PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1XS5T5F
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1XS5T5F
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 31 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
Angiopoietin receptor Tie2-mediated signaling 161
Signaling events mediated by the Hedgehog family 143
Endothelins 93
Fc-epsilon receptor I signaling in mast cells 67
Thromboxane A2 receptor signaling 61
IL4-mediated signaling events 59
Aurora B signaling 59
Signaling mediated by p38-alpha and p38-beta 56
amb2 Integrin signaling 55
TCGA08_retinoblastoma 55
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 489 . 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 ( 489 ).

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
Angiopoietin receptor Tie2-mediated signaling 0.3292 161 14194 88 -0.71 0.075 1000 -1000 -0.062 -1000
Signaling events mediated by the Hedgehog family 0.2924 143 7466 52 -0.44 0.23 1000 -1000 -0.038 -1000
Endothelins 0.1902 93 8967 96 -0.38 0.11 1000 -1000 -0.054 -1000
Fc-epsilon receptor I signaling in mast cells 0.1370 67 6585 97 -0.14 0.023 1000 -1000 -0.059 -1000
Thromboxane A2 receptor signaling 0.1247 61 6430 105 -0.2 0.055 1000 -1000 -0.039 -1000
IL4-mediated signaling events 0.1207 59 5438 91 -0.81 0.49 1000 -1000 -0.12 -1000
Aurora B signaling 0.1207 59 3953 67 -0.3 0.29 1000 -1000 -0.029 -1000
Signaling mediated by p38-alpha and p38-beta 0.1145 56 2486 44 -0.11 0.022 1000 -1000 -0.028 -1000
amb2 Integrin signaling 0.1125 55 4536 82 -0.5 0.035 1000 -1000 -0.04 -1000
TCGA08_retinoblastoma 0.1125 55 443 8 -0.01 0.096 1000 -1000 -0.002 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.1063 52 2722 52 -0.26 0.048 1000 -1000 -0.042 -1000
Aurora C signaling 0.1022 50 353 7 0 0.15 1000 -1000 -0.013 -1000
Signaling events regulated by Ret tyrosine kinase 0.0838 41 3427 82 -0.11 0.055 1000 -1000 -0.061 -1000
Nongenotropic Androgen signaling 0.0777 38 1980 52 -0.11 0.075 1000 -1000 -0.033 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0777 38 2964 78 -0.16 0.05 1000 -1000 -0.049 -1000
BMP receptor signaling 0.0757 37 3077 81 -0.27 0.15 1000 -1000 -0.044 -1000
Integrins in angiogenesis 0.0716 35 2952 84 -0.33 0.13 1000 -1000 -0.044 -1000
Calcium signaling in the CD4+ TCR pathway 0.0716 35 1112 31 -0.17 0.024 1000 -1000 -0.039 -1000
Arf6 signaling events 0.0675 33 2075 62 -0.14 0.043 1000 -1000 -0.041 -1000
PLK1 signaling events 0.0675 33 2828 85 -0.027 0.16 1000 -1000 -0.025 -1000
Canonical Wnt signaling pathway 0.0613 30 1544 51 -0.34 0.16 1000 -1000 -0.045 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0593 29 3720 125 -0.13 0.051 1000 -1000 -0.052 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0573 28 1962 68 -0.18 0.04 1000 -1000 -0.072 -1000
Presenilin action in Notch and Wnt signaling 0.0552 27 1653 61 -0.34 0.16 1000 -1000 -0.041 -1000
Reelin signaling pathway 0.0552 27 1556 56 -0.068 0.059 1000 -1000 -0.052 -1000
Glypican 2 network 0.0552 27 108 4 0.028 0.057 1000 -1000 0.013 -1000
IL6-mediated signaling events 0.0552 27 2071 75 -0.46 0.048 1000 -1000 -0.066 -1000
Coregulation of Androgen receptor activity 0.0532 26 1978 76 -0.32 0.095 1000 -1000 -0.027 -1000
Visual signal transduction: Cones 0.0511 25 967 38 -0.04 0.13 1000 -1000 -0.026 -1000
Syndecan-3-mediated signaling events 0.0511 25 893 35 -0.24 0.056 1000 -1000 -0.027 -1000
FOXM1 transcription factor network 0.0511 25 1316 51 0.022 0.35 1000 -1000 -0.12 -1000
LPA4-mediated signaling events 0.0491 24 289 12 -0.098 0 1000 -1000 -0.025 -1000
IL23-mediated signaling events 0.0491 24 1481 60 -0.2 0.023 1000 -1000 -0.12 -1000
HIF-1-alpha transcription factor network 0.0470 23 1750 76 -0.11 0.14 1000 -1000 -0.11 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0470 23 2025 85 -0.1 0.031 1000 -1000 -0.044 -1000
FOXA2 and FOXA3 transcription factor networks 0.0470 23 1084 46 -0.69 0.11 1000 -1000 -0.12 -1000
TCR signaling in naïve CD8+ T cells 0.0470 23 2153 93 -0.06 0.032 1000 -1000 -0.048 -1000
Plasma membrane estrogen receptor signaling 0.0470 23 1997 86 -0.11 0.038 1000 -1000 -0.052 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0470 23 760 33 -0.16 0.095 1000 -1000 -0.025 -1000
Regulation of Androgen receptor activity 0.0470 23 1615 70 -0.35 0.14 1000 -1000 -0.042 -1000
Glucocorticoid receptor regulatory network 0.0450 22 2580 114 -0.33 0.074 1000 -1000 -0.057 -1000
IL12-mediated signaling events 0.0429 21 1864 87 -0.18 0.044 1000 -1000 -0.078 -1000
Syndecan-1-mediated signaling events 0.0429 21 734 34 -0.09 0.15 1000 -1000 -0.048 -1000
Nectin adhesion pathway 0.0409 20 1292 63 -0.031 0.12 1000 -1000 -0.042 -1000
Wnt signaling 0.0409 20 145 7 0.007 0.056 1000 -1000 -0.015 -1000
Caspase cascade in apoptosis 0.0389 19 1408 74 -0.068 0.083 1000 -1000 -0.031 -1000
ErbB4 signaling events 0.0389 19 1351 69 -0.13 0.16 1000 -1000 -0.05 -1000
Glypican 1 network 0.0389 19 950 48 -0.14 0.086 1000 -1000 -0.031 -1000
S1P1 pathway 0.0368 18 657 36 -0.1 0.022 1000 -1000 -0.04 -1000
FAS signaling pathway (CD95) 0.0368 18 863 47 -0.2 0.061 1000 -1000 -0.035 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0348 17 941 54 -0.068 0.072 1000 -1000 -0.055 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0348 17 2117 120 -0.14 0.06 1000 -1000 -0.046 -1000
TCGA08_p53 0.0327 16 118 7 -0.03 0.022 1000 -1000 -0.014 -1000
Visual signal transduction: Rods 0.0327 16 851 52 -0.04 0.093 1000 -1000 -0.036 -1000
JNK signaling in the CD4+ TCR pathway 0.0286 14 251 17 -0.035 0.032 1000 -1000 -0.035 -1000
p75(NTR)-mediated signaling 0.0286 14 1821 125 -0.049 0.15 1000 -1000 -0.075 -1000
PDGFR-alpha signaling pathway 0.0286 14 627 44 -0.13 0.046 1000 -1000 -0.042 -1000
Ras signaling in the CD4+ TCR pathway 0.0286 14 240 17 -0.017 0.031 1000 -1000 -0.025 -1000
Noncanonical Wnt signaling pathway 0.0266 13 362 26 -0.052 0.056 1000 -1000 -0.045 -1000
Signaling events mediated by PTP1B 0.0266 13 1028 76 -0.047 0.057 1000 -1000 -0.036 -1000
Effects of Botulinum toxin 0.0266 13 338 26 -0.036 0.03 1000 -1000 -0.017 -1000
BCR signaling pathway 0.0266 13 1340 99 -0.089 0.053 1000 -1000 -0.053 -1000
S1P4 pathway 0.0266 13 331 25 -0.029 0.032 1000 -1000 -0.026 -1000
Osteopontin-mediated events 0.0245 12 473 38 -0.047 0.13 1000 -1000 -0.048 -1000
Aurora A signaling 0.0245 12 734 60 -0.04 0.21 1000 -1000 -0.027 -1000
Ephrin B reverse signaling 0.0245 12 604 48 -0.058 0.063 1000 -1000 -0.03 -1000
EGFR-dependent Endothelin signaling events 0.0245 12 266 21 -0.025 0.049 1000 -1000 -0.044 -1000
Regulation of nuclear SMAD2/3 signaling 0.0225 11 1515 136 -0.2 0.14 1000 -1000 -0.041 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0225 11 320 28 -0.11 0.043 1000 -1000 -0.031 -1000
Hedgehog signaling events mediated by Gli proteins 0.0225 11 753 65 -0.52 0.055 1000 -1000 -0.039 -1000
mTOR signaling pathway 0.0225 11 589 53 -0.018 0.092 1000 -1000 -0.039 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0225 11 848 74 -0.14 0.049 1000 -1000 -0.071 -1000
HIF-2-alpha transcription factor network 0.0204 10 464 43 -0.072 0.074 1000 -1000 -0.062 -1000
Syndecan-4-mediated signaling events 0.0204 10 692 67 -0.032 0.086 1000 -1000 -0.043 -1000
Syndecan-2-mediated signaling events 0.0184 9 677 69 -0.034 0.086 1000 -1000 -0.041 -1000
Cellular roles of Anthrax toxin 0.0184 9 351 39 -0.06 0.023 1000 -1000 -0.022 -1000
Retinoic acid receptors-mediated signaling 0.0184 9 522 58 -0.16 0.045 1000 -1000 -0.036 -1000
LPA receptor mediated events 0.0184 9 947 102 -0.061 0.041 1000 -1000 -0.055 -1000
ErbB2/ErbB3 signaling events 0.0164 8 552 65 -0.038 0.033 1000 -1000 -0.058 -1000
IL2 signaling events mediated by PI3K 0.0164 8 466 58 -0.02 0.12 1000 -1000 -0.038 -1000
EPHB forward signaling 0.0164 8 685 85 -0.043 0.072 1000 -1000 -0.069 -1000
Regulation of p38-alpha and p38-beta 0.0164 8 435 54 -0.043 0.053 1000 -1000 -0.046 -1000
IL27-mediated signaling events 0.0164 8 446 51 -0.068 0.029 1000 -1000 -0.049 -1000
IL2 signaling events mediated by STAT5 0.0164 8 182 22 0.004 0.076 1000 -1000 -0.039 -1000
IGF1 pathway 0.0164 8 459 57 -0.055 0.058 1000 -1000 -0.053 -1000
PDGFR-beta signaling pathway 0.0164 8 808 97 -0.046 0.066 1000 -1000 -0.057 -1000
TCGA08_rtk_signaling 0.0143 7 196 26 -0.064 0.081 1000 -1000 -0.016 -1000
Insulin Pathway 0.0143 7 525 74 -0.089 0.06 1000 -1000 -0.061 -1000
IFN-gamma pathway 0.0123 6 444 68 -0.027 0.066 1000 -1000 -0.057 -1000
Ceramide signaling pathway 0.0123 6 522 76 -0.012 0.06 1000 -1000 -0.032 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0123 6 561 83 -0.067 0.041 1000 -1000 -0.039 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0123 6 306 45 -0.019 0.051 1000 -1000 -0.051 -1000
Class I PI3K signaling events 0.0123 6 467 73 -0.029 0.042 1000 -1000 -0.044 -1000
S1P3 pathway 0.0123 6 274 42 -0.11 0.043 1000 -1000 -0.041 -1000
Signaling events mediated by PRL 0.0123 6 229 34 -0.036 0.064 1000 -1000 -0.048 -1000
E-cadherin signaling in keratinocytes 0.0123 6 260 43 -0.05 0.063 1000 -1000 -0.042 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0102 5 171 34 -0.032 0.051 1000 -1000 -0.033 -1000
Ephrin A reverse signaling 0.0102 5 37 7 -0.011 0.03 1000 -1000 -0.022 -1000
EPO signaling pathway 0.0102 5 276 55 -0.011 0.06 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class III 0.0102 5 203 40 -0.079 0.042 1000 -1000 -0.031 -1000
TRAIL signaling pathway 0.0102 5 263 48 -0.037 0.059 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0102 5 273 49 0 0.033 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class I 0.0102 5 533 104 -0.043 0.055 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class II 0.0082 4 307 75 -0.034 0.056 1000 -1000 -0.036 -1000
BARD1 signaling events 0.0082 4 244 57 -0.042 0.089 1000 -1000 -0.037 -1000
IL1-mediated signaling events 0.0082 4 268 62 -0.02 0.041 1000 -1000 -0.059 -1000
FoxO family signaling 0.0082 4 258 64 -0.022 0.072 1000 -1000 -0.057 -1000
E-cadherin signaling in the nascent adherens junction 0.0082 4 325 76 -0.013 0.06 1000 -1000 -0.061 -1000
VEGFR1 specific signals 0.0082 4 266 56 -0.13 0.056 1000 -1000 -0.048 -1000
a4b1 and a4b7 Integrin signaling 0.0061 3 17 5 0.017 0.028 1000 -1000 0.007 -1000
Insulin-mediated glucose transport 0.0061 3 97 32 -0.009 0.043 1000 -1000 -0.031 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0061 3 124 37 -0.013 0.052 1000 -1000 -0.032 -1000
Regulation of Telomerase 0.0061 3 374 102 -0.041 0.068 1000 -1000 -0.05 -1000
p38 MAPK signaling pathway 0.0061 3 149 44 -0.003 0.054 1000 -1000 -0.028 -1000
Canonical NF-kappaB pathway 0.0041 2 102 39 -0.006 0.046 1000 -1000 -0.03 -1000
Arf6 downstream pathway 0.0041 2 115 43 -0.045 0.046 1000 -1000 -0.023 -1000
Class I PI3K signaling events mediated by Akt 0.0041 2 155 68 -0.034 0.048 1000 -1000 -0.042 -1000
Paxillin-dependent events mediated by a4b1 0.0041 2 98 36 -0.041 0.043 1000 -1000 -0.038 -1000
Arf6 trafficking events 0.0041 2 196 71 -0.055 0.04 1000 -1000 -0.035 -1000
Circadian rhythm pathway 0.0020 1 29 22 -0.006 0.048 1000 -1000 -0.034 -1000
S1P5 pathway 0.0020 1 32 17 -0.015 0.03 1000 -1000 -0.013 -1000
Signaling mediated by p38-gamma and p38-delta 0.0020 1 27 15 -0.011 0.022 1000 -1000 -0.031 -1000
Rapid glucocorticoid signaling 0.0020 1 31 20 -0.011 0.024 1000 -1000 -0.012 -1000
Class IB PI3K non-lipid kinase events 0.0020 1 3 3 -0.021 0.021 1000 -1000 -0.008 -1000
Arf1 pathway 0.0020 1 71 54 -0.005 0.031 1000 -1000 -0.019 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 12 23 0.003 0.042 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 0.0000 0 1 3 -0.01 0.022 1000 -1000 -0.032 -1000
Atypical NF-kappaB pathway 0.0000 0 13 31 -0.008 0.023 1000 -1000 -0.029 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 10 27 -0.01 0.053 1000 -1000 -0.041 -1000
E-cadherin signaling events 0.0000 0 0 5 0.021 0.042 1000 -1000 0.01 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 0 0.06 1000 -1000 0 -1000
Total NA 2465 159775 7203 -14 9.5 131000 -131000 -5.4 -131000
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.53 0.5 -10000 0 -0.97 266 266
NCK1/PAK1/Dok-R -0.24 0.21 -10000 0 -0.44 266 266
NCK1/Dok-R -0.61 0.63 -10000 0 -1.1 264 264
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
mol:beta2-estradiol 0.063 0.098 0.24 114 -10000 0 114
RELA 0.023 0.002 -10000 0 -10000 0 0
SHC1 0.02 0.005 -10000 0 -10000 0 0
Rac/GDP 0.017 0.003 -10000 0 -10000 0 0
F2 0.075 0.12 0.27 117 -10000 0 117
TNIP2 0.021 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.55 0.57 -10000 0 -1.1 264 264
FN1 0.01 0.082 -10000 0 -0.56 10 10
PLD2 -0.64 0.65 -10000 0 -1.2 262 262
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GRB14 -0.013 0.14 0.24 1 -0.56 30 31
ELK1 -0.57 0.56 -10000 0 -1.1 266 266
GRB7 0.025 0.032 0.37 4 -10000 0 4
PAK1 0.023 0.016 0.37 1 -10000 0 1
Tie2/Ang1/alpha5/beta1 Integrin -0.59 0.62 -10000 0 -1.1 264 264
CDKN1A -0.37 0.33 -10000 0 -0.66 265 265
ITGA5 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.62 0.64 -10000 0 -1.2 265 265
CRK 0.022 0.005 -10000 0 -10000 0 0
mol:NO -0.38 0.35 -10000 0 -0.69 266 266
PLG -0.64 0.65 -10000 0 -1.2 263 263
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.5 0.46 -10000 0 -0.91 266 266
GRB2 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.006 -10000 0 -10000 0 0
ANGPT2 -0.3 0.32 -10000 0 -0.73 146 146
BMX -0.69 0.67 -10000 0 -1.3 264 264
ANGPT1 -0.36 0.56 -10000 0 -1.3 117 117
tube development -0.42 0.37 -10000 0 -0.75 265 265
ANGPT4 -0.24 0.28 -10000 0 -0.56 209 209
response to hypoxia -0.036 0.033 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.68 0.68 -10000 0 -1.2 264 264
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
FGF2 0.007 0.093 -10000 0 -0.56 13 13
STAT5A (dimer) -0.48 0.44 -10000 0 -0.87 264 264
mol:L-citrulline -0.38 0.35 -10000 0 -0.69 266 266
AGTR1 -0.14 0.25 -10000 0 -0.56 127 127
MAPK14 -0.69 0.67 -10000 0 -1.3 266 266
Tie2/SHP2 -0.57 0.6 -10000 0 -1.2 236 236
TEK -0.63 0.66 -10000 0 -1.3 236 236
RPS6KB1 -0.51 0.47 -10000 0 -0.93 266 266
Angiotensin II/AT1 -0.098 0.18 -10000 0 -0.41 127 127
Tie2/Ang1/GRB2 -0.66 0.68 -10000 0 -1.2 264 264
MAPK3 -0.58 0.57 -10000 0 -1.1 262 262
MAPK1 -0.57 0.57 -10000 0 -1.1 263 263
Tie2/Ang1/GRB7 -0.66 0.68 -10000 0 -1.2 264 264
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.64 0.65 -10000 0 -1.2 264 264
PI3K -0.63 0.59 -10000 0 -1.1 266 266
FES -0.68 0.66 -10000 0 -1.3 266 266
Crk/Dok-R -0.62 0.64 -10000 0 -1.2 265 265
Tie2/Ang1/ABIN2 -0.66 0.68 -10000 0 -1.2 264 264
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.46 0.43 -10000 0 -0.85 266 266
STAT5A 0.023 0.003 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.5 0.47 -10000 0 -0.92 266 266
Tie2/Ang2 -0.6 0.55 -10000 0 -1.1 264 264
Tie2/Ang1 -0.71 0.74 -10000 0 -1.3 264 264
FOXO1 -0.47 0.44 -10000 0 -0.86 266 266
ELF1 -0.037 0.068 -10000 0 -10000 0 0
ELF2 -0.64 0.65 -10000 0 -1.2 264 264
mol:Choline -0.6 0.6 -10000 0 -1.1 263 263
cell migration -0.13 0.12 -10000 0 -0.24 266 266
FYN -0.49 0.44 -10000 0 -0.87 265 265
DOK2 -0.021 0.15 -10000 0 -0.56 35 35
negative regulation of cell cycle -0.33 0.3 -10000 0 -0.6 265 265
ETS1 -0.068 0.14 -10000 0 -0.29 114 114
PXN -0.41 0.38 -10000 0 -0.75 265 265
ITGB1 0.022 0.004 -10000 0 -10000 0 0
NOS3 -0.44 0.4 -10000 0 -0.8 266 266
RAC1 0.022 0.004 -10000 0 -10000 0 0
TNF -0.068 0.14 0.24 1 -0.29 116 117
MAPKKK cascade -0.6 0.6 -10000 0 -1.1 263 263
RASA1 0.021 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.66 0.68 -10000 0 -1.2 263 263
NCK1 0.019 0.008 -10000 0 -10000 0 0
vasculogenesis -0.34 0.31 -10000 0 -0.61 266 266
mol:Phosphatidic acid -0.6 0.6 -10000 0 -1.1 263 263
mol:Angiotensin II 0 0.001 -10000 0 -10000 0 0
mol:NADP -0.38 0.35 -10000 0 -0.69 266 266
Rac1/GTP -0.46 0.44 -10000 0 -0.86 266 266
MMP2 -0.64 0.65 -10000 0 -1.2 263 263
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.16 0.23 -10000 0 -0.75 28 28
IHH -0.3 0.31 -10000 0 -0.59 262 262
SHH Np/Cholesterol/GAS1 -0.029 0.12 0.2 1 -0.33 67 68
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.029 0.12 0.32 67 -0.19 1 68
SMO/beta Arrestin2 -0.2 0.22 -10000 0 -0.4 256 256
SMO -0.22 0.23 -10000 0 -0.41 260 260
AKT1 -0.11 0.16 -10000 0 -0.58 29 29
ARRB2 0.022 0.005 -10000 0 -10000 0 0
BOC 0.019 0.04 0.24 2 -0.56 2 4
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
heart looping -0.22 0.22 -10000 0 -0.41 260 260
STIL -0.17 0.19 0.24 1 -0.46 76 77
DHH N/PTCH2 0 0.12 -10000 0 -0.41 36 36
DHH N/PTCH1 -0.18 0.21 -10000 0 -0.33 292 292
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DHH -0.022 0.15 -10000 0 -0.56 34 34
PTHLH -0.2 0.26 -10000 0 -0.75 27 27
determination of left/right symmetry -0.22 0.22 -10000 0 -0.41 260 260
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
skeletal system development -0.2 0.26 -10000 0 -0.74 27 27
IHH N/Hhip -0.44 0.29 -10000 0 -0.57 382 382
DHH N/Hhip -0.28 0.23 -10000 0 -0.42 332 332
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.22 0.22 -10000 0 -0.41 260 260
pancreas development -0.34 0.28 -10000 0 -0.56 299 299
HHAT 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.014 0.069 -10000 0 -0.56 7 7
somite specification -0.22 0.22 -10000 0 -0.41 260 260
SHH Np/Cholesterol/PTCH1 -0.18 0.2 -10000 0 -0.32 281 281
SHH Np/Cholesterol/PTCH2 -0.026 0.12 0.2 1 -0.32 63 64
SHH Np/Cholesterol/Megalin -0.19 0.2 -10000 0 -0.36 263 263
SHH -0.06 0.13 0.3 1 -0.41 60 61
catabolic process -0.18 0.21 -10000 0 -0.35 275 275
SMO/Vitamin D3 -0.2 0.22 -10000 0 -0.38 257 257
SHH Np/Cholesterol/Hhip -0.23 0.19 -10000 0 -0.36 307 307
LRP2 -0.27 0.29 -10000 0 -0.56 245 245
receptor-mediated endocytosis -0.32 0.26 -10000 0 -0.58 203 203
SHH Np/Cholesterol/BOC -0.023 0.11 -10000 0 -0.33 53 53
SHH Np/Cholesterol/CDO -0.027 0.12 0.2 1 -0.32 65 66
mesenchymal cell differentiation 0.23 0.19 0.36 307 -10000 0 307
mol:Vitamin D3 -0.18 0.2 0.24 1 -0.4 130 131
IHH N/PTCH2 -0.19 0.2 -10000 0 -0.37 263 263
CDON 0.016 0.059 -10000 0 -0.56 5 5
IHH N/PTCH1 -0.17 0.22 -10000 0 -0.36 275 275
Megalin/LRPAP1 -0.19 0.22 -10000 0 -0.41 243 243
PTCH2 0.02 0.048 0.24 2 -0.56 3 5
SHH Np/Cholesterol -0.033 0.11 -10000 0 -0.32 60 60
PTCH1 -0.18 0.21 -10000 0 -0.35 275 275
HHIP -0.34 0.28 -10000 0 -0.56 299 299
Endothelins

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 -0.1 0.15 -10000 0 -0.4 76 76
PTK2B 0.021 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.28 -10000 0 -0.83 52 52
EDN1 -0.094 0.17 -10000 0 -0.46 68 68
EDN3 -0.05 0.18 0.24 13 -0.56 49 62
EDN2 0.042 0.1 0.24 64 -0.56 7 71
HRAS/GDP -0.22 0.26 -10000 0 -0.56 143 143
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.1 0.19 -10000 0 -0.43 92 92
ADCY4 -0.098 0.16 -10000 0 -0.38 91 91
ADCY5 -0.1 0.17 -10000 0 -0.4 91 91
ADCY6 -0.084 0.14 -10000 0 -0.36 71 71
ADCY7 -0.082 0.14 -10000 0 -0.36 69 69
ADCY1 -0.083 0.14 -10000 0 -0.36 70 70
ADCY2 -0.069 0.15 0.26 9 -0.38 61 70
ADCY3 -0.083 0.14 -10000 0 -0.36 72 72
ADCY8 -0.16 0.18 -10000 0 -0.36 184 184
ADCY9 -0.084 0.14 -10000 0 -0.36 73 73
arachidonic acid secretion -0.2 0.24 -10000 0 -0.5 160 160
ETB receptor/Endothelin-1/Gq/GTP -0.27 0.28 -10000 0 -0.44 303 303
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.077 0.15 -10000 0 -0.38 72 72
ETA receptor/Endothelin-1/Gs/GTP -0.076 0.15 -10000 0 -0.37 76 76
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
COL3A1 -0.1 0.15 -10000 0 -0.41 72 72
EDNRB -0.3 0.29 -10000 0 -0.56 271 271
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.11 0.18 -10000 0 -0.46 76 76
CYSLTR1 -0.15 0.24 -10000 0 -0.58 98 98
SLC9A1 -0.056 0.096 -10000 0 -0.27 60 60
mol:GDP -0.24 0.28 -10000 0 -0.6 147 147
SLC9A3 -0.38 0.37 -10000 0 -0.74 194 194
RAF1 -0.23 0.27 -10000 0 -0.57 158 158
JUN -0.14 0.24 -10000 0 -0.72 44 44
JAK2 -0.1 0.15 -10000 0 -0.41 77 77
mol:IP3 -0.21 0.25 -10000 0 -0.55 145 145
ETA receptor/Endothelin-1 -0.11 0.18 -10000 0 -0.44 95 95
PLCB1 0.02 0.008 -10000 0 -10000 0 0
PLCB2 0.01 0.074 -10000 0 -0.56 8 8
ETA receptor/Endothelin-3 -0.069 0.14 -10000 0 -0.42 56 56
FOS -0.24 0.32 -10000 0 -0.75 106 106
Gai/GDP -0.088 0.29 -10000 0 -0.87 53 53
CRK 0.021 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.28 -10000 0 -0.62 153 153
BCAR1 0.022 0.006 -10000 0 -10000 0 0
PRKCB1 -0.2 0.24 -10000 0 -0.53 145 145
GNAQ 0.017 0.03 -10000 0 -0.56 1 1
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
GNAL 0.018 0.046 -10000 0 -0.56 3 3
Gs family/GDP -0.21 0.25 -10000 0 -0.54 141 141
ETA receptor/Endothelin-1/Gq/GTP -0.12 0.2 -10000 0 -0.43 116 116
MAPK14 -0.22 0.23 -10000 0 -0.5 165 165
TRPC6 -0.17 0.3 -10000 0 -0.93 48 48
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.25 -10000 0 -0.51 169 169
ETB receptor/Endothelin-2 -0.22 0.23 0.27 1 -0.42 277 278
ETB receptor/Endothelin-3 -0.26 0.24 -10000 0 -0.44 297 297
ETB receptor/Endothelin-1 -0.29 0.24 -10000 0 -0.46 294 294
MAPK3 -0.25 0.32 -10000 0 -0.67 146 146
MAPK1 -0.25 0.32 -10000 0 -0.67 147 147
Rac1/GDP -0.21 0.26 -10000 0 -0.56 140 140
cAMP biosynthetic process -0.092 0.16 0.26 8 -0.44 50 58
MAPK8 -0.17 0.3 -10000 0 -0.72 83 83
SRC 0.022 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.17 0.16 -10000 0 -0.3 231 231
p130Cas/CRK/Src/PYK2 -0.23 0.28 -10000 0 -0.61 139 139
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.21 0.26 -10000 0 -0.56 140 140
COL1A2 -0.26 0.22 -10000 0 -0.57 106 106
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.014 0.11 0.26 3 -0.35 21 24
mol:DAG -0.21 0.25 -10000 0 -0.55 145 145
MAP2K2 -0.24 0.28 -10000 0 -0.6 153 153
MAP2K1 -0.24 0.28 -10000 0 -0.6 152 152
EDNRA -0.05 0.093 -10000 0 -0.3 34 34
positive regulation of muscle contraction -0.084 0.13 -10000 0 -0.37 66 66
Gq family/GDP -0.19 0.27 -10000 0 -0.58 137 137
HRAS/GTP -0.23 0.27 -10000 0 -0.57 157 157
PRKCH -0.2 0.24 -10000 0 -0.53 139 139
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.2 0.24 0.21 2 -0.53 141 143
PRKCB -0.22 0.26 -10000 0 -0.57 141 141
PRKCE -0.2 0.24 0.21 1 -0.53 137 138
PRKCD -0.2 0.24 0.21 1 -0.54 135 136
PRKCG -0.21 0.24 -10000 0 -0.54 140 140
regulation of vascular smooth muscle contraction -0.28 0.38 -10000 0 -0.91 103 103
PRKCQ -0.22 0.27 -10000 0 -0.58 149 149
PLA2G4A -0.21 0.27 -10000 0 -0.54 160 160
GNA14 -0.11 0.24 -10000 0 -0.56 111 111
GNA15 0.02 0.01 -10000 0 -10000 0 0
GNA12 0.022 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.01 -10000 0 -10000 0 0
Rac1/GTP -0.078 0.15 -10000 0 -0.38 72 72
MMP1 0.11 0.1 0.36 32 -10000 0 32
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.006 -10000 0 -10000 0 0
LAT2 -0.11 0.21 -10000 0 -0.45 99 99
AP1 -0.11 0.26 -10000 0 -0.55 98 98
mol:PIP3 -0.13 0.24 0.3 10 -0.49 105 115
IKBKB -0.06 0.14 0.19 26 -0.3 78 104
AKT1 -0.056 0.2 0.41 19 -0.43 54 73
IKBKG -0.069 0.13 0.23 9 -0.29 78 87
MS4A2 -0.11 0.24 -10000 0 -0.56 107 107
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.012 0.011 -10000 0 -10000 0 0
MAP3K1 -0.028 0.22 0.24 95 -0.47 57 152
mol:Ca2+ -0.095 0.18 0.27 11 -0.36 104 115
LYN 0.012 0.042 -10000 0 -0.58 2 2
CBLB -0.1 0.2 -10000 0 -0.44 92 92
SHC1 0.022 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK -0.002 0.11 -10000 0 -0.32 51 51
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
PLD2 -0.14 0.21 0.32 13 -0.38 174 187
PTPN13 -0.099 0.21 0.41 1 -0.54 61 62
PTPN11 0.007 0.028 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.039 0.18 0.35 19 -0.35 54 73
SYK 0.015 0.018 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.23 -10000 0 -0.46 136 136
LAT -0.11 0.2 -10000 0 -0.43 98 98
PAK2 -0.035 0.24 0.25 93 -0.52 60 153
NFATC2 -0.13 0.26 -10000 0 -0.72 67 67
HRAS -0.11 0.24 0.23 8 -0.51 97 105
GAB2 0.007 0.094 -10000 0 -0.56 13 13
PLA2G1B -0.081 0.25 -10000 0 -0.92 38 38
Fc epsilon R1 -0.14 0.26 -10000 0 -0.46 179 179
Antigen/IgE/Fc epsilon R1 -0.13 0.24 -10000 0 -0.42 179 179
mol:GDP -0.12 0.26 0.27 1 -0.55 100 101
JUN 0.022 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
FOS -0.042 0.18 -10000 0 -0.56 54 54
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.11 0.21 -10000 0 -0.4 131 131
CHUK -0.071 0.13 0.23 9 -0.29 80 89
KLRG1 -0.1 0.19 -10000 0 -0.36 128 128
VAV1 -0.11 0.2 -10000 0 -0.44 100 100
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.11 0.2 -10000 0 -0.43 99 99
negative regulation of mast cell degranulation -0.088 0.19 0.2 1 -0.47 64 65
BTK -0.14 0.28 -10000 0 -0.66 87 87
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.14 0.25 -10000 0 -0.41 172 172
GAB2/PI3K/SHP2 -0.11 0.16 -10000 0 -0.37 112 112
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.11 0.2 -10000 0 -0.34 168 168
RAF1 -0.045 0.27 -10000 0 -0.96 38 38
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.25 -10000 0 -0.41 179 179
FCER1G 0.001 0.097 -10000 0 -0.57 13 13
FCER1A -0.14 0.26 -10000 0 -0.57 134 134
Antigen/IgE/Fc epsilon R1/Fyn -0.11 0.24 -10000 0 -0.4 178 178
MAPK3 -0.044 0.25 -10000 0 -0.9 38 38
MAPK1 -0.045 0.25 -10000 0 -0.9 38 38
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.051 0.25 0.38 1 -0.85 35 36
DUSP1 -0.043 0.18 -10000 0 -0.56 54 54
NF-kappa-B/RelA -0.038 0.083 -10000 0 -0.21 33 33
actin cytoskeleton reorganization -0.098 0.22 0.43 1 -0.56 61 62
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.089 0.2 -10000 0 -0.5 67 67
FER -0.11 0.2 -10000 0 -0.43 99 99
RELA 0.023 0.002 -10000 0 -10000 0 0
ITK -0.065 0.15 -10000 0 -0.44 58 58
SOS1 0.022 0.004 -10000 0 -10000 0 0
PLCG1 -0.12 0.26 0.36 4 -0.55 100 104
cytokine secretion -0.03 0.057 -10000 0 -10000 0 0
SPHK1 -0.1 0.2 -10000 0 -0.44 98 98
PTK2 -0.1 0.23 0.43 1 -0.59 60 61
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.25 -10000 0 -0.47 137 137
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.13 0.23 0.31 10 -0.48 109 119
MAP2K2 -0.047 0.25 -10000 0 -0.9 38 38
MAP2K1 -0.047 0.25 -10000 0 -0.9 38 38
MAP2K7 0.022 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.085 0.18 0.2 8 -0.46 63 71
MAP2K4 -0.037 0.27 -10000 0 -0.97 34 34
Fc epsilon R1/FcgammaRIIB -0.12 0.26 -10000 0 -0.43 179 179
mol:Choline -0.13 0.21 0.32 13 -0.38 174 187
SHC/Grb2/SOS1 -0.078 0.2 -10000 0 -0.44 83 83
FYN 0.022 0.026 -10000 0 -0.56 1 1
DOK1 0.022 0.004 -10000 0 -10000 0 0
PXN -0.097 0.21 0.59 1 -0.54 60 61
HCLS1 -0.099 0.2 -10000 0 -0.44 93 93
PRKCB -0.1 0.18 0.26 9 -0.39 98 107
FCGR2B 0.015 0.064 -10000 0 -0.56 6 6
IGHE -0.003 0.009 -10000 0 -10000 0 0
KLRG1/SHIP -0.09 0.19 0.2 1 -0.48 64 65
LCP2 0.014 0.064 -10000 0 -0.56 6 6
PLA2G4A -0.11 0.2 -10000 0 -0.44 100 100
RASA1 0.021 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.13 0.21 0.32 13 -0.38 174 187
IKK complex -0.042 0.11 0.17 26 -0.23 65 91
WIPF1 0.023 0.003 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 -0.025 0.16 -10000 0 -0.56 39 39
GNB1/GNG2 -0.067 0.093 -10000 0 -0.19 163 163
AKT1 -0.061 0.12 0.19 1 -0.24 53 54
EGF 0.015 0.071 0.24 3 -0.56 7 10
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.026 0.1 0.25 2 -0.37 27 29
mol:Ca2+ -0.097 0.16 -10000 0 -0.31 172 172
LYN -0.013 0.071 0.27 3 -0.37 8 11
RhoA/GTP -0.038 0.07 -10000 0 -0.14 75 75
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.11 0.18 -10000 0 -0.35 163 163
GNG2 0.016 0.059 -10000 0 -0.56 5 5
ARRB2 0.022 0.005 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.044 0.15 -10000 0 -0.6 21 21
G beta5/gamma2 -0.086 0.13 -10000 0 -0.26 161 161
PRKCH -0.12 0.19 -10000 0 -0.36 165 165
DNM1 0.023 0.014 0.24 2 -10000 0 2
TXA2/TP beta/beta Arrestin3 0.012 0.065 -10000 0 -0.58 5 5
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.009 0.086 -10000 0 -0.56 11 11
G12 family/GTP -0.097 0.16 -10000 0 -0.31 165 165
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
ADRBK2 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.027 0.01 -10000 0 -10000 0 0
mol:GDP 0.055 0.12 0.38 28 -10000 0 28
mol:NADP 0.019 0.046 -10000 0 -0.56 3 3
RAB11A 0.023 0.002 -10000 0 -10000 0 0
PRKG1 -0.025 0.16 -10000 0 -0.56 39 39
mol:IP3 -0.12 0.2 -10000 0 -0.39 172 172
cell morphogenesis 0.027 0.01 -10000 0 -10000 0 0
PLCB2 -0.18 0.28 -10000 0 -0.54 171 171
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.014 0.083 0.27 3 -0.33 17 20
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.013 0.074 0.27 3 -0.42 8 11
RHOA 0.021 0.007 -10000 0 -10000 0 0
PTGIR 0.008 0.09 -10000 0 -0.56 12 12
PRKCB1 -0.12 0.2 -10000 0 -0.39 171 171
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
mol:L-citrulline 0.019 0.046 -10000 0 -0.56 3 3
TXA2/TXA2-R family -0.18 0.28 -10000 0 -0.54 168 168
LCK -0.013 0.072 0.27 3 -0.39 8 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.009 0.077 -10000 0 -0.36 13 13
TXA2-R family/G12 family/GDP/G beta/gamma -0.002 0.11 -10000 0 -0.45 23 23
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.012 0.076 -10000 0 -0.33 18 18
MAPK14 -0.073 0.12 -10000 0 -0.24 158 158
TGM2/GTP -0.15 0.24 -10000 0 -0.45 174 174
MAPK11 -0.072 0.12 -10000 0 -0.24 157 157
ARHGEF1 -0.055 0.095 -10000 0 -0.18 150 150
GNAI2 0.021 0.007 -10000 0 -10000 0 0
JNK cascade -0.12 0.2 -10000 0 -0.4 168 168
RAB11/GDP 0.023 0.003 -10000 0 -10000 0 0
ICAM1 -0.097 0.17 -10000 0 -0.32 165 165
cAMP biosynthetic process -0.12 0.19 -10000 0 -0.36 174 174
Gq family/GTP/EBP50 -0.036 0.098 0.24 3 -0.2 106 109
actin cytoskeleton reorganization 0.027 0.01 -10000 0 -10000 0 0
SRC -0.012 0.069 0.27 3 -0.4 6 9
GNB5 0.023 0.003 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
EGF/EGFR -0.007 0.092 0.22 9 -0.31 20 29
VCAM1 -0.091 0.15 -10000 0 -0.3 165 165
TP beta/Gq family/GDP/G beta5/gamma2 -0.044 0.15 -10000 0 -0.6 21 21
platelet activation -0.097 0.16 -10000 0 -0.31 167 167
PGI2/IP 0.006 0.066 -10000 0 -0.41 12 12
PRKACA -0.002 0.079 -10000 0 -0.36 19 19
Gq family/GDP/G beta5/gamma2 -0.042 0.14 -10000 0 -0.53 23 23
TXA2/TP beta/beta Arrestin2 0.009 0.045 -10000 0 -0.37 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.076 -10000 0 -0.36 19 19
mol:DAG -0.14 0.23 -10000 0 -0.44 171 171
EGFR 0.022 0.083 0.36 11 -0.56 6 17
TXA2/TP alpha -0.16 0.26 -10000 0 -0.5 173 173
Gq family/GTP -0.058 0.12 -10000 0 -0.25 125 125
YES1 -0.014 0.067 0.25 2 -0.38 7 9
GNAI2/GTP -0.006 0.069 -10000 0 -0.35 13 13
PGD2/DP 0.006 0.064 -10000 0 -0.37 13 13
SLC9A3R1 0.024 0.023 0.27 4 -10000 0 4
FYN -0.013 0.072 0.27 3 -0.44 6 9
mol:NO 0.019 0.046 -10000 0 -0.56 3 3
GNA15 0.022 0.004 -10000 0 -10000 0 0
PGK/cGMP -0.004 0.11 -10000 0 -0.36 41 41
RhoA/GDP 0.021 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.002 0.13 -10000 0 -0.37 42 42
NOS3 0.019 0.046 -10000 0 -0.56 3 3
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.11 0.19 -10000 0 -0.36 165 165
PRKCB -0.12 0.2 -10000 0 -0.38 168 168
PRKCE -0.11 0.19 0.27 1 -0.37 158 159
PRKCD -0.12 0.2 -10000 0 -0.39 166 166
PRKCG -0.13 0.21 -10000 0 -0.4 166 166
muscle contraction -0.16 0.26 -10000 0 -0.5 169 169
PRKCZ -0.11 0.18 -10000 0 -0.35 167 167
ARR3 -0.011 0.016 -10000 0 -10000 0 0
TXA2/TP beta 0.009 0.079 -10000 0 -0.38 14 14
PRKCQ -0.13 0.2 -10000 0 -0.39 171 171
MAPKKK cascade -0.16 0.25 -10000 0 -0.47 172 172
SELE -0.12 0.2 -10000 0 -0.4 165 165
TP beta/GNAI2/GDP/G beta/gamma 0.02 0.09 -10000 0 -0.45 11 11
ROCK1 0.022 0.004 -10000 0 -10000 0 0
GNA14 -0.11 0.24 -10000 0 -0.56 111 111
chemotaxis -0.2 0.31 -10000 0 -0.62 165 165
GNA12 0.022 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.003 -10000 0 -10000 0 0
IL4-mediated signaling events

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.42 0.53 -10000 0 -1.2 109 109
STAT6 (cleaved dimer) -0.44 0.54 -10000 0 -1.2 121 121
IGHG1 -0.13 0.18 -10000 0 -0.46 12 12
IGHG3 -0.42 0.51 -10000 0 -1.1 118 118
AKT1 -0.21 0.3 -10000 0 -0.92 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.26 -10000 0 -0.85 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.21 0.32 -10000 0 -1 38 38
THY1 -0.44 0.53 -10000 0 -1.2 108 108
MYB 0.027 0.053 0.24 15 -0.56 2 17
HMGA1 0.024 0.017 0.24 3 -10000 0 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.33 -10000 0 -0.66 118 118
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.33 -10000 0 -1 39 39
SP1 0.027 0.004 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
SOCS5 0.02 0.03 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.43 0.54 -10000 0 -1.2 119 119
SOCS1 -0.28 0.34 -10000 0 -0.75 110 110
SOCS3 -0.21 0.27 -10000 0 -0.83 28 28
FCER2 -0.41 0.51 -10000 0 -1.1 130 130
PARP14 0.021 0.009 -10000 0 -10000 0 0
CCL17 -0.5 0.6 -10000 0 -1.4 127 127
GRB2 0.022 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.26 -10000 0 -0.78 40 40
T cell proliferation -0.43 0.54 -10000 0 -1.2 113 113
IL4R/JAK1 -0.43 0.53 -10000 0 -1.2 109 109
EGR2 -0.45 0.55 -10000 0 -1.3 114 114
JAK2 -0.019 0.047 -10000 0 -10000 0 0
JAK3 0.027 0.009 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
JAK1 0 0.026 -10000 0 -10000 0 0
COL1A2 -0.11 0.16 -10000 0 -10000 0 0
CCL26 -0.43 0.53 -10000 0 -1.2 109 109
IL4R -0.46 0.56 -10000 0 -1.3 109 109
PTPN6 0.026 0.022 -10000 0 -10000 0 0
IL13RA2 -0.46 0.56 -10000 0 -1.3 117 117
IL13RA1 -0.018 0.05 -10000 0 -10000 0 0
IRF4 -0.2 0.37 -10000 0 -0.89 92 92
ARG1 -0.12 0.22 -10000 0 -0.79 28 28
CBL -0.23 0.31 -10000 0 -0.64 111 111
GTF3A 0.028 0.012 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.018 0.067 -10000 0 -10000 0 0
IRF4/BCL6 -0.16 0.32 -10000 0 -0.76 86 86
CD40LG -0.074 0.22 -10000 0 -0.56 83 83
MAPK14 -0.23 0.31 -10000 0 -0.7 78 78
mitosis -0.2 0.28 -10000 0 -0.85 38 38
STAT6 -0.51 0.66 -10000 0 -1.5 116 116
SPI1 -0.014 0.15 -10000 0 -0.56 33 33
RPS6KB1 -0.19 0.27 -10000 0 -0.82 36 36
STAT6 (dimer) -0.51 0.66 -10000 0 -1.5 116 116
STAT6 (dimer)/PARP14 -0.46 0.58 -10000 0 -1.3 112 112
mast cell activation 0.009 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.34 -10000 0 -0.85 64 64
FRAP1 -0.21 0.3 -10000 0 -0.92 38 38
LTA -0.44 0.53 -10000 0 -1.2 109 109
FES 0.021 0.026 -10000 0 -0.56 1 1
T-helper 1 cell differentiation 0.49 0.61 1.4 116 -10000 0 116
CCL11 -0.43 0.51 -10000 0 -1.2 112 112
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.19 0.3 -10000 0 -0.89 37 37
IL2RG 0.019 0.069 -10000 0 -0.55 7 7
IL10 -0.44 0.53 -10000 0 -1.2 109 109
IRS1 0.022 0.004 -10000 0 -10000 0 0
IRS2 0.018 0.046 -10000 0 -0.56 3 3
IL4 -0.14 0.27 -10000 0 -1.1 29 29
IL5 -0.44 0.53 -10000 0 -1.2 109 109
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.45 -10000 0 -0.97 120 120
COL1A1 -0.14 0.25 -10000 0 -1 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.45 0.55 -10000 0 -1.3 108 108
IL2R gamma/JAK3 0.029 0.054 -10000 0 -0.4 7 7
TFF3 -0.48 0.6 -10000 0 -1.4 114 114
ALOX15 -0.65 0.73 -10000 0 -1.5 188 188
MYBL1 0.023 0.011 0.24 1 -10000 0 1
T-helper 2 cell differentiation -0.48 0.51 -10000 0 -1.1 154 154
SHC1 0.022 0.005 -10000 0 -10000 0 0
CEBPB 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.31 -10000 0 -0.94 39 39
mol:PI-3-4-5-P3 -0.21 0.3 -10000 0 -0.92 38 38
PI3K -0.22 0.33 -10000 0 -1 38 38
DOK2 -0.021 0.15 -10000 0 -0.56 35 35
ETS1 0.008 0.085 -10000 0 -0.52 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.23 -10000 0 -0.7 34 34
ITGB3 -0.44 0.54 -10000 0 -1.3 110 110
PIGR -0.81 0.78 -10000 0 -1.5 258 258
IGHE 0.046 0.053 0.2 12 -10000 0 12
MAPKKK cascade -0.15 0.22 -10000 0 -0.68 34 34
BCL6 0.013 0.011 -10000 0 -10000 0 0
OPRM1 -0.44 0.53 -10000 0 -1.2 109 109
RETNLB -0.42 0.53 -10000 0 -1.2 106 106
SELP -0.58 0.7 -10000 0 -1.5 150 150
AICDA -0.41 0.51 -10000 0 -1.2 109 109
Aurora B signaling

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.058 0.089 0.28 16 -0.32 8 24
STMN1 0.011 0.06 -10000 0 -0.2 12 12
Aurora B/RasGAP/Survivin 0.22 0.14 0.32 288 -0.19 11 299
Chromosomal passenger complex/Cul3 protein complex 0.041 0.08 0.2 10 -0.29 14 24
BIRC5 0.21 0.085 0.25 411 -0.3 1 412
DES -0.3 0.31 -10000 0 -0.51 308 308
Aurora C/Aurora B/INCENP 0.12 0.09 0.3 1 -0.35 1 2
Aurora B/TACC1 0.092 0.093 -10000 0 -0.18 18 18
Aurora B/PP2A 0.12 0.099 -10000 0 -0.2 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.018 0.03 0.13 4 -10000 0 4
mitotic metaphase/anaphase transition -0.003 0.005 -10000 0 -10000 0 0
NDC80 -0.015 0.11 0.35 21 -0.22 19 40
Cul3 protein complex 0.04 0.03 0.25 1 -10000 0 1
KIF2C 0.07 0.085 0.14 84 -0.37 11 95
PEBP1 0.021 0.006 -10000 0 -10000 0 0
KIF20A 0.12 0.13 0.24 236 -0.29 15 251
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.098 -10000 0 -0.2 6 6
SEPT1 0.023 0.01 0.24 1 -10000 0 1
SMC2 0.022 0.004 -10000 0 -10000 0 0
SMC4 0.016 0.011 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.073 0.18 0.28 3 -0.57 30 33
PSMA3 0.022 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.003 -10000 0 -10000 0 0
H3F3B 0.044 0.062 0.18 8 -0.22 19 27
AURKB 0.16 0.14 0.25 326 -0.29 22 348
AURKC 0.021 0.028 0.24 1 -0.56 1 2
CDCA8 0.084 0.1 0.25 132 -0.3 1 133
cytokinesis 0.048 0.12 0.23 7 -0.39 23 30
Aurora B/Septin1 0.13 0.14 0.31 16 -0.38 21 37
AURKA 0.028 0.049 0.24 22 -10000 0 22
INCENP 0.024 0.009 -10000 0 -10000 0 0
KLHL13 0.029 0.04 0.27 12 -10000 0 12
BUB1 0.042 0.067 0.25 45 -10000 0 45
hSgo1/Aurora B/Survivin 0.26 0.2 0.39 316 -0.24 28 344
EVI5 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.1 0.096 0.26 36 -0.27 7 43
SGOL1 0.11 0.14 0.24 232 -0.29 21 253
CENPA 0.081 0.08 0.19 32 -0.23 12 44
NCAPG 0.056 0.088 0.24 83 -0.29 4 87
Aurora B/HC8 Proteasome 0.12 0.099 -10000 0 -0.2 3 3
NCAPD2 0.022 0.017 0.37 1 -10000 0 1
Aurora B/PP1-gamma 0.13 0.098 -10000 0 -0.2 22 22
RHOA 0.021 0.007 -10000 0 -10000 0 0
NCAPH 0.13 0.11 0.24 247 -10000 0 247
NPM1 0.019 0.18 -10000 0 -0.62 30 30
RASA1 0.021 0.006 -10000 0 -10000 0 0
KLHL9 0.019 0.009 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.098 -10000 0 -0.2 3 3
PPP1CC 0.023 0.002 -10000 0 -10000 0 0
Centraspindlin 0.11 0.11 0.26 77 -0.3 8 85
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
NSUN2 0.063 0.12 0.23 2 -0.34 27 29
MYLK 0.051 0.071 0.17 44 -0.22 19 63
KIF23 0.068 0.087 0.24 96 -10000 0 96
VIM 0.002 0.091 0.28 3 -0.44 10 13
RACGAP1 0.026 0.008 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.036 0.14 -10000 0 -0.46 27 27
Chromosomal passenger complex 0.066 0.081 0.18 21 -0.27 15 36
Chromosomal passenger complex/EVI5 0.29 0.17 0.39 312 -0.22 9 321
TACC1 0.018 0.028 -10000 0 -0.56 1 1
PPP2R5D 0.022 0.004 -10000 0 -10000 0 0
CUL3 0.022 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.34 -10000 0 -1.1 50 50
MKNK1 0.022 0.004 -10000 0 -10000 0 0
MAPK14 -0.014 0.13 -10000 0 -0.32 68 68
ATF2/c-Jun -0.021 0.097 -10000 0 -0.4 5 5
MAPK11 -0.016 0.13 -10000 0 -0.32 70 70
MITF -0.039 0.15 -10000 0 -0.38 77 77
MAPKAPK5 -0.031 0.14 -10000 0 -0.37 73 73
KRT8 -0.031 0.14 -10000 0 -0.37 72 72
MAPKAPK3 0.021 0.007 -10000 0 -10000 0 0
MAPKAPK2 0.022 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.028 0.19 -10000 0 -0.47 71 71
CEBPB -0.03 0.14 -10000 0 -0.36 72 72
SLC9A1 -0.032 0.15 -10000 0 -0.38 71 71
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.027 0.14 -10000 0 -0.36 69 69
p38alpha-beta/MNK1 -0.008 0.16 -10000 0 -0.39 66 66
JUN -0.02 0.096 -10000 0 -0.4 5 5
PPARGC1A -0.11 0.24 -10000 0 -0.44 135 135
USF1 -0.03 0.14 -10000 0 -0.36 70 70
RAB5/GDP/GDI1 -0.017 0.11 -10000 0 -0.28 64 64
NOS2 -0.064 0.28 -10000 0 -1.1 28 28
DDIT3 -0.03 0.14 -10000 0 -0.36 72 72
RAB5A 0.021 0.006 -10000 0 -10000 0 0
HSPB1 -0.028 0.12 0.27 8 -0.31 64 72
p38alpha-beta/HBP1 -0.008 0.16 -10000 0 -0.38 67 67
CREB1 -0.032 0.15 -10000 0 -0.39 71 71
RAB5/GDP 0.016 0.005 -10000 0 -10000 0 0
EIF4E -0.032 0.13 -10000 0 -0.35 65 65
RPS6KA4 -0.031 0.14 -10000 0 -0.37 72 72
PLA2G4A -0.033 0.14 0.26 1 -0.35 68 69
GDI1 -0.028 0.14 -10000 0 -0.37 68 68
TP53 -0.051 0.18 -10000 0 -0.47 70 70
RPS6KA5 -0.031 0.14 -10000 0 -0.37 71 71
ESR1 -0.049 0.18 -10000 0 -0.41 86 86
HBP1 0.022 0.005 -10000 0 -10000 0 0
MEF2C -0.038 0.15 -10000 0 -0.38 76 76
MEF2A -0.03 0.14 -10000 0 -0.37 71 71
EIF4EBP1 -0.03 0.15 -10000 0 -0.39 69 69
KRT19 -0.037 0.16 -10000 0 -0.39 75 75
ELK4 -0.03 0.14 -10000 0 -0.37 71 71
ATF6 -0.03 0.14 -10000 0 -0.36 70 70
ATF1 -0.032 0.15 -10000 0 -0.38 71 71
p38alpha-beta/MAPKAPK2 -0.008 0.16 -10000 0 -0.39 67 67
p38alpha-beta/MAPKAPK3 -0.011 0.16 -10000 0 -0.39 67 67
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.013 0.16 -10000 0 -0.52 39 39
alphaM/beta2 Integrin/GPIbA -0.014 0.16 -10000 0 -0.51 40 40
alphaM/beta2 Integrin/proMMP-9 -0.003 0.16 -10000 0 -0.5 37 37
PLAUR 0.022 0.005 -10000 0 -10000 0 0
HMGB1 0.014 0.021 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.011 0.15 -10000 0 -0.49 38 38
AGER -0.5 0.18 -10000 0 -0.56 433 433
RAP1A 0.022 0.005 -10000 0 -10000 0 0
SELPLG -0.014 0.14 -10000 0 -0.56 31 31
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.35 0.2 -10000 0 -0.39 431 431
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.034 0.049 0.24 25 -10000 0 25
CYR61 -0.004 0.12 -10000 0 -0.56 22 22
TLN1 0.021 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.15 0.26 -10000 0 -0.52 116 116
RHOA 0.021 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.24 -10000 0 -0.56 108 108
MYH2 -0.24 0.29 -10000 0 -0.62 147 147
MST1R -0.007 0.12 -10000 0 -0.56 23 23
leukocyte activation during inflammatory response -0.018 0.16 -10000 0 -0.41 57 57
APOB -0.013 0.13 0.24 4 -0.56 27 31
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.017 0.053 -10000 0 -0.56 4 4
JAM3 0.022 0.005 -10000 0 -10000 0 0
GP1BA 0.016 0.054 0.24 1 -0.56 4 5
alphaM/beta2 Integrin/CTGF -0.022 0.18 -10000 0 -0.53 46 46
alphaM/beta2 Integrin -0.19 0.31 -10000 0 -0.6 121 121
JAM3 homodimer 0.022 0.005 -10000 0 -10000 0 0
ICAM2 -0.013 0.14 -10000 0 -0.56 30 30
ICAM1 -0.022 0.15 -10000 0 -0.56 37 37
phagocytosis triggered by activation of immune response cell surface activating receptor -0.18 0.3 -10000 0 -0.59 121 121
cell adhesion -0.014 0.16 -10000 0 -0.51 40 40
NFKB1 -0.36 0.23 -10000 0 -0.71 110 110
THY1 0.022 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
Lipoprotein(a) 0.012 0.092 0.24 2 -0.35 27 29
alphaM/beta2 Integrin/LRP/tPA 0.001 0.15 -10000 0 -0.47 38 38
IL6 -0.39 0.32 -10000 0 -0.93 107 107
ITGB2 -0.006 0.11 -10000 0 -0.56 17 17
elevation of cytosolic calcium ion concentration 0.007 0.15 0.25 1 -0.47 37 38
alphaM/beta2 Integrin/JAM2/JAM3 -0.046 0.21 -10000 0 -0.46 84 84
JAM2 -0.058 0.2 -10000 0 -0.56 67 67
alphaM/beta2 Integrin/ICAM1 -0.024 0.21 -10000 0 -0.46 76 76
alphaM/beta2 Integrin/uPA/Plg 0.007 0.15 -10000 0 -0.47 38 38
RhoA/GTP -0.22 0.3 -10000 0 -0.67 122 122
positive regulation of phagocytosis -0.13 0.24 -10000 0 -0.58 77 77
Ron/MSP 0.008 0.096 -10000 0 -0.41 23 23
alphaM/beta2 Integrin/uPAR/uPA 0.008 0.15 0.26 1 -0.47 37 38
alphaM/beta2 Integrin/uPAR -0.011 0.15 -10000 0 -0.5 38 38
PLAU 0.035 0.053 0.24 30 -10000 0 30
PLAT 0.025 0.035 0.33 6 -10000 0 6
actin filament polymerization -0.23 0.27 -10000 0 -0.57 150 150
MST1 0.021 0.012 0.24 1 -10000 0 1
alphaM/beta2 Integrin/lipoprotein(a) -0.015 0.16 -10000 0 -0.42 57 57
TNF -0.34 0.22 -10000 0 -0.69 105 105
RAP1B 0.022 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.003 0.16 0.26 1 -0.51 38 39
fibrinolysis 0.005 0.15 -10000 0 -0.46 38 38
HCK 0.018 0.046 -10000 0 -0.56 3 3
dendritic cell antigen processing and presentation -0.18 0.3 -10000 0 -0.59 121 121
VTN -0.2 0.28 0.24 2 -0.56 186 188
alphaM/beta2 Integrin/CYR61 -0.027 0.18 -10000 0 -0.52 51 51
LPA 0.02 0.049 0.25 18 -10000 0 18
LRP1 0.023 0.002 -10000 0 -10000 0 0
cell migration -0.014 0.15 -10000 0 -0.48 38 38
FN1 0.01 0.082 -10000 0 -0.56 10 10
alphaM/beta2 Integrin/Thy1 -0.011 0.15 -10000 0 -0.5 38 38
MPO -0.002 0.12 -10000 0 -0.56 20 20
KNG1 0.006 0.051 0.3 12 -10000 0 12
RAP1/GDP 0.029 0.009 -10000 0 -10000 0 0
ROCK1 -0.2 0.28 -10000 0 -0.62 119 119
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.006 0.026 0.24 3 -10000 0 3
CTGF 0.004 0.1 -10000 0 -0.56 16 16
alphaM/beta2 Integrin/Hck -0.011 0.15 -10000 0 -0.5 37 37
ITGAM -0.031 0.16 -10000 0 -0.57 38 38
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.092 0.26 -10000 0 -0.48 122 122
HP -0.14 0.26 -10000 0 -0.56 139 139
leukocyte adhesion -0.34 0.23 -10000 0 -0.61 145 145
SELP -0.11 0.24 -10000 0 -0.56 108 108
TCGA08_retinoblastoma

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
CDKN2B 0.017 0.038 -10000 0 -0.53 2 2
CDKN2C 0.024 0.02 -10000 0 -10000 0 0
CDKN2A 0.096 0.14 0.24 204 -0.28 20 224
CCND2 -0.01 0.055 0.23 5 -0.38 7 12
RB1 -0.006 0.082 0.43 6 -0.24 35 41
CDK4 -0.002 0.073 0.25 21 -0.43 6 27
CDK6 -0.003 0.073 0.25 21 -0.44 6 27
G1/S progression 0.033 0.1 0.21 104 -0.42 6 110
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.018 0.064 0.36 11 -10000 0 11
VDR 0.022 0.026 -10000 0 -0.56 1 1
FAM120B 0.022 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.12 0.15 -10000 0 -0.41 21 21
RXRs/LXRs/DNA/Oxysterols -0.099 0.14 -10000 0 -0.47 19 19
MED1 0.022 0.004 -10000 0 -10000 0 0
mol:9cRA 0.001 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.001 0.071 -10000 0 -0.27 18 18
RXRs/NUR77 -0.17 0.22 -10000 0 -0.37 259 259
RXRs/PPAR -0.15 0.17 -10000 0 -0.3 255 255
NCOR2 0.022 0.026 -10000 0 -0.56 1 1
VDR/VDR/Vit D3 0.016 0.019 -10000 0 -0.41 1 1
RARs/VDR/DNA/Vit D3 0.047 0.029 -10000 0 -0.3 2 2
RARA 0.022 0.004 -10000 0 -10000 0 0
NCOA1 0.023 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.022 0.026 -10000 0 -0.56 1 1
RARs/RARs/DNA/9cRA 0.036 0.022 -10000 0 -0.28 1 1
RARG 0.023 0.002 -10000 0 -10000 0 0
RPS6KB1 0.038 0.083 0.65 7 -10000 0 7
RARs/THRs/DNA/SMRT 0 0.073 -10000 0 -0.28 19 19
THRA 0.022 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.019 -10000 0 -0.41 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.13 0.18 -10000 0 -0.32 235 235
NR1H4 -0.001 0.029 0.24 4 -10000 0 4
RXRs/LXRs/DNA -0.12 0.19 -10000 0 -0.3 234 234
NR1H2 0.023 0.012 -10000 0 -10000 0 0
NR1H3 0.024 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.18 -10000 0 -0.3 232 232
NR4A1 -0.055 0.2 -10000 0 -0.56 65 65
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.1 0.12 -10000 0 -0.23 235 235
RXRG -0.26 0.29 -10000 0 -0.56 237 237
RXR alpha/CCPG 0.033 0.012 -10000 0 -10000 0 0
RXRA 0.023 0.011 -10000 0 -10000 0 0
RXRB 0.023 0.011 -10000 0 -10000 0 0
THRB 0.002 0.1 -10000 0 -0.56 16 16
PPARG -0.04 0.18 -10000 0 -0.56 51 51
PPARD 0.023 0.003 -10000 0 -10000 0 0
TNF -0.1 0.19 -10000 0 -1.1 12 12
mol:Oxysterols 0.002 0.007 -10000 0 -10000 0 0
cholesterol transport -0.098 0.14 -10000 0 -0.47 19 19
PPARA 0.022 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.02 0.027 -10000 0 -0.56 1 1
RXRs/NUR77/BCL2 -0.16 0.17 -10000 0 -0.3 259 259
SREBF1 -0.09 0.13 -10000 0 -0.55 9 9
RXRs/RXRs/DNA/9cRA -0.13 0.18 -10000 0 -0.32 235 235
ABCA1 -0.091 0.13 -10000 0 -0.56 9 9
RARs/THRs 0.048 0.07 -10000 0 -0.31 16 16
RXRs/FXR -0.13 0.19 -10000 0 -0.33 235 235
BCL2 0.023 0.016 0.37 1 -10000 0 1
Aurora C signaling

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
INCENP 0.023 0.002 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.087 0.3 1 -0.36 1 2
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.004 0.022 -10000 0 -0.42 1 1
AURKB 0.15 0.14 0.24 326 -0.29 22 348
AURKC 0.021 0.028 0.24 1 -0.56 1 2
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.022 0.092 -10000 0 -0.39 23 23
Crk/p130 Cas/Paxillin -0.052 0.12 -10000 0 -0.3 50 50
JUN -0.019 0.12 0.26 7 -0.35 6 13
HRAS 0.022 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.005 0.16 0.36 4 -0.33 75 79
RAP1A 0.022 0.005 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.016 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.006 0.17 0.35 4 -0.33 79 83
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.022 0.16 0.24 18 -0.33 86 104
RHOA 0.021 0.007 -10000 0 -10000 0 0
RAP1A/GTP -0.01 0.15 0.32 3 -0.3 80 83
GRB7 0.025 0.032 0.37 4 -10000 0 4
RET51/GFRalpha1/GDNF -0.008 0.16 0.36 3 -0.33 78 81
MAPKKK cascade -0.028 0.14 0.27 2 -0.31 67 69
BCAR1 0.022 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.021 0.16 0.24 19 -0.33 86 105
lamellipodium assembly -0.039 0.12 -10000 0 -0.28 53 53
RET51/GFRalpha1/GDNF/SHC -0.008 0.16 0.34 4 -0.33 77 81
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.022 0.16 0.24 17 -0.33 81 98
RET9/GFRalpha1/GDNF/Shank3 -0.023 0.16 0.24 17 -0.33 85 102
MAPK3 -0.043 0.13 0.33 1 -0.29 77 78
DOK1 0.022 0.004 -10000 0 -10000 0 0
DOK6 -0.026 0.16 -10000 0 -0.56 40 40
PXN 0.023 0.002 -10000 0 -10000 0 0
neurite development -0.048 0.13 0.32 1 -0.37 17 18
DOK5 0.021 0.04 0.24 2 -0.56 2 4
GFRA1 -0.11 0.24 -10000 0 -0.56 111 111
MAPK8 -0.033 0.12 0.28 7 -0.34 8 15
HRAS/GTP -0.019 0.15 0.32 3 -0.33 70 73
tube development -0.021 0.15 0.32 1 -0.32 85 86
MAPK1 -0.042 0.13 0.27 2 -0.29 71 73
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.033 0.12 -10000 0 -0.26 83 83
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
PDLIM7 0.021 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.024 0.19 0.36 4 -0.36 102 106
SHC1 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.008 0.17 0.38 3 -0.33 80 83
RET51/GFRalpha1/GDNF/Dok5 -0.009 0.17 0.4 4 -0.34 80 84
PRKCA 0.02 0.037 -10000 0 -0.56 2 2
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
CREB1 -0.037 0.13 0.27 3 -0.29 68 71
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.035 0.12 -10000 0 -0.27 83 83
RET51/GFRalpha1/GDNF/Grb7 -0.006 0.17 0.28 24 -0.33 80 104
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.03 0.04 0.24 16 -10000 0 16
DOK4 0.022 0.005 -10000 0 -10000 0 0
JNK cascade -0.018 0.12 0.26 7 -0.34 6 13
RET9/GFRalpha1/GDNF/FRS2 -0.02 0.16 0.24 18 -0.33 82 100
SHANK3 0.021 0.027 -10000 0 -0.56 1 1
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.033 0.12 -10000 0 -0.26 79 79
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.029 0.12 0.26 2 -0.26 82 84
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.032 0.12 0.28 2 -0.27 76 78
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.027 0.12 0.28 2 -0.26 65 67
PI3K -0.038 0.18 0.34 3 -0.4 55 58
SOS1 0.022 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.015 0.16 -10000 0 -0.32 85 85
GRB10 0.022 0.005 -10000 0 -10000 0 0
activation of MAPKK activity -0.027 0.11 0.31 1 -0.3 1 2
RET51/GFRalpha1/GDNF/FRS2 -0.007 0.16 0.36 4 -0.33 79 83
GAB1 0.022 0.006 -10000 0 -10000 0 0
IRS1 0.022 0.004 -10000 0 -10000 0 0
IRS2 0.018 0.046 -10000 0 -0.56 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.03 0.12 -10000 0 -0.27 71 71
RET51/GFRalpha1/GDNF/PKC alpha -0.009 0.17 0.36 4 -0.33 83 87
GRB2 0.022 0.004 -10000 0 -10000 0 0
PRKACA 0.022 0.004 -10000 0 -10000 0 0
GDNF 0.055 0.1 0.28 79 -10000 0 79
RAC1 0.022 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.008 0.17 0.36 4 -0.33 82 86
Rac1/GTP -0.034 0.14 -10000 0 -0.33 51 51
RET9/GFRalpha1/GDNF -0.034 0.17 0.24 19 -0.34 92 111
GFRalpha1/GDNF -0.043 0.19 0.26 19 -0.36 112 131
Nongenotropic Androgen signaling

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
PTK2 -0.005 0.002 -10000 0 -10000 0 0
GNB1/GNG2 -0.037 0.15 -10000 0 -0.32 101 101
regulation of S phase of mitotic cell cycle -0.034 0.093 -10000 0 -0.27 47 47
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
SHBG/T-DHT 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.021 0.006 -10000 0 -10000 0 0
AKT1 -0.004 0.003 -10000 0 -10000 0 0
MAP2K1 -0.073 0.12 -10000 0 -0.29 89 89
T-DHT/AR -0.073 0.17 -10000 0 -0.4 102 102
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 55 55
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP -0.081 0.16 -10000 0 -0.38 100 100
cell proliferation -0.097 0.17 -10000 0 -0.43 70 70
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
FOS -0.11 0.26 -10000 0 -0.8 57 57
mol:Ca2+ -0.009 0.023 -10000 0 -0.072 34 34
MAPK3 -0.089 0.14 -10000 0 -0.35 71 71
MAPK1 -0.044 0.099 -10000 0 -0.33 26 26
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 55 55
cAMP biosynthetic process 0.002 0.017 -10000 0 -10000 0 0
GNG2 0.016 0.059 -10000 0 -0.56 5 5
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 55 55
HRAS/GTP -0.036 0.14 -10000 0 -0.3 96 96
actin cytoskeleton reorganization 0.017 0.018 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 55 55
PI3K 0.015 0.016 -10000 0 -10000 0 0
apoptosis 0.075 0.16 0.43 63 -10000 0 63
T-DHT/AR/PELP1 -0.053 0.15 -10000 0 -0.35 99 99
HRAS/GDP -0.067 0.16 -10000 0 -0.36 100 100
CREB1 -0.081 0.17 -10000 0 -0.47 63 63
RAC1-CDC42/GTP 0.022 0.023 -10000 0 -10000 0 0
AR -0.098 0.23 -10000 0 -0.56 99 99
GNB1 0.021 0.027 -10000 0 -0.56 1 1
RAF1 -0.07 0.12 0.2 1 -0.29 94 95
RAC1-CDC42/GDP -0.026 0.17 -10000 0 -0.35 97 97
T-DHT/AR/PELP1/Src -0.039 0.14 -10000 0 -0.32 96 96
MAP2K2 -0.073 0.12 -10000 0 -0.29 94 94
T-DHT/AR/PELP1/Src/PI3K -0.035 0.094 -10000 0 -0.28 47 47
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
SHBG 0.02 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.034 0.17 -10000 0 -0.53 37 37
mol:T-DHT 0 0.001 0.002 1 -0.002 36 37
RAC1 0.022 0.004 -10000 0 -10000 0 0
GNRH1 -0.006 0.026 -10000 0 -0.41 2 2
Gi family/GTP -0.032 0.091 -10000 0 -0.33 23 23
CDC42 0.022 0.004 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.024 0.14 0.33 3 -0.38 50 53
CRKL -0.037 0.13 -10000 0 -0.4 51 51
HRAS -0.03 0.14 -10000 0 -0.4 45 45
mol:PIP3 -0.004 0.13 0.25 1 -0.35 49 50
SPRED1 0.023 0.003 -10000 0 -10000 0 0
SPRED2 0.022 0.006 -10000 0 -10000 0 0
GAB1 -0.039 0.15 -10000 0 -0.42 60 60
FOXO3 -0.024 0.14 0.28 1 -0.36 62 63
AKT1 -0.025 0.15 0.3 1 -0.39 64 65
BAD -0.025 0.14 0.27 2 -0.36 62 64
megakaryocyte differentiation -0.055 0.17 -10000 0 -0.43 73 73
GSK3B -0.006 0.15 0.28 9 -0.37 52 61
RAF1 -0.021 0.12 0.24 2 -0.32 43 45
SHC1 0.022 0.005 -10000 0 -10000 0 0
STAT3 -0.041 0.15 -10000 0 -0.42 60 60
STAT1 -0.11 0.36 -10000 0 -1 60 60
HRAS/SPRED1 -0.012 0.13 -10000 0 -0.4 16 16
cell proliferation -0.039 0.14 -10000 0 -0.41 61 61
PIK3CA 0.012 0.011 -10000 0 -10000 0 0
TEC 0.018 0.046 -10000 0 -0.56 3 3
RPS6KB1 -0.031 0.15 -10000 0 -0.4 62 62
HRAS/SPRED2 -0.013 0.12 -10000 0 -0.35 31 31
LYN/TEC/p62DOK -0.012 0.15 -10000 0 -0.42 51 51
MAPK3 -0.016 0.097 0.28 4 -0.3 17 21
STAP1 -0.053 0.17 -10000 0 -0.44 70 70
GRAP2 -0.005 0.12 -10000 0 -0.56 23 23
JAK2 -0.093 0.32 -10000 0 -0.91 60 60
STAT1 (dimer) -0.11 0.34 -10000 0 -1 60 60
mol:Gleevec 0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.012 0.16 -10000 0 -0.41 57 57
actin filament polymerization -0.039 0.14 -10000 0 -0.41 55 55
LYN 0.02 0.037 -10000 0 -0.56 2 2
STAP1/STAT5A (dimer) -0.077 0.24 -10000 0 -0.65 63 63
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.011 0.14 -10000 0 -0.38 50 50
PI3K -0.019 0.12 -10000 0 -0.4 28 28
PTEN 0.02 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.42 -10000 0 -1.2 60 60
MAPK8 -0.039 0.15 -10000 0 -0.42 61 61
STAT3 (dimer) -0.04 0.14 -10000 0 -0.41 60 60
positive regulation of transcription -0.011 0.082 0.27 4 -0.24 16 20
mol:GDP -0.029 0.15 -10000 0 -0.4 50 50
PIK3C2B -0.039 0.14 -10000 0 -0.42 59 59
CBL/CRKL -0.021 0.14 -10000 0 -0.39 52 52
FER -0.038 0.15 -10000 0 -0.42 60 60
SH2B3 -0.042 0.15 -10000 0 -0.42 62 62
PDPK1 -0.001 0.13 -10000 0 -0.33 44 44
SNAI2 -0.04 0.14 -10000 0 -0.42 60 60
positive regulation of cell proliferation -0.081 0.27 -10000 0 -0.76 61 61
KITLG 0.017 0.022 -10000 0 -10000 0 0
cell motility -0.081 0.27 -10000 0 -0.76 61 61
PTPN6 0.022 0.011 -10000 0 -10000 0 0
EPOR -0.033 0.19 -10000 0 -0.88 14 14
STAT5A (dimer) -0.064 0.22 -10000 0 -0.62 61 61
SOCS1 0.021 0.027 -10000 0 -0.56 1 1
cell migration 0.05 0.16 0.42 70 -10000 0 70
SOS1 0.022 0.004 -10000 0 -10000 0 0
EPO 0.019 0.03 0.24 6 -10000 0 6
VAV1 0.019 0.046 -10000 0 -0.56 3 3
GRB10 -0.038 0.14 -10000 0 -0.41 59 59
PTPN11 0.023 0.007 -10000 0 -10000 0 0
SCF/KIT -0.04 0.16 -10000 0 -0.44 61 61
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.017 0.099 0.3 4 -0.32 14 18
CBL 0.022 0.004 -10000 0 -10000 0 0
KIT -0.16 0.46 -10000 0 -1.2 69 69
MAP2K2 -0.017 0.1 0.3 4 -0.31 15 19
SHC/Grb2/SOS1 -0.008 0.15 -10000 0 -0.4 52 52
STAT5A -0.064 0.23 -10000 0 -0.65 60 60
GRB2 0.022 0.004 -10000 0 -10000 0 0
response to radiation -0.039 0.14 -10000 0 -0.41 59 59
SHC/GRAP2 0.01 0.095 -10000 0 -0.41 23 23
PTPRO -0.056 0.17 -10000 0 -0.44 73 73
SH2B2 -0.04 0.14 -10000 0 -0.42 55 55
DOK1 0.022 0.004 -10000 0 -10000 0 0
MATK -0.051 0.16 -10000 0 -0.42 70 70
CREBBP 0.017 0.045 -10000 0 -10000 0 0
BCL2 -0.041 0.22 -10000 0 -0.96 18 18
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.071 0.15 0.3 25 -0.32 42 67
SMAD6-7/SMURF1 0.004 0.11 -10000 0 -0.35 42 42
NOG 0.002 0.11 0.24 1 -0.56 17 18
SMAD9 -0.088 0.22 -10000 0 -0.53 92 92
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD5 -0.036 0.14 -10000 0 -0.47 30 30
BMP7/USAG1 -0.013 0.22 0.26 3 -0.42 94 97
SMAD5/SKI -0.038 0.16 0.26 1 -0.46 43 44
SMAD1 0.007 0.061 -10000 0 -0.62 2 2
BMP2 -0.05 0.19 -10000 0 -0.56 60 60
SMAD1/SMAD1/SMAD4 -0.015 0.11 -10000 0 -0.46 6 6
BMPR1A 0.022 0.005 -10000 0 -10000 0 0
BMPR1B -0.021 0.15 -10000 0 -0.56 36 36
BMPR1A-1B/BAMBI 0.011 0.11 0.25 1 -0.35 39 40
AHSG 0.019 0.063 0.35 16 -10000 0 16
CER1 -0.008 0.024 0.24 1 -0.29 1 2
BMP2-4/CER1 -0.017 0.14 -10000 0 -0.37 64 64
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.15 -10000 0 -0.46 37 37
BMP2-4 (homodimer) -0.031 0.16 -10000 0 -0.42 66 66
RGMB 0.021 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.016 0.12 -10000 0 -0.33 45 45
RGMA 0.048 0.073 0.25 53 -10000 0 53
SMURF1 0.022 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.03 0.12 -10000 0 -0.45 25 25
BMP2-4/USAG1 -0.082 0.21 -10000 0 -0.4 132 132
SMAD6/SMURF1/SMAD5 -0.035 0.16 0.31 2 -0.46 42 44
SOSTDC1 -0.085 0.22 0.24 1 -0.56 90 91
BMP7/BMPR2/BMPR1A-1B 0.052 0.14 0.25 2 -0.34 41 43
SKI 0.022 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.009 0.086 -10000 0 -0.56 11 11
HFE2 -0.003 0.024 0.24 2 -10000 0 2
ZFYVE16 0.021 0.006 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD -0.017 0.12 0.25 1 -0.38 40 41
SMAD5/SMAD5/SMAD4 -0.038 0.16 0.31 2 -0.46 43 45
MAPK1 0.022 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.016 0.12 -10000 0 -0.39 25 25
BMP7 (homodimer) 0.086 0.13 0.24 162 -0.49 8 170
NUP214 0.023 0.003 -10000 0 -10000 0 0
BMP6/FETUA 0.018 0.069 0.26 11 -0.41 7 18
SMAD1/SKI 0.007 0.087 -10000 0 -0.53 4 4
SMAD6 -0.038 0.18 -10000 0 -0.56 51 51
CTDSP2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.01 0.12 0.25 12 -0.37 41 53
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.15 0.11 0.24 288 -0.29 2 290
BMPR2 (homodimer) 0.022 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.042 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.002 0.12 -10000 0 -0.41 36 36
CHRDL1 -0.27 0.29 -10000 0 -0.56 248 248
ENDOFIN/SMAD1 0.009 0.085 -10000 0 -0.53 4 4
SMAD6-7/SMURF1/SMAD1 -0.006 0.12 -10000 0 -0.51 6 6
SMAD6/SMURF1 0.022 0.006 -10000 0 -10000 0 0
BAMBI 0.02 0.049 0.3 2 -0.56 3 5
SMURF2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.2 0.23 -10000 0 -0.4 261 261
BMP2-4/GREM1 0.051 0.18 0.25 1 -0.38 64 65
SMAD7 0.021 0.027 -10000 0 -0.56 1 1
SMAD8A/SMAD8A/SMAD4 -0.087 0.23 -10000 0 -0.51 99 99
SMAD1/SMAD6 0.006 0.086 -10000 0 -0.54 4 4
TAK1/SMAD6 0.032 0.009 -10000 0 -10000 0 0
BMP7 0.086 0.13 0.24 162 -0.49 8 170
BMP6 0.009 0.086 -10000 0 -0.56 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.024 0.12 -10000 0 -0.4 32 32
PPM1A 0.022 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.006 0.086 -10000 0 -0.5 4 4
SMAD7/SMURF1 0.03 0.023 -10000 0 -0.41 1 1
CTDSPL 0.021 0.007 -10000 0 -10000 0 0
PPP1CA 0.022 0.004 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
CTDSP1 0.022 0.004 -10000 0 -10000 0 0
PPP1R15A 0.022 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.036 0.15 -10000 0 -0.44 40 40
CHRD 0.011 0.042 0.37 1 -0.56 2 3
BMPR2 0.022 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.038 0.13 0.2 1 -0.45 27 28
BMP4 0.012 0.079 0.24 1 -0.56 9 10
FST 0.049 0.091 0.24 72 -0.33 7 79
BMP2-4/NOG -0.024 0.16 -10000 0 -0.39 73 73
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.059 0.13 -10000 0 -0.32 35 35
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.009 0.096 -10000 0 -0.41 24 24
alphaV beta3 Integrin 0.026 0.083 -10000 0 -0.37 19 19
PTK2 -0.17 0.19 0.33 2 -0.54 59 61
IGF1R 0.022 0.004 -10000 0 -10000 0 0
PI4KB 0.022 0.006 -10000 0 -10000 0 0
MFGE8 0.023 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
CDKN1B -0.18 0.25 -10000 0 -0.49 184 184
VEGFA 0.022 0.004 -10000 0 -10000 0 0
ILK -0.18 0.25 -10000 0 -0.5 186 186
ROCK1 0.022 0.004 -10000 0 -10000 0 0
AKT1 -0.17 0.23 -10000 0 -0.46 181 181
PTK2B -0.019 0.096 0.35 2 -0.35 26 28
alphaV/beta3 Integrin/JAM-A -0.096 0.18 -10000 0 -0.33 174 174
CBL 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.037 0.053 -10000 0 -0.35 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.044 0.066 -10000 0 -0.32 14 14
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.097 0.16 -10000 0 -0.44 52 52
alphaV/beta3 Integrin/Syndecan-1 0.037 0.055 -10000 0 -0.36 9 9
PI4KA 0.021 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.017 0.11 -10000 0 -0.35 36 36
PI4 Kinase 0.03 0.012 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.099 0.097 0.25 1 -0.29 13 14
RPS6KB1 -0.037 0.099 0.32 1 -0.48 10 11
TLN1 0.021 0.007 -10000 0 -10000 0 0
MAPK3 -0.084 0.17 -10000 0 -0.57 37 37
GPR124 0.019 0.009 -10000 0 -10000 0 0
MAPK1 -0.082 0.17 -10000 0 -0.58 36 36
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.2 0.2 -10000 0 -0.36 289 289
cell adhesion 0.026 0.051 -10000 0 -0.34 7 7
ANGPTL3 0.007 0.029 0.24 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.023 0.083 -10000 0 -0.35 21 21
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
TGFBR2 -0.011 0.13 -10000 0 -0.56 27 27
ITGB3 0.013 0.074 -10000 0 -0.56 8 8
IGF1 0.004 0.1 0.24 1 -0.56 16 17
RAC1 0.022 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.032 0.048 -10000 0 -0.35 6 6
apoptosis 0.023 0.003 -10000 0 -10000 0 0
CD47 0.019 0.027 -10000 0 -0.56 1 1
alphaV/beta3 Integrin/CD47 0.033 0.052 -10000 0 -0.36 7 7
VCL 0.022 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.016 0.1 -10000 0 -0.38 29 29
CSF1 0.017 0.053 -10000 0 -0.56 4 4
PIK3C2A -0.18 0.25 -10000 0 -0.49 186 186
PI4 Kinase/Pyk2 -0.096 0.17 -10000 0 -0.51 26 26
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.029 0.1 -10000 0 -0.37 26 26
FAK1/Vinculin -0.13 0.16 0.31 2 -0.43 52 54
alphaV beta3/Integrin/ppsTEM5 0.032 0.049 -10000 0 -0.36 6 6
RHOA 0.021 0.007 -10000 0 -10000 0 0
VTN -0.2 0.28 0.24 2 -0.56 186 188
BCAR1 0.022 0.006 -10000 0 -10000 0 0
FGF2 0.006 0.094 -10000 0 -0.56 13 13
F11R -0.019 0.063 -10000 0 -0.41 12 12
alphaV/beta3 Integrin/Lactadherin 0.038 0.052 -10000 0 -0.36 8 8
alphaV/beta3 Integrin/TGFBR2 0.012 0.12 -10000 0 -0.41 30 30
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.05 0.036 -10000 0 -0.33 3 3
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.046 -10000 0 -0.32 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.082 -10000 0 -0.56 10 10
alphaV/beta3 Integrin/Pyk2 0.019 0.097 -10000 0 -0.35 26 26
SDC1 0.021 0.027 -10000 0 -0.56 1 1
VAV3 -0.013 0.041 -10000 0 -0.31 4 4
PTPN11 0.023 0.002 -10000 0 -10000 0 0
IRS1 0.022 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.14 0.16 0.34 1 -0.44 52 53
cell migration -0.12 0.14 0.26 3 -0.4 50 53
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PI3K -0.057 0.14 -10000 0 -0.31 82 82
SPP1 0.13 0.12 0.24 247 -0.29 6 253
KDR -0.009 0.13 -10000 0 -0.56 25 25
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.023 0.003 -10000 0 -10000 0 0
COL4A3 -0.33 0.28 -10000 0 -0.56 296 296
angiogenesis -0.11 0.19 0.27 1 -0.58 38 39
Rac1/GTP 0.019 0.037 -10000 0 -0.29 4 4
EDIL3 -0.006 0.12 -10000 0 -0.56 23 23
cell proliferation 0.011 0.11 -10000 0 -0.41 30 30
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.005 0.035 -10000 0 -0.43 1 1
NFATC2 -0.05 0.13 -10000 0 -0.38 62 62
NFATC3 -0.004 0.03 -10000 0 -10000 0 0
CD40LG -0.17 0.29 0.34 2 -0.64 112 114
PTGS2 -0.15 0.26 0.34 2 -0.6 99 101
JUNB 0.021 0.027 -10000 0 -0.56 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.024 -10000 0 -10000 0 0
CaM/Ca2+ 0.003 0.024 -10000 0 -10000 0 0
CALM1 0.01 0.023 -10000 0 -10000 0 0
JUN 0.01 0.023 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.013 -10000 0 -10000 0 0
FOSL1 0.024 0.014 0.24 2 -10000 0 2
CREM 0.022 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.055 0.17 -10000 0 -0.41 60 60
FOS -0.054 0.18 -10000 0 -0.56 54 54
IFNG -0.13 0.23 0.34 1 -0.54 84 85
AP-1/NFAT1-c-4 -0.14 0.28 -10000 0 -0.62 88 88
FASLG -0.13 0.24 0.34 2 -0.58 82 84
NFAT1-c-4/ICER1 -0.047 0.14 -10000 0 -0.36 59 59
IL2RA -0.13 0.23 0.34 1 -0.54 84 85
FKBP12/FK506 0.016 0.004 -10000 0 -10000 0 0
CSF2 -0.15 0.26 0.34 2 -0.58 109 111
JunB/Fra1/NFAT1-c-4 -0.039 0.14 -10000 0 -0.36 56 56
IL4 -0.13 0.23 0.33 2 -0.53 86 88
IL2 -0.033 0.21 -10000 0 -0.93 25 25
IL3 -0.046 0.19 -10000 0 -0.71 36 36
FKBP1A 0.022 0.005 -10000 0 -10000 0 0
BATF3 0.022 0.004 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.022 0.006 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.017 0.062 -10000 0 -0.36 12 12
ARNO/beta Arrestin1-2 -0.1 0.22 -10000 0 -0.6 50 50
EGFR 0.022 0.083 0.36 11 -0.56 6 17
EPHA2 0.018 0.046 -10000 0 -0.56 3 3
USP6 0.022 0.006 -10000 0 -10000 0 0
IQSEC1 0.021 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.023 0.082 0.26 8 -0.44 12 20
ARRB2 0.007 0.004 -10000 0 -10000 0 0
mol:GTP 0.038 0.063 0.16 27 -0.18 8 35
ARRB1 -0.085 0.22 -10000 0 -0.56 90 90
FBXO8 0.021 0.006 -10000 0 -10000 0 0
TSHR 0.027 0.04 0.24 16 -10000 0 16
EGF 0.015 0.071 0.24 3 -0.56 7 10
somatostatin receptor activity 0 0 0.001 4 -0.001 104 108
ARAP2 0.02 0.027 -10000 0 -0.56 1 1
mol:GDP -0.091 0.16 0.2 1 -0.33 110 111
mol:PI-3-4-5-P3 0 0 0.001 1 -0.001 57 58
ITGA2B 0.006 0.097 -10000 0 -0.56 14 14
ARF6 0.022 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.039 -10000 0 -0.33 3 3
ADAP1 0.014 0.069 -10000 0 -0.56 7 7
KIF13B 0.015 0.059 -10000 0 -0.56 5 5
HGF/MET -0.054 0.18 0.26 1 -0.41 93 94
PXN 0.023 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.085 0.14 0.2 7 -0.3 108 115
EGFR/EGFR/EGF/EGF/ARFGEP100 0.034 0.075 0.25 8 -0.38 12 20
ADRB2 -0.12 0.25 -10000 0 -0.56 121 121
receptor agonist activity 0 0 0 8 0 98 106
actin filament binding 0 0 0 4 -0.001 109 113
SRC 0.022 0.004 -10000 0 -10000 0 0
ITGB3 0.013 0.074 -10000 0 -0.56 8 8
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 12 -0.001 74 86
ARF6/GDP -0.019 0.17 0.25 9 -0.53 31 40
ARF6/GDP/GULP/ACAP1 -0.073 0.16 -10000 0 -0.38 71 71
alphaIIb/beta3 Integrin/paxillin/GIT1 0.039 0.081 -10000 0 -0.33 22 22
ACAP1 0.021 0.029 0.24 1 -0.56 1 2
ACAP2 0.014 0.011 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.018 0.2 1 -10000 0 1
EFNA1 0.022 0.005 -10000 0 -10000 0 0
HGF -0.09 0.23 -10000 0 -0.56 94 94
CYTH3 -0.005 0.002 -10000 0 -10000 0 0
CYTH2 -0.01 0.16 -10000 0 -1 12 12
NCK1 0.019 0.008 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 7 0 89 96
endosomal lumen acidification 0 0 0.001 24 0 71 95
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.014 0.069 -10000 0 -0.56 7 7
GNAQ/ARNO 0.002 0.15 -10000 0 -0.96 12 12
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 4 0 18 22
MET 0.02 0.041 0.37 1 -0.56 2 3
GNA14 -0.11 0.24 -10000 0 -0.56 111 111
GNA15 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 10 -0.001 87 97
GNA11 0.022 0.004 -10000 0 -10000 0 0
LHCGR -0.007 0.021 0.24 1 -10000 0 1
AGTR1 -0.14 0.25 -10000 0 -0.56 127 127
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.018 0.2 1 -10000 0 1
IPCEF1/ARNO 0.008 0.15 -10000 0 -0.84 13 13
alphaIIb/beta3 Integrin 0.013 0.093 -10000 0 -0.41 22 22
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.01 0.054 0.16 36 -0.11 1 37
BUB1B 0.024 0.031 -10000 0 -0.23 3 3
PLK1 0.01 0.018 0.085 5 -10000 0 5
PLK1S1 0.01 0.022 -10000 0 -0.19 4 4
KIF2A 0.008 0.022 0.23 3 -10000 0 3
regulation of mitotic centrosome separation 0.01 0.018 0.085 5 -10000 0 5
GOLGA2 0.023 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.12 0.11 0.23 225 -0.28 1 226
WEE1 0.009 0.058 -10000 0 -0.34 11 11
cytokinesis 0.021 0.076 0.2 4 -0.3 14 18
PP2A-alpha B56 0.057 0.05 -10000 0 -0.49 2 2
AURKA 0.013 0.025 0.14 3 -0.19 3 6
PICH/PLK1 0.036 0.053 0.22 11 -0.22 1 12
CENPE 0.002 0.024 0.27 1 -0.19 1 2
RhoA/GTP 0.015 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.023 0.23 3 -10000 0 3
PPP2CA 0.021 0.006 -10000 0 -10000 0 0
FZR1 0.022 0.004 -10000 0 -10000 0 0
TPX2 0.056 0.042 0.16 40 -10000 0 40
PAK1 0.023 0.016 0.36 1 -10000 0 1
SPC24 0.088 0.1 0.24 146 -0.29 1 147
FBXW11 0.021 0.006 -10000 0 -10000 0 0
CLSPN 0.014 0.045 -10000 0 -0.22 13 13
GORASP1 0.021 0.006 -10000 0 -10000 0 0
metaphase 0 0.002 0.013 7 -0.012 2 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.01 0.046 6 -10000 0 6
G2 phase of mitotic cell cycle -0.001 0.002 0.016 3 -0.013 1 4
STAG2 0.023 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.027 0.15 -10000 0 -0.53 41 41
spindle elongation 0.01 0.018 0.085 5 -10000 0 5
ODF2 0.023 0.004 -10000 0 -10000 0 0
BUB1 0.035 0.054 -10000 0 -0.54 2 2
TPT1 -0.003 0.051 -10000 0 -0.19 33 33
CDC25C 0.044 0.099 0.2 2 -0.29 34 36
CDC25B 0.021 0.011 -10000 0 -10000 0 0
SGOL1 0.01 0.054 0.11 1 -0.16 36 37
RHOA 0.021 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.04 0.055 -10000 0 -0.22 2 2
CDC14B -0.005 0.003 -10000 0 -10000 0 0
CDC20 0.16 0.11 0.24 307 -0.29 4 311
PLK1/PBIP1 0.004 0.011 -10000 0 -10000 0 0
mitosis -0.002 0.004 0.024 3 -0.018 11 14
FBXO5 0.006 0.021 0.14 2 -10000 0 2
CDC2 0.001 0.003 -10000 0 -0.012 6 6
NDC80 0.1 0.11 0.25 170 -0.29 1 171
metaphase plate congression 0.004 0.049 -10000 0 -0.23 20 20
ERCC6L 0.032 0.055 0.2 9 -0.26 1 10
NLP/gamma Tubulin 0.006 0.015 0.12 1 -0.099 2 3
microtubule cytoskeleton organization -0.003 0.05 -10000 0 -0.18 33 33
G2/M transition DNA damage checkpoint -0.001 0.002 0.013 1 -10000 0 1
PPP1R12A 0.023 0.003 -10000 0 -10000 0 0
interphase -0.001 0.002 0.013 1 -10000 0 1
PLK1/PRC1-2 0.11 0.1 0.25 79 -0.19 4 83
GRASP65/GM130/RAB1/GTP/PLK1 0.039 0.02 -10000 0 -10000 0 0
RAB1A 0.022 0.006 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.015 0.079 5 -10000 0 5
mitotic prometaphase 0 0.004 0.018 19 -10000 0 19
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.099 -10000 0 -0.46 17 17
microtubule-based process 0.089 0.085 0.17 234 -0.17 11 245
Golgi organization 0.01 0.018 0.085 5 -10000 0 5
Cohesin/SA2 0.023 0.015 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.033 0.007 -10000 0 -10000 0 0
KIF20A 0.12 0.13 0.24 236 -0.29 15 251
APC/C/CDC20 0.11 0.079 0.17 303 -0.16 4 307
PPP2R1A 0.022 0.004 -10000 0 -10000 0 0
chromosome segregation 0.004 0.011 -10000 0 -10000 0 0
PRC1 0.046 0.07 0.25 48 -10000 0 48
ECT2 0.099 0.11 0.22 216 -10000 0 216
C13orf34 0.008 0.015 0.074 5 -10000 0 5
NUDC 0.004 0.05 -10000 0 -0.23 20 20
regulation of attachment of spindle microtubules to kinetochore 0.024 0.031 -10000 0 -0.23 3 3
spindle assembly 0.008 0.017 0.12 2 -10000 0 2
spindle stabilization 0.01 0.022 -10000 0 -0.18 4 4
APC/C/HCDH1 0.019 0.005 -10000 0 -10000 0 0
MKLP2/PLK1 0.089 0.086 0.17 234 -0.17 11 245
CCNB1 0.045 0.072 0.24 54 -0.3 2 56
PPP1CB 0.023 0.004 -10000 0 -10000 0 0
BTRC 0.022 0.005 -10000 0 -10000 0 0
ROCK2 0.006 0.047 -10000 0 -0.28 3 3
TUBG1 0.008 0.024 0.11 1 -0.18 6 7
G2/M transition of mitotic cell cycle 0.005 0.029 -10000 0 -0.22 2 2
MLF1IP -0.006 0.011 -10000 0 -10000 0 0
INCENP 0.022 0.002 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.016 -10000 0 -10000 0 0
AES 0.023 0.013 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.011 -10000 0 -10000 0 0
SMAD4 0.022 0.005 -10000 0 -10000 0 0
DKK2 -0.074 0.22 -10000 0 -0.56 80 80
TLE1 0.023 0.012 -10000 0 -10000 0 0
MACF1 0.02 0.037 -10000 0 -0.56 2 2
CTNNB1 0.09 0.13 0.29 36 -0.38 6 42
WIF1 -0.34 0.28 0.23 1 -0.56 300 301
beta catenin/RanBP3 0.009 0.1 0.44 17 -0.44 1 18
KREMEN2 0.16 0.11 0.24 310 -0.29 6 316
DKK1 0.02 0.093 0.25 20 -0.53 10 30
beta catenin/beta TrCP1 0.098 0.12 0.3 29 -0.34 6 35
FZD1 0.022 0.006 -10000 0 -10000 0 0
AXIN2 -0.04 0.28 0.57 7 -1.4 18 25
AXIN1 0.023 0.005 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.025 0.11 -10000 0 -0.56 13 13
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.053 0.13 -10000 0 -0.54 14 14
Axin1/APC/GSK3 0.056 0.077 0.27 8 -0.34 2 10
Axin1/APC/GSK3/beta catenin/Macf1 0.047 0.1 0.3 7 -0.4 3 10
HNF1A 0.027 0.03 0.23 8 -10000 0 8
CTBP1 0.021 0.014 -10000 0 -10000 0 0
MYC 0.056 0.18 0.58 48 -10000 0 48
RANBP3 0.022 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.028 0.2 -10000 0 -0.38 79 79
NKD1 -0.024 0.16 0.24 4 -0.56 39 43
TCF4 0.021 0.03 -10000 0 -0.56 1 1
TCF3 0.022 0.013 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.052 0.024 -10000 0 -10000 0 0
Ran/GTP 0.017 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.005 0.11 0.39 16 -0.4 13 29
LEF1 0.023 0.017 0.23 1 -10000 0 1
DVL1 0.054 0.079 -10000 0 -0.52 4 4
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.05 0.16 -10000 0 -0.61 14 14
DKK1/LRP6/Kremen 2 0.11 0.11 0.32 14 -0.37 10 24
LRP6 0.022 0.006 -10000 0 -10000 0 0
CSNK1A1 0.022 0.015 -10000 0 -10000 0 0
NLK 0.021 0.009 -10000 0 -10000 0 0
CCND1 0.062 0.26 0.57 66 -1.4 6 72
WNT1 0.022 0.017 0.24 2 -10000 0 2
GSK3A 0.023 0.005 -10000 0 -10000 0 0
GSK3B 0.02 0.008 -10000 0 -10000 0 0
FRAT1 0.02 0.027 -10000 0 -0.56 1 1
PPP2R5D 0.067 0.088 0.32 38 -0.32 2 40
APC 0.014 0.067 0.35 6 -10000 0 6
WNT1/LRP6/FZD1 0.14 0.12 0.23 276 -10000 0 276
CREBBP 0.022 0.013 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.026 0.057 -10000 0 -0.41 8 8
AKT1 -0.007 0.19 0.36 11 -0.55 31 42
PTK2B -0.062 0.19 0.37 6 -0.69 26 32
VEGFR2 homodimer/Frs2 -0.06 0.2 -10000 0 -0.46 81 81
CAV1 -0.13 0.25 -10000 0 -0.56 127 127
CALM1 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.044 0.19 -10000 0 -0.44 78 78
endothelial cell proliferation -0.012 0.18 0.37 14 -0.54 30 44
mol:Ca2+ -0.044 0.18 0.36 3 -0.66 23 26
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.031 0.19 -10000 0 -0.43 70 70
RP11-342D11.1 -0.06 0.17 -10000 0 -0.68 23 23
CDH5 -0.086 0.22 -10000 0 -0.56 90 90
VEGFA homodimer 0.051 0.022 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
SHC2 0.019 0.046 -10000 0 -0.56 3 3
HRAS/GDP -0.027 0.15 -10000 0 -0.57 23 23
SH2D2A 0.021 0.027 -10000 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.025 0.18 -10000 0 -0.57 30 30
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.043 0.19 -10000 0 -0.43 78 78
VEGFR1 homodimer 0.022 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.016 0.17 -10000 0 -0.63 23 23
GRB10 -0.045 0.18 0.35 2 -0.67 23 25
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
PAK1 0.023 0.016 0.37 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.078 0.25 -10000 0 -0.68 52 52
HRAS 0.022 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.039 0.13 -10000 0 -0.44 34 34
HIF1A 0.022 0.004 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.032 0.18 -10000 0 -0.42 70 70
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.005 0.12 -10000 0 -0.56 22 22
Nck/Pak 0.028 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.045 0.2 -10000 0 -0.44 81 81
mol:GDP -0.023 0.16 -10000 0 -0.61 23 23
mol:NADP -0.017 0.17 0.35 9 -0.5 32 41
eNOS/Hsp90 -0.009 0.16 0.36 7 -0.47 32 39
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
mol:IP3 -0.045 0.18 0.36 3 -0.67 23 26
HIF1A/ARNT 0.031 0.01 -10000 0 -10000 0 0
SHB 0.021 0.007 -10000 0 -10000 0 0
VEGFA 0.023 0.004 -10000 0 -10000 0 0
VEGFC 0.019 0.038 -10000 0 -0.56 2 2
FAK1/Vinculin -0.043 0.21 0.34 4 -0.66 35 39
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.037 0.2 -10000 0 -0.44 76 76
PTPN6 0.021 0.006 -10000 0 -10000 0 0
EPAS1 -0.08 0.23 -10000 0 -0.56 88 88
mol:L-citrulline -0.017 0.17 0.35 9 -0.5 32 41
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.031 0.18 -10000 0 -0.43 69 69
VEGFR2 homodimer/VEGFA homodimer -0.042 0.19 -10000 0 -0.45 73 73
VEGFR2/3 heterodimer -0.075 0.22 -10000 0 -0.48 92 92
VEGFB 0.023 0.002 -10000 0 -10000 0 0
MAPK11 -0.045 0.18 0.41 5 -0.61 29 34
VEGFR2 homodimer -0.078 0.22 -10000 0 -0.53 81 81
FLT1 0.022 0.006 -10000 0 -10000 0 0
NEDD4 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.052 0.18 0.35 8 -0.61 26 34
MAPK1 -0.051 0.18 0.34 8 -0.62 26 34
VEGFA145/NRP2 0.031 0.036 -10000 0 -0.4 3 3
VEGFR1/2 heterodimer -0.062 0.2 -10000 0 -0.46 84 84
KDR -0.078 0.22 -10000 0 -0.53 81 81
VEGFA165/NRP1/VEGFR2 homodimer -0.038 0.19 -10000 0 -0.71 23 23
SRC 0.022 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.049 0.18 0.36 8 -0.62 26 34
PI3K -0.038 0.16 -10000 0 -0.63 23 23
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.04 0.18 -10000 0 -0.45 63 63
FES -0.048 0.19 0.36 1 -0.71 23 24
GAB1 -0.049 0.19 -10000 0 -0.63 30 30
VEGFR2 homodimer/VEGFA homodimer/Src -0.043 0.19 -10000 0 -0.43 80 80
CTNNB1 0.021 0.006 -10000 0 -10000 0 0
SOS1 0.022 0.004 -10000 0 -10000 0 0
ARNT 0.022 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.071 0.2 0.33 4 -0.48 59 63
VEGFR2 homodimer/VEGFA homodimer/Yes -0.044 0.19 -10000 0 -0.44 77 77
PI3K/GAB1 -0.01 0.17 -10000 0 -0.55 26 26
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.021 0.17 -10000 0 -0.64 22 22
PRKACA 0.022 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.061 0.22 -10000 0 -0.47 83 83
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
CDC42 -0.045 0.19 0.36 3 -0.69 23 26
actin cytoskeleton reorganization -0.042 0.19 -10000 0 -0.43 78 78
PTK2 -0.06 0.22 0.32 4 -0.66 41 45
EDG1 -0.06 0.17 -10000 0 -0.68 23 23
mol:DAG -0.045 0.18 0.36 3 -0.67 23 26
CaM/Ca2+ -0.034 0.17 -10000 0 -0.62 23 23
MAP2K3 -0.048 0.14 -10000 0 -0.57 23 23
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.037 0.19 -10000 0 -0.7 23 23
PLCG1 -0.046 0.18 0.36 3 -0.68 23 26
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.033 0.18 -10000 0 -0.43 68 68
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
YES1 0.021 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.044 0.19 -10000 0 -0.44 80 80
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.043 0.19 -10000 0 -0.43 76 76
cell migration -0.058 0.21 0.4 2 -0.6 42 44
mol:PI-3-4-5-P3 -0.035 0.15 -10000 0 -0.58 23 23
FYN 0.022 0.026 -10000 0 -0.56 1 1
VEGFB/NRP1 -0.04 0.17 -10000 0 -0.64 23 23
mol:NO -0.017 0.17 0.35 9 -0.5 32 41
PXN 0.023 0.002 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.15 -10000 0 -0.57 23 23
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.046 0.18 -10000 0 -0.7 23 23
VHL 0.021 0.006 -10000 0 -10000 0 0
ITGB3 0.013 0.074 -10000 0 -0.56 8 8
NOS3 -0.023 0.19 0.37 8 -0.57 32 40
VEGFR2 homodimer/VEGFA homodimer/Sck -0.046 0.2 -10000 0 -0.44 80 80
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.057 0.17 0.35 3 -0.64 24 27
PRKCB -0.069 0.18 0.35 3 -0.65 27 30
VCL 0.022 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.04 0.18 -10000 0 -0.41 73 73
VEGFR1/2 heterodimer/VEGFA homodimer -0.045 0.19 -10000 0 -0.44 77 77
VEGFA165/NRP2 0.031 0.036 -10000 0 -0.4 3 3
MAPKKK cascade -0.038 0.15 -10000 0 -0.57 23 23
NRP2 0.019 0.046 -10000 0 -0.56 3 3
VEGFC homodimer 0.019 0.037 -10000 0 -0.56 2 2
NCK1 0.019 0.008 -10000 0 -10000 0 0
ROCK1 0.022 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.043 0.22 0.38 4 -0.65 37 41
MAP3K13 -0.04 0.15 -10000 0 -0.6 23 23
PDPK1 -0.036 0.13 -10000 0 -0.51 23 23
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.031 0.034 0.24 12 -10000 0 12
NFATC2 -0.043 0.23 -10000 0 -0.58 65 65
NFATC3 0.012 0.064 -10000 0 -0.27 9 9
CD40LG -0.18 0.36 -10000 0 -0.91 68 68
ITCH -0.019 0.097 -10000 0 -10000 0 0
CBLB -0.019 0.095 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.1 0.28 -10000 0 -0.78 50 50
JUNB 0.021 0.027 -10000 0 -0.56 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.024 0.12 -10000 0 -0.3 74 74
T cell anergy -0.052 0.16 -10000 0 -0.42 65 65
TLE4 -0.032 0.17 -10000 0 -0.56 25 25
Jun/NFAT1-c-4/p21SNFT -0.049 0.26 -10000 0 -0.87 27 27
AP-1/NFAT1-c-4 -0.13 0.37 -10000 0 -1 44 44
IKZF1 -0.035 0.19 -10000 0 -0.58 37 37
T-helper 2 cell differentiation -0.074 0.26 -10000 0 -0.76 42 42
AP-1/NFAT1 -0.069 0.21 -10000 0 -0.46 67 67
CALM1 -0.004 0.076 -10000 0 -10000 0 0
EGR2 -0.061 0.27 -10000 0 -0.99 26 26
EGR3 -0.064 0.28 -10000 0 -1 26 26
NFAT1/FOXP3 -0.008 0.18 -10000 0 -0.42 57 57
EGR1 0.012 0.07 -10000 0 -0.56 7 7
JUN 0.004 0.035 -10000 0 -10000 0 0
EGR4 0.026 0.036 0.25 11 -10000 0 11
mol:Ca2+ -0.023 0.067 -10000 0 -0.27 2 2
GBP3 -0.047 0.21 -10000 0 -0.56 51 51
FOSL1 0.024 0.014 0.24 2 -10000 0 2
NFAT1-c-4/MAF/IRF4 -0.035 0.25 -10000 0 -0.85 27 27
DGKA -0.031 0.16 -10000 0 -0.47 39 39
CREM 0.022 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.078 0.27 -10000 0 -0.84 32 32
CTLA4 -0.023 0.14 -10000 0 -0.49 22 22
NFAT1-c-4 (dimer)/EGR1 -0.044 0.26 -10000 0 -0.9 26 26
NFAT1-c-4 (dimer)/EGR4 -0.037 0.25 -10000 0 -0.85 27 27
FOS -0.06 0.18 -10000 0 -0.57 54 54
IFNG -0.12 0.32 -10000 0 -0.91 50 50
T cell activation -0.067 0.19 -10000 0 -0.68 17 17
MAF 0.022 0.005 -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 0.031 0.16 0.69 16 -10000 0 16
TNF -0.063 0.24 -10000 0 -0.82 32 32
FASLG -0.13 0.42 -10000 0 -1.4 37 37
TBX21 -0.034 0.18 -10000 0 -0.56 49 49
BATF3 0.022 0.004 -10000 0 -10000 0 0
PRKCQ -0.028 0.16 -10000 0 -0.56 41 41
PTPN1 -0.031 0.16 -10000 0 -0.55 23 23
NFAT1-c-4/ICER1 -0.041 0.24 -10000 0 -0.86 25 25
GATA3 0.008 0.095 0.24 3 -0.56 13 16
T-helper 1 cell differentiation -0.11 0.31 -10000 0 -0.88 51 51
IL2RA -0.096 0.28 -10000 0 -0.75 55 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.028 0.16 -10000 0 -0.55 22 22
E2F1 0.025 0.006 -10000 0 -10000 0 0
PPARG -0.04 0.18 -10000 0 -0.56 51 51
SLC3A2 -0.031 0.16 -10000 0 -0.47 38 38
IRF4 0.015 0.064 -10000 0 -0.56 6 6
PTGS2 -0.16 0.33 -10000 0 -0.86 63 63
CSF2 -0.16 0.33 -10000 0 -0.88 55 55
JunB/Fra1/NFAT1-c-4 -0.03 0.24 -10000 0 -0.82 26 26
IL4 -0.078 0.27 -10000 0 -0.79 42 42
IL5 -0.14 0.3 -10000 0 -0.86 43 43
IL2 -0.068 0.19 -10000 0 -0.7 16 16
IL3 -0.044 0.17 -10000 0 -0.71 23 23
RNF128 -0.085 0.24 -10000 0 -0.64 79 79
NFATC1 -0.03 0.16 -10000 0 -0.7 16 16
CDK4 0.04 0.14 0.61 8 -10000 0 8
PTPRK -0.031 0.16 -10000 0 -0.55 22 22
IL8 -0.14 0.3 -10000 0 -0.86 45 45
POU2F1 0.022 0.006 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.03 0.066 -10000 0 -0.38 12 12
HDAC1 0.021 0.005 -10000 0 -10000 0 0
AES 0.022 0.004 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.014 0.24 2 -10000 0 2
LRP6/FZD1 0.03 0.011 -10000 0 -10000 0 0
TLE1 0.022 0.004 -10000 0 -10000 0 0
AP1 -0.051 0.15 -10000 0 -0.34 84 84
NCSTN 0.022 0.005 -10000 0 -10000 0 0
ADAM10 0.023 0.002 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.011 0.17 -10000 0 -0.75 23 23
NICD/RBPSUH 0.026 0.065 -10000 0 -0.37 12 12
WIF1 -0.34 0.28 0.24 1 -0.56 300 301
NOTCH1 0.011 0.062 -10000 0 -0.4 11 11
PSENEN 0.021 0.007 -10000 0 -10000 0 0
KREMEN2 0.16 0.11 0.24 310 -0.29 6 316
DKK1 0.02 0.093 0.25 20 -0.53 10 30
beta catenin/beta TrCP1 -0.002 0.11 0.28 2 -0.4 14 16
APH1B 0.023 0.002 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
AXIN1 -0.002 0.082 0.27 1 -0.52 8 9
CtBP/CBP/TCF1/TLE1/AES 0.01 0.033 -10000 0 -10000 0 0
PSEN1 0.022 0.005 -10000 0 -10000 0 0
FOS -0.042 0.18 -10000 0 -0.56 54 54
JUN 0.022 0.004 -10000 0 -10000 0 0
MAP3K7 0.022 0.003 -10000 0 -10000 0 0
CTNNB1 -0.009 0.11 0.29 2 -0.42 15 17
MAPK3 0.023 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.028 0.2 -10000 0 -0.38 79 79
HNF1A 0.026 0.027 0.24 8 -10000 0 8
CTBP1 0.021 0.007 -10000 0 -10000 0 0
MYC 0.02 0.019 -10000 0 -10000 0 0
NKD1 -0.023 0.16 0.24 4 -0.56 39 43
FZD1 0.022 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.029 0.067 -10000 0 -0.38 12 12
apoptosis -0.05 0.15 -10000 0 -0.34 84 84
Delta 1/NOTCHprecursor 0.028 0.066 -10000 0 -0.38 12 12
DLL1 0.022 0.004 -10000 0 -10000 0 0
PPARD 0.006 0.13 -10000 0 -0.95 9 9
Gamma Secretase 0.056 0.027 -10000 0 -10000 0 0
APC -0.019 0.11 0.27 1 -0.42 26 27
DVL1 -0.044 0.092 -10000 0 -0.61 6 6
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.11 0.11 0.32 14 -0.37 10 24
LRP6 0.022 0.006 -10000 0 -10000 0 0
CSNK1A1 0.022 0.006 -10000 0 -10000 0 0
NLK 0.009 0.004 -10000 0 -10000 0 0
CCND1 0.004 0.15 -10000 0 -1.4 6 6
WNT1 0.018 0.02 0.24 2 -10000 0 2
Axin1/APC/beta catenin -0.016 0.14 0.32 4 -0.46 26 30
DKK2 -0.074 0.22 -10000 0 -0.56 80 80
NOTCH1 precursor/DVL1 -0.029 0.12 -10000 0 -0.55 13 13
GSK3B 0.02 0.007 -10000 0 -10000 0 0
FRAT1 0.02 0.027 -10000 0 -0.56 1 1
NOTCH/Deltex homolog 1 0.031 0.067 -10000 0 -0.38 12 12
PPP2R5D 0.013 0.098 0.28 38 -0.42 7 45
MAPK1 0.022 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.17 0.18 -10000 0 -0.33 273 273
RBPJ 0.021 0.006 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.021 -10000 0 -10000 0 0
VLDLR 0.019 0.027 -10000 0 -0.56 1 1
CRKL 0.021 0.006 -10000 0 -10000 0 0
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.56 1 1
ITGA3 0.017 0.059 -10000 0 -0.56 5 5
RELN/VLDLR/Fyn -0.022 0.14 -10000 0 -0.36 74 74
MAPK8IP1/MKK7/MAP3K11/JNK1 0.059 0.03 -10000 0 -0.31 1 1
AKT1 -0.023 0.081 0.21 1 -0.27 28 29
MAP2K7 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
DAB1 0.028 0.06 0.24 31 -10000 0 31
RELN/LRP8/DAB1 -0.01 0.14 0.3 1 -0.32 76 77
LRPAP1/LRP8 0.032 0.014 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.001 0.14 0.29 1 -0.31 76 77
DAB1/alpha3/beta1 Integrin -0.009 0.12 -10000 0 -0.3 65 65
long-term memory -0.011 0.16 0.3 2 -0.32 84 86
DAB1/LIS1 0.003 0.13 -10000 0 -0.3 69 69
DAB1/CRLK/C3G -0.005 0.12 -10000 0 -0.29 57 57
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DAB1/NCK2 0.005 0.13 -10000 0 -0.3 69 69
ARHGEF2 0.022 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.006 0.13 0.24 24 -0.56 21 45
CDK5R1 0.028 0.033 0.25 10 -10000 0 10
RELN -0.068 0.21 0.24 3 -0.56 76 79
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.019 0.15 -10000 0 -0.36 76 76
GRIN2A/RELN/LRP8/DAB1/Fyn -0.001 0.17 0.31 2 -0.33 88 90
MAPK8 0.022 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.013 0.14 0.33 2 -0.32 75 77
ITGB1 0.022 0.004 -10000 0 -10000 0 0
MAP1B -0.049 0.12 0.28 2 -0.31 74 76
RELN/LRP8 -0.021 0.14 -10000 0 -0.35 76 76
GRIN2B/RELN/LRP8/DAB1/Fyn 0.009 0.14 0.3 2 -0.32 71 73
PI3K 0.017 0.017 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.029 0.042 -10000 0 -0.37 5 5
RAP1A -0.037 0.12 0.34 8 -0.31 1 9
PAFAH1B1 0.022 0.005 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.028 0.24 1 -0.56 1 2
CRLK/C3G 0.031 0.01 -10000 0 -10000 0 0
GRIN2B 0 0.029 0.24 4 -10000 0 4
NCK2 0.023 0.003 -10000 0 -10000 0 0
neuron differentiation -0.012 0.093 0.19 2 -0.35 12 14
neuron adhesion -0.04 0.12 0.34 10 -0.33 1 11
LRP8 0.024 0.017 0.24 3 -10000 0 3
GSK3B -0.022 0.072 0.2 1 -0.28 16 17
RELN/VLDLR/DAB1/Fyn -0.004 0.14 0.32 2 -0.31 74 76
MAP3K11 0.023 0.002 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.022 0.089 -10000 0 -0.28 38 38
CDK5 0.022 0.004 -10000 0 -10000 0 0
MAPT 0.004 0.11 0.75 8 -0.51 6 14
neuron migration -0.015 0.12 0.31 2 -0.34 30 32
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.012 0.093 0.2 1 -0.35 12 13
RELN/VLDLR -0.009 0.14 -10000 0 -0.32 74 74
Glypican 2 network

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
MDK 0.028 0.037 0.28 10 -9999 0 10
GPC2 0.057 0.086 0.26 72 -9999 0 72
GPC2/Midkine 0.057 0.063 0.28 13 -9999 0 13
neuron projection morphogenesis 0.057 0.063 0.28 13 -9999 0 13
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.15 0.23 -10000 0 -0.7 14 14
CRP -0.15 0.23 -10000 0 -0.71 14 14
cell cycle arrest -0.18 0.26 -10000 0 -0.66 44 44
TIMP1 -0.12 0.21 -10000 0 -0.62 16 16
IL6ST -0.009 0.097 -10000 0 -0.55 14 14
Rac1/GDP -0.069 0.16 -10000 0 -0.42 51 51
AP1 0.037 0.16 -10000 0 -0.52 9 9
GAB2 0.014 0.095 -10000 0 -0.55 13 13
TNFSF11 -0.16 0.23 -10000 0 -0.72 13 13
HSP90B1 -0.002 0.089 -10000 0 -0.76 5 5
GAB1 0.026 0.01 -10000 0 -10000 0 0
MAPK14 -0.047 0.14 -10000 0 -0.57 18 18
AKT1 0.04 0.072 0.3 4 -0.37 2 6
FOXO1 0.038 0.069 0.32 2 -0.36 1 3
MAP2K6 -0.058 0.14 -10000 0 -0.4 48 48
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.091 0.17 -10000 0 -0.46 50 50
MITF -0.066 0.15 -10000 0 -0.41 53 53
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.022 0.004 -10000 0 -10000 0 0
A2M -0.43 0.65 -10000 0 -1.4 159 159
CEBPB 0.026 0.005 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.027 0.12 0.27 2 -0.48 11 13
STAT3 -0.18 0.27 -10000 0 -0.7 44 44
STAT1 -0.006 0.1 -10000 0 -0.85 7 7
CEBPD -0.15 0.24 -10000 0 -0.76 14 14
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.018 -10000 0 -10000 0 0
JUN 0.022 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.059 0.15 -10000 0 -0.4 50 50
MAPK11 -0.046 0.14 -10000 0 -0.57 18 18
STAT3 (dimer)/FOXO1 -0.2 0.3 0.4 1 -0.66 92 93
GRB2/SOS1/GAB family 0.004 0.16 -10000 0 -0.46 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.049 0.15 -10000 0 -0.37 65 65
GRB2 0.027 0.008 -10000 0 -10000 0 0
JAK2 0.02 0.007 -10000 0 -10000 0 0
LBP -0.093 0.19 -10000 0 -0.63 8 8
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
JAK1 0.014 0.02 -10000 0 -10000 0 0
MYC -0.14 0.24 -10000 0 -0.68 15 15
FGG -0.46 0.53 -10000 0 -1 226 226
macrophage differentiation -0.18 0.26 -10000 0 -0.66 44 44
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.033 0.16 -10000 0 -0.36 77 77
JUNB -0.15 0.23 -10000 0 -0.72 13 13
FOS -0.042 0.18 -10000 0 -0.56 54 54
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.067 0.16 -10000 0 -0.42 56 56
STAT1/PIAS1 -0.07 0.16 -10000 0 -0.42 53 53
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.07 -10000 0 -0.37 4 4
STAT3 (dimer) -0.18 0.27 -10000 0 -0.69 44 44
PRKCD -0.11 0.2 0.31 2 -0.52 44 46
IL6R 0.001 0.087 -10000 0 -0.56 11 11
SOCS3 -0.035 0.15 -10000 0 -0.69 12 12
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.076 -10000 0 -0.34 14 14
Rac1/GTP -0.078 0.17 -10000 0 -0.44 52 52
HCK 0.02 0.046 -10000 0 -0.55 3 3
MAPKKK cascade 0.046 0.13 -10000 0 -0.55 9 9
bone resorption -0.15 0.22 -10000 0 -0.68 13 13
IRF1 -0.16 0.23 -10000 0 -0.72 13 13
mol:GDP -0.07 0.15 -10000 0 -0.42 52 52
SOS1 0.029 0.012 -10000 0 -10000 0 0
VAV1 -0.071 0.16 -10000 0 -0.43 52 52
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.036 0.17 -10000 0 -0.61 24 24
PTPN11 0.008 0.058 -10000 0 -0.82 2 2
IL6/IL6RA -0.055 0.17 -10000 0 -0.42 81 81
gp130 (dimer)/TYK2/TYK2/LMO4 0.017 0.072 -10000 0 -0.35 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 0.015 0.072 -10000 0 -0.35 14 14
IL6 -0.082 0.21 -10000 0 -0.56 77 77
PIAS3 0.021 0.007 -10000 0 -10000 0 0
PTPRE 0.02 0.042 -10000 0 -0.55 2 2
PIAS1 0.023 0.002 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.058 0.15 -10000 0 -0.34 84 84
LMO4 0.009 0.026 0.21 1 -10000 0 1
STAT3 (dimer)/PIAS3 -0.16 0.26 -10000 0 -0.67 44 44
MCL1 0.048 0.081 0.45 2 -10000 0 2
Coregulation of Androgen receptor activity

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
NRIP1 0.022 0.006 -10000 0 -10000 0 0
SVIL 0.022 0.004 -10000 0 -10000 0 0
ZNF318 0.022 0.005 -10000 0 -10000 0 0
JMJD2C 0.006 0.012 0.059 1 -10000 0 1
T-DHT/AR/Ubc9 -0.079 0.16 -10000 0 -0.38 99 99
CARM1 0.022 0.004 -10000 0 -10000 0 0
PRDX1 0.022 0.004 -10000 0 -10000 0 0
PELP1 0.022 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.022 0.005 -10000 0 -10000 0 0
PTK2B 0.021 0.007 -10000 0 -10000 0 0
MED1 0.022 0.004 -10000 0 -10000 0 0
MAK -0.018 0.15 -10000 0 -0.56 33 33
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.023 0.004 -10000 0 -10000 0 0
GSN 0.023 0.003 -10000 0 -10000 0 0
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA6 0.022 0.005 -10000 0 -10000 0 0
DNA-PK 0.043 0.013 -10000 0 -10000 0 0
NCOA4 0.022 0.005 -10000 0 -10000 0 0
PIAS3 0.021 0.007 -10000 0 -10000 0 0
cell proliferation -0.075 0.22 -10000 0 -0.78 41 41
XRCC5 0.022 0.004 -10000 0 -10000 0 0
UBE3A 0.023 0.004 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.089 0.18 -10000 0 -0.4 108 108
FHL2 -0.029 0.072 -10000 0 -0.35 3 3
RANBP9 0.023 0.004 -10000 0 -10000 0 0
JMJD1A -0.037 0.064 -10000 0 -0.13 155 155
CDK6 0.023 0.023 0.37 2 -10000 0 2
TGFB1I1 0.023 0.003 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.073 0.16 0.26 1 -0.38 93 94
XRCC6 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR -0.095 0.18 -10000 0 -0.39 107 107
CTDSP1 0.022 0.004 -10000 0 -10000 0 0
CTDSP2 0.022 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.003 -10000 0 -10000 0 0
TCF4 0.021 0.027 -10000 0 -0.56 1 1
CDKN2A 0.095 0.14 0.24 204 -0.3 20 224
SRF 0.026 0.005 -10000 0 -10000 0 0
NKX3-1 -0.1 0.17 -10000 0 -0.45 62 62
KLK3 0.013 0.045 -10000 0 -10000 0 0
TMF1 0.021 0.007 -10000 0 -10000 0 0
HNRNPA1 0.023 0.002 -10000 0 -10000 0 0
AOF2 0 0.001 -10000 0 -10000 0 0
APPL1 -0.009 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.077 0.16 -10000 0 -0.38 98 98
AR -0.12 0.24 -10000 0 -0.58 99 99
UBA3 0.021 0.007 -10000 0 -10000 0 0
PATZ1 0.022 0.005 -10000 0 -10000 0 0
PAWR 0.023 0.003 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
PA2G4 0.023 0.002 -10000 0 -10000 0 0
UBE2I 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.07 0.15 -10000 0 -0.35 99 99
RPS6KA3 0.022 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.078 0.16 -10000 0 -0.38 98 98
LATS2 0.02 0.027 -10000 0 -0.56 1 1
T-DHT/AR/PRX1 -0.071 0.15 -10000 0 -0.35 99 99
Cyclin D3/CDK11 p58 0.016 0.003 -10000 0 -10000 0 0
VAV3 0.021 0.027 -10000 0 -0.56 1 1
KLK2 -0.036 0.09 -10000 0 -0.49 6 6
CASP8 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.062 0.16 -10000 0 -0.35 97 97
TMPRSS2 -0.32 0.47 -10000 0 -0.99 157 157
CCND1 0.013 0.066 0.37 1 -0.56 6 7
PIAS1 0.023 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.029 -10000 0 -0.065 116 116
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.073 0.16 0.24 2 -0.37 93 95
CMTM2 -0.05 0.19 -10000 0 -0.56 59 59
SNURF 0.005 0.097 -10000 0 -0.56 14 14
ZMIZ1 -0.002 0.043 -10000 0 -10000 0 0
CCND3 0.022 0.004 -10000 0 -10000 0 0
TGIF1 0.022 0.005 -10000 0 -10000 0 0
FKBP4 0.022 0.017 0.37 1 -10000 0 1
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.028 0.062 0.22 2 -0.3 14 16
RGS9BP 0.009 0.082 -10000 0 -0.56 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.004 0.03 0.37 2 -10000 0 2
mol:Na + 0.091 0.071 0.23 10 -0.16 2 12
mol:ADP -0.004 0.059 0.34 12 -10000 0 12
GNAT2 0.018 0.013 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.007 0.13 -10000 0 -0.36 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.009 -10000 0 -10000 0 0
GRK7 0.029 0.062 0.3 22 -10000 0 22
CNGB3 0.13 0.12 0.24 237 -0.29 2 239
Cone Metarhodopsin II/X-Arrestin 0.014 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0.009 0.079 0.22 28 -10000 0 28
Cone PDE6 0.007 0.12 -10000 0 -0.32 54 54
Cone Metarhodopsin II 0.027 0.036 0.22 10 -10000 0 10
Na + (4 Units) 0.11 0.095 0.29 49 -0.18 2 51
GNAT2/GDP 0.003 0.12 -10000 0 -0.31 58 58
GNB5 0.023 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.005 0.045 0.18 28 -10000 0 28
Cone Transducin 0.031 0.067 0.24 2 -0.32 14 16
SLC24A2 0.055 0.097 0.25 88 -0.29 5 93
GNB3/GNGT2 0.021 0.08 0.26 2 -0.41 14 16
GNB3 0.026 0.034 0.27 9 -10000 0 9
GNAT2/GTP 0.016 0.004 -10000 0 -10000 0 0
CNGA3 0.011 0.027 0.3 2 -10000 0 2
ARR3 -0.011 0.016 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.092 0.072 0.23 10 -0.16 2 12
mol:Pi -0.007 0.13 -10000 0 -0.36 58 58
Cone CNG Channel 0.079 0.064 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.055 0.097 0.25 88 -0.29 5 93
RGS9 -0.04 0.18 -10000 0 -0.56 52 52
PDE6C -0.008 0.017 -10000 0 -10000 0 0
GNGT2 0.004 0.1 -10000 0 -0.56 16 16
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.011 0.015 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.008 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.028 0.078 -10000 0 -0.31 18 18
Syndecan-3/Neurocan 0.026 0.072 -10000 0 -0.36 10 10
POMC 0.039 0.08 0.24 43 -0.56 3 46
EGFR 0.022 0.083 0.36 11 -0.56 6 17
Syndecan-3/EGFR 0.018 0.071 0.25 9 -0.35 11 20
AGRP -0.24 0.28 -10000 0 -0.56 211 211
NCSTN 0.022 0.005 -10000 0 -10000 0 0
PSENEN 0.021 0.007 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.002 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
NCAN 0.029 0.061 0.24 34 -10000 0 34
long-term memory 0.025 0.065 -10000 0 -0.35 11 11
Syndecan-3/IL8 0.021 0.071 0.24 3 -0.35 12 15
PSEN1 0.022 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.028 0.013 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.56 1 1
limb bud formation 0.001 0.056 -10000 0 -0.38 10 10
MC4R 0.025 0.051 0.25 21 -10000 0 21
SRC 0.022 0.004 -10000 0 -10000 0 0
PTN 0.012 0.084 0.24 3 -0.56 10 13
FGFR/FGF/Syndecan-3 0.001 0.056 -10000 0 -0.39 10 10
neuron projection morphogenesis 0.029 0.091 0.27 9 -0.35 8 17
Syndecan-3/AgRP -0.11 0.16 -10000 0 -0.29 181 181
Syndecan-3/AgRP/MC4R -0.1 0.16 0.32 1 -0.29 180 181
Fyn/Cortactin 0.028 0.024 -10000 0 -0.41 1 1
SDC3 0.001 0.057 -10000 0 -0.39 10 10
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.02 0.07 0.24 3 -0.35 12 15
IL8 0.026 0.062 0.25 16 -0.56 3 19
Syndecan-3/Fyn/Cortactin 0.026 0.066 -10000 0 -0.36 11 11
Syndecan-3/CASK -0.001 0.057 -10000 0 -0.35 12 12
alpha-MSH/MC4R 0.048 0.065 0.28 6 -0.42 3 9
Gamma Secretase 0.056 0.027 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.28 0.23 0.6 8 -1.2 2 10
PLK1 0.12 0.096 -10000 0 -10000 0 0
BIRC5 0.15 0.07 -10000 0 -0.51 1 1
HSPA1B 0.28 0.23 0.6 4 -1.2 2 6
MAP2K1 0.069 0.042 -10000 0 -10000 0 0
BRCA2 0.27 0.23 0.58 6 -1.2 2 8
FOXM1 0.3 0.27 0.63 14 -1.5 3 17
XRCC1 0.28 0.24 0.67 10 -1.2 2 12
FOXM1B/p19 0.15 0.27 0.59 15 -1.2 4 19
Cyclin D1/CDK4 0.23 0.24 0.6 16 -1.1 3 19
CDC2 0.28 0.24 0.58 22 -1.1 3 25
TGFA 0.25 0.22 0.55 24 -0.96 3 27
SKP2 0.31 0.26 0.69 43 -1.1 2 45
CCNE1 0.086 0.11 0.29 107 -10000 0 107
CKS1B 0.28 0.24 0.69 15 -1.2 2 17
RB1 0.16 0.2 0.45 37 -0.8 6 43
FOXM1C/SP1 0.27 0.24 0.58 2 -1.3 3 5
AURKB 0.1 0.18 -10000 0 -0.8 10 10
CENPF 0.29 0.24 0.64 20 -1.2 2 22
CDK4 0.042 0.025 0.38 1 -10000 0 1
MYC 0.23 0.22 0.52 20 -0.91 3 23
CHEK2 0.067 0.042 -10000 0 -10000 0 0
ONECUT1 0.28 0.24 0.58 30 -1.1 3 33
CDKN2A 0.075 0.14 0.22 204 -0.32 20 224
LAMA4 0.27 0.26 0.62 2 -1.2 6 8
FOXM1B/HNF6 0.28 0.26 0.63 12 -1.4 3 15
FOS 0.18 0.45 0.68 7 -0.95 57 64
SP1 0.024 0.002 -10000 0 -10000 0 0
CDC25B 0.28 0.24 0.67 14 -1.2 2 16
response to radiation 0.039 0.029 -10000 0 -10000 0 0
CENPB 0.28 0.24 0.65 17 -1.1 3 20
CENPA 0.3 0.24 0.62 24 -1.2 2 26
NEK2 0.3 0.24 0.68 13 -1.2 2 15
HIST1H2BA 0.27 0.23 0.6 3 -1.2 2 5
CCNA2 0.086 0.1 0.26 122 -0.28 2 124
EP300 0.022 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.27 0.25 0.62 2 -1.5 2 4
CCNB2 0.29 0.24 0.6 12 -1.1 3 15
CCNB1 0.28 0.24 0.62 8 -1.3 2 10
ETV5 0.35 0.29 0.68 92 -1.1 5 97
ESR1 0.24 0.34 0.67 4 -1.1 20 24
CCND1 0.22 0.24 0.58 9 -1.2 3 12
GSK3A 0.058 0.036 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.14 0.11 0.3 121 -10000 0 121
CDK2 0.032 0.013 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.048 0.035 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.25 0.24 0.57 1 -1.2 3 4
GAS1 0.26 0.28 0.6 9 -1.1 9 18
MMP2 0.27 0.26 0.66 3 -1.3 5 8
RB1/FOXM1C 0.23 0.26 0.58 33 -1.2 3 36
CREBBP 0.022 0.005 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.029 0.085 -10000 0 -0.36 29 29
ADCY5 -0.035 0.097 -10000 0 -0.36 39 39
ADCY6 -0.009 0.022 -10000 0 -0.35 2 2
ADCY7 -0.008 0.016 -10000 0 -0.35 1 1
ADCY1 -0.01 0.027 -10000 0 -0.35 3 3
ADCY2 -0.009 0.081 0.27 16 -0.35 15 31
ADCY3 -0.009 0.016 -10000 0 -0.35 1 1
ADCY8 -0.098 0.15 0.22 1 -0.35 126 127
PRKCE -0.006 0.018 -10000 0 -0.41 1 1
ADCY9 -0.009 0.022 -10000 0 -0.35 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.016 0.12 0.25 33 -0.28 20 53
IL23-mediated signaling events

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
CCL2 -0.1 0.42 -10000 0 -1.2 45 45
IL23A -0.081 0.39 -10000 0 -1.3 25 25
NF kappa B1 p50/RelA/I kappa B alpha -0.071 0.4 -10000 0 -1.1 39 39
positive regulation of T cell mediated cytotoxicity -0.1 0.45 -10000 0 -1.2 44 44
ITGA3 -0.093 0.4 -10000 0 -1.1 40 40
IL17F -0.002 0.28 -10000 0 -0.71 31 31
IL12B 0.02 0.041 -10000 0 -10000 0 0
STAT1 (dimer) -0.098 0.43 -10000 0 -1.2 42 42
CD4 -0.089 0.42 -10000 0 -1.2 39 39
IL23 -0.072 0.38 -10000 0 -1.2 25 25
IL23R -0.001 0.17 -10000 0 -0.96 11 11
IL1B -0.09 0.41 -10000 0 -1.3 28 28
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.084 0.38 -10000 0 -1.2 29 29
TYK2 0.016 0.034 -10000 0 -10000 0 0
STAT4 0.013 0.074 -10000 0 -0.56 8 8
STAT3 0.023 0.003 -10000 0 -10000 0 0
IL18RAP -0.003 0.12 -10000 0 -0.56 22 22
IL12RB1 -0.016 0.14 -10000 0 -0.58 28 28
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.002 0.12 -10000 0 -0.42 30 30
IL23R/JAK2 0.014 0.17 -10000 0 -0.91 9 9
positive regulation of chronic inflammatory response -0.1 0.45 -10000 0 -1.2 44 44
natural killer cell activation 0 0.006 -10000 0 -10000 0 0
JAK2 0.02 0.04 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
NFKB1 0.02 0.012 -10000 0 -10000 0 0
RELA 0.021 0.011 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.066 0.36 -10000 0 -1.1 25 25
ALOX12B -0.081 0.38 -10000 0 -1.1 33 33
CXCL1 -0.11 0.44 -10000 0 -1.2 48 48
T cell proliferation -0.1 0.45 -10000 0 -1.2 44 44
NFKBIA 0.02 0.012 -10000 0 -10000 0 0
IL17A 0.006 0.23 -10000 0 -0.58 21 21
PI3K -0.097 0.38 -10000 0 -1.2 33 33
IFNG -0.001 0.036 0.1 3 -0.12 23 26
STAT3 (dimer) -0.089 0.36 -10000 0 -1.1 31 31
IL18R1 0.017 0.059 -10000 0 -0.55 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.059 0.31 -10000 0 -0.88 38 38
IL18/IL18R 0.023 0.1 -10000 0 -0.41 24 24
macrophage activation -0.004 0.018 0.032 1 -0.045 16 17
TNF -0.095 0.42 -10000 0 -1.3 32 32
STAT3/STAT4 -0.09 0.42 -10000 0 -1.2 42 42
STAT4 (dimer) -0.1 0.44 -10000 0 -1.2 43 43
IL18 0.019 0.046 -10000 0 -0.56 3 3
IL19 -0.085 0.38 -10000 0 -1.1 35 35
STAT5A (dimer) -0.098 0.43 -10000 0 -1.2 43 43
STAT1 0.022 0.004 -10000 0 -10000 0 0
SOCS3 0.02 0.037 -10000 0 -0.56 2 2
CXCL9 -0.1 0.42 -10000 0 -1.2 43 43
MPO -0.12 0.44 -10000 0 -1.2 45 45
positive regulation of humoral immune response -0.1 0.45 -10000 0 -1.2 44 44
IL23/IL23R/JAK2/TYK2 -0.12 0.51 -10000 0 -1.4 44 44
IL6 -0.2 0.56 -10000 0 -1.3 92 92
STAT5A 0.023 0.003 -10000 0 -10000 0 0
IL2 0.008 0.022 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.006 -10000 0 -10000 0 0
CD3E -0.095 0.4 -10000 0 -1.2 33 33
keratinocyte proliferation -0.1 0.45 -10000 0 -1.2 44 44
NOS2 -0.12 0.45 -10000 0 -1.2 52 52
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 0.014 0.3 0.48 1 -0.87 29 30
HDAC7 0.023 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.088 0.3 -10000 0 -0.81 17 17
SMAD4 0.022 0.009 -10000 0 -10000 0 0
ID2 0.013 0.3 0.48 1 -0.88 29 30
AP1 -0.023 0.14 -10000 0 -0.42 54 54
ABCG2 -0.022 0.35 0.48 1 -0.88 46 47
HIF1A 0.019 0.075 -10000 0 -0.28 4 4
TFF3 -0.011 0.33 -10000 0 -0.88 40 40
GATA2 -0.039 0.17 -10000 0 -0.56 46 46
AKT1 0.019 0.069 -10000 0 -10000 0 0
response to hypoxia 0.002 0.066 -10000 0 -0.27 7 7
MCL1 0.006 0.29 0.48 1 -0.87 28 29
NDRG1 0.013 0.29 0.48 1 -0.88 26 27
SERPINE1 0.013 0.29 0.48 1 -0.87 27 28
FECH 0.012 0.29 0.48 1 -0.88 28 29
FURIN 0.014 0.29 0.48 1 -0.88 28 29
NCOA2 0.022 0.027 -10000 0 -0.56 1 1
EP300 0.022 0.074 -10000 0 -0.3 4 4
HMOX1 0.014 0.3 0.48 1 -0.88 28 29
BHLHE40 0.011 0.29 0.48 1 -0.87 29 30
BHLHE41 0.008 0.3 0.48 1 -0.94 27 28
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.063 0.13 -10000 0 -0.43 7 7
ENG 0.012 0.12 0.36 3 -0.64 7 10
JUN 0.018 0.017 -10000 0 -10000 0 0
RORA 0.014 0.3 0.48 1 -0.87 29 30
ABCB1 -0.11 0.39 -10000 0 -1.1 61 61
TFRC -0.015 0.26 -10000 0 -0.85 24 24
CXCR4 0.014 0.3 0.48 1 -0.87 29 30
TF 0.006 0.29 -10000 0 -0.86 31 31
CITED2 0.009 0.3 0.48 1 -0.91 29 30
HIF1A/ARNT 0.14 0.4 0.6 9 -0.98 29 38
LDHA 0.023 0.13 -10000 0 -0.78 9 9
ETS1 0.006 0.31 0.48 1 -0.96 29 30
PGK1 0.012 0.3 0.48 1 -0.87 29 30
NOS2 0.005 0.33 0.48 1 -0.89 35 36
ITGB2 0.001 0.32 -10000 0 -0.93 33 33
ALDOA 0.014 0.3 0.48 1 -0.87 29 30
Cbp/p300/CITED2 0.025 0.31 -10000 0 -0.97 24 24
FOS -0.046 0.18 -10000 0 -0.56 54 54
HK2 0.014 0.29 0.48 1 -0.88 29 30
SP1 0.008 0.051 -10000 0 -0.2 1 1
GCK 0.036 0.11 -10000 0 -10000 0 0
HK1 0.013 0.3 0.48 1 -0.87 29 30
NPM1 0.012 0.29 0.48 1 -0.87 29 30
EGLN1 0.013 0.29 0.48 1 -0.88 28 29
CREB1 0.026 0.004 -10000 0 -10000 0 0
PGM1 0.013 0.3 0.48 1 -0.87 29 30
SMAD3 0.023 0.008 -10000 0 -10000 0 0
EDN1 -0.11 0.38 0.41 1 -1.1 50 51
IGFBP1 0.013 0.29 0.47 1 -0.86 29 30
VEGFA 0.023 0.23 -10000 0 -0.74 12 12
HIF1A/JAB1 0.03 0.059 -10000 0 -0.3 1 1
CP -0.008 0.29 0.48 1 -0.9 30 31
CXCL12 -0.007 0.34 0.48 1 -0.99 36 37
COPS5 0.023 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.032 0.014 -10000 0 -10000 0 0
BNIP3 0.014 0.3 0.48 1 -0.87 29 30
EGLN3 0.024 0.3 0.46 3 -0.88 29 32
CA9 0.079 0.34 0.51 9 -0.92 27 36
TERT 0.052 0.3 0.5 8 -0.87 25 33
ENO1 0.012 0.29 0.48 1 -0.87 29 30
PFKL 0.012 0.29 -10000 0 -0.87 29 29
NCOA1 0.023 0.003 -10000 0 -10000 0 0
ADM 0.013 0.3 0.48 1 -0.88 28 29
ARNT 0.02 0.07 -10000 0 -0.32 1 1
HNF4A 0.027 0.031 0.26 8 -10000 0 8
ADFP 0.003 0.29 -10000 0 -0.86 30 30
SLC2A1 0.078 0.27 0.41 6 -0.71 20 26
LEP 0.027 0.3 0.48 1 -0.88 28 29
HIF1A/ARNT/Cbp/p300 0.084 0.3 -10000 0 -0.81 21 21
EPO 0.05 0.19 -10000 0 -0.75 4 4
CREBBP 0.02 0.078 -10000 0 -0.3 7 7
HIF1A/ARNT/Cbp/p300/HDAC7 0.12 0.32 -10000 0 -0.83 17 17
PFKFB3 0.013 0.29 0.48 1 -0.87 29 30
NT5E 0.013 0.3 0.48 1 -0.88 29 30
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.031 0.032 0.26 1 -0.41 2 3
CRKL -0.047 0.18 0.34 2 -0.6 32 34
mol:PIP3 0.012 0.018 -10000 0 -10000 0 0
AKT1 0.012 0.043 -10000 0 -10000 0 0
PTK2B 0.021 0.007 -10000 0 -10000 0 0
RAPGEF1 -0.046 0.17 0.42 2 -0.57 32 34
RANBP10 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.033 0.16 0.25 1 -0.36 89 90
MAP3K5 -0.042 0.17 0.34 2 -0.55 34 36
HGF/MET/CIN85/CBL/ENDOPHILINS -0.022 0.15 -10000 0 -0.33 92 92
AP1 -0.026 0.12 -10000 0 -0.36 54 54
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis -0.1 0.3 -10000 0 -0.78 76 76
STAT3 (dimer) -0.041 0.12 -10000 0 -0.36 21 21
GAB1/CRKL/SHP2/PI3K -0.02 0.14 -10000 0 -0.53 22 22
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
CBL/CRK -0.045 0.17 -10000 0 -0.58 31 31
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.022 0.004 -10000 0 -10000 0 0
PTEN 0.02 0.007 -10000 0 -10000 0 0
ELK1 -0.004 0.076 0.28 24 -0.21 2 26
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.028 0.089 -10000 0 -0.31 21 21
PAK1 0.012 0.049 0.39 1 -10000 0 1
HGF/MET/RANBP10 -0.034 0.16 0.25 1 -0.35 92 93
HRAS -0.056 0.16 -10000 0 -0.59 17 17
DOCK1 -0.047 0.17 0.4 1 -0.57 32 33
GAB1 -0.057 0.18 -10000 0 -0.65 31 31
CRK -0.057 0.17 -10000 0 -0.61 31 31
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.088 0.22 -10000 0 -0.5 99 99
JUN 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.035 0.091 0.17 1 -0.22 93 94
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
cell morphogenesis 0.02 0.16 0.33 19 -0.44 15 34
GRB2/SHC -0.008 0.091 -10000 0 -0.29 9 9
FOS -0.042 0.18 -10000 0 -0.56 54 54
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.004 0.075 0.28 24 -0.21 2 26
HGF/MET/MUC20 -0.045 0.15 0.24 1 -0.35 93 94
cell migration -0.008 0.09 -10000 0 -0.28 9 9
GRB2 0.022 0.004 -10000 0 -10000 0 0
CBL 0.022 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.03 0.032 0.26 1 -0.41 2 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.035 0.12 -10000 0 -0.28 81 81
MET/MUC20 0.015 0.029 0.24 1 -0.41 2 3
RAP1B -0.039 0.16 0.37 4 -0.53 32 36
RAP1A -0.045 0.16 0.56 1 -0.54 31 32
HGF/MET/RANBP9 -0.034 0.16 0.25 1 -0.35 92 93
RAF1 -0.052 0.15 -10000 0 -0.59 14 14
STAT3 -0.041 0.12 -10000 0 -0.36 21 21
cell proliferation -0.055 0.16 0.25 4 -0.38 76 80
RPS6KB1 -0.006 0.041 -10000 0 -0.25 3 3
MAPK3 -0.005 0.1 0.75 7 -10000 0 7
MAPK1 -0.002 0.11 0.68 9 -10000 0 9
RANBP9 0.022 0.004 -10000 0 -10000 0 0
MAPK8 -0.022 0.16 0.34 3 -0.5 32 35
SRC -0.043 0.1 -10000 0 -0.34 17 17
PI3K 0 0.064 -10000 0 -0.27 6 6
MET/Glomulin 0.014 0.034 0.27 1 -0.36 2 3
SOS1 0.022 0.004 -10000 0 -10000 0 0
MAP2K1 -0.05 0.14 -10000 0 -0.55 14 14
MET 0.02 0.041 0.37 1 -0.56 2 3
MAP4K1 -0.044 0.18 0.35 2 -0.58 36 38
PTK2 0.021 0.006 -10000 0 -10000 0 0
MAP2K2 -0.05 0.14 -10000 0 -0.55 14 14
BAD 0.01 0.042 -10000 0 -10000 0 0
MAP2K4 -0.039 0.15 0.32 2 -0.5 32 34
SHP2/GRB2/SOS1/GAB1 -0.032 0.16 -10000 0 -0.54 30 30
INPPL1 0.022 0.005 -10000 0 -10000 0 0
PXN 0.023 0.002 -10000 0 -10000 0 0
SH3KBP1 0.02 0.037 -10000 0 -0.56 2 2
HGS -0.035 0.084 0.15 1 -0.2 87 88
PLCgamma1/PKC 0.017 0.003 -10000 0 -10000 0 0
HGF -0.09 0.23 -10000 0 -0.56 94 94
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
PTPRJ 0.021 0.026 -10000 0 -0.56 1 1
NCK/PLCgamma1 -0.01 0.091 -10000 0 -0.27 4 4
PDPK1 0.009 0.022 -10000 0 -10000 0 0
HGF/MET/SHIP -0.034 0.16 0.25 1 -0.36 93 94
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.21 0.27 -10000 0 -0.76 30 30
PCK1 -0.1 0.17 -10000 0 -0.67 9 9
HNF4A -0.25 0.34 -10000 0 -0.91 55 55
KCNJ11 -0.22 0.3 -10000 0 -0.94 21 21
AKT1 -0.015 0.097 -10000 0 -0.45 1 1
response to starvation -0.008 0.031 -10000 0 -0.19 3 3
DLK1 -0.2 0.29 -10000 0 -0.75 26 26
NKX2-1 -0.69 0.7 -10000 0 -1.4 251 251
ACADM -0.21 0.27 -10000 0 -0.76 30 30
TAT -0.11 0.19 -10000 0 -0.77 14 14
CEBPB 0.023 0.005 -10000 0 -10000 0 0
CEBPA 0.021 0.027 -10000 0 -0.55 1 1
TTR -0.023 0.18 0.66 2 -0.67 19 21
PKLR -0.2 0.27 -10000 0 -0.76 28 28
APOA1 -0.36 0.49 -10000 0 -1.3 67 67
CPT1C -0.21 0.27 -10000 0 -0.76 29 29
ALAS1 -0.11 0.17 -10000 0 -0.83 1 1
TFRC -0.089 0.2 -10000 0 -0.75 10 10
FOXF1 0.044 0.18 0.24 49 -0.44 48 97
NF1 0.025 0.005 -10000 0 -10000 0 0
HNF1A (dimer) 0.035 0.031 0.25 8 -10000 0 8
CPT1A -0.2 0.27 -10000 0 -0.77 26 26
HMGCS1 -0.17 0.28 -10000 0 -0.76 22 22
NR3C1 0.026 0.008 -10000 0 -10000 0 0
CPT1B -0.21 0.27 -10000 0 -0.76 29 29
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.03 0.012 -10000 0 -10000 0 0
GCK -0.21 0.27 -10000 0 -0.76 29 29
CREB1 0.026 0.007 -10000 0 -10000 0 0
IGFBP1 -0.099 0.16 -10000 0 -0.63 6 6
PDX1 -0.096 0.17 -10000 0 -10000 0 0
UCP2 -0.21 0.27 -10000 0 -0.76 29 29
ALDOB -0.21 0.28 -10000 0 -0.8 14 14
AFP 0.046 0.077 0.36 1 -10000 0 1
BDH1 -0.12 0.27 0.53 1 -0.75 26 27
HADH -0.21 0.28 -10000 0 -0.8 14 14
F2 -0.27 0.35 -10000 0 -0.95 41 41
HNF1A 0.035 0.031 0.25 8 -10000 0 8
G6PC 0.022 0.06 -10000 0 -10000 0 0
SLC2A2 -0.09 0.17 -10000 0 -0.81 1 1
INS -0.023 0.006 -10000 0 -10000 0 0
FOXA1 0.11 0.12 0.29 53 -0.37 10 63
FOXA3 0.03 0.1 0.36 4 -0.55 13 17
FOXA2 -0.24 0.33 -10000 0 -0.82 31 31
ABCC8 -0.22 0.3 -10000 0 -0.89 23 23
ALB 0.046 0.076 0.36 1 -10000 0 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.014 0.17 0.32 12 -0.58 25 37
FYN -0.013 0.22 0.3 13 -0.71 33 46
LAT/GRAP2/SLP76 -0.006 0.18 0.28 3 -0.6 32 35
IKBKB 0.022 0.017 0.37 1 -10000 0 1
AKT1 -0.005 0.15 0.25 16 -0.44 36 52
B2M 0.021 0.012 -10000 0 -10000 0 0
IKBKG 0.003 0.044 0.098 10 -0.14 20 30
MAP3K8 0.021 0.027 -10000 0 -0.56 1 1
mol:Ca2+ -0.013 0.016 0.087 2 -0.091 6 8
integrin-mediated signaling pathway 0.029 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.017 0.21 0.32 10 -0.66 36 46
TRPV6 0.006 0.17 1.1 9 -0.58 8 17
CD28 0.018 0.053 -10000 0 -0.56 4 4
SHC1 -0.01 0.21 0.32 17 -0.74 27 44
receptor internalization -0.024 0.22 0.23 4 -0.7 37 41
PRF1 -0.06 0.33 -10000 0 -1 45 45
KRAS 0.021 0.006 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
COT/AKT1 0.01 0.12 0.26 10 -0.36 32 42
LAT -0.015 0.2 0.27 7 -0.75 26 33
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D 0.011 0.08 -10000 0 -0.57 9 9
CD3E 0.012 0.076 -10000 0 -0.57 8 8
CD3G -0.011 0.14 -10000 0 -0.56 28 28
RASGRP2 -0.017 0.06 -10000 0 -0.17 63 63
RASGRP1 -0.005 0.14 0.26 12 -0.44 33 45
HLA-A 0.02 0.029 -10000 0 -0.57 1 1
RASSF5 0.022 0.004 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.029 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.059 0.16 25 -0.13 22 47
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.06 -10000 0 -0.23 24 24
PRKCA -0.001 0.086 0.16 12 -0.29 26 38
GRAP2 -0.005 0.12 -10000 0 -0.56 23 23
mol:IP3 -0.016 0.12 0.24 4 -0.44 29 33
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.026 0.19 -10000 0 -0.74 26 26
ORAI1 -0.013 0.13 0.63 1 -0.95 8 9
CSK -0.015 0.2 0.28 7 -0.75 27 34
B7 family/CD28 -0.012 0.23 -10000 0 -0.77 32 32
CHUK 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.034 0.23 0.25 1 -0.79 33 34
PTPN6 -0.015 0.2 0.25 4 -0.76 27 31
VAV1 -0.018 0.2 0.3 6 -0.74 28 34
Monovalent TCR/CD3 -0.022 0.16 -10000 0 -0.52 35 35
CBL 0.022 0.004 -10000 0 -10000 0 0
LCK -0.014 0.22 0.3 13 -0.73 32 45
PAG1 -0.014 0.21 0.28 10 -0.73 28 38
RAP1A 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.033 0.23 0.32 3 -0.8 32 35
CD80 0.002 0.1 -10000 0 -0.56 15 15
CD86 0.013 0.065 -10000 0 -0.56 6 6
PDK1/CARD11/BCL10/MALT1 -0.008 0.076 -10000 0 -0.28 25 25
HRAS 0.022 0.004 -10000 0 -10000 0 0
GO:0035030 -0.028 0.17 -10000 0 -0.59 34 34
CD8A 0.013 0.071 -10000 0 -0.57 7 7
CD8B 0.01 0.091 0.24 4 -0.57 11 15
PTPRC -0.013 0.14 -10000 0 -0.56 30 30
PDK1/PKC theta -0.018 0.18 0.27 11 -0.53 37 48
CSK/PAG1 -0.014 0.2 0.29 11 -0.71 27 38
SOS1 0.022 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.03 0.032 -10000 0 -0.54 1 1
GRAP2/SLP76 -0.009 0.21 0.3 2 -0.7 33 35
STIM1 -0.003 0.079 1.3 1 -0.93 1 2
RAS family/GTP 0.022 0.073 0.19 23 -0.19 17 40
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.028 0.24 0.23 4 -0.76 37 41
mol:DAG -0.026 0.1 -10000 0 -0.39 30 30
RAP1A/GDP 0.009 0.028 0.092 14 -10000 0 14
PLCG1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.008 0.088 -10000 0 -0.57 11 11
cytotoxic T cell degranulation -0.054 0.3 -10000 0 -0.94 45 45
RAP1A/GTP -0.006 0.023 -10000 0 -0.065 56 56
mol:PI-3-4-5-P3 -0.008 0.17 0.27 15 -0.53 36 51
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.014 0.16 0.26 4 -0.59 29 33
NRAS 0.022 0.005 -10000 0 -10000 0 0
ZAP70 0.013 0.074 -10000 0 -0.56 8 8
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.017 0.16 -10000 0 -0.59 30 30
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.019 0.1 -10000 0 -0.55 13 13
CARD11 0.022 0.033 0.3 2 -0.56 1 3
PRKCB -0.007 0.1 0.16 12 -0.31 35 47
PRKCE -0.004 0.083 0.16 7 -0.28 27 34
PRKCQ -0.023 0.2 0.29 10 -0.61 38 48
LCP2 0.014 0.064 -10000 0 -0.56 6 6
BCL10 0.022 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0 0.13 0.23 18 -0.37 35 53
IKK complex 0.013 0.055 0.14 35 -0.12 19 54
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.005 0.093 0.17 18 -0.27 32 50
PDPK1 -0.003 0.14 0.25 15 -0.42 33 48
TCR/CD3/MHC I/CD8/Fyn -0.028 0.23 -10000 0 -0.84 28 28
Plasma membrane estrogen 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
GNB1/GNG2 0.03 0.087 -10000 0 -0.34 23 23
ER alpha/Gai/GDP/Gbeta gamma -0.038 0.19 -10000 0 -0.56 42 42
AKT1 -0.026 0.2 -10000 0 -0.82 27 27
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.021 0.2 -10000 0 -0.82 27 27
mol:Ca2+ -0.096 0.18 -10000 0 -0.42 109 109
IGF1R 0.022 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.014 0.077 -10000 0 -0.35 20 20
SHC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis 0.023 0.19 0.77 27 -10000 0 27
RhoA/GTP 0.007 0.057 -10000 0 -0.28 18 18
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.008 0.16 -10000 0 -0.47 40 40
regulation of stress fiber formation 0.01 0.068 0.45 1 -0.22 3 4
E2/ERA-ERB (dimer) 0.013 0.076 -10000 0 -0.34 21 21
KRAS 0.021 0.006 -10000 0 -10000 0 0
G13/GTP 0.014 0.069 -10000 0 -0.32 19 19
pseudopodium formation -0.01 0.068 0.22 3 -0.45 1 4
E2/ER alpha (dimer)/PELP1 0.013 0.077 -10000 0 -0.35 21 21
GRB2 0.022 0.004 -10000 0 -10000 0 0
GNG2 0.016 0.059 -10000 0 -0.56 5 5
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.026 0.18 -10000 0 -0.52 42 42
E2/ER beta (dimer) 0.016 0.004 -10000 0 -10000 0 0
mol:GDP -0.004 0.086 -10000 0 -0.4 21 21
mol:NADP -0.026 0.18 -10000 0 -0.52 42 42
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
mol:IP3 -0.1 0.19 -10000 0 -0.44 109 109
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
PLCB1 -0.094 0.19 -10000 0 -0.44 109 109
PLCB2 -0.1 0.2 -10000 0 -0.45 117 117
IGF1 0.004 0.1 0.24 1 -0.56 16 17
mol:L-citrulline -0.026 0.18 -10000 0 -0.52 42 42
RHOA 0.021 0.007 -10000 0 -10000 0 0
Gai/GDP -0.04 0.21 -10000 0 -0.62 53 53
JNK cascade 0.016 0.004 -10000 0 -10000 0 0
BCAR1 0.022 0.006 -10000 0 -10000 0 0
ESR2 0.022 0.005 -10000 0 -10000 0 0
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
ESR1 -0.002 0.12 -10000 0 -0.56 21 21
Gq family/GDP/Gbeta gamma -0.07 0.21 -10000 0 -0.68 34 34
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.075 -10000 0 -0.47 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.007 0.15 -10000 0 -0.47 38 38
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
E2/ER alpha (dimer) -0.002 0.087 -10000 0 -0.4 22 22
STRN 0.023 0.003 -10000 0 -10000 0 0
GNAL 0.018 0.046 -10000 0 -0.56 3 3
PELP1 0.022 0.005 -10000 0 -10000 0 0
MAPK11 0.01 0.003 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
HBEGF -0.036 0.19 0.3 8 -0.54 45 53
cAMP biosynthetic process 0.01 0.066 -10000 0 -0.3 19 19
SRC -0.034 0.18 0.26 2 -0.53 42 44
PI3K 0.017 0.017 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
G13/GDP/Gbeta gamma 0.017 0.096 -10000 0 -0.39 21 21
SOS1 0.022 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.026 0.12 -10000 0 -0.41 36 36
Gs family/GTP 0.016 0.068 -10000 0 -0.3 19 19
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.038 0.016 -10000 0 -10000 0 0
vasodilation -0.024 0.16 -10000 0 -0.5 42 42
mol:DAG -0.1 0.19 -10000 0 -0.44 109 109
Gs family/GDP/Gbeta gamma 0.001 0.089 -10000 0 -0.39 19 19
MSN -0.011 0.071 0.23 3 -0.49 1 4
Gq family/GTP -0.095 0.21 -10000 0 -0.46 116 116
mol:PI-3-4-5-P3 -0.019 0.19 -10000 0 -0.78 27 27
NRAS 0.022 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.024 0.16 0.5 42 -10000 0 42
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.086 -10000 0 -0.38 21 21
NOS3 -0.029 0.19 -10000 0 -0.56 41 41
GNA11 0.022 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.16 0.32 1 -0.63 26 27
E2/ER alpha (dimer)/PELP1/Src -0.014 0.17 0.25 1 -0.49 41 42
ruffle organization -0.01 0.068 0.22 3 -0.45 1 4
ROCK2 -0.008 0.074 0.24 3 -0.27 13 16
GNA14 -0.11 0.24 -10000 0 -0.56 111 111
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
MMP9 -0.028 0.17 0.32 9 -0.51 38 47
MMP2 -0.028 0.17 0.29 4 -0.51 41 45
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.27 -10000 0 -0.56 156 156
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.022 0.004 -10000 0 -10000 0 0
TCEB1 0.022 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.012 0.065 0.25 2 -0.27 20 22
HIF1A -0.004 0.048 -10000 0 -0.27 15 15
COPS5 0.022 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.058 0.025 -10000 0 -10000 0 0
FIH (dimer) 0.022 0.005 -10000 0 -10000 0 0
CDKN2A 0.095 0.14 0.24 204 -0.3 20 224
ARNT/IPAS -0.11 0.2 -10000 0 -0.41 143 143
HIF1AN 0.022 0.005 -10000 0 -10000 0 0
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.01 0.062 -10000 0 -0.28 18 18
CUL2 0.022 0.004 -10000 0 -10000 0 0
OS9 0.023 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.012 0.063 0.26 1 -0.27 19 20
PHD1-3/OS9 0.068 0.051 0.25 2 -10000 0 2
HIF1A/RACK1/Elongin B/Elongin C 0.031 0.062 -10000 0 -0.28 7 7
VHL 0.021 0.006 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.013 0.062 0.25 2 -0.28 16 18
EGLN3 0.054 0.078 0.24 72 -10000 0 72
EGLN2 0.021 0.006 -10000 0 -10000 0 0
EGLN1 0.022 0.004 -10000 0 -10000 0 0
TP53 0.022 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.015 0.17 -10000 0 -0.58 38 38
ARNT 0.022 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.022 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.056 0.11 0.35 4 -0.32 21 25
Regulation of Androgen receptor activity

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
HDAC1 -0.01 0.003 -10000 0 -10000 0 0
SMARCC1 0.004 0.023 -10000 0 -10000 0 0
REL 0.021 0.007 -10000 0 -10000 0 0
HDAC7 -0.073 0.11 0.21 1 -0.31 35 36
JUN 0.022 0.004 -10000 0 -10000 0 0
EP300 0.022 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.006 -10000 0 -10000 0 0
KAT5 0.023 0.002 -10000 0 -10000 0 0
MAPK14 -0.009 0.023 -10000 0 -10000 0 0
FOXO1 0.022 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.054 0.13 -10000 0 -0.32 36 36
MAP2K6 0.007 0.026 0.22 1 -10000 0 1
BRM/BAF57 0.029 0.023 -10000 0 -0.41 1 1
MAP2K4 0.007 0.024 -10000 0 -10000 0 0
SMARCA2 0.019 0.027 -10000 0 -0.56 1 1
PDE9A -0.083 0.22 -10000 0 -0.95 20 20
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
CEBPA 0.02 0.027 -10000 0 -0.56 1 1
EHMT2 0.022 0.004 -10000 0 -10000 0 0
cell proliferation -0.078 0.16 0.33 4 -0.45 43 47
NR0B1 0.07 0.12 0.24 147 -0.29 7 154
EGR1 0.013 0.069 -10000 0 -0.56 7 7
RXRs/9cRA -0.14 0.18 -10000 0 -0.32 235 235
AR/RACK1/Src -0.025 0.078 0.35 2 -0.28 1 3
AR/GR -0.045 0.12 -10000 0 -0.28 88 88
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
PKN1 0.022 0.005 -10000 0 -10000 0 0
RCHY1 0.022 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.009 0.023 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.018 0.082 0.28 1 -0.33 2 3
SRC -0.028 0.036 0.2 3 -10000 0 3
NR3C1 0.021 0.006 -10000 0 -10000 0 0
KLK3 -0.04 0.13 -10000 0 -0.49 7 7
APPBP2 0.007 0.024 -10000 0 -10000 0 0
TRIM24 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.032 0.075 0.22 1 -0.3 1 2
TMPRSS2 -0.35 0.52 -10000 0 -1.1 162 162
RXRG -0.26 0.28 -10000 0 -0.56 237 237
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.022 0.004 -10000 0 -10000 0 0
RXRB 0.023 0.004 -10000 0 -10000 0 0
CARM1 0.022 0.005 -10000 0 -10000 0 0
NR2C2 0.021 0.006 -10000 0 -10000 0 0
KLK2 -0.012 0.075 0.44 1 -0.36 1 2
AR -0.062 0.12 -10000 0 -0.3 92 92
SENP1 0.023 0.003 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
MDM2 0.023 0.017 0.37 1 -10000 0 1
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 -0.034 0.17 -10000 0 -0.56 46 46
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.14 0.11 0.24 286 -10000 0 286
T-DHT/AR/RACK1/Src -0.025 0.078 0.3 3 -0.29 1 4
positive regulation of transcription -0.034 0.17 -10000 0 -0.56 46 46
DNAJA1 0.007 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.01 0.21 1 -10000 0 1
NCOA1 0.031 0.02 -10000 0 -10000 0 0
SPDEF -0.048 0.19 0.24 4 -0.56 60 64
T-DHT/AR/TIF2 -0.024 0.085 -10000 0 -0.37 13 13
T-DHT/AR/Hsp90 -0.03 0.074 0.21 2 -0.3 1 3
GSK3B 0.017 0.013 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.029 0.034 -10000 0 -10000 0 0
SIRT1 0.022 0.005 -10000 0 -10000 0 0
ZMIZ2 0.022 0.005 -10000 0 -10000 0 0
POU2F1 -0.011 0.061 -10000 0 -0.18 5 5
T-DHT/AR/DAX-1 -0.019 0.11 0.27 5 -0.31 2 7
CREBBP 0.022 0.005 -10000 0 -10000 0 0
SMARCE1 0.022 0.004 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.009 0.093 -10000 0 -0.43 4 4
SMARCC2 0.024 0.002 -10000 0 -10000 0 0
SMARCC1 0.022 0.007 -10000 0 -10000 0 0
TBX21 -0.073 0.3 0.43 2 -0.9 50 52
SUMO2 0.022 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.026 0.005 -10000 0 -10000 0 0
FKBP4 0.022 0.017 0.37 1 -10000 0 1
FKBP5 0.023 0.003 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.01 0.11 0.32 8 -10000 0 8
PRL 0.014 0.092 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.002 0.25 0.52 43 -0.4 36 79
RELA -0.061 0.13 -10000 0 -0.29 61 61
FGG -0.24 0.34 0.47 13 -0.6 206 219
GR beta/TIF2 0 0.12 0.3 20 -0.32 1 21
IFNG 0.027 0.19 -10000 0 -0.9 8 8
apoptosis -0.006 0.11 0.51 3 -0.52 5 8
CREB1 0.026 0.01 -10000 0 -10000 0 0
histone acetylation 0 0.11 0.32 1 -0.36 13 14
BGLAP 0.021 0.11 -10000 0 -0.53 1 1
GR/PKAc 0.01 0.11 0.31 8 -10000 0 8
NF kappa B1 p50/RelA -0.12 0.24 -10000 0 -0.4 172 172
SMARCD1 0.024 0.002 -10000 0 -10000 0 0
MDM2 0.003 0.08 0.24 20 -10000 0 20
GATA3 0.011 0.096 0.24 3 -0.56 13 16
AKT1 0.019 0.005 -10000 0 -10000 0 0
CSF2 -0.12 0.37 -10000 0 -1.2 52 52
GSK3B 0.02 0.01 -10000 0 -10000 0 0
NR1I3 0.003 0.11 0.57 3 -0.63 1 4
CSN2 -0.048 0.17 0.36 19 -0.36 40 59
BRG1/BAF155/BAF170/BAF60A 0.056 0.021 -10000 0 -10000 0 0
NFATC1 0.021 0.027 -10000 0 -0.56 1 1
POU2F1 0.023 0.007 -10000 0 -10000 0 0
CDKN1A 0.009 0.042 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
SFN 0.039 0.071 0.24 45 -0.38 3 48
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.025 0.12 0.32 7 -0.24 1 8
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.009 0.14 0.51 2 -0.8 9 11
JUN 0.038 0.1 0.38 2 -0.4 5 7
IL4 0.009 0.11 -10000 0 -0.43 5 5
CDK5R1 0.027 0.033 0.25 10 -10000 0 10
PRKACA 0.022 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.15 -10000 0 -0.4 80 80
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.016 0.11 0.32 8 -10000 0 8
cortisol/GR alpha (monomer) -0.005 0.3 0.59 46 -0.46 42 88
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.002 0.2 -10000 0 -0.55 54 54
AP-1/NFAT1-c-4 0.07 0.19 0.38 2 -0.53 8 10
AFP 0.041 0.093 -10000 0 -10000 0 0
SUV420H1 0.022 0.004 -10000 0 -10000 0 0
IRF1 0 0.13 0.42 8 -0.39 1 9
TP53 0.031 0.008 -10000 0 -10000 0 0
PPP5C 0.022 0.004 -10000 0 -10000 0 0
KRT17 0.066 0.17 -10000 0 -0.62 6 6
KRT14 0.043 0.13 0.46 1 -0.66 4 5
TBP 0.027 0.005 -10000 0 -10000 0 0
CREBBP -0.013 0.045 0.34 1 -10000 0 1
HDAC1 0.021 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.024 -10000 0 -10000 0 0
AP-1 0.071 0.19 0.38 2 -0.52 9 11
MAPK14 0.022 0.008 -10000 0 -10000 0 0
MAPK10 0.013 0.069 -10000 0 -0.56 7 7
MAPK11 0.021 0.008 -10000 0 -10000 0 0
KRT5 0.066 0.18 -10000 0 -0.86 5 5
interleukin-1 receptor activity 0.007 0.023 -10000 0 -10000 0 0
NCOA1 0.024 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.005 -10000 0 -10000 0 0
CGA 0.015 0.11 0.32 1 -0.44 3 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.033 0.19 0.46 38 -0.34 17 55
MAPK3 0.022 0.008 -10000 0 -10000 0 0
MAPK1 0.021 0.008 -10000 0 -10000 0 0
ICAM1 -0.14 0.39 -10000 0 -1 60 60
NFKB1 -0.059 0.13 -10000 0 -0.3 58 58
MAPK8 0.031 0.13 0.29 4 -0.38 16 20
MAPK9 0.02 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.009 0.11 0.5 2 -0.55 5 7
BAX 0.007 0.041 -10000 0 -10000 0 0
POMC -0.027 0.2 0.51 2 -0.9 8 10
EP300 -0.013 0.046 0.34 1 -10000 0 1
cortisol/GR alpha (dimer)/p53 0.002 0.25 0.52 40 -0.4 34 74
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.069 0.23 14 -0.2 1 15
SGK1 -0.005 0.075 -10000 0 -10000 0 0
IL13 0.01 0.16 -10000 0 -0.65 9 9
IL6 -0.21 0.47 -10000 0 -1.1 94 94
PRKACG -0.01 0.019 0.24 1 -10000 0 1
IL5 0.008 0.14 -10000 0 -0.64 6 6
IL2 0.023 0.16 -10000 0 -0.64 5 5
CDK5 0.022 0.005 -10000 0 -10000 0 0
PRKACB 0.022 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
IL8 -0.071 0.24 -10000 0 -0.58 51 51
CDK5R1/CDK5 0.035 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.064 0.2 -10000 0 -0.44 55 55
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.011 0.24 0.5 41 -0.38 30 71
SMARCA4 0.023 0.005 -10000 0 -10000 0 0
chromatin remodeling 0 0.14 0.36 17 -0.37 2 19
NF kappa B1 p50/RelA/Cbp -0.09 0.2 0.36 1 -0.43 76 77
JUN (dimer) 0.038 0.1 0.38 2 -0.4 5 7
YWHAH 0.022 0.004 -10000 0 -10000 0 0
VIPR1 -0.28 0.46 -10000 0 -0.91 165 165
NR3C1 -0.009 0.17 0.43 24 -0.27 4 28
NR4A1 -0.053 0.2 -10000 0 -0.55 68 68
TIF2/SUV420H1 0.031 0.022 -10000 0 -0.41 1 1
MAPKKK cascade -0.006 0.11 0.51 3 -0.52 5 8
cortisol/GR alpha (dimer)/Src-1 0.006 0.26 0.51 46 -0.4 38 84
PBX1 0.021 0.038 -10000 0 -0.56 2 2
POU1F1 0.004 0.027 0.24 3 -10000 0 3
SELE -0.33 0.55 -10000 0 -1.1 155 155
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0 0.14 0.37 16 -0.37 2 18
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.011 0.24 0.5 41 -0.38 30 71
mol:cortisol -0.01 0.16 0.33 46 -0.24 44 90
MMP1 0.074 0.11 -10000 0 -0.54 6 6
IL12-mediated signaling 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
IL12/IL12R/TYK2/JAK2/SOCS1 0.008 0.12 0.22 1 -0.38 28 29
TBX21 -0.12 0.47 -10000 0 -1.3 58 58
B2M 0.022 0.01 -10000 0 -10000 0 0
TYK2 0.014 0.031 -10000 0 -10000 0 0
IL12RB1 -0.018 0.14 -10000 0 -0.59 28 28
GADD45B -0.067 0.36 -10000 0 -1.1 40 40
IL12RB2 0.037 0.075 0.24 49 -0.28 1 50
GADD45G -0.049 0.32 -10000 0 -0.98 38 38
natural killer cell activation 0 0.017 -10000 0 -10000 0 0
RELB 0.023 0.016 0.37 1 -10000 0 1
RELA 0.023 0.002 -10000 0 -10000 0 0
IL18 0.016 0.05 -10000 0 -0.57 3 3
IL2RA 0.021 0.041 0.24 3 -0.56 2 5
IFNG 0.016 0.055 0.24 2 -0.56 4 6
STAT3 (dimer) -0.046 0.29 -10000 0 -0.78 49 49
HLA-DRB5 -0.037 0.17 -10000 0 -0.56 46 46
FASLG -0.079 0.39 -10000 0 -1.2 42 42
NF kappa B2 p52/RelB -0.057 0.34 -10000 0 -0.94 47 47
CD4 0.001 0.094 -10000 0 -0.56 13 13
SOCS1 0.021 0.027 -10000 0 -0.56 1 1
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D 0.006 0.08 -10000 0 -0.56 9 9
CD3E 0.008 0.076 -10000 0 -0.56 8 8
CD3G -0.016 0.14 -10000 0 -0.56 28 28
IL12Rbeta2/JAK2 0.035 0.065 0.22 1 -10000 0 1
CCL3 -0.067 0.34 -10000 0 -1 39 39
CCL4 -0.069 0.35 -10000 0 -1.1 36 36
HLA-A 0.021 0.028 -10000 0 -0.56 1 1
IL18/IL18R 0.03 0.12 -10000 0 -0.44 24 24
NOS2 -0.091 0.41 -10000 0 -1.2 53 53
IL12/IL12R/TYK2/JAK2/SPHK2 0.009 0.12 0.22 1 -0.39 24 25
IL1R1 -0.064 0.33 -10000 0 -1 40 40
IL4 -0.007 0.031 -10000 0 -10000 0 0
JAK2 0.013 0.03 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.043 0.27 -10000 0 -1.1 23 23
RAB7A -0.019 0.28 0.51 1 -0.81 37 38
lysosomal transport -0.015 0.27 0.51 1 -0.76 37 38
FOS -0.18 0.47 -10000 0 -1.2 84 84
STAT4 (dimer) -0.052 0.33 0.44 2 -0.9 49 51
STAT5A (dimer) -0.06 0.34 -10000 0 -0.94 47 47
GZMA -0.07 0.35 -10000 0 -1.1 39 39
GZMB -0.07 0.36 -10000 0 -1.1 39 39
HLX 0.022 0.004 -10000 0 -10000 0 0
LCK -0.074 0.37 -10000 0 -1 47 47
TCR/CD3/MHC II/CD4 -0.079 0.28 -10000 0 -0.76 48 48
IL2/IL2R 0.044 0.072 -10000 0 -0.45 8 8
MAPK14 -0.056 0.35 -10000 0 -0.98 46 46
CCR5 -0.072 0.36 -10000 0 -1.1 41 41
IL1B 0.002 0.091 -10000 0 -0.59 10 10
STAT6 0.007 0.091 -10000 0 -10000 0 0
STAT4 0.013 0.074 -10000 0 -0.56 8 8
STAT3 0.023 0.003 -10000 0 -10000 0 0
STAT1 0.022 0.004 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
NFKB2 0.022 0.005 -10000 0 -10000 0 0
IL12B 0.013 0.03 -10000 0 -10000 0 0
CD8A 0.014 0.07 -10000 0 -0.56 7 7
CD8B 0.011 0.09 0.24 4 -0.57 11 15
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.008 0.12 0.38 28 -0.22 1 29
IL2RB 0.019 0.046 -10000 0 -0.56 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.041 0.3 0.44 2 -0.8 49 51
IL2RG 0.014 0.069 -10000 0 -0.56 7 7
IL12 0.012 0.06 -10000 0 -0.42 6 6
STAT5A 0.023 0.003 -10000 0 -10000 0 0
CD247 0.003 0.088 -10000 0 -0.56 11 11
IL2 0.001 0.02 -10000 0 -10000 0 0
SPHK2 0.022 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.069 -10000 0 -0.57 6 6
IL12/IL12R/TYK2/JAK2 -0.098 0.4 -10000 0 -1.1 49 49
MAP2K3 -0.063 0.36 -10000 0 -1 44 44
RIPK2 0.022 0.005 -10000 0 -10000 0 0
MAP2K6 -0.053 0.34 -10000 0 -0.99 43 43
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.029 0.16 -10000 0 -0.56 39 39
IL18RAP -0.006 0.12 -10000 0 -0.57 22 22
IL12Rbeta1/TYK2 -0.003 0.12 -10000 0 -0.42 31 31
EOMES -0.058 0.25 -10000 0 -0.92 28 28
STAT1 (dimer) -0.043 0.28 -10000 0 -0.77 46 46
T cell proliferation -0.027 0.24 0.43 2 -0.66 43 45
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.013 0.062 -10000 0 -0.57 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.046 0.27 -10000 0 -0.72 49 49
ATF2 -0.047 0.31 -10000 0 -0.92 41 41
Syndecan-1-mediated signaling events

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
TGFB1 0.022 0.005 -10000 0 -10000 0 0
CCL5 0.012 0.078 -10000 0 -0.56 9 9
SDCBP 0.022 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.023 0.065 0.28 6 -0.39 3 9
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.03 0.072 0.26 8 -0.35 4 12
Syndecan-1/Syntenin 0.032 0.07 0.26 8 -0.34 4 12
MAPK3 0.024 0.065 0.24 8 -0.37 2 10
HGF/MET -0.054 0.18 0.26 1 -0.41 93 94
TGFB1/TGF beta receptor Type II 0.022 0.005 -10000 0 -10000 0 0
BSG 0.022 0.004 -10000 0 -10000 0 0
keratinocyte migration 0.03 0.072 0.26 8 -0.34 4 12
Syndecan-1/RANTES 0.025 0.089 0.26 7 -0.43 8 15
Syndecan-1/CD147 0.042 0.071 0.29 3 -0.36 3 6
Syndecan-1/Syntenin/PIP2 0.03 0.067 0.24 8 -0.33 4 12
LAMA5 0.021 0.027 -10000 0 -0.56 1 1
positive regulation of cell-cell adhesion 0.029 0.066 0.24 8 -0.33 4 12
MMP7 0.021 0.091 0.24 21 -0.56 9 30
HGF -0.09 0.23 -10000 0 -0.56 94 94
Syndecan-1/CASK 0.014 0.064 0.22 5 -0.31 6 11
Syndecan-1/HGF/MET -0.018 0.15 0.29 3 -0.42 21 24
regulation of cell adhesion 0.013 0.059 0.31 1 -0.36 2 3
HPSE 0.022 0.005 -10000 0 -10000 0 0
positive regulation of cell migration 0.023 0.065 0.28 6 -0.39 3 9
SDC1 0.024 0.06 0.26 5 -0.42 2 7
Syndecan-1/Collagen 0.023 0.065 0.28 6 -0.39 3 9
PPIB 0.023 0.002 -10000 0 -10000 0 0
MET 0.02 0.041 0.37 1 -0.56 2 3
PRKACA 0.022 0.004 -10000 0 -10000 0 0
MMP9 0.034 0.049 0.24 25 -10000 0 25
MAPK1 0.02 0.061 0.22 5 -0.37 2 7
homophilic cell adhesion 0.023 0.066 0.28 6 -0.38 3 9
MMP1 0.15 0.11 0.24 295 -0.29 4 299
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
alphaV beta3 Integrin 0.026 0.057 -10000 0 -0.41 8 8
PTK2 0.012 0.14 -10000 0 -0.44 30 30
positive regulation of JNK cascade 0.002 0.1 -10000 0 -0.32 32 32
CDC42/GDP 0.019 0.14 0.36 1 -0.43 35 36
Rac1/GDP 0.018 0.14 -10000 0 -0.42 34 34
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.01 0.13 -10000 0 -0.4 32 32
nectin-3/I-afadin 0.001 0.11 -10000 0 -0.4 33 33
RAPGEF1 0.001 0.14 -10000 0 -0.47 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.004 0.15 -10000 0 -0.53 30 30
PDGFB-D/PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
TLN1 -0.031 0.099 -10000 0 -0.43 22 22
Rap1/GTP -0.001 0.1 -10000 0 -0.34 28 28
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.001 0.11 -10000 0 -0.4 33 33
PVR 0.022 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.005 -10000 0 -10000 0 0
mol:GDP 0.004 0.17 0.39 1 -0.52 36 37
MLLT4 0.022 0.004 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.018 0.069 -10000 0 -0.3 12 12
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.1 0.077 0.26 1 -0.2 1 2
positive regulation of lamellipodium assembly 0.006 0.11 -10000 0 -0.34 33 33
PVRL1 0.12 0.11 0.24 234 -0.29 1 235
PVRL3 -0.017 0.14 -10000 0 -0.56 31 31
PVRL2 0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
CDH1 0.022 0.005 -10000 0 -10000 0 0
CLDN1 0.066 0.12 0.31 88 -0.56 2 90
JAM-A/CLDN1 0.042 0.1 0.25 30 -0.32 15 45
SRC -0.01 0.17 -10000 0 -0.58 31 31
ITGB3 0.013 0.074 -10000 0 -0.56 8 8
nectin-1(dimer)/I-afadin/I-afadin 0.1 0.077 0.26 1 -0.2 1 2
FARP2 0.003 0.18 -10000 0 -0.54 33 33
RAC1 0.022 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.013 0.098 -10000 0 -0.35 31 31
nectin-1/I-afadin 0.1 0.077 0.26 1 -0.2 1 2
nectin-2/I-afadin 0.032 0.008 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.03 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.063 0.13 -10000 0 -0.36 31 31
CDC42/GTP/IQGAP1/filamentous actin 0.029 0.008 -10000 0 -10000 0 0
F11R 0.022 0.005 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.002 0.1 -10000 0 -0.32 32 32
alphaV/beta3 Integrin/Talin 0.008 0.12 0.27 5 -0.45 21 26
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.008 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.008 -10000 0 -10000 0 0
PIP5K1C -0.029 0.11 -10000 0 -0.33 44 44
VAV2 0.005 0.17 -10000 0 -0.53 37 37
RAP1/GDP 0.018 0.13 0.36 1 -0.39 34 35
ITGAV 0.023 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.014 0.098 -10000 0 -0.35 31 31
nectin-3(dimer)/I-afadin/I-afadin 0.001 0.11 -10000 0 -0.4 33 33
Rac1/GTP 0.012 0.14 -10000 0 -0.41 33 33
PTPRM -0.027 0.12 -10000 0 -0.35 48 48
E-cadherin/beta catenin/alpha catenin 0.1 0.062 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD 0.01 0.074 0.28 1 -0.29 19 20
FZD6 0.022 0.006 -10000 0 -10000 0 0
WNT6 0.056 0.083 0.24 80 -0.29 1 81
WNT4 0.019 0.056 0.24 4 -0.56 4 8
FZD3 0.021 0.007 -10000 0 -10000 0 0
WNT5A 0.024 0.032 0.24 8 -0.29 1 9
WNT11 0.007 0.11 0.25 10 -0.56 17 27
Caspase cascade in apoptosis

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
TOP1 -0.025 0.16 0.28 1 -0.48 39 40
ACTA1 -0.035 0.15 0.27 3 -0.52 31 34
NUMA1 -0.029 0.16 0.28 1 -0.48 43 44
SPTAN1 -0.037 0.15 0.32 3 -0.53 30 33
LIMK1 -0.035 0.15 0.31 2 -0.53 30 32
BIRC3 0.015 0.064 -10000 0 -0.56 6 6
BIRC2 0.022 0.004 -10000 0 -10000 0 0
BAX 0.022 0.004 -10000 0 -10000 0 0
CASP10 -0.032 0.098 -10000 0 -0.45 23 23
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
PTK2 -0.025 0.15 0.26 1 -0.47 40 41
DIABLO 0.023 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.036 0.14 0.32 3 -0.52 30 33
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
GSN -0.038 0.15 0.31 2 -0.53 30 32
MADD 0.022 0.004 -10000 0 -10000 0 0
TFAP2A 0.083 0.18 -10000 0 -0.7 21 21
BID -0.008 0.053 -10000 0 -0.26 19 19
MAP3K1 -0.037 0.16 -10000 0 -0.52 41 41
TRADD 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.028 0.15 0.32 3 -0.55 27 30
CASP9 0.022 0.005 -10000 0 -10000 0 0
DNA repair 0.002 0.047 0.22 5 -0.18 1 6
neuron apoptosis -0.011 0.15 -10000 0 -0.73 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.036 0.17 0.28 1 -0.5 43 44
APAF1 0.023 0.002 -10000 0 -10000 0 0
CASP6 -0.034 0.22 -10000 0 -0.98 22 22
TRAF2 0.022 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.037 0.14 0.33 3 -0.52 30 33
CASP7 -0.005 0.067 0.32 5 -0.27 4 9
KRT18 0.009 0.047 -10000 0 -0.62 1 1
apoptosis -0.042 0.16 0.41 1 -0.54 38 39
DFFA -0.037 0.15 0.29 1 -0.53 30 31
DFFB -0.036 0.15 0.29 1 -0.53 30 31
PARP1 -0.002 0.048 0.18 1 -0.22 5 6
actin filament polymerization 0.031 0.14 0.48 30 -0.33 7 37
TNF 0.011 0.083 0.24 1 -0.56 10 11
CYCS -0.002 0.062 0.18 8 -0.24 19 27
SATB1 -0.035 0.2 -10000 0 -0.92 22 22
SLK -0.037 0.15 0.32 1 -0.53 30 31
p15 BID/BAX 0.006 0.066 0.2 3 -0.25 20 23
CASP2 0.006 0.053 0.2 2 -0.38 2 4
JNK cascade 0.037 0.16 0.51 41 -10000 0 41
CASP3 -0.037 0.16 0.32 1 -0.51 35 36
LMNB2 -0.005 0.13 0.28 3 -0.42 27 30
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CASP4 0.021 0.027 -10000 0 -0.56 1 1
Mammalian IAPs/DIABLO 0.051 0.045 -10000 0 -0.33 6 6
negative regulation of DNA binding 0.083 0.18 -10000 0 -0.68 21 21
stress fiber formation -0.037 0.14 0.31 1 -0.52 30 31
GZMB -0.035 0.12 -10000 0 -0.52 24 24
CASP1 0.008 0.041 -10000 0 -0.58 2 2
LMNB1 -0.025 0.19 0.28 3 -0.54 43 46
APP -0.011 0.15 -10000 0 -0.74 18 18
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.002 -10000 0 -10000 0 0
VIM -0.04 0.17 0.4 1 -0.54 39 40
LMNA 0.003 0.1 0.28 3 -0.38 21 24
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.009 0.057 -10000 0 -0.25 11 11
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.037 0.15 0.32 2 -0.53 30 32
APAF-1/Caspase 9 -0.008 0.13 -10000 0 -0.66 18 18
nuclear fragmentation during apoptosis -0.028 0.16 0.27 1 -0.47 43 44
CFL2 -0.032 0.14 0.34 7 -0.5 30 37
GAS2 -0.068 0.17 -10000 0 -0.44 66 66
positive regulation of apoptosis -0.009 0.15 0.29 3 -0.48 32 35
PRF1 -0.003 0.12 -10000 0 -0.56 21 21
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.047 0.11 -10000 0 -0.39 13 13
epithelial cell differentiation -0.024 0.088 -10000 0 -0.46 3 3
ITCH 0.037 0.022 -10000 0 -10000 0 0
WWP1 -0.04 0.078 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.56 1 1
EGFR 0.022 0.083 0.36 11 -0.56 6 17
PRL 0.001 0.036 0.24 8 -10000 0 8
neuron projection morphogenesis -0.03 0.079 -10000 0 -0.36 5 5
PTPRZ1 0.16 0.13 0.24 317 -0.49 8 325
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.011 0.092 -10000 0 -0.38 5 5
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.036 0.083 -10000 0 -0.36 12 12
ADAM17 0.037 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.054 0.093 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.18 -10000 0 -0.4 118 118
NCOR1 0.022 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.032 0.087 -10000 0 -0.39 7 7
GRIN2B -0.034 0.083 -10000 0 -0.39 5 5
ErbB4/ErbB2/betacellulin -0.043 0.11 -10000 0 -0.4 19 19
STAT1 0.022 0.004 -10000 0 -10000 0 0
HBEGF 0.005 0.097 -10000 0 -0.56 14 14
PRLR 0.018 0.1 0.3 21 -0.56 10 31
E4ICDs/ETO2 -0.042 0.099 -10000 0 -0.41 5 5
axon guidance -0.037 0.073 -10000 0 -0.43 2 2
NEDD4 0.038 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.026 0.079 0.28 9 -0.41 10 19
CBFA2T3 0.016 0.059 -10000 0 -0.56 5 5
ErbB4/ErbB2/HBEGF -0.029 0.088 -10000 0 -0.37 8 8
MAPK3 -0.022 0.086 -10000 0 -0.37 5 5
STAT1 (dimer) -0.038 0.092 -10000 0 -10000 0 0
MAPK1 -0.021 0.083 -10000 0 -0.37 5 5
JAK2 0.02 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.035 0.083 -10000 0 -0.39 6 6
NRG1 -0.006 0.07 -10000 0 -0.41 13 13
NRG3 -0.13 0.25 -10000 0 -0.56 120 120
NRG2 -0.038 0.17 -10000 0 -0.56 46 46
NRG4 0.047 0.071 0.24 58 -0.29 1 59
heart development -0.037 0.073 -10000 0 -0.43 2 2
neural crest cell migration -0.034 0.082 -10000 0 -0.39 6 6
ERBB2 0.008 0.029 0.31 2 -10000 0 2
WWOX/E4ICDs -0.036 0.09 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.02 0.12 -10000 0 -0.44 3 3
apoptosis 0.16 0.25 0.52 129 -10000 0 129
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.07 0.14 -10000 0 -0.4 43 43
ErbB4/ErbB2/epiregulin -0.073 0.15 -10000 0 -0.4 50 50
ErbB4/ErbB4/betacellulin/betacellulin -0.063 0.13 -10000 0 -0.4 36 36
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.022 0.11 0.37 1 -0.43 8 9
MDM2 -0.043 0.088 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.022 0.074 -10000 0 -0.34 11 11
STAT5A -0.037 0.069 -10000 0 -0.41 2 2
ErbB4/EGFR/neuregulin 1 beta -0.029 0.1 0.28 1 -0.44 11 12
DLG4 0.022 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.031 0.009 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.037 0.084 -10000 0 -10000 0 0
STAT5A (dimer) -0.021 0.097 -10000 0 -0.55 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.026 0.078 -10000 0 -0.41 2 2
LRIG1 0.02 0.027 -10000 0 -0.56 1 1
EREG -0.077 0.23 0.25 14 -0.56 88 102
BTC -0.022 0.15 -10000 0 -0.56 36 36
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.037 0.071 -10000 0 -0.43 2 2
ERBB4 -0.054 0.094 -10000 0 -10000 0 0
STAT5B 0.023 0.003 -10000 0 -10000 0 0
YAP1 -0.009 0.077 -10000 0 -0.52 9 9
GRB2 0.022 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.015 0.091 0.33 2 -10000 0 2
glial cell differentiation 0.037 0.084 -10000 0 -10000 0 0
WWOX 0.021 0.007 -10000 0 -10000 0 0
cell proliferation -0.059 0.13 0.32 1 -0.48 13 14
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.074 -10000 0 -0.35 13 13
fibroblast growth factor receptor signaling pathway 0.029 0.073 -10000 0 -0.35 13 13
LAMA1 0.086 0.1 0.24 140 -0.29 1 141
PRNP 0.022 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 -0.056 0.18 -10000 0 -0.41 94 94
SMAD2 -0.031 0.072 0.18 4 -0.32 25 29
GPC1/PrPc/Cu2+ 0.035 0.03 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.082 0.083 0.31 23 -0.2 1 24
TDGF1 0.014 0.024 0.24 3 -10000 0 3
CRIPTO/GPC1 0.038 0.035 -10000 0 -10000 0 0
APP/GPC1 0.039 0.034 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.013 0.011 -10000 0 -10000 0 0
FLT1 0.022 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.023 0.099 -10000 0 -0.35 26 26
SERPINC1 0.014 0.031 0.24 6 -10000 0 6
FYN -0.015 0.017 -10000 0 -0.32 1 1
FGR -0.034 0.08 -10000 0 -0.35 28 28
positive regulation of MAPKKK cascade -0.017 0.1 0.3 2 -0.36 22 24
SLIT2 -0.091 0.23 -10000 0 -0.56 94 94
GPC1/NRG 0.025 0.08 -10000 0 -0.41 13 13
NRG1 0.005 0.093 -10000 0 -0.56 13 13
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.033 -10000 0 -10000 0 0
LYN -0.015 0.024 -10000 0 -0.35 2 2
mol:Spermine -0.008 0.012 -10000 0 -10000 0 0
cell growth 0.029 0.073 -10000 0 -0.35 13 13
BMP signaling pathway -0.033 0.047 -10000 0 -0.24 25 25
SRC -0.014 0.011 -10000 0 -10000 0 0
TGFBR1 0.022 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.26 0.24 2 -0.56 133 135
GPC1 0.033 0.047 0.24 25 -10000 0 25
TGFBR1 (dimer) 0.022 0.004 -10000 0 -10000 0 0
VEGFA 0.022 0.004 -10000 0 -10000 0 0
BLK -0.018 0.053 -10000 0 -0.36 10 10
HCK -0.016 0.029 -10000 0 -0.36 3 3
FGF2 0.006 0.094 -10000 0 -0.56 13 13
FGFR1 0.017 0.028 -10000 0 -0.56 1 1
VEGFR1 homodimer 0.022 0.006 -10000 0 -10000 0 0
TGFBR2 -0.011 0.13 -10000 0 -0.56 27 27
cell death 0.039 0.033 -10000 0 -10000 0 0
ATIII/GPC1 0.039 0.036 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.088 0.2 -10000 0 -0.41 133 133
LCK -0.015 0.019 -10000 0 -0.36 1 1
neuron differentiation 0.025 0.08 -10000 0 -0.41 13 13
PrPc/Cu2+ 0.016 0.004 -10000 0 -10000 0 0
APP 0.022 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.011 0.13 -10000 0 -0.56 27 27
S1P1 pathway

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.004 0.097 -10000 0 -0.41 24 24
PDGFRB 0.019 0.028 -10000 0 -0.56 1 1
SPHK1 0 0.054 -10000 0 -0.73 2 2
mol:S1P -0.004 0.053 -10000 0 -0.64 2 2
S1P1/S1P/Gi -0.05 0.16 -10000 0 -0.43 62 62
GNAO1 0.017 0.033 0.23 2 -0.56 1 3
PDGFB-D/PDGFRB/PLCgamma1 -0.033 0.15 0.25 3 -0.39 60 63
PLCG1 -0.052 0.15 -10000 0 -0.4 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.028 -10000 0 -0.56 1 1
GNAI2 0.017 0.016 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.016 0.031 -10000 0 -0.57 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.026 0.075 -10000 0 -0.35 24 24
S1P1/S1P -0.019 0.082 -10000 0 -0.36 11 11
negative regulation of cAMP metabolic process -0.048 0.16 -10000 0 -0.42 62 62
MAPK3 -0.073 0.21 -10000 0 -0.56 68 68
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
KDR -0.012 0.13 -10000 0 -0.56 25 25
PLCB2 -0.01 0.092 0.25 4 -0.34 9 13
RAC1 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.072 -10000 0 -0.33 9 9
receptor internalization -0.019 0.077 -10000 0 -0.34 11 11
PTGS2 -0.1 0.33 0.34 1 -0.95 58 59
Rac1/GTP -0.013 0.073 -10000 0 -0.32 10 10
RHOA 0.021 0.007 -10000 0 -10000 0 0
VEGFA 0.019 0.013 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.048 0.16 -10000 0 -0.42 62 62
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.012 0.06 -10000 0 -0.56 5 5
MAPK1 -0.064 0.2 -10000 0 -0.54 64 64
S1P1/S1P/PDGFB-D/PDGFRB -0.009 0.096 0.28 1 -0.39 11 12
ABCC1 0.019 0.017 0.24 1 -10000 0 1
FAS signaling pathway (CD95)

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
SPTAN1 -0.008 0.025 0.24 1 -0.22 2 3
RFC1 -0.006 0.031 0.22 5 -0.2 4 9
PRKDC -0.003 0.046 0.22 14 -0.22 2 16
RIPK1 0.024 0.006 -10000 0 -10000 0 0
CASP7 -0.017 0.12 -10000 0 -0.6 18 18
FASLG/FAS/FADD/FAF1 -0.006 0.063 0.22 4 -0.29 18 22
MAP2K4 -0.021 0.15 0.31 4 -0.43 23 27
mol:ceramide -0.018 0.098 -10000 0 -0.38 20 20
GSN -0.008 0.025 0.24 1 -0.25 1 2
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.088 -10000 0 -0.35 20 20
FAS 0.012 0.033 -10000 0 -0.57 1 1
BID -0.014 0.056 0.52 4 -10000 0 4
MAP3K1 0.01 0.14 0.34 6 -0.46 20 26
MAP3K7 0.017 0.015 -10000 0 -10000 0 0
RB1 -0.007 0.027 0.23 2 -0.2 4 6
CFLAR 0.024 0.006 -10000 0 -10000 0 0
HGF/MET -0.037 0.16 0.25 1 -0.36 94 95
ARHGDIB 0 0.054 0.22 22 -0.2 5 27
FADD 0.013 0.018 -10000 0 -10000 0 0
actin filament polymerization 0.019 0.047 0.25 1 -0.24 1 2
NFKB1 -0.034 0.14 -10000 0 -0.67 16 16
MAPK8 -0.05 0.2 0.45 1 -0.44 80 81
DFFA -0.008 0.029 0.21 3 -0.21 3 6
DNA fragmentation during apoptosis -0.015 0.048 0.21 5 -0.22 2 7
FAS/FADD/MET 0.026 0.044 0.25 1 -0.36 3 4
CFLAR/RIP1 0.034 0.011 -10000 0 -10000 0 0
FAIM3 0.019 0.053 0.24 1 -0.56 4 5
FAF1 0.014 0.022 -10000 0 -10000 0 0
PARP1 -0.007 0.037 0.22 6 -0.25 1 7
DFFB -0.007 0.032 0.21 5 -0.2 7 12
CHUK -0.031 0.13 -10000 0 -0.61 16 16
FASLG -0.009 0.11 -10000 0 -0.56 19 19
FAS/FADD 0.018 0.033 -10000 0 -0.44 1 1
HGF -0.09 0.23 -10000 0 -0.56 94 94
LMNA -0.011 0.043 0.19 9 -0.24 1 10
CASP6 -0.006 0.027 0.23 3 -0.25 1 4
CASP10 0.013 0.033 -10000 0 -0.56 1 1
CASP3 -0.003 0.021 0.25 2 -0.28 1 3
PTPN13 0.017 0.053 -10000 0 -0.56 4 4
CASP8 -0.016 0.046 0.45 4 -10000 0 4
IL6 -0.2 0.5 -10000 0 -1.2 89 89
MET 0.02 0.041 0.37 1 -0.56 2 3
ICAD/CAD -0.008 0.033 0.25 4 -0.24 1 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.018 0.099 -10000 0 -0.38 20 20
activation of caspase activity by cytochrome c -0.014 0.056 0.51 4 -10000 0 4
PAK2 0.061 0.11 0.22 149 -10000 0 149
BCL2 0.023 0.017 0.37 1 -10000 0 1
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.022 0.005 -10000 0 -10000 0 0
VLDLR 0.019 0.027 -10000 0 -0.56 1 1
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
NUDC 0.022 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.021 0.14 -10000 0 -0.35 76 76
CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
KATNA1 0.023 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.054 0.12 -10000 0 -0.32 76 76
IQGAP1/CaM 0.032 0.009 -10000 0 -10000 0 0
DAB1 0.028 0.06 0.24 31 -10000 0 31
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
PLA2G7 0.018 0.052 -10000 0 -0.56 4 4
CALM1 0.022 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.032 0.014 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.002 -10000 0 -10000 0 0
CDK5R1 0.028 0.033 0.25 10 -10000 0 10
LIS1/Poliovirus Protein 3A -0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.072 0.098 0.24 123 -0.29 2 125
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.016 0.15 0.35 2 -0.35 75 77
YWHAE 0.022 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.017 0.12 0.31 2 -0.34 2 4
MAP1B 0.005 0.01 0.21 1 -10000 0 1
RAC1 0.009 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.048 0.11 0.28 1 -0.3 62 63
RELN -0.068 0.21 0.24 3 -0.56 76 79
PAFAH/LIS1 0.018 0.031 -10000 0 -0.35 3 3
LIS1/CLIP170 0.021 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.01 0.096 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.036 0.12 -10000 0 -0.29 78 78
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.034 0.12 0.34 1 -0.34 8 9
LIS1/IQGAP1 0.021 0.008 -10000 0 -10000 0 0
RHOA 0.009 0.004 -10000 0 -10000 0 0
PAFAH1B1 -0.009 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.025 0.029 0.34 4 -10000 0 4
PAFAH1B2 0.022 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.015 0.027 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.008 0.12 0.3 2 -0.35 2 4
LRP8 0.024 0.017 0.24 3 -10000 0 3
NDEL1/Katanin 60 -0.019 0.12 0.31 2 -0.34 5 7
P39/CDK5 -0.019 0.14 0.31 7 -0.31 64 71
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.008 -10000 0 -10000 0 0
CDK5 -0.054 0.11 -10000 0 -0.3 72 72
PPP2R5D 0.022 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.007 -10000 0 -10000 0 0
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.006 0.13 0.27 3 -0.31 66 69
RELN/VLDLR -0.009 0.14 -10000 0 -0.32 74 74
CDC42 0.009 0.004 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.021 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.041 0.093 -10000 0 -0.27 22 22
NT3 (dimer)/TRKC -0.091 0.2 -10000 0 -0.42 127 127
NT3 (dimer)/TRKB 0.041 0.13 0.31 2 -0.38 32 34
SHC/Grb2/SOS1/GAB1/PI3K 0.009 0.023 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
BDNF -0.049 0.19 -10000 0 -0.56 60 60
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DYNLT1 0.023 0.003 -10000 0 -10000 0 0
NTRK1 0.015 0.059 -10000 0 -0.56 5 5
NTRK2 0.02 0.17 0.24 76 -0.55 31 107
NTRK3 -0.14 0.26 0.24 2 -0.56 135 137
NT-4/5 (dimer)/TRKB 0.043 0.14 0.28 4 -0.38 35 39
neuron apoptosis 0.042 0.18 0.42 48 -10000 0 48
SHC 2-3/Grb2 -0.047 0.19 -10000 0 -0.47 48 48
SHC1 0.022 0.005 -10000 0 -10000 0 0
SHC2 0.005 0.12 -10000 0 -0.42 18 18
SHC3 -0.073 0.23 -10000 0 -0.53 83 83
STAT3 (dimer) 0.022 0.043 -10000 0 -0.36 6 6
NT3 (dimer)/TRKA 0.044 0.067 0.25 1 -0.36 8 9
RIN/GDP -0.028 0.091 0.25 3 -0.28 6 9
GIPC1 0.022 0.005 -10000 0 -10000 0 0
KRAS 0.021 0.006 -10000 0 -10000 0 0
DNAJA3 0.029 0.059 0.2 2 -0.25 5 7
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.001 0.092 0.37 1 -0.81 6 7
MAGED1 0.022 0.004 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.013 0.074 -10000 0 -0.56 8 8
SHC/GRB2/SOS1 0.042 0.015 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.017 0.098 0.25 1 -0.35 30 31
TRKA/NEDD4-2 0.027 0.046 -10000 0 -0.41 5 5
ELMO1 0.012 0.074 -10000 0 -0.56 8 8
RhoG/GTP/ELMO1/DOCK1 0.022 0.05 -10000 0 -0.35 8 8
NGF 0.013 0.077 0.28 3 -0.56 8 11
HRAS 0.022 0.004 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
GAB2 0.007 0.094 -10000 0 -0.56 13 13
RIT2 -0.015 0.011 -10000 0 -10000 0 0
RIT1 0.022 0.005 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
DNM1 0.023 0.014 0.24 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.036 0.065 -10000 0 -0.26 8 8
mol:GDP -0.042 0.13 0.33 4 -0.39 12 16
NGF (dimer) 0.013 0.077 0.28 3 -0.56 8 11
RhoG/GDP 0.009 0.055 -10000 0 -0.36 10 10
RIT1/GDP -0.024 0.089 0.26 3 -0.27 7 10
TIAM1 0.021 0.027 -10000 0 -0.56 1 1
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.007 0.18 0.25 1 -0.41 76 77
KIDINS220/CRKL/C3G 0.031 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.03 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2 0.043 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.05 0.022 -10000 0 -10000 0 0
RIT1/GTP 0.016 0.004 -10000 0 -10000 0 0
NT3 (dimer) 0.016 0.06 0.24 2 -0.56 5 7
RAP1/GDP -0.025 0.073 -10000 0 -0.24 6 6
KIDINS220/CRKL 0.021 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.049 0.19 -10000 0 -0.56 60 60
ubiquitin-dependent protein catabolic process 0.031 0.067 0.25 1 -0.35 13 14
Schwann cell development -0.04 0.03 -10000 0 -10000 0 0
EHD4 0.023 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.052 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.011 0.054 -10000 0 -0.32 4 4
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.096 0.21 -10000 0 -0.36 164 164
ABL1 0.023 0.003 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.017 0.094 -10000 0 -0.37 11 11
STAT3 0.022 0.043 -10000 0 -0.36 6 6
axon guidance -0.099 0.19 -10000 0 -0.34 164 164
MAPK3 -0.027 0.082 0.2 1 -0.32 29 30
MAPK1 -0.026 0.08 0.18 13 -0.32 28 41
CDC42/GDP -0.023 0.094 0.25 5 -0.26 9 14
NTF3 0.016 0.06 0.24 2 -0.56 5 7
NTF4 0.013 0.074 -10000 0 -0.56 8 8
NGF (dimer)/TRKA/FAIM 0.026 0.066 0.25 1 -0.36 12 13
PI3K 0.017 0.017 -10000 0 -10000 0 0
FRS3 0.022 0.004 -10000 0 -10000 0 0
FAIM 0.019 0.009 -10000 0 -10000 0 0
GAB1 0.022 0.006 -10000 0 -10000 0 0
RASGRF1 -0.13 0.15 -10000 0 -0.3 139 139
SOS1 0.022 0.004 -10000 0 -10000 0 0
MCF2L -0.1 0.16 0.25 1 -0.36 126 127
RGS19 0.022 0.004 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.024 0.083 0.37 1 -0.43 4 5
Rac1/GDP -0.024 0.092 0.24 4 -0.27 8 12
NGF (dimer)/TRKA/GRIT 0.019 0.064 0.24 1 -0.35 13 14
neuron projection morphogenesis 0.035 0.13 -10000 0 -0.82 7 7
NGF (dimer)/TRKA/NEDD4-2 0.031 0.068 0.25 1 -0.36 13 14
MAP2K1 0.002 0.058 0.55 1 -10000 0 1
NGFR 0.042 0.062 0.24 42 -10000 0 42
NGF (dimer)/TRKA/GIPC/GAIP 0.013 0.047 -10000 0 -0.27 11 11
RAS family/GTP/PI3K 0.009 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.06 0.023 -10000 0 -10000 0 0
NRAS 0.022 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.026 0.14 -10000 0 -0.56 23 23
RASA1 0.021 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.027 0.046 -10000 0 -0.41 5 5
SQSTM1 0.021 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.005 0.18 -10000 0 -0.38 72 72
NGF (dimer)/TRKA/p62/Atypical PKCs 0.027 0.06 -10000 0 -0.31 9 9
MATK 0 0.11 -10000 0 -0.56 19 19
NEDD4L 0.022 0.005 -10000 0 -10000 0 0
RAS family/GDP -0.038 0.057 -10000 0 -0.2 7 7
NGF (dimer)/TRKA 0.005 0.046 0.19 1 -0.25 7 8
Rac1/GTP -0.11 0.1 -10000 0 -0.27 68 68
FRS2 family/SHP2/CRK family 0.056 0.027 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.03 0.058 0.3 6 -0.2 20 26
TP53 -0.001 0.045 -10000 0 -0.18 23 23
Senescence -0.001 0.045 -10000 0 -0.18 23 23
Apoptosis -0.001 0.045 -10000 0 -0.18 23 23
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.003 0.073 0.32 17 -0.21 6 23
MDM4 0.022 0.004 -10000 0 -10000 0 0
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.023 0.002 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.021 -10000 0 -0.19 1 1
Metarhodopsin II/Arrestin 0.023 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.021 0.055 -10000 0 -0.33 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.008 0.036 0.24 7 -0.29 1 8
GRK1 -0.004 0.03 0.37 2 -10000 0 2
CNG Channel 0.027 0.081 -10000 0 -0.29 24 24
mol:Na + 0.059 0.059 -10000 0 -10000 0 0
mol:ADP -0.004 0.03 0.37 2 -10000 0 2
RGS9-1/Gbeta5/R9AP -0.007 0.13 -10000 0 -0.36 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.075 0.07 0.26 22 -10000 0 22
CNGB1 0.041 0.063 0.24 44 -10000 0 44
RDH5 0.02 0.037 -10000 0 -0.56 2 2
SAG -0.013 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.089 0.35 13 -10000 0 13
Na + (4 Units) 0.044 0.044 -10000 0 -10000 0 0
RGS9 -0.04 0.18 -10000 0 -0.56 52 52
GNB1/GNGT1 0.077 0.078 0.26 18 -0.41 1 19
GNAT1/GDP 0.002 0.12 -10000 0 -0.31 58 58
GUCY2D 0.02 0.009 -10000 0 -10000 0 0
GNGT1 0.093 0.11 0.26 149 -10000 0 149
GUCY2F -0.006 0.019 -10000 0 -10000 0 0
GNB5 0.023 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.001 0.071 -10000 0 -0.3 24 24
mol:11-cis-retinal 0.02 0.037 -10000 0 -0.56 2 2
mol:cGMP 0.063 0.062 0.28 3 -10000 0 3
GNB1 0.021 0.027 -10000 0 -0.56 1 1
Rhodopsin 0.027 0.032 -10000 0 -0.42 2 2
SLC24A1 0.023 0.002 -10000 0 -10000 0 0
CNGA1 0.024 0.024 0.24 6 -10000 0 6
Metarhodopsin II 0.022 0.017 0.22 2 -10000 0 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.073 0.064 -10000 0 -10000 0 0
RGS9BP 0.009 0.082 -10000 0 -0.56 10 10
Metarhodopsin II/Transducin 0.024 0.045 0.17 14 -0.27 1 15
GCAP Family/Ca ++ 0.063 0.06 -10000 0 -10000 0 0
PDE6A/B 0.015 0.082 -10000 0 -0.41 16 16
mol:Pi -0.007 0.13 -10000 0 -0.36 58 58
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.072 0.07 0.24 18 -0.32 1 19
PDE6B 0.015 0.06 0.24 1 -0.56 5 6
PDE6A 0.008 0.088 0.24 2 -0.56 11 13
PDE6G 0.012 0.078 -10000 0 -0.56 9 9
RHO 0 0.025 0.24 2 -10000 0 2
PDE6 -0.003 0.14 -10000 0 -0.33 69 69
GUCA1A 0.077 0.098 0.24 128 -0.29 2 130
GC2/GCAP Family 0.072 0.062 -10000 0 -10000 0 0
GUCA1C -0.016 0.006 -10000 0 -10000 0 0
GUCA1B 0.022 0.005 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.025 0.096 -10000 0 -0.35 26 26
MAP4K1 0.016 0.053 -10000 0 -0.56 4 4
MAP3K8 0.021 0.027 -10000 0 -0.56 1 1
PRKCB -0.005 0.12 -10000 0 -0.56 23 23
DBNL 0.022 0.005 -10000 0 -10000 0 0
CRKL 0.021 0.006 -10000 0 -10000 0 0
MAP3K1 -0.001 0.08 -10000 0 -0.49 7 7
JUN -0.035 0.19 -10000 0 -0.65 41 41
MAP3K7 -0.008 0.089 -10000 0 -0.4 13 13
GRAP2 -0.005 0.12 -10000 0 -0.56 23 23
CRK 0.022 0.005 -10000 0 -10000 0 0
MAP2K4 0.003 0.098 0.27 6 -0.51 9 15
LAT 0.023 0.003 -10000 0 -10000 0 0
LCP2 0.014 0.064 -10000 0 -0.56 6 6
MAPK8 -0.034 0.21 -10000 0 -0.68 41 41
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0 0.093 -10000 0 -0.34 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55 0.032 0.093 -10000 0 -0.33 25 25
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.027 0.046 -10000 0 -0.37 6 6
Necdin/E2F1 0.026 0.051 -10000 0 -0.38 7 7
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.059 0.075 -10000 0 -0.31 13 13
NGF (dimer)/p75(NTR)/BEX1 0.015 0.14 0.29 5 -0.36 49 54
NT-4/5 (dimer)/p75(NTR) 0.038 0.072 0.26 2 -0.41 8 10
IKBKB 0.022 0.017 0.37 1 -10000 0 1
AKT1 0.053 0.1 0.35 4 -0.32 6 10
IKBKG 0.022 0.004 -10000 0 -10000 0 0
BDNF -0.049 0.19 -10000 0 -0.56 60 60
MGDIs/NGR/p75(NTR)/LINGO1 0.063 0.061 0.32 7 -0.36 1 8
FURIN 0.023 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.001 0.15 0.25 2 -0.36 64 66
LINGO1 0.042 0.062 0.24 43 -10000 0 43
Sortilin/TRAF6/NRIF 0.022 0.032 -10000 0 -0.29 4 4
proBDNF (dimer) -0.049 0.19 -10000 0 -0.56 60 60
NTRK1 0.015 0.059 -10000 0 -0.56 5 5
RTN4R 0.02 0.029 0.24 1 -0.56 1 2
neuron apoptosis -0.047 0.15 0.3 1 -0.53 18 19
IRAK1 0.022 0.004 -10000 0 -10000 0 0
SHC1 -0.019 0.05 0.23 3 -0.36 8 11
ARHGDIA 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.056 0.027 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.054 0.076 -10000 0 -0.33 13 13
MAGEH1 0.023 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.05 0.088 0.25 3 -0.34 17 20
Mammalian IAPs/DIABLO 0.051 0.045 -10000 0 -0.33 6 6
proNGF (dimer) 0.013 0.077 0.28 3 -0.56 8 11
MAGED1 0.022 0.004 -10000 0 -10000 0 0
APP 0.022 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.013 0.074 -10000 0 -0.56 8 8
ZNF274 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.017 0.051 -10000 0 -0.31 8 8
NGF 0.013 0.077 0.28 3 -0.56 8 11
cell cycle arrest -0.016 0.068 0.21 7 -0.3 13 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.014 0.048 -10000 0 -0.26 7 7
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.049 0.066 0.25 2 -0.36 8 10
NCSTN 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0.047 0.067 0.25 3 -0.36 8 11
PSENEN 0.021 0.007 -10000 0 -10000 0 0
mol:ceramide -0.022 0.059 0.18 9 -0.33 13 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.036 0.24 1 -10000 0 1
p75(NTR)/beta APP 0.044 0.042 0.26 2 -10000 0 2
BEX1 -0.021 0.17 0.24 21 -0.56 42 63
mol:GDP -0.016 0.05 0.22 3 -0.36 8 11
NGF (dimer) 0.043 0.081 -10000 0 -0.35 16 16
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.072 0.06 0.34 5 -0.33 1 6
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
RAC1/GTP 0.041 0.059 0.22 3 -0.31 8 11
MYD88 0.021 0.006 -10000 0 -10000 0 0
CHUK 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.048 0.068 0.25 3 -0.36 8 11
RHOB 0.021 0.027 -10000 0 -0.56 1 1
RHOA 0.021 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.032 0.009 -10000 0 -10000 0 0
NT3 (dimer) 0.016 0.06 0.24 2 -0.56 5 7
TP53 -0.049 0.11 0.33 3 -0.3 64 67
PRDM4 -0.022 0.059 0.18 9 -0.33 13 22
BDNF (dimer) 0.061 0.18 0.31 15 -0.36 65 80
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
SORT1 0.016 0.059 -10000 0 -0.56 5 5
activation of caspase activity 0.053 0.072 -10000 0 -0.31 13 13
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.054 0.077 0.25 3 -0.33 13 16
RHOC 0.022 0.005 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
MAPK10 -0.033 0.1 0.35 4 -0.42 8 12
DIABLO 0.023 0.002 -10000 0 -10000 0 0
SMPD2 -0.022 0.059 0.18 9 -0.33 13 22
APH1B 0.023 0.002 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.079 0.25 3 -0.36 13 16
PSEN1 0.022 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.038 0.062 0.26 1 -0.41 5 6
MAPK8 -0.029 0.099 0.33 5 -0.42 4 9
MAPK9 -0.03 0.098 0.37 3 -0.39 6 9
APAF1 0.023 0.002 -10000 0 -10000 0 0
NTF3 0.016 0.06 0.24 2 -0.56 5 7
NTF4 0.013 0.074 -10000 0 -0.56 8 8
NDN 0.015 0.064 -10000 0 -0.56 6 6
RAC1/GDP 0.017 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.061 -10000 0 -0.3 9 9
p75 CTF/Sortilin/TRAF6/NRIF 0.049 0.041 -10000 0 -0.33 4 4
RhoA-B-C/GTP 0.047 0.067 0.25 3 -0.36 8 11
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.019 0.14 -10000 0 -0.32 64 64
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.012 0.14 0.25 2 -0.33 64 66
PRKACB 0.022 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.023 0.15 -10000 0 -0.41 59 59
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.015 0.064 -10000 0 -0.56 6 6
BIRC2 0.022 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.004 0.074 0.23 3 -0.32 13 16
BAD -0.032 0.1 0.32 5 -0.4 5 10
RIPK2 0.022 0.005 -10000 0 -10000 0 0
NGFR 0.042 0.062 0.24 42 -10000 0 42
CYCS -0.021 0.057 -10000 0 -0.31 12 12
ADAM17 0.022 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.056 0.067 0.25 3 -0.34 8 11
BCL2L11 -0.032 0.1 0.34 4 -0.4 5 9
BDNF (dimer)/p75(NTR) -0.012 0.16 0.26 2 -0.42 60 62
PI3K 0.03 0.064 -10000 0 -0.33 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.054 0.077 -10000 0 -0.33 13 13
NDNL2 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.005 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.037 0.074 0.26 3 -0.42 8 11
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.054 0.077 -10000 0 -0.33 13 13
TRAF6 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
PLG -0.006 0.026 0.24 3 -10000 0 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.031 0.12 0.21 2 -0.31 70 72
SQSTM1 0.021 0.006 -10000 0 -10000 0 0
NGFRAP1 0.023 0.003 -10000 0 -10000 0 0
CASP3 -0.033 0.1 0.33 4 -0.35 9 13
E2F1 0.022 0.005 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
IKK complex 0.046 0.079 -10000 0 -0.34 7 7
NGF (dimer)/TRKA 0.02 0.074 0.26 1 -0.41 13 14
MMP7 0.021 0.091 0.24 21 -0.56 9 30
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.06 0.075 -10000 0 -0.32 13 13
MMP3 0.15 0.11 0.24 287 -0.29 4 291
APAF-1/Caspase 9 -0.036 0.049 -10000 0 -0.48 1 1
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.01 0.059 0.35 1 -0.57 4 5
PDGF/PDGFRA/CRKL 0.021 0.039 0.25 1 -0.34 3 4
positive regulation of JUN kinase activity 0.044 0.04 -10000 0 -0.31 4 4
CRKL 0.021 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.049 0.16 0.25 1 -0.4 81 82
AP1 -0.11 0.3 -10000 0 -0.94 55 55
mol:IP3 -0.014 0.037 0.3 1 -0.41 2 3
PLCG1 -0.014 0.037 0.3 1 -0.41 2 3
PDGF/PDGFRA/alphaV Integrin 0.021 0.046 0.25 1 -0.41 4 5
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
CRK 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.037 0.3 1 -0.41 2 3
CAV3 -0.091 0.2 -10000 0 -0.56 72 72
CAV1 -0.13 0.25 -10000 0 -0.56 127 127
SHC/Grb2/SOS1 0.046 0.04 -10000 0 -0.31 4 4
PDGF/PDGFRA/Shf 0.022 0.046 0.25 1 -0.4 4 5
FOS -0.11 0.29 -10000 0 -0.93 55 55
JUN -0.022 0.025 -10000 0 -10000 0 0
oligodendrocyte development 0.021 0.046 0.25 1 -0.41 4 5
GRB2 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
mol:DAG -0.014 0.037 0.3 1 -0.41 2 3
PDGF/PDGFRA 0.01 0.059 0.35 1 -0.56 4 5
actin cytoskeleton reorganization 0.02 0.045 0.25 1 -0.4 4 5
SRF -0.006 0.014 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.017 0.04 0.24 1 -0.34 3 4
PDGF/PDGFRA/Crk/C3G 0.031 0.043 0.24 1 -0.32 4 5
JAK1 -0.013 0.04 0.28 1 -0.4 4 5
ELK1/SRF -0.01 0.051 0.24 2 -0.3 3 5
SHB 0.021 0.007 -10000 0 -10000 0 0
SHF 0.023 0.003 -10000 0 -10000 0 0
CSNK2A1 0.024 0.02 -10000 0 -10000 0 0
GO:0007205 -0.012 0.04 0.3 1 -0.4 3 4
SOS1 0.022 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.044 0.04 -10000 0 -0.31 4 4
PDGF/PDGFRA/SHB 0.02 0.045 0.25 1 -0.4 4 5
PDGF/PDGFRA/Caveolin-1 -0.094 0.2 0.25 1 -0.42 130 131
ITGAV 0.023 0.003 -10000 0 -10000 0 0
ELK1 -0.017 0.042 0.23 1 -0.36 3 4
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.021 0.045 0.25 1 -0.39 4 5
JAK-STAT cascade -0.013 0.039 0.28 1 -0.4 4 5
cell proliferation 0.022 0.046 0.25 1 -0.4 4 5
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.017 0.15 -10000 0 -0.38 53 53
MAP3K8 0.017 0.029 -10000 0 -0.56 1 1
FOS -0.012 0.12 -10000 0 -0.5 13 13
PRKCA 0.015 0.04 -10000 0 -0.56 2 2
PTPN7 0.016 0.036 0.37 1 -0.56 1 2
HRAS 0.022 0.004 -10000 0 -10000 0 0
PRKCB -0.01 0.12 -10000 0 -0.56 23 23
NRAS 0.021 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.025 -10000 0 -10000 0 0
MAPK3 0.001 0.095 -10000 0 -0.6 8 8
MAP2K1 -0.015 0.12 -10000 0 -0.44 28 28
ELK1 0.016 0.02 -10000 0 -10000 0 0
BRAF -0.011 0.1 -10000 0 -0.43 23 23
mol:GTP -0.001 0.002 -10000 0 -0.005 55 55
MAPK1 0.002 0.089 -10000 0 -0.47 9 9
RAF1 -0.014 0.11 -10000 0 -0.48 23 23
KRAS 0.021 0.006 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.052 0.19 -10000 0 -0.56 62 62
GNB1/GNG2 0.018 0.093 0.26 1 -0.33 9 10
mol:DAG -0.003 0.076 0.22 2 -0.34 6 8
PLCG1 -0.003 0.078 0.22 2 -0.35 6 8
YES1 -0.003 0.07 0.25 3 -0.34 6 9
FZD3 0.021 0.007 -10000 0 -10000 0 0
FZD6 0.022 0.006 -10000 0 -10000 0 0
G protein 0.014 0.089 -10000 0 -0.35 6 6
MAP3K7 -0.026 0.094 0.19 2 -0.4 13 15
mol:Ca2+ -0.003 0.074 0.22 2 -0.33 6 8
mol:IP3 -0.003 0.076 0.22 2 -0.34 6 8
NLK 0.005 0.073 -10000 0 -0.79 4 4
GNB1 0.021 0.027 -10000 0 -0.56 1 1
CAMK2A -0.019 0.1 0.2 2 -0.42 14 16
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.01 0.074 0.28 1 -0.29 19 20
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
GNAS -0.003 0.07 0.25 3 -0.28 18 21
GO:0007205 -0.011 0.074 0.21 2 -0.36 5 7
WNT6 0.056 0.083 0.24 80 -0.29 1 81
WNT4 0.019 0.056 0.24 4 -0.56 4 8
NFAT1/CK1 alpha -0.012 0.14 0.28 1 -0.42 21 22
GNG2 0.016 0.059 -10000 0 -0.56 5 5
WNT5A 0.024 0.032 0.24 8 -0.29 1 9
WNT11 0.007 0.11 0.25 10 -0.56 17 27
CDC42 -0.004 0.066 0.23 3 -0.36 4 7
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
Jak2/Leptin Receptor -0.018 0.15 -10000 0 -0.45 35 35
PTP1B/AKT1 0.001 0.085 0.26 1 -0.32 18 19
FYN 0.022 0.026 -10000 0 -0.56 1 1
p210 bcr-abl/PTP1B -0.01 0.089 0.24 2 -0.31 24 26
EGFR 0.02 0.083 0.35 11 -0.57 6 17
EGF/EGFR 0.005 0.1 0.24 8 -0.33 26 34
CSF1 0.017 0.053 -10000 0 -0.56 4 4
AKT1 0.021 0.007 -10000 0 -10000 0 0
INSR 0.022 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.006 0.094 0.24 7 -0.32 19 26
Insulin Receptor/Insulin 0.013 0.084 -10000 0 -0.32 13 13
HCK 0.018 0.046 -10000 0 -0.56 3 3
CRK 0.022 0.005 -10000 0 -10000 0 0
TYK2 -0.011 0.086 0.26 4 -0.31 20 24
EGF 0.015 0.073 0.24 3 -0.56 7 10
YES1 0.021 0.006 -10000 0 -10000 0 0
CAV1 -0.047 0.13 0.25 5 -0.39 37 42
TXN 0.022 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.012 0.089 -10000 0 -0.34 14 14
cell migration 0.01 0.089 0.31 24 -0.24 2 26
STAT3 0.023 0.003 -10000 0 -10000 0 0
PRLR 0.018 0.1 0.29 21 -0.56 10 31
ITGA2B 0.006 0.097 -10000 0 -0.56 14 14
CSF1R 0.014 0.064 -10000 0 -0.56 6 6
Prolactin Receptor/Prolactin 0.026 0.079 0.28 9 -0.41 10 19
FGR -0.011 0.14 -10000 0 -0.56 28 28
PTP1B/p130 Cas 0.004 0.085 0.25 1 -0.32 18 19
Crk/p130 Cas 0.013 0.087 0.25 1 -0.32 13 14
DOK1 -0.01 0.1 0.37 1 -0.34 31 32
JAK2 -0.016 0.15 0.27 2 -0.44 41 43
Jak2/Leptin Receptor/Leptin 0.03 0.12 0.28 1 -0.41 12 13
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
PTPN1 -0.01 0.089 0.24 2 -0.31 24 26
LYN 0.02 0.037 -10000 0 -0.56 2 2
CDH2 0.034 0.062 0.26 28 -0.56 1 29
SRC 0.013 0.073 -10000 0 -0.62 5 5
ITGB3 0.013 0.074 -10000 0 -0.56 8 8
CAT1/PTP1B -0.018 0.14 0.26 3 -0.42 36 39
CAPN1 0.023 0.004 -10000 0 -10000 0 0
CSK 0.023 0.002 -10000 0 -10000 0 0
PI3K 0.01 0.065 -10000 0 -0.34 4 4
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.1 0.26 1 -0.38 12 13
negative regulation of transcription -0.015 0.14 0.27 2 -0.43 41 43
FCGR2A 0.011 0.078 -10000 0 -0.56 9 9
FER 0.021 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.013 0.093 -10000 0 -0.42 22 22
BLK 0.013 0.09 0.24 12 -0.56 10 22
Insulin Receptor/Insulin/Shc 0.039 0.014 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
LEPR -0.011 0.13 -10000 0 -0.55 28 28
BCAR1 0.022 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.022 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.014 0.14 0.27 1 -0.43 31 32
PRL 0.003 0.036 0.24 8 -10000 0 8
SOCS3 0.015 0.11 -10000 0 -1.2 4 4
SPRY2 0.018 0.046 -10000 0 -0.56 3 3
Insulin Receptor/Insulin/IRS1 0.04 0.012 -10000 0 -10000 0 0
CSF1/CSF1R 0.006 0.1 0.25 1 -0.36 20 21
Ras protein signal transduction 0.011 0.1 0.57 14 -10000 0 14
IRS1 0.022 0.004 -10000 0 -10000 0 0
INS 0.01 0.016 -10000 0 -10000 0 0
LEP 0.057 0.085 0.24 85 -0.29 1 86
STAT5B -0.008 0.11 0.31 1 -0.37 28 29
STAT5A -0.008 0.11 0.31 1 -0.37 28 29
GRB2 0.022 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.086 0.25 1 -0.31 20 21
CSN2 0.017 0.066 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
LAT 0.002 0.1 -10000 0 -0.51 15 15
YBX1 0.026 0.005 -10000 0 -10000 0 0
LCK 0.021 0.027 -10000 0 -0.56 1 1
SHC1 0.022 0.005 -10000 0 -10000 0 0
NOX4 0.023 0.016 0.37 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A -0.006 0.005 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.012 0.13 -10000 0 -0.4 47 47
STXBP1 0.019 0.046 -10000 0 -0.56 3 3
ACh/CHRNA1 0.014 0.052 0.18 9 -0.29 8 17
RAB3GAP2/RIMS1/UNC13B 0.002 0.12 -10000 0 -0.36 42 42
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.036 0.17 0.24 1 -0.56 46 47
mol:ACh 0 0.031 0.094 8 -0.15 10 18
RAB3GAP2 0.022 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0 0.098 -10000 0 -0.28 42 42
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.014 0.052 0.18 9 -0.29 8 17
UNC13B 0.018 0.038 -10000 0 -0.56 2 2
CHRNA1 0.02 0.066 0.24 9 -0.56 5 14
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.021 0.04 0.18 16 -0.15 3 19
SNAP25 -0.002 0.041 -10000 0 -0.3 9 9
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 0.03 0.04 0.24 16 -10000 0 16
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.018 0.03 -10000 0 -0.35 3 3
STX1A/SNAP25 fragment 1/VAMP2 0 0.098 -10000 0 -0.28 42 42
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.01 0.11 0.61 1 -0.4 21 22
IKBKB 0.027 0.082 0.34 7 -0.3 5 12
AKT1 0.049 0.11 0.25 57 -0.24 9 66
IKBKG 0.024 0.073 0.34 4 -0.29 5 9
CALM1 -0.005 0.094 0.26 1 -0.39 16 17
PIK3CA 0.012 0.011 -10000 0 -10000 0 0
MAP3K1 -0.006 0.14 0.69 1 -0.53 20 21
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.096 0.25 2 -0.4 17 19
DOK1 0.022 0.004 -10000 0 -10000 0 0
AP-1 -0.016 0.082 0.31 3 -0.25 13 16
LYN 0.02 0.037 -10000 0 -0.56 2 2
BLNK 0.021 0.027 -10000 0 -0.56 1 1
SHC1 0.022 0.005 -10000 0 -10000 0 0
BCR complex 0.022 0.085 0.34 1 -0.44 14 15
CD22 -0.039 0.16 0.26 1 -0.45 49 50
CAMK2G -0.006 0.09 0.3 2 -0.38 14 16
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
SHC/GRB2/SOS1 0.016 0.06 -10000 0 -0.5 2 2
GO:0007205 -0.005 0.099 0.25 2 -0.41 18 20
SYK 0.022 0.004 -10000 0 -10000 0 0
ELK1 -0.008 0.098 0.25 2 -0.4 17 19
NFATC1 -0.014 0.1 0.37 3 -0.48 13 16
B-cell antigen/BCR complex 0.022 0.085 0.34 1 -0.44 14 15
PAG1/CSK 0.027 0.05 -10000 0 -0.41 6 6
NFKBIB 0.023 0.047 0.2 5 -0.12 22 27
HRAS -0.006 0.092 0.32 3 -0.39 13 16
NFKBIA 0.022 0.046 0.18 6 -0.12 22 28
NF-kappa-B/RelA/I kappa B beta 0.026 0.041 0.2 5 -10000 0 5
RasGAP/Csk 0.046 0.084 0.3 1 -0.35 16 17
mol:GDP -0.008 0.1 0.25 2 -0.42 17 19
PTEN 0.02 0.007 -10000 0 -10000 0 0
CD79B 0.019 0.047 0.24 1 -0.56 3 4
NF-kappa-B/RelA/I kappa B alpha 0.026 0.041 0.2 5 -10000 0 5
GRB2 0.022 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.009 0.14 0.58 1 -0.53 20 21
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
mol:IP3 -0.005 0.094 0.28 1 -0.41 16 17
CSK 0.023 0.002 -10000 0 -10000 0 0
FOS -0.036 0.12 0.33 2 -0.41 20 22
CHUK 0.015 0.09 0.34 4 -0.29 17 21
IBTK 0.023 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.014 0.093 -10000 0 -0.39 12 12
PTPN6 -0.039 0.15 0.25 1 -0.56 26 27
RELA 0.023 0.002 -10000 0 -10000 0 0
BCL2A1 0.017 0.034 0.24 2 -0.12 3 5
VAV2 -0.013 0.12 -10000 0 -0.62 14 14
ubiquitin-dependent protein catabolic process 0.024 0.046 0.2 5 -0.12 22 27
BTK -0.089 0.33 -10000 0 -1.1 47 47
CD19 -0.018 0.12 0.26 2 -0.56 15 17
MAP4K1 0.016 0.053 -10000 0 -0.56 4 4
CD72 0.021 0.012 0.24 1 -10000 0 1
PAG1 0.015 0.064 -10000 0 -0.56 6 6
MAPK14 -0.004 0.12 0.46 2 -0.45 19 21
SH3BP5 0.015 0.059 -10000 0 -0.56 5 5
PIK3AP1 -0.004 0.11 0.3 1 -0.48 17 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.008 0.14 -10000 0 -0.57 21 21
RAF1 -0.007 0.085 0.3 3 -0.36 12 15
RasGAP/p62DOK/SHIP 0.045 0.083 -10000 0 -0.36 15 15
CD79A 0.012 0.1 0.24 13 -0.56 13 26
re-entry into mitotic cell cycle -0.016 0.081 0.3 3 -0.25 13 16
RASA1 0.021 0.006 -10000 0 -10000 0 0
MAPK3 -0.009 0.074 0.31 2 -0.34 8 10
MAPK1 -0.002 0.083 0.35 5 -0.36 5 10
CD72/SHP1 -0.008 0.15 0.29 5 -0.52 24 29
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 0.66 1 -0.45 19 20
actin cytoskeleton organization -0.009 0.11 0.29 1 -0.55 12 13
NF-kappa-B/RelA 0.053 0.078 0.34 5 -0.2 5 10
Calcineurin 0.017 0.09 -10000 0 -0.43 7 7
PI3K -0.018 0.09 -10000 0 -0.42 16 16
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.003 0.091 0.26 3 -0.42 14 17
SOS1 0.022 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.013 0.19 -10000 0 -0.68 29 29
DAPP1 -0.029 0.2 -10000 0 -0.77 28 28
cytokine secretion -0.013 0.098 0.32 4 -0.44 13 17
mol:DAG -0.005 0.094 0.28 1 -0.41 16 17
PLCG2 0.022 0.005 -10000 0 -10000 0 0
MAP2K1 -0.009 0.08 0.32 2 -0.35 10 12
B-cell antigen/BCR complex/FcgammaRIIB 0.03 0.089 0.31 1 -0.41 16 17
mol:PI-3-4-5-P3 0.003 0.084 0.23 3 -0.34 9 12
ETS1 -0.013 0.096 0.29 2 -0.39 16 18
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.048 0.082 0.31 1 -0.35 15 16
B-cell antigen/BCR complex/LYN -0.01 0.12 0.28 2 -0.53 19 21
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.004 -10000 0 -10000 0 0
RAC1 -0.012 0.12 -10000 0 -0.6 12 12
B-cell antigen/BCR complex/LYN/SYK 0.012 0.16 0.34 2 -0.53 25 27
CARD11 -0.006 0.1 0.3 3 -0.42 16 19
FCGR2B 0.015 0.064 -10000 0 -0.56 6 6
PPP3CA 0.022 0.005 -10000 0 -10000 0 0
BCL10 0.022 0.004 -10000 0 -10000 0 0
IKK complex 0.028 0.054 0.16 27 -0.13 3 30
PTPRC -0.014 0.14 -10000 0 -0.56 30 30
PDPK1 0.028 0.098 0.23 43 -0.24 7 50
PPP3CB 0.022 0.005 -10000 0 -10000 0 0
PPP3CC 0.021 0.007 -10000 0 -10000 0 0
POU2F2 0.02 0.031 0.24 3 -10000 0 3
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
CDC42/GTP -0.008 0.097 -10000 0 -0.28 36 36
PLCG1 -0.014 0.085 -10000 0 -0.3 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
G12/G13 0.032 0.008 -10000 0 -10000 0 0
cell migration -0.008 0.095 -10000 0 -0.28 36 36
S1PR5 0.024 0.037 0.24 7 -0.56 1 8
S1PR4 -0.023 0.16 -10000 0 -0.56 38 38
MAPK3 -0.013 0.084 -10000 0 -0.29 30 30
MAPK1 -0.012 0.08 -10000 0 -0.3 27 27
S1P/S1P5/Gi 0.017 0.036 -10000 0 -0.23 5 5
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
CDC42/GDP 0.016 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.024 -10000 0 -0.35 1 1
RHOA -0.029 0.086 0.36 1 -0.3 37 38
S1P/S1P4/Gi -0.007 0.09 -10000 0 -0.29 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
S1P/S1P4/G12/G13 0.012 0.098 -10000 0 -0.32 37 37
GNA12 0.022 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.007 0.061 -10000 0 -0.32 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.069 0.32 2 -0.33 1 3
alphaV/beta3 Integrin/Osteopontin/Src 0.11 0.083 0.2 17 -0.19 6 23
AP1 0.005 0.12 -10000 0 -0.57 2 2
ILK -0.016 0.059 -10000 0 -0.34 8 8
bone resorption -0.015 0.058 -10000 0 -0.31 4 4
PTK2B 0.021 0.007 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.094 0.29 2 -0.31 8 10
ITGAV 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.031 0.022 -10000 0 -0.41 1 1
alphaV/beta3 Integrin/Osteopontin 0.11 0.098 0.26 1 -0.37 8 9
MAP3K1 -0.015 0.059 -10000 0 -0.34 8 8
JUN 0.022 0.005 -10000 0 -10000 0 0
MAPK3 -0.017 0.056 0.38 1 -0.32 8 9
MAPK1 -0.017 0.056 0.38 1 -0.32 8 9
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.024 0.053 -10000 0 -0.33 8 8
ITGB3 0.015 0.074 -10000 0 -0.56 8 8
NFKBIA -0.01 0.051 0.35 1 -0.32 7 8
FOS -0.042 0.18 -10000 0 -0.56 54 54
CD44 0.021 0.027 -10000 0 -0.56 1 1
CHUK 0.022 0.005 -10000 0 -10000 0 0
PLAU 0.002 0.068 0.43 1 -10000 0 1
NF kappa B1 p50/RelA 0.01 0.076 -10000 0 -10000 0 0
BCAR1 0.022 0.006 -10000 0 -10000 0 0
RELA 0.023 0.002 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.03 0.058 -10000 0 -0.41 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.017 0.058 -10000 0 -0.34 8 8
VAV3 -0.026 0.058 0.38 1 -0.35 8 9
MAP3K14 -0.013 0.059 -10000 0 -0.34 8 8
ROCK2 0.022 0.004 -10000 0 -10000 0 0
SPP1 0.13 0.12 0.24 247 -0.28 6 253
RAC1 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.016 0.059 0.33 1 -0.33 8 9
MMP2 -0.047 0.1 -10000 0 -0.63 4 4
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.021 0.034 -10000 0 -10000 0 0
BIRC5 0.21 0.084 0.24 411 -0.29 1 412
NFKBIA -0.024 0.026 0.24 1 -10000 0 1
CPEB1 -0.017 0.14 -10000 0 -0.56 32 32
AKT1 -0.024 0.023 -10000 0 -10000 0 0
NDEL1 0.022 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.019 0.03 -10000 0 -10000 0 0
NDEL1/TACC3 -0.009 0.041 -10000 0 -10000 0 0
GADD45A 0.022 0.004 -10000 0 -10000 0 0
GSK3B -0.02 0.02 -10000 0 -10000 0 0
PAK1/Aurora A -0.02 0.036 0.31 1 -10000 0 1
MDM2 0.023 0.017 0.37 1 -10000 0 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.019 0.094 0.3 36 -10000 0 36
TP53 -0.01 0.044 0.21 1 -0.24 1 2
DLG7 -0.021 0.022 -10000 0 -10000 0 0
AURKAIP1 0.022 0.005 -10000 0 -10000 0 0
ARHGEF7 0.021 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.01 0.044 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.019 0.03 -10000 0 -10000 0 0
AURKA -0.025 0.031 -10000 0 -10000 0 0
AURKB 0.079 0.06 0.14 53 -0.17 4 57
CDC25B -0.012 0.023 -10000 0 -0.3 1 1
G2/M transition checkpoint -0.02 0.023 -10000 0 -10000 0 0
mRNA polyadenylation -0.039 0.082 -10000 0 -0.33 31 31
Aurora A/CPEB -0.04 0.082 -10000 0 -0.33 31 31
Aurora A/TACC1/TRAP/chTOG -0.005 0.046 -10000 0 -10000 0 0
BRCA1 0.023 0.003 -10000 0 -10000 0 0
centrosome duplication -0.02 0.036 0.31 1 -10000 0 1
regulation of centrosome cycle -0.009 0.041 -10000 0 -10000 0 0
spindle assembly -0.005 0.045 -10000 0 -10000 0 0
TDRD7 0.022 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.081 0.27 6 -10000 0 6
CENPA 0.1 0.052 0.17 72 -10000 0 72
Aurora A/PP2A -0.022 0.033 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.012 0.032 0.24 1 -10000 0 1
negative regulation of DNA binding -0.01 0.045 0.21 1 -0.24 1 2
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.01 -10000 0 -10000 0 0
RASA1 0.021 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A -0.021 0.023 -10000 0 -10000 0 0
mitotic prometaphase -0.02 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.031 -10000 0 -10000 0 0
TACC1 0.018 0.028 -10000 0 -0.56 1 1
TACC3 0.021 0.022 0.37 1 -0.29 1 2
Aurora A/Antizyme1 -0.011 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP -0.018 0.03 -10000 0 -10000 0 0
OAZ1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.022 0.019 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.042 0.017 0.25 1 -10000 0 1
Importin alpha/Importin beta/TPX2 -0.019 0.094 0.3 36 -10000 0 36
PPP2R5D 0.022 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.02 0.081 0.29 6 -10000 0 6
PAK1 0.023 0.016 0.37 1 -10000 0 1
CKAP5 0.022 0.004 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.02 0.027 -10000 0 -0.56 1 1
EPHB2 0.026 0.028 0.24 8 -10000 0 8
EFNB1 -0.004 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.063 0.053 0.28 1 -10000 0 1
Ephrin B2/EPHB1-2 0.052 0.056 0.24 16 -0.33 1 17
neuron projection morphogenesis 0.045 0.039 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.06 0.056 0.3 1 -10000 0 1
DNM1 0.024 0.014 0.24 2 -10000 0 2
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.021 0.1 0.24 1 -0.43 27 28
YES1 -0.025 0.16 -10000 0 -0.66 28 28
Ephrin B1/EPHB1-2/NCK2 0.06 0.056 0.3 1 -10000 0 1
PI3K -0.002 0.094 -10000 0 -0.43 17 17
mol:GDP 0.058 0.055 0.29 1 -10000 0 1
ITGA2B 0.006 0.097 -10000 0 -0.56 14 14
endothelial cell proliferation 0.027 0.02 -10000 0 -0.35 1 1
FYN -0.025 0.16 -10000 0 -0.66 28 28
MAP3K7 -0.022 0.11 0.23 1 -0.46 28 29
FGR -0.031 0.16 -10000 0 -0.68 27 27
TIAM1 0.021 0.027 -10000 0 -0.56 1 1
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
RGS3 0.022 0.004 -10000 0 -10000 0 0
cell adhesion -0.017 0.099 -10000 0 -0.37 27 27
LYN -0.025 0.16 -10000 0 -0.66 28 28
Ephrin B1/EPHB1-2/Src Family Kinases -0.025 0.14 -10000 0 -0.59 28 28
Ephrin B1/EPHB1-2 -0.022 0.12 -10000 0 -0.5 26 26
SRC -0.022 0.16 -10000 0 -0.65 28 28
ITGB3 0.013 0.074 -10000 0 -0.56 8 8
EPHB1 0.052 0.088 0.28 60 -10000 0 60
EPHB4 0.022 0.006 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.02 -10000 0 -0.35 1 1
alphaIIb/beta3 Integrin 0.013 0.093 -10000 0 -0.41 22 22
BLK -0.027 0.16 -10000 0 -0.67 27 27
HCK -0.024 0.16 -10000 0 -0.65 28 28
regulation of stress fiber formation -0.058 0.055 -10000 0 -0.29 1 1
MAPK8 -0.021 0.099 -10000 0 -0.41 26 26
Ephrin B1/EPHB1-2/RGS3 0.06 0.056 0.3 1 -10000 0 1
endothelial cell migration -0.011 0.1 0.39 1 -0.37 26 27
NCK2 0.023 0.003 -10000 0 -10000 0 0
PTPN13 0.016 0.062 -10000 0 -0.66 4 4
regulation of focal adhesion formation -0.058 0.055 -10000 0 -0.29 1 1
chemotaxis -0.058 0.055 -10000 0 -0.29 1 1
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.055 0.047 0.25 1 -10000 0 1
angiogenesis -0.022 0.12 -10000 0 -0.5 27 27
LCK -0.022 0.16 -10000 0 -0.66 27 27
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.022 0.004 -10000 0 -10000 0 0
EGFR 0.022 0.083 0.36 11 -0.56 6 17
EGF/EGFR 0.005 0.12 -10000 0 -0.33 47 47
EGF/EGFR dimer/SHC/GRB2/SOS1 0.049 0.072 -10000 0 -0.33 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.018 0.046 -10000 0 -0.56 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.015 0.071 0.24 3 -0.56 7 10
EGF/EGFR dimer/SHC 0.033 0.074 0.25 7 -0.38 12 19
mol:GDP 0.044 0.07 -10000 0 -0.33 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.025 0.16 -10000 0 -0.56 40 40
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.029 0.06 -10000 0 -0.31 12 12
SHC1 0.022 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.042 0.066 -10000 0 -0.32 12 12
FRAP1 -0.018 0.053 0.16 7 -0.32 12 19
EGF/EGFR dimer 0.024 0.082 0.26 8 -0.44 12 20
SOS1 0.022 0.004 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.009 0.13 -10000 0 -0.41 43 43
Regulation of nuclear SMAD2/3 signaling

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.023 0.006 -10000 0 -10000 0 0
HSPA8 0.022 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.016 0.098 -10000 0 -0.4 20 20
AKT1 0.014 0.03 -10000 0 -10000 0 0
GSC 0.019 0.074 -10000 0 -0.47 2 2
NKX2-5 0.11 0.14 0.24 225 -0.28 23 248
muscle cell differentiation -0.029 0.099 0.45 8 -10000 0 8
SMAD2-3/SMAD4/SP1 0.054 0.071 -10000 0 -10000 0 0
SMAD4 0.017 0.038 -10000 0 -10000 0 0
CBFB 0.022 0.005 -10000 0 -10000 0 0
SAP18 0.022 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.043 0.024 -10000 0 -0.36 1 1
SMAD3/SMAD4/VDR 0.053 0.051 -10000 0 -0.31 1 1
MYC 0.022 0.013 -10000 0 -10000 0 0
CDKN2B -0.2 0.47 -10000 0 -1.5 46 46
AP1 0 0.1 -10000 0 -0.29 51 51
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.034 0.068 -10000 0 -0.37 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.011 0.1 -10000 0 -0.34 37 37
SP3 0.024 0.003 -10000 0 -10000 0 0
CREB1 0.023 0.003 -10000 0 -10000 0 0
FOXH1 0.046 0.073 0.27 42 -10000 0 42
SMAD3/SMAD4/GR 0.034 0.047 -10000 0 -10000 0 0
GATA3 0.008 0.096 0.24 2 -0.51 15 17
SKI/SIN3/HDAC complex/NCoR1 -0.001 0.086 -10000 0 -0.41 14 14
MEF2C/TIF2 -0.008 0.094 0.28 2 -0.6 6 8
endothelial cell migration -0.02 0.037 0.49 1 -10000 0 1
MAX 0.021 0.004 -10000 0 -10000 0 0
RBBP7 0.022 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
RUNX2 0.023 0.003 -10000 0 -10000 0 0
RUNX3 0.022 0.004 -10000 0 -10000 0 0
RUNX1 0.022 0.004 -10000 0 -10000 0 0
CTBP1 0.021 0.007 -10000 0 -10000 0 0
NR3C1 0.021 0.006 -10000 0 -10000 0 0
VDR 0.022 0.026 -10000 0 -0.56 1 1
CDKN1A 0.014 0.052 -10000 0 -0.5 1 1
KAT2B 0.021 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.056 0.065 0.27 5 -0.25 1 6
DCP1A 0.021 0.007 -10000 0 -10000 0 0
SKI 0.022 0.005 -10000 0 -10000 0 0
SERPINE1 0.02 0.037 -10000 0 -0.49 1 1
SMAD3/SMAD4/ATF2 0.036 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.036 0.051 -10000 0 -0.41 1 1
SAP30 0.021 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.04 0.019 -10000 0 -10000 0 0
JUN -0.009 0.1 -10000 0 -0.28 49 49
SMAD3/SMAD4/IRF7 0.038 0.049 -10000 0 -10000 0 0
TFE3 0.026 0.004 -10000 0 -10000 0 0
COL1A2 0.026 0.031 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.036 0.048 -10000 0 -10000 0 0
DLX1 0.14 0.11 0.24 280 -0.29 1 281
TCF3 0.022 0.004 -10000 0 -10000 0 0
FOS -0.04 0.18 -10000 0 -0.56 54 54
SMAD3/SMAD4/Max 0.034 0.048 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.043 0.014 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.014 0.034 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.036 0.047 -10000 0 -10000 0 0
IRF7 0.023 0.004 -10000 0 -10000 0 0
ESR1 -0.004 0.12 -10000 0 -0.56 21 21
HNF4A 0.021 0.034 0.25 8 -10000 0 8
MEF2C -0.008 0.094 0.37 3 -0.59 6 9
SMAD2-3/SMAD4 0.036 0.061 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.043 0.015 -10000 0 -10000 0 0
IGHV3OR16-13 0.006 0.033 -10000 0 -0.35 4 4
TGIF2/HDAC complex 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.006 -10000 0 -10000 0 0
SKIL 0.013 0.011 -10000 0 -10000 0 0
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.002 -10000 0 -10000 0 0
SNIP1 0.023 0.016 0.37 1 -10000 0 1
GCN5L2 0 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.042 0.049 -10000 0 -10000 0 0
MSG1/HSC70 0.032 0.022 -10000 0 -0.41 1 1
SMAD2 0.017 0.03 -10000 0 -10000 0 0
SMAD3 0.016 0.036 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.037 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.003 0.066 0.23 2 -0.41 7 9
NCOR1 0.022 0.005 -10000 0 -10000 0 0
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA1 0.023 0.003 -10000 0 -10000 0 0
MYOD/E2A 0.049 0.056 0.26 1 -0.19 3 4
SMAD2-3/SMAD4/SP1/MIZ-1 0.062 0.075 -10000 0 -10000 0 0
IFNB1 0.009 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.024 0.1 -10000 0 -0.58 6 6
CITED1 0.021 0.029 0.24 1 -0.56 1 2
SMAD2-3/SMAD4/ARC105 0.043 0.06 -10000 0 -10000 0 0
RBL1 0.022 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.026 0.16 -10000 0 -0.52 41 41
RUNX1-3/PEBPB2 0.043 0.014 -10000 0 -10000 0 0
SMAD7 0.004 0.11 -10000 0 -0.92 1 1
MYC/MIZ-1 0.032 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 0.013 0.04 -10000 0 -10000 0 0
IL10 0.001 0.076 -10000 0 -0.38 14 14
PIASy/HDAC complex 0.02 0.011 -10000 0 -10000 0 0
PIAS3 0.021 0.007 -10000 0 -10000 0 0
CDK2 0.023 0.003 -10000 0 -10000 0 0
IL5 0 0.07 -10000 0 -0.34 15 15
CDK4 0.024 0.016 0.37 1 -10000 0 1
PIAS4 0.02 0.011 -10000 0 -10000 0 0
ATF3 0.021 0.027 -10000 0 -0.56 1 1
SMAD3/SMAD4/SP1 0.043 0.054 -10000 0 -10000 0 0
FOXG1 0.027 0.078 0.24 51 -0.29 1 52
FOXO3 0.002 0.031 -10000 0 -10000 0 0
FOXO1 0.003 0.029 -10000 0 -10000 0 0
FOXO4 0.002 0.031 -10000 0 -10000 0 0
heart looping -0.008 0.094 0.36 3 -0.58 6 9
CEBPB 0.017 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.11 0.093 0.27 6 -10000 0 6
MYOD1 0.032 0.088 0.24 68 -0.29 3 71
SMAD3/SMAD4/HNF4 0.038 0.053 0.27 1 -10000 0 1
SMAD3/SMAD4/GATA3 0.027 0.088 -10000 0 -0.37 16 16
SnoN/SIN3/HDAC complex/NCoR1 0.013 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.051 0.054 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.055 0.056 -10000 0 -10000 0 0
MED15 0.021 0.006 -10000 0 -10000 0 0
SP1 0.023 0.015 -10000 0 -10000 0 0
SIN3B 0.022 0.004 -10000 0 -10000 0 0
SIN3A 0.023 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.11 0.12 0.34 16 -0.36 5 21
ITGB5 0.014 0.039 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.005 0.073 -10000 0 -0.34 16 16
SMAD3/SMAD4/AR -0.047 0.17 -10000 0 -0.38 98 98
AR -0.097 0.23 -10000 0 -0.56 99 99
negative regulation of cell growth 0.013 0.047 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.052 0.072 0.27 1 -10000 0 1
E2F5 0.022 0.005 -10000 0 -10000 0 0
E2F4 0.022 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.066 0.062 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.011 0.11 -10000 0 -0.37 39 39
TFDP1 0.023 0.028 0.37 3 -10000 0 3
SMAD3/SMAD4/AP1 0.014 0.11 -10000 0 -0.29 49 49
SMAD3/SMAD4/RUNX2 0.036 0.048 -10000 0 -10000 0 0
TGIF2 0.022 0.005 -10000 0 -10000 0 0
TGIF1 0.022 0.005 -10000 0 -10000 0 0
ATF2 0.023 0.003 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.022 0.004 -10000 0 -10000 0 0
SPHK1 0.022 0.004 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
mol:S1P 0.011 0.003 -10000 0 -10000 0 0
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
mol:Sphinganine-1-P -0.01 0.002 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.043 0.034 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
G12/G13 0.032 0.008 -10000 0 -10000 0 0
S1PR3 0.022 0.004 -10000 0 -10000 0 0
S1PR2 0.022 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.003 0.026 -10000 0 -0.2 4 4
S1PR5 0.024 0.037 0.24 7 -0.56 1 8
S1PR4 -0.023 0.16 -10000 0 -0.56 38 38
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
S1P/S1P5/G12 0.033 0.039 -10000 0 -0.31 1 1
S1P/S1P3/Gq -0.051 0.14 -10000 0 -0.28 115 115
S1P/S1P4/Gi -0.004 0.093 0.26 1 -0.31 31 32
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
GNA14 -0.11 0.24 -10000 0 -0.56 111 111
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA12 0.022 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
ABCC1 0.023 0.01 0.24 1 -10000 0 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.024 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.047 0.24 1 -0.36 6 7
forebrain development -0.1 0.16 -10000 0 -0.56 20 20
GNAO1 0.015 0.033 0.24 2 -0.57 1 3
SMO/beta Arrestin2 0.007 0.03 0.23 1 -10000 0 1
SMO 0.004 0.032 0.37 2 -10000 0 2
ARRB2 0.005 0.019 -10000 0 -10000 0 0
GLI3/SPOP 0.024 0.094 -10000 0 -0.4 10 10
mol:GTP -0.003 0.004 -10000 0 -10000 0 0
GSK3B 0.02 0.007 -10000 0 -10000 0 0
GNAI2 0.014 0.014 -10000 0 -10000 0 0
SIN3/HDAC complex 0.055 0.022 -10000 0 -10000 0 0
GNAI1 0.015 0.029 -10000 0 -0.56 1 1
XPO1 0 0.024 -10000 0 -10000 0 0
GLI1/Su(fu) -0.1 0.16 -10000 0 -0.58 19 19
SAP30 0.022 0.007 -10000 0 -10000 0 0
mol:GDP 0.004 0.032 0.37 2 -10000 0 2
MIM/GLI2A -0.041 0.069 -10000 0 -10000 0 0
IFT88 0.022 0.006 -10000 0 -10000 0 0
GNAI3 0.016 0.013 -10000 0 -10000 0 0
GLI2 0.016 0.076 0.31 2 -0.34 9 11
GLI3 0.013 0.098 0.41 1 -0.36 18 19
CSNK1D 0.022 0.004 -10000 0 -10000 0 0
CSNK1E 0.022 0.004 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.021 0.006 -10000 0 -10000 0 0
GNG2 0.016 0.059 -10000 0 -0.56 5 5
Gi family/GTP -0.01 0.051 -10000 0 -0.27 7 7
SIN3B 0.023 0.005 -10000 0 -10000 0 0
SIN3A 0.024 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.011 0.11 -10000 0 -0.43 20 20
GLI2/Su(fu) 0.01 0.088 -10000 0 -0.4 12 12
FOXA2 -0.52 0.56 -10000 0 -1.1 244 244
neural tube patterning -0.1 0.16 -10000 0 -0.56 20 20
SPOP 0.023 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.008 0.046 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
CSNK1G2 0.022 0.004 -10000 0 -10000 0 0
CSNK1G3 0.021 0.006 -10000 0 -10000 0 0
MTSS1 -0.041 0.069 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.1 0.16 -10000 0 -0.56 20 20
SUFU 0.004 0.016 -10000 0 -10000 0 0
LGALS3 0.022 0.004 -10000 0 -10000 0 0
catabolic process 0.026 0.12 -10000 0 -0.46 18 18
GLI3A/CBP 0.005 0.03 -10000 0 -0.36 1 1
KIF3A 0.021 0.006 -10000 0 -10000 0 0
GLI1 -0.1 0.16 -10000 0 -0.57 20 20
RAB23 0.022 0.004 -10000 0 -10000 0 0
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
IFT172 0.023 0.003 -10000 0 -10000 0 0
RBBP7 0.023 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.01 0.041 -10000 0 -10000 0 0
GNAZ 0.01 0.059 -10000 0 -0.56 5 5
RBBP4 0.023 0.004 -10000 0 -10000 0 0
CSNK1G1 0.023 0.002 -10000 0 -10000 0 0
PIAS1 0.023 0.002 -10000 0 -10000 0 0
PRKACA 0.022 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.023 0.079 0.23 1 -0.34 11 12
STK36 -0.001 0.025 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.011 0.067 -10000 0 -0.33 14 14
PTCH1 -0.1 0.17 -10000 0 -0.73 15 15
MIM/GLI1 -0.22 0.28 -10000 0 -0.5 227 227
CREBBP 0.005 0.03 -10000 0 -0.36 1 1
Su(fu)/SIN3/HDAC complex 0.007 0.089 -10000 0 -0.4 16 16
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.022 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.005 0.017 -10000 0 -10000 0 0
FRAP1 0.049 0.058 0.26 2 -0.37 2 4
AKT1 0.054 0.08 0.19 17 -10000 0 17
INSR 0.022 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0.081 0.076 0.26 20 -10000 0 20
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.013 -10000 0 -10000 0 0
TSC2 0.022 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.008 0.017 -10000 0 -10000 0 0
TSC1 0.023 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.019 0.032 -10000 0 -0.18 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.015 0.024 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.004 -10000 0 -10000 0 0
RPS6KB1 0.076 0.078 0.23 39 -0.31 1 40
MAP3K5 0 0.025 0.19 2 -0.18 7 9
PIK3R1 0.022 0.007 -10000 0 -10000 0 0
apoptosis 0 0.025 0.19 2 -0.18 7 9
mol:LY294002 0 0 -10000 0 -0.001 12 12
EIF4B 0.071 0.075 0.23 40 -0.27 1 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.074 0.066 0.23 20 -10000 0 20
eIF4E/eIF4G1/eIF4A1 0.008 0.017 -10000 0 -0.27 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.016 0.027 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.056 0.071 0.2 48 -10000 0 48
FKBP1A 0.023 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.063 0.059 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 12 12
FKBP12/Rapamycin 0.019 0.006 -10000 0 -10000 0 0
PDPK1 -0.002 0.033 0.17 14 -10000 0 14
EIF4E 0.022 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.052 0.084 -10000 0 -0.52 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.006 0.064 -10000 0 -0.87 1 1
TSC1/TSC2 0.092 0.085 0.29 24 -10000 0 24
tumor necrosis factor receptor activity 0 0 0.001 12 -10000 0 12
RPS6 0.021 0.007 -10000 0 -10000 0 0
PPP5C 0.022 0.004 -10000 0 -10000 0 0
EIF4G1 0.013 0.011 -10000 0 -10000 0 0
IRS1 0.005 0.032 -10000 0 -0.19 12 12
INS -0.018 0.003 -10000 0 -10000 0 0
PTEN 0.02 0.007 -10000 0 -10000 0 0
PDK2 -0.002 0.031 0.16 13 -10000 0 13
EIF4EBP1 0.01 0.17 -10000 0 -1 11 11
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PPP2R5D 0.048 0.06 0.24 9 -0.34 2 11
peptide biosynthetic process -0.013 0.015 0.17 3 -10000 0 3
RHEB 0.023 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.002 0.003 223 -10000 0 223
EEF2 -0.013 0.015 0.18 3 -10000 0 3
eIF4E/4E-BP1 0.015 0.15 -10000 0 -0.93 11 11
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.018 0.006 -10000 0 -10000 0 0
epithelial cell differentiation 0.044 0.016 -10000 0 -10000 0 0
CYFIP2 0.009 0.082 -10000 0 -0.56 10 10
ENAH 0.006 0.068 0.26 12 -10000 0 12
EGFR 0.022 0.083 0.36 11 -0.56 6 17
EPHA2 0.018 0.046 -10000 0 -0.56 3 3
MYO6 -0.009 0.028 0.34 1 -10000 0 1
CTNNB1 0.021 0.006 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.033 0.056 -10000 0 -0.36 8 8
AQP5 -0.14 0.22 -10000 0 -0.48 143 143
CTNND1 0.023 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.026 0.34 1 -10000 0 1
regulation of calcium-dependent cell-cell adhesion -0.085 0.13 0.34 1 -0.29 127 128
EGF 0.015 0.071 0.24 3 -0.56 7 10
NCKAP1 0.022 0.004 -10000 0 -10000 0 0
AQP3 -0.061 0.17 -10000 0 -0.47 66 66
cortical microtubule organization 0.044 0.016 -10000 0 -10000 0 0
GO:0000145 -0.01 0.024 0.33 1 -10000 0 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.049 0.017 -10000 0 -10000 0 0
MLLT4 0.022 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.023 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.039 -10000 0 -0.33 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.002 0.009 -10000 0 -10000 0 0
PVRL2 0.022 0.005 -10000 0 -10000 0 0
ZYX -0.01 0.022 -10000 0 -10000 0 0
ARF6/GTP 0.046 0.04 -10000 0 -0.31 3 3
CDH1 0.022 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.031 0.061 -10000 0 -0.32 12 12
RhoA/GDP 0.045 0.017 -10000 0 -10000 0 0
actin cytoskeleton organization -0.012 0.019 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
IGF1R 0.022 0.004 -10000 0 -10000 0 0
IGF1 0.004 0.1 0.24 1 -0.56 16 17
DIAPH1 -0.013 0.16 -10000 0 -0.59 16 16
Wnt receptor signaling pathway -0.044 0.016 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.023 -10000 0 -10000 0 0
CTNNA1 0.021 0.006 -10000 0 -10000 0 0
VCL -0.012 0.019 -10000 0 -10000 0 0
EFNA1 0.022 0.005 -10000 0 -10000 0 0
LPP -0.008 0.021 0.34 1 -10000 0 1
Ephrin A1/EPHA2 0.036 0.031 -10000 0 -0.29 3 3
SEC6/SEC8 -0.016 0.011 -10000 0 -10000 0 0
MGAT3 -0.086 0.13 0.34 1 -0.3 127 128
HGF/MET -0.024 0.13 -10000 0 -0.29 83 83
HGF -0.09 0.23 -10000 0 -0.56 94 94
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.018 0.006 -10000 0 -10000 0 0
actin cable formation 0.047 0.1 0.33 27 -10000 0 27
KIAA1543 -0.01 0.023 0.34 1 -10000 0 1
KIFC3 -0.011 0.026 0.34 1 -10000 0 1
NCK1 0.019 0.008 -10000 0 -10000 0 0
EXOC3 0.018 0.009 -10000 0 -10000 0 0
ACTN1 -0.01 0.027 0.34 1 -10000 0 1
NCK1/GIT1 0.028 0.013 -10000 0 -10000 0 0
mol:GDP 0.044 0.016 -10000 0 -10000 0 0
EXOC4 0.022 0.004 -10000 0 -10000 0 0
STX4 -0.01 0.027 0.34 1 -10000 0 1
PIP5K1C -0.01 0.026 0.34 1 -10000 0 1
LIMA1 0.023 0.002 -10000 0 -10000 0 0
ABI1 0.022 0.004 -10000 0 -10000 0 0
ROCK1 0.015 0.086 0.31 18 -10000 0 18
adherens junction assembly -0.014 0.093 0.31 3 -0.71 6 9
IGF-1R heterotetramer/IGF1 0.029 0.058 -10000 0 -0.29 13 13
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.008 -10000 0 -10000 0 0
MET 0.02 0.041 0.37 1 -0.56 2 3
PLEKHA7 -0.01 0.025 0.34 1 -10000 0 1
mol:GTP 0.042 0.038 -10000 0 -0.32 3 3
establishment of epithelial cell apical/basal polarity 0.025 0.089 0.38 9 -10000 0 9
cortical actin cytoskeleton stabilization 0.018 0.006 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.012 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.018 0.006 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.017 0.12 -10000 0 -0.7 12 12
oxygen homeostasis 0.002 0.009 -10000 0 -10000 0 0
TCEB2 0.022 0.004 -10000 0 -10000 0 0
TCEB1 0.022 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.011 0.13 0.28 5 -0.34 19 24
EPO 0.032 0.16 0.36 2 -0.5 2 4
FIH (dimer) 0.019 0.019 -10000 0 -10000 0 0
APEX1 0.023 0.024 -10000 0 -10000 0 0
SERPINE1 0.019 0.17 0.4 2 -0.52 5 7
FLT1 -0.034 0.22 -10000 0 -0.79 31 31
ADORA2A 0.007 0.16 0.38 3 -0.49 7 10
germ cell development 0.022 0.17 0.39 2 -0.5 8 10
SLC11A2 0.021 0.17 0.4 2 -0.51 6 8
BHLHE40 0.019 0.17 0.42 1 -0.5 6 7
HIF1AN 0.019 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.026 0.14 0.31 5 -0.4 11 16
ETS1 0.01 0.091 -10000 0 -0.56 11 11
CITED2 0.006 0.17 -10000 0 -1 11 11
KDR -0.068 0.32 -10000 0 -1 46 46
PGK1 0.021 0.17 0.4 2 -0.5 7 9
SIRT1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.074 0.22 0.46 2 -0.55 9 11
EPAS1 -0.017 0.12 0.26 7 -0.34 28 35
SP1 0.026 0.003 -10000 0 -10000 0 0
ABCG2 -0.018 0.25 0.42 1 -0.63 53 54
EFNA1 0.018 0.16 -10000 0 -0.51 6 6
FXN 0.008 0.16 0.45 5 -0.49 7 12
POU5F1 0.021 0.17 0.4 2 -0.52 8 10
neuron apoptosis -0.072 0.22 0.54 9 -0.46 2 11
EP300 0.022 0.004 -10000 0 -10000 0 0
EGLN3 0.053 0.081 0.24 72 -10000 0 72
EGLN2 0.018 0.02 -10000 0 -10000 0 0
EGLN1 0.02 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.041 0.016 -10000 0 -10000 0 0
VHL 0.021 0.006 -10000 0 -10000 0 0
ARNT 0.023 0.023 -10000 0 -10000 0 0
SLC2A1 0.022 0.18 0.41 9 -0.49 7 16
TWIST1 0.017 0.17 0.39 7 -0.5 6 13
ELK1 0.024 0.014 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.028 0.15 0.33 1 -0.4 10 11
VEGFA 0.021 0.17 0.4 2 -0.51 5 7
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.013 0.14 -10000 0 -0.57 20 20
Syndecan-4/Syndesmos 0.02 0.094 -10000 0 -0.66 5 5
positive regulation of JNK cascade 0.008 0.12 -10000 0 -0.57 9 9
Syndecan-4/ADAM12 0.049 0.12 -10000 0 -0.68 5 5
CCL5 0.012 0.078 -10000 0 -0.56 9 9
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
DNM2 0.022 0.004 -10000 0 -10000 0 0
ITGA5 0.023 0.003 -10000 0 -10000 0 0
SDCBP 0.022 0.005 -10000 0 -10000 0 0
PLG 0.012 0.026 0.22 3 -10000 0 3
ADAM12 0.078 0.098 0.24 130 -0.29 2 132
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.053 0.12 0.35 1 -0.67 5 6
Syndecan-4/CXCL12/CXCR4 0.008 0.12 -10000 0 -0.61 9 9
Syndecan-4/Laminin alpha3 0.011 0.096 -10000 0 -0.6 5 5
MDK 0.028 0.037 0.28 10 -10000 0 10
Syndecan-4/FZD7 0.02 0.093 -10000 0 -0.63 5 5
Syndecan-4/Midkine 0.021 0.097 0.41 1 -0.62 5 6
FZD7 0.023 0.016 0.37 1 -10000 0 1
Syndecan-4/FGFR1/FGF 0.015 0.095 -10000 0 -0.59 5 5
THBS1 0.014 0.069 -10000 0 -0.56 7 7
integrin-mediated signaling pathway 0.02 0.094 -10000 0 -0.63 5 5
positive regulation of MAPKKK cascade 0.008 0.12 -10000 0 -0.57 9 9
Syndecan-4/TACI 0.021 0.098 -10000 0 -0.65 5 5
CXCR4 0.023 0.003 -10000 0 -10000 0 0
cell adhesion 0.005 0.054 0.19 5 -0.31 11 16
Syndecan-4/Dynamin 0.019 0.094 -10000 0 -0.66 5 5
Syndecan-4/TSP1 0.016 0.11 -10000 0 -0.65 8 8
Syndecan-4/GIPC 0.02 0.092 -10000 0 -0.72 4 4
Syndecan-4/RANTES 0.014 0.1 -10000 0 -0.61 7 7
ITGB1 0.022 0.004 -10000 0 -10000 0 0
LAMA1 0.086 0.1 0.24 140 -0.29 1 141
LAMA3 0.008 0.086 -10000 0 -0.56 11 11
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA 0.004 0.11 0.76 9 -0.49 1 10
Syndecan-4/alpha-Actinin 0.021 0.093 -10000 0 -0.66 5 5
TFPI -0.023 0.16 -10000 0 -0.56 38 38
F2 0.026 0.038 0.24 14 -10000 0 14
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.016 0.1 0.38 1 -0.59 5 6
ACTN1 0.022 0.005 -10000 0 -10000 0 0
TNC 0.025 0.038 0.24 8 -0.56 1 9
Syndecan-4/CXCL12 -0.001 0.13 -10000 0 -0.62 10 10
FGF6 -0.017 0.006 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
CXCL12 -0.021 0.15 -10000 0 -0.56 36 36
TNFRSF13B 0.019 0.06 0.24 8 -0.56 4 12
FGF2 0.006 0.094 -10000 0 -0.56 13 13
FGFR1 0.017 0.028 -10000 0 -0.56 1 1
Syndecan-4/PI-4-5-P2 0.003 0.088 -10000 0 -0.66 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.008 0.081 -10000 0 -0.54 10 10
cell migration -0.017 0.01 -10000 0 -10000 0 0
PRKCD 0.018 0.014 -10000 0 -10000 0 0
vasculogenesis 0.016 0.1 -10000 0 -0.62 8 8
SDC4 0.013 0.08 -10000 0 -0.76 3 3
Syndecan-4/Tenascin C 0.02 0.097 -10000 0 -0.66 5 5
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.019 0.092 -10000 0 -0.63 5 5
MMP9 0.034 0.049 0.24 25 -10000 0 25
Rac1/GTP 0.005 0.055 0.19 5 -0.32 11 16
cytoskeleton organization 0.02 0.09 -10000 0 -0.63 5 5
GIPC1 0.022 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.002 0.13 -10000 0 -0.66 8 8
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.012 0.061 -10000 0 -0.37 11 11
EPHB2 0.026 0.028 0.24 8 -10000 0 8
Syndecan-2/TACI 0.018 0.048 -10000 0 -0.34 7 7
LAMA1 0.086 0.1 0.24 140 -0.29 1 141
Syndecan-2/alpha2 ITGB1 0.033 0.055 -10000 0 -0.3 11 11
HRAS 0.022 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK 0.004 0.027 -10000 0 -0.34 3 3
ITGA5 0.023 0.003 -10000 0 -10000 0 0
BAX -0.006 0.02 -10000 0 -10000 0 0
EPB41 0.022 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.027 -10000 0 -0.31 3 3
LAMA3 0.008 0.086 -10000 0 -0.56 11 11
EZR 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.007 0.094 -10000 0 -0.56 13 13
Syndecan-2/MMP2 0.016 0.048 -10000 0 -0.4 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.031 0.01 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.032 -10000 0 -0.35 2 2
Syndecan-2/GM-CSF -0.015 0.11 -10000 0 -0.35 45 45
determination of left/right symmetry 0.005 0.032 -10000 0 -0.4 3 3
Syndecan-2/PKC delta 0.018 0.029 -10000 0 -0.33 3 3
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
MAPK3 -0.018 0.1 0.19 16 -0.32 45 61
MAPK1 -0.017 0.097 0.19 13 -0.32 41 54
Syndecan-2/RACK1 0.029 0.028 -10000 0 -0.29 3 3
NF1 0.022 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.005 0.032 -10000 0 -0.4 3 3
ITGA2 0.021 0.006 -10000 0 -10000 0 0
MAPK8 0.003 0.027 -10000 0 -0.34 3 3
Syndecan-2/alpha2/beta1 Integrin 0.075 0.073 0.25 13 -0.29 3 16
Syndecan-2/Kininogen 0.016 0.036 0.25 6 -10000 0 6
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC -0.002 0.042 -10000 0 -0.29 2 2
Syndecan-2/CASK/Protein 4.1 0.018 0.027 -10000 0 -0.32 3 3
extracellular matrix organization 0.019 0.029 -10000 0 -0.34 3 3
actin cytoskeleton reorganization 0.012 0.061 -10000 0 -0.37 11 11
Syndecan-2/Caveolin-2/Ras 0.023 0.061 -10000 0 -0.34 11 11
Syndecan-2/Laminin alpha3 0.01 0.06 -10000 0 -0.35 13 13
Syndecan-2/RasGAP 0.037 0.029 -10000 0 -0.27 3 3
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
PRKCD 0.021 0.007 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.032 -10000 0 -0.35 2 2
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.023 0.025 -10000 0 -0.28 2 2
RHOA 0.021 0.007 -10000 0 -10000 0 0
SDCBP 0.022 0.005 -10000 0 -10000 0 0
TNFRSF13B 0.019 0.06 0.24 8 -0.56 4 12
RASA1 0.021 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.031 0.01 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.019 0.03 -10000 0 -0.35 3 3
TGFB1 0.022 0.005 -10000 0 -10000 0 0
CASP3 0.013 0.042 0.19 18 -0.29 3 21
FN1 0.01 0.082 -10000 0 -0.56 10 10
Syndecan-2/IL8 0.022 0.051 0.18 15 -0.35 6 21
SDC2 0.005 0.032 -10000 0 -0.4 3 3
KNG1 0.006 0.051 0.3 12 -10000 0 12
Syndecan-2/Neurofibromin 0.019 0.03 -10000 0 -0.35 3 3
TRAPPC4 0.022 0.004 -10000 0 -10000 0 0
CSF2 -0.034 0.17 -10000 0 -0.56 45 45
Syndecan-2/TGFB1 0.019 0.029 -10000 0 -0.34 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.027 -10000 0 -0.32 3 3
Syndecan-2/Ezrin 0.03 0.029 -10000 0 -0.3 3 3
PRKACA 0.015 0.045 0.19 21 -0.31 3 24
angiogenesis 0.021 0.051 0.18 15 -0.35 6 21
MMP2 0.017 0.053 -10000 0 -0.56 4 4
IL8 0.026 0.062 0.25 16 -0.56 3 19
calcineurin-NFAT signaling pathway 0.018 0.048 -10000 0 -0.34 7 7
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.037 -10000 0 -0.56 2 2
ANTXR2 0.015 0.064 -10000 0 -0.56 6 6
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.08 7 7
monocyte activation -0.009 0.1 -10000 0 -0.38 32 32
MAP2K2 -0.009 0.11 -10000 0 -0.57 18 18
MAP2K1 -0.005 0.009 -10000 0 -0.11 1 1
MAP2K7 -0.005 0.008 -10000 0 -0.11 1 1
MAP2K6 -0.005 0.011 0.12 1 -0.11 2 3
CYAA -0.011 0.045 -10000 0 -0.39 6 6
MAP2K4 -0.005 0.008 -10000 0 -0.099 2 2
IL1B -0.009 0.053 0.24 2 -0.3 13 15
Channel 0.022 0.052 -10000 0 -0.42 6 6
NLRP1 -0.007 0.027 -10000 0 -0.33 3 3
CALM1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.07 -10000 0 -0.4 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.08 7 -10000 0 7
MAPK3 -0.005 0.009 -10000 0 -0.11 2 2
MAPK1 -0.005 0.009 -10000 0 -0.11 1 1
PGR -0.06 0.12 -10000 0 -0.3 92 92
PA/Cellular Receptors 0.023 0.056 -10000 0 -0.45 6 6
apoptosis -0.002 0.01 -10000 0 -0.08 7 7
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.049 -10000 0 -0.35 7 7
macrophage activation -0.008 0.009 -10000 0 -10000 0 0
TNF 0.011 0.083 0.24 1 -0.56 10 11
VCAM1 -0.007 0.099 -10000 0 -0.38 30 30
platelet activation -0.004 0.07 -10000 0 -0.4 14 14
MAPKKK cascade 0.001 0.021 0.13 2 -0.14 3 5
IL18 -0.006 0.034 0.11 1 -0.27 6 7
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.08 7 7
LEF -0.002 0.01 -10000 0 -0.08 7 7
CASP1 -0.003 0.024 -10000 0 -0.19 5 5
mol:cAMP -0.004 0.07 -10000 0 -0.4 14 14
necrosis -0.002 0.01 -10000 0 -0.08 7 7
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.05 -10000 0 -0.39 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC3 0.022 0.006 -10000 0 -10000 0 0
VDR 0.022 0.026 -10000 0 -0.56 1 1
Cbp/p300/PCAF 0.041 0.017 -10000 0 -10000 0 0
EP300 0.022 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.018 0.049 0.23 1 -0.37 6 7
KAT2B 0.021 0.006 -10000 0 -10000 0 0
MAPK14 0.022 0.004 -10000 0 -10000 0 0
AKT1 -0.009 0.055 -10000 0 -0.28 3 3
RAR alpha/9cRA/Cyclin H 0.037 0.045 -10000 0 -0.32 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.001 0.087 -10000 0 -0.34 24 24
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.021 0.03 -10000 0 -0.23 3 3
NCOR2 0.022 0.026 -10000 0 -0.56 1 1
VDR/VDR/Vit D3 0.016 0.019 -10000 0 -0.41 1 1
RXRs/RARs/NRIP1/9cRA -0.034 0.11 -10000 0 -0.56 11 11
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA3 0.022 0.004 -10000 0 -10000 0 0
NCOA1 0.023 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.022 0.026 -10000 0 -0.56 1 1
RARG 0.023 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.03 0.007 -10000 0 -10000 0 0
MAPK3 0.023 0.003 -10000 0 -10000 0 0
MAPK1 0.022 0.006 -10000 0 -10000 0 0
MAPK8 0.023 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.028 0.093 -10000 0 -0.49 7 7
RARA 0.015 0.024 0.2 1 -0.22 3 4
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.087 -10000 0 -0.35 23 23
PRKCA 0.022 0.037 -10000 0 -0.56 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.046 0.12 0.34 1 -0.55 15 16
RXRG -0.16 0.18 -10000 0 -0.34 233 233
RXRA 0.012 0.03 -10000 0 -0.33 2 2
RXRB 0.018 0.033 0.25 1 -0.28 4 5
VDR/Vit D3/DNA 0.016 0.019 -10000 0 -0.41 1 1
RBP1 0.028 0.049 0.28 17 -10000 0 17
CRBP1/9-cic-RA 0.02 0.033 0.19 17 -10000 0 17
RARB 0.021 0.027 -10000 0 -0.56 1 1
PRKCG 0.036 0.059 0.24 33 -0.29 2 35
MNAT1 0.022 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.04 0.098 -10000 0 -0.53 10 10
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.024 0.092 0.24 1 -0.47 11 12
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.1 0.29 1 -0.36 27 28
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.047 0.12 0.34 1 -0.56 15 16
positive regulation of DNA binding 0.029 0.04 -10000 0 -0.31 2 2
NRIP1 -0.044 0.12 -10000 0 -0.61 9 9
RXRs/RARs -0.05 0.13 -10000 0 -0.55 18 18
RXRs/RXRs/DNA/9cRA -0.037 0.086 -10000 0 -0.46 9 9
PRKACA 0.022 0.004 -10000 0 -10000 0 0
CDK7 0.021 0.006 -10000 0 -10000 0 0
TFIIH 0.042 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.045 0.035 -10000 0 -10000 0 0
CCNH 0.021 0.006 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.04 0.016 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.034 0.064 -10000 0 -0.41 8 8
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.077 -10000 0 -0.31 7 7
AP1 -0.003 0.11 -10000 0 -0.29 59 59
mol:PIP3 -0.017 0.048 -10000 0 -0.32 9 9
AKT1 0.006 0.099 0.31 9 -0.42 3 12
PTK2B -0.018 0.081 -10000 0 -0.34 13 13
RHOA -0.015 0.084 -10000 0 -0.31 31 31
PIK3CB 0.019 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.067 -10000 0 -0.29 10 10
MAGI3 0.022 0.005 -10000 0 -10000 0 0
RELA 0.023 0.002 -10000 0 -10000 0 0
apoptosis 0.009 0.042 0.19 1 -0.29 8 9
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.002 0.096 0.3 5 -0.31 13 18
NF kappa B1 p50/RelA -0.006 0.078 -10000 0 -0.34 8 8
endothelial cell migration 0.007 0.066 -10000 0 -0.71 4 4
ADCY4 -0.004 0.077 -10000 0 -0.4 8 8
ADCY5 -0.008 0.073 -10000 0 -0.42 5 5
ADCY6 0.007 0.058 -10000 0 -0.36 6 6
ADCY7 0.008 0.054 -10000 0 -0.37 5 5
ADCY1 0.006 0.055 -10000 0 -0.37 5 5
ADCY2 0.002 0.066 0.21 2 -0.4 4 6
ADCY3 0.007 0.056 -10000 0 -0.37 5 5
ADCY8 -0.046 0.1 -10000 0 -0.4 11 11
ADCY9 0.007 0.059 -10000 0 -0.39 6 6
GSK3B 0 0.094 0.26 4 -0.36 9 13
arachidonic acid secretion 0.004 0.062 -10000 0 -0.42 6 6
GNG2 0.016 0.059 -10000 0 -0.56 5 5
TRIP6 0.015 0.008 -10000 0 -10000 0 0
GNAO1 0.009 0.041 -10000 0 -0.36 5 5
HRAS 0.022 0.004 -10000 0 -10000 0 0
NFKBIA -0.019 0.074 0.22 1 -0.32 11 12
GAB1 0.022 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.007 0.16 -10000 0 -0.82 18 18
JUN 0.022 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.028 0.029 -10000 0 -0.35 2 2
TIAM1 -0.01 0.18 -10000 0 -0.94 18 18
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
mol:IP3 -0.027 0.066 -10000 0 -0.3 10 10
PLCB3 0.011 0.035 0.18 11 -0.32 2 13
FOS -0.042 0.18 -10000 0 -0.56 54 54
positive regulation of mitosis 0.004 0.062 -10000 0 -0.42 6 6
LPA/LPA1-2-3 0.041 0.054 0.24 1 -0.32 8 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.006 -10000 0 -10000 0 0
stress fiber formation 0 0.066 0.35 1 -0.38 6 7
GNAZ 0.006 0.051 -10000 0 -0.35 9 9
EGFR/PI3K-beta/Gab1 0.009 0.055 -10000 0 -0.33 9 9
positive regulation of dendritic cell cytokine production 0.039 0.054 0.24 1 -0.32 8 9
LPA/LPA2/MAGI-3 0.028 0.016 -10000 0 -10000 0 0
ARHGEF1 0.009 0.047 -10000 0 -0.53 1 1
GNAI2 0.009 0.036 -10000 0 -0.35 4 4
GNAI3 0.01 0.036 -10000 0 -0.35 4 4
GNAI1 0.01 0.047 -10000 0 -0.42 4 4
LPA/LPA3 0.017 0.046 0.17 10 -0.41 4 14
LPA/LPA2 0.017 0.012 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.042 -10000 0 -0.41 4 4
HB-EGF/EGFR 0.01 0.084 0.26 8 -0.37 18 26
HBEGF -0.023 0.066 -10000 0 -0.41 13 13
mol:DAG -0.027 0.066 -10000 0 -0.3 10 10
cAMP biosynthetic process -0.004 0.069 0.33 2 -0.39 5 7
NFKB1 0.022 0.005 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.027 -10000 0 -0.56 1 1
LYN -0.018 0.078 0.26 2 -0.34 12 14
GNAQ 0.009 0.034 0.19 1 -0.3 5 6
LPAR2 0.022 0.005 -10000 0 -10000 0 0
LPAR3 0.022 0.062 0.25 10 -0.56 4 14
LPAR1 0.022 0.038 -10000 0 -0.32 4 4
IL8 -0.016 0.12 0.3 3 -0.43 15 18
PTK2 0.004 0.05 -10000 0 -0.3 8 8
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
CASP3 0.009 0.042 0.19 1 -0.3 8 9
EGFR 0.022 0.083 0.36 11 -0.56 6 17
PLCG1 -0.02 0.066 -10000 0 -0.24 15 15
PLD2 0.006 0.054 0.36 1 -0.35 5 6
G12/G13 0.041 0.038 -10000 0 -0.32 4 4
PI3K-beta -0.009 0.075 -10000 0 -0.36 9 9
cell migration 0.013 0.059 0.17 1 -0.25 18 19
SLC9A3R2 0.02 0.037 -10000 0 -0.56 2 2
PXN -0.001 0.067 0.35 1 -0.39 6 7
HRAS/GTP 0.004 0.063 -10000 0 -0.44 6 6
RAC1 0.022 0.004 -10000 0 -10000 0 0
MMP9 0.034 0.049 0.24 25 -10000 0 25
PRKCE 0.02 0.027 -10000 0 -0.56 1 1
PRKCD -0.027 0.063 -10000 0 -0.28 9 9
Gi(beta/gamma) 0.008 0.068 -10000 0 -0.45 6 6
mol:LPA 0 0.014 -10000 0 -0.18 3 3
TRIP6/p130 Cas/FAK1/Paxillin 0.021 0.058 0.26 1 -0.39 2 3
MAPKKK cascade 0.004 0.062 -10000 0 -0.42 6 6
contractile ring contraction involved in cytokinesis -0.021 0.096 -10000 0 -0.32 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.061 0.14 -10000 0 -0.31 110 110
GNA15 0.01 0.031 0.19 1 -0.3 4 5
GNA12 0.022 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.003 -10000 0 -10000 0 0
MAPT -0.003 0.098 0.3 5 -0.32 13 18
GNA11 0.01 0.031 0.19 1 -0.3 4 5
Rac1/GTP 0.007 0.17 -10000 0 -0.86 18 18
MMP2 0.007 0.067 -10000 0 -0.72 4 4
ErbB2/ErbB3 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
USP8 -0.007 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.029 0.062 -10000 0 -0.29 3 3
NFATC4 -0.012 0.059 0.24 4 -0.25 1 5
ERBB2IP 0.021 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.022 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis 0.008 0.06 -10000 0 -0.3 12 12
JUN 0.013 0.06 0.24 2 -0.45 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
DOCK7 -0.016 0.063 0.28 1 -0.3 3 4
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.025 0.058 -10000 0 -0.32 11 11
AKT1 -0.004 0.006 -10000 0 -10000 0 0
BAD -0.008 0.004 -10000 0 -10000 0 0
MAPK10 -0.01 0.055 0.18 6 -0.25 7 13
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.009 0.064 -10000 0 -0.32 12 12
RAF1 0.019 0.076 0.27 11 -0.3 3 14
ErbB2/ErbB3/neuregulin 2 -0.008 0.1 0.21 1 -0.33 42 43
STAT3 0.012 0.1 -10000 0 -0.79 8 8
cell migration -0.005 0.054 0.22 7 -0.27 2 9
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.014 0.17 0.38 2 -0.5 21 23
FOS -0.031 0.19 0.31 3 -0.47 63 66
NRAS 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.06 -10000 0 -0.3 12 12
MAPK3 -0.005 0.14 0.37 2 -0.5 17 19
MAPK1 -0.006 0.15 0.36 2 -0.52 19 21
JAK2 -0.017 0.059 -10000 0 -0.29 10 10
NF2 -0.003 0.072 -10000 0 -0.56 8 8
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.01 0.053 0.19 1 -0.29 10 11
NRG1 0.005 0.094 -10000 0 -0.56 13 13
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.002 0.067 0.24 1 -0.29 12 13
MAPK9 -0.009 0.044 0.18 4 -10000 0 4
ERBB2 -0.016 0.021 0.29 2 -10000 0 2
ERBB3 0.023 0.003 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
apoptosis 0.005 0.017 -10000 0 -0.17 3 3
STAT3 (dimer) 0.014 0.1 -10000 0 -0.77 8 8
RNF41 -0.01 0.007 -10000 0 -10000 0 0
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.025 0.035 -10000 0 -0.22 11 11
ErbB2/ErbB2/HSP90 (dimer) -0.014 0.018 0.21 2 -10000 0 2
CHRNA1 0.004 0.13 0.34 2 -0.45 15 17
myelination -0.001 0.077 0.29 12 -10000 0 12
PPP3CB -0.015 0.059 0.27 1 -0.27 12 13
KRAS 0.021 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.033 0.059 -10000 0 -0.26 10 10
NRG2 -0.038 0.17 -10000 0 -0.56 46 46
mol:GDP 0.01 0.053 0.19 1 -0.29 10 11
SOS1 0.022 0.004 -10000 0 -10000 0 0
MAP2K2 0.013 0.077 0.26 10 -0.34 2 12
SRC 0.022 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.015 0.064 0.28 1 -0.29 12 13
MAP2K1 -0.01 0.15 0.4 1 -0.48 17 18
heart morphogenesis 0.008 0.06 -10000 0 -0.3 12 12
RAS family/GDP 0.033 0.063 -10000 0 -0.29 2 2
GRB2 0.022 0.004 -10000 0 -10000 0 0
PRKACA 0 0.08 -10000 0 -0.58 9 9
CHRNE 0.007 0.017 0.099 1 -0.21 1 2
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.004 0.006 -10000 0 -10000 0 0
nervous system development 0.008 0.06 -10000 0 -0.3 12 12
CDC42 0.022 0.004 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.04 0.074 -10000 0 -0.56 2 2
UGCG 0.015 0.084 -10000 0 -0.7 6 6
AKT1/mTOR/p70S6K/Hsp90/TERT 0.074 0.11 0.28 14 -0.43 11 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.017 0.083 -10000 0 -0.69 6 6
mol:DAG -0.02 0.16 -10000 0 -0.8 19 19
CaM/Ca2+/Calcineurin A alpha-beta B1 0.049 0.095 -10000 0 -0.41 8 8
FRAP1 0.048 0.11 0.49 1 -0.46 9 10
FOXO3 0.044 0.11 0.34 3 -0.43 11 14
AKT1 0.045 0.11 -10000 0 -0.46 11 11
GAB2 0.007 0.094 -10000 0 -0.56 13 13
SMPD1 0.006 0.12 -10000 0 -0.7 13 13
SGMS1 0 0.13 -10000 0 -0.64 18 18
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 -0.003 0.003 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
cell proliferation 0.032 0.11 0.48 1 -0.45 16 17
EIF3A 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.018 0.019 -10000 0 -10000 0 0
RPS6KB1 0.025 0.043 -10000 0 -0.82 1 1
mol:sphingomyelin -0.02 0.16 -10000 0 -0.8 19 19
natural killer cell activation 0 0 -10000 0 -10000 0 0
JAK3 0.024 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.007 -10000 0 -10000 0 0
JAK1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MYC 0.06 0.11 0.36 9 -0.49 4 13
MYB 0.018 0.084 -10000 0 -1.2 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.091 -10000 0 -0.49 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.045 0.045 -10000 0 -0.74 1 1
mol:PI-3-4-5-P3 0.043 0.092 -10000 0 -0.48 7 7
Rac1/GDP 0.01 0.01 -10000 0 -10000 0 0
T cell proliferation 0.042 0.088 0.26 2 -0.46 6 8
SHC1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.005 -10000 0 -0.064 2 2
PRKCZ 0.041 0.089 -10000 0 -0.48 6 6
NF kappa B1 p50/RelA 0.062 0.1 0.46 1 -0.43 6 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.007 0.055 -10000 0 -0.46 5 5
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
RELA 0.023 0.002 -10000 0 -10000 0 0
IL2RA 0.021 0.041 0.24 3 -0.56 2 5
IL2RB 0.02 0.046 -10000 0 -0.56 3 3
TERT 0.12 0.13 0.28 189 -0.29 1 190
E2F1 0.024 0.038 -10000 0 -0.41 3 3
SOS1 0.023 0.004 -10000 0 -10000 0 0
RPS6 0.021 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.003 0.03 2 -10000 0 2
PTPN11 0.023 0.002 -10000 0 -10000 0 0
IL2RG 0.016 0.069 -10000 0 -0.56 7 7
actin cytoskeleton organization 0.042 0.088 0.26 2 -0.46 6 8
GRB2 0.023 0.004 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.024 -10000 0 -10000 0 0
LCK 0.023 0.027 -10000 0 -0.56 1 1
BCL2 0.046 0.095 0.4 4 -0.46 3 7
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.029 0.027 -10000 0 -0.35 1 1
cell-cell adhesion 0.019 0.018 0.27 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.06 0.035 -10000 0 -0.31 1 1
ITSN1 0.022 0.004 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.025 0.042 0.24 15 -10000 0 15
Ephrin B1/EPHB1 0.046 0.053 0.24 18 -10000 0 18
HRAS/GDP -0.024 0.09 -10000 0 -0.29 3 3
Ephrin B/EPHB1/GRB7 0.066 0.057 -10000 0 -0.31 1 1
Endophilin/SYNJ1 -0.011 0.027 -10000 0 -0.29 1 1
KRAS 0.021 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.064 0.056 -10000 0 -0.31 1 1
endothelial cell migration 0.022 0.029 -10000 0 -0.3 1 1
GRB2 0.022 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.032 0.37 4 -10000 0 4
PAK1 0.005 0.071 0.31 3 -0.3 3 6
HRAS 0.022 0.004 -10000 0 -10000 0 0
RRAS -0.012 0.025 -10000 0 -0.3 1 1
DNM1 0.023 0.014 0.24 2 -10000 0 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.009 0.068 0.34 1 -0.3 1 2
lamellipodium assembly -0.019 0.018 -10000 0 -0.27 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.022 0.042 0.26 1 -0.26 2 3
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
EPHB2 0.026 0.028 0.24 8 -10000 0 8
EPHB3 0.025 0.065 0.35 18 -10000 0 18
EPHB1 0.052 0.088 0.28 60 -10000 0 60
EPHB4 0.022 0.006 -10000 0 -10000 0 0
mol:GDP -0.039 0.07 -10000 0 -0.32 2 2
Ephrin B/EPHB2 0.049 0.03 -10000 0 -0.31 1 1
Ephrin B/EPHB3 0.034 0.048 -10000 0 -0.31 1 1
JNK cascade 0.035 0.13 0.35 63 -10000 0 63
Ephrin B/EPHB1 0.055 0.052 -10000 0 -0.31 1 1
RAP1/GDP -0.029 0.086 -10000 0 -0.3 3 3
EFNB2 0.02 0.027 -10000 0 -0.56 1 1
EFNB3 0.023 0.015 0.24 2 -10000 0 2
EFNB1 0.023 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.052 0.057 0.24 16 -0.32 1 17
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.04 0.045 -10000 0 -0.32 1 1
Rap1/GTP 0.011 0.027 -10000 0 -10000 0 0
axon guidance 0.029 0.027 -10000 0 -0.35 1 1
MAPK3 0.011 0.039 0.23 4 -10000 0 4
MAPK1 0.011 0.043 0.25 6 -10000 0 6
Rac1/GDP -0.038 0.084 0.21 1 -0.29 5 6
actin cytoskeleton reorganization -0.039 0.044 -10000 0 -0.26 1 1
CDC42/GDP -0.038 0.084 0.21 1 -0.29 6 7
PI3K 0.025 0.031 -10000 0 -0.31 1 1
EFNA5 0.02 0.027 -10000 0 -0.56 1 1
Ephrin B2/EPHB4 0.027 0.02 -10000 0 -0.35 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.015 0.035 -10000 0 -0.26 1 1
CDC42 0.022 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.02 0.019 -10000 0 -10000 0 0
PTK2 0.028 0.14 0.54 32 -10000 0 32
MAP4K4 0.035 0.13 0.35 63 -10000 0 63
SRC 0.022 0.004 -10000 0 -10000 0 0
KALRN 0.017 0.046 -10000 0 -0.56 3 3
Intersectin/N-WASP 0.032 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis 0.017 0.1 0.29 47 -10000 0 47
MAP2K1 0.014 0.038 0.24 1 -10000 0 1
WASL 0.022 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.058 0.048 0.31 1 -10000 0 1
cell migration 0.014 0.072 0.32 5 -10000 0 5
NRAS 0.022 0.005 -10000 0 -10000 0 0
SYNJ1 -0.011 0.027 -10000 0 -0.3 1 1
PXN 0.023 0.002 -10000 0 -10000 0 0
TF -0.014 0.041 0.19 2 -0.29 5 7
HRAS/GTP 0.041 0.035 -10000 0 -0.28 1 1
Ephrin B1/EPHB1-2 0.056 0.055 0.24 18 -10000 0 18
cell adhesion mediated by integrin -0.02 0.051 0.3 1 -0.21 4 5
RAC1 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0.045 0.041 -10000 0 -0.29 1 1
RAC1-CDC42/GTP -0.015 0.02 -10000 0 -0.27 1 1
RASA1 0.021 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.031 0.087 -10000 0 -0.3 3 3
ruffle organization 0.011 0.082 0.35 9 -10000 0 9
NCK1 0.019 0.008 -10000 0 -10000 0 0
receptor internalization -0.014 0.026 0.2 1 -0.29 1 2
Ephrin B/EPHB2/KALRN 0.052 0.048 -10000 0 -0.3 4 4
ROCK1 0.072 0.095 0.18 209 -10000 0 209
RAS family/GDP -0.043 0.046 -10000 0 -0.27 1 1
Rac1/GTP -0.019 0.02 -10000 0 -0.28 1 1
Ephrin B/EPHB1/Src/Paxillin 0.02 0.042 -10000 0 -0.26 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.03 0.007 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.023 0.01 0.24 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.006 0.017 -10000 0 -0.21 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.021 0.006 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.56 1 1
MAP3K12 0.023 0.002 -10000 0 -10000 0 0
FGR -0.011 0.14 -10000 0 -0.56 28 28
p38 alpha/TAB1 -0.028 0.084 -10000 0 -0.34 25 25
PRKG1 -0.025 0.16 -10000 0 -0.56 39 39
DUSP8 0.014 0.069 -10000 0 -0.56 7 7
PGK/cGMP/p38 alpha -0.009 0.13 -10000 0 -0.34 44 44
apoptosis -0.027 0.08 -10000 0 -0.33 25 25
RAL/GTP 0.03 0.007 -10000 0 -10000 0 0
LYN 0.02 0.037 -10000 0 -0.56 2 2
DUSP1 -0.043 0.18 -10000 0 -0.56 54 54
PAK1 0.023 0.016 0.37 1 -10000 0 1
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.053 0.019 -10000 0 -10000 0 0
TRAF6 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.022 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.029 0.008 -10000 0 -10000 0 0
MAPK11 0.014 0.099 0.26 3 -0.35 15 18
BLK 0.013 0.09 0.24 12 -0.56 10 22
HCK 0.018 0.046 -10000 0 -0.56 3 3
MAP2K3 0.022 0.005 -10000 0 -10000 0 0
DUSP16 0.022 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.027 -10000 0 -0.56 1 1
TRAF6/MEKK3 0.028 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0.11 0.21 2 -0.4 21 23
positive regulation of innate immune response 0.013 0.12 0.26 3 -0.42 21 24
LCK 0.021 0.027 -10000 0 -0.56 1 1
p38alpha-beta/MKP7 0.02 0.12 0.25 1 -0.42 19 20
p38alpha-beta/MKP5 0.021 0.12 0.25 1 -0.43 18 19
PGK/cGMP -0.018 0.12 -10000 0 -0.4 40 40
PAK2 0.014 0.011 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.006 0.14 0.31 1 -0.41 30 31
CDC42 0.022 0.004 -10000 0 -10000 0 0
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.022 0.005 -10000 0 -10000 0 0
PAK3 0.012 0.055 0.24 1 -0.56 4 5
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 0.025 0.008 -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 0.011 0.094 0.42 9 -10000 0 9
IL27/IL27R/JAK1 0.029 0.085 -10000 0 -0.41 3 3
TBX21 -0.048 0.15 -10000 0 -0.49 40 40
IL12B 0.019 0.012 -10000 0 -10000 0 0
IL12A -0.003 0.046 -10000 0 -0.41 6 6
IL6ST 0.002 0.098 -10000 0 -0.56 14 14
IL27RA/JAK1 0.016 0.034 -10000 0 -10000 0 0
IL27 0.017 0.016 -10000 0 -10000 0 0
TYK2 0.022 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.028 0.13 0.42 3 -0.62 2 5
T-helper 2 cell differentiation 0.011 0.094 0.42 9 -10000 0 9
T cell proliferation during immune response 0.011 0.094 0.42 9 -10000 0 9
MAPKKK cascade -0.011 0.094 -10000 0 -0.42 9 9
STAT3 0.023 0.003 -10000 0 -10000 0 0
STAT2 0.023 0.003 -10000 0 -10000 0 0
STAT1 0.02 0.011 -10000 0 -10000 0 0
IL12RB1 -0.011 0.14 -10000 0 -0.56 28 28
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.024 0.099 -10000 0 -0.44 5 5
IL27/IL27R/JAK2/TYK2 -0.012 0.095 -10000 0 -0.42 9 9
positive regulation of T cell mediated cytotoxicity -0.011 0.094 -10000 0 -0.42 9 9
STAT1 (dimer) 0.013 0.13 0.5 3 -0.57 5 8
JAK2 0.02 0.009 -10000 0 -10000 0 0
JAK1 0.02 0.011 -10000 0 -10000 0 0
STAT2 (dimer) -0.004 0.1 -10000 0 -0.4 10 10
T cell proliferation -0.059 0.14 -10000 0 -0.49 21 21
IL12/IL12R/TYK2/JAK2 -0.054 0.24 -10000 0 -0.81 40 40
IL17A -0.028 0.13 0.42 3 -0.62 2 5
mast cell activation 0.011 0.094 0.42 9 -10000 0 9
IFNG 0.002 0.029 -10000 0 -0.11 16 16
T cell differentiation -0.002 0.005 -10000 0 -0.019 14 14
STAT3 (dimer) -0.004 0.1 -10000 0 -0.4 10 10
STAT5A (dimer) -0.004 0.1 -10000 0 -0.4 11 11
STAT4 (dimer) -0.008 0.11 -10000 0 -0.44 9 9
STAT4 0.013 0.074 -10000 0 -0.56 8 8
T cell activation -0.005 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.022 0.068 -10000 0 -10000 0 0
GATA3 -0.042 0.22 0.57 2 -1.3 14 16
IL18 -0.008 0.032 -10000 0 -0.41 3 3
positive regulation of mast cell cytokine production -0.004 0.1 -10000 0 -0.4 10 10
IL27/EBI3 0.029 0.024 -10000 0 -0.18 2 2
IL27RA 0.004 0.026 -10000 0 -10000 0 0
IL6 -0.068 0.21 -10000 0 -0.56 77 77
STAT5A 0.023 0.003 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.012 0.018 -10000 0 -10000 0 0
IL1B -0.014 0.057 -10000 0 -0.41 10 10
EBI3 0.02 0.031 0.24 1 -0.56 1 2
TNF -0.014 0.057 -10000 0 -0.41 10 10
IL2 signaling events mediated by STAT5

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
GAB2 0.007 0.094 -10000 0 -0.56 13 13
ELF1 0.025 0.02 -10000 0 -0.36 1 1
CCNA2 0.076 0.098 0.24 124 -0.29 2 126
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
JAK3 0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
JAK1 0.022 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.037 0.095 -10000 0 -0.49 7 7
SHC1 0.022 0.005 -10000 0 -10000 0 0
SP1 0.024 0.03 -10000 0 -0.36 3 3
IL2RA 0.01 0.046 -10000 0 -0.68 2 2
IL2RB 0.019 0.046 -10000 0 -0.56 3 3
SOS1 0.023 0.004 -10000 0 -10000 0 0
IL2RG 0.015 0.069 -10000 0 -0.56 7 7
G1/S transition of mitotic cell cycle 0.035 0.096 0.38 3 -0.64 3 6
PTPN11 0.023 0.002 -10000 0 -10000 0 0
CCND2 0.006 0.065 -10000 0 -0.81 3 3
LCK 0.022 0.027 -10000 0 -0.56 1 1
GRB2 0.023 0.004 -10000 0 -10000 0 0
IL2 0.004 0.02 -10000 0 -10000 0 0
CDK6 0.023 0.023 0.37 2 -10000 0 2
CCND3 0.035 0.093 0.32 5 -0.53 3 8
IGF1 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
NCK2 0.023 0.003 -10000 0 -10000 0 0
PTK2 0.021 0.006 -10000 0 -10000 0 0
CRKL 0.002 0.049 -10000 0 -0.29 13 13
GRB2/SOS1/SHC 0.042 0.015 -10000 0 -10000 0 0
HRAS 0.022 0.004 -10000 0 -10000 0 0
IRS1/Crk 0.01 0.054 -10000 0 -0.29 14 14
IGF-1R heterotetramer/IGF1/PTP1B 0.033 0.062 -10000 0 -0.34 12 12
AKT1 0.056 0.096 0.26 11 -10000 0 11
BAD 0.05 0.091 0.25 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.001 0.051 -10000 0 -0.29 14 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.016 0.055 -10000 0 -0.3 14 14
RAF1 0.055 0.12 0.28 12 -0.43 9 21
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.041 0.059 -10000 0 -0.29 13 13
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.018 0.06 -10000 0 -0.32 14 14
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
RPS6KB1 0.058 0.097 0.26 12 -10000 0 12
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.053 0.1 0.27 17 -0.34 4 21
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.018 0.046 -10000 0 -0.27 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.052 0.057 -10000 0 -0.28 10 10
IGF-1R heterotetramer 0.021 0.021 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.058 -10000 0 -0.3 13 13
Crk/p130 Cas/Paxillin 0.036 0.057 -10000 0 -0.28 12 12
IGF1R 0.021 0.021 -10000 0 -10000 0 0
IGF1 0.006 0.11 0.27 1 -0.56 16 17
IRS2/Crk 0.008 0.054 -10000 0 -0.29 15 15
PI3K 0.022 0.045 -10000 0 -0.29 4 4
apoptosis -0.055 0.093 -10000 0 -0.27 13 13
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
PRKCD -0.002 0.07 -10000 0 -0.37 15 15
RAF1/14-3-3 E 0.054 0.12 0.28 13 -0.37 11 24
BAD/14-3-3 0.057 0.096 0.29 12 -10000 0 12
PRKCZ 0.055 0.096 0.26 10 -10000 0 10
Crk/p130 Cas/Paxillin/FAK1 0.053 0.062 -10000 0 -10000 0 0
PTPN1 0.022 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.002 0.075 -10000 0 -0.39 15 15
BCAR1 0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.043 0.056 -10000 0 -0.29 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.022 0.004 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.056 -10000 0 -0.29 13 13
GRB10 0.022 0.005 -10000 0 -10000 0 0
PTPN11 0.001 0.052 -10000 0 -0.29 14 14
IRS1 0.004 0.059 -10000 0 -0.32 14 14
IRS2 0 0.054 -10000 0 -0.3 15 15
IGF-1R heterotetramer/IGF1 0.019 0.08 -10000 0 -0.43 14 14
GRB2 0.022 0.004 -10000 0 -10000 0 0
PDPK1 0.057 0.099 0.27 11 -0.28 4 15
YWHAE 0.022 0.005 -10000 0 -10000 0 0
PRKD1 -0.013 0.095 -10000 0 -0.38 26 26
SHC1 0.022 0.005 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.004 0.092 0.25 1 -0.34 21 22
PDGFB-D/PDGFRB/SLAP 0.009 0.098 -10000 0 -0.42 23 23
PDGFB-D/PDGFRB/APS/CBL 0.04 0.024 -10000 0 -0.36 1 1
AKT1 0.066 0.1 0.32 24 -10000 0 24
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.11 0.24 1 -0.38 24 25
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
FGR -0.043 0.19 0.32 1 -0.59 45 46
mol:Ca2+ -0.004 0.12 -10000 0 -0.4 31 31
MYC 0.021 0.1 0.35 3 -0.38 6 9
SHC1 0.022 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.026 0.036 -10000 0 -0.3 1 1
LRP1/PDGFRB/PDGFB 0.042 0.023 -10000 0 -0.36 1 1
GRB10 0.022 0.005 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GO:0007205 -0.004 0.12 -10000 0 -0.4 31 31
PTEN 0.02 0.007 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.032 0.37 4 -10000 0 4
PDGFB-D/PDGFRB/SHP2 0.031 0.022 -10000 0 -0.41 1 1
PDGFB-D/PDGFRB/GRB10 0.03 0.023 -10000 0 -0.41 1 1
cell cycle arrest 0.009 0.098 -10000 0 -0.42 23 23
HRAS 0.022 0.004 -10000 0 -10000 0 0
HIF1A 0.058 0.097 0.29 28 -10000 0 28
GAB1 -0.001 0.11 0.24 1 -0.4 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.001 0.098 0.27 3 -0.37 16 19
PDGFB-D/PDGFRB 0.041 0.025 -10000 0 -0.37 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.023 -10000 0 -0.41 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.007 0.073 -10000 0 -0.37 6 6
positive regulation of MAPKKK cascade 0.031 0.022 -10000 0 -0.41 1 1
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
mol:IP3 -0.004 0.12 -10000 0 -0.4 31 31
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.022 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.033 0.031 0.26 4 -0.41 1 5
SHB 0.021 0.007 -10000 0 -10000 0 0
BLK -0.046 0.17 -10000 0 -0.48 59 59
PTPN2 0.022 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.031 0.022 -10000 0 -0.41 1 1
BCAR1 0.022 0.006 -10000 0 -10000 0 0
VAV2 -0.001 0.12 -10000 0 -0.41 24 24
CBL 0.022 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.031 -10000 0 -0.42 2 2
LCK -0.006 0.11 0.32 1 -0.54 15 16
PDGFRB 0.021 0.027 -10000 0 -0.57 1 1
ACP1 0.022 0.004 -10000 0 -10000 0 0
HCK 0.003 0.072 0.32 1 -0.5 6 7
ABL1 -0.002 0.1 0.22 7 -0.4 20 27
PDGFB-D/PDGFRB/CBL -0.005 0.13 -10000 0 -0.44 31 31
PTPN1 0.023 0.005 -10000 0 -10000 0 0
SNX15 0.023 0.002 -10000 0 -10000 0 0
STAT3 0.023 0.003 -10000 0 -10000 0 0
STAT1 0.022 0.004 -10000 0 -10000 0 0
cell proliferation 0.021 0.099 0.35 3 -0.35 6 9
SLA -0.006 0.12 -10000 0 -0.56 23 23
actin cytoskeleton reorganization 0.022 0.083 0.33 8 -0.3 1 9
SRC 0.005 0.068 0.31 1 -0.65 3 4
PI3K -0.011 0.018 -10000 0 -0.28 1 1
PDGFB-D/PDGFRB/GRB7/SHC 0.043 0.026 0.25 4 -10000 0 4
SH2B2 0.022 0.005 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.007 0.11 0.24 1 -0.39 24 25
LYN 0 0.083 0.3 1 -0.54 8 9
LRP1 0.023 0.002 -10000 0 -10000 0 0
SOS1 0.022 0.004 -10000 0 -10000 0 0
STAT5B 0.023 0.003 -10000 0 -10000 0 0
STAT5A 0.023 0.003 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.05 0.037 -10000 0 -0.31 1 1
SPHK1 0.022 0.005 -10000 0 -10000 0 0
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG -0.004 0.12 -10000 0 -0.4 31 31
PLCG1 -0.005 0.12 -10000 0 -0.41 31 31
NHERF/PDGFRB 0.041 0.037 0.25 1 -0.31 4 5
YES1 0 0.076 -10000 0 -0.54 7 7
cell migration 0.041 0.037 0.25 1 -0.3 4 5
SHC/Grb2/SOS1 0.057 0.031 -10000 0 -10000 0 0
SLC9A3R2 0.02 0.037 -10000 0 -0.56 2 2
SLC9A3R1 0.024 0.023 0.27 4 -10000 0 4
NHERF1-2/PDGFRB/PTEN 0.047 0.039 -10000 0 -0.32 3 3
FYN 0.004 0.067 -10000 0 -0.52 5 5
DOK1 -0.003 0.041 0.18 2 -0.33 1 3
HRAS/GTP 0.017 0.003 -10000 0 -10000 0 0
PDGFB 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.003 0.11 0.3 1 -0.41 18 19
PRKCD -0.002 0.044 0.18 18 -0.34 1 19
FER -0.002 0.044 0.18 11 -0.34 1 12
MAPKKK cascade 0.007 0.075 0.4 7 -10000 0 7
RASA1 -0.002 0.044 0.18 10 -0.34 1 11
NCK1 0.019 0.008 -10000 0 -10000 0 0
NCK2 0.023 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.027 0.035 -10000 0 -0.31 1 1
PDGFB-D/PDGFRB/SHB 0.029 0.023 -10000 0 -0.41 1 1
chemotaxis -0.002 0.1 0.22 7 -0.38 20 27
STAT1-3-5/STAT1-3-5 0.048 0.028 -10000 0 -0.3 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.02 -10000 0 -0.41 1 1
PTPRJ 0.021 0.026 -10000 0 -0.56 1 1
TCGA08_rtk_signaling

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
PDGFRA 0.017 0.055 0.37 1 -0.56 4 5
HRAS 0.022 0.004 -10000 0 -10000 0 0
EGFR 0.022 0.083 0.36 11 -0.56 6 17
AKT 0.065 0.077 0.26 20 -0.28 1 21
FOXO3 0.023 0.003 -10000 0 -10000 0 0
AKT1 0.022 0.005 -10000 0 -10000 0 0
FOXO1 0.022 0.006 -10000 0 -10000 0 0
AKT3 0.021 0.027 -10000 0 -0.56 1 1
FOXO4 0.023 0.003 -10000 0 -10000 0 0
MET 0.02 0.041 0.37 1 -0.56 2 3
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PIK3CB 0.019 0.009 -10000 0 -10000 0 0
NRAS 0.022 0.005 -10000 0 -10000 0 0
PIK3CG -0.025 0.16 -10000 0 -0.56 39 39
PIK3R3 0.022 0.004 -10000 0 -10000 0 0
PIK3R2 0.022 0.004 -10000 0 -10000 0 0
NF1 0.022 0.004 -10000 0 -10000 0 0
RAS 0.023 0.049 0.2 11 -0.18 11 22
ERBB2 0.024 0.023 0.37 2 -10000 0 2
proliferation/survival/translation -0.064 0.071 0.28 3 -0.26 12 15
PI3K 0.046 0.074 0.23 33 -0.21 6 39
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
KRAS 0.021 0.006 -10000 0 -10000 0 0
FOXO 0.081 0.063 0.23 32 -10000 0 32
AKT2 0.021 0.007 -10000 0 -10000 0 0
PTEN 0.02 0.007 -10000 0 -10000 0 0
Insulin Pathway

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.009 0.096 -10000 0 -0.29 40 40
TC10/GTP 0.007 0.089 -10000 0 -0.29 36 36
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.018 -10000 0 -10000 0 0
HRAS 0.022 0.004 -10000 0 -10000 0 0
APS homodimer 0.022 0.005 -10000 0 -10000 0 0
GRB14 -0.013 0.14 0.24 1 -0.56 30 31
FOXO3 0.031 0.054 -10000 0 -0.54 3 3
AKT1 0.045 0.11 0.31 7 -10000 0 7
INSR 0.024 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.043 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.005 -10000 0 -10000 0 0
SORBS1 -0.038 0.18 -10000 0 -0.56 50 50
CRK 0.022 0.005 -10000 0 -10000 0 0
PTPN1 0.002 0.037 -10000 0 -10000 0 0
CAV1 -0.089 0.13 -10000 0 -0.31 126 126
CBL/APS/CAP/Crk-II/C3G 0.023 0.11 -10000 0 -0.31 39 39
Insulin Receptor/Insulin/IRS1/NCK2 0.053 0.018 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.023 0.024 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.055 -10000 0 -0.32 8 8
RPS6KB1 0.038 0.11 0.29 6 -10000 0 6
PARD6A 0.022 0.005 -10000 0 -10000 0 0
CBL 0.022 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.017 0.007 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.049 0.088 -10000 0 -10000 0 0
HRAS/GTP -0.019 0.018 -10000 0 -0.28 1 1
Insulin Receptor 0.024 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.059 0.025 -10000 0 -10000 0 0
PRKCI 0.009 0.031 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.001 0.066 -10000 0 -0.29 21 21
SHC1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.032 0.021 -10000 0 -10000 0 0
PI3K 0.028 0.029 -10000 0 -10000 0 0
NCK2 0.023 0.003 -10000 0 -10000 0 0
RHOQ 0.022 0.006 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
AKT2 0.039 0.11 0.31 7 -10000 0 7
PRKCZ 0.005 0.044 -10000 0 -10000 0 0
SH2B2 0.022 0.005 -10000 0 -10000 0 0
SHC/SHIP 0.021 0.022 -10000 0 -0.3 1 1
F2RL2 0.048 0.097 0.24 77 -0.35 9 86
TRIP10 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.04 0.015 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.059 0.025 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.014 0.11 -10000 0 -0.32 40 40
TC10/GDP 0.016 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.051 0.022 -10000 0 -10000 0 0
INPP5D -0.011 0.025 -10000 0 -0.32 1 1
SOS1 0.022 0.004 -10000 0 -10000 0 0
SGK1 0.001 0.056 -10000 0 -0.6 4 4
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
IRS1 0.022 0.004 -10000 0 -10000 0 0
p62DOK/RasGAP 0.033 0.022 -10000 0 -10000 0 0
INS 0.019 0.008 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.011 0.025 -10000 0 -0.31 1 1
GRB2 0.022 0.004 -10000 0 -10000 0 0
EIF4EBP1 0.039 0.11 0.31 16 -10000 0 16
PTPRA 0.023 0.006 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.029 0.009 -10000 0 -10000 0 0
PDPK1 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.018 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.04 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.032 0.012 -10000 0 -10000 0 0
Par3/Par6 0.06 0.057 -10000 0 -0.31 1 1
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.045 -10000 0 -0.3 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.021 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.038 0.045 0.28 1 -10000 0 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.022 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.002 0.034 -10000 0 -10000 0 0
CaM/Ca2+ 0.042 0.045 -10000 0 -0.28 4 4
RAP1A 0.022 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.023 0.042 -10000 0 -0.29 3 3
AKT1 0.066 0.097 0.29 19 -10000 0 19
MAP2K1 -0.009 0.048 0.27 1 -0.28 4 5
MAP3K11 -0.007 0.047 0.27 1 -0.29 4 5
IFNGR1 0.024 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.004 0.12 -10000 0 -0.41 29 29
Rap1/GTP -0.02 0.02 -10000 0 -10000 0 0
CRKL/C3G 0.031 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.053 0.044 -10000 0 -0.31 4 4
CEBPB -0.014 0.14 -10000 0 -0.48 29 29
STAT3 0.023 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.037 0.13 -10000 0 -0.7 13 13
STAT1 -0.004 0.046 0.27 1 -0.29 3 4
CALM1 0.022 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.017 0.056 0.25 2 -0.56 4 6
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.023 0.046 0.27 1 -0.28 3 4
CEBPB/PTGES2/Cbp/p300 0.002 0.094 -10000 0 -0.38 9 9
mol:Ca2+ 0.04 0.043 -10000 0 -0.29 4 4
MAPK3 -0.004 0.11 -10000 0 -0.68 8 8
STAT1 (dimer) 0.006 0.047 -10000 0 -10000 0 0
MAPK1 -0.006 0.1 -10000 0 -0.62 8 8
JAK2 0.021 0.01 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
JAK1 0.023 0.009 -10000 0 -10000 0 0
CAMK2D 0.022 0.005 -10000 0 -10000 0 0
DAPK1 -0.027 0.17 0.32 1 -0.6 36 37
SMAD7 0.031 0.05 0.16 19 -0.3 1 20
CBL/CRKL/C3G 0.03 0.045 0.27 1 -10000 0 1
PI3K 0.023 0.038 -10000 0 -0.27 2 2
IFNG 0.017 0.056 0.25 2 -0.56 4 6
apoptosis -0.009 0.13 -10000 0 -0.43 35 35
CAMK2G 0.022 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.003 -10000 0 -10000 0 0
CAMK2A -0.014 0.14 -10000 0 -0.56 29 29
CAMK2B 0.047 0.074 0.25 56 -0.29 1 57
FRAP1 0.061 0.091 0.28 19 -10000 0 19
PRKCD 0.064 0.099 0.3 19 -10000 0 19
RAP1B 0.022 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.002 0.034 -10000 0 -10000 0 0
PTPN2 0.022 0.005 -10000 0 -10000 0 0
EP300 0.023 0.004 -10000 0 -10000 0 0
IRF1 0.002 0.048 0.26 2 -0.33 1 3
STAT1 (dimer)/PIASy 0.02 0.046 0.27 1 -0.3 1 2
SOCS1 -0.005 0.17 -10000 0 -1 13 13
mol:GDP 0.027 0.042 0.25 1 -10000 0 1
CASP1 0.032 0.052 0.17 20 -0.26 2 22
PTGES2 0.023 0.003 -10000 0 -10000 0 0
IRF9 0.009 0.044 0.14 1 -0.19 1 2
mol:PI-3-4-5-P3 0.016 0.032 -10000 0 -0.27 2 2
RAP1/GDP 0.025 0.032 -10000 0 -10000 0 0
CBL -0.006 0.047 0.27 1 -0.28 4 5
MAP3K1 -0.007 0.047 0.27 1 -0.29 4 5
PIAS1 0.023 0.002 -10000 0 -10000 0 0
PIAS4 0.022 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.002 0.034 -10000 0 -10000 0 0
PTPN11 -0.002 0.05 0.29 1 -0.29 4 5
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.012 0.026 -10000 0 -0.41 2 2
MAP4K4 0.005 0.062 -10000 0 -0.34 5 5
BAG4 0.02 0.018 0.37 1 -10000 0 1
PKC zeta/ceramide 0.012 0.043 -10000 0 -0.23 10 10
NFKBIA 0.022 0.005 -10000 0 -10000 0 0
BIRC3 0.015 0.064 -10000 0 -0.56 6 6
BAX 0.001 0.057 -10000 0 -0.33 13 13
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.013 0.12 0.65 16 -10000 0 16
BAD -0.004 0.043 0.17 4 -0.23 10 14
SMPD1 0.007 0.054 0.2 4 -0.2 12 16
RB1 -0.004 0.042 0.18 3 -0.23 10 13
FADD/Caspase 8 0.022 0.08 -10000 0 -0.45 3 3
MAP2K4 -0.006 0.042 0.18 4 -0.23 9 13
NSMAF 0.022 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.002 0.048 0.2 13 -0.2 10 23
EGF 0.015 0.071 0.24 3 -0.56 7 10
mol:ceramide -0.001 0.043 0.17 2 -0.24 10 12
MADD 0.022 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.011 0.025 -10000 0 -0.39 2 2
ASAH1 0.021 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle -0.004 0.041 0.18 3 -0.22 10 13
cell proliferation 0.011 0.061 -10000 0 -0.25 16 16
BID 0 0.13 -10000 0 -0.61 16 16
MAP3K1 -0.004 0.042 0.18 3 -0.23 10 13
EIF2A 0.048 0.096 0.3 20 -0.26 1 21
TRADD 0.022 0.005 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
MAPK3 -0.002 0.046 0.19 12 -0.42 1 13
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.002 0.045 0.18 12 -0.43 1 13
Cathepsin D/ceramide 0.013 0.043 0.17 1 -0.23 10 11
FADD 0.003 0.056 -10000 0 -0.4 3 3
KSR1 0.001 0.048 0.19 14 -0.21 10 24
MAPK8 -0.005 0.052 -10000 0 -0.34 3 3
PRKRA 0.001 0.052 0.19 15 -0.24 9 24
PDGFA 0.02 0.037 -10000 0 -0.56 2 2
TRAF2 0.022 0.004 -10000 0 -10000 0 0
IGF1 0.004 0.1 0.24 1 -0.56 16 17
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.001 0.043 0.17 2 -0.24 10 12
CTSD 0.022 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.032 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.012 0.065 -10000 0 -0.27 16 16
PRKCD 0.021 0.007 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.011 0.025 -10000 0 -0.39 2 2
RelA/NF kappa B1 0.032 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.006 0.055 -10000 0 -0.36 4 4
TNFR1A/BAG4/TNF-alpha 0.028 0.056 0.25 1 -0.35 8 9
mol:Sphingosine-1-phosphate -0.012 0.026 -10000 0 -0.41 2 2
MAP2K1 -0.004 0.046 0.21 6 -0.43 1 7
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.002 -10000 0 -10000 0 0
CYCS -0.001 0.044 -10000 0 -0.22 9 9
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.018 0.26 1 -10000 0 1
EIF2AK2 0.002 0.053 0.19 21 -0.44 1 22
TNF-alpha/TNFR1A/FAN 0.034 0.052 -10000 0 -0.36 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.081 -10000 0 -0.38 12 12
MAP2K2 -0.004 0.045 0.18 13 -0.3 2 15
SMPD3 0.002 0.075 0.18 1 -0.27 26 27
TNF 0.011 0.083 0.24 1 -0.56 10 11
PKC zeta/PAR4 0.032 0.008 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.006 0.041 0.24 7 -0.19 3 10
NF kappa B1/RelA/I kappa B alpha 0.06 0.023 -10000 0 -10000 0 0
AIFM1 0 0.041 -10000 0 -0.22 7 7
BCL2 0.023 0.016 0.37 1 -10000 0 1
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 0.021 0.006 -10000 0 -10000 0 0
NFATC1 0.027 0.08 0.49 2 -0.38 3 5
NFATC2 -0.02 0.096 0.19 2 -0.28 38 40
NFATC3 0.012 0.009 -10000 0 -10000 0 0
YWHAE 0.022 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.022 0.12 -10000 0 -0.43 30 30
Exportin 1/Ran/NUP214 0.041 0.015 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.002 0.12 -10000 0 -0.39 28 28
BCL2/BAX 0.033 0.013 0.26 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.014 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.014 -10000 0 -10000 0 0
BAX 0.022 0.004 -10000 0 -10000 0 0
MAPK14 0.022 0.004 -10000 0 -10000 0 0
BAD 0.023 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D -0.011 0.12 -10000 0 -0.4 32 32
Calcineurin A alpha-beta B1/BCL2 0.023 0.016 0.37 1 -10000 0 1
FKBP8 0.022 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.011 0.12 0.39 32 -10000 0 32
KPNB1 0.023 0.003 -10000 0 -10000 0 0
KPNA2 0.022 0.004 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
SFN 0.039 0.071 0.24 45 -0.38 3 48
MAP3K8 0.017 0.029 -10000 0 -0.56 1 1
NFAT4/CK1 alpha 0.017 0.021 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.02 0.14 -10000 0 -0.33 63 63
CABIN1 -0.022 0.13 -10000 0 -0.43 29 29
CALM1 0.017 0.015 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
MAP3K1 0.021 0.006 -10000 0 -10000 0 0
CAMK4 0.019 0.038 -10000 0 -0.56 2 2
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.003 -10000 0 -10000 0 0
YWHAH 0.022 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0.03 -10000 0 -0.41 2 2
YWHAB 0.022 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.013 -10000 0 -10000 0 0
MAPK9 0.021 0.007 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
FKBP1A 0.022 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.015 0.093 0.28 1 -0.41 5 6
PRKCH 0.022 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.023 0.025 -10000 0 -10000 0 0
CASP3 0.02 0.007 -10000 0 -10000 0 0
PIM1 0.022 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.009 -10000 0 -10000 0 0
apoptosis 0.015 0.01 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.04 -10000 0 -0.26 5 5
PRKCB -0.005 0.12 -10000 0 -0.56 23 23
PRKCE 0.02 0.027 -10000 0 -0.56 1 1
JNK2/NFAT4 0.023 0.026 -10000 0 -10000 0 0
BAD/BCL-XL 0.031 0.01 -10000 0 -10000 0 0
PRKCD 0.021 0.007 -10000 0 -10000 0 0
NUP214 0.022 0.003 -10000 0 -10000 0 0
PRKCZ 0.018 0.013 -10000 0 -10000 0 0
PRKCA 0.02 0.037 -10000 0 -0.56 2 2
PRKCG 0.028 0.063 0.24 33 -0.29 2 35
PRKCQ -0.027 0.16 -10000 0 -0.56 41 41
FKBP38/BCL2 0.032 0.014 0.26 1 -10000 0 1
EP300 0.016 0.017 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.036 0.078 0.46 2 -0.36 3 5
CaM/Ca2+/FKBP38 0.023 0.019 -10000 0 -10000 0 0
FKBP12/FK506 0.016 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.02 0.032 -10000 0 -0.36 2 2
NFATc/ERK1 0.039 0.078 0.46 2 -0.36 3 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0 0.12 -10000 0 -0.4 29 29
NR4A1 -0.067 0.21 0.23 1 -0.54 72 73
GSK3B 0.017 0.013 -10000 0 -10000 0 0
positive T cell selection 0.012 0.009 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.011 0.072 -10000 0 -0.31 12 12
RCH1/ KPNB1 0.033 0.006 -10000 0 -10000 0 0
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
PRKACA 0.021 0.005 -10000 0 -10000 0 0
AKAP5 0.02 0.037 -10000 0 -0.56 2 2
MEF2D 0.016 0.018 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.038 0.078 0.66 1 -0.36 3 4
CREBBP 0.016 0.017 -10000 0 -10000 0 0
BCL2 0.023 0.016 0.37 1 -10000 0 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.02 0.018 0.37 1 -10000 0 1
Caspase 8 (4 units) 0.028 0.069 -10000 0 -0.29 3 3
NEF -0.005 0.038 -10000 0 -0.2 15 15
NFKBIA 0.022 0.015 -10000 0 -10000 0 0
BIRC3 0.012 0.069 -10000 0 -0.53 6 6
CYCS 0.01 0.065 0.25 2 -0.32 3 5
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.003 0.1 -10000 0 -0.39 24 24
MAP2K7 0.009 0.14 0.29 1 -0.6 18 19
protein ubiquitination 0.021 0.074 0.32 4 -0.33 4 8
CRADD 0.023 0.002 -10000 0 -10000 0 0
DAXX 0.022 0.004 -10000 0 -10000 0 0
FAS 0.021 0.027 -10000 0 -0.56 1 1
BID 0.012 0.067 -10000 0 -0.28 13 13
NF-kappa-B/RelA/I kappa B alpha 0.044 0.037 -10000 0 -0.29 5 5
TRADD 0.022 0.005 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
CFLAR 0.022 0.004 -10000 0 -10000 0 0
FADD 0.02 0.008 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.037 -10000 0 -0.29 5 5
MAPK8 0.009 0.13 0.27 2 -0.57 17 19
APAF1 0.023 0.002 -10000 0 -10000 0 0
TRAF1 0.023 0.003 -10000 0 -10000 0 0
TRAF2 0.022 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.012 0.069 -10000 0 -0.29 19 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.075 -10000 0 -0.39 6 6
CHUK 0.02 0.072 0.23 3 -0.36 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.051 0.034 -10000 0 -0.31 1 1
TCRz/NEF -0.002 0.1 -10000 0 -0.42 24 24
TNF 0.011 0.083 0.24 1 -0.56 10 11
FASLG -0.019 0.15 -10000 0 -0.62 25 25
NFKB1 0.022 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.028 0.056 0.25 1 -0.35 8 9
CASP6 0.018 0.13 -10000 0 -0.51 14 14
CASP7 0.017 0.11 0.36 6 -0.47 11 17
RELA 0.023 0.017 -10000 0 -0.17 1 1
CASP2 0.022 0.004 -10000 0 -10000 0 0
CASP3 0.011 0.11 0.36 6 -0.48 10 16
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.018 0.26 1 -10000 0 1
CASP8 0.022 0.004 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
MAP3K14 0.021 0.079 -10000 0 -0.38 5 5
APAF-1/Caspase 9 0.014 0.07 -10000 0 -0.39 6 6
BCL2 0.008 0.12 0.32 3 -0.51 17 20
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.009 0.049 -10000 0 -10000 0 0
DAPP1 -0.01 0.12 0.23 2 -0.39 30 32
Src family/SYK family/BLNK-LAT/BTK-ITK -0.021 0.17 0.31 1 -0.55 34 35
mol:DAG 0.001 0.087 0.18 19 -0.25 22 41
HRAS 0.024 0.008 -10000 0 -10000 0 0
RAP1A 0.024 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.016 0.081 -10000 0 -0.38 10 10
PLCG2 0.022 0.005 -10000 0 -10000 0 0
PLCG1 0.022 0.004 -10000 0 -10000 0 0
ARF5 0.022 0.004 -10000 0 -10000 0 0
mol:GTP -0.007 0.046 -10000 0 -0.27 2 2
ARF1/GTP -0.004 0.041 0.23 1 -0.27 2 3
RHOA 0.021 0.007 -10000 0 -10000 0 0
YES1 0.021 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.007 0.048 -10000 0 -0.27 2 2
ADAP1 -0.011 0.053 -10000 0 -0.29 5 5
ARAP3 -0.007 0.045 -10000 0 -0.27 2 2
INPPL1 0.022 0.005 -10000 0 -10000 0 0
PREX1 0.016 0.059 -10000 0 -0.56 5 5
ARHGEF6 0.004 0.1 -10000 0 -0.56 16 16
ARHGEF7 0.021 0.006 -10000 0 -10000 0 0
ARF1 0.022 0.004 -10000 0 -10000 0 0
NRAS 0.023 0.009 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.56 1 1
ARF6 0.022 0.005 -10000 0 -10000 0 0
FGR -0.011 0.14 -10000 0 -0.56 28 28
mol:Ca2+ 0.005 0.056 0.2 9 -10000 0 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.021 0.027 -10000 0 -0.56 1 1
ZAP70 0.013 0.074 -10000 0 -0.56 8 8
mol:IP3 0.002 0.071 0.18 30 -0.2 9 39
LYN 0.02 0.037 -10000 0 -0.56 2 2
ARF1/GDP 0.015 0.083 -10000 0 -0.36 12 12
RhoA/GDP 0.023 0.058 0.33 1 -0.33 1 2
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
BLNK 0.021 0.027 -10000 0 -0.56 1 1
actin cytoskeleton reorganization 0.008 0.088 0.27 6 -0.4 6 12
SRC 0.022 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.01 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PTEN 0.018 0.014 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.011 0.046 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.048 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.009 0.11 -10000 0 -0.43 21 21
BLK 0.013 0.09 0.24 12 -0.56 10 22
PDPK1 0.022 0.004 -10000 0 -10000 0 0
CYTH1 -0.009 0.044 -10000 0 -0.26 2 2
HCK 0.018 0.046 -10000 0 -0.56 3 3
CYTH3 -0.009 0.044 -10000 0 -10000 0 0
CYTH2 -0.009 0.044 -10000 0 -0.26 2 2
KRAS 0.022 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.014 0.032 -10000 0 -10000 0 0
SGK1 0.019 0.032 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP 0.003 0.083 -10000 0 -0.34 15 15
SOS1 0.022 0.004 -10000 0 -10000 0 0
SYK 0.022 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.004 0.058 0.27 2 -0.34 1 3
mol:PI-3-4-5-P3 -0.009 0.042 -10000 0 -0.27 2 2
ARAP3/RAP1A/GTP -0.007 0.048 -10000 0 -0.27 2 2
VAV1 0.019 0.046 -10000 0 -0.56 3 3
mol:PI-3-4-P2 -0.011 0.018 -10000 0 -0.41 1 1
RAS family/GTP/PI3K Class I 0.038 0.049 -10000 0 -0.27 2 2
PLEKHA1 -0.012 0.016 -10000 0 -0.35 1 1
Rac1/GDP 0.014 0.083 -10000 0 -0.36 12 12
LAT 0.023 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.002 0.086 -10000 0 -0.38 18 18
ITK -0.024 0.075 -10000 0 -0.3 23 23
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.006 0.11 0.27 7 -0.34 25 32
LCK 0.021 0.027 -10000 0 -0.56 1 1
BTK -0.029 0.083 -10000 0 -0.29 33 33
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
mol:S1P 0.001 0.001 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.003 0.055 -10000 0 -0.26 13 13
GNAO1 0.022 0.03 0.24 2 -0.56 1 3
S1P/S1P3/G12/G13 0.043 0.012 -10000 0 -10000 0 0
AKT1 0.013 0.079 -10000 0 -0.45 13 13
AKT3 0.016 0.083 -10000 0 -1.2 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
GNAI2 0.022 0.007 -10000 0 -10000 0 0
GNAI3 0.023 0.005 -10000 0 -10000 0 0
GNAI1 0.022 0.027 -10000 0 -0.56 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.023 0.005 -10000 0 -10000 0 0
S1PR2 0.022 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.039 -10000 0 -0.24 2 2
MAPK3 0.01 0.042 -10000 0 -0.25 1 1
MAPK1 0.009 0.036 -10000 0 -10000 0 0
JAK2 0.013 0.048 -10000 0 -0.27 1 1
CXCR4 0.01 0.042 -10000 0 -0.25 1 1
FLT1 0.023 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
SRC 0.009 0.043 -10000 0 -0.25 1 1
S1P/S1P3/Gi 0.02 0.039 -10000 0 -0.24 2 2
RAC1 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.021 0.053 -10000 0 -10000 0 0
VEGFA 0.024 0.004 -10000 0 -10000 0 0
S1P/S1P2/Gi 0.02 0.034 -10000 0 -0.22 4 4
VEGFR1 homodimer/VEGFA homodimer 0.035 0.011 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.048 0.12 -10000 0 -0.27 111 111
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
G12/G13 0.032 0.008 -10000 0 -10000 0 0
GNA14 -0.11 0.24 -10000 0 -0.56 111 111
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA12 0.022 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.057 -10000 0 -0.24 1 1
Signaling events mediated by PRL

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
CCNE1 0.078 0.11 0.27 107 -10000 0 107
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0.016 0.053 -10000 0 -0.56 4 4
CDKN1A 0.009 0.039 -10000 0 -0.31 6 6
PRL-3/alpha Tubulin 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.085 -10000 0 -0.42 23 23
AGT -0.006 0.13 0.24 1 -0.56 24 25
CCNA2 -0.015 0.047 0.39 1 -10000 0 1
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
EGR1 0.004 0.049 -10000 0 -0.4 7 7
CDK2/Cyclin E1 0.064 0.097 0.33 5 -0.34 4 9
MAPK3 -0.01 0.003 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.033 0.007 -10000 0 -10000 0 0
MAPK1 -0.009 0.004 -10000 0 -10000 0 0
PTP4A1 -0.009 0.034 -10000 0 -10000 0 0
PTP4A3 0.021 0.006 -10000 0 -10000 0 0
PTP4A2 0.022 0.004 -10000 0 -10000 0 0
ITGB1 -0.009 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.01 0.03 -10000 0 -0.31 3 3
Rab GGTase beta/Rab GGTase alpha 0.032 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 0.021 0.057 0.3 1 -10000 0 1
RABGGTA 0.022 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.006 -10000 0 -10000 0 0
RHOC 0.006 0.046 -10000 0 -0.31 9 9
RHOA 0.005 0.049 -10000 0 -0.31 10 10
cell motility 0.011 0.065 -10000 0 -0.28 10 10
PRL-1/alpha Tubulin 0.02 0.054 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.042 -10000 0 -0.41 4 4
ROCK1 0.018 0.051 -10000 0 -0.33 3 3
RABGGTB 0.022 0.004 -10000 0 -10000 0 0
CDK2 0.023 0.002 -10000 0 -10000 0 0
mitosis -0.009 0.034 -10000 0 -10000 0 0
ATF5 0.026 0.026 0.24 7 -10000 0 7
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.046 0.078 0.2 4 -0.29 4 8
adherens junction organization 0.013 0.099 -10000 0 -0.41 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.062 0.088 0.32 3 -10000 0 3
FMN1 0.008 0.1 -10000 0 -0.35 23 23
mol:IP3 0.003 0.037 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.031 0.082 -10000 0 -0.41 11 11
CTNNB1 0.022 0.007 -10000 0 -10000 0 0
AKT1 0.002 0.042 -10000 0 -0.29 2 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.003 0.15 -10000 0 -0.72 17 17
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.08 -10000 0 -0.38 11 11
VASP 0.027 0.074 -10000 0 -0.38 8 8
ZYX 0.025 0.081 -10000 0 -0.39 11 11
JUB 0.027 0.083 -10000 0 -0.39 11 11
EGFR(dimer) 0.034 0.098 0.27 9 -0.35 15 24
E-cadherin/beta catenin-gamma catenin 0.038 0.014 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.01 0.051 -10000 0 -0.3 3 3
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.011 0.052 -10000 0 -0.31 3 3
FYN 0.04 0.079 0.2 4 -0.31 3 7
mol:Ca2+ 0.003 0.037 -10000 0 -0.24 1 1
JUP 0.024 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.008 -10000 0 -10000 0 0
mol:DAG 0.001 0.036 -10000 0 -10000 0 0
CDH1 0.023 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.063 0.087 0.32 3 -10000 0 3
establishment of polarity of embryonic epithelium 0.026 0.075 -10000 0 -0.37 9 9
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
EGFR 0.022 0.083 0.36 11 -0.56 6 17
CASR 0.039 0.076 0.2 4 -10000 0 4
RhoA/GTP 0.06 0.069 -10000 0 -10000 0 0
AKT2 0.001 0.044 -10000 0 -0.28 3 3
actin cable formation 0.006 0.099 0.24 3 -0.39 12 15
apoptosis -0.05 0.085 0.3 9 -0.22 8 17
CTNNA1 0.025 0.008 -10000 0 -10000 0 0
mol:GDP 0.05 0.087 0.32 3 -0.27 4 7
PIP5K1A 0.023 0.08 -10000 0 -0.4 10 10
PLCG1 0.001 0.036 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.093 0.29 4 -0.35 11 15
homophilic cell adhesion 0.003 0.004 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.032 0.06 0.33 7 -0.23 1 8
KIRREL 0.016 0.069 -10000 0 -0.55 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.032 0.06 0.24 1 -0.33 7 8
PLCG1 0.022 0.004 -10000 0 -10000 0 0
ARRB2 0.022 0.005 -10000 0 -10000 0 0
WASL 0.022 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.05 0.055 0.32 1 -0.34 4 5
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.013 0.035 -10000 0 -0.3 2 2
FYN 0.009 0.079 0.29 18 -0.37 4 22
mol:Ca2+ 0.047 0.049 0.31 1 -0.32 2 3
mol:DAG 0.048 0.05 0.32 1 -0.32 2 3
NPHS2 -0.005 0.031 0.26 3 -10000 0 3
mol:IP3 0.048 0.05 0.32 1 -0.32 2 3
regulation of endocytosis 0.039 0.051 -10000 0 -0.34 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.037 0.052 0.31 1 -0.34 4 5
establishment of cell polarity 0.032 0.06 0.23 1 -0.33 7 8
Nephrin/NEPH1/podocin/NCK1-2 0.051 0.057 0.32 1 -0.32 4 5
Nephrin/NEPH1/beta Arrestin2 0.043 0.053 -10000 0 -0.35 4 4
NPHS1 0.024 0.059 0.26 24 -10000 0 24
Nephrin/NEPH1/podocin 0.039 0.055 0.31 1 -0.37 4 5
TJP1 0.022 0.004 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
NCK2 0.023 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.049 0.05 0.32 1 -0.32 2 3
CD2AP 0.022 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.05 0.053 0.32 1 -0.35 3 4
GRB2 0.022 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.011 0.098 0.28 15 -0.36 19 34
cytoskeleton organization -0.002 0.041 -10000 0 -0.36 2 2
Nephrin/NEPH1 0.028 0.045 0.19 1 -0.31 4 5
Nephrin/NEPH1/ZO-1 0.042 0.052 -10000 0 -0.35 4 4
Ephrin A reverse signaling

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
MAPKKK cascade 0.03 0.032 0.23 1 -0.35 1 2
EFNA5 0.02 0.027 -10000 0 -0.56 1 1
FYN -0.011 0.033 0.18 8 -0.32 2 10
neuron projection morphogenesis 0.03 0.032 0.23 1 -0.35 1 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.03 0.032 0.24 1 -0.36 1 2
EPHA5 0.019 0.052 0.25 20 -10000 0 20
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.041 0.05 0.34 2 -10000 0 2
CRKL 0.011 0.064 0.3 8 -0.28 1 9
mol:DAG 0.026 0.038 -10000 0 -0.33 1 1
HRAS 0.015 0.076 0.28 15 -10000 0 15
MAPK8 0.003 0.051 0.19 12 -0.33 1 13
RAP1A 0.011 0.069 0.33 9 -0.28 2 11
GAB1 0.012 0.069 0.33 9 -0.28 1 10
MAPK14 0.004 0.054 0.19 14 -0.33 1 15
EPO 0.025 0.028 0.26 6 -10000 0 6
PLCG1 0.026 0.039 -10000 0 -0.33 1 1
EPOR/TRPC2/IP3 Receptors 0.026 0.01 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.044 0.036 -10000 0 -0.37 2 2
GAB1/SHC/GRB2/SOS1 0.046 0.049 0.26 5 -10000 0 5
EPO/EPOR (dimer) 0.036 0.023 0.23 1 -10000 0 1
IRS2 0.008 0.068 0.3 8 -0.29 4 12
STAT1 0.031 0.038 -10000 0 -10000 0 0
STAT5B 0.029 0.04 -10000 0 -0.33 1 1
cell proliferation 0.001 0.055 0.21 14 -0.31 1 15
GAB1/SHIP/PIK3R1/SHP2/SHC 0.035 0.038 -10000 0 -10000 0 0
TEC 0.009 0.071 0.33 8 -0.28 5 13
SOCS3 0.02 0.037 -10000 0 -0.56 2 2
STAT1 (dimer) 0.03 0.037 -10000 0 -10000 0 0
JAK2 0.023 0.012 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.06 0.049 0.33 1 -0.29 2 3
EPO/EPOR 0.036 0.023 0.23 1 -10000 0 1
LYN 0.02 0.037 -10000 0 -0.56 2 2
TEC/VAV2 0.032 0.064 0.27 6 -0.35 5 11
elevation of cytosolic calcium ion concentration 0.026 0.01 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.047 0.032 -10000 0 -0.37 1 1
mol:IP3 0.026 0.038 -10000 0 -0.33 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.042 0.062 0.3 7 -10000 0 7
SH2B3 0.024 0.038 -10000 0 -0.56 2 2
NFKB1 0.005 0.054 0.19 13 -0.33 1 14
EPO/EPOR (dimer)/JAK2/SOCS3 0.009 0.033 0.26 2 -0.23 2 4
PTPN6 0.016 0.047 0.3 2 -0.28 2 4
TEC/VAV2/GRB2 0.041 0.062 0.27 6 -0.39 3 9
EPOR 0.026 0.01 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP 0.046 0.049 0.26 5 -10000 0 5
SOS1 0.022 0.004 -10000 0 -10000 0 0
PLCG2 0.022 0.005 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.044 0.052 0.27 6 -0.27 1 7
VAV2 0.009 0.069 0.3 8 -0.31 4 12
CBL 0.012 0.07 0.33 9 -0.28 2 11
SHC/Grb2/SOS1 0.029 0.03 -10000 0 -10000 0 0
STAT5A 0.029 0.04 -10000 0 -0.33 1 1
GRB2 0.022 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.044 0.044 -10000 0 -0.3 1 1
LYN/PLCgamma2 0.03 0.03 -10000 0 -0.41 2 2
PTPN11 0.023 0.002 -10000 0 -10000 0 0
BTK -0.011 0.1 0.33 8 -0.31 33 41
BCL2 0.042 0.054 0.34 2 -10000 0 2
Signaling events mediated by HDAC Class III

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
EP300 0.022 0.004 -10000 0 -10000 0 0
HDAC4 0.022 0.004 -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 0.021 -10000 0 -0.3 2 2
CDKN1A -0.009 0.003 -10000 0 -10000 0 0
KAT2B 0.021 0.006 -10000 0 -10000 0 0
BAX 0.022 0.004 -10000 0 -10000 0 0
FOXO3 -0.004 0.003 -10000 0 -10000 0 0
FOXO1 0.022 0.006 -10000 0 -10000 0 0
FOXO4 0.01 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
TAT 0.016 0.025 0.3 2 -10000 0 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.018 0.023 0.3 1 -10000 0 1
PPARGC1A -0.079 0.22 -10000 0 -0.56 84 84
FHL2 0.025 0.019 0.24 4 -10000 0 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.03 0.008 -10000 0 -10000 0 0
HIST2H4A -0.009 0.021 0.3 2 -10000 0 2
SIRT1/FOXO3a 0.011 0.031 -10000 0 -0.2 9 9
SIRT1 0.02 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.041 0.014 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.02 0.036 -10000 0 -0.2 5 5
apoptosis -0.041 0.012 -10000 0 -10000 0 0
SIRT1/PGC1A -0.043 0.14 -10000 0 -0.35 84 84
p53/SIRT1 0.025 0.008 -10000 0 -10000 0 0
SIRT1/FOXO4 0.019 0.032 -10000 0 -0.21 1 1
FOXO1/FHL2/SIRT1 0.04 0.017 -10000 0 -10000 0 0
HIST1H1E 0.013 0.015 0.16 2 -10000 0 2
SIRT1/p300 0.03 0.008 -10000 0 -10000 0 0
muscle cell differentiation -0.014 0.034 -10000 0 -0.21 3 3
TP53 0.02 0.005 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.042 0.013 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
MEF2D 0.022 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.015 0.26 1 -10000 0 1
ACSS2 -0.01 0.003 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.014 0.035 0.21 3 -10000 0 3
TRAIL signaling 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
TNFSF10 0.013 0.011 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0.009 0.055 -10000 0 -0.24 17 17
MAP2K4 0.012 0.031 -10000 0 -10000 0 0
IKBKB 0.022 0.017 0.37 1 -10000 0 1
TNFRSF10B 0.021 0.007 -10000 0 -10000 0 0
TNFRSF10A 0.019 0.027 -10000 0 -0.56 1 1
SMPD1 0.006 0.005 -10000 0 -10000 0 0
IKBKG 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.003 0.1 -10000 0 -0.56 15 15
TRAIL/TRAILR2 0.018 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR3 -0.01 0.094 -10000 0 -0.26 49 49
TRAIL/TRAILR1 0.017 0.027 -10000 0 -0.28 2 2
TRAIL/TRAILR4 0.009 0.055 -10000 0 -0.25 17 17
TRAIL/TRAILR1/DAP3/GTP 0.022 0.028 -10000 0 -0.32 1 1
IKK complex 0.006 0.031 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.016 0.004 -10000 0 -10000 0 0
MAPK3 -0.006 0.005 -10000 0 -10000 0 0
MAP3K1 0.016 0.029 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.003 0.1 -10000 0 -0.56 15 15
TRADD 0.022 0.005 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.019 0.027 -10000 0 -0.56 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.008 0.025 -10000 0 -0.29 2 2
CFLAR 0.022 0.004 -10000 0 -10000 0 0
MAPK1 -0.006 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.029 0.038 -10000 0 -0.31 1 1
mol:ceramide 0.006 0.005 -10000 0 -10000 0 0
FADD 0.02 0.008 -10000 0 -10000 0 0
MAPK8 0.042 0.055 0.28 1 -10000 0 1
TRAF2 0.022 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.037 0.17 -10000 0 -0.56 48 48
CHUK 0.022 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.02 0.03 -10000 0 -0.36 1 1
DAP3 0.022 0.005 -10000 0 -10000 0 0
CASP10 0.059 0.094 0.36 15 -10000 0 15
JNK cascade 0.009 0.055 -10000 0 -0.24 17 17
TRAIL (trimer) 0.013 0.011 -10000 0 -10000 0 0
TNFRSF10C -0.037 0.17 -10000 0 -0.56 48 48
TRAIL/TRAILR1/DAP3/GTP/FADD 0.024 0.032 -10000 0 -0.31 1 1
TRAIL/TRAILR2/FADD 0.021 0.023 -10000 0 -10000 0 0
cell death 0.006 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.01 0.016 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.021 0.007 -10000 0 -10000 0 0
CASP8 -0.004 0.074 -10000 0 -0.48 10 10
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.03 0.034 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.006 0.081 0.24 1 -0.43 7 8
BAG4 0.02 0.018 0.37 1 -10000 0 1
BAD 0.002 0.033 0.16 3 -0.15 2 5
NFKBIA 0.022 0.005 -10000 0 -10000 0 0
BIRC3 0.015 0.064 -10000 0 -0.56 6 6
BAX 0.003 0.033 0.31 1 -0.15 2 3
EnzymeConsortium:3.1.4.12 0.004 0.022 0.11 1 -0.088 8 9
IKBKB 0.017 0.09 0.28 2 -0.46 5 7
MAP2K2 0.002 0.038 0.19 9 -10000 0 9
MAP2K1 0.002 0.04 0.2 9 -10000 0 9
SMPD1 0.003 0.028 0.11 1 -0.13 7 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.033 0.1 0.27 15 -0.45 5 20
MAP2K4 0.003 0.026 0.16 2 -10000 0 2
protein ubiquitination 0.012 0.084 -10000 0 -0.41 7 7
EnzymeConsortium:2.7.1.37 0 0.042 0.2 9 -10000 0 9
response to UV 0 0 0.002 10 -10000 0 10
RAF1 0.006 0.039 0.2 10 -10000 0 10
CRADD 0.023 0.002 -10000 0 -10000 0 0
mol:ceramide 0.005 0.033 0.13 2 -0.14 7 9
I-kappa-B-alpha/RELA/p50/ubiquitin 0.03 0.007 -10000 0 -10000 0 0
MADD 0.022 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.03 0.16 2 -0.15 1 3
TRADD 0.022 0.005 -10000 0 -10000 0 0
RELA/p50 0.023 0.002 -10000 0 -10000 0 0
MAPK3 0.003 0.043 0.2 9 -0.21 2 11
MAPK1 0.003 0.041 0.19 8 -0.2 1 9
p50/RELA/I-kappa-B-alpha 0.032 0.008 -10000 0 -10000 0 0
FADD 0.028 0.097 0.26 13 -0.48 4 17
KSR1 0.005 0.041 0.19 11 -0.14 2 13
MAPK8 0 0.028 0.16 3 -10000 0 3
TRAF2 0.022 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK 0.007 0.077 -10000 0 -0.42 6 6
TNF R/SODD 0.026 0.018 0.26 1 -10000 0 1
TNF 0.011 0.083 0.24 1 -0.56 10 11
CYCS 0.002 0.037 0.2 2 -0.22 2 4
IKBKG 0.008 0.08 0.24 2 -0.39 7 9
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.009 0.083 -10000 0 -0.38 11 11
RELA 0.023 0.002 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AIFM1 0.002 0.034 0.22 1 -0.18 1 2
TNF/TNF R/SODD 0.028 0.056 0.25 1 -0.35 8 9
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.017 0.078 -10000 0 -0.56 8 8
NSMAF 0.01 0.08 0.27 3 -0.44 6 9
response to hydrogen peroxide 0 0 0.002 10 -10000 0 10
BCL2 0.023 0.016 0.37 1 -10000 0 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.031 0.074 -10000 0 -0.35 10 10
Ran/GTP/Exportin 1/HDAC1 -0.01 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.082 -10000 0 -0.33 12 12
SUMO1 0.022 0.004 -10000 0 -10000 0 0
ZFPM1 0.021 0.027 -10000 0 -0.56 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.01 0.003 -10000 0 -10000 0 0
FKBP3 0.022 0.005 -10000 0 -10000 0 0
Histones 0.04 0.065 -10000 0 -0.24 1 1
YY1/LSF 0.012 0.063 -10000 0 -0.29 5 5
SMG5 0.022 0.005 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.012 0.041 -10000 0 -0.27 8 8
I kappa B alpha/HDAC1 0.019 0.057 -10000 0 -0.26 1 1
SAP18 0.022 0.006 -10000 0 -10000 0 0
RELA 0.018 0.05 -10000 0 -0.27 8 8
HDAC1/Smad7 0.04 0.024 -10000 0 -0.36 1 1
RANGAP1 0.022 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.017 0.062 -10000 0 -0.26 1 1
NuRD/MBD3 Complex 0.023 0.043 -10000 0 -0.36 3 3
NF kappa B1 p50/RelA 0.016 0.079 -10000 0 -0.29 15 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.034 0.17 -10000 0 -0.56 46 46
GATA1 -0.033 0.16 -10000 0 -0.56 42 42
Mad/Max 0.032 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.003 0.093 -10000 0 -0.38 10 10
RBBP7 0.022 0.005 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
MAX 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
NFKBIA 0.011 0.031 -10000 0 -0.21 8 8
KAT2B 0.021 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.014 0.031 -10000 0 -0.36 1 1
SIN3 complex 0.052 0.02 -10000 0 -10000 0 0
SMURF1 0.022 0.006 -10000 0 -10000 0 0
CHD3 0.022 0.006 -10000 0 -10000 0 0
SAP30 0.021 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.005 -10000 0 -10000 0 0
YY1/HDAC3 0.011 0.057 -10000 0 -0.36 6 6
YY1/HDAC2 0.013 0.063 -10000 0 -0.3 5 5
YY1/HDAC1 0.013 0.061 -10000 0 -0.29 5 5
NuRD/MBD2 Complex (MeCP1) 0.023 0.036 -10000 0 -0.25 1 1
PPARG -0.02 0.13 -10000 0 -0.34 57 57
HDAC8/hEST1B 0.043 0.013 -10000 0 -10000 0 0
UBE2I 0.022 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.018 0.063 -10000 0 -0.36 2 2
MBD3L2 -0.018 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.024 -10000 0 -0.35 1 1
CREBBP 0.022 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.019 0.062 -10000 0 -0.32 7 7
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC3 0.011 0.031 -10000 0 -0.21 8 8
HDAC2 0.023 0.002 -10000 0 -10000 0 0
YY1 0.012 0.011 -10000 0 -0.2 1 1
HDAC8 0.023 0.003 -10000 0 -10000 0 0
SMAD7 0.021 0.027 -10000 0 -0.56 1 1
NCOR2 0.022 0.026 -10000 0 -0.56 1 1
MXD1 0.022 0.004 -10000 0 -10000 0 0
STAT3 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.025 0.061 -10000 0 -0.26 5 5
YY1/SAP30/HDAC1 0.025 0.059 -10000 0 -0.26 5 5
EP300 0.022 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.015 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.031 -10000 0 -0.21 8 8
histone deacetylation 0.023 0.036 -10000 0 -0.25 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.015 0.033 -10000 0 -0.25 1 1
nuclear export -0.043 0.013 -10000 0 -10000 0 0
PRKACA 0.022 0.004 -10000 0 -10000 0 0
GATAD2B 0.022 0.005 -10000 0 -10000 0 0
GATAD2A 0.022 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 -0.015 0.12 -10000 0 -0.35 44 44
GATA1/HDAC1 -0.007 0.12 -10000 0 -0.41 42 42
GATA1/HDAC3 -0.012 0.11 -10000 0 -0.33 41 41
CHD4 0.021 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.022 0.06 -10000 0 -0.37 10 10
SIN3/HDAC complex/Mad/Max 0.01 0.059 -10000 0 -0.28 12 12
NuRD Complex 0.021 0.057 -10000 0 -0.34 3 3
positive regulation of chromatin silencing 0.038 0.063 -10000 0 -0.24 1 1
SIN3B 0.022 0.004 -10000 0 -10000 0 0
MTA2 0.023 0.002 -10000 0 -10000 0 0
SIN3A 0.023 0.002 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
SUMO1/HDAC1 0.032 0.03 -10000 0 -0.26 1 1
HDAC complex 0.055 0.015 -10000 0 -10000 0 0
GATA1/Fog1 -0.008 0.13 -10000 0 -0.41 43 43
FKBP25/HDAC1/HDAC2 0.043 0.013 -10000 0 -10000 0 0
TNF 0.011 0.083 0.24 1 -0.56 10 11
negative regulation of cell growth 0.01 0.058 -10000 0 -0.28 12 12
NuRD/MBD2/PRMT5 Complex 0.023 0.036 -10000 0 -0.25 1 1
Ran/GTP/Exportin 1 0.03 0.029 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.004 0.066 -10000 0 -0.33 12 12
SIN3/HDAC complex/NCoR1 -0.001 0.078 -10000 0 -0.37 11 11
TFCP2 0.023 0.002 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
MBD3 0.021 0.027 -10000 0 -0.56 1 1
MBD2 0.022 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.041 -10000 0 -0.33 4 4
HDAC3 0.022 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 -0.006 0.12 -10000 0 -0.41 42 42
GATA1/HDAC5 -0.006 0.12 -10000 0 -0.41 42 42
GATA2/HDAC5 -0.011 0.13 -10000 0 -0.4 46 46
HDAC5/BCL6/BCoR 0.027 0.023 -10000 0 -10000 0 0
HDAC9 0.022 0.032 0.24 3 -0.56 1 4
Glucocorticoid receptor/Hsp90/HDAC6 0.042 0.015 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.031 0.01 -10000 0 -10000 0 0
HDAC5/YWHAB 0.033 0.008 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.01 0.003 -10000 0 -10000 0 0
GATA2 -0.034 0.17 -10000 0 -0.56 46 46
HDAC4/RFXANK 0.032 0.008 -10000 0 -10000 0 0
BCOR 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.022 0.005 -10000 0 -10000 0 0
HDAC5 0.023 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.026 0.05 -10000 0 -0.41 6 6
Histones 0.018 0.036 -10000 0 -0.26 3 3
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
HDAC4 0.022 0.004 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.031 0.01 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.008 -10000 0 -10000 0 0
HDAC7 0.023 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.032 0.009 -10000 0 -10000 0 0
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
HDAC6 0.023 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.032 0.008 -10000 0 -10000 0 0
CAMK4 0.019 0.038 -10000 0 -0.56 2 2
Tubulin/HDAC6 0.044 0.011 -10000 0 -10000 0 0
SUMO1 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.022 0.004 -10000 0 -10000 0 0
GATA1 -0.033 0.16 -10000 0 -0.56 42 42
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.005 -10000 0 -10000 0 0
NR3C1 0.021 0.006 -10000 0 -10000 0 0
SUMO1/HDAC4 0.032 0.029 -10000 0 -0.24 1 1
SRF 0.022 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.007 -10000 0 -10000 0 0
Tubulin 0.033 0.006 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.032 0.009 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
RANGAP1 0.022 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.02 0.017 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.042 0.021 -10000 0 -0.34 1 1
HDAC4/SRF 0.04 0.03 -10000 0 -0.36 2 2
HDAC4/ER alpha 0.014 0.091 -10000 0 -0.41 21 21
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.018 0.036 -10000 0 -0.26 3 3
cell motility 0.044 0.011 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.022 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.032 0.009 -10000 0 -10000 0 0
BCL6 0.014 0.011 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.022 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.032 0.009 -10000 0 -10000 0 0
ESR1 -0.002 0.12 -10000 0 -0.56 21 21
HDAC6/HDAC11 0.031 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.029 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
MEF2C 0.013 0.069 -10000 0 -0.56 7 7
RAN 0.023 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.056 0.05 -10000 0 -0.3 7 7
GNG2 0.016 0.059 -10000 0 -0.56 5 5
NCOR2 0.022 0.026 -10000 0 -0.56 1 1
TUBB2A 0.022 0.004 -10000 0 -10000 0 0
HDAC11 0.021 0.006 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
ANKRA2 0.021 0.006 -10000 0 -10000 0 0
RFXANK 0.022 0.004 -10000 0 -10000 0 0
nuclear import -0.026 0.009 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.033 0.007 -10000 0 -10000 0 0
ATM 0.022 0.004 -10000 0 -10000 0 0
UBE2D3 0.022 0.005 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
ATR 0.018 0.009 -10000 0 -10000 0 0
UBE2L3 0.021 0.006 -10000 0 -10000 0 0
FANCD2 0.012 0.007 -10000 0 -10000 0 0
protein ubiquitination 0.08 0.057 -10000 0 -10000 0 0
XRCC5 0.022 0.004 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.041 0.016 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
DNA-PK 0.043 0.013 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.011 0.1 0.3 1 -0.49 15 16
FANCF 0.022 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.003 -10000 0 -10000 0 0
CCNE1 0.078 0.11 0.27 107 -10000 0 107
CDK2/Cyclin E1 0.07 0.073 0.26 30 -10000 0 30
FANCG 0.022 0.024 0.37 2 -10000 0 2
BRCA1/BACH1/BARD1 0.033 0.007 -10000 0 -10000 0 0
FANCE 0.023 0.003 -10000 0 -10000 0 0
FANCC 0.022 0.004 -10000 0 -10000 0 0
NBN 0.022 0.005 -10000 0 -10000 0 0
FANCA 0.023 0.019 0.3 2 -10000 0 2
DNA repair 0.014 0.082 0.28 8 -0.39 7 15
BRCA1/BARD1/ubiquitin 0.033 0.007 -10000 0 -10000 0 0
BARD1/DNA-PK 0.054 0.017 -10000 0 -10000 0 0
FANCL 0.022 0.017 0.37 1 -10000 0 1
mRNA polyadenylation -0.033 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.02 0.033 -10000 0 -0.27 1 1
BRCA1/BACH1/BARD1/TopBP1 0.039 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.044 0.026 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.044 0.011 -10000 0 -10000 0 0
BRCA1/BACH1 0.023 0.003 -10000 0 -10000 0 0
BARD1 0.022 0.004 -10000 0 -10000 0 0
PCNA 0.022 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.043 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.042 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.07 0.048 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.06 0.023 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.033 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.033 0.012 -10000 0 -10000 0 0
FA complex 0.032 0.042 0.41 1 -0.26 2 3
BARD1/EWS 0.032 0.009 -10000 0 -10000 0 0
RBBP8 -0.01 0.003 -10000 0 -10000 0 0
TP53 0.022 0.006 -10000 0 -10000 0 0
TOPBP1 0.02 0.008 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.042 0.025 -10000 0 -10000 0 0
BRCA1/BARD1 0.089 0.062 -10000 0 -10000 0 0
CSTF1 0.023 0.003 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.017 0.003 -10000 0 -10000 0 0
CDK2 0.023 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.052 0.074 0.24 67 -10000 0 67
RAD50 0.021 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.033 0.007 -10000 0 -10000 0 0
EWSR1 0.022 0.004 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.032 0.007 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.021 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0 0.055 -10000 0 -0.38 3 3
IRAK/TOLLIP 0.023 0.007 -10000 0 -10000 0 0
IKBKB 0.022 0.017 0.37 1 -10000 0 1
IKBKG 0.022 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.029 0.099 0.3 2 -0.41 19 21
IL1A 0.009 0.12 0.24 20 -0.56 19 39
IL1B -0.02 0.062 -10000 0 -0.41 12 12
IRAK/TRAF6/p62/Atypical PKCs 0.03 0.032 -10000 0 -10000 0 0
IL1R2 0.034 0.048 0.24 24 -10000 0 24
IL1R1 0.022 0.026 -10000 0 -0.56 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.028 0.062 0.3 3 -10000 0 3
TOLLIP 0.022 0.004 -10000 0 -10000 0 0
TICAM2 0.015 0.059 -10000 0 -0.56 5 5
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.034 0.055 0.38 1 -0.33 1 2
JUN -0.011 0.038 0.25 2 -10000 0 2
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.022 0.051 -10000 0 -0.3 8 8
IL1 alpha/IL1R1/IL1RAP/MYD88 0.025 0.075 -10000 0 -0.35 12 12
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.031 0.075 -10000 0 -0.33 12 12
IL1 beta fragment/IL1R1/IL1RAP 0.014 0.05 -10000 0 -0.32 8 8
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.008 0.041 0.26 2 -10000 0 2
IRAK1 -0.013 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 0.033 0.044 0.26 1 -0.57 2 3
IRAK4 0.023 0.003 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
TRAF6 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.055 -10000 0 -0.38 3 3
CHUK 0.022 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.014 0.05 -10000 0 -0.32 8 8
IL1 beta/IL1R2 0.027 0.07 0.3 2 -0.36 12 14
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.017 0.045 -10000 0 -0.29 6 6
IRAK3 0.008 0.09 -10000 0 -0.56 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.022 0.064 -10000 0 -0.3 13 13
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.062 -10000 0 -0.32 13 13
IL1 alpha/IL1R1/IL1RAP 0.019 0.077 -10000 0 -0.38 12 12
RELA 0.023 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.006 -10000 0 -10000 0 0
MYD88 0.021 0.006 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.039 0.023 -10000 0 -10000 0 0
IL1RAP 0.014 0.011 -10000 0 -10000 0 0
UBE2N 0.023 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 -0.003 0.05 -10000 0 -10000 0 0
CASP1 0.02 0.037 -10000 0 -0.56 2 2
IL1RN/IL1R2 0.041 0.047 0.29 3 -0.41 2 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.02 0.051 -10000 0 -0.31 8 8
TMEM189-UBE2V1 0.01 0.019 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.07 -10000 0 -0.41 6 6
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL1RN 0.023 0.044 0.27 4 -0.56 2 6
TRAF6/TAK1/TAB1/TAB2 0.041 0.012 -10000 0 -10000 0 0
MAP2K6 -0.005 0.044 0.27 2 -10000 0 2
FoxO family signaling

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
G6PC 0.002 0.045 -10000 0 -10000 0 0
PLK1 0.066 0.12 -10000 0 -0.96 1 1
CDKN1B 0.072 0.1 0.3 4 -0.37 10 14
FOXO3 0.071 0.11 -10000 0 -0.73 3 3
KAT2B 0.028 0.017 -10000 0 -10000 0 0
FOXO1/SIRT1 0.019 0.037 -10000 0 -10000 0 0
CAT 0.051 0.14 -10000 0 -1.1 3 3
CTNNB1 0.021 0.006 -10000 0 -10000 0 0
AKT1 0.03 0.017 -10000 0 -10000 0 0
FOXO1 0.007 0.044 -10000 0 -10000 0 0
MAPK10 0.018 0.05 0.19 18 -0.3 7 25
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.035 0.061 0.36 1 -10000 0 1
response to oxidative stress 0.01 0.01 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.071 0.1 -10000 0 -0.92 1 1
XPO1 0.021 0.007 -10000 0 -10000 0 0
EP300 0.023 0.004 -10000 0 -10000 0 0
BCL2L11 0.033 0.044 -10000 0 -0.78 1 1
FOXO1/SKP2 0.017 0.04 0.25 2 -10000 0 2
mol:GDP 0.01 0.01 -10000 0 -10000 0 0
RAN 0.024 0.002 -10000 0 -10000 0 0
GADD45A 0.051 0.15 -10000 0 -0.63 15 15
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.014 0.12 -10000 0 -0.45 21 21
MST1 0.028 0.02 0.24 1 -10000 0 1
CSNK1D 0.022 0.004 -10000 0 -10000 0 0
CSNK1E 0.022 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.017 0.088 -10000 0 -0.41 13 13
YWHAB 0.022 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.032 0.19 17 -10000 0 17
MAPK9 0.022 0.033 0.19 17 -10000 0 17
YWHAG 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.005 -10000 0 -10000 0 0
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
SIRT1 0.021 0.013 -10000 0 -10000 0 0
SOD2 0.062 0.099 -10000 0 -0.62 2 2
RBL2 0.037 0.2 -10000 0 -0.81 23 23
RAL/GDP 0.038 0.014 -10000 0 -10000 0 0
CHUK 0.029 0.016 -10000 0 -10000 0 0
Ran/GTP 0.019 0.002 -10000 0 -10000 0 0
CSNK1G2 0.022 0.004 -10000 0 -10000 0 0
RAL/GTP 0.04 0.012 -10000 0 -10000 0 0
CSNK1G1 0.023 0.002 -10000 0 -10000 0 0
FASLG -0.022 0.28 -10000 0 -1.3 21 21
SKP2 0.02 0.026 0.33 3 -10000 0 3
USP7 0.023 0.005 -10000 0 -10000 0 0
IKBKB 0.028 0.024 0.38 1 -10000 0 1
CCNB1 0.063 0.1 -10000 0 -0.96 1 1
FOXO1-3a-4/beta catenin 0.072 0.09 0.33 2 -0.39 1 3
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.04 0.25 2 -10000 0 2
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
SGK1 0.03 0.016 -10000 0 -10000 0 0
CSNK1G3 0.021 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.01 -10000 0 -10000 0 0
ZFAND5 0.031 0.068 0.39 3 -10000 0 3
SFN 0.039 0.071 0.24 45 -0.38 3 48
CDK2 0.023 0.003 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.026 0.09 -10000 0 -0.4 14 14
CREBBP 0.022 0.005 -10000 0 -10000 0 0
FBXO32 0.066 0.12 -10000 0 -0.97 1 1
BCL6 0.054 0.097 -10000 0 -0.69 1 1
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.023 0.005 -10000 0 -10000 0 0
YWHAH 0.022 0.004 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.009 0.09 -10000 0 -0.34 26 26
KLHL20 0.016 0.058 0.17 1 -0.25 9 10
CYFIP2 0.009 0.082 -10000 0 -0.56 10 10
Rac1/GDP 0.013 0.07 0.25 2 -10000 0 2
ENAH -0.009 0.095 -10000 0 -0.34 29 29
AP1M1 0.022 0.004 -10000 0 -10000 0 0
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.014 0.029 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.036 -10000 0 -0.19 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.026 -10000 0 -0.33 1 1
RAPGEF1 -0.004 0.08 -10000 0 -0.32 1 1
CTNND1 0.023 0.001 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.005 0.098 -10000 0 -0.34 30 30
CRK -0.004 0.072 -10000 0 -0.32 12 12
E-cadherin/gamma catenin/alpha catenin 0.043 0.014 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.031 0.022 -10000 0 -0.41 1 1
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
NCKAP1 0.022 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.014 -10000 0 -10000 0 0
DLG1 -0.001 0.064 -10000 0 -0.34 14 14
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.011 -10000 0 -10000 0 0
MLLT4 0.022 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.041 0.015 -10000 0 -10000 0 0
PI3K -0.009 0.014 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.032 0.009 -10000 0 -10000 0 0
TIAM1 0.021 0.027 -10000 0 -0.56 1 1
E-cadherin(dimer)/Ca2+ 0.049 0.017 -10000 0 -10000 0 0
AKT1 0.005 0.031 0.12 2 -10000 0 2
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
CDH1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.065 0.25 2 -10000 0 2
actin cytoskeleton organization 0.015 0.046 0.15 5 -0.18 8 13
CDC42/GDP 0.016 0.068 0.25 2 -10000 0 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.014 0.005 -10000 0 -10000 0 0
ITGB7 0.022 0.026 -10000 0 -0.56 1 1
RAC1 0.022 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.053 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.037 0.013 -10000 0 -10000 0 0
mol:GDP 0.002 0.074 0.26 2 -0.31 1 3
CDC42/GTP/IQGAP1 0.029 0.008 -10000 0 -10000 0 0
JUP 0.023 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.023 0.064 0.27 1 -10000 0 1
RAC1/GTP/IQGAP1 0.03 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.032 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.009 0.04 0.14 4 -0.24 6 10
NME1 0.023 0.01 0.24 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.006 0.091 -10000 0 -0.34 26 26
regulation of cell-cell adhesion 0.009 0.024 -10000 0 -10000 0 0
WASF2 0.008 0.025 -10000 0 -10000 0 0
Rap1/GTP 0.018 0.04 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.028 -10000 0 -0.31 1 1
CCND1 0.01 0.048 0.16 4 -0.3 6 10
VAV2 -0.011 0.12 -10000 0 -0.64 9 9
RAP1/GDP 0.02 0.055 0.25 1 -10000 0 1
adherens junction assembly -0.007 0.089 -10000 0 -0.33 28 28
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.022 0.004 -10000 0 -10000 0 0
PIP5K1C 0.022 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.044 0.026 -10000 0 -0.3 1 1
E-cadherin/beta catenin 0.01 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.008 0.092 -10000 0 -0.34 26 26
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
Rac1/GTP -0.013 0.077 -10000 0 -0.42 10 10
E-cadherin/beta catenin/alpha catenin 0.042 0.015 -10000 0 -10000 0 0
ITGAE 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.006 0.1 -10000 0 -0.35 30 30
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.008 0.003 -10000 0 -10000 0 0
mol:DAG -0.01 0.021 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.022 -10000 0 -10000 0 0
HIF1A 0.026 0.005 -10000 0 -10000 0 0
GAB1 0.022 0.006 -10000 0 -10000 0 0
AKT1 0.054 0.078 0.31 3 -10000 0 3
PLCG1 -0.01 0.022 -10000 0 -10000 0 0
NOS3 0.034 0.052 0.31 1 -10000 0 1
CBL 0.022 0.004 -10000 0 -10000 0 0
mol:NO 0.04 0.075 0.42 6 -0.4 2 8
FLT1 0.011 0.004 -10000 0 -10000 0 0
PGF 0.033 0.049 0.24 25 -10000 0 25
VEGFR1 homodimer/NRP2/VEGFR121 0.033 0.03 -10000 0 -0.32 2 2
CALM1 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
eNOS/Hsp90 0.043 0.071 0.3 1 -0.38 3 4
endothelial cell proliferation 0.008 0.054 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.021 -10000 0 -10000 0 0
MAPK3 -0.011 0.038 0.34 3 -10000 0 3
MAPK1 -0.011 0.037 0.34 3 -10000 0 3
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
PLGF homodimer 0.033 0.049 0.24 25 -10000 0 25
PRKACA 0.022 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.13 0.25 -10000 0 -0.56 127 127
VEGFA homodimer 0.022 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.012 0.042 0.32 5 -10000 0 5
PI3K 0.028 0.035 -10000 0 -10000 0 0
PRKCA -0.013 0.024 -10000 0 -0.29 1 1
PRKCB -0.024 0.061 -10000 0 -0.31 17 17
VEGFR1 homodimer/PLGF homodimer 0.03 0.033 0.26 1 -10000 0 1
VEGFA 0.022 0.004 -10000 0 -10000 0 0
VEGFB 0.023 0.002 -10000 0 -10000 0 0
mol:IP3 -0.01 0.021 -10000 0 -10000 0 0
RASA1 -0.008 0.02 -10000 0 -10000 0 0
NRP2 0.019 0.046 -10000 0 -0.56 3 3
VEGFR1 homodimer 0.011 0.004 -10000 0 -10000 0 0
VEGFB homodimer 0.023 0.002 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.027 0.15 0.46 4 -0.44 13 17
PTPN11 0.023 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.033 -10000 0 -10000 0 0
mol:L-citrulline 0.04 0.075 0.42 6 -0.4 2 8
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.046 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.03 0.017 -10000 0 -10000 0 0
CD2AP 0.022 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.034 0.04 -10000 0 -10000 0 0
PDPK1 0.056 0.088 0.34 2 -10000 0 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.035 0.013 -10000 0 -10000 0 0
mol:NADP 0.04 0.075 0.42 6 -0.4 2 8
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.022 0.03 -10000 0 -0.34 3 3
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.022 0.004 -9999 0 -10000 0 0
ITGB7 0.022 0.026 -9999 0 -0.56 1 1
ITGA4 0.017 0.059 -9999 0 -0.56 5 5
alpha4/beta7 Integrin 0.028 0.05 -9999 0 -0.41 6 6
alpha4/beta1 Integrin 0.028 0.046 -9999 0 -0.41 5 5
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.04 0.11 -10000 0 -0.4 11 11
CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
AKT1 0.022 0.005 -10000 0 -10000 0 0
AKT2 0.021 0.007 -10000 0 -10000 0 0
STXBP4 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.028 0.12 0.44 1 -0.4 16 17
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
TBC1D4 -0.009 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.022 0.004 -10000 0 -10000 0 0
YWHAB 0.022 0.004 -10000 0 -10000 0 0
SNARE/Synip 0.043 0.014 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
ASIP 0.008 0.028 0.3 2 -10000 0 2
PRKCI 0.013 0.011 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
RHOQ 0.022 0.006 -10000 0 -10000 0 0
GYS1 0.005 0.003 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
TRIP10 0.022 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.04 -10000 0 -0.3 2 2
VAMP2 0.022 0.006 -10000 0 -10000 0 0
SLC2A4 0.027 0.13 0.45 1 -0.45 16 17
STX4 0.023 0.003 -10000 0 -10000 0 0
GSK3B 0.013 0.007 -10000 0 -10000 0 0
SFN 0.039 0.071 0.24 45 -0.38 3 48
LNPEP 0.021 0.006 -10000 0 -10000 0 0
YWHAE 0.022 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.036 -10000 0 -0.3 6 6
CRKL 0.021 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
ITGA4 0.017 0.059 -10000 0 -0.56 5 5
alpha4/beta7 Integrin/MAdCAM1 0.048 0.047 -10000 0 -0.31 6 6
EPO 0.017 0.029 0.24 6 -10000 0 6
alpha4/beta7 Integrin 0.028 0.05 -10000 0 -0.41 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.046 -10000 0 -0.41 5 5
EPO/EPOR (dimer) 0.032 0.019 -10000 0 -10000 0 0
lamellipodium assembly 0.043 0.12 -10000 0 -0.61 9 9
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
JAK2 0.015 0.029 -10000 0 -0.32 3 3
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
MADCAM1 0.02 0.023 0.24 4 -10000 0 4
cell adhesion 0.046 0.046 -10000 0 -0.31 6 6
CRKL/CBL 0.031 0.01 -10000 0 -10000 0 0
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC -0.012 0.053 0.18 14 -0.4 5 19
ITGB7 0.022 0.026 -10000 0 -0.56 1 1
RAC1 0.022 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.038 0.06 -10000 0 -0.45 6 6
p130Cas/Crk/Dock1 0.023 0.049 -10000 0 -0.37 4 4
VCAM1 0.02 0.049 0.24 3 -0.56 3 6
RHOA 0.021 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.038 -10000 0 -0.32 4 4
BCAR1 -0.013 0.051 0.18 14 -0.38 5 19
EPOR 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.043 0.12 -10000 0 -0.64 9 9
Regulation of Telomerase

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
Telomerase catalytic core complex 0.054 0.11 0.38 1 -0.54 3 4
RAD9A 0.022 0.004 -10000 0 -10000 0 0
AP1 -0.015 0.14 -10000 0 -0.41 54 54
IFNAR2 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.007 0.057 -10000 0 -0.27 14 14
ER alpha/Oestrogen 0 0.087 -10000 0 -0.4 22 22
NFX1/SIN3/HDAC complex 0.013 0.059 -10000 0 -0.29 12 12
EGF 0.016 0.071 0.24 3 -0.56 7 10
SMG5 0.022 0.005 -10000 0 -10000 0 0
SMG6 0.022 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.011 -10000 0 -10000 0 0
TERT/c-Abl 0.059 0.1 -10000 0 -0.5 3 3
SAP18 0.022 0.006 -10000 0 -10000 0 0
MRN complex 0.041 0.016 -10000 0 -10000 0 0
WT1 0.037 0.05 0.24 26 -10000 0 26
WRN 0.021 0.007 -10000 0 -10000 0 0
SP1 0.027 0.008 -10000 0 -10000 0 0
SP3 0.024 0.006 -10000 0 -10000 0 0
TERF2IP 0.022 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.061 0.095 -10000 0 -0.56 1 1
Mad/Max 0.035 0.012 -10000 0 -10000 0 0
TERT 0.055 0.11 0.38 1 -0.55 3 4
CCND1 0.066 0.17 0.54 1 -1.1 6 7
MAX 0.023 0.006 -10000 0 -10000 0 0
RBBP7 0.023 0.005 -10000 0 -10000 0 0
RBBP4 0.023 0.004 -10000 0 -10000 0 0
TERF2 0.019 0.008 -10000 0 -10000 0 0
PTGES3 0.023 0.002 -10000 0 -10000 0 0
SIN3A 0.023 0.002 -10000 0 -10000 0 0
Telomerase/911 0.045 0.073 -10000 0 -0.5 3 3
CDKN1B 0.011 0.033 -10000 0 -0.34 4 4
RAD1 0.018 0.009 -10000 0 -10000 0 0
XRCC5 0.022 0.004 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.03 0.011 -10000 0 -10000 0 0
UBE3A 0.024 0.004 -10000 0 -10000 0 0
JUN 0.023 0.006 -10000 0 -10000 0 0
E6 0.001 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.005 -10000 0 -10000 0 0
FOS -0.041 0.18 -10000 0 -0.56 54 54
IFN-gamma/IRF1 0.034 0.043 -10000 0 -0.4 4 4
PARP2 0.022 0.005 -10000 0 -10000 0 0
BLM 0.028 0.035 0.26 10 -10000 0 10
Telomerase 0.024 0.057 -10000 0 -10000 0 0
IRF1 0.025 0.007 -10000 0 -10000 0 0
ESR1 -0.002 0.12 -10000 0 -0.56 21 21
KU/TER 0.032 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.032 0.009 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.018 0.056 -10000 0 -0.3 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.018 0.057 -10000 0 -0.3 4 4
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.026 0.007 -10000 0 -10000 0 0
ATM 0.011 0.013 -10000 0 -10000 0 0
SMAD3 -0.012 0.004 -10000 0 -10000 0 0
ABL1 0.023 0.003 -10000 0 -10000 0 0
MXD1 0.023 0.006 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
HUS1 0.022 0.005 -10000 0 -10000 0 0
RPS6KB1 0.023 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.063 0.12 -10000 0 -0.59 4 4
NR2F2 0.019 0.006 -10000 0 -10000 0 0
MAPK3 -0.001 0.013 -10000 0 -10000 0 0
MAPK1 -0.001 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
HNRNPC 0.022 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.013 -10000 0 -10000 0 0
NBN 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.023 0.082 0.36 11 -0.56 6 17
mol:Oestrogen 0.001 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.026 0.082 0.27 8 -0.44 12 20
MYC 0.022 0.009 -10000 0 -10000 0 0
IL2 0.023 0.009 -10000 0 -10000 0 0
KU 0.032 0.008 -10000 0 -10000 0 0
RAD50 0.021 0.006 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
TGFB1 0.021 0.005 -10000 0 -10000 0 0
TRF2/BLM 0.034 0.024 0.25 2 -10000 0 2
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.068 0.1 -10000 0 -0.54 2 2
SP1/HDAC2 0.042 0.013 -10000 0 -10000 0 0
PINX1 0.02 0.007 -10000 0 -10000 0 0
Telomerase/EST1A 0.061 0.094 -10000 0 -0.54 1 1
Smad3/Myc 0.019 0.008 -10000 0 -10000 0 0
911 complex 0.035 0.021 -10000 0 -10000 0 0
IFNG 0.021 0.054 0.24 2 -0.55 4 6
Telomerase/PinX1 0.056 0.094 -10000 0 -0.54 1 1
Telomerase/AKT1/mTOR/p70S6K 0.022 0.095 -10000 0 -0.5 11 11
SIN3B 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.005 -10000 0 -10000 0 0
Telomerase/EST1B 0.06 0.093 -10000 0 -0.56 1 1
response to DNA damage stimulus 0.003 0.016 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.056 0.023 -10000 0 -10000 0 0
TRF2/WRN 0.029 0.014 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.059 0.094 -10000 0 -0.54 1 1
E2F1 0.024 0.008 -10000 0 -10000 0 0
ZNFX1 0.023 0.004 -10000 0 -10000 0 0
PIF1 0.043 0.063 0.24 47 -10000 0 47
NCL 0.022 0.004 -10000 0 -10000 0 0
DKC1 0.022 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.01 -10000 0 -10000 0 0
TRAF2/ASK1 0.03 0.007 -10000 0 -10000 0 0
ATM 0.022 0.004 -10000 0 -10000 0 0
MAP2K3 -0.001 0.095 0.3 1 -0.35 20 21
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0 0.078 0.31 1 -0.35 12 13
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.018 0.053 -10000 0 -0.56 4 4
TXN 0.005 0.001 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
GADD45A 0.022 0.004 -10000 0 -10000 0 0
GADD45B 0.007 0.094 -10000 0 -0.56 13 13
MAP3K1 0.021 0.006 -10000 0 -10000 0 0
MAP3K6 0.022 0.004 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
MAP3K4 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.008 -10000 0 -10000 0 0
TAK1/TAB family -0.003 0.018 -10000 0 -0.14 5 5
RAC1/OSM/MEKK3 0.042 0.011 -10000 0 -10000 0 0
TRAF2 0.022 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.017 0.08 -10000 0 -0.33 9 9
TRAF6 0.005 0.001 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.047 0.074 0.25 56 -0.29 1 57
CCM2 0.022 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.044 0.046 0.24 4 -0.16 1 5
MAPK11 0.022 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.054 0.046 0.24 4 -10000 0 4
OSM/MEKK3 0.032 0.008 -10000 0 -10000 0 0
TAOK1 0.01 0.011 -10000 0 -0.22 1 1
TAOK2 0.01 0.002 -10000 0 -10000 0 0
TAOK3 0.011 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.022 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
MAP3K10 0.022 0.017 0.37 1 -10000 0 1
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.013 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.037 0.07 -10000 0 -0.32 16 16
Canonical NF-kappaB 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
FBXW11 0.023 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.09 0.26 1 -0.34 11 12
ERC1 0.021 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.023 -10000 0 -0.41 1 1
NFKBIA -0.006 0.017 -10000 0 -10000 0 0
BIRC2 0.022 0.004 -10000 0 -10000 0 0
IKBKB 0.022 0.017 0.37 1 -10000 0 1
RIPK2 0.022 0.005 -10000 0 -10000 0 0
IKBKG 0.016 0.025 -10000 0 -10000 0 0
IKK complex/A20 0.023 0.1 -10000 0 -0.42 11 11
NEMO/A20/RIP2 0.022 0.005 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
NEMO/ATM 0.015 0.099 -10000 0 -0.38 23 23
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.028 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.02 0.088 -10000 0 -0.42 9 9
BCL10/MALT1/TRAF6 0.043 0.013 -10000 0 -10000 0 0
NOD2 0.02 0.027 -10000 0 -0.56 1 1
NFKB1 0.023 0.005 -10000 0 -10000 0 0
RELA 0.024 0.002 -10000 0 -10000 0 0
MALT1 0.022 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.031 0.009 -10000 0 -10000 0 0
ATM 0.022 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.022 0.06 -10000 0 -0.37 10 10
TRAF6 0.022 0.004 -10000 0 -10000 0 0
PRKCA 0.02 0.037 -10000 0 -0.56 2 2
CHUK 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.005 -10000 0 -10000 0 0
TNF 0.011 0.083 0.24 1 -0.56 10 11
NF kappa B1 p50/RelA 0.046 0.016 -10000 0 -10000 0 0
BCL10 0.022 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.017 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
IKK complex 0.024 0.097 -10000 0 -0.43 11 11
CYLD 0.022 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.031 0.1 -10000 0 -0.47 10 10
Arf6 downstream 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
PLAUR 0.016 0.017 -10000 0 -10000 0 0
regulation of axonogenesis -0.005 0.021 0.24 2 -0.17 3 5
myoblast fusion -0.027 0.036 0.34 1 -10000 0 1
mol:GTP 0.016 0.027 -10000 0 -0.15 8 8
regulation of calcium-dependent cell-cell adhesion -0.045 0.029 -10000 0 -10000 0 0
ARF1/GTP 0.027 0.027 -10000 0 -10000 0 0
mol:GM1 0.007 0.02 -10000 0 -10000 0 0
mol:Choline 0.005 0.02 0.23 3 -10000 0 3
lamellipodium assembly 0.009 0.043 -10000 0 -0.33 6 6
MAPK3 0.017 0.017 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.046 0.029 -10000 0 -10000 0 0
ARF1 0.022 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.027 0.036 -10000 0 -0.34 1 1
ARF1/GDP 0.025 0.047 -10000 0 -0.27 3 3
ARF6 0.03 0.012 -10000 0 -10000 0 0
RAB11A 0.023 0.002 -10000 0 -10000 0 0
TIAM1 0.022 0.025 -10000 0 -0.52 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.017 -10000 0 -10000 0 0
actin filament bundle formation -0.025 0.043 0.25 3 -10000 0 3
KALRN 0.007 0.03 -10000 0 -0.3 4 4
RAB11FIP3/RAB11A 0.033 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.044 -10000 0 -0.25 3 3
NME1 0.024 0.012 0.24 1 -10000 0 1
Rac1/GDP 0.026 0.045 -10000 0 -0.25 3 3
substrate adhesion-dependent cell spreading 0.016 0.027 -10000 0 -0.15 8 8
cortical actin cytoskeleton organization 0.009 0.044 -10000 0 -0.33 6 6
RAC1 0.022 0.004 -10000 0 -10000 0 0
liver development 0.016 0.027 -10000 0 -0.15 8 8
ARF6/GTP 0.016 0.027 -10000 0 -0.15 8 8
RhoA/GTP 0.026 0.025 -10000 0 -10000 0 0
mol:GDP 0.007 0.027 -10000 0 -0.21 7 7
ARF6/GTP/RAB11FIP3/RAB11A 0.04 0.027 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
PLD1 0.009 0.027 0.28 3 -10000 0 3
RAB11FIP3 0.022 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.009 0.043 -10000 0 -0.33 6 6
ruffle organization 0.005 0.021 0.17 3 -0.24 2 5
regulation of epithelial cell migration 0.016 0.027 -10000 0 -0.15 8 8
PLD2 0.015 0.018 -10000 0 -10000 0 0
PIP5K1A 0.005 0.021 0.17 3 -0.24 2 5
mol:Phosphatidic acid 0.005 0.02 0.23 3 -10000 0 3
Rac1/GTP 0.009 0.044 -10000 0 -0.34 6 6
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.009 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.031 0.014 -10000 0 -10000 0 0
CDKN1B 0.019 0.064 -10000 0 -0.6 2 2
CDKN1A 0.015 0.048 -10000 0 -0.6 1 1
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
FOXO3 0.014 0.057 -10000 0 -0.6 2 2
AKT1 0.005 0.052 -10000 0 -0.43 5 5
BAD 0.023 0.002 -10000 0 -10000 0 0
AKT3 0.01 0.016 -10000 0 -0.34 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.013 0.057 -10000 0 -0.6 2 2
AKT1/ASK1 0.032 0.064 -10000 0 -0.59 2 2
BAD/YWHAZ 0.042 0.014 -10000 0 -10000 0 0
RICTOR 0.018 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.006 -10000 0 -10000 0 0
JNK cascade -0.031 0.062 0.57 2 -10000 0 2
TSC1 0.012 0.057 -10000 0 -0.6 2 2
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.035 0.067 -10000 0 -0.59 2 2
EP300 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0.006 0.054 -10000 0 -0.41 6 6
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.016 0.035 -10000 0 -0.3 1 1
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
TBC1D4 0.003 0.001 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
MAPKAP1 0.023 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.025 0.068 0.37 6 -0.29 1 7
YWHAH 0.022 0.004 -10000 0 -10000 0 0
AKT1S1 0.015 0.046 -10000 0 -0.6 1 1
CASP9 0.014 0.045 -10000 0 -0.6 1 1
YWHAB 0.022 0.004 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.072 0.3 1 -0.58 2 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
YWHAE 0.022 0.005 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.012 0.054 0.25 1 -0.42 4 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.052 -10000 0 -0.33 9 9
CHUK 0.015 0.043 -10000 0 -0.6 1 1
BAD/BCL-XL 0.033 0.064 -10000 0 -0.58 2 2
mTORC2 0.023 0.012 -10000 0 -10000 0 0
AKT2 0.01 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.031 0.087 0.3 1 -0.49 6 7
PDPK1 0.022 0.004 -10000 0 -10000 0 0
MDM2 0.016 0.062 -10000 0 -0.5 3 3
MAPKKK cascade -0.034 0.066 0.57 2 -10000 0 2
MDM2/Cbp/p300 0.048 0.074 0.3 1 -0.54 2 3
TSC1/TSC2 0.012 0.054 0.25 1 -0.57 2 3
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.071 0.29 1 -0.51 2 3
glucose import -0.004 0.028 0.2 2 -0.31 3 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.015 0.049 0.3 1 -0.35 4 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.005 0.024 -10000 0 -0.31 3 3
GSK3A 0.016 0.048 -10000 0 -0.6 1 1
FOXO1 0.015 0.05 -10000 0 -0.6 2 2
GSK3B 0.025 0.072 -10000 0 -0.6 2 2
SFN 0.039 0.071 0.24 45 -0.38 3 48
G1/S transition of mitotic cell cycle 0.036 0.078 0.3 8 -0.59 1 9
p27Kip1/14-3-3 family 0.028 0.055 -10000 0 -0.54 2 2
PRKACA 0.022 0.004 -10000 0 -10000 0 0
KPNA1 0.02 0.007 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
RHEB 0.022 0.004 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.021 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.01 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
ITGA4 0.017 0.059 -10000 0 -0.56 5 5
RAC1 0.022 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.028 0.05 -10000 0 -0.41 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.04 0.036 -10000 0 -0.36 3 3
alpha4/beta7 Integrin/Paxillin 0.031 0.035 -10000 0 -0.33 4 4
lamellipodium assembly -0.015 0.1 -10000 0 -0.4 25 25
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
TLN1 0.021 0.007 -10000 0 -10000 0 0
PXN -0.01 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.032 -10000 0 -0.29 3 3
cell adhesion 0.038 0.031 -10000 0 -0.31 2 2
CRKL/CBL 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.031 0.031 -10000 0 -0.33 3 3
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.022 0.026 -10000 0 -0.56 1 1
ARF6/GDP 0.022 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.041 0.049 -10000 0 -0.38 5 5
p130Cas/Crk/Dock1 0.042 0.015 -10000 0 -10000 0 0
VCAM1 0.02 0.049 0.24 3 -0.56 3 6
alpha4/beta1 Integrin/Paxillin/Talin 0.04 0.031 -10000 0 -0.31 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.043 0.033 -10000 0 -0.31 3 3
BCAR1 0.022 0.006 -10000 0 -10000 0 0
mol:GDP -0.041 0.032 0.31 3 -10000 0 3
CBL 0.022 0.004 -10000 0 -10000 0 0
PRKACA 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.04 0.031 -10000 0 -0.31 2 2
Rac1/GTP -0.017 0.11 -10000 0 -0.45 25 25
Arf6 trafficking events

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
SLC2A4 0.018 0.046 -10000 0 -0.56 3 3
CLTC 0.019 0.07 -10000 0 -0.38 12 12
calcium ion-dependent exocytosis 0.006 0.024 -10000 0 -0.24 2 2
Dynamin 2/GTP 0.02 0.006 -10000 0 -10000 0 0
EXOC4 0.022 0.004 -10000 0 -10000 0 0
CD59 0.004 0.041 -10000 0 -0.33 6 6
CPE 0.009 0.017 -10000 0 -0.35 1 1
CTNNB1 0.021 0.006 -10000 0 -10000 0 0
membrane fusion 0.007 0.015 -10000 0 -10000 0 0
CTNND1 -0.007 0.033 0.18 15 -10000 0 15
DNM2 0.022 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.005 0.043 0.25 2 -0.33 3 5
TSHR 0.012 0.017 -10000 0 -10000 0 0
INS 0.001 0.1 -10000 0 -0.54 16 16
BIN1 0.02 0.037 -10000 0 -0.56 2 2
mol:Choline 0.007 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.006 -10000 0 -10000 0 0
JUP 0.003 0.044 -10000 0 -0.34 7 7
ASAP2/amphiphysin II 0.039 0.026 -10000 0 -0.31 2 2
ARF6/GTP 0.016 0.004 -10000 0 -10000 0 0
CDH1 0.005 0.035 -10000 0 -0.35 4 4
clathrin-independent pinocytosis 0.016 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.022 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.016 0.004 -10000 0 -10000 0 0
EXOC2 0.022 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.006 0.044 -10000 0 -0.32 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.023 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.053 0.32 5 -10000 0 5
positive regulation of phagocytosis 0.01 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.029 0.008 -10000 0 -10000 0 0
ACAP1 0.009 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.04 0.097 -10000 0 -0.46 7 7
clathrin heavy chain/ACAP1 0.004 0.054 0.24 3 -0.35 7 10
JIP4/KLC1 0.04 0.013 -10000 0 -10000 0 0
EXOC1 0.021 0.006 -10000 0 -10000 0 0
exocyst 0.01 0.038 -10000 0 -0.32 3 3
RALA/GTP 0.016 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.008 -10000 0 -10000 0 0
receptor recycling 0.016 0.004 -10000 0 -10000 0 0
CTNNA1 -0.007 0.031 0.18 13 -10000 0 13
NME1 0.01 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.022 0.072 0.31 1 -0.37 12 13
IL2RA 0.004 0.038 -10000 0 -0.32 5 5
VAMP3 0.01 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.029 0.063 -10000 0 -0.36 6 6
EXOC6 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.007 0.015 0.18 3 -10000 0 3
PLD2 0.009 0.008 -10000 0 -10000 0 0
EXOC5 0.022 0.004 -10000 0 -10000 0 0
PIP5K1C 0.004 0.038 -10000 0 -0.34 3 3
SDC1 0.003 0.046 -10000 0 -0.34 7 7
ARF6/GDP 0.019 0.005 -10000 0 -10000 0 0
EXOC7 0.022 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.055 -10000 0 -0.33 5 5
mol:Phosphatidic acid 0.007 0.015 -10000 0 -10000 0 0
endocytosis -0.038 0.025 0.31 2 -10000 0 2
SCAMP2 0.023 0.002 -10000 0 -10000 0 0
ADRB2 -0.055 0.13 -10000 0 -0.42 13 13
EXOC3 0.018 0.009 -10000 0 -10000 0 0
ASAP2 0.022 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.023 0.008 -10000 0 -10000 0 0
KLC1 0.022 0.005 -10000 0 -10000 0 0
AVPR2 -0.045 0.14 0.24 2 -0.39 21 23
RALA 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.051 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.036 0.024 -10000 0 -10000 0 0
CLOCK 0.022 0.007 -10000 0 -10000 0 0
TIMELESS/CRY2 0.032 0.018 -10000 0 -10000 0 0
DEC1/BMAL1 0.039 0.034 -10000 0 -10000 0 0
ATR 0.018 0.009 -10000 0 -10000 0 0
NR1D1 0.014 0.006 -10000 0 -10000 0 0
ARNTL 0.024 0.005 -10000 0 -10000 0 0
TIMELESS 0.014 0.006 -10000 0 -10000 0 0
NPAS2 0.024 0.003 -10000 0 -10000 0 0
CRY2 0.022 0.004 -10000 0 -10000 0 0
mol:CO -0.006 0 -10000 0 -10000 0 0
CHEK1 0.023 0.01 0.24 1 -10000 0 1
mol:HEME 0.006 0 -10000 0 -10000 0 0
PER1 0.019 0.037 -10000 0 -0.56 2 2
BMAL/CLOCK/NPAS2 0.048 0.018 -10000 0 -10000 0 0
BMAL1/CLOCK 0.022 0.049 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.036 0.024 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.036 0.024 -10000 0 -10000 0 0
mol:NADPH 0.006 0 -10000 0 -10000 0 0
PER1/TIMELESS 0.031 0.026 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.014 0.056 0.24 26 -10000 0 26
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.015 0.054 0.24 2 -10000 0 2
GNAI2 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.024 -10000 0 -0.35 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
RhoA/GTP 0.016 0.055 -10000 0 -0.25 2 2
negative regulation of cAMP metabolic process 0.017 0.036 -10000 0 -0.23 5 5
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNA12 0.022 0.004 -10000 0 -10000 0 0
S1PR5 0.024 0.037 0.24 7 -0.56 1 8
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.017 0.036 -10000 0 -0.23 5 5
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.004 -10000 0 -10000 0 0
SNTA1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.004 -10000 0 -10000 0 0
MAPK12 -0.004 0.002 -10000 0 -10000 0 0
CCND1 0.003 0.05 -10000 0 -0.42 6 6
p38 gamma/SNTA1 0.019 0.036 0.28 1 -10000 0 1
MAP2K3 0.022 0.005 -10000 0 -10000 0 0
PKN1 0.022 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint 0.001 0.031 0.2 11 -10000 0 11
MAP2K6 0.003 0.002 -10000 0 -10000 0 0
MAPT 0.003 0.054 0.22 3 -0.33 6 9
MAPK13 -0.01 0.003 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.003 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.031 0.049 -10000 0 -0.34 7 7
MAPK9 0.005 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.024 0.043 -10000 0 -0.35 6 6
GNB1 0.021 0.027 -10000 0 -0.56 1 1
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 0.005 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.012 0.027 -10000 0 -0.27 4 4
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.002 0.007 0.07 4 -10000 0 4
GNAL 0.018 0.046 -10000 0 -0.56 3 3
GNG2 0.016 0.059 -10000 0 -0.56 5 5
CRH -0.011 0.019 0.24 1 -10000 0 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.001 -10000 0 -10000 0 0
MAPK11 0.005 0.001 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.021 0.027 0.56 1 -10000 0 1
PI3K Class IB/PDE3B 0.021 0.027 -10000 0 -0.56 1 1
PDE3B 0.021 0.027 -10000 0 -0.56 1 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.004 0.018 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.012 0.031 0.13 9 -0.17 3 12
AP2 0.018 0.02 0.26 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.029 0.012 -10000 0 -10000 0 0
CLTB 0.021 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0.006 -10000 0 -10000 0 0
CD4 0.006 0.094 -10000 0 -0.56 13 13
CLTA 0.021 0.007 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.005 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.008 -10000 0 -10000 0 0
ARF1/GTP 0.026 0.011 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.006 0.003 -10000 0 -10000 0 0
mol:Choline 0.004 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.023 0.007 -10000 0 -10000 0 0
DDEF1 0.003 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.015 -10000 0 -10000 0 0
AP2M1 0.013 0.02 0.37 1 -10000 0 1
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.005 -10000 0 -10000 0 0
Rac/GTP 0.017 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.031 0.011 -10000 0 -10000 0 0
ARFIP2 0.018 0.013 -10000 0 -10000 0 0
COPA 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.009 0.034 -10000 0 -0.21 4 4
ARF1/GTP/ARHGAP10 0.015 0.006 -10000 0 -10000 0 0
GGA3 0.022 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.02 0.017 -10000 0 -0.25 1 1
AP2A1 0.022 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.001 0.041 -10000 0 -0.21 9 9
ARF1/GDP/Membrin 0.021 0.021 -10000 0 -0.24 2 2
Arfaptin 2/Rac/GDP 0.029 0.009 -10000 0 -10000 0 0
CYTH2 0.024 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.03 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.007 0.028 -10000 0 -0.24 4 4
PLD2 0.004 0.008 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.004 0.008 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.014 0.019 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.008 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.005 0.001 -10000 0 -10000 0 0
GOSR2 0.009 0.016 -10000 0 -0.33 1 1
USO1 0.005 0.037 -10000 0 -0.32 6 6
GBF1 0.001 0.053 -10000 0 -0.32 13 13
ARF1/GTP/Arfaptin 2 0.03 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.018 0.046 0.25 1 -0.36 3 4
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD2 0.003 0.043 0.21 1 -0.25 3 4
SMAD3 0.019 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.057 -10000 0 -0.46 4 4
SMAD4/Ubc9/PIASy 0.042 0.014 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.053 -10000 0 -10000 0 0
PPM1A 0.022 0.004 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.011 0.051 -10000 0 -0.25 4 4
MAP3K1 0.021 0.006 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.032 0.008 -10000 0 -10000 0 0
MAPK3 0.023 0.003 -10000 0 -10000 0 0
MAPK1 0.022 0.006 -10000 0 -10000 0 0
NUP214 0.023 0.003 -10000 0 -10000 0 0
CTDSP1 0.022 0.004 -10000 0 -10000 0 0
CTDSP2 0.023 0.003 -10000 0 -10000 0 0
CTDSPL 0.021 0.007 -10000 0 -10000 0 0
KPNB1 0.023 0.003 -10000 0 -10000 0 0
TGFBRAP1 0.023 0.002 -10000 0 -10000 0 0
UBE2I 0.022 0.004 -10000 0 -10000 0 0
NUP153 0.022 0.004 -10000 0 -10000 0 0
KPNA2 0.022 0.004 -10000 0 -10000 0 0
PIAS4 0.022 0.004 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.021 0.006 -10000 0 -9999 0 0
PLK4 0.022 0.011 0.24 1 -9999 0 1
regulation of centriole replication -0.01 0.004 -10000 0 -9999 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.033 0.007 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.019 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.039 -10000 0 -10000 0 0
NFKBIA 0.011 0.022 -10000 0 -0.22 1 1
MAPK14 0.022 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.019 0.009 -10000 0 -10000 0 0
ARRB2 0.01 0.003 -10000 0 -10000 0 0
REL 0.021 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.02 0.008 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.017 0.029 0.42 2 -10000 0 2
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
NFKB1 -0.008 0.027 0.58 1 -10000 0 1
RELA 0.023 0.002 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.018 0.034 0.24 1 -0.23 1 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.022 0.043 -10000 0 -0.27 1 1
SRC 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.018 0.034 0.24 1 -0.23 1 2
IKBKB 0.022 0.017 0.37 1 -10000 0 1
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -10000 0 0
SYK 0.022 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.035 -10000 0 -0.25 1 1
cell death 0.021 0.042 -10000 0 -0.26 1 1
NF kappa B1 p105/c-Rel 0.019 0.01 -10000 0 -10000 0 0
LCK 0.021 0.027 -10000 0 -0.56 1 1
BCL3 0.022 0.005 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.022 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.007 -10000 0 -10000 0 0
MDM2/SUMO1 0.031 0.032 0.24 1 -0.26 1 2
HDAC4 0.022 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.01 0.006 -10000 0 -10000 0 0
SUMO1 0.022 0.004 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.005 0.002 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.032 0.029 -10000 0 -0.24 1 1
SUMO1/HDAC1 0.032 0.03 -10000 0 -0.26 1 1
RANGAP1 0.022 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.053 0.021 0.25 1 -10000 0 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.01 0.003 -10000 0 -10000 0 0
Ran/GTP 0.022 0.028 -10000 0 -0.24 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.017 0.37 1 -10000 0 1
UBE2I 0.022 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.032 0.053 0.24 3 -10000 0 3
NPC 0.014 0.001 -10000 0 -10000 0 0
PIAS2 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.023 0.002 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.042 0.015 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.031 0.01 -9999 0 -9999 0 0
CTNNB1 0.021 0.006 -9999 0 -9999 0 0
JUP 0.023 0.003 -9999 0 -9999 0 0
CDH1 0.022 0.005 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.032 0.009 -10000 0 -9999 0 0
FBXW11 0.021 0.006 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -9999 0 0
CHUK 0.022 0.005 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.06 0.025 -10000 0 -9999 0 0
NFKB1 0.022 0.005 -10000 0 -9999 0 0
MAP3K14 0.023 0.003 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.032 0.014 0.26 1 -9999 0 1
RELB 0.023 0.016 0.37 1 -9999 0 1
NFKB2 0.022 0.005 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.029 0.013 0.24 1 -9999 0 1
regulation of B cell activation 0.029 0.012 0.23 1 -9999 0 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 486 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.O2.A5IB TCGA.O2.A52W TCGA.O2.A52V TCGA.O2.A52S
109_MAP3K5 -0.17 0.02 0.02 -0.18
47_PPARGC1A 0 0.023 0.023 -0.56
105_BMP4 0.023 0.023 0.023 0.023
105_BMP6 0.023 0.023 0.023 0.023
105_BMP7 0.023 0.24 0.24 0.023
105_BMP2 -0.56 0.023 0.023 0.023
131_RELN/VLDLR 0.059 0.059 0.059 -0.33
30_TGFB1/TGF beta receptor Type II 0.028 0.021 0.021 0.021
84_STAT5B -0.34 0.024 0.024 -0.074
84_STAT5A -0.34 0.024 0.024 -0.074
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/9830261/LUSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LUSC-TP/10006028/GDAC_Gistic2Report_10008722/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle