PARADIGM pathway analysis of mRNASeq expression and copy number data
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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/C1Q52NHN
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 35 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
HIF-1-alpha transcription factor network 112
IL4-mediated signaling events 101
Syndecan-1-mediated signaling events 84
Glypican 2 network 69
TCGA08_retinoblastoma 64
Endothelins 56
amb2 Integrin signaling 53
Syndecan-4-mediated signaling events 50
Osteopontin-mediated events 49
Syndecan-2-mediated signaling events 48
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 497 . 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 ( 497 ).

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
HIF-1-alpha transcription factor network 0.2254 112 8546 76 -0.69 0.038 1000 -1000 -0.14 -1000
IL4-mediated signaling events 0.2032 101 9217 91 -1.2 1 1000 -1000 -0.18 -1000
Syndecan-1-mediated signaling events 0.1690 84 2861 34 -0.32 0.027 1000 -1000 -0.051 -1000
Glypican 2 network 0.1388 69 278 4 -0.045 -0.027 1000 -1000 -0.001 -1000
TCGA08_retinoblastoma 0.1288 64 514 8 -0.14 0.082 1000 -1000 -0.005 -1000
Endothelins 0.1127 56 5422 96 -0.23 0.027 1000 -1000 -0.07 -1000
amb2 Integrin signaling 0.1066 53 4359 82 -0.27 0.035 1000 -1000 -0.045 -1000
Syndecan-4-mediated signaling events 0.1006 50 3400 67 -0.29 0.041 1000 -1000 -0.05 -1000
Osteopontin-mediated events 0.0986 49 1884 38 -0.2 0.032 1000 -1000 -0.049 -1000
Syndecan-2-mediated signaling events 0.0966 48 3354 69 -0.21 0.037 1000 -1000 -0.047 -1000
Signaling events regulated by Ret tyrosine kinase 0.0946 47 3903 82 -0.087 0.027 1000 -1000 -0.068 -1000
IL23-mediated signaling events 0.0885 44 2666 60 -0.54 0.027 1000 -1000 -0.13 -1000
Nongenotropic Androgen signaling 0.0805 40 2094 52 -0.11 0.067 1000 -1000 -0.042 -1000
TCGA08_p53 0.0785 39 278 7 -0.1 0.06 1000 -1000 -0.008 -1000
TCR signaling in naïve CD8+ T cells 0.0785 39 3719 93 -0.19 0.1 1000 -1000 -0.056 -1000
Coregulation of Androgen receptor activity 0.0765 38 2931 76 -0.44 0.066 1000 -1000 -0.026 -1000
p75(NTR)-mediated signaling 0.0744 37 4730 125 -0.24 0.073 1000 -1000 -0.077 -1000
BMP receptor signaling 0.0744 37 3045 81 -0.22 0.047 1000 -1000 -0.061 -1000
Calcium signaling in the CD4+ TCR pathway 0.0744 37 1152 31 -0.31 0.027 1000 -1000 -0.054 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0744 37 2962 78 -0.14 0.042 1000 -1000 -0.064 -1000
Effects of Botulinum toxin 0.0724 36 946 26 -0.12 0.027 1000 -1000 -0.019 -1000
Visual signal transduction: Rods 0.0704 35 1829 52 -0.21 0.039 1000 -1000 -0.042 -1000
FOXA2 and FOXA3 transcription factor networks 0.0684 34 1599 46 -0.44 0.032 1000 -1000 -0.13 -1000
Glypican 1 network 0.0664 33 1602 48 -0.27 0.046 1000 -1000 -0.033 -1000
Canonical Wnt signaling pathway 0.0644 32 1675 51 -0.19 0.14 1000 -1000 -0.063 -1000
IGF1 pathway 0.0644 32 1841 57 -0.054 0.053 1000 -1000 -0.051 -1000
Fc-epsilon receptor I signaling in mast cells 0.0624 31 3008 97 -0.14 0.034 1000 -1000 -0.063 -1000
Reelin signaling pathway 0.0604 30 1682 56 -0.17 0.066 1000 -1000 -0.056 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0604 30 3643 120 -0.16 0.072 1000 -1000 -0.059 -1000
LPA4-mediated signaling events 0.0584 29 351 12 -0.087 0.007 1000 -1000 -0.028 -1000
Thromboxane A2 receptor signaling 0.0563 28 2948 105 -0.083 0.031 1000 -1000 -0.063 -1000
Presenilin action in Notch and Wnt signaling 0.0543 27 1677 61 -0.19 0.073 1000 -1000 -0.054 -1000
LPA receptor mediated events 0.0543 27 2821 102 -0.27 0.027 1000 -1000 -0.057 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0543 27 1884 68 -0.33 0.042 1000 -1000 -0.11 -1000
IL12-mediated signaling events 0.0523 26 2290 87 -0.17 0.035 1000 -1000 -0.11 -1000
Visual signal transduction: Cones 0.0483 24 943 38 -0.061 0.049 1000 -1000 -0.017 -1000
Signaling mediated by p38-gamma and p38-delta 0.0483 24 374 15 -0.13 0.026 1000 -1000 -0.039 -1000
PDGFR-beta signaling pathway 0.0483 24 2330 97 -0.058 0.056 1000 -1000 -0.056 -1000
Arf6 signaling events 0.0463 23 1452 62 -0.11 0.051 1000 -1000 -0.049 -1000
BCR signaling pathway 0.0463 23 2360 99 -0.067 0.047 1000 -1000 -0.06 -1000
Integrins in angiogenesis 0.0443 22 1864 84 -0.2 0.053 1000 -1000 -0.055 -1000
Regulation of Androgen receptor activity 0.0443 22 1590 70 -0.47 0.033 1000 -1000 -0.055 -1000
ErbB2/ErbB3 signaling events 0.0423 21 1400 65 -0.24 0.039 1000 -1000 -0.064 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0423 21 1138 54 -0.13 0.038 1000 -1000 -0.065 -1000
Signaling events mediated by the Hedgehog family 0.0423 21 1132 52 -0.22 0.03 1000 -1000 -0.051 -1000
Signaling events mediated by PTP1B 0.0423 21 1659 76 -0.087 0.044 1000 -1000 -0.046 -1000
IL1-mediated signaling events 0.0423 21 1340 62 -0.11 0.045 1000 -1000 -0.051 -1000
Ephrin B reverse signaling 0.0423 21 1019 48 -0.065 0.032 1000 -1000 -0.038 -1000
Plasma membrane estrogen receptor signaling 0.0423 21 1870 86 -0.13 0.045 1000 -1000 -0.064 -1000
EGFR-dependent Endothelin signaling events 0.0402 20 431 21 -0.06 0.04 1000 -1000 -0.05 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0402 20 1784 88 -0.16 0.045 1000 -1000 -0.089 -1000
Caspase cascade in apoptosis 0.0382 19 1448 74 -0.094 0.053 1000 -1000 -0.049 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0382 19 675 34 -0.03 0.031 1000 -1000 -0.036 -1000
Ephrin A reverse signaling 0.0382 19 138 7 -0.008 0.015 1000 -1000 -0.014 -1000
Glucocorticoid receptor regulatory network 0.0362 18 2135 114 -0.34 0.18 1000 -1000 -0.064 -1000
Signaling mediated by p38-alpha and p38-beta 0.0362 18 810 44 -0.13 0.027 1000 -1000 -0.034 -1000
EPHB forward signaling 0.0362 18 1536 85 -0.16 0.09 1000 -1000 -0.073 -1000
Wnt signaling 0.0362 18 131 7 -0.019 0.023 1000 -1000 -0.025 -1000
ErbB4 signaling events 0.0342 17 1178 69 -0.24 0.039 1000 -1000 -0.065 -1000
Signaling events mediated by HDAC Class III 0.0342 17 705 40 -0.13 0.049 1000 -1000 -0.021 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0342 17 584 33 -0.14 0.062 1000 -1000 -0.043 -1000
Syndecan-3-mediated signaling events 0.0322 16 582 35 -0.15 0.073 1000 -1000 -0.034 -1000
IL27-mediated signaling events 0.0322 16 847 51 -0.11 0.053 1000 -1000 -0.055 -1000
Regulation of nuclear SMAD2/3 signaling 0.0282 14 1906 136 -0.35 0.16 1000 -1000 -0.052 -1000
Noncanonical Wnt signaling pathway 0.0282 14 388 26 -0.052 0.026 1000 -1000 -0.051 -1000
PDGFR-alpha signaling pathway 0.0282 14 641 44 -0.11 0.059 1000 -1000 -0.044 -1000
Ceramide signaling pathway 0.0282 14 1106 76 -0.06 0.069 1000 -1000 -0.05 -1000
S1P1 pathway 0.0262 13 484 36 -0.049 0.026 1000 -1000 -0.052 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0241 12 1036 85 -0.087 0.072 1000 -1000 -0.048 -1000
EPO signaling pathway 0.0241 12 666 55 -0.015 0.049 1000 -1000 -0.048 -1000
IFN-gamma pathway 0.0241 12 831 68 -0.13 0.04 1000 -1000 -0.068 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0241 12 657 52 -0.14 0.042 1000 -1000 -0.066 -1000
FAS signaling pathway (CD95) 0.0241 12 567 47 -0.06 0.042 1000 -1000 -0.048 -1000
IL6-mediated signaling events 0.0241 12 919 75 -0.11 0.05 1000 -1000 -0.072 -1000
Signaling events mediated by PRL 0.0241 12 434 34 -0.066 0.039 1000 -1000 -0.039 -1000
Cellular roles of Anthrax toxin 0.0221 11 464 39 -0.025 0.029 1000 -1000 -0.026 -1000
Nectin adhesion pathway 0.0221 11 699 63 -0.049 0.061 1000 -1000 -0.057 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0221 11 834 74 -0.28 0.059 1000 -1000 -0.073 -1000
S1P3 pathway 0.0221 11 481 42 -0.049 0.045 1000 -1000 -0.045 -1000
Rapid glucocorticoid signaling 0.0221 11 234 20 -0.03 0.034 1000 -1000 -0.006 -1000
BARD1 signaling events 0.0201 10 580 57 -0.033 0.05 1000 -1000 -0.059 -1000
ceramide signaling pathway 0.0201 10 520 49 0 0.064 1000 -1000 -0.052 -1000
Retinoic acid receptors-mediated signaling 0.0201 10 618 58 -0.053 0.05 1000 -1000 -0.063 -1000
p38 MAPK signaling pathway 0.0201 10 478 44 -0.094 0.055 1000 -1000 -0.039 -1000
PLK1 signaling events 0.0181 9 782 85 -0.038 0.066 1000 -1000 -0.04 -1000
Class I PI3K signaling events mediated by Akt 0.0181 9 635 68 -0.093 0.061 1000 -1000 -0.043 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0181 9 338 37 -0.022 0.061 1000 -1000 -0.038 -1000
IL2 signaling events mediated by PI3K 0.0181 9 578 58 -0.089 0.081 1000 -1000 -0.053 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0181 9 441 45 -0.029 0.05 1000 -1000 -0.065 -1000
Regulation of p38-alpha and p38-beta 0.0181 9 486 54 -0.036 0.059 1000 -1000 -0.058 -1000
Ras signaling in the CD4+ TCR pathway 0.0181 9 153 17 -0.001 0.043 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0161 8 196 22 -0.059 0.055 1000 -1000 -0.052 -1000
JNK signaling in the CD4+ TCR pathway 0.0161 8 149 17 0.01 0.049 1000 -1000 -0.044 -1000
Regulation of Telomerase 0.0161 8 879 102 -0.071 0.058 1000 -1000 -0.069 -1000
FOXM1 transcription factor network 0.0161 8 438 51 -0.14 0.14 1000 -1000 -0.17 -1000
Aurora B signaling 0.0161 8 590 67 -0.31 0.087 1000 -1000 -0.045 -1000
mTOR signaling pathway 0.0141 7 389 53 -0.021 0.066 1000 -1000 -0.044 -1000
TCGA08_rtk_signaling 0.0141 7 197 26 -0.066 0.086 1000 -1000 -0.024 -1000
VEGFR1 specific signals 0.0141 7 400 56 -0.046 0.05 1000 -1000 -0.058 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0121 6 190 28 -0.044 0.05 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 0.0121 6 401 65 -0.024 0.063 1000 -1000 -0.061 -1000
HIF-2-alpha transcription factor network 0.0121 6 267 43 -0.1 0.044 1000 -1000 -0.08 -1000
IL2 signaling events mediated by STAT5 0.0121 6 140 22 -0.017 0.043 1000 -1000 -0.055 -1000
Insulin Pathway 0.0121 6 461 74 -0.095 0.071 1000 -1000 -0.053 -1000
Class IB PI3K non-lipid kinase events 0.0121 6 18 3 -0.021 0.021 1000 -1000 -0.004 -1000
a4b1 and a4b7 Integrin signaling 0.0101 5 28 5 0.02 0.033 1000 -1000 -0.002 -1000
Class I PI3K signaling events 0.0101 5 396 73 -0.036 0.048 1000 -1000 -0.053 -1000
Arf6 trafficking events 0.0101 5 413 71 -0.18 0.048 1000 -1000 -0.037 -1000
E-cadherin signaling in keratinocytes 0.0101 5 246 43 -0.042 0.061 1000 -1000 -0.045 -1000
S1P4 pathway 0.0101 5 139 25 0 0.037 1000 -1000 -0.035 -1000
TRAIL signaling pathway 0.0080 4 214 48 0 0.07 1000 -1000 -0.044 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0080 4 370 83 -0.031 0.053 1000 -1000 -0.054 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0080 4 560 125 -0.039 0.07 1000 -1000 -0.065 -1000
E-cadherin signaling in the nascent adherens junction 0.0080 4 354 76 -0.02 0.068 1000 -1000 -0.062 -1000
Canonical NF-kappaB pathway 0.0060 3 142 39 0 0.059 1000 -1000 -0.046 -1000
Aurora A signaling 0.0060 3 221 60 -0.035 0.055 1000 -1000 -0.028 -1000
Aurora C signaling 0.0060 3 25 7 0 0.041 1000 -1000 -0.011 -1000
Insulin-mediated glucose transport 0.0060 3 115 32 -0.069 0.052 1000 -1000 -0.037 -1000
S1P5 pathway 0.0060 3 59 17 -0.022 0.032 1000 -1000 -0.025 -1000
FoxO family signaling 0.0060 3 249 64 -0.019 0.086 1000 -1000 -0.075 -1000
E-cadherin signaling events 0.0060 3 17 5 0.021 0.043 1000 -1000 -0.002 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 2 56 23 0.004 0.048 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 0.0040 2 159 75 -0.033 0.066 1000 -1000 -0.031 -1000
Arf6 downstream pathway 0.0040 2 125 43 -0.04 0.041 1000 -1000 -0.04 -1000
Paxillin-dependent events mediated by a4b1 0.0040 2 106 36 -0.051 0.053 1000 -1000 -0.046 -1000
Atypical NF-kappaB pathway 0.0040 2 68 31 0 0.033 1000 -1000 -0.04 -1000
PLK2 and PLK4 events 0.0020 1 4 3 0.012 0.027 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class I 0.0020 1 199 104 -0.072 0.065 1000 -1000 -0.049 -1000
Alternative NF-kappaB pathway 0.0020 1 16 13 0 0.072 1000 -1000 -0.004 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 9 27 0 0.06 1000 -1000 -0.038 -1000
Arf1 pathway 0.0000 0 44 54 -0.001 0.037 1000 -1000 -0.026 -1000
Total NA 2582 157571 7203 -16 7.7 131000 -131000 -6.7 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.57 0.38 -10000 0 -0.94 199 199
HDAC7 0.028 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.42 0.29 -10000 0 -0.8 89 89
SMAD4 0.025 0.008 -10000 0 -10000 0 0
ID2 -0.57 0.39 -10000 0 -0.97 178 178
AP1 -0.006 0.12 -10000 0 -0.32 60 60
ABCG2 -0.57 0.39 -10000 0 -0.98 179 179
HIF1A -0.09 0.066 -10000 0 -0.59 1 1
TFF3 -0.66 0.44 -10000 0 -1 228 228
GATA2 0.023 0.03 -10000 0 -0.42 2 2
AKT1 -0.092 0.069 -10000 0 -0.41 2 2
response to hypoxia -0.1 0.076 -10000 0 -0.3 27 27
MCL1 -0.57 0.39 -10000 0 -0.97 177 177
NDRG1 -0.55 0.38 -10000 0 -0.97 165 165
SERPINE1 -0.65 0.42 -10000 0 -1 212 212
FECH -0.57 0.39 -10000 0 -0.98 173 173
FURIN -0.57 0.39 -10000 0 -1 161 161
NCOA2 -0.008 0.12 -10000 0 -0.45 32 32
EP300 -0.091 0.085 -10000 0 -0.37 13 13
HMOX1 -0.57 0.39 -10000 0 -0.98 171 171
BHLHE40 -0.57 0.39 -10000 0 -1 161 161
BHLHE41 -0.57 0.39 -10000 0 -0.98 175 175
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.082 0.093 -10000 0 -0.38 2 2
ENG -0.078 0.085 0.33 5 -0.38 1 6
JUN 0.027 0.006 -10000 0 -10000 0 0
RORA -0.57 0.4 -10000 0 -1 162 162
ABCB1 -0.18 0.31 -10000 0 -1.2 36 36
TFRC -0.54 0.38 -10000 0 -0.99 146 146
CXCR4 -0.57 0.39 -10000 0 -0.99 173 173
TF -0.68 0.44 -10000 0 -1 242 242
CITED2 -0.57 0.39 -10000 0 -0.97 177 177
HIF1A/ARNT -0.63 0.46 -10000 0 -1.1 178 178
LDHA -0.08 0.16 -10000 0 -0.79 20 20
ETS1 -0.57 0.39 -10000 0 -0.97 179 179
PGK1 -0.57 0.39 -10000 0 -0.98 172 172
NOS2 -0.6 0.4 -10000 0 -0.99 192 192
ITGB2 -0.57 0.39 -10000 0 -0.97 184 184
ALDOA -0.57 0.39 -10000 0 -0.98 170 170
Cbp/p300/CITED2 -0.56 0.39 -10000 0 -1 142 142
FOS -0.032 0.16 -10000 0 -0.45 60 60
HK2 -0.57 0.39 -10000 0 -1 160 160
SP1 0.026 0.03 -10000 0 -10000 0 0
GCK -0.15 0.15 -10000 0 -0.7 10 10
HK1 -0.57 0.39 -10000 0 -1 161 161
NPM1 -0.57 0.39 -10000 0 -1 161 161
EGLN1 -0.57 0.39 -10000 0 -0.97 176 176
CREB1 0.032 0.006 -10000 0 -10000 0 0
PGM1 -0.57 0.39 -10000 0 -0.97 178 178
SMAD3 0.028 0.005 -10000 0 -10000 0 0
EDN1 -0.091 0.16 -10000 0 -0.99 8 8
IGFBP1 -0.57 0.39 -10000 0 -0.98 178 178
VEGFA -0.37 0.25 -10000 0 -0.72 71 71
HIF1A/JAB1 -0.049 0.049 -10000 0 -10000 0 0
CP -0.62 0.43 -10000 0 -1 208 208
CXCL12 -0.59 0.41 -10000 0 -1 184 184
COPS5 0.023 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.013 -10000 0 -10000 0 0
BNIP3 -0.57 0.39 -10000 0 -1 160 160
EGLN3 -0.57 0.4 -10000 0 -0.98 183 183
CA9 -0.69 0.41 -10000 0 -1 234 234
TERT -0.58 0.4 -10000 0 -0.99 187 187
ENO1 -0.57 0.39 -10000 0 -0.97 177 177
PFKL -0.57 0.39 -10000 0 -0.97 178 178
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.57 0.39 -10000 0 -0.98 178 178
ARNT -0.097 0.068 -10000 0 -0.35 8 8
HNF4A -0.02 0.12 -10000 0 -0.4 46 46
ADFP -0.57 0.38 -10000 0 -0.94 199 199
SLC2A1 -0.37 0.25 -10000 0 -0.72 75 75
LEP -0.6 0.41 -10000 0 -1 189 189
HIF1A/ARNT/Cbp/p300 -0.43 0.3 -10000 0 -0.81 95 95
EPO -0.34 0.25 -10000 0 -0.83 52 52
CREBBP -0.09 0.082 -10000 0 -0.36 11 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.41 0.3 -10000 0 -0.81 84 84
PFKFB3 -0.57 0.39 -10000 0 -0.99 167 167
NT5E -0.6 0.41 -10000 0 -1 182 182
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.87 0.46 -10000 0 -1.3 227 227
STAT6 (cleaved dimer) -0.89 0.48 -10000 0 -1.3 269 269
IGHG1 -0.31 0.16 -10000 0 -0.53 60 60
IGHG3 -0.85 0.44 -10000 0 -1.2 263 263
AKT1 -0.37 0.2 -10000 0 -0.85 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.17 -10000 0 -0.79 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.38 0.21 -10000 0 -0.92 26 26
THY1 -0.92 0.48 -10000 0 -1.3 248 248
MYB -0.022 0.14 -10000 0 -0.45 50 50
HMGA1 0.026 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.45 0.21 -10000 0 -0.78 50 50
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.38 0.21 -10000 0 -0.93 25 25
SP1 0.003 0.04 -10000 0 -10000 0 0
INPP5D 0.024 0.031 -10000 0 -0.45 2 2
SOCS5 0.048 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.88 0.47 -10000 0 -1.3 246 246
SOCS1 -0.57 0.26 -10000 0 -0.8 203 203
SOCS3 -0.39 0.18 -10000 0 -0.91 9 9
FCER2 -0.7 0.36 -10000 0 -1.1 147 147
PARP14 0.023 0.021 -10000 0 -0.4 1 1
CCL17 -0.9 0.48 -10000 0 -1.3 239 239
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.32 0.18 -10000 0 -0.76 26 26
T cell proliferation -0.88 0.48 -10000 0 -1.3 233 233
IL4R/JAK1 -0.88 0.46 -10000 0 -1.3 237 237
EGR2 -0.9 0.47 -10000 0 -1.3 217 217
JAK2 -0.048 0.03 -10000 0 -10000 0 0
JAK3 0.018 0.079 -10000 0 -0.4 17 17
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
JAK1 -0.011 0.016 -10000 0 -10000 0 0
COL1A2 -0.34 0.21 -10000 0 -0.95 5 5
CCL26 -0.9 0.47 -10000 0 -1.3 230 230
IL4R -0.94 0.5 -10000 0 -1.4 236 236
PTPN6 0.044 0.014 -10000 0 -10000 0 0
IL13RA2 -0.91 0.48 -10000 0 -1.3 244 244
IL13RA1 -0.052 0.027 -10000 0 -10000 0 0
IRF4 -0.25 0.32 -10000 0 -0.88 82 82
ARG1 -0.5 0.54 -10000 0 -1.5 115 115
CBL -0.43 0.2 -10000 0 -0.75 44 44
GTF3A -0.018 0.04 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.06 0.041 -10000 0 -10000 0 0
IRF4/BCL6 -0.2 0.29 -10000 0 -0.81 73 73
CD40LG -0.036 0.16 -10000 0 -0.45 64 64
MAPK14 -0.42 0.2 -10000 0 -0.78 37 37
mitosis -0.35 0.19 -10000 0 -0.79 31 31
STAT6 -1 0.58 -10000 0 -1.5 254 254
SPI1 -0.014 0.073 -10000 0 -0.44 3 3
RPS6KB1 -0.34 0.18 -10000 0 -0.76 30 30
STAT6 (dimer) -1 0.58 -10000 0 -1.5 254 254
STAT6 (dimer)/PARP14 -0.94 0.53 -10000 0 -1.4 248 248
mast cell activation 0.02 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.36 0.21 -10000 0 -0.92 29 29
FRAP1 -0.37 0.2 -10000 0 -0.85 31 31
LTA -0.9 0.46 -10000 0 -1.3 237 237
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 1 0.55 1.4 257 -10000 0 257
CCL11 -0.93 0.44 -10000 0 -1.3 263 263
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.35 0.19 -10000 0 -0.85 23 23
IL2RG 0.018 0.08 -10000 0 -0.4 17 17
IL10 -0.88 0.46 -10000 0 -1.3 224 224
IRS1 0.023 0.038 -10000 0 -0.45 3 3
IRS2 0.025 0.031 -10000 0 -0.45 2 2
IL4 -0.23 0.24 -10000 0 -1.2 27 27
IL5 -0.89 0.46 -10000 0 -1.3 234 234
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.69 0.34 -10000 0 -0.99 200 200
COL1A1 -0.46 0.26 -10000 0 -0.7 163 163
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.91 0.49 -10000 0 -1.4 221 221
IL2R gamma/JAK3 0.019 0.09 -10000 0 -0.32 30 30
TFF3 -1.1 0.6 -10000 0 -1.6 288 288
ALOX15 -0.96 0.52 -10000 0 -1.4 249 249
MYBL1 0.02 0.043 -10000 0 -0.4 5 5
T-helper 2 cell differentiation -0.79 0.39 -10000 0 -1.1 258 258
SHC1 0.027 0.004 -10000 0 -10000 0 0
CEBPB -0.01 0.063 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.36 0.19 -10000 0 -0.86 23 23
mol:PI-3-4-5-P3 -0.37 0.2 -10000 0 -0.85 31 31
PI3K -0.39 0.22 -10000 0 -0.92 31 31
DOK2 0.022 0.04 -10000 0 -0.41 4 4
ETS1 0.04 0.037 -10000 0 -0.38 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.29 0.16 -10000 0 -0.69 22 22
ITGB3 -0.89 0.47 -10000 0 -1.3 234 234
PIGR -1.2 0.62 -10000 0 -1.6 339 339
IGHE 0.047 0.053 0.2 10 -10000 0 10
MAPKKK cascade -0.29 0.15 -10000 0 -0.67 22 22
BCL6 0.02 0.012 -10000 0 -10000 0 0
OPRM1 -0.89 0.46 -10000 0 -1.3 237 237
RETNLB -0.88 0.48 -10000 0 -1.3 228 228
SELP -0.96 0.54 -10000 0 -1.4 245 245
AICDA -0.86 0.44 -10000 0 -1.2 229 229
Syndecan-1-mediated signaling events

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
TGFB1 0.025 0.027 -10000 0 -0.4 2 2
CCL5 -0.037 0.15 -10000 0 -0.4 75 75
SDCBP 0.025 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.18 0.14 0.27 10 -0.34 118 128
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 -0.18 0.13 0.2 6 -0.33 118 124
Syndecan-1/Syntenin -0.16 0.13 0.31 3 -0.33 108 111
MAPK3 -0.16 0.12 0.29 4 -0.39 37 41
HGF/MET 0.02 0.078 -10000 0 -0.3 26 26
TGFB1/TGF beta receptor Type II 0.025 0.027 -10000 0 -0.4 2 2
BSG 0.027 0.005 -10000 0 -10000 0 0
keratinocyte migration -0.18 0.12 0.2 6 -0.33 118 124
Syndecan-1/RANTES -0.2 0.15 0.25 9 -0.36 171 180
Syndecan-1/CD147 -0.17 0.13 0.31 4 -0.32 110 114
Syndecan-1/Syntenin/PIP2 -0.16 0.13 0.29 3 -0.32 108 111
LAMA5 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.16 0.12 0.29 3 -0.31 108 111
MMP7 -0.065 0.17 -10000 0 -0.4 102 102
HGF 0.007 0.092 -10000 0 -0.44 20 20
Syndecan-1/CASK -0.18 0.12 -10000 0 -0.33 120 120
Syndecan-1/HGF/MET -0.17 0.14 0.31 3 -0.33 125 128
regulation of cell adhesion -0.16 0.12 0.28 4 -0.39 33 37
HPSE 0.023 0.043 -10000 0 -0.45 4 4
positive regulation of cell migration -0.18 0.14 0.27 10 -0.34 118 128
SDC1 -0.19 0.12 0.22 1 -0.35 115 116
Syndecan-1/Collagen -0.18 0.14 0.27 10 -0.34 118 128
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET 0.021 0.049 -10000 0 -0.42 6 6
PRKACA 0.027 0.003 -10000 0 -10000 0 0
MMP9 -0.27 0.19 -10000 0 -0.4 349 349
MAPK1 -0.16 0.12 0.29 4 -0.39 36 40
homophilic cell adhesion -0.18 0.14 0.27 10 -0.34 119 129
MMP1 -0.32 0.16 -10000 0 -0.4 405 405
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.009 0.084 -9999 0 -0.4 20 20
GPC2 -0.045 0.16 -9999 0 -0.4 82 82
GPC2/Midkine -0.027 0.14 -9999 0 -0.31 88 88
neuron projection morphogenesis -0.027 0.14 -9999 0 -0.31 88 88
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.01 0.07 -10000 0 -0.42 12 12
CDKN2C 0.019 0.071 -10000 0 -0.36 14 14
CDKN2A -0.14 0.2 -10000 0 -0.4 183 183
CCND2 0.04 0.063 0.18 46 -10000 0 46
RB1 -0.06 0.087 0.3 1 -0.24 62 63
CDK4 0.048 0.074 0.2 49 -10000 0 49
CDK6 0.044 0.07 0.21 39 -10000 0 39
G1/S progression 0.082 0.096 0.23 107 -0.3 1 108
Endothelins

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
AKT1 -0.12 0.19 0.25 2 -0.44 63 65
PTK2B 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.18 -10000 0 -0.58 15 15
EDN1 -0.073 0.15 -10000 0 -0.31 48 48
EDN3 -0.18 0.22 -10000 0 -0.45 197 197
EDN2 -0.04 0.16 -10000 0 -0.43 71 71
HRAS/GDP -0.066 0.16 0.29 5 -0.43 33 38
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.059 0.13 -10000 0 -0.35 48 48
ADCY4 -0.12 0.17 0.27 5 -0.39 83 88
ADCY5 -0.16 0.18 0.24 2 -0.41 120 122
ADCY6 -0.13 0.17 0.3 3 -0.39 88 91
ADCY7 -0.12 0.17 0.26 7 -0.38 87 94
ADCY1 -0.12 0.17 0.26 6 -0.39 91 97
ADCY2 -0.18 0.18 0.26 2 -0.41 139 141
ADCY3 -0.12 0.17 0.27 5 -0.38 86 91
ADCY8 -0.12 0.16 0.32 2 -0.39 80 82
ADCY9 -0.12 0.17 0.27 5 -0.39 84 89
arachidonic acid secretion -0.092 0.2 0.27 3 -0.48 68 71
ETB receptor/Endothelin-1/Gq/GTP -0.055 0.12 -10000 0 -0.33 48 48
GNAO1 0.022 0.04 -10000 0 -0.41 4 4
HRAS 0.025 0.02 -10000 0 -0.41 1 1
ETA receptor/Endothelin-1/G12/GTP -0.043 0.23 0.32 8 -0.4 62 70
ETA receptor/Endothelin-1/Gs/GTP -0.079 0.22 0.28 10 -0.4 88 98
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.22 0.27 -10000 0 -0.48 210 210
EDNRB -0.01 0.061 -10000 0 -0.45 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.14 0.22 -10000 0 -0.52 74 74
CYSLTR1 -0.16 0.25 -10000 0 -0.54 104 104
SLC9A1 -0.05 0.11 -10000 0 -0.32 23 23
mol:GDP -0.075 0.16 0.29 5 -0.44 39 44
SLC9A3 -0.16 0.3 -10000 0 -0.65 106 106
RAF1 -0.094 0.18 0.27 5 -0.45 61 66
JUN -0.052 0.17 -10000 0 -0.61 13 13
JAK2 -0.12 0.19 0.25 3 -0.44 63 66
mol:IP3 -0.071 0.14 -10000 0 -0.38 54 54
ETA receptor/Endothelin-1 -0.08 0.28 0.4 6 -0.48 80 86
PLCB1 0.024 0.023 -10000 0 -0.45 1 1
PLCB2 0.021 0.041 -10000 0 -0.42 4 4
ETA receptor/Endothelin-3 -0.17 0.19 -10000 0 -0.37 200 200
FOS -0.14 0.32 0.31 1 -0.9 66 67
Gai/GDP -0.07 0.26 -10000 0 -0.72 64 64
CRK 0.026 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.13 0.19 0.24 1 -0.44 78 79
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.069 0.14 0.25 2 -0.36 53 55
GNAQ 0.026 0.009 -10000 0 -10000 0 0
GNAZ 0.01 0.083 -10000 0 -0.42 18 18
GNAL -0.03 0.15 -10000 0 -0.45 57 57
Gs family/GDP -0.087 0.16 0.25 1 -0.42 50 51
ETA receptor/Endothelin-1/Gq/GTP -0.07 0.15 -10000 0 -0.37 56 56
MAPK14 -0.041 0.11 0.24 1 -0.38 19 20
TRPC6 -0.051 0.18 -10000 0 -0.61 15 15
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.025 0.022 -10000 0 -0.45 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.045 0.12 -10000 0 -0.35 33 33
ETB receptor/Endothelin-2 -0.041 0.12 -10000 0 -0.32 75 75
ETB receptor/Endothelin-3 -0.13 0.17 -10000 0 -0.34 195 195
ETB receptor/Endothelin-1 -0.052 0.14 -10000 0 -0.27 60 60
MAPK3 -0.13 0.28 0.3 2 -0.75 70 72
MAPK1 -0.13 0.28 0.3 2 -0.76 69 71
Rac1/GDP -0.066 0.15 0.29 4 -0.42 34 38
cAMP biosynthetic process -0.14 0.17 0.28 6 -0.42 74 80
MAPK8 -0.063 0.19 0.34 1 -0.59 29 30
SRC 0.026 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.021 0.088 -10000 0 -0.36 15 15
p130Cas/CRK/Src/PYK2 -0.073 0.16 0.3 6 -0.5 26 32
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.066 0.15 0.29 4 -0.42 34 38
COL1A2 -0.16 0.25 -10000 0 -0.46 158 158
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.082 0.15 -10000 0 -0.36 75 75
mol:DAG -0.071 0.14 -10000 0 -0.38 54 54
MAP2K2 -0.11 0.22 0.3 3 -0.57 69 72
MAP2K1 -0.11 0.22 0.27 5 -0.56 72 77
EDNRA -0.068 0.14 -10000 0 -0.29 57 57
positive regulation of muscle contraction -0.091 0.17 0.27 8 -0.39 57 65
Gq family/GDP -0.055 0.17 -10000 0 -0.43 39 39
HRAS/GTP -0.085 0.16 0.28 4 -0.41 53 57
PRKCH -0.064 0.14 0.24 7 -0.4 37 44
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.07 0.14 0.25 3 -0.38 45 48
PRKCB -0.071 0.14 0.24 4 -0.37 53 57
PRKCE -0.069 0.14 0.25 2 -0.39 40 42
PRKCD -0.066 0.13 -10000 0 -0.4 33 33
PRKCG -0.09 0.15 0.25 2 -0.39 55 57
regulation of vascular smooth muscle contraction -0.17 0.37 -10000 0 -1 67 67
PRKCQ -0.075 0.15 0.29 3 -0.39 54 57
PLA2G4A -0.1 0.21 0.29 2 -0.52 68 70
GNA14 -0.044 0.17 -10000 0 -0.45 72 72
GNA15 0.024 0.032 -10000 0 -0.46 2 2
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.038 -10000 0 -0.45 3 3
Rac1/GTP -0.044 0.23 0.33 7 -0.4 62 69
MMP1 -0.23 0.2 0.48 19 -0.36 182 201
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.018 0.14 -9999 0 -0.28 90 90
alphaM/beta2 Integrin/GPIbA 0.006 0.11 -9999 0 -0.31 46 46
alphaM/beta2 Integrin/proMMP-9 -0.18 0.15 -9999 0 -0.26 350 350
PLAUR 0.003 0.098 -9999 0 -0.4 28 28
HMGB1 0.019 0.025 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.012 0.097 -9999 0 -0.29 35 35
AGER 0.013 0.055 -9999 0 -0.4 7 7
RAP1A 0.027 0.005 -9999 0 -10000 0 0
SELPLG 0.027 0.002 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.016 0.12 -9999 0 -0.39 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.27 0.19 -9999 0 -0.4 349 349
CYR61 0.022 0.044 -9999 0 -0.41 5 5
TLN1 0.024 0.009 -9999 0 -10000 0 0
Rap1/GTP -0.073 0.12 -9999 0 -0.33 32 32
RHOA 0.024 0.009 -9999 0 -10000 0 0
P-selectin oligomer -0.059 0.18 -9999 0 -0.45 88 88
MYH2 -0.21 0.18 -9999 0 -0.39 207 207
MST1R 0.019 0.049 -9999 0 -0.45 5 5
leukocyte activation during inflammatory response 0.009 0.1 -9999 0 -0.3 26 26
APOB 0.006 0.07 -9999 0 -0.4 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.029 0.14 -9999 0 -0.4 64 64
JAM3 0.024 0.02 -9999 0 -0.4 1 1
GP1BA 0.007 0.081 -9999 0 -0.41 17 17
alphaM/beta2 Integrin/CTGF 0.013 0.1 -9999 0 -0.3 40 40
alphaM/beta2 Integrin -0.098 0.12 -9999 0 -0.28 95 95
JAM3 homodimer 0.024 0.02 -9999 0 -0.4 1 1
ICAM2 0.024 0.036 -9999 0 -0.43 3 3
ICAM1 0.005 0.095 -9999 0 -0.4 26 26
phagocytosis triggered by activation of immune response cell surface activating receptor -0.091 0.13 -9999 0 -0.29 90 90
cell adhesion 0.005 0.11 -9999 0 -0.31 46 46
NFKB1 -0.028 0.14 -9999 0 -0.39 46 46
THY1 -0.09 0.19 -9999 0 -0.4 134 134
RhoA/GDP 0.018 0.007 -9999 0 -10000 0 0
Lipoprotein(a) 0.019 0.056 -9999 0 -0.24 22 22
alphaM/beta2 Integrin/LRP/tPA 0.024 0.1 -9999 0 -0.35 19 19
IL6 -0.057 0.2 -9999 0 -0.66 41 41
ITGB2 0.007 0.074 -9999 0 -0.4 14 14
elevation of cytosolic calcium ion concentration -0.093 0.17 -9999 0 -0.38 62 62
alphaM/beta2 Integrin/JAM2/JAM3 0.023 0.11 -9999 0 -0.32 27 27
JAM2 0.015 0.074 -9999 0 -0.45 12 12
alphaM/beta2 Integrin/ICAM1 0.02 0.12 -9999 0 -0.38 21 21
alphaM/beta2 Integrin/uPA/Plg -0.088 0.15 -9999 0 -0.33 49 49
RhoA/GTP -0.13 0.14 -9999 0 -0.35 103 103
positive regulation of phagocytosis -0.062 0.11 -9999 0 -0.34 28 28
Ron/MSP 0.029 0.05 -9999 0 -0.3 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.092 0.17 -9999 0 -0.38 62 62
alphaM/beta2 Integrin/uPAR 0.001 0.12 -9999 0 -0.3 56 56
PLAU -0.15 0.21 -9999 0 -0.4 209 209
PLAT 0.015 0.066 -9999 0 -0.4 12 12
actin filament polymerization -0.21 0.17 -9999 0 -0.37 205 205
MST1 0.02 0.044 -9999 0 -0.41 5 5
alphaM/beta2 Integrin/lipoprotein(a) 0.013 0.1 -9999 0 -0.31 26 26
TNF -0.039 0.15 -9999 0 -0.57 13 13
RAP1B 0.026 0.006 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.099 0.16 -9999 0 -0.26 231 231
fibrinolysis -0.088 0.15 -9999 0 -0.33 50 50
HCK 0.023 0.03 -9999 0 -0.42 2 2
dendritic cell antigen processing and presentation -0.091 0.13 -9999 0 -0.29 90 90
VTN 0 0.1 -9999 0 -0.4 30 30
alphaM/beta2 Integrin/CYR61 0.014 0.1 -9999 0 -0.3 38 38
LPA 0.001 0.058 -9999 0 -0.4 9 9
LRP1 0.026 0.022 -9999 0 -0.45 1 1
cell migration -0.18 0.16 -9999 0 -0.39 116 116
FN1 -0.16 0.21 -9999 0 -0.4 217 217
alphaM/beta2 Integrin/Thy1 -0.057 0.16 -9999 0 -0.28 139 139
MPO 0.008 0.085 -9999 0 -0.44 17 17
KNG1 -0.01 0.061 -9999 0 -0.4 11 11
RAP1/GDP 0.035 0.01 -9999 0 -10000 0 0
ROCK1 -0.11 0.14 -9999 0 -0.35 81 81
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.014 0.038 -9999 0 -0.4 4 4
CTGF 0.021 0.051 -9999 0 -0.43 6 6
alphaM/beta2 Integrin/Hck 0.015 0.098 -9999 0 -0.3 33 33
ITGAM -0.007 0.1 -9999 0 -0.4 31 31
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.02 0.15 -9999 0 -0.28 94 94
HP -0.15 0.22 -9999 0 -0.45 174 174
leukocyte adhesion -0.049 0.14 -9999 0 -0.39 37 37
SELP -0.059 0.18 -9999 0 -0.45 88 88
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.1 0.17 -10000 0 -0.55 32 32
Syndecan-4/Syndesmos -0.16 0.16 -10000 0 -0.67 16 16
positive regulation of JNK cascade -0.17 0.15 -10000 0 -0.52 35 35
Syndecan-4/ADAM12 -0.29 0.19 -10000 0 -0.45 203 203
CCL5 -0.037 0.15 -10000 0 -0.4 75 75
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DNM2 0.027 0.003 -10000 0 -10000 0 0
ITGA5 -0.1 0.2 -10000 0 -0.4 152 152
SDCBP 0.025 0.008 -10000 0 -10000 0 0
PLG 0.015 0.042 -10000 0 -0.39 4 4
ADAM12 -0.28 0.19 -10000 0 -0.4 352 352
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.079 0.043 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.22 0.18 -10000 0 -0.47 105 105
Syndecan-4/CXCL12/CXCR4 -0.18 0.16 -10000 0 -0.55 35 35
Syndecan-4/Laminin alpha3 -0.2 0.18 -10000 0 -0.46 91 91
MDK 0.009 0.084 -10000 0 -0.4 20 20
Syndecan-4/FZD7 -0.16 0.16 -10000 0 -0.65 18 18
Syndecan-4/Midkine -0.17 0.16 -10000 0 -0.63 19 19
FZD7 0.021 0.048 -10000 0 -0.4 6 6
Syndecan-4/FGFR1/FGF -0.15 0.15 -10000 0 -0.64 15 15
THBS1 0.012 0.081 -10000 0 -0.42 17 17
integrin-mediated signaling pathway -0.19 0.17 -10000 0 -0.46 73 73
positive regulation of MAPKKK cascade -0.17 0.15 -10000 0 -0.52 35 35
Syndecan-4/TACI -0.18 0.16 -10000 0 -0.54 34 34
CXCR4 0.013 0.077 -10000 0 -0.4 17 17
cell adhesion -0.072 0.1 0.2 4 -0.22 111 115
Syndecan-4/Dynamin -0.16 0.16 -10000 0 -0.66 17 17
Syndecan-4/TSP1 -0.17 0.16 -10000 0 -0.57 27 27
Syndecan-4/GIPC -0.16 0.16 -10000 0 -0.67 16 16
Syndecan-4/RANTES -0.19 0.17 -10000 0 -0.51 48 48
ITGB1 0.027 0.005 -10000 0 -10000 0 0
LAMA1 -0.13 0.2 -10000 0 -0.4 177 177
LAMA3 -0.088 0.19 -10000 0 -0.4 132 132
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.041 0.092 0.86 5 -0.4 2 7
Syndecan-4/alpha-Actinin -0.16 0.16 -10000 0 -0.66 17 17
TFPI 0.022 0.045 -10000 0 -0.42 5 5
F2 -0.034 0.12 -10000 0 -0.4 46 46
alpha5/beta1 Integrin -0.059 0.15 -10000 0 -0.28 152 152
positive regulation of cell adhesion -0.25 0.2 -10000 0 -0.49 142 142
ACTN1 0.026 0.006 -10000 0 -10000 0 0
TNC -0.05 0.16 -10000 0 -0.4 89 89
Syndecan-4/CXCL12 -0.18 0.16 -10000 0 -0.6 28 28
FGF6 -0.009 0.017 -10000 0 -10000 0 0
RHOA 0.024 0.009 -10000 0 -10000 0 0
CXCL12 -0.022 0.14 -10000 0 -0.45 50 50
TNFRSF13B -0.027 0.13 -10000 0 -0.4 56 56
FGF2 0.011 0.083 -10000 0 -0.44 16 16
FGFR1 0.02 0.044 -10000 0 -0.41 5 5
Syndecan-4/PI-4-5-P2 -0.17 0.15 -10000 0 -0.52 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.16 0.21 -10000 0 -0.39 217 217
cell migration -0.031 0.017 -10000 0 -10000 0 0
PRKCD 0.029 0.015 -10000 0 -10000 0 0
vasculogenesis -0.16 0.15 -10000 0 -0.54 27 27
SDC4 -0.17 0.16 -10000 0 -0.53 34 34
Syndecan-4/Tenascin C -0.19 0.18 -10000 0 -0.48 73 73
Syndecan-4/PI-4-5-P2/PKC alpha -0.063 0.034 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.15 0.15 -10000 0 -0.65 17 17
MMP9 -0.27 0.19 -10000 0 -0.39 349 349
Rac1/GTP -0.074 0.1 0.21 4 -0.22 111 115
cytoskeleton organization -0.16 0.15 -10000 0 -0.64 16 16
GIPC1 0.027 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.16 -10000 0 -0.62 19 19
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.12 0.13 -10000 0 -0.31 41 41
NF kappa B1 p50/RelA/I kappa B alpha -0.11 0.13 0.32 1 -0.4 9 10
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.16 -10000 0 -0.29 252 252
AP1 -0.16 0.18 -10000 0 -0.44 82 82
ILK -0.12 0.13 -10000 0 -0.32 37 37
bone resorption -0.094 0.12 0.33 1 -0.38 15 16
PTK2B 0.025 0.007 -10000 0 -10000 0 0
PYK2/p130Cas -0.084 0.14 -10000 0 -0.39 11 11
ITGAV 0.019 0.031 -10000 0 -0.41 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.032 0.049 -10000 0 -0.32 9 9
alphaV/beta3 Integrin/Osteopontin -0.13 0.15 -10000 0 -0.28 156 156
MAP3K1 -0.12 0.13 -10000 0 -0.31 45 45
JUN 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.14 0.13 0.2 2 -0.31 127 129
MAPK1 -0.14 0.13 0.2 2 -0.3 123 125
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.12 0.12 -10000 0 -0.33 37 37
ITGB3 0.005 0.087 -10000 0 -0.42 19 19
NFKBIA -0.13 0.13 0.2 2 -0.31 114 116
FOS -0.033 0.16 -10000 0 -0.45 60 60
CD44 0.025 0.022 -10000 0 -0.45 1 1
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.2 0.19 -10000 0 -0.47 116 116
NF kappa B1 p50/RelA -0.12 0.15 -10000 0 -0.44 7 7
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.011 0.073 -10000 0 -0.31 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.12 0.13 -10000 0 -0.3 46 46
VAV3 -0.13 0.13 -10000 0 -0.4 34 34
MAP3K14 -0.13 0.13 -10000 0 -0.29 128 128
ROCK2 0.018 0.064 -10000 0 -0.45 9 9
SPP1 -0.2 0.21 -10000 0 -0.4 263 263
RAC1 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.11 0.12 -10000 0 -0.38 32 32
MMP2 -0.16 0.17 -10000 0 -0.47 80 80
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.081 0.14 -10000 0 -0.24 194 194
EPHB2 -0.065 0.17 -10000 0 -0.4 107 107
Syndecan-2/TACI -0.011 0.09 -10000 0 -0.23 69 69
LAMA1 -0.13 0.2 -10000 0 -0.4 177 177
Syndecan-2/alpha2 ITGB1 -0.015 0.11 -10000 0 -0.37 7 7
HRAS 0.025 0.02 -10000 0 -0.41 1 1
Syndecan-2/CASK 0 0.044 -10000 0 -0.22 18 18
ITGA5 -0.1 0.2 -10000 0 -0.4 152 152
BAX 0 0.046 -10000 0 -0.42 1 1
EPB41 0.027 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.016 0.042 -10000 0 -0.2 17 17
LAMA3 -0.088 0.19 -10000 0 -0.4 132 132
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.024 0.031 -10000 0 -0.45 2 2
Syndecan-2/MMP2 -0.015 0.1 -10000 0 -0.26 68 68
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.036 0.025 -10000 0 -0.32 2 2
dendrite morphogenesis -0.028 0.11 -10000 0 -0.24 100 100
Syndecan-2/GM-CSF -0.11 0.14 -10000 0 -0.24 243 243
determination of left/right symmetry 0.002 0.053 -10000 0 -0.27 18 18
Syndecan-2/PKC delta 0.015 0.048 -10000 0 -0.22 18 18
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.09 0.13 0.19 23 -0.4 13 36
MAPK1 -0.087 0.13 0.19 23 -0.4 11 34
Syndecan-2/RACK1 0.027 0.047 -10000 0 -0.19 18 18
NF1 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.002 0.053 -10000 0 -0.27 18 18
ITGA2 0.023 0.038 -10000 0 -0.45 3 3
MAPK8 0.002 0.049 -10000 0 -0.36 2 2
Syndecan-2/alpha2/beta1 Integrin -0.039 0.12 -10000 0 -0.37 10 10
Syndecan-2/Kininogen 0.006 0.052 -10000 0 -0.25 17 17
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.027 0.066 0.19 43 -10000 0 43
Syndecan-2/CASK/Protein 4.1 0.016 0.044 -10000 0 -0.2 18 18
extracellular matrix organization 0.016 0.051 -10000 0 -0.24 18 18
actin cytoskeleton reorganization -0.081 0.14 -10000 0 -0.24 194 194
Syndecan-2/Caveolin-2/Ras 0.027 0.053 -10000 0 -0.22 18 18
Syndecan-2/Laminin alpha3 -0.041 0.12 -10000 0 -0.24 124 124
Syndecan-2/RasGAP 0.037 0.053 -10000 0 -0.4 1 1
alpha5/beta1 Integrin -0.059 0.15 -10000 0 -0.28 152 152
PRKCD 0.024 0.009 -10000 0 -10000 0 0
Syndecan-2 dimer -0.028 0.11 -10000 0 -0.24 100 100
GO:0007205 0.003 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.026 0.05 -10000 0 -0.39 1 1
RHOA 0.024 0.009 -10000 0 -10000 0 0
SDCBP 0.025 0.008 -10000 0 -10000 0 0
TNFRSF13B -0.027 0.13 -10000 0 -0.4 56 56
RASA1 0.024 0.031 -10000 0 -0.45 2 2
alpha2/beta1 Integrin 0.036 0.025 -10000 0 -0.32 2 2
Syndecan-2/Synbindin 0.015 0.049 -10000 0 -0.23 18 18
TGFB1 0.025 0.027 -10000 0 -0.4 2 2
CASP3 0.024 0.068 0.19 48 -10000 0 48
FN1 -0.16 0.21 -10000 0 -0.4 217 217
Syndecan-2/IL8 -0.032 0.11 -10000 0 -0.24 106 106
SDC2 0.002 0.053 -10000 0 -0.27 18 18
KNG1 -0.01 0.061 -10000 0 -0.4 11 11
Syndecan-2/Neurofibromin 0.017 0.048 -10000 0 -0.22 18 18
TRAPPC4 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.21 0.21 -10000 0 -0.4 271 271
Syndecan-2/TGFB1 0.016 0.051 -10000 0 -0.24 18 18
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.043 -10000 0 -0.2 17 17
Syndecan-2/Ezrin 0.027 0.048 -10000 0 -0.2 16 16
PRKACA 0.029 0.072 0.19 57 -10000 0 57
angiogenesis -0.032 0.11 -10000 0 -0.24 106 106
MMP2 -0.029 0.14 -10000 0 -0.4 64 64
IL8 -0.064 0.17 -10000 0 -0.4 105 105
calcineurin-NFAT signaling pathway -0.011 0.089 -10000 0 -0.23 69 69
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.032 0.12 -10000 0 -0.48 25 25
Crk/p130 Cas/Paxillin -0.065 0.11 -10000 0 -0.35 26 26
JUN -0.041 0.12 -10000 0 -0.33 31 31
HRAS 0.025 0.02 -10000 0 -0.41 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.047 0.16 -10000 0 -0.28 139 139
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.051 0.16 -10000 0 -0.28 153 153
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.04 0.14 -10000 0 -0.26 127 127
RHOA 0.024 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.044 0.14 -10000 0 -0.31 57 57
GRB7 0.025 0.031 -10000 0 -0.45 2 2
RET51/GFRalpha1/GDNF -0.051 0.16 -10000 0 -0.28 152 152
MAPKKK cascade -0.049 0.13 -10000 0 -0.36 28 28
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.04 0.14 -10000 0 -0.26 127 127
lamellipodium assembly -0.044 0.12 -10000 0 -0.27 66 66
RET51/GFRalpha1/GDNF/SHC -0.052 0.16 -10000 0 -0.3 112 112
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.039 0.14 -10000 0 -0.26 126 126
RET9/GFRalpha1/GDNF/Shank3 -0.038 0.14 -10000 0 -0.26 125 125
MAPK3 -0.056 0.14 0.34 4 -0.38 28 32
DOK1 0.026 0.019 -10000 0 -0.4 1 1
DOK6 0.014 0.068 -10000 0 -0.43 11 11
PXN 0.027 0.002 -10000 0 -10000 0 0
neurite development -0.052 0.13 0.33 4 -0.36 23 27
DOK5 0.002 0.1 -10000 0 -0.44 25 25
GFRA1 -0.087 0.2 -10000 0 -0.45 117 117
MAPK8 -0.052 0.11 -10000 0 -0.33 33 33
HRAS/GTP -0.048 0.14 -10000 0 -0.31 86 86
tube development -0.035 0.13 -10000 0 -0.26 96 96
MAPK1 -0.056 0.13 0.34 4 -0.38 25 29
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.04 0.11 -10000 0 -0.24 95 95
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
PDLIM7 0.022 0.038 -10000 0 -0.4 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.044 0.16 -10000 0 -0.29 101 101
SHC1 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.051 0.16 -10000 0 -0.28 150 150
RET51/GFRalpha1/GDNF/Dok5 -0.062 0.17 -10000 0 -0.29 159 159
PRKCA 0.025 0.029 -10000 0 -0.42 2 2
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
CREB1 -0.054 0.13 -10000 0 -0.32 54 54
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.043 0.11 -10000 0 -0.27 44 44
RET51/GFRalpha1/GDNF/Grb7 -0.05 0.16 -10000 0 -0.28 150 150
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.02 0.14 -10000 0 -0.4 54 54
DOK4 0.026 0.006 -10000 0 -10000 0 0
JNK cascade -0.04 0.11 -10000 0 -0.34 25 25
RET9/GFRalpha1/GDNF/FRS2 -0.038 0.14 -10000 0 -0.26 122 122
SHANK3 0.026 0.005 -10000 0 -10000 0 0
RASA1 0.024 0.031 -10000 0 -0.45 2 2
NCK1 0.023 0.011 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.041 0.11 -10000 0 -0.24 97 97
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.049 0.12 -10000 0 -0.34 28 28
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.051 0.11 -10000 0 -0.26 94 94
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.051 0.12 -10000 0 -0.36 32 32
PI3K -0.061 0.17 -10000 0 -0.39 70 70
SOS1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.026 0.13 -10000 0 -0.26 98 98
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.039 0.12 -10000 0 -0.33 27 27
RET51/GFRalpha1/GDNF/FRS2 -0.05 0.16 -10000 0 -0.3 108 108
GAB1 0.026 0.005 -10000 0 -10000 0 0
IRS1 0.023 0.038 -10000 0 -0.45 3 3
IRS2 0.025 0.031 -10000 0 -0.45 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.053 0.12 -10000 0 -0.37 30 30
RET51/GFRalpha1/GDNF/PKC alpha -0.051 0.16 -10000 0 -0.3 110 110
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GDNF -0.016 0.11 -10000 0 -0.4 37 37
RAC1 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.053 0.16 -10000 0 -0.28 153 153
Rac1/GTP -0.046 0.14 -10000 0 -0.35 42 42
RET9/GFRalpha1/GDNF -0.055 0.14 -10000 0 -0.29 126 126
GFRalpha1/GDNF -0.064 0.17 -10000 0 -0.34 126 126
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.43 0.4 -10000 0 -1.2 71 71
IL23A -0.41 0.36 -10000 0 -1.1 59 59
NF kappa B1 p50/RelA/I kappa B alpha -0.4 0.37 -10000 0 -1.1 66 66
positive regulation of T cell mediated cytotoxicity -0.45 0.41 -10000 0 -1.2 80 80
ITGA3 -0.41 0.36 -10000 0 -1.1 62 62
IL17F -0.27 0.25 -10000 0 -0.7 59 59
IL12B -0.062 0.12 -10000 0 -0.43 43 43
STAT1 (dimer) -0.44 0.4 -10000 0 -1.1 78 78
CD4 -0.4 0.35 -10000 0 -1.1 59 59
IL23 -0.4 0.36 -10000 0 -1.1 61 61
IL23R -0.068 0.12 -10000 0 -0.91 7 7
IL1B -0.42 0.38 -10000 0 -1.1 73 73
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.49 0.35 -10000 0 -1.1 81 81
TYK2 -0.021 0.032 -10000 0 -0.43 1 1
STAT4 0.017 0.063 -10000 0 -0.4 11 11
STAT3 0.027 0.004 -10000 0 -10000 0 0
IL18RAP 0.004 0.085 -10000 0 -0.42 18 18
IL12RB1 -0.056 0.12 -10000 0 -0.43 44 44
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.046 0.093 -10000 0 -0.32 45 45
IL23R/JAK2 -0.078 0.12 -10000 0 -0.87 6 6
positive regulation of chronic inflammatory response -0.45 0.41 -10000 0 -1.2 80 80
natural killer cell activation 0.007 0.006 0.042 4 -10000 0 4
JAK2 -0.023 0.03 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
NFKB1 0.024 0.005 -10000 0 -10000 0 0
RELA 0.023 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.39 0.34 -10000 0 -1 63 63
ALOX12B -0.47 0.42 -10000 0 -1.2 87 87
CXCL1 -0.43 0.39 -10000 0 -1.1 82 82
T cell proliferation -0.45 0.41 -10000 0 -1.2 80 80
NFKBIA 0.023 0.006 -10000 0 -10000 0 0
IL17A -0.21 0.2 -10000 0 -0.56 41 41
PI3K -0.39 0.37 -10000 0 -1.1 70 70
IFNG -0.025 0.035 0.096 4 -0.12 8 12
STAT3 (dimer) -0.37 0.35 -10000 0 -1.1 64 64
IL18R1 0.019 0.033 -10000 0 -0.43 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.25 0.22 -10000 0 -0.76 28 28
IL18/IL18R 0.019 0.086 -10000 0 -0.27 30 30
macrophage activation -0.023 0.015 -10000 0 -0.045 25 25
TNF -0.42 0.37 -10000 0 -1.1 63 63
STAT3/STAT4 -0.42 0.38 -10000 0 -1.1 73 73
STAT4 (dimer) -0.43 0.4 -10000 0 -1.2 75 75
IL18 0.007 0.074 -10000 0 -0.45 12 12
IL19 -0.54 0.5 -10000 0 -1.3 133 133
STAT5A (dimer) -0.43 0.4 -10000 0 -1.1 80 80
STAT1 0.008 0.085 -10000 0 -0.4 21 21
SOCS3 0.026 0.022 -10000 0 -0.45 1 1
CXCL9 -0.47 0.37 -10000 0 -1.1 80 80
MPO -0.42 0.38 -10000 0 -1.1 75 75
positive regulation of humoral immune response -0.45 0.41 -10000 0 -1.2 80 80
IL23/IL23R/JAK2/TYK2 -0.46 0.44 -10000 0 -1.3 78 78
IL6 -0.43 0.42 -10000 0 -1.2 77 77
STAT5A 0.027 0.003 -10000 0 -10000 0 0
IL2 0.013 0.029 -10000 0 -0.39 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.007 0.006 0.042 4 -10000 0 4
CD3E -0.41 0.36 -10000 0 -1.1 65 65
keratinocyte proliferation -0.45 0.41 -10000 0 -1.2 80 80
NOS2 -0.44 0.38 -10000 0 -1.1 73 73
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.03 0.13 -10000 0 -0.25 127 127
regulation of S phase of mitotic cell cycle -0.027 0.093 -10000 0 -0.23 83 83
GNAO1 0.022 0.04 -10000 0 -0.41 4 4
HRAS 0.025 0.02 -10000 0 -0.41 1 1
SHBG/T-DHT 0.017 0.004 -10000 0 -10000 0 0
PELP1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.052 0.11 0.32 1 -0.31 15 16
T-DHT/AR -0.072 0.15 -10000 0 -0.32 131 131
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 63 63
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.025 0.022 -10000 0 -0.45 1 1
mol:GDP -0.085 0.15 -10000 0 -0.34 122 122
cell proliferation -0.084 0.17 0.28 3 -0.44 66 69
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
FOS -0.1 0.27 0.3 2 -0.78 64 66
mol:Ca2+ -0.009 0.022 -10000 0 -0.064 36 36
MAPK3 -0.073 0.14 0.29 2 -0.4 31 33
MAPK1 -0.033 0.097 -10000 0 -0.4 9 9
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
mol:IP3 0 0.002 -10000 0 -0.004 63 63
cAMP biosynthetic process 0.006 0.022 0.21 2 -10000 0 2
GNG2 0.025 0.02 -10000 0 -0.4 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 63 63
HRAS/GTP -0.031 0.12 -10000 0 -0.23 121 121
actin cytoskeleton reorganization 0.026 0.026 -10000 0 -0.22 2 2
SRC 0.025 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 63 63
PI3K 0.024 0.026 -10000 0 -0.27 2 2
apoptosis 0.067 0.16 0.42 68 -0.25 2 70
T-DHT/AR/PELP1 -0.049 0.14 -10000 0 -0.27 131 131
HRAS/GDP -0.072 0.15 -10000 0 -0.33 119 119
CREB1 -0.072 0.17 0.25 2 -0.45 68 70
RAC1-CDC42/GTP 0.033 0.031 -10000 0 -0.22 2 2
AR -0.11 0.21 -10000 0 -0.45 131 131
GNB1 0.026 0.005 -10000 0 -10000 0 0
RAF1 -0.045 0.11 0.33 1 -0.28 16 17
RAC1-CDC42/GDP -0.04 0.16 -10000 0 -0.32 113 113
T-DHT/AR/PELP1/Src -0.031 0.13 -10000 0 -0.25 122 122
MAP2K2 -0.052 0.11 0.2 5 -0.31 16 21
T-DHT/AR/PELP1/Src/PI3K -0.028 0.094 -10000 0 -0.23 83 83
GNAZ 0.01 0.083 -10000 0 -0.42 18 18
SHBG 0.024 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.028 0.13 -10000 0 -0.46 30 30
mol:T-DHT 0 0.001 0.002 2 -0.002 39 41
RAC1 0.026 0.007 -10000 0 -10000 0 0
GNRH1 -0.004 0.055 -10000 0 -0.28 19 19
Gi family/GTP -0.031 0.083 -10000 0 -0.28 26 26
CDC42 0.027 0.005 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.1 0.14 -10000 0 -0.28 183 183
TP53 -0.032 0.064 -10000 0 -0.3 19 19
Senescence -0.035 0.071 -10000 0 -0.3 25 25
Apoptosis -0.035 0.071 -10000 0 -0.3 25 25
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.06 0.093 0.3 26 -10000 0 26
MDM4 0.027 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.011 0.16 0.26 18 -0.4 45 63
FYN -0.026 0.18 0.27 19 -0.45 50 69
LAT/GRAP2/SLP76 -0.018 0.17 0.24 8 -0.44 45 53
IKBKB 0.025 0.008 -10000 0 -10000 0 0
AKT1 -0.022 0.14 0.23 16 -0.36 46 62
B2M 0.025 0.012 -10000 0 -10000 0 0
IKBKG -0.003 0.049 0.096 19 -0.14 15 34
MAP3K8 0.024 0.038 -10000 0 -0.45 3 3
mol:Ca2+ -0.035 0.03 -10000 0 -0.091 46 46
integrin-mediated signaling pathway 0.034 0.021 -10000 0 -0.27 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.037 0.19 0.26 16 -0.47 53 69
TRPV6 -0.19 0.26 1.1 5 -0.45 219 224
CD28 0.012 0.079 -10000 0 -0.41 17 17
SHC1 -0.034 0.18 0.26 18 -0.46 54 72
receptor internalization -0.041 0.19 0.18 5 -0.45 66 71
PRF1 -0.048 0.21 -10000 0 -0.63 42 42
KRAS 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.01 0.12 0.21 14 -0.3 40 54
LAT -0.039 0.19 0.22 16 -0.48 55 71
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D 0.009 0.081 -10000 0 -0.43 16 16
CD3E 0.012 0.07 -10000 0 -0.42 12 12
CD3G -0.002 0.11 -10000 0 -0.44 27 27
RASGRP2 0.006 0.02 0.066 2 -0.09 6 8
RASGRP1 -0.025 0.15 0.24 17 -0.39 47 64
HLA-A 0 0.005 -10000 0 -10000 0 0
RASSF5 0.025 0.031 -10000 0 -0.45 2 2
RAP1A/GTP/RAPL 0.034 0.021 -10000 0 -0.27 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.06 0.13 37 -0.12 19 56
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.027 0.064 -10000 0 -0.22 27 27
PRKCA -0.007 0.091 0.14 20 -0.26 23 43
GRAP2 0.015 0.071 -10000 0 -0.43 12 12
mol:IP3 0.031 0.17 0.21 170 -0.36 33 203
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.031 0.15 -10000 0 -0.44 50 50
ORAI1 0.1 0.16 0.6 2 -0.94 5 7
CSK -0.033 0.18 0.21 16 -0.46 53 69
B7 family/CD28 -0.055 0.19 0.23 2 -0.5 51 53
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.051 0.19 0.2 5 -0.47 63 68
PTPN6 -0.035 0.17 0.22 14 -0.44 54 68
VAV1 -0.038 0.18 0.21 15 -0.47 54 69
Monovalent TCR/CD3 -0.009 0.11 -10000 0 -0.36 35 35
CBL 0.025 0.008 -10000 0 -10000 0 0
LCK -0.029 0.18 0.25 19 -0.46 50 69
PAG1 -0.029 0.18 0.22 29 -0.46 51 80
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.05 0.19 0.22 8 -0.46 63 71
CD80 -0.075 0.18 -10000 0 -0.4 115 115
CD86 0.023 0.021 -10000 0 -0.4 1 1
PDK1/CARD11/BCL10/MALT1 -0.022 0.082 -10000 0 -0.26 29 29
HRAS 0.025 0.02 -10000 0 -0.41 1 1
GO:0035030 -0.063 0.15 0.18 5 -0.42 53 58
CD8A -0.015 0.13 -10000 0 -0.42 46 46
CD8B -0.022 0.14 -10000 0 -0.42 53 53
PTPRC 0.015 0.073 -10000 0 -0.43 13 13
PDK1/PKC theta -0.031 0.17 0.27 16 -0.44 43 59
CSK/PAG1 -0.024 0.18 0.22 35 -0.45 49 84
SOS1 0.027 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 -0.02 0.19 0.22 12 -0.47 49 61
STIM1 0.057 0.12 1.2 4 -10000 0 4
RAS family/GTP 0.013 0.074 0.15 28 -0.17 17 45
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.043 0.2 0.18 5 -0.48 64 69
mol:DAG -0.017 0.12 0.11 20 -0.31 43 63
RAP1A/GDP 0.011 0.029 0.081 19 -0.066 1 20
PLCG1 0.026 0.006 -10000 0 -10000 0 0
CD247 0.007 0.089 -10000 0 -0.41 21 21
cytotoxic T cell degranulation -0.045 0.21 -10000 0 -0.6 42 42
RAP1A/GTP 0.002 0.008 -10000 0 -0.052 1 1
mol:PI-3-4-5-P3 -0.028 0.16 0.24 18 -0.4 50 68
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.029 0.2 0.23 151 -0.47 34 185
NRAS 0.026 0.005 -10000 0 -10000 0 0
ZAP70 0.005 0.095 -10000 0 -0.41 25 25
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.026 0.16 0.28 3 -0.44 45 48
MALT1 0.025 0.008 -10000 0 -10000 0 0
TRAF6 0.026 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.022 0.16 -10000 0 -0.39 72 72
CARD11 0.001 0.099 -10000 0 -0.4 28 28
PRKCB -0.008 0.094 0.14 20 -0.28 25 45
PRKCE -0.006 0.09 0.14 22 -0.26 23 45
PRKCQ -0.036 0.18 0.26 17 -0.47 49 66
LCP2 0.023 0.033 -10000 0 -0.4 3 3
BCL10 0.027 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.017 0.13 0.2 21 -0.31 46 67
IKK complex 0.014 0.06 0.14 40 -0.12 6 46
RAS family/GDP -0.002 0.01 -10000 0 -0.053 1 1
MAP3K14 -0.008 0.096 0.17 16 -0.24 32 48
PDPK1 -0.02 0.14 0.23 16 -0.34 42 58
TCR/CD3/MHC I/CD8/Fyn -0.054 0.21 -10000 0 -0.49 66 66
Coregulation of Androgen receptor activity

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
NRIP1 0.007 0.046 -10000 0 -0.45 1 1
SVIL 0.009 0.043 -10000 0 -0.45 1 1
ZNF318 0.051 0.06 0.19 58 -10000 0 58
JMJD2C 0.006 0.016 0.05 1 -0.068 12 13
T-DHT/AR/Ubc9 -0.093 0.15 -10000 0 -0.31 131 131
CARM1 0.023 0.013 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.03 0.012 -10000 0 -10000 0 0
CTNNB1 0.011 0.032 -10000 0 -10000 0 0
AKT1 0.033 0.019 -10000 0 -10000 0 0
PTK2B 0.012 0.03 -10000 0 -10000 0 0
MED1 0.035 0.019 -10000 0 -10000 0 0
MAK 0.042 0.083 0.2 6 -0.41 8 14
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 0.009 0.043 -10000 0 -0.45 1 1
GSN 0.008 0.042 -10000 0 -10000 0 0
NCOA2 -0.01 0.12 -10000 0 -0.46 32 32
NCOA6 0.009 0.037 -10000 0 -10000 0 0
DNA-PK 0.066 0.058 0.26 2 -10000 0 2
NCOA4 0.025 0.006 -10000 0 -10000 0 0
PIAS3 0.012 0.033 -10000 0 -10000 0 0
cell proliferation -0.011 0.12 -10000 0 -0.53 16 16
XRCC5 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.004 0.052 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.16 -10000 0 -0.33 145 145
FHL2 -0.016 0.096 -10000 0 -0.51 6 6
RANBP9 0.01 0.037 -10000 0 -10000 0 0
JMJD1A -0.06 0.068 -10000 0 -0.13 229 229
CDK6 0.023 0.037 -10000 0 -0.43 3 3
TGFB1I1 -0.002 0.078 -10000 0 -0.4 14 14
T-DHT/AR/CyclinD1 -0.08 0.13 -10000 0 -0.32 98 98
XRCC6 0.033 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.12 0.17 -10000 0 -0.34 134 134
CTDSP1 0.017 0.022 -10000 0 -10000 0 0
CTDSP2 0.045 0.04 -10000 0 -10000 0 0
BRCA1 0.01 0.038 -10000 0 -10000 0 0
TCF4 0.037 0.031 -10000 0 -10000 0 0
CDKN2A -0.13 0.2 -10000 0 -0.38 183 183
SRF 0.04 0.021 -10000 0 -10000 0 0
NKX3-1 -0.13 0.12 -10000 0 -0.23 288 288
KLK3 -0.22 0.51 -10000 0 -1.3 84 84
TMF1 0.018 0.017 -10000 0 -10000 0 0
HNRNPA1 0.037 0.023 -10000 0 -10000 0 0
AOF2 -0.012 0.026 -10000 0 -0.07 83 83
APPL1 0.026 0.035 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.084 0.15 -10000 0 -0.31 129 129
AR -0.14 0.21 -10000 0 -0.48 131 131
UBA3 0.015 0.022 -10000 0 -10000 0 0
PATZ1 0.037 0.023 -10000 0 -10000 0 0
PAWR 0.02 0.017 -10000 0 -10000 0 0
PRKDC 0.029 0.017 -10000 0 -10000 0 0
PA2G4 0.039 0.027 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.077 0.13 -10000 0 -0.28 128 128
RPS6KA3 0.006 0.052 -10000 0 -0.45 2 2
T-DHT/AR/ARA70 -0.095 0.14 -10000 0 -0.31 128 128
LATS2 0.035 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.07 0.14 0.18 1 -0.28 129 130
Cyclin D3/CDK11 p58 0.021 0.006 -10000 0 -10000 0 0
VAV3 -0.018 0.12 -10000 0 -0.46 31 31
KLK2 -0.054 0.09 -10000 0 -0.4 15 15
CASP8 0.029 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.095 0.15 -10000 0 -0.31 137 137
TMPRSS2 -0.44 0.46 -10000 0 -0.91 234 234
CCND1 0.01 0.043 -10000 0 -0.46 3 3
PIAS1 0.004 0.052 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.03 0.038 1 -0.062 163 164
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.006 0.073 -10000 0 -0.23 1 1
T-DHT/AR/CDK6 -0.088 0.14 -10000 0 -0.31 125 125
CMTM2 0.014 0.071 -10000 0 -0.39 14 14
SNURF -0.002 0.1 -10000 0 -0.45 23 23
ZMIZ1 -0.011 0.044 -10000 0 -10000 0 0
CCND3 0.027 0.006 -10000 0 -10000 0 0
TGIF1 0.033 0.025 -10000 0 -10000 0 0
FKBP4 0.01 0.037 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.028 0.061 -10000 0 -0.32 14 14
Necdin/E2F1 0.019 0.079 -10000 0 -0.31 25 25
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.001 0.13 -10000 0 -0.27 32 32
NGF (dimer)/p75(NTR)/BEX1 -0.033 0.14 -10000 0 -0.25 138 138
NT-4/5 (dimer)/p75(NTR) 0.022 0.079 -10000 0 -0.32 24 24
IKBKB 0.025 0.008 -10000 0 -10000 0 0
AKT1 0.005 0.12 -10000 0 -0.38 1 1
IKBKG 0.026 0.006 -10000 0 -10000 0 0
BDNF -0.005 0.12 -10000 0 -0.43 34 34
MGDIs/NGR/p75(NTR)/LINGO1 0.01 0.11 -10000 0 -0.26 64 64
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.007 0.12 -10000 0 -0.27 68 68
LINGO1 -0.004 0.11 -10000 0 -0.4 36 36
Sortilin/TRAF6/NRIF 0.025 0.043 -10000 0 -10000 0 0
proBDNF (dimer) -0.005 0.12 -10000 0 -0.43 34 34
NTRK1 -0.008 0.12 -10000 0 -0.4 40 40
RTN4R 0.013 0.073 -10000 0 -0.4 15 15
neuron apoptosis -0.037 0.12 0.46 1 -0.45 18 19
IRAK1 0.026 0.006 -10000 0 -10000 0 0
SHC1 -0.042 0.11 -10000 0 -0.24 110 110
ARHGDIA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.007 -10000 0 -10000 0 0
Gamma Secretase 0.073 0.026 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.01 0.13 -10000 0 -0.23 124 124
MAGEH1 0.026 0.02 -10000 0 -0.4 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.014 0.14 -10000 0 -0.24 127 127
Mammalian IAPs/DIABLO 0.053 0.049 -10000 0 -10000 0 0
proNGF (dimer) -0.053 0.16 -10000 0 -0.4 91 91
MAGED1 0.023 0.041 -10000 0 -0.42 4 4
APP 0.026 0.02 -10000 0 -0.4 1 1
NT-4/5 (dimer) 0.025 0.029 -10000 0 -0.42 2 2
ZNF274 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.019 0.1 -10000 0 -0.21 97 97
NGF -0.053 0.17 -10000 0 -0.4 91 91
cell cycle arrest -0.064 0.1 -10000 0 -0.3 17 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.006 0.066 -10000 0 -0.25 5 5
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.037 0.07 -10000 0 -0.27 22 22
NCSTN 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.017 0.12 -10000 0 -0.24 115 115
PSENEN 0.026 0.005 -10000 0 -10000 0 0
mol:ceramide -0.046 0.11 -10000 0 -0.28 33 33
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.001 0.049 -10000 0 -0.28 2 2
p75(NTR)/beta APP 0.021 0.076 -10000 0 -0.3 26 26
BEX1 -0.009 0.1 -10000 0 -0.4 31 31
mol:GDP -0.051 0.1 -10000 0 -0.24 114 114
NGF (dimer) -0.051 0.14 -10000 0 -0.25 142 142
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.024 0.11 -10000 0 -0.25 57 57
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
RAC1/GTP -0.01 0.1 -10000 0 -0.2 105 105
MYD88 0.024 0.009 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.016 0.13 -10000 0 -0.24 115 115
RHOB 0.027 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.009 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.024 0.062 -10000 0 -0.28 19 19
NT3 (dimer) -0.11 0.21 -10000 0 -0.45 138 138
TP53 -0.014 0.095 0.53 1 -0.43 5 6
PRDM4 -0.047 0.11 -10000 0 -0.28 33 33
BDNF (dimer) -0.18 0.16 -10000 0 -0.28 326 326
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
SORT1 0.011 0.085 -10000 0 -0.45 16 16
activation of caspase activity -0.005 0.13 -10000 0 -0.26 32 32
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.007 0.13 -10000 0 -0.23 117 117
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.027 0.004 -10000 0 -10000 0 0
MAPK10 -0.044 0.12 0.31 3 -0.36 25 28
DIABLO 0.027 0.002 -10000 0 -10000 0 0
SMPD2 -0.047 0.11 -10000 0 -0.28 33 33
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.026 0.14 -10000 0 -0.25 126 126
PSEN1 0.026 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.079 0.17 -10000 0 -0.33 154 154
MAPK8 -0.035 0.1 0.35 2 -0.35 14 16
MAPK9 -0.034 0.11 0.34 3 -0.35 13 16
APAF1 0.027 0.002 -10000 0 -10000 0 0
NTF3 -0.11 0.21 -10000 0 -0.45 138 138
NTF4 0.025 0.029 -10000 0 -0.42 2 2
NDN 0.018 0.064 -10000 0 -0.45 9 9
RAC1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.004 0.11 -10000 0 -0.36 1 1
p75 CTF/Sortilin/TRAF6/NRIF 0.053 0.059 -10000 0 -0.25 15 15
RhoA-B-C/GTP -0.017 0.12 -10000 0 -0.24 115 115
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.032 0.11 -10000 0 -0.26 36 36
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.023 0.11 -10000 0 -0.25 65 65
PRKACB 0.026 0.022 -10000 0 -0.45 1 1
proBDNF (dimer)/p75 ECD 0.014 0.089 -10000 0 -0.31 35 35
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.012 0.071 -10000 0 -0.4 14 14
BIRC2 0.024 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.047 0.1 0.21 1 -0.29 34 35
BAD -0.038 0.11 0.38 2 -0.38 11 13
RIPK2 0.024 0.009 -10000 0 -10000 0 0
NGFR 0.005 0.099 -10000 0 -0.42 25 25
CYCS -0.042 0.1 -10000 0 -0.42 6 6
ADAM17 0.025 0.031 -10000 0 -0.45 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.003 0.11 -10000 0 -0.22 90 90
BCL2L11 -0.039 0.11 0.38 2 -0.38 11 13
BDNF (dimer)/p75(NTR) -0.001 0.11 -10000 0 -0.3 58 58
PI3K -0.01 0.11 -10000 0 -0.22 89 89
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.01 0.13 -10000 0 -0.23 123 123
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.026 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.012 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.037 0.14 -10000 0 -0.29 114 114
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.012 0.14 -10000 0 -0.28 37 37
TRAF6 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.025 0.022 -10000 0 -0.45 1 1
PLG -0.014 0.038 -10000 0 -0.4 4 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.048 0.12 -10000 0 -0.31 48 48
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.025 0.027 -10000 0 -0.4 2 2
CASP3 -0.036 0.1 0.37 2 -0.35 14 16
E2F1 0.009 0.081 -10000 0 -0.4 19 19
CASP9 0.026 0.006 -10000 0 -10000 0 0
IKK complex 0.008 0.11 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.045 0.14 -10000 0 -0.29 124 124
MMP7 -0.065 0.17 -10000 0 -0.4 102 102
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.003 0.13 -10000 0 -0.26 29 29
MMP3 -0.24 0.2 -10000 0 -0.4 305 305
APAF-1/Caspase 9 -0.031 0.087 -10000 0 -0.35 5 5
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.063 0.16 -10000 0 -0.36 57 57
SMAD6-7/SMURF1 0.047 0.02 -10000 0 -10000 0 0
NOG -0.018 0.13 -10000 0 -0.42 45 45
SMAD9 -0.071 0.19 -10000 0 -0.54 63 63
SMAD4 0.025 0.008 -10000 0 -10000 0 0
SMAD5 -0.047 0.12 -10000 0 -0.42 26 26
BMP7/USAG1 -0.069 0.18 -10000 0 -0.35 132 132
SMAD5/SKI -0.043 0.14 0.24 1 -0.42 29 30
SMAD1 0.024 0.041 -10000 0 -10000 0 0
BMP2 0.011 0.078 -10000 0 -0.4 17 17
SMAD1/SMAD1/SMAD4 0.026 0.05 -10000 0 -10000 0 0
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.015 0.13 -10000 0 -0.41 47 47
BMPR1A-1B/BAMBI 0.014 0.1 -10000 0 -0.24 62 62
AHSG -0.001 0.067 -10000 0 -0.4 13 13
CER1 -0.01 0.043 -10000 0 -0.4 5 5
BMP2-4/CER1 0.021 0.074 -10000 0 -0.25 30 30
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.078 0.16 -10000 0 -0.43 49 49
BMP2-4 (homodimer) 0.018 0.078 -10000 0 -0.3 26 26
RGMB 0.026 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.033 0.089 -10000 0 -0.22 47 47
RGMA -0.028 0.15 -10000 0 -0.45 56 56
SMURF1 0.025 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.073 0.14 -10000 0 -0.38 53 53
BMP2-4/USAG1 -0.043 0.14 -10000 0 -0.27 133 133
SMAD6/SMURF1/SMAD5 -0.044 0.13 0.24 1 -0.42 29 30
SOSTDC1 -0.094 0.2 -10000 0 -0.44 123 123
BMP7/BMPR2/BMPR1A-1B 0.014 0.12 -10000 0 -0.24 73 73
SKI 0.026 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.021 0.048 -10000 0 -0.4 6 6
HFE2 -0.13 0.21 -10000 0 -0.45 144 144
ZFYVE16 0.026 0.006 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.017 0.077 -10000 0 -0.26 30 30
SMAD5/SMAD5/SMAD4 -0.041 0.13 0.24 1 -0.42 29 30
MAPK1 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.057 0.13 -10000 0 -0.36 42 42
BMP7 (homodimer) -0.007 0.12 -10000 0 -0.45 34 34
NUP214 0.027 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.015 0.058 -10000 0 -0.28 17 17
SMAD1/SKI 0.026 0.067 -10000 0 -0.36 1 1
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.015 0.076 -10000 0 -0.25 32 32
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.16 0.21 -10000 0 -0.4 216 216
BMPR2 (homodimer) 0.026 0.006 -10000 0 -10000 0 0
GADD34/PP1CA 0.047 0.02 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.008 0.097 -10000 0 -0.29 47 47
CHRDL1 -0.22 0.24 -10000 0 -0.45 245 245
ENDOFIN/SMAD1 0.028 0.066 -10000 0 -0.34 1 1
SMAD6-7/SMURF1/SMAD1 0.045 0.065 -10000 0 -10000 0 0
SMAD6/SMURF1 0.025 0.007 -10000 0 -10000 0 0
BAMBI 0.012 0.081 -10000 0 -0.43 16 16
SMURF2 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.12 0.17 -10000 0 -0.29 235 235
BMP2-4/GREM1 -0.079 0.15 -10000 0 -0.25 206 206
SMAD7 0.025 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.064 0.19 -10000 0 -0.5 70 70
SMAD1/SMAD6 0.023 0.067 -10000 0 -0.34 1 1
TAK1/SMAD6 0.036 0.013 -10000 0 -10000 0 0
BMP7 -0.007 0.12 -10000 0 -0.45 34 34
BMP6 0.021 0.048 -10000 0 -0.4 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.062 0.14 -10000 0 -0.38 51 51
PPM1A 0.026 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.026 0.068 -10000 0 -0.36 1 1
SMAD7/SMURF1 0.035 0.015 -10000 0 -10000 0 0
CTDSPL 0.024 0.009 -10000 0 -10000 0 0
PPP1CA 0.025 0.008 -10000 0 -10000 0 0
XIAP 0.027 0.004 -10000 0 -10000 0 0
CTDSP1 0.026 0.005 -10000 0 -10000 0 0
PPP1R15A 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.16 -10000 0 -0.36 104 104
CHRD 0.01 0.063 -10000 0 -0.4 11 11
BMPR2 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.082 0.15 -10000 0 -0.39 58 58
BMP4 0.016 0.067 -10000 0 -0.45 10 10
FST -0.13 0.2 -10000 0 -0.4 177 177
BMP2-4/NOG 0.007 0.11 -10000 0 -0.26 66 66
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.021 0.11 -10000 0 -0.26 37 37
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.022 0.033 -10000 0 -10000 0 0
NFATC2 -0.055 0.093 -10000 0 -0.3 53 53
NFATC3 -0.025 0.033 -10000 0 -10000 0 0
CD40LG -0.24 0.26 0.35 6 -0.63 107 113
PTGS2 -0.24 0.25 0.34 5 -0.61 110 115
JUNB 0.027 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.014 0.025 -10000 0 -10000 0 0
CaM/Ca2+ -0.014 0.025 -10000 0 -10000 0 0
CALM1 0.006 0.025 -10000 0 -10000 0 0
JUN 0.006 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.007 0.014 -10000 0 -10000 0 0
FOSL1 0.015 0.066 -10000 0 -0.4 12 12
CREM 0.027 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.12 0.14 -10000 0 -0.4 39 39
FOS -0.053 0.16 -10000 0 -0.46 60 60
IFNG -0.25 0.26 0.35 4 -0.61 113 117
AP-1/NFAT1-c-4 -0.25 0.27 -10000 0 -0.65 98 98
FASLG -0.23 0.25 0.34 4 -0.64 88 92
NFAT1-c-4/ICER1 -0.079 0.1 -10000 0 -0.32 37 37
IL2RA -0.23 0.25 0.35 6 -0.62 90 96
FKBP12/FK506 0.019 0.005 -10000 0 -10000 0 0
CSF2 -0.31 0.27 0.35 5 -0.6 171 176
JunB/Fra1/NFAT1-c-4 -0.077 0.11 -10000 0 -0.34 29 29
IL4 -0.22 0.22 0.35 4 -0.6 75 79
IL2 -0.01 0.15 -10000 0 -0.92 12 12
IL3 -0.038 0.17 -10000 0 -0.79 20 20
FKBP1A 0.026 0.006 -10000 0 -10000 0 0
BATF3 0.024 0.038 -10000 0 -0.4 4 4
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.004 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.033 0.14 0.3 4 -0.38 56 60
CRKL -0.038 0.14 -10000 0 -0.4 58 58
HRAS -0.026 0.14 -10000 0 -0.37 40 40
mol:PIP3 -0.018 0.14 0.31 1 -0.37 55 56
SPRED1 0.027 0.003 -10000 0 -10000 0 0
SPRED2 0.025 0.031 -10000 0 -0.45 2 2
GAB1 -0.038 0.15 -10000 0 -0.42 61 61
FOXO3 -0.025 0.15 0.36 1 -0.37 58 59
AKT1 -0.028 0.16 -10000 0 -0.39 62 62
BAD -0.022 0.15 0.31 1 -0.37 51 52
megakaryocyte differentiation -0.042 0.15 -10000 0 -0.4 64 64
GSK3B -0.006 0.15 0.32 2 -0.37 40 42
RAF1 -0.017 0.11 -10000 0 -0.34 14 14
SHC1 0.027 0.004 -10000 0 -10000 0 0
STAT3 -0.039 0.15 -10000 0 -0.42 61 61
STAT1 -0.11 0.35 -10000 0 -1 63 63
HRAS/SPRED1 -0.01 0.12 -10000 0 -0.36 13 13
cell proliferation -0.04 0.15 -10000 0 -0.42 61 61
PIK3CA 0.019 0.012 -10000 0 -10000 0 0
TEC 0.007 0.092 -10000 0 -0.45 19 19
RPS6KB1 -0.029 0.15 -10000 0 -0.4 65 65
HRAS/SPRED2 -0.011 0.12 -10000 0 -0.36 16 16
LYN/TEC/p62DOK -0.015 0.16 -10000 0 -0.41 51 51
MAPK3 -0.011 0.092 0.21 1 -0.3 7 8
STAP1 -0.05 0.15 0.25 1 -0.41 65 66
GRAP2 0.015 0.071 -10000 0 -0.43 12 12
JAK2 -0.095 0.31 -10000 0 -0.86 63 63
STAT1 (dimer) -0.11 0.34 -10000 0 -0.97 63 63
mol:Gleevec 0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.022 0.17 -10000 0 -0.4 60 60
actin filament polymerization -0.041 0.14 -10000 0 -0.41 61 61
LYN 0.024 0.021 -10000 0 -0.4 1 1
STAP1/STAT5A (dimer) -0.069 0.22 -10000 0 -0.59 64 64
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
CBL/CRKL/GRB2 -0.008 0.14 0.28 1 -0.37 52 53
PI3K -0.016 0.14 -10000 0 -0.4 45 45
PTEN 0.026 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.13 0.41 -10000 0 -1.2 62 62
MAPK8 -0.041 0.16 -10000 0 -0.43 61 61
STAT3 (dimer) -0.038 0.15 -10000 0 -0.41 61 61
positive regulation of transcription -0.007 0.078 0.19 1 -0.25 6 7
mol:GDP -0.027 0.15 -10000 0 -0.38 53 53
PIK3C2B -0.039 0.15 -10000 0 -0.42 62 62
CBL/CRKL -0.018 0.14 0.28 1 -0.38 56 57
FER -0.038 0.15 -10000 0 -0.41 63 63
SH2B3 -0.038 0.15 -10000 0 -0.42 62 62
PDPK1 -0.015 0.13 0.3 1 -0.36 42 43
SNAI2 -0.037 0.14 -10000 0 -0.41 52 52
positive regulation of cell proliferation -0.077 0.26 -10000 0 -0.72 63 63
KITLG 0.017 0.045 -10000 0 -0.47 3 3
cell motility -0.077 0.26 -10000 0 -0.72 63 63
PTPN6 0.027 0.011 -10000 0 -10000 0 0
EPOR -0.016 0.17 -10000 0 -0.77 13 13
STAT5A (dimer) -0.058 0.22 -10000 0 -0.59 63 63
SOCS1 -0.004 0.11 -10000 0 -0.4 36 36
cell migration 0.042 0.15 0.42 62 -10000 0 62
SOS1 0.027 0.003 -10000 0 -10000 0 0
EPO -0.023 0.12 -10000 0 -0.4 49 49
VAV1 0.019 0.06 -10000 0 -0.45 8 8
GRB10 -0.037 0.15 -10000 0 -0.42 56 56
PTPN11 0.028 0.007 -10000 0 -10000 0 0
SCF/KIT -0.038 0.16 -10000 0 -0.44 62 62
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.013 0.093 0.19 1 -0.31 6 7
CBL 0.025 0.008 -10000 0 -10000 0 0
KIT -0.14 0.44 -10000 0 -1.2 67 67
MAP2K2 -0.013 0.093 0.23 2 -0.31 6 8
SHC/Grb2/SOS1 -0.004 0.16 -10000 0 -0.4 57 57
STAT5A -0.057 0.22 -10000 0 -0.61 63 63
GRB2 0.027 0.004 -10000 0 -10000 0 0
response to radiation -0.036 0.14 -10000 0 -0.4 52 52
SHC/GRAP2 0.03 0.054 -10000 0 -0.3 12 12
PTPRO -0.043 0.15 -10000 0 -0.41 64 64
SH2B2 -0.042 0.15 -10000 0 -0.42 61 61
DOK1 0.026 0.019 -10000 0 -0.4 1 1
MATK -0.043 0.15 -10000 0 -0.42 62 62
CREBBP 0.024 0.051 -10000 0 -10000 0 0
BCL2 -0.064 0.28 -10000 0 -0.98 29 29
Effects of Botulinum toxin

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
STX1A -0.004 0.056 -10000 0 -0.28 20 20
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.007 0.091 -10000 0 -0.32 34 34
STXBP1 0.027 0.004 -10000 0 -10000 0 0
ACh/CHRNA1 -0.075 0.14 -10000 0 -0.27 156 156
RAB3GAP2/RIMS1/UNC13B 0.022 0.082 -10000 0 -0.27 33 33
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 -0.019 0.12 -10000 0 -0.45 34 34
mol:ACh 0 0.034 0.081 36 -0.11 7 43
RAB3GAP2 0.027 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.007 0.08 -10000 0 -0.28 4 4
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.075 0.14 -10000 0 -0.27 156 156
UNC13B 0.022 0.032 -10000 0 -0.45 2 2
CHRNA1 -0.12 0.21 -10000 0 -0.43 156 156
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.05 0.12 -10000 0 -0.25 125 125
SNAP25 -0.004 0.036 -10000 0 -0.14 34 34
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.081 0.18 -10000 0 -0.4 125 125
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.014 0.051 -10000 0 -0.23 20 20
STX1A/SNAP25 fragment 1/VAMP2 0.007 0.08 -10000 0 -0.28 4 4
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.024 -10000 0 -0.28 3 3
Metarhodopsin II/Arrestin 0.02 0.023 -10000 0 -0.24 3 3
PDE6G/GNAT1/GTP 0.019 0.051 -10000 0 -0.23 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.003 0.038 -10000 0 -0.4 3 3
GRK1 -0.009 0.025 -10000 0 -0.4 1 1
CNG Channel -0.21 0.17 -10000 0 -0.41 155 155
mol:Na + -0.11 0.14 -10000 0 -0.39 46 46
mol:ADP -0.009 0.025 -10000 0 -0.4 1 1
RGS9-1/Gbeta5/R9AP 0.039 0.064 -10000 0 -0.26 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.11 0.15 -10000 0 -0.4 46 46
CNGB1 -0.19 0.21 -10000 0 -0.4 253 253
RDH5 0.025 0.029 -10000 0 -0.42 2 2
SAG -0.012 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.11 0.15 0.35 6 -0.38 46 52
Na + (4 Units) -0.11 0.13 -10000 0 -0.37 46 46
RGS9 0.017 0.064 -10000 0 -0.41 11 11
GNB1/GNGT1 -0.002 0.1 -10000 0 -0.28 58 58
GNAT1/GDP 0.039 0.064 -10000 0 -0.24 20 20
GUCY2D 0.003 0.094 -10000 0 -0.4 26 26
GNGT1 -0.03 0.14 -10000 0 -0.4 58 58
GUCY2F -0.009 0.026 -10000 0 -0.4 1 1
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.11 0.14 -10000 0 -0.26 213 213
mol:11-cis-retinal 0.025 0.029 -10000 0 -0.42 2 2
mol:cGMP 0.005 0.092 -10000 0 -0.36 5 5
GNB1 0.026 0.005 -10000 0 -10000 0 0
Rhodopsin 0.027 0.035 -10000 0 -0.29 5 5
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 -0.005 0.12 -10000 0 -0.45 32 32
Metarhodopsin II 0.02 0.021 -10000 0 -0.21 3 3
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.012 0.099 -10000 0 -0.29 9 9
RGS9BP 0.015 0.071 -10000 0 -0.45 11 11
Metarhodopsin II/Transducin -0.006 0.052 -10000 0 -0.27 8 8
GCAP Family/Ca ++ 0.011 0.08 -10000 0 -0.22 51 51
PDE6A/B -0.14 0.19 -10000 0 -0.34 230 230
mol:Pi 0.038 0.064 -10000 0 -0.26 21 21
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.007 0.083 -10000 0 -0.21 58 58
PDE6B -0.01 0.12 -10000 0 -0.42 39 39
PDE6A -0.18 0.23 -10000 0 -0.45 207 207
PDE6G 0.014 0.073 -10000 0 -0.4 15 15
RHO -0.006 0.036 -10000 0 -0.4 3 3
PDE6 -0.092 0.17 -10000 0 -0.4 36 36
GUCA1A -0.018 0.13 -10000 0 -0.4 50 50
GC2/GCAP Family 0.019 0.086 -10000 0 -0.31 3 3
GUCA1C -0.016 0.006 -10000 0 -10000 0 0
GUCA1B 0.022 0.042 -10000 0 -0.44 4 4
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.17 0.27 -10000 0 -0.82 32 32
PCK1 -0.44 0.57 -10000 0 -1.2 164 164
HNF4A -0.2 0.3 -10000 0 -0.93 34 34
KCNJ11 -0.26 0.39 -10000 0 -0.97 84 84
AKT1 -0.087 0.15 -10000 0 -0.5 10 10
response to starvation -0.002 0.014 -10000 0 -10000 0 0
DLK1 -0.34 0.46 -10000 0 -0.98 144 144
NKX2-1 -0.012 0.18 0.32 48 -0.38 14 62
ACADM -0.18 0.28 -10000 0 -0.86 31 31
TAT -0.13 0.19 -10000 0 -0.71 12 12
CEBPB 0.026 0.008 -10000 0 -10000 0 0
CEBPA 0.024 0.038 -10000 0 -0.45 3 3
TTR -0.25 0.29 -10000 0 -0.85 56 56
PKLR -0.19 0.29 -10000 0 -0.79 50 50
APOA1 -0.2 0.32 -10000 0 -1 28 28
CPT1C -0.17 0.27 -10000 0 -0.8 37 37
ALAS1 -0.082 0.16 -10000 0 -0.7 4 4
TFRC -0.15 0.22 -10000 0 -0.76 11 11
FOXF1 0.021 0.048 -10000 0 -0.4 6 6
NF1 0.032 0.005 -10000 0 -10000 0 0
HNF1A (dimer) 0.018 0.062 -10000 0 -0.39 9 9
CPT1A -0.15 0.27 -10000 0 -0.81 31 31
HMGCS1 -0.16 0.27 -10000 0 -0.79 33 33
NR3C1 0.028 0.023 -10000 0 -10000 0 0
CPT1B -0.18 0.28 -10000 0 -0.82 42 42
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.025 0.024 -10000 0 -10000 0 0
GCK -0.18 0.28 -10000 0 -0.83 34 34
CREB1 -0.038 0.1 -10000 0 -0.23 50 50
IGFBP1 -0.078 0.15 -10000 0 -0.65 4 4
PDX1 -0.092 0.17 -10000 0 -0.66 7 7
UCP2 -0.16 0.27 -10000 0 -0.79 38 38
ALDOB -0.19 0.3 -10000 0 -0.85 38 38
AFP -0.15 0.16 -10000 0 -0.45 58 58
BDH1 -0.14 0.27 -10000 0 -0.81 28 28
HADH -0.18 0.29 -10000 0 -0.83 36 36
F2 -0.21 0.32 -10000 0 -0.96 33 33
HNF1A 0.018 0.062 -10000 0 -0.39 9 9
G6PC -0.055 0.1 -10000 0 -0.49 1 1
SLC2A2 -0.098 0.16 -10000 0 -0.96 1 1
INS -0.023 0.033 -10000 0 -0.41 2 2
FOXA1 -0.16 0.24 -10000 0 -0.46 183 183
FOXA3 -0.094 0.17 -10000 0 -0.43 65 65
FOXA2 -0.22 0.32 -10000 0 -0.89 46 46
ABCC8 -0.19 0.29 -10000 0 -0.83 36 36
ALB -0.16 0.18 -10000 0 -0.55 47 47
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.035 0.063 -10000 0 -0.27 17 17
fibroblast growth factor receptor signaling pathway 0.034 0.063 -10000 0 -0.27 17 17
LAMA1 -0.13 0.2 -10000 0 -0.4 177 177
PRNP 0.026 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.008 0.12 -10000 0 -0.32 62 62
SMAD2 0.016 0.028 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.033 0.017 -10000 0 -0.23 1 1
GPC1/Laminin alpha1 -0.079 0.15 -10000 0 -0.28 177 177
TDGF1 0.003 0.05 -10000 0 -0.4 6 6
CRIPTO/GPC1 0.028 0.039 -10000 0 -0.27 7 7
APP/GPC1 0.037 0.023 -10000 0 -0.28 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.003 0.025 -10000 0 -0.22 4 4
FLT1 0.025 0.02 -10000 0 -0.4 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.045 0.031 -10000 0 -0.24 3 3
SERPINC1 0.013 0.061 -10000 0 -0.4 10 10
FYN 0.001 0.033 -10000 0 -0.23 8 8
FGR 0.002 0.032 -10000 0 -0.23 7 7
positive regulation of MAPKKK cascade 0.003 0.094 0.26 14 -0.35 9 23
SLIT2 -0.034 0.16 -10000 0 -0.45 61 61
GPC1/NRG -0.013 0.11 -10000 0 -0.28 75 75
NRG1 -0.039 0.15 -10000 0 -0.4 74 74
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.046 0.036 -10000 0 -0.24 6 6
LYN 0.001 0.033 -10000 0 -0.23 8 8
mol:Spermine 0.007 0.013 -10000 0 -0.28 1 1
cell growth 0.034 0.063 -10000 0 -0.27 17 17
BMP signaling pathway -0.025 0.02 0.4 1 -10000 0 1
SRC 0.001 0.031 -10000 0 -0.23 7 7
TGFBR1 0.027 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.27 0.23 -10000 0 -0.45 306 306
GPC1 0.025 0.02 -10000 0 -0.4 1 1
TGFBR1 (dimer) 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.022 0.043 -10000 0 -0.4 5 5
BLK -0.032 0.086 -10000 0 -0.24 71 71
HCK 0.001 0.035 -10000 0 -0.26 7 7
FGF2 0.011 0.083 -10000 0 -0.44 16 16
FGFR1 0.02 0.044 -10000 0 -0.41 5 5
VEGFR1 homodimer 0.025 0.02 -10000 0 -0.4 1 1
TGFBR2 0.022 0.032 -10000 0 -0.45 2 2
cell death 0.037 0.022 -10000 0 -0.28 2 2
ATIII/GPC1 0.03 0.048 -10000 0 -0.28 11 11
PLA2G2A/GPC1 -0.19 0.17 -10000 0 -0.32 307 307
LCK -0.004 0.047 -10000 0 -0.23 18 18
neuron differentiation -0.013 0.11 -10000 0 -0.28 75 75
PrPc/Cu2+ 0.019 0.005 -10000 0 -10000 0 0
APP 0.026 0.02 -10000 0 -0.4 1 1
TGFBR2 (dimer) 0.022 0.032 -10000 0 -0.45 2 2
Canonical Wnt 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
HDAC1 0.025 0.017 0.24 1 -10000 0 1
AES 0.026 0.015 0.21 1 -10000 0 1
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.034 0.03 -10000 0 -0.31 3 3
SMAD4 0.025 0.008 -10000 0 -10000 0 0
DKK2 0.013 0.077 -10000 0 -0.42 15 15
TLE1 0.026 0.015 0.21 1 -10000 0 1
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.035 0.12 0.26 20 -0.39 10 30
WIF1 -0.19 0.22 -10000 0 -0.45 207 207
beta catenin/RanBP3 -0.008 0.1 0.38 14 -0.4 5 19
KREMEN2 -0.13 0.2 -10000 0 -0.4 181 181
DKK1 -0.13 0.21 -10000 0 -0.4 180 180
beta catenin/beta TrCP1 0.046 0.12 0.26 20 -0.39 6 26
FZD1 0.024 0.03 -10000 0 -0.42 2 2
AXIN2 -0.018 0.2 0.58 3 -1.3 10 13
AXIN1 0.028 0.004 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.026 0.093 -10000 0 -0.61 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.13 0.33 2 -0.52 12 14
Axin1/APC/GSK3 0.041 0.069 0.25 5 -0.43 2 7
Axin1/APC/GSK3/beta catenin/Macf1 0.039 0.096 0.3 7 -0.43 4 11
HNF1A 0.018 0.059 0.2 2 -0.4 9 11
CTBP1 0.025 0.017 0.22 1 -10000 0 1
MYC 0.11 0.23 0.58 95 -0.51 2 97
RANBP3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.059 0.14 -10000 0 -0.24 183 183
NKD1 0.011 0.078 -10000 0 -0.4 17 17
TCF4 0.024 0.017 0.22 1 -10000 0 1
TCF3 0.025 0.016 0.22 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.056 0.041 -10000 0 -0.25 2 2
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.001 0.11 0.5 11 -0.43 5 16
LEF1 0.021 0.045 0.22 1 -0.4 5 6
DVL1 0.047 0.062 0.22 1 -0.49 2 3
CSNK2A1 0.026 0.007 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.061 0.1 0.29 2 -0.51 6 8
DKK1/LRP6/Kremen 2 -0.14 0.18 -10000 0 -0.29 275 275
LRP6 0.025 0.023 -10000 0 -0.45 1 1
CSNK1A1 0.025 0.018 0.25 1 -10000 0 1
NLK 0.027 0.007 -10000 0 -10000 0 0
CCND1 0.14 0.28 0.58 122 -1.4 3 125
WNT1 0.016 0.045 -10000 0 -0.4 5 5
GSK3A 0.027 0.004 -10000 0 -10000 0 0
GSK3B 0.024 0.009 -10000 0 -10000 0 0
FRAT1 0.026 0.004 -10000 0 -10000 0 0
PPP2R5D 0.035 0.078 0.24 9 -0.4 7 16
APC 0.026 0.065 0.2 31 -10000 0 31
WNT1/LRP6/FZD1 0.075 0.094 0.2 155 -10000 0 155
CREBBP 0.026 0.016 0.22 1 -10000 0 1
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTK2 0.022 0.011 -10000 0 -10000 0 0
CRKL -0.022 0.091 -10000 0 -0.24 73 73
GRB2/SOS1/SHC 0.053 0.012 -10000 0 -10000 0 0
HRAS 0.025 0.02 -10000 0 -0.41 1 1
IRS1/Crk -0.016 0.096 -10000 0 -0.24 77 77
IGF-1R heterotetramer/IGF1/PTP1B 0.001 0.11 -10000 0 -0.26 77 77
AKT1 0.009 0.11 0.23 14 -0.39 2 16
BAD 0.006 0.1 0.23 12 -0.37 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.024 0.093 -10000 0 -0.23 77 77
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.012 0.1 0.2 1 -0.24 77 78
RAF1 -0.007 0.16 0.28 10 -0.45 31 41
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.017 0.1 -10000 0 -0.23 72 72
YWHAZ 0.024 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.013 0.11 -10000 0 -0.25 81 81
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
RPS6KB1 0.013 0.11 0.18 114 -0.39 2 116
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.004 0.13 0.26 14 -0.37 25 39
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.005 0.086 -10000 0 -0.38 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.032 0.1 -10000 0 -0.26 1 1
IGF-1R heterotetramer 0.012 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.004 0.1 -10000 0 -0.24 75 75
Crk/p130 Cas/Paxillin 0.014 0.1 -10000 0 -0.35 1 1
IGF1R 0.012 0.038 -10000 0 -10000 0 0
IGF1 -0.054 0.18 -10000 0 -0.46 84 84
IRS2/Crk -0.014 0.093 -10000 0 -0.23 69 69
PI3K 0.008 0.093 -10000 0 -0.23 54 54
apoptosis -0.027 0.096 0.31 1 -0.26 14 15
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
PRKCD -0.035 0.13 -10000 0 -0.33 75 75
RAF1/14-3-3 E 0.003 0.15 0.28 12 -0.39 31 43
BAD/14-3-3 0.028 0.1 0.27 14 -0.33 1 15
PRKCZ 0.007 0.11 0.24 13 -0.39 2 15
Crk/p130 Cas/Paxillin/FAK1 0.021 0.083 -10000 0 -0.3 1 1
PTPN1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.039 0.14 -10000 0 -0.34 79 79
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.016 0.11 -10000 0 -0.23 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.009 0.099 -10000 0 -0.24 75 75
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.024 0.094 -10000 0 -0.24 77 77
IRS1 -0.026 0.1 -10000 0 -0.25 81 81
IRS2 -0.024 0.094 -10000 0 -0.24 75 75
IGF-1R heterotetramer/IGF1 -0.021 0.14 -10000 0 -0.34 79 79
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDPK1 0.021 0.11 0.26 10 -0.4 2 12
YWHAE 0.026 0.006 -10000 0 -10000 0 0
PRKD1 -0.04 0.13 -10000 0 -0.34 75 75
SHC1 0.027 0.004 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.006 -10000 0 -10000 0 0
LAT2 -0.046 0.11 -10000 0 -0.33 28 28
AP1 -0.02 0.14 0.3 1 -0.4 16 17
mol:PIP3 -0.061 0.15 0.31 12 -0.41 24 36
IKBKB -0.024 0.1 0.22 25 -0.25 12 37
AKT1 -0.025 0.15 0.39 18 -0.38 12 30
IKBKG -0.024 0.1 0.24 19 -0.25 12 31
MS4A2 0.007 0.091 -10000 0 -0.46 18 18
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.019 0.012 -10000 0 -10000 0 0
MAP3K1 0.02 0.14 0.25 74 -0.36 8 82
mol:Ca2+ -0.045 0.12 0.27 14 -0.31 24 38
LYN 0.023 0.022 -10000 0 -0.4 1 1
CBLB -0.043 0.11 -10000 0 -0.32 25 25
SHC1 0.027 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.034 0.065 -10000 0 -0.25 24 24
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.031 -10000 0 -0.45 2 2
PLD2 -0.073 0.14 0.34 9 -0.34 29 38
PTPN13 -0.034 0.12 0.36 1 -0.46 14 15
PTPN11 0.014 0.026 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.002 0.14 0.3 30 -0.32 8 38
SYK 0.024 0.039 -10000 0 -0.47 3 3
GRB2 0.027 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.067 0.14 -10000 0 -0.4 26 26
LAT -0.05 0.12 -10000 0 -0.34 30 30
PAK2 0.016 0.15 0.26 78 -0.36 12 90
NFATC2 -0.087 0.19 -10000 0 -0.58 58 58
HRAS -0.026 0.12 0.24 7 -0.38 19 26
GAB2 0.022 0.038 -10000 0 -0.45 3 3
PLA2G1B -0.061 0.27 -10000 0 -0.82 55 55
Fc epsilon R1 -0.079 0.18 -10000 0 -0.3 182 182
Antigen/IgE/Fc epsilon R1 -0.07 0.16 -10000 0 -0.27 182 182
mol:GDP -0.026 0.12 0.25 2 -0.39 18 20
JUN 0.027 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
FOS -0.032 0.16 -10000 0 -0.45 60 60
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.047 0.12 -10000 0 -0.34 29 29
CHUK -0.03 0.097 0.25 12 -0.25 12 24
KLRG1 -0.05 0.11 -10000 0 -0.35 24 24
VAV1 -0.047 0.12 -10000 0 -0.35 28 28
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.044 0.11 -10000 0 -0.33 26 26
negative regulation of mast cell degranulation -0.032 0.12 0.2 7 -0.35 22 29
BTK -0.029 0.11 -10000 0 -0.4 14 14
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.081 0.15 -10000 0 -0.39 50 50
GAB2/PI3K/SHP2 -0.06 0.11 -10000 0 -0.4 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.055 0.12 -10000 0 -0.35 26 26
RAF1 -0.07 0.3 -10000 0 -0.9 55 55
Fc epsilon R1/FcgammaRIIB/SHIP -0.052 0.17 -10000 0 -0.28 133 133
FCER1G 0.016 0.067 -10000 0 -0.4 12 12
FCER1A -0.14 0.23 -10000 0 -0.46 170 170
Antigen/IgE/Fc epsilon R1/Fyn -0.056 0.16 -10000 0 -0.26 179 179
MAPK3 -0.063 0.27 -10000 0 -0.83 55 55
MAPK1 -0.063 0.27 -10000 0 -0.83 55 55
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.008 0.14 0.33 1 -0.57 17 18
DUSP1 0.005 0.097 -10000 0 -0.45 21 21
NF-kappa-B/RelA -0.013 0.061 0.12 4 -0.19 1 5
actin cytoskeleton reorganization -0.031 0.12 0.37 1 -0.47 13 14
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.023 0.11 -10000 0 -0.38 12 12
FER -0.045 0.11 -10000 0 -0.34 27 27
RELA 0.026 0.006 -10000 0 -10000 0 0
ITK -0.021 0.072 -10000 0 -0.27 27 27
SOS1 0.027 0.003 -10000 0 -10000 0 0
PLCG1 -0.026 0.13 0.28 9 -0.4 17 26
cytokine secretion -0.013 0.041 -10000 0 -10000 0 0
SPHK1 -0.048 0.12 -10000 0 -0.33 35 35
PTK2 -0.032 0.13 0.38 1 -0.49 13 14
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.064 0.14 -10000 0 -0.41 26 26
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.056 0.15 0.34 9 -0.4 24 33
MAP2K2 -0.068 0.28 -10000 0 -0.84 55 55
MAP2K1 -0.068 0.28 -10000 0 -0.84 55 55
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.037 0.12 0.21 14 -0.34 23 37
MAP2K4 0.005 0.17 -10000 0 -0.81 21 21
Fc epsilon R1/FcgammaRIIB -0.063 0.17 -10000 0 -0.28 182 182
mol:Choline -0.072 0.14 0.33 9 -0.34 28 37
SHC/Grb2/SOS1 -0.013 0.13 0.25 1 -0.38 15 16
FYN 0.026 0.02 -10000 0 -0.4 1 1
DOK1 0.026 0.019 -10000 0 -0.4 1 1
PXN -0.031 0.12 0.33 2 -0.47 11 13
HCLS1 -0.043 0.11 0.18 1 -0.33 26 27
PRKCB -0.043 0.12 0.28 12 -0.31 21 33
FCGR2B 0.02 0.057 -10000 0 -0.45 7 7
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.033 0.12 0.2 7 -0.35 22 29
LCP2 0.023 0.033 -10000 0 -0.4 3 3
PLA2G4A -0.056 0.12 -10000 0 -0.35 42 42
RASA1 0.024 0.031 -10000 0 -0.45 2 2
mol:Phosphatidic acid -0.072 0.14 0.33 9 -0.34 28 37
IKK complex -0.011 0.091 0.22 27 -0.22 2 29
WIPF1 0.023 0.038 -10000 0 -0.4 4 4
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.023 -10000 0 -0.28 2 2
VLDLR 0.017 0.057 -10000 0 -0.45 7 7
CRKL 0.025 0.02 -10000 0 -0.4 1 1
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.026 0.02 -10000 0 -0.4 1 1
ITGA3 0.012 0.08 -10000 0 -0.4 18 18
RELN/VLDLR/Fyn -0.021 0.13 -10000 0 -0.27 99 99
MAPK8IP1/MKK7/MAP3K11/JNK1 0.066 0.045 -10000 0 -10000 0 0
AKT1 -0.022 0.079 -10000 0 -0.33 7 7
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
DAB1 -0.002 0.075 -10000 0 -0.4 16 16
RELN/LRP8/DAB1 -0.026 0.13 -10000 0 -0.25 115 115
LRPAP1/LRP8 0.032 0.045 -10000 0 -0.28 10 10
RELN/LRP8/DAB1/Fyn -0.015 0.13 -10000 0 -0.25 93 93
DAB1/alpha3/beta1 Integrin -0.024 0.12 -10000 0 -0.4 6 6
long-term memory -0.063 0.16 -10000 0 -0.44 30 30
DAB1/LIS1 -0.01 0.13 -10000 0 -0.39 6 6
DAB1/CRLK/C3G -0.018 0.12 -10000 0 -0.4 6 6
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
DAB1/NCK2 -0.009 0.13 -10000 0 -0.41 5 5
ARHGEF2 0.027 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.073 0.19 -10000 0 -0.43 105 105
CDK5R1 0.025 0.027 -10000 0 -0.4 2 2
RELN -0.071 0.19 -10000 0 -0.45 98 98
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
RELN/LRP8/Fyn -0.022 0.14 -10000 0 -0.28 106 106
GRIN2A/RELN/LRP8/DAB1/Fyn -0.06 0.17 -10000 0 -0.4 38 38
MAPK8 0.021 0.053 -10000 0 -0.45 6 6
RELN/VLDLR/DAB1 -0.026 0.12 -10000 0 -0.25 110 110
ITGB1 0.027 0.005 -10000 0 -10000 0 0
MAP1B -0.038 0.13 0.2 1 -0.27 85 86
RELN/LRP8 -0.021 0.13 -10000 0 -0.28 104 104
GRIN2B/RELN/LRP8/DAB1/Fyn -0.01 0.13 -10000 0 -0.27 38 38
PI3K 0.026 0.029 -10000 0 -0.32 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.027 0.061 -10000 0 -0.28 18 18
RAP1A -0.028 0.13 0.34 10 -0.38 6 16
PAFAH1B1 0.026 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.023 0.04 -10000 0 -0.41 4 4
CRLK/C3G 0.037 0.018 -10000 0 -0.28 1 1
GRIN2B -0.009 0.044 -10000 0 -0.4 5 5
NCK2 0.027 0.003 -10000 0 -10000 0 0
neuron differentiation -0.015 0.089 -10000 0 -0.35 7 7
neuron adhesion -0.033 0.12 0.34 9 -0.37 6 15
LRP8 0.018 0.06 -10000 0 -0.4 10 10
GSK3B -0.014 0.086 -10000 0 -0.32 7 7
RELN/VLDLR/DAB1/Fyn -0.017 0.12 -10000 0 -0.24 97 97
MAP3K11 0.026 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.023 0.089 -10000 0 -0.24 64 64
CDK5 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.17 0.21 0.8 1 -0.42 204 205
neuron migration -0.023 0.13 0.3 8 -0.42 3 11
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.015 0.09 -10000 0 -0.36 7 7
RELN/VLDLR -0.012 0.13 -10000 0 -0.26 95 95
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.025 0.02 -10000 0 -0.4 1 1
RAS family/GTP/Tiam1 -0.06 0.1 -10000 0 -0.24 68 68
NT3 (dimer)/TRKC -0.14 0.22 -10000 0 -0.38 208 208
NT3 (dimer)/TRKB -0.13 0.21 -10000 0 -0.34 218 218
SHC/Grb2/SOS1/GAB1/PI3K 0.021 0.022 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
BDNF -0.005 0.12 -10000 0 -0.43 34 34
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 -0.008 0.12 -10000 0 -0.4 40 40
NTRK2 -0.099 0.21 -10000 0 -0.44 132 132
NTRK3 -0.1 0.21 -10000 0 -0.45 126 126
NT-4/5 (dimer)/TRKB -0.047 0.16 -10000 0 -0.28 146 146
neuron apoptosis 0.042 0.12 0.38 17 -10000 0 17
SHC 2-3/Grb2 -0.045 0.13 -10000 0 -0.41 17 17
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 -0.047 0.12 -10000 0 -0.38 26 26
SHC3 -0.043 0.12 -10000 0 -0.43 18 18
STAT3 (dimer) 0.025 0.058 -10000 0 -0.34 12 12
NT3 (dimer)/TRKA -0.074 0.17 -10000 0 -0.29 178 178
RIN/GDP -0.028 0.095 0.2 10 -0.24 11 21
GIPC1 0.027 0.004 -10000 0 -10000 0 0
KRAS 0.026 0.006 -10000 0 -10000 0 0
DNAJA3 -0.012 0.087 0.21 2 -0.28 11 13
RIN/GTP 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.011 0.057 -10000 0 -0.71 3 3
MAGED1 0.023 0.041 -10000 0 -0.42 4 4
PTPN11 0.027 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.025 0.029 -10000 0 -0.42 2 2
SHC/GRB2/SOS1 0.053 0.012 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.031 0.14 -10000 0 -0.25 133 133
TRKA/NEDD4-2 0.012 0.084 -10000 0 -0.28 38 38
ELMO1 0.025 0.022 -10000 0 -0.45 1 1
RhoG/GTP/ELMO1/DOCK1 0.033 0.022 -10000 0 -0.27 2 2
NGF -0.053 0.17 -10000 0 -0.4 91 91
HRAS 0.025 0.02 -10000 0 -0.41 1 1
DOCK1 0.026 0.022 -10000 0 -0.45 1 1
GAB2 0.022 0.038 -10000 0 -0.45 3 3
RIT2 -0.014 0.011 -10000 0 -10000 0 0
RIT1 0.027 0.004 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
DNM1 -0.002 0.11 -10000 0 -0.4 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.002 0.088 0.21 1 -0.28 11 12
mol:GDP -0.045 0.13 0.25 10 -0.34 15 25
NGF (dimer) -0.053 0.16 -10000 0 -0.4 91 91
RhoG/GDP 0.018 0.016 -10000 0 -0.32 1 1
RIT1/GDP -0.027 0.095 0.18 9 -0.24 10 19
TIAM1 0.021 0.053 -10000 0 -0.45 6 6
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
BDNF (dimer)/TRKB -0.053 0.16 -10000 0 -0.28 155 155
KIDINS220/CRKL/C3G 0.037 0.018 -10000 0 -0.28 1 1
SHC/RasGAP 0.037 0.02 -10000 0 -0.32 1 1
FRS2 family/SHP2 0.051 0.016 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.065 0.019 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.003 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.21 -10000 0 -0.45 138 138
RAP1/GDP -0.028 0.077 -10000 0 -0.2 9 9
KIDINS220/CRKL 0.025 0.02 -10000 0 -0.4 1 1
BDNF (dimer) -0.005 0.12 -10000 0 -0.43 34 34
ubiquitin-dependent protein catabolic process -0.024 0.13 -10000 0 -0.24 122 122
Schwann cell development -0.036 0.032 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.062 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.029 0.042 -10000 0 -0.25 1 1
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.22 -10000 0 -0.47 128 128
ABL1 0.027 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.079 -10000 0 -0.36 7 7
STAT3 0.025 0.058 -10000 0 -0.34 12 12
axon guidance -0.16 0.2 -10000 0 -0.45 128 128
MAPK3 -0.047 0.11 0.18 7 -0.34 15 22
MAPK1 -0.045 0.11 0.18 7 -0.34 15 22
CDC42/GDP -0.025 0.098 0.2 13 -0.24 11 24
NTF3 -0.11 0.21 -10000 0 -0.45 138 138
NTF4 0.025 0.029 -10000 0 -0.42 2 2
NGF (dimer)/TRKA/FAIM -0.026 0.12 -10000 0 -0.24 113 113
PI3K 0.026 0.029 -10000 0 -0.32 2 2
FRS3 0.026 0.006 -10000 0 -10000 0 0
FAIM 0.022 0.011 -10000 0 -10000 0 0
GAB1 0.026 0.005 -10000 0 -10000 0 0
RASGRF1 -0.047 0.12 0.21 2 -0.3 48 50
SOS1 0.027 0.003 -10000 0 -10000 0 0
MCF2L -0.14 0.2 -10000 0 -0.35 210 210
RGS19 0.026 0.006 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.027 0.07 -10000 0 -0.38 2 2
Rac1/GDP -0.025 0.092 0.18 9 -0.24 10 19
NGF (dimer)/TRKA/GRIT -0.036 0.12 -10000 0 -0.24 124 124
neuron projection morphogenesis 0.005 0.12 -10000 0 -0.81 4 4
NGF (dimer)/TRKA/NEDD4-2 -0.024 0.13 -10000 0 -0.24 122 122
MAP2K1 0.022 0.036 0.36 1 -10000 0 1
NGFR 0.005 0.099 -10000 0 -0.42 25 25
NGF (dimer)/TRKA/GIPC/GAIP -0.015 0.072 -10000 0 -0.33 1 1
RAS family/GTP/PI3K 0.016 0.021 -10000 0 -0.22 2 2
FRS2 family/SHP2/GRB2/SOS1 0.072 0.026 -10000 0 -10000 0 0
NRAS 0.026 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
PRKCI 0.02 0.012 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.025 0.022 -10000 0 -0.45 1 1
MAPKKK cascade -0.027 0.11 -10000 0 -0.49 12 12
RASA1 0.024 0.031 -10000 0 -0.45 2 2
TRKA/c-Abl 0.013 0.087 -10000 0 -0.28 40 40
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.035 0.15 -10000 0 -0.26 149 149
NGF (dimer)/TRKA/p62/Atypical PKCs -0.01 0.11 -10000 0 -0.38 5 5
MATK 0.016 0.066 -10000 0 -0.4 12 12
NEDD4L 0.025 0.008 -10000 0 -10000 0 0
RAS family/GDP -0.046 0.058 -10000 0 -0.2 7 7
NGF (dimer)/TRKA -0.027 0.075 0.23 2 -0.26 21 23
Rac1/GTP -0.068 0.082 -10000 0 -0.26 27 27
FRS2 family/SHP2/CRK family 0.068 0.033 -10000 0 -10000 0 0
LPA4-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
ADCY4 -0.005 0.012 -10000 0 -0.27 1 1
ADCY5 -0.062 0.11 -10000 0 -0.27 108 108
ADCY6 -0.011 0.043 -10000 0 -0.27 13 13
ADCY7 -0.005 0.012 -10000 0 -0.27 1 1
ADCY1 -0.013 0.046 -10000 0 -0.24 20 20
ADCY2 -0.087 0.12 -10000 0 -0.27 152 152
ADCY3 -0.005 0.012 -10000 0 -0.27 1 1
ADCY8 -0.013 0.035 -10000 0 -0.23 12 12
PRKCE 0.007 0.015 -10000 0 -0.32 1 1
ADCY9 -0.006 0.021 -10000 0 -0.27 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.009 0.11 0.22 33 -0.28 6 39
Thromboxane A2 receptor signaling

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
TGM2 -0.001 0.1 -10000 0 -0.4 31 31
GNB1/GNG2 -0.044 0.068 -10000 0 -0.19 62 62
AKT1 -0.017 0.11 0.2 11 -0.31 13 24
EGF -0.06 0.18 -10000 0 -0.45 88 88
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.015 0.078 0.27 8 -0.25 7 15
mol:Ca2+ -0.032 0.14 0.24 3 -0.3 61 64
LYN 0.012 0.074 0.28 6 -0.26 10 16
RhoA/GTP -0.014 0.058 0.1 2 -10000 0 2
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.039 0.15 0.28 5 -0.34 66 71
GNG2 0.025 0.02 -10000 0 -0.4 1 1
ARRB2 0.026 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.013 0.12 0.27 1 -0.53 17 18
G beta5/gamma2 -0.056 0.088 -10000 0 -0.25 60 60
PRKCH -0.038 0.16 0.29 10 -0.35 63 73
DNM1 -0.002 0.11 -10000 0 -0.4 34 34
TXA2/TP beta/beta Arrestin3 0.005 0.042 -10000 0 -0.47 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.017 0.06 -10000 0 -0.42 9 9
G12 family/GTP -0.047 0.12 -10000 0 -0.3 61 61
ADRBK1 0.025 0.008 -10000 0 -10000 0 0
ADRBK2 0.026 0.02 -10000 0 -0.4 1 1
RhoA/GTP/ROCK1 0.031 0.014 -10000 0 -10000 0 0
mol:GDP 0.013 0.099 0.33 13 -0.21 2 15
mol:NADP 0.019 0.054 -10000 0 -0.4 8 8
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 0.003 0.1 -10000 0 -0.43 25 25
mol:IP3 -0.044 0.17 0.3 1 -0.38 62 63
cell morphogenesis 0.031 0.013 -10000 0 -10000 0 0
PLCB2 -0.068 0.22 0.33 1 -0.51 64 65
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.1 0.27 8 -0.29 12 20
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.013 0.075 0.27 8 -0.25 6 14
RHOA 0.024 0.009 -10000 0 -10000 0 0
PTGIR 0.011 0.079 -10000 0 -0.4 18 18
PRKCB1 -0.045 0.16 0.28 1 -0.37 70 71
GNAQ 0.027 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.019 0.054 -10000 0 -0.4 8 8
TXA2/TXA2-R family -0.07 0.22 0.33 1 -0.51 71 72
LCK 0.012 0.082 0.27 8 -0.26 6 14
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.012 0.073 -10000 0 -0.3 11 11
TXA2-R family/G12 family/GDP/G beta/gamma 0.014 0.086 -10000 0 -0.44 15 15
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.017 0.073 -10000 0 -0.3 10 10
MAPK14 -0.021 0.11 0.2 16 -0.24 27 43
TGM2/GTP -0.061 0.18 -10000 0 -0.44 39 39
MAPK11 -0.021 0.11 0.22 17 -0.24 26 43
ARHGEF1 -0.019 0.081 0.14 5 -0.19 23 28
GNAI2 0.024 0.009 -10000 0 -10000 0 0
JNK cascade -0.046 0.17 0.27 3 -0.38 71 74
RAB11/GDP 0.027 0.004 -10000 0 -10000 0 0
ICAM1 -0.032 0.13 0.23 3 -0.28 72 75
cAMP biosynthetic process -0.044 0.15 0.27 2 -0.36 46 48
Gq family/GTP/EBP50 -0.01 0.089 0.24 7 -0.35 9 16
actin cytoskeleton reorganization 0.031 0.013 -10000 0 -10000 0 0
SRC 0.014 0.075 0.27 8 -0.25 7 15
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
EGF/EGFR 0.007 0.098 0.23 31 -0.26 7 38
VCAM1 -0.039 0.14 0.22 4 -0.31 85 89
TP beta/Gq family/GDP/G beta5/gamma2 -0.013 0.12 0.27 1 -0.53 17 18
platelet activation -0.026 0.14 0.27 14 -0.3 55 69
PGI2/IP 0.009 0.056 -10000 0 -0.28 18 18
PRKACA 0.011 0.039 -10000 0 -0.25 5 5
Gq family/GDP/G beta5/gamma2 -0.007 0.1 0.28 1 -0.46 16 17
TXA2/TP beta/beta Arrestin2 0.001 0.05 -10000 0 -0.32 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.008 0.068 -10000 0 -0.23 35 35
mol:DAG -0.051 0.18 0.31 1 -0.42 69 70
EGFR 0.019 0.049 -10000 0 -0.45 5 5
TXA2/TP alpha -0.062 0.2 0.35 1 -0.48 58 59
Gq family/GTP -0.025 0.09 0.28 2 -0.22 82 84
YES1 0.014 0.07 0.27 6 -0.26 4 10
GNAI2/GTP 0.005 0.061 -10000 0 -0.27 10 10
PGD2/DP 0.013 0.042 -10000 0 -0.29 9 9
SLC9A3R1 0.023 0.043 -10000 0 -0.45 4 4
FYN 0.015 0.077 0.27 7 -0.25 10 17
mol:NO 0.019 0.054 -10000 0 -0.4 8 8
GNA15 0.025 0.031 -10000 0 -0.45 2 2
PGK/cGMP 0.015 0.072 -10000 0 -0.25 33 33
RhoA/GDP 0.024 0.009 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.015 0.096 -10000 0 -0.35 16 16
NOS3 0.019 0.054 -10000 0 -0.4 8 8
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.041 0.16 0.27 2 -0.35 60 62
PRKCB -0.043 0.16 0.29 4 -0.35 70 74
PRKCE -0.041 0.16 0.28 2 -0.35 62 64
PRKCD -0.048 0.16 0.27 1 -0.37 74 75
PRKCG -0.054 0.17 0.27 2 -0.39 73 75
muscle contraction -0.062 0.2 0.31 2 -0.47 72 74
PRKCZ -0.04 0.15 0.26 3 -0.34 67 70
ARR3 -0.012 0.016 -10000 0 -10000 0 0
TXA2/TP beta 0.016 0.073 -10000 0 -0.29 11 11
PRKCQ -0.045 0.16 0.28 1 -0.36 71 72
MAPKKK cascade -0.058 0.19 0.32 1 -0.44 68 69
SELE -0.045 0.16 0.23 3 -0.38 71 74
TP beta/GNAI2/GDP/G beta/gamma 0.026 0.076 -10000 0 -0.3 10 10
ROCK1 0.026 0.006 -10000 0 -10000 0 0
GNA14 -0.044 0.17 -10000 0 -0.45 72 72
chemotaxis -0.083 0.25 -10000 0 -0.59 76 76
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.003 -10000 0 -10000 0 0
GNA11 0.024 0.038 -10000 0 -0.45 3 3
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.028 0.087 -10000 0 -0.41 12 12
HDAC1 0.024 0.005 -10000 0 -10000 0 0
AES 0.026 0.005 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.036 -10000 0 -0.43 3 3
LRP6/FZD1 0.034 0.03 -10000 0 -0.31 3 3
TLE1 0.026 0.004 -10000 0 -10000 0 0
AP1 -0.018 0.093 -10000 0 -0.25 57 57
NCSTN 0.027 0.004 -10000 0 -10000 0 0
ADAM10 0.025 0.031 -10000 0 -0.45 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.017 0.12 -10000 0 -0.71 11 11
NICD/RBPSUH 0.029 0.084 -10000 0 -0.41 10 10
WIF1 -0.19 0.22 -10000 0 -0.45 207 207
NOTCH1 0.014 0.081 -10000 0 -0.42 13 13
PSENEN 0.026 0.005 -10000 0 -10000 0 0
KREMEN2 -0.13 0.2 -10000 0 -0.4 181 181
DKK1 -0.13 0.21 -10000 0 -0.4 180 180
beta catenin/beta TrCP1 -0.004 0.1 -10000 0 -0.38 17 17
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.005 -10000 0 -10000 0 0
AXIN1 0.006 0.06 -10000 0 -0.4 5 5
CtBP/CBP/TCF1/TLE1/AES 0.016 0.03 -10000 0 -0.26 1 1
PSEN1 0.026 0.006 -10000 0 -10000 0 0
FOS -0.032 0.16 -10000 0 -0.45 60 60
JUN 0.027 0.004 -10000 0 -10000 0 0
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 -0.016 0.11 -10000 0 -0.38 22 22
MAPK3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.059 0.14 -10000 0 -0.24 183 183
HNF1A 0.019 0.057 -10000 0 -0.4 9 9
CTBP1 0.025 0.007 -10000 0 -10000 0 0
MYC 0.022 0.041 -10000 0 -0.77 1 1
NKD1 0.011 0.078 -10000 0 -0.4 17 17
FZD1 0.024 0.03 -10000 0 -0.42 2 2
NOTCH1 precursor/Deltex homolog 1 0.03 0.089 -10000 0 -0.42 12 12
apoptosis -0.018 0.093 -10000 0 -0.25 57 57
Delta 1/NOTCHprecursor 0.027 0.087 -10000 0 -0.4 12 12
DLL1 0.021 0.053 -10000 0 -0.45 6 6
PPARD 0.005 0.15 -10000 0 -0.84 14 14
Gamma Secretase 0.073 0.026 -10000 0 -10000 0 0
APC -0.008 0.097 -10000 0 -0.41 20 20
DVL1 -0.012 0.071 -10000 0 -0.32 17 17
CSNK2A1 0.026 0.007 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.14 0.18 -10000 0 -0.29 275 275
LRP6 0.025 0.023 -10000 0 -0.45 1 1
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
NLK 0.012 0.005 -10000 0 -10000 0 0
CCND1 -0.002 0.15 -10000 0 -0.99 9 9
WNT1 0.011 0.046 -10000 0 -0.4 5 5
Axin1/APC/beta catenin -0.002 0.12 0.26 4 -0.47 16 20
DKK2 0.013 0.077 -10000 0 -0.42 15 15
NOTCH1 precursor/DVL1 -0.002 0.11 -10000 0 -0.5 12 12
GSK3B 0.024 0.009 -10000 0 -10000 0 0
FRAT1 0.026 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.03 0.089 -10000 0 -0.42 12 12
PPP2R5D 0.005 0.079 0.22 3 -0.38 13 16
MAPK1 0.026 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.07 0.15 -10000 0 -0.25 178 178
RBPJ 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.017 0.085 -10000 0 -0.27 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.077 0.28 2 -0.33 1 3
AP1 -0.03 0.11 -10000 0 -0.24 77 77
mol:PIP3 -0.015 0.071 -10000 0 -0.41 5 5
AKT1 0.013 0.1 0.28 10 -0.31 3 13
PTK2B -0.013 0.074 0.19 2 -0.25 16 18
RHOA -0.023 0.093 0.19 1 -0.3 38 39
PIK3CB 0.022 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.061 0.19 10 -0.31 2 12
MAGI3 0.024 0.031 -10000 0 -0.45 2 2
RELA 0.026 0.006 -10000 0 -10000 0 0
apoptosis -0.013 0.082 -10000 0 -0.27 28 28
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
positive regulation of microtubule depolymerization -0.084 0.13 0.2 24 -0.3 46 70
NF kappa B1 p50/RelA -0.017 0.085 -10000 0 -0.35 6 6
endothelial cell migration -0.037 0.13 -10000 0 -0.36 72 72
ADCY4 -0.008 0.082 -10000 0 -0.35 14 14
ADCY5 -0.044 0.11 -10000 0 -0.38 21 21
ADCY6 -0.012 0.092 -10000 0 -0.38 16 16
ADCY7 -0.006 0.08 -10000 0 -0.35 13 13
ADCY1 -0.011 0.083 0.22 1 -0.35 14 15
ADCY2 -0.059 0.11 0.22 1 -0.38 22 23
ADCY3 -0.008 0.082 -10000 0 -0.35 14 14
ADCY8 -0.015 0.079 -10000 0 -0.34 14 14
ADCY9 -0.008 0.084 -10000 0 -0.36 14 14
GSK3B 0.007 0.094 0.21 50 -0.26 8 58
arachidonic acid secretion -0.006 0.083 -10000 0 -0.35 14 14
GNG2 0.025 0.02 -10000 0 -0.39 1 1
TRIP6 0.015 0.017 -10000 0 -10000 0 0
GNAO1 -0.014 0.079 -10000 0 -0.19 75 75
HRAS 0.025 0.02 -10000 0 -0.41 1 1
NFKBIA -0.007 0.078 0.28 3 -0.32 5 8
GAB1 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.003 0.19 -10000 0 -0.82 25 25
JUN 0.027 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.022 0.04 -10000 0 -0.29 1 1
TIAM1 -0.019 0.22 -10000 0 -0.96 25 25
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
mol:IP3 -0.012 0.06 0.19 10 -0.32 2 12
PLCB3 0.008 0.036 0.19 4 -0.26 1 5
FOS -0.033 0.16 -10000 0 -0.45 60 60
positive regulation of mitosis -0.006 0.083 -10000 0 -0.35 14 14
LPA/LPA1-2-3 0.011 0.098 -10000 0 -0.28 26 26
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation 0.002 0.074 0.21 5 -0.33 4 9
GNAZ -0.022 0.093 -10000 0 -0.26 42 42
EGFR/PI3K-beta/Gab1 -0.009 0.077 -10000 0 -0.43 5 5
positive regulation of dendritic cell cytokine production 0.01 0.097 -10000 0 -0.28 26 26
LPA/LPA2/MAGI-3 0.02 0.042 -10000 0 -0.27 2 2
ARHGEF1 0.005 0.088 0.35 2 -0.25 16 18
GNAI2 -0.014 0.078 -10000 0 -0.24 23 23
GNAI3 -0.014 0.082 -10000 0 -0.23 36 36
GNAI1 -0.014 0.082 -10000 0 -0.2 76 76
LPA/LPA3 -0.001 0.062 -10000 0 -0.27 16 16
LPA/LPA2 0.007 0.037 -10000 0 -0.13 7 7
LPA/LPA1 -0.015 0.098 -10000 0 -0.23 78 78
HB-EGF/EGFR -0.14 0.12 -10000 0 -0.24 302 302
HBEGF -0.19 0.13 -10000 0 -0.28 347 347
mol:DAG -0.012 0.06 0.19 10 -0.32 2 12
cAMP biosynthetic process -0.017 0.084 0.24 1 -0.35 14 15
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN 0.001 0.083 0.28 6 -0.32 5 11
GNAQ 0.002 0.047 -10000 0 -0.25 11 11
LPAR2 0.027 0.003 -10000 0 -10000 0 0
LPAR3 0.016 0.071 -10000 0 -0.45 11 11
LPAR1 -0.004 0.091 -10000 0 -0.38 17 17
IL8 -0.12 0.13 0.36 2 -0.4 32 34
PTK2 -0.013 0.08 0.19 6 -0.27 22 28
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
CASP3 -0.014 0.083 -10000 0 -0.27 28 28
EGFR 0.019 0.049 -10000 0 -0.45 5 5
PLCG1 -0.013 0.062 0.16 1 -0.26 15 16
PLD2 -0.011 0.085 0.19 10 -0.26 25 35
G12/G13 0.017 0.085 -10000 0 -0.26 16 16
PI3K-beta -0.017 0.077 -10000 0 -0.32 6 6
cell migration 0.009 0.069 -10000 0 -0.24 21 21
SLC9A3R2 0.026 0.019 -10000 0 -0.4 1 1
PXN 0.002 0.075 0.21 5 -0.34 4 9
HRAS/GTP -0.008 0.083 -10000 0 -0.36 14 14
RAC1 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.27 0.19 -10000 0 -0.4 349 349
PRKCE 0.026 0.022 -10000 0 -0.45 1 1
PRKCD -0.011 0.057 0.2 5 -0.33 1 6
Gi(beta/gamma) -0.003 0.079 -10000 0 -0.32 13 13
mol:LPA -0.016 0.047 -10000 0 -0.2 7 7
TRIP6/p130 Cas/FAK1/Paxillin 0.013 0.079 -10000 0 -0.38 3 3
MAPKKK cascade -0.006 0.083 -10000 0 -0.35 14 14
contractile ring contraction involved in cytokinesis -0.029 0.1 0.19 1 -0.31 42 43
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.036 0.1 -10000 0 -0.25 82 82
GNA15 0.001 0.053 -10000 0 -0.28 12 12
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.003 -10000 0 -10000 0 0
MAPT -0.086 0.13 0.2 24 -0.31 46 70
GNA11 0.001 0.051 -10000 0 -0.25 14 14
Rac1/GTP 0.002 0.2 -10000 0 -0.86 25 25
MMP2 -0.037 0.14 -10000 0 -0.36 72 72
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.049 0.17 -10000 0 -0.46 68 68
NFATC2 -0.029 0.19 -10000 0 -0.57 30 30
NFATC3 -0.006 0.068 -10000 0 -0.28 3 3
CD40LG -0.26 0.31 -10000 0 -0.86 54 54
ITCH 0.004 0.077 -10000 0 -10000 0 0
CBLB 0.001 0.079 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.21 0.31 -10000 0 -0.83 69 69
JUNB 0.027 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.098 -10000 0 -0.26 55 55
T cell anergy -0.011 0.14 0.3 6 -0.38 46 52
TLE4 -0.017 0.13 -10000 0 -0.5 12 12
Jun/NFAT1-c-4/p21SNFT -0.099 0.23 -10000 0 -0.85 16 16
AP-1/NFAT1-c-4 -0.26 0.31 -10000 0 -0.93 43 43
IKZF1 -0.021 0.15 -10000 0 -0.5 26 26
T-helper 2 cell differentiation -0.068 0.2 -10000 0 -0.71 24 24
AP-1/NFAT1 -0.09 0.17 -10000 0 -0.45 50 50
CALM1 0.013 0.062 -10000 0 -10000 0 0
EGR2 -0.064 0.25 -10000 0 -1.4 12 12
EGR3 -0.058 0.23 -10000 0 -1.2 11 11
NFAT1/FOXP3 -0.061 0.21 -10000 0 -0.52 57 57
EGR1 0.004 0.097 -10000 0 -0.45 21 21
JUN -0.023 0.042 -10000 0 -0.2 1 1
EGR4 -0.027 0.14 -10000 0 -0.4 60 60
mol:Ca2+ -0.011 0.056 -10000 0 -0.21 3 3
GBP3 -0.033 0.17 -10000 0 -0.56 32 32
FOSL1 0.015 0.066 -10000 0 -0.4 12 12
NFAT1-c-4/MAF/IRF4 -0.057 0.22 -10000 0 -0.84 17 17
DGKA -0.017 0.13 -10000 0 -0.47 14 14
CREM 0.026 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.24 -10000 0 -0.89 19 19
CTLA4 -0.088 0.22 -10000 0 -0.56 69 69
NFAT1-c-4 (dimer)/EGR1 -0.065 0.23 -10000 0 -0.92 16 16
NFAT1-c-4 (dimer)/EGR4 -0.08 0.22 -10000 0 -0.86 17 17
FOS -0.08 0.15 -10000 0 -0.47 60 60
IFNG -0.12 0.23 -10000 0 -0.76 26 26
T cell activation -0.092 0.16 -10000 0 -0.62 10 10
MAF 0.021 0.048 -10000 0 -0.45 5 5
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.042 0.15 0.68 13 -10000 0 13
TNF -0.099 0.22 -10000 0 -0.78 25 25
FASLG -0.12 0.34 -10000 0 -1.3 26 26
TBX21 -0.015 0.11 -10000 0 -0.44 29 29
BATF3 0.024 0.038 -10000 0 -0.4 4 4
PRKCQ 0.012 0.073 -10000 0 -0.44 11 11
PTPN1 -0.017 0.13 -10000 0 -0.46 16 16
NFAT1-c-4/ICER1 -0.056 0.21 -10000 0 -0.88 14 14
GATA3 0.01 0.083 -10000 0 -0.4 19 19
T-helper 1 cell differentiation -0.12 0.23 -10000 0 -0.74 26 26
IL2RA -0.19 0.28 -10000 0 -0.74 71 71
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.13 -10000 0 -0.46 14 14
E2F1 0.013 0.081 -10000 0 -0.39 19 19
PPARG -0.14 0.22 -10000 0 -0.45 165 165
SLC3A2 -0.017 0.13 -10000 0 -0.44 21 21
IRF4 -0.003 0.11 -10000 0 -0.41 33 33
PTGS2 -0.26 0.3 -10000 0 -0.82 64 64
CSF2 -0.33 0.32 -10000 0 -0.83 78 78
JunB/Fra1/NFAT1-c-4 -0.045 0.21 -10000 0 -0.86 14 14
IL4 -0.07 0.21 -10000 0 -0.76 22 22
IL5 -0.24 0.28 -10000 0 -0.83 43 43
IL2 -0.093 0.16 -10000 0 -0.64 9 9
IL3 -0.057 0.14 -10000 0 -0.72 18 18
RNF128 -0.038 0.19 -10000 0 -0.52 62 62
NFATC1 -0.042 0.15 -10000 0 -0.68 13 13
CDK4 0.04 0.12 0.57 6 -10000 0 6
PTPRK -0.016 0.13 -10000 0 -0.43 21 21
IL8 -0.27 0.31 -10000 0 -0.82 64 64
POU2F1 0.027 0.004 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.028 0.13 -10000 0 -0.35 32 32
TBX21 -0.094 0.34 -10000 0 -0.99 42 42
B2M 0.02 0.02 -10000 0 -10000 0 0
TYK2 0.017 0.038 -10000 0 -0.42 1 1
IL12RB1 -0.018 0.13 -10000 0 -0.42 44 44
GADD45B -0.045 0.24 -10000 0 -0.75 18 18
IL12RB2 -0.059 0.17 -10000 0 -0.4 91 91
GADD45G -0.048 0.25 -10000 0 -0.82 18 18
natural killer cell activation 0.001 0.02 0.04 5 -0.043 21 26
RELB 0.023 0.038 -10000 0 -0.4 4 4
RELA 0.026 0.006 -10000 0 -10000 0 0
IL18 0.011 0.075 -10000 0 -0.45 12 12
IL2RA -0.013 0.12 -10000 0 -0.4 46 46
IFNG -0.064 0.17 -10000 0 -0.4 101 101
STAT3 (dimer) -0.055 0.25 -10000 0 -0.7 35 35
HLA-DRB5 -0.002 0.007 -10000 0 -0.023 34 34
FASLG -0.099 0.35 0.55 1 -1 43 44
NF kappa B2 p52/RelB -0.068 0.3 -10000 0 -0.85 37 37
CD4 0.019 0.034 -10000 0 -0.43 2 2
SOCS1 -0.004 0.11 -10000 0 -0.4 36 36
EntrezGene:6955 -0.004 0.012 -10000 0 -0.028 64 64
CD3D 0.001 0.083 -10000 0 -0.43 16 16
CD3E 0.005 0.072 -10000 0 -0.42 12 12
CD3G -0.01 0.11 -10000 0 -0.44 27 27
IL12Rbeta2/JAK2 -0.028 0.12 -10000 0 -0.28 82 82
CCL3 -0.085 0.31 -10000 0 -0.96 33 33
CCL4 -0.081 0.3 -10000 0 -0.94 33 33
HLA-A -0.002 0.008 -10000 0 -0.027 26 26
IL18/IL18R 0.035 0.096 -10000 0 -0.28 30 30
NOS2 -0.089 0.32 -10000 0 -0.93 38 38
IL12/IL12R/TYK2/JAK2/SPHK2 -0.017 0.12 0.2 1 -0.32 28 29
IL1R1 -0.075 0.3 0.52 2 -0.9 32 34
IL4 -0.003 0.035 -10000 0 -10000 0 0
JAK2 0.015 0.031 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.012 -10000 0 -0.03 38 38
TCR/CD3/MHC I/CD8 -0.069 0.23 -10000 0 -0.65 46 46
RAB7A -0.013 0.23 0.48 3 -0.7 10 13
lysosomal transport -0.01 0.22 0.48 3 -0.66 10 13
FOS -0.17 0.46 -10000 0 -1.2 73 73
STAT4 (dimer) -0.044 0.27 0.42 3 -0.78 28 31
STAT5A (dimer) -0.1 0.32 -10000 0 -0.86 49 49
GZMA -0.1 0.34 -10000 0 -1.1 38 38
GZMB -0.094 0.33 -10000 0 -0.99 34 34
HLX 0.024 0.033 -10000 0 -0.4 3 3
LCK -0.089 0.32 -10000 0 -0.94 38 38
TCR/CD3/MHC II/CD4 -0.028 0.13 -10000 0 -0.33 51 51
IL2/IL2R 0.021 0.11 -10000 0 -0.38 11 11
MAPK14 -0.044 0.25 -10000 0 -0.74 24 24
CCR5 -0.079 0.29 -10000 0 -0.94 25 25
IL1B -0.026 0.14 -10000 0 -0.4 53 53
STAT6 -0.007 0.11 -10000 0 -0.9 2 2
STAT4 0.017 0.063 -10000 0 -0.4 11 11
STAT3 0.027 0.003 -10000 0 -10000 0 0
STAT1 0.008 0.085 -10000 0 -0.4 21 21
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B -0.019 0.12 -10000 0 -0.41 43 43
CD8A -0.019 0.13 -10000 0 -0.42 46 46
CD8B -0.026 0.14 -10000 0 -0.43 53 53
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.027 0.13 0.35 32 -10000 0 32
IL2RB 0.021 0.051 -10000 0 -0.4 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.038 0.25 0.42 3 -0.72 27 30
IL2RG 0.012 0.079 -10000 0 -0.4 17 17
IL12 -0.013 0.11 -10000 0 -0.3 51 51
STAT5A 0.027 0.003 -10000 0 -10000 0 0
CD247 -0.002 0.091 -10000 0 -0.42 21 21
IL2 -0.003 0.028 -10000 0 -0.4 1 1
SPHK2 0.027 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.001 0.082 -10000 0 -0.45 14 14
IL12/IL12R/TYK2/JAK2 -0.089 0.33 -10000 0 -0.97 38 38
MAP2K3 -0.044 0.25 -10000 0 -0.69 28 28
RIPK2 0.024 0.009 -10000 0 -10000 0 0
MAP2K6 -0.051 0.26 -10000 0 -0.78 24 24
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.008 -10000 0 -0.026 44 44
IL18RAP 0.009 0.086 -10000 0 -0.42 18 18
IL12Rbeta1/TYK2 0.002 0.11 -10000 0 -0.31 45 45
EOMES -0.11 0.28 -10000 0 -0.87 38 38
STAT1 (dimer) -0.072 0.27 -10000 0 -0.72 41 41
T cell proliferation -0.015 0.21 0.36 3 -0.56 26 29
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.023 0.033 -10000 0 -0.44 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.064 0.21 -10000 0 -0.64 24 24
ATF2 -0.035 0.24 0.45 1 -0.7 22 23
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.034 0.049 -10000 0 -0.21 18 18
RGS9BP 0.015 0.071 -10000 0 -0.45 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.009 0.025 -10000 0 -0.4 1 1
mol:Na + -0.007 0.09 -10000 0 -0.23 65 65
mol:ADP -0.022 0.063 -10000 0 -0.28 26 26
GNAT2 0.02 0.017 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.039 0.064 -10000 0 -0.26 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0.009 -10000 0 -10000 0 0
GRK7 -0.004 0.095 -10000 0 -0.4 27 27
CNGB3 -0.038 0.14 -10000 0 -0.4 66 66
Cone Metarhodopsin II/X-Arrestin 0.013 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.13 0.18 30 -0.24 128 158
Cone PDE6 0.049 0.062 -10000 0 -0.24 12 12
Cone Metarhodopsin II 0.01 0.054 -10000 0 -0.21 26 26
Na + (4 Units) -0.039 0.12 -10000 0 -0.23 133 133
GNAT2/GDP 0.046 0.059 -10000 0 -0.22 20 20
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.039 0.18 21 -10000 0 21
Cone Transducin 0.037 0.052 -10000 0 -0.22 18 18
SLC24A2 -0.061 0.16 -10000 0 -0.4 93 93
GNB3/GNGT2 0.026 0.062 -10000 0 -0.29 18 18
GNB3 0.012 0.074 -10000 0 -0.4 15 15
GNAT2/GTP 0.019 0.004 -10000 0 -10000 0 0
CNGA3 0.009 0.029 -10000 0 -0.4 1 1
ARR3 -0.012 0.016 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.006 0.09 -10000 0 -0.24 65 65
mol:Pi 0.038 0.064 -10000 0 -0.26 21 21
Cone CNG Channel 0.013 0.084 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.061 0.16 -10000 0 -0.4 93 93
RGS9 0.017 0.064 -10000 0 -0.41 11 11
PDE6C -0.011 0.017 -10000 0 -10000 0 0
GNGT2 0.024 0.036 -10000 0 -0.43 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.011 0.016 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.021 -10000 0 -0.27 3 3
SNTA1 0.025 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.009 0.027 -10000 0 -0.26 5 5
MAPK12 -0.017 0.066 0.18 2 -0.24 38 40
CCND1 -0.002 0.061 -10000 0 -0.45 7 7
p38 gamma/SNTA1 0.004 0.074 0.22 8 -0.24 25 33
MAP2K3 0.026 0.005 -10000 0 -10000 0 0
PKN1 0.025 0.027 -10000 0 -0.4 2 2
G2/M transition checkpoint -0.017 0.066 0.18 2 -0.24 38 40
MAP2K6 -0.01 0.059 -10000 0 -0.26 25 25
MAPT -0.13 0.15 0.2 2 -0.3 212 214
MAPK13 0.012 0.027 -10000 0 -0.32 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.011 -10000 0 -0.16 2 2
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.003 0.094 -10000 0 -0.34 11 11
PDGFB-D/PDGFRB/SLAP -0.022 0.12 -10000 0 -0.27 85 85
PDGFB-D/PDGFRB/APS/CBL -0.001 0.1 -10000 0 -0.23 82 82
AKT1 0.024 0.12 0.36 15 -0.33 2 17
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.11 0.27 14 -0.36 16 30
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
FGR -0.018 0.11 0.34 1 -0.46 13 14
mol:Ca2+ 0 0.12 0.27 14 -0.38 21 35
MYC 0.056 0.13 0.38 32 -10000 0 32
SHC1 0.027 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.003 0.093 -10000 0 -0.23 2 2
LRP1/PDGFRB/PDGFB -0.002 0.12 -10000 0 -0.24 89 89
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 0.027 0.002 -10000 0 -10000 0 0
GO:0007205 -0.001 0.12 0.26 14 -0.39 21 35
PTEN 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.031 -10000 0 -0.45 2 2
PDGFB-D/PDGFRB/SHP2 -0.017 0.12 -10000 0 -0.27 88 88
PDGFB-D/PDGFRB/GRB10 -0.015 0.12 -10000 0 -0.27 83 83
cell cycle arrest -0.022 0.12 -10000 0 -0.27 85 85
HRAS 0.025 0.02 -10000 0 -0.41 1 1
HIF1A 0.019 0.11 0.34 15 -0.31 1 16
GAB1 0.004 0.11 0.28 8 -0.38 11 19
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.004 0.1 0.26 14 -0.36 7 21
PDGFB-D/PDGFRB 0.001 0.1 -10000 0 -0.23 82 82
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.017 0.12 -10000 0 -0.27 88 88
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.004 0.08 -10000 0 -0.39 2 2
positive regulation of MAPKKK cascade -0.017 0.12 -10000 0 -0.27 88 88
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
mol:IP3 -0.001 0.12 0.27 14 -0.39 21 35
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.018 0.12 -10000 0 -0.28 88 88
SHB 0.024 0.009 -10000 0 -10000 0 0
BLK -0.058 0.15 -10000 0 -0.5 36 36
PTPN2 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.017 0.12 -10000 0 -0.27 86 86
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.01 0.11 0.31 12 -0.4 10 22
CBL 0.025 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.016 0.12 -10000 0 -0.27 86 86
LCK -0.019 0.11 0.34 1 -0.61 6 7
PDGFRB -0.048 0.16 -10000 0 -0.39 88 88
ACP1 0.027 0.003 -10000 0 -10000 0 0
HCK -0.011 0.093 -10000 0 -0.76 3 3
ABL1 0.001 0.11 0.27 14 -0.39 10 24
PDGFB-D/PDGFRB/CBL 0.001 0.12 0.3 4 -0.42 18 22
PTPN1 0.026 0.006 -10000 0 -10000 0 0
SNX15 0.026 0.006 -10000 0 -10000 0 0
STAT3 0.027 0.003 -10000 0 -10000 0 0
STAT1 0.008 0.085 -10000 0 -0.4 21 21
cell proliferation 0.056 0.13 0.36 37 -10000 0 37
SLA 0.02 0.034 -10000 0 -0.4 3 3
actin cytoskeleton reorganization 0.029 0.11 0.34 10 -10000 0 10
SRC -0.013 0.1 -10000 0 -0.66 6 6
PI3K -0.017 0.066 -10000 0 -0.35 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.001 0.11 -10000 0 -0.23 87 87
SH2B2 0.025 0.02 -10000 0 -0.4 1 1
PLCgamma1/SPHK1 0.006 0.12 0.27 14 -0.38 15 29
LYN -0.009 0.073 -10000 0 -10000 0 0
LRP1 0.026 0.022 -10000 0 -0.45 1 1
SOS1 0.027 0.003 -10000 0 -10000 0 0
STAT5B 0.027 0.003 -10000 0 -10000 0 0
STAT5A 0.027 0.003 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.018 0.093 -10000 0 -10000 0 0
SPHK1 0.018 0.062 -10000 0 -0.39 11 11
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG -0.001 0.12 0.27 14 -0.39 21 35
PLCG1 -0.001 0.12 0.27 14 -0.4 21 35
NHERF/PDGFRB 0 0.11 -10000 0 -0.24 89 89
YES1 -0.021 0.097 0.35 1 -0.55 8 9
cell migration -0.001 0.11 -10000 0 -0.24 89 89
SHC/Grb2/SOS1 0.026 0.098 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.019 -10000 0 -0.4 1 1
SLC9A3R1 0.023 0.043 -10000 0 -0.45 4 4
NHERF1-2/PDGFRB/PTEN 0.012 0.11 -10000 0 -0.22 81 81
FYN -0.015 0.092 -10000 0 -0.37 10 10
DOK1 -0.01 0.097 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.014 -10000 0 -0.28 1 1
PDGFB 0.02 0.054 -10000 0 -0.4 8 8
RAC1 0.023 0.12 0.34 16 -0.4 6 22
PRKCD -0.01 0.094 -10000 0 -10000 0 0
FER -0.009 0.097 0.19 2 -10000 0 2
MAPKKK cascade -0.017 0.097 0.36 7 -10000 0 7
RASA1 -0.009 0.099 0.18 16 -0.25 2 18
NCK1 0.023 0.011 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.002 0.095 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.018 0.12 -10000 0 -0.27 86 86
chemotaxis 0.002 0.11 0.27 14 -0.38 10 24
STAT1-3-5/STAT1-3-5 0.006 0.1 -10000 0 -0.36 6 6
Bovine Papilomavirus E5/PDGFRB -0.032 0.11 -10000 0 -0.27 88 88
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
Arf6 signaling events

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.028 0.036 -10000 0 -0.27 6 6
ARNO/beta Arrestin1-2 0.012 0.12 -10000 0 -0.75 8 8
EGFR 0.019 0.049 -10000 0 -0.45 5 5
EPHA2 0.019 0.057 -10000 0 -0.45 7 7
USP6 0.025 0.02 -10000 0 -0.4 1 1
IQSEC1 0.024 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.025 0.14 -10000 0 -0.33 80 80
ARRB2 0.009 0.003 -10000 0 -10000 0 0
mol:GTP 0.036 0.05 0.12 71 -0.16 2 73
ARRB1 0.023 0.031 -10000 0 -0.45 2 2
FBXO8 0.026 0.006 -10000 0 -10000 0 0
TSHR 0.007 0.071 -10000 0 -0.4 14 14
EGF -0.06 0.18 -10000 0 -0.45 88 88
somatostatin receptor activity 0 0 0.001 28 -0.001 22 50
ARAP2 0.021 0.048 -10000 0 -0.45 5 5
mol:GDP -0.004 0.091 0.18 12 -0.26 26 38
mol:PI-3-4-5-P3 0 0 0.001 14 -0.001 8 22
ITGA2B -0.013 0.12 -10000 0 -0.4 47 47
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.051 0.043 -10000 0 -0.25 5 5
ADAP1 0.024 0.023 -10000 0 -0.45 1 1
KIF13B 0.02 0.048 -10000 0 -0.45 5 5
HGF/MET 0.02 0.078 -10000 0 -0.3 26 26
PXN 0.027 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.007 0.11 0.21 23 -0.28 20 43
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.012 0.12 -10000 0 -0.28 80 80
ADRB2 -0.006 0.12 -10000 0 -0.45 33 33
receptor agonist activity 0 0 0 26 0 13 39
actin filament binding 0 0 0 28 -0.001 21 49
SRC 0.026 0.007 -10000 0 -10000 0 0
ITGB3 0.01 0.086 -10000 0 -0.42 19 19
GNAQ 0.027 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 51 -0.001 15 66
ARF6/GDP 0.036 0.12 0.25 23 -0.5 10 33
ARF6/GDP/GULP/ACAP1 -0.044 0.15 0.25 1 -0.34 50 51
alphaIIb/beta3 Integrin/paxillin/GIT1 0.032 0.1 -10000 0 -0.31 9 9
ACAP1 0.016 0.065 -10000 0 -0.4 12 12
ACAP2 0.02 0.012 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.016 0.014 -10000 0 -10000 0 0
EFNA1 0.027 0.004 -10000 0 -10000 0 0
HGF 0.007 0.092 -10000 0 -0.44 20 20
CYTH3 0.007 0.002 -10000 0 -10000 0 0
CYTH2 0.003 0.13 -10000 0 -0.98 8 8
NCK1 0.023 0.011 -10000 0 -10000 0 0
fibronectin binding 0 0 0 19 0 18 37
endosomal lumen acidification 0 0 0 40 0 18 58
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.11 0.22 -10000 0 -0.45 142 142
GNAQ/ARNO 0.02 0.12 -10000 0 -0.91 8 8
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 14 0 4 18
MET 0.021 0.049 -10000 0 -0.42 6 6
GNA14 -0.044 0.17 -10000 0 -0.45 72 72
GNA15 0.025 0.031 -10000 0 -0.45 2 2
GIT1 0.027 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 34 -0.001 17 51
GNA11 0.024 0.038 -10000 0 -0.45 3 3
LHCGR -0.012 0.016 -10000 0 -10000 0 0
AGTR1 -0.018 0.12 -10000 0 -0.45 36 36
desensitization of G-protein coupled receptor protein signaling pathway 0.016 0.014 -10000 0 -10000 0 0
IPCEF1/ARNO -0.012 0.14 -10000 0 -0.82 8 8
alphaIIb/beta3 Integrin -0.002 0.11 -10000 0 -0.3 63 63
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.022 0.12 0.25 6 -0.38 22 28
IKBKB 0.006 0.096 0.26 12 -0.32 9 21
AKT1 0.003 0.11 0.27 32 -0.23 18 50
IKBKG 0.015 0.081 0.24 10 -0.27 5 15
CALM1 -0.007 0.1 0.28 9 -0.38 12 21
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
MAP3K1 -0.031 0.15 0.31 5 -0.53 21 26
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.1 0.27 3 -0.38 14 17
DOK1 0.026 0.019 -10000 0 -0.4 1 1
AP-1 -0.013 0.092 0.22 15 -0.24 14 29
LYN 0.024 0.021 -10000 0 -0.4 1 1
BLNK -0.017 0.14 -10000 0 -0.45 45 45
SHC1 0.027 0.004 -10000 0 -10000 0 0
BCR complex -0.041 0.16 -10000 0 -0.34 105 105
CD22 -0.054 0.15 -10000 0 -0.43 51 51
CAMK2G -0.006 0.097 0.27 9 -0.37 10 19
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
INPP5D 0.024 0.031 -10000 0 -0.45 2 2
SHC/GRB2/SOS1 -0.04 0.12 -10000 0 -0.39 26 26
GO:0007205 -0.013 0.1 0.27 3 -0.39 14 17
SYK 0.024 0.038 -10000 0 -0.45 3 3
ELK1 -0.012 0.099 0.25 4 -0.38 13 17
NFATC1 -0.047 0.13 0.26 6 -0.39 32 38
B-cell antigen/BCR complex -0.041 0.16 -10000 0 -0.34 105 105
PAG1/CSK 0.035 0.02 -10000 0 -0.28 1 1
NFKBIB 0.018 0.045 0.13 16 -0.13 13 29
HRAS -0.015 0.1 0.27 4 -0.38 12 16
NFKBIA 0.018 0.044 0.13 16 -0.13 11 27
NF-kappa-B/RelA/I kappa B beta 0.022 0.039 0.13 16 -10000 0 16
RasGAP/Csk 0.001 0.14 -10000 0 -0.32 47 47
mol:GDP -0.01 0.098 0.25 3 -0.38 13 16
PTEN 0.026 0.006 -10000 0 -10000 0 0
CD79B 0.006 0.095 -10000 0 -0.42 23 23
NF-kappa-B/RelA/I kappa B alpha 0.022 0.039 0.13 16 -10000 0 16
GRB2 0.027 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.051 0.16 0.29 2 -0.48 28 30
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
mol:IP3 -0.014 0.1 0.23 6 -0.38 15 21
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.032 0.12 0.27 10 -0.36 25 35
CHUK 0.008 0.092 0.24 9 -0.33 11 20
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.003 0.11 0.24 5 -0.35 17 22
PTPN6 -0.053 0.14 -10000 0 -0.41 50 50
RELA 0.026 0.006 -10000 0 -10000 0 0
BCL2A1 0.014 0.033 0.11 5 -10000 0 5
VAV2 -0.063 0.16 -10000 0 -0.51 31 31
ubiquitin-dependent protein catabolic process 0.021 0.044 0.13 17 -0.13 13 30
BTK 0.018 0.051 -10000 0 -1 1 1
CD19 -0.067 0.16 -10000 0 -0.4 75 75
MAP4K1 0.014 0.072 -10000 0 -0.41 14 14
CD72 -0.025 0.14 -10000 0 -0.4 57 57
PAG1 0.024 0.021 -10000 0 -0.4 1 1
MAPK14 -0.024 0.13 0.28 6 -0.44 21 27
SH3BP5 0.021 0.038 -10000 0 -0.45 3 3
PIK3AP1 -0.019 0.11 -10000 0 -0.38 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.04 0.14 -10000 0 -0.45 26 26
RAF1 -0.015 0.097 0.27 4 -0.37 11 15
RasGAP/p62DOK/SHIP -0.001 0.14 -10000 0 -0.42 23 23
CD79A -0.065 0.18 -10000 0 -0.41 102 102
re-entry into mitotic cell cycle -0.013 0.092 0.22 15 -0.24 14 29
RASA1 0.024 0.031 -10000 0 -0.45 2 2
MAPK3 -0.01 0.088 0.26 5 -0.32 10 15
MAPK1 -0.007 0.091 0.26 8 -0.32 9 17
CD72/SHP1 -0.05 0.17 0.32 4 -0.44 53 57
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.028 0.13 0.29 6 -0.44 22 28
actin cytoskeleton organization -0.047 0.14 0.3 3 -0.43 31 34
NF-kappa-B/RelA 0.047 0.075 0.24 16 -10000 0 16
Calcineurin 0.014 0.098 0.27 6 -0.35 10 16
PI3K -0.054 0.13 -10000 0 -0.41 43 43
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.013 0.1 0.22 3 -0.39 19 22
SOS1 0.027 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.034 0.2 -10000 0 -0.7 31 31
DAPP1 -0.047 0.21 -10000 0 -0.77 31 31
cytokine secretion -0.044 0.12 0.26 6 -0.37 31 37
mol:DAG -0.014 0.1 0.23 6 -0.38 15 21
PLCG2 0.025 0.022 -10000 0 -0.45 1 1
MAP2K1 -0.012 0.095 0.27 4 -0.35 11 15
B-cell antigen/BCR complex/FcgammaRIIB -0.023 0.15 -10000 0 -0.3 106 106
mol:PI-3-4-5-P3 -0.035 0.11 -10000 0 -0.29 41 41
ETS1 -0.008 0.092 0.25 10 -0.34 10 20
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.022 0.15 -10000 0 -0.3 75 75
B-cell antigen/BCR complex/LYN -0.036 0.14 -10000 0 -0.38 48 48
MALT1 0.025 0.008 -10000 0 -10000 0 0
TRAF6 0.026 0.006 -10000 0 -10000 0 0
RAC1 -0.053 0.15 0.28 2 -0.46 31 33
B-cell antigen/BCR complex/LYN/SYK -0.025 0.17 0.36 1 -0.44 47 48
CARD11 -0.012 0.12 0.27 11 -0.39 19 30
FCGR2B 0.02 0.057 -10000 0 -0.45 7 7
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.016 0.052 0.16 24 -0.12 5 29
PTPRC 0.015 0.073 -10000 0 -0.43 13 13
PDPK1 -0.006 0.1 0.23 31 -0.23 18 49
PPP3CB 0.027 0.004 -10000 0 -10000 0 0
PPP3CC 0.025 0.007 -10000 0 -10000 0 0
POU2F2 0.015 0.034 0.13 6 -10000 0 6
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.034 0.037 -10000 0 -0.29 6 6
alphaV beta3 Integrin 0.029 0.084 -10000 0 -0.27 34 34
PTK2 0.003 0.1 0.31 8 -0.49 4 12
IGF1R 0.026 0.005 -10000 0 -10000 0 0
PI4KB 0.027 0.004 -10000 0 -10000 0 0
MFGE8 0.026 0.02 -10000 0 -0.4 1 1
SRC 0.026 0.007 -10000 0 -10000 0 0
CDKN1B 0.005 0.051 -10000 0 -10000 0 0
VEGFA 0.022 0.043 -10000 0 -0.4 5 5
ILK 0.005 0.055 -10000 0 -0.28 4 4
ROCK1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.001 0.048 -10000 0 -0.4 1 1
PTK2B 0.01 0.063 -10000 0 -0.36 2 2
alphaV/beta3 Integrin/JAM-A 0.021 0.097 -10000 0 -0.28 20 20
CBL 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.033 0.065 -10000 0 -0.25 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.013 0.12 -10000 0 -0.25 81 81
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.01 0.049 -10000 0 -0.32 3 3
alphaV/beta3 Integrin/Syndecan-1 0.039 0.063 -10000 0 -0.25 21 21
PI4KA 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.1 0.16 -10000 0 -0.41 46 46
PI4 Kinase 0.038 0.011 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.11 0.15 -10000 0 -0.24 263 263
RPS6KB1 -0.12 0.13 0.22 1 -0.39 46 47
TLN1 0.024 0.009 -10000 0 -10000 0 0
MAPK3 -0.059 0.13 -10000 0 -0.48 31 31
GPR124 0.022 0.034 -10000 0 -0.4 3 3
MAPK1 -0.058 0.13 -10000 0 -0.47 32 32
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
alphaV/beta3 Integrin/Tumstatin 0.004 0.11 -10000 0 -0.26 72 72
cell adhesion 0.027 0.06 -10000 0 -0.29 8 8
ANGPTL3 -0.004 0.038 -10000 0 -0.4 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.037 -10000 0 -0.24 6 6
IGF-1R heterotetramer 0.026 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
TGFBR2 0.022 0.032 -10000 0 -0.45 2 2
ITGB3 0.01 0.086 -10000 0 -0.42 19 19
IGF1 -0.054 0.18 -10000 0 -0.45 84 84
RAC1 0.026 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.033 0.065 -10000 0 -0.26 21 21
apoptosis 0.024 0.027 -10000 0 -0.4 2 2
CD47 0.024 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.033 0.063 -10000 0 -0.25 21 21
VCL 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.003 0.12 -10000 0 -0.27 81 81
CSF1 0.021 0.053 -10000 0 -0.45 6 6
PIK3C2A 0.005 0.055 -10000 0 -0.43 1 1
PI4 Kinase/Pyk2 0.006 0.083 -10000 0 -0.42 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.069 -10000 0 -0.29 7 7
FAK1/Vinculin 0.015 0.096 0.27 11 -0.38 4 15
alphaV beta3/Integrin/ppsTEM5 0.034 0.066 -10000 0 -0.26 21 21
RHOA 0.024 0.009 -10000 0 -10000 0 0
VTN 0 0.1 -10000 0 -0.4 30 30
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 0.011 0.083 -10000 0 -0.44 16 16
F11R 0.003 0.06 -10000 0 -0.31 17 17
alphaV/beta3 Integrin/Lactadherin 0.038 0.065 -10000 0 -0.26 20 20
alphaV/beta3 Integrin/TGFBR2 0.032 0.066 -10000 0 -0.25 23 23
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.053 0.045 -10000 0 -0.24 7 7
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.032 0.058 -10000 0 -0.22 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.16 0.21 -10000 0 -0.4 217 217
alphaV/beta3 Integrin/Pyk2 0.033 0.064 -10000 0 -0.27 7 7
SDC1 0.027 0.003 -10000 0 -10000 0 0
VAV3 0 0.076 -10000 0 -0.45 3 3
PTPN11 0.027 0.002 -10000 0 -10000 0 0
IRS1 0.023 0.038 -10000 0 -0.45 3 3
FAK1/Paxillin 0.013 0.097 0.28 10 -0.38 4 14
cell migration 0.011 0.09 0.25 14 -0.35 4 18
ITGAV 0.024 0.027 -10000 0 -0.4 2 2
PI3K 0.014 0.093 -10000 0 -0.42 5 5
SPP1 -0.2 0.21 -10000 0 -0.4 263 263
KDR 0.025 0.029 -10000 0 -0.42 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.027 -10000 0 -0.4 2 2
COL4A3 -0.027 0.14 -10000 0 -0.41 57 57
angiogenesis -0.051 0.14 -10000 0 -0.49 30 30
Rac1/GTP 0.013 0.071 -10000 0 -0.42 3 3
EDIL3 -0.038 0.16 -10000 0 -0.42 70 70
cell proliferation 0.032 0.066 -10000 0 -0.25 23 23
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.01 0.011 -10000 0 -10000 0 0
SMARCC1 0.004 0.036 -10000 0 -0.6 1 1
REL 0.021 0.065 -10000 0 -0.45 9 9
HDAC7 -0.092 0.14 0.23 2 -0.47 25 27
JUN 0.025 0.005 -10000 0 -10000 0 0
EP300 0.024 0.031 -10000 0 -0.45 2 2
KAT2B 0.006 0.09 -10000 0 -0.45 18 18
KAT5 0.026 0.006 -10000 0 -10000 0 0
MAPK14 -0.024 0.078 -10000 0 -0.34 25 25
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.086 0.16 -10000 0 -0.47 29 29
MAP2K6 -0.018 0.11 -10000 0 -0.47 25 25
BRM/BAF57 0.023 0.033 -10000 0 -0.32 1 1
MAP2K4 0.005 0.025 -10000 0 -10000 0 0
SMARCA2 0.015 0.029 -10000 0 -0.45 1 1
PDE9A -0.083 0.22 -10000 0 -0.97 22 22
NCOA2 -0.007 0.12 -10000 0 -0.45 32 32
CEBPA 0.024 0.038 -10000 0 -0.45 3 3
EHMT2 0.024 0.007 -10000 0 -10000 0 0
cell proliferation -0.078 0.16 0.28 12 -0.44 29 41
NR0B1 -0.02 0.086 -10000 0 -0.4 23 23
EGR1 -0.001 0.097 -10000 0 -0.45 21 21
RXRs/9cRA 0.004 0.096 -10000 0 -0.25 56 56
AR/RACK1/Src -0.042 0.11 0.23 6 -0.38 22 28
AR/GR -0.061 0.13 0.19 1 -0.32 69 70
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.027 -10000 0 -0.4 2 2
RCHY1 0.026 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.009 0.04 -10000 0 -0.34 4 4
T-DHT/AR/TIF2/CARM1 -0.049 0.12 -10000 0 -0.38 27 27
SRC -0.036 0.078 0.2 13 -0.3 23 36
NR3C1 0.026 0.006 -10000 0 -10000 0 0
KLK3 -0.25 0.43 0.37 1 -1.1 87 88
APPBP2 0.006 0.026 -10000 0 -10000 0 0
TRIM24 0.017 0.028 -10000 0 -0.45 1 1
T-DHT/AR/TIP60 -0.046 0.11 0.23 1 -0.4 20 21
TMPRSS2 -0.47 0.53 -10000 0 -1 234 234
RXRG -0.035 0.15 -10000 0 -0.45 59 59
mol:9cRA -0.001 0.003 -10000 0 -0.011 2 2
RXRA 0.026 0.005 -10000 0 -10000 0 0
RXRB 0.026 0.006 -10000 0 -10000 0 0
CARM1 0.027 0.004 -10000 0 -10000 0 0
NR2C2 0.018 0.053 -10000 0 -0.45 6 6
KLK2 -0.042 0.11 -10000 0 -0.4 15 15
AR -0.073 0.13 0.16 2 -0.3 110 112
SENP1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
MDM2 0.031 0.013 -10000 0 -10000 0 0
SRY 0.005 0.011 0.029 87 -10000 0 87
GATA2 0.022 0.03 -10000 0 -0.42 2 2
MYST2 0.001 0.001 -10000 0 -10000 0 0
HOXB13 -0.14 0.2 -10000 0 -0.4 179 179
T-DHT/AR/RACK1/Src -0.039 0.11 0.23 8 -0.38 23 31
positive regulation of transcription 0.022 0.03 -10000 0 -0.42 2 2
DNAJA1 0.004 0.025 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.008 -10000 0 -10000 0 0
NCOA1 0.033 0.028 -10000 0 -10000 0 0
SPDEF -0.11 0.21 -10000 0 -0.45 137 137
T-DHT/AR/TIF2 -0.049 0.13 0.2 2 -0.41 31 33
T-DHT/AR/Hsp90 -0.049 0.11 0.22 1 -0.4 23 24
GSK3B 0.022 0.009 -10000 0 -10000 0 0
NR2C1 0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.043 0.073 -10000 0 -0.31 25 25
SIRT1 0.026 0.022 -10000 0 -0.45 1 1
ZMIZ2 0.031 0.014 -10000 0 -10000 0 0
POU2F1 -0.025 0.07 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.063 0.11 0.21 1 -0.39 27 28
CREBBP 0.026 0.004 -10000 0 -10000 0 0
SMARCE1 0.018 0.02 -10000 0 -10000 0 0
ErbB2/ErbB3 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
USP8 -0.004 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.083 -10000 0 -0.31 2 2
NFATC4 -0.022 0.072 0.27 6 -0.34 2 8
ERBB2IP 0.027 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis -0.015 0.076 -10000 0 -0.25 1 1
JUN -0.004 0.075 0.19 9 -0.36 4 13
HRAS 0.025 0.02 -10000 0 -0.41 1 1
DOCK7 -0.021 0.076 0.28 2 -10000 0 2
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.003 0.094 -10000 0 -0.27 10 10
AKT1 0.005 0.006 -10000 0 -10000 0 0
BAD -0.004 0.004 -10000 0 -10000 0 0
MAPK10 -0.016 0.067 0.2 12 -0.25 4 16
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.016 0.081 -10000 0 -0.27 1 1
RAF1 -0.017 0.091 0.28 6 -0.31 2 8
ErbB2/ErbB3/neuregulin 2 -0.13 0.14 -10000 0 -0.26 259 259
STAT3 0.014 0.12 -10000 0 -0.81 10 10
cell migration -0.008 0.067 0.23 12 -0.23 2 14
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.15 0.27 0.33 2 -0.58 110 112
FOS -0.11 0.21 0.33 6 -0.4 143 149
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.076 -10000 0 -0.25 1 1
MAPK3 -0.12 0.22 0.3 5 -0.48 99 104
MAPK1 -0.11 0.22 0.32 2 -0.49 91 93
JAK2 -0.02 0.07 -10000 0 -10000 0 0
NF2 0.008 0.042 -10000 0 -0.63 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.007 0.063 0.16 1 -0.26 10 11
NRG1 -0.04 0.15 -10000 0 -0.4 74 74
GRB2/SOS1 0.039 0.007 -10000 0 -10000 0 0
MAPK8 -0.008 0.078 0.23 4 -0.3 7 11
MAPK9 -0.01 0.057 0.2 10 -10000 0 10
ERBB2 -0.019 0.007 -10000 0 -10000 0 0
ERBB3 0.019 0.057 -10000 0 -0.46 7 7
SHC1 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
apoptosis 0.009 0.033 -10000 0 -0.17 13 13
STAT3 (dimer) 0.014 0.12 -10000 0 -0.79 10 10
RNF41 -0.006 0.007 -10000 0 -10000 0 0
FRAP1 -0.002 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.021 0.051 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.001 0.019 -10000 0 -10000 0 0
CHRNA1 -0.14 0.26 0.29 3 -0.6 98 101
myelination -0.014 0.085 0.29 13 -0.31 2 15
PPP3CB -0.019 0.073 0.27 2 -10000 0 2
KRAS 0.025 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.019 0.069 -10000 0 -10000 0 0
NRG2 -0.24 0.24 -10000 0 -0.45 267 267
mol:GDP -0.006 0.062 0.16 1 -0.26 10 11
SOS1 0.026 0.004 -10000 0 -10000 0 0
MAP2K2 -0.032 0.1 0.27 6 -0.32 2 8
SRC 0.026 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.026 0.075 0.28 2 -10000 0 2
MAP2K1 -0.1 0.21 -10000 0 -0.56 38 38
heart morphogenesis -0.015 0.076 -10000 0 -0.25 1 1
RAS family/GDP 0.012 0.08 -10000 0 -0.3 2 2
GRB2 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.01 0.043 -10000 0 -0.66 2 2
CHRNE 0.004 0.023 0.083 2 -0.14 6 8
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.005 0.006 -10000 0 -10000 0 0
nervous system development -0.015 0.076 -10000 0 -0.25 1 1
CDC42 0.027 0.005 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.026 0.007 -10000 0 -10000 0 0
VLDLR 0.017 0.057 -10000 0 -0.45 7 7
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.021 0.13 -10000 0 -0.28 104 104
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.031 0.12 0.18 28 -0.26 91 119
IQGAP1/CaM 0.038 0.011 -10000 0 -10000 0 0
DAB1 -0.002 0.075 -10000 0 -0.4 16 16
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.13 0.2 -10000 0 -0.4 187 187
CALM1 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.032 0.045 -10000 0 -0.28 10 10
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.022 -10000 0 -0.45 1 1
CDK5R1 0.025 0.027 -10000 0 -0.4 2 2
LIS1/Poliovirus Protein 3A 0.01 0.003 -10000 0 -10000 0 0
CDK5R2 -0.043 0.14 -10000 0 -0.4 68 68
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.031 0.14 -10000 0 -0.28 110 110
YWHAE 0.026 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.029 0.12 0.3 5 -0.33 10 15
MAP1B 0.002 0.028 -10000 0 -0.33 2 2
RAC1 0.013 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.023 0.11 0.2 1 -0.4 4 5
RELN -0.071 0.19 -10000 0 -0.45 98 98
PAFAH/LIS1 -0.068 0.13 -10000 0 -0.23 179 179
LIS1/CLIP170 0.028 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.021 0.096 -10000 0 -0.38 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.037 0.12 -10000 0 -0.37 24 24
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.04 0.12 0.33 3 -0.34 11 14
LIS1/IQGAP1 0.028 0.01 -10000 0 -10000 0 0
RHOA 0.013 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.025 0.027 -10000 0 -0.4 2 2
PAFAH1B2 0.023 0.031 -10000 0 -0.45 2 2
MAP1B/LIS1/Dynein heavy chain 0.019 0.034 -10000 0 -0.26 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.02 0.12 0.3 4 -0.38 3 7
LRP8 0.018 0.06 -10000 0 -0.4 10 10
NDEL1/Katanin 60 -0.03 0.12 0.3 5 -0.33 10 15
P39/CDK5 -0.051 0.13 -10000 0 -0.4 13 13
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.01 -10000 0 -10000 0 0
CDK5 -0.046 0.11 0.18 24 -0.41 3 27
PPP2R5D 0.026 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0.009 -10000 0 -10000 0 0
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.018 0.12 -10000 0 -0.35 4 4
RELN/VLDLR -0.012 0.13 -10000 0 -0.26 95 95
CDC42 0.014 0.005 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.16 0.14 -10000 0 -0.58 12 12
IHH -0.04 0.059 -10000 0 -0.38 3 3
SHH Np/Cholesterol/GAS1 0.002 0.069 -10000 0 -0.22 44 44
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.002 0.068 0.21 44 -10000 0 44
SMO/beta Arrestin2 -0.085 0.12 -10000 0 -0.47 20 20
SMO -0.091 0.12 -10000 0 -0.48 24 24
AKT1 -0.039 0.1 -10000 0 -0.51 14 14
ARRB2 0.026 0.006 -10000 0 -10000 0 0
BOC -0.017 0.13 -10000 0 -0.45 42 42
ADRBK1 0.025 0.008 -10000 0 -10000 0 0
heart looping -0.09 0.12 -10000 0 -0.47 24 24
STIL -0.086 0.098 -10000 0 -0.41 12 12
DHH N/PTCH2 0.03 0.055 -10000 0 -0.3 13 13
DHH N/PTCH1 -0.085 0.099 -10000 0 -0.51 7 7
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
DHH 0.021 0.03 -10000 0 -0.4 2 2
PTHLH -0.22 0.18 -10000 0 -0.6 25 25
determination of left/right symmetry -0.09 0.12 -10000 0 -0.47 24 24
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
skeletal system development -0.22 0.18 -10000 0 -0.59 25 25
IHH N/Hhip -0.033 0.085 -10000 0 -0.32 32 32
DHH N/Hhip 0.017 0.078 -10000 0 -0.28 31 31
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.09 0.12 -10000 0 -0.47 24 24
pancreas development -0.007 0.1 -10000 0 -0.4 29 29
HHAT 0.025 0.031 -10000 0 -0.45 2 2
PI3K 0.026 0.029 -10000 0 -0.32 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.021 0.049 -10000 0 -0.42 6 6
somite specification -0.09 0.12 -10000 0 -0.47 24 24
SHH Np/Cholesterol/PTCH1 -0.092 0.098 -10000 0 -0.34 32 32
SHH Np/Cholesterol/PTCH2 0 0.076 -10000 0 -0.23 47 47
SHH Np/Cholesterol/Megalin -0.01 0.085 -10000 0 -0.24 55 55
SHH -0.02 0.078 -10000 0 -0.28 39 39
catabolic process -0.1 0.1 -10000 0 -0.52 8 8
SMO/Vitamin D3 -0.087 0.11 -10000 0 -0.46 13 13
SHH Np/Cholesterol/Hhip -0.013 0.088 -10000 0 -0.24 60 60
LRP2 -0.003 0.094 -10000 0 -0.4 26 26
receptor-mediated endocytosis -0.09 0.11 -10000 0 -0.48 15 15
SHH Np/Cholesterol/BOC -0.017 0.092 -10000 0 -0.24 72 72
SHH Np/Cholesterol/CDO -0.002 0.075 -10000 0 -0.22 48 48
mesenchymal cell differentiation 0.013 0.088 0.24 60 -10000 0 60
mol:Vitamin D3 -0.088 0.1 0.37 1 -0.38 20 21
IHH N/PTCH2 -0.02 0.066 -10000 0 -0.33 14 14
CDON 0.015 0.068 -10000 0 -0.45 10 10
IHH N/PTCH1 -0.099 0.11 -10000 0 -0.46 11 11
Megalin/LRPAP1 0.02 0.07 -10000 0 -0.28 26 26
PTCH2 0.016 0.067 -10000 0 -0.43 11 11
SHH Np/Cholesterol -0.003 0.062 -10000 0 -0.21 39 39
PTCH1 -0.1 0.1 -10000 0 -0.52 8 8
HHIP -0.007 0.1 -10000 0 -0.4 29 29
Signaling events mediated by PTP1B

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
PDGFRB -0.049 0.16 -10000 0 -0.4 88 88
Jak2/Leptin Receptor -0.063 0.17 -10000 0 -0.44 53 53
PTP1B/AKT1 -0.021 0.098 -10000 0 -0.35 15 15
FYN 0.026 0.02 -10000 0 -0.4 1 1
p210 bcr-abl/PTP1B -0.03 0.1 0.22 3 -0.32 28 31
EGFR 0.012 0.051 -10000 0 -0.46 5 5
EGF/EGFR -0.049 0.13 -10000 0 -0.34 45 45
CSF1 0.021 0.053 -10000 0 -0.45 6 6
AKT1 0.026 0.007 -10000 0 -10000 0 0
INSR 0.026 0.022 -10000 0 -0.46 1 1
PTP1B/N-cadherin -0.041 0.12 0.26 1 -0.32 38 39
Insulin Receptor/Insulin -0.009 0.097 -10000 0 -0.41 6 6
HCK 0.023 0.03 -10000 0 -0.42 2 2
CRK 0.026 0.006 -10000 0 -10000 0 0
TYK2 -0.029 0.098 0.22 2 -0.35 17 19
EGF -0.06 0.18 -10000 0 -0.46 88 88
YES1 0.024 0.009 -10000 0 -10000 0 0
CAV1 -0.036 0.12 0.22 9 -0.34 30 39
TXN 0.026 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.012 0.11 0.27 1 -0.37 14 15
cell migration 0.03 0.1 0.32 28 -0.22 3 31
STAT3 0.027 0.003 -10000 0 -10000 0 0
PRLR -0.068 0.19 -10000 0 -0.45 94 94
ITGA2B -0.013 0.12 -10000 0 -0.4 47 47
CSF1R 0.024 0.031 -10000 0 -0.45 2 2
Prolactin Receptor/Prolactin -0.041 0.14 -10000 0 -0.33 95 95
FGR 0.026 0.02 -10000 0 -0.4 1 1
PTP1B/p130 Cas -0.02 0.1 0.23 2 -0.33 20 22
Crk/p130 Cas -0.009 0.1 0.27 1 -0.37 12 13
DOK1 -0.04 0.11 0.28 2 -0.35 22 24
JAK2 -0.074 0.17 -10000 0 -0.44 60 60
Jak2/Leptin Receptor/Leptin -0.047 0.14 -10000 0 -0.44 17 17
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
PTPN1 -0.031 0.1 0.23 3 -0.32 28 31
LYN 0.024 0.021 -10000 0 -0.4 1 1
CDH2 -0.028 0.14 -10000 0 -0.4 60 60
SRC 0.001 0.11 -10000 0 -0.56 15 15
ITGB3 0.01 0.086 -10000 0 -0.42 19 19
CAT1/PTP1B -0.087 0.14 0.21 7 -0.41 37 44
CAPN1 0.025 0.006 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.01 0.081 -10000 0 -0.39 3 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.041 0.12 -10000 0 -0.38 18 18
negative regulation of transcription -0.072 0.17 -10000 0 -0.43 60 60
FCGR2A 0.005 0.093 -10000 0 -0.4 25 25
FER 0.023 0.032 -10000 0 -0.46 2 2
alphaIIb/beta3 Integrin -0.003 0.11 -10000 0 -0.3 63 63
BLK -0.036 0.15 -10000 0 -0.4 67 67
Insulin Receptor/Insulin/Shc 0.044 0.027 -10000 0 -0.25 3 3
RHOA 0.024 0.009 -10000 0 -10000 0 0
LEPR 0.025 0.031 -10000 0 -0.45 2 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.027 0.004 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.077 0.14 0.24 3 -0.44 30 33
PRL -0.003 0.045 -10000 0 -0.4 5 5
SOCS3 0.024 0.11 -10000 0 -1.1 4 4
SPRY2 0.02 0.053 -10000 0 -0.46 6 6
Insulin Receptor/Insulin/IRS1 0.041 0.037 -10000 0 -0.27 6 6
CSF1/CSF1R -0.013 0.11 0.27 1 -0.35 18 19
Ras protein signal transduction 0.011 0.067 0.55 6 -10000 0 6
IRS1 0.023 0.038 -10000 0 -0.45 3 3
INS -0.012 0.029 -10000 0 -0.4 2 2
LEP -0.05 0.16 -10000 0 -0.43 73 73
STAT5B -0.04 0.12 0.21 3 -0.35 37 40
STAT5A -0.04 0.12 0.21 3 -0.36 35 38
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.052 0.13 0.23 2 -0.33 34 36
CSN2 -0.015 0.092 -10000 0 -0.52 1 1
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
LAT 0.001 0.081 -10000 0 -0.56 6 6
YBX1 0.033 0.006 -10000 0 -10000 0 0
LCK 0.017 0.065 -10000 0 -0.4 12 12
SHC1 0.027 0.004 -10000 0 -10000 0 0
NOX4 -0.056 0.16 -10000 0 -0.4 94 94
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.02 0.002 -10000 0 -10000 0 0
PRKCZ 0.025 0.022 -10000 0 -0.45 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.067 -10000 0 -0.43 3 3
IRAK/TOLLIP 0.03 0.009 -10000 0 -10000 0 0
IKBKB 0.025 0.008 -10000 0 -10000 0 0
IKBKG 0.026 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.1 0.18 -10000 0 -0.31 203 203
IL1A -0.083 0.19 -10000 0 -0.4 128 128
IL1B -0.018 0.091 -10000 0 -0.28 52 52
IRAK/TRAF6/p62/Atypical PKCs 0.045 0.034 -10000 0 -10000 0 0
IL1R2 -0.059 0.18 -10000 0 -0.45 89 89
IL1R1 0.026 0.022 -10000 0 -0.45 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.015 0.057 0.24 1 -0.61 1 2
TOLLIP 0.026 0.006 -10000 0 -10000 0 0
TICAM2 0.025 0.008 -10000 0 -10000 0 0
MAP3K3 0.027 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.04 0.053 0.24 1 -0.33 1 2
JUN -0.013 0.052 0.16 12 -0.38 1 13
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.024 0.082 -10000 0 -0.64 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.014 0.11 -10000 0 -0.4 3 3
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.11 -10000 0 -0.66 1 1
IL1 beta fragment/IL1R1/IL1RAP 0.007 0.078 -10000 0 -0.22 42 42
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.013 0.056 0.17 12 -0.41 1 13
IRAK1 0.015 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.054 0.16 -10000 0 -0.33 126 126
IRAK4 0.026 0.022 -10000 0 -0.45 1 1
PRKCI 0.02 0.012 -10000 0 -10000 0 0
TRAF6 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.026 0.029 -10000 0 -0.32 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.016 0.065 -10000 0 -0.44 3 3
CHUK 0.027 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.007 0.078 -10000 0 -0.22 42 42
IL1 beta/IL1R2 -0.048 0.14 0.22 1 -0.27 133 134
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.013 0.072 -10000 0 -0.6 1 1
IRAK3 0.022 0.045 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.025 0.082 -10000 0 -0.64 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.011 0.069 -10000 0 -0.3 10 10
IL1 alpha/IL1R1/IL1RAP -0.023 0.12 -10000 0 -0.24 103 103
RELA 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
MYD88 0.024 0.009 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.016 -10000 0 -10000 0 0
IL1RAP 0.018 0.031 -10000 0 -0.42 2 2
UBE2N 0.027 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 0.006 0.063 -10000 0 -0.55 1 1
CASP1 0.024 0.023 -10000 0 -0.45 1 1
IL1RN/IL1R2 -0.11 0.21 -10000 0 -0.38 176 176
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.015 0.079 -10000 0 -0.66 1 1
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.077 -10000 0 -0.32 10 10
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
IL1RN -0.096 0.21 -10000 0 -0.45 126 126
TRAF6/TAK1/TAB1/TAB2 0.038 0.011 -10000 0 -10000 0 0
MAP2K6 0.008 0.059 0.19 14 -0.22 24 38
Ephrin B reverse signaling

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.025 0.031 -10000 0 -0.45 2 2
EPHB2 -0.065 0.17 -10000 0 -0.4 107 107
EFNB1 -0.005 0.072 -10000 0 -0.28 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.016 0.12 -10000 0 -0.37 11 11
Ephrin B2/EPHB1-2 -0.015 0.11 -10000 0 -0.22 99 99
neuron projection morphogenesis -0.025 0.1 -10000 0 -0.35 11 11
Ephrin B1/EPHB1-2/Tiam1 -0.022 0.12 -10000 0 -0.39 11 11
DNM1 -0.002 0.11 -10000 0 -0.39 34 34
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.018 0.11 0.42 1 -0.44 29 30
YES1 -0.026 0.16 -10000 0 -0.68 28 28
Ephrin B1/EPHB1-2/NCK2 -0.017 0.12 -10000 0 -0.39 10 10
PI3K 0.006 0.11 -10000 0 -0.46 21 21
mol:GDP -0.023 0.12 -10000 0 -0.37 12 12
ITGA2B -0.013 0.12 -10000 0 -0.4 47 47
endothelial cell proliferation 0.032 0.023 -10000 0 -0.27 2 2
FYN -0.026 0.16 -10000 0 -0.69 28 28
MAP3K7 -0.022 0.11 0.24 1 -0.48 27 28
FGR -0.022 0.16 -10000 0 -0.67 29 29
TIAM1 0.021 0.053 -10000 0 -0.45 6 6
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
RGS3 0.027 0.004 -10000 0 -10000 0 0
cell adhesion -0.02 0.12 -10000 0 -0.46 26 26
LYN -0.025 0.16 -10000 0 -0.68 28 28
Ephrin B1/EPHB1-2/Src Family Kinases -0.029 0.15 -10000 0 -0.63 29 29
Ephrin B1/EPHB1-2 -0.02 0.12 -10000 0 -0.53 24 24
SRC -0.022 0.16 -10000 0 -0.66 29 29
ITGB3 0.01 0.086 -10000 0 -0.42 19 19
EPHB1 0.005 0.088 -10000 0 -0.42 20 20
EPHB4 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.032 0.023 -10000 0 -0.27 2 2
alphaIIb/beta3 Integrin -0.003 0.11 -10000 0 -0.3 63 63
BLK -0.03 0.16 -10000 0 -0.67 28 28
HCK -0.021 0.16 -10000 0 -0.67 28 28
regulation of stress fiber formation 0.018 0.12 0.38 10 -10000 0 10
MAPK8 -0.018 0.11 -10000 0 -0.44 28 28
Ephrin B1/EPHB1-2/RGS3 -0.018 0.12 -10000 0 -0.39 10 10
endothelial cell migration -0.005 0.099 0.27 3 -0.4 22 25
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTPN13 0.014 0.083 -10000 0 -0.56 10 10
regulation of focal adhesion formation 0.018 0.12 0.38 10 -10000 0 10
chemotaxis 0.019 0.12 0.38 10 -10000 0 10
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
Rac1/GTP -0.02 0.11 -10000 0 -0.36 11 11
angiogenesis -0.024 0.12 -10000 0 -0.51 28 28
LCK -0.023 0.16 -10000 0 -0.67 29 29
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.037 0.075 -10000 0 -0.25 10 10
ER alpha/Gai/GDP/Gbeta gamma -0.025 0.16 -10000 0 -0.53 33 33
AKT1 -0.008 0.17 -10000 0 -0.73 23 23
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.004 0.17 -10000 0 -0.75 23 23
mol:Ca2+ -0.034 0.13 -10000 0 -0.35 64 64
IGF1R 0.026 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.007 0.089 -10000 0 -0.26 47 47
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis 0.007 0.16 0.7 23 -10000 0 23
RhoA/GTP 0.011 0.047 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.012 0.14 -10000 0 -0.47 23 23
regulation of stress fiber formation 0.006 0.059 0.31 1 -0.17 4 5
E2/ERA-ERB (dimer) 0.013 0.076 -10000 0 -0.25 36 36
KRAS 0.026 0.006 -10000 0 -10000 0 0
G13/GTP 0.02 0.059 -10000 0 -0.22 27 27
pseudopodium formation -0.006 0.059 0.17 4 -0.31 1 5
E2/ER alpha (dimer)/PELP1 0.02 0.063 -10000 0 -0.24 26 26
GRB2 0.027 0.004 -10000 0 -10000 0 0
GNG2 0.025 0.02 -10000 0 -0.4 1 1
GNAO1 0.022 0.04 -10000 0 -0.41 4 4
HRAS 0.025 0.02 -10000 0 -0.41 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.009 0.16 0.26 6 -0.54 29 35
E2/ER beta (dimer) 0.012 0.045 -10000 0 -0.28 11 11
mol:GDP 0.001 0.073 -10000 0 -0.35 13 13
mol:NADP -0.009 0.16 0.26 6 -0.54 29 35
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
mol:IP3 -0.041 0.13 -10000 0 -0.36 64 64
IGF-1R heterotetramer 0.026 0.005 -10000 0 -10000 0 0
PLCB1 -0.037 0.14 -10000 0 -0.37 65 65
PLCB2 -0.04 0.14 -10000 0 -0.37 69 69
IGF1 -0.054 0.18 -10000 0 -0.45 84 84
mol:L-citrulline -0.009 0.16 0.26 6 -0.54 29 35
RHOA 0.024 0.009 -10000 0 -10000 0 0
Gai/GDP -0.048 0.23 -10000 0 -0.61 65 65
JNK cascade 0.012 0.045 -10000 0 -0.28 11 11
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.016 0.064 -10000 0 -0.4 11 11
GNAQ 0.027 0.004 -10000 0 -10000 0 0
ESR1 0.002 0.1 -10000 0 -0.42 27 27
Gq family/GDP/Gbeta gamma -0.026 0.16 -10000 0 -0.7 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.028 0.09 -10000 0 -0.86 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.011 0.14 -10000 0 -0.46 25 25
GNAZ 0.01 0.083 -10000 0 -0.42 18 18
E2/ER alpha (dimer) 0.003 0.072 -10000 0 -0.3 27 27
STRN 0.006 0.099 -10000 0 -0.45 22 22
GNAL -0.03 0.15 -10000 0 -0.45 57 57
PELP1 0.026 0.006 -10000 0 -10000 0 0
MAPK11 0.008 0.037 -10000 0 -0.24 11 11
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.025 0.022 -10000 0 -0.45 1 1
HBEGF -0.088 0.17 0.32 13 -0.52 40 53
cAMP biosynthetic process -0.016 0.097 -10000 0 -0.23 81 81
SRC -0.019 0.16 0.22 3 -0.52 31 34
PI3K 0.026 0.029 -10000 0 -0.32 2 2
GNB1 0.026 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.028 0.077 -10000 0 -0.33 10 10
SOS1 0.027 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.041 0.12 -10000 0 -0.42 26 26
Gs family/GTP -0.011 0.1 -10000 0 -0.23 81 81
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.045 0.022 -10000 0 -0.22 1 1
vasodilation -0.008 0.15 0.26 6 -0.51 29 35
mol:DAG -0.041 0.13 -10000 0 -0.36 64 64
Gs family/GDP/Gbeta gamma -0.014 0.093 -10000 0 -0.35 13 13
MSN -0.007 0.061 0.19 1 -0.33 1 2
Gq family/GTP -0.038 0.15 -10000 0 -0.38 70 70
mol:PI-3-4-5-P3 -0.003 0.16 -10000 0 -0.72 23 23
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.008 0.15 0.51 29 -0.26 6 35
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.074 -10000 0 -0.34 11 11
NOS3 -0.011 0.17 0.27 5 -0.57 28 33
GNA11 0.024 0.038 -10000 0 -0.45 3 3
MAPKKK cascade 0 0.16 -10000 0 -0.56 23 23
E2/ER alpha (dimer)/PELP1/Src 0.011 0.15 0.27 4 -0.46 28 32
ruffle organization -0.006 0.059 0.17 4 -0.31 1 5
ROCK2 -0.006 0.066 0.2 1 -0.36 1 2
GNA14 -0.044 0.17 -10000 0 -0.45 72 72
GNA15 0.025 0.031 -10000 0 -0.45 2 2
GNA13 0.027 0.003 -10000 0 -10000 0 0
MMP9 -0.13 0.18 0.36 15 -0.53 41 56
MMP2 -0.029 0.16 0.25 12 -0.5 27 39
EGFR-dependent Endothelin signaling events

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
HRAS 0.025 0.02 -9999 0 -0.41 1 1
EGFR 0.019 0.049 -9999 0 -0.45 5 5
EGF/EGFR -0.007 0.11 -9999 0 -0.24 79 79
EGF/EGFR dimer/SHC/GRB2/SOS1 0.015 0.12 -9999 0 -0.38 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.024 0.033 -9999 0 -0.4 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.06 0.18 -9999 0 -0.45 88 88
EGF/EGFR dimer/SHC -0.009 0.12 -9999 0 -0.28 79 79
mol:GDP 0.01 0.11 -9999 0 -0.38 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.021 0.048 -9999 0 -0.45 5 5
GRB2/SOS1 0.04 0.007 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.099 -9999 0 -0.42 2 2
SHC1 0.027 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.01 0.11 -9999 0 -0.43 2 2
FRAP1 -0.043 0.082 -9999 0 -0.23 73 73
EGF/EGFR dimer -0.025 0.14 -9999 0 -0.33 80 80
SOS1 0.027 0.003 -9999 0 -10000 0 0
GRB2 0.027 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.032 0.045 -9999 0 -0.31 8 8
Angiopoietin receptor Tie2-mediated signaling

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.016 0.2 -10000 0 -0.86 20 20
NCK1/PAK1/Dok-R -0.025 0.081 -10000 0 -0.4 17 17
NCK1/Dok-R 0.008 0.22 -10000 0 -0.99 20 20
PIK3CA 0.019 0.012 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.04 0.24 13 -10000 0 13
RELA 0.026 0.006 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -10000 0 -10000 0 0
F2 -0.039 0.13 0.27 13 -0.41 46 59
TNIP2 0.026 0.007 -10000 0 -10000 0 0
NF kappa B/RelA 0.028 0.21 -10000 0 -0.94 20 20
FN1 -0.16 0.21 -10000 0 -0.4 217 217
PLD2 -0.007 0.23 -10000 0 -1.1 20 20
PTPN11 0.027 0.002 -10000 0 -10000 0 0
GRB14 -0.018 0.14 -10000 0 -0.44 45 45
ELK1 0.001 0.21 -10000 0 -0.96 20 20
GRB7 0.025 0.031 -10000 0 -0.45 2 2
PAK1 0.025 0.008 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.26 -10000 0 -1 20 20
CDKN1A 0.031 0.16 0.44 1 -0.62 14 15
ITGA5 -0.1 0.2 -10000 0 -0.4 152 152
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.013 0.23 -10000 0 -1 20 20
CRK 0.026 0.006 -10000 0 -10000 0 0
mol:NO 0.024 0.16 0.39 3 -0.63 20 23
PLG -0.012 0.23 -10000 0 -1.1 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.017 0.19 -10000 0 -0.81 21 21
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.46 3 3
ANGPT2 0.015 0.16 0.37 2 -0.56 8 10
BMX -0.031 0.24 -10000 0 -1.1 20 20
ANGPT1 -0.006 0.2 -10000 0 -1.2 13 13
tube development 0.021 0.17 0.38 1 -0.65 18 19
ANGPT4 0.016 0.017 -10000 0 -10000 0 0
response to hypoxia -0.002 0.014 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.015 0.25 -10000 0 -1.1 20 20
alpha5/beta1 Integrin -0.059 0.15 -10000 0 -0.28 152 152
FGF2 0.011 0.083 -10000 0 -0.44 16 16
STAT5A (dimer) 0.031 0.2 -10000 0 -0.76 16 16
mol:L-citrulline 0.024 0.16 0.39 3 -0.63 20 23
AGTR1 -0.017 0.12 -10000 0 -0.45 36 36
MAPK14 -0.003 0.25 -10000 0 -1.1 22 22
Tie2/SHP2 -0.005 0.2 -10000 0 -1.1 13 13
TEK -0.002 0.21 -10000 0 -1.2 13 13
RPS6KB1 0.017 0.2 -10000 0 -0.82 21 21
Angiotensin II/AT1 -0.01 0.088 -10000 0 -0.32 36 36
Tie2/Ang1/GRB2 0.005 0.24 -10000 0 -1.1 20 20
MAPK3 -0.006 0.21 -10000 0 -0.98 20 20
MAPK1 -0.003 0.21 -10000 0 -0.98 20 20
Tie2/Ang1/GRB7 0.004 0.24 -10000 0 -1.1 20 20
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.008 0.23 -10000 0 -1.1 20 20
PI3K -0.007 0.22 -10000 0 -0.98 21 21
FES 0.002 0.24 -10000 0 -1 22 22
Crk/Dok-R 0.015 0.23 -10000 0 -1 20 20
Tie2/Ang1/ABIN2 0.005 0.24 -10000 0 -1.1 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.022 0.19 0.4 1 -0.76 20 21
STAT5A 0.027 0.003 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.041 0.21 0.45 2 -0.8 19 21
Tie2/Ang2 0.011 0.22 -10000 0 -0.89 17 17
Tie2/Ang1 -0.006 0.25 -10000 0 -1.1 20 20
FOXO1 0.023 0.19 -10000 0 -0.77 20 20
ELF1 0.027 0.045 -10000 0 -0.46 3 3
ELF2 -0.004 0.23 -10000 0 -1.1 20 20
mol:Choline -0.005 0.22 -10000 0 -1 20 20
cell migration -0.045 0.061 -10000 0 -0.23 21 21
FYN 0.015 0.19 -10000 0 -0.76 16 16
DOK2 0.022 0.04 -10000 0 -0.41 4 4
negative regulation of cell cycle 0.033 0.15 0.4 2 -0.56 14 16
ETS1 0.022 0.055 -10000 0 -0.28 15 15
PXN 0.045 0.18 0.4 6 -0.67 19 25
ITGB1 0.027 0.005 -10000 0 -10000 0 0
NOS3 0.021 0.18 0.43 2 -0.72 20 22
RAC1 0.026 0.007 -10000 0 -10000 0 0
TNF 0.007 0.098 -10000 0 -0.34 34 34
MAPKKK cascade -0.005 0.22 -10000 0 -1 20 20
RASA1 0.024 0.031 -10000 0 -0.45 2 2
Tie2/Ang1/Shc 0.006 0.24 -10000 0 -1.1 20 20
NCK1 0.023 0.011 -10000 0 -10000 0 0
vasculogenesis 0.026 0.15 0.38 3 -0.56 20 23
mol:Phosphatidic acid -0.005 0.22 -10000 0 -1 20 20
mol:Angiotensin II 0 0.004 -10000 0 -10000 0 0
mol:NADP 0.024 0.16 0.39 3 -0.63 20 23
Rac1/GTP 0.02 0.18 -10000 0 -0.76 21 21
MMP2 -0.03 0.23 -10000 0 -1.1 20 20
Caspase cascade in apoptosis

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
TOP1 -0.021 0.13 0.26 3 -0.45 14 17
ACTA1 -0.094 0.12 0.21 2 -0.33 73 75
NUMA1 -0.03 0.14 0.25 3 -0.51 15 18
SPTAN1 -0.033 0.12 0.3 5 -0.32 38 43
LIMK1 -0.032 0.12 0.27 5 -0.32 38 43
BIRC3 0.012 0.071 -10000 0 -0.4 14 14
BIRC2 0.024 0.009 -10000 0 -10000 0 0
BAX 0.027 0.004 -10000 0 -10000 0 0
CASP10 -0.06 0.12 -10000 0 -0.32 87 87
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.004 -10000 0 -10000 0 0
PTK2 -0.018 0.1 0.24 3 -0.34 11 14
DIABLO 0.027 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.033 0.12 0.3 5 -0.32 38 43
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.002 -10000 0 -10000 0 0
GSN -0.034 0.12 0.27 4 -0.32 38 42
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.01 0.2 -10000 0 -0.81 23 23
BID -0.021 0.064 -10000 0 -0.2 34 34
MAP3K1 -0.02 0.1 -10000 0 -0.42 23 23
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.029 0.12 0.4 3 -0.32 37 40
CASP9 0.026 0.006 -10000 0 -10000 0 0
DNA repair 0.004 0.051 0.19 3 -0.18 3 6
neuron apoptosis 0.004 0.12 -10000 0 -0.66 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.037 0.14 0.27 4 -0.37 38 42
APAF1 0.027 0.002 -10000 0 -10000 0 0
CASP6 -0.008 0.15 -10000 0 -0.91 10 10
TRAF2 0.021 0.047 -10000 0 -0.4 6 6
ICAD/CAD -0.036 0.11 0.26 5 -0.32 38 43
CASP7 -0.008 0.084 0.29 4 -0.48 2 6
KRT18 0.005 0.075 -10000 0 -0.49 9 9
apoptosis -0.031 0.12 0.26 3 -0.41 11 14
DFFA -0.036 0.11 0.26 4 -0.32 38 42
DFFB -0.036 0.12 0.27 5 -0.32 43 48
PARP1 -0.004 0.051 0.18 3 -0.19 3 6
actin filament polymerization 0.025 0.12 0.3 36 -0.34 14 50
TNF 0.007 0.088 -10000 0 -0.4 22 22
CYCS -0.006 0.066 0.21 3 -0.27 4 7
SATB1 -0.016 0.14 -10000 0 -0.84 10 10
SLK -0.037 0.11 0.27 3 -0.32 42 45
p15 BID/BAX 0 0.073 0.2 2 -0.26 2 4
CASP2 0.015 0.06 0.21 4 -0.38 4 8
JNK cascade 0.02 0.1 0.42 23 -10000 0 23
CASP3 -0.038 0.12 0.27 4 -0.33 42 46
LMNB2 0.011 0.12 0.24 2 -0.51 15 17
RIPK1 0.026 0.006 -10000 0 -10000 0 0
CASP4 0.024 0.023 -10000 0 -0.45 1 1
Mammalian IAPs/DIABLO 0.053 0.049 -10000 0 -10000 0 0
negative regulation of DNA binding -0.009 0.19 -10000 0 -0.8 23 23
stress fiber formation -0.036 0.11 0.27 3 -0.31 42 45
GZMB -0.055 0.15 -10000 0 -0.37 88 88
CASP1 0.013 0.032 -10000 0 -0.68 1 1
LMNB1 0.004 0.13 0.26 1 -0.59 13 14
APP 0.004 0.12 -10000 0 -0.67 14 14
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM -0.029 0.12 0.26 3 -0.4 13 16
LMNA 0.019 0.088 0.26 1 -0.48 9 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.019 0.059 -10000 0 -0.35 5 5
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.036 0.11 0.27 3 -0.32 38 41
APAF-1/Caspase 9 -0.006 0.11 -10000 0 -0.62 14 14
nuclear fragmentation during apoptosis -0.029 0.13 0.25 3 -0.5 15 18
CFL2 -0.026 0.12 0.34 14 -0.31 36 50
GAS2 -0.063 0.13 0.26 4 -0.34 56 60
positive regulation of apoptosis 0.014 0.11 0.24 2 -0.53 13 15
PRF1 -0.007 0.12 -10000 0 -0.4 39 39
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0 0.11 0.32 47 -10000 0 47
KIRREL 0.002 0.1 -10000 0 -0.45 22 22
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0 0.11 -10000 0 -0.32 47 47
PLCG1 0.026 0.006 -10000 0 -10000 0 0
ARRB2 0.026 0.006 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.023 0.097 -10000 0 -0.3 22 22
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.001 0.062 -10000 0 -0.26 18 18
FYN -0.016 0.085 0.27 9 -0.28 23 32
mol:Ca2+ 0.021 0.094 -10000 0 -0.3 21 21
mol:DAG 0.022 0.095 -10000 0 -0.3 21 21
NPHS2 -0.025 0.064 -10000 0 -0.41 12 12
mol:IP3 0.022 0.095 -10000 0 -0.3 21 21
regulation of endocytosis 0.02 0.084 -10000 0 -0.27 21 21
Nephrin/NEPH1/podocin/Cholesterol 0.01 0.092 -10000 0 -0.24 52 52
establishment of cell polarity 0 0.11 -10000 0 -0.32 47 47
Nephrin/NEPH1/podocin/NCK1-2 0.031 0.089 -10000 0 -0.36 8 8
Nephrin/NEPH1/beta Arrestin2 0.022 0.085 -10000 0 -0.28 20 20
NPHS1 -0.022 0.1 -10000 0 -0.41 29 29
Nephrin/NEPH1/podocin 0.014 0.086 -10000 0 -0.28 24 24
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.023 0.011 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.023 0.096 -10000 0 -0.3 21 21
CD2AP 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.024 0.098 -10000 0 -0.3 23 23
GRB2 0.027 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.03 0.096 0.28 7 -0.25 48 55
cytoskeleton organization -0.01 0.071 0.23 3 -0.3 17 20
Nephrin/NEPH1 0.005 0.076 -10000 0 -0.22 46 46
Nephrin/NEPH1/ZO-1 0.018 0.091 -10000 0 -0.25 46 46
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.015 0.068 -10000 0 -0.27 27 27
EFNA5 0.005 0.097 -10000 0 -0.45 21 21
FYN -0.008 0.061 0.18 4 -0.25 26 30
neuron projection morphogenesis 0.015 0.068 -10000 0 -0.27 27 27
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.015 0.069 -10000 0 -0.27 27 27
EPHA5 0.002 0.049 -10000 0 -0.4 6 6
Glucocorticoid receptor regulatory network

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
PCK2 0.053 0.064 -10000 0 -10000 0 0
SMARCC2 0.028 0.009 -10000 0 -10000 0 0
SMARCC1 0.025 0.012 -10000 0 -10000 0 0
TBX21 -0.087 0.16 -10000 0 -0.55 37 37
SUMO2 0.026 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.014 0.085 -10000 0 -0.39 21 21
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 0.023 0.036 -10000 0 -0.43 3 3
GR alpha/HSP90/FKBP51/HSP90 0.089 0.081 0.31 19 -0.25 1 20
PRL -0.079 0.13 -10000 0 -0.6 6 6
cortisol/GR alpha (dimer)/TIF2 0.12 0.18 0.53 41 -10000 0 41
RELA -0.01 0.088 -10000 0 -0.26 6 6
FGG 0.082 0.17 0.46 27 -0.38 13 40
GR beta/TIF2 0.057 0.11 0.32 19 -0.28 15 34
IFNG -0.21 0.2 -10000 0 -0.66 38 38
apoptosis 0.017 0.15 0.49 9 -0.55 11 20
CREB1 0.028 0.015 -10000 0 -10000 0 0
histone acetylation -0.01 0.1 0.27 13 -0.37 11 24
BGLAP -0.045 0.096 -10000 0 -0.45 9 9
GR/PKAc 0.1 0.077 0.32 13 -0.28 1 14
NF kappa B1 p50/RelA -0.02 0.15 -10000 0 -0.42 21 21
SMARCD1 0.028 0.009 -10000 0 -10000 0 0
MDM2 0.055 0.066 0.23 29 -10000 0 29
GATA3 0.012 0.085 -10000 0 -0.4 19 19
AKT1 0.021 0.006 -10000 0 -10000 0 0
CSF2 -0.15 0.14 -10000 0 -0.54 13 13
GSK3B 0.023 0.013 -10000 0 -10000 0 0
NR1I3 0.024 0.15 0.46 9 -0.6 6 15
CSN2 0.079 0.12 0.39 22 -10000 0 22
BRG1/BAF155/BAF170/BAF60A 0.064 0.037 -10000 0 -0.4 1 1
NFATC1 0.024 0.01 -10000 0 -10000 0 0
POU2F1 0.027 0.014 -10000 0 -10000 0 0
CDKN1A 0.016 0.049 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.006 -10000 0 -10000 0 0
SFN 0.022 0.045 -10000 0 -0.42 5 5
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.096 0.082 0.32 13 -10000 0 13
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0 0.21 0.44 9 -0.8 24 33
JUN -0.15 0.13 -10000 0 -0.5 31 31
IL4 -0.053 0.091 -10000 0 -0.56 3 3
CDK5R1 0.025 0.027 -10000 0 -0.4 2 2
PRKACA 0.027 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.099 0.2 0.18 4 -0.41 86 90
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.099 0.081 0.33 13 -10000 0 13
cortisol/GR alpha (monomer) 0.18 0.22 0.62 52 -10000 0 52
NCOA2 -0.007 0.12 -10000 0 -0.45 32 32
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.11 0.15 -10000 0 -0.5 60 60
AP-1/NFAT1-c-4 -0.25 0.19 -10000 0 -0.61 59 59
AFP -0.11 0.13 -10000 0 -0.63 9 9
SUV420H1 0.025 0.008 -10000 0 -10000 0 0
IRF1 0.086 0.11 0.41 17 -10000 0 17
TP53 0.038 0.044 -10000 0 -0.44 4 4
PPP5C 0.027 0.004 -10000 0 -10000 0 0
KRT17 -0.22 0.23 -10000 0 -0.71 47 47
KRT14 -0.16 0.31 0.38 1 -0.97 50 51
TBP 0.032 0.017 -10000 0 -10000 0 0
CREBBP 0.066 0.074 0.32 27 -0.34 1 28
HDAC1 0.026 0.007 -10000 0 -10000 0 0
HDAC2 0.042 0.017 -10000 0 -10000 0 0
AP-1 -0.25 0.19 -10000 0 -0.61 60 60
MAPK14 0.025 0.011 -10000 0 -10000 0 0
MAPK10 -0.001 0.11 -10000 0 -0.44 27 27
MAPK11 0.025 0.011 -10000 0 -10000 0 0
KRT5 -0.17 0.2 -10000 0 -0.75 28 28
interleukin-1 receptor activity 0.016 0.016 -10000 0 -10000 0 0
NCOA1 0.029 0.004 -10000 0 -10000 0 0
STAT1 0.014 0.085 -10000 0 -0.39 21 21
CGA -0.052 0.095 -10000 0 -0.47 9 9
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.14 0.38 65 -0.33 1 66
MAPK3 0.026 0.011 -10000 0 -10000 0 0
MAPK1 0.026 0.01 -10000 0 -10000 0 0
ICAM1 -0.092 0.18 -10000 0 -0.56 24 24
NFKB1 -0.012 0.093 -10000 0 -0.31 5 5
MAPK8 -0.12 0.12 -10000 0 -0.48 29 29
MAPK9 0.025 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.017 0.16 0.5 9 -0.58 11 20
BAX 0.016 0.051 -10000 0 -10000 0 0
POMC -0.12 0.25 -10000 0 -1.2 18 18
EP300 0.063 0.077 0.3 28 -0.37 3 31
cortisol/GR alpha (dimer)/p53 0.17 0.18 0.55 47 -0.39 1 48
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.055 0.24 11 -10000 0 11
SGK1 0.071 0.12 0.54 2 -1.1 2 4
IL13 -0.14 0.15 -10000 0 -0.67 14 14
IL6 -0.13 0.29 -10000 0 -0.87 52 52
PRKACG -0.008 0.019 -10000 0 -10000 0 0
IL5 -0.13 0.13 -10000 0 -0.61 9 9
IL2 -0.17 0.16 -10000 0 -0.63 21 21
CDK5 0.026 0.007 -10000 0 -10000 0 0
PRKACB 0.026 0.022 -10000 0 -0.45 1 1
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
IL8 -0.13 0.21 -10000 0 -0.66 31 31
CDK5R1/CDK5 0.037 0.024 -10000 0 -0.28 2 2
NF kappa B1 p50/RelA/PKAc 0.01 0.13 -10000 0 -0.35 8 8
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.18 0.52 48 -10000 0 48
SMARCA4 0.027 0.01 -10000 0 -10000 0 0
chromatin remodeling 0.092 0.1 0.37 22 -0.48 1 23
NF kappa B1 p50/RelA/Cbp 0.055 0.15 0.39 11 -0.39 7 18
JUN (dimer) -0.15 0.13 -10000 0 -0.5 31 31
YWHAH 0.027 0.004 -10000 0 -10000 0 0
VIPR1 -0.078 0.16 -10000 0 -0.74 21 21
NR3C1 0.1 0.13 0.42 37 -10000 0 37
NR4A1 -0.004 0.11 -10000 0 -0.47 19 19
TIF2/SUV420H1 0.013 0.084 -10000 0 -0.32 28 28
MAPKKK cascade 0.017 0.15 0.49 9 -0.55 11 20
cortisol/GR alpha (dimer)/Src-1 0.17 0.18 0.54 53 -10000 0 53
PBX1 -0.059 0.18 -10000 0 -0.45 89 89
POU1F1 -0.001 0.023 -10000 0 -10000 0 0
SELE -0.17 0.34 -10000 0 -0.95 71 71
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.092 0.1 0.37 22 -0.49 1 23
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.18 0.52 48 -10000 0 48
mol:cortisol 0.086 0.12 0.36 50 -10000 0 50
MMP1 -0.34 0.17 -10000 0 -0.78 35 35
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.054 0.17 -10000 0 -0.58 20 20
MKNK1 0.027 0.003 -10000 0 -10000 0 0
MAPK14 -0.017 0.097 -10000 0 -0.3 21 21
ATF2/c-Jun -0.011 0.07 -10000 0 -0.33 4 4
MAPK11 -0.019 0.098 -10000 0 -0.3 22 22
MITF -0.03 0.11 -10000 0 -0.34 34 34
MAPKAPK5 -0.023 0.1 -10000 0 -0.37 14 14
KRT8 -0.071 0.15 -10000 0 -0.34 84 84
MAPKAPK3 0.024 0.009 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.027 0.14 -10000 0 -0.42 23 23
CEBPB -0.024 0.1 -10000 0 -0.37 16 16
SLC9A1 -0.024 0.1 -10000 0 -0.37 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.022 0.1 -10000 0 -0.36 15 15
p38alpha-beta/MNK1 -0.005 0.12 -10000 0 -0.35 21 21
JUN -0.008 0.072 -10000 0 -0.33 4 4
PPARGC1A -0.13 0.2 -10000 0 -0.48 74 74
USF1 -0.022 0.1 -10000 0 -0.37 14 14
RAB5/GDP/GDI1 -0.007 0.074 -10000 0 -0.28 13 13
NOS2 -0.065 0.2 -10000 0 -0.7 27 27
DDIT3 -0.026 0.1 -10000 0 -0.36 18 18
RAB5A 0.024 0.009 -10000 0 -10000 0 0
HSPB1 -0.017 0.092 0.29 11 -0.31 14 25
p38alpha-beta/HBP1 -0.005 0.12 -10000 0 -0.35 21 21
CREB1 -0.02 0.1 -10000 0 -0.37 15 15
RAB5/GDP 0.018 0.006 -10000 0 -10000 0 0
EIF4E -0.019 0.094 0.24 1 -0.34 13 14
RPS6KA4 -0.024 0.1 -10000 0 -0.37 14 14
PLA2G4A -0.034 0.11 -10000 0 -0.34 18 18
GDI1 -0.021 0.099 -10000 0 -0.37 13 13
TP53 -0.038 0.12 -10000 0 -0.42 23 23
RPS6KA5 -0.026 0.1 -10000 0 -0.36 14 14
ESR1 -0.037 0.12 -10000 0 -0.37 29 29
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.029 0.11 -10000 0 -0.38 16 16
MEF2A -0.023 0.1 -10000 0 -0.37 14 14
EIF4EBP1 -0.019 0.098 -10000 0 -0.39 13 13
KRT19 -0.13 0.17 -10000 0 -0.45 52 52
ELK4 -0.022 0.1 -10000 0 -0.33 22 22
ATF6 -0.022 0.1 -10000 0 -0.37 14 14
ATF1 -0.02 0.099 -10000 0 -0.37 13 13
p38alpha-beta/MAPKAPK2 -0.003 0.12 -10000 0 -0.35 21 21
p38alpha-beta/MAPKAPK3 -0.006 0.11 -10000 0 -0.35 21 21
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.036 0.13 -10000 0 -0.25 120 120
cell-cell adhesion 0.036 0.084 0.4 5 -10000 0 5
Ephrin B/EPHB2/RasGAP -0.007 0.13 -10000 0 -0.43 4 4
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.02 0.044 -10000 0 -0.27 9 9
Ephrin B1/EPHB1 0.019 0.056 -10000 0 -0.25 19 19
HRAS/GDP -0.026 0.095 -10000 0 -0.34 8 8
Ephrin B/EPHB1/GRB7 0.038 0.089 -10000 0 -0.45 2 2
Endophilin/SYNJ1 -0.04 0.1 0.21 1 -0.39 3 4
KRAS 0.026 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.038 0.085 -10000 0 -0.45 2 2
endothelial cell migration 0.035 0.036 -10000 0 -0.23 3 3
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.031 -10000 0 -0.45 2 2
PAK1 -0.034 0.12 0.36 3 -0.42 8 11
HRAS 0.025 0.02 -10000 0 -0.41 1 1
RRAS -0.04 0.1 0.21 1 -0.4 3 4
DNM1 -0.002 0.11 -10000 0 -0.4 34 34
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.018 0.093 0.35 3 -0.43 2 5
lamellipodium assembly -0.036 0.084 -10000 0 -0.4 5 5
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.009 0.066 -10000 0 -0.37 3 3
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
EPHB2 -0.065 0.17 -10000 0 -0.4 107 107
EPHB3 0.01 0.068 -10000 0 -0.45 10 10
EPHB1 0.005 0.088 -10000 0 -0.42 20 20
EPHB4 0.025 0.007 -10000 0 -10000 0 0
mol:GDP -0.035 0.091 0.29 1 -0.33 15 16
Ephrin B/EPHB2 -0.014 0.12 -10000 0 -0.25 28 28
Ephrin B/EPHB3 0.026 0.071 -10000 0 -0.24 27 27
JNK cascade 0.013 0.15 0.36 50 -0.41 1 51
Ephrin B/EPHB1 0.028 0.081 -10000 0 -0.25 26 26
RAP1/GDP -0.015 0.1 0.3 2 -0.35 5 7
EFNB2 0.025 0.031 -10000 0 -0.45 2 2
EFNB3 -0.002 0.11 -10000 0 -0.45 29 29
EFNB1 0.027 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.015 0.11 -10000 0 -0.22 101 101
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.012 0.11 -10000 0 -0.44 5 5
Rap1/GTP -0.028 0.093 -10000 0 -0.41 5 5
axon guidance -0.036 0.13 -10000 0 -0.25 120 120
MAPK3 0.004 0.061 0.19 4 -0.37 2 6
MAPK1 0.006 0.065 0.19 12 -0.34 3 15
Rac1/GDP -0.025 0.096 0.32 1 -0.35 6 7
actin cytoskeleton reorganization -0.042 0.079 -10000 0 -0.32 7 7
CDC42/GDP -0.022 0.099 0.3 2 -0.35 6 8
PI3K 0.039 0.038 -10000 0 -0.23 3 3
EFNA5 0.005 0.097 -10000 0 -0.45 21 21
Ephrin B2/EPHB4 0.032 0.023 -10000 0 -0.27 2 2
Ephrin B/EPHB2/Intersectin/N-WASP -0.019 0.086 -10000 0 -0.31 14 14
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.03 0.089 -10000 0 -0.4 5 5
PTK2 0.09 0.21 0.59 72 -10000 0 72
MAP4K4 0.013 0.15 0.36 50 -0.42 1 51
SRC 0.026 0.007 -10000 0 -10000 0 0
KALRN -0.009 0.12 -10000 0 -0.45 34 34
Intersectin/N-WASP 0.037 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.001 0.13 0.31 34 -0.36 9 43
MAP2K1 0.005 0.06 -10000 0 -0.36 3 3
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.004 0.11 -10000 0 -0.27 10 10
cell migration 0.01 0.093 0.29 3 -0.41 3 6
NRAS 0.026 0.005 -10000 0 -10000 0 0
SYNJ1 -0.041 0.1 0.21 1 -0.4 3 4
PXN 0.027 0.002 -10000 0 -10000 0 0
TF -0.16 0.15 0.2 2 -0.4 81 83
HRAS/GTP -0.015 0.11 -10000 0 -0.42 5 5
Ephrin B1/EPHB1-2 -0.015 0.11 -10000 0 -0.22 102 102
cell adhesion mediated by integrin 0.001 0.068 0.23 16 -0.26 8 24
RAC1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP -0.013 0.11 -10000 0 -0.45 5 5
RAC1-CDC42/GTP -0.036 0.088 -10000 0 -0.4 5 5
RASA1 0.024 0.031 -10000 0 -0.45 2 2
RAC1-CDC42/GDP -0.016 0.099 0.29 2 -0.35 5 7
ruffle organization -0.014 0.13 0.36 14 -0.41 5 19
NCK1 0.023 0.011 -10000 0 -10000 0 0
receptor internalization -0.063 0.1 0.2 3 -0.36 20 23
Ephrin B/EPHB2/KALRN -0.018 0.13 -10000 0 -0.42 9 9
ROCK1 0.055 0.078 0.18 123 -0.25 4 127
RAS family/GDP -0.047 0.079 -10000 0 -0.33 6 6
Rac1/GTP -0.033 0.091 -10000 0 -0.42 5 5
Ephrin B/EPHB1/Src/Paxillin 0.006 0.067 -10000 0 -0.33 5 5
Wnt signaling

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
Noncanonical Wnts/FZD -0.016 0.1 -9999 0 -0.47 13 13
FZD6 0.023 0.023 -9999 0 -0.45 1 1
WNT6 -0.01 0.12 -9999 0 -0.41 41 41
WNT4 0.013 0.077 -9999 0 -0.44 14 14
FZD3 0.019 0.057 -9999 0 -0.45 7 7
WNT5A 0.018 0.052 -9999 0 -0.44 6 6
WNT11 -0.019 0.13 -9999 0 -0.41 49 49
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.005 0.081 -10000 0 -10000 0 0
epithelial cell differentiation -0.03 0.1 -10000 0 -0.4 2 2
ITCH 0.037 0.02 -10000 0 -10000 0 0
WWP1 -0.004 0.076 -10000 0 -10000 0 0
FYN 0.026 0.02 -10000 0 -0.4 1 1
EGFR 0.019 0.049 -10000 0 -0.45 5 5
PRL -0.007 0.045 -10000 0 -0.4 5 5
neuron projection morphogenesis -0.02 0.095 0.27 3 -10000 0 3
PTPRZ1 0.007 0.092 -10000 0 -0.45 19 19
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.005 0.11 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.037 0.097 -10000 0 -0.38 2 2
ADAM17 0.038 0.036 -10000 0 -0.44 2 2
ErbB4/ErbB4 -0.021 0.072 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.015 0.093 -10000 0 -0.39 5 5
NCOR1 0.026 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.025 0.1 -10000 0 -0.36 3 3
GRIN2B -0.03 0.099 0.27 3 -0.35 3 6
ErbB4/ErbB2/betacellulin -0.069 0.13 -10000 0 -10000 0 0
STAT1 0.008 0.085 -10000 0 -0.4 21 21
HBEGF 0.025 0.02 -10000 0 -0.4 1 1
PRLR -0.068 0.19 -10000 0 -0.45 94 94
E4ICDs/ETO2 -0.005 0.081 -10000 0 -10000 0 0
axon guidance -0.007 0.072 0.38 1 -10000 0 1
NEDD4 0.039 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.04 0.14 -10000 0 -0.33 95 95
CBFA2T3 0.025 0.022 -10000 0 -0.45 1 1
ErbB4/ErbB2/HBEGF 0.008 0.066 -10000 0 -10000 0 0
MAPK3 -0.017 0.099 0.27 3 -10000 0 3
STAT1 (dimer) -0.014 0.095 -10000 0 -0.34 8 8
MAPK1 -0.016 0.1 0.28 4 -10000 0 4
JAK2 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.031 0.096 -10000 0 -0.36 2 2
NRG1 -0.026 0.11 -10000 0 -0.28 75 75
NRG3 -0.004 0.073 -10000 0 -0.44 12 12
NRG2 -0.24 0.24 -10000 0 -0.45 267 267
NRG4 -0.007 0.12 -10000 0 -0.45 33 33
heart development -0.007 0.072 0.38 1 -10000 0 1
neural crest cell migration -0.031 0.095 -10000 0 -0.36 2 2
ERBB2 0.021 0.025 -10000 0 -0.3 2 2
WWOX/E4ICDs -0.004 0.079 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.013 0.1 -10000 0 -0.36 13 13
apoptosis 0.036 0.12 0.58 10 -10000 0 10
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.14 0.16 -10000 0 -0.38 76 76
ErbB4/ErbB2/epiregulin -0.05 0.12 -10000 0 -0.41 1 1
ErbB4/ErbB4/betacellulin/betacellulin -0.086 0.14 -10000 0 -0.38 38 38
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.029 0.13 -10000 0 -0.44 2 2
MDM2 -0.01 0.078 0.27 7 -10000 0 7
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.022 0.088 -10000 0 -0.32 2 2
STAT5A -0.005 0.07 0.34 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta -0.027 0.098 -10000 0 -0.34 3 3
DLG4 0.025 0.022 -10000 0 -0.45 1 1
GRB2/SHC 0.039 0.008 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.006 0.075 -10000 0 -10000 0 0
STAT5A (dimer) -0.027 0.12 -10000 0 -0.42 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.005 0.081 0.33 1 -10000 0 1
LRIG1 0.015 0.064 -10000 0 -0.45 9 9
EREG -0.094 0.21 -10000 0 -0.45 124 124
BTC -0.13 0.22 -10000 0 -0.45 154 154
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.007 0.071 0.38 1 -10000 0 1
ERBB4 -0.021 0.072 -10000 0 -10000 0 0
STAT5B 0.027 0.003 -10000 0 -10000 0 0
YAP1 -0.013 0.1 -10000 0 -0.46 21 21
GRB2 0.027 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.007 0.092 -10000 0 -0.41 1 1
glial cell differentiation 0.006 0.074 -10000 0 -10000 0 0
WWOX 0.025 0.008 -10000 0 -10000 0 0
cell proliferation -0.097 0.16 0.29 3 -0.44 33 36
Signaling events mediated by HDAC Class III

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
EP300 0.025 0.031 -10000 0 -0.45 2 2
HDAC4 0.026 0.006 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.001 0.061 0.28 22 -10000 0 22
CDKN1A -0.006 0.011 -10000 0 -10000 0 0
KAT2B 0.007 0.09 -10000 0 -0.45 18 18
BAX 0.027 0.004 -10000 0 -10000 0 0
FOXO3 -0.004 0.025 0.37 2 -10000 0 2
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.029 -10000 0 -0.29 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
TAT 0.002 0.046 -10000 0 -0.4 5 5
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.054 0.12 -10000 0 -0.33 81 81
PPARGC1A -0.13 0.22 -10000 0 -0.45 164 164
FHL2 0.025 0.031 -10000 0 -0.45 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.018 -10000 0 -0.32 1 1
HIST2H4A -0.001 0.061 -10000 0 -0.28 22 22
SIRT1/FOXO3a 0.013 0.029 0.27 1 -0.2 6 7
SIRT1 0.022 0.022 -10000 0 -0.45 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.048 0.021 -10000 0 -0.28 1 1
SIRT1/Histone H1b 0.018 0.049 -10000 0 -0.25 5 5
apoptosis -0.049 0.019 0.28 1 -10000 0 1
SIRT1/PGC1A -0.072 0.14 -10000 0 -0.28 163 163
p53/SIRT1 0.025 0.036 -10000 0 -0.32 5 5
SIRT1/FOXO4 0.024 0.038 -10000 0 -0.25 5 5
FOXO1/FHL2/SIRT1 0.045 0.027 -10000 0 -0.25 3 3
HIST1H1E 0.008 0.038 -10000 0 -0.29 4 4
SIRT1/p300 0.034 0.028 -10000 0 -0.32 3 3
muscle cell differentiation 0.025 0.12 0.28 86 -10000 0 86
TP53 0.019 0.043 -10000 0 -0.45 4 4
KU70/SIRT1/BAX 0.049 0.02 -10000 0 -0.28 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
MEF2D 0.027 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.028 0.036 -10000 0 -0.29 6 6
ACSS2 0.011 0.016 -10000 0 -0.32 1 1
SIRT1/PCAF/MYOD -0.025 0.12 -10000 0 -0.28 86 86
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.095 0.2 -10000 0 -0.45 123 123
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.027 -10000 0 -0.4 2 2
TCEB1 0.024 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.023 0.065 0.25 3 -0.3 9 12
HIF1A 0.005 0.044 -10000 0 -0.27 9 9
COPS5 0.025 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.062 0.035 -10000 0 -10000 0 0
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.14 0.2 -10000 0 -0.4 183 183
ARNT/IPAS -0.049 0.15 -10000 0 -0.32 119 119
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.023 0.059 0.25 2 -0.27 11 13
CUL2 0.027 0.005 -10000 0 -10000 0 0
OS9 0.027 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.046 0.021 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.02 0.054 0.26 1 -0.27 10 11
PHD1-3/OS9 0.049 0.064 -10000 0 -0.25 5 5
HIF1A/RACK1/Elongin B/Elongin C 0.038 0.057 -10000 0 -0.3 3 3
VHL 0.024 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.02 0.055 -10000 0 -0.27 10 10
EGLN3 0.003 0.097 -10000 0 -0.41 26 26
EGLN2 0.027 0.005 -10000 0 -10000 0 0
EGLN1 0.027 0.004 -10000 0 -10000 0 0
TP53 0.022 0.043 -10000 0 -0.45 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.011 0.16 -10000 0 -0.49 47 47
ARNT 0.027 0.004 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF -0.057 0.1 -10000 0 -0.31 17 17
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.019 0.012 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.035 0.11 -9999 0 -0.34 6 6
Syndecan-3/Neurocan 0.011 0.074 -9999 0 -0.36 12 12
POMC -0.025 0.14 -9999 0 -0.41 59 59
EGFR 0.019 0.049 -9999 0 -0.45 5 5
Syndecan-3/EGFR 0.017 0.065 -9999 0 -0.36 11 11
AGRP -0.002 0.022 -9999 0 -10000 0 0
NCSTN 0.027 0.004 -9999 0 -10000 0 0
PSENEN 0.026 0.005 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.027 0.005 -9999 0 -10000 0 0
NCAN -0.005 0.091 -9999 0 -0.4 24 24
long-term memory 0.026 0.057 -9999 0 -0.34 8 8
Syndecan-3/IL8 -0.022 0.11 -9999 0 -0.4 13 13
PSEN1 0.026 0.006 -9999 0 -10000 0 0
Src/Cortactin 0.027 0.019 -9999 0 -10000 0 0
FYN 0.026 0.02 -9999 0 -0.4 1 1
limb bud formation 0.004 0.06 -9999 0 -0.37 12 12
MC4R 0.002 0.028 -9999 0 -0.4 1 1
SRC 0.026 0.007 -9999 0 -10000 0 0
PTN -0.15 0.23 -9999 0 -0.45 177 177
FGFR/FGF/Syndecan-3 0.004 0.06 -9999 0 -0.37 12 12
neuron projection morphogenesis -0.03 0.13 -9999 0 -0.34 8 8
Syndecan-3/AgRP 0.017 0.061 -9999 0 -0.36 12 12
Syndecan-3/AgRP/MC4R 0.027 0.062 -9999 0 -0.34 12 12
Fyn/Cortactin 0.028 0.019 -9999 0 -10000 0 0
SDC3 0.004 0.061 -9999 0 -0.38 12 12
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.021 0.1 -9999 0 -0.4 13 13
IL8 -0.064 0.17 -9999 0 -0.4 105 105
Syndecan-3/Fyn/Cortactin 0.027 0.058 -9999 0 -0.35 8 8
Syndecan-3/CASK 0.003 0.058 -9999 0 -0.36 12 12
alpha-MSH/MC4R -0.006 0.11 -9999 0 -0.29 59 59
Gamma Secretase 0.073 0.026 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.036 -10000 0 -0.39 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.053 0.14 0.5 19 -10000 0 19
IL27/IL27R/JAK1 -0.035 0.15 -10000 0 -0.57 8 8
TBX21 -0.084 0.17 -10000 0 -0.56 23 23
IL12B -0.018 0.12 -10000 0 -0.4 43 43
IL12A -0.006 0.053 -10000 0 -0.32 14 14
IL6ST -0.038 0.16 -10000 0 -0.46 57 57
IL27RA/JAK1 -0.002 0.066 -10000 0 -10000 0 0
IL27 -0.007 0.091 -10000 0 -0.41 23 23
TYK2 0.016 0.029 -10000 0 -0.41 1 1
T-helper cell lineage commitment 0.003 0.1 0.43 1 -0.42 2 3
T-helper 2 cell differentiation 0.053 0.14 0.5 19 -10000 0 19
T cell proliferation during immune response 0.053 0.14 0.5 19 -10000 0 19
MAPKKK cascade -0.053 0.14 -10000 0 -0.5 19 19
STAT3 0.027 0.003 -10000 0 -10000 0 0
STAT2 0.027 0.003 -10000 0 -10000 0 0
STAT1 0.008 0.086 -10000 0 -0.4 21 21
IL12RB1 -0.012 0.12 -10000 0 -0.4 44 44
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.11 0.19 -10000 0 -0.54 37 37
IL27/IL27R/JAK2/TYK2 -0.054 0.14 -10000 0 -0.5 19 19
positive regulation of T cell mediated cytotoxicity -0.053 0.14 -10000 0 -0.5 19 19
STAT1 (dimer) -0.073 0.21 0.52 1 -0.67 15 16
JAK2 0.016 0.02 -10000 0 -10000 0 0
JAK1 0.026 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.043 0.14 -10000 0 -0.49 18 18
T cell proliferation -0.067 0.15 -10000 0 -0.5 26 26
IL12/IL12R/TYK2/JAK2 -0.052 0.19 -10000 0 -0.75 25 25
IL17A 0.002 0.1 0.43 1 -0.42 2 3
mast cell activation 0.053 0.14 0.5 19 -10000 0 19
IFNG -0.012 0.039 -10000 0 -0.098 16 16
T cell differentiation -0.005 0.007 -10000 0 -0.02 52 52
STAT3 (dimer) -0.043 0.14 -10000 0 -0.49 18 18
STAT5A (dimer) -0.043 0.14 -10000 0 -0.49 18 18
STAT4 (dimer) -0.045 0.14 -10000 0 -0.5 20 20
STAT4 0.017 0.063 -10000 0 -0.4 11 11
T cell activation -0.005 0.011 0.051 16 -10000 0 16
IL27R/JAK2/TYK2 -0.019 0.12 -10000 0 -0.66 1 1
GATA3 -0.004 0.13 0.6 4 -1.3 3 7
IL18 -0.002 0.051 -10000 0 -0.32 12 12
positive regulation of mast cell cytokine production -0.043 0.14 -10000 0 -0.48 18 18
IL27/EBI3 0.003 0.087 -10000 0 -0.3 33 33
IL27RA -0.01 0.067 -10000 0 -10000 0 0
IL6 -0.012 0.13 -10000 0 -0.44 42 42
STAT5A 0.027 0.003 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.001 0.046 -10000 0 -10000 0 0
IL1B -0.024 0.089 -10000 0 -0.28 53 53
EBI3 0.01 0.067 -10000 0 -0.42 11 11
TNF -0.006 0.06 -10000 0 -0.28 22 22
Regulation of nuclear SMAD2/3 signaling

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.004 0.038 -10000 0 -0.45 2 2
HSPA8 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.054 0.1 -10000 0 -0.28 15 15
AKT1 0.005 0.046 -10000 0 -10000 0 0
GSC 0.007 0.14 -10000 0 -1.1 3 3
NKX2-5 0 0.008 -10000 0 -10000 0 0
muscle cell differentiation 0.04 0.14 0.37 40 -10000 0 40
SMAD2-3/SMAD4/SP1 -0.005 0.11 -10000 0 -0.32 2 2
SMAD4 0.009 0.046 -10000 0 -10000 0 0
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.015 0.053 -10000 0 -0.24 9 9
SMAD3/SMAD4/VDR 0.056 0.057 -10000 0 -10000 0 0
MYC 0.028 0.023 -10000 0 -10000 0 0
CDKN2B -0.35 0.64 -10000 0 -1.5 111 111
AP1 0.008 0.092 -10000 0 -0.26 9 9
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.036 0.08 -10000 0 -0.43 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.067 0.16 -10000 0 -0.36 95 95
SP3 0.028 0.006 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 -0.022 0.12 -10000 0 -0.4 48 48
SMAD3/SMAD4/GR 0.063 0.065 -10000 0 -10000 0 0
GATA3 0.01 0.084 -10000 0 -0.4 19 19
SKI/SIN3/HDAC complex/NCoR1 0.03 0.056 -10000 0 -0.52 3 3
MEF2C/TIF2 -0.01 0.13 0.32 1 -0.43 19 20
endothelial cell migration 0.16 0.17 0.5 10 -10000 0 10
MAX 0.038 0.015 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.022 -10000 0 -0.45 1 1
RUNX2 0.024 0.029 -10000 0 -0.42 2 2
RUNX3 0.021 0.047 -10000 0 -0.4 6 6
RUNX1 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.007 -10000 0 -10000 0 0
NR3C1 0.038 0.015 -10000 0 -10000 0 0
VDR 0.025 0.031 -10000 0 -0.45 2 2
CDKN1A -0.011 0.1 -10000 0 -0.58 7 7
KAT2B 0.005 0.09 -10000 0 -0.45 18 18
SMAD2/SMAD2/SMAD4/FOXH1 -0.002 0.1 -10000 0 -0.31 15 15
DCP1A 0.024 0.009 -10000 0 -10000 0 0
SKI 0.027 0.006 -10000 0 -10000 0 0
SERPINE1 -0.16 0.17 -10000 0 -0.52 9 9
SMAD3/SMAD4/ATF2 0.035 0.06 -10000 0 -0.26 1 1
SMAD3/SMAD4/ATF3 0.032 0.072 -10000 0 -0.3 7 7
SAP30 0.026 0.02 -10000 0 -0.39 1 1
Cbp/p300/PIAS3 0.013 0.048 -10000 0 -0.26 2 2
JUN 0.001 0.089 0.29 1 -0.26 4 5
SMAD3/SMAD4/IRF7 0.026 0.084 -10000 0 -0.36 5 5
TFE3 -0.002 0.03 -10000 0 -10000 0 0
COL1A2 -0.097 0.17 -10000 0 -0.52 1 1
mesenchymal cell differentiation -0.034 0.063 0.3 2 -10000 0 2
DLX1 -0.14 0.21 -10000 0 -0.4 198 198
TCF3 0.027 0.005 -10000 0 -10000 0 0
FOS -0.03 0.16 -10000 0 -0.45 60 60
SMAD3/SMAD4/Max 0.062 0.064 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.044 0.024 -10000 0 -0.26 2 2
ZBTB17 0.029 0.013 -10000 0 -10000 0 0
LAMC1 0.001 0.044 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.035 0.059 -10000 0 -10000 0 0
IRF7 0.011 0.079 -10000 0 -0.41 16 16
ESR1 0.01 0.1 -10000 0 -0.42 27 27
HNF4A -0.024 0.12 -10000 0 -0.4 46 46
MEF2C 0.008 0.12 0.43 2 -0.42 12 14
SMAD2-3/SMAD4 0.029 0.079 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.037 0.03 -10000 0 -0.26 2 2
IGHV3OR16-13 0.007 0.045 -10000 0 -0.33 8 8
TGIF2/HDAC complex 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.008 0.023 -10000 0 -10000 0 0
SKIL 0.02 0.012 -10000 0 -10000 0 0
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
SNIP1 0.028 0.004 -10000 0 -10000 0 0
GCN5L2 -0.005 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.018 0.059 -10000 0 -10000 0 0
MSG1/HSC70 0.034 0.043 -10000 0 -0.28 8 8
SMAD2 0.007 0.044 -10000 0 -10000 0 0
SMAD3 0.013 0.045 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.018 0.041 -10000 0 -0.39 1 1
SMAD2/SMAD2/SMAD4 -0.049 0.12 0.21 3 -0.4 45 48
NCOR1 0.027 0.006 -10000 0 -10000 0 0
NCOA2 -0.007 0.12 -10000 0 -0.45 32 32
NCOA1 0.027 0.003 -10000 0 -10000 0 0
MYOD/E2A -0.019 0.13 -10000 0 -0.32 75 75
SMAD2-3/SMAD4/SP1/MIZ-1 0.011 0.12 -10000 0 -0.34 2 2
IFNB1 -0.003 0.08 -10000 0 -0.4 9 9
SMAD3/SMAD4/MEF2C 0.02 0.13 -10000 0 -0.42 11 11
CITED1 0.02 0.054 -10000 0 -0.4 8 8
SMAD2-3/SMAD4/ARC105 0.04 0.078 -10000 0 -10000 0 0
RBL1 0.025 0.023 -10000 0 -0.45 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.085 0.23 -10000 0 -0.54 98 98
RUNX1-3/PEBPB2 0.047 0.035 -10000 0 -0.23 6 6
SMAD7 -0.013 0.1 -10000 0 -0.4 3 3
MYC/MIZ-1 0.04 0.038 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.067 0.11 0.28 4 -0.35 13 17
IL10 0.003 0.079 -10000 0 -0.37 8 8
PIASy/HDAC complex 0.031 0.014 -10000 0 -10000 0 0
PIAS3 0.023 0.007 -10000 0 -10000 0 0
CDK2 0.012 0.021 -10000 0 -10000 0 0
IL5 -0.003 0.07 -10000 0 -0.38 3 3
CDK4 0.009 0.023 -10000 0 -10000 0 0
PIAS4 0.031 0.013 -10000 0 -10000 0 0
ATF3 0.02 0.058 -10000 0 -0.43 8 8
SMAD3/SMAD4/SP1 -0.01 0.1 -10000 0 -0.3 3 3
FOXG1 -0.066 0.16 -10000 0 -0.42 80 80
FOXO3 -0.007 0.049 -10000 0 -10000 0 0
FOXO1 -0.008 0.048 -10000 0 -10000 0 0
FOXO4 -0.008 0.051 -10000 0 -0.32 1 1
heart looping 0.008 0.12 0.43 2 -0.42 12 14
CEBPB 0.012 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.077 0.15 -10000 0 -0.28 82 82
MYOD1 -0.065 0.16 -10000 0 -0.45 75 75
SMAD3/SMAD4/HNF4 0.007 0.099 -10000 0 -0.29 11 11
SMAD3/SMAD4/GATA3 0.029 0.085 -10000 0 -0.31 4 4
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.057 0.067 -10000 0 -0.28 1 1
SMAD3/SMAD4/SP1-3 0.007 0.096 -10000 0 -10000 0 0
MED15 0.025 0.02 -10000 0 -0.4 1 1
SP1 -0.018 0.061 -10000 0 -0.18 1 1
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.002 0.098 -10000 0 -0.29 15 15
ITGB5 -0.01 0.073 0.35 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP 0.035 0.038 -10000 0 -0.32 1 1
SMAD3/SMAD4/AR -0.048 0.15 -10000 0 -0.28 119 119
AR -0.1 0.21 -10000 0 -0.45 131 131
negative regulation of cell growth 0.01 0.063 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.016 0.13 -10000 0 -0.29 70 70
E2F5 0.021 0.038 -10000 0 -0.45 3 3
E2F4 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.011 0.095 -10000 0 -0.32 4 4
SMAD2-3/SMAD4/FOXO1-3a-4 -0.044 0.16 -10000 0 -0.36 94 94
TFDP1 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.024 0.1 -10000 0 -0.27 4 4
SMAD3/SMAD4/RUNX2 0.035 0.063 -10000 0 -0.3 2 2
TGIF2 0.026 0.007 -10000 0 -10000 0 0
TGIF1 0.024 0.009 -10000 0 -10000 0 0
ATF2 0.025 0.022 -10000 0 -0.45 1 1
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.03 0.15 -10000 0 -0.45 56 56
GNB1/GNG2 0 0.12 -10000 0 -0.5 9 9
mol:DAG -0.014 0.1 0.19 3 -0.46 9 12
PLCG1 -0.014 0.1 0.2 3 -0.47 9 12
YES1 -0.018 0.095 -10000 0 -0.5 9 9
FZD3 0.019 0.057 -10000 0 -0.45 7 7
FZD6 0.023 0.023 -10000 0 -0.45 1 1
G protein 0.002 0.12 0.27 3 -0.53 7 10
MAP3K7 -0.051 0.12 0.29 5 -0.41 19 24
mol:Ca2+ -0.013 0.097 0.19 3 -0.44 9 12
mol:IP3 -0.014 0.1 0.19 3 -0.46 9 12
NLK 0.006 0.063 -10000 0 -0.79 3 3
GNB1 0.026 0.005 -10000 0 -10000 0 0
CAMK2A -0.052 0.13 0.3 5 -0.41 24 29
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.1 -10000 0 -0.47 13 13
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.02 0.097 -10000 0 -0.51 9 9
GO:0007205 -0.017 0.099 0.25 5 -0.47 9 14
WNT6 -0.01 0.12 -10000 0 -0.41 41 41
WNT4 0.013 0.077 -10000 0 -0.44 14 14
NFAT1/CK1 alpha -0.013 0.14 0.27 5 -0.49 12 17
GNG2 0.025 0.02 -10000 0 -0.4 1 1
WNT5A 0.018 0.052 -10000 0 -0.44 6 6
WNT11 -0.019 0.13 -10000 0 -0.41 49 49
CDC42 -0.008 0.1 0.19 21 -0.52 7 28
PDGFR-alpha signaling pathway

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
PDGFRA 0.01 0.068 -10000 0 -0.45 9 9
PDGF/PDGFRA/CRKL 0.023 0.054 -10000 0 -0.31 10 10
positive regulation of JUN kinase activity 0.057 0.042 -10000 0 -0.24 6 6
CRKL 0.025 0.02 -10000 0 -0.4 1 1
PDGF/PDGFRA/Caveolin-3 -0.049 0.15 -10000 0 -0.33 101 101
AP1 -0.098 0.3 0.31 2 -0.86 63 65
mol:IP3 -0.001 0.052 -10000 0 -0.32 9 9
PLCG1 -0.001 0.052 -10000 0 -0.32 9 9
PDGF/PDGFRA/alphaV Integrin 0.022 0.054 -10000 0 -0.3 10 10
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
CRK 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.052 -10000 0 -0.32 9 9
CAV3 -0.085 0.18 -10000 0 -0.45 96 96
CAV1 -0.007 0.11 -10000 0 -0.4 38 38
SHC/Grb2/SOS1 0.059 0.042 -10000 0 -0.24 6 6
PDGF/PDGFRA/Shf 0.019 0.072 -10000 0 -0.35 15 15
FOS -0.11 0.29 0.32 2 -0.85 63 65
JUN -0.023 0.025 -10000 0 -10000 0 0
oligodendrocyte development 0.022 0.054 -10000 0 -0.3 10 10
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
mol:DAG -0.001 0.052 -10000 0 -0.32 9 9
PDGF/PDGFRA 0.01 0.068 -10000 0 -0.45 9 9
actin cytoskeleton reorganization 0.022 0.051 -10000 0 -0.3 9 9
SRF 0.014 0.011 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.032 0.043 -10000 0 -0.26 6 6
PDGF/PDGFRA/Crk/C3G 0.044 0.044 -10000 0 -0.25 9 9
JAK1 0.004 0.046 -10000 0 -0.31 9 9
ELK1/SRF 0.004 0.045 -10000 0 -0.27 5 5
SHB 0.024 0.009 -10000 0 -10000 0 0
SHF 0.019 0.061 -10000 0 -0.45 8 8
CSNK2A1 0.028 0.02 -10000 0 -10000 0 0
GO:0007205 -0.007 0.052 -10000 0 -0.34 9 9
SOS1 0.027 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.057 0.042 -10000 0 -0.24 6 6
PDGF/PDGFRA/SHB 0.022 0.051 -10000 0 -0.3 9 9
PDGF/PDGFRA/Caveolin-1 0 0.098 -10000 0 -0.29 47 47
ITGAV 0.024 0.027 -10000 0 -0.4 2 2
ELK1 -0.013 0.052 -10000 0 -0.29 9 9
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.024 0.051 -10000 0 -0.31 9 9
JAK-STAT cascade 0.004 0.046 -10000 0 -0.31 9 9
cell proliferation 0.019 0.072 -10000 0 -0.35 15 15
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.023 -10000 0 -0.28 3 3
MAP4K4 0.018 0.065 0.21 2 -0.4 5 7
BAG4 0.023 0.023 -10000 0 -0.45 1 1
PKC zeta/ceramide -0.008 0.068 -10000 0 -0.22 31 31
NFKBIA 0.026 0.006 -10000 0 -10000 0 0
BIRC3 0.012 0.071 -10000 0 -0.4 14 14
BAX -0.003 0.052 -10000 0 -0.34 9 9
RIPK1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.023 0.13 0.69 18 -10000 0 18
BAD -0.018 0.068 0.2 10 -0.22 30 40
SMPD1 0.02 0.064 0.18 23 -0.23 7 30
RB1 -0.021 0.062 0.2 1 -0.22 30 31
FADD/Caspase 8 0.056 0.1 0.23 64 -0.41 3 67
MAP2K4 -0.02 0.059 0.18 4 -0.27 9 13
NSMAF 0.025 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.019 0.06 0.18 6 -0.26 10 16
EGF -0.06 0.18 -10000 0 -0.45 88 88
mol:ceramide -0.022 0.065 -10000 0 -0.22 32 32
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.011 0.023 -10000 0 -0.27 3 3
ASAH1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle -0.021 0.061 0.19 1 -0.22 30 31
cell proliferation -0.029 0.096 -10000 0 -0.32 8 8
BID 0.014 0.11 -10000 0 -0.67 7 7
MAP3K1 -0.021 0.061 0.19 2 -0.22 28 30
EIF2A 0.023 0.1 0.24 31 -0.27 8 39
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.002 -10000 0 -10000 0 0
MAPK3 -0.014 0.06 -10000 0 -0.55 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.061 -10000 0 -0.44 2 2
Cathepsin D/ceramide -0.007 0.067 -10000 0 -0.21 32 32
FADD 0.044 0.083 0.2 74 -0.38 3 77
KSR1 -0.021 0.064 0.19 4 -0.22 30 34
MAPK8 -0.017 0.071 -10000 0 -0.27 15 15
PRKRA -0.016 0.069 0.19 14 -0.22 28 42
PDGFA 0.023 0.034 -10000 0 -0.4 3 3
TRAF2 0.021 0.047 -10000 0 -0.4 6 6
IGF1 -0.054 0.18 -10000 0 -0.45 84 84
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.022 0.064 -10000 0 -0.22 32 32
CTSD 0.026 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.037 0.011 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.03 0.1 -10000 0 -0.34 8 8
PRKCD 0.024 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.022 -10000 0 -0.45 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.011 0.023 -10000 0 -0.27 3 3
RelA/NF kappa B1 0.038 0.011 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.054 -10000 0 -0.39 5 5
TNFR1A/BAG4/TNF-alpha 0.032 0.061 -10000 0 -0.24 20 20
mol:Sphingosine-1-phosphate 0.012 0.023 -10000 0 -0.28 3 3
MAP2K1 -0.018 0.06 0.21 1 -0.3 5 6
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
CYCS 0.003 0.047 0.18 3 -0.21 5 8
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.033 0.022 -10000 0 -0.32 1 1
EIF2AK2 -0.016 0.068 0.19 14 -0.27 11 25
TNF-alpha/TNFR1A/FAN 0.033 0.061 -10000 0 -0.24 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.025 0.071 -10000 0 -0.42 7 7
MAP2K2 -0.019 0.059 -10000 0 -0.32 4 4
SMPD3 0 0.095 0.2 3 -0.3 35 38
TNF 0.007 0.088 -10000 0 -0.4 22 22
PKC zeta/PAR4 0.038 0.019 -10000 0 -0.32 1 1
mol:PHOSPHOCHOLINE 0.029 0.084 0.21 71 -0.18 4 75
NF kappa B1/RelA/I kappa B alpha 0.069 0.032 -10000 0 -10000 0 0
AIFM1 0 0.054 0.17 4 -0.23 4 8
BCL2 0.021 0.04 -10000 0 -0.41 4 4
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.032 0.038 -10000 0 -0.29 6 6
PDGFRB -0.049 0.16 -10000 0 -0.4 88 88
SPHK1 0 0.057 -10000 0 -0.64 3 3
mol:S1P -0.004 0.055 -10000 0 -0.54 3 3
S1P1/S1P/Gi -0.033 0.12 -10000 0 -0.39 33 33
GNAO1 0.02 0.041 -10000 0 -0.42 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.037 0.13 0.26 1 -0.37 25 26
PLCG1 -0.036 0.11 -10000 0 -0.37 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.049 0.16 -10000 0 -0.4 88 88
GNAI2 0.022 0.012 -10000 0 -10000 0 0
GNAI3 0.025 0.008 -10000 0 -10000 0 0
GNAI1 0.024 0.023 -10000 0 -0.46 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0 0.029 -10000 0 -0.24 6 6
S1P1/S1P -0.006 0.056 -10000 0 -0.33 3 3
negative regulation of cAMP metabolic process -0.032 0.12 -10000 0 -0.38 33 33
MAPK3 -0.041 0.14 -10000 0 -0.42 31 31
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
KDR 0.024 0.029 -10000 0 -0.42 2 2
PLCB2 -0.001 0.062 0.2 3 -0.3 5 8
RAC1 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.048 -10000 0 -0.28 3 3
receptor internalization -0.007 0.052 -10000 0 -0.31 3 3
PTGS2 -0.045 0.17 -10000 0 -0.6 16 16
Rac1/GTP -0.005 0.048 -10000 0 -0.29 3 3
RHOA 0.024 0.009 -10000 0 -10000 0 0
VEGFA 0.021 0.043 -10000 0 -0.4 5 5
negative regulation of T cell proliferation -0.032 0.12 -10000 0 -0.38 33 33
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.009 0.083 -10000 0 -0.42 18 18
MAPK1 -0.041 0.13 -10000 0 -0.43 29 29
S1P1/S1P/PDGFB-D/PDGFRB -0.016 0.089 -10000 0 -0.31 5 5
ABCC1 0.024 0.033 -10000 0 -0.4 3 3
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.034 0.035 -10000 0 -0.29 5 5
CRKL 0.017 0.12 0.3 8 -0.45 18 26
mol:PIP3 0 0.035 -10000 0 -0.74 1 1
AKT1 0.004 0.05 -10000 0 -0.64 1 1
PTK2B 0.025 0.007 -10000 0 -10000 0 0
RAPGEF1 0.02 0.12 0.28 14 -0.43 17 31
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.031 0.066 -10000 0 -0.26 22 22
MAP3K5 0.016 0.12 0.28 7 -0.48 16 23
HGF/MET/CIN85/CBL/ENDOPHILINS 0.043 0.071 -10000 0 -0.23 26 26
AP1 -0.01 0.11 -10000 0 -0.29 60 60
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.087 0.28 -10000 0 -0.74 77 77
STAT3 (dimer) 0.018 0.067 -10000 0 -0.32 6 6
GAB1/CRKL/SHP2/PI3K 0.031 0.098 0.32 2 -0.43 9 11
INPP5D 0.024 0.031 -10000 0 -0.45 2 2
CBL/CRK 0.024 0.11 0.31 1 -0.42 17 18
PTPN11 0.027 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
ELK1 -0.006 0.07 0.29 18 -0.21 1 19
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.012 0.051 0.15 1 -0.24 8 9
PAK1 0.011 0.066 0.39 4 -0.62 1 5
HGF/MET/RANBP10 0.033 0.071 -10000 0 -0.26 26 26
HRAS 0 0.12 -10000 0 -0.48 20 20
DOCK1 0.015 0.11 0.29 7 -0.43 17 24
GAB1 0.01 0.11 0.25 1 -0.46 19 20
CRK 0.012 0.11 0.28 2 -0.45 18 20
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.12 -10000 0 -0.46 24 24
JUN 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.002 0.044 -10000 0 -0.2 19 19
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
cell morphogenesis 0.072 0.13 0.32 49 -0.41 5 54
GRB2/SHC 0.033 0.057 -10000 0 -0.22 6 6
FOS -0.032 0.16 -10000 0 -0.45 60 60
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.006 0.07 0.28 18 -0.21 1 19
HGF/MET/MUC20 0.019 0.066 -10000 0 -0.26 26 26
cell migration 0.03 0.054 -10000 0 -0.22 6 6
GRB2 0.027 0.004 -10000 0 -10000 0 0
CBL 0.025 0.008 -10000 0 -10000 0 0
MET/RANBP10 0.033 0.038 -10000 0 -0.29 6 6
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.013 0.052 -10000 0 -0.32 4 4
MET/MUC20 0.016 0.034 -10000 0 -0.29 6 6
RAP1B 0.026 0.12 0.28 19 -0.42 14 33
RAP1A 0.019 0.11 0.27 13 -0.42 15 28
HGF/MET/RANBP9 0.034 0.069 -10000 0 -0.26 24 24
RAF1 0.008 0.11 -10000 0 -0.46 17 17
STAT3 0.018 0.067 -10000 0 -0.32 6 6
cell proliferation 0.02 0.099 0.3 8 -0.35 17 25
RPS6KB1 0.011 0.023 -10000 0 -0.26 1 1
MAPK3 -0.008 0.098 0.68 7 -10000 0 7
MAPK1 -0.011 0.085 0.73 4 -10000 0 4
RANBP9 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.029 0.12 0.29 7 -0.44 17 24
SRC 0.007 0.047 -10000 0 -0.31 4 4
PI3K 0.023 0.05 -10000 0 -0.24 6 6
MET/Glomulin 0.015 0.037 -10000 0 -0.24 7 7
SOS1 0.027 0.003 -10000 0 -10000 0 0
MAP2K1 0.008 0.11 0.3 1 -0.45 14 15
MET 0.021 0.049 -10000 0 -0.42 6 6
MAP4K1 0.014 0.13 0.31 5 -0.51 16 21
PTK2 0.022 0.011 -10000 0 -10000 0 0
MAP2K2 0.008 0.11 -10000 0 -0.44 14 14
BAD 0.008 0.06 0.38 3 -0.62 1 4
MAP2K4 0.017 0.11 0.27 9 -0.43 16 25
SHP2/GRB2/SOS1/GAB1 0.031 0.1 -10000 0 -0.39 18 18
INPPL1 0.024 0.01 -10000 0 -10000 0 0
PXN 0.027 0.002 -10000 0 -10000 0 0
SH3KBP1 0.025 0.027 -10000 0 -0.4 2 2
HGS 0 0.042 -10000 0 -0.23 6 6
PLCgamma1/PKC 0.019 0.005 -10000 0 -10000 0 0
HGF 0.007 0.092 -10000 0 -0.44 20 20
RASA1 0.024 0.031 -10000 0 -0.45 2 2
NCK1 0.023 0.011 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.029 0.049 -10000 0 -0.23 4 4
PDPK1 -0.002 0.036 -10000 0 -0.68 1 1
HGF/MET/SHIP 0.032 0.075 -10000 0 -0.27 27 27
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.046 0.081 0.34 1 -0.41 1 2
CRKL 0.021 0.084 0.31 6 -0.32 1 7
mol:DAG 0.02 0.065 -10000 0 -0.28 3 3
HRAS 0.026 0.086 0.3 13 -10000 0 13
MAPK8 0.019 0.099 0.2 41 -0.3 6 47
RAP1A 0.023 0.086 0.31 7 -0.32 1 8
GAB1 0.022 0.085 0.31 7 -0.32 1 8
MAPK14 0.022 0.094 0.19 46 -0.37 2 48
EPO -0.015 0.12 -10000 0 -0.39 49 49
PLCG1 0.021 0.066 -10000 0 -0.28 3 3
EPOR/TRPC2/IP3 Receptors 0.018 0.062 -10000 0 -0.39 10 10
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.022 0.09 -10000 0 -0.23 48 48
GAB1/SHC/GRB2/SOS1 0.049 0.082 0.27 6 -0.3 1 7
EPO/EPOR (dimer) 0.005 0.1 -10000 0 -0.28 56 56
IRS2 0.022 0.087 0.31 7 -0.32 1 8
STAT1 0.02 0.071 -10000 0 -0.35 1 1
STAT5B 0.024 0.068 -10000 0 -0.34 1 1
cell proliferation 0.013 0.097 0.2 47 -0.35 2 49
GAB1/SHIP/PIK3R1/SHP2/SHC 0.029 0.075 -10000 0 -0.34 2 2
TEC 0.013 0.099 0.29 6 -0.37 8 14
SOCS3 0.026 0.022 -10000 0 -0.45 1 1
STAT1 (dimer) 0.02 0.07 -10000 0 -0.34 1 1
JAK2 0.021 0.02 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
EPO/EPOR (dimer)/JAK2 0.044 0.086 -10000 0 -0.34 1 1
EPO/EPOR 0.005 0.1 -10000 0 -0.28 56 56
LYN 0.025 0.021 -10000 0 -0.39 1 1
TEC/VAV2 0.017 0.1 0.28 2 -0.39 10 12
elevation of cytosolic calcium ion concentration 0.018 0.062 -10000 0 -0.39 10 10
SHC1 0.027 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.022 0.09 -10000 0 -0.23 48 48
mol:IP3 0.02 0.065 -10000 0 -0.28 3 3
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.041 0.092 0.31 6 -0.34 3 9
SH2B3 0.025 0.027 -10000 0 -0.4 1 1
NFKB1 0.023 0.095 0.19 47 -0.37 2 49
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.052 -10000 0 -0.25 9 9
PTPN6 0.018 0.083 0.3 4 -0.33 1 5
TEC/VAV2/GRB2 0.027 0.1 0.28 2 -0.38 10 12
EPOR 0.018 0.062 -10000 0 -0.39 10 10
INPP5D 0.024 0.031 -10000 0 -0.45 2 2
mol:GDP 0.048 0.082 0.27 6 -0.3 1 7
SOS1 0.027 0.003 -10000 0 -10000 0 0
PLCG2 0.025 0.022 -10000 0 -0.45 1 1
CRKL/CBL/C3G 0.035 0.08 0.28 2 -0.31 1 3
VAV2 0.018 0.092 0.31 7 -0.34 4 11
CBL 0.021 0.084 0.31 7 -0.32 1 8
SHC/Grb2/SOS1 0.019 0.064 -10000 0 -0.31 1 1
STAT5A 0.024 0.068 -10000 0 -0.34 1 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.078 -10000 0 -0.38 1 1
LYN/PLCgamma2 0.034 0.026 -10000 0 -0.3 2 2
PTPN11 0.027 0.002 -10000 0 -10000 0 0
BTK 0.022 0.085 0.31 6 -0.32 1 7
BCL2 0.041 0.11 0.34 1 -0.61 6 7
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.015 0.09 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.02 -10000 0 -0.4 1 1
STAT1 (dimer)/Cbp/p300 0.018 0.099 -10000 0 -0.31 10 10
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.03 0.044 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.03 0.069 -10000 0 -0.24 9 9
CaM/Ca2+ 0.016 0.087 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.001 0.096 -10000 0 -0.34 10 10
AKT1 0.04 0.11 0.3 19 -10000 0 19
MAP2K1 -0.008 0.079 0.22 2 -10000 0 2
MAP3K11 -0.005 0.082 -10000 0 -10000 0 0
IFNGR1 0.019 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.13 0.21 -10000 0 -0.43 120 120
Rap1/GTP -0.009 0.06 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.018 -10000 0 -0.28 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.016 0.1 -10000 0 -10000 0 0
CEBPB 0.02 0.11 0.32 2 -0.53 4 6
STAT3 0.027 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.005 0.15 -10000 0 -0.7 8 8
STAT1 -0.01 0.092 -10000 0 -0.34 10 10
CALM1 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.061 0.17 -10000 0 -0.39 101 101
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.004 0.095 -10000 0 -0.32 10 10
CEBPB/PTGES2/Cbp/p300 0.014 0.069 -10000 0 -0.34 2 2
mol:Ca2+ 0.013 0.088 -10000 0 -10000 0 0
MAPK3 0.002 0.12 -10000 0 -0.65 10 10
STAT1 (dimer) -0.034 0.095 -10000 0 -0.36 5 5
MAPK1 0.005 0.1 -10000 0 -0.58 7 7
JAK2 0.015 0.023 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
JAK1 0.019 0.023 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 0.022 0.096 0.29 5 -0.58 4 9
SMAD7 0.004 0.062 0.17 20 -10000 0 20
CBL/CRKL/C3G 0.015 0.086 0.27 1 -10000 0 1
PI3K 0.007 0.077 -10000 0 -10000 0 0
IFNG -0.061 0.17 -10000 0 -0.39 101 101
apoptosis 0.019 0.084 0.26 4 -0.44 5 9
CAMK2G 0.027 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.003 -10000 0 -10000 0 0
CAMK2A -0.085 0.2 -10000 0 -0.45 114 114
CAMK2B -0.093 0.21 -10000 0 -0.45 123 123
FRAP1 0.028 0.1 0.28 21 -10000 0 21
PRKCD 0.034 0.11 0.31 15 -10000 0 15
RAP1B 0.026 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.03 0.069 -10000 0 -0.24 9 9
PTPN2 0.025 0.007 -10000 0 -10000 0 0
EP300 0.025 0.031 -10000 0 -0.45 2 2
IRF1 -0.009 0.092 0.28 7 -0.38 1 8
STAT1 (dimer)/PIASy 0.004 0.095 0.23 3 -0.33 9 12
SOCS1 -0.013 0.16 -10000 0 -1 8 8
mol:GDP 0.012 0.082 0.25 1 -10000 0 1
CASP1 0.005 0.063 0.18 19 -0.3 1 20
PTGES2 0.027 0.004 -10000 0 -10000 0 0
IRF9 0.025 0.047 0.16 12 -10000 0 12
mol:PI-3-4-5-P3 0 0.069 -10000 0 -10000 0 0
RAP1/GDP 0.007 0.072 -10000 0 -10000 0 0
CBL -0.003 0.081 0.27 1 -10000 0 1
MAP3K1 -0.004 0.083 0.27 1 -10000 0 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.027 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.03 0.069 -10000 0 -0.24 9 9
PTPN11 -0.002 0.088 0.28 1 -10000 0 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.01 0.054 0.89 1 -10000 0 1
VDR 0.025 0.031 -10000 0 -0.45 2 2
FAM120B 0.027 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.007 0.089 -10000 0 -0.35 5 5
RXRs/LXRs/DNA/Oxysterols 0.015 0.093 -10000 0 -0.38 4 4
MED1 0.027 0.003 -10000 0 -10000 0 0
mol:9cRA 0.003 0.008 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.009 0.091 -10000 0 -0.22 63 63
RXRs/NUR77 0.026 0.11 -10000 0 -0.28 3 3
RXRs/PPAR -0.08 0.13 -10000 0 -0.34 30 30
NCOR2 0.027 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.022 -10000 0 -0.32 2 2
RARs/VDR/DNA/Vit D3 0.033 0.082 -10000 0 -0.24 36 36
RARA 0.027 0.004 -10000 0 -10000 0 0
NCOA1 0.027 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.031 -10000 0 -0.45 2 2
RARs/RARs/DNA/9cRA 0.022 0.074 -10000 0 -0.23 36 36
RARG 0.026 0.022 -10000 0 -0.45 1 1
RPS6KB1 0.016 0.039 0.54 2 -10000 0 2
RARs/THRs/DNA/SMRT -0.01 0.093 -10000 0 -0.23 63 63
THRA 0.027 0.003 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.022 -10000 0 -0.32 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.021 0.099 -10000 0 -0.3 2 2
NR1H4 -0.005 0.028 -10000 0 -0.4 1 1
RXRs/LXRs/DNA 0.042 0.11 -10000 0 -0.34 3 3
NR1H2 0.028 0.015 -10000 0 -10000 0 0
NR1H3 0.023 0.049 -10000 0 -0.39 6 6
RXRs/VDR/DNA/Vit D3 0.028 0.097 -10000 0 -0.27 2 2
NR4A1 0.018 0.064 -10000 0 -0.45 9 9
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.003 0.071 -10000 0 -0.25 6 6
RXRG -0.03 0.15 -10000 0 -0.44 59 59
RXR alpha/CCPG 0.04 0.013 -10000 0 -10000 0 0
RXRA 0.028 0.015 -10000 0 -10000 0 0
RXRB 0.028 0.016 -10000 0 -10000 0 0
THRB -0.004 0.11 -10000 0 -0.45 29 29
PPARG -0.14 0.22 -10000 0 -0.45 165 165
PPARD 0.026 0.006 -10000 0 -10000 0 0
TNF 0.004 0.12 -10000 0 -0.73 5 5
mol:Oxysterols 0.003 0.007 -10000 0 -10000 0 0
cholesterol transport 0.015 0.092 -10000 0 -0.38 4 4
PPARA 0.026 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.01 0.12 -10000 0 -0.45 35 35
RXRs/NUR77/BCL2 -0.01 0.088 -10000 0 -0.35 8 8
SREBF1 0.012 0.085 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.021 0.099 -10000 0 -0.3 2 2
ABCA1 0.007 0.1 -10000 0 -1 2 2
RARs/THRs 0.028 0.11 -10000 0 -0.24 61 61
RXRs/FXR 0.027 0.1 -10000 0 -0.29 2 2
BCL2 0.021 0.04 -10000 0 -0.41 4 4
FAS signaling pathway (CD95)

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
SPTAN1 0.001 0.034 0.21 10 -10000 0 10
RFC1 -0.001 0.024 0.2 4 -0.19 1 5
PRKDC 0.018 0.067 0.22 45 -0.19 1 46
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 0.011 0.085 -10000 0 -0.55 9 9
FASLG/FAS/FADD/FAF1 -0.001 0.059 0.22 8 -0.25 12 20
MAP2K4 0.026 0.12 0.3 7 -0.43 11 18
mol:ceramide 0.008 0.085 -10000 0 -0.33 11 11
GSN 0.001 0.035 0.21 10 -10000 0 10
FASLG/FAS/FADD/FAF1/Caspase 8 0.016 0.082 0.25 2 -0.32 8 10
FAS 0.022 0.026 -10000 0 -0.45 1 1
BID -0.015 0.024 0.26 1 -0.24 2 3
MAP3K1 0.042 0.1 0.32 6 -0.39 7 13
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
RB1 -0.002 0.02 0.18 2 -10000 0 2
CFLAR 0.027 0.006 -10000 0 -10000 0 0
HGF/MET 0.027 0.084 -10000 0 -0.27 35 35
ARHGDIB 0.004 0.041 0.22 14 -10000 0 14
FADD 0.017 0.016 -10000 0 -10000 0 0
actin filament polymerization 0.003 0.044 -10000 0 -0.21 10 10
NFKB1 0.005 0.094 -10000 0 -0.52 8 8
MAPK8 0.011 0.16 0.29 7 -0.46 34 41
DFFA -0.002 0.021 0.2 1 -10000 0 1
DNA fragmentation during apoptosis -0.006 0.04 0.2 4 -0.31 2 6
FAS/FADD/MET 0.03 0.042 -10000 0 -0.26 5 5
CFLAR/RIP1 0.038 0.012 -10000 0 -10000 0 0
FAIM3 0.02 0.055 -10000 0 -0.4 8 8
FAF1 0.023 0.017 -10000 0 -10000 0 0
PARP1 -0.001 0.025 0.2 4 -10000 0 4
DFFB -0.003 0.032 0.2 4 -0.27 3 7
CHUK 0.003 0.084 -10000 0 -0.52 6 6
FASLG -0.017 0.13 -10000 0 -0.42 45 45
FAS/FADD 0.023 0.029 -10000 0 -0.32 1 1
HGF 0.007 0.092 -10000 0 -0.44 20 20
LMNA -0.006 0.031 0.19 2 -10000 0 2
CASP6 -0.002 0.021 0.18 2 -0.19 1 3
CASP10 0.023 0.014 -10000 0 -10000 0 0
CASP3 0 0.023 0.19 5 -0.18 1 6
PTPN13 0.016 0.068 -10000 0 -0.45 10 10
CASP8 -0.015 0.029 0.2 8 -10000 0 8
IL6 -0.06 0.34 -10000 0 -1.1 41 41
MET 0.021 0.049 -10000 0 -0.42 6 6
ICAD/CAD -0.003 0.029 0.19 2 -0.29 2 4
FASLG/FAS/FADD/FAF1/Caspase 10 0.008 0.085 -10000 0 -0.33 11 11
activation of caspase activity by cytochrome c -0.015 0.024 0.26 1 -0.24 2 3
PAK2 0.04 0.093 0.22 97 -0.19 3 100
BCL2 0.021 0.04 -10000 0 -0.41 4 4
IL6-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
BCL2L1 -0.013 0.15 -10000 0 -10000 0 0
CRP -0.031 0.16 0.49 2 -0.66 1 3
cell cycle arrest -0.032 0.16 -10000 0 -0.58 2 2
TIMP1 -0.014 0.16 -10000 0 -0.55 10 10
IL6ST -0.029 0.15 -10000 0 -0.45 57 57
Rac1/GDP -0.023 0.12 -10000 0 -0.45 15 15
AP1 0.009 0.14 -10000 0 -0.51 8 8
GAB2 0.022 0.038 -10000 0 -0.45 3 3
TNFSF11 -0.055 0.18 -10000 0 -0.63 1 1
HSP90B1 0.023 0.093 -10000 0 -0.69 5 5
GAB1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.028 0.12 -10000 0 -0.45 16 16
AKT1 0.048 0.063 0.3 8 -0.57 1 9
FOXO1 0.045 0.059 0.3 5 -0.55 1 6
MAP2K6 -0.035 0.12 -10000 0 -0.45 19 19
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.023 0.12 -10000 0 -0.45 13 13
MITF -0.031 0.12 -10000 0 -0.41 23 23
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.019 -10000 0 -0.4 1 1
A2M 0.017 0.1 -10000 0 -1.1 4 4
CEBPB 0.028 0.014 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.006 0.11 -10000 0 -0.47 13 13
STAT3 -0.037 0.16 -10000 0 -0.61 2 2
STAT1 0.006 0.076 -10000 0 -0.74 4 4
CEBPD -0.009 0.16 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.027 0.03 -10000 0 -0.32 2 2
JUN 0.027 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.019 0.12 -10000 0 -0.41 20 20
MAPK11 -0.028 0.12 -10000 0 -0.46 17 17
STAT3 (dimer)/FOXO1 0.012 0.15 0.39 2 -10000 0 2
GRB2/SOS1/GAB family 0.017 0.12 -10000 0 -0.41 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.02 0.12 -10000 0 -0.36 27 27
GRB2 0.027 0.004 -10000 0 -10000 0 0
JAK2 0.024 0.01 -10000 0 -10000 0 0
LBP -0.11 0.33 -10000 0 -0.87 68 68
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
JAK1 0.028 0.006 -10000 0 -10000 0 0
MYC 0.006 0.16 0.49 2 -10000 0 2
FGG -0.042 0.16 -10000 0 -0.63 1 1
macrophage differentiation -0.032 0.16 -10000 0 -0.58 2 2
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.01 0.13 -10000 0 -0.32 30 30
JUNB -0.024 0.14 -10000 0 -10000 0 0
FOS -0.033 0.16 -10000 0 -0.45 60 60
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.025 0.12 -10000 0 -0.4 23 23
STAT1/PIAS1 -0.014 0.12 -10000 0 -0.41 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.044 0.057 -10000 0 -0.48 2 2
STAT3 (dimer) -0.035 0.16 -10000 0 -0.6 2 2
PRKCD -0.015 0.14 0.35 8 -0.47 7 15
IL6R 0.021 0.057 -10000 0 -0.45 7 7
SOCS3 -0.022 0.13 -10000 0 -0.76 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.017 0.1 -10000 0 -0.27 56 56
Rac1/GTP -0.023 0.12 -10000 0 -0.45 15 15
HCK 0.023 0.03 -10000 0 -0.42 2 2
MAPKKK cascade 0.023 0.11 -10000 0 -0.5 10 10
bone resorption -0.051 0.18 -10000 0 -0.6 1 1
IRF1 -0.025 0.15 -10000 0 -10000 0 0
mol:GDP -0.031 0.12 -10000 0 -0.41 22 22
SOS1 0.027 0.004 -10000 0 -10000 0 0
VAV1 -0.032 0.12 -10000 0 -0.42 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.019 0.13 -10000 0 -0.5 18 18
PTPN11 0.016 0.049 -10000 0 -0.7 2 2
IL6/IL6RA 0.006 0.11 -10000 0 -0.32 47 47
gp130 (dimer)/TYK2/TYK2/LMO4 0.015 0.11 -10000 0 -0.27 57 57
gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.1 -10000 0 -0.27 52 52
IL6 -0.013 0.13 -10000 0 -0.44 42 42
PIAS3 0.026 0.006 -10000 0 -10000 0 0
PTPRE 0.024 0.012 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.027 0.12 -10000 0 -0.32 42 42
LMO4 0.028 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.027 0.16 -10000 0 -0.6 2 2
MCL1 0.05 0.071 0.54 2 -0.51 1 3
Signaling events mediated by PRL

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
CCNE1 0.024 0.033 -10000 0 -0.4 3 3
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 -0.035 0.15 -10000 0 -0.4 71 71
CDKN1A 0.012 0.048 -10000 0 -0.3 9 9
PRL-3/alpha Tubulin 0.029 0.038 -10000 0 -0.28 6 6
mol:Ca2+ -0.061 0.12 0.18 4 -0.33 75 79
AGT -0.066 0.19 -10000 0 -0.45 96 96
CCNA2 -0.006 0.045 -10000 0 -0.41 1 1
TUBA1B 0.027 0.003 -10000 0 -10000 0 0
EGR1 0.002 0.066 -10000 0 -0.31 21 21
CDK2/Cyclin E1 0.039 0.079 0.27 1 -0.36 4 5
MAPK3 0.008 0.032 -10000 0 -0.28 6 6
PRL-2 /Rab GGTase beta 0.039 0.007 -10000 0 -10000 0 0
MAPK1 0.008 0.032 -10000 0 -0.28 6 6
PTP4A1 -0.003 0.047 -10000 0 -10000 0 0
PTP4A3 0.017 0.047 -10000 0 -0.4 6 6
PTP4A2 0.027 0.004 -10000 0 -10000 0 0
ITGB1 0.009 0.03 -10000 0 -0.28 5 5
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1 0.013 0.027 -10000 0 -0.3 1 1
Rab GGTase beta/Rab GGTase alpha 0.038 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 0.02 0.07 -10000 0 -10000 0 0
RABGGTA 0.026 0.006 -10000 0 -10000 0 0
BCAR1 -0.013 0.023 0.18 6 -10000 0 6
RHOC 0.011 0.037 -10000 0 -0.3 4 4
RHOA 0 0.068 -10000 0 -0.3 21 21
cell motility 0.022 0.069 0.31 2 -0.31 3 5
PRL-1/alpha Tubulin 0.023 0.065 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.013 0.11 -10000 0 -0.28 70 70
ROCK1 0.024 0.058 -10000 0 -0.29 3 3
RABGGTB 0.027 0.004 -10000 0 -10000 0 0
CDK2 0.027 0.003 -10000 0 -10000 0 0
mitosis -0.003 0.047 -10000 0 -10000 0 0
ATF5 0.018 0.06 -10000 0 -0.4 10 10
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 0.025 0.033 -10000 0 -0.4 3 3
ANTXR2 0.017 0.063 -10000 0 -0.4 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.048 13 13
monocyte activation -0.017 0.1 -10000 0 -0.37 33 33
MAP2K2 0.002 0.089 -10000 0 -0.56 12 12
MAP2K1 -0.003 0.007 -10000 0 -10000 0 0
MAP2K7 -0.003 0.007 -10000 0 -10000 0 0
MAP2K6 -0.014 0.05 -10000 0 -0.23 24 24
CYAA -0.008 0.031 -10000 0 -0.2 13 13
MAP2K4 -0.003 0.007 -10000 0 -10000 0 0
IL1B -0.02 0.064 0.18 5 -0.19 53 58
Channel 0.028 0.04 -10000 0 -0.21 13 13
NLRP1 -0.003 0.011 -10000 0 -0.2 1 1
CALM1 0.026 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.074 -10000 0 -0.38 18 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.048 13 -10000 0 13
MAPK3 -0.003 0.007 -10000 0 -10000 0 0
MAPK1 -0.003 0.01 0.15 1 -10000 0 1
PGR -0.025 0.067 0.15 1 -0.22 49 50
PA/Cellular Receptors 0.029 0.044 -10000 0 -0.23 13 13
apoptosis -0.002 0.008 -10000 0 -0.048 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.027 0.035 -10000 0 -0.18 13 13
macrophage activation -0.004 0.009 0.14 1 -10000 0 1
TNF 0.007 0.088 -10000 0 -0.4 22 22
VCAM1 -0.015 0.1 -10000 0 -0.37 31 31
platelet activation -0.003 0.074 -10000 0 -0.38 18 18
MAPKKK cascade 0.003 0.021 0.11 1 -0.092 3 4
IL18 -0.005 0.038 0.15 3 -0.23 11 14
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.048 13 13
LEF -0.002 0.008 -10000 0 -0.048 13 13
CASP1 0 0.009 -10000 0 -0.089 2 2
mol:cAMP -0.003 0.075 -10000 0 -0.38 18 18
necrosis -0.002 0.008 -10000 0 -0.048 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.037 -10000 0 -0.2 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.049 0.16 -10000 0 -0.4 88 88
alphaV beta3 Integrin 0.024 0.068 -10000 0 -0.3 21 21
PTK2 0.008 0.086 -10000 0 -0.42 8 8
positive regulation of JNK cascade 0.009 0.091 -10000 0 -0.32 19 19
CDC42/GDP 0.042 0.12 0.32 3 -0.4 16 19
Rac1/GDP 0.038 0.12 0.3 2 -0.39 16 18
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
CDC42/GTP 0.025 0.12 -10000 0 -0.39 19 19
nectin-3/I-afadin 0.023 0.065 -10000 0 -0.31 17 17
RAPGEF1 0.026 0.11 0.32 5 -0.45 9 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0.11 -10000 0 -0.48 12 12
PDGFB-D/PDGFRB -0.049 0.16 -10000 0 -0.4 88 88
TLN1 0.001 0.03 0.17 2 -0.3 1 3
Rap1/GTP 0.013 0.074 -10000 0 -0.33 9 9
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.016 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.023 0.065 -10000 0 -0.31 17 17
PVR 0.027 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0.03 0.14 0.33 4 -0.48 18 22
MLLT4 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
PI3K 0.005 0.1 -10000 0 -0.36 3 3
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.034 0.031 -10000 0 -0.32 3 3
positive regulation of lamellipodium assembly 0.016 0.081 -10000 0 -0.31 13 13
PVRL1 0.022 0.038 -10000 0 -0.45 3 3
PVRL3 0.008 0.085 -10000 0 -0.44 17 17
PVRL2 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
CDH1 0.021 0.048 -10000 0 -0.45 5 5
CLDN1 0.004 0.085 -10000 0 -0.44 17 17
JAM-A/CLDN1 0.029 0.077 -10000 0 -0.25 28 28
SRC 0.002 0.12 -10000 0 -0.51 14 14
ITGB3 0.01 0.086 -10000 0 -0.42 19 19
nectin-1(dimer)/I-afadin/I-afadin 0.034 0.031 -10000 0 -0.32 3 3
FARP2 0.018 0.16 -10000 0 -0.54 21 21
RAC1 0.026 0.007 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.035 0.06 -10000 0 -0.26 17 17
nectin-1/I-afadin 0.034 0.031 -10000 0 -0.32 3 3
nectin-2/I-afadin 0.038 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.034 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.031 0.065 -10000 0 -0.26 20 20
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.008 -10000 0 -10000 0 0
F11R 0.026 0.022 -10000 0 -0.45 1 1
positive regulation of filopodium formation 0.009 0.091 -10000 0 -0.32 19 19
alphaV/beta3 Integrin/Talin 0.046 0.087 0.26 15 -0.33 5 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.01 -10000 0 -10000 0 0
PIP5K1C 0.002 0.035 -10000 0 -0.34 2 2
VAV2 0.033 0.12 0.3 1 -0.48 12 13
RAP1/GDP 0.042 0.11 0.3 5 -0.37 13 18
ITGAV 0.024 0.027 -10000 0 -0.4 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.035 0.06 -10000 0 -0.26 17 17
nectin-3(dimer)/I-afadin/I-afadin 0.023 0.065 -10000 0 -0.31 17 17
Rac1/GTP 0.03 0.1 -10000 0 -0.37 13 13
PTPRM 0.006 0.039 -10000 0 -0.21 12 12
E-cadherin/beta catenin/alpha catenin 0.061 0.051 -10000 0 -0.43 2 2
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.021 0.03 -10000 0 -0.25 5 5
epithelial cell differentiation 0.047 0.033 -10000 0 -0.23 4 4
CYFIP2 0.024 0.029 -10000 0 -0.42 2 2
ENAH 0.02 0.071 0.23 11 -0.45 1 12
EGFR 0.019 0.049 -10000 0 -0.45 5 5
EPHA2 0.019 0.057 -10000 0 -0.45 7 7
MYO6 0.017 0.037 0.21 2 -10000 0 2
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.026 -10000 0 -0.26 2 2
AQP5 -0.28 0.22 -10000 0 -0.45 274 274
CTNND1 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.036 0.21 2 -10000 0 2
regulation of calcium-dependent cell-cell adhesion 0.001 0.062 -10000 0 -10000 0 0
EGF -0.06 0.18 -10000 0 -0.45 88 88
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.086 0.19 -10000 0 -0.42 113 113
cortical microtubule organization 0.047 0.033 -10000 0 -0.23 4 4
GO:0000145 -0.001 0.036 0.2 3 -10000 0 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.052 0.035 -10000 0 -0.23 4 4
MLLT4 0.027 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.012 0.028 -10000 0 -0.39 1 1
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.051 0.043 -10000 0 -0.25 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.008 0.029 0.21 1 -10000 0 1
PVRL2 0.027 0.005 -10000 0 -10000 0 0
ZYX 0.017 0.035 0.21 2 -10000 0 2
ARF6/GTP 0.055 0.045 -10000 0 -10000 0 0
CDH1 0.021 0.048 -10000 0 -0.45 5 5
EGFR/EGFR/EGF/EGF -0.007 0.1 -10000 0 -0.38 5 5
RhoA/GDP 0.049 0.033 -10000 0 -10000 0 0
actin cytoskeleton organization 0.01 0.035 0.2 2 -10000 0 2
IGF-1R heterotetramer 0.026 0.005 -10000 0 -10000 0 0
GIT1 0.027 0.002 -10000 0 -10000 0 0
IGF1R 0.026 0.005 -10000 0 -10000 0 0
IGF1 -0.054 0.18 -10000 0 -0.45 84 84
DIAPH1 0.02 0.11 -10000 0 -0.55 1 1
Wnt receptor signaling pathway -0.047 0.033 0.23 4 -10000 0 4
RHOA 0.024 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.012 0.028 -10000 0 -0.39 1 1
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL -0.002 0.037 0.2 2 -10000 0 2
EFNA1 0.027 0.004 -10000 0 -10000 0 0
LPP -0.002 0.03 0.2 2 -10000 0 2
Ephrin A1/EPHA2 0.038 0.045 -10000 0 -0.42 1 1
SEC6/SEC8 0.01 0.02 -10000 0 -10000 0 0
MGAT3 0.001 0.063 -10000 0 -10000 0 0
HGF/MET 0.029 0.064 -10000 0 -0.37 2 2
HGF 0.007 0.092 -10000 0 -0.44 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.021 0.03 -10000 0 -0.25 5 5
actin cable formation 0.059 0.095 0.23 80 -0.32 1 81
KIAA1543 -0.014 0.064 0.2 3 -0.37 4 7
KIFC3 0.015 0.03 -10000 0 -10000 0 0
NCK1 0.023 0.011 -10000 0 -10000 0 0
EXOC3 0.024 0.009 -10000 0 -10000 0 0
ACTN1 0.017 0.035 0.21 2 -10000 0 2
NCK1/GIT1 0.033 0.016 -10000 0 -10000 0 0
mol:GDP 0.047 0.033 -10000 0 -0.23 4 4
EXOC4 0.026 0.007 -10000 0 -10000 0 0
STX4 0.018 0.036 0.21 2 -10000 0 2
PIP5K1C 0.018 0.036 0.21 2 -10000 0 2
LIMA1 0.027 0.003 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
ROCK1 0.026 0.078 0.27 10 -0.34 1 11
adherens junction assembly -0.009 0.096 0.28 6 -0.5 8 14
IGF-1R heterotetramer/IGF1 0.001 0.098 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.01 -10000 0 -10000 0 0
MET 0.021 0.049 -10000 0 -0.42 6 6
PLEKHA7 0.003 0.07 0.21 2 -0.38 4 6
mol:GTP 0.049 0.042 -10000 0 -0.25 5 5
establishment of epithelial cell apical/basal polarity 0.026 0.083 0.33 12 -10000 0 12
cortical actin cytoskeleton stabilization 0.021 0.03 -10000 0 -0.25 5 5
regulation of cell-cell adhesion 0.01 0.035 0.2 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.021 0.03 -10000 0 -0.25 5 5
S1P3 pathway

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
PDGFRB -0.049 0.16 -9999 0 -0.4 88 88
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.006 0.062 -9999 0 -0.26 14 14
GNAO1 0.023 0.041 -9999 0 -0.42 4 4
S1P/S1P3/G12/G13 0.045 0.035 -9999 0 -0.24 5 5
AKT1 -0.008 0.11 -9999 0 -0.48 19 19
AKT3 0.019 0.09 -9999 0 -0.59 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.049 0.16 -9999 0 -0.4 88 88
GNAI2 0.025 0.011 -9999 0 -10000 0 0
GNAI3 0.027 0.007 -9999 0 -10000 0 0
GNAI1 0.026 0.023 -9999 0 -0.45 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.022 0.048 -9999 0 -0.44 5 5
S1PR2 0.027 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.066 -9999 0 -0.34 9 9
MAPK3 0.016 0.06 -9999 0 -0.38 5 5
MAPK1 0.013 0.061 -9999 0 -0.38 5 5
JAK2 0.016 0.082 -9999 0 -0.43 8 8
CXCR4 0.009 0.078 -9999 0 -0.36 10 10
FLT1 0.026 0.021 -9999 0 -0.39 1 1
RhoA/GDP 0.018 0.007 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.005 -9999 0 -10000 0 0
SRC 0.015 0.061 -9999 0 -0.32 9 9
S1P/S1P3/Gi 0.021 0.067 -9999 0 -0.34 9 9
RAC1 0.026 0.007 -9999 0 -10000 0 0
RhoA/GTP 0.026 0.071 -9999 0 -0.36 5 5
VEGFA 0.023 0.043 -9999 0 -0.39 5 5
S1P/S1P2/Gi 0.023 0.051 -9999 0 -0.29 5 5
VEGFR1 homodimer/VEGFA homodimer 0.037 0.039 -9999 0 -0.28 6 6
RHOA 0.024 0.009 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.015 0.1 -9999 0 -0.24 77 77
GNAQ 0.027 0.004 -9999 0 -10000 0 0
GNAZ 0.01 0.083 -9999 0 -0.42 18 18
G12/G13 0.037 0.012 -9999 0 -10000 0 0
GNA14 -0.044 0.17 -9999 0 -0.45 72 72
GNA15 0.025 0.031 -9999 0 -0.45 2 2
GNA12 0.025 0.007 -9999 0 -10000 0 0
GNA13 0.027 0.003 -9999 0 -10000 0 0
GNA11 0.024 0.038 -9999 0 -0.45 3 3
Rac1/GTP 0.021 0.073 -9999 0 -0.35 6 6
Rapid glucocorticoid signaling

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.01 0.088 -10000 0 -0.23 55 55
MAPK9 0.007 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.009 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.016 -10000 0 -0.23 1 1
GNB1 0.026 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.002 -10000 0 -10000 0 0
Gs family/GTP -0.014 0.084 -10000 0 -0.24 57 57
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 0.008 0.021 0.067 57 -10000 0 57
GNAL -0.03 0.15 -10000 0 -0.45 57 57
GNG2 0.025 0.02 -10000 0 -0.4 1 1
CRH -0.014 0.011 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.034 -10000 0 -0.3 6 6
MAPK11 0.008 0.001 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.016 0.086 -10000 0 -0.32 29 29
ATM 0.025 0.008 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.024 0.009 -10000 0 -10000 0 0
ATR 0.022 0.011 -10000 0 -10000 0 0
UBE2L3 0.026 0.006 -10000 0 -10000 0 0
FANCD2 0.016 0.011 -10000 0 -10000 0 0
protein ubiquitination 0.043 0.076 -10000 0 -0.41 1 1
XRCC5 0.026 0.005 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.043 0.024 -10000 0 -10000 0 0
MRE11A 0.025 0.008 -10000 0 -10000 0 0
DNA-PK 0.047 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.013 0.094 -10000 0 -0.53 8 8
FANCF 0.023 0.043 -10000 0 -0.45 4 4
BRCA1 0.027 0.003 -10000 0 -10000 0 0
CCNE1 0.024 0.033 -10000 0 -0.4 3 3
CDK2/Cyclin E1 0.037 0.026 -10000 0 -0.28 3 3
FANCG 0.024 0.009 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.016 0.087 -10000 0 -0.32 30 30
FANCE 0.026 0.006 -10000 0 -10000 0 0
FANCC 0.026 0.005 -10000 0 -10000 0 0
NBN 0.024 0.009 -10000 0 -10000 0 0
FANCA 0.024 0.027 -10000 0 -0.4 2 2
DNA repair 0.013 0.083 0.28 6 -0.38 4 10
BRCA1/BARD1/ubiquitin 0.016 0.087 -10000 0 -0.32 30 30
BARD1/DNA-PK 0.044 0.07 -10000 0 -0.25 22 22
FANCL 0.026 0.019 -10000 0 -0.4 1 1
mRNA polyadenylation -0.016 0.086 0.32 29 -10000 0 29
BRCA1/BARD1/CTIP/M/R/N Complex 0.01 0.073 -10000 0 -0.27 5 5
BRCA1/BACH1/BARD1/TopBP1 0.028 0.074 -10000 0 -0.27 25 25
BRCA1/BARD1/P53 0.034 0.075 -10000 0 -0.25 27 27
BARD1/CSTF1/BRCA1 0.031 0.078 -10000 0 -0.28 29 29
BRCA1/BACH1 0.027 0.003 -10000 0 -10000 0 0
BARD1 -0.003 0.12 -10000 0 -0.45 30 30
PCNA 0.026 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.032 0.079 -10000 0 -0.28 30 30
BRCA1/BARD1/UbcH7 0.031 0.078 -10000 0 -0.28 29 29
BRCA1/BARD1/RAD51/PCNA 0.043 0.077 -10000 0 -0.25 29 29
BARD1/DNA-PK/P53 0.05 0.073 -10000 0 -0.24 23 23
BRCA1/BARD1/Ubiquitin 0.016 0.087 -10000 0 -0.32 30 30
BRCA1/BARD1/CTIP 0.021 0.07 -10000 0 -0.25 29 29
FA complex 0.036 0.039 -10000 0 -10000 0 0
BARD1/EWS 0.016 0.086 -10000 0 -0.32 29 29
RBBP8 0.013 0.005 -10000 0 -10000 0 0
TP53 0.022 0.043 -10000 0 -0.45 4 4
TOPBP1 0.023 0.01 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.033 0.074 0.25 27 -10000 0 27
BRCA1/BARD1 0.048 0.079 -10000 0 -0.42 1 1
CSTF1 0.026 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.001 0.082 -10000 0 -0.32 30 30
CDK2 0.027 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.019 -10000 0 -0.4 1 1
RAD50 0.026 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.016 0.087 -10000 0 -0.32 30 30
EWSR1 0.027 0.005 -10000 0 -10000 0 0
ceramide signaling pathway

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.014 0.095 0.27 4 -0.47 8 12
BAG4 0.023 0.023 -10000 0 -0.45 1 1
BAD 0.017 0.048 0.17 20 -0.18 3 23
NFKBIA 0.026 0.006 -10000 0 -10000 0 0
BIRC3 0.012 0.071 -10000 0 -0.4 14 14
BAX 0.014 0.041 0.17 8 -0.19 2 10
EnzymeConsortium:3.1.4.12 0.007 0.026 0.069 12 -0.094 10 22
IKBKB 0.024 0.094 0.29 10 -0.48 6 16
MAP2K2 0.015 0.041 0.18 9 -10000 0 9
MAP2K1 0.015 0.042 0.18 8 -10000 0 8
SMPD1 0.009 0.034 0.12 6 -0.14 7 13
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.064 0.12 0.27 43 -0.45 6 49
MAP2K4 0.014 0.04 0.19 6 -0.19 1 7
protein ubiquitination 0.022 0.098 0.28 8 -0.47 7 15
EnzymeConsortium:2.7.1.37 0.015 0.046 0.18 8 -10000 0 8
response to UV 0 0 0.002 9 -10000 0 9
RAF1 0.014 0.04 0.19 7 -10000 0 7
CRADD 0.027 0.002 -10000 0 -10000 0 0
mol:ceramide 0.014 0.041 0.11 15 -0.15 8 23
I-kappa-B-alpha/RELA/p50/ubiquitin 0.033 0.012 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.013 0.039 0.18 4 -0.21 1 5
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.026 0.006 -10000 0 -10000 0 0
MAPK3 0.017 0.046 0.18 7 -0.22 1 8
MAPK1 0.017 0.043 0.18 7 -10000 0 7
p50/RELA/I-kappa-B-alpha 0.036 0.013 -10000 0 -10000 0 0
FADD 0.055 0.12 0.26 31 -0.45 7 38
KSR1 0.013 0.043 0.17 8 -0.19 2 10
MAPK8 0.011 0.045 0.18 9 -0.23 1 10
TRAF2 0.021 0.047 -10000 0 -0.4 6 6
response to radiation 0 0 0.002 2 -10000 0 2
CHUK 0.016 0.092 0.27 5 -0.48 6 11
TNF R/SODD 0.033 0.022 -10000 0 -0.32 1 1
TNF 0.007 0.088 -10000 0 -0.4 22 22
CYCS 0.023 0.051 0.14 35 -0.16 1 36
IKBKG 0.023 0.1 0.31 10 -0.48 6 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.017 0.094 -10000 0 -0.49 8 8
RELA 0.026 0.006 -10000 0 -10000 0 0
RIPK1 0.026 0.006 -10000 0 -10000 0 0
AIFM1 0.02 0.048 0.14 26 -10000 0 26
TNF/TNF R/SODD 0.032 0.061 -10000 0 -0.24 20 20
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.022 0.086 -10000 0 -0.54 10 10
NSMAF 0.027 0.1 0.27 15 -0.45 8 23
response to hydrogen peroxide 0 0 0.002 9 -10000 0 9
BCL2 0.021 0.04 -10000 0 -0.41 4 4
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.004 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.025 0.031 -10000 0 -0.45 2 2
Cbp/p300/PCAF 0.035 0.068 -10000 0 -0.28 19 19
EP300 0.025 0.031 -10000 0 -0.45 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.085 -10000 0 -0.39 13 13
KAT2B 0.007 0.09 -10000 0 -0.45 18 18
MAPK14 0.026 0.006 -10000 0 -10000 0 0
AKT1 -0.013 0.092 0.19 4 -0.33 12 16
RAR alpha/9cRA/Cyclin H 0.034 0.06 -10000 0 -0.38 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.015 0.11 -10000 0 -0.36 27 27
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.012 0.059 -10000 0 -0.37 6 6
NCOR2 0.027 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.022 -10000 0 -0.32 2 2
RXRs/RARs/NRIP1/9cRA -0.015 0.12 0.28 1 -0.68 5 6
NCOA2 -0.007 0.12 -10000 0 -0.45 32 32
NCOA3 0.026 0.006 -10000 0 -10000 0 0
NCOA1 0.027 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.031 -10000 0 -0.45 2 2
RARG 0.027 0.022 -10000 0 -0.45 1 1
RAR gamma1/9cRA 0.036 0.015 -10000 0 -0.27 1 1
MAPK3 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.022 0.053 -10000 0 -0.45 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.012 0.085 -10000 0 -0.5 4 4
RARA 0.005 0.044 -10000 0 -0.22 6 6
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.029 0.14 -10000 0 -0.42 38 38
PRKCA 0.027 0.03 -10000 0 -0.43 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.025 0.13 -10000 0 -0.6 9 9
RXRG -0.033 0.12 -10000 0 -0.33 52 52
RXRA 0.007 0.046 -10000 0 -0.3 1 1
RXRB 0.002 0.061 -10000 0 -0.33 4 4
VDR/Vit D3/DNA 0.019 0.022 -10000 0 -0.32 2 2
RBP1 -0.053 0.16 -10000 0 -0.4 88 88
CRBP1/9-cic-RA -0.037 0.11 -10000 0 -0.28 88 88
RARB -0.008 0.12 -10000 0 -0.45 35 35
PRKCG -0.02 0.13 -10000 0 -0.39 54 54
MNAT1 0.026 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs -0.012 0.11 0.31 1 -0.55 5 6
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.007 0.1 -10000 0 -0.52 5 5
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.12 0.22 1 -0.38 33 34
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.026 0.13 -10000 0 -0.6 9 9
positive regulation of DNA binding 0.026 0.054 -10000 0 -0.36 1 1
NRIP1 -0.029 0.15 -10000 0 -0.92 5 5
RXRs/RARs -0.031 0.14 -10000 0 -0.52 17 17
RXRs/RXRs/DNA/9cRA -0.004 0.074 -10000 0 -0.46 4 4
PRKACA 0.027 0.003 -10000 0 -10000 0 0
CDK7 0.026 0.006 -10000 0 -10000 0 0
TFIIH 0.05 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.041 0.052 -10000 0 -10000 0 0
CCNH 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.046 0.024 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.02 0.014 -10000 0 -10000 0 0
TRAF2/ASK1 0.031 0.03 -10000 0 -0.23 6 6
ATM 0.025 0.008 -10000 0 -10000 0 0
MAP2K3 -0.017 0.11 0.42 2 -0.35 22 24
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.017 0.11 0.31 3 -0.37 17 20
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.02 0.054 -10000 0 -0.43 7 7
TXN 0.008 0.001 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
GADD45A 0.026 0.019 -10000 0 -0.4 1 1
GADD45B 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.006 -10000 0 -10000 0 0
MAP3K6 0.026 0.022 -10000 0 -0.45 1 1
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.019 -10000 0 -0.32 1 1
TAK1/TAB family -0.005 0.017 -10000 0 -0.13 7 7
RAC1/OSM/MEKK3 0.045 0.032 -10000 0 -0.21 6 6
TRAF2 0.021 0.047 -10000 0 -0.4 6 6
RAC1/OSM/MEKK3/MKK3 -0.004 0.089 -10000 0 -0.32 9 9
TRAF6 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.094 0.21 -10000 0 -0.45 123 123
CCM2 0.02 0.05 -10000 0 -0.4 7 7
CaM/Ca2+/CAMKIIB -0.041 0.13 -10000 0 -0.27 119 119
MAPK11 0.026 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.025 0.12 -10000 0 -0.24 118 118
OSM/MEKK3 0.034 0.036 -10000 0 -0.28 6 6
TAOK1 0.005 0.054 -10000 0 -0.32 13 13
TAOK2 0.014 0.005 -10000 0 -10000 0 0
TAOK3 0.014 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
MAP3K10 0.026 0.005 -10000 0 -10000 0 0
MAP3K3 0.027 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.008 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.055 0.039 -10000 0 -0.24 4 4
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.007 0.043 0.13 41 -0.12 1 42
BUB1B 0.01 0.03 0.12 5 -0.15 3 8
PLK1 0.01 0.025 0.093 13 -10000 0 13
PLK1S1 0.013 0.025 0.11 10 -0.19 3 13
KIF2A 0.008 0.022 0.19 1 -10000 0 1
regulation of mitotic centrosome separation 0.01 0.025 0.093 13 -10000 0 13
GOLGA2 0.027 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.031 0.044 -10000 0 -0.21 9 9
WEE1 0.01 0.061 -10000 0 -0.3 15 15
cytokinesis 0.008 0.051 -10000 0 -0.21 4 4
PP2A-alpha B56 0.058 0.049 -10000 0 -0.53 3 3
AURKA 0.01 0.03 0.11 2 -0.18 7 9
PICH/PLK1 0.015 0.04 0.16 4 -0.2 1 5
CENPE 0.008 0.021 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.007 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.022 0.19 1 -10000 0 1
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.027 0.005 -10000 0 -10000 0 0
TPX2 0.015 0.025 0.12 8 -0.16 2 10
PAK1 0.025 0.008 -10000 0 -10000 0 0
SPC24 0.017 0.063 -10000 0 -0.4 11 11
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN 0.01 0.033 -10000 0 -0.24 6 6
GORASP1 0.024 0.009 -10000 0 -10000 0 0
metaphase 0 0.002 0.015 8 -0.011 3 11
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.014 0.049 19 -10000 0 19
G2 phase of mitotic cell cycle -0.001 0.002 0.012 2 -10000 0 2
STAG2 0.027 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.038 0.17 -10000 0 -0.5 60 60
spindle elongation 0.01 0.025 0.093 13 -10000 0 13
ODF2 0.027 0.005 -10000 0 -10000 0 0
BUB1 0.028 0.049 -10000 0 -0.58 3 3
TPT1 0.001 0.049 -10000 0 -0.18 29 29
CDC25C 0.002 0.062 -10000 0 -0.27 22 22
CDC25B 0.012 0.075 -10000 0 -0.4 16 16
SGOL1 -0.007 0.043 0.12 1 -0.13 41 42
RHOA 0.024 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.045 -10000 0 -0.22 3 3
CDC14B 0.005 0.021 -10000 0 -0.33 2 2
CDC20 0.021 0.05 -10000 0 -0.4 7 7
PLK1/PBIP1 0.009 0.021 0.092 1 -0.15 2 3
mitosis -0.001 0.005 0.023 12 -10000 0 12
FBXO5 0.008 0.025 0.13 5 -10000 0 5
CDC2 0.001 0.002 -10000 0 -0.014 2 2
NDC80 0.024 0.021 -10000 0 -0.4 1 1
metaphase plate congression 0.007 0.047 -10000 0 -0.24 16 16
ERCC6L 0.013 0.042 -10000 0 -0.23 2 2
NLP/gamma Tubulin 0.008 0.017 0.064 7 -0.11 2 9
microtubule cytoskeleton organization 0.001 0.048 -10000 0 -0.18 29 29
G2/M transition DNA damage checkpoint 0 0.003 0.013 11 -10000 0 11
PPP1R12A 0.027 0.003 -10000 0 -10000 0 0
interphase 0 0.003 0.013 11 -10000 0 11
PLK1/PRC1-2 0.039 0.027 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.044 0.029 -10000 0 -10000 0 0
RAB1A 0.027 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.022 0.085 18 -10000 0 18
mitotic prometaphase 0 0.003 0.017 16 -10000 0 16
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.054 -10000 0 -0.48 4 4
microtubule-based process 0.025 0.024 -10000 0 -10000 0 0
Golgi organization 0.01 0.025 0.093 13 -10000 0 13
Cohesin/SA2 0.023 0.021 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.04 0.006 -10000 0 -10000 0 0
KIF20A 0.026 0.006 -10000 0 -10000 0 0
APC/C/CDC20 0.022 0.035 -10000 0 -0.21 6 6
PPP2R1A 0.027 0.004 -10000 0 -10000 0 0
chromosome segregation 0.009 0.021 0.091 1 -0.15 2 3
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.066 0.098 0.22 138 -10000 0 138
C13orf34 0.009 0.022 0.079 17 -10000 0 17
NUDC 0.007 0.047 -10000 0 -0.24 16 16
regulation of attachment of spindle microtubules to kinetochore 0.01 0.03 0.12 5 -0.15 3 8
spindle assembly 0.009 0.021 0.077 14 -10000 0 14
spindle stabilization 0.013 0.025 0.11 10 -0.19 3 13
APC/C/HCDH1 0.023 0.02 -10000 0 -0.26 2 2
MKLP2/PLK1 0.025 0.024 -10000 0 -10000 0 0
CCNB1 0.027 0.007 -10000 0 -10000 0 0
PPP1CB 0.027 0.003 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 -0.002 0.075 -10000 0 -0.35 14 14
TUBG1 0.011 0.022 -10000 0 -0.21 3 3
G2/M transition of mitotic cell cycle 0.004 0.035 -10000 0 -0.23 2 2
MLF1IP 0.005 0.018 -10000 0 -0.28 2 2
INCENP 0.027 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.036 0.02 -10000 0 -10000 0 0
CDKN1B 0.017 0.061 -10000 0 -0.29 1 1
CDKN1A 0.016 0.051 -10000 0 -0.28 6 6
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.009 -10000 0 -10000 0 0
FOXO3 0.013 0.055 -10000 0 -0.28 12 12
AKT1 0.01 0.043 -10000 0 -0.29 7 7
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.012 0.025 -10000 0 -0.3 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.013 0.057 -10000 0 -0.29 1 1
AKT1/ASK1 0.039 0.066 -10000 0 -0.27 8 8
BAD/YWHAZ 0.046 0.021 -10000 0 -10000 0 0
RICTOR 0.024 0.009 -10000 0 -10000 0 0
RAF1 0.024 0.009 -10000 0 -10000 0 0
JNK cascade -0.036 0.062 0.26 8 -10000 0 8
TSC1 0.013 0.054 -10000 0 -0.29 1 1
YWHAZ 0.024 0.009 -10000 0 -10000 0 0
AKT1/RAF1 0.04 0.072 0.28 3 -0.28 5 8
EP300 0.025 0.031 -10000 0 -0.45 2 2
mol:GDP 0.009 0.055 -10000 0 -0.29 12 12
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.014 0.053 -10000 0 -10000 0 0
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
TBC1D4 0.008 0.012 -10000 0 -0.26 1 1
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
MAPKAP1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.07 0.28 9 -0.21 13 22
YWHAH 0.027 0.004 -10000 0 -10000 0 0
AKT1S1 0.015 0.052 -10000 0 -0.28 6 6
CASP9 0.015 0.045 -10000 0 -0.28 4 4
YWHAB 0.026 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.046 0.072 0.3 10 -10000 0 10
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.048 0.024 -10000 0 -0.28 1 1
YWHAE 0.026 0.006 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.02 0.055 -10000 0 -0.3 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.002 0.081 -10000 0 -0.34 24 24
CHUK 0.013 0.054 -10000 0 -0.29 1 1
BAD/BCL-XL 0.043 0.063 0.26 1 -10000 0 1
mTORC2 0.03 0.012 -10000 0 -10000 0 0
AKT2 0.014 0.014 -10000 0 -0.3 1 1
FOXO1-3a-4/14-3-3 family 0.048 0.09 0.25 13 -0.39 8 21
PDPK1 0.026 0.022 -10000 0 -0.45 1 1
MDM2 0.017 0.061 -10000 0 -0.29 1 1
MAPKKK cascade -0.04 0.071 0.28 5 -0.28 3 8
MDM2/Cbp/p300 0.061 0.078 0.27 9 -10000 0 9
TSC1/TSC2 0.015 0.056 0.29 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.074 0.26 9 -10000 0 9
glucose import -0.092 0.12 0.21 6 -0.24 200 206
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.061 0.18 1 -0.34 7 8
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.093 0.12 0.21 4 -0.24 200 204
GSK3A 0.015 0.052 -10000 0 -0.29 1 1
FOXO1 0.014 0.049 -10000 0 -0.28 6 6
GSK3B 0.03 0.065 -10000 0 -0.29 1 1
SFN 0.022 0.045 -10000 0 -0.42 5 5
G1/S transition of mitotic cell cycle 0.04 0.068 0.25 8 -10000 0 8
p27Kip1/14-3-3 family 0.029 0.063 -10000 0 -0.43 3 3
PRKACA 0.027 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.017 0.032 -10000 0 -0.24 2 2
CRKL 0.025 0.02 -10000 0 -0.4 1 1
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DOCK1 0.026 0.022 -10000 0 -0.45 1 1
ITGA4 0.02 0.054 -10000 0 -0.4 8 8
alpha4/beta7 Integrin/MAdCAM1 0.043 0.066 -10000 0 -0.25 2 2
EPO -0.022 0.12 -10000 0 -0.4 49 49
alpha4/beta7 Integrin 0.033 0.047 -10000 0 -0.29 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.033 0.041 -10000 0 -0.28 8 8
EPO/EPOR (dimer) -0.001 0.1 -10000 0 -0.28 56 56
lamellipodium assembly 0.038 0.082 -10000 0 -0.39 6 6
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
PI3K 0.026 0.029 -10000 0 -0.32 2 2
ARF6 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.002 0.06 -10000 0 -0.28 9 9
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
MADCAM1 0 0.075 -10000 0 -0.4 16 16
cell adhesion 0.041 0.065 -10000 0 -0.25 2 2
CRKL/CBL 0.034 0.02 -10000 0 -0.28 1 1
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC -0.005 0.082 0.18 11 -0.28 10 21
ITGB7 0.025 0.031 -10000 0 -0.45 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.017 0.097 -10000 0 -0.25 56 56
p130Cas/Crk/Dock1 0.015 0.077 -10000 0 -0.36 2 2
VCAM1 -0.018 0.13 -10000 0 -0.41 51 51
RHOA 0.024 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.061 0.04 -10000 0 -10000 0 0
BCAR1 -0.022 0.071 0.18 12 -0.38 2 14
EPOR 0.018 0.06 -10000 0 -0.4 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.027 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.083 -10000 0 -0.4 6 6
IL2 signaling events mediated by PI3K

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
BCL2L1 0.045 0.068 -10000 0 -10000 0 0
UGCG 0.005 0.11 -10000 0 -0.56 18 18
AKT1/mTOR/p70S6K/Hsp90/TERT 0.034 0.12 0.28 6 -0.42 13 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.006 0.11 -10000 0 -0.55 18 18
mol:DAG 0.003 0.095 -10000 0 -0.76 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.048 0.095 -10000 0 -0.44 4 4
FRAP1 0.046 0.11 0.29 1 -0.47 6 7
FOXO3 0.048 0.093 0.35 2 -0.39 4 6
AKT1 0.049 0.092 -10000 0 -0.4 3 3
GAB2 0.022 0.038 -10000 0 -0.45 3 3
SMPD1 0.01 0.1 -10000 0 -0.57 14 14
SGMS1 0.019 0.071 -10000 0 -0.58 6 6
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 0.004 0.019 -10000 0 -0.28 2 2
CALM1 0.026 0.007 -10000 0 -10000 0 0
cell proliferation 0.047 0.086 0.27 2 -0.39 6 8
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.031 -10000 0 -0.33 2 2
RPS6KB1 0.009 0.085 -10000 0 -0.83 2 2
mol:sphingomyelin 0.003 0.095 -10000 0 -0.76 7 7
natural killer cell activation 0 0.001 -10000 0 -0.011 2 2
JAK3 0.014 0.077 -10000 0 -0.39 17 17
PIK3R1 0.025 0.038 -10000 0 -0.45 3 3
JAK1 0.029 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC 0.081 0.11 0.36 13 -10000 0 13
MYB -0.089 0.36 -10000 0 -1.2 48 48
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.041 0.079 -10000 0 -0.35 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.086 -10000 0 -0.75 2 2
mol:PI-3-4-5-P3 0.043 0.08 -10000 0 -0.34 2 2
Rac1/GDP 0.016 0.022 -10000 0 -0.25 2 2
T cell proliferation 0.043 0.079 0.27 7 -0.32 1 8
SHC1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.003 0.021 -10000 0 -0.063 52 52
PRKCZ 0.041 0.077 0.25 3 -0.33 1 4
NF kappa B1 p50/RelA 0.06 0.1 -10000 0 -0.47 3 3
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.016 0.052 -10000 0 -0.38 2 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
IL2RA -0.013 0.12 -10000 0 -0.4 46 46
IL2RB 0.023 0.051 -10000 0 -0.4 7 7
TERT -0.057 0.16 -10000 0 -0.4 92 92
E2F1 -0.016 0.14 -10000 0 -0.42 50 50
SOS1 0.027 0.004 -10000 0 -10000 0 0
RPS6 0.025 0.008 -10000 0 -10000 0 0
mol:cAMP 0.001 0.01 0.03 52 -10000 0 52
PTPN11 0.028 0.003 -10000 0 -10000 0 0
IL2RG 0.015 0.079 -10000 0 -0.4 17 17
actin cytoskeleton organization 0.043 0.079 0.27 7 -0.32 1 8
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL2 0.018 0.023 -10000 0 -0.39 1 1
PIK3CA 0.021 0.014 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.033 -10000 0 -0.24 2 2
LCK 0.019 0.065 -10000 0 -0.39 12 12
BCL2 0.043 0.12 -10000 0 -0.76 5 5
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.023 0.023 -10000 0 -0.45 1 1
Caspase 8 (4 units) 0.041 0.077 -10000 0 -0.4 1 1
NEF -0.008 0.037 -10000 0 -10000 0 0
NFKBIA 0.023 0.026 -10000 0 -10000 0 0
BIRC3 0.017 0.081 -10000 0 -0.39 13 13
CYCS 0.017 0.077 0.22 13 -0.44 1 14
RIPK1 0.026 0.006 -10000 0 -10000 0 0
CD247 -0.003 0.11 -10000 0 -0.48 21 21
MAP2K7 0.032 0.14 0.31 2 -0.79 9 11
protein ubiquitination 0.04 0.096 0.24 16 -0.39 9 25
CRADD 0.027 0.002 -10000 0 -10000 0 0
DAXX 0.026 0.006 -10000 0 -10000 0 0
FAS 0.026 0.022 -10000 0 -0.45 1 1
BID 0.015 0.074 0.19 3 -0.46 1 4
NF-kappa-B/RelA/I kappa B alpha 0.043 0.068 -10000 0 -0.34 9 9
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
CFLAR 0.026 0.005 -10000 0 -10000 0 0
FADD 0.019 0.012 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.069 -10000 0 -0.34 9 9
MAPK8 0.029 0.13 0.28 4 -0.72 9 13
APAF1 0.027 0.002 -10000 0 -10000 0 0
TRAF1 0.016 0.065 -10000 0 -0.4 12 12
TRAF2 0.021 0.047 -10000 0 -0.4 6 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.022 0.078 0.2 3 -0.27 10 13
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.029 0.1 -10000 0 -0.48 11 11
CHUK 0.041 0.1 0.25 15 -0.42 9 24
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.05 0.042 -10000 0 -0.24 1 1
TCRz/NEF -0.008 0.11 -10000 0 -0.3 53 53
TNF 0.007 0.088 -10000 0 -0.4 22 22
FASLG -0.029 0.15 -10000 0 -0.48 46 46
NFKB1 0.023 0.029 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.032 0.061 -10000 0 -0.24 20 20
CASP6 0.04 0.11 -10000 0 -0.54 7 7
CASP7 0.042 0.12 0.3 28 -0.43 7 35
RELA 0.022 0.028 -10000 0 -0.21 1 1
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.039 0.12 0.3 28 -0.42 7 35
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.033 0.022 -10000 0 -0.32 1 1
CASP8 0.026 0.005 -10000 0 -10000 0 0
CASP9 0.026 0.006 -10000 0 -10000 0 0
MAP3K14 0.039 0.1 0.25 8 -0.46 10 18
APAF-1/Caspase 9 0.01 0.076 -10000 0 -0.34 2 2
BCL2 0.026 0.12 0.28 3 -0.66 9 12
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.003 0.1 -10000 0 -0.45 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.009 0.023 -10000 0 -0.18 2 2
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.024 0.009 -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 0.027 0.003 -10000 0 -10000 0 0
FYN 0.026 0.02 -10000 0 -0.4 1 1
MAP3K12 0.025 0.029 -10000 0 -0.42 2 2
FGR 0.026 0.02 -10000 0 -0.4 1 1
p38 alpha/TAB1 -0.024 0.068 -10000 0 -0.31 17 17
PRKG1 0.003 0.1 -10000 0 -0.43 25 25
DUSP8 0.026 0.006 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.016 0.099 0.16 4 -0.34 14 18
apoptosis -0.023 0.066 -10000 0 -0.3 17 17
RAL/GTP 0.035 0.009 -10000 0 -10000 0 0
LYN 0.024 0.021 -10000 0 -0.4 1 1
DUSP1 0.005 0.097 -10000 0 -0.45 21 21
PAK1 0.025 0.008 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.059 0.038 -10000 0 -10000 0 0
TRAF6 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -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 0.02 0.05 -10000 0 -0.4 7 7
RAC1-CDC42/GTP 0.034 0.011 -10000 0 -10000 0 0
MAPK11 0.029 0.11 0.24 24 -0.35 14 38
BLK -0.036 0.15 -10000 0 -0.4 67 67
HCK 0.023 0.03 -10000 0 -0.42 2 2
MAP2K3 0.026 0.005 -10000 0 -10000 0 0
DUSP16 0.026 0.007 -10000 0 -10000 0 0
DUSP10 0.026 0.019 -10000 0 -0.4 1 1
TRAF6/MEKK3 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.028 0.1 0.21 24 -0.37 13 37
positive regulation of innate immune response 0.033 0.12 0.25 29 -0.41 15 44
LCK 0.017 0.065 -10000 0 -0.4 12 12
p38alpha-beta/MKP7 0.039 0.12 0.28 20 -0.4 12 32
p38alpha-beta/MKP5 0.04 0.12 0.26 21 -0.4 13 34
PGK/cGMP 0.003 0.072 -10000 0 -0.31 25 25
PAK2 0.02 0.012 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.034 0.13 0.26 26 -0.41 14 40
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.027 0.004 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
PAK3 0.003 0.078 -10000 0 -0.4 17 17
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.001 0.15 -9999 0 -0.49 17 17
MAP3K8 0.023 0.038 -9999 0 -0.45 3 3
FOS 0.001 0.11 -9999 0 -0.51 10 10
PRKCA 0.02 0.033 -9999 0 -0.42 2 2
PTPN7 0.002 0.092 -9999 0 -0.4 23 23
HRAS 0.025 0.02 -9999 0 -0.41 1 1
PRKCB 0.015 0.057 -9999 0 -0.41 8 8
NRAS 0.026 0.005 -9999 0 -10000 0 0
RAS family/GTP 0.043 0.023 -9999 0 -0.22 1 1
MAPK3 0.009 0.097 -9999 0 -0.6 8 8
MAP2K1 0.011 0.076 -9999 0 -0.43 8 8
ELK1 0.02 0.02 -9999 0 -10000 0 0
BRAF 0.012 0.041 -9999 0 -0.33 3 3
mol:GTP -0.001 0.002 -9999 0 -0.005 63 63
MAPK1 0.013 0.081 -9999 0 -0.63 4 4
RAF1 0.01 0.046 -9999 0 -0.38 2 2
KRAS 0.026 0.006 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.041 0.03 -9999 0 -10000 0 0
CLOCK 0.023 0.053 -9999 0 -0.45 6 6
TIMELESS/CRY2 0.04 0.022 -9999 0 -10000 0 0
DEC1/BMAL1 -0.016 0.12 -9999 0 -0.28 84 84
ATR 0.022 0.011 -9999 0 -10000 0 0
NR1D1 0.024 0.014 -9999 0 -10000 0 0
ARNTL 0.029 0.006 -9999 0 -10000 0 0
TIMELESS 0.024 0.014 -9999 0 -10000 0 0
NPAS2 0.022 0.061 -9999 0 -0.45 8 8
CRY2 0.026 0.006 -9999 0 -10000 0 0
mol:CO -0.01 0 -9999 0 -10000 0 0
CHEK1 0.025 0.008 -9999 0 -10000 0 0
mol:HEME 0.01 0 -9999 0 -10000 0 0
PER1 0.025 0.022 -9999 0 -0.45 1 1
BMAL/CLOCK/NPAS2 0.055 0.058 -9999 0 -0.29 12 12
BMAL1/CLOCK 0.011 0.07 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.041 0.03 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.042 0.03 -9999 0 -10000 0 0
mol:NADPH 0.01 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.039 0.024 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.059 0.16 -9999 0 -0.4 85 85
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.041 0.1 -10000 0 -0.39 20 20
MAP4K1 0.014 0.072 -10000 0 -0.41 14 14
MAP3K8 0.024 0.038 -10000 0 -0.45 3 3
PRKCB 0.02 0.054 -10000 0 -0.4 8 8
DBNL 0.026 0.006 -10000 0 -10000 0 0
CRKL 0.025 0.02 -10000 0 -0.4 1 1
MAP3K1 0.012 0.058 -10000 0 -0.38 4 4
JUN 0.01 0.12 -10000 0 -0.56 17 17
MAP3K7 0.011 0.061 -10000 0 -0.37 5 5
GRAP2 0.015 0.071 -10000 0 -0.43 12 12
CRK 0.026 0.006 -10000 0 -10000 0 0
MAP2K4 0.015 0.074 0.26 9 -0.4 4 13
LAT 0.015 0.07 -10000 0 -0.4 14 14
LCP2 0.023 0.033 -10000 0 -0.4 3 3
MAPK8 0.012 0.12 -10000 0 -0.59 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.016 0.067 -10000 0 -0.39 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55 0.049 0.1 -10000 0 -0.45 13 13
Regulation of Telomerase

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
Telomerase catalytic core complex -0.049 0.18 -10000 0 -0.63 13 13
RAD9A 0.025 0.008 -10000 0 -10000 0 0
AP1 -0.009 0.12 -10000 0 -0.33 60 60
IFNAR2 0.019 0.018 -10000 0 -10000 0 0
AKT1 0.001 0.051 -10000 0 -0.34 5 5
ER alpha/Oestrogen 0 0.072 -10000 0 -0.3 27 27
NFX1/SIN3/HDAC complex 0.021 0.046 -10000 0 -0.3 4 4
EGF -0.06 0.18 -10000 0 -0.45 88 88
SMG5 0.027 0.004 -10000 0 -10000 0 0
SMG6 0.026 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.027 0.028 -10000 0 -10000 0 0
TERT/c-Abl -0.043 0.18 -10000 0 -0.58 14 14
SAP18 0.026 0.006 -10000 0 -10000 0 0
MRN complex 0.043 0.024 -10000 0 -10000 0 0
WT1 -0.071 0.17 -10000 0 -0.4 101 101
WRN 0.025 0.008 -10000 0 -10000 0 0
SP1 0.018 0.022 -10000 0 -10000 0 0
SP3 0.025 0.007 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.026 0.17 -10000 0 -0.56 10 10
Mad/Max 0.033 0.036 -10000 0 -0.33 4 4
TERT -0.051 0.19 -10000 0 -0.64 13 13
CCND1 -0.004 0.2 0.49 1 -0.95 5 6
MAX 0.025 0.007 -10000 0 -10000 0 0
RBBP7 0.026 0.004 -10000 0 -10000 0 0
RBBP4 0.025 0.022 -10000 0 -0.46 1 1
TERF2 0.025 0.013 -10000 0 -10000 0 0
PTGES3 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.005 -10000 0 -10000 0 0
Telomerase/911 0.035 0.049 0.2 1 -10000 0 1
CDKN1B -0.028 0.1 -10000 0 -10000 0 0
RAD1 0.024 0.009 -10000 0 -10000 0 0
XRCC5 0.026 0.005 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
SAP30 0.025 0.02 -10000 0 -0.4 1 1
TRF2/PARP2 0.037 0.015 -10000 0 -10000 0 0
UBE3A 0.026 0.005 -10000 0 -10000 0 0
JUN 0.026 0.006 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.014 0.015 -10000 0 -10000 0 0
FOS -0.033 0.16 -10000 0 -0.45 60 60
IFN-gamma/IRF1 -0.023 0.13 -10000 0 -0.27 100 100
PARP2 0.026 0.006 -10000 0 -10000 0 0
BLM 0.026 0.019 -10000 0 -0.4 1 1
Telomerase 0.008 0.1 0.23 1 -0.5 10 11
IRF1 0.028 0.008 -10000 0 -10000 0 0
ESR1 0.002 0.1 -10000 0 -0.42 27 27
KU/TER 0.038 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.015 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.025 0.059 -10000 0 -0.4 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.025 0.061 -10000 0 -0.41 5 5
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.017 0.022 -10000 0 -10000 0 0
ATM 0.01 0.008 -10000 0 -10000 0 0
SMAD3 0.014 0.019 -10000 0 -0.28 2 2
ABL1 0.027 0.004 -10000 0 -10000 0 0
MXD1 0.021 0.049 -10000 0 -0.46 5 5
MRE11A 0.025 0.008 -10000 0 -10000 0 0
HUS1 0.026 0.007 -10000 0 -10000 0 0
RPS6KB1 0.027 0.002 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.023 0.19 -10000 0 -0.63 11 11
NR2F2 0.028 0.02 -10000 0 -0.38 1 1
MAPK3 -0.007 0.019 -10000 0 -0.28 1 1
MAPK1 -0.007 0.019 -10000 0 -0.28 1 1
TGFB1/TGF beta receptor Type II 0.025 0.027 -10000 0 -0.4 2 2
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.026 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.008 -10000 0 -10000 0 0
NBN 0.024 0.009 -10000 0 -10000 0 0
EGFR 0.019 0.049 -10000 0 -0.46 5 5
mol:Oestrogen -0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.027 0.14 -10000 0 -0.33 80 80
MYC 0.021 0.011 -10000 0 -10000 0 0
IL2 0.009 0.029 -10000 0 -0.39 1 1
KU 0.038 0.01 -10000 0 -10000 0 0
RAD50 0.026 0.007 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
TGFB1 0.025 0.027 -10000 0 -0.4 2 2
TRF2/BLM 0.038 0.019 -10000 0 -0.26 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.031 0.18 -10000 0 -0.6 12 12
SP1/HDAC2 0.027 0.033 -10000 0 -10000 0 0
PINX1 0.025 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.026 0.17 -10000 0 -0.58 9 9
Smad3/Myc 0.024 0.018 -10000 0 -0.24 1 1
911 complex 0.042 0.024 -10000 0 -10000 0 0
IFNG -0.058 0.17 -10000 0 -0.39 101 101
Telomerase/PinX1 -0.026 0.17 -10000 0 -0.58 9 9
Telomerase/AKT1/mTOR/p70S6K 0 0.096 0.26 1 -0.43 11 12
SIN3B 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.026 0.006 -10000 0 -10000 0 0
Telomerase/EST1B -0.025 0.17 -10000 0 -0.57 10 10
response to DNA damage stimulus -0.002 0.027 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.058 0.035 -10000 0 -10000 0 0
TRF2/WRN 0.036 0.016 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.025 0.17 -10000 0 -0.58 9 9
E2F1 0.003 0.084 -10000 0 -0.41 19 19
ZNFX1 0.026 0.006 -10000 0 -10000 0 0
PIF1 0.003 0.098 -10000 0 -0.4 28 28
NCL 0.026 0.006 -10000 0 -10000 0 0
DKC1 0.026 0.005 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.088 0.24 -10000 0 -1.1 3 3
PLK1 0.053 0.1 -10000 0 -0.68 7 7
BIRC5 0.046 0.11 -10000 0 -0.89 3 3
HSPA1B 0.088 0.24 -10000 0 -1.1 3 3
MAP2K1 0.035 0.038 -10000 0 -10000 0 0
BRCA2 0.081 0.26 -10000 0 -1.1 6 6
FOXM1 0.085 0.27 0.57 1 -1.4 3 4
XRCC1 0.086 0.24 -10000 0 -1.1 3 3
FOXM1B/p19 -0.018 0.24 -10000 0 -1.1 5 5
Cyclin D1/CDK4 0.027 0.24 -10000 0 -1 5 5
CDC2 0.088 0.25 0.55 1 -1.2 3 4
TGFA 0.071 0.26 0.56 1 -0.99 7 8
SKP2 0.11 0.25 0.62 3 -1 3 6
CCNE1 0.027 0.034 -10000 0 -0.39 3 3
CKS1B 0.086 0.24 0.52 1 -1.1 3 4
RB1 0.029 0.18 -10000 0 -0.81 8 8
FOXM1C/SP1 0.093 0.25 -10000 0 -1.2 3 3
AURKB 0.033 0.16 -10000 0 -0.77 13 13
CENPF 0.088 0.24 0.63 1 -1.1 3 4
CDK4 0.032 0.02 -10000 0 -10000 0 0
MYC 0.061 0.21 0.49 1 -0.92 3 4
CHEK2 0.034 0.038 -10000 0 -10000 0 0
ONECUT1 0.072 0.27 -10000 0 -1 6 6
CDKN2A -0.14 0.2 -10000 0 -0.4 183 183
LAMA4 0.078 0.25 -10000 0 -1.1 3 3
FOXM1B/HNF6 0.07 0.29 -10000 0 -1.2 6 6
FOS -0.007 0.44 -10000 0 -1.1 64 64
SP1 0.028 0.003 -10000 0 -10000 0 0
CDC25B 0.088 0.24 -10000 0 -1.1 3 3
response to radiation 0.015 0.023 -10000 0 -10000 0 0
CENPB 0.093 0.24 -10000 0 -1.1 3 3
CENPA 0.085 0.24 -10000 0 -1.2 3 3
NEK2 0.087 0.24 0.63 1 -1.1 3 4
HIST1H2BA 0.082 0.24 -10000 0 -1.1 3 3
CCNA2 0.029 0.022 -10000 0 -0.41 1 1
EP300 0.025 0.031 -10000 0 -0.45 2 2
CCNB1/CDK1 0.083 0.26 -10000 0 -1.3 3 3
CCNB2 0.085 0.24 0.73 1 -1.2 3 4
CCNB1 0.088 0.25 0.55 1 -1.1 3 4
ETV5 0.14 0.26 0.6 5 -1.1 3 8
ESR1 0.061 0.3 -10000 0 -1.1 16 16
CCND1 0.022 0.24 -10000 0 -1 5 5
GSK3A 0.035 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.061 0.048 -10000 0 -0.25 2 2
CDK2 0.03 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.015 0.026 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.091 0.25 -10000 0 -1.1 4 4
GAS1 0.084 0.26 -10000 0 -1.2 6 6
MMP2 0.069 0.26 -10000 0 -1.1 3 3
RB1/FOXM1C 0.08 0.26 0.6 1 -1.1 5 6
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.018 0.027 -10000 0 -10000 0 0
STMN1 0.01 0.049 -10000 0 -0.32 10 10
Aurora B/RasGAP/Survivin 0.041 0.078 -10000 0 -0.27 24 24
Chromosomal passenger complex/Cul3 protein complex 0.011 0.054 -10000 0 -0.28 6 6
BIRC5 0.01 0.088 -10000 0 -0.4 22 22
DES -0.31 0.29 -10000 0 -0.56 279 279
Aurora C/Aurora B/INCENP 0.048 0.048 -10000 0 -0.23 11 11
Aurora B/TACC1 0.031 0.039 -10000 0 -0.24 9 9
Aurora B/PP2A 0.037 0.042 -10000 0 -0.27 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.01 0.01 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0 0.003 -10000 0 -10000 0 0
NDC80 0.011 0.035 -10000 0 -0.27 7 7
Cul3 protein complex 0.042 0.038 -10000 0 -0.28 4 4
KIF2C 0.017 0.025 -10000 0 -0.18 2 2
PEBP1 0.028 0.003 -10000 0 -10000 0 0
KIF20A 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.046 -10000 0 -0.31 7 7
SEPT1 0.018 0.06 -10000 0 -0.4 10 10
SMC2 0.027 0.004 -10000 0 -10000 0 0
SMC4 0.02 0.012 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.008 0.12 -10000 0 -0.56 17 17
PSMA3 0.026 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.015 0.022 -10000 0 -0.15 8 8
AURKB 0.026 0.055 -10000 0 -0.4 8 8
AURKC 0.021 0.049 -10000 0 -0.42 6 6
CDCA8 0.028 0.02 -10000 0 -0.4 1 1
cytokinesis -0.002 0.058 -10000 0 -0.36 5 5
Aurora B/Septin1 0.03 0.081 -10000 0 -0.36 5 5
AURKA 0.021 0.047 -10000 0 -0.4 6 6
INCENP 0.028 0.006 -10000 0 -10000 0 0
KLHL13 0.023 0.043 -10000 0 -0.45 4 4
BUB1 0.027 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.038 0.069 -10000 0 -0.24 22 22
EVI5 0.028 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.05 0.052 -10000 0 -10000 0 0
SGOL1 0.024 0.009 -10000 0 -10000 0 0
CENPA 0.017 0.05 -10000 0 -0.27 5 5
NCAPG 0.026 0.006 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.037 0.042 -10000 0 -0.27 8 8
NCAPD2 0.026 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.038 0.041 -10000 0 -0.27 8 8
RHOA 0.024 0.009 -10000 0 -10000 0 0
NCAPH 0.027 0.004 -10000 0 -10000 0 0
NPM1 -0.007 0.11 -10000 0 -0.46 16 16
RASA1 0.024 0.031 -10000 0 -0.45 2 2
KLHL9 0.024 0.01 -10000 0 -10000 0 0
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.042 -10000 0 -0.27 8 8
PPP1CC 0.027 0.002 -10000 0 -10000 0 0
Centraspindlin 0.047 0.054 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
NSUN2 0.01 0.056 -10000 0 -0.27 14 14
MYLK 0.012 0.032 -10000 0 -0.19 9 9
KIF23 0.028 0.005 -10000 0 -10000 0 0
VIM 0.011 0.044 -10000 0 -0.3 9 9
RACGAP1 0.028 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0 0.093 -10000 0 -0.41 17 17
Chromosomal passenger complex 0.018 0.044 0.17 2 -0.24 3 5
Chromosomal passenger complex/EVI5 0.087 0.086 -10000 0 -0.37 6 6
TACC1 0.023 0.031 -10000 0 -0.45 2 2
PPP2R5D 0.026 0.006 -10000 0 -10000 0 0
CUL3 0.026 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.003 -10000 0 -10000 0 0
mol:PIP3 0.001 0.029 -10000 0 -0.22 2 2
FRAP1 0.03 0.064 -10000 0 -0.43 5 5
AKT1 0.033 0.072 0.18 11 -0.24 1 12
INSR 0.026 0.022 -10000 0 -0.45 1 1
Insulin Receptor/Insulin 0.027 0.023 -10000 0 -0.25 3 3
mol:GTP 0.059 0.071 0.28 5 -10000 0 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.01 0.02 -10000 0 -10000 0 0
TSC2 0.027 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.013 0.029 -10000 0 -10000 0 0
TSC1 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.017 0.05 -10000 0 -0.2 22 22
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.029 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.048 0.07 0.23 12 -0.25 3 15
MAP3K5 0.005 0.034 0.19 7 -0.18 9 16
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
apoptosis 0.005 0.034 0.19 7 -0.18 9 16
mol:LY294002 0 0 -10000 0 -0.001 22 22
EIF4B 0.045 0.067 0.24 13 -10000 0 13
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.058 0.06 0.22 8 -10000 0 8
eIF4E/eIF4G1/eIF4A1 0.012 0.03 -10000 0 -0.27 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.022 0.041 -10000 0 -0.22 4 4
mTOR/RHEB/GTP/Raptor/GBL 0.038 0.06 0.22 19 -0.19 1 20
FKBP1A 0.027 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.053 0.058 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 22 22
FKBP12/Rapamycin 0.021 0.006 -10000 0 -10000 0 0
PDPK1 -0.005 0.036 0.17 10 -0.21 2 12
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.039 0.097 -10000 0 -0.49 13 13
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.005 0.099 -10000 0 -0.83 5 5
TSC1/TSC2 0.066 0.077 0.3 6 -10000 0 6
tumor necrosis factor receptor activity 0 0 0.001 22 -10000 0 22
RPS6 0.025 0.008 -10000 0 -10000 0 0
PPP5C 0.027 0.004 -10000 0 -10000 0 0
EIF4G1 0.02 0.012 -10000 0 -10000 0 0
IRS1 0 0.049 -10000 0 -0.21 23 23
INS -0.018 0.026 -10000 0 -0.4 2 2
PTEN 0.025 0.006 -10000 0 -10000 0 0
PDK2 -0.004 0.037 0.17 12 -0.21 1 13
EIF4EBP1 -0.021 0.21 -10000 0 -1 20 20
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
PPP2R5D 0.031 0.064 0.24 5 -0.38 5 10
peptide biosynthetic process -0.009 0.025 0.18 4 -0.22 3 7
RHEB 0.026 0.007 -10000 0 -10000 0 0
EIF4A1 0.026 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.003 36 -10000 0 36
EEF2 -0.009 0.025 0.18 4 -0.22 3 7
eIF4E/4E-BP1 -0.006 0.2 -10000 0 -0.95 20 20
TCGA08_rtk_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
PDGFRA 0.018 0.063 -10000 0 -0.44 9 9
HRAS 0.025 0.02 -10000 0 -0.41 1 1
EGFR 0.019 0.049 -10000 0 -0.45 5 5
AKT 0.069 0.073 0.28 16 -0.27 1 17
FOXO3 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.007 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.021 0.05 -10000 0 -0.4 7 7
FOXO4 0.025 0.031 -10000 0 -0.45 2 2
MET 0.021 0.049 -10000 0 -0.42 6 6
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
PIK3CB 0.022 0.011 -10000 0 -10000 0 0
NRAS 0.026 0.005 -10000 0 -10000 0 0
PIK3CG 0.008 0.086 -10000 0 -0.41 20 20
PIK3R3 0.027 0.003 -10000 0 -10000 0 0
PIK3R2 0.027 0.003 -10000 0 -10000 0 0
NF1 0.027 0.004 -10000 0 -10000 0 0
RAS 0.025 0.042 0.16 1 -0.24 3 4
ERBB2 0.027 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.066 0.073 0.25 6 -0.21 51 57
PI3K 0.054 0.073 0.23 31 -0.31 1 32
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
KRAS 0.026 0.006 -10000 0 -10000 0 0
FOXO 0.086 0.063 0.22 34 -10000 0 34
AKT2 0.026 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.03 0.024 -10000 0 -0.3 1 1
VEGFR1 homodimer/NRP1 0.013 0.019 -10000 0 -0.28 2 2
mol:DAG -0.02 0.087 -10000 0 -0.43 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.032 -10000 0 -0.27 1 1
CaM/Ca2+ -0.007 0.087 -10000 0 -0.41 1 1
HIF1A 0.03 0.025 -10000 0 -0.44 1 1
GAB1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.02 0.1 0.35 5 -0.5 2 7
PLCG1 -0.02 0.087 -10000 0 -0.43 1 1
NOS3 0.009 0.094 0.35 6 -0.4 2 8
CBL 0.025 0.008 -10000 0 -10000 0 0
mol:NO 0.021 0.12 0.47 16 -0.38 2 18
FLT1 0.017 0.023 -10000 0 -0.34 2 2
PGF -0.046 0.16 -10000 0 -0.4 84 84
VEGFR1 homodimer/NRP2/VEGFR121 0.039 0.038 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
eNOS/Hsp90 0.018 0.1 0.47 3 -0.41 1 4
endothelial cell proliferation -0.003 0.091 0.37 9 -0.42 1 10
mol:Ca2+ -0.02 0.086 -10000 0 -0.42 1 1
MAPK3 -0.025 0.089 0.34 10 -0.38 1 11
MAPK1 -0.025 0.089 0.34 10 -0.38 1 11
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
PLGF homodimer -0.046 0.16 -10000 0 -0.4 84 84
PRKACA 0.027 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.007 0.11 -10000 0 -0.4 38 38
VEGFA homodimer 0.022 0.043 -10000 0 -0.4 5 5
VEGFR1 homodimer/VEGFA homodimer 0.027 0.035 -10000 0 -0.3 1 1
platelet activating factor biosynthetic process -0.026 0.084 0.33 9 -0.37 1 10
PI3K 0.009 0.087 -10000 0 -0.41 2 2
PRKCA -0.022 0.085 0.35 4 -0.4 1 5
PRKCB -0.024 0.089 0.35 5 -0.4 1 6
VEGFR1 homodimer/PLGF homodimer -0.014 0.1 -10000 0 -0.39 2 2
VEGFA 0.022 0.043 -10000 0 -0.4 5 5
VEGFB 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.02 0.087 -10000 0 -0.43 1 1
RASA1 0.02 0.042 -10000 0 -0.47 1 1
NRP2 0.025 0.027 -10000 0 -0.4 2 2
VEGFR1 homodimer 0.017 0.023 -10000 0 -0.34 2 2
VEGFB homodimer 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.023 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.014 0.13 0.47 14 -0.41 2 16
PTPN11 0.027 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.086 -10000 0 -0.41 2 2
mol:L-citrulline 0.021 0.12 0.47 16 -0.38 2 18
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.05 0.039 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.035 0.035 -10000 0 -10000 0 0
CD2AP 0.026 0.006 -10000 0 -10000 0 0
PI3K/GAB1 0.017 0.089 -10000 0 -0.4 2 2
PDPK1 0.025 0.12 0.37 10 -0.49 2 12
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.04 0.037 -10000 0 -10000 0 0
mol:NADP 0.021 0.12 0.47 16 -0.38 2 18
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.038 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.029 0.028 -10000 0 -0.3 1 1
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.027 0.004 -10000 0 -10000 0 0
SPHK1 0.018 0.063 -10000 0 -0.4 11 11
GNAI2 0.024 0.009 -10000 0 -10000 0 0
mol:S1P 0.013 0.023 -10000 0 -10000 0 0
GNAO1 0.022 0.04 -10000 0 -0.41 4 4
mol:Sphinganine-1-P 0.008 0.043 -10000 0 -0.28 11 11
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.05 0.039 -10000 0 -10000 0 0
GNAI3 0.027 0.004 -10000 0 -10000 0 0
G12/G13 0.037 0.012 -10000 0 -10000 0 0
S1PR3 0.022 0.047 -10000 0 -0.44 5 5
S1PR2 0.027 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.005 0.029 -10000 0 -0.24 2 2
S1PR5 0.023 0.041 -10000 0 -0.42 4 4
S1PR4 0.002 0.1 -10000 0 -0.4 29 29
GNAI1 0.025 0.022 -10000 0 -0.45 1 1
S1P/S1P5/G12 0.036 0.041 -10000 0 -0.24 3 3
S1P/S1P3/Gq -0.014 0.11 -10000 0 -0.39 12 12
S1P/S1P4/Gi 0.014 0.073 0.18 1 -0.36 9 10
GNAQ 0.027 0.004 -10000 0 -10000 0 0
GNAZ 0.01 0.083 -10000 0 -0.42 18 18
GNA14 -0.044 0.17 -10000 0 -0.45 72 72
GNA15 0.025 0.031 -10000 0 -0.45 2 2
GNA12 0.025 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.003 -10000 0 -10000 0 0
GNA11 0.024 0.038 -10000 0 -0.45 3 3
ABCC1 0.024 0.033 -10000 0 -0.4 3 3
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.004 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.062 -10000 0 -0.27 17 17
forebrain development -0.023 0.13 -10000 0 -0.47 19 19
GNAO1 0.022 0.04 -10000 0 -0.41 4 4
SMO/beta Arrestin2 0.023 0.068 -10000 0 -0.32 17 17
SMO 0.007 0.09 -10000 0 -0.45 18 18
ARRB2 0.026 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.049 0.079 0.26 3 -0.38 2 5
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.009 -10000 0 -10000 0 0
GNAI2 0.024 0.009 -10000 0 -10000 0 0
SIN3/HDAC complex 0.063 0.025 -10000 0 -0.21 1 1
GNAI1 0.025 0.022 -10000 0 -0.45 1 1
XPO1 0.023 0.016 -10000 0 -10000 0 0
GLI1/Su(fu) -0.022 0.14 -10000 0 -0.54 15 15
SAP30 0.025 0.02 -10000 0 -0.4 1 1
mol:GDP 0.007 0.09 -10000 0 -0.45 18 18
MIM/GLI2A 0.017 0.029 -10000 0 -10000 0 0
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GLI2 0.016 0.071 0.2 2 -10000 0 2
GLI3 0.037 0.079 0.26 5 -0.37 3 8
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.025 0.02 -10000 0 -0.4 1 1
Gi family/GTP 0.008 0.073 -10000 0 -0.33 10 10
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.038 0.081 -10000 0 -0.41 6 6
GLI2/Su(fu) 0.022 0.075 0.2 1 -0.31 5 6
FOXA2 -0.019 0.14 -10000 0 -0.88 3 3
neural tube patterning -0.023 0.13 -10000 0 -0.47 19 19
SPOP 0.027 0.002 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.054 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
MTSS1 0.017 0.029 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.023 0.13 -10000 0 -0.47 19 19
SUFU 0.016 0.037 -10000 0 -10000 0 0
LGALS3 0.024 0.031 -10000 0 -0.45 2 2
catabolic process 0.048 0.097 0.27 3 -0.42 5 8
GLI3A/CBP 0.002 0.081 -10000 0 -0.21 62 62
KIF3A 0.026 0.006 -10000 0 -10000 0 0
GLI1 -0.024 0.14 -10000 0 -0.48 18 18
RAB23 0.024 0.027 -10000 0 -0.4 2 2
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.027 0.003 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.02 0.057 -10000 0 -0.38 1 1
GNAZ 0.01 0.083 -10000 0 -0.42 18 18
RBBP4 0.026 0.022 -10000 0 -0.45 1 1
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.028 0.072 -10000 0 -10000 0 0
STK36 0.023 0.016 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.005 0.074 -10000 0 -0.39 10 10
PTCH1 -0.024 0.16 -10000 0 -0.93 7 7
MIM/GLI1 -0.018 0.14 -10000 0 -0.54 9 9
CREBBP 0.002 0.081 -10000 0 -0.21 62 62
Su(fu)/SIN3/HDAC complex 0.014 0.089 -10000 0 -0.45 11 11
HIF-2-alpha transcription factor network

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
MMP14 0.012 0.13 -10000 0 -0.6 17 17
oxygen homeostasis -0.002 0.011 -10000 0 -10000 0 0
TCEB2 0.025 0.027 -10000 0 -0.4 2 2
TCEB1 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.028 0.084 -10000 0 -0.44 1 1
EPO -0.026 0.17 -10000 0 -0.56 9 9
FIH (dimer) 0.021 0.021 -10000 0 -10000 0 0
APEX1 0.019 0.024 -10000 0 -10000 0 0
SERPINE1 -0.1 0.2 -10000 0 -0.6 14 14
FLT1 -0.014 0.18 -10000 0 -0.64 34 34
ADORA2A -0.026 0.16 0.37 3 -0.59 7 10
germ cell development -0.034 0.17 -10000 0 -0.64 6 6
SLC11A2 -0.024 0.16 -10000 0 -0.62 6 6
BHLHE40 -0.027 0.16 -10000 0 -0.62 6 6
HIF1AN 0.021 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.012 0.12 0.3 1 -0.4 2 3
ETS1 0.032 0.035 -10000 0 -0.39 3 3
CITED2 0.016 0.11 -10000 0 -0.67 9 9
KDR -0.01 0.18 -10000 0 -0.65 29 29
PGK1 -0.024 0.16 -10000 0 -0.62 6 6
SIRT1 0.026 0.022 -10000 0 -0.45 1 1
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT -0.017 0.19 -10000 0 -0.67 8 8
EPAS1 -0.004 0.078 0.22 1 -0.32 6 7
SP1 0.031 0.012 -10000 0 -10000 0 0
ABCG2 -0.029 0.17 -10000 0 -0.63 9 9
EFNA1 -0.023 0.16 -10000 0 -0.6 6 6
FXN -0.025 0.16 0.37 3 -0.63 5 8
POU5F1 -0.036 0.17 -10000 0 -0.67 6 6
neuron apoptosis 0.017 0.18 0.65 8 -10000 0 8
EP300 0.025 0.031 -10000 0 -0.45 2 2
EGLN3 -0.003 0.1 -10000 0 -0.42 26 26
EGLN2 0.021 0.021 -10000 0 -10000 0 0
EGLN1 0.021 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.044 0.023 -10000 0 -10000 0 0
VHL 0.024 0.009 -10000 0 -10000 0 0
ARNT 0.02 0.023 -10000 0 -10000 0 0
SLC2A1 -0.029 0.17 0.37 3 -0.61 9 12
TWIST1 -0.027 0.16 0.37 3 -0.63 9 12
ELK1 0.032 0.007 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.029 0.12 0.31 1 -10000 0 1
VEGFA -0.028 0.16 -10000 0 -0.63 6 6
CREBBP 0.027 0.004 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.038 -10000 0 -0.45 3 3
ELF1 0.007 0.076 -10000 0 -0.44 3 3
CCNA2 0.026 0.02 -10000 0 -0.4 1 1
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
JAK3 0.013 0.077 -10000 0 -0.4 17 17
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
JAK1 0.027 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.04 0.081 -10000 0 -0.38 2 2
SHC1 0.027 0.004 -10000 0 -10000 0 0
SP1 0.028 0.048 -10000 0 -0.37 6 6
IL2RA -0.017 0.11 -10000 0 -0.35 49 49
IL2RB 0.021 0.051 -10000 0 -0.4 7 7
SOS1 0.028 0.004 -10000 0 -10000 0 0
IL2RG 0.013 0.079 -10000 0 -0.4 17 17
G1/S transition of mitotic cell cycle 0.032 0.092 0.3 5 -0.49 7 12
PTPN11 0.028 0.002 -10000 0 -10000 0 0
CCND2 0.015 0.053 -10000 0 -0.53 4 4
LCK 0.017 0.065 -10000 0 -0.4 12 12
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL2 -0.002 0.028 -10000 0 -0.4 1 1
CDK6 0.022 0.037 -10000 0 -0.43 3 3
CCND3 0.043 0.078 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.002 0.1 -10000 0 -0.41 4 4
TC10/GTP 0.004 0.093 -10000 0 -0.39 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.058 0.039 -10000 0 -0.26 4 4
HRAS 0.025 0.02 -10000 0 -0.41 1 1
APS homodimer 0.025 0.02 -10000 0 -0.4 1 1
GRB14 -0.018 0.14 -10000 0 -0.44 45 45
FOXO3 0.02 0.093 -10000 0 -0.59 10 10
AKT1 0.019 0.1 0.35 3 -0.4 1 4
INSR 0.028 0.023 -10000 0 -0.46 1 1
Insulin Receptor/Insulin 0.051 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.006 -10000 0 -10000 0 0
SORBS1 -0.047 0.17 -10000 0 -0.45 76 76
CRK 0.026 0.006 -10000 0 -10000 0 0
PTPN1 0.009 0.026 -10000 0 -10000 0 0
CAV1 -0.005 0.064 0.18 2 -0.23 4 6
CBL/APS/CAP/Crk-II/C3G 0.021 0.11 -10000 0 -0.42 1 1
Insulin Receptor/Insulin/IRS1/NCK2 0.058 0.039 -10000 0 -0.26 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.037 -10000 0 -0.23 3 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.025 0.063 -10000 0 -0.37 6 6
RPS6KB1 0.017 0.099 0.27 6 -0.37 1 7
PARD6A 0.024 0.029 -10000 0 -0.42 2 2
CBL 0.025 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.021 0.011 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.036 0.084 -10000 0 -0.38 1 1
HRAS/GTP 0.015 0.028 -10000 0 -10000 0 0
Insulin Receptor 0.028 0.023 -10000 0 -0.45 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.067 0.042 -10000 0 -10000 0 0
PRKCI 0.018 0.038 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.001 0.07 -10000 0 -0.34 2 2
SHC1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.038 0.029 -10000 0 -10000 0 0
PI3K 0.041 0.042 -10000 0 -0.23 3 3
NCK2 0.027 0.003 -10000 0 -10000 0 0
RHOQ 0.027 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
AKT2 0.022 0.11 0.3 6 -0.4 1 7
PRKCZ 0.014 0.056 -10000 0 -0.4 3 3
SH2B2 0.025 0.02 -10000 0 -0.4 1 1
SHC/SHIP 0.027 0.035 -10000 0 -10000 0 0
F2RL2 -0.095 0.19 -10000 0 -0.4 141 141
TRIP10 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.045 0.025 -10000 0 -0.24 1 1
TC10/GTP/CIP4/Exocyst 0.036 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.071 0.032 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
RASA1 0.024 0.031 -10000 0 -0.45 2 2
NCK1 0.023 0.011 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.01 0.11 -10000 0 -0.25 74 74
TC10/GDP 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.058 0.032 -10000 0 -0.24 1 1
INPP5D 0.011 0.034 0.19 1 -0.24 4 5
SOS1 0.027 0.003 -10000 0 -10000 0 0
SGK1 -0.004 0.097 -10000 0 -0.64 11 11
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.002 -10000 0 -10000 0 0
IRS1 0.023 0.038 -10000 0 -0.45 3 3
p62DOK/RasGAP 0.038 0.029 -10000 0 -10000 0 0
INS 0.017 0.028 -10000 0 -0.39 2 2
mol:PI-3-4-P2 0.011 0.034 0.19 1 -0.24 4 5
GRB2 0.027 0.004 -10000 0 -10000 0 0
EIF4EBP1 0.01 0.096 0.33 3 -0.36 2 5
PTPRA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.036 0.007 -10000 0 -10000 0 0
PDPK1 0.026 0.022 -10000 0 -0.45 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.024 0.029 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.042 0.035 -10000 0 -0.23 6 6
Insulin Receptor/Insulin/IRS3 0.034 0.029 -10000 0 -0.3 3 3
Par3/Par6 -0.015 0.12 -10000 0 -0.3 3 3
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.021 0.049 0.41 6 -10000 0 6
PI3K Class IB/PDE3B 0.021 0.049 -10000 0 -0.41 6 6
PDE3B 0.021 0.049 -10000 0 -0.42 6 6
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.005 -9999 0 -10000 0 0
ITGB7 0.025 0.031 -9999 0 -0.45 2 2
ITGA4 0.02 0.054 -9999 0 -0.4 8 8
alpha4/beta7 Integrin 0.033 0.047 -9999 0 -0.29 10 10
alpha4/beta1 Integrin 0.033 0.041 -9999 0 -0.28 8 8
Class I PI3K signaling events

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
ARF5/GTP 0.001 0.048 -10000 0 -10000 0 0
DAPP1 0.024 0.1 0.27 13 -0.37 10 23
Src family/SYK family/BLNK-LAT/BTK-ITK 0.01 0.13 0.26 9 -0.45 12 21
mol:DAG 0.016 0.076 0.2 24 -0.22 2 26
HRAS 0.026 0.02 -10000 0 -0.39 1 1
RAP1A 0.028 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.028 0.065 -10000 0 -0.3 6 6
PLCG2 0.025 0.022 -10000 0 -0.45 1 1
PLCG1 0.026 0.006 -10000 0 -10000 0 0
ARF5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.004 0.039 0.17 1 -10000 0 1
ARF1/GTP 0.007 0.039 0.24 2 -10000 0 2
RHOA 0.024 0.009 -10000 0 -10000 0 0
YES1 0.024 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.003 0.041 0.17 1 -10000 0 1
ADAP1 -0.005 0.038 -10000 0 -10000 0 0
ARAP3 -0.004 0.038 0.17 1 -10000 0 1
INPPL1 0.024 0.01 -10000 0 -10000 0 0
PREX1 0.026 0.006 -10000 0 -10000 0 0
ARHGEF6 0.022 0.048 -10000 0 -0.45 5 5
ARHGEF7 0.026 0.005 -10000 0 -10000 0 0
ARF1 0.027 0.004 -10000 0 -10000 0 0
NRAS 0.028 0.007 -10000 0 -10000 0 0
FYN 0.026 0.02 -10000 0 -0.4 1 1
ARF6 0.026 0.007 -10000 0 -10000 0 0
FGR 0.026 0.02 -10000 0 -0.4 1 1
mol:Ca2+ 0.012 0.047 0.18 8 -10000 0 8
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.021 0.053 -10000 0 -0.45 6 6
ZAP70 0.005 0.095 -10000 0 -0.4 25 25
mol:IP3 0.011 0.058 0.19 15 -10000 0 15
LYN 0.024 0.021 -10000 0 -0.4 1 1
ARF1/GDP 0.029 0.067 -10000 0 -0.3 6 6
RhoA/GDP 0.039 0.046 0.24 4 -10000 0 4
PDK1/Src/Hsp90 0.048 0.024 -10000 0 -0.28 1 1
BLNK -0.017 0.14 -10000 0 -0.45 45 45
actin cytoskeleton reorganization 0.024 0.071 0.24 9 -0.39 1 10
SRC 0.026 0.007 -10000 0 -10000 0 0
PLEKHA2 -0.005 0.012 -10000 0 -0.27 1 1
RAC1 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.024 0.012 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.006 0.036 -10000 0 -10000 0 0
RhoA/GTP -0.004 0.039 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.005 0.1 -10000 0 -0.34 19 19
BLK -0.036 0.15 -10000 0 -0.4 67 67
PDPK1 0.026 0.022 -10000 0 -0.45 1 1
CYTH1 -0.004 0.038 -10000 0 -10000 0 0
HCK 0.023 0.03 -10000 0 -0.42 2 2
CYTH3 -0.004 0.036 -10000 0 -10000 0 0
CYTH2 -0.005 0.036 -10000 0 -10000 0 0
KRAS 0.027 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.017 0.045 -10000 0 -0.44 1 1
SGK1 0.018 0.055 -10000 0 -0.48 1 1
INPP5D 0.024 0.031 -10000 0 -0.45 2 2
mol:GDP 0.015 0.065 -10000 0 -0.32 6 6
SOS1 0.027 0.003 -10000 0 -10000 0 0
SYK 0.024 0.038 -10000 0 -0.45 3 3
ARF6/GDP 0.024 0.043 0.23 4 -10000 0 4
mol:PI-3-4-5-P3 -0.005 0.034 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP -0.003 0.041 0.17 1 -10000 0 1
VAV1 0.019 0.06 -10000 0 -0.45 8 8
mol:PI-3-4-P2 0.012 0.016 -10000 0 -0.32 1 1
RAS family/GTP/PI3K Class I 0.042 0.034 -10000 0 -10000 0 0
PLEKHA1 -0.006 0.012 -10000 0 -0.27 1 1
Rac1/GDP 0.027 0.064 -10000 0 -0.3 6 6
LAT 0.015 0.07 -10000 0 -0.4 14 14
Rac1/GTP 0.02 0.061 0.19 1 -0.29 7 8
ITK -0.011 0.046 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.015 0.093 0.23 22 -0.29 5 27
LCK 0.017 0.065 -10000 0 -0.4 12 12
BTK -0.005 0.04 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.18 0.24 -10000 0 -0.45 211 211
CLTC 0.023 0.064 -10000 0 -0.35 10 10
calcium ion-dependent exocytosis 0.013 0.029 -10000 0 -10000 0 0
Dynamin 2/GTP 0.026 0.013 -10000 0 -0.21 1 1
EXOC4 0.026 0.007 -10000 0 -10000 0 0
CD59 0.014 0.031 -10000 0 -0.32 2 2
CPE 0.011 0.027 -10000 0 -0.23 6 6
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
membrane fusion 0.014 0.025 -10000 0 -10000 0 0
CTNND1 0.018 0.034 0.18 18 -10000 0 18
DNM2 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.051 0.21 8 -0.4 2 10
TSHR 0.004 0.04 -10000 0 -0.23 13 13
INS 0.004 0.089 -10000 0 -0.46 16 16
BIN1 0.02 0.055 -10000 0 -0.41 8 8
mol:Choline 0.014 0.025 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.012 -10000 0 -0.23 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.013 -10000 0 -0.21 1 1
JUP 0.013 0.031 -10000 0 -0.32 2 2
ASAP2/amphiphysin II 0.044 0.037 -10000 0 -0.22 8 8
ARF6/GTP 0.019 0.005 -10000 0 -10000 0 0
CDH1 0.014 0.03 -10000 0 -0.32 1 1
clathrin-independent pinocytosis 0.019 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.027 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.005 -10000 0 -10000 0 0
EXOC2 0.026 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.022 0.03 -10000 0 -0.29 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.027 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.035 0.051 0.35 3 -10000 0 3
positive regulation of phagocytosis 0.014 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.034 0.01 -10000 0 -10000 0 0
ACAP1 0.017 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.012 0.023 -10000 0 -0.32 1 1
clathrin heavy chain/ACAP1 0.027 0.056 -10000 0 -0.4 4 4
JIP4/KLC1 0.048 0.015 -10000 0 -10000 0 0
EXOC1 0.027 0.005 -10000 0 -10000 0 0
exocyst 0.022 0.03 -10000 0 -0.29 3 3
RALA/GTP 0.019 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.009 -10000 0 -10000 0 0
receptor recycling 0.019 0.005 -10000 0 -10000 0 0
CTNNA1 0.019 0.035 0.18 20 -10000 0 20
NME1 0.014 0.012 -10000 0 -0.23 1 1
clathrin coat assembly 0.026 0.065 -10000 0 -0.34 10 10
IL2RA 0.004 0.039 -10000 0 -0.32 2 2
VAMP3 0.014 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.057 0.11 -10000 0 -0.33 9 9
EXOC6 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.009 0.022 -10000 0 -0.25 3 3
PLD2 0.014 0.006 -10000 0 -10000 0 0
EXOC5 0.026 0.006 -10000 0 -10000 0 0
PIP5K1C 0.015 0.026 -10000 0 -10000 0 0
SDC1 0.013 0.029 -10000 0 -0.32 2 2
ARF6/GDP 0.024 0.013 -10000 0 -0.23 1 1
EXOC7 0.027 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.037 0.053 -10000 0 -0.36 3 3
mol:Phosphatidic acid 0.014 0.025 -10000 0 -10000 0 0
endocytosis -0.043 0.036 0.22 8 -10000 0 8
SCAMP2 0.027 0.005 -10000 0 -10000 0 0
ADRB2 0.009 0.079 0.27 1 -0.39 6 7
EXOC3 0.024 0.009 -10000 0 -10000 0 0
ASAP2 0.027 0.003 -10000 0 -10000 0 0
Dynamin 2/GDP 0.029 0.014 -10000 0 -0.21 1 1
KLC1 0.026 0.007 -10000 0 -10000 0 0
AVPR2 0.019 0.09 0.24 14 -0.36 8 22
RALA 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.052 -10000 0 -0.37 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.036 0.073 0.22 3 -0.36 2 5
adherens junction organization 0.012 0.094 0.22 1 -0.36 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.083 0.27 3 -0.43 2 5
FMN1 0.007 0.098 -10000 0 -0.37 13 13
mol:IP3 0.011 0.044 -10000 0 -0.35 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.023 0.085 -10000 0 -0.34 13 13
CTNNB1 0.025 0.009 -10000 0 -10000 0 0
AKT1 0.011 0.049 0.19 1 -0.39 2 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.16 -10000 0 -0.67 18 18
CTNND1 0.03 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.078 -10000 0 -0.33 11 11
VASP 0.02 0.078 -10000 0 -0.34 11 11
ZYX 0.022 0.074 -10000 0 -0.33 10 10
JUB 0.02 0.08 -10000 0 -0.32 13 13
EGFR(dimer) 0.025 0.09 -10000 0 -0.34 13 13
E-cadherin/beta catenin-gamma catenin 0.041 0.043 -10000 0 -0.36 4 4
mol:PI-3-4-5-P3 0.022 0.06 0.21 1 -0.41 2 3
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.022 0.061 0.22 1 -0.42 2 3
FYN 0.025 0.073 0.23 6 -0.47 1 7
mol:Ca2+ 0.011 0.043 -10000 0 -0.34 2 2
JUP 0.027 0.03 -10000 0 -0.44 2 2
PIK3R1 0.026 0.038 -10000 0 -0.45 3 3
mol:DAG 0.011 0.043 -10000 0 -0.35 2 2
CDH1 0.022 0.048 -10000 0 -0.44 5 5
RhoA/GDP 0.061 0.08 0.26 4 -0.42 2 6
establishment of polarity of embryonic epithelium 0.02 0.077 -10000 0 -0.33 11 11
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.009 -10000 0 -10000 0 0
EGFR 0.019 0.049 -10000 0 -0.45 5 5
CASR 0.024 0.063 0.22 4 -0.33 2 6
RhoA/GTP 0.048 0.065 -10000 0 -0.31 2 2
AKT2 0.011 0.05 0.19 1 -0.39 2 3
actin cable formation 0.004 0.098 0.2 4 -0.39 10 14
apoptosis -0.042 0.08 0.33 4 -0.23 9 13
CTNNA1 0.029 0.007 -10000 0 -10000 0 0
mol:GDP 0.033 0.076 -10000 0 -0.46 2 2
PIP5K1A 0.019 0.08 -10000 0 -0.34 11 11
PLCG1 0.011 0.044 -10000 0 -0.36 2 2
Rac1/GTP 0.032 0.085 -10000 0 -0.41 5 5
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
S1P4 pathway

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.022 0.04 -9999 0 -0.41 4 4
CDC42/GTP 0.013 0.074 -9999 0 -0.32 7 7
PLCG1 0.007 0.06 -9999 0 -0.32 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.024 0.009 -9999 0 -10000 0 0
GNAI3 0.027 0.004 -9999 0 -10000 0 0
G12/G13 0.037 0.012 -9999 0 -10000 0 0
cell migration 0.012 0.072 -9999 0 -0.32 7 7
S1PR5 0.023 0.041 -9999 0 -0.42 4 4
S1PR4 0.002 0.1 -9999 0 -0.4 29 29
MAPK3 0.007 0.06 -9999 0 -0.33 7 7
MAPK1 0.005 0.056 -9999 0 -0.3 7 7
S1P/S1P5/Gi 0.019 0.053 -9999 0 -0.27 8 8
GNAI1 0.025 0.022 -9999 0 -0.45 1 1
CDC42/GDP 0.02 0.004 -9999 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 -9999 0 -0.25 4 4
RHOA 0.012 0.064 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.012 0.064 -9999 0 -0.33 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.083 -9999 0 -0.42 18 18
S1P/S1P4/G12/G13 0.033 0.061 -9999 0 -0.21 27 27
GNA12 0.025 0.007 -9999 0 -10000 0 0
GNA13 0.027 0.003 -9999 0 -10000 0 0
CDC42 0.027 0.005 -9999 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.016 0.041 -10000 0 -0.41 4 4
positive regulation of NF-kappaB transcription factor activity 0.018 0.053 -10000 0 -0.28 13 13
MAP2K4 0.029 0.05 0.2 3 -0.41 1 4
IKBKB 0.025 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.025 0.007 -10000 0 -10000 0 0
TNFRSF10A 0.024 0.023 -10000 0 -0.45 1 1
SMPD1 0.009 0.015 -10000 0 -0.18 1 1
IKBKG 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.012 0.074 -10000 0 -0.4 15 15
TRAIL/TRAILR2 0.024 0.034 -10000 0 -0.29 4 4
TRAIL/TRAILR3 0.018 0.054 -10000 0 -0.29 13 13
TRAIL/TRAILR1 0.024 0.034 -10000 0 -0.29 4 4
TRAIL/TRAILR4 0.019 0.053 -10000 0 -0.28 13 13
TRAIL/TRAILR1/DAP3/GTP 0.032 0.034 -10000 0 -0.22 4 4
IKK complex 0.013 0.027 -10000 0 -10000 0 0
RIPK1 0.026 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.003 -10000 0 -10000 0 0
MAPK3 0.008 0.028 -10000 0 -0.29 4 4
MAP3K1 0.031 0.052 -10000 0 -0.43 1 1
TRAILR4 (trimer) 0.012 0.074 -10000 0 -0.4 15 15
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.024 0.023 -10000 0 -0.45 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.031 -10000 0 -0.36 1 1
CFLAR 0.026 0.005 -10000 0 -10000 0 0
MAPK1 0.008 0.028 -10000 0 -0.29 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.036 0.046 -10000 0 -0.24 1 1
mol:ceramide 0.009 0.015 -10000 0 -0.18 1 1
FADD 0.019 0.012 -10000 0 -10000 0 0
MAPK8 0.052 0.065 0.24 6 -0.4 1 7
TRAF2 0.021 0.047 -10000 0 -0.4 6 6
TRAILR3 (trimer) 0.012 0.074 -10000 0 -0.4 15 15
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.025 0.037 -10000 0 -0.24 4 4
DAP3 0.027 0.004 -10000 0 -10000 0 0
CASP10 0.07 0.096 0.33 26 -0.29 1 27
JNK cascade 0.018 0.053 -10000 0 -0.28 13 13
TRAIL (trimer) 0.016 0.04 -10000 0 -0.41 4 4
TNFRSF10C 0.012 0.074 -10000 0 -0.4 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD 0.03 0.039 -10000 0 -0.21 4 4
TRAIL/TRAILR2/FADD 0.025 0.037 -10000 0 -0.24 4 4
cell death 0.009 0.015 -10000 0 -0.18 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.012 0.031 -10000 0 -0.36 1 1
TRAILR2 (trimer) 0.025 0.007 -10000 0 -10000 0 0
CASP8 0.003 0.07 -10000 0 -0.48 8 8
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.036 0.046 -10000 0 -0.24 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.025 0.008 -10000 0 -10000 0 0
NFATC1 0.025 0.093 0.25 6 -0.38 6 12
NFATC2 0.008 0.082 0.21 4 -0.31 15 19
NFATC3 0.02 0.018 -10000 0 -0.34 1 1
YWHAE 0.026 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0 0.076 0.24 2 -0.33 8 10
Exportin 1/Ran/NUP214 0.053 0.013 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.013 0.088 -10000 0 -0.33 7 7
BCL2/BAX 0.034 0.032 -10000 0 -0.29 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.026 0.006 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.01 0.077 0.26 1 -0.33 7 8
Calcineurin A alpha-beta B1/BCL2 0.021 0.04 -10000 0 -0.41 4 4
FKBP8 0.027 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.01 0.077 0.32 7 -0.25 1 8
KPNB1 0.027 0.002 -10000 0 -10000 0 0
KPNA2 0.027 0.003 -10000 0 -10000 0 0
XPO1 0.027 0.004 -10000 0 -10000 0 0
SFN 0.022 0.045 -10000 0 -0.42 5 5
MAP3K8 0.024 0.038 -10000 0 -0.45 3 3
NFAT4/CK1 alpha 0.029 0.021 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.046 0.095 0.25 1 -0.4 6 7
CABIN1 -0.001 0.077 0.24 2 -0.33 8 10
CALM1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
MAP3K1 0.026 0.006 -10000 0 -10000 0 0
CAMK4 0.002 0.098 -10000 0 -0.4 27 27
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.027 0.004 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.022 0.07 -10000 0 -0.28 25 25
YWHAB 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.053 -10000 0 -0.45 6 6
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
FKBP1A 0.026 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.034 0.098 0.26 4 -0.4 4 8
PRKCH 0.026 0.007 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.037 0.026 -10000 0 -0.31 2 2
CASP3 0.026 0.006 -10000 0 -10000 0 0
PIM1 0.025 0.022 -10000 0 -0.45 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.005 -10000 0 -10000 0 0
apoptosis 0.018 0.012 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.039 -10000 0 -0.28 2 2
PRKCB 0.02 0.054 -10000 0 -0.4 8 8
PRKCE 0.026 0.022 -10000 0 -0.45 1 1
JNK2/NFAT4 0.029 0.04 -10000 0 -0.32 1 1
BAD/BCL-XL 0.036 0.013 -10000 0 -10000 0 0
PRKCD 0.024 0.009 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.45 1 1
PRKCA 0.025 0.029 -10000 0 -0.42 2 2
PRKCG -0.031 0.13 -10000 0 -0.4 54 54
PRKCQ 0.016 0.07 -10000 0 -0.44 11 11
FKBP38/BCL2 0.034 0.031 -10000 0 -0.28 4 4
EP300 0.024 0.031 -10000 0 -0.45 2 2
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.036 0.096 0.25 5 -0.37 5 10
CaM/Ca2+/FKBP38 0.034 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.005 -10000 0 -10000 0 0
CSNK1A1 0.014 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.019 0.061 -10000 0 -0.23 26 26
NFATc/ERK1 0.037 0.094 0.25 6 -0.38 4 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.012 0.088 -10000 0 -0.33 7 7
NR4A1 0.019 0.1 0.25 4 -0.45 12 16
GSK3B 0.024 0.009 -10000 0 -10000 0 0
positive T cell selection 0.02 0.018 -10000 0 -0.34 1 1
NFAT1/CK1 alpha 0.009 0.059 0.16 1 -0.29 7 8
RCH1/ KPNB1 0.04 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
PRKACA 0.027 0.004 -10000 0 -10000 0 0
AKAP5 0.004 0.093 -10000 0 -0.4 25 25
MEF2D 0.027 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.024 0.009 -10000 0 -10000 0 0
NFATc/p38 alpha 0.037 0.093 0.25 6 -0.37 4 10
CREBBP 0.026 0.007 -10000 0 -10000 0 0
BCL2 0.021 0.04 -10000 0 -0.41 4 4
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.024 0.068 -10000 0 -0.3 21 21
AKT1 0.06 0.087 0.34 8 -0.51 1 9
PTK2B 0.017 0.069 -10000 0 -0.72 1 1
VEGFR2 homodimer/Frs2 0.033 0.036 -10000 0 -0.46 2 2
CAV1 -0.007 0.11 -10000 0 -0.4 38 38
CALM1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.046 0.043 -10000 0 -0.58 1 1
endothelial cell proliferation 0.057 0.1 0.34 20 -0.46 1 21
mol:Ca2+ 0.024 0.045 -10000 0 -0.44 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.056 0.046 -10000 0 -0.56 1 1
RP11-342D11.1 0.013 0.043 -10000 0 -0.44 2 2
CDH5 0.024 0.029 -10000 0 -0.42 2 2
VEGFA homodimer 0.054 0.041 -10000 0 -0.25 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 0.02 0.053 -10000 0 -0.42 7 7
HRAS/GDP 0.043 0.041 -10000 0 -0.48 1 1
SH2D2A -0.039 0.15 -10000 0 -0.4 77 77
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.051 0.1 0.36 2 -0.44 5 7
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.008 0.1 -10000 0 -0.51 3 3
VEGFR1 homodimer 0.025 0.02 -10000 0 -0.4 1 1
SHC/GRB2/SOS1 0.07 0.05 -10000 0 -0.52 1 1
GRB10 0.024 0.043 -10000 0 -0.53 1 1
PTPN11 0.027 0.002 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
PAK1 0.025 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.064 0.055 -10000 0 -0.54 1 1
HRAS 0.025 0.02 -10000 0 -0.41 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.017 0.053 -10000 0 -0.35 4 4
HIF1A 0.025 0.023 -10000 0 -0.45 1 1
FRS2 0.026 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.054 0.045 -10000 0 -0.55 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.02 0.051 -10000 0 -0.4 7 7
Nck/Pak 0.031 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.046 0.045 -10000 0 -0.58 1 1
mol:GDP 0.056 0.045 -10000 0 -0.5 1 1
mol:NADP 0.036 0.1 0.31 4 -0.4 8 12
eNOS/Hsp90 0.043 0.095 0.28 2 -0.39 5 7
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
mol:IP3 0.024 0.046 -10000 0 -0.44 2 2
HIF1A/ARNT 0.037 0.02 -10000 0 -0.32 1 1
SHB 0.024 0.009 -10000 0 -10000 0 0
VEGFA 0.023 0.043 -10000 0 -0.39 5 5
VEGFC -0.03 0.14 -10000 0 -0.4 65 65
FAK1/Vinculin 0.045 0.085 0.3 1 -0.7 1 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.072 -10000 0 -0.76 1 1
PTPN6 0.026 0.006 -10000 0 -10000 0 0
EPAS1 0.034 0.02 -10000 0 -0.33 1 1
mol:L-citrulline 0.036 0.1 0.31 4 -0.4 8 12
ITGAV 0.024 0.027 -10000 0 -0.4 2 2
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.058 0.045 -10000 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer 0.05 0.047 -10000 0 -0.47 2 2
VEGFR2/3 heterodimer 0.029 0.05 -10000 0 -0.56 2 2
VEGFB 0.026 0.005 -10000 0 -10000 0 0
MAPK11 0.013 0.054 0.25 8 -0.55 1 9
VEGFR2 homodimer 0.021 0.038 -10000 0 -0.53 2 2
FLT1 0.025 0.02 -10000 0 -0.4 1 1
NEDD4 0.028 0.007 -10000 0 -10000 0 0
MAPK3 0.011 0.057 0.3 2 -0.41 2 4
MAPK1 0.012 0.058 0.29 4 -0.49 1 5
VEGFA145/NRP2 0.035 0.036 -10000 0 -0.27 6 6
VEGFR1/2 heterodimer 0.033 0.037 -10000 0 -0.46 2 2
KDR 0.021 0.038 -10000 0 -0.53 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.05 0.046 -10000 0 -0.43 2 2
SRC 0.026 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.02 0.064 0.3 4 -0.5 1 5
PI3K 0.032 0.05 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.04 0.044 -10000 0 -0.58 1 1
FES 0.025 0.046 -10000 0 -0.45 2 2
GAB1 0.034 0.052 -10000 0 -0.59 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.045 -10000 0 -0.58 1 1
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
SOS1 0.027 0.003 -10000 0 -10000 0 0
ARNT 0.027 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.033 0.11 0.33 2 -0.38 6 8
VEGFR2 homodimer/VEGFA homodimer/Yes 0.043 0.044 -10000 0 -0.58 1 1
PI3K/GAB1 0.057 0.081 0.28 4 -0.53 1 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.056 0.053 -10000 0 -0.54 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.009 0.098 -10000 0 -0.61 2 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.025 0.046 -10000 0 -0.45 2 2
actin cytoskeleton reorganization 0.007 0.1 -10000 0 -0.51 3 3
PTK2 0.022 0.061 0.3 1 -0.76 1 2
EDG1 0.013 0.043 -10000 0 -0.44 2 2
mol:DAG 0.024 0.046 -10000 0 -0.44 2 2
CaM/Ca2+ 0.037 0.049 -10000 0 -0.41 2 2
MAP2K3 0.009 0.048 -10000 0 -0.52 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.058 0.058 -10000 0 -0.55 1 1
PLCG1 0.024 0.046 -10000 0 -0.45 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.051 0.049 -10000 0 -0.56 1 1
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.024 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.047 0.043 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.045 0.043 -10000 0 -0.58 1 1
cell migration 0.053 0.087 0.31 8 -0.6 1 9
mol:PI-3-4-5-P3 0.032 0.048 -10000 0 -0.53 1 1
FYN 0.026 0.02 -10000 0 -0.4 1 1
VEGFB/NRP1 0.028 0.043 -10000 0 -0.42 2 2
mol:NO 0.036 0.1 0.31 4 -0.4 8 12
PXN 0.027 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.024 0.035 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.04 0.042 -10000 0 -0.55 1 1
VHL 0.024 0.009 -10000 0 -10000 0 0
ITGB3 0.01 0.086 -10000 0 -0.42 19 19
NOS3 0.036 0.11 0.32 4 -0.45 8 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.044 0.053 -10000 0 -0.48 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.017 0.051 -10000 0 -0.42 2 2
PRKCB 0.014 0.055 -10000 0 -0.42 2 2
VCL 0.027 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.032 0.045 -10000 0 -0.44 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.046 -10000 0 -0.58 1 1
VEGFA165/NRP2 0.035 0.036 -10000 0 -0.27 6 6
MAPKKK cascade 0.036 0.046 -10000 0 -0.48 1 1
NRP2 0.025 0.027 -10000 0 -0.4 2 2
VEGFC homodimer -0.03 0.14 -10000 0 -0.4 65 65
NCK1 0.023 0.011 -10000 0 -10000 0 0
ROCK1 0.026 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.044 0.086 0.3 1 -0.7 1 2
MAP3K13 0.013 0.046 -10000 0 -0.55 1 1
PDPK1 0.022 0.045 -10000 0 -0.48 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.001 0.08 -10000 0 -0.33 16 16
KLHL20 0.026 0.068 0.19 8 -0.25 7 15
CYFIP2 0.024 0.029 -10000 0 -0.42 2 2
Rac1/GDP 0.025 0.075 0.33 5 -0.3 1 6
ENAH -0.005 0.1 -10000 0 -0.36 18 18
AP1M1 0.027 0.003 -10000 0 -10000 0 0
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
CDC42/GTP 0.021 0.034 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.03 -10000 0 -0.17 7 7
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.041 -10000 0 -0.25 5 5
RAPGEF1 0.002 0.093 0.29 2 -0.38 5 7
CTNND1 0.027 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.1 -10000 0 -0.34 23 23
CRK 0.007 0.091 -10000 0 -0.38 7 7
E-cadherin/gamma catenin/alpha catenin 0.046 0.047 -10000 0 -0.37 5 5
alphaE/beta7 Integrin 0.037 0.025 -10000 0 -0.32 2 2
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.016 -10000 0 -10000 0 0
DLG1 0.002 0.077 -10000 0 -0.35 11 11
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.002 0.018 -10000 0 -10000 0 0
MLLT4 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.044 0.036 -10000 0 -0.24 6 6
PI3K 0.006 0.024 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.034 0.05 -10000 0 -0.43 5 5
TIAM1 0.021 0.053 -10000 0 -0.45 6 6
E-cadherin(dimer)/Ca2+ 0.052 0.036 -10000 0 -0.23 4 4
AKT1 0.012 0.029 0.14 1 -10000 0 1
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
CDH1 0.021 0.048 -10000 0 -0.45 5 5
RhoA/GDP 0.033 0.071 0.33 6 -10000 0 6
actin cytoskeleton organization 0.023 0.053 0.14 17 -0.19 6 23
CDC42/GDP 0.029 0.078 0.33 6 -10000 0 6
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.017 0.034 -10000 0 -0.33 4 4
ITGB7 0.025 0.031 -10000 0 -0.45 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.057 0.038 -10000 0 -0.24 4 4
E-cadherin/Ca2+/beta catenin/alpha catenin 0.039 0.032 -10000 0 -0.22 5 5
mol:GDP 0.015 0.083 0.34 6 -0.33 1 7
CDC42/GTP/IQGAP1 0.035 0.008 -10000 0 -10000 0 0
JUP 0.025 0.031 -10000 0 -0.45 2 2
p120 catenin/RhoA/GDP 0.035 0.073 0.34 4 -10000 0 4
RAC1/GTP/IQGAP1 0.034 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.039 0.008 -10000 0 -10000 0 0
RHOA 0.024 0.009 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.036 0.12 4 -0.17 6 10
NME1 0.026 0.019 -10000 0 -0.4 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.003 0.096 -10000 0 -0.35 17 17
regulation of cell-cell adhesion 0.013 0.028 -10000 0 -10000 0 0
WASF2 0.014 0.027 -10000 0 -10000 0 0
Rap1/GTP 0.03 0.048 0.24 1 -10000 0 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.068 0.049 -10000 0 -0.45 2 2
CCND1 0.013 0.043 0.14 3 -0.21 6 9
VAV2 0.005 0.11 -10000 0 -0.54 4 4
RAP1/GDP 0.037 0.065 0.32 5 -10000 0 5
adherens junction assembly -0.002 0.094 -10000 0 -0.33 21 21
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.027 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.05 0.046 -10000 0 -0.43 2 2
E-cadherin/beta catenin 0.009 0.035 -10000 0 -0.33 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.004 0.097 -10000 0 -0.34 22 22
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
Rac1/GTP -0.02 0.071 -10000 0 -0.39 10 10
E-cadherin/beta catenin/alpha catenin 0.044 0.037 -10000 0 -0.26 5 5
ITGAE 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.1 -10000 0 -0.35 23 23
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 0.028 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.059 0.081 0.23 22 -0.35 4 26
ERC1 0.025 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.031 0.037 -10000 0 -0.31 5 5
NFKBIA 0.023 0.042 -10000 0 -10000 0 0
BIRC2 0.024 0.01 -10000 0 -10000 0 0
IKBKB 0.025 0.008 -10000 0 -10000 0 0
RIPK2 0.024 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.028 -10000 0 -10000 0 0
IKK complex/A20 0.048 0.094 0.27 1 -0.4 9 10
NEMO/A20/RIP2 0.024 0.009 -10000 0 -10000 0 0
XPO1 0.027 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.042 0.087 0.26 1 -0.37 15 16
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.043 0.08 -10000 0 -0.39 9 9
BCL10/MALT1/TRAF6 0.048 0.019 -10000 0 -10000 0 0
NOD2 0.021 0.046 -10000 0 -0.43 5 5
NFKB1 0.029 0.009 -10000 0 -10000 0 0
RELA 0.028 0.01 -10000 0 -10000 0 0
MALT1 0.025 0.008 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.035 0.015 -10000 0 -10000 0 0
ATM 0.025 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.022 0.067 -10000 0 -0.28 22 22
TRAF6 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.025 0.029 -10000 0 -0.42 2 2
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF 0.007 0.088 -10000 0 -0.4 22 22
NF kappa B1 p50/RelA 0.056 0.029 -10000 0 -0.38 1 1
BCL10 0.027 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.042 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.01 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
IKK complex 0.052 0.092 0.26 2 -0.41 10 12
CYLD 0.026 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.059 0.094 0.27 1 -0.4 11 12
Aurora A signaling

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
Aurora A/GADD45A 0.025 0.028 -10000 0 -0.22 1 1
BIRC5 0.008 0.087 -10000 0 -0.4 22 22
NFKBIA 0.012 0.039 0.25 11 -10000 0 11
CPEB1 -0.035 0.15 -10000 0 -0.44 62 62
AKT1 0.012 0.041 0.25 12 -10000 0 12
NDEL1 0.026 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 0.023 0.024 -10000 0 -10000 0 0
NDEL1/TACC3 0.046 0.034 -10000 0 -10000 0 0
GADD45A 0.026 0.019 -10000 0 -0.4 1 1
GSK3B 0.023 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.024 0.026 -10000 0 -10000 0 0
MDM2 0.026 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.013 0.004 -10000 0 -10000 0 0
TP53 0.017 0.024 -10000 0 -0.29 2 2
DLG7 0.008 0.016 -10000 0 -10000 0 0
AURKAIP1 0.025 0.027 -10000 0 -0.4 2 2
ARHGEF7 0.026 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.049 0.035 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.022 0.024 -10000 0 -10000 0 0
AURKA 0.014 0.02 -10000 0 -10000 0 0
AURKB 0.012 0.017 -10000 0 -0.15 2 2
CDC25B 0.01 0.029 -10000 0 -0.24 1 1
G2/M transition checkpoint 0.007 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.007 0.085 -10000 0 -0.25 44 44
Aurora A/CPEB -0.007 0.085 -10000 0 -0.25 44 44
Aurora A/TACC1/TRAP/chTOG 0.055 0.043 -10000 0 -10000 0 0
BRCA1 0.027 0.003 -10000 0 -10000 0 0
centrosome duplication 0.024 0.026 -10000 0 -10000 0 0
regulation of centrosome cycle 0.044 0.033 -10000 0 -10000 0 0
spindle assembly 0.054 0.042 -10000 0 -10000 0 0
TDRD7 0.027 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.048 0.064 -10000 0 -0.29 5 5
CENPA 0.014 0.021 -10000 0 -0.19 3 3
Aurora A/PP2A 0.025 0.026 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.013 0.025 -10000 0 -10000 0 0
negative regulation of DNA binding 0.017 0.024 -10000 0 -0.29 2 2
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.039 0.008 -10000 0 -10000 0 0
RASA1 0.024 0.031 -10000 0 -0.45 2 2
Ajuba/Aurora A 0.007 0.018 -10000 0 -10000 0 0
mitotic prometaphase 0 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.02 -10000 0 -10000 0 0
TACC1 0.023 0.031 -10000 0 -0.45 2 2
TACC3 0.025 0.02 -10000 0 -0.4 1 1
Aurora A/Antizyme1 0.049 0.035 -10000 0 -10000 0 0
Aurora A/RasGAP 0.024 0.031 -10000 0 -0.26 2 2
OAZ1 0.027 0.005 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.004 -10000 0 -10000 0 0
GIT1 0.027 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.049 0.019 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.013 0.004 -10000 0 -10000 0 0
PPP2R5D 0.026 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.017 0.019 -10000 0 -10000 0 0
PAK1 0.025 0.008 -10000 0 -10000 0 0
CKAP5 0.026 0.005 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.027 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.041 0.046 -9999 0 -0.23 11 11
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.012 0.013 -9999 0 -10000 0 0
AURKB 0.019 0.054 -9999 0 -0.4 8 8
AURKC 0.021 0.049 -9999 0 -0.42 6 6
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.05 0.14 0.26 3 -0.35 22 25
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.007 -10000 0 -10000 0 0
AKT2 0.026 0.005 -10000 0 -10000 0 0
STXBP4 0.027 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.062 0.14 0.26 8 -0.37 27 35
YWHAZ 0.024 0.009 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
TBC1D4 0.013 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
YWHAB 0.026 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.052 0.014 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
ASIP 0.002 0.064 -10000 0 -0.4 11 11
PRKCI 0.02 0.012 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.003 -10000 0 -10000 0 0
GYS1 0.012 0.012 0.24 1 -10000 0 1
PRKCZ 0.025 0.022 -10000 0 -0.45 1 1
TRIP10 0.027 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.007 -10000 0 -10000 0 0
AS160/14-3-3 0.03 0.041 -10000 0 -0.3 1 1
VAMP2 0.026 0.006 -10000 0 -10000 0 0
SLC2A4 -0.069 0.15 0.28 6 -0.4 28 34
STX4 0.027 0.004 -10000 0 -10000 0 0
GSK3B 0.019 0.009 -10000 0 -10000 0 0
SFN 0.022 0.045 -10000 0 -0.42 5 5
LNPEP 0.024 0.031 -10000 0 -0.45 2 2
YWHAE 0.026 0.006 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.022 0.06 0.26 6 -10000 0 6
GNAI2 0.024 0.009 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 -10000 0 -0.25 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.04 -10000 0 -0.41 4 4
RhoA/GTP 0.023 0.062 -10000 0 -0.26 6 6
negative regulation of cAMP metabolic process 0.019 0.052 -10000 0 -0.27 8 8
GNAZ 0.01 0.083 -10000 0 -0.42 18 18
GNAI3 0.027 0.004 -10000 0 -10000 0 0
GNA12 0.025 0.007 -10000 0 -10000 0 0
S1PR5 0.023 0.041 -10000 0 -0.42 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.019 0.053 -10000 0 -0.27 8 8
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.009 -10000 0 -10000 0 0
GNAI1 0.025 0.022 -10000 0 -0.45 1 1
FoxO family signaling

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.008 0.044 -10000 0 -10000 0 0
PLK1 0.041 0.12 -10000 0 -0.82 2 2
CDKN1B 0.081 0.098 0.31 8 -0.41 1 9
FOXO3 0.056 0.11 -10000 0 -0.67 4 4
KAT2B 0.013 0.092 -10000 0 -0.45 18 18
FOXO1/SIRT1 0.029 0.043 -10000 0 -10000 0 0
CAT 0.046 0.13 -10000 0 -0.91 3 3
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
AKT1 0.033 0.016 -10000 0 -10000 0 0
FOXO1 0.016 0.045 0.23 2 -10000 0 2
MAPK10 0.024 0.069 0.2 27 -0.22 24 51
mol:GTP 0.002 0 -10000 0 -10000 0 0
FOXO4 0.054 0.065 0.3 5 -0.39 1 6
response to oxidative stress 0.01 0.009 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.057 0.11 -10000 0 -0.77 3 3
XPO1 0.027 0.004 -10000 0 -10000 0 0
EP300 0.026 0.031 -10000 0 -0.45 2 2
BCL2L11 0.035 0.024 -10000 0 -10000 0 0
FOXO1/SKP2 0.025 0.041 -10000 0 -10000 0 0
mol:GDP 0.01 0.009 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
GADD45A 0.067 0.11 -10000 0 -0.57 8 8
YWHAQ 0.027 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.038 0.096 -10000 0 -0.45 7 7
MST1 0.026 0.046 -10000 0 -0.4 5 5
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.034 0.077 0.23 1 -0.38 7 8
YWHAB 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.035 0.049 0.2 28 -0.22 5 33
MAPK9 0.035 0.042 0.2 27 -10000 0 27
YWHAG 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.006 -10000 0 -10000 0 0
YWHAZ 0.024 0.009 -10000 0 -10000 0 0
SIRT1 0.026 0.024 -10000 0 -0.45 1 1
SOD2 0.071 0.092 -10000 0 -0.56 1 1
RBL2 0.04 0.17 -10000 0 -0.69 18 18
RAL/GDP 0.044 0.014 -10000 0 -10000 0 0
CHUK 0.033 0.015 -10000 0 -10000 0 0
Ran/GTP 0.023 0.003 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
RAL/GTP 0.048 0.014 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.019 0.23 -10000 0 -1.3 13 13
SKP2 0.024 0.009 -10000 0 -10000 0 0
USP7 0.028 0.004 -10000 0 -10000 0 0
IKBKB 0.031 0.016 -10000 0 -10000 0 0
CCNB1 0.043 0.11 -10000 0 -0.76 2 2
FOXO1-3a-4/beta catenin 0.086 0.092 0.33 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.041 -10000 0 -10000 0 0
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
SGK1 0.031 0.032 -10000 0 -0.42 2 2
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.041 0.007 -10000 0 -10000 0 0
ZFAND5 0.052 0.066 0.39 2 -10000 0 2
SFN 0.022 0.045 -10000 0 -0.42 5 5
CDK2 0.027 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.037 0.081 -10000 0 -0.38 6 6
CREBBP 0.027 0.007 -10000 0 -10000 0 0
FBXO32 0.069 0.16 0.45 2 -1.1 3 5
BCL6 0.054 0.093 -10000 0 -10000 0 0
RALB 0.028 0.004 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.043 0.047 -9999 0 -0.36 5 5
E-cadherin/beta catenin 0.031 0.038 -9999 0 -0.31 5 5
CTNNB1 0.024 0.009 -9999 0 -10000 0 0
JUP 0.025 0.031 -9999 0 -0.45 2 2
CDH1 0.021 0.048 -9999 0 -0.45 5 5
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.025 0.008 -10000 0 -10000 0 0
SMAD2 0.004 0.048 0.25 2 -0.26 3 5
SMAD3 0.026 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 0.026 0.087 -10000 0 -0.44 14 14
SMAD4/Ubc9/PIASy 0.048 0.019 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.046 0.057 -10000 0 -10000 0 0
PPM1A 0.026 0.006 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.048 0.24 1 -0.25 4 5
MAP3K1 0.026 0.006 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.025 0.065 -10000 0 -0.32 16 16
MAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPK1 0.026 0.005 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
CTDSP1 0.026 0.005 -10000 0 -10000 0 0
CTDSP2 0.027 0.004 -10000 0 -10000 0 0
CTDSPL 0.024 0.009 -10000 0 -10000 0 0
KPNB1 0.027 0.002 -10000 0 -10000 0 0
TGFBRAP1 0.012 0.085 -10000 0 -0.45 16 16
UBE2I 0.027 0.004 -10000 0 -10000 0 0
NUP153 0.026 0.006 -10000 0 -10000 0 0
KPNA2 0.027 0.003 -10000 0 -10000 0 0
PIAS4 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.058 0.029 -9999 0 -10000 0 0
HDAC3 0.026 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.036 0.017 -9999 0 -0.28 1 1
GATA1/HDAC5 0.038 0.016 -9999 0 -0.28 1 1
GATA2/HDAC5 0.034 0.026 -9999 0 -0.3 2 2
HDAC5/BCL6/BCoR 0.039 0.026 -9999 0 -10000 0 0
HDAC9 0.006 0.089 -9999 0 -0.4 23 23
Glucocorticoid receptor/Hsp90/HDAC6 0.049 0.018 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.037 0.011 -9999 0 -10000 0 0
HDAC5/YWHAB 0.038 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.005 -9999 0 -10000 0 0
GATA2 0.022 0.03 -9999 0 -0.42 2 2
HDAC4/RFXANK 0.038 0.017 -9999 0 -0.28 1 1
BCOR 0.026 0.022 -9999 0 -0.45 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.026 0.005 -9999 0 -10000 0 0
HDAC5 0.027 0.002 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.018 -9999 0 -0.28 1 1
Histones 0.024 0.04 -9999 0 -10000 0 0
ADRBK1 0.025 0.008 -9999 0 -10000 0 0
HDAC4 0.026 0.006 -9999 0 -10000 0 0
XPO1 0.027 0.004 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.01 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.01 -9999 0 -10000 0 0
HDAC7 0.027 0.003 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.039 0.009 -9999 0 -10000 0 0
TUBA1B 0.027 0.003 -9999 0 -10000 0 0
HDAC6 0.027 0.004 -9999 0 -10000 0 0
HDAC5/RFXANK 0.039 0.015 -9999 0 -0.28 1 1
CAMK4 0.002 0.098 -9999 0 -0.4 27 27
Tubulin/HDAC6 0.051 0.015 -9999 0 -10000 0 0
SUMO1 0.026 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.026 0.006 -9999 0 -10000 0 0
GATA1 0.017 0.026 -9999 0 -0.4 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.006 -9999 0 -10000 0 0
NR3C1 0.026 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.041 0.025 -9999 0 -10000 0 0
SRF 0.026 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.037 0.012 -9999 0 -10000 0 0
Tubulin 0.038 0.01 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.037 0.011 -9999 0 -10000 0 0
GNB1 0.026 0.005 -9999 0 -10000 0 0
RANGAP1 0.027 0.004 -9999 0 -10000 0 0
BCL6/BCoR 0.029 0.019 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.051 0.016 -9999 0 -10000 0 0
HDAC4/SRF 0.034 0.067 -9999 0 -0.24 26 26
HDAC4/ER alpha 0.02 0.076 -9999 0 -0.29 27 27
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.039 -9999 0 -10000 0 0
cell motility 0.051 0.015 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.027 0.004 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -9999 0 -10000 0 0
BCL6 0.02 0.012 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.026 0.006 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.011 -9999 0 -10000 0 0
ESR1 0.002 0.1 -9999 0 -0.42 27 27
HDAC6/HDAC11 0.035 0.021 -9999 0 -0.32 1 1
Ran/GTP/Exportin 1 0.042 0.029 -9999 0 -10000 0 0
NPC 0.016 0.002 -9999 0 -10000 0 0
MEF2C 0.017 0.064 -9999 0 -0.42 10 10
RAN 0.027 0.003 -9999 0 -10000 0 0
HDAC4/MEF2C 0.066 0.048 -9999 0 -0.24 4 4
GNG2 0.025 0.02 -9999 0 -0.4 1 1
NCOR2 0.027 0.003 -9999 0 -10000 0 0
TUBB2A 0.026 0.006 -9999 0 -10000 0 0
HDAC11 0.023 0.023 -9999 0 -0.45 1 1
HSP90AA1 0.026 0.007 -9999 0 -10000 0 0
RANBP2 0.027 0.003 -9999 0 -10000 0 0
ANKRA2 0.026 0.006 -9999 0 -10000 0 0
RFXANK 0.026 0.019 -9999 0 -0.4 1 1
nuclear import -0.033 0.013 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.008 0.08 -10000 0 -10000 0 0
regulation of axonogenesis -0.004 0.026 0.23 1 -10000 0 1
myoblast fusion -0.016 0.062 0.3 3 -10000 0 3
mol:GTP 0.011 0.039 -10000 0 -0.16 4 4
regulation of calcium-dependent cell-cell adhesion -0.04 0.058 0.24 7 -10000 0 7
ARF1/GTP 0.027 0.038 -10000 0 -10000 0 0
mol:GM1 0.004 0.029 -10000 0 -10000 0 0
mol:Choline 0.002 0.03 -10000 0 -0.27 3 3
lamellipodium assembly 0 0.061 -10000 0 -0.36 5 5
MAPK3 0.013 0.047 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.041 0.058 -10000 0 -0.24 7 7
ARF1 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.016 0.062 -10000 0 -0.3 3 3
ARF1/GDP 0.019 0.067 -10000 0 -0.26 6 6
ARF6 0.028 0.029 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 0.02 0.054 -10000 0 -0.45 6 6
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.046 -10000 0 -10000 0 0
actin filament bundle formation -0.016 0.063 0.28 3 -10000 0 3
KALRN -0.008 0.071 -10000 0 -0.25 29 29
RAB11FIP3/RAB11A 0.039 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.064 -10000 0 -0.28 3 3
NME1 0.026 0.022 -10000 0 -0.39 1 1
Rac1/GDP 0.019 0.064 -10000 0 -0.26 6 6
substrate adhesion-dependent cell spreading 0.011 0.039 -10000 0 -0.16 3 3
cortical actin cytoskeleton organization 0 0.062 -10000 0 -0.36 5 5
RAC1 0.026 0.007 -10000 0 -10000 0 0
liver development 0.011 0.039 -10000 0 -0.16 3 3
ARF6/GTP 0.011 0.039 -10000 0 -0.16 3 3
RhoA/GTP 0.024 0.036 -10000 0 -10000 0 0
mol:GDP 0 0.052 -10000 0 -0.3 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.041 0.039 -10000 0 -10000 0 0
RHOA 0.024 0.009 -10000 0 -10000 0 0
PLD1 0.005 0.037 -10000 0 -0.31 3 3
RAB11FIP3 0.027 0.004 -10000 0 -10000 0 0
tube morphogenesis 0 0.061 -10000 0 -0.36 5 5
ruffle organization 0.004 0.026 -10000 0 -0.23 1 1
regulation of epithelial cell migration 0.011 0.039 -10000 0 -0.16 3 3
PLD2 0.013 0.032 -10000 0 -10000 0 0
PIP5K1A 0.004 0.026 -10000 0 -0.23 1 1
mol:Phosphatidic acid 0.002 0.03 -10000 0 -0.27 3 3
Rac1/GTP 0 0.062 -10000 0 -0.36 5 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.02 -9999 0 -0.4 1 1
Rac1/GDP 0.024 0.01 -9999 0 -10000 0 0
DOCK1 0.026 0.022 -9999 0 -0.45 1 1
ITGA4 0.02 0.054 -9999 0 -0.4 8 8
RAC1 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.033 0.047 -9999 0 -0.29 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.047 0.039 -9999 0 -0.24 8 8
alpha4/beta7 Integrin/Paxillin 0.039 0.039 -9999 0 -0.25 2 2
lamellipodium assembly 0.011 0.063 -9999 0 -0.36 7 7
PIK3CA 0.019 0.013 -9999 0 -10000 0 0
PI3K 0.026 0.029 -9999 0 -0.32 2 2
ARF6 0.026 0.007 -9999 0 -10000 0 0
TLN1 0.024 0.009 -9999 0 -10000 0 0
PXN 0.015 0.002 -9999 0 -10000 0 0
PIK3R1 0.023 0.038 -9999 0 -0.45 3 3
ARF6/GTP 0.049 0.037 -9999 0 -10000 0 0
cell adhesion 0.046 0.036 -9999 0 -10000 0 0
CRKL/CBL 0.034 0.02 -9999 0 -0.28 1 1
alpha4/beta1 Integrin/Paxillin 0.039 0.035 -9999 0 -10000 0 0
ITGB1 0.027 0.005 -9999 0 -10000 0 0
ITGB7 0.025 0.031 -9999 0 -0.45 2 2
ARF6/GDP 0.024 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.027 0.087 -9999 0 -0.38 2 2
p130Cas/Crk/Dock1 0.05 0.022 -9999 0 -0.28 1 1
VCAM1 -0.018 0.13 -9999 0 -0.41 51 51
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.037 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.053 0.037 -9999 0 -10000 0 0
BCAR1 0.026 0.006 -9999 0 -10000 0 0
mol:GDP -0.051 0.036 -9999 0 -10000 0 0
CBL 0.025 0.008 -9999 0 -10000 0 0
PRKACA 0.027 0.003 -9999 0 -10000 0 0
GIT1 0.027 0.002 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.037 -9999 0 -10000 0 0
Rac1/GTP 0.011 0.068 -9999 0 -0.39 7 7
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.036 0.02 -10000 0 -0.32 1 1
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.023 0.038 -10000 0 -0.27 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.047 0.22 3 -0.28 1 4
NFKBIA 0.016 0.034 -10000 0 -0.23 3 3
MAPK14 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.011 -10000 0 -10000 0 0
ARRB2 0.014 0.004 -10000 0 -10000 0 0
REL 0.018 0.064 -10000 0 -0.45 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.017 -10000 0 -0.28 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.011 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.02 0.007 -10000 0 -10000 0 0
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
NFKB1 0.013 0.004 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.018 0.033 -10000 0 -0.28 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.033 0.05 0.27 1 -10000 0 1
SRC 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.026 0.029 -10000 0 -0.32 2 2
NF kappa B1 p50/RelA 0.018 0.033 -10000 0 -0.28 1 1
IKBKB 0.025 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.024 0.038 -10000 0 -0.45 3 3
I kappa B alpha/PIK3R1 0.03 0.053 0.22 6 -0.26 3 9
cell death 0.032 0.048 0.26 1 -10000 0 1
NF kappa B1 p105/c-Rel 0.023 0.038 -10000 0 -0.27 8 8
LCK 0.017 0.065 -10000 0 -0.4 12 12
BCL3 0.026 0.022 -10000 0 -0.45 1 1
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.031 -9999 0 -0.45 2 2
PLK4 0.027 0.005 -9999 0 -10000 0 0
regulation of centriole replication 0.012 0.022 -9999 0 -0.32 2 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.046 0.065 -10000 0 -0.29 2 2
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.067 -10000 0 -0.28 3 3
SUMO1 0.026 0.005 -10000 0 -10000 0 0
ZFPM1 0.026 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.005 -10000 0 -10000 0 0
FKBP3 0.026 0.006 -10000 0 -10000 0 0
Histones 0.053 0.057 -10000 0 -10000 0 0
YY1/LSF 0.008 0.079 -10000 0 -0.25 22 22
SMG5 0.027 0.004 -10000 0 -10000 0 0
RAN 0.027 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.017 0.036 -10000 0 -0.22 2 2
I kappa B alpha/HDAC1 0.026 0.05 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
RELA 0.021 0.045 0.28 1 -0.3 2 3
HDAC1/Smad7 0.047 0.021 -10000 0 -10000 0 0
RANGAP1 0.027 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.028 0.049 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.036 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.032 0.065 0.24 1 -0.33 3 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.022 0.03 -10000 0 -0.42 2 2
GATA1 0.017 0.026 -10000 0 -0.4 1 1
Mad/Max 0.035 0.034 -10000 0 -0.32 4 4
NuRD/MBD3 Complex/GATA1/Fog1 0.031 0.052 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
NPC 0.016 0.002 -10000 0 -10000 0 0
RBBP4 0.026 0.022 -10000 0 -0.45 1 1
MAX 0.026 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NFKBIA 0.015 0.029 -10000 0 -10000 0 0
KAT2B 0.007 0.09 -10000 0 -0.45 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.027 0.014 -10000 0 -10000 0 0
SIN3 complex 0.063 0.025 -10000 0 -0.21 1 1
SMURF1 0.025 0.007 -10000 0 -10000 0 0
CHD3 0.026 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.02 -10000 0 -0.4 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.007 0.07 -10000 0 -0.37 5 5
YY1/HDAC2 0.009 0.079 -10000 0 -0.34 7 7
YY1/HDAC1 0.009 0.079 -10000 0 -0.34 7 7
NuRD/MBD2 Complex (MeCP1) 0.034 0.028 -10000 0 -10000 0 0
PPARG -0.072 0.14 -10000 0 -0.4 15 15
HDAC8/hEST1B 0.053 0.012 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.029 0.048 -10000 0 -10000 0 0
MBD3L2 -0.017 0.026 -10000 0 -0.4 2 2
ubiquitin-dependent protein catabolic process 0.046 0.02 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.03 0.049 -10000 0 -0.3 1 1
HDAC1 0.027 0.004 -10000 0 -10000 0 0
HDAC3 0.016 0.029 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.008 0.055 -10000 0 -0.27 17 17
HDAC8 0.027 0.002 -10000 0 -10000 0 0
SMAD7 0.025 0.008 -10000 0 -10000 0 0
NCOR2 0.027 0.003 -10000 0 -10000 0 0
MXD1 0.022 0.048 -10000 0 -0.45 5 5
STAT3 0.02 0.026 -10000 0 -0.36 2 2
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.078 -10000 0 -0.33 6 6
YY1/SAP30/HDAC1 0.022 0.079 -10000 0 -0.37 5 5
EP300 0.025 0.031 -10000 0 -0.45 2 2
STAT3 (dimer non-phopshorylated) 0.02 0.026 -10000 0 -0.36 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.029 -10000 0 -10000 0 0
histone deacetylation 0.03 0.035 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.037 -10000 0 -0.32 1 1
nuclear export -0.053 0.011 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GATAD2B 0.027 0.004 -10000 0 -10000 0 0
GATAD2A 0.027 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.024 0.049 -10000 0 -0.26 2 2
GATA1/HDAC1 0.037 0.017 -10000 0 -0.28 1 1
GATA1/HDAC3 0.027 0.049 -10000 0 -10000 0 0
CHD4 0.026 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.022 0.067 -10000 0 -0.28 22 22
SIN3/HDAC complex/Mad/Max 0.031 0.035 -10000 0 -0.27 1 1
NuRD Complex 0.03 0.053 -10000 0 -0.31 4 4
positive regulation of chromatin silencing 0.05 0.055 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.04 0.029 -10000 0 -10000 0 0
HDAC complex 0.065 0.019 -10000 0 -10000 0 0
GATA1/Fog1 0.036 0.018 -10000 0 -0.28 1 1
FKBP25/HDAC1/HDAC2 0.05 0.017 -10000 0 -10000 0 0
TNF 0.007 0.088 -10000 0 -0.4 22 22
negative regulation of cell growth 0.028 0.039 -10000 0 -0.27 1 1
NuRD/MBD2/PRMT5 Complex 0.034 0.028 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.029 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.018 0.049 -10000 0 -0.28 3 3
SIN3/HDAC complex/NCoR1 0.026 0.039 -10000 0 -0.45 1 1
TFCP2 0.027 0.003 -10000 0 -10000 0 0
NR2C1 0.027 0.003 -10000 0 -10000 0 0
MBD3 0.027 0.005 -10000 0 -10000 0 0
MBD2 0.025 0.008 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.04 0.007 -9999 0 -10000 0 0
FBXW11 0.026 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -10000 0 0
CHUK 0.027 0.004 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.072 0.033 -9999 0 -10000 0 0
NFKB1 0.027 0.004 -9999 0 -10000 0 0
MAP3K14 0.027 0.002 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.036 0.03 -9999 0 -0.28 4 4
RELB 0.023 0.038 -9999 0 -0.4 4 4
NFKB2 0.027 0.004 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.033 0.025 -9999 0 -0.23 4 4
regulation of B cell activation 0.033 0.025 -9999 0 -0.23 4 4
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.027 0.004 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.006 -10000 0 -9999 0 0
MDM2/SUMO1 0.038 0.03 -10000 0 -9999 0 0
HDAC4 0.026 0.006 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0.007 0.007 -10000 0 -9999 0 0
SUMO1 0.026 0.005 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.012 0.012 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0.011 0.008 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0.027 0.003 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0.027 0.003 -10000 0 -9999 0 0
SUMO1/HDAC4 0.041 0.025 -10000 0 -9999 0 0
SUMO1/HDAC1 0.04 0.029 -10000 0 -9999 0 0
RANGAP1 0.027 0.004 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.06 0.026 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.005 -10000 0 -9999 0 0
Ran/GTP 0.029 0.026 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0.026 0.006 -10000 0 -9999 0 0
UBE2I 0.027 0.004 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0.03 0.035 0.21 9 -9999 0 9
NPC 0.016 0.002 -10000 0 -9999 0 0
PIAS2 0.025 0.008 -10000 0 -9999 0 0
PIAS1 0.027 0.004 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
Arf1 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
coatomer protein complex 0.012 0.029 0.21 3 -10000 0 3
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.017 0.023 0.14 4 -10000 0 4
AP2 0.028 0.019 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.034 0.013 -10000 0 -10000 0 0
CLTB 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.009 -10000 0 -10000 0 0
CD4 0.024 0.029 -10000 0 -0.42 2 2
CLTA 0.024 0.009 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.007 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.01 -10000 0 -10000 0 0
ARF1/GTP 0.032 0.011 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.011 0.006 -10000 0 -10000 0 0
mol:Choline 0.007 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.005 -10000 0 -10000 0 0
DDEF1 0.006 0.01 -10000 0 -10000 0 0
ARF1/GDP 0.006 0.011 -10000 0 -10000 0 0
AP2M1 0.019 0.013 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.037 0.013 -10000 0 -10000 0 0
ARFIP2 0.023 0.011 -10000 0 -10000 0 0
COPA 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.044 -10000 0 -0.2 5 5
ARF1/GTP/ARHGAP10 0.018 0.006 -10000 0 -10000 0 0
GGA3 0.027 0.003 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.026 0.018 -10000 0 -0.22 2 2
AP2A1 0.027 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.039 -10000 0 -0.2 11 11
ARF1/GDP/Membrin 0.026 0.021 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.033 0.012 -10000 0 -10000 0 0
CYTH2 0.028 0.005 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.036 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -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 0.017 0.028 -10000 0 -0.24 1 1
PLD2 0.007 0.01 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.002 -10000 0 -10000 0 0
PIP5K1A 0.008 0.01 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.021 0.018 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.01 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.002 -10000 0 -10000 0 0
GOSR2 0.012 0.021 -10000 0 -0.31 2 2
USO1 0.011 0.03 -10000 0 -0.31 4 4
GBF1 0.01 0.036 -10000 0 -0.31 6 6
ARF1/GTP/Arfaptin 2 0.037 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.036 0.032 -10000 0 -0.26 2 2
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 493 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WA.A7H4 TCGA.WA.A7GZ TCGA.UP.A6WW TCGA.UF.A7JV
109_MAP3K5 0.034 0.034 0 0.034
47_PPARGC1A 0.027 0.027 0.027 -0.45
105_BMP4 0.027 0.027 0.027 0.027
105_BMP6 0.027 0.027 0 0.027
105_BMP7 0.027 0.027 0.027 0.027
105_BMP2 0.027 0.027 0.027 -0.4
131_RELN/VLDLR 0.071 0.071 0.071 0
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.03 0.027
84_STAT5B 0.03 0.03 -0.42 0.032
84_STAT5A 0.03 0.03 -0.42 0.032
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/HNSC-TP/11493471/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/HNSC-TP/11541450/GDAC_Gistic2Report_11544267/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)