PARADIGM pathway analysis of mRNASeq expression and copy number data
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1W957X4
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1W957X4
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 40 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
IL4-mediated signaling events 131
HIF-1-alpha transcription factor network 101
Syndecan-1-mediated signaling events 82
Glypican 2 network 68
TCGA08_retinoblastoma 63
Endothelins 56
Syndecan-4-mediated signaling events 56
Syndecan-2-mediated signaling events 55
amb2 Integrin signaling 54
Osteopontin-mediated events 46
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
IL4-mediated signaling events 0.2636 131 11941 91 -1.2 0.99 1000 -1000 -0.13 -1000
HIF-1-alpha transcription factor network 0.2032 101 7698 76 -0.68 0.038 1000 -1000 -0.16 -1000
Syndecan-1-mediated signaling events 0.1650 82 2815 34 -0.32 0.028 1000 -1000 -0.049 -1000
Glypican 2 network 0.1368 68 275 4 -0.043 -0.025 1000 -1000 0.002 -1000
TCGA08_retinoblastoma 0.1268 63 506 8 -0.14 0.082 1000 -1000 -0.004 -1000
Endothelins 0.1127 56 5469 96 -0.23 0.027 1000 -1000 -0.064 -1000
Syndecan-4-mediated signaling events 0.1127 56 3779 67 -0.28 0.04 1000 -1000 -0.047 -1000
Syndecan-2-mediated signaling events 0.1107 55 3846 69 -0.2 0.037 1000 -1000 -0.045 -1000
amb2 Integrin signaling 0.1087 54 4498 82 -0.27 0.035 1000 -1000 -0.044 -1000
Osteopontin-mediated events 0.0926 46 1775 38 -0.2 0.032 1000 -1000 -0.049 -1000
IL23-mediated signaling events 0.0926 46 2807 60 -0.53 0.028 1000 -1000 -0.14 -1000
Signaling events regulated by Ret tyrosine kinase 0.0885 44 3663 82 -0.086 0.028 1000 -1000 -0.065 -1000
Nongenotropic Androgen signaling 0.0825 41 2168 52 -0.1 0.068 1000 -1000 -0.035 -1000
Visual signal transduction: Rods 0.0805 40 2117 52 -0.21 0.04 1000 -1000 -0.037 -1000
TCGA08_p53 0.0785 39 279 7 -0.1 0.059 1000 -1000 -0.008 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0785 39 3065 78 -0.14 0.042 1000 -1000 -0.06 -1000
IGF1 pathway 0.0765 38 2191 57 -0.053 0.054 1000 -1000 -0.042 -1000
Reelin signaling pathway 0.0744 37 2102 56 -0.17 0.068 1000 -1000 -0.047 -1000
Calcium signaling in the CD4+ TCR pathway 0.0744 37 1162 31 -0.3 0.028 1000 -1000 -0.056 -1000
Coregulation of Androgen receptor activity 0.0724 36 2750 76 -0.43 0.067 1000 -1000 -0.032 -1000
p75(NTR)-mediated signaling 0.0724 36 4515 125 -0.24 0.074 1000 -1000 -0.071 -1000
TCR signaling in naïve CD8+ T cells 0.0724 36 3412 93 -0.19 0.099 1000 -1000 -0.06 -1000
BMP receptor signaling 0.0704 35 2905 81 -0.21 0.048 1000 -1000 -0.063 -1000
Effects of Botulinum toxin 0.0704 35 925 26 -0.12 0.028 1000 -1000 -0.017 -1000
FOXA2 and FOXA3 transcription factor networks 0.0664 33 1537 46 -0.45 0.033 1000 -1000 -0.12 -1000
Glypican 1 network 0.0664 33 1598 48 -0.27 0.047 1000 -1000 -0.036 -1000
Canonical Wnt signaling pathway 0.0644 32 1652 51 -0.19 0.14 1000 -1000 -0.062 -1000
Fc-epsilon receptor I signaling in mast cells 0.0604 30 2973 97 -0.14 0.035 1000 -1000 -0.061 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0604 30 3662 120 -0.16 0.074 1000 -1000 -0.053 -1000
LPA4-mediated signaling events 0.0584 29 352 12 -0.086 0.007 1000 -1000 -0.029 -1000
Thromboxane A2 receptor signaling 0.0584 29 3061 105 -0.083 0.032 1000 -1000 -0.057 -1000
Presenilin action in Notch and Wnt signaling 0.0563 28 1754 61 -0.19 0.074 1000 -1000 -0.045 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0543 27 1863 68 -0.32 0.042 1000 -1000 -0.11 -1000
EGFR-dependent Endothelin signaling events 0.0543 27 568 21 -0.059 0.04 1000 -1000 -0.046 -1000
IL12-mediated signaling events 0.0503 25 2200 87 -0.17 0.036 1000 -1000 -0.096 -1000
Visual signal transduction: Cones 0.0503 25 951 38 -0.059 0.05 1000 -1000 -0.019 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0503 25 1354 54 -0.13 0.038 1000 -1000 -0.05 -1000
Arf6 signaling events 0.0503 25 1552 62 -0.11 0.053 1000 -1000 -0.038 -1000
Signaling mediated by p38-gamma and p38-delta 0.0503 25 377 15 -0.13 0.027 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 0.0503 25 2520 97 -0.06 0.057 1000 -1000 -0.054 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0483 24 840 34 -0.03 0.033 1000 -1000 -0.03 -1000
Signaling events mediated by PTP1B 0.0483 24 1884 76 -0.087 0.045 1000 -1000 -0.045 -1000
LPA receptor mediated events 0.0483 24 2496 102 -0.27 0.028 1000 -1000 -0.075 -1000
Signaling events mediated by the Hedgehog family 0.0443 22 1171 52 -0.22 0.031 1000 -1000 -0.046 -1000
IL1-mediated signaling events 0.0443 22 1368 62 -0.11 0.049 1000 -1000 -0.053 -1000
Ephrin B reverse signaling 0.0443 22 1090 48 -0.064 0.033 1000 -1000 -0.034 -1000
Integrins in angiogenesis 0.0443 22 1885 84 -0.2 0.054 1000 -1000 -0.056 -1000
BCR signaling pathway 0.0443 22 2263 99 -0.067 0.048 1000 -1000 -0.064 -1000
Plasma membrane estrogen receptor signaling 0.0443 22 1944 86 -0.13 0.046 1000 -1000 -0.061 -1000
Regulation of Androgen receptor activity 0.0443 22 1585 70 -0.47 0.034 1000 -1000 -0.061 -1000
ErbB2/ErbB3 signaling events 0.0423 21 1416 65 -0.23 0.04 1000 -1000 -0.058 -1000
EPHB forward signaling 0.0423 21 1807 85 -0.16 0.091 1000 -1000 -0.068 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0423 21 1852 88 -0.16 0.045 1000 -1000 -0.063 -1000
Caspase cascade in apoptosis 0.0402 20 1510 74 -0.093 0.054 1000 -1000 -0.052 -1000
ErbB4 signaling events 0.0402 20 1421 69 -0.23 0.04 1000 -1000 -0.051 -1000
Ephrin A reverse signaling 0.0382 19 138 7 -0.008 0.016 1000 -1000 -0.01 -1000
Glucocorticoid receptor regulatory network 0.0382 19 2209 114 -0.34 0.17 1000 -1000 -0.061 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0382 19 637 33 -0.14 0.063 1000 -1000 -0.043 -1000
Wnt signaling 0.0362 18 131 7 -0.018 0.023 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class III 0.0342 17 694 40 -0.13 0.05 1000 -1000 -0.021 -1000
Signaling mediated by p38-alpha and p38-beta 0.0342 17 753 44 -0.13 0.028 1000 -1000 -0.037 -1000
IL27-mediated signaling events 0.0342 17 893 51 -0.11 0.053 1000 -1000 -0.056 -1000
Regulation of nuclear SMAD2/3 signaling 0.0322 16 2228 136 -0.36 0.16 1000 -1000 -0.052 -1000
Noncanonical Wnt signaling pathway 0.0322 16 418 26 -0.05 0.027 1000 -1000 -0.046 -1000
Ceramide signaling pathway 0.0322 16 1249 76 -0.059 0.07 1000 -1000 -0.044 -1000
Syndecan-3-mediated signaling events 0.0322 16 581 35 -0.14 0.074 1000 -1000 -0.032 -1000
PDGFR-alpha signaling pathway 0.0282 14 652 44 -0.11 0.061 1000 -1000 -0.044 -1000
mTOR signaling pathway 0.0282 14 781 53 -0.022 0.066 1000 -1000 -0.04 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0282 14 734 52 -0.13 0.043 1000 -1000 -0.054 -1000
S1P1 pathway 0.0262 13 499 36 -0.048 0.026 1000 -1000 -0.052 -1000
Signaling events mediated by PRL 0.0262 13 456 34 -0.065 0.04 1000 -1000 -0.041 -1000
Cellular roles of Anthrax toxin 0.0241 12 468 39 -0.025 0.029 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0241 12 1046 85 -0.091 0.071 1000 -1000 -0.048 -1000
IFN-gamma pathway 0.0241 12 820 68 -0.13 0.04 1000 -1000 -0.064 -1000
ceramide signaling pathway 0.0241 12 627 49 0 0.065 1000 -1000 -0.048 -1000
FAS signaling pathway (CD95) 0.0241 12 574 47 -0.06 0.041 1000 -1000 -0.039 -1000
IL6-mediated signaling events 0.0241 12 919 75 -0.11 0.049 1000 -1000 -0.071 -1000
S1P3 pathway 0.0241 12 504 42 -0.048 0.046 1000 -1000 -0.037 -1000
Class I PI3K signaling events mediated by Akt 0.0221 11 750 68 -0.092 0.06 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0221 11 649 58 -0.053 0.05 1000 -1000 -0.051 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0221 11 863 74 -0.27 0.058 1000 -1000 -0.07 -1000
Rapid glucocorticoid signaling 0.0221 11 233 20 -0.029 0.034 1000 -1000 -0.009 -1000
p38 MAPK signaling pathway 0.0221 11 495 44 -0.092 0.056 1000 -1000 -0.029 -1000
BARD1 signaling events 0.0201 10 626 57 -0.034 0.052 1000 -1000 -0.044 -1000
EPO signaling pathway 0.0201 10 589 55 -0.015 0.05 1000 -1000 -0.048 -1000
PLK1 signaling events 0.0201 10 880 85 -0.04 0.066 1000 -1000 -0.032 -1000
Nectin adhesion pathway 0.0201 10 684 63 -0.048 0.062 1000 -1000 -0.063 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0201 10 375 37 -0.022 0.062 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 0.0201 10 613 58 -0.089 0.081 1000 -1000 -0.054 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0201 10 473 45 -0.028 0.051 1000 -1000 -0.057 -1000
JNK signaling in the CD4+ TCR pathway 0.0181 9 166 17 0.009 0.05 1000 -1000 -0.034 -1000
Regulation of p38-alpha and p38-beta 0.0181 9 508 54 -0.035 0.06 1000 -1000 -0.053 -1000
Insulin Pathway 0.0181 9 687 74 -0.094 0.073 1000 -1000 -0.046 -1000
Ras signaling in the CD4+ TCR pathway 0.0181 9 157 17 -0.001 0.044 1000 -1000 -0.031 -1000
Circadian rhythm pathway 0.0161 8 197 22 -0.058 0.056 1000 -1000 -0.042 -1000
Regulation of Telomerase 0.0161 8 848 102 -0.07 0.059 1000 -1000 -0.076 -1000
FOXM1 transcription factor network 0.0161 8 435 51 -0.14 0.14 1000 -1000 -0.16 -1000
Aurora B signaling 0.0161 8 595 67 -0.31 0.088 1000 -1000 -0.041 -1000
TCGA08_rtk_signaling 0.0141 7 198 26 -0.064 0.087 1000 -1000 -0.025 -1000
VEGFR1 specific signals 0.0141 7 422 56 -0.045 0.051 1000 -1000 -0.057 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0121 6 191 28 -0.043 0.051 1000 -1000 -0.029 -1000
IL2 signaling events mediated by STAT5 0.0121 6 145 22 -0.017 0.043 1000 -1000 -0.055 -1000
Class IB PI3K non-lipid kinase events 0.0121 6 18 3 -0.022 0.022 1000 -1000 -0.001 -1000
S1P4 pathway 0.0121 6 170 25 0 0.038 1000 -1000 -0.032 -1000
a4b1 and a4b7 Integrin signaling 0.0101 5 28 5 0.021 0.034 1000 -1000 -0.003 -1000
HIF-2-alpha transcription factor network 0.0101 5 251 43 -0.1 0.044 1000 -1000 -0.072 -1000
Class I PI3K signaling events 0.0101 5 397 73 -0.035 0.049 1000 -1000 -0.052 -1000
Arf6 trafficking events 0.0101 5 409 71 -0.18 0.049 1000 -1000 -0.034 -1000
E-cadherin signaling in keratinocytes 0.0101 5 249 43 -0.042 0.061 1000 -1000 -0.038 -1000
Hedgehog signaling events mediated by Gli proteins 0.0080 4 300 65 -0.023 0.064 1000 -1000 -0.058 -1000
TRAIL signaling pathway 0.0080 4 207 48 0 0.07 1000 -1000 -0.043 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0080 4 392 83 -0.031 0.054 1000 -1000 -0.052 -1000
FoxO family signaling 0.0080 4 259 64 -0.018 0.084 1000 -1000 -0.07 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0080 4 568 125 -0.038 0.073 1000 -1000 -0.063 -1000
E-cadherin signaling in the nascent adherens junction 0.0080 4 349 76 -0.02 0.069 1000 -1000 -0.068 -1000
Canonical NF-kappaB pathway 0.0060 3 125 39 0 0.06 1000 -1000 -0.041 -1000
Aurora A signaling 0.0060 3 221 60 -0.034 0.057 1000 -1000 -0.03 -1000
Arf6 downstream pathway 0.0060 3 158 43 -0.04 0.042 1000 -1000 -0.024 -1000
Aurora C signaling 0.0060 3 25 7 0 0.042 1000 -1000 -0.014 -1000
Insulin-mediated glucose transport 0.0060 3 96 32 -0.068 0.054 1000 -1000 -0.035 -1000
S1P5 pathway 0.0060 3 61 17 -0.023 0.032 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class I 0.0060 3 324 104 -0.07 0.067 1000 -1000 -0.045 -1000
Paxillin-dependent events mediated by a4b1 0.0060 3 112 36 -0.052 0.054 1000 -1000 -0.032 -1000
E-cadherin signaling events 0.0060 3 17 5 0.022 0.044 1000 -1000 0.001 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 2 56 23 0.004 0.049 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class II 0.0040 2 162 75 -0.033 0.068 1000 -1000 -0.026 -1000
Atypical NF-kappaB pathway 0.0040 2 79 31 0 0.034 1000 -1000 -0.028 -1000
PLK2 and PLK4 events 0.0020 1 4 3 0.012 0.027 1000 -1000 -0.015 -1000
Alternative NF-kappaB pathway 0.0020 1 16 13 0 0.074 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 16 27 0 0.061 1000 -1000 -0.033 -1000
Arf1 pathway 0.0000 0 42 54 -0.001 0.038 1000 -1000 -0.026 -1000
Total NA 2685 164070 7203 -16 7.8 131000 -131000 -6.2 -131000
IL4-mediated signaling events

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
BCL2L1 -0.87 0.46 -10000 0 -1.2 281 281
STAT6 (cleaved dimer) -0.88 0.48 -10000 0 -1.2 316 316
IGHG1 -0.3 0.16 -10000 0 -0.47 117 117
IGHG3 -0.85 0.44 -10000 0 -1.1 309 309
AKT1 -0.37 0.2 -10000 0 -0.75 50 50
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.17 -10000 0 -0.66 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.38 0.21 -10000 0 -0.74 55 55
THY1 -0.91 0.48 -10000 0 -1.3 289 289
MYB -0.021 0.14 -10000 0 -0.44 50 50
HMGA1 0.027 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.45 0.21 -10000 0 -0.61 220 220
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.38 0.21 -10000 0 -0.73 56 56
SP1 0.003 0.04 -10000 0 -10000 0 0
INPP5D 0.025 0.031 -10000 0 -0.45 2 2
SOCS5 0.048 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.87 0.47 -10000 0 -1.2 296 296
SOCS1 -0.57 0.26 -10000 0 -0.76 263 263
SOCS3 -0.38 0.18 -10000 0 -0.7 38 38
FCER2 -0.69 0.36 -10000 0 -0.97 249 249
PARP14 0.024 0.021 -10000 0 -0.39 1 1
CCL17 -0.9 0.48 -10000 0 -1.2 286 286
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.31 0.18 -10000 0 -0.63 56 56
T cell proliferation -0.88 0.48 -10000 0 -1.2 292 292
IL4R/JAK1 -0.88 0.46 -10000 0 -1.2 287 287
EGR2 -0.89 0.47 -10000 0 -1.2 275 275
JAK2 -0.048 0.03 -10000 0 -10000 0 0
JAK3 0.019 0.079 -10000 0 -0.39 17 17
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
JAK1 -0.012 0.016 -10000 0 -10000 0 0
COL1A2 -0.34 0.2 -10000 0 -0.6 136 136
CCL26 -0.9 0.47 -10000 0 -1.2 274 274
IL4R -0.93 0.5 -10000 0 -1.3 286 286
PTPN6 0.045 0.014 -10000 0 -10000 0 0
IL13RA2 -0.9 0.48 -10000 0 -1.3 278 278
IL13RA1 -0.052 0.027 -10000 0 -10000 0 0
IRF4 -0.25 0.32 -10000 0 -0.88 81 81
ARG1 -0.5 0.54 -10000 0 -1.3 131 131
CBL -0.43 0.2 -10000 0 -0.59 183 183
GTF3A -0.017 0.04 -10000 0 -10000 0 0
PIK3CA 0.02 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 -0.035 0.16 -10000 0 -0.45 64 64
MAPK14 -0.42 0.2 -10000 0 -0.61 155 155
mitosis -0.35 0.19 -10000 0 -0.71 49 49
STAT6 -1 0.58 -10000 0 -1.4 305 305
SPI1 -0.014 0.073 -10000 0 -0.43 3 3
RPS6KB1 -0.34 0.18 -10000 0 -0.7 45 45
STAT6 (dimer) -1 0.58 -10000 0 -1.4 305 305
STAT6 (dimer)/PARP14 -0.93 0.52 -10000 0 -1.3 298 298
mast cell activation 0.02 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.36 0.22 -10000 0 -0.72 66 66
FRAP1 -0.37 0.2 -10000 0 -0.75 50 50
LTA -0.89 0.46 -10000 0 -1.2 292 292
FES 0.027 0.005 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.99 0.54 1.3 305 -10000 0 305
CCL11 -0.92 0.44 -10000 0 -1.2 292 292
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.35 0.19 -10000 0 -0.71 49 49
IL2RG 0.019 0.08 -10000 0 -0.4 17 17
IL10 -0.88 0.46 -10000 0 -1.2 285 285
IRS1 0.024 0.037 -10000 0 -0.45 3 3
IRS2 0.025 0.031 -10000 0 -0.45 2 2
IL4 -0.23 0.25 -10000 0 -1.1 30 30
IL5 -0.88 0.46 -10000 0 -1.2 283 283
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.69 0.34 -10000 0 -0.91 296 296
COL1A1 -0.46 0.26 -10000 0 -0.7 174 174
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.9 0.49 -10000 0 -1.3 283 283
IL2R gamma/JAK3 0.02 0.09 -10000 0 -0.32 30 30
TFF3 -1.1 0.6 -10000 0 -1.5 322 322
ALOX15 -0.95 0.52 -10000 0 -1.3 276 276
MYBL1 0.021 0.043 -10000 0 -0.39 5 5
T-helper 2 cell differentiation -0.78 0.39 -10000 0 -1 309 309
SHC1 0.028 0.004 -10000 0 -10000 0 0
CEBPB -0.009 0.063 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.36 0.19 -10000 0 -0.7 48 48
mol:PI-3-4-5-P3 -0.37 0.2 -10000 0 -0.75 50 50
PI3K -0.38 0.22 -10000 0 -0.81 50 50
DOK2 0.022 0.04 -10000 0 -0.41 4 4
ETS1 0.041 0.037 -10000 0 -0.38 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.29 0.16 -10000 0 -0.57 51 51
ITGB3 -0.89 0.47 -10000 0 -1.2 286 286
PIGR -1.2 0.62 -10000 0 -1.6 346 346
IGHE 0.046 0.054 0.19 18 -0.16 1 19
MAPKKK cascade -0.29 0.15 -10000 0 -0.56 51 51
BCL6 0.02 0.013 -10000 0 -10000 0 0
OPRM1 -0.88 0.46 -10000 0 -1.2 284 284
RETNLB -0.87 0.47 -10000 0 -1.2 285 285
SELP -0.96 0.53 -10000 0 -1.3 296 296
AICDA -0.85 0.44 -10000 0 -1.2 288 288
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.56 0.39 -10000 0 -0.99 161 161
HDAC7 0.028 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.41 0.29 -10000 0 -0.8 85 85
SMAD4 0.026 0.009 -10000 0 -10000 0 0
ID2 -0.56 0.39 -10000 0 -1 148 148
AP1 -0.005 0.12 -10000 0 -0.32 60 60
ABCG2 -0.56 0.39 -10000 0 -1 151 151
HIF1A -0.088 0.067 -10000 0 -0.31 5 5
TFF3 -0.65 0.44 -10000 0 -1.1 214 214
GATA2 0.023 0.03 -10000 0 -0.42 2 2
AKT1 -0.09 0.071 -10000 0 -0.41 2 2
response to hypoxia -0.1 0.077 -10000 0 -0.32 22 22
MCL1 -0.56 0.39 -10000 0 -1 149 149
NDRG1 -0.54 0.38 -10000 0 -1 140 140
SERPINE1 -0.64 0.42 -10000 0 -1 197 197
FECH -0.56 0.39 -10000 0 -1 155 155
FURIN -0.56 0.39 -10000 0 -1 155 155
NCOA2 -0.007 0.12 -10000 0 -0.45 31 31
EP300 -0.09 0.087 -10000 0 -0.36 15 15
HMOX1 -0.56 0.39 -10000 0 -1 147 147
BHLHE40 -0.56 0.39 -10000 0 -0.99 159 159
BHLHE41 -0.56 0.39 -10000 0 -1 146 146
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.079 0.095 -10000 0 -0.36 3 3
ENG -0.076 0.086 0.33 5 -0.38 1 6
JUN 0.028 0.007 -10000 0 -10000 0 0
RORA -0.56 0.4 -10000 0 -1 150 150
ABCB1 -0.18 0.3 -10000 0 -1.2 36 36
TFRC -0.53 0.38 -10000 0 -0.98 143 143
CXCR4 -0.56 0.39 -10000 0 -1 151 151
TF -0.66 0.44 -10000 0 -1 228 228
CITED2 -0.56 0.39 -10000 0 -1 149 149
HIF1A/ARNT -0.61 0.46 -10000 0 -1.1 161 161
LDHA -0.078 0.16 -10000 0 -0.77 21 21
ETS1 -0.56 0.39 -10000 0 -1 152 152
PGK1 -0.56 0.39 -10000 0 -1 148 148
NOS2 -0.59 0.4 -10000 0 -1 172 172
ITGB2 -0.56 0.39 -10000 0 -1 154 154
ALDOA -0.56 0.39 -10000 0 -1 143 143
Cbp/p300/CITED2 -0.55 0.39 -10000 0 -1 136 136
FOS -0.031 0.16 -10000 0 -0.45 60 60
HK2 -0.56 0.39 -10000 0 -1 157 157
SP1 0.027 0.03 -10000 0 -10000 0 0
GCK -0.15 0.15 -10000 0 -0.73 9 9
HK1 -0.56 0.39 -10000 0 -1 152 152
NPM1 -0.56 0.39 -10000 0 -1 153 153
EGLN1 -0.56 0.39 -10000 0 -1 155 155
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.56 0.39 -10000 0 -1 149 149
SMAD3 0.028 0.005 -10000 0 -10000 0 0
EDN1 -0.09 0.16 -10000 0 -0.98 8 8
IGFBP1 -0.56 0.39 -10000 0 -0.99 163 163
VEGFA -0.36 0.25 -10000 0 -0.74 52 52
HIF1A/JAB1 -0.047 0.05 -10000 0 -10000 0 0
CP -0.6 0.43 -10000 0 -1 205 205
CXCL12 -0.58 0.41 -10000 0 -1 154 154
COPS5 0.023 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.014 -10000 0 -10000 0 0
BNIP3 -0.56 0.39 -10000 0 -1 149 149
EGLN3 -0.56 0.4 -10000 0 -1 164 164
CA9 -0.68 0.4 -10000 0 -1 229 229
TERT -0.57 0.4 -10000 0 -1 166 166
ENO1 -0.56 0.39 -10000 0 -1 144 144
PFKL -0.56 0.39 -10000 0 -1 149 149
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.56 0.39 -10000 0 -1 159 159
ARNT -0.097 0.069 -10000 0 -0.35 8 8
HNF4A -0.019 0.12 -10000 0 -0.39 46 46
ADFP -0.56 0.38 -10000 0 -0.95 186 186
SLC2A1 -0.37 0.25 -10000 0 -0.76 53 53
LEP -0.59 0.41 -10000 0 -1 170 170
HIF1A/ARNT/Cbp/p300 -0.42 0.3 -10000 0 -0.82 91 91
EPO -0.33 0.25 -10000 0 -0.81 56 56
CREBBP -0.09 0.084 -10000 0 -0.37 10 10
HIF1A/ARNT/Cbp/p300/HDAC7 -0.41 0.3 -10000 0 -0.82 78 78
PFKFB3 -0.56 0.39 -10000 0 -1 146 146
NT5E -0.59 0.41 -10000 0 -1 180 180
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 0.026 0.027 -10000 0 -0.39 2 2
CCL5 -0.036 0.15 -10000 0 -0.4 75 75
SDCBP 0.025 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.18 0.14 0.27 10 -0.34 119 129
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 -0.33 119 125
Syndecan-1/Syntenin -0.16 0.13 0.25 8 -0.32 108 116
MAPK3 -0.16 0.12 0.24 9 -0.39 37 46
HGF/MET 0.021 0.077 -10000 0 -0.3 26 26
TGFB1/TGF beta receptor Type II 0.026 0.027 -10000 0 -0.39 2 2
BSG 0.027 0.005 -10000 0 -10000 0 0
keratinocyte migration -0.17 0.12 0.2 6 -0.32 119 125
Syndecan-1/RANTES -0.2 0.15 0.25 9 -0.35 172 181
Syndecan-1/CD147 -0.16 0.13 0.31 4 -0.4 39 43
Syndecan-1/Syntenin/PIP2 -0.16 0.13 0.23 8 -0.31 108 116
LAMA5 0.027 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.15 0.12 0.23 8 -0.31 108 116
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 -0.33 121 121
Syndecan-1/HGF/MET -0.17 0.14 0.32 3 -0.33 116 119
regulation of cell adhesion -0.15 0.12 0.28 4 -0.38 34 38
HPSE 0.023 0.043 -10000 0 -0.45 4 4
positive regulation of cell migration -0.18 0.14 0.27 10 -0.34 119 129
SDC1 -0.18 0.13 0.29 2 -0.34 119 121
Syndecan-1/Collagen -0.18 0.14 0.27 10 -0.34 119 129
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET 0.021 0.049 -10000 0 -0.41 6 6
PRKACA 0.028 0.004 -10000 0 -10000 0 0
MMP9 -0.27 0.19 -10000 0 -0.39 349 349
MAPK1 -0.16 0.12 0.3 4 -0.39 35 39
homophilic cell adhesion -0.18 0.14 0.27 10 -0.34 121 131
MMP1 -0.32 0.16 -10000 0 -0.39 405 405
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 0.01 0.084 -9999 0 -0.4 20 20
GPC2 -0.043 0.16 -9999 0 -0.39 81 81
GPC2/Midkine -0.025 0.14 -9999 0 -0.31 87 87
neuron projection morphogenesis -0.025 0.14 -9999 0 -0.31 87 87
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 0.011 0.067 -10000 0 -0.42 11 11
CDKN2C 0.02 0.071 -10000 0 -0.36 14 14
CDKN2A -0.14 0.2 -10000 0 -0.4 183 183
CCND2 0.039 0.062 0.18 43 -10000 0 43
RB1 -0.058 0.086 0.3 1 -0.24 60 61
CDK4 0.047 0.072 0.2 48 -10000 0 48
CDK6 0.043 0.069 0.21 38 -10000 0 38
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 0.18 0.25 2 -0.4 76 78
PTK2B 0.026 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.17 -10000 0 -0.58 14 14
EDN1 -0.071 0.15 -10000 0 -0.29 58 58
EDN3 -0.18 0.22 -10000 0 -0.45 197 197
EDN2 -0.039 0.16 -10000 0 -0.43 71 71
HRAS/GDP -0.065 0.16 0.31 4 -0.43 31 35
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.058 0.13 -10000 0 -0.35 44 44
ADCY4 -0.12 0.16 0.27 5 -0.38 83 88
ADCY5 -0.16 0.18 0.24 2 -0.4 122 124
ADCY6 -0.12 0.17 0.28 4 -0.38 92 96
ADCY7 -0.12 0.16 0.27 5 -0.38 85 90
ADCY1 -0.12 0.17 0.27 5 -0.38 93 98
ADCY2 -0.18 0.18 0.26 2 -0.4 142 144
ADCY3 -0.12 0.17 0.27 5 -0.38 86 91
ADCY8 -0.11 0.16 0.29 3 -0.38 84 87
ADCY9 -0.12 0.16 0.24 4 -0.38 87 91
arachidonic acid secretion -0.092 0.19 0.28 2 -0.49 59 61
ETB receptor/Endothelin-1/Gq/GTP -0.053 0.12 -10000 0 -0.32 49 49
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
HRAS 0.026 0.021 -10000 0 -0.41 1 1
ETA receptor/Endothelin-1/G12/GTP -0.04 0.23 0.3 14 -0.38 72 86
ETA receptor/Endothelin-1/Gs/GTP -0.077 0.22 0.32 4 -0.38 97 101
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.22 0.26 -10000 0 -0.45 250 250
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 0.25 3 -0.47 91 94
CYSLTR1 -0.16 0.24 -10000 0 -0.52 107 107
SLC9A1 -0.049 0.11 -10000 0 -0.28 36 36
mol:GDP -0.074 0.16 0.31 4 -0.44 37 41
SLC9A3 -0.15 0.29 -10000 0 -0.69 89 89
RAF1 -0.093 0.17 0.27 5 -0.45 56 61
JUN -0.052 0.16 -10000 0 -0.66 10 10
JAK2 -0.12 0.18 0.25 3 -0.41 72 75
mol:IP3 -0.07 0.14 -10000 0 -0.39 45 45
ETA receptor/Endothelin-1 -0.078 0.28 0.38 7 -0.44 92 99
PLCB1 0.024 0.023 -10000 0 -0.45 1 1
PLCB2 0.022 0.04 -10000 0 -0.41 4 4
ETA receptor/Endothelin-3 -0.17 0.19 -10000 0 -0.37 205 205
FOS -0.14 0.32 0.31 1 -0.9 66 67
Gai/GDP -0.074 0.26 -10000 0 -0.71 68 68
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.13 0.18 -10000 0 -0.43 77 77
BCAR1 0.027 0.006 -10000 0 -10000 0 0
PRKCB1 -0.067 0.14 0.25 2 -0.37 47 49
GNAQ 0.026 0.009 -10000 0 -10000 0 0
GNAZ 0.011 0.083 -10000 0 -0.41 18 18
GNAL -0.029 0.15 -10000 0 -0.45 57 57
Gs family/GDP -0.085 0.16 0.25 1 -0.44 43 44
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.14 -10000 0 -0.36 56 56
MAPK14 -0.039 0.1 0.24 1 -0.39 15 16
TRPC6 -0.051 0.18 -10000 0 -0.61 14 14
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.45 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.044 0.11 -10000 0 -0.38 25 25
ETB receptor/Endothelin-2 -0.04 0.12 -10000 0 -0.31 75 75
ETB receptor/Endothelin-3 -0.13 0.17 -10000 0 -0.33 195 195
ETB receptor/Endothelin-1 -0.051 0.14 -10000 0 -0.26 59 59
MAPK3 -0.13 0.28 0.3 2 -0.74 71 73
MAPK1 -0.13 0.28 0.3 2 -0.75 69 71
Rac1/GDP -0.064 0.15 0.32 3 -0.43 27 30
cAMP biosynthetic process -0.14 0.17 0.28 5 -0.41 80 85
MAPK8 -0.062 0.19 0.34 1 -0.61 27 28
SRC 0.026 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.021 0.087 -10000 0 -0.32 20 20
p130Cas/CRK/Src/PYK2 -0.072 0.16 0.39 2 -0.5 24 26
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.064 0.15 0.32 3 -0.43 27 30
COL1A2 -0.15 0.24 -10000 0 -0.44 173 173
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.082 0.16 -10000 0 -0.35 84 84
mol:DAG -0.07 0.14 -10000 0 -0.39 45 45
MAP2K2 -0.11 0.21 0.29 4 -0.56 70 74
MAP2K1 -0.11 0.21 0.28 3 -0.55 73 76
EDNRA -0.07 0.15 -10000 0 -0.29 65 65
positive regulation of muscle contraction -0.088 0.16 0.27 8 -0.38 59 67
Gq family/GDP -0.053 0.17 -10000 0 -0.43 38 38
HRAS/GTP -0.084 0.15 0.28 4 -0.42 45 49
PRKCH -0.062 0.14 0.25 6 -0.39 36 42
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.069 0.14 0.25 3 -0.39 36 39
PRKCB -0.07 0.14 0.25 3 -0.38 43 46
PRKCE -0.068 0.13 0.25 2 -0.39 37 39
PRKCD -0.065 0.13 -10000 0 -0.39 33 33
PRKCG -0.089 0.14 0.25 2 -0.4 48 50
regulation of vascular smooth muscle contraction -0.17 0.37 -10000 0 -1.1 66 66
PRKCQ -0.073 0.14 0.29 3 -0.41 43 46
PLA2G4A -0.1 0.21 0.29 2 -0.53 59 61
GNA14 -0.043 0.17 -10000 0 -0.45 72 72
GNA15 0.025 0.031 -10000 0 -0.45 2 2
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.038 -10000 0 -0.45 3 3
Rac1/GTP -0.042 0.23 0.32 8 -0.38 72 80
MMP1 -0.23 0.19 0.46 20 -0.35 186 206
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.099 0.17 -10000 0 -0.54 33 33
Syndecan-4/Syndesmos -0.16 0.16 -10000 0 -0.5 38 38
positive regulation of JNK cascade -0.17 0.15 -10000 0 -0.51 35 35
Syndecan-4/ADAM12 -0.28 0.19 -10000 0 -0.44 216 216
CCL5 -0.036 0.15 -10000 0 -0.4 75 75
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DNM2 0.028 0.004 -10000 0 -10000 0 0
ITGA5 -0.1 0.19 -10000 0 -0.39 152 152
SDCBP 0.025 0.009 -10000 0 -10000 0 0
PLG 0.015 0.042 -10000 0 -0.38 4 4
ADAM12 -0.27 0.19 -10000 0 -0.39 352 352
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.08 0.043 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.21 0.18 -10000 0 -0.46 118 118
Syndecan-4/CXCL12/CXCR4 -0.18 0.16 -10000 0 -0.55 35 35
Syndecan-4/Laminin alpha3 -0.2 0.18 -10000 0 -0.45 105 105
MDK 0.01 0.084 -10000 0 -0.4 20 20
Syndecan-4/FZD7 -0.16 0.16 -10000 0 -0.49 40 40
Syndecan-4/Midkine -0.16 0.16 -10000 0 -0.48 44 44
FZD7 0.023 0.044 -10000 0 -0.4 5 5
Syndecan-4/FGFR1/FGF -0.15 0.15 -10000 0 -0.6 17 17
THBS1 0.012 0.081 -10000 0 -0.41 17 17
integrin-mediated signaling pathway -0.18 0.17 -10000 0 -0.44 91 91
positive regulation of MAPKKK cascade -0.17 0.15 -10000 0 -0.51 35 35
Syndecan-4/TACI -0.18 0.16 -10000 0 -0.47 54 54
CXCR4 0.013 0.077 -10000 0 -0.39 17 17
cell adhesion -0.07 0.099 0.2 4 -0.22 104 108
Syndecan-4/Dynamin -0.16 0.16 -10000 0 -0.5 38 38
Syndecan-4/TSP1 -0.16 0.16 -10000 0 -0.48 49 49
Syndecan-4/GIPC -0.16 0.16 -10000 0 -0.5 37 37
Syndecan-4/RANTES -0.18 0.17 -10000 0 -0.46 70 70
ITGB1 0.027 0.005 -10000 0 -10000 0 0
LAMA1 -0.13 0.2 -10000 0 -0.39 177 177
LAMA3 -0.087 0.19 -10000 0 -0.39 132 132
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.04 0.092 0.85 5 -0.4 2 7
Syndecan-4/alpha-Actinin -0.16 0.16 -10000 0 -0.5 36 36
TFPI 0.023 0.045 -10000 0 -0.42 5 5
F2 -0.033 0.12 -10000 0 -0.39 46 46
alpha5/beta1 Integrin -0.057 0.15 -10000 0 -0.28 151 151
positive regulation of cell adhesion -0.25 0.2 -10000 0 -0.48 151 151
ACTN1 0.026 0.007 -10000 0 -10000 0 0
TNC -0.049 0.16 -10000 0 -0.39 89 89
Syndecan-4/CXCL12 -0.18 0.16 -10000 0 -0.5 47 47
FGF6 -0.009 0.018 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
CXCL12 -0.021 0.14 -10000 0 -0.45 50 50
TNFRSF13B -0.027 0.13 -10000 0 -0.39 56 56
FGF2 0.012 0.082 -10000 0 -0.44 16 16
FGFR1 0.02 0.044 -10000 0 -0.4 5 5
Syndecan-4/PI-4-5-P2 -0.16 0.15 -10000 0 -0.49 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.16 0.21 -10000 0 -0.39 217 217
cell migration -0.032 0.017 -10000 0 -10000 0 0
PRKCD 0.029 0.015 -10000 0 -10000 0 0
vasculogenesis -0.16 0.15 -10000 0 -0.46 49 49
SDC4 -0.17 0.16 -10000 0 -0.5 38 38
Syndecan-4/Tenascin C -0.19 0.18 -10000 0 -0.46 91 91
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 -0.5 37 37
MMP9 -0.27 0.19 -10000 0 -0.39 349 349
Rac1/GTP -0.072 0.1 0.21 4 -0.22 103 107
cytoskeleton organization -0.15 0.15 -10000 0 -0.47 38 38
GIPC1 0.028 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.16 -10000 0 -0.48 41 41
Syndecan-2-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
Syndecan-2/Fibronectin -0.08 0.14 -10000 0 -0.24 194 194
EPHB2 -0.064 0.17 -10000 0 -0.39 107 107
Syndecan-2/TACI -0.011 0.089 -10000 0 -0.23 69 69
LAMA1 -0.13 0.2 -10000 0 -0.39 177 177
Syndecan-2/alpha2 ITGB1 -0.014 0.11 -10000 0 -0.36 7 7
HRAS 0.026 0.021 -10000 0 -0.41 1 1
Syndecan-2/CASK 0.001 0.044 -10000 0 -0.22 18 18
ITGA5 -0.1 0.19 -10000 0 -0.39 152 152
BAX 0 0.045 -10000 0 -0.42 1 1
EPB41 0.027 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.042 -10000 0 -0.2 17 17
LAMA3 -0.087 0.19 -10000 0 -0.39 132 132
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.025 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 0.037 0.026 -10000 0 -0.32 2 2
dendrite morphogenesis -0.026 0.11 -10000 0 -0.24 99 99
Syndecan-2/GM-CSF -0.1 0.14 -10000 0 -0.24 241 241
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 0.007 -10000 0 -10000 0 0
MAPK3 -0.089 0.13 0.19 25 -0.22 235 260
MAPK1 -0.086 0.13 0.19 24 -0.21 230 254
Syndecan-2/RACK1 0.027 0.047 -10000 0 -0.19 17 17
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 0.024 0.038 -10000 0 -0.45 3 3
MAPK8 0.002 0.049 -10000 0 -0.24 19 19
Syndecan-2/alpha2/beta1 Integrin -0.038 0.12 -10000 0 -0.36 10 10
Syndecan-2/Kininogen 0.007 0.052 -10000 0 -0.25 17 17
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.028 0.067 0.19 45 -10000 0 45
Syndecan-2/CASK/Protein 4.1 0.016 0.044 -10000 0 -0.2 18 18
extracellular matrix organization 0.017 0.051 -10000 0 -0.24 18 18
actin cytoskeleton reorganization -0.08 0.14 -10000 0 -0.24 194 194
Syndecan-2/Caveolin-2/Ras 0.028 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 -0.3 2 2
alpha5/beta1 Integrin -0.057 0.15 -10000 0 -0.28 151 151
PRKCD 0.024 0.009 -10000 0 -10000 0 0
Syndecan-2 dimer -0.027 0.11 -10000 0 -0.24 99 99
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 0.049 -10000 0 -0.39 1 1
RHOA 0.025 0.009 -10000 0 -10000 0 0
SDCBP 0.025 0.009 -10000 0 -10000 0 0
TNFRSF13B -0.027 0.13 -10000 0 -0.39 56 56
RASA1 0.024 0.031 -10000 0 -0.45 2 2
alpha2/beta1 Integrin 0.037 0.026 -10000 0 -0.32 2 2
Syndecan-2/Synbindin 0.015 0.048 -10000 0 -0.22 18 18
TGFB1 0.026 0.027 -10000 0 -0.39 2 2
CASP3 0.025 0.068 0.19 49 -0.2 14 63
FN1 -0.16 0.21 -10000 0 -0.39 217 217
Syndecan-2/IL8 -0.031 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 -0.39 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 -0.2 0.21 -10000 0 -0.39 271 271
Syndecan-2/TGFB1 0.017 0.051 -10000 0 -0.24 18 18
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.043 -10000 0 -0.2 17 17
Syndecan-2/Ezrin 0.027 0.048 -10000 0 -0.2 16 16
PRKACA 0.03 0.073 0.19 59 -0.2 17 76
angiogenesis -0.031 0.11 -10000 0 -0.24 106 106
MMP2 -0.028 0.14 -10000 0 -0.39 64 64
IL8 -0.063 0.17 -10000 0 -0.4 105 105
calcineurin-NFAT signaling pathway -0.011 0.089 -10000 0 -0.23 69 69
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.017 0.14 -10000 0 -0.28 86 86
alphaM/beta2 Integrin/GPIbA 0.007 0.11 -10000 0 -0.3 48 48
alphaM/beta2 Integrin/proMMP-9 -0.18 0.15 -10000 0 -0.26 351 351
PLAUR 0.003 0.097 -10000 0 -0.39 28 28
HMGB1 0.019 0.026 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.013 0.097 -10000 0 -0.29 35 35
AGER 0.014 0.055 -10000 0 -0.4 7 7
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.028 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.017 0.12 -10000 0 -0.38 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.27 0.19 -10000 0 -0.39 349 349
CYR61 0.023 0.044 -10000 0 -0.4 5 5
TLN1 0.024 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.071 0.12 -10000 0 -0.33 31 31
RHOA 0.025 0.009 -10000 0 -10000 0 0
P-selectin oligomer -0.058 0.18 -10000 0 -0.45 88 88
MYH2 -0.21 0.18 -10000 0 -0.4 176 176
MST1R 0.02 0.048 -10000 0 -0.45 5 5
leukocyte activation during inflammatory response 0.01 0.1 -10000 0 -0.29 30 30
APOB 0.007 0.07 -10000 0 -0.4 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.028 0.14 -10000 0 -0.39 64 64
JAM3 0.025 0.02 -10000 0 -0.39 1 1
GP1BA 0.007 0.08 -10000 0 -0.41 17 17
alphaM/beta2 Integrin/CTGF 0.014 0.1 -10000 0 -0.3 40 40
alphaM/beta2 Integrin -0.091 0.12 -10000 0 -0.34 44 44
JAM3 homodimer 0.025 0.02 -10000 0 -0.39 1 1
ICAM2 0.025 0.036 -10000 0 -0.43 3 3
ICAM1 0.005 0.094 -10000 0 -0.39 26 26
phagocytosis triggered by activation of immune response cell surface activating receptor -0.09 0.12 -10000 0 -0.34 43 43
cell adhesion 0.006 0.11 -10000 0 -0.3 48 48
NFKB1 -0.028 0.14 -10000 0 -0.38 48 48
THY1 -0.089 0.19 -10000 0 -0.39 134 134
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
Lipoprotein(a) 0.02 0.056 -10000 0 -0.24 22 22
alphaM/beta2 Integrin/LRP/tPA 0.025 0.1 -10000 0 -0.34 19 19
IL6 -0.057 0.2 -10000 0 -0.66 41 41
ITGB2 0.007 0.074 -10000 0 -0.4 14 14
elevation of cytosolic calcium ion concentration -0.092 0.17 -10000 0 -0.37 64 64
alphaM/beta2 Integrin/JAM2/JAM3 0.023 0.11 -10000 0 -0.32 27 27
JAM2 0.015 0.074 -10000 0 -0.45 12 12
alphaM/beta2 Integrin/ICAM1 0.021 0.12 -10000 0 -0.38 21 21
alphaM/beta2 Integrin/uPA/Plg -0.087 0.15 -10000 0 -0.24 219 219
RhoA/GTP -0.13 0.14 -10000 0 -0.35 96 96
positive regulation of phagocytosis -0.061 0.11 -10000 0 -0.35 24 24
Ron/MSP 0.03 0.05 -10000 0 -0.3 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.091 0.17 -10000 0 -0.37 64 64
alphaM/beta2 Integrin/uPAR 0.002 0.12 -10000 0 -0.3 56 56
PLAU -0.15 0.21 -10000 0 -0.39 209 209
PLAT 0.015 0.066 -10000 0 -0.4 12 12
actin filament polymerization -0.2 0.17 0.23 1 -0.39 168 169
MST1 0.02 0.044 -10000 0 -0.41 5 5
alphaM/beta2 Integrin/lipoprotein(a) 0.014 0.1 -10000 0 -0.29 30 30
TNF -0.039 0.14 -10000 0 -0.57 13 13
RAP1B 0.027 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.098 0.16 -10000 0 -0.26 231 231
fibrinolysis -0.087 0.15 -10000 0 -0.24 219 219
HCK 0.024 0.029 -10000 0 -0.42 2 2
dendritic cell antigen processing and presentation -0.09 0.12 -10000 0 -0.34 43 43
VTN 0.001 0.1 -10000 0 -0.39 30 30
alphaM/beta2 Integrin/CYR61 0.014 0.1 -10000 0 -0.3 38 38
LPA 0.001 0.058 -10000 0 -0.39 9 9
LRP1 0.027 0.022 -10000 0 -0.45 1 1
cell migration -0.18 0.17 -10000 0 -0.39 112 112
FN1 -0.16 0.21 -10000 0 -0.39 217 217
alphaM/beta2 Integrin/Thy1 -0.057 0.16 -10000 0 -0.27 148 148
MPO 0.009 0.085 -10000 0 -0.44 17 17
KNG1 -0.01 0.061 -10000 0 -0.39 11 11
RAP1/GDP 0.035 0.01 -10000 0 -10000 0 0
ROCK1 -0.11 0.15 -10000 0 -0.35 78 78
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.015 0.038 -10000 0 -0.39 4 4
CTGF 0.022 0.051 -10000 0 -0.43 6 6
alphaM/beta2 Integrin/Hck 0.015 0.098 -10000 0 -0.3 33 33
ITGAM -0.007 0.1 -10000 0 -0.4 31 31
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.018 0.15 -10000 0 -0.27 101 101
HP -0.15 0.22 -10000 0 -0.45 174 174
leukocyte adhesion -0.048 0.14 -10000 0 -0.38 37 37
SELP -0.058 0.18 -10000 0 -0.45 88 88
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.12 0.13 -10000 0 -0.3 49 49
NF kappa B1 p50/RelA/I kappa B alpha -0.11 0.13 0.32 1 -0.37 13 14
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.16 -10000 0 -0.29 252 252
AP1 -0.16 0.18 -10000 0 -0.46 64 64
ILK -0.12 0.13 -10000 0 -0.38 14 14
bone resorption -0.094 0.12 0.33 1 -0.38 15 16
PTK2B 0.026 0.008 -10000 0 -10000 0 0
PYK2/p130Cas -0.082 0.14 -10000 0 -0.39 11 11
ITGAV 0.021 0.03 -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 -0.12 0.15 -10000 0 -0.28 156 156
MAP3K1 -0.12 0.13 -10000 0 -0.31 45 45
JUN 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.14 0.13 0.2 2 -0.3 128 130
MAPK1 -0.14 0.13 -10000 0 -0.3 122 122
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.12 0.12 0.2 1 -0.33 38 39
ITGB3 0.007 0.087 -10000 0 -0.42 19 19
NFKBIA -0.13 0.13 0.2 2 -0.3 122 124
FOS -0.033 0.16 -10000 0 -0.45 60 60
CD44 0.026 0.022 -10000 0 -0.45 1 1
CHUK 0.027 0.005 -10000 0 -10000 0 0
PLAU -0.2 0.19 -10000 0 -0.5 50 50
NF kappa B1 p50/RelA -0.12 0.15 -10000 0 -0.41 10 10
BCAR1 0.027 0.006 -10000 0 -10000 0 0
RELA 0.027 0.007 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.012 0.073 -10000 0 -0.3 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.12 0.13 -10000 0 -0.3 42 42
VAV3 -0.12 0.13 0.19 1 -0.4 31 32
MAP3K14 -0.13 0.13 -10000 0 -0.29 126 126
ROCK2 0.019 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 29 29
MMP2 -0.16 0.17 -10000 0 -0.49 66 66
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.43 0.4 -10000 0 -1.2 76 76
IL23A -0.4 0.36 -10000 0 -1.1 65 65
NF kappa B1 p50/RelA/I kappa B alpha -0.39 0.37 -10000 0 -1.1 78 78
positive regulation of T cell mediated cytotoxicity -0.44 0.41 -10000 0 -1.2 84 84
ITGA3 -0.4 0.35 -10000 0 -1.1 69 69
IL17F -0.26 0.25 -10000 0 -0.7 64 64
IL12B -0.062 0.12 -10000 0 -0.43 43 43
STAT1 (dimer) -0.43 0.4 -10000 0 -1.1 86 86
CD4 -0.39 0.35 -10000 0 -1.1 64 64
IL23 -0.4 0.36 -10000 0 -1.1 66 66
IL23R -0.07 0.13 -10000 0 -0.93 8 8
IL1B -0.42 0.37 -10000 0 -1.1 73 73
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.48 0.35 -10000 0 -1.1 79 79
TYK2 -0.021 0.032 -10000 0 -0.43 1 1
STAT4 0.018 0.063 -10000 0 -0.4 11 11
STAT3 0.028 0.004 -10000 0 -10000 0 0
IL18RAP 0.006 0.085 -10000 0 -0.42 18 18
IL12RB1 -0.055 0.12 -10000 0 -0.42 44 44
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.046 0.093 -10000 0 -0.32 45 45
IL23R/JAK2 -0.08 0.13 -10000 0 -0.86 7 7
positive regulation of chronic inflammatory response -0.44 0.41 -10000 0 -1.2 84 84
natural killer cell activation 0.007 0.006 0.041 4 -10000 0 4
JAK2 -0.023 0.03 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
NFKB1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.024 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.38 0.34 -10000 0 -1 67 67
ALOX12B -0.47 0.41 -10000 0 -1.2 87 87
CXCL1 -0.43 0.39 -10000 0 -1.1 81 81
T cell proliferation -0.44 0.41 -10000 0 -1.2 84 84
NFKBIA 0.024 0.007 -10000 0 -10000 0 0
IL17A -0.21 0.2 -10000 0 -0.56 42 42
PI3K -0.38 0.37 -10000 0 -1.1 79 79
IFNG -0.025 0.035 0.095 4 -0.12 8 12
STAT3 (dimer) -0.37 0.35 -10000 0 -1 73 73
IL18R1 0.02 0.033 -10000 0 -0.43 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.25 0.22 -10000 0 -0.77 29 29
IL18/IL18R 0.02 0.086 -10000 0 -0.27 30 30
macrophage activation -0.023 0.015 -10000 0 -0.045 27 27
TNF -0.41 0.37 -10000 0 -1.1 69 69
STAT3/STAT4 -0.41 0.38 -10000 0 -1.1 82 82
STAT4 (dimer) -0.43 0.39 -10000 0 -1.1 84 84
IL18 0.008 0.074 -10000 0 -0.45 12 12
IL19 -0.53 0.5 -10000 0 -1.3 132 132
STAT5A (dimer) -0.43 0.39 -10000 0 -1.1 84 84
STAT1 0.009 0.085 -10000 0 -0.39 21 21
SOCS3 0.027 0.022 -10000 0 -0.45 1 1
CXCL9 -0.47 0.37 -10000 0 -1.1 84 84
MPO -0.42 0.38 -10000 0 -1.1 77 77
positive regulation of humoral immune response -0.44 0.41 -10000 0 -1.2 84 84
IL23/IL23R/JAK2/TYK2 -0.46 0.44 -10000 0 -1.2 84 84
IL6 -0.43 0.42 -10000 0 -1.2 78 78
STAT5A 0.028 0.003 -10000 0 -10000 0 0
IL2 0.014 0.029 -10000 0 -0.38 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.007 0.006 0.041 4 -10000 0 4
CD3E -0.4 0.36 -10000 0 -1.1 66 66
keratinocyte proliferation -0.44 0.41 -10000 0 -1.2 84 84
NOS2 -0.43 0.38 -10000 0 -1.1 75 75
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.031 0.12 -10000 0 -0.42 37 37
Crk/p130 Cas/Paxillin -0.065 0.11 -10000 0 -0.34 28 28
JUN -0.04 0.12 -10000 0 -0.35 25 25
HRAS 0.026 0.021 -10000 0 -0.41 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.045 0.16 -10000 0 -0.28 138 138
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.049 0.16 -10000 0 -0.3 111 111
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.039 0.14 -10000 0 -0.26 127 127
RHOA 0.025 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.042 0.14 -10000 0 -0.38 30 30
GRB7 0.026 0.031 -10000 0 -0.45 2 2
RET51/GFRalpha1/GDNF -0.049 0.16 -10000 0 -0.3 109 109
MAPKKK cascade -0.048 0.12 -10000 0 -0.36 27 27
BCAR1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.039 0.14 -10000 0 -0.26 127 127
lamellipodium assembly -0.044 0.11 -10000 0 -0.27 65 65
RET51/GFRalpha1/GDNF/SHC -0.05 0.16 -10000 0 -0.3 111 111
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.038 0.14 -10000 0 -0.26 126 126
RET9/GFRalpha1/GDNF/Shank3 -0.037 0.14 -10000 0 -0.26 125 125
MAPK3 -0.055 0.14 0.34 4 -0.38 27 31
DOK1 0.027 0.019 -10000 0 -0.39 1 1
DOK6 0.015 0.067 -10000 0 -0.42 11 11
PXN 0.028 0.003 -10000 0 -10000 0 0
neurite development -0.051 0.12 0.33 4 -0.35 26 30
DOK5 0.003 0.1 -10000 0 -0.44 25 25
GFRA1 -0.086 0.2 -10000 0 -0.45 117 117
MAPK8 -0.051 0.11 -10000 0 -0.34 32 32
HRAS/GTP -0.046 0.14 -10000 0 -0.3 84 84
tube development -0.034 0.13 -10000 0 -0.26 99 99
MAPK1 -0.055 0.13 0.32 5 -0.38 24 29
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.04 0.1 -10000 0 -0.24 96 96
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
PDLIM7 0.023 0.038 -10000 0 -0.39 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.042 0.16 -10000 0 -0.29 99 99
SHC1 0.028 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.049 0.16 -10000 0 -0.3 110 110
RET51/GFRalpha1/GDNF/Dok5 -0.06 0.17 -10000 0 -0.32 113 113
PRKCA 0.026 0.029 -10000 0 -0.42 2 2
HRAS/GDP 0.019 0.015 -10000 0 -0.29 1 1
CREB1 -0.053 0.13 -10000 0 -0.37 33 33
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.042 0.11 -10000 0 -0.24 100 100
RET51/GFRalpha1/GDNF/Grb7 -0.048 0.16 -10000 0 -0.28 149 149
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.019 0.13 -10000 0 -0.4 53 53
DOK4 0.027 0.006 -10000 0 -10000 0 0
JNK cascade -0.04 0.11 -10000 0 -0.34 25 25
RET9/GFRalpha1/GDNF/FRS2 -0.037 0.14 -10000 0 -0.26 122 122
SHANK3 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
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.041 0.11 -10000 0 -0.24 97 97
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.047 0.12 -10000 0 -0.28 52 52
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.049 0.11 -10000 0 -0.33 33 33
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.049 0.12 -10000 0 -0.36 29 29
PI3K -0.06 0.17 -10000 0 -0.39 72 72
SOS1 0.028 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.025 0.13 -10000 0 -0.26 99 99
GRB10 0.026 0.007 -10000 0 -10000 0 0
activation of MAPKK activity -0.038 0.12 -10000 0 -0.32 28 28
RET51/GFRalpha1/GDNF/FRS2 -0.048 0.16 -10000 0 -0.3 107 107
GAB1 0.027 0.005 -10000 0 -10000 0 0
IRS1 0.024 0.037 -10000 0 -0.45 3 3
IRS2 0.025 0.031 -10000 0 -0.45 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.051 0.12 -10000 0 -0.37 30 30
RET51/GFRalpha1/GDNF/PKC alpha -0.049 0.16 -10000 0 -0.3 109 109
GRB2 0.028 0.004 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GDNF -0.016 0.11 -10000 0 -0.39 37 37
RAC1 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.051 0.16 -10000 0 -0.3 112 112
Rac1/GTP -0.045 0.14 -10000 0 -0.35 41 41
RET9/GFRalpha1/GDNF -0.053 0.14 -10000 0 -0.29 126 126
GFRalpha1/GDNF -0.063 0.17 -10000 0 -0.34 126 126
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 -0.028 0.13 -10000 0 -0.24 125 125
regulation of S phase of mitotic cell cycle -0.027 0.093 -10000 0 -0.23 83 83
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
HRAS 0.026 0.021 -10000 0 -0.41 1 1
SHBG/T-DHT 0.018 0.004 -10000 0 -10000 0 0
PELP1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.051 0.1 0.18 15 -0.31 15 30
T-DHT/AR -0.071 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 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.45 1 1
mol:GDP -0.084 0.15 -10000 0 -0.34 121 121
cell proliferation -0.085 0.17 0.28 3 -0.43 69 72
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
FOS -0.1 0.27 0.28 3 -0.77 66 69
mol:Ca2+ -0.009 0.021 -10000 0 -0.063 37 37
MAPK3 -0.074 0.14 0.3 2 -0.32 67 69
MAPK1 -0.033 0.097 0.2 1 -0.31 23 24
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
mol:IP3 0 0.002 -10000 0 -0.004 63 63
cAMP biosynthetic process 0.005 0.022 0.21 2 -10000 0 2
GNG2 0.025 0.02 -10000 0 -0.39 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 63 63
HRAS/GTP -0.029 0.12 -10000 0 -0.22 120 120
actin cytoskeleton reorganization 0.027 0.027 -10000 0 -0.22 2 2
SRC 0.026 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 0.068 0.16 0.42 73 -0.25 2 75
T-DHT/AR/PELP1 -0.048 0.13 -10000 0 -0.27 131 131
HRAS/GDP -0.071 0.15 -10000 0 -0.32 118 118
CREB1 -0.073 0.17 0.26 2 -0.44 73 75
RAC1-CDC42/GTP 0.033 0.031 -10000 0 -0.22 2 2
AR -0.1 0.21 -10000 0 -0.45 131 131
GNB1 0.027 0.006 -10000 0 -10000 0 0
RAF1 -0.045 0.11 0.26 2 -0.28 16 18
RAC1-CDC42/GDP -0.038 0.16 -10000 0 -0.32 111 111
T-DHT/AR/PELP1/Src -0.029 0.13 -10000 0 -0.25 121 121
MAP2K2 -0.051 0.1 0.22 3 -0.3 16 19
T-DHT/AR/PELP1/Src/PI3K -0.027 0.094 -10000 0 -0.23 83 83
GNAZ 0.011 0.083 -10000 0 -0.41 18 18
SHBG 0.024 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.029 0.13 -10000 0 -0.46 30 30
mol:T-DHT 0 0.001 0.002 3 -0.002 38 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 0.082 -10000 0 -0.27 27 27
CDC42 0.027 0.005 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.024 -10000 0 -0.27 3 3
Metarhodopsin II/Arrestin 0.021 0.023 -10000 0 -0.24 3 3
PDE6G/GNAT1/GTP 0.02 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 -0.39 3 3
GRK1 -0.009 0.026 -10000 0 -0.39 1 1
CNG Channel -0.21 0.17 -10000 0 -0.4 160 160
mol:Na + -0.11 0.14 -10000 0 -0.38 46 46
mol:ADP -0.009 0.026 -10000 0 -0.39 1 1
RGS9-1/Gbeta5/R9AP 0.04 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 -0.39 46 46
CNGB1 -0.19 0.21 -10000 0 -0.39 253 253
RDH5 0.026 0.029 -10000 0 -0.42 2 2
SAG -0.012 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.11 0.15 0.36 7 -0.38 45 52
Na + (4 Units) -0.11 0.13 -10000 0 -0.37 45 45
RGS9 0.018 0.064 -10000 0 -0.4 11 11
GNB1/GNGT1 -0.001 0.1 -10000 0 -0.28 57 57
GNAT1/GDP 0.04 0.064 -10000 0 -0.24 20 20
GUCY2D 0.004 0.094 -10000 0 -0.39 26 26
GNGT1 -0.028 0.13 -10000 0 -0.39 57 57
GUCY2F -0.009 0.026 -10000 0 -0.39 1 1
GNB5 0.027 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.11 0.14 -10000 0 -0.25 229 229
mol:11-cis-retinal 0.026 0.029 -10000 0 -0.42 2 2
mol:cGMP 0.006 0.092 -10000 0 -0.3 9 9
GNB1 0.027 0.006 -10000 0 -10000 0 0
Rhodopsin 0.028 0.035 -10000 0 -0.29 5 5
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 -0.004 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 0.014 0.099 -10000 0 -0.23 64 64
RGS9BP 0.015 0.071 -10000 0 -0.45 11 11
Metarhodopsin II/Transducin -0.005 0.052 -10000 0 -0.26 9 9
GCAP Family/Ca ++ 0.012 0.08 -10000 0 -0.22 51 51
PDE6A/B -0.14 0.19 -10000 0 -0.34 227 227
mol:Pi 0.039 0.064 -10000 0 -0.26 21 21
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.009 0.083 -10000 0 -0.21 57 57
PDE6B -0.01 0.12 -10000 0 -0.42 39 39
PDE6A -0.18 0.23 -10000 0 -0.45 206 206
PDE6G 0.015 0.072 -10000 0 -0.39 15 15
RHO -0.006 0.036 -10000 0 -0.39 3 3
PDE6 -0.089 0.16 -10000 0 -0.26 204 204
GUCA1A -0.018 0.13 -10000 0 -0.39 50 50
GC2/GCAP Family 0.02 0.086 -10000 0 -0.23 50 50
GUCA1C -0.017 0.006 -10000 0 -10000 0 0
GUCA1B 0.023 0.042 -10000 0 -0.44 4 4
TCGA08_p53

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
CDKN2A -0.1 0.14 -10000 0 -0.28 183 183
TP53 -0.031 0.064 -10000 0 -0.3 19 19
Senescence -0.035 0.07 -10000 0 -0.3 25 25
Apoptosis -0.035 0.07 -10000 0 -0.3 25 25
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.059 0.093 0.29 27 -10000 0 27
MDM4 0.028 0.004 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.034 0.14 0.3 4 -0.38 58 62
CRKL -0.038 0.14 -10000 0 -0.4 58 58
HRAS -0.026 0.14 -10000 0 -0.36 53 53
mol:PIP3 -0.018 0.14 0.31 1 -0.36 58 59
SPRED1 0.028 0.004 -10000 0 -10000 0 0
SPRED2 0.026 0.031 -10000 0 -0.45 2 2
GAB1 -0.038 0.15 -10000 0 -0.42 61 61
FOXO3 -0.026 0.15 0.36 1 -0.37 59 60
AKT1 -0.029 0.16 -10000 0 -0.39 66 66
BAD -0.023 0.15 0.28 2 -0.37 60 62
megakaryocyte differentiation -0.042 0.15 -10000 0 -0.4 64 64
GSK3B -0.007 0.16 0.32 2 -0.37 49 51
RAF1 -0.018 0.11 -10000 0 -0.32 20 20
SHC1 0.028 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 -0.99 64 64
HRAS/SPRED1 -0.01 0.12 -10000 0 -0.33 20 20
cell proliferation -0.04 0.15 -10000 0 -0.42 61 61
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
TEC 0.008 0.092 -10000 0 -0.45 19 19
RPS6KB1 -0.03 0.16 -10000 0 -0.4 65 65
HRAS/SPRED2 -0.011 0.13 -10000 0 -0.35 18 18
LYN/TEC/p62DOK -0.015 0.16 -10000 0 -0.41 50 50
MAPK3 -0.011 0.091 -10000 0 -0.27 15 15
STAP1 -0.05 0.15 0.25 1 -0.41 65 66
GRAP2 0.016 0.07 -10000 0 -0.43 12 12
JAK2 -0.096 0.31 -10000 0 -0.85 64 64
STAT1 (dimer) -0.11 0.34 -10000 0 -0.96 64 64
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 -0.04 0.14 -10000 0 -0.41 60 60
LYN 0.024 0.021 -10000 0 -0.39 1 1
STAP1/STAT5A (dimer) -0.069 0.22 0.27 1 -0.58 65 66
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
CBL/CRKL/GRB2 -0.008 0.14 0.28 1 -0.37 52 53
PI3K -0.015 0.14 -10000 0 -0.4 46 46
PTEN 0.027 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 0.077 -10000 0 -0.23 11 11
mol:GDP -0.026 0.15 -10000 0 -0.37 55 55
PIK3C2B -0.039 0.15 -10000 0 -0.42 62 62
CBL/CRKL -0.019 0.14 0.28 1 -0.38 57 58
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 -0.35 52 53
SNAI2 -0.037 0.14 -10000 0 -0.4 53 53
positive regulation of cell proliferation -0.078 0.26 -10000 0 -0.72 64 64
KITLG 0.018 0.045 -10000 0 -0.47 3 3
cell motility -0.078 0.26 -10000 0 -0.72 64 64
PTPN6 0.027 0.011 -10000 0 -10000 0 0
EPOR -0.016 0.17 -10000 0 -0.8 11 11
STAT5A (dimer) -0.059 0.22 -10000 0 -0.59 65 65
SOCS1 -0.003 0.11 -10000 0 -0.39 36 36
cell migration 0.042 0.15 0.41 63 -10000 0 63
SOS1 0.028 0.004 -10000 0 -10000 0 0
EPO -0.022 0.12 -10000 0 -0.39 49 49
VAV1 0.02 0.06 -10000 0 -0.44 8 8
GRB10 -0.037 0.15 -10000 0 -0.41 57 57
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.038 0.16 -10000 0 -0.43 63 63
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.013 0.093 0.19 1 -0.29 9 10
CBL 0.025 0.008 -10000 0 -10000 0 0
KIT -0.14 0.44 -10000 0 -1.2 70 70
MAP2K2 -0.014 0.093 0.19 1 -0.29 9 10
SHC/Grb2/SOS1 -0.003 0.16 -10000 0 -0.39 57 57
STAT5A -0.058 0.22 -10000 0 -0.61 64 64
GRB2 0.028 0.004 -10000 0 -10000 0 0
response to radiation -0.036 0.14 0.21 2 -0.4 53 55
SHC/GRAP2 0.031 0.054 -10000 0 -0.3 12 12
PTPRO -0.043 0.15 -10000 0 -0.41 64 64
SH2B2 -0.041 0.15 -10000 0 -0.42 60 60
DOK1 0.027 0.019 -10000 0 -0.39 1 1
MATK -0.043 0.15 -10000 0 -0.42 63 63
CREBBP 0.024 0.052 -10000 0 -10000 0 0
BCL2 -0.065 0.28 -10000 0 -0.98 29 29
IGF1 pathway

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
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTK2 0.023 0.011 -10000 0 -10000 0 0
CRKL -0.022 0.091 -10000 0 -0.23 73 73
GRB2/SOS1/SHC 0.054 0.012 -10000 0 -10000 0 0
HRAS 0.026 0.021 -10000 0 -0.41 1 1
IRS1/Crk -0.016 0.096 -10000 0 -0.23 77 77
IGF-1R heterotetramer/IGF1/PTP1B 0.002 0.11 -10000 0 -0.26 77 77
AKT1 0.009 0.11 0.18 102 -0.38 2 104
BAD 0.005 0.1 0.22 12 -0.36 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.023 0.092 -10000 0 -0.23 76 76
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.011 0.099 0.21 1 -0.24 77 78
RAF1 -0.011 0.16 0.28 10 -0.44 38 48
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.018 0.1 -10000 0 -0.22 70 70
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.012 0.11 -10000 0 -0.25 81 81
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
RPS6KB1 0.012 0.11 0.18 114 -0.38 2 116
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.008 0.14 0.26 13 -0.37 28 41
PXN 0.028 0.003 -10000 0 -10000 0 0
PIK3R1 0.024 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 0.033 0.1 -10000 0 -0.26 1 1
IGF-1R heterotetramer 0.013 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.005 0.1 -10000 0 -0.24 75 75
Crk/p130 Cas/Paxillin 0.015 0.1 0.22 2 -0.22 66 68
IGF1R 0.013 0.039 -10000 0 -10000 0 0
IGF1 -0.053 0.18 -10000 0 -0.46 84 84
IRS2/Crk -0.014 0.093 -10000 0 -0.23 74 74
PI3K 0.009 0.093 -10000 0 -0.23 55 55
apoptosis -0.026 0.095 0.31 1 -0.25 17 18
HRAS/GDP 0.019 0.015 -10000 0 -0.29 1 1
PRKCD -0.035 0.13 -10000 0 -0.33 72 72
RAF1/14-3-3 E 0 0.16 0.28 12 -0.39 35 47
BAD/14-3-3 0.027 0.099 0.27 14 -0.33 1 15
PRKCZ 0.007 0.11 0.18 102 -0.38 2 104
Crk/p130 Cas/Paxillin/FAK1 0.021 0.083 -10000 0 -0.3 1 1
PTPN1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.039 0.14 -10000 0 -0.35 78 78
BCAR1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.017 0.11 -10000 0 -0.23 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.008 0.099 -10000 0 -0.23 75 75
GRB10 0.026 0.007 -10000 0 -10000 0 0
PTPN11 -0.023 0.093 -10000 0 -0.23 77 77
IRS1 -0.026 0.1 -10000 0 -0.25 81 81
IRS2 -0.024 0.093 -10000 0 -0.24 75 75
IGF-1R heterotetramer/IGF1 -0.02 0.14 -10000 0 -0.34 79 79
GRB2 0.028 0.004 -10000 0 -10000 0 0
PDPK1 0.02 0.11 0.18 106 -0.4 2 108
YWHAE 0.027 0.006 -10000 0 -10000 0 0
PRKD1 -0.04 0.13 -10000 0 -0.34 69 69
SHC1 0.028 0.004 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.038 0.023 -10000 0 -0.28 2 2
VLDLR 0.018 0.057 -10000 0 -0.45 7 7
CRKL 0.026 0.02 -10000 0 -0.39 1 1
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.019 -10000 0 -0.39 1 1
ITGA3 0.012 0.08 -10000 0 -0.4 18 18
RELN/VLDLR/Fyn -0.02 0.13 -10000 0 -0.27 99 99
MAPK8IP1/MKK7/MAP3K11/JNK1 0.068 0.045 -10000 0 -0.24 3 3
AKT1 -0.021 0.079 -10000 0 -0.22 57 57
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
DAB1 -0.001 0.075 -10000 0 -0.39 16 16
RELN/LRP8/DAB1 -0.025 0.13 -10000 0 -0.25 116 116
LRPAP1/LRP8 0.032 0.045 -10000 0 -0.27 10 10
RELN/LRP8/DAB1/Fyn -0.014 0.13 -10000 0 -0.24 116 116
DAB1/alpha3/beta1 Integrin -0.023 0.12 -10000 0 -0.38 7 7
long-term memory -0.06 0.16 -10000 0 -0.39 38 38
DAB1/LIS1 -0.009 0.13 -10000 0 -0.38 6 6
DAB1/CRLK/C3G -0.018 0.12 -10000 0 -0.38 7 7
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DAB1/NCK2 -0.008 0.13 -10000 0 -0.24 84 84
ARHGEF2 0.028 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.072 0.18 -10000 0 -0.43 105 105
CDK5R1 0.026 0.027 -10000 0 -0.39 2 2
RELN -0.07 0.19 -10000 0 -0.45 98 98
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
RELN/LRP8/Fyn -0.02 0.14 -10000 0 -0.27 106 106
GRIN2A/RELN/LRP8/DAB1/Fyn -0.059 0.17 -10000 0 -0.28 133 133
MAPK8 0.022 0.052 -10000 0 -0.45 6 6
RELN/VLDLR/DAB1 -0.025 0.12 -10000 0 -0.25 110 110
ITGB1 0.027 0.005 -10000 0 -10000 0 0
MAP1B -0.037 0.13 0.2 1 -0.26 93 94
RELN/LRP8 -0.02 0.13 -10000 0 -0.27 104 104
GRIN2B/RELN/LRP8/DAB1/Fyn -0.009 0.13 -10000 0 -0.25 89 89
PI3K 0.027 0.03 -10000 0 -0.32 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.06 -10000 0 -0.28 18 18
RAP1A -0.028 0.13 0.34 10 -0.38 6 16
PAFAH1B1 0.027 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.023 0.039 -10000 0 -0.41 4 4
CRLK/C3G 0.038 0.018 -10000 0 -0.28 1 1
GRIN2B -0.009 0.044 -10000 0 -0.39 5 5
NCK2 0.028 0.003 -10000 0 -10000 0 0
neuron differentiation -0.014 0.089 -10000 0 -0.29 17 17
neuron adhesion -0.033 0.12 0.34 9 -0.37 6 15
LRP8 0.019 0.059 -10000 0 -0.39 10 10
GSK3B -0.012 0.087 -10000 0 -0.31 8 8
RELN/VLDLR/DAB1/Fyn -0.016 0.12 -10000 0 -0.23 111 111
MAP3K11 0.027 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.022 0.089 -10000 0 -0.24 65 65
CDK5 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.17 0.21 0.8 1 -0.41 204 205
neuron migration -0.023 0.13 0.27 12 -0.29 54 66
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.014 0.09 -10000 0 -0.29 17 17
RELN/VLDLR -0.011 0.13 -10000 0 -0.25 104 104
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 -0.054 0.092 -10000 0 -0.3 52 52
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 -0.61 108 113
JUNB 0.028 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 0.026 -10000 0 -10000 0 0
CALM1 0.006 0.026 -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 0.015 -10000 0 -10000 0 0
FOSL1 0.016 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 -0.052 0.15 -10000 0 -0.46 60 60
IFNG -0.24 0.26 0.35 4 -0.6 116 120
AP-1/NFAT1-c-4 -0.25 0.27 -10000 0 -0.65 96 96
FASLG -0.23 0.25 0.34 4 -0.63 90 94
NFAT1-c-4/ICER1 -0.079 0.1 -10000 0 -0.32 37 37
IL2RA -0.23 0.25 0.35 6 -0.62 89 95
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.3 0.27 0.35 5 -0.6 171 176
JunB/Fra1/NFAT1-c-4 -0.077 0.11 -10000 0 -0.32 36 36
IL4 -0.22 0.23 0.34 6 -0.6 75 81
IL2 -0.012 0.15 -10000 0 -0.93 13 13
IL3 -0.04 0.17 -10000 0 -0.79 21 21
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
BATF3 0.024 0.038 -10000 0 -0.39 4 4
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.028 0.004 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.008 0.046 -10000 0 -0.45 1 1
SVIL 0.009 0.044 -10000 0 -0.45 1 1
ZNF318 0.052 0.06 0.2 13 -10000 0 13
JMJD2C 0.006 0.016 -10000 0 -0.068 12 12
T-DHT/AR/Ubc9 -0.09 0.14 -10000 0 -0.31 131 131
CARM1 0.023 0.014 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.031 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 0.031 -10000 0 -10000 0 0
MED1 0.036 0.019 -10000 0 -10000 0 0
MAK 0.042 0.083 0.19 74 -0.41 8 82
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 0.043 -10000 0 -10000 0 0
NCOA2 -0.009 0.12 -10000 0 -0.45 31 31
NCOA6 0.01 0.037 -10000 0 -10000 0 0
DNA-PK 0.067 0.058 0.26 2 -10000 0 2
NCOA4 0.026 0.006 -10000 0 -10000 0 0
PIAS3 0.012 0.033 -10000 0 -10000 0 0
cell proliferation -0.008 0.12 -10000 0 -0.55 14 14
XRCC5 0.033 0.015 -10000 0 -10000 0 0
UBE3A 0.004 0.052 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.1 0.16 -10000 0 -0.32 145 145
FHL2 -0.013 0.09 -10000 0 -0.48 4 4
RANBP9 0.011 0.037 -10000 0 -10000 0 0
JMJD1A -0.057 0.069 -10000 0 -0.13 233 233
CDK6 0.024 0.037 -10000 0 -0.43 3 3
TGFB1I1 -0.001 0.078 -10000 0 -0.4 14 14
T-DHT/AR/CyclinD1 -0.078 0.13 -10000 0 -0.31 97 97
XRCC6 0.033 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.12 0.17 -10000 0 -0.34 133 133
CTDSP1 0.018 0.022 -10000 0 -10000 0 0
CTDSP2 0.045 0.04 -10000 0 -10000 0 0
BRCA1 0.01 0.039 -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 0.16 -10000 0 -0.49 32 32
KLK3 -0.22 0.51 -10000 0 -1.3 84 84
TMF1 0.018 0.017 -10000 0 -10000 0 0
HNRNPA1 0.038 0.023 -10000 0 -10000 0 0
AOF2 -0.012 0.026 -10000 0 -0.07 82 82
APPL1 0.025 0.034 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.082 0.15 -10000 0 -0.3 129 129
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 0.021 0.017 -10000 0 -10000 0 0
PRKDC 0.03 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 -0.075 0.13 -10000 0 -0.28 127 127
RPS6KA3 0.006 0.052 -10000 0 -0.45 2 2
T-DHT/AR/ARA70 -0.093 0.14 -10000 0 -0.31 128 128
LATS2 0.036 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.068 0.14 0.17 2 -0.28 129 131
Cyclin D3/CDK11 p58 0.021 0.006 -10000 0 -10000 0 0
VAV3 -0.014 0.11 -10000 0 -0.46 28 28
KLK2 -0.053 0.09 -10000 0 -0.43 12 12
CASP8 0.03 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.092 0.15 -10000 0 -0.3 135 135
TMPRSS2 -0.43 0.45 -10000 0 -0.9 234 234
CCND1 0.01 0.043 -10000 0 -0.46 3 3
PIAS1 0.004 0.052 -10000 0 -10000 0 0
mol:T-DHT -0.023 0.03 -10000 0 -0.061 161 161
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.005 0.073 -10000 0 -0.17 68 68
T-DHT/AR/CDK6 -0.086 0.14 -10000 0 -0.3 126 126
CMTM2 0.015 0.07 -10000 0 -0.39 14 14
SNURF -0.001 0.1 -10000 0 -0.45 23 23
ZMIZ1 -0.01 0.045 -10000 0 -10000 0 0
CCND3 0.027 0.007 -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 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
Sortilin/TRAF6 0.028 0.061 -10000 0 -0.32 14 14
Necdin/E2F1 0.02 0.079 -10000 0 -0.31 25 25
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.001 0.13 -10000 0 -0.26 32 32
NGF (dimer)/p75(NTR)/BEX1 -0.032 0.14 -10000 0 -0.25 138 138
NT-4/5 (dimer)/p75(NTR) 0.023 0.079 -10000 0 -0.32 24 24
IKBKB 0.026 0.008 -10000 0 -10000 0 0
AKT1 0.005 0.12 -10000 0 -0.38 1 1
IKBKG 0.027 0.006 -10000 0 -10000 0 0
BDNF -0.004 0.12 -10000 0 -0.42 34 34
MGDIs/NGR/p75(NTR)/LINGO1 0.011 0.11 -10000 0 -0.26 64 64
FURIN 0.027 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.008 0.12 -10000 0 -0.27 68 68
LINGO1 -0.003 0.11 -10000 0 -0.39 36 36
Sortilin/TRAF6/NRIF 0.026 0.043 -10000 0 -10000 0 0
proBDNF (dimer) -0.004 0.12 -10000 0 -0.42 34 34
NTRK1 -0.007 0.12 -10000 0 -0.39 40 40
RTN4R 0.014 0.073 -10000 0 -0.39 15 15
neuron apoptosis -0.037 0.12 0.46 1 -0.45 19 20
IRAK1 0.027 0.006 -10000 0 -10000 0 0
SHC1 -0.042 0.11 -10000 0 -0.24 111 111
ARHGDIA 0.028 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.007 -10000 0 -10000 0 0
Gamma Secretase 0.074 0.028 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.009 0.13 -10000 0 -0.23 124 124
MAGEH1 0.026 0.019 -10000 0 -0.39 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.013 0.14 -10000 0 -0.3 41 41
Mammalian IAPs/DIABLO 0.054 0.05 -10000 0 -0.21 6 6
proNGF (dimer) -0.052 0.16 -10000 0 -0.4 91 91
MAGED1 0.024 0.041 -10000 0 -0.42 4 4
APP 0.026 0.02 -10000 0 -0.39 1 1
NT-4/5 (dimer) 0.025 0.029 -10000 0 -0.42 2 2
ZNF274 0.027 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.019 0.1 -10000 0 -0.24 18 18
NGF -0.052 0.16 -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 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.038 0.07 -10000 0 -0.27 22 22
NCSTN 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.015 0.12 -10000 0 -0.24 115 115
PSENEN 0.027 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 0.022 0.076 -10000 0 -0.3 26 26
BEX1 -0.009 0.1 -10000 0 -0.39 31 31
mol:GDP -0.051 0.1 -10000 0 -0.24 114 114
NGF (dimer) -0.049 0.14 -10000 0 -0.24 162 162
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.026 0.11 -10000 0 -0.24 57 57
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
RAC1/GTP -0.009 0.1 -10000 0 -0.2 104 104
MYD88 0.025 0.009 -10000 0 -10000 0 0
CHUK 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.015 0.13 -10000 0 -0.24 115 115
RHOB 0.028 0.003 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.025 0.062 -10000 0 -0.28 19 19
NT3 (dimer) -0.11 0.21 -10000 0 -0.45 138 138
TP53 -0.014 0.094 0.53 1 -0.43 5 6
PRDM4 -0.047 0.11 -10000 0 -0.28 34 34
BDNF (dimer) -0.18 0.16 -10000 0 -0.27 335 335
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
SORT1 0.012 0.085 -10000 0 -0.45 16 16
activation of caspase activity -0.004 0.13 -10000 0 -0.26 32 32
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.006 0.13 -10000 0 -0.23 116 116
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
MAPK10 -0.043 0.12 0.31 3 -0.36 24 27
DIABLO 0.028 0.003 -10000 0 -10000 0 0
SMPD2 -0.046 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 -0.024 0.14 -10000 0 -0.25 126 126
PSEN1 0.026 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.077 0.17 -10000 0 -0.33 154 154
MAPK8 -0.035 0.1 0.35 2 -0.34 14 16
MAPK9 -0.033 0.1 0.34 3 -0.35 13 16
APAF1 0.028 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 0.019 0.064 -10000 0 -0.45 9 9
RAC1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.005 0.11 -10000 0 -0.36 1 1
p75 CTF/Sortilin/TRAF6/NRIF 0.054 0.059 -10000 0 -0.25 15 15
RhoA-B-C/GTP -0.016 0.12 -10000 0 -0.24 115 115
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.034 0.11 -10000 0 -0.26 36 36
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.024 0.11 -10000 0 -0.25 65 65
PRKACB 0.026 0.022 -10000 0 -0.45 1 1
proBDNF (dimer)/p75 ECD 0.015 0.089 -10000 0 -0.3 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 -0.049 0.1 0.21 1 -0.29 34 35
BAD -0.037 0.11 0.38 2 -0.39 10 12
RIPK2 0.025 0.009 -10000 0 -10000 0 0
NGFR 0.005 0.098 -10000 0 -0.42 25 25
CYCS -0.042 0.1 0.18 3 -0.41 6 9
ADAM17 0.026 0.031 -10000 0 -0.45 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.004 0.11 -10000 0 -0.26 16 16
BCL2L11 -0.039 0.11 0.38 2 -0.39 10 12
BDNF (dimer)/p75(NTR) 0 0.11 -10000 0 -0.3 58 58
PI3K -0.009 0.11 -10000 0 -0.22 89 89
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.008 0.13 -10000 0 -0.28 34 34
NDNL2 0.028 0.004 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.013 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.036 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 -0.011 0.13 -10000 0 -0.23 124 124
TRAF6 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.45 1 1
PLG -0.015 0.038 -10000 0 -0.39 4 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.048 0.12 -10000 0 -0.34 36 36
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
NGFRAP1 0.026 0.027 -10000 0 -0.39 2 2
CASP3 -0.036 0.1 0.37 2 -0.35 14 16
E2F1 0.009 0.081 -10000 0 -0.39 19 19
CASP9 0.027 0.006 -10000 0 -10000 0 0
IKK complex 0.008 0.11 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.044 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 0.004 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 -0.34 6 6
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.011 0.17 0.3 12 -0.43 40 52
FYN -0.027 0.19 0.28 19 -0.49 45 64
LAT/GRAP2/SLP76 -0.019 0.18 0.3 4 -0.47 40 44
IKBKB 0.026 0.008 -10000 0 -10000 0 0
AKT1 -0.023 0.15 0.24 17 -0.38 45 62
B2M 0.026 0.012 -10000 0 -10000 0 0
IKBKG -0.003 0.051 0.096 21 -0.14 13 34
MAP3K8 0.024 0.037 -10000 0 -0.45 3 3
mol:Ca2+ -0.035 0.03 -10000 0 -0.089 49 49
integrin-mediated signaling pathway 0.034 0.021 -10000 0 -0.27 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.037 0.2 0.28 15 -0.51 48 63
TRPV6 -0.19 0.26 1.1 5 -0.45 219 224
CD28 0.012 0.079 -10000 0 -0.4 17 17
SHC1 -0.034 0.19 0.31 10 -0.49 49 59
receptor internalization -0.041 0.19 -10000 0 -0.48 62 62
PRF1 -0.048 0.22 -10000 0 -0.68 35 35
KRAS 0.026 0.007 -10000 0 -10000 0 0
GRB2 0.028 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.008 0.13 0.22 15 -0.32 37 52
LAT -0.039 0.19 0.28 5 -0.52 48 53
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D 0.01 0.081 -10000 0 -0.42 16 16
CD3E 0.013 0.07 -10000 0 -0.42 12 12
CD3G -0.001 0.1 -10000 0 -0.44 27 27
RASGRP2 0.006 0.02 0.072 1 -0.16 1 2
RASGRP1 -0.025 0.16 0.27 15 -0.41 43 58
HLA-A 0.019 0.049 -10000 0 -0.4 6 6
RASSF5 0.026 0.031 -10000 0 -0.45 2 2
RAP1A/GTP/RAPL 0.035 0.021 -10000 0 -0.27 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.063 0.14 39 -0.12 12 51
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.027 0.066 -10000 0 -0.22 29 29
PRKCA -0.008 0.093 0.16 14 -0.26 25 39
GRAP2 0.016 0.07 -10000 0 -0.43 12 12
mol:IP3 0.03 0.17 0.21 165 -0.38 32 197
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.03 0.16 -10000 0 -0.43 53 53
ORAI1 0.099 0.16 0.6 2 -0.94 5 7
CSK -0.033 0.18 0.24 9 -0.5 47 56
B7 family/CD28 -0.055 0.19 0.24 2 -0.51 46 48
CHUK 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.051 0.2 0.22 6 -0.53 52 58
PTPN6 -0.037 0.18 0.26 6 -0.48 47 53
VAV1 -0.038 0.19 0.24 6 -0.51 48 54
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 0.19 0.27 18 -0.49 46 64
PAG1 -0.029 0.19 0.27 12 -0.5 45 57
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.051 0.19 0.22 10 -0.51 55 65
CD80 -0.074 0.18 -10000 0 -0.39 115 115
CD86 0.023 0.021 -10000 0 -0.39 1 1
PDK1/CARD11/BCL10/MALT1 -0.024 0.084 -10000 0 -0.26 31 31
HRAS 0.026 0.021 -10000 0 -0.41 1 1
GO:0035030 -0.063 0.16 0.2 4 -0.42 52 56
CD8A -0.014 0.13 -10000 0 -0.42 46 46
CD8B -0.021 0.14 -10000 0 -0.42 53 53
PTPRC 0.015 0.073 -10000 0 -0.43 13 13
PDK1/PKC theta -0.032 0.18 0.3 14 -0.46 42 56
CSK/PAG1 -0.022 0.19 0.29 16 -0.49 44 60
SOS1 0.028 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.032 0.04 -10000 0 -0.28 6 6
GRAP2/SLP76 -0.021 0.19 0.29 3 -0.5 46 49
STIM1 0.057 0.12 1.2 4 -10000 0 4
RAS family/GTP 0.014 0.077 0.16 31 -0.18 16 47
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.045 0.2 -10000 0 -0.5 63 63
mol:DAG -0.018 0.12 0.12 8 -0.33 38 46
RAP1A/GDP 0.012 0.03 0.081 22 -10000 0 22
PLCG1 0.027 0.006 -10000 0 -10000 0 0
CD247 0.008 0.089 -10000 0 -0.41 21 21
cytotoxic T cell degranulation -0.046 0.21 -10000 0 -0.64 36 36
RAP1A/GTP 0.002 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.028 0.17 0.26 18 -0.43 46 64
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.026 0.2 0.23 143 -0.48 34 177
NRAS 0.027 0.006 -10000 0 -10000 0 0
ZAP70 0.006 0.095 -10000 0 -0.4 25 25
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.026 0.17 0.36 2 -0.47 39 41
MALT1 0.025 0.008 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.021 0.16 -10000 0 -0.39 72 72
CARD11 0.003 0.097 -10000 0 -0.4 27 27
PRKCB -0.009 0.096 0.16 12 -0.28 26 38
PRKCE -0.007 0.092 0.16 13 -0.26 24 37
PRKCQ -0.037 0.19 0.29 14 -0.51 45 59
LCP2 0.024 0.033 -10000 0 -0.39 3 3
BCL10 0.027 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.017 0.13 0.23 17 -0.32 45 62
IKK complex 0.015 0.063 0.15 42 -0.12 8 50
RAS family/GDP -0.002 0.01 -10000 0 -10000 0 0
MAP3K14 -0.008 0.1 0.18 17 -0.26 31 48
PDPK1 -0.02 0.14 0.24 18 -0.36 40 58
TCR/CD3/MHC I/CD8/Fyn -0.055 0.21 -10000 0 -0.59 47 47
BMP receptor signaling

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.062 0.16 -10000 0 -0.41 39 39
SMAD6-7/SMURF1 0.048 0.021 -10000 0 -10000 0 0
NOG -0.018 0.13 -10000 0 -0.42 45 45
SMAD9 -0.074 0.2 -10000 0 -0.54 66 66
SMAD4 0.025 0.008 -10000 0 -10000 0 0
SMAD5 -0.048 0.12 -10000 0 -0.42 27 27
BMP7/USAG1 -0.068 0.18 -10000 0 -0.35 132 132
SMAD5/SKI -0.044 0.14 0.26 3 -0.43 29 32
SMAD1 0.024 0.041 -10000 0 -10000 0 0
BMP2 0.012 0.077 -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 -0.014 0.13 -10000 0 -0.4 47 47
BMPR1A-1B/BAMBI 0.016 0.1 -10000 0 -0.24 62 62
AHSG -0.001 0.067 -10000 0 -0.39 13 13
CER1 -0.009 0.043 -10000 0 -0.39 5 5
BMP2-4/CER1 0.022 0.074 -10000 0 -0.25 30 30
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.077 0.16 -10000 0 -0.44 47 47
BMP2-4 (homodimer) 0.019 0.078 -10000 0 -0.3 26 26
RGMB 0.027 0.007 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.034 0.089 -10000 0 -0.25 11 11
RGMA -0.027 0.15 -10000 0 -0.45 56 56
SMURF1 0.026 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.073 0.14 -10000 0 -0.38 54 54
BMP2-4/USAG1 -0.042 0.14 -10000 0 -0.27 133 133
SMAD6/SMURF1/SMAD5 -0.045 0.13 0.26 2 -0.42 31 33
SOSTDC1 -0.093 0.2 -10000 0 -0.44 123 123
BMP7/BMPR2/BMPR1A-1B 0.015 0.12 -10000 0 -0.27 42 42
SKI 0.027 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.021 0.048 -10000 0 -0.4 6 6
HFE2 -0.13 0.2 -10000 0 -0.45 144 144
ZFYVE16 0.026 0.007 -10000 0 -10000 0 0
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/CHRD 0.018 0.077 -10000 0 -0.26 30 30
SMAD5/SMAD5/SMAD4 -0.042 0.14 0.26 3 -0.42 30 33
MAPK1 0.027 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.056 0.14 -10000 0 -0.36 44 44
BMP7 (homodimer) -0.006 0.12 -10000 0 -0.45 34 34
NUP214 0.027 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.016 0.058 -10000 0 -0.28 17 17
SMAD1/SKI 0.025 0.068 -10000 0 -0.36 1 1
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.016 0.076 -10000 0 -0.25 32 32
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.16 0.21 -10000 0 -0.39 216 216
BMPR2 (homodimer) 0.027 0.006 -10000 0 -10000 0 0
GADD34/PP1CA 0.048 0.021 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.009 0.096 -10000 0 -0.29 47 47
CHRDL1 -0.21 0.24 -10000 0 -0.45 245 245
ENDOFIN/SMAD1 0.028 0.067 -10000 0 -0.35 1 1
SMAD6-7/SMURF1/SMAD1 0.045 0.065 -10000 0 -10000 0 0
SMAD6/SMURF1 0.026 0.008 -10000 0 -10000 0 0
BAMBI 0.013 0.08 -10000 0 -0.42 16 16
SMURF2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.12 0.17 -10000 0 -0.29 233 233
BMP2-4/GREM1 -0.077 0.15 -10000 0 -0.25 206 206
SMAD7 0.026 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.069 0.2 -10000 0 -0.51 71 71
SMAD1/SMAD6 0.023 0.067 -10000 0 -0.35 1 1
TAK1/SMAD6 0.037 0.013 -10000 0 -10000 0 0
BMP7 -0.006 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 53 53
PPM1A 0.026 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.025 0.069 -10000 0 -0.36 1 1
SMAD7/SMURF1 0.035 0.015 -10000 0 -10000 0 0
CTDSPL 0.025 0.009 -10000 0 -10000 0 0
PPP1CA 0.026 0.008 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
CTDSP1 0.027 0.006 -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 -0.42 67 67
CHRD 0.01 0.063 -10000 0 -0.4 11 11
BMPR2 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.081 0.15 -10000 0 -0.39 58 58
BMP4 0.017 0.067 -10000 0 -0.44 10 10
FST -0.12 0.2 -10000 0 -0.39 177 177
BMP2-4/NOG 0.008 0.11 -10000 0 -0.26 66 66
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.023 0.11 -10000 0 -0.4 5 5
Effects of Botulinum toxin

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
STX1A -0.004 0.056 -10000 0 -0.28 20 20
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.008 0.091 -10000 0 -0.32 34 34
STXBP1 0.027 0.004 -10000 0 -10000 0 0
ACh/CHRNA1 -0.074 0.13 -10000 0 -0.27 156 156
RAB3GAP2/RIMS1/UNC13B 0.023 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 0.001 0.034 0.1 15 -0.11 7 22
RAB3GAP2 0.028 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.008 0.08 -10000 0 -0.27 4 4
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.074 0.13 -10000 0 -0.26 156 156
UNC13B 0.022 0.032 -10000 0 -0.45 2 2
CHRNA1 -0.12 0.21 -10000 0 -0.42 156 156
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.049 0.12 -10000 0 -0.24 125 125
SNAP25 -0.004 0.035 -10000 0 -0.13 34 34
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.08 0.18 -10000 0 -0.4 125 125
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.015 0.051 -10000 0 -0.23 20 20
STX1A/SNAP25 fragment 1/VAMP2 0.008 0.08 -10000 0 -0.27 4 4
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.18 0.28 -10000 0 -0.84 33 33
PCK1 -0.45 0.57 -10000 0 -1.2 163 163
HNF4A -0.21 0.3 -10000 0 -0.97 31 31
KCNJ11 -0.27 0.39 -10000 0 -1 80 80
AKT1 -0.093 0.15 -10000 0 -0.51 11 11
response to starvation -0.002 0.014 -10000 0 -10000 0 0
DLK1 -0.35 0.46 -10000 0 -0.99 142 142
NKX2-1 -0.046 0.22 0.46 3 -0.63 10 13
ACADM -0.18 0.28 -10000 0 -0.86 34 34
TAT -0.13 0.19 -10000 0 -0.75 10 10
CEBPB 0.027 0.008 -10000 0 -10000 0 0
CEBPA 0.025 0.038 -10000 0 -0.45 3 3
TTR -0.25 0.29 -10000 0 -0.83 62 62
PKLR -0.2 0.29 -10000 0 -0.86 40 40
APOA1 -0.22 0.32 -10000 0 -1 29 29
CPT1C -0.18 0.28 -10000 0 -0.84 34 34
ALAS1 -0.089 0.16 -10000 0 -0.69 4 4
TFRC -0.16 0.22 -10000 0 -0.75 14 14
FOXF1 0.031 0.055 -10000 0 -0.37 6 6
NF1 0.033 0.005 -10000 0 -10000 0 0
HNF1A (dimer) 0.018 0.061 -10000 0 -0.39 9 9
CPT1A -0.16 0.28 -10000 0 -0.83 31 31
HMGCS1 -0.17 0.27 -10000 0 -0.83 31 31
NR3C1 0.029 0.022 -10000 0 -10000 0 0
CPT1B -0.19 0.29 -10000 0 -0.88 36 36
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.025 0.024 -10000 0 -10000 0 0
GCK -0.2 0.28 -10000 0 -0.85 34 34
CREB1 -0.037 0.1 -10000 0 -0.23 44 44
IGFBP1 -0.083 0.15 -10000 0 -0.57 11 11
PDX1 -0.099 0.17 -10000 0 -0.73 5 5
UCP2 -0.17 0.28 -10000 0 -0.83 37 37
ALDOB -0.2 0.3 -10000 0 -0.85 44 44
AFP -0.14 0.16 -10000 0 -0.43 67 67
BDH1 -0.15 0.27 0.52 1 -0.83 29 30
HADH -0.19 0.29 -10000 0 -0.87 33 33
F2 -0.22 0.32 -10000 0 -1 27 27
HNF1A 0.018 0.061 -10000 0 -0.39 9 9
G6PC -0.054 0.1 -10000 0 -10000 0 0
SLC2A2 -0.1 0.16 -10000 0 -1 1 1
INS -0.023 0.032 -10000 0 -0.4 2 2
FOXA1 -0.15 0.24 -10000 0 -0.46 181 181
FOXA3 -0.093 0.17 -10000 0 -0.41 72 72
FOXA2 -0.23 0.33 -10000 0 -0.93 44 44
ABCC8 -0.2 0.29 -10000 0 -0.85 36 36
ALB -0.15 0.18 -10000 0 -0.55 44 44
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.036 0.063 -10000 0 -0.27 17 17
fibroblast growth factor receptor signaling pathway 0.035 0.063 -10000 0 -0.27 17 17
LAMA1 -0.13 0.2 -10000 0 -0.39 177 177
PRNP 0.026 0.007 -10000 0 -10000 0 0
GPC1/SLIT2 -0.007 0.12 -10000 0 -0.32 62 62
SMAD2 0.015 0.028 0.18 7 -0.24 2 9
GPC1/PrPc/Cu2+ 0.034 0.017 -10000 0 -0.23 1 1
GPC1/Laminin alpha1 -0.078 0.15 -10000 0 -0.28 177 177
TDGF1 0.003 0.05 -10000 0 -0.4 6 6
CRIPTO/GPC1 0.029 0.039 -10000 0 -0.28 7 7
APP/GPC1 0.038 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 0.026 0.02 -10000 0 -0.39 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.031 -10000 0 -0.24 3 3
SERPINC1 0.014 0.06 -10000 0 -0.39 10 10
FYN 0.001 0.033 -10000 0 -0.23 7 7
FGR 0.002 0.032 -10000 0 -0.23 7 7
positive regulation of MAPKKK cascade 0.004 0.094 0.3 8 -0.36 7 15
SLIT2 -0.033 0.16 -10000 0 -0.45 61 61
GPC1/NRG -0.012 0.11 -10000 0 -0.28 75 75
NRG1 -0.039 0.15 -10000 0 -0.4 74 74
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.034 -10000 0 -0.23 5 5
LYN 0.001 0.033 -10000 0 -0.23 7 7
mol:Spermine 0.007 0.013 -10000 0 -0.27 1 1
cell growth 0.035 0.063 -10000 0 -0.27 17 17
BMP signaling pathway -0.026 0.02 0.39 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 0.026 0.02 -10000 0 -0.39 1 1
TGFBR1 (dimer) 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.023 0.038 -10000 0 -0.39 4 4
BLK -0.031 0.085 -10000 0 -0.24 70 70
HCK 0.001 0.035 -10000 0 -0.26 7 7
FGF2 0.012 0.082 -10000 0 -0.44 16 16
FGFR1 0.02 0.044 -10000 0 -0.4 5 5
VEGFR1 homodimer 0.026 0.02 -10000 0 -0.39 1 1
TGFBR2 0.022 0.032 -10000 0 -0.45 2 2
cell death 0.037 0.023 -10000 0 -0.28 2 2
ATIII/GPC1 0.031 0.048 -10000 0 -0.28 11 11
PLA2G2A/GPC1 -0.18 0.17 -10000 0 -0.32 307 307
LCK -0.004 0.047 -10000 0 -0.23 18 18
neuron differentiation -0.012 0.11 -10000 0 -0.28 75 75
PrPc/Cu2+ 0.02 0.005 -10000 0 -10000 0 0
APP 0.026 0.02 -10000 0 -0.39 1 1
TGFBR2 (dimer) 0.022 0.032 -10000 0 -0.45 2 2
Canonical Wnt signaling pathway

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
HDAC1 0.026 0.017 0.22 2 -10000 0 2
AES 0.026 0.015 0.21 1 -10000 0 1
FBXW11 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 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 0.027 0.015 0.21 1 -10000 0 1
MACF1 0.028 0.005 -10000 0 -10000 0 0
CTNNB1 0.034 0.12 0.28 16 -0.37 13 29
WIF1 -0.19 0.22 -10000 0 -0.44 207 207
beta catenin/RanBP3 -0.008 0.1 0.39 13 -0.4 5 18
KREMEN2 -0.13 0.2 -10000 0 -0.39 181 181
DKK1 -0.13 0.2 -10000 0 -0.4 179 179
beta catenin/beta TrCP1 0.046 0.12 0.28 16 -0.36 9 25
FZD1 0.025 0.029 -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 0.028 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.026 0.095 -10000 0 -0.56 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.13 0.33 2 -0.56 10 12
Axin1/APC/GSK3 0.041 0.071 0.25 6 -0.34 4 10
Axin1/APC/GSK3/beta catenin/Macf1 0.039 0.098 0.3 8 -0.39 6 14
HNF1A 0.019 0.059 0.2 2 -0.4 9 11
CTBP1 0.025 0.017 0.2 2 -10000 0 2
MYC 0.12 0.24 0.58 96 -10000 0 96
RANBP3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.058 0.14 -10000 0 -0.24 183 183
NKD1 0.012 0.077 -10000 0 -0.4 17 17
TCF4 0.024 0.017 0.22 1 -10000 0 1
TCF3 0.026 0.016 0.22 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.057 0.042 -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 0.52 10 -0.43 5 15
LEF1 0.022 0.045 0.22 1 -0.4 5 6
DVL1 0.047 0.062 0.23 1 -0.49 2 3
CSNK2A1 0.027 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 -0.28 274 274
LRP6 0.026 0.023 -10000 0 -0.45 1 1
CSNK1A1 0.026 0.018 0.22 2 -10000 0 2
NLK 0.028 0.007 -10000 0 -10000 0 0
CCND1 0.14 0.28 0.58 122 -1.2 4 126
WNT1 0.017 0.044 -10000 0 -0.39 5 5
GSK3A 0.028 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.009 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
PPP2R5D 0.036 0.078 0.24 9 -0.38 8 17
APC 0.026 0.065 0.35 4 -10000 0 4
WNT1/LRP6/FZD1 0.075 0.094 0.2 155 -10000 0 155
CREBBP 0.026 0.016 0.22 1 -10000 0 1
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.006 -10000 0 -10000 0 0
LAT2 -0.045 0.11 -10000 0 -0.34 24 24
AP1 -0.019 0.14 0.3 1 -0.41 12 13
mol:PIP3 -0.06 0.15 0.35 9 -0.41 24 33
IKBKB -0.024 0.1 0.22 25 -0.25 12 37
AKT1 -0.025 0.15 0.39 18 -0.37 12 30
IKBKG -0.024 0.1 0.24 19 -0.25 11 30
MS4A2 0.008 0.09 -10000 0 -0.45 18 18
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.019 0.013 -10000 0 -10000 0 0
MAP3K1 0.02 0.14 0.25 76 -0.36 8 84
mol:Ca2+ -0.045 0.12 0.28 13 -0.31 24 37
LYN 0.024 0.022 -10000 0 -0.4 1 1
CBLB -0.042 0.1 -10000 0 -0.34 20 20
SHC1 0.028 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.035 0.065 -10000 0 -0.24 24 24
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.025 0.031 -10000 0 -0.45 2 2
PLD2 -0.08 0.14 0.3 12 -0.36 24 36
PTPN13 -0.033 0.12 0.36 1 -0.48 12 13
PTPN11 0.015 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 -0.46 3 3
GRB2 0.027 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.066 0.14 -10000 0 -0.41 24 24
LAT -0.049 0.12 -10000 0 -0.35 26 26
PAK2 0.017 0.15 0.26 77 -0.38 10 87
NFATC2 -0.087 0.19 -10000 0 -0.58 58 58
HRAS -0.025 0.12 0.24 7 -0.38 18 25
GAB2 0.022 0.038 -10000 0 -0.45 3 3
PLA2G1B -0.069 0.28 -10000 0 -0.82 60 60
Fc epsilon R1 -0.078 0.18 -10000 0 -0.3 182 182
Antigen/IgE/Fc epsilon R1 -0.068 0.16 -10000 0 -0.27 182 182
mol:GDP -0.025 0.12 0.25 2 -0.4 16 18
JUN 0.027 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.024 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 -0.045 0.12 -10000 0 -0.34 28 28
CHUK -0.031 0.097 0.25 12 -0.25 12 24
KLRG1 -0.049 0.11 -10000 0 -0.35 24 24
VAV1 -0.047 0.12 -10000 0 -0.36 26 26
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.043 0.11 -10000 0 -0.34 24 24
negative regulation of mast cell degranulation -0.031 0.12 0.2 7 -0.34 22 29
BTK -0.026 0.11 -10000 0 -0.42 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.08 0.15 -10000 0 -0.41 44 44
GAB2/PI3K/SHP2 -0.059 0.11 -10000 0 -0.4 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.055 0.12 -10000 0 -0.4 20 20
RAF1 -0.079 0.31 -10000 0 -0.9 60 60
Fc epsilon R1/FcgammaRIIB/SHIP -0.05 0.17 -10000 0 -0.27 149 149
FCER1G 0.016 0.066 -10000 0 -0.4 12 12
FCER1A -0.14 0.23 -10000 0 -0.46 170 170
Antigen/IgE/Fc epsilon R1/Fyn -0.055 0.16 -10000 0 -0.26 178 178
MAPK3 -0.072 0.28 -10000 0 -0.83 60 60
MAPK1 -0.071 0.28 -10000 0 -0.82 60 60
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.008 0.14 0.33 1 -0.54 21 22
DUSP1 0.006 0.096 -10000 0 -0.45 21 21
NF-kappa-B/RelA -0.012 0.061 0.13 2 -0.19 1 3
actin cytoskeleton reorganization -0.029 0.12 0.38 1 -0.47 13 14
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.021 0.11 -10000 0 -0.38 11 11
FER -0.044 0.11 -10000 0 -0.34 26 26
RELA 0.027 0.007 -10000 0 -10000 0 0
ITK -0.021 0.073 -10000 0 -0.27 28 28
SOS1 0.028 0.004 -10000 0 -10000 0 0
PLCG1 -0.026 0.13 0.28 8 -0.41 16 24
cytokine secretion -0.012 0.041 -10000 0 -10000 0 0
SPHK1 -0.047 0.12 -10000 0 -0.34 29 29
PTK2 -0.031 0.13 0.38 1 -0.5 12 13
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.06 0.14 -10000 0 -0.42 24 24
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.056 0.15 0.34 9 -0.4 24 33
MAP2K2 -0.077 0.28 -10000 0 -0.84 60 60
MAP2K1 -0.076 0.28 -10000 0 -0.84 60 60
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.037 0.12 0.21 14 -0.33 23 37
MAP2K4 0.006 0.17 -10000 0 -0.81 21 21
Fc epsilon R1/FcgammaRIIB -0.061 0.17 -10000 0 -0.28 181 181
mol:Choline -0.079 0.14 0.29 12 -0.36 24 36
SHC/Grb2/SOS1 -0.012 0.13 0.25 1 -0.4 12 13
FYN 0.027 0.019 -10000 0 -0.39 1 1
DOK1 0.027 0.019 -10000 0 -0.39 1 1
PXN -0.029 0.12 0.33 2 -0.47 11 13
HCLS1 -0.042 0.11 0.18 1 -0.35 21 22
PRKCB -0.043 0.12 0.28 12 -0.32 19 31
FCGR2B 0.021 0.057 -10000 0 -0.45 7 7
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.032 0.12 0.24 2 -0.35 22 24
LCP2 0.024 0.033 -10000 0 -0.39 3 3
PLA2G4A -0.055 0.12 -10000 0 -0.36 37 37
RASA1 0.024 0.031 -10000 0 -0.45 2 2
mol:Phosphatidic acid -0.079 0.14 0.29 12 -0.36 24 36
IKK complex -0.011 0.091 0.21 30 -0.21 3 33
WIPF1 0.023 0.038 -10000 0 -0.39 4 4
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 0.026 0.02 -10000 0 -0.39 1 1
RAS family/GTP/Tiam1 -0.059 0.1 -10000 0 -0.23 67 67
NT3 (dimer)/TRKC -0.14 0.22 -10000 0 -0.38 208 208
NT3 (dimer)/TRKB -0.12 0.21 -10000 0 -0.34 218 218
SHC/Grb2/SOS1/GAB1/PI3K 0.021 0.022 -10000 0 -0.21 2 2
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
BDNF -0.004 0.12 -10000 0 -0.42 34 34
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DYNLT1 0.027 0.005 -10000 0 -10000 0 0
NTRK1 -0.007 0.12 -10000 0 -0.39 40 40
NTRK2 -0.098 0.21 -10000 0 -0.44 132 132
NTRK3 -0.098 0.2 -10000 0 -0.45 125 125
NT-4/5 (dimer)/TRKB -0.045 0.16 -10000 0 -0.28 146 146
neuron apoptosis 0.041 0.12 0.36 20 -10000 0 20
SHC 2-3/Grb2 -0.044 0.13 -10000 0 -0.39 20 20
SHC1 0.028 0.004 -10000 0 -10000 0 0
SHC2 -0.046 0.12 -10000 0 -0.37 27 27
SHC3 -0.042 0.12 -10000 0 -0.44 17 17
STAT3 (dimer) 0.026 0.058 -10000 0 -0.34 12 12
NT3 (dimer)/TRKA -0.072 0.17 -10000 0 -0.28 178 178
RIN/GDP -0.028 0.096 0.21 10 -0.24 11 21
GIPC1 0.028 0.004 -10000 0 -10000 0 0
KRAS 0.026 0.007 -10000 0 -10000 0 0
DNAJA3 -0.012 0.087 0.24 3 -0.28 10 13
RIN/GTP 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.011 0.057 -10000 0 -0.71 3 3
MAGED1 0.024 0.041 -10000 0 -0.42 4 4
PTPN11 0.028 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 0.054 0.012 -10000 0 -10000 0 0
GRB2 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.03 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 0.034 0.022 -10000 0 -0.27 2 2
NGF -0.052 0.16 -10000 0 -0.4 91 91
HRAS 0.026 0.021 -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 -0.015 0.012 -10000 0 -10000 0 0
RIT1 0.027 0.004 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
DNM1 -0.002 0.11 -10000 0 -0.39 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 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 12 13
mol:GDP -0.044 0.13 0.26 10 -0.34 16 26
NGF (dimer) -0.052 0.16 -10000 0 -0.4 91 91
RhoG/GDP 0.019 0.016 -10000 0 -0.32 1 1
RIT1/GDP -0.026 0.095 0.18 9 -0.24 10 19
TIAM1 0.021 0.053 -10000 0 -0.45 6 6
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
BDNF (dimer)/TRKB -0.052 0.16 -10000 0 -0.28 155 155
KIDINS220/CRKL/C3G 0.038 0.018 -10000 0 -0.28 1 1
SHC/RasGAP 0.038 0.02 -10000 0 -0.32 1 1
FRS2 family/SHP2 0.052 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.067 0.02 -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 -0.027 0.077 0.13 1 -0.2 8 9
KIDINS220/CRKL 0.026 0.02 -10000 0 -0.39 1 1
BDNF (dimer) -0.004 0.12 -10000 0 -0.42 34 34
ubiquitin-dependent protein catabolic process -0.023 0.13 -10000 0 -0.24 122 122
Schwann cell development -0.035 0.032 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.064 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.029 0.043 -10000 0 -0.25 1 1
RAP1B 0.027 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 -0.46 128 128
ABL1 0.027 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.082 -10000 0 -0.39 7 7
STAT3 0.026 0.057 -10000 0 -0.34 12 12
axon guidance -0.16 0.2 -10000 0 -0.44 129 129
MAPK3 -0.047 0.11 0.18 7 -0.33 15 22
MAPK1 -0.045 0.11 0.18 7 -0.33 15 22
CDC42/GDP -0.024 0.099 0.2 13 -0.24 10 23
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 -0.025 0.12 -10000 0 -0.24 113 113
PI3K 0.027 0.03 -10000 0 -0.32 2 2
FRS3 0.027 0.006 -10000 0 -10000 0 0
FAIM 0.023 0.011 -10000 0 -10000 0 0
GAB1 0.027 0.005 -10000 0 -10000 0 0
RASGRF1 -0.047 0.12 0.2 2 -0.3 48 50
SOS1 0.028 0.004 -10000 0 -10000 0 0
MCF2L -0.14 0.19 -10000 0 -0.35 210 210
RGS19 0.027 0.006 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.029 0.07 0.25 2 -0.38 2 4
Rac1/GDP -0.024 0.093 0.18 9 -0.24 11 20
NGF (dimer)/TRKA/GRIT -0.035 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 -0.023 0.13 -10000 0 -0.24 122 122
MAP2K1 0.021 0.035 0.36 1 -10000 0 1
NGFR 0.005 0.098 -10000 0 -0.42 25 25
NGF (dimer)/TRKA/GIPC/GAIP -0.014 0.072 -10000 0 -0.32 1 1
RAS family/GTP/PI3K 0.016 0.021 -10000 0 -0.22 2 2
FRS2 family/SHP2/GRB2/SOS1 0.074 0.027 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
PRKCI 0.02 0.013 -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 0.026 0.022 -10000 0 -0.45 1 1
MAPKKK cascade -0.027 0.11 -10000 0 -0.46 19 19
RASA1 0.024 0.031 -10000 0 -0.45 2 2
TRKA/c-Abl 0.014 0.087 -10000 0 -0.28 40 40
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.033 0.15 -10000 0 -0.25 149 149
NGF (dimer)/TRKA/p62/Atypical PKCs -0.009 0.11 -10000 0 -0.38 5 5
MATK 0.017 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 0.074 0.23 2 -0.26 21 23
Rac1/GTP -0.067 0.082 -10000 0 -0.25 28 28
FRS2 family/SHP2/CRK family 0.07 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 -0.012 0.043 -10000 0 -0.27 13 13
ADCY7 -0.005 0.012 -10000 0 -0.27 1 1
ADCY1 -0.014 0.045 -10000 0 -0.23 20 20
ADCY2 -0.086 0.12 -10000 0 -0.27 151 151
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 -0.007 0.11 0.22 35 -0.27 6 41
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 0.1 -10000 0 -0.39 31 31
GNB1/GNG2 -0.044 0.067 -10000 0 -0.18 66 66
AKT1 -0.018 0.11 0.2 10 -0.3 15 25
EGF -0.059 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 -0.31 1 9
mol:Ca2+ -0.032 0.14 0.24 3 -0.3 64 67
LYN 0.012 0.074 0.28 6 -0.27 6 12
RhoA/GTP -0.014 0.057 0.11 1 -10000 0 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.039 0.15 0.27 6 -0.34 69 75
GNG2 0.025 0.02 -10000 0 -0.39 1 1
ARRB2 0.027 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 -0.24 62 62
PRKCH -0.038 0.16 0.29 10 -0.35 65 75
DNM1 -0.002 0.11 -10000 0 -0.39 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 0.018 0.059 -10000 0 -0.41 9 9
G12 family/GTP -0.046 0.12 -10000 0 -0.3 61 61
ADRBK1 0.026 0.008 -10000 0 -10000 0 0
ADRBK2 0.026 0.02 -10000 0 -0.39 1 1
RhoA/GTP/ROCK1 0.032 0.014 -10000 0 -10000 0 0
mol:GDP 0.012 0.099 0.32 13 -0.21 2 15
mol:NADP 0.019 0.053 -10000 0 -0.39 8 8
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 0.004 0.1 -10000 0 -0.43 25 25
mol:IP3 -0.044 0.17 0.3 1 -0.38 65 66
cell morphogenesis 0.031 0.014 -10000 0 -10000 0 0
PLCB2 -0.068 0.22 0.33 1 -0.51 68 69
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.099 0.27 8 -0.28 12 20
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.013 0.075 0.27 8 -0.26 4 12
RHOA 0.025 0.009 -10000 0 -10000 0 0
PTGIR 0.012 0.079 -10000 0 -0.39 18 18
PRKCB1 -0.045 0.16 0.28 1 -0.37 70 71
GNAQ 0.027 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0.019 0.053 -10000 0 -0.39 8 8
TXA2/TXA2-R family -0.069 0.22 0.33 1 -0.51 75 76
LCK 0.012 0.082 0.27 8 -0.28 2 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.013 0.073 -10000 0 -0.3 11 11
TXA2-R family/G12 family/GDP/G beta/gamma 0.014 0.087 -10000 0 -0.44 15 15
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.018 0.073 -10000 0 -0.3 10 10
MAPK14 -0.02 0.11 0.2 16 -0.23 55 71
TGM2/GTP -0.061 0.18 -10000 0 -0.42 62 62
MAPK11 -0.02 0.11 0.23 16 -0.24 30 46
ARHGEF1 -0.019 0.081 0.14 4 -0.19 20 24
GNAI2 0.024 0.009 -10000 0 -10000 0 0
JNK cascade -0.046 0.17 0.27 3 -0.38 74 77
RAB11/GDP 0.027 0.005 -10000 0 -10000 0 0
ICAM1 -0.032 0.13 0.23 3 -0.28 78 81
cAMP biosynthetic process -0.043 0.15 0.27 2 -0.35 61 63
Gq family/GTP/EBP50 -0.009 0.089 0.24 7 -0.35 9 16
actin cytoskeleton reorganization 0.031 0.014 -10000 0 -10000 0 0
SRC 0.013 0.074 0.27 8 -0.25 6 14
GNB5 0.027 0.005 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
EGF/EGFR 0.008 0.098 0.22 35 -0.26 7 42
VCAM1 -0.039 0.14 0.22 4 -0.31 86 90
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 0.28 14 -0.3 59 73
PGI2/IP 0.009 0.055 -10000 0 -0.28 18 18
PRKACA 0.011 0.038 -10000 0 -0.25 5 5
Gq family/GDP/G beta5/gamma2 -0.007 0.1 0.28 1 -0.44 17 18
TXA2/TP beta/beta Arrestin2 0.001 0.05 -10000 0 -0.29 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.008 0.067 -10000 0 -0.26 21 21
mol:DAG -0.051 0.18 0.3 1 -0.42 71 72
EGFR 0.02 0.048 -10000 0 -0.45 5 5
TXA2/TP alpha -0.062 0.2 0.35 1 -0.47 62 63
Gq family/GTP -0.025 0.09 0.28 2 -0.21 84 86
YES1 0.013 0.071 0.27 6 -0.26 4 10
GNAI2/GTP 0.005 0.061 -10000 0 -0.27 9 9
PGD2/DP 0.014 0.042 -10000 0 -0.29 9 9
SLC9A3R1 0.024 0.043 -10000 0 -0.45 4 4
FYN 0.014 0.077 0.27 7 -0.26 6 13
mol:NO 0.019 0.053 -10000 0 -0.39 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 0.016 0.096 -10000 0 -0.35 16 16
NOS3 0.019 0.053 -10000 0 -0.39 8 8
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.041 0.16 0.27 2 -0.35 68 70
PRKCB -0.042 0.16 0.29 4 -0.35 75 79
PRKCE -0.04 0.16 0.28 2 -0.35 67 69
PRKCD -0.048 0.16 0.27 1 -0.37 76 77
PRKCG -0.054 0.17 0.27 2 -0.39 76 78
muscle contraction -0.062 0.2 0.31 2 -0.47 72 74
PRKCZ -0.04 0.15 0.25 3 -0.34 70 73
ARR3 -0.012 0.016 -10000 0 -10000 0 0
TXA2/TP beta 0.017 0.073 -10000 0 -0.3 9 9
PRKCQ -0.045 0.16 0.28 1 -0.36 73 74
MAPKKK cascade -0.057 0.19 0.32 1 -0.44 68 69
SELE -0.045 0.16 0.22 4 -0.37 74 78
TP beta/GNAI2/GDP/G beta/gamma 0.026 0.076 -10000 0 -0.3 10 10
ROCK1 0.027 0.007 -10000 0 -10000 0 0
GNA14 -0.043 0.17 -10000 0 -0.45 72 72
chemotaxis -0.083 0.25 -10000 0 -0.59 76 76
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.028 0.003 -10000 0 -10000 0 0
GNA11 0.024 0.037 -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) 0.029 0.089 -10000 0 -0.39 18 18
HDAC1 0.025 0.005 -10000 0 -10000 0 0
AES 0.027 0.005 -10000 0 -10000 0 0
FBXW11 0.027 0.007 -10000 0 -10000 0 0
DTX1 0.025 0.036 -10000 0 -0.43 3 3
LRP6/FZD1 0.034 0.03 -10000 0 -0.31 3 3
TLE1 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.019 0.094 -10000 0 -0.25 61 61
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 0.016 0.12 -10000 0 -0.7 12 12
NICD/RBPSUH 0.029 0.086 -10000 0 -0.38 19 19
WIF1 -0.19 0.22 -10000 0 -0.44 207 207
NOTCH1 0.013 0.083 -10000 0 -0.4 18 18
PSENEN 0.027 0.005 -10000 0 -10000 0 0
KREMEN2 -0.13 0.2 -10000 0 -0.39 181 181
DKK1 -0.13 0.2 -10000 0 -0.4 179 179
beta catenin/beta TrCP1 -0.004 0.1 -10000 0 -0.39 17 17
APH1B 0.028 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.005 -10000 0 -10000 0 0
AXIN1 0.005 0.066 -10000 0 -0.43 6 6
CtBP/CBP/TCF1/TLE1/AES 0.017 0.029 -10000 0 -0.26 1 1
PSEN1 0.026 0.007 -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 -0.017 0.11 0.25 1 -0.37 25 26
MAPK3 0.028 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.058 0.14 -10000 0 -0.24 183 183
HNF1A 0.019 0.057 -10000 0 -0.39 9 9
CTBP1 0.025 0.007 -10000 0 -10000 0 0
MYC 0.022 0.041 -10000 0 -0.77 1 1
NKD1 0.012 0.078 -10000 0 -0.4 17 17
FZD1 0.024 0.029 -10000 0 -0.42 2 2
NOTCH1 precursor/Deltex homolog 1 0.03 0.091 -10000 0 -0.4 19 19
apoptosis -0.019 0.093 -10000 0 -0.25 61 61
Delta 1/NOTCHprecursor 0.028 0.089 -10000 0 -0.38 18 18
DLL1 0.021 0.052 -10000 0 -0.45 6 6
PPARD 0.005 0.15 -10000 0 -0.84 14 14
Gamma Secretase 0.074 0.028 -10000 0 -10000 0 0
APC -0.01 0.1 -10000 0 -0.39 26 26
DVL1 -0.011 0.071 -10000 0 -0.32 17 17
CSNK2A1 0.027 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 -0.28 274 274
LRP6 0.025 0.022 -10000 0 -0.45 1 1
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.013 0.005 -10000 0 -10000 0 0
CCND1 -0.002 0.15 -10000 0 -0.99 9 9
WNT1 0.012 0.046 -10000 0 -0.39 5 5
Axin1/APC/beta catenin -0.002 0.12 0.28 5 -0.47 18 23
DKK2 0.013 0.077 -10000 0 -0.42 15 15
NOTCH1 precursor/DVL1 -0.002 0.11 -10000 0 -0.48 16 16
GSK3B 0.024 0.009 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.032 0.091 -10000 0 -0.4 19 19
PPP2R5D 0.006 0.078 0.22 3 -0.37 13 16
MAPK1 0.027 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.068 0.15 -10000 0 -0.25 190 190
RBPJ 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.048 0.17 -10000 0 -0.45 70 70
NFATC2 -0.028 0.19 -10000 0 -0.57 30 30
NFATC3 -0.006 0.069 -10000 0 -0.27 5 5
CD40LG -0.26 0.3 -10000 0 -0.87 50 50
ITCH 0.004 0.076 -10000 0 -10000 0 0
CBLB 0.001 0.078 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.21 0.31 -10000 0 -0.83 68 68
JUNB 0.028 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.097 -10000 0 -0.26 55 55
T cell anergy -0.011 0.14 0.3 6 -0.39 43 49
TLE4 -0.017 0.13 -10000 0 -0.45 19 19
Jun/NFAT1-c-4/p21SNFT -0.099 0.23 -10000 0 -0.87 15 15
AP-1/NFAT1-c-4 -0.25 0.31 -10000 0 -0.94 40 40
IKZF1 -0.021 0.15 -10000 0 -0.54 21 21
T-helper 2 cell differentiation -0.068 0.2 -10000 0 -0.65 36 36
AP-1/NFAT1 -0.089 0.17 -10000 0 -0.46 44 44
CALM1 0.014 0.063 -10000 0 -10000 0 0
EGR2 -0.064 0.25 -10000 0 -1.4 12 12
EGR3 -0.058 0.22 -10000 0 -1.3 10 10
NFAT1/FOXP3 -0.06 0.21 -10000 0 -0.51 59 59
EGR1 0.005 0.097 -10000 0 -0.45 21 21
JUN -0.023 0.042 -10000 0 -10000 0 0
EGR4 -0.026 0.14 -10000 0 -0.4 60 60
mol:Ca2+ -0.011 0.056 -10000 0 -0.23 2 2
GBP3 -0.031 0.17 -10000 0 -0.56 31 31
FOSL1 0.016 0.066 -10000 0 -0.4 12 12
NFAT1-c-4/MAF/IRF4 -0.056 0.22 -10000 0 -0.83 17 17
DGKA -0.017 0.13 -10000 0 -0.44 18 18
CREM 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.24 -10000 0 -0.9 18 18
CTLA4 -0.087 0.22 -10000 0 -0.54 73 73
NFAT1-c-4 (dimer)/EGR1 -0.064 0.23 -10000 0 -0.92 16 16
NFAT1-c-4 (dimer)/EGR4 -0.079 0.22 -10000 0 -0.87 16 16
FOS -0.079 0.15 -10000 0 -0.47 60 60
IFNG -0.12 0.23 -10000 0 -0.67 39 39
T cell activation -0.091 0.16 -10000 0 -0.7 5 5
MAF 0.022 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 0.14 0.69 12 -10000 0 12
TNF -0.098 0.22 -10000 0 -0.84 19 19
FASLG -0.12 0.34 -10000 0 -1.3 26 26
TBX21 -0.014 0.11 -10000 0 -0.44 29 29
BATF3 0.024 0.038 -10000 0 -0.39 4 4
PRKCQ 0.012 0.073 -10000 0 -0.44 11 11
PTPN1 -0.017 0.13 -10000 0 -0.46 14 14
NFAT1-c-4/ICER1 -0.056 0.2 -10000 0 -0.88 14 14
GATA3 0.011 0.083 -10000 0 -0.4 19 19
T-helper 1 cell differentiation -0.12 0.23 -10000 0 -0.66 39 39
IL2RA -0.19 0.28 -10000 0 -0.73 72 72
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.017 0.13 -10000 0 -0.46 14 14
E2F1 0.014 0.081 -10000 0 -0.39 19 19
PPARG -0.13 0.22 -10000 0 -0.45 163 163
SLC3A2 -0.017 0.13 -10000 0 -0.43 21 21
IRF4 -0.003 0.11 -10000 0 -0.41 33 33
PTGS2 -0.26 0.3 -10000 0 -0.86 52 52
CSF2 -0.32 0.32 -10000 0 -0.84 75 75
JunB/Fra1/NFAT1-c-4 -0.044 0.21 -10000 0 -0.86 14 14
IL4 -0.07 0.21 -10000 0 -0.68 35 35
IL5 -0.24 0.27 -10000 0 -0.84 40 40
IL2 -0.092 0.16 -10000 0 -0.71 5 5
IL3 -0.058 0.15 -10000 0 -0.7 20 20
RNF128 -0.038 0.18 -10000 0 -0.52 62 62
NFATC1 -0.042 0.15 -10000 0 -0.7 11 11
CDK4 0.04 0.12 0.63 3 -10000 0 3
PTPRK -0.016 0.13 -10000 0 -0.48 12 12
IL8 -0.27 0.3 -10000 0 -0.86 49 49
POU2F1 0.028 0.004 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.026 0.021 -9999 0 -0.41 1 1
EGFR 0.02 0.048 -9999 0 -0.45 5 5
EGF/EGFR -0.005 0.11 -9999 0 -0.23 82 82
EGF/EGFR dimer/SHC/GRB2/SOS1 0.017 0.12 -9999 0 -0.24 72 72
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.024 0.033 -9999 0 -0.39 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.059 0.18 -9999 0 -0.45 88 88
EGF/EGFR dimer/SHC -0.007 0.12 -9999 0 -0.28 78 78
mol:GDP 0.012 0.11 -9999 0 -0.24 72 72
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.023 0.043 -9999 0 -0.45 4 4
GRB2/SOS1 0.04 0.007 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.098 -9999 0 -0.35 3 3
SHC1 0.028 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.11 -9999 0 -0.42 2 2
FRAP1 -0.043 0.08 -9999 0 -0.23 72 72
EGF/EGFR dimer -0.024 0.13 -9999 0 -0.33 79 79
SOS1 0.028 0.004 -9999 0 -10000 0 0
GRB2 0.028 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.034 0.042 -9999 0 -0.3 7 7
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 -0.027 0.13 -10000 0 -0.34 36 36
TBX21 -0.093 0.33 -10000 0 -1 39 39
B2M 0.021 0.02 -10000 0 -10000 0 0
TYK2 0.017 0.038 -10000 0 -0.41 1 1
IL12RB1 -0.017 0.13 -10000 0 -0.42 44 44
GADD45B -0.044 0.24 -10000 0 -0.7 24 24
IL12RB2 -0.058 0.17 -10000 0 -0.4 91 91
GADD45G -0.047 0.25 -10000 0 -0.79 20 20
natural killer cell activation 0.001 0.019 -10000 0 -10000 0 0
RELB 0.024 0.038 -10000 0 -0.39 4 4
RELA 0.027 0.007 -10000 0 -10000 0 0
IL18 0.012 0.074 -10000 0 -0.45 12 12
IL2RA -0.012 0.12 -10000 0 -0.39 46 46
IFNG -0.063 0.17 -10000 0 -0.39 101 101
STAT3 (dimer) -0.054 0.25 -10000 0 -0.68 37 37
HLA-DRB5 0.01 0.074 -10000 0 -0.43 13 13
FASLG -0.098 0.35 0.57 1 -0.99 48 49
NF kappa B2 p52/RelB -0.067 0.29 -10000 0 -0.83 38 38
CD4 0.02 0.034 -10000 0 -0.43 2 2
SOCS1 -0.003 0.11 -10000 0 -0.39 36 36
EntrezGene:6955 -0.004 0.012 -10000 0 -10000 0 0
CD3D 0.001 0.083 -10000 0 -0.43 16 16
CD3E 0.005 0.071 -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 -0.084 0.31 -10000 0 -0.92 35 35
CCL4 -0.08 0.3 -10000 0 -0.91 35 35
HLA-A 0.015 0.05 -10000 0 -0.4 6 6
IL18/IL18R 0.036 0.095 -10000 0 -0.27 30 30
NOS2 -0.088 0.32 -10000 0 -0.89 42 42
IL12/IL12R/TYK2/JAK2/SPHK2 -0.016 0.12 0.2 1 -0.33 26 27
IL1R1 -0.074 0.29 0.57 1 -0.88 33 34
IL4 -0.003 0.036 -10000 0 -10000 0 0
JAK2 0.015 0.031 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.069 0.23 -10000 0 -0.71 39 39
RAB7A -0.012 0.23 0.45 6 -0.66 14 20
lysosomal transport -0.01 0.22 0.44 7 -0.62 16 23
FOS -0.17 0.46 -10000 0 -1.2 76 76
STAT4 (dimer) -0.044 0.27 0.42 3 -0.73 34 37
STAT5A (dimer) -0.099 0.32 -10000 0 -0.81 55 55
GZMA -0.1 0.34 -10000 0 -0.97 46 46
GZMB -0.092 0.32 0.47 1 -0.91 42 43
HLX 0.025 0.033 -10000 0 -0.39 3 3
LCK -0.088 0.31 -10000 0 -0.92 38 38
TCR/CD3/MHC II/CD4 -0.03 0.15 -10000 0 -0.44 37 37
IL2/IL2R 0.022 0.11 -10000 0 -0.28 31 31
MAPK14 -0.043 0.25 -10000 0 -0.71 28 28
CCR5 -0.08 0.28 -10000 0 -0.89 28 28
IL1B -0.026 0.13 -10000 0 -0.4 53 53
STAT6 -0.006 0.11 -10000 0 -0.9 2 2
STAT4 0.018 0.063 -10000 0 -0.4 11 11
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.009 0.085 -10000 0 -0.39 21 21
NFKB1 0.027 0.005 -10000 0 -10000 0 0
NFKB2 0.027 0.005 -10000 0 -10000 0 0
IL12B -0.018 0.12 -10000 0 -0.4 43 43
CD8A -0.018 0.13 -10000 0 -0.42 46 46
CD8B -0.025 0.14 -10000 0 -0.42 53 53
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.026 0.13 0.34 36 -0.3 1 37
IL2RB 0.021 0.051 -10000 0 -0.4 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.25 0.42 3 -0.68 33 36
IL2RG 0.013 0.078 -10000 0 -0.4 17 17
IL12 -0.012 0.11 -10000 0 -0.3 51 51
STAT5A 0.028 0.003 -10000 0 -10000 0 0
CD247 -0.001 0.09 -10000 0 -0.41 21 21
IL2 -0.003 0.028 -10000 0 -0.39 1 1
SPHK2 0.027 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.001 0.081 -10000 0 -0.44 14 14
IL12/IL12R/TYK2/JAK2 -0.087 0.32 -10000 0 -0.93 41 41
MAP2K3 -0.043 0.25 -10000 0 -0.68 30 30
RIPK2 0.025 0.009 -10000 0 -10000 0 0
MAP2K6 -0.05 0.26 -10000 0 -0.71 33 33
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.041 -10000 0 -0.45 3 3
IL18RAP 0.01 0.086 -10000 0 -0.42 18 18
IL12Rbeta1/TYK2 0.003 0.11 -10000 0 -0.31 45 45
EOMES -0.12 0.28 -10000 0 -0.84 42 42
STAT1 (dimer) -0.07 0.26 -10000 0 -0.69 45 45
T cell proliferation -0.015 0.21 0.38 2 -0.55 28 30
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.024 0.033 -10000 0 -0.43 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.056 0.22 -10000 0 -0.62 28 28
ATF2 -0.034 0.24 0.45 1 -0.68 26 27
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 0.035 0.049 -10000 0 -0.2 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 0.026 -10000 0 -0.39 1 1
mol:Na + -0.005 0.089 -10000 0 -0.23 64 64
mol:ADP -0.022 0.062 -10000 0 -0.28 26 26
GNAT2 0.02 0.017 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.04 0.064 -10000 0 -0.26 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.009 -10000 0 -10000 0 0
GRK7 -0.004 0.095 -10000 0 -0.39 27 27
CNGB3 -0.036 0.14 -10000 0 -0.39 65 65
Cone Metarhodopsin II/X-Arrestin 0.014 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.046 0.13 0.18 44 -0.23 130 174
Cone PDE6 0.05 0.063 -10000 0 -0.24 12 12
Cone Metarhodopsin II 0.01 0.054 -10000 0 -0.21 26 26
Na + (4 Units) -0.037 0.12 -10000 0 -0.23 131 131
GNAT2/GDP 0.048 0.059 -10000 0 -0.22 20 20
GNB5 0.027 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.038 0.18 20 -10000 0 20
Cone Transducin 0.038 0.053 -10000 0 -0.22 18 18
SLC24A2 -0.059 0.16 -10000 0 -0.39 92 92
GNB3/GNGT2 0.027 0.062 -10000 0 -0.29 18 18
GNB3 0.013 0.074 -10000 0 -0.4 15 15
GNAT2/GTP 0.019 0.004 -10000 0 -10000 0 0
CNGA3 0.01 0.029 -10000 0 -0.39 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 -0.005 0.089 -10000 0 -0.23 64 64
mol:Pi 0.039 0.064 -10000 0 -0.26 21 21
Cone CNG Channel 0.014 0.084 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.059 0.16 -10000 0 -0.39 92 92
RGS9 0.018 0.064 -10000 0 -0.4 11 11
PDE6C -0.011 0.017 -10000 0 -10000 0 0
GNGT2 0.025 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
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.007 -10000 0 -10000 0 0
VLDLR 0.018 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 -0.02 0.13 -10000 0 -0.27 104 104
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 29 -0.25 101 130
IQGAP1/CaM 0.038 0.012 -10000 0 -10000 0 0
DAB1 -0.001 0.075 -10000 0 -0.39 16 16
IQGAP1 0.027 0.005 -10000 0 -10000 0 0
PLA2G7 -0.13 0.2 -10000 0 -0.39 187 187
CALM1 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.032 0.045 -10000 0 -0.27 10 10
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.022 -10000 0 -0.45 1 1
CDK5R1 0.026 0.027 -10000 0 -0.39 2 2
LIS1/Poliovirus Protein 3A 0.01 0.003 -10000 0 -10000 0 0
CDK5R2 -0.043 0.14 -10000 0 -0.39 68 68
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.03 0.14 -10000 0 -0.27 110 110
YWHAE 0.027 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.028 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 -0.39 4 5
RELN -0.07 0.19 -10000 0 -0.45 98 98
PAFAH/LIS1 -0.067 0.12 -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 -0.02 0.096 -10000 0 -0.32 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.037 0.12 -10000 0 -0.35 30 30
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.039 0.12 0.33 3 -0.32 17 20
LIS1/IQGAP1 0.028 0.01 -10000 0 -10000 0 0
RHOA 0.013 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.026 0.027 -10000 0 -0.39 2 2
PAFAH1B2 0.023 0.031 -10000 0 -0.45 2 2
MAP1B/LIS1/Dynein heavy chain 0.019 0.035 -10000 0 -0.26 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.018 0.12 0.3 4 -0.32 9 13
LRP8 0.019 0.059 -10000 0 -0.39 10 10
NDEL1/Katanin 60 -0.029 0.12 0.3 5 -0.32 11 16
P39/CDK5 -0.05 0.13 0.2 1 -0.4 13 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.011 -10000 0 -10000 0 0
CDK5 -0.046 0.11 0.18 24 -0.24 89 113
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0.01 -10000 0 -10000 0 0
CSNK2A1 0.026 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.018 0.12 -10000 0 -0.24 92 92
RELN/VLDLR -0.011 0.13 -10000 0 -0.25 104 104
CDC42 0.014 0.006 -10000 0 -10000 0 0
Arf6 signaling events

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.029 0.034 -10000 0 -0.27 5 5
ARNO/beta Arrestin1-2 0.012 0.12 -10000 0 -0.75 9 9
EGFR 0.02 0.048 -10000 0 -0.45 5 5
EPHA2 0.02 0.057 -10000 0 -0.45 7 7
USP6 0.026 0.02 -10000 0 -0.39 1 1
IQSEC1 0.025 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.024 0.13 -10000 0 -0.33 79 79
ARRB2 0.01 0.003 -10000 0 -10000 0 0
mol:GTP 0.036 0.05 0.12 74 -0.16 2 76
ARRB1 0.024 0.031 -10000 0 -0.45 2 2
FBXO8 0.027 0.006 -10000 0 -10000 0 0
TSHR 0.007 0.071 -10000 0 -0.39 14 14
EGF -0.059 0.18 -10000 0 -0.45 88 88
somatostatin receptor activity 0 0 0.001 28 -0.001 23 51
ARAP2 0.021 0.048 -10000 0 -0.45 5 5
mol:GDP -0.004 0.091 0.18 13 -0.26 27 40
mol:PI-3-4-5-P3 0 0 0.001 15 -0.001 11 26
ITGA2B -0.012 0.12 -10000 0 -0.39 47 47
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.043 -10000 0 -0.25 5 5
ADAP1 0.025 0.023 -10000 0 -0.45 1 1
KIF13B 0.021 0.048 -10000 0 -0.45 5 5
HGF/MET 0.021 0.077 -10000 0 -0.3 26 26
PXN 0.028 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.006 0.11 0.2 27 -0.26 24 51
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.011 0.12 -10000 0 -0.28 79 79
ADRB2 -0.004 0.12 -10000 0 -0.45 32 32
receptor agonist activity 0 0 0 28 0 14 42
actin filament binding 0 0 0 25 -0.001 21 46
SRC 0.026 0.007 -10000 0 -10000 0 0
ITGB3 0.011 0.085 -10000 0 -0.41 19 19
GNAQ 0.027 0.005 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 41 -0.001 16 57
ARF6/GDP 0.036 0.12 0.23 38 -0.44 14 52
ARF6/GDP/GULP/ACAP1 -0.043 0.15 0.23 2 -0.33 55 57
alphaIIb/beta3 Integrin/paxillin/GIT1 0.033 0.1 -10000 0 -0.22 61 61
ACAP1 0.017 0.065 -10000 0 -0.39 12 12
ACAP2 0.02 0.013 -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 0.002 0.13 -10000 0 -0.98 9 9
NCK1 0.023 0.011 -10000 0 -10000 0 0
fibronectin binding 0 0 0 21 0 19 40
endosomal lumen acidification 0 0 0 43 0 24 67
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.11 0.22 -10000 0 -0.45 141 141
GNAQ/ARNO 0.019 0.13 -10000 0 -0.91 9 9
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 14 0 5 19
MET 0.021 0.049 -10000 0 -0.41 6 6
GNA14 -0.043 0.17 -10000 0 -0.45 72 72
GNA15 0.025 0.031 -10000 0 -0.45 2 2
GIT1 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 34 -0.001 17 51
GNA11 0.024 0.037 -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 -0.74 11 11
alphaIIb/beta3 Integrin -0.001 0.11 -10000 0 -0.29 63 63
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.021 -10000 0 -0.27 3 3
SNTA1 0.026 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.009 0.027 -10000 0 -0.25 6 6
MAPK12 -0.013 0.067 0.2 3 -0.23 37 40
CCND1 -0.001 0.062 -10000 0 -0.45 7 7
p38 gamma/SNTA1 0.011 0.076 0.23 10 -0.24 23 33
MAP2K3 0.027 0.005 -10000 0 -10000 0 0
PKN1 0.026 0.027 -10000 0 -0.39 2 2
G2/M transition checkpoint -0.011 0.07 0.21 8 -0.23 37 45
MAP2K6 -0.005 0.057 -10000 0 -0.26 24 24
MAPT -0.13 0.15 0.21 3 -0.29 211 214
MAPK13 0.012 0.026 -10000 0 -0.32 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.014 0.012 -10000 0 -10000 0 0
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.002 0.095 0.21 2 -0.33 15 17
PDGFB-D/PDGFRB/SLAP -0.021 0.12 -10000 0 -0.27 85 85
PDGFB-D/PDGFRB/APS/CBL 0 0.1 -10000 0 -0.23 83 83
AKT1 0.024 0.12 0.36 16 -0.33 2 18
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.008 0.12 0.27 16 -0.36 18 34
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
FGR -0.018 0.11 0.34 1 -0.5 13 14
mol:Ca2+ 0 0.12 0.27 16 -0.39 22 38
MYC 0.057 0.13 0.4 29 -10000 0 29
SHC1 0.028 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.003 0.092 -10000 0 -0.22 2 2
LRP1/PDGFRB/PDGFB 0 0.12 -10000 0 -0.24 89 89
GRB10 0.026 0.007 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 -0.001 0.12 0.27 16 -0.39 22 38
PTEN 0.027 0.006 -10000 0 -10000 0 0
GRB2 0.028 0.004 -10000 0 -10000 0 0
GRB7 0.026 0.031 -10000 0 -0.45 2 2
PDGFB-D/PDGFRB/SHP2 -0.016 0.12 -10000 0 -0.27 88 88
PDGFB-D/PDGFRB/GRB10 -0.014 0.12 -10000 0 -0.27 83 83
cell cycle arrest -0.021 0.12 -10000 0 -0.27 85 85
HRAS 0.026 0.021 -10000 0 -0.41 1 1
HIF1A 0.018 0.11 0.33 16 -0.3 2 18
GAB1 0.004 0.11 0.29 8 -0.37 15 23
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.004 0.1 0.27 14 -0.34 10 24
PDGFB-D/PDGFRB 0.002 0.1 -10000 0 -0.23 82 82
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.016 0.12 -10000 0 -0.27 88 88
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.003 0.08 -10000 0 -0.35 3 3
positive regulation of MAPKKK cascade -0.016 0.12 -10000 0 -0.27 88 88
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
mol:IP3 0 0.12 0.27 16 -0.4 22 38
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.027 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.017 0.12 -10000 0 -0.28 88 88
SHB 0.025 0.009 -10000 0 -10000 0 0
BLK -0.06 0.16 -10000 0 -0.5 40 40
PTPN2 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.016 0.12 -10000 0 -0.27 86 86
BCAR1 0.027 0.006 -10000 0 -10000 0 0
VAV2 0.01 0.12 0.31 14 -0.38 13 27
CBL 0.025 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.015 0.12 -10000 0 -0.27 86 86
LCK -0.019 0.11 0.34 1 -0.52 11 12
PDGFRB -0.047 0.16 -10000 0 -0.39 88 88
ACP1 0.028 0.003 -10000 0 -10000 0 0
HCK -0.01 0.093 -10000 0 -0.76 3 3
ABL1 0.001 0.11 0.27 16 -0.37 13 29
PDGFB-D/PDGFRB/CBL 0.001 0.12 0.33 4 -0.41 22 26
PTPN1 0.027 0.007 -10000 0 -10000 0 0
SNX15 0.027 0.007 -10000 0 -10000 0 0
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.009 0.085 -10000 0 -0.39 21 21
cell proliferation 0.056 0.13 0.37 35 -10000 0 35
SLA 0.02 0.034 -10000 0 -0.39 3 3
actin cytoskeleton reorganization 0.029 0.11 0.34 11 -10000 0 11
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 0.002 0.11 -10000 0 -0.23 87 87
SH2B2 0.025 0.02 -10000 0 -0.39 1 1
PLCgamma1/SPHK1 0.008 0.12 0.28 16 -0.37 17 33
LYN -0.009 0.073 -10000 0 -10000 0 0
LRP1 0.027 0.022 -10000 0 -0.45 1 1
SOS1 0.028 0.004 -10000 0 -10000 0 0
STAT5B 0.028 0.003 -10000 0 -10000 0 0
STAT5A 0.028 0.003 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.019 0.093 -10000 0 -10000 0 0
SPHK1 0.019 0.062 -10000 0 -0.39 11 11
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0 0.12 0.27 16 -0.4 22 38
PLCG1 -0.001 0.12 0.27 16 -0.4 22 38
NHERF/PDGFRB 0.001 0.11 -10000 0 -0.24 89 89
YES1 -0.02 0.097 0.35 1 -0.51 9 10
cell migration 0 0.11 -10000 0 -0.23 89 89
SHC/Grb2/SOS1 0.027 0.099 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.019 -10000 0 -0.39 1 1
SLC9A3R1 0.024 0.043 -10000 0 -0.45 4 4
NHERF1-2/PDGFRB/PTEN 0.013 0.11 -10000 0 -0.21 88 88
FYN -0.014 0.092 -10000 0 -0.37 10 10
DOK1 -0.01 0.097 0.18 32 -0.22 3 35
HRAS/GTP 0.019 0.015 -10000 0 -0.29 1 1
PDGFB 0.02 0.053 -10000 0 -0.39 8 8
RAC1 0.024 0.12 0.34 16 -0.38 9 25
PRKCD -0.01 0.094 0.18 27 -0.22 1 28
FER -0.009 0.096 0.18 33 -0.22 1 34
MAPKKK cascade -0.018 0.097 0.36 7 -10000 0 7
RASA1 -0.009 0.098 0.18 34 -0.24 3 37
NCK1 0.023 0.011 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.003 0.095 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.017 0.12 -10000 0 -0.27 86 86
chemotaxis 0.002 0.11 0.27 16 -0.36 13 29
STAT1-3-5/STAT1-3-5 0.007 0.1 -10000 0 -0.35 6 6
Bovine Papilomavirus E5/PDGFRB -0.031 0.11 -10000 0 -0.27 88 88
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.001 0.11 0.32 47 -10000 0 47
KIRREL 0.002 0.099 -10000 0 -0.45 22 22
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.001 0.11 -10000 0 -0.32 47 47
PLCG1 0.027 0.006 -10000 0 -10000 0 0
ARRB2 0.027 0.006 -10000 0 -10000 0 0
WASL 0.027 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.024 0.097 -10000 0 -0.29 25 25
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.002 0.061 -10000 0 -0.25 19 19
FYN -0.016 0.085 0.27 9 -0.27 24 33
mol:Ca2+ 0.023 0.094 -10000 0 -0.24 50 50
mol:DAG 0.024 0.095 -10000 0 -0.24 50 50
NPHS2 -0.013 0.068 -10000 0 -0.41 12 12
mol:IP3 0.024 0.095 -10000 0 -0.24 50 50
regulation of endocytosis 0.021 0.084 -10000 0 -0.26 23 23
Nephrin/NEPH1/podocin/Cholesterol 0.011 0.092 -10000 0 -0.24 52 52
establishment of cell polarity 0.001 0.11 -10000 0 -0.32 47 47
Nephrin/NEPH1/podocin/NCK1-2 0.033 0.09 -10000 0 -0.28 18 18
Nephrin/NEPH1/beta Arrestin2 0.023 0.085 -10000 0 -0.26 23 23
NPHS1 -0.02 0.1 -10000 0 -0.4 29 29
Nephrin/NEPH1/podocin 0.015 0.085 -10000 0 -0.23 46 46
TJP1 0.028 0.004 -10000 0 -10000 0 0
NCK1 0.023 0.011 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.025 0.096 -10000 0 -0.24 50 50
CD2AP 0.027 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.025 0.098 -10000 0 -0.29 25 25
GRB2 0.028 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 51 58
cytoskeleton organization -0.01 0.071 0.23 3 -0.29 18 21
Nephrin/NEPH1 0.006 0.075 -10000 0 -0.22 47 47
Nephrin/NEPH1/ZO-1 0.019 0.091 -10000 0 -0.25 46 46
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.048 0.16 -10000 0 -0.39 88 88
Jak2/Leptin Receptor -0.063 0.17 -10000 0 -0.45 53 53
PTP1B/AKT1 -0.022 0.099 0.19 1 -0.3 27 28
FYN 0.027 0.019 -10000 0 -0.39 1 1
p210 bcr-abl/PTP1B -0.031 0.1 0.21 4 -0.3 35 39
EGFR 0.012 0.051 -10000 0 -0.46 5 5
EGF/EGFR -0.049 0.13 -10000 0 -0.3 79 79
CSF1 0.021 0.052 -10000 0 -0.45 6 6
AKT1 0.026 0.008 -10000 0 -10000 0 0
INSR 0.027 0.022 -10000 0 -0.45 1 1
PTP1B/N-cadherin -0.041 0.12 0.22 2 -0.29 52 54
Insulin Receptor/Insulin -0.009 0.099 -10000 0 -0.32 14 14
HCK 0.024 0.029 -10000 0 -0.42 2 2
CRK 0.027 0.006 -10000 0 -10000 0 0
TYK2 -0.03 0.099 0.21 3 -0.31 26 29
EGF -0.059 0.18 -10000 0 -0.45 88 88
YES1 0.025 0.009 -10000 0 -10000 0 0
CAV1 -0.036 0.12 0.21 11 -0.33 33 44
TXN 0.026 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.012 0.11 0.24 2 -0.34 18 20
cell migration 0.031 0.1 0.3 35 -0.21 4 39
STAT3 0.027 0.003 -10000 0 -10000 0 0
PRLR -0.067 0.19 -10000 0 -0.45 94 94
ITGA2B -0.013 0.12 -10000 0 -0.39 47 47
CSF1R 0.025 0.031 -10000 0 -0.45 2 2
Prolactin Receptor/Prolactin -0.039 0.14 -10000 0 -0.33 94 94
FGR 0.027 0.019 -10000 0 -0.39 1 1
PTP1B/p130 Cas -0.021 0.1 0.22 3 -0.3 30 33
Crk/p130 Cas -0.009 0.1 0.22 3 -0.32 20 23
DOK1 -0.041 0.11 0.23 4 -0.34 28 32
JAK2 -0.075 0.17 0.21 1 -0.45 58 59
Jak2/Leptin Receptor/Leptin -0.048 0.14 0.23 1 -0.42 21 22
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
PTPN1 -0.031 0.1 0.21 4 -0.3 35 39
LYN 0.024 0.021 -10000 0 -0.39 1 1
CDH2 -0.027 0.14 -10000 0 -0.4 60 60
SRC 0 0.11 -10000 0 -0.56 16 16
ITGB3 0.01 0.085 -10000 0 -0.42 19 19
CAT1/PTP1B -0.087 0.15 0.21 8 -0.39 44 52
CAPN1 0.026 0.007 -10000 0 -10000 0 0
CSK 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.01 0.082 -10000 0 -0.35 5 5
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.04 0.13 0.21 1 -0.38 19 20
negative regulation of transcription -0.073 0.17 0.21 1 -0.45 58 59
FCGR2A 0.006 0.092 -10000 0 -0.39 25 25
FER 0.023 0.031 -10000 0 -0.46 2 2
alphaIIb/beta3 Integrin -0.002 0.11 -10000 0 -0.29 63 63
BLK -0.035 0.15 -10000 0 -0.4 67 67
Insulin Receptor/Insulin/Shc 0.045 0.027 -10000 0 -0.25 3 3
RHOA 0.024 0.009 -10000 0 -10000 0 0
LEPR 0.026 0.031 -10000 0 -0.45 2 2
BCAR1 0.027 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.028 0.004 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.076 0.14 0.24 3 -0.41 36 39
PRL -0.003 0.046 -10000 0 -0.4 5 5
SOCS3 0.023 0.12 -10000 0 -1.1 5 5
SPRY2 0.021 0.053 -10000 0 -0.46 6 6
Insulin Receptor/Insulin/IRS1 0.042 0.037 -10000 0 -0.27 6 6
CSF1/CSF1R -0.014 0.11 0.24 2 -0.33 21 23
Ras protein signal transduction 0.011 0.067 0.55 6 -10000 0 6
IRS1 0.024 0.037 -10000 0 -0.45 3 3
INS -0.004 0.032 -10000 0 -0.4 2 2
LEP -0.049 0.16 -10000 0 -0.43 73 73
STAT5B -0.04 0.12 0.21 3 -0.35 40 43
STAT5A -0.04 0.12 0.21 3 -0.36 37 40
GRB2 0.028 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.053 0.13 0.22 3 -0.27 82 85
CSN2 -0.014 0.092 -10000 0 -0.5 3 3
PIK3CA 0.02 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 -0.39 12 12
SHC1 0.028 0.004 -10000 0 -10000 0 0
NOX4 -0.056 0.16 -10000 0 -0.39 94 94
LPA receptor mediated 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
GNB1/GNG2 0.018 0.085 -10000 0 -0.27 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.078 0.28 2 -0.3 3 5
AP1 -0.029 0.11 -10000 0 -0.36 16 16
mol:PIP3 -0.015 0.07 -10000 0 -0.41 5 5
AKT1 0.012 0.1 0.28 10 -0.32 4 14
PTK2B -0.013 0.074 0.19 2 -0.29 9 11
RHOA -0.026 0.098 0.19 1 -0.31 41 42
PIK3CB 0.023 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.06 0.19 10 -0.31 2 12
MAGI3 0.025 0.031 -10000 0 -0.45 2 2
RELA 0.026 0.007 -10000 0 -10000 0 0
apoptosis -0.013 0.082 -10000 0 -0.27 28 28
HRAS/GDP 0.019 0.015 -10000 0 -0.29 1 1
positive regulation of microtubule depolymerization -0.083 0.13 0.24 7 -0.32 40 47
NF kappa B1 p50/RelA -0.017 0.084 -10000 0 -0.35 6 6
endothelial cell migration -0.036 0.13 -10000 0 -0.35 72 72
ADCY4 -0.008 0.081 -10000 0 -0.35 14 14
ADCY5 -0.043 0.11 -10000 0 -0.38 21 21
ADCY6 -0.011 0.091 -10000 0 -0.39 15 15
ADCY7 -0.006 0.079 -10000 0 -0.36 12 12
ADCY1 -0.01 0.082 0.22 1 -0.36 13 14
ADCY2 -0.059 0.11 0.22 1 -0.37 22 23
ADCY3 -0.007 0.08 -10000 0 -0.34 14 14
ADCY8 -0.014 0.078 -10000 0 -0.34 14 14
ADCY9 -0.008 0.083 -10000 0 -0.36 13 13
GSK3B 0.007 0.094 0.21 42 -0.28 5 47
arachidonic acid secretion -0.006 0.082 -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 -0.013 0.078 -10000 0 -0.28 15 15
HRAS 0.026 0.021 -10000 0 -0.41 1 1
NFKBIA -0.008 0.078 0.28 3 -0.32 5 8
GAB1 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.19 -10000 0 -0.81 26 26
JUN 0.027 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.023 0.041 -10000 0 -0.28 1 1
TIAM1 -0.02 0.22 -10000 0 -0.96 26 26
PIK3R1 0.023 0.038 -10000 0 -0.45 3 3
mol:IP3 -0.012 0.059 0.19 10 -0.32 2 12
PLCB3 0.008 0.036 0.19 4 -0.26 1 5
FOS -0.032 0.16 -10000 0 -0.45 60 60
positive regulation of mitosis -0.006 0.082 -10000 0 -0.35 14 14
LPA/LPA1-2-3 0.012 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 0.027 0.006 -10000 0 -10000 0 0
stress fiber formation 0.003 0.073 0.23 2 -0.33 4 6
GNAZ -0.021 0.093 -10000 0 -0.28 34 34
EGFR/PI3K-beta/Gab1 -0.008 0.076 -10000 0 -0.43 5 5
positive regulation of dendritic cell cytokine production 0.011 0.097 -10000 0 -0.28 26 26
LPA/LPA2/MAGI-3 0.021 0.042 -10000 0 -0.27 2 2
ARHGEF1 0.005 0.089 0.35 2 -0.28 6 8
GNAI2 -0.013 0.077 -10000 0 -0.29 14 14
GNAI3 -0.013 0.081 -10000 0 -0.28 17 17
GNAI1 -0.014 0.081 -10000 0 -0.28 18 18
LPA/LPA3 0 0.061 -10000 0 -0.25 18 18
LPA/LPA2 0.008 0.037 -10000 0 -10000 0 0
LPA/LPA1 -0.014 0.097 -10000 0 -0.23 78 78
HB-EGF/EGFR -0.14 0.12 -10000 0 -0.24 311 311
HBEGF -0.19 0.13 -10000 0 -0.28 347 347
mol:DAG -0.012 0.059 0.19 10 -0.32 2 12
cAMP biosynthetic process -0.017 0.084 0.24 1 -0.34 14 15
NFKB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
LYN 0.001 0.082 0.28 6 -0.32 5 11
GNAQ 0.003 0.046 -10000 0 -0.25 11 11
LPAR2 0.028 0.003 -10000 0 -10000 0 0
LPAR3 0.017 0.071 -10000 0 -0.45 11 11
LPAR1 -0.003 0.09 -10000 0 -0.38 17 17
IL8 -0.12 0.13 0.36 2 -0.4 30 32
PTK2 -0.013 0.079 -10000 0 -0.33 8 8
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
CASP3 -0.013 0.082 -10000 0 -0.27 28 28
EGFR 0.02 0.048 -10000 0 -0.45 5 5
PLCG1 -0.013 0.062 0.16 1 -0.25 17 18
PLD2 -0.011 0.084 -10000 0 -0.32 10 10
G12/G13 0.017 0.085 -10000 0 -0.26 16 16
PI3K-beta -0.018 0.079 -10000 0 -0.32 9 9
cell migration 0.009 0.07 -10000 0 -0.25 19 19
SLC9A3R2 0.027 0.019 -10000 0 -0.39 1 1
PXN 0.003 0.074 0.25 1 -0.34 4 5
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 -0.39 349 349
PRKCE 0.027 0.022 -10000 0 -0.45 1 1
PRKCD -0.011 0.056 0.19 9 -0.33 1 10
Gi(beta/gamma) -0.003 0.078 -10000 0 -0.33 12 12
mol:LPA -0.015 0.046 -10000 0 -0.19 8 8
TRIP6/p130 Cas/FAK1/Paxillin 0.014 0.079 -10000 0 -0.42 2 2
MAPKKK cascade -0.006 0.082 -10000 0 -0.35 14 14
contractile ring contraction involved in cytokinesis -0.031 0.1 0.19 1 -0.31 45 46
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.035 0.1 -10000 0 -0.25 82 82
GNA15 0.001 0.053 -10000 0 -0.27 12 12
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.028 0.003 -10000 0 -10000 0 0
MAPT -0.085 0.13 0.24 7 -0.32 40 47
GNA11 0.001 0.051 -10000 0 -0.25 14 14
Rac1/GTP 0.002 0.2 -10000 0 -0.86 26 26
MMP2 -0.036 0.13 -10000 0 -0.35 72 72
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.15 0.14 -10000 0 -0.54 14 14
IHH -0.039 0.059 -10000 0 -0.33 4 4
SHH Np/Cholesterol/GAS1 0.003 0.068 -10000 0 -0.21 44 44
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.003 0.068 0.21 44 -10000 0 44
SMO/beta Arrestin2 -0.084 0.12 -10000 0 -0.45 23 23
SMO -0.09 0.12 -10000 0 -0.47 24 24
AKT1 -0.039 0.11 -10000 0 -0.5 16 16
ARRB2 0.027 0.006 -10000 0 -10000 0 0
BOC -0.016 0.13 -10000 0 -0.45 42 42
ADRBK1 0.026 0.008 -10000 0 -10000 0 0
heart looping -0.088 0.12 -10000 0 -0.46 24 24
STIL -0.086 0.097 -10000 0 -0.39 14 14
DHH N/PTCH2 0.031 0.055 -10000 0 -0.3 13 13
DHH N/PTCH1 -0.084 0.098 -10000 0 -0.5 7 7
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DHH 0.021 0.03 -10000 0 -0.39 2 2
PTHLH -0.22 0.18 -10000 0 -0.59 25 25
determination of left/right symmetry -0.088 0.12 -10000 0 -0.46 24 24
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
skeletal system development -0.21 0.18 -10000 0 -0.59 25 25
IHH N/Hhip -0.033 0.085 -10000 0 -0.32 32 32
DHH N/Hhip 0.018 0.078 -10000 0 -0.28 31 31
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.088 0.12 -10000 0 -0.46 24 24
pancreas development -0.006 0.1 -10000 0 -0.4 29 29
HHAT 0.026 0.031 -10000 0 -0.45 2 2
PI3K 0.027 0.03 -10000 0 -0.32 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.022 0.048 -10000 0 -0.41 6 6
somite specification -0.088 0.12 -10000 0 -0.46 24 24
SHH Np/Cholesterol/PTCH1 -0.091 0.097 -10000 0 -0.34 32 32
SHH Np/Cholesterol/PTCH2 0 0.076 -10000 0 -0.23 47 47
SHH Np/Cholesterol/Megalin -0.009 0.085 -10000 0 -0.24 55 55
SHH -0.021 0.077 -10000 0 -0.28 39 39
catabolic process -0.099 0.1 -10000 0 -0.43 13 13
SMO/Vitamin D3 -0.086 0.11 -10000 0 -0.44 15 15
SHH Np/Cholesterol/Hhip -0.012 0.088 -10000 0 -0.24 60 60
LRP2 -0.003 0.094 -10000 0 -0.39 26 26
receptor-mediated endocytosis -0.089 0.11 -10000 0 -0.45 18 18
SHH Np/Cholesterol/BOC -0.016 0.091 -10000 0 -0.23 72 72
SHH Np/Cholesterol/CDO -0.001 0.074 -10000 0 -0.22 48 48
mesenchymal cell differentiation 0.012 0.088 0.24 60 -10000 0 60
mol:Vitamin D3 -0.087 0.1 0.37 1 -0.34 32 33
IHH N/PTCH2 -0.02 0.066 -10000 0 -0.33 14 14
CDON 0.016 0.067 -10000 0 -0.45 10 10
IHH N/PTCH1 -0.097 0.11 -10000 0 -0.43 13 13
Megalin/LRPAP1 0.021 0.07 -10000 0 -0.27 26 26
PTCH2 0.017 0.067 -10000 0 -0.42 11 11
SHH Np/Cholesterol -0.002 0.061 -10000 0 -0.21 39 39
PTCH1 -0.099 0.1 -10000 0 -0.43 13 13
HHIP -0.006 0.1 -10000 0 -0.4 29 29
IL1-mediated signaling events

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
UBC13/UEV1A 0.038 0.01 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.45 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.068 -10000 0 -0.43 3 3
IRAK/TOLLIP 0.03 0.011 -10000 0 -10000 0 0
IKBKB 0.026 0.008 -10000 0 -10000 0 0
IKBKG 0.027 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.1 0.18 -10000 0 -0.31 202 202
IL1A -0.081 0.18 -10000 0 -0.4 127 127
IL1B -0.018 0.09 -10000 0 -0.28 52 52
IRAK/TRAF6/p62/Atypical PKCs 0.048 0.039 -10000 0 -10000 0 0
IL1R2 -0.057 0.18 -10000 0 -0.44 88 88
IL1R1 0.027 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 0.027 0.006 -10000 0 -10000 0 0
TICAM2 0.026 0.008 -10000 0 -10000 0 0
MAP3K3 0.028 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.019 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.043 0.059 0.27 6 -10000 0 6
JUN -0.011 0.062 0.32 2 -0.39 1 3
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.025 0.082 -10000 0 -0.64 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.012 0.11 -10000 0 -0.22 91 91
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.11 -10000 0 -0.45 2 2
IL1 beta fragment/IL1R1/IL1RAP 0.007 0.078 -10000 0 -0.45 2 2
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.01 0.066 0.18 26 -0.41 1 27
IRAK1 0.01 0.013 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.052 0.16 -10000 0 -0.32 125 125
IRAK4 0.027 0.022 -10000 0 -0.45 1 1
PRKCI 0.02 0.013 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.027 0.03 -10000 0 -0.32 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.016 0.065 -10000 0 -0.43 3 3
CHUK 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.007 0.078 -10000 0 -0.45 2 2
IL1 beta/IL1R2 -0.046 0.14 0.22 1 -0.26 132 133
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.014 0.072 -10000 0 -0.59 1 1
IRAK3 0.022 0.045 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.025 0.083 -10000 0 -0.64 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.011 0.069 -10000 0 -0.28 12 12
IL1 alpha/IL1R1/IL1RAP -0.021 0.12 -10000 0 -0.24 101 101
RELA 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
MYD88 0.025 0.009 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.049 0.028 -10000 0 -10000 0 0
IL1RAP 0.018 0.031 -10000 0 -0.42 2 2
UBE2N 0.028 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.006 0.063 -10000 0 -0.56 1 1
CASP1 0.024 0.023 -10000 0 -0.45 1 1
IL1RN/IL1R2 -0.11 0.21 -10000 0 -0.38 175 175
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.015 0.079 -10000 0 -0.66 1 1
TMEM189-UBE2V1 0.016 0.02 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.091 -10000 0 -0.3 15 15
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
IL1RN -0.093 0.21 -10000 0 -0.45 125 125
TRAF6/TAK1/TAB1/TAB2 0.048 0.017 -10000 0 -10000 0 0
MAP2K6 0.007 0.069 0.19 27 -0.22 24 51
Ephrin B reverse signaling

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
EFNB2 0.025 0.031 -10000 0 -0.45 2 2
EPHB2 -0.064 0.17 -10000 0 -0.39 107 107
EFNB1 -0.005 0.072 -10000 0 -0.27 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.12 -10000 0 -0.37 10 10
Ephrin B2/EPHB1-2 -0.014 0.11 -10000 0 -0.22 100 100
neuron projection morphogenesis -0.023 0.1 -10000 0 -0.35 10 10
Ephrin B1/EPHB1-2/Tiam1 -0.021 0.12 -10000 0 -0.31 22 22
DNM1 -0.001 0.11 -10000 0 -0.39 34 34
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.019 0.11 0.42 1 -0.44 30 31
YES1 -0.026 0.17 -10000 0 -0.68 29 29
Ephrin B1/EPHB1-2/NCK2 -0.016 0.12 -10000 0 -0.32 17 17
PI3K 0.005 0.11 -10000 0 -0.44 23 23
mol:GDP -0.022 0.12 -10000 0 -0.31 22 22
ITGA2B -0.012 0.12 -10000 0 -0.39 47 47
endothelial cell proliferation 0.032 0.023 -10000 0 -0.27 2 2
FYN -0.026 0.17 -10000 0 -0.68 29 29
MAP3K7 -0.023 0.11 0.24 1 -0.48 28 29
FGR -0.023 0.16 -10000 0 -0.66 30 30
TIAM1 0.021 0.053 -10000 0 -0.45 6 6
PIK3R1 0.024 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 -0.45 28 28
LYN -0.026 0.16 -10000 0 -0.68 29 29
Ephrin B1/EPHB1-2/Src Family Kinases -0.03 0.15 -10000 0 -0.62 30 30
Ephrin B1/EPHB1-2 -0.021 0.12 -10000 0 -0.52 25 25
SRC -0.023 0.16 -10000 0 -0.66 30 30
ITGB3 0.011 0.085 -10000 0 -0.41 19 19
EPHB1 0.005 0.087 -10000 0 -0.42 20 20
EPHB4 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.023 -10000 0 -0.27 2 2
alphaIIb/beta3 Integrin -0.001 0.11 -10000 0 -0.29 63 63
BLK -0.031 0.16 -10000 0 -0.67 29 29
HCK -0.021 0.16 -10000 0 -0.67 29 29
regulation of stress fiber formation 0.017 0.12 0.32 17 -10000 0 17
MAPK8 -0.019 0.11 -10000 0 -0.44 29 29
Ephrin B1/EPHB1-2/RGS3 -0.017 0.12 -10000 0 -0.32 17 17
endothelial cell migration -0.003 0.1 0.39 2 -0.4 22 24
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTPN13 0.015 0.083 -10000 0 -0.56 10 10
regulation of focal adhesion formation 0.017 0.12 0.32 17 -10000 0 17
chemotaxis 0.017 0.12 0.32 17 -10000 0 17
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
Rac1/GTP -0.018 0.11 -10000 0 -0.36 10 10
angiogenesis -0.024 0.12 -10000 0 -0.51 29 29
LCK -0.024 0.17 -10000 0 -0.67 30 30
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.035 0.037 -10000 0 -0.28 6 6
alphaV beta3 Integrin 0.03 0.084 -10000 0 -0.27 34 34
PTK2 0.004 0.11 0.31 9 -0.48 4 13
IGF1R 0.027 0.005 -10000 0 -10000 0 0
PI4KB 0.027 0.005 -10000 0 -10000 0 0
MFGE8 0.026 0.019 -10000 0 -0.39 1 1
SRC 0.026 0.007 -10000 0 -10000 0 0
CDKN1B 0.006 0.051 -10000 0 -10000 0 0
VEGFA 0.023 0.038 -10000 0 -0.39 4 4
ILK 0.006 0.054 -10000 0 -0.43 1 1
ROCK1 0.027 0.007 -10000 0 -10000 0 0
AKT1 0.001 0.047 -10000 0 -0.4 1 1
PTK2B 0.011 0.065 0.34 1 -0.36 2 3
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 0.034 0.065 -10000 0 -0.25 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.014 0.12 -10000 0 -0.25 81 81
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.01 0.048 -10000 0 -0.32 3 3
alphaV/beta3 Integrin/Syndecan-1 0.04 0.063 -10000 0 -0.25 21 21
PI4KA 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.1 0.16 -10000 0 -0.41 46 46
PI4 Kinase 0.039 0.011 -10000 0 -10000 0 0
PIK3CA 0.02 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 0.01 -10000 0 -10000 0 0
MAPK3 -0.06 0.13 -10000 0 -0.47 32 32
GPR124 0.022 0.034 -10000 0 -0.39 3 3
MAPK1 -0.059 0.13 -10000 0 -0.47 32 32
PXN 0.028 0.003 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
alphaV/beta3 Integrin/Tumstatin 0.005 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 -0.39 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.037 -10000 0 -0.24 6 6
IGF-1R heterotetramer 0.027 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 0.011 0.085 -10000 0 -0.41 19 19
IGF1 -0.053 0.18 -10000 0 -0.45 84 84
RAC1 0.026 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.034 0.065 -10000 0 -0.26 21 21
apoptosis 0.025 0.027 -10000 0 -0.39 2 2
CD47 0.025 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.034 0.063 -10000 0 -0.25 21 21
VCL 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.002 0.12 -10000 0 -0.27 81 81
CSF1 0.021 0.052 -10000 0 -0.45 6 6
PIK3C2A 0.006 0.054 -10000 0 -0.43 1 1
PI4 Kinase/Pyk2 0.007 0.083 -10000 0 -0.42 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.069 -10000 0 -0.24 22 22
FAK1/Vinculin 0.015 0.098 0.28 11 -0.38 4 15
alphaV beta3/Integrin/ppsTEM5 0.035 0.066 -10000 0 -0.26 21 21
RHOA 0.025 0.009 -10000 0 -10000 0 0
VTN 0.001 0.1 -10000 0 -0.39 30 30
BCAR1 0.027 0.006 -10000 0 -10000 0 0
FGF2 0.012 0.082 -10000 0 -0.44 16 16
F11R 0.003 0.06 -10000 0 -0.31 17 17
alphaV/beta3 Integrin/Lactadherin 0.039 0.065 -10000 0 -0.26 21 21
alphaV/beta3 Integrin/TGFBR2 0.033 0.066 -10000 0 -0.25 23 23
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.054 0.046 -10000 0 -0.24 7 7
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.058 -10000 0 -0.22 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.16 0.21 -10000 0 -0.39 217 217
alphaV/beta3 Integrin/Pyk2 0.034 0.064 -10000 0 -0.27 7 7
SDC1 0.028 0.003 -10000 0 -10000 0 0
VAV3 0.001 0.074 -10000 0 -0.45 3 3
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.024 0.037 -10000 0 -0.45 3 3
FAK1/Paxillin 0.014 0.099 0.28 11 -0.38 4 15
cell migration 0.011 0.092 0.25 16 -0.35 4 20
ITGAV 0.025 0.027 -10000 0 -0.39 2 2
PI3K 0.017 0.093 -10000 0 -0.4 6 6
SPP1 -0.2 0.21 -10000 0 -0.39 263 263
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 0.025 0.027 -10000 0 -0.39 2 2
COL4A3 -0.026 0.14 -10000 0 -0.41 57 57
angiogenesis -0.052 0.14 -10000 0 -0.48 32 32
Rac1/GTP 0.016 0.07 -10000 0 -0.42 3 3
EDIL3 -0.037 0.16 -10000 0 -0.42 70 70
cell proliferation 0.032 0.066 -10000 0 -0.25 23 23
BCR signaling pathway

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
JUN -0.022 0.12 0.24 6 -0.38 21 27
IKBKB 0.008 0.097 0.27 12 -0.32 9 21
AKT1 0.003 0.11 0.26 33 -0.23 19 52
IKBKG 0.017 0.081 0.24 11 -0.29 3 14
CALM1 -0.007 0.1 0.28 9 -0.38 11 20
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
MAP3K1 -0.031 0.15 0.31 5 -0.52 21 26
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.1 0.26 4 -0.39 13 17
DOK1 0.027 0.019 -10000 0 -0.39 1 1
AP-1 -0.013 0.093 0.21 17 -0.24 14 31
LYN 0.024 0.021 -10000 0 -0.39 1 1
BLNK -0.016 0.14 -10000 0 -0.45 45 45
SHC1 0.028 0.004 -10000 0 -10000 0 0
BCR complex -0.039 0.16 -10000 0 -0.33 105 105
CD22 -0.053 0.15 -10000 0 -0.42 51 51
CAMK2G -0.005 0.097 0.27 9 -0.37 10 19
CSNK2A1 0.026 0.007 -10000 0 -10000 0 0
INPP5D 0.025 0.031 -10000 0 -0.45 2 2
SHC/GRB2/SOS1 -0.039 0.12 -10000 0 -0.39 26 26
GO:0007205 -0.012 0.1 0.26 4 -0.4 13 17
SYK 0.024 0.037 -10000 0 -0.45 3 3
ELK1 -0.011 0.099 0.25 5 -0.38 13 18
NFATC1 -0.046 0.13 0.26 6 -0.46 18 24
B-cell antigen/BCR complex -0.039 0.16 -10000 0 -0.33 105 105
PAG1/CSK 0.035 0.02 -10000 0 -0.28 1 1
NFKBIB 0.018 0.045 0.12 18 -0.13 14 32
HRAS -0.015 0.1 0.26 5 -0.39 11 16
NFKBIA 0.018 0.045 0.12 20 -0.12 14 34
NF-kappa-B/RelA/I kappa B beta 0.022 0.04 0.13 18 -10000 0 18
RasGAP/Csk 0.002 0.14 -10000 0 -0.32 46 46
mol:GDP -0.009 0.099 0.26 3 -0.38 13 16
PTEN 0.027 0.006 -10000 0 -10000 0 0
CD79B 0.007 0.094 -10000 0 -0.42 23 23
NF-kappa-B/RelA/I kappa B alpha 0.022 0.04 0.13 18 -10000 0 18
GRB2 0.028 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.05 0.16 0.29 2 -0.52 22 24
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
mol:IP3 -0.013 0.1 0.25 4 -0.4 13 17
CSK 0.027 0.005 -10000 0 -10000 0 0
FOS -0.031 0.12 0.27 11 -0.36 25 36
CHUK 0.008 0.094 0.23 11 -0.33 11 22
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.004 0.11 0.24 2 -0.37 12 14
PTPN6 -0.053 0.14 -10000 0 -0.41 48 48
RELA 0.027 0.007 -10000 0 -10000 0 0
BCL2A1 0.014 0.033 0.11 8 -0.11 1 9
VAV2 -0.062 0.16 -10000 0 -0.5 31 31
ubiquitin-dependent protein catabolic process 0.021 0.045 0.12 20 -0.12 14 34
BTK 0.019 0.051 -10000 0 -1 1 1
CD19 -0.067 0.16 -10000 0 -0.39 74 74
MAP4K1 0.015 0.072 -10000 0 -0.4 14 14
CD72 -0.025 0.13 -10000 0 -0.39 57 57
PAG1 0.024 0.021 -10000 0 -0.39 1 1
MAPK14 -0.023 0.13 0.31 6 -0.46 19 25
SH3BP5 0.022 0.038 -10000 0 -0.45 3 3
PIK3AP1 -0.018 0.11 -10000 0 -0.38 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.039 0.14 -10000 0 -0.44 27 27
RAF1 -0.014 0.097 0.26 5 -0.37 11 16
RasGAP/p62DOK/SHIP 0.001 0.14 -10000 0 -0.42 23 23
CD79A -0.063 0.18 -10000 0 -0.41 102 102
re-entry into mitotic cell cycle -0.013 0.092 0.21 17 -0.24 13 30
RASA1 0.024 0.031 -10000 0 -0.45 2 2
MAPK3 -0.01 0.088 0.25 6 -0.32 11 17
MAPK1 -0.006 0.091 0.25 9 -0.31 9 18
CD72/SHP1 -0.05 0.17 0.33 4 -0.52 35 39
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.13 0.3 5 -0.44 21 26
actin cytoskeleton organization -0.046 0.14 0.33 2 -0.44 28 30
NF-kappa-B/RelA 0.048 0.077 0.23 18 -0.21 3 21
Calcineurin 0.015 0.099 0.27 7 -0.36 7 14
PI3K -0.054 0.13 -10000 0 -0.4 42 42
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.012 0.1 0.22 3 -0.4 17 20
SOS1 0.028 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.034 0.2 -10000 0 -0.7 32 32
DAPP1 -0.047 0.21 -10000 0 -0.77 32 32
cytokine secretion -0.043 0.12 0.26 6 -0.43 18 24
mol:DAG -0.013 0.1 0.25 4 -0.4 13 17
PLCG2 0.026 0.022 -10000 0 -0.45 1 1
MAP2K1 -0.011 0.094 0.26 5 -0.34 11 16
B-cell antigen/BCR complex/FcgammaRIIB -0.022 0.15 -10000 0 -0.29 106 106
mol:PI-3-4-5-P3 -0.034 0.11 0.22 1 -0.3 38 39
ETS1 -0.007 0.092 0.25 10 -0.34 10 20
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.02 0.15 -10000 0 -0.36 39 39
B-cell antigen/BCR complex/LYN -0.035 0.14 -10000 0 -0.46 29 29
MALT1 0.025 0.008 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
RAC1 -0.051 0.15 0.33 1 -0.48 28 29
B-cell antigen/BCR complex/LYN/SYK -0.024 0.17 0.36 1 -0.44 46 47
CARD11 -0.01 0.12 0.27 12 -0.4 17 29
FCGR2B 0.021 0.057 -10000 0 -0.45 7 7
PPP3CA 0.027 0.005 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.017 0.053 0.15 31 -0.12 5 36
PTPRC 0.016 0.073 -10000 0 -0.42 13 13
PDPK1 -0.007 0.1 0.22 33 -0.22 18 51
PPP3CB 0.028 0.004 -10000 0 -10000 0 0
PPP3CC 0.026 0.008 -10000 0 -10000 0 0
POU2F2 0.016 0.034 0.12 8 -10000 0 8
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 0.038 0.075 -10000 0 -0.22 34 34
ER alpha/Gai/GDP/Gbeta gamma -0.026 0.16 -10000 0 -0.5 38 38
AKT1 -0.007 0.17 -10000 0 -0.73 23 23
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.002 0.17 -10000 0 -0.75 23 23
mol:Ca2+ -0.034 0.13 -10000 0 -0.35 64 64
IGF1R 0.027 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.008 0.089 -10000 0 -0.26 47 47
SHC1 0.028 0.004 -10000 0 -10000 0 0
apoptosis 0.006 0.16 0.7 23 -10000 0 23
RhoA/GTP 0.012 0.048 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.012 0.14 -10000 0 -0.45 26 26
regulation of stress fiber formation 0.007 0.059 0.31 1 -0.17 5 6
E2/ERA-ERB (dimer) 0.014 0.076 -10000 0 -0.25 36 36
KRAS 0.026 0.007 -10000 0 -10000 0 0
G13/GTP 0.021 0.059 -10000 0 -0.22 27 27
pseudopodium formation -0.007 0.059 0.17 5 -0.31 1 6
E2/ER alpha (dimer)/PELP1 0.021 0.063 -10000 0 -0.24 26 26
GRB2 0.028 0.004 -10000 0 -10000 0 0
GNG2 0.025 0.02 -10000 0 -0.39 1 1
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
HRAS 0.026 0.021 -10000 0 -0.41 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.01 0.16 0.26 6 -0.52 31 37
E2/ER beta (dimer) 0.013 0.045 -10000 0 -0.28 11 11
mol:GDP 0.001 0.073 -10000 0 -0.34 14 14
mol:NADP -0.01 0.16 0.26 6 -0.52 31 37
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
mol:IP3 -0.041 0.13 -10000 0 -0.36 64 64
IGF-1R heterotetramer 0.027 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 -0.053 0.18 -10000 0 -0.45 84 84
mol:L-citrulline -0.01 0.16 0.26 6 -0.52 31 37
RHOA 0.025 0.009 -10000 0 -10000 0 0
Gai/GDP -0.051 0.23 -10000 0 -0.61 68 68
JNK cascade 0.013 0.044 -10000 0 -0.28 11 11
BCAR1 0.027 0.006 -10000 0 -10000 0 0
ESR2 0.017 0.063 -10000 0 -0.4 11 11
GNAQ 0.027 0.005 -10000 0 -10000 0 0
ESR1 0.003 0.1 -10000 0 -0.42 27 27
Gq family/GDP/Gbeta gamma -0.025 0.16 -10000 0 -0.69 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.028 0.093 -10000 0 -0.78 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.011 0.14 -10000 0 -0.45 28 28
GNAZ 0.011 0.083 -10000 0 -0.41 18 18
E2/ER alpha (dimer) 0.003 0.072 -10000 0 -0.29 27 27
STRN 0.006 0.099 -10000 0 -0.45 22 22
GNAL -0.029 0.15 -10000 0 -0.45 57 57
PELP1 0.027 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 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.45 1 1
HBEGF -0.089 0.18 0.32 14 -0.52 41 55
cAMP biosynthetic process -0.015 0.096 -10000 0 -0.22 81 81
SRC -0.019 0.16 0.22 3 -0.51 32 35
PI3K 0.027 0.03 -10000 0 -0.32 2 2
GNB1 0.027 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.029 0.077 -10000 0 -0.32 11 11
SOS1 0.028 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.041 0.12 -10000 0 -0.4 30 30
Gs family/GTP -0.01 0.1 -10000 0 -0.23 81 81
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.022 -10000 0 -0.22 1 1
vasodilation -0.008 0.16 0.25 8 -0.5 31 39
mol:DAG -0.041 0.13 -10000 0 -0.36 64 64
Gs family/GDP/Gbeta gamma -0.013 0.092 -10000 0 -0.34 14 14
MSN -0.007 0.061 0.19 2 -0.33 1 3
Gq family/GTP -0.037 0.15 -10000 0 -0.38 70 70
mol:PI-3-4-5-P3 -0.001 0.16 -10000 0 -0.72 23 23
NRAS 0.027 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.008 0.16 0.5 31 -0.25 8 39
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.074 -10000 0 -0.34 11 11
NOS3 -0.012 0.17 0.27 6 -0.55 31 37
GNA11 0.024 0.037 -10000 0 -0.45 3 3
MAPKKK cascade 0 0.16 -10000 0 -0.55 25 25
E2/ER alpha (dimer)/PELP1/Src 0.011 0.15 0.28 5 -0.46 28 33
ruffle organization -0.007 0.059 0.17 5 -0.31 1 6
ROCK2 -0.006 0.067 0.2 2 -0.36 1 3
GNA14 -0.043 0.17 -10000 0 -0.45 72 72
GNA15 0.025 0.031 -10000 0 -0.45 2 2
GNA13 0.028 0.003 -10000 0 -10000 0 0
MMP9 -0.13 0.18 0.36 16 -0.53 42 58
MMP2 -0.03 0.16 0.27 9 -0.51 27 36
Regulation of Androgen receptor activity

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
HDAC1 0.01 0.012 -10000 0 -10000 0 0
SMARCC1 0.004 0.035 -10000 0 -0.6 1 1
REL 0.022 0.065 -10000 0 -0.45 9 9
HDAC7 -0.091 0.14 0.23 2 -0.47 25 27
JUN 0.026 0.005 -10000 0 -10000 0 0
EP300 0.025 0.031 -10000 0 -0.45 2 2
KAT2B 0.009 0.084 -10000 0 -0.45 16 16
KAT5 0.027 0.007 -10000 0 -10000 0 0
MAPK14 -0.024 0.078 -10000 0 -0.34 25 25
FOXO1 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.085 0.16 0.25 1 -0.47 28 29
MAP2K6 -0.018 0.11 -10000 0 -0.46 25 25
BRM/BAF57 0.023 0.034 -10000 0 -0.32 1 1
MAP2K4 0.005 0.026 -10000 0 -10000 0 0
SMARCA2 0.015 0.029 -10000 0 -0.45 1 1
PDE9A -0.08 0.22 -10000 0 -0.96 22 22
NCOA2 -0.005 0.12 -10000 0 -0.45 31 31
CEBPA 0.025 0.037 -10000 0 -0.45 3 3
EHMT2 0.025 0.007 -10000 0 -10000 0 0
cell proliferation -0.076 0.16 0.28 13 -0.44 29 42
NR0B1 -0.02 0.085 -10000 0 -0.39 23 23
EGR1 -0.001 0.096 -10000 0 -0.45 21 21
RXRs/9cRA 0.005 0.095 -10000 0 -0.25 56 56
AR/RACK1/Src -0.041 0.11 0.25 3 -0.38 22 25
AR/GR -0.061 0.13 0.19 1 -0.31 70 71
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
PKN1 0.026 0.027 -10000 0 -0.39 2 2
RCHY1 0.027 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 -0.37 31 31
SRC -0.037 0.077 0.2 12 -0.3 23 35
NR3C1 0.027 0.006 -10000 0 -10000 0 0
KLK3 -0.25 0.43 0.37 1 -1.1 86 87
APPBP2 0.006 0.026 -10000 0 -10000 0 0
TRIM24 0.017 0.029 -10000 0 -0.45 1 1
T-DHT/AR/TIP60 -0.045 0.11 0.23 1 -0.39 20 21
TMPRSS2 -0.47 0.53 -10000 0 -1 234 234
RXRG -0.034 0.15 -10000 0 -0.44 59 59
mol:9cRA -0.001 0.003 -10000 0 -0.012 1 1
RXRA 0.027 0.005 -10000 0 -10000 0 0
RXRB 0.026 0.006 -10000 0 -10000 0 0
CARM1 0.028 0.004 -10000 0 -10000 0 0
NR2C2 0.019 0.048 -10000 0 -0.45 5 5
KLK2 -0.041 0.11 -10000 0 -0.42 11 11
AR -0.073 0.13 0.16 2 -0.3 109 111
SENP1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
MDM2 0.032 0.013 -10000 0 -10000 0 0
SRY 0.005 0.011 0.029 87 -10000 0 87
GATA2 0.023 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 0.24 5 -0.39 22 27
positive regulation of transcription 0.023 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 0.034 0.029 -10000 0 -10000 0 0
SPDEF -0.11 0.21 -10000 0 -0.44 137 137
T-DHT/AR/TIF2 -0.048 0.13 0.2 2 -0.37 38 40
T-DHT/AR/Hsp90 -0.048 0.11 0.22 1 -0.39 23 24
GSK3B 0.022 0.009 -10000 0 -10000 0 0
NR2C1 0.029 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.043 0.072 -10000 0 -0.31 25 25
SIRT1 0.026 0.022 -10000 0 -0.45 1 1
ZMIZ2 0.032 0.014 -10000 0 -10000 0 0
POU2F1 -0.025 0.07 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.062 0.11 0.21 1 -0.38 28 29
CREBBP 0.027 0.005 -10000 0 -10000 0 0
SMARCE1 0.019 0.02 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.005 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.005 0.083 -10000 0 -0.3 2 2
NFATC4 -0.023 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 -10000 0 0
JUN -0.004 0.075 0.19 9 -0.36 4 13
HRAS 0.025 0.021 -10000 0 -0.41 1 1
DOCK7 -0.028 0.074 0.29 2 -10000 0 2
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.004 0.094 -10000 0 -0.24 23 23
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 -0.015 0.082 -10000 0 -10000 0 0
RAF1 -0.017 0.09 0.28 6 -0.31 2 8
ErbB2/ErbB3/neuregulin 2 -0.13 0.14 -10000 0 -0.26 258 258
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 0.31 8 -0.4 143 151
NRAS 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.076 -10000 0 -10000 0 0
MAPK3 -0.12 0.22 0.31 3 -0.48 99 102
MAPK1 -0.12 0.22 0.31 3 -0.49 96 99
JAK2 -0.027 0.068 -10000 0 -10000 0 0
NF2 0.008 0.042 -10000 0 -0.63 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.062 -10000 0 -0.26 10 10
NRG1 -0.039 0.15 -10000 0 -0.4 74 74
GRB2/SOS1 0.04 0.007 -10000 0 -10000 0 0
MAPK8 -0.008 0.078 0.22 7 -0.29 10 17
MAPK9 -0.011 0.056 0.21 9 -10000 0 9
ERBB2 -0.019 0.007 -10000 0 -10000 0 0
ERBB3 0.02 0.057 -10000 0 -0.45 7 7
SHC1 0.027 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) 0.015 0.12 -10000 0 -0.79 10 10
RNF41 -0.007 0.007 -10000 0 -10000 0 0
FRAP1 -0.002 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.021 0.05 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0 0.02 -10000 0 -10000 0 0
CHRNA1 -0.14 0.26 0.29 3 -0.6 98 101
myelination -0.014 0.084 0.29 13 -0.31 2 15
PPP3CB -0.026 0.071 0.28 2 -10000 0 2
KRAS 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.02 0.069 -10000 0 -10000 0 0
NRG2 -0.23 0.23 -10000 0 -0.45 266 266
mol:GDP -0.006 0.062 -10000 0 -0.25 10 10
SOS1 0.027 0.004 -10000 0 -10000 0 0
MAP2K2 -0.031 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 -0.027 0.075 0.28 2 -10000 0 2
MAP2K1 -0.11 0.22 -10000 0 -0.57 40 40
heart morphogenesis -0.015 0.076 -10000 0 -10000 0 0
RAS family/GDP 0.013 0.08 -10000 0 -0.34 1 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.011 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 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.035 0.13 -10000 0 -0.25 120 120
cell-cell adhesion 0.035 0.083 0.4 5 -10000 0 5
Ephrin B/EPHB2/RasGAP -0.005 0.13 -10000 0 -0.26 26 26
ITSN1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.021 0.044 -10000 0 -0.27 9 9
Ephrin B1/EPHB1 0.02 0.056 -10000 0 -0.25 19 19
HRAS/GDP -0.027 0.095 -10000 0 -0.32 14 14
Ephrin B/EPHB1/GRB7 0.04 0.088 -10000 0 -0.25 26 26
Endophilin/SYNJ1 -0.039 0.1 0.21 1 -0.39 3 4
KRAS 0.026 0.007 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.04 0.085 -10000 0 -0.25 23 23
endothelial cell migration 0.036 0.036 -10000 0 -0.23 3 3
GRB2 0.028 0.004 -10000 0 -10000 0 0
GRB7 0.026 0.031 -10000 0 -0.45 2 2
PAK1 -0.034 0.12 0.32 5 -0.41 8 13
HRAS 0.026 0.021 -10000 0 -0.41 1 1
RRAS -0.039 0.1 0.2 3 -0.4 3 6
DNM1 -0.002 0.11 -10000 0 -0.39 34 34
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.019 0.094 0.35 5 -0.43 2 7
lamellipodium assembly -0.035 0.083 -10000 0 -0.4 5 5
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.01 0.065 -10000 0 -0.37 3 3
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
EPHB2 -0.064 0.17 -10000 0 -0.39 107 107
EPHB3 0.01 0.067 -10000 0 -0.45 10 10
EPHB1 0.005 0.088 -10000 0 -0.42 20 20
EPHB4 0.026 0.008 -10000 0 -10000 0 0
mol:GDP -0.034 0.091 0.29 1 -0.33 17 18
Ephrin B/EPHB2 -0.013 0.12 -10000 0 -0.21 127 127
Ephrin B/EPHB3 0.028 0.07 -10000 0 -0.23 26 26
JNK cascade 0.013 0.15 0.36 50 -0.41 1 51
Ephrin B/EPHB1 0.03 0.081 -10000 0 -0.25 25 25
RAP1/GDP -0.014 0.1 0.3 2 -0.35 6 8
EFNB2 0.025 0.031 -10000 0 -0.45 2 2
EFNB3 -0.001 0.11 -10000 0 -0.45 29 29
EFNB1 0.028 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.015 0.11 -10000 0 -0.22 104 104
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.11 -10000 0 -0.41 6 6
Rap1/GTP -0.027 0.092 -10000 0 -0.41 5 5
axon guidance -0.035 0.13 -10000 0 -0.25 120 120
MAPK3 0.004 0.061 0.19 4 -0.33 3 7
MAPK1 0.006 0.065 0.19 12 -0.34 3 15
Rac1/GDP -0.025 0.097 0.27 2 -0.32 12 14
actin cytoskeleton reorganization -0.042 0.079 -10000 0 -0.32 7 7
CDC42/GDP -0.022 0.099 0.26 5 -0.32 12 17
PI3K 0.04 0.039 -10000 0 -0.23 3 3
EFNA5 0.006 0.096 -10000 0 -0.45 21 21
Ephrin B2/EPHB4 0.033 0.023 -10000 0 -0.27 2 2
Ephrin B/EPHB2/Intersectin/N-WASP -0.019 0.085 -10000 0 -0.25 36 36
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.03 0.089 -10000 0 -0.4 5 5
PTK2 0.091 0.21 0.59 73 -10000 0 73
MAP4K4 0.013 0.15 0.36 50 -0.41 1 51
SRC 0.026 0.007 -10000 0 -10000 0 0
KALRN -0.008 0.12 -10000 0 -0.45 34 34
Intersectin/N-WASP 0.038 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis 0 0.13 0.31 35 -0.36 9 44
MAP2K1 0.006 0.062 -10000 0 -0.35 3 3
WASL 0.027 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.003 0.11 -10000 0 -0.27 10 10
cell migration 0.01 0.093 0.27 4 -0.38 4 8
NRAS 0.027 0.006 -10000 0 -10000 0 0
SYNJ1 -0.039 0.1 0.21 1 -0.4 3 4
PXN 0.028 0.003 -10000 0 -10000 0 0
TF -0.16 0.14 0.2 2 -0.4 81 83
HRAS/GTP -0.014 0.11 -10000 0 -0.42 5 5
Ephrin B1/EPHB1-2 -0.014 0.11 -10000 0 -0.22 104 104
cell adhesion mediated by integrin 0 0.067 0.23 17 -0.26 8 25
RAC1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP -0.012 0.11 -10000 0 -0.44 5 5
RAC1-CDC42/GTP -0.035 0.087 -10000 0 -0.4 5 5
RASA1 0.024 0.031 -10000 0 -0.45 2 2
RAC1-CDC42/GDP -0.016 0.1 0.27 3 -0.33 9 12
ruffle organization -0.012 0.13 0.37 15 -0.41 5 20
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 -0.016 0.13 -10000 0 -0.27 43 43
ROCK1 0.055 0.079 0.18 124 -0.24 4 128
RAS family/GDP -0.047 0.078 -10000 0 -0.32 7 7
Rac1/GTP -0.032 0.09 -10000 0 -0.42 5 5
Ephrin B/EPHB1/Src/Paxillin 0.008 0.067 -10000 0 -0.33 5 5
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.016 0.2 0.4 1 -0.84 21 22
NCK1/PAK1/Dok-R -0.025 0.08 -10000 0 -0.38 20 20
NCK1/Dok-R 0.007 0.22 -10000 0 -0.98 20 20
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.041 0.24 13 -10000 0 13
RELA 0.027 0.007 -10000 0 -10000 0 0
SHC1 0.028 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 -0.92 21 21
FN1 -0.16 0.21 -10000 0 -0.39 217 217
PLD2 -0.007 0.23 -10000 0 -1 21 21
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB14 -0.017 0.14 -10000 0 -0.44 45 45
ELK1 0.001 0.21 -10000 0 -0.93 21 21
GRB7 0.026 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 21 21
CDKN1A 0.03 0.16 0.44 1 -0.6 16 17
ITGA5 -0.1 0.19 -10000 0 -0.39 152 152
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.014 0.23 -10000 0 -1 21 21
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:NO 0.023 0.16 0.4 3 -0.62 21 24
PLG -0.012 0.23 -10000 0 -1 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.017 0.19 -10000 0 -0.8 21 21
GRB2 0.028 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
ANGPT2 0.015 0.16 0.36 2 -0.55 8 10
BMX -0.03 0.24 -10000 0 -1.1 21 21
ANGPT1 -0.006 0.2 -10000 0 -1.2 13 13
tube development 0.021 0.17 0.37 2 -0.63 20 22
ANGPT4 0.017 0.017 -10000 0 -10000 0 0
response to hypoxia -0.002 0.014 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.014 0.24 -10000 0 -1.1 21 21
alpha5/beta1 Integrin -0.057 0.15 -10000 0 -0.28 151 151
FGF2 0.012 0.082 -10000 0 -0.44 16 16
STAT5A (dimer) 0.031 0.2 -10000 0 -0.72 19 19
mol:L-citrulline 0.023 0.16 0.4 3 -0.62 21 24
AGTR1 -0.016 0.12 -10000 0 -0.44 36 36
MAPK14 -0.002 0.25 -10000 0 -1 24 24
Tie2/SHP2 -0.006 0.2 -10000 0 -1.1 13 13
TEK -0.001 0.21 -10000 0 -1.2 13 13
RPS6KB1 0.016 0.2 -10000 0 -0.81 21 21
Angiotensin II/AT1 -0.009 0.087 -10000 0 -0.32 36 36
Tie2/Ang1/GRB2 0.005 0.24 -10000 0 -1.1 21 21
MAPK3 -0.007 0.21 -10000 0 -0.95 21 21
MAPK1 -0.004 0.21 -10000 0 -0.95 21 21
Tie2/Ang1/GRB7 0.004 0.24 -10000 0 -1.1 20 20
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.007 0.23 -10000 0 -1.1 20 20
PI3K -0.007 0.22 -10000 0 -0.97 21 21
FES 0.002 0.24 -10000 0 -1 22 22
Crk/Dok-R 0.015 0.23 -10000 0 -1 21 21
Tie2/Ang1/ABIN2 0.005 0.24 -10000 0 -1.1 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.021 0.19 0.39 1 -0.75 21 22
STAT5A 0.028 0.003 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.041 0.21 0.4 7 -0.77 21 28
Tie2/Ang2 0.011 0.21 -10000 0 -0.84 20 20
Tie2/Ang1 -0.005 0.25 -10000 0 -1.1 21 21
FOXO1 0.023 0.19 0.39 1 -0.75 21 22
ELF1 0.027 0.045 -10000 0 -0.45 3 3
ELF2 -0.002 0.22 -10000 0 -1 20 20
mol:Choline -0.005 0.22 -10000 0 -0.98 21 21
cell migration -0.044 0.061 -10000 0 -0.22 23 23
FYN 0.014 0.19 0.39 1 -0.71 20 21
DOK2 0.022 0.04 -10000 0 -0.41 4 4
negative regulation of cell cycle 0.032 0.15 0.4 2 -0.54 16 18
ETS1 0.022 0.056 -10000 0 -0.28 15 15
PXN 0.045 0.18 0.37 11 -0.64 21 32
ITGB1 0.027 0.005 -10000 0 -10000 0 0
NOS3 0.021 0.18 0.41 3 -0.71 21 24
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 -0.98 21 21
RASA1 0.024 0.031 -10000 0 -0.45 2 2
Tie2/Ang1/Shc 0.005 0.24 -10000 0 -1.1 21 21
NCK1 0.023 0.011 -10000 0 -10000 0 0
vasculogenesis 0.025 0.15 0.39 3 -0.56 21 24
mol:Phosphatidic acid -0.005 0.22 -10000 0 -0.98 21 21
mol:Angiotensin II 0 0.004 -10000 0 -10000 0 0
mol:NADP 0.023 0.16 0.4 3 -0.62 21 24
Rac1/GTP 0.019 0.18 -10000 0 -0.75 21 21
MMP2 -0.03 0.23 -10000 0 -1 21 21
Caspase cascade in apoptosis

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
TOP1 -0.021 0.13 0.26 3 -0.46 14 17
ACTA1 -0.093 0.12 0.21 2 -0.32 72 74
NUMA1 -0.029 0.14 0.25 3 -0.47 18 21
SPTAN1 -0.033 0.12 0.3 5 -0.31 42 47
LIMK1 -0.032 0.12 0.27 5 -0.31 43 48
BIRC3 0.012 0.071 -10000 0 -0.4 14 14
BIRC2 0.024 0.01 -10000 0 -10000 0 0
BAX 0.027 0.005 -10000 0 -10000 0 0
CASP10 -0.06 0.12 -10000 0 -0.31 87 87
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
PTK2 -0.017 0.1 0.24 3 -0.34 12 15
DIABLO 0.028 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.032 0.12 0.3 5 -0.31 42 47
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.028 0.002 -10000 0 -10000 0 0
GSN -0.033 0.12 0.27 4 -0.31 42 46
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.01 0.2 -10000 0 -0.82 23 23
BID -0.021 0.063 -10000 0 -0.2 39 39
MAP3K1 -0.02 0.1 -10000 0 -0.43 24 24
TRADD 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 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 0.027 0.006 -10000 0 -10000 0 0
DNA repair 0.004 0.051 0.2 2 -0.19 2 4
neuron apoptosis 0.003 0.12 -10000 0 -0.65 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.036 0.14 0.28 4 -0.36 39 43
APAF1 0.028 0.002 -10000 0 -10000 0 0
CASP6 -0.008 0.15 -10000 0 -0.91 11 11
TRAF2 0.022 0.046 -10000 0 -0.39 6 6
ICAD/CAD -0.035 0.11 0.28 6 -0.31 39 45
CASP7 -0.008 0.085 0.28 5 -0.36 4 9
KRT18 0.006 0.076 -10000 0 -0.49 9 9
apoptosis -0.031 0.12 0.26 3 -0.41 12 15
DFFA -0.036 0.11 0.26 4 -0.32 39 43
DFFB -0.036 0.12 0.27 5 -0.31 43 48
PARP1 -0.004 0.052 0.19 2 -0.2 2 4
actin filament polymerization 0.025 0.12 0.3 37 -0.34 14 51
TNF 0.008 0.088 -10000 0 -0.4 22 22
CYCS -0.005 0.066 0.21 3 -0.27 4 7
SATB1 -0.017 0.14 -10000 0 -0.84 11 11
SLK -0.036 0.11 0.27 3 -0.31 43 46
p15 BID/BAX 0.001 0.074 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 24 -10000 0 24
CASP3 -0.037 0.12 0.27 4 -0.32 44 48
LMNB2 0.011 0.12 0.24 3 -0.51 15 18
RIPK1 0.027 0.006 -10000 0 -10000 0 0
CASP4 0.024 0.023 -10000 0 -0.45 1 1
Mammalian IAPs/DIABLO 0.054 0.05 -10000 0 -0.21 10 10
negative regulation of DNA binding -0.008 0.19 -10000 0 -0.8 23 23
stress fiber formation -0.036 0.11 0.27 3 -0.31 43 46
GZMB -0.054 0.15 -10000 0 -0.36 88 88
CASP1 0.013 0.032 -10000 0 -0.68 1 1
LMNB1 0.002 0.13 0.25 2 -0.61 14 16
APP 0.003 0.13 -10000 0 -0.66 15 15
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.002 -10000 0 -10000 0 0
VIM -0.028 0.12 0.26 3 -0.42 13 16
LMNA 0.02 0.09 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 -0.035 0.11 0.27 3 -0.32 38 41
APAF-1/Caspase 9 -0.005 0.11 -10000 0 -0.62 14 14
nuclear fragmentation during apoptosis -0.028 0.13 0.25 3 -0.46 18 21
CFL2 -0.025 0.12 0.34 14 -0.3 37 51
GAS2 -0.063 0.13 0.26 4 -0.33 59 63
positive regulation of apoptosis 0.014 0.12 0.24 3 -0.53 14 17
PRF1 -0.006 0.12 -10000 0 -0.4 39 39
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.004 0.081 -10000 0 -10000 0 0
epithelial cell differentiation -0.029 0.1 -10000 0 -0.38 3 3
ITCH 0.038 0.02 -10000 0 -10000 0 0
WWP1 -0.003 0.077 -10000 0 -10000 0 0
FYN 0.027 0.019 -10000 0 -0.39 1 1
EGFR 0.02 0.048 -10000 0 -0.45 5 5
PRL -0.007 0.045 -10000 0 -0.4 5 5
neuron projection morphogenesis -0.02 0.095 0.25 7 -10000 0 7
PTPRZ1 0.008 0.092 -10000 0 -0.45 19 19
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.004 0.11 -10000 0 -0.33 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.036 0.097 -10000 0 -0.3 20 20
ADAM17 0.039 0.036 -10000 0 -0.44 2 2
ErbB4/ErbB4 -0.013 0.08 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.014 0.093 -10000 0 -0.37 6 6
NCOR1 0.027 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.024 0.1 -10000 0 -0.29 19 19
GRIN2B -0.029 0.099 0.26 4 -0.35 3 7
ErbB4/ErbB2/betacellulin -0.068 0.13 -10000 0 -0.31 37 37
STAT1 0.009 0.085 -10000 0 -0.39 21 21
HBEGF 0.026 0.02 -10000 0 -0.39 1 1
PRLR -0.067 0.19 -10000 0 -0.45 94 94
E4ICDs/ETO2 -0.004 0.081 -10000 0 -10000 0 0
axon guidance -0.006 0.073 0.38 1 -10000 0 1
NEDD4 0.04 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.038 0.14 -10000 0 -0.33 94 94
CBFA2T3 0.026 0.022 -10000 0 -0.45 1 1
ErbB4/ErbB2/HBEGF 0.009 0.066 -10000 0 -10000 0 0
MAPK3 -0.017 0.099 0.25 7 -0.32 2 9
STAT1 (dimer) -0.013 0.095 -10000 0 -0.34 8 8
MAPK1 -0.016 0.1 0.28 5 -10000 0 5
JAK2 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.03 0.096 -10000 0 -0.29 19 19
NRG1 -0.026 0.11 -10000 0 -0.28 75 75
NRG3 -0.004 0.073 -10000 0 -0.44 12 12
NRG2 -0.23 0.23 -10000 0 -0.45 266 266
NRG4 -0.006 0.12 -10000 0 -0.45 33 33
heart development -0.006 0.073 0.38 1 -10000 0 1
neural crest cell migration -0.03 0.095 -10000 0 -0.29 19 19
ERBB2 0.022 0.028 0.23 2 -0.3 2 4
WWOX/E4ICDs -0.003 0.079 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.012 0.1 -10000 0 -0.34 17 17
apoptosis 0.035 0.12 0.5 14 -10000 0 14
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.14 0.16 -10000 0 -0.36 86 86
ErbB4/ErbB2/epiregulin -0.049 0.12 -10000 0 -0.31 34 34
ErbB4/ErbB4/betacellulin/betacellulin -0.084 0.14 -10000 0 -0.36 47 47
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.027 0.13 -10000 0 -0.34 21 21
MDM2 -0.01 0.078 0.27 9 -10000 0 9
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.021 0.089 -10000 0 -0.32 2 2
STAT5A -0.005 0.071 0.34 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta -0.026 0.098 -10000 0 -0.29 18 18
DLG4 0.026 0.022 -10000 0 -0.45 1 1
GRB2/SHC 0.04 0.008 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.005 0.075 -10000 0 -10000 0 0
STAT5A (dimer) -0.026 0.12 -10000 0 -0.41 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.082 0.33 1 -10000 0 1
LRIG1 0.016 0.064 -10000 0 -0.45 9 9
EREG -0.092 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 0.028 0.003 -10000 0 -10000 0 0
YAP1 -0.013 0.1 -10000 0 -0.43 26 26
GRB2 0.028 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.006 0.092 -10000 0 -0.32 12 12
glial cell differentiation 0.005 0.074 -10000 0 -10000 0 0
WWOX 0.025 0.008 -10000 0 -10000 0 0
cell proliferation -0.096 0.16 0.29 3 -0.42 42 45
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.016 0.068 -10000 0 -0.26 27 27
EFNA5 0.006 0.096 -10000 0 -0.45 21 21
FYN -0.008 0.061 0.18 4 -0.25 26 30
neuron projection morphogenesis 0.016 0.068 -10000 0 -0.26 27 27
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.016 0.068 -10000 0 -0.26 27 27
EPHA5 0.002 0.049 -10000 0 -0.39 6 6
Glucocorticoid receptor regulatory network

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
PCK2 0.051 0.063 -10000 0 -10000 0 0
SMARCC2 0.028 0.009 -10000 0 -10000 0 0
SMARCC1 0.025 0.013 -10000 0 -10000 0 0
TBX21 -0.085 0.16 -10000 0 -0.59 30 30
SUMO2 0.027 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.085 -10000 0 -0.39 21 21
FKBP4 0.026 0.008 -10000 0 -10000 0 0
FKBP5 0.024 0.036 -10000 0 -0.43 3 3
GR alpha/HSP90/FKBP51/HSP90 0.087 0.079 0.3 17 -0.25 1 18
PRL -0.077 0.13 -10000 0 -0.58 5 5
cortisol/GR alpha (dimer)/TIF2 0.12 0.18 0.53 39 -10000 0 39
RELA -0.01 0.088 -10000 0 -0.25 11 11
FGG 0.079 0.17 0.45 24 -0.37 14 38
GR beta/TIF2 0.057 0.11 0.3 20 -0.27 18 38
IFNG -0.2 0.2 -10000 0 -0.57 71 71
apoptosis 0.018 0.15 0.49 9 -0.54 11 20
CREB1 0.029 0.015 -10000 0 -10000 0 0
histone acetylation -0.009 0.1 0.28 10 -0.41 8 18
BGLAP -0.043 0.093 -10000 0 -0.48 5 5
GR/PKAc 0.1 0.076 0.34 9 -0.28 1 10
NF kappa B1 p50/RelA -0.02 0.15 -10000 0 -0.4 26 26
SMARCD1 0.029 0.009 -10000 0 -10000 0 0
MDM2 0.054 0.065 0.23 29 -10000 0 29
GATA3 0.013 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 -0.51 17 17
GSK3B 0.024 0.013 -10000 0 -10000 0 0
NR1I3 0.024 0.15 0.46 10 -0.58 6 16
CSN2 0.076 0.12 0.39 18 -10000 0 18
BRG1/BAF155/BAF170/BAF60A 0.065 0.038 -10000 0 -0.4 1 1
NFATC1 0.025 0.01 -10000 0 -10000 0 0
POU2F1 0.028 0.014 -10000 0 -10000 0 0
CDKN1A 0.017 0.057 0.68 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.006 -10000 0 -10000 0 0
SFN 0.023 0.045 -10000 0 -0.42 5 5
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.095 0.081 0.31 16 -10000 0 16
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.21 0.45 8 -0.79 24 32
JUN -0.15 0.13 -10000 0 -0.47 34 34
IL4 -0.051 0.087 -10000 0 -0.47 4 4
CDK5R1 0.026 0.027 -10000 0 -0.39 2 2
PRKACA 0.028 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.099 0.2 0.18 5 -0.4 91 96
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.08 0.31 17 -10000 0 17
cortisol/GR alpha (monomer) 0.17 0.21 0.61 50 -10000 0 50
NCOA2 -0.005 0.12 -10000 0 -0.45 31 31
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.11 0.15 -10000 0 -0.49 60 60
AP-1/NFAT1-c-4 -0.25 0.18 -10000 0 -0.57 74 74
AFP -0.11 0.12 -10000 0 -0.59 9 9
SUV420H1 0.026 0.008 -10000 0 -10000 0 0
IRF1 0.084 0.11 0.41 15 -10000 0 15
TP53 0.038 0.044 -10000 0 -0.44 4 4
PPP5C 0.027 0.005 -10000 0 -10000 0 0
KRT17 -0.22 0.23 -10000 0 -0.62 73 73
KRT14 -0.16 0.31 -10000 0 -1.2 37 37
TBP 0.033 0.017 -10000 0 -10000 0 0
CREBBP 0.066 0.074 0.32 26 -0.34 1 27
HDAC1 0.027 0.007 -10000 0 -10000 0 0
HDAC2 0.043 0.017 -10000 0 -10000 0 0
AP-1 -0.25 0.19 -10000 0 -0.57 74 74
MAPK14 0.026 0.011 -10000 0 -10000 0 0
MAPK10 0 0.11 -10000 0 -0.44 27 27
MAPK11 0.026 0.011 -10000 0 -10000 0 0
KRT5 -0.17 0.2 -10000 0 -0.76 26 26
interleukin-1 receptor activity 0.015 0.016 -10000 0 -10000 0 0
NCOA1 0.03 0.004 -10000 0 -10000 0 0
STAT1 0.015 0.085 -10000 0 -0.39 21 21
CGA -0.049 0.092 -10000 0 -0.49 6 6
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.14 0.38 62 -0.33 1 63
MAPK3 0.027 0.011 -10000 0 -10000 0 0
MAPK1 0.026 0.011 -10000 0 -10000 0 0
ICAM1 -0.091 0.17 -10000 0 -0.54 26 26
NFKB1 -0.012 0.093 -10000 0 -0.27 14 14
MAPK8 -0.12 0.12 -10000 0 -0.44 33 33
MAPK9 0.026 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.018 0.16 0.5 9 -0.57 11 20
BAX 0.015 0.051 -10000 0 -10000 0 0
POMC -0.11 0.25 -10000 0 -1.1 18 18
EP300 0.064 0.077 0.32 25 -0.37 3 28
cortisol/GR alpha (dimer)/p53 0.16 0.18 0.55 45 -0.38 1 46
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.054 0.24 10 -10000 0 10
SGK1 0.07 0.12 0.54 2 -1.1 2 4
IL13 -0.14 0.15 -10000 0 -0.66 15 15
IL6 -0.13 0.28 -10000 0 -0.9 47 47
PRKACG -0.008 0.019 -10000 0 -10000 0 0
IL5 -0.12 0.13 -10000 0 -0.6 9 9
IL2 -0.17 0.16 -10000 0 -0.64 18 18
CDK5 0.027 0.008 -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 29 29
CDK5R1/CDK5 0.038 0.024 -10000 0 -0.28 2 2
NF kappa B1 p50/RelA/PKAc 0.01 0.13 -10000 0 -0.35 9 9
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.17 0.51 46 -10000 0 46
SMARCA4 0.028 0.01 -10000 0 -10000 0 0
chromatin remodeling 0.089 0.1 0.36 23 -0.48 1 24
NF kappa B1 p50/RelA/Cbp 0.055 0.15 0.39 11 -0.37 10 21
JUN (dimer) -0.15 0.13 -10000 0 -0.47 34 34
YWHAH 0.027 0.004 -10000 0 -10000 0 0
VIPR1 -0.075 0.16 -10000 0 -0.73 20 20
NR3C1 0.1 0.13 0.41 37 -10000 0 37
NR4A1 -0.003 0.11 -10000 0 -0.47 19 19
TIF2/SUV420H1 0.014 0.082 -10000 0 -0.32 27 27
MAPKKK cascade 0.018 0.15 0.49 9 -0.54 11 20
cortisol/GR alpha (dimer)/Src-1 0.17 0.18 0.54 49 -10000 0 49
PBX1 -0.058 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 -0.91 75 75
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.089 0.1 0.36 23 -0.49 1 24
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.17 0.51 46 -10000 0 46
mol:cortisol 0.084 0.12 0.36 47 -10000 0 47
MMP1 -0.34 0.17 -10000 0 -0.7 45 45
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.093 0.2 -10000 0 -0.44 123 123
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.027 -10000 0 -0.39 2 2
TCEB1 0.025 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.022 0.067 0.25 2 -0.28 14 16
HIF1A 0.004 0.046 -10000 0 -0.26 12 12
COPS5 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.063 0.037 -10000 0 -10000 0 0
FIH (dimer) 0.027 0.005 -10000 0 -10000 0 0
CDKN2A -0.14 0.2 -10000 0 -0.4 183 183
ARNT/IPAS -0.048 0.15 -10000 0 -0.32 119 119
HIF1AN 0.027 0.005 -10000 0 -10000 0 0
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
HIF1A/ARNT 0.022 0.062 0.25 1 -0.27 14 15
CUL2 0.027 0.005 -10000 0 -10000 0 0
OS9 0.028 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.047 0.022 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.02 0.057 -10000 0 -0.27 14 14
PHD1-3/OS9 0.05 0.064 -10000 0 -0.22 22 22
HIF1A/RACK1/Elongin B/Elongin C 0.037 0.061 -10000 0 -0.28 7 7
VHL 0.025 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.019 0.059 -10000 0 -0.27 13 13
EGLN3 0.004 0.097 -10000 0 -0.4 26 26
EGLN2 0.027 0.005 -10000 0 -10000 0 0
EGLN1 0.027 0.004 -10000 0 -10000 0 0
TP53 0.023 0.043 -10000 0 -0.45 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.016 0.17 -10000 0 -0.5 51 51
ARNT 0.027 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p19ARF -0.058 0.11 -10000 0 -0.29 30 30
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.016 0.1 -9999 0 -0.46 13 13
FZD6 0.023 0.023 -9999 0 -0.45 1 1
WNT6 -0.009 0.12 -9999 0 -0.4 41 41
WNT4 0.014 0.077 -9999 0 -0.43 14 14
FZD3 0.019 0.057 -9999 0 -0.45 7 7
WNT5A 0.019 0.052 -9999 0 -0.44 6 6
WNT11 -0.018 0.13 -9999 0 -0.41 49 49
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 0.027 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 0.06 0.28 22 -10000 0 22
CDKN1A -0.006 0.011 -10000 0 -10000 0 0
KAT2B 0.009 0.084 -10000 0 -0.45 16 16
BAX 0.027 0.005 -10000 0 -10000 0 0
FOXO3 -0.004 0.024 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 -0.39 5 5
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.053 0.12 -10000 0 -0.33 80 80
PPARGC1A -0.13 0.22 -10000 0 -0.45 162 162
FHL2 0.027 0.022 -10000 0 -0.45 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 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 0.023 0.022 -10000 0 -0.45 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.021 -10000 0 -0.27 1 1
SIRT1/Histone H1b 0.018 0.049 -10000 0 -0.25 5 5
apoptosis -0.05 0.02 0.27 1 -10000 0 1
SIRT1/PGC1A -0.07 0.14 -10000 0 -0.27 161 161
p53/SIRT1 0.026 0.036 -10000 0 -0.32 5 5
SIRT1/FOXO4 0.025 0.038 -10000 0 -0.25 5 5
FOXO1/FHL2/SIRT1 0.046 0.024 -10000 0 -0.25 2 2
HIST1H1E 0.009 0.038 -10000 0 -0.29 4 4
SIRT1/p300 0.035 0.028 -10000 0 -0.31 3 3
muscle cell differentiation 0.024 0.12 0.28 85 -10000 0 85
TP53 0.019 0.043 -10000 0 -0.45 4 4
KU70/SIRT1/BAX 0.05 0.02 -10000 0 -0.27 1 1
CREBBP 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.027 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.036 -10000 0 -0.29 6 6
ACSS2 0.011 0.016 -10000 0 -0.32 1 1
SIRT1/PCAF/MYOD -0.024 0.12 -10000 0 -0.28 85 85
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.052 0.17 -10000 0 -0.59 19 19
MKNK1 0.028 0.003 -10000 0 -10000 0 0
MAPK14 -0.016 0.096 -10000 0 -0.3 21 21
ATF2/c-Jun -0.011 0.071 -10000 0 -0.46 1 1
MAPK11 -0.017 0.097 -10000 0 -0.3 21 21
MITF -0.03 0.11 -10000 0 -0.36 27 27
MAPKAPK5 -0.022 0.1 -10000 0 -0.37 15 15
KRT8 -0.07 0.15 -10000 0 -0.4 45 45
MAPKAPK3 0.024 0.009 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.026 0.14 -10000 0 -0.42 23 23
CEBPB -0.023 0.1 -10000 0 -0.37 17 17
SLC9A1 -0.023 0.1 -10000 0 -0.37 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.02 0.1 -10000 0 -0.35 14 14
p38alpha-beta/MNK1 -0.003 0.12 -10000 0 -0.35 20 20
JUN -0.007 0.073 -10000 0 -0.46 1 1
PPARGC1A -0.12 0.19 -10000 0 -0.48 71 71
USF1 -0.021 0.1 -10000 0 -0.37 15 15
RAB5/GDP/GDI1 -0.006 0.074 -10000 0 -0.28 14 14
NOS2 -0.064 0.2 -10000 0 -0.71 26 26
DDIT3 -0.025 0.1 -10000 0 -0.37 18 18
RAB5A 0.025 0.009 -10000 0 -10000 0 0
HSPB1 -0.016 0.092 0.29 11 -0.31 15 26
p38alpha-beta/HBP1 -0.003 0.12 -10000 0 -0.35 20 20
CREB1 -0.02 0.1 -10000 0 -0.37 16 16
RAB5/GDP 0.018 0.007 -10000 0 -10000 0 0
EIF4E -0.017 0.093 0.24 1 -0.34 13 14
RPS6KA4 -0.023 0.1 -10000 0 -0.36 16 16
PLA2G4A -0.033 0.11 -10000 0 -0.34 18 18
GDI1 -0.02 0.098 -10000 0 -0.37 14 14
TP53 -0.037 0.12 -10000 0 -0.42 23 23
RPS6KA5 -0.025 0.1 -10000 0 -0.36 15 15
ESR1 -0.036 0.12 -10000 0 -0.37 30 30
HBP1 0.026 0.007 -10000 0 -10000 0 0
MEF2C -0.028 0.11 -10000 0 -0.38 17 17
MEF2A -0.022 0.1 -10000 0 -0.37 15 15
EIF4EBP1 -0.02 0.1 -10000 0 -0.41 15 15
KRT19 -0.13 0.17 -10000 0 -0.48 45 45
ELK4 -0.021 0.1 -10000 0 -0.37 15 15
ATF6 -0.021 0.1 -10000 0 -0.37 15 15
ATF1 -0.021 0.1 -10000 0 -0.39 15 15
p38alpha-beta/MAPKAPK2 -0.002 0.12 -10000 0 -0.34 21 21
p38alpha-beta/MAPKAPK3 -0.005 0.11 -10000 0 -0.35 20 20
IL27-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
TGFB1 0.027 0.035 -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 0.49 19 -10000 0 19
IL27/IL27R/JAK1 -0.034 0.15 -10000 0 -0.52 13 13
TBX21 -0.084 0.17 -10000 0 -0.54 28 28
IL12B -0.016 0.12 -10000 0 -0.4 43 43
IL12A -0.006 0.053 -10000 0 -0.31 14 14
IL6ST -0.037 0.15 -10000 0 -0.46 57 57
IL27RA/JAK1 -0.002 0.065 -10000 0 -10000 0 0
IL27 -0.006 0.091 -10000 0 -0.41 23 23
TYK2 0.017 0.029 -10000 0 -0.41 1 1
T-helper cell lineage commitment 0.004 0.11 0.43 2 -10000 0 2
T-helper 2 cell differentiation 0.053 0.14 0.49 19 -10000 0 19
T cell proliferation during immune response 0.053 0.14 0.49 19 -10000 0 19
MAPKKK cascade -0.053 0.14 -10000 0 -0.49 19 19
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT2 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.008 0.086 -10000 0 -0.4 21 21
IL12RB1 -0.011 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 -0.52 41 41
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 -0.49 19 19
STAT1 (dimer) -0.072 0.21 0.52 1 -0.62 22 23
JAK2 0.016 0.02 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.043 0.14 -10000 0 -0.48 18 18
T cell proliferation -0.066 0.14 -10000 0 -0.49 26 26
IL12/IL12R/TYK2/JAK2 -0.052 0.19 -10000 0 -0.75 26 26
IL17A 0.004 0.11 0.43 2 -10000 0 2
mast cell activation 0.053 0.14 0.49 19 -10000 0 19
IFNG -0.012 0.038 -10000 0 -0.096 18 18
T cell differentiation -0.005 0.007 -10000 0 -0.019 72 72
STAT3 (dimer) -0.043 0.14 -10000 0 -0.48 18 18
STAT5A (dimer) -0.043 0.14 -10000 0 -0.48 18 18
STAT4 (dimer) -0.045 0.14 -10000 0 -0.49 21 21
STAT4 0.018 0.063 -10000 0 -0.4 11 11
T cell activation -0.005 0.011 0.05 16 -10000 0 16
IL27R/JAK2/TYK2 -0.018 0.12 -10000 0 -0.53 3 3
GATA3 -0.003 0.13 0.59 5 -1.3 3 8
IL18 -0.002 0.05 -10000 0 -0.32 12 12
positive regulation of mast cell cytokine production -0.042 0.14 -10000 0 -0.47 18 18
IL27/EBI3 0.004 0.087 -10000 0 -0.3 33 33
IL27RA -0.01 0.066 -10000 0 -10000 0 0
IL6 -0.011 0.13 -10000 0 -0.44 42 42
STAT5A 0.028 0.003 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.002 0.045 -10000 0 -10000 0 0
IL1B -0.024 0.088 -10000 0 -0.28 53 53
EBI3 0.011 0.067 -10000 0 -0.42 11 11
TNF -0.006 0.059 -10000 0 -0.28 22 22
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.005 0.039 -10000 0 -0.44 2 2
HSPA8 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.054 0.1 0.23 2 -0.28 15 17
AKT1 0.006 0.046 -10000 0 -10000 0 0
GSC 0.006 0.14 0.4 1 -0.93 4 5
NKX2-5 -0.075 0.18 -10000 0 -0.41 112 112
muscle cell differentiation 0.062 0.16 0.44 48 -10000 0 48
SMAD2-3/SMAD4/SP1 -0.003 0.12 -10000 0 -0.31 3 3
SMAD4 0.01 0.047 -10000 0 -10000 0 0
CBFB 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.016 0.053 -10000 0 -0.24 9 9
SMAD3/SMAD4/VDR 0.058 0.058 -10000 0 -10000 0 0
MYC 0.028 0.023 -10000 0 -10000 0 0
CDKN2B -0.36 0.64 -10000 0 -1.4 120 120
AP1 0.008 0.092 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.035 0.082 -10000 0 -0.43 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.067 0.16 -10000 0 -0.36 99 99
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 -0.39 48 48
SMAD3/SMAD4/GR 0.063 0.065 -10000 0 -10000 0 0
GATA3 0.011 0.084 -10000 0 -0.4 19 19
SKI/SIN3/HDAC complex/NCoR1 0.029 0.058 -10000 0 -0.47 4 4
MEF2C/TIF2 -0.051 0.15 0.35 2 -0.48 25 27
endothelial cell migration 0.16 0.17 0.66 3 -10000 0 3
MAX 0.038 0.016 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
RBBP4 0.027 0.022 -10000 0 -0.45 1 1
RUNX2 0.025 0.029 -10000 0 -0.42 2 2
RUNX3 0.022 0.046 -10000 0 -0.39 6 6
RUNX1 0.027 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.007 -10000 0 -10000 0 0
NR3C1 0.039 0.015 -10000 0 -10000 0 0
VDR 0.026 0.03 -10000 0 -0.45 2 2
CDKN1A -0.011 0.1 -10000 0 -0.62 5 5
KAT2B 0.007 0.084 -10000 0 -0.45 16 16
SMAD2/SMAD2/SMAD4/FOXH1 -0.001 0.1 -10000 0 -0.3 19 19
DCP1A 0.024 0.009 -10000 0 -10000 0 0
SKI 0.028 0.006 -10000 0 -10000 0 0
SERPINE1 -0.16 0.17 -10000 0 -0.75 2 2
SMAD3/SMAD4/ATF2 0.036 0.061 -10000 0 -0.25 1 1
SMAD3/SMAD4/ATF3 0.033 0.073 -10000 0 -0.3 7 7
SAP30 0.027 0.02 -10000 0 -0.39 1 1
Cbp/p300/PIAS3 0.014 0.048 -10000 0 -0.25 2 2
JUN 0.001 0.089 0.29 1 -10000 0 1
SMAD3/SMAD4/IRF7 0.027 0.084 -10000 0 -0.32 7 7
TFE3 -0.002 0.03 -10000 0 -10000 0 0
COL1A2 -0.095 0.17 -10000 0 -0.32 161 161
mesenchymal cell differentiation -0.035 0.063 0.3 2 -10000 0 2
DLX1 -0.14 0.21 -10000 0 -0.39 198 198
TCF3 0.027 0.005 -10000 0 -10000 0 0
FOS -0.029 0.16 -10000 0 -0.45 60 60
SMAD3/SMAD4/Max 0.061 0.066 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.046 0.025 -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 0.036 0.06 -10000 0 -10000 0 0
IRF7 0.012 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 -0.39 46 46
MEF2C -0.039 0.15 0.41 3 -0.44 20 23
SMAD2-3/SMAD4 0.03 0.079 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.039 0.03 -10000 0 -0.26 2 2
IGHV3OR16-13 0.006 0.048 -10000 0 -0.34 9 9
TGIF2/HDAC complex 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.009 0.023 -10000 0 -10000 0 0
SKIL 0.02 0.013 -10000 0 -10000 0 0
HDAC1 0.028 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.005 -10000 0 -10000 0 0
SNIP1 0.029 0.004 -10000 0 -10000 0 0
GCN5L2 -0.005 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.06 -10000 0 -10000 0 0
MSG1/HSC70 0.035 0.043 -10000 0 -0.28 8 8
SMAD2 0.008 0.043 -10000 0 -10000 0 0
SMAD3 0.013 0.046 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.018 0.041 -10000 0 -0.32 2 2
SMAD2/SMAD2/SMAD4 -0.049 0.12 0.2 4 -0.4 45 49
NCOR1 0.028 0.006 -10000 0 -10000 0 0
NCOA2 -0.005 0.12 -10000 0 -0.45 31 31
NCOA1 0.028 0.003 -10000 0 -10000 0 0
MYOD/E2A -0.018 0.13 -10000 0 -0.32 75 75
SMAD2-3/SMAD4/SP1/MIZ-1 0.012 0.12 -10000 0 -0.33 3 3
IFNB1 -0.004 0.079 0.23 1 -0.39 10 11
SMAD3/SMAD4/MEF2C -0.028 0.16 0.41 1 -0.46 16 17
CITED1 0.02 0.054 -10000 0 -0.39 8 8
SMAD2-3/SMAD4/ARC105 0.041 0.079 -10000 0 -10000 0 0
RBL1 0.025 0.022 -10000 0 -0.45 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.086 0.23 -10000 0 -0.53 102 102
RUNX1-3/PEBPB2 0.048 0.035 -10000 0 -0.23 6 6
SMAD7 -0.013 0.1 -10000 0 -10000 0 0
MYC/MIZ-1 0.041 0.038 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.066 0.11 0.28 4 -0.41 7 11
IL10 0.003 0.077 -10000 0 -0.36 8 8
PIASy/HDAC complex 0.031 0.013 -10000 0 -10000 0 0
PIAS3 0.024 0.007 -10000 0 -10000 0 0
CDK2 0.016 0.018 -10000 0 -10000 0 0
IL5 -0.002 0.069 -10000 0 -0.38 3 3
CDK4 0.01 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 -0.064 0.16 -10000 0 -0.41 79 79
FOXO3 -0.007 0.049 -10000 0 -10000 0 0
FOXO1 -0.007 0.048 -10000 0 -10000 0 0
FOXO4 -0.008 0.051 -10000 0 -0.32 1 1
heart looping -0.038 0.15 0.41 3 -0.44 20 23
CEBPB 0.012 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.076 0.15 -10000 0 -0.28 72 72
MYOD1 -0.065 0.16 -10000 0 -0.45 75 75
SMAD3/SMAD4/HNF4 0.007 0.099 -10000 0 -0.26 28 28
SMAD3/SMAD4/GATA3 0.03 0.085 -10000 0 -0.29 7 7
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.068 -10000 0 -0.28 1 1
SMAD3/SMAD4/SP1-3 0.008 0.097 -10000 0 -10000 0 0
MED15 0.026 0.02 -10000 0 -0.39 1 1
SP1 -0.017 0.061 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.04 0.14 -10000 0 -0.37 23 23
ITGB5 -0.01 0.073 0.35 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP 0.034 0.039 -10000 0 -0.32 1 1
SMAD3/SMAD4/AR -0.046 0.15 -10000 0 -0.28 123 123
AR -0.1 0.21 -10000 0 -0.45 131 131
negative regulation of cell growth 0.01 0.066 -10000 0 -0.26 1 1
SMAD3/SMAD4/MYOD -0.015 0.13 -10000 0 -0.29 70 70
E2F5 0.022 0.038 -10000 0 -0.45 3 3
E2F4 0.027 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.095 -10000 0 -0.32 4 4
SMAD2-3/SMAD4/FOXO1-3a-4 -0.043 0.16 -10000 0 -0.36 94 94
TFDP1 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.024 0.1 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.036 0.064 -10000 0 -0.3 2 2
TGIF2 0.026 0.007 -10000 0 -10000 0 0
TGIF1 0.025 0.009 -10000 0 -10000 0 0
ATF2 0.026 0.022 -10000 0 -0.45 1 1
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.029 0.15 -10000 0 -0.45 56 56
GNB1/GNG2 0 0.12 -10000 0 -0.46 11 11
mol:DAG -0.014 0.1 0.2 3 -0.42 11 14
PLCG1 -0.015 0.1 0.2 3 -0.43 11 14
YES1 -0.018 0.094 -10000 0 -0.47 10 10
FZD3 0.019 0.057 -10000 0 -0.45 7 7
FZD6 0.023 0.023 -10000 0 -0.45 1 1
G protein 0.003 0.12 0.26 4 -0.47 9 13
MAP3K7 -0.05 0.12 0.29 5 -0.38 23 28
mol:Ca2+ -0.013 0.097 0.19 3 -0.4 11 14
mol:IP3 -0.014 0.1 0.2 3 -0.42 11 14
NLK 0.007 0.063 -10000 0 -0.79 3 3
GNB1 0.027 0.006 -10000 0 -10000 0 0
CAMK2A -0.05 0.13 0.3 5 -0.4 26 31
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.1 -10000 0 -0.46 13 13
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
GNAS -0.02 0.097 -10000 0 -0.46 11 11
GO:0007205 -0.016 0.1 0.25 8 -0.46 9 17
WNT6 -0.009 0.12 -10000 0 -0.4 41 41
WNT4 0.014 0.077 -10000 0 -0.43 14 14
NFAT1/CK1 alpha -0.013 0.14 0.28 5 -0.44 16 21
GNG2 0.025 0.02 -10000 0 -0.39 1 1
WNT5A 0.019 0.052 -10000 0 -0.44 6 6
WNT11 -0.018 0.13 -10000 0 -0.41 49 49
CDC42 -0.008 0.1 0.19 21 -0.49 8 29
Ceramide 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
SPHK2 0.012 0.019 -10000 0 -0.28 2 2
MAP4K4 0.018 0.065 0.21 2 -0.37 6 8
BAG4 0.024 0.023 -10000 0 -0.45 1 1
PKC zeta/ceramide -0.008 0.069 -10000 0 -0.22 34 34
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.012 0.071 -10000 0 -0.4 14 14
BAX -0.004 0.055 -10000 0 -0.34 10 10
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.023 0.13 0.69 18 -10000 0 18
BAD -0.018 0.069 0.2 10 -0.21 33 43
SMPD1 0.02 0.066 0.18 24 -0.23 8 32
RB1 -0.022 0.062 0.2 1 -0.21 34 35
FADD/Caspase 8 0.056 0.1 0.23 65 -0.36 5 70
MAP2K4 -0.021 0.059 0.18 4 -0.27 10 14
NSMAF 0.025 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.02 0.061 0.18 6 -0.22 20 26
EGF -0.059 0.18 -10000 0 -0.45 88 88
mol:ceramide -0.023 0.066 -10000 0 -0.22 34 34
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 0.012 0.019 -10000 0 -0.28 2 2
ASAH1 0.026 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.022 0.062 0.19 1 -0.21 34 35
cell proliferation -0.029 0.097 -10000 0 -0.27 21 21
BID 0.014 0.11 -10000 0 -0.66 7 7
MAP3K1 -0.022 0.062 0.19 2 -0.22 30 32
EIF2A 0.022 0.1 0.23 32 -0.27 9 41
TRADD 0.027 0.006 -10000 0 -10000 0 0
CRADD 0.028 0.002 -10000 0 -10000 0 0
MAPK3 -0.015 0.061 0.17 6 -0.24 11 17
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.061 0.17 6 -0.26 9 15
Cathepsin D/ceramide -0.007 0.068 -10000 0 -0.21 34 34
FADD 0.044 0.083 0.2 75 -0.35 4 79
KSR1 -0.022 0.064 0.19 4 -0.21 33 37
MAPK8 -0.018 0.071 -10000 0 -0.27 17 17
PRKRA -0.017 0.07 0.19 14 -0.22 30 44
PDGFA 0.024 0.028 -10000 0 -0.39 2 2
TRAF2 0.022 0.046 -10000 0 -0.39 6 6
IGF1 -0.053 0.18 -10000 0 -0.45 84 84
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.023 0.065 -10000 0 -0.22 34 34
CTSD 0.027 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 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 -0.29 21 21
PRKCD 0.024 0.009 -10000 0 -10000 0 0
PRKCZ 0.026 0.022 -10000 0 -0.45 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.012 0.019 -10000 0 -0.28 2 2
RelA/NF kappa B1 0.038 0.011 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.053 -10000 0 -0.38 5 5
TNFR1A/BAG4/TNF-alpha 0.033 0.061 -10000 0 -0.24 20 20
mol:Sphingosine-1-phosphate 0.012 0.019 -10000 0 -0.28 2 2
MAP2K1 -0.019 0.06 0.17 8 -0.25 10 18
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.007 -10000 0 -10000 0 0
CYCS 0.003 0.047 0.18 2 -0.2 6 8
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.022 -10000 0 -0.32 1 1
EIF2AK2 -0.017 0.069 0.19 14 -0.26 12 26
TNF-alpha/TNFR1A/FAN 0.034 0.061 -10000 0 -0.24 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.024 0.074 -10000 0 -0.36 13 13
MAP2K2 -0.02 0.06 0.17 8 -0.25 11 19
SMPD3 0.001 0.096 0.18 9 -0.3 35 44
TNF 0.008 0.088 -10000 0 -0.4 22 22
PKC zeta/PAR4 0.039 0.019 -10000 0 -0.32 1 1
mol:PHOSPHOCHOLINE 0.028 0.084 0.21 71 -0.18 4 75
NF kappa B1/RelA/I kappa B alpha 0.07 0.033 -10000 0 -0.23 1 1
AIFM1 -0.001 0.054 0.17 4 -0.22 5 9
BCL2 0.022 0.04 -10000 0 -0.41 4 4
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.013 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.033 0.11 -9999 0 -0.34 6 6
Syndecan-3/Neurocan 0.012 0.075 -9999 0 -0.36 12 12
POMC -0.024 0.14 -9999 0 -0.4 59 59
EGFR 0.02 0.048 -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 0.027 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 0.09 -9999 0 -0.39 24 24
long-term memory 0.027 0.058 -9999 0 -0.34 8 8
Syndecan-3/IL8 -0.021 0.11 -9999 0 -0.4 13 13
PSEN1 0.026 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.028 0.02 -9999 0 -10000 0 0
FYN 0.027 0.019 -9999 0 -0.39 1 1
limb bud formation 0.005 0.06 -9999 0 -0.37 12 12
MC4R 0.002 0.028 -9999 0 -0.39 1 1
SRC 0.026 0.007 -9999 0 -10000 0 0
PTN -0.14 0.23 -9999 0 -0.45 176 176
FGFR/FGF/Syndecan-3 0.004 0.061 -9999 0 -0.37 12 12
neuron projection morphogenesis -0.029 0.13 -9999 0 -0.34 8 8
Syndecan-3/AgRP 0.018 0.062 -9999 0 -0.36 12 12
Syndecan-3/AgRP/MC4R 0.028 0.063 -9999 0 -0.34 12 12
Fyn/Cortactin 0.029 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 -0.02 0.1 -9999 0 -0.4 13 13
IL8 -0.063 0.17 -9999 0 -0.4 105 105
Syndecan-3/Fyn/Cortactin 0.028 0.059 -9999 0 -0.35 8 8
Syndecan-3/CASK 0.003 0.058 -9999 0 -0.36 12 12
alpha-MSH/MC4R -0.005 0.11 -9999 0 -0.29 59 59
Gamma Secretase 0.074 0.028 -9999 0 -10000 0 0
PDGFR-alpha 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
PDGFRA 0.011 0.067 -10000 0 -0.44 9 9
PDGF/PDGFRA/CRKL 0.024 0.054 -10000 0 -0.3 10 10
positive regulation of JUN kinase activity 0.058 0.042 -10000 0 -0.24 6 6
CRKL 0.026 0.02 -10000 0 -0.39 1 1
PDGF/PDGFRA/Caveolin-3 -0.048 0.15 -10000 0 -0.33 101 101
AP1 -0.097 0.3 0.31 2 -0.86 62 64
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 0.023 0.053 -10000 0 -0.3 10 10
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.052 -10000 0 -0.32 9 9
CAV3 -0.084 0.18 -10000 0 -0.45 96 96
CAV1 -0.006 0.11 -10000 0 -0.39 38 38
SHC/Grb2/SOS1 0.061 0.043 -10000 0 -0.24 6 6
PDGF/PDGFRA/Shf 0.02 0.072 -10000 0 -0.35 15 15
FOS -0.11 0.28 0.32 2 -0.85 62 64
JUN -0.023 0.025 -10000 0 -10000 0 0
oligodendrocyte development 0.023 0.053 -10000 0 -0.3 10 10
GRB2 0.028 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
mol:DAG -0.001 0.052 -10000 0 -0.32 9 9
PDGF/PDGFRA 0.011 0.067 -10000 0 -0.44 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 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.032 0.043 -10000 0 -0.26 6 6
PDGF/PDGFRA/Crk/C3G 0.045 0.044 -10000 0 -0.25 9 9
JAK1 0.004 0.045 -10000 0 -0.31 9 9
ELK1/SRF 0.004 0.045 0.16 12 -0.26 6 18
SHB 0.025 0.009 -10000 0 -10000 0 0
SHF 0.02 0.06 -10000 0 -0.45 8 8
CSNK2A1 0.029 0.02 -10000 0 -10000 0 0
GO:0007205 -0.007 0.052 -10000 0 -0.33 9 9
SOS1 0.028 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.058 0.042 -10000 0 -0.24 6 6
PDGF/PDGFRA/SHB 0.023 0.051 -10000 0 -0.3 9 9
PDGF/PDGFRA/Caveolin-1 0.001 0.097 -10000 0 -0.29 47 47
ITGAV 0.025 0.027 -10000 0 -0.39 2 2
ELK1 -0.016 0.051 -10000 0 -0.29 9 9
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.025 0.052 -10000 0 -0.3 9 9
JAK-STAT cascade 0.004 0.045 -10000 0 -0.31 9 9
cell proliferation 0.02 0.072 -10000 0 -0.35 15 15
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.028 0.003 -10000 0 -10000 0 0
mol:PIP3 0.001 0.029 -10000 0 -0.21 2 2
FRAP1 0.03 0.065 -10000 0 -0.43 5 5
AKT1 0.035 0.074 0.16 106 -0.23 2 108
INSR 0.027 0.022 -10000 0 -0.45 1 1
Insulin Receptor/Insulin 0.028 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 0.021 -10000 0 -10000 0 0
TSC2 0.027 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.013 0.03 -10000 0 -10000 0 0
TSC1 0.028 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.05 -10000 0 -0.2 23 23
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.03 -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 0.049 0.071 0.23 14 -0.25 3 17
MAP3K5 0.005 0.034 0.19 7 -0.18 9 16
PIK3R1 0.024 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 0.046 0.069 0.24 15 -0.24 1 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.059 0.061 0.22 10 -10000 0 10
eIF4E/eIF4G1/eIF4A1 0.013 0.031 -10000 0 -0.27 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.042 -10000 0 -0.19 9 9
mTOR/RHEB/GTP/Raptor/GBL 0.037 0.062 0.21 20 -0.19 1 21
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
RHEB/GTP 0.053 0.059 -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 0.023 0.072 0.16 100 -0.21 3 103
EIF4E 0.027 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.04 0.097 -10000 0 -0.51 12 12
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.004 0.1 -10000 0 -0.83 5 5
TSC1/TSC2 0.066 0.078 0.3 7 -10000 0 7
tumor necrosis factor receptor activity 0 0 0.001 22 -10000 0 22
RPS6 0.025 0.009 -10000 0 -10000 0 0
PPP5C 0.027 0.005 -10000 0 -10000 0 0
EIF4G1 0.02 0.013 -10000 0 -10000 0 0
IRS1 0 0.049 -10000 0 -0.21 23 23
INS -0.018 0.026 -10000 0 -0.39 2 2
PTEN 0.026 0.006 -10000 0 -10000 0 0
PDK2 0.024 0.072 0.16 103 -0.21 2 105
EIF4EBP1 -0.022 0.21 -10000 0 -1 21 21
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PPP2R5D 0.032 0.066 0.25 7 -0.38 5 12
peptide biosynthetic process -0.01 0.025 0.18 4 -0.22 3 7
RHEB 0.027 0.007 -10000 0 -10000 0 0
EIF4A1 0.027 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.003 131 -10000 0 131
EEF2 -0.01 0.025 0.18 4 -0.22 3 7
eIF4E/4E-BP1 -0.007 0.2 -10000 0 -0.94 21 21
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.054 0.44 5 -10000 0 5
VDR 0.026 0.03 -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 -0.34 7 7
RXRs/LXRs/DNA/Oxysterols 0.015 0.092 -10000 0 -0.37 10 10
MED1 0.028 0.003 -10000 0 -10000 0 0
mol:9cRA 0.003 0.008 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.008 0.091 -10000 0 -0.35 4 4
RXRs/NUR77 0.027 0.11 -10000 0 -0.27 5 5
RXRs/PPAR -0.079 0.13 -10000 0 -0.34 30 30
NCOR2 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.022 -10000 0 -0.32 2 2
RARs/VDR/DNA/Vit D3 0.035 0.081 -10000 0 -0.24 35 35
RARA 0.027 0.004 -10000 0 -10000 0 0
NCOA1 0.028 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.03 -10000 0 -0.45 2 2
RARs/RARs/DNA/9cRA 0.024 0.073 -10000 0 -0.23 35 35
RARG 0.027 0.022 -10000 0 -0.45 1 1
RPS6KB1 0.015 0.039 0.54 2 -10000 0 2
RARs/THRs/DNA/SMRT -0.009 0.091 -10000 0 -0.35 4 4
THRA 0.028 0.004 -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 0.022 0.099 -10000 0 -0.24 47 47
NR1H4 -0.005 0.028 -10000 0 -0.39 1 1
RXRs/LXRs/DNA 0.043 0.11 -10000 0 -0.34 3 3
NR1H2 0.029 0.015 -10000 0 -10000 0 0
NR1H3 0.023 0.048 -10000 0 -0.39 6 6
RXRs/VDR/DNA/Vit D3 0.029 0.097 -10000 0 -0.27 2 2
NR4A1 0.019 0.064 -10000 0 -0.45 9 9
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.004 0.071 -10000 0 -0.25 6 6
RXRG -0.029 0.15 -10000 0 -0.44 59 59
RXR alpha/CCPG 0.041 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 -0.003 0.11 -10000 0 -0.45 28 28
PPARG -0.13 0.22 -10000 0 -0.45 163 163
PPARD 0.027 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 -0.36 10 10
PPARA 0.027 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.008 0.12 -10000 0 -0.45 34 34
RXRs/NUR77/BCL2 -0.01 0.088 -10000 0 -0.23 58 58
SREBF1 0.012 0.084 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.022 0.099 -10000 0 -0.24 47 47
ABCA1 0.007 0.1 -10000 0 -1 2 2
RARs/THRs 0.03 0.11 -10000 0 -0.24 59 59
RXRs/FXR 0.028 0.1 -10000 0 -0.25 45 45
BCL2 0.022 0.04 -10000 0 -0.41 4 4
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.038 -10000 0 -0.29 6 6
PDGFRB -0.048 0.16 -10000 0 -0.39 88 88
SPHK1 -0.001 0.062 -10000 0 -0.62 4 4
mol:S1P -0.005 0.058 -10000 0 -0.52 4 4
S1P1/S1P/Gi -0.033 0.12 0.31 1 -0.39 33 34
GNAO1 0.022 0.04 -10000 0 -0.41 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.037 0.13 0.26 1 -0.34 36 37
PLCG1 -0.035 0.11 0.3 2 -0.37 30 32
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.048 0.16 -10000 0 -0.39 88 88
GNAI2 0.023 0.011 -10000 0 -10000 0 0
GNAI3 0.026 0.007 -10000 0 -10000 0 0
GNAI1 0.025 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 -0.007 0.056 -10000 0 -0.33 3 3
negative regulation of cAMP metabolic process -0.032 0.12 0.31 1 -0.38 33 34
MAPK3 -0.042 0.14 0.3 1 -0.42 31 32
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 0.025 0.029 -10000 0 -0.42 2 2
PLCB2 -0.001 0.066 0.31 3 -0.31 3 6
RAC1 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.006 0.048 -10000 0 -0.28 3 3
receptor internalization -0.007 0.053 -10000 0 -0.31 3 3
PTGS2 -0.044 0.17 -10000 0 -0.61 15 15
Rac1/GTP -0.005 0.048 -10000 0 -0.29 3 3
RHOA 0.025 0.009 -10000 0 -10000 0 0
VEGFA 0.023 0.039 -10000 0 -0.4 4 4
negative regulation of T cell proliferation -0.032 0.12 0.31 1 -0.38 33 34
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.009 0.083 -10000 0 -0.41 18 18
MAPK1 -0.041 0.13 0.3 1 -0.43 28 29
S1P1/S1P/PDGFB-D/PDGFRB -0.015 0.089 0.25 1 -0.3 5 6
ABCC1 0.025 0.033 -10000 0 -0.39 3 3
Signaling events mediated by PRL

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
CCNE1 0.024 0.033 -10000 0 -0.39 3 3
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 -0.034 0.15 -10000 0 -0.39 71 71
CDKN1A 0.012 0.048 -10000 0 -0.3 9 9
PRL-3/alpha Tubulin 0.03 0.038 -10000 0 -0.28 6 6
mol:Ca2+ -0.061 0.11 0.18 4 -0.33 74 78
AGT -0.065 0.19 -10000 0 -0.45 96 96
CCNA2 -0.006 0.045 -10000 0 -0.4 1 1
TUBA1B 0.028 0.003 -10000 0 -10000 0 0
EGR1 0.002 0.066 -10000 0 -0.31 21 21
CDK2/Cyclin E1 0.04 0.079 0.28 1 -0.36 4 5
MAPK3 0.008 0.032 -10000 0 -0.28 6 6
PRL-2 /Rab GGTase beta 0.04 0.008 -10000 0 -10000 0 0
MAPK1 0.008 0.032 -10000 0 -0.28 6 6
PTP4A1 -0.004 0.047 -10000 0 -10000 0 0
PTP4A3 0.018 0.047 -10000 0 -0.39 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 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 0.019 0.069 -10000 0 -10000 0 0
RABGGTA 0.026 0.007 -10000 0 -10000 0 0
BCAR1 -0.013 0.022 0.18 6 -10000 0 6
RHOC 0.01 0.042 -10000 0 -0.3 6 6
RHOA -0.001 0.069 -10000 0 -0.3 22 22
cell motility 0.021 0.074 0.31 4 -0.26 13 17
PRL-1/alpha Tubulin 0.023 0.064 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.013 0.11 -10000 0 -0.28 70 70
ROCK1 0.025 0.064 0.33 3 -0.27 8 11
RABGGTB 0.027 0.004 -10000 0 -10000 0 0
CDK2 0.028 0.003 -10000 0 -10000 0 0
mitosis -0.004 0.046 -10000 0 -10000 0 0
ATF5 0.019 0.059 -10000 0 -0.39 10 10
Cellular roles of Anthrax toxin

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
ANTXR1 0.025 0.033 -10000 0 -0.39 3 3
ANTXR2 0.018 0.062 -10000 0 -0.39 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.048 13 13
monocyte activation -0.016 0.1 -10000 0 -0.37 34 34
MAP2K2 0.003 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 0.049 -10000 0 -0.23 24 24
CYAA -0.009 0.03 -10000 0 -0.19 13 13
MAP2K4 -0.003 0.007 -10000 0 -10000 0 0
IL1B -0.02 0.064 0.17 6 -0.19 53 59
Channel 0.028 0.04 -10000 0 -0.21 13 13
NLRP1 -0.004 0.011 -10000 0 -0.19 1 1
CALM1 0.026 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.076 -10000 0 -0.38 19 19
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) 0.028 0.035 -10000 0 -0.18 13 13
macrophage activation -0.004 0.009 0.14 1 -10000 0 1
TNF 0.008 0.088 -10000 0 -0.4 22 22
VCAM1 -0.015 0.1 -10000 0 -0.37 31 31
platelet activation -0.003 0.076 -10000 0 -0.38 19 19
MAPKKK cascade 0.003 0.021 0.11 1 -0.092 3 4
IL18 -0.005 0.038 0.18 2 -0.23 11 13
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 -0.004 0.077 -10000 0 -0.38 19 19
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) 0.028 0.037 -10000 0 -0.2 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.034 0.035 -10000 0 -0.29 5 5
CRKL 0.017 0.12 0.3 8 -0.46 19 27
mol:PIP3 0 0.035 -10000 0 -0.74 1 1
AKT1 0.004 0.051 -10000 0 -0.64 1 1
PTK2B 0.026 0.008 -10000 0 -10000 0 0
RAPGEF1 0.02 0.12 0.28 14 -0.44 18 32
RANBP10 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.032 0.066 -10000 0 -0.26 22 22
MAP3K5 0.015 0.12 0.28 7 -0.47 17 24
HGF/MET/CIN85/CBL/ENDOPHILINS 0.044 0.071 -10000 0 -0.23 26 26
AP1 -0.009 0.11 -10000 0 -0.29 60 60
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
apoptosis -0.091 0.29 -10000 0 -0.73 80 80
STAT3 (dimer) 0.019 0.066 -10000 0 -0.32 6 6
GAB1/CRKL/SHP2/PI3K 0.031 0.1 0.32 2 -0.42 11 13
INPP5D 0.025 0.031 -10000 0 -0.45 2 2
CBL/CRK 0.024 0.11 0.31 1 -0.42 19 20
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.006 -10000 0 -10000 0 0
PTEN 0.027 0.006 -10000 0 -10000 0 0
ELK1 -0.006 0.07 0.27 21 -0.2 2 23
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.012 0.051 0.15 1 -0.24 9 10
PAK1 0.011 0.067 0.4 4 -0.62 1 5
HGF/MET/RANBP10 0.035 0.071 -10000 0 -0.26 26 26
HRAS 0.001 0.12 -10000 0 -0.48 20 20
DOCK1 0.015 0.12 0.29 7 -0.44 18 25
GAB1 0.01 0.12 0.25 1 -0.47 20 21
CRK 0.012 0.11 0.28 2 -0.45 19 21
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.12 -10000 0 -0.47 23 23
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 0.024 0.038 -10000 0 -0.45 3 3
cell morphogenesis 0.071 0.13 0.32 50 -0.41 5 55
GRB2/SHC 0.034 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 0.27 21 -0.2 2 23
HGF/MET/MUC20 0.02 0.066 -10000 0 -0.25 26 26
cell migration 0.031 0.054 -10000 0 -0.22 6 6
GRB2 0.028 0.004 -10000 0 -10000 0 0
CBL 0.025 0.008 -10000 0 -10000 0 0
MET/RANBP10 0.034 0.038 -10000 0 -0.29 6 6
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.051 -10000 0 -0.32 4 4
MET/MUC20 0.016 0.034 -10000 0 -0.29 6 6
RAP1B 0.025 0.12 0.3 14 -0.43 14 28
RAP1A 0.018 0.11 0.29 9 -0.42 16 25
HGF/MET/RANBP9 0.036 0.068 -10000 0 -0.26 23 23
RAF1 0.007 0.11 -10000 0 -0.47 15 15
STAT3 0.019 0.067 -10000 0 -0.32 6 6
cell proliferation 0.02 0.098 0.3 8 -0.39 9 17
RPS6KB1 0.011 0.023 -10000 0 -0.26 1 1
MAPK3 -0.008 0.099 0.52 12 -10000 0 12
MAPK1 -0.011 0.085 0.72 4 -10000 0 4
RANBP9 0.026 0.007 -10000 0 -10000 0 0
MAPK8 0.027 0.13 0.29 7 -0.44 20 27
SRC 0.007 0.047 -10000 0 -0.3 4 4
PI3K 0.024 0.051 -10000 0 -0.24 6 6
MET/Glomulin 0.016 0.037 -10000 0 -0.24 7 7
SOS1 0.028 0.004 -10000 0 -10000 0 0
MAP2K1 0.008 0.11 0.3 1 -0.46 12 13
MET 0.021 0.049 -10000 0 -0.41 6 6
MAP4K1 0.013 0.13 0.3 6 -0.49 19 25
PTK2 0.023 0.011 -10000 0 -10000 0 0
MAP2K2 0.008 0.11 -10000 0 -0.47 11 11
BAD 0.008 0.06 0.38 3 -0.62 1 4
MAP2K4 0.016 0.11 0.27 8 -0.44 16 24
SHP2/GRB2/SOS1/GAB1 0.031 0.1 -10000 0 -0.4 18 18
INPPL1 0.024 0.01 -10000 0 -10000 0 0
PXN 0.028 0.003 -10000 0 -10000 0 0
SH3KBP1 0.026 0.027 -10000 0 -0.39 2 2
HGS 0 0.042 -10000 0 -0.23 6 6
PLCgamma1/PKC 0.02 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 0.03 0.05 -10000 0 -0.23 4 4
PDPK1 -0.002 0.037 0.3 1 -0.68 1 2
HGF/MET/SHIP 0.034 0.075 -10000 0 -0.27 27 27
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.016 0.091 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.026 0.02 -10000 0 -0.39 1 1
STAT1 (dimer)/Cbp/p300 0.019 0.099 -10000 0 -0.31 10 10
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.03 0.045 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.03 0.069 -10000 0 -0.28 3 3
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 0.27 1 -10000 0 1
MAP3K11 -0.005 0.081 -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 -0.43 121 121
Rap1/GTP -0.009 0.06 -10000 0 -10000 0 0
CRKL/C3G 0.038 0.018 -10000 0 -0.28 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.017 0.1 -10000 0 -10000 0 0
CEBPB 0.019 0.11 0.31 3 -0.49 8 11
STAT3 0.028 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.003 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) -0.058 0.17 -10000 0 -0.39 101 101
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.004 0.094 -10000 0 -0.32 10 10
CEBPB/PTGES2/Cbp/p300 0.014 0.072 -10000 0 -0.34 5 5
mol:Ca2+ 0.013 0.088 -10000 0 -10000 0 0
MAPK3 0.001 0.12 -10000 0 -0.65 11 11
STAT1 (dimer) -0.034 0.095 -10000 0 -0.38 3 3
MAPK1 0.004 0.1 -10000 0 -0.58 8 8
JAK2 0.016 0.023 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
JAK1 0.02 0.023 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 0.021 0.097 0.28 7 -0.47 7 14
SMAD7 0.005 0.062 0.18 16 -10000 0 16
CBL/CRKL/C3G 0.015 0.086 0.27 1 -10000 0 1
PI3K 0.008 0.077 -10000 0 -10000 0 0
IFNG -0.058 0.17 -10000 0 -0.39 101 101
apoptosis 0.019 0.085 0.26 4 -0.41 6 10
CAMK2G 0.028 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.003 -10000 0 -10000 0 0
CAMK2A -0.084 0.2 -10000 0 -0.45 114 114
CAMK2B -0.092 0.2 -10000 0 -0.45 123 123
FRAP1 0.028 0.1 0.28 20 -10000 0 20
PRKCD 0.034 0.11 0.31 15 -10000 0 15
RAP1B 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.03 0.069 -10000 0 -0.28 3 3
PTPN2 0.026 0.008 -10000 0 -10000 0 0
EP300 0.026 0.031 -10000 0 -0.45 2 2
IRF1 -0.01 0.092 0.28 7 -0.38 1 8
STAT1 (dimer)/PIASy 0.005 0.095 0.23 2 -0.32 10 12
SOCS1 -0.012 0.16 -10000 0 -1 8 8
mol:GDP 0.013 0.082 0.25 1 -10000 0 1
CASP1 0.005 0.063 0.18 18 -0.3 1 19
PTGES2 0.027 0.005 -10000 0 -10000 0 0
IRF9 0.025 0.047 0.17 11 -10000 0 11
mol:PI-3-4-5-P3 0 0.069 -10000 0 -10000 0 0
RAP1/GDP 0.008 0.072 -10000 0 -10000 0 0
CBL -0.003 0.08 0.27 1 -10000 0 1
MAP3K1 -0.003 0.082 0.27 1 -10000 0 1
PIAS1 0.027 0.005 -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 -0.28 3 3
PTPN11 -0.001 0.088 0.28 1 -10000 0 1
CREBBP 0.028 0.005 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.014 0.094 0.24 4 -0.46 8 12
BAG4 0.024 0.023 -10000 0 -0.45 1 1
BAD 0.017 0.049 0.18 19 -0.18 3 22
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.012 0.071 -10000 0 -0.4 14 14
BAX 0.014 0.042 0.17 9 -0.21 1 10
EnzymeConsortium:3.1.4.12 0.008 0.027 0.074 13 -0.092 11 24
IKBKB 0.025 0.096 0.31 10 -0.44 8 18
MAP2K2 0.015 0.042 0.18 11 -10000 0 11
MAP2K1 0.015 0.043 0.18 11 -10000 0 11
SMPD1 0.009 0.034 0.13 7 -0.13 10 17
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.065 0.12 0.27 46 -0.43 7 53
MAP2K4 0.014 0.042 0.2 7 -10000 0 7
protein ubiquitination 0.022 0.1 0.29 9 -0.45 8 17
EnzymeConsortium:2.7.1.37 0.015 0.047 0.19 9 -10000 0 9
response to UV 0 0 0.002 9 -10000 0 9
RAF1 0.014 0.041 0.18 10 -0.19 1 11
CRADD 0.028 0.002 -10000 0 -10000 0 0
mol:ceramide 0.014 0.042 0.11 23 -0.15 9 32
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.012 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.013 0.04 0.16 7 -0.18 3 10
TRADD 0.027 0.006 -10000 0 -10000 0 0
RELA/p50 0.026 0.006 -10000 0 -10000 0 0
MAPK3 0.017 0.047 0.18 9 -0.22 1 10
MAPK1 0.017 0.044 0.18 9 -10000 0 9
p50/RELA/I-kappa-B-alpha 0.037 0.013 -10000 0 -10000 0 0
FADD 0.054 0.12 0.23 70 -0.45 7 77
KSR1 0.014 0.044 0.17 9 -0.19 2 11
MAPK8 0.011 0.045 0.18 10 -0.23 1 11
TRAF2 0.022 0.046 -10000 0 -0.39 6 6
response to radiation 0 0 0.002 3 -10000 0 3
CHUK 0.017 0.093 0.3 5 -0.45 7 12
TNF R/SODD 0.034 0.022 -10000 0 -0.32 1 1
TNF 0.008 0.088 -10000 0 -0.4 22 22
CYCS 0.023 0.052 0.16 29 -10000 0 29
IKBKG 0.023 0.1 0.32 11 -0.44 8 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.016 0.094 -10000 0 -0.47 9 9
RELA 0.027 0.007 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AIFM1 0.021 0.049 0.15 27 -0.16 1 28
TNF/TNF R/SODD 0.033 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 3 -10000 0 3
CASP8 0.021 0.089 -10000 0 -0.54 11 11
NSMAF 0.027 0.1 0.23 37 -0.45 8 45
response to hydrogen peroxide 0 0 0.002 9 -10000 0 9
BCL2 0.022 0.04 -10000 0 -0.41 4 4
FAS signaling pathway (CD95)

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
SPTAN1 0.001 0.035 0.21 9 -10000 0 9
RFC1 -0.002 0.027 0.21 3 -10000 0 3
PRKDC 0.017 0.069 0.22 45 -10000 0 45
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 0.009 0.091 -10000 0 -0.54 11 11
FASLG/FAS/FADD/FAF1 -0.001 0.059 0.22 8 -0.24 14 22
MAP2K4 0.026 0.12 0.3 8 -0.42 13 21
mol:ceramide 0.008 0.085 -10000 0 -0.32 13 13
GSN 0.001 0.036 0.21 9 -10000 0 9
FASLG/FAS/FADD/FAF1/Caspase 8 0.016 0.082 0.22 3 -0.29 12 15
FAS 0.023 0.026 -10000 0 -0.45 1 1
BID -0.015 0.024 0.26 1 -0.24 2 3
MAP3K1 0.041 0.1 0.31 7 -0.36 10 17
MAP3K7 0.027 0.006 -10000 0 -10000 0 0
RB1 -0.003 0.023 0.2 1 -10000 0 1
CFLAR 0.027 0.006 -10000 0 -10000 0 0
HGF/MET 0.028 0.084 -10000 0 -0.27 35 35
ARHGDIB 0.003 0.042 0.22 14 -10000 0 14
FADD 0.017 0.017 -10000 0 -10000 0 0
actin filament polymerization 0.003 0.044 -10000 0 -0.21 9 9
NFKB1 0.005 0.098 -10000 0 -0.49 11 11
MAPK8 0.011 0.16 0.3 6 -0.47 34 40
DFFA -0.003 0.024 0.2 1 -10000 0 1
DNA fragmentation during apoptosis -0.006 0.04 0.21 3 -0.31 2 5
FAS/FADD/MET 0.031 0.042 -10000 0 -0.26 5 5
CFLAR/RIP1 0.039 0.013 -10000 0 -10000 0 0
FAIM3 0.021 0.054 -10000 0 -0.4 8 8
FAF1 0.023 0.017 -10000 0 -10000 0 0
PARP1 -0.002 0.028 0.2 4 -10000 0 4
DFFB -0.004 0.034 0.21 3 -0.31 2 5
CHUK 0.002 0.088 -10000 0 -0.48 9 9
FASLG -0.016 0.13 -10000 0 -0.41 45 45
FAS/FADD 0.024 0.029 -10000 0 -0.32 1 1
HGF 0.007 0.092 -10000 0 -0.44 20 20
LMNA -0.006 0.029 0.19 1 -10000 0 1
CASP6 -0.003 0.022 0.2 1 -10000 0 1
CASP10 0.024 0.015 -10000 0 -10000 0 0
CASP3 0 0.023 0.22 2 -0.18 1 3
PTPN13 0.017 0.067 -10000 0 -0.45 10 10
CASP8 -0.016 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 -0.41 6 6
ICAD/CAD -0.004 0.029 0.19 2 -0.29 2 4
FASLG/FAS/FADD/FAF1/Caspase 10 0.008 0.086 -10000 0 -0.32 13 13
activation of caspase activity by cytochrome c -0.015 0.024 0.26 1 -0.24 2 3
PAK2 0.041 0.093 0.22 98 -10000 0 98
BCL2 0.022 0.04 -10000 0 -0.41 4 4
IL6-mediated signaling events

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
BCL2L1 -0.012 0.15 -10000 0 -10000 0 0
CRP -0.031 0.16 0.49 2 -0.66 1 3
cell cycle arrest -0.031 0.16 -10000 0 -0.57 2 2
TIMP1 -0.013 0.16 -10000 0 -0.54 10 10
IL6ST -0.028 0.15 -10000 0 -0.45 57 57
Rac1/GDP -0.022 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 -0.054 0.18 -10000 0 -0.62 1 1
HSP90B1 0.024 0.093 -10000 0 -0.68 5 5
GAB1 0.027 0.006 -10000 0 -10000 0 0
MAPK14 -0.027 0.12 -10000 0 -0.43 18 18
AKT1 0.048 0.064 0.29 9 -0.49 2 11
FOXO1 0.045 0.06 0.29 8 -0.46 2 10
MAP2K6 -0.034 0.12 -10000 0 -0.43 21 21
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.023 0.12 -10000 0 -0.45 13 13
MITF -0.03 0.12 -10000 0 -0.4 23 23
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.019 -10000 0 -0.39 1 1
A2M 0.018 0.1 -10000 0 -1.1 4 4
CEBPB 0.028 0.015 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.007 0.11 -10000 0 -0.46 14 14
STAT3 -0.036 0.16 -10000 0 -0.6 2 2
STAT1 0.005 0.084 -10000 0 -0.76 5 5
CEBPD -0.008 0.16 -10000 0 -10000 0 0
PIK3CA 0.021 0.013 -10000 0 -10000 0 0
PI3K 0.028 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 19 19
MAPK11 -0.027 0.12 -10000 0 -0.45 17 17
STAT3 (dimer)/FOXO1 0.012 0.15 0.39 2 -10000 0 2
GRB2/SOS1/GAB family 0.019 0.12 -10000 0 -0.4 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.019 0.12 -10000 0 -0.39 22 22
GRB2 0.028 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 0.007 0.16 0.49 2 -10000 0 2
FGG -0.041 0.16 -10000 0 -0.62 1 1
macrophage differentiation -0.031 0.16 -10000 0 -0.57 2 2
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.13 -10000 0 -0.36 19 19
JUNB -0.024 0.14 -10000 0 -10000 0 0
FOS -0.032 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 -0.013 0.12 -10000 0 -0.42 12 12
GRB2/SOS1/GAB family/SHP2/PI3K 0.044 0.058 -10000 0 -0.53 2 2
STAT3 (dimer) -0.034 0.16 -10000 0 -0.59 2 2
PRKCD -0.014 0.14 0.35 8 -0.49 5 13
IL6R 0.022 0.057 -10000 0 -0.45 7 7
SOCS3 -0.022 0.13 0.32 1 -0.59 7 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.018 0.1 -10000 0 -0.27 56 56
Rac1/GTP -0.022 0.12 -10000 0 -0.45 15 15
HCK 0.024 0.029 -10000 0 -0.42 2 2
MAPKKK cascade 0.023 0.11 -10000 0 -0.48 12 12
bone resorption -0.051 0.17 -10000 0 -0.59 1 1
IRF1 -0.025 0.15 -10000 0 -10000 0 0
mol:GDP -0.03 0.12 -10000 0 -0.41 22 22
SOS1 0.028 0.004 -10000 0 -10000 0 0
VAV1 -0.031 0.12 -10000 0 -0.42 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.019 0.13 -10000 0 -0.49 20 20
PTPN11 0.017 0.049 -10000 0 -0.69 2 2
IL6/IL6RA 0.007 0.1 -10000 0 -0.31 47 47
gp130 (dimer)/TYK2/TYK2/LMO4 0.016 0.11 -10000 0 -0.27 57 57
gp130 (dimer)/JAK2/JAK2/LMO4 0.014 0.1 -10000 0 -0.27 52 52
IL6 -0.012 0.13 -10000 0 -0.44 42 42
PIAS3 0.027 0.006 -10000 0 -10000 0 0
PTPRE 0.024 0.012 -10000 0 -10000 0 0
PIAS1 0.027 0.005 -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 41 41
LMO4 0.028 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.026 0.16 -10000 0 -0.59 2 2
MCL1 0.049 0.071 0.54 2 -0.51 1 3
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.048 0.16 -9999 0 -0.39 88 88
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.006 0.062 -9999 0 -0.25 15 15
GNAO1 0.024 0.041 -9999 0 -0.42 4 4
S1P/S1P3/G12/G13 0.046 0.035 -9999 0 -0.24 5 5
AKT1 -0.008 0.11 -9999 0 -0.47 20 20
AKT3 0.018 0.093 -9999 0 -0.7 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.048 0.16 -9999 0 -0.39 88 88
GNAI2 0.025 0.011 -9999 0 -10000 0 0
GNAI3 0.028 0.008 -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 0.023 0.048 -9999 0 -0.44 5 5
S1PR2 0.028 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.066 -9999 0 -0.32 10 10
MAPK3 0.016 0.06 -9999 0 -0.32 9 9
MAPK1 0.013 0.06 -9999 0 -0.32 9 9
JAK2 0.015 0.083 -9999 0 -0.41 10 10
CXCR4 0.009 0.078 -9999 0 -0.33 14 14
FLT1 0.027 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 0.06 -9999 0 -0.32 9 9
S1P/S1P3/Gi 0.021 0.066 -9999 0 -0.33 10 10
RAC1 0.026 0.007 -9999 0 -10000 0 0
RhoA/GTP 0.026 0.071 -9999 0 -0.32 7 7
VEGFA 0.024 0.039 -9999 0 -0.39 4 4
S1P/S1P2/Gi 0.023 0.051 -9999 0 -0.27 7 7
VEGFR1 homodimer/VEGFA homodimer 0.038 0.036 -9999 0 -0.27 5 5
RHOA 0.025 0.009 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.014 0.1 -9999 0 -0.24 77 77
GNAQ 0.027 0.005 -9999 0 -10000 0 0
GNAZ 0.011 0.083 -9999 0 -0.41 18 18
G12/G13 0.038 0.012 -9999 0 -10000 0 0
GNA14 -0.043 0.17 -9999 0 -0.45 72 72
GNA15 0.025 0.031 -9999 0 -0.45 2 2
GNA12 0.026 0.007 -9999 0 -10000 0 0
GNA13 0.028 0.003 -9999 0 -10000 0 0
GNA11 0.024 0.037 -9999 0 -0.45 3 3
Rac1/GTP 0.02 0.074 -9999 0 -0.31 9 9
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.037 0.021 -10000 0 -10000 0 0
CDKN1B 0.017 0.061 -10000 0 -0.28 9 9
CDKN1A 0.015 0.052 -10000 0 -0.28 11 11
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.009 -10000 0 -10000 0 0
FOXO3 0.013 0.055 -10000 0 -0.28 13 13
AKT1 0.009 0.047 -10000 0 -0.29 9 9
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 0.058 -10000 0 -0.28 13 13
AKT1/ASK1 0.039 0.068 -10000 0 -0.27 13 13
BAD/YWHAZ 0.047 0.022 -10000 0 -10000 0 0
RICTOR 0.025 0.009 -10000 0 -10000 0 0
RAF1 0.025 0.009 -10000 0 -10000 0 0
JNK cascade -0.036 0.065 0.26 13 -10000 0 13
TSC1 0.013 0.054 -10000 0 -0.28 13 13
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.039 0.074 0.28 3 -0.28 9 12
EP300 0.025 0.031 -10000 0 -0.45 2 2
mol:GDP 0.015 0.058 -10000 0 -0.29 13 13
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.014 0.055 -10000 0 -0.28 10 10
YWHAQ 0.028 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 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.071 0.28 9 -0.22 11 20
YWHAH 0.027 0.004 -10000 0 -10000 0 0
AKT1S1 0.015 0.052 -10000 0 -0.28 8 8
CASP9 0.015 0.048 -10000 0 -0.28 9 9
YWHAB 0.026 0.007 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.046 0.075 0.3 10 -10000 0 10
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.049 0.025 -10000 0 -0.27 1 1
YWHAE 0.027 0.006 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.02 0.057 0.2 3 -0.3 1 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.002 0.083 -10000 0 -0.34 24 24
CHUK 0.013 0.054 -10000 0 -0.28 12 12
BAD/BCL-XL 0.043 0.065 0.26 1 -10000 0 1
mTORC2 0.031 0.013 -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 0.091 0.25 13 -0.38 8 21
PDPK1 0.027 0.022 -10000 0 -0.45 1 1
MDM2 0.017 0.061 -10000 0 -0.28 12 12
MAPKKK cascade -0.039 0.073 0.27 9 -0.28 3 12
MDM2/Cbp/p300 0.06 0.08 0.27 9 -10000 0 9
TSC1/TSC2 0.014 0.058 0.29 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.077 0.26 9 -10000 0 9
glucose import -0.091 0.12 0.21 6 -0.24 199 205
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.062 0.18 1 -0.34 8 9
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.092 0.12 0.21 4 -0.24 199 203
GSK3A 0.015 0.052 -10000 0 -0.28 11 11
FOXO1 0.014 0.05 -10000 0 -0.28 7 7
GSK3B 0.029 0.067 -10000 0 -0.28 6 6
SFN 0.023 0.045 -10000 0 -0.42 5 5
G1/S transition of mitotic cell cycle 0.04 0.069 0.25 8 -10000 0 8
p27Kip1/14-3-3 family 0.029 0.063 -10000 0 -0.37 5 5
PRKACA 0.028 0.004 -10000 0 -10000 0 0
KPNA1 0.025 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.027 0.005 -10000 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.027 0.006 -10000 0 -10000 0 0
VDR 0.026 0.03 -10000 0 -0.45 2 2
Cbp/p300/PCAF 0.036 0.065 -10000 0 -0.28 17 17
EP300 0.025 0.031 -10000 0 -0.45 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.004 0.082 -10000 0 -0.38 12 12
KAT2B 0.009 0.084 -10000 0 -0.45 16 16
MAPK14 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.014 0.093 0.19 4 -0.26 28 32
RAR alpha/9cRA/Cyclin H 0.034 0.061 0.22 1 -0.38 1 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.015 0.11 -10000 0 -0.37 26 26
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.013 0.059 -10000 0 -0.34 7 7
NCOR2 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.022 -10000 0 -0.32 2 2
RXRs/RARs/NRIP1/9cRA -0.016 0.12 0.28 1 -0.57 8 9
NCOA2 -0.005 0.12 -10000 0 -0.45 31 31
NCOA3 0.027 0.006 -10000 0 -10000 0 0
NCOA1 0.028 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.03 -10000 0 -0.45 2 2
RARG 0.027 0.022 -10000 0 -0.45 1 1
RAR gamma1/9cRA 0.037 0.015 -10000 0 -0.27 1 1
MAPK3 0.028 0.005 -10000 0 -10000 0 0
MAPK1 0.027 0.006 -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 -0.028 0.13 -10000 0 -0.43 34 34
PRKCA 0.028 0.03 -10000 0 -0.43 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.026 0.13 -10000 0 -0.54 13 13
RXRG -0.032 0.12 -10000 0 -0.32 52 52
RXRA 0.008 0.046 -10000 0 -0.3 1 1
RXRB 0.003 0.06 -10000 0 -0.32 4 4
VDR/Vit D3/DNA 0.019 0.022 -10000 0 -0.32 2 2
RBP1 -0.053 0.16 -10000 0 -0.39 88 88
CRBP1/9-cic-RA -0.036 0.11 -10000 0 -0.28 88 88
RARB -0.007 0.12 -10000 0 -0.45 34 34
PRKCG -0.019 0.13 -10000 0 -0.39 54 54
MNAT1 0.026 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs -0.013 0.11 0.31 1 -0.54 6 7
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.007 0.1 -10000 0 -0.42 11 11
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.12 0.3 1 -0.36 36 37
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.027 0.13 -10000 0 -0.52 14 14
positive regulation of DNA binding 0.026 0.054 -10000 0 -0.36 1 1
NRIP1 -0.03 0.15 -10000 0 -0.92 5 5
RXRs/RARs -0.032 0.14 -10000 0 -0.5 20 20
RXRs/RXRs/DNA/9cRA -0.003 0.075 -10000 0 -0.46 4 4
PRKACA 0.028 0.004 -10000 0 -10000 0 0
CDK7 0.027 0.006 -10000 0 -10000 0 0
TFIIH 0.05 0.019 -10000 0 -10000 0 0
RAR alpha/9cRA 0.041 0.053 -10000 0 -10000 0 0
CCNH 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.027 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.047 0.024 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.021 0.032 -10000 0 -0.26 5 5
epithelial cell differentiation 0.048 0.034 -10000 0 -0.23 3 3
CYFIP2 0.025 0.029 -10000 0 -0.42 2 2
ENAH 0.019 0.071 0.25 8 -0.45 1 9
EGFR 0.02 0.048 -10000 0 -0.45 5 5
EPHA2 0.02 0.057 -10000 0 -0.45 7 7
MYO6 0.017 0.037 0.21 2 -10000 0 2
CTNNB1 0.025 0.009 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.027 -10000 0 -0.25 2 2
AQP5 -0.27 0.22 -10000 0 -0.43 313 313
CTNND1 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.017 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 -0.059 0.18 -10000 0 -0.45 88 88
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.086 0.18 -10000 0 -0.43 103 103
cortical microtubule organization 0.048 0.034 -10000 0 -0.23 3 3
GO:0000145 -0.001 0.036 0.19 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.053 0.036 -10000 0 -0.23 3 3
MLLT4 0.027 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.013 0.028 -10000 0 -0.39 1 1
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.053 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 0.056 0.046 -10000 0 -0.23 5 5
CDH1 0.022 0.048 -10000 0 -0.45 5 5
EGFR/EGFR/EGF/EGF -0.005 0.1 -10000 0 -0.38 5 5
RhoA/GDP 0.05 0.033 -10000 0 -0.22 3 3
actin cytoskeleton organization -0.002 0.036 0.2 2 -10000 0 2
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
IGF1R 0.027 0.005 -10000 0 -10000 0 0
IGF1 -0.053 0.18 -10000 0 -0.45 84 84
DIAPH1 0.017 0.12 -10000 0 -0.55 1 1
Wnt receptor signaling pathway -0.048 0.034 0.23 3 -10000 0 3
RHOA 0.025 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.028 -10000 0 -0.39 1 1
CTNNA1 0.027 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 -0.003 0.03 0.2 3 -10000 0 3
Ephrin A1/EPHA2 0.039 0.045 -10000 0 -0.42 1 1
SEC6/SEC8 0.01 0.02 -10000 0 -10000 0 0
MGAT3 0.001 0.062 -10000 0 -10000 0 0
HGF/MET 0.03 0.063 -10000 0 -0.36 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 0.032 -10000 0 -0.26 5 5
actin cable formation 0.058 0.095 0.23 77 -0.32 1 78
KIAA1543 -0.014 0.063 0.19 4 -0.4 3 7
KIFC3 0.014 0.029 -10000 0 -10000 0 0
NCK1 0.023 0.011 -10000 0 -10000 0 0
EXOC3 0.024 0.01 -10000 0 -10000 0 0
ACTN1 0.017 0.035 0.21 2 -10000 0 2
NCK1/GIT1 0.034 0.016 -10000 0 -10000 0 0
mol:GDP 0.048 0.034 -10000 0 -0.23 3 3
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 0.028 0.003 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
ROCK1 0.025 0.078 0.27 10 -0.34 1 11
adherens junction assembly -0.01 0.096 0.28 6 -0.5 8 14
IGF-1R heterotetramer/IGF1 0.003 0.098 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.01 -10000 0 -10000 0 0
MET 0.021 0.049 -10000 0 -0.41 6 6
PLEKHA7 0.003 0.069 0.21 2 -0.42 3 5
mol:GTP 0.051 0.042 -10000 0 -0.25 5 5
establishment of epithelial cell apical/basal polarity 0.025 0.084 0.33 14 -10000 0 14
cortical actin cytoskeleton stabilization 0.021 0.032 -10000 0 -0.26 5 5
regulation of cell-cell adhesion -0.002 0.036 0.2 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.021 0.032 -10000 0 -0.26 5 5
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.011 0.087 -10000 0 -0.23 54 54
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 0.027 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0.002 -10000 0 -10000 0 0
Gs family/GTP -0.013 0.083 -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 0.066 57 -10000 0 57
GNAL -0.029 0.15 -10000 0 -0.45 57 57
GNG2 0.025 0.02 -10000 0 -0.39 1 1
CRH -0.014 0.012 -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 0.002 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.02 0.014 -10000 0 -10000 0 0
TRAF2/ASK1 0.032 0.03 -10000 0 -0.23 6 6
ATM 0.025 0.008 -10000 0 -10000 0 0
MAP2K3 -0.018 0.11 0.41 2 -0.34 25 27
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.018 0.11 0.3 3 -0.34 25 28
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.021 0.054 -10000 0 -0.42 7 7
TXN 0.008 0.001 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
GADD45A 0.027 0.019 -10000 0 -0.39 1 1
GADD45B 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.027 0.007 -10000 0 -10000 0 0
MAP3K6 0.026 0.022 -10000 0 -0.45 1 1
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
MAP3K4 0.027 0.005 -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 0.018 -10000 0 -0.14 7 7
RAC1/OSM/MEKK3 0.046 0.033 -10000 0 -0.21 6 6
TRAF2 0.022 0.046 -10000 0 -0.39 6 6
RAC1/OSM/MEKK3/MKK3 -0.004 0.09 -10000 0 -0.3 12 12
TRAF6 0.008 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 -0.092 0.2 -10000 0 -0.45 123 123
CCM2 0.021 0.05 -10000 0 -0.39 7 7
CaM/Ca2+/CAMKIIB -0.04 0.13 -10000 0 -0.27 119 119
MAPK11 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.024 0.12 -10000 0 -0.24 118 118
OSM/MEKK3 0.035 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 0.027 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 0.027 0.005 -10000 0 -10000 0 0
MAP3K3 0.028 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.008 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.056 0.04 -10000 0 -0.22 7 7
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.017 0.085 -10000 0 -0.32 29 29
ATM 0.025 0.008 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.009 -10000 0 -10000 0 0
ATR 0.022 0.011 -10000 0 -10000 0 0
UBE2L3 0.027 0.006 -10000 0 -10000 0 0
FANCD2 0.016 0.011 -10000 0 -10000 0 0
protein ubiquitination 0.044 0.077 -10000 0 -0.24 26 26
XRCC5 0.027 0.006 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.043 0.025 -10000 0 -10000 0 0
MRE11A 0.025 0.008 -10000 0 -10000 0 0
DNA-PK 0.048 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.012 0.095 -10000 0 -0.53 8 8
FANCF 0.023 0.043 -10000 0 -0.45 4 4
BRCA1 0.028 0.003 -10000 0 -10000 0 0
CCNE1 0.024 0.033 -10000 0 -0.39 3 3
CDK2/Cyclin E1 0.038 0.026 -10000 0 -0.28 3 3
FANCG 0.024 0.01 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.018 0.087 -10000 0 -0.32 30 30
FANCE 0.027 0.006 -10000 0 -10000 0 0
FANCC 0.027 0.005 -10000 0 -10000 0 0
NBN 0.025 0.009 -10000 0 -10000 0 0
FANCA 0.025 0.027 -10000 0 -0.39 2 2
DNA repair 0.011 0.083 0.25 5 -0.38 4 9
BRCA1/BARD1/ubiquitin 0.018 0.087 -10000 0 -0.32 30 30
BARD1/DNA-PK 0.046 0.069 -10000 0 -0.25 21 21
FANCL 0.027 0.019 -10000 0 -0.39 1 1
mRNA polyadenylation -0.017 0.085 0.32 29 -10000 0 29
BRCA1/BARD1/CTIP/M/R/N Complex 0.01 0.072 -10000 0 -0.28 4 4
BRCA1/BACH1/BARD1/TopBP1 0.029 0.074 -10000 0 -0.27 25 25
BRCA1/BARD1/P53 0.035 0.076 -10000 0 -0.25 27 27
BARD1/CSTF1/BRCA1 0.032 0.078 -10000 0 -0.27 29 29
BRCA1/BACH1 0.028 0.003 -10000 0 -10000 0 0
BARD1 -0.002 0.11 -10000 0 -0.45 30 30
PCNA 0.026 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.033 0.079 -10000 0 -0.27 30 30
BRCA1/BARD1/UbcH7 0.032 0.078 -10000 0 -0.27 29 29
BRCA1/BARD1/RAD51/PCNA 0.044 0.077 -10000 0 -0.25 29 29
BARD1/DNA-PK/P53 0.052 0.073 -10000 0 -0.24 22 22
BRCA1/BARD1/Ubiquitin 0.018 0.087 -10000 0 -0.32 30 30
BRCA1/BARD1/CTIP 0.022 0.07 -10000 0 -0.25 29 29
FA complex 0.037 0.039 -10000 0 -10000 0 0
BARD1/EWS 0.018 0.085 -10000 0 -0.32 29 29
RBBP8 0.013 0.005 -10000 0 -10000 0 0
TP53 0.023 0.043 -10000 0 -0.45 4 4
TOPBP1 0.024 0.01 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.034 0.074 0.24 27 -10000 0 27
BRCA1/BARD1 0.05 0.08 -10000 0 -0.24 26 26
CSTF1 0.027 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.001 0.081 -10000 0 -0.32 30 30
CDK2 0.028 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.027 0.019 -10000 0 -0.39 1 1
RAD50 0.026 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.018 0.087 -10000 0 -0.32 30 30
EWSR1 0.027 0.005 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.047 0.081 0.34 1 -0.41 1 2
CRKL 0.021 0.085 0.31 6 -0.32 1 7
mol:DAG 0.02 0.065 -10000 0 -0.3 1 1
HRAS 0.025 0.085 0.3 13 -10000 0 13
MAPK8 0.02 0.099 0.22 9 -0.3 6 15
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 0.22 9 -0.37 2 11
EPO -0.015 0.12 -10000 0 -0.39 49 49
PLCG1 0.021 0.065 -10000 0 -0.3 1 1
EPOR/TRPC2/IP3 Receptors 0.019 0.062 -10000 0 -0.39 10 10
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.023 0.09 -10000 0 -0.23 49 49
GAB1/SHC/GRB2/SOS1 0.05 0.082 0.27 6 -0.29 1 7
EPO/EPOR (dimer) 0.006 0.1 -10000 0 -0.27 56 56
IRS2 0.022 0.086 0.31 7 -0.32 1 8
STAT1 0.02 0.071 -10000 0 -0.34 1 1
STAT5B 0.024 0.068 -10000 0 -0.34 1 1
cell proliferation 0.014 0.097 0.2 47 -0.35 2 49
GAB1/SHIP/PIK3R1/SHP2/SHC 0.03 0.075 -10000 0 -0.34 2 2
TEC 0.013 0.1 0.29 6 -0.37 8 14
SOCS3 0.027 0.022 -10000 0 -0.45 1 1
STAT1 (dimer) 0.02 0.07 -10000 0 -0.34 1 1
JAK2 0.022 0.02 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
EPO/EPOR (dimer)/JAK2 0.045 0.087 -10000 0 -0.33 1 1
EPO/EPOR 0.006 0.1 -10000 0 -0.27 56 56
LYN 0.025 0.021 -10000 0 -0.39 1 1
TEC/VAV2 0.018 0.1 0.28 2 -0.39 10 12
elevation of cytosolic calcium ion concentration 0.019 0.061 -10000 0 -0.39 10 10
SHC1 0.028 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.023 0.09 -10000 0 -0.23 47 47
mol:IP3 0.02 0.065 -10000 0 -0.3 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.042 0.092 0.31 6 -0.34 3 9
SH2B3 0.025 0.028 -10000 0 -0.39 1 1
NFKB1 0.024 0.097 0.2 43 -0.37 2 45
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.054 -10000 0 -0.26 11 11
PTPN6 0.019 0.083 0.3 4 -0.33 1 5
TEC/VAV2/GRB2 0.028 0.11 0.28 2 -0.38 10 12
EPOR 0.019 0.062 -10000 0 -0.39 10 10
INPP5D 0.025 0.031 -10000 0 -0.45 2 2
mol:GDP 0.049 0.083 0.27 6 -0.3 1 7
SOS1 0.028 0.004 -10000 0 -10000 0 0
PLCG2 0.026 0.022 -10000 0 -0.45 1 1
CRKL/CBL/C3G 0.035 0.08 0.28 2 -0.3 1 3
VAV2 0.019 0.092 0.31 7 -0.33 4 11
CBL 0.021 0.084 0.31 7 -0.32 1 8
SHC/Grb2/SOS1 0.019 0.064 -10000 0 -0.3 1 1
STAT5A 0.024 0.068 -10000 0 -0.34 1 1
GRB2 0.028 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.078 -10000 0 -0.38 1 1
LYN/PLCgamma2 0.035 0.026 -10000 0 -0.3 2 2
PTPN11 0.028 0.002 -10000 0 -10000 0 0
BTK 0.022 0.086 0.31 6 -0.32 1 7
BCL2 0.042 0.11 0.34 1 -0.61 6 7
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.009 0.044 0.12 59 -0.12 1 60
BUB1B 0.01 0.031 0.12 5 -0.15 5 10
PLK1 0.01 0.025 0.085 20 -10000 0 20
PLK1S1 0.013 0.025 0.12 5 -0.19 3 8
KIF2A 0.008 0.022 0.19 1 -10000 0 1
regulation of mitotic centrosome separation 0.01 0.025 0.084 20 -10000 0 20
GOLGA2 0.027 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.032 0.044 -10000 0 -0.21 10 10
WEE1 0.01 0.061 0.17 1 -0.3 15 16
cytokinesis 0.008 0.052 -10000 0 -0.23 6 6
PP2A-alpha B56 0.059 0.056 -10000 0 -0.52 4 4
AURKA 0.011 0.03 0.12 2 -0.18 7 9
PICH/PLK1 0.015 0.04 0.17 3 -0.2 1 4
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 0.027 0.006 -10000 0 -10000 0 0
FZR1 0.027 0.005 -10000 0 -10000 0 0
TPX2 0.016 0.025 0.11 12 -0.16 2 14
PAK1 0.025 0.009 -10000 0 -10000 0 0
SPC24 0.018 0.062 -10000 0 -0.39 11 11
FBXW11 0.027 0.007 -10000 0 -10000 0 0
CLSPN 0.01 0.033 -10000 0 -0.24 6 6
GORASP1 0.025 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 0.048 21 -10000 0 21
G2 phase of mitotic cell cycle -0.001 0.002 0.012 2 -10000 0 2
STAG2 0.028 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.04 0.17 -10000 0 -0.49 63 63
spindle elongation 0.01 0.025 0.084 20 -10000 0 20
ODF2 0.028 0.005 -10000 0 -10000 0 0
BUB1 0.027 0.056 -10000 0 -0.57 4 4
TPT1 0 0.051 -10000 0 -0.18 34 34
CDC25C 0.001 0.063 -10000 0 -0.27 23 23
CDC25B 0.013 0.075 -10000 0 -0.39 16 16
SGOL1 -0.009 0.044 0.12 1 -0.12 59 60
RHOA 0.025 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.031 0.045 -10000 0 -0.23 2 2
CDC14B 0.005 0.021 -10000 0 -0.32 2 2
CDC20 0.022 0.05 -10000 0 -0.39 7 7
PLK1/PBIP1 0.009 0.021 0.091 2 -0.17 2 4
mitosis -0.001 0.005 0.024 11 -10000 0 11
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 -0.39 1 1
metaphase plate congression 0.007 0.048 -10000 0 -0.23 17 17
ERCC6L 0.014 0.042 -10000 0 -0.22 2 2
NLP/gamma Tubulin 0.008 0.017 0.064 7 -0.11 2 9
microtubule cytoskeleton organization 0 0.051 -10000 0 -0.18 34 34
G2/M transition DNA damage checkpoint 0 0.003 0.013 12 -10000 0 12
PPP1R12A 0.028 0.003 -10000 0 -10000 0 0
interphase 0 0.003 0.013 12 -10000 0 12
PLK1/PRC1-2 0.04 0.027 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.044 0.03 -10000 0 -10000 0 0
RAB1A 0.028 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.022 0.084 19 -10000 0 19
mitotic prometaphase 0 0.003 0.017 17 -10000 0 17
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.059 -10000 0 -0.48 5 5
microtubule-based process 0.025 0.024 0.12 1 -10000 0 1
Golgi organization 0.01 0.025 0.084 20 -10000 0 20
Cohesin/SA2 0.023 0.021 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.041 0.006 -10000 0 -10000 0 0
KIF20A 0.027 0.006 -10000 0 -10000 0 0
APC/C/CDC20 0.023 0.035 0.12 1 -0.21 6 7
PPP2R1A 0.027 0.005 -10000 0 -10000 0 0
chromosome segregation 0.009 0.021 0.09 2 -0.17 2 4
PRC1 0.027 0.005 -10000 0 -10000 0 0
ECT2 0.066 0.098 0.22 141 -10000 0 141
C13orf34 0.009 0.022 0.078 19 -10000 0 19
NUDC 0.007 0.048 -10000 0 -0.24 17 17
regulation of attachment of spindle microtubules to kinetochore 0.01 0.031 0.12 5 -0.15 5 10
spindle assembly 0.008 0.021 0.077 14 -10000 0 14
spindle stabilization 0.013 0.025 0.12 5 -0.19 3 8
APC/C/HCDH1 0.023 0.019 -10000 0 -0.26 2 2
MKLP2/PLK1 0.026 0.024 0.12 1 -10000 0 1
CCNB1 0.028 0.007 -10000 0 -10000 0 0
PPP1CB 0.028 0.003 -10000 0 -10000 0 0
BTRC 0.027 0.005 -10000 0 -10000 0 0
ROCK2 -0.003 0.075 -10000 0 -0.34 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 0.006 0.018 -10000 0 -0.28 2 2
INCENP 0.028 0.004 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.048 0.16 -10000 0 -0.39 88 88
alphaV beta3 Integrin 0.025 0.068 -10000 0 -0.29 21 21
PTK2 0.009 0.087 -10000 0 -0.42 8 8
positive regulation of JNK cascade 0.009 0.092 -10000 0 -0.32 18 18
CDC42/GDP 0.042 0.12 0.32 3 -0.41 15 18
Rac1/GDP 0.038 0.12 0.3 2 -0.4 15 17
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.025 0.009 -10000 0 -10000 0 0
CDC42/GTP 0.026 0.12 -10000 0 -0.39 18 18
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 0.009 0.11 -10000 0 -0.48 11 11
PDGFB-D/PDGFRB -0.048 0.16 -10000 0 -0.39 88 88
TLN1 0.001 0.03 0.17 2 -0.3 1 3
Rap1/GTP 0.012 0.075 -10000 0 -0.32 9 9
IQGAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.017 -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 0.35 3 -0.48 17 20
MLLT4 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.006 0.1 -10000 0 -0.27 11 11
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 0.017 0.082 -10000 0 -0.32 10 10
PVRL1 0.022 0.038 -10000 0 -0.45 3 3
PVRL3 0.008 0.084 -10000 0 -0.43 17 17
PVRL2 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
CDH1 0.022 0.048 -10000 0 -0.45 5 5
CLDN1 0.004 0.085 -10000 0 -0.44 17 17
JAM-A/CLDN1 0.03 0.077 -10000 0 -0.25 28 28
SRC 0.002 0.12 -10000 0 -0.52 13 13
ITGB3 0.011 0.085 -10000 0 -0.41 19 19
nectin-1(dimer)/I-afadin/I-afadin 0.034 0.031 -10000 0 -0.32 3 3
FARP2 0.019 0.16 -10000 0 -0.55 20 20
RAC1 0.026 0.007 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.036 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 0.039 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.032 0.065 -10000 0 -0.26 20 20
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.027 0.022 -10000 0 -0.45 1 1
positive regulation of filopodium formation 0.009 0.092 -10000 0 -0.32 18 18
alphaV/beta3 Integrin/Talin 0.048 0.088 0.26 16 -0.31 6 22
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.039 0.01 -10000 0 -10000 0 0
PIP5K1C 0.002 0.034 -10000 0 -0.34 2 2
VAV2 0.034 0.13 -10000 0 -0.56 5 5
RAP1/GDP 0.042 0.11 0.31 4 -0.37 13 17
ITGAV 0.025 0.027 -10000 0 -0.39 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.036 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 -0.38 10 10
PTPRM 0.006 0.039 -10000 0 -0.21 12 12
E-cadherin/beta catenin/alpha catenin 0.062 0.052 -10000 0 -0.42 2 2
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.017 0.032 -10000 0 -0.24 2 2
CRKL 0.026 0.02 -10000 0 -0.39 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 0.021 0.053 -10000 0 -0.39 8 8
alpha4/beta7 Integrin/MAdCAM1 0.044 0.066 -10000 0 -0.22 23 23
EPO -0.021 0.12 -10000 0 -0.39 49 49
alpha4/beta7 Integrin 0.034 0.047 -10000 0 -0.29 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.041 -10000 0 -0.28 8 8
EPO/EPOR (dimer) 0 0.1 -10000 0 -0.28 56 56
lamellipodium assembly 0.037 0.085 -10000 0 -0.39 8 8
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.027 0.03 -10000 0 -0.32 2 2
ARF6 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.002 0.063 -10000 0 -0.3 10 10
PXN 0.028 0.003 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
MADCAM1 0 0.075 -10000 0 -0.39 16 16
cell adhesion 0.043 0.065 -10000 0 -0.21 23 23
CRKL/CBL 0.035 0.02 -10000 0 -0.28 1 1
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC -0.005 0.082 -10000 0 -0.28 10 10
ITGB7 0.026 0.03 -10000 0 -0.45 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.018 0.097 -10000 0 -0.25 56 56
p130Cas/Crk/Dock1 0.016 0.078 -10000 0 -0.35 2 2
VCAM1 -0.017 0.13 -10000 0 -0.4 51 51
RHOA 0.025 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.04 -10000 0 -10000 0 0
BCAR1 -0.022 0.072 0.18 13 -0.38 2 15
EPOR 0.019 0.059 -10000 0 -0.39 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.037 0.085 -10000 0 -0.4 8 8
IL2 signaling events mediated by PI3K

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
BCL2L1 0.044 0.069 -10000 0 -10000 0 0
UGCG 0.005 0.11 -10000 0 -0.56 18 18
AKT1/mTOR/p70S6K/Hsp90/TERT 0.035 0.12 0.25 11 -0.38 16 27
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.007 0.11 -10000 0 -0.55 18 18
mol:DAG 0.002 0.1 -10000 0 -0.76 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.049 0.096 0.24 1 -0.41 5 6
FRAP1 0.046 0.11 0.27 3 -0.43 9 12
FOXO3 0.048 0.095 0.3 4 -0.38 5 9
AKT1 0.05 0.093 0.26 2 -0.38 5 7
GAB2 0.023 0.038 -10000 0 -0.45 3 3
SMPD1 0.01 0.1 -10000 0 -0.57 14 14
SGMS1 0.018 0.075 -10000 0 -0.58 7 7
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 0.046 0.087 0.27 2 -0.39 6 8
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.031 -10000 0 -0.32 2 2
RPS6KB1 0.009 0.085 -10000 0 -0.83 2 2
mol:sphingomyelin 0.002 0.1 -10000 0 -0.76 8 8
natural killer cell activation 0 0.001 -10000 0 -0.012 1 1
JAK3 0.015 0.077 -10000 0 -0.39 17 17
PIK3R1 0.026 0.038 -10000 0 -0.45 3 3
JAK1 0.03 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MYC 0.081 0.12 0.38 9 -10000 0 9
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 0.043 0.081 -10000 0 -0.33 5 5
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 -0.32 5 5
Rac1/GDP 0.016 0.022 -10000 0 -0.25 2 2
T cell proliferation 0.044 0.079 0.27 8 -0.32 1 9
SHC1 0.028 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 -0.062 52 52
PRKCZ 0.041 0.076 0.24 4 -0.33 1 5
NF kappa B1 p50/RelA 0.06 0.1 0.26 2 -0.43 5 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.016 0.051 -10000 0 -0.3 5 5
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.007 -10000 0 -10000 0 0
IL2RA -0.012 0.12 -10000 0 -0.39 46 46
IL2RB 0.024 0.051 -10000 0 -0.4 7 7
TERT -0.055 0.16 -10000 0 -0.39 91 91
E2F1 -0.015 0.14 -10000 0 -0.42 50 50
SOS1 0.028 0.004 -10000 0 -10000 0 0
RPS6 0.025 0.009 -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 0.078 -10000 0 -0.4 17 17
actin cytoskeleton organization 0.044 0.079 0.27 8 -0.32 1 9
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL2 0.019 0.023 -10000 0 -0.39 1 1
PIK3CA 0.021 0.014 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.034 -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 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
BAG4 0.024 0.023 -10000 0 -0.45 1 1
Caspase 8 (4 units) 0.042 0.078 -10000 0 -0.4 1 1
NEF -0.008 0.036 -10000 0 -10000 0 0
NFKBIA 0.024 0.027 -10000 0 -10000 0 0
BIRC3 0.017 0.082 -10000 0 -0.39 13 13
CYCS 0.019 0.079 0.21 21 -0.44 1 22
RIPK1 0.027 0.006 -10000 0 -10000 0 0
CD247 -0.002 0.11 -10000 0 -0.48 21 21
MAP2K7 0.033 0.14 0.34 3 -0.71 11 14
protein ubiquitination 0.041 0.097 0.25 16 -0.39 9 25
CRADD 0.028 0.002 -10000 0 -10000 0 0
DAXX 0.027 0.006 -10000 0 -10000 0 0
FAS 0.026 0.022 -10000 0 -0.45 1 1
BID 0.016 0.074 0.19 3 -0.26 9 12
NF-kappa-B/RelA/I kappa B alpha 0.044 0.069 -10000 0 -0.32 10 10
TRADD 0.027 0.006 -10000 0 -10000 0 0
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
CFLAR 0.027 0.006 -10000 0 -10000 0 0
FADD 0.02 0.013 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.069 -10000 0 -0.33 10 10
MAPK8 0.031 0.13 0.28 5 -0.65 11 16
APAF1 0.028 0.002 -10000 0 -10000 0 0
TRAF1 0.017 0.065 -10000 0 -0.39 12 12
TRAF2 0.022 0.046 -10000 0 -0.39 6 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.023 0.078 0.2 3 -0.27 10 13
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.031 0.1 -10000 0 -0.48 11 11
CHUK 0.041 0.1 0.26 15 -0.42 9 24
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.051 0.043 -10000 0 -10000 0 0
TCRz/NEF -0.008 0.11 -10000 0 -0.3 53 53
TNF 0.008 0.088 -10000 0 -0.4 22 22
FASLG -0.028 0.15 -10000 0 -0.48 46 46
NFKB1 0.024 0.029 -10000 0 -0.21 1 1
TNFR1A/BAG4/TNF-alpha 0.033 0.061 -10000 0 -0.24 20 20
CASP6 0.041 0.11 -10000 0 -0.52 9 9
CASP7 0.042 0.12 0.3 28 -0.43 7 35
RELA 0.023 0.029 -10000 0 -0.21 1 1
CASP2 0.026 0.007 -10000 0 -10000 0 0
CASP3 0.038 0.12 0.3 26 -0.41 8 34
TNFRSF1A 0.026 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.022 -10000 0 -0.32 1 1
CASP8 0.027 0.006 -10000 0 -10000 0 0
CASP9 0.027 0.006 -10000 0 -10000 0 0
MAP3K14 0.04 0.1 0.24 9 -0.44 11 20
APAF-1/Caspase 9 0.012 0.077 -10000 0 -0.32 4 4
BCL2 0.027 0.12 0.27 5 -0.63 10 15
JNK 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
LAT/GRAP2/SLP76/HPK1 0.042 0.1 -10000 0 -0.35 26 26
MAP4K1 0.015 0.072 -10000 0 -0.4 14 14
MAP3K8 0.024 0.037 -10000 0 -0.45 3 3
PRKCB 0.02 0.054 -10000 0 -0.4 8 8
DBNL 0.027 0.006 -10000 0 -10000 0 0
CRKL 0.026 0.02 -10000 0 -0.39 1 1
MAP3K1 0.011 0.059 0.18 1 -0.38 4 5
JUN 0.009 0.12 -10000 0 -0.56 18 18
MAP3K7 0.009 0.063 -10000 0 -0.37 5 5
GRAP2 0.016 0.07 -10000 0 -0.43 12 12
CRK 0.027 0.006 -10000 0 -10000 0 0
MAP2K4 0.015 0.074 0.26 9 -0.4 4 13
LAT 0.016 0.07 -10000 0 -0.39 14 14
LCP2 0.024 0.033 -10000 0 -0.39 3 3
MAPK8 0.012 0.12 -10000 0 -0.57 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.017 0.066 -10000 0 -0.36 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.05 0.1 -10000 0 -0.38 19 19
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.036 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 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 0.027 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 0.025 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 0.028 0.003 -10000 0 -10000 0 0
FYN 0.027 0.019 -10000 0 -0.39 1 1
MAP3K12 0.026 0.029 -10000 0 -0.42 2 2
FGR 0.027 0.019 -10000 0 -0.39 1 1
p38 alpha/TAB1 -0.024 0.068 -10000 0 -0.29 22 22
PRKG1 0.004 0.1 -10000 0 -0.43 25 25
DUSP8 0.027 0.006 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.019 0.1 0.17 5 -0.33 16 21
apoptosis -0.023 0.066 -10000 0 -0.28 22 22
RAL/GTP 0.035 0.01 -10000 0 -10000 0 0
LYN 0.024 0.021 -10000 0 -0.39 1 1
DUSP1 0.006 0.096 -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 0.06 0.039 -10000 0 -0.21 6 6
TRAF6 0.027 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 0.021 0.05 -10000 0 -0.39 7 7
RAC1-CDC42/GTP 0.034 0.012 -10000 0 -10000 0 0
MAPK11 0.029 0.11 0.24 24 -0.34 14 38
BLK -0.035 0.15 -10000 0 -0.4 67 67
HCK 0.024 0.029 -10000 0 -0.42 2 2
MAP2K3 0.027 0.005 -10000 0 -10000 0 0
DUSP16 0.026 0.007 -10000 0 -10000 0 0
DUSP10 0.027 0.019 -10000 0 -0.39 1 1
TRAF6/MEKK3 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.029 0.11 0.22 22 -0.35 16 38
positive regulation of innate immune response 0.034 0.13 0.26 29 -0.39 17 46
LCK 0.017 0.065 -10000 0 -0.39 12 12
p38alpha-beta/MKP7 0.041 0.12 0.29 18 -0.39 14 32
p38alpha-beta/MKP5 0.041 0.12 0.26 21 -0.38 15 36
PGK/cGMP 0.004 0.071 -10000 0 -0.3 25 25
PAK2 0.02 0.013 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.035 0.13 0.27 22 -0.39 16 38
CDC42 0.027 0.005 -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
PAK3 0.003 0.077 -10000 0 -0.39 17 17
Insulin 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
CBL/APS/CAP 0.003 0.1 -10000 0 -0.4 4 4
TC10/GTP 0.005 0.092 -10000 0 -0.39 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.06 0.039 -10000 0 -0.25 4 4
HRAS 0.026 0.021 -10000 0 -0.41 1 1
APS homodimer 0.025 0.02 -10000 0 -0.39 1 1
GRB14 -0.017 0.14 -10000 0 -0.44 45 45
FOXO3 0.021 0.093 -10000 0 -0.6 10 10
AKT1 0.019 0.1 0.28 6 -0.39 1 7
INSR 0.029 0.023 -10000 0 -0.45 1 1
Insulin Receptor/Insulin 0.052 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.007 -10000 0 -10000 0 0
SORBS1 -0.045 0.17 -10000 0 -0.45 75 75
CRK 0.027 0.006 -10000 0 -10000 0 0
PTPN1 0.01 0.027 -10000 0 -10000 0 0
CAV1 -0.005 0.063 0.18 2 -0.23 4 6
CBL/APS/CAP/Crk-II/C3G 0.024 0.11 -10000 0 -0.24 58 58
Insulin Receptor/Insulin/IRS1/NCK2 0.06 0.039 -10000 0 -0.24 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.034 0.038 -10000 0 -0.23 3 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.026 0.065 -10000 0 -0.33 11 11
RPS6KB1 0.016 0.099 0.24 10 -0.36 1 11
PARD6A 0.025 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 0.02 0.029 -10000 0 -0.57 1 1
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.037 0.084 -10000 0 -0.38 1 1
HRAS/GTP 0.016 0.028 -10000 0 -10000 0 0
Insulin Receptor 0.029 0.023 -10000 0 -0.45 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.069 0.042 -10000 0 -0.24 3 3
PRKCI 0.018 0.038 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.002 0.07 -10000 0 -0.34 2 2
SHC1 0.028 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.038 0.038 -10000 0 -0.49 1 1
PI3K 0.042 0.043 -10000 0 -0.23 3 3
NCK2 0.028 0.003 -10000 0 -10000 0 0
RHOQ 0.028 0.003 -10000 0 -10000 0 0
mol:H2O2 0.001 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.015 -10000 0 -0.29 1 1
AKT2 0.022 0.11 0.28 8 -0.39 1 9
PRKCZ 0.015 0.054 -10000 0 -0.43 2 2
SH2B2 0.025 0.02 -10000 0 -0.39 1 1
SHC/SHIP 0.027 0.035 0.2 1 -0.23 4 5
F2RL2 -0.094 0.19 -10000 0 -0.4 141 141
TRIP10 0.028 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.046 0.025 -10000 0 -0.21 3 3
TC10/GTP/CIP4/Exocyst 0.037 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.073 0.033 -10000 0 -0.22 1 1
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 0.012 0.11 -10000 0 -0.25 73 73
TC10/GDP 0.021 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.059 0.032 -10000 0 -0.24 1 1
INPP5D 0.011 0.034 0.18 2 -0.23 6 8
SOS1 0.028 0.004 -10000 0 -10000 0 0
SGK1 -0.004 0.098 -10000 0 -0.64 11 11
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.024 0.037 -10000 0 -0.45 3 3
p62DOK/RasGAP 0.038 0.038 -10000 0 -0.49 1 1
INS 0.019 0.027 -10000 0 -0.39 2 2
mol:PI-3-4-P2 0.011 0.034 0.18 2 -0.23 6 8
GRB2 0.028 0.004 -10000 0 -10000 0 0
EIF4EBP1 0.01 0.096 0.28 5 -0.36 2 7
PTPRA 0.028 0.009 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.037 0.007 -10000 0 -10000 0 0
PDPK1 0.027 0.022 -10000 0 -0.45 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.025 0.029 -10000 0 -0.22 4 4
Insulin Receptor/Insulin/IRS1 0.044 0.035 -10000 0 -0.23 6 6
Insulin Receptor/Insulin/IRS3 0.035 0.029 -10000 0 -0.29 3 3
Par3/Par6 -0.014 0.12 -10000 0 -0.2 133 133
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.001 0.15 -9999 0 -0.47 20 20
MAP3K8 0.024 0.038 -9999 0 -0.45 3 3
FOS 0.002 0.11 -9999 0 -0.51 10 10
PRKCA 0.021 0.033 -9999 0 -0.42 2 2
PTPN7 0.002 0.091 -9999 0 -0.4 23 23
HRAS 0.026 0.021 -9999 0 -0.41 1 1
PRKCB 0.015 0.057 -9999 0 -0.41 8 8
NRAS 0.027 0.006 -9999 0 -10000 0 0
RAS family/GTP 0.044 0.024 -9999 0 -0.22 1 1
MAPK3 0.01 0.097 -9999 0 -0.6 8 8
MAP2K1 0.012 0.072 -9999 0 -0.42 7 7
ELK1 0.021 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 0.014 0.081 -9999 0 -0.57 5 5
RAF1 0.01 0.047 -9999 0 -0.33 3 3
KRAS 0.026 0.007 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.042 0.03 -9999 0 -10000 0 0
CLOCK 0.024 0.052 -9999 0 -0.45 6 6
TIMELESS/CRY2 0.04 0.022 -9999 0 -10000 0 0
DEC1/BMAL1 -0.015 0.12 -9999 0 -0.27 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 0.06 -9999 0 -0.45 8 8
CRY2 0.027 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 0.026 0.022 -9999 0 -0.45 1 1
BMAL/CLOCK/NPAS2 0.056 0.058 -9999 0 -0.28 12 12
BMAL1/CLOCK 0.011 0.07 -9999 0 -0.42 1 1
S phase of mitotic cell cycle 0.042 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 0.04 0.024 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.058 0.15 -9999 0 -0.39 85 85
Regulation of Telomerase

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
Telomerase catalytic core complex -0.048 0.18 -10000 0 -0.64 11 11
RAD9A 0.026 0.008 -10000 0 -10000 0 0
AP1 -0.008 0.12 -10000 0 -0.32 60 60
IFNAR2 0.02 0.018 -10000 0 -10000 0 0
AKT1 0.001 0.053 -10000 0 -0.37 5 5
ER alpha/Oestrogen 0.001 0.072 -10000 0 -0.3 27 27
NFX1/SIN3/HDAC complex 0.021 0.047 -10000 0 -0.3 4 4
EGF -0.059 0.18 -10000 0 -0.45 88 88
SMG5 0.028 0.004 -10000 0 -10000 0 0
SMG6 0.027 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.028 0.028 -10000 0 -10000 0 0
TERT/c-Abl -0.041 0.18 -10000 0 -0.6 11 11
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.043 0.025 -10000 0 -10000 0 0
WT1 -0.07 0.17 -10000 0 -0.4 101 101
WRN 0.026 0.008 -10000 0 -10000 0 0
SP1 0.018 0.023 -10000 0 -10000 0 0
SP3 0.026 0.007 -10000 0 -10000 0 0
TERF2IP 0.027 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.025 0.17 -10000 0 -0.62 6 6
Mad/Max 0.033 0.035 -10000 0 -0.33 4 4
TERT -0.049 0.19 -10000 0 -0.66 11 11
CCND1 -0.003 0.2 0.49 1 -0.94 5 6
MAX 0.025 0.008 -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
TERF2 0.026 0.014 -10000 0 -10000 0 0
PTGES3 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
Telomerase/911 0.036 0.049 -10000 0 -10000 0 0
CDKN1B -0.028 0.1 -10000 0 -10000 0 0
RAD1 0.025 0.009 -10000 0 -10000 0 0
XRCC5 0.027 0.006 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
SAP30 0.026 0.02 -10000 0 -0.4 1 1
TRF2/PARP2 0.038 0.015 -10000 0 -10000 0 0
UBE3A 0.027 0.005 -10000 0 -10000 0 0
JUN 0.027 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 -0.022 0.13 -10000 0 -0.27 100 100
PARP2 0.027 0.006 -10000 0 -10000 0 0
BLM 0.027 0.019 -10000 0 -0.39 1 1
Telomerase 0.008 0.1 0.23 1 -0.53 9 10
IRF1 0.029 0.008 -10000 0 -10000 0 0
ESR1 0.003 0.1 -10000 0 -0.42 27 27
KU/TER 0.039 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.015 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.024 0.061 -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 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.018 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 0.005 -10000 0 -10000 0 0
MXD1 0.022 0.048 -10000 0 -0.45 5 5
MRE11A 0.025 0.008 -10000 0 -10000 0 0
HUS1 0.026 0.007 -10000 0 -10000 0 0
RPS6KB1 0.028 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.022 0.19 -10000 0 -0.65 10 10
NR2F2 0.028 0.02 -10000 0 -0.38 1 1
MAPK3 -0.008 0.019 -10000 0 -0.28 1 1
MAPK1 -0.008 0.019 -10000 0 -0.28 1 1
TGFB1/TGF beta receptor Type II 0.026 0.027 -10000 0 -0.39 2 2
NFKB1 0.027 0.005 -10000 0 -10000 0 0
HNRNPC 0.026 0.007 -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 0.025 0.009 -10000 0 -10000 0 0
EGFR 0.019 0.049 -10000 0 -0.45 5 5
mol:Oestrogen -0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.026 0.14 -10000 0 -0.33 79 79
MYC 0.021 0.012 -10000 0 -10000 0 0
IL2 0.01 0.03 -10000 0 -0.39 1 1
KU 0.039 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 0.026 0.027 -10000 0 -0.39 2 2
TRF2/BLM 0.039 0.02 -10000 0 -0.26 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.029 0.18 -10000 0 -0.62 9 9
SP1/HDAC2 0.028 0.033 -10000 0 -10000 0 0
PINX1 0.026 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.025 0.17 -10000 0 -0.62 6 6
Smad3/Myc 0.024 0.019 -10000 0 -0.23 1 1
911 complex 0.043 0.025 -10000 0 -10000 0 0
IFNG -0.057 0.17 -10000 0 -0.39 101 101
Telomerase/PinX1 -0.024 0.17 -10000 0 -0.62 6 6
Telomerase/AKT1/mTOR/p70S6K -0.001 0.099 0.26 1 -0.46 9 10
SIN3B 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
Telomerase/EST1B -0.023 0.17 -10000 0 -0.6 7 7
response to DNA damage stimulus -0.003 0.028 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.059 0.036 -10000 0 -10000 0 0
TRF2/WRN 0.037 0.016 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.024 0.17 -10000 0 -0.6 7 7
E2F1 0.003 0.083 -10000 0 -0.4 19 19
ZNFX1 0.026 0.006 -10000 0 -10000 0 0
PIF1 0.004 0.097 -10000 0 -0.39 28 28
NCL 0.027 0.006 -10000 0 -10000 0 0
DKC1 0.027 0.006 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.094 0.24 -10000 0 -1.1 3 3
PLK1 0.055 0.1 -10000 0 -0.69 7 7
BIRC5 0.047 0.11 -10000 0 -0.88 3 3
HSPA1B 0.095 0.24 -10000 0 -1.1 3 3
MAP2K1 0.037 0.038 -10000 0 -10000 0 0
BRCA2 0.088 0.26 -10000 0 -1.2 6 6
FOXM1 0.091 0.28 -10000 0 -1.4 4 4
XRCC1 0.093 0.24 -10000 0 -1.1 3 3
FOXM1B/p19 -0.013 0.25 -10000 0 -1.2 5 5
Cyclin D1/CDK4 0.065 0.26 -10000 0 -1.1 4 4
CDC2 0.095 0.25 0.55 1 -1.1 4 5
TGFA 0.077 0.26 0.56 1 -1.1 6 7
SKP2 0.11 0.25 0.66 2 -1.1 3 5
CCNE1 0.028 0.034 -10000 0 -0.38 3 3
CKS1B 0.092 0.25 0.65 1 -1.1 4 5
RB1 0.032 0.18 -10000 0 -0.84 7 7
FOXM1C/SP1 0.099 0.26 -10000 0 -1.3 3 3
AURKB 0.035 0.16 -10000 0 -0.73 15 15
CENPF 0.094 0.24 0.65 1 -1.1 3 4
CDK4 0.033 0.02 -10000 0 -10000 0 0
MYC 0.065 0.21 0.5 1 -0.95 3 4
CHEK2 0.036 0.038 -10000 0 -10000 0 0
ONECUT1 0.079 0.27 -10000 0 -1.1 5 5
CDKN2A -0.14 0.2 -10000 0 -0.4 183 183
LAMA4 0.085 0.25 -10000 0 -1.1 3 3
FOXM1B/HNF6 0.076 0.29 -10000 0 -1.4 5 5
FOS 0 0.44 -10000 0 -1.1 64 64
SP1 0.029 0.003 -10000 0 -10000 0 0
CDC25B 0.095 0.25 -10000 0 -1.1 3 3
response to radiation 0.016 0.024 -10000 0 -10000 0 0
CENPB 0.1 0.24 -10000 0 -1.1 3 3
CENPA 0.091 0.24 0.59 1 -1.2 3 4
NEK2 0.093 0.24 0.65 1 -1.2 3 4
HIST1H2BA 0.088 0.24 -10000 0 -1.1 3 3
CCNA2 0.03 0.022 -10000 0 -0.41 1 1
EP300 0.025 0.031 -10000 0 -0.45 2 2
CCNB1/CDK1 0.09 0.26 -10000 0 -1.4 3 3
CCNB2 0.092 0.25 0.74 1 -1.2 3 4
CCNB1 0.095 0.25 -10000 0 -1.2 3 3
ETV5 0.14 0.26 0.63 4 -1.1 3 7
ESR1 0.067 0.3 -10000 0 -1.1 16 16
CCND1 0.027 0.24 -10000 0 -1.1 5 5
GSK3A 0.038 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.063 0.048 -10000 0 -0.24 3 3
CDK2 0.031 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.016 0.026 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.097 0.25 -10000 0 -1.2 4 4
GAS1 0.09 0.26 -10000 0 -1.2 6 6
MMP2 0.076 0.26 -10000 0 -1.1 3 3
RB1/FOXM1C 0.085 0.27 0.6 1 -1.1 4 5
CREBBP 0.027 0.005 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.017 0.028 -10000 0 -10000 0 0
STMN1 0.01 0.049 -10000 0 -0.31 10 10
Aurora B/RasGAP/Survivin 0.042 0.078 -10000 0 -0.28 23 23
Chromosomal passenger complex/Cul3 protein complex 0.012 0.052 -10000 0 -0.29 5 5
BIRC5 0.011 0.087 -10000 0 -0.39 22 22
DES -0.31 0.29 -10000 0 -0.56 279 279
Aurora C/Aurora B/INCENP 0.049 0.048 -10000 0 -0.23 11 11
Aurora B/TACC1 0.032 0.039 -10000 0 -0.23 9 9
Aurora B/PP2A 0.038 0.042 -10000 0 -0.27 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 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 0.043 0.038 -10000 0 -0.27 4 4
KIF2C 0.017 0.027 -10000 0 -0.19 3 3
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 0.037 0.046 -10000 0 -0.31 7 7
SEPT1 0.019 0.059 -10000 0 -0.39 10 10
SMC2 0.027 0.005 -10000 0 -10000 0 0
SMC4 0.021 0.012 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.008 0.12 -10000 0 -0.58 17 17
PSMA3 0.026 0.007 -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 0.027 0.055 -10000 0 -0.39 8 8
AURKC 0.022 0.049 -10000 0 -0.41 6 6
CDCA8 0.028 0.02 -10000 0 -0.4 1 1
cytokinesis -0.002 0.058 -10000 0 -0.35 6 6
Aurora B/Septin1 0.03 0.082 -10000 0 -0.34 8 8
AURKA 0.021 0.046 -10000 0 -0.39 6 6
INCENP 0.029 0.006 -10000 0 -10000 0 0
KLHL13 0.024 0.043 -10000 0 -0.45 4 4
BUB1 0.028 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.039 0.069 -10000 0 -0.23 25 25
EVI5 0.029 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.051 0.053 -10000 0 -10000 0 0
SGOL1 0.025 0.009 -10000 0 -10000 0 0
CENPA 0.018 0.049 -10000 0 -0.28 4 4
NCAPG 0.026 0.007 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.038 0.042 -10000 0 -0.27 8 8
NCAPD2 0.026 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.039 0.041 -10000 0 -0.27 8 8
RHOA 0.025 0.009 -10000 0 -10000 0 0
NCAPH 0.027 0.004 -10000 0 -10000 0 0
NPM1 -0.008 0.12 -10000 0 -0.45 20 20
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 0.038 0.042 -10000 0 -0.27 8 8
PPP1CC 0.028 0.003 -10000 0 -10000 0 0
Centraspindlin 0.048 0.055 -10000 0 -0.25 1 1
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
NSUN2 0.011 0.055 -10000 0 -0.28 8 8
MYLK 0.012 0.032 -10000 0 -0.19 9 9
KIF23 0.029 0.005 -10000 0 -10000 0 0
VIM 0.011 0.044 -10000 0 -0.3 9 9
RACGAP1 0.029 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.001 0.094 -10000 0 -0.45 14 14
Chromosomal passenger complex 0.018 0.045 0.17 2 -0.21 7 9
Chromosomal passenger complex/EVI5 0.088 0.087 -10000 0 -0.36 6 6
TACC1 0.023 0.031 -10000 0 -0.45 2 2
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
CUL3 0.027 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA 0.019 0.062 -10000 0 -0.44 9 9
HRAS 0.026 0.021 -10000 0 -0.41 1 1
EGFR 0.02 0.048 -10000 0 -0.45 5 5
AKT 0.07 0.073 0.28 18 -0.27 1 19
FOXO3 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.021 0.05 -10000 0 -0.39 7 7
FOXO4 0.026 0.03 -10000 0 -0.45 2 2
MET 0.021 0.049 -10000 0 -0.41 6 6
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PIK3CB 0.023 0.011 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
PIK3CG 0.009 0.086 -10000 0 -0.41 20 20
PIK3R3 0.028 0.004 -10000 0 -10000 0 0
PIK3R2 0.028 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 -0.064 0.077 0.25 7 -0.21 49 56
PI3K 0.055 0.072 0.23 31 -0.31 1 32
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
KRAS 0.026 0.007 -10000 0 -10000 0 0
FOXO 0.087 0.063 0.23 34 -10000 0 34
AKT2 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.027 0.006 -10000 0 -10000 0 0
VEGFR1 specific signals

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
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 0.085 -10000 0 -0.42 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.03 -10000 0 -0.27 1 1
CaM/Ca2+ -0.007 0.086 -10000 0 -0.4 1 1
HIF1A 0.031 0.025 -10000 0 -0.44 1 1
GAB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.02 0.1 0.38 5 -0.49 2 7
PLCG1 -0.02 0.086 -10000 0 -0.43 1 1
NOS3 0.012 0.098 0.37 9 -0.39 2 11
CBL 0.025 0.008 -10000 0 -10000 0 0
mol:NO 0.021 0.12 0.46 17 -0.38 4 21
FLT1 0.017 0.023 -10000 0 -0.33 2 2
PGF -0.045 0.16 -10000 0 -0.39 84 84
VEGFR1 homodimer/NRP2/VEGFR121 0.04 0.036 -10000 0 -0.27 1 1
CALM1 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
eNOS/Hsp90 0.019 0.1 0.37 6 -0.38 3 9
endothelial cell proliferation -0.003 0.091 0.37 10 -0.42 1 11
mol:Ca2+ -0.02 0.085 -10000 0 -0.42 1 1
MAPK3 -0.025 0.089 0.34 11 -0.38 1 12
MAPK1 -0.025 0.089 0.34 11 -0.38 1 12
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
PLGF homodimer -0.045 0.16 -10000 0 -0.39 84 84
PRKACA 0.028 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.006 0.11 -10000 0 -0.39 38 38
VEGFA homodimer 0.023 0.038 -10000 0 -0.39 4 4
VEGFR1 homodimer/VEGFA homodimer 0.027 0.033 -10000 0 -0.3 1 1
platelet activating factor biosynthetic process -0.026 0.084 0.33 10 -0.37 1 11
PI3K 0.01 0.087 -10000 0 -0.41 2 2
PRKCA -0.023 0.084 0.35 4 -0.4 1 5
PRKCB -0.024 0.088 0.35 5 -0.4 1 6
VEGFR1 homodimer/PLGF homodimer -0.013 0.1 -10000 0 -0.38 2 2
VEGFA 0.023 0.038 -10000 0 -0.39 4 4
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.02 0.085 -10000 0 -0.42 1 1
RASA1 0.02 0.042 -10000 0 -0.46 1 1
NRP2 0.025 0.027 -10000 0 -0.39 2 2
VEGFR1 homodimer 0.017 0.023 -10000 0 -0.33 2 2
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.023 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.015 0.13 0.45 16 -0.38 3 19
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.009 0.085 -10000 0 -0.4 2 2
mol:L-citrulline 0.021 0.12 0.46 17 -0.38 4 21
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.051 0.038 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.035 0.036 -10000 0 -10000 0 0
CD2AP 0.027 0.006 -10000 0 -10000 0 0
PI3K/GAB1 0.018 0.088 -10000 0 -0.39 2 2
PDPK1 0.025 0.11 0.37 9 -0.49 2 11
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.041 0.035 -10000 0 -10000 0 0
mol:NADP 0.021 0.12 0.46 17 -0.38 4 21
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.037 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.029 0.028 -10000 0 -0.3 1 1
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.004 -10000 0 -10000 0 0
SPHK1 0.018 0.062 -10000 0 -0.39 11 11
GNAI2 0.024 0.009 -10000 0 -10000 0 0
mol:S1P 0.013 0.023 -10000 0 -10000 0 0
GNAO1 0.023 0.039 -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 0.051 0.04 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.012 -10000 0 -10000 0 0
S1PR3 0.023 0.047 -10000 0 -0.44 5 5
S1PR2 0.028 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 0.024 0.041 -10000 0 -0.42 4 4
S1PR4 0.002 0.1 -10000 0 -0.4 29 29
GNAI1 0.026 0.022 -10000 0 -0.45 1 1
S1P/S1P5/G12 0.036 0.042 -10000 0 -0.24 3 3
S1P/S1P3/Gq -0.014 0.11 -10000 0 -0.38 13 13
S1P/S1P4/Gi 0.014 0.074 0.18 1 -0.36 9 10
GNAQ 0.027 0.005 -10000 0 -10000 0 0
GNAZ 0.011 0.083 -10000 0 -0.41 18 18
GNA14 -0.043 0.17 -10000 0 -0.45 72 72
GNA15 0.025 0.031 -10000 0 -0.45 2 2
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.028 0.003 -10000 0 -10000 0 0
GNA11 0.024 0.037 -10000 0 -0.45 3 3
ABCC1 0.025 0.033 -10000 0 -0.39 3 3
IL2 signaling events mediated by STAT5

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
GAB2 0.023 0.038 -10000 0 -0.45 3 3
ELF1 0.008 0.075 -10000 0 -0.44 3 3
CCNA2 0.026 0.02 -10000 0 -0.39 1 1
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
JAK3 0.014 0.077 -10000 0 -0.39 17 17
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
JAK1 0.028 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 0.23 3 -0.38 3 6
SHC1 0.028 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 0.022 0.051 -10000 0 -0.4 7 7
SOS1 0.028 0.004 -10000 0 -10000 0 0
IL2RG 0.014 0.078 -10000 0 -0.4 17 17
G1/S transition of mitotic cell cycle 0.031 0.093 0.3 5 -0.49 7 12
PTPN11 0.029 0.002 -10000 0 -10000 0 0
CCND2 0.015 0.052 -10000 0 -0.53 4 4
LCK 0.018 0.065 -10000 0 -0.39 12 12
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL2 0 0.028 -10000 0 -0.39 1 1
CDK6 0.023 0.036 -10000 0 -0.43 3 3
CCND3 0.043 0.081 0.35 1 -10000 0 1
Class IB PI3K non-lipid kinase events

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.022 0.048 0.41 6 -10000 0 6
PI3K Class IB/PDE3B 0.022 0.048 -10000 0 -0.41 6 6
PDE3B 0.022 0.049 -10000 0 -0.41 6 6
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.023 0.039 -10000 0 -0.41 4 4
CDC42/GTP 0.013 0.074 -10000 0 -0.32 7 7
PLCG1 0.004 0.063 -10000 0 -0.32 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.012 -10000 0 -10000 0 0
cell migration 0.012 0.073 -10000 0 -0.31 7 7
S1PR5 0.024 0.041 -10000 0 -0.42 4 4
S1PR4 0.002 0.1 -10000 0 -0.4 29 29
MAPK3 0.004 0.063 -10000 0 -0.32 8 8
MAPK1 0.002 0.06 -10000 0 -0.29 8 8
S1P/S1P5/Gi 0.019 0.052 -10000 0 -0.27 8 8
GNAI1 0.026 0.022 -10000 0 -0.45 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 -10000 0 -0.25 4 4
RHOA 0.012 0.065 0.18 29 -10000 0 29
S1P/S1P4/Gi 0.012 0.064 -10000 0 -0.33 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.011 0.083 -10000 0 -0.41 18 18
S1P/S1P4/G12/G13 0.034 0.062 -10000 0 -0.21 27 27
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.028 0.003 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.005 -9999 0 -10000 0 0
ITGB7 0.026 0.03 -9999 0 -0.45 2 2
ITGA4 0.021 0.053 -9999 0 -0.39 8 8
alpha4/beta7 Integrin 0.034 0.047 -9999 0 -0.29 10 10
alpha4/beta1 Integrin 0.034 0.041 -9999 0 -0.28 8 8
HIF-2-alpha transcription factor network

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
MMP14 0.013 0.13 -10000 0 -0.63 14 14
oxygen homeostasis -0.002 0.011 -10000 0 -10000 0 0
TCEB2 0.026 0.027 -10000 0 -0.39 2 2
TCEB1 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.027 0.084 -10000 0 -0.44 1 1
EPO -0.026 0.16 -10000 0 -0.55 10 10
FIH (dimer) 0.021 0.021 -10000 0 -10000 0 0
APEX1 0.021 0.023 -10000 0 -10000 0 0
SERPINE1 -0.1 0.2 -10000 0 -0.62 12 12
FLT1 -0.019 0.19 -10000 0 -0.65 31 31
ADORA2A -0.027 0.16 0.37 3 -0.59 7 10
germ cell development -0.034 0.16 -10000 0 -0.64 6 6
SLC11A2 -0.025 0.16 -10000 0 -0.61 6 6
BHLHE40 -0.027 0.16 -10000 0 -0.61 6 6
HIF1AN 0.021 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.011 0.12 -10000 0 -0.38 4 4
ETS1 0.033 0.035 -10000 0 -0.39 3 3
CITED2 0.016 0.11 -10000 0 -0.73 7 7
KDR -0.012 0.18 -10000 0 -0.7 20 20
PGK1 -0.025 0.16 -10000 0 -0.61 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 -0.005 0.077 0.22 1 -0.32 6 7
SP1 0.032 0.012 -10000 0 -10000 0 0
ABCG2 -0.029 0.16 -10000 0 -0.62 9 9
EFNA1 -0.024 0.16 -10000 0 -0.6 6 6
FXN -0.025 0.16 0.37 3 -0.59 7 10
POU5F1 -0.036 0.17 -10000 0 -0.66 6 6
neuron apoptosis 0.017 0.18 0.67 7 -10000 0 7
EP300 0.025 0.031 -10000 0 -0.45 2 2
EGLN3 -0.002 0.1 -10000 0 -0.42 26 26
EGLN2 0.021 0.021 -10000 0 -10000 0 0
EGLN1 0.022 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.044 0.024 -10000 0 -10000 0 0
VHL 0.025 0.009 -10000 0 -10000 0 0
ARNT 0.021 0.024 -10000 0 -10000 0 0
SLC2A1 -0.03 0.16 0.37 3 -0.6 9 12
TWIST1 -0.028 0.16 0.37 3 -0.61 10 13
ELK1 0.033 0.007 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.029 0.12 -10000 0 -10000 0 0
VEGFA -0.027 0.16 -10000 0 -0.62 6 6
CREBBP 0.027 0.005 -10000 0 -10000 0 0
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 0.049 -10000 0 -10000 0 0
DAPP1 0.024 0.1 0.24 18 -0.35 13 31
Src family/SYK family/BLNK-LAT/BTK-ITK 0.01 0.13 0.28 5 -0.46 11 16
mol:DAG 0.016 0.076 0.2 23 -0.22 2 25
HRAS 0.027 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 0.026 0.022 -10000 0 -0.45 1 1
PLCG1 0.027 0.006 -10000 0 -10000 0 0
ARF5 0.026 0.007 -10000 0 -10000 0 0
mol:GTP -0.004 0.039 0.17 2 -10000 0 2
ARF1/GTP 0.007 0.04 0.24 2 -10000 0 2
RHOA 0.025 0.009 -10000 0 -10000 0 0
YES1 0.025 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.004 0.041 0.17 1 -10000 0 1
ADAP1 -0.005 0.038 -10000 0 -10000 0 0
ARAP3 -0.004 0.039 0.17 2 -10000 0 2
INPPL1 0.024 0.01 -10000 0 -10000 0 0
PREX1 0.027 0.006 -10000 0 -10000 0 0
ARHGEF6 0.023 0.048 -10000 0 -0.45 5 5
ARHGEF7 0.027 0.006 -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 0.027 0.019 -10000 0 -0.39 1 1
ARF6 0.026 0.007 -10000 0 -10000 0 0
FGR 0.027 0.019 -10000 0 -0.39 1 1
mol:Ca2+ 0.011 0.047 0.18 7 -10000 0 7
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.021 0.053 -10000 0 -0.45 6 6
ZAP70 0.006 0.094 -10000 0 -0.4 25 25
mol:IP3 0.01 0.057 0.18 14 -10000 0 14
LYN 0.024 0.021 -10000 0 -0.39 1 1
ARF1/GDP 0.029 0.067 -10000 0 -0.31 5 5
RhoA/GDP 0.039 0.046 0.23 6 -10000 0 6
PDK1/Src/Hsp90 0.049 0.025 -10000 0 -0.27 1 1
BLNK -0.016 0.14 -10000 0 -0.45 45 45
actin cytoskeleton reorganization 0.024 0.071 0.23 12 -0.39 1 13
SRC 0.026 0.007 -10000 0 -10000 0 0
PLEKHA2 -0.006 0.012 -10000 0 -0.27 1 1
RAC1 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.024 0.013 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.007 0.037 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.038 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.004 0.1 -10000 0 -0.34 17 17
BLK -0.035 0.15 -10000 0 -0.4 67 67
PDPK1 0.027 0.022 -10000 0 -0.45 1 1
CYTH1 -0.005 0.039 -10000 0 -10000 0 0
HCK 0.024 0.029 -10000 0 -0.42 2 2
CYTH3 -0.005 0.037 -10000 0 -10000 0 0
CYTH2 -0.006 0.036 -10000 0 -10000 0 0
KRAS 0.027 0.008 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.016 0.046 -10000 0 -0.44 1 1
SGK1 0.018 0.057 -10000 0 -0.34 5 5
INPP5D 0.025 0.031 -10000 0 -0.45 2 2
mol:GDP 0.015 0.065 -10000 0 -0.31 6 6
SOS1 0.028 0.004 -10000 0 -10000 0 0
SYK 0.024 0.037 -10000 0 -0.45 3 3
ARF6/GDP 0.024 0.044 0.23 4 -10000 0 4
mol:PI-3-4-5-P3 -0.006 0.034 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP -0.004 0.041 0.17 1 -10000 0 1
VAV1 0.02 0.06 -10000 0 -0.44 8 8
mol:PI-3-4-P2 0.012 0.016 -10000 0 -0.32 1 1
RAS family/GTP/PI3K Class I 0.043 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 -0.31 5 5
LAT 0.016 0.07 -10000 0 -0.39 14 14
Rac1/GTP 0.02 0.06 0.19 1 -0.35 2 3
ITK -0.012 0.045 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.014 0.093 0.23 21 -0.28 5 26
LCK 0.017 0.065 -10000 0 -0.39 12 12
BTK -0.006 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 0.024 0.064 -10000 0 -0.35 10 10
calcium ion-dependent exocytosis 0.013 0.031 -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 -0.22 6 6
CTNNB1 0.025 0.009 -10000 0 -10000 0 0
membrane fusion 0.014 0.025 -10000 0 -10000 0 0
CTNND1 0.019 0.035 0.18 19 -10000 0 19
DNM2 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.051 0.2 9 -0.4 2 11
TSHR 0.004 0.04 -10000 0 -0.23 13 13
INS 0.004 0.089 -10000 0 -0.46 16 16
BIN1 0.021 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+ 0.026 0.013 -10000 0 -0.21 1 1
JUP 0.013 0.031 -10000 0 -0.29 3 3
ASAP2/amphiphysin II 0.045 0.037 -10000 0 -0.22 8 8
ARF6/GTP 0.02 0.005 -10000 0 -10000 0 0
CDH1 0.014 0.03 -10000 0 -0.28 2 2
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 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.022 0.029 -10000 0 -0.28 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.028 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.035 0.052 0.33 4 -10000 0 4
positive regulation of phagocytosis 0.014 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 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 0.029 0.058 -10000 0 -0.4 4 4
JIP4/KLC1 0.049 0.016 -10000 0 -10000 0 0
EXOC1 0.027 0.005 -10000 0 -10000 0 0
exocyst 0.022 0.029 -10000 0 -0.28 2 2
RALA/GTP 0.02 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.019 0.005 -10000 0 -10000 0 0
CTNNA1 0.019 0.036 0.18 21 -10000 0 21
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 0.005 0.039 -10000 0 -0.32 2 2
VAMP3 0.014 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.055 0.11 -10000 0 -0.32 10 10
EXOC6 0.027 0.005 -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 0.007 -10000 0 -10000 0 0
PIP5K1C 0.015 0.027 -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 0.028 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.037 0.054 -10000 0 -0.34 4 4
mol:Phosphatidic acid 0.014 0.025 -10000 0 -10000 0 0
endocytosis -0.044 0.037 0.22 8 -10000 0 8
SCAMP2 0.027 0.005 -10000 0 -10000 0 0
ADRB2 0.01 0.079 0.27 1 -0.4 5 6
EXOC3 0.024 0.01 -10000 0 -10000 0 0
ASAP2 0.028 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.03 0.014 -10000 0 -0.21 1 1
KLC1 0.026 0.007 -10000 0 -10000 0 0
AVPR2 0.02 0.09 0.28 5 -0.36 8 13
RALA 0.027 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 0.074 0.22 3 -0.35 3 6
adherens junction organization 0.011 0.095 0.22 1 -0.36 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.084 0.27 3 -0.46 2 5
FMN1 0.006 0.099 -10000 0 -0.37 13 13
mol:IP3 0.011 0.045 -10000 0 -0.38 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.023 0.086 -10000 0 -0.34 13 13
CTNNB1 0.025 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.05 0.19 1 -0.42 2 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.001 0.16 -10000 0 -0.68 18 18
CTNND1 0.03 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.08 -10000 0 -0.34 11 11
VASP 0.019 0.079 -10000 0 -0.34 11 11
ZYX 0.021 0.075 -10000 0 -0.34 10 10
JUB 0.02 0.081 -10000 0 -0.33 13 13
EGFR(dimer) 0.026 0.091 -10000 0 -0.35 13 13
E-cadherin/beta catenin-gamma catenin 0.042 0.043 -10000 0 -0.36 4 4
mol:PI-3-4-5-P3 0.022 0.062 0.21 1 -0.44 2 3
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.022 0.063 0.22 1 -0.45 2 3
FYN 0.024 0.074 0.23 6 -0.4 2 8
mol:Ca2+ 0.011 0.044 -10000 0 -0.37 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 0.045 -10000 0 -0.38 2 2
CDH1 0.023 0.047 -10000 0 -0.44 5 5
RhoA/GDP 0.061 0.081 0.26 4 -0.45 2 6
establishment of polarity of embryonic epithelium 0.019 0.078 -10000 0 -0.34 11 11
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
EGFR 0.02 0.048 -10000 0 -0.45 5 5
CASR 0.024 0.064 0.22 4 -0.36 2 6
RhoA/GTP 0.048 0.066 -10000 0 -0.34 2 2
AKT2 0.01 0.052 0.19 1 -0.42 2 3
actin cable formation 0.003 0.098 0.25 1 -0.36 14 15
apoptosis -0.042 0.08 0.35 4 -0.23 9 13
CTNNA1 0.029 0.008 -10000 0 -10000 0 0
mol:GDP 0.036 0.079 -10000 0 -0.49 2 2
PIP5K1A 0.018 0.081 -10000 0 -0.34 11 11
PLCG1 0.011 0.045 -10000 0 -0.39 2 2
Rac1/GTP 0.033 0.087 -10000 0 -0.43 5 5
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.062 -10000 0 -0.27 17 17
forebrain development -0.022 0.13 -10000 0 -0.47 17 17
GNAO1 0.023 0.04 -10000 0 -0.41 4 4
SMO/beta Arrestin2 0.024 0.067 -10000 0 -0.32 17 17
SMO 0.008 0.089 -10000 0 -0.45 18 18
ARRB2 0.026 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.048 0.081 0.25 5 -0.37 3 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.025 0.009 -10000 0 -10000 0 0
GNAI2 0.024 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.026 -10000 0 -0.21 1 1
GNAI1 0.026 0.022 -10000 0 -0.45 1 1
XPO1 0.024 0.016 -10000 0 -10000 0 0
GLI1/Su(fu) -0.02 0.14 -10000 0 -0.52 15 15
SAP30 0.026 0.02 -10000 0 -0.39 1 1
mol:GDP 0.008 0.089 -10000 0 -0.45 18 18
MIM/GLI2A 0.017 0.029 -10000 0 -10000 0 0
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GLI2 0.016 0.073 0.21 1 -0.34 1 2
GLI3 0.036 0.082 0.25 6 -0.37 4 10
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.02 -10000 0 -0.39 1 1
Gi family/GTP 0.008 0.072 -10000 0 -0.26 23 23
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.084 -10000 0 -0.42 6 6
GLI2/Su(fu) 0.021 0.079 -10000 0 -0.33 6 6
FOXA2 -0.017 0.13 -10000 0 -0.88 3 3
neural tube patterning -0.022 0.13 -10000 0 -0.47 17 17
SPOP 0.028 0.002 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.055 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
CSNK1G3 0.026 0.007 -10000 0 -10000 0 0
MTSS1 0.017 0.029 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.022 0.13 -10000 0 -0.47 17 17
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 0.1 0.27 3 -0.44 5 8
GLI3A/CBP 0.003 0.08 -10000 0 -0.34 4 4
KIF3A 0.026 0.007 -10000 0 -10000 0 0
GLI1 -0.023 0.14 -10000 0 -0.48 17 17
RAB23 0.025 0.027 -10000 0 -0.39 2 2
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
IFT172 0.028 0.003 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.058 -10000 0 -0.32 2 2
GNAZ 0.011 0.083 -10000 0 -0.41 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 0.005 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.027 0.075 -10000 0 -0.32 1 1
STK36 0.023 0.016 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.005 0.073 -10000 0 -0.4 9 9
PTCH1 -0.023 0.16 -10000 0 -0.83 9 9
MIM/GLI1 -0.017 0.14 -10000 0 -0.51 9 9
CREBBP 0.003 0.08 -10000 0 -0.34 4 4
Su(fu)/SIN3/HDAC complex 0.013 0.091 -10000 0 -0.45 12 12
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 0.017 0.04 -10000 0 -0.41 4 4
positive regulation of NF-kappaB transcription factor activity 0.019 0.053 -10000 0 -0.28 13 13
MAP2K4 0.043 0.054 0.22 1 -0.41 1 2
IKBKB 0.026 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.025 0.023 -10000 0 -0.45 1 1
SMPD1 0.009 0.015 -10000 0 -0.18 1 1
IKBKG 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.013 0.074 -10000 0 -0.4 15 15
TRAIL/TRAILR2 0.025 0.035 -10000 0 -0.29 4 4
TRAIL/TRAILR3 0.019 0.054 -10000 0 -0.28 13 13
TRAIL/TRAILR1 0.025 0.035 -10000 0 -0.29 4 4
TRAIL/TRAILR4 0.019 0.053 -10000 0 -0.28 13 13
TRAIL/TRAILR1/DAP3/GTP 0.033 0.035 -10000 0 -0.22 4 4
IKK complex 0.021 0.035 -10000 0 -10000 0 0
RIPK1 0.027 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) 0.013 0.074 -10000 0 -0.4 15 15
TRADD 0.027 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.025 0.023 -10000 0 -0.45 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.021 0.04 -10000 0 -0.36 1 1
CFLAR 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.008 0.028 -10000 0 -0.29 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.036 0.047 -10000 0 -10000 0 0
mol:ceramide 0.009 0.015 -10000 0 -0.18 1 1
FADD 0.02 0.013 -10000 0 -10000 0 0
MAPK8 0.052 0.065 0.28 3 -0.39 1 4
TRAF2 0.022 0.046 -10000 0 -0.39 6 6
TRAILR3 (trimer) 0.013 0.074 -10000 0 -0.4 15 15
CHUK 0.027 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.026 0.037 -10000 0 -0.24 4 4
DAP3 0.028 0.004 -10000 0 -10000 0 0
CASP10 0.07 0.097 0.34 25 -0.29 1 26
JNK cascade 0.019 0.053 -10000 0 -0.28 13 13
TRAIL (trimer) 0.017 0.04 -10000 0 -0.41 4 4
TNFRSF10C 0.013 0.074 -10000 0 -0.4 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD 0.03 0.04 -10000 0 -0.23 1 1
TRAIL/TRAILR2/FADD 0.026 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 0.021 0.04 -10000 0 -0.29 2 2
TRAILR2 (trimer) 0.026 0.008 -10000 0 -10000 0 0
CASP8 0.001 0.08 -10000 0 -0.51 10 10
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.036 0.047 -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 0.026 0.008 -10000 0 -10000 0 0
NFATC1 0.026 0.093 0.25 6 -0.38 4 10
NFATC2 0.008 0.083 0.21 4 -0.29 18 22
NFATC3 0.02 0.018 -10000 0 -0.34 1 1
YWHAE 0.027 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.001 0.078 0.2 5 -0.29 14 19
Exportin 1/Ran/NUP214 0.054 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.012 0.09 -10000 0 -0.32 9 9
BCL2/BAX 0.034 0.032 -10000 0 -0.29 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.02 0.008 -10000 0 -10000 0 0
BAX 0.027 0.005 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.01 0.079 0.23 2 -0.32 8 10
Calcineurin A alpha-beta B1/BCL2 0.022 0.04 -10000 0 -0.41 4 4
FKBP8 0.028 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.01 0.079 0.31 8 -0.22 2 10
KPNB1 0.028 0.002 -10000 0 -10000 0 0
KPNA2 0.028 0.004 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
SFN 0.023 0.045 -10000 0 -0.42 5 5
MAP3K8 0.024 0.037 -10000 0 -0.45 3 3
NFAT4/CK1 alpha 0.03 0.021 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.046 0.096 0.26 1 -0.4 6 7
CABIN1 -0.001 0.078 0.21 5 -0.29 14 19
CALM1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
MAP3K1 0.027 0.007 -10000 0 -10000 0 0
CAMK4 0.003 0.097 -10000 0 -0.4 27 27
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.028 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 0.007 -10000 0 -10000 0 0
MAPK8 0.022 0.052 -10000 0 -0.45 6 6
MAPK9 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.036 0.098 0.26 3 -0.39 4 7
PRKCH 0.026 0.007 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.038 0.026 -10000 0 -0.31 2 2
CASP3 0.027 0.007 -10000 0 -10000 0 0
PIM1 0.026 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 0.041 -10000 0 -0.28 2 2
PRKCB 0.02 0.054 -10000 0 -0.4 8 8
PRKCE 0.027 0.022 -10000 0 -0.45 1 1
JNK2/NFAT4 0.029 0.041 -10000 0 -0.31 1 1
BAD/BCL-XL 0.037 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 0.026 0.029 -10000 0 -0.42 2 2
PRKCG -0.031 0.13 -10000 0 -0.39 54 54
PRKCQ 0.017 0.069 -10000 0 -0.44 11 11
FKBP38/BCL2 0.035 0.032 -10000 0 -0.28 4 4
EP300 0.025 0.031 -10000 0 -0.45 2 2
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.007 -10000 0 -10000 0 0
NFATc/JNK1 0.037 0.095 0.26 3 -0.35 5 8
CaM/Ca2+/FKBP38 0.035 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.02 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 0.038 0.094 0.26 5 -0.36 4 9
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.012 0.09 -10000 0 -0.32 9 9
NR4A1 0.019 0.1 0.25 5 -0.45 12 17
GSK3B 0.025 0.009 -10000 0 -10000 0 0
positive T cell selection 0.02 0.018 -10000 0 -0.34 1 1
NFAT1/CK1 alpha 0.01 0.059 0.16 1 -0.27 9 10
RCH1/ KPNB1 0.041 0.006 -10000 0 -10000 0 0
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
AKAP5 0.005 0.092 -10000 0 -0.39 25 25
MEF2D 0.027 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.038 0.092 0.26 3 -0.35 3 6
CREBBP 0.027 0.008 -10000 0 -10000 0 0
BCL2 0.022 0.04 -10000 0 -0.41 4 4
FoxO family signaling

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
G6PC 0.007 0.046 -10000 0 -10000 0 0
PLK1 0.039 0.12 -10000 0 -0.82 2 2
CDKN1B 0.078 0.1 0.31 8 -0.37 4 12
FOXO3 0.056 0.11 -10000 0 -0.67 4 4
KAT2B 0.015 0.087 -10000 0 -0.45 16 16
FOXO1/SIRT1 0.028 0.045 -10000 0 -10000 0 0
CAT 0.044 0.13 -10000 0 -0.9 3 3
CTNNB1 0.024 0.009 -10000 0 -10000 0 0
AKT1 0.033 0.016 -10000 0 -10000 0 0
FOXO1 0.014 0.047 0.23 2 -10000 0 2
MAPK10 0.025 0.07 0.2 29 -0.22 22 51
mol:GTP 0.002 0 -10000 0 -10000 0 0
FOXO4 0.053 0.066 0.3 5 -0.39 1 6
response to oxidative stress 0.01 0.008 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.056 0.11 -10000 0 -0.77 3 3
XPO1 0.028 0.004 -10000 0 -10000 0 0
EP300 0.026 0.031 -10000 0 -0.45 2 2
BCL2L11 0.033 0.04 -10000 0 -0.66 1 1
FOXO1/SKP2 0.024 0.043 -10000 0 -10000 0 0
mol:GDP 0.01 0.008 -10000 0 -10000 0 0
RAN 0.029 0.003 -10000 0 -10000 0 0
GADD45A 0.064 0.12 -10000 0 -0.56 10 10
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.037 0.1 -10000 0 -0.44 11 11
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 0.078 0.23 1 -0.38 7 8
YWHAB 0.026 0.007 -10000 0 -10000 0 0
MAPK8 0.035 0.05 0.2 29 -0.22 5 34
MAPK9 0.036 0.042 0.2 28 -10000 0 28
YWHAG 0.027 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
SIRT1 0.027 0.024 -10000 0 -0.44 1 1
SOD2 0.069 0.092 -10000 0 -0.54 1 1
RBL2 0.039 0.17 -10000 0 -0.71 16 16
RAL/GDP 0.045 0.014 -10000 0 -10000 0 0
CHUK 0.033 0.015 -10000 0 -10000 0 0
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
RAL/GTP 0.048 0.015 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.018 0.23 -10000 0 -1.3 13 13
SKP2 0.025 0.009 -10000 0 -10000 0 0
USP7 0.029 0.005 -10000 0 -10000 0 0
IKBKB 0.031 0.016 -10000 0 -10000 0 0
CCNB1 0.042 0.11 -10000 0 -0.75 2 2
FOXO1-3a-4/beta catenin 0.084 0.092 0.33 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.042 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
SGK1 0.031 0.032 -10000 0 -0.41 2 2
CSNK1G3 0.026 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.008 -10000 0 -10000 0 0
ZFAND5 0.052 0.066 0.39 2 -10000 0 2
SFN 0.023 0.045 -10000 0 -0.42 5 5
CDK2 0.028 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.037 0.081 -10000 0 -0.36 8 8
CREBBP 0.027 0.007 -10000 0 -10000 0 0
FBXO32 0.068 0.16 0.45 2 -1.1 3 5
BCL6 0.054 0.092 -10000 0 -10000 0 0
RALB 0.029 0.004 -10000 0 -10000 0 0
RALA 0.028 0.007 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.025 0.068 -10000 0 -0.29 21 21
AKT1 0.059 0.091 0.35 9 -0.47 2 11
PTK2B 0.018 0.071 0.34 1 -0.72 1 2
VEGFR2 homodimer/Frs2 0.034 0.035 -10000 0 -0.62 1 1
CAV1 -0.006 0.11 -10000 0 -0.39 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 0.11 0.36 18 -0.42 2 20
mol:Ca2+ 0.023 0.045 -10000 0 -0.44 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.057 0.047 -10000 0 -0.55 1 1
RP11-342D11.1 0.013 0.043 -10000 0 -0.43 2 2
CDH5 0.025 0.029 -10000 0 -0.42 2 2
VEGFA homodimer 0.055 0.04 -10000 0 -0.22 4 4
SHC1 0.028 0.004 -10000 0 -10000 0 0
SHC2 0.021 0.053 -10000 0 -0.42 7 7
HRAS/GDP 0.044 0.041 -10000 0 -0.47 1 1
SH2D2A -0.038 0.15 -10000 0 -0.39 77 77
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.05 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 0.026 0.02 -10000 0 -0.39 1 1
SHC/GRB2/SOS1 0.073 0.051 -10000 0 -0.51 1 1
GRB10 0.023 0.043 -10000 0 -0.53 1 1
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB2 0.028 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 0.065 0.056 -10000 0 -0.54 1 1
HRAS 0.026 0.021 -10000 0 -0.41 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.016 0.054 -10000 0 -0.37 3 3
HIF1A 0.025 0.023 -10000 0 -0.45 1 1
FRS2 0.027 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.055 0.046 -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 0.032 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.047 0.045 -10000 0 -0.58 1 1
mol:GDP 0.057 0.046 -10000 0 -0.5 1 1
mol:NADP 0.036 0.1 0.34 6 -0.4 8 14
eNOS/Hsp90 0.044 0.099 0.33 4 -0.39 6 10
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
mol:IP3 0.024 0.045 -10000 0 -0.44 2 2
HIF1A/ARNT 0.037 0.02 -10000 0 -0.32 1 1
SHB 0.025 0.009 -10000 0 -10000 0 0
VEGFA 0.024 0.038 -10000 0 -0.39 4 4
VEGFC -0.029 0.14 -10000 0 -0.39 65 65
FAK1/Vinculin 0.045 0.087 0.37 2 -0.7 1 3
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 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 0.007 -10000 0 -10000 0 0
EPAS1 0.034 0.02 -10000 0 -0.33 1 1
mol:L-citrulline 0.036 0.1 0.34 6 -0.4 8 14
ITGAV 0.025 0.027 -10000 0 -0.39 2 2
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.059 0.046 -10000 0 -0.55 1 1
VEGFR2 homodimer/VEGFA homodimer 0.051 0.047 -10000 0 -0.47 2 2
VEGFR2/3 heterodimer 0.03 0.05 -10000 0 -0.56 2 2
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.013 0.056 0.42 1 -0.55 1 2
VEGFR2 homodimer 0.021 0.038 -10000 0 -0.52 2 2
FLT1 0.026 0.02 -10000 0 -0.39 1 1
NEDD4 0.029 0.007 -10000 0 -10000 0 0
MAPK3 0.011 0.061 0.37 3 -0.49 1 4
MAPK1 0.013 0.062 0.33 5 -0.49 1 6
VEGFA145/NRP2 0.036 0.033 -10000 0 -0.27 5 5
VEGFR1/2 heterodimer 0.033 0.037 -10000 0 -0.62 1 1
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 0.069 0.34 6 -0.5 1 7
PI3K 0.033 0.051 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.04 0.044 -10000 0 -0.58 1 1
FES 0.025 0.048 0.35 1 -0.45 2 3
GAB1 0.033 0.053 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.045 -10000 0 -0.58 1 1
CTNNB1 0.025 0.009 -10000 0 -10000 0 0
SOS1 0.028 0.004 -10000 0 -10000 0 0
ARNT 0.027 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.034 0.11 0.35 4 -0.39 6 10
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 0.057 0.053 -10000 0 -0.54 1 1
PRKACA 0.028 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.01 0.098 -10000 0 -0.61 2 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.025 0.048 0.35 1 -0.45 2 3
actin cytoskeleton reorganization 0.008 0.1 -10000 0 -0.5 3 3
PTK2 0.022 0.061 0.3 1 -0.76 1 2
EDG1 0.013 0.043 -10000 0 -0.43 2 2
mol:DAG 0.024 0.045 -10000 0 -0.44 2 2
CaM/Ca2+ 0.037 0.049 -10000 0 -0.5 1 1
MAP2K3 0.008 0.047 -10000 0 -0.52 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.057 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 0.052 0.049 -10000 0 -0.55 1 1
IQGAP1 0.027 0.005 -10000 0 -10000 0 0
YES1 0.025 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.048 0.044 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.046 0.043 -10000 0 -0.58 1 1
cell migration 0.052 0.089 0.33 8 -0.6 1 9
mol:PI-3-4-5-P3 0.032 0.049 -10000 0 -0.53 1 1
FYN 0.027 0.019 -10000 0 -0.39 1 1
VEGFB/NRP1 0.028 0.043 -10000 0 -0.42 2 2
mol:NO 0.036 0.1 0.34 6 -0.4 8 14
PXN 0.028 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.035 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.04 0.042 -10000 0 -0.55 1 1
VHL 0.025 0.009 -10000 0 -10000 0 0
ITGB3 0.011 0.085 -10000 0 -0.41 19 19
NOS3 0.036 0.11 0.36 5 -0.45 8 13
VEGFR2 homodimer/VEGFA homodimer/Sck 0.045 0.051 -10000 0 -0.48 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.016 0.05 -10000 0 -0.51 1 1
PRKCB 0.013 0.054 -10000 0 -0.51 1 1
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 0.036 0.033 -10000 0 -0.27 5 5
MAPKKK cascade 0.036 0.046 -10000 0 -0.47 1 1
NRP2 0.025 0.027 -10000 0 -0.39 2 2
VEGFC homodimer -0.029 0.14 -10000 0 -0.39 65 65
NCK1 0.023 0.011 -10000 0 -10000 0 0
ROCK1 0.027 0.007 -10000 0 -10000 0 0
FAK1/Paxillin 0.044 0.088 0.37 2 -0.7 1 3
MAP3K13 0.013 0.046 -10000 0 -0.55 1 1
PDPK1 0.022 0.046 -10000 0 -0.48 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0 0.087 -10000 0 -0.35 13 13
KLHL20 0.026 0.069 0.19 9 -0.26 6 15
CYFIP2 0.025 0.029 -10000 0 -0.42 2 2
Rac1/GDP 0.025 0.077 0.33 5 -0.34 1 6
ENAH -0.006 0.1 -10000 0 -0.36 18 18
AP1M1 0.028 0.004 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.025 0.009 -10000 0 -10000 0 0
CDC42/GTP 0.021 0.035 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.03 -10000 0 -0.19 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.057 0.041 -10000 0 -0.24 5 5
RAPGEF1 0.001 0.095 0.29 2 -0.39 5 7
CTNND1 0.028 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.11 -10000 0 -0.35 23 23
CRK 0.006 0.093 -10000 0 -0.4 6 6
E-cadherin/gamma catenin/alpha catenin 0.048 0.046 -10000 0 -0.36 5 5
alphaE/beta7 Integrin 0.038 0.025 -10000 0 -0.32 2 2
IQGAP1 0.027 0.005 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.017 -10000 0 -10000 0 0
DLG1 0.001 0.079 -10000 0 -0.35 12 12
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 0.045 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 0.035 0.049 -10000 0 -0.43 5 5
TIAM1 0.021 0.053 -10000 0 -0.45 6 6
E-cadherin(dimer)/Ca2+ 0.053 0.036 -10000 0 -0.23 3 3
AKT1 0.011 0.029 0.14 1 -10000 0 1
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
CDH1 0.022 0.048 -10000 0 -0.45 5 5
RhoA/GDP 0.032 0.072 0.33 6 -0.32 1 7
actin cytoskeleton organization 0.023 0.054 0.15 17 -0.21 3 20
CDC42/GDP 0.028 0.079 0.33 6 -0.32 1 7
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.017 0.037 -10000 0 -0.36 4 4
ITGB7 0.026 0.03 -10000 0 -0.45 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.058 0.038 -10000 0 -0.25 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin 0.04 0.032 -10000 0 -0.22 5 5
mol:GDP 0.014 0.085 0.34 6 -0.39 1 7
CDC42/GTP/IQGAP1 0.036 0.008 -10000 0 -10000 0 0
JUP 0.026 0.03 -10000 0 -0.45 2 2
p120 catenin/RhoA/GDP 0.035 0.074 0.34 4 -0.3 1 5
RAC1/GTP/IQGAP1 0.035 0.011 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.04 0.008 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.037 0.12 6 -0.17 6 12
NME1 0.027 0.019 -10000 0 -0.39 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.004 0.098 -10000 0 -0.35 17 17
regulation of cell-cell adhesion 0.013 0.029 -10000 0 -10000 0 0
WASF2 0.013 0.028 -10000 0 -10000 0 0
Rap1/GTP 0.033 0.056 0.3 5 -0.29 1 6
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.069 0.049 -10000 0 -0.32 5 5
CCND1 0.013 0.044 0.15 5 -0.21 6 11
VAV2 0.016 0.11 -10000 0 -0.55 4 4
RAP1/GDP 0.037 0.066 0.33 5 -0.3 1 6
adherens junction assembly -0.003 0.096 -10000 0 -0.34 17 17
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 0.051 0.046 -10000 0 -0.42 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 -0.005 0.099 -10000 0 -0.35 18 18
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
Rac1/GTP -0.02 0.072 -10000 0 -0.41 8 8
E-cadherin/beta catenin/alpha catenin 0.045 0.037 -10000 0 -0.26 5 5
ITGAE 0.027 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.001 0.11 -10000 0 -0.36 23 23
Canonical NF-kappaB pathway

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.083 0.26 14 -0.34 4 18
ERC1 0.026 0.008 -10000 0 -10000 0 0
RIP2/NOD2 0.031 0.037 -10000 0 -0.3 5 5
NFKBIA 0.022 0.042 -10000 0 -10000 0 0
BIRC2 0.024 0.01 -10000 0 -10000 0 0
IKBKB 0.026 0.008 -10000 0 -10000 0 0
RIPK2 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.029 -10000 0 -10000 0 0
IKK complex/A20 0.048 0.094 0.27 1 -0.4 8 9
NEMO/A20/RIP2 0.025 0.009 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.042 0.087 0.26 1 -0.4 10 11
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.037 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.043 0.08 -10000 0 -0.39 8 8
BCL10/MALT1/TRAF6 0.049 0.02 -10000 0 -10000 0 0
NOD2 0.022 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 0.023 0.067 -10000 0 -0.28 22 22
TRAF6 0.027 0.006 -10000 0 -10000 0 0
PRKCA 0.026 0.029 -10000 0 -0.42 2 2
CHUK 0.027 0.005 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
TNF 0.008 0.088 -10000 0 -0.4 22 22
NF kappa B1 p50/RelA 0.057 0.029 -10000 0 -0.38 1 1
BCL10 0.027 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 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 0.053 0.092 0.26 2 -0.41 9 11
CYLD 0.027 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.06 0.095 0.27 1 -0.39 10 11
Aurora A 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
Aurora A/GADD45A 0.026 0.028 -10000 0 -0.22 1 1
BIRC5 0.009 0.087 -10000 0 -0.39 22 22
NFKBIA 0.012 0.041 0.25 12 -10000 0 12
CPEB1 -0.034 0.15 -10000 0 -0.44 62 62
AKT1 0.012 0.041 0.25 12 -10000 0 12
NDEL1 0.027 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 0.023 0.024 -10000 0 -10000 0 0
NDEL1/TACC3 0.046 0.035 -10000 0 -10000 0 0
GADD45A 0.027 0.019 -10000 0 -0.39 1 1
GSK3B 0.023 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.025 0.026 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.014 0.004 -10000 0 -10000 0 0
TP53 0.018 0.024 -10000 0 -0.29 2 2
DLG7 0.008 0.015 -10000 0 -10000 0 0
AURKAIP1 0.025 0.027 -10000 0 -0.39 2 2
ARHGEF7 0.027 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.049 0.036 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.023 0.024 -10000 0 -10000 0 0
AURKA 0.014 0.02 -10000 0 -10000 0 0
AURKB 0.012 0.016 -10000 0 -0.15 2 2
CDC25B 0.011 0.029 -10000 0 -0.23 1 1
G2/M transition checkpoint 0.007 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.007 0.084 -10000 0 -0.24 44 44
Aurora A/CPEB -0.007 0.085 -10000 0 -0.25 44 44
Aurora A/TACC1/TRAP/chTOG 0.057 0.044 -10000 0 -10000 0 0
BRCA1 0.028 0.003 -10000 0 -10000 0 0
centrosome duplication 0.025 0.026 -10000 0 -10000 0 0
regulation of centrosome cycle 0.045 0.034 -10000 0 -10000 0 0
spindle assembly 0.055 0.043 -10000 0 -10000 0 0
TDRD7 0.027 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.049 0.064 -10000 0 -0.31 4 4
CENPA 0.014 0.021 -10000 0 -0.18 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 0.012 0.026 -10000 0 -10000 0 0
negative regulation of DNA binding 0.017 0.028 -10000 0 -0.29 2 2
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.039 0.01 -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 -0.39 1 1
Aurora A/Antizyme1 0.05 0.036 -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 0.028 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.049 0.02 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.014 0.004 -10000 0 -10000 0 0
PPP2R5D 0.027 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 0.027 0.005 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.009 0.079 -10000 0 -10000 0 0
regulation of axonogenesis -0.005 0.026 0.23 1 -10000 0 1
myoblast fusion -0.017 0.061 0.29 3 -10000 0 3
mol:GTP 0.012 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 0.028 0.038 -10000 0 -10000 0 0
mol:GM1 0.004 0.028 -10000 0 -10000 0 0
mol:Choline 0.002 0.029 -10000 0 -0.27 3 3
lamellipodium assembly 0 0.061 -10000 0 -0.32 8 8
MAPK3 0.013 0.047 -10000 0 -0.19 5 5
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 0.017 0.061 -10000 0 -0.3 3 3
ARF1/GDP 0.02 0.066 -10000 0 -0.25 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 0.053 -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 -0.017 0.063 0.24 6 -10000 0 6
KALRN -0.008 0.07 -10000 0 -0.25 31 31
RAB11FIP3/RAB11A 0.04 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.063 -10000 0 -0.24 6 6
NME1 0.026 0.022 -10000 0 -0.39 1 1
Rac1/GDP 0.019 0.064 -10000 0 -0.25 7 7
substrate adhesion-dependent cell spreading 0.012 0.039 -10000 0 -0.16 4 4
cortical actin cytoskeleton organization 0 0.061 -10000 0 -0.32 8 8
RAC1 0.026 0.007 -10000 0 -10000 0 0
liver development 0.012 0.039 -10000 0 -0.16 4 4
ARF6/GTP 0.012 0.039 -10000 0 -0.16 4 4
RhoA/GTP 0.025 0.037 -10000 0 -10000 0 0
mol:GDP 0 0.052 -10000 0 -0.25 6 6
ARF6/GTP/RAB11FIP3/RAB11A 0.042 0.039 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
PLD1 0.005 0.037 -10000 0 -0.3 3 3
RAB11FIP3 0.027 0.004 -10000 0 -10000 0 0
tube morphogenesis 0 0.061 -10000 0 -0.32 8 8
ruffle organization 0.005 0.026 -10000 0 -0.23 1 1
regulation of epithelial cell migration 0.012 0.039 -10000 0 -0.16 4 4
PLD2 0.013 0.032 -10000 0 -10000 0 0
PIP5K1A 0.005 0.026 -10000 0 -0.23 1 1
mol:Phosphatidic acid 0.002 0.029 -10000 0 -0.27 3 3
Rac1/GTP 0 0.061 -10000 0 -0.32 8 8
Aurora C signaling

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
INCENP 0.027 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.042 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 0.02 0.053 -9999 0 -0.39 8 8
AURKC 0.022 0.049 -9999 0 -0.41 6 6
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.049 0.14 0.31 1 -0.37 18 19
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
AKT2 0.027 0.005 -10000 0 -10000 0 0
STXBP4 0.028 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.061 0.14 0.31 4 -0.38 24 28
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
YWHAQ 0.028 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 0.007 -10000 0 -10000 0 0
SNARE/Synip 0.054 0.014 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
ASIP 0.002 0.063 -10000 0 -0.39 11 11
PRKCI 0.02 0.013 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
RHOQ 0.028 0.003 -10000 0 -10000 0 0
GYS1 0.012 0.012 0.25 1 -10000 0 1
PRKCZ 0.026 0.022 -10000 0 -0.45 1 1
TRIP10 0.028 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.007 -10000 0 -10000 0 0
AS160/14-3-3 0.03 0.041 -10000 0 -0.3 1 1
VAMP2 0.027 0.006 -10000 0 -10000 0 0
SLC2A4 -0.068 0.15 0.32 4 -0.42 24 28
STX4 0.028 0.004 -10000 0 -10000 0 0
GSK3B 0.019 0.01 -10000 0 -10000 0 0
SFN 0.023 0.045 -10000 0 -0.42 5 5
LNPEP 0.025 0.031 -10000 0 -0.45 2 2
YWHAE 0.027 0.006 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.023 0.061 0.25 7 -10000 0 7
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 0.023 0.039 -10000 0 -0.41 4 4
RhoA/GTP 0.023 0.062 -10000 0 -0.26 7 7
negative regulation of cAMP metabolic process 0.019 0.052 -10000 0 -0.27 8 8
GNAZ 0.011 0.083 -10000 0 -0.41 18 18
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.007 -10000 0 -10000 0 0
S1PR5 0.024 0.041 -10000 0 -0.42 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.019 0.052 -10000 0 -0.27 8 8
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
RHOA 0.025 0.009 -10000 0 -10000 0 0
GNAI1 0.026 0.022 -10000 0 -0.45 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.048 0.065 -10000 0 -0.28 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 0.068 -10000 0 -0.29 1 1
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.027 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.005 -10000 0 -10000 0 0
FKBP3 0.027 0.006 -10000 0 -10000 0 0
Histones 0.053 0.058 -10000 0 -10000 0 0
YY1/LSF 0.008 0.079 -10000 0 -0.32 8 8
SMG5 0.028 0.004 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.018 0.036 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.026 0.05 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA 0.021 0.046 0.28 1 -0.28 3 4
HDAC1/Smad7 0.048 0.021 -10000 0 -10000 0 0
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
HDAC3/TR2 0.029 0.05 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.037 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.033 0.067 0.25 2 -0.33 3 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.023 0.03 -10000 0 -0.42 2 2
GATA1 0.018 0.026 -10000 0 -0.39 1 1
Mad/Max 0.036 0.034 -10000 0 -0.32 4 4
NuRD/MBD3 Complex/GATA1/Fog1 0.032 0.052 -10000 0 -0.3 1 1
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 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.007 -10000 0 -10000 0 0
NFKBIA 0.015 0.029 -10000 0 -10000 0 0
KAT2B 0.009 0.084 -10000 0 -0.45 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.027 0.014 -10000 0 -10000 0 0
SIN3 complex 0.064 0.026 -10000 0 -0.21 1 1
SMURF1 0.026 0.008 -10000 0 -10000 0 0
CHD3 0.027 0.006 -10000 0 -10000 0 0
SAP30 0.026 0.02 -10000 0 -0.39 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.027 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.007 0.07 -10000 0 -0.35 5 5
YY1/HDAC2 0.008 0.079 -10000 0 -0.32 8 8
YY1/HDAC1 0.008 0.079 -10000 0 -0.32 8 8
NuRD/MBD2 Complex (MeCP1) 0.034 0.028 -10000 0 -10000 0 0
PPARG -0.07 0.14 -10000 0 -0.28 152 152
HDAC8/hEST1B 0.055 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 0.049 -10000 0 -10000 0 0
MBD3L2 -0.018 0.026 -10000 0 -0.39 2 2
ubiquitin-dependent protein catabolic process 0.047 0.021 -10000 0 -10000 0 0
CREBBP 0.027 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.03 0.049 -10000 0 -0.31 1 1
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.016 0.029 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
YY1 0.01 0.05 -10000 0 -0.26 15 15
HDAC8 0.028 0.003 -10000 0 -10000 0 0
SMAD7 0.026 0.008 -10000 0 -10000 0 0
NCOR2 0.028 0.004 -10000 0 -10000 0 0
MXD1 0.023 0.048 -10000 0 -0.45 5 5
STAT3 0.021 0.026 -10000 0 -0.36 2 2
NFKB1 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.079 -10000 0 -0.3 7 7
YY1/SAP30/HDAC1 0.022 0.079 -10000 0 -0.3 8 8
EP300 0.025 0.031 -10000 0 -0.45 2 2
STAT3 (dimer non-phopshorylated) 0.021 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 0.036 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.024 0.037 -10000 0 -0.32 1 1
nuclear export -0.054 0.012 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GATAD2B 0.028 0.004 -10000 0 -10000 0 0
GATAD2A 0.028 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.025 0.049 -10000 0 -0.29 1 1
GATA1/HDAC1 0.038 0.017 -10000 0 -0.28 1 1
GATA1/HDAC3 0.027 0.05 -10000 0 -10000 0 0
CHD4 0.026 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.023 0.067 -10000 0 -0.28 22 22
SIN3/HDAC complex/Mad/Max 0.03 0.038 -10000 0 -0.3 2 2
NuRD Complex 0.03 0.054 -10000 0 -0.33 2 2
positive regulation of chromatin silencing 0.051 0.056 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.04 0.032 -10000 0 -0.22 1 1
HDAC complex 0.067 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.037 0.018 -10000 0 -0.28 1 1
FKBP25/HDAC1/HDAC2 0.052 0.017 -10000 0 -10000 0 0
TNF 0.008 0.088 -10000 0 -0.4 22 22
negative regulation of cell growth 0.026 0.043 -10000 0 -0.3 2 2
NuRD/MBD2/PRMT5 Complex 0.034 0.028 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.032 -10000 0 -0.23 1 1
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 0.028 0.003 -10000 0 -10000 0 0
NR2C1 0.028 0.003 -10000 0 -10000 0 0
MBD3 0.027 0.005 -10000 0 -10000 0 0
MBD2 0.026 0.008 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.02 -9999 0 -0.39 1 1
Rac1/GDP 0.025 0.011 -9999 0 -10000 0 0
DOCK1 0.026 0.022 -9999 0 -0.45 1 1
ITGA4 0.021 0.053 -9999 0 -0.39 8 8
RAC1 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.034 0.047 -9999 0 -0.29 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.039 -9999 0 -0.23 8 8
alpha4/beta7 Integrin/Paxillin 0.04 0.039 -9999 0 -0.25 2 2
lamellipodium assembly 0.012 0.062 -9999 0 -0.34 10 10
PIK3CA 0.02 0.013 -9999 0 -10000 0 0
PI3K 0.027 0.03 -9999 0 -0.32 2 2
ARF6 0.026 0.007 -9999 0 -10000 0 0
TLN1 0.024 0.01 -9999 0 -10000 0 0
PXN 0.015 0.002 -9999 0 -10000 0 0
PIK3R1 0.024 0.038 -9999 0 -0.45 3 3
ARF6/GTP 0.049 0.037 -9999 0 -10000 0 0
cell adhesion 0.046 0.037 -9999 0 -10000 0 0
CRKL/CBL 0.035 0.02 -9999 0 -0.28 1 1
alpha4/beta1 Integrin/Paxillin 0.04 0.035 -9999 0 -10000 0 0
ITGB1 0.027 0.005 -9999 0 -10000 0 0
ITGB7 0.026 0.03 -9999 0 -0.45 2 2
ARF6/GDP 0.025 0.011 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.028 0.087 -9999 0 -0.38 2 2
p130Cas/Crk/Dock1 0.051 0.022 -9999 0 -0.27 1 1
VCAM1 -0.017 0.13 -9999 0 -0.4 51 51
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.038 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.038 -9999 0 -10000 0 0
BCAR1 0.027 0.006 -9999 0 -10000 0 0
mol:GDP -0.052 0.037 -9999 0 -10000 0 0
CBL 0.025 0.008 -9999 0 -10000 0 0
PRKACA 0.028 0.004 -9999 0 -10000 0 0
GIT1 0.028 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.038 -9999 0 -10000 0 0
Rac1/GTP 0.011 0.068 -9999 0 -0.37 10 10
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.044 0.047 -9999 0 -0.36 5 5
E-cadherin/beta catenin 0.032 0.038 -9999 0 -0.31 5 5
CTNNB1 0.025 0.009 -9999 0 -10000 0 0
JUP 0.026 0.03 -9999 0 -0.45 2 2
CDH1 0.022 0.048 -9999 0 -0.45 5 5
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.025 0.008 -10000 0 -10000 0 0
SMAD2 0.004 0.05 0.26 2 -0.26 3 5
SMAD3 0.026 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 0.026 0.088 -10000 0 -0.45 14 14
SMAD4/Ubc9/PIASy 0.049 0.02 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.046 0.059 0.24 1 -10000 0 1
PPM1A 0.026 0.007 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.049 0.24 1 -0.24 3 4
MAP3K1 0.027 0.007 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.026 0.065 -10000 0 -0.32 16 16
MAPK3 0.028 0.004 -10000 0 -10000 0 0
MAPK1 0.027 0.006 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
CTDSP1 0.027 0.006 -10000 0 -10000 0 0
CTDSP2 0.028 0.004 -10000 0 -10000 0 0
CTDSPL 0.025 0.009 -10000 0 -10000 0 0
KPNB1 0.028 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 0.027 0.006 -10000 0 -10000 0 0
KPNA2 0.028 0.004 -10000 0 -10000 0 0
PIAS4 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.06 0.03 -9999 0 -0.21 1 1
HDAC3 0.027 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.037 0.017 -9999 0 -0.28 1 1
GATA1/HDAC5 0.039 0.016 -9999 0 -0.28 1 1
GATA2/HDAC5 0.035 0.026 -9999 0 -0.3 2 2
HDAC5/BCL6/BCoR 0.04 0.027 -9999 0 -10000 0 0
HDAC9 0.007 0.089 -9999 0 -0.39 23 23
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.019 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.038 0.012 -9999 0 -10000 0 0
HDAC5/YWHAB 0.039 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.005 -9999 0 -10000 0 0
GATA2 0.023 0.03 -9999 0 -0.42 2 2
HDAC4/RFXANK 0.039 0.017 -9999 0 -0.28 1 1
BCOR 0.027 0.022 -9999 0 -0.45 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.027 0.005 -9999 0 -10000 0 0
HDAC5 0.028 0.003 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.018 -9999 0 -0.28 1 1
Histones 0.025 0.039 -9999 0 -10000 0 0
ADRBK1 0.026 0.008 -9999 0 -10000 0 0
HDAC4 0.027 0.006 -9999 0 -10000 0 0
XPO1 0.028 0.004 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.01 -9999 0 -10000 0 0
HDAC4/Ubc9 0.039 0.01 -9999 0 -10000 0 0
HDAC7 0.028 0.003 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.04 0.009 -9999 0 -10000 0 0
TUBA1B 0.028 0.003 -9999 0 -10000 0 0
HDAC6 0.028 0.004 -9999 0 -10000 0 0
HDAC5/RFXANK 0.04 0.015 -9999 0 -0.28 1 1
CAMK4 0.003 0.097 -9999 0 -0.4 27 27
Tubulin/HDAC6 0.053 0.016 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.026 0.007 -9999 0 -10000 0 0
GATA1 0.018 0.026 -9999 0 -0.39 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.027 0.006 -9999 0 -10000 0 0
NR3C1 0.027 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.041 0.028 -9999 0 -0.2 1 1
SRF 0.027 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.038 0.012 -9999 0 -10000 0 0
Tubulin 0.039 0.01 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.038 0.012 -9999 0 -10000 0 0
GNB1 0.027 0.006 -9999 0 -10000 0 0
RANGAP1 0.027 0.005 -9999 0 -10000 0 0
BCL6/BCoR 0.029 0.019 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.017 -9999 0 -10000 0 0
HDAC4/SRF 0.034 0.067 -9999 0 -0.24 26 26
HDAC4/ER alpha 0.021 0.076 -9999 0 -0.29 27 27
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.025 0.039 -9999 0 -10000 0 0
cell motility 0.052 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 0.01 -9999 0 -10000 0 0
BCL6 0.02 0.013 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.027 0.006 -9999 0 -10000 0 0
Hsp90/HDAC6 0.038 0.012 -9999 0 -10000 0 0
ESR1 0.003 0.1 -9999 0 -0.42 27 27
HDAC6/HDAC11 0.035 0.022 -9999 0 -0.32 1 1
Ran/GTP/Exportin 1 0.042 0.032 -9999 0 -0.23 1 1
NPC 0.016 0.002 -9999 0 -10000 0 0
MEF2C 0.017 0.064 -9999 0 -0.42 10 10
RAN 0.028 0.003 -9999 0 -10000 0 0
HDAC4/MEF2C 0.068 0.049 -9999 0 -0.24 4 4
GNG2 0.025 0.02 -9999 0 -0.39 1 1
NCOR2 0.028 0.004 -9999 0 -10000 0 0
TUBB2A 0.027 0.006 -9999 0 -10000 0 0
HDAC11 0.024 0.023 -9999 0 -0.45 1 1
HSP90AA1 0.026 0.007 -9999 0 -10000 0 0
RANBP2 0.028 0.003 -9999 0 -10000 0 0
ANKRA2 0.027 0.006 -9999 0 -10000 0 0
RFXANK 0.027 0.019 -9999 0 -0.39 1 1
nuclear import -0.033 0.013 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.037 0.02 -10000 0 -0.32 1 1
FBXW11 0.027 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.024 0.038 -10000 0 -0.26 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.049 0.22 5 -0.28 1 6
NFKBIA 0.016 0.034 -10000 0 -0.23 3 3
MAPK14 0.027 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0.011 -10000 0 -10000 0 0
ARRB2 0.015 0.004 -10000 0 -10000 0 0
REL 0.019 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 -0.27 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.012 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.02 0.007 -10000 0 -10000 0 0
PIK3R1 0.024 0.038 -10000 0 -0.45 3 3
NFKB1 0.013 0.005 -10000 0 -10000 0 0
RELA 0.027 0.007 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.018 0.032 -10000 0 -0.27 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.034 0.051 0.23 3 -0.27 2 5
SRC 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.027 0.03 -10000 0 -0.32 2 2
NF kappa B1 p50/RelA 0.018 0.033 -10000 0 -0.27 1 1
IKBKB 0.026 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 0.037 -10000 0 -0.45 3 3
I kappa B alpha/PIK3R1 0.031 0.055 0.22 8 -0.26 3 11
cell death 0.032 0.049 0.22 2 -0.26 2 4
NF kappa B1 p105/c-Rel 0.024 0.038 -10000 0 -0.26 8 8
LCK 0.017 0.065 -10000 0 -0.39 12 12
BCL3 0.026 0.022 -10000 0 -0.45 1 1
PLK2 and PLK4 events

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
PLK2 0.025 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
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 0.008 -9999 0 -10000 0 0
FBXW11 0.027 0.007 -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 0.005 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.074 0.034 -9999 0 -10000 0 0
NFKB1 0.027 0.005 -9999 0 -10000 0 0
MAP3K14 0.028 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.037 0.03 -9999 0 -0.28 4 4
RELB 0.024 0.038 -9999 0 -0.39 4 4
NFKB2 0.027 0.005 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.034 0.025 -9999 0 -0.22 4 4
regulation of B cell activation 0.033 0.025 -9999 0 -0.22 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 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.007 -10000 0 -10000 0 0
MDM2/SUMO1 0.038 0.033 -10000 0 -0.22 1 1
HDAC4 0.027 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.007 0.007 -10000 0 -10000 0 0
SUMO1 0.027 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.011 0.017 -10000 0 -0.25 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.011 0.008 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.041 0.028 -10000 0 -0.2 1 1
SUMO1/HDAC1 0.04 0.032 -10000 0 -0.22 1 1
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.061 0.027 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.005 -10000 0 -10000 0 0
Ran/GTP 0.029 0.029 -10000 0 -0.23 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.038 0.21 10 -0.23 1 11
NPC 0.016 0.002 -10000 0 -10000 0 0
PIAS2 0.026 0.008 -10000 0 -10000 0 0
PIAS1 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 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 0.024 0.14 4 -10000 0 4
AP2 0.029 0.019 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.035 0.013 -10000 0 -10000 0 0
CLTB 0.026 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.009 -10000 0 -10000 0 0
CD4 0.025 0.029 -10000 0 -0.42 2 2
CLTA 0.025 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 0.033 0.012 -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 0.02 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 0.038 0.013 -10000 0 -10000 0 0
ARFIP2 0.024 0.012 -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 -0.22 2 2
ARF1/GTP/ARHGAP10 0.019 0.006 -10000 0 -10000 0 0
GGA3 0.028 0.004 -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 0.041 -10000 0 -0.21 11 11
ARF1/GDP/Membrin 0.026 0.021 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.034 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.037 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 0.029 -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 0.019 -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 0.013 0.022 -10000 0 -0.31 2 2
USO1 0.011 0.03 -10000 0 -0.31 4 4
GBF1 0.009 0.039 -10000 0 -0.31 7 7
ARF1/GTP/Arfaptin 2 0.038 0.012 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.033 -10000 0 -0.25 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 0.028 0.028 0.028 -0.45
105_BMP4 0.028 0.028 0.028 0.028
105_BMP6 0.028 0.028 0 0.028
105_BMP7 0.028 0.028 0.028 0.028
105_BMP2 0.028 0.028 0.028 -0.39
131_RELN/VLDLR 0.072 0.072 0.072 0
30_TGFB1/TGF beta receptor Type II 0.028 0.028 0.03 0.028
84_STAT5B 0.031 0.03 -0.42 0.033
84_STAT5A 0.031 0.03 -0.42 0.033
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/9908695/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/HNSC-TP/10005928/Gistic2_Analysis_10006195/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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