PARADIGM pathway analysis of mRNASeq expression and copy number data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1F76BS7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1F76BS7
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
HIF-1-alpha transcription factor network 276
Nephrin/Neph1 signaling in the kidney podocyte 257
EGFR-dependent Endothelin signaling events 179
TCR signaling in naïve CD8+ T cells 139
FOXA2 and FOXA3 transcription factor networks 131
IL12-mediated signaling events 114
PDGFR-alpha signaling pathway 113
FOXM1 transcription factor network 87
Glypican 1 network 76
BMP receptor signaling 72
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 533 . 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 ( 533 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 0.5178 276 21023 76 -0.045 0.61 1000 -1000 -0.12 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.4822 257 8760 34 -0.34 0.02 1000 -1000 -0.03 -1000
EGFR-dependent Endothelin signaling events 0.3358 179 3762 21 -0.37 0.032 1000 -1000 -0.038 -1000
TCR signaling in naïve CD8+ T cells 0.2608 139 13008 93 -0.24 0.2 1000 -1000 -0.045 -1000
FOXA2 and FOXA3 transcription factor networks 0.2458 131 6040 46 -0.83 0.022 1000 -1000 -0.13 -1000
IL12-mediated signaling events 0.2139 114 9951 87 -0.14 0.32 1000 -1000 -0.096 -1000
PDGFR-alpha signaling pathway 0.2120 113 5015 44 -0.15 0.028 1000 -1000 -0.034 -1000
FOXM1 transcription factor network 0.1632 87 4475 51 0.019 0.27 1000 -1000 -0.15 -1000
Glypican 1 network 0.1426 76 3666 48 -0.21 0.093 1000 -1000 -0.029 -1000
BMP receptor signaling 0.1351 72 5857 81 -0.32 0.039 1000 -1000 -0.041 -1000
TCGA08_p53 0.1276 68 478 7 -0.066 0.036 1000 -1000 -0.014 -1000
HIF-2-alpha transcription factor network 0.1182 63 2731 43 -0.25 0.25 1000 -1000 -0.064 -1000
TCGA08_retinoblastoma 0.1182 63 507 8 -0.048 0.17 1000 -1000 -0.002 -1000
Reelin signaling pathway 0.1107 59 3308 56 -0.11 0.053 1000 -1000 -0.038 -1000
JNK signaling in the CD4+ TCR pathway 0.0938 50 853 17 0.018 0.1 1000 -1000 -0.034 -1000
Calcium signaling in the CD4+ TCR pathway 0.0938 50 1575 31 -0.003 0.19 1000 -1000 -0.049 -1000
amb2 Integrin signaling 0.0882 47 3916 82 -0.29 0.1 1000 -1000 -0.037 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0863 46 3463 74 -0.37 0.046 1000 -1000 -0.061 -1000
IL23-mediated signaling events 0.0844 45 2729 60 -0.01 0.23 1000 -1000 -0.14 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0807 43 2365 54 -0.11 0.14 1000 -1000 -0.052 -1000
Coregulation of Androgen receptor activity 0.0769 41 3170 76 -0.71 0.17 1000 -1000 -0.026 -1000
Ephrin A reverse signaling 0.0732 39 275 7 -0.014 0.021 1000 -1000 -0.016 -1000
Arf6 signaling events 0.0732 39 2472 62 -0.37 0.084 1000 -1000 -0.045 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0732 39 2682 68 -0.19 0.21 1000 -1000 -0.085 -1000
IL27-mediated signaling events 0.0694 37 1928 51 -0.59 0.32 1000 -1000 -0.053 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0694 37 1229 33 -0.12 0.17 1000 -1000 -0.039 -1000
Aurora B signaling 0.0694 37 2512 67 -0.091 0.13 1000 -1000 -0.044 -1000
Syndecan-1-mediated signaling events 0.0638 34 1179 34 -0.052 0.094 1000 -1000 -0.041 -1000
Aurora C signaling 0.0638 34 242 7 0 0.096 1000 -1000 -0.013 -1000
Fc-epsilon receptor I signaling in mast cells 0.0638 34 3335 97 -0.25 0.1 1000 -1000 -0.052 -1000
Effects of Botulinum toxin 0.0638 34 894 26 -0.046 0.089 1000 -1000 -0.01 -1000
Noncanonical Wnt signaling pathway 0.0582 31 827 26 -0.091 0.025 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.0582 31 700 22 -0.017 0.11 1000 -1000 -0.04 -1000
Signaling events mediated by the Hedgehog family 0.0563 30 1580 52 -0.074 0.094 1000 -1000 -0.048 -1000
IL4-mediated signaling events 0.0563 30 2794 91 -0.49 0.15 1000 -1000 -0.17 -1000
Ceramide signaling pathway 0.0525 28 2190 76 -0.37 0.17 1000 -1000 -0.038 -1000
Glypican 2 network 0.0525 28 114 4 0.032 0.047 1000 -1000 0.014 -1000
IL6-mediated signaling events 0.0525 28 2156 75 -0.014 0.15 1000 -1000 -0.073 -1000
PLK1 signaling events 0.0507 27 2347 85 -0.12 0.071 1000 -1000 -0.026 -1000
Wnt signaling 0.0507 27 189 7 -0.05 0.025 1000 -1000 -0.02 -1000
Signaling events mediated by PTP1B 0.0450 24 1879 76 -0.37 0.076 1000 -1000 -0.039 -1000
FoxO family signaling 0.0450 24 1582 64 -0.54 0.1 1000 -1000 -0.074 -1000
IL2 signaling events mediated by PI3K 0.0432 23 1339 58 -0.015 0.11 1000 -1000 -0.048 -1000
Integrins in angiogenesis 0.0432 23 1958 84 -0.17 0.093 1000 -1000 -0.053 -1000
Syndecan-4-mediated signaling events 0.0432 23 1590 67 -0.19 0.1 1000 -1000 -0.04 -1000
Class I PI3K signaling events 0.0413 22 1650 73 -0.02 0.11 1000 -1000 -0.045 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0413 22 1985 88 -0.15 0.061 1000 -1000 -0.063 -1000
Endothelins 0.0394 21 2058 96 -0.32 0.065 1000 -1000 -0.05 -1000
Thromboxane A2 receptor signaling 0.0375 20 2176 105 -0.37 0.042 1000 -1000 -0.048 -1000
Syndecan-2-mediated signaling events 0.0375 20 1408 69 -0.29 0.037 1000 -1000 -0.029 -1000
Signaling mediated by p38-alpha and p38-beta 0.0375 20 880 44 -0.049 0.025 1000 -1000 -0.035 -1000
LPA receptor mediated events 0.0375 20 2113 102 -0.072 0.094 1000 -1000 -0.062 -1000
VEGFR1 specific signals 0.0375 20 1154 56 -0.021 0.11 1000 -1000 -0.045 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0375 20 1591 78 -0.14 0.07 1000 -1000 -0.069 -1000
Caspase cascade in apoptosis 0.0356 19 1472 74 -0.26 0.064 1000 -1000 -0.045 -1000
p75(NTR)-mediated signaling 0.0356 19 2376 125 -0.19 0.072 1000 -1000 -0.059 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0356 19 866 45 0.005 0.12 1000 -1000 -0.054 -1000
BCR signaling pathway 0.0356 19 1926 99 -0.017 0.088 1000 -1000 -0.053 -1000
IFN-gamma pathway 0.0338 18 1241 68 -0.1 0.09 1000 -1000 -0.055 -1000
Signaling events regulated by Ret tyrosine kinase 0.0338 18 1500 82 -0.076 0.025 1000 -1000 -0.053 -1000
TCGA08_rtk_signaling 0.0338 18 469 26 -0.15 0.022 1000 -1000 -0.031 -1000
Regulation of Telomerase 0.0319 17 1734 102 -0.37 0.095 1000 -1000 -0.059 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0319 17 2102 120 -0.068 0.054 1000 -1000 -0.049 -1000
S1P1 pathway 0.0300 16 576 36 -0.038 0.093 1000 -1000 -0.045 -1000
Nongenotropic Androgen signaling 0.0300 16 858 52 -0.056 0.037 1000 -1000 -0.03 -1000
E-cadherin signaling in the nascent adherens junction 0.0300 16 1276 76 -0.069 0.035 1000 -1000 -0.053 -1000
Plasma membrane estrogen receptor signaling 0.0300 16 1384 86 -0.14 0.058 1000 -1000 -0.048 -1000
Visual signal transduction: Rods 0.0300 16 848 52 -0.063 0.067 1000 -1000 -0.047 -1000
Presenilin action in Notch and Wnt signaling 0.0281 15 960 61 -0.09 0.052 1000 -1000 -0.041 -1000
Glucocorticoid receptor regulatory network 0.0281 15 1784 114 -0.23 0.058 1000 -1000 -0.068 -1000
FAS signaling pathway (CD95) 0.0281 15 741 47 -0.029 0.1 1000 -1000 -0.035 -1000
E-cadherin signaling in keratinocytes 0.0281 15 667 43 -0.15 0.02 1000 -1000 -0.037 -1000
Regulation of Androgen receptor activity 0.0281 15 1063 70 -0.84 0.054 1000 -1000 -0.051 -1000
Aurora A signaling 0.0263 14 855 60 -0.054 0.067 1000 -1000 -0.03 -1000
IGF1 pathway 0.0263 14 808 57 -0.1 0.055 1000 -1000 -0.045 -1000
EPO signaling pathway 0.0244 13 760 55 -0.002 0.072 1000 -1000 -0.051 -1000
PLK2 and PLK4 events 0.0225 12 38 3 -0.013 -1000 1000 -1000 -0.022 -1000
mTOR signaling pathway 0.0225 12 686 53 -0.053 0.025 1000 -1000 -0.038 -1000
Class I PI3K signaling events mediated by Akt 0.0225 12 847 68 -0.022 0.038 1000 -1000 -0.04 -1000
ceramide signaling pathway 0.0225 12 605 49 -0.004 0.045 1000 -1000 -0.044 -1000
Canonical Wnt signaling pathway 0.0225 12 635 51 -0.09 0.064 1000 -1000 -0.051 -1000
PDGFR-beta signaling pathway 0.0225 12 1176 97 -0.03 0.048 1000 -1000 -0.052 -1000
Regulation of nuclear SMAD2/3 signaling 0.0206 11 1607 136 -0.19 0.11 1000 -1000 -0.047 -1000
E-cadherin signaling events 0.0206 11 56 5 0.005 0.017 1000 -1000 0.013 -1000
ErbB4 signaling events 0.0188 10 757 69 -0.15 0.1 1000 -1000 -0.042 -1000
Osteopontin-mediated events 0.0188 10 381 38 -0.037 0.034 1000 -1000 -0.045 -1000
EPHB forward signaling 0.0188 10 882 85 -0.043 0.049 1000 -1000 -0.057 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0169 9 813 85 -0.05 0.043 1000 -1000 -0.045 -1000
Nectin adhesion pathway 0.0169 9 603 63 -0.035 0.04 1000 -1000 -0.052 -1000
Syndecan-3-mediated signaling events 0.0169 9 347 35 -0.02 0.052 1000 -1000 -0.031 -1000
ErbB2/ErbB3 signaling events 0.0150 8 548 65 -0.04 0.035 1000 -1000 -0.054 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0150 8 245 28 -0.009 0.049 1000 -1000 -0.028 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0150 8 1058 125 -0.022 0.1 1000 -1000 -0.053 -1000
Signaling events mediated by PRL 0.0150 8 282 34 -0.04 0.032 1000 -1000 -0.037 -1000
LPA4-mediated signaling events 0.0131 7 90 12 -0.022 0.019 1000 -1000 -0.021 -1000
Arf6 downstream pathway 0.0131 7 323 43 -0.033 0.034 1000 -1000 -0.028 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0131 7 293 37 -0.028 0.072 1000 -1000 -0.035 -1000
IL1-mediated signaling events 0.0131 7 484 62 -0.047 0.041 1000 -1000 -0.053 -1000
Ephrin B reverse signaling 0.0131 7 367 48 -0.032 0.035 1000 -1000 -0.033 -1000
Arf6 trafficking events 0.0131 7 545 71 -0.09 0.035 1000 -1000 -0.033 -1000
S1P3 pathway 0.0131 7 307 42 -0.016 0.094 1000 -1000 -0.055 -1000
Class IB PI3K non-lipid kinase events 0.0131 7 21 3 -0.019 0.019 1000 -1000 -0.014 -1000
S1P5 pathway 0.0113 6 113 17 -0.004 0.049 1000 -1000 -0.014 -1000
Regulation of p38-alpha and p38-beta 0.0113 6 346 54 -0.025 0.045 1000 -1000 -0.047 -1000
S1P4 pathway 0.0113 6 174 25 -0.006 0.049 1000 -1000 -0.026 -1000
Ras signaling in the CD4+ TCR pathway 0.0113 6 112 17 -0.017 0.035 1000 -1000 -0.033 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0094 5 117 23 -0.044 0.038 1000 -1000 -0.029 -1000
Visual signal transduction: Cones 0.0094 5 226 38 -0.018 0.041 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 0.0094 5 206 39 -0.019 0.026 1000 -1000 -0.02 -1000
Insulin-mediated glucose transport 0.0094 5 181 32 -0.018 0.038 1000 -1000 -0.032 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0094 5 260 52 -0.054 0.054 1000 -1000 -0.051 -1000
Insulin Pathway 0.0094 5 417 74 -0.043 0.055 1000 -1000 -0.046 -1000
p38 MAPK signaling pathway 0.0094 5 247 44 -0.033 0.041 1000 -1000 -0.027 -1000
Canonical NF-kappaB pathway 0.0075 4 182 39 -0.019 0.057 1000 -1000 -0.033 -1000
Hedgehog signaling events mediated by Gli proteins 0.0075 4 297 65 -0.022 0.052 1000 -1000 -0.051 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0075 4 348 83 -0.025 0.037 1000 -1000 -0.032 -1000
Signaling mediated by p38-gamma and p38-delta 0.0075 4 61 15 -0.023 0.02 1000 -1000 -0.031 -1000
BARD1 signaling events 0.0056 3 218 57 -0.043 0.053 1000 -1000 -0.035 -1000
a4b1 and a4b7 Integrin signaling 0.0056 3 16 5 0.02 0.032 1000 -1000 0.01 -1000
Signaling events mediated by HDAC Class III 0.0056 3 140 40 -0.038 0.038 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class I 0.0056 3 325 104 -0.038 0.052 1000 -1000 -0.037 -1000
Retinoic acid receptors-mediated signaling 0.0056 3 196 58 -0.048 0.034 1000 -1000 -0.044 -1000
Atypical NF-kappaB pathway 0.0056 3 107 31 -0.026 0.025 1000 -1000 -0.031 -1000
Arf1 pathway 0.0056 3 212 54 -0.013 0.04 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 0.0019 1 77 75 -0.02 0.041 1000 -1000 -0.031 -1000
Paxillin-dependent events mediated by a4b1 0.0019 1 43 36 -0.038 0.042 1000 -1000 -0.026 -1000
Circadian rhythm pathway 0.0000 0 20 22 -0.001 0.038 1000 -1000 -0.038 -1000
TRAIL signaling pathway 0.0000 0 43 48 -0.019 0.047 1000 -1000 -0.035 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 19 27 -0.02 0.047 1000 -1000 -0.036 -1000
Rapid glucocorticoid signaling 0.0000 0 12 20 -0.009 0.025 1000 -1000 -0.014 -1000
Alternative NF-kappaB pathway 0.0000 0 6 13 0 0.043 1000 -1000 0 -1000
Total NA 3642 204643 7203 -15 -990 131000 -131000 -5.7 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.42 0.25 0.54 374 -0.81 2 376
HDAC7 0.032 0.016 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.5 0.3 0.65 382 -0.62 2 384
SMAD4 0.02 0.003 -10000 0 -10000 0 0
ID2 0.43 0.24 0.56 365 -0.81 2 367
AP1 0.022 0.049 -10000 0 -0.3 11 11
ABCG2 0.43 0.24 0.56 366 -0.81 2 368
HIF1A 0.16 0.1 0.23 304 -0.28 2 306
TFF3 0.42 0.26 0.56 359 -0.9 2 361
GATA2 0.011 0.063 -10000 0 -0.42 11 11
AKT1 0.17 0.1 0.24 268 -10000 0 268
response to hypoxia 0.15 0.094 0.2 359 -0.35 2 361
MCL1 0.42 0.25 0.56 361 -0.81 2 363
NDRG1 0.42 0.25 0.56 357 -0.81 2 359
SERPINE1 0.42 0.28 0.58 343 -0.81 2 345
FECH 0.42 0.25 0.56 360 -0.81 2 362
FURIN 0.43 0.24 0.56 367 -0.81 2 369
NCOA2 0.026 0.065 -10000 0 -0.4 10 10
EP300 0.23 0.14 0.31 346 -0.26 1 347
HMOX1 0.44 0.25 0.57 367 -0.81 2 369
BHLHE40 0.33 0.29 0.57 281 -0.81 2 283
BHLHE41 0.46 0.27 0.59 374 -0.89 2 376
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.21 0.16 0.33 285 -10000 0 285
ENG 0.15 0.11 0.27 144 -10000 0 144
JUN 0.02 0.006 -10000 0 -10000 0 0
RORA 0.43 0.24 0.56 369 -0.81 2 371
ABCB1 -0.045 0.18 0.55 2 -0.65 39 41
TFRC 0.42 0.25 0.56 360 -0.81 2 362
CXCR4 0.48 0.28 0.61 376 -0.81 2 378
TF 0.45 0.28 0.6 359 -0.81 2 361
CITED2 0.41 0.26 0.56 350 -0.81 2 352
HIF1A/ARNT 0.61 0.38 0.8 393 -0.89 2 395
LDHA 0.001 0.076 0.49 6 -0.54 5 11
ETS1 0.43 0.24 0.56 370 -0.81 2 372
PGK1 0.44 0.24 0.56 370 -0.81 2 372
NOS2 0.44 0.24 0.56 369 -0.81 2 371
ITGB2 0.45 0.27 0.59 368 -0.81 2 370
ALDOA 0.42 0.25 0.56 361 -0.81 2 363
Cbp/p300/CITED2 0.44 0.28 0.6 353 -0.81 2 355
FOS 0.01 0.063 0.19 1 -0.42 11 12
HK2 0.53 0.26 0.64 412 -0.81 2 414
SP1 -0.007 0.079 -10000 0 -0.22 61 61
GCK 0.28 0.22 0.48 189 -1 3 192
HK1 0.43 0.25 0.56 361 -0.81 2 363
NPM1 0.33 0.28 0.56 283 -0.81 2 285
EGLN1 0.42 0.25 0.56 359 -0.81 2 361
CREB1 0.02 0.007 -10000 0 -10000 0 0
PGM1 0.43 0.25 0.56 365 -0.81 2 367
SMAD3 0.02 0.002 -10000 0 -10000 0 0
EDN1 0.18 0.15 0.4 45 -0.74 2 47
IGFBP1 0.42 0.29 0.59 345 -0.81 2 347
VEGFA 0.46 0.25 0.57 396 -0.59 1 397
HIF1A/JAB1 0.14 0.089 0.22 231 -0.18 2 233
CP 0.51 0.29 0.64 398 -0.99 2 400
CXCL12 0.43 0.25 0.56 363 -0.84 2 365
COPS5 0.03 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4 0.029 0.006 -10000 0 -10000 0 0
BNIP3 0.42 0.25 0.56 364 -0.81 2 366
EGLN3 0.54 0.28 0.65 422 -0.99 2 424
CA9 0.56 0.26 0.65 439 -0.81 2 441
TERT 0.41 0.27 0.57 345 -0.81 2 347
ENO1 0.43 0.25 0.56 365 -0.81 2 367
PFKL 0.42 0.25 0.56 363 -0.81 2 365
NCOA1 0.025 0.009 -10000 0 -10000 0 0
ADM 0.47 0.26 0.59 385 -0.81 2 387
ARNT 0.16 0.092 0.23 260 -0.26 1 261
HNF4A -0.012 0.11 -10000 0 -0.4 40 40
ADFP 0.42 0.25 0.54 374 -0.81 2 376
SLC2A1 0.42 0.24 0.52 395 -0.59 1 396
LEP 0.41 0.27 0.57 341 -0.81 2 343
HIF1A/ARNT/Cbp/p300 0.5 0.31 0.66 384 -0.64 2 386
EPO 0.4 0.28 0.59 317 -10000 0 317
CREBBP 0.23 0.15 0.31 343 -10000 0 343
HIF1A/ARNT/Cbp/p300/HDAC7 0.5 0.31 0.66 389 -0.62 2 391
PFKFB3 0.43 0.24 0.56 368 -0.84 2 370
NT5E 0.42 0.25 0.56 358 -0.81 2 360
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.25 0.15 0.34 392 -10000 0 392
KIRREL -0.058 0.061 -10000 0 -0.46 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.25 0.16 -10000 0 -0.34 392 392
PLCG1 0.019 0.004 -10000 0 -10000 0 0
ARRB2 0.02 0.003 -10000 0 -10000 0 0
WASL 0.018 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.26 0.18 -10000 0 -0.34 417 417
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.26 0.18 -10000 0 -0.35 387 387
FYN -0.25 0.15 0.26 1 -0.32 417 418
mol:Ca2+ -0.25 0.18 -10000 0 -0.33 409 409
mol:DAG -0.25 0.18 -10000 0 -0.33 409 409
NPHS2 -0.23 0.21 -10000 0 -0.46 240 240
mol:IP3 -0.25 0.18 -10000 0 -0.33 409 409
regulation of endocytosis -0.24 0.16 -10000 0 -0.3 417 417
Nephrin/NEPH1/podocin/Cholesterol -0.26 0.17 -10000 0 -0.33 417 417
establishment of cell polarity -0.25 0.15 -10000 0 -0.34 392 392
Nephrin/NEPH1/podocin/NCK1-2 -0.24 0.17 -10000 0 -0.31 410 410
Nephrin/NEPH1/beta Arrestin2 -0.24 0.16 -10000 0 -0.31 417 417
NPHS1 -0.34 0.18 -10000 0 -0.44 404 404
Nephrin/NEPH1/podocin -0.25 0.16 -10000 0 -0.32 417 417
TJP1 0.02 0.002 -10000 0 -10000 0 0
NCK1 0.018 0.02 -10000 0 -0.42 1 1
NCK2 0.019 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.25 0.18 -10000 0 -0.34 409 409
CD2AP 0.019 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.26 0.18 -10000 0 -0.34 415 415
GRB2 0.02 0.003 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.25 0.15 0.27 1 -0.31 415 416
cytoskeleton organization -0.31 0.2 -10000 0 -0.41 383 383
Nephrin/NEPH1 -0.17 0.11 -10000 0 -0.23 392 392
Nephrin/NEPH1/ZO-1 -0.2 0.13 -10000 0 -0.27 390 390
EGFR-dependent Endothelin 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
HRAS 0.02 0.008 0.19 1 -10000 0 1
EGFR 0.019 0.026 0.19 5 -0.42 1 6
EGF/EGFR -0.17 0.085 -10000 0 -0.21 422 422
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.18 0.097 -10000 0 -0.23 403 403
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.02 0.008 0.19 1 -10000 0 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.37 0.14 -10000 0 -0.42 467 467
EGF/EGFR dimer/SHC -0.2 0.1 -10000 0 -0.26 411 411
mol:GDP -0.18 0.096 -10000 0 -0.23 403 403
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.024 0.036 0.19 17 -0.42 1 18
GRB2/SOS1 0.029 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.17 0.089 -10000 0 -0.22 402 402
SHC1 0.019 0.004 -10000 0 -10000 0 0
HRAS/GDP -0.17 0.093 -10000 0 -0.22 402 402
FRAP1 -0.18 0.08 -10000 0 -0.22 403 403
EGF/EGFR dimer -0.24 0.12 -10000 0 -0.3 422 422
SOS1 0.02 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.032 0.026 -10000 0 -0.3 1 1
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.15 0.16 0.31 200 -0.33 7 207
FYN 0.14 0.18 0.32 207 -0.44 7 214
LAT/GRAP2/SLP76 0.13 0.18 0.36 168 -0.36 6 174
IKBKB 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.17 0.19 0.34 241 -0.3 8 249
B2M 0.026 0.011 -10000 0 -10000 0 0
IKBKG 0.063 0.082 0.15 198 -10000 0 198
MAP3K8 0.02 0.011 0.19 2 -10000 0 2
mol:Ca2+ -0.023 0.025 -10000 0 -0.06 120 120
integrin-mediated signaling pathway 0.029 0.02 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.19 0.21 0.38 234 -0.38 8 242
TRPV6 -0.24 0.39 0.94 46 -0.41 405 451
CD28 0.034 0.046 0.2 39 -10000 0 39
SHC1 0.15 0.18 0.34 213 -0.4 7 220
receptor internalization 0.15 0.17 0.32 218 -0.41 8 226
PRF1 0.15 0.22 0.45 115 -0.66 14 129
KRAS 0.019 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.003 -10000 0 -10000 0 0
COT/AKT1 0.16 0.17 0.32 238 -0.24 8 246
LAT 0.16 0.19 0.36 222 -0.38 8 230
EntrezGene:6955 0.005 0.007 -10000 0 -10000 0 0
CD3D 0.1 0.09 0.2 235 -10000 0 235
CD3E 0.093 0.089 0.2 211 -10000 0 211
CD3G 0.089 0.087 0.2 202 -10000 0 202
RASGRP2 0.039 0.044 0.099 142 -0.13 1 143
RASGRP1 0.18 0.2 0.35 251 -0.34 11 262
HLA-A 0.007 0.01 0.071 1 -10000 0 1
RASSF5 0.025 0.03 0.19 17 -10000 0 17
RAP1A/GTP/RAPL 0.029 0.02 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.14 0.15 0.24 269 -0.11 7 276
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.004 0.022 -10000 0 -0.16 6 6
PRKCA 0.1 0.13 0.24 206 -0.19 6 212
GRAP2 0.03 0.046 0.19 34 -0.42 1 35
mol:IP3 0.18 0.17 0.28 347 -0.29 6 353
EntrezGene:6957 0.006 0.009 0.042 1 -10000 0 1
TCR/CD3/MHC I/CD8 0.13 0.15 0.28 232 -0.29 6 238
ORAI1 0.099 0.28 0.54 7 -0.78 45 52
CSK 0.15 0.17 0.33 210 -0.37 8 218
B7 family/CD28 0.18 0.2 0.41 193 -0.37 6 199
CHUK 0.019 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.16 0.18 0.35 215 -0.43 8 223
PTPN6 0.14 0.17 0.31 210 -0.38 7 217
VAV1 0.16 0.19 0.36 217 -0.39 8 225
Monovalent TCR/CD3 0.12 0.12 0.25 214 -10000 0 214
CBL 0.019 0.019 -10000 0 -0.42 1 1
LCK 0.14 0.18 0.32 207 -0.4 11 218
PAG1 0.15 0.17 0.33 211 -0.37 8 219
RAP1A 0.019 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.15 0.18 0.33 212 -0.41 8 220
CD80 0.056 0.072 0.19 113 -10000 0 113
CD86 0.046 0.063 0.19 81 -10000 0 81
PDK1/CARD11/BCL10/MALT1 0.005 0.035 0.12 11 -0.18 6 17
HRAS 0.02 0.008 0.19 1 -10000 0 1
GO:0035030 0.13 0.17 0.31 204 -0.31 7 211
CD8A 0.1 0.09 0.2 232 -10000 0 232
CD8B 0.085 0.087 0.2 185 -10000 0 185
PTPRC 0.038 0.052 0.19 53 -10000 0 53
PDK1/PKC theta 0.19 0.21 0.38 241 -0.35 8 249
CSK/PAG1 0.14 0.17 0.32 211 -0.34 8 219
SOS1 0.02 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.025 0.017 -10000 0 -10000 0 0
GRAP2/SLP76 0.14 0.19 0.37 166 -0.39 7 173
STIM1 0.057 0.079 0.96 1 -0.79 1 2
RAS family/GTP 0.13 0.14 0.25 251 -0.18 9 260
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.15 0.17 0.33 218 -0.42 8 226
mol:DAG 0.018 0.054 0.11 44 -0.26 7 51
RAP1A/GDP 0.068 0.089 0.12 247 -10000 0 247
PLCG1 0.019 0.004 -10000 0 -10000 0 0
CD247 0.078 0.085 0.2 169 -10000 0 169
cytotoxic T cell degranulation 0.15 0.22 0.44 116 -0.62 15 131
RAP1A/GTP 0.002 0.004 -10000 0 -0.047 1 1
mol:PI-3-4-5-P3 0.19 0.2 0.37 241 -0.32 8 249
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.2 0.2 0.33 317 -0.36 6 323
NRAS 0.019 0.004 -10000 0 -10000 0 0
ZAP70 0.11 0.084 0.19 291 -10000 0 291
GRB2/SOS1 0.029 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.12 0.18 0.36 158 -0.35 7 165
MALT1 0.02 0.003 -10000 0 -10000 0 0
TRAF6 0.02 0.002 -10000 0 -10000 0 0
CD8 heterodimer 0.13 0.12 0.29 188 -10000 0 188
CARD11 0.049 0.067 0.19 98 -10000 0 98
PRKCB 0.1 0.13 0.24 203 -0.22 6 209
PRKCE 0.1 0.13 0.24 205 -0.19 6 211
PRKCQ 0.19 0.21 0.38 239 -0.39 8 247
LCP2 0.024 0.04 0.19 29 -10000 0 29
BCL10 0.019 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.16 0.18 0.32 248 -0.26 8 256
IKK complex 0.12 0.15 0.23 261 -0.11 6 267
RAS family/GDP 0 0.005 -10000 0 -10000 0 0
MAP3K14 0.13 0.15 0.26 243 -0.19 4 247
PDPK1 0.17 0.19 0.34 244 -0.28 7 251
TCR/CD3/MHC I/CD8/Fyn 0.15 0.18 0.35 203 -0.4 8 211
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.39 0.32 0.47 1 -0.89 97 98
PCK1 -0.83 0.57 0.42 1 -1.2 301 302
HNF4A -0.4 0.38 0.56 2 -1 102 104
KCNJ11 -0.43 0.34 0.46 1 -0.87 138 139
AKT1 -0.23 0.17 0.31 1 -0.45 94 95
response to starvation 0.003 0.013 -10000 0 -10000 0 0
DLK1 -0.49 0.41 0.48 2 -0.98 169 171
NKX2-1 -0.13 0.14 -10000 0 -0.41 29 29
ACADM -0.39 0.32 0.47 1 -0.87 105 106
TAT -0.42 0.25 0.57 2 -0.65 216 218
CEBPB -0.03 0.051 0.19 2 -0.16 1 3
CEBPA -0.026 0.05 0.2 3 -0.16 2 5
TTR -0.74 0.47 0.71 1 -0.99 330 331
PKLR -0.42 0.38 0.47 1 -0.93 132 133
APOA1 -0.46 0.41 0.63 2 -1.1 104 106
CPT1C -0.39 0.32 0.47 1 -0.86 110 111
ALAS1 -0.24 0.19 -10000 0 -0.62 31 31
TFRC -0.62 0.33 0.59 1 -0.82 334 335
FOXF1 0.022 0.021 0.19 8 -10000 0 8
NF1 0.02 0.003 -10000 0 -10000 0 0
HNF1A (dimer) -0.032 0.074 -10000 0 -0.24 30 30
CPT1A -0.39 0.32 0.47 1 -0.84 120 121
HMGCS1 -0.38 0.33 0.56 2 -0.88 98 100
NR3C1 0.025 0.042 0.26 1 -0.16 8 9
CPT1B -0.4 0.33 0.47 1 -0.88 109 110
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.02 0.005 -10000 0 -10000 0 0
GCK -0.38 0.33 0.56 2 -0.85 112 114
CREB1 -0.06 0.084 -10000 0 -0.19 102 102
IGFBP1 -0.14 0.23 0.5 3 -1.3 13 16
PDX1 -0.22 0.17 -10000 0 -0.71 11 11
UCP2 -0.39 0.32 0.47 1 -0.89 97 98
ALDOB -0.76 0.45 -10000 0 -1 378 378
AFP -0.48 0.34 -10000 0 -0.65 329 329
BDH1 -0.48 0.4 0.47 1 -0.96 179 180
HADH -0.43 0.33 0.46 1 -0.82 167 168
F2 -0.44 0.4 0.63 2 -1.1 97 99
HNF1A -0.032 0.074 -10000 0 -0.23 30 30
G6PC -0.72 0.56 -10000 0 -1.3 246 246
SLC2A2 -0.32 0.36 0.55 1 -1.2 53 54
INS -0.029 0.043 0.19 5 -10000 0 5
FOXA1 -0.16 0.14 0.28 5 -0.26 283 288
FOXA3 -0.47 0.2 0.39 1 -0.5 484 485
FOXA2 -0.49 0.38 0.63 2 -0.92 168 170
ABCC8 -0.43 0.33 0.46 1 -0.87 131 132
ALB -0.83 0.34 0.33 1 -0.97 439 440
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.14 0.16 0.32 186 -0.29 2 188
TBX21 0.3 0.3 0.68 157 -0.88 1 158
B2M 0.028 0.01 -10000 0 -10000 0 0
TYK2 0.065 0.049 0.17 39 -10000 0 39
IL12RB1 0.12 0.12 0.28 161 -10000 0 161
GADD45B 0.25 0.25 0.58 144 -0.91 1 145
IL12RB2 0.088 0.084 0.2 139 -0.4 2 141
GADD45G 0.25 0.26 0.58 149 -0.81 3 152
natural killer cell activation 0.048 0.051 0.088 268 -0.045 2 270
RELB 0.02 0.002 -10000 0 -10000 0 0
RELA 0.02 0.002 -10000 0 -10000 0 0
IL18 0.037 0.024 0.19 5 -10000 0 5
IL2RA 0.052 0.066 0.19 100 -10000 0 100
IFNG 0.094 0.084 0.19 232 -10000 0 232
STAT3 (dimer) 0.24 0.24 0.5 197 -0.57 7 204
HLA-DRB5 0 0.004 -10000 0 -0.027 10 10
FASLG 0.32 0.31 0.67 182 -0.88 1 183
NF kappa B2 p52/RelB 0.12 0.16 0.41 39 -0.66 3 42
CD4 0.021 0.023 0.19 8 -10000 0 8
SOCS1 0.021 0.018 0.19 6 -10000 0 6
EntrezGene:6955 0.008 0.011 0.02 201 -0.029 11 212
CD3D 0.1 0.091 0.2 233 -10000 0 233
CD3E 0.095 0.09 0.2 211 -10000 0 211
CD3G 0.091 0.091 0.2 201 -10000 0 201
IL12Rbeta2/JAK2 0.12 0.095 0.24 154 -0.28 2 156
CCL3 0.28 0.3 0.66 150 -1.3 2 152
CCL4 0.29 0.3 0.68 149 -1.4 1 150
HLA-A 0.008 0.01 0.021 177 -10000 0 177
IL18/IL18R 0.14 0.1 0.26 154 -0.24 3 157
NOS2 0.27 0.28 0.63 156 -0.68 2 158
IL12/IL12R/TYK2/JAK2/SPHK2 0.14 0.16 0.32 185 -0.29 2 187
IL1R1 0.27 0.27 0.63 146 -0.88 1 147
IL4 -0.049 0.057 -10000 0 -0.18 24 24
JAK2 0.063 0.051 0.18 26 -10000 0 26
EntrezGene:6957 0.008 0.011 0.02 194 -0.026 9 203
TCR/CD3/MHC I/CD8 0.15 0.17 0.36 186 -0.33 1 187
RAB7A 0.24 0.24 0.55 134 -0.76 2 136
lysosomal transport 0.24 0.23 0.54 143 -0.72 2 145
FOS 0.17 0.32 0.5 145 -0.74 31 176
STAT4 (dimer) 0.27 0.26 0.54 194 -0.76 3 197
STAT5A (dimer) 0.27 0.26 0.56 198 -0.66 3 201
GZMA 0.3 0.3 0.65 175 -0.72 2 177
GZMB 0.28 0.29 0.66 150 -0.88 1 151
HLX 0.038 0.054 0.19 60 -10000 0 60
LCK 0.27 0.28 0.6 177 -0.71 4 181
TCR/CD3/MHC II/CD4 0.093 0.11 0.21 211 -0.21 7 218
IL2/IL2R 0.13 0.09 0.28 87 -0.23 1 88
MAPK14 0.26 0.26 0.57 157 -0.83 3 160
CCR5 0.22 0.32 0.63 159 -10000 0 159
IL1B 0.065 0.056 0.19 31 -0.42 1 32
STAT6 0.17 0.17 0.39 164 -10000 0 164
STAT4 0.029 0.039 0.19 30 -10000 0 30
STAT3 0.02 0.003 -10000 0 -10000 0 0
STAT1 0.02 0.009 0.19 1 -10000 0 1
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
NFKB2 0.019 0.004 -10000 0 -10000 0 0
IL12B 0.069 0.084 0.23 86 -10000 0 86
CD8A 0.1 0.091 0.2 232 -10000 0 232
CD8B 0.087 0.087 0.2 185 -10000 0 185
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.14 0.15 0.28 2 -0.32 186 188
IL2RB 0.11 0.084 0.19 272 -10000 0 272
proteasomal ubiquitin-dependent protein catabolic process 0.27 0.25 0.53 197 -0.7 3 200
IL2RG 0.03 0.045 0.19 33 -0.42 1 34
IL12 0.091 0.099 0.24 120 -10000 0 120
STAT5A 0.02 0.003 -10000 0 -10000 0 0
CD247 0.08 0.086 0.2 169 -10000 0 169
IL2 0.022 0.023 0.19 10 -10000 0 10
SPHK2 0.018 0.027 -10000 0 -0.42 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.062 0.05 0.17 48 -10000 0 48
IL12/IL12R/TYK2/JAK2 0.3 0.32 0.68 180 -0.73 3 183
MAP2K3 0.26 0.26 0.57 159 -0.83 3 162
RIPK2 0.019 0.009 0.19 1 -10000 0 1
MAP2K6 0.26 0.26 0.56 159 -0.77 4 163
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.005 -10000 0 -0.031 11 11
IL18RAP 0.077 0.079 0.21 136 -10000 0 136
IL12Rbeta1/TYK2 0.12 0.1 0.26 171 -10000 0 171
EOMES -0.1 0.21 -10000 0 -0.48 89 89
STAT1 (dimer) 0.28 0.28 0.56 215 -0.62 4 219
T cell proliferation 0.23 0.23 0.48 184 -0.57 3 187
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.034 0.042 0.2 4 -0.42 3 7
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.032 0.097 0.36 6 -0.62 3 9
ATF2 0.24 0.24 0.53 162 -0.76 3 165
PDGFR-alpha signaling pathway

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
PDGFRA -0.15 0.21 -10000 0 -0.42 199 199
PDGF/PDGFRA/CRKL -0.093 0.16 -10000 0 -0.3 196 196
positive regulation of JUN kinase activity -0.052 0.13 -10000 0 -0.23 181 181
CRKL 0.02 0.002 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.095 0.15 0.17 1 -0.29 199 200
AP1 -0.11 0.15 0.45 1 -0.87 11 12
mol:IP3 -0.12 0.14 -10000 0 -0.31 191 191
PLCG1 -0.12 0.14 -10000 0 -0.31 191 191
PDGF/PDGFRA/alphaV Integrin -0.09 0.16 -10000 0 -0.3 190 190
RAPGEF1 0.019 0.004 -10000 0 -10000 0 0
CRK 0.02 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.14 -10000 0 -0.31 191 191
CAV3 0.014 0.014 0.19 2 -10000 0 2
CAV1 0.028 0.04 0.19 30 -10000 0 30
SHC/Grb2/SOS1 -0.052 0.13 -10000 0 -0.23 181 181
PDGF/PDGFRA/Shf -0.094 0.16 -10000 0 -0.3 198 198
FOS -0.11 0.15 -10000 0 -0.86 11 11
JUN -0.031 0.018 -10000 0 -10000 0 0
oligodendrocyte development -0.09 0.15 -10000 0 -0.29 190 190
GRB2 0.02 0.003 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
mol:DAG -0.12 0.14 -10000 0 -0.31 191 191
PDGF/PDGFRA -0.15 0.21 -10000 0 -0.42 199 199
actin cytoskeleton reorganization -0.094 0.16 -10000 0 -0.29 198 198
SRF -0.016 0.007 -10000 0 -10000 0 0
SHC1 0.019 0.004 -10000 0 -10000 0 0
PI3K -0.061 0.13 -10000 0 -0.25 171 171
PDGF/PDGFRA/Crk/C3G -0.07 0.14 -10000 0 -0.25 196 196
JAK1 -0.12 0.13 -10000 0 -0.3 188 188
ELK1/SRF -0.11 0.11 0.15 1 -0.25 188 189
SHB 0.019 0.004 -10000 0 -10000 0 0
SHF 0.019 0.019 -10000 0 -0.42 1 1
CSNK2A1 0.028 0.013 -10000 0 -10000 0 0
GO:0007205 -0.13 0.15 -10000 0 -0.33 191 191
SOS1 0.02 0.003 -10000 0 -10000 0 0
Ras protein signal transduction -0.052 0.13 -10000 0 -0.23 181 181
PDGF/PDGFRA/SHB -0.094 0.16 -10000 0 -0.29 198 198
PDGF/PDGFRA/Caveolin-1 -0.076 0.16 0.16 1 -0.29 174 175
ITGAV 0.019 0.004 -10000 0 -10000 0 0
ELK1 -0.12 0.13 -10000 0 -0.29 189 189
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
PDGF/PDGFRA/Crk -0.093 0.16 -10000 0 -0.3 197 197
JAK-STAT cascade -0.12 0.13 -10000 0 -0.29 188 188
cell proliferation -0.094 0.16 -10000 0 -0.29 198 198
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.25 0.33 0.79 98 -1.1 3 101
PLK1 0.12 0.17 0.5 39 -10000 0 39
BIRC5 0.12 0.2 0.5 41 -0.95 5 46
HSPA1B 0.24 0.32 0.77 97 -1.1 3 100
MAP2K1 0.073 0.079 0.23 83 -10000 0 83
BRCA2 0.25 0.33 0.78 98 -1.1 3 101
FOXM1 0.27 0.38 0.89 98 -1.5 3 101
XRCC1 0.25 0.33 0.8 96 -1.1 3 99
FOXM1B/p19 0.15 0.21 0.66 12 -1.3 3 15
Cyclin D1/CDK4 0.22 0.29 0.7 89 -1 3 92
CDC2 0.26 0.35 0.81 109 -1.2 3 112
TGFA 0.21 0.3 0.68 105 -1.1 5 110
SKP2 0.26 0.34 0.8 108 -1.1 3 111
CCNE1 0.032 0.03 0.22 7 -10000 0 7
CKS1B 0.25 0.32 0.75 110 -1.1 3 113
RB1 0.16 0.21 0.51 98 -0.75 1 99
FOXM1C/SP1 0.23 0.3 0.73 90 -1.3 3 93
AURKB 0.15 0.2 0.53 24 -0.91 6 30
CENPF 0.26 0.34 0.83 100 -1.1 3 103
CDK4 0.036 0.031 0.21 1 -10000 0 1
MYC 0.21 0.28 0.68 99 -0.93 3 102
CHEK2 0.073 0.081 0.23 85 -10000 0 85
ONECUT1 0.23 0.31 0.72 101 -1.1 3 104
CDKN2A 0.14 0.071 0.18 359 -0.15 1 360
LAMA4 0.26 0.33 0.8 101 -1.1 3 104
FOXM1B/HNF6 0.23 0.32 0.74 95 -1.5 3 98
FOS 0.23 0.35 0.78 98 -1.2 6 104
SP1 0.021 0.008 -10000 0 -10000 0 0
CDC25B 0.25 0.33 0.79 100 -1.1 3 103
response to radiation 0.043 0.059 0.17 72 -10000 0 72
CENPB 0.25 0.33 0.8 98 -1.1 3 101
CENPA 0.27 0.36 0.82 118 -1.1 3 121
NEK2 0.27 0.35 0.84 107 -1.1 3 110
HIST1H2BA 0.24 0.32 0.78 96 -1.1 3 99
CCNA2 0.06 0.078 0.22 99 -10000 0 99
EP300 0.019 0.019 -10000 0 -0.42 1 1
CCNB1/CDK1 0.26 0.35 0.83 95 -1.4 3 98
CCNB2 0.26 0.35 0.84 106 -1.1 3 109
CCNB1 0.27 0.35 0.84 103 -1.2 3 106
ETV5 0.25 0.33 0.79 99 -1.1 3 102
ESR1 0.24 0.33 0.78 96 -1.3 3 99
CCND1 0.23 0.31 0.72 102 -1.1 3 105
GSK3A 0.06 0.061 0.19 68 -10000 0 68
Cyclin A-E1/CDK1-2 0.099 0.098 0.29 92 -10000 0 92
CDK2 0.029 0.021 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.054 0.075 0.19 95 -10000 0 95
FOXM1B/Cbp/p300 0.19 0.26 0.65 67 -1.2 3 70
GAS1 0.2 0.41 0.79 94 -1 24 118
MMP2 0.25 0.33 0.79 98 -1.2 3 101
RB1/FOXM1C 0.2 0.29 0.68 90 -1.1 3 93
CREBBP 0.019 0.004 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.033 0.032 -10000 0 -0.26 5 5
fibroblast growth factor receptor signaling pathway 0.032 0.032 -10000 0 -0.26 5 5
LAMA1 0.012 0.06 0.19 1 -0.42 10 11
PRNP 0.019 0.004 -10000 0 -10000 0 0
GPC1/SLIT2 -0.038 0.13 -10000 0 -0.3 106 106
SMAD2 -0.017 0.023 0.17 4 -0.24 1 5
GPC1/PrPc/Cu2+ 0.025 0.014 -10000 0 -0.25 1 1
GPC1/Laminin alpha1 0.022 0.045 -10000 0 -0.3 10 10
TDGF1 -0.21 0.21 -10000 0 -0.42 273 273
CRIPTO/GPC1 -0.15 0.16 -10000 0 -0.3 272 272
APP/GPC1 0.027 0.017 -10000 0 -0.3 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.15 0.11 -10000 0 -0.26 268 268
FLT1 0.021 0.017 0.19 5 -10000 0 5
GPC1/TGFB/TGFBR1/TGFBR2 0.027 0.023 -10000 0 -0.26 1 1
SERPINC1 -0.01 0.11 0.19 6 -0.42 37 43
FYN -0.15 0.12 -10000 0 -0.26 267 267
FGR -0.15 0.11 -10000 0 -0.26 268 268
positive regulation of MAPKKK cascade -0.21 0.14 0.35 3 -0.31 289 292
SLIT2 -0.069 0.18 0.19 2 -0.42 108 110
GPC1/NRG 0.017 0.053 -10000 0 -0.3 14 14
NRG1 0.007 0.068 -10000 0 -0.42 13 13
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.081 0.059 0.26 3 -10000 0 3
LYN -0.15 0.11 -10000 0 -0.26 262 262
mol:Spermine -0.01 0.013 -10000 0 -0.29 1 1
cell growth 0.032 0.032 -10000 0 -0.26 5 5
BMP signaling pathway -0.018 0.02 0.42 1 -10000 0 1
SRC -0.15 0.11 -10000 0 -0.26 264 264
TGFBR1 0.019 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.032 0.047 0.19 43 -10000 0 43
GPC1 0.018 0.02 -10000 0 -0.42 1 1
TGFBR1 (dimer) 0.019 0.004 -10000 0 -10000 0 0
VEGFA 0.093 0.084 0.19 232 -10000 0 232
BLK -0.14 0.12 -10000 0 -0.25 270 270
HCK -0.14 0.12 0.1 10 -0.26 264 274
FGF2 0.017 0.039 0.19 1 -0.42 4 5
FGFR1 0.018 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer 0.021 0.017 0.19 5 -10000 0 5
TGFBR2 0.014 0.009 -10000 0 -10000 0 0
cell death 0.027 0.017 -10000 0 -0.3 1 1
ATIII/GPC1 0.005 0.087 -10000 0 -0.3 38 38
PLA2G2A/GPC1 0.036 0.037 -10000 0 -0.3 1 1
LCK -0.15 0.11 0.1 6 -0.26 270 276
neuron differentiation 0.017 0.053 -10000 0 -0.3 14 14
PrPc/Cu2+ 0.014 0.003 -10000 0 -10000 0 0
APP 0.019 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.014 0.009 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.28 0.18 -10000 0 -0.35 425 425
SMAD6-7/SMURF1 0.036 0.014 -10000 0 -10000 0 0
NOG 0.03 0.094 0.19 70 -0.42 14 84
SMAD9 -0.07 0.16 -10000 0 -0.6 39 39
SMAD4 0.02 0.003 -10000 0 -10000 0 0
SMAD5 -0.13 0.12 -10000 0 -0.41 29 29
BMP7/USAG1 -0.32 0.21 -10000 0 -0.42 402 402
SMAD5/SKI -0.13 0.13 0.28 3 -0.39 37 40
SMAD1 -0.052 0.057 -10000 0 -0.39 3 3
BMP2 0.017 0.033 -10000 0 -0.42 3 3
SMAD1/SMAD1/SMAD4 -0.051 0.063 -10000 0 -0.36 3 3
BMPR1A 0.019 0.004 -10000 0 -10000 0 0
BMPR1B -0.28 0.2 0.19 1 -0.42 358 359
BMPR1A-1B/BAMBI -0.17 0.14 -10000 0 -0.26 357 357
AHSG 0.022 0.025 0.19 11 -10000 0 11
CER1 0.018 0.004 -10000 0 -10000 0 0
BMP2-4/CER1 0.033 0.029 -10000 0 -0.26 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.099 -10000 0 -0.36 14 14
BMP2-4 (homodimer) 0.025 0.03 -10000 0 -0.3 4 4
RGMB 0.018 0.013 0.19 2 -10000 0 2
BMP6/BMPR2/BMPR1A-1B -0.15 0.13 -10000 0 -0.24 346 346
RGMA 0.016 0.042 -10000 0 -0.42 5 5
SMURF1 0.018 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.1 -10000 0 -0.31 31 31
BMP2-4/USAG1 -0.14 0.14 -10000 0 -0.26 297 297
SMAD6/SMURF1/SMAD5 -0.13 0.13 0.28 1 -0.4 35 36
SOSTDC1 -0.23 0.22 0.19 1 -0.42 298 299
BMP7/BMPR2/BMPR1A-1B -0.28 0.17 -10000 0 -0.35 430 430
SKI 0.019 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) 0.014 0.05 -10000 0 -0.42 7 7
HFE2 0.025 0.031 0.19 18 -10000 0 18
ZFYVE16 0.018 0.006 -10000 0 -10000 0 0
MAP3K7 0.019 0.005 -10000 0 -10000 0 0
BMP2-4/CHRD 0.032 0.042 -10000 0 -0.29 7 7
SMAD5/SMAD5/SMAD4 -0.14 0.13 0.26 2 -0.39 40 42
MAPK1 0.02 0.002 -10000 0 -10000 0 0
TAK1/TAB family -0.1 0.099 -10000 0 -0.29 29 29
BMP7 (homodimer) -0.26 0.21 -10000 0 -0.42 340 340
NUP214 0.019 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.027 0.034 -10000 0 -0.3 4 4
SMAD1/SKI -0.05 0.066 0.31 1 -0.36 4 5
SMAD6 0.02 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA 0.036 0.031 -10000 0 -0.26 3 3
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.078 0.19 0.19 10 -0.42 122 132
BMPR2 (homodimer) 0.019 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.036 0.013 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.19 0.15 -10000 0 -0.3 355 355
CHRDL1 -0.2 0.22 -10000 0 -0.42 270 270
ENDOFIN/SMAD1 -0.046 0.065 0.31 1 -0.37 4 5
SMAD6-7/SMURF1/SMAD1 -0.046 0.067 -10000 0 -0.36 4 4
SMAD6/SMURF1 0.018 0.006 -10000 0 -10000 0 0
BAMBI 0.015 0.046 -10000 0 -0.42 6 6
SMURF2 0.019 0.019 -10000 0 -0.42 1 1
BMP2-4/CHRDL1 -0.11 0.15 -10000 0 -0.26 264 264
BMP2-4/GREM1 -0.03 0.13 -10000 0 -0.26 120 120
SMAD7 0.02 0.003 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.076 0.16 -10000 0 -0.55 48 48
SMAD1/SMAD6 -0.048 0.062 -10000 0 -0.37 4 4
TAK1/SMAD6 0.025 0.011 -10000 0 -10000 0 0
BMP7 -0.26 0.21 -10000 0 -0.42 340 340
BMP6 0.014 0.05 -10000 0 -0.42 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.089 0.097 -10000 0 -0.3 26 26
PPM1A 0.019 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.052 0.066 0.31 1 -0.37 4 5
SMAD7/SMURF1 0.026 0.01 -10000 0 -10000 0 0
CTDSPL 0.014 0.009 -10000 0 -10000 0 0
PPP1CA 0.02 0.002 -10000 0 -10000 0 0
XIAP 0.02 0.002 -10000 0 -10000 0 0
CTDSP1 0.019 0.005 -10000 0 -10000 0 0
PPP1R15A 0.02 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.14 0.14 -10000 0 -0.41 61 61
CHRD 0.015 0.048 0.19 3 -0.42 6 9
BMPR2 0.019 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.11 0.11 -10000 0 -0.32 34 34
BMP4 0.016 0.033 -10000 0 -0.42 3 3
FST -0.016 0.12 0.19 10 -0.42 45 55
BMP2-4/NOG 0.039 0.067 -10000 0 -0.25 18 18
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.26 0.17 -10000 0 -0.34 412 412
TCGA08_p53

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
CDKN2A 0.094 0.032 0.1 474 -10000 0 474
TP53 0.036 0.018 -10000 0 -0.16 1 1
Senescence 0.036 0.018 -10000 0 -0.16 1 1
Apoptosis 0.036 0.018 -10000 0 -0.16 1 1
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.066 0.028 0.29 1 -10000 0 1
MDM4 0.019 0.004 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.009 0.1 -10000 0 -0.54 15 15
oxygen homeostasis 0.016 0.014 -10000 0 -10000 0 0
TCEB2 0.019 0.022 0.19 2 -0.42 1 3
TCEB1 0.019 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.084 0.091 0.25 25 -0.31 1 26
EPO 0.21 0.18 0.45 140 -10000 0 140
FIH (dimer) 0.034 0.015 -10000 0 -10000 0 0
APEX1 0.038 0.02 -10000 0 -10000 0 0
SERPINE1 0.18 0.16 0.42 105 -10000 0 105
FLT1 0.018 0.082 -10000 0 -0.63 4 4
ADORA2A 0.18 0.14 0.39 93 -10000 0 93
germ cell development 0.21 0.17 0.42 164 -10000 0 164
SLC11A2 0.18 0.14 0.4 86 -10000 0 86
BHLHE40 0.14 0.15 0.4 68 -10000 0 68
HIF1AN 0.034 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.19 0.14 0.35 144 -10000 0 144
ETS1 0.022 0.011 -10000 0 -10000 0 0
CITED2 -0.008 0.13 -10000 0 -0.61 12 12
KDR 0.019 0.063 -10000 0 -0.63 2 2
PGK1 0.19 0.14 0.4 90 -10000 0 90
SIRT1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0.002 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.25 0.18 0.46 148 -10000 0 148
EPAS1 0.12 0.087 0.22 158 -0.33 1 159
SP1 0.022 0.011 -10000 0 -10000 0 0
ABCG2 0.19 0.14 0.4 90 -10000 0 90
EFNA1 0.19 0.14 0.4 89 -10000 0 89
FXN 0.18 0.14 0.38 92 -10000 0 92
POU5F1 0.22 0.17 0.42 164 -10000 0 164
neuron apoptosis -0.25 0.18 -10000 0 -0.45 150 150
EP300 0.019 0.019 -10000 0 -0.42 1 1
EGLN3 0.17 0.079 0.2 437 -0.41 2 439
EGLN2 0.036 0.015 -10000 0 -10000 0 0
EGLN1 0.034 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.027 0.025 -10000 0 -0.26 1 1
VHL 0.014 0.009 -10000 0 -10000 0 0
ARNT 0.038 0.02 -10000 0 -10000 0 0
SLC2A1 0.18 0.14 0.4 98 -10000 0 98
TWIST1 0.16 0.14 0.39 86 -10000 0 86
ELK1 0.021 0.006 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.16 0.12 0.33 78 -10000 0 78
VEGFA 0.22 0.17 0.42 184 -10000 0 184
CREBBP 0.019 0.004 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.022 0.19 7 -10000 0 7
CDKN2C -0.03 0.012 -10000 0 -10000 0 0
CDKN2A 0.17 0.055 0.19 473 -10000 0 473
CCND2 -0.042 0.024 -10000 0 -0.14 5 5
RB1 0.045 0.029 0.17 6 -10000 0 6
CDK4 -0.048 0.027 -10000 0 -0.14 6 6
CDK6 -0.047 0.026 -10000 0 -0.14 6 6
G1/S progression -0.045 0.032 0.18 2 -0.26 2 4
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.026 0.01 -10000 0 -10000 0 0
VLDLR 0.019 0.004 -10000 0 -10000 0 0
CRKL 0.02 0.002 -10000 0 -10000 0 0
LRPAP1 0.02 0.003 -10000 0 -10000 0 0
FYN 0.019 0.005 -10000 0 -10000 0 0
ITGA3 0.02 0.008 0.19 1 -10000 0 1
RELN/VLDLR/Fyn -0.051 0.13 -10000 0 -0.26 153 153
MAPK8IP1/MKK7/MAP3K11/JNK1 0.053 0.033 -10000 0 -0.3 3 3
AKT1 -0.065 0.098 -10000 0 -0.22 137 137
MAP2K7 0.02 0.002 -10000 0 -10000 0 0
RAPGEF1 0.019 0.004 -10000 0 -10000 0 0
DAB1 0.023 0.027 0.19 13 -10000 0 13
RELN/LRP8/DAB1 -0.042 0.12 -10000 0 -0.23 153 153
LRPAP1/LRP8 0.029 0.009 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.035 0.12 -10000 0 -0.22 153 153
DAB1/alpha3/beta1 Integrin -0.037 0.12 -10000 0 -0.22 142 142
long-term memory -0.034 0.13 0.31 1 -0.23 144 145
DAB1/LIS1 -0.03 0.13 -10000 0 -0.22 149 149
DAB1/CRLK/C3G -0.038 0.12 -10000 0 -0.22 151 151
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
DAB1/NCK2 -0.03 0.13 -10000 0 -0.22 150 150
ARHGEF2 0.019 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.023 0.091 0.19 52 -0.42 15 67
CDK5R1 0.02 0.003 -10000 0 -10000 0 0
RELN -0.11 0.2 0.19 5 -0.42 153 158
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
RELN/LRP8/Fyn -0.051 0.13 -10000 0 -0.26 153 153
GRIN2A/RELN/LRP8/DAB1/Fyn -0.029 0.14 0.25 4 -0.23 159 163
MAPK8 0.018 0.027 -10000 0 -0.42 2 2
RELN/VLDLR/DAB1 -0.043 0.12 -10000 0 -0.23 153 153
ITGB1 0.02 0.003 -10000 0 -10000 0 0
MAP1B -0.07 0.11 -10000 0 -0.24 141 141
RELN/LRP8 -0.05 0.13 -10000 0 -0.26 153 153
GRIN2B/RELN/LRP8/DAB1/Fyn -0.03 0.13 -10000 0 -0.23 150 150
PI3K 0.025 0.022 -10000 0 -0.3 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.029 0.008 -10000 0 -10000 0 0
RAP1A -0.067 0.12 0.35 9 -10000 0 9
PAFAH1B1 0.02 0.003 -10000 0 -10000 0 0
MAPK8IP1 0.018 0.027 -10000 0 -0.42 2 2
CRLK/C3G 0.029 0.006 -10000 0 -10000 0 0
GRIN2B 0.019 0.011 0.19 2 -10000 0 2
NCK2 0.019 0.004 -10000 0 -10000 0 0
neuron differentiation -0.051 0.11 -10000 0 -0.37 30 30
neuron adhesion -0.071 0.12 0.35 13 -10000 0 13
LRP8 0.02 0.008 0.19 1 -10000 0 1
GSK3B -0.066 0.093 -10000 0 -0.22 132 132
RELN/VLDLR/DAB1/Fyn -0.037 0.12 -10000 0 -0.22 153 153
MAP3K11 0.019 0.019 -10000 0 -0.42 1 1
RELN/VLDLR/DAB1/P13K -0.06 0.11 -10000 0 -0.23 142 142
CDK5 0.018 0.006 -10000 0 -10000 0 0
MAPT 0.003 0.081 0.74 5 -0.37 4 9
neuron migration -0.086 0.14 0.39 4 -0.3 133 137
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.051 0.11 -10000 0 -0.37 30 30
RELN/VLDLR -0.039 0.13 -10000 0 -0.24 153 153
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.11 0.12 0.32 101 -0.24 1 102
MAP4K1 0.088 0.083 0.19 214 -10000 0 214
MAP3K8 0.02 0.011 0.19 2 -10000 0 2
PRKCB 0.018 0.03 0.19 3 -0.42 2 5
DBNL 0.018 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.002 -10000 0 -10000 0 0
MAP3K1 0.032 0.059 0.2 28 -0.21 1 29
JUN 0.023 0.11 0.31 2 -0.52 16 18
MAP3K7 0.033 0.059 0.2 30 -0.21 1 31
GRAP2 0.03 0.046 0.19 34 -0.42 1 35
CRK 0.02 0.003 -10000 0 -10000 0 0
MAP2K4 0.067 0.088 0.23 83 -0.25 1 84
LAT 0.065 0.076 0.19 144 -10000 0 144
LCP2 0.024 0.04 0.19 29 -10000 0 29
MAPK8 0.028 0.11 -10000 0 -0.55 16 16
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.045 0.065 0.21 44 -0.22 1 45
LAT/GRAP2/SLP76/HPK1/HIP-55 0.1 0.12 0.31 98 -0.23 1 99
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.027 0.04 0.12 26 -10000 0 26
NFATC2 0.025 0.045 0.12 27 -0.22 3 30
NFATC3 0.027 0.04 0.12 25 -10000 0 25
CD40LG 0.12 0.17 0.37 103 -0.48 2 105
PTGS2 0.098 0.17 0.34 91 -0.42 13 104
JUNB 0.018 0.027 -10000 0 -0.42 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.022 -10000 0 -10000 0 0
CaM/Ca2+ 0.029 0.022 -10000 0 -10000 0 0
CALM1 0.026 0.015 -10000 0 -10000 0 0
JUN 0.027 0.016 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.011 -10000 0 -0.1 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.009 -10000 0 -10000 0 0
FOSL1 0.028 0.036 0.19 26 -10000 0 26
CREM 0.019 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.12 0.13 0.32 94 -10000 0 94
FOS 0.018 0.065 0.19 1 -0.41 11 12
IFNG 0.15 0.18 0.34 212 -0.39 2 214
AP-1/NFAT1-c-4 0.19 0.2 0.39 215 -0.44 2 217
FASLG 0.16 0.19 0.35 220 -0.39 2 222
NFAT1-c-4/ICER1 0.059 0.088 0.2 75 -10000 0 75
IL2RA 0.12 0.17 0.39 106 -0.39 2 108
FKBP12/FK506 0.014 0.003 -10000 0 -10000 0 0
CSF2 0.089 0.15 0.35 81 -0.39 2 83
JunB/Fra1/NFAT1-c-4 0.071 0.093 0.21 89 -10000 0 89
IL4 0.086 0.14 0.33 79 -0.39 2 81
IL2 -0.001 0.1 -10000 0 -0.87 7 7
IL3 -0.003 0.082 -10000 0 -0.59 9 9
FKBP1A 0.019 0.004 -10000 0 -10000 0 0
BATF3 0.034 0.047 0.19 45 -10000 0 45
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.004 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.058 0.066 0.24 22 -0.31 1 23
alphaM/beta2 Integrin/GPIbA 0.057 0.065 0.25 18 -0.26 1 19
alphaM/beta2 Integrin/proMMP-9 0.1 0.095 0.27 82 -10000 0 82
PLAUR 0.028 0.036 0.19 25 -10000 0 25
HMGB1 0.016 0.021 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.056 0.064 0.26 16 -10000 0 16
AGER 0.046 0.069 0.19 93 -10000 0 93
RAP1A 0.019 0.004 -10000 0 -10000 0 0
SELPLG 0.03 0.04 0.19 32 -10000 0 32
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.078 0.1 0.26 52 -0.23 23 75
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.094 0.084 0.19 234 -10000 0 234
CYR61 0.017 0.033 -10000 0 -0.42 3 3
TLN1 0.019 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.1 0.11 -10000 0 -0.34 55 55
RHOA 0.014 0.009 -10000 0 -10000 0 0
P-selectin oligomer 0.002 0.085 -10000 0 -0.42 21 21
MYH2 -0.17 0.14 -10000 0 -0.36 116 116
MST1R 0.012 0.04 0.19 2 -0.42 4 6
leukocyte activation during inflammatory response 0.073 0.082 0.23 50 -0.22 7 57
APOB 0.06 0.1 0.19 154 -0.42 10 164
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.02 0.025 0.19 5 -0.42 1 6
JAM3 0.02 0.002 -10000 0 -10000 0 0
GP1BA 0.019 0.019 -10000 0 -0.42 1 1
alphaM/beta2 Integrin/CTGF 0.052 0.071 0.25 18 -0.27 5 23
alphaM/beta2 Integrin -0.12 0.12 0.16 2 -0.33 77 79
JAM3 homodimer 0.02 0.002 -10000 0 -10000 0 0
ICAM2 0.02 0.003 -10000 0 -10000 0 0
ICAM1 0.024 0.024 0.19 11 -10000 0 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.12 0.15 2 -0.35 66 68
cell adhesion 0.056 0.065 0.25 18 -0.26 1 19
NFKB1 0.006 0.12 0.28 15 -0.38 26 41
THY1 0.019 0.019 -10000 0 -0.42 1 1
RhoA/GDP 0.011 0.007 -10000 0 -10000 0 0
Lipoprotein(a) 0.049 0.065 0.14 56 -0.25 10 66
alphaM/beta2 Integrin/LRP/tPA 0.057 0.072 0.26 17 -0.23 7 24
IL6 -0.016 0.17 0.27 24 -0.63 29 53
ITGB2 0.048 0.071 0.19 98 -10000 0 98
elevation of cytosolic calcium ion concentration 0.063 0.077 0.27 22 -0.27 6 28
alphaM/beta2 Integrin/JAM2/JAM3 0.066 0.063 0.26 17 -10000 0 17
JAM2 0.019 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 0.057 0.075 0.26 21 -0.23 3 24
alphaM/beta2 Integrin/uPA/Plg -0.075 0.15 0.25 11 -0.23 228 239
RhoA/GTP -0.17 0.15 -10000 0 -0.36 128 128
positive regulation of phagocytosis -0.072 0.11 0.22 13 -0.3 44 57
Ron/MSP 0.02 0.038 0.15 8 -0.3 5 13
alphaM/beta2 Integrin/uPAR/uPA 0.066 0.078 0.28 22 -0.27 6 28
alphaM/beta2 Integrin/uPAR 0.062 0.071 0.28 23 -10000 0 23
PLAU 0.014 0.047 -10000 0 -0.42 6 6
PLAT 0.011 0.057 -10000 0 -0.42 9 9
actin filament polymerization -0.16 0.13 -10000 0 -0.34 115 115
MST1 0.015 0.028 0.19 6 -0.42 1 7
alphaM/beta2 Integrin/lipoprotein(a) 0.08 0.087 0.25 50 -0.22 7 57
TNF -0.005 0.12 0.33 6 -0.43 22 28
RAP1B 0.019 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.054 0.073 0.25 18 -0.27 7 25
fibrinolysis -0.076 0.15 0.24 11 -0.23 228 239
HCK 0.028 0.037 0.19 27 -10000 0 27
dendritic cell antigen processing and presentation -0.12 0.12 0.15 2 -0.35 66 68
VTN -0.037 0.15 0.19 6 -0.42 70 76
alphaM/beta2 Integrin/CYR61 0.055 0.07 0.25 18 -0.33 3 21
LPA 0.018 0.012 0.19 2 -10000 0 2
LRP1 0.02 0.003 -10000 0 -10000 0 0
cell migration 0.075 0.08 0.23 73 -0.29 1 74
FN1 0.031 0.043 0.19 36 -10000 0 36
alphaM/beta2 Integrin/Thy1 0.057 0.065 0.25 18 -0.26 1 19
MPO 0.025 0.03 0.19 17 -10000 0 17
KNG1 -0.29 0.2 -10000 0 -0.42 373 373
RAP1/GDP 0.025 0.007 -10000 0 -10000 0 0
ROCK1 -0.17 0.14 -10000 0 -0.36 117 117
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.19 0.22 -10000 0 -0.42 246 246
CTGF 0.013 0.05 -10000 0 -0.42 7 7
alphaM/beta2 Integrin/Hck 0.062 0.078 0.3 31 -10000 0 31
ITGAM 0.023 0.039 0.19 20 -10000 0 20
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.06 0.088 0.27 34 -0.23 13 47
HP 0.057 0.08 0.19 124 -0.42 3 127
leukocyte adhesion 0.053 0.086 0.24 28 -0.26 5 33
SELP 0.002 0.086 -10000 0 -0.42 21 21
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.015 0.053 -10000 0 -0.24 14 14
epithelial cell differentiation 0.017 0.046 -10000 0 -0.22 14 14
CYFIP2 0.009 0.05 -10000 0 -0.42 7 7
ENAH -0.002 0.097 0.32 19 -10000 0 19
EGFR 0.019 0.026 0.19 5 -0.42 1 6
EPHA2 0.018 0.019 -10000 0 -0.42 1 1
MYO6 0.016 0.1 0.18 116 -0.22 15 131
CTNNB1 0.014 0.009 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.025 0.038 -10000 0 -0.26 7 7
AQP5 -0.11 0.2 -10000 0 -0.42 139 139
CTNND1 0.02 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.1 0.18 121 -0.21 13 134
regulation of calcium-dependent cell-cell adhesion 0.019 0.1 0.19 120 -0.21 15 135
EGF -0.37 0.14 -10000 0 -0.42 467 467
NCKAP1 0.019 0.004 -10000 0 -10000 0 0
AQP3 -0.031 0.13 -10000 0 -0.44 38 38
cortical microtubule organization 0.017 0.046 -10000 0 -0.22 14 14
GO:0000145 0.017 0.099 0.18 121 -0.2 13 134
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.048 -10000 0 -0.22 14 14
MLLT4 0.018 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.036 0.035 -10000 0 -10000 0 0
ARF6 0.019 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.025 -10000 0 -0.24 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.004 0.07 0.28 3 -10000 0 3
PVRL2 0.02 0.002 -10000 0 -10000 0 0
ZYX 0.006 0.085 0.17 93 -0.22 14 107
ARF6/GTP 0.046 0.03 -10000 0 -0.23 2 2
CDH1 0.005 0.077 -10000 0 -0.42 17 17
EGFR/EGFR/EGF/EGF -0.15 0.1 -10000 0 -0.22 337 337
RhoA/GDP 0.019 0.045 -10000 0 -0.21 14 14
actin cytoskeleton organization 0.009 0.091 0.16 114 -0.22 14 128
IGF-1R heterotetramer 0.02 0.002 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
IGF1R 0.02 0.002 -10000 0 -10000 0 0
IGF1 0.021 0.017 0.19 5 -10000 0 5
DIAPH1 0.01 0.1 -10000 0 -0.59 10 10
Wnt receptor signaling pathway -0.017 0.046 0.22 14 -10000 0 14
RHOA 0.014 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.035 0.037 -10000 0 -0.22 12 12
CTNNA1 0.015 0.009 -10000 0 -10000 0 0
VCL 0.009 0.092 0.16 114 -0.22 14 128
EFNA1 0.019 0.009 0.19 1 -10000 0 1
LPP 0.003 0.086 0.17 93 -0.21 12 105
Ephrin A1/EPHA2 0.012 0.045 -10000 0 -0.22 14 14
SEC6/SEC8 -0.033 0.035 -10000 0 -0.21 13 13
MGAT3 0.019 0.1 0.19 120 -0.22 15 135
HGF/MET 0.011 0.05 -10000 0 -0.21 18 18
HGF 0.014 0.062 0.19 10 -0.42 9 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.015 0.054 -10000 0 -0.24 14 14
actin cable formation 0.033 0.13 0.3 54 -0.3 1 55
KIAA1543 0.013 0.094 0.17 118 -0.22 16 134
KIFC3 0.007 0.085 0.16 106 -0.22 15 121
NCK1 0.018 0.02 -10000 0 -0.42 1 1
EXOC3 0.018 0.006 -10000 0 -10000 0 0
ACTN1 0.01 0.094 0.18 101 -0.22 12 113
NCK1/GIT1 0.027 0.016 -10000 0 -0.3 1 1
mol:GDP 0.017 0.046 -10000 0 -0.22 14 14
EXOC4 0.018 0.006 -10000 0 -10000 0 0
STX4 0.007 0.084 0.16 104 -0.22 14 118
PIP5K1C 0.018 0.1 0.19 121 -0.22 13 134
LIMA1 0.02 0.003 -10000 0 -10000 0 0
ABI1 0.02 0.003 -10000 0 -10000 0 0
ROCK1 0.005 0.11 0.35 21 -10000 0 21
adherens junction assembly 0.025 0.13 0.44 19 -0.43 4 23
IGF-1R heterotetramer/IGF1 0.014 0.043 -10000 0 -0.22 12 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.027 0.009 -10000 0 -10000 0 0
MET 0.019 0.012 0.19 2 -10000 0 2
PLEKHA7 0.013 0.098 0.18 118 -0.23 16 134
mol:GTP 0.043 0.025 -10000 0 -0.24 2 2
establishment of epithelial cell apical/basal polarity 0.018 0.13 0.34 50 -10000 0 50
cortical actin cytoskeleton stabilization -0.015 0.053 -10000 0 -0.24 14 14
regulation of cell-cell adhesion 0.009 0.091 0.16 114 -0.22 14 128
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.015 0.054 -10000 0 -0.24 14 14
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 0.2 0.28 0.64 33 -1.2 7 40
IL23A 0.2 0.26 0.64 26 -1.1 6 32
NF kappa B1 p50/RelA/I kappa B alpha 0.19 0.24 0.55 16 -1.1 5 21
positive regulation of T cell mediated cytotoxicity 0.22 0.29 0.66 57 -1.3 5 62
ITGA3 0.2 0.25 0.64 23 -1.1 5 28
IL17F 0.16 0.21 0.47 70 -0.74 4 74
IL12B 0.073 0.089 0.24 87 -10000 0 87
STAT1 (dimer) 0.2 0.26 0.6 31 -1.2 5 36
CD4 0.21 0.26 0.64 40 -1.1 5 45
IL23 0.16 0.25 0.62 24 -1.1 5 29
IL23R 0.088 0.17 0.5 6 -0.62 14 20
IL1B 0.2 0.26 0.66 24 -1.2 5 29
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.2 0.26 0.64 38 -1.1 5 43
TYK2 0.045 0.037 0.18 1 -10000 0 1
STAT4 0.029 0.039 0.19 30 -10000 0 30
STAT3 0.02 0.003 -10000 0 -10000 0 0
IL18RAP 0.068 0.077 0.2 136 -10000 0 136
IL12RB1 0.099 0.1 0.25 159 -10000 0 159
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
IL12Rbeta1/TYK2 0.097 0.084 0.22 149 -10000 0 149
IL23R/JAK2 0.12 0.18 0.47 19 -0.77 4 23
positive regulation of chronic inflammatory response 0.22 0.29 0.66 57 -1.3 5 62
natural killer cell activation -0.01 0.011 -10000 0 -0.039 25 25
JAK2 0.064 0.062 0.21 27 -10000 0 27
PIK3R1 0.018 0.02 -10000 0 -0.42 1 1
NFKB1 0.021 0.023 -10000 0 -0.42 1 1
RELA 0.022 0.012 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.15 0.24 0.61 27 -1 5 32
ALOX12B 0.21 0.27 0.65 42 -1.1 5 47
CXCL1 0.18 0.32 0.66 36 -1.1 13 49
T cell proliferation 0.22 0.29 0.66 57 -1.3 5 62
NFKBIA 0.021 0.013 -10000 0 -10000 0 0
IL17A 0.15 0.18 0.41 93 -0.57 4 97
PI3K 0.18 0.25 0.57 28 -1.2 5 33
IFNG 0.059 0.063 0.13 211 -0.11 4 215
STAT3 (dimer) 0.17 0.24 0.56 19 -1.2 4 23
IL18R1 0.022 0.039 0.19 4 -0.42 3 7
IL23/IL23R/JAK2/TYK2/SOCS3 0.19 0.21 0.49 88 -1.1 1 89
IL18/IL18R 0.096 0.072 0.22 89 -0.24 3 92
macrophage activation 0.009 0.017 0.033 121 -0.045 3 124
TNF 0.2 0.28 0.64 30 -1.1 8 38
STAT3/STAT4 0.2 0.26 0.59 39 -1.2 5 44
STAT4 (dimer) 0.2 0.27 0.62 40 -1.2 5 45
IL18 0.025 0.022 0.19 5 -10000 0 5
IL19 0.2 0.26 0.63 37 -1.1 5 42
STAT5A (dimer) 0.2 0.26 0.6 32 -1.2 5 37
STAT1 0.02 0.009 0.19 1 -10000 0 1
SOCS3 0.021 0.015 0.19 4 -10000 0 4
CXCL9 0.23 0.28 0.67 55 -1.1 5 60
MPO 0.2 0.26 0.64 38 -1.1 5 43
positive regulation of humoral immune response 0.22 0.29 0.66 57 -1.3 5 62
IL23/IL23R/JAK2/TYK2 0.22 0.3 0.67 52 -1.4 5 57
IL6 0.18 0.35 0.66 36 -1.1 23 59
STAT5A 0.02 0.003 -10000 0 -10000 0 0
IL2 0.027 0.041 0.21 9 -10000 0 9
positive regulation of tyrosine phosphorylation of STAT protein -0.01 0.011 -10000 0 -0.039 25 25
CD3E 0.23 0.28 0.66 59 -1.1 5 64
keratinocyte proliferation 0.22 0.29 0.66 57 -1.3 5 62
NOS2 0.2 0.26 0.63 36 -1.1 5 41
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.019 0.005 -10000 0 -10000 0 0
VLDLR 0.019 0.004 -10000 0 -10000 0 0
LRPAP1 0.02 0.003 -10000 0 -10000 0 0
NUDC 0.019 0.004 -10000 0 -10000 0 0
RELN/LRP8 -0.05 0.13 -10000 0 -0.26 153 153
CaM/Ca2+ 0.014 0.004 -10000 0 -10000 0 0
KATNA1 0.018 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.072 0.12 0.17 35 -0.24 153 188
IQGAP1/CaM 0.028 0.008 -10000 0 -10000 0 0
DAB1 0.023 0.027 0.19 13 -10000 0 13
IQGAP1 0.02 0.002 -10000 0 -10000 0 0
PLA2G7 0.14 0.076 0.19 382 -10000 0 382
CALM1 0.019 0.005 -10000 0 -10000 0 0
DYNLT1 0.018 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.029 0.009 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.019 0.004 -10000 0 -10000 0 0
CDK5R1 0.02 0.003 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.014 0.004 -10000 0 -10000 0 0
CDK5R2 0.038 0.054 0.19 60 -10000 0 60
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.049 0.14 -10000 0 -0.26 153 153
YWHAE 0.02 0.003 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.048 0.13 0.3 40 -0.27 3 43
MAP1B 0.002 0.001 -10000 0 -10000 0 0
RAC1 0.003 0.001 -10000 0 -10000 0 0
p35/CDK5 -0.081 0.09 0.16 2 -0.22 136 138
RELN -0.11 0.2 0.19 5 -0.42 153 158
PAFAH/LIS1 0.095 0.072 0.14 379 -10000 0 379
LIS1/CLIP170 -0.021 0.006 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.075 0.076 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.061 0.11 -10000 0 -0.32 17 17
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.063 0.1 0.35 9 -0.26 3 12
LIS1/IQGAP1 -0.021 0.006 -10000 0 -10000 0 0
RHOA 0.003 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.018 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.019 0.019 -10000 0 -0.42 1 1
PAFAH1B2 0.019 0.019 -10000 0 -0.42 1 1
MAP1B/LIS1/Dynein heavy chain 0.019 0.02 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.054 0.12 0.3 31 -10000 0 31
LRP8 0.02 0.008 0.19 1 -10000 0 1
NDEL1/Katanin 60 -0.05 0.13 0.3 36 -0.27 3 39
P39/CDK5 -0.062 0.12 0.34 13 -0.22 126 139
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.021 0.006 -10000 0 -10000 0 0
CDK5 -0.081 0.094 0.16 3 -0.23 150 153
PPP2R5D 0.019 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.017 0.005 -10000 0 -10000 0 0
CSNK2A1 0.019 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.041 0.12 -10000 0 -0.23 151 151
RELN/VLDLR -0.039 0.13 -10000 0 -0.24 153 153
CDC42 0.004 0.001 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.02 0.005 -10000 0 -10000 0 0
SVIL 0.02 0.004 -10000 0 -10000 0 0
ZNF318 0.018 0.011 -10000 0 -10000 0 0
JMJD2C 0.003 0.015 0.083 18 -10000 0 18
T-DHT/AR/Ubc9 -0.084 0.061 -10000 0 -0.26 29 29
CARM1 0.02 0.002 -10000 0 -10000 0 0
PRDX1 0.019 0.006 -10000 0 -10000 0 0
PELP1 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.015 0.01 -10000 0 -10000 0 0
AKT1 0.017 0.01 -10000 0 -10000 0 0
PTK2B 0.018 0.006 -10000 0 -10000 0 0
MED1 0.019 0.007 -10000 0 -10000 0 0
MAK 0.018 0.013 0.19 1 -10000 0 1
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.015 0.038 -10000 0 -0.41 4 4
GSN 0.02 0.005 -10000 0 -10000 0 0
NCOA2 0.011 0.06 -10000 0 -0.42 10 10
NCOA6 0.02 0.005 -10000 0 -10000 0 0
DNA-PK 0.034 0.018 -10000 0 -10000 0 0
NCOA4 0.02 0.003 -10000 0 -10000 0 0
PIAS3 0.019 0.005 -10000 0 -10000 0 0
cell proliferation -0.054 0.091 -10000 0 -0.54 17 17
XRCC5 0.018 0.008 -10000 0 -10000 0 0
UBE3A 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.095 0.076 -10000 0 -0.29 43 43
FHL2 -0.072 0.084 -10000 0 -0.46 17 17
RANBP9 0.02 0.005 -10000 0 -10000 0 0
JMJD1A -0.11 0.046 -10000 0 -0.13 454 454
CDK6 0.017 0.02 -10000 0 -0.42 1 1
TGFB1I1 0.02 0.009 0.19 1 -10000 0 1
T-DHT/AR/CyclinD1 -0.084 0.062 0.18 1 -0.26 28 29
XRCC6 0.018 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.15 0.078 -10000 0 -0.18 447 447
CTDSP1 0.019 0.005 -10000 0 -10000 0 0
CTDSP2 0.018 0.011 -10000 0 -10000 0 0
BRCA1 0.02 0.004 -10000 0 -10000 0 0
TCF4 0.018 0.01 -10000 0 -10000 0 0
CDKN2A 0.17 0.055 0.19 474 -10000 0 474
SRF 0.018 0.015 -10000 0 -0.15 3 3
NKX3-1 -0.2 0.074 -10000 0 -0.22 464 464
KLK3 -0.004 0.053 -10000 0 -10000 0 0
TMF1 0.016 0.008 -10000 0 -10000 0 0
HNRNPA1 0.018 0.009 -10000 0 -10000 0 0
AOF2 0.001 0.003 -10000 0 -10000 0 0
APPL1 -0.014 0.01 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.086 0.06 -10000 0 -0.26 29 29
AR -0.084 0.086 -10000 0 -0.44 25 25
UBA3 0.016 0.008 -10000 0 -10000 0 0
PATZ1 0.018 0.009 -10000 0 -10000 0 0
PAWR 0.019 0.019 -10000 0 -0.42 1 1
PRKDC 0.017 0.009 -10000 0 -10000 0 0
PA2G4 0.018 0.009 -10000 0 -10000 0 0
UBE2I 0.019 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.078 0.054 -10000 0 -0.23 31 31
RPS6KA3 0.02 0.019 -10000 0 -0.41 1 1
T-DHT/AR/ARA70 -0.087 0.059 -10000 0 -0.28 24 24
LATS2 0.018 0.009 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.078 0.053 -10000 0 -0.26 25 25
Cyclin D3/CDK11 p58 0.014 0.004 -10000 0 -10000 0 0
VAV3 0.008 0.07 -10000 0 -0.42 14 14
KLK2 -0.061 0.054 -10000 0 -0.52 1 1
CASP8 0.018 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.082 0.069 -10000 0 -0.3 26 26
TMPRSS2 -0.71 0.28 -10000 0 -0.82 456 456
CCND1 0.026 0.031 0.19 18 -10000 0 18
PIAS1 0.021 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.052 0.022 -10000 0 -0.06 453 453
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.021 0.006 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.063 -10000 0 -0.26 25 25
CMTM2 0.022 0.025 0.19 11 -10000 0 11
SNURF 0.006 0.077 -10000 0 -0.42 17 17
ZMIZ1 -0.062 0.035 -10000 0 -0.15 1 1
CCND3 0.019 0.004 -10000 0 -10000 0 0
TGIF1 0.018 0.009 -10000 0 -10000 0 0
FKBP4 0.02 0.005 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.003 0.072 -10000 0 -0.25 38 38
EFNA5 -0.014 0.11 0.19 2 -0.42 38 40
FYN -0.005 0.091 0.17 76 -0.23 38 114
neuron projection morphogenesis 0.003 0.072 -10000 0 -0.25 38 38
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.003 0.073 -10000 0 -0.25 38 38
EPHA5 0.021 0.02 0.19 7 -10000 0 7
Arf6 signaling events

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
CENTA1/KIF3B 0.02 0.026 -10000 0 -0.25 4 4
ARNO/beta Arrestin1-2 0.022 0.043 -10000 0 -0.8 1 1
EGFR 0.019 0.026 0.19 5 -0.42 1 6
EPHA2 0.018 0.019 -10000 0 -0.42 1 1
USP6 0.02 0.008 0.19 1 -10000 0 1
IQSEC1 0.014 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.24 0.12 -10000 0 -0.3 422 422
ARRB2 0.011 0.022 -10000 0 -10000 0 0
mol:GTP 0.017 0.038 0.17 9 -0.16 6 15
ARRB1 0.02 0.002 -10000 0 -10000 0 0
FBXO8 0.02 0.003 -10000 0 -10000 0 0
TSHR 0.038 0.054 0.19 60 -10000 0 60
EGF -0.37 0.14 -10000 0 -0.42 467 467
somatostatin receptor activity 0 0 0.001 29 -0.001 31 60
ARAP2 0.018 0.027 -10000 0 -0.42 2 2
mol:GDP -0.032 0.088 0.18 19 -0.29 23 42
mol:PI-3-4-5-P3 0 0 0.001 24 -0.001 15 39
ITGA2B 0.025 0.036 0.19 18 -0.42 1 19
ARF6 0.019 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.025 -10000 0 -0.24 2 2
ADAP1 0.015 0.038 -10000 0 -0.42 4 4
KIF13B 0.018 0.006 -10000 0 -10000 0 0
HGF/MET 0.023 0.048 0.27 1 -0.3 9 10
PXN 0.019 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.046 0.1 0.23 28 -0.28 31 59
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.2 0.1 -10000 0 -0.25 422 422
ADRB2 0.014 0.028 -10000 0 -0.42 2 2
receptor agonist activity 0 0 0 30 0 19 49
actin filament binding 0 0 0.001 29 -0.001 32 61
SRC 0.019 0.004 -10000 0 -10000 0 0
ITGB3 0.015 0.043 -10000 0 -0.42 5 5
GNAQ 0.019 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 35 -0.001 19 54
ARF6/GDP -0.002 0.099 0.26 7 -0.39 15 22
ARF6/GDP/GULP/ACAP1 0.006 0.11 0.24 12 -0.31 14 26
alphaIIb/beta3 Integrin/paxillin/GIT1 0.049 0.037 -10000 0 -0.23 6 6
ACAP1 0.084 0.082 0.19 203 -10000 0 203
ACAP2 0.019 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.026 0.037 0.16 38 -10000 0 38
EFNA1 0.019 0.009 0.19 1 -10000 0 1
HGF 0.014 0.062 0.19 10 -0.42 9 19
CYTH3 -0.009 0.003 -10000 0 -10000 0 0
CYTH2 0.012 0.044 -10000 0 -1 1 1
NCK1 0.018 0.02 -10000 0 -0.42 1 1
fibronectin binding 0 0 0.001 47 0 24 71
endosomal lumen acidification 0 0 0.001 10 0 32 42
microtubule-based process 0 0 -10000 0 0 3 3
GULP1 0.006 0.075 0.19 1 -0.42 16 17
GNAQ/ARNO 0.022 0.043 -10000 0 -0.94 1 1
mol:Phosphatidic acid 0 0 0 8 -10000 0 8
PIP3-E 0 0 0 3 0 10 13
MET 0.019 0.012 0.19 2 -10000 0 2
GNA14 0.014 0.05 -10000 0 -0.42 7 7
GNA15 0.025 0.028 0.19 15 -10000 0 15
GIT1 0.02 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 34 -0.001 24 58
GNA11 0.017 0.033 -10000 0 -0.42 3 3
LHCGR 0.022 0.05 0.19 39 -10000 0 39
AGTR1 -0.001 0.091 -10000 0 -0.42 24 24
desensitization of G-protein coupled receptor protein signaling pathway 0.026 0.037 0.16 38 -10000 0 38
IPCEF1/ARNO -0.14 0.082 -10000 0 -0.9 1 1
alphaIIb/beta3 Integrin 0.029 0.041 -10000 0 -0.29 6 6
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.079 0.083 0.27 68 -10000 0 68
NFATC2 0.13 0.13 0.36 44 -0.55 3 47
NFATC3 0.046 0.054 -10000 0 -0.26 6 6
CD40LG 0.12 0.22 0.48 55 -0.88 9 64
ITCH -0.016 0.031 -10000 0 -10000 0 0
CBLB -0.015 0.032 -10000 0 -0.23 10 10
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.18 0.22 0.48 116 -0.82 5 121
JUNB 0.018 0.027 -10000 0 -0.42 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.044 -10000 0 -0.27 12 12
T cell anergy -0.001 0.056 -10000 0 -0.37 10 10
TLE4 0.069 0.089 0.27 1 -0.43 2 3
Jun/NFAT1-c-4/p21SNFT 0.18 0.22 0.48 63 -0.82 10 73
AP-1/NFAT1-c-4 0.21 0.28 0.58 84 -1 9 93
IKZF1 0.097 0.14 0.35 94 -0.43 2 96
T-helper 2 cell differentiation -0.084 0.26 0.46 1 -0.77 8 9
AP-1/NFAT1 0.13 0.14 0.32 103 -0.41 5 108
CALM1 0.015 0.029 -10000 0 -0.17 11 11
EGR2 0.12 0.21 0.47 5 -1 11 16
EGR3 0.11 0.21 0.47 3 -1.1 9 12
NFAT1/FOXP3 0.16 0.15 0.38 124 -0.44 2 126
EGR1 0.008 0.057 -10000 0 -0.42 9 9
JUN 0.032 0.026 -10000 0 -10000 0 0
EGR4 0.02 0.018 0.19 5 -10000 0 5
mol:Ca2+ -0.004 0.03 -10000 0 -0.18 14 14
GBP3 0.068 0.098 0.28 6 -0.51 4 10
FOSL1 0.028 0.036 0.19 26 -10000 0 26
NFAT1-c-4/MAF/IRF4 0.17 0.21 0.44 85 -0.84 9 94
DGKA 0.07 0.098 0.36 6 -0.58 2 8
CREM 0.018 0.009 -10000 0 -10000 0 0
NFAT1-c-4/PPARG 0.11 0.19 0.43 13 -0.86 9 22
CTLA4 0.14 0.16 0.32 210 -0.36 2 212
NFAT1-c-4 (dimer)/EGR1 0.12 0.19 0.43 10 -0.84 10 20
NFAT1-c-4 (dimer)/EGR4 0.15 0.19 0.44 11 -0.87 9 20
FOS 0.023 0.068 0.17 2 -0.4 11 13
IFNG 0.16 0.17 0.39 106 -0.72 2 108
T cell activation 0.091 0.13 0.43 13 -0.6 4 17
MAF 0.019 0.004 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.1 0.15 0.63 10 -0.41 1 11
TNF 0.11 0.18 0.41 8 -0.8 10 18
FASLG 0.15 0.25 0.53 4 -1.2 11 15
TBX21 0.11 0.099 0.24 172 -10000 0 172
BATF3 0.034 0.048 0.19 45 -10000 0 45
PRKCQ 0.031 0.072 -10000 0 -0.41 12 12
PTPN1 0.069 0.09 0.27 1 -0.43 2 3
NFAT1-c-4/ICER1 0.14 0.19 0.42 7 -0.86 9 16
GATA3 -0.19 0.22 -10000 0 -0.42 255 255
T-helper 1 cell differentiation 0.16 0.17 0.39 111 -0.7 2 113
IL2RA 0.17 0.21 0.48 98 -0.82 5 103
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.069 0.09 0.25 7 -0.43 2 9
E2F1 0.037 0.051 0.19 54 -10000 0 54
PPARG 0.014 0.009 -10000 0 -10000 0 0
SLC3A2 0.069 0.09 0.27 1 -0.43 2 3
IRF4 0.056 0.073 0.19 116 -0.42 1 117
PTGS2 0.1 0.22 0.44 37 -0.84 11 48
CSF2 0.096 0.2 0.45 39 -0.86 8 47
JunB/Fra1/NFAT1-c-4 0.15 0.18 0.44 12 -0.83 9 21
IL4 -0.088 0.27 0.46 1 -0.81 8 9
IL5 0.093 0.2 0.43 34 -0.86 8 42
IL2 0.091 0.14 0.44 10 -0.61 4 14
IL3 -0.002 0.068 -10000 0 -0.68 2 2
RNF128 -0.023 0.076 0.2 2 -0.51 12 14
NFATC1 0.1 0.15 0.41 1 -0.63 10 11
CDK4 -0.089 0.12 0.54 2 -10000 0 2
PTPRK 0.067 0.093 0.25 5 -0.49 3 8
IL8 0.12 0.22 0.46 43 -0.87 10 53
POU2F1 0.019 0.004 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.021 0.015 0.19 4 -10000 0 4
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.084 0.092 0.35 1 -0.29 6 7
IL27/IL27R/JAK1 0.21 0.16 0.42 106 -10000 0 106
TBX21 0.2 0.15 0.38 135 -10000 0 135
IL12B 0.037 0.056 0.2 54 -10000 0 54
IL12A -0.001 0.01 -10000 0 -10000 0 0
IL6ST 0.018 0.08 -10000 0 -0.41 17 17
IL27RA/JAK1 0.062 0.046 0.34 3 -10000 0 3
IL27 0.043 0.044 0.2 32 -10000 0 32
TYK2 0.036 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.005 0.068 -10000 0 -0.41 1 1
T-helper 2 cell differentiation -0.084 0.092 0.35 1 -0.29 6 7
T cell proliferation during immune response -0.084 0.092 0.35 1 -0.29 6 7
MAPKKK cascade 0.084 0.092 0.29 6 -0.35 1 7
STAT3 0.02 0.003 -10000 0 -10000 0 0
STAT2 0.02 0.003 -10000 0 -10000 0 0
STAT1 0.027 0.012 0.19 1 -10000 0 1
IL12RB1 0.074 0.079 0.19 159 -10000 0 159
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.2 0.15 0.38 133 -0.39 1 134
IL27/IL27R/JAK2/TYK2 0.084 0.091 0.28 5 -0.35 1 6
positive regulation of T cell mediated cytotoxicity 0.084 0.092 0.29 6 -0.35 1 7
STAT1 (dimer) 0.32 0.24 0.53 257 -10000 0 257
JAK2 0.028 0.016 -10000 0 -10000 0 0
JAK1 0.027 0.009 -10000 0 -10000 0 0
STAT2 (dimer) 0.1 0.089 0.35 4 -0.34 1 5
T cell proliferation 0.072 0.1 0.29 27 -0.36 2 29
IL12/IL12R/TYK2/JAK2 0.11 0.11 -10000 0 -0.74 2 2
IL17A -0.006 0.067 -10000 0 -0.41 1 1
mast cell activation -0.084 0.092 0.35 1 -0.29 6 7
IFNG 0.053 0.044 0.1 213 -10000 0 213
T cell differentiation 0.006 0.006 0.012 179 -0.017 1 180
STAT3 (dimer) 0.1 0.089 0.35 4 -0.34 1 5
STAT5A (dimer) 0.1 0.089 0.35 4 -0.34 1 5
STAT4 (dimer) 0.1 0.096 0.32 21 -0.34 1 22
STAT4 0.029 0.039 0.19 30 -10000 0 30
T cell activation -0.002 0.004 -10000 0 -0.073 1 1
IL27R/JAK2/TYK2 0.087 0.082 -10000 0 -10000 0 0
GATA3 -0.59 0.57 0.55 1 -1.2 258 259
IL18 -0.007 0.011 0.1 5 -10000 0 5
positive regulation of mast cell cytokine production 0.099 0.088 0.34 4 -0.33 1 5
IL27/EBI3 0.082 0.066 0.23 65 -10000 0 65
IL27RA 0.036 0.038 -10000 0 -10000 0 0
IL6 0.009 0.1 0.19 37 -0.42 25 62
STAT5A 0.02 0.003 -10000 0 -10000 0 0
monocyte differentiation 0.002 0.002 -10000 0 -10000 0 0
IL2 -0.028 0.031 -10000 0 -10000 0 0
IL1B -0.007 0.017 0.11 5 -0.29 1 6
EBI3 0.059 0.061 0.21 74 -10000 0 74
TNF -0.009 0.027 0.11 4 -0.29 4 8
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.012 0.064 0.19 3 -0.42 11 14
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.019 0.022 0.19 2 -0.42 1 3
TCEB1 0.019 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.063 0.2 3 -0.27 17 20
HIF1A 0.005 0.052 -10000 0 -0.27 16 16
COPS5 0.019 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.035 0.038 -10000 0 -0.23 1 1
FIH (dimer) 0.019 0.004 -10000 0 -10000 0 0
CDKN2A 0.17 0.054 0.19 474 -10000 0 474
ARNT/IPAS 0.022 0.049 -10000 0 -0.3 11 11
HIF1AN 0.019 0.004 -10000 0 -10000 0 0
GNB2L1 0.015 0.009 -10000 0 -10000 0 0
HIF1A/ARNT 0.014 0.062 0.24 1 -0.28 17 18
CUL2 0.02 0.003 -10000 0 -10000 0 0
OS9 0.02 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.029 0.024 -10000 0 -0.26 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.018 0.06 -10000 0 -0.28 17 17
PHD1-3/OS9 0.12 0.06 -10000 0 -0.24 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.021 0.061 -10000 0 -0.28 15 15
VHL 0.014 0.009 -10000 0 -10000 0 0
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.013 0.062 -10000 0 -0.28 17 17
EGLN3 0.16 0.074 0.19 437 -0.42 2 439
EGLN2 0.02 0.002 -10000 0 -10000 0 0
EGLN1 0.019 0.004 -10000 0 -10000 0 0
TP53 0.02 0.003 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.12 0.24 -10000 0 -0.49 143 143
ARNT 0.019 0.004 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.003 -10000 0 -10000 0 0
HIF1A/p19ARF 0.11 0.08 0.21 22 -0.24 16 38
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.047 0.065 0.17 72 -10000 0 72
STMN1 0.035 0.058 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.1 0.091 0.24 123 -0.21 1 124
Chromosomal passenger complex/Cul3 protein complex 0.025 0.069 0.19 1 -0.38 6 7
BIRC5 0.07 0.077 0.19 148 -10000 0 148
DES -0.091 0.28 -10000 0 -0.55 109 109
Aurora C/Aurora B/INCENP 0.083 0.05 0.24 1 -10000 0 1
Aurora B/TACC1 0.068 0.053 -10000 0 -10000 0 0
Aurora B/PP2A 0.078 0.058 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.019 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.005 0.004 -10000 0 -10000 0 0
NDC80 0.059 0.09 0.21 103 -10000 0 103
Cul3 protein complex 0.029 0.051 -10000 0 -0.26 15 15
KIF2C 0.05 0.078 0.17 49 -0.54 5 54
PEBP1 0.022 0.005 -10000 0 -10000 0 0
KIF20A 0.066 0.084 0.18 175 -10000 0 175
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.071 0.062 -10000 0 -0.3 1 1
SEPT1 0.041 0.057 0.19 68 -10000 0 68
SMC2 0.019 0.004 -10000 0 -10000 0 0
SMC4 0.019 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.077 0.13 0.33 26 -0.63 9 35
PSMA3 0.019 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.003 -10000 0 -10000 0 0
H3F3B 0.042 0.041 -10000 0 -10000 0 0
AURKB 0.092 0.084 0.18 239 -10000 0 239
AURKC 0.021 0.011 0.19 2 -10000 0 2
CDCA8 0.029 0.033 0.2 19 -10000 0 19
cytokinesis 0.056 0.091 0.26 21 -0.34 5 26
Aurora B/Septin1 0.097 0.12 0.29 79 -0.32 5 84
AURKA 0.006 0.026 0.18 5 -10000 0 5
INCENP 0.024 0.008 -10000 0 -10000 0 0
KLHL13 0.007 0.073 -10000 0 -0.42 15 15
BUB1 0.079 0.09 0.18 223 -10000 0 223
hSgo1/Aurora B/Survivin 0.085 0.094 0.24 114 -10000 0 114
EVI5 0.021 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.063 0.08 0.3 9 -0.32 5 14
SGOL1 0.019 0.03 0.19 15 -10000 0 15
CENPA 0.075 0.096 0.19 156 -0.44 5 161
NCAPG 0.074 0.079 0.19 171 -10000 0 171
Aurora B/HC8 Proteasome 0.075 0.059 -10000 0 -10000 0 0
NCAPD2 0.019 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.078 0.058 -10000 0 -10000 0 0
RHOA 0.014 0.009 -10000 0 -10000 0 0
NCAPH 0.047 0.062 0.19 85 -10000 0 85
NPM1 0.05 0.075 0.21 1 -0.29 6 7
RASA1 0.017 0.02 -10000 0 -0.42 1 1
KLHL9 0.019 0.004 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.075 0.059 -10000 0 -10000 0 0
PPP1CC 0.019 0.004 -10000 0 -10000 0 0
Centraspindlin 0.09 0.082 0.25 23 -0.32 6 29
RhoA/GDP 0.011 0.007 -10000 0 -10000 0 0
NSUN2 0.049 0.07 -10000 0 -0.29 6 6
MYLK 0.041 0.041 -10000 0 -10000 0 0
KIF23 0.025 0.022 0.2 8 -10000 0 8
VIM 0.045 0.071 0.15 79 -10000 0 79
RACGAP1 0.023 0.011 0.2 1 -10000 0 1
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.038 0.11 -10000 0 -0.8 7 7
Chromosomal passenger complex 0.081 0.092 0.19 153 -0.4 5 158
Chromosomal passenger complex/EVI5 0.13 0.087 0.25 131 -10000 0 131
TACC1 0.018 0.006 -10000 0 -10000 0 0
PPP2R5D 0.019 0.004 -10000 0 -10000 0 0
CUL3 0.019 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.015 0.19 4 -10000 0 4
CCL5 0.09 0.083 0.19 220 -10000 0 220
SDCBP 0.019 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.009 0.11 0.23 9 -0.28 33 42
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 -0.007 0.11 0.21 3 -0.37 14 17
Syndecan-1/Syntenin -0.005 0.11 0.26 5 -0.36 15 20
MAPK3 -0.019 0.1 0.18 5 -0.35 12 17
HGF/MET 0.024 0.048 0.27 1 -0.3 9 10
TGFB1/TGF beta receptor Type II 0.021 0.015 0.19 4 -10000 0 4
BSG 0.02 0.008 0.19 1 -10000 0 1
keratinocyte migration -0.007 0.11 0.21 3 -0.36 14 17
Syndecan-1/RANTES 0.042 0.14 0.24 41 -0.34 15 56
Syndecan-1/CD147 0.006 0.12 0.23 6 -0.37 12 18
Syndecan-1/Syntenin/PIP2 -0.007 0.11 0.21 4 -0.34 15 19
LAMA5 0.019 0.021 0.19 1 -0.42 1 2
positive regulation of cell-cell adhesion -0.007 0.1 0.21 4 -0.34 15 19
MMP7 -0.052 0.16 0.19 6 -0.42 88 94
HGF 0.014 0.062 0.19 10 -0.42 9 19
Syndecan-1/CASK -0.015 0.1 0.17 3 -0.27 34 37
Syndecan-1/HGF/MET 0.001 0.12 0.24 5 -0.36 18 23
regulation of cell adhesion -0.026 0.099 0.27 4 -0.35 12 16
HPSE 0.018 0.027 -10000 0 -0.42 2 2
positive regulation of cell migration -0.009 0.11 0.23 9 -0.28 33 42
SDC1 -0.011 0.11 0.22 5 -0.28 33 38
Syndecan-1/Collagen -0.009 0.11 0.23 9 -0.28 33 42
PPIB 0.02 0.002 -10000 0 -10000 0 0
MET 0.019 0.012 0.19 2 -10000 0 2
PRKACA 0.02 0.002 -10000 0 -10000 0 0
MMP9 0.094 0.084 0.19 234 -10000 0 234
MAPK1 -0.018 0.1 0.2 7 -0.35 12 19
homophilic cell adhesion -0.009 0.11 0.22 10 -0.28 33 43
MMP1 0.018 0.12 0.19 72 -0.42 30 102
Aurora C 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
INCENP 0.02 0.002 -10000 0 -9999 0 0
Aurora C/Aurora B/INCENP 0.083 0.053 0.24 1 -9999 0 1
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.013 0.01 -10000 0 -9999 0 0
AURKB 0.096 0.084 0.19 239 -9999 0 239
AURKC 0.021 0.011 0.19 2 -9999 0 2
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.018 0.006 -10000 0 -10000 0 0
LAT2 0.019 0.07 0.24 10 -0.34 5 15
AP1 0.057 0.11 0.26 7 -0.51 9 16
mol:PIP3 0.1 0.16 0.33 104 -0.31 5 109
IKBKB 0.082 0.14 0.27 117 -0.28 1 118
AKT1 -0.003 0.098 0.33 22 -0.38 1 23
IKBKG 0.083 0.13 0.26 119 -0.28 1 120
MS4A2 0.048 0.074 0.19 114 -10000 0 114
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
MAP3K1 0.053 0.12 0.27 63 -0.33 5 68
mol:Ca2+ 0.095 0.14 0.28 126 -0.25 4 130
LYN 0.019 0.01 -10000 0 -10000 0 0
CBLB 0.01 0.06 -10000 0 -0.32 6 6
SHC1 0.019 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.028 0.021 -10000 0 -0.23 1 1
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.02 0.015 0.19 4 -10000 0 4
PLD2 0.005 0.077 0.32 18 -0.22 10 28
PTPN13 0.03 0.12 0.36 4 -0.66 9 13
PTPN11 0.017 0.015 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.033 0.13 0.36 40 -0.34 5 45
SYK 0.019 0.022 -10000 0 -0.42 1 1
GRB2 0.02 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.022 0.065 0.21 11 -0.3 6 17
LAT 0.027 0.072 0.19 12 -0.33 5 17
PAK2 0.047 0.1 0.27 41 -0.36 5 46
NFATC2 0.004 0.039 -10000 0 -0.44 3 3
HRAS 0.045 0.093 0.24 29 -0.35 7 36
GAB2 0.02 0.002 -10000 0 -10000 0 0
PLA2G1B -0.23 0.37 -10000 0 -0.81 150 150
Fc epsilon R1 0.074 0.082 0.25 15 -0.25 15 30
Antigen/IgE/Fc epsilon R1 0.072 0.077 0.22 23 -0.23 14 37
mol:GDP 0.049 0.095 0.25 20 -0.34 10 30
JUN 0.019 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.017 0.021 -10000 0 -0.42 1 1
FOS 0.01 0.063 0.19 1 -0.42 11 12
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.024 0.067 0.16 1 -0.28 10 11
CHUK 0.082 0.13 0.27 113 -0.28 1 114
KLRG1 0.009 0.058 -10000 0 -0.28 7 7
VAV1 0.024 0.075 0.19 17 -0.34 6 23
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL 0.01 0.062 -10000 0 -0.34 5 5
negative regulation of mast cell degranulation 0.017 0.06 0.19 5 -0.3 5 10
BTK 0.046 0.087 0.23 18 -0.39 5 23
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0.035 0.082 0.18 14 -0.34 13 27
GAB2/PI3K/SHP2 -0.017 0.049 -10000 0 -0.24 10 10
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.018 0.055 0.17 1 -0.26 11 12
RAF1 -0.25 0.41 -10000 0 -0.89 150 150
Fc epsilon R1/FcgammaRIIB/SHIP 0.1 0.096 0.27 73 -0.24 11 84
FCER1G 0.039 0.071 0.19 94 -10000 0 94
FCER1A 0.008 0.077 0.19 3 -0.42 16 19
Antigen/IgE/Fc epsilon R1/Fyn 0.074 0.076 0.23 17 -0.22 14 31
MAPK3 -0.23 0.38 -10000 0 -0.82 150 150
MAPK1 -0.23 0.38 -10000 0 -0.82 150 150
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
MAPK8 0.028 0.14 -10000 0 -0.69 16 16
DUSP1 0.015 0.012 0.19 1 -10000 0 1
NF-kappa-B/RelA 0.029 0.05 0.12 55 -0.18 1 56
actin cytoskeleton reorganization 0.039 0.12 0.38 3 -0.66 9 12
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.039 0.077 0.29 1 -0.36 6 7
FER 0.015 0.074 0.25 18 -0.34 5 23
RELA 0.02 0.002 -10000 0 -10000 0 0
ITK 0.033 0.047 0.14 27 -10000 0 27
SOS1 0.02 0.003 -10000 0 -10000 0 0
PLCG1 0.063 0.11 0.28 42 -0.37 6 48
cytokine secretion 0.007 0.025 -10000 0 -10000 0 0
SPHK1 0.019 0.062 0.23 7 -0.34 3 10
PTK2 0.038 0.12 0.38 3 -0.71 9 12
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.035 0.075 0.22 16 -0.32 6 22
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.1 0.16 0.33 115 -0.31 5 120
MAP2K2 -0.24 0.38 -10000 0 -0.84 150 150
MAP2K1 -0.24 0.38 -10000 0 -0.84 150 150
MAP2K7 0.02 0.002 -10000 0 -10000 0 0
KLRG1/SHP2 0.009 0.057 0.24 3 -0.28 6 9
MAP2K4 0.01 0.14 -10000 0 -0.84 12 12
Fc epsilon R1/FcgammaRIIB 0.099 0.099 0.27 73 -0.24 14 87
mol:Choline 0.005 0.077 0.32 18 -0.22 10 28
SHC/Grb2/SOS1 0.053 0.07 0.23 2 -0.31 5 7
FYN 0.019 0.005 -10000 0 -10000 0 0
DOK1 0.02 0.003 -10000 0 -10000 0 0
PXN 0.038 0.12 0.41 12 -0.64 9 21
HCLS1 0.012 0.062 0.17 3 -0.34 5 8
PRKCB 0.097 0.15 0.29 125 -0.32 2 127
FCGR2B 0.047 0.067 0.19 89 -0.42 1 90
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP 0.017 0.061 0.19 5 -0.3 5 10
LCP2 0.025 0.041 0.19 29 -10000 0 29
PLA2G4A 0.011 0.057 -10000 0 -0.34 3 3
RASA1 0.017 0.02 -10000 0 -0.42 1 1
mol:Phosphatidic acid 0.005 0.077 0.32 18 -0.22 10 28
IKK complex 0.072 0.13 0.26 108 -0.21 1 109
WIPF1 0.019 0.004 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.009 0.015 0.1 3 -0.29 1 4
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.029 0.018 -10000 0 -10000 0 0
STXBP1 0.019 0.019 -10000 0 -0.42 1 1
ACh/CHRNA1 0.075 0.068 0.15 219 -10000 0 219
RAB3GAP2/RIMS1/UNC13B 0.038 0.02 -10000 0 -10000 0 0
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 0.022 0.024 0.19 10 -10000 0 10
mol:ACh 0.013 0.035 0.1 54 -0.11 2 56
RAB3GAP2 0.019 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.029 0.028 -10000 0 -0.2 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.075 0.068 0.15 219 -10000 0 219
UNC13B 0.019 0.004 -10000 0 -10000 0 0
CHRNA1 0.089 0.084 0.19 219 -10000 0 219
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.02 0.099 0.16 2 -0.25 77 79
SNAP25 0.01 0.03 -10000 0 -0.25 2 2
VAMP2 0.001 0 -10000 0 -10000 0 0
SYT1 -0.046 0.16 0.19 2 -0.42 79 81
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.013 0.018 -10000 0 -0.25 2 2
STX1A/SNAP25 fragment 1/VAMP2 0.029 0.028 -10000 0 -0.2 1 1
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.018 0.035 0.19 2 -0.42 3 5
GNB1/GNG2 -0.043 0.12 -10000 0 -0.32 45 45
mol:DAG -0.07 0.096 -10000 0 -0.32 40 40
PLCG1 -0.071 0.099 -10000 0 -0.33 40 40
YES1 -0.059 0.1 -10000 0 -0.28 74 74
FZD3 0.018 0.006 -10000 0 -10000 0 0
FZD6 0.019 0.005 -10000 0 -10000 0 0
G protein -0.046 0.12 0.24 2 -0.33 39 41
MAP3K7 -0.088 0.12 0.31 1 -0.32 63 64
mol:Ca2+ -0.068 0.094 -10000 0 -0.31 40 40
mol:IP3 -0.07 0.096 -10000 0 -0.32 40 40
NLK -0.007 0.09 -10000 0 -0.84 6 6
GNB1 0.019 0.004 -10000 0 -10000 0 0
CAMK2A -0.091 0.12 0.32 1 -0.34 64 65
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.05 0.12 -10000 0 -0.29 76 76
CSNK1A1 0.015 0.009 -10000 0 -10000 0 0
GNAS -0.059 0.1 -10000 0 -0.28 75 75
GO:0007205 -0.067 0.096 -10000 0 -0.32 40 40
WNT6 0.025 0.032 0.19 19 -10000 0 19
WNT4 -0.023 0.13 0.19 3 -0.42 52 55
NFAT1/CK1 alpha -0.033 0.1 0.24 1 -0.35 21 22
GNG2 0.019 0.005 -10000 0 -10000 0 0
WNT5A 0.014 0.021 -10000 0 -0.42 1 1
WNT11 -0.005 0.11 0.19 6 -0.42 32 38
CDC42 -0.06 0.1 -10000 0 -0.33 41 41
IL2 signaling events mediated by STAT5

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
GAB2 0.02 0.002 -10000 0 -10000 0 0
ELF1 0.039 0.043 0.16 2 -0.42 1 3
CCNA2 0.052 0.066 0.19 99 -10000 0 99
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
JAK3 0.054 0.067 0.19 105 -10000 0 105
PIK3R1 0.018 0.02 -10000 0 -0.42 1 1
JAK1 0.019 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.047 0.095 0.24 15 -0.5 7 22
SHC1 0.019 0.004 -10000 0 -10000 0 0
SP1 0.021 0.007 -10000 0 -10000 0 0
IL2RA 0.025 0.088 0.2 102 -0.3 1 103
IL2RB 0.11 0.084 0.19 272 -10000 0 272
SOS1 0.02 0.003 -10000 0 -10000 0 0
IL2RG 0.03 0.045 0.19 33 -0.42 1 34
G1/S transition of mitotic cell cycle 0.04 0.086 0.39 15 -0.4 1 16
PTPN11 0.02 0.004 -10000 0 -10000 0 0
CCND2 -0.017 0.014 0.2 2 -10000 0 2
LCK 0.024 0.042 0.19 20 -0.42 2 22
GRB2 0.02 0.003 -10000 0 -10000 0 0
IL2 0.022 0.023 0.19 10 -10000 0 10
CDK6 0.017 0.02 -10000 0 -0.42 1 1
CCND3 0.045 0.09 0.37 2 -0.43 7 9
Signaling events mediated by the Hedgehog family

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
TGFB2 0.078 0.11 0.32 1 -0.44 1 2
IHH 0.021 0.13 0.21 5 -0.42 40 45
SHH Np/Cholesterol/GAS1 -0.029 0.051 0.12 1 -0.23 29 30
LRPAP1 0.02 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.029 0.05 0.23 29 -0.12 1 30
SMO/beta Arrestin2 0.05 0.12 0.29 1 -0.33 13 14
SMO 0.033 0.11 -10000 0 -0.34 14 14
AKT1 0.02 0.098 -10000 0 -0.41 14 14
ARRB2 0.02 0.003 -10000 0 -10000 0 0
BOC 0.019 0.006 -10000 0 -10000 0 0
ADRBK1 0.02 0.002 -10000 0 -10000 0 0
heart looping 0.032 0.11 -10000 0 -0.34 14 14
STIL 0.036 0.095 0.24 36 -0.29 2 38
DHH N/PTCH2 0.027 0.054 -10000 0 -0.3 11 11
DHH N/PTCH1 0.055 0.1 -10000 0 -0.27 19 19
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
DHH 0.01 0.065 -10000 0 -0.42 12 12
PTHLH 0.094 0.14 0.34 7 -0.52 1 8
determination of left/right symmetry 0.032 0.11 -10000 0 -0.34 14 14
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
skeletal system development 0.094 0.14 0.34 7 -0.52 1 8
IHH N/Hhip -0.049 0.18 0.22 5 -0.33 142 147
DHH N/Hhip -0.048 0.14 -10000 0 -0.31 123 123
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.032 0.11 -10000 0 -0.34 14 14
pancreas development -0.074 0.18 0.19 10 -0.42 116 126
HHAT 0.019 0.004 -10000 0 -10000 0 0
PI3K 0.025 0.022 -10000 0 -0.3 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.002 0.095 0.19 1 -0.42 26 27
somite specification 0.032 0.11 -10000 0 -0.34 14 14
SHH Np/Cholesterol/PTCH1 0.029 0.086 -10000 0 -0.27 4 4
SHH Np/Cholesterol/PTCH2 -0.015 0.041 0.12 21 -0.23 10 31
SHH Np/Cholesterol/Megalin -0.032 0.061 0.12 1 -0.25 35 36
SHH -0.021 0.036 -10000 0 -0.3 8 8
catabolic process 0.06 0.1 -10000 0 -0.28 14 14
SMO/Vitamin D3 0.037 0.11 0.31 10 -0.36 4 14
SHH Np/Cholesterol/Hhip -0.061 0.095 0.12 7 -0.24 109 116
LRP2 -0.01 0.11 0.19 1 -0.42 36 37
receptor-mediated endocytosis 0.01 0.12 0.25 8 -0.42 13 21
SHH Np/Cholesterol/BOC -0.02 0.03 -10000 0 -0.23 10 10
SHH Np/Cholesterol/CDO -0.007 0.053 0.12 52 -0.23 10 62
mesenchymal cell differentiation 0.061 0.094 0.24 109 -0.12 7 116
mol:Vitamin D3 0.061 0.12 0.3 38 -0.29 3 41
IHH N/PTCH2 0.034 0.087 0.19 17 -0.25 39 56
CDON 0.039 0.053 0.19 59 -10000 0 59
IHH N/PTCH1 0.078 0.11 0.26 4 -0.29 14 18
Megalin/LRPAP1 0.007 0.081 -10000 0 -0.3 34 34
PTCH2 0.027 0.036 0.19 25 -10000 0 25
SHH Np/Cholesterol -0.016 0.03 -10000 0 -0.22 10 10
PTCH1 0.061 0.1 -10000 0 -0.28 14 14
HHIP -0.074 0.18 0.19 10 -0.42 116 126
IL4-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
BCL2L1 -0.14 0.38 0.64 6 -1.1 13 19
STAT6 (cleaved dimer) -0.14 0.36 0.5 12 -1 22 34
IGHG1 -0.029 0.19 0.38 28 -10000 0 28
IGHG3 -0.14 0.37 0.57 6 -0.99 20 26
AKT1 -0.032 0.26 0.44 34 -0.76 13 47
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0 0.2 0.42 35 -0.74 4 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.047 0.27 0.45 27 -0.88 14 41
THY1 -0.14 0.39 0.64 6 -1.2 14 20
MYB 0.061 0.074 0.19 132 -10000 0 132
HMGA1 0.02 0.008 0.19 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.04 0.29 0.53 37 -0.67 10 47
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.045 0.27 0.45 29 -0.86 15 44
SP1 0.031 0.028 -10000 0 -10000 0 0
INPP5D 0.02 0.015 0.19 4 -10000 0 4
SOCS5 -0.001 0.041 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.12 0.38 0.56 15 -1 19 34
SOCS1 -0.081 0.3 0.46 25 -0.7 15 40
SOCS3 -0.042 0.24 0.52 14 -0.66 2 16
FCER2 -0.092 0.34 0.65 15 -1 10 25
PARP14 0.021 0.009 -10000 0 -10000 0 0
CCL17 -0.14 0.39 0.66 8 -1.1 13 21
GRB2 0.02 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.034 0.23 0.41 31 -0.72 15 46
T cell proliferation -0.12 0.38 0.61 9 -1.1 18 27
IL4R/JAK1 -0.14 0.38 0.58 6 -1.1 15 21
EGR2 -0.15 0.41 0.65 9 -1.2 21 30
JAK2 -0.004 0.059 0.18 1 -10000 0 1
JAK3 0.059 0.074 0.2 105 -10000 0 105
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
JAK1 0.007 0.036 0.14 1 -10000 0 1
COL1A2 -0.008 0.18 0.48 7 -10000 0 7
CCL26 -0.12 0.39 0.66 11 -1.1 13 24
IL4R -0.14 0.41 0.66 13 -1.1 15 28
PTPN6 0.008 0.032 -10000 0 -10000 0 0
IL13RA2 -0.21 0.49 0.64 7 -1.3 44 51
IL13RA1 -0.003 0.06 0.18 1 -10000 0 1
IRF4 0.039 0.22 0.5 36 -0.76 11 47
ARG1 -0.017 0.18 0.47 5 -1.1 1 6
CBL -0.045 0.26 0.48 33 -0.64 10 43
GTF3A 0.054 0.043 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
IL13RA1/JAK2 0.003 0.084 0.2 17 -10000 0 17
IRF4/BCL6 0.028 0.19 0.42 12 -0.74 10 22
CD40LG 0.057 0.075 0.25 54 -0.44 1 55
MAPK14 -0.045 0.26 0.48 32 -0.66 8 40
mitosis -0.028 0.25 0.44 34 -0.71 13 47
STAT6 -0.15 0.44 0.68 20 -1.2 18 38
SPI1 0.045 0.059 0.19 73 -10000 0 73
RPS6KB1 -0.03 0.24 0.43 35 -0.69 13 48
STAT6 (dimer) -0.15 0.44 0.68 20 -1.2 18 38
STAT6 (dimer)/PARP14 -0.15 0.39 0.61 6 -1.1 18 24
mast cell activation 0.001 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.029 0.25 0.47 33 -0.77 6 39
FRAP1 -0.032 0.26 0.44 34 -0.76 13 47
LTA -0.12 0.4 0.68 13 -1.1 13 26
FES 0.018 0.027 -10000 0 -0.42 2 2
T-helper 1 cell differentiation 0.15 0.43 1.2 17 -0.68 20 37
CCL11 -0.35 0.59 0.57 5 -1.2 145 150
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.022 0.24 0.46 31 -0.71 6 37
IL2RG 0.035 0.054 0.22 33 -0.42 1 34
IL10 -0.14 0.39 0.63 11 -1.1 14 25
IRS1 0.016 0.038 -10000 0 -0.42 4 4
IRS2 0.022 0.02 0.19 7 -10000 0 7
IL4 -0.018 0.16 0.6 1 -0.97 2 3
IL5 -0.1 0.4 0.65 13 -1.1 12 25
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.12 0.36 0.58 20 -0.87 21 41
COL1A1 0.023 0.26 0.51 29 -1 8 37
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.14 0.38 0.59 2 -1.1 13 15
IL2R gamma/JAK3 0.071 0.081 0.25 62 -0.31 1 63
TFF3 -0.16 0.42 0.63 7 -1.2 23 30
ALOX15 -0.14 0.38 0.64 6 -1.1 13 19
MYBL1 0.029 0.04 0.19 30 -10000 0 30
T-helper 2 cell differentiation -0.11 0.36 0.55 19 -0.96 24 43
SHC1 0.019 0.004 -10000 0 -10000 0 0
CEBPB 0.024 0.025 0.21 8 -10000 0 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.044 0.26 0.43 28 -0.82 15 43
mol:PI-3-4-5-P3 -0.031 0.26 0.44 34 -0.76 13 47
PI3K -0.035 0.27 0.45 31 -0.81 13 44
DOK2 0.027 0.044 0.19 30 -0.42 1 31
ETS1 0.002 0.04 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.034 0.23 0.39 33 -0.73 15 48
ITGB3 -0.15 0.4 0.64 6 -1.2 15 21
PIGR -0.49 0.65 0.64 7 -1.2 202 209
IGHE 0.008 0.067 0.2 15 -0.17 8 23
MAPKKK cascade -0.032 0.22 0.39 33 -0.71 15 48
BCL6 0.016 0.014 -10000 0 -10000 0 0
OPRM1 -0.14 0.39 0.66 6 -1.1 14 20
RETNLB -0.14 0.39 0.63 7 -1.1 13 20
SELP -0.17 0.44 0.64 7 -1.3 30 37
AICDA -0.11 0.38 0.63 9 -1.1 12 21
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.019 0.022 -10000 0 -0.3 3 3
MAP4K4 -0.001 0.039 -10000 0 -0.27 1 1
BAG4 0.018 0.02 -10000 0 -0.42 1 1
PKC zeta/ceramide -0.074 0.079 -10000 0 -0.26 59 59
NFKBIA 0.019 0.005 -10000 0 -10000 0 0
BIRC3 0.045 0.06 0.19 79 -10000 0 79
BAX -0.026 0.035 -10000 0 -0.28 4 4
RIPK1 0.019 0.004 -10000 0 -10000 0 0
AKT1 0 0.066 0.84 3 -10000 0 3
BAD -0.074 0.076 -10000 0 -0.26 55 55
SMPD1 0.005 0.05 0.23 12 -0.23 1 13
RB1 -0.073 0.077 -10000 0 -0.26 55 55
FADD/Caspase 8 -0.001 0.062 0.22 1 -0.35 8 9
MAP2K4 -0.061 0.075 0.17 2 -0.25 42 44
NSMAF 0.019 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.061 0.078 -10000 0 -0.25 52 52
EGF -0.37 0.14 -10000 0 -0.42 467 467
mol:ceramide -0.074 0.081 0.13 1 -0.27 57 58
MADD 0.02 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.015 -10000 0 -0.3 1 1
ASAH1 0.018 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.073 0.075 -10000 0 -0.26 55 55
cell proliferation -0.06 0.066 0.21 1 -0.23 38 39
BID -0.007 0.061 -10000 0 -0.52 4 4
MAP3K1 -0.058 0.08 0.19 2 -0.26 43 45
EIF2A -0.066 0.083 0.32 7 -0.26 41 48
TRADD 0.019 0.004 -10000 0 -10000 0 0
CRADD 0.02 0.004 -10000 0 -10000 0 0
MAPK3 -0.069 0.067 -10000 0 -0.25 44 44
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.069 0.067 -10000 0 -0.25 44 44
Cathepsin D/ceramide -0.073 0.078 -10000 0 -0.26 55 55
FADD -0.003 0.046 0.23 1 -0.27 2 3
KSR1 -0.073 0.077 -10000 0 -0.26 54 54
MAPK8 -0.066 0.084 -10000 0 -0.26 55 55
PRKRA -0.069 0.082 0.19 1 -0.26 53 54
PDGFA 0.017 0.02 -10000 0 -0.42 1 1
TRAF2 0.019 0.004 -10000 0 -10000 0 0
IGF1 0.021 0.017 0.19 5 -10000 0 5
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.074 0.08 0.13 1 -0.27 57 58
CTSD 0.019 0.019 -10000 0 -0.42 1 1
regulation of nitric oxide biosynthetic process 0.029 0.015 -10000 0 -0.3 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.063 0.071 0.22 1 -0.27 23 24
PRKCD 0.015 0.012 0.19 1 -10000 0 1
PRKCZ 0.017 0.033 -10000 0 -0.42 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.015 -10000 0 -0.3 1 1
RelA/NF kappa B1 0.029 0.015 -10000 0 -0.3 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.019 0.019 -10000 0 -0.42 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.005 0.046 -10000 0 -0.28 2 2
TNFR1A/BAG4/TNF-alpha 0.033 0.033 -10000 0 -0.26 5 5
mol:Sphingosine-1-phosphate -0.019 0.022 -10000 0 -0.3 3 3
MAP2K1 -0.071 0.07 -10000 0 -0.25 45 45
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.02 0.002 -10000 0 -10000 0 0
CYCS -0.038 0.033 -10000 0 -0.22 8 8
TNFRSF1A 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
TNFR1A/BAG4 0.026 0.017 -10000 0 -0.3 1 1
EIF2AK2 -0.069 0.087 0.29 8 -0.26 53 61
TNF-alpha/TNFR1A/FAN 0.035 0.031 -10000 0 -0.26 4 4
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.068 -10000 0 -0.41 10 10
MAP2K2 -0.072 0.068 -10000 0 -0.25 46 46
SMPD3 0.001 0.047 0.19 4 -0.32 5 9
TNF 0.017 0.041 0.19 4 -0.42 4 8
PKC zeta/PAR4 0.025 0.03 -10000 0 -0.3 4 4
mol:PHOSPHOCHOLINE 0.17 0.075 0.2 424 -0.12 7 431
NF kappa B1/RelA/I kappa B alpha 0.05 0.032 -10000 0 -0.23 3 3
AIFM1 -0.046 0.048 -10000 0 -0.17 48 48
BCL2 0.02 0.003 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.032 0.043 0.19 37 -9999 0 37
GPC2 0.036 0.053 0.19 55 -9999 0 55
GPC2/Midkine 0.047 0.053 0.27 11 -9999 0 11
neuron projection morphogenesis 0.047 0.053 0.27 11 -9999 0 11
IL6-mediated 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
BCL2L1 0.12 0.2 0.55 39 -0.71 1 40
CRP 0.13 0.22 0.53 68 -0.71 1 69
cell cycle arrest 0.12 0.21 0.49 67 -0.82 1 68
TIMP1 0.14 0.2 0.52 57 -0.65 1 58
IL6ST 0.01 0.08 -10000 0 -0.41 17 17
Rac1/GDP 0.061 0.12 0.28 54 -0.48 2 56
AP1 0.059 0.14 0.37 23 -0.55 8 31
GAB2 0.015 0.014 -10000 0 -10000 0 0
TNFSF11 0.12 0.2 0.53 51 -0.71 1 52
HSP90B1 0.065 0.083 0.67 1 -0.59 1 2
GAB1 0.019 0.006 -10000 0 -10000 0 0
MAPK14 0.004 0.07 0.25 3 -0.35 1 4
AKT1 0.014 0.037 -10000 0 -0.45 1 1
FOXO1 0.015 0.048 -10000 0 -0.43 1 1
MAP2K6 0.018 0.09 0.23 17 -0.48 2 19
mol:GTP 0.002 0.003 -10000 0 -10000 0 0
MAP2K4 0.075 0.15 0.34 80 -0.48 2 82
MITF 0.029 0.099 0.24 41 -0.33 5 46
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.002 -10000 0 -10000 0 0
A2M 0.01 0.069 -10000 0 -1.1 2 2
CEBPB 0.016 0.032 0.2 8 -10000 0 8
GRB2/SOS1/GAB family/SHP2 0.034 0.094 0.24 3 -0.58 6 9
STAT3 0.12 0.21 0.51 56 -0.9 1 57
STAT1 0.018 0.1 -10000 0 -0.69 9 9
CEBPD 0.12 0.2 0.51 52 -0.71 1 53
PIK3CA 0.019 0.02 -10000 0 -0.42 1 1
PI3K 0.025 0.023 -10000 0 -0.3 2 2
JUN 0.014 0.014 -10000 0 -10000 0 0
PIAS3/MITF 0.036 0.1 0.28 21 -0.6 1 22
MAPK11 0.003 0.075 0.25 3 -0.46 2 5
STAT3 (dimer)/FOXO1 0.087 0.19 0.43 65 -0.76 1 66
GRB2/SOS1/GAB family 0.043 0.1 0.24 4 -0.48 2 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.021 0.089 0.22 15 -0.32 8 23
GRB2 0.019 0.007 -10000 0 -10000 0 0
JAK2 0.019 0.005 -10000 0 -10000 0 0
LBP 0.013 0.42 0.52 81 -0.82 87 168
PIK3R1 0.018 0.02 -10000 0 -0.42 1 1
JAK1 0.02 0.017 -10000 0 -10000 0 0
MYC 0.12 0.2 0.51 55 -0.71 1 56
FGG 0.14 0.22 0.52 70 -0.71 1 71
macrophage differentiation 0.12 0.21 0.49 67 -0.82 1 68
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.041 0.094 0.23 12 -0.24 30 42
JUNB 0.11 0.2 0.51 35 -0.74 3 38
FOS 0.005 0.064 0.19 1 -0.42 11 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.044 0.11 0.27 45 -0.34 5 50
STAT1/PIAS1 0.074 0.13 0.3 64 -0.56 1 65
GRB2/SOS1/GAB family/SHP2/PI3K 0.021 0.036 -10000 0 -0.3 1 1
STAT3 (dimer) 0.12 0.21 0.51 57 -0.86 1 58
PRKCD 0.082 0.17 0.38 80 -0.58 1 81
IL6R 0.02 0.017 -10000 0 -10000 0 0
SOCS3 0.007 0.09 0.41 1 -0.72 1 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.039 0.067 0.18 2 -0.24 17 19
Rac1/GTP 0.067 0.13 0.3 59 -0.49 2 61
HCK 0.028 0.038 0.19 27 -10000 0 27
MAPKKK cascade 0.045 0.11 0.36 7 -0.6 7 14
bone resorption 0.12 0.2 0.51 55 -0.67 1 56
IRF1 0.15 0.22 0.54 63 -0.71 1 64
mol:GDP 0.054 0.12 0.26 72 -0.35 5 77
SOS1 0.014 0.014 -10000 0 -10000 0 0
VAV1 0.053 0.12 0.26 71 -0.36 5 76
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.005 0.094 -10000 0 -0.45 11 11
PTPN11 0.028 0.049 -10000 0 -0.77 1 1
IL6/IL6RA 0.027 0.085 0.18 30 -0.3 24 54
gp130 (dimer)/TYK2/TYK2/LMO4 0.033 0.062 -10000 0 -0.25 17 17
gp130 (dimer)/JAK2/JAK2/LMO4 0.031 0.062 -10000 0 -0.25 17 17
IL6 0.016 0.11 0.21 37 -0.42 25 62
PIAS3 0.019 0.004 -10000 0 -10000 0 0
PTPRE -0.014 0.036 -10000 0 -0.15 1 1
PIAS1 0.02 0.002 -10000 0 -10000 0 0
RAC1 0.02 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.019 0.08 0.2 11 -0.24 24 35
LMO4 0.026 0.023 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.1 0.19 0.48 39 -0.89 1 40
MCL1 0.021 0.058 0.37 2 -10000 0 2
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.035 0.065 0.14 143 -0.12 4 147
BUB1B 0.018 0.039 0.15 22 -10000 0 22
PLK1 0.013 0.032 0.12 22 -0.092 1 23
PLK1S1 0.012 0.026 0.14 14 -0.13 1 15
KIF2A 0.025 0.079 0.26 50 -0.22 1 51
regulation of mitotic centrosome separation 0.014 0.032 0.12 21 -0.091 1 22
GOLGA2 0.019 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.064 0.074 0.2 99 -10000 0 99
WEE1 0.021 0.035 0.21 6 -0.25 1 7
cytokinesis 0.062 0.075 0.19 67 -0.19 2 69
PP2A-alpha B56 0.058 0.083 -10000 0 -0.49 7 7
AURKA 0.013 0.024 0.14 9 -10000 0 9
PICH/PLK1 0.003 0.04 0.17 18 -10000 0 18
CENPE 0.012 0.04 0.16 12 -10000 0 12
RhoA/GTP 0.011 0.007 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.025 0.079 0.26 50 -0.22 1 51
PPP2CA 0.015 0.009 -10000 0 -10000 0 0
FZR1 0.019 0.019 -10000 0 -0.42 1 1
TPX2 0.027 0.041 0.14 28 -10000 0 28
PAK1 0.02 0.003 -10000 0 -10000 0 0
SPC24 0.036 0.05 0.19 51 -10000 0 51
FBXW11 0.015 0.009 -10000 0 -10000 0 0
CLSPN 0.011 0.059 0.13 7 -0.24 21 28
GORASP1 0.014 0.009 -10000 0 -10000 0 0
metaphase 0.001 0.003 0.015 24 -10000 0 24
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.007 0.018 0.065 26 -0.046 1 27
G2 phase of mitotic cell cycle -0.001 0.002 0.012 8 -10000 0 8
STAG2 0.02 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.12 0.22 -10000 0 -0.48 147 147
spindle elongation 0.014 0.032 0.12 21 -0.091 1 22
ODF2 0.019 0.007 -10000 0 -10000 0 0
BUB1 0.06 0.087 -10000 0 -0.52 7 7
TPT1 0.007 0.033 0.11 9 -0.17 11 20
CDC25C 0.054 0.051 0.16 18 -0.27 1 19
CDC25B 0.022 0.016 0.19 4 -10000 0 4
SGOL1 -0.035 0.065 0.12 4 -0.14 143 147
RHOA 0.014 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.031 0.024 0.24 2 -10000 0 2
CDC14B -0.01 0.003 -10000 0 -10000 0 0
CDC20 0.032 0.045 0.19 40 -10000 0 40
PLK1/PBIP1 0.009 0.027 0.1 19 -10000 0 19
mitosis -0.002 0.002 0.017 2 -10000 0 2
FBXO5 0.004 0.039 0.15 14 -0.12 6 20
CDC2 0.001 0.001 0.014 3 -0.01 1 4
NDC80 0.054 0.068 0.19 109 -10000 0 109
metaphase plate congression 0.005 0.054 0.14 2 -0.23 22 24
ERCC6L 0.006 0.037 0.22 9 -10000 0 9
NLP/gamma Tubulin 0.008 0.024 0.094 14 -0.12 6 20
microtubule cytoskeleton organization 0.007 0.033 0.11 9 -0.17 11 20
G2/M transition DNA damage checkpoint -0.001 0.002 0.015 2 -10000 0 2
PPP1R12A 0.02 0.005 -10000 0 -10000 0 0
interphase -0.001 0.002 0.015 2 -10000 0 2
PLK1/PRC1-2 0.06 0.067 0.16 135 -10000 0 135
GRASP65/GM130/RAB1/GTP/PLK1 0.028 0.027 -10000 0 -10000 0 0
RAB1A 0.02 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.009 0.027 0.11 23 -0.071 1 24
mitotic prometaphase 0.001 0.004 0.019 22 -10000 0 22
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.028 0.19 1 -0.25 1 2
microtubule-based process 0.054 0.066 0.15 171 -10000 0 171
Golgi organization 0.014 0.032 0.12 21 -0.091 1 22
Cohesin/SA2 0.024 0.024 0.13 9 -10000 0 9
PPP1CB/MYPT1 0.029 0.007 -10000 0 -10000 0 0
KIF20A 0.071 0.083 0.19 175 -10000 0 175
APC/C/CDC20 0.034 0.045 0.16 47 -10000 0 47
PPP2R1A 0.02 0.002 -10000 0 -10000 0 0
chromosome segregation 0.008 0.027 0.1 19 -10000 0 19
PRC1 0.022 0.016 0.19 5 -10000 0 5
ECT2 0.012 0.052 0.23 22 -10000 0 22
C13orf34 0.01 0.026 0.1 23 -0.077 1 24
NUDC 0.005 0.054 0.14 2 -0.24 22 24
regulation of attachment of spindle microtubules to kinetochore 0.017 0.039 0.15 22 -10000 0 22
spindle assembly 0.01 0.029 0.11 22 -0.081 6 28
spindle stabilization 0.012 0.026 0.14 14 -0.13 1 15
APC/C/HCDH1 -0.012 0.015 -10000 0 -0.26 1 1
MKLP2/PLK1 0.054 0.067 0.15 171 -10000 0 171
CCNB1 0.022 0.022 0.19 8 -10000 0 8
PPP1CB 0.02 0.004 -10000 0 -10000 0 0
BTRC 0.019 0.004 -10000 0 -10000 0 0
ROCK2 -0.02 0.075 0.18 3 -0.37 9 12
TUBG1 0.009 0.032 0.13 6 -0.24 6 12
G2/M transition of mitotic cell cycle 0.002 0.019 0.19 2 -10000 0 2
MLF1IP -0.006 0.021 0.11 17 -10000 0 17
INCENP 0.02 0.005 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.05 0.12 -10000 0 -0.29 76 76
FZD6 0.019 0.005 -10000 0 -10000 0 0
WNT6 0.025 0.032 0.19 19 -10000 0 19
WNT4 -0.023 0.13 0.19 3 -0.42 52 55
FZD3 0.018 0.006 -10000 0 -10000 0 0
WNT5A 0.014 0.021 -10000 0 -0.42 1 1
WNT11 -0.005 0.11 0.19 6 -0.42 32 38
Signaling events mediated by PTP1B

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
PDGFRB 0.015 0.009 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.081 0.12 -10000 0 -0.38 45 45
PTP1B/AKT1 -0.072 0.068 0.23 1 -0.27 14 15
FYN 0.019 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.076 0.07 0.28 2 -0.28 16 18
EGFR -0.022 0.03 0.17 5 -0.43 1 6
EGF/EGFR -0.21 0.099 -10000 0 -0.26 380 380
CSF1 0.019 0.019 -10000 0 -0.42 1 1
AKT1 0.009 0.017 -10000 0 -10000 0 0
INSR 0.008 0.019 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.081 0.073 -10000 0 -0.28 24 24
Insulin Receptor/Insulin -0.067 0.073 0.3 1 -0.27 11 12
HCK 0.028 0.037 0.19 27 -10000 0 27
CRK 0.02 0.003 -10000 0 -10000 0 0
TYK2 -0.077 0.068 0.24 3 -0.28 14 17
EGF -0.37 0.14 -10000 0 -0.42 467 467
YES1 0.02 0.003 -10000 0 -10000 0 0
CAV1 -0.13 0.096 0.28 7 -0.28 34 41
TXN -0.015 0.015 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.077 0.07 0.31 1 -0.28 16 17
cell migration 0.076 0.07 0.28 16 -0.28 2 18
STAT3 0.018 0.007 -10000 0 -10000 0 0
PRLR -0.033 0.14 -10000 0 -0.42 61 61
ITGA2B 0.023 0.037 0.19 18 -0.42 1 19
CSF1R 0.017 0.019 0.19 5 -10000 0 5
Prolactin Receptor/Prolactin -0.014 0.1 -10000 0 -0.3 61 61
FGR 0.02 0.013 0.19 3 -10000 0 3
PTP1B/p130 Cas -0.076 0.066 -10000 0 -0.27 16 16
Crk/p130 Cas -0.078 0.066 -10000 0 -0.28 12 12
DOK1 -0.049 0.08 0.26 6 -0.29 11 17
JAK2 -0.08 0.13 0.3 1 -0.4 47 48
Jak2/Leptin Receptor/Leptin -0.067 0.084 -10000 0 -0.33 13 13
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
PTPN1 -0.076 0.071 0.28 2 -0.28 16 18
LYN 0.019 0.005 -10000 0 -10000 0 0
CDH2 0.007 0.073 -10000 0 -0.42 15 15
SRC -0.015 0.045 0.32 1 -0.54 2 3
ITGB3 0.015 0.043 -10000 0 -0.42 5 5
CAT1/PTP1B -0.19 0.14 0.34 7 -0.37 101 108
CAPN1 0.006 0.018 -10000 0 -10000 0 0
CSK 0.02 0.002 -10000 0 -10000 0 0
PI3K -0.069 0.07 -10000 0 -0.29 8 8
mol:H2O2 -0.004 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.062 0.078 -10000 0 -0.3 12 12
negative regulation of transcription -0.079 0.13 0.3 1 -0.39 47 48
FCGR2A 0.027 0.035 0.19 23 -10000 0 23
FER -0.015 0.029 -10000 0 -0.43 2 2
alphaIIb/beta3 Integrin 0.028 0.041 -10000 0 -0.29 6 6
BLK 0.029 0.042 0.19 34 -10000 0 34
Insulin Receptor/Insulin/Shc 0.034 0.017 -10000 0 -10000 0 0
RHOA 0.01 0.012 -10000 0 -10000 0 0
LEPR 0.02 0.006 -10000 0 -10000 0 0
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
p210 bcr-abl/Grb2 0.02 0.003 -10000 0 -10000 0 0
mol:NADPH -0.005 0.003 -10000 0 -10000 0 0
TRPV6 -0.16 0.15 0.34 4 -0.44 61 65
PRL 0 0.018 -10000 0 -10000 0 0
SOCS3 0.013 0.11 -10000 0 -1 6 6
SPRY2 -0.013 0.017 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.031 0.031 -10000 0 -0.26 4 4
CSF1/CSF1R -0.062 0.068 0.31 1 -0.29 10 11
Ras protein signal transduction 0.02 0.072 0.51 10 -10000 0 10
IRS1 0.016 0.038 -10000 0 -0.42 4 4
INS -0.01 0.017 -10000 0 -10000 0 0
LEP 0.024 0.054 0.19 47 -10000 0 47
STAT5B -0.073 0.088 0.26 2 -0.34 23 25
STAT5A -0.073 0.088 0.26 2 -0.32 28 30
GRB2 0.02 0.003 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.061 0.066 0.31 1 -0.27 13 14
CSN2 0.006 0.06 -10000 0 -0.49 1 1
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
LAT 0.009 0.083 -10000 0 -0.43 9 9
YBX1 -0.01 0.018 -10000 0 -10000 0 0
LCK 0.024 0.042 0.19 20 -0.42 2 22
SHC1 0.019 0.004 -10000 0 -10000 0 0
NOX4 -0.016 0.035 -10000 0 -0.42 3 3
FoxO family signaling

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
G6PC -0.54 0.58 -10000 0 -1.2 245 245
PLK1 0.016 0.17 0.43 4 -0.72 1 5
CDKN1B -0.071 0.11 0.34 2 -0.35 13 15
FOXO3 0.039 0.11 0.36 4 -0.7 2 6
KAT2B 0.024 0.029 -10000 0 -0.45 1 1
FOXO1/SIRT1 -0.18 0.21 -10000 0 -0.4 239 239
CAT -0.01 0.17 0.46 2 -1.3 2 4
CTNNB1 0.014 0.009 -10000 0 -10000 0 0
AKT1 -0.009 0.046 -10000 0 -0.33 1 1
FOXO1 -0.19 0.22 0.28 1 -0.42 240 241
MAPK10 -0.001 0.066 0.18 55 -0.21 4 59
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.023 0.086 0.33 16 -10000 0 16
response to oxidative stress -0.014 0.032 -10000 0 -0.22 2 2
FOXO3A/SIRT1 -0.036 0.14 -10000 0 -0.48 10 10
XPO1 0.02 0.004 -10000 0 -10000 0 0
EP300 -0.025 0.053 -10000 0 -0.25 4 4
BCL2L11 0.017 0.091 -10000 0 -0.8 6 6
FOXO1/SKP2 -0.16 0.2 0.23 1 -0.39 216 217
mol:GDP -0.014 0.032 -10000 0 -0.22 2 2
RAN 0.02 0.004 -10000 0 -10000 0 0
GADD45A -0.005 0.15 0.37 1 -0.61 20 21
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.016 0.1 -10000 0 -0.55 10 10
MST1 0.026 0.033 0.2 6 -0.39 1 7
CSNK1D 0.02 0.003 -10000 0 -10000 0 0
CSNK1E 0.02 0.002 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.001 0.096 -10000 0 -0.55 10 10
YWHAB 0.019 0.004 -10000 0 -10000 0 0
MAPK8 0 0.063 0.17 55 -0.23 2 57
MAPK9 -0.004 0.048 0.18 28 -10000 0 28
YWHAG 0.018 0.006 -10000 0 -10000 0 0
YWHAE 0.02 0.003 -10000 0 -10000 0 0
YWHAZ 0.019 0.005 -10000 0 -10000 0 0
SIRT1 -0.006 0.028 -10000 0 -10000 0 0
SOD2 -0.085 0.15 0.35 2 -0.5 20 22
RBL2 0.009 0.15 -10000 0 -0.92 6 6
RAL/GDP 0.003 0.033 -10000 0 -10000 0 0
CHUK 0.032 0.015 -10000 0 -10000 0 0
Ran/GTP 0.015 0.003 -10000 0 -10000 0 0
CSNK1G2 0.019 0.019 -10000 0 -0.42 1 1
RAL/GTP 0.005 0.031 -10000 0 -10000 0 0
CSNK1G1 0.02 0.002 -10000 0 -10000 0 0
FASLG 0.1 0.15 -10000 0 -0.77 8 8
SKP2 0.018 0.006 -10000 0 -10000 0 0
USP7 0.019 0.005 -10000 0 -10000 0 0
IKBKB 0.03 0.016 -10000 0 -10000 0 0
CCNB1 0.008 0.16 0.41 2 -0.64 2 4
FOXO1-3a-4/beta catenin -0.049 0.12 0.32 5 -0.43 1 6
proteasomal ubiquitin-dependent protein catabolic process -0.16 0.2 0.23 1 -0.39 216 217
CSNK1A1 0.015 0.009 -10000 0 -10000 0 0
SGK1 0.031 0.017 -10000 0 -10000 0 0
CSNK1G3 0.016 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.007 -10000 0 -10000 0 0
ZFAND5 0.02 0.084 0.4 9 -10000 0 9
SFN 0.022 0.081 0.19 41 -0.42 12 53
CDK2 -0.035 0.062 -10000 0 -0.15 11 11
FOXO3A/14-3-3 0.001 0.099 0.26 1 -0.57 9 10
CREBBP -0.033 0.06 -10000 0 -0.14 8 8
FBXO32 -0.001 0.16 0.44 7 -0.64 2 9
BCL6 0.003 0.17 -10000 0 -0.77 12 12
RALB 0.02 0.004 -10000 0 -10000 0 0
RALA 0.018 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.002 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.041 0.077 0.36 3 -10000 0 3
UGCG 0.007 0.11 -10000 0 -0.56 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT 0.066 0.12 0.26 34 -0.45 10 44
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.009 0.11 -10000 0 -0.55 19 19
mol:DAG -0.009 0.13 -10000 0 -0.83 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.064 0.094 0.3 8 -0.41 6 14
FRAP1 0.066 0.11 0.33 9 -0.46 6 15
FOXO3 0.055 0.1 0.3 11 -0.46 6 17
AKT1 0.06 0.1 0.31 10 -0.46 8 18
GAB2 0.021 0.003 -10000 0 -10000 0 0
SMPD1 0.026 0.041 -10000 0 -0.71 1 1
SGMS1 0.012 0.11 -10000 0 -0.69 12 12
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 -0.012 0.016 -10000 0 -0.25 2 2
CALM1 0.019 0.005 -10000 0 -10000 0 0
cell proliferation 0.029 0.12 0.27 8 -0.45 18 26
EIF3A 0.019 0.004 -10000 0 -10000 0 0
PI3K 0.027 0.023 -10000 0 -0.3 2 2
RPS6KB1 0.034 0.11 -10000 0 -0.89 6 6
mol:sphingomyelin -0.009 0.13 -10000 0 -0.83 12 12
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 0.055 0.067 0.19 105 -10000 0 105
PIK3R1 0.018 0.02 -10000 0 -0.42 1 1
JAK1 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
MYC 0.063 0.11 0.39 12 -0.43 5 17
MYB 0.07 0.094 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.059 0.097 0.26 20 -0.5 7 27
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.051 0.1 -10000 0 -0.81 6 6
mol:PI-3-4-5-P3 0.059 0.097 0.25 21 -0.49 7 28
Rac1/GDP -0.015 0.018 -10000 0 -0.23 2 2
T cell proliferation 0.056 0.091 0.25 23 -0.44 8 31
SHC1 0.02 0.005 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.016 0.026 0.06 139 -10000 0 139
PRKCZ 0.054 0.091 0.25 19 -0.46 8 27
NF kappa B1 p50/RelA 0.075 0.099 0.3 8 -0.42 6 14
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.05 0.067 0.22 17 -0.37 3 20
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
RELA 0.02 0.002 -10000 0 -10000 0 0
IL2RA 0.052 0.066 0.19 100 -10000 0 100
IL2RB 0.11 0.084 0.19 272 -10000 0 272
TERT 0.036 0.055 0.19 60 -10000 0 60
E2F1 0.066 0.077 0.26 23 -10000 0 23
SOS1 0.02 0.004 -10000 0 -10000 0 0
RPS6 0.02 0.011 0.19 2 -10000 0 2
mol:cAMP -0.008 0.014 -10000 0 -0.032 137 137
PTPN11 0.02 0.004 -10000 0 -10000 0 0
IL2RG 0.031 0.045 0.19 33 -0.42 1 34
actin cytoskeleton organization 0.056 0.091 0.25 23 -0.44 8 31
GRB2 0.02 0.004 -10000 0 -10000 0 0
IL2 0.023 0.024 0.19 10 -10000 0 10
PIK3CA 0.019 0.02 -10000 0 -0.42 1 1
Rac1/GTP 0.034 0.027 -10000 0 -0.22 2 2
LCK 0.025 0.043 0.19 20 -0.42 2 22
BCL2 0.059 0.094 0.36 4 -0.41 1 5
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.079 0.062 -10000 0 -0.24 1 1
alphaV beta3 Integrin 0.033 0.042 -10000 0 -0.28 8 8
PTK2 -0.017 0.12 0.43 7 -0.42 12 19
IGF1R 0.02 0.002 -10000 0 -10000 0 0
PI4KB 0.019 0.004 -10000 0 -10000 0 0
MFGE8 0.02 0.008 0.19 1 -10000 0 1
SRC 0.019 0.004 -10000 0 -10000 0 0
CDKN1B -0.043 0.14 -10000 0 -0.4 67 67
VEGFA 0.093 0.084 0.19 232 -10000 0 232
ILK -0.045 0.14 -10000 0 -0.39 70 70
ROCK1 0.02 0.003 -10000 0 -10000 0 0
AKT1 -0.056 0.13 -10000 0 -0.38 69 69
PTK2B 0.008 0.058 0.21 19 -0.23 5 24
alphaV/beta3 Integrin/JAM-A 0.001 0.094 0.22 1 -0.23 69 70
CBL 0.019 0.019 -10000 0 -0.42 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.091 0.14 -10000 0 -0.26 222 222
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.045 0.03 -10000 0 -0.24 4 4
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.023 0.1 -10000 0 -0.3 37 37
alphaV/beta3 Integrin/Syndecan-1 0.032 0.044 -10000 0 -0.26 11 11
PI4KA 0.02 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.039 0.049 -10000 0 -0.26 10 10
PI4 Kinase 0.028 0.007 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Osteopontin 0.034 0.036 -10000 0 -0.26 7 7
RPS6KB1 -0.021 0.092 0.45 13 -0.39 2 15
TLN1 0.019 0.004 -10000 0 -10000 0 0
MAPK3 -0.027 0.077 0.24 1 -0.44 8 9
GPR124 0.019 0.012 0.19 2 -10000 0 2
MAPK1 -0.026 0.077 0.24 1 -0.44 8 9
PXN 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Tumstatin 0.004 0.096 -10000 0 -0.27 57 57
cell adhesion -0.085 0.12 -10000 0 -0.23 217 217
ANGPTL3 -0.17 0.22 -10000 0 -0.42 224 224
VEGFR2 homodimer/VEGFA homodimer/Src 0.083 0.057 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.02 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.005 -10000 0 -10000 0 0
TGFBR2 0.014 0.009 -10000 0 -10000 0 0
ITGB3 0.015 0.043 -10000 0 -0.42 5 5
IGF1 0.021 0.017 0.19 5 -10000 0 5
RAC1 0.018 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.033 0.032 -10000 0 -0.26 5 5
apoptosis 0.019 0.004 -10000 0 -10000 0 0
CD47 0.018 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.033 0.032 -10000 0 -0.26 5 5
VCL 0.019 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.028 0.051 -10000 0 -0.27 12 12
CSF1 0.019 0.019 -10000 0 -0.42 1 1
PIK3C2A -0.046 0.14 -10000 0 -0.4 71 71
PI4 Kinase/Pyk2 -0.03 0.08 -10000 0 -0.23 30 30
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.085 0.066 -10000 0 -0.23 6 6
FAK1/Vinculin -0.011 0.1 0.41 6 -0.34 12 18
alphaV beta3/Integrin/ppsTEM5 0.033 0.032 -10000 0 -0.26 5 5
RHOA 0.014 0.009 -10000 0 -10000 0 0
VTN -0.037 0.15 0.19 6 -0.42 70 76
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
FGF2 0.017 0.039 0.19 1 -0.42 4 5
F11R -0.02 0.029 0.32 1 -0.3 4 5
alphaV/beta3 Integrin/Lactadherin 0.035 0.031 -10000 0 -0.26 5 5
alphaV/beta3 Integrin/TGFBR2 0.026 0.033 -10000 0 -0.26 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.045 0.029 -10000 0 -0.34 2 2
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.029 -10000 0 -0.23 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.031 0.043 0.19 36 -10000 0 36
alphaV/beta3 Integrin/Pyk2 0.015 0.06 0.18 1 -0.23 5 6
SDC1 0.014 0.047 -10000 0 -0.42 6 6
VAV3 -0.023 0.067 0.21 27 -0.24 14 41
PTPN11 0.019 0.004 -10000 0 -10000 0 0
IRS1 0.016 0.038 -10000 0 -0.42 4 4
FAK1/Paxillin -0.013 0.099 0.34 5 -0.34 12 17
cell migration -0.017 0.091 0.3 6 -0.31 12 18
ITGAV 0.019 0.004 -10000 0 -10000 0 0
PI3K 0.006 0.091 -10000 0 -0.23 61 61
SPP1 0.017 0.033 -10000 0 -0.42 3 3
KDR 0.019 0.019 -10000 0 -0.42 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.019 0.004 -10000 0 -10000 0 0
COL4A3 -0.026 0.13 -10000 0 -0.42 54 54
angiogenesis -0.034 0.1 0.26 5 -0.46 8 13
Rac1/GTP -0.028 0.044 0.16 14 -0.23 11 25
EDIL3 0.013 0.056 0.19 5 -0.42 8 13
cell proliferation 0.025 0.033 -10000 0 -0.26 5 5
Syndecan-4-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
PTK2 -0.058 0.15 0.24 1 -0.62 15 16
Syndecan-4/Syndesmos -0.046 0.14 0.35 1 -10000 0 1
positive regulation of JNK cascade -0.016 0.15 0.32 10 -0.46 2 12
Syndecan-4/ADAM12 -0.019 0.16 0.34 17 -10000 0 17
CCL5 0.09 0.083 0.19 220 -10000 0 220
Rac1/GDP 0.013 0.005 -10000 0 -10000 0 0
DNM2 0.02 0.002 -10000 0 -10000 0 0
ITGA5 0.031 0.042 0.19 35 -10000 0 35
SDCBP 0.019 0.005 -10000 0 -10000 0 0
PLG -0.19 0.21 -10000 0 -0.41 246 246
ADAM12 0.063 0.074 0.19 136 -10000 0 136
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.019 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.021 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.049 0.14 0.36 2 -0.38 2 4
Syndecan-4/CXCL12/CXCR4 -0.016 0.16 0.34 10 -0.48 2 12
Syndecan-4/Laminin alpha3 -0.045 0.14 0.34 4 -10000 0 4
MDK 0.032 0.043 0.19 37 -10000 0 37
Syndecan-4/FZD7 -0.047 0.14 0.35 1 -10000 0 1
Syndecan-4/Midkine -0.041 0.14 0.36 3 -10000 0 3
FZD7 0.018 0.02 -10000 0 -0.42 1 1
Syndecan-4/FGFR1/FGF -0.048 0.13 -10000 0 -10000 0 0
THBS1 0.017 0.033 -10000 0 -0.42 3 3
integrin-mediated signaling pathway -0.049 0.14 0.33 3 -0.45 4 7
positive regulation of MAPKKK cascade -0.016 0.15 0.32 10 -0.46 2 12
Syndecan-4/TACI -0.038 0.14 0.34 4 -10000 0 4
CXCR4 0.078 0.08 0.19 182 -10000 0 182
cell adhesion 0.02 0.032 0.19 7 -10000 0 7
Syndecan-4/Dynamin -0.047 0.14 0.36 2 -10000 0 2
Syndecan-4/TSP1 -0.048 0.14 0.36 2 -0.38 1 3
Syndecan-4/GIPC -0.047 0.14 0.36 2 -0.38 1 3
Syndecan-4/RANTES -0.008 0.16 0.36 9 -10000 0 9
ITGB1 0.02 0.003 -10000 0 -10000 0 0
LAMA1 0.012 0.06 0.19 1 -0.42 10 11
LAMA3 0.022 0.018 0.19 6 -10000 0 6
RAC1 0.018 0.006 -10000 0 -10000 0 0
PRKCA 0.018 0.11 0.82 9 -10000 0 9
Syndecan-4/alpha-Actinin -0.048 0.14 0.35 1 -10000 0 1
TFPI 0.019 0.032 0.19 5 -0.42 2 7
F2 0.09 0.085 0.2 195 -10000 0 195
alpha5/beta1 Integrin 0.037 0.03 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.054 0.14 0.32 4 -0.38 2 6
ACTN1 0.018 0.02 -10000 0 -0.42 1 1
TNC 0.009 0.065 -10000 0 -0.42 12 12
Syndecan-4/CXCL12 -0.049 0.14 0.35 1 -0.49 2 3
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.014 0.009 -10000 0 -10000 0 0
CXCL12 0.013 0.054 -10000 0 -0.42 8 8
TNFRSF13B 0.036 0.051 0.19 52 -10000 0 52
FGF2 0.017 0.039 0.19 1 -0.42 4 5
FGFR1 0.018 0.006 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.053 0.13 0.31 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.035 0.047 0.19 36 -10000 0 36
cell migration -0.014 0.011 -10000 0 -10000 0 0
PRKCD 0.012 0.021 0.22 1 -10000 0 1
vasculogenesis -0.046 0.14 0.33 3 -0.37 1 4
SDC4 -0.043 0.13 0.34 2 -10000 0 2
Syndecan-4/Tenascin C -0.051 0.14 0.36 2 -0.46 4 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.017 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.05 0.13 -10000 0 -10000 0 0
MMP9 0.1 0.087 0.2 234 -10000 0 234
Rac1/GTP 0.02 0.032 0.19 7 -10000 0 7
cytoskeleton organization -0.045 0.13 0.34 1 -10000 0 1
GIPC1 0.019 0.019 -10000 0 -0.42 1 1
Syndecan-4/TFPI -0.046 0.14 0.33 2 -0.38 1 3
Class I PI3K signaling events

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.006 0.061 0.28 1 -10000 0 1
DAPP1 -0.007 0.1 0.31 8 -0.39 18 26
Src family/SYK family/BLNK-LAT/BTK-ITK 0.043 0.14 0.26 16 -0.51 14 30
mol:DAG 0.068 0.11 0.23 125 -0.21 4 129
HRAS 0.024 0.01 0.18 1 -10000 0 1
RAP1A 0.023 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.03 0.061 0.23 2 -0.38 6 8
PLCG2 0.018 0.036 0.19 4 -0.42 3 7
PLCG1 0.019 0.004 -10000 0 -10000 0 0
ARF5 0.018 0.006 -10000 0 -10000 0 0
mol:GTP -0.019 0.032 0.25 3 -10000 0 3
ARF1/GTP 0.003 0.059 0.29 3 -10000 0 3
RHOA 0.014 0.009 -10000 0 -10000 0 0
YES1 0.02 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.019 0.029 0.16 9 -10000 0 9
ADAP1 0 0.07 0.27 3 -0.22 4 7
ARAP3 -0.019 0.032 0.24 3 -10000 0 3
INPPL1 0.02 0.002 -10000 0 -10000 0 0
PREX1 0.019 0.004 -10000 0 -10000 0 0
ARHGEF6 0.02 0.002 -10000 0 -10000 0 0
ARHGEF7 0.02 0.003 -10000 0 -10000 0 0
ARF1 0.019 0.004 -10000 0 -10000 0 0
NRAS 0.023 0.008 -10000 0 -10000 0 0
FYN 0.019 0.005 -10000 0 -10000 0 0
ARF6 0.019 0.005 -10000 0 -10000 0 0
FGR 0.02 0.013 0.19 3 -10000 0 3
mol:Ca2+ 0.042 0.079 0.17 82 -10000 0 82
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.019 0.004 -10000 0 -10000 0 0
ZAP70 0.11 0.084 0.19 291 -10000 0 291
mol:IP3 0.048 0.088 0.17 121 -0.17 1 122
LYN 0.019 0.005 -10000 0 -10000 0 0
ARF1/GDP 0.039 0.067 0.23 8 -0.37 6 14
RhoA/GDP -0.004 0.038 0.25 3 -10000 0 3
PDK1/Src/Hsp90 0.035 0.019 -10000 0 -0.26 1 1
BLNK 0.019 0.019 -10000 0 -0.42 1 1
actin cytoskeleton reorganization 0.016 0.088 0.28 24 -0.31 4 28
SRC 0.019 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.019 0.011 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
PTEN 0.01 0.022 -10000 0 -10000 0 0
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.006 0.062 0.28 1 -10000 0 1
RhoA/GTP -0.018 0.031 0.24 3 -10000 0 3
Src family/SYK family/BLNK-LAT 0.029 0.1 0.2 13 -0.34 17 30
BLK 0.029 0.042 0.19 34 -10000 0 34
PDPK1 0.018 0.019 -10000 0 -0.42 1 1
CYTH1 0.01 0.08 0.27 11 -10000 0 11
HCK 0.028 0.037 0.19 27 -10000 0 27
CYTH3 0.001 0.068 0.27 3 -10000 0 3
CYTH2 0.009 0.079 0.27 11 -10000 0 11
KRAS 0.022 0.008 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.007 0.051 -10000 0 -0.32 3 3
SGK1 0.006 0.084 0.21 2 -0.34 21 23
INPP5D 0.02 0.015 0.19 4 -10000 0 4
mol:GDP 0.03 0.07 0.21 15 -0.39 6 21
SOS1 0.02 0.003 -10000 0 -10000 0 0
SYK 0.019 0.019 -10000 0 -0.42 1 1
ARF6/GDP -0.013 0.036 0.29 2 -10000 0 2
mol:PI-3-4-5-P3 0.015 0.082 0.16 119 -10000 0 119
ARAP3/RAP1A/GTP -0.02 0.029 0.16 9 -10000 0 9
VAV1 0.058 0.074 0.19 122 -0.42 1 123
mol:PI-3-4-P2 -0.017 0.012 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.018 0.087 0.17 124 -10000 0 124
PLEKHA1 -0.02 0.01 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.06 0.21 1 -0.38 6 7
LAT 0.065 0.076 0.19 144 -10000 0 144
Rac1/GTP 0.025 0.047 0.19 1 -0.4 2 3
ITK -0.003 0.04 0.23 4 -10000 0 4
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.068 0.12 0.24 116 -0.28 5 121
LCK 0.024 0.042 0.19 20 -0.42 2 22
BTK 0.027 0.082 0.24 27 -10000 0 27
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.003 0.24 -10000 0 -0.88 31 31
NCK1/PAK1/Dok-R -0.035 0.098 -10000 0 -0.41 30 30
NCK1/Dok-R -0.037 0.25 -10000 0 -0.98 30 30
PIK3CA 0.019 0.02 -10000 0 -0.42 1 1
mol:beta2-estradiol 0.003 0.028 0.22 8 -10000 0 8
RELA 0.02 0.002 -10000 0 -10000 0 0
SHC1 0.018 0.01 -10000 0 -10000 0 0
Rac/GDP 0.013 0.005 -10000 0 -10000 0 0
F2 0.061 0.1 0.2 118 -10000 0 118
TNIP2 0.02 0.003 -10000 0 -10000 0 0
NF kappa B/RelA -0.034 0.24 -10000 0 -0.95 30 30
FN1 0.031 0.043 0.19 36 -10000 0 36
PLD2 -0.064 0.25 -10000 0 -1 30 30
PTPN11 0.019 0.004 -10000 0 -10000 0 0
GRB14 -0.003 0.096 -10000 0 -0.42 27 27
ELK1 -0.059 0.22 0.37 2 -0.93 30 32
GRB7 0.014 0.05 -10000 0 -0.42 7 7
PAK1 0.02 0.002 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.022 0.25 -10000 0 -0.95 30 30
CDKN1A 0.017 0.19 0.39 1 -0.62 32 33
ITGA5 0.031 0.042 0.19 35 -10000 0 35
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.037 0.24 -10000 0 -0.97 30 30
CRK 0.02 0.003 -10000 0 -10000 0 0
mol:NO 0.023 0.19 0.34 20 -0.63 31 51
PLG -0.15 0.26 -10000 0 -1.1 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.014 0.22 -10000 0 -0.82 31 31
GRB2 0.02 0.003 -10000 0 -10000 0 0
PIK3R1 0.016 0.022 -10000 0 -0.42 1 1
ANGPT2 0.026 0.18 -10000 0 -0.63 16 16
BMX -0.059 0.25 -10000 0 -1 30 30
ANGPT1 -0.033 0.16 -10000 0 -1.2 8 8
tube development 0.008 0.21 -10000 0 -0.7 31 31
ANGPT4 0.027 0.031 0.19 16 -10000 0 16
response to hypoxia -0.005 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.065 0.27 -10000 0 -1.1 30 30
alpha5/beta1 Integrin 0.037 0.03 -10000 0 -10000 0 0
FGF2 -0.004 0.043 0.18 1 -0.42 4 5
STAT5A (dimer) 0.016 0.23 -10000 0 -0.79 31 31
mol:L-citrulline 0.023 0.19 0.34 20 -0.63 31 51
AGTR1 0.007 0.093 -10000 0 -0.41 24 24
MAPK14 -0.05 0.3 -10000 0 -1.1 35 35
Tie2/SHP2 -0.046 0.24 -10000 0 -0.99 30 30
TEK -0.057 0.27 -10000 0 -1 33 33
RPS6KB1 -0.006 0.23 0.36 1 -0.85 30 31
Angiotensin II/AT1 0.019 0.07 -10000 0 -0.29 24 24
Tie2/Ang1/GRB2 -0.055 0.26 -10000 0 -1.1 30 30
MAPK3 -0.061 0.23 -10000 0 -0.93 30 30
MAPK1 -0.064 0.22 -10000 0 -0.94 30 30
Tie2/Ang1/GRB7 -0.057 0.26 -10000 0 -1.1 30 30
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
MAPK8 -0.066 0.25 -10000 0 -1 30 30
PI3K -0.015 0.27 -10000 0 -1 30 30
FES -0.04 0.28 -10000 0 -1.1 30 30
Crk/Dok-R -0.036 0.25 -10000 0 -0.98 30 30
Tie2/Ang1/ABIN2 -0.056 0.26 -10000 0 -1.1 30 30
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.005 0.22 0.35 1 -0.78 31 32
STAT5A 0.02 0.003 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.004 0.23 0.36 1 -0.85 30 31
Tie2/Ang2 -0.001 0.27 -10000 0 -0.97 31 31
Tie2/Ang1 -0.062 0.28 -10000 0 -1.1 30 30
FOXO1 0.009 0.22 0.37 1 -0.79 31 32
ELF1 0.013 0.037 -10000 0 -0.19 5 5
ELF2 -0.062 0.25 -10000 0 -1 30 30
mol:Choline -0.061 0.24 -10000 0 -0.98 30 30
cell migration -0.02 0.056 -10000 0 -0.23 29 29
FYN 0.001 0.23 -10000 0 -0.8 31 31
DOK2 0.027 0.044 0.19 30 -0.42 1 31
negative regulation of cell cycle 0.02 0.18 0.38 1 -0.56 32 33
ETS1 -0.002 0.037 -10000 0 -0.24 8 8
PXN 0.004 0.2 0.4 6 -0.71 28 34
ITGB1 0.02 0.003 -10000 0 -10000 0 0
NOS3 0.017 0.21 0.39 8 -0.72 31 39
RAC1 0.018 0.006 -10000 0 -10000 0 0
TNF 0.013 0.054 0.19 4 -0.3 12 16
MAPKKK cascade -0.061 0.24 -10000 0 -0.98 30 30
RASA1 0.017 0.02 -10000 0 -0.42 1 1
Tie2/Ang1/Shc -0.05 0.26 -10000 0 -1.1 30 30
NCK1 0.018 0.02 -10000 0 -0.42 1 1
vasculogenesis 0.026 0.18 0.33 21 -0.56 31 52
mol:Phosphatidic acid -0.061 0.24 -10000 0 -0.98 30 30
mol:Angiotensin II 0.008 0.008 -10000 0 -10000 0 0
mol:NADP 0.023 0.19 0.34 20 -0.63 31 51
Rac1/GTP -0.002 0.21 -10000 0 -0.77 31 31
MMP2 -0.065 0.25 -10000 0 -1 30 30
Endothelins

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
AKT1 0.011 0.085 0.24 26 -0.25 7 33
PTK2B 0.018 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.13 0.45 2 -0.58 15 17
EDN1 0.041 0.076 0.22 30 -0.26 3 33
EDN3 0.022 0.025 0.19 11 -10000 0 11
EDN2 0.02 0.09 0.19 43 -0.42 16 59
HRAS/GDP 0.004 0.11 0.29 5 -0.43 15 20
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.019 0.079 0.2 10 -0.46 6 16
ADCY4 0.005 0.067 0.24 9 -0.24 1 10
ADCY5 -0.001 0.078 0.25 7 -0.29 7 14
ADCY6 0.005 0.068 0.24 7 -0.24 1 8
ADCY7 0.008 0.069 0.22 10 -0.24 1 11
ADCY1 0.002 0.07 0.23 8 -0.28 3 11
ADCY2 0.028 0.087 0.26 17 -0.25 3 20
ADCY3 0.007 0.07 0.24 11 -0.24 1 12
ADCY8 0.039 0.083 0.24 23 -0.24 1 24
ADCY9 0.006 0.067 0.23 10 -10000 0 10
arachidonic acid secretion -0.008 0.12 0.34 6 -0.42 23 29
ETB receptor/Endothelin-1/Gq/GTP 0.012 0.06 -10000 0 -0.34 7 7
GNAO1 0.019 0.023 0.19 3 -0.42 1 4
HRAS 0.02 0.009 0.19 1 -10000 0 1
ETA receptor/Endothelin-1/G12/GTP 0.059 0.096 0.34 24 -0.22 6 30
ETA receptor/Endothelin-1/Gs/GTP 0.06 0.095 0.32 29 -0.21 7 36
mol:GTP 0 0.002 -10000 0 -10000 0 0
COL3A1 0.025 0.11 0.26 77 -0.25 7 84
EDNRB 0.025 0.027 0.19 1 -0.42 1 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.017 0.12 0.24 58 -0.45 11 69
CYSLTR1 0.014 0.091 0.25 29 -0.32 3 32
SLC9A1 0.021 0.062 0.24 7 -0.3 4 11
mol:GDP 0.001 0.11 0.3 7 -0.45 15 22
SLC9A3 -0.32 0.26 0.45 1 -0.52 249 250
RAF1 -0.007 0.11 0.36 4 -0.43 18 22
JUN -0.001 0.13 -10000 0 -0.58 13 13
JAK2 0.013 0.089 0.24 31 -0.25 7 38
mol:IP3 0.013 0.09 0.19 6 -0.45 11 17
ETA receptor/Endothelin-1 0.065 0.12 0.4 31 -0.29 8 39
PLCB1 0.011 0.057 -10000 0 -0.42 9 9
PLCB2 0.037 0.053 0.19 57 -10000 0 57
ETA receptor/Endothelin-3 0.038 0.051 0.19 8 -10000 0 8
FOS -0.018 0.15 0.35 5 -0.75 16 21
Gai/GDP -0.14 0.27 -10000 0 -0.56 143 143
CRK 0.02 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0.017 0.098 0.25 10 -0.48 6 16
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
PRKCB1 0.007 0.093 0.19 1 -0.36 19 20
GNAQ 0.019 0.008 -10000 0 -10000 0 0
GNAZ 0.017 0.033 -10000 0 -0.42 3 3
GNAL 0.02 0.003 -10000 0 -10000 0 0
Gs family/GDP 0.002 0.1 0.27 5 -0.41 15 20
ETA receptor/Endothelin-1/Gq/GTP 0.019 0.072 0.2 5 -0.39 4 9
MAPK14 0.007 0.062 -10000 0 -0.44 6 6
TRPC6 -0.002 0.14 0.46 2 -0.61 15 17
GNAI2 0.014 0.009 -10000 0 -10000 0 0
GNAI3 0.019 0.004 -10000 0 -10000 0 0
GNAI1 0.017 0.02 -10000 0 -0.42 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.012 0.074 0.17 2 -0.48 7 9
ETB receptor/Endothelin-2 0.032 0.07 0.19 2 -0.3 17 19
ETB receptor/Endothelin-3 0.034 0.027 0.18 2 -0.3 1 3
ETB receptor/Endothelin-1 0.048 0.071 0.25 1 -0.54 1 2
MAPK3 -0.013 0.14 0.36 5 -0.66 16 21
MAPK1 -0.013 0.14 0.37 5 -0.67 16 21
Rac1/GDP -0.001 0.1 0.25 1 -0.42 15 16
cAMP biosynthetic process 0.03 0.09 0.28 17 -0.34 5 22
MAPK8 0.001 0.15 0.34 1 -0.61 19 20
SRC 0.019 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.008 0.072 0.16 2 -0.34 10 12
p130Cas/CRK/Src/PYK2 -0.005 0.12 0.38 8 -0.44 16 24
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0 0.1 0.25 1 -0.43 14 15
COL1A2 0.045 0.11 0.3 41 -0.51 1 42
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.037 0.081 0.24 12 -0.28 16 28
mol:DAG 0.013 0.09 0.19 6 -0.45 11 17
MAP2K2 -0.012 0.12 0.43 4 -0.48 22 26
MAP2K1 -0.01 0.12 0.36 5 -0.49 20 25
EDNRA 0.033 0.066 0.21 30 -0.18 6 36
positive regulation of muscle contraction 0.021 0.091 0.22 57 -0.21 6 63
Gq family/GDP 0.014 0.097 -10000 0 -0.39 13 13
HRAS/GTP 0 0.1 0.29 5 -0.39 20 25
PRKCH 0.005 0.081 -10000 0 -0.38 11 11
RAC1 0.018 0.006 -10000 0 -10000 0 0
PRKCA 0.005 0.092 0.22 1 -0.38 16 17
PRKCB 0.006 0.1 0.22 5 -0.38 19 24
PRKCE 0.004 0.092 0.22 1 -0.36 18 19
PRKCD 0.006 0.079 -10000 0 -0.42 10 10
PRKCG 0.004 0.09 0.21 2 -0.39 12 14
regulation of vascular smooth muscle contraction -0.022 0.18 0.38 5 -0.86 16 21
PRKCQ -0.003 0.1 -10000 0 -0.42 16 16
PLA2G4A -0.01 0.13 0.34 6 -0.46 23 29
GNA14 0.013 0.051 -10000 0 -0.42 7 7
GNA15 0.024 0.029 0.19 15 -10000 0 15
GNA12 0.018 0.006 -10000 0 -10000 0 0
GNA11 0.017 0.034 -10000 0 -0.42 3 3
Rac1/GTP 0.059 0.098 0.34 25 -0.22 6 31
MMP1 -0.043 0.19 0.25 6 -0.76 30 36
Thromboxane A2 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
TGM2 0.019 0.021 0.19 6 -10000 0 6
GNB1/GNG2 -0.022 0.043 -10000 0 -0.18 31 31
AKT1 -0.011 0.094 0.24 8 -0.29 27 35
EGF -0.37 0.14 -10000 0 -0.42 467 467
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.012 0.043 0.3 5 -10000 0 5
mol:Ca2+ 0.006 0.096 0.29 8 -0.29 30 38
LYN -0.013 0.04 0.32 4 -10000 0 4
RhoA/GTP -0.008 0.036 0.11 4 -0.13 20 24
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.004 0.1 0.28 8 -0.33 33 41
GNG2 0.019 0.005 -10000 0 -10000 0 0
ARRB2 0.02 0.003 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.006 0.077 0.29 2 -0.38 14 16
G beta5/gamma2 -0.027 0.056 -10000 0 -0.24 31 31
PRKCH -0.001 0.1 0.28 9 -0.33 31 40
DNM1 0.023 0.024 0.19 11 -10000 0 11
TXA2/TP beta/beta Arrestin3 0.01 0.023 -10000 0 -0.44 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.042 0.059 0.19 74 -10000 0 74
G12 family/GTP -0.015 0.076 -10000 0 -0.29 30 30
ADRBK1 0.02 0.002 -10000 0 -10000 0 0
ADRBK2 0.02 0.003 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.019 0.013 -10000 0 -10000 0 0
mol:GDP -0.011 0.07 0.44 3 -0.26 5 8
mol:NADP 0.018 0.006 -10000 0 -10000 0 0
RAB11A 0.02 0.002 -10000 0 -10000 0 0
PRKG1 0.008 0.07 -10000 0 -0.42 14 14
mol:IP3 0.004 0.11 0.32 7 -0.35 32 39
cell morphogenesis 0.019 0.012 -10000 0 -10000 0 0
PLCB2 -0.003 0.14 0.36 6 -0.48 32 38
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.007 0.048 0.35 3 -10000 0 3
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.01 0.04 0.35 1 -10000 0 1
RHOA 0.014 0.009 -10000 0 -10000 0 0
PTGIR 0.019 0.021 0.19 1 -0.42 1 2
PRKCB1 0.001 0.11 0.29 8 -0.35 33 41
GNAQ 0.019 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.018 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.008 0.15 0.35 6 -0.49 34 40
LCK -0.009 0.048 0.3 5 -0.21 1 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.013 0.034 -10000 0 -0.2 1 1
TXA2-R family/G12 family/GDP/G beta/gamma -0.005 0.096 -10000 0 -0.44 22 22
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.012 0.034 -10000 0 -10000 0 0
MAPK14 -0.003 0.075 0.23 12 -0.22 31 43
TGM2/GTP 0 0.12 0.31 5 -0.4 28 33
MAPK11 -0.002 0.074 0.22 12 -0.22 28 40
ARHGEF1 -0.009 0.051 0.15 5 -0.18 27 32
GNAI2 0.014 0.009 -10000 0 -10000 0 0
JNK cascade -0.001 0.12 0.31 8 -0.36 34 42
RAB11/GDP 0.017 0.01 -10000 0 -10000 0 0
ICAM1 0.002 0.089 0.26 10 -0.27 32 42
cAMP biosynthetic process 0.002 0.11 0.31 7 -0.33 29 36
Gq family/GTP/EBP50 -0.001 0.046 0.22 3 -0.2 19 22
actin cytoskeleton reorganization 0.019 0.012 -10000 0 -10000 0 0
SRC -0.015 0.032 0.35 1 -10000 0 1
GNB5 0.02 0.002 -10000 0 -10000 0 0
GNB1 0.019 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.097 0.065 0.29 3 -0.25 24 27
VCAM1 0 0.094 0.27 8 -0.3 32 40
TP beta/Gq family/GDP/G beta5/gamma2 -0.006 0.077 0.29 2 -0.38 14 16
platelet activation -0.002 0.098 0.29 12 -0.29 30 42
PGI2/IP 0.014 0.015 0.13 1 -0.29 1 2
PRKACA 0.015 0.024 -10000 0 -0.22 1 1
Gq family/GDP/G beta5/gamma2 -0.004 0.064 0.25 1 -0.34 13 14
TXA2/TP beta/beta Arrestin2 0.004 0.031 0.18 1 -0.35 1 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.005 0.028 -10000 0 -0.22 1 1
mol:DAG 0.001 0.12 0.32 7 -0.39 33 40
EGFR 0.019 0.026 0.19 5 -0.42 1 6
TXA2/TP alpha -0.002 0.14 0.36 7 -0.45 31 38
Gq family/GTP -0.003 0.039 -10000 0 -0.24 12 12
YES1 -0.013 0.042 0.29 5 -10000 0 5
GNAI2/GTP -0.013 0.028 -10000 0 -0.21 1 1
PGD2/DP 0.03 0.041 0.13 74 -10000 0 74
SLC9A3R1 0.02 0.003 -10000 0 -10000 0 0
FYN -0.013 0.041 0.3 5 -10000 0 5
mol:NO 0.018 0.006 -10000 0 -10000 0 0
GNA15 0.025 0.028 0.19 15 -10000 0 15
PGK/cGMP 0.017 0.042 -10000 0 -0.25 12 12
RhoA/GDP 0.012 0.012 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.032 0.033 -10000 0 -10000 0 0
NOS3 0.018 0.006 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
PRKCA 0.001 0.11 0.29 10 -0.34 30 40
PRKCB 0.001 0.11 0.29 14 -0.34 33 47
PRKCE -0.001 0.11 0.27 9 -0.34 32 41
PRKCD -0.008 0.11 0.3 8 -0.36 34 42
PRKCG 0 0.11 0.3 9 -0.36 32 41
muscle contraction -0.008 0.14 0.35 6 -0.46 33 39
PRKCZ -0.005 0.1 0.28 8 -0.33 33 41
ARR3 0.018 0.001 -10000 0 -10000 0 0
TXA2/TP beta 0.02 0.033 -10000 0 -0.21 1 1
PRKCQ -0.004 0.11 0.29 9 -0.35 32 41
MAPKKK cascade -0.004 0.13 0.34 6 -0.43 31 37
SELE -0.006 0.11 0.26 9 -0.37 36 45
TP beta/GNAI2/GDP/G beta/gamma 0.024 0.032 -10000 0 -10000 0 0
ROCK1 0.02 0.003 -10000 0 -10000 0 0
GNA14 0.014 0.05 -10000 0 -0.42 7 7
chemotaxis -0.014 0.17 0.41 3 -0.57 35 38
GNA12 0.018 0.006 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.017 0.033 -10000 0 -0.42 3 3
Rac1/GTP 0.013 0.005 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.024 0.035 0.15 36 -10000 0 36
EPHB2 0.017 0.04 0.19 2 -0.42 4 6
Syndecan-2/TACI 0.024 0.038 0.14 50 -10000 0 50
LAMA1 0.012 0.06 0.19 1 -0.42 10 11
Syndecan-2/alpha2 ITGB1 0.033 0.027 -10000 0 -0.22 3 3
HRAS 0.02 0.008 0.19 1 -10000 0 1
Syndecan-2/CASK -0.007 0.002 -10000 0 -10000 0 0
ITGA5 0.031 0.042 0.19 35 -10000 0 35
BAX -0.018 0.014 -10000 0 -10000 0 0
EPB41 0.019 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.014 0.004 -10000 0 -10000 0 0
LAMA3 0.022 0.018 0.19 6 -10000 0 6
EZR 0.018 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.019 0.026 0.19 5 -0.42 1 6
Syndecan-2/MMP2 0.016 0.019 0.26 1 -0.25 1 2
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.024 0.03 -10000 0 -0.3 4 4
dendrite morphogenesis 0.014 0.028 0.26 2 -0.25 4 6
Syndecan-2/GM-CSF 0.003 0.027 0.26 1 -10000 0 1
determination of left/right symmetry -0.008 0.002 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.012 0.009 -10000 0 -10000 0 0
GNB2L1 0.015 0.009 -10000 0 -10000 0 0
MAPK3 -0.009 0.03 0.19 9 -10000 0 9
MAPK1 -0.008 0.033 0.18 11 -10000 0 11
Syndecan-2/RACK1 0.02 0.013 -10000 0 -10000 0 0
NF1 0.02 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.008 0.002 -10000 0 -10000 0 0
ITGA2 0.015 0.038 -10000 0 -0.42 4 4
MAPK8 -0.014 0.015 -10000 0 -0.25 2 2
Syndecan-2/alpha2/beta1 Integrin 0.028 0.041 -10000 0 -0.22 11 11
Syndecan-2/Kininogen -0.18 0.11 -10000 0 -0.25 361 361
ITGB1 0.02 0.003 -10000 0 -10000 0 0
SRC 0.017 0.074 0.16 112 -10000 0 112
Syndecan-2/CASK/Protein 4.1 0.014 0.004 -10000 0 -10000 0 0
extracellular matrix organization 0.016 0.011 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.024 0.035 0.15 36 -10000 0 36
Syndecan-2/Caveolin-2/Ras 0.026 0.021 0.24 1 -0.23 1 2
Syndecan-2/Laminin alpha3 0.017 0.016 0.16 6 -10000 0 6
Syndecan-2/RasGAP 0.026 0.019 -10000 0 -0.17 1 1
alpha5/beta1 Integrin 0.037 0.03 -10000 0 -10000 0 0
PRKCD 0.015 0.012 0.19 1 -10000 0 1
Syndecan-2 dimer 0.014 0.028 0.26 2 -0.25 4 6
GO:0007205 0 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.059 0.16 59 -10000 0 59
RHOA 0.014 0.009 -10000 0 -10000 0 0
SDCBP 0.019 0.005 -10000 0 -10000 0 0
TNFRSF13B 0.036 0.051 0.19 52 -10000 0 52
RASA1 0.017 0.02 -10000 0 -0.42 1 1
alpha2/beta1 Integrin 0.024 0.03 -10000 0 -0.3 4 4
Syndecan-2/Synbindin 0.016 0.004 -10000 0 -10000 0 0
TGFB1 0.021 0.015 0.19 4 -10000 0 4
CASP3 -0.009 0.031 0.18 13 -10000 0 13
FN1 0.031 0.043 0.19 36 -10000 0 36
Syndecan-2/IL8 0.018 0.043 0.26 2 -0.25 7 9
SDC2 -0.008 0.002 -10000 0 -10000 0 0
KNG1 -0.29 0.2 -10000 0 -0.42 373 373
Syndecan-2/Neurofibromin 0.015 0.004 -10000 0 -10000 0 0
TRAPPC4 0.02 0.002 -10000 0 -10000 0 0
CSF2 0.019 0.029 0.19 14 -10000 0 14
Syndecan-2/TGFB1 0.016 0.011 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.014 0.004 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.019 0.014 -10000 0 -10000 0 0
PRKACA -0.012 0.034 0.18 16 -10000 0 16
angiogenesis 0.018 0.043 0.26 2 -0.25 7 9
MMP2 0.02 0.025 0.19 5 -0.42 1 6
IL8 0.022 0.063 0.19 26 -0.42 7 33
calcineurin-NFAT signaling pathway 0.024 0.038 0.14 50 -10000 0 50
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.025 0.19 -10000 0 -0.95 21 21
MKNK1 0.019 0.004 -10000 0 -10000 0 0
MAPK14 0.011 0.066 -10000 0 -0.3 21 21
ATF2/c-Jun -0.017 0.05 -10000 0 -0.31 2 2
MAPK11 0.012 0.069 -10000 0 -0.3 22 22
MITF -0.006 0.082 -10000 0 -0.38 22 22
MAPKAPK5 -0.002 0.074 -10000 0 -0.35 21 21
KRT8 -0.002 0.074 -10000 0 -0.35 21 21
MAPKAPK3 0.014 0.009 -10000 0 -10000 0 0
MAPKAPK2 0.019 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.013 0.099 -10000 0 -0.44 22 22
CEBPB -0.001 0.075 -10000 0 -0.35 21 21
SLC9A1 -0.003 0.076 -10000 0 -0.36 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.003 0.074 -10000 0 -0.35 21 21
p38alpha-beta/MNK1 0.024 0.084 -10000 0 -0.37 21 21
JUN -0.014 0.052 -10000 0 -0.31 2 2
PPARGC1A -0.028 0.11 -10000 0 -0.31 66 66
USF1 -0.002 0.071 -10000 0 -0.34 21 21
RAB5/GDP/GDI1 0.001 0.059 -10000 0 -0.26 21 21
NOS2 -0.001 0.075 -10000 0 -0.47 2 2
DDIT3 -0.002 0.074 -10000 0 -0.36 20 20
RAB5A 0.014 0.009 -10000 0 -10000 0 0
HSPB1 0.005 0.095 0.26 42 -0.3 19 61
p38alpha-beta/HBP1 0.023 0.081 -10000 0 -0.36 19 19
CREB1 -0.003 0.078 -10000 0 -0.39 20 20
RAB5/GDP 0.011 0.007 -10000 0 -10000 0 0
EIF4E -0.033 0.065 -10000 0 -0.33 20 20
RPS6KA4 -0.001 0.071 -10000 0 -0.35 20 20
PLA2G4A -0.036 0.066 -10000 0 -0.32 23 23
GDI1 -0.003 0.075 -10000 0 -0.35 22 22
TP53 -0.027 0.09 -10000 0 -0.44 22 22
RPS6KA5 -0.003 0.078 -10000 0 -0.38 20 20
ESR1 -0.005 0.08 -10000 0 -0.36 23 23
HBP1 0.018 0.006 -10000 0 -10000 0 0
MEF2C -0.002 0.071 -10000 0 -0.36 18 18
MEF2A -0.001 0.071 -10000 0 -0.36 19 19
EIF4EBP1 -0.002 0.081 -10000 0 -0.4 19 19
KRT19 -0.049 0.14 -10000 0 -0.32 100 100
ELK4 -0.002 0.073 -10000 0 -0.35 21 21
ATF6 -0.002 0.071 -10000 0 -0.34 21 21
ATF1 -0.003 0.078 -10000 0 -0.39 20 20
p38alpha-beta/MAPKAPK2 0.025 0.082 -10000 0 -0.36 22 22
p38alpha-beta/MAPKAPK3 0.016 0.083 -10000 0 -0.36 22 22
LPA receptor mediated events

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
GNB1/GNG2 0.025 0.056 -10000 0 -0.23 22 22
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.068 0.23 3 -0.3 3 6
AP1 0.016 0.063 -10000 0 -0.22 32 32
mol:PIP3 -0.033 0.037 -10000 0 -0.22 16 16
AKT1 -0.053 0.1 0.27 12 -0.32 17 29
PTK2B -0.023 0.078 0.2 3 -0.3 15 18
RHOA -0.071 0.12 0.16 6 -0.28 122 128
PIK3CB 0.018 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.054 0.26 8 -0.29 2 10
MAGI3 0.017 0.033 -10000 0 -0.42 3 3
RELA 0.02 0.002 -10000 0 -10000 0 0
apoptosis -0.017 0.05 -10000 0 -0.24 22 22
HRAS/GDP 0.015 0.005 0.13 1 -10000 0 1
positive regulation of microtubule depolymerization -0.028 0.079 0.26 8 -0.33 8 16
NF kappa B1 p50/RelA -0.026 0.057 -10000 0 -0.27 2 2
endothelial cell migration -0.021 0.055 0.2 5 -0.26 22 27
ADCY4 -0.018 0.077 -10000 0 -0.34 26 26
ADCY5 -0.023 0.085 -10000 0 -0.33 33 33
ADCY6 -0.02 0.08 -10000 0 -0.32 31 31
ADCY7 -0.019 0.08 -10000 0 -0.32 31 31
ADCY1 -0.023 0.079 -10000 0 -0.32 31 31
ADCY2 -0.015 0.084 0.17 1 -0.32 31 32
ADCY3 -0.019 0.08 -10000 0 -0.32 30 30
ADCY8 -0.009 0.082 -10000 0 -0.34 25 25
ADCY9 -0.02 0.079 -10000 0 -0.32 30 30
GSK3B -0.025 0.078 0.26 6 -0.36 8 14
arachidonic acid secretion -0.026 0.083 -10000 0 -0.33 32 32
GNG2 0.018 0.008 -10000 0 -10000 0 0
TRIP6 0.009 0.005 -10000 0 -10000 0 0
GNAO1 -0.022 0.051 0.11 3 -0.25 23 26
HRAS 0.02 0.008 0.19 1 -10000 0 1
NFKBIA -0.018 0.074 0.32 6 -0.32 4 10
GAB1 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.002 0.17 -10000 0 -0.84 20 20
JUN 0.019 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.026 0.015 -10000 0 -0.25 1 1
TIAM1 -0.015 0.2 -10000 0 -1 20 20
PIK3R1 0.017 0.021 -10000 0 -0.42 1 1
mol:IP3 -0.006 0.049 0.2 21 -0.29 2 23
PLCB3 -0.011 0.04 0.17 22 -0.23 1 23
FOS 0.01 0.063 0.19 1 -0.42 11 12
positive regulation of mitosis -0.026 0.083 -10000 0 -0.33 32 32
LPA/LPA1-2-3 0.026 0.057 -10000 0 -0.23 22 22
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
stress fiber formation -0.014 0.072 0.25 3 -0.3 13 16
GNAZ -0.023 0.05 0.1 1 -0.25 24 25
EGFR/PI3K-beta/Gab1 -0.033 0.04 -10000 0 -0.24 7 7
positive regulation of dendritic cell cytokine production 0.025 0.056 -10000 0 -0.23 22 22
LPA/LPA2/MAGI-3 0.024 0.023 -10000 0 -0.25 3 3
ARHGEF1 -0.009 0.076 0.19 47 -0.22 16 63
GNAI2 -0.012 0.03 -10000 0 -0.25 7 7
GNAI3 -0.021 0.048 0.1 1 -0.25 21 22
GNAI1 -0.02 0.046 -10000 0 -0.25 19 19
LPA/LPA3 0.015 0.011 0.13 3 -10000 0 3
LPA/LPA2 0.015 0.008 -10000 0 -0.11 1 1
LPA/LPA1 0.004 0.063 0.16 1 -0.29 22 23
HB-EGF/EGFR 0.024 0.054 0.17 5 -0.26 1 6
HBEGF 0.058 0.099 0.15 234 -10000 0 234
mol:DAG -0.006 0.049 0.2 21 -0.29 2 23
cAMP biosynthetic process -0.014 0.099 0.29 17 -0.32 26 43
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
SRC 0.019 0.004 -10000 0 -10000 0 0
GNB1 0.018 0.009 -10000 0 -10000 0 0
LYN -0.014 0.075 0.31 8 -0.3 6 14
GNAQ -0.008 0.013 -10000 0 -10000 0 0
LPAR2 0.02 0.003 -10000 0 -10000 0 0
LPAR3 0.019 0.014 0.19 3 -10000 0 3
LPAR1 0.002 0.086 -10000 0 -0.4 22 22
IL8 0.03 0.11 0.34 5 -0.44 9 14
PTK2 -0.026 0.046 0.17 6 -0.22 20 26
Rac1/GDP 0.013 0.005 -10000 0 -10000 0 0
CASP3 -0.017 0.05 -10000 0 -0.24 22 22
EGFR 0.019 0.026 0.19 5 -0.42 1 6
PLCG1 -0.001 0.021 0.16 1 -10000 0 1
PLD2 -0.027 0.047 0.17 7 -0.22 21 28
G12/G13 0.026 0.049 -10000 0 -0.23 16 16
PI3K-beta -0.069 0.09 -10000 0 -0.31 28 28
cell migration -0.004 0.055 -10000 0 -0.26 16 16
SLC9A3R2 0.018 0.019 -10000 0 -0.42 1 1
PXN -0.014 0.073 0.29 2 -0.31 13 15
HRAS/GTP -0.025 0.083 -10000 0 -0.35 28 28
RAC1 0.018 0.006 -10000 0 -10000 0 0
MMP9 0.094 0.085 0.19 234 -10000 0 234
PRKCE 0.017 0.021 -10000 0 -0.42 1 1
PRKCD -0.006 0.055 0.28 8 -0.28 2 10
Gi(beta/gamma) -0.022 0.078 -10000 0 -0.32 30 30
mol:LPA 0.001 0.009 -10000 0 -0.15 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.002 0.069 -10000 0 -0.31 7 7
MAPKKK cascade -0.026 0.083 -10000 0 -0.33 32 32
contractile ring contraction involved in cytokinesis -0.072 0.12 0.17 6 -0.28 123 129
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.011 0.028 -10000 0 -0.24 6 6
GNA15 -0.006 0.021 0.15 1 -10000 0 1
GNA12 0.018 0.007 -10000 0 -10000 0 0
GNA13 0.018 0.008 -10000 0 -10000 0 0
MAPT -0.029 0.081 0.28 7 -0.34 8 15
GNA11 -0.01 0.022 -10000 0 -0.24 3 3
Rac1/GTP -0.003 0.18 -10000 0 -0.9 20 20
MMP2 -0.021 0.056 0.2 5 -0.26 22 27
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.02 0.022 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.013 0.02 -10000 0 -0.25 2 2
mol:DAG 0.025 0.048 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.04 0.071 0.25 3 -10000 0 3
CaM/Ca2+ 0.026 0.052 -10000 0 -10000 0 0
HIF1A 0.019 0.029 -10000 0 -0.42 2 2
GAB1 0.02 0.003 -10000 0 -10000 0 0
AKT1 0.019 0.061 0.34 2 -0.6 1 3
PLCG1 0.025 0.048 -10000 0 -10000 0 0
NOS3 0.025 0.046 0.28 1 -10000 0 1
CBL 0.019 0.019 -10000 0 -0.42 1 1
mol:NO 0.027 0.063 0.41 3 -10000 0 3
FLT1 -0.016 0.026 -10000 0 -0.3 2 2
PGF 0.11 0.086 0.19 277 -10000 0 277
VEGFR1 homodimer/NRP2/VEGFR121 0.068 0.061 0.26 3 -10000 0 3
CALM1 0.019 0.005 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
eNOS/Hsp90 0.034 0.066 0.31 5 -10000 0 5
endothelial cell proliferation 0.021 0.051 0.39 3 -10000 0 3
mol:Ca2+ 0.025 0.048 -10000 0 -10000 0 0
MAPK3 0.002 0.041 0.43 2 -10000 0 2
MAPK1 0.002 0.041 0.43 2 -10000 0 2
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
PLGF homodimer 0.11 0.085 0.19 277 -10000 0 277
PRKACA 0.02 0.002 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.028 0.04 0.19 30 -10000 0 30
VEGFA homodimer 0.093 0.084 0.19 232 -10000 0 232
VEGFR1 homodimer/VEGFA homodimer 0.045 0.08 0.28 4 -10000 0 4
platelet activating factor biosynthetic process -0.001 0.046 0.22 12 -10000 0 12
PI3K 0.08 0.066 0.26 3 -0.3 2 5
PRKCA 0.01 0.036 -10000 0 -10000 0 0
PRKCB 0.009 0.038 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.062 0.08 0.28 3 -10000 0 3
VEGFA 0.093 0.084 0.19 232 -10000 0 232
VEGFB 0.02 0.002 -10000 0 -10000 0 0
mol:IP3 0.025 0.048 -10000 0 -10000 0 0
RASA1 -0.021 0.028 -10000 0 -0.44 1 1
NRP2 0.021 0.02 0.19 7 -10000 0 7
VEGFR1 homodimer -0.016 0.026 -10000 0 -0.3 2 2
VEGFB homodimer 0.02 0.002 -10000 0 -10000 0 0
NCK1 0.018 0.02 -10000 0 -0.42 1 1
eNOS/Caveolin-1 0.026 0.062 0.27 2 -10000 0 2
PTPN11 0.019 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.078 0.064 0.25 3 -0.3 2 5
mol:L-citrulline 0.027 0.063 0.41 3 -10000 0 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.077 0.063 0.26 4 -0.42 1 5
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.067 0.064 0.26 4 -0.44 1 5
CD2AP 0.019 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.084 0.065 -10000 0 -0.36 1 1
PDPK1 0.02 0.066 0.34 3 -0.54 1 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.068 0.061 0.26 4 -10000 0 4
mol:NADP 0.027 0.063 0.41 3 -10000 0 3
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.074 0.061 0.25 4 -0.42 1 5
VEGFR1 homodimer/NRP2 -0.018 0.026 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.002 0.097 0.23 2 -0.39 22 24
CRKL -0.017 0.1 0.25 1 -0.44 23 24
HRAS 0.008 0.093 -10000 0 -0.38 18 18
mol:PIP3 0.004 0.1 0.24 2 -0.42 19 21
SPRED1 0.02 0.002 -10000 0 -10000 0 0
SPRED2 0.019 0.019 -10000 0 -0.42 1 1
GAB1 -0.012 0.11 -10000 0 -0.46 24 24
FOXO3 -0.012 0.14 0.31 3 -0.44 31 34
AKT1 -0.009 0.15 0.27 3 -0.48 31 34
BAD -0.011 0.14 0.3 5 -0.45 31 36
megakaryocyte differentiation -0.043 0.13 -10000 0 -0.5 25 25
GSK3B -0.01 0.14 0.29 4 -0.44 31 35
RAF1 -0.003 0.076 0.24 2 -0.33 13 15
SHC1 0.019 0.004 -10000 0 -10000 0 0
STAT3 -0.012 0.11 -10000 0 -0.46 24 24
STAT1 -0.028 0.23 -10000 0 -1 24 24
HRAS/SPRED1 0.019 0.082 0.22 1 -0.33 13 14
cell proliferation -0.013 0.11 -10000 0 -0.47 24 24
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
TEC 0.02 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.005 0.12 -10000 0 -0.48 25 25
HRAS/SPRED2 0.018 0.081 0.22 1 -0.33 13 14
LYN/TEC/p62DOK 0.018 0.11 -10000 0 -0.43 24 24
MAPK3 0.003 0.071 0.24 13 -0.28 6 19
STAP1 -0.14 0.14 0.22 2 -0.54 30 32
GRAP2 0.03 0.046 0.19 34 -0.42 1 35
JAK2 -0.023 0.21 -10000 0 -0.93 24 24
STAT1 (dimer) -0.025 0.22 -10000 0 -1 24 24
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.04 0.12 -10000 0 -0.43 23 23
actin filament polymerization -0.013 0.1 -10000 0 -0.45 22 22
LYN 0.019 0.005 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.12 0.17 -10000 0 -0.71 26 26
PIK3R1 0.018 0.02 -10000 0 -0.42 1 1
CBL/CRKL/GRB2 0.003 0.099 0.25 1 -0.4 23 24
PI3K 0.011 0.12 -10000 0 -0.47 21 21
PTEN 0.019 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.009 0.26 -10000 0 -1.1 24 24
MAPK8 -0.013 0.11 -10000 0 -0.48 24 24
STAT3 (dimer) -0.012 0.1 -10000 0 -0.45 24 24
positive regulation of transcription 0.005 0.064 0.23 14 -0.22 6 20
mol:GDP 0.016 0.097 -10000 0 -0.39 18 18
PIK3C2B -0.013 0.1 -10000 0 -0.45 24 24
CBL/CRKL -0.014 0.1 0.25 1 -0.42 23 24
FER -0.013 0.1 -10000 0 -0.46 22 22
SH2B3 -0.011 0.11 -10000 0 -0.46 24 24
PDPK1 0.006 0.11 0.28 11 -0.39 18 29
SNAI2 -0.012 0.11 -10000 0 -0.46 24 24
positive regulation of cell proliferation -0.01 0.18 -10000 0 -0.76 24 24
KITLG 0.011 0.064 -10000 0 -0.44 10 10
cell motility -0.01 0.18 -10000 0 -0.76 24 24
PTPN6 0.015 0.015 -10000 0 -10000 0 0
EPOR 0.012 0.092 -10000 0 -1.1 2 2
STAT5A (dimer) 0.004 0.16 -10000 0 -0.62 24 24
SOCS1 0.021 0.018 0.19 6 -10000 0 6
cell migration 0.006 0.11 0.44 24 -10000 0 24
SOS1 0.02 0.003 -10000 0 -10000 0 0
EPO 0.07 0.082 0.19 168 -10000 0 168
VAV1 0.058 0.074 0.19 122 -0.42 1 123
GRB10 -0.014 0.1 -10000 0 -0.46 22 22
PTPN11 0.014 0.015 -10000 0 -10000 0 0
SCF/KIT -0.005 0.12 -10000 0 -0.48 24 24
GO:0007205 0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.006 0.064 0.24 3 -0.29 7 10
CBL 0.019 0.019 -10000 0 -0.42 1 1
KIT -0.03 0.26 -10000 0 -1.2 24 24
MAP2K2 -0.006 0.066 0.29 4 -0.28 8 12
SHC/Grb2/SOS1 0.019 0.11 -10000 0 -0.43 22 22
STAT5A 0.003 0.16 -10000 0 -0.64 24 24
GRB2 0.02 0.003 -10000 0 -10000 0 0
response to radiation -0.012 0.1 0.25 1 -0.45 24 25
SHC/GRAP2 0.035 0.033 -10000 0 -0.3 1 1
PTPRO -0.044 0.13 -10000 0 -0.51 25 25
SH2B2 -0.014 0.1 -10000 0 -0.46 22 22
DOK1 0.02 0.003 -10000 0 -10000 0 0
MATK -0.007 0.11 -10000 0 -0.46 24 24
CREBBP 0.018 0.03 -10000 0 -10000 0 0
BCL2 0.008 0.089 -10000 0 -1.1 1 1
Caspase cascade in apoptosis

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
TOP1 0.028 0.067 -10000 0 -0.35 5 5
ACTA1 0.014 0.063 0.2 3 -10000 0 3
NUMA1 0.027 0.079 -10000 0 -0.44 6 6
SPTAN1 0.012 0.061 0.25 1 -10000 0 1
LIMK1 0.029 0.08 0.28 14 -10000 0 14
BIRC3 0.045 0.06 0.19 79 -10000 0 79
BIRC2 0.02 0.002 -10000 0 -10000 0 0
BAX 0.02 0.002 -10000 0 -10000 0 0
CASP10 0.025 0.065 0.14 106 -10000 0 106
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.02 0.002 -10000 0 -10000 0 0
PTK2 0.024 0.074 -10000 0 -0.34 8 8
DIABLO 0.019 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes 0.011 0.061 0.25 1 -10000 0 1
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.02 0.004 -10000 0 -10000 0 0
GSN 0.012 0.061 0.25 1 -10000 0 1
MADD 0.02 0.002 -10000 0 -10000 0 0
TFAP2A -0.26 0.28 -10000 0 -0.48 299 299
BID 0.021 0.038 0.16 2 -10000 0 2
MAP3K1 0.017 0.035 -10000 0 -0.41 1 1
TRADD 0.019 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.028 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.016 0.067 0.26 4 -10000 0 4
CASP9 0.019 0.005 -10000 0 -10000 0 0
DNA repair 0.002 0.059 0.28 15 -10000 0 15
neuron apoptosis 0.005 0.12 -10000 0 -0.65 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.018 0.074 -10000 0 -0.41 5 5
APAF1 0.019 0.004 -10000 0 -10000 0 0
CASP6 0.024 0.12 0.37 1 -0.89 7 8
TRAF2 0.019 0.004 -10000 0 -10000 0 0
ICAD/CAD 0.006 0.058 -10000 0 -10000 0 0
CASP7 -0.026 0.067 -10000 0 -0.31 11 11
KRT18 0.021 0.027 -10000 0 -10000 0 0
apoptosis 0.011 0.08 0.42 2 -0.43 7 9
DFFA 0.011 0.06 -10000 0 -10000 0 0
DFFB 0.011 0.06 -10000 0 -10000 0 0
PARP1 -0.002 0.059 -10000 0 -0.28 15 15
actin filament polymerization -0.024 0.076 -10000 0 -0.27 14 14
TNF 0.017 0.041 0.19 4 -0.42 4 8
CYCS 0.026 0.041 0.17 9 -0.25 1 10
SATB1 0.016 0.11 0.42 2 -0.83 7 9
SLK 0.012 0.062 0.33 1 -10000 0 1
p15 BID/BAX 0.018 0.045 0.15 4 -10000 0 4
CASP2 0.011 0.067 0.19 42 -0.27 2 44
JNK cascade -0.016 0.035 0.41 1 -10000 0 1
CASP3 0.017 0.065 -10000 0 -10000 0 0
LMNB2 0.03 0.1 0.33 13 -0.58 6 19
RIPK1 0.019 0.004 -10000 0 -10000 0 0
CASP4 0.02 0.002 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.064 0.038 -10000 0 -10000 0 0
negative regulation of DNA binding -0.26 0.27 -10000 0 -0.48 299 299
stress fiber formation 0.011 0.062 0.33 1 -10000 0 1
GZMB 0.047 0.091 0.16 185 -10000 0 185
CASP1 0.006 0.001 -10000 0 -10000 0 0
LMNB1 0.028 0.09 0.32 13 -0.4 6 19
APP 0.004 0.12 -10000 0 -0.66 14 14
TNFRSF1A 0.019 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.002 -10000 0 -10000 0 0
VIM 0.015 0.08 0.31 1 -0.44 7 8
LMNA 0.028 0.1 0.33 13 -0.41 12 25
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.046 -10000 0 -0.26 3 3
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.012 0.062 0.29 1 -10000 0 1
APAF-1/Caspase 9 -0.003 0.12 -10000 0 -0.6 21 21
nuclear fragmentation during apoptosis 0.027 0.077 -10000 0 -0.44 6 6
CFL2 0.025 0.075 0.27 14 -10000 0 14
GAS2 0.009 0.069 0.24 2 -0.33 2 4
positive regulation of apoptosis 0.031 0.099 0.31 15 -0.44 8 23
PRF1 0.062 0.073 0.19 132 -10000 0 132
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.028 0.016 -10000 0 -0.3 1 1
Necdin/E2F1 0.04 0.04 -10000 0 -0.3 1 1
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.069 0.043 0.25 7 -0.23 1 8
NGF (dimer)/p75(NTR)/BEX1 -0.052 0.15 0.26 5 -0.25 186 191
NT-4/5 (dimer)/p75(NTR) 0.036 0.03 -10000 0 -10000 0 0
IKBKB 0.019 0.006 -10000 0 -10000 0 0
AKT1 0 0.068 0.19 44 -0.23 1 45
IKBKG 0.02 0.002 -10000 0 -10000 0 0
BDNF 0.04 0.063 0.19 67 -0.42 2 69
MGDIs/NGR/p75(NTR)/LINGO1 0.05 0.04 0.26 4 -0.26 1 5
FURIN 0.02 0.002 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.057 0.049 0.26 6 -0.23 2 8
LINGO1 0.027 0.033 0.19 21 -10000 0 21
Sortilin/TRAF6/NRIF -0.04 0.014 -10000 0 -0.22 1 1
proBDNF (dimer) 0.04 0.063 0.19 67 -0.42 2 69
NTRK1 -0.007 0.1 0.19 2 -0.42 32 34
RTN4R 0.021 0.025 0.19 5 -0.42 1 6
neuron apoptosis 0.018 0.068 0.4 7 -0.43 1 8
IRAK1 0.02 0.002 -10000 0 -10000 0 0
SHC1 -0.007 0.038 0.16 8 -10000 0 8
ARHGDIA 0.019 0.019 -10000 0 -0.42 1 1
RhoA/GTP 0.011 0.007 -10000 0 -10000 0 0
Gamma Secretase 0.052 0.022 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.064 0.044 0.26 7 -0.24 1 8
MAGEH1 0.02 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.063 0.048 0.26 7 -0.24 3 10
Mammalian IAPs/DIABLO 0.064 0.038 -10000 0 -10000 0 0
proNGF (dimer) 0.034 0.048 0.19 47 -10000 0 47
MAGED1 0.02 0.002 -10000 0 -10000 0 0
APP 0.019 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.019 0.013 0.19 3 -10000 0 3
ZNF274 0.02 0.002 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.006 0.034 0.14 4 -0.22 1 5
NGF 0.034 0.048 0.19 47 -10000 0 47
cell cycle arrest 0.028 0.074 0.2 33 -10000 0 33
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.012 0.059 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.045 0.028 -10000 0 -10000 0 0
NCSTN 0.019 0.004 -10000 0 -10000 0 0
mol:GTP 0.054 0.043 0.25 7 -10000 0 7
PSENEN 0.02 0.002 -10000 0 -10000 0 0
mol:ceramide -0.011 0.038 0.18 5 -0.24 1 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.009 0.052 0.19 1 -0.36 4 5
p75(NTR)/beta APP 0.035 0.029 -10000 0 -10000 0 0
BEX1 -0.14 0.21 0.19 5 -0.42 188 193
mol:GDP -0.002 0.034 0.16 8 -10000 0 8
NGF (dimer) -0.13 0.16 -10000 0 -0.25 299 299
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.059 0.043 0.26 4 -0.44 1 5
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
RAC1/GTP 0.044 0.039 0.22 7 -10000 0 7
MYD88 0.014 0.009 -10000 0 -10000 0 0
CHUK 0.019 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.055 0.043 0.26 7 -10000 0 7
RHOB 0.019 0.004 -10000 0 -10000 0 0
RHOA 0.014 0.009 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.04 0.037 -10000 0 -10000 0 0
NT3 (dimer) 0.017 0.035 0.19 2 -0.42 3 5
TP53 -0.017 0.045 0.3 4 -0.22 1 5
PRDM4 -0.011 0.037 0.18 5 -10000 0 5
BDNF (dimer) -0.12 0.16 0.25 1 -0.25 293 294
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
SORT1 0.019 0.019 -10000 0 -0.42 1 1
activation of caspase activity 0.063 0.04 0.23 7 -0.23 1 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.064 0.044 0.26 7 -0.24 1 8
RHOC 0.019 0.004 -10000 0 -10000 0 0
XIAP 0.02 0.002 -10000 0 -10000 0 0
MAPK10 0.005 0.074 0.34 11 -0.38 1 12
DIABLO 0.02 0.004 -10000 0 -10000 0 0
SMPD2 -0.011 0.038 0.18 5 -0.24 1 6
APH1B 0.02 0.002 -10000 0 -10000 0 0
APH1A 0.019 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.054 0.045 0.26 7 -0.26 1 8
PSEN1 0.019 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.028 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.034 0.038 -10000 0 -0.28 3 3
MAPK8 0.004 0.07 0.32 11 -10000 0 11
MAPK9 0.003 0.063 0.32 12 -10000 0 12
APAF1 0.019 0.004 -10000 0 -10000 0 0
NTF3 0.018 0.035 0.19 2 -0.42 3 5
NTF4 0.019 0.013 0.19 3 -10000 0 3
NDN 0.018 0.027 -10000 0 -0.42 2 2
RAC1/GDP 0.013 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.039 0.045 0.2 4 -10000 0 4
p75 CTF/Sortilin/TRAF6/NRIF 0.048 0.018 -10000 0 -0.24 1 1
RhoA-B-C/GTP 0.053 0.042 0.25 7 -10000 0 7
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.072 0.047 0.25 6 -0.21 2 8
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.067 0.048 0.26 6 -0.21 2 8
PRKACB 0.019 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.042 0.045 -10000 0 -0.29 2 2
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.045 0.06 0.19 79 -10000 0 79
BIRC2 0.02 0.002 -10000 0 -10000 0 0
neuron projection morphogenesis 0.041 0.07 0.15 71 -10000 0 71
BAD 0.012 0.092 0.33 20 -0.28 1 21
RIPK2 0.019 0.009 0.19 1 -10000 0 1
NGFR 0.03 0.04 0.19 31 -10000 0 31
CYCS -0.013 0.045 0.37 3 -0.23 1 4
ADAM17 0.02 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.062 0.044 0.26 7 -10000 0 7
BCL2L11 0.012 0.091 0.32 20 -0.28 1 21
BDNF (dimer)/p75(NTR) 0.05 0.052 0.27 6 -0.3 1 7
PI3K 0.056 0.048 0.26 7 -0.21 2 9
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.064 0.044 0.26 7 -0.24 1 8
NDNL2 0.02 0.002 -10000 0 -10000 0 0
YWHAE 0.02 0.003 -10000 0 -10000 0 0
PRKCI 0.019 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.046 0.047 0.27 7 -10000 0 7
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.063 0.044 0.26 7 -0.24 1 8
TRAF6 0.02 0.002 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
PRKCZ 0.017 0.033 -10000 0 -0.42 3 3
PLG -0.19 0.22 -10000 0 -0.42 246 246
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.001 0.045 0.2 3 -0.22 2 5
SQSTM1 0.015 0.009 -10000 0 -10000 0 0
NGFRAP1 0.02 0.002 -10000 0 -10000 0 0
CASP3 0.013 0.09 0.32 20 -0.29 2 22
E2F1 0.037 0.051 0.19 54 -10000 0 54
CASP9 0.019 0.004 -10000 0 -10000 0 0
IKK complex 0.035 0.084 0.23 1 -0.32 5 6
NGF (dimer)/TRKA 0.019 0.088 -10000 0 -0.3 32 32
MMP7 -0.052 0.16 0.19 6 -0.42 88 94
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.043 0.25 7 -0.23 1 8
MMP3 0.034 0.048 0.19 46 -10000 0 46
APAF-1/Caspase 9 -0.025 0.037 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.02 -10000 0 -0.42 1 1
Caspase 8 (4 units) 0.046 0.062 -10000 0 -0.24 6 6
NEF 0.028 0.028 -10000 0 -10000 0 0
NFKBIA 0.024 0.012 -10000 0 -10000 0 0
BIRC3 0.009 0.08 -10000 0 -10000 0 0
CYCS 0.04 0.068 0.22 27 -0.27 1 28
RIPK1 0.019 0.004 -10000 0 -10000 0 0
CD247 0.098 0.095 0.23 169 -10000 0 169
MAP2K7 0.038 0.14 0.32 3 -0.64 13 16
protein ubiquitination 0.01 0.088 0.3 13 -0.37 6 19
CRADD 0.02 0.004 -10000 0 -10000 0 0
DAXX 0.019 0.004 -10000 0 -10000 0 0
FAS 0.019 0.004 -10000 0 -10000 0 0
BID 0.045 0.056 0.18 12 -10000 0 12
NF-kappa-B/RelA/I kappa B alpha 0.055 0.046 -10000 0 -0.26 1 1
TRADD 0.019 0.004 -10000 0 -10000 0 0
MAP3K5 0.019 0.005 -10000 0 -10000 0 0
CFLAR 0.019 0.004 -10000 0 -10000 0 0
FADD 0.02 0.002 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.056 0.046 -10000 0 -0.26 1 1
MAPK8 0.033 0.13 0.36 4 -0.6 13 17
APAF1 0.019 0.004 -10000 0 -10000 0 0
TRAF1 0.02 0.008 0.19 1 -10000 0 1
TRAF2 0.019 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.058 0.058 0.22 7 -10000 0 7
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.005 0.087 -10000 0 -0.36 20 20
CHUK 0.008 0.082 0.24 11 -0.35 10 21
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.052 0.023 -10000 0 -10000 0 0
TCRz/NEF 0.1 0.094 0.24 151 -10000 0 151
TNF 0.017 0.041 0.19 4 -0.42 4 8
FASLG 0.12 0.13 0.24 258 -10000 0 258
NFKB1 0.024 0.022 -10000 0 -0.42 1 1
TNFR1A/BAG4/TNF-alpha 0.033 0.033 -10000 0 -0.26 5 5
CASP6 0.035 0.12 -10000 0 -0.53 15 15
CASP7 0.042 0.11 0.3 10 -0.45 6 16
RELA 0.025 0.011 -10000 0 -10000 0 0
CASP2 0.018 0.006 -10000 0 -10000 0 0
CASP3 0.045 0.095 0.3 10 -0.36 2 12
TNFRSF1A 0.019 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.017 -10000 0 -0.3 1 1
CASP8 0.019 0.004 -10000 0 -10000 0 0
CASP9 0.019 0.004 -10000 0 -10000 0 0
MAP3K14 0.007 0.079 -10000 0 -0.36 14 14
APAF-1/Caspase 9 0.03 0.078 0.18 49 -10000 0 49
BCL2 0.029 0.12 0.38 4 -0.55 13 17
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.039 0.12 0.32 17 -0.46 11 28
IKBKB 0.038 0.1 0.32 21 -0.27 8 29
AKT1 0.035 0.11 0.33 43 -0.21 2 45
IKBKG 0.052 0.075 0.29 21 -0.24 2 23
CALM1 0.036 0.066 0.33 3 -0.3 5 8
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
MAP3K1 0.058 0.13 0.35 28 -0.47 8 36
MAP3K7 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.044 0.069 0.25 6 -0.31 5 11
DOK1 0.02 0.003 -10000 0 -10000 0 0
AP-1 0.037 0.087 0.26 26 -0.24 14 40
LYN 0.019 0.005 -10000 0 -10000 0 0
BLNK 0.019 0.019 -10000 0 -0.42 1 1
SHC1 0.019 0.004 -10000 0 -10000 0 0
BCR complex 0.057 0.056 0.27 3 -0.3 1 4
CD22 0.02 0.059 0.24 4 -0.29 7 11
CAMK2G 0.032 0.064 0.28 5 -0.3 4 9
CSNK2A1 0.019 0.004 -10000 0 -10000 0 0
INPP5D 0.02 0.015 0.19 4 -10000 0 4
SHC/GRB2/SOS1 -0.017 0.044 -10000 0 -0.21 3 3
GO:0007205 0.044 0.069 0.26 5 -0.32 5 10
SYK 0.019 0.019 -10000 0 -0.42 1 1
ELK1 0.039 0.069 0.27 6 -0.31 5 11
NFATC1 0.025 0.08 0.31 10 -0.35 2 12
B-cell antigen/BCR complex 0.057 0.056 0.27 3 -0.3 1 4
PAG1/CSK 0.028 0.008 -10000 0 -10000 0 0
NFKBIB 0.028 0.044 0.14 23 -0.12 8 31
HRAS 0.032 0.062 0.25 9 -0.25 5 14
NFKBIA 0.028 0.043 0.14 24 -0.12 8 32
NF-kappa-B/RelA/I kappa B beta 0.03 0.041 0.14 24 -0.14 1 25
RasGAP/Csk 0.083 0.076 0.26 41 -0.32 2 43
mol:GDP 0.042 0.071 0.31 2 -0.33 5 7
PTEN 0.019 0.004 -10000 0 -10000 0 0
CD79B 0.02 0.013 0.19 3 -10000 0 3
NF-kappa-B/RelA/I kappa B alpha 0.031 0.041 0.14 24 -0.14 1 25
GRB2 0.02 0.003 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.061 0.11 0.36 20 -0.47 4 24
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
mol:IP3 0.043 0.068 0.24 8 -0.32 5 13
CSK 0.02 0.002 -10000 0 -10000 0 0
FOS 0.029 0.077 0.29 7 -0.35 6 13
CHUK 0.044 0.092 0.3 20 -0.28 14 34
IBTK 0.019 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.066 0.075 0.28 12 -0.27 3 15
PTPN6 0.013 0.056 0.21 5 -0.29 7 12
RELA 0.02 0.002 -10000 0 -10000 0 0
BCL2A1 0.028 0.035 0.14 14 -10000 0 14
VAV2 0.022 0.083 0.31 3 -0.35 6 9
ubiquitin-dependent protein catabolic process 0.029 0.043 0.14 24 -0.12 8 32
BTK 0.027 0.15 -10000 0 -0.91 11 11
CD19 0.025 0.07 0.23 8 -0.31 7 15
MAP4K1 0.088 0.083 0.19 214 -10000 0 214
CD72 0.058 0.071 0.19 122 -10000 0 122
PAG1 0.019 0.005 -10000 0 -10000 0 0
MAPK14 0.052 0.12 0.32 32 -0.4 8 40
SH3BP5 0.014 0.021 -10000 0 -0.42 1 1
PIK3AP1 0.039 0.066 0.25 3 -0.38 4 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.03 0.093 0.2 4 -0.35 11 15
RAF1 0.021 0.06 0.25 9 -0.26 2 11
RasGAP/p62DOK/SHIP 0.076 0.071 0.24 42 -0.32 2 44
CD79A 0.06 0.075 0.19 127 -0.42 1 128
re-entry into mitotic cell cycle 0.037 0.086 0.25 26 -0.24 13 39
RASA1 0.017 0.02 -10000 0 -0.42 1 1
MAPK3 0.025 0.077 0.27 27 -0.26 1 28
MAPK1 0.02 0.066 0.26 15 -0.26 1 16
CD72/SHP1 0.049 0.096 0.25 40 -0.28 6 46
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
MAPK8 0.051 0.12 0.32 31 -0.4 8 39
actin cytoskeleton organization 0.035 0.096 0.32 15 -0.32 5 20
NF-kappa-B/RelA 0.06 0.076 0.26 24 -0.2 3 27
Calcineurin 0.049 0.059 0.23 1 -0.28 4 5
PI3K -0.009 0.05 -10000 0 -0.33 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.038 0.068 0.28 2 -0.37 5 7
SOS1 0.02 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.083 0.14 0.39 1 -0.58 14 15
DAPP1 0.028 0.12 -10000 0 -0.64 14 14
cytokine secretion 0.025 0.078 0.3 11 -0.33 2 13
mol:DAG 0.043 0.068 0.24 8 -0.32 5 13
PLCG2 0.018 0.036 0.19 4 -0.42 3 7
MAP2K1 0.025 0.064 0.27 11 -0.27 1 12
B-cell antigen/BCR complex/FcgammaRIIB 0.08 0.077 0.26 44 -0.47 1 45
mol:PI-3-4-5-P3 0.008 0.066 0.22 17 -0.28 1 18
ETS1 0.027 0.065 0.3 6 -0.28 4 10
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.07 0.057 0.25 3 -0.23 3 6
B-cell antigen/BCR complex/LYN 0.035 0.06 0.25 1 -0.32 7 8
MALT1 0.019 0.003 -10000 0 -10000 0 0
TRAF6 0.02 0.002 -10000 0 -10000 0 0
RAC1 0.032 0.096 0.32 12 -0.33 6 18
B-cell antigen/BCR complex/LYN/SYK 0.057 0.067 0.3 6 -0.3 2 8
CARD11 0.064 0.091 0.28 35 -0.3 5 40
FCGR2B 0.047 0.067 0.19 89 -0.42 1 90
PPP3CA 0.02 0.002 -10000 0 -10000 0 0
BCL10 0.019 0.004 -10000 0 -10000 0 0
IKK complex 0.029 0.063 0.19 37 -10000 0 37
PTPRC 0.036 0.051 0.19 53 -10000 0 53
PDPK1 0.01 0.078 0.26 27 -0.22 2 29
PPP3CB 0.019 0.004 -10000 0 -10000 0 0
PPP3CC 0.018 0.006 -10000 0 -10000 0 0
POU2F2 0.025 0.034 0.15 13 -10000 0 13
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.077 0.06 0.28 1 -10000 0 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.002 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.016 0.062 0.27 10 -10000 0 10
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.044 0.024 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.037 0.061 -10000 0 -0.21 14 14
CaM/Ca2+ 0.068 0.055 0.24 1 -10000 0 1
RAP1A 0.019 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.013 0.047 0.18 4 -10000 0 4
AKT1 0.016 0.079 0.26 28 -0.23 1 29
MAP2K1 0.001 0.047 0.23 11 -10000 0 11
MAP3K11 0.01 0.057 0.25 15 -10000 0 15
IFNGR1 0.021 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.1 0.18 -10000 0 -0.38 124 124
Rap1/GTP -0.011 0.034 -10000 0 -0.2 1 1
CRKL/C3G 0.029 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.087 0.062 0.25 1 -10000 0 1
CEBPB 0.033 0.094 0.45 11 -0.44 3 14
STAT3 0.02 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.09 0.07 -10000 0 -0.72 1 1
STAT1 0.012 0.059 0.26 17 -10000 0 17
CALM1 0.019 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.088 0.087 0.18 232 -10000 0 232
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
STAT1 (dimer)/PIAS1 0.015 0.06 0.24 16 -10000 0 16
CEBPB/PTGES2/Cbp/p300 0.014 0.041 -10000 0 -0.3 3 3
mol:Ca2+ 0.073 0.057 0.27 1 -10000 0 1
MAPK3 0.018 0.064 0.39 3 -0.7 1 4
STAT1 (dimer) -0.046 0.082 -10000 0 -0.28 11 11
MAPK1 0.019 0.075 0.42 4 -0.68 2 6
JAK2 0.02 0.013 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
JAK1 0.021 0.013 -10000 0 -10000 0 0
CAMK2D 0.02 0.003 -10000 0 -10000 0 0
DAPK1 0.026 0.09 0.37 14 -0.57 3 17
SMAD7 -0.01 0.059 0.17 27 -10000 0 27
CBL/CRKL/C3G 0.015 0.063 0.24 14 -10000 0 14
PI3K 0.058 0.053 0.21 1 -0.23 2 3
IFNG 0.088 0.087 0.18 232 -10000 0 232
apoptosis 0.022 0.092 0.33 16 -0.43 8 24
CAMK2G 0.019 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.02 0.003 -10000 0 -10000 0 0
CAMK2A -0.089 0.18 0.19 1 -0.42 126 127
CAMK2B -0.033 0.14 0.19 7 -0.42 64 71
FRAP1 0.01 0.074 0.25 28 -0.22 1 29
PRKCD 0.014 0.068 0.25 25 -0.23 1 26
RAP1B 0.019 0.004 -10000 0 -10000 0 0
negative regulation of cell growth -0.037 0.061 -10000 0 -0.21 14 14
PTPN2 0.02 0.003 -10000 0 -10000 0 0
EP300 0.019 0.019 -10000 0 -0.42 1 1
IRF1 0 0.053 0.3 9 -10000 0 9
STAT1 (dimer)/PIASy 0.014 0.063 0.27 14 -10000 0 14
SOCS1 0.014 0.051 -10000 0 -1 1 1
mol:GDP 0.013 0.06 0.23 14 -10000 0 14
CASP1 -0.01 0.059 0.16 32 -10000 0 32
PTGES2 0.018 0.027 -10000 0 -0.42 2 2
IRF9 0.012 0.045 0.2 14 -10000 0 14
mol:PI-3-4-5-P3 0.042 0.042 0.17 1 -0.22 2 3
RAP1/GDP -0.002 0.045 -10000 0 -10000 0 0
CBL 0.01 0.057 0.24 17 -0.22 1 18
MAP3K1 0.009 0.052 0.24 13 -10000 0 13
PIAS1 0.02 0.002 -10000 0 -10000 0 0
PIAS4 0.019 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.037 0.061 -10000 0 -0.21 14 14
PTPN11 0.009 0.04 0.17 4 -10000 0 4
CREBBP 0.019 0.004 -10000 0 -10000 0 0
RAPGEF1 0.019 0.004 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.076 0.15 -10000 0 -0.33 127 127
Crk/p130 Cas/Paxillin -0.044 0.067 -10000 0 -0.27 28 28
JUN -0.024 0.063 -10000 0 -0.36 7 7
HRAS 0.02 0.008 0.19 1 -10000 0 1
RET51/GFRalpha1/GDNF/GRB10 0.023 0.074 0.26 1 -0.25 31 32
RAP1A 0.019 0.004 -10000 0 -10000 0 0
FRS2 0.019 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.014 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.023 0.079 0.26 1 -0.24 38 39
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.019 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.016 0.057 -10000 0 -0.23 21 21
RHOA 0.014 0.009 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.072 0.21 1 -0.22 37 38
GRB7 0.014 0.05 -10000 0 -0.42 7 7
RET51/GFRalpha1/GDNF 0.023 0.079 0.26 1 -0.24 38 39
MAPKKK cascade -0.044 0.059 0.15 1 -0.25 31 32
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/IRS1 0.016 0.068 -10000 0 -0.24 32 32
lamellipodium assembly -0.029 0.065 -10000 0 -0.26 30 30
RET51/GFRalpha1/GDNF/SHC 0.023 0.077 0.26 1 -0.24 36 37
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC 0.019 0.062 -10000 0 -0.23 27 27
RET9/GFRalpha1/GDNF/Shank3 0.018 0.064 -10000 0 -0.23 29 29
MAPK3 -0.029 0.075 0.5 1 -0.39 1 2
DOK1 0.02 0.003 -10000 0 -10000 0 0
DOK6 0.011 0.06 -10000 0 -0.42 10 10
PXN 0.019 0.004 -10000 0 -10000 0 0
neurite development -0.032 0.067 -10000 0 -0.31 5 5
DOK5 0.012 0.057 0.19 1 -0.42 9 10
GFRA1 -0.005 0.1 0.19 3 -0.42 30 33
MAPK8 -0.025 0.064 -10000 0 -0.25 33 33
HRAS/GTP 0.016 0.082 0.21 1 -0.26 33 34
tube development 0.016 0.064 0.19 8 -0.22 29 37
MAPK1 -0.024 0.089 0.41 6 -0.39 1 7
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.006 0.056 -10000 0 -0.22 29 29
Rac1/GDP 0.013 0.005 -10000 0 -10000 0 0
SRC 0.019 0.004 -10000 0 -10000 0 0
PDLIM7 0.016 0.014 0.19 2 -10000 0 2
RET51/GFRalpha1/GDNF/Dok6 0.025 0.087 0.25 1 -0.25 41 42
SHC1 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.023 0.078 0.26 1 -0.24 37 38
RET51/GFRalpha1/GDNF/Dok5 0.02 0.086 0.26 1 -0.26 39 40
PRKCA 0.02 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.005 0.13 1 -10000 0 1
CREB1 -0.013 0.077 -10000 0 -0.28 30 30
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.009 0.062 -10000 0 -0.24 31 31
RET51/GFRalpha1/GDNF/Grb7 0.02 0.087 0.26 1 -0.26 41 42
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.009 0.072 0.19 3 -0.42 14 17
DOK4 0.019 0.004 -10000 0 -10000 0 0
JNK cascade -0.024 0.062 -10000 0 -0.36 7 7
RET9/GFRalpha1/GDNF/FRS2 0.019 0.061 -10000 0 -0.23 26 26
SHANK3 0.02 0.002 -10000 0 -10000 0 0
RASA1 0.017 0.02 -10000 0 -0.42 1 1
NCK1 0.018 0.02 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.004 0.056 -10000 0 -0.23 27 27
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.011 0.07 -10000 0 -0.24 39 39
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.012 0.074 -10000 0 -0.26 38 38
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.01 0.071 -10000 0 -0.24 38 38
PI3K -0.036 0.1 0.21 2 -0.36 33 35
SOS1 0.02 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.025 0.065 -10000 0 -0.22 29 29
GRB10 0.018 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.009 0.059 -10000 0 -0.23 29 29
RET51/GFRalpha1/GDNF/FRS2 0.023 0.077 0.26 1 -0.24 35 36
GAB1 0.02 0.003 -10000 0 -10000 0 0
IRS1 0.016 0.038 -10000 0 -0.42 4 4
IRS2 0.022 0.02 0.19 7 -10000 0 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.012 0.074 -10000 0 -0.25 40 40
RET51/GFRalpha1/GDNF/PKC alpha 0.022 0.079 0.26 1 -0.24 38 39
GRB2 0.02 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.002 -10000 0 -10000 0 0
GDNF 0.018 0.014 0.19 3 -10000 0 3
RAC1 0.018 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.019 0.082 -10000 0 -0.25 41 41
Rac1/GTP -0.032 0.078 -10000 0 -0.3 30 30
RET9/GFRalpha1/GDNF 0.008 0.065 -10000 0 -0.25 29 29
GFRalpha1/GDNF 0.008 0.077 -10000 0 -0.3 29 29
TCGA08_rtk_signaling

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.15 0.21 -10000 0 -0.42 199 199
HRAS 0.02 0.008 0.19 1 -10000 0 1
EGFR 0.019 0.026 0.19 5 -0.42 1 6
AKT -0.027 0.088 0.25 28 -10000 0 28
FOXO3 0.019 0.005 -10000 0 -10000 0 0
AKT1 0.019 0.005 -10000 0 -10000 0 0
FOXO1 0.02 0.003 -10000 0 -10000 0 0
AKT3 0.019 0.004 -10000 0 -10000 0 0
FOXO4 0.02 0.001 -10000 0 -10000 0 0
MET 0.019 0.012 0.19 2 -10000 0 2
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
PIK3CB 0.019 0.005 -10000 0 -10000 0 0
NRAS 0.019 0.004 -10000 0 -10000 0 0
PIK3CG 0.019 0.014 0.19 3 -10000 0 3
PIK3R3 0.019 0.004 -10000 0 -10000 0 0
PIK3R2 0.02 0.002 -10000 0 -10000 0 0
NF1 0.02 0.003 -10000 0 -10000 0 0
RAS -0.038 0.068 -10000 0 -0.14 161 161
ERBB2 0.018 0.027 -10000 0 -0.42 2 2
proliferation/survival/translation -0.017 0.059 0.28 8 -0.21 2 10
PI3K -0.016 0.088 0.27 23 -0.21 4 27
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
KRAS 0.019 0.004 -10000 0 -10000 0 0
FOXO 0.022 0.069 0.22 28 -10000 0 28
AKT2 0.02 0.002 -10000 0 -10000 0 0
PTEN 0.019 0.004 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.049 0.13 0.44 1 -10000 0 1
RAD9A 0.02 0.002 -10000 0 -10000 0 0
AP1 0.023 0.048 -10000 0 -0.3 11 11
IFNAR2 0.022 0.007 -10000 0 -10000 0 0
AKT1 0.013 0.027 -10000 0 -0.27 2 2
ER alpha/Oestrogen 0.014 0.024 0.13 1 -0.29 3 4
NFX1/SIN3/HDAC complex 0.003 0.062 -10000 0 -0.34 11 11
EGF -0.37 0.14 -10000 0 -0.42 467 467
SMG5 0.019 0.004 -10000 0 -10000 0 0
SMG6 0.02 0.003 -10000 0 -10000 0 0
SP3/HDAC2 0.031 0.014 -10000 0 -10000 0 0
TERT/c-Abl -0.051 0.12 -10000 0 -10000 0 0
SAP18 0.02 0.003 -10000 0 -10000 0 0
MRN complex 0.03 0.018 -10000 0 -10000 0 0
WT1 -0.18 0.22 -10000 0 -0.42 241 241
WRN 0.018 0.006 -10000 0 -10000 0 0
SP1 0.023 0.009 -10000 0 -10000 0 0
SP3 0.02 0.005 -10000 0 -10000 0 0
TERF2IP 0.019 0.004 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.057 0.12 -10000 0 -10000 0 0
Mad/Max 0.03 0.012 -10000 0 -10000 0 0
TERT -0.05 0.13 0.44 1 -10000 0 1
CCND1 -0.047 0.13 0.6 1 -10000 0 1
MAX 0.02 0.006 -10000 0 -10000 0 0
RBBP7 0.02 0.002 -10000 0 -10000 0 0
RBBP4 0.019 0.019 -10000 0 -0.42 1 1
TERF2 -0.021 0.009 -10000 0 -10000 0 0
PTGES3 0.02 0.003 -10000 0 -10000 0 0
SIN3A 0.02 0.002 -10000 0 -10000 0 0
Telomerase/911 0.013 0.047 0.22 3 -10000 0 3
CDKN1B 0.026 0.056 0.25 13 -10000 0 13
RAD1 0.018 0.006 -10000 0 -10000 0 0
XRCC5 0.019 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
SAP30 0.026 0.031 0.19 18 -10000 0 18
TRF2/PARP2 0.026 0.009 -10000 0 -10000 0 0
UBE3A 0.021 0.003 -10000 0 -10000 0 0
JUN 0.021 0.005 -10000 0 -10000 0 0
E6 0.001 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.017 0.006 -10000 0 -10000 0 0
FOS 0.011 0.063 0.19 1 -0.42 11 12
IFN-gamma/IRF1 0.069 0.066 0.27 1 -10000 0 1
PARP2 0.019 0.005 -10000 0 -10000 0 0
BLM 0.023 0.024 0.19 11 -10000 0 11
Telomerase -0.028 0.087 -10000 0 -0.36 15 15
IRF1 0.017 0.012 0.19 1 -10000 0 1
ESR1 0.017 0.034 0.19 1 -0.41 3 4
KU/TER 0.028 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.027 0.016 -10000 0 -0.28 1 1
ubiquitin-dependent protein catabolic process 0.007 0.055 -10000 0 -0.29 11 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.007 0.057 -10000 0 -0.3 11 11
HDAC1 0.02 0.004 -10000 0 -10000 0 0
HDAC2 0.022 0.009 -10000 0 -10000 0 0
ATM 0.008 0.017 -10000 0 -0.34 1 1
SMAD3 -0.02 0.011 0.1 2 -10000 0 2
ABL1 0.019 0.004 -10000 0 -10000 0 0
MXD1 0.021 0.005 -10000 0 -10000 0 0
MRE11A 0.02 0.002 -10000 0 -10000 0 0
HUS1 0.018 0.006 -10000 0 -10000 0 0
RPS6KB1 0.02 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.035 0.13 -10000 0 -10000 0 0
NR2F2 0.011 0.019 -10000 0 -10000 0 0
MAPK3 -0.011 0.021 0.12 2 -10000 0 2
MAPK1 -0.012 0.021 0.11 10 -10000 0 10
TGFB1/TGF beta receptor Type II 0.015 0.021 0.18 4 -10000 0 4
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
HNRNPC 0.019 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.008 0.017 -10000 0 -0.34 1 1
NBN 0.019 0.005 -10000 0 -10000 0 0
EGFR 0.019 0.026 0.19 5 -0.42 1 6
mol:Oestrogen 0.001 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.24 0.12 -10000 0 -0.3 422 422
MYC 0.027 0.032 0.19 19 -10000 0 19
IL2 0.026 0.025 0.19 10 -10000 0 10
KU 0.028 0.007 -10000 0 -10000 0 0
RAD50 0.015 0.009 -10000 0 -10000 0 0
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
TGFB1 0.015 0.021 0.18 4 -10000 0 4
TRF2/BLM 0.029 0.018 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.049 0.13 -10000 0 -10000 0 0
SP1/HDAC2 0.034 0.019 -10000 0 -10000 0 0
PINX1 0.018 0.006 -10000 0 -10000 0 0
Telomerase/EST1A -0.057 0.12 -10000 0 -10000 0 0
Smad3/Myc -0.016 0.031 0.14 19 -10000 0 19
911 complex 0.034 0.016 -10000 0 -10000 0 0
IFNG 0.095 0.084 0.19 232 -10000 0 232
Telomerase/PinX1 -0.059 0.12 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K -0.012 0.088 0.23 1 -0.34 12 13
SIN3B 0.021 0.002 -10000 0 -10000 0 0
YWHAE 0.02 0.003 -10000 0 -10000 0 0
Telomerase/EST1B -0.056 0.12 -10000 0 -10000 0 0
response to DNA damage stimulus 0.003 0.011 -10000 0 -0.12 1 1
MRN complex/TRF2/Rap1 0.04 0.027 -10000 0 -10000 0 0
TRF2/WRN 0.025 0.01 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.056 0.12 -10000 0 -10000 0 0
E2F1 0.039 0.052 0.19 54 -10000 0 54
ZNFX1 0.02 0.004 -10000 0 -10000 0 0
PIF1 0.049 0.064 0.19 92 -10000 0 92
NCL 0.019 0.005 -10000 0 -10000 0 0
DKC1 0.02 0.002 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0.002 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.001 0.041 -10000 0 -0.27 4 4
NT3 (dimer)/TRKC 0.013 0.075 -10000 0 -0.32 24 24
NT3 (dimer)/TRKB -0.002 0.11 -10000 0 -0.26 76 76
SHC/Grb2/SOS1/GAB1/PI3K 0.007 0.021 -10000 0 -0.22 1 1
RAPGEF1 0.019 0.004 -10000 0 -10000 0 0
BDNF 0.04 0.063 0.19 67 -0.42 2 69
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
DYNLT1 0.018 0.006 -10000 0 -10000 0 0
NTRK1 -0.007 0.1 0.19 2 -0.42 32 34
NTRK2 -0.055 0.16 -10000 0 -0.42 90 90
NTRK3 -0.003 0.098 -10000 0 -0.42 28 28
NT-4/5 (dimer)/TRKB -0.004 0.11 -10000 0 -0.25 82 82
neuron apoptosis 0.043 0.14 0.34 70 -10000 0 70
SHC 2-3/Grb2 -0.046 0.16 -10000 0 -0.37 70 70
SHC1 0.019 0.004 -10000 0 -10000 0 0
SHC2 -0.014 0.1 -10000 0 -0.39 20 20
SHC3 -0.068 0.19 -10000 0 -0.47 81 81
STAT3 (dimer) 0.024 0.017 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.025 0.079 -10000 0 -0.25 34 34
RIN/GDP 0.009 0.076 0.26 16 -0.27 12 28
GIPC1 0.019 0.019 -10000 0 -0.42 1 1
KRAS 0.019 0.004 -10000 0 -10000 0 0
DNAJA3 -0.01 0.066 0.15 2 -0.23 29 31
RIN/GTP 0.014 0.006 0.13 1 -10000 0 1
CCND1 -0.01 0.039 0.2 18 -10000 0 18
MAGED1 0.02 0.002 -10000 0 -10000 0 0
PTPN11 0.019 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.019 0.013 0.19 3 -10000 0 3
SHC/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
GRB2 0.02 0.003 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.04 0.089 0.26 8 -0.25 32 40
TRKA/NEDD4-2 0.009 0.078 -10000 0 -0.3 31 31
ELMO1 0.018 0.01 0.19 1 -10000 0 1
RhoG/GTP/ELMO1/DOCK1 0.023 0.016 -10000 0 -0.25 1 1
NGF 0.034 0.048 0.19 47 -10000 0 47
HRAS 0.02 0.008 0.19 1 -10000 0 1
DOCK1 0.019 0.019 -10000 0 -0.42 1 1
GAB2 0.02 0.002 -10000 0 -10000 0 0
RIT2 0.018 0.008 0.19 1 -10000 0 1
RIT1 0.019 0.004 -10000 0 -10000 0 0
FRS2 0.019 0.004 -10000 0 -10000 0 0
DNM1 0.023 0.024 0.19 11 -10000 0 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.003 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.013 0.068 -10000 0 -0.22 28 28
mol:GDP 0.004 0.11 0.35 17 -0.4 13 30
NGF (dimer) 0.034 0.048 0.19 47 -10000 0 47
RhoG/GDP 0.014 0.007 0.13 1 -10000 0 1
RIT1/GDP 0.007 0.071 0.28 11 -0.26 12 23
TIAM1 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
BDNF (dimer)/TRKB 0 0.12 -10000 0 -0.26 88 88
KIDINS220/CRKL/C3G 0.029 0.006 -10000 0 -10000 0 0
SHC/RasGAP 0.025 0.018 -10000 0 -0.3 1 1
FRS2 family/SHP2 0.038 0.011 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.047 0.015 -10000 0 -10000 0 0
RIT1/GTP 0.014 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.017 0.035 0.19 2 -0.42 3 5
RAP1/GDP 0.002 0.051 -10000 0 -0.24 10 10
KIDINS220/CRKL 0.02 0.002 -10000 0 -10000 0 0
BDNF (dimer) 0.04 0.063 0.19 67 -0.42 2 69
ubiquitin-dependent protein catabolic process 0.029 0.079 -10000 0 -0.26 31 31
Schwann cell development -0.016 0.017 -10000 0 -10000 0 0
EHD4 0.02 0.002 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.047 0.016 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.005 0.034 -10000 0 -0.28 1 1
RAP1B 0.019 0.004 -10000 0 -10000 0 0
RAP1A 0.019 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.058 0.097 0.14 1 -0.25 72 73
ABL1 0.019 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.029 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.014 0.08 -10000 0 -0.37 11 11
STAT3 0.024 0.017 -10000 0 -10000 0 0
axon guidance -0.059 0.09 -10000 0 -0.24 81 81
MAPK3 -0.018 0.067 0.17 9 -0.24 28 37
MAPK1 -0.018 0.068 0.17 11 -0.24 28 39
CDC42/GDP 0.012 0.081 0.29 17 -0.26 12 29
NTF3 0.018 0.035 0.19 2 -0.42 3 5
NTF4 0.019 0.013 0.19 3 -10000 0 3
NGF (dimer)/TRKA/FAIM 0.028 0.079 -10000 0 -0.26 31 31
PI3K 0.025 0.022 -10000 0 -0.3 2 2
FRS3 0.019 0.004 -10000 0 -10000 0 0
FAIM 0.019 0.005 -10000 0 -10000 0 0
GAB1 0.02 0.003 -10000 0 -10000 0 0
RASGRF1 -0.009 0.068 0.15 2 -0.23 30 32
SOS1 0.02 0.003 -10000 0 -10000 0 0
MCF2L -0.033 0.055 -10000 0 -0.28 24 24
RGS19 0.019 0.004 -10000 0 -10000 0 0
CDC42 0.019 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.014 0.083 0.27 7 -0.52 7 14
Rac1/GDP 0.004 0.064 0.24 8 -0.27 11 19
NGF (dimer)/TRKA/GRIT 0.018 0.075 -10000 0 -0.25 32 32
neuron projection morphogenesis 0.009 0.13 0.39 1 -1 6 7
NGF (dimer)/TRKA/NEDD4-2 0.029 0.079 -10000 0 -0.26 31 31
MAP2K1 -0.017 0.054 0.19 31 -10000 0 31
NGFR 0.03 0.04 0.19 31 -10000 0 31
NGF (dimer)/TRKA/GIPC/GAIP -0.007 0.074 -10000 0 -0.25 31 31
RAS family/GTP/PI3K 0.005 0.026 -10000 0 -0.23 3 3
FRS2 family/SHP2/GRB2/SOS1 0.053 0.02 -10000 0 -10000 0 0
NRAS 0.019 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.029 0.006 -10000 0 -10000 0 0
PRKCI 0.019 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
PRKCZ 0.017 0.033 -10000 0 -0.42 3 3
MAPKKK cascade -0.04 0.19 -10000 0 -0.56 53 53
RASA1 0.017 0.02 -10000 0 -0.42 1 1
TRKA/c-Abl 0.008 0.079 -10000 0 -0.3 32 32
SQSTM1 0.015 0.009 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.007 0.12 -10000 0 -0.24 89 89
NGF (dimer)/TRKA/p62/Atypical PKCs 0.034 0.066 -10000 0 -0.23 19 19
MATK 0.037 0.05 0.19 52 -10000 0 52
NEDD4L 0.019 0.019 -10000 0 -0.42 1 1
RAS family/GDP -0.015 0.036 -10000 0 -0.2 11 11
NGF (dimer)/TRKA 0.002 0.067 -10000 0 -0.23 28 28
Rac1/GTP -0.026 0.049 -10000 0 -0.24 12 12
FRS2 family/SHP2/CRK family 0.054 0.02 -10000 0 -10000 0 0
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.079 0.064 0.16 5 -0.23 1 6
PDGFRB 0.013 0.012 -10000 0 -10000 0 0
SPHK1 0.004 0.077 -10000 0 -0.65 6 6
mol:S1P 0 0.068 -10000 0 -0.56 6 6
S1P1/S1P/Gi -0.023 0.1 0.25 2 -0.39 26 28
GNAO1 0.018 0.026 0.19 3 -0.41 1 4
PDGFB-D/PDGFRB/PLCgamma1 -0.021 0.084 0.28 1 -0.34 20 21
PLCG1 -0.024 0.096 0.23 4 -0.36 26 30
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.012 -10000 0 -10000 0 0
GNAI2 0.013 0.012 -10000 0 -10000 0 0
GNAI3 0.018 0.011 -10000 0 -10000 0 0
GNAI1 0.016 0.023 -10000 0 -0.43 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.023 0.043 0.086 12 -0.18 1 13
S1P1/S1P 0.029 0.074 0.23 12 -0.39 6 18
negative regulation of cAMP metabolic process -0.022 0.1 0.25 2 -0.38 26 28
MAPK3 -0.033 0.13 0.33 4 -0.54 25 29
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.011 0.007 -10000 0 -10000 0 0
KDR 0.018 0.021 -10000 0 -0.41 1 1
PLCB2 0.038 0.083 0.26 23 -0.36 6 29
RAC1 0.018 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.004 0.05 -10000 0 -0.34 6 6
receptor internalization 0.025 0.066 0.2 7 -0.37 6 13
PTGS2 -0.038 0.21 0.45 7 -0.9 24 31
Rac1/GTP 0.009 0.053 -10000 0 -0.34 6 6
RHOA 0.014 0.009 -10000 0 -10000 0 0
VEGFA 0.093 0.086 0.19 232 -10000 0 232
negative regulation of T cell proliferation -0.022 0.1 0.25 2 -0.38 26 28
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.016 0.035 -10000 0 -0.42 3 3
MAPK1 -0.036 0.13 0.25 2 -0.55 26 28
S1P1/S1P/PDGFB-D/PDGFRB 0.016 0.064 0.23 3 -0.33 6 9
ABCC1 0.018 0.011 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.009 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.023 0.057 -10000 0 -0.23 25 25
regulation of S phase of mitotic cell cycle -0.001 0.052 -10000 0 -0.25 19 19
GNAO1 0.019 0.023 0.19 3 -0.42 1 4
HRAS 0.019 0.01 0.19 1 -10000 0 1
SHBG/T-DHT -0.013 0.078 -10000 0 -0.24 53 53
PELP1 0.019 0.007 -10000 0 -10000 0 0
AKT1 -0.009 0.003 -10000 0 -10000 0 0
MAP2K1 -0.026 0.051 0.16 10 -0.22 18 28
T-DHT/AR 0 0.066 -10000 0 -0.29 25 25
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 0.002 1 -0.009 12 13
GNAI2 0.014 0.009 -10000 0 -10000 0 0
GNAI3 0.019 0.004 -10000 0 -10000 0 0
GNAI1 0.017 0.02 -10000 0 -0.42 1 1
mol:GDP -0.027 0.073 -10000 0 -0.35 24 24
cell proliferation -0.056 0.093 0.28 7 -0.4 15 22
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
FOS -0.042 0.12 0.24 2 -0.66 15 17
mol:Ca2+ -0.003 0.012 -10000 0 -0.064 12 12
MAPK3 -0.045 0.076 0.25 10 -0.32 13 23
MAPK1 -0.021 0.056 -10000 0 -0.4 5 5
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
mol:IP3 0 0.001 0.003 1 -0.005 12 13
cAMP biosynthetic process -0.024 0.07 0.24 2 -0.23 52 54
GNG2 0.019 0.005 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 0.003 1 -0.005 12 13
HRAS/GTP 0.026 0.051 -10000 0 -0.22 20 20
actin cytoskeleton reorganization 0.024 0.02 -10000 0 -0.21 2 2
SRC 0.019 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 0.003 1 -0.005 12 13
PI3K 0.023 0.019 -10000 0 -0.25 2 2
apoptosis 0.037 0.091 0.41 19 -0.22 5 24
T-DHT/AR/PELP1 0.013 0.059 -10000 0 -0.25 24 24
HRAS/GDP -0.03 0.069 -10000 0 -0.34 23 23
CREB1 -0.039 0.097 0.23 5 -0.44 19 24
RAC1-CDC42/GTP 0.03 0.023 -10000 0 -0.21 2 2
AR -0.001 0.093 -10000 0 -0.42 25 25
GNB1 0.019 0.004 -10000 0 -10000 0 0
RAF1 -0.023 0.051 0.18 10 -0.22 20 30
RAC1-CDC42/GDP -0.025 0.073 -10000 0 -0.35 20 20
T-DHT/AR/PELP1/Src 0.026 0.053 -10000 0 -0.23 20 20
MAP2K2 -0.026 0.05 0.17 8 -0.22 18 26
T-DHT/AR/PELP1/Src/PI3K -0.001 0.052 -10000 0 -0.25 19 19
GNAZ 0.017 0.033 -10000 0 -0.42 3 3
SHBG -0.025 0.13 -10000 0 -0.42 53 53
Gi family/GNB1/GNG2/GDP -0.048 0.12 -10000 0 -0.46 20 20
mol:T-DHT 0 0.001 -10000 0 -0.006 9 9
RAC1 0.018 0.006 -10000 0 -10000 0 0
GNRH1 0.021 0.05 0.1 135 -10000 0 135
Gi family/GTP -0.012 0.041 -10000 0 -0.25 10 10
CDC42 0.019 0.004 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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 -0.069 0.12 -10000 0 -0.3 89 89
KLHL20 -0.022 0.06 0.16 2 -0.22 11 13
CYFIP2 0.009 0.05 -10000 0 -0.42 7 7
Rac1/GDP -0.034 0.078 0.24 6 -0.28 12 18
ENAH -0.065 0.12 -10000 0 -0.31 85 85
AP1M1 0.02 0.002 -10000 0 -10000 0 0
RAP1B 0.019 0.004 -10000 0 -10000 0 0
RAP1A 0.019 0.004 -10000 0 -10000 0 0
CTNNB1 0.014 0.009 -10000 0 -10000 0 0
CDC42/GTP -0.028 0.045 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.022 0.034 -10000 0 -0.15 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.026 0.054 -10000 0 -0.24 17 17
RAPGEF1 -0.063 0.12 0.22 6 -0.36 18 24
CTNND1 0.02 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.06 0.13 -10000 0 -0.31 92 92
CRK -0.068 0.12 -10000 0 -0.3 69 69
E-cadherin/gamma catenin/alpha catenin 0.02 0.056 -10000 0 -0.27 16 16
alphaE/beta7 Integrin 0.028 0.007 -10000 0 -10000 0 0
IQGAP1 0.02 0.002 -10000 0 -10000 0 0
NCKAP1 0.019 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.013 -10000 0 -10000 0 0
DLG1 -0.06 0.12 -10000 0 -0.3 79 79
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.031 0.028 -10000 0 -0.16 2 2
MLLT4 0.018 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.035 0.014 -10000 0 -10000 0 0
PI3K -0.038 0.035 -10000 0 -0.21 2 2
ARF6 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.016 0.065 -10000 0 -0.31 19 19
TIAM1 0.019 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.02 0.048 -10000 0 -0.22 14 14
AKT1 -0.023 0.029 0.11 1 -10000 0 1
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
CDH1 0.005 0.077 -10000 0 -0.42 17 17
RhoA/GDP -0.026 0.086 0.29 10 -0.28 13 23
actin cytoskeleton organization -0.014 0.05 0.14 13 -0.16 10 23
CDC42/GDP -0.03 0.1 0.32 16 -0.28 13 29
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.002 0.046 -10000 0 -0.24 16 16
ITGB7 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.023 0.05 -10000 0 -0.24 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin 0.015 0.042 -10000 0 -0.22 14 14
mol:GDP -0.033 0.11 0.33 16 -0.31 13 29
CDC42/GTP/IQGAP1 0.026 0.006 -10000 0 -10000 0 0
JUP 0.017 0.033 -10000 0 -0.42 3 3
p120 catenin/RhoA/GDP -0.043 0.069 0.26 3 -0.28 13 16
RAC1/GTP/IQGAP1 0.024 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.03 0.003 -10000 0 -10000 0 0
RHOA 0.014 0.009 -10000 0 -10000 0 0
CDC42 0.019 0.004 -10000 0 -10000 0 0
CTNNA1 0.015 0.009 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.004 0.044 0.13 22 -10000 0 22
NME1 0.02 0.008 0.19 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.068 0.12 -10000 0 -0.3 89 89
regulation of cell-cell adhesion -0.027 0.037 -10000 0 -0.19 1 1
WASF2 -0.005 0.031 -10000 0 -10000 0 0
Rap1/GTP -0.025 0.054 0.21 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.034 0.057 -10000 0 -0.24 16 16
CCND1 -0.006 0.05 0.16 18 -10000 0 18
VAV2 -0.065 0.16 0.36 1 -0.52 27 28
RAP1/GDP -0.024 0.066 0.24 6 -0.26 5 11
adherens junction assembly -0.067 0.12 -10000 0 -0.3 91 91
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.02 0.003 -10000 0 -10000 0 0
PIP5K1C 0.02 0.002 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.024 0.066 -10000 0 -0.24 16 16
E-cadherin/beta catenin -0.007 0.059 -10000 0 -0.32 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.067 0.12 -10000 0 -0.3 88 88
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
Rac1/GTP -0.039 0.08 0.16 6 -0.34 13 19
E-cadherin/beta catenin/alpha catenin 0.017 0.05 -10000 0 -0.26 14 14
ITGAE 0.02 0.003 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.062 0.13 -10000 0 -0.31 92 92
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.039 0.032 -10000 0 -0.22 4 4
ER alpha/Gai/GDP/Gbeta gamma -0.072 0.18 -10000 0 -0.54 47 47
AKT1 -0.062 0.23 -10000 0 -0.73 51 51
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.06 0.24 -10000 0 -0.75 52 52
mol:Ca2+ -0.012 0.053 -10000 0 -0.37 7 7
IGF1R 0.02 0.002 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.021 0.032 -10000 0 -0.24 7 7
SHC1 0.019 0.004 -10000 0 -10000 0 0
apoptosis 0.058 0.22 0.7 51 -10000 0 51
RhoA/GTP -0.027 0.017 -10000 0 -0.2 3 3
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.042 0.15 -10000 0 -0.44 46 46
regulation of stress fiber formation 0.024 0.05 0.33 1 -0.24 8 9
E2/ERA-ERB (dimer) 0.022 0.029 -10000 0 -0.25 4 4
KRAS 0.019 0.004 -10000 0 -10000 0 0
G13/GTP 0.022 0.021 -10000 0 -0.23 3 3
pseudopodium formation -0.024 0.05 0.24 8 -0.33 1 9
E2/ER alpha (dimer)/PELP1 0.023 0.023 -10000 0 -0.25 3 3
GRB2 0.02 0.003 -10000 0 -10000 0 0
GNG2 0.019 0.005 -10000 0 -10000 0 0
GNAO1 0.019 0.023 0.19 3 -0.42 1 4
HRAS 0.02 0.008 0.19 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.049 0.18 0.28 5 -0.56 46 51
E2/ER beta (dimer) 0.014 0.018 0.13 5 -0.29 1 6
mol:GDP -0.03 0.052 -10000 0 -0.31 5 5
mol:NADP -0.049 0.18 0.28 5 -0.56 46 51
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
mol:IP3 -0.013 0.055 -10000 0 -0.38 7 7
IGF-1R heterotetramer 0.02 0.002 -10000 0 -10000 0 0
PLCB1 -0.014 0.055 -10000 0 -0.39 8 8
PLCB2 -0.005 0.055 -10000 0 -0.36 9 9
IGF1 0.021 0.017 0.19 5 -10000 0 5
mol:L-citrulline -0.049 0.18 0.28 5 -0.56 46 51
RHOA 0.014 0.009 -10000 0 -10000 0 0
Gai/GDP -0.14 0.26 -10000 0 -0.56 147 147
JNK cascade 0.014 0.018 0.13 5 -0.29 1 6
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
ESR2 0.019 0.026 0.19 5 -0.42 1 6
GNAQ 0.019 0.004 -10000 0 -10000 0 0
ESR1 0.016 0.034 0.19 1 -0.42 3 4
Gq family/GDP/Gbeta gamma -0.007 0.11 -10000 0 -0.62 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.007 0.14 -10000 0 -0.97 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.041 0.15 -10000 0 -0.43 46 46
GNAZ 0.017 0.033 -10000 0 -0.42 3 3
E2/ER alpha (dimer) 0.012 0.024 0.13 1 -0.29 3 4
STRN 0.016 0.038 -10000 0 -0.42 4 4
GNAL 0.02 0.003 -10000 0 -10000 0 0
PELP1 0.02 0.003 -10000 0 -10000 0 0
MAPK11 -0.013 0.016 0.11 2 -0.25 1 3
GNAI2 0.014 0.009 -10000 0 -10000 0 0
GNAI3 0.019 0.004 -10000 0 -10000 0 0
GNAI1 0.017 0.02 -10000 0 -0.42 1 1
HBEGF -0.051 0.17 0.36 10 -0.47 47 57
cAMP biosynthetic process 0.018 0.023 -10000 0 -0.21 4 4
SRC -0.071 0.17 -10000 0 -0.51 48 48
PI3K 0.025 0.022 -10000 0 -0.3 2 2
GNB1 0.019 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.017 0.06 -10000 0 -0.3 4 4
SOS1 0.02 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.043 0.12 -10000 0 -0.36 45 45
Gs family/GTP 0.023 0.026 -10000 0 -0.21 4 4
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.011 -10000 0 -10000 0 0
vasodilation -0.046 0.17 0.26 6 -0.53 46 52
mol:DAG -0.013 0.055 -10000 0 -0.38 7 7
Gs family/GDP/Gbeta gamma -0.038 0.044 -10000 0 -0.29 4 4
MSN -0.026 0.052 0.3 5 -0.35 1 6
Gq family/GTP 0.005 0.055 -10000 0 -0.38 9 9
mol:PI-3-4-5-P3 -0.057 0.23 -10000 0 -0.72 52 52
NRAS 0.019 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.046 0.17 0.53 46 -0.26 6 52
GRB2/SOS1 0.029 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.001 0.059 -10000 0 -0.29 5 5
NOS3 -0.053 0.19 0.28 5 -0.59 46 51
GNA11 0.017 0.033 -10000 0 -0.42 3 3
MAPKKK cascade -0.047 0.18 0.33 4 -0.58 47 51
E2/ER alpha (dimer)/PELP1/Src -0.046 0.15 0.24 1 -0.45 47 48
ruffle organization -0.024 0.05 0.24 8 -0.33 1 9
ROCK2 -0.022 0.056 0.31 5 -0.38 1 6
GNA14 0.014 0.05 -10000 0 -0.42 7 7
GNA15 0.025 0.028 0.19 15 -10000 0 15
GNA13 0.02 0.004 -10000 0 -10000 0 0
MMP9 -0.048 0.17 0.33 7 -0.47 48 55
MMP2 -0.069 0.16 0.3 2 -0.49 46 48
Visual signal transduction: Rods

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
mol:K + 0.02 0.002 -10000 0 -10000 0 0
GNAT1/GTP 0.011 0.013 0.13 5 -10000 0 5
Metarhodopsin II/Arrestin 0.026 0.02 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.017 0.029 -10000 0 -0.25 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.015 0.019 0.19 5 -10000 0 5
GRK1 0.018 0.003 -10000 0 -10000 0 0
CNG Channel -0.017 0.088 0.23 1 -0.22 73 74
mol:Na + -0.056 0.077 0.18 3 -0.22 69 72
mol:ADP 0.018 0.003 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.026 0.066 -10000 0 -0.26 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.003 0.1 0.21 3 -0.22 74 77
CNGB1 0.021 0.022 0.19 9 -10000 0 9
RDH5 0.02 0.032 0.19 5 -0.42 2 7
SAG 0.017 0.009 0.19 1 -10000 0 1
mol:Ca2+ -0.058 0.086 0.3 7 -10000 0 7
Na + (4 Units) -0.063 0.07 0.13 3 -0.22 63 66
RGS9 0.019 0.044 0.19 9 -0.42 4 13
GNB1/GNGT1 0.058 0.057 -10000 0 -10000 0 0
GNAT1/GDP 0.017 0.061 -10000 0 -0.22 25 25
GUCY2D 0.027 0.037 0.19 26 -10000 0 26
GNGT1 0.067 0.078 0.19 154 -10000 0 154
GUCY2F 0.018 0.002 -10000 0 -10000 0 0
GNB5 0.02 0.002 -10000 0 -10000 0 0
mol:GMP (4 units) -0.015 0.036 0.16 1 -0.24 8 9
mol:11-cis-retinal 0.02 0.032 0.19 5 -0.42 2 7
mol:cGMP 0.036 0.031 0.22 2 -0.23 2 4
GNB1 0.019 0.004 -10000 0 -10000 0 0
Rhodopsin 0.03 0.032 -10000 0 -0.3 2 2
SLC24A1 0.02 0.002 -10000 0 -10000 0 0
CNGA1 -0.059 0.17 -10000 0 -0.42 95 95
Metarhodopsin II 0.025 0.018 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.049 0.038 0.26 2 -0.24 2 4
RGS9BP 0.001 0.089 -10000 0 -0.42 23 23
Metarhodopsin II/Transducin 0.015 0.044 0.23 1 -0.18 14 15
GCAP Family/Ca ++ 0.034 0.027 0.24 1 -0.23 2 3
PDE6A/B 0.022 0.038 -10000 0 -0.29 5 5
mol:Pi 0.026 0.066 -10000 0 -0.26 25 25
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.047 0.053 0.24 2 -10000 0 2
PDE6B 0.016 0.042 -10000 0 -0.42 5 5
PDE6A 0.019 0.027 0.19 12 -10000 0 12
PDE6G 0.017 0.039 0.19 1 -0.42 4 5
RHO 0.023 0.029 0.19 15 -10000 0 15
PDE6 0.029 0.073 -10000 0 -0.24 28 28
GUCA1A 0.021 0.022 0.19 9 -10000 0 9
GC2/GCAP Family 0.044 0.03 0.25 1 -0.24 2 3
GUCA1C 0.015 0.027 -10000 0 -0.42 2 2
GUCA1B 0.021 0.017 0.19 5 -10000 0 5
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.015 0.081 -10000 0 -0.4 19 19
HDAC1 0.015 0.014 -10000 0 -10000 0 0
AES 0.017 0.01 -10000 0 -10000 0 0
FBXW11 0.015 0.009 -10000 0 -10000 0 0
DTX1 -0.017 0.12 -10000 0 -0.42 44 44
LRP6/FZD1 0.026 0.01 -10000 0 -10000 0 0
TLE1 0.017 0.011 -10000 0 -10000 0 0
AP1 -0.062 0.12 -10000 0 -0.25 136 136
NCSTN 0.019 0.004 -10000 0 -10000 0 0
ADAM10 0.019 0.019 -10000 0 -0.42 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.022 0.044 -10000 0 -0.72 1 1
NICD/RBPSUH 0.014 0.082 -10000 0 -0.4 19 19
WIF1 0.016 0.039 0.19 1 -0.42 4 5
NOTCH1 0 0.082 -10000 0 -0.42 19 19
PSENEN 0.02 0.002 -10000 0 -10000 0 0
KREMEN2 0.038 0.054 0.19 60 -10000 0 60
DKK1 0.018 0.057 0.19 14 -0.42 7 21
beta catenin/beta TrCP1 0.011 0.081 0.26 3 -0.31 7 10
APH1B 0.02 0.002 -10000 0 -10000 0 0
APH1A 0.019 0.004 -10000 0 -10000 0 0
AXIN1 0.011 0.063 0.26 6 -0.32 2 8
CtBP/CBP/TCF1/TLE1/AES -0.004 0.041 -10000 0 -0.28 3 3
PSEN1 0.019 0.005 -10000 0 -10000 0 0
FOS 0.01 0.063 0.19 1 -0.42 11 12
JUN 0.019 0.004 -10000 0 -10000 0 0
MAP3K7 0.016 0.012 -10000 0 -10000 0 0
CTNNB1 0.01 0.1 0.25 12 -0.31 12 24
MAPK3 0.019 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.049 0.05 0.26 1 -0.26 5 6
HNF1A 0.013 0.039 -10000 0 -0.42 4 4
CTBP1 0.017 0.01 -10000 0 -10000 0 0
MYC 0.017 0.1 -10000 0 -0.74 8 8
NKD1 -0.09 0.19 -10000 0 -0.42 130 130
FZD1 0.018 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.003 0.1 -10000 0 -0.43 17 17
apoptosis -0.061 0.12 -10000 0 -0.25 136 136
Delta 1/NOTCHprecursor 0.013 0.081 -10000 0 -0.4 19 19
DLL1 0.018 0.006 -10000 0 -10000 0 0
PPARD -0.007 0.15 -10000 0 -0.78 19 19
Gamma Secretase 0.052 0.022 -10000 0 -10000 0 0
APC 0.012 0.07 0.27 6 -0.41 3 9
DVL1 0.001 0.033 -10000 0 -0.3 3 3
CSNK2A1 0.02 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.048 0.049 0.26 3 -0.23 5 8
LRP6 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.016 0.009 -10000 0 -10000 0 0
NLK 0.004 0.006 -10000 0 -10000 0 0
CCND1 0.025 0.063 -10000 0 -0.77 2 2
WNT1 0.027 0.036 0.19 25 -10000 0 25
Axin1/APC/beta catenin 0.042 0.095 0.35 16 -0.33 1 17
DKK2 0.019 0.059 0.19 17 -0.42 7 24
NOTCH1 precursor/DVL1 0.011 0.083 -10000 0 -0.4 13 13
GSK3B 0.019 0.005 -10000 0 -10000 0 0
FRAT1 0.016 0.011 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.001 0.1 -10000 0 -0.43 17 17
PPP2R5D 0.051 0.11 0.24 107 -0.39 10 117
MAPK1 0.02 0.002 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.047 0.038 -10000 0 -0.24 4 4
RBPJ 0.02 0.003 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.004 0.056 -10000 0 -0.7 1 1
SMARCC2 0.02 0.003 -10000 0 -10000 0 0
SMARCC1 0.015 0.009 -10000 0 -10000 0 0
TBX21 0.045 0.11 0.28 30 -10000 0 30
SUMO2 0.008 0.021 -10000 0 -10000 0 0
STAT1 (dimer) 0.021 0.012 0.27 1 -10000 0 1
FKBP4 0.019 0.004 -10000 0 -10000 0 0
FKBP5 0.02 0.027 0.19 6 -0.42 1 7
GR alpha/HSP90/FKBP51/HSP90 0.003 0.066 0.24 1 -10000 0 1
PRL -0.008 0.067 -10000 0 -0.54 2 2
cortisol/GR alpha (dimer)/TIF2 -0.008 0.13 0.46 3 -0.39 6 9
RELA 0.006 0.069 -10000 0 -0.25 15 15
FGG 0.058 0.17 0.39 45 -0.34 1 46
GR beta/TIF2 -0.005 0.079 0.25 1 -0.34 8 9
IFNG 0.039 0.17 0.37 25 -0.51 2 27
apoptosis -0.1 0.21 -10000 0 -0.52 84 84
CREB1 -0.011 0.1 -10000 0 -0.36 43 43
histone acetylation -0.008 0.06 -10000 0 -0.32 3 3
BGLAP 0.006 0.058 -10000 0 -10000 0 0
GR/PKAc 0.007 0.068 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.009 0.13 0.33 1 -0.35 48 49
SMARCD1 0.02 0.003 -10000 0 -10000 0 0
MDM2 0.004 0.052 0.18 2 -10000 0 2
GATA3 -0.19 0.22 -10000 0 -0.42 255 255
AKT1 0.018 0.009 0.19 1 -10000 0 1
CSF2 -0.011 0.05 -10000 0 -10000 0 0
GSK3B 0.008 0.02 -10000 0 -10000 0 0
NR1I3 -0.072 0.21 0.4 1 -0.53 48 49
CSN2 0.016 0.14 0.34 14 -0.31 2 16
BRG1/BAF155/BAF170/BAF60A 0.037 0.025 -10000 0 -10000 0 0
NFATC1 0.02 0.004 -10000 0 -10000 0 0
POU2F1 0.02 0.004 -10000 0 -10000 0 0
CDKN1A 0.004 0.06 0.87 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN 0.022 0.081 0.19 41 -0.42 12 53
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.01 0.079 0.27 3 -0.25 8 11
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.043 0.24 0.41 5 -0.58 30 35
JUN -0.029 0.16 0.27 15 -0.4 39 54
IL4 0.004 0.059 -10000 0 -10000 0 0
CDK5R1 0.009 0.019 -10000 0 -10000 0 0
PRKACA 0.02 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 0.009 0.073 0.21 32 -0.25 3 35
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.008 0.069 -10000 0 -10000 0 0
cortisol/GR alpha (monomer) -0.009 0.15 0.52 3 -0.39 2 5
NCOA2 0.011 0.06 -10000 0 -0.42 10 10
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.032 0.085 0.17 14 -0.35 14 28
AP-1/NFAT1-c-4 0.008 0.2 0.38 16 -0.49 20 36
AFP -0.23 0.49 0.43 1 -1.2 104 105
SUV420H1 0.02 0.002 -10000 0 -10000 0 0
IRF1 -0.002 0.076 -10000 0 -0.34 1 1
TP53 0.022 0.007 -10000 0 -10000 0 0
PPP5C 0.02 0.002 -10000 0 -10000 0 0
KRT17 -0.042 0.27 0.38 4 -0.94 34 38
KRT14 0.024 0.092 0.42 1 -10000 0 1
TBP 0.02 0.007 -10000 0 -10000 0 0
CREBBP 0.002 0.04 -10000 0 -10000 0 0
HDAC1 0.019 0.004 -10000 0 -10000 0 0
HDAC2 0.017 0.01 -10000 0 -10000 0 0
AP-1 0.008 0.2 0.39 16 -0.5 20 36
MAPK14 0.008 0.021 -10000 0 -10000 0 0
MAPK10 0.005 0.047 -10000 0 -0.43 5 5
MAPK11 0.009 0.024 0.19 2 -10000 0 2
KRT5 0.015 0.16 0.38 17 -0.57 1 18
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.019 0.007 -10000 0 -10000 0 0
STAT1 0.021 0.012 0.28 1 -10000 0 1
CGA -0.069 0.28 -10000 0 -0.97 44 44
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.018 0.078 -10000 0 -0.41 3 3
MAPK3 0.009 0.02 -10000 0 -10000 0 0
MAPK1 0.008 0.021 -10000 0 -10000 0 0
ICAM1 -0.011 0.13 0.35 3 -0.46 15 18
NFKB1 0.005 0.074 -10000 0 -0.26 20 20
MAPK8 -0.006 0.11 0.23 17 -0.3 9 26
MAPK9 0.007 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.11 0.22 -10000 0 -0.54 86 86
BAX 0.008 0.029 -10000 0 -10000 0 0
POMC -0.02 0.12 -10000 0 -1.3 1 1
EP300 0.001 0.046 -10000 0 -0.47 1 1
cortisol/GR alpha (dimer)/p53 -0.003 0.13 0.46 3 -0.34 2 5
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.044 0.28 1 -10000 0 1
SGK1 -0.008 0.075 -10000 0 -10000 0 0
IL13 -0.11 0.21 0.43 2 -0.59 36 38
IL6 -0.032 0.24 0.33 11 -0.9 30 41
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.093 0.18 -10000 0 -0.61 6 6
IL2 -0.006 0.15 0.35 6 -0.58 3 9
CDK5 0.009 0.018 -10000 0 -10000 0 0
PRKACB 0.019 0.004 -10000 0 -10000 0 0
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
IL8 -0.016 0.17 0.34 6 -0.71 17 23
CDK5R1/CDK5 0.014 0.025 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.036 0.11 0.29 1 -0.34 21 22
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.001 0.12 0.44 3 -0.31 2 5
SMARCA4 0.02 0.002 -10000 0 -10000 0 0
chromatin remodeling -0.015 0.082 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp 0.01 0.12 0.3 1 -0.41 17 18
JUN (dimer) -0.029 0.16 0.27 15 -0.4 39 54
YWHAH 0.02 0.002 -10000 0 -10000 0 0
VIPR1 -0.005 0.098 -10000 0 -0.67 8 8
NR3C1 -0.01 0.091 0.32 3 -0.23 2 5
NR4A1 0.009 0.072 -10000 0 -0.42 14 14
TIF2/SUV420H1 0.022 0.046 -10000 0 -0.3 10 10
MAPKKK cascade -0.1 0.21 -10000 0 -0.52 84 84
cortisol/GR alpha (dimer)/Src-1 -0.004 0.13 0.46 3 -0.34 2 5
PBX1 0.006 0.075 -10000 0 -0.42 16 16
POU1F1 0.016 0.007 -10000 0 -10000 0 0
SELE -0.051 0.25 0.34 1 -0.88 37 38
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.016 0.083 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.001 0.12 0.44 3 -0.31 2 5
mol:cortisol -0.006 0.093 0.26 5 -0.2 11 16
MMP1 -0.02 0.26 0.35 7 -1 30 37
FAS signaling pathway (CD95)

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
SPTAN1 -0.016 0.032 0.22 1 -0.19 13 14
RFC1 -0.016 0.027 -10000 0 -0.18 10 10
PRKDC -0.014 0.04 0.22 6 -0.19 14 20
RIPK1 0.016 0.013 -10000 0 -10000 0 0
CASP7 0.004 0.093 -10000 0 -0.6 11 11
FASLG/FAS/FADD/FAF1 0.032 0.047 0.19 7 -10000 0 7
MAP2K4 0.014 0.14 0.26 8 -0.45 26 34
mol:ceramide 0.04 0.071 0.17 23 -0.26 3 26
GSN -0.016 0.032 0.22 1 -0.19 13 14
FASLG/FAS/FADD/FAF1/Caspase 8 0.036 0.055 0.23 3 -10000 0 3
FAS 0.017 0.014 -10000 0 -10000 0 0
BID -0.029 0.024 -10000 0 -10000 0 0
MAP3K1 0.016 0.12 0.26 8 -0.45 18 26
MAP3K7 0.017 0.011 -10000 0 -10000 0 0
RB1 -0.016 0.036 0.22 3 -0.19 14 17
CFLAR 0.016 0.013 -10000 0 -10000 0 0
HGF/MET 0.03 0.056 0.26 1 -0.27 14 15
ARHGDIB -0.013 0.044 0.22 10 -0.18 14 24
FADD 0.018 0.014 -10000 0 -10000 0 0
actin filament polymerization 0.016 0.032 0.19 13 -0.22 1 14
NFKB1 0.019 0.09 -10000 0 -0.57 7 7
MAPK8 0.003 0.16 0.28 9 -0.51 34 43
DFFA -0.016 0.028 -10000 0 -0.18 11 11
DNA fragmentation during apoptosis -0.016 0.028 -10000 0 -0.19 1 1
FAS/FADD/MET 0.033 0.025 -10000 0 -10000 0 0
CFLAR/RIP1 0.024 0.019 -10000 0 -10000 0 0
FAIM3 0.029 0.044 0.19 36 -10000 0 36
FAF1 0.018 0.015 -10000 0 -10000 0 0
PARP1 -0.017 0.032 -10000 0 -0.19 14 14
DFFB -0.016 0.028 -10000 0 -0.19 5 5
CHUK 0.011 0.075 -10000 0 -0.55 5 5
FASLG 0.1 0.088 0.19 258 -10000 0 258
FAS/FADD 0.026 0.02 -10000 0 -10000 0 0
HGF 0.014 0.062 0.19 10 -0.42 9 19
LMNA -0.019 0.027 0.19 1 -0.18 1 2
CASP6 -0.016 0.027 -10000 0 -0.18 10 10
CASP10 0.018 0.013 -10000 0 -10000 0 0
CASP3 -0.008 0.022 -10000 0 -0.25 2 2
PTPN13 0.012 0.057 -10000 0 -0.42 9 9
CASP8 -0.028 0.028 -10000 0 -10000 0 0
IL6 -0.019 0.27 -10000 0 -1 31 31
MET 0.019 0.012 0.19 2 -10000 0 2
ICAD/CAD -0.02 0.026 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 0.04 0.072 0.17 23 -0.26 3 26
activation of caspase activity by cytochrome c -0.029 0.024 -10000 0 -10000 0 0
PAK2 -0.012 0.046 0.22 11 -0.19 14 25
BCL2 0.02 0.003 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.003 0.065 0.22 20 -0.26 4 24
adherens junction organization -0.033 0.084 0.23 4 -0.28 22 26
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.012 0.068 0.22 19 -0.25 3 22
FMN1 -0.041 0.08 -10000 0 -0.28 29 29
mol:IP3 -0.016 0.045 -10000 0 -0.23 5 5
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.026 0.073 -10000 0 -0.28 22 22
CTNNB1 0.015 0.01 -10000 0 -10000 0 0
AKT1 -0.021 0.052 0.19 3 -0.25 4 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.076 0.13 -10000 0 -0.5 23 23
CTNND1 0.02 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.03 0.066 -10000 0 -0.26 22 22
VASP -0.033 0.069 -10000 0 -0.27 21 21
ZYX -0.031 0.067 -10000 0 -0.27 21 21
JUB -0.027 0.069 -10000 0 -0.26 22 22
EGFR(dimer) -0.019 0.076 -10000 0 -0.28 21 21
E-cadherin/beta catenin-gamma catenin 0.017 0.056 -10000 0 -0.25 19 19
mol:PI-3-4-5-P3 0.003 0.063 0.22 4 -0.27 5 9
PIK3CA 0.018 0.022 -10000 0 -0.42 1 1
PI3K 0.003 0.064 0.23 4 -0.28 5 9
FYN -0.15 0.11 0.2 5 -0.31 77 82
mol:Ca2+ -0.014 0.048 0.16 6 -0.23 5 11
JUP 0.02 0.033 -10000 0 -0.42 3 3
PIK3R1 0.017 0.022 -10000 0 -0.42 1 1
mol:DAG -0.016 0.045 -10000 0 -0.23 5 5
CDH1 0.007 0.077 -10000 0 -0.41 17 17
RhoA/GDP -0.005 0.064 0.22 19 -0.25 3 22
establishment of polarity of embryonic epithelium -0.033 0.068 -10000 0 -0.27 21 21
SRC 0.019 0.004 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
RHOA 0.014 0.009 -10000 0 -10000 0 0
EGFR 0.019 0.026 0.19 5 -0.42 1 6
CASR -0.15 0.1 0.2 5 -0.26 70 75
RhoA/GTP -0.019 0.041 0.16 1 -0.24 2 3
AKT2 -0.022 0.055 0.2 4 -0.28 4 8
actin cable formation -0.044 0.079 -10000 0 -0.29 27 27
apoptosis 0.004 0.078 0.26 5 -0.24 26 31
CTNNA1 0.014 0.011 -10000 0 -10000 0 0
mol:GDP -0.021 0.044 -10000 0 -0.25 5 5
PIP5K1A -0.031 0.067 -10000 0 -0.26 22 22
PLCG1 -0.016 0.046 -10000 0 -0.24 5 5
Rac1/GTP -0.011 0.077 -10000 0 -0.26 20 20
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 -0.018 0.005 -10000 0 -10000 0 0
SMARCC1 -0.04 0.066 -10000 0 -0.68 2 2
REL 0.016 0.034 -10000 0 -0.42 3 3
HDAC7 -0.17 0.082 -10000 0 -0.33 23 23
JUN 0.019 0.004 -10000 0 -10000 0 0
EP300 0.019 0.019 -10000 0 -0.42 1 1
KAT2B 0.014 0.021 -10000 0 -0.42 1 1
KAT5 0.02 0.002 -10000 0 -10000 0 0
MAPK14 -0.039 0.028 -10000 0 -0.33 3 3
FOXO1 0.02 0.003 -10000 0 -10000 0 0
T-DHT/AR -0.18 0.084 -10000 0 -0.34 24 24
MAP2K6 -0.028 0.036 -10000 0 -0.44 3 3
BRM/BAF57 0.028 0.008 -10000 0 -10000 0 0
MAP2K4 -0.025 0.019 -10000 0 -10000 0 0
SMARCA2 0.019 0.005 -10000 0 -10000 0 0
PDE9A -0.15 0.13 -10000 0 -0.75 18 18
NCOA2 0.011 0.06 -10000 0 -0.42 10 10
CEBPA 0.022 0.024 0.19 10 -10000 0 10
EHMT2 0.019 0.004 -10000 0 -10000 0 0
cell proliferation -0.17 0.13 0.46 5 -0.39 44 49
NR0B1 0.028 0.04 0.19 31 -10000 0 31
EGR1 0.008 0.056 -10000 0 -0.41 9 9
RXRs/9cRA 0.036 0.014 -10000 0 -10000 0 0
AR/RACK1/Src -0.064 0.064 0.23 4 -0.32 5 9
AR/GR -0.048 0.074 -10000 0 -0.32 25 25
GNB2L1 0.016 0.009 -10000 0 -10000 0 0
PKN1 0.02 0.002 -10000 0 -10000 0 0
RCHY1 0.02 0.002 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.04 0.023 -10000 0 -0.31 2 2
T-DHT/AR/TIF2/CARM1 -0.087 0.068 0.22 2 -0.36 13 15
SRC -0.069 0.038 0.22 1 -0.27 4 5
NR3C1 0.016 0.011 0.19 1 -10000 0 1
KLK3 0.024 0.07 0.37 1 -10000 0 1
APPBP2 -0.026 0.018 -10000 0 -10000 0 0
TRIM24 0.018 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.089 0.055 0.22 2 -0.33 9 11
TMPRSS2 -0.84 0.32 -10000 0 -0.96 461 461
RXRG 0.02 0.014 0.19 3 -10000 0 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.02 0.004 -10000 0 -10000 0 0
RXRB 0.019 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.002 -10000 0 -10000 0 0
NR2C2 0.014 0.021 -10000 0 -0.41 1 1
KLK2 -0.052 0.07 0.33 2 -0.36 7 9
AR -0.053 0.063 -10000 0 -0.3 23 23
SENP1 0.02 0.003 -10000 0 -10000 0 0
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
MDM2 0.018 0.01 -10000 0 -10000 0 0
SRY -0.001 0.003 -10000 0 -0.017 18 18
GATA2 0.01 0.063 -10000 0 -0.42 11 11
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.052 0.067 0.19 101 -10000 0 101
T-DHT/AR/RACK1/Src -0.069 0.063 0.25 3 -0.3 7 10
positive regulation of transcription 0.01 0.062 -10000 0 -0.42 11 11
DNAJA1 -0.025 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.002 -10000 0 -10000 0 0
NCOA1 0.041 0.029 -10000 0 -10000 0 0
SPDEF 0.054 0.068 0.19 106 -10000 0 106
T-DHT/AR/TIF2 -0.076 0.085 0.18 1 -0.37 20 21
T-DHT/AR/Hsp90 -0.084 0.057 0.22 2 -0.32 8 10
GSK3B -0.015 0.015 -10000 0 -10000 0 0
NR2C1 0.019 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.072 0.037 -10000 0 -0.28 5 5
SIRT1 0.02 0.004 -10000 0 -10000 0 0
ZMIZ2 0.016 0.011 -10000 0 -10000 0 0
POU2F1 -0.091 0.046 -10000 0 -0.17 6 6
T-DHT/AR/DAX-1 -0.084 0.059 0.24 2 -0.32 9 11
CREBBP 0.019 0.004 -10000 0 -10000 0 0
SMARCE1 0.02 0.003 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A -0.006 0.037 -10000 0 -10000 0 0
BIRC5 0.067 0.076 0.19 148 -10000 0 148
NFKBIA -0.015 0.025 0.26 2 -10000 0 2
CPEB1 -0.054 0.17 0.19 13 -0.42 93 106
AKT1 -0.015 0.022 0.28 1 -10000 0 1
NDEL1 0.02 0.003 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.005 0.034 -10000 0 -10000 0 0
NDEL1/TACC3 0.003 0.043 -10000 0 -10000 0 0
GADD45A 0.019 0.004 -10000 0 -10000 0 0
GSK3B 0.002 0.025 -10000 0 -10000 0 0
PAK1/Aurora A -0.005 0.04 -10000 0 -10000 0 0
MDM2 0.019 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.009 0.053 0.11 112 -10000 0 112
TP53 0.002 0.016 -10000 0 -0.22 1 1
DLG7 -0.01 0.017 -10000 0 -10000 0 0
AURKAIP1 0.018 0.028 0.19 1 -0.42 2 3
ARHGEF7 0.02 0.003 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.003 0.046 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.034 -10000 0 -10000 0 0
AURKA -0.011 0.023 -10000 0 -10000 0 0
AURKB 0.047 0.047 0.11 155 -10000 0 155
CDC25B -0.001 0.017 -10000 0 -10000 0 0
G2/M transition checkpoint -0.014 0.026 -10000 0 -10000 0 0
mRNA polyadenylation -0.043 0.096 0.18 1 -0.23 91 92
Aurora A/CPEB -0.043 0.096 0.18 1 -0.23 91 92
Aurora A/TACC1/TRAP/chTOG 0.007 0.049 -10000 0 -10000 0 0
BRCA1 0.02 0.003 -10000 0 -10000 0 0
centrosome duplication -0.005 0.04 -10000 0 -10000 0 0
regulation of centrosome cycle 0.003 0.042 -10000 0 -10000 0 0
spindle assembly 0.007 0.048 -10000 0 -10000 0 0
TDRD7 0.019 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.041 0.057 0.24 1 -10000 0 1
CENPA 0.045 0.046 0.15 15 -10000 0 15
Aurora A/PP2A -0.005 0.037 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.017 0.036 -10000 0 -0.2 3 3
negative regulation of DNA binding 0.002 0.016 -10000 0 -0.22 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.029 0.005 -10000 0 -10000 0 0
RASA1 0.017 0.02 -10000 0 -0.42 1 1
Ajuba/Aurora A -0.014 0.026 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.013 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.023 -10000 0 -10000 0 0
TACC1 0.018 0.006 -10000 0 -10000 0 0
TACC3 0.021 0.015 0.19 4 -10000 0 4
Aurora A/Antizyme1 0.002 0.047 -10000 0 -0.24 2 2
Aurora A/RasGAP -0.004 0.038 -10000 0 -0.25 1 1
OAZ1 0.02 0.008 0.19 1 -10000 0 1
RAN 0.019 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.003 0.025 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.008 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.009 0.053 0.11 112 -10000 0 112
PPP2R5D 0.019 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.006 0.044 0.21 2 -10000 0 2
PAK1 0.02 0.002 -10000 0 -10000 0 0
CKAP5 0.02 0.002 -10000 0 -10000 0 0
IGF1 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
NCK2 0.019 0.004 -10000 0 -10000 0 0
PTK2 0.019 0.004 -10000 0 -10000 0 0
CRKL -0.014 0.028 0.15 9 -0.14 4 13
GRB2/SOS1/SHC 0.038 0.011 -10000 0 -10000 0 0
HRAS 0.02 0.008 0.19 1 -10000 0 1
IRS1/Crk -0.018 0.014 -10000 0 -0.14 4 4
IGF-1R heterotetramer/IGF1/PTP1B 0.04 0.022 0.19 3 -10000 0 3
AKT1 -0.01 0.062 0.17 42 -0.39 1 43
BAD -0.015 0.06 0.15 42 -0.27 2 44
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.015 0.026 0.15 9 -10000 0 9
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.021 0.025 0.19 1 -10000 0 1
RAF1 -0.1 0.19 0.28 5 -0.43 129 134
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.044 0.025 -10000 0 -0.14 4 4
YWHAZ 0.019 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.023 0.019 -10000 0 -0.15 4 4
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
RPS6KB1 -0.008 0.068 0.17 50 -0.39 1 51
GNB2L1 0.015 0.009 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.086 0.16 0.27 13 -0.35 131 144
PXN 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.029 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.028 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.055 0.023 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.023 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.035 0.023 -10000 0 -0.14 4 4
Crk/p130 Cas/Paxillin 0.039 0.029 0.2 2 -0.22 1 3
IGF1R 0.023 0.013 -10000 0 -10000 0 0
IGF1 0.023 0.021 0.2 5 -10000 0 5
IRS2/Crk -0.019 0.028 0.14 10 -10000 0 10
PI3K 0.041 0.033 -10000 0 -0.16 5 5
apoptosis 0.013 0.067 0.29 1 -0.25 13 14
HRAS/GDP 0.015 0.005 0.13 1 -10000 0 1
PRKCD 0.004 0.024 -10000 0 -10000 0 0
RAF1/14-3-3 E -0.1 0.17 0.28 8 -0.37 139 147
BAD/14-3-3 -0.014 0.069 0.26 13 -0.31 1 14
PRKCZ -0.01 0.064 0.16 45 -0.3 2 47
Crk/p130 Cas/Paxillin/FAK1 -0.03 0.05 -10000 0 -0.36 1 1
PTPN1 0.019 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.005 0.017 -10000 0 -10000 0 0
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.043 0.024 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.019 0.022 -10000 0 -0.14 4 4
GRB10 0.018 0.006 -10000 0 -10000 0 0
PTPN11 -0.014 0.029 0.15 10 -10000 0 10
IRS1 -0.011 0.025 0.11 15 -0.15 4 19
IRS2 -0.013 0.032 0.15 12 -0.14 4 16
IGF-1R heterotetramer/IGF1 0.032 0.024 0.21 3 -10000 0 3
GRB2 0.02 0.003 -10000 0 -10000 0 0
PDPK1 -0.005 0.068 0.18 45 -0.4 1 46
YWHAE 0.02 0.003 -10000 0 -10000 0 0
PRKD1 0.009 0.035 -10000 0 -0.34 1 1
SHC1 0.019 0.004 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.034 0.053 0.41 3 -10000 0 3
CRKL 0.02 0.078 0.31 20 -10000 0 20
mol:DAG 0.018 0.048 0.17 1 -10000 0 1
HRAS 0.01 0.088 0.33 22 -10000 0 22
MAPK8 0.018 0.061 0.16 53 -0.22 2 55
RAP1A 0.021 0.079 0.32 20 -10000 0 20
GAB1 0.019 0.075 0.3 18 -10000 0 18
MAPK14 0.019 0.06 0.16 55 -10000 0 55
EPO 0.068 0.082 0.18 168 -10000 0 168
PLCG1 0.018 0.048 0.17 1 -10000 0 1
EPOR/TRPC2/IP3 Receptors 0.024 0.012 -10000 0 -10000 0 0
RAPGEF1 0.019 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.07 0.055 0.22 5 -10000 0 5
GAB1/SHC/GRB2/SOS1 0.013 0.065 0.24 9 -10000 0 9
EPO/EPOR (dimer) 0.064 0.058 0.19 2 -10000 0 2
IRS2 0.021 0.078 0.31 21 -10000 0 21
STAT1 0.02 0.049 0.19 1 -10000 0 1
STAT5B 0.019 0.049 0.19 1 -10000 0 1
cell proliferation 0.012 0.069 0.18 58 -0.21 2 60
GAB1/SHIP/PIK3R1/SHP2/SHC -0.002 0.049 -10000 0 -10000 0 0
TEC 0.019 0.075 0.3 18 -10000 0 18
SOCS3 0.021 0.015 0.19 4 -10000 0 4
STAT1 (dimer) 0.02 0.048 0.19 1 -10000 0 1
JAK2 0.023 0.01 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
EPO/EPOR (dimer)/JAK2 0.072 0.054 0.28 1 -10000 0 1
EPO/EPOR 0.064 0.058 0.19 2 -10000 0 2
LYN 0.019 0.005 -10000 0 -10000 0 0
TEC/VAV2 0.016 0.061 0.23 9 -10000 0 9
elevation of cytosolic calcium ion concentration 0.024 0.012 -10000 0 -10000 0 0
SHC1 0.019 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.066 0.053 -10000 0 -10000 0 0
mol:IP3 0.018 0.048 0.17 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.014 0.067 0.28 10 -10000 0 10
SH2B3 0.022 0.009 -10000 0 -10000 0 0
NFKB1 0.019 0.061 0.16 56 -0.2 1 57
EPO/EPOR (dimer)/JAK2/SOCS3 0.027 0.037 0.15 1 -0.2 2 3
PTPN6 0.016 0.055 0.15 50 -10000 0 50
TEC/VAV2/GRB2 0.016 0.064 0.23 9 -10000 0 9
EPOR 0.024 0.012 -10000 0 -10000 0 0
INPP5D 0.02 0.015 0.19 4 -10000 0 4
mol:GDP 0.013 0.066 0.24 9 -10000 0 9
SOS1 0.02 0.003 -10000 0 -10000 0 0
PLCG2 0.018 0.036 0.19 4 -0.42 3 7
CRKL/CBL/C3G 0.015 0.065 0.23 9 -10000 0 9
VAV2 0.02 0.076 0.3 19 -10000 0 19
CBL 0.018 0.073 0.3 17 -10000 0 17
SHC/Grb2/SOS1 0.004 0.049 -10000 0 -10000 0 0
STAT5A 0.019 0.049 0.18 3 -10000 0 3
GRB2 0.02 0.003 -10000 0 -10000 0 0
STAT5 (dimer) 0.041 0.043 -10000 0 -10000 0 0
LYN/PLCgamma2 0.027 0.024 -10000 0 -0.3 2 2
PTPN11 0.019 0.004 -10000 0 -10000 0 0
BTK 0.044 0.085 0.21 57 -10000 0 57
BCL2 0.037 0.058 0.37 5 -10000 0 5
PLK2 and PLK4 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
PLK2 0.023 0.03 0.19 16 -9999 0 16
PLK4 0.021 0.013 0.19 3 -9999 0 3
regulation of centriole replication -0.013 0.023 0.1 19 -9999 0 19
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.019 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.015 0.039 0.14 1 -0.22 14 15
FRAP1 0.013 0.045 0.3 2 -10000 0 2
AKT1 0.001 0.064 0.16 45 -0.29 6 51
INSR 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.003 -10000 0 -10000 0 0
mol:GTP -0.011 0.063 0.17 12 -0.25 6 18
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.018 0.025 -10000 0 -0.23 2 2
TSC2 0.019 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.027 0.033 -10000 0 -0.25 4 4
TSC1 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.01 0.049 -10000 0 -0.22 22 22
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.011 0.037 -10000 0 -0.26 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.019 0.004 -10000 0 -10000 0 0
RPS6KB1 0.014 0.072 0.28 10 -0.3 6 16
MAP3K5 -0.013 0.051 0.18 1 -0.19 41 42
PIK3R1 0.018 0.02 -10000 0 -0.42 1 1
apoptosis -0.013 0.051 0.18 1 -0.19 41 42
mol:LY294002 0 0 0.001 1 -0.001 21 22
EIF4B 0.013 0.077 0.31 14 -0.27 6 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.025 0.058 0.26 5 -0.32 2 7
eIF4E/eIF4G1/eIF4A1 -0.013 0.022 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.018 0.05 -10000 0 -0.21 21 21
mTOR/RHEB/GTP/Raptor/GBL -0.003 0.045 0.21 8 -0.16 2 10
FKBP1A 0.019 0.004 -10000 0 -10000 0 0
RHEB/GTP -0.019 0.05 0.16 1 -0.27 3 4
mol:Amino Acids 0 0 0.001 1 -0.001 21 22
FKBP12/Rapamycin 0.014 0.006 -10000 0 -10000 0 0
PDPK1 -0.01 0.057 0.15 36 -0.23 13 49
EIF4E 0.02 0.002 -10000 0 -10000 0 0
ASK1/PP5C -0.016 0.16 -10000 0 -0.55 41 41
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.007 0.031 -10000 0 -0.24 5 5
TSC1/TSC2 -0.009 0.07 0.19 16 -0.27 6 22
tumor necrosis factor receptor activity 0 0 0.001 21 -0.001 1 22
RPS6 0.02 0.011 0.19 2 -10000 0 2
PPP5C 0.02 0.002 -10000 0 -10000 0 0
EIF4G1 0.019 0.004 -10000 0 -10000 0 0
IRS1 -0.003 0.049 -10000 0 -0.23 22 22
INS 0.018 0.002 -10000 0 -10000 0 0
PTEN 0.016 0.011 -10000 0 -10000 0 0
PDK2 -0.007 0.062 0.16 44 -0.22 12 56
EIF4EBP1 -0.053 0.28 -10000 0 -1 41 41
PIK3CA 0.019 0.02 -10000 0 -0.42 1 1
PPP2R5D 0.009 0.049 0.3 6 -10000 0 6
peptide biosynthetic process -0.019 0.015 0.17 3 -10000 0 3
RHEB 0.018 0.006 -10000 0 -10000 0 0
EIF4A1 0.02 0.003 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 48 -0.003 1 49
EEF2 -0.019 0.015 0.17 3 -10000 0 3
eIF4E/4E-BP1 -0.041 0.26 -10000 0 -0.94 41 41
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 -0.019 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.026 0.015 -10000 0 -0.24 1 1
CDKN1B -0.016 0.085 -10000 0 -0.34 22 22
CDKN1A -0.013 0.076 -10000 0 -0.32 26 26
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.019 0.005 -10000 0 -10000 0 0
FOXO3 -0.013 0.074 -10000 0 -0.36 16 16
AKT1 -0.015 0.079 -10000 0 -0.31 33 33
BAD 0.02 0.02 0.19 1 -0.42 1 2
AKT3 0.005 0.013 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.018 0.084 -10000 0 -0.32 35 35
AKT1/ASK1 -0.003 0.094 -10000 0 -0.32 31 31
BAD/YWHAZ 0.038 0.017 -10000 0 -0.26 1 1
RICTOR 0.018 0.006 -10000 0 -10000 0 0
RAF1 0.014 0.009 -10000 0 -10000 0 0
JNK cascade 0.004 0.091 0.31 32 -10000 0 32
TSC1 -0.013 0.075 -10000 0 -0.36 15 15
YWHAZ 0.019 0.005 -10000 0 -10000 0 0
AKT1/RAF1 -0.007 0.094 -10000 0 -0.34 25 25
EP300 0.019 0.019 -10000 0 -0.42 1 1
mol:GDP -0.014 0.079 -10000 0 -0.31 33 33
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.02 0.083 -10000 0 -0.32 35 35
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
TBC1D4 -0.008 0.011 -10000 0 -0.25 1 1
MAP3K5 0.019 0.005 -10000 0 -10000 0 0
MAPKAP1 0.019 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.005 0.079 0.32 12 -0.23 13 25
YWHAH 0.02 0.002 -10000 0 -10000 0 0
AKT1S1 -0.018 0.083 -10000 0 -0.34 22 22
CASP9 -0.013 0.073 -10000 0 -0.31 27 27
YWHAB 0.019 0.004 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.004 0.098 0.32 7 -0.33 23 30
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.035 0.019 -10000 0 -0.26 1 1
YWHAE 0.02 0.003 -10000 0 -10000 0 0
SRC 0.019 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.022 0.077 -10000 0 -0.31 23 23
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.001 0.026 -10000 0 -10000 0 0
CHUK -0.016 0.08 -10000 0 -0.32 30 30
BAD/BCL-XL -0.004 0.093 0.23 1 -0.34 23 24
mTORC2 0.023 0.009 -10000 0 -10000 0 0
AKT2 0.005 0.013 -10000 0 -0.28 1 1
FOXO1-3a-4/14-3-3 family -0.005 0.1 0.27 9 -0.41 13 22
PDPK1 0.018 0.019 -10000 0 -0.42 1 1
MDM2 -0.016 0.086 -10000 0 -0.32 34 34
MAPKKK cascade 0.007 0.093 0.33 25 -10000 0 25
MDM2/Cbp/p300 0.005 0.096 0.28 4 -0.33 23 27
TSC1/TSC2 -0.018 0.089 0.25 12 -0.34 22 34
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.092 0.27 4 -0.32 23 27
glucose import -0.013 0.03 0.19 5 -0.22 5 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 -0.003 0.052 0.22 3 -0.22 7 10
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.015 0.022 -10000 0 -0.23 5 5
GSK3A -0.017 0.083 -10000 0 -0.34 22 22
FOXO1 -0.017 0.083 -10000 0 -0.32 33 33
GSK3B -0.013 0.073 -10000 0 -0.34 17 17
SFN 0.022 0.081 0.19 41 -0.42 12 53
G1/S transition of mitotic cell cycle -0.021 0.089 0.28 5 -0.34 22 27
p27Kip1/14-3-3 family 0.013 0.058 0.26 2 -0.37 5 7
PRKACA 0.02 0.002 -10000 0 -10000 0 0
KPNA1 0.019 0.005 -10000 0 -10000 0 0
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
YWHAG 0.018 0.006 -10000 0 -10000 0 0
RHEB 0.018 0.006 -10000 0 -10000 0 0
CREBBP 0.019 0.004 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.004 0.069 -10000 0 -0.46 5 5
BAG4 0.018 0.02 -10000 0 -0.42 1 1
BAD 0.001 0.05 0.28 8 -0.19 3 11
NFKBIA 0.019 0.005 -10000 0 -10000 0 0
BIRC3 0.045 0.06 0.19 79 -10000 0 79
BAX 0.002 0.046 0.22 13 -0.18 2 15
EnzymeConsortium:3.1.4.12 0.005 0.028 0.11 14 -0.1 5 19
IKBKB 0 0.075 0.29 5 -0.44 5 10
MAP2K2 -0.004 0.052 0.23 14 -0.19 2 16
MAP2K1 -0.003 0.054 0.25 14 -0.19 1 15
SMPD1 0.005 0.032 0.2 7 -0.15 2 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.003 0.079 0.28 2 -0.48 5 7
MAP2K4 0.011 0.07 0.19 51 -0.18 2 53
protein ubiquitination 0.005 0.089 0.34 10 -0.45 5 15
EnzymeConsortium:2.7.1.37 -0.002 0.063 0.25 16 -0.22 1 17
response to UV 0 0.001 0.003 19 -0.002 1 20
RAF1 0.001 0.049 0.24 13 -0.19 2 15
CRADD 0.019 0.004 -10000 0 -10000 0 0
mol:ceramide 0.006 0.041 0.18 12 -0.15 5 17
I-kappa-B-alpha/RELA/p50/ubiquitin 0.026 0.007 -10000 0 -10000 0 0
MADD 0.02 0.002 -10000 0 -10000 0 0
MAP3K1 0.014 0.069 0.2 50 -0.19 2 52
TRADD 0.019 0.004 -10000 0 -10000 0 0
RELA/p50 0.02 0.002 -10000 0 -10000 0 0
MAPK3 -0.002 0.053 0.23 15 -0.19 1 16
MAPK1 -0.002 0.053 0.23 15 -0.2 1 16
p50/RELA/I-kappa-B-alpha 0.028 0.008 -10000 0 -10000 0 0
FADD 0 0.073 0.29 2 -0.46 5 7
KSR1 0.003 0.046 0.22 12 -0.19 2 14
MAPK8 0.005 0.073 0.19 49 -0.18 4 53
TRAF2 0.019 0.004 -10000 0 -10000 0 0
response to radiation 0 0.001 0.003 8 -10000 0 8
CHUK 0.002 0.07 0.26 2 -0.44 5 7
TNF R/SODD 0.026 0.017 -10000 0 -0.3 1 1
TNF 0.017 0.041 0.19 4 -0.42 4 8
CYCS 0.005 0.056 0.24 16 -0.18 2 18
IKBKG 0.001 0.076 0.27 4 -0.44 5 9
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.006 0.074 -10000 0 -0.48 5 5
RELA 0.02 0.002 -10000 0 -10000 0 0
RIPK1 0.019 0.004 -10000 0 -10000 0 0
AIFM1 -0.001 0.048 0.21 15 -0.18 2 17
TNF/TNF R/SODD 0.033 0.033 -10000 0 -0.26 5 5
TNFRSF1A 0.019 0.004 -10000 0 -10000 0 0
response to heat 0 0.001 0.003 8 -10000 0 8
CASP8 0.011 0.092 -10000 0 -0.66 9 9
NSMAF 0.003 0.073 0.27 3 -0.45 5 8
response to hydrogen peroxide 0 0.001 0.003 19 -0.002 1 20
BCL2 0.02 0.003 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0.015 -10000 0 -10000 0 0
AES 0.016 0.014 -10000 0 -10000 0 0
FBXW11 0.015 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.027 0.01 -10000 0 -10000 0 0
SMAD4 0.02 0.003 -10000 0 -10000 0 0
DKK2 0.02 0.059 0.19 17 -0.42 7 24
TLE1 0.015 0.014 -10000 0 -10000 0 0
MACF1 0.02 0.005 -10000 0 -10000 0 0
CTNNB1 0.018 0.11 0.31 26 -0.27 4 30
WIF1 0.004 0.042 0.19 1 -0.42 4 5
beta catenin/RanBP3 -0.002 0.074 0.34 2 -10000 0 2
KREMEN2 0.038 0.054 0.19 60 -10000 0 60
DKK1 0.018 0.057 0.19 14 -0.42 7 21
beta catenin/beta TrCP1 0.003 0.072 0.28 3 -0.26 3 6
FZD1 0.018 0.007 -10000 0 -10000 0 0
AXIN2 -0.007 0.11 0.55 9 -1.3 2 11
AXIN1 0.02 0.005 -10000 0 -10000 0 0
RAN 0.019 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin -0.018 0.12 -10000 0 -0.51 24 24
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.017 0.08 0.38 2 -0.48 4 6
Axin1/APC/GSK3 0.043 0.079 0.25 35 -10000 0 35
Axin1/APC/GSK3/beta catenin/Macf1 0.021 0.087 0.32 18 -0.29 1 19
HNF1A 0.012 0.04 -10000 0 -0.42 4 4
CTBP1 0.016 0.014 -10000 0 -10000 0 0
MYC 0.011 0.11 0.54 15 -10000 0 15
RANBP3 0.02 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.049 0.05 0.26 1 -0.26 5 6
NKD1 -0.09 0.19 -10000 0 -0.42 130 130
TCF4 0.016 0.014 -10000 0 -10000 0 0
TCF3 0.016 0.014 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.049 0.03 -10000 0 -10000 0 0
Ran/GTP 0.014 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.012 0.066 0.44 2 -0.48 3 5
LEF1 0.02 0.037 0.19 15 -0.42 1 16
DVL1 0.002 0.03 -10000 0 -0.26 2 2
CSNK2A1 0.02 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.023 0.083 0.38 2 -0.47 6 8
DKK1/LRP6/Kremen 2 0.048 0.049 0.26 3 -0.23 5 8
LRP6 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.012 0.014 -10000 0 -10000 0 0
NLK 0.02 0.004 -10000 0 -10000 0 0
CCND1 -0.005 0.061 0.67 1 -10000 0 1
WNT1 0.028 0.036 0.19 25 -10000 0 25
GSK3A 0.021 0.004 -10000 0 -10000 0 0
GSK3B 0.019 0.006 -10000 0 -10000 0 0
FRAT1 0.016 0.012 -10000 0 -10000 0 0
PPP2R5D 0.064 0.12 0.24 115 -0.35 12 127
APC -0.001 0.072 0.21 42 -10000 0 42
WNT1/LRP6/FZD1 0.022 0.033 0.18 3 -10000 0 3
CREBBP 0.016 0.014 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.019 0.048 0.27 4 -10000 0 4
PDGFB-D/PDGFRB/SLAP 0.028 0.03 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.03 0.024 -10000 0 -0.26 1 1
AKT1 0.022 0.13 0.34 58 -10000 0 58
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.044 0.065 0.28 14 -10000 0 14
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
FGR 0.024 0.11 0.32 7 -0.39 19 26
mol:Ca2+ 0.03 0.063 0.27 16 -0.29 2 18
MYC 0.048 0.11 0.44 21 -10000 0 21
SHC1 0.019 0.004 -10000 0 -10000 0 0
HRAS/GDP -0.001 0.059 0.15 66 -10000 0 66
LRP1/PDGFRB/PDGFB 0.031 0.018 -10000 0 -10000 0 0
GRB10 0.018 0.006 -10000 0 -10000 0 0
PTPN11 0.019 0.004 -10000 0 -10000 0 0
GO:0007205 0.03 0.063 0.27 16 -0.29 2 18
PTEN 0.019 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.003 -10000 0 -10000 0 0
GRB7 0.014 0.05 -10000 0 -0.42 7 7
PDGFB-D/PDGFRB/SHP2 0.023 0.014 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.022 0.014 -10000 0 -10000 0 0
cell cycle arrest 0.028 0.03 -10000 0 -10000 0 0
HRAS 0.02 0.008 0.19 1 -10000 0 1
HIF1A 0.015 0.13 0.32 56 -0.35 1 57
GAB1 0.033 0.071 0.31 11 -0.4 2 13
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.03 0.072 0.3 18 -0.32 2 20
PDGFB-D/PDGFRB 0.032 0.021 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.023 0.014 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.016 0.042 0.22 4 -10000 0 4
positive regulation of MAPKKK cascade 0.023 0.014 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
mol:IP3 0.03 0.063 0.27 16 -0.29 2 18
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.009 0.018 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.019 0.037 -10000 0 -0.3 6 6
SHB 0.019 0.004 -10000 0 -10000 0 0
BLK 0.009 0.13 0.31 4 -0.36 41 45
PTPN2 0.02 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.023 0.014 -10000 0 -10000 0 0
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
VAV2 0.034 0.077 0.31 15 -0.43 2 17
CBL 0.019 0.019 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/DEP1 0.023 0.014 -10000 0 -10000 0 0
LCK 0.025 0.11 0.32 8 -0.39 21 29
PDGFRB 0.015 0.011 -10000 0 -10000 0 0
ACP1 0.02 0.003 -10000 0 -10000 0 0
HCK 0.04 0.067 0.31 4 -10000 0 4
ABL1 0.034 0.084 0.28 18 -0.51 2 20
PDGFB-D/PDGFRB/CBL 0.028 0.067 0.28 8 -0.47 2 10
PTPN1 0.02 0.008 -10000 0 -10000 0 0
SNX15 0.02 0.002 -10000 0 -10000 0 0
STAT3 0.02 0.003 -10000 0 -10000 0 0
STAT1 0.02 0.009 0.19 1 -10000 0 1
cell proliferation 0.047 0.11 0.39 27 -10000 0 27
SLA 0.027 0.037 0.19 26 -10000 0 26
actin cytoskeleton reorganization -0.02 0.047 0.32 3 -10000 0 3
SRC 0.035 0.064 0.31 4 -10000 0 4
PI3K -0.03 0.024 -10000 0 -0.22 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.027 0.034 -10000 0 -0.26 5 5
SH2B2 0.019 0.016 0.19 4 -10000 0 4
PLCgamma1/SPHK1 0.044 0.066 0.29 13 -10000 0 13
LYN 0.022 0.099 0.31 5 -0.38 17 22
LRP1 0.02 0.003 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
STAT5B 0.02 0.003 -10000 0 -10000 0 0
STAT5A 0.02 0.003 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.042 0.036 -10000 0 -0.23 2 2
SPHK1 0.034 0.046 0.19 42 -10000 0 42
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG 0.03 0.063 0.27 16 -0.29 2 18
PLCG1 0.03 0.064 0.27 16 -0.3 2 18
NHERF/PDGFRB 0.03 0.022 -10000 0 -0.26 1 1
YES1 0.032 0.08 0.33 4 -0.6 3 7
cell migration 0.03 0.022 -10000 0 -0.26 1 1
SHC/Grb2/SOS1 0.043 0.03 -10000 0 -10000 0 0
SLC9A3R2 0.018 0.019 -10000 0 -0.42 1 1
SLC9A3R1 0.02 0.003 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.036 0.027 -10000 0 -0.24 1 1
FYN 0.011 0.12 0.31 6 -0.36 33 39
DOK1 0.016 0.076 0.16 115 -10000 0 115
HRAS/GTP 0.015 0.005 0.13 1 -10000 0 1
PDGFB 0.02 0.002 -10000 0 -10000 0 0
RAC1 0.047 0.1 0.39 20 -0.4 2 22
PRKCD 0.004 0.058 0.16 60 -10000 0 60
FER -0.007 0.051 0.16 39 -0.24 2 41
MAPKKK cascade 0.006 0.086 0.35 15 -10000 0 15
RASA1 0.001 0.062 0.16 66 -0.24 1 67
NCK1 0.018 0.02 -10000 0 -0.42 1 1
NCK2 0.019 0.004 -10000 0 -10000 0 0
p62DOK/Csk 0.013 0.077 0.16 113 -10000 0 113
PDGFB-D/PDGFRB/SHB 0.022 0.014 -10000 0 -10000 0 0
chemotaxis 0.034 0.083 0.27 20 -0.49 2 22
STAT1-3-5/STAT1-3-5 0.036 0.025 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.011 0.008 -10000 0 -10000 0 0
PTPRJ 0.02 0.002 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.017 0.024 -10000 0 -0.42 1 1
HSPA8 0.015 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.019 0.046 -10000 0 -0.28 3 3
AKT1 0.019 0.006 -10000 0 -10000 0 0
GSC 0 0.12 -10000 0 -0.42 4 4
NKX2-5 0 0 -10000 0 -10000 0 0
muscle cell differentiation -0.038 0.041 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.064 0.04 0.24 1 -10000 0 1
SMAD4 0.017 0.025 -10000 0 -10000 0 0
CBFB 0.019 0.004 -10000 0 -10000 0 0
SAP18 0.019 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.036 0.029 -10000 0 -0.27 1 1
SMAD3/SMAD4/VDR 0.055 0.04 -10000 0 -0.23 4 4
MYC 0.024 0.033 0.19 19 -10000 0 19
CDKN2B -0.015 0.11 -10000 0 -0.47 13 13
AP1 0.014 0.041 -10000 0 -0.22 7 7
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.005 0.072 -10000 0 -0.39 11 11
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.024 -10000 0 -10000 0 0
SP3 0.019 0.004 -10000 0 -10000 0 0
CREB1 0.019 0.004 -10000 0 -10000 0 0
FOXH1 0.034 0.047 0.2 40 -10000 0 40
SMAD3/SMAD4/GR 0.023 0.039 -10000 0 -10000 0 0
GATA3 -0.19 0.22 -10000 0 -0.41 255 255
SKI/SIN3/HDAC complex/NCoR1 -0.011 0.087 -10000 0 -0.39 21 21
MEF2C/TIF2 -0.008 0.054 0.3 6 -10000 0 6
endothelial cell migration -0.026 0.082 -10000 0 -10000 0 0
MAX 0.009 0.023 -10000 0 -10000 0 0
RBBP7 0.02 0.003 -10000 0 -10000 0 0
RBBP4 0.018 0.02 -10000 0 -0.42 1 1
RUNX2 0.024 0.027 0.19 14 -10000 0 14
RUNX3 0.092 0.084 0.19 227 -10000 0 227
RUNX1 0.03 0.042 0.19 35 -10000 0 35
CTBP1 0.02 0.003 -10000 0 -10000 0 0
NR3C1 0.008 0.023 0.19 1 -10000 0 1
VDR 0.017 0.033 -10000 0 -0.42 3 3
CDKN1A 0 0.081 -10000 0 -0.57 3 3
KAT2B 0.012 0.023 -10000 0 -0.42 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.057 0.047 0.25 12 -10000 0 12
DCP1A 0.015 0.009 -10000 0 -10000 0 0
SKI 0.019 0.005 -10000 0 -10000 0 0
SERPINE1 0.027 0.08 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 0.034 0.035 -10000 0 -0.27 1 1
SMAD3/SMAD4/ATF3 0.031 0.043 -10000 0 -0.28 4 4
SAP30 0.025 0.031 0.19 18 -10000 0 18
Cbp/p300/PIAS3 0.035 0.032 -10000 0 -0.27 1 1
JUN -0.014 0.039 0.26 1 -10000 0 1
SMAD3/SMAD4/IRF7 0.039 0.041 -10000 0 -0.28 1 1
TFE3 0.023 0.007 -10000 0 -10000 0 0
COL1A2 0.037 0.065 0.3 1 -10000 0 1
mesenchymal cell differentiation -0.037 0.038 -10000 0 -0.2 3 3
DLX1 0.11 0.085 0.19 272 -10000 0 272
TCF3 0.02 0.002 -10000 0 -10000 0 0
FOS 0.007 0.065 0.18 1 -0.42 11 12
SMAD3/SMAD4/Max 0.027 0.042 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.034 0.025 -10000 0 -0.27 1 1
ZBTB17 0.016 0.029 -10000 0 -0.43 2 2
LAMC1 -0.013 0.03 0.22 2 -10000 0 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.035 0.033 -10000 0 -10000 0 0
IRF7 0.025 0.036 0.19 18 -0.42 1 19
ESR1 0.008 0.04 0.16 1 -0.42 3 4
HNF4A -0.012 0.11 -10000 0 -0.42 38 38
MEF2C 0.001 0.056 0.31 9 -10000 0 9
SMAD2-3/SMAD4 0.04 0.035 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.034 0.028 -10000 0 -0.27 1 1
IGHV3OR16-13 0.003 0.05 -10000 0 -0.35 10 10
TGIF2/HDAC complex 0.019 0.004 -10000 0 -10000 0 0
CREBBP 0.017 0.013 -10000 0 -10000 0 0
SKIL 0.019 0.005 -10000 0 -10000 0 0
HDAC1 0.019 0.005 -10000 0 -10000 0 0
HDAC2 0.018 0.006 -10000 0 -10000 0 0
SNIP1 0.014 0.014 -10000 0 -10000 0 0
GCN5L2 0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.049 0.031 -10000 0 -10000 0 0
MSG1/HSC70 0.028 0.013 -10000 0 -10000 0 0
SMAD2 0.023 0.008 -10000 0 -10000 0 0
SMAD3 0.012 0.026 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.023 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.032 0.068 0.18 1 -0.43 4 5
NCOR1 0.019 0.004 -10000 0 -10000 0 0
NCOA2 0.011 0.06 -10000 0 -0.42 10 10
NCOA1 0.02 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.035 0.027 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.069 0.044 0.26 2 -10000 0 2
IFNB1 -0.015 0.033 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.034 0.042 -10000 0 -10000 0 0
CITED1 0.021 0.011 0.19 2 -10000 0 2
SMAD2-3/SMAD4/ARC105 0.054 0.03 -10000 0 -10000 0 0
RBL1 0.019 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.002 0.025 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.086 0.063 0.26 12 -10000 0 12
SMAD7 0.013 0.05 -10000 0 -10000 0 0
MYC/MIZ-1 0.029 0.034 -10000 0 -0.33 2 2
SMAD3/SMAD4 0.01 0.054 -10000 0 -0.42 1 1
IL10 -0.12 0.12 0.24 3 -0.26 28 31
PIASy/HDAC complex 0.014 0.017 -10000 0 -10000 0 0
PIAS3 0.017 0.012 -10000 0 -10000 0 0
CDK2 0.017 0.013 -10000 0 -10000 0 0
IL5 -0.09 0.11 -10000 0 -0.28 3 3
CDK4 0.017 0.013 -10000 0 -10000 0 0
PIAS4 0.014 0.017 -10000 0 -10000 0 0
ATF3 0.016 0.038 -10000 0 -0.42 4 4
SMAD3/SMAD4/SP1 0.048 0.039 -10000 0 -10000 0 0
FOXG1 0.023 0.032 0.19 18 -10000 0 18
FOXO3 -0.016 0.009 -10000 0 -10000 0 0
FOXO1 -0.017 0.008 -10000 0 -10000 0 0
FOXO4 -0.017 0.008 -10000 0 -10000 0 0
heart looping 0.001 0.056 0.31 9 -10000 0 9
CEBPB 0.022 0.021 0.19 8 -10000 0 8
SMAD3/SMAD4/DLX1 0.092 0.069 0.21 8 -10000 0 8
MYOD1 0.028 0.039 0.19 29 -10000 0 29
SMAD3/SMAD4/HNF4 0.012 0.085 -10000 0 -0.27 38 38
SMAD3/SMAD4/GATA3 -0.11 0.16 -10000 0 -0.28 235 235
SnoN/SIN3/HDAC complex/NCoR1 0.019 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.098 0.069 0.26 12 -10000 0 12
SMAD3/SMAD4/SP1-3 0.058 0.038 -10000 0 -10000 0 0
MED15 0.02 0.002 -10000 0 -10000 0 0
SP1 0.025 0.011 -10000 0 -10000 0 0
SIN3B 0.02 0.003 -10000 0 -10000 0 0
SIN3A 0.02 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.055 0.045 0.24 12 -10000 0 12
ITGB5 -0.005 0.055 0.31 4 -10000 0 4
TGIF/SIN3/HDAC complex/CtBP 0.001 0.054 -10000 0 -0.37 7 7
SMAD3/SMAD4/AR 0.021 0.073 -10000 0 -0.27 25 25
AR -0.001 0.093 -10000 0 -0.42 25 25
negative regulation of cell growth 0.007 0.033 -10000 0 -0.31 1 1
SMAD3/SMAD4/MYOD 0.04 0.043 0.22 1 -10000 0 1
E2F5 0.018 0.02 -10000 0 -0.42 1 1
E2F4 0.019 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.051 0.053 0.23 8 -10000 0 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.006 0.016 -10000 0 -10000 0 0
TFDP1 0.02 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.034 0.044 -10000 0 -0.22 7 7
SMAD3/SMAD4/RUNX2 0.038 0.038 0.21 3 -10000 0 3
TGIF2 0.019 0.004 -10000 0 -10000 0 0
TGIF1 0.02 0.003 -10000 0 -10000 0 0
ATF2 0.018 0.019 -10000 0 -0.42 1 1
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.017 0.059 -9999 0 -0.27 19 19
E-cadherin/beta catenin 0.01 0.058 -9999 0 -0.3 17 17
CTNNB1 0.014 0.009 -9999 0 -10000 0 0
JUP 0.017 0.033 -9999 0 -0.42 3 3
CDH1 0.005 0.077 -9999 0 -0.42 17 17
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.086 0.078 -10000 0 -0.33 1 1
epithelial cell differentiation -0.066 0.085 -10000 0 -0.37 3 3
ITCH 0.046 0.017 -10000 0 -10000 0 0
WWP1 -0.096 0.057 -10000 0 -10000 0 0
FYN 0.019 0.005 -10000 0 -10000 0 0
EGFR 0.019 0.026 0.19 5 -0.42 1 6
PRL 0.018 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.09 0.069 0.3 4 -0.34 2 6
PTPRZ1 -0.024 0.13 0.19 6 -0.42 52 58
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.087 0.067 -10000 0 -0.31 9 9
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.091 0.062 -10000 0 -0.35 9 9
ADAM17 0.046 0.017 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.074 -10000 0 -0.36 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.071 -10000 0 -0.33 1 1
NCOR1 0.02 0.003 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.086 0.064 -10000 0 -0.33 9 9
GRIN2B -0.092 0.055 -10000 0 -0.32 9 9
ErbB4/ErbB2/betacellulin -0.12 0.089 -10000 0 -0.31 62 62
STAT1 0.02 0.009 0.19 1 -10000 0 1
HBEGF 0.015 0.009 -10000 0 -10000 0 0
PRLR -0.033 0.14 -10000 0 -0.42 61 61
E4ICDs/ETO2 -0.11 0.068 -10000 0 -0.33 1 1
axon guidance -0.064 0.072 -10000 0 -10000 0 0
NEDD4 0.045 0.032 -10000 0 -0.4 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.013 0.1 -10000 0 -0.3 61 61
CBFA2T3 0.02 0.011 0.19 2 -10000 0 2
ErbB4/ErbB2/HBEGF -0.065 0.061 -10000 0 -0.31 1 1
MAPK3 -0.09 0.066 0.33 2 -0.31 6 8
STAT1 (dimer) -0.11 0.069 -10000 0 -0.32 1 1
MAPK1 -0.09 0.067 0.32 3 -0.3 9 12
JAK2 0.019 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.095 0.056 -10000 0 -0.33 10 10
NRG1 0.009 0.043 -10000 0 -0.29 9 9
NRG3 0.022 0.023 0.19 10 -10000 0 10
NRG2 0.017 0.03 0.19 8 -0.42 1 9
NRG4 -0.009 0.11 0.19 8 -0.42 37 45
heart development -0.064 0.072 -10000 0 -10000 0 0
neural crest cell migration -0.094 0.055 -10000 0 -0.33 10 10
ERBB2 0.014 0.025 -10000 0 -0.3 2 2
WWOX/E4ICDs -0.11 0.069 -10000 0 -0.33 1 1
SHC1 0.019 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.11 0.091 -10000 0 -0.34 30 30
apoptosis 0.094 0.072 0.37 12 -10000 0 12
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.085 0.081 0.29 1 -0.32 2 3
ErbB4/ErbB2/epiregulin -0.082 0.062 -10000 0 -0.31 2 2
ErbB4/ErbB4/betacellulin/betacellulin -0.15 0.1 -10000 0 -0.36 63 63
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.097 0.098 -10000 0 -0.33 34 34
MDM2 -0.11 0.065 -10000 0 -0.33 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.068 0.053 -10000 0 -0.31 9 9
STAT5A -0.066 0.067 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.084 0.065 -10000 0 -0.34 10 10
DLG4 0.02 0.003 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.008 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.1 0.06 -10000 0 -0.3 1 1
STAT5A (dimer) -0.067 0.092 -10000 0 -0.39 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.063 0.077 0.33 1 -10000 0 1
LRIG1 0.016 0.008 -10000 0 -10000 0 0
EREG 0.029 0.044 0.19 31 -0.42 1 32
BTC -0.043 0.15 -10000 0 -0.42 76 76
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.061 0.071 -10000 0 -10000 0 0
ERBB4 -0.12 0.074 -10000 0 -0.36 1 1
STAT5B 0.02 0.003 -10000 0 -10000 0 0
YAP1 -0.026 0.037 -10000 0 -0.54 2 2
GRB2 0.02 0.003 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.099 0.079 -10000 0 -0.31 32 32
glial cell differentiation 0.1 0.06 0.3 1 -10000 0 1
WWOX 0.019 0.009 0.19 1 -10000 0 1
cell proliferation -0.093 0.12 0.31 1 -0.44 22 23
Osteopontin-mediated 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
IKK alpha homodimer -0.025 0.046 0.17 16 -0.23 7 23
NF kappa B1 p50/RelA/I kappa B alpha -0.025 0.073 0.3 10 -0.33 4 14
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.027 -10000 0 -0.29 3 3
AP1 -0.029 0.071 -10000 0 -0.4 4 4
ILK -0.02 0.046 -10000 0 -10000 0 0
bone resorption -0.033 0.053 0.22 1 -0.4 2 3
PTK2B 0.018 0.006 -10000 0 -10000 0 0
PYK2/p130Cas 0.034 0.046 -10000 0 -0.22 9 9
ITGAV 0.019 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.031 0.034 -10000 0 -0.3 3 3
alphaV/beta3 Integrin/Osteopontin 0.034 0.039 -10000 0 -0.26 7 7
MAP3K1 -0.019 0.046 0.17 19 -0.24 7 26
JUN 0.019 0.005 -10000 0 -10000 0 0
MAPK3 -0.026 0.047 0.17 14 -0.24 12 26
MAPK1 -0.026 0.046 0.17 16 -0.23 11 27
Rac1/GDP 0.013 0.005 -10000 0 -10000 0 0
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
MAPK8 -0.022 0.052 0.18 20 -0.28 7 27
ITGB3 0.015 0.043 -10000 0 -0.42 5 5
NFKBIA -0.022 0.048 0.23 1 -0.29 8 9
FOS 0.01 0.063 0.19 1 -0.42 11 12
CD44 0.026 0.031 0.19 18 -10000 0 18
CHUK 0.019 0.004 -10000 0 -10000 0 0
PLAU -0.026 0.14 0.49 3 -1 8 11
NF kappa B1 p50/RelA -0.037 0.067 0.28 5 -0.35 6 11
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
RELA 0.02 0.002 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.025 0.034 -10000 0 -0.3 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.02 0.048 0.17 22 -0.24 8 30
VAV3 -0.028 0.056 0.16 20 -0.24 18 38
MAP3K14 -0.021 0.048 0.18 18 -0.23 8 26
ROCK2 0.017 0.033 -10000 0 -0.42 3 3
SPP1 0.017 0.034 -10000 0 -0.41 3 3
RAC1 0.018 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.029 0.048 0.16 15 -0.23 15 30
MMP2 -0.028 0.07 0.34 3 -0.42 3 6
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0 0.075 -10000 0 -0.25 41 41
cell-cell adhesion 0.036 0.033 0.22 11 -10000 0 11
Ephrin B/EPHB2/RasGAP 0.043 0.046 -10000 0 -0.23 10 10
ITSN1 0.019 0.004 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
SHC1 0.019 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.02 0.04 -10000 0 -0.25 11 11
Ephrin B1/EPHB1 0.025 0.02 -10000 0 -0.25 2 2
HRAS/GDP 0.021 0.046 -10000 0 -0.25 9 9
Ephrin B/EPHB1/GRB7 0.047 0.049 -10000 0 -0.23 13 13
Endophilin/SYNJ1 -0.028 0.037 0.17 7 -0.22 11 18
KRAS 0.019 0.004 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.049 0.041 -10000 0 -0.23 8 8
endothelial cell migration 0.034 0.024 -10000 0 -0.22 2 2
GRB2 0.02 0.003 -10000 0 -10000 0 0
GRB7 0.014 0.05 -10000 0 -0.42 7 7
PAK1 -0.032 0.042 0.22 3 -0.22 9 12
HRAS 0.02 0.008 0.19 1 -10000 0 1
RRAS -0.028 0.038 0.17 9 -0.22 9 18
DNM1 0.023 0.024 0.19 11 -10000 0 11
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.026 0.037 0.16 12 -0.22 7 19
lamellipodium assembly -0.036 0.033 -10000 0 -0.22 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.006 0.039 -10000 0 -0.3 4 4
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
EPHB2 0.017 0.04 0.19 2 -0.42 4 6
EPHB3 0.01 0.063 -10000 0 -0.42 11 11
EPHB1 0.018 0.029 0.19 2 -0.42 2 4
EPHB4 0.018 0.006 -10000 0 -10000 0 0
mol:GDP -0.015 0.044 0.26 5 -0.27 6 11
Ephrin B/EPHB2 0.039 0.038 -10000 0 -0.22 9 9
Ephrin B/EPHB3 0.035 0.051 -10000 0 -0.24 16 16
JNK cascade -0.026 0.046 0.29 7 -0.27 5 12
Ephrin B/EPHB1 0.04 0.037 -10000 0 -0.22 8 8
RAP1/GDP -0.007 0.076 0.21 38 -0.29 2 40
EFNB2 0.02 0.003 -10000 0 -10000 0 0
EFNB3 0.015 0.047 -10000 0 -0.42 6 6
EFNB1 0.02 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.032 0.033 -10000 0 -0.29 4 4
RAP1B 0.019 0.004 -10000 0 -10000 0 0
RAP1A 0.019 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.022 0.051 -10000 0 -0.28 10 10
Rap1/GTP -0.042 0.034 -10000 0 -0.23 10 10
axon guidance 0 0.075 -10000 0 -0.25 41 41
MAPK3 -0.018 0.046 0.17 3 -0.3 6 9
MAPK1 -0.017 0.046 0.17 3 -0.3 6 9
Rac1/GDP -0.019 0.05 0.23 6 -0.25 9 15
actin cytoskeleton reorganization -0.037 0.035 -10000 0 -0.22 9 9
CDC42/GDP -0.003 0.078 0.21 45 -0.26 7 52
PI3K 0.037 0.025 -10000 0 -0.22 2 2
EFNA5 -0.014 0.11 0.19 2 -0.42 38 40
Ephrin B2/EPHB4 0.024 0.009 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.002 0.042 -10000 0 -0.23 11 11
CDC42 0.019 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.042 0.033 -10000 0 -0.23 10 10
PTK2 0 0.089 0.54 14 -10000 0 14
MAP4K4 -0.026 0.046 0.29 7 -0.27 5 12
SRC 0.019 0.004 -10000 0 -10000 0 0
KALRN 0.019 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.026 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.002 0.12 0.34 42 -0.31 2 44
MAP2K1 -0.01 0.043 -10000 0 -0.3 7 7
WASL 0.018 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.044 0.039 -10000 0 -0.29 5 5
cell migration -0.002 0.078 0.28 14 -0.32 6 20
NRAS 0.019 0.004 -10000 0 -10000 0 0
SYNJ1 -0.029 0.037 0.17 7 -0.22 11 18
PXN 0.019 0.004 -10000 0 -10000 0 0
TF -0.014 0.048 0.17 7 -0.22 9 16
HRAS/GTP 0.024 0.043 -10000 0 -0.23 10 10
Ephrin B1/EPHB1-2 0.033 0.034 -10000 0 -0.29 4 4
cell adhesion mediated by integrin 0.021 0.038 0.24 6 -0.19 7 13
RAC1 0.018 0.006 -10000 0 -10000 0 0
mol:GTP 0.025 0.044 -10000 0 -0.24 11 11
RAC1-CDC42/GTP -0.043 0.045 -10000 0 -0.25 16 16
RASA1 0.017 0.02 -10000 0 -0.42 1 1
RAC1-CDC42/GDP -0.021 0.05 0.23 6 -0.29 2 8
ruffle organization 0.006 0.13 0.35 51 -0.38 1 52
NCK1 0.018 0.02 -10000 0 -0.42 1 1
receptor internalization -0.031 0.036 0.16 5 -0.22 11 16
Ephrin B/EPHB2/KALRN 0.046 0.044 -10000 0 -0.23 9 9
ROCK1 -0.02 0.042 0.17 11 -0.23 11 22
RAS family/GDP -0.037 0.035 -10000 0 -0.23 9 9
Rac1/GTP -0.037 0.035 -10000 0 -0.24 11 11
Ephrin B/EPHB1/Src/Paxillin 0.002 0.042 -10000 0 -0.23 8 8
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.026 0.013 -10000 0 -10000 0 0
CRKL 0.019 0.092 0.39 7 -0.47 7 14
mol:PIP3 0.007 0.046 -10000 0 -0.72 2 2
AKT1 0.002 0.057 -10000 0 -0.63 2 2
PTK2B 0.018 0.006 -10000 0 -10000 0 0
RAPGEF1 0.015 0.094 0.36 12 -0.45 7 19
RANBP10 0.019 0.004 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
HGF/MET/SHIP2 0.033 0.045 0.26 1 -0.26 9 10
MAP3K5 0.043 0.098 0.36 16 -0.41 8 24
HGF/MET/CIN85/CBL/ENDOPHILINS 0.042 0.048 0.26 1 -0.26 9 10
AP1 -0.015 0.054 0.14 5 -0.25 11 16
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0.004 -10000 0 -10000 0 0
apoptosis -0.05 0.24 -10000 0 -0.72 55 55
STAT3 (dimer) 0 0.056 0.2 1 -0.36 5 6
GAB1/CRKL/SHP2/PI3K 0.029 0.076 0.4 1 -0.41 9 10
INPP5D 0.02 0.015 0.19 4 -10000 0 4
CBL/CRK 0.03 0.092 0.33 11 -0.44 8 19
PTPN11 0.019 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.019 0.004 -10000 0 -10000 0 0
PTEN 0.019 0.004 -10000 0 -10000 0 0
ELK1 0.022 0.12 0.34 56 -10000 0 56
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.002 0.034 -10000 0 -0.26 5 5
PAK1 -0.003 0.056 0.39 1 -0.61 2 3
HGF/MET/RANBP10 0.032 0.045 0.26 1 -0.26 9 10
HRAS -0.004 0.088 -10000 0 -0.42 19 19
DOCK1 0.017 0.097 0.37 13 -0.44 8 21
GAB1 0.012 0.077 0.22 3 -0.46 8 11
CRK 0.017 0.086 0.29 8 -0.47 7 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.089 -10000 0 -0.46 15 15
JUN 0.019 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.002 0.026 0.12 1 -0.17 10 11
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
cell morphogenesis 0.026 0.14 0.36 52 -0.4 5 57
GRB2/SHC 0.023 0.03 -10000 0 -0.16 6 6
FOS 0.01 0.063 0.19 1 -0.42 11 12
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.022 0.11 0.34 56 -10000 0 56
HGF/MET/MUC20 0.022 0.041 0.24 1 -0.25 9 10
cell migration 0.023 0.029 -10000 0 -0.16 6 6
GRB2 0.02 0.003 -10000 0 -10000 0 0
CBL 0.019 0.019 -10000 0 -0.42 1 1
MET/RANBP10 0.026 0.013 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0 0.048 0.21 1 -0.28 9 10
MET/MUC20 0.014 0.009 0.13 2 -10000 0 2
RAP1B 0.018 0.11 0.4 19 -0.42 7 26
RAP1A 0.012 0.094 0.36 13 -0.42 7 20
HGF/MET/RANBP9 0.032 0.044 0.26 1 -0.25 9 10
RAF1 -0.004 0.087 -10000 0 -0.45 11 11
STAT3 -0.001 0.057 0.2 1 -0.36 5 6
cell proliferation 0.001 0.071 0.25 7 -0.36 9 16
RPS6KB1 0.003 0.039 -10000 0 -0.34 6 6
MAPK3 0.014 0.11 0.53 6 -10000 0 6
MAPK1 0.015 0.11 0.58 7 -10000 0 7
RANBP9 0.019 0.004 -10000 0 -10000 0 0
MAPK8 0.037 0.11 0.41 16 -0.39 11 27
SRC -0.015 0.044 0.19 1 -0.26 9 10
PI3K 0.023 0.035 -10000 0 -0.22 7 7
MET/Glomulin 0.011 0.023 0.14 2 -10000 0 2
SOS1 0.02 0.003 -10000 0 -10000 0 0
MAP2K1 0.002 0.091 0.26 2 -0.42 11 13
MET 0.019 0.012 0.19 2 -10000 0 2
MAP4K1 0.05 0.1 0.37 16 -0.43 8 24
PTK2 0.019 0.004 -10000 0 -10000 0 0
MAP2K2 0.003 0.094 0.33 4 -0.42 11 15
BAD -0.004 0.057 0.39 1 -0.61 2 3
MAP2K4 0.039 0.095 0.34 19 -0.38 8 27
SHP2/GRB2/SOS1/GAB1 0.022 0.061 -10000 0 -0.39 7 7
INPPL1 0.02 0.002 -10000 0 -10000 0 0
PXN 0.019 0.004 -10000 0 -10000 0 0
SH3KBP1 0.02 0.002 -10000 0 -10000 0 0
HGS -0.007 0.021 -10000 0 -0.16 7 7
PLCgamma1/PKC 0.014 0.003 -10000 0 -10000 0 0
HGF 0.014 0.062 0.19 10 -0.42 9 19
RASA1 0.017 0.02 -10000 0 -0.42 1 1
NCK1 0.018 0.02 -10000 0 -0.42 1 1
PTPRJ 0.02 0.002 -10000 0 -10000 0 0
NCK/PLCgamma1 0.024 0.035 -10000 0 -0.2 9 9
PDPK1 0.008 0.061 -10000 0 -0.67 2 2
HGF/MET/SHIP 0.033 0.045 0.26 1 -0.25 9 10
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.015 0.009 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.025 0.033 -10000 0 -0.3 5 5
PTK2 -0.015 0.084 -10000 0 -0.46 2 2
positive regulation of JNK cascade -0.018 0.1 -10000 0 -0.35 21 21
CDC42/GDP -0.016 0.14 0.33 3 -0.41 36 39
Rac1/GDP -0.019 0.13 -10000 0 -0.42 31 31
RAP1B 0.019 0.004 -10000 0 -10000 0 0
RAP1A 0.019 0.004 -10000 0 -10000 0 0
CTNNB1 0.014 0.009 -10000 0 -10000 0 0
CDC42/GTP -0.019 0.13 -10000 0 -0.43 21 21
nectin-3/I-afadin 0.024 0.023 -10000 0 -0.3 2 2
RAPGEF1 -0.032 0.12 0.26 2 -0.35 59 61
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.034 0.14 -10000 0 -0.39 62 62
PDGFB-D/PDGFRB 0.015 0.009 -10000 0 -10000 0 0
TLN1 -0.018 0.015 -10000 0 -10000 0 0
Rap1/GTP -0.02 0.097 -10000 0 -0.29 22 22
IQGAP1 0.02 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.024 0.023 -10000 0 -0.3 2 2
PVR 0.02 0.002 -10000 0 -10000 0 0
Necl-5(dimer) 0.02 0.002 -10000 0 -10000 0 0
mol:GDP -0.033 0.17 0.35 3 -0.5 36 39
MLLT4 0.018 0.006 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
PI3K 0.036 0.038 -10000 0 -0.23 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.027 0.009 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.016 0.1 -10000 0 -0.32 30 30
PVRL1 0.02 0.002 -10000 0 -10000 0 0
PVRL3 0.017 0.027 -10000 0 -0.42 2 2
PVRL2 0.02 0.002 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
CDH1 0.005 0.077 -10000 0 -0.42 17 17
CLDN1 0.017 0.035 0.19 2 -0.42 3 5
JAM-A/CLDN1 0.04 0.034 -10000 0 -0.24 5 5
SRC -0.035 0.15 -10000 0 -0.42 64 64
ITGB3 0.015 0.043 -10000 0 -0.42 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.027 0.009 -10000 0 -10000 0 0
FARP2 -0.032 0.17 -10000 0 -0.62 21 21
RAC1 0.018 0.006 -10000 0 -10000 0 0
CTNNA1 0.015 0.009 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.033 0.024 -10000 0 -0.26 2 2
nectin-1/I-afadin 0.027 0.009 -10000 0 -10000 0 0
nectin-2/I-afadin 0.027 0.009 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.024 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.034 0.024 -10000 0 -0.26 2 2
CDC42/GTP/IQGAP1/filamentous actin 0.026 0.006 -10000 0 -10000 0 0
F11R 0.019 0.004 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.018 0.1 -10000 0 -0.35 21 21
alphaV/beta3 Integrin/Talin -0.025 0.04 0.24 3 -0.34 1 4
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.027 0.009 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.027 0.009 -10000 0 -10000 0 0
PIP5K1C -0.009 0.011 -10000 0 -10000 0 0
VAV2 -0.031 0.17 -10000 0 -0.53 30 30
RAP1/GDP -0.014 0.13 -10000 0 -0.37 34 34
ITGAV 0.019 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.033 0.024 -10000 0 -0.26 2 2
nectin-3(dimer)/I-afadin/I-afadin 0.024 0.023 -10000 0 -0.3 2 2
Rac1/GTP -0.018 0.13 -10000 0 -0.4 29 29
PTPRM 0.003 0.012 -10000 0 -0.17 2 2
E-cadherin/beta catenin/alpha catenin 0.024 0.052 -10000 0 -0.22 13 13
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.019 0.004 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.002 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.019 0.085 -10000 0 -0.38 17 17
Syndecan-3/Neurocan 0.005 0.08 -10000 0 -0.39 20 20
POMC 0.019 0.019 -10000 0 -0.42 1 1
EGFR 0.019 0.026 0.19 5 -0.42 1 6
Syndecan-3/EGFR 0.003 0.076 -10000 0 -0.4 16 16
AGRP 0.017 0.027 -10000 0 -0.42 2 2
NCSTN 0.019 0.004 -10000 0 -10000 0 0
PSENEN 0.02 0.002 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.02 0.002 -10000 0 -10000 0 0
APH1A 0.019 0.004 -10000 0 -10000 0 0
NCAN 0.024 0.026 0.19 13 -10000 0 13
long-term memory 0.015 0.078 -10000 0 -0.37 20 20
Syndecan-3/IL8 0.006 0.087 -10000 0 -0.39 20 20
PSEN1 0.019 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.029 0.006 -10000 0 -10000 0 0
FYN 0.019 0.005 -10000 0 -10000 0 0
limb bud formation -0.01 0.077 -10000 0 -0.4 20 20
MC4R 0.021 0.022 0.19 9 -10000 0 9
SRC 0.019 0.004 -10000 0 -10000 0 0
PTN 0.008 0.066 0.19 1 -0.42 12 13
FGFR/FGF/Syndecan-3 -0.01 0.078 -10000 0 -0.4 20 20
neuron projection morphogenesis -0.02 0.087 -10000 0 -0.38 16 16
Syndecan-3/AgRP 0.001 0.079 -10000 0 -0.39 20 20
Syndecan-3/AgRP/MC4R 0.015 0.083 -10000 0 -0.38 20 20
Fyn/Cortactin 0.028 0.008 -10000 0 -10000 0 0
SDC3 -0.01 0.078 -10000 0 -0.4 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.006 0.086 -10000 0 -0.38 20 20
IL8 0.022 0.063 0.19 26 -0.42 7 33
Syndecan-3/Fyn/Cortactin 0.016 0.08 -10000 0 -0.38 20 20
Syndecan-3/CASK -0.01 0.074 -10000 0 -0.38 20 20
alpha-MSH/MC4R 0.029 0.022 -10000 0 -0.3 1 1
Gamma Secretase 0.052 0.022 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.015 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.086 0.21 2 -0.32 12 14
NFATC4 -0.033 0.05 0.24 7 -10000 0 7
ERBB2IP 0.017 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.019 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.015 0.059 -10000 0 -0.24 18 18
JUN 0.025 0.064 0.25 10 -10000 0 10
HRAS 0.021 0.008 0.19 1 -10000 0 1
DOCK7 -0.039 0.046 -10000 0 -0.24 13 13
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.054 -10000 0 -0.23 20 20
AKT1 -0.01 0.005 -10000 0 -10000 0 0
BAD -0.015 0.012 -10000 0 -0.26 1 1
MAPK10 -0.023 0.047 0.17 7 -0.23 2 9
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.016 0.063 -10000 0 -0.25 18 18
RAF1 0.013 0.089 0.31 11 -0.42 6 17
ErbB2/ErbB3/neuregulin 2 -0.007 0.042 0.14 2 -0.24 9 11
STAT3 0.013 0.098 -10000 0 -0.9 6 6
cell migration -0.004 0.078 0.24 26 -0.2 5 31
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation 0.002 0.17 0.46 6 -0.53 3 9
FOS 0.008 0.14 0.37 8 -0.45 12 20
NRAS 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.059 -10000 0 -0.24 18 18
MAPK3 0.004 0.15 0.44 6 -0.47 3 9
MAPK1 0.004 0.15 0.42 7 -0.53 4 11
JAK2 -0.037 0.045 -10000 0 -0.23 12 12
NF2 0.002 0.032 -10000 0 -0.7 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.011 0.07 0.17 4 -0.33 19 23
NRG1 0.007 0.068 -10000 0 -0.42 13 13
GRB2/SOS1 0.029 0.007 -10000 0 -10000 0 0
MAPK8 -0.021 0.07 -10000 0 -0.28 18 18
MAPK9 -0.022 0.037 0.17 4 -0.21 1 5
ERBB2 -0.02 0.019 -10000 0 -0.3 2 2
ERBB3 0.01 0.054 -10000 0 -0.42 8 8
SHC1 0.02 0.005 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
apoptosis 0.008 0.016 0.23 1 -0.17 2 3
STAT3 (dimer) 0.014 0.096 -10000 0 -0.87 6 6
RNF41 -0.02 0.007 -10000 0 -10000 0 0
FRAP1 -0.008 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.036 0.032 -10000 0 -0.19 12 12
ErbB2/ErbB2/HSP90 (dimer) -0.021 0.018 -10000 0 -0.26 2 2
CHRNA1 0.032 0.15 0.37 11 -0.4 5 16
myelination -0.029 0.068 0.31 11 -10000 0 11
PPP3CB -0.037 0.043 -10000 0 -0.22 10 10
KRAS 0.02 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.008 0.074 0.26 1 -0.29 18 19
NRG2 0.017 0.03 0.19 8 -0.42 1 9
mol:GDP -0.011 0.069 0.17 4 -0.32 19 23
SOS1 0.02 0.004 -10000 0 -10000 0 0
MAP2K2 0.012 0.086 0.3 9 -0.4 6 15
SRC 0.019 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.04 0.044 -10000 0 -0.23 13 13
MAP2K1 -0.036 0.19 0.4 6 -0.48 22 28
heart morphogenesis -0.015 0.059 -10000 0 -0.24 18 18
RAS family/GDP 0.027 0.081 -10000 0 -0.33 12 12
GRB2 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.009 0.033 -10000 0 -0.73 1 1
CHRNE 0.008 0.02 0.13 7 -10000 0 7
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.01 0.005 -10000 0 -10000 0 0
nervous system development -0.015 0.059 -10000 0 -0.24 18 18
CDC42 0.019 0.004 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.018 0.027 -10000 0 -0.42 2 2
SPHK1 0.033 0.046 0.19 42 -10000 0 42
GNAI2 0.014 0.009 -10000 0 -10000 0 0
mol:S1P 0.009 0.025 -10000 0 -0.25 2 2
GNAO1 0.019 0.023 0.19 3 -0.42 1 4
mol:Sphinganine-1-P -0.009 0.04 0.32 1 -0.3 2 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.038 0.03 -10000 0 -0.2 2 2
GNAI3 0.019 0.004 -10000 0 -10000 0 0
G12/G13 0.026 0.01 -10000 0 -10000 0 0
S1PR3 0.019 0.004 -10000 0 -10000 0 0
S1PR2 0.02 0.002 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.004 0.022 -10000 0 -0.21 2 2
S1PR5 0.049 0.064 0.19 91 -10000 0 91
S1PR4 0.03 0.039 0.19 30 -10000 0 30
GNAI1 0.017 0.02 -10000 0 -0.42 1 1
S1P/S1P5/G12 0.046 0.051 0.18 12 -0.21 2 14
S1P/S1P3/Gq 0.006 0.072 -10000 0 -0.34 19 19
S1P/S1P4/Gi 0.009 0.045 0.2 2 -0.29 3 5
GNAQ 0.019 0.004 -10000 0 -10000 0 0
GNAZ 0.017 0.033 -10000 0 -0.42 3 3
GNA14 0.014 0.05 -10000 0 -0.42 7 7
GNA15 0.025 0.028 0.19 15 -10000 0 15
GNA12 0.018 0.006 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.017 0.033 -10000 0 -0.42 3 3
ABCC1 0.019 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.025 0.033 -10000 0 -0.3 5 5
AKT1 0.023 0.095 0.36 8 -0.5 4 12
PTK2B 0.004 0.063 0.25 12 -0.46 1 13
VEGFR2 homodimer/Frs2 -0.022 0.028 -10000 0 -0.43 2 2
CAV1 0.028 0.04 0.19 30 -10000 0 30
CALM1 0.019 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.072 0.064 0.25 3 -0.37 2 5
endothelial cell proliferation 0.034 0.11 0.4 25 -0.34 3 28
mol:Ca2+ 0.011 0.052 0.22 5 -0.31 1 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.073 0.061 0.25 2 -0.27 2 4
RP11-342D11.1 0.01 0.048 0.22 3 -0.47 1 4
CDH5 0.02 0.008 0.19 1 -10000 0 1
VEGFA homodimer 0.061 0.063 -10000 0 -0.23 2 2
SHC1 0.019 0.004 -10000 0 -10000 0 0
SHC2 0.02 0.031 0.19 4 -0.42 2 6
HRAS/GDP 0.011 0.06 -10000 0 -0.29 1 1
SH2D2A 0.072 0.079 0.19 164 -10000 0 164
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.06 0.067 0.29 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.1 0.077 0.24 62 -0.33 1 63
VEGFR1 homodimer 0.021 0.017 0.19 5 -10000 0 5
SHC/GRB2/SOS1 0.077 0.056 -10000 0 -0.3 1 1
GRB10 0.009 0.049 0.22 2 -0.31 1 3
PTPN11 0.019 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.003 -10000 0 -10000 0 0
PAK1 0.02 0.002 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.057 0.065 -10000 0 -0.48 1 1
HRAS 0.02 0.008 0.19 1 -10000 0 1
VEGF/Rho/ROCK1/Integrin Complex 0.003 0.067 -10000 0 -0.36 10 10
HIF1A 0.017 0.027 -10000 0 -0.42 2 2
FRS2 0.019 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.071 0.059 0.24 2 -0.27 2 4
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.015 0.009 -10000 0 -10000 0 0
Nck/Pak 0.028 0.016 -10000 0 -0.3 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.07 0.064 0.25 3 -0.37 2 5
mol:GDP 0.062 0.048 -10000 0 -0.3 1 1
mol:NADP 0.027 0.068 0.35 9 -10000 0 9
eNOS/Hsp90 0.027 0.057 0.28 5 -10000 0 5
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
mol:IP3 0.011 0.052 0.22 5 -0.31 1 6
HIF1A/ARNT 0.025 0.022 -10000 0 -0.3 2 2
SHB 0.019 0.004 -10000 0 -10000 0 0
VEGFA 0.094 0.084 0.19 232 -10000 0 232
VEGFC 0.02 0.008 0.19 1 -10000 0 1
FAK1/Vinculin 0.001 0.089 0.33 4 -0.4 7 11
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.014 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.075 0.068 -10000 0 -0.27 7 7
PTPN6 0.019 0.004 -10000 0 -10000 0 0
EPAS1 0.019 0.025 -10000 0 -0.37 2 2
mol:L-citrulline 0.027 0.068 0.35 9 -10000 0 9
ITGAV 0.019 0.004 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.079 0.063 0.25 3 -0.36 2 5
VEGFR2 homodimer/VEGFA homodimer 0.073 0.066 0.25 3 -0.31 4 7
VEGFR2/3 heterodimer -0.017 0.022 -10000 0 -0.33 2 2
VEGFB 0.02 0.002 -10000 0 -10000 0 0
MAPK11 0.008 0.048 0.28 5 -10000 0 5
VEGFR2 homodimer -0.019 0.031 -10000 0 -0.48 2 2
FLT1 0.021 0.017 0.19 5 -10000 0 5
NEDD4 0.019 0.027 -10000 0 -0.42 2 2
MAPK3 -0.001 0.051 0.31 4 -0.32 1 5
MAPK1 0.001 0.054 0.26 10 -10000 0 10
VEGFA145/NRP2 0.079 0.062 0.27 2 -10000 0 2
VEGFR1/2 heterodimer -0.02 0.031 -10000 0 -0.42 2 2
KDR -0.019 0.031 -10000 0 -0.49 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.068 0.063 0.24 5 -0.43 1 6
SRC 0.019 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.008 0.071 0.31 15 -0.3 1 16
PI3K 0.017 0.069 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.07 0.062 0.25 2 -0.27 3 5
FES 0.009 0.056 0.23 3 -0.49 1 4
GAB1 0.024 0.067 0.3 1 -0.42 1 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.073 0.061 0.25 3 -0.28 2 5
CTNNB1 0.014 0.009 -10000 0 -10000 0 0
SOS1 0.02 0.003 -10000 0 -10000 0 0
ARNT 0.019 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.023 0.054 0.27 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/Yes 0.072 0.063 0.25 3 -0.37 2 5
PI3K/GAB1 0.033 0.078 0.31 3 -0.38 3 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.081 0.061 -10000 0 -0.31 1 1
PRKACA 0.02 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.02 0.025 -10000 0 -0.31 2 2
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
CDC42 0.011 0.055 0.22 4 -0.47 1 5
actin cytoskeleton reorganization 0.1 0.076 0.24 62 -0.32 1 63
PTK2 0.005 0.066 0.26 3 -0.36 5 8
EDG1 0.01 0.048 0.22 3 -0.47 1 4
mol:DAG 0.011 0.052 0.22 5 -0.31 1 6
CaM/Ca2+ 0.01 0.051 0.21 2 -0.28 1 3
MAP2K3 0 0.048 0.24 4 -0.3 1 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.058 0.1 0.3 26 -0.32 1 27
PLCG1 0.011 0.053 0.22 5 -0.31 1 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.079 0.061 0.25 3 -0.27 2 5
IQGAP1 0.02 0.002 -10000 0 -10000 0 0
YES1 0.02 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.072 0.064 0.25 3 -0.37 2 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.072 0.064 0.25 3 -0.37 2 5
cell migration 0.001 0.094 0.34 5 -0.42 7 12
mol:PI-3-4-5-P3 0.017 0.066 0.21 2 -0.44 1 3
FYN 0.019 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.012 0.053 0.21 3 -0.45 1 4
mol:NO 0.027 0.068 0.35 9 -10000 0 9
PXN 0.019 0.004 -10000 0 -10000 0 0
HRAS/GTP -0.001 0.046 -10000 0 -0.28 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.045 0.088 0.24 26 -0.32 1 27
VHL 0.014 0.009 -10000 0 -10000 0 0
ITGB3 0.015 0.043 -10000 0 -0.42 5 5
NOS3 0.028 0.071 0.37 8 -10000 0 8
VEGFR2 homodimer/VEGFA homodimer/Sck 0.073 0.066 0.25 4 -0.33 3 7
RAC1 0.018 0.006 -10000 0 -10000 0 0
PRKCA 0 0.045 0.2 5 -0.3 1 6
PRKCB -0.002 0.044 0.2 4 -0.3 1 5
VCL 0.019 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.04 0.077 0.26 5 -0.47 1 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.073 0.064 0.25 6 -0.37 2 8
VEGFA165/NRP2 0.079 0.062 0.27 2 -10000 0 2
MAPKKK cascade 0.029 0.084 0.32 9 -10000 0 9
NRP2 0.021 0.02 0.19 7 -10000 0 7
VEGFC homodimer 0.02 0.008 0.19 1 -10000 0 1
NCK1 0.018 0.02 -10000 0 -0.42 1 1
ROCK1 0.02 0.003 -10000 0 -10000 0 0
FAK1/Paxillin 0.002 0.092 0.3 7 -0.4 7 14
MAP3K13 0.011 0.053 0.22 5 -0.31 1 6
PDPK1 0.005 0.06 0.26 2 -0.55 1 3
Signaling events mediated by PRL

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
CCNE1 0.022 0.019 0.19 7 -10000 0 7
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.018 0.006 -10000 0 -10000 0 0
CDKN1A -0.002 0.047 -10000 0 -0.32 10 10
PRL-3/alpha Tubulin 0.032 0.023 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.031 -10000 0 -0.3 1 1
AGT 0.021 0.048 0.19 16 -0.42 4 20
CCNA2 -0.003 0.052 0.23 19 -10000 0 19
TUBA1B 0.02 0.003 -10000 0 -10000 0 0
EGR1 -0.011 0.037 -10000 0 -0.29 9 9
CDK2/Cyclin E1 0.031 0.096 0.25 2 -0.33 26 28
MAPK3 -0.014 0.022 0.1 17 -10000 0 17
PRL-2 /Rab GGTase beta 0.029 0.006 -10000 0 -10000 0 0
MAPK1 -0.014 0.022 0.1 17 -10000 0 17
PTP4A1 -0.016 0.026 -10000 0 -10000 0 0
PTP4A3 0.025 0.03 0.19 17 -10000 0 17
PTP4A2 0.019 0.004 -10000 0 -10000 0 0
ITGB1 -0.014 0.022 0.1 17 -10000 0 17
SRC 0.019 0.004 -10000 0 -10000 0 0
RAC1 0.006 0.025 -10000 0 -0.32 1 1
Rab GGTase beta/Rab GGTase alpha 0.026 0.022 -10000 0 -0.3 2 2
PRL-1/ATF-5 0.016 0.083 -10000 0 -10000 0 0
RABGGTA 0.017 0.027 -10000 0 -0.42 2 2
BCAR1 -0.024 0.024 -10000 0 -0.3 1 1
RHOC 0.002 0.047 -10000 0 -0.35 7 7
RHOA -0.04 0.12 -10000 0 -0.33 73 73
cell motility -0.003 0.09 0.27 7 -0.32 10 17
PRL-1/alpha Tubulin 0.014 0.082 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.03 0.023 -10000 0 -10000 0 0
ROCK1 0 0.08 0.25 6 -0.31 8 14
RABGGTB 0.019 0.004 -10000 0 -10000 0 0
CDK2 0.02 0.003 -10000 0 -10000 0 0
mitosis -0.016 0.026 -10000 0 -10000 0 0
ATF5 0.021 0.013 0.19 3 -10000 0 3
LPA4-mediated signaling events

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
ADCY4 -0.015 0.011 -10000 0 -0.25 1 1
ADCY5 -0.022 0.044 -10000 0 -0.25 18 18
ADCY6 -0.015 0.02 -10000 0 -0.47 1 1
ADCY7 -0.012 0.018 -10000 0 -0.25 1 1
ADCY1 -0.018 0.035 -10000 0 -0.25 11 11
ADCY2 0 0.047 0.29 1 -0.25 8 9
ADCY3 -0.015 0.011 -10000 0 -0.25 1 1
ADCY8 0.009 0.042 0.29 1 -0.25 2 3
PRKCE -0.01 0.013 -10000 0 -0.29 1 1
ADCY9 -0.015 0.011 -10000 0 -0.25 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.019 0.081 0.23 39 -0.26 4 43
Arf6 downstream pathway

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.01 0.055 0.34 2 -10000 0 2
regulation of axonogenesis 0.012 0.051 0.25 21 -10000 0 21
myoblast fusion -0.02 0.026 -10000 0 -0.18 1 1
mol:GTP 0.009 0.046 -10000 0 -0.17 27 27
regulation of calcium-dependent cell-cell adhesion -0.033 0.039 -10000 0 -0.18 1 1
ARF1/GTP 0.02 0.04 -10000 0 -10000 0 0
mol:GM1 0 0.033 -10000 0 -0.14 7 7
mol:Choline -0.015 0.027 -10000 0 -10000 0 0
lamellipodium assembly 0.003 0.061 -10000 0 -0.35 13 13
MAPK3 0.01 0.039 0.16 4 -10000 0 4
ARF6/GTP/NME1/Tiam1 0.034 0.039 0.19 1 -10000 0 1
ARF1 0.019 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.026 0.18 1 -10000 0 1
ARF1/GDP 0.01 0.06 -10000 0 -0.28 6 6
ARF6 0.026 0.013 -10000 0 -10000 0 0
RAB11A 0.02 0.002 -10000 0 -10000 0 0
TIAM1 0.02 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.01 0.04 0.16 4 -10000 0 4
actin filament bundle formation -0.009 0.058 0.27 6 -10000 0 6
KALRN 0.01 0.018 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.028 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.009 0.059 -10000 0 -0.27 6 6
NME1 0.02 0.01 0.19 1 -10000 0 1
Rac1/GDP 0.015 0.055 -10000 0 -0.26 7 7
substrate adhesion-dependent cell spreading 0.009 0.046 -10000 0 -0.17 27 27
cortical actin cytoskeleton organization 0.003 0.061 -10000 0 -0.35 13 13
RAC1 0.018 0.006 -10000 0 -10000 0 0
liver development 0.009 0.046 -10000 0 -0.17 27 27
ARF6/GTP 0.009 0.046 -10000 0 -0.17 27 27
RhoA/GTP 0.015 0.038 -10000 0 -10000 0 0
mol:GDP 0 0.059 0.2 1 -0.24 24 25
ARF6/GTP/RAB11FIP3/RAB11A 0.032 0.038 -10000 0 -10000 0 0
RHOA 0.014 0.009 -10000 0 -10000 0 0
PLD1 0.004 0.033 -10000 0 -0.15 1 1
RAB11FIP3 0.019 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.003 0.061 -10000 0 -0.35 13 13
ruffle organization -0.012 0.051 -10000 0 -0.25 21 21
regulation of epithelial cell migration 0.009 0.046 -10000 0 -0.17 27 27
PLD2 0.003 0.037 -10000 0 -10000 0 0
PIP5K1A -0.012 0.051 -10000 0 -0.25 21 21
mol:Phosphatidic acid -0.015 0.027 -10000 0 -10000 0 0
Rac1/GTP 0.003 0.061 -10000 0 -0.35 13 13
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.008 0.019 -10000 0 -10000 0 0
CRKL 0.02 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.005 -10000 0 -10000 0 0
DOCK1 0.019 0.019 -10000 0 -0.42 1 1
ITGA4 0.024 0.029 0.19 16 -10000 0 16
alpha4/beta7 Integrin/MAdCAM1 0.039 0.034 -10000 0 -10000 0 0
EPO 0.072 0.08 0.19 168 -10000 0 168
alpha4/beta7 Integrin 0.031 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.032 0.022 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.064 0.058 -10000 0 -10000 0 0
lamellipodium assembly -0.006 0.088 0.26 1 -0.37 20 21
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
PI3K 0.025 0.022 -10000 0 -0.3 2 2
ARF6 0.019 0.005 -10000 0 -10000 0 0
JAK2 0.028 0.032 -10000 0 -10000 0 0
PXN 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
MADCAM1 0.023 0.023 0.19 10 -10000 0 10
cell adhesion 0.038 0.033 -10000 0 -10000 0 0
CRKL/CBL 0.029 0.015 -10000 0 -0.3 1 1
ITGB1 0.02 0.003 -10000 0 -10000 0 0
SRC -0.016 0.037 0.17 14 -0.22 1 15
ITGB7 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.042 0.029 -10000 0 -0.24 1 1
p130Cas/Crk/Dock1 -0.028 0.038 0.17 10 -0.22 1 11
VCAM1 0.021 0.029 0.19 9 -0.42 1 10
RHOA 0.014 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.05 0.024 -10000 0 -10000 0 0
BCAR1 -0.021 0.034 0.16 12 -0.22 1 13
EPOR 0.02 0.002 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.019 0.019 -10000 0 -0.42 1 1
GIT1 0.02 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.09 0.26 1 -0.38 20 21
IL1-mediated signaling events

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
UBC13/UEV1A 0.014 0.003 -10000 0 -10000 0 0
PRKCZ 0.017 0.033 -10000 0 -0.42 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.019 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.045 0.1 -10000 0 -0.21 133 133
IRAK/TOLLIP -0.019 0.004 -10000 0 -10000 0 0
IKBKB 0.019 0.006 -10000 0 -10000 0 0
IKBKG 0.02 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.016 0.087 0.27 1 -0.3 33 34
IL1A 0.024 0.027 0.19 14 -10000 0 14
IL1B -0.018 0.018 0.1 5 -0.3 1 6
IRAK/TRAF6/p62/Atypical PKCs 0.031 0.029 -10000 0 -0.22 1 1
IL1R2 -0.001 0.11 0.19 23 -0.42 33 56
IL1R1 0.02 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.028 0.059 -10000 0 -0.25 14 14
TOLLIP 0.02 0.002 -10000 0 -10000 0 0
TICAM2 0.016 0.008 -10000 0 -10000 0 0
MAP3K3 0.02 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.013 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.003 0.064 -10000 0 -0.41 1 1
JUN -0.024 0.038 0.16 17 -0.2 4 21
MAP3K7 0.019 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.041 0.031 -10000 0 -0.31 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88 0.038 0.033 -10000 0 -0.24 1 1
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.038 0.041 -10000 0 -0.23 1 1
IL1 beta fragment/IL1R1/IL1RAP 0.026 0.021 -10000 0 -0.24 2 2
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
MAPK8 -0.02 0.04 0.17 17 -0.21 4 21
IRAK1 -0.015 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.033 0.021 -10000 0 -10000 0 0
IRAK4 0.02 0.003 -10000 0 -10000 0 0
PRKCI 0.019 0.005 -10000 0 -10000 0 0
TRAF6 0.02 0.002 -10000 0 -10000 0 0
PI3K 0.025 0.022 -10000 0 -0.3 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.036 0.079 -10000 0 -0.24 14 14
CHUK 0.019 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.026 0.021 -10000 0 -0.24 2 2
IL1 beta/IL1R2 -0.029 0.068 0.14 22 -0.26 33 55
IRAK/TRAF6/TAK1/TAB1/TAB2 0.022 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.037 0.031 -10000 0 -0.56 1 1
IRAK3 0.02 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.036 0.028 -10000 0 -0.23 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.013 0.05 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP 0.04 0.026 -10000 0 -0.26 1 1
RELA 0.02 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.015 0.009 -10000 0 -10000 0 0
MYD88 0.014 0.009 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.033 0.023 -10000 0 -10000 0 0
IL1RAP 0.019 0.023 0.19 3 -0.42 1 4
UBE2N 0.02 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.033 0.024 -10000 0 -10000 0 0
CASP1 0.02 0.002 -10000 0 -10000 0 0
IL1RN/IL1R2 0.017 0.089 0.27 2 -0.3 33 35
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.027 0.027 -10000 0 -0.23 2 2
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.047 0.1 -10000 0 -0.29 18 18
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
IL1RN 0.025 0.029 0.19 16 -10000 0 16
TRAF6/TAK1/TAB1/TAB2 0.027 0.009 -10000 0 -10000 0 0
MAP2K6 -0.016 0.041 0.18 17 -0.21 3 20
Ephrin B reverse 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
EFNB2 0.02 0.003 -10000 0 -10000 0 0
EPHB2 0.016 0.04 0.19 2 -0.42 4 6
EFNB1 -0.016 0.019 0.12 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.035 0.037 -10000 0 -0.28 4 4
Ephrin B2/EPHB1-2 0.032 0.033 -10000 0 -0.3 4 4
neuron projection morphogenesis -0.026 0.032 0.14 1 -0.27 4 5
Ephrin B1/EPHB1-2/Tiam1 0.033 0.036 0.22 2 -0.29 4 6
DNM1 0.023 0.025 0.19 11 -10000 0 11
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.017 0.075 0.22 1 -0.47 13 14
YES1 -0.007 0.11 -10000 0 -0.68 14 14
Ephrin B1/EPHB1-2/NCK2 0.032 0.035 0.2 1 -0.29 4 5
PI3K 0.015 0.082 -10000 0 -0.45 14 14
mol:GDP 0.032 0.035 0.22 2 -0.29 4 6
ITGA2B 0.025 0.036 0.19 18 -0.42 1 19
endothelial cell proliferation 0.024 0.009 -10000 0 -10000 0 0
FYN -0.012 0.12 -10000 0 -0.69 14 14
MAP3K7 -0.015 0.079 -10000 0 -0.49 14 14
FGR -0.006 0.11 -10000 0 -0.68 14 14
TIAM1 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
RGS3 0.019 0.004 -10000 0 -10000 0 0
cell adhesion -0.024 0.077 -10000 0 -0.48 11 11
LYN -0.007 0.11 -10000 0 -0.68 14 14
Ephrin B1/EPHB1-2/Src Family Kinases -0.01 0.1 -10000 0 -0.63 14 14
Ephrin B1/EPHB1-2 -0.01 0.086 -10000 0 -0.53 14 14
SRC -0.005 0.11 -10000 0 -0.66 14 14
ITGB3 0.015 0.043 -10000 0 -0.42 5 5
EPHB1 0.018 0.03 0.19 2 -0.42 2 4
EPHB4 0.018 0.006 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.024 0.009 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.029 0.041 -10000 0 -0.29 6 6
BLK -0.006 0.12 -10000 0 -0.68 14 14
HCK -0.003 0.11 -10000 0 -0.66 14 14
regulation of stress fiber formation -0.031 0.034 0.28 4 -0.2 1 5
MAPK8 -0.021 0.075 0.3 2 -0.45 13 15
Ephrin B1/EPHB1-2/RGS3 0.033 0.035 0.2 1 -0.29 4 5
endothelial cell migration 0.001 0.09 0.24 15 -0.42 12 27
NCK2 0.019 0.004 -10000 0 -10000 0 0
PTPN13 0.013 0.07 -10000 0 -0.52 9 9
regulation of focal adhesion formation -0.031 0.034 0.28 4 -0.2 1 5
chemotaxis -0.032 0.034 0.29 4 -0.2 1 5
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
Rac1/GTP 0.029 0.034 -10000 0 -0.27 4 4
angiogenesis -0.01 0.086 -10000 0 -0.52 14 14
LCK -0.005 0.12 -10000 0 -0.69 14 14
Arf6 trafficking events

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
SLC2A4 0.016 0.044 0.19 3 -0.42 5 8
CLTC -0.009 0.088 -10000 0 -0.36 29 29
calcium ion-dependent exocytosis 0.004 0.032 0.19 1 -0.16 5 6
Dynamin 2/GTP -0.018 0.007 -10000 0 -10000 0 0
EXOC4 0.018 0.006 -10000 0 -10000 0 0
CD59 -0.01 0.071 -10000 0 -0.32 21 21
CPE -0.01 0.023 0.11 20 -10000 0 20
CTNNB1 0.014 0.009 -10000 0 -10000 0 0
membrane fusion 0.005 0.026 -10000 0 -10000 0 0
CTNND1 -0.021 0.023 0.17 7 -10000 0 7
DNM2 0.02 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.006 0.051 0.21 2 -0.28 5 7
TSHR 0 0.038 0.11 60 -10000 0 60
INS 0.006 0.039 -10000 0 -0.8 1 1
BIN1 0.02 0.003 -10000 0 -10000 0 0
mol:Choline 0.005 0.026 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.007 0.11 1 -10000 0 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.007 -10000 0 -10000 0 0
JUP -0.011 0.071 -10000 0 -0.32 21 21
ASAP2/amphiphysin II 0.035 0.016 -10000 0 -0.23 1 1
ARF6/GTP 0.014 0.004 -10000 0 -10000 0 0
CDH1 -0.013 0.075 -10000 0 -0.34 19 19
clathrin-independent pinocytosis 0.014 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.031 0.043 0.19 36 -10000 0 36
positive regulation of endocytosis 0.014 0.004 -10000 0 -10000 0 0
EXOC2 0.019 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.051 -10000 0 -0.31 9 9
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.02 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.077 0.31 21 -10000 0 21
positive regulation of phagocytosis -0.014 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.031 0.027 -10000 0 -10000 0 0
ACAP1 0.022 0.032 0.13 12 -0.17 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.01 0.066 -10000 0 -0.32 21 21
clathrin heavy chain/ACAP1 -0.005 0.073 0.19 1 -0.3 22 23
JIP4/KLC1 0.035 0.012 -10000 0 -10000 0 0
EXOC1 0.02 0.002 -10000 0 -10000 0 0
exocyst -0.005 0.052 -10000 0 -0.31 9 9
RALA/GTP 0.013 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.025 0.008 -10000 0 -10000 0 0
receptor recycling 0.014 0.004 -10000 0 -10000 0 0
CTNNA1 -0.016 0.024 0.17 7 -10000 0 7
NME1 -0.014 0.007 0.11 1 -10000 0 1
clathrin coat assembly -0.011 0.091 -10000 0 -0.36 29 29
IL2RA -0.002 0.073 -10000 0 -0.31 21 21
VAMP3 -0.014 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.007 0.073 -10000 0 -0.29 22 22
EXOC6 0.019 0.004 -10000 0 -10000 0 0
PLD1 0.002 0.009 -10000 0 -10000 0 0
PLD2 0.002 0.011 -10000 0 -10000 0 0
EXOC5 0.019 0.005 -10000 0 -10000 0 0
PIP5K1C -0.006 0.049 0.18 1 -0.28 5 6
SDC1 -0.011 0.074 -10000 0 -0.33 21 21
ARF6/GDP 0.015 0.006 -10000 0 -10000 0 0
EXOC7 0.02 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0.079 -10000 0 -0.32 21 21
mol:Phosphatidic acid 0.005 0.026 -10000 0 -10000 0 0
endocytosis -0.033 0.016 0.23 1 -10000 0 1
SCAMP2 0.02 0.002 -10000 0 -10000 0 0
ADRB2 0.028 0.11 0.24 23 -0.35 13 36
EXOC3 0.018 0.006 -10000 0 -10000 0 0
ASAP2 0.019 0.019 -10000 0 -0.42 1 1
Dynamin 2/GDP -0.018 0.008 0.1 1 -10000 0 1
KLC1 0.019 0.005 -10000 0 -10000 0 0
AVPR2 -0.09 0.13 0.28 1 -0.45 33 34
RALA 0.018 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.01 0.079 0.25 1 -0.33 9 10
S1P3 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
PDGFRB 0.015 0.009 -10000 0 -10000 0 0
mol:S1P 0 0 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.016 0.049 -10000 0 -0.21 10 10
GNAO1 0.02 0.023 0.19 3 -0.42 1 4
S1P/S1P3/G12/G13 0.033 0.014 -10000 0 -10000 0 0
AKT1 0.006 0.049 -10000 0 -0.4 7 7
AKT3 0.016 0.076 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.009 -10000 0 -10000 0 0
GNAI2 0.014 0.009 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.017 0.02 -10000 0 -0.42 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.02 0.004 -10000 0 -10000 0 0
S1PR2 0.02 0.002 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.029 -10000 0 -10000 0 0
MAPK3 -0.006 0.03 -10000 0 -0.31 1 1
MAPK1 -0.005 0.027 -10000 0 -10000 0 0
JAK2 -0.006 0.055 -10000 0 -0.47 1 1
CXCR4 0.011 0.039 0.19 1 -0.31 1 2
FLT1 0.022 0.017 0.19 5 -10000 0 5
RhoA/GDP 0.011 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.005 -10000 0 -10000 0 0
SRC -0.006 0.029 -10000 0 -0.31 1 1
S1P/S1P3/Gi 0.005 0.03 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.052 -10000 0 -0.29 1 1
VEGFA 0.094 0.084 0.19 232 -10000 0 232
S1P/S1P2/Gi 0.005 0.031 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.081 0.063 0.27 4 -10000 0 4
RHOA 0.014 0.009 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.008 0.037 -10000 0 -0.25 9 9
GNAQ 0.019 0.004 -10000 0 -10000 0 0
GNAZ 0.018 0.033 -10000 0 -0.42 3 3
G12/G13 0.026 0.01 -10000 0 -10000 0 0
GNA14 0.014 0.05 -10000 0 -0.42 7 7
GNA15 0.025 0.028 0.19 15 -10000 0 15
GNA12 0.018 0.006 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.017 0.033 -10000 0 -0.42 3 3
Rac1/GTP -0.01 0.053 -10000 0 -0.3 1 1
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.019 0.036 0.42 3 -0.19 4 7
PI3K Class IB/PDE3B 0.019 0.036 0.19 4 -0.42 3 7
PDE3B 0.019 0.036 0.19 4 -0.42 3 7
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.004 0.054 0.22 3 -10000 0 3
GNAI2 0.014 0.009 -10000 0 -10000 0 0
S1P/S1P5/G12 0.041 0.041 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.023 0.19 3 -0.42 1 4
RhoA/GTP 0.004 0.055 -10000 0 -0.22 3 3
negative regulation of cAMP metabolic process 0.012 0.038 -10000 0 -0.19 4 4
GNAZ 0.017 0.033 -10000 0 -0.42 3 3
GNAI3 0.019 0.004 -10000 0 -10000 0 0
GNA12 0.018 0.006 -10000 0 -10000 0 0
S1PR5 0.049 0.064 0.19 91 -10000 0 91
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.012 0.038 -10000 0 -0.19 4 4
RhoA/GDP 0.011 0.007 -10000 0 -10000 0 0
RHOA 0.014 0.009 -10000 0 -10000 0 0
GNAI1 0.017 0.02 -10000 0 -0.42 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.026 0.006 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.019 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.033 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0 0.025 -10000 0 -0.18 2 2
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.003 -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 0.02 0.003 -10000 0 -10000 0 0
FYN 0.019 0.005 -10000 0 -10000 0 0
MAP3K12 0.019 0.019 -10000 0 -0.42 1 1
FGR 0.02 0.013 0.19 3 -10000 0 3
p38 alpha/TAB1 -0.025 0.092 -10000 0 -0.42 18 18
PRKG1 0.008 0.07 -10000 0 -0.42 14 14
DUSP8 0.019 0.019 -10000 0 -0.42 1 1
PGK/cGMP/p38 alpha 0 0.1 -10000 0 -0.4 20 20
apoptosis -0.024 0.086 -10000 0 -0.4 18 18
RAL/GTP 0.024 0.009 -10000 0 -10000 0 0
LYN 0.019 0.005 -10000 0 -10000 0 0
DUSP1 0.015 0.012 0.19 1 -10000 0 1
PAK1 0.02 0.002 -10000 0 -10000 0 0
SRC 0.019 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.045 0.018 -10000 0 -10000 0 0
TRAF6 0.02 0.002 -10000 0 -10000 0 0
RAC1 0.018 0.006 -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 0.018 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.024 0.009 -10000 0 -10000 0 0
MAPK11 0.009 0.11 0.3 18 -0.44 13 31
BLK 0.029 0.042 0.19 34 -10000 0 34
HCK 0.028 0.037 0.19 27 -10000 0 27
MAP2K3 0.02 0.003 -10000 0 -10000 0 0
DUSP16 0.019 0.004 -10000 0 -10000 0 0
DUSP10 0.02 0.011 0.19 2 -10000 0 2
TRAF6/MEKK3 0.025 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.004 0.12 0.27 13 -0.46 18 31
positive regulation of innate immune response 0.008 0.13 0.32 17 -0.54 14 31
LCK 0.024 0.042 0.19 20 -0.42 2 22
p38alpha-beta/MKP7 0.011 0.12 0.3 7 -0.52 13 20
p38alpha-beta/MKP5 0.016 0.13 0.37 11 -0.52 13 24
PGK/cGMP 0.006 0.05 -10000 0 -0.29 14 14
PAK2 0.019 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.006 0.11 0.35 5 -0.56 11 16
CDC42 0.019 0.004 -10000 0 -10000 0 0
RALB 0.02 0.003 -10000 0 -10000 0 0
RALA 0.018 0.006 -10000 0 -10000 0 0
PAK3 0.02 0.04 0.19 10 -0.42 3 13
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.023 0.19 3 -0.42 1 4
CDC42/GTP -0.006 0.057 -10000 0 -0.25 2 2
PLCG1 -0.004 0.034 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.014 0.009 -10000 0 -10000 0 0
GNAI3 0.019 0.004 -10000 0 -10000 0 0
G12/G13 0.026 0.01 -10000 0 -10000 0 0
cell migration -0.006 0.056 -10000 0 -0.24 2 2
S1PR5 0.049 0.064 0.19 91 -10000 0 91
S1PR4 0.03 0.039 0.19 30 -10000 0 30
MAPK3 -0.004 0.035 -10000 0 -0.31 1 1
MAPK1 -0.003 0.032 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.012 0.038 -10000 0 -0.19 4 4
GNAI1 0.017 0.02 -10000 0 -0.42 1 1
CDC42/GDP 0.014 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.041 0.041 -10000 0 -10000 0 0
RHOA -0.001 0.054 0.19 31 -10000 0 31
S1P/S1P4/Gi 0.008 0.035 -10000 0 -0.19 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.017 0.033 -10000 0 -0.42 3 3
S1P/S1P4/G12/G13 0.039 0.028 -10000 0 -10000 0 0
GNA12 0.018 0.006 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.019 0.004 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.008 0.1 0.35 2 -0.58 8 10
MAP3K8 0.02 0.013 0.19 2 -10000 0 2
FOS 0.004 0.093 0.32 4 -0.5 10 14
PRKCA 0.019 0.008 -10000 0 -10000 0 0
PTPN7 0.028 0.046 0.19 33 -0.42 1 34
HRAS 0.02 0.009 0.19 1 -10000 0 1
PRKCB 0.018 0.031 0.18 3 -0.42 2 5
NRAS 0.019 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.015 -10000 0 -10000 0 0
MAPK3 0.003 0.083 -10000 0 -0.54 9 9
MAP2K1 -0.017 0.06 -10000 0 -0.32 8 8
ELK1 0.019 0.01 -10000 0 -10000 0 0
BRAF 0.004 0.026 -10000 0 -0.33 3 3
mol:GTP 0 0.001 0.002 1 -0.006 12 13
MAPK1 0.004 0.084 -10000 0 -0.51 10 10
RAF1 0.003 0.027 -10000 0 -0.33 3 3
KRAS 0.019 0.007 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.02 0.003 -10000 0 -10000 0 0
SMAD2 -0.044 0.075 0.22 1 -0.25 36 37
SMAD3 -0.017 0.039 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.007 0.096 -10000 0 -0.48 19 19
SMAD4/Ubc9/PIASy 0.038 0.011 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.016 0.09 -10000 0 -0.26 22 22
PPM1A 0.019 0.005 -10000 0 -10000 0 0
CALM1 0.019 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.036 0.08 -10000 0 -0.25 39 39
MAP3K1 0.018 0.006 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.028 0.007 -10000 0 -10000 0 0
MAPK3 0.019 0.004 -10000 0 -10000 0 0
MAPK1 0.02 0.002 -10000 0 -10000 0 0
NUP214 0.019 0.004 -10000 0 -10000 0 0
CTDSP1 0.019 0.005 -10000 0 -10000 0 0
CTDSP2 0.02 0.003 -10000 0 -10000 0 0
CTDSPL 0.014 0.009 -10000 0 -10000 0 0
KPNB1 0.02 0.003 -10000 0 -10000 0 0
TGFBRAP1 0.02 0.003 -10000 0 -10000 0 0
UBE2I 0.019 0.004 -10000 0 -10000 0 0
NUP153 0.019 0.004 -10000 0 -10000 0 0
KPNA2 0.02 0.003 -10000 0 -10000 0 0
PIAS4 0.02 0.002 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.038 0.023 -10000 0 -10000 0 0
RGS9BP 0.001 0.089 -10000 0 -0.42 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.018 0.003 -10000 0 -10000 0 0
mol:Na + 0.024 0.012 -10000 0 -10000 0 0
mol:ADP -0.018 0.009 0.1 2 -10000 0 2
GNAT2 0.019 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.026 0.066 -10000 0 -0.26 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.024 0.007 -10000 0 -10000 0 0
GRK7 0.019 0.011 0.19 2 -10000 0 2
CNGB3 0.019 0.017 0.19 5 -10000 0 5
Cone Metarhodopsin II/X-Arrestin 0.014 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.038 0.17 20 -10000 0 20
Cone PDE6 0.04 0.064 -10000 0 -0.23 24 24
Cone Metarhodopsin II 0.023 0.009 0.12 2 -10000 0 2
Na + (4 Units) 0.033 0.018 0.24 1 -10000 0 1
GNAT2/GDP 0.032 0.06 -10000 0 -0.22 25 25
GNB5 0.02 0.002 -10000 0 -10000 0 0
mol:GMP (4 units) -0.013 0.035 0.17 17 -10000 0 17
Cone Transducin 0.041 0.025 -10000 0 -10000 0 0
SLC24A2 0.019 0.017 0.19 5 -10000 0 5
GNB3/GNGT2 0.034 0.027 -10000 0 -10000 0 0
GNB3 0.028 0.037 0.19 26 -10000 0 26
GNAT2/GTP 0.014 0.003 -10000 0 -10000 0 0
CNGA3 0.019 0.013 0.19 3 -10000 0 3
ARR3 0.018 0.001 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.024 0.012 -10000 0 -10000 0 0
mol:Pi 0.026 0.066 -10000 0 -0.26 25 25
Cone CNG Channel 0.04 0.02 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.019 0.017 0.19 5 -10000 0 5
RGS9 0.019 0.044 0.19 9 -0.42 4 13
PDE6C 0.019 0.011 0.19 2 -10000 0 2
GNGT2 0.02 0.008 0.19 1 -10000 0 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.018 0.004 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.003 -10000 0 -10000 0 0
ANTXR2 0.02 0.002 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.001 -10000 0 -10000 0 0
monocyte activation -0.008 0.095 -10000 0 -0.36 33 33
MAP2K2 0.004 0.059 -10000 0 -0.59 5 5
MAP2K1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K7 -0.009 0.002 -10000 0 -10000 0 0
MAP2K6 -0.009 0.013 -10000 0 -0.21 2 2
CYAA -0.012 0.003 -10000 0 -10000 0 0
MAP2K4 -0.009 0.002 -10000 0 -10000 0 0
IL1B -0.006 0.028 0.21 7 -0.21 1 8
Channel 0.025 0.006 -10000 0 -10000 0 0
NLRP1 -0.008 0.005 0.046 4 -10000 0 4
CALM1 0.019 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.019 0.097 -10000 0 -0.39 33 33
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.001 -10000 0 -10000 0 0
MAPK3 -0.009 0.002 -10000 0 -10000 0 0
MAPK1 -0.009 0.002 -10000 0 -10000 0 0
PGR -0.014 0.033 0.046 1 -0.21 14 15
PA/Cellular Receptors 0.026 0.007 -10000 0 -10000 0 0
apoptosis -0.003 0.001 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.024 0.006 -10000 0 -10000 0 0
macrophage activation -0.014 0.004 -10000 0 -10000 0 0
TNF 0.017 0.041 0.19 4 -0.42 4 8
VCAM1 -0.002 0.082 -10000 0 -0.35 25 25
platelet activation -0.019 0.097 -10000 0 -0.39 33 33
MAPKKK cascade 0.006 0.019 -10000 0 -0.11 6 6
IL18 -0.008 0.008 0.1 1 -10000 0 1
negative regulation of macrophage activation -0.003 0.001 -10000 0 -10000 0 0
LEF -0.003 0.001 -10000 0 -10000 0 0
CASP1 -0.004 0.003 -10000 0 -10000 0 0
mol:cAMP -0.019 0.097 -10000 0 -0.4 33 33
necrosis -0.003 0.001 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.024 0.006 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0 0.1 -10000 0 -0.42 18 18
CaM/Ca2+ 0.014 0.004 -10000 0 -10000 0 0
AKT1 0.019 0.005 -10000 0 -10000 0 0
AKT2 0.02 0.002 -10000 0 -10000 0 0
STXBP4 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.013 0.11 0.32 3 -0.41 25 28
YWHAZ 0.019 0.005 -10000 0 -10000 0 0
CALM1 0.019 0.005 -10000 0 -10000 0 0
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
TBC1D4 -0.018 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.002 -10000 0 -10000 0 0
YWHAB 0.019 0.004 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.011 -10000 0 -10000 0 0
YWHAG 0.018 0.006 -10000 0 -10000 0 0
ASIP 0.033 0.048 0.19 45 -10000 0 45
PRKCI 0.019 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.014 0.004 -10000 0 -10000 0 0
RHOQ 0.02 0.003 -10000 0 -10000 0 0
GYS1 -0.008 0.003 -10000 0 -10000 0 0
PRKCZ 0.017 0.033 -10000 0 -0.42 3 3
TRIP10 0.02 0.002 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.005 -10000 0 -10000 0 0
AS160/14-3-3 -0.002 0.052 -10000 0 -0.4 4 4
VAMP2 0.02 0.003 -10000 0 -10000 0 0
SLC2A4 -0.015 0.12 0.33 3 -0.47 25 28
STX4 0.019 0.004 -10000 0 -10000 0 0
GSK3B 0.008 0.003 -10000 0 -10000 0 0
SFN 0.022 0.081 0.19 41 -0.42 12 53
LNPEP 0.016 0.028 -10000 0 -0.42 2 2
YWHAE 0.02 0.003 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.007 0.065 0.69 2 -10000 0 2
VDR 0.017 0.033 -10000 0 -0.42 3 3
FAM120B 0.018 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.007 0.039 -10000 0 -0.26 4 4
RXRs/LXRs/DNA/Oxysterols 0.004 0.048 -10000 0 -0.39 4 4
MED1 0.02 0.003 -10000 0 -10000 0 0
mol:9cRA 0.001 0.005 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.051 0.094 -10000 0 -0.22 33 33
RXRs/NUR77 0.039 0.051 -10000 0 -0.24 13 13
RXRs/PPAR -0.016 0.051 -10000 0 -10000 0 0
NCOR2 0.019 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0.023 -10000 0 -0.29 3 3
RARs/VDR/DNA/Vit D3 0.027 0.036 -10000 0 -0.22 5 5
RARA 0.02 0.003 -10000 0 -10000 0 0
NCOA1 0.02 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.017 0.033 -10000 0 -0.42 3 3
RARs/RARs/DNA/9cRA 0.023 0.023 -10000 0 -0.22 2 2
RARG 0.02 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.003 0.073 0.54 9 -10000 0 9
RARs/THRs/DNA/SMRT -0.054 0.095 -10000 0 -0.22 33 33
THRA 0.019 0.019 -10000 0 -0.42 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0.023 -10000 0 -0.29 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.036 0.026 -10000 0 -10000 0 0
NR1H4 0.008 0.07 -10000 0 -0.42 14 14
RXRs/LXRs/DNA 0.054 0.038 -10000 0 -0.23 1 1
NR1H2 0.019 0.021 -10000 0 -0.42 1 1
NR1H3 0.02 0.008 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.041 0.031 -10000 0 -0.22 3 3
NR4A1 0.009 0.068 0.19 1 -0.42 13 14
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.005 0.061 -10000 0 -0.3 17 17
RXRG 0.02 0.016 0.19 3 -10000 0 3
RXR alpha/CCPG 0.027 0.012 -10000 0 -10000 0 0
RXRA 0.019 0.009 -10000 0 -10000 0 0
RXRB 0.019 0.01 -10000 0 -10000 0 0
THRB -0.006 0.092 -10000 0 -0.42 25 25
PPARG 0.014 0.009 -10000 0 -10000 0 0
PPARD 0.019 0.004 -10000 0 -10000 0 0
TNF -0.003 0.089 -10000 0 -0.96 4 4
mol:Oxysterols 0.001 0.004 -10000 0 -10000 0 0
cholesterol transport 0.004 0.048 -10000 0 -0.39 4 4
PPARA 0.02 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.013 0.028 -10000 0 -0.42 2 2
RXRs/NUR77/BCL2 -0.001 0.046 -10000 0 -0.23 13 13
SREBF1 0 0.043 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.036 0.026 -10000 0 -10000 0 0
ABCA1 0.002 0.043 -10000 0 -10000 0 0
RARs/THRs 0.025 0.067 -10000 0 -0.23 27 27
RXRs/FXR 0.039 0.052 -10000 0 -0.24 14 14
BCL2 0.02 0.003 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.031 0.034 -10000 0 -0.22 6 6
TC10/GTP 0.03 0.024 -10000 0 -0.22 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.045 0.03 -10000 0 -0.25 4 4
HRAS 0.02 0.008 0.19 1 -10000 0 1
APS homodimer 0.019 0.016 0.19 4 -10000 0 4
GRB14 -0.003 0.096 -10000 0 -0.42 27 27
FOXO3 -0.035 0.17 -10000 0 -0.66 37 37
AKT1 -0.018 0.099 0.34 20 -0.38 2 22
INSR 0.022 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.037 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.018 0.006 -10000 0 -10000 0 0
SORBS1 0.019 0.019 -10000 0 -0.42 1 1
CRK 0.02 0.003 -10000 0 -10000 0 0
PTPN1 -0.018 0.011 -10000 0 -10000 0 0
CAV1 -0.013 0.043 0.17 9 -0.23 4 13
CBL/APS/CAP/Crk-II/C3G 0.049 0.031 -10000 0 -0.23 2 2
Insulin Receptor/Insulin/IRS1/NCK2 0.046 0.03 -10000 0 -0.25 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.031 0.032 -10000 0 -0.22 6 6
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.009 0.046 -10000 0 -0.31 7 7
RPS6KB1 -0.023 0.089 0.31 18 -0.36 2 20
PARD6A 0.017 0.033 -10000 0 -0.42 3 3
CBL 0.019 0.019 -10000 0 -0.42 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.009 0.06 -10000 0 -0.55 6 6
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.038 0.063 0.16 3 -0.36 2 5
HRAS/GTP -0.037 0.022 -10000 0 -0.21 3 3
Insulin Receptor 0.022 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.051 0.033 -10000 0 -0.24 4 4
PRKCI 0.006 0.054 -10000 0 -0.33 12 12
Insulin Receptor/Insulin/GRB14/PDK1 -0.041 0.046 -10000 0 -0.23 24 24
SHC1 0.019 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.022 0.06 -10000 0 -0.46 7 7
PI3K 0.039 0.035 -10000 0 -0.22 6 6
NCK2 0.019 0.004 -10000 0 -10000 0 0
RHOQ 0.02 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.003 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.005 0.13 1 -10000 0 1
AKT2 -0.014 0.11 0.34 25 -0.38 2 27
PRKCZ -0.002 0.079 -10000 0 -0.38 20 20
SH2B2 0.019 0.016 0.19 4 -10000 0 4
SHC/SHIP -0.025 0.028 0.18 1 -0.22 3 4
F2RL2 0.027 0.038 0.19 27 -10000 0 27
TRIP10 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.012 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.055 0.019 -10000 0 -10000 0 0
RAPGEF1 0.019 0.004 -10000 0 -10000 0 0
RASA1 0.017 0.02 -10000 0 -0.42 1 1
NCK1 0.018 0.02 -10000 0 -0.42 1 1
CBL/APS/CAP/Crk-II 0.044 0.027 -10000 0 -0.24 2 2
TC10/GDP 0.015 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.019 -10000 0 -10000 0 0
INPP5D -0.021 0.029 0.16 5 -0.22 4 9
SOS1 0.02 0.003 -10000 0 -10000 0 0
SGK1 -0.043 0.18 -10000 0 -0.65 40 40
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.019 0.004 -10000 0 -10000 0 0
IRS1 0.016 0.038 -10000 0 -0.42 4 4
p62DOK/RasGAP 0.023 0.061 -10000 0 -0.47 7 7
INS -0.017 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.021 0.029 0.16 5 -0.21 4 9
GRB2 0.02 0.003 -10000 0 -10000 0 0
EIF4EBP1 -0.02 0.089 0.32 18 -0.33 2 20
PTPRA 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
TC10/GTP/CIP4 0.026 0.005 -10000 0 -10000 0 0
PDPK1 0.018 0.019 -10000 0 -0.42 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.007 0.026 -10000 0 -0.22 4 4
Insulin Receptor/Insulin/IRS1 0.035 0.027 -10000 0 -0.24 4 4
Insulin Receptor/Insulin/IRS3 0.03 0.011 -10000 0 -10000 0 0
Par3/Par6 0.042 0.034 -10000 0 -0.22 3 3
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.006 -10000 0 -10000 0 0
TRAF2/ASK1 0.025 0.008 -10000 0 -10000 0 0
ATM 0.019 0.019 -10000 0 -0.42 1 1
MAP2K3 0.002 0.065 0.39 4 -0.32 3 7
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.005 0.066 0.39 3 -0.31 8 11
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.021 0.028 0.19 8 -0.42 1 9
TXN 0.003 0.001 -10000 0 -10000 0 0
CALM1 0.019 0.005 -10000 0 -10000 0 0
GADD45A 0.019 0.004 -10000 0 -10000 0 0
GADD45B 0.02 0.002 -10000 0 -10000 0 0
MAP3K1 0.018 0.006 -10000 0 -10000 0 0
MAP3K6 0.019 0.019 -10000 0 -0.42 1 1
MAP3K7 0.019 0.005 -10000 0 -10000 0 0
MAP3K4 0.018 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.026 0.017 -10000 0 -0.3 1 1
TAK1/TAB family 0.001 0.013 -10000 0 -0.13 4 4
RAC1/OSM/MEKK3 0.034 0.013 -10000 0 -10000 0 0
TRAF2 0.019 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.006 0.048 -10000 0 -0.3 2 2
TRAF6 0.003 0 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.033 0.14 0.19 7 -0.42 64 71
CCM2 0.018 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.009 0.092 -10000 0 -0.25 64 64
MAPK11 0.021 0.011 0.19 2 -10000 0 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0 0.088 -10000 0 -0.23 64 64
OSM/MEKK3 0.026 0.01 -10000 0 -10000 0 0
TAOK1 0.003 0.031 -10000 0 -0.28 6 6
TAOK2 0.005 0.013 -10000 0 -0.28 1 1
TAOK3 0.005 0.013 -10000 0 -0.28 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.019 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.019 0.005 -10000 0 -10000 0 0
MAP3K10 0.019 0.019 -10000 0 -0.42 1 1
MAP3K3 0.02 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.013 0.018 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.041 0.022 -10000 0 -0.2 1 1
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.015 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.059 0.28 5 -10000 0 5
ERC1 0.019 0.004 -10000 0 -10000 0 0
RIP2/NOD2 0.053 0.054 0.27 1 -0.3 1 2
NFKBIA -0.019 0.015 -10000 0 -10000 0 0
BIRC2 0.02 0.002 -10000 0 -10000 0 0
IKBKB 0.019 0.006 -10000 0 -10000 0 0
RIPK2 0.019 0.009 0.19 1 -10000 0 1
IKBKG 0.012 0.053 -10000 0 -0.34 6 6
IKK complex/A20 0.04 0.064 -10000 0 -0.33 7 7
NEMO/A20/RIP2 0.019 0.009 0.19 1 -10000 0 1
XPO1 0.02 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.026 0.059 0.25 1 -0.33 6 7
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.019 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.026 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.031 0.053 -10000 0 -0.31 6 6
BCL10/MALT1/TRAF6 0.038 0.01 -10000 0 -10000 0 0
NOD2 0.057 0.074 0.19 119 -0.42 1 120
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
RELA 0.02 0.002 -10000 0 -10000 0 0
MALT1 0.02 0.003 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.029 0.005 -10000 0 -10000 0 0
ATM 0.019 0.019 -10000 0 -0.42 1 1
TNF/TNFR1A 0.026 0.032 -10000 0 -0.3 4 4
TRAF6 0.02 0.002 -10000 0 -10000 0 0
PRKCA 0.02 0.003 -10000 0 -10000 0 0
CHUK 0.019 0.004 -10000 0 -10000 0 0
UBE2D3 0.02 0.002 -10000 0 -10000 0 0
TNF 0.017 0.041 0.19 4 -0.42 4 8
NF kappa B1 p50/RelA 0.031 0.022 -10000 0 -0.26 1 1
BCL10 0.019 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.019 0.015 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.009 -10000 0 -10000 0 0
TNFRSF1A 0.019 0.004 -10000 0 -10000 0 0
IKK complex 0.035 0.06 -10000 0 -0.32 6 6
CYLD 0.019 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.04 0.06 -10000 0 -0.32 6 6
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.019 0.004 -10000 0 -10000 0 0
HDAC2 0.019 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.033 0.021 -10000 0 -0.26 1 1
forebrain development 0.011 0.1 0.44 7 -0.49 6 13
GNAO1 0.019 0.024 0.19 3 -0.42 1 4
SMO/beta Arrestin2 0.025 0.019 -10000 0 -0.3 1 1
SMO 0.017 0.021 -10000 0 -0.42 1 1
ARRB2 0.019 0.007 -10000 0 -10000 0 0
GLI3/SPOP 0.014 0.091 0.24 2 -0.54 8 10
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.019 0.005 -10000 0 -10000 0 0
GNAI2 0.014 0.011 -10000 0 -10000 0 0
SIN3/HDAC complex 0.052 0.022 -10000 0 -10000 0 0
GNAI1 0.017 0.021 -10000 0 -0.42 1 1
XPO1 0.019 0.009 -10000 0 -10000 0 0
GLI1/Su(fu) 0.005 0.07 -10000 0 -0.47 4 4
SAP30 0.025 0.031 0.19 18 -10000 0 18
mol:GDP 0.017 0.021 -10000 0 -0.42 1 1
MIM/GLI2A 0.021 0.029 -10000 0 -0.12 11 11
IFT88 0.019 0.019 -10000 0 -0.42 1 1
GNAI3 0.019 0.007 -10000 0 -10000 0 0
GLI2 0.035 0.078 0.27 13 -10000 0 13
GLI3 0.005 0.095 0.28 3 -0.5 11 14
CSNK1D 0.02 0.003 -10000 0 -10000 0 0
CSNK1E 0.02 0.002 -10000 0 -10000 0 0
SAP18 0.02 0.004 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.019 0.019 -10000 0 -0.42 1 1
GNG2 0.019 0.005 -10000 0 -10000 0 0
Gi family/GTP 0.001 0.034 -10000 0 -0.29 4 4
SIN3B 0.02 0.002 -10000 0 -10000 0 0
SIN3A 0.02 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) -0.003 0.1 -10000 0 -0.5 16 16
GLI2/Su(fu) 0.025 0.062 0.22 3 -0.29 2 5
FOXA2 0.003 0.16 -10000 0 -0.79 19 19
neural tube patterning 0.011 0.1 0.44 7 -0.49 6 13
SPOP 0.02 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.044 -10000 0 -10000 0 0
GNB1 0.019 0.004 -10000 0 -10000 0 0
CSNK1G2 0.019 0.019 -10000 0 -0.42 1 1
CSNK1G3 0.016 0.008 -10000 0 -10000 0 0
MTSS1 0.021 0.029 -10000 0 -0.12 11 11
embryonic limb morphogenesis 0.011 0.1 0.44 7 -0.49 6 13
SUFU 0.008 0.01 -10000 0 -10000 0 0
LGALS3 0.022 0.024 0.19 10 -10000 0 10
catabolic process 0.043 0.12 0.33 10 -0.52 9 19
GLI3A/CBP 0.02 0.026 -10000 0 -0.33 2 2
KIF3A 0.015 0.009 -10000 0 -10000 0 0
GLI1 0.011 0.1 0.46 6 -0.5 6 12
RAB23 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.015 0.009 -10000 0 -10000 0 0
IFT172 0.02 0.003 -10000 0 -10000 0 0
RBBP7 0.02 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.019 0.042 0.22 1 -10000 0 1
GNAZ 0.017 0.034 -10000 0 -0.42 3 3
RBBP4 0.018 0.019 -10000 0 -0.42 1 1
CSNK1G1 0.02 0.002 -10000 0 -10000 0 0
PIAS1 0.02 0.002 -10000 0 -10000 0 0
PRKACA 0.02 0.002 -10000 0 -10000 0 0
GLI2/SPOP 0.043 0.069 0.24 11 -10000 0 11
STK36 0.019 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.022 0.061 -10000 0 -0.32 7 7
PTCH1 0.006 0.1 0.44 6 -0.56 5 11
MIM/GLI1 0.015 0.12 0.4 7 -0.45 16 23
CREBBP 0.02 0.026 -10000 0 -0.33 2 2
Su(fu)/SIN3/HDAC complex -0.005 0.095 0.22 1 -0.44 18 19
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.019 0.004 -10000 0 -10000 0 0
NFATC1 -0.008 0.074 0.34 3 -0.33 12 15
NFATC2 -0.001 0.066 0.19 8 -0.25 20 28
NFATC3 0.008 0.016 -10000 0 -0.35 1 1
YWHAE 0.02 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.025 0.073 0.29 2 -0.3 11 13
Exportin 1/Ran/NUP214 0.037 0.012 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.002 0.069 -10000 0 -0.3 10 10
BCL2/BAX 0.029 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.008 -10000 0 -10000 0 0
BAX 0.02 0.002 -10000 0 -10000 0 0
MAPK14 0.018 0.008 -10000 0 -10000 0 0
BAD 0.02 0.02 0.19 1 -0.42 1 2
CABIN1/MEF2D -0.015 0.072 0.29 1 -0.29 11 12
Calcineurin A alpha-beta B1/BCL2 0.02 0.003 -10000 0 -10000 0 0
FKBP8 0.019 0.019 -10000 0 -0.42 1 1
activation-induced cell death of T cells 0.015 0.072 0.29 11 -0.29 1 12
KPNB1 0.02 0.003 -10000 0 -10000 0 0
KPNA2 0.02 0.003 -10000 0 -10000 0 0
XPO1 0.019 0.004 -10000 0 -10000 0 0
SFN 0.022 0.081 0.19 41 -0.42 12 53
MAP3K8 0.019 0.013 0.19 2 -10000 0 2
NFAT4/CK1 alpha -0.019 0.016 -10000 0 -0.22 1 1
MEF2D/NFAT1/Cbp/p300 0.019 0.078 -10000 0 -0.27 21 21
CABIN1 -0.024 0.072 0.29 2 -0.31 11 13
CALM1 0.018 0.009 -10000 0 -10000 0 0
RAN 0.019 0.004 -10000 0 -10000 0 0
MAP3K1 0.018 0.006 -10000 0 -10000 0 0
CAMK4 0.015 0.02 -10000 0 -0.42 1 1
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.019 0.004 -10000 0 -10000 0 0
YWHAH 0.02 0.002 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.026 0.022 -10000 0 -0.3 2 2
YWHAB 0.019 0.004 -10000 0 -10000 0 0
MAPK8 0.017 0.028 -10000 0 -0.42 2 2
MAPK9 0.015 0.009 -10000 0 -10000 0 0
YWHAG 0.018 0.006 -10000 0 -10000 0 0
FKBP1A 0.019 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.004 0.079 -10000 0 -0.33 11 11
PRKCH 0.019 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.026 0.019 -10000 0 -0.3 1 1
CASP3 0.019 0.007 -10000 0 -10000 0 0
PIM1 0.019 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.005 -10000 0 -10000 0 0
apoptosis 0.013 0.009 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.051 -10000 0 -0.29 8 8
PRKCB 0.018 0.03 0.19 3 -0.42 2 5
PRKCE 0.019 0.019 -10000 0 -0.42 1 1
JNK2/NFAT4 0.007 0.04 -10000 0 -0.25 2 2
BAD/BCL-XL 0.028 0.016 -10000 0 -0.3 1 1
PRKCD 0.015 0.012 0.19 1 -10000 0 1
NUP214 0.019 0.005 -10000 0 -10000 0 0
PRKCZ 0.016 0.034 -10000 0 -0.42 3 3
PRKCA 0.02 0.003 -10000 0 -10000 0 0
PRKCG 0.025 0.033 0.19 20 -10000 0 20
PRKCQ 0.01 0.065 -10000 0 -0.42 12 12
FKBP38/BCL2 0.028 0.015 -10000 0 -0.3 1 1
EP300 0.018 0.021 -10000 0 -0.42 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.019 0.004 -10000 0 -10000 0 0
NFATc/JNK1 0 0.075 0.3 2 -0.31 12 14
CaM/Ca2+/FKBP38 0.024 0.017 -10000 0 -0.26 1 1
FKBP12/FK506 0.014 0.003 -10000 0 -10000 0 0
CSNK1A1 -0.011 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.019 0.018 -10000 0 -0.24 1 1
NFATc/ERK1 -0.002 0.071 -10000 0 -0.32 12 12
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.003 0.07 -10000 0 -0.3 10 10
NR4A1 -0.019 0.09 0.19 11 -0.36 21 32
GSK3B 0.018 0.009 -10000 0 -10000 0 0
positive T cell selection 0.008 0.016 -10000 0 -0.34 1 1
NFAT1/CK1 alpha -0.013 0.035 -10000 0 -0.21 8 8
RCH1/ KPNB1 0.029 0.005 -10000 0 -10000 0 0
YWHAQ 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.019 0.007 -10000 0 -10000 0 0
AKAP5 0.017 0.027 -10000 0 -0.42 2 2
MEF2D 0.018 0.01 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.003 0.074 0.33 3 -0.32 8 11
CREBBP 0.018 0.009 -10000 0 -10000 0 0
BCL2 0.02 0.003 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.023 0.024 -10000 0 -0.26 5 5
SNTA1 0.019 0.019 -10000 0 -0.42 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.022 0.016 -10000 0 -0.26 2 2
MAPK12 -0.013 0.02 0.2 1 -0.22 3 4
CCND1 0.003 0.03 -10000 0 -0.37 2 2
p38 gamma/SNTA1 -0.013 0.038 0.18 12 -0.28 3 15
MAP2K3 0.02 0.003 -10000 0 -10000 0 0
PKN1 0.02 0.002 -10000 0 -10000 0 0
G2/M transition checkpoint -0.013 0.02 0.2 1 -0.22 3 4
MAP2K6 -0.009 0.018 -10000 0 -0.24 3 3
MAPT -0.015 0.068 0.28 4 -0.34 16 20
MAPK13 -0.021 0.028 -10000 0 -0.3 5 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.026 0.022 -10000 0 -0.3 2 2
ATM 0.019 0.019 -10000 0 -0.42 1 1
UBE2D3 0.02 0.002 -10000 0 -10000 0 0
PRKDC 0.019 0.005 -10000 0 -10000 0 0
ATR 0.019 0.005 -10000 0 -10000 0 0
UBE2L3 0.02 0.002 -10000 0 -10000 0 0
FANCD2 0.006 0.013 -10000 0 -0.28 1 1
protein ubiquitination 0.048 0.028 -10000 0 -0.21 3 3
XRCC5 0.019 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
M/R/N Complex 0.03 0.018 -10000 0 -10000 0 0
MRE11A 0.02 0.002 -10000 0 -10000 0 0
DNA-PK 0.036 0.013 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.016 0.11 -10000 0 -0.46 21 21
FANCF 0.02 0.002 -10000 0 -10000 0 0
BRCA1 0.02 0.003 -10000 0 -10000 0 0
CCNE1 0.022 0.019 0.19 7 -10000 0 7
CDK2/Cyclin E1 0.031 0.015 -10000 0 -10000 0 0
FANCG 0.019 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.027 0.022 -10000 0 -0.3 2 2
FANCE 0.02 0.008 0.19 1 -10000 0 1
FANCC 0.019 0.004 -10000 0 -10000 0 0
NBN 0.019 0.005 -10000 0 -10000 0 0
FANCA 0.053 0.068 0.19 105 -10000 0 105
DNA repair -0.017 0.08 0.29 10 -0.35 7 17
BRCA1/BARD1/ubiquitin 0.027 0.022 -10000 0 -0.3 2 2
BARD1/DNA-PK 0.045 0.025 -10000 0 -0.24 2 2
FANCL 0.02 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.022 0.3 2 -10000 0 2
BRCA1/BARD1/CTIP/M/R/N Complex -0.006 0.033 -10000 0 -0.29 4 4
BRCA1/BACH1/BARD1/TopBP1 0.035 0.023 -10000 0 -0.26 2 2
BRCA1/BARD1/P53 0.045 0.025 -10000 0 -0.24 2 2
BARD1/CSTF1/BRCA1 0.036 0.022 -10000 0 -0.26 2 2
BRCA1/BACH1 0.02 0.003 -10000 0 -10000 0 0
BARD1 0.017 0.027 -10000 0 -0.42 2 2
PCNA 0.019 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.037 0.022 -10000 0 -0.26 2 2
BRCA1/BARD1/UbcH7 0.037 0.022 -10000 0 -0.26 2 2
BRCA1/BARD1/RAD51/PCNA 0.048 0.029 -10000 0 -0.24 2 2
BARD1/DNA-PK/P53 0.05 0.029 -10000 0 -0.23 2 2
BRCA1/BARD1/Ubiquitin 0.027 0.022 -10000 0 -0.3 2 2
BRCA1/BARD1/CTIP 0.024 0.028 -10000 0 -0.31 3 3
FA complex 0.015 0.047 0.2 1 -0.28 1 2
BARD1/EWS 0.027 0.022 -10000 0 -0.3 2 2
RBBP8 -0.02 0.023 -10000 0 -0.54 1 1
TP53 0.02 0.003 -10000 0 -10000 0 0
TOPBP1 0.019 0.005 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.043 0.024 0.24 2 -10000 0 2
BRCA1/BARD1 0.053 0.029 -10000 0 -0.22 3 3
CSTF1 0.019 0.004 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.013 0.019 -10000 0 -0.29 2 2
CDK2 0.02 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.024 0.026 0.19 13 -10000 0 13
RAD50 0.015 0.009 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.022 -10000 0 -0.3 2 2
EWSR1 0.02 0.002 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.02 0.003 -10000 0 -9999 0 0
ITGB7 0.02 0.003 -10000 0 -9999 0 0
ITGA4 0.024 0.029 0.19 16 -9999 0 16
alpha4/beta7 Integrin 0.031 0.022 -10000 0 -9999 0 0
alpha4/beta1 Integrin 0.032 0.022 -10000 0 -9999 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.019 0.019 -10000 0 -0.42 1 1
HDAC4 0.019 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.018 0.005 -10000 0 -10000 0 0
CDKN1A -0.012 0.009 -10000 0 -10000 0 0
KAT2B 0.014 0.021 -10000 0 -0.42 1 1
BAX 0.02 0.002 -10000 0 -10000 0 0
FOXO3 0.003 0.015 0.35 1 -10000 0 1
FOXO1 0.02 0.003 -10000 0 -10000 0 0
FOXO4 0.004 0.011 -10000 0 -0.25 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.003 -10000 0 -10000 0 0
TAT 0.022 0.023 0.19 10 -10000 0 10
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.009 0.029 -10000 0 -0.3 1 1
PPARGC1A -0.022 0.13 -10000 0 -0.42 50 50
FHL2 0.017 0.034 0.19 1 -0.42 3 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.028 0.008 -10000 0 -10000 0 0
HIST2H4A -0.018 0.005 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.01 0.029 0.25 1 -0.2 7 8
SIRT1 0.019 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.036 0.014 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.016 0.029 -10000 0 -0.22 1 1
apoptosis -0.038 0.011 -10000 0 -10000 0 0
SIRT1/PGC1A -0.001 0.082 -10000 0 -0.25 50 50
p53/SIRT1 0.027 0.009 -10000 0 -10000 0 0
SIRT1/FOXO4 0.019 0.022 -10000 0 -0.22 1 1
FOXO1/FHL2/SIRT1 0.035 0.023 -10000 0 -0.23 3 3
HIST1H1E 0.004 0.012 -10000 0 -0.25 1 1
SIRT1/p300 0.027 0.016 -10000 0 -0.3 1 1
muscle cell differentiation 0.012 0.027 0.26 1 -0.2 2 3
TP53 0.019 0.006 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.038 0.011 -10000 0 -10000 0 0
CREBBP 0.019 0.004 -10000 0 -10000 0 0
MEF2D 0.019 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.018 -10000 0 -10000 0 0
ACSS2 -0.019 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.012 0.027 0.21 2 -0.26 1 3
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.031 0.042 -10000 0 -0.3 3 3
Ran/GTP/Exportin 1/HDAC1 -0.02 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.04 -10000 0 -0.29 3 3
SUMO1 0.019 0.004 -10000 0 -10000 0 0
ZFPM1 0.017 0.033 -10000 0 -0.42 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.004 0.001 -10000 0 -10000 0 0
FKBP3 0.019 0.005 -10000 0 -10000 0 0
Histones 0.031 0.029 -10000 0 -10000 0 0
YY1/LSF -0.02 0.07 -10000 0 -0.24 19 19
SMG5 0.019 0.004 -10000 0 -10000 0 0
RAN 0.019 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.004 0.024 -10000 0 -0.22 2 2
I kappa B alpha/HDAC1 0.012 0.031 -10000 0 -10000 0 0
SAP18 0.02 0.003 -10000 0 -10000 0 0
RELA 0.003 0.027 -10000 0 -10000 0 0
HDAC1/Smad7 0.035 0.015 -10000 0 -10000 0 0
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
HDAC3/TR2 0.015 0.02 -10000 0 -10000 0 0
NuRD/MBD3 Complex -0.001 0.064 -10000 0 -0.36 12 12
NF kappa B1 p50/RelA 0.045 0.065 0.26 8 -0.4 1 9
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.01 0.063 -10000 0 -0.42 11 11
GATA1 0.026 0.032 0.19 20 -10000 0 20
Mad/Max 0.027 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.002 0.067 -10000 0 -0.39 8 8
RBBP7 0.02 0.002 -10000 0 -10000 0 0
NPC 0.012 0.002 -10000 0 -10000 0 0
RBBP4 0.019 0.019 -10000 0 -0.42 1 1
MAX 0.019 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.015 0.009 -10000 0 -10000 0 0
NFKBIA 0.007 0.013 -10000 0 -10000 0 0
KAT2B 0.014 0.021 -10000 0 -0.42 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.002 0.047 -10000 0 -0.32 7 7
SIN3 complex 0.052 0.022 -10000 0 -10000 0 0
SMURF1 0.018 0.006 -10000 0 -10000 0 0
CHD3 0.02 0.003 -10000 0 -10000 0 0
SAP30 0.026 0.031 0.19 18 -10000 0 18
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.02 0.003 -10000 0 -10000 0 0
YY1/HDAC3 -0.01 0.047 -10000 0 -0.3 3 3
YY1/HDAC2 -0.016 0.068 -10000 0 -0.24 20 20
YY1/HDAC1 -0.019 0.07 -10000 0 -0.24 20 20
NuRD/MBD2 Complex (MeCP1) 0 0.065 -10000 0 -0.38 11 11
PPARG 0.004 0.02 -10000 0 -0.27 2 2
HDAC8/hEST1B 0.039 0.009 -10000 0 -10000 0 0
UBE2I 0.019 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.009 -10000 0 -10000 0 0
TNFRSF1A 0.019 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.014 0.02 -10000 0 -10000 0 0
MBD3L2 0.018 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.015 -10000 0 -10000 0 0
CREBBP 0.019 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.003 0.062 -10000 0 -0.34 12 12
HDAC1 0.019 0.004 -10000 0 -10000 0 0
HDAC3 0.007 0.013 -10000 0 -10000 0 0
HDAC2 0.019 0.005 -10000 0 -10000 0 0
YY1 0.003 0.024 -10000 0 -0.55 1 1
HDAC8 0.02 0.001 -10000 0 -10000 0 0
SMAD7 0.02 0.003 -10000 0 -10000 0 0
NCOR2 0.019 0.004 -10000 0 -10000 0 0
MXD1 0.02 0.003 -10000 0 -10000 0 0
STAT3 0.008 0.013 -10000 0 -0.28 1 1
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 -0.011 0.071 -10000 0 -0.22 19 19
YY1/SAP30/HDAC1 -0.007 0.076 0.2 1 -0.23 15 16
EP300 0.019 0.019 -10000 0 -0.42 1 1
STAT3 (dimer non-phopshorylated) 0.008 0.013 -10000 0 -0.28 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.013 -10000 0 -10000 0 0
histone deacetylation -0.001 0.069 -10000 0 -0.38 13 13
STAT3 (dimer non-phopshorylated)/HDAC3 0.007 0.023 -10000 0 -10000 0 0
nuclear export -0.038 0.009 -10000 0 -10000 0 0
PRKACA 0.02 0.002 -10000 0 -10000 0 0
GATAD2B 0.019 0.004 -10000 0 -10000 0 0
GATAD2A 0.02 0.002 -10000 0 -10000 0 0
GATA2/HDAC3 0.011 0.036 -10000 0 -0.23 8 8
GATA1/HDAC1 0.033 0.024 -10000 0 -10000 0 0
GATA1/HDAC3 0.018 0.029 -10000 0 -10000 0 0
CHD4 0.019 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.026 0.032 -10000 0 -0.3 4 4
SIN3/HDAC complex/Mad/Max -0.005 0.068 -10000 0 -0.4 11 11
NuRD Complex 0.003 0.063 -10000 0 -0.33 13 13
positive regulation of chromatin silencing 0.03 0.028 -10000 0 -10000 0 0
SIN3B 0.02 0.002 -10000 0 -10000 0 0
MTA2 0.02 0.002 -10000 0 -10000 0 0
SIN3A 0.02 0.002 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.026 0.03 -10000 0 -10000 0 0
HDAC complex 0.046 0.02 -10000 0 -0.24 1 1
GATA1/Fog1 0.031 0.034 -10000 0 -0.3 3 3
FKBP25/HDAC1/HDAC2 0.035 0.014 -10000 0 -10000 0 0
TNF 0.017 0.041 0.19 4 -0.42 4 8
negative regulation of cell growth -0.006 0.068 -10000 0 -0.38 12 12
NuRD/MBD2/PRMT5 Complex 0 0.065 -10000 0 -0.38 11 11
Ran/GTP/Exportin 1 0.025 0.029 -10000 0 -0.17 6 6
NF kappa B/RelA/I kappa B alpha 0.003 0.031 -10000 0 -0.29 2 2
SIN3/HDAC complex/NCoR1 0.001 0.05 -10000 0 -0.34 6 6
TFCP2 0.02 0.003 -10000 0 -10000 0 0
NR2C1 0.019 0.004 -10000 0 -10000 0 0
MBD3 0.019 0.021 0.19 1 -0.42 1 2
MBD2 0.02 0.003 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.019 0.004 -10000 0 -10000 0 0
HDAC3 0.015 0.009 -10000 0 -10000 0 0
VDR 0.017 0.033 -10000 0 -0.42 3 3
Cbp/p300/PCAF 0.027 0.029 -10000 0 -0.47 1 1
EP300 0.019 0.019 -10000 0 -0.42 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.039 -10000 0 -0.29 7 7
KAT2B 0.014 0.021 -10000 0 -0.42 1 1
MAPK14 0.019 0.004 -10000 0 -10000 0 0
AKT1 -0.022 0.054 0.17 1 -0.23 5 6
RAR alpha/9cRA/Cyclin H 0.022 0.045 -10000 0 -0.3 4 4
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.037 0.088 0.16 1 -0.25 11 12
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.014 0.043 -10000 0 -0.31 8 8
NCOR2 0.019 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0.023 -10000 0 -0.29 3 3
RXRs/RARs/NRIP1/9cRA -0.025 0.079 0.29 2 -0.42 4 6
NCOA2 0.011 0.06 -10000 0 -0.42 10 10
NCOA3 0.019 0.004 -10000 0 -10000 0 0
NCOA1 0.02 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.017 0.033 -10000 0 -0.42 3 3
RARG 0.02 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.019 0.004 -10000 0 -10000 0 0
MAPK1 0.02 0.002 -10000 0 -10000 0 0
MAPK8 0.018 0.027 -10000 0 -0.42 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.017 0.045 -10000 0 -10000 0 0
RARA 0.007 0.018 -10000 0 -0.22 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.039 0.097 0.16 2 -0.34 15 17
PRKCA 0.02 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.034 0.095 0.33 1 -0.45 5 6
RXRG 0.012 0.017 -10000 0 -10000 0 0
RXRA 0.002 0.018 0.16 1 -0.19 2 3
RXRB 0.011 0.015 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0.023 -10000 0 -0.29 3 3
RBP1 0.019 0.023 0.19 3 -0.42 1 4
CRBP1/9-cic-RA 0.014 0.016 0.13 3 -0.29 1 4
RARB 0.013 0.028 -10000 0 -0.42 2 2
PRKCG 0.025 0.033 0.19 20 -10000 0 20
MNAT1 0.019 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.014 0.064 0.36 1 -0.41 4 5
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.016 0.071 0.28 2 -0.39 4 6
proteasomal ubiquitin-dependent protein catabolic process -0.046 0.11 0.24 10 -0.29 23 33
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.024 0.093 0.38 1 -0.43 4 5
positive regulation of DNA binding 0.016 0.041 -10000 0 -0.28 4 4
NRIP1 -0.045 0.11 -10000 0 -0.56 1 1
RXRs/RARs -0.048 0.12 0.27 1 -0.4 7 8
RXRs/RXRs/DNA/9cRA 0.005 0.037 -10000 0 -10000 0 0
PRKACA 0.02 0.002 -10000 0 -10000 0 0
CDK7 0.018 0.006 -10000 0 -10000 0 0
TFIIH 0.034 0.016 -10000 0 -10000 0 0
RAR alpha/9cRA 0.032 0.044 -10000 0 -0.27 6 6
CCNH 0.018 0.007 -10000 0 -10000 0 0
CREBBP 0.019 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.03 0.019 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.03 0.008 -10000 0 -10000 0 0
FBXW11 0.015 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.022 0.022 -10000 0 -0.26 4 4
NF kappa B1 p50/RelA/I kappa B alpha -0.024 0.049 -10000 0 -0.26 7 7
NFKBIA 0.001 0.019 -10000 0 -0.26 2 2
MAPK14 0.019 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.016 0.015 -10000 0 -0.26 1 1
ARRB2 0.006 0.001 -10000 0 -10000 0 0
REL 0.017 0.033 -10000 0 -0.42 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.021 0.014 0.13 1 -0.26 1 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.021 0.012 -10000 0 -0.26 1 1
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
NF kappa B1 p50 dimer -0.018 0.014 -10000 0 -0.3 1 1
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
NFKB1 -0.018 0.014 -10000 0 -0.3 1 1
RELA 0.02 0.002 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.002 0.037 -10000 0 -0.22 9 9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.026 0.053 -10000 0 -0.27 9 9
SRC 0.019 0.004 -10000 0 -10000 0 0
PI3K 0.025 0.022 -10000 0 -0.3 2 2
NF kappa B1 p50/RelA -0.002 0.037 -10000 0 -0.22 9 9
IKBKB 0.019 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.009 -10000 0 -10000 0 0
SYK 0.019 0.019 -10000 0 -0.42 1 1
I kappa B alpha/PIK3R1 0.002 0.056 0.22 2 -0.24 14 16
cell death -0.025 0.051 -10000 0 -0.26 9 9
NF kappa B1 p105/c-Rel -0.022 0.022 -10000 0 -0.26 4 4
LCK 0.024 0.042 0.19 20 -0.42 2 22
BCL3 0.021 0.011 0.19 2 -10000 0 2
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.034 0.076 0.17 119 -0.33 1 120
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.001 0.053 0.13 11 -0.3 10 21
AP2 0.028 0.007 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.025 0.011 -10000 0 -10000 0 0
CLTB 0.015 0.009 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.005 0.004 -10000 0 -10000 0 0
CD4 0.022 0.022 0.19 9 -10000 0 9
CLTA 0.019 0.004 -10000 0 -10000 0 0
mol:GTP -0.003 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.01 0.013 -10000 0 -0.29 1 1
mol:PI-4-5-P2 -0.004 0.013 -10000 0 -0.27 1 1
ARF1/GTP 0.024 0.012 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.007 0.018 -10000 0 -0.27 1 1
mol:Choline -0.005 0.013 -10000 0 -0.27 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.02 0.005 -10000 0 -10000 0 0
DDEF1 -0.003 0.013 -10000 0 -0.28 1 1
ARF1/GDP 0.001 0.016 -10000 0 -0.11 8 8
AP2M1 0.019 0.004 -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 0.013 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.014 -10000 0 -0.22 1 1
ARFIP2 0.018 0.012 -10000 0 -10000 0 0
COPA 0.019 0.004 -10000 0 -10000 0 0
RAC1 0.018 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex -0.005 0.043 -10000 0 -0.3 8 8
ARF1/GTP/ARHGAP10 0.013 0.004 -10000 0 -10000 0 0
GGA3 0.02 0.003 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.013 0.031 -10000 0 -0.26 6 6
AP2A1 0.02 0.002 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.017 -10000 0 -0.15 2 2
ARF1/GDP/Membrin 0.013 0.038 -10000 0 -0.33 6 6
Arfaptin 2/Rac/GDP 0.024 0.011 -10000 0 -10000 0 0
CYTH2 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.007 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.013 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 0.027 -10000 0 -0.18 7 7
PLD2 -0.005 0.013 -10000 0 -0.27 1 1
ARF-GAP1/v-SNARE -0.01 0.012 -10000 0 -0.29 1 1
PIP5K1A -0.005 0.013 -10000 0 -0.28 1 1
ARF1/GTP/Membrin/GBF1/p115 0.009 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.005 0.013 -10000 0 -0.27 1 1
KDEL Receptor/Ligand/ARF-GAP1 -0.01 0.012 -10000 0 -0.29 1 1
GOSR2 0.006 0.006 -10000 0 -10000 0 0
USO1 0.004 0.025 -10000 0 -0.32 3 3
GBF1 -0.001 0.047 -10000 0 -0.32 11 11
ARF1/GTP/Arfaptin 2 0.028 0.009 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.04 0.018 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.046 0.021 -10000 0 -0.24 1 1
HDAC3 0.015 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.02 0.006 -10000 0 -10000 0 0
GATA1/HDAC4 0.032 0.024 -10000 0 -10000 0 0
GATA1/HDAC5 0.033 0.028 -10000 0 -0.3 1 1
GATA2/HDAC5 0.021 0.048 -10000 0 -0.3 11 11
HDAC5/BCL6/BCoR 0.037 0.017 -10000 0 -0.26 1 1
HDAC9 0.018 0.006 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.03 0.019 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.026 0.011 -10000 0 -10000 0 0
HDAC5/YWHAB 0.028 0.016 -10000 0 -0.3 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.004 0.001 -10000 0 -10000 0 0
GATA2 0.01 0.063 -10000 0 -0.42 11 11
HDAC4/RFXANK 0.028 0.009 -10000 0 -10000 0 0
BCOR 0.02 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.019 -10000 0 -0.42 1 1
HDAC5 0.019 0.019 -10000 0 -0.42 1 1
GNB1/GNG2 0.027 0.009 -10000 0 -10000 0 0
Histones 0.005 0.039 -10000 0 -0.52 1 1
ADRBK1 0.02 0.002 -10000 0 -10000 0 0
HDAC4 0.019 0.005 -10000 0 -10000 0 0
XPO1 0.02 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.026 0.017 -10000 0 -0.3 1 1
HDAC4/Ubc9 0.027 0.009 -10000 0 -10000 0 0
HDAC7 0.02 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0.015 -10000 0 -0.3 1 1
TUBA1B 0.02 0.003 -10000 0 -10000 0 0
HDAC6 0.02 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.029 0.016 -10000 0 -0.3 1 1
CAMK4 0.015 0.02 -10000 0 -0.42 1 1
Tubulin/HDAC6 0.037 0.017 -10000 0 -0.26 1 1
SUMO1 0.019 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.019 0.004 -10000 0 -10000 0 0
GATA1 0.026 0.032 0.19 20 -10000 0 20
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.02 0.003 -10000 0 -10000 0 0
NR3C1 0.016 0.011 0.19 1 -10000 0 1
SUMO1/HDAC4 0.027 0.03 -10000 0 -10000 0 0
SRF 0.019 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.028 0.008 -10000 0 -10000 0 0
Tubulin 0.027 0.016 -10000 0 -0.3 1 1
HDAC4/14-3-3 E 0.028 0.008 -10000 0 -10000 0 0
GNB1 0.019 0.004 -10000 0 -10000 0 0
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
BCL6/BCoR 0.028 0.007 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.029 0.019 -10000 0 -10000 0 0
HDAC4/SRF 0.03 0.022 -10000 0 -0.26 1 1
HDAC4/ER alpha 0.025 0.027 -10000 0 -0.3 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.005 0.039 -10000 0 -0.51 1 1
cell motility 0.037 0.017 -10000 0 -0.26 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.019 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.023 0.013 -10000 0 -10000 0 0
BCL6 0.019 0.004 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.019 0.005 -10000 0 -10000 0 0
Hsp90/HDAC6 0.028 0.008 -10000 0 -10000 0 0
ESR1 0.016 0.034 0.19 1 -0.42 3 4
HDAC6/HDAC11 0.021 0.02 -10000 0 -0.3 1 1
Ran/GTP/Exportin 1 0.025 0.029 -10000 0 -0.17 6 6
NPC 0.012 0.002 -10000 0 -10000 0 0
MEF2C 0.018 0.007 -10000 0 -10000 0 0
RAN 0.019 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.041 0.029 -10000 0 -10000 0 0
GNG2 0.019 0.005 -10000 0 -10000 0 0
NCOR2 0.019 0.004 -10000 0 -10000 0 0
TUBB2A 0.019 0.019 -10000 0 -0.42 1 1
HDAC11 0.014 0.021 -10000 0 -0.42 1 1
HSP90AA1 0.019 0.005 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
ANKRA2 0.018 0.006 -10000 0 -10000 0 0
RFXANK 0.02 0.008 0.19 1 -10000 0 1
nuclear import -0.019 0.014 0.26 1 -10000 0 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.013 -10000 0 -10000 0 0
DOCK1 0.019 0.019 -10000 0 -0.42 1 1
ITGA4 0.024 0.029 0.19 16 -10000 0 16
RAC1 0.018 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.031 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.021 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.03 0.02 -10000 0 -10000 0 0
lamellipodium assembly 0.003 0.051 -10000 0 -0.52 3 3
PIK3CA 0.018 0.02 -10000 0 -0.42 1 1
PI3K 0.025 0.022 -10000 0 -0.3 2 2
ARF6 0.019 0.005 -10000 0 -10000 0 0
TLN1 0.019 0.004 -10000 0 -10000 0 0
PXN -0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.02 -10000 0 -0.42 1 1
ARF6/GTP 0.036 0.023 -10000 0 -10000 0 0
cell adhesion 0.037 0.022 -10000 0 -10000 0 0
CRKL/CBL 0.029 0.015 -10000 0 -0.3 1 1
alpha4/beta1 Integrin/Paxillin 0.029 0.021 -10000 0 -10000 0 0
ITGB1 0.02 0.003 -10000 0 -10000 0 0
ITGB7 0.02 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.019 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.04 0.029 -10000 0 -0.22 1 1
p130Cas/Crk/Dock1 0.036 0.022 -10000 0 -0.26 2 2
VCAM1 0.021 0.029 0.19 9 -0.42 1 10
alpha4/beta1 Integrin/Paxillin/Talin 0.039 0.022 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.039 0.022 -10000 0 -10000 0 0
BCAR1 0.019 0.019 -10000 0 -0.42 1 1
mol:GDP -0.038 0.021 -10000 0 -10000 0 0
CBL 0.019 0.019 -10000 0 -0.42 1 1
PRKACA 0.02 0.002 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.039 0.022 -10000 0 -10000 0 0
Rac1/GTP 0.003 0.057 -10000 0 -0.6 3 3
Circadian rhythm 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
chromatin modification 0.027 0.024 -10000 0 -10000 0 0
CLOCK 0.019 0.02 -10000 0 -0.42 1 1
TIMELESS/CRY2 0.017 0.023 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.009 -10000 0 -10000 0 0
ATR 0.019 0.005 -10000 0 -10000 0 0
NR1D1 0 0.051 -10000 0 -1.2 1 1
ARNTL 0.02 0.005 -10000 0 -10000 0 0
TIMELESS 0.001 0.018 -10000 0 -10000 0 0
NPAS2 0.016 0.043 -10000 0 -0.42 5 5
CRY2 0.02 0.002 -10000 0 -10000 0 0
mol:CO -0.001 0.007 0.13 1 -0.069 1 2
CHEK1 0.02 0.002 -10000 0 -10000 0 0
mol:HEME 0.001 0.007 0.069 1 -0.13 1 2
PER1 0.02 0.003 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.038 0.031 -10000 0 -0.24 5 5
BMAL1/CLOCK 0.005 0.054 -10000 0 -0.79 1 1
S phase of mitotic cell cycle 0.027 0.024 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.027 0.024 -10000 0 -10000 0 0
mol:NADPH 0.001 0.007 0.069 1 -0.13 1 2
PER1/TIMELESS 0.017 0.022 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.008 0.19 1 -10000 0 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.018 0.02 -10000 0 -0.42 1 1
positive regulation of NF-kappaB transcription factor activity 0.025 0.018 -10000 0 -0.3 1 1
MAP2K4 -0.002 0.038 0.19 1 -0.27 3 4
IKBKB 0.019 0.006 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.01 0.19 1 -10000 0 1
TNFRSF10A 0.018 0.006 -10000 0 -10000 0 0
SMPD1 0.004 0.008 -10000 0 -0.17 1 1
IKBKG 0.02 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.018 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.025 0.018 -10000 0 -0.3 1 1
TRAIL/TRAILR3 0.025 0.018 -10000 0 -0.3 1 1
TRAIL/TRAILR1 0.025 0.018 -10000 0 -0.3 1 1
TRAIL/TRAILR4 0.025 0.018 -10000 0 -0.3 1 1
TRAIL/TRAILR1/DAP3/GTP 0.032 0.019 -10000 0 -0.23 1 1
IKK complex -0.009 0.06 -10000 0 -10000 0 0
RIPK1 0.019 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.003 -10000 0 -10000 0 0
MAPK3 -0.018 0.013 -10000 0 -0.3 1 1
MAP3K1 0.005 0.035 -10000 0 -0.28 3 3
TRAILR4 (trimer) 0.018 0.006 -10000 0 -10000 0 0
TRADD 0.019 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.004 0.044 -10000 0 -0.22 1 1
CFLAR 0.019 0.004 -10000 0 -10000 0 0
MAPK1 -0.019 0.013 -10000 0 -0.3 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.047 0.029 -10000 0 -0.23 1 1
mol:ceramide 0.004 0.008 -10000 0 -0.17 1 1
FADD 0.02 0.002 -10000 0 -10000 0 0
MAPK8 -0.011 0.044 0.25 1 -0.32 1 2
TRAF2 0.019 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.018 0.006 -10000 0 -10000 0 0
CHUK 0.019 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.035 0.019 -10000 0 -0.26 1 1
DAP3 0.019 0.004 -10000 0 -10000 0 0
CASP10 -0.011 0.028 0.18 1 -0.28 1 2
JNK cascade 0.025 0.018 -10000 0 -0.3 1 1
TRAIL (trimer) 0.018 0.019 -10000 0 -0.42 1 1
TNFRSF10C 0.018 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.038 0.024 -10000 0 -0.22 1 1
TRAIL/TRAILR2/FADD 0.035 0.019 -10000 0 -0.26 1 1
cell death 0.004 0.008 -10000 0 -0.17 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.004 0.044 -10000 0 -0.22 1 1
TRAILR2 (trimer) 0.018 0.01 0.19 1 -10000 0 1
CASP8 -0.001 0.082 -10000 0 -0.61 9 9
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.047 0.029 -10000 0 -0.23 1 1
Sumoylation by RanBP2 regulates transcriptional repression

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.019 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.02 0.007 -10000 0 -10000 0 0
MDM2/SUMO1 0.026 0.029 -10000 0 -0.17 6 6
HDAC4 0.019 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.02 0.007 -10000 0 -10000 0 0
SUMO1 0.019 0.004 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.001 0.023 -10000 0 -0.2 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.006 0.01 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.019 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.02 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.027 0.03 -10000 0 -10000 0 0
SUMO1/HDAC1 0.026 0.03 -10000 0 -10000 0 0
RANGAP1 0.02 0.003 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.047 0.016 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.004 0.001 -10000 0 -10000 0 0
Ran/GTP 0.015 0.028 -10000 0 -0.18 6 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.019 0.004 -10000 0 -10000 0 0
UBE2I 0.019 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.01 0.028 0.24 1 -10000 0 1
NPC 0.012 0.002 -10000 0 -10000 0 0
PIAS2 0.02 0.003 -10000 0 -10000 0 0
PIAS1 0.02 0.002 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.032 0.012 -10000 0 -10000 0 0
MAPK9 0.002 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.009 0.01 0.1 4 -10000 0 4
GNB1/GNG2 0.025 0.008 -10000 0 -10000 0 0
GNB1 0.019 0.004 -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 0.003 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.013 0.002 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.002 0 -10000 0 -10000 0 0
GNAL 0.02 0.003 -10000 0 -10000 0 0
GNG2 0.019 0.005 -10000 0 -10000 0 0
CRH 0.018 0.016 0.19 4 -10000 0 4
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.018 -10000 0 -0.28 2 2
MAPK11 0.003 0.005 0.088 2 -10000 0 2
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.029 0.012 -10000 0 -10000 0 0
FBXW11 0.015 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.009 -10000 0 -10000 0 0
CHUK 0.019 0.004 -10000 0 -10000 0 0
NF kappa B2 p100/RelB 0.043 0.028 -10000 0 -10000 0 0
NFKB1 0.019 0.019 -10000 0 -0.42 1 1
MAP3K14 0.021 0.015 0.19 4 -10000 0 4
NF kappa B1 p50/RelB 0.029 0.015 -10000 0 -0.3 1 1
RELB 0.02 0.002 -10000 0 -10000 0 0
NFKB2 0.019 0.004 -10000 0 -10000 0 0
NF kappa B2 p52/RelB 0.026 0.006 -10000 0 -10000 0 0
regulation of B cell activation 0.026 0.006 -10000 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 525 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.T7.A92I TCGA.MW.A4EC TCGA.MM.A84U TCGA.MM.A564
109_MAP3K5 0.0037 0 0.057 0.0037
47_PPARGC1A 0.02 0.02 0.02 0.02
105_BMP4 0.02 0.02 0.02 0.02
105_BMP6 0.02 0.02 0.02 0.02
105_BMP7 0.02 0.018 -0.42 -0.42
105_BMP2 0.02 0.02 0.02 0.02
131_RELN/VLDLR -0.23 -0.24 0.052 -0.24
30_TGFB1/TGF beta receptor Type II 0.02 0.02 0.02 -0.022
84_STAT5B -0.046 -0.063 -0.14 -0.14
84_STAT5A -0.046 -0.063 -0.14 -0.14
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIRC-TP/19438817/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/KIRC-TP/19775260/GDAC_Gistic2Report_19781651/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)
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