PARADIGM pathway analysis of mRNASeq expression and copy number data
Colon Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1G15ZJD
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1G15ZJD
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
TCGA08_retinoblastoma 123
Reelin signaling pathway 110
Signaling events regulated by Ret tyrosine kinase 68
IL4-mediated signaling events 66
Ephrin A reverse signaling 64
Lissencephaly gene (LIS1) in neuronal migration and development 62
p75(NTR)-mediated signaling 52
BCR signaling pathway 52
Signaling events mediated by Stem cell factor receptor (c-Kit) 52
Glypican 1 network 51
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 432 . 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 ( 432 ).

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
TCGA08_retinoblastoma 0.2847 123 991 8 -0.12 0.094 1000 -1000 -0.003 -1000
Reelin signaling pathway 0.2546 110 6165 56 -0.33 0.071 1000 -1000 -0.049 -1000
Signaling events regulated by Ret tyrosine kinase 0.1574 68 5592 82 -0.13 0.032 1000 -1000 -0.059 -1000
IL4-mediated signaling events 0.1528 66 6033 91 -0.82 0.58 1000 -1000 -0.15 -1000
Ephrin A reverse signaling 0.1481 64 452 7 -0.055 0 1000 -1000 -0.015 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1435 62 3379 54 -0.3 0.035 1000 -1000 -0.054 -1000
p75(NTR)-mediated signaling 0.1204 52 6547 125 -0.44 0.067 1000 -1000 -0.075 -1000
BCR signaling pathway 0.1204 52 5211 99 -0.21 0.027 1000 -1000 -0.063 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1204 52 4096 78 -0.2 0.085 1000 -1000 -0.049 -1000
Glypican 1 network 0.1181 51 2480 48 -0.16 0.05 1000 -1000 -0.036 -1000
FOXA2 and FOXA3 transcription factor networks 0.1065 46 2120 46 -0.62 0.03 1000 -1000 -0.13 -1000
Fc-epsilon receptor I signaling in mast cells 0.1042 45 4432 97 -0.15 0.047 1000 -1000 -0.077 -1000
HIF-1-alpha transcription factor network 0.1019 44 3395 76 -0.55 0.035 1000 -1000 -0.15 -1000
Visual signal transduction: Rods 0.0880 38 2011 52 -0.22 0.041 1000 -1000 -0.041 -1000
IL1-mediated signaling events 0.0810 35 2174 62 -0.14 0.084 1000 -1000 -0.049 -1000
Signaling events mediated by the Hedgehog family 0.0787 34 1813 52 -0.064 0.061 1000 -1000 -0.036 -1000
BMP receptor signaling 0.0764 33 2715 81 -0.2 0.049 1000 -1000 -0.053 -1000
Syndecan-1-mediated signaling events 0.0741 32 1112 34 -0.4 0.03 1000 -1000 -0.05 -1000
JNK signaling in the CD4+ TCR pathway 0.0741 32 549 17 -0.13 0.031 1000 -1000 -0.044 -1000
Syndecan-2-mediated signaling events 0.0741 32 2257 69 -0.24 0.044 1000 -1000 -0.036 -1000
Visual signal transduction: Cones 0.0718 31 1183 38 -0.11 0.036 1000 -1000 -0.019 -1000
LPA receptor mediated events 0.0694 30 3156 102 -0.16 0.035 1000 -1000 -0.057 -1000
amb2 Integrin signaling 0.0671 29 2425 82 -0.083 0.035 1000 -1000 -0.043 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0671 29 1543 52 -0.22 0.057 1000 -1000 -0.038 -1000
Endothelins 0.0671 29 2837 96 -0.26 0.06 1000 -1000 -0.07 -1000
IGF1 pathway 0.0648 28 1621 57 -0.083 0.051 1000 -1000 -0.051 -1000
Plasma membrane estrogen receptor signaling 0.0625 27 2352 86 -0.17 0.072 1000 -1000 -0.06 -1000
TCR signaling in naïve CD8+ T cells 0.0602 26 2497 93 -0.04 0.038 1000 -1000 -0.051 -1000
Effects of Botulinum toxin 0.0602 26 689 26 -0.069 0.045 1000 -1000 -0.013 -1000
Ras signaling in the CD4+ TCR pathway 0.0602 26 454 17 -0.068 0.047 1000 -1000 -0.03 -1000
Osteopontin-mediated events 0.0579 25 951 38 -0.19 0.039 1000 -1000 -0.048 -1000
IL23-mediated signaling events 0.0579 25 1526 60 -0.27 0.027 1000 -1000 -0.12 -1000
S1P5 pathway 0.0556 24 408 17 -0.088 0.036 1000 -1000 -0.021 -1000
Canonical Wnt signaling pathway 0.0556 24 1254 51 -0.26 0.13 1000 -1000 -0.054 -1000
Presenilin action in Notch and Wnt signaling 0.0532 23 1438 61 -0.26 0.13 1000 -1000 -0.037 -1000
EPHB forward signaling 0.0532 23 1962 85 -0.085 0.094 1000 -1000 -0.067 -1000
Wnt signaling 0.0532 23 161 7 -0.065 0.023 1000 -1000 -0.023 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0532 23 2084 88 -0.13 0.06 1000 -1000 -0.067 -1000
TCGA08_p53 0.0509 22 154 7 -0.059 0.026 1000 -1000 -0.009 -1000
S1P4 pathway 0.0509 22 558 25 -0.088 0.039 1000 -1000 -0.032 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0486 21 795 37 -0.18 0.055 1000 -1000 -0.041 -1000
Calcium signaling in the CD4+ TCR pathway 0.0486 21 660 31 -0.27 0.026 1000 -1000 -0.057 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0486 21 2637 120 -0.12 0.1 1000 -1000 -0.049 -1000
LPA4-mediated signaling events 0.0463 20 242 12 -0.1 0.007 1000 -1000 -0.026 -1000
Ephrin B reverse signaling 0.0463 20 998 48 -0.084 0.031 1000 -1000 -0.029 -1000
Signaling events mediated by PRL 0.0463 20 712 34 -0.055 0.084 1000 -1000 -0.048 -1000
Signaling mediated by p38-alpha and p38-beta 0.0440 19 849 44 -0.039 0.026 1000 -1000 -0.041 -1000
IL12-mediated signaling events 0.0417 18 1585 87 -0.13 0.047 1000 -1000 -0.1 -1000
Syndecan-3-mediated signaling events 0.0417 18 637 35 -0.24 0.067 1000 -1000 -0.026 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0417 18 1259 68 -0.29 0.041 1000 -1000 -0.11 -1000
PDGFR-beta signaling pathway 0.0417 18 1822 97 -0.14 0.096 1000 -1000 -0.067 -1000
Arf6 signaling events 0.0394 17 1082 62 -0.12 0.059 1000 -1000 -0.034 -1000
HIF-2-alpha transcription factor network 0.0394 17 754 43 -0.36 0.17 1000 -1000 -0.079 -1000
Syndecan-4-mediated signaling events 0.0394 17 1140 67 -0.25 0.04 1000 -1000 -0.061 -1000
Thromboxane A2 receptor signaling 0.0370 16 1734 105 -0.19 0.069 1000 -1000 -0.063 -1000
Nectin adhesion pathway 0.0370 16 1058 63 -0.38 0.074 1000 -1000 -0.044 -1000
Glucocorticoid receptor regulatory network 0.0370 16 1866 114 -0.3 0.19 1000 -1000 -0.068 -1000
a4b1 and a4b7 Integrin signaling 0.0347 15 75 5 0.01 0.027 1000 -1000 0 -1000
Integrins in angiogenesis 0.0347 15 1332 84 -0.19 0.063 1000 -1000 -0.049 -1000
Regulation of Androgen receptor activity 0.0347 15 1080 70 -0.23 0.057 1000 -1000 -0.055 -1000
Nongenotropic Androgen signaling 0.0324 14 739 52 -0.088 0.063 1000 -1000 -0.046 -1000
EGFR-dependent Endothelin signaling events 0.0324 14 302 21 -0.061 0.038 1000 -1000 -0.051 -1000
Caspase cascade in apoptosis 0.0301 13 1002 74 -0.087 0.061 1000 -1000 -0.04 -1000
Noncanonical Wnt signaling pathway 0.0301 13 359 26 -0.065 0.026 1000 -1000 -0.05 -1000
Signaling events mediated by PTP1B 0.0301 13 1001 76 -0.21 0.045 1000 -1000 -0.039 -1000
Ceramide signaling pathway 0.0301 13 1030 76 -0.08 0.067 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class III 0.0301 13 526 40 -0.14 0.05 1000 -1000 -0.021 -1000
Regulation of p38-alpha and p38-beta 0.0301 13 734 54 -0.1 0.05 1000 -1000 -0.049 -1000
PLK1 signaling events 0.0278 12 1047 85 -0.01 0.059 1000 -1000 -0.03 -1000
S1P1 pathway 0.0278 12 434 36 -0.088 0.04 1000 -1000 -0.052 -1000
FAS signaling pathway (CD95) 0.0278 12 605 47 -0.027 0.044 1000 -1000 -0.035 -1000
S1P3 pathway 0.0278 12 526 42 -0.088 0.044 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 0.0255 11 1552 136 -0.48 0.069 1000 -1000 -0.054 -1000
FoxO family signaling 0.0255 11 706 64 -0.13 0.047 1000 -1000 -0.064 -1000
Glypican 2 network 0.0255 11 45 4 0.015 0.026 1000 -1000 0.002 -1000
IL6-mediated signaling events 0.0255 11 898 75 -0.071 0.075 1000 -1000 -0.069 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0255 11 386 33 -0.071 0.063 1000 -1000 -0.034 -1000
Aurora B signaling 0.0255 11 763 67 -0.38 0.089 1000 -1000 -0.044 -1000
ErbB2/ErbB3 signaling events 0.0231 10 706 65 -0.047 0.038 1000 -1000 -0.049 -1000
Coregulation of Androgen receptor activity 0.0231 10 823 76 -0.2 0.062 1000 -1000 -0.028 -1000
ErbB4 signaling events 0.0231 10 710 69 -0.16 0.074 1000 -1000 -0.053 -1000
Arf6 downstream pathway 0.0231 10 437 43 -0.027 0.041 1000 -1000 -0.023 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0208 9 272 28 -0.088 0.041 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 0.0208 9 371 39 -0.039 0.032 1000 -1000 -0.018 -1000
PDGFR-alpha signaling pathway 0.0208 9 415 44 -0.014 0.06 1000 -1000 -0.051 -1000
Class I PI3K signaling events 0.0208 9 718 73 -0.1 0.043 1000 -1000 -0.045 -1000
VEGFR1 specific signals 0.0208 9 510 56 -0.013 0.093 1000 -1000 -0.052 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0185 8 277 34 -0.028 0.063 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 0.0185 8 544 68 -0.051 0.062 1000 -1000 -0.034 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0185 8 714 83 -0.12 0.068 1000 -1000 -0.041 -1000
Signaling mediated by p38-gamma and p38-delta 0.0185 8 134 15 -0.055 0.026 1000 -1000 -0.038 -1000
Retinoic acid receptors-mediated signaling 0.0185 8 500 58 -0.14 0.048 1000 -1000 -0.045 -1000
IL27-mediated signaling events 0.0185 8 415 51 -0.064 0.036 1000 -1000 -0.05 -1000
Arf6 trafficking events 0.0185 8 597 71 -0.045 0.047 1000 -1000 -0.027 -1000
Insulin-mediated glucose transport 0.0162 7 248 32 -0.14 0.043 1000 -1000 -0.031 -1000
EPO signaling pathway 0.0139 6 368 55 -0.016 0.061 1000 -1000 -0.049 -1000
ceramide signaling pathway 0.0139 6 338 49 0 0.043 1000 -1000 -0.042 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0139 6 288 45 -0.018 0.072 1000 -1000 -0.05 -1000
Regulation of Telomerase 0.0139 6 638 102 -0.19 0.06 1000 -1000 -0.066 -1000
FOXM1 transcription factor network 0.0139 6 314 51 -0.089 0.12 1000 -1000 -0.15 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0116 5 472 85 -0.034 0.068 1000 -1000 -0.045 -1000
Hedgehog signaling events mediated by Gli proteins 0.0116 5 375 65 -0.088 0.049 1000 -1000 -0.045 -1000
mTOR signaling pathway 0.0116 5 299 53 -0.073 0.037 1000 -1000 -0.04 -1000
IFN-gamma pathway 0.0116 5 341 68 -0.034 0.039 1000 -1000 -0.06 -1000
IL2 signaling events mediated by PI3K 0.0116 5 331 58 -0.012 0.046 1000 -1000 -0.047 -1000
TCGA08_rtk_signaling 0.0116 5 148 26 -0.035 0.06 1000 -1000 -0.024 -1000
E-cadherin signaling in the nascent adherens junction 0.0116 5 406 76 -0.015 0.088 1000 -1000 -0.062 -1000
Rapid glucocorticoid signaling 0.0116 5 119 20 -0.018 0.025 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class II 0.0093 4 372 75 -0.034 0.067 1000 -1000 -0.034 -1000
Paxillin-dependent events mediated by a4b1 0.0093 4 156 36 -0.045 0.047 1000 -1000 -0.04 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0093 4 297 74 -0.08 0.062 1000 -1000 -0.066 -1000
Class IB PI3K non-lipid kinase events 0.0093 4 12 3 -0.022 0.022 1000 -1000 0 -1000
Aurora A signaling 0.0069 3 236 60 -0.079 0.073 1000 -1000 -0.022 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0069 3 443 125 -0.011 0.095 1000 -1000 -0.055 -1000
Insulin Pathway 0.0069 3 224 74 -0.035 0.081 1000 -1000 -0.06 -1000
Arf1 pathway 0.0069 3 201 54 -0.001 0.04 1000 -1000 -0.024 -1000
PLK2 and PLK4 events 0.0046 2 8 3 0.009 0.026 1000 -1000 -0.021 -1000
TRAIL signaling pathway 0.0046 2 127 48 -0.006 0.057 1000 -1000 -0.042 -1000
IL2 signaling events mediated by STAT5 0.0046 2 54 22 -0.006 0.042 1000 -1000 -0.054 -1000
p38 MAPK signaling pathway 0.0046 2 129 44 -0.013 0.057 1000 -1000 -0.033 -1000
Canonical NF-kappaB pathway 0.0023 1 67 39 0 0.058 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 0.0023 1 161 104 -0.051 0.064 1000 -1000 -0.041 -1000
Atypical NF-kappaB pathway 0.0023 1 31 31 0 0.056 1000 -1000 -0.029 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 9 23 0.012 0.04 1000 -1000 -0.032 -1000
BARD1 signaling events 0.0000 0 31 57 -0.054 0.075 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0000 0 16 22 -0.009 0.062 1000 -1000 -0.041 -1000
Aurora C signaling 0.0000 0 5 7 0 0.04 1000 -1000 -0.013 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 18 27 0 0.05 1000 -1000 -0.04 -1000
E-cadherin signaling in keratinocytes 0.0000 0 28 43 -0.046 0.086 1000 -1000 -0.038 -1000
E-cadherin signaling events 0.0000 0 2 5 0.025 0.051 1000 -1000 0 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.073 1000 -1000 -0.001 -1000
Total NA 2421 143204 7203 -16 7.8 131000 -131000 -6 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.12 0.19 -10000 0 -0.37 157 157
CDKN2C 0.034 0.026 -10000 0 -10000 0 0
CDKN2A -0.075 0.19 0.37 1 -0.44 91 92
CCND2 0.084 0.099 0.2 158 -0.36 1 159
RB1 -0.07 0.1 0.28 4 -0.2 130 134
CDK4 0.084 0.1 0.21 150 -0.25 2 152
CDK6 0.094 0.11 0.22 162 -0.38 1 163
G1/S progression 0.073 0.1 0.2 131 -0.32 3 134
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.019 -10000 0 -0.3 1 1
VLDLR -0.011 0.12 -10000 0 -0.4 37 37
CRKL 0.025 0.005 -10000 0 -10000 0 0
LRPAP1 0.026 0.004 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
ITGA3 0.025 0.021 -10000 0 -0.4 1 1
RELN/VLDLR/Fyn -0.085 0.16 -10000 0 -0.27 175 175
MAPK8IP1/MKK7/MAP3K11/JNK1 0.071 0.038 -10000 0 -0.57 1 1
AKT1 -0.095 0.13 -10000 0 -0.35 48 48
MAP2K7 0.025 0.021 -10000 0 -0.4 1 1
RAPGEF1 0.025 0.021 -10000 0 -0.4 1 1
DAB1 -0.025 0.13 -10000 0 -0.43 39 39
RELN/LRP8/DAB1 -0.26 0.17 -10000 0 -0.32 348 348
LRPAP1/LRP8 -0.21 0.16 0.26 1 -0.3 303 304
RELN/LRP8/DAB1/Fyn -0.24 0.16 -10000 0 -0.3 343 343
DAB1/alpha3/beta1 Integrin -0.24 0.17 -10000 0 -0.42 159 159
long-term memory -0.33 0.2 -10000 0 -0.47 241 241
DAB1/LIS1 -0.24 0.17 -10000 0 -0.42 164 164
DAB1/CRLK/C3G -0.24 0.17 -10000 0 -0.42 159 159
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
DAB1/NCK2 -0.25 0.18 -10000 0 -0.42 164 164
ARHGEF2 0.026 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.095 0.18 -10000 0 -0.4 108 108
CDK5R1 0.025 0.022 -10000 0 -0.42 1 1
RELN -0.15 0.21 -10000 0 -0.4 172 172
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.26 0.18 0.25 1 -0.33 336 337
GRIN2A/RELN/LRP8/DAB1/Fyn -0.29 0.19 -10000 0 -0.37 320 320
MAPK8 0.026 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.099 0.16 -10000 0 -0.26 199 199
ITGB1 0.026 0.002 -10000 0 -10000 0 0
MAP1B -0.25 0.18 -10000 0 -0.42 179 179
RELN/LRP8 -0.26 0.18 0.25 1 -0.33 336 337
GRIN2B/RELN/LRP8/DAB1/Fyn -0.29 0.18 -10000 0 -0.36 327 327
PI3K 0.038 0.008 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.038 0.017 -10000 0 -0.28 1 1
RAP1A -0.24 0.15 0.3 1 -0.4 158 159
PAFAH1B1 0.022 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.025 0.021 -10000 0 -0.4 1 1
CRLK/C3G 0.037 0.018 -10000 0 -0.28 1 1
GRIN2B -0.083 0.19 -10000 0 -0.42 102 102
NCK2 0.027 0 -10000 0 -10000 0 0
neuron differentiation -0.12 0.12 0.23 1 -0.26 137 138
neuron adhesion -0.23 0.15 0.3 2 -0.39 153 155
LRP8 -0.3 0.2 0.37 1 -0.42 304 305
GSK3B -0.091 0.13 -10000 0 -0.34 46 46
RELN/VLDLR/DAB1/Fyn -0.088 0.16 -10000 0 -0.24 191 191
MAP3K11 0.025 0.021 -10000 0 -0.4 1 1
RELN/VLDLR/DAB1/P13K -0.1 0.14 -10000 0 -0.25 178 178
CDK5 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.059 0.18 0.85 5 -0.35 89 94
neuron migration -0.22 0.17 0.23 3 -0.41 153 156
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.12 0.12 0.23 1 -0.26 137 138
RELN/VLDLR -0.25 0.18 0.26 1 -0.32 332 333
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.02 0.079 -10000 0 -0.43 10 10
Crk/p130 Cas/Paxillin -0.094 0.12 -10000 0 -0.33 39 39
JUN -0.088 0.13 -10000 0 -0.36 46 46
HRAS 0.025 0.021 -10000 0 -0.4 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.072 0.16 -10000 0 -0.26 167 167
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.075 0.17 -10000 0 -0.26 177 177
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.049 0.13 -10000 0 -0.22 151 151
RHOA 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.067 0.15 -10000 0 -0.27 94 94
GRB7 0.032 0.047 0.37 8 -10000 0 8
RET51/GFRalpha1/GDNF -0.075 0.17 -10000 0 -0.26 177 177
MAPKKK cascade -0.086 0.15 -10000 0 -0.39 40 40
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.049 0.13 -10000 0 -0.22 151 151
lamellipodium assembly -0.081 0.12 -10000 0 -0.25 116 116
RET51/GFRalpha1/GDNF/SHC -0.075 0.17 -10000 0 -0.26 176 176
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.048 0.12 -10000 0 -0.22 148 148
RET9/GFRalpha1/GDNF/Shank3 -0.049 0.13 -10000 0 -0.22 151 151
MAPK3 -0.1 0.12 -10000 0 -0.36 40 40
DOK1 0.026 0.002 -10000 0 -10000 0 0
DOK6 0.011 0.058 -10000 0 -0.4 8 8
PXN 0.026 0.002 -10000 0 -10000 0 0
neurite development -0.076 0.11 -10000 0 -0.35 29 29
DOK5 0.011 0.05 0.37 1 -0.4 5 6
GFRA1 -0.13 0.2 -10000 0 -0.4 156 156
MAPK8 -0.091 0.14 -10000 0 -0.37 48 48
HRAS/GTP -0.086 0.18 -10000 0 -0.33 89 89
tube development -0.045 0.12 0.2 1 -0.21 136 137
MAPK1 -0.1 0.12 -10000 0 -0.36 39 39
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.058 0.11 -10000 0 -0.21 146 146
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC 0.016 0.013 -10000 0 -10000 0 0
PDLIM7 0.026 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.055 0.14 -10000 0 -0.26 112 112
SHC1 0.026 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.076 0.17 -10000 0 -0.26 178 178
RET51/GFRalpha1/GDNF/Dok5 -0.057 0.14 0.26 1 -0.26 121 122
PRKCA 0.025 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.015 -10000 0 -0.28 1 1
CREB1 -0.091 0.15 -10000 0 -0.28 149 149
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.058 0.11 -10000 0 -0.21 144 144
RET51/GFRalpha1/GDNF/Grb7 -0.07 0.17 0.26 4 -0.26 173 177
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.041 0.16 -10000 0 -0.4 66 66
DOK4 0.025 0.021 -10000 0 -0.4 1 1
JNK cascade -0.086 0.13 -10000 0 -0.35 46 46
RET9/GFRalpha1/GDNF/FRS2 -0.048 0.13 -10000 0 -0.22 150 150
SHANK3 0.024 0.021 -10000 0 -0.4 1 1
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.059 0.11 -10000 0 -0.21 144 144
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.09 0.14 -10000 0 -0.25 176 176
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.092 0.15 -10000 0 -0.25 175 175
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.097 0.16 -10000 0 -0.27 173 173
PI3K -0.12 0.18 -10000 0 -0.36 124 124
SOS1 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.036 0.12 -10000 0 -0.21 136 136
GRB10 0.024 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.075 0.13 -10000 0 -0.32 42 42
RET51/GFRalpha1/GDNF/FRS2 -0.075 0.17 -10000 0 -0.26 178 178
GAB1 0.026 0.004 -10000 0 -10000 0 0
IRS1 0.026 0.002 -10000 0 -10000 0 0
IRS2 0.02 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.098 0.16 -10000 0 -0.27 174 174
RET51/GFRalpha1/GDNF/PKC alpha -0.073 0.16 -10000 0 -0.26 176 176
GRB2 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GDNF 0.013 0.02 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.076 0.17 -10000 0 -0.26 178 178
Rac1/GTP -0.092 0.14 -10000 0 -0.29 116 116
RET9/GFRalpha1/GDNF -0.065 0.13 -10000 0 -0.24 151 151
GFRalpha1/GDNF -0.079 0.15 -10000 0 -0.28 151 151
IL4-mediated signaling events

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
BCL2L1 -0.46 0.49 -10000 0 -1.1 104 104
STAT6 (cleaved dimer) -0.58 0.52 -10000 0 -1.2 150 150
IGHG1 -0.17 0.16 -10000 0 -10000 0 0
IGHG3 -0.5 0.46 -10000 0 -1.1 137 137
AKT1 -0.28 0.29 -10000 0 -0.72 72 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.24 -10000 0 -0.68 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.28 0.28 -10000 0 -0.8 42 42
THY1 -0.53 0.48 -10000 0 -1.2 115 115
MYB 0.026 0.004 -10000 0 -10000 0 0
HMGA1 0.027 0.017 0.37 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.36 -10000 0 -0.81 132 132
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.28 -10000 0 -0.79 44 44
SP1 0.026 0.02 -10000 0 -10000 0 0
INPP5D 0.026 0.002 -10000 0 -10000 0 0
SOCS5 0.045 0.026 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.57 0.52 -10000 0 -1.2 146 146
SOCS1 -0.38 0.31 -10000 0 -0.75 110 110
SOCS3 -0.33 0.29 -10000 0 -0.75 87 87
FCER2 -0.82 0.66 -10000 0 -1.4 230 230
PARP14 0.008 0.029 -10000 0 -10000 0 0
CCL17 -0.53 0.48 -10000 0 -1.2 113 113
GRB2 0.026 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.21 -10000 0 -0.72 18 18
T cell proliferation -0.53 0.5 -10000 0 -1.2 124 124
IL4R/JAK1 -0.53 0.49 -10000 0 -1.2 123 123
EGR2 -0.61 0.52 -10000 0 -1.2 130 130
JAK2 -0.035 0.053 -10000 0 -0.43 3 3
JAK3 0.01 0.035 -10000 0 -0.42 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 -0.008 0.025 -10000 0 -10000 0 0
COL1A2 -0.16 0.16 -10000 0 -0.7 1 1
CCL26 -0.54 0.49 -10000 0 -1.2 118 118
IL4R -0.56 0.52 -10000 0 -1.2 116 116
PTPN6 0.036 0.016 -10000 0 -10000 0 0
IL13RA2 -0.54 0.48 -10000 0 -1.2 113 113
IL13RA1 -0.032 0.041 -10000 0 -10000 0 0
IRF4 -0.54 0.67 -10000 0 -1.4 144 144
ARG1 -0.091 0.14 -10000 0 -0.62 5 5
CBL -0.37 0.33 -10000 0 -0.78 129 129
GTF3A 0.022 0.071 0.35 14 -0.42 1 15
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.039 0.062 -10000 0 -0.31 3 3
IRF4/BCL6 -0.47 0.63 -10000 0 -1.3 144 144
CD40LG -0.053 0.12 -10000 0 -0.42 34 34
MAPK14 -0.37 0.33 -10000 0 -0.78 124 124
mitosis -0.27 0.27 -10000 0 -0.68 70 70
STAT6 -0.59 0.57 -10000 0 -1.3 135 135
SPI1 0.022 0.051 -10000 0 -0.4 6 6
RPS6KB1 -0.26 0.26 -10000 0 -0.67 64 64
STAT6 (dimer) -0.59 0.57 -10000 0 -1.3 135 135
STAT6 (dimer)/PARP14 -0.6 0.55 -10000 0 -1.2 148 148
mast cell activation 0.014 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.31 0.29 -10000 0 -0.71 88 88
FRAP1 -0.28 0.29 -10000 0 -0.72 72 72
LTA -0.53 0.49 -10000 0 -1.2 116 116
FES 0.024 0.021 -10000 0 -0.4 1 1
T-helper 1 cell differentiation 0.58 0.55 1.2 135 -10000 0 135
CCL11 -0.56 0.55 -10000 0 -1.3 128 128
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.27 -10000 0 -0.68 68 68
IL2RG 0.009 0.039 -10000 0 -0.39 2 2
IL10 -0.55 0.52 -10000 0 -1.2 123 123
IRS1 0.026 0.002 -10000 0 -10000 0 0
IRS2 0.02 0.011 -10000 0 -10000 0 0
IL4 -0.14 0.2 -10000 0 -1.1 11 11
IL5 -0.53 0.48 -10000 0 -1.2 113 113
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.42 0.38 -10000 0 -0.88 118 118
COL1A1 -0.19 0.2 -10000 0 -0.61 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.54 0.5 -10000 0 -1.2 113 113
IL2R gamma/JAK3 0.011 0.047 -10000 0 -0.29 3 3
TFF3 -0.54 0.51 -10000 0 -1.2 120 120
ALOX15 -0.55 0.5 -10000 0 -1.2 119 119
MYBL1 0.021 0.032 -10000 0 -0.42 2 2
T-helper 2 cell differentiation -0.44 0.4 -10000 0 -0.93 121 121
SHC1 0.026 0.004 -10000 0 -10000 0 0
CEBPB 0.016 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.25 0.27 -10000 0 -0.82 33 33
mol:PI-3-4-5-P3 -0.28 0.29 -10000 0 -0.72 72 72
PI3K -0.3 0.31 -10000 0 -0.78 72 72
DOK2 0.013 0.055 -10000 0 -0.4 7 7
ETS1 0.036 0.021 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.2 -10000 0 -0.64 21 21
ITGB3 -0.53 0.49 -10000 0 -1.2 114 114
PIGR -0.7 0.65 -10000 0 -1.4 165 165
IGHE 0.085 0.074 0.19 83 -10000 0 83
MAPKKK cascade -0.2 0.19 -10000 0 -0.63 21 21
BCL6 0.032 0.01 -10000 0 -10000 0 0
OPRM1 -0.53 0.48 -10000 0 -1.2 114 114
RETNLB -0.76 0.66 -10000 0 -1.4 188 188
SELP -0.59 0.57 -10000 0 -1.3 130 130
AICDA -0.51 0.46 -10000 0 -1.1 114 114
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.029 0.12 -10000 0 -0.24 90 90
EFNA5 -0.055 0.16 -10000 0 -0.4 79 79
FYN -0.045 0.095 0.18 1 -0.22 87 88
neuron projection morphogenesis -0.029 0.12 -10000 0 -0.24 90 90
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.029 0.12 -10000 0 -0.25 90 90
EPHA5 -0.009 0.078 -10000 0 -0.4 15 15
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.007 -10000 0 -10000 0 0
VLDLR -0.011 0.12 -10000 0 -0.4 37 37
LRPAP1 0.026 0.004 -10000 0 -10000 0 0
NUDC 0.025 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.26 0.18 0.25 1 -0.33 336 337
CaM/Ca2+ 0.018 0.005 -10000 0 -10000 0 0
KATNA1 0.026 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.24 0.16 0.18 8 -0.31 325 333
IQGAP1/CaM 0.035 0.012 -10000 0 -10000 0 0
DAB1 -0.025 0.13 -10000 0 -0.43 39 39
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
PLA2G7 0.022 0.041 -10000 0 -0.4 4 4
CALM1 0.025 0.007 -10000 0 -10000 0 0
DYNLT1 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.21 0.16 0.26 1 -0.3 303 304
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.025 0.021 -10000 0 -0.4 1 1
CDK5R1 0.025 0.022 -10000 0 -0.42 1 1
LIS1/Poliovirus Protein 3A 0.007 0.004 -10000 0 -10000 0 0
CDK5R2 -0.024 0.13 -10000 0 -0.4 43 43
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.17 -10000 0 -0.28 199 199
YWHAE 0.022 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.2 0.15 0.32 4 -0.36 147 151
MAP1B 0 0.038 -10000 0 -0.27 8 8
RAC1 0.009 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.21 0.14 0.18 3 -0.38 127 130
RELN -0.15 0.21 -10000 0 -0.4 172 172
PAFAH/LIS1 0.019 0.024 -10000 0 -0.22 3 3
LIS1/CLIP170 0.02 0.018 -10000 0 -0.24 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.16 0.12 -10000 0 -0.31 126 126
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.088 0.15 -10000 0 -0.37 58 58
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.22 0.16 0.32 3 -0.38 152 155
LIS1/IQGAP1 0.02 0.013 -10000 0 -10000 0 0
RHOA 0.01 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.009 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.019 0.057 -10000 0 -0.42 7 7
PAFAH1B2 0.026 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.012 0.039 -10000 0 -0.24 2 2
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.15 0.32 5 -0.36 147 152
LRP8 -0.3 0.2 0.37 1 -0.42 304 305
NDEL1/Katanin 60 -0.21 0.15 0.32 5 -0.37 148 153
P39/CDK5 -0.23 0.15 0.18 2 -0.4 151 153
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.02 0.014 -10000 0 -10000 0 0
CDK5 -0.23 0.14 0.18 4 -0.4 130 134
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.017 0.016 -10000 0 -0.2 1 1
CSNK2A1 0.021 0.011 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.084 0.14 -10000 0 -0.38 36 36
RELN/VLDLR -0.25 0.18 0.26 1 -0.32 332 333
CDC42 0.009 0.019 -10000 0 -0.37 1 1
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.037 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.018 0.06 0.26 6 -0.29 11 17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.017 0.13 -10000 0 -0.22 99 99
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.19 -10000 0 -0.3 189 189
NT-4/5 (dimer)/p75(NTR) -0.066 0.15 -10000 0 -0.3 128 128
IKBKB 0.023 0.009 -10000 0 -10000 0 0
AKT1 -0.069 0.095 -10000 0 -0.38 8 8
IKBKG 0.025 0.021 -10000 0 -0.4 1 1
BDNF 0.015 0.068 -10000 0 -0.42 10 10
MGDIs/NGR/p75(NTR)/LINGO1 -0.053 0.15 -10000 0 -0.26 142 142
FURIN 0.024 0.021 -10000 0 -0.4 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.035 0.13 -10000 0 -0.24 124 124
LINGO1 0.003 0.097 -10000 0 -0.42 21 21
Sortilin/TRAF6/NRIF 0.028 0.028 -10000 0 -10000 0 0
proBDNF (dimer) 0.015 0.068 -10000 0 -0.42 10 10
NTRK1 0.017 0.045 -10000 0 -0.42 4 4
RTN4R 0.008 0.086 -10000 0 -0.42 16 16
neuron apoptosis -0.062 0.15 0.32 2 -0.41 27 29
IRAK1 0.026 0.002 -10000 0 -10000 0 0
SHC1 -0.061 0.12 -10000 0 -0.25 118 118
ARHGDIA 0.025 0.021 -10000 0 -0.4 1 1
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.067 0.031 -10000 0 -0.21 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.024 0.14 -10000 0 -0.23 122 122
MAGEH1 0.021 0.046 -10000 0 -0.4 5 5
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.029 0.14 -10000 0 -0.25 112 112
Mammalian IAPs/DIABLO 0.061 0.041 -10000 0 -0.22 8 8
proNGF (dimer) 0.005 0.084 -10000 0 -0.4 17 17
MAGED1 0.026 0.003 -10000 0 -10000 0 0
APP 0.024 0.021 -10000 0 -0.4 1 1
NT-4/5 (dimer) -0.02 0.09 -10000 0 -0.43 18 18
ZNF274 0.022 0.041 -10000 0 -0.4 4 4
RhoA/GDP/RHOGDI -0.037 0.12 -10000 0 -0.22 112 112
NGF 0.005 0.084 -10000 0 -0.4 17 17
cell cycle arrest -0.044 0.1 0.23 2 -0.35 9 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.043 0.11 -10000 0 -0.22 108 108
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.043 0.14 -10000 0 -0.25 128 128
NCSTN 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.071 0.17 -10000 0 -0.28 156 156
PSENEN 0.025 0.021 -10000 0 -0.4 1 1
mol:ceramide -0.057 0.11 0.18 1 -0.3 18 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.037 0.1 -10000 0 -0.32 19 19
p75(NTR)/beta APP -0.05 0.14 -10000 0 -0.28 116 116
BEX1 -0.098 0.18 -10000 0 -0.4 115 115
mol:GDP -0.077 0.11 -10000 0 -0.25 123 123
NGF (dimer) -0.27 0.11 0.23 1 -0.28 407 408
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.038 0.14 -10000 0 -0.24 134 134
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.03 0.12 -10000 0 -0.21 113 113
MYD88 0.026 0.003 -10000 0 -10000 0 0
CHUK 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.071 0.17 -10000 0 -0.28 156 156
RHOB 0.026 0.001 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.025 0.043 0.26 7 -0.3 2 9
NT3 (dimer) 0.015 0.062 -10000 0 -0.4 9 9
TP53 -0.062 0.095 0.35 3 -0.38 3 6
PRDM4 -0.057 0.11 0.18 1 -0.23 113 114
BDNF (dimer) -0.44 0.14 0.31 2 -0.45 415 417
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
SORT1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.02 0.13 -10000 0 -0.22 99 99
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.022 0.14 -10000 0 -0.23 119 119
RHOC 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
MAPK10 -0.084 0.16 0.32 4 -0.44 43 47
DIABLO 0.026 0.003 -10000 0 -10000 0 0
SMPD2 -0.057 0.11 0.18 1 -0.31 18 19
APH1B 0.025 0.006 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.037 0.14 -10000 0 -0.25 123 123
PSEN1 0.025 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.055 0.15 -10000 0 -0.29 119 119
MAPK8 -0.06 0.14 0.35 3 -0.36 18 21
MAPK9 -0.059 0.14 0.35 3 -0.37 16 19
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 0.015 0.062 -10000 0 -0.4 9 9
NTF4 -0.02 0.09 -10000 0 -0.43 18 18
NDN 0.011 0.076 -10000 0 -0.4 14 14
RAC1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.041 0.15 -10000 0 -0.38 26 26
p75 CTF/Sortilin/TRAF6/NRIF 0.061 0.03 -10000 0 -0.22 3 3
RhoA-B-C/GTP -0.071 0.16 -10000 0 -0.27 156 156
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.012 0.13 -10000 0 -0.26 13 13
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.019 0.13 -10000 0 -0.22 124 124
PRKACB -0.031 0.14 -10000 0 -0.4 56 56
proBDNF (dimer)/p75 ECD 0.031 0.052 -10000 0 -0.3 10 10
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.018 0.058 -10000 0 -0.4 8 8
BIRC2 0.026 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.069 0.14 -10000 0 -0.28 83 83
BAD -0.076 0.15 0.31 4 -0.37 43 47
RIPK2 0.023 0.01 -10000 0 -10000 0 0
NGFR -0.09 0.19 -10000 0 -0.4 115 115
CYCS -0.065 0.094 -10000 0 -0.39 8 8
ADAM17 0.026 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.022 0.13 -10000 0 -0.23 104 104
BCL2L11 -0.076 0.15 0.31 4 -0.37 43 47
BDNF (dimer)/p75(NTR) -0.057 0.15 -10000 0 -0.29 124 124
PI3K -0.021 0.14 -10000 0 -0.23 111 111
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.022 0.14 -10000 0 -0.23 109 109
NDNL2 0.025 0.007 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
PRKCI 0.024 0.029 -10000 0 -0.4 2 2
NGF (dimer)/p75(NTR) -0.06 0.16 -10000 0 -0.3 123 123
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.02 0.14 -10000 0 -0.23 113 113
TRAF6 0.026 0.003 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.025 0.006 -10000 0 -10000 0 0
PLG -0.083 0.16 -10000 0 -0.42 79 79
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.063 0.13 -10000 0 -0.26 111 111
SQSTM1 0.026 0.003 -10000 0 -10000 0 0
NGFRAP1 0.025 0.021 -10000 0 -0.4 1 1
CASP3 -0.074 0.14 0.34 3 -0.35 44 47
E2F1 0.021 0.058 0.37 8 -0.42 2 10
CASP9 0.025 0.006 -10000 0 -10000 0 0
IKK complex -0.01 0.12 -10000 0 -0.38 11 11
NGF (dimer)/TRKA 0.02 0.071 -10000 0 -0.29 21 21
MMP7 -0.4 0.11 0.37 3 -0.43 405 408
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.014 0.14 -10000 0 -0.38 11 11
MMP3 -0.35 0.18 0.37 1 -0.43 350 351
APAF-1/Caspase 9 -0.064 0.08 -10000 0 -0.33 11 11
BCR signaling pathway

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
JUN -0.13 0.21 0.24 1 -0.48 88 89
IKBKB -0.04 0.11 0.21 3 -0.29 34 37
AKT1 -0.085 0.11 0.18 4 -0.26 86 90
IKBKG -0.042 0.1 0.23 1 -0.28 35 36
CALM1 -0.11 0.23 0.3 1 -0.54 75 76
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 -0.15 0.28 0.27 1 -0.65 85 86
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.24 0.32 1 -0.56 79 80
DOK1 0.026 0.002 -10000 0 -10000 0 0
AP-1 -0.075 0.12 0.19 2 -0.28 77 79
LYN 0.023 0.009 -10000 0 -10000 0 0
BLNK 0.021 0.041 -10000 0 -0.4 4 4
SHC1 0.026 0.004 -10000 0 -10000 0 0
BCR complex -0.11 0.2 -10000 0 -0.36 155 155
CD22 -0.2 0.32 -10000 0 -0.68 107 107
CAMK2G -0.1 0.21 0.27 2 -0.52 67 69
CSNK2A1 0.021 0.011 -10000 0 -10000 0 0
INPP5D 0.026 0.002 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.059 0.13 -10000 0 -0.36 42 42
GO:0007205 -0.12 0.25 0.32 1 -0.57 79 80
SYK 0.026 0.003 -10000 0 -10000 0 0
ELK1 -0.12 0.23 0.3 1 -0.55 75 76
NFATC1 -0.17 0.26 -10000 0 -0.53 113 113
B-cell antigen/BCR complex -0.11 0.2 -10000 0 -0.36 155 155
PAG1/CSK 0.027 0.042 -10000 0 -0.28 7 7
NFKBIB -0.001 0.046 0.12 3 -0.13 18 21
HRAS -0.094 0.2 0.27 2 -0.49 66 68
NFKBIA 0 0.045 0.12 3 -0.12 17 20
NF-kappa-B/RelA/I kappa B beta 0.005 0.039 0.12 3 -10000 0 3
RasGAP/Csk -0.07 0.2 -10000 0 -0.46 63 63
mol:GDP -0.11 0.24 0.31 1 -0.55 75 76
PTEN 0.025 0.006 -10000 0 -10000 0 0
CD79B -0.033 0.15 -10000 0 -0.4 58 58
NF-kappa-B/RelA/I kappa B alpha 0.006 0.038 0.12 3 -10000 0 3
GRB2 0.026 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.18 0.27 0.3 1 -0.56 122 123
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.12 0.26 0.32 1 -0.57 81 82
CSK 0.025 0.005 -10000 0 -10000 0 0
FOS -0.11 0.21 0.29 1 -0.52 72 73
CHUK -0.05 0.12 0.23 1 -0.3 49 50
IBTK 0.025 0.021 -10000 0 -0.4 1 1
CARD11/BCL10/MALT1/TAK1 -0.079 0.21 0.26 1 -0.53 57 58
PTPN6 -0.19 0.3 -10000 0 -0.65 105 105
RELA 0.026 0.004 -10000 0 -10000 0 0
BCL2A1 0.005 0.028 -10000 0 -0.13 1 1
VAV2 -0.2 0.32 -10000 0 -0.66 114 114
ubiquitin-dependent protein catabolic process 0.002 0.045 0.12 3 -0.13 17 20
BTK -0.12 0.36 -10000 0 -1.1 54 54
CD19 -0.2 0.32 -10000 0 -0.64 116 116
MAP4K1 -0.016 0.13 -10000 0 -0.4 42 42
CD72 0.025 0.021 -10000 0 -0.4 1 1
PAG1 0.015 0.055 -10000 0 -0.4 7 7
MAPK14 -0.13 0.23 0.26 1 -0.53 84 85
SH3BP5 0.023 0.036 -10000 0 -0.4 3 3
PIK3AP1 -0.11 0.25 0.34 2 -0.6 71 73
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.16 0.3 -10000 0 -0.66 84 84
RAF1 -0.09 0.18 0.26 2 -0.48 59 61
RasGAP/p62DOK/SHIP -0.066 0.2 -10000 0 -0.45 62 62
CD79A -0.13 0.2 -10000 0 -0.4 156 156
re-entry into mitotic cell cycle -0.075 0.12 0.19 2 -0.28 77 79
RASA1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.077 0.15 0.27 1 -0.41 55 56
MAPK1 -0.075 0.15 0.27 1 -0.41 53 54
CD72/SHP1 -0.16 0.29 0.33 1 -0.61 103 104
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.13 0.23 0.26 1 -0.54 83 84
actin cytoskeleton organization -0.16 0.26 -10000 0 -0.55 109 109
NF-kappa-B/RelA 0.014 0.076 0.22 3 -0.2 10 13
Calcineurin -0.077 0.2 0.28 1 -0.49 60 61
PI3K -0.16 0.23 -10000 0 -0.49 121 121
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.12 0.26 0.36 1 -0.59 80 81
SOS1 0.026 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.18 0.36 -10000 0 -0.87 80 80
DAPP1 -0.21 0.4 -10000 0 -0.97 80 80
cytokine secretion -0.15 0.23 0.19 1 -0.49 112 113
mol:DAG -0.12 0.26 0.32 1 -0.57 81 82
PLCG2 -0.016 0.13 -10000 0 -0.4 42 42
MAP2K1 -0.084 0.17 0.29 1 -0.45 58 59
B-cell antigen/BCR complex/FcgammaRIIB -0.1 0.22 -10000 0 -0.36 156 156
mol:PI-3-4-5-P3 -0.12 0.15 0.24 1 -0.34 112 113
ETS1 -0.096 0.19 0.26 2 -0.48 64 66
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.048 0.16 -10000 0 -0.39 44 44
B-cell antigen/BCR complex/LYN -0.15 0.29 -10000 0 -0.69 80 80
MALT1 0.019 0.023 -10000 0 -0.4 1 1
TRAF6 0.026 0.003 -10000 0 -10000 0 0
RAC1 -0.17 0.28 -10000 0 -0.59 109 109
B-cell antigen/BCR complex/LYN/SYK -0.16 0.3 -10000 0 -0.63 98 98
CARD11 -0.11 0.25 0.27 6 -0.57 74 80
FCGR2B -0.019 0.13 -10000 0 -0.4 44 44
PPP3CA 0.026 0.004 -10000 0 -10000 0 0
BCL10 0.025 0.021 -10000 0 -0.4 1 1
IKK complex -0.013 0.048 0.14 6 -0.12 10 16
PTPRC -0.006 0.11 -10000 0 -0.4 32 32
PDPK1 -0.084 0.1 0.16 5 -0.25 84 89
PPP3CB 0.026 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.011 -10000 0 -10000 0 0
POU2F2 0.003 0.031 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.079 0.18 -10000 0 -0.42 83 83
CRKL -0.066 0.17 -10000 0 -0.41 78 78
HRAS -0.051 0.17 -10000 0 -0.37 80 80
mol:PIP3 -0.052 0.16 0.26 2 -0.39 74 76
SPRED1 0.025 0.007 -10000 0 -10000 0 0
SPRED2 0.026 0.002 -10000 0 -10000 0 0
GAB1 -0.067 0.18 -10000 0 -0.43 79 79
FOXO3 -0.06 0.19 -10000 0 -0.41 81 81
AKT1 -0.064 0.21 -10000 0 -0.44 81 81
BAD -0.06 0.19 -10000 0 -0.41 81 81
megakaryocyte differentiation -0.085 0.19 -10000 0 -0.45 81 81
GSK3B -0.059 0.19 -10000 0 -0.41 80 80
RAF1 -0.042 0.14 0.24 1 -0.31 79 80
SHC1 0.026 0.004 -10000 0 -10000 0 0
STAT3 -0.068 0.18 -10000 0 -0.43 78 78
STAT1 -0.17 0.42 -10000 0 -0.98 85 85
HRAS/SPRED1 -0.031 0.14 -10000 0 -0.31 76 76
cell proliferation -0.066 0.18 -10000 0 -0.42 79 79
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
TEC 0.025 0.022 -10000 0 -0.42 1 1
RPS6KB1 -0.061 0.2 -10000 0 -0.44 82 82
HRAS/SPRED2 -0.03 0.15 -10000 0 -0.31 79 79
LYN/TEC/p62DOK -0.032 0.18 -10000 0 -0.41 66 66
MAPK3 -0.028 0.1 0.21 2 -0.26 30 32
STAP1 -0.11 0.2 -10000 0 -0.48 85 85
GRAP2 0.013 0.071 -10000 0 -0.4 12 12
JAK2 -0.14 0.36 -10000 0 -0.83 83 83
STAT1 (dimer) -0.16 0.41 -10000 0 -0.95 85 85
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.044 0.2 -10000 0 -0.44 76 76
actin filament polymerization -0.065 0.17 0.21 1 -0.42 74 75
LYN 0.023 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.13 0.27 -10000 0 -0.64 81 81
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.039 0.17 -10000 0 -0.39 75 75
PI3K -0.037 0.2 -10000 0 -0.42 78 78
PTEN 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.18 0.49 -10000 0 -1.2 77 77
MAPK8 -0.068 0.18 -10000 0 -0.43 79 79
STAT3 (dimer) -0.066 0.18 -10000 0 -0.42 78 78
positive regulation of transcription -0.021 0.087 0.2 2 -0.22 28 30
mol:GDP -0.049 0.18 -10000 0 -0.39 78 78
PIK3C2B -0.067 0.18 -10000 0 -0.44 75 75
CBL/CRKL -0.05 0.17 -10000 0 -0.39 77 77
FER -0.068 0.18 -10000 0 -0.43 78 78
SH2B3 -0.067 0.18 -10000 0 -0.43 78 78
PDPK1 -0.049 0.15 0.24 2 -0.36 74 76
SNAI2 -0.067 0.17 -10000 0 -0.43 73 73
positive regulation of cell proliferation -0.12 0.31 -10000 0 -0.71 85 85
KITLG 0.007 0.072 -10000 0 -0.42 10 10
cell motility -0.12 0.31 -10000 0 -0.71 85 85
PTPN6 0.029 0.01 -10000 0 -10000 0 0
EPOR -0.022 0.14 -10000 0 -0.99 1 1
STAT5A (dimer) -0.091 0.25 -10000 0 -0.6 79 79
SOCS1 0.018 0.067 0.37 1 -0.42 9 10
cell migration 0.085 0.19 0.46 79 -10000 0 79
SOS1 0.026 0.002 -10000 0 -10000 0 0
EPO 0.01 0.047 0.37 1 -0.43 3 4
VAV1 0.007 0.088 -10000 0 -0.4 19 19
GRB10 -0.066 0.17 -10000 0 -0.43 71 71
PTPN11 0.028 0.007 -10000 0 -10000 0 0
SCF/KIT -0.068 0.19 -10000 0 -0.45 79 79
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.034 0.11 0.22 2 -0.28 31 33
CBL 0.026 0.003 -10000 0 -10000 0 0
KIT -0.2 0.5 -10000 0 -1.2 78 78
MAP2K2 -0.034 0.11 0.22 2 -0.28 33 35
SHC/Grb2/SOS1 -0.031 0.19 -10000 0 -0.42 73 73
STAT5A -0.095 0.26 -10000 0 -0.62 79 79
GRB2 0.026 0.004 -10000 0 -10000 0 0
response to radiation -0.065 0.17 -10000 0 -0.42 73 73
SHC/GRAP2 0.027 0.054 -10000 0 -0.28 12 12
PTPRO -0.087 0.19 -10000 0 -0.46 81 81
SH2B2 -0.067 0.18 0.21 1 -0.43 74 75
DOK1 0.026 0.002 -10000 0 -10000 0 0
MATK -0.087 0.2 -10000 0 -0.48 79 79
CREBBP 0.012 0.061 -10000 0 -10000 0 0
BCL2 -0.19 0.43 -10000 0 -1.2 49 49
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.026 0.074 -10000 0 -0.24 29 29
fibroblast growth factor receptor signaling pathway 0.025 0.073 -10000 0 -0.24 29 29
LAMA1 -0.055 0.16 -10000 0 -0.4 76 76
PRNP 0.02 0.023 -10000 0 -0.4 1 1
GPC1/SLIT2 -0.046 0.14 -10000 0 -0.28 111 111
SMAD2 0.011 0.025 0.18 3 -0.23 1 4
GPC1/PrPc/Cu2+ 0.026 0.027 -10000 0 -0.24 3 3
GPC1/Laminin alpha1 -0.027 0.12 -10000 0 -0.28 78 78
TDGF1 -0.16 0.22 -10000 0 -0.42 173 173
CRIPTO/GPC1 -0.1 0.17 -10000 0 -0.3 174 174
APP/GPC1 0.035 0.029 -10000 0 -0.29 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.094 0.13 -10000 0 -0.25 174 174
FLT1 0.02 0.011 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.05 0.027 -10000 0 -0.24 3 3
SERPINC1 0.005 0.047 -10000 0 -0.42 4 4
FYN -0.095 0.13 -10000 0 -0.25 172 172
FGR -0.096 0.13 -10000 0 -0.26 174 174
positive regulation of MAPKKK cascade -0.038 0.13 0.21 26 -0.37 18 44
SLIT2 -0.085 0.18 -10000 0 -0.4 109 109
GPC1/NRG -0.002 0.096 -10000 0 -0.28 43 43
NRG1 -0.021 0.12 -10000 0 -0.4 41 41
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.039 0.033 0.25 1 -0.25 2 3
LYN -0.086 0.13 -10000 0 -0.26 153 153
mol:Spermine 0.005 0.02 -10000 0 -0.29 2 2
cell growth 0.025 0.073 -10000 0 -0.24 29 29
BMP signaling pathway -0.024 0.03 0.41 2 -10000 0 2
SRC -0.05 0.1 -10000 0 -0.26 77 77
TGFBR1 0.025 0.021 -10000 0 -0.4 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.065 0.17 -10000 0 -0.4 88 88
GPC1 0.024 0.03 -10000 0 -0.41 2 2
TGFBR1 (dimer) 0.025 0.021 -10000 0 -0.4 1 1
VEGFA 0.027 0.017 0.37 1 -10000 0 1
BLK -0.16 0.16 -10000 0 -0.29 243 243
HCK -0.051 0.1 -10000 0 -0.26 78 78
FGF2 -0.003 0.11 -10000 0 -0.4 29 29
FGFR1 0.02 0.037 -10000 0 -0.4 3 3
VEGFR1 homodimer 0.02 0.011 -10000 0 -10000 0 0
TGFBR2 0.026 0.003 -10000 0 -10000 0 0
cell death 0.035 0.029 -10000 0 -0.29 3 3
ATIII/GPC1 0.031 0.04 -10000 0 -0.3 6 6
PLA2G2A/GPC1 -0.032 0.13 -10000 0 -0.28 90 90
LCK -0.099 0.13 -10000 0 -0.25 179 179
neuron differentiation -0.002 0.095 -10000 0 -0.28 43 43
PrPc/Cu2+ 0.015 0.016 -10000 0 -0.28 1 1
APP 0.024 0.021 -10000 0 -0.4 1 1
TGFBR2 (dimer) 0.026 0.003 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.28 0.27 -10000 0 -0.77 54 54
PCK1 -0.62 0.6 -10000 0 -1.3 193 193
HNF4A -0.26 0.28 -10000 0 -0.91 29 29
KCNJ11 -0.29 0.28 -10000 0 -0.81 52 52
AKT1 -0.21 0.17 -10000 0 -0.56 35 35
response to starvation -0.016 0.027 -10000 0 -10000 0 0
DLK1 -0.3 0.29 -10000 0 -0.78 70 70
NKX2-1 -0.15 0.16 -10000 0 -0.54 14 14
ACADM -0.29 0.28 -10000 0 -0.79 57 57
TAT -0.6 0.58 -10000 0 -1.3 165 165
CEBPB 0.003 0.032 -10000 0 -10000 0 0
CEBPA 0 0.056 -10000 0 -0.4 3 3
TTR -0.3 0.44 0.52 1 -1.2 75 76
PKLR -0.34 0.34 -10000 0 -0.91 86 86
APOA1 -0.3 0.31 -10000 0 -0.95 34 34
CPT1C -0.29 0.27 -10000 0 -0.78 55 55
ALAS1 -0.14 0.15 -10000 0 -0.62 1 1
TFRC -0.28 0.23 -10000 0 -0.65 52 52
FOXF1 0.028 0.065 -10000 0 -0.4 8 8
NF1 0.03 0.006 -10000 0 -10000 0 0
HNF1A (dimer) -0.075 0.057 -10000 0 -0.28 8 8
CPT1A -0.29 0.27 -10000 0 -0.79 49 49
HMGCS1 -0.28 0.27 -10000 0 -0.78 52 52
NR3C1 -0.077 0.14 -10000 0 -0.39 39 39
CPT1B -0.28 0.27 -10000 0 -0.78 52 52
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.062 0.037 -10000 0 -10000 0 0
GCK -0.28 0.28 -10000 0 -0.83 52 52
CREB1 -0.074 0.1 -10000 0 -0.22 85 85
IGFBP1 -0.21 0.18 -10000 0 -0.61 24 24
PDX1 -0.29 0.18 -10000 0 -0.55 58 58
UCP2 -0.29 0.27 -10000 0 -0.78 51 51
ALDOB -0.32 0.32 -10000 0 -0.88 64 64
AFP -0.11 0.13 -10000 0 -0.4 49 49
BDH1 -0.29 0.27 -10000 0 -0.79 53 53
HADH -0.29 0.28 -10000 0 -0.81 49 49
F2 -0.31 0.32 -10000 0 -1 29 29
HNF1A -0.075 0.057 -10000 0 -0.28 8 8
G6PC -0.23 0.4 -10000 0 -1.2 57 57
SLC2A2 -0.21 0.18 -10000 0 -0.67 10 10
INS -0.008 0.038 -10000 0 -10000 0 0
FOXA1 -0.028 0.12 -10000 0 -0.38 37 37
FOXA3 -0.16 0.14 -10000 0 -0.32 123 123
FOXA2 -0.33 0.32 -10000 0 -0.86 67 67
ABCC8 -0.34 0.34 -10000 0 -0.96 65 65
ALB -0.12 0.14 -10000 0 -0.39 55 55
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.022 0.041 -10000 0 -0.4 4 4
LAT2 -0.091 0.16 -10000 0 -0.37 74 74
AP1 -0.12 0.24 -10000 0 -0.52 85 85
mol:PIP3 -0.12 0.2 0.23 6 -0.46 75 81
IKBKB -0.069 0.14 0.19 26 -0.28 83 109
AKT1 -0.088 0.12 0.3 7 -0.33 40 47
IKBKG -0.082 0.13 0.22 6 -0.29 89 95
MS4A2 -0.096 0.19 -10000 0 -0.4 119 119
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 -0.11 0.17 0.24 3 -0.42 74 77
mol:Ca2+ -0.09 0.15 0.21 7 -0.35 73 80
LYN 0.021 0.011 -10000 0 -10000 0 0
CBLB -0.091 0.16 -10000 0 -0.38 66 66
SHC1 0.026 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.047 0.024 -10000 0 -0.22 3 3
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.026 0.002 -10000 0 -10000 0 0
PLD2 -0.092 0.14 0.32 7 -0.36 56 63
PTPN13 -0.1 0.19 -10000 0 -0.52 32 32
PTPN11 0.014 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.079 0.12 0.22 4 -0.31 42 46
SYK 0.024 0.009 -10000 0 -10000 0 0
GRB2 0.025 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.21 -10000 0 -0.47 76 76
LAT -0.093 0.16 -10000 0 -0.38 67 67
PAK2 -0.12 0.2 0.25 3 -0.45 79 82
NFATC2 -0.034 0.1 -10000 0 -0.53 13 13
HRAS -0.12 0.21 0.24 4 -0.48 82 86
GAB2 0.026 0.003 -10000 0 -10000 0 0
PLA2G1B 0.021 0.1 -10000 0 -0.89 5 5
Fc epsilon R1 -0.097 0.19 -10000 0 -0.31 168 168
Antigen/IgE/Fc epsilon R1 -0.086 0.17 -10000 0 -0.28 160 160
mol:GDP -0.14 0.24 0.24 2 -0.53 87 89
JUN 0.026 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.025 0.005 -10000 0 -10000 0 0
FOS 0.022 0.036 -10000 0 -0.4 3 3
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.093 0.16 -10000 0 -0.33 109 109
CHUK -0.082 0.13 0.2 6 -0.28 91 97
KLRG1 -0.082 0.14 -10000 0 -0.35 64 64
VAV1 -0.1 0.17 -10000 0 -0.39 76 76
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.091 0.16 -10000 0 -0.39 63 63
negative regulation of mast cell degranulation -0.067 0.14 -10000 0 -0.33 61 61
BTK -0.15 0.27 -10000 0 -0.58 93 93
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.13 0.22 -10000 0 -0.52 82 82
GAB2/PI3K/SHP2 -0.1 0.12 -10000 0 -0.35 52 52
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.091 0.16 -10000 0 -0.41 63 63
RAF1 0.024 0.11 -10000 0 -0.98 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.084 0.2 -10000 0 -0.43 77 77
FCER1G 0.026 0.044 -10000 0 -0.41 4 4
FCER1A -0.097 0.19 -10000 0 -0.41 115 115
Antigen/IgE/Fc epsilon R1/Fyn -0.072 0.17 -10000 0 -0.3 108 108
MAPK3 0.022 0.1 -10000 0 -0.9 5 5
MAPK1 0.017 0.11 -10000 0 -0.92 5 5
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.11 0.27 -10000 0 -0.7 61 61
DUSP1 0.023 0.036 -10000 0 -0.4 3 3
NF-kappa-B/RelA -0.043 0.084 0.16 1 -0.2 41 42
actin cytoskeleton reorganization -0.096 0.19 -10000 0 -0.46 56 56
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.097 0.19 0.28 2 -0.44 71 73
FER -0.087 0.16 -10000 0 -0.38 66 66
RELA 0.026 0.004 -10000 0 -10000 0 0
ITK -0.034 0.091 -10000 0 -0.37 22 22
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG1 -0.087 0.24 0.27 6 -0.5 71 77
cytokine secretion -0.034 0.058 -10000 0 -0.17 2 2
SPHK1 -0.1 0.16 -10000 0 -0.38 74 74
PTK2 -0.1 0.2 -10000 0 -0.48 54 54
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.22 0.2 7 -0.49 76 83
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.12 0.2 0.25 5 -0.45 78 83
MAP2K2 0.017 0.1 -10000 0 -0.88 5 5
MAP2K1 0.016 0.1 -10000 0 -0.91 5 5
MAP2K7 0.025 0.021 -10000 0 -0.4 1 1
KLRG1/SHP2 -0.064 0.13 0.18 1 -0.32 55 56
MAP2K4 -0.14 0.37 -10000 0 -0.9 80 80
Fc epsilon R1/FcgammaRIIB -0.098 0.21 -10000 0 -0.37 121 121
mol:Choline -0.091 0.14 0.32 7 -0.36 56 63
SHC/Grb2/SOS1 -0.062 0.17 -10000 0 -0.38 60 60
FYN 0.026 0.004 -10000 0 -10000 0 0
DOK1 0.026 0.002 -10000 0 -10000 0 0
PXN -0.095 0.18 -10000 0 -0.5 29 29
HCLS1 -0.093 0.16 -10000 0 -0.39 65 65
PRKCB -0.12 0.18 0.21 5 -0.39 100 105
FCGR2B -0.019 0.13 -10000 0 -0.4 44 44
IGHE -0.003 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.069 0.14 -10000 0 -0.34 61 61
LCP2 0.021 0.042 -10000 0 -0.4 4 4
PLA2G4A -0.11 0.18 -10000 0 -0.39 93 93
RASA1 0.026 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.091 0.14 0.32 7 -0.36 56 63
IKK complex -0.049 0.11 0.19 24 -0.23 45 69
WIPF1 0.023 0.036 -10000 0 -0.4 3 3
HIF-1-alpha transcription factor network

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
PKM2 -0.39 0.3 -10000 0 -0.87 67 67
HDAC7 0.026 0.007 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.31 0.25 -10000 0 -0.87 25 25
SMAD4 0.02 0.012 -10000 0 -10000 0 0
ID2 -0.39 0.3 -10000 0 -0.87 66 66
AP1 0.035 0.029 -10000 0 -0.27 3 3
ABCG2 -0.55 0.32 -10000 0 -0.88 149 149
HIF1A -0.075 0.055 -10000 0 -10000 0 0
TFF3 -0.4 0.31 -10000 0 -0.89 67 67
GATA2 0.018 0.062 -10000 0 -0.4 9 9
AKT1 -0.075 0.059 -10000 0 -10000 0 0
response to hypoxia -0.077 0.051 -10000 0 -0.22 11 11
MCL1 -0.39 0.3 -10000 0 -0.87 64 64
NDRG1 -0.38 0.3 -10000 0 -0.87 61 61
SERPINE1 -0.43 0.32 -10000 0 -0.89 87 87
FECH -0.39 0.3 -10000 0 -0.87 64 64
FURIN -0.39 0.3 -10000 0 -0.87 66 66
NCOA2 0.022 0.023 -10000 0 -0.4 1 1
EP300 -0.07 0.079 -10000 0 -0.34 16 16
HMOX1 -0.4 0.3 -10000 0 -0.87 70 70
BHLHE40 -0.4 0.3 -10000 0 -0.88 65 65
BHLHE41 -0.4 0.3 -10000 0 -0.88 68 68
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.07 0.088 -10000 0 -10000 0 0
ENG -0.074 0.073 0.24 1 -10000 0 1
JUN 0.026 0.006 -10000 0 -10000 0 0
RORA -0.39 0.3 -10000 0 -0.87 69 69
ABCB1 -0.29 0.44 -10000 0 -1.1 92 92
TFRC -0.39 0.3 -10000 0 -0.87 66 66
CXCR4 -0.39 0.3 -10000 0 -0.87 66 66
TF -0.42 0.32 -10000 0 -0.91 72 72
CITED2 -0.39 0.3 -10000 0 -0.86 66 66
HIF1A/ARNT -0.43 0.34 -10000 0 -0.96 66 66
LDHA -0.037 0.055 -10000 0 -0.67 1 1
ETS1 -0.39 0.3 -10000 0 -0.87 66 66
PGK1 -0.39 0.3 -10000 0 -0.87 66 66
NOS2 -0.4 0.31 -10000 0 -0.89 70 70
ITGB2 -0.4 0.3 -10000 0 -0.87 68 68
ALDOA -0.39 0.3 -10000 0 -0.87 65 65
Cbp/p300/CITED2 -0.39 0.31 -10000 0 -1 39 39
FOS 0.022 0.036 -10000 0 -0.4 3 3
HK2 -0.39 0.3 -10000 0 -0.87 66 66
SP1 0.003 0.055 -10000 0 -10000 0 0
GCK -0.094 0.2 -10000 0 -1.3 9 9
HK1 -0.39 0.3 -10000 0 -0.87 65 65
NPM1 -0.39 0.3 -10000 0 -0.87 66 66
EGLN1 -0.39 0.3 -10000 0 -0.87 65 65
CREB1 0.032 0 -10000 0 -10000 0 0
PGM1 -0.4 0.3 -10000 0 -0.86 71 71
SMAD3 0.026 0.006 -10000 0 -10000 0 0
EDN1 -0.08 0.15 -10000 0 -0.87 7 7
IGFBP1 -0.41 0.31 -10000 0 -0.9 75 75
VEGFA -0.28 0.22 -10000 0 -0.78 20 20
HIF1A/JAB1 -0.038 0.046 -10000 0 -10000 0 0
CP -0.48 0.34 -10000 0 -0.88 126 126
CXCL12 -0.42 0.33 -10000 0 -0.89 92 92
COPS5 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.03 0.018 -10000 0 -10000 0 0
BNIP3 -0.39 0.3 -10000 0 -0.88 66 66
EGLN3 -0.39 0.3 -10000 0 -0.87 66 66
CA9 -0.53 0.32 -10000 0 -0.89 129 129
TERT -0.41 0.31 -10000 0 -0.89 72 72
ENO1 -0.39 0.3 -10000 0 -0.87 66 66
PFKL -0.39 0.3 -10000 0 -0.87 66 66
NCOA1 0.027 0.001 -10000 0 -10000 0 0
ADM -0.39 0.3 -10000 0 -0.87 66 66
ARNT -0.078 0.055 -10000 0 -0.45 1 1
HNF4A 0.015 0.019 -10000 0 -10000 0 0
ADFP -0.4 0.29 -10000 0 -0.86 67 67
SLC2A1 -0.29 0.23 -10000 0 -0.81 24 24
LEP -0.4 0.31 -10000 0 -0.9 69 69
HIF1A/ARNT/Cbp/p300 -0.33 0.25 -10000 0 -0.88 28 28
EPO -0.22 0.18 -10000 0 -0.83 6 6
CREBBP -0.07 0.077 -10000 0 -0.36 12 12
HIF1A/ARNT/Cbp/p300/HDAC7 -0.31 0.26 -10000 0 -0.87 28 28
PFKFB3 -0.39 0.3 -10000 0 -0.87 66 66
NT5E -0.4 0.3 -10000 0 -0.88 66 66
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.025 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.012 0.002 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.022 0.024 -10000 0 -0.25 3 3
PDE6G/GNAT1/GTP 0.013 0.062 -10000 0 -0.24 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.018 0.003 -10000 0 -10000 0 0
GRK1 -0.012 0.032 -10000 0 -0.42 2 2
CNG Channel -0.16 0.16 -10000 0 -0.41 78 78
mol:Na + -0.03 0.12 -10000 0 -0.41 18 18
mol:ADP -0.012 0.032 -10000 0 -0.42 2 2
RGS9-1/Gbeta5/R9AP 0.005 0.1 0.25 1 -0.24 63 64
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.024 0.13 -10000 0 -0.42 18 18
CNGB1 -0.046 0.13 -10000 0 -0.4 49 49
RDH5 -0.016 0.13 -10000 0 -0.4 42 42
SAG -0.01 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.066 0.11 0.3 7 -0.4 18 25
Na + (4 Units) -0.034 0.12 -10000 0 -0.39 18 18
RGS9 -0.039 0.15 -10000 0 -0.4 63 63
GNB1/GNGT1 -0.044 0.15 0.26 11 -0.3 106 117
GNAT1/GDP 0.012 0.093 0.23 1 -0.21 55 56
GUCY2D -0.004 0.082 -10000 0 -0.42 15 15
GNGT1 -0.089 0.2 0.37 12 -0.42 106 118
GUCY2F -0.017 0.022 -10000 0 -0.42 1 1
GNB5 0.025 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.13 0.13 -10000 0 -0.23 255 255
mol:11-cis-retinal -0.016 0.13 -10000 0 -0.4 42 42
mol:cGMP 0.016 0.078 -10000 0 -0.26 28 28
GNB1 0.025 0.006 -10000 0 -10000 0 0
Rhodopsin -0.002 0.099 -10000 0 -0.29 45 45
SLC24A1 0.025 0.005 -10000 0 -10000 0 0
CNGA1 -0.015 0.13 -10000 0 -0.4 41 41
Metarhodopsin II 0.014 0.032 -10000 0 -0.28 4 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.026 0.082 -10000 0 -0.26 28 28
RGS9BP 0.02 0.032 0.37 1 -0.42 1 2
Metarhodopsin II/Transducin -0.019 0.063 0.15 10 -0.2 10 20
GCAP Family/Ca ++ 0.031 0.053 -10000 0 -0.24 16 16
PDE6A/B -0.16 0.17 -10000 0 -0.3 250 250
mol:Pi 0.005 0.1 0.25 1 -0.24 63 64
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.025 0.12 0.23 11 -0.23 106 117
PDE6B 0.007 0.086 -10000 0 -0.4 18 18
PDE6A -0.22 0.21 -10000 0 -0.4 246 246
PDE6G 0.001 0.098 -10000 0 -0.4 24 24
RHO -0.018 0.036 -10000 0 -0.42 3 3
PDE6 -0.14 0.17 -10000 0 -0.41 60 60
GUCA1A -0.001 0.087 0.37 1 -0.42 16 17
GC2/GCAP Family 0.041 0.06 -10000 0 -0.25 16 16
GUCA1C -0.018 0.002 -10000 0 -10000 0 0
GUCA1B 0.028 0.024 0.37 2 -10000 0 2
IL1-mediated signaling events

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
UBC13/UEV1A 0.01 0.099 0.26 20 -0.3 28 48
PRKCZ 0.025 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.044 -10000 0 -0.2 1 1
IRAK/TOLLIP 0.008 0.074 0.19 19 -0.23 27 46
IKBKB 0.023 0.009 -10000 0 -10000 0 0
IKBKG 0.025 0.021 -10000 0 -0.4 1 1
IL1 alpha/IL1R2 -0.14 0.18 -10000 0 -0.31 218 218
IL1A -0.12 0.21 -10000 0 -0.42 139 139
IL1B -0.024 0.1 -10000 0 -0.3 49 49
IRAK/TRAF6/p62/Atypical PKCs 0.084 0.1 -10000 0 -10000 0 0
IL1R2 -0.064 0.17 -10000 0 -0.4 90 90
IL1R1 0.02 0.05 -10000 0 -0.4 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.034 0.066 0.24 5 -0.32 1 6
TOLLIP 0.026 0.003 -10000 0 -10000 0 0
TICAM2 0.014 0.055 -10000 0 -0.4 7 7
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.06 0.098 0.27 5 -10000 0 5
JUN 0.039 0.1 0.23 5 -0.34 1 6
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.031 0.095 -10000 0 -0.36 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.034 0.14 -10000 0 -0.24 142 142
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.024 0.14 -10000 0 -0.22 137 137
IL1 beta fragment/IL1R1/IL1RAP 0.008 0.093 -10000 0 -0.23 54 54
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.046 0.11 0.16 154 -0.36 1 155
IRAK1 -0.008 0.079 0.21 20 -0.25 27 47
IL1RN/IL1R1 -0.02 0.13 -10000 0 -0.3 74 74
IRAK4 0.026 0.002 -10000 0 -10000 0 0
PRKCI 0.024 0.029 -10000 0 -0.4 2 2
TRAF6 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.038 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.05 -10000 0 -0.33 1 1
CHUK 0.025 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.008 0.093 -10000 0 -0.23 54 54
IL1 beta/IL1R2 -0.056 0.13 -10000 0 -0.25 135 135
IRAK/TRAF6/TAK1/TAB1/TAB2 0.013 0.066 -10000 0 -0.2 27 27
NF kappa B1 p50/RelA 0.02 0.086 -10000 0 -0.32 1 1
IRAK3 0.015 0.068 -10000 0 -0.4 11 11
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.026 0.099 -10000 0 -0.38 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.014 0.065 -10000 0 -0.25 7 7
IL1 alpha/IL1R1/IL1RAP -0.051 0.15 -10000 0 -0.26 142 142
RELA 0.026 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.003 -10000 0 -10000 0 0
MYD88 0.026 0.003 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.079 0.1 -10000 0 -0.22 25 25
IL1RAP 0.026 0.002 -10000 0 -10000 0 0
UBE2N 0.026 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.018 0.088 -10000 0 -0.36 7 7
CASP1 0.025 0.021 -10000 0 -0.4 1 1
IL1RN/IL1R2 -0.084 0.16 -10000 0 -0.29 158 158
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.022 0.094 -10000 0 -0.22 45 45
TMEM189-UBE2V1 -0.01 0.14 0.37 21 -0.42 28 49
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.028 0.085 0.19 1 -0.41 2 3
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
IL1RN -0.046 0.16 -10000 0 -0.42 68 68
TRAF6/TAK1/TAB1/TAB2 0.02 0.075 0.2 19 -0.21 28 47
MAP2K6 0.051 0.11 0.18 157 -0.38 1 158
Signaling events mediated by the Hedgehog family

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
TGFB2 0.013 0.098 -10000 0 -0.4 18 18
IHH 0.018 0.085 -10000 0 -0.45 12 12
SHH Np/Cholesterol/GAS1 -0.044 0.12 0.19 1 -0.25 105 106
LRPAP1 0.026 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.044 0.12 0.25 105 -0.19 1 106
SMO/beta Arrestin2 0.018 0.09 -10000 0 -0.46 6 6
SMO 0.006 0.085 -10000 0 -0.38 14 14
AKT1 0.001 0.1 -10000 0 -0.34 27 27
ARRB2 0.022 0.01 -10000 0 -10000 0 0
BOC 0.017 0.061 -10000 0 -0.4 9 9
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
heart looping 0.007 0.085 -10000 0 -0.37 14 14
STIL -0.015 0.11 -10000 0 -0.36 8 8
DHH N/PTCH2 0.023 0.067 -10000 0 -0.28 19 19
DHH N/PTCH1 0.02 0.091 -10000 0 -0.41 8 8
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
DHH 0.005 0.086 -10000 0 -0.4 18 18
PTHLH 0.008 0.12 -10000 0 -0.74 8 8
determination of left/right symmetry 0.007 0.085 -10000 0 -0.37 14 14
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development 0.008 0.12 -10000 0 -0.73 8 8
IHH N/Hhip -0.041 0.15 -10000 0 -0.32 95 95
DHH N/Hhip -0.041 0.15 -10000 0 -0.3 97 97
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.007 0.085 -10000 0 -0.37 14 14
pancreas development -0.064 0.17 -10000 0 -0.4 88 88
HHAT 0.022 0.041 -10000 0 -0.4 4 4
PI3K 0.038 0.008 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.029 0.14 -10000 0 -0.4 55 55
somite specification 0.007 0.085 -10000 0 -0.37 14 14
SHH Np/Cholesterol/PTCH1 -0.016 0.1 0.2 4 -0.34 11 15
SHH Np/Cholesterol/PTCH2 -0.017 0.097 0.19 4 -0.23 72 76
SHH Np/Cholesterol/Megalin -0.038 0.12 0.18 4 -0.24 98 102
SHH -0.038 0.12 0.28 4 -0.3 70 74
catabolic process 0.018 0.078 -10000 0 -0.32 16 16
SMO/Vitamin D3 -0.013 0.11 -10000 0 -0.41 8 8
SHH Np/Cholesterol/Hhip -0.061 0.13 0.18 3 -0.23 141 144
LRP2 -0.032 0.12 -10000 0 -0.42 36 36
receptor-mediated endocytosis -0.026 0.11 -10000 0 -0.42 10 10
SHH Np/Cholesterol/BOC -0.02 0.1 0.19 3 -0.23 76 79
SHH Np/Cholesterol/CDO -0.017 0.096 0.19 3 -0.23 71 74
mesenchymal cell differentiation 0.061 0.13 0.23 141 -0.18 3 144
mol:Vitamin D3 -0.009 0.11 0.2 21 -0.34 11 32
IHH N/PTCH2 0.03 0.057 -10000 0 -0.27 13 13
CDON 0.026 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.026 0.08 -10000 0 -0.32 16 16
Megalin/LRPAP1 0.006 0.094 -10000 0 -0.3 36 36
PTCH2 0.024 0.023 -10000 0 -0.42 1 1
SHH Np/Cholesterol -0.026 0.09 -10000 0 -0.23 71 71
PTCH1 0.018 0.078 -10000 0 -0.32 16 16
HHIP -0.064 0.17 -10000 0 -0.4 88 88
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.01 0.16 0.26 55 -0.42 10 65
SMAD6-7/SMURF1 0.039 0.028 -10000 0 -0.24 1 1
NOG 0.013 0.029 -10000 0 -0.42 1 1
SMAD9 -0.047 0.18 -10000 0 -0.56 41 41
SMAD4 0.02 0.012 -10000 0 -10000 0 0
SMAD5 -0.036 0.12 -10000 0 -0.38 31 31
BMP7/USAG1 -0.055 0.2 0.26 52 -0.34 122 174
SMAD5/SKI -0.036 0.13 -10000 0 -0.37 31 31
SMAD1 0.01 0.045 -10000 0 -0.35 2 2
BMP2 0.006 0.078 -10000 0 -0.4 15 15
SMAD1/SMAD1/SMAD4 0.019 0.054 -10000 0 -0.34 3 3
BMPR1A 0.025 0.006 -10000 0 -10000 0 0
BMPR1B -0.007 0.11 -10000 0 -0.42 27 27
BMPR1A-1B/BAMBI 0.012 0.1 0.25 1 -0.25 54 55
AHSG -0.052 0.16 0.37 2 -0.42 62 64
CER1 -0.02 0.082 -10000 0 -0.42 16 16
BMP2-4/CER1 0.001 0.098 -10000 0 -0.26 49 49
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.039 0.13 -10000 0 -0.36 33 33
BMP2-4 (homodimer) 0.001 0.097 -10000 0 -0.31 36 36
RGMB 0.025 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.024 0.1 -10000 0 -0.24 19 19
RGMA -0.061 0.17 -10000 0 -0.4 86 86
SMURF1 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.039 0.12 -10000 0 -0.32 43 43
BMP2-4/USAG1 -0.029 0.13 -10000 0 -0.27 89 89
SMAD6/SMURF1/SMAD5 -0.036 0.13 -10000 0 -0.38 29 29
SOSTDC1 -0.051 0.16 -10000 0 -0.4 73 73
BMP7/BMPR2/BMPR1A-1B -0.006 0.16 0.26 62 -0.24 105 167
SKI 0.025 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) -0.005 0.11 -10000 0 -0.4 31 31
HFE2 -0.01 0.027 -10000 0 -0.42 1 1
ZFYVE16 0.024 0.029 -10000 0 -0.4 2 2
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.015 0.089 -10000 0 -0.26 37 37
SMAD5/SMAD5/SMAD4 -0.031 0.12 -10000 0 -0.38 27 27
MAPK1 0.025 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.024 0.11 -10000 0 -0.32 26 26
BMP7 (homodimer) -0.025 0.25 0.37 71 -0.42 97 168
NUP214 0.026 0.003 -10000 0 -10000 0 0
BMP6/FETUA -0.034 0.14 -10000 0 -0.31 85 85
SMAD1/SKI 0.015 0.065 -10000 0 -0.39 4 4
SMAD6 0.025 0.006 -10000 0 -10000 0 0
CTDSP2 0.026 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA -0.023 0.13 0.25 1 -0.28 83 84
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.002 0.097 -10000 0 -0.41 22 22
BMPR2 (homodimer) 0.025 0.021 -10000 0 -0.4 1 1
GADD34/PP1CA 0.049 0.024 -10000 0 -0.24 2 2
BMPR1A-1B (homodimer) 0.015 0.081 -10000 0 -0.29 27 27
CHRDL1 -0.2 0.21 -10000 0 -0.4 221 221
ENDOFIN/SMAD1 0.015 0.067 -10000 0 -0.4 4 4
SMAD6-7/SMURF1/SMAD1 0.031 0.066 -10000 0 -0.38 3 3
SMAD6/SMURF1 0.025 0.006 -10000 0 -10000 0 0
BAMBI -0.003 0.11 0.37 1 -0.42 28 29
SMURF2 0.025 0.021 -10000 0 -0.4 1 1
BMP2-4/CHRDL1 -0.11 0.16 -10000 0 -0.26 206 206
BMP2-4/GREM1 -0.001 0.1 -10000 0 -0.26 56 56
SMAD7 0.019 0.023 -10000 0 -0.4 1 1
SMAD8A/SMAD8A/SMAD4 -0.043 0.18 -10000 0 -0.49 52 52
SMAD1/SMAD6 0.014 0.067 -10000 0 -0.37 5 5
TAK1/SMAD6 0.037 0.01 -10000 0 -10000 0 0
BMP7 -0.025 0.25 0.37 71 -0.42 97 168
BMP6 -0.005 0.11 -10000 0 -0.4 31 31
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.041 0.13 -10000 0 -0.38 37 37
PPM1A 0.025 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.015 0.066 -10000 0 -0.37 5 5
SMAD7/SMURF1 0.028 0.023 -10000 0 -0.28 1 1
CTDSPL 0.026 0.003 -10000 0 -10000 0 0
PPP1CA 0.026 0.004 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
CTDSP1 0.026 0.001 -10000 0 -10000 0 0
PPP1R15A 0.026 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.055 0.15 -10000 0 -0.4 49 49
CHRD 0.025 0.021 -10000 0 -0.4 1 1
BMPR2 0.025 0.021 -10000 0 -0.4 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.044 0.12 -10000 0 -0.36 39 39
BMP4 -0.001 0.1 -10000 0 -0.42 24 24
FST 0.008 0.084 -10000 0 -0.4 17 17
BMP2-4/NOG 0.013 0.089 -10000 0 -0.26 37 37
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.003 0.16 0.26 55 -0.41 5 60
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.022 -10000 0 -0.42 1 1
CCL5 0.009 0.084 -10000 0 -0.4 17 17
SDCBP 0.022 0.022 -10000 0 -0.4 1 1
FGFR/FGF2/Syndecan-1 -0.11 0.099 0.3 3 -0.29 29 32
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 -0.081 0.099 0.24 3 -0.38 9 12
Syndecan-1/Syntenin -0.097 0.098 0.28 2 -0.37 12 14
MAPK3 -0.1 0.091 0.26 2 -0.37 10 12
HGF/MET 0.03 0.048 -10000 0 -0.29 9 9
TGFB1/TGF beta receptor Type II 0.025 0.022 -10000 0 -0.42 1 1
BSG 0.025 0.021 -10000 0 -0.4 1 1
keratinocyte migration -0.08 0.098 0.24 3 -0.38 9 12
Syndecan-1/RANTES -0.11 0.1 0.27 3 -0.35 21 24
Syndecan-1/CD147 -0.1 0.099 0.36 1 -0.39 10 11
Syndecan-1/Syntenin/PIP2 -0.094 0.094 0.34 1 -0.36 12 13
LAMA5 0.017 0.038 0.37 3 -0.4 1 4
positive regulation of cell-cell adhesion -0.093 0.092 0.33 1 -0.35 12 13
MMP7 -0.4 0.11 0.37 3 -0.43 405 408
HGF 0.018 0.055 -10000 0 -0.4 7 7
Syndecan-1/CASK -0.11 0.093 0.28 2 -0.29 30 32
Syndecan-1/HGF/MET -0.1 0.1 0.24 1 -0.4 12 13
regulation of cell adhesion -0.099 0.087 0.32 1 -0.38 8 9
HPSE 0.021 0.046 -10000 0 -0.4 5 5
positive regulation of cell migration -0.11 0.099 0.3 3 -0.29 29 32
SDC1 -0.11 0.099 0.3 3 -0.29 30 33
Syndecan-1/Collagen -0.11 0.099 0.3 3 -0.29 29 32
PPIB 0.025 0.006 -10000 0 -10000 0 0
MET 0.022 0.047 0.37 1 -0.42 4 5
PRKACA 0.026 0.003 -10000 0 -10000 0 0
MMP9 -0.002 0.12 0.37 11 -0.42 25 36
MAPK1 -0.099 0.091 0.34 1 -0.38 9 10
homophilic cell adhesion -0.11 0.1 0.3 3 -0.3 30 33
MMP1 -0.27 0.22 0.37 2 -0.43 278 280
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.026 0.11 -10000 0 -0.28 45 45
MAP4K1 -0.016 0.13 -10000 0 -0.4 42 42
MAP3K8 0.026 0.003 -10000 0 -10000 0 0
PRKCB -0.068 0.18 -10000 0 -0.4 94 94
DBNL 0.024 0.008 -10000 0 -10000 0 0
CRKL 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 -0.013 0.11 -10000 0 -0.35 29 29
JUN -0.13 0.28 -10000 0 -0.6 105 105
MAP3K7 -0.011 0.1 -10000 0 -0.35 29 29
GRAP2 0.013 0.071 -10000 0 -0.4 12 12
CRK 0.022 0.01 -10000 0 -10000 0 0
MAP2K4 -0.02 0.12 0.23 1 -0.38 31 32
LAT 0.023 0.036 -10000 0 -0.41 3 3
LCP2 0.022 0.041 -10000 0 -0.4 4 4
MAPK8 -0.13 0.3 -10000 0 -0.63 105 105
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.007 0.11 -10000 0 -0.36 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55 0.031 0.1 -10000 0 -0.32 19 19
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.011 0.06 -10000 0 -0.25 21 21
EPHB2 0.023 0.031 -10000 0 -0.42 2 2
Syndecan-2/TACI -0.058 0.11 -10000 0 -0.23 127 127
LAMA1 -0.055 0.16 -10000 0 -0.4 76 76
Syndecan-2/alpha2 ITGB1 0.04 0.03 -10000 0 -0.21 1 1
HRAS 0.025 0.021 -10000 0 -0.4 1 1
Syndecan-2/CASK 0.008 0.003 -10000 0 -10000 0 0
ITGA5 0.024 0.031 -10000 0 -0.42 2 2
BAX 0.005 0.002 -10000 0 -10000 0 0
EPB41 0.025 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.021 0.015 -10000 0 -0.21 1 1
LAMA3 0.019 0.037 -10000 0 -0.41 3 3
EZR 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.019 0.052 -10000 0 -0.42 6 6
Syndecan-2/MMP2 0.022 0.028 -10000 0 -0.24 4 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.038 0.007 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.022 -10000 0 -0.25 2 2
Syndecan-2/GM-CSF -0.066 0.14 -10000 0 -0.25 146 146
determination of left/right symmetry 0.01 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.024 0.011 -10000 0 -10000 0 0
GNB2L1 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.057 0.13 0.19 35 -0.23 144 179
MAPK1 -0.057 0.13 0.19 35 -0.23 144 179
Syndecan-2/RACK1 0.034 0.019 -10000 0 -0.2 1 1
NF1 0.026 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.004 -10000 0 -10000 0 0
ITGA2 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.009 0.004 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.001 0.09 -10000 0 -10000 0 0
Syndecan-2/Kininogen -0.03 0.1 -10000 0 -0.23 86 86
ITGB1 0.026 0.002 -10000 0 -10000 0 0
SRC 0.017 0.039 0.18 20 -10000 0 20
Syndecan-2/CASK/Protein 4.1 0.021 0.011 -10000 0 -10000 0 0
extracellular matrix organization 0.023 0.017 -10000 0 -0.25 1 1
actin cytoskeleton reorganization 0.011 0.059 -10000 0 -0.24 21 21
Syndecan-2/Caveolin-2/Ras 0.033 0.033 -10000 0 -0.22 5 5
Syndecan-2/Laminin alpha3 0.02 0.019 -10000 0 -0.25 1 1
Syndecan-2/RasGAP 0.044 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.037 0.024 -10000 0 -0.3 2 2
PRKCD 0.026 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.022 -10000 0 -0.25 2 2
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.02 0.023 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
SDCBP 0.022 0.022 -10000 0 -0.4 1 1
TNFRSF13B -0.13 0.2 -10000 0 -0.4 144 144
RASA1 0.026 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.038 0.007 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.024 0.01 -10000 0 -10000 0 0
TGFB1 0.025 0.022 -10000 0 -0.42 1 1
CASP3 0.035 0.059 0.19 52 -10000 0 52
FN1 0.002 0.1 -10000 0 -0.42 23 23
Syndecan-2/IL8 -0.11 0.15 0.39 1 -0.25 219 220
SDC2 0.01 0.004 -10000 0 -10000 0 0
KNG1 -0.083 0.18 -10000 0 -0.4 98 98
Syndecan-2/Neurofibromin 0.024 0.011 -10000 0 -10000 0 0
TRAPPC4 0.026 0.003 -10000 0 -10000 0 0
CSF2 -0.16 0.22 -10000 0 -0.43 168 168
Syndecan-2/TGFB1 0.023 0.017 -10000 0 -0.25 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.021 0.015 -10000 0 -0.21 1 1
Syndecan-2/Ezrin 0.037 0.017 -10000 0 -10000 0 0
PRKACA 0.038 0.06 0.19 56 -10000 0 56
angiogenesis -0.11 0.15 0.38 1 -0.25 219 220
MMP2 0.022 0.042 -10000 0 -0.41 4 4
IL8 -0.24 0.22 0.37 1 -0.43 251 252
calcineurin-NFAT signaling pathway -0.058 0.11 -10000 0 -0.23 127 127
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.033 0.051 -10000 0 -0.21 17 17
RGS9BP 0.02 0.032 0.37 1 -0.42 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.012 0.032 -10000 0 -0.42 2 2
mol:Na + -0.053 0.13 0.23 4 -0.25 122 126
mol:ADP -0.014 0.034 -10000 0 -0.39 3 3
GNAT2 0.013 0.058 -10000 0 -0.42 7 7
RGS9-1/Gbeta5/R9AP 0.005 0.1 0.25 1 -0.24 63 64
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.022 0.039 -10000 0 -0.26 8 8
GRK7 0.008 0.037 -10000 0 -0.42 2 2
CNGB3 -0.014 0.092 0.37 6 -0.42 15 21
Cone Metarhodopsin II/X-Arrestin 0.013 0.022 -10000 0 -0.3 2 2
mol:Ca2+ -0.07 0.14 0.18 37 -0.24 142 179
Cone PDE6 0.018 0.099 0.26 1 -0.23 1 2
Cone Metarhodopsin II 0.018 0.03 -10000 0 -0.3 3 3
Na + (4 Units) -0.06 0.14 0.23 4 -0.24 144 148
GNAT2/GDP 0.012 0.097 0.24 1 -0.21 59 60
GNB5 0.025 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.018 0.034 0.18 2 -0.24 8 10
Cone Transducin 0.036 0.055 -10000 0 -0.22 17 17
SLC24A2 -0.03 0.13 0.37 2 -0.42 38 40
GNB3/GNGT2 0.03 0.05 -10000 0 -0.29 10 10
GNB3 0.021 0.043 -10000 0 -0.42 4 4
GNAT2/GTP 0.013 0.041 -10000 0 -0.3 7 7
CNGA3 -0.11 0.19 -10000 0 -0.4 128 128
ARR3 -0.009 0.035 -10000 0 -0.42 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.053 0.13 0.24 4 -0.25 122 126
mol:Pi 0.005 0.1 0.25 1 -0.24 63 64
Cone CNG Channel -0.038 0.12 -10000 0 -0.26 19 19
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.03 0.13 0.37 2 -0.42 38 40
RGS9 -0.039 0.15 -10000 0 -0.4 63 63
PDE6C -0.006 0.02 -10000 0 -10000 0 0
GNGT2 0.02 0.05 -10000 0 -0.4 6 6
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.016 0.023 -10000 0 -0.42 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.003 0.11 -10000 0 -0.24 62 62
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.091 -10000 0 -0.3 10 10
AP1 -0.039 0.092 -10000 0 -0.35 8 8
mol:PIP3 -0.032 0.08 -10000 0 -0.33 7 7
AKT1 0.002 0.079 0.24 1 -0.35 4 5
PTK2B -0.052 0.11 -10000 0 -0.33 30 30
RHOA 0.007 0.062 0.23 2 -0.35 7 9
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.056 0.21 1 -0.27 1 2
MAGI3 0.025 0.021 -10000 0 -0.4 1 1
RELA 0.026 0.004 -10000 0 -10000 0 0
apoptosis -0.036 0.11 -10000 0 -0.24 83 83
HRAS/GDP 0.019 0.015 -10000 0 -0.28 1 1
positive regulation of microtubule depolymerization -0.084 0.12 0.23 1 -0.35 48 49
NF kappa B1 p50/RelA -0.04 0.09 -10000 0 -0.4 7 7
endothelial cell migration -0.019 0.095 -10000 0 -0.24 61 61
ADCY4 -0.083 0.18 -10000 0 -0.45 71 71
ADCY5 -0.16 0.24 -10000 0 -0.5 114 114
ADCY6 -0.079 0.18 -10000 0 -0.46 65 65
ADCY7 -0.078 0.18 -10000 0 -0.46 64 64
ADCY1 -0.077 0.18 -10000 0 -0.46 63 63
ADCY2 -0.096 0.21 -10000 0 -0.49 78 78
ADCY3 -0.079 0.18 -10000 0 -0.46 65 65
ADCY8 -0.078 0.17 -10000 0 -0.45 64 64
ADCY9 -0.078 0.18 -10000 0 -0.46 66 66
GSK3B -0.051 0.1 -10000 0 -0.33 26 26
arachidonic acid secretion -0.093 0.19 -10000 0 -0.46 72 72
GNG2 0.009 0.081 -10000 0 -0.4 16 16
TRIP6 0.012 0.02 -10000 0 -0.32 1 1
GNAO1 -0.08 0.16 -10000 0 -0.3 130 130
HRAS 0.025 0.021 -10000 0 -0.4 1 1
NFKBIA -0.028 0.089 0.19 1 -0.32 13 14
GAB1 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.081 0.31 -10000 0 -0.85 59 59
JUN 0.026 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.035 0.017 -10000 0 -0.23 1 1
TIAM1 -0.11 0.36 -10000 0 -1 59 59
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.013 0.052 0.21 1 -0.27 1 2
PLCB3 0.015 0.018 0.18 2 -0.21 1 3
FOS 0.021 0.036 -10000 0 -0.4 3 3
positive regulation of mitosis -0.093 0.19 -10000 0 -0.46 72 72
LPA/LPA1-2-3 -0.008 0.12 -10000 0 -0.23 87 87
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade -0.001 0 -10000 0 -10000 0 0
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
stress fiber formation -0.033 0.097 -10000 0 -0.3 24 24
GNAZ -0.018 0.089 -10000 0 -0.24 59 59
EGFR/PI3K-beta/Gab1 -0.017 0.089 -10000 0 -0.34 7 7
positive regulation of dendritic cell cytokine production -0.01 0.11 -10000 0 -0.22 87 87
LPA/LPA2/MAGI-3 0.035 0.018 -10000 0 -0.23 1 1
ARHGEF1 0.006 0.093 0.19 38 -0.37 1 39
GNAI2 -0.015 0.085 -10000 0 -0.23 55 55
GNAI3 -0.018 0.088 -10000 0 -0.23 59 59
GNAI1 -0.023 0.1 -10000 0 -0.27 60 60
LPA/LPA3 -0.006 0.081 -10000 0 -0.28 34 34
LPA/LPA2 0.02 0.01 -10000 0 -10000 0 0
LPA/LPA1 -0.018 0.11 -10000 0 -0.27 62 62
HB-EGF/EGFR 0.002 0.072 0.21 10 -0.26 25 35
HBEGF -0.006 0.088 0.28 11 -0.3 27 38
mol:DAG -0.013 0.052 0.21 1 -0.27 1 2
cAMP biosynthetic process -0.1 0.19 0.32 1 -0.44 83 84
NFKB1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.016 0.013 -10000 0 -10000 0 0
GNB1 0.025 0.006 -10000 0 -10000 0 0
LYN -0.009 0.094 0.22 2 -0.35 8 10
GNAQ -0.004 0.064 -10000 0 -0.21 35 35
LPAR2 0.026 0.003 -10000 0 -10000 0 0
LPAR3 -0.018 0.12 -10000 0 -0.4 34 34
LPAR1 -0.032 0.15 -10000 0 -0.4 59 59
IL8 -0.091 0.13 0.28 1 -0.37 15 16
PTK2 -0.029 0.089 0.18 1 -0.38 7 8
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
CASP3 -0.036 0.11 -10000 0 -0.24 83 83
EGFR 0.022 0.022 -10000 0 -0.4 1 1
PLCG1 -0.011 0.06 -10000 0 -0.22 29 29
PLD2 -0.035 0.092 0.18 1 -0.37 7 8
G12/G13 0.016 0.087 -10000 0 -0.21 50 50
PI3K-beta -0.01 0.077 -10000 0 -0.37 6 6
cell migration -0.018 0.1 -10000 0 -0.25 56 56
SLC9A3R2 0.025 0.021 -10000 0 -0.4 1 1
PXN -0.034 0.098 -10000 0 -0.3 24 24
HRAS/GTP -0.095 0.2 -10000 0 -0.47 72 72
RAC1 0.024 0.008 -10000 0 -10000 0 0
MMP9 -0.002 0.12 0.37 11 -0.42 25 36
PRKCE 0.026 0.003 -10000 0 -10000 0 0
PRKCD -0.006 0.057 0.26 2 -0.26 1 3
Gi(beta/gamma) -0.085 0.19 0.16 1 -0.43 77 78
mol:LPA 0.002 0.012 -10000 0 -0.15 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.002 0.11 -10000 0 -0.38 8 8
MAPKKK cascade -0.093 0.19 -10000 0 -0.46 72 72
contractile ring contraction involved in cytokinesis 0.008 0.062 0.23 2 -0.35 7 9
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.005 0.065 -10000 0 -0.22 36 36
GNA15 -0.005 0.064 -10000 0 -0.21 38 38
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.004 -10000 0 -10000 0 0
MAPT -0.087 0.13 0.24 1 -0.36 48 49
GNA11 -0.004 0.064 -10000 0 -0.21 36 36
Rac1/GTP -0.087 0.33 -10000 0 -0.9 59 59
MMP2 -0.019 0.095 -10000 0 -0.24 61 61
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.014 0.095 -10000 0 -0.3 29 29
alphaM/beta2 Integrin/GPIbA 0.006 0.092 -10000 0 -0.28 31 31
alphaM/beta2 Integrin/proMMP-9 0 0.1 0.25 11 -0.27 38 49
PLAUR 0.026 0.003 -10000 0 -10000 0 0
HMGB1 0.013 0.022 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.016 0.09 -10000 0 -0.29 26 26
AGER 0.016 0.034 -10000 0 -0.46 1 1
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.023 0.036 -10000 0 -0.4 3 3
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.013 0.098 -10000 0 -0.42 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.002 0.12 0.37 11 -0.42 25 36
CYR61 0.023 0.038 -10000 0 -0.42 3 3
TLN1 0.026 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.028 0.1 -10000 0 -0.3 20 20
RHOA 0.026 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.03 0.14 -10000 0 -0.4 55 55
MYH2 -0.046 0.1 -10000 0 -0.3 24 24
MST1R 0.026 0.004 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.024 0.12 -10000 0 -0.24 92 92
APOB -0.053 0.15 -10000 0 -0.41 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.042 -10000 0 -0.41 4 4
JAM3 0.026 0.004 -10000 0 -10000 0 0
GP1BA 0.012 0.048 -10000 0 -0.4 5 5
alphaM/beta2 Integrin/CTGF 0.013 0.094 -10000 0 -0.29 30 30
alphaM/beta2 Integrin -0.045 0.11 -10000 0 -0.28 40 40
JAM3 homodimer 0.026 0.004 -10000 0 -10000 0 0
ICAM2 0.026 0.005 -10000 0 -10000 0 0
ICAM1 0.025 0.022 -10000 0 -0.42 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.044 0.11 -10000 0 -0.28 40 40
cell adhesion 0.006 0.092 -10000 0 -0.28 31 31
NFKB1 0.017 0.14 0.32 2 -0.43 10 12
THY1 0.009 0.086 -10000 0 -0.42 16 16
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.021 0.11 -10000 0 -0.25 77 77
alphaM/beta2 Integrin/LRP/tPA 0.031 0.086 -10000 0 -0.26 28 28
IL6 -0.015 0.16 -10000 0 -0.54 8 8
ITGB2 0.009 0.058 -10000 0 -0.4 7 7
elevation of cytosolic calcium ion concentration 0.014 0.11 -10000 0 -0.25 58 58
alphaM/beta2 Integrin/JAM2/JAM3 -0.016 0.15 -10000 0 -0.27 91 91
JAM2 -0.065 0.17 -10000 0 -0.4 89 89
alphaM/beta2 Integrin/ICAM1 0.003 0.13 -10000 0 -0.25 72 72
alphaM/beta2 Integrin/uPA/Plg -0.045 0.15 -10000 0 -0.25 130 130
RhoA/GTP -0.048 0.11 -10000 0 -0.31 30 30
positive regulation of phagocytosis -0.027 0.095 0.18 2 -0.42 10 12
Ron/MSP -0.014 0.12 -10000 0 -0.3 65 65
alphaM/beta2 Integrin/uPAR/uPA 0.016 0.11 -10000 0 -0.26 58 58
alphaM/beta2 Integrin/uPAR 0.016 0.09 -10000 0 -0.29 26 26
PLAU -0.008 0.12 -10000 0 -0.42 32 32
PLAT 0.021 0.03 -10000 0 -0.4 2 2
actin filament polymerization -0.046 0.1 0.24 2 -0.3 25 27
MST1 -0.043 0.16 -10000 0 -0.43 65 65
alphaM/beta2 Integrin/lipoprotein(a) -0.021 0.13 -10000 0 -0.24 92 92
TNF 0.01 0.13 -10000 0 -0.52 7 7
RAP1B 0.026 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.004 0.12 -10000 0 -0.28 58 58
fibrinolysis -0.046 0.14 -10000 0 -0.25 130 130
HCK 0.011 0.047 -10000 0 -0.4 5 5
dendritic cell antigen processing and presentation -0.044 0.11 -10000 0 -0.28 40 40
VTN 0.007 0.072 -10000 0 -0.42 11 11
alphaM/beta2 Integrin/CYR61 0.015 0.093 -10000 0 -0.29 29 29
LPA -0.009 0.08 -10000 0 -0.44 13 13
LRP1 0.024 0.029 -10000 0 -0.4 2 2
cell migration -0.004 0.095 0.21 10 -0.27 37 47
FN1 0.002 0.1 -10000 0 -0.42 23 23
alphaM/beta2 Integrin/Thy1 0.006 0.1 -10000 0 -0.28 42 42
MPO 0.002 0.095 -10000 0 -0.42 20 20
KNG1 -0.083 0.18 -10000 0 -0.4 98 98
RAP1/GDP 0.035 0.007 -10000 0 -10000 0 0
ROCK1 -0.043 0.1 0.19 1 -0.31 21 22
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.083 0.16 -10000 0 -0.42 79 79
CTGF 0.022 0.044 -10000 0 -0.42 4 4
alphaM/beta2 Integrin/Hck 0.009 0.074 -10000 0 -0.3 16 16
ITGAM -0.008 0.1 -10000 0 -0.4 25 25
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.004 0.14 -10000 0 -0.29 62 62
HP -0.006 0.1 -10000 0 -0.42 23 23
leukocyte adhesion -0.034 0.13 -10000 0 -0.42 24 24
SELP -0.03 0.14 -10000 0 -0.4 55 55
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.073 0.43 7 -10000 0 7
VDR 0.026 0.003 -10000 0 -10000 0 0
FAM120B 0.026 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.048 0.11 -10000 0 -0.3 10 10
RXRs/LXRs/DNA/Oxysterols -0.032 0.11 -10000 0 -0.4 7 7
MED1 0.026 0.017 0.37 1 -10000 0 1
mol:9cRA 0.003 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.036 0.11 0.17 1 -0.21 115 116
RXRs/NUR77 -0.041 0.14 -10000 0 -0.33 8 8
RXRs/PPAR -0.058 0.12 -10000 0 -0.31 16 16
NCOR2 0.025 0.021 -10000 0 -0.4 1 1
VDR/VDR/Vit D3 0.019 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.057 0.033 0.24 1 -0.2 5 6
RARA 0.025 0.027 0.37 1 -0.4 1 2
NCOA1 0.026 0.001 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.043 0.031 0.23 1 -0.2 5 6
RARG 0.026 0.002 -10000 0 -10000 0 0
RPS6KB1 0.035 0.092 0.62 9 -0.38 1 10
RARs/THRs/DNA/SMRT -0.036 0.11 0.17 1 -0.36 6 7
THRA 0.026 0.017 0.37 1 -10000 0 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.043 0.13 -10000 0 -0.21 155 155
NR1H4 -0.22 0.2 -10000 0 -0.4 232 232
RXRs/LXRs/DNA -0.02 0.14 -10000 0 -0.37 2 2
NR1H2 0.028 0.023 -10000 0 -0.4 1 1
NR1H3 0.029 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.035 0.13 -10000 0 -0.22 3 3
NR4A1 0.019 0.057 -10000 0 -0.42 7 7
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.16 0.15 -10000 0 -0.27 222 222
RXRG -0.13 0.2 -10000 0 -0.4 158 158
RXR alpha/CCPG 0.039 0.02 -10000 0 -0.28 1 1
RXRA 0.028 0.023 -10000 0 -0.4 1 1
RXRB 0.029 0.011 -10000 0 -10000 0 0
THRB -0.091 0.19 -10000 0 -0.4 116 116
PPARG 0.024 0.029 -10000 0 -0.4 2 2
PPARD 0.025 0.021 -10000 0 -0.4 1 1
TNF -0.035 0.12 -10000 0 -0.78 3 3
mol:Oxysterols 0.003 0.006 -10000 0 -10000 0 0
cholesterol transport -0.032 0.11 -10000 0 -0.4 7 7
PPARA 0.025 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.022 0.041 -10000 0 -0.4 4 4
RXRs/NUR77/BCL2 -0.081 0.13 -10000 0 -0.23 159 159
SREBF1 -0.026 0.093 -10000 0 -0.45 2 2
RXRs/RXRs/DNA/9cRA -0.043 0.13 -10000 0 -0.21 155 155
ABCA1 -0.04 0.14 -10000 0 -0.88 6 6
RARs/THRs -0.003 0.13 0.26 1 -0.39 2 3
RXRs/FXR -0.17 0.17 -10000 0 -0.4 96 96
BCL2 0.011 0.062 -10000 0 -0.4 9 9
Endothelins

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
AKT1 -0.029 0.16 -10000 0 -0.43 29 29
PTK2B 0.02 0.023 -10000 0 -0.4 1 1
mol:Ca2+ -0.012 0.23 -10000 0 -0.88 24 24
EDN1 0.015 0.12 -10000 0 -0.32 14 14
EDN3 -0.12 0.19 -10000 0 -0.4 130 130
EDN2 -0.093 0.19 -10000 0 -0.4 117 117
HRAS/GDP 0.001 0.14 0.29 2 -0.41 16 18
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.014 0.11 -10000 0 -0.38 10 10
ADCY4 -0.043 0.13 -10000 0 -0.39 31 31
ADCY5 -0.12 0.17 -10000 0 -0.41 74 74
ADCY6 -0.045 0.13 -10000 0 -0.39 31 31
ADCY7 -0.044 0.13 -10000 0 -0.39 30 30
ADCY1 -0.044 0.13 0.39 1 -0.4 29 30
ADCY2 -0.059 0.15 -10000 0 -0.41 42 42
ADCY3 -0.044 0.13 -10000 0 -0.39 30 30
ADCY8 -0.044 0.12 0.22 1 -0.39 24 25
ADCY9 -0.044 0.13 -10000 0 -0.39 31 31
arachidonic acid secretion -0.022 0.16 0.25 3 -0.47 22 25
ETB receptor/Endothelin-1/Gq/GTP 0.005 0.078 -10000 0 -0.32 14 14
GNAO1 -0.088 0.19 -10000 0 -0.4 114 114
HRAS 0.025 0.021 -10000 0 -0.4 1 1
ETA receptor/Endothelin-1/G12/GTP 0.06 0.19 0.32 2 -0.4 26 28
ETA receptor/Endothelin-1/Gs/GTP 0.032 0.19 0.3 2 -0.4 32 34
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.033 0.17 -10000 0 -0.44 37 37
EDNRB 0.002 0.08 -10000 0 -0.4 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.04 0.18 -10000 0 -0.6 28 28
CYSLTR1 -0.073 0.24 -10000 0 -0.55 74 74
SLC9A1 -0.008 0.1 -10000 0 -0.27 35 35
mol:GDP -0.01 0.14 0.29 2 -0.43 18 20
SLC9A3 -0.26 0.33 -10000 0 -0.68 100 100
RAF1 -0.013 0.12 0.26 3 -0.48 8 11
JUN 0.01 0.15 -10000 0 -0.65 6 6
JAK2 -0.031 0.16 -10000 0 -0.44 30 30
mol:IP3 0.022 0.1 0.21 9 -0.5 4 13
ETA receptor/Endothelin-1 0.045 0.24 0.38 2 -0.49 32 34
PLCB1 0.024 0.031 0.37 3 -10000 0 3
PLCB2 0.025 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.086 0.16 -10000 0 -0.31 131 131
FOS -0.014 0.15 -10000 0 -0.9 8 8
Gai/GDP -0.16 0.34 -10000 0 -0.69 116 116
CRK 0.022 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.006 0.15 -10000 0 -0.43 22 22
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
PRKCB1 0.019 0.1 0.2 9 -0.48 4 13
GNAQ 0.025 0.024 -10000 0 -0.4 1 1
GNAZ 0.021 0.042 -10000 0 -0.4 4 4
GNAL 0.004 0.083 -10000 0 -0.4 17 17
Gs family/GDP -0.013 0.14 0.29 1 -0.39 24 25
ETA receptor/Endothelin-1/Gq/GTP 0.008 0.12 0.24 1 -0.5 5 6
MAPK14 0.009 0.074 0.23 3 -0.42 4 7
TRPC6 -0.016 0.25 -10000 0 -0.95 24 24
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.011 0.076 -10000 0 -0.4 14 14
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.011 0.076 -10000 0 -0.31 10 10
ETB receptor/Endothelin-2 -0.047 0.13 -10000 0 -0.29 95 95
ETB receptor/Endothelin-3 -0.078 0.14 -10000 0 -0.3 123 123
ETB receptor/Endothelin-1 0.013 0.11 -10000 0 -0.37 16 16
MAPK3 -0.011 0.14 0.3 1 -0.67 9 10
MAPK1 -0.017 0.16 -10000 0 -0.8 9 9
Rac1/GDP -0.003 0.13 0.29 2 -0.41 17 19
cAMP biosynthetic process -0.086 0.15 0.24 1 -0.42 40 41
MAPK8 0.007 0.18 -10000 0 -0.61 22 22
SRC 0.016 0.013 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.048 0.14 -10000 0 -0.37 49 49
p130Cas/CRK/Src/PYK2 -0.01 0.18 0.28 13 -0.56 19 32
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.003 0.13 0.29 2 -0.41 17 19
COL1A2 -0.001 0.17 0.33 1 -0.43 30 31
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.075 0.18 -10000 0 -0.32 131 131
mol:DAG 0.022 0.1 0.21 9 -0.5 4 13
MAP2K2 -0.015 0.13 0.27 2 -0.56 9 11
MAP2K1 -0.013 0.13 0.27 2 -0.55 9 11
EDNRA -0.006 0.15 -10000 0 -0.38 38 38
positive regulation of muscle contraction -0.007 0.15 0.25 25 -0.39 24 49
Gq family/GDP 0 0.13 -10000 0 -0.46 8 8
HRAS/GTP -0.014 0.13 0.25 2 -0.38 16 18
PRKCH 0.017 0.1 0.2 8 -0.49 4 12
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA 0.022 0.1 0.22 12 -0.56 3 15
PRKCB -0.015 0.14 0.2 6 -0.38 29 35
PRKCE 0.019 0.1 0.2 9 -0.55 3 12
PRKCD 0.018 0.1 0.2 1 -0.55 3 4
PRKCG -0.044 0.14 0.25 3 -0.4 19 22
regulation of vascular smooth muscle contraction -0.019 0.17 -10000 0 -1 8 8
PRKCQ 0.017 0.11 0.2 2 -0.44 7 9
PLA2G4A -0.025 0.17 0.26 3 -0.52 22 25
GNA14 0.024 0.031 -10000 0 -0.4 2 2
GNA15 0.021 0.045 -10000 0 -0.42 4 4
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA11 0.023 0.031 -10000 0 -0.4 2 2
Rac1/GTP 0.06 0.19 0.32 2 -0.4 26 28
MMP1 -0.19 0.18 0.29 2 -0.33 224 226
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.027 0 -10000 0 -10000 0 0
PTK2 0.022 0.01 -10000 0 -10000 0 0
CRKL -0.036 0.093 -10000 0 -0.21 96 96
GRB2/SOS1/SHC 0.051 0.012 -10000 0 -10000 0 0
HRAS 0.025 0.021 -10000 0 -0.4 1 1
IRS1/Crk -0.032 0.097 -10000 0 -0.21 74 74
IGF-1R heterotetramer/IGF1/PTP1B -0.011 0.092 -10000 0 -0.23 60 60
AKT1 -0.052 0.075 -10000 0 -10000 0 0
BAD -0.051 0.071 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.028 0.084 -10000 0 -0.21 74 74
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.028 0.1 -10000 0 -0.21 104 104
RAF1 -0.034 0.086 -10000 0 -0.46 4 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.003 0.11 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.03 0.11 -10000 0 -0.22 105 105
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.051 0.075 -10000 0 -10000 0 0
GNB2L1 0.026 0.003 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.016 0.081 0.26 2 -0.39 2 4
PXN 0.026 0.002 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.02 0.092 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.013 0.11 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.005 0.041 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.016 0.11 -10000 0 -0.21 105 105
Crk/p130 Cas/Paxillin -0.002 0.11 -10000 0 -10000 0 0
IGF1R 0.005 0.041 -10000 0 -10000 0 0
IGF1 -0.083 0.19 -10000 0 -0.41 105 105
IRS2/Crk -0.022 0.082 -10000 0 -10000 0 0
PI3K -0.004 0.11 -10000 0 -10000 0 0
apoptosis 0.04 0.062 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.015 -10000 0 -0.28 1 1
PRKCD -0.065 0.14 -10000 0 -0.31 98 98
RAF1/14-3-3 E -0.019 0.082 -10000 0 -0.39 5 5
BAD/14-3-3 -0.042 0.065 -10000 0 -10000 0 0
PRKCZ -0.051 0.075 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.014 0.08 -10000 0 -10000 0 0
PTPN1 0.015 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.063 0.15 -10000 0 -0.32 105 105
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.002 0.11 -10000 0 -0.2 84 84
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.028 0.1 -10000 0 -0.21 105 105
GRB10 0.024 0.008 -10000 0 -10000 0 0
PTPN11 -0.04 0.095 -10000 0 -0.21 104 104
IRS1 -0.044 0.1 -10000 0 -0.22 105 105
IRS2 -0.029 0.084 -10000 0 -0.21 77 77
IGF-1R heterotetramer/IGF1 -0.047 0.15 -10000 0 -0.3 105 105
GRB2 0.026 0.004 -10000 0 -10000 0 0
PDPK1 -0.038 0.087 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
PRKD1 -0.065 0.14 0.2 1 -0.31 98 99
SHC1 0.026 0.004 -10000 0 -10000 0 0
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.021 0.093 -10000 0 -0.23 41 41
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.27 -10000 0 -0.63 69 69
AKT1 -0.065 0.28 -10000 0 -0.82 50 50
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.064 0.29 -10000 0 -0.84 50 50
mol:Ca2+ 0.023 0.066 -10000 0 -0.4 2 2
IGF1R 0.025 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.011 0.077 -10000 0 -0.24 37 37
SHC1 0.026 0.004 -10000 0 -10000 0 0
apoptosis 0.061 0.27 0.78 50 -10000 0 50
RhoA/GTP 0.005 0.061 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.035 0.22 -10000 0 -0.52 52 52
regulation of stress fiber formation 0.021 0.054 0.3 2 -10000 0 2
E2/ERA-ERB (dimer) 0.007 0.081 -10000 0 -0.24 40 40
KRAS 0.026 0.003 -10000 0 -10000 0 0
G13/GTP 0.011 0.069 -10000 0 -0.21 37 37
pseudopodium formation -0.021 0.054 -10000 0 -0.3 2 2
E2/ER alpha (dimer)/PELP1 0.007 0.074 -10000 0 -0.23 38 38
GRB2 0.026 0.004 -10000 0 -10000 0 0
GNG2 0.009 0.081 -10000 0 -0.4 16 16
GNAO1 -0.088 0.19 -10000 0 -0.4 114 114
HRAS 0.025 0.021 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.077 0.24 0.23 1 -0.61 56 57
E2/ER beta (dimer) 0.016 0.025 -10000 0 -0.28 3 3
mol:GDP -0.019 0.1 -10000 0 -0.33 38 38
mol:NADP -0.077 0.24 0.23 1 -0.61 56 57
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.004 0.04 -10000 0 -0.42 2 2
IGF-1R heterotetramer 0.025 0.005 -10000 0 -10000 0 0
PLCB1 0.007 0.049 0.17 2 -0.44 3 5
PLCB2 0.007 0.052 -10000 0 -0.48 3 3
IGF1 -0.08 0.18 -10000 0 -0.4 105 105
mol:L-citrulline -0.077 0.24 0.23 1 -0.61 56 57
RHOA 0.026 0.004 -10000 0 -10000 0 0
Gai/GDP -0.17 0.34 -10000 0 -0.7 117 117
JNK cascade 0.016 0.025 -10000 0 -0.28 3 3
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
ESR2 0.021 0.037 -10000 0 -0.4 3 3
GNAQ 0.025 0.021 -10000 0 -0.4 1 1
ESR1 -0.014 0.12 -10000 0 -0.4 38 38
Gq family/GDP/Gbeta gamma -0.001 0.12 -10000 0 -0.65 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.007 0.13 -10000 0 -0.55 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.033 0.22 -10000 0 -0.52 51 51
GNAZ 0.021 0.042 -10000 0 -0.4 4 4
E2/ER alpha (dimer) -0.008 0.085 -10000 0 -0.28 38 38
STRN 0.026 0.003 -10000 0 -10000 0 0
GNAL 0.004 0.083 -10000 0 -0.4 17 17
PELP1 0.022 0.01 -10000 0 -10000 0 0
MAPK11 0.009 0.028 -10000 0 -0.24 5 5
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.011 0.076 -10000 0 -0.4 14 14
HBEGF -0.005 0.26 0.3 100 -0.55 49 149
cAMP biosynthetic process -0.004 0.079 -10000 0 -0.21 50 50
SRC -0.055 0.25 0.21 77 -0.59 57 134
PI3K 0.038 0.008 -10000 0 -10000 0 0
GNB1 0.025 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.003 0.11 -10000 0 -0.32 36 36
SOS1 0.026 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.093 0.18 -10000 0 -0.45 71 71
Gs family/GTP 0.001 0.083 -10000 0 -0.21 50 50
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.025 -10000 0 -0.22 3 3
vasodilation -0.072 0.22 0.23 1 -0.58 56 57
mol:DAG 0.004 0.04 -10000 0 -0.42 2 2
Gs family/GDP/Gbeta gamma -0.021 0.11 -10000 0 -0.32 38 38
MSN -0.023 0.057 -10000 0 -0.32 2 2
Gq family/GTP 0.013 0.057 -10000 0 -0.52 3 3
mol:PI-3-4-5-P3 -0.06 0.28 -10000 0 -0.8 50 50
NRAS 0.024 0.029 -10000 0 -0.4 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.072 0.22 0.58 56 -0.23 1 57
GRB2/SOS1 0.038 0.007 -10000 0 -10000 0 0
RhoA/GDP -0.005 0.11 -10000 0 -0.32 38 38
NOS3 -0.083 0.25 0.24 1 -0.65 56 57
GNA11 0.024 0.029 -10000 0 -0.4 2 2
MAPKKK cascade -0.037 0.23 0.24 1 -0.61 50 51
E2/ER alpha (dimer)/PELP1/Src -0.034 0.23 0.26 6 -0.54 53 59
ruffle organization -0.021 0.054 -10000 0 -0.3 2 2
ROCK2 -0.022 0.062 -10000 0 -0.34 2 2
GNA14 0.024 0.029 -10000 0 -0.4 2 2
GNA15 0.022 0.044 -10000 0 -0.42 4 4
GNA13 0.026 0.004 -10000 0 -10000 0 0
MMP9 -0.009 0.26 0.37 80 -0.54 47 127
MMP2 -0.051 0.24 0.27 7 -0.57 55 62
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.001 0.16 0.28 7 -0.5 29 36
FYN -0.026 0.2 0.3 2 -0.56 40 42
LAT/GRAP2/SLP76 -0.007 0.17 -10000 0 -0.51 34 34
IKBKB 0.023 0.009 -10000 0 -10000 0 0
AKT1 -0.021 0.14 0.18 3 -0.42 38 41
B2M 0.024 0.023 -10000 0 -0.4 1 1
IKBKG 0 0.049 0.091 25 -0.15 17 42
MAP3K8 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.035 0.088 5 -0.11 49 54
integrin-mediated signaling pathway 0.031 0.027 -10000 0 -0.23 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.035 0.2 0.21 2 -0.6 39 41
TRPV6 -0.009 0.27 1.1 17 -0.42 48 65
CD28 0.008 0.087 -10000 0 -0.4 18 18
SHC1 -0.026 0.19 0.3 7 -0.57 37 44
receptor internalization -0.035 0.21 -10000 0 -0.63 39 39
PRF1 -0.031 0.23 -10000 0 -0.86 23 23
KRAS 0.026 0.003 -10000 0 -10000 0 0
GRB2 0.026 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.006 0.12 0.17 3 -0.33 37 40
LAT -0.031 0.19 0.2 2 -0.57 38 40
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.014 0.072 -10000 0 -0.41 12 12
CD3E 0.015 0.07 -10000 0 -0.41 11 11
CD3G -0.008 0.12 -10000 0 -0.4 33 33
RASGRP2 -0.012 0.058 0.059 2 -0.17 46 48
RASGRP1 0.001 0.15 0.21 7 -0.41 35 42
HLA-A 0.025 0.022 -10000 0 -0.4 1 1
RASSF5 0.022 0.041 -10000 0 -0.4 4 4
RAP1A/GTP/RAPL 0.031 0.027 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.059 0.13 20 -0.13 23 43
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.019 0.067 -10000 0 -0.22 29 29
PRKCA 0.02 0.096 0.16 28 -0.26 24 52
GRAP2 0.013 0.071 -10000 0 -0.4 12 12
mol:IP3 -0.005 0.13 0.2 44 -0.39 30 74
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.027 0.18 -10000 0 -0.56 36 36
ORAI1 -0.01 0.21 0.36 1 -0.96 17 18
CSK -0.027 0.19 -10000 0 -0.58 35 35
B7 family/CD28 -0.006 0.21 -10000 0 -0.61 36 36
CHUK 0.025 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.034 0.22 0.21 1 -0.65 38 39
PTPN6 -0.03 0.19 0.26 3 -0.58 36 39
VAV1 -0.035 0.2 0.21 3 -0.58 40 43
Monovalent TCR/CD3 -0.018 0.15 -10000 0 -0.4 40 40
CBL 0.026 0.003 -10000 0 -10000 0 0
LCK -0.03 0.2 0.28 2 -0.56 41 43
PAG1 -0.016 0.2 0.24 4 -0.6 33 37
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.032 0.22 0.21 2 -0.64 39 41
CD80 0.025 0.022 -10000 0 -0.4 1 1
CD86 0.015 0.068 -10000 0 -0.4 11 11
PDK1/CARD11/BCL10/MALT1 -0.014 0.085 -10000 0 -0.27 30 30
HRAS 0.025 0.021 -10000 0 -0.4 1 1
GO:0035030 -0.029 0.16 0.18 1 -0.48 39 40
CD8A -0.003 0.11 -10000 0 -0.4 30 30
CD8B 0.013 0.075 -10000 0 -0.41 13 13
PTPRC -0.007 0.11 -10000 0 -0.4 32 32
PDK1/PKC theta -0.018 0.17 0.21 4 -0.51 35 39
CSK/PAG1 -0.014 0.19 0.24 4 -0.59 31 35
SOS1 0.026 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.035 0.021 -10000 0 -0.28 1 1
GRAP2/SLP76 -0.008 0.2 -10000 0 -0.59 35 35
STIM1 0.014 0.12 1.2 4 -10000 0 4
RAS family/GTP 0.024 0.069 0.15 14 -0.18 20 34
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.04 0.23 -10000 0 -0.68 39 39
mol:DAG -0.021 0.1 0.1 2 -0.35 30 32
RAP1A/GDP 0.011 0.028 0.065 16 -0.064 11 27
PLCG1 0.016 0.013 -10000 0 -10000 0 0
CD247 0.014 0.072 -10000 0 -0.4 12 12
cytotoxic T cell degranulation -0.028 0.22 -10000 0 -0.76 26 26
RAP1A/GTP -0.005 0.022 -10000 0 -0.067 36 36
mol:PI-3-4-5-P3 -0.025 0.16 0.19 3 -0.49 38 41
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.008 0.16 0.22 40 -0.51 30 70
NRAS 0.024 0.029 -10000 0 -0.4 2 2
ZAP70 0.013 0.074 -10000 0 -0.4 13 13
GRB2/SOS1 0.038 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.017 0.17 0.21 1 -0.51 35 36
MALT1 0.019 0.023 -10000 0 -0.4 1 1
TRAF6 0.026 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.009 0.11 -10000 0 -0.34 36 36
CARD11 0.002 0.1 0.37 2 -0.41 23 25
PRKCB -0.003 0.12 0.16 24 -0.28 46 70
PRKCE 0.021 0.098 0.16 29 -0.26 26 55
PRKCQ -0.021 0.19 0.21 4 -0.56 37 41
LCP2 0.022 0.041 -10000 0 -0.4 4 4
BCL10 0.025 0.021 -10000 0 -0.4 1 1
regulation of survival gene product expression -0.016 0.12 0.16 4 -0.35 38 42
IKK complex 0.023 0.066 0.11 108 -0.12 24 132
RAS family/GDP -0.003 0.012 -10000 0 -0.068 1 1
MAP3K14 -0.006 0.09 0.14 4 -0.26 33 37
PDPK1 -0.018 0.13 0.17 4 -0.4 35 39
TCR/CD3/MHC I/CD8/Fyn -0.036 0.22 -10000 0 -0.67 37 37
Effects of Botulinum toxin

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
STX1A -0.007 0.07 0.27 3 -0.3 21 24
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.032 0.034 -10000 0 -0.3 4 4
STXBP1 0.021 0.049 -10000 0 -0.42 5 5
ACh/CHRNA1 -0.04 0.096 -10000 0 -0.23 59 59
RAB3GAP2/RIMS1/UNC13B 0.045 0.035 -10000 0 -0.25 5 5
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 0.005 0.051 -10000 0 -0.42 5 5
mol:ACh -0.035 0.067 0.08 36 -0.12 137 173
RAB3GAP2 0.025 0.021 -10000 0 -0.4 1 1
STX1A/SNAP25/VAMP2 -0.034 0.11 -10000 0 -0.29 12 12
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.039 0.095 -10000 0 -0.23 59 59
UNC13B 0.026 0.004 -10000 0 -10000 0 0
CHRNA1 -0.013 0.12 -10000 0 -0.4 38 38
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.052 0.11 -10000 0 -0.24 81 81
SNAP25 -0.069 0.11 0.19 1 -0.25 122 123
VAMP2 0.004 0.002 -10000 0 -10000 0 0
SYT1 -0.035 0.15 -10000 0 -0.4 60 60
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.008 0.067 0.21 3 -0.25 25 28
STX1A/SNAP25 fragment 1/VAMP2 -0.034 0.11 -10000 0 -0.29 12 12
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.011 0.15 -9999 0 -0.52 22 22
MAP3K8 0.026 0.003 -9999 0 -10000 0 0
FOS -0.024 0.14 -9999 0 -0.5 23 23
PRKCA 0.026 0.007 -9999 0 -10000 0 0
PTPN7 0.017 0.063 -9999 0 -0.41 9 9
HRAS 0.025 0.021 -9999 0 -0.4 1 1
PRKCB -0.068 0.18 -9999 0 -0.4 94 94
NRAS 0.024 0.029 -9999 0 -0.4 2 2
RAS family/GTP 0.047 0.026 -9999 0 -0.21 3 3
MAPK3 -0.004 0.1 -9999 0 -0.6 7 7
MAP2K1 -0.059 0.17 -9999 0 -0.36 93 93
ELK1 0.026 0.006 -9999 0 -10000 0 0
BRAF -0.052 0.15 -9999 0 -0.35 84 84
mol:GTP 0 0 -9999 0 -0.004 7 7
MAPK1 -0.023 0.16 -9999 0 -0.64 21 21
RAF1 -0.056 0.16 -9999 0 -0.35 88 88
KRAS 0.026 0.003 -9999 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.087 0.13 -10000 0 -0.27 28 28
NF kappa B1 p50/RelA/I kappa B alpha -0.073 0.12 0.3 4 -0.32 3 7
alphaV/beta3 Integrin/Osteopontin/Src -0.12 0.17 -10000 0 -0.3 206 206
AP1 -0.07 0.13 -10000 0 -0.47 2 2
ILK -0.097 0.13 -10000 0 -0.31 4 4
bone resorption -0.081 0.12 0.33 1 -0.42 2 3
PTK2B 0.02 0.023 -10000 0 -0.4 1 1
PYK2/p130Cas -0.07 0.14 -10000 0 -0.4 3 3
ITGAV 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.037 0.023 -10000 0 -0.28 2 2
alphaV/beta3 Integrin/Osteopontin -0.094 0.16 -10000 0 -0.25 209 209
MAP3K1 -0.1 0.13 -10000 0 -0.27 28 28
JUN 0.026 0.004 -10000 0 -10000 0 0
MAPK3 -0.1 0.12 0.19 1 -0.3 29 30
MAPK1 -0.1 0.12 0.19 1 -0.29 29 30
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.098 0.12 0.19 5 -0.32 4 9
ITGB3 0.024 0.041 -10000 0 -0.39 4 4
NFKBIA -0.088 0.11 0.19 1 -0.29 30 31
FOS 0.022 0.036 -10000 0 -0.4 3 3
CD44 0.026 0.003 -10000 0 -10000 0 0
CHUK 0.025 0.006 -10000 0 -10000 0 0
PLAU -0.087 0.13 0.32 1 -0.44 3 4
NF kappa B1 p50/RelA -0.072 0.13 -10000 0 -0.33 3 3
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
RELA 0.026 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.039 0.032 -10000 0 -0.28 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.099 0.13 -10000 0 -0.26 28 28
VAV3 -0.12 0.14 0.19 5 -0.39 34 39
MAP3K14 -0.1 0.13 -10000 0 -0.28 29 29
ROCK2 0.024 0.029 -10000 0 -0.4 2 2
SPP1 -0.19 0.22 -10000 0 -0.42 206 206
RAC1 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.097 0.13 -10000 0 -0.36 32 32
MMP2 -0.077 0.1 -10000 0 -0.5 3 3
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.23 0.33 -10000 0 -1.1 31 31
IL23A -0.27 0.35 -10000 0 -1.1 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.34 -10000 0 -0.99 39 39
positive regulation of T cell mediated cytotoxicity -0.24 0.35 -10000 0 -1.1 38 38
ITGA3 -0.23 0.32 -10000 0 -0.98 37 37
IL17F -0.2 0.25 -10000 0 -0.66 50 50
IL12B -0.018 0.056 -10000 0 -0.44 4 4
STAT1 (dimer) -0.23 0.34 -10000 0 -1 38 38
CD4 -0.24 0.36 -10000 0 -1.1 44 44
IL23 -0.26 0.34 -10000 0 -1 36 36
IL23R -0.076 0.26 -10000 0 -1.1 21 21
IL1B -0.26 0.35 -10000 0 -1.1 38 38
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.27 0.33 -10000 0 -0.98 39 39
TYK2 -0.006 0.032 -10000 0 -10000 0 0
STAT4 0.003 0.097 -10000 0 -0.4 23 23
STAT3 0.025 0.006 -10000 0 -10000 0 0
IL18RAP 0.002 0.094 -10000 0 -0.4 22 22
IL12RB1 -0.022 0.086 -10000 0 -0.43 16 16
PIK3CA 0.026 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.015 0.071 -10000 0 -0.31 16 16
IL23R/JAK2 -0.08 0.25 -10000 0 -1.1 19 19
positive regulation of chronic inflammatory response -0.24 0.35 -10000 0 -1.1 38 38
natural killer cell activation 0.005 0.013 0.079 11 -10000 0 11
JAK2 -0.011 0.051 -10000 0 -0.42 3 3
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.32 -10000 0 -0.97 36 36
ALOX12B -0.23 0.34 -10000 0 -0.99 42 42
CXCL1 -0.27 0.34 -10000 0 -1 35 35
T cell proliferation -0.24 0.35 -10000 0 -1.1 38 38
NFKBIA 0.023 0.007 -10000 0 -10000 0 0
IL17A -0.18 0.22 -10000 0 -0.54 59 59
PI3K -0.23 0.34 -10000 0 -0.98 42 42
IFNG -0.01 0.037 0.14 11 -0.11 6 17
STAT3 (dimer) -0.24 0.34 -10000 0 -0.95 43 43
IL18R1 0.015 0.062 -10000 0 -0.4 9 9
IL23/IL23R/JAK2/TYK2/SOCS3 -0.15 0.23 -10000 0 -0.72 32 32
IL18/IL18R 0.027 0.081 -10000 0 -0.23 33 33
macrophage activation -0.017 0.016 -10000 0 -0.044 23 23
TNF -0.25 0.34 -10000 0 -1 36 36
STAT3/STAT4 -0.24 0.35 -10000 0 -0.99 43 43
STAT4 (dimer) -0.24 0.36 -10000 0 -1 43 43
IL18 0.022 0.031 -10000 0 -0.4 2 2
IL19 -0.22 0.32 -10000 0 -0.96 36 36
STAT5A (dimer) -0.23 0.34 -10000 0 -1 37 37
STAT1 0.025 0.022 -10000 0 -0.42 1 1
SOCS3 0.026 0.004 -10000 0 -10000 0 0
CXCL9 -0.25 0.34 -10000 0 -1 38 38
MPO -0.23 0.32 -10000 0 -0.98 33 33
positive regulation of humoral immune response -0.24 0.35 -10000 0 -1.1 38 38
IL23/IL23R/JAK2/TYK2 -0.25 0.37 -10000 0 -1.1 38 38
IL6 -0.24 0.35 -10000 0 -1 37 37
STAT5A 0.026 0.004 -10000 0 -10000 0 0
IL2 0.013 0.021 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.013 0.079 11 -10000 0 11
CD3E -0.24 0.36 -10000 0 -1.1 42 42
keratinocyte proliferation -0.24 0.35 -10000 0 -1.1 38 38
NOS2 -0.26 0.38 -10000 0 -1.1 45 45
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.036 0.12 0.32 26 -10000 0 26
GNAI2 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.028 0.036 -10000 0 -0.25 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.088 0.19 -10000 0 -0.4 114 114
RhoA/GTP -0.036 0.12 -10000 0 -0.33 26 26
negative regulation of cAMP metabolic process -0.048 0.12 -10000 0 -0.24 106 106
GNAZ 0.021 0.042 -10000 0 -0.4 4 4
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNA12 0.024 0.008 -10000 0 -10000 0 0
S1PR5 0.02 0.053 -10000 0 -0.42 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.049 0.12 -10000 0 -0.24 106 106
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
GNAI1 0.011 0.076 -10000 0 -0.4 14 14
Canonical Wnt signaling pathway

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
HDAC1 0.025 0.01 -10000 0 -10000 0 0
AES 0.025 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.036 0.019 -10000 0 -0.28 1 1
SMAD4 0.02 0.012 -10000 0 -10000 0 0
DKK2 -0.06 0.18 -10000 0 -0.43 79 79
TLE1 0.025 0.022 -10000 0 -0.39 1 1
MACF1 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.039 0.075 0.24 10 -0.37 2 12
WIF1 -0.075 0.17 -10000 0 -0.42 83 83
beta catenin/RanBP3 0.022 0.076 0.28 9 -0.4 1 10
KREMEN2 -0.02 0.14 0.37 2 -0.42 45 47
DKK1 -0.07 0.18 -10000 0 -0.42 85 85
beta catenin/beta TrCP1 0.05 0.072 0.24 8 -0.43 1 9
FZD1 0.024 0.022 -10000 0 -0.4 1 1
AXIN2 -0.004 0.13 0.57 8 -1.3 1 9
AXIN1 0.025 0.021 -10000 0 -0.4 1 1
RAN 0.026 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.029 0.066 -10000 0 -0.49 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.022 0.14 -10000 0 -0.46 21 21
Axin1/APC/GSK3 0.053 0.067 0.22 11 -0.29 4 15
Axin1/APC/GSK3/beta catenin/Macf1 0.025 0.074 0.28 2 -0.35 3 5
HNF1A 0.024 0.03 -10000 0 -0.4 2 2
CTBP1 0.025 0.009 -10000 0 -10000 0 0
MYC 0.1 0.22 0.57 72 -10000 0 72
RANBP3 0.026 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.037 0.15 0.26 2 -0.27 116 118
NKD1 -0.26 0.22 0.37 3 -0.42 268 271
TCF4 0.018 0.024 -10000 0 -0.4 1 1
TCF3 0.025 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.058 0.037 -10000 0 -0.23 5 5
Ran/GTP 0.019 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.016 0.084 0.35 2 -0.38 5 7
LEF1 -0.027 0.14 -10000 0 -0.43 49 49
DVL1 0.023 0.056 0.18 2 -0.35 4 6
CSNK2A1 0.021 0.011 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.025 0.089 -10000 0 -0.54 5 5
DKK1/LRP6/Kremen 2 -0.04 0.15 0.25 2 -0.27 120 122
LRP6 0.026 0.004 -10000 0 -10000 0 0
CSNK1A1 0.025 0.009 -10000 0 -10000 0 0
NLK 0.026 0.005 -10000 0 -10000 0 0
CCND1 0.005 0.057 0.58 2 -10000 0 2
WNT1 0.012 0.041 -10000 0 -0.42 3 3
GSK3A 0.026 0.004 -10000 0 -10000 0 0
GSK3B 0.027 0.002 -10000 0 -10000 0 0
FRAT1 0.025 0.005 -10000 0 -10000 0 0
PPP2R5D 0.13 0.099 0.22 169 -0.25 3 172
APC 0.005 0.059 0.18 28 -10000 0 28
WNT1/LRP6/FZD1 0.038 0.05 0.2 6 -10000 0 6
CREBBP 0.025 0.008 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.024 0.091 -10000 0 -0.35 21 21
HDAC1 0.023 0.006 -10000 0 -10000 0 0
AES 0.025 0.003 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
DTX1 0.022 0.041 -10000 0 -0.4 4 4
LRP6/FZD1 0.036 0.019 -10000 0 -0.28 1 1
TLE1 0.025 0.021 -10000 0 -0.4 1 1
AP1 -0.076 0.093 0.18 3 -0.29 38 41
NCSTN 0.026 0.004 -10000 0 -10000 0 0
ADAM10 0.025 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.039 0.085 -10000 0 -0.57 7 7
NICD/RBPSUH 0.025 0.089 -10000 0 -0.35 21 21
WIF1 -0.075 0.17 -10000 0 -0.42 83 83
NOTCH1 0.007 0.087 -10000 0 -0.37 21 21
PSENEN 0.025 0.021 -10000 0 -0.4 1 1
KREMEN2 -0.02 0.14 0.37 2 -0.42 45 47
DKK1 -0.07 0.18 -10000 0 -0.42 85 85
beta catenin/beta TrCP1 0.089 0.076 0.25 11 -0.3 1 12
APH1B 0.025 0.006 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
AXIN1 -0.026 0.067 -10000 0 -0.45 6 6
CtBP/CBP/TCF1/TLE1/AES 0.017 0.026 -10000 0 -0.29 1 1
PSEN1 0.025 0.007 -10000 0 -10000 0 0
FOS 0.022 0.036 -10000 0 -0.4 3 3
JUN 0.026 0.004 -10000 0 -10000 0 0
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
CTNNB1 0.078 0.079 0.24 13 -0.31 1 14
MAPK3 0.025 0.021 -10000 0 -0.4 1 1
DKK2/LRP6/Kremen 2 -0.037 0.15 0.25 2 -0.27 116 118
HNF1A 0.024 0.029 -10000 0 -0.4 2 2
CTBP1 0.025 0.004 -10000 0 -10000 0 0
MYC 0.024 0.036 -10000 0 -10000 0 0
NKD1 -0.26 0.22 0.37 3 -0.42 268 271
FZD1 0.024 0.021 -10000 0 -0.4 1 1
NOTCH1 precursor/Deltex homolog 1 0.023 0.092 -10000 0 -0.35 21 21
apoptosis -0.076 0.093 0.18 3 -0.29 38 41
Delta 1/NOTCHprecursor 0.023 0.091 -10000 0 -0.35 21 21
DLL1 0.023 0.036 -10000 0 -0.4 3 3
PPARD 0.029 0.073 -10000 0 -0.99 2 2
Gamma Secretase 0.067 0.031 -10000 0 -0.21 1 1
APC -0.045 0.11 -10000 0 -0.41 29 29
DVL1 0.001 0.079 -10000 0 -0.36 15 15
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.04 0.15 0.25 2 -0.27 120 122
LRP6 0.026 0.004 -10000 0 -10000 0 0
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
NLK 0.011 0.004 -10000 0 -10000 0 0
CCND1 0.018 0.11 -10000 0 -0.82 7 7
WNT1 0.01 0.042 -10000 0 -0.42 3 3
Axin1/APC/beta catenin 0.023 0.11 0.23 1 -0.43 12 13
DKK2 -0.06 0.18 -10000 0 -0.43 79 79
NOTCH1 precursor/DVL1 0.006 0.13 -10000 0 -0.49 18 18
GSK3B 0.026 0.002 -10000 0 -10000 0 0
FRAT1 0.025 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.024 0.091 -10000 0 -0.35 21 21
PPP2R5D 0.13 0.1 0.22 199 -0.28 3 202
MAPK1 0.025 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.002 0.12 -10000 0 -0.24 78 78
RBPJ 0.026 0.004 -10000 0 -10000 0 0
CREBBP 0.028 0.005 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.019 0.1 -10000 0 -0.23 81 81
cell-cell adhesion 0.04 0.068 0.36 3 -10000 0 3
Ephrin B/EPHB2/RasGAP 0.046 0.048 -10000 0 -0.22 4 4
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
SHC1 0.026 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.021 0.063 -10000 0 -0.25 21 21
Ephrin B1/EPHB1 -0.036 0.13 0.24 2 -0.25 106 108
HRAS/GDP -0.026 0.1 -10000 0 -0.3 15 15
Ephrin B/EPHB1/GRB7 0.006 0.11 0.25 5 -0.22 52 57
Endophilin/SYNJ1 0.032 0.081 0.18 91 -10000 0 91
KRAS 0.026 0.003 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.01 0.085 0.26 1 -0.23 34 35
endothelial cell migration 0.04 0.026 -10000 0 -10000 0 0
GRB2 0.026 0.004 -10000 0 -10000 0 0
GRB7 0.032 0.047 0.37 8 -10000 0 8
PAK1 0.031 0.084 0.19 25 -10000 0 25
HRAS 0.025 0.021 -10000 0 -0.4 1 1
RRAS 0.034 0.083 0.18 95 -10000 0 95
DNM1 0.024 0.041 0.37 1 -0.42 3 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.023 0.097 0.18 42 -0.4 1 43
lamellipodium assembly -0.04 0.068 -10000 0 -0.36 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.056 0.17 1 -10000 0 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.023 0.031 -10000 0 -0.42 2 2
EPHB3 0.004 0.098 -10000 0 -0.42 21 21
EPHB1 -0.085 0.2 0.37 2 -0.42 106 108
EPHB4 0.025 0.006 -10000 0 -10000 0 0
mol:GDP -0.016 0.087 -10000 0 -0.28 16 16
Ephrin B/EPHB2 0.036 0.041 -10000 0 -0.22 5 5
Ephrin B/EPHB3 0.026 0.065 -10000 0 -0.21 23 23
JNK cascade -0.062 0.096 0.33 2 -0.38 3 5
Ephrin B/EPHB1 -0.004 0.1 0.24 1 -0.22 67 68
RAP1/GDP -0.001 0.11 0.29 11 -0.27 11 22
EFNB2 0.02 0.011 -10000 0 -10000 0 0
EFNB3 0.018 0.043 -10000 0 -0.41 4 4
EFNB1 0.026 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.009 0.1 0.24 2 -0.23 65 67
RAP1B 0.026 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.095 -10000 0 -0.34 3 3
Rap1/GTP -0.018 0.081 -10000 0 -0.36 3 3
axon guidance -0.019 0.1 -10000 0 -0.23 81 81
MAPK3 0.008 0.052 0.19 2 -10000 0 2
MAPK1 0.008 0.049 0.17 1 -10000 0 1
Rac1/GDP -0.017 0.097 0.24 4 -0.27 14 18
actin cytoskeleton reorganization -0.036 0.075 -10000 0 -0.24 13 13
CDC42/GDP -0.007 0.11 0.28 13 -0.28 14 27
PI3K 0.044 0.029 -10000 0 -10000 0 0
EFNA5 -0.055 0.16 -10000 0 -0.4 79 79
Ephrin B2/EPHB4 0.027 0.016 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.016 0.023 -10000 0 -0.2 1 1
CDC42 0.024 0.022 -10000 0 -0.4 1 1
RAS family/GTP -0.022 0.081 -10000 0 -0.36 4 4
PTK2 0.094 0.21 0.58 65 -10000 0 65
MAP4K4 -0.063 0.096 0.34 2 -0.39 3 5
SRC 0.016 0.013 -10000 0 -10000 0 0
KALRN 0.025 0.021 -10000 0 -0.4 1 1
Intersectin/N-WASP 0.036 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.006 0.098 0.27 17 -10000 0 17
MAP2K1 0.011 0.052 0.16 2 -10000 0 2
WASL 0.025 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.012 0.13 -10000 0 -0.24 106 106
cell migration 0.03 0.081 0.21 32 -10000 0 32
NRAS 0.024 0.029 -10000 0 -0.4 2 2
SYNJ1 0.032 0.082 0.18 91 -10000 0 91
PXN 0.026 0.002 -10000 0 -10000 0 0
TF 0.008 0.1 0.17 85 -0.39 2 87
HRAS/GTP -0.007 0.092 -10000 0 -0.38 3 3
Ephrin B1/EPHB1-2 -0.022 0.12 0.24 2 -0.23 106 108
cell adhesion mediated by integrin -0.041 0.094 0.2 3 -0.2 96 99
RAC1 0.024 0.008 -10000 0 -10000 0 0
mol:GTP -0.006 0.096 -10000 0 -0.39 3 3
RAC1-CDC42/GTP -0.034 0.092 -10000 0 -0.38 10 10
RASA1 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.01 0.098 0.26 2 -0.27 13 15
ruffle organization -0.003 0.12 0.36 20 -0.36 3 23
NCK1 0.026 0.002 -10000 0 -10000 0 0
receptor internalization 0.029 0.08 0.17 90 -10000 0 90
Ephrin B/EPHB2/KALRN 0.045 0.05 -10000 0 -0.22 4 4
ROCK1 0.001 0.053 0.18 1 -0.22 22 23
RAS family/GDP -0.044 0.062 -10000 0 -0.27 1 1
Rac1/GTP -0.024 0.08 -10000 0 -0.38 3 3
Ephrin B/EPHB1/Src/Paxillin 0.003 0.049 0.17 1 -0.2 2 3
Wnt signaling

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
Noncanonical Wnts/FZD -0.027 0.098 0.17 1 -0.31 23 24
FZD6 0.023 0.009 -10000 0 -10000 0 0
WNT6 -0.003 0.1 -10000 0 -0.41 24 24
WNT4 0.004 0.091 -10000 0 -0.4 20 20
FZD3 0.021 0.034 0.37 2 -0.42 1 3
WNT5A 0.022 0.044 -10000 0 -0.42 4 4
WNT11 -0.065 0.18 -10000 0 -0.42 86 86
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.035 0.24 0.43 1 -0.78 29 30
NCK1/PAK1/Dok-R -0.029 0.098 -10000 0 -0.39 27 27
NCK1/Dok-R 0.005 0.26 -10000 0 -0.91 28 28
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
mol:beta2-estradiol 0.002 0.05 0.25 16 -10000 0 16
RELA 0.026 0.004 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -10000 0 -10000 0 0
F2 -0.13 0.22 0.29 17 -0.44 129 146
TNIP2 0.026 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.04 0.25 -10000 0 -0.85 29 29
FN1 0.002 0.1 -10000 0 -0.42 23 23
PLD2 -0.028 0.26 -10000 0 -0.94 28 28
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB14 -0.009 0.11 -10000 0 -0.41 30 30
ELK1 0.007 0.25 -10000 0 -0.85 29 29
GRB7 0.032 0.047 0.37 8 -10000 0 8
PAK1 0.026 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.032 0.27 -10000 0 -0.91 28 28
CDKN1A 0.035 0.2 0.46 2 -0.62 23 25
ITGA5 0.024 0.031 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.005 0.26 -10000 0 -0.91 28 28
CRK 0.022 0.01 -10000 0 -10000 0 0
mol:NO 0.049 0.2 0.41 13 -0.59 29 42
PLG -0.055 0.26 -10000 0 -0.95 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.026 0.23 -10000 0 -0.75 29 29
GRB2 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
ANGPT2 -0.025 0.21 0.39 2 -0.6 20 22
BMX -0.076 0.28 -10000 0 -1 28 28
ANGPT1 0.01 0.23 -10000 0 -1.1 16 16
tube development 0.025 0.21 0.38 9 -0.67 22 31
ANGPT4 0.002 0.045 -10000 0 -0.42 4 4
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.006 0.28 -10000 0 -0.96 29 29
alpha5/beta1 Integrin 0.037 0.024 -10000 0 -0.3 2 2
FGF2 -0.004 0.11 -10000 0 -0.4 29 29
STAT5A (dimer) 0.033 0.24 0.42 1 -0.74 24 25
mol:L-citrulline 0.049 0.2 0.41 13 -0.59 29 42
AGTR1 -0.12 0.2 -10000 0 -0.4 141 141
MAPK14 -0.003 0.28 -10000 0 -0.99 29 29
Tie2/SHP2 0.013 0.21 -10000 0 -0.98 17 17
TEK -0.012 0.23 -10000 0 -1.1 17 17
RPS6KB1 0.035 0.24 0.56 1 -0.76 28 29
Angiotensin II/AT1 -0.08 0.14 -10000 0 -0.28 141 141
Tie2/Ang1/GRB2 0.018 0.28 -10000 0 -0.96 28 28
MAPK3 -0.017 0.24 -10000 0 -0.87 28 28
MAPK1 -0.017 0.24 -10000 0 -0.87 28 28
Tie2/Ang1/GRB7 0.02 0.28 -10000 0 -0.94 29 29
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.025 0.26 -10000 0 -0.93 29 29
PI3K 0.021 0.27 -10000 0 -0.9 29 29
FES -0.012 0.29 -10000 0 -1 29 29
Crk/Dok-R 0.002 0.26 -10000 0 -0.9 28 28
Tie2/Ang1/ABIN2 0.017 0.28 -10000 0 -0.95 29 29
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.043 0.22 0.39 3 -0.7 29 32
STAT5A 0.026 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.056 0.25 0.46 10 -0.76 27 37
Tie2/Ang2 -0.012 0.25 0.48 1 -0.91 22 23
Tie2/Ang1 -0.022 0.28 -10000 0 -1 28 28
FOXO1 0.06 0.23 0.41 12 -0.73 24 36
ELF1 0.02 0.029 -10000 0 -10000 0 0
ELF2 -0.021 0.26 -10000 0 -0.95 28 28
mol:Choline -0.025 0.24 -10000 0 -0.9 28 28
cell migration -0.014 0.06 -10000 0 -0.22 28 28
FYN 0.018 0.23 0.4 5 -0.76 22 27
DOK2 0.013 0.055 -10000 0 -0.4 7 7
negative regulation of cell cycle 0.038 0.19 0.4 5 -0.56 23 28
ETS1 0.021 0.057 -10000 0 -0.26 16 16
PXN 0.06 0.22 0.39 20 -0.64 27 47
ITGB1 0.026 0.002 -10000 0 -10000 0 0
NOS3 0.045 0.22 0.44 10 -0.67 29 39
RAC1 0.024 0.008 -10000 0 -10000 0 0
TNF 0.02 0.063 -10000 0 -0.28 17 17
MAPKKK cascade -0.025 0.24 -10000 0 -0.9 28 28
RASA1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.017 0.28 -10000 0 -0.96 29 29
NCK1 0.026 0.002 -10000 0 -10000 0 0
vasculogenesis 0.051 0.18 0.39 14 -0.53 29 43
mol:Phosphatidic acid -0.025 0.24 -10000 0 -0.9 28 28
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.049 0.2 0.41 13 -0.59 29 42
Rac1/GTP 0.028 0.22 -10000 0 -0.71 28 28
MMP2 -0.026 0.26 -10000 0 -0.94 29 29
TCGA08_p53

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
CDKN2A -0.059 0.13 0.27 1 -0.3 91 92
TP53 -0.018 0.061 -10000 0 -0.27 19 19
Senescence -0.017 0.061 -10000 0 -0.27 19 19
Apoptosis -0.017 0.061 -10000 0 -0.27 19 19
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.064 0.27 3 -0.2 2 5
MDM4 0.026 0.004 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.088 0.19 -10000 0 -0.4 114 114
CDC42/GTP -0.041 0.13 -10000 0 -0.35 30 30
PLCG1 -0.034 0.099 -10000 0 -0.38 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.034 0.013 -10000 0 -10000 0 0
cell migration -0.041 0.12 -10000 0 -0.34 30 30
S1PR5 0.02 0.053 -10000 0 -0.42 6 6
S1PR4 0.016 0.065 -10000 0 -0.4 10 10
MAPK3 -0.056 0.12 -10000 0 -0.36 31 31
MAPK1 -0.047 0.12 -10000 0 -0.38 22 22
S1P/S1P5/Gi -0.049 0.12 -10000 0 -0.24 106 106
GNAI1 0.011 0.076 -10000 0 -0.4 14 14
CDC42/GDP 0.018 0.015 -10000 0 -0.28 1 1
S1P/S1P5/G12 0.028 0.036 -10000 0 -0.25 6 6
RHOA 0.027 0.063 0.18 47 -10000 0 47
S1P/S1P4/Gi -0.053 0.13 -10000 0 -0.25 113 113
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.021 0.042 -10000 0 -0.4 4 4
S1P/S1P4/G12/G13 0.039 0.039 -10000 0 -0.21 8 8
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.004 -10000 0 -10000 0 0
CDC42 0.024 0.022 -10000 0 -0.4 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.003 0.072 -10000 0 -0.29 22 22
CRKL 0.025 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DOCK1 0.026 0.005 -10000 0 -10000 0 0
ITGA4 0.01 0.081 -10000 0 -0.4 16 16
alpha4/beta7 Integrin/MAdCAM1 -0.081 0.16 -10000 0 -0.24 198 198
EPO 0.003 0.046 0.37 1 -0.42 3 4
alpha4/beta7 Integrin 0.016 0.088 -10000 0 -0.31 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.027 0.061 -10000 0 -0.28 16 16
EPO/EPOR (dimer) 0.031 0.036 0.26 1 -0.3 4 5
lamellipodium assembly 0.006 0.075 -10000 0 -0.33 9 9
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.038 0.008 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
JAK2 0.012 0.058 -10000 0 -0.25 16 16
PXN 0.026 0.002 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
MADCAM1 -0.18 0.21 -10000 0 -0.4 197 197
cell adhesion -0.082 0.16 -10000 0 -0.24 198 198
CRKL/CBL 0.037 0.009 -10000 0 -10000 0 0
ITGB1 0.026 0.002 -10000 0 -10000 0 0
SRC 0.001 0.053 -10000 0 -0.38 7 7
ITGB7 0.011 0.079 -10000 0 -0.4 15 15
RAC1 0.024 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.036 0.078 -10000 0 -0.32 18 18
p130Cas/Crk/Dock1 0.051 0.078 -10000 0 -0.35 6 6
VCAM1 0.016 0.061 -10000 0 -0.4 9 9
RHOA 0.026 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.054 -10000 0 -0.22 15 15
BCAR1 -0.014 0.049 -10000 0 -0.39 6 6
EPOR 0.025 0.022 -10000 0 -0.42 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.003 -10000 0 -10000 0 0
GIT1 0.025 0.021 -10000 0 -0.4 1 1
Rac1/GTP 0.006 0.077 -10000 0 -0.35 8 8
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.015 0.038 -10000 0 -0.25 2 2
NFATC2 -0.016 0.046 -10000 0 -0.25 10 10
NFATC3 -0.016 0.038 -10000 0 -10000 0 0
CD40LG -0.067 0.22 0.36 1 -0.54 33 34
PTGS2 -0.066 0.21 0.36 1 -0.54 35 36
JUNB 0.024 0.029 -10000 0 -0.4 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.029 -10000 0 -10000 0 0
CaM/Ca2+ -0.006 0.029 -10000 0 -10000 0 0
CALM1 0.007 0.026 -10000 0 -10000 0 0
JUN 0.007 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.013 -10000 0 -10000 0 0
FOSL1 -0.27 0.21 -10000 0 -0.42 276 276
CREM 0.026 0.002 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.016 0.13 -10000 0 -0.38 6 6
FOS 0.004 0.043 -10000 0 -0.4 3 3
IFNG -0.07 0.22 0.36 1 -0.52 38 39
AP-1/NFAT1-c-4 -0.06 0.21 -10000 0 -0.48 47 47
FASLG -0.064 0.2 0.36 1 -0.51 26 27
NFAT1-c-4/ICER1 -0.027 0.07 -10000 0 -0.28 6 6
IL2RA -0.057 0.2 0.36 1 -0.52 22 23
FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
CSF2 -0.12 0.24 0.36 1 -0.53 59 60
JunB/Fra1/NFAT1-c-4 -0.1 0.16 -10000 0 -0.34 50 50
IL4 -0.058 0.19 0.36 1 -0.51 18 19
IL2 -0.01 0.12 -10000 0 -0.83 9 9
IL3 0 0.083 -10000 0 -0.64 6 6
FKBP1A 0.021 0.011 -10000 0 -10000 0 0
BATF3 0.02 0.048 -10000 0 -0.42 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.005 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.032 0.1 -10000 0 -0.26 45 45
NT3 (dimer)/TRKC -0.028 0.13 -10000 0 -0.3 80 80
NT3 (dimer)/TRKB -0.11 0.19 -10000 0 -0.31 184 184
SHC/Grb2/SOS1/GAB1/PI3K 0.028 0.009 -10000 0 -10000 0 0
RAPGEF1 0.025 0.021 -10000 0 -0.4 1 1
BDNF 0.015 0.068 -10000 0 -0.42 10 10
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
DYNLT1 0.026 0.004 -10000 0 -10000 0 0
NTRK1 0.017 0.045 -10000 0 -0.42 4 4
NTRK2 -0.1 0.19 -10000 0 -0.4 125 125
NTRK3 -0.06 0.16 -10000 0 -0.4 78 78
NT-4/5 (dimer)/TRKB -0.12 0.19 -10000 0 -0.31 196 196
neuron apoptosis 0.1 0.16 0.39 73 -10000 0 73
SHC 2-3/Grb2 -0.11 0.18 -10000 0 -0.42 73 73
SHC1 0.026 0.004 -10000 0 -10000 0 0
SHC2 -0.11 0.18 -10000 0 -0.43 76 76
SHC3 -0.11 0.17 -10000 0 -0.43 69 69
STAT3 (dimer) 0.03 0.019 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.034 0.13 -10000 0 -0.24 118 118
RIN/GDP -0.007 0.081 0.22 5 -0.26 4 9
GIPC1 0.025 0.021 -10000 0 -0.4 1 1
KRAS 0.026 0.003 -10000 0 -10000 0 0
DNAJA3 -0.073 0.13 -10000 0 -0.28 104 104
RIN/GTP 0.009 0.016 -10000 0 -0.3 1 1
CCND1 0.015 0.029 -10000 0 -0.32 3 3
MAGED1 0.026 0.003 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.02 0.09 -10000 0 -0.43 18 18
SHC/GRB2/SOS1 0.051 0.012 -10000 0 -10000 0 0
GRB2 0.026 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.005 0.11 -10000 0 -0.24 63 63
TRKA/NEDD4-2 0.025 0.039 -10000 0 -0.3 5 5
ELMO1 0.023 0.022 -10000 0 -0.4 1 1
RhoG/GTP/ELMO1/DOCK1 0.031 0.018 -10000 0 -0.24 1 1
NGF 0.005 0.084 -10000 0 -0.4 17 17
HRAS 0.025 0.021 -10000 0 -0.4 1 1
DOCK1 0.026 0.005 -10000 0 -10000 0 0
GAB2 0.026 0.003 -10000 0 -10000 0 0
RIT2 -0.013 0.023 -10000 0 -0.42 1 1
RIT1 0.026 0.004 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
DNM1 0.024 0.041 0.37 1 -0.42 3 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.056 0.13 -10000 0 -0.28 98 98
mol:GDP -0.016 0.12 0.26 7 -0.36 9 16
NGF (dimer) 0.005 0.084 -10000 0 -0.4 17 17
RhoG/GDP 0.017 0.016 -10000 0 -0.28 1 1
RIT1/GDP -0.005 0.085 0.2 5 -0.26 6 11
TIAM1 -0.015 0.12 -10000 0 -0.4 40 40
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.043 0.14 -10000 0 -0.24 134 134
KIDINS220/CRKL/C3G 0.037 0.018 -10000 0 -0.28 1 1
SHC/RasGAP 0.037 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.053 0.013 0.25 1 -10000 0 1
SHC/GRB2/SOS1/GAB1 0.064 0.018 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.015 0.062 -10000 0 -0.4 9 9
RAP1/GDP -0.008 0.07 -10000 0 -0.22 6 6
KIDINS220/CRKL 0.025 0.005 -10000 0 -10000 0 0
BDNF (dimer) 0.015 0.068 -10000 0 -0.42 10 10
ubiquitin-dependent protein catabolic process 0.024 0.066 -10000 0 -0.24 22 22
Schwann cell development -0.028 0.028 -10000 0 -10000 0 0
EHD4 0.025 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.018 0.25 1 -10000 0 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.014 0.04 0.25 1 -0.25 1 2
RAP1B 0.026 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.063 0.13 -10000 0 -0.38 28 28
ABL1 0.026 0.003 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.02 0.097 -10000 0 -0.41 13 13
STAT3 0.03 0.019 -10000 0 -10000 0 0
axon guidance -0.066 0.12 -10000 0 -0.36 28 28
MAPK3 -0.021 0.089 0.18 6 -0.26 6 12
MAPK1 -0.021 0.088 0.18 6 -0.26 6 12
CDC42/GDP -0.002 0.087 0.21 8 -0.25 6 14
NTF3 0.015 0.062 -10000 0 -0.4 9 9
NTF4 -0.02 0.09 -10000 0 -0.43 18 18
NGF (dimer)/TRKA/FAIM 0.035 0.065 -10000 0 -0.24 21 21
PI3K 0.038 0.008 -10000 0 -10000 0 0
FRS3 0.027 0.017 0.37 1 -10000 0 1
FAIM 0.026 0.003 -10000 0 -10000 0 0
GAB1 0.026 0.004 -10000 0 -10000 0 0
RASGRF1 -0.088 0.14 -10000 0 -0.3 112 112
SOS1 0.026 0.002 -10000 0 -10000 0 0
MCF2L -0.035 0.097 -10000 0 -0.25 66 66
RGS19 0.016 0.013 -10000 0 -10000 0 0
CDC42 0.024 0.022 -10000 0 -0.4 1 1
RAS family/GTP 0.002 0.072 -10000 0 -0.37 2 2
Rac1/GDP -0.008 0.081 0.23 4 -0.24 6 10
NGF (dimer)/TRKA/GRIT 0.019 0.06 -10000 0 -0.24 21 21
neuron projection morphogenesis -0.058 0.14 -10000 0 -0.48 12 12
NGF (dimer)/TRKA/NEDD4-2 0.024 0.066 -10000 0 -0.24 22 22
MAP2K1 -0.005 0.036 -10000 0 -10000 0 0
NGFR -0.09 0.19 -10000 0 -0.4 115 115
NGF (dimer)/TRKA/GIPC/GAIP 0.008 0.04 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.022 0.02 -10000 0 -0.2 3 3
FRS2 family/SHP2/GRB2/SOS1 0.075 0.02 0.25 1 -10000 0 1
NRAS 0.024 0.029 -10000 0 -0.4 2 2
GRB2/SOS1 0.038 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.029 -10000 0 -0.4 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.025 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.051 0.15 -10000 0 -0.58 29 29
RASA1 0.026 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.034 0.034 -10000 0 -0.3 4 4
SQSTM1 0.026 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.025 0.13 -10000 0 -0.22 131 131
NGF (dimer)/TRKA/p62/Atypical PKCs 0.054 0.069 -10000 0 -0.41 1 1
MATK -0.02 0.13 -10000 0 -0.4 46 46
NEDD4L 0.019 0.023 -10000 0 -0.4 1 1
RAS family/GDP -0.028 0.047 -10000 0 -0.23 1 1
NGF (dimer)/TRKA -0.071 0.14 -10000 0 -0.29 114 114
Rac1/GTP -0.069 0.11 -10000 0 -0.27 55 55
FRS2 family/SHP2/CRK family 0.063 0.033 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.006 0.002 -10000 0 -10000 0 0
ADCY5 -0.1 0.11 -10000 0 -0.24 174 174
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.001 -10000 0 -10000 0 0
ADCY1 -0.01 0.037 0.21 1 -0.25 9 10
ADCY2 -0.024 0.062 -10000 0 -0.24 33 33
ADCY3 -0.006 0.001 -10000 0 -10000 0 0
ADCY8 -0.012 0.031 0.21 1 -0.25 6 7
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.007 0.016 -10000 0 -0.24 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.012 0.075 0.2 14 -0.22 2 16
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.02 0.011 -10000 0 -10000 0 0
EPHB2 0.023 0.032 -10000 0 -0.42 2 2
EFNB1 0.006 0.031 0.28 1 -0.29 3 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.025 0.13 0.23 1 -0.38 10 11
Ephrin B2/EPHB1-2 -0.007 0.1 0.25 2 -0.23 65 67
neuron projection morphogenesis -0.035 0.12 -10000 0 -0.34 12 12
Ephrin B1/EPHB1-2/Tiam1 -0.038 0.14 0.24 1 -0.26 53 54
DNM1 0.024 0.041 0.37 1 -0.42 3 4
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.006 0.06 -10000 0 -0.38 10 10
YES1 -0.008 0.1 -10000 0 -0.6 11 11
Ephrin B1/EPHB1-2/NCK2 -0.013 0.12 0.27 2 -0.23 46 48
PI3K 0.031 0.076 -10000 0 -0.37 13 13
mol:GDP -0.038 0.13 0.24 1 -0.26 53 54
ITGA2B 0.003 0.091 -10000 0 -0.42 18 18
endothelial cell proliferation 0.026 0.016 -10000 0 -10000 0 0
FYN -0.005 0.1 -10000 0 -0.6 12 12
MAP3K7 -0.01 0.065 -10000 0 -0.4 11 11
FGR -0.008 0.1 -10000 0 -0.61 12 12
TIAM1 -0.015 0.12 -10000 0 -0.4 40 40
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.026 0.003 -10000 0 -10000 0 0
cell adhesion 0.009 0.085 -10000 0 -0.36 13 13
LYN -0.006 0.1 -10000 0 -0.59 13 13
Ephrin B1/EPHB1-2/Src Family Kinases -0.007 0.085 -10000 0 -0.49 12 12
Ephrin B1/EPHB1-2 -0.01 0.069 -10000 0 -0.44 10 10
SRC -0.005 0.093 -10000 0 -0.57 11 11
ITGB3 0.022 0.041 -10000 0 -0.4 4 4
EPHB1 -0.084 0.2 0.37 2 -0.42 106 108
EPHB4 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.016 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.02 0.075 -10000 0 -0.3 22 22
BLK -0.043 0.12 -10000 0 -0.64 10 10
HCK -0.009 0.096 -10000 0 -0.58 11 11
regulation of stress fiber formation 0.014 0.12 0.23 46 -0.26 2 48
MAPK8 -0.006 0.06 -10000 0 -0.36 11 11
Ephrin B1/EPHB1-2/RGS3 -0.013 0.12 0.27 2 -0.22 91 93
endothelial cell migration 0.024 0.086 0.22 54 -0.34 4 58
NCK2 0.027 0 -10000 0 -10000 0 0
PTPN13 0.008 0.08 -10000 0 -0.4 15 15
regulation of focal adhesion formation 0.014 0.12 0.23 46 -0.26 2 48
chemotaxis 0.014 0.12 0.22 91 -0.26 2 93
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.03 0.12 0.21 1 -0.35 12 13
angiogenesis -0.008 0.069 -10000 0 -0.44 10 10
LCK -0.007 0.1 -10000 0 -0.6 12 12
Signaling events mediated by PRL

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
CCNE1 0.027 0.032 0.37 2 -0.42 1 3
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.026 0.004 -10000 0 -10000 0 0
CDKN1A 0.006 0.047 -10000 0 -0.3 9 9
PRL-3/alpha Tubulin 0.023 0.12 0.26 32 -0.3 36 68
mol:Ca2+ -0.055 0.12 0.43 2 -0.3 76 78
AGT -0.024 0.14 0.37 2 -0.42 48 50
CCNA2 -0.003 0.009 -10000 0 -10000 0 0
TUBA1B 0.026 0.002 -10000 0 -10000 0 0
EGR1 0.014 0.014 -10000 0 -0.27 1 1
CDK2/Cyclin E1 0.072 0.077 0.31 3 -10000 0 3
MAPK3 0.004 0.12 0.28 32 -0.3 37 69
PRL-2 /Rab GGTase beta 0.037 0.009 -10000 0 -10000 0 0
MAPK1 0.004 0.12 0.28 31 -0.3 36 67
PTP4A1 0.002 0.01 -10000 0 -10000 0 0
PTP4A3 0.012 0.16 0.37 32 -0.42 36 68
PTP4A2 0.025 0.005 -10000 0 -10000 0 0
ITGB1 0.005 0.12 0.28 32 -0.3 36 68
SRC 0.016 0.013 -10000 0 -10000 0 0
RAC1 0.024 0.071 0.3 16 -0.3 4 20
Rab GGTase beta/Rab GGTase alpha 0.036 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 0.082 0.082 -10000 0 -10000 0 0
RABGGTA 0.025 0.006 -10000 0 -10000 0 0
BCAR1 -0.022 0.083 -10000 0 -0.26 33 33
RHOC 0.026 0.086 0.31 22 -0.32 7 29
RHOA 0.027 0.079 0.28 29 -0.3 5 34
cell motility 0.05 0.11 0.31 18 -0.35 6 24
PRL-1/alpha Tubulin 0.084 0.082 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.022 0.12 0.26 30 -0.3 36 66
ROCK1 0.051 0.1 0.31 18 -0.38 4 22
RABGGTB 0.026 0.005 -10000 0 -10000 0 0
CDK2 0.026 0.002 -10000 0 -10000 0 0
mitosis 0.002 0.01 -10000 0 -10000 0 0
ATF5 0.026 0.003 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.013 0.14 -10000 0 -0.82 5 5
MKNK1 0.026 0.004 -10000 0 -10000 0 0
MAPK14 0.005 0.09 -10000 0 -0.3 21 21
ATF2/c-Jun 0.002 0.067 -10000 0 -0.48 1 1
MAPK11 0.005 0.093 -10000 0 -0.32 23 23
MITF -0.01 0.11 -10000 0 -0.35 27 27
MAPKAPK5 -0.004 0.1 -10000 0 -0.34 28 28
KRT8 -0.003 0.097 -10000 0 -0.34 27 27
MAPKAPK3 0.026 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.004 0.13 -10000 0 -0.44 24 24
CEBPB -0.004 0.076 -10000 0 -0.35 14 14
SLC9A1 -0.005 0.1 -10000 0 -0.37 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.001 0.098 -10000 0 -0.34 23 23
p38alpha-beta/MNK1 0.021 0.11 -10000 0 -0.37 22 22
JUN 0.001 0.066 -10000 0 -0.47 1 1
PPARGC1A -0.039 0.14 -10000 0 -0.4 32 32
USF1 0.001 0.091 -10000 0 -0.34 23 23
RAB5/GDP/GDI1 0.004 0.078 -10000 0 -0.26 22 22
NOS2 -0.039 0.23 -10000 0 -0.93 24 24
DDIT3 -0.003 0.099 -10000 0 -0.34 26 26
RAB5A 0.024 0.029 -10000 0 -0.4 2 2
HSPB1 0.001 0.098 0.28 16 -0.29 24 40
p38alpha-beta/HBP1 0.019 0.11 -10000 0 -0.37 21 21
CREB1 -0.002 0.1 -10000 0 -0.38 25 25
RAB5/GDP 0.018 0.021 -10000 0 -0.28 2 2
EIF4E -0.008 0.092 -10000 0 -0.33 22 22
RPS6KA4 -0.004 0.099 -10000 0 -0.34 28 28
PLA2G4A -0.026 0.11 -10000 0 -0.37 19 19
GDI1 -0.003 0.097 -10000 0 -0.34 27 27
TP53 -0.019 0.11 -10000 0 -0.44 22 22
RPS6KA5 -0.006 0.1 -10000 0 -0.38 24 24
ESR1 -0.027 0.14 -10000 0 -0.41 28 28
HBP1 0.025 0.006 -10000 0 -10000 0 0
MEF2C -0.009 0.11 -10000 0 -0.35 27 27
MEF2A -0.005 0.1 -10000 0 -0.36 27 27
EIF4EBP1 -0.005 0.1 -10000 0 -0.39 24 24
KRT19 -0.004 0.099 -10000 0 -0.34 28 28
ELK4 0 0.092 -10000 0 -0.34 24 24
ATF6 0.001 0.091 -10000 0 -0.34 23 23
ATF1 -0.002 0.1 -10000 0 -0.38 25 25
p38alpha-beta/MAPKAPK2 0.024 0.11 -10000 0 -0.36 20 20
p38alpha-beta/MAPKAPK3 0.022 0.11 -10000 0 -0.36 22 22
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0 0.11 0.21 2 -0.34 22 24
TBX21 -0.1 0.4 -10000 0 -1.2 39 39
B2M 0.021 0.027 -10000 0 -0.4 1 1
TYK2 0.018 0.032 -10000 0 -10000 0 0
IL12RB1 0.003 0.09 -10000 0 -0.43 16 16
GADD45B -0.043 0.29 -10000 0 -0.91 28 28
IL12RB2 0.013 0.062 -10000 0 -0.43 6 6
GADD45G -0.043 0.29 -10000 0 -0.97 23 23
natural killer cell activation 0 0.018 -10000 0 -10000 0 0
RELB 0.026 0.003 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL18 0.024 0.032 -10000 0 -0.4 2 2
IL2RA 0.016 0.065 -10000 0 -0.4 10 10
IFNG -0.025 0.13 -10000 0 -0.42 42 42
STAT3 (dimer) -0.045 0.27 0.34 1 -0.77 37 38
HLA-DRB5 -0.001 0.11 0.37 1 -0.41 27 28
FASLG -0.1 0.4 0.58 1 -1.2 40 41
NF kappa B2 p52/RelB -0.066 0.33 -10000 0 -0.95 36 36
CD4 0.01 0.081 -10000 0 -0.4 16 16
SOCS1 0.018 0.067 0.37 1 -0.42 9 10
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D 0.011 0.073 -10000 0 -0.4 12 12
CD3E 0.012 0.07 -10000 0 -0.4 11 11
CD3G -0.01 0.12 -10000 0 -0.41 33 33
IL12Rbeta2/JAK2 0.023 0.068 -10000 0 -0.33 9 9
CCL3 -0.076 0.33 -10000 0 -0.98 32 32
CCL4 -0.072 0.33 -10000 0 -0.99 32 32
HLA-A 0.022 0.027 -10000 0 -0.4 1 1
IL18/IL18R 0.044 0.093 -10000 0 -0.25 32 32
NOS2 -0.093 0.39 -10000 0 -1.2 39 39
IL12/IL12R/TYK2/JAK2/SPHK2 0.002 0.1 0.22 1 -0.33 23 24
IL1R1 -0.081 0.34 -10000 0 -1 35 35
IL4 -0.003 0.034 -10000 0 -10000 0 0
JAK2 0.014 0.049 -10000 0 -0.43 3 3
EntrezGene:6957 -0.001 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.07 0.3 -10000 0 -0.89 43 43
RAB7A -0.03 0.25 -10000 0 -0.78 25 25
lysosomal transport -0.026 0.24 -10000 0 -0.73 25 25
FOS -0.073 0.32 -10000 0 -0.92 40 40
STAT4 (dimer) -0.046 0.31 0.43 1 -0.9 35 36
STAT5A (dimer) -0.079 0.33 -10000 0 -0.94 37 37
GZMA -0.13 0.44 -10000 0 -1.3 47 47
GZMB -0.099 0.33 -10000 0 -1 31 31
HLX 0.025 0.021 -10000 0 -0.4 1 1
LCK -0.086 0.35 -10000 0 -1 38 38
TCR/CD3/MHC II/CD4 -0.03 0.19 -10000 0 -0.56 35 35
IL2/IL2R 0.047 0.071 -10000 0 -0.3 14 14
MAPK14 -0.045 0.3 -10000 0 -0.95 28 28
CCR5 -0.053 0.32 -10000 0 -1 28 28
IL1B -0.031 0.14 -10000 0 -0.42 48 48
STAT6 0.004 0.094 -10000 0 -10000 0 0
STAT4 0.003 0.097 -10000 0 -0.4 23 23
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.025 0.022 -10000 0 -0.42 1 1
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.025 0.006 -10000 0 -10000 0 0
IL12B 0.009 0.054 -10000 0 -0.42 4 4
CD8A -0.006 0.11 -10000 0 -0.41 30 30
CD8B 0.01 0.077 -10000 0 -0.41 13 13
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0 0.11 0.34 22 -0.21 2 24
IL2RB 0.017 0.058 -10000 0 -0.4 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.28 0.4 2 -0.81 35 37
IL2RG 0.024 0.029 -10000 0 -0.4 2 2
IL12 0.018 0.071 -10000 0 -0.3 11 11
STAT5A 0.026 0.004 -10000 0 -10000 0 0
CD247 0.011 0.073 -10000 0 -0.4 12 12
IL2 -0.006 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.021 -10000 0 -0.4 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.011 0.064 -10000 0 -0.42 7 7
IL12/IL12R/TYK2/JAK2 -0.087 0.38 -10000 0 -1.1 38 38
MAP2K3 -0.065 0.32 -10000 0 -0.94 36 36
RIPK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K6 -0.04 0.3 -10000 0 -0.93 28 28
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.016 0.065 -10000 0 -0.4 10 10
IL18RAP 0.003 0.097 -10000 0 -0.4 22 22
IL12Rbeta1/TYK2 0.017 0.078 -10000 0 -0.32 16 16
EOMES -0.062 0.3 -10000 0 -1.2 26 26
STAT1 (dimer) -0.041 0.27 -10000 0 -0.76 35 35
T cell proliferation -0.025 0.23 0.36 2 -0.66 31 33
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.017 0.064 -10000 0 -0.4 9 9
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.031 0.25 -10000 0 -0.72 32 32
ATF2 -0.041 0.28 -10000 0 -0.86 28 28
Syndecan-3-mediated signaling events

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
CTTN 0.026 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.002 0.098 -10000 0 -0.38 12 12
Syndecan-3/Neurocan 0.006 0.087 -10000 0 -0.37 20 20
POMC 0.01 0.079 -10000 0 -0.4 15 15
EGFR 0.023 0.022 -10000 0 -0.4 1 1
Syndecan-3/EGFR 0.007 0.085 -10000 0 -0.37 19 19
AGRP -0.005 0.041 -10000 0 -0.42 3 3
NCSTN 0.026 0.004 -10000 0 -10000 0 0
PSENEN 0.025 0.021 -10000 0 -0.4 1 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.025 0.006 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
NCAN 0.001 0.037 -10000 0 -0.42 2 2
long-term memory 0.026 0.087 -10000 0 -0.35 20 20
Syndecan-3/IL8 -0.12 0.14 0.23 1 -0.45 23 24
PSEN1 0.025 0.007 -10000 0 -10000 0 0
Src/Cortactin 0.023 0.019 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
limb bud formation -0.006 0.083 -10000 0 -0.38 20 20
MC4R -0.009 0.044 -10000 0 -0.42 4 4
SRC 0.016 0.013 -10000 0 -10000 0 0
PTN -0.041 0.15 -10000 0 -0.4 66 66
FGFR/FGF/Syndecan-3 -0.006 0.084 -10000 0 -0.38 20 20
neuron projection morphogenesis 0.024 0.12 -10000 0 -0.37 12 12
Syndecan-3/AgRP 0.005 0.088 -10000 0 -0.37 20 20
Syndecan-3/AgRP/MC4R 0.009 0.088 -10000 0 -0.34 21 21
Fyn/Cortactin 0.038 0.008 -10000 0 -10000 0 0
SDC3 -0.006 0.085 -10000 0 -0.39 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.12 0.14 0.23 1 -0.45 23 24
IL8 -0.24 0.22 0.37 1 -0.43 251 252
Syndecan-3/Fyn/Cortactin 0.027 0.089 -10000 0 -0.36 20 20
Syndecan-3/CASK -0.008 0.082 -10000 0 -0.36 21 21
alpha-MSH/MC4R 0.012 0.065 -10000 0 -0.28 19 19
Gamma Secretase 0.067 0.031 -10000 0 -0.21 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.007 0.1 -10000 0 -0.46 18 18
NFATC2 -0.005 0.13 -10000 0 -0.62 7 7
NFATC3 -0.024 0.067 -10000 0 -0.3 3 3
CD40LG -0.19 0.28 -10000 0 -0.8 38 38
ITCH 0.017 0.022 -10000 0 -10000 0 0
CBLB 0.027 0.035 -10000 0 -0.39 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.21 -10000 0 -0.8 21 21
JUNB 0.024 0.029 -10000 0 -0.4 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.035 0.032 -10000 0 -0.27 4 4
T cell anergy 0.037 0.059 0.24 1 -0.32 2 3
TLE4 -0.004 0.086 -10000 0 -0.46 6 6
Jun/NFAT1-c-4/p21SNFT -0.084 0.18 -10000 0 -0.76 10 10
AP-1/NFAT1-c-4 -0.21 0.28 -10000 0 -0.86 30 30
IKZF1 -0.014 0.13 -10000 0 -0.68 13 13
T-helper 2 cell differentiation -0.069 0.17 -10000 0 -0.69 16 16
AP-1/NFAT1 -0.035 0.1 -10000 0 -0.42 6 6
CALM1 0.032 0.021 -10000 0 -10000 0 0
EGR2 -0.043 0.17 -10000 0 -0.97 9 9
EGR3 -0.046 0.17 -10000 0 -0.96 9 9
NFAT1/FOXP3 -0.003 0.12 -10000 0 -0.49 13 13
EGR1 0.026 0.021 -10000 0 -0.4 1 1
JUN -0.034 0.045 -10000 0 -10000 0 0
EGR4 -0.054 0.17 -10000 0 -0.42 74 74
mol:Ca2+ 0.008 0.016 -10000 0 -0.19 1 1
GBP3 -0.025 0.15 -10000 0 -0.62 23 23
FOSL1 -0.27 0.21 -10000 0 -0.42 276 276
NFAT1-c-4/MAF/IRF4 -0.092 0.2 -10000 0 -0.78 17 17
DGKA -0.005 0.086 -10000 0 -0.46 6 6
CREM 0.026 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.047 0.16 -10000 0 -0.76 8 8
CTLA4 -0.018 0.12 -10000 0 -0.54 12 12
NFAT1-c-4 (dimer)/EGR1 -0.044 0.16 -10000 0 -0.79 7 7
NFAT1-c-4 (dimer)/EGR4 -0.076 0.17 -10000 0 -0.89 6 6
FOS -0.034 0.055 -10000 0 -0.42 3 3
IFNG -0.066 0.19 -10000 0 -0.67 23 23
T cell activation -0.027 0.14 -10000 0 -0.6 2 2
MAF 0.014 0.071 -10000 0 -0.4 12 12
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.041 0.14 0.77 10 -10000 0 10
TNF -0.069 0.15 -10000 0 -0.84 6 6
FASLG -0.11 0.36 -10000 0 -1.2 37 37
TBX21 -0.005 0.1 -10000 0 -0.4 24 24
BATF3 0.02 0.048 -10000 0 -0.42 5 5
PRKCQ 0.015 0.06 -10000 0 -0.41 6 6
PTPN1 -0.004 0.086 -10000 0 -0.46 6 6
NFAT1-c-4/ICER1 -0.046 0.16 -10000 0 -0.78 7 7
GATA3 0.021 0.047 -10000 0 -0.4 5 5
T-helper 1 cell differentiation -0.065 0.18 -10000 0 -0.66 23 23
IL2RA -0.11 0.21 -10000 0 -0.75 25 25
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.005 0.084 -10000 0 -0.46 6 6
E2F1 0.023 0.059 0.37 8 -0.42 2 10
PPARG 0.024 0.029 -10000 0 -0.4 2 2
SLC3A2 -0.004 0.085 -10000 0 -0.46 6 6
IRF4 -0.11 0.2 -10000 0 -0.4 137 137
PTGS2 -0.19 0.28 -10000 0 -0.77 44 44
CSF2 -0.25 0.32 -10000 0 -0.77 60 60
JunB/Fra1/NFAT1-c-4 -0.16 0.18 -10000 0 -0.78 13 13
IL4 -0.071 0.18 -10000 0 -0.73 15 15
IL5 -0.19 0.26 -10000 0 -0.77 32 32
IL2 -0.027 0.14 -10000 0 -0.61 2 2
IL3 -0.036 0.095 -10000 0 -0.7 6 6
RNF128 0.026 0.041 -10000 0 -0.42 3 3
NFATC1 -0.041 0.14 -10000 0 -0.78 10 10
CDK4 0.023 0.095 0.64 3 -10000 0 3
PTPRK -0.003 0.084 -10000 0 -0.46 6 6
IL8 -0.29 0.32 -10000 0 -0.77 69 69
POU2F1 0.026 0.005 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.039 0.1 0.21 52 -0.28 2 54
PDGFB-D/PDGFRB/SLAP 0.029 0.042 -10000 0 -0.29 6 6
PDGFB-D/PDGFRB/APS/CBL 0.046 0.043 0.26 1 -0.25 7 8
AKT1 0.054 0.094 0.27 10 -10000 0 10
mol:PI-4-5-P2 0.001 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.068 0.12 0.24 68 -0.38 1 69
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
FGR 0.009 0.12 0.34 2 -0.46 18 20
mol:Ca2+ 0.063 0.11 0.24 63 -0.45 1 64
MYC 0.096 0.16 0.39 60 -10000 0 60
SHC1 0.026 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.061 0.074 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.047 0.038 -10000 0 -0.25 6 6
GRB10 0.024 0.008 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0.063 0.11 0.24 61 -0.46 1 62
PTEN 0.025 0.006 -10000 0 -10000 0 0
GRB2 0.026 0.004 -10000 0 -10000 0 0
GRB7 0.032 0.047 0.37 8 -10000 0 8
PDGFB-D/PDGFRB/SHP2 0.037 0.033 -10000 0 -0.3 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.031 -10000 0 -0.3 3 3
cell cycle arrest 0.029 0.042 -10000 0 -0.29 6 6
HRAS 0.025 0.021 -10000 0 -0.4 1 1
HIF1A 0.047 0.087 0.24 12 -10000 0 12
GAB1 0.047 0.12 0.25 15 -0.32 3 18
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.06 0.11 0.23 68 -0.3 1 69
PDGFB-D/PDGFRB 0.026 0.039 -10000 0 -0.26 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.037 0.033 -10000 0 -0.3 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.006 0.058 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.036 0.033 -10000 0 -0.3 4 4
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.063 0.11 0.24 61 -0.46 1 62
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.04 0.046 0.27 8 -0.3 4 12
SHB 0.026 0.004 -10000 0 -10000 0 0
BLK -0.14 0.23 -10000 0 -0.46 136 136
PTPN2 0.024 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.036 0.034 -10000 0 -0.3 4 4
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
VAV2 0.057 0.13 0.26 66 -0.36 2 68
CBL 0.026 0.003 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.036 0.034 -10000 0 -0.3 4 4
LCK 0.018 0.1 0.34 2 -0.44 11 13
PDGFRB 0.024 0.044 -10000 0 -0.42 4 4
ACP1 0.026 0.002 -10000 0 -10000 0 0
HCK 0.006 0.071 -10000 0 -0.48 6 6
ABL1 0.04 0.12 0.23 58 -0.32 8 66
PDGFB-D/PDGFRB/CBL 0.035 0.12 0.32 1 -0.37 4 5
PTPN1 0.015 0.013 -10000 0 -10000 0 0
SNX15 0.026 0.004 -10000 0 -10000 0 0
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.025 0.022 -10000 0 -0.42 1 1
cell proliferation 0.094 0.15 0.38 63 -10000 0 63
SLA 0.02 0.03 -10000 0 -0.4 2 2
actin cytoskeleton reorganization 0.084 0.087 0.34 4 -10000 0 4
SRC 0.01 0.039 -10000 0 -10000 0 0
PI3K -0.003 0.025 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.052 0.042 0.26 7 -0.25 4 11
SH2B2 0.023 0.042 0.37 1 -0.42 3 4
PLCgamma1/SPHK1 0.069 0.13 0.24 67 -0.39 1 68
LYN 0.022 0.078 0.33 1 -0.56 3 4
LRP1 0.024 0.029 -10000 0 -0.4 2 2
SOS1 0.026 0.002 -10000 0 -10000 0 0
STAT5B 0.026 0.004 -10000 0 -10000 0 0
STAT5A 0.026 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.039 0.049 -10000 0 -10000 0 0
SPHK1 -0.003 0.12 -10000 0 -0.42 30 30
EDG1 0.003 0.004 -10000 0 -10000 0 0
mol:DAG 0.063 0.11 0.24 61 -0.46 1 62
PLCG1 0.064 0.11 0.24 60 -0.48 1 61
NHERF/PDGFRB 0.049 0.035 -10000 0 -0.25 5 5
YES1 -0.001 0.14 0.34 2 -0.48 25 27
cell migration 0.048 0.035 -10000 0 -0.25 5 5
SHC/Grb2/SOS1 0.038 0.048 -10000 0 -10000 0 0
SLC9A3R2 0.025 0.021 -10000 0 -0.4 1 1
SLC9A3R1 0.026 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.059 0.038 -10000 0 -0.23 5 5
FYN 0.021 0.079 0.33 1 -0.39 6 7
DOK1 0.056 0.082 0.18 116 -0.23 1 117
HRAS/GTP 0.019 0.015 -10000 0 -0.28 1 1
PDGFB 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.073 0.14 0.34 45 -0.38 1 46
PRKCD 0.051 0.086 0.18 111 -0.24 1 112
FER 0.051 0.086 0.18 110 -0.23 4 114
MAPKKK cascade 0.066 0.1 0.33 11 -10000 0 11
RASA1 0.051 0.086 0.18 109 -0.24 1 110
NCK1 0.026 0.002 -10000 0 -10000 0 0
NCK2 0.027 0 -10000 0 -10000 0 0
p62DOK/Csk 0.062 0.073 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.036 0.034 -10000 0 -0.3 4 4
chemotaxis 0.04 0.12 0.23 60 -0.32 8 68
STAT1-3-5/STAT1-3-5 0.031 0.043 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.018 0.031 -10000 0 -0.3 4 4
PTPRJ 0.026 0.003 -10000 0 -10000 0 0
Arf6 signaling 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
CENTA1/KIF3B 0.025 0.028 -10000 0 -0.44 1 1
ARNO/beta Arrestin1-2 0 0.095 -10000 0 -0.8 2 2
EGFR 0.023 0.022 -10000 0 -0.4 1 1
EPHA2 0.024 0.023 -10000 0 -0.42 1 1
USP6 0.021 0.024 -10000 0 -0.42 1 1
IQSEC1 0.026 0.003 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.022 0.12 -10000 0 -0.29 73 73
ARRB2 0.007 0.004 -10000 0 -10000 0 0
mol:GTP 0.004 0.041 0.12 5 -0.26 2 7
ARRB1 0.025 0.021 -10000 0 -0.4 1 1
FBXO8 0.024 0.021 -10000 0 -0.4 1 1
TSHR 0.005 0.059 -10000 0 -0.4 8 8
EGF -0.061 0.17 -10000 0 -0.4 82 82
somatostatin receptor activity 0 0 0.001 22 -0.001 20 42
ARAP2 0.025 0.021 -10000 0 -0.4 1 1
mol:GDP -0.035 0.11 0.18 10 -0.25 44 54
mol:PI-3-4-5-P3 0 0 0.001 13 -0.001 7 20
ITGA2B 0.003 0.091 -10000 0 -0.42 18 18
ARF6 0.025 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.059 0.029 -10000 0 -0.22 2 2
ADAP1 0.023 0.022 -10000 0 -0.4 1 1
KIF13B 0.02 0.023 -10000 0 -0.4 1 1
HGF/MET 0.03 0.048 -10000 0 -0.29 9 9
PXN 0.026 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.1 0.22 19 -0.26 22 41
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.005 0.11 -10000 0 -0.24 72 72
ADRB2 -0.04 0.15 -10000 0 -0.4 65 65
receptor agonist activity 0 0 0 7 0 20 27
actin filament binding 0 0 0 21 0 23 44
SRC 0.016 0.013 -10000 0 -10000 0 0
ITGB3 0.022 0.041 -10000 0 -0.4 4 4
GNAQ 0.025 0.021 -10000 0 -0.4 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 28 -0.001 10 38
ARF6/GDP -0.047 0.16 0.2 3 -0.4 53 56
ARF6/GDP/GULP/ACAP1 -0.026 0.12 0.22 2 -0.34 19 21
alphaIIb/beta3 Integrin/paxillin/GIT1 0.049 0.067 -10000 0 -0.23 22 22
ACAP1 0.011 0.068 -10000 0 -0.4 11 11
ACAP2 0.025 0.021 -10000 0 -0.4 1 1
LHCGR/beta Arrestin2 0.006 0.026 -10000 0 -10000 0 0
EFNA1 0.026 0.004 -10000 0 -10000 0 0
HGF 0.018 0.055 -10000 0 -0.4 7 7
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 0.014 0.07 -10000 0 -1 2 2
NCK1 0.026 0.002 -10000 0 -10000 0 0
fibronectin binding 0 0 0 29 0 12 41
endosomal lumen acidification 0 0 0 33 0 10 43
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.005 0.092 -10000 0 -0.4 21 21
GNAQ/ARNO 0.029 0.067 -10000 0 -0.93 2 2
mol:Phosphatidic acid 0 0 0 5 -10000 0 5
PIP3-E 0 0 0 9 0 3 12
MET 0.022 0.047 0.37 1 -0.42 4 5
GNA14 0.024 0.029 -10000 0 -0.4 2 2
GNA15 0.022 0.044 -10000 0 -0.42 4 4
GIT1 0.025 0.021 -10000 0 -0.4 1 1
mol:PI-4-5-P2 0 0 0.001 23 -0.001 17 40
GNA11 0.024 0.029 -10000 0 -0.4 2 2
LHCGR -0.014 0.013 -10000 0 -10000 0 0
AGTR1 -0.12 0.2 -10000 0 -0.4 141 141
desensitization of G-protein coupled receptor protein signaling pathway 0.006 0.026 -10000 0 -10000 0 0
IPCEF1/ARNO -0.001 0.098 -10000 0 -0.85 2 2
alphaIIb/beta3 Integrin 0.02 0.075 -10000 0 -0.3 22 22
HIF-2-alpha transcription factor network

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
MMP14 -0.028 0.15 -10000 0 -0.63 22 22
oxygen homeostasis -0.011 0.01 -10000 0 -10000 0 0
TCEB2 0.025 0.022 -10000 0 -0.42 1 1
TCEB1 0.023 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.044 0.073 -10000 0 -0.34 1 1
EPO -0.15 0.15 -10000 0 -0.54 10 10
FIH (dimer) 0.006 0.023 -10000 0 -10000 0 0
APEX1 -0.016 0.024 -10000 0 -10000 0 0
SERPINE1 -0.2 0.22 -10000 0 -0.57 81 81
FLT1 -0.002 0.085 -10000 0 -0.66 5 5
ADORA2A -0.16 0.17 0.36 1 -0.52 37 38
germ cell development -0.16 0.17 -10000 0 -0.52 40 40
SLC11A2 -0.16 0.17 -10000 0 -0.53 36 36
BHLHE40 -0.17 0.17 -10000 0 -0.54 37 37
HIF1AN 0.006 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.091 0.11 -10000 0 -0.4 3 3
ETS1 0.036 0.008 -10000 0 -10000 0 0
CITED2 -0.006 0.1 -10000 0 -0.75 7 7
KDR -0.011 0.13 -10000 0 -0.69 12 12
PGK1 -0.16 0.17 -10000 0 -0.53 36 36
SIRT1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.18 0.2 -10000 0 -0.61 36 36
EPAS1 -0.053 0.065 -10000 0 -0.26 2 2
SP1 0.03 0.009 -10000 0 -10000 0 0
ABCG2 -0.36 0.24 -10000 0 -0.64 109 109
EFNA1 -0.16 0.17 -10000 0 -0.53 36 36
FXN -0.16 0.17 0.36 1 -0.52 36 37
POU5F1 -0.17 0.18 -10000 0 -0.53 40 40
neuron apoptosis 0.17 0.2 0.59 36 -10000 0 36
EP300 0.025 0.006 -10000 0 -10000 0 0
EGLN3 0.003 0.037 -10000 0 -0.41 2 2
EGLN2 0.005 0.031 -10000 0 -0.41 1 1
EGLN1 0.006 0.023 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.045 0.02 -10000 0 -10000 0 0
VHL 0.026 0.003 -10000 0 -10000 0 0
ARNT -0.015 0.031 -10000 0 -0.42 1 1
SLC2A1 -0.16 0.18 0.36 1 -0.53 44 45
TWIST1 -0.16 0.19 0.36 1 -0.59 42 43
ELK1 0.031 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.091 0.11 -10000 0 -0.42 2 2
VEGFA -0.16 0.17 -10000 0 -0.53 35 35
CREBBP 0.026 0.004 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.013 0.069 -10000 0 -0.39 5 5
Syndecan-4/Syndesmos 0.039 0.13 0.31 4 -0.54 2 6
positive regulation of JNK cascade 0.012 0.14 0.3 4 -0.57 2 6
Syndecan-4/ADAM12 -0.061 0.18 -10000 0 -0.45 8 8
CCL5 0.009 0.084 -10000 0 -0.4 17 17
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DNM2 0.026 0.003 -10000 0 -10000 0 0
ITGA5 0.024 0.031 -10000 0 -0.42 2 2
SDCBP 0.022 0.022 -10000 0 -0.4 1 1
PLG -0.091 0.17 -10000 0 -0.44 79 79
ADAM12 -0.25 0.22 -10000 0 -0.43 260 260
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.04 0.049 -10000 0 -0.14 30 30
Syndecan-4/Laminin alpha1 -0.009 0.13 0.31 4 -0.54 2 6
Syndecan-4/CXCL12/CXCR4 0.013 0.15 0.31 3 -0.61 2 5
Syndecan-4/Laminin alpha3 0.024 0.12 0.31 4 -0.54 2 6
MDK 0.022 0.044 -10000 0 -0.42 4 4
Syndecan-4/FZD7 0.04 0.13 0.31 4 -0.54 2 6
Syndecan-4/Midkine 0.038 0.13 0.31 4 -0.53 2 6
FZD7 0.027 0 -10000 0 -10000 0 0
Syndecan-4/FGFR1/FGF 0.014 0.13 -10000 0 -0.52 2 2
THBS1 0.024 0.023 -10000 0 -0.42 1 1
integrin-mediated signaling pathway 0.034 0.13 0.31 4 -0.6 2 6
positive regulation of MAPKKK cascade 0.012 0.14 0.3 4 -0.57 2 6
Syndecan-4/TACI -0.037 0.14 0.31 2 -0.57 3 5
CXCR4 0.026 0.003 -10000 0 -10000 0 0
cell adhesion 0.009 0.048 0.19 11 -0.23 5 16
Syndecan-4/Dynamin 0.038 0.13 0.31 4 -0.54 2 6
Syndecan-4/TSP1 0.037 0.13 0.31 4 -0.54 2 6
Syndecan-4/GIPC 0.038 0.13 0.31 4 -0.54 2 6
Syndecan-4/RANTES 0.031 0.13 0.31 4 -0.54 2 6
ITGB1 0.026 0.002 -10000 0 -10000 0 0
LAMA1 -0.055 0.16 -10000 0 -0.4 76 76
LAMA3 0.019 0.037 -10000 0 -0.41 3 3
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA 0.022 0.13 0.75 13 -10000 0 13
Syndecan-4/alpha-Actinin 0.034 0.12 0.31 4 -0.54 2 6
TFPI 0.023 0.036 -10000 0 -0.4 3 3
F2 -0.11 0.21 0.41 1 -0.41 136 137
alpha5/beta1 Integrin 0.037 0.024 -10000 0 -0.3 2 2
positive regulation of cell adhesion -0.011 0.13 0.3 4 -0.49 3 7
ACTN1 0.025 0.006 -10000 0 -10000 0 0
TNC 0.015 0.07 -10000 0 -0.41 11 11
Syndecan-4/CXCL12 0.009 0.15 0.31 4 -0.62 2 6
FGF6 -0.018 0.021 -10000 0 -0.42 1 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
CXCL12 -0.049 0.16 -10000 0 -0.4 75 75
TNFRSF13B -0.13 0.2 -10000 0 -0.4 144 144
FGF2 -0.003 0.11 -10000 0 -0.4 29 29
FGFR1 0.02 0.037 -10000 0 -0.4 3 3
Syndecan-4/PI-4-5-P2 -0.007 0.094 0.29 4 -0.54 2 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.014 0.1 -10000 0 -0.42 23 23
cell migration -0.021 0.02 -10000 0 -10000 0 0
PRKCD 0.011 0.025 -10000 0 -10000 0 0
vasculogenesis 0.036 0.12 0.31 4 -0.52 2 6
SDC4 -0.005 0.099 0.32 4 -0.57 2 6
Syndecan-4/Tenascin C 0.034 0.13 0.31 4 -0.62 2 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.033 0.037 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.029 0.12 0.31 3 -0.54 2 5
MMP9 -0.003 0.12 0.38 11 -0.42 25 36
Rac1/GTP 0.009 0.049 0.2 11 -0.23 5 16
cytoskeleton organization 0.038 0.12 0.31 4 -0.52 2 6
GIPC1 0.025 0.021 -10000 0 -0.4 1 1
Syndecan-4/TFPI 0.038 0.13 0.31 4 -0.54 2 6
Thromboxane A2 receptor signaling

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
TGM2 0.012 0.039 -10000 0 -0.42 3 3
GNB1/GNG2 -0.053 0.049 -10000 0 -0.2 12 12
AKT1 -0.042 0.091 -10000 0 -0.29 28 28
EGF -0.061 0.17 -10000 0 -0.4 82 82
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.074 0.08 -10000 0 -0.31 2 2
mol:Ca2+ -0.053 0.094 -10000 0 -0.29 24 24
LYN -0.063 0.077 -10000 0 -10000 0 0
RhoA/GTP -0.024 0.042 -10000 0 -0.14 3 3
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.059 0.097 -10000 0 -0.35 10 10
GNG2 0.009 0.081 -10000 0 -0.4 16 16
ARRB2 0.022 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.026 0.11 -10000 0 -0.61 9 9
G beta5/gamma2 -0.061 0.066 -10000 0 -0.27 12 12
PRKCH -0.056 0.099 -10000 0 -0.35 11 11
DNM1 0.024 0.041 0.37 1 -0.42 3 4
TXA2/TP beta/beta Arrestin3 -0.01 0.039 -10000 0 -0.65 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.19 0.21 -10000 0 -0.4 211 211
G12 family/GTP -0.054 0.086 -10000 0 -0.31 10 10
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
ADRBK2 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.028 0.019 -10000 0 -0.24 1 1
mol:GDP 0.069 0.1 0.36 23 -10000 0 23
mol:NADP 0.018 0.063 0.37 1 -0.42 8 9
RAB11A 0.025 0.005 -10000 0 -10000 0 0
PRKG1 0.005 0.088 -10000 0 -0.4 19 19
mol:IP3 -0.066 0.11 -10000 0 -0.36 26 26
cell morphogenesis 0.028 0.019 -10000 0 -0.24 1 1
PLCB2 -0.089 0.14 -10000 0 -0.49 26 26
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.12 0.11 -10000 0 -0.31 70 70
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.043 0.073 -10000 0 -0.31 3 3
RHOA 0.026 0.004 -10000 0 -10000 0 0
PTGIR 0.026 0.004 -10000 0 -10000 0 0
PRKCB1 -0.06 0.1 -10000 0 -0.36 15 15
GNAQ 0.025 0.021 -10000 0 -0.4 1 1
mol:L-citrulline 0.018 0.063 0.37 1 -0.42 8 9
TXA2/TXA2-R family -0.085 0.14 -10000 0 -0.53 11 11
LCK -0.077 0.083 -10000 0 -0.31 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.081 0.1 -10000 0 -0.24 3 3
TXA2-R family/G12 family/GDP/G beta/gamma -0.03 0.11 -10000 0 -0.48 20 20
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.075 0.1 -10000 0 -0.24 2 2
MAPK14 -0.041 0.068 -10000 0 -0.24 8 8
TGM2/GTP -0.077 0.12 -10000 0 -0.42 15 15
MAPK11 -0.042 0.069 -10000 0 -0.24 10 10
ARHGEF1 -0.034 0.054 -10000 0 -0.18 9 9
GNAI2 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.065 0.11 -10000 0 -0.39 11 11
RAB11/GDP 0.026 0.006 -10000 0 -10000 0 0
ICAM1 -0.044 0.08 -10000 0 -0.28 10 10
cAMP biosynthetic process -0.069 0.11 -10000 0 -0.35 22 22
Gq family/GTP/EBP50 0.015 0.047 0.24 3 -0.34 4 7
actin cytoskeleton reorganization 0.028 0.019 -10000 0 -0.24 1 1
SRC -0.042 0.07 -10000 0 -10000 0 0
GNB5 0.025 0.006 -10000 0 -10000 0 0
GNB1 0.025 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.065 0.099 0.18 4 -0.28 24 28
VCAM1 -0.049 0.089 -10000 0 -0.39 9 9
TP beta/Gq family/GDP/G beta5/gamma2 -0.026 0.11 -10000 0 -0.61 9 9
platelet activation -0.054 0.092 -10000 0 -0.31 11 11
PGI2/IP 0.019 0.003 -10000 0 -10000 0 0
PRKACA -0.098 0.11 -10000 0 -0.21 204 204
Gq family/GDP/G beta5/gamma2 -0.033 0.11 -10000 0 -0.54 10 10
TXA2/TP beta/beta Arrestin2 -0.027 0.06 -10000 0 -0.33 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.094 0.1 -10000 0 -0.2 200 200
mol:DAG -0.067 0.12 -10000 0 -0.4 15 15
EGFR 0.023 0.022 -10000 0 -0.4 1 1
TXA2/TP alpha -0.089 0.14 -10000 0 -0.47 24 24
Gq family/GTP 0.01 0.05 0.28 2 -0.24 9 11
YES1 -0.069 0.078 -10000 0 -10000 0 0
GNAI2/GTP -0.073 0.095 -10000 0 -0.24 2 2
PGD2/DP -0.13 0.15 -10000 0 -0.28 211 211
SLC9A3R1 0.026 0.004 -10000 0 -10000 0 0
FYN -0.074 0.078 -10000 0 -10000 0 0
mol:NO 0.018 0.063 0.37 1 -0.42 8 9
GNA15 0.022 0.044 -10000 0 -0.42 4 4
PGK/cGMP 0.015 0.068 -10000 0 -0.25 25 25
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.045 0.1 -10000 0 -0.35 7 7
NOS3 0.018 0.064 0.37 1 -0.42 8 9
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.056 0.098 -10000 0 -0.34 11 11
PRKCB -0.079 0.12 -10000 0 -0.4 20 20
PRKCE -0.053 0.099 -10000 0 -0.34 11 11
PRKCD -0.058 0.1 -10000 0 -0.38 10 10
PRKCG -0.083 0.12 -10000 0 -0.4 15 15
muscle contraction -0.083 0.13 -10000 0 -0.48 13 13
PRKCZ -0.06 0.096 -10000 0 -0.34 11 11
ARR3 -0.009 0.035 -10000 0 -0.42 2 2
TXA2/TP beta -0.075 0.11 -10000 0 -0.25 3 3
PRKCQ -0.056 0.1 -10000 0 -0.34 13 13
MAPKKK cascade -0.078 0.13 -10000 0 -0.44 20 20
SELE -0.057 0.093 -10000 0 -0.3 11 11
TP beta/GNAI2/GDP/G beta/gamma -0.076 0.12 -10000 0 -0.34 11 11
ROCK1 0.021 0.023 -10000 0 -0.4 1 1
GNA14 0.024 0.029 -10000 0 -0.4 2 2
chemotaxis -0.086 0.14 -10000 0 -0.6 10 10
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.004 -10000 0 -10000 0 0
GNA11 0.024 0.029 -10000 0 -0.4 2 2
Rac1/GTP 0.017 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.022 0.044 -10000 0 -0.42 4 4
alphaV beta3 Integrin 0.035 0.032 -10000 0 -0.28 4 4
PTK2 0.013 0.07 -10000 0 -0.34 10 10
positive regulation of JNK cascade 0.025 0.069 -10000 0 -0.28 8 8
CDC42/GDP 0.053 0.097 -10000 0 -0.36 10 10
Rac1/GDP 0.048 0.096 -10000 0 -0.34 14 14
RAP1B 0.026 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.043 0.087 -10000 0 -0.35 7 7
nectin-3/I-afadin 0.029 0.054 -10000 0 -0.28 12 12
RAPGEF1 0.029 0.091 0.25 1 -0.38 10 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.003 0.086 -10000 0 -0.41 12 12
PDGFB-D/PDGFRB 0.022 0.044 -10000 0 -0.42 4 4
TLN1 -0.003 0.031 -10000 0 -0.28 3 3
Rap1/GTP 0.019 0.066 -10000 0 -0.3 6 6
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.012 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.029 0.054 -10000 0 -0.28 12 12
PVR 0.026 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.003 -10000 0 -10000 0 0
mol:GDP 0.046 0.11 -10000 0 -0.41 14 14
MLLT4 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.063 0.057 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.007 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.025 0.079 -10000 0 -0.28 14 14
PVRL1 0.026 0.003 -10000 0 -10000 0 0
PVRL3 0.014 0.071 -10000 0 -0.4 12 12
PVRL2 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.002 -10000 0 -10000 0 0
CLDN1 -0.38 0.13 0.37 1 -0.42 385 386
JAM-A/CLDN1 -0.21 0.094 -10000 0 -0.24 375 375
SRC 0.004 0.097 -10000 0 -0.44 15 15
ITGB3 0.022 0.041 -10000 0 -0.4 4 4
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.007 -10000 0 -10000 0 0
FARP2 0.047 0.11 -10000 0 -0.45 9 9
RAC1 0.024 0.008 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.043 0.049 -10000 0 -0.24 12 12
nectin-1/I-afadin 0.038 0.007 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.007 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.043 0.049 -10000 0 -0.24 12 12
CDC42/GTP/IQGAP1/filamentous actin 0.032 0.017 -10000 0 -0.24 1 1
F11R 0.026 0.004 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.025 0.069 -10000 0 -0.28 8 8
alphaV/beta3 Integrin/Talin 0.006 0.069 -10000 0 -0.3 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.007 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.007 -10000 0 -10000 0 0
PIP5K1C 0.001 0.034 -10000 0 -0.29 3 3
VAV2 0.04 0.12 -10000 0 -0.43 14 14
RAP1/GDP 0.056 0.091 -10000 0 -0.34 8 8
ITGAV 0.026 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.043 0.049 -10000 0 -0.24 12 12
nectin-3(dimer)/I-afadin/I-afadin 0.029 0.054 -10000 0 -0.28 12 12
Rac1/GTP 0.033 0.096 -10000 0 -0.34 14 14
PTPRM 0.005 0.037 -10000 0 -0.2 12 12
E-cadherin/beta catenin/alpha catenin 0.074 0.021 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.024 0.022 -10000 0 -0.4 1 1
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.054 0.061 -10000 0 -10000 0 0
SMARCC2 0.023 0.02 -10000 0 -10000 0 0
SMARCC1 0.023 0.021 -10000 0 -10000 0 0
TBX21 -0.1 0.18 0.32 1 -0.68 29 30
SUMO2 0.026 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.031 0.022 -10000 0 -0.41 1 1
FKBP4 0.027 0.017 0.37 1 -10000 0 1
FKBP5 0.025 0.021 -10000 0 -0.4 1 1
GR alpha/HSP90/FKBP51/HSP90 0.084 0.1 0.29 15 -0.3 8 23
PRL -0.044 0.092 -10000 0 -0.49 3 3
cortisol/GR alpha (dimer)/TIF2 0.16 0.18 0.51 39 -0.43 3 42
RELA -0.043 0.069 -10000 0 -0.22 1 1
FGG 0.079 0.17 0.44 20 -0.46 9 29
GR beta/TIF2 0.073 0.11 0.29 17 -0.31 15 32
IFNG -0.18 0.16 -10000 0 -0.55 35 35
apoptosis -0.004 0.15 0.47 14 -0.49 7 21
CREB1 0.024 0.025 -10000 0 -10000 0 0
histone acetylation -0.044 0.11 0.34 5 -0.35 18 23
BGLAP -0.044 0.087 -10000 0 -10000 0 0
GR/PKAc 0.057 0.14 0.29 10 -0.38 13 23
NF kappa B1 p50/RelA -0.07 0.12 -10000 0 -0.3 20 20
SMARCD1 0.023 0.021 -10000 0 -10000 0 0
MDM2 0.056 0.057 0.22 20 -0.26 1 21
GATA3 0.022 0.05 -10000 0 -0.4 5 5
AKT1 0.02 0.006 -10000 0 -10000 0 0
CSF2 -0.11 0.11 -10000 0 -0.42 7 7
GSK3B 0.027 0.007 -10000 0 -10000 0 0
NR1I3 -0.002 0.16 0.49 12 -0.77 5 17
CSN2 0.07 0.12 0.37 15 -0.42 2 17
BRG1/BAF155/BAF170/BAF60A 0.057 0.061 -10000 0 -0.27 5 5
NFATC1 0.019 0.031 -10000 0 -0.4 2 2
POU2F1 0.025 0.019 -10000 0 -10000 0 0
CDKN1A -0.013 0.12 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.023 0.022 -10000 0 -0.4 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.089 0.1 0.3 9 -0.33 3 12
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.003 0.14 0.44 12 -0.66 2 14
JUN -0.17 0.12 -10000 0 -0.4 38 38
IL4 -0.051 0.081 -10000 0 -0.45 3 3
CDK5R1 0.025 0.022 -10000 0 -0.42 1 1
PRKACA 0.026 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.15 -10000 0 -0.41 109 109
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.094 0.1 0.3 13 -0.3 5 18
cortisol/GR alpha (monomer) 0.19 0.21 0.59 42 -0.47 3 45
NCOA2 0.022 0.022 -10000 0 -0.4 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.07 0.051 -10000 0 -0.45 3 3
AP-1/NFAT1-c-4 -0.26 0.16 -10000 0 -0.55 55 55
AFP -0.13 0.1 -10000 0 -10000 0 0
SUV420H1 0.026 0.004 -10000 0 -10000 0 0
IRF1 0.09 0.1 0.4 9 -0.37 1 10
TP53 0.032 0.029 -10000 0 -0.48 1 1
PPP5C 0.026 0.003 -10000 0 -10000 0 0
KRT17 -0.3 0.16 -10000 0 -0.53 77 77
KRT14 -0.079 0.2 0.4 6 -1.1 11 17
TBP 0.032 0.008 -10000 0 -10000 0 0
CREBBP 0.03 0.075 0.32 8 -0.25 17 25
HDAC1 0.025 0.008 -10000 0 -10000 0 0
HDAC2 0.034 0.012 -10000 0 -10000 0 0
AP-1 -0.26 0.16 -10000 0 -0.55 57 57
MAPK14 0.027 0.007 -10000 0 -10000 0 0
MAPK10 -0.033 0.15 -10000 0 -0.4 59 59
MAPK11 0.023 0.033 -10000 0 -0.43 2 2
KRT5 -0.19 0.17 -10000 0 -0.57 33 33
interleukin-1 receptor activity 0.008 0.011 -10000 0 -10000 0 0
NCOA1 0.028 0.001 -10000 0 -10000 0 0
STAT1 0.031 0.022 -10000 0 -0.42 1 1
CGA -0.058 0.095 -10000 0 -0.41 4 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.074 0.14 0.32 27 -0.42 8 35
MAPK3 0.026 0.022 -10000 0 -0.4 1 1
MAPK1 0.026 0.009 -10000 0 -10000 0 0
ICAM1 -0.1 0.13 -10000 0 -0.52 9 9
NFKB1 -0.043 0.069 -10000 0 -0.22 2 2
MAPK8 -0.13 0.11 -10000 0 -0.38 27 27
MAPK9 0.027 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.006 0.16 0.48 14 -0.52 7 21
BAX -0.007 0.075 -10000 0 -10000 0 0
POMC -0.094 0.25 0.45 1 -1.3 14 15
EP300 0.028 0.078 0.31 8 -0.25 19 27
cortisol/GR alpha (dimer)/p53 0.16 0.19 0.52 39 -0.44 2 41
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.058 0.26 14 -0.23 1 15
SGK1 -0.017 0.3 -10000 0 -1.2 24 24
IL13 -0.13 0.12 -10000 0 -0.52 9 9
IL6 -0.12 0.18 0.34 1 -0.51 45 46
PRKACG -0.006 0.029 -10000 0 -0.42 1 1
IL5 -0.11 0.11 -10000 0 -0.6 3 3
IL2 -0.17 0.13 -10000 0 -0.57 14 14
CDK5 0.026 0.006 -10000 0 -10000 0 0
PRKACB -0.031 0.14 -10000 0 -0.4 56 56
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
IL8 -0.2 0.19 -10000 0 -0.45 95 95
CDK5R1/CDK5 0.037 0.021 -10000 0 -0.3 1 1
NF kappa B1 p50/RelA/PKAc -0.067 0.12 -10000 0 -0.34 15 15
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.17 0.18 0.51 39 -0.42 2 41
SMARCA4 0.023 0.02 -10000 0 -10000 0 0
chromatin remodeling 0.074 0.16 0.35 21 -0.48 18 39
NF kappa B1 p50/RelA/Cbp -0.021 0.13 0.36 5 -0.39 9 14
JUN (dimer) -0.17 0.11 -10000 0 -0.4 38 38
YWHAH 0.025 0.006 -10000 0 -10000 0 0
VIPR1 -0.096 0.18 -10000 0 -0.74 26 26
NR3C1 0.089 0.16 0.41 23 -0.4 22 45
NR4A1 0.007 0.12 -10000 0 -0.5 19 19
TIF2/SUV420H1 0.033 0.021 -10000 0 -0.28 1 1
MAPKKK cascade -0.004 0.15 0.47 14 -0.49 7 21
cortisol/GR alpha (dimer)/Src-1 0.18 0.18 0.51 44 -0.45 2 46
PBX1 0.013 0.073 -10000 0 -0.4 12 12
POU1F1 0.001 0.036 -10000 0 -0.51 1 1
SELE -0.13 0.17 -10000 0 -0.52 31 31
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.074 0.16 0.35 21 -0.48 18 39
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.17 0.18 0.51 39 -0.42 2 41
mol:cortisol 0.091 0.1 0.33 41 -10000 0 41
MMP1 -0.22 0.16 -10000 0 -0.84 7 7
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.026 0.002 -9999 0 -10000 0 0
ITGB7 0.011 0.079 -9999 0 -0.4 15 15
ITGA4 0.01 0.081 -9999 0 -0.4 16 16
alpha4/beta7 Integrin 0.016 0.088 -9999 0 -0.31 28 28
alpha4/beta1 Integrin 0.027 0.061 -9999 0 -0.28 16 16
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.038 0.021 0.26 1 -0.28 1 2
alphaV beta3 Integrin 0.029 0.08 -10000 0 -0.24 32 32
PTK2 0.027 0.11 0.3 13 -0.4 3 16
IGF1R 0.025 0.005 -10000 0 -10000 0 0
PI4KB 0.026 0.004 -10000 0 -10000 0 0
MFGE8 0.026 0.005 -10000 0 -10000 0 0
SRC 0.016 0.013 -10000 0 -10000 0 0
CDKN1B 0.009 0.047 -10000 0 -0.4 2 2
VEGFA 0.027 0.017 0.37 1 -10000 0 1
ILK 0.011 0.038 -10000 0 -10000 0 0
ROCK1 0.021 0.023 -10000 0 -0.4 1 1
AKT1 0.004 0.032 -10000 0 -10000 0 0
PTK2B -0.009 0.034 0.18 7 -10000 0 7
alphaV/beta3 Integrin/JAM-A 0.028 0.081 -10000 0 -0.4 2 2
CBL 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.044 0.033 -10000 0 -0.24 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.004 0.12 -10000 0 -0.22 96 96
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.033 0.15 1 -0.43 1 2
alphaV/beta3 Integrin/Syndecan-1 0.05 0.029 -10000 0 -0.24 4 4
PI4KA 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.032 0.14 -10000 0 -0.39 28 28
PI4 Kinase 0.037 0.01 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.1 0.15 -10000 0 -0.26 210 210
RPS6KB1 -0.077 0.11 -10000 0 -0.37 27 27
TLN1 0.026 0.004 -10000 0 -10000 0 0
MAPK3 -0.045 0.15 -10000 0 -0.51 36 36
GPR124 0.021 0.023 -10000 0 -0.4 1 1
MAPK1 -0.045 0.15 -10000 0 -0.5 37 37
PXN 0.026 0.002 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.019 0.092 -10000 0 -0.24 47 47
cell adhesion 0.039 0.034 -10000 0 -0.24 4 4
ANGPTL3 -0.003 0.03 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.032 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.025 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
TGFBR2 0.026 0.003 -10000 0 -10000 0 0
ITGB3 0.022 0.041 -10000 0 -0.4 4 4
IGF1 -0.08 0.18 -10000 0 -0.4 105 105
RAC1 0.024 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.041 0.036 -10000 0 -0.23 5 5
apoptosis 0.026 0.002 -10000 0 -10000 0 0
CD47 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.049 0.03 -10000 0 -0.24 4 4
VCL 0.026 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.002 0.12 -10000 0 -0.25 74 74
CSF1 0.025 0.021 -10000 0 -0.4 1 1
PIK3C2A 0.01 0.043 -10000 0 -0.4 1 1
PI4 Kinase/Pyk2 0.01 0.069 -10000 0 -0.36 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.061 0.036 0.26 1 -0.22 5 6
FAK1/Vinculin 0.04 0.1 0.25 23 -0.32 3 26
alphaV beta3/Integrin/ppsTEM5 0.042 0.036 -10000 0 -0.23 5 5
RHOA 0.026 0.004 -10000 0 -10000 0 0
VTN 0.007 0.072 -10000 0 -0.42 11 11
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
FGF2 -0.003 0.11 -10000 0 -0.4 29 29
F11R -0.008 0.073 -10000 0 -0.28 28 28
alphaV/beta3 Integrin/Lactadherin 0.048 0.03 -10000 0 -0.23 4 4
alphaV/beta3 Integrin/TGFBR2 0.049 0.03 -10000 0 -0.24 4 4
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.063 0.025 -10000 0 -0.22 2 2
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.046 0.028 -10000 0 -0.22 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.002 0.1 -10000 0 -0.42 23 23
alphaV/beta3 Integrin/Pyk2 0.035 0.039 -10000 0 -10000 0 0
SDC1 0.026 0.001 -10000 0 -10000 0 0
VAV3 -0.033 0.063 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.04 0.1 0.24 24 -0.32 3 27
cell migration 0.035 0.097 0.22 34 -0.3 3 37
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PI3K 0.041 0.083 -10000 0 -0.37 2 2
SPP1 -0.19 0.22 -10000 0 -0.42 206 206
KDR 0.025 0.021 -10000 0 -0.4 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.002 -10000 0 -10000 0 0
COL4A3 -0.025 0.13 -10000 0 -0.4 43 43
angiogenesis -0.04 0.16 -10000 0 -0.51 36 36
Rac1/GTP 0 0.067 -10000 0 -10000 0 0
EDIL3 -0.051 0.16 -10000 0 -0.4 76 76
cell proliferation 0.049 0.03 -10000 0 -0.24 4 4
Regulation of Androgen receptor activity

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
HDAC1 0.007 0.012 -10000 0 -10000 0 0
SMARCC1 0.012 0.011 -10000 0 -10000 0 0
REL 0.029 0.008 -10000 0 -10000 0 0
HDAC7 -0.023 0.085 -10000 0 -0.4 3 3
JUN 0.024 0.006 -10000 0 -10000 0 0
EP300 0.025 0.006 -10000 0 -10000 0 0
KAT2B 0.008 0.084 -10000 0 -0.4 17 17
KAT5 0.026 0.004 -10000 0 -10000 0 0
MAPK14 0 0.033 -10000 0 -0.31 3 3
FOXO1 0.019 0.023 -10000 0 -0.4 1 1
T-DHT/AR -0.005 0.1 -10000 0 -0.42 3 3
MAP2K6 0.014 0.041 -10000 0 -0.42 3 3
BRM/BAF57 0.025 0.033 -10000 0 -0.31 1 1
MAP2K4 0.015 0.019 -10000 0 -10000 0 0
SMARCA2 0.017 0.029 -10000 0 -0.42 1 1
PDE9A -0.16 0.39 -10000 0 -0.96 77 77
NCOA2 0.022 0.022 -10000 0 -0.4 1 1
CEBPA 0.023 0.036 -10000 0 -0.4 3 3
EHMT2 0.025 0.018 0.37 1 -10000 0 1
cell proliferation 0.032 0.13 0.24 30 -0.38 4 34
NR0B1 -0.008 0.05 -10000 0 -0.42 5 5
EGR1 0.018 0.027 -10000 0 -0.4 1 1
RXRs/9cRA -0.06 0.12 -10000 0 -0.22 157 157
AR/RACK1/Src 0.049 0.098 0.27 3 -0.3 3 6
AR/GR -0.018 0.089 -10000 0 -0.3 14 14
GNB2L1 0.026 0.003 -10000 0 -10000 0 0
PKN1 0.026 0.003 -10000 0 -10000 0 0
RCHY1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.011 1 1
MAPK8 0.002 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.005 0.062 -10000 0 -0.32 3 3
SRC 0.024 0.086 0.19 83 -0.26 3 86
NR3C1 -0.003 0.11 -10000 0 -0.4 29 29
KLK3 -0.23 0.43 -10000 0 -1.2 71 71
APPBP2 0.017 0.028 -10000 0 -0.4 1 1
TRIM24 0.017 0.019 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.006 0.057 0.2 2 -0.32 3 5
TMPRSS2 -0.017 0.13 -10000 0 -0.59 14 14
RXRG -0.15 0.2 -10000 0 -0.4 158 158
mol:9cRA -0.001 0.002 -10000 0 -0.009 2 2
RXRA 0.025 0.021 -10000 0 -0.4 1 1
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.026 0.003 -10000 0 -10000 0 0
NR2C2 0.026 0.004 -10000 0 -10000 0 0
KLK2 0.023 0.084 -10000 0 -10000 0 0
AR -0.011 0.063 0.16 1 -0.25 22 23
SENP1 0.026 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
MDM2 0.03 0.024 -10000 0 -0.4 1 1
SRY 0.004 0.011 0.028 74 -10000 0 74
GATA2 0.017 0.061 -10000 0 -0.4 9 9
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.14 0.22 0.37 3 -0.43 150 153
T-DHT/AR/RACK1/Src 0.057 0.1 0.27 6 -0.32 3 9
positive regulation of transcription 0.017 0.061 -10000 0 -0.4 9 9
DNAJA1 0.018 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.016 -10000 0 -0.29 1 1
NCOA1 0.023 0.019 -10000 0 -10000 0 0
SPDEF -0.061 0.17 -10000 0 -0.4 81 81
T-DHT/AR/TIF2 -0.003 0.067 -10000 0 -0.28 7 7
T-DHT/AR/Hsp90 -0.007 0.054 0.2 1 -0.32 3 4
GSK3B 0.025 0.004 -10000 0 -10000 0 0
NR2C1 0.027 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.035 0.22 1 -0.27 3 4
SIRT1 0.026 0.004 -10000 0 -10000 0 0
ZMIZ2 0.028 0.015 -10000 0 -10000 0 0
POU2F1 0.014 0.051 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.016 0.058 -10000 0 -0.33 3 3
CREBBP 0.026 0.004 -10000 0 -10000 0 0
SMARCE1 0.018 0.019 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.005 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.02 0.08 -10000 0 -0.22 38 38
regulation of S phase of mitotic cell cycle 0.006 0.04 -10000 0 -0.2 13 13
GNAO1 -0.088 0.19 -10000 0 -0.4 114 114
HRAS 0.025 0.021 -10000 0 -0.4 1 1
SHBG/T-DHT 0.011 0.034 -10000 0 -0.32 4 4
PELP1 0.022 0.01 -10000 0 -10000 0 0
AKT1 0.006 0.002 -10000 0 -10000 0 0
MAP2K1 0.047 0.097 0.2 35 -10000 0 35
T-DHT/AR 0.001 0.069 -10000 0 -0.28 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.009 7 7
GNAI2 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.011 0.076 -10000 0 -0.4 14 14
mol:GDP -0.014 0.07 -10000 0 -0.3 22 22
cell proliferation 0.043 0.1 0.29 2 -0.37 4 6
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
FOS 0.034 0.12 0.26 1 -0.74 7 8
mol:Ca2+ -0.013 0.029 -10000 0 -0.078 42 42
MAPK3 0.047 0.098 0.3 4 -0.32 1 5
MAPK1 0.022 0.096 0.21 1 -0.36 16 17
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 7 7
cAMP biosynthetic process 0.006 0.038 0.11 1 -0.29 4 5
GNG2 0.009 0.081 -10000 0 -0.4 16 16
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 7 7
HRAS/GTP 0.019 0.05 -10000 0 -0.21 2 2
actin cytoskeleton reorganization 0.033 0.02 -10000 0 -0.19 1 1
SRC 0.016 0.013 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 7 7
PI3K 0.034 0.007 -10000 0 -10000 0 0
apoptosis -0.043 0.092 0.36 7 -0.27 1 8
T-DHT/AR/PELP1 0.014 0.062 -10000 0 -0.23 24 24
HRAS/GDP -0.003 0.071 -10000 0 -0.3 18 18
CREB1 0.043 0.095 0.28 1 -0.38 7 8
RAC1-CDC42/GTP 0.041 0.024 -10000 0 -0.2 1 1
AR -0.005 0.098 -10000 0 -0.4 24 24
GNB1 0.025 0.006 -10000 0 -10000 0 0
RAF1 0.063 0.097 0.2 29 -10000 0 29
RAC1-CDC42/GDP 0.035 0.085 -10000 0 -0.33 13 13
T-DHT/AR/PELP1/Src 0.018 0.052 -10000 0 -0.22 15 15
MAP2K2 0.048 0.098 0.19 37 -0.35 1 38
T-DHT/AR/PELP1/Src/PI3K 0.006 0.04 -10000 0 -0.2 13 13
GNAZ 0.021 0.042 -10000 0 -0.4 4 4
SHBG 0.01 0.056 -10000 0 -0.52 4 4
Gi family/GNB1/GNG2/GDP -0.076 0.19 -10000 0 -0.38 92 92
mol:T-DHT 0 0.001 -10000 0 -0.005 7 7
RAC1 0.024 0.008 -10000 0 -10000 0 0
GNRH1 0.005 0.004 -10000 0 -10000 0 0
Gi family/GTP -0.05 0.11 -10000 0 -0.3 45 45
CDC42 0.024 0.022 -10000 0 -0.4 1 1
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.021 -9999 0 -0.4 1 1
EGFR 0.023 0.022 -9999 0 -0.4 1 1
EGF/EGFR -0.009 0.11 -9999 0 -0.26 26 26
EGF/EGFR dimer/SHC/GRB2/SOS1 0.018 0.1 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.004 0.098 -9999 0 -0.42 21 21
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.061 0.17 -9999 0 -0.4 82 82
EGF/EGFR dimer/SHC -0.004 0.11 -9999 0 -0.24 71 71
mol:GDP 0.013 0.1 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.023 0.036 -9999 0 -0.4 3 3
GRB2/SOS1 0.038 0.007 -9999 0 -10000 0 0
HRAS/GTP 0.001 0.089 -9999 0 -10000 0 0
SHC1 0.026 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.013 0.098 -9999 0 -10000 0 0
FRAP1 -0.042 0.07 -9999 0 -10000 0 0
EGF/EGFR dimer -0.022 0.12 -9999 0 -0.29 73 73
SOS1 0.026 0.002 -9999 0 -10000 0 0
GRB2 0.026 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.019 0.078 -9999 0 -0.3 24 24
Caspase cascade in apoptosis

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
TOP1 -0.035 0.1 -10000 0 -0.33 24 24
ACTA1 -0.052 0.1 -10000 0 -0.34 23 23
NUMA1 -0.034 0.11 -10000 0 -0.37 21 21
SPTAN1 -0.053 0.098 -10000 0 -0.34 21 21
LIMK1 -0.046 0.1 0.27 3 -0.35 18 21
BIRC3 0.018 0.058 -10000 0 -0.4 8 8
BIRC2 0.026 0.005 -10000 0 -10000 0 0
BAX 0.026 0.003 -10000 0 -10000 0 0
CASP10 -0.074 0.12 -10000 0 -0.27 106 106
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
PTK2 -0.034 0.1 -10000 0 -0.33 26 26
DIABLO 0.026 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.052 0.097 -10000 0 -0.34 21 21
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.003 -10000 0 -10000 0 0
GSN -0.056 0.1 -10000 0 -0.35 25 25
MADD 0.026 0.003 -10000 0 -10000 0 0
TFAP2A 0.002 0.083 -10000 0 -0.57 7 7
BID -0.027 0.062 -10000 0 -0.22 17 17
MAP3K1 -0.019 0.075 -10000 0 -0.4 11 11
TRADD 0.026 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.052 0.099 -10000 0 -0.34 22 22
CASP9 0.025 0.006 -10000 0 -10000 0 0
DNA repair 0.008 0.041 0.2 2 -0.15 3 5
neuron apoptosis -0.015 0.16 -10000 0 -0.69 21 21
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.044 0.11 -10000 0 -0.37 21 21
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 -0.019 0.14 -10000 0 -0.87 10 10
TRAF2 0.025 0.021 -10000 0 -0.4 1 1
ICAD/CAD -0.051 0.095 -10000 0 -0.36 14 14
CASP7 0.002 0.058 0.24 7 -0.23 15 22
KRT18 0.012 0.028 -10000 0 -10000 0 0
apoptosis -0.047 0.11 0.34 1 -0.38 23 24
DFFA -0.053 0.097 -10000 0 -0.34 21 21
DFFB -0.052 0.098 -10000 0 -0.34 21 21
PARP1 -0.008 0.042 -10000 0 -0.2 2 2
actin filament polymerization 0.045 0.095 0.34 14 -0.3 1 15
TNF 0.024 0.03 -10000 0 -0.4 2 2
CYCS -0.013 0.055 0.19 1 -0.2 6 7
SATB1 -0.023 0.14 -10000 0 -0.82 10 10
SLK -0.053 0.099 0.34 1 -0.34 21 22
p15 BID/BAX -0.017 0.067 -10000 0 -0.22 13 13
CASP2 0.022 0.049 0.21 15 -10000 0 15
JNK cascade 0.019 0.074 0.4 11 -10000 0 11
CASP3 -0.054 0.1 -10000 0 -0.35 22 22
LMNB2 0.014 0.095 0.28 1 -0.62 5 6
RIPK1 0.026 0.003 -10000 0 -10000 0 0
CASP4 0.026 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.061 0.041 -10000 0 -0.22 8 8
negative regulation of DNA binding 0.003 0.083 -10000 0 -0.57 7 7
stress fiber formation -0.052 0.098 0.34 1 -0.34 21 22
GZMB -0.071 0.15 -10000 0 -0.32 106 106
CASP1 0.013 0.014 -10000 0 -0.28 1 1
LMNB1 0.009 0.1 0.23 2 -0.41 14 16
APP -0.016 0.16 -10000 0 -0.7 21 21
TNFRSF1A 0.026 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0 -10000 0 -10000 0 0
VIM -0.044 0.11 -10000 0 -0.38 24 24
LMNA 0.019 0.062 0.23 2 -0.27 4 6
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.021 0.034 -10000 0 -0.22 1 1
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.048 0.096 -10000 0 -0.34 20 20
APAF-1/Caspase 9 -0.02 0.15 -10000 0 -0.62 23 23
nuclear fragmentation during apoptosis -0.034 0.11 -10000 0 -0.36 21 21
CFL2 -0.046 0.096 0.3 1 -0.34 14 15
GAS2 -0.087 0.13 -10000 0 -0.38 44 44
positive regulation of apoptosis 0.018 0.086 0.2 11 -0.4 11 22
PRF1 0.019 0.055 -10000 0 -0.4 7 7
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.005 0.064 -10000 0 -0.4 10 10
GNB1/GNG2 -0.023 0.11 -10000 0 -0.32 18 18
mol:DAG -0.022 0.08 0.19 1 -0.32 12 13
PLCG1 -0.022 0.082 0.19 1 -0.32 12 13
YES1 -0.031 0.088 -10000 0 -0.3 19 19
FZD3 0.021 0.034 0.37 2 -0.42 1 3
FZD6 0.023 0.009 -10000 0 -10000 0 0
G protein 0.024 0.12 0.28 8 -0.35 9 17
MAP3K7 -0.03 0.076 -10000 0 -0.33 6 6
mol:Ca2+ -0.021 0.078 0.19 1 -0.31 12 13
mol:IP3 -0.022 0.08 0.19 1 -0.32 12 13
NLK -0.001 0.082 -10000 0 -0.74 5 5
GNB1 0.025 0.006 -10000 0 -10000 0 0
CAMK2A -0.029 0.082 0.18 1 -0.32 11 12
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.027 0.098 0.17 1 -0.31 23 24
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
GNAS -0.017 0.085 0.33 1 -0.33 13 14
GO:0007205 -0.025 0.078 0.18 1 -0.32 10 11
WNT6 -0.003 0.1 -10000 0 -0.41 24 24
WNT4 0.004 0.091 -10000 0 -0.4 20 20
NFAT1/CK1 alpha -0.014 0.089 -10000 0 -0.4 7 7
GNG2 0.009 0.081 -10000 0 -0.4 16 16
WNT5A 0.022 0.044 -10000 0 -0.42 4 4
WNT11 -0.065 0.18 -10000 0 -0.42 86 86
CDC42 -0.031 0.085 -10000 0 -0.33 11 11
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.044 -10000 0 -0.42 4 4
Jak2/Leptin Receptor 0.02 0.086 -10000 0 -0.36 9 9
PTP1B/AKT1 0.017 0.073 -10000 0 -0.32 3 3
FYN 0.026 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.014 0.08 0.2 8 -0.32 4 12
EGFR 0.017 0.027 -10000 0 -0.4 1 1
EGF/EGFR -0.012 0.11 -10000 0 -0.28 28 28
CSF1 0.025 0.021 -10000 0 -0.4 1 1
AKT1 0.025 0.007 -10000 0 -10000 0 0
INSR 0.027 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.005 0.081 0.21 3 -0.29 9 12
Insulin Receptor/Insulin 0.022 0.068 -10000 0 -0.32 2 2
HCK 0.011 0.047 -10000 0 -0.4 5 5
CRK 0.022 0.01 -10000 0 -10000 0 0
TYK2 0.012 0.078 0.25 6 -0.33 3 9
EGF -0.058 0.17 -10000 0 -0.41 82 82
YES1 0.021 0.023 -10000 0 -0.4 1 1
CAV1 0.025 0.1 0.22 32 -0.31 4 36
TXN 0.026 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.028 0.083 -10000 0 -0.36 2 2
cell migration -0.014 0.08 0.32 4 -0.2 8 12
STAT3 0.026 0.004 -10000 0 -10000 0 0
PRLR 0.015 0.065 -10000 0 -0.4 10 10
ITGA2B 0.003 0.09 -10000 0 -0.42 18 18
CSF1R 0.001 0.1 -10000 0 -0.4 25 25
Prolactin Receptor/Prolactin 0.016 0.075 -10000 0 -0.3 21 21
FGR 0.021 0.042 -10000 0 -0.4 4 4
PTP1B/p130 Cas 0.02 0.081 0.21 3 -0.33 3 6
Crk/p130 Cas 0.018 0.078 -10000 0 -0.35 2 2
DOK1 0.017 0.073 0.21 2 -0.33 3 5
JAK2 0.015 0.086 0.22 1 -0.32 14 15
Jak2/Leptin Receptor/Leptin 0.018 0.091 -10000 0 -0.33 4 4
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0.014 0.08 0.2 8 -0.32 4 12
LYN 0.023 0.009 -10000 0 -10000 0 0
CDH2 0.003 0.084 -10000 0 -0.4 17 17
SRC 0.026 0.082 -10000 0 -0.41 8 8
ITGB3 0.022 0.041 -10000 0 -0.4 4 4
CAT1/PTP1B 0.003 0.16 0.24 51 -0.43 15 66
CAPN1 0.025 0.004 -10000 0 -10000 0 0
CSK 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.04 0.064 -10000 0 -0.34 1 1
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.02 0.084 -10000 0 -0.35 1 1
negative regulation of transcription 0.015 0.085 0.22 1 -0.32 14 15
FCGR2A 0.024 0.031 -10000 0 -0.42 2 2
FER 0.025 0.006 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.019 0.074 -10000 0 -0.3 22 22
BLK -0.1 0.19 -10000 0 -0.4 121 121
Insulin Receptor/Insulin/Shc 0.044 0.013 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
LEPR 0.02 0.046 -10000 0 -0.4 5 5
BCAR1 0.025 0.021 -10000 0 -0.4 1 1
p210 bcr-abl/Grb2 0.026 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.069 0.18 0.24 13 -0.4 59 72
PRL -0.009 0.074 -10000 0 -0.42 12 12
SOCS3 0.01 0.12 -10000 0 -1.1 5 5
SPRY2 0.021 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.045 0.011 -10000 0 -10000 0 0
CSF1/CSF1R 0.015 0.096 0.26 1 -0.34 7 8
Ras protein signal transduction -0.004 0.062 0.46 6 -10000 0 6
IRS1 0.026 0.002 -10000 0 -10000 0 0
INS -0.005 0.017 -10000 0 -10000 0 0
LEP -0.02 0.11 -10000 0 -0.4 31 31
STAT5B 0.02 0.077 0.19 6 -0.31 5 11
STAT5A 0.02 0.077 0.19 5 -0.31 5 10
GRB2 0.026 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.085 0.21 4 -0.32 6 10
CSN2 -0.007 0.05 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
LAT 0.028 0.06 -10000 0 -0.46 4 4
YBX1 0.035 0.008 -10000 0 -10000 0 0
LCK 0.016 0.064 -10000 0 -0.42 9 9
SHC1 0.026 0.004 -10000 0 -10000 0 0
NOX4 -0.21 0.23 0.36 1 -0.42 218 219
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.015 -10000 0 -0.28 1 1
MAP4K4 0.016 0.037 -10000 0 -0.23 1 1
BAG4 0.022 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.016 0.068 -10000 0 -0.19 46 46
NFKBIA 0.025 0.007 -10000 0 -10000 0 0
BIRC3 0.018 0.058 -10000 0 -0.4 8 8
BAX -0.004 0.04 -10000 0 -0.34 3 3
RIPK1 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.002 0.012 -10000 0 -10000 0 0
BAD -0.031 0.061 -10000 0 -0.19 46 46
SMPD1 0.019 0.049 0.21 1 -0.24 5 6
RB1 0.014 0.093 0.19 65 -0.19 26 91
FADD/Caspase 8 0.023 0.036 0.2 1 -10000 0 1
MAP2K4 -0.029 0.058 -10000 0 -0.22 10 10
NSMAF 0.023 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.026 0.064 0.18 7 -0.23 8 15
EGF -0.061 0.17 -10000 0 -0.4 82 82
mol:ceramide -0.03 0.065 -10000 0 -0.2 47 47
MADD 0.026 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.006 -10000 0 -10000 0 0
ASAH1 0.02 0.011 -10000 0 -10000 0 0
negative regulation of cell cycle 0.013 0.092 0.19 65 -0.19 26 91
cell proliferation -0.046 0.099 -10000 0 -0.31 11 11
BID -0.002 0.13 -10000 0 -0.6 18 18
MAP3K1 -0.031 0.062 -10000 0 -0.19 48 48
EIF2A -0.031 0.059 0.17 1 -0.22 8 9
TRADD 0.026 0.002 -10000 0 -10000 0 0
CRADD 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.023 0.061 0.18 7 -0.22 7 14
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.027 0.063 0.17 5 -0.23 9 14
Cathepsin D/ceramide -0.017 0.068 -10000 0 -0.19 47 47
FADD 0.017 0.037 0.2 1 -0.23 1 2
KSR1 -0.026 0.067 0.18 8 -0.19 45 53
MAPK8 -0.025 0.067 -10000 0 -0.23 10 10
PRKRA -0.031 0.061 -10000 0 -0.19 47 47
PDGFA 0.024 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.021 -10000 0 -0.4 1 1
IGF1 -0.08 0.18 -10000 0 -0.4 105 105
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.03 0.065 -10000 0 -0.2 47 47
CTSD 0.025 0.021 -10000 0 -0.4 1 1
regulation of nitric oxide biosynthetic process 0.038 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.048 0.1 -10000 0 -0.33 11 11
PRKCD 0.026 0.004 -10000 0 -10000 0 0
PRKCZ 0.025 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.038 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.021 0.031 -10000 0 -0.25 1 1
TNFR1A/BAG4/TNF-alpha 0.043 0.028 -10000 0 -0.24 2 2
mol:Sphingosine-1-phosphate 0.011 0.015 -10000 0 -0.28 1 1
MAP2K1 -0.027 0.061 0.18 7 -0.22 7 14
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
CYCS 0.017 0.05 0.16 7 -10000 0 7
TNFRSF1A 0.026 0.004 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.033 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.031 0.06 0.18 1 -0.23 9 10
TNF-alpha/TNFR1A/FAN 0.044 0.028 -10000 0 -0.24 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.029 0.044 -10000 0 -0.29 1 1
MAP2K2 -0.027 0.062 0.17 8 -0.22 7 15
SMPD3 0.019 0.057 0.19 1 -0.3 9 10
TNF 0.024 0.03 -10000 0 -0.4 2 2
PKC zeta/PAR4 0.037 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.026 0.082 0.19 59 -10000 0 59
NF kappa B1/RelA/I kappa B alpha 0.067 0.028 -10000 0 -10000 0 0
AIFM1 0.009 0.059 0.15 7 -0.15 4 11
BCL2 0.011 0.062 -10000 0 -0.4 9 9
Signaling events mediated by HDAC Class III

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
EP300 0.025 0.006 -10000 0 -10000 0 0
HDAC4 0.026 0.002 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.008 0.034 0.3 4 -0.27 1 5
CDKN1A -0.009 0.037 -10000 0 -0.53 2 2
KAT2B 0.009 0.084 -10000 0 -0.4 17 17
BAX 0.026 0.003 -10000 0 -10000 0 0
FOXO3 -0.005 0.003 -10000 0 -10000 0 0
FOXO1 0.019 0.023 -10000 0 -0.4 1 1
FOXO4 0.014 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.025 0.006 -10000 0 -10000 0 0
TAT -0.14 0.2 -10000 0 -0.4 157 157
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.026 0.054 -10000 0 -0.29 17 17
PPARGC1A -0.029 0.14 -10000 0 -0.4 55 55
FHL2 0.026 0.021 -10000 0 -0.4 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.035 0.011 -10000 0 -10000 0 0
HIST2H4A 0.008 0.034 0.27 1 -0.3 4 5
SIRT1/FOXO3a 0.017 0.025 -10000 0 -0.2 2 2
SIRT1 0.024 0.01 0.2 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.013 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.015 0.044 -10000 0 -0.2 3 3
apoptosis -0.048 0.015 -10000 0 -10000 0 0
SIRT1/PGC1A -0.002 0.09 -10000 0 -0.24 54 54
p53/SIRT1 0.026 0.021 0.37 1 -10000 0 1
SIRT1/FOXO4 0.022 0.031 -10000 0 -0.2 2 2
FOXO1/FHL2/SIRT1 0.036 0.028 -10000 0 -0.22 2 2
HIST1H1E 0.006 0.035 0.2 2 -0.24 1 3
SIRT1/p300 0.035 0.012 -10000 0 -10000 0 0
muscle cell differentiation -0.018 0.056 0.24 17 -0.21 3 20
TP53 0.02 0.012 0.2 1 -10000 0 1
KU70/SIRT1/BAX 0.048 0.015 -10000 0 -10000 0 0
CREBBP 0.026 0.004 -10000 0 -10000 0 0
MEF2D 0.026 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.084 0.15 -10000 0 -0.28 156 156
ACSS2 0.007 0.018 0.35 1 -10000 0 1
SIRT1/PCAF/MYOD 0.018 0.056 0.21 3 -0.24 17 20
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.023 0.036 -10000 0 -0.4 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.013 0.012 -10000 0 -0.18 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.021 0.023 -10000 0 -0.4 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
MAP3K12 0.026 0.002 -10000 0 -10000 0 0
FGR 0.021 0.042 -10000 0 -0.4 4 4
p38 alpha/TAB1 -0.061 0.11 -10000 0 -0.32 49 49
PRKG1 0.005 0.088 -10000 0 -0.4 19 19
DUSP8 0.025 0.021 -10000 0 -0.4 1 1
PGK/cGMP/p38 alpha -0.029 0.14 0.16 9 -0.34 45 54
apoptosis -0.059 0.1 -10000 0 -0.3 49 49
RAL/GTP 0.032 0.011 -10000 0 -10000 0 0
LYN 0.023 0.009 -10000 0 -10000 0 0
DUSP1 0.023 0.036 -10000 0 -0.4 3 3
PAK1 0.026 0.003 -10000 0 -10000 0 0
SRC 0.016 0.013 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.05 0.032 -10000 0 -0.22 1 1
TRAF6 0.026 0.003 -10000 0 -10000 0 0
RAC1 0.024 0.008 -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 0.023 0.022 -10000 0 -0.4 1 1
RAC1-CDC42/GTP 0.029 0.019 -10000 0 -0.24 1 1
MAPK11 -0.009 0.14 0.22 33 -0.35 25 58
BLK -0.1 0.19 -10000 0 -0.4 121 121
HCK 0.011 0.047 -10000 0 -0.4 5 5
MAP2K3 0.023 0.009 -10000 0 -10000 0 0
DUSP16 0.026 0.004 -10000 0 -10000 0 0
DUSP10 0.022 0.044 -10000 0 -0.42 4 4
TRAF6/MEKK3 0.033 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.02 0.15 0.2 29 -0.35 46 75
positive regulation of innate immune response -0.021 0.17 0.25 31 -0.41 36 67
LCK 0.016 0.064 -10000 0 -0.42 9 9
p38alpha-beta/MKP7 -0.012 0.17 0.25 30 -0.4 34 64
p38alpha-beta/MKP5 -0.012 0.17 0.26 27 -0.4 34 61
PGK/cGMP 0.005 0.062 -10000 0 -0.28 19 19
PAK2 0.026 0.002 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.014 0.17 0.25 29 -0.4 34 63
CDC42 0.024 0.022 -10000 0 -0.4 1 1
RALB 0.026 0.001 -10000 0 -10000 0 0
RALA 0.024 0.008 -10000 0 -10000 0 0
PAK3 0.008 0.022 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.01 0.018 0.1 6 -0.12 1 7
BUB1B 0.019 0.037 -10000 0 -0.13 1 1
PLK1 0.024 0.027 0.068 59 -0.099 2 61
PLK1S1 0.023 0.047 0.098 53 -0.17 13 66
KIF2A 0.018 0.027 0.25 1 -10000 0 1
regulation of mitotic centrosome separation 0.023 0.027 0.068 59 -0.099 2 61
GOLGA2 0.026 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.038 0.042 -10000 0 -0.19 8 8
WEE1 0.032 0.035 -10000 0 -0.3 1 1
cytokinesis 0.025 0.034 0.19 1 -10000 0 1
PP2A-alpha B56 0.052 0.086 -10000 0 -0.5 9 9
AURKA 0.025 0.022 -10000 0 -10000 0 0
PICH/PLK1 0.019 0.048 0.18 13 -0.19 3 16
CENPE 0.017 0.027 -10000 0 -0.22 1 1
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.019 0.027 0.25 1 -10000 0 1
PPP2CA 0.026 0.004 -10000 0 -10000 0 0
FZR1 0.025 0.021 -10000 0 -0.4 1 1
TPX2 0.04 0.04 0.1 62 -10000 0 62
PAK1 0.027 0.004 -10000 0 -10000 0 0
SPC24 0.019 0.064 0.37 1 -0.42 8 9
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN 0.014 0.043 -10000 0 -0.21 13 13
GORASP1 0.026 0.003 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 4 -0.011 1 5
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.011 0.015 0.037 59 -0.052 2 61
G2 phase of mitotic cell cycle 0.001 0.003 0.014 6 -10000 0 6
STAG2 0.026 0.001 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.014 0.046 -10000 0 -0.44 4 4
spindle elongation 0.023 0.027 0.068 59 -0.099 2 61
ODF2 0.029 0.004 -10000 0 -10000 0 0
BUB1 0.016 0.083 -10000 0 -0.54 9 9
TPT1 0.027 0.039 0.11 3 -0.16 7 10
CDC25C 0.019 0.037 -10000 0 -0.24 7 7
CDC25B 0.019 0.091 0.36 11 -0.42 11 22
SGOL1 0.01 0.018 0.12 1 -0.1 6 7
RHOA 0.026 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.036 0.049 0.24 11 -10000 0 11
CDC14B 0.006 0.014 -10000 0 -0.28 1 1
CDC20 0.026 0.004 -10000 0 -10000 0 0
PLK1/PBIP1 0.017 0.021 -10000 0 -10000 0 0
mitosis -0.001 0.001 -10000 0 -10000 0 0
FBXO5 0.018 0.029 0.13 1 -10000 0 1
CDC2 0.002 0.003 0.015 11 -10000 0 11
NDC80 0.022 0.01 -10000 0 -10000 0 0
metaphase plate congression 0.005 0.066 -10000 0 -0.22 32 32
ERCC6L 0.02 0.046 0.2 11 -0.24 1 12
NLP/gamma Tubulin 0.012 0.015 0.071 4 -10000 0 4
microtubule cytoskeleton organization 0.027 0.039 0.11 3 -0.16 7 10
G2/M transition DNA damage checkpoint 0 0.002 0.014 6 -10000 0 6
PPP1R12A 0.025 0.03 -10000 0 -0.4 2 2
interphase 0 0.002 0.014 6 -10000 0 6
PLK1/PRC1-2 0.048 0.026 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.059 0.024 -10000 0 -10000 0 0
RAB1A 0.026 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.027 0.03 0.064 154 -10000 0 154
mitotic prometaphase 0.001 0.005 0.018 32 -10000 0 32
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.026 -10000 0 -10000 0 0
microtubule-based process 0.035 0.026 -10000 0 -10000 0 0
Golgi organization 0.023 0.027 0.068 59 -0.099 2 61
Cohesin/SA2 0.034 0.021 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.038 0.031 -10000 0 -0.4 2 2
KIF20A 0.026 0.004 -10000 0 -10000 0 0
APC/C/CDC20 0.036 0.026 -10000 0 -10000 0 0
PPP2R1A 0.026 0.003 -10000 0 -10000 0 0
chromosome segregation 0.017 0.02 -10000 0 -10000 0 0
PRC1 0.025 0.005 -10000 0 -10000 0 0
ECT2 0.017 0.032 0.24 1 -0.2 3 4
C13orf34 0.022 0.025 0.063 59 -0.071 2 61
NUDC 0.005 0.066 -10000 0 -0.22 32 32
regulation of attachment of spindle microtubules to kinetochore 0.019 0.037 -10000 0 -0.13 1 1
spindle assembly 0.018 0.023 0.089 7 -0.085 2 9
spindle stabilization 0.023 0.047 0.098 53 -0.17 13 66
APC/C/HCDH1 0.023 0.019 -10000 0 -0.24 2 2
MKLP2/PLK1 0.035 0.026 -10000 0 -10000 0 0
CCNB1 0.026 0.01 -10000 0 -10000 0 0
PPP1CB 0.026 0.021 -10000 0 -0.41 1 1
BTRC 0.025 0.006 -10000 0 -10000 0 0
ROCK2 0.025 0.036 -10000 0 -0.36 2 2
TUBG1 0.018 0.017 0.096 1 -0.13 1 2
G2/M transition of mitotic cell cycle 0.013 0.04 0.18 11 -10000 0 11
MLF1IP 0.006 0.003 -10000 0 -10000 0 0
INCENP 0.027 0.004 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.039 0.021 0.26 1 -0.28 1 2
PDGFRB 0.023 0.044 -10000 0 -0.42 4 4
SPHK1 -0.002 0.055 -10000 0 -0.6 3 3
mol:S1P -0.005 0.05 -10000 0 -0.5 3 3
S1P1/S1P/Gi -0.042 0.16 0.24 2 -0.4 36 38
GNAO1 -0.088 0.19 -10000 0 -0.4 114 114
PDGFB-D/PDGFRB/PLCgamma1 0.009 0.16 0.28 15 -0.4 20 35
PLCG1 -0.045 0.13 0.29 6 -0.38 28 34
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.044 -10000 0 -0.42 4 4
GNAI2 0.027 0.007 -10000 0 -10000 0 0
GNAI3 0.026 0.007 -10000 0 -10000 0 0
GNAI1 0.012 0.077 -10000 0 -0.4 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.005 0.017 0.2 1 -0.22 1 2
S1P1/S1P 0.02 0.06 0.22 2 -0.29 3 5
negative regulation of cAMP metabolic process -0.04 0.15 0.24 2 -0.39 36 38
MAPK3 -0.046 0.16 0.26 2 -0.47 27 29
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
KDR 0.025 0.021 -10000 0 -0.4 1 1
PLCB2 0.022 0.062 0.24 6 -0.32 1 7
RAC1 0.024 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.048 -10000 0 -0.26 3 3
receptor internalization 0.018 0.056 0.21 1 -0.27 3 4
PTGS2 -0.044 0.18 -10000 0 -0.65 14 14
Rac1/GTP 0.013 0.047 -10000 0 -0.26 3 3
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.027 0.017 0.37 1 -10000 0 1
negative regulation of T cell proliferation -0.04 0.15 0.24 2 -0.39 36 38
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.022 0.042 -10000 0 -0.4 4 4
MAPK1 -0.042 0.16 0.27 1 -0.48 24 25
S1P1/S1P/PDGFB-D/PDGFRB 0.04 0.081 0.24 7 -0.28 2 9
ABCC1 0.027 0.004 -10000 0 -10000 0 0
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 0.004 0.044 0.23 14 -10000 0 14
RFC1 0.002 0.039 0.22 11 -10000 0 11
PRKDC 0.019 0.073 0.24 40 -10000 0 40
RIPK1 0.027 0.004 -10000 0 -10000 0 0
CASP7 0.005 0.1 -10000 0 -0.55 11 11
FASLG/FAS/FADD/FAF1 0.004 0.066 0.21 11 -0.23 19 30
MAP2K4 -0.018 0.097 -10000 0 -0.33 18 18
mol:ceramide 0 0.083 -10000 0 -0.29 25 25
GSN 0.001 0.046 0.24 11 -0.22 3 14
FASLG/FAS/FADD/FAF1/Caspase 8 0 0.074 0.27 1 -0.28 18 19
FAS 0.022 0.031 -10000 0 -0.41 2 2
BID -0.009 0.05 0.25 14 -0.26 1 15
MAP3K1 0.004 0.084 0.21 5 -0.37 11 16
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
RB1 0.027 0.079 0.22 56 -10000 0 56
CFLAR 0.027 0.002 -10000 0 -10000 0 0
HGF/MET 0.032 0.072 -10000 0 -0.26 23 23
ARHGDIB 0.002 0.039 0.21 13 -10000 0 13
FADD 0.025 0.007 -10000 0 -10000 0 0
actin filament polymerization 0.002 0.053 0.22 3 -0.24 11 14
NFKB1 -0.004 0.11 -10000 0 -0.7 9 9
MAPK8 -0.025 0.1 -10000 0 -0.4 14 14
DFFA 0.001 0.034 0.21 9 -10000 0 9
DNA fragmentation during apoptosis -0.001 0.047 0.22 12 -10000 0 12
FAS/FADD/MET 0.044 0.041 0.26 1 -0.25 6 7
CFLAR/RIP1 0.04 0.006 -10000 0 -10000 0 0
FAIM3 0.005 0.092 -10000 0 -0.4 21 21
FAF1 0.02 0.017 -10000 0 -10000 0 0
PARP1 0.002 0.039 0.22 11 -10000 0 11
DFFB 0.003 0.039 0.22 12 -10000 0 12
CHUK -0.007 0.1 -10000 0 -0.64 9 9
FASLG -0.007 0.1 -10000 0 -0.4 26 26
FAS/FADD 0.034 0.026 -10000 0 -0.29 2 2
HGF 0.018 0.055 -10000 0 -0.4 7 7
LMNA -0.003 0.043 0.24 5 -10000 0 5
CASP6 0.002 0.039 0.22 11 -10000 0 11
CASP10 0.025 0.006 -10000 0 -10000 0 0
CASP3 0.006 0.048 0.26 13 -10000 0 13
PTPN13 0.01 0.082 -10000 0 -0.42 15 15
CASP8 -0.003 0.075 0.32 21 -10000 0 21
IL6 -0.027 0.17 -10000 0 -0.83 10 10
MET 0.022 0.047 0.37 1 -0.42 4 5
ICAD/CAD -0.001 0.031 0.23 3 -10000 0 3
FASLG/FAS/FADD/FAF1/Caspase 10 0 0.084 -10000 0 -0.29 25 25
activation of caspase activity by cytochrome c -0.009 0.05 0.25 14 -0.26 1 15
PAK2 0.003 0.041 0.22 13 -10000 0 13
BCL2 0.011 0.062 -10000 0 -0.4 9 9
S1P3 pathway

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
PDGFRB 0.022 0.044 -10000 0 -0.42 4 4
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.04 0.11 -10000 0 -0.31 35 35
GNAO1 -0.088 0.19 -10000 0 -0.4 114 114
S1P/S1P3/G12/G13 0.044 0.024 -10000 0 -0.23 1 1
AKT1 -0.029 0.14 -10000 0 -0.46 34 34
AKT3 -0.016 0.15 -10000 0 -1.2 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.044 -10000 0 -0.42 4 4
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.026 0.008 -10000 0 -10000 0 0
GNAI1 0.011 0.076 -10000 0 -0.4 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.025 0.023 -10000 0 -0.42 1 1
S1PR2 0.026 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.044 0.13 -10000 0 -0.38 31 31
MAPK3 -0.047 0.12 -10000 0 -0.36 32 32
MAPK1 -0.039 0.12 -10000 0 -0.38 23 23
JAK2 0.001 0.14 0.22 8 -0.35 27 35
CXCR4 -0.046 0.12 -10000 0 -0.36 31 31
FLT1 0.02 0.014 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC -0.032 0.1 -10000 0 -0.35 19 19
S1P/S1P3/Gi -0.044 0.13 -10000 0 -0.38 31 31
RAC1 0.024 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.13 -10000 0 -0.34 31 31
VEGFA 0.028 0.019 0.37 1 -10000 0 1
S1P/S1P2/Gi -0.045 0.13 -10000 0 -0.35 32 32
VEGFR1 homodimer/VEGFA homodimer 0.032 0.025 0.27 1 -10000 0 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.038 -10000 0 -0.3 4 4
GNAQ 0.025 0.021 -10000 0 -0.4 1 1
GNAZ 0.021 0.042 -10000 0 -0.4 4 4
G12/G13 0.034 0.013 -10000 0 -10000 0 0
GNA14 0.024 0.029 -10000 0 -0.4 2 2
GNA15 0.022 0.044 -10000 0 -0.42 4 4
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.004 -10000 0 -10000 0 0
GNA11 0.024 0.029 -10000 0 -0.4 2 2
Rac1/GTP -0.031 0.12 -10000 0 -0.36 29 29
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.022 -10000 0 -10000 0 0
HSPA8 0.025 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.004 0.11 -10000 0 -0.31 27 27
AKT1 -0.012 0.054 -10000 0 -10000 0 0
GSC -0.033 0.13 -10000 0 -0.5 9 9
NKX2-5 0.005 0.071 -10000 0 -0.42 11 11
muscle cell differentiation 0.046 0.13 0.36 18 -10000 0 18
SMAD2-3/SMAD4/SP1 -0.014 0.11 -10000 0 -0.29 2 2
SMAD4 0.001 0.047 -10000 0 -10000 0 0
CBFB 0.026 0.002 -10000 0 -10000 0 0
SAP18 0.02 0.011 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.038 0.14 -10000 0 -0.25 127 127
SMAD3/SMAD4/VDR 0.057 0.058 -10000 0 -10000 0 0
MYC 0.047 0.059 0.38 4 -0.36 2 6
CDKN2B -0.48 0.64 -10000 0 -1.3 164 164
AP1 0.013 0.054 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.018 0.12 -10000 0 -0.38 26 26
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.15 0.22 -10000 0 -0.42 151 151
SP3 0.028 0.001 -10000 0 -10000 0 0
CREB1 0.027 0 -10000 0 -10000 0 0
FOXH1 0.004 0.078 0.37 1 -0.4 13 14
SMAD3/SMAD4/GR 0.008 0.1 -10000 0 -0.3 25 25
GATA3 0.015 0.059 -10000 0 -0.42 5 5
SKI/SIN3/HDAC complex/NCoR1 0.02 0.054 -10000 0 -0.33 2 2
MEF2C/TIF2 -0.012 0.089 -10000 0 -0.4 8 8
endothelial cell migration 0.02 0.12 0.47 1 -10000 0 1
MAX 0.028 0.011 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
RBBP4 0.025 0.006 -10000 0 -10000 0 0
RUNX2 0.026 0.003 -10000 0 -10000 0 0
RUNX3 0.024 0.022 -10000 0 -0.4 1 1
RUNX1 0.025 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.004 -10000 0 -10000 0 0
NR3C1 0 0.11 -10000 0 -0.4 29 29
VDR 0.026 0.003 -10000 0 -10000 0 0
CDKN1A -0.016 0.11 -10000 0 -1 3 3
KAT2B 0.01 0.082 -10000 0 -0.39 17 17
SMAD2/SMAD2/SMAD4/FOXH1 -0.004 0.081 0.28 1 -0.3 8 9
DCP1A 0.026 0.004 -10000 0 -10000 0 0
SKI 0.025 0.006 -10000 0 -10000 0 0
SERPINE1 -0.02 0.12 -10000 0 -0.47 1 1
SMAD3/SMAD4/ATF2 0.018 0.064 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.016 0.068 -10000 0 -0.28 2 2
SAP30 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.053 0.047 -10000 0 -10000 0 0
JUN 0.003 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.017 0.065 -10000 0 -0.27 1 1
TFE3 0.018 0.024 -10000 0 -10000 0 0
COL1A2 0.003 0.081 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.017 0.063 -10000 0 -10000 0 0
DLX1 -0.001 0.083 -10000 0 -0.42 15 15
TCF3 0.026 0.004 -10000 0 -10000 0 0
FOS 0.019 0.039 -10000 0 -0.41 3 3
SMAD3/SMAD4/Max 0.026 0.069 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.053 0.019 -10000 0 -10000 0 0
ZBTB17 0.044 0.039 -10000 0 -0.4 1 1
LAMC1 -0.004 0.042 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.016 0.056 0.29 3 -0.31 1 4
IRF7 0.025 0.021 -10000 0 -0.4 1 1
ESR1 -0.015 0.12 -10000 0 -0.4 38 38
HNF4A 0.015 0.013 -10000 0 -10000 0 0
MEF2C -0.011 0.1 0.34 1 -0.42 8 9
SMAD2-3/SMAD4 -0.005 0.091 -10000 0 -0.28 1 1
Cbp/p300/Src-1 0.056 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 0.01 0.011 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.021 0.052 0.37 7 -0.42 1 8
CREBBP 0.026 0.016 -10000 0 -10000 0 0
SKIL 0.025 0.021 -10000 0 -0.4 1 1
HDAC1 0.025 0.006 -10000 0 -10000 0 0
HDAC2 0.025 0.004 -10000 0 -10000 0 0
SNIP1 0.025 0.005 -10000 0 -10000 0 0
GCN5L2 0.004 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.015 0.062 -10000 0 -10000 0 0
MSG1/HSC70 -0.068 0.16 -10000 0 -0.3 130 130
SMAD2 -0.009 0.048 -10000 0 -10000 0 0
SMAD3 0 0.051 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.042 0.21 3 -0.23 1 4
SMAD2/SMAD2/SMAD4 -0.053 0.12 -10000 0 -0.38 31 31
NCOR1 0.021 0.01 -10000 0 -10000 0 0
NCOA2 0.022 0.022 -10000 0 -0.4 1 1
NCOA1 0.026 0.001 -10000 0 -10000 0 0
MYOD/E2A 0.031 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.004 0.12 -10000 0 -0.32 1 1
IFNB1 -0.009 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.12 0.35 1 -0.42 8 9
CITED1 -0.11 0.21 -10000 0 -0.42 130 130
SMAD2-3/SMAD4/ARC105 0.007 0.09 -10000 0 -0.25 2 2
RBL1 0.016 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.16 0.27 -10000 0 -0.52 142 142
RUNX1-3/PEBPB2 0.048 0.017 -10000 0 -10000 0 0
SMAD7 -0.011 0.098 -10000 0 -0.47 4 4
MYC/MIZ-1 0.069 0.078 0.27 5 -0.3 2 7
SMAD3/SMAD4 0.007 0.1 0.25 9 -0.34 5 14
IL10 -0.022 0.11 -10000 0 -0.45 24 24
PIASy/HDAC complex 0.011 0.024 -10000 0 -10000 0 0
PIAS3 0.027 0.007 -10000 0 -10000 0 0
CDK2 0.028 0.013 -10000 0 -10000 0 0
IL5 -0.015 0.077 -10000 0 -0.37 6 6
CDK4 0.025 0.029 -10000 0 -0.42 1 1
PIAS4 0.011 0.024 -10000 0 -10000 0 0
ATF3 0.023 0.038 -10000 0 -0.42 3 3
SMAD3/SMAD4/SP1 0 0.083 -10000 0 -10000 0 0
FOXG1 -0.067 0.15 -10000 0 -0.43 57 57
FOXO3 -0.028 0.06 -10000 0 -10000 0 0
FOXO1 -0.02 0.052 -10000 0 -0.35 1 1
FOXO4 -0.027 0.058 -10000 0 -10000 0 0
heart looping -0.011 0.099 0.34 1 -0.42 8 9
CEBPB 0 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.006 0.081 -10000 0 -0.28 8 8
MYOD1 -0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.014 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.01 0.093 -10000 0 -0.32 7 7
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.021 -10000 0 -0.4 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.033 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.013 0.084 -10000 0 -10000 0 0
MED15 0.024 0.021 -10000 0 -0.4 1 1
SP1 0 0.039 -10000 0 -10000 0 0
SIN3B 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.025 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.005 0.09 0.28 1 -0.29 11 12
ITGB5 -0.012 0.056 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.026 0.05 -10000 0 -0.56 1 1
SMAD3/SMAD4/AR 0.002 0.092 -10000 0 -0.31 13 13
AR -0.005 0.099 -10000 0 -0.4 24 24
negative regulation of cell growth -0.004 0.061 -10000 0 -0.31 3 3
SMAD3/SMAD4/MYOD 0.012 0.063 -10000 0 -10000 0 0
E2F5 0.025 0.049 0.37 5 -0.42 2 7
E2F4 0.026 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.019 0.075 0.27 1 -0.3 1 2
SMAD2-3/SMAD4/FOXO1-3a-4 -0.13 0.24 -10000 0 -0.44 149 149
TFDP1 0.02 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.025 0.064 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.018 0.064 -10000 0 -10000 0 0
TGIF2 0.021 0.052 0.37 7 -0.42 1 8
TGIF1 0.022 0.01 -10000 0 -10000 0 0
ATF2 0.026 0.003 -10000 0 -10000 0 0
FoxO family 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
G6PC -0.13 0.41 -10000 0 -1.2 55 55
PLK1 0.014 0.14 -10000 0 -0.68 4 4
CDKN1B 0.041 0.12 0.3 1 -0.38 7 8
FOXO3 0.023 0.14 -10000 0 -0.62 8 8
KAT2B 0.013 0.085 -10000 0 -0.4 17 17
FOXO1/SIRT1 -0.006 0.15 -10000 0 -0.36 54 54
CAT 0.016 0.14 -10000 0 -0.65 5 5
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
AKT1 0.018 0.035 -10000 0 -10000 0 0
FOXO1 -0.018 0.15 -10000 0 -0.38 54 54
MAPK10 0.003 0.09 0.19 34 -0.2 53 87
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.031 0.077 -10000 0 -10000 0 0
response to oxidative stress 0 0.023 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.036 0.13 -10000 0 -0.54 8 8
XPO1 0.027 0.001 -10000 0 -10000 0 0
EP300 0.013 0.034 -10000 0 -10000 0 0
BCL2L11 0.03 0.025 -10000 0 -10000 0 0
FOXO1/SKP2 -0.006 0.14 -10000 0 -0.36 51 51
mol:GDP 0 0.023 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
GADD45A 0.039 0.13 -10000 0 -0.55 12 12
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.034 0.11 0.2 18 -0.39 14 32
MST1 -0.039 0.16 -10000 0 -0.42 65 65
CSNK1D 0.026 0.004 -10000 0 -10000 0 0
CSNK1E 0.025 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.007 0.1 -10000 0 -0.37 19 19
YWHAB 0.015 0.013 -10000 0 -10000 0 0
MAPK8 0.034 0.053 0.19 41 -10000 0 41
MAPK9 0.034 0.053 0.19 42 -10000 0 42
YWHAG 0.025 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
SIRT1 0.027 0.014 -10000 0 -10000 0 0
SOD2 0.037 0.11 0.31 1 -0.5 1 2
RBL2 0.039 0.12 -10000 0 -0.79 2 2
RAL/GDP 0.032 0.026 -10000 0 -10000 0 0
CHUK 0.03 0.017 -10000 0 -10000 0 0
Ran/GTP 0.022 0.002 -10000 0 -10000 0 0
CSNK1G2 0.025 0.021 -10000 0 -0.4 1 1
RAL/GTP 0.035 0.026 -10000 0 -10000 0 0
CSNK1G1 0.024 0.021 -10000 0 -0.4 1 1
FASLG -0.049 0.32 -10000 0 -1.3 27 27
SKP2 0.026 0.004 -10000 0 -10000 0 0
USP7 0.027 0.003 -10000 0 -10000 0 0
IKBKB 0.027 0.018 -10000 0 -10000 0 0
CCNB1 0.017 0.13 -10000 0 -0.68 4 4
FOXO1-3a-4/beta catenin 0.047 0.12 0.28 10 -0.36 2 12
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.14 -10000 0 -0.35 51 51
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
SGK1 0.008 0.097 -10000 0 -0.4 22 22
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.004 -10000 0 -10000 0 0
ZFAND5 0.029 0.071 -10000 0 -10000 0 0
SFN 0.023 0.022 -10000 0 -0.4 1 1
CDK2 0.01 0.045 -10000 0 -0.21 1 1
FOXO3A/14-3-3 0.001 0.091 -10000 0 -0.38 12 12
CREBBP 0.009 0.045 -10000 0 -0.2 2 2
FBXO32 0.043 0.17 -10000 0 -0.81 4 4
BCL6 0.039 0.12 -10000 0 -0.72 2 2
RALB 0.027 0.001 -10000 0 -10000 0 0
RALA 0.025 0.008 -10000 0 -10000 0 0
YWHAH 0.025 0.006 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.022 0.044 -10000 0 -0.42 4 4
GPC2 0.015 0.07 0.37 1 -0.42 10 11
GPC2/Midkine 0.026 0.062 0.26 1 -0.3 14 15
neuron projection morphogenesis 0.026 0.062 0.26 1 -0.3 14 15
IL6-mediated signaling events

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 0.071 0.15 0.41 2 -0.66 2 4
CRP 0.008 0.14 0.48 2 -0.77 2 4
cell cycle arrest 0.007 0.14 -10000 0 -0.78 3 3
TIMP1 0.01 0.14 -10000 0 -0.58 6 6
IL6ST 0.02 0.059 -10000 0 -0.4 8 8
Rac1/GDP -0.034 0.12 -10000 0 -0.38 24 24
AP1 0.053 0.087 -10000 0 -0.44 4 4
GAB2 0.027 0.004 -10000 0 -10000 0 0
TNFSF11 0.037 0.18 0.48 2 -0.88 5 7
HSP90B1 0.034 0.052 -10000 0 -0.58 1 1
GAB1 0.026 0.004 -10000 0 -10000 0 0
MAPK14 -0.033 0.12 -10000 0 -0.38 14 14
AKT1 0.031 0.042 -10000 0 -0.4 1 1
FOXO1 0.06 0.078 0.25 3 -0.37 1 4
MAP2K6 -0.042 0.11 -10000 0 -0.39 17 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.028 0.12 0.4 1 -0.44 11 12
MITF -0.043 0.11 -10000 0 -0.4 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.003 -10000 0 -10000 0 0
A2M 0.001 0.17 -10000 0 -1.2 9 9
CEBPB 0.018 0.016 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.025 0.071 -10000 0 -0.4 3 3
STAT3 -0.001 0.14 -10000 0 -0.84 3 3
STAT1 0.02 0.016 -10000 0 -10000 0 0
CEBPD 0.023 0.14 0.48 1 -0.98 2 3
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.04 0.008 -10000 0 -10000 0 0
JUN 0.026 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.027 0.12 -10000 0 -0.38 18 18
MAPK11 -0.03 0.11 -10000 0 -0.39 13 13
STAT3 (dimer)/FOXO1 0.051 0.14 0.35 14 -0.63 2 16
GRB2/SOS1/GAB family 0.014 0.12 0.24 1 -0.38 11 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.028 0.11 0.23 2 -0.37 20 22
GRB2 0.026 0.005 -10000 0 -10000 0 0
JAK2 0.023 0.036 -10000 0 -0.4 3 3
LBP 0.075 0.15 0.4 4 -0.58 1 5
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.027 0.008 -10000 0 -10000 0 0
MYC 0.036 0.15 0.46 3 -0.77 2 5
FGG -0.006 0.14 -10000 0 -0.77 2 2
macrophage differentiation 0.007 0.14 -10000 0 -0.78 3 3
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.027 0.15 0.26 4 -0.33 28 32
JUNB 0.005 0.13 -10000 0 -0.94 3 3
FOS 0.022 0.036 -10000 0 -0.4 3 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.038 0.12 0.21 2 -0.38 23 25
STAT1/PIAS1 -0.005 0.11 -10000 0 -0.36 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.035 0.041 -10000 0 -0.34 3 3
STAT3 (dimer) 0.005 0.14 -10000 0 -0.82 3 3
PRKCD -0.008 0.14 0.33 18 -0.49 7 25
IL6R -0.067 0.18 -10000 0 -0.4 94 94
SOCS3 -0.029 0.11 -10000 0 -0.52 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.052 0.045 -10000 0 -0.23 8 8
Rac1/GTP -0.032 0.12 -10000 0 -0.38 22 22
HCK 0.011 0.047 -10000 0 -0.4 5 5
MAPKKK cascade 0.041 0.078 -10000 0 -0.48 4 4
bone resorption 0.039 0.17 0.48 2 -0.81 5 7
IRF1 0.008 0.12 -10000 0 -0.76 2 2
mol:GDP -0.039 0.13 -10000 0 -0.39 24 24
SOS1 0.027 0.003 -10000 0 -10000 0 0
VAV1 -0.045 0.12 -10000 0 -0.4 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.066 0.17 -10000 0 -0.37 83 83
PTPN11 0.015 0.07 -10000 0 -0.79 3 3
IL6/IL6RA -0.071 0.16 0.27 4 -0.3 137 141
gp130 (dimer)/TYK2/TYK2/LMO4 0.049 0.043 -10000 0 -0.24 8 8
gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.049 -10000 0 -0.24 11 11
IL6 -0.037 0.17 0.37 5 -0.42 64 69
PIAS3 0.025 0.005 -10000 0 -10000 0 0
PTPRE 0.02 0.012 -10000 0 -10000 0 0
PIAS1 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.043 0.12 0.18 3 -0.31 34 37
LMO4 0.028 0.009 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.009 0.14 -10000 0 -0.78 3 3
MCL1 0.033 0.049 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.055 0.17 -10000 0 -0.4 80 80
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.022 -10000 0 -0.42 1 1
TCEB1 0.023 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.012 0.058 0.18 2 -0.25 17 19
HIF1A 0.003 0.047 -10000 0 -0.26 12 12
COPS5 0.023 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.063 0.032 -10000 0 -10000 0 0
FIH (dimer) 0.025 0.006 -10000 0 -10000 0 0
CDKN2A -0.071 0.19 0.37 1 -0.43 91 92
ARNT/IPAS -0.022 0.12 -10000 0 -0.28 79 79
HIF1AN 0.025 0.006 -10000 0 -10000 0 0
GNB2L1 0.026 0.003 -10000 0 -10000 0 0
HIF1A/ARNT 0.01 0.061 0.18 1 -0.26 17 18
CUL2 0.026 0.002 -10000 0 -10000 0 0
OS9 0.026 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.045 0.02 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.015 0.059 0.18 2 -0.25 17 19
PHD1-3/OS9 0.059 0.03 -10000 0 -0.22 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.029 0.065 -10000 0 -0.26 14 14
VHL 0.026 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.01 0.06 0.18 1 -0.26 16 17
EGLN3 0.023 0.03 -10000 0 -0.4 2 2
EGLN2 0.025 0.021 -10000 0 -0.4 1 1
EGLN1 0.026 0.005 -10000 0 -10000 0 0
TP53 0.022 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.071 -10000 0 -0.48 7 7
ARNT 0.025 0.021 -10000 0 -0.4 1 1
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.024 0.021 -10000 0 -0.4 1 1
HIF1A/p19ARF -0.033 0.11 0.22 1 -0.31 20 21
Aurora B signaling

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
Condensin I complex 0.008 0.046 -10000 0 -0.38 1 1
STMN1 0.012 0.016 -10000 0 -0.28 1 1
Aurora B/RasGAP/Survivin 0.05 0.027 0.26 1 -10000 0 1
Chromosomal passenger complex/Cul3 protein complex -0.012 0.08 0.16 1 -0.27 16 17
BIRC5 0.029 0.017 0.37 1 -10000 0 1
DES -0.38 0.32 -10000 0 -0.6 278 278
Aurora C/Aurora B/INCENP 0.045 0.03 -10000 0 -0.21 2 2
Aurora B/TACC1 0.03 0.018 -10000 0 -10000 0 0
Aurora B/PP2A 0.036 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.008 0.004 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.004 -10000 0 -10000 0 0
NDC80 0.012 0.008 -10000 0 -10000 0 0
Cul3 protein complex 0.017 0.095 -10000 0 -0.24 52 52
KIF2C 0.015 0.046 -10000 0 -0.35 5 5
PEBP1 0.028 0.002 -10000 0 -10000 0 0
KIF20A 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.017 -10000 0 -10000 0 0
SEPT1 0.02 0.05 -10000 0 -0.4 6 6
SMC2 0.025 0.021 -10000 0 -0.4 1 1
SMC4 0.024 0.029 -10000 0 -0.4 2 2
NSUN2/NPM1/Nucleolin -0.069 0.2 -10000 0 -0.49 72 72
PSMA3 0.025 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.014 0.007 -10000 0 -10000 0 0
AURKB 0.027 0.014 -10000 0 -10000 0 0
AURKC 0.022 0.031 -10000 0 -0.4 2 2
CDCA8 0.028 0.005 -10000 0 -10000 0 0
cytokinesis 0.006 0.039 -10000 0 -0.37 2 2
Aurora B/Septin1 0.002 0.11 -10000 0 -0.33 7 7
AURKA 0.016 0.013 -10000 0 -10000 0 0
INCENP 0.028 0.005 -10000 0 -10000 0 0
KLHL13 -0.026 0.14 -10000 0 -0.4 52 52
BUB1 0.028 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.048 0.029 0.24 1 -0.21 1 2
EVI5 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.045 0.061 -10000 0 -0.29 1 1
SGOL1 0.025 0.022 -10000 0 -0.42 1 1
CENPA 0.034 0.05 -10000 0 -0.19 2 2
NCAPG 0.026 0.005 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.036 0.018 -10000 0 -10000 0 0
NCAPD2 0.026 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.036 0.017 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
NCAPH 0.027 0 -10000 0 -10000 0 0
NPM1 -0.039 0.14 -10000 0 -0.32 61 61
RASA1 0.026 0.005 -10000 0 -10000 0 0
KLHL9 0.026 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.017 -10000 0 -10000 0 0
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin 0.041 0.061 -10000 0 -0.31 1 1
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
NSUN2 -0.033 0.11 -10000 0 -0.28 67 67
MYLK -0.023 0.095 -10000 0 -0.27 54 54
KIF23 0.025 0.023 -10000 0 -0.43 1 1
VIM 0.013 0.007 -10000 0 -10000 0 0
RACGAP1 0.027 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.033 0.11 -10000 0 -0.28 68 68
Chromosomal passenger complex 0.02 0.046 0.17 1 -0.2 1 2
Chromosomal passenger complex/EVI5 0.089 0.054 0.31 1 -10000 0 1
TACC1 0.023 0.01 -10000 0 -10000 0 0
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
CUL3 0.026 0.001 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.016 -10000 0 -0.23 2 2
RAS family/GTP 0.01 0.092 0.23 1 -0.26 7 8
NFATC4 -0.023 0.061 0.25 2 -10000 0 2
ERBB2IP 0.02 0.05 -10000 0 -0.39 6 6
HSP90 (dimer) 0.025 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis -0.001 0.073 0.19 1 -10000 0 1
JUN 0.005 0.063 -10000 0 -0.18 1 1
HRAS 0.025 0.021 -10000 0 -0.4 1 1
DOCK7 -0.029 0.066 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.015 0.08 0.21 7 -0.22 37 44
AKT1 0.003 0.006 -10000 0 -10000 0 0
BAD -0.006 0.012 -10000 0 -0.24 1 1
MAPK10 -0.023 0.072 0.19 4 -0.24 12 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.001 0.08 0.21 1 -10000 0 1
RAF1 -0.008 0.088 0.26 3 -0.3 7 10
ErbB2/ErbB3/neuregulin 2 -0.003 0.087 0.2 9 -0.23 48 57
STAT3 0.018 0.043 -10000 0 -0.79 1 1
cell migration -0.016 0.07 0.19 7 -0.22 11 18
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.044 0.22 -10000 0 -0.59 50 50
FOS -0.019 0.14 -10000 0 -0.36 52 52
NRAS 0.024 0.029 -10000 0 -0.4 2 2
mol:Ca2+ -0.001 0.073 0.19 1 -10000 0 1
MAPK3 -0.027 0.17 -10000 0 -0.49 38 38
MAPK1 -0.043 0.2 -10000 0 -0.54 47 47
JAK2 -0.029 0.068 -10000 0 -10000 0 0
NF2 0.003 0.059 -10000 0 -0.6 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.072 0.18 1 -0.22 37 38
NRG1 -0.021 0.12 -10000 0 -0.4 41 41
GRB2/SOS1 0.038 0.007 -10000 0 -10000 0 0
MAPK8 -0.017 0.09 -10000 0 -0.24 32 32
MAPK9 -0.007 0.054 0.19 4 -10000 0 4
ERBB2 -0.012 0.048 0.3 10 -10000 0 10
ERBB3 0.026 0.003 -10000 0 -10000 0 0
SHC1 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
apoptosis 0.006 0.013 0.21 1 -10000 0 1
STAT3 (dimer) 0.018 0.043 -10000 0 -0.77 1 1
RNF41 -0.009 0.015 -10000 0 -0.2 2 2
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.011 0.049 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.011 0.037 0.22 10 -10000 0 10
CHRNA1 -0.035 0.2 0.25 1 -0.6 41 42
myelination -0.02 0.064 0.24 3 -10000 0 3
PPP3CB -0.027 0.062 -10000 0 -10000 0 0
KRAS 0.026 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.01 0.078 0.24 1 -10000 0 1
NRG2 -0.042 0.14 -10000 0 -0.4 56 56
mol:GDP -0.006 0.071 0.18 1 -0.22 37 38
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.015 0.093 0.25 3 -0.33 9 12
SRC 0.016 0.013 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.029 0.067 -10000 0 -10000 0 0
MAP2K1 -0.047 0.2 -10000 0 -0.57 37 37
heart morphogenesis -0.001 0.073 0.19 1 -10000 0 1
RAS family/GDP 0.013 0.092 0.24 1 -10000 0 1
GRB2 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.006 0.063 -10000 0 -0.64 4 4
CHRNE 0.005 0.023 -10000 0 -0.13 7 7
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.006 -10000 0 -10000 0 0
nervous system development -0.001 0.073 0.19 1 -10000 0 1
CDC42 0.024 0.022 -10000 0 -0.4 1 1
Coregulation of Androgen receptor activity

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
NRIP1 0.005 0.051 -10000 0 -0.4 2 2
SVIL 0.01 0.037 -10000 0 -10000 0 0
ZNF318 0.05 0.058 0.18 69 -10000 0 69
JMJD2C 0.005 0.019 -10000 0 -0.069 16 16
T-DHT/AR/Ubc9 0.022 0.071 -10000 0 -0.24 24 24
CARM1 0.018 0.02 -10000 0 -10000 0 0
PRDX1 0.028 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.015 -10000 0 -10000 0 0
CTNNB1 0.011 0.034 -10000 0 -10000 0 0
AKT1 0.031 0.019 -10000 0 -10000 0 0
PTK2B 0.011 0.033 -10000 0 -0.4 1 1
MED1 0.035 0.027 0.37 1 -10000 0 1
MAK 0.033 0.11 0.19 22 -0.42 15 37
response to oxidative stress 0.002 0.005 -10000 0 -10000 0 0
HIP1 0.009 0.041 -10000 0 -0.4 1 1
GSN -0.001 0.076 -10000 0 -0.42 9 9
NCOA2 0.016 0.027 -10000 0 -0.4 1 1
NCOA6 0.009 0.027 -10000 0 -10000 0 0
DNA-PK 0.062 0.055 -10000 0 -10000 0 0
NCOA4 0.022 0.023 -10000 0 -0.4 1 1
PIAS3 0.011 0.034 -10000 0 -10000 0 0
cell proliferation 0.029 0.073 0.28 1 -0.37 4 5
XRCC5 0.032 0.013 -10000 0 -10000 0 0
UBE3A 0.004 0.052 -10000 0 -0.4 1 1
T-DHT/AR/SNURF -0.004 0.1 -10000 0 -0.26 56 56
FHL2 0.041 0.075 -10000 0 -1 1 1
RANBP9 0.007 0.047 -10000 0 -0.4 1 1
JMJD1A 0.003 0.021 -10000 0 -0.11 12 12
CDK6 0.026 0.008 -10000 0 -10000 0 0
TGFB1I1 0.01 0.037 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.007 0.077 -10000 0 -0.24 28 28
XRCC6 0.03 0.015 -10000 0 -10000 0 0
T-DHT/AR 0.032 0.083 -10000 0 -0.25 24 24
CTDSP1 0.016 0.024 -10000 0 -10000 0 0
CTDSP2 0.043 0.039 -10000 0 -10000 0 0
BRCA1 0.011 0.036 -10000 0 -10000 0 0
TCF4 0.027 0.035 -10000 0 -0.4 1 1
CDKN2A -0.061 0.19 0.37 1 -0.42 91 92
SRF 0.039 0.022 -10000 0 -10000 0 0
NKX3-1 -0.011 0.12 -10000 0 -0.58 16 16
KLK3 -0.2 0.49 -10000 0 -1.3 71 71
TMF1 0.017 0.028 -10000 0 -0.4 1 1
HNRNPA1 0.036 0.023 -10000 0 -10000 0 0
AOF2 -0.013 0.03 -10000 0 -0.079 71 71
APPL1 0.024 0.042 0.15 3 -0.28 2 5
T-DHT/AR/Caspase 8 0.032 0.076 -10000 0 -0.24 24 24
AR 0 0.1 -10000 0 -0.4 24 24
UBA3 0.016 0.023 -10000 0 -10000 0 0
PATZ1 0.034 0.022 -10000 0 -10000 0 0
PAWR 0.018 0.019 -10000 0 -10000 0 0
PRKDC 0.027 0.016 -10000 0 -10000 0 0
PA2G4 0.037 0.025 -10000 0 -10000 0 0
UBE2I 0.026 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.028 0.068 -10000 0 -0.21 24 24
RPS6KA3 0.007 0.044 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.016 0.072 -10000 0 -0.24 25 25
LATS2 0.027 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.035 0.075 0.17 3 -0.22 21 24
Cyclin D3/CDK11 p58 0.021 0.005 -10000 0 -10000 0 0
VAV3 -0.033 0.13 -10000 0 -0.41 45 45
KLK2 0.003 0.064 -10000 0 -0.36 2 2
CASP8 0.03 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.019 0.071 -10000 0 -0.25 9 9
TMPRSS2 0.006 0.077 -10000 0 -0.56 5 5
CCND1 0.012 0.045 -10000 0 -0.42 3 3
PIAS1 0.005 0.049 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.013 -10000 0 -0.061 12 12
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.004 0.07 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.025 0.073 -10000 0 -0.24 24 24
CMTM2 0.009 0.089 -10000 0 -0.42 17 17
SNURF -0.023 0.12 -10000 0 -0.4 37 37
ZMIZ1 0.025 0.021 -10000 0 -10000 0 0
CCND3 0.027 0.004 -10000 0 -10000 0 0
TGIF1 0.029 0.023 -10000 0 -10000 0 0
FKBP4 0.008 0.046 0.37 1 -10000 0 1
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.055 0.054 -10000 0 -0.58 1 1
epithelial cell differentiation 0.042 0.079 -10000 0 -0.63 1 1
ITCH 0.017 0.015 -10000 0 -10000 0 0
WWP1 0.013 0.068 -10000 0 -1.2 1 1
FYN 0.026 0.004 -10000 0 -10000 0 0
EGFR 0.023 0.022 -10000 0 -0.4 1 1
PRL -0.01 0.074 -10000 0 -0.42 12 12
neuron projection morphogenesis 0.023 0.086 0.29 12 -0.38 2 14
PTPRZ1 -0.12 0.19 -10000 0 -0.4 134 134
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.03 0.079 -10000 0 -0.46 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.071 -10000 0 -0.52 1 1
ADAM17 0.02 0.015 -10000 0 -10000 0 0
ErbB4/ErbB4 0.014 0.04 -10000 0 -0.64 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.052 0.052 -10000 0 -0.59 1 1
NCOR1 0.022 0.01 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.018 0.074 -10000 0 -0.49 1 1
GRIN2B -0.034 0.11 0.26 4 -0.38 5 9
ErbB4/ErbB2/betacellulin 0.051 0.047 0.28 1 -0.49 1 2
STAT1 0.025 0.022 -10000 0 -0.42 1 1
HBEGF 0.024 0.031 -10000 0 -0.42 2 2
PRLR 0.016 0.065 -10000 0 -0.4 10 10
E4ICDs/ETO2 0.034 0.083 -10000 0 -0.58 1 1
axon guidance 0.038 0.086 0.29 11 -0.72 1 12
NEDD4 0.018 0.015 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.017 0.075 -10000 0 -0.3 21 21
CBFA2T3 -0.029 0.14 -10000 0 -0.4 55 55
ErbB4/ErbB2/HBEGF 0.052 0.047 0.26 2 -0.49 1 3
MAPK3 0.02 0.08 0.27 7 -0.39 2 9
STAT1 (dimer) 0.056 0.052 -10000 0 -0.58 1 1
MAPK1 0.019 0.078 0.27 7 -0.44 1 8
JAK2 0.023 0.036 -10000 0 -0.4 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.005 0.069 0.24 2 -0.49 1 3
NRG1 -0.024 0.087 -10000 0 -0.29 41 41
NRG3 0.004 0.03 -10000 0 -0.42 1 1
NRG2 -0.042 0.14 -10000 0 -0.4 56 56
NRG4 -0.027 0.13 -10000 0 -0.4 43 43
heart development 0.038 0.086 0.29 11 -0.72 1 12
neural crest cell migration 0.005 0.069 0.24 2 -0.49 1 3
ERBB2 0.009 0.03 0.28 4 -10000 0 4
WWOX/E4ICDs 0.052 0.053 -10000 0 -0.58 1 1
SHC1 0.026 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.033 0.083 -10000 0 -0.56 1 1
apoptosis -0.038 0.076 0.39 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.031 0.082 -10000 0 -0.59 1 1
ErbB4/ErbB2/epiregulin -0.034 0.12 0.3 2 -0.36 3 5
ErbB4/ErbB4/betacellulin/betacellulin 0.054 0.054 -10000 0 -0.58 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.067 0.08 -10000 0 -0.45 2 2
MDM2 0.01 0.036 0.25 1 -0.58 1 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.001 0.061 -10000 0 -0.4 1 1
STAT5A 0.045 0.085 0.3 8 -0.7 1 9
ErbB4/EGFR/neuregulin 1 beta 0.016 0.073 -10000 0 -0.49 1 1
DLG4 0.021 0.024 -10000 0 -0.42 1 1
GRB2/SHC 0.037 0.009 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.04 0.046 -10000 0 -0.55 1 1
STAT5A (dimer) 0.068 0.099 0.31 3 -0.69 1 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.074 0.088 0.31 4 -0.7 1 5
LRIG1 0.026 0.003 -10000 0 -10000 0 0
EREG -0.16 0.22 0.37 1 -0.42 173 174
BTC 0.023 0.036 -10000 0 -0.4 3 3
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.023 0.073 0.29 5 -0.73 1 6
ERBB4 0.01 0.034 -10000 0 -0.64 1 1
STAT5B 0.026 0.004 -10000 0 -10000 0 0
YAP1 0.011 0.054 -10000 0 -0.44 5 5
GRB2 0.026 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.03 0.077 0.26 2 -0.5 1 3
glial cell differentiation -0.04 0.046 0.54 1 -10000 0 1
WWOX 0.024 0.008 -10000 0 -10000 0 0
cell proliferation 0.019 0.094 0.32 6 -0.53 1 7
Arf6 downstream 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
PLAUR 0.014 0.03 -10000 0 -10000 0 0
regulation of axonogenesis -0.007 0.033 0.23 7 -10000 0 7
myoblast fusion -0.027 0.02 -10000 0 -10000 0 0
mol:GTP 0.014 0.034 -10000 0 -0.15 18 18
regulation of calcium-dependent cell-cell adhesion -0.015 0.096 0.25 42 -10000 0 42
ARF1/GTP 0.027 0.035 -10000 0 -10000 0 0
mol:GM1 0.003 0.028 -10000 0 -10000 0 0
mol:Choline 0.007 0.019 -10000 0 -0.22 1 1
lamellipodium assembly 0.001 0.085 -10000 0 -0.34 24 24
MAPK3 0.016 0.029 -10000 0 -0.25 1 1
ARF6/GTP/NME1/Tiam1 0.015 0.097 -10000 0 -0.25 42 42
ARF1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.027 0.02 -10000 0 -10000 0 0
ARF1/GDP 0.022 0.057 -10000 0 -0.24 6 6
ARF6 0.031 0.009 -10000 0 -10000 0 0
RAB11A 0.025 0.005 -10000 0 -10000 0 0
TIAM1 -0.014 0.12 -10000 0 -0.4 40 40
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.025 -10000 0 -10000 0 0
actin filament bundle formation -0.024 0.058 0.2 24 -10000 0 24
KALRN 0.019 0.019 -10000 0 -0.2 1 1
RAB11FIP3/RAB11A 0.037 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.058 -10000 0 -0.2 24 24
NME1 0.018 0.067 0.37 1 -0.42 9 10
Rac1/GDP 0.021 0.056 -10000 0 -0.2 22 22
substrate adhesion-dependent cell spreading 0.014 0.034 -10000 0 -0.15 18 18
cortical actin cytoskeleton organization 0.002 0.083 -10000 0 -0.34 22 22
RAC1 0.024 0.008 -10000 0 -10000 0 0
liver development 0.014 0.034 -10000 0 -0.15 18 18
ARF6/GTP 0.014 0.034 -10000 0 -0.15 18 18
RhoA/GTP 0.027 0.036 -10000 0 -10000 0 0
mol:GDP 0.011 0.051 -10000 0 -0.2 19 19
ARF6/GTP/RAB11FIP3/RAB11A 0.041 0.036 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
PLD1 0.012 0.034 -10000 0 -0.25 1 1
RAB11FIP3 0.026 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.085 -10000 0 -0.34 24 24
ruffle organization 0.007 0.033 -10000 0 -0.23 7 7
regulation of epithelial cell migration 0.014 0.034 -10000 0 -0.15 18 18
PLD2 0.015 0.019 -10000 0 -10000 0 0
PIP5K1A 0.007 0.033 -10000 0 -0.23 7 7
mol:Phosphatidic acid 0.007 0.019 -10000 0 -0.22 1 1
Rac1/GTP 0.002 0.084 -10000 0 -0.34 22 22
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.025 0.021 -9999 0 -0.4 1 1
SPHK1 -0.006 0.12 -9999 0 -0.42 30 30
GNAI2 0.026 0.004 -9999 0 -10000 0 0
mol:S1P 0.005 0.034 -9999 0 -0.24 1 1
GNAO1 -0.088 0.19 -9999 0 -0.4 114 114
mol:Sphinganine-1-P -0.011 0.082 -9999 0 -0.3 31 31
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.041 0.045 -9999 0 -10000 0 0
GNAI3 0.026 0.005 -9999 0 -10000 0 0
G12/G13 0.034 0.013 -9999 0 -10000 0 0
S1PR3 0.025 0.022 -9999 0 -0.42 1 1
S1PR2 0.026 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.001 0.031 -9999 0 -0.21 1 1
S1PR5 0.02 0.053 -9999 0 -0.42 6 6
S1PR4 0.016 0.065 -9999 0 -0.4 10 10
GNAI1 0.011 0.076 -9999 0 -0.4 14 14
S1P/S1P5/G12 0.027 0.053 -9999 0 -0.24 6 6
S1P/S1P3/Gq 0.023 0.054 -9999 0 -0.38 5 5
S1P/S1P4/Gi -0.049 0.13 -9999 0 -0.35 39 39
GNAQ 0.025 0.021 -9999 0 -0.4 1 1
GNAZ 0.021 0.042 -9999 0 -0.4 4 4
GNA14 0.024 0.029 -9999 0 -0.4 2 2
GNA15 0.022 0.044 -9999 0 -0.42 4 4
GNA12 0.024 0.008 -9999 0 -10000 0 0
GNA13 0.026 0.004 -9999 0 -10000 0 0
GNA11 0.024 0.029 -9999 0 -0.4 2 2
ABCC1 0.026 0.003 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.022 0.043 -10000 0 -0.42 4 4
ANTXR2 0.025 0.021 -10000 0 -0.4 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.006 -10000 0 -0.052 5 5
monocyte activation -0.004 0.09 -10000 0 -0.33 30 30
MAP2K2 0.006 0.076 -10000 0 -0.58 7 7
MAP2K1 -0.004 0.005 -10000 0 -10000 0 0
MAP2K7 -0.004 0.011 -10000 0 -0.2 1 1
MAP2K6 -0.005 0.017 -10000 0 -0.2 3 3
CYAA -0.007 0.022 -10000 0 -0.21 5 5
MAP2K4 -0.003 0.005 -10000 0 -10000 0 0
IL1B -0.026 0.066 -10000 0 -0.21 48 48
Channel 0.03 0.028 -10000 0 -0.22 5 5
NLRP1 -0.005 0.018 -10000 0 -0.21 3 3
CALM1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.016 0.1 -10000 0 -0.38 30 30
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.006 0.052 5 -10000 0 5
MAPK3 -0.004 0.011 -10000 0 -0.2 1 1
MAPK1 -0.004 0.005 -10000 0 -10000 0 0
PGR -0.039 0.076 -10000 0 -0.2 77 77
PA/Cellular Receptors 0.032 0.031 -10000 0 -0.25 5 5
apoptosis -0.001 0.006 -10000 0 -0.052 5 5
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.03 0.025 -10000 0 -0.2 5 5
macrophage activation -0.005 0.019 0.18 3 -0.19 1 4
TNF 0.024 0.03 -10000 0 -0.4 2 2
VCAM1 -0.004 0.09 -10000 0 -0.33 30 30
platelet activation -0.016 0.1 -10000 0 -0.38 30 30
MAPKKK cascade 0.001 0.015 0.14 1 -0.07 8 9
IL18 -0.003 0.017 -10000 0 -0.19 2 2
negative regulation of macrophage activation -0.001 0.006 -10000 0 -0.052 5 5
LEF -0.001 0.006 -10000 0 -0.052 5 5
CASP1 -0.001 0.011 -10000 0 -0.1 4 4
mol:cAMP -0.017 0.1 -10000 0 -0.38 30 30
necrosis -0.001 0.006 -10000 0 -0.052 5 5
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.03 0.026 -10000 0 -0.21 5 5
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.019 0.072 -10000 0 -0.39 12 12
PDGF/PDGFRA/CRKL 0.032 0.052 -10000 0 -0.26 12 12
positive regulation of JUN kinase activity 0.057 0.046 -10000 0 -0.21 8 8
CRKL 0.025 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.025 0.057 -10000 0 -0.28 14 14
AP1 0.02 0.087 0.29 2 -0.52 3 5
mol:IP3 0.002 0.043 -10000 0 -0.29 9 9
PLCG1 0.002 0.043 -10000 0 -0.29 9 9
PDGF/PDGFRA/alphaV Integrin 0.033 0.053 -10000 0 -0.27 12 12
RAPGEF1 0.025 0.021 -10000 0 -0.4 1 1
CRK 0.022 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.043 -10000 0 -0.29 9 9
CAV3 -0.014 0.032 -10000 0 -0.42 2 2
CAV1 0.022 0.036 -10000 0 -0.4 3 3
SHC/Grb2/SOS1 0.06 0.047 -10000 0 -0.21 8 8
PDGF/PDGFRA/Shf 0.02 0.08 -10000 0 -0.29 26 26
FOS -0.005 0.073 0.31 9 -0.52 3 12
JUN -0.007 0.019 -10000 0 -10000 0 0
oligodendrocyte development 0.033 0.053 -10000 0 -0.27 12 12
GRB2 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG 0.002 0.043 -10000 0 -0.29 9 9
PDGF/PDGFRA 0.019 0.072 -10000 0 -0.39 12 12
actin cytoskeleton reorganization 0.032 0.052 -10000 0 -0.26 12 12
SRF 0.005 0.012 -10000 0 -10000 0 0
SHC1 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.047 0.046 -10000 0 -0.23 8 8
PDGF/PDGFRA/Crk/C3G 0.039 0.05 -10000 0 -0.23 10 10
JAK1 0.009 0.046 -10000 0 -0.27 11 11
ELK1/SRF 0.02 0.075 0.15 84 -10000 0 84
SHB 0.026 0.004 -10000 0 -10000 0 0
SHF 0.01 0.08 -10000 0 -0.42 14 14
CSNK2A1 0.012 0.019 -10000 0 -10000 0 0
GO:0007205 -0.003 0.046 -10000 0 -0.31 9 9
SOS1 0.026 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.057 0.046 -10000 0 -0.21 8 8
PDGF/PDGFRA/SHB 0.033 0.052 -10000 0 -0.27 12 12
PDGF/PDGFRA/Caveolin-1 0.03 0.059 -10000 0 -0.29 13 13
ITGAV 0.026 0.002 -10000 0 -10000 0 0
ELK1 -0.008 0.041 0.25 1 -0.27 9 10
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.027 0.052 -10000 0 -0.26 12 12
JAK-STAT cascade 0.009 0.046 -10000 0 -0.27 11 11
cell proliferation 0.02 0.08 -10000 0 -0.29 26 26
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.006 0.049 -10000 0 -10000 0 0
DAPP1 -0.015 0.14 0.22 18 -0.37 28 46
Src family/SYK family/BLNK-LAT/BTK-ITK -0.068 0.2 0.23 11 -0.52 41 52
mol:DAG -0.006 0.094 0.18 47 -0.24 14 61
HRAS 0.025 0.022 -10000 0 -0.4 1 1
RAP1A 0.026 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.028 0.11 -10000 0 -0.41 14 14
PLCG2 -0.016 0.13 -10000 0 -0.4 42 42
PLCG1 0.016 0.013 -10000 0 -10000 0 0
ARF5 0.025 0.005 -10000 0 -10000 0 0
mol:GTP -0.015 0.026 -10000 0 -10000 0 0
ARF1/GTP 0.002 0.039 0.24 1 -10000 0 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
YES1 0.021 0.023 -10000 0 -0.4 1 1
RAP1A/GTP -0.015 0.027 -10000 0 -10000 0 0
ADAP1 -0.015 0.029 -10000 0 -0.37 1 1
ARAP3 -0.015 0.025 -10000 0 -10000 0 0
INPPL1 0.026 0.003 -10000 0 -10000 0 0
PREX1 0.014 0.024 -10000 0 -0.4 1 1
ARHGEF6 0.016 0.065 -10000 0 -0.4 10 10
ARHGEF7 0.02 0.011 -10000 0 -10000 0 0
ARF1 0.026 0.005 -10000 0 -10000 0 0
NRAS 0.024 0.03 -10000 0 -0.4 2 2
FYN 0.026 0.004 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
FGR 0.021 0.042 -10000 0 -0.4 4 4
mol:Ca2+ 0.002 0.057 0.16 5 -10000 0 5
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.015 0.12 -10000 0 -0.4 40 40
ZAP70 0.013 0.074 -10000 0 -0.4 13 13
mol:IP3 -0.004 0.072 0.17 16 -0.19 4 20
LYN 0.023 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.028 0.12 0.19 1 -0.41 15 16
RhoA/GDP 0.038 0.067 0.23 4 -0.32 2 6
PDK1/Src/Hsp90 0.032 0.027 -10000 0 -10000 0 0
BLNK 0.021 0.041 -10000 0 -0.4 4 4
actin cytoskeleton reorganization 0.035 0.091 0.23 23 -0.37 5 28
SRC 0.016 0.013 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.003 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
PTEN 0.025 0.009 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.015 0.032 -10000 0 -10000 0 0
RhoA/GTP -0.016 0.027 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.036 0.11 -10000 0 -0.39 19 19
BLK -0.1 0.19 -10000 0 -0.4 121 121
PDPK1 0.026 0.003 -10000 0 -10000 0 0
CYTH1 -0.016 0.026 -10000 0 -10000 0 0
HCK 0.011 0.047 -10000 0 -0.4 5 5
CYTH3 -0.015 0.025 -10000 0 -10000 0 0
CYTH2 -0.016 0.026 -10000 0 -10000 0 0
KRAS 0.027 0.006 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.009 0.086 -10000 0 -0.38 20 20
SGK1 -0.008 0.093 -10000 0 -0.4 21 21
INPP5D 0.026 0.002 -10000 0 -10000 0 0
mol:GDP 0.018 0.12 0.18 4 -0.42 16 20
SOS1 0.026 0.002 -10000 0 -10000 0 0
SYK 0.026 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.023 0.063 0.22 4 -0.31 2 6
mol:PI-3-4-5-P3 -0.015 0.026 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP -0.015 0.027 -10000 0 -10000 0 0
VAV1 0.007 0.088 -10000 0 -0.4 19 19
mol:PI-3-4-P2 0.013 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.043 0.041 0.21 1 -10000 0 1
PLEKHA1 -0.009 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.11 -10000 0 -0.42 13 13
LAT 0.023 0.036 -10000 0 -0.41 3 3
Rac1/GTP -0.016 0.11 -10000 0 -0.38 25 25
ITK -0.023 0.041 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.016 0.12 0.2 45 -0.31 23 68
LCK 0.016 0.064 -10000 0 -0.42 9 9
BTK -0.037 0.063 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.01 0.006 -10000 0 -10000 0 0
mol:DAG 0.017 0.056 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.017 0.23 1 -10000 0 1
CaM/Ca2+ 0.025 0.055 -10000 0 -10000 0 0
HIF1A 0.031 0.008 -10000 0 -10000 0 0
GAB1 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.039 0.073 -10000 0 -10000 0 0
PLCG1 0.017 0.056 -10000 0 -10000 0 0
NOS3 0.081 0.1 0.3 58 -10000 0 58
CBL 0.026 0.003 -10000 0 -10000 0 0
mol:NO 0.082 0.1 0.29 59 -10000 0 59
FLT1 0.013 0.008 -10000 0 -10000 0 0
PGF 0.012 0.075 -10000 0 -0.42 12 12
VEGFR1 homodimer/NRP2/VEGFR121 0.033 0.032 0.25 1 -10000 0 1
CALM1 0.025 0.007 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
eNOS/Hsp90 0.093 0.1 0.29 59 -10000 0 59
endothelial cell proliferation 0.048 0.12 0.33 41 -10000 0 41
mol:Ca2+ 0.017 0.056 -10000 0 -10000 0 0
MAPK3 0.003 0.052 -10000 0 -10000 0 0
MAPK1 0.003 0.05 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.012 0.074 -10000 0 -0.42 12 12
PRKACA 0.026 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.022 0.036 -10000 0 -0.4 3 3
VEGFA homodimer 0.027 0.017 0.37 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer 0.024 0.019 0.26 1 -10000 0 1
platelet activating factor biosynthetic process 0.044 0.12 0.34 54 -10000 0 54
PI3K 0.039 0.047 -10000 0 -10000 0 0
PRKCA 0.005 0.054 -10000 0 -10000 0 0
PRKCB -0.013 0.075 0.18 21 -10000 0 21
VEGFR1 homodimer/PLGF homodimer 0.019 0.043 -10000 0 -10000 0 0
VEGFA 0.027 0.017 0.37 1 -10000 0 1
VEGFB 0.026 0.004 -10000 0 -10000 0 0
mol:IP3 0.017 0.056 -10000 0 -10000 0 0
RASA1 0.049 0.073 -10000 0 -10000 0 0
NRP2 0.024 0.036 -10000 0 -0.4 3 3
VEGFR1 homodimer 0.013 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.026 0.004 -10000 0 -10000 0 0
NCK1 0.026 0.002 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.085 0.1 0.28 50 -10000 0 50
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.037 0.046 -10000 0 -10000 0 0
mol:L-citrulline 0.082 0.1 0.29 59 -10000 0 59
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.039 0.048 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.035 0.024 0.25 1 -10000 0 1
CD2AP 0.013 0.073 -10000 0 -0.4 13 13
PI3K/GAB1 0.081 0.065 -10000 0 -10000 0 0
PDPK1 0.041 0.077 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.035 0.024 0.25 1 -10000 0 1
mol:NADP 0.082 0.1 0.29 59 -10000 0 59
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.047 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.022 0.026 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.028 0.056 0.3 11 -0.24 1 12
KIRREL 0.022 0.044 -10000 0 -0.41 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.029 0.056 0.24 1 -0.3 11 12
PLCG1 0.016 0.013 -10000 0 -10000 0 0
ARRB2 0.022 0.01 -10000 0 -10000 0 0
WASL 0.025 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.042 0.074 0.23 1 -0.24 26 27
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.02 0.029 0.16 1 -0.21 4 5
FYN 0.013 0.062 0.27 12 -0.2 13 25
mol:Ca2+ 0.027 0.052 -10000 0 -0.23 10 10
mol:DAG 0.028 0.052 -10000 0 -0.23 10 10
NPHS2 -0.005 0.047 -10000 0 -0.42 4 4
mol:IP3 0.028 0.052 -10000 0 -0.23 10 10
regulation of endocytosis 0.036 0.047 0.21 1 -0.24 3 4
Nephrin/NEPH1/podocin/Cholesterol 0.036 0.051 0.22 1 -0.23 13 14
establishment of cell polarity 0.028 0.056 0.24 1 -0.3 11 12
Nephrin/NEPH1/podocin/NCK1-2 0.063 0.055 0.24 1 -0.38 1 2
Nephrin/NEPH1/beta Arrestin2 0.037 0.048 0.22 1 -0.24 3 4
NPHS1 0.014 0.062 0.34 1 -0.43 7 8
Nephrin/NEPH1/podocin 0.038 0.046 0.22 1 -0.2 13 14
TJP1 0.025 0.006 -10000 0 -10000 0 0
NCK1 0.026 0.002 -10000 0 -10000 0 0
NCK2 0.027 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.029 0.053 -10000 0 -0.24 10 10
CD2AP 0.013 0.073 -10000 0 -0.4 13 13
Nephrin/NEPH1/podocin/GRB2 0.05 0.055 0.23 1 -0.23 13 14
GRB2 0.026 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.01 0.078 0.28 10 -0.24 19 29
cytoskeleton organization 0.01 0.041 0.2 6 -0.24 4 10
Nephrin/NEPH1 0.025 0.04 0.2 1 -0.2 11 12
Nephrin/NEPH1/ZO-1 0.04 0.049 0.23 1 -0.23 11 12
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.008 0.006 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.024 0.025 -10000 0 -0.22 1 1
CDKN1B 0.024 0.058 -10000 0 -0.35 5 5
CDKN1A 0.023 0.062 0.2 1 -0.32 8 9
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.023 0.009 -10000 0 -10000 0 0
FOXO3 0.026 0.05 -10000 0 -0.27 5 5
AKT1 0.003 0.053 -10000 0 -0.31 10 10
BAD 0.025 0.021 -10000 0 -0.4 1 1
AKT3 0.009 0.034 -10000 0 -0.28 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.024 0.06 -10000 0 -0.32 7 7
AKT1/ASK1 0.041 0.087 -10000 0 -0.33 8 8
BAD/YWHAZ 0.044 0.025 -10000 0 -0.24 1 1
RICTOR 0.022 0.041 -10000 0 -0.4 4 4
RAF1 0.026 0.003 -10000 0 -10000 0 0
JNK cascade -0.038 0.084 0.32 8 -10000 0 8
TSC1 0.023 0.062 -10000 0 -0.33 7 7
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.045 0.09 -10000 0 -0.34 8 8
EP300 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0.026 0.064 -10000 0 -0.31 10 10
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.024 0.058 -10000 0 -0.35 5 5
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
TBC1D4 0.005 0.003 -10000 0 -10000 0 0
MAP3K5 0.026 0.004 -10000 0 -10000 0 0
MAPKAP1 0.026 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.051 0.089 0.29 5 -0.2 47 52
YWHAH 0.025 0.006 -10000 0 -10000 0 0
AKT1S1 0.024 0.061 -10000 0 -0.34 6 6
CASP9 0.025 0.053 -10000 0 -0.36 4 4
YWHAB 0.015 0.013 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.042 0.088 0.26 2 -0.35 6 8
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0.027 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
SRC 0.016 0.013 -10000 0 -10000 0 0
AKT2/p21CIP1 0.021 0.072 0.23 2 -0.32 8 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.028 -10000 0 -0.24 1 1
CHUK 0.026 0.048 -10000 0 -0.28 4 4
BAD/BCL-XL 0.018 0.059 -10000 0 -0.44 2 2
mTORC2 0.03 0.025 -10000 0 -0.21 4 4
AKT2 0.014 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.062 0.12 0.23 66 -0.35 10 76
PDPK1 0.026 0.003 -10000 0 -10000 0 0
MDM2 0.024 0.06 -10000 0 -0.34 6 6
MAPKKK cascade -0.044 0.088 0.34 8 -10000 0 8
MDM2/Cbp/p300 0.05 0.086 -10000 0 -0.49 2 2
TSC1/TSC2 0.023 0.058 0.34 1 -0.34 5 6
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.083 -10000 0 -0.47 2 2
glucose import 0.014 0.098 0.21 62 -0.2 37 99
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.044 0.18 3 -0.34 1 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.014 0.099 0.21 62 -0.2 37 99
GSK3A 0.025 0.06 0.2 2 -0.34 6 8
FOXO1 0.025 0.068 0.2 22 -0.33 6 28
GSK3B 0.024 0.063 0.2 1 -0.33 7 8
SFN 0.023 0.022 -10000 0 -0.4 1 1
G1/S transition of mitotic cell cycle 0.035 0.074 0.25 3 -0.35 7 10
p27Kip1/14-3-3 family 0.045 0.051 0.2 1 -10000 0 1
PRKACA 0.026 0.003 -10000 0 -10000 0 0
KPNA1 0.026 0.002 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
YWHAG 0.025 0.005 -10000 0 -10000 0 0
RHEB 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.004 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.016 0.013 -10000 0 -10000 0 0
NFATC1 -0.013 0.12 0.24 1 -0.38 25 26
NFATC2 0.033 0.05 0.14 4 -0.2 4 8
NFATC3 0.019 0.007 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.054 0.11 -10000 0 -0.29 50 50
Exportin 1/Ran/NUP214 0.053 0.008 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.038 0.12 -10000 0 -0.35 28 28
BCL2/BAX 0.023 0.048 -10000 0 -0.28 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.026 0.003 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
BAD 0.025 0.021 -10000 0 -0.4 1 1
CABIN1/MEF2D -0.042 0.11 -10000 0 -0.35 22 22
Calcineurin A alpha-beta B1/BCL2 0.011 0.061 -10000 0 -0.4 9 9
FKBP8 0.025 0.021 -10000 0 -0.4 1 1
activation-induced cell death of T cells 0.042 0.11 0.35 22 -10000 0 22
KPNB1 0.026 0.004 -10000 0 -10000 0 0
KPNA2 0.027 0.017 0.37 1 -10000 0 1
XPO1 0.026 0.001 -10000 0 -10000 0 0
SFN 0.023 0.022 -10000 0 -0.4 1 1
MAP3K8 0.026 0.003 -10000 0 -10000 0 0
NFAT4/CK1 alpha 0.026 0.023 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.068 0.065 -10000 0 -0.33 1 1
CABIN1 -0.055 0.11 -10000 0 -0.29 50 50
CALM1 0.025 0.007 -10000 0 -10000 0 0
RAN 0.026 0.002 -10000 0 -10000 0 0
MAP3K1 0.025 0.021 -10000 0 -0.4 1 1
CAMK4 0.002 0.094 -10000 0 -0.4 22 22
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.025 0.021 -10000 0 -0.4 1 1
YWHAH 0.025 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.022 0.067 -10000 0 -0.28 19 19
YWHAB 0.015 0.013 -10000 0 -10000 0 0
MAPK8 0.026 0.004 -10000 0 -10000 0 0
MAPK9 0.026 0.003 -10000 0 -10000 0 0
YWHAG 0.025 0.005 -10000 0 -10000 0 0
FKBP1A 0.021 0.011 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.015 0.12 0.22 3 -0.37 18 21
PRKCH 0.024 0.022 -10000 0 -0.4 1 1
CABIN1/Cbp/p300 0.036 0.013 -10000 0 -10000 0 0
CASP3 0.025 0.007 -10000 0 -10000 0 0
PIM1 0.026 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.007 -10000 0 -10000 0 0
apoptosis 0.009 0.016 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.044 -10000 0 -0.37 1 1
PRKCB -0.068 0.18 -10000 0 -0.4 94 94
PRKCE 0.026 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.024 0.036 -10000 0 -10000 0 0
BAD/BCL-XL 0.023 0.024 -10000 0 -0.28 1 1
PRKCD 0.026 0.004 -10000 0 -10000 0 0
NUP214 0.026 0.003 -10000 0 -10000 0 0
PRKCZ 0.025 0.006 -10000 0 -10000 0 0
PRKCA 0.025 0.005 -10000 0 -10000 0 0
PRKCG -0.12 0.22 0.37 4 -0.42 139 143
PRKCQ 0.02 0.05 -10000 0 -0.4 6 6
FKBP38/BCL2 0.022 0.05 -10000 0 -0.28 10 10
EP300 0.025 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.021 0.011 -10000 0 -10000 0 0
NFATc/JNK1 0.001 0.12 0.25 1 -0.36 24 25
CaM/Ca2+/FKBP38 0.033 0.018 -10000 0 -0.24 1 1
FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
CSNK1A1 0.013 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.018 0.06 -10000 0 -0.23 22 22
NFATc/ERK1 0 0.12 0.25 1 -0.36 23 24
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.04 0.12 -10000 0 -0.35 30 30
NR4A1 0.038 0.071 0.22 3 -0.37 7 10
GSK3B 0.027 0.002 -10000 0 -10000 0 0
positive T cell selection 0.019 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.03 0.037 -10000 0 -10000 0 0
RCH1/ KPNB1 0.038 0.007 -10000 0 -10000 0 0
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
AKAP5 0.005 0.088 -10000 0 -0.4 19 19
MEF2D 0.025 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha -0.001 0.12 0.25 1 -0.36 24 25
CREBBP 0.026 0.007 -10000 0 -10000 0 0
BCL2 0.011 0.062 -10000 0 -0.4 9 9
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.004 -10000 0 -10000 0 0
SNTA1 0.015 0.024 -10000 0 -0.4 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.008 0.012 -10000 0 -0.24 1 1
MAPK12 0.002 0.045 0.21 8 -0.28 6 14
CCND1 0.008 0.039 -10000 0 -0.32 4 4
p38 gamma/SNTA1 0.009 0.042 0.19 4 -0.39 2 6
MAP2K3 0.023 0.009 -10000 0 -10000 0 0
PKN1 0.026 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint 0.002 0.045 0.21 8 -0.28 6 14
MAP2K6 0.005 0.019 -10000 0 -0.22 3 3
MAPT -0.055 0.12 0.23 3 -0.28 88 91
MAPK13 0.011 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.014 0.002 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.004 -10000 0 -10000 0 0
VDR 0.026 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.039 0.057 -10000 0 -0.24 16 16
EP300 0.025 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.038 -10000 0 -0.32 1 1
KAT2B 0.009 0.084 -10000 0 -0.4 17 17
MAPK14 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.003 0.047 0.19 1 -0.2 4 5
RAR alpha/9cRA/Cyclin H 0.011 0.067 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.004 0.055 0.18 1 -0.23 11 12
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.003 0.053 -10000 0 -0.26 2 2
NCOR2 0.025 0.021 -10000 0 -0.4 1 1
VDR/VDR/Vit D3 0.019 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.028 0.081 0.3 1 -0.45 5 6
NCOA2 0.022 0.022 -10000 0 -0.4 1 1
NCOA3 0.015 0.013 -10000 0 -10000 0 0
NCOA1 0.026 0.001 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.003 -10000 0 -10000 0 0
RARG 0.027 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.035 0.005 -10000 0 -10000 0 0
MAPK3 0.025 0.021 -10000 0 -0.4 1 1
MAPK1 0.025 0.006 -10000 0 -10000 0 0
MAPK8 0.026 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.028 0.079 0.26 1 -0.36 5 6
RARA -0.013 0.054 0.18 3 -0.21 6 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.002 0.051 0.18 1 -0.22 10 11
PRKCA 0.027 0.009 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.033 0.085 0.32 1 -0.46 5 6
RXRG -0.14 0.16 0.28 3 -0.32 156 159
RXRA -0.009 0.053 0.26 1 -0.2 2 3
RXRB -0.027 0.08 0.27 4 -0.34 2 6
VDR/Vit D3/DNA 0.019 0.002 -10000 0 -10000 0 0
RBP1 0.002 0.1 0.37 1 -0.42 24 25
CRBP1/9-cic-RA 0.002 0.074 0.24 1 -0.3 24 25
RARB 0.023 0.042 -10000 0 -0.4 4 4
PRKCG -0.12 0.22 0.37 4 -0.42 139 143
MNAT1 0.024 0.023 -10000 0 -0.42 1 1
RAR alpha/RXRs -0.028 0.075 -10000 0 -0.41 5 5
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.02 0.071 0.3 1 -0.36 4 5
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.072 0.24 4 -0.27 3 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.032 0.086 0.32 1 -0.46 5 6
positive regulation of DNA binding 0.004 0.06 -10000 0 -10000 0 0
NRIP1 -0.033 0.11 -10000 0 -1.1 2 2
RXRs/RARs -0.032 0.085 0.34 1 -0.38 5 6
RXRs/RXRs/DNA/9cRA -0.037 0.07 -10000 0 -0.37 5 5
PRKACA 0.026 0.003 -10000 0 -10000 0 0
CDK7 0.026 0.004 -10000 0 -10000 0 0
TFIIH 0.048 0.021 -10000 0 -0.26 1 1
RAR alpha/9cRA 0.019 0.065 0.23 1 -0.25 2 3
CCNH 0.026 0.004 -10000 0 -10000 0 0
CREBBP 0.026 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.047 0.021 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.002 0.063 -10000 0 -0.42 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.008 0.091 0.41 3 -10000 0 3
IL27/IL27R/JAK1 0.028 0.11 -10000 0 -0.56 1 1
TBX21 -0.027 0.13 -10000 0 -0.5 16 16
IL12B 0.005 0.047 -10000 0 -0.43 4 4
IL12A 0 0.037 -10000 0 -0.28 7 7
IL6ST 0.016 0.06 -10000 0 -0.41 8 8
IL27RA/JAK1 0.021 0.027 -10000 0 -10000 0 0
IL27 0.004 0.081 -10000 0 -0.42 14 14
TYK2 0.022 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.037 0.14 0.42 1 -10000 0 1
T-helper 2 cell differentiation 0.008 0.091 0.41 3 -10000 0 3
T cell proliferation during immune response 0.008 0.091 0.41 3 -10000 0 3
MAPKKK cascade -0.008 0.091 -10000 0 -0.41 3 3
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT2 0.026 0.002 -10000 0 -10000 0 0
STAT1 0.026 0.022 -10000 0 -0.43 1 1
IL12RB1 0.01 0.081 -10000 0 -0.4 16 16
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.021 0.11 -10000 0 -0.45 15 15
IL27/IL27R/JAK2/TYK2 -0.008 0.092 -10000 0 -0.42 3 3
positive regulation of T cell mediated cytotoxicity -0.008 0.091 -10000 0 -0.41 3 3
STAT1 (dimer) 0.028 0.16 -10000 0 -0.51 15 15
JAK2 0.021 0.039 -10000 0 -0.4 3 3
JAK1 0.026 0.005 -10000 0 -10000 0 0
STAT2 (dimer) 0.003 0.096 -10000 0 -0.4 3 3
T cell proliferation -0.048 0.12 -10000 0 -0.38 16 16
IL12/IL12R/TYK2/JAK2 0.004 0.14 -10000 0 -0.78 10 10
IL17A -0.037 0.14 0.43 1 -10000 0 1
mast cell activation 0.008 0.091 0.41 3 -10000 0 3
IFNG 0.001 0.026 -10000 0 -0.089 4 4
T cell differentiation -0.001 0.004 -10000 0 -0.017 3 3
STAT3 (dimer) 0.003 0.095 -10000 0 -0.4 3 3
STAT5A (dimer) 0.003 0.095 -10000 0 -0.4 3 3
STAT4 (dimer) -0.007 0.12 -10000 0 -0.39 17 17
STAT4 0.003 0.097 -10000 0 -0.4 23 23
T cell activation -0.006 0.002 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.036 0.06 -10000 0 -10000 0 0
GATA3 -0.015 0.12 -10000 0 -1.2 4 4
IL18 0.004 0.02 -10000 0 -0.28 2 2
positive regulation of mast cell cytokine production 0.003 0.094 -10000 0 -0.39 3 3
IL27/EBI3 -0.003 0.11 -10000 0 -0.3 47 47
IL27RA 0.008 0.025 -10000 0 -10000 0 0
IL6 -0.064 0.17 0.34 5 -0.44 64 69
STAT5A 0.026 0.004 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.016 0.013 -10000 0 -10000 0 0
IL1B -0.029 0.096 -10000 0 -0.3 48 48
EBI3 -0.009 0.12 -10000 0 -0.4 34 34
TNF 0.004 0.02 -10000 0 -0.28 2 2
Arf6 trafficking events

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
SLC2A4 -0.022 0.13 -10000 0 -0.4 44 44
CLTC -0.004 0.1 -10000 0 -0.39 26 26
calcium ion-dependent exocytosis 0.012 0.046 -10000 0 -10000 0 0
Dynamin 2/GTP 0.019 0.038 0.19 1 -0.22 9 10
EXOC4 0.025 0.005 -10000 0 -10000 0 0
CD59 0.001 0.077 -10000 0 -0.32 21 21
CPE -0.005 0.064 -10000 0 -0.24 30 30
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
membrane fusion 0.019 0.031 -10000 0 -10000 0 0
CTNND1 0.008 0.04 0.18 7 -0.22 7 14
DNM2 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.064 -10000 0 -0.24 19 19
TSHR 0.001 0.035 -10000 0 -0.24 8 8
INS 0.007 0.041 -10000 0 -0.51 2 2
BIN1 0.025 0.021 -10000 0 -0.4 1 1
mol:Choline 0.019 0.031 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.008 0.039 0.24 1 -0.25 9 10
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.037 0.19 1 -0.22 9 10
JUP 0.001 0.077 0.21 1 -0.31 21 22
ASAP2/amphiphysin II 0.047 0.019 -10000 0 -0.22 1 1
ARF6/GTP 0.018 0.005 -10000 0 -10000 0 0
CDH1 0.001 0.076 -10000 0 -0.31 21 21
clathrin-independent pinocytosis 0.018 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.024 0.03 -10000 0 -0.41 2 2
positive regulation of endocytosis 0.018 0.005 -10000 0 -10000 0 0
EXOC2 0.025 0.021 -10000 0 -0.4 1 1
substrate adhesion-dependent cell spreading 0.023 0.046 -10000 0 -0.41 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.093 0.32 25 -10000 0 25
positive regulation of phagocytosis 0.012 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.032 0.021 -10000 0 -0.24 2 2
ACAP1 0.018 0.033 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.04 0.12 -10000 0 -0.39 24 24
clathrin heavy chain/ACAP1 0 0.089 0.18 2 -0.32 24 26
JIP4/KLC1 0.046 0.015 -10000 0 -10000 0 0
EXOC1 0.025 0.021 -10000 0 -0.4 1 1
exocyst 0.02 0.044 -10000 0 -0.41 3 3
RALA/GTP 0.018 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.033 0.01 -10000 0 -10000 0 0
receptor recycling 0.018 0.005 -10000 0 -10000 0 0
CTNNA1 0.008 0.04 0.18 8 -0.21 9 17
NME1 0.008 0.039 0.24 1 -0.25 9 10
clathrin coat assembly -0.002 0.1 -10000 0 -0.38 26 26
IL2RA -0.001 0.078 -10000 0 -0.31 22 22
VAMP3 0.012 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.011 0.1 -10000 0 -0.29 28 28
EXOC6 0.025 0.006 -10000 0 -10000 0 0
PLD1 0.011 0.014 -10000 0 -0.24 1 1
PLD2 0.011 0.007 -10000 0 -10000 0 0
EXOC5 0.022 0.036 -10000 0 -0.4 3 3
PIP5K1C 0.006 0.056 -10000 0 -0.22 16 16
SDC1 0.001 0.076 -10000 0 -0.31 21 21
ARF6/GDP 0.017 0.04 0.2 1 -0.25 9 10
EXOC7 0.026 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.019 0.096 -10000 0 -0.32 25 25
mol:Phosphatidic acid 0.019 0.031 -10000 0 -10000 0 0
endocytosis -0.045 0.018 0.21 1 -10000 0 1
SCAMP2 0.025 0.005 -10000 0 -10000 0 0
ADRB2 -0.032 0.12 -10000 0 -0.41 29 29
EXOC3 0.026 0.004 -10000 0 -10000 0 0
ASAP2 0.026 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.023 0.038 0.21 1 -0.22 9 10
KLC1 0.025 0.007 -10000 0 -10000 0 0
AVPR2 -0.017 0.11 0.23 2 -0.39 27 29
RALA 0.024 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.015 0.09 -10000 0 -0.32 22 22
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.17 -10000 0 -0.4 75 75
CaM/Ca2+ 0.018 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.007 -10000 0 -10000 0 0
AKT2 0.026 0.004 -10000 0 -10000 0 0
STXBP4 0.025 0.021 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.18 -10000 0 -0.42 81 81
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
TBC1D4 0.009 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.025 0.006 -10000 0 -10000 0 0
YWHAB 0.015 0.013 -10000 0 -10000 0 0
SNARE/Synip 0.043 0.025 -10000 0 -0.24 1 1
YWHAG 0.025 0.005 -10000 0 -10000 0 0
ASIP 0.003 0.042 0.37 2 -0.42 2 4
PRKCI 0.024 0.029 -10000 0 -0.4 2 2
AS160/CaM/Ca2+ 0.018 0.005 -10000 0 -10000 0 0
RHOQ 0.026 0.003 -10000 0 -10000 0 0
GYS1 0.01 0.003 -10000 0 -10000 0 0
PRKCZ 0.025 0.006 -10000 0 -10000 0 0
TRIP10 0.025 0.021 -10000 0 -0.4 1 1
TC10/GTP/CIP4/Exocyst 0.034 0.014 -10000 0 -0.24 1 1
AS160/14-3-3 0.014 0.037 -10000 0 -10000 0 0
VAMP2 0.022 0.01 -10000 0 -10000 0 0
SLC2A4 -0.14 0.2 -10000 0 -0.48 81 81
STX4 0.026 0.003 -10000 0 -10000 0 0
GSK3B 0.019 0.006 -10000 0 -10000 0 0
SFN 0.023 0.022 -10000 0 -0.4 1 1
LNPEP 0.025 0.006 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
EPO signaling 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
BCL2L1 0.021 0.065 -10000 0 -10000 0 0
CRKL 0.02 0.052 0.29 1 -0.29 2 3
mol:DAG 0.018 0.031 -10000 0 -10000 0 0
HRAS 0.002 0.06 0.27 2 -10000 0 2
MAPK8 0.027 0.068 0.19 44 -10000 0 44
RAP1A 0.019 0.052 0.29 1 -0.29 2 3
GAB1 0.019 0.052 0.29 1 -0.29 2 3
MAPK14 0.028 0.069 0.19 45 -10000 0 45
EPO 0.018 0.044 0.35 1 -0.43 3 4
PLCG1 0.018 0.031 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.025 0.024 -10000 0 -0.39 1 1
RAPGEF1 0.025 0.021 -10000 0 -0.4 1 1
EPO/EPOR (dimer)/SOCS3 0.045 0.036 0.24 1 -0.24 4 5
GAB1/SHC/GRB2/SOS1 0.048 0.052 0.27 1 -0.3 1 2
EPO/EPOR (dimer) 0.032 0.039 0.25 1 -0.3 4 5
IRS2 0.013 0.042 -10000 0 -0.33 1 1
STAT1 0.026 0.052 -10000 0 -10000 0 0
STAT5B 0.024 0.048 -10000 0 -10000 0 0
cell proliferation 0.019 0.077 0.2 49 -10000 0 49
GAB1/SHIP/PIK3R1/SHP2/SHC 0.039 0.045 -10000 0 -0.29 1 1
TEC 0.019 0.053 0.29 1 -0.3 2 3
SOCS3 0.026 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.025 0.052 -10000 0 -10000 0 0
JAK2 0.024 0.038 -10000 0 -0.41 3 3
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.061 0.055 0.25 1 -0.31 2 3
EPO/EPOR 0.032 0.039 0.25 1 -0.3 4 5
LYN 0.022 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.03 0.057 0.28 1 -0.26 1 2
elevation of cytosolic calcium ion concentration 0.025 0.024 -10000 0 -0.39 1 1
SHC1 0.026 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.042 0.039 0.24 1 -0.23 3 4
mol:IP3 0.018 0.031 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.033 0.047 -10000 0 -0.31 1 1
SH2B3 0.027 0.011 -10000 0 -10000 0 0
NFKB1 0.027 0.068 0.19 44 -10000 0 44
EPO/EPOR (dimer)/JAK2/SOCS3 0.01 0.032 -10000 0 -0.26 3 3
PTPN6 0.019 0.051 -10000 0 -0.3 2 2
TEC/VAV2/GRB2 0.041 0.059 0.28 1 -10000 0 1
EPOR 0.025 0.024 -10000 0 -0.39 1 1
INPP5D 0.026 0.002 -10000 0 -10000 0 0
mol:GDP 0.047 0.053 0.27 1 -0.31 1 2
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG2 -0.016 0.13 -10000 0 -0.4 42 42
CRKL/CBL/C3G 0.045 0.052 0.28 1 -10000 0 1
VAV2 0.017 0.056 0.29 1 -0.26 1 2
CBL 0.019 0.053 0.29 1 -0.29 2 3
SHC/Grb2/SOS1 0.034 0.044 -10000 0 -0.31 1 1
STAT5A 0.024 0.048 -10000 0 -10000 0 0
GRB2 0.026 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.035 0.073 -10000 0 -0.3 5 5
LYN/PLCgamma2 0.007 0.088 -10000 0 -0.28 35 35
PTPN11 0.026 0.003 -10000 0 -10000 0 0
BTK -0.005 0.088 0.29 1 -0.3 10 11
BCL2 0.004 0.18 -10000 0 -0.72 24 24
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.02 0.053 -10000 0 -0.31 2 2
BAG4 0.022 0.01 -10000 0 -10000 0 0
BAD 0.012 0.031 -10000 0 -0.36 1 1
NFKBIA 0.025 0.007 -10000 0 -10000 0 0
BIRC3 0.018 0.058 -10000 0 -0.4 8 8
BAX 0.013 0.033 0.16 7 -0.19 1 8
EnzymeConsortium:3.1.4.12 0.008 0.016 0.059 4 -0.071 1 5
IKBKB 0.035 0.07 0.21 26 -0.32 1 27
MAP2K2 0.012 0.042 0.19 11 -0.31 1 12
MAP2K1 0.011 0.038 0.19 10 -10000 0 10
SMPD1 0.008 0.03 0.12 3 -0.19 6 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.057 0.21 1 -0.36 1 2
MAP2K4 0.008 0.026 0.14 1 -0.23 1 2
protein ubiquitination 0.026 0.059 -10000 0 -0.31 2 2
EnzymeConsortium:2.7.1.37 0.013 0.042 0.19 12 -0.23 1 13
response to UV 0 0 0.002 12 -10000 0 12
RAF1 0.014 0.039 0.19 11 -0.19 1 12
CRADD 0.026 0.003 -10000 0 -10000 0 0
mol:ceramide 0.014 0.03 0.1 5 -0.2 1 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0.033 0.01 -10000 0 -10000 0 0
MADD 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 0.011 0.03 0.12 1 -0.22 2 3
TRADD 0.026 0.002 -10000 0 -10000 0 0
RELA/p50 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.015 0.041 0.19 11 -0.25 1 12
MAPK1 0.012 0.043 0.2 9 -0.25 1 10
p50/RELA/I-kappa-B-alpha 0.036 0.011 -10000 0 -10000 0 0
FADD 0.022 0.052 0.21 1 -0.3 2 3
KSR1 0.015 0.039 0.18 12 -0.19 1 13
MAPK8 0.008 0.028 -10000 0 -0.22 1 1
TRAF2 0.025 0.021 -10000 0 -0.4 1 1
response to radiation 0 0 0.002 5 -10000 0 5
CHUK 0.019 0.051 0.2 1 -0.29 1 2
TNF R/SODD 0.033 0.015 -10000 0 -10000 0 0
TNF 0.024 0.03 -10000 0 -0.4 2 2
CYCS 0.035 0.049 0.13 38 -0.28 1 39
IKBKG 0.019 0.057 -10000 0 -0.36 2 2
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.025 0.056 -10000 0 -0.3 3 3
RELA 0.026 0.004 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
AIFM1 0.029 0.045 0.13 24 -0.28 1 25
TNF/TNF R/SODD 0.043 0.028 -10000 0 -0.24 2 2
TNFRSF1A 0.026 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 5 -10000 0 5
CASP8 0.024 0.089 -10000 0 -0.57 9 9
NSMAF 0.04 0.077 0.21 48 -0.32 1 49
response to hydrogen peroxide 0 0 0.002 12 -10000 0 12
BCL2 0.011 0.062 -10000 0 -0.4 9 9
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.022 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.028 0.07 -10000 0 -0.36 4 4
NEF -0.006 0.036 -10000 0 -0.23 2 2
NFKBIA 0.024 0.018 -10000 0 -10000 0 0
BIRC3 0.011 0.064 -10000 0 -0.44 8 8
CYCS 0.011 0.084 0.18 39 -0.39 4 43
RIPK1 0.026 0.003 -10000 0 -10000 0 0
CD247 0.006 0.093 -10000 0 -0.49 12 12
MAP2K7 0.019 0.1 -10000 0 -0.61 7 7
protein ubiquitination 0.025 0.045 0.2 4 -0.29 1 5
CRADD 0.026 0.003 -10000 0 -10000 0 0
DAXX 0.026 0.003 -10000 0 -10000 0 0
FAS 0.023 0.03 -10000 0 -0.4 2 2
BID 0.002 0.073 0.18 7 -0.26 24 31
NF-kappa-B/RelA/I kappa B alpha 0.049 0.044 -10000 0 -0.24 8 8
TRADD 0.026 0.002 -10000 0 -10000 0 0
MAP3K5 0.026 0.004 -10000 0 -10000 0 0
CFLAR 0.027 0 -10000 0 -10000 0 0
FADD 0.026 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.049 0.044 -10000 0 -0.24 8 8
MAPK8 0.017 0.097 -10000 0 -0.56 7 7
APAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF2 0.025 0.021 -10000 0 -0.4 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.078 0.19 8 -0.27 25 33
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.03 0.048 -10000 0 -0.39 1 1
CHUK 0.026 0.047 0.22 2 -0.32 1 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.072 0.028 -10000 0 -10000 0 0
TCRz/NEF 0.001 0.094 -10000 0 -0.32 30 30
TNF 0.024 0.03 -10000 0 -0.4 2 2
FASLG -0.018 0.14 -10000 0 -0.5 30 30
NFKB1 0.026 0.017 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.043 0.028 -10000 0 -0.24 2 2
CASP6 0.035 0.094 -10000 0 -0.48 7 7
CASP7 0.012 0.095 -10000 0 -0.43 11 11
RELA 0.026 0.017 -10000 0 -10000 0 0
CASP2 0.025 0.005 -10000 0 -10000 0 0
CASP3 0.009 0.095 0.28 1 -0.45 10 11
TNFRSF1A 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.033 0.015 -10000 0 -10000 0 0
CASP8 0.027 0 -10000 0 -10000 0 0
CASP9 0.025 0.006 -10000 0 -10000 0 0
MAP3K14 0.028 0.05 0.2 4 -0.36 1 5
APAF-1/Caspase 9 0.021 0.079 -10000 0 -0.31 8 8
BCL2 0.008 0.089 -10000 0 -0.5 7 7
Regulation of Telomerase

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
Telomerase catalytic core complex 0.005 0.13 -10000 0 -1.1 2 2
RAD9A 0.026 0.004 -10000 0 -10000 0 0
AP1 0.034 0.029 -10000 0 -0.27 3 3
IFNAR2 0.023 0.013 -10000 0 -10000 0 0
AKT1 -0.004 0.064 -10000 0 -0.32 8 8
ER alpha/Oestrogen -0.008 0.085 -10000 0 -0.28 38 38
NFX1/SIN3/HDAC complex 0.036 0.043 -10000 0 -0.24 1 1
EGF -0.061 0.17 -10000 0 -0.4 82 82
SMG5 0.026 0.004 -10000 0 -10000 0 0
SMG6 0.022 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.035 0.02 -10000 0 -10000 0 0
TERT/c-Abl 0.015 0.12 -10000 0 -1 2 2
SAP18 0.021 0.011 -10000 0 -10000 0 0
MRN complex 0.043 0.025 -10000 0 -0.24 1 1
WT1 -0.19 0.23 0.37 4 -0.42 203 207
WRN 0.02 0.023 -10000 0 -0.4 1 1
SP1 0.024 0.015 -10000 0 -10000 0 0
SP3 0.026 0.004 -10000 0 -10000 0 0
TERF2IP 0.026 0.002 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.03 0.12 -10000 0 -0.89 2 2
Mad/Max 0.035 0.025 -10000 0 -0.28 2 2
TERT 0.005 0.13 -10000 0 -1.1 2 2
CCND1 0.005 0.12 -10000 0 -0.92 2 2
MAX 0.025 0.007 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
RBBP4 0.025 0.006 -10000 0 -10000 0 0
TERF2 0.023 0.007 -10000 0 -10000 0 0
PTGES3 0.026 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.006 -10000 0 -10000 0 0
Telomerase/911 0.042 0.042 -10000 0 -0.31 1 1
CDKN1B -0.008 0.084 -10000 0 -0.39 2 2
RAD1 0.027 0.017 0.37 1 -10000 0 1
XRCC5 0.026 0.001 -10000 0 -10000 0 0
XRCC6 0.025 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.036 0.011 -10000 0 -10000 0 0
UBE3A 0.024 0.022 -10000 0 -0.4 1 1
JUN 0.026 0.006 -10000 0 -10000 0 0
E6 0 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.016 0.018 -10000 0 -0.28 1 1
FOS 0.022 0.036 -10000 0 -0.4 3 3
IFN-gamma/IRF1 0.009 0.1 -10000 0 -0.29 43 43
PARP2 0.025 0.006 -10000 0 -10000 0 0
BLM 0.025 0.005 -10000 0 -10000 0 0
Telomerase 0.001 0.1 -10000 0 -0.65 6 6
IRF1 0.028 0.011 -10000 0 -10000 0 0
ESR1 -0.014 0.12 -10000 0 -0.4 38 38
KU/TER 0.037 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.039 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.032 0.054 -10000 0 -0.29 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.033 0.054 -10000 0 -0.3 3 3
HDAC1 0.025 0.006 -10000 0 -10000 0 0
HDAC2 0.023 0.015 -10000 0 -10000 0 0
ATM 0.01 0.002 -10000 0 -10000 0 0
SMAD3 0.011 0.016 -10000 0 -0.3 1 1
ABL1 0.026 0.003 -10000 0 -10000 0 0
MXD1 0.024 0.029 -10000 0 -0.4 2 2
MRE11A 0.026 0.004 -10000 0 -10000 0 0
HUS1 0.024 0.008 -10000 0 -10000 0 0
RPS6KB1 0.025 0.021 -10000 0 -0.4 1 1
TERT/NF kappa B1/14-3-3 0.015 0.14 -10000 0 -0.98 2 2
NR2F2 0.025 0.007 -10000 0 -10000 0 0
MAPK3 -0.009 0.019 -10000 0 -0.3 1 1
MAPK1 -0.008 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.025 0.022 -10000 0 -0.42 1 1
NFKB1 0.026 0.004 -10000 0 -10000 0 0
HNRNPC 0.025 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.002 -10000 0 -10000 0 0
NBN 0.022 0.023 -10000 0 -0.4 1 1
EGFR 0.023 0.022 -10000 0 -0.4 1 1
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.022 0.12 -10000 0 -0.29 73 73
MYC 0.023 0.047 0.37 4 -0.42 2 6
IL2 0.016 0.016 -10000 0 -10000 0 0
KU 0.037 0.009 -10000 0 -10000 0 0
RAD50 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
TGFB1 0.025 0.022 -10000 0 -0.42 1 1
TRF2/BLM 0.037 0.009 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.025 0.13 -10000 0 -1 2 2
SP1/HDAC2 0.036 0.023 -10000 0 -10000 0 0
PINX1 0.021 0.011 -10000 0 -10000 0 0
Telomerase/EST1A 0.025 0.12 -10000 0 -0.89 2 2
Smad3/Myc 0.023 0.035 0.25 4 -0.26 3 7
911 complex 0.047 0.021 0.25 1 -10000 0 1
IFNG -0.017 0.13 -10000 0 -0.42 42 42
Telomerase/PinX1 0.019 0.11 -10000 0 -0.89 2 2
Telomerase/AKT1/mTOR/p70S6K 0.003 0.092 0.22 1 -0.38 12 13
SIN3B 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.029 0.12 -10000 0 -0.89 2 2
response to DNA damage stimulus 0.003 0.014 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.06 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.029 0.021 -10000 0 -0.26 1 1
Telomerase/hnRNP C1/C2 0.031 0.12 -10000 0 -0.89 2 2
E2F1 0.019 0.059 0.37 8 -0.43 2 10
ZNFX1 0.015 0.013 -10000 0 -10000 0 0
PIF1 0.016 0.065 -10000 0 -0.42 9 9
NCL 0.026 0.002 -10000 0 -10000 0 0
DKC1 0.026 0.002 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.08 0.23 -10000 0 -1 1 1
PLK1 0.042 0.091 -10000 0 -0.83 4 4
BIRC5 0.039 0.1 -10000 0 -0.82 5 5
HSPA1B 0.073 0.24 -10000 0 -1 1 1
MAP2K1 0.036 0.036 -10000 0 -10000 0 0
BRCA2 0.12 0.24 0.57 1 -1 1 2
FOXM1 0.082 0.25 -10000 0 -0.99 3 3
XRCC1 0.081 0.23 -10000 0 -1 1 1
FOXM1B/p19 0.046 0.25 -10000 0 -0.9 4 4
Cyclin D1/CDK4 0.086 0.22 -10000 0 -0.93 1 1
CDC2 0.082 0.24 -10000 0 -0.88 3 3
TGFA 0.078 0.21 -10000 0 -0.89 1 1
SKP2 0.083 0.23 -10000 0 -1 1 1
CCNE1 0.029 0.033 0.36 2 -0.41 1 3
CKS1B 0.084 0.23 -10000 0 -1 1 1
RB1 0.057 0.13 -10000 0 -0.7 2 2
FOXM1C/SP1 0.086 0.24 -10000 0 -0.92 3 3
AURKB -0.089 0.33 -10000 0 -0.83 61 61
CENPF 0.084 0.23 -10000 0 -1 1 1
CDK4 0.029 0.027 -10000 0 -0.42 1 1
MYC 0.062 0.21 -10000 0 -0.89 1 1
CHEK2 0.036 0.036 -10000 0 -10000 0 0
ONECUT1 0.079 0.22 -10000 0 -0.98 1 1
CDKN2A -0.074 0.19 0.37 1 -0.43 91 92
LAMA4 0.08 0.23 -10000 0 -1 1 1
FOXM1B/HNF6 0.078 0.24 -10000 0 -1.1 1 1
FOS 0.069 0.27 -10000 0 -1.1 8 8
SP1 0.026 0.007 -10000 0 -10000 0 0
CDC25B 0.1 0.24 0.57 1 -1.1 1 2
response to radiation 0.014 0.021 -10000 0 -10000 0 0
CENPB 0.11 0.24 0.57 1 -1 1 2
CENPA 0.079 0.23 -10000 0 -1 1 1
NEK2 0.084 0.23 -10000 0 -1 1 1
HIST1H2BA 0.076 0.23 -10000 0 -1 1 1
CCNA2 0.028 0.011 -10000 0 -10000 0 0
EP300 0.025 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.077 0.24 -10000 0 -1.2 1 1
CCNB2 0.08 0.23 -10000 0 -1 1 1
CCNB1 0.081 0.24 -10000 0 -1.1 1 1
ETV5 0.078 0.23 -10000 0 -1 1 1
ESR1 0.015 0.39 -10000 0 -1.1 39 39
CCND1 0.078 0.22 -10000 0 -0.94 1 1
GSK3A 0.033 0.033 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.063 0.041 0.23 2 -0.23 1 3
CDK2 0.029 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.016 0.024 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.089 0.24 -10000 0 -0.95 2 2
GAS1 -0.009 0.42 -10000 0 -1.1 52 52
MMP2 0.077 0.24 -10000 0 -1.2 2 2
RB1/FOXM1C 0.058 0.21 -10000 0 -0.99 1 1
CREBBP 0.026 0.004 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.034 0.039 0.26 1 -0.3 5 6
CRKL 0.032 0.077 0.25 7 -0.38 7 14
mol:PIP3 -0.004 0.041 -10000 0 -0.82 1 1
AKT1 -0.01 0.038 -10000 0 -0.72 1 1
PTK2B 0.02 0.023 -10000 0 -0.4 1 1
RAPGEF1 0.032 0.077 0.25 7 -0.38 6 13
RANBP10 0.026 0.001 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.044 0.045 -10000 0 -0.24 9 9
MAP3K5 0.017 0.11 0.23 3 -0.39 13 16
HGF/MET/CIN85/CBL/ENDOPHILINS 0.057 0.045 -10000 0 -0.23 6 6
AP1 0.028 0.034 -10000 0 -0.25 2 2
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.004 -10000 0 -10000 0 0
apoptosis -0.034 0.22 -10000 0 -0.74 38 38
STAT3 (dimer) 0.007 0.045 -10000 0 -0.31 2 2
GAB1/CRKL/SHP2/PI3K 0.068 0.076 0.28 3 -0.36 6 9
INPP5D 0.026 0.002 -10000 0 -10000 0 0
CBL/CRK 0.051 0.078 0.26 6 -0.38 6 12
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.013 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
ELK1 0.006 0.091 0.29 31 -10000 0 31
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.033 -10000 0 -0.19 2 2
PAK1 -0.01 0.039 -10000 0 -0.69 1 1
HGF/MET/RANBP10 0.044 0.045 -10000 0 -0.25 9 9
HRAS 0.021 0.057 0.33 1 -0.42 2 3
DOCK1 0.032 0.072 0.25 6 -0.39 5 11
GAB1 0.024 0.066 -10000 0 -0.41 6 6
CRK 0.029 0.071 0.26 5 -0.38 6 11
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.067 0.26 1 -0.39 8 9
JUN 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.01 0.035 -10000 0 -0.18 7 7
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.05 0.091 0.3 9 -0.34 1 10
GRB2/SHC 0.01 0.051 0.18 1 -0.2 2 3
FOS 0.022 0.036 -10000 0 -0.4 3 3
GLMN 0.002 0.011 -10000 0 -0.22 1 1
cell motility 0.006 0.09 0.29 31 -10000 0 31
HGF/MET/MUC20 0.028 0.041 -10000 0 -0.24 9 9
cell migration 0.009 0.051 0.18 1 -0.2 2 3
GRB2 0.026 0.004 -10000 0 -10000 0 0
CBL 0.026 0.003 -10000 0 -10000 0 0
MET/RANBP10 0.035 0.036 0.26 1 -0.3 4 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.041 -10000 0 -0.28 5 5
MET/MUC20 0.016 0.033 0.24 1 -0.3 4 5
RAP1B 0.03 0.074 0.24 8 -0.36 6 14
RAP1A 0.029 0.073 0.24 7 -0.36 6 13
HGF/MET/RANBP9 0.043 0.047 -10000 0 -0.25 10 10
RAF1 0.024 0.06 0.31 1 -0.4 2 3
STAT3 0.007 0.045 -10000 0 -0.32 2 2
cell proliferation 0.026 0.062 0.25 2 -0.35 3 5
RPS6KB1 0.004 0.035 -10000 0 -0.28 5 5
MAPK3 -0.011 0.082 0.43 8 -10000 0 8
MAPK1 0.017 0.16 0.63 22 -10000 0 22
RANBP9 0.025 0.021 -10000 0 -0.4 1 1
MAPK8 0.026 0.1 0.24 2 -0.45 5 7
SRC 0.006 0.031 -10000 0 -0.27 3 3
PI3K 0.011 0.051 -10000 0 -0.2 1 1
MET/Glomulin -0.014 0.053 0.21 1 -0.2 12 13
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K1 0.021 0.058 0.3 1 -0.38 2 3
MET 0.022 0.047 0.37 1 -0.42 4 5
MAP4K1 0.018 0.11 0.23 5 -0.41 14 19
PTK2 0.022 0.01 -10000 0 -10000 0 0
MAP2K2 0.021 0.06 0.3 1 -0.37 3 4
BAD -0.011 0.038 -10000 0 -0.69 1 1
MAP2K4 0.012 0.096 0.24 2 -0.37 11 13
SHP2/GRB2/SOS1/GAB1 0.051 0.064 0.26 1 -0.35 5 6
INPPL1 0.026 0.003 -10000 0 -10000 0 0
PXN 0.026 0.002 -10000 0 -10000 0 0
SH3KBP1 0.026 0.003 -10000 0 -10000 0 0
HGS -0.013 0.031 -10000 0 -0.21 2 2
PLCgamma1/PKC 0.012 0.01 -10000 0 -10000 0 0
HGF 0.018 0.055 -10000 0 -0.4 7 7
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.002 -10000 0 -10000 0 0
PTPRJ 0.026 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.025 0.029 -10000 0 -10000 0 0
PDPK1 -0.008 0.041 -10000 0 -0.76 1 1
HGF/MET/SHIP 0.044 0.045 -10000 0 -0.25 9 9
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.036 0.056 -10000 0 -0.24 15 15
forebrain development 0.003 0.095 -10000 0 -0.52 6 6
GNAO1 -0.088 0.19 -10000 0 -0.4 114 114
SMO/beta Arrestin2 0.033 0.018 -10000 0 -10000 0 0
SMO 0.026 0.007 -10000 0 -10000 0 0
ARRB2 0.023 0.01 -10000 0 -10000 0 0
GLI3/SPOP 0.044 0.085 0.23 3 -0.35 3 6
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.026 0.002 -10000 0 -10000 0 0
GNAI2 0.026 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.049 0.031 -10000 0 -10000 0 0
GNAI1 0.012 0.076 -10000 0 -0.4 14 14
XPO1 0.027 0.008 -10000 0 -10000 0 0
GLI1/Su(fu) 0 0.097 -10000 0 -0.59 3 3
SAP30 0.025 0.005 -10000 0 -10000 0 0
mol:GDP 0.026 0.007 -10000 0 -10000 0 0
MIM/GLI2A 0.018 0.053 -10000 0 -0.4 6 6
IFT88 0.02 0.011 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GLI2 0.011 0.059 0.17 1 -0.28 10 11
GLI3 0.031 0.088 0.24 3 -0.36 5 8
CSNK1D 0.026 0.004 -10000 0 -10000 0 0
CSNK1E 0.025 0.006 -10000 0 -10000 0 0
SAP18 0.021 0.011 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.011 -10000 0 -10000 0 0
GNG2 0.009 0.081 -10000 0 -0.4 16 16
Gi family/GTP -0.045 0.12 -10000 0 -0.34 30 30
SIN3B 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.025 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.078 0.24 3 -0.36 4 7
GLI2/Su(fu) 0.019 0.061 -10000 0 -0.34 6 6
FOXA2 -0.006 0.16 -10000 0 -0.74 14 14
neural tube patterning 0.003 0.095 -10000 0 -0.52 6 6
SPOP 0.026 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.039 -10000 0 -10000 0 0
GNB1 0.025 0.006 -10000 0 -10000 0 0
CSNK1G2 0.025 0.021 -10000 0 -0.4 1 1
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
MTSS1 0.018 0.053 -10000 0 -0.4 6 6
embryonic limb morphogenesis 0.003 0.095 -10000 0 -0.52 6 6
SUFU 0.019 0.011 -10000 0 -10000 0 0
LGALS3 0.024 0.022 -10000 0 -0.4 1 1
catabolic process 0.047 0.098 0.25 1 -0.35 9 10
GLI3A/CBP 0.029 0.034 -10000 0 -0.32 4 4
KIF3A 0.026 0.005 -10000 0 -10000 0 0
GLI1 0.003 0.097 -10000 0 -0.53 6 6
RAB23 0.026 0.003 -10000 0 -10000 0 0
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
IFT172 0.026 0.001 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.026 0.041 -10000 0 -10000 0 0
GNAZ 0.021 0.042 -10000 0 -0.4 4 4
RBBP4 0.025 0.005 -10000 0 -10000 0 0
CSNK1G1 0.024 0.021 -10000 0 -0.4 1 1
PIAS1 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.025 0.06 -10000 0 -0.3 5 5
STK36 0.027 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.047 0.14 -10000 0 -0.37 41 41
PTCH1 0.001 0.11 -10000 0 -1 3 3
MIM/GLI1 0.01 0.11 -10000 0 -0.54 7 7
CREBBP 0.029 0.034 -10000 0 -0.32 4 4
Su(fu)/SIN3/HDAC complex 0.025 0.082 0.24 1 -0.34 13 14
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.026 0.004 -10000 0 -10000 0 0
mol:PIP3 0.007 0.012 -10000 0 -10000 0 0
FRAP1 -0.008 0.1 -10000 0 -0.42 23 23
AKT1 0 0.026 0.16 4 -10000 0 4
INSR 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.028 0.006 -10000 0 -10000 0 0
mol:GTP 0.029 0.041 0.22 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.039 -10000 0 -0.22 5 5
TSC2 0.026 0.003 -10000 0 -10000 0 0
RHEB/GDP 0.015 0.028 -10000 0 -10000 0 0
TSC1 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.023 0.017 -10000 0 -0.18 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.017 0.048 -10000 0 -0.25 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.008 0.072 0.21 1 -0.31 12 13
MAP3K5 0.005 0.026 0.2 2 -0.17 6 8
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
apoptosis 0.005 0.026 0.2 2 -0.17 6 8
mol:LY294002 0 0 -10000 0 -0.001 1 1
EIF4B 0.007 0.066 0.2 1 -0.31 7 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.067 0.2 1 -0.32 5 6
eIF4E/eIF4G1/eIF4A1 0.004 0.063 -10000 0 -0.26 20 20
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.037 0.022 -10000 0 -0.2 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.028 0.16 3 -10000 0 3
FKBP1A 0.021 0.011 -10000 0 -10000 0 0
RHEB/GTP 0.033 0.037 0.2 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 1 1
FKBP12/Rapamycin 0.016 0.008 -10000 0 -10000 0 0
PDPK1 -0.005 0.016 0.16 2 -10000 0 2
EIF4E 0.024 0.029 -10000 0 -0.4 2 2
ASK1/PP5C 0.01 0.12 -10000 0 -0.43 26 26
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.008 0.047 -10000 0 -0.27 8 8
TSC1/TSC2 0.033 0.044 0.24 1 -10000 0 1
tumor necrosis factor receptor activity 0 0 0.001 1 -10000 0 1
RPS6 0.025 0.022 -10000 0 -0.42 1 1
PPP5C 0.026 0.003 -10000 0 -10000 0 0
EIF4G1 0.026 0.002 -10000 0 -10000 0 0
IRS1 0.006 0.016 -10000 0 -0.21 2 2
INS -0.018 0.004 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
PDK2 -0.006 0.02 0.16 2 -10000 0 2
EIF4EBP1 -0.073 0.3 -10000 0 -1 38 38
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
PPP2R5D -0.005 0.096 -10000 0 -0.38 23 23
peptide biosynthetic process -0.007 0.035 0.18 13 -0.23 1 14
RHEB 0.026 0.005 -10000 0 -10000 0 0
EIF4A1 0.022 0.01 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 17 -10000 0 17
EEF2 -0.007 0.035 0.18 13 -0.24 1 14
eIF4E/4E-BP1 -0.056 0.29 -10000 0 -0.96 38 38
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.033 0.079 -10000 0 -0.23 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.026 0.073 0.3 1 -0.34 1 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.038 0.043 -10000 0 -0.25 3 3
antigen processing and presentation of peptide antigen via MHC class I -0.006 0.056 -10000 0 -0.24 3 3
CaM/Ca2+ 0.033 0.077 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.009 0.07 -10000 0 -0.37 1 1
AKT1 -0.01 0.057 -10000 0 -10000 0 0
MAP2K1 -0.024 0.059 0.28 1 -0.26 1 2
MAP3K11 -0.008 0.065 0.29 1 -10000 0 1
IFNGR1 0.021 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.026 0.14 -10000 0 -0.38 43 43
Rap1/GTP 0 0.055 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.018 -10000 0 -0.28 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.033 0.089 -10000 0 -10000 0 0
CEBPB 0.017 0.14 0.29 1 -0.52 10 11
STAT3 0.026 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.039 0.11 -10000 0 -0.67 3 3
STAT1 -0.006 0.066 0.29 1 -0.37 1 2
CALM1 0.025 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.024 0.13 -10000 0 -0.42 42 42
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.008 0.069 0.29 1 -0.36 1 2
CEBPB/PTGES2/Cbp/p300 0.022 0.092 -10000 0 -0.41 3 3
mol:Ca2+ 0.03 0.077 -10000 0 -0.23 1 1
MAPK3 -0.008 0.093 -10000 0 -0.74 3 3
STAT1 (dimer) 0.002 0.078 -10000 0 -0.32 3 3
MAPK1 -0.034 0.17 -10000 0 -0.73 19 19
JAK2 0.018 0.04 -10000 0 -0.4 3 3
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.021 0.019 -10000 0 -10000 0 0
CAMK2D 0.025 0.021 -10000 0 -0.4 1 1
DAPK1 0.007 0.15 0.25 3 -0.56 21 24
SMAD7 0.001 0.034 0.13 1 -0.24 1 2
CBL/CRKL/C3G 0.018 0.071 0.29 1 -10000 0 1
PI3K 0.033 0.076 -10000 0 -10000 0 0
IFNG -0.024 0.13 -10000 0 -0.42 42 42
apoptosis 0.002 0.13 0.22 1 -0.43 28 29
CAMK2G 0.026 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.004 -10000 0 -10000 0 0
CAMK2A -0.011 0.11 -10000 0 -0.4 33 33
CAMK2B -0.013 0.11 0.37 1 -0.4 32 33
FRAP1 -0.022 0.05 -10000 0 -10000 0 0
PRKCD -0.022 0.057 0.28 1 -10000 0 1
RAP1B 0.026 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.006 0.056 -10000 0 -0.24 3 3
PTPN2 0.022 0.01 -10000 0 -10000 0 0
EP300 0.025 0.006 -10000 0 -10000 0 0
IRF1 -0.007 0.056 0.25 1 -10000 0 1
STAT1 (dimer)/PIASy 0.007 0.068 0.29 1 -0.36 1 2
SOCS1 0.016 0.096 -10000 0 -1 3 3
mol:GDP 0.016 0.068 0.27 1 -10000 0 1
CASP1 0.001 0.036 0.13 1 -0.27 1 2
PTGES2 0.026 0.003 -10000 0 -10000 0 0
IRF9 0.022 0.048 0.14 6 -0.18 1 7
mol:PI-3-4-5-P3 0.02 0.069 -10000 0 -10000 0 0
RAP1/GDP 0.017 0.064 -10000 0 -10000 0 0
CBL -0.008 0.064 0.29 1 -10000 0 1
MAP3K1 -0.007 0.065 0.29 1 -10000 0 1
PIAS1 0.025 0.005 -10000 0 -10000 0 0
PIAS4 0.026 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.006 0.056 -10000 0 -0.24 3 3
PTPN11 -0.006 0.065 -10000 0 -0.23 1 1
CREBBP 0.026 0.004 -10000 0 -10000 0 0
RAPGEF1 0.025 0.021 -10000 0 -0.4 1 1
IL2 signaling events mediated by PI3K

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
BCL2L1 0.08 0.098 -10000 0 -10000 0 0
UGCG 0.021 0.046 -10000 0 -0.59 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT 0.01 0.13 -10000 0 -0.44 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.02 0.046 -10000 0 -0.58 2 2
mol:DAG -0.005 0.12 -10000 0 -0.82 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.13 -10000 0 -0.41 27 27
FRAP1 0.01 0.14 -10000 0 -0.46 29 29
FOXO3 0.017 0.11 -10000 0 -0.4 13 13
AKT1 0.019 0.11 -10000 0 -0.42 14 14
GAB2 0.026 0.004 -10000 0 -10000 0 0
SMPD1 0.011 0.092 -10000 0 -0.63 8 8
SGMS1 0.01 0.096 -10000 0 -0.62 9 9
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 0.006 0.006 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
cell proliferation 0.034 0.085 -10000 0 -0.41 7 7
EIF3A 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.041 0.009 -10000 0 -10000 0 0
RPS6KB1 0.014 0.1 -10000 0 -0.83 6 6
mol:sphingomyelin -0.005 0.12 -10000 0 -0.82 9 9
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.027 0.022 -10000 0 -0.42 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.028 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MYC 0.046 0.12 0.29 7 -0.45 4 11
MYB 0.033 0.033 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.026 0.091 -10000 0 -0.41 9 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.1 -10000 0 -0.77 6 6
mol:PI-3-4-5-P3 0.025 0.091 -10000 0 -0.4 9 9
Rac1/GDP 0.02 0.013 -10000 0 -10000 0 0
T cell proliferation 0.023 0.08 -10000 0 -0.43 5 5
SHC1 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0 -10000 0 -10000 0 0
PRKCZ 0.024 0.081 -10000 0 -0.44 5 5
NF kappa B1 p50/RelA 0.033 0.14 -10000 0 -0.42 24 24
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.056 -10000 0 -0.42 4 4
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL2RA 0.016 0.065 -10000 0 -0.4 10 10
IL2RB 0.019 0.058 -10000 0 -0.4 8 8
TERT -0.012 0.13 0.37 2 -0.42 37 39
E2F1 0.033 0.037 -10000 0 -10000 0 0
SOS1 0.027 0.003 -10000 0 -10000 0 0
RPS6 0.025 0.022 -10000 0 -0.42 1 1
mol:cAMP -0.002 0 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
IL2RG 0.026 0.03 -10000 0 -0.4 2 2
actin cytoskeleton organization 0.023 0.08 -10000 0 -0.43 5 5
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL2 0.018 0.012 -10000 0 -10000 0 0
PIK3CA 0.028 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.045 0.024 -10000 0 -10000 0 0
LCK 0.018 0.064 -10000 0 -0.42 9 9
BCL2 -0.007 0.21 -10000 0 -0.8 25 25
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.014 0.071 -10000 0 -0.4 12 12
HRAS 0.025 0.021 -10000 0 -0.4 1 1
EGFR 0.023 0.022 -10000 0 -0.4 1 1
AKT 0.037 0.072 0.25 8 -0.3 4 12
FOXO3 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.025 0.007 -10000 0 -10000 0 0
FOXO1 0.019 0.023 -10000 0 -0.4 1 1
AKT3 0.019 0.05 -10000 0 -0.4 6 6
FOXO4 0.026 0.001 -10000 0 -10000 0 0
MET 0.022 0.047 0.37 1 -0.42 4 5
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
NRAS 0.024 0.029 -10000 0 -0.4 2 2
PIK3CG -0.035 0.15 -10000 0 -0.4 59 59
PIK3R3 0.026 0.004 -10000 0 -10000 0 0
PIK3R2 0.026 0.003 -10000 0 -10000 0 0
NF1 0.026 0.005 -10000 0 -10000 0 0
RAS 0.021 0.042 0.19 3 -0.24 2 5
ERBB2 0.029 0.034 0.37 4 -10000 0 4
proliferation/survival/translation -0.023 0.068 0.29 7 -0.23 1 8
PI3K 0.022 0.063 0.24 12 -0.22 6 18
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.026 0.003 -10000 0 -10000 0 0
FOXO 0.06 0.051 0.22 14 -10000 0 14
AKT2 0.026 0.004 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.021 0.034 -10000 0 -0.31 3 3
KLHL20 0.042 0.074 0.21 26 -0.22 7 33
CYFIP2 0.025 0.021 -10000 0 -0.4 1 1
Rac1/GDP 0.068 0.08 0.27 7 -10000 0 7
ENAH 0.02 0.034 -10000 0 -0.31 3 3
AP1M1 0.026 0.003 -10000 0 -10000 0 0
RAP1B 0.026 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.017 0.021 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.027 -10000 0 -0.16 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.049 0.053 -10000 0 -0.2 14 14
RAPGEF1 0.055 0.081 0.3 5 -10000 0 5
CTNND1 0.026 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.029 0.036 -10000 0 -0.31 3 3
CRK 0.055 0.076 -10000 0 -0.3 1 1
E-cadherin/gamma catenin/alpha catenin 0.051 0.018 -10000 0 -0.24 1 1
alphaE/beta7 Integrin 0.023 0.058 -10000 0 -0.27 15 15
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
NCKAP1 0.027 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.012 -10000 0 -10000 0 0
DLG1 0.02 0.035 -10000 0 -0.31 3 3
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.004 0.01 -10000 0 -10000 0 0
MLLT4 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.017 0.087 -10000 0 -0.23 42 42
PI3K 0.008 0.014 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.017 -10000 0 -0.28 1 1
TIAM1 -0.015 0.12 -10000 0 -0.4 40 40
E-cadherin(dimer)/Ca2+ 0.061 0.013 -10000 0 -10000 0 0
AKT1 0.025 0.045 0.1 24 -10000 0 24
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.08 0.081 0.27 6 -10000 0 6
actin cytoskeleton organization 0.039 0.06 0.17 29 -0.17 6 35
CDC42/GDP 0.075 0.08 0.24 11 -10000 0 11
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.019 0.012 -10000 0 -0.21 1 1
ITGB7 0.011 0.079 -10000 0 -0.4 15 15
RAC1 0.024 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.066 0.014 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.008 -10000 0 -10000 0 0
mol:GDP 0.072 0.088 0.28 7 -0.29 1 8
CDC42/GTP/IQGAP1 0.032 0.017 -10000 0 -0.24 1 1
JUP 0.025 0.021 -10000 0 -0.4 1 1
p120 catenin/RhoA/GDP 0.088 0.08 0.28 5 -10000 0 5
RAC1/GTP/IQGAP1 0.031 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.038 0.016 -10000 0 -0.28 1 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
CDC42 0.024 0.022 -10000 0 -0.4 1 1
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.032 0.047 0.13 30 -0.15 4 34
NME1 0.017 0.067 0.37 1 -0.42 9 10
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.019 0.034 -10000 0 -0.31 3 3
regulation of cell-cell adhesion 0.012 0.015 -10000 0 -10000 0 0
WASF2 0.014 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.079 0.071 0.29 4 -10000 0 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.057 0.055 -10000 0 -10000 0 0
CCND1 0.036 0.054 0.15 29 -0.19 4 33
VAV2 0.072 0.13 -10000 0 -0.6 10 10
RAP1/GDP 0.087 0.078 0.28 6 -10000 0 6
adherens junction assembly 0.019 0.033 -10000 0 -0.3 3 3
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.003 -10000 0 -10000 0 0
PIP5K1C 0.025 0.021 -10000 0 -0.4 1 1
regulation of heterotypic cell-cell adhesion 0.043 0.049 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.013 0.011 -10000 0 -0.16 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.013 0.029 -10000 0 -0.31 2 2
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.063 -10000 0 -0.34 9 9
E-cadherin/beta catenin/alpha catenin 0.052 0.009 -10000 0 -10000 0 0
ITGAE 0.022 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.036 -10000 0 -0.32 3 3
Rapid glucocorticoid signaling

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.019 0.069 -10000 0 -0.21 30 30
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.011 0.02 -10000 0 -0.3 2 2
GNB1/GNG2 0.022 0.052 -10000 0 -0.23 16 16
GNB1 0.025 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.004 0.045 -10000 0 -0.21 17 17
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 0.003 0.011 0.059 17 -10000 0 17
GNAL 0.004 0.083 -10000 0 -0.4 17 17
GNG2 0.009 0.081 -10000 0 -0.4 16 16
CRH -0.018 0.029 -10000 0 -0.42 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.001 -10000 0 -10000 0 0
MAPK11 0.006 0.011 -10000 0 -0.15 2 2
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.058 -10000 0 -0.22 14 14
HDAC3 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0.036 0.006 -10000 0 -10000 0 0
GATA1/HDAC5 0.035 0.017 -10000 0 -0.29 1 1
GATA2/HDAC5 0.031 0.049 -10000 0 -0.28 10 10
HDAC5/BCL6/BCoR 0.051 0.017 -10000 0 -0.24 1 1
HDAC9 -0.034 0.14 -10000 0 -0.4 57 57
Glucocorticoid receptor/Hsp90/HDAC6 0.03 0.073 -10000 0 -0.23 29 29
HDAC4/ANKRA2 0.038 0.007 -10000 0 -10000 0 0
HDAC5/YWHAB 0.021 0.025 -10000 0 -0.28 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.014 -10000 0 -0.18 2 2
GATA2 0.017 0.061 -10000 0 -0.4 9 9
HDAC4/RFXANK 0.039 0.004 -10000 0 -10000 0 0
BCOR 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.024 0.021 -10000 0 -0.4 1 1
HDAC5 0.025 0.021 -10000 0 -0.4 1 1
GNB1/GNG2 0.023 0.061 -10000 0 -0.28 16 16
Histones 0 0.084 -10000 0 -0.32 7 7
ADRBK1 0.026 0.004 -10000 0 -10000 0 0
HDAC4 0.026 0.002 -10000 0 -10000 0 0
XPO1 0.026 0.001 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.037 0.018 -10000 0 -0.28 1 1
HDAC4/Ubc9 0.038 0.006 -10000 0 -10000 0 0
HDAC7 0.026 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.032 0.021 -10000 0 -0.28 1 1
TUBA1B 0.026 0.002 -10000 0 -10000 0 0
HDAC6 0.026 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.038 0.017 -10000 0 -0.28 1 1
CAMK4 0.002 0.094 -10000 0 -0.4 22 22
Tubulin/HDAC6 0.046 0.043 -10000 0 -0.26 8 8
SUMO1 0.025 0.029 -10000 0 -0.4 2 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0.013 -10000 0 -10000 0 0
GATA1 0.01 0.022 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.01 -10000 0 -10000 0 0
NR3C1 -0.003 0.11 -10000 0 -0.4 29 29
SUMO1/HDAC4 0.035 0.036 -10000 0 -0.28 2 2
SRF 0.026 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.022 0.02 -10000 0 -10000 0 0
Tubulin 0.032 0.047 -10000 0 -0.3 8 8
HDAC4/14-3-3 E 0.033 0.015 -10000 0 -10000 0 0
GNB1 0.025 0.006 -10000 0 -10000 0 0
RANGAP1 0.025 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.039 0.005 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.017 -10000 0 -0.24 1 1
HDAC4/SRF 0.035 0.066 -10000 0 -0.24 22 22
HDAC4/ER alpha 0.009 0.092 -10000 0 -0.28 38 38
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0 0.083 -10000 0 -0.31 7 7
cell motility 0.046 0.043 -10000 0 -0.25 8 8
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.026 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.038 0.006 -10000 0 -10000 0 0
BCL6 0.026 0.002 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.026 0.002 -10000 0 -10000 0 0
Hsp90/HDAC6 0.036 0.01 -10000 0 -10000 0 0
ESR1 -0.014 0.12 -10000 0 -0.4 38 38
HDAC6/HDAC11 0.039 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0.032 -10000 0 -10000 0 0
NPC 0.016 0 -10000 0 -10000 0 0
MEF2C 0.016 0.061 -10000 0 -0.4 9 9
RAN 0.026 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.067 0.046 -10000 0 -10000 0 0
GNG2 0.009 0.081 -10000 0 -0.4 16 16
NCOR2 0.025 0.021 -10000 0 -0.4 1 1
TUBB2A 0.018 0.061 -10000 0 -0.42 8 8
HDAC11 0.026 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
RANBP2 0.027 0 -10000 0 -10000 0 0
ANKRA2 0.026 0.004 -10000 0 -10000 0 0
RFXANK 0.026 0.003 -10000 0 -10000 0 0
nuclear import -0.018 0.022 0.25 1 -10000 0 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.005 -9999 0 -10000 0 0
Rac1/GDP 0.024 0.011 -9999 0 -10000 0 0
DOCK1 0.026 0.005 -9999 0 -10000 0 0
ITGA4 0.01 0.081 -9999 0 -0.4 16 16
RAC1 0.024 0.008 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.016 0.088 -9999 0 -0.31 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.022 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.056 -9999 0 -0.24 16 16
alpha4/beta7 Integrin/Paxillin 0.025 0.072 -9999 0 -0.24 28 28
lamellipodium assembly 0.008 0.074 -9999 0 -0.41 9 9
PIK3CA 0.026 0.003 -9999 0 -10000 0 0
PI3K 0.038 0.008 -9999 0 -10000 0 0
ARF6 0.025 0.007 -9999 0 -10000 0 0
TLN1 0.026 0.004 -9999 0 -10000 0 0
PXN 0.013 0.002 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
ARF6/GTP 0.043 0.048 -9999 0 -10000 0 0
cell adhesion 0.045 0.051 -9999 0 -10000 0 0
CRKL/CBL 0.037 0.009 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.034 0.05 -9999 0 -0.22 16 16
ITGB1 0.026 0.002 -9999 0 -10000 0 0
ITGB7 0.011 0.079 -9999 0 -0.4 15 15
ARF6/GDP 0.025 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.042 0.071 -9999 0 -0.39 7 7
p130Cas/Crk/Dock1 0.043 0.025 -9999 0 -0.24 1 1
VCAM1 0.016 0.061 -9999 0 -0.4 9 9
alpha4/beta1 Integrin/Paxillin/Talin 0.047 0.052 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.047 0.05 -9999 0 -10000 0 0
BCAR1 0.025 0.021 -9999 0 -0.4 1 1
mol:GDP -0.045 0.05 -9999 0 -10000 0 0
CBL 0.026 0.003 -9999 0 -10000 0 0
PRKACA 0.026 0.003 -9999 0 -10000 0 0
GIT1 0.025 0.021 -9999 0 -0.4 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.047 0.052 -9999 0 -10000 0 0
Rac1/GTP 0.007 0.081 -9999 0 -0.46 9 9
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.021 0.027 -10000 0 -0.2 6 6
epithelial cell differentiation 0.055 0.012 -10000 0 -10000 0 0
CYFIP2 0.025 0.021 -10000 0 -0.4 1 1
ENAH -0.012 0.026 -10000 0 -10000 0 0
EGFR 0.023 0.022 -10000 0 -0.4 1 1
EPHA2 0.024 0.023 -10000 0 -0.42 1 1
MYO6 -0.01 0.015 0.18 2 -10000 0 2
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.052 0.017 -10000 0 -0.24 1 1
AQP5 -0.007 0.042 -10000 0 -10000 0 0
CTNND1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.017 0.17 2 -10000 0 2
regulation of calcium-dependent cell-cell adhesion -0.018 0.039 0.17 1 -10000 0 1
EGF -0.061 0.17 -10000 0 -0.4 82 82
NCKAP1 0.027 0 -10000 0 -10000 0 0
AQP3 0.009 0.036 0.24 1 -0.43 1 2
cortical microtubule organization 0.055 0.012 -10000 0 -10000 0 0
GO:0000145 -0.01 0.016 0.16 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.06 0.013 -10000 0 -10000 0 0
MLLT4 0.026 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.014 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.059 0.029 -10000 0 -0.22 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.005 0.011 -10000 0 -10000 0 0
PVRL2 0.026 0.003 -10000 0 -10000 0 0
ZYX -0.01 0.012 0.18 1 -10000 0 1
ARF6/GTP 0.062 0.034 -10000 0 -0.22 1 1
CDH1 0.026 0.002 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.001 0.092 -10000 0 -10000 0 0
RhoA/GDP 0.056 0.013 -10000 0 -10000 0 0
actin cytoskeleton organization -0.009 0.013 0.16 2 -10000 0 2
IGF-1R heterotetramer 0.025 0.005 -10000 0 -10000 0 0
GIT1 0.025 0.021 -10000 0 -0.4 1 1
IGF1R 0.025 0.005 -10000 0 -10000 0 0
IGF1 -0.08 0.18 -10000 0 -0.4 105 105
DIAPH1 0.038 0.095 -10000 0 -0.52 7 7
Wnt receptor signaling pathway -0.055 0.012 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.014 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.009 0.013 0.17 2 -10000 0 2
EFNA1 0.026 0.004 -10000 0 -10000 0 0
LPP -0.011 0.017 0.17 2 -10000 0 2
Ephrin A1/EPHA2 0.046 0.021 -10000 0 -10000 0 0
SEC6/SEC8 -0.015 0.006 -10000 0 -10000 0 0
MGAT3 -0.018 0.039 0.18 1 -10000 0 1
HGF/MET 0.042 0.039 -10000 0 -10000 0 0
HGF 0.018 0.055 -10000 0 -0.4 7 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.021 0.027 -10000 0 -0.2 6 6
actin cable formation 0.008 0.053 0.21 13 -0.29 1 14
KIAA1543 -0.009 0.013 0.16 2 -10000 0 2
KIFC3 -0.018 0.04 0.18 1 -10000 0 1
NCK1 0.026 0.002 -10000 0 -10000 0 0
EXOC3 0.026 0.004 -10000 0 -10000 0 0
ACTN1 -0.009 0.014 0.18 2 -10000 0 2
NCK1/GIT1 0.037 0.017 -10000 0 -0.28 1 1
mol:GDP 0.055 0.012 -10000 0 -10000 0 0
EXOC4 0.025 0.005 -10000 0 -10000 0 0
STX4 -0.01 0.015 0.18 2 -10000 0 2
PIP5K1C -0.01 0.017 0.18 2 -10000 0 2
LIMA1 0.02 0.05 -10000 0 -0.4 6 6
ABI1 0.026 0.003 -10000 0 -10000 0 0
ROCK1 -0.008 0.039 0.29 1 -10000 0 1
adherens junction assembly 0.001 0.037 0.26 1 -0.3 1 2
IGF-1R heterotetramer/IGF1 -0.011 0.1 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.007 -10000 0 -10000 0 0
MET 0.022 0.047 0.37 1 -0.42 4 5
PLEKHA7 -0.01 0.014 0.18 2 -10000 0 2
mol:GTP 0.057 0.029 -10000 0 -0.22 2 2
establishment of epithelial cell apical/basal polarity -0.003 0.052 0.32 3 -10000 0 3
cortical actin cytoskeleton stabilization 0.021 0.027 -10000 0 -0.2 6 6
regulation of cell-cell adhesion -0.009 0.013 0.16 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.021 0.027 -10000 0 -0.2 6 6
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.022 0.041 0.4 4 -10000 0 4
PI3K Class IB/PDE3B 0.022 0.041 -10000 0 -0.4 4 4
PDE3B 0.022 0.041 -10000 0 -0.4 4 4
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.018 0.016 -10000 0 -10000 0 0
BIRC5 0.027 0.017 0.37 1 -10000 0 1
NFKBIA 0.005 0.012 0.25 1 -10000 0 1
CPEB1 -0.079 0.17 -10000 0 -0.4 96 96
AKT1 0.004 0.004 -10000 0 -10000 0 0
NDEL1 0.022 0.01 -10000 0 -10000 0 0
Aurora A/BRCA1 0.016 0.014 -10000 0 -10000 0 0
NDEL1/TACC3 0.053 0.035 -10000 0 -10000 0 0
GADD45A 0.026 0.005 -10000 0 -10000 0 0
GSK3B 0.024 0.002 -10000 0 -10000 0 0
PAK1/Aurora A 0.018 0.016 -10000 0 -10000 0 0
MDM2 0.025 0.021 -10000 0 -0.4 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.01 0.027 0.28 4 -10000 0 4
TP53 0.012 0.012 -10000 0 -10000 0 0
DLG7 0.005 0.004 -10000 0 -10000 0 0
AURKAIP1 0.025 0.006 -10000 0 -10000 0 0
ARHGEF7 0.02 0.011 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.056 0.037 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.016 0.014 -10000 0 -10000 0 0
AURKA 0.01 0.008 -10000 0 -10000 0 0
AURKB 0.009 0.008 -10000 0 -10000 0 0
CDC25B 0.014 0.045 0.3 9 -10000 0 9
G2/M transition checkpoint 0.006 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.08 -10000 0 -0.2 56 56
Aurora A/CPEB -0.026 0.08 -10000 0 -0.21 56 56
Aurora A/TACC1/TRAP/chTOG 0.068 0.04 -10000 0 -10000 0 0
BRCA1 0.026 0.003 -10000 0 -10000 0 0
centrosome duplication 0.018 0.016 -10000 0 -10000 0 0
regulation of centrosome cycle 0.051 0.034 -10000 0 -10000 0 0
spindle assembly 0.066 0.039 -10000 0 -10000 0 0
TDRD7 0.026 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.073 0.032 -10000 0 -10000 0 0
CENPA 0.011 0.01 -10000 0 -10000 0 0
Aurora A/PP2A 0.018 0.016 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.035 0.04 0.2 1 -10000 0 1
negative regulation of DNA binding 0.011 0.018 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.029 0.023 -10000 0 -0.28 1 1
RASA1 0.026 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.006 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0.01 0.027 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.008 -10000 0 -10000 0 0
TACC1 0.023 0.01 -10000 0 -10000 0 0
TACC3 0.026 0.004 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.066 0.033 -10000 0 -10000 0 0
Aurora A/RasGAP 0.018 0.016 -10000 0 -10000 0 0
OAZ1 0.026 0.003 -10000 0 -10000 0 0
RAN 0.026 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.025 0.021 -10000 0 -0.4 1 1
GIT1/beta-PIX/PAK1 0.039 0.027 -10000 0 -0.24 1 1
Importin alpha/Importin beta/TPX2 0.01 0.027 0.28 4 -10000 0 4
PPP2R5D 0.026 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.015 0.028 0.28 4 -10000 0 4
PAK1 0.026 0.003 -10000 0 -10000 0 0
CKAP5 0.026 0.003 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.035 0.032 -10000 0 -0.28 4 4
AKT1 0.086 0.089 0.34 9 -0.4 1 10
PTK2B 0.012 0.039 -10000 0 -0.49 1 1
VEGFR2 homodimer/Frs2 0.033 0.031 -10000 0 -0.58 1 1
CAV1 0.022 0.036 -10000 0 -0.4 3 3
CALM1 0.025 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.049 0.032 0.25 1 -0.54 1 2
endothelial cell proliferation 0.094 0.12 0.27 106 -0.34 1 107
mol:Ca2+ 0.012 0.022 -10000 0 -0.33 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.054 0.039 -10000 0 -0.51 1 1
RP11-342D11.1 0.01 0.028 -10000 0 -0.5 1 1
CDH5 0.026 0.001 -10000 0 -10000 0 0
VEGFA homodimer 0.062 0.024 0.26 1 -10000 0 1
SHC1 0.026 0.004 -10000 0 -10000 0 0
SHC2 0.017 0.063 -10000 0 -0.41 9 9
HRAS/GDP 0.044 0.033 -10000 0 -0.45 1 1
SH2D2A 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.095 0.079 0.28 7 -0.36 1 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.048 0.033 0.25 1 -0.54 1 2
VEGFR1 homodimer 0.02 0.011 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.07 0.04 -10000 0 -0.48 1 1
GRB10 0.019 0.03 -10000 0 -0.5 1 1
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB2 0.026 0.004 -10000 0 -10000 0 0
PAK1 0.026 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.071 0.038 -10000 0 -0.5 1 1
HRAS 0.025 0.021 -10000 0 -0.4 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.003 0.077 -10000 0 -0.54 2 2
HIF1A 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.052 0.038 -10000 0 -0.51 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.041 -10000 0 -0.4 4 4
Nck/Pak 0.039 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.049 0.033 0.25 1 -0.54 1 2
mol:GDP 0.056 0.035 -10000 0 -0.47 1 1
mol:NADP 0.086 0.084 0.29 15 -0.32 1 16
eNOS/Hsp90 0.089 0.082 0.28 15 -10000 0 15
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.012 0.022 -10000 0 -0.34 1 1
HIF1A/ARNT 0.035 0.019 -10000 0 -0.28 1 1
SHB 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.028 0.017 0.37 1 -10000 0 1
VEGFC 0.021 0.042 -10000 0 -0.4 4 4
FAK1/Vinculin 0.054 0.075 0.28 6 -0.57 1 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.059 0.042 -10000 0 -0.51 1 1
PTPN6 0.026 0.004 -10000 0 -10000 0 0
EPAS1 0.032 0.017 -10000 0 -0.32 1 1
mol:L-citrulline 0.086 0.084 0.29 15 -0.32 1 16
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.062 0.034 -10000 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer 0.051 0.035 0.26 1 -0.54 1 2
VEGFR2/3 heterodimer 0.03 0.04 -10000 0 -0.58 1 1
VEGFB 0.026 0.004 -10000 0 -10000 0 0
MAPK11 0.006 0.041 0.43 1 -0.53 1 2
VEGFR2 homodimer 0.019 0.033 -10000 0 -0.66 1 1
FLT1 0.02 0.011 -10000 0 -10000 0 0
NEDD4 0.026 0.007 -10000 0 -10000 0 0
MAPK3 0.034 0.082 0.31 5 -0.32 1 6
MAPK1 0.034 0.081 0.3 6 -0.32 1 7
VEGFA145/NRP2 0.038 0.03 0.26 1 -0.28 3 4
VEGFR1/2 heterodimer 0.025 0.033 -10000 0 -0.58 1 1
KDR 0.019 0.033 -10000 0 -0.66 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.05 0.039 0.25 1 -0.5 1 2
SRC 0.016 0.013 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.046 0.087 0.33 6 -0.34 1 7
PI3K 0.047 0.055 0.3 1 -0.42 1 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.049 0.032 0.25 1 -0.54 1 2
FES 0.02 0.032 -10000 0 -0.51 1 1
GAB1 0.028 0.037 -10000 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.03 0.032 -10000 0 -0.36 1 1
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
ARNT 0.025 0.021 -10000 0 -0.4 1 1
eNOS/Caveolin-1 0.087 0.081 0.31 7 -10000 0 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.041 0.044 0.25 1 -0.72 1 2
PI3K/GAB1 0.051 0.054 0.27 1 -0.44 1 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.073 0.036 -10000 0 -0.5 1 1
PRKACA 0.026 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.049 -10000 0 -0.47 2 2
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
CDC42 0.02 0.03 -10000 0 -0.51 1 1
actin cytoskeleton reorganization 0.047 0.033 0.25 1 -0.53 1 2
PTK2 0.027 0.054 0.27 1 -0.61 1 2
EDG1 0.01 0.028 -10000 0 -0.5 1 1
mol:DAG 0.012 0.022 -10000 0 -0.34 1 1
CaM/Ca2+ 0.02 0.027 -10000 0 -0.31 1 1
MAP2K3 0.011 0.035 -10000 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.063 0.061 -10000 0 -0.51 1 1
PLCG1 0.012 0.022 -10000 0 -0.34 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.038 0.038 -10000 0 -0.34 1 1
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
YES1 0.021 0.023 -10000 0 -0.4 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.049 0.033 0.25 1 -0.54 1 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.048 0.033 0.25 1 -0.54 1 2
cell migration 0.063 0.077 0.28 10 -0.51 1 11
mol:PI-3-4-5-P3 0.052 0.055 0.29 1 -0.39 1 2
FYN 0.026 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.025 0.029 -10000 0 -0.47 1 1
mol:NO 0.086 0.084 0.29 15 -0.32 1 16
PXN 0.026 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.027 -10000 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.038 0.034 -10000 0 -0.51 1 1
VHL 0.026 0.003 -10000 0 -10000 0 0
ITGB3 0.022 0.041 -10000 0 -0.4 4 4
NOS3 0.089 0.088 0.3 13 -0.36 1 14
VEGFR2 homodimer/VEGFA homodimer/Sck 0.043 0.049 -10000 0 -0.54 1 1
RAC1 0.024 0.008 -10000 0 -10000 0 0
PRKCA 0.006 0.022 -10000 0 -0.32 1 1
PRKCB -0.011 0.054 -10000 0 -0.32 1 1
VCL 0.026 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.029 0.031 0.23 1 -0.5 1 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.037 0.038 0.25 1 -0.54 1 2
VEGFA165/NRP2 0.038 0.03 0.26 1 -0.28 3 4
MAPKKK cascade 0.032 0.042 -10000 0 -0.45 1 1
NRP2 0.024 0.036 -10000 0 -0.4 3 3
VEGFC homodimer 0.021 0.041 -10000 0 -0.4 4 4
NCK1 0.026 0.002 -10000 0 -10000 0 0
ROCK1 0.021 0.023 -10000 0 -0.4 1 1
FAK1/Paxillin 0.054 0.075 0.28 6 -0.57 1 7
MAP3K13 0.021 0.03 -10000 0 -0.51 1 1
PDPK1 0.078 0.087 0.25 61 -0.36 1 62
Insulin Pathway

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.047 0.05 -10000 0 -10000 0 0
TC10/GTP 0.032 0.046 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.074 0.027 -10000 0 -10000 0 0
HRAS 0.025 0.021 -10000 0 -0.4 1 1
APS homodimer 0.023 0.042 0.37 1 -0.42 3 4
GRB14 -0.009 0.11 -10000 0 -0.41 30 30
FOXO3 -0.013 0.15 -10000 0 -0.56 28 28
AKT1 -0.004 0.061 0.24 2 -10000 0 2
INSR 0.038 0.015 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.071 0.069 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.008 -10000 0 -10000 0 0
SORBS1 0.014 0.068 -10000 0 -0.4 11 11
CRK 0.022 0.01 -10000 0 -10000 0 0
PTPN1 0.006 0.026 0.31 1 -10000 0 1
CAV1 0.014 0.045 0.22 4 -10000 0 4
CBL/APS/CAP/Crk-II/C3G 0.052 0.059 0.26 1 -10000 0 1
Insulin Receptor/Insulin/IRS1/NCK2 0.075 0.026 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.058 0.022 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.066 0.06 -10000 0 -10000 0 0
RPS6KB1 -0.009 0.056 0.22 2 -10000 0 2
PARD6A 0.022 0.043 -10000 0 -0.42 4 4
CBL 0.026 0.003 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.008 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.027 0.057 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.013 -10000 0 -10000 0 0
Insulin Receptor 0.038 0.015 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.081 0.032 -10000 0 -10000 0 0
PRKCI 0.024 0.059 -10000 0 -0.42 4 4
Insulin Receptor/Insulin/GRB14/PDK1 0.021 0.057 -10000 0 -10000 0 0
SHC1 0.026 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.04 0.026 -10000 0 -10000 0 0
PI3K 0.07 0.026 -10000 0 -10000 0 0
NCK2 0.027 0 -10000 0 -10000 0 0
RHOQ 0.026 0.003 -10000 0 -10000 0 0
mol:H2O2 0.001 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.015 -10000 0 -0.28 1 1
AKT2 -0.003 0.062 0.22 4 -10000 0 4
PRKCZ 0.018 0.071 -10000 0 -0.41 3 3
SH2B2 0.023 0.042 0.37 1 -0.42 3 4
SHC/SHIP 0.044 0.032 0.29 1 -10000 0 1
F2RL2 -0.007 0.12 -10000 0 -0.43 31 31
TRIP10 0.025 0.021 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/Shc 0.057 0.025 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.014 -10000 0 -0.24 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.081 0.032 -10000 0 -10000 0 0
RAPGEF1 0.025 0.021 -10000 0 -0.4 1 1
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.002 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.044 0.056 0.26 1 -0.23 2 3
TC10/GDP 0.019 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.064 0.034 -10000 0 -10000 0 0
INPP5D 0.017 0.043 0.19 9 -10000 0 9
SOS1 0.026 0.002 -10000 0 -10000 0 0
SGK1 -0.035 0.19 -10000 0 -0.76 28 28
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.002 -10000 0 -10000 0 0
p62DOK/RasGAP 0.04 0.027 -10000 0 -10000 0 0
INS 0.028 0.015 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.017 0.043 0.19 9 -10000 0 9
GRB2 0.026 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.011 0.052 0.19 1 -10000 0 1
PTPRA 0.027 0.016 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.034 0.014 -10000 0 -0.24 1 1
PDPK1 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.035 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.059 0.024 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.05 0.025 -10000 0 -10000 0 0
Par3/Par6 0.036 0.079 -10000 0 -0.22 34 34
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.058 0.074 0.15 119 -0.45 1 120
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.01 0.034 0.14 9 -0.17 1 10
AP2 0.038 0.017 -10000 0 -0.28 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.013 -10000 0 -10000 0 0
CLTB 0.025 0.021 -10000 0 -0.4 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.012 -10000 0 -0.2 1 1
CD4 0.01 0.081 -10000 0 -0.4 16 16
CLTA 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.004 0.019 0.27 1 -0.28 1 2
mol:PI-4-5-P2 0.005 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.034 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.006 0.02 0.19 1 -0.34 1 2
mol:Choline 0.005 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.027 0.006 -10000 0 -10000 0 0
DDEF1 0.004 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.018 0.18 1 -0.24 1 2
AP2M1 0.026 0.002 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.006 -10000 0 -10000 0 0
Rac/GTP 0.019 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.022 0.024 0.19 1 -0.2 1 2
ARFIP2 0.016 0.021 -10000 0 -10000 0 0
COPA 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.018 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.019 0.006 -10000 0 -10000 0 0
GGA3 0.026 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.023 0.027 -10000 0 -0.24 4 4
AP2A1 0.025 0.021 -10000 0 -0.4 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.027 0.14 1 -0.33 2 3
ARF1/GDP/Membrin 0.017 0.034 -10000 0 -0.28 4 4
Arfaptin 2/Rac/GDP 0.03 0.012 -10000 0 -10000 0 0
CYTH2 0.028 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.035 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -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 0.015 0.043 -10000 0 -0.32 1 1
PLD2 0.005 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.004 0.019 0.27 1 -0.28 1 2
PIP5K1A 0.005 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.012 0.026 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.005 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.004 0.019 0.27 1 -0.28 1 2
GOSR2 0.01 0.017 -10000 0 -0.31 1 1
USO1 0.009 0.028 -10000 0 -0.31 3 3
GBF1 0.006 0.039 -10000 0 -0.31 6 6
ARF1/GTP/Arfaptin 2 0.035 0.009 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.04 0.058 -10000 0 -0.24 17 17
PLK2 and PLK4 events

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
PLK2 0.022 0.044 -9999 0 -0.42 4 4
PLK4 0.026 0.005 -9999 0 -10000 0 0
regulation of centriole replication 0.009 0.03 -9999 0 -0.3 4 4
TRAIL signaling pathway

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.024 0.029 -9999 0 -0.4 2 2
positive regulation of NF-kappaB transcription factor activity 0.028 0.027 -9999 0 -0.28 2 2
MAP2K4 0.016 0.027 -9999 0 -10000 0 0
IKBKB 0.023 0.009 -9999 0 -10000 0 0
TNFRSF10B 0.02 0.011 -9999 0 -10000 0 0
TNFRSF10A 0.02 0.011 -9999 0 -10000 0 0
SMPD1 0.005 0.048 -9999 0 -0.37 6 6
IKBKG 0.025 0.021 -9999 0 -0.4 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.02 0.011 -9999 0 -10000 0 0
TRAIL/TRAILR2 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR3 0.008 0.082 -9999 0 -0.3 27 27
TRAIL/TRAILR1 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR4 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR1/DAP3/GTP 0.037 0.028 -9999 0 -0.22 2 2
IKK complex 0.018 0.04 -9999 0 -0.35 1 1
RIPK1 0.026 0.003 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.019 0.003 -9999 0 -10000 0 0
MAPK3 0.011 0.025 -9999 0 -0.28 3 3
MAP3K1 0.02 0.029 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.02 0.011 -9999 0 -10000 0 0
TRADD 0.026 0.002 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.02 0.011 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.021 0.023 -9999 0 -10000 0 0
CFLAR 0.027 0 -9999 0 -10000 0 0
MAPK1 0.011 0.02 -9999 0 -0.28 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.057 0.039 -9999 0 -10000 0 0
mol:ceramide 0.005 0.047 -9999 0 -0.37 6 6
FADD 0.026 0.004 -9999 0 -10000 0 0
MAPK8 0.013 0.026 -9999 0 -10000 0 0
TRAF2 0.025 0.021 -9999 0 -0.4 1 1
TRAILR3 (trimer) -0.006 0.1 -9999 0 -0.42 25 25
CHUK 0.025 0.006 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.039 0.03 -9999 0 -0.24 2 2
DAP3 0.026 0.004 -9999 0 -10000 0 0
CASP10 0.005 0.021 -9999 0 -0.26 2 2
JNK cascade 0.028 0.027 -9999 0 -0.28 2 2
TRAIL (trimer) 0.024 0.029 -9999 0 -0.4 2 2
TNFRSF10C -0.006 0.1 -9999 0 -0.42 25 25
TRAIL/TRAILR1/DAP3/GTP/FADD 0.045 0.033 -9999 0 -0.2 2 2
TRAIL/TRAILR2/FADD 0.039 0.03 -9999 0 -0.24 2 2
cell death 0.005 0.047 -9999 0 -0.37 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.023 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.02 0.011 -9999 0 -10000 0 0
CASP8 0.015 0.014 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.057 0.039 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.003 -10000 0 -10000 0 0
ELF1 0.02 0.043 -10000 0 -0.32 6 6
CCNA2 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
JAK3 0.026 0.022 -10000 0 -0.42 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.026 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.042 0.089 -10000 0 -0.46 6 6
SHC1 0.026 0.004 -10000 0 -10000 0 0
SP1 0.028 0.038 -10000 0 -0.32 5 5
IL2RA 0.005 0.08 -10000 0 -0.66 6 6
IL2RB 0.018 0.058 -10000 0 -0.4 8 8
SOS1 0.027 0.002 -10000 0 -10000 0 0
IL2RG 0.025 0.029 -10000 0 -0.4 2 2
G1/S transition of mitotic cell cycle 0.025 0.083 0.3 1 -0.63 4 5
PTPN11 0.027 0.003 -10000 0 -10000 0 0
CCND2 0.012 0.066 -10000 0 -0.66 4 4
LCK 0.016 0.064 -10000 0 -0.42 9 9
GRB2 0.026 0.004 -10000 0 -10000 0 0
IL2 -0.006 0.02 -10000 0 -10000 0 0
CDK6 0.025 0.007 -10000 0 -10000 0 0
CCND3 0.041 0.084 0.34 1 -0.71 1 2
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.02 0.008 -10000 0 -10000 0 0
TRAF2/ASK1 0.034 0.015 -10000 0 -0.24 1 1
ATM 0.026 0.004 -10000 0 -10000 0 0
MAP2K3 0.009 0.067 -10000 0 -0.34 5 5
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.016 0.06 0.23 1 -0.35 4 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.025 0.035 0.37 1 -0.41 2 3
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
GADD45A 0.026 0.005 -10000 0 -10000 0 0
GADD45B 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 0.025 0.021 -10000 0 -0.4 1 1
MAP3K6 0.024 0.022 -10000 0 -0.4 1 1
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
MAP3K4 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.035 0.019 -10000 0 -0.28 1 1
TAK1/TAB family 0 0.016 -10000 0 -0.14 1 1
RAC1/OSM/MEKK3 0.043 0.022 -10000 0 -0.22 1 1
TRAF2 0.025 0.021 -10000 0 -0.4 1 1
RAC1/OSM/MEKK3/MKK3 0.018 0.06 -10000 0 -0.28 4 4
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.013 0.11 0.37 1 -0.4 32 33
CCM2 0.023 0.022 -10000 0 -0.4 1 1
CaM/Ca2+/CAMKIIB 0.009 0.072 0.24 1 -0.24 32 33
MAPK11 0.023 0.031 -10000 0 -0.42 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.023 0.07 0.24 1 -0.22 31 32
OSM/MEKK3 0.034 0.02 -10000 0 -0.28 1 1
TAOK1 0.013 0.003 -10000 0 -10000 0 0
TAOK2 0.014 0.002 -10000 0 -10000 0 0
TAOK3 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.004 -10000 0 -10000 0 0
MAP3K10 0.026 0.004 -10000 0 -10000 0 0
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.024 0.009 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.057 0.027 0.24 1 -0.21 2 3
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.074 0.22 26 -0.27 1 27
ERC1 0.026 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.05 -10000 0 -0.3 9 9
NFKBIA 0.012 0.006 -10000 0 -10000 0 0
BIRC2 0.026 0.005 -10000 0 -10000 0 0
IKBKB 0.023 0.009 -10000 0 -10000 0 0
RIPK2 0.023 0.01 -10000 0 -10000 0 0
IKBKG 0.027 0.043 -10000 0 -0.36 2 2
IKK complex/A20 0.052 0.057 -10000 0 -0.33 2 2
NEMO/A20/RIP2 0.022 0.009 -10000 0 -10000 0 0
XPO1 0.026 0.001 -10000 0 -10000 0 0
NEMO/ATM 0.045 0.054 0.27 1 -0.34 3 4
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.042 0.048 -10000 0 -0.34 1 1
BCL10/MALT1/TRAF6 0.039 0.03 -10000 0 -0.24 2 2
NOD2 0.016 0.068 -10000 0 -0.42 10 10
NFKB1 0.028 0.004 -10000 0 -10000 0 0
RELA 0.028 0.004 -10000 0 -10000 0 0
MALT1 0.019 0.023 -10000 0 -0.4 1 1
cIAP1/UbcH5C 0.038 0.008 -10000 0 -10000 0 0
ATM 0.026 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.036 0.023 -10000 0 -0.28 2 2
TRAF6 0.026 0.003 -10000 0 -10000 0 0
PRKCA 0.025 0.005 -10000 0 -10000 0 0
CHUK 0.025 0.006 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
TNF 0.024 0.03 -10000 0 -0.4 2 2
NF kappa B1 p50/RelA 0.058 0.014 -10000 0 -10000 0 0
BCL10 0.025 0.021 -10000 0 -0.4 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.004 -10000 0 -10000 0 0
IKK complex 0.045 0.052 -10000 0 -0.33 2 2
CYLD 0.025 0.021 -10000 0 -0.4 1 1
IKK complex/PKC alpha 0.052 0.055 -10000 0 -0.35 1 1
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.057 0.043 -9999 0 -0.26 2 2
Ran/GTP/Exportin 1/HDAC1 -0.008 0.002 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.051 -9999 0 -0.26 2 2
SUMO1 0.025 0.029 -9999 0 -0.4 2 2
ZFPM1 0.018 0.061 -9999 0 -0.42 8 8
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.014 -9999 0 -0.18 2 2
FKBP3 0.024 0.022 -9999 0 -0.4 1 1
Histones 0.059 0.036 -9999 0 -10000 0 0
YY1/LSF 0.009 0.069 -9999 0 -0.28 6 6
SMG5 0.026 0.004 -9999 0 -10000 0 0
RAN 0.026 0.002 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.023 0.018 -9999 0 -0.21 2 2
I kappa B alpha/HDAC1 0.025 0.046 -9999 0 -10000 0 0
SAP18 0.021 0.011 -9999 0 -10000 0 0
RELA 0.024 0.024 -9999 0 -10000 0 0
HDAC1/Smad7 0.038 0.028 -9999 0 -0.24 1 1
RANGAP1 0.025 0.006 -9999 0 -10000 0 0
HDAC3/TR2 0.034 0.03 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.018 0.039 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.028 0.056 -9999 0 -0.26 4 4
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.017 0.061 -9999 0 -0.4 9 9
GATA1 0.01 0.022 -9999 0 -10000 0 0
Mad/Max 0.035 0.024 -9999 0 -0.28 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.01 0.066 -9999 0 -0.36 2 2
RBBP7 0.026 0.003 -9999 0 -10000 0 0
NPC 0.016 0 -9999 0 -10000 0 0
RBBP4 0.025 0.005 -9999 0 -10000 0 0
MAX 0.025 0.006 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.026 0.004 -9999 0 -10000 0 0
NFKBIA 0.02 0.014 -9999 0 -10000 0 0
KAT2B 0.009 0.084 -9999 0 -0.4 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.02 0.013 -9999 0 -10000 0 0
SIN3 complex 0.049 0.031 -9999 0 -10000 0 0
SMURF1 0.025 0.006 -9999 0 -10000 0 0
CHD3 0.022 0.01 -9999 0 -10000 0 0
SAP30 0.025 0.005 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.022 0.01 -9999 0 -10000 0 0
YY1/HDAC3 0.012 0.057 -9999 0 -0.32 3 3
YY1/HDAC2 0.01 0.067 -9999 0 -0.29 5 5
YY1/HDAC1 0.01 0.066 -9999 0 -0.29 5 5
NuRD/MBD2 Complex (MeCP1) 0.014 0.047 -9999 0 -0.44 2 2
PPARG 0.02 0.035 -9999 0 -0.25 4 4
HDAC8/hEST1B 0.052 0.011 -9999 0 -10000 0 0
UBE2I 0.026 0.004 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -10000 0 0
TNFRSF1A 0.026 0.004 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.033 0.033 -9999 0 -10000 0 0
MBD3L2 -0.018 0.002 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.027 -9999 0 -0.24 1 1
CREBBP 0.026 0.004 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.01 0.069 -9999 0 -0.34 4 4
HDAC1 0.025 0.005 -9999 0 -10000 0 0
HDAC3 0.021 0.013 -9999 0 -10000 0 0
HDAC2 0.026 0.004 -9999 0 -10000 0 0
YY1 0.007 0.053 -9999 0 -0.25 16 16
HDAC8 0.026 0.001 -9999 0 -10000 0 0
SMAD7 0.019 0.023 -9999 0 -0.4 1 1
NCOR2 0.025 0.021 -9999 0 -0.4 1 1
MXD1 0.024 0.029 -9999 0 -0.4 2 2
STAT3 0.019 0.006 -9999 0 -10000 0 0
NFKB1 0.026 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.023 0.067 -9999 0 -0.29 4 4
YY1/SAP30/HDAC1 0.024 0.065 -9999 0 -0.29 4 4
EP300 0.025 0.006 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.019 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.014 -9999 0 -10000 0 0
histone deacetylation 0.014 0.046 -9999 0 -0.44 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.029 0.018 -9999 0 -10000 0 0
nuclear export -0.051 0.011 -9999 0 -10000 0 0
PRKACA 0.026 0.003 -9999 0 -10000 0 0
GATAD2B 0.026 0.004 -9999 0 -10000 0 0
GATAD2A 0.026 0.003 -9999 0 -10000 0 0
GATA2/HDAC3 0.029 0.045 -9999 0 -10000 0 0
GATA1/HDAC1 0.035 0.009 -9999 0 -10000 0 0
GATA1/HDAC3 0.032 0.029 -9999 0 -10000 0 0
CHD4 0.026 0.004 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0.036 0.023 -9999 0 -0.28 2 2
SIN3/HDAC complex/Mad/Max 0.032 0.043 -9999 0 -0.33 1 1
NuRD Complex -0.006 0.09 -9999 0 -0.3 16 16
positive regulation of chromatin silencing 0.056 0.035 -9999 0 -10000 0 0
SIN3B 0.026 0.003 -9999 0 -10000 0 0
MTA2 0.026 0.004 -9999 0 -10000 0 0
SIN3A 0.025 0.005 -9999 0 -10000 0 0
XPO1 0.026 0.001 -9999 0 -10000 0 0
SUMO1/HDAC1 0.036 0.033 -9999 0 -0.28 2 2
HDAC complex 0.064 0.018 -9999 0 -10000 0 0
GATA1/Fog1 0.03 0.047 -9999 0 -0.3 8 8
FKBP25/HDAC1/HDAC2 0.047 0.023 -9999 0 -0.24 1 1
TNF 0.024 0.03 -9999 0 -0.4 2 2
negative regulation of cell growth 0.032 0.043 -9999 0 -0.33 1 1
NuRD/MBD2/PRMT5 Complex 0.014 0.047 -9999 0 -0.44 2 2
Ran/GTP/Exportin 1 0.036 0.032 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.018 0.04 -9999 0 -0.26 2 2
SIN3/HDAC complex/NCoR1 0.008 0.05 -9999 0 -0.28 8 8
TFCP2 0.025 0.021 -9999 0 -0.4 1 1
NR2C1 0.026 0.003 -9999 0 -10000 0 0
MBD3 0.025 0.021 -9999 0 -0.4 1 1
MBD2 0.02 0.011 -9999 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 0.038 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.025 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.053 0.21 5 -10000 0 5
NFKBIA 0.044 0.055 -10000 0 -0.18 1 1
MAPK14 0.026 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.025 0.01 -10000 0 -10000 0 0
ARRB2 0.012 0.005 -10000 0 -10000 0 0
REL 0.026 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.025 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0.01 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.017 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.011 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.037 0.045 -10000 0 -0.18 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.045 0.052 0.2 5 -10000 0 5
SRC 0.016 0.013 -10000 0 -10000 0 0
PI3K 0.038 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.037 0.045 -10000 0 -0.19 1 1
IKBKB 0.023 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
SYK 0.026 0.003 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.056 0.056 0.21 5 -10000 0 5
cell death 0.043 0.049 0.18 4 -10000 0 4
NF kappa B1 p105/c-Rel 0.025 0.01 -10000 0 -10000 0 0
LCK 0.016 0.064 -10000 0 -0.42 9 9
BCL3 0.026 0.003 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.02 0.012 -10000 0 -10000 0 0
SMAD2 0.012 0.03 -10000 0 -10000 0 0
SMAD3 0.018 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.059 -10000 0 -0.43 6 6
SMAD4/Ubc9/PIASy 0.04 0.024 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.044 -10000 0 -10000 0 0
PPM1A 0.025 0.006 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.022 -10000 0 -10000 0 0
MAP3K1 0.025 0.021 -10000 0 -0.4 1 1
TRAP-1/SMAD4 0.029 0.017 -10000 0 -10000 0 0
MAPK3 0.025 0.021 -10000 0 -0.4 1 1
MAPK1 0.025 0.006 -10000 0 -10000 0 0
NUP214 0.026 0.003 -10000 0 -10000 0 0
CTDSP1 0.026 0.001 -10000 0 -10000 0 0
CTDSP2 0.026 0.002 -10000 0 -10000 0 0
CTDSPL 0.026 0.003 -10000 0 -10000 0 0
KPNB1 0.026 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.027 0 -10000 0 -10000 0 0
UBE2I 0.026 0.004 -10000 0 -10000 0 0
NUP153 0.026 0.004 -10000 0 -10000 0 0
KPNA2 0.027 0.017 0.37 1 -10000 0 1
PIAS4 0.026 0.004 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.023 0.019 -10000 0 -10000 0 0
ATM 0.026 0.004 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
PRKDC 0.023 0.009 -10000 0 -10000 0 0
ATR 0.026 0.002 -10000 0 -10000 0 0
UBE2L3 0.025 0.005 -10000 0 -10000 0 0
FANCD2 0.02 0.015 -10000 0 -0.27 1 1
protein ubiquitination 0.068 0.024 0.24 2 -0.22 1 3
XRCC5 0.026 0.001 -10000 0 -10000 0 0
XRCC6 0.025 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.043 0.025 -10000 0 -0.24 1 1
MRE11A 0.026 0.004 -10000 0 -10000 0 0
DNA-PK 0.045 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.029 0.04 -10000 0 -0.36 3 3
FANCF 0.026 0.003 -10000 0 -10000 0 0
BRCA1 0.026 0.003 -10000 0 -10000 0 0
CCNE1 0.027 0.032 0.37 2 -0.42 1 3
CDK2/Cyclin E1 0.039 0.024 0.26 2 -0.3 1 3
FANCG 0.026 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.039 0.005 -10000 0 -10000 0 0
FANCE 0.026 0.003 -10000 0 -10000 0 0
FANCC 0.026 0.004 -10000 0 -10000 0 0
NBN 0.022 0.023 -10000 0 -0.4 1 1
FANCA 0.026 0.003 -10000 0 -10000 0 0
DNA repair 0.046 0.067 0.27 6 -0.3 1 7
BRCA1/BARD1/ubiquitin 0.039 0.005 -10000 0 -10000 0 0
BARD1/DNA-PK 0.057 0.026 -10000 0 -10000 0 0
FANCL 0.026 0.001 -10000 0 -10000 0 0
mRNA polyadenylation -0.023 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.025 0.043 -10000 0 -0.26 4 4
BRCA1/BACH1/BARD1/TopBP1 0.053 0.008 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.056 0.027 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.031 0.027 -10000 0 -10000 0 0
BRCA1/BACH1 0.026 0.003 -10000 0 -10000 0 0
BARD1 0.026 0.001 -10000 0 -10000 0 0
PCNA 0.021 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.052 0.01 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.051 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.051 0.03 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.057 0.035 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.039 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.035 0.022 -10000 0 -0.22 1 1
FA complex 0.029 0.015 -10000 0 -10000 0 0
BARD1/EWS 0.038 0.008 -10000 0 -10000 0 0
RBBP8 0.01 0.015 -10000 0 -0.28 1 1
TP53 0.022 0.01 -10000 0 -10000 0 0
TOPBP1 0.026 0.002 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.054 0.026 -10000 0 -10000 0 0
BRCA1/BARD1 0.075 0.026 0.26 2 -0.22 1 3
CSTF1 0.015 0.013 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.02 0.001 -10000 0 -10000 0 0
CDK2 0.026 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.025 0.007 -10000 0 -10000 0 0
RAD50 0.026 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.039 0.005 -10000 0 -10000 0 0
EWSR1 0.025 0.006 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.052 0.013 -10000 0 -10000 0 0
CLOCK 0.028 0.005 -10000 0 -10000 0 0
TIMELESS/CRY2 0.038 0.012 -10000 0 -10000 0 0
DEC1/BMAL1 0.03 0.04 -10000 0 -0.3 6 6
ATR 0.026 0.002 -10000 0 -10000 0 0
NR1D1 0.022 0.01 -10000 0 -10000 0 0
ARNTL 0.028 0.005 -10000 0 -10000 0 0
TIMELESS 0.023 0.009 -10000 0 -10000 0 0
NPAS2 0.029 0.003 -10000 0 -10000 0 0
CRY2 0.026 0.003 -10000 0 -10000 0 0
mol:CO -0.009 0.004 0.064 1 -10000 0 1
CHEK1 0.026 0.004 -10000 0 -10000 0 0
mol:HEME 0.009 0.004 -10000 0 -0.064 1 1
PER1 0.021 0.023 -10000 0 -0.4 1 1
BMAL/CLOCK/NPAS2 0.062 0.013 -10000 0 -10000 0 0
BMAL1/CLOCK 0.023 0.043 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.052 0.013 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.053 0.014 -10000 0 -10000 0 0
mol:NADPH 0.009 0.004 -10000 0 -0.064 1 1
PER1/TIMELESS 0.032 0.02 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.009 0.054 -10000 0 -0.42 6 6
Aurora C signaling

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
INCENP 0.026 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.04 0.027 -9999 0 -0.22 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.01 0.017 -9999 0 -0.3 1 1
AURKB 0.022 0.01 -9999 0 -10000 0 0
AURKC 0.022 0.031 -9999 0 -0.4 2 2
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.025 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.005 0.01 -10000 0 -10000 0 0
MDM2/SUMO1 0.035 0.04 -10000 0 -0.37 2 2
HDAC4 0.026 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.005 0.009 -10000 0 -10000 0 0
SUMO1 0.025 0.029 -10000 0 -0.4 2 2
NPC/RanGAP1/SUMO1 0.011 0.014 -10000 0 -0.18 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.009 0.013 -10000 0 -0.17 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.026 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0 -10000 0 -10000 0 0
SUMO1/HDAC4 0.035 0.036 -10000 0 -0.28 2 2
SUMO1/HDAC1 0.036 0.033 -10000 0 -0.28 2 2
RANGAP1 0.025 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.05 0.039 -10000 0 -0.32 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.014 -10000 0 -0.18 2 2
Ran/GTP 0.023 0.028 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.025 0.021 -10000 0 -0.4 1 1
UBE2I 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.029 0.19 1 -10000 0 1
NPC 0.016 0 -10000 0 -10000 0 0
PIAS2 0.02 0.011 -10000 0 -10000 0 0
PIAS1 0.025 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.011 0.019 -10000 0 -10000 0 0
adherens junction organization 0.034 0.039 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.023 -10000 0 -10000 0 0
FMN1 0.034 0.035 -10000 0 -10000 0 0
mol:IP3 0.012 0.016 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.042 0.034 -10000 0 -0.22 1 1
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.051 0.047 0.18 4 -10000 0 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.062 0.061 -10000 0 -0.29 1 1
CTNND1 0.029 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.034 -10000 0 -10000 0 0
VASP 0.037 0.033 -10000 0 -10000 0 0
ZYX 0.035 0.033 -10000 0 -10000 0 0
JUB 0.038 0.033 -10000 0 -0.21 1 1
EGFR(dimer) 0.049 0.039 -10000 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin 0.048 0.017 -10000 0 -0.22 1 1
mol:PI-3-4-5-P3 0.084 0.059 0.21 5 -10000 0 5
PIK3CA 0.03 0.005 -10000 0 -10000 0 0
PI3K 0.086 0.06 0.22 5 -10000 0 5
FYN -0.005 0.046 -10000 0 -0.32 1 1
mol:Ca2+ 0.012 0.016 -10000 0 -10000 0 0
JUP 0.026 0.021 -10000 0 -0.4 1 1
PIK3R1 0.029 0.007 -10000 0 -10000 0 0
mol:DAG 0.012 0.016 -10000 0 -10000 0 0
CDH1 0.027 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.034 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.037 0.034 -10000 0 -10000 0 0
SRC 0.016 0.013 -10000 0 -10000 0 0
RAC1 0.024 0.008 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
EGFR 0.023 0.022 -10000 0 -0.4 1 1
CASR -0.007 0.047 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.022 -10000 0 -10000 0 0
AKT2 0.055 0.047 0.18 4 -10000 0 4
actin cable formation 0.031 0.035 -10000 0 -10000 0 0
apoptosis -0.046 0.046 -10000 0 -0.18 3 3
CTNNA1 0.029 0.005 -10000 0 -10000 0 0
mol:GDP 0.009 0.017 -10000 0 -10000 0 0
PIP5K1A 0.036 0.033 -10000 0 -10000 0 0
PLCG1 0.012 0.017 -10000 0 -10000 0 0
Rac1/GTP 0.054 0.04 -10000 0 -10000 0 0
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.051 0.017 -9999 0 -0.24 1 1
E-cadherin/beta catenin 0.039 0.005 -9999 0 -10000 0 0
CTNNB1 0.026 0.003 -9999 0 -10000 0 0
JUP 0.025 0.021 -9999 0 -0.4 1 1
CDH1 0.026 0.002 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.037 0.009 -9999 0 -9999 0 0
FBXW11 0.026 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -9999 0 0
CHUK 0.025 0.006 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.073 0.022 -9999 0 -9999 0 0
NFKB1 0.026 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.007 -9999 0 -9999 0 0
RELB 0.026 0.003 -9999 0 -9999 0 0
NFKB2 0.025 0.006 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.008 -9999 0 -9999 0 0
regulation of B cell activation 0.033 0.008 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 423 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QG.A5Z2 TCGA.QG.A5Z1 TCGA.QG.A5YX TCGA.QG.A5YW
109_MAP3K5 0.029 0.0051 0.11 0.029
47_PPARGC1A 0.027 0.027 0.027 0.027
105_BMP4 0.027 0.027 0.027 0.027
105_BMP6 0.027 -0.4 -0.4 0.027
105_BMP7 0.027 0.37 0.027 0.027
105_BMP2 0.027 0.027 0 0.027
131_RELN/VLDLR -0.43 -0.23 -0.43 -0.23
30_TGFB1/TGF beta receptor Type II 0.026 0.026 0.026 0.026
84_STAT5B 0.015 0.03 0.096 0.028
84_STAT5A 0.015 0.03 0.096 0.028
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/COAD-TP/9829541/COAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/COAD-TP/10005850/Gistic2_Analysis_10006058/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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