PARADIGM pathway analysis of mRNASeq expression and copy number data
Stomach Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1B857MS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1B857MS
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 37 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
Reelin signaling pathway 92
FOXA2 and FOXA3 transcription factor networks 75
Effects of Botulinum toxin 54
Lissencephaly gene (LIS1) in neuronal migration and development 51
Signaling events regulated by Ret tyrosine kinase 50
p75(NTR)-mediated signaling 49
Signaling events mediated by Stem cell factor receptor (c-Kit) 48
HIF-1-alpha transcription factor network 44
Wnt signaling 44
Signaling events mediated by the Hedgehog family 40
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 415 . 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 ( 415 ).

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
Reelin signaling pathway 0.2217 92 5184 56 -0.24 0.062 1000 -1000 -0.051 -1000
FOXA2 and FOXA3 transcription factor networks 0.1807 75 3469 46 -0.77 0.031 1000 -1000 -0.17 -1000
Effects of Botulinum toxin 0.1301 54 1407 26 -0.15 0.027 1000 -1000 -0.012 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1229 51 2806 54 -0.19 0.038 1000 -1000 -0.046 -1000
Signaling events regulated by Ret tyrosine kinase 0.1205 50 4177 82 -0.12 0.028 1000 -1000 -0.062 -1000
p75(NTR)-mediated signaling 0.1181 49 6146 125 -0.17 0.072 1000 -1000 -0.073 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1157 48 3765 78 -0.22 0.073 1000 -1000 -0.064 -1000
HIF-1-alpha transcription factor network 0.1060 44 3381 76 -0.38 0.036 1000 -1000 -0.15 -1000
Wnt signaling 0.1060 44 310 7 -0.08 -0.004 1000 -1000 -0.022 -1000
Signaling events mediated by the Hedgehog family 0.0964 40 2103 52 -0.067 0.043 1000 -1000 -0.046 -1000
IL4-mediated signaling events 0.0964 40 3664 91 -0.68 0.55 1000 -1000 -0.18 -1000
IL23-mediated signaling events 0.0940 39 2381 60 -0.49 0.028 1000 -1000 -0.15 -1000
Syndecan-1-mediated signaling events 0.0916 38 1293 34 -0.15 0.027 1000 -1000 -0.042 -1000
Glypican 2 network 0.0892 37 148 4 -0.006 0.002 1000 -1000 0.009 -1000
Noncanonical Wnt signaling pathway 0.0867 36 936 26 -0.08 0.027 1000 -1000 -0.043 -1000
Fc-epsilon receptor I signaling in mast cells 0.0867 36 3508 97 -0.12 0.042 1000 -1000 -0.06 -1000
EPHB forward signaling 0.0867 36 3112 85 -0.16 0.11 1000 -1000 -0.064 -1000
Visual signal transduction: Cones 0.0843 35 1361 38 -0.065 0.048 1000 -1000 -0.018 -1000
Glypican 1 network 0.0843 35 1715 48 -0.12 0.049 1000 -1000 -0.03 -1000
Syndecan-2-mediated signaling events 0.0795 33 2300 69 -0.16 0.042 1000 -1000 -0.042 -1000
Ephrin B reverse signaling 0.0795 33 1607 48 -0.16 0.089 1000 -1000 -0.033 -1000
TCGA08_p53 0.0795 33 232 7 -0.067 0.045 1000 -1000 -0.006 -1000
BMP receptor signaling 0.0723 30 2493 81 -0.16 0.049 1000 -1000 -0.059 -1000
TCGA08_retinoblastoma 0.0675 28 231 8 -0.086 0.04 1000 -1000 -0.003 -1000
Canonical Wnt signaling pathway 0.0651 27 1391 51 -0.15 0.12 1000 -1000 -0.06 -1000
Endothelins 0.0602 25 2461 96 -0.15 0.042 1000 -1000 -0.066 -1000
BCR signaling pathway 0.0602 25 2506 99 -0.11 0.034 1000 -1000 -0.059 -1000
Nongenotropic Androgen signaling 0.0578 24 1272 52 -0.074 0.043 1000 -1000 -0.042 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0554 23 800 34 -0.022 0.04 1000 -1000 -0.029 -1000
amb2 Integrin signaling 0.0554 23 1967 82 -0.14 0.038 1000 -1000 -0.049 -1000
Glucocorticoid receptor regulatory network 0.0554 23 2710 114 -0.32 0.21 1000 -1000 -0.065 -1000
TCR signaling in naïve CD8+ T cells 0.0554 23 2180 93 -0.12 0.059 1000 -1000 -0.048 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0554 23 2845 120 -0.11 0.09 1000 -1000 -0.05 -1000
Osteopontin-mediated events 0.0530 22 848 38 -0.15 0.039 1000 -1000 -0.052 -1000
Presenilin action in Notch and Wnt signaling 0.0530 22 1378 61 -0.15 0.072 1000 -1000 -0.047 -1000
LPA receptor mediated events 0.0530 22 2343 102 -0.11 0.037 1000 -1000 -0.052 -1000
Ephrin A reverse signaling 0.0506 21 147 7 -0.003 0.016 1000 -1000 -0.017 -1000
S1P5 pathway 0.0482 20 353 17 -0.055 0.029 1000 -1000 -0.016 -1000
Visual signal transduction: Rods 0.0458 19 1027 52 -0.058 0.037 1000 -1000 -0.036 -1000
Plasma membrane estrogen receptor signaling 0.0434 18 1580 86 -0.13 0.046 1000 -1000 -0.051 -1000
S1P4 pathway 0.0434 18 461 25 -0.055 0.044 1000 -1000 -0.027 -1000
Arf6 signaling events 0.0410 17 1070 62 -0.079 0.059 1000 -1000 -0.04 -1000
Integrins in angiogenesis 0.0410 17 1460 84 -0.15 0.061 1000 -1000 -0.041 -1000
LPA4-mediated signaling events 0.0361 15 187 12 -0.053 0.007 1000 -1000 -0.025 -1000
ErbB4 signaling events 0.0361 15 1078 69 -0.11 0.055 1000 -1000 -0.051 -1000
PDGFR-beta signaling pathway 0.0361 15 1469 97 -0.05 0.082 1000 -1000 -0.058 -1000
Regulation of Androgen receptor activity 0.0361 15 1085 70 -0.22 0.032 1000 -1000 -0.058 -1000
IL1-mediated signaling events 0.0337 14 901 62 -0.054 0.055 1000 -1000 -0.045 -1000
Syndecan-3-mediated signaling events 0.0337 14 511 35 -0.16 0.072 1000 -1000 -0.029 -1000
Syndecan-4-mediated signaling events 0.0337 14 973 67 -0.19 0.033 1000 -1000 -0.048 -1000
Aurora B signaling 0.0337 14 947 67 -0.3 0.08 1000 -1000 -0.044 -1000
ErbB2/ErbB3 signaling events 0.0313 13 897 65 -0.099 0.04 1000 -1000 -0.067 -1000
Coregulation of Androgen receptor activity 0.0313 13 1023 76 -0.087 0.05 1000 -1000 -0.024 -1000
IL12-mediated signaling events 0.0313 13 1206 87 -0.13 0.034 1000 -1000 -0.1 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0313 13 686 52 -0.14 0.056 1000 -1000 -0.064 -1000
S1P1 pathway 0.0313 13 486 36 -0.057 0.028 1000 -1000 -0.052 -1000
Calcium signaling in the CD4+ TCR pathway 0.0313 13 403 31 -0.11 0.027 1000 -1000 -0.056 -1000
IL27-mediated signaling events 0.0313 13 694 51 -0.24 0.062 1000 -1000 -0.065 -1000
IGF1 pathway 0.0313 13 791 57 -0.021 0.053 1000 -1000 -0.047 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0313 13 440 33 -0.088 0.064 1000 -1000 -0.041 -1000
Cellular roles of Anthrax toxin 0.0289 12 491 39 -0.022 0.027 1000 -1000 -0.023 -1000
PLK1 signaling events 0.0289 12 1071 85 -0.05 0.05 1000 -1000 -0.038 -1000
S1P3 pathway 0.0289 12 510 42 -0.054 0.046 1000 -1000 -0.047 -1000
JNK signaling in the CD4+ TCR pathway 0.0265 11 202 17 -0.032 0.056 1000 -1000 -0.037 -1000
Signaling events mediated by PTP1B 0.0265 11 863 76 -0.14 0.046 1000 -1000 -0.044 -1000
Nectin adhesion pathway 0.0265 11 708 63 -0.24 0.051 1000 -1000 -0.058 -1000
Ceramide signaling pathway 0.0265 11 883 76 -0.022 0.072 1000 -1000 -0.043 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0265 11 412 37 -0.086 0.062 1000 -1000 -0.034 -1000
ceramide signaling pathway 0.0265 11 542 49 0 0.04 1000 -1000 -0.046 -1000
Signaling mediated by p38-alpha and p38-beta 0.0265 11 516 44 -0.12 0.028 1000 -1000 -0.036 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0265 11 748 68 -0.21 0.032 1000 -1000 -0.11 -1000
EGFR-dependent Endothelin signaling events 0.0265 11 243 21 -0.028 0.04 1000 -1000 -0.043 -1000
FOXM1 transcription factor network 0.0265 11 599 51 -0.11 0.037 1000 -1000 -0.18 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0241 10 880 85 -0.035 0.041 1000 -1000 -0.055 -1000
FAS signaling pathway (CD95) 0.0241 10 497 47 -0.093 0.04 1000 -1000 -0.043 -1000
Ras signaling in the CD4+ TCR pathway 0.0241 10 170 17 0 0.043 1000 -1000 -0.027 -1000
Caspase cascade in apoptosis 0.0217 9 680 74 -0.048 0.063 1000 -1000 -0.04 -1000
Class I PI3K signaling events mediated by Akt 0.0217 9 630 68 -0.042 0.048 1000 -1000 -0.044 -1000
Signaling mediated by p38-gamma and p38-delta 0.0217 9 146 15 -0.05 0.027 1000 -1000 -0.037 -1000
Retinoic acid receptors-mediated signaling 0.0217 9 524 58 -0.15 0.05 1000 -1000 -0.049 -1000
Regulation of p38-alpha and p38-beta 0.0217 9 488 54 -0.041 0.06 1000 -1000 -0.052 -1000
IL6-mediated signaling events 0.0217 9 680 75 -0.18 0.04 1000 -1000 -0.088 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0217 9 667 74 -0.1 0.064 1000 -1000 -0.061 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0217 9 814 88 -0.077 0.063 1000 -1000 -0.079 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0193 8 238 28 -0.055 0.047 1000 -1000 -0.021 -1000
IFN-gamma pathway 0.0193 8 588 68 -0.066 0.039 1000 -1000 -0.059 -1000
IL2 signaling events mediated by PI3K 0.0193 8 496 58 -0.077 0.051 1000 -1000 -0.069 -1000
Class I PI3K signaling events 0.0193 8 603 73 -0.041 0.046 1000 -1000 -0.047 -1000
FoxO family signaling 0.0169 7 495 64 -0.1 0.057 1000 -1000 -0.08 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0169 7 325 45 -0.003 0.069 1000 -1000 -0.053 -1000
Regulation of nuclear SMAD2/3 signaling 0.0145 6 861 136 -0.085 0.068 1000 -1000 -0.048 -1000
PLK2 and PLK4 events 0.0145 6 20 3 0.006 0.023 1000 -1000 -0.015 -1000
Hedgehog signaling events mediated by Gli proteins 0.0145 6 451 65 -0.055 0.061 1000 -1000 -0.051 -1000
Aurora A signaling 0.0145 6 416 60 -0.08 0.055 1000 -1000 -0.02 -1000
Aurora C signaling 0.0145 6 44 7 0 0.035 1000 -1000 -0.021 -1000
E-cadherin signaling in the nascent adherens junction 0.0145 6 529 76 -0.01 0.059 1000 -1000 -0.057 -1000
Regulation of Telomerase 0.0145 6 641 102 -0.078 0.063 1000 -1000 -0.059 -1000
Rapid glucocorticoid signaling 0.0145 6 127 20 -0.012 0.035 1000 -1000 -0.006 -1000
Thromboxane A2 receptor signaling 0.0120 5 540 105 -0.053 0.04 1000 -1000 -0.061 -1000
EPO signaling pathway 0.0120 5 322 55 0.007 0.057 1000 -1000 -0.049 -1000
PDGFR-alpha signaling pathway 0.0120 5 244 44 -0.042 0.063 1000 -1000 -0.045 -1000
mTOR signaling pathway 0.0120 5 306 53 -0.031 0.043 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class III 0.0120 5 212 40 -0.049 0.05 1000 -1000 -0.019 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0120 5 470 83 -0.13 0.054 1000 -1000 -0.043 -1000
TCGA08_rtk_signaling 0.0120 5 143 26 -0.041 0.073 1000 -1000 -0.028 -1000
IL2 signaling events mediated by STAT5 0.0120 5 110 22 -0.011 0.038 1000 -1000 -0.059 -1000
Arf6 trafficking events 0.0120 5 356 71 -0.091 0.05 1000 -1000 -0.034 -1000
Insulin Pathway 0.0120 5 384 74 -0.037 0.076 1000 -1000 -0.049 -1000
Signaling events mediated by PRL 0.0120 5 174 34 -0.048 0.04 1000 -1000 -0.048 -1000
E-cadherin signaling in keratinocytes 0.0120 5 219 43 -0.031 0.047 1000 -1000 -0.039 -1000
E-cadherin signaling events 0.0120 5 27 5 0.018 0.042 1000 -1000 0.007 -1000
p38 MAPK signaling pathway 0.0120 5 259 44 -0.047 0.057 1000 -1000 -0.033 -1000
Insulin-mediated glucose transport 0.0096 4 158 32 -0.075 0.052 1000 -1000 -0.037 -1000
VEGFR1 specific signals 0.0096 4 249 56 -0.014 0.06 1000 -1000 -0.049 -1000
Class IB PI3K non-lipid kinase events 0.0072 3 9 3 -0.025 0.025 1000 -1000 -0.01 -1000
Canonical NF-kappaB pathway 0.0048 2 114 39 0 0.058 1000 -1000 -0.045 -1000
a4b1 and a4b7 Integrin signaling 0.0048 2 13 5 0.025 0.036 1000 -1000 0.004 -1000
Arf6 downstream pathway 0.0048 2 119 43 -0.043 0.047 1000 -1000 -0.028 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0048 2 342 125 0 0.07 1000 -1000 -0.061 -1000
Signaling events mediated by HDAC Class II 0.0024 1 123 75 -0.027 0.07 1000 -1000 -0.035 -1000
BARD1 signaling events 0.0024 1 74 57 -0.059 0.066 1000 -1000 -0.045 -1000
TRAIL signaling pathway 0.0024 1 79 48 0 0.058 1000 -1000 -0.038 -1000
HIF-2-alpha transcription factor network 0.0024 1 79 43 -0.05 0.052 1000 -1000 -0.085 -1000
Signaling events mediated by HDAC Class I 0.0024 1 195 104 -0.052 0.066 1000 -1000 -0.046 -1000
Paxillin-dependent events mediated by a4b1 0.0024 1 60 36 -0.051 0.053 1000 -1000 -0.042 -1000
Atypical NF-kappaB pathway 0.0024 1 38 31 0 0.036 1000 -1000 -0.029 -1000
Arf1 pathway 0.0024 1 85 54 -0.001 0.048 1000 -1000 -0.025 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 16 23 0.011 0.047 1000 -1000 -0.04 -1000
Circadian rhythm pathway 0.0000 0 17 22 -0.008 0.062 1000 -1000 -0.04 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 10 27 0 0.059 1000 -1000 -0.036 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 0 0.072 1000 -1000 0 -1000
Total NA 2120 125653 7203 -13 7.1 131000 -131000 -6.3 -131000
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.03 -10000 0 -0.25 4 4
VLDLR -0.021 0.13 -10000 0 -0.38 45 45
CRKL 0.027 0.006 -10000 0 -10000 0 0
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ITGA3 0.026 0.027 -10000 0 -0.35 2 2
RELN/VLDLR/Fyn -0.046 0.15 -10000 0 -0.28 116 116
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.057 -10000 0 -10000 0 0
AKT1 -0.16 0.17 -10000 0 -0.4 108 108
MAP2K7 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
DAB1 -0.19 0.2 -10000 0 -0.38 213 213
RELN/LRP8/DAB1 -0.2 0.2 -10000 0 -0.31 283 283
LRPAP1/LRP8 -0.072 0.14 -10000 0 -0.24 161 161
RELN/LRP8/DAB1/Fyn -0.19 0.19 -10000 0 -0.3 275 275
DAB1/alpha3/beta1 Integrin -0.19 0.19 -10000 0 -0.4 148 148
long-term memory -0.24 0.22 -10000 0 -0.45 174 174
DAB1/LIS1 -0.19 0.2 -10000 0 -0.41 150 150
DAB1/CRLK/C3G -0.19 0.19 -10000 0 -0.4 147 147
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DAB1/NCK2 -0.19 0.2 -10000 0 -0.42 149 149
ARHGEF2 0.027 0.006 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.068 0.17 -10000 0 -0.38 95 95
CDK5R1 0.024 0.038 -10000 0 -0.35 4 4
RELN -0.082 0.18 -10000 0 -0.38 108 108
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.11 0.17 -10000 0 -0.27 198 198
GRIN2A/RELN/LRP8/DAB1/Fyn -0.23 0.22 -10000 0 -0.44 175 175
MAPK8 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.15 0.18 -10000 0 -0.28 239 239
ITGB1 0.026 0.02 -10000 0 -0.35 1 1
MAP1B -0.22 0.19 -10000 0 -0.36 229 229
RELN/LRP8 -0.11 0.17 -10000 0 -0.27 197 197
GRIN2B/RELN/LRP8/DAB1/Fyn -0.2 0.2 -10000 0 -0.42 156 156
PI3K 0.036 0.014 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.026 -10000 0 -0.25 3 3
RAP1A -0.19 0.17 0.23 3 -0.38 146 149
PAFAH1B1 0.026 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.009 0.084 -10000 0 -0.38 18 18
CRLK/C3G 0.039 0.011 -10000 0 -10000 0 0
GRIN2B -0.015 0.12 -10000 0 -0.35 43 43
NCK2 0.028 0.004 -10000 0 -10000 0 0
neuron differentiation -0.16 0.17 -10000 0 -0.36 138 138
neuron adhesion -0.18 0.17 0.29 4 -0.38 138 142
LRP8 -0.12 0.19 -10000 0 -0.35 165 165
GSK3B -0.15 0.17 -10000 0 -0.39 104 104
RELN/VLDLR/DAB1/Fyn -0.14 0.17 -10000 0 -0.27 236 236
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.17 0.19 -10000 0 -0.3 233 233
CDK5 0.027 0.006 -10000 0 -10000 0 0
MAPT -0.043 0.19 0.85 8 -0.33 86 94
neuron migration -0.22 0.18 0.22 1 -0.41 150 151
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.17 -10000 0 -0.36 143 143
RELN/VLDLR -0.11 0.18 -10000 0 -0.28 188 188
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.51 0.36 -9999 0 -0.93 128 128
PCK1 -0.36 0.34 -9999 0 -0.94 76 76
HNF4A -0.59 0.44 -9999 0 -1.1 159 159
KCNJ11 -0.49 0.35 -9999 0 -0.96 102 102
AKT1 -0.28 0.2 -9999 0 -0.7 37 37
response to starvation -0.025 0.037 -9999 0 -0.22 4 4
DLK1 -0.52 0.38 -9999 0 -1 114 114
NKX2-1 -0.2 0.15 -9999 0 -0.39 69 69
ACADM -0.51 0.36 -9999 0 -0.94 121 121
TAT -0.36 0.34 -9999 0 -1.1 55 55
CEBPB 0.002 0.037 -9999 0 -0.17 1 1
CEBPA -0.005 0.059 -9999 0 -0.34 6 6
TTR -0.46 0.49 -9999 0 -1.2 120 120
PKLR -0.53 0.37 -9999 0 -0.96 130 130
APOA1 -0.77 0.58 -9999 0 -1.4 171 171
CPT1C -0.52 0.36 -9999 0 -0.95 126 126
ALAS1 -0.23 0.15 -9999 0 -0.6 8 8
TFRC -0.34 0.25 -9999 0 -0.87 37 37
FOXF1 0.013 0.072 -9999 0 -0.38 13 13
NF1 0.031 0.005 -9999 0 -10000 0 0
HNF1A (dimer) -0.073 0.11 -9999 0 -0.26 57 57
CPT1A -0.51 0.35 -9999 0 -0.94 120 120
HMGCS1 -0.49 0.36 -9999 0 -0.94 114 114
NR3C1 -0.018 0.074 -9999 0 -0.28 12 12
CPT1B -0.51 0.36 -9999 0 -0.94 124 124
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.025 0.027 -9999 0 -10000 0 0
GCK -0.52 0.37 -9999 0 -0.95 133 133
CREB1 -0.014 0.068 -9999 0 -0.19 12 12
IGFBP1 -0.32 0.21 -9999 0 -0.73 33 33
PDX1 -0.3 0.28 -9999 0 -1.1 23 23
UCP2 -0.51 0.35 -9999 0 -0.94 121 121
ALDOB -0.6 0.43 -9999 0 -1 164 164
AFP -0.077 0.13 -9999 0 -0.42 30 30
BDH1 -0.51 0.36 -9999 0 -0.95 119 119
HADH -0.48 0.35 -9999 0 -0.95 104 104
F2 -0.61 0.43 -9999 0 -1.2 119 119
HNF1A -0.073 0.11 -9999 0 -0.26 57 57
G6PC -0.16 0.34 -9999 0 -1.1 45 45
SLC2A2 -0.71 0.54 -9999 0 -1.2 204 204
INS 0.014 0.05 -9999 0 -10000 0 0
FOXA1 -0.04 0.11 -9999 0 -0.33 33 33
FOXA3 -0.072 0.12 -9999 0 -0.37 33 33
FOXA2 -0.56 0.39 -9999 0 -1 130 130
ABCC8 -0.62 0.43 -9999 0 -1 174 174
ALB -0.088 0.14 -9999 0 -0.44 31 31
Effects of Botulinum toxin

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
STX1A 0.003 0.03 -10000 0 -0.24 6 6
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.055 0.14 -10000 0 -0.27 122 122
STXBP1 0.022 0.042 -10000 0 -0.35 5 5
ACh/CHRNA1 -0.1 0.12 -10000 0 -0.22 195 195
RAB3GAP2/RIMS1/UNC13B -0.03 0.12 -10000 0 -0.23 117 117
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 -0.099 0.19 -10000 0 -0.38 125 125
mol:ACh -0.014 0.055 0.082 37 -0.11 74 111
RAB3GAP2 0.027 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.048 0.12 -10000 0 -0.28 44 44
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.1 0.12 -10000 0 -0.22 195 195
UNC13B 0.026 0.008 -10000 0 -10000 0 0
CHRNA1 -0.15 0.19 -10000 0 -0.35 188 188
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.04 0.11 -10000 0 -0.23 83 83
SNAP25 -0.042 0.095 -10000 0 -0.23 82 82
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.049 0.15 -10000 0 -0.36 80 80
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.019 0.036 -10000 0 -0.2 10 10
STX1A/SNAP25 fragment 1/VAMP2 -0.048 0.12 -10000 0 -0.28 44 44
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.006 -10000 0 -10000 0 0
VLDLR -0.021 0.13 -10000 0 -0.38 45 45
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
NUDC 0.026 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.11 0.17 -10000 0 -0.27 197 197
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.1 0.15 0.18 11 -0.31 98 109
IQGAP1/CaM 0.038 0.012 -10000 0 -10000 0 0
DAB1 -0.19 0.2 -10000 0 -0.38 213 213
IQGAP1 0.026 0.007 -10000 0 -10000 0 0
PLA2G7 -0.14 0.19 -10000 0 -0.35 176 176
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.072 0.14 -10000 0 -0.24 161 161
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.019 -10000 0 -0.35 1 1
CDK5R1 0.024 0.038 -10000 0 -0.35 4 4
LIS1/Poliovirus Protein 3A 0.008 0.004 -10000 0 -10000 0 0
CDK5R2 -0.063 0.17 -10000 0 -0.38 91 91
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.19 -10000 0 -0.31 239 239
YWHAE 0.026 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.11 0.16 0.29 5 -0.33 93 98
MAP1B 0.002 0.021 -10000 0 -0.24 1 1
RAC1 0.011 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.091 0.14 0.18 14 -0.34 61 75
RELN -0.082 0.18 -10000 0 -0.38 108 108
PAFAH/LIS1 -0.07 0.11 -10000 0 -0.21 166 166
LIS1/CLIP170 0.025 0.017 -10000 0 -0.21 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.089 0.13 -10000 0 -0.3 54 54
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.18 0.21 -10000 0 -0.46 115 115
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.12 0.16 0.21 10 -0.35 101 111
LIS1/IQGAP1 0.024 0.013 -10000 0 -10000 0 0
RHOA 0.012 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.011 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.006 -10000 0 -10000 0 0
PAFAH1B2 0.027 0.006 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.013 0.037 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.1 0.16 0.31 4 -0.32 95 99
LRP8 -0.12 0.19 -10000 0 -0.35 165 165
NDEL1/Katanin 60 -0.11 0.16 0.29 5 -0.33 95 100
P39/CDK5 -0.13 0.16 0.18 13 -0.36 100 113
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.013 -10000 0 -10000 0 0
CDK5 -0.11 0.14 0.18 17 -0.35 60 77
PPP2R5D 0.026 0.007 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.021 0.014 -10000 0 -0.18 1 1
CSNK2A1 0.025 0.009 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.13 0.17 -10000 0 -0.36 98 98
RELN/VLDLR -0.11 0.18 -10000 0 -0.28 188 188
CDC42 0.011 0.006 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.013 0.075 -10000 0 -0.41 10 10
Crk/p130 Cas/Paxillin -0.083 0.13 -10000 0 -0.33 46 46
JUN -0.072 0.13 -10000 0 -0.34 48 48
HRAS 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.053 0.16 -10000 0 -0.25 144 144
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.057 0.16 -10000 0 -0.25 152 152
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.043 0.12 -10000 0 -0.21 137 137
RHOA 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.048 0.14 -10000 0 -0.35 37 37
GRB7 0.019 0.044 -10000 0 -0.37 5 5
RET51/GFRalpha1/GDNF -0.055 0.16 -10000 0 -0.25 150 150
MAPKKK cascade -0.065 0.14 -10000 0 -0.37 36 36
BCAR1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.04 0.12 -10000 0 -0.22 131 131
lamellipodium assembly -0.069 0.12 -10000 0 -0.3 48 48
RET51/GFRalpha1/GDNF/SHC -0.053 0.16 -10000 0 -0.25 144 144
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.038 0.12 -10000 0 -0.22 127 127
RET9/GFRalpha1/GDNF/Shank3 -0.04 0.12 -10000 0 -0.21 131 131
MAPK3 -0.075 0.12 0.19 20 -0.35 35 55
DOK1 0.027 0.019 -10000 0 -0.35 1 1
DOK6 0.017 0.053 -10000 0 -0.36 8 8
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.063 0.12 0.3 1 -0.33 34 35
DOK5 0.006 0.077 -10000 0 -0.36 17 17
GFRA1 -0.12 0.2 -10000 0 -0.38 142 142
MAPK8 -0.074 0.13 -10000 0 -0.35 49 49
HRAS/GTP -0.063 0.16 -10000 0 -0.32 74 74
tube development -0.038 0.12 0.21 1 -0.2 121 122
MAPK1 -0.072 0.13 0.2 23 -0.35 35 58
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.051 0.11 -10000 0 -0.23 57 57
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC 0.024 0.01 -10000 0 -10000 0 0
PDLIM7 0.022 0.042 -10000 0 -0.35 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.042 0.14 -10000 0 -0.28 67 67
SHC1 0.027 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.055 0.16 -10000 0 -0.25 147 147
RET51/GFRalpha1/GDNF/Dok5 -0.054 0.14 -10000 0 -0.25 136 136
PRKCA 0.027 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.005 -10000 0 -10000 0 0
CREB1 -0.078 0.14 -10000 0 -0.38 43 43
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.05 0.11 -10000 0 -0.21 122 122
RET51/GFRalpha1/GDNF/Grb7 -0.05 0.15 -10000 0 -0.25 131 131
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.027 0.14 -10000 0 -0.37 56 56
DOK4 0.026 0.021 -10000 0 -0.38 1 1
JNK cascade -0.071 0.13 -10000 0 -0.33 48 48
RET9/GFRalpha1/GDNF/FRS2 -0.04 0.12 -10000 0 -0.22 128 128
SHANK3 0.026 0.007 -10000 0 -10000 0 0
RASA1 0.025 0.008 -10000 0 -10000 0 0
NCK1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.051 0.11 -10000 0 -0.21 124 124
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.07 0.14 -10000 0 -0.37 43 43
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.073 0.14 -10000 0 -0.29 91 91
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.076 0.15 -10000 0 -0.43 43 43
PI3K -0.1 0.18 -10000 0 -0.45 52 52
SOS1 0.028 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.03 0.12 -10000 0 -0.2 127 127
GRB10 0.026 0.02 -10000 0 -0.35 1 1
activation of MAPKK activity -0.061 0.13 -10000 0 -0.33 41 41
RET51/GFRalpha1/GDNF/FRS2 -0.057 0.16 -10000 0 -0.26 135 135
GAB1 0.027 0.006 -10000 0 -10000 0 0
IRS1 0.027 0.021 -10000 0 -0.38 1 1
IRS2 0.012 0.074 -10000 0 -0.38 14 14
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.075 0.16 -10000 0 -0.42 47 47
RET51/GFRalpha1/GDNF/PKC alpha -0.057 0.16 -10000 0 -0.25 149 149
GRB2 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.027 0.005 -10000 0 -10000 0 0
GDNF 0.012 0.068 -10000 0 -0.38 12 12
RAC1 0.026 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.056 0.16 -10000 0 -0.26 138 138
Rac1/GTP -0.077 0.15 -10000 0 -0.36 47 47
RET9/GFRalpha1/GDNF -0.055 0.13 -10000 0 -0.24 132 132
GFRalpha1/GDNF -0.068 0.15 -10000 0 -0.28 132 132
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.04 0.01 -10000 0 -10000 0 0
Necdin/E2F1 0.025 0.058 -10000 0 -0.27 14 14
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.026 0.15 -10000 0 -0.41 22 22
NGF (dimer)/p75(NTR)/BEX1 -0.14 0.19 -10000 0 -0.29 235 235
NT-4/5 (dimer)/p75(NTR) -0.074 0.15 -10000 0 -0.27 150 150
IKBKB 0.025 0.009 -10000 0 -10000 0 0
AKT1 -0.065 0.12 0.19 20 -0.37 17 37
IKBKG 0.027 0.006 -10000 0 -10000 0 0
BDNF 0.017 0.062 -10000 0 -0.36 11 11
MGDIs/NGR/p75(NTR)/LINGO1 -0.053 0.14 -10000 0 -0.23 153 153
FURIN 0.027 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.04 0.13 -10000 0 -0.23 136 136
LINGO1 -0.005 0.11 -10000 0 -0.35 35 35
Sortilin/TRAF6/NRIF 0.03 0.027 -10000 0 -10000 0 0
proBDNF (dimer) 0.017 0.062 -10000 0 -0.36 11 11
NTRK1 0.009 0.084 -10000 0 -0.38 18 18
RTN4R 0.024 0.033 -10000 0 -0.35 3 3
neuron apoptosis -0.071 0.16 0.31 2 -0.51 22 24
IRAK1 0.027 0.005 -10000 0 -10000 0 0
SHC1 -0.07 0.13 -10000 0 -0.25 130 130
ARHGDIA 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.072 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.035 0.15 -10000 0 -0.24 135 135
MAGEH1 0.021 0.053 -10000 0 -0.38 7 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.037 0.15 -10000 0 -0.24 137 137
Mammalian IAPs/DIABLO 0.063 0.036 -10000 0 -10000 0 0
proNGF (dimer) 0.003 0.096 -10000 0 -0.38 24 24
MAGED1 0.025 0.035 -10000 0 -0.38 3 3
APP 0.026 0.008 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0.092 -10000 0 -0.35 26 26
ZNF274 0.023 0.041 -10000 0 -0.38 4 4
RhoA/GDP/RHOGDI -0.046 0.12 -10000 0 -0.22 134 134
NGF 0.003 0.096 -10000 0 -0.38 24 24
cell cycle arrest -0.042 0.12 0.29 6 -0.34 18 24
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.04 0.11 -10000 0 -0.34 24 24
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.049 0.13 -10000 0 -0.23 147 147
NCSTN 0.027 0.005 -10000 0 -10000 0 0
mol:GTP -0.048 0.15 -10000 0 -0.25 136 136
PSENEN 0.027 0.007 -10000 0 -10000 0 0
mol:ceramide -0.061 0.12 0.18 5 -0.24 115 120
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.035 0.1 -10000 0 -0.3 33 33
p75(NTR)/beta APP -0.058 0.14 -10000 0 -0.27 130 130
BEX1 -0.14 0.2 -10000 0 -0.38 163 163
mol:GDP -0.087 0.12 -10000 0 -0.25 136 136
NGF (dimer) -0.075 0.13 -10000 0 -0.2 198 198
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.036 0.14 -10000 0 -0.22 147 147
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
RAC1/GTP -0.036 0.12 -10000 0 -0.21 128 128
MYD88 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.048 0.15 -10000 0 -0.25 136 136
RHOB 0.028 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.029 0.043 -10000 0 -0.24 9 9
NT3 (dimer) -0.007 0.11 -10000 0 -0.38 33 33
TP53 -0.059 0.1 0.31 4 -0.35 6 10
PRDM4 -0.064 0.12 0.18 5 -0.24 119 124
BDNF (dimer) -0.17 0.15 -10000 0 -0.36 102 102
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.029 0.15 -10000 0 -0.4 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.03 0.14 -10000 0 -0.23 130 130
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
MAPK10 -0.09 0.17 0.27 6 -0.43 52 58
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 -0.061 0.12 0.18 5 -0.24 115 120
APH1B 0.027 0.005 -10000 0 -10000 0 0
APH1A 0.027 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.047 0.15 -10000 0 -0.25 136 136
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.078 0.16 -10000 0 -0.3 144 144
MAPK8 -0.065 0.14 0.29 7 -0.36 27 34
MAPK9 -0.068 0.14 0.28 6 -0.36 29 35
APAF1 0.028 0.004 -10000 0 -10000 0 0
NTF3 -0.007 0.11 -10000 0 -0.38 33 33
NTF4 0 0.092 -10000 0 -0.35 26 26
NDN 0.017 0.064 -10000 0 -0.38 10 10
RAC1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.022 0.13 -10000 0 -0.36 18 18
p75 CTF/Sortilin/TRAF6/NRIF 0.061 0.036 -10000 0 -0.21 4 4
RhoA-B-C/GTP -0.048 0.15 -10000 0 -0.25 136 136
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.014 0.13 -10000 0 -0.37 6 6
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.024 0.13 -10000 0 -0.21 110 110
PRKACB 0.026 0.029 -10000 0 -0.38 2 2
proBDNF (dimer)/p75 ECD 0.032 0.047 -10000 0 -0.25 11 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.021 0.047 -10000 0 -0.36 6 6
BIRC2 0.027 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.043 0.14 0.25 5 -0.27 79 84
BAD -0.081 0.16 0.25 11 -0.36 57 68
RIPK2 0.024 0.01 -10000 0 -10000 0 0
NGFR -0.1 0.19 -10000 0 -0.38 130 130
CYCS -0.072 0.11 0.24 6 -0.38 17 23
ADAM17 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.021 0.13 -10000 0 -0.23 111 111
BCL2L11 -0.081 0.16 0.25 12 -0.36 57 69
BDNF (dimer)/p75(NTR) -0.064 0.15 -10000 0 -0.27 138 138
PI3K -0.034 0.14 -10000 0 -0.24 107 107
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.031 0.14 -10000 0 -0.23 134 134
NDNL2 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
PRKCI 0.024 0.027 -10000 0 -0.35 2 2
NGF (dimer)/p75(NTR) -0.072 0.16 -10000 0 -0.3 136 136
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.033 0.15 -10000 0 -0.24 134 134
TRAF6 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
PLG 0.015 0.041 -10000 0 -0.35 5 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.07 0.14 -10000 0 -0.26 117 117
SQSTM1 0.027 0.006 -10000 0 -10000 0 0
NGFRAP1 0.018 0.064 -10000 0 -0.38 10 10
CASP3 -0.08 0.15 0.25 10 -0.35 58 68
E2F1 0.016 0.056 -10000 0 -0.35 9 9
CASP9 0.027 0.006 -10000 0 -10000 0 0
IKK complex -0.012 0.13 -10000 0 -0.36 20 20
NGF (dimer)/TRKA 0.008 0.095 -10000 0 -0.28 39 39
MMP7 -0.15 0.19 -10000 0 -0.35 193 193
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.021 0.14 -10000 0 -0.38 20 20
MMP3 -0.16 0.19 -10000 0 -0.36 199 199
APAF-1/Caspase 9 -0.07 0.083 -10000 0 -0.32 16 16
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.065 0.16 0.3 2 -0.39 75 77
CRKL -0.068 0.16 0.27 1 -0.39 78 79
HRAS -0.048 0.16 -10000 0 -0.35 66 66
mol:PIP3 -0.055 0.16 -10000 0 -0.36 70 70
SPRED1 0.027 0.006 -10000 0 -10000 0 0
SPRED2 0.028 0.003 -10000 0 -10000 0 0
GAB1 -0.07 0.17 -10000 0 -0.4 80 80
FOXO3 -0.058 0.17 0.35 1 -0.38 71 72
AKT1 -0.062 0.18 0.26 1 -0.4 80 81
BAD -0.058 0.17 0.25 1 -0.38 73 74
megakaryocyte differentiation -0.09 0.18 -10000 0 -0.42 80 80
GSK3B -0.056 0.17 0.27 2 -0.37 70 72
RAF1 -0.041 0.13 0.26 2 -0.34 20 22
SHC1 0.027 0.005 -10000 0 -10000 0 0
STAT3 -0.07 0.17 -10000 0 -0.4 79 79
STAT1 -0.18 0.39 -10000 0 -0.95 81 81
HRAS/SPRED1 -0.029 0.14 0.26 1 -0.33 24 25
cell proliferation -0.07 0.17 -10000 0 -0.39 81 81
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
TEC 0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.062 0.18 -10000 0 -0.4 79 79
HRAS/SPRED2 -0.029 0.14 0.26 1 -0.35 20 21
LYN/TEC/p62DOK -0.034 0.18 -10000 0 -0.39 66 66
MAPK3 -0.027 0.1 0.22 3 -0.28 12 15
STAP1 -0.09 0.19 -10000 0 -0.44 82 82
GRAP2 0.016 0.067 -10000 0 -0.38 11 11
JAK2 -0.15 0.36 -10000 0 -0.84 81 81
STAT1 (dimer) -0.17 0.38 -10000 0 -0.92 81 81
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.039 0.19 -10000 0 -0.4 76 76
actin filament polymerization -0.069 0.16 -10000 0 -0.4 72 72
LYN 0.025 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.12 0.25 -10000 0 -0.6 82 82
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.037 0.16 0.27 1 -0.37 70 71
PI3K -0.041 0.18 -10000 0 -0.39 71 71
PTEN 0.026 0.008 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.19 0.45 -10000 0 -1.1 82 82
MAPK8 -0.071 0.17 -10000 0 -0.4 80 80
STAT3 (dimer) -0.069 0.17 -10000 0 -0.4 80 80
positive regulation of transcription -0.021 0.085 0.19 4 -0.23 12 16
mol:GDP -0.043 0.17 -10000 0 -0.37 70 70
PIK3C2B -0.069 0.17 -10000 0 -0.4 78 78
CBL/CRKL -0.049 0.16 0.27 1 -0.38 72 73
FER -0.068 0.17 -10000 0 -0.41 79 79
SH2B3 -0.067 0.17 -10000 0 -0.4 80 80
PDPK1 -0.051 0.15 0.37 1 -0.35 63 64
SNAI2 -0.069 0.17 -10000 0 -0.41 69 69
positive regulation of cell proliferation -0.13 0.29 -10000 0 -0.7 81 81
KITLG 0.015 0.034 -10000 0 -0.38 1 1
cell motility -0.13 0.29 -10000 0 -0.7 81 81
PTPN6 0.028 0.021 -10000 0 -0.33 1 1
EPOR -0.067 0.23 -10000 0 -0.88 18 18
STAT5A (dimer) -0.1 0.24 -10000 0 -0.58 81 81
SOCS1 0.021 0.047 -10000 0 -0.36 6 6
cell migration 0.073 0.18 0.41 82 -10000 0 82
SOS1 0.028 0.003 -10000 0 -10000 0 0
EPO 0.004 0.058 -10000 0 -0.36 9 9
VAV1 0.022 0.043 -10000 0 -0.36 5 5
GRB10 -0.068 0.17 -10000 0 -0.41 72 72
PTPN11 0.029 0.008 -10000 0 -10000 0 0
SCF/KIT -0.072 0.18 -10000 0 -0.42 81 81
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.031 0.1 0.23 3 -0.29 14 17
CBL 0.027 0.006 -10000 0 -10000 0 0
KIT -0.22 0.48 -10000 0 -1.1 89 89
MAP2K2 -0.031 0.1 0.23 3 -0.29 14 17
SHC/Grb2/SOS1 -0.034 0.18 -10000 0 -0.39 71 71
STAT5A -0.1 0.25 -10000 0 -0.59 81 81
GRB2 0.027 0.005 -10000 0 -10000 0 0
response to radiation -0.068 0.16 -10000 0 -0.4 70 70
SHC/GRAP2 0.031 0.051 -10000 0 -0.27 11 11
PTPRO -0.092 0.18 -10000 0 -0.43 80 80
SH2B2 -0.07 0.17 -10000 0 -0.41 71 71
DOK1 0.027 0.019 -10000 0 -0.35 1 1
MATK -0.074 0.18 -10000 0 -0.42 82 82
CREBBP 0.013 0.057 -10000 0 -10000 0 0
BCL2 -0.12 0.32 -10000 0 -0.94 39 39
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.33 0.33 -10000 0 -0.84 76 76
HDAC7 0.026 0.012 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.26 0.33 -10000 0 -0.92 45 45
SMAD4 0.025 0.01 -10000 0 -10000 0 0
ID2 -0.32 0.34 0.41 1 -0.87 65 66
AP1 0.024 0.07 -10000 0 -0.27 21 21
ABCG2 -0.33 0.34 0.41 1 -0.9 62 63
HIF1A -0.063 0.065 -10000 0 -0.25 1 1
TFF3 -0.38 0.37 0.41 1 -0.91 85 86
GATA2 0.023 0.046 -10000 0 -0.38 5 5
AKT1 -0.066 0.076 -10000 0 -0.26 3 3
response to hypoxia -0.069 0.066 -10000 0 -0.22 27 27
MCL1 -0.32 0.33 -10000 0 -0.89 60 60
NDRG1 -0.31 0.33 0.41 1 -0.88 60 61
SERPINE1 -0.34 0.34 0.41 1 -0.89 67 68
FECH -0.32 0.33 0.41 1 -0.88 64 65
FURIN -0.32 0.33 0.41 1 -0.88 60 61
NCOA2 0.024 0.023 -10000 0 -0.38 1 1
EP300 -0.064 0.1 -10000 0 -0.35 29 29
HMOX1 -0.32 0.34 0.41 1 -0.88 64 65
BHLHE40 -0.32 0.34 0.41 1 -0.88 63 64
BHLHE41 -0.32 0.33 -10000 0 -0.9 58 58
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.034 0.098 -10000 0 -10000 0 0
ENG -0.043 0.082 0.31 2 -10000 0 2
JUN 0.028 0.006 -10000 0 -10000 0 0
RORA -0.32 0.34 0.41 1 -0.88 65 66
ABCB1 -0.1 0.2 -10000 0 -0.9 20 20
TFRC -0.32 0.33 0.41 1 -0.88 64 65
CXCR4 -0.33 0.34 0.41 1 -0.88 67 68
TF -0.38 0.37 0.41 1 -0.91 87 88
CITED2 -0.32 0.34 0.41 1 -0.88 64 65
HIF1A/ARNT -0.34 0.39 -10000 0 -0.97 65 65
LDHA -0.039 0.11 -10000 0 -0.74 7 7
ETS1 -0.32 0.34 0.41 1 -0.87 65 66
PGK1 -0.32 0.34 0.41 1 -0.88 65 66
NOS2 -0.38 0.36 0.41 1 -0.92 82 83
ITGB2 -0.32 0.34 0.41 1 -0.88 65 66
ALDOA -0.32 0.34 0.41 1 -0.88 64 65
Cbp/p300/CITED2 -0.33 0.37 -10000 0 -1 58 58
FOS 0.006 0.091 -10000 0 -0.38 21 21
HK2 -0.33 0.34 0.41 1 -0.89 66 67
SP1 0.027 0.026 -10000 0 -10000 0 0
GCK -0.13 0.31 -10000 0 -1.3 24 24
HK1 -0.32 0.33 0.41 1 -0.88 64 65
NPM1 -0.32 0.33 0.41 1 -0.88 64 65
EGLN1 -0.32 0.33 -10000 0 -0.9 58 58
CREB1 0.032 0.004 -10000 0 -10000 0 0
PGM1 -0.32 0.34 0.41 1 -0.88 65 66
SMAD3 0.028 0.005 -10000 0 -10000 0 0
EDN1 -0.082 0.17 -10000 0 -0.74 12 12
IGFBP1 -0.37 0.36 0.41 1 -0.92 76 77
VEGFA -0.23 0.27 0.37 1 -0.79 41 42
HIF1A/JAB1 -0.024 0.054 -10000 0 -10000 0 0
CP -0.35 0.35 0.41 1 -0.92 70 71
CXCL12 -0.33 0.34 0.41 1 -0.88 72 73
COPS5 0.025 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.016 -10000 0 -10000 0 0
BNIP3 -0.32 0.34 0.41 1 -0.88 66 67
EGLN3 -0.32 0.33 0.41 1 -0.88 64 65
CA9 -0.37 0.36 0.41 1 -0.89 86 87
TERT -0.35 0.35 0.41 1 -0.91 72 73
ENO1 -0.32 0.33 0.41 1 -0.87 65 66
PFKL -0.32 0.34 0.41 1 -0.88 65 66
NCOA1 0.028 0.003 -10000 0 -10000 0 0
ADM -0.32 0.34 0.41 1 -0.87 67 68
ARNT -0.058 0.062 -10000 0 -10000 0 0
HNF4A 0.01 0.063 -10000 0 -0.38 9 9
ADFP -0.33 0.33 -10000 0 -0.84 76 76
SLC2A1 -0.25 0.29 0.37 1 -0.82 48 49
LEP -0.34 0.35 0.41 1 -0.9 71 72
HIF1A/ARNT/Cbp/p300 -0.28 0.34 -10000 0 -0.93 48 48
EPO -0.17 0.2 -10000 0 -0.74 11 11
CREBBP -0.068 0.11 -10000 0 -0.34 36 36
HIF1A/ARNT/Cbp/p300/HDAC7 -0.26 0.34 -10000 0 -0.95 43 43
PFKFB3 -0.32 0.33 0.41 1 -0.87 62 63
NT5E -0.32 0.34 0.41 1 -0.89 65 66
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.08 0.14 -9999 0 -0.38 51 51
FZD6 0.022 0.03 -9999 0 -0.38 2 2
WNT6 -0.031 0.14 -9999 0 -0.38 59 59
WNT4 -0.036 0.15 -9999 0 -0.38 62 62
FZD3 0.024 0.022 -9999 0 -0.38 1 1
WNT5A -0.004 0.1 -9999 0 -0.35 34 34
WNT11 -0.068 0.17 -9999 0 -0.36 101 101
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.039 0.17 -10000 0 -0.54 27 27
IHH -0.028 0.15 -10000 0 -0.43 48 48
SHH Np/Cholesterol/GAS1 -0.017 0.095 -10000 0 -0.22 71 71
LRPAP1 0.026 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.017 0.094 0.22 71 -10000 0 71
SMO/beta Arrestin2 -0.027 0.16 -10000 0 -0.5 26 26
SMO -0.042 0.16 -10000 0 -0.51 27 27
AKT1 -0.025 0.15 -10000 0 -0.53 21 21
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC -0.014 0.12 -10000 0 -0.38 41 41
ADRBK1 0.027 0.006 -10000 0 -10000 0 0
heart looping -0.039 0.16 -10000 0 -0.5 27 27
STIL -0.056 0.14 -10000 0 -0.38 40 40
DHH N/PTCH2 -0.005 0.11 -10000 0 -0.25 64 64
DHH N/PTCH1 -0.016 0.13 -10000 0 -0.38 31 31
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DHH 0.016 0.067 -10000 0 -0.38 11 11
PTHLH -0.062 0.23 -10000 0 -0.76 32 32
determination of left/right symmetry -0.039 0.16 -10000 0 -0.5 27 27
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
skeletal system development -0.061 0.23 -10000 0 -0.75 32 32
IHH N/Hhip -0.067 0.17 -10000 0 -0.34 113 113
DHH N/Hhip -0.039 0.14 -10000 0 -0.28 99 99
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.039 0.16 -10000 0 -0.5 27 27
pancreas development -0.067 0.17 -10000 0 -0.38 94 94
HHAT 0.021 0.05 -10000 0 -0.38 6 6
PI3K 0.036 0.014 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.021 0.13 -10000 0 -0.38 48 48
somite specification -0.039 0.16 -10000 0 -0.5 27 27
SHH Np/Cholesterol/PTCH1 -0.031 0.12 -10000 0 -0.4 23 23
SHH Np/Cholesterol/PTCH2 -0.022 0.094 -10000 0 -0.2 85 85
SHH Np/Cholesterol/Megalin -0.019 0.092 -10000 0 -0.2 79 79
SHH -0.012 0.082 -10000 0 -0.28 34 34
catabolic process -0.026 0.14 -10000 0 -0.41 27 27
SMO/Vitamin D3 -0.038 0.15 -10000 0 -0.46 25 25
SHH Np/Cholesterol/Hhip -0.043 0.12 -10000 0 -0.24 105 105
LRP2 -0.025 0.13 -10000 0 -0.35 55 55
receptor-mediated endocytosis -0.052 0.14 -10000 0 -0.44 28 28
SHH Np/Cholesterol/BOC -0.013 0.093 -10000 0 -0.22 65 65
SHH Np/Cholesterol/CDO 0.001 0.072 -10000 0 -0.21 41 41
mesenchymal cell differentiation 0.043 0.12 0.24 105 -10000 0 105
mol:Vitamin D3 -0.029 0.13 -10000 0 -0.4 23 23
IHH N/PTCH2 -0.037 0.14 -10000 0 -0.27 99 99
CDON 0.018 0.058 -10000 0 -0.37 9 9
IHH N/PTCH1 -0.019 0.14 -10000 0 -0.42 27 27
Megalin/LRPAP1 0 0.096 -10000 0 -0.25 54 54
PTCH2 -0.022 0.13 -10000 0 -0.36 54 54
SHH Np/Cholesterol -0.003 0.064 -10000 0 -0.21 34 34
PTCH1 -0.026 0.14 -10000 0 -0.41 27 27
HHIP -0.067 0.17 -10000 0 -0.38 94 94
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.48 0.44 -10000 0 -1.2 67 67
STAT6 (cleaved dimer) -0.5 0.45 -10000 0 -1.2 89 89
IGHG1 -0.17 0.14 -10000 0 -10000 0 0
IGHG3 -0.48 0.42 -10000 0 -1.1 86 86
AKT1 -0.26 0.27 -10000 0 -0.92 35 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.2 0.27 -10000 0 -0.98 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.28 -10000 0 -0.99 27 27
THY1 -0.51 0.44 -10000 0 -1.2 81 81
MYB -0.039 0.14 -10000 0 -0.35 71 71
HMGA1 0.026 0.02 -10000 0 -0.35 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.31 0.29 -10000 0 -0.87 45 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.26 0.28 -10000 0 -1 27 27
SP1 0.019 0.031 -10000 0 -10000 0 0
INPP5D 0.025 0.034 -10000 0 -0.36 3 3
SOCS5 0.04 0.019 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.49 0.45 -10000 0 -1.2 83 83
SOCS1 -0.34 0.28 -10000 0 -0.77 60 60
SOCS3 -0.26 0.24 -10000 0 -0.82 24 24
FCER2 -0.58 0.56 -10000 0 -1.4 111 111
PARP14 0.015 0.046 -10000 0 -0.35 5 5
CCL17 -0.53 0.48 -10000 0 -1.3 80 80
GRB2 0.027 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.21 -10000 0 -0.75 26 26
T cell proliferation -0.49 0.45 -10000 0 -1.2 73 73
IL4R/JAK1 -0.5 0.44 -10000 0 -1.2 76 76
EGR2 -0.54 0.48 -10000 0 -1.3 79 79
JAK2 -0.03 0.038 -10000 0 -10000 0 0
JAK3 0.013 0.079 -10000 0 -0.35 18 18
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
JAK1 -0.003 0.024 -10000 0 -10000 0 0
COL1A2 -0.2 0.21 -10000 0 -0.87 12 12
CCL26 -0.52 0.45 -10000 0 -1.2 79 79
IL4R -0.53 0.47 -10000 0 -1.3 72 72
PTPN6 0.037 0.024 -10000 0 -0.34 1 1
IL13RA2 -0.54 0.44 -10000 0 -1.2 82 82
IL13RA1 -0.032 0.039 -10000 0 -10000 0 0
IRF4 -0.16 0.3 -10000 0 -1.1 31 31
ARG1 -0.11 0.14 -10000 0 -0.81 4 4
CBL -0.3 0.27 -10000 0 -0.82 43 43
GTF3A 0.001 0.041 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.037 0.051 -10000 0 -10000 0 0
IRF4/BCL6 -0.13 0.27 -10000 0 -1 28 28
CD40LG 0.007 0.078 -10000 0 -0.38 14 14
MAPK14 -0.29 0.27 -10000 0 -0.86 38 38
mitosis -0.24 0.25 -10000 0 -0.84 35 35
STAT6 -0.57 0.53 -10000 0 -1.4 82 82
SPI1 0.027 0.03 -10000 0 -0.35 2 2
RPS6KB1 -0.24 0.24 -10000 0 -0.81 35 35
STAT6 (dimer) -0.57 0.53 -10000 0 -1.4 82 82
STAT6 (dimer)/PARP14 -0.55 0.5 -10000 0 -1.3 87 87
mast cell activation 0.013 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.26 0.3 -10000 0 -1 34 34
FRAP1 -0.26 0.27 -10000 0 -0.91 35 35
LTA -0.5 0.45 -10000 0 -1.3 71 71
FES 0.023 0.04 -10000 0 -0.38 4 4
T-helper 1 cell differentiation 0.55 0.5 1.3 82 -10000 0 82
CCL11 -0.53 0.49 -10000 0 -1.3 93 93
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.28 -10000 0 -0.96 33 33
IL2RG 0.022 0.06 -10000 0 -0.37 9 9
IL10 -0.5 0.44 -10000 0 -1.2 73 73
IRS1 0.027 0.021 -10000 0 -0.38 1 1
IRS2 0.012 0.074 -10000 0 -0.38 14 14
IL4 -0.17 0.26 -10000 0 -1.1 24 24
IL5 -0.5 0.44 -10000 0 -1.3 67 67
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.43 0.37 -10000 0 -1 77 77
COL1A1 -0.25 0.23 -10000 0 -0.82 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.51 0.46 -10000 0 -1.3 64 64
IL2R gamma/JAK3 0.02 0.074 -10000 0 -0.25 27 27
TFF3 -0.57 0.47 -10000 0 -1.3 93 93
ALOX15 -0.53 0.46 -10000 0 -1.3 77 77
MYBL1 0.015 0.062 -10000 0 -0.35 11 11
T-helper 2 cell differentiation -0.44 0.38 -10000 0 -1 77 77
SHC1 0.027 0.005 -10000 0 -10000 0 0
CEBPB 0.023 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.25 0.26 -10000 0 -0.96 25 25
mol:PI-3-4-5-P3 -0.26 0.27 -10000 0 -0.91 35 35
PI3K -0.27 0.3 -10000 0 -1 35 35
DOK2 0.023 0.03 -10000 0 -0.38 2 2
ETS1 0.037 0.02 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.69 22 22
ITGB3 -0.5 0.44 -10000 0 -1.2 72 72
PIGR -0.68 0.6 -10000 0 -1.4 154 154
IGHE 0.06 0.073 0.19 55 -10000 0 55
MAPKKK cascade -0.19 0.19 -10000 0 -0.68 22 22
BCL6 0.029 0.01 -10000 0 -10000 0 0
OPRM1 -0.5 0.44 -10000 0 -1.2 75 75
RETNLB -0.59 0.52 -10000 0 -1.3 101 101
SELP -0.57 0.53 -10000 0 -1.4 90 90
AICDA -0.49 0.43 -10000 0 -1.2 71 71
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.43 0.36 -10000 0 -1.1 60 60
IL23A -0.44 0.37 -10000 0 -1.1 52 52
NF kappa B1 p50/RelA/I kappa B alpha -0.44 0.36 -10000 0 -1 70 70
positive regulation of T cell mediated cytotoxicity -0.47 0.4 -10000 0 -1.1 73 73
ITGA3 -0.42 0.35 -10000 0 -1.1 51 51
IL17F -0.34 0.25 -10000 0 -0.72 71 71
IL12B -0.034 0.049 -10000 0 -0.39 5 5
STAT1 (dimer) -0.46 0.39 -10000 0 -1.1 72 72
CD4 -0.42 0.35 -10000 0 -1.1 54 54
IL23 -0.43 0.35 -10000 0 -1.1 50 50
IL23R -0.11 0.25 -10000 0 -1.1 20 20
IL1B -0.45 0.38 -10000 0 -1.2 58 58
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.46 0.36 -10000 0 -1 72 72
TYK2 -0.022 0.027 -10000 0 -10000 0 0
STAT4 0.024 0.038 -10000 0 -0.35 4 4
STAT3 0.027 0.007 -10000 0 -10000 0 0
IL18RAP 0.006 0.069 -10000 0 -0.38 12 12
IL12RB1 -0.026 0.046 -10000 0 -0.41 4 4
PIK3CA 0.025 0.008 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.024 0.047 -10000 0 -0.3 4 4
IL23R/JAK2 -0.11 0.24 -10000 0 -1.1 18 18
positive regulation of chronic inflammatory response -0.47 0.4 -10000 0 -1.1 73 73
natural killer cell activation 0.009 0.013 0.075 12 -10000 0 12
JAK2 -0.025 0.031 -10000 0 -10000 0 0
PIK3R1 0.025 0.009 -10000 0 -10000 0 0
NFKB1 0.024 0.005 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.41 0.34 -10000 0 -1 51 51
ALOX12B -0.46 0.36 -10000 0 -1 70 70
CXCL1 -0.48 0.36 -10000 0 -1 75 75
T cell proliferation -0.47 0.4 -10000 0 -1.1 73 73
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
IL17A -0.31 0.21 -10000 0 -0.58 92 92
PI3K -0.44 0.37 -10000 0 -1.1 68 68
IFNG -0.023 0.043 0.14 12 -0.12 9 21
STAT3 (dimer) -0.44 0.37 -10000 0 -1.1 68 68
IL18R1 0.016 0.034 -10000 0 -0.37 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.27 0.24 -10000 0 -0.83 32 32
IL18/IL18R 0.025 0.069 -10000 0 -0.23 15 15
macrophage activation -0.024 0.015 -10000 0 -0.045 30 30
TNF -0.44 0.37 -10000 0 -1.2 50 50
STAT3/STAT4 -0.44 0.38 -10000 0 -1.1 71 71
STAT4 (dimer) -0.45 0.39 -10000 0 -1.1 73 73
IL18 0.013 0.043 -10000 0 -0.36 4 4
IL19 -0.49 0.43 -10000 0 -1.2 86 86
STAT5A (dimer) -0.45 0.39 -10000 0 -1.1 71 71
STAT1 0.018 0.059 -10000 0 -0.35 10 10
SOCS3 0.027 0.005 -10000 0 -10000 0 0
CXCL9 -0.47 0.36 -10000 0 -1 75 75
MPO -0.43 0.35 -10000 0 -1 60 60
positive regulation of humoral immune response -0.47 0.4 -10000 0 -1.1 73 73
IL23/IL23R/JAK2/TYK2 -0.48 0.43 -10000 0 -1.2 73 73
IL6 -0.46 0.41 -10000 0 -1.2 73 73
STAT5A 0.028 0.004 -10000 0 -10000 0 0
IL2 0.013 0.035 -10000 0 -0.35 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.009 0.013 0.075 12 -10000 0 12
CD3E -0.42 0.35 -10000 0 -1.1 55 55
keratinocyte proliferation -0.47 0.4 -10000 0 -1.1 73 73
NOS2 -0.48 0.37 -10000 0 -1 88 88
Syndecan-1-mediated signaling events

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
TGFB1 0.027 0.006 -10000 0 -10000 0 0
CCL5 0.019 0.059 -10000 0 -0.38 9 9
SDCBP 0.025 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.079 0.12 0.24 8 -0.31 43 51
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 -0.076 0.11 0.23 3 -0.3 42 45
Syndecan-1/Syntenin -0.069 0.12 0.25 6 -0.29 41 47
MAPK3 -0.072 0.11 0.21 5 -0.29 33 38
HGF/MET 0.014 0.082 -10000 0 -0.26 33 33
TGFB1/TGF beta receptor Type II 0.027 0.006 -10000 0 -10000 0 0
BSG 0.027 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.076 0.11 0.22 3 -0.3 42 45
Syndecan-1/RANTES -0.075 0.12 0.24 8 -0.3 44 52
Syndecan-1/CD147 -0.065 0.12 0.24 8 -0.29 39 47
Syndecan-1/Syntenin/PIP2 -0.068 0.11 0.24 6 -0.28 41 47
LAMA5 0.022 0.022 -10000 0 -0.35 1 1
positive regulation of cell-cell adhesion -0.067 0.11 0.23 6 -0.27 41 47
MMP7 -0.15 0.19 -10000 0 -0.35 193 193
HGF 0.014 0.07 -10000 0 -0.37 13 13
Syndecan-1/CASK -0.084 0.11 -10000 0 -0.29 44 44
Syndecan-1/HGF/MET -0.078 0.13 0.31 3 -0.36 23 26
regulation of cell adhesion -0.07 0.11 0.23 8 -0.34 15 23
HPSE 0.016 0.065 -10000 0 -0.36 12 12
positive regulation of cell migration -0.079 0.12 0.24 8 -0.31 43 51
SDC1 -0.083 0.12 0.18 1 -0.31 44 45
Syndecan-1/Collagen -0.079 0.12 0.24 8 -0.31 43 51
PPIB 0.027 0.005 -10000 0 -10000 0 0
MET 0.005 0.088 -10000 0 -0.36 23 23
PRKACA 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.062 0.16 -10000 0 -0.35 92 92
MAPK1 -0.068 0.11 0.22 8 -0.29 33 41
homophilic cell adhesion -0.078 0.12 0.26 9 -0.31 43 52
MMP1 -0.13 0.19 -10000 0 -0.36 165 165
Glypican 2 network

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
MDK 0.012 0.074 -9999 0 -0.36 16 16
GPC2 -0.006 0.1 -9999 0 -0.35 34 34
GPC2/Midkine 0.002 0.095 -9999 0 -0.25 49 49
neuron projection morphogenesis 0.002 0.094 -9999 0 -0.25 49 49
Noncanonical Wnt signaling pathway

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.019 0.036 -10000 0 -0.38 3 3
GNB1/GNG2 -0.06 0.15 -10000 0 -0.36 50 50
mol:DAG -0.059 0.13 0.21 7 -0.34 42 49
PLCG1 -0.061 0.13 0.21 7 -0.35 42 49
YES1 -0.078 0.14 -10000 0 -0.37 49 49
FZD3 0.024 0.022 -10000 0 -0.38 1 1
FZD6 0.022 0.03 -10000 0 -0.38 2 2
G protein -0.034 0.16 0.26 8 -0.36 40 48
MAP3K7 -0.062 0.12 0.2 11 -0.34 32 43
mol:Ca2+ -0.057 0.13 0.21 7 -0.33 42 49
mol:IP3 -0.059 0.13 0.21 7 -0.34 42 49
NLK 0.007 0.047 -10000 0 -0.91 1 1
GNB1 0.026 0.007 -10000 0 -10000 0 0
CAMK2A -0.064 0.13 0.21 11 -0.32 46 57
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.08 0.14 -10000 0 -0.38 51 51
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
GNAS -0.07 0.13 0.18 1 -0.37 43 44
GO:0007205 -0.059 0.13 0.23 10 -0.34 43 53
WNT6 -0.031 0.14 -10000 0 -0.38 59 59
WNT4 -0.036 0.15 -10000 0 -0.38 62 62
NFAT1/CK1 alpha -0.051 0.14 0.33 3 -0.4 27 30
GNG2 0.027 0.019 -10000 0 -0.35 1 1
WNT5A -0.004 0.1 -10000 0 -0.35 34 34
WNT11 -0.068 0.17 -10000 0 -0.36 101 101
CDC42 -0.07 0.13 0.19 4 -0.36 47 51
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.007 -10000 0 -10000 0 0
LAT2 -0.07 0.13 -10000 0 -0.34 52 52
AP1 -0.06 0.17 0.26 2 -0.4 53 55
mol:PIP3 -0.084 0.16 0.3 9 -0.4 45 54
IKBKB -0.043 0.11 0.22 17 -0.24 43 60
AKT1 -0.069 0.13 0.36 10 -0.31 24 34
IKBKG -0.047 0.11 0.22 14 -0.24 47 61
MS4A2 -0.036 0.15 -10000 0 -0.39 62 62
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
MAP3K1 -0.054 0.13 0.29 11 -0.33 43 54
mol:Ca2+ -0.064 0.13 0.26 10 -0.31 45 55
LYN 0.024 0.01 -10000 0 -10000 0 0
CBLB -0.07 0.13 -10000 0 -0.34 51 51
SHC1 0.027 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK 0.042 0.043 -10000 0 -0.2 10 10
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.025 0.034 -10000 0 -0.36 3 3
PLD2 -0.085 0.13 0.28 13 -0.34 44 57
PTPN13 -0.074 0.16 0.36 1 -0.49 20 21
PTPN11 0.012 0.026 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.055 0.12 0.32 8 -0.28 25 33
SYK 0.025 0.022 -10000 0 -0.4 1 1
GRB2 0.027 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.079 0.16 0.17 1 -0.4 50 51
LAT -0.07 0.13 -10000 0 -0.34 55 55
PAK2 -0.059 0.15 0.28 14 -0.36 47 61
NFATC2 -0.025 0.066 -10000 0 -0.58 3 3
HRAS -0.071 0.15 0.27 7 -0.38 51 58
GAB2 0.027 0.006 -10000 0 -10000 0 0
PLA2G1B 0.007 0.1 -10000 0 -0.87 5 5
Fc epsilon R1 -0.085 0.18 -10000 0 -0.29 166 166
Antigen/IgE/Fc epsilon R1 -0.075 0.16 -10000 0 -0.26 166 166
mol:GDP -0.074 0.15 0.23 1 -0.39 53 54
JUN 0.028 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
FOS 0.006 0.091 -10000 0 -0.38 21 21
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.072 0.14 -10000 0 -0.33 65 65
CHUK -0.051 0.1 0.22 11 -0.24 48 59
KLRG1 -0.068 0.12 -10000 0 -0.31 53 53
VAV1 -0.07 0.13 -10000 0 -0.34 55 55
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.068 0.13 -10000 0 -0.33 54 54
negative regulation of mast cell degranulation -0.057 0.12 0.18 3 -0.3 48 51
BTK -0.076 0.16 0.23 1 -0.41 54 55
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.18 -10000 0 -0.44 66 66
GAB2/PI3K/SHP2 -0.088 0.1 -10000 0 -0.32 37 37
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.077 0.14 -10000 0 -0.36 55 55
RAF1 0.025 0.11 -10000 0 -0.94 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.061 0.17 -10000 0 -0.27 148 148
FCER1G 0.02 0.057 -10000 0 -0.36 9 9
FCER1A -0.12 0.2 -10000 0 -0.4 147 147
Antigen/IgE/Fc epsilon R1/Fyn -0.061 0.15 -10000 0 -0.24 161 161
MAPK3 0.021 0.099 -10000 0 -0.83 5 5
MAPK1 0.019 0.1 -10000 0 -0.87 5 5
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.058 0.22 -10000 0 -0.63 43 43
DUSP1 0.017 0.064 -10000 0 -0.38 10 10
NF-kappa-B/RelA -0.024 0.066 -10000 0 -0.19 6 6
actin cytoskeleton reorganization -0.069 0.16 0.37 1 -0.47 21 22
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.056 0.14 0.23 1 -0.36 42 43
FER -0.065 0.13 -10000 0 -0.34 53 53
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.025 0.061 -10000 0 -0.24 18 18
SOS1 0.028 0.003 -10000 0 -10000 0 0
PLCG1 -0.055 0.16 0.26 10 -0.39 45 55
cytokine secretion -0.02 0.046 -10000 0 -10000 0 0
SPHK1 -0.077 0.14 -10000 0 -0.34 64 64
PTK2 -0.072 0.16 0.37 1 -0.5 19 20
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.078 0.17 0.19 2 -0.41 49 51
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.083 0.16 0.28 9 -0.4 48 57
MAP2K2 0.016 0.1 -10000 0 -0.87 5 5
MAP2K1 0.019 0.099 -10000 0 -0.84 5 5
MAP2K7 0.027 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.057 0.12 0.19 3 -0.3 42 45
MAP2K4 -0.091 0.33 -10000 0 -0.92 55 55
Fc epsilon R1/FcgammaRIIB -0.072 0.18 -10000 0 -0.27 169 169
mol:Choline -0.084 0.13 0.28 13 -0.34 44 57
SHC/Grb2/SOS1 -0.04 0.15 0.24 1 -0.34 44 45
FYN 0.027 0.005 -10000 0 -10000 0 0
DOK1 0.027 0.019 -10000 0 -0.35 1 1
PXN -0.067 0.15 0.36 1 -0.46 19 20
HCLS1 -0.07 0.13 -10000 0 -0.34 51 51
PRKCB -0.071 0.14 0.25 10 -0.32 58 68
FCGR2B 0.012 0.077 -10000 0 -0.38 15 15
IGHE -0.002 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.058 0.13 0.18 3 -0.31 48 51
LCP2 0.027 0.006 -10000 0 -10000 0 0
PLA2G4A -0.076 0.14 -10000 0 -0.34 60 60
RASA1 0.025 0.008 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.084 0.13 0.28 13 -0.34 44 57
IKK complex -0.028 0.09 0.21 20 -0.21 8 28
WIPF1 0.027 0.021 -10000 0 -0.38 1 1
EPHB forward 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
Ephrin A5/EPHB2 -0.092 0.13 -10000 0 -0.22 205 205
cell-cell adhesion 0.097 0.1 0.3 55 -10000 0 55
Ephrin B/EPHB2/RasGAP -0.053 0.13 -10000 0 -0.35 9 9
ITSN1 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.04 -10000 0 -0.23 9 9
Ephrin B1/EPHB1 -0.009 0.094 -10000 0 -0.2 77 77
HRAS/GDP -0.023 0.11 -10000 0 -0.29 19 19
Ephrin B/EPHB1/GRB7 0.01 0.1 -10000 0 -0.35 3 3
Endophilin/SYNJ1 -0.076 0.097 0.17 12 -0.33 9 21
KRAS 0.025 0.009 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.014 0.1 -10000 0 -0.24 11 11
endothelial cell migration 0.046 0.026 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.044 -10000 0 -0.37 5 5
PAK1 -0.075 0.1 0.18 15 -0.34 8 23
HRAS 0.026 0.007 -10000 0 -10000 0 0
RRAS -0.079 0.097 0.17 8 -0.36 8 16
DNM1 0.016 0.064 -10000 0 -0.35 12 12
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.029 0.091 0.21 23 -0.34 3 26
lamellipodium assembly -0.097 0.1 -10000 0 -0.3 55 55
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.002 0.064 -10000 0 -0.28 2 2
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
EPHB2 -0.16 0.19 -10000 0 -0.35 204 204
EPHB3 0.017 0.06 -10000 0 -0.38 9 9
EPHB1 -0.044 0.15 -10000 0 -0.35 77 77
EPHB4 0.026 0.008 -10000 0 -10000 0 0
mol:GDP -0.046 0.093 0.24 2 -0.3 17 19
Ephrin B/EPHB2 -0.058 0.12 -10000 0 -0.19 174 174
Ephrin B/EPHB3 0.039 0.062 -10000 0 -0.19 23 23
JNK cascade -0.11 0.13 0.3 9 -0.33 57 66
Ephrin B/EPHB1 0.006 0.099 -10000 0 -0.19 76 76
RAP1/GDP -0.034 0.1 0.23 8 -0.3 12 20
EFNB2 0.026 0.008 -10000 0 -10000 0 0
EFNB3 0.008 0.083 -10000 0 -0.38 18 18
EFNB1 0.027 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.092 0.14 -10000 0 -0.23 203 203
RAP1B 0.027 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.078 0.13 -10000 0 -0.3 59 59
Rap1/GTP -0.086 0.12 -10000 0 -0.3 61 61
axon guidance -0.092 0.13 -10000 0 -0.22 205 205
MAPK3 -0.004 0.056 0.19 1 -0.26 2 3
MAPK1 -0.004 0.058 0.19 2 -0.26 2 4
Rac1/GDP -0.042 0.097 0.23 4 -0.28 16 20
actin cytoskeleton reorganization -0.078 0.097 -10000 0 -0.26 54 54
CDC42/GDP -0.038 0.1 0.23 9 -0.28 18 27
PI3K 0.051 0.029 -10000 0 -10000 0 0
EFNA5 0.008 0.084 -10000 0 -0.38 18 18
Ephrin B2/EPHB4 0.032 0.014 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.04 0.078 -10000 0 -0.29 11 11
CDC42 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.082 0.12 -10000 0 -0.29 58 58
PTK2 0.11 0.23 0.66 61 -10000 0 61
MAP4K4 -0.11 0.14 0.3 9 -0.34 57 66
SRC 0.024 0.01 -10000 0 -10000 0 0
KALRN 0.022 0.045 -10000 0 -0.38 5 5
Intersectin/N-WASP 0.038 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis -0.057 0.12 0.28 15 -0.31 8 23
MAP2K1 -0.003 0.058 -10000 0 -0.26 2 2
WASL 0.027 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.094 0.16 -10000 0 -0.24 208 208
cell migration 0.004 0.09 0.25 9 -0.3 4 13
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 -0.077 0.098 0.17 12 -0.33 9 21
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.14 0.12 0.17 3 -0.34 74 77
HRAS/GTP -0.081 0.13 -10000 0 -0.31 61 61
Ephrin B1/EPHB1-2 -0.1 0.15 -10000 0 -0.23 216 216
cell adhesion mediated by integrin 0.004 0.061 0.2 10 -0.2 18 28
RAC1 0.026 0.008 -10000 0 -10000 0 0
mol:GTP -0.084 0.14 -10000 0 -0.32 61 61
RAC1-CDC42/GTP -0.091 0.12 -10000 0 -0.3 58 58
RASA1 0.025 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.099 0.23 4 -0.3 8 12
ruffle organization -0.073 0.15 0.37 14 -0.3 52 66
NCK1 0.027 0.005 -10000 0 -10000 0 0
receptor internalization -0.078 0.1 0.17 7 -0.33 16 23
Ephrin B/EPHB2/KALRN -0.056 0.13 -10000 0 -0.35 10 10
ROCK1 0.021 0.054 0.18 28 -0.21 9 37
RAS family/GDP -0.084 0.087 -10000 0 -0.25 48 48
Rac1/GTP -0.089 0.12 -10000 0 -0.31 55 55
Ephrin B/EPHB1/Src/Paxillin -0.003 0.06 -10000 0 -0.27 4 4
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.045 0.024 -10000 0 -0.18 3 3
RGS9BP -0.011 0.12 -10000 0 -0.38 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.015 0.041 -10000 0 -0.35 5 5
mol:Na + -0.052 0.12 -10000 0 -0.22 132 132
mol:ADP -0.016 0.04 -10000 0 -0.25 11 11
GNAT2 0.027 0.005 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.023 0.13 -10000 0 -0.25 101 101
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.029 0.022 -10000 0 -0.2 3 3
GRK7 0.019 0.046 -10000 0 -0.35 6 6
CNGB3 -0.065 0.16 -10000 0 -0.35 95 95
Cone Metarhodopsin II/X-Arrestin 0.015 0.019 -10000 0 -0.24 2 2
mol:Ca2+ -0.055 0.12 0.18 35 -0.22 123 158
Cone PDE6 -0.007 0.13 -10000 0 -0.22 84 84
Cone Metarhodopsin II 0.021 0.036 -10000 0 -0.18 11 11
Na + (4 Units) -0.048 0.12 -10000 0 -0.21 141 141
GNAT2/GDP -0.009 0.12 -10000 0 -0.21 98 98
GNB5 0.027 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.035 0.18 8 -0.24 3 11
Cone Transducin 0.048 0.025 -10000 0 -0.19 3 3
SLC24A2 0.003 0.085 -10000 0 -0.35 22 22
GNB3/GNGT2 0.037 0.028 -10000 0 -0.26 3 3
GNB3 0.024 0.035 -10000 0 -0.38 3 3
GNAT2/GTP 0.02 0.003 -10000 0 -10000 0 0
CNGA3 -0.027 0.14 -10000 0 -0.38 54 54
ARR3 0.02 0.027 -10000 0 -0.35 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.052 0.12 -10000 0 -0.22 132 132
mol:Pi -0.024 0.13 -10000 0 -0.25 101 101
Cone CNG Channel -0.029 0.11 -10000 0 -0.23 32 32
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.003 0.085 -10000 0 -0.35 22 22
RGS9 -0.058 0.17 -10000 0 -0.38 85 85
PDE6C 0.022 0.02 -10000 0 -0.35 1 1
GNGT2 0.028 0.002 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.032 -10000 0 -0.35 3 3
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.035 0.064 -10000 0 -0.23 20 20
fibroblast growth factor receptor signaling pathway 0.034 0.064 -10000 0 -0.23 20 20
LAMA1 -0.044 0.15 -10000 0 -0.36 76 76
PRNP 0.024 0.022 -10000 0 -0.38 1 1
GPC1/SLIT2 -0.014 0.12 -10000 0 -0.27 71 71
SMAD2 0.012 0.027 0.18 3 -0.19 4 7
GPC1/PrPc/Cu2+ 0.03 0.03 -10000 0 -0.21 5 5
GPC1/Laminin alpha1 -0.017 0.12 -10000 0 -0.25 78 78
TDGF1 -0.035 0.14 -10000 0 -0.37 65 65
CRIPTO/GPC1 -0.01 0.11 -10000 0 -0.26 68 68
APP/GPC1 0.034 0.031 -10000 0 -0.25 4 4
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.022 0.084 -10000 0 -0.22 63 63
FLT1 0.025 0.02 -10000 0 -0.35 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.049 0.033 -10000 0 -0.2 5 5
SERPINC1 0.017 0.053 -10000 0 -0.35 8 8
FYN -0.022 0.086 -10000 0 -0.22 65 65
FGR -0.023 0.086 -10000 0 -0.22 66 66
positive regulation of MAPKKK cascade -0.015 0.13 0.22 23 -0.33 30 53
SLIT2 -0.041 0.15 -10000 0 -0.38 68 68
GPC1/NRG -0.027 0.12 -10000 0 -0.27 84 84
NRG1 -0.056 0.16 -10000 0 -0.38 81 81
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.046 0.033 -10000 0 -0.21 4 4
LYN -0.018 0.08 -10000 0 -0.22 55 55
mol:Spermine 0.005 0.025 -10000 0 -0.24 4 4
cell growth 0.034 0.064 -10000 0 -0.23 20 20
BMP signaling pathway -0.024 0.038 0.35 4 -10000 0 4
SRC -0.015 0.076 -10000 0 -0.22 47 47
TGFBR1 0.026 0.019 -10000 0 -0.35 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.12 0.19 -10000 0 -0.36 157 157
GPC1 0.024 0.038 -10000 0 -0.35 4 4
TGFBR1 (dimer) 0.026 0.019 -10000 0 -0.35 1 1
VEGFA 0.025 0.02 -10000 0 -0.35 1 1
BLK -0.056 0.12 -10000 0 -0.25 105 105
HCK -0.014 0.076 -10000 0 -0.22 47 47
FGF2 0.009 0.084 -10000 0 -0.38 18 18
FGFR1 0.022 0.035 -10000 0 -0.38 3 3
VEGFR1 homodimer 0.025 0.02 -10000 0 -0.35 1 1
TGFBR2 0.027 0.005 -10000 0 -10000 0 0
cell death 0.034 0.031 -10000 0 -0.25 4 4
ATIII/GPC1 0.029 0.049 -10000 0 -0.25 12 12
PLA2G2A/GPC1 -0.075 0.14 -10000 0 -0.26 157 157
LCK -0.029 0.092 -10000 0 -0.22 76 76
neuron differentiation -0.027 0.12 -10000 0 -0.27 84 84
PrPc/Cu2+ 0.018 0.016 -10000 0 -0.27 1 1
APP 0.026 0.008 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.027 0.005 -10000 0 -10000 0 0
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 0.003 0.069 -10000 0 -0.2 41 41
EPHB2 -0.16 0.19 -10000 0 -0.35 204 204
Syndecan-2/TACI -0.025 0.097 -10000 0 -0.22 78 78
LAMA1 -0.044 0.15 -10000 0 -0.36 76 76
Syndecan-2/alpha2 ITGB1 0.03 0.065 -10000 0 -0.25 7 7
HRAS 0.026 0.007 -10000 0 -10000 0 0
Syndecan-2/CASK 0.007 0.015 -10000 0 -0.21 2 2
ITGA5 0.021 0.049 -10000 0 -0.35 7 7
BAX 0.004 0.01 -10000 0 -10000 0 0
EPB41 0.027 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.022 0.018 -10000 0 -0.19 2 2
LAMA3 0.014 0.066 -10000 0 -0.36 12 12
EZR 0.027 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.024 0.027 -10000 0 -0.35 2 2
Syndecan-2/MMP2 0.022 0.026 -10000 0 -0.21 4 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.025 0.059 -10000 0 -0.24 18 18
dendrite morphogenesis -0.067 0.11 -10000 0 -0.2 168 168
Syndecan-2/GM-CSF -0.025 0.093 -10000 0 -0.2 89 89
determination of left/right symmetry 0.009 0.019 -10000 0 -0.25 2 2
Syndecan-2/PKC delta 0.024 0.02 -10000 0 -0.21 2 2
GNB2L1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.012 0.1 0.19 36 -0.18 85 121
MAPK1 -0.014 0.099 0.19 33 -0.18 83 116
Syndecan-2/RACK1 0.034 0.023 -10000 0 -0.18 2 2
NF1 0.028 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.009 0.019 -10000 0 -0.25 2 2
ITGA2 0.008 0.082 -10000 0 -0.35 20 20
MAPK8 0.008 0.015 -10000 0 -0.22 1 1
Syndecan-2/alpha2/beta1 Integrin 0.008 0.089 -10000 0 -0.32 2 2
Syndecan-2/Kininogen 0.009 0.057 -10000 0 -0.21 25 25
ITGB1 0.026 0.02 -10000 0 -0.35 1 1
SRC 0.028 0.049 0.18 38 -10000 0 38
Syndecan-2/CASK/Protein 4.1 0.021 0.018 -10000 0 -0.19 2 2
extracellular matrix organization 0.024 0.017 -10000 0 -0.22 1 1
actin cytoskeleton reorganization 0.003 0.069 -10000 0 -0.2 41 41
Syndecan-2/Caveolin-2/Ras 0.034 0.027 -10000 0 -0.19 3 3
Syndecan-2/Laminin alpha3 0.018 0.039 -10000 0 -0.21 11 11
Syndecan-2/RasGAP 0.042 0.029 -10000 0 -0.18 1 1
alpha5/beta1 Integrin 0.033 0.043 -10000 0 -0.28 7 7
PRKCD 0.027 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer -0.067 0.11 -10000 0 -0.2 168 168
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.028 0.022 0.18 3 -10000 0 3
RHOA 0.027 0.006 -10000 0 -10000 0 0
SDCBP 0.025 0.009 -10000 0 -10000 0 0
TNFRSF13B -0.069 0.17 -10000 0 -0.38 94 94
RASA1 0.025 0.008 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.025 0.059 -10000 0 -0.24 18 18
Syndecan-2/Synbindin 0.024 0.02 -10000 0 -0.21 2 2
TGFB1 0.027 0.006 -10000 0 -10000 0 0
CASP3 0.032 0.058 0.19 45 -0.2 1 46
FN1 -0.01 0.11 -10000 0 -0.35 41 41
Syndecan-2/IL8 -0.072 0.11 -10000 0 -0.2 176 176
SDC2 0.009 0.019 -10000 0 -0.25 2 2
KNG1 -0.004 0.098 -10000 0 -0.35 30 30
Syndecan-2/Neurofibromin 0.024 0.02 -10000 0 -0.21 2 2
TRAPPC4 0.027 0.006 -10000 0 -10000 0 0
CSF2 -0.066 0.16 -10000 0 -0.35 99 99
Syndecan-2/TGFB1 0.024 0.017 -10000 0 -0.22 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.022 0.018 -10000 0 -0.19 2 2
Syndecan-2/Ezrin 0.036 0.024 -10000 0 -0.19 2 2
PRKACA 0.035 0.06 0.19 50 -0.19 2 52
angiogenesis -0.072 0.11 -10000 0 -0.2 176 176
MMP2 0.025 0.028 -10000 0 -0.37 2 2
IL8 -0.16 0.19 -10000 0 -0.35 198 198
calcineurin-NFAT signaling pathway -0.025 0.097 -10000 0 -0.22 78 78
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.008 -10000 0 -10000 0 0
EPHB2 -0.16 0.19 -10000 0 -0.35 204 204
EFNB1 -0.003 0.044 -10000 0 -0.25 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.083 0.14 -10000 0 -0.33 60 60
Ephrin B2/EPHB1-2 -0.09 0.14 -10000 0 -0.22 200 200
neuron projection morphogenesis -0.086 0.13 -10000 0 -0.31 60 60
Ephrin B1/EPHB1-2/Tiam1 -0.096 0.15 -10000 0 -0.34 65 65
DNM1 0.016 0.064 -10000 0 -0.35 12 12
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.025 0.11 0.26 1 -0.45 23 24
YES1 -0.027 0.16 -10000 0 -0.65 26 26
Ephrin B1/EPHB1-2/NCK2 -0.089 0.15 -10000 0 -0.34 60 60
PI3K 0.007 0.12 -10000 0 -0.43 26 26
mol:GDP -0.096 0.15 -10000 0 -0.34 65 65
ITGA2B 0.015 0.067 -10000 0 -0.36 13 13
endothelial cell proliferation 0.032 0.014 -10000 0 -10000 0 0
FYN -0.028 0.17 -10000 0 -0.65 27 27
MAP3K7 -0.026 0.12 0.22 1 -0.47 25 26
FGR -0.024 0.16 -10000 0 -0.66 24 24
TIAM1 0.017 0.062 -10000 0 -0.37 10 10
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
RGS3 0.027 0.006 -10000 0 -10000 0 0
cell adhesion -0.009 0.12 -10000 0 -0.43 23 23
LYN -0.026 0.16 -10000 0 -0.66 25 25
Ephrin B1/EPHB1-2/Src Family Kinases -0.03 0.15 -10000 0 -0.58 27 27
Ephrin B1/EPHB1-2 -0.022 0.12 -10000 0 -0.54 19 19
SRC -0.026 0.16 -10000 0 -0.64 26 26
ITGB3 0.023 0.042 -10000 0 -0.36 5 5
EPHB1 -0.044 0.15 -10000 0 -0.35 77 77
EPHB4 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.032 0.014 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.028 0.06 -10000 0 -0.25 18 18
BLK -0.044 0.17 -10000 0 -0.69 24 24
HCK -0.025 0.16 -10000 0 -0.64 25 25
regulation of stress fiber formation 0.089 0.15 0.34 60 -10000 0 60
MAPK8 -0.025 0.11 0.24 1 -0.43 22 23
Ephrin B1/EPHB1-2/RGS3 -0.089 0.15 -10000 0 -0.34 61 61
endothelial cell migration 0.003 0.11 0.24 16 -0.41 17 33
NCK2 0.028 0.004 -10000 0 -10000 0 0
PTPN13 0.009 0.096 -10000 0 -0.45 17 17
regulation of focal adhesion formation 0.089 0.15 0.34 60 -10000 0 60
chemotaxis 0.089 0.15 0.34 61 -10000 0 61
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.085 0.14 -10000 0 -0.32 60 60
angiogenesis -0.025 0.12 -10000 0 -0.51 23 23
LCK -0.027 0.16 -10000 0 -0.65 26 26
TCGA08_p53

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
CDKN2A -0.067 0.11 -10000 0 -0.24 121 121
TP53 -0.025 0.065 0.18 1 -0.25 24 25
Senescence -0.026 0.067 0.18 1 -0.25 25 26
Apoptosis -0.026 0.067 0.18 1 -0.25 25 26
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.045 0.094 0.27 33 -0.34 1 34
MDM4 0.027 0.005 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.021 0.14 -10000 0 -0.4 18 18
SMAD6-7/SMURF1 0.045 0.023 -10000 0 -10000 0 0
NOG 0.002 0.097 -10000 0 -0.37 26 26
SMAD9 -0.053 0.19 -10000 0 -0.58 44 44
SMAD4 0.024 0.01 -10000 0 -10000 0 0
SMAD5 -0.037 0.12 -10000 0 -0.34 36 36
BMP7/USAG1 -0.12 0.18 -10000 0 -0.33 176 176
SMAD5/SKI -0.041 0.14 -10000 0 -0.35 41 41
SMAD1 0.014 0.062 -10000 0 -0.43 4 4
BMP2 0.023 0.03 -10000 0 -0.38 2 2
SMAD1/SMAD1/SMAD4 0.024 0.059 -10000 0 -0.36 3 3
BMPR1A 0.025 0.021 -10000 0 -0.38 1 1
BMPR1B -0.026 0.14 -10000 0 -0.38 53 53
BMPR1A-1B/BAMBI -0.023 0.13 -10000 0 -0.24 106 106
AHSG 0.008 0.075 -10000 0 -0.35 17 17
CER1 0.01 0.057 -10000 0 -0.35 10 10
BMP2-4/CER1 0.031 0.055 -10000 0 -0.23 14 14
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.06 0.14 -10000 0 -0.36 51 51
BMP2-4 (homodimer) 0.031 0.046 -10000 0 -0.29 7 7
RGMB 0.025 0.022 -10000 0 -0.38 1 1
BMP6/BMPR2/BMPR1A-1B 0.027 0.094 -10000 0 -0.22 44 44
RGMA -0.098 0.19 -10000 0 -0.38 125 125
SMURF1 0.025 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.051 0.13 -10000 0 -0.33 49 49
BMP2-4/USAG1 -0.079 0.14 -10000 0 -0.23 181 181
SMAD6/SMURF1/SMAD5 -0.039 0.13 -10000 0 -0.34 45 45
SOSTDC1 -0.16 0.2 -10000 0 -0.38 189 189
BMP7/BMPR2/BMPR1A-1B -0.011 0.12 -10000 0 -0.24 76 76
SKI 0.026 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.025 0.021 -10000 0 -0.38 1 1
HFE2 0.012 0.061 -10000 0 -0.35 11 11
ZFYVE16 0.026 0.008 -10000 0 -10000 0 0
MAP3K7 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD 0.039 0.057 -10000 0 -0.28 10 10
SMAD5/SMAD5/SMAD4 -0.041 0.14 -10000 0 -0.34 42 42
MAPK1 0.027 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.034 0.12 -10000 0 -0.31 36 36
BMP7 (homodimer) -0.037 0.14 -10000 0 -0.38 60 60
NUP214 0.027 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.024 0.055 -10000 0 -0.24 16 16
SMAD1/SKI 0.02 0.078 0.25 1 -0.42 6 7
SMAD6 0.027 0.005 -10000 0 -10000 0 0
CTDSP2 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA 0.035 0.057 -10000 0 -0.22 16 16
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.045 0.15 -10000 0 -0.36 77 77
BMPR2 (homodimer) 0.028 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.049 0.02 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.002 0.1 -10000 0 -0.27 52 52
CHRDL1 -0.13 0.2 -10000 0 -0.38 153 153
ENDOFIN/SMAD1 0.02 0.077 0.25 1 -0.42 6 7
SMAD6-7/SMURF1/SMAD1 0.039 0.072 -10000 0 -0.39 4 4
SMAD6/SMURF1 0.025 0.009 -10000 0 -10000 0 0
BAMBI -0.033 0.14 -10000 0 -0.35 65 65
SMURF2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.047 0.14 -10000 0 -0.24 135 135
BMP2-4/GREM1 -0.003 0.11 -10000 0 -0.21 80 80
SMAD7 0.025 0.009 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.048 0.19 -10000 0 -0.52 52 52
SMAD1/SMAD6 0.018 0.074 0.25 1 -0.4 5 6
TAK1/SMAD6 0.036 0.015 -10000 0 -10000 0 0
BMP7 -0.037 0.14 -10000 0 -0.38 60 60
BMP6 0.025 0.021 -10000 0 -0.38 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.045 0.14 -10000 0 -0.35 47 47
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.021 0.077 -10000 0 -0.44 5 5
SMAD7/SMURF1 0.033 0.017 -10000 0 -10000 0 0
CTDSPL 0.027 0.005 -10000 0 -10000 0 0
PPP1CA 0.027 0.006 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
CTDSP1 0.028 0.004 -10000 0 -10000 0 0
PPP1R15A 0.027 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.085 0.18 -10000 0 -0.4 77 77
CHRD 0.018 0.057 -10000 0 -0.38 8 8
BMPR2 0.028 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.061 0.14 -10000 0 -0.33 61 61
BMP4 0.021 0.051 -10000 0 -0.36 7 7
FST -0.009 0.11 -10000 0 -0.37 36 36
BMP2-4/NOG 0.027 0.077 -10000 0 -0.22 33 33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.003 0.12 -10000 0 -0.39 9 9
TCGA08_retinoblastoma

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
CDKN2B 0.022 0.031 -10000 0 -0.35 2 2
CDKN2C 0.033 0.028 -10000 0 -0.32 1 1
CDKN2A -0.086 0.17 -10000 0 -0.35 121 121
CCND2 0.017 0.041 0.14 9 -10000 0 9
RB1 -0.021 0.051 0.3 1 -0.18 11 12
CDK4 0.024 0.053 0.19 14 -10000 0 14
CDK6 0.023 0.052 0.17 21 -10000 0 21
G1/S progression 0.04 0.075 0.2 50 -0.3 1 51
Canonical Wnt signaling pathway

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.014 -10000 0 -10000 0 0
AES 0.026 0.013 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.016 -10000 0 -10000 0 0
SMAD4 0.024 0.01 -10000 0 -10000 0 0
DKK2 -0.075 0.17 -10000 0 -0.35 111 111
TLE1 0.026 0.024 -10000 0 -0.39 1 1
MACF1 0.027 0.019 -10000 0 -0.35 1 1
CTNNB1 0.016 0.12 0.33 11 -0.46 7 18
WIF1 -0.065 0.16 -10000 0 -0.38 86 86
beta catenin/RanBP3 0 0.11 0.38 11 -0.48 4 15
KREMEN2 -0.049 0.15 -10000 0 -0.35 82 82
DKK1 -0.15 0.19 -10000 0 -0.36 186 186
beta catenin/beta TrCP1 0.027 0.11 0.33 11 -0.48 5 16
FZD1 0.025 0.009 -10000 0 -10000 0 0
AXIN2 -0.012 0.19 0.64 7 -1.3 6 13
AXIN1 0.027 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.007 0.13 -10000 0 -0.56 16 16
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.016 0.19 0.32 2 -0.64 25 27
Axin1/APC/GSK3 0.038 0.071 0.24 8 -0.36 3 11
Axin1/APC/GSK3/beta catenin/Macf1 0.013 0.11 0.25 6 -0.41 12 18
HNF1A 0.018 0.06 -10000 0 -0.35 10 10
CTBP1 0.026 0.013 -10000 0 -10000 0 0
MYC 0.12 0.26 0.59 81 -1.2 2 83
RANBP3 0.027 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.066 0.14 -10000 0 -0.22 171 171
NKD1 -0.02 0.13 -10000 0 -0.37 48 48
TCF4 0.024 0.014 -10000 0 -10000 0 0
TCF3 0.026 0.013 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.046 0.062 -10000 0 -0.2 17 17
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.015 0.12 0.41 6 -0.47 12 18
LEF1 0.016 0.064 -10000 0 -0.35 12 12
DVL1 0.026 0.044 -10000 0 -0.34 1 1
CSNK2A1 0.025 0.009 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.007 0.16 0.35 2 -0.6 19 21
DKK1/LRP6/Kremen 2 -0.11 0.15 -10000 0 -0.23 228 228
LRP6 0.027 0.007 -10000 0 -10000 0 0
CSNK1A1 0.027 0.014 -10000 0 -10000 0 0
NLK 0.028 0.005 -10000 0 -10000 0 0
CCND1 0.037 0.14 0.58 23 -10000 0 23
WNT1 0.006 0.09 -10000 0 -0.38 21 21
GSK3A 0.027 0.006 -10000 0 -10000 0 0
GSK3B 0.028 0.005 -10000 0 -10000 0 0
FRAT1 0.027 0.006 -10000 0 -10000 0 0
PPP2R5D 0.044 0.071 0.24 28 -0.34 2 30
APC 0.012 0.079 0.2 46 -10000 0 46
WNT1/LRP6/FZD1 0.035 0.083 0.2 58 -0.31 3 61
CREBBP 0.026 0.014 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.013 0.14 0.25 7 -0.42 11 18
PTK2B 0.025 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.14 -10000 0 -0.62 6 6
EDN1 0.007 0.11 0.21 3 -0.33 12 15
EDN3 -0.06 0.16 -10000 0 -0.38 82 82
EDN2 -0.049 0.16 -10000 0 -0.38 77 77
HRAS/GDP -0.019 0.13 0.26 4 -0.42 15 19
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.008 0.095 -10000 0 -0.34 12 12
ADCY4 -0.021 0.12 0.21 10 -0.37 15 25
ADCY5 -0.059 0.16 0.21 8 -0.36 53 61
ADCY6 -0.02 0.12 0.22 5 -0.38 14 19
ADCY7 -0.02 0.12 0.21 9 -0.37 15 24
ADCY1 -0.025 0.12 0.2 11 -0.36 18 29
ADCY2 -0.047 0.14 0.22 4 -0.36 36 40
ADCY3 -0.02 0.12 0.21 10 -0.37 15 25
ADCY8 -0.026 0.12 0.22 4 -0.36 15 19
ADCY9 -0.023 0.12 0.21 7 -0.37 15 22
arachidonic acid secretion -0.026 0.15 0.24 5 -0.47 27 32
ETB receptor/Endothelin-1/Gq/GTP 0.004 0.07 -10000 0 -0.26 10 10
GNAO1 -0.055 0.16 -10000 0 -0.38 82 82
HRAS 0.026 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.042 0.16 0.3 8 -0.39 10 18
ETA receptor/Endothelin-1/Gs/GTP 0.021 0.16 0.29 7 -0.38 15 22
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
COL3A1 -0.037 0.18 0.25 6 -0.42 58 64
EDNRB 0.01 0.053 -10000 0 -0.38 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.02 0.15 0.25 7 -0.5 13 20
CYSLTR1 -0.03 0.17 0.25 7 -0.49 31 38
SLC9A1 0 0.081 0.18 4 -0.25 12 16
mol:GDP -0.029 0.14 0.25 5 -0.42 20 25
SLC9A3 -0.14 0.27 -10000 0 -0.6 65 65
RAF1 -0.036 0.14 0.24 7 -0.44 26 33
JUN 0.002 0.14 -10000 0 -0.68 6 6
JAK2 -0.015 0.13 0.25 7 -0.32 30 37
mol:IP3 0.005 0.091 -10000 0 -0.36 10 10
ETA receptor/Endothelin-1 0.028 0.19 0.36 6 -0.37 30 36
PLCB1 0.023 0.028 -10000 0 -0.35 2 2
PLCB2 0.023 0.038 -10000 0 -0.36 4 4
ETA receptor/Endothelin-3 -0.047 0.14 -10000 0 -0.29 91 91
FOS -0.054 0.22 0.33 1 -0.82 27 28
Gai/GDP -0.15 0.32 -10000 0 -0.68 104 104
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.011 0.13 0.23 6 -0.41 13 19
BCAR1 0.027 0.007 -10000 0 -10000 0 0
PRKCB1 0 0.1 0.19 2 -0.37 15 17
GNAQ 0.027 0.009 -10000 0 -10000 0 0
GNAZ 0.001 0.1 -10000 0 -0.38 26 26
GNAL -0.001 0.1 -10000 0 -0.38 27 27
Gs family/GDP -0.033 0.14 0.25 4 -0.4 21 25
ETA receptor/Endothelin-1/Gq/GTP 0.007 0.095 0.19 3 -0.34 9 12
MAPK14 0.001 0.074 0.23 2 -0.31 8 10
TRPC6 0.005 0.14 -10000 0 -0.66 6 6
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.054 -10000 0 -0.38 7 7
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.006 0.074 -10000 0 -0.31 7 7
ETB receptor/Endothelin-2 -0.029 0.12 -10000 0 -0.28 75 75
ETB receptor/Endothelin-3 -0.039 0.12 -10000 0 -0.28 81 81
ETB receptor/Endothelin-1 0.013 0.11 -10000 0 -0.3 12 12
MAPK3 -0.05 0.2 0.33 1 -0.7 28 29
MAPK1 -0.052 0.2 0.34 1 -0.7 28 29
Rac1/GDP -0.02 0.13 0.22 2 -0.42 16 18
cAMP biosynthetic process -0.042 0.15 0.24 11 -0.39 31 42
MAPK8 -0.001 0.16 -10000 0 -0.62 14 14
SRC 0.024 0.01 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.039 0.12 -10000 0 -0.36 34 34
p130Cas/CRK/Src/PYK2 -0.023 0.15 0.3 10 -0.54 11 21
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.019 0.13 0.22 3 -0.41 16 19
COL1A2 -0.027 0.18 0.25 4 -0.42 52 56
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.037 0.14 -10000 0 -0.28 83 83
mol:DAG 0.005 0.091 -10000 0 -0.36 10 10
MAP2K2 -0.041 0.16 0.3 2 -0.52 30 32
MAP2K1 -0.043 0.16 0.3 2 -0.52 30 32
EDNRA 0.004 0.12 0.21 3 -0.35 16 19
positive regulation of muscle contraction -0.002 0.12 0.22 25 -0.38 10 35
Gq family/GDP -0.012 0.12 -10000 0 -0.4 15 15
HRAS/GTP -0.032 0.13 0.25 5 -0.41 24 29
PRKCH 0.003 0.092 0.2 2 -0.35 12 14
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCA 0 0.1 0.2 4 -0.37 15 19
PRKCB -0.01 0.11 0.19 1 -0.39 20 21
PRKCE -0.001 0.1 0.25 3 -0.38 14 17
PRKCD 0.002 0.091 0.19 1 -0.34 12 13
PRKCG -0.065 0.13 0.22 5 -0.37 24 29
regulation of vascular smooth muscle contraction -0.066 0.26 0.34 1 -0.95 27 28
PRKCQ -0.005 0.11 0.22 3 -0.4 15 18
PLA2G4A -0.03 0.16 0.24 5 -0.52 27 32
GNA14 0.021 0.053 -10000 0 -0.38 7 7
GNA15 0.023 0.042 -10000 0 -0.35 5 5
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA11 0.027 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.042 0.16 0.3 8 -0.39 10 18
MMP1 -0.12 0.19 0.4 2 -0.34 157 159
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.058 0.16 0.41 3 -0.43 42 45
IKBKB -0.025 0.1 0.47 2 -0.33 17 19
AKT1 -0.028 0.11 0.32 9 -0.25 21 30
IKBKG -0.017 0.091 0.42 2 -0.28 14 16
CALM1 -0.039 0.13 0.28 1 -0.41 32 33
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
MAP3K1 -0.067 0.2 0.44 2 -0.55 43 45
MAP3K7 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.037 0.14 -10000 0 -0.42 34 34
DOK1 0.027 0.019 -10000 0 -0.35 1 1
AP-1 -0.034 0.1 0.31 5 -0.26 34 39
LYN 0.025 0.009 -10000 0 -10000 0 0
BLNK 0.011 0.08 -10000 0 -0.38 16 16
SHC1 0.027 0.005 -10000 0 -10000 0 0
BCR complex -0.031 0.15 -10000 0 -0.33 78 78
CD22 -0.073 0.18 -10000 0 -0.54 38 38
CAMK2G -0.032 0.13 0.27 2 -0.38 30 32
CSNK2A1 0.025 0.009 -10000 0 -10000 0 0
INPP5D 0.025 0.034 -10000 0 -0.36 3 3
SHC/GRB2/SOS1 -0.015 0.11 -10000 0 -0.36 22 22
GO:0007205 -0.04 0.14 0.3 1 -0.42 37 38
SYK 0.026 0.021 -10000 0 -0.38 1 1
ELK1 -0.039 0.14 0.28 1 -0.41 34 35
NFATC1 -0.061 0.16 0.28 3 -0.42 50 53
B-cell antigen/BCR complex -0.031 0.15 -10000 0 -0.33 78 78
PAG1/CSK 0.034 0.021 -10000 0 -0.25 1 1
NFKBIB 0.007 0.047 0.18 4 -0.12 15 19
HRAS -0.034 0.13 0.3 2 -0.4 30 32
NFKBIA 0.007 0.047 0.18 4 -0.12 15 19
NF-kappa-B/RelA/I kappa B beta 0.012 0.042 0.18 4 -10000 0 4
RasGAP/Csk 0.006 0.14 -10000 0 -0.28 61 61
mol:GDP -0.037 0.14 0.28 1 -0.41 35 36
PTEN 0.026 0.008 -10000 0 -10000 0 0
CD79B -0.002 0.1 -10000 0 -0.38 30 30
NF-kappa-B/RelA/I kappa B alpha 0.012 0.041 0.18 4 -10000 0 4
GRB2 0.027 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.081 0.2 0.45 2 -0.52 50 52
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
mol:IP3 -0.039 0.14 -10000 0 -0.44 34 34
CSK 0.027 0.005 -10000 0 -10000 0 0
FOS -0.045 0.14 0.28 3 -0.42 33 36
CHUK -0.024 0.1 0.42 2 -0.3 26 28
IBTK 0.027 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.043 0.15 0.27 4 -0.4 32 36
PTPN6 -0.071 0.17 -10000 0 -0.57 31 31
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.007 0.033 0.22 2 -10000 0 2
VAV2 -0.075 0.19 -10000 0 -0.54 47 47
ubiquitin-dependent protein catabolic process 0.01 0.046 0.18 4 -0.12 15 19
BTK -0.006 0.16 -10000 0 -0.98 11 11
CD19 -0.075 0.19 -10000 0 -0.52 50 50
MAP4K1 0.013 0.073 -10000 0 -0.37 14 14
CD72 -0.029 0.13 -10000 0 -0.35 59 59
PAG1 0.023 0.021 -10000 0 -0.35 1 1
MAPK14 -0.054 0.18 0.43 3 -0.47 41 44
SH3BP5 0.028 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.038 0.15 -10000 0 -0.45 34 34
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.068 0.19 -10000 0 -0.52 46 46
RAF1 -0.032 0.12 0.3 2 -0.4 26 28
RasGAP/p62DOK/SHIP 0.007 0.14 -10000 0 -0.39 28 28
CD79A -0.048 0.16 -10000 0 -0.38 75 75
re-entry into mitotic cell cycle -0.034 0.1 0.31 5 -0.26 33 38
RASA1 0.025 0.008 -10000 0 -10000 0 0
MAPK3 -0.026 0.11 0.35 3 -0.37 18 21
MAPK1 -0.026 0.11 0.3 3 -0.36 19 22
CD72/SHP1 -0.073 0.18 0.27 3 -0.48 47 50
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.056 0.17 0.44 3 -0.46 41 44
actin cytoskeleton organization -0.059 0.17 0.27 2 -0.46 43 45
NF-kappa-B/RelA 0.026 0.078 0.28 5 -0.2 6 11
Calcineurin -0.009 0.12 0.26 1 -0.39 20 21
PI3K -0.064 0.15 -10000 0 -0.42 48 48
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.034 0.15 -10000 0 -0.46 35 35
SOS1 0.028 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.083 0.27 -10000 0 -0.79 45 45
DAPP1 -0.11 0.3 -10000 0 -0.9 46 46
cytokine secretion -0.056 0.15 0.28 3 -0.39 50 53
mol:DAG -0.039 0.14 -10000 0 -0.44 34 34
PLCG2 0.019 0.055 -10000 0 -0.37 8 8
MAP2K1 -0.03 0.12 0.28 2 -0.37 25 27
B-cell antigen/BCR complex/FcgammaRIIB -0.017 0.15 -10000 0 -0.3 80 80
mol:PI-3-4-5-P3 -0.057 0.1 0.21 1 -0.32 37 38
ETS1 -0.03 0.12 0.28 3 -0.36 28 31
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.008 0.13 -10000 0 -0.39 22 22
B-cell antigen/BCR complex/LYN -0.052 0.17 -10000 0 -0.54 33 33
MALT1 0.025 0.009 -10000 0 -10000 0 0
TRAF6 0.027 0.005 -10000 0 -10000 0 0
RAC1 -0.062 0.18 0.29 1 -0.5 41 42
B-cell antigen/BCR complex/LYN/SYK -0.043 0.18 -10000 0 -0.55 31 31
CARD11 -0.067 0.16 0.29 5 -0.41 48 53
FCGR2B 0.012 0.077 -10000 0 -0.38 15 15
PPP3CA 0.026 0.027 -10000 0 -0.35 2 2
BCL10 0.028 0.004 -10000 0 -10000 0 0
IKK complex 0 0.053 0.18 9 -0.12 9 18
PTPRC 0.01 0.08 -10000 0 -0.36 19 19
PDPK1 -0.035 0.082 0.2 8 -0.23 28 36
PPP3CB 0.027 0.006 -10000 0 -10000 0 0
PPP3CC 0.025 0.009 -10000 0 -10000 0 0
POU2F2 0.01 0.033 0.42 1 -10000 0 1
Nongenotropic Androgen signaling

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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.018 0.084 -10000 0 -0.2 50 50
regulation of S phase of mitotic cell cycle -0.004 0.071 -10000 0 -0.21 39 39
GNAO1 -0.055 0.16 -10000 0 -0.38 82 82
HRAS 0.026 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.007 0.044 -10000 0 -0.2 17 17
PELP1 0.026 0.007 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.006 0.089 0.18 48 -0.28 3 51
T-DHT/AR -0.016 0.095 -10000 0 -0.27 51 51
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.008 23 23
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.054 -10000 0 -0.38 7 7
mol:GDP -0.037 0.11 -10000 0 -0.32 51 51
cell proliferation -0.015 0.13 0.29 7 -0.4 20 27
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
FOS -0.026 0.19 0.26 2 -0.72 24 26
mol:Ca2+ -0.014 0.031 -10000 0 -0.08 57 57
MAPK3 -0.009 0.11 0.27 10 -0.3 17 27
MAPK1 -0.008 0.1 0.21 4 -0.43 13 17
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 23 23
cAMP biosynthetic process 0 0.048 0.25 1 -0.19 17 18
GNG2 0.027 0.019 -10000 0 -0.35 1 1
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 23 23
HRAS/GTP 0.016 0.073 -10000 0 -0.19 33 33
actin cytoskeleton reorganization 0.034 0.019 -10000 0 -10000 0 0
SRC 0.024 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 23 23
PI3K 0.033 0.013 -10000 0 -10000 0 0
apoptosis 0.006 0.12 0.37 26 -0.26 5 31
T-DHT/AR/PELP1 0.003 0.085 -10000 0 -0.22 51 51
HRAS/GDP -0.023 0.11 -10000 0 -0.31 46 46
CREB1 -0.008 0.12 0.27 5 -0.4 26 31
RAC1-CDC42/GTP 0.043 0.023 -10000 0 -10000 0 0
AR -0.024 0.14 -10000 0 -0.38 51 51
GNB1 0.026 0.007 -10000 0 -10000 0 0
RAF1 0.012 0.091 0.19 50 -0.26 3 53
RAC1-CDC42/GDP 0.003 0.11 -10000 0 -0.32 36 36
T-DHT/AR/PELP1/Src 0.017 0.077 -10000 0 -0.2 42 42
MAP2K2 -0.007 0.086 0.18 44 -0.28 3 47
T-DHT/AR/PELP1/Src/PI3K -0.004 0.071 -10000 0 -0.21 39 39
GNAZ 0.001 0.1 -10000 0 -0.38 26 26
SHBG 0.008 0.075 -10000 0 -0.35 17 17
Gi family/GNB1/GNG2/GDP -0.074 0.19 -10000 0 -0.4 80 80
mol:T-DHT 0 0.001 -10000 0 -0.003 17 17
RAC1 0.026 0.008 -10000 0 -10000 0 0
GNRH1 0.005 0.019 -10000 0 -0.27 2 2
Gi family/GTP -0.051 0.12 -10000 0 -0.32 57 57
CDC42 0.026 0.007 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0 0.1 0.26 53 -10000 0 53
KIRREL 0.017 0.046 -10000 0 -0.37 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.001 0.1 -10000 0 -0.26 53 53
PLCG1 0.023 0.011 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.027 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.029 0.086 -10000 0 -0.22 17 17
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.004 0.061 -10000 0 -0.22 19 19
FYN -0.004 0.08 0.24 12 -0.2 21 33
mol:Ca2+ 0.024 0.081 -10000 0 -0.19 44 44
mol:DAG 0.025 0.081 -10000 0 -0.19 44 44
NPHS2 0.013 0.041 -10000 0 -0.36 3 3
mol:IP3 0.025 0.081 -10000 0 -0.19 44 44
regulation of endocytosis 0.022 0.075 -10000 0 -0.19 17 17
Nephrin/NEPH1/podocin/Cholesterol 0.015 0.082 -10000 0 -0.19 55 55
establishment of cell polarity 0 0.1 -10000 0 -0.26 53 53
Nephrin/NEPH1/podocin/NCK1-2 0.04 0.087 -10000 0 -0.31 1 1
Nephrin/NEPH1/beta Arrestin2 0.024 0.077 -10000 0 -0.2 17 17
NPHS1 -0.022 0.13 -10000 0 -0.36 51 51
Nephrin/NEPH1/podocin 0.018 0.077 -10000 0 -0.18 41 41
TJP1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.005 -10000 0 -10000 0 0
NCK2 0.028 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.026 0.082 -10000 0 -0.19 44 44
CD2AP 0.026 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.028 0.09 -10000 0 -0.2 41 41
GRB2 0.027 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.078 0.21 18 -0.19 18 36
cytoskeleton organization -0.008 0.073 0.21 6 -0.26 19 25
Nephrin/NEPH1 0.006 0.07 -10000 0 -0.17 53 53
Nephrin/NEPH1/ZO-1 0.019 0.087 -10000 0 -0.2 52 52
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.025 0.065 -10000 0 -0.22 14 14
alphaM/beta2 Integrin/GPIbA 0.016 0.08 -10000 0 -0.23 28 28
alphaM/beta2 Integrin/proMMP-9 -0.032 0.12 -10000 0 -0.23 90 90
PLAUR 0.023 0.038 -10000 0 -0.35 4 4
HMGB1 0.016 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.027 0.06 -10000 0 -0.22 11 11
AGER 0.014 0.035 -10000 0 -0.35 1 1
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.028 0.004 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.021 0.1 -10000 0 -0.29 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.062 0.16 -10000 0 -0.35 92 92
CYR61 0.023 0.043 -10000 0 -0.37 5 5
TLN1 0.026 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.023 0.092 -10000 0 -0.29 14 14
RHOA 0.027 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.024 0.14 -10000 0 -0.38 51 51
MYH2 -0.044 0.097 -10000 0 -0.3 20 20
MST1R 0.023 0.04 -10000 0 -0.38 4 4
leukocyte activation during inflammatory response -0.075 0.13 -10000 0 -0.27 52 52
APOB -0.14 0.2 -10000 0 -0.38 176 176
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.025 0.028 -10000 0 -0.37 2 2
JAM3 0.027 0.006 -10000 0 -10000 0 0
GP1BA 0.01 0.078 -10000 0 -0.38 16 16
alphaM/beta2 Integrin/CTGF 0.026 0.066 -10000 0 -0.22 15 15
alphaM/beta2 Integrin -0.036 0.092 -10000 0 -0.28 26 26
JAM3 homodimer 0.027 0.006 -10000 0 -10000 0 0
ICAM2 0.026 0.028 -10000 0 -0.37 2 2
ICAM1 0.018 0.059 -10000 0 -0.35 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.036 0.093 -10000 0 -0.28 26 26
cell adhesion 0.016 0.079 -10000 0 -0.23 28 28
NFKB1 -0.015 0.14 0.38 2 -0.37 37 39
THY1 -0.003 0.1 -10000 0 -0.35 32 32
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.09 0.14 -10000 0 -0.23 192 192
alphaM/beta2 Integrin/LRP/tPA 0.038 0.063 -10000 0 -0.22 5 5
IL6 -0.05 0.2 0.37 1 -0.59 37 38
ITGB2 0.009 0.057 -10000 0 -0.36 7 7
elevation of cytosolic calcium ion concentration 0.015 0.094 -10000 0 -0.25 18 18
alphaM/beta2 Integrin/JAM2/JAM3 0.022 0.094 -10000 0 -0.23 35 35
JAM2 -0.009 0.12 -10000 0 -0.38 35 35
alphaM/beta2 Integrin/ICAM1 0.025 0.098 -10000 0 -0.31 5 5
alphaM/beta2 Integrin/uPA/Plg 0.01 0.093 -10000 0 -0.24 16 16
RhoA/GTP -0.047 0.1 -10000 0 -0.29 30 30
positive regulation of phagocytosis -0.019 0.082 -10000 0 -0.29 7 7
Ron/MSP 0.014 0.085 -10000 0 -0.25 37 37
alphaM/beta2 Integrin/uPAR/uPA 0.017 0.095 -10000 0 -0.25 17 17
alphaM/beta2 Integrin/uPAR 0.024 0.067 -10000 0 -0.22 17 17
PLAU -0.007 0.11 -10000 0 -0.35 36 36
PLAT 0.025 0.009 -10000 0 -10000 0 0
actin filament polymerization -0.043 0.094 -10000 0 -0.29 21 21
MST1 -0.004 0.1 -10000 0 -0.35 34 34
alphaM/beta2 Integrin/lipoprotein(a) -0.074 0.13 -10000 0 -0.27 52 52
TNF -0.032 0.15 -10000 0 -0.56 15 15
RAP1B 0.027 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.093 -10000 0 -0.22 47 47
fibrinolysis 0.009 0.092 -10000 0 -0.24 16 16
HCK 0.024 0.01 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.036 0.093 -10000 0 -0.28 26 26
VTN -0.051 0.16 -10000 0 -0.37 81 81
alphaM/beta2 Integrin/CYR61 0.025 0.07 -10000 0 -0.23 18 18
LPA -0.005 0.098 -10000 0 -0.35 30 30
LRP1 0.027 0.005 -10000 0 -10000 0 0
cell migration -0.032 0.1 -10000 0 -0.3 20 20
FN1 -0.01 0.11 -10000 0 -0.35 41 41
alphaM/beta2 Integrin/Thy1 0.009 0.091 -10000 0 -0.23 42 42
MPO 0.022 0.046 -10000 0 -0.35 6 6
KNG1 -0.004 0.098 -10000 0 -0.35 30 30
RAP1/GDP 0.035 0.01 -10000 0 -10000 0 0
ROCK1 -0.041 0.098 0.2 3 -0.3 20 23
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.015 0.041 -10000 0 -0.35 5 5
CTGF 0.025 0.028 -10000 0 -0.37 2 2
alphaM/beta2 Integrin/Hck 0.024 0.062 -10000 0 -0.22 13 13
ITGAM 0.011 0.054 -10000 0 -0.37 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.013 0.1 -10000 0 -0.22 50 50
HP -0.03 0.13 -10000 0 -0.35 60 60
leukocyte adhesion -0.013 0.11 -10000 0 -0.33 14 14
SELP -0.024 0.14 -10000 0 -0.38 51 51
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.066 0.07 -10000 0 -10000 0 0
SMARCC2 0.028 0.01 -10000 0 -10000 0 0
SMARCC1 0.028 0.01 -10000 0 -10000 0 0
TBX21 -0.083 0.12 0.34 1 -0.46 18 19
SUMO2 0.027 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.059 -10000 0 -0.35 10 10
FKBP4 0.026 0.007 -10000 0 -10000 0 0
FKBP5 0.025 0.029 -10000 0 -0.38 2 2
GR alpha/HSP90/FKBP51/HSP90 0.1 0.093 0.28 29 -0.27 1 30
PRL -0.059 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.2 0.52 62 -10000 0 62
RELA -0.045 0.075 -10000 0 -0.22 10 10
FGG 0.089 0.22 0.42 50 -0.38 37 87
GR beta/TIF2 0.091 0.099 0.28 36 -0.32 1 37
IFNG -0.24 0.21 -10000 0 -0.6 72 72
apoptosis -0.007 0.16 0.48 11 -0.51 11 22
CREB1 0.002 0.089 -10000 0 -0.31 24 24
histone acetylation -0.032 0.12 0.35 10 -0.34 16 26
BGLAP -0.063 0.11 -10000 0 -1 1 1
GR/PKAc 0.1 0.094 0.29 17 -0.22 3 20
NF kappa B1 p50/RelA -0.072 0.13 -10000 0 -0.32 28 28
SMARCD1 0.028 0.009 -10000 0 -10000 0 0
MDM2 0.064 0.074 0.2 55 -0.2 2 57
GATA3 0.019 0.061 -10000 0 -0.35 10 10
AKT1 0.023 0.005 -10000 0 -10000 0 0
CSF2 -0.095 0.14 -10000 0 -0.51 10 10
GSK3B 0.027 0.009 -10000 0 -10000 0 0
NR1I3 0 0.16 0.46 12 -0.57 6 18
CSN2 0.1 0.14 0.36 39 -0.28 2 41
BRG1/BAF155/BAF170/BAF60A 0.068 0.033 -10000 0 -0.25 2 2
NFATC1 0.021 0.037 -10000 0 -0.38 2 2
POU2F1 0.024 0.031 -10000 0 -0.35 1 1
CDKN1A 0.007 0.081 -10000 0 -1.2 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.007 -10000 0 -10000 0 0
SFN 0.015 0.067 -10000 0 -0.37 12 12
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.098 0.1 0.29 21 -0.21 5 26
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.014 0.18 0.44 11 -0.71 14 25
JUN -0.18 0.13 -10000 0 -0.43 43 43
IL4 -0.072 0.11 -10000 0 -0.47 9 9
CDK5R1 0.024 0.038 -10000 0 -0.35 4 4
PRKACA 0.027 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.16 0.16 0.19 6 -0.36 113 119
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.092 0.3 19 -0.24 1 20
cortisol/GR alpha (monomer) 0.21 0.23 0.6 68 -0.36 1 69
NCOA2 0.024 0.022 -10000 0 -0.38 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.082 0.095 -10000 0 -0.42 22 22
AP-1/NFAT1-c-4 -0.28 0.19 -10000 0 -0.56 87 87
AFP -0.15 0.12 -10000 0 -0.55 5 5
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.11 0.12 0.39 19 -10000 0 19
TP53 0.037 0.029 -10000 0 -0.5 1 1
PPP5C 0.027 0.006 -10000 0 -10000 0 0
KRT17 -0.32 0.23 -10000 0 -0.64 83 83
KRT14 -0.16 0.3 -10000 0 -0.97 38 38
TBP 0.031 0.018 -10000 0 -0.29 1 1
CREBBP 0.059 0.078 0.31 26 -0.26 2 28
HDAC1 0.026 0.009 -10000 0 -10000 0 0
HDAC2 0.033 0.014 -10000 0 -10000 0 0
AP-1 -0.28 0.2 -10000 0 -0.56 87 87
MAPK14 0.027 0.01 -10000 0 -10000 0 0
MAPK10 -0.023 0.13 -10000 0 -0.38 50 50
MAPK11 0.026 0.01 -10000 0 -10000 0 0
KRT5 -0.25 0.22 -10000 0 -0.61 77 77
interleukin-1 receptor activity 0.006 0.013 -10000 0 -10000 0 0
NCOA1 0.03 0.003 -10000 0 -10000 0 0
STAT1 0.023 0.059 -10000 0 -0.35 10 10
CGA -0.13 0.25 -10000 0 -0.9 31 31
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.1 0.14 0.37 49 -0.3 1 50
MAPK3 0.027 0.01 -10000 0 -10000 0 0
MAPK1 0.027 0.01 -10000 0 -10000 0 0
ICAM1 -0.13 0.16 -10000 0 -0.52 25 25
NFKB1 -0.046 0.077 -10000 0 -0.23 13 13
MAPK8 -0.14 0.12 -10000 0 -0.37 46 46
MAPK9 0.027 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.008 0.16 0.49 11 -0.54 11 22
BAX 0.01 0.063 -10000 0 -10000 0 0
POMC -0.15 0.32 -10000 0 -1.3 25 25
EP300 0.061 0.078 0.31 27 -0.26 2 29
cortisol/GR alpha (dimer)/p53 0.19 0.2 0.53 61 -10000 0 61
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.065 0.22 18 -0.18 2 20
SGK1 0.063 0.14 -10000 0 -1.2 2 2
IL13 -0.16 0.15 -10000 0 -0.55 22 22
IL6 -0.18 0.27 -10000 0 -0.72 63 63
PRKACG 0.018 0.042 -10000 0 -0.35 5 5
IL5 -0.14 0.13 -10000 0 -0.58 7 7
IL2 -0.21 0.18 -10000 0 -0.59 34 34
CDK5 0.027 0.007 -10000 0 -10000 0 0
PRKACB 0.026 0.029 -10000 0 -0.38 2 2
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
IL8 -0.22 0.21 -10000 0 -0.5 97 97
CDK5R1/CDK5 0.037 0.031 -10000 0 -0.25 4 4
NF kappa B1 p50/RelA/PKAc -0.039 0.11 -10000 0 -0.28 10 10
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.19 0.5 60 -10000 0 60
SMARCA4 0.027 0.01 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.12 0.34 39 -0.32 1 40
NF kappa B1 p50/RelA/Cbp 0.001 0.13 0.37 9 -0.38 4 13
JUN (dimer) -0.18 0.13 -10000 0 -0.43 44 44
YWHAH 0.027 0.005 -10000 0 -10000 0 0
VIPR1 -0.098 0.16 -10000 0 -0.57 30 30
NR3C1 0.12 0.14 0.38 59 -0.37 2 61
NR4A1 -0.01 0.14 -10000 0 -0.46 34 34
TIF2/SUV420H1 0.035 0.021 -10000 0 -0.27 1 1
MAPKKK cascade -0.007 0.16 0.48 11 -0.51 11 22
cortisol/GR alpha (dimer)/Src-1 0.2 0.2 0.52 67 -10000 0 67
PBX1 0.017 0.061 -10000 0 -0.38 8 8
POU1F1 0.019 0.031 -10000 0 -0.35 1 1
SELE -0.16 0.2 -10000 0 -0.5 68 68
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.12 0.34 39 -0.32 1 40
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.19 0.5 60 -10000 0 60
mol:cortisol 0.11 0.13 0.34 67 -10000 0 67
MMP1 -0.2 0.22 -10000 0 -0.48 96 96
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.014 0.13 0.28 13 -0.4 20 33
FYN -0.008 0.14 0.26 15 -0.42 27 42
LAT/GRAP2/SLP76 0.006 0.13 0.25 7 -0.42 23 30
IKBKB 0.025 0.009 -10000 0 -10000 0 0
AKT1 -0.01 0.11 0.24 10 -0.35 26 36
B2M 0.027 0.008 -10000 0 -10000 0 0
IKBKG -0.011 0.045 0.1 14 -0.14 11 25
MAP3K8 0.026 0.02 -10000 0 -0.35 1 1
mol:Ca2+ -0.021 0.021 0.086 1 -0.082 8 9
integrin-mediated signaling pathway 0.035 0.016 -10000 0 -0.23 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.018 0.15 0.26 9 -0.48 27 36
TRPV6 -0.12 0.23 1.1 5 -0.54 4 9
CD28 0.011 0.079 -10000 0 -0.36 18 18
SHC1 -0.012 0.15 0.28 13 -0.47 24 37
receptor internalization -0.013 0.15 0.19 1 -0.51 27 28
PRF1 -0.009 0.18 -10000 0 -0.78 16 16
KRAS 0.025 0.009 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
COT/AKT1 0.003 0.096 0.23 10 -0.29 22 32
LAT -0.014 0.14 0.25 8 -0.44 27 35
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.022 0.047 -10000 0 -0.39 5 5
CD3E 0.023 0.04 -10000 0 -0.38 4 4
CD3G 0.019 0.058 -10000 0 -0.39 8 8
RASGRP2 -0.005 0.05 0.072 3 -0.15 38 41
RASGRP1 0.002 0.12 0.26 12 -0.36 24 36
HLA-A 0 0.003 -10000 0 -10000 0 0
RASSF5 0.026 0.021 -10000 0 -0.38 1 1
RAP1A/GTP/RAPL 0.035 0.016 -10000 0 -0.23 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.054 0.14 27 -0.13 9 36
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.032 0.061 -10000 0 -0.21 19 19
PRKCA 0.012 0.074 0.16 24 -0.23 12 36
GRAP2 0.016 0.067 -10000 0 -0.38 11 11
mol:IP3 0.033 0.12 0.19 98 -0.35 15 113
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.004 0.12 -10000 0 -0.56 15 15
ORAI1 0.059 0.16 0.48 5 -0.97 5 10
CSK -0.013 0.14 0.22 11 -0.44 28 39
B7 family/CD28 -0.017 0.16 0.25 5 -0.39 32 37
CHUK 0.027 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.021 0.16 0.19 6 -0.48 30 36
PTPN6 -0.016 0.14 0.26 8 -0.45 25 33
VAV1 -0.019 0.14 0.22 7 -0.45 28 35
Monovalent TCR/CD3 0.009 0.077 -10000 0 -0.36 12 12
CBL 0.027 0.006 -10000 0 -10000 0 0
LCK -0.012 0.14 0.26 13 -0.42 29 42
PAG1 -0.005 0.15 0.21 37 -0.43 28 65
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.02 0.15 0.2 7 -0.49 27 34
CD80 -0.071 0.17 -10000 0 -0.35 107 107
CD86 0.02 0.053 -10000 0 -0.36 8 8
PDK1/CARD11/BCL10/MALT1 -0.029 0.078 -10000 0 -0.25 21 21
HRAS 0.026 0.007 -10000 0 -10000 0 0
GO:0035030 -0.037 0.12 0.2 7 -0.34 35 42
CD8A 0.016 0.07 -10000 0 -0.39 12 12
CD8B -0.001 0.11 -10000 0 -0.38 30 30
PTPRC 0.01 0.08 -10000 0 -0.36 19 19
PDK1/PKC theta -0.009 0.13 0.3 11 -0.43 22 33
CSK/PAG1 -0.005 0.15 0.21 39 -0.44 24 63
SOS1 0.028 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.02 0.009 -10000 0 -10000 0 0
GRAP2/SLP76 0.005 0.15 0.25 5 -0.46 27 32
STIM1 0.036 0.12 1.3 3 -10000 0 3
RAS family/GTP 0.022 0.069 0.18 21 -0.18 13 34
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.015 0.16 0.19 1 -0.54 27 28
mol:DAG -0.006 0.084 -10000 0 -0.29 20 20
RAP1A/GDP 0.013 0.026 0.078 17 -0.064 3 20
PLCG1 0.023 0.011 -10000 0 -10000 0 0
CD247 0.021 0.05 -10000 0 -0.39 6 6
cytotoxic T cell degranulation -0.007 0.18 -10000 0 -0.75 16 16
RAP1A/GTP -0.002 0.019 -10000 0 -0.06 36 36
mol:PI-3-4-5-P3 -0.013 0.13 0.25 10 -0.4 27 37
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.035 0.14 0.21 61 -0.43 17 78
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 0.008 0.085 -10000 0 -0.36 21 21
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.005 0.13 0.25 3 -0.41 22 25
MALT1 0.025 0.009 -10000 0 -10000 0 0
TRAF6 0.027 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.013 0.1 -10000 0 -0.32 34 34
CARD11 -0.069 0.16 -10000 0 -0.35 103 103
PRKCB 0.004 0.083 0.16 21 -0.28 15 36
PRKCE 0.011 0.076 0.16 25 -0.24 13 38
PRKCQ -0.012 0.15 0.3 9 -0.48 24 33
LCP2 0.027 0.006 -10000 0 -10000 0 0
BCL10 0.028 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.007 0.1 0.21 13 -0.3 25 38
IKK complex 0.017 0.056 0.13 44 -0.11 10 54
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 -0.001 0.073 0.16 11 -0.23 19 30
PDPK1 -0.009 0.11 0.25 10 -0.34 22 32
TCR/CD3/MHC I/CD8/Fyn -0.02 0.18 -10000 0 -0.54 34 34
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.027 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.027 0.086 -10000 0 -0.25 29 29
NT3 (dimer)/TRKC -0.051 0.15 -10000 0 -0.3 107 107
NT3 (dimer)/TRKB -0.09 0.19 -10000 0 -0.3 165 165
SHC/Grb2/SOS1/GAB1/PI3K 0.026 0.013 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
BDNF 0.017 0.062 -10000 0 -0.36 11 11
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.006 -10000 0 -10000 0 0
NTRK1 0.009 0.084 -10000 0 -0.38 18 18
NTRK2 -0.042 0.15 -10000 0 -0.38 70 70
NTRK3 -0.065 0.17 -10000 0 -0.38 91 91
NT-4/5 (dimer)/TRKB -0.087 0.17 -10000 0 -0.28 174 174
neuron apoptosis 0.09 0.18 0.41 68 -10000 0 68
SHC 2-3/Grb2 -0.098 0.2 -10000 0 -0.45 68 68
SHC1 0.027 0.005 -10000 0 -10000 0 0
SHC2 -0.1 0.2 -10000 0 -0.45 80 80
SHC3 -0.11 0.19 -10000 0 -0.46 74 74
STAT3 (dimer) 0.03 0.032 -10000 0 -0.28 4 4
NT3 (dimer)/TRKA -0.059 0.16 -10000 0 -0.26 143 143
RIN/GDP -0.006 0.092 0.22 8 -0.26 10 18
GIPC1 0.027 0.005 -10000 0 -10000 0 0
KRAS 0.025 0.009 -10000 0 -10000 0 0
DNAJA3 -0.081 0.14 -10000 0 -0.3 105 105
RIN/GTP 0.012 0.019 -10000 0 -0.24 2 2
CCND1 0.016 0.018 -10000 0 -0.32 1 1
MAGED1 0.025 0.035 -10000 0 -0.38 3 3
PTPN11 0.028 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0.092 -10000 0 -0.35 26 26
SHC/GRB2/SOS1 0.053 0.015 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.016 0.097 -10000 0 -0.24 47 47
TRKA/NEDD4-2 0.021 0.066 -10000 0 -0.27 19 19
ELMO1 0.026 0.02 -10000 0 -0.35 1 1
RhoG/GTP/ELMO1/DOCK1 0.034 0.017 -10000 0 -0.2 1 1
NGF 0.003 0.096 -10000 0 -0.38 24 24
HRAS 0.026 0.007 -10000 0 -10000 0 0
DOCK1 0.027 0.006 -10000 0 -10000 0 0
GAB2 0.027 0.006 -10000 0 -10000 0 0
RIT2 0.016 0.027 -10000 0 -0.35 2 2
RIT1 0.027 0.006 -10000 0 -10000 0 0
FRS2 0.026 0.007 -10000 0 -10000 0 0
DNM1 0.016 0.064 -10000 0 -0.35 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.066 0.15 -10000 0 -0.3 104 104
mol:GDP -0.016 0.13 0.27 11 -0.4 12 23
NGF (dimer) 0.003 0.096 -10000 0 -0.38 24 24
RhoG/GDP 0.019 0.014 -10000 0 -0.24 1 1
RIT1/GDP -0.004 0.092 0.21 7 -0.27 9 16
TIAM1 0.017 0.062 -10000 0 -0.37 10 10
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.002 0.11 -10000 0 -0.23 78 78
KIDINS220/CRKL/C3G 0.039 0.011 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2 0.05 0.019 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.065 0.023 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.007 0.11 -10000 0 -0.38 33 33
RAP1/GDP -0.008 0.074 0.13 4 -0.22 9 13
KIDINS220/CRKL 0.027 0.006 -10000 0 -10000 0 0
BDNF (dimer) 0.017 0.062 -10000 0 -0.36 11 11
ubiquitin-dependent protein catabolic process 0.019 0.087 -10000 0 -0.24 40 40
Schwann cell development -0.025 0.028 -10000 0 -10000 0 0
EHD4 0.027 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.061 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.027 0.033 -10000 0 -10000 0 0
RAP1B 0.027 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.046 0.14 -10000 0 -0.36 45 45
ABL1 0.027 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
Rap1/GTP 0.008 0.078 -10000 0 -0.44 4 4
STAT3 0.03 0.032 -10000 0 -0.28 4 4
axon guidance -0.052 0.13 -10000 0 -0.35 45 45
MAPK3 -0.011 0.082 0.18 11 -0.22 43 54
MAPK1 -0.009 0.082 0.18 12 -0.23 41 53
CDC42/GDP 0 0.095 0.22 11 -0.26 11 22
NTF3 -0.007 0.11 -10000 0 -0.38 33 33
NTF4 0 0.092 -10000 0 -0.35 26 26
NGF (dimer)/TRKA/FAIM 0.023 0.088 -10000 0 -0.24 38 38
PI3K 0.036 0.014 -10000 0 -10000 0 0
FRS3 0.026 0.007 -10000 0 -10000 0 0
FAIM 0.026 0.021 -10000 0 -0.38 1 1
GAB1 0.027 0.006 -10000 0 -10000 0 0
RASGRF1 -0.09 0.15 -10000 0 -0.32 105 105
SOS1 0.028 0.003 -10000 0 -10000 0 0
MCF2L -0.048 0.12 -10000 0 -0.25 94 94
RGS19 0.022 0.022 -10000 0 -0.35 1 1
CDC42 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.012 0.099 0.27 7 -0.45 5 12
Rac1/GDP -0.003 0.093 0.25 8 -0.26 11 19
NGF (dimer)/TRKA/GRIT 0.009 0.081 -10000 0 -0.24 39 39
neuron projection morphogenesis -0.069 0.16 -10000 0 -0.82 4 4
NGF (dimer)/TRKA/NEDD4-2 0.019 0.087 -10000 0 -0.24 40 40
MAP2K1 0 0.052 0.2 24 -10000 0 24
NGFR -0.1 0.19 -10000 0 -0.38 130 130
NGF (dimer)/TRKA/GIPC/GAIP 0.003 0.064 -10000 0 -0.28 6 6
RAS family/GTP/PI3K 0.02 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.071 0.031 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
PRKCI 0.024 0.027 -10000 0 -0.35 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.066 0.2 -10000 0 -0.59 48 48
RASA1 0.025 0.008 -10000 0 -10000 0 0
TRKA/c-Abl 0.025 0.064 -10000 0 -0.27 18 18
SQSTM1 0.027 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.013 0.11 -10000 0 -0.21 62 62
NGF (dimer)/TRKA/p62/Atypical PKCs 0.04 0.085 -10000 0 -0.38 2 2
MATK 0.016 0.066 -10000 0 -0.38 11 11
NEDD4L 0.023 0.022 -10000 0 -0.38 1 1
RAS family/GDP -0.028 0.049 -10000 0 -0.22 3 3
NGF (dimer)/TRKA -0.085 0.15 -10000 0 -0.31 118 118
Rac1/GTP -0.065 0.1 -10000 0 -0.25 65 65
FRS2 family/SHP2/CRK family 0.067 0.034 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.064 0.11 -10000 0 -0.28 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.047 0.11 0.33 1 -0.28 3 4
alphaV/beta3 Integrin/Osteopontin/Src -0.094 0.14 -10000 0 -0.24 194 194
AP1 -0.057 0.12 -10000 0 -0.37 7 7
ILK -0.074 0.11 -10000 0 -0.31 3 3
bone resorption -0.052 0.1 -10000 0 -0.32 3 3
PTK2B 0.025 0.009 -10000 0 -10000 0 0
PYK2/p130Cas -0.042 0.12 -10000 0 -0.34 3 3
ITGAV 0.027 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.039 0.011 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.069 0.13 -10000 0 -0.21 186 186
MAP3K1 -0.075 0.1 0.19 3 -0.23 28 31
JUN 0.028 0.004 -10000 0 -10000 0 0
MAPK3 -0.076 0.1 0.23 5 -0.27 30 35
MAPK1 -0.075 0.1 0.19 4 -0.27 30 34
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.074 0.095 0.19 3 -0.3 3 6
ITGB3 0.024 0.043 -10000 0 -0.36 5 5
NFKBIA -0.068 0.096 0.19 3 -0.27 29 32
FOS 0.006 0.091 -10000 0 -0.38 21 21
CD44 0.026 0.007 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
PLAU -0.072 0.13 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.049 0.12 -10000 0 -0.32 2 2
BCAR1 0.027 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.037 0.035 -10000 0 -0.24 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.076 0.11 0.19 5 -0.31 5 10
VAV3 -0.086 0.1 0.19 2 -0.33 14 16
MAP3K14 -0.075 0.11 0.19 5 -0.25 29 34
ROCK2 0.028 0.004 -10000 0 -10000 0 0
SPP1 -0.15 0.19 -10000 0 -0.35 195 195
RAC1 0.026 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.068 0.1 -10000 0 -0.31 13 13
MMP2 -0.061 0.096 0.31 1 -0.47 3 4
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) 0.032 0.082 -10000 0 -0.37 15 15
HDAC1 0.025 0.006 -10000 0 -10000 0 0
AES 0.026 0.007 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.039 -10000 0 -0.37 4 4
LRP6/FZD1 0.035 0.016 -10000 0 -10000 0 0
TLE1 0.026 0.021 -10000 0 -0.39 1 1
AP1 -0.016 0.087 -10000 0 -0.24 44 44
NCSTN 0.027 0.005 -10000 0 -10000 0 0
ADAM10 0.027 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.006 0.17 -10000 0 -0.62 26 26
NICD/RBPSUH 0.03 0.083 -10000 0 -0.38 15 15
WIF1 -0.063 0.16 -10000 0 -0.38 86 86
NOTCH1 0.014 0.075 -10000 0 -0.39 13 13
PSENEN 0.027 0.007 -10000 0 -10000 0 0
KREMEN2 -0.049 0.15 -10000 0 -0.35 82 82
DKK1 -0.15 0.19 -10000 0 -0.36 186 186
beta catenin/beta TrCP1 0.037 0.077 0.25 4 -0.46 3 7
APH1B 0.027 0.005 -10000 0 -10000 0 0
APH1A 0.027 0.006 -10000 0 -10000 0 0
AXIN1 -0.011 0.092 -10000 0 -0.37 20 20
CtBP/CBP/TCF1/TLE1/AES 0.011 0.04 -10000 0 -10000 0 0
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS 0.006 0.091 -10000 0 -0.38 21 21
JUN 0.028 0.004 -10000 0 -10000 0 0
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
CTNNB1 0.024 0.079 0.25 4 -0.39 5 9
MAPK3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.066 0.14 -10000 0 -0.22 171 171
HNF1A 0.017 0.061 -10000 0 -0.37 10 10
CTBP1 0.026 0.007 -10000 0 -10000 0 0
MYC 0.012 0.1 -10000 0 -1.1 3 3
NKD1 -0.02 0.13 -10000 0 -0.37 48 48
FZD1 0.025 0.009 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.029 0.084 -10000 0 -0.38 15 15
apoptosis -0.015 0.087 -10000 0 -0.24 44 44
Delta 1/NOTCHprecursor 0.03 0.082 -10000 0 -0.37 15 15
DLL1 0.026 0.02 -10000 0 -0.35 1 1
PPARD 0.012 0.12 -10000 0 -0.85 7 7
Gamma Secretase 0.072 0.03 -10000 0 -10000 0 0
APC -0.024 0.12 -10000 0 -0.39 31 31
DVL1 0.005 0.046 -10000 0 -0.43 2 2
CSNK2A1 0.025 0.009 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.15 -10000 0 -0.23 226 226
LRP6 0.026 0.007 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.012 0.005 -10000 0 -10000 0 0
CCND1 0.014 0.097 -10000 0 -0.88 4 4
WNT1 0.006 0.09 -10000 0 -0.38 21 21
Axin1/APC/beta catenin 0.015 0.12 0.32 4 -0.41 14 18
DKK2 -0.075 0.17 -10000 0 -0.35 111 111
NOTCH1 precursor/DVL1 0.015 0.11 -10000 0 -0.57 9 9
GSK3B 0.027 0.005 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.031 0.084 -10000 0 -0.38 15 15
PPP2R5D 0.033 0.06 0.23 25 -0.29 1 26
MAPK1 0.027 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.002 0.11 -10000 0 -0.22 72 72
RBPJ 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.038 0.064 -10000 0 -0.21 23 23
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.098 0.3 1 -0.36 5 6
AP1 -0.026 0.093 -10000 0 -0.33 8 8
mol:PIP3 -0.022 0.076 -10000 0 -0.35 6 6
AKT1 0.021 0.073 0.27 8 -0.31 2 10
PTK2B -0.016 0.083 0.2 1 -0.28 22 23
RHOA 0.005 0.063 0.21 7 -0.34 8 15
PIK3CB 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.073 0.21 5 -0.34 4 9
MAGI3 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.023 0.094 -10000 0 -0.23 62 62
HRAS/GDP 0.02 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.047 0.11 0.21 12 -0.33 24 36
NF kappa B1 p50/RelA -0.032 0.092 -10000 0 -0.36 7 7
endothelial cell migration 0.004 0.063 -10000 0 -0.24 23 23
ADCY4 -0.039 0.13 -10000 0 -0.39 35 35
ADCY5 -0.08 0.18 -10000 0 -0.44 71 71
ADCY6 -0.038 0.12 -10000 0 -0.39 34 34
ADCY7 -0.039 0.13 -10000 0 -0.39 35 35
ADCY1 -0.042 0.12 -10000 0 -0.39 34 34
ADCY2 -0.061 0.16 -10000 0 -0.42 53 53
ADCY3 -0.039 0.12 -10000 0 -0.39 35 35
ADCY8 -0.038 0.12 -10000 0 -0.38 33 33
ADCY9 -0.042 0.13 -10000 0 -0.39 39 39
GSK3B -0.013 0.085 0.19 11 -0.29 17 28
arachidonic acid secretion -0.049 0.13 -10000 0 -0.38 41 41
GNG2 0.026 0.019 -10000 0 -0.35 1 1
TRIP6 0.018 0.01 -10000 0 -10000 0 0
GNAO1 -0.039 0.12 -10000 0 -0.25 85 85
HRAS 0.026 0.007 -10000 0 -10000 0 0
NFKBIA -0.025 0.095 0.3 1 -0.36 7 8
GAB1 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.024 0.23 -10000 0 -0.78 35 35
JUN 0.027 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.036 0.012 -10000 0 -10000 0 0
TIAM1 -0.046 0.27 -10000 0 -0.92 35 35
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
mol:IP3 -0.016 0.065 0.21 5 -0.27 2 7
PLCB3 0.017 0.02 0.19 5 -10000 0 5
FOS 0.006 0.091 -10000 0 -0.38 21 21
positive regulation of mitosis -0.049 0.13 -10000 0 -0.38 41 41
LPA/LPA1-2-3 0.009 0.1 -10000 0 -0.21 65 65
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.027 0.006 -10000 0 -10000 0 0
stress fiber formation -0.009 0.087 0.23 2 -0.32 16 18
GNAZ -0.011 0.081 -10000 0 -0.23 48 48
EGFR/PI3K-beta/Gab1 -0.011 0.084 -10000 0 -0.36 6 6
positive regulation of dendritic cell cytokine production 0.008 0.098 -10000 0 -0.21 65 65
LPA/LPA2/MAGI-3 0.037 0.012 -10000 0 -10000 0 0
ARHGEF1 0.02 0.073 0.2 30 -0.36 1 31
GNAI2 0.004 0.058 -10000 0 -0.23 23 23
GNAI3 0.005 0.057 -10000 0 -0.23 22 22
GNAI1 0.001 0.07 -10000 0 -0.26 25 25
LPA/LPA3 -0.014 0.092 -10000 0 -0.26 50 50
LPA/LPA2 0.021 0.007 -10000 0 -10000 0 0
LPA/LPA1 0.008 0.07 -10000 0 -0.27 24 24
HB-EGF/EGFR -0.031 0.096 -10000 0 -0.21 90 90
HBEGF -0.047 0.11 -10000 0 -0.25 91 91
mol:DAG -0.016 0.065 0.21 5 -0.27 2 7
cAMP biosynthetic process -0.059 0.15 0.34 3 -0.41 40 43
NFKB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.024 0.01 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
LYN -0.019 0.1 0.3 4 -0.35 9 13
GNAQ -0.009 0.07 -10000 0 -0.21 41 41
LPAR2 0.027 0.005 -10000 0 -10000 0 0
LPAR3 -0.026 0.13 -10000 0 -0.38 50 50
LPAR1 0.006 0.096 -10000 0 -0.39 23 23
IL8 -0.11 0.14 -10000 0 -0.36 35 35
PTK2 -0.019 0.076 0.18 2 -0.36 3 5
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
CASP3 -0.023 0.094 -10000 0 -0.23 62 62
EGFR 0.017 0.057 -10000 0 -0.38 8 8
PLCG1 -0.015 0.072 0.16 1 -0.22 43 44
PLD2 -0.02 0.083 0.18 5 -0.36 4 9
G12/G13 0.037 0.063 -10000 0 -0.21 21 21
PI3K-beta 0.006 0.056 -10000 0 -0.33 3 3
cell migration -0.003 0.081 -10000 0 -0.24 30 30
SLC9A3R2 0.027 0.006 -10000 0 -10000 0 0
PXN -0.009 0.088 0.23 2 -0.32 16 18
HRAS/GTP -0.049 0.14 -10000 0 -0.39 39 39
RAC1 0.026 0.008 -10000 0 -10000 0 0
MMP9 -0.063 0.16 -10000 0 -0.35 92 92
PRKCE 0.027 0.004 -10000 0 -10000 0 0
PRKCD -0.02 0.074 0.2 5 -0.35 5 10
Gi(beta/gamma) -0.035 0.12 -10000 0 -0.36 36 36
mol:LPA 0.002 0.007 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin 0.006 0.093 -10000 0 -0.32 8 8
MAPKKK cascade -0.049 0.13 -10000 0 -0.38 41 41
contractile ring contraction involved in cytokinesis 0.005 0.069 0.21 7 -0.33 9 16
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.013 0.075 -10000 0 -0.21 47 47
GNA15 -0.011 0.074 -10000 0 -0.22 45 45
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.048 0.12 0.21 12 -0.34 24 36
GNA11 -0.01 0.071 -10000 0 -0.22 41 41
Rac1/GTP -0.026 0.24 -10000 0 -0.82 35 35
MMP2 0.004 0.063 -10000 0 -0.24 23 23
Ephrin A reverse 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
MAPKKK cascade 0.015 0.066 -10000 0 -0.22 29 29
EFNA5 0.008 0.084 -10000 0 -0.38 18 18
FYN -0.003 0.056 0.18 3 -0.2 28 31
neuron projection morphogenesis 0.015 0.066 -10000 0 -0.22 29 29
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.015 0.066 -10000 0 -0.22 29 29
EPHA5 0.016 0.064 -10000 0 -0.37 11 11
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.029 0.12 0.31 33 -10000 0 33
GNAI2 0.027 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.037 -10000 0 -0.2 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.055 0.16 -10000 0 -0.38 82 82
RhoA/GTP -0.03 0.12 -10000 0 -0.32 31 31
negative regulation of cAMP metabolic process -0.035 0.12 -10000 0 -0.25 77 77
GNAZ 0.001 0.1 -10000 0 -0.38 26 26
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.008 -10000 0 -10000 0 0
S1PR5 0.017 0.062 -10000 0 -0.35 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.035 0.12 -10000 0 -0.25 77 77
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.054 -10000 0 -0.38 7 7
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.01 0.04 -10000 0 -0.24 10 10
Metarhodopsin II/Arrestin 0.024 0.034 -10000 0 -0.24 6 6
PDE6G/GNAT1/GTP 0.02 0.054 -10000 0 -0.21 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.013 0.058 -10000 0 -0.35 10 10
GRK1 0.015 0.041 -10000 0 -0.35 5 5
CNG Channel -0.001 0.1 -10000 0 -0.34 14 14
mol:Na + 0.001 0.095 -10000 0 -0.34 8 8
mol:ADP 0.015 0.041 -10000 0 -0.35 5 5
RGS9-1/Gbeta5/R9AP -0.023 0.13 -10000 0 -0.25 101 101
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.009 0.1 -10000 0 -0.35 8 8
CNGB1 0.007 0.082 -10000 0 -0.36 20 20
RDH5 0.022 0.045 -10000 0 -0.38 5 5
SAG 0.02 0.019 -10000 0 -0.35 1 1
mol:Ca2+ -0.024 0.12 0.35 26 -0.33 8 34
Na + (4 Units) -0.003 0.089 -10000 0 -0.32 8 8
RGS9 -0.058 0.17 -10000 0 -0.38 85 85
GNB1/GNGT1 0.009 0.078 -10000 0 -0.24 35 35
GNAT1/GDP -0.017 0.12 -10000 0 -0.22 107 107
GUCY2D 0.013 0.064 -10000 0 -0.35 12 12
GNGT1 -0.011 0.1 -10000 0 -0.35 35 35
GUCY2F 0.02 0.004 -10000 0 -10000 0 0
GNB5 0.027 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.003 0.076 -10000 0 -0.22 41 41
mol:11-cis-retinal 0.022 0.045 -10000 0 -0.38 5 5
mol:cGMP 0.022 0.072 -10000 0 -0.34 2 2
GNB1 0.026 0.007 -10000 0 -10000 0 0
Rhodopsin 0.028 0.046 -10000 0 -0.26 10 10
SLC24A1 0.028 0.004 -10000 0 -10000 0 0
CNGA1 0.002 0.098 -10000 0 -0.38 25 25
Metarhodopsin II 0.019 0.039 -10000 0 -0.22 9 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.032 0.078 -10000 0 -0.21 26 26
RGS9BP -0.011 0.12 -10000 0 -0.38 37 37
Metarhodopsin II/Transducin -0.004 0.053 -10000 0 -0.24 13 13
GCAP Family/Ca ++ 0.027 0.063 -10000 0 -0.19 30 30
PDE6A/B 0.015 0.08 -10000 0 -0.26 30 30
mol:Pi -0.024 0.13 -10000 0 -0.25 101 101
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.016 0.074 -10000 0 -0.2 41 41
PDE6B 0.013 0.072 -10000 0 -0.37 14 14
PDE6A 0.009 0.082 -10000 0 -0.36 19 19
PDE6G 0.016 0.065 -10000 0 -0.36 12 12
RHO 0.016 0.045 -10000 0 -0.35 6 6
PDE6 -0.019 0.14 -10000 0 -0.36 25 25
GUCA1A 0.001 0.092 -10000 0 -0.35 26 26
GC2/GCAP Family 0.037 0.068 -10000 0 -0.2 20 20
GUCA1C 0.018 0.027 -10000 0 -0.37 2 2
GUCA1B 0.024 0.028 -10000 0 -0.37 2 2
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.046 0.061 -10000 0 -0.19 22 22
ER alpha/Gai/GDP/Gbeta gamma -0.072 0.2 -10000 0 -0.52 47 47
AKT1 -0.02 0.2 -10000 0 -0.78 25 25
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.018 0.2 -10000 0 -0.79 25 25
mol:Ca2+ 0.012 0.076 0.18 28 -0.32 9 37
IGF1R 0.025 0.028 -10000 0 -0.37 2 2
E2/ER alpha (dimer)/Striatin 0.026 0.049 -10000 0 -0.22 15 15
SHC1 0.027 0.005 -10000 0 -10000 0 0
apoptosis 0.018 0.19 0.74 25 -10000 0 25
RhoA/GTP 0.016 0.036 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.02 0.17 0.21 1 -0.44 36 37
regulation of stress fiber formation -0.005 0.063 -10000 0 -0.19 8 8
E2/ERA-ERB (dimer) 0.022 0.057 -10000 0 -0.22 22 22
KRAS 0.025 0.009 -10000 0 -10000 0 0
G13/GTP 0.025 0.045 -10000 0 -0.2 15 15
pseudopodium formation 0.005 0.063 0.19 8 -10000 0 8
E2/ER alpha (dimer)/PELP1 0.025 0.049 -10000 0 -0.22 15 15
GRB2 0.027 0.005 -10000 0 -10000 0 0
GNG2 0.027 0.019 -10000 0 -0.35 1 1
GNAO1 -0.055 0.16 -10000 0 -0.38 82 82
HRAS 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.039 0.18 0.21 2 -0.54 31 33
E2/ER beta (dimer) 0.015 0.037 -10000 0 -0.24 8 8
mol:GDP 0.004 0.065 -10000 0 -0.32 12 12
mol:NADP -0.039 0.18 0.21 2 -0.54 31 33
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
mol:IP3 0 0.063 0.16 3 -0.32 10 13
IGF-1R heterotetramer 0.025 0.028 -10000 0 -0.37 2 2
PLCB1 0.007 0.057 -10000 0 -0.34 8 8
PLCB2 0.007 0.059 -10000 0 -0.34 8 8
IGF1 -0.022 0.13 -10000 0 -0.37 51 51
mol:L-citrulline -0.039 0.18 0.21 2 -0.54 31 33
RHOA 0.027 0.006 -10000 0 -10000 0 0
Gai/GDP -0.13 0.3 -10000 0 -0.63 104 104
JNK cascade 0.015 0.036 -10000 0 -0.24 8 8
BCAR1 0.027 0.006 -10000 0 -10000 0 0
ESR2 0.02 0.053 -10000 0 -0.35 8 8
GNAQ 0.027 0.006 -10000 0 -10000 0 0
ESR1 0.012 0.077 -10000 0 -0.38 15 15
Gq family/GDP/Gbeta gamma -0.018 0.18 -10000 0 -0.67 25 25
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.018 0.1 -10000 0 -0.76 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.018 0.17 0.21 1 -0.44 35 36
GNAZ 0.001 0.1 -10000 0 -0.38 26 26
E2/ER alpha (dimer) 0.009 0.054 -10000 0 -0.27 15 15
STRN 0.028 0.004 -10000 0 -10000 0 0
GNAL -0.001 0.1 -10000 0 -0.38 27 27
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.009 0.03 -10000 0 -0.2 8 8
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.054 -10000 0 -0.38 7 7
HBEGF -0.04 0.21 0.32 35 -0.46 45 80
cAMP biosynthetic process 0.005 0.072 -10000 0 -0.2 43 43
SRC -0.048 0.19 0.21 28 -0.5 42 70
PI3K 0.036 0.014 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.03 0.07 -10000 0 -0.28 13 13
SOS1 0.028 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.052 0.13 -10000 0 -0.38 39 39
Gs family/GTP 0.011 0.075 -10000 0 -0.2 43 43
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.021 -10000 0 -10000 0 0
vasodilation -0.037 0.16 0.21 2 -0.51 31 33
mol:DAG 0 0.063 0.16 3 -0.32 10 13
Gs family/GDP/Gbeta gamma 0 0.079 -10000 0 -0.33 13 13
MSN 0.005 0.065 0.2 8 -10000 0 8
Gq family/GTP 0.015 0.06 -10000 0 -0.36 8 8
mol:PI-3-4-5-P3 -0.016 0.19 -10000 0 -0.75 25 25
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.037 0.16 0.51 31 -0.21 2 33
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.069 -10000 0 -0.31 12 12
NOS3 -0.043 0.19 0.22 1 -0.58 31 32
GNA11 0.026 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.17 0.28 5 -0.58 25 30
E2/ER alpha (dimer)/PELP1/Src -0.021 0.18 0.25 8 -0.46 36 44
ruffle organization 0.005 0.063 0.19 8 -10000 0 8
ROCK2 0.01 0.072 0.21 10 -10000 0 10
GNA14 0.02 0.053 -10000 0 -0.38 7 7
GNA15 0.022 0.042 -10000 0 -0.35 5 5
GNA13 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.059 0.21 0.32 38 -0.45 52 90
MMP2 -0.04 0.19 0.28 12 -0.49 38 50
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.055 0.16 -10000 0 -0.38 82 82
CDC42/GTP -0.031 0.12 -10000 0 -0.31 33 33
PLCG1 -0.032 0.1 -10000 0 -0.34 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.013 -10000 0 -10000 0 0
cell migration -0.031 0.12 -10000 0 -0.3 33 33
S1PR5 0.017 0.062 -10000 0 -0.35 11 11
S1PR4 0.023 0.038 -10000 0 -0.35 4 4
MAPK3 -0.038 0.11 -10000 0 -0.34 25 25
MAPK1 -0.036 0.11 -10000 0 -0.35 23 23
S1P/S1P5/Gi -0.035 0.12 -10000 0 -0.25 77 77
GNAI1 0.02 0.054 -10000 0 -0.38 7 7
CDC42/GDP 0.02 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.037 -10000 0 -0.2 9 9
RHOA 0.023 0.05 0.19 29 -10000 0 29
S1P/S1P4/Gi -0.035 0.12 -10000 0 -0.25 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.001 0.1 -10000 0 -0.38 26 26
S1P/S1P4/G12/G13 0.044 0.03 -10000 0 -0.19 4 4
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.026 0.007 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.03 0.022 -10000 0 -0.2 2 2
ARNO/beta Arrestin1-2 -0.03 0.16 -10000 0 -0.81 11 11
EGFR 0.017 0.057 -10000 0 -0.38 8 8
EPHA2 0.021 0.047 -10000 0 -0.36 6 6
USP6 0.022 0.039 -10000 0 -0.37 4 4
IQSEC1 0.028 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.001 0.093 -10000 0 -0.25 48 48
ARRB2 0.009 0.019 -10000 0 -10000 0 0
mol:GTP 0.014 0.041 0.14 16 -0.14 2 18
ARRB1 0.027 0.005 -10000 0 -10000 0 0
FBXO8 0.026 0.007 -10000 0 -10000 0 0
TSHR 0.013 0.075 -10000 0 -0.38 14 14
EGF -0.016 0.12 -10000 0 -0.36 44 44
somatostatin receptor activity 0 0 0.001 10 -0.001 27 37
ARAP2 0.027 0.005 -10000 0 -10000 0 0
mol:GDP -0.046 0.12 0.23 3 -0.27 54 57
mol:PI-3-4-5-P3 0 0 0.001 3 -0.001 8 11
ITGA2B 0.015 0.067 -10000 0 -0.36 13 13
ARF6 0.027 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.059 0.039 -10000 0 -0.19 6 6
ADAP1 0.024 0.028 -10000 0 -0.35 2 2
KIF13B 0.025 0.009 -10000 0 -10000 0 0
HGF/MET 0.014 0.082 -10000 0 -0.26 33 33
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.032 0.11 0.23 10 -0.27 29 39
EGFR/EGFR/EGF/EGF/ARFGEP100 0.017 0.086 -10000 0 -0.21 48 48
ADRB2 -0.079 0.18 -10000 0 -0.38 106 106
receptor agonist activity 0 0 0 8 0 28 36
actin filament binding 0 0 0.001 9 0 32 41
SRC 0.024 0.01 -10000 0 -10000 0 0
ITGB3 0.023 0.042 -10000 0 -0.36 5 5
GNAQ 0.027 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 15 -0.001 19 34
ARF6/GDP -0.017 0.14 0.22 5 -0.45 26 31
ARF6/GDP/GULP/ACAP1 -0.029 0.13 0.23 3 -0.32 35 38
alphaIIb/beta3 Integrin/paxillin/GIT1 0.057 0.056 -10000 0 -0.19 18 18
ACAP1 0.017 0.06 -10000 0 -0.36 10 10
ACAP2 0.026 0.007 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.033 -10000 0 -0.2 6 6
EFNA1 0.026 0.019 -10000 0 -0.35 1 1
HGF 0.014 0.07 -10000 0 -0.37 13 13
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 -0.007 0.16 -10000 0 -1 11 11
NCK1 0.027 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 8 0 23 31
endosomal lumen acidification 0 0 0.001 26 0 13 39
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.014 0.072 -10000 0 -0.38 13 13
GNAQ/ARNO 0.009 0.15 -10000 0 -0.92 11 11
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 3 0 4 7
MET 0.005 0.088 -10000 0 -0.36 23 23
GNA14 0.02 0.053 -10000 0 -0.38 7 7
GNA15 0.022 0.042 -10000 0 -0.35 5 5
GIT1 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 12 -0.001 25 37
GNA11 0.026 0.007 -10000 0 -10000 0 0
LHCGR 0.017 0.046 -10000 0 -0.35 6 6
AGTR1 -0.075 0.18 -10000 0 -0.38 102 102
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.033 -10000 0 -0.2 6 6
IPCEF1/ARNO -0.005 0.15 -10000 0 -0.86 11 11
alphaIIb/beta3 Integrin 0.028 0.06 -10000 0 -0.25 18 18
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.037 0.019 -10000 0 -0.25 1 1
alphaV beta3 Integrin 0.036 0.065 -10000 0 -0.22 23 23
PTK2 0.01 0.12 0.29 25 -0.35 5 30
IGF1R 0.025 0.028 -10000 0 -0.37 2 2
PI4KB 0.027 0.006 -10000 0 -10000 0 0
MFGE8 0.027 0.006 -10000 0 -10000 0 0
SRC 0.024 0.01 -10000 0 -10000 0 0
CDKN1B -0.042 0.14 -10000 0 -0.42 45 45
VEGFA 0.025 0.02 -10000 0 -0.35 1 1
ILK -0.042 0.14 -10000 0 -0.41 45 45
ROCK1 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.043 0.13 -10000 0 -0.39 43 43
PTK2B 0 0.054 0.19 23 -10000 0 23
alphaV/beta3 Integrin/JAM-A -0.001 0.11 -10000 0 -0.23 48 48
CBL 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.033 0.07 -10000 0 -0.22 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.033 0.09 -10000 0 -0.2 49 49
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.007 0.07 -10000 0 -0.29 6 6
alphaV/beta3 Integrin/Syndecan-1 0.047 0.04 -10000 0 -0.21 8 8
PI4KA 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.005 0.12 -10000 0 -0.35 18 18
PI4 Kinase 0.038 0.013 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.074 0.13 -10000 0 -0.21 197 197
RPS6KB1 -0.045 0.1 0.24 3 -0.34 18 21
TLN1 0.026 0.008 -10000 0 -10000 0 0
MAPK3 -0.041 0.13 -10000 0 -0.5 20 20
GPR124 0.025 0.009 -10000 0 -10000 0 0
MAPK1 -0.043 0.13 -10000 0 -0.48 22 22
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.008 0.1 -10000 0 -0.22 67 67
cell adhesion 0.03 0.058 -10000 0 -0.2 11 11
ANGPTL3 0.001 0.096 -10000 0 -0.37 26 26
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.027 -10000 0 -0.21 1 1
IGF-1R heterotetramer 0.025 0.028 -10000 0 -0.37 2 2
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
TGFBR2 0.027 0.005 -10000 0 -10000 0 0
ITGB3 0.023 0.042 -10000 0 -0.36 5 5
IGF1 -0.022 0.13 -10000 0 -0.37 51 51
RAC1 0.026 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.044 0.035 -10000 0 -0.21 5 5
apoptosis 0.026 0.007 -10000 0 -10000 0 0
CD47 0.028 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.049 0.033 -10000 0 -0.21 5 5
VCL 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.042 0.049 -10000 0 -0.24 10 10
CSF1 0.026 0.019 -10000 0 -0.35 1 1
PIK3C2A -0.042 0.14 -10000 0 -0.41 45 45
PI4 Kinase/Pyk2 -0.012 0.092 -10000 0 -0.32 8 8
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.057 0.04 -10000 0 -0.19 6 6
FAK1/Vinculin 0.021 0.11 0.28 25 -0.32 3 28
alphaV beta3/Integrin/ppsTEM5 0.044 0.035 -10000 0 -0.21 5 5
RHOA 0.027 0.006 -10000 0 -10000 0 0
VTN -0.051 0.16 -10000 0 -0.37 81 81
BCAR1 0.027 0.006 -10000 0 -10000 0 0
FGF2 0.009 0.084 -10000 0 -0.38 18 18
F11R 0.002 0.053 -10000 0 -0.27 15 15
alphaV/beta3 Integrin/Lactadherin 0.048 0.034 -10000 0 -0.21 5 5
alphaV/beta3 Integrin/TGFBR2 0.048 0.033 -10000 0 -0.21 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.061 0.029 -10000 0 -0.19 1 1
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
alphaV/beta3 Integrin/Talin 0.044 0.032 -10000 0 -0.19 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.01 0.11 -10000 0 -0.35 41 41
alphaV/beta3 Integrin/Pyk2 0.046 0.047 -10000 0 -10000 0 0
SDC1 0.024 0.035 -10000 0 -0.38 3 3
VAV3 -0.017 0.052 0.18 10 -10000 0 10
PTPN11 0.028 0.004 -10000 0 -10000 0 0
IRS1 0.027 0.021 -10000 0 -0.38 1 1
FAK1/Paxillin 0.022 0.11 0.27 26 -0.32 3 29
cell migration 0.016 0.1 0.25 31 -0.29 3 34
ITGAV 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.01 0.11 -10000 0 -0.34 9 9
SPP1 -0.15 0.19 -10000 0 -0.35 195 195
KDR 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.007 -10000 0 -10000 0 0
COL4A3 -0.033 0.14 -10000 0 -0.37 63 63
angiogenesis -0.05 0.14 -10000 0 -0.48 25 25
Rac1/GTP 0.018 0.051 -10000 0 -10000 0 0
EDIL3 0.02 0.05 -10000 0 -0.38 6 6
cell proliferation 0.048 0.033 -10000 0 -0.21 5 5
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 0.001 -10000 0 -10000 0 0
ADCY5 -0.053 0.09 -10000 0 -0.23 88 88
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.012 0.035 -10000 0 -0.2 13 13
ADCY2 -0.035 0.075 -10000 0 -0.22 56 56
ADCY3 -0.006 0.001 -10000 0 -10000 0 0
ADCY8 -0.01 0.02 -10000 0 -0.2 4 4
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.007 0.015 -10000 0 -0.23 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0 0.084 0.22 22 -0.24 2 24
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.026 0.06 -10000 0 -10000 0 0
epithelial cell differentiation 0.018 0.076 -10000 0 -10000 0 0
ITCH 0.029 0.017 -10000 0 -10000 0 0
WWP1 0.017 0.062 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.017 0.057 -10000 0 -0.38 8 8
PRL 0.01 0.068 -10000 0 -0.35 14 14
neuron projection morphogenesis -0.007 0.1 0.29 20 -10000 0 20
PTPRZ1 -0.11 0.19 -10000 0 -0.38 133 133
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.003 0.1 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.026 0.091 -10000 0 -0.29 10 10
ADAM17 0.031 0.014 -10000 0 -10000 0 0
ErbB4/ErbB4 0.012 0.054 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.006 0.09 -10000 0 -0.34 6 6
NCOR1 0.026 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.014 0.094 -10000 0 -0.31 1 1
GRIN2B -0.029 0.1 0.25 9 -0.33 3 12
ErbB4/ErbB2/betacellulin 0.018 0.068 -10000 0 -0.43 2 2
STAT1 0.018 0.059 -10000 0 -0.35 10 10
HBEGF 0.026 0.021 -10000 0 -0.38 1 1
PRLR -0.01 0.12 -10000 0 -0.38 36 36
E4ICDs/ETO2 0.016 0.073 -10000 0 -0.31 3 3
axon guidance 0.035 0.08 0.31 7 -10000 0 7
NEDD4 0.031 0.015 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0 0.096 -10000 0 -0.27 45 45
CBFA2T3 0 0.1 -10000 0 -0.38 26 26
ErbB4/ErbB2/HBEGF 0.024 0.05 -10000 0 -0.32 1 1
MAPK3 -0.004 0.11 0.3 16 -10000 0 16
STAT1 (dimer) 0.022 0.068 -10000 0 -10000 0 0
MAPK1 -0.002 0.11 0.3 16 -10000 0 16
JAK2 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.019 0.092 -10000 0 -0.3 12 12
NRG1 -0.042 0.11 -10000 0 -0.27 79 79
NRG3 -0.019 0.13 -10000 0 -0.38 45 45
NRG2 -0.099 0.19 -10000 0 -0.38 125 125
NRG4 -0.11 0.19 -10000 0 -0.38 135 135
heart development 0.035 0.08 0.31 7 -10000 0 7
neural crest cell migration -0.018 0.092 -10000 0 -0.29 12 12
ERBB2 0.01 0.031 -10000 0 -0.28 4 4
WWOX/E4ICDs 0.021 0.048 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.034 0.12 -10000 0 -0.31 18 18
apoptosis 0.019 0.12 0.37 29 -10000 0 29
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.034 0.12 -10000 0 -0.32 14 14
ErbB4/ErbB2/epiregulin -0.016 0.094 -10000 0 -0.33 3 3
ErbB4/ErbB4/betacellulin/betacellulin 0.017 0.08 -10000 0 -0.33 4 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.025 0.094 -10000 0 -0.32 1 1
MDM2 0.014 0.062 0.26 12 -10000 0 12
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.017 0.086 -10000 0 -0.28 1 1
STAT5A 0.037 0.083 0.29 11 -10000 0 11
ErbB4/EGFR/neuregulin 1 beta -0.017 0.096 -10000 0 -0.33 6 6
DLG4 0.026 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.039 0.01 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.024 0.053 -10000 0 -10000 0 0
STAT5A (dimer) 0.034 0.094 0.29 2 -10000 0 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.055 0.085 0.32 5 -10000 0 5
LRIG1 0.026 0.021 -10000 0 -0.38 1 1
EREG -0.09 0.18 -10000 0 -0.35 127 127
BTC 0.003 0.098 -10000 0 -0.38 25 25
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.028 0.074 0.31 7 -10000 0 7
ERBB4 0.004 0.043 -10000 0 -10000 0 0
STAT5B 0.027 0.005 -10000 0 -10000 0 0
YAP1 0.019 0.068 -10000 0 -0.39 8 8
GRB2 0.027 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.029 0.1 -10000 0 -0.38 4 4
glial cell differentiation -0.024 0.053 -10000 0 -10000 0 0
WWOX 0.019 0.013 -10000 0 -10000 0 0
cell proliferation -0.013 0.13 0.32 9 -0.45 5 14
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.029 0.083 0.23 12 -0.32 3 15
PDGFB-D/PDGFRB/SLAP 0.017 0.069 -10000 0 -0.24 26 26
PDGFB-D/PDGFRB/APS/CBL 0.034 0.064 -10000 0 -0.2 25 25
AKT1 0.032 0.1 0.28 26 -10000 0 26
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.048 0.1 0.26 27 -0.37 3 30
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
FGR 0.008 0.1 0.35 2 -0.44 12 14
mol:Ca2+ 0.041 0.1 0.25 27 -0.38 5 32
MYC 0.082 0.15 0.4 32 -0.74 2 34
SHC1 0.027 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.036 0.073 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.035 0.069 -10000 0 -0.22 26 26
GRB10 0.026 0.02 -10000 0 -0.35 1 1
PTPN11 0.028 0.004 -10000 0 -10000 0 0
GO:0007205 0.04 0.1 0.25 27 -0.38 5 32
PTEN 0.026 0.008 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.044 -10000 0 -0.37 5 5
PDGFB-D/PDGFRB/SHP2 0.023 0.068 -10000 0 -0.24 25 25
PDGFB-D/PDGFRB/GRB10 0.021 0.069 -10000 0 -0.24 26 26
cell cycle arrest 0.017 0.069 -10000 0 -0.24 26 26
HRAS 0.026 0.007 -10000 0 -10000 0 0
HIF1A 0.027 0.098 0.26 28 -10000 0 28
GAB1 0.038 0.099 0.28 11 -0.37 3 14
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.04 0.099 0.25 32 -0.32 2 34
PDGFB-D/PDGFRB 0.026 0.064 -10000 0 -0.2 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.024 0.067 -10000 0 -0.24 24 24
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.015 0.061 0.23 1 -10000 0 1
positive regulation of MAPKKK cascade 0.023 0.068 -10000 0 -0.24 25 25
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
mol:IP3 0.041 0.1 0.25 27 -0.39 5 32
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.014 0.074 -10000 0 -0.24 30 30
SHB 0.026 0.007 -10000 0 -10000 0 0
BLK -0.05 0.17 0.35 2 -0.47 51 53
PTPN2 0.028 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.023 0.068 -10000 0 -0.24 25 25
BCAR1 0.027 0.006 -10000 0 -10000 0 0
VAV2 0.044 0.11 0.27 24 -0.4 3 27
CBL 0.027 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.022 0.07 -10000 0 -0.24 26 26
LCK 0.011 0.097 0.35 2 -0.41 9 11
PDGFRB 0.006 0.091 -10000 0 -0.35 25 25
ACP1 0.028 0.004 -10000 0 -10000 0 0
HCK 0.019 0.063 0.36 3 -10000 0 3
ABL1 0.036 0.1 0.24 29 -0.36 5 34
PDGFB-D/PDGFRB/CBL 0.034 0.1 0.29 7 -0.42 5 12
PTPN1 0.022 0.012 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.018 0.059 -10000 0 -0.35 10 10
cell proliferation 0.081 0.14 0.38 37 -0.66 2 39
SLA 0.022 0.028 -10000 0 -0.35 2 2
actin cytoskeleton reorganization 0.05 0.095 0.34 13 -10000 0 13
SRC 0.014 0.062 0.35 2 -0.34 1 3
PI3K -0.005 0.041 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.028 0.069 -10000 0 -0.2 30 30
SH2B2 0.024 0.027 -10000 0 -0.35 2 2
PLCgamma1/SPHK1 0.048 0.11 0.26 27 -0.38 3 30
LYN 0.013 0.089 0.35 3 -0.42 7 10
LRP1 0.027 0.005 -10000 0 -10000 0 0
SOS1 0.028 0.003 -10000 0 -10000 0 0
STAT5B 0.027 0.005 -10000 0 -10000 0 0
STAT5A 0.028 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.045 0.067 -10000 0 -10000 0 0
SPHK1 0.013 0.078 -10000 0 -0.35 18 18
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.041 0.1 0.25 27 -0.39 5 32
PLCG1 0.041 0.1 0.26 26 -0.4 5 31
NHERF/PDGFRB 0.037 0.063 -10000 0 -0.2 25 25
YES1 0.015 0.093 0.36 1 -0.59 5 6
cell migration 0.036 0.063 -10000 0 -0.2 25 25
SHC/Grb2/SOS1 0.045 0.067 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.028 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.047 0.064 -10000 0 -10000 0 0
FYN 0.008 0.095 0.35 3 -0.38 11 14
DOK1 0.031 0.084 0.18 76 -10000 0 76
HRAS/GTP 0.02 0.005 -10000 0 -10000 0 0
PDGFB 0.024 0.033 -10000 0 -0.35 3 3
RAC1 0.054 0.12 0.36 21 -0.39 4 25
PRKCD 0.032 0.085 0.18 76 -10000 0 76
FER 0.027 0.081 0.18 63 -10000 0 63
MAPKKK cascade 0.016 0.092 0.29 12 -10000 0 12
RASA1 0.028 0.082 0.18 65 -10000 0 65
NCK1 0.027 0.005 -10000 0 -10000 0 0
NCK2 0.028 0.004 -10000 0 -10000 0 0
p62DOK/Csk 0.042 0.078 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.022 0.068 -10000 0 -0.24 25 25
chemotaxis 0.036 0.1 0.24 30 -0.35 5 35
STAT1-3-5/STAT1-3-5 0.031 0.068 -10000 0 -0.32 1 1
Bovine Papilomavirus E5/PDGFRB 0.005 0.063 -10000 0 -0.24 25 25
PTPRJ 0.027 0.019 -10000 0 -0.35 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.007 -10000 0 -10000 0 0
SMARCC1 0.013 0.011 -10000 0 -10000 0 0
REL 0.028 0.004 -10000 0 -10000 0 0
HDAC7 -0.017 0.089 0.22 2 -0.39 3 5
JUN 0.027 0.004 -10000 0 -10000 0 0
EP300 0.027 0.005 -10000 0 -10000 0 0
KAT2B 0.024 0.041 -10000 0 -0.38 4 4
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 0.002 0.039 -10000 0 -0.28 6 6
FOXO1 0.026 0.008 -10000 0 -10000 0 0
T-DHT/AR 0.003 0.1 0.25 1 -0.41 3 4
MAP2K6 0.015 0.053 -10000 0 -0.39 6 6
BRM/BAF57 0.032 0.023 -10000 0 -0.27 1 1
MAP2K4 0.019 0.019 -10000 0 -10000 0 0
SMARCA2 0.023 0.023 -10000 0 -0.38 1 1
PDE9A -0.11 0.33 -10000 0 -0.92 52 52
NCOA2 0.024 0.022 -10000 0 -0.38 1 1
CEBPA 0.021 0.044 -10000 0 -0.37 5 5
EHMT2 0.026 0.007 -10000 0 -10000 0 0
cell proliferation 0.009 0.13 0.28 23 -0.4 8 31
NR0B1 0.018 0.037 -10000 0 -0.35 4 4
EGR1 0.017 0.064 -10000 0 -0.38 10 10
RXRs/9cRA -0.052 0.12 -10000 0 -0.21 159 159
AR/RACK1/Src 0.013 0.086 0.2 23 -0.3 2 25
AR/GR -0.014 0.094 0.2 1 -0.26 30 31
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
PKN1 0.027 0.005 -10000 0 -10000 0 0
RCHY1 0.027 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.015 2 2
MAPK8 0.006 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.007 0.071 0.24 2 -0.28 1 3
SRC -0.01 0.049 0.19 14 -0.26 3 17
NR3C1 0.022 0.045 -10000 0 -0.38 5 5
KLK3 -0.1 0.12 -10000 0 -0.48 8 8
APPBP2 0.022 0.019 -10000 0 -10000 0 0
TRIM24 0.026 0.02 -10000 0 -0.35 1 1
T-DHT/AR/TIP60 -0.004 0.065 0.2 4 -0.32 2 6
TMPRSS2 -0.06 0.23 -10000 0 -0.83 27 27
RXRG -0.14 0.2 -10000 0 -0.38 165 165
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.026 0.021 -10000 0 -0.39 1 1
RXRB 0.027 0.006 -10000 0 -10000 0 0
CARM1 0.027 0.006 -10000 0 -10000 0 0
NR2C2 0.028 0.004 -10000 0 -10000 0 0
KLK2 -0.003 0.087 0.33 1 -0.32 5 6
AR -0.021 0.085 0.17 2 -0.25 45 47
SENP1 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
MDM2 0.025 0.028 -10000 0 -0.35 2 2
SRY 0 0.004 0.014 24 -10000 0 24
GATA2 0.022 0.045 -10000 0 -0.38 5 5
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.22 0.18 -10000 0 -0.36 270 270
T-DHT/AR/RACK1/Src 0.017 0.09 0.21 35 -0.31 2 37
positive regulation of transcription 0.022 0.045 -10000 0 -0.38 5 5
DNAJA1 0.02 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.011 -10000 0 -10000 0 0
NCOA1 0.032 0.013 -10000 0 -10000 0 0
SPDEF -0.054 0.16 -10000 0 -0.38 79 79
T-DHT/AR/TIF2 0.003 0.072 0.22 4 -0.35 4 8
T-DHT/AR/Hsp90 -0.006 0.066 0.2 4 -0.32 2 6
GSK3B 0.027 0.005 -10000 0 -10000 0 0
NR2C1 0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.038 0.25 1 -0.25 5 6
SIRT1 0.027 0.005 -10000 0 -10000 0 0
ZMIZ2 0.027 0.008 -10000 0 -10000 0 0
POU2F1 0.016 0.05 -10000 0 -0.35 1 1
T-DHT/AR/DAX-1 -0.01 0.069 0.22 3 -0.29 4 7
CREBBP 0.026 0.007 -10000 0 -10000 0 0
SMARCE1 0.026 0.008 -10000 0 -10000 0 0
IL1-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
UBC13/UEV1A 0.02 0.003 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.006 0.056 -10000 0 -0.42 2 2
IRAK/TOLLIP 0.03 0.009 -10000 0 -10000 0 0
IKBKB 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.027 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.054 0.14 -10000 0 -0.26 129 129
IL1A -0.039 0.14 -10000 0 -0.35 72 72
IL1B -0.017 0.085 -10000 0 -0.26 45 45
IRAK/TRAF6/p62/Atypical PKCs 0.055 0.034 -10000 0 -10000 0 0
IL1R2 -0.033 0.15 -10000 0 -0.38 61 61
IL1R1 0.027 0.019 -10000 0 -0.35 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.064 0.24 1 -0.42 3 4
TOLLIP 0.027 0.006 -10000 0 -10000 0 0
TICAM2 0.022 0.041 -10000 0 -0.38 4 4
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.022 0.067 -10000 0 -0.34 2 2
JUN -0.009 0.032 0.16 10 -10000 0 10
MAP3K7 0.027 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.03 0.084 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 0.018 0.1 -10000 0 -0.2 70 70
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.027 0.1 -10000 0 -0.34 3 3
IL1 beta fragment/IL1R1/IL1RAP 0.011 0.08 -10000 0 -0.19 53 53
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.007 0.034 0.17 10 -10000 0 10
IRAK1 0.014 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.01 0.093 -10000 0 -0.27 42 42
IRAK4 0.027 0.005 -10000 0 -10000 0 0
PRKCI 0.024 0.027 -10000 0 -0.35 2 2
TRAF6 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.036 0.014 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.054 -10000 0 -0.36 1 1
CHUK 0.027 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.011 0.08 -10000 0 -0.19 53 53
IL1 beta/IL1R2 -0.03 0.12 -10000 0 -0.23 100 100
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.02 0.075 -10000 0 -10000 0 0
IRAK3 0.02 0.053 -10000 0 -0.38 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.028 0.087 -10000 0 -0.33 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.053 -10000 0 -0.27 2 2
IL1 alpha/IL1R1/IL1RAP 0.005 0.1 -10000 0 -0.22 72 72
RELA 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.027 0.006 -10000 0 -10000 0 0
MYD88 0.027 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.016 -10000 0 -10000 0 0
IL1RAP 0.019 0.053 -10000 0 -0.35 8 8
UBE2N 0.028 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.006 0.068 -10000 0 -0.3 1 1
CASP1 0.021 0.049 -10000 0 -0.35 7 7
IL1RN/IL1R2 -0.032 0.15 -10000 0 -0.32 84 84
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.023 0.082 -10000 0 -10000 0 0
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.059 -10000 0 -0.28 4 4
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
IL1RN -0.013 0.12 -10000 0 -0.38 41 41
TRAF6/TAK1/TAB1/TAB2 0.038 0.011 -10000 0 -10000 0 0
MAP2K6 0.014 0.034 0.18 10 -10000 0 10
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 0.007 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.017 0.093 -9999 0 -0.34 9 9
Syndecan-3/Neurocan 0.012 0.078 -9999 0 -0.37 13 13
POMC 0.001 0.1 -9999 0 -0.38 27 27
EGFR 0.017 0.057 -9999 0 -0.38 8 8
Syndecan-3/EGFR 0.015 0.071 -9999 0 -0.37 10 10
AGRP 0.015 0.058 -9999 0 -0.35 10 10
NCSTN 0.027 0.005 -9999 0 -10000 0 0
PSENEN 0.027 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.005 -9999 0 -10000 0 0
APH1A 0.027 0.006 -9999 0 -10000 0 0
NCAN 0.011 0.071 -9999 0 -0.35 15 15
long-term memory 0.034 0.069 -9999 0 -0.35 11 11
Syndecan-3/IL8 -0.067 0.12 -9999 0 -0.48 13 13
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.034 0.017 -9999 0 -10000 0 0
FYN 0.027 0.005 -9999 0 -10000 0 0
limb bud formation 0.001 0.069 -9999 0 -0.38 13 13
MC4R 0.021 0.009 -9999 0 -10000 0 0
SRC 0.024 0.01 -9999 0 -10000 0 0
PTN -0.032 0.14 -9999 0 -0.38 59 59
FGFR/FGF/Syndecan-3 0.001 0.069 -9999 0 -0.38 13 13
neuron projection morphogenesis 0.005 0.098 -9999 0 -0.33 10 10
Syndecan-3/AgRP 0.013 0.075 -9999 0 -0.36 13 13
Syndecan-3/AgRP/MC4R 0.023 0.076 -9999 0 -0.34 13 13
Fyn/Cortactin 0.038 0.012 -9999 0 -10000 0 0
SDC3 0.001 0.07 -9999 0 -0.38 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.067 0.12 -9999 0 -0.48 13 13
IL8 -0.16 0.19 -9999 0 -0.35 198 198
Syndecan-3/Fyn/Cortactin 0.035 0.07 -9999 0 -0.35 11 11
Syndecan-3/CASK 0 0.067 -9999 0 -0.36 13 13
alpha-MSH/MC4R 0.015 0.074 -9999 0 -0.26 26 26
Gamma Secretase 0.072 0.03 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.002 0.072 -10000 0 -0.3 2 2
Syndecan-4/Syndesmos -0.004 0.11 0.3 1 -0.44 1 2
positive regulation of JNK cascade -0.013 0.13 0.29 2 -0.36 7 9
Syndecan-4/ADAM12 -0.09 0.15 0.3 1 -0.38 23 24
CCL5 0.019 0.059 -10000 0 -0.38 9 9
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DNM2 0.027 0.005 -10000 0 -10000 0 0
ITGA5 0.021 0.049 -10000 0 -0.35 7 7
SDCBP 0.025 0.009 -10000 0 -10000 0 0
PLG 0.004 0.047 -10000 0 -0.35 5 5
ADAM12 -0.19 0.19 -10000 0 -0.35 230 230
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.041 0.034 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.032 0.14 0.3 2 -0.37 15 17
Syndecan-4/CXCL12/CXCR4 -0.013 0.14 0.31 2 -0.39 6 8
Syndecan-4/Laminin alpha3 -0.008 0.12 0.31 1 -0.45 3 4
MDK 0.012 0.074 -10000 0 -0.36 16 16
Syndecan-4/FZD7 -0.002 0.12 0.3 2 -0.44 1 3
Syndecan-4/Midkine -0.01 0.12 0.3 2 -0.44 3 5
FZD7 0.025 0.033 -10000 0 -0.36 3 3
Syndecan-4/FGFR1/FGF -0.007 0.12 0.29 1 -0.4 4 5
THBS1 0.018 0.059 -10000 0 -0.36 10 10
integrin-mediated signaling pathway -0.012 0.12 0.29 1 -0.36 6 7
positive regulation of MAPKKK cascade -0.013 0.13 0.29 2 -0.36 7 9
Syndecan-4/TACI -0.042 0.13 0.3 1 -0.39 14 15
CXCR4 0.005 0.091 -10000 0 -0.35 25 25
cell adhesion 0.002 0.05 0.19 6 -0.2 8 14
Syndecan-4/Dynamin 0 0.12 0.3 2 -0.44 1 3
Syndecan-4/TSP1 -0.006 0.12 0.3 2 -0.39 3 5
Syndecan-4/GIPC 0 0.12 0.3 2 -0.44 1 3
Syndecan-4/RANTES -0.005 0.12 0.3 2 -0.44 1 3
ITGB1 0.026 0.02 -10000 0 -0.35 1 1
LAMA1 -0.044 0.15 -10000 0 -0.36 76 76
LAMA3 0.014 0.066 -10000 0 -0.36 12 12
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCA 0.017 0.1 0.77 7 -10000 0 7
Syndecan-4/alpha-Actinin -0.003 0.12 0.3 1 -0.44 1 2
TFPI 0.026 0.019 -10000 0 -0.35 1 1
F2 -0.031 0.13 -10000 0 -0.35 60 60
alpha5/beta1 Integrin 0.033 0.043 -10000 0 -0.28 7 7
positive regulation of cell adhesion -0.039 0.13 0.28 2 -0.38 14 16
ACTN1 0.024 0.033 -10000 0 -0.35 3 3
TNC 0.001 0.096 -10000 0 -0.36 28 28
Syndecan-4/CXCL12 -0.012 0.12 0.3 2 -0.41 4 6
FGF6 0.017 0.026 -10000 0 -0.35 2 2
RHOA 0.027 0.006 -10000 0 -10000 0 0
CXCL12 0.001 0.1 -10000 0 -0.38 26 26
TNFRSF13B -0.069 0.17 -10000 0 -0.38 94 94
FGF2 0.009 0.084 -10000 0 -0.38 18 18
FGFR1 0.022 0.035 -10000 0 -0.38 3 3
Syndecan-4/PI-4-5-P2 -0.036 0.082 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.02 0.11 -10000 0 -0.35 41 41
cell migration -0.019 0.014 -10000 0 -10000 0 0
PRKCD 0.017 0.025 -10000 0 -10000 0 0
vasculogenesis -0.005 0.12 0.3 2 -0.38 3 5
SDC4 -0.034 0.085 -10000 0 -0.46 1 1
Syndecan-4/Tenascin C -0.012 0.13 0.3 1 -0.38 6 7
Syndecan-4/PI-4-5-P2/PKC alpha -0.033 0.027 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.004 0.11 0.3 2 -0.42 1 3
MMP9 -0.063 0.16 -10000 0 -0.35 92 92
Rac1/GTP 0.002 0.051 0.19 6 -0.2 8 14
cytoskeleton organization -0.004 0.11 0.29 1 -0.43 1 2
GIPC1 0.027 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.003 0.12 0.3 1 -0.44 1 2
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.011 0.05 -9999 0 -0.26 7 7
STMN1 0.009 0.036 -9999 0 -0.24 8 8
Aurora B/RasGAP/Survivin 0.037 0.073 -9999 0 -0.24 20 20
Chromosomal passenger complex/Cul3 protein complex -0.017 0.089 -9999 0 -0.31 18 18
BIRC5 0.01 0.084 -9999 0 -0.36 20 20
DES -0.3 0.32 -9999 0 -0.59 217 217
Aurora C/Aurora B/INCENP 0.04 0.06 -9999 0 -0.21 20 20
Aurora B/TACC1 0.031 0.034 -9999 0 -0.2 7 7
Aurora B/PP2A 0.035 0.042 -9999 0 -0.24 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.008 0.012 -9999 0 -0.14 1 1
mitotic metaphase/anaphase transition 0.001 0.004 -9999 0 -10000 0 0
NDC80 0 0.064 -9999 0 -0.28 20 20
Cul3 protein complex 0.017 0.089 -9999 0 -0.23 46 46
KIF2C 0.004 0.067 -9999 0 -0.34 9 9
PEBP1 0.027 0.006 -9999 0 -10000 0 0
KIF20A 0.004 0.091 -9999 0 -0.35 25 25
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.033 0.044 -9999 0 -0.24 9 9
SEPT1 0.023 0.038 -9999 0 -0.36 4 4
SMC2 0.027 0.005 -9999 0 -10000 0 0
SMC4 0.027 0.006 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.026 0.16 -9999 0 -0.54 31 31
PSMA3 0.027 0.005 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -9999 0 -10000 0 0
H3F3B 0.012 0.026 -9999 0 -0.28 1 1
AURKB 0.023 0.058 -9999 0 -0.36 9 9
AURKC 0.014 0.068 -9999 0 -0.36 13 13
CDCA8 0.027 0.021 -9999 0 -0.37 1 1
cytokinesis -0.025 0.1 -9999 0 -0.44 13 13
Aurora B/Septin1 -0.002 0.12 -9999 0 -0.4 14 14
AURKA 0.011 0.064 -9999 0 -0.36 12 12
INCENP 0.028 0.008 -9999 0 -10000 0 0
KLHL13 -0.021 0.13 -9999 0 -0.38 49 49
BUB1 -0.024 0.13 -9999 0 -0.35 57 57
hSgo1/Aurora B/Survivin 0.029 0.087 -9999 0 -0.23 37 37
EVI5 0.028 0.005 -9999 0 -10000 0 0
RhoA/GTP 0.014 0.11 -9999 0 -0.37 11 11
SGOL1 0.011 0.078 -9999 0 -0.35 18 18
CENPA 0.01 0.079 -9999 0 -0.31 13 13
NCAPG 0.021 0.046 -9999 0 -0.35 6 6
Aurora B/HC8 Proteasome 0.036 0.044 -9999 0 -0.24 9 9
NCAPD2 0.027 0.006 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.036 0.044 -9999 0 -0.24 9 9
RHOA 0.027 0.006 -9999 0 -10000 0 0
NCAPH 0.026 0.027 -9999 0 -0.35 2 2
NPM1 -0.02 0.12 -9999 0 -0.39 29 29
RASA1 0.025 0.008 -9999 0 -10000 0 0
KLHL9 0.024 0.01 -9999 0 -10000 0 0
mitotic prometaphase 0 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.044 -9999 0 -0.24 9 9
PPP1CC 0.028 0.004 -9999 0 -10000 0 0
Centraspindlin 0.007 0.11 -9999 0 -0.35 17 17
RhoA/GDP 0.02 0.004 -9999 0 -10000 0 0
NSUN2 -0.01 0.096 -9999 0 -0.33 27 27
MYLK -0.002 0.058 -9999 0 -0.26 13 13
KIF23 -0.02 0.13 -9999 0 -0.35 52 52
VIM 0.009 0.038 -9999 0 -0.24 9 9
RACGAP1 0.028 0.006 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.099 -9999 0 -0.33 29 29
Chromosomal passenger complex -0.001 0.081 -9999 0 -0.34 13 13
Chromosomal passenger complex/EVI5 0.08 0.087 -9999 0 -0.34 5 5
TACC1 0.025 0.009 -9999 0 -10000 0 0
PPP2R5D 0.026 0.007 -9999 0 -10000 0 0
CUL3 0.028 0.004 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
ErbB2/ErbB3 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
USP8 -0.004 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.015 0.094 0.23 1 -0.54 1 2
NFATC4 -0.019 0.093 0.28 13 -0.38 1 14
ERBB2IP 0.026 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.025 0.027 -10000 0 -0.35 2 2
mammary gland morphogenesis -0.032 0.087 -10000 0 -0.29 4 4
JUN -0.009 0.07 0.18 9 -0.23 7 16
HRAS 0.026 0.007 -10000 0 -10000 0 0
DOCK7 -0.034 0.092 0.26 3 -0.47 1 4
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.002 0.1 -10000 0 -0.22 66 66
AKT1 0.004 0.008 -10000 0 -10000 0 0
BAD -0.005 0.007 -10000 0 -10000 0 0
MAPK10 -0.02 0.08 0.19 17 -0.23 11 28
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.034 0.093 -10000 0 -0.31 4 4
RAF1 -0.024 0.099 0.26 6 -0.55 1 7
ErbB2/ErbB3/neuregulin 2 -0.043 0.11 -10000 0 -0.22 103 103
STAT3 0.024 0.056 -10000 0 -0.74 2 2
cell migration -0.012 0.088 0.24 20 -0.22 9 29
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.08 0.17 -10000 0 -0.58 9 9
FOS -0.058 0.14 0.31 3 -0.44 27 30
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.032 0.087 -10000 0 -0.29 4 4
MAPK3 -0.063 0.15 0.3 2 -0.52 9 11
MAPK1 -0.069 0.16 0.31 2 -0.58 11 13
JAK2 -0.035 0.086 0.26 1 -0.47 1 2
NF2 -0.006 0.091 -10000 0 -0.65 8 8
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.019 0.097 0.18 8 -0.22 61 69
NRG1 -0.056 0.16 -10000 0 -0.38 81 81
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
MAPK8 -0.03 0.1 0.21 4 -0.24 55 59
MAPK9 -0.007 0.074 0.19 24 -0.24 1 25
ERBB2 -0.02 0.025 -10000 0 -0.29 3 3
ERBB3 0.024 0.03 -10000 0 -0.39 2 2
SHC1 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
apoptosis 0.008 0.011 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.055 -10000 0 -0.73 2 2
RNF41 -0.007 0.011 -10000 0 -10000 0 0
FRAP1 -0.002 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.03 0.059 -10000 0 -0.34 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.006 0.03 -10000 0 -0.24 4 4
CHRNA1 -0.081 0.15 0.28 2 -0.43 10 12
myelination -0.007 0.11 0.28 28 -0.37 1 29
PPP3CB -0.033 0.082 0.25 1 -0.44 1 2
KRAS 0.024 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.005 0.098 -10000 0 -0.38 2 2
NRG2 -0.099 0.19 -10000 0 -0.38 125 125
mol:GDP -0.019 0.096 0.18 8 -0.22 61 69
SOS1 0.027 0.003 -10000 0 -10000 0 0
MAP2K2 -0.035 0.098 0.26 5 -0.54 1 6
SRC 0.024 0.01 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.034 0.091 0.26 3 -0.47 1 4
MAP2K1 -0.063 0.16 -10000 0 -0.57 10 10
heart morphogenesis -0.032 0.087 -10000 0 -0.29 4 4
RAS family/GDP 0.009 0.098 0.25 1 -0.53 1 2
GRB2 0.027 0.005 -10000 0 -10000 0 0
PRKACA -0.008 0.11 -10000 0 -0.66 11 11
CHRNE 0.001 0.026 0.08 2 -0.14 9 11
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
activation of caspase activity -0.004 0.008 -10000 0 -10000 0 0
nervous system development -0.032 0.087 -10000 0 -0.29 4 4
CDC42 0.026 0.007 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.023 0.015 -9999 0 -10000 0 0
SVIL 0.022 0.03 -9999 0 -0.35 2 2
ZNF318 0.028 0.014 -9999 0 -10000 0 0
JMJD2C -0.002 0.019 -9999 0 -0.073 26 26
T-DHT/AR/Ubc9 -0.002 0.091 -9999 0 -0.22 53 53
CARM1 0.027 0.005 -9999 0 -10000 0 0
PRDX1 0.028 0.004 -9999 0 -10000 0 0
PELP1 0.026 0.008 -9999 0 -10000 0 0
CTNNB1 0.024 0.014 -9999 0 -10000 0 0
AKT1 0.027 0.007 -9999 0 -10000 0 0
PTK2B 0.022 0.015 -9999 0 -10000 0 0
MED1 0.027 0.008 -9999 0 -10000 0 0
MAK 0.017 0.068 -9999 0 -0.35 13 13
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.024 0.014 -9999 0 -10000 0 0
GSN 0.017 0.055 -9999 0 -0.38 7 7
NCOA2 0.024 0.022 -9999 0 -0.38 1 1
NCOA6 0.022 0.015 -9999 0 -10000 0 0
DNA-PK 0.05 0.025 -9999 0 -10000 0 0
NCOA4 0.027 0.006 -9999 0 -10000 0 0
PIAS3 0.024 0.013 -9999 0 -10000 0 0
cell proliferation -0.006 0.084 -9999 0 -0.44 11 11
XRCC5 0.028 0.005 -9999 0 -10000 0 0
UBE3A 0.024 0.017 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.046 0.13 -9999 0 -0.25 113 113
FHL2 0.005 0.1 -9999 0 -0.71 6 6
RANBP9 0.024 0.015 -9999 0 -10000 0 0
JMJD1A -0.001 0.025 -9999 0 -0.13 15 15
CDK6 0.021 0.038 -9999 0 -0.35 4 4
TGFB1I1 0.02 0.04 -9999 0 -0.36 4 4
T-DHT/AR/CyclinD1 -0.002 0.09 -9999 0 -0.22 52 52
XRCC6 0.027 0.006 -9999 0 -10000 0 0
T-DHT/AR 0.002 0.1 -9999 0 -0.23 51 51
CTDSP1 0.027 0.004 -9999 0 -10000 0 0
CTDSP2 0.028 0.01 -9999 0 -10000 0 0
BRCA1 0.024 0.023 -9999 0 -0.35 1 1
TCF4 0.025 0.011 -9999 0 -10000 0 0
CDKN2A -0.087 0.17 -9999 0 -0.35 121 121
SRF 0.029 0.019 -9999 0 -10000 0 0
NKX3-1 -0.015 0.055 -9999 0 -0.21 19 19
KLK3 -0.005 0.081 -9999 0 -10000 0 0
TMF1 0.027 0.005 -9999 0 -10000 0 0
HNRNPA1 0.028 0.007 -9999 0 -10000 0 0
AOF2 -0.001 0.005 -9999 0 -10000 0 0
APPL1 0.014 0.008 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.001 0.091 -9999 0 -0.23 50 50
AR -0.028 0.14 -9999 0 -0.38 51 51
UBA3 0.027 0.005 -9999 0 -10000 0 0
PATZ1 0.028 0.007 -9999 0 -10000 0 0
PAWR 0.027 0.005 -9999 0 -10000 0 0
PRKDC 0.025 0.01 -9999 0 -10000 0 0
PA2G4 0.028 0.008 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.001 0.081 -9999 0 -0.2 48 48
RPS6KA3 0.024 0.015 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.001 0.091 -9999 0 -0.22 53 53
LATS2 0.027 0.008 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.003 0.083 -9999 0 -0.2 50 50
Cyclin D3/CDK11 p58 0.019 0.006 -9999 0 -10000 0 0
VAV3 -0.001 0.096 -9999 0 -0.36 28 28
KLK2 -0.02 0.09 -9999 0 -0.31 29 29
CASP8 0.028 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.011 0.087 -9999 0 -0.21 46 46
TMPRSS2 -0.031 0.17 -9999 0 -0.73 20 20
CCND1 0.025 0.02 -9999 0 -0.35 1 1
PIAS1 0.024 0.016 -9999 0 -10000 0 0
mol:T-DHT -0.002 0.017 -9999 0 -0.07 17 17
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.022 0.021 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0 0.088 -9999 0 -0.23 47 47
CMTM2 0.015 0.065 -9999 0 -0.36 12 12
SNURF -0.048 0.16 -9999 0 -0.38 72 72
ZMIZ1 0.021 0.027 -9999 0 -10000 0 0
CCND3 0.026 0.008 -9999 0 -10000 0 0
TGIF1 0.027 0.008 -9999 0 -10000 0 0
FKBP4 0.024 0.014 -9999 0 -10000 0 0
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.014 0.11 -10000 0 -0.39 14 14
TBX21 -0.088 0.26 0.52 1 -0.91 20 21
B2M 0.016 0.023 -10000 0 -10000 0 0
TYK2 0.015 0.031 -10000 0 -10000 0 0
IL12RB1 0.011 0.052 -10000 0 -0.41 4 4
GADD45B -0.07 0.24 -10000 0 -0.78 20 20
IL12RB2 0.004 0.078 -10000 0 -0.38 14 14
GADD45G -0.065 0.23 -10000 0 -0.78 17 17
natural killer cell activation -0.002 0.017 0.044 1 -0.041 20 21
RELB 0.026 0.02 -10000 0 -0.35 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 0.016 0.042 -10000 0 -0.36 4 4
IL2RA -0.004 0.1 -10000 0 -0.35 33 33
IFNG -0.067 0.16 -10000 0 -0.35 101 101
STAT3 (dimer) -0.068 0.22 -10000 0 -0.66 25 25
HLA-DRB5 0 0.005 -10000 0 -0.025 11 11
FASLG -0.095 0.29 -10000 0 -1 23 23
NF kappa B2 p52/RelB -0.078 0.25 -10000 0 -0.74 27 27
CD4 0.022 0.03 -10000 0 -0.35 2 2
SOCS1 0.021 0.047 -10000 0 -0.36 6 6
EntrezGene:6955 -0.004 0.011 -10000 0 -0.03 22 22
CD3D 0.009 0.051 -10000 0 -0.39 5 5
CD3E 0.011 0.046 -10000 0 -0.38 4 4
CD3G 0.006 0.061 -10000 0 -0.39 8 8
IL12Rbeta2/JAK2 0.017 0.064 -10000 0 -0.27 11 11
CCL3 -0.11 0.28 -10000 0 -0.84 25 25
CCL4 -0.089 0.27 -10000 0 -0.87 25 25
HLA-A -0.004 0.009 -10000 0 -0.026 13 13
IL18/IL18R 0.021 0.077 -10000 0 -0.25 13 13
NOS2 -0.13 0.28 -10000 0 -0.85 30 30
IL12/IL12R/TYK2/JAK2/SPHK2 -0.012 0.11 -10000 0 -0.36 17 17
IL1R1 -0.082 0.25 0.51 1 -0.85 18 19
IL4 0.002 0.056 -10000 0 -0.35 7 7
JAK2 0.014 0.029 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.01 -10000 0 -0.031 14 14
TCR/CD3/MHC I/CD8 -0.045 0.16 -10000 0 -0.64 16 16
RAB7A -0.053 0.21 -10000 0 -0.73 11 11
lysosomal transport -0.05 0.2 -10000 0 -0.69 11 11
FOS -0.085 0.31 -10000 0 -1 33 33
STAT4 (dimer) -0.056 0.24 0.38 3 -0.78 19 22
STAT5A (dimer) -0.12 0.26 -10000 0 -0.77 29 29
GZMA -0.1 0.3 -10000 0 -1 26 26
GZMB -0.095 0.27 -10000 0 -0.92 22 22
HLX 0.026 0.019 -10000 0 -0.35 1 1
LCK -0.096 0.26 -10000 0 -0.81 26 26
TCR/CD3/MHC II/CD4 -0.007 0.087 -10000 0 -0.4 12 12
IL2/IL2R 0.034 0.082 -10000 0 -0.26 6 6
MAPK14 -0.068 0.24 -10000 0 -0.81 17 17
CCR5 -0.067 0.23 -10000 0 -0.81 15 15
IL1B -0.022 0.12 -10000 0 -0.38 41 41
STAT6 -0.014 0.1 -10000 0 -0.9 2 2
STAT4 0.024 0.038 -10000 0 -0.35 4 4
STAT3 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.018 0.059 -10000 0 -0.35 10 10
NFKB1 0.027 0.005 -10000 0 -10000 0 0
NFKB2 0.027 0.006 -10000 0 -10000 0 0
IL12B 0.009 0.051 -10000 0 -0.35 5 5
CD8A 0.005 0.071 -10000 0 -0.38 12 12
CD8B -0.012 0.1 -10000 0 -0.38 30 30
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.014 0.11 0.39 14 -10000 0 14
IL2RB 0.026 0.021 -10000 0 -0.38 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.05 0.22 0.38 3 -0.71 19 22
IL2RG 0.019 0.059 -10000 0 -0.38 9 9
IL12 0.003 0.083 -10000 0 -0.27 26 26
STAT5A 0.028 0.004 -10000 0 -10000 0 0
CD247 0.009 0.055 -10000 0 -0.39 6 6
IL2 0.021 0.027 -10000 0 -0.35 2 2
SPHK2 0.027 0.006 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.006 0.095 -10000 0 -0.4 21 21
IL12/IL12R/TYK2/JAK2 -0.097 0.27 -10000 0 -0.82 29 29
MAP2K3 -0.077 0.25 -10000 0 -0.77 24 24
RIPK2 0.024 0.01 -10000 0 -10000 0 0
MAP2K6 -0.066 0.24 -10000 0 -0.76 21 21
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.006 -10000 0 -0.026 18 18
IL18RAP 0.008 0.07 -10000 0 -0.38 12 12
IL12Rbeta1/TYK2 0.021 0.053 -10000 0 -0.3 4 4
EOMES -0.038 0.15 -10000 0 -1 4 4
STAT1 (dimer) -0.088 0.22 -10000 0 -0.68 24 24
T cell proliferation -0.041 0.19 0.41 2 -0.55 20 22
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.033 -10000 0 -0.38 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.057 0.2 -10000 0 -0.62 19 19
ATF2 -0.063 0.23 0.51 1 -0.75 17 18
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.02 0.076 0.38 14 -10000 0 14
VDR 0.027 0.005 -10000 0 -10000 0 0
FAM120B 0.026 0.007 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.055 0.12 -10000 0 -0.31 17 17
RXRs/LXRs/DNA/Oxysterols -0.044 0.11 -10000 0 -0.37 7 7
MED1 0.026 0.008 -10000 0 -10000 0 0
mol:9cRA 0.002 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.01 0.061 -10000 0 -0.29 2 2
RXRs/NUR77 -0.045 0.14 -10000 0 -0.31 15 15
RXRs/PPAR -0.061 0.12 -10000 0 -0.32 19 19
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.004 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.056 0.032 -10000 0 -0.2 2 2
RARA 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.028 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.005 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.042 0.027 -10000 0 -0.19 3 3
RARG 0.026 0.02 -10000 0 -0.35 1 1
RPS6KB1 0.032 0.072 0.59 6 -10000 0 6
RARs/THRs/DNA/SMRT 0.009 0.062 -10000 0 -0.33 2 2
THRA 0.025 0.009 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.004 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.047 0.12 -10000 0 -0.26 9 9
NR1H4 -0.055 0.16 -10000 0 -0.37 85 85
RXRs/LXRs/DNA -0.026 0.14 -10000 0 -0.28 9 9
NR1H2 0.027 0.015 -10000 0 -10000 0 0
NR1H3 0.028 0.016 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.038 0.12 -10000 0 -0.23 9 9
NR4A1 0.016 0.067 -10000 0 -0.38 11 11
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.078 0.12 -10000 0 -0.29 45 45
RXRG -0.14 0.2 -10000 0 -0.38 165 165
RXR alpha/CCPG 0.039 0.021 -10000 0 -0.27 1 1
RXRA 0.027 0.025 -10000 0 -0.38 1 1
RXRB 0.027 0.015 -10000 0 -10000 0 0
THRB -0.002 0.11 -10000 0 -0.38 30 30
PPARG 0.022 0.045 -10000 0 -0.38 5 5
PPARD 0.027 0.005 -10000 0 -10000 0 0
TNF -0.052 0.14 -10000 0 -0.9 5 5
mol:Oxysterols 0.002 0.007 -10000 0 -10000 0 0
cholesterol transport -0.043 0.11 -10000 0 -0.37 7 7
PPARA 0.026 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.025 0.035 -10000 0 -0.38 3 3
RXRs/NUR77/BCL2 -0.075 0.13 -10000 0 -0.22 162 162
SREBF1 -0.039 0.1 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.047 0.13 -10000 0 -0.26 9 9
ABCA1 -0.041 0.1 -10000 0 -10000 0 0
RARs/THRs 0.05 0.077 -10000 0 -10000 0 0
RXRs/FXR -0.086 0.15 -10000 0 -0.35 41 41
BCL2 0.024 0.022 -10000 0 -0.38 1 1
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.037 0.02 -10000 0 -0.24 1 1
PDGFRB 0.004 0.091 -10000 0 -0.35 25 25
SPHK1 -0.006 0.074 -10000 0 -0.61 5 5
mol:S1P -0.01 0.067 -10000 0 -0.51 5 5
S1P1/S1P/Gi -0.05 0.15 -10000 0 -0.41 36 36
GNAO1 -0.057 0.16 -10000 0 -0.39 82 82
PDGFB-D/PDGFRB/PLCgamma1 -0.029 0.15 0.27 14 -0.38 28 42
PLCG1 -0.052 0.13 0.27 2 -0.4 29 31
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.091 -10000 0 -0.35 25 25
GNAI2 0.026 0.01 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.019 0.054 -10000 0 -0.39 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.002 0.014 -10000 0 -0.2 1 1
S1P1/S1P -0.001 0.059 -10000 0 -0.32 5 5
negative regulation of cAMP metabolic process -0.049 0.14 -10000 0 -0.4 36 36
MAPK3 -0.055 0.15 0.31 2 -0.45 30 32
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
KDR 0.028 0.005 -10000 0 -10000 0 0
PLCB2 0.011 0.076 0.22 13 -0.29 5 18
RAC1 0.026 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.051 -10000 0 -0.28 5 5
receptor internalization -0.002 0.055 -10000 0 -0.3 5 5
PTGS2 -0.057 0.18 0.38 1 -0.65 14 15
Rac1/GTP 0 0.05 -10000 0 -0.28 5 5
RHOA 0.027 0.006 -10000 0 -10000 0 0
VEGFA 0.025 0.02 -10000 0 -0.35 1 1
negative regulation of T cell proliferation -0.049 0.14 -10000 0 -0.4 36 36
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0 0.1 -10000 0 -0.39 26 26
MAPK1 -0.053 0.15 -10000 0 -0.46 27 27
S1P1/S1P/PDGFB-D/PDGFRB 0.013 0.09 0.24 13 -0.33 2 15
ABCC1 0.027 0.006 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.014 0.037 -10000 0 -0.22 2 2
NFATC2 -0.011 0.035 -10000 0 -0.22 3 3
NFATC3 -0.013 0.036 -10000 0 -10000 0 0
CD40LG -0.079 0.19 0.35 1 -0.52 27 28
PTGS2 -0.088 0.2 0.35 1 -0.52 40 41
JUNB 0.027 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.028 -10000 0 -10000 0 0
CaM/Ca2+ -0.005 0.028 -10000 0 -10000 0 0
CALM1 0.011 0.026 -10000 0 -10000 0 0
JUN 0.012 0.026 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.013 -10000 0 -10000 0 0
FOSL1 -0.001 0.1 -10000 0 -0.36 31 31
CREM 0.027 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.024 0.12 -10000 0 -0.34 5 5
FOS -0.009 0.093 -10000 0 -0.39 21 21
IFNG -0.11 0.22 0.35 1 -0.52 55 56
AP-1/NFAT1-c-4 -0.077 0.21 -10000 0 -0.57 27 27
FASLG -0.08 0.19 0.35 1 -0.53 29 30
NFAT1-c-4/ICER1 -0.023 0.07 -10000 0 -10000 0 0
IL2RA -0.086 0.2 0.35 1 -0.54 36 37
FKBP12/FK506 0.019 0.007 -10000 0 -10000 0 0
CSF2 -0.11 0.21 -10000 0 -0.53 49 49
JunB/Fra1/NFAT1-c-4 -0.01 0.1 -10000 0 -0.3 7 7
IL4 -0.082 0.18 -10000 0 -0.5 28 28
IL2 -0.017 0.16 -10000 0 -0.84 15 15
IL3 -0.025 0.14 -10000 0 -0.59 19 19
FKBP1A 0.025 0.009 -10000 0 -10000 0 0
BATF3 0.025 0.033 -10000 0 -0.35 3 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.021 -10000 0 -0.35 1 1
IL27-mediated signaling events

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
TGFB1 -0.056 0.18 -10000 0 -0.42 78 78
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.019 0.099 0.39 3 -10000 0 3
IL27/IL27R/JAK1 0.047 0.12 0.4 1 -0.41 1 2
TBX21 0.008 0.12 0.34 2 -0.43 1 3
IL12B 0.018 0.043 -10000 0 -0.36 5 5
IL12A -0.011 0.06 -10000 0 -0.27 21 21
IL6ST 0.016 0.041 -10000 0 -0.4 3 3
IL27RA/JAK1 0.019 0.041 -10000 0 -10000 0 0
IL27 0.005 0.071 -10000 0 -0.36 14 14
TYK2 0.016 0.023 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.24 0.51 0.43 4 -1.2 85 89
T-helper 2 cell differentiation 0.019 0.099 0.39 3 -10000 0 3
T cell proliferation during immune response 0.019 0.099 0.39 3 -10000 0 3
MAPKKK cascade -0.019 0.099 -10000 0 -0.39 3 3
STAT3 0.028 0.004 -10000 0 -10000 0 0
STAT2 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.02 0.059 -10000 0 -0.35 10 10
IL12RB1 0.022 0.041 -10000 0 -0.38 4 4
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.002 0.13 0.34 2 -0.42 6 8
IL27/IL27R/JAK2/TYK2 -0.019 0.098 -10000 0 -0.39 3 3
positive regulation of T cell mediated cytotoxicity -0.019 0.099 -10000 0 -0.39 3 3
STAT1 (dimer) 0.062 0.18 0.42 39 -10000 0 39
JAK2 0.014 0.022 -10000 0 -10000 0 0
JAK1 0.029 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.013 0.1 -10000 0 -0.4 2 2
T cell proliferation -0.07 0.12 -10000 0 -0.4 16 16
IL12/IL12R/TYK2/JAK2 -0.047 0.21 -10000 0 -0.78 28 28
IL17A -0.23 0.51 0.43 4 -1.2 84 88
mast cell activation 0.019 0.099 0.39 3 -10000 0 3
IFNG -0.011 0.037 -10000 0 -0.1 10 10
T cell differentiation -0.002 0.006 0.01 2 -0.017 12 14
STAT3 (dimer) -0.014 0.1 -10000 0 -0.37 4 4
STAT5A (dimer) -0.014 0.1 -10000 0 -0.37 4 4
STAT4 (dimer) -0.016 0.1 -10000 0 -0.36 4 4
STAT4 0.024 0.038 -10000 0 -0.35 4 4
T cell activation -0.005 0.005 0.048 2 -10000 0 2
IL27R/JAK2/TYK2 0.024 0.065 -10000 0 -10000 0 0
GATA3 0.014 0.12 0.65 12 -10000 0 12
IL18 0.001 0.026 -10000 0 -0.25 4 4
positive regulation of mast cell cytokine production -0.013 0.1 -10000 0 -0.36 4 4
IL27/EBI3 0.013 0.074 -10000 0 -0.26 24 24
IL27RA 0.004 0.034 -10000 0 -10000 0 0
IL6 -0.095 0.22 -10000 0 -0.44 108 108
STAT5A 0.028 0.004 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.011 0.026 -10000 0 -10000 0 0
IL1B -0.022 0.077 -10000 0 -0.25 41 41
EBI3 0.011 0.064 -10000 0 -0.37 10 10
TNF -0.008 0.052 -10000 0 -0.25 18 18
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.028 0.004 -10000 0 -10000 0 0
PTK2 0.024 0.01 -10000 0 -10000 0 0
CRKL -0.006 0.063 0.16 2 -0.21 24 26
GRB2/SOS1/SHC 0.053 0.015 -10000 0 -10000 0 0
HRAS 0.026 0.007 -10000 0 -10000 0 0
IRS1/Crk 0.002 0.065 -10000 0 -0.2 25 25
IGF-1R heterotetramer/IGF1/PTP1B 0.016 0.078 -10000 0 -0.2 41 41
AKT1 -0.013 0.07 0.19 21 -0.32 1 22
BAD -0.014 0.067 0.18 21 -0.31 1 22
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.005 0.06 0.16 2 -0.21 20 22
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.008 0.07 0.21 2 -0.21 25 27
RAF1 0.004 0.08 0.3 3 -0.42 4 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.033 0.077 -10000 0 -0.2 23 23
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.008 0.074 -10000 0 -0.19 49 49
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.013 0.07 0.18 22 -0.32 1 23
GNB2L1 0.027 0.005 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.005 0.075 0.33 5 -0.33 1 6
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.009 0.061 -10000 0 -0.3 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.045 0.081 -10000 0 -0.34 1 1
IGF-1R heterotetramer 0.016 0.041 -10000 0 -0.4 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck 0.022 0.076 -10000 0 -0.21 25 25
Crk/p130 Cas/Paxillin 0.032 0.074 0.22 2 -0.19 19 21
IGF1R 0.016 0.041 -10000 0 -0.4 2 2
IGF1 -0.021 0.13 -10000 0 -0.38 51 51
IRS2/Crk -0.004 0.07 0.16 1 -0.2 30 31
PI3K 0.029 0.076 -10000 0 -0.2 20 20
apoptosis 0.011 0.058 0.27 1 -0.25 3 4
HRAS/GDP 0.02 0.005 -10000 0 -10000 0 0
PRKCD -0.012 0.083 -10000 0 -0.31 22 22
RAF1/14-3-3 E 0.013 0.082 0.31 3 -0.35 5 8
BAD/14-3-3 -0.012 0.06 0.26 3 -0.29 1 4
PRKCZ -0.012 0.069 0.18 21 -0.32 1 22
Crk/p130 Cas/Paxillin/FAK1 0.017 0.059 -10000 0 -0.26 1 1
PTPN1 0.022 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.011 0.091 -10000 0 -0.3 29 29
BCAR1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.033 0.08 -10000 0 -0.2 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.01 0.072 -10000 0 -0.2 25 25
GRB10 0.026 0.02 -10000 0 -0.35 1 1
PTPN11 -0.007 0.064 0.16 2 -0.21 25 27
IRS1 -0.005 0.07 -10000 0 -0.19 47 47
IRS2 -0.013 0.07 0.16 1 -0.21 35 36
IGF-1R heterotetramer/IGF1 0.001 0.1 -10000 0 -0.27 49 49
GRB2 0.027 0.005 -10000 0 -10000 0 0
PDPK1 0.003 0.072 0.19 19 -0.33 1 20
YWHAE 0.026 0.008 -10000 0 -10000 0 0
PRKD1 -0.017 0.094 -10000 0 -0.33 27 27
SHC1 0.027 0.005 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.082 0.18 -10000 0 -0.38 110 110
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.007 -10000 0 -10000 0 0
TCEB1 0.024 0.01 -10000 0 -10000 0 0
HIF1A/p53 0.022 0.056 -10000 0 -0.24 14 14
HIF1A 0.006 0.051 -10000 0 -0.26 13 13
COPS5 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.064 0.036 -10000 0 -10000 0 0
FIH (dimer) 0.027 0.006 -10000 0 -10000 0 0
CDKN2A -0.088 0.17 -10000 0 -0.35 121 121
ARNT/IPAS -0.039 0.13 -10000 0 -0.27 103 103
HIF1AN 0.027 0.006 -10000 0 -10000 0 0
GNB2L1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.057 -10000 0 -0.25 14 14
CUL2 0.027 0.006 -10000 0 -10000 0 0
OS9 0.027 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.046 0.023 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.022 0.058 -10000 0 -0.25 13 13
PHD1-3/OS9 0.063 0.028 -10000 0 -0.21 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.037 0.058 -10000 0 -0.24 7 7
VHL 0.028 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
HIF1A/JAB1 0.018 0.057 0.18 1 -0.25 14 15
EGLN3 0.026 0.021 -10000 0 -0.38 1 1
EGLN2 0.027 0.006 -10000 0 -10000 0 0
EGLN1 0.027 0.005 -10000 0 -10000 0 0
TP53 0.026 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.028 0.078 -10000 0 -0.5 8 8
ARNT 0.027 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p19ARF -0.029 0.096 -10000 0 -0.31 18 18
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.01 0.08 -10000 0 -0.35 19 19
ANTXR2 0.024 0.035 -10000 0 -0.38 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.01 -10000 0 -0.044 22 22
monocyte activation 0.001 0.079 -10000 0 -0.35 18 18
MAP2K2 -0.018 0.14 -10000 0 -0.56 24 24
MAP2K1 -0.005 0.009 -10000 0 -10000 0 0
MAP2K7 -0.005 0.009 -10000 0 -10000 0 0
MAP2K6 -0.008 0.024 -10000 0 -0.19 6 6
CYAA -0.014 0.038 -10000 0 -0.17 22 22
MAP2K4 -0.005 0.009 -10000 0 -10000 0 0
IL1B -0.02 0.055 0.19 3 -0.17 40 43
Channel 0.022 0.05 -10000 0 -0.19 22 22
NLRP1 -0.008 0.024 -10000 0 -0.17 7 7
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.072 -10000 0 -0.38 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.01 0.044 22 -10000 0 22
MAPK3 -0.005 0.009 -10000 0 -10000 0 0
MAPK1 -0.005 0.009 -10000 0 -10000 0 0
PGR -0.022 0.055 -10000 0 -0.19 38 38
PA/Cellular Receptors 0.023 0.056 -10000 0 -0.21 22 22
apoptosis -0.003 0.01 -10000 0 -0.044 22 22
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.023 0.045 -10000 0 -0.16 22 22
macrophage activation -0.007 0.009 -10000 0 -10000 0 0
TNF 0.01 0.08 -10000 0 -0.36 18 18
VCAM1 0.005 0.069 -10000 0 -0.34 14 14
platelet activation -0.003 0.072 -10000 0 -0.38 14 14
MAPKKK cascade 0.003 0.016 -10000 0 -0.067 6 6
IL18 -0.006 0.024 0.19 1 -0.17 4 5
negative regulation of macrophage activation -0.003 0.01 -10000 0 -0.044 22 22
LEF -0.003 0.01 -10000 0 -0.045 22 22
CASP1 -0.003 0.014 -10000 0 -0.089 6 6
mol:cAMP -0.003 0.072 -10000 0 -0.38 14 14
necrosis -0.003 0.01 -10000 0 -0.044 22 22
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.022 0.047 -10000 0 -0.18 22 22
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
PLK1 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
regulation of centriole-centriole cohesion -0.003 0.028 0.11 15 -0.1 1 16
BUB1B -0.006 0.057 0.12 6 -0.14 23 29
PLK1 0.013 0.029 0.083 26 -0.096 1 27
PLK1S1 0.016 0.036 0.12 7 -0.2 5 12
KIF2A 0.009 0.029 0.16 5 -10000 0 5
regulation of mitotic centrosome separation 0.013 0.029 0.083 26 -0.096 1 27
GOLGA2 0.027 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.033 0.051 -10000 0 -0.18 13 13
WEE1 0.014 0.062 0.18 2 -0.33 10 12
cytokinesis 0.006 0.058 0.15 2 -0.22 8 10
PP2A-alpha B56 0.035 0.091 -10000 0 -0.53 7 7
AURKA 0.015 0.025 0.11 3 -10000 0 3
PICH/PLK1 0.009 0.039 0.15 2 -0.19 4 6
CENPE -0.05 0.087 -10000 0 -0.17 120 120
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.01 0.03 0.16 5 -10000 0 5
PPP2CA 0.026 0.007 -10000 0 -10000 0 0
FZR1 0.026 0.007 -10000 0 -10000 0 0
TPX2 0.017 0.035 0.1 31 -10000 0 31
PAK1 0.028 0.006 -10000 0 -10000 0 0
SPC24 0.024 0.033 -10000 0 -0.35 3 3
FBXW11 0.027 0.006 -10000 0 -10000 0 0
CLSPN -0.013 0.053 0.15 1 -0.23 7 8
GORASP1 0.027 0.005 -10000 0 -10000 0 0
metaphase 0.001 0.003 0.016 15 -0.009 1 16
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.016 0.046 28 -0.047 1 29
G2 phase of mitotic cell cycle 0 0.003 0.013 12 -10000 0 12
STAG2 0.027 0.005 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.006 0.088 -10000 0 -0.49 12 12
spindle elongation 0.013 0.029 0.083 26 -0.096 1 27
ODF2 0.028 0.007 -10000 0 -10000 0 0
BUB1 0.006 0.087 -10000 0 -0.57 7 7
TPT1 0.014 0.031 0.1 10 -0.19 5 15
CDC25C 0.003 0.06 -10000 0 -0.25 19 19
CDC25B 0.022 0.029 -10000 0 -0.35 2 2
SGOL1 0.003 0.028 0.1 1 -0.11 15 16
RHOA 0.027 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.031 0.039 -10000 0 -10000 0 0
CDC14B 0.007 0.003 -10000 0 -10000 0 0
CDC20 0.021 0.049 -10000 0 -0.35 7 7
PLK1/PBIP1 0.009 0.023 0.092 3 -0.16 1 4
mitosis -0.001 0.004 0.017 12 -10000 0 12
FBXO5 0.011 0.034 0.13 13 -0.12 3 16
CDC2 0.001 0.002 -10000 0 -0.01 7 7
NDC80 0.013 0.071 -10000 0 -0.35 15 15
metaphase plate congression 0 0.066 -10000 0 -0.23 29 29
ERCC6L 0.008 0.044 -10000 0 -0.21 4 4
NLP/gamma Tubulin 0.009 0.018 0.076 11 -0.08 1 12
microtubule cytoskeleton organization 0.014 0.031 0.1 10 -0.19 5 15
G2/M transition DNA damage checkpoint 0 0.002 0.018 3 -10000 0 3
PPP1R12A 0.027 0.019 -10000 0 -0.35 1 1
interphase 0 0.002 0.018 3 -10000 0 3
PLK1/PRC1-2 0.026 0.061 -10000 0 -0.19 17 17
GRASP65/GM130/RAB1/GTP/PLK1 0.05 0.03 -10000 0 -10000 0 0
RAB1A 0.028 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.014 0.03 0.081 36 -0.075 1 37
mitotic prometaphase 0 0.005 0.017 29 -10000 0 29
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.031 0.17 1 -0.26 1 2
microtubule-based process 0.015 0.054 0.13 2 -0.17 25 27
Golgi organization 0.013 0.029 0.083 26 -0.096 1 27
Cohesin/SA2 0.025 0.024 0.11 3 -10000 0 3
PPP1CB/MYPT1 0.04 0.017 -10000 0 -0.25 1 1
KIF20A 0.004 0.091 -10000 0 -0.35 25 25
APC/C/CDC20 0.024 0.041 0.12 3 -0.21 7 10
PPP2R1A 0.027 0.006 -10000 0 -10000 0 0
chromosome segregation 0.009 0.023 0.091 3 -0.16 1 4
PRC1 0.021 0.046 -10000 0 -0.35 6 6
ECT2 -0.014 0.1 0.21 31 -0.18 81 112
C13orf34 0.012 0.026 0.075 28 -10000 0 28
NUDC 0 0.066 -10000 0 -0.23 29 29
regulation of attachment of spindle microtubules to kinetochore -0.006 0.056 0.12 6 -0.14 23 29
spindle assembly 0.011 0.026 0.094 16 -10000 0 16
spindle stabilization 0.016 0.036 0.12 7 -0.2 5 12
APC/C/HCDH1 0.024 0.008 -10000 0 -10000 0 0
MKLP2/PLK1 0.015 0.054 0.13 2 -0.17 25 27
CCNB1 0.024 0.033 -10000 0 -0.35 3 3
PPP1CB 0.028 0.003 -10000 0 -10000 0 0
BTRC 0.027 0.006 -10000 0 -10000 0 0
ROCK2 0.016 0.046 0.16 1 -0.28 5 6
TUBG1 0.013 0.022 0.15 1 -0.18 2 3
G2/M transition of mitotic cell cycle 0.002 0.03 -10000 0 -10000 0 0
MLF1IP 0.005 0.013 -10000 0 -0.25 1 1
INCENP 0.028 0.004 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.091 -9999 0 -0.35 25 25
mol:S1P 0.001 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.031 0.11 -9999 0 -0.28 36 36
GNAO1 -0.054 0.16 -9999 0 -0.38 82 82
S1P/S1P3/G12/G13 0.046 0.03 -9999 0 -0.2 4 4
AKT1 -0.016 0.11 -9999 0 -0.44 21 21
AKT3 0.006 0.071 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.091 -9999 0 -0.35 25 25
GNAI2 0.028 0.006 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.02 0.054 -9999 0 -0.38 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.024 0.039 -9999 0 -0.37 4 4
S1PR2 0.026 0.019 -9999 0 -0.35 1 1
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.028 0.12 -9999 0 -0.37 25 25
MAPK3 -0.033 0.11 -9999 0 -0.34 25 25
MAPK1 -0.029 0.11 -9999 0 -0.36 20 20
JAK2 -0.03 0.13 -9999 0 -0.37 29 29
CXCR4 -0.044 0.12 -9999 0 -0.34 29 29
FLT1 0.027 0.02 -9999 0 -0.35 1 1
RhoA/GDP 0.02 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.006 -9999 0 -10000 0 0
SRC -0.03 0.11 -9999 0 -0.36 23 23
S1P/S1P3/Gi -0.028 0.12 -9999 0 -0.37 25 25
RAC1 0.026 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.024 0.12 -9999 0 -0.33 28 28
VEGFA 0.026 0.021 -9999 0 -0.35 1 1
S1P/S1P2/Gi -0.029 0.12 -9999 0 -0.35 26 26
VEGFR1 homodimer/VEGFA homodimer 0.039 0.022 -9999 0 -0.24 1 1
RHOA 0.027 0.006 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.018 0.04 -9999 0 -0.23 8 8
GNAQ 0.027 0.006 -9999 0 -10000 0 0
GNAZ 0.002 0.1 -9999 0 -0.38 26 26
G12/G13 0.038 0.013 -9999 0 -10000 0 0
GNA14 0.02 0.053 -9999 0 -0.38 7 7
GNA15 0.022 0.042 -9999 0 -0.35 5 5
GNA12 0.026 0.008 -9999 0 -10000 0 0
GNA13 0.027 0.005 -9999 0 -10000 0 0
GNA11 0.026 0.007 -9999 0 -10000 0 0
Rac1/GTP -0.023 0.12 -9999 0 -0.34 26 26
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.047 0.074 -10000 0 -0.24 21 21
MAP4K1 0.013 0.073 -10000 0 -0.37 14 14
MAP3K8 0.026 0.02 -10000 0 -0.35 1 1
PRKCB 0.003 0.096 -10000 0 -0.38 24 24
DBNL 0.026 0.007 -10000 0 -10000 0 0
CRKL 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 0.008 0.06 -10000 0 -0.31 9 9
JUN -0.032 0.19 -10000 0 -0.57 42 42
MAP3K7 0.009 0.062 -10000 0 -0.32 9 9
GRAP2 0.016 0.067 -10000 0 -0.38 11 11
CRK 0.026 0.008 -10000 0 -10000 0 0
MAP2K4 0.008 0.066 0.27 1 -0.32 8 9
LAT 0.026 0.019 -10000 0 -0.35 1 1
LCP2 0.027 0.006 -10000 0 -10000 0 0
MAPK8 -0.031 0.2 -10000 0 -0.6 42 42
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.017 0.064 -10000 0 -0.32 9 9
LAT/GRAP2/SLP76/HPK1/HIP-55 0.056 0.07 -10000 0 -0.27 10 10
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 0.004 0.091 -10000 0 -0.35 25 25
Jak2/Leptin Receptor -0.032 0.14 -10000 0 -0.41 25 25
PTP1B/AKT1 0.001 0.073 -10000 0 -0.32 4 4
FYN 0.027 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.008 0.074 -10000 0 -0.32 5 5
EGFR 0.016 0.058 -10000 0 -0.39 8 8
EGF/EGFR -0.014 0.087 -10000 0 -0.29 9 9
CSF1 0.026 0.019 -10000 0 -0.35 1 1
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.027 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.014 0.084 -10000 0 -0.4 4 4
Insulin Receptor/Insulin 0.012 0.072 -10000 0 -0.29 2 2
HCK 0.024 0.01 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
TYK2 -0.008 0.071 0.32 1 -0.31 5 6
EGF -0.018 0.12 -10000 0 -0.36 44 44
YES1 0.026 0.007 -10000 0 -10000 0 0
CAV1 0.003 0.088 0.22 13 -0.32 7 20
TXN 0.027 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.007 0.081 -10000 0 -0.32 4 4
cell migration 0.008 0.074 0.32 5 -10000 0 5
STAT3 0.027 0.004 -10000 0 -10000 0 0
PRLR -0.012 0.12 -10000 0 -0.38 36 36
ITGA2B 0.014 0.067 -10000 0 -0.36 13 13
CSF1R 0.023 0.041 -10000 0 -0.38 4 4
Prolactin Receptor/Prolactin -0.002 0.098 -10000 0 -0.27 45 45
FGR 0.027 0.006 -10000 0 -10000 0 0
PTP1B/p130 Cas 0 0.073 -10000 0 -0.3 5 5
Crk/p130 Cas 0.006 0.077 -10000 0 -0.3 4 4
DOK1 -0.01 0.076 -10000 0 -0.34 5 5
JAK2 -0.043 0.14 -10000 0 -0.4 31 31
Jak2/Leptin Receptor/Leptin -0.022 0.1 -10000 0 -0.37 4 4
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
PTPN1 -0.008 0.074 -10000 0 -0.33 5 5
LYN 0.025 0.009 -10000 0 -10000 0 0
CDH2 -0.005 0.11 -10000 0 -0.37 32 32
SRC 0.015 0.079 -10000 0 -0.51 7 7
ITGB3 0.023 0.043 -10000 0 -0.36 5 5
CAT1/PTP1B -0.042 0.15 0.25 16 -0.42 23 39
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.065 -10000 0 -0.3 1 1
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.015 0.096 -10000 0 -0.35 3 3
negative regulation of transcription -0.043 0.13 -10000 0 -0.39 32 32
FCGR2A 0.022 0.046 -10000 0 -0.35 6 6
FER 0.025 0.009 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.027 0.06 -10000 0 -0.25 18 18
BLK -0.041 0.15 -10000 0 -0.38 66 66
Insulin Receptor/Insulin/Shc 0.046 0.017 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
LEPR 0.025 0.034 -10000 0 -0.37 3 3
BCAR1 0.027 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.027 0.005 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.057 0.17 0.28 4 -0.45 34 38
PRL 0.003 0.07 -10000 0 -0.36 14 14
SOCS3 0.018 0.12 -10000 0 -1 5 5
SPRY2 0.026 0.022 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/IRS1 0.046 0.021 -10000 0 -0.24 1 1
CSF1/CSF1R 0.006 0.081 -10000 0 -0.32 3 3
Ras protein signal transduction 0.004 0.066 0.51 6 -10000 0 6
IRS1 0.027 0.021 -10000 0 -0.38 1 1
INS 0.015 0.012 -10000 0 -10000 0 0
LEP -0.015 0.12 -10000 0 -0.38 41 41
STAT5B -0.015 0.087 -10000 0 -0.34 12 12
STAT5A -0.015 0.087 -10000 0 -0.34 12 12
GRB2 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.01 0.088 -10000 0 -0.3 6 6
CSN2 -0.008 0.072 -10000 0 -0.42 1 1
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
LAT 0.015 0.067 -10000 0 -0.44 6 6
YBX1 0.035 0.007 -10000 0 -10000 0 0
LCK 0.017 0.062 -10000 0 -0.35 11 11
SHC1 0.027 0.005 -10000 0 -10000 0 0
NOX4 -0.14 0.19 -10000 0 -0.35 179 179
Nectin adhesion 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
PDGFRB 0.004 0.091 -10000 0 -0.35 25 25
alphaV beta3 Integrin 0.035 0.033 -10000 0 -0.25 5 5
PTK2 0.014 0.074 -10000 0 -0.36 7 7
positive regulation of JNK cascade 0.012 0.084 -10000 0 -0.32 5 5
CDC42/GDP 0.038 0.12 0.3 2 -0.39 10 12
Rac1/GDP 0.035 0.11 0.31 2 -0.39 10 12
RAP1B 0.027 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.026 0.11 -10000 0 -0.4 5 5
nectin-3/I-afadin 0.027 0.061 -10000 0 -0.27 16 16
RAPGEF1 0.022 0.1 0.3 5 -0.41 6 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.007 0.098 -10000 0 -0.45 7 7
PDGFB-D/PDGFRB 0.004 0.091 -10000 0 -0.35 25 25
TLN1 -0.001 0.02 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.072 -10000 0 -0.3 6 6
IQGAP1 0.026 0.007 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.018 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.027 0.061 -10000 0 -0.27 16 16
PVR 0.026 0.02 -10000 0 -0.35 1 1
Necl-5(dimer) 0.026 0.02 -10000 0 -0.35 1 1
mol:GDP 0.027 0.13 0.32 2 -0.48 10 12
MLLT4 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.043 0.081 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.026 0.056 -10000 0 -0.25 16 16
positive regulation of lamellipodium assembly 0.017 0.088 -10000 0 -0.31 11 11
PVRL1 0.012 0.074 -10000 0 -0.35 16 16
PVRL3 0.011 0.08 -10000 0 -0.38 16 16
PVRL2 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
CDH1 0.018 0.06 -10000 0 -0.38 9 9
CLDN1 -0.24 0.17 -10000 0 -0.35 288 288
JAM-A/CLDN1 -0.12 0.12 -10000 0 -0.3 15 15
SRC 0.007 0.11 -10000 0 -0.49 8 8
ITGB3 0.023 0.042 -10000 0 -0.36 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.026 0.056 -10000 0 -0.25 16 16
FARP2 0.022 0.14 -10000 0 -0.56 5 5
RAC1 0.026 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.039 0.056 -10000 0 -0.23 15 15
nectin-1/I-afadin 0.026 0.056 -10000 0 -0.25 16 16
nectin-2/I-afadin 0.038 0.013 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.033 0.071 -10000 0 -0.23 25 25
CDC42/GTP/IQGAP1/filamentous actin 0.034 0.012 -10000 0 -10000 0 0
F11R 0.027 0.005 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.012 0.084 -10000 0 -0.32 5 5
alphaV/beta3 Integrin/Talin 0.033 0.059 0.2 15 -10000 0 15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.013 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.013 -10000 0 -10000 0 0
PIP5K1C 0.001 0.031 -10000 0 -0.33 1 1
VAV2 0.027 0.14 -10000 0 -0.52 9 9
RAP1/GDP 0.04 0.1 0.27 2 -0.36 8 10
ITGAV 0.026 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.041 0.053 -10000 0 -0.23 13 13
nectin-3(dimer)/I-afadin/I-afadin 0.027 0.061 -10000 0 -0.27 16 16
Rac1/GTP 0.025 0.11 -10000 0 -0.38 11 11
PTPRM 0.006 0.036 -10000 0 -0.36 1 1
E-cadherin/beta catenin/alpha catenin 0.051 0.067 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.026 0.007 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.014 -10000 0 -0.25 1 1
MAP4K4 0.015 0.054 0.2 5 -0.39 2 7
BAG4 0.025 0.009 -10000 0 -10000 0 0
PKC zeta/ceramide -0.004 0.067 -10000 0 -0.2 36 36
NFKBIA 0.028 0.004 -10000 0 -10000 0 0
BIRC3 0.021 0.047 -10000 0 -0.36 6 6
BAX -0.006 0.068 -10000 0 -0.36 12 12
RIPK1 0.026 0.007 -10000 0 -10000 0 0
AKT1 -0.005 0.011 -10000 0 -10000 0 0
BAD -0.02 0.065 0.2 3 -0.2 38 41
SMPD1 0.014 0.067 0.18 13 -0.27 9 22
RB1 -0.009 0.073 0.19 18 -0.2 30 48
FADD/Caspase 8 0.023 0.076 0.22 17 -0.48 3 20
MAP2K4 -0.022 0.057 -10000 0 -0.2 21 21
NSMAF 0.025 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.017 0.062 0.19 7 -0.24 8 15
EGF -0.016 0.12 -10000 0 -0.36 44 44
mol:ceramide -0.02 0.066 -10000 0 -0.21 38 38
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.014 -10000 0 -0.25 1 1
ASAH1 0.025 0.01 -10000 0 -10000 0 0
negative regulation of cell cycle -0.009 0.072 0.19 18 -0.2 30 48
cell proliferation -0.012 0.085 0.19 2 -0.29 7 9
BID -0.004 0.16 -10000 0 -0.67 19 19
MAP3K1 -0.021 0.061 -10000 0 -0.2 37 37
EIF2A -0.014 0.069 0.17 17 -0.27 6 23
TRADD 0.027 0.006 -10000 0 -10000 0 0
CRADD 0.028 0.004 -10000 0 -10000 0 0
MAPK3 -0.015 0.061 0.19 3 -0.26 4 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.062 0.19 3 -0.26 6 9
Cathepsin D/ceramide -0.004 0.069 -10000 0 -0.2 38 38
FADD 0.021 0.062 0.21 17 -0.39 2 19
KSR1 -0.018 0.062 0.2 4 -0.2 36 40
MAPK8 -0.016 0.071 -10000 0 -0.28 12 12
PRKRA -0.02 0.065 0.19 3 -0.2 38 41
PDGFA 0.025 0.02 -10000 0 -0.35 1 1
TRAF2 0.027 0.006 -10000 0 -10000 0 0
IGF1 -0.022 0.13 -10000 0 -0.37 51 51
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.02 0.066 -10000 0 -0.21 38 38
CTSD 0.027 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.04 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.012 0.09 0.21 2 -0.31 7 9
PRKCD 0.027 0.005 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.014 -10000 0 -0.25 1 1
RelA/NF kappa B1 0.04 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.017 0.041 -10000 0 -0.41 2 2
TNFR1A/BAG4/TNF-alpha 0.036 0.054 -10000 0 -0.21 16 16
mol:Sphingosine-1-phosphate 0.011 0.013 -10000 0 -0.25 1 1
MAP2K1 -0.018 0.06 0.18 4 -0.24 7 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS 0.004 0.05 0.22 1 -0.21 8 9
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.036 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.019 0.064 0.18 7 -0.2 24 31
TNF-alpha/TNFR1A/FAN 0.036 0.055 -10000 0 -0.21 16 16
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.053 -10000 0 -0.32 4 4
MAP2K2 -0.019 0.059 0.19 3 -0.24 6 9
SMPD3 0 0.091 0.26 3 -0.3 27 30
TNF 0.01 0.08 -10000 0 -0.36 18 18
PKC zeta/PAR4 0.038 0.012 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.004 0.056 0.19 5 -0.19 3 8
NF kappa B1/RelA/I kappa B alpha 0.072 0.029 -10000 0 -10000 0 0
AIFM1 -0.001 0.057 0.14 4 -0.23 9 13
BCL2 0.024 0.022 -10000 0 -0.38 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.017 0.025 -10000 0 -0.27 1 1
CRKL 0.027 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DOCK1 0.027 0.006 -10000 0 -10000 0 0
ITGA4 0.025 0.033 -10000 0 -0.35 3 3
alpha4/beta7 Integrin/MAdCAM1 -0.013 0.12 -10000 0 -0.21 112 112
EPO 0.013 0.055 -10000 0 -0.35 9 9
alpha4/beta7 Integrin 0.036 0.03 -10000 0 -0.25 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.03 -10000 0 -0.25 4 4
EPO/EPOR (dimer) 0.028 0.042 -10000 0 -0.24 9 9
lamellipodium assembly 0.016 0.069 -10000 0 -0.5 4 4
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.036 0.014 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
JAK2 0.016 0.032 -10000 0 -0.27 2 2
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
MADCAM1 -0.086 0.18 -10000 0 -0.38 113 113
cell adhesion -0.014 0.12 -10000 0 -0.21 112 112
CRKL/CBL 0.038 0.012 -10000 0 -10000 0 0
ITGB1 0.026 0.02 -10000 0 -0.35 1 1
SRC 0.013 0.038 0.18 10 -10000 0 10
ITGB7 0.026 0.021 -10000 0 -0.38 1 1
RAC1 0.026 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.047 0.038 -10000 0 -0.21 7 7
p130Cas/Crk/Dock1 0.042 0.05 -10000 0 -10000 0 0
VCAM1 0.025 0.033 -10000 0 -0.35 3 3
RHOA 0.027 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.034 -10000 0 -0.19 4 4
BCAR1 -0.009 0.036 0.18 9 -10000 0 9
EPOR 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.027 0.006 -10000 0 -10000 0 0
GIT1 0.028 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.07 -10000 0 -0.52 4 4
ceramide signaling pathway

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.006 0.11 0.22 5 -0.49 12 17
BAG4 0.025 0.009 -10000 0 -10000 0 0
BAD 0.009 0.043 0.16 7 -0.18 7 14
NFKBIA 0.028 0.004 -10000 0 -10000 0 0
BIRC3 0.021 0.047 -10000 0 -0.36 6 6
BAX 0.012 0.049 0.18 14 -0.18 6 20
EnzymeConsortium:3.1.4.12 0.005 0.026 0.07 9 -0.1 11 20
IKBKB 0.017 0.11 0.25 9 -0.5 9 18
MAP2K2 0.009 0.048 0.19 12 -0.25 2 14
MAP2K1 0.009 0.049 0.19 13 -0.24 2 15
SMPD1 0.006 0.034 0.1 6 -0.17 8 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.021 0.11 0.22 19 -0.52 10 29
MAP2K4 0.009 0.035 0.15 4 -0.24 2 6
protein ubiquitination 0.014 0.11 0.24 5 -0.5 11 16
EnzymeConsortium:2.7.1.37 0.009 0.052 0.19 14 -0.28 2 16
response to UV 0 0.001 0.002 15 -0.002 2 17
RAF1 0.01 0.051 0.2 12 -0.22 4 16
CRADD 0.028 0.004 -10000 0 -10000 0 0
mol:ceramide 0.01 0.043 0.12 9 -0.17 10 19
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.008 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.008 0.04 0.14 5 -0.2 5 10
TRADD 0.027 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.011 0.053 0.19 13 -0.29 2 15
MAPK1 0.01 0.055 0.19 12 -0.28 3 15
p50/RELA/I-kappa-B-alpha 0.04 0.009 -10000 0 -10000 0 0
FADD 0.014 0.11 0.21 19 -0.5 10 29
KSR1 0.011 0.049 0.19 11 -0.21 5 16
MAPK8 0.007 0.041 0.21 4 -0.22 2 6
TRAF2 0.027 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 4 -10000 0 4
CHUK 0.011 0.098 0.22 3 -0.48 10 13
TNF R/SODD 0.036 0.015 -10000 0 -10000 0 0
TNF 0.01 0.08 -10000 0 -0.36 18 18
CYCS 0.021 0.052 0.16 23 -0.17 3 26
IKBKG 0.013 0.11 0.24 6 -0.49 10 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.006 0.11 -10000 0 -0.54 11 11
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.026 0.007 -10000 0 -10000 0 0
AIFM1 0.017 0.048 0.15 21 -0.17 3 24
TNF/TNF R/SODD 0.036 0.054 -10000 0 -0.21 16 16
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 4 -10000 0 4
CASP8 0.023 0.084 -10000 0 -0.62 6 6
NSMAF 0.017 0.11 0.21 27 -0.47 11 38
response to hydrogen peroxide 0 0.001 0.002 15 -0.002 2 17
BCL2 0.024 0.022 -10000 0 -0.38 1 1
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.066 0.14 -10000 0 -0.54 17 17
MKNK1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 -0.045 0.096 -10000 0 -0.26 19 19
ATF2/c-Jun -0.03 0.066 -10000 0 -0.34 1 1
MAPK11 -0.048 0.097 -10000 0 -0.28 20 20
MITF -0.052 0.11 -10000 0 -0.38 16 16
MAPKAPK5 -0.047 0.093 -10000 0 -0.32 11 11
KRT8 -0.047 0.097 -10000 0 -0.35 12 12
MAPKAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.06 0.13 -10000 0 -0.37 18 18
CEBPB -0.038 0.083 -10000 0 -0.33 7 7
SLC9A1 -0.046 0.091 -10000 0 -0.32 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.046 0.094 -10000 0 -0.32 9 9
p38alpha-beta/MNK1 -0.035 0.11 -10000 0 -0.3 18 18
JUN -0.03 0.065 -10000 0 -0.34 1 1
PPARGC1A -0.067 0.12 -10000 0 -0.38 24 24
USF1 -0.046 0.093 -10000 0 -0.32 11 11
RAB5/GDP/GDI1 -0.03 0.072 -10000 0 -0.24 9 9
NOS2 -0.12 0.19 -10000 0 -0.51 30 30
DDIT3 -0.047 0.093 -10000 0 -0.28 22 22
RAB5A 0.028 0.004 -10000 0 -10000 0 0
HSPB1 -0.034 0.092 0.28 11 -0.3 11 22
p38alpha-beta/HBP1 -0.035 0.11 -10000 0 -0.3 18 18
CREB1 -0.04 0.091 -10000 0 -0.34 11 11
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.046 0.084 -10000 0 -0.29 7 7
RPS6KA4 -0.045 0.092 -10000 0 -0.28 21 21
PLA2G4A -0.052 0.092 -10000 0 -0.34 11 11
GDI1 -0.046 0.092 -10000 0 -0.32 10 10
TP53 -0.063 0.1 -10000 0 -0.34 20 20
RPS6KA5 -0.047 0.093 -10000 0 -0.32 11 11
ESR1 -0.056 0.1 -10000 0 -0.34 16 16
HBP1 0.027 0.006 -10000 0 -10000 0 0
MEF2C -0.05 0.098 -10000 0 -0.34 14 14
MEF2A -0.044 0.09 -10000 0 -0.32 10 10
EIF4EBP1 -0.043 0.097 -10000 0 -0.38 10 10
KRT19 -0.046 0.1 -10000 0 -0.36 14 14
ELK4 -0.045 0.092 -10000 0 -0.32 10 10
ATF6 -0.046 0.093 -10000 0 -0.32 11 11
ATF1 -0.041 0.091 -10000 0 -0.34 11 11
p38alpha-beta/MAPKAPK2 -0.036 0.11 -10000 0 -0.3 17 17
p38alpha-beta/MAPKAPK3 -0.036 0.11 -10000 0 -0.3 18 18
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.027 0.14 -10000 0 -0.41 45 45
NFATC2 0.01 0.1 -10000 0 -0.52 1 1
NFATC3 -0.013 0.065 -10000 0 -0.27 7 7
CD40LG -0.14 0.25 -10000 0 -0.8 21 21
ITCH 0.021 0.034 -10000 0 -10000 0 0
CBLB 0.024 0.036 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.21 -10000 0 -0.71 20 20
JUNB 0.027 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.043 -10000 0 -0.24 8 8
T cell anergy 0.026 0.066 -10000 0 -0.35 9 9
TLE4 0.002 0.091 -10000 0 -0.64 5 5
Jun/NFAT1-c-4/p21SNFT -0.05 0.19 -10000 0 -0.76 10 10
AP-1/NFAT1-c-4 -0.15 0.27 -10000 0 -0.86 19 19
IKZF1 -0.001 0.085 -10000 0 -0.37 4 4
T-helper 2 cell differentiation -0.024 0.11 -10000 0 -0.56 2 2
AP-1/NFAT1 -0.023 0.11 -10000 0 -0.39 6 6
CALM1 0.032 0.029 -10000 0 -10000 0 0
EGR2 -0.023 0.16 -10000 0 -1 6 6
EGR3 -0.03 0.2 -10000 0 -1.1 11 11
NFAT1/FOXP3 -0.013 0.15 -10000 0 -0.46 22 22
EGR1 0.015 0.065 -10000 0 -0.38 10 10
JUN -0.018 0.045 -10000 0 -10000 0 0
EGR4 -0.042 0.15 -10000 0 -0.36 74 74
mol:Ca2+ 0.005 0.023 -10000 0 -10000 0 0
GBP3 0.003 0.082 -10000 0 -0.62 3 3
FOSL1 -0.001 0.1 -10000 0 -0.36 31 31
NFAT1-c-4/MAF/IRF4 -0.018 0.17 -10000 0 -0.78 9 9
DGKA 0.006 0.063 -10000 0 -10000 0 0
CREM 0.026 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.026 0.17 -10000 0 -0.77 10 10
CTLA4 -0.042 0.16 -10000 0 -0.46 40 40
NFAT1-c-4 (dimer)/EGR1 -0.027 0.18 -10000 0 -0.85 10 10
NFAT1-c-4 (dimer)/EGR4 -0.051 0.18 -10000 0 -0.78 10 10
FOS -0.037 0.095 -10000 0 -0.4 21 21
IFNG -0.061 0.15 -10000 0 -0.56 4 4
T cell activation -0.023 0.12 -10000 0 -0.59 1 1
MAF 0.021 0.05 -10000 0 -0.38 6 6
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.023 0.14 0.65 13 -10000 0 13
TNF -0.061 0.18 -10000 0 -0.79 10 10
FASLG -0.053 0.29 -10000 0 -1.2 20 20
TBX21 0 0.065 -10000 0 -0.39 6 6
BATF3 0.025 0.033 -10000 0 -0.35 3 3
PRKCQ 0.01 0.08 -10000 0 -0.39 15 15
PTPN1 0.007 0.065 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 -0.022 0.16 -10000 0 -0.79 9 9
GATA3 0.017 0.059 -10000 0 -0.35 10 10
T-helper 1 cell differentiation -0.06 0.15 -10000 0 -0.55 4 4
IL2RA -0.095 0.19 -10000 0 -0.66 16 16
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.005 0.062 -10000 0 -0.36 1 1
E2F1 0.019 0.056 -10000 0 -0.35 9 9
PPARG 0.023 0.045 -10000 0 -0.38 5 5
SLC3A2 0.007 0.065 -10000 0 -0.36 1 1
IRF4 0.012 0.074 -10000 0 -0.38 14 14
PTGS2 -0.15 0.26 -10000 0 -0.74 34 34
CSF2 -0.18 0.28 -10000 0 -0.73 39 39
JunB/Fra1/NFAT1-c-4 -0.024 0.17 -10000 0 -0.74 10 10
IL4 -0.026 0.11 -10000 0 -0.58 2 2
IL5 -0.14 0.24 -10000 0 -0.77 19 19
IL2 -0.024 0.13 -10000 0 -0.6 1 1
IL3 -0.04 0.13 -10000 0 -0.61 11 11
RNF128 0.018 0.077 -10000 0 -0.46 10 10
NFATC1 -0.023 0.14 -10000 0 -0.66 13 13
CDK4 0.011 0.087 0.59 2 -10000 0 2
PTPRK 0.007 0.063 -10000 0 -0.36 1 1
IL8 -0.21 0.29 -10000 0 -0.73 44 44
POU2F1 0.026 0.021 -10000 0 -0.35 1 1
EGFR-dependent Endothelin signaling events

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
HRAS 0.026 0.007 -9999 0 -10000 0 0
EGFR 0.017 0.057 -9999 0 -0.38 8 8
EGF/EGFR 0.01 0.084 -9999 0 -0.18 59 59
EGF/EGFR dimer/SHC/GRB2/SOS1 0.04 0.083 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.017 0.062 -9999 0 -0.35 11 11
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.016 0.12 -9999 0 -0.36 44 44
EGF/EGFR dimer/SHC 0.018 0.084 -9999 0 -0.21 45 45
mol:GDP 0.034 0.08 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.02 0.05 -9999 0 -0.36 7 7
GRB2/SOS1 0.04 0.008 -9999 0 -10000 0 0
HRAS/GTP 0.019 0.069 -9999 0 -10000 0 0
SHC1 0.027 0.005 -9999 0 -10000 0 0
HRAS/GDP 0.032 0.078 -9999 0 -10000 0 0
FRAP1 -0.028 0.051 -9999 0 -0.19 3 3
EGF/EGFR dimer 0.001 0.093 -9999 0 -0.25 48 48
SOS1 0.028 0.003 -9999 0 -10000 0 0
GRB2 0.027 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.025 0.06 -9999 0 -0.25 18 18
FOXM1 transcription factor network

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.037 0.31 0.57 1 -1 8 9
PLK1 0.003 0.19 -10000 0 -1 11 11
BIRC5 0.008 0.16 -10000 0 -1 7 7
HSPA1B -0.036 0.31 -10000 0 -1.1 7 7
MAP2K1 0.02 0.042 -10000 0 -10000 0 0
BRCA2 -0.033 0.31 -10000 0 -1 9 9
FOXM1 -0.051 0.35 -10000 0 -1.1 14 14
XRCC1 -0.035 0.31 0.57 1 -1 7 8
FOXM1B/p19 -0.091 0.33 -10000 0 -1.1 13 13
Cyclin D1/CDK4 -0.044 0.3 -10000 0 -0.94 10 10
CDC2 -0.041 0.32 -10000 0 -0.98 14 14
TGFA -0.044 0.3 -10000 0 -0.92 9 9
SKP2 -0.025 0.31 0.55 2 -1.1 7 9
CCNE1 0.01 0.072 -10000 0 -0.36 15 15
CKS1B -0.039 0.31 -10000 0 -0.94 14 14
RB1 -0.001 0.18 -10000 0 -0.91 6 6
FOXM1C/SP1 -0.04 0.33 -10000 0 -1 13 13
AURKB -0.034 0.26 -10000 0 -0.92 30 30
CENPF -0.072 0.33 0.57 1 -1 13 14
CDK4 0.022 0.023 -10000 0 -10000 0 0
MYC -0.033 0.26 -10000 0 -0.93 6 6
CHEK2 0.021 0.041 -10000 0 -10000 0 0
ONECUT1 -0.048 0.32 -10000 0 -0.94 15 15
CDKN2A -0.089 0.17 -10000 0 -0.35 121 121
LAMA4 -0.039 0.31 -10000 0 -1.1 7 7
FOXM1B/HNF6 -0.058 0.34 -10000 0 -1.1 13 13
FOS -0.072 0.38 -10000 0 -1.1 28 28
SP1 0.027 0.007 -10000 0 -10000 0 0
CDC25B -0.025 0.31 0.54 1 -1 7 8
response to radiation 0.004 0.023 -10000 0 -10000 0 0
CENPB -0.023 0.3 0.54 1 -1 7 8
CENPA -0.042 0.32 -10000 0 -1.1 8 8
NEK2 -0.047 0.32 0.57 1 -1 13 14
HIST1H2BA -0.041 0.31 -10000 0 -1 8 8
CCNA2 0.026 0.015 -10000 0 -10000 0 0
EP300 0.027 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 -0.049 0.33 -10000 0 -1.2 8 8
CCNB2 -0.039 0.31 -10000 0 -1.1 7 7
CCNB1 -0.041 0.32 -10000 0 -1.1 8 8
ETV5 -0.032 0.31 0.57 1 -1.1 8 9
ESR1 -0.055 0.36 -10000 0 -1.2 19 19
CCND1 -0.052 0.3 -10000 0 -0.96 10 10
GSK3A 0.02 0.037 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.037 0.063 -10000 0 -0.22 9 9
CDK2 0.025 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.027 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.032 0.32 -10000 0 -1 12 12
GAS1 -0.11 0.44 0.57 1 -1.1 50 51
MMP2 -0.04 0.31 0.57 1 -1.1 8 9
RB1/FOXM1C -0.034 0.3 -10000 0 -0.99 9 9
CREBBP 0.026 0.007 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.021 0.067 -10000 0 -0.25 23 23
CRKL 0.013 0.11 0.29 4 -0.47 12 16
mol:PIP3 -0.004 0.058 -10000 0 -0.82 2 2
AKT1 -0.007 0.054 -10000 0 -0.72 2 2
PTK2B 0.025 0.009 -10000 0 -10000 0 0
RAPGEF1 0.015 0.11 0.3 6 -0.46 11 17
RANBP10 0.027 0.007 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.028 0.076 -10000 0 -0.22 33 33
MAP3K5 0.013 0.11 0.29 4 -0.43 13 17
HGF/MET/CIN85/CBL/ENDOPHILINS 0.041 0.075 -10000 0 -0.24 6 6
AP1 0.015 0.072 0.17 2 -0.24 21 23
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.035 0.22 -10000 0 -0.71 39 39
STAT3 (dimer) 0.008 0.057 -10000 0 -0.27 8 8
GAB1/CRKL/SHP2/PI3K 0.039 0.11 0.31 2 -0.45 9 11
INPP5D 0.025 0.034 -10000 0 -0.36 3 3
CBL/CRK 0.027 0.11 0.29 5 -0.45 11 16
PTPN11 0.028 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.011 -10000 0 -10000 0 0
PTEN 0.026 0.008 -10000 0 -10000 0 0
ELK1 0.003 0.11 0.31 29 -0.32 1 30
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.006 0.047 -10000 0 -0.22 8 8
PAK1 -0.003 0.061 -10000 0 -0.69 2 2
HGF/MET/RANBP10 0.029 0.074 -10000 0 -0.22 32 32
HRAS -0.002 0.11 -10000 0 -0.47 13 13
DOCK1 0.016 0.11 0.28 9 -0.45 11 20
GAB1 0.009 0.095 0.24 1 -0.48 10 11
CRK 0.011 0.11 0.29 5 -0.46 12 17
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.001 0.1 -10000 0 -0.43 16 16
JUN 0.028 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.006 0.041 -10000 0 -0.2 7 7
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
cell morphogenesis 0.034 0.11 0.3 27 -0.44 3 30
GRB2/SHC 0.02 0.059 -10000 0 -0.21 4 4
FOS 0.006 0.091 -10000 0 -0.38 21 21
GLMN 0.003 0.006 -10000 0 -10000 0 0
cell motility 0.003 0.1 0.31 29 -0.32 1 30
HGF/MET/MUC20 0.014 0.069 -10000 0 -0.22 33 33
cell migration 0.02 0.058 -10000 0 -0.21 4 4
GRB2 0.027 0.005 -10000 0 -10000 0 0
CBL 0.027 0.006 -10000 0 -10000 0 0
MET/RANBP10 0.022 0.065 -10000 0 -0.25 22 22
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.011 0.044 -10000 0 -0.24 7 7
MET/MUC20 0.005 0.061 -10000 0 -0.24 23 23
RAP1B 0.02 0.11 0.27 14 -0.43 11 25
RAP1A 0.014 0.1 0.29 7 -0.43 11 18
HGF/MET/RANBP9 0.028 0.076 -10000 0 -0.22 33 33
RAF1 0.001 0.11 -10000 0 -0.45 12 12
STAT3 0.008 0.057 -10000 0 -0.27 8 8
cell proliferation 0.015 0.084 0.3 9 -0.34 7 16
RPS6KB1 0.007 0.031 -10000 0 -0.34 2 2
MAPK3 -0.004 0.12 0.62 11 -10000 0 11
MAPK1 0.006 0.15 0.64 17 -10000 0 17
RANBP9 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.11 0.3 5 -0.44 10 15
SRC 0.007 0.037 -10000 0 -0.25 3 3
PI3K 0.019 0.055 -10000 0 -0.22 2 2
MET/Glomulin -0.005 0.06 -10000 0 -0.21 25 25
SOS1 0.028 0.003 -10000 0 -10000 0 0
MAP2K1 0 0.1 -10000 0 -0.44 10 10
MET 0.005 0.088 -10000 0 -0.36 23 23
MAP4K1 0.012 0.12 0.3 3 -0.44 16 19
PTK2 0.024 0.01 -10000 0 -10000 0 0
MAP2K2 0.001 0.1 -10000 0 -0.44 10 10
BAD -0.007 0.054 -10000 0 -0.69 2 2
MAP2K4 0.012 0.1 0.28 4 -0.42 10 14
SHP2/GRB2/SOS1/GAB1 0.025 0.099 -10000 0 -0.44 9 9
INPPL1 0.026 0.02 -10000 0 -0.35 1 1
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.028 0.004 -10000 0 -10000 0 0
HGS -0.007 0.037 -10000 0 -0.19 5 5
PLCgamma1/PKC 0.017 0.008 -10000 0 -10000 0 0
HGF 0.014 0.07 -10000 0 -0.37 13 13
RASA1 0.025 0.008 -10000 0 -10000 0 0
NCK1 0.027 0.005 -10000 0 -10000 0 0
PTPRJ 0.027 0.019 -10000 0 -0.35 1 1
NCK/PLCgamma1 0.026 0.052 -10000 0 -0.22 2 2
PDPK1 -0.006 0.058 -10000 0 -0.76 2 2
HGF/MET/SHIP 0.027 0.078 -10000 0 -0.22 36 36
FAS signaling pathway (CD95)

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
SPTAN1 -0.001 0.033 0.23 5 -0.19 3 8
RFC1 -0.002 0.026 0.22 2 -0.19 2 4
PRKDC 0.011 0.057 0.22 26 -0.19 3 29
RIPK1 0.027 0.008 -10000 0 -10000 0 0
CASP7 0.002 0.11 -10000 0 -0.63 10 10
FASLG/FAS/FADD/FAF1 0.009 0.053 0.18 4 -0.25 6 10
MAP2K4 -0.018 0.14 0.32 2 -0.41 27 29
mol:ceramide 0.007 0.073 -10000 0 -0.28 10 10
GSN -0.004 0.037 0.24 3 -0.24 5 8
FASLG/FAS/FADD/FAF1/Caspase 8 0.007 0.065 -10000 0 -0.27 9 9
FAS 0.022 0.016 -10000 0 -10000 0 0
BID -0.014 0.023 -10000 0 -10000 0 0
MAP3K1 -0.001 0.1 0.3 2 -0.44 11 13
MAP3K7 0.026 0.008 -10000 0 -10000 0 0
RB1 0.006 0.047 0.22 17 -0.19 1 18
CFLAR 0.029 0.005 -10000 0 -10000 0 0
HGF/MET 0.019 0.092 -10000 0 -0.23 45 45
ARHGDIB -0.002 0.031 0.22 4 -0.19 4 8
FADD 0.022 0.017 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.054 0.25 4 -0.24 3 7
NFKB1 -0.007 0.11 -10000 0 -0.61 10 10
MAPK8 -0.034 0.17 0.31 3 -0.49 41 44
DFFA -0.001 0.03 0.22 4 -0.19 3 7
DNA fragmentation during apoptosis -0.011 0.048 0.22 3 -10000 0 3
FAS/FADD/MET 0.028 0.064 -10000 0 -0.21 23 23
CFLAR/RIP1 0.04 0.012 -10000 0 -10000 0 0
FAIM3 0.011 0.078 -10000 0 -0.35 18 18
FAF1 0.021 0.02 -10000 0 -10000 0 0
PARP1 -0.003 0.025 0.22 1 -0.19 4 5
DFFB -0.002 0.028 0.22 3 -0.19 2 5
CHUK -0.007 0.097 -10000 0 -0.57 8 8
FASLG 0.007 0.077 -10000 0 -0.38 15 15
FAS/FADD 0.031 0.023 -10000 0 -10000 0 0
HGF 0.014 0.07 -10000 0 -0.37 13 13
LMNA -0.012 0.043 0.19 3 -10000 0 3
CASP6 -0.003 0.02 -10000 0 -0.19 2 2
CASP10 0.022 0.026 -10000 0 -0.38 1 1
CASP3 0 0.017 -10000 0 -10000 0 0
PTPN13 0.01 0.081 -10000 0 -0.38 17 17
CASP8 -0.013 0.037 0.16 18 -10000 0 18
IL6 -0.093 0.35 -10000 0 -1.1 41 41
MET 0.005 0.088 -10000 0 -0.36 23 23
ICAD/CAD -0.001 0.041 0.36 4 -10000 0 4
FASLG/FAS/FADD/FAF1/Caspase 10 0.006 0.073 -10000 0 -0.29 10 10
activation of caspase activity by cytochrome c -0.014 0.023 -10000 0 -10000 0 0
PAK2 0.004 0.046 0.22 15 -0.19 3 18
BCL2 0.024 0.022 -10000 0 -0.38 1 1
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.021 0.12 0.25 1 -0.41 12 13
MAP3K8 0.026 0.02 -10000 0 -0.36 1 1
FOS 0.011 0.1 0.26 1 -0.38 13 14
PRKCA 0.025 0.012 -10000 0 -10000 0 0
PTPN7 0.02 0.048 -10000 0 -0.36 6 6
HRAS 0.026 0.007 -10000 0 -10000 0 0
PRKCB 0.001 0.097 -10000 0 -0.38 24 24
NRAS 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.023 -10000 0 -10000 0 0
MAPK3 0.015 0.092 -10000 0 -0.51 9 9
MAP2K1 0.003 0.098 -10000 0 -0.36 22 22
ELK1 0.025 0.014 -10000 0 -10000 0 0
BRAF 0.001 0.084 -10000 0 -0.34 22 22
mol:GTP 0 0.001 -10000 0 -0.005 23 23
MAPK1 0.011 0.096 -10000 0 -0.42 14 14
RAF1 0.001 0.084 -10000 0 -0.34 22 22
KRAS 0.025 0.009 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.006 0.085 0.2 1 -0.34 13 14
ACTA1 -0.019 0.074 0.19 1 -0.27 10 11
NUMA1 -0.006 0.098 0.22 1 -0.38 14 15
SPTAN1 -0.013 0.073 0.24 4 -0.27 6 10
LIMK1 -0.012 0.079 0.3 4 -0.27 6 10
BIRC3 0.021 0.047 -10000 0 -0.36 6 6
BIRC2 0.027 0.006 -10000 0 -10000 0 0
BAX 0.027 0.006 -10000 0 -10000 0 0
CASP10 -0.024 0.053 -10000 0 -0.21 30 30
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.004 -10000 0 -10000 0 0
PTK2 -0.009 0.11 -10000 0 -0.43 14 14
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.012 0.072 0.24 4 -0.27 6 10
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.028 0.004 -10000 0 -10000 0 0
GSN -0.018 0.075 -10000 0 -0.29 10 10
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.048 0.18 -10000 0 -0.64 27 27
BID -0.003 0.035 -10000 0 -0.18 8 8
MAP3K1 -0.024 0.12 -10000 0 -0.4 32 32
TRADD 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.013 0.073 0.35 1 -0.26 8 9
CASP9 0.027 0.006 -10000 0 -10000 0 0
DNA repair -0.003 0.036 0.19 2 -10000 0 2
neuron apoptosis -0.03 0.19 -10000 0 -0.63 34 34
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.009 0.093 -10000 0 -0.38 10 10
APAF1 0.028 0.004 -10000 0 -10000 0 0
CASP6 -0.011 0.17 -10000 0 -0.9 13 13
TRAF2 0.027 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.011 0.079 0.35 6 -0.27 5 11
CASP7 -0.005 0.069 -10000 0 -0.41 4 4
KRT18 0 0.11 -10000 0 -0.56 12 12
apoptosis -0.012 0.1 0.43 3 -0.42 14 17
DFFA -0.013 0.075 0.27 4 -0.27 7 11
DFFB -0.015 0.07 -10000 0 -0.27 6 6
PARP1 0.003 0.036 -10000 0 -0.19 2 2
actin filament polymerization 0.014 0.078 0.3 2 -0.27 5 7
TNF 0.01 0.08 -10000 0 -0.36 18 18
CYCS 0.01 0.036 0.16 3 -0.17 1 4
SATB1 -0.012 0.16 -10000 0 -0.84 13 13
SLK -0.015 0.071 0.34 2 -0.27 6 8
p15 BID/BAX 0.014 0.046 0.2 1 -0.25 2 3
CASP2 0.009 0.055 0.21 3 -0.33 5 8
JNK cascade 0.024 0.12 0.4 32 -10000 0 32
CASP3 -0.017 0.072 0.21 1 -0.28 8 9
LMNB2 -0.001 0.12 0.23 2 -0.47 18 20
RIPK1 0.026 0.007 -10000 0 -10000 0 0
CASP4 0.027 0.006 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.063 0.036 -10000 0 -10000 0 0
negative regulation of DNA binding -0.046 0.18 -10000 0 -0.62 27 27
stress fiber formation -0.014 0.071 0.34 2 -0.27 6 8
GZMB -0.006 0.068 -10000 0 -0.25 29 29
CASP1 0.012 0.02 -10000 0 -0.14 7 7
LMNB1 -0.007 0.14 0.23 2 -0.59 17 19
APP -0.031 0.19 -10000 0 -0.64 34 34
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM -0.012 0.1 0.32 3 -0.43 15 18
LMNA 0.014 0.093 0.23 2 -0.44 10 12
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.012 0.056 -10000 0 -0.32 6 6
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.015 0.069 0.22 1 -0.27 6 7
APAF-1/Caspase 9 0.009 0.088 -10000 0 -0.63 7 7
nuclear fragmentation during apoptosis -0.006 0.096 0.22 1 -0.38 14 15
CFL2 -0.014 0.079 0.27 5 -0.27 4 9
GAS2 -0.023 0.078 -10000 0 -0.28 10 10
positive regulation of apoptosis 0.003 0.13 0.23 2 -0.52 16 18
PRF1 0.023 0.041 -10000 0 -0.39 4 4
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.034 0.021 -10000 0 -10000 0 0
CDKN1B 0.01 0.065 -10000 0 -0.3 12 12
CDKN1A 0.009 0.067 -10000 0 -0.3 11 11
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.009 -10000 0 -10000 0 0
FOXO3 0.009 0.068 0.2 2 -0.3 12 14
AKT1 0.005 0.058 -10000 0 -0.32 8 8
BAD 0.028 0.004 -10000 0 -10000 0 0
AKT3 0.013 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.069 -10000 0 -0.3 13 13
AKT1/ASK1 0.033 0.08 -10000 0 -0.29 12 12
BAD/YWHAZ 0.046 0.023 -10000 0 -10000 0 0
RICTOR 0.025 0.009 -10000 0 -10000 0 0
RAF1 0.028 0.004 -10000 0 -10000 0 0
JNK cascade -0.031 0.078 0.28 12 -10000 0 12
TSC1 0.01 0.064 -10000 0 -0.3 10 10
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.035 0.085 0.27 1 -0.3 14 15
EP300 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0.01 0.071 -10000 0 -0.31 13 13
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.011 0.061 -10000 0 -0.31 9 9
YWHAQ 0.028 0.004 -10000 0 -10000 0 0
TBC1D4 0.004 0.028 0.22 2 -0.19 6 8
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
MAPKAP1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.038 0.084 0.3 8 -0.2 20 28
YWHAH 0.027 0.005 -10000 0 -10000 0 0
AKT1S1 0.007 0.069 -10000 0 -0.3 13 13
CASP9 0.012 0.056 -10000 0 -0.28 8 8
YWHAB 0.022 0.011 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.087 0.3 5 -0.3 9 14
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.044 0.029 -10000 0 -0.21 2 2
YWHAE 0.026 0.008 -10000 0 -10000 0 0
SRC 0.024 0.01 -10000 0 -10000 0 0
AKT2/p21CIP1 0.012 0.072 0.26 3 -0.33 6 9
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.068 -10000 0 -0.32 14 14
CHUK 0.007 0.069 -10000 0 -0.3 13 13
BAD/BCL-XL 0.029 0.075 0.26 1 -0.5 1 2
mTORC2 0.032 0.012 -10000 0 -10000 0 0
AKT2 0.014 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.041 0.11 0.24 22 -0.43 8 30
PDPK1 0.027 0.007 -10000 0 -10000 0 0
MDM2 0.014 0.074 0.2 7 -0.3 12 19
MAPKKK cascade -0.035 0.084 0.29 14 -0.27 1 15
MDM2/Cbp/p300 0.048 0.089 0.3 5 -0.37 2 7
TSC1/TSC2 0.01 0.059 0.31 1 -0.31 7 8
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.086 0.29 5 -0.36 2 7
glucose import -0.041 0.099 0.2 15 -0.2 98 113
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.012 0.063 0.18 5 -0.47 2 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.042 0.098 0.2 13 -0.2 98 111
GSK3A 0.008 0.068 -10000 0 -0.3 13 13
FOXO1 0.008 0.072 -10000 0 -0.3 14 14
GSK3B 0.008 0.07 -10000 0 -0.3 13 13
SFN 0.015 0.067 -10000 0 -0.37 12 12
G1/S transition of mitotic cell cycle 0.019 0.081 0.24 8 -0.3 9 17
p27Kip1/14-3-3 family 0.033 0.057 -10000 0 -0.39 2 2
PRKACA 0.027 0.005 -10000 0 -10000 0 0
KPNA1 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
YWHAG 0.026 0.007 -10000 0 -10000 0 0
RHEB 0.027 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.009 0.011 -10000 0 -0.23 1 1
SNTA1 0.013 0.067 -10000 0 -0.38 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.009 0.011 -10000 0 -0.23 1 1
MAPK12 -0.008 0.031 -10000 0 -0.19 11 11
CCND1 0.007 0.03 -10000 0 -0.32 2 2
p38 gamma/SNTA1 0.009 0.051 0.19 6 -0.2 14 20
MAP2K3 0.026 0.008 -10000 0 -10000 0 0
PKN1 0.027 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.008 0.031 -10000 0 -0.19 11 11
MAP2K6 0 0.026 -10000 0 -0.21 6 6
MAPT -0.05 0.12 0.22 1 -0.28 81 82
MAPK13 0.011 0.015 -10000 0 -0.27 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.001 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.027 0.006 -10000 0 -10000 0 0
VDR 0.027 0.005 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.048 0.033 -10000 0 -0.23 4 4
EP300 0.027 0.005 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.004 0.056 -10000 0 -0.35 5 5
KAT2B 0.024 0.041 -10000 0 -0.38 4 4
MAPK14 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.009 0.061 0.22 4 -0.24 6 10
RAR alpha/9cRA/Cyclin H -0.001 0.075 -10000 0 -0.32 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.061 0.23 1 -0.28 9 10
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.006 0.062 -10000 0 -0.31 2 2
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.047 0.098 -10000 0 -0.42 6 6
NCOA2 0.024 0.022 -10000 0 -0.38 1 1
NCOA3 0.023 0.011 -10000 0 -10000 0 0
NCOA1 0.028 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.005 -10000 0 -10000 0 0
RARG 0.027 0.02 -10000 0 -0.35 1 1
RAR gamma1/9cRA 0.035 0.015 -10000 0 -0.2 1 1
MAPK3 0.028 0.005 -10000 0 -10000 0 0
MAPK1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.028 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.053 0.096 -10000 0 -0.38 7 7
RARA -0.025 0.057 -10000 0 -0.22 9 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.001 0.058 -10000 0 -0.28 9 9
PRKCA 0.029 0.005 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.054 0.1 0.35 1 -0.39 6 7
RXRG -0.15 0.17 -10000 0 -0.34 161 161
RXRA -0.019 0.06 -10000 0 -0.27 4 4
RXRB -0.045 0.082 -10000 0 -0.28 8 8
VDR/Vit D3/DNA 0.02 0.004 -10000 0 -10000 0 0
RBP1 0.013 0.073 -10000 0 -0.36 15 15
CRBP1/9-cic-RA 0.01 0.051 -10000 0 -0.25 15 15
RARB 0.026 0.035 -10000 0 -0.38 3 3
PRKCG -0.13 0.19 -10000 0 -0.35 174 174
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.051 0.095 0.26 2 -0.4 9 11
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.041 0.098 0.21 1 -0.36 11 12
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.078 0.25 2 -0.3 7 9
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.054 0.1 0.35 1 -0.38 7 8
positive regulation of DNA binding -0.007 0.067 -10000 0 -0.31 2 2
NRIP1 -0.05 0.097 -10000 0 -10000 0 0
RXRs/RARs -0.056 0.1 -10000 0 -0.36 13 13
RXRs/RXRs/DNA/9cRA -0.062 0.09 -10000 0 -0.38 8 8
PRKACA 0.027 0.005 -10000 0 -10000 0 0
CDK7 0.026 0.008 -10000 0 -10000 0 0
TFIIH 0.05 0.019 -10000 0 -10000 0 0
RAR alpha/9cRA 0.01 0.07 0.2 1 -0.25 2 3
CCNH 0.026 0.008 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.046 0.024 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.022 0.049 -10000 0 -0.38 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.007 0.062 -10000 0 -0.18 47 47
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
MAP3K12 0.027 0.006 -10000 0 -10000 0 0
FGR 0.027 0.006 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.036 0.097 -10000 0 -0.4 21 21
PRKG1 0.022 0.044 -10000 0 -0.37 5 5
DUSP8 0.025 0.029 -10000 0 -0.38 2 2
PGK/cGMP/p38 alpha 0.005 0.12 0.17 3 -0.43 17 20
apoptosis -0.034 0.093 -10000 0 -0.38 21 21
RAL/GTP 0.036 0.009 -10000 0 -10000 0 0
LYN 0.025 0.009 -10000 0 -10000 0 0
DUSP1 0.017 0.064 -10000 0 -0.38 10 10
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.024 0.01 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.06 0.028 -10000 0 -10000 0 0
TRAF6 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.026 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 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.013 -10000 0 -10000 0 0
MAPK11 0.014 0.12 0.26 18 -0.44 13 31
BLK -0.041 0.15 -10000 0 -0.38 66 66
HCK 0.024 0.01 -10000 0 -10000 0 0
MAP2K3 0.026 0.008 -10000 0 -10000 0 0
DUSP16 0.026 0.007 -10000 0 -10000 0 0
DUSP10 0.026 0.027 -10000 0 -0.35 2 2
TRAF6/MEKK3 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0.13 0.21 24 -0.44 20 44
positive regulation of innate immune response 0.014 0.15 0.26 21 -0.52 15 36
LCK 0.017 0.062 -10000 0 -0.35 11 11
p38alpha-beta/MKP7 0.024 0.14 0.27 19 -0.49 14 33
p38alpha-beta/MKP5 0.021 0.14 0.28 17 -0.51 14 31
PGK/cGMP 0.016 0.031 -10000 0 -0.26 5 5
PAK2 0.026 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.02 0.15 0.27 18 -0.47 18 36
CDC42 0.026 0.007 -10000 0 -10000 0 0
RALB 0.028 0.003 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
PAK3 -0.033 0.14 -10000 0 -0.38 61 61
IL6-mediated signaling events

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
BCL2L1 -0.099 0.18 -10000 0 -0.66 4 4
CRP -0.12 0.19 -10000 0 -0.64 12 12
cell cycle arrest -0.13 0.2 -10000 0 -0.65 13 13
TIMP1 -0.094 0.17 -10000 0 -0.61 8 8
IL6ST 0.013 0.04 -10000 0 -0.39 3 3
Rac1/GDP -0.047 0.098 -10000 0 -0.35 10 10
AP1 0.022 0.1 -10000 0 -0.47 6 6
GAB2 0.027 0.006 -10000 0 -10000 0 0
TNFSF11 -0.17 0.21 -10000 0 -0.62 27 27
HSP90B1 -0.003 0.099 -10000 0 -0.64 8 8
GAB1 0.027 0.006 -10000 0 -10000 0 0
MAPK14 -0.021 0.084 -10000 0 -0.39 5 5
AKT1 0.027 0.049 -10000 0 -0.41 2 2
FOXO1 0.035 0.058 0.25 3 -0.38 2 5
MAP2K6 -0.034 0.085 -10000 0 -0.35 10 10
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
MAP2K4 -0.064 0.11 -10000 0 -0.39 8 8
MITF -0.044 0.094 -10000 0 -0.34 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.005 -10000 0 -10000 0 0
A2M -0.02 0.23 -10000 0 -1.1 17 17
CEBPB 0.025 0.014 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.009 0.081 -10000 0 -0.45 7 7
STAT3 -0.14 0.2 -10000 0 -0.69 12 12
STAT1 0.001 0.08 -10000 0 -0.76 4 4
CEBPD -0.11 0.18 -10000 0 -0.7 6 6
PIK3CA 0.027 0.007 -10000 0 -10000 0 0
PI3K 0.038 0.015 -10000 0 -10000 0 0
JUN 0.027 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.038 0.1 0.24 1 -0.35 15 16
MAPK11 -0.019 0.08 -10000 0 -0.4 4 4
STAT3 (dimer)/FOXO1 -0.084 0.16 -10000 0 -0.57 4 4
GRB2/SOS1/GAB family 0.028 0.094 -10000 0 -0.33 4 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.083 -10000 0 -0.3 17 17
GRB2 0.028 0.005 -10000 0 -10000 0 0
JAK2 0.024 0.01 -10000 0 -10000 0 0
LBP -0.095 0.19 0.41 1 -0.54 14 15
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
JAK1 0.023 0.014 -10000 0 -10000 0 0
MYC -0.088 0.2 -10000 0 -0.8 5 5
FGG -0.18 0.3 -10000 0 -0.94 46 46
macrophage differentiation -0.13 0.2 -10000 0 -0.65 13 13
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.016 0.099 -10000 0 -0.26 13 13
JUNB -0.12 0.17 -10000 0 -0.62 6 6
FOS 0.006 0.091 -10000 0 -0.38 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.042 0.096 -10000 0 -0.33 20 20
STAT1/PIAS1 -0.048 0.11 -10000 0 -0.33 11 11
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.053 -10000 0 -0.4 3 3
STAT3 (dimer) -0.14 0.2 -10000 0 -0.69 12 12
PRKCD -0.077 0.14 0.32 2 -0.45 8 10
IL6R 0.011 0.07 -10000 0 -0.39 12 12
SOCS3 -0.005 0.085 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.031 0.05 -10000 0 -0.23 6 6
Rac1/GTP -0.054 0.1 -10000 0 -0.37 10 10
HCK 0.024 0.01 -10000 0 -10000 0 0
MAPKKK cascade 0.018 0.088 -10000 0 -0.5 7 7
bone resorption -0.17 0.2 -10000 0 -0.58 28 28
IRF1 -0.12 0.17 -10000 0 -0.64 6 6
mol:GDP -0.044 0.09 -10000 0 -0.33 16 16
SOS1 0.028 0.003 -10000 0 -10000 0 0
VAV1 -0.044 0.09 -10000 0 -0.33 15 15
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.005 0.099 -10000 0 -0.5 6 6
PTPN11 0.001 0.096 -10000 0 -0.77 6 6
IL6/IL6RA -0.013 0.11 -10000 0 -0.28 55 55
gp130 (dimer)/TYK2/TYK2/LMO4 0.04 0.04 -10000 0 -0.23 6 6
gp130 (dimer)/JAK2/JAK2/LMO4 0.037 0.041 -10000 0 -0.23 6 6
IL6 -0.031 0.13 -10000 0 -0.38 49 49
PIAS3 0.027 0.006 -10000 0 -10000 0 0
PTPRE 0.03 0.029 -10000 0 -0.35 2 2
PIAS1 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.007 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.027 0.09 -10000 0 -0.28 28 28
LMO4 0.014 0.039 -10000 0 -0.37 3 3
STAT3 (dimer)/PIAS3 -0.13 0.19 -10000 0 -0.65 12 12
MCL1 0.033 0.063 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.017 0.038 -10000 0 -0.22 9 9
epithelial cell differentiation 0.047 0.041 -10000 0 -0.19 9 9
CYFIP2 0.02 0.053 -10000 0 -0.38 7 7
ENAH -0.007 0.053 0.23 5 -0.24 1 6
EGFR 0.017 0.057 -10000 0 -0.38 8 8
EPHA2 0.021 0.047 -10000 0 -0.36 6 6
MYO6 -0.006 0.043 0.18 13 -10000 0 13
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.046 0.04 -10000 0 -0.22 7 7
AQP5 -0.1 0.18 -10000 0 -0.42 89 89
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.007 0.042 0.18 12 -10000 0 12
regulation of calcium-dependent cell-cell adhesion -0.009 0.046 0.18 12 -0.34 1 13
EGF -0.016 0.12 -10000 0 -0.36 44 44
NCKAP1 0.028 0.004 -10000 0 -10000 0 0
AQP3 -0.008 0.088 -10000 0 -0.42 13 13
cortical microtubule organization 0.047 0.041 -10000 0 -0.19 9 9
GO:0000145 -0.008 0.039 0.16 11 -10000 0 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.052 0.043 -10000 0 -0.19 9 9
MLLT4 0.026 0.007 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.031 -10000 0 -0.33 1 1
ARF6 0.027 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.039 -10000 0 -0.19 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.004 0.04 0.18 9 -0.33 1 10
PVRL2 0.027 0.006 -10000 0 -10000 0 0
ZYX -0.007 0.043 0.18 13 -10000 0 13
ARF6/GTP 0.064 0.042 -10000 0 -0.2 1 1
CDH1 0.018 0.06 -10000 0 -0.38 9 9
EGFR/EGFR/EGF/EGF 0.012 0.078 -10000 0 -0.34 2 2
RhoA/GDP 0.048 0.041 -10000 0 -0.19 6 6
actin cytoskeleton organization -0.007 0.04 0.16 13 -10000 0 13
IGF-1R heterotetramer 0.025 0.028 -10000 0 -0.37 2 2
GIT1 0.028 0.004 -10000 0 -10000 0 0
IGF1R 0.025 0.028 -10000 0 -0.37 2 2
IGF1 -0.022 0.13 -10000 0 -0.37 51 51
DIAPH1 0.013 0.15 -10000 0 -0.53 19 19
Wnt receptor signaling pathway -0.047 0.041 0.19 9 -10000 0 9
RHOA 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.021 0.03 -10000 0 -0.31 1 1
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
VCL -0.007 0.041 0.17 13 -10000 0 13
EFNA1 0.026 0.019 -10000 0 -0.35 1 1
LPP -0.011 0.047 0.17 9 -0.4 2 11
Ephrin A1/EPHA2 0.037 0.048 -10000 0 -0.35 1 1
SEC6/SEC8 -0.016 0.024 -10000 0 -10000 0 0
MGAT3 -0.009 0.047 0.18 12 -0.34 1 13
HGF/MET 0.023 0.07 -10000 0 -0.34 2 2
HGF 0.014 0.07 -10000 0 -0.37 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.017 0.038 -10000 0 -0.22 9 9
actin cable formation 0.019 0.081 0.26 19 -0.34 1 20
KIAA1543 -0.007 0.041 0.17 13 -10000 0 13
KIFC3 -0.009 0.039 0.18 9 -10000 0 9
NCK1 0.027 0.005 -10000 0 -10000 0 0
EXOC3 0.025 0.009 -10000 0 -10000 0 0
ACTN1 -0.008 0.046 0.18 12 -0.34 1 13
NCK1/GIT1 0.04 0.009 -10000 0 -10000 0 0
mol:GDP 0.047 0.041 -10000 0 -0.19 9 9
EXOC4 0.027 0.006 -10000 0 -10000 0 0
STX4 -0.008 0.041 0.18 11 -10000 0 11
PIP5K1C -0.008 0.042 0.18 12 -10000 0 12
LIMA1 0.027 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.006 -10000 0 -10000 0 0
ROCK1 0 0.069 0.29 9 -0.28 1 10
adherens junction assembly -0.012 0.099 0.27 3 -0.66 6 9
IGF-1R heterotetramer/IGF1 0.014 0.082 -10000 0 -0.33 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.013 -10000 0 -10000 0 0
MET 0.005 0.088 -10000 0 -0.36 23 23
PLEKHA7 -0.007 0.043 0.18 13 -10000 0 13
mol:GTP 0.057 0.038 -10000 0 -0.19 6 6
establishment of epithelial cell apical/basal polarity 0.013 0.083 0.32 12 -10000 0 12
cortical actin cytoskeleton stabilization 0.017 0.038 -10000 0 -0.22 9 9
regulation of cell-cell adhesion -0.007 0.04 0.16 13 -10000 0 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.017 0.038 -10000 0 -0.22 9 9
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.032 0.14 -10000 0 -0.78 6 6
NCK1/PAK1/Dok-R -0.015 0.055 -10000 0 -0.4 5 5
NCK1/Dok-R 0.047 0.12 -10000 0 -0.81 6 6
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol -0.005 0.022 0.24 3 -10000 0 3
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.028 0.006 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -10000 0 -10000 0 0
F2 -0.054 0.13 0.26 3 -0.36 60 63
TNIP2 0.026 0.007 -10000 0 -10000 0 0
NF kappa B/RelA 0.063 0.12 -10000 0 -0.81 6 6
FN1 -0.01 0.11 -10000 0 -0.35 41 41
PLD2 0.019 0.12 -10000 0 -0.86 6 6
PTPN11 0.028 0.004 -10000 0 -10000 0 0
GRB14 -0.037 0.14 -10000 0 -0.36 68 68
ELK1 0.03 0.11 -10000 0 -0.81 6 6
GRB7 0.019 0.044 -10000 0 -0.37 5 5
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.04 0.14 -10000 0 -0.83 6 6
CDKN1A 0.027 0.14 0.35 1 -0.64 6 7
ITGA5 0.021 0.049 -10000 0 -0.35 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.045 0.12 -10000 0 -0.81 6 6
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:NO 0.036 0.12 0.36 6 -0.59 6 12
PLG 0.015 0.12 -10000 0 -0.87 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.029 0.12 -10000 0 -0.75 6 6
GRB2 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
ANGPT2 -0.018 0.17 0.34 1 -0.56 13 14
BMX 0.003 0.13 -10000 0 -0.92 6 6
ANGPT1 0.023 0.11 0.31 1 -1.1 3 4
tube development 0.015 0.14 0.35 2 -0.65 6 8
ANGPT4 0.016 0.043 -10000 0 -0.36 5 5
response to hypoxia 0.001 0.01 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.016 0.14 -10000 0 -0.93 6 6
alpha5/beta1 Integrin 0.033 0.043 -10000 0 -0.28 7 7
FGF2 0.009 0.084 -10000 0 -0.38 18 18
STAT5A (dimer) 0.027 0.16 -10000 0 -0.76 6 6
mol:L-citrulline 0.036 0.12 0.36 6 -0.59 6 12
AGTR1 -0.077 0.18 -10000 0 -0.38 102 102
MAPK14 0.021 0.14 -10000 0 -0.93 6 6
Tie2/SHP2 0.027 0.11 -10000 0 -0.93 3 3
TEK 0.026 0.1 -10000 0 -1 3 3
RPS6KB1 0.033 0.13 -10000 0 -0.76 6 6
Angiotensin II/AT1 -0.052 0.12 -10000 0 -0.26 102 102
Tie2/Ang1/GRB2 0.042 0.12 -10000 0 -0.88 6 6
MAPK3 0.018 0.11 -10000 0 -0.82 6 6
MAPK1 0.017 0.11 -10000 0 -0.82 6 6
Tie2/Ang1/GRB7 0.031 0.13 -10000 0 -0.91 6 6
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.12 -10000 0 -0.87 6 6
PI3K 0.025 0.14 -10000 0 -0.88 6 6
FES 0.025 0.14 -10000 0 -0.97 6 6
Crk/Dok-R 0.047 0.12 -10000 0 -0.81 6 6
Tie2/Ang1/ABIN2 0.042 0.12 -10000 0 -0.88 6 6
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.035 0.13 0.36 2 -0.7 6 8
STAT5A 0.028 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.048 0.15 0.4 5 -0.8 5 10
Tie2/Ang2 0.002 0.15 -10000 0 -0.86 6 6
Tie2/Ang1 0.025 0.12 -10000 0 -0.91 6 6
FOXO1 0.038 0.14 0.4 4 -0.74 5 9
ELF1 0.032 0.018 -10000 0 -10000 0 0
ELF2 0.023 0.12 -10000 0 -0.87 6 6
mol:Choline 0.02 0.11 -10000 0 -0.84 6 6
cell migration -0.006 0.04 -10000 0 -0.23 5 5
FYN 0.013 0.15 -10000 0 -0.73 6 6
DOK2 0.023 0.03 -10000 0 -0.38 2 2
negative regulation of cell cycle 0.028 0.13 0.34 2 -0.58 6 8
ETS1 0.031 0.026 -10000 0 -0.25 3 3
PXN 0.057 0.14 0.36 19 -0.67 5 24
ITGB1 0.026 0.02 -10000 0 -0.35 1 1
NOS3 0.034 0.13 0.38 5 -0.67 6 11
RAC1 0.026 0.008 -10000 0 -10000 0 0
TNF 0.014 0.084 -10000 0 -0.34 21 21
MAPKKK cascade 0.02 0.11 -10000 0 -0.84 6 6
RASA1 0.025 0.008 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.041 0.12 -10000 0 -0.86 6 6
NCK1 0.027 0.005 -10000 0 -10000 0 0
vasculogenesis 0.037 0.11 0.34 7 -0.53 6 13
mol:Phosphatidic acid 0.02 0.11 -10000 0 -0.84 6 6
mol:Angiotensin II 0 0.005 -10000 0 -10000 0 0
mol:NADP 0.036 0.12 0.36 6 -0.59 6 12
Rac1/GTP 0.033 0.12 -10000 0 -0.71 6 6
MMP2 0.018 0.12 -10000 0 -0.87 6 6
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.027 0.006 -9999 0 -10000 0 0
SPHK1 0.011 0.078 -9999 0 -0.35 18 18
GNAI2 0.027 0.005 -9999 0 -10000 0 0
mol:S1P 0.009 0.028 -9999 0 -0.24 1 1
GNAO1 -0.055 0.16 -9999 0 -0.38 82 82
mol:Sphinganine-1-P 0.002 0.051 -9999 0 -0.24 17 17
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.047 0.046 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.038 0.013 -9999 0 -10000 0 0
S1PR3 0.023 0.039 -9999 0 -0.37 4 4
S1PR2 0.026 0.019 -9999 0 -0.35 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.002 0.033 -9999 0 -0.2 4 4
S1PR5 0.017 0.062 -9999 0 -0.35 11 11
S1PR4 0.023 0.038 -9999 0 -0.35 4 4
GNAI1 0.02 0.054 -9999 0 -0.38 7 7
S1P/S1P5/G12 0.031 0.053 -9999 0 -0.26 3 3
S1P/S1P3/Gq 0.016 0.07 -9999 0 -0.3 15 15
S1P/S1P4/Gi -0.033 0.12 -9999 0 -0.35 33 33
GNAQ 0.027 0.006 -9999 0 -10000 0 0
GNAZ 0.001 0.1 -9999 0 -0.38 26 26
GNA14 0.02 0.053 -9999 0 -0.38 7 7
GNA15 0.022 0.042 -9999 0 -0.35 5 5
GNA12 0.026 0.008 -9999 0 -10000 0 0
GNA13 0.027 0.005 -9999 0 -10000 0 0
GNA11 0.026 0.007 -9999 0 -10000 0 0
ABCC1 0.027 0.005 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.008 0.094 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.027 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.01 0.097 0.29 4 -0.28 8 12
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.026 0.047 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.023 0.064 -10000 0 -0.23 9 9
CaM/Ca2+ 0.01 0.091 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.089 -10000 0 -0.3 8 8
AKT1 -0.006 0.088 0.3 6 -10000 0 6
MAP2K1 -0.027 0.075 0.28 3 -10000 0 3
MAP3K11 -0.017 0.078 0.28 1 -10000 0 1
IFNGR1 0.016 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.044 0.13 -10000 0 -0.34 36 36
Rap1/GTP -0.014 0.063 -10000 0 -10000 0 0
CRKL/C3G 0.039 0.011 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.01 0.1 -10000 0 -10000 0 0
CEBPB 0.01 0.11 0.31 3 -0.52 5 8
STAT3 0.028 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.002 0.15 -10000 0 -0.66 12 12
STAT1 -0.021 0.086 0.22 2 -0.3 8 10
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.066 0.16 -10000 0 -0.35 101 101
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.005 0.093 0.28 4 -0.29 8 12
CEBPB/PTGES2/Cbp/p300 0.011 0.073 -10000 0 -0.37 3 3
mol:Ca2+ 0.006 0.091 -10000 0 -10000 0 0
MAPK3 -0.015 0.12 -10000 0 -0.68 8 8
STAT1 (dimer) -0.025 0.088 -10000 0 -0.36 4 4
MAPK1 -0.027 0.14 -10000 0 -0.67 15 15
JAK2 0.013 0.025 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
JAK1 0.016 0.025 -10000 0 -10000 0 0
CAMK2D 0.027 0.005 -10000 0 -10000 0 0
DAPK1 0.013 0.096 0.28 5 -0.44 6 11
SMAD7 -0.001 0.049 0.15 12 -10000 0 12
CBL/CRKL/C3G 0.006 0.088 0.28 3 -10000 0 3
PI3K 0.007 0.087 -10000 0 -10000 0 0
IFNG -0.066 0.16 -10000 0 -0.35 101 101
apoptosis 0.006 0.095 0.26 4 -0.42 9 13
CAMK2G 0.027 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.004 -10000 0 -10000 0 0
CAMK2A 0.004 0.092 -10000 0 -0.36 24 24
CAMK2B -0.047 0.16 -10000 0 -0.38 73 73
FRAP1 -0.015 0.081 0.29 6 -10000 0 6
PRKCD -0.013 0.089 0.28 6 -10000 0 6
RAP1B 0.027 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.023 0.064 -10000 0 -0.23 9 9
PTPN2 0.026 0.007 -10000 0 -10000 0 0
EP300 0.027 0.005 -10000 0 -10000 0 0
IRF1 -0.014 0.075 0.27 5 -10000 0 5
STAT1 (dimer)/PIASy -0.006 0.094 0.28 4 -0.29 8 12
SOCS1 -0.005 0.18 -10000 0 -1 12 12
mol:GDP 0.004 0.083 0.26 3 -10000 0 3
CASP1 -0.003 0.055 0.15 11 -0.22 7 18
PTGES2 0.027 0.006 -10000 0 -10000 0 0
IRF9 0.018 0.047 0.16 13 -10000 0 13
mol:PI-3-4-5-P3 -0.004 0.077 -10000 0 -10000 0 0
RAP1/GDP 0 0.073 -10000 0 -10000 0 0
CBL -0.019 0.077 0.2 4 -10000 0 4
MAP3K1 -0.016 0.077 0.28 1 -10000 0 1
PIAS1 0.027 0.005 -10000 0 -10000 0 0
PIAS4 0.026 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.023 0.064 -10000 0 -0.23 9 9
PTPN11 -0.013 0.087 0.28 5 -10000 0 5
CREBBP 0.027 0.007 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.03 0.072 -10000 0 -10000 0 0
UGCG 0.008 0.095 -10000 0 -0.61 9 9
AKT1/mTOR/p70S6K/Hsp90/TERT 0.003 0.11 0.24 1 -0.44 12 13
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.01 0.094 -10000 0 -0.6 9 9
mol:DAG -0.004 0.12 -10000 0 -0.79 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.1 -10000 0 -0.49 5 5
FRAP1 0.016 0.11 -10000 0 -0.55 6 6
FOXO3 0.02 0.096 -10000 0 -0.46 3 3
AKT1 0.019 0.1 -10000 0 -0.46 4 4
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 0.001 0.12 -10000 0 -0.64 13 13
SGMS1 0.009 0.09 -10000 0 -0.57 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 0.004 0.006 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation 0.034 0.091 0.23 2 -0.38 8 10
EIF3A 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.016 -10000 0 -10000 0 0
RPS6KB1 0.005 0.074 -10000 0 -0.88 2 2
mol:sphingomyelin -0.004 0.12 -10000 0 -0.79 9 9
natural killer cell activation 0 0.001 -10000 0 -0.011 2 2
JAK3 0.012 0.078 -10000 0 -0.35 18 18
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
JAK1 0.029 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MYC 0.051 0.13 0.36 3 -0.9 2 5
MYB -0.024 0.12 -10000 0 -0.52 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.022 0.079 -10000 0 -0.37 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.029 0.077 -10000 0 -0.8 2 2
mol:PI-3-4-5-P3 0.021 0.081 -10000 0 -0.35 4 4
Rac1/GDP 0.02 0.012 -10000 0 -10000 0 0
T cell proliferation 0.025 0.074 0.24 5 -0.33 3 8
SHC1 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.003 0.014 -10000 0 -0.033 76 76
PRKCZ 0.026 0.074 0.25 5 -0.34 3 8
NF kappa B1 p50/RelA 0.038 0.11 -10000 0 -0.5 5 5
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.019 0.047 -10000 0 -0.3 1 1
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.004 0.1 -10000 0 -0.35 33 33
IL2RB 0.028 0.021 -10000 0 -0.39 1 1
TERT -0.077 0.17 -10000 0 -0.35 111 111
E2F1 -0.009 0.081 -10000 0 -0.41 3 3
SOS1 0.028 0.003 -10000 0 -10000 0 0
RPS6 0.025 0.009 -10000 0 -10000 0 0
mol:cAMP 0.001 0.007 0.016 75 -10000 0 75
PTPN11 0.028 0.005 -10000 0 -10000 0 0
IL2RG 0.02 0.059 -10000 0 -0.37 9 9
actin cytoskeleton organization 0.025 0.074 0.24 5 -0.33 3 8
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL2 0.022 0.028 -10000 0 -0.35 2 2
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.044 0.024 -10000 0 -10000 0 0
LCK 0.019 0.062 -10000 0 -0.35 11 11
BCL2 0.014 0.12 -10000 0 -0.81 6 6
Class I PI3K signaling events

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
ARF5/GTP 0.002 0.057 0.3 1 -10000 0 1
DAPP1 0.013 0.12 0.25 14 -0.36 14 28
Src family/SYK family/BLNK-LAT/BTK-ITK 0.002 0.14 0.27 1 -0.48 15 16
mol:DAG 0.023 0.086 0.2 40 -0.21 4 44
HRAS 0.028 0.009 -10000 0 -10000 0 0
RAP1A 0.029 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.037 0.071 0.2 3 -0.3 6 9
PLCG2 0.019 0.055 -10000 0 -0.37 8 8
PLCG1 0.023 0.011 -10000 0 -10000 0 0
ARF5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.05 0.17 4 -10000 0 4
ARF1/GTP 0.009 0.049 0.23 6 -10000 0 6
RHOA 0.027 0.006 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0 0.052 0.15 40 -10000 0 40
ADAP1 -0.003 0.046 0.16 3 -10000 0 3
ARAP3 -0.001 0.05 0.16 4 -10000 0 4
INPPL1 0.026 0.02 -10000 0 -0.35 1 1
PREX1 0.023 0.011 -10000 0 -10000 0 0
ARHGEF6 0.023 0.041 -10000 0 -0.38 4 4
ARHGEF7 0.026 0.008 -10000 0 -10000 0 0
ARF1 0.027 0.005 -10000 0 -10000 0 0
NRAS 0.029 0.008 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
FGR 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.018 0.058 0.17 23 -10000 0 23
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.017 0.062 -10000 0 -0.37 10 10
ZAP70 0.008 0.085 -10000 0 -0.36 21 21
mol:IP3 0.016 0.067 0.19 22 -10000 0 22
LYN 0.025 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.038 0.072 0.2 4 -0.3 6 10
RhoA/GDP 0.046 0.057 0.21 16 -10000 0 16
PDK1/Src/Hsp90 0.044 0.029 -10000 0 -0.21 2 2
BLNK 0.011 0.08 -10000 0 -0.38 16 16
actin cytoskeleton reorganization 0.043 0.078 0.24 27 -10000 0 27
SRC 0.024 0.01 -10000 0 -10000 0 0
PLEKHA2 -0.01 0.017 -10000 0 -0.2 3 3
RAC1 0.026 0.008 -10000 0 -10000 0 0
PTEN 0.022 0.016 -10000 0 -10000 0 0
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
ARF6/GTP -0.002 0.052 0.16 1 -10000 0 1
RhoA/GTP -0.002 0.051 0.15 26 -10000 0 26
Src family/SYK family/BLNK-LAT -0.004 0.099 -10000 0 -0.36 15 15
BLK -0.041 0.15 -10000 0 -0.38 66 66
PDPK1 0.027 0.007 -10000 0 -10000 0 0
CYTH1 -0.002 0.05 0.16 4 -10000 0 4
HCK 0.024 0.01 -10000 0 -10000 0 0
CYTH3 -0.003 0.045 0.16 3 -10000 0 3
CYTH2 -0.002 0.049 0.16 5 -10000 0 5
KRAS 0.025 0.011 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.015 0.049 -10000 0 -0.38 3 3
SGK1 0.018 0.057 -10000 0 -0.36 5 5
INPP5D 0.025 0.034 -10000 0 -0.36 3 3
mol:GDP 0.026 0.071 0.19 6 -0.32 6 12
SOS1 0.028 0.003 -10000 0 -10000 0 0
SYK 0.026 0.021 -10000 0 -0.38 1 1
ARF6/GDP 0.033 0.056 0.21 16 -10000 0 16
mol:PI-3-4-5-P3 -0.003 0.046 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0 0.052 0.16 40 -10000 0 40
VAV1 0.022 0.043 -10000 0 -0.36 5 5
mol:PI-3-4-P2 0.01 0.026 -10000 0 -0.25 4 4
RAS family/GTP/PI3K Class I 0.04 0.04 -10000 0 -10000 0 0
PLEKHA1 -0.01 0.017 -10000 0 -0.2 3 3
Rac1/GDP 0.033 0.07 0.19 3 -0.3 6 9
LAT 0.026 0.019 -10000 0 -0.35 1 1
Rac1/GTP 0.015 0.059 -10000 0 -0.41 3 3
ITK -0.009 0.059 0.16 2 -10000 0 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.02 0.098 0.21 35 -0.28 6 41
LCK 0.017 0.062 -10000 0 -0.35 11 11
BTK -0.008 0.056 0.16 4 -10000 0 4
FoxO family signaling

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
G6PC -0.1 0.36 0.35 2 -1.2 40 42
PLK1 0.026 0.13 -10000 0 -1.4 1 1
CDKN1B 0.044 0.12 0.31 5 -0.36 6 11
FOXO3 0.04 0.11 -10000 0 -0.73 3 3
KAT2B 0.027 0.044 -10000 0 -0.38 4 4
FOXO1/SIRT1 -0.008 0.13 0.26 2 -0.39 36 38
CAT 0.035 0.12 0.43 1 -0.89 3 4
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.022 0.032 -10000 0 -10000 0 0
FOXO1 -0.021 0.14 0.33 2 -0.41 39 41
MAPK10 0.001 0.078 0.2 15 -0.19 46 61
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.023 0.078 0.34 3 -0.36 1 4
response to oxidative stress 0.002 0.02 -10000 0 -0.13 1 1
FOXO3A/SIRT1 0.044 0.11 -10000 0 -0.55 5 5
XPO1 0.028 0.003 -10000 0 -10000 0 0
EP300 0.018 0.029 -10000 0 -10000 0 0
BCL2L11 0.029 0.062 -10000 0 -0.8 2 2
FOXO1/SKP2 -0.01 0.13 0.27 2 -0.39 36 38
mol:GDP 0.002 0.02 -10000 0 -0.13 1 1
RAN 0.028 0.005 -10000 0 -10000 0 0
GADD45A 0.043 0.12 -10000 0 -0.66 6 6
YWHAQ 0.028 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.019 0.13 0.24 1 -0.45 18 19
MST1 -0.001 0.11 -10000 0 -0.35 34 34
CSNK1D 0.027 0.005 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.006 0.12 -10000 0 -0.45 16 16
YWHAB 0.022 0.011 -10000 0 -10000 0 0
MAPK8 0.026 0.042 0.2 19 -10000 0 19
MAPK9 0.027 0.043 0.2 21 -10000 0 21
YWHAG 0.026 0.007 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
SIRT1 0.027 0.01 -10000 0 -10000 0 0
SOD2 0.034 0.12 0.37 1 -0.53 3 4
RBL2 0.023 0.17 -10000 0 -0.69 16 16
RAL/GDP 0.036 0.026 -10000 0 -10000 0 0
CHUK 0.03 0.018 -10000 0 -10000 0 0
Ran/GTP 0.023 0.004 -10000 0 -10000 0 0
CSNK1G2 0.026 0.007 -10000 0 -10000 0 0
RAL/GTP 0.039 0.024 -10000 0 -10000 0 0
CSNK1G1 0.027 0.005 -10000 0 -10000 0 0
FASLG -0.003 0.2 -10000 0 -1.2 11 11
SKP2 0.023 0.028 -10000 0 -0.35 2 2
USP7 0.028 0.006 -10000 0 -10000 0 0
IKBKB 0.028 0.018 -10000 0 -10000 0 0
CCNB1 0.032 0.11 -10000 0 -0.94 1 1
FOXO1-3a-4/beta catenin 0.048 0.11 0.28 10 -0.39 1 11
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.13 0.27 2 -0.38 36 38
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
SGK1 0.028 0.034 -10000 0 -0.4 2 2
CSNK1G3 0.026 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.008 -10000 0 -10000 0 0
ZFAND5 0.024 0.073 0.43 2 -10000 0 2
SFN 0.015 0.067 -10000 0 -0.37 12 12
CDK2 0.015 0.038 -10000 0 -0.2 1 1
FOXO3A/14-3-3 0.014 0.11 -10000 0 -0.45 12 12
CREBBP 0.015 0.037 -10000 0 -0.19 1 1
FBXO32 0.057 0.16 0.44 4 -0.95 5 9
BCL6 0.046 0.098 -10000 0 -0.67 2 2
RALB 0.029 0.003 -10000 0 -10000 0 0
RALA 0.027 0.007 -10000 0 -10000 0 0
YWHAH 0.027 0.005 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.025 0.009 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.04 0.055 -10000 0 -0.25 1 1
NEF -0.003 0.029 -10000 0 -0.16 9 9
NFKBIA 0.028 0.013 -10000 0 -10000 0 0
BIRC3 0.018 0.05 -10000 0 -0.34 6 6
CYCS 0.019 0.055 0.19 23 -10000 0 23
RIPK1 0.026 0.007 -10000 0 -10000 0 0
CD247 0.018 0.06 -10000 0 -0.4 6 6
MAP2K7 0 0.17 0.28 1 -0.62 23 24
protein ubiquitination 0.021 0.085 0.22 13 -0.36 8 21
CRADD 0.028 0.004 -10000 0 -10000 0 0
DAXX 0.027 0.006 -10000 0 -10000 0 0
FAS 0.026 0.007 -10000 0 -10000 0 0
BID 0.014 0.048 0.18 6 -0.23 7 13
NF-kappa-B/RelA/I kappa B alpha 0.056 0.034 -10000 0 -0.2 5 5
TRADD 0.027 0.006 -10000 0 -10000 0 0
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
CFLAR 0.028 0.003 -10000 0 -10000 0 0
FADD 0.026 0.007 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.056 0.035 -10000 0 -0.2 5 5
MAPK8 0.001 0.16 0.32 3 -0.57 23 26
APAF1 0.028 0.004 -10000 0 -10000 0 0
TRAF1 0.025 0.027 -10000 0 -0.35 2 2
TRAF2 0.027 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.021 0.05 0.19 6 -0.24 7 13
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.019 0.09 -10000 0 -0.44 10 10
CHUK 0.02 0.089 0.23 13 -0.39 8 21
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.069 0.032 -10000 0 -10000 0 0
TCRz/NEF 0.013 0.061 -10000 0 -0.25 20 20
TNF 0.01 0.08 -10000 0 -0.36 18 18
FASLG 0 0.09 -10000 0 -0.43 15 15
NFKB1 0.028 0.014 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.036 0.054 -10000 0 -0.21 16 16
CASP6 0.039 0.097 -10000 0 -0.47 6 6
CASP7 0.033 0.079 0.26 9 -0.45 2 11
RELA 0.028 0.014 -10000 0 -10000 0 0
CASP2 0.027 0.006 -10000 0 -10000 0 0
CASP3 0.022 0.085 0.25 9 -0.42 3 12
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.036 0.015 -10000 0 -10000 0 0
CASP8 0.028 0.003 -10000 0 -10000 0 0
CASP9 0.027 0.006 -10000 0 -10000 0 0
MAP3K14 0.018 0.092 0.2 4 -0.4 11 15
APAF-1/Caspase 9 0.027 0.056 -10000 0 -0.28 1 1
BCL2 0 0.14 0.31 3 -0.52 23 26
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.02 0.022 -10000 0 -10000 0 0
HSPA8 0.026 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.05 0.082 -10000 0 -0.26 10 10
AKT1 0.026 0.019 -10000 0 -10000 0 0
GSC -0.061 0.25 -10000 0 -1.1 19 19
NKX2-5 0.001 0 -10000 0 -10000 0 0
muscle cell differentiation -0.001 0.1 0.33 12 -10000 0 12
SMAD2-3/SMAD4/SP1 0.046 0.082 -10000 0 -10000 0 0
SMAD4 0.021 0.039 -10000 0 -10000 0 0
CBFB 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.016 0.082 -10000 0 -0.21 39 39
SMAD3/SMAD4/VDR 0.068 0.056 -10000 0 -10000 0 0
MYC 0.019 0.031 -10000 0 -0.39 2 2
CDKN2B -0.085 0.26 -10000 0 -0.92 21 21
AP1 0.03 0.061 -10000 0 -0.25 2 2
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.011 0.098 -10000 0 -0.44 9 9
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.004 0.084 -10000 0 -0.35 15 15
SP3 0.029 0.004 -10000 0 -10000 0 0
CREB1 0.028 0.004 -10000 0 -10000 0 0
FOXH1 -0.05 0.15 -10000 0 -0.36 74 74
SMAD3/SMAD4/GR 0.053 0.064 -10000 0 -0.25 5 5
GATA3 0.017 0.061 -10000 0 -0.35 10 10
SKI/SIN3/HDAC complex/NCoR1 0.018 0.069 -10000 0 -0.39 7 7
MEF2C/TIF2 -0.005 0.093 0.22 1 -0.36 4 5
endothelial cell migration 0.036 0.13 0.52 6 -10000 0 6
MAX 0.031 0.011 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
RUNX2 0.022 0.042 -10000 0 -0.35 5 5
RUNX3 0.025 0.027 -10000 0 -0.35 2 2
RUNX1 0.018 0.053 -10000 0 -0.35 8 8
CTBP1 0.026 0.007 -10000 0 -10000 0 0
NR3C1 0.025 0.047 -10000 0 -0.39 5 5
VDR 0.027 0.005 -10000 0 -10000 0 0
CDKN1A 0.008 0.094 -10000 0 -0.73 4 4
KAT2B 0.023 0.04 -10000 0 -0.38 4 4
SMAD2/SMAD2/SMAD4/FOXH1 -0.009 0.12 -10000 0 -0.27 29 29
DCP1A 0.027 0.005 -10000 0 -10000 0 0
SKI 0.027 0.007 -10000 0 -10000 0 0
SERPINE1 -0.037 0.13 -10000 0 -0.53 6 6
SMAD3/SMAD4/ATF2 0.051 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.048 0.057 -10000 0 -0.24 5 5
SAP30 0.026 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.039 0.043 -10000 0 -10000 0 0
JUN 0.017 0.056 -10000 0 -0.25 2 2
SMAD3/SMAD4/IRF7 0.049 0.059 -10000 0 -0.26 1 1
TFE3 0.018 0.029 -10000 0 -0.16 2 2
COL1A2 -0.023 0.11 -10000 0 -0.29 58 58
mesenchymal cell differentiation -0.046 0.059 0.27 4 -10000 0 4
DLX1 -0.028 0.14 -10000 0 -0.38 56 56
TCF3 0.026 0.007 -10000 0 -10000 0 0
FOS 0.008 0.092 -10000 0 -0.39 21 21
SMAD3/SMAD4/Max 0.057 0.054 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.05 0.02 -10000 0 -10000 0 0
ZBTB17 0.026 0.009 -10000 0 -10000 0 0
LAMC1 0.015 0.042 -10000 0 -0.31 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.048 0.047 -10000 0 -10000 0 0
IRF7 0.024 0.027 -10000 0 -0.35 1 1
ESR1 0.014 0.078 -10000 0 -0.38 15 15
HNF4A 0.013 0.06 -10000 0 -0.38 9 9
MEF2C -0.006 0.099 0.2 3 -0.35 4 7
SMAD2-3/SMAD4 0.048 0.059 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.047 0.027 -10000 0 -10000 0 0
IGHV3OR16-13 0.011 0.026 -10000 0 -0.32 2 2
TGIF2/HDAC complex 0.024 0.01 -10000 0 -10000 0 0
CREBBP 0.019 0.02 -10000 0 -10000 0 0
SKIL 0.026 0.008 -10000 0 -10000 0 0
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
SNIP1 0.028 0.005 -10000 0 -10000 0 0
GCN5L2 0 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.048 0.057 -10000 0 -0.33 2 2
MSG1/HSC70 0.012 0.084 -10000 0 -0.25 39 39
SMAD2 0.018 0.034 -10000 0 -0.15 4 4
SMAD3 0.027 0.036 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.021 0.036 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.016 0.062 -10000 0 -0.28 6 6
NCOR1 0.026 0.008 -10000 0 -10000 0 0
NCOA2 0.024 0.022 -10000 0 -0.38 1 1
NCOA1 0.028 0.003 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.035 -10000 0 -0.25 6 6
SMAD2-3/SMAD4/SP1/MIZ-1 0.057 0.083 -10000 0 -10000 0 0
IFNB1 0.006 0.064 -10000 0 -0.42 7 7
SMAD3/SMAD4/MEF2C 0.016 0.11 0.24 1 -0.34 3 4
CITED1 -0.009 0.11 -10000 0 -0.36 39 39
SMAD2-3/SMAD4/ARC105 0.059 0.062 -10000 0 -0.26 1 1
RBL1 0.024 0.01 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.013 0.098 -10000 0 -0.54 8 8
RUNX1-3/PEBPB2 0.043 0.046 -10000 0 -0.22 9 9
SMAD7 0.024 0.07 -10000 0 -0.38 2 2
MYC/MIZ-1 0.028 0.028 -10000 0 -0.27 2 2
SMAD3/SMAD4 -0.006 0.083 0.26 10 -0.3 1 11
IL10 0.012 0.068 -10000 0 -0.34 7 7
PIASy/HDAC complex 0.024 0.017 -10000 0 -10000 0 0
PIAS3 0.026 0.007 -10000 0 -10000 0 0
CDK2 0.021 0.018 -10000 0 -10000 0 0
IL5 0.009 0.063 -10000 0 -0.32 5 5
CDK4 0.021 0.02 -10000 0 -10000 0 0
PIAS4 0.024 0.017 -10000 0 -10000 0 0
ATF3 0.022 0.045 -10000 0 -0.38 5 5
SMAD3/SMAD4/SP1 0.035 0.075 -10000 0 -10000 0 0
FOXG1 -0.009 0.061 -10000 0 -0.35 11 11
FOXO3 0.013 0.019 -10000 0 -10000 0 0
FOXO1 0.012 0.018 -10000 0 -10000 0 0
FOXO4 0.012 0.024 -10000 0 -0.27 1 1
heart looping -0.006 0.098 0.2 4 -0.35 4 8
CEBPB 0.022 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.013 0.11 -10000 0 -0.25 40 40
MYOD1 0.014 0.045 -10000 0 -0.35 6 6
SMAD3/SMAD4/HNF4 0.039 0.063 -10000 0 -0.28 7 7
SMAD3/SMAD4/GATA3 0.044 0.071 -10000 0 -10000 0 0
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.062 0.07 -10000 0 -0.31 2 2
SMAD3/SMAD4/SP1-3 0.049 0.076 -10000 0 -10000 0 0
MED15 0.026 0.02 -10000 0 -0.35 1 1
SP1 0.014 0.042 -10000 0 -10000 0 0
SIN3B 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.003 0.1 -10000 0 -0.26 19 19
ITGB5 0.01 0.049 0.22 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP 0.023 0.055 -10000 0 -0.37 4 4
SMAD3/SMAD4/AR 0.018 0.11 -10000 0 -0.25 34 34
AR -0.024 0.14 -10000 0 -0.38 51 51
negative regulation of cell growth 0.014 0.06 -10000 0 -0.28 4 4
SMAD3/SMAD4/MYOD 0.042 0.057 -10000 0 -0.28 1 1
E2F5 0.023 0.028 -10000 0 -0.35 2 2
E2F4 0.027 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.011 0.11 -10000 0 -0.27 10 10
SMAD2-3/SMAD4/FOXO1-3a-4 0.018 0.082 -10000 0 -0.4 11 11
TFDP1 0.026 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.049 0.07 -10000 0 -0.25 2 2
SMAD3/SMAD4/RUNX2 0.046 0.059 -10000 0 -0.28 4 4
TGIF2 0.024 0.01 -10000 0 -10000 0 0
TGIF1 0.027 0.006 -10000 0 -10000 0 0
ATF2 0.028 0.004 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.02 0.046 -9999 0 -0.35 6 6
PLK4 0.023 0.038 -9999 0 -0.35 4 4
regulation of centriole replication 0.006 0.039 -9999 0 -0.24 10 10
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.044 0.048 -10000 0 -0.23 11 11
forebrain development -0.015 0.14 -10000 0 -0.57 14 14
GNAO1 -0.055 0.16 -10000 0 -0.38 82 82
SMO/beta Arrestin2 0.029 0.049 -10000 0 -0.26 10 10
SMO 0.016 0.064 -10000 0 -0.39 10 10
ARRB2 0.026 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.031 0.091 0.24 1 -0.53 4 5
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.027 0.005 -10000 0 -10000 0 0
GNAI2 0.027 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.061 0.027 -10000 0 -10000 0 0
GNAI1 0.02 0.054 -10000 0 -0.38 7 7
XPO1 0.026 0.013 -10000 0 -10000 0 0
GLI1/Su(fu) -0.008 0.13 -10000 0 -0.57 11 11
SAP30 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.016 0.064 -10000 0 -0.38 10 10
MIM/GLI2A 0.019 0.038 -10000 0 -0.41 1 1
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GLI2 0.007 0.072 0.21 1 -0.27 14 15
GLI3 0.019 0.092 0.24 1 -0.46 6 7
CSNK1D 0.027 0.005 -10000 0 -10000 0 0
CSNK1E 0.027 0.005 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.027 0.019 -10000 0 -0.35 1 1
Gi family/GTP -0.036 0.13 -10000 0 -0.38 32 32
SIN3B 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.026 0.088 0.23 1 -0.46 7 8
GLI2/Su(fu) 0.014 0.081 0.2 1 -0.35 7 8
FOXA2 -0.024 0.21 -10000 0 -0.93 20 20
neural tube patterning -0.015 0.14 -10000 0 -0.57 14 14
SPOP 0.028 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.044 -10000 0 -0.32 1 1
GNB1 0.026 0.007 -10000 0 -10000 0 0
CSNK1G2 0.026 0.007 -10000 0 -10000 0 0
CSNK1G3 0.026 0.008 -10000 0 -10000 0 0
MTSS1 0.019 0.038 -10000 0 -0.41 1 1
embryonic limb morphogenesis -0.015 0.14 -10000 0 -0.57 14 14
SUFU 0.018 0.031 -10000 0 -0.34 1 1
LGALS3 0.025 0.029 -10000 0 -0.38 2 2
catabolic process 0.03 0.12 0.24 3 -0.45 12 15
GLI3A/CBP 0.021 0.057 -10000 0 -0.31 10 10
KIF3A 0.025 0.02 -10000 0 -0.35 1 1
GLI1 -0.016 0.14 -10000 0 -0.59 14 14
RAB23 0.013 0.071 -10000 0 -0.35 15 15
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
IFT172 0.028 0.003 -10000 0 -10000 0 0
RBBP7 0.027 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.026 0.048 -10000 0 -0.32 1 1
GNAZ 0.001 0.1 -10000 0 -0.38 26 26
RBBP4 0.027 0.005 -10000 0 -10000 0 0
CSNK1G1 0.027 0.005 -10000 0 -10000 0 0
PIAS1 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.027 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.018 0.077 0.2 1 -0.31 8 9
STK36 0.026 0.013 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.031 0.12 -10000 0 -0.37 30 30
PTCH1 -0.014 0.14 0.41 1 -0.74 7 8
MIM/GLI1 -0.015 0.16 -10000 0 -0.58 15 15
CREBBP 0.021 0.057 -10000 0 -0.31 10 10
Su(fu)/SIN3/HDAC complex 0.017 0.088 -10000 0 -0.43 12 12
Aurora A signaling

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
Aurora A/GADD45A 0.024 0.041 -10000 0 -0.26 3 3
BIRC5 0.009 0.083 -10000 0 -0.36 20 20
NFKBIA 0.003 0.034 0.25 2 -0.26 3 5
CPEB1 -0.08 0.18 -10000 0 -0.38 106 106
AKT1 0.002 0.029 -10000 0 -0.26 3 3
NDEL1 0.026 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.016 0.036 -10000 0 -0.22 4 4
NDEL1/TACC3 0.042 0.045 -10000 0 -0.3 2 2
GADD45A 0.028 0.004 -10000 0 -10000 0 0
GSK3B 0.026 0.007 -10000 0 -10000 0 0
PAK1/Aurora A 0.025 0.041 -10000 0 -0.26 3 3
MDM2 0.025 0.027 -10000 0 -0.35 2 2
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.001 0.056 -10000 0 -0.25 20 20
TP53 0.014 0.026 -10000 0 -0.2 1 1
DLG7 0.003 0.028 -10000 0 -0.25 3 3
AURKAIP1 0.026 0.007 -10000 0 -10000 0 0
ARHGEF7 0.026 0.008 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.045 0.047 -10000 0 -0.32 2 2
G2/M transition of mitotic cell cycle 0.016 0.035 -10000 0 -0.22 4 4
AURKA 0.008 0.036 -10000 0 -0.3 3 3
AURKB 0.009 0.022 -10000 0 -0.15 3 3
CDC25B 0.009 0.028 -10000 0 -0.24 3 3
G2/M transition checkpoint 0.003 0.028 -10000 0 -0.23 3 3
mRNA polyadenylation -0.031 0.094 -10000 0 -0.21 79 79
Aurora A/CPEB -0.031 0.094 -10000 0 -0.21 79 79
Aurora A/TACC1/TRAP/chTOG 0.055 0.049 -10000 0 -0.22 3 3
BRCA1 0.027 0.019 -10000 0 -0.35 1 1
centrosome duplication 0.025 0.041 -10000 0 -0.26 3 3
regulation of centrosome cycle 0.041 0.044 -10000 0 -0.29 2 2
spindle assembly 0.054 0.048 -10000 0 -0.21 3 3
TDRD7 0.027 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.046 0.064 -10000 0 -0.25 6 6
CENPA 0.011 0.027 -10000 0 -0.21 2 2
Aurora A/PP2A 0.023 0.042 -10000 0 -0.26 3 3
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.012 0.036 -10000 0 -0.25 3 3
negative regulation of DNA binding 0.013 0.03 -10000 0 -0.2 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.038 0.013 -10000 0 -10000 0 0
RASA1 0.025 0.008 -10000 0 -10000 0 0
Ajuba/Aurora A 0.003 0.028 -10000 0 -0.23 3 3
mitotic prometaphase 0.003 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.036 -10000 0 -0.3 3 3
TACC1 0.025 0.009 -10000 0 -10000 0 0
TACC3 0.025 0.02 -10000 0 -0.35 1 1
Aurora A/Antizyme1 0.047 0.043 -10000 0 -0.22 3 3
Aurora A/RasGAP 0.023 0.04 -10000 0 -0.24 3 3
OAZ1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.026 0.007 -10000 0 -10000 0 0
GIT1 0.028 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.019 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.001 0.056 -10000 0 -0.25 20 20
PPP2R5D 0.026 0.007 -10000 0 -10000 0 0
Aurora A/TPX2 0.005 0.058 -10000 0 -0.3 8 8
PAK1 0.027 0.005 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.028 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.035 0.059 -9999 0 -0.21 20 20
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.008 0.026 -9999 0 -0.29 2 2
AURKB 0.018 0.056 -9999 0 -0.36 9 9
AURKC 0.014 0.068 -9999 0 -0.36 13 13
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.002 0.091 -10000 0 -0.36 18 18
KLHL20 0.026 0.064 0.18 12 -0.2 3 15
CYFIP2 0.02 0.053 -10000 0 -0.38 7 7
Rac1/GDP 0.034 0.084 0.25 14 -0.28 2 16
ENAH 0.004 0.089 -10000 0 -0.37 16 16
AP1M1 0.027 0.005 -10000 0 -10000 0 0
RAP1B 0.027 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.016 0.038 -10000 0 -0.22 1 1
ABI1/Sra1/Nap1 -0.01 0.029 -10000 0 -0.16 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.054 0.049 -10000 0 -0.2 10 10
RAPGEF1 0.017 0.096 0.23 7 -0.33 15 22
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.098 -10000 0 -0.36 20 20
CRK 0.016 0.092 -10000 0 -0.35 15 15
E-cadherin/gamma catenin/alpha catenin 0.042 0.045 -10000 0 -0.23 9 9
alphaE/beta7 Integrin 0.037 0.02 -10000 0 -0.27 1 1
IQGAP1 0.026 0.007 -10000 0 -10000 0 0
NCKAP1 0.028 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.018 -10000 0 -10000 0 0
DLG1 0.003 0.091 -10000 0 -0.36 18 18
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.001 0.024 -10000 0 -10000 0 0
MLLT4 0.026 0.007 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.043 0.042 -10000 0 -0.2 10 10
PI3K 0.004 0.031 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.03 0.047 -10000 0 -0.27 9 9
TIAM1 0.017 0.062 -10000 0 -0.37 10 10
E-cadherin(dimer)/Ca2+ 0.052 0.043 -10000 0 -0.19 9 9
AKT1 0.005 0.038 0.13 4 -10000 0 4
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
CDH1 0.018 0.06 -10000 0 -0.38 9 9
RhoA/GDP 0.041 0.087 0.24 19 -0.27 2 21
actin cytoskeleton organization 0.024 0.053 0.16 18 -0.15 1 19
CDC42/GDP 0.04 0.087 0.25 17 -0.27 3 20
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.013 0.035 -10000 0 -0.21 9 9
ITGB7 0.026 0.021 -10000 0 -0.38 1 1
RAC1 0.026 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.056 0.047 -10000 0 -0.2 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin 0.039 0.038 -10000 0 -0.19 9 9
mol:GDP 0.028 0.095 0.26 16 -0.28 9 25
CDC42/GTP/IQGAP1 0.034 0.012 -10000 0 -10000 0 0
JUP 0.026 0.008 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.049 0.088 0.24 22 -0.27 2 24
RAC1/GTP/IQGAP1 0.033 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.039 0.011 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
CDC42 0.026 0.007 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.02 0.039 0.13 14 -0.14 1 15
NME1 0.028 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.003 0.091 -10000 0 -0.36 19 19
regulation of cell-cell adhesion 0.01 0.031 -10000 0 -0.19 1 1
WASF2 0.012 0.025 0.089 1 -10000 0 1
Rap1/GTP 0.036 0.064 0.28 3 -0.24 1 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.059 0.053 -10000 0 -0.2 7 7
CCND1 0.022 0.046 0.16 12 -0.17 1 13
VAV2 0.02 0.13 -10000 0 -0.53 10 10
RAP1/GDP 0.046 0.078 0.25 14 -0.25 1 15
adherens junction assembly 0.004 0.089 -10000 0 -0.35 19 19
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.006 -10000 0 -10000 0 0
PIP5K1C 0.026 0.007 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.052 0.054 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.004 0.048 -10000 0 -0.28 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.001 0.089 -10000 0 -0.36 18 18
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.066 -10000 0 -0.3 7 7
E-cadherin/beta catenin/alpha catenin 0.044 0.044 -10000 0 -0.22 9 9
ITGAE 0.026 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.008 0.1 -10000 0 -0.37 20 20
Regulation of Telomerase

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
Telomerase catalytic core complex -0.077 0.16 -10000 0 -0.53 9 9
RAD9A 0.027 0.006 -10000 0 -10000 0 0
AP1 0.019 0.07 -10000 0 -0.28 21 21
IFNAR2 0.014 0.022 -10000 0 -10000 0 0
AKT1 0.001 0.044 -10000 0 -0.3 3 3
ER alpha/Oestrogen 0.005 0.054 -10000 0 -0.27 15 15
NFX1/SIN3/HDAC complex 0.025 0.04 -10000 0 -0.28 3 3
EGF -0.02 0.12 -10000 0 -0.36 44 44
SMG5 0.027 0.005 -10000 0 -10000 0 0
SMG6 0.026 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.02 0.033 -10000 0 -10000 0 0
TERT/c-Abl -0.065 0.15 -10000 0 -0.52 7 7
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.046 0.023 -10000 0 -10000 0 0
WT1 -0.078 0.16 -10000 0 -0.36 101 101
WRN 0.025 0.009 -10000 0 -10000 0 0
SP1 0.012 0.026 -10000 0 -10000 0 0
SP3 0.026 0.006 -10000 0 -10000 0 0
TERF2IP 0.027 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.048 0.16 -10000 0 -0.5 5 5
Mad/Max 0.034 0.015 -10000 0 -10000 0 0
TERT -0.078 0.16 -10000 0 -0.54 9 9
CCND1 -0.061 0.15 0.44 1 -0.58 4 5
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.005 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
TERF2 0.023 0.022 -10000 0 -0.37 1 1
PTGES3 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
Telomerase/911 0.026 0.053 -10000 0 -0.28 1 1
CDKN1B -0.038 0.092 -10000 0 -10000 0 0
RAD1 0.026 0.008 -10000 0 -10000 0 0
XRCC5 0.028 0.004 -10000 0 -10000 0 0
XRCC6 0.027 0.006 -10000 0 -10000 0 0
SAP30 0.026 0.007 -10000 0 -10000 0 0
TRF2/PARP2 0.037 0.02 -10000 0 -0.29 1 1
UBE3A 0.026 0.006 -10000 0 -10000 0 0
JUN 0.026 0.005 -10000 0 -10000 0 0
E6 -0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.01 0.017 -10000 0 -10000 0 0
FOS 0.005 0.091 -10000 0 -0.39 21 21
IFN-gamma/IRF1 -0.031 0.12 -10000 0 -0.24 100 100
PARP2 0.028 0.004 -10000 0 -10000 0 0
BLM 0.014 0.069 -10000 0 -0.35 14 14
Telomerase 0.006 0.09 -10000 0 -0.41 8 8
IRF1 0.027 0.01 -10000 0 -10000 0 0
ESR1 0.011 0.077 -10000 0 -0.38 15 15
KU/TER 0.039 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.023 -10000 0 -0.24 2 2
ubiquitin-dependent protein catabolic process 0.024 0.056 -10000 0 -0.33 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.024 0.057 -10000 0 -0.34 4 4
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.011 0.025 -10000 0 -10000 0 0
ATM 0.012 0.016 -10000 0 -0.2 1 1
SMAD3 0.014 0.006 -10000 0 -10000 0 0
ABL1 0.027 0.006 -10000 0 -10000 0 0
MXD1 0.026 0.005 -10000 0 -10000 0 0
MRE11A 0.027 0.005 -10000 0 -10000 0 0
HUS1 0.026 0.007 -10000 0 -10000 0 0
RPS6KB1 0.028 0.004 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.054 0.16 -10000 0 -0.56 5 5
NR2F2 0.03 0.01 -10000 0 -10000 0 0
MAPK3 -0.007 0.023 -10000 0 -0.24 2 2
MAPK1 -0.007 0.023 -10000 0 -0.24 2 2
TGFB1/TGF beta receptor Type II 0.027 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
HNRNPC 0.028 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.016 -10000 0 -0.2 1 1
NBN 0.025 0.01 -10000 0 -10000 0 0
EGFR 0.016 0.057 -10000 0 -0.39 8 8
mol:Oestrogen -0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.005 0.093 -10000 0 -0.26 48 48
MYC 0.019 0.031 -10000 0 -0.39 2 2
IL2 0.005 0.036 -10000 0 -0.35 2 2
KU 0.039 0.01 -10000 0 -10000 0 0
RAD50 0.026 0.007 -10000 0 -10000 0 0
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
TGFB1 0.027 0.007 -10000 0 -10000 0 0
TRF2/BLM 0.027 0.053 -10000 0 -0.25 13 13
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.058 0.16 -10000 0 -0.52 7 7
SP1/HDAC2 0.018 0.037 -10000 0 -10000 0 0
PINX1 0.024 0.01 -10000 0 -10000 0 0
Telomerase/EST1A -0.049 0.15 -10000 0 -0.5 5 5
Smad3/Myc 0.022 0.023 -10000 0 -0.23 2 2
911 complex 0.047 0.022 -10000 0 -10000 0 0
IFNG -0.067 0.16 -10000 0 -0.35 101 101
Telomerase/PinX1 -0.048 0.15 -10000 0 -0.5 5 5
Telomerase/AKT1/mTOR/p70S6K -0.012 0.094 -10000 0 -0.39 11 11
SIN3B 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
Telomerase/EST1B -0.048 0.15 -10000 0 -0.5 5 5
response to DNA damage stimulus 0.002 0.02 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.063 0.037 -10000 0 -0.22 1 1
TRF2/WRN 0.034 0.022 -10000 0 -0.29 1 1
Telomerase/hnRNP C1/C2 -0.047 0.15 -10000 0 -0.5 5 5
E2F1 0.006 0.058 -10000 0 -0.36 9 9
ZNFX1 0.022 0.011 -10000 0 -10000 0 0
PIF1 0.018 0.059 -10000 0 -0.35 10 10
NCL 0.028 0.003 -10000 0 -10000 0 0
DKC1 0.027 0.006 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.028 0.062 -10000 0 -0.2 26 26
MAPK9 0.007 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.012 0.035 -10000 0 -0.24 9 9
GNB1/GNG2 0.035 0.016 -10000 0 -0.2 1 1
GNB1 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.002 -10000 0 -10000 0 0
Gs family/GTP 0.003 0.054 -10000 0 -0.2 27 27
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 0.005 0.014 0.057 27 -10000 0 27
GNAL -0.001 0.1 -10000 0 -0.38 27 27
GNG2 0.027 0.019 -10000 0 -0.35 1 1
CRH 0.01 0.055 -10000 0 -0.35 9 9
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.001 -10000 0 -10000 0 0
MAPK11 0.007 0.002 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.017 0.05 -10000 0 -0.36 7 7
GNB1/GNG2 -0.032 0.039 -10000 0 -0.17 4 4
AKT1 -0.016 0.084 0.26 2 -0.3 10 12
EGF -0.016 0.12 -10000 0 -0.36 44 44
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.008 0.049 0.25 1 -10000 0 1
mol:Ca2+ -0.025 0.089 0.28 2 -0.29 4 6
LYN 0.007 0.045 0.25 1 -10000 0 1
RhoA/GTP -0.013 0.039 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.03 0.095 0.51 1 -0.31 2 3
GNG2 0.027 0.019 -10000 0 -0.35 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.012 0.14 -10000 0 -0.59 19 19
G beta5/gamma2 -0.034 0.054 -10000 0 -0.22 4 4
PRKCH -0.028 0.095 0.29 2 -0.32 2 4
DNM1 0.016 0.064 -10000 0 -0.35 12 12
TXA2/TP beta/beta Arrestin3 -0.002 0.082 -10000 0 -0.53 9 9
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.007 0.09 -10000 0 -0.38 21 21
G12 family/GTP -0.032 0.077 -10000 0 -0.28 2 2
ADRBK1 0.027 0.006 -10000 0 -10000 0 0
ADRBK2 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.035 0.011 -10000 0 -10000 0 0
mol:GDP 0.017 0.088 0.35 13 -0.27 1 14
mol:NADP 0.023 0.038 -10000 0 -0.35 4 4
RAB11A 0.027 0.005 -10000 0 -10000 0 0
PRKG1 0.022 0.044 -10000 0 -0.37 5 5
mol:IP3 -0.031 0.1 0.38 1 -0.35 6 7
cell morphogenesis 0.034 0.01 -10000 0 -10000 0 0
PLCB2 -0.044 0.13 0.41 1 -0.46 6 7
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.02 0.075 0.25 1 -0.27 6 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.005 0.044 0.25 1 -10000 0 1
RHOA 0.027 0.006 -10000 0 -10000 0 0
PTGIR 0.027 0.006 -10000 0 -10000 0 0
PRKCB1 -0.03 0.099 0.35 1 -0.33 4 5
GNAQ 0.027 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.023 0.038 -10000 0 -0.35 4 4
TXA2/TXA2-R family -0.045 0.12 0.4 1 -0.45 4 5
LCK 0.004 0.055 0.25 1 -10000 0 1
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.02 0.053 -10000 0 -0.22 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.013 0.081 -10000 0 -0.4 14 14
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.024 0.051 -10000 0 -10000 0 0
MAPK14 -0.018 0.073 0.25 5 -0.22 1 6
TGM2/GTP -0.042 0.11 0.43 1 -0.4 6 7
MAPK11 -0.019 0.069 0.25 3 -0.22 1 4
ARHGEF1 -0.018 0.051 -10000 0 -0.18 1 1
GNAI2 0.027 0.005 -10000 0 -10000 0 0
JNK cascade -0.034 0.1 0.38 1 -0.34 4 5
RAB11/GDP 0.027 0.005 -10000 0 -10000 0 0
ICAM1 -0.024 0.082 0.32 1 -0.28 5 6
cAMP biosynthetic process -0.035 0.1 0.37 1 -0.34 4 5
Gq family/GTP/EBP50 0.013 0.039 0.24 3 -0.24 1 4
actin cytoskeleton reorganization 0.034 0.01 -10000 0 -10000 0 0
SRC 0.005 0.041 -10000 0 -10000 0 0
GNB5 0.027 0.005 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
EGF/EGFR 0.011 0.085 0.21 20 -0.26 8 28
VCAM1 -0.025 0.082 0.34 1 -0.28 3 4
TP beta/Gq family/GDP/G beta5/gamma2 -0.012 0.14 -10000 0 -0.59 19 19
platelet activation -0.023 0.093 0.31 4 -0.28 2 6
PGI2/IP 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.007 0.048 -10000 0 -0.21 19 19
Gq family/GDP/G beta5/gamma2 -0.009 0.13 0.2 1 -0.53 19 20
TXA2/TP beta/beta Arrestin2 -0.002 0.056 -10000 0 -0.33 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.04 -10000 0 -0.19 17 17
mol:DAG -0.033 0.11 0.38 1 -0.37 4 5
EGFR 0.017 0.057 -10000 0 -0.38 8 8
TXA2/TP alpha -0.045 0.13 0.42 1 -0.46 4 5
Gq family/GTP -0.004 0.056 -10000 0 -0.2 27 27
YES1 0.008 0.049 0.25 1 -10000 0 1
GNAI2/GTP 0.015 0.044 -10000 0 -0.22 1 1
PGD2/DP 0.006 0.063 -10000 0 -0.27 21 21
SLC9A3R1 0.028 0.004 -10000 0 -10000 0 0
FYN 0.008 0.05 0.25 1 -10000 0 1
mol:NO 0.023 0.038 -10000 0 -0.35 4 4
GNA15 0.022 0.042 -10000 0 -0.35 5 5
PGK/cGMP 0.029 0.038 -10000 0 -0.21 9 9
RhoA/GDP 0.027 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.033 0.058 -10000 0 -0.28 2 2
NOS3 0.023 0.038 -10000 0 -0.35 4 4
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCA -0.027 0.095 0.29 2 -0.31 3 5
PRKCB -0.032 0.097 0.43 1 -0.37 4 5
PRKCE -0.027 0.093 0.29 1 -0.31 2 3
PRKCD -0.029 0.096 0.35 1 -0.34 2 3
PRKCG -0.053 0.12 0.32 2 -0.36 8 10
muscle contraction -0.044 0.12 0.45 1 -0.43 4 5
PRKCZ -0.029 0.093 0.35 1 -0.32 2 3
ARR3 0.02 0.027 -10000 0 -0.35 2 2
TXA2/TP beta 0.026 0.054 -10000 0 -0.23 1 1
PRKCQ -0.03 0.098 0.31 3 -0.34 3 6
MAPKKK cascade -0.039 0.11 0.39 1 -0.42 4 5
SELE -0.034 0.095 0.34 1 -0.31 3 4
TP beta/GNAI2/GDP/G beta/gamma 0.04 0.056 -10000 0 -0.23 1 1
ROCK1 0.027 0.006 -10000 0 -10000 0 0
GNA14 0.02 0.053 -10000 0 -0.38 7 7
chemotaxis -0.05 0.13 0.42 1 -0.5 3 4
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.019 0.006 -10000 0 -10000 0 0
EPO signaling pathway

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.039 0.062 0.38 1 -10000 0 1
CRKL 0.028 0.057 0.29 6 -10000 0 6
mol:DAG 0.023 0.036 -10000 0 -10000 0 0
HRAS 0.014 0.071 0.29 12 -10000 0 12
MAPK8 0.032 0.062 0.19 32 -10000 0 32
RAP1A 0.028 0.056 0.3 5 -10000 0 5
GAB1 0.027 0.057 0.29 6 -10000 0 6
MAPK14 0.033 0.06 0.19 30 -10000 0 30
EPO 0.016 0.056 -10000 0 -0.35 9 9
PLCG1 0.024 0.037 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.029 0.013 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.042 -10000 0 -0.19 9 9
GAB1/SHC/GRB2/SOS1 0.057 0.05 0.27 4 -10000 0 4
EPO/EPOR (dimer) 0.032 0.045 -10000 0 -0.24 9 9
IRS2 0.019 0.061 0.29 4 -0.32 1 5
STAT1 0.028 0.048 0.25 2 -10000 0 2
STAT5B 0.028 0.043 0.25 1 -10000 0 1
cell proliferation 0.018 0.079 0.19 60 -10000 0 60
GAB1/SHIP/PIK3R1/SHP2/SHC 0.04 0.043 -10000 0 -0.28 1 1
TEC 0.027 0.058 0.29 6 -10000 0 6
SOCS3 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.028 0.048 0.24 2 -10000 0 2
JAK2 0.026 0.015 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.057 0.05 -10000 0 -10000 0 0
EPO/EPOR 0.032 0.045 -10000 0 -0.24 9 9
LYN 0.025 0.011 -10000 0 -10000 0 0
TEC/VAV2 0.036 0.054 0.28 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.029 0.013 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.044 0.041 -10000 0 -0.2 6 6
mol:IP3 0.023 0.036 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.04 0.068 0.29 4 -0.45 1 5
SH2B3 0.029 0.012 -10000 0 -10000 0 0
NFKB1 0.034 0.063 0.19 33 -10000 0 33
EPO/EPOR (dimer)/JAK2/SOCS3 0.007 0.032 -10000 0 -0.22 5 5
PTPN6 0.027 0.053 0.3 1 -10000 0 1
TEC/VAV2/GRB2 0.047 0.056 0.28 5 -10000 0 5
EPOR 0.029 0.013 -10000 0 -10000 0 0
INPP5D 0.025 0.034 -10000 0 -0.36 3 3
mol:GDP 0.056 0.05 0.28 4 -10000 0 4
SOS1 0.028 0.003 -10000 0 -10000 0 0
PLCG2 0.019 0.055 -10000 0 -0.37 8 8
CRKL/CBL/C3G 0.049 0.054 0.28 6 -10000 0 6
VAV2 0.025 0.057 0.29 5 -10000 0 5
CBL 0.026 0.056 0.29 6 -10000 0 6
SHC/Grb2/SOS1 0.035 0.036 -10000 0 -10000 0 0
STAT5A 0.029 0.043 0.25 1 -10000 0 1
GRB2 0.027 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.044 0.054 0.26 2 -10000 0 2
LYN/PLCgamma2 0.032 0.038 -10000 0 -0.25 6 6
PTPN11 0.028 0.004 -10000 0 -10000 0 0
BTK 0.021 0.069 0.29 6 -0.29 2 8
BCL2 0.036 0.1 -10000 0 -0.7 5 5
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.022 0.05 -10000 0 -0.4 5 5
PDGF/PDGFRA/CRKL 0.034 0.038 -10000 0 -0.26 5 5
positive regulation of JUN kinase activity 0.061 0.036 -10000 0 -0.2 5 5
CRKL 0.027 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.03 0.04 -10000 0 -0.27 6 6
AP1 -0.032 0.18 0.32 4 -0.72 22 26
mol:IP3 0.007 0.03 -10000 0 -0.28 3 3
PLCG1 0.007 0.03 -10000 0 -0.28 3 3
PDGF/PDGFRA/alphaV Integrin 0.033 0.038 -10000 0 -0.26 5 5
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.007 0.03 -10000 0 -0.28 3 3
CAV3 0.021 0.019 -10000 0 -0.35 1 1
CAV1 0.024 0.033 -10000 0 -0.35 3 3
SHC/Grb2/SOS1 0.063 0.037 -10000 0 -0.2 5 5
PDGF/PDGFRA/Shf 0.021 0.076 -10000 0 -0.29 21 21
FOS -0.042 0.16 0.31 1 -0.7 22 23
JUN -0.016 0.02 -10000 0 -10000 0 0
oligodendrocyte development 0.033 0.038 -10000 0 -0.26 5 5
GRB2 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
mol:DAG 0.007 0.03 -10000 0 -0.28 3 3
PDGF/PDGFRA 0.022 0.05 -10000 0 -0.4 5 5
actin cytoskeleton reorganization 0.034 0.035 -10000 0 -0.27 4 4
SRF 0.01 0.01 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.047 0.031 -10000 0 -0.22 3 3
PDGF/PDGFRA/Crk/C3G 0.047 0.036 -10000 0 -0.22 5 5
JAK1 0.009 0.033 -10000 0 -0.27 5 5
ELK1/SRF 0 0.05 0.16 27 -0.27 1 28
SHB 0.026 0.007 -10000 0 -10000 0 0
SHF 0.009 0.084 -10000 0 -0.38 18 18
CSNK2A1 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0.001 0.03 -10000 0 -0.31 3 3
SOS1 0.028 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.061 0.036 -10000 0 -0.2 5 5
PDGF/PDGFRA/SHB 0.034 0.035 -10000 0 -0.27 4 4
PDGF/PDGFRA/Caveolin-1 0.031 0.046 -10000 0 -0.27 8 8
ITGAV 0.026 0.007 -10000 0 -10000 0 0
ELK1 -0.008 0.029 -10000 0 -0.28 3 3
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.033 0.038 -10000 0 -0.26 5 5
JAK-STAT cascade 0.009 0.033 -10000 0 -0.27 5 5
cell proliferation 0.021 0.076 -10000 0 -0.29 21 21
mTOR signaling pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.028 0.004 -10000 0 -10000 0 0
mol:PIP3 0.007 0.02 -10000 0 -0.26 1 1
FRAP1 0.015 0.061 0.22 1 -0.42 5 6
AKT1 0.01 0.045 0.18 5 -0.22 1 6
INSR 0.027 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.029 0.009 -10000 0 -10000 0 0
mol:GTP 0.037 0.051 0.26 6 -10000 0 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.013 0.02 -10000 0 -10000 0 0
TSC2 0.027 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.02 0.025 -10000 0 -10000 0 0
TSC1 0.027 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.023 0.029 -10000 0 -0.2 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.028 0.03 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 0.031 0.063 0.26 11 -0.26 2 13
MAP3K5 0.005 0.036 0.19 7 -0.18 9 16
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
apoptosis 0.005 0.036 0.19 7 -0.18 9 16
mol:LY294002 0 0 -10000 0 -0.001 6 6
EIF4B 0.031 0.062 0.25 12 -10000 0 12
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.043 0.048 0.23 5 -10000 0 5
eIF4E/eIF4G1/eIF4A1 0.015 0.034 -10000 0 -0.25 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.036 0.029 -10000 0 -0.28 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.044 0.2 13 -10000 0 13
FKBP1A 0.025 0.009 -10000 0 -10000 0 0
RHEB/GTP 0.039 0.043 0.23 5 -10000 0 5
mol:Amino Acids 0 0 -10000 0 -0.001 6 6
FKBP12/Rapamycin 0.019 0.007 -10000 0 -10000 0 0
PDPK1 0 0.038 0.16 17 -0.24 1 18
EIF4E 0.027 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.027 0.098 -10000 0 -0.5 12 12
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0 0.078 -10000 0 -0.29 18 18
TSC1/TSC2 0.043 0.058 0.28 8 -10000 0 8
tumor necrosis factor receptor activity 0 0 0.001 6 -10000 0 6
RPS6 0.025 0.009 -10000 0 -10000 0 0
PPP5C 0.027 0.006 -10000 0 -10000 0 0
EIF4G1 0.026 0.007 -10000 0 -10000 0 0
IRS1 0.006 0.028 -10000 0 -0.21 6 6
INS 0.018 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.008 -10000 0 -10000 0 0
PDK2 0 0.04 0.16 17 -0.24 1 18
EIF4EBP1 -0.031 0.23 -10000 0 -1 22 22
PIK3CA 0.027 0.007 -10000 0 -10000 0 0
PPP2R5D 0.025 0.072 0.26 8 -0.38 5 13
peptide biosynthetic process -0.008 0.022 0.18 5 -10000 0 5
RHEB 0.027 0.006 -10000 0 -10000 0 0
EIF4A1 0.026 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 30 -10000 0 30
EEF2 -0.008 0.022 0.18 5 -10000 0 5
eIF4E/4E-BP1 -0.016 0.22 -10000 0 -0.94 22 22
Signaling events mediated by HDAC Class III

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
EP300 0.027 0.005 -10000 0 -10000 0 0
HDAC4 0.027 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.006 0.036 0.25 8 -0.13 1 9
CDKN1A -0.009 0.03 -10000 0 -0.61 1 1
KAT2B 0.024 0.041 -10000 0 -0.38 4 4
BAX 0.027 0.006 -10000 0 -10000 0 0
FOXO3 -0.005 0.003 -10000 0 -10000 0 0
FOXO1 0.026 0.008 -10000 0 -10000 0 0
FOXO4 0.014 0.013 -10000 0 -0.23 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.006 -10000 0 -10000 0 0
TAT -0.004 0.1 -10000 0 -0.38 29 29
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.04 -10000 0 -0.26 10 10
PPARGC1A -0.005 0.11 -10000 0 -0.38 33 33
FHL2 0.024 0.041 -10000 0 -0.38 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.012 -10000 0 -10000 0 0
HIST2H4A 0.006 0.036 0.13 1 -0.25 8 9
SIRT1/FOXO3a 0.017 0.022 -10000 0 -0.19 1 1
SIRT1 0.025 0.01 0.2 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.017 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.014 0.051 -10000 0 -0.21 10 10
apoptosis -0.049 0.018 -10000 0 -10000 0 0
SIRT1/PGC1A 0.013 0.07 -10000 0 -0.22 33 33
p53/SIRT1 0.031 0.02 0.37 1 -10000 0 1
SIRT1/FOXO4 0.017 0.044 -10000 0 -0.2 5 5
FOXO1/FHL2/SIRT1 0.044 0.027 -10000 0 -0.21 2 2
HIST1H1E 0.01 0.028 -10000 0 -0.23 4 4
SIRT1/p300 0.037 0.012 -10000 0 -10000 0 0
muscle cell differentiation -0.026 0.041 0.22 10 -0.22 2 12
TP53 0.023 0.011 0.2 1 -10000 0 1
KU70/SIRT1/BAX 0.049 0.019 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
MEF2D 0.027 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.014 0.079 -10000 0 -0.27 29 29
ACSS2 0.01 0.016 -10000 0 -0.27 1 1
SIRT1/PCAF/MYOD 0.026 0.042 0.22 2 -0.22 10 12
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.01 -10000 0 -10000 0 0
NFATC1 0.011 0.1 0.24 1 -0.43 9 10
NFATC2 0.021 0.057 0.14 7 -0.29 5 12
NFATC3 0.02 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.035 0.096 0.22 2 -0.32 26 28
Exportin 1/Ran/NUP214 0.054 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.021 0.099 -10000 0 -0.38 12 12
BCL2/BAX 0.035 0.021 -10000 0 -0.27 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.02 0.007 -10000 0 -10000 0 0
BAX 0.027 0.006 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
BAD 0.028 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.026 0.095 -10000 0 -0.34 18 18
Calcineurin A alpha-beta B1/BCL2 0.024 0.022 -10000 0 -0.38 1 1
FKBP8 0.027 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.026 0.094 0.33 18 -10000 0 18
KPNB1 0.028 0.002 -10000 0 -10000 0 0
KPNA2 0.027 0.019 -10000 0 -0.35 1 1
XPO1 0.028 0.003 -10000 0 -10000 0 0
SFN 0.015 0.067 -10000 0 -0.37 12 12
MAP3K8 0.026 0.02 -10000 0 -0.35 1 1
NFAT4/CK1 alpha 0.027 0.02 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.054 0.076 -10000 0 -0.3 3 3
CABIN1 -0.036 0.096 0.22 2 -0.32 26 28
CALM1 0.027 0.005 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.008 -10000 0 -10000 0 0
CAMK4 0.016 0.063 -10000 0 -0.38 10 10
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.027 0.005 -10000 0 -10000 0 0
YWHAH 0.027 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.033 -10000 0 -0.25 5 5
YWHAB 0.022 0.011 -10000 0 -10000 0 0
MAPK8 0.027 0.005 -10000 0 -10000 0 0
MAPK9 0.027 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.007 -10000 0 -10000 0 0
FKBP1A 0.025 0.009 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.032 0.11 0.24 4 -0.41 9 13
PRKCH 0.026 0.021 -10000 0 -0.38 1 1
CABIN1/Cbp/p300 0.036 0.017 -10000 0 -10000 0 0
CASP3 0.025 0.009 -10000 0 -10000 0 0
PIM1 0.025 0.029 -10000 0 -0.38 2 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.006 -10000 0 -10000 0 0
apoptosis 0.017 0.011 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.046 -10000 0 -0.45 1 1
PRKCB 0.003 0.096 -10000 0 -0.38 24 24
PRKCE 0.028 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.026 0.04 -10000 0 -10000 0 0
BAD/BCL-XL 0.036 0.015 -10000 0 -10000 0 0
PRKCD 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
PRKCZ 0.027 0.007 -10000 0 -10000 0 0
PRKCA 0.027 0.005 -10000 0 -10000 0 0
PRKCG -0.13 0.19 -10000 0 -0.35 174 174
PRKCQ 0.011 0.077 -10000 0 -0.38 15 15
FKBP38/BCL2 0.035 0.021 -10000 0 -0.27 1 1
EP300 0.026 0.01 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.025 0.009 -10000 0 -10000 0 0
NFATc/JNK1 0.024 0.1 0.24 1 -0.42 8 9
CaM/Ca2+/FKBP38 0.035 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.007 -10000 0 -10000 0 0
CSNK1A1 0.013 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.027 0.042 -10000 0 -0.22 10 10
NFATc/ERK1 0.025 0.1 0.24 1 -0.43 7 8
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.022 0.1 0.22 1 -0.37 13 14
NR4A1 0.024 0.088 0.22 7 -0.39 12 19
GSK3B 0.027 0.005 -10000 0 -10000 0 0
positive T cell selection 0.02 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.022 0.041 0.15 1 -0.23 2 3
RCH1/ KPNB1 0.04 0.016 -10000 0 -0.25 1 1
YWHAQ 0.028 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.005 -10000 0 -10000 0 0
AKAP5 0.023 0.042 -10000 0 -0.35 5 5
MEF2D 0.026 0.01 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.024 0.1 0.24 1 -0.42 8 9
CREBBP 0.025 0.011 -10000 0 -10000 0 0
BCL2 0.024 0.022 -10000 0 -0.38 1 1
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.022 0.045 -10000 0 -0.38 5 5
HRAS 0.026 0.007 -10000 0 -10000 0 0
EGFR 0.017 0.057 -10000 0 -0.38 8 8
AKT 0.055 0.068 0.23 17 -0.24 1 18
FOXO3 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.027 0.006 -10000 0 -10000 0 0
FOXO1 0.026 0.008 -10000 0 -10000 0 0
AKT3 0.026 0.019 -10000 0 -0.35 1 1
FOXO4 0.027 0.021 -10000 0 -0.38 1 1
MET 0.005 0.088 -10000 0 -0.36 23 23
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PIK3CB 0.027 0.006 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.016 0.065 -10000 0 -0.38 11 11
PIK3R3 0.028 0.003 -10000 0 -10000 0 0
PIK3R2 0.027 0.005 -10000 0 -10000 0 0
NF1 0.028 0.004 -10000 0 -10000 0 0
RAS 0.025 0.052 0.16 5 -0.28 5 10
ERBB2 0.02 0.041 -10000 0 -0.38 4 4
proliferation/survival/translation -0.041 0.054 0.27 2 -0.21 7 9
PI3K 0.038 0.061 0.21 20 -0.24 2 22
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
KRAS 0.025 0.009 -10000 0 -10000 0 0
FOXO 0.073 0.058 0.2 31 -10000 0 31
AKT2 0.027 0.006 -10000 0 -10000 0 0
PTEN 0.026 0.008 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.006 -10000 0 -10000 0 0
ELF1 0.014 0.059 -10000 0 -10000 0 0
CCNA2 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.027 0.007 -10000 0 -10000 0 0
JAK3 0.011 0.078 -10000 0 -0.35 18 18
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
JAK1 0.028 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.031 0.07 0.24 2 -0.37 1 3
SHC1 0.028 0.005 -10000 0 -10000 0 0
SP1 0.025 0.047 -10000 0 -0.28 9 9
IL2RA -0.011 0.092 -10000 0 -0.32 33 33
IL2RB 0.027 0.021 -10000 0 -0.38 1 1
SOS1 0.028 0.003 -10000 0 -10000 0 0
IL2RG 0.019 0.059 -10000 0 -0.37 9 9
G1/S transition of mitotic cell cycle 0.016 0.13 0.31 4 -0.69 8 12
PTPN11 0.028 0.004 -10000 0 -10000 0 0
CCND2 0.011 0.065 -10000 0 -0.64 4 4
LCK 0.017 0.062 -10000 0 -0.35 11 11
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL2 0.021 0.027 -10000 0 -0.35 2 2
CDK6 0.021 0.038 -10000 0 -0.35 4 4
CCND3 0.038 0.083 0.35 4 -10000 0 4
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.091 0.18 -10000 0 -0.38 117 117
CLTC 0.015 0.071 -10000 0 -0.42 9 9
calcium ion-dependent exocytosis 0.015 0.03 0.2 1 -0.26 1 2
Dynamin 2/GTP 0.026 0.008 -10000 0 -10000 0 0
EXOC4 0.027 0.006 -10000 0 -10000 0 0
CD59 0.013 0.046 -10000 0 -0.33 6 6
CPE -0.011 0.072 -10000 0 -0.23 42 42
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
membrane fusion 0.016 0.021 -10000 0 -10000 0 0
CTNND1 0.015 0.031 0.2 11 -10000 0 11
DNM2 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.051 0.2 4 -0.36 4 8
TSHR 0.005 0.044 -10000 0 -0.23 14 14
INS -0.006 0.11 -10000 0 -0.5 17 17
BIN1 0.028 0.003 -10000 0 -10000 0 0
mol:Choline 0.016 0.021 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.008 -10000 0 -10000 0 0
JUP 0.016 0.048 -10000 0 -0.32 6 6
ASAP2/amphiphysin II 0.05 0.015 -10000 0 -10000 0 0
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.008 0.051 -10000 0 -0.33 6 6
clathrin-independent pinocytosis 0.02 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.021 -10000 0 -0.38 1 1
positive regulation of endocytosis 0.02 0.004 -10000 0 -10000 0 0
EXOC2 0.026 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.019 0.042 -10000 0 -0.31 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.028 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.033 0.057 0.3 7 -10000 0 7
positive regulation of phagocytosis 0.013 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.034 0.017 -10000 0 -0.23 1 1
ACAP1 0.019 0.027 0.2 1 -0.21 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.047 0.096 -10000 0 -0.46 7 7
clathrin heavy chain/ACAP1 0.018 0.059 0.36 1 -0.35 7 8
JIP4/KLC1 0.049 0.016 -10000 0 -10000 0 0
EXOC1 0.027 0.005 -10000 0 -10000 0 0
exocyst 0.02 0.039 -10000 0 -0.31 3 3
RALA/GTP 0.02 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.036 0.009 -10000 0 -10000 0 0
receptor recycling 0.02 0.004 -10000 0 -10000 0 0
CTNNA1 0.015 0.031 0.2 11 -10000 0 11
NME1 0.014 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.016 0.071 0.3 1 -0.41 9 10
IL2RA 0.006 0.052 -10000 0 -0.33 6 6
VAMP3 0.013 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.023 0.099 -10000 0 -0.36 9 9
EXOC6 0.027 0.006 -10000 0 -10000 0 0
PLD1 0.013 0.009 -10000 0 -10000 0 0
PLD2 0.013 0.007 -10000 0 -10000 0 0
EXOC5 0.028 0.004 -10000 0 -10000 0 0
PIP5K1C 0.012 0.045 0.19 1 -0.37 4 5
SDC1 0.012 0.047 -10000 0 -0.32 6 6
ARF6/GDP 0.025 0.006 -10000 0 -10000 0 0
EXOC7 0.028 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.036 0.059 -10000 0 -0.3 7 7
mol:Phosphatidic acid 0.016 0.021 -10000 0 -10000 0 0
endocytosis -0.048 0.014 -10000 0 -10000 0 0
SCAMP2 0.027 0.005 -10000 0 -10000 0 0
ADRB2 -0.032 0.1 0.22 1 -0.39 12 13
EXOC3 0.025 0.009 -10000 0 -10000 0 0
ASAP2 0.027 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.03 0.009 -10000 0 -10000 0 0
KLC1 0.027 0.006 -10000 0 -10000 0 0
AVPR2 0.007 0.087 0.27 7 -0.41 8 15
RALA 0.027 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.057 -10000 0 -0.32 3 3
Insulin Pathway

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
CBL/APS/CAP 0.023 0.077 -10000 0 -0.36 1 1
TC10/GTP 0.018 0.071 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.067 0.032 -10000 0 -0.22 1 1
HRAS 0.026 0.007 -10000 0 -10000 0 0
APS homodimer 0.024 0.027 -10000 0 -0.35 2 2
GRB14 -0.037 0.14 -10000 0 -0.36 68 68
FOXO3 0.003 0.11 -10000 0 -0.55 16 16
AKT1 -0.013 0.08 0.26 7 -10000 0 7
INSR 0.033 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.063 0.053 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.02 -10000 0 -0.35 1 1
SORBS1 -0.022 0.13 -10000 0 -0.38 49 49
CRK 0.026 0.008 -10000 0 -10000 0 0
PTPN1 0.006 0.02 -10000 0 -10000 0 0
CAV1 0.001 0.039 0.18 8 -0.2 1 9
CBL/APS/CAP/Crk-II/C3G 0.037 0.086 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.066 0.032 -10000 0 -0.22 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.048 0.029 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.033 0.084 -10000 0 -0.37 4 4
RPS6KB1 -0.015 0.074 0.24 9 -10000 0 9
PARD6A 0.027 0.006 -10000 0 -10000 0 0
CBL 0.027 0.006 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.029 -10000 0 -0.52 1 1
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.016 0.072 -10000 0 -10000 0 0
HRAS/GTP 0.018 0.021 -10000 0 -10000 0 0
Insulin Receptor 0.033 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.074 0.037 -10000 0 -10000 0 0
PRKCI 0.014 0.066 -10000 0 -0.38 2 2
Insulin Receptor/Insulin/GRB14/PDK1 0.003 0.069 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.043 0.034 -10000 0 -0.44 1 1
PI3K 0.059 0.034 -10000 0 -10000 0 0
NCK2 0.028 0.004 -10000 0 -10000 0 0
RHOQ 0.028 0.002 -10000 0 -10000 0 0
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.005 -10000 0 -10000 0 0
AKT2 -0.013 0.077 0.24 8 -10000 0 8
PRKCZ 0.009 0.079 -10000 0 -0.39 4 4
SH2B2 0.024 0.027 -10000 0 -0.35 2 2
SHC/SHIP 0.035 0.035 0.2 6 -10000 0 6
F2RL2 -0.03 0.14 -10000 0 -0.35 61 61
TRIP10 0.027 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.052 0.024 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.076 0.034 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
RASA1 0.025 0.008 -10000 0 -10000 0 0
NCK1 0.027 0.005 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.029 0.085 -10000 0 -0.21 36 36
TC10/GDP 0.021 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.063 0.032 -10000 0 -10000 0 0
INPP5D 0.002 0.039 0.18 8 -0.2 2 10
SOS1 0.028 0.003 -10000 0 -10000 0 0
SGK1 -0.002 0.11 -10000 0 -0.67 10 10
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.004 -10000 0 -10000 0 0
IRS1 0.027 0.021 -10000 0 -0.38 1 1
p62DOK/RasGAP 0.043 0.034 -10000 0 -0.45 1 1
INS 0.025 0.013 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.002 0.039 0.18 8 -0.2 2 10
GRB2 0.027 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.016 0.069 0.24 6 -10000 0 6
PTPRA 0.029 0.012 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.036 0.009 -10000 0 -10000 0 0
PDPK1 0.027 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.027 0.028 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.051 0.027 -10000 0 -0.22 1 1
Insulin Receptor/Insulin/IRS3 0.043 0.023 -10000 0 -10000 0 0
Par3/Par6 0.021 0.085 -10000 0 -0.18 56 56
Signaling events mediated by PRL

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
CCNE1 0.011 0.071 -10000 0 -0.35 15 15
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.018 0.056 -10000 0 -0.35 9 9
CDKN1A 0.01 0.052 -10000 0 -0.54 1 1
PRL-3/alpha Tubulin 0.035 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.079 -10000 0 -0.26 52 52
AGT -0.022 0.13 -10000 0 -0.36 53 53
CCNA2 -0.006 0.024 -10000 0 -10000 0 0
TUBA1B 0.028 0.004 -10000 0 -10000 0 0
EGR1 0.008 0.042 -10000 0 -0.26 10 10
CDK2/Cyclin E1 0.037 0.082 -10000 0 -0.42 3 3
MAPK3 0.011 0.005 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.04 0.009 -10000 0 -10000 0 0
MAPK1 0.011 0.005 -10000 0 -10000 0 0
PTP4A1 -0.001 0.028 -10000 0 -10000 0 0
PTP4A3 0.024 0.01 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.011 0.014 -10000 0 -0.25 1 1
SRC 0.024 0.01 -10000 0 -10000 0 0
RAC1 0.013 0.031 -10000 0 -0.3 3 3
Rab GGTase beta/Rab GGTase alpha 0.04 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 0.036 0.065 -10000 0 -10000 0 0
RABGGTA 0.028 0.004 -10000 0 -10000 0 0
BCAR1 -0.017 0.008 -10000 0 -10000 0 0
RHOC 0.011 0.045 -10000 0 -0.47 1 1
RHOA 0.011 0.045 -10000 0 -0.33 6 6
cell motility 0.039 0.069 0.3 4 -0.31 2 6
PRL-1/alpha Tubulin 0.038 0.065 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.027 0.044 -10000 0 -0.25 9 9
ROCK1 0.039 0.061 0.28 3 -0.3 1 4
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.006 -10000 0 -10000 0 0
mitosis -0.001 0.028 -10000 0 -10000 0 0
ATF5 0.026 0.019 -10000 0 -0.35 1 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.015 0.049 0.22 3 -0.27 1 4
adherens junction organization 0.018 0.074 0.22 4 -0.37 6 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.059 0.23 4 -0.27 1 5
FMN1 0.016 0.069 -10000 0 -0.36 5 5
mol:IP3 0.011 0.038 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.021 0.069 -10000 0 -0.34 6 6
CTNNB1 0.027 0.007 -10000 0 -10000 0 0
AKT1 0.027 0.055 0.2 8 -10000 0 8
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.014 0.12 -10000 0 -0.46 14 14
CTNND1 0.03 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.068 0.18 5 -0.32 6 11
VASP 0.018 0.063 -10000 0 -0.32 5 5
ZYX 0.019 0.061 0.16 1 -0.32 4 5
JUB 0.018 0.066 0.16 3 -0.32 6 9
EGFR(dimer) 0.028 0.078 0.22 2 -0.32 8 10
E-cadherin/beta catenin-gamma catenin 0.041 0.043 -10000 0 -0.21 9 9
mol:PI-3-4-5-P3 0.046 0.069 0.23 9 -0.24 1 10
PIK3CA 0.028 0.008 -10000 0 -10000 0 0
PI3K 0.047 0.07 0.23 9 -0.25 1 10
FYN -0.001 0.063 0.24 2 -0.34 3 5
mol:Ca2+ 0.011 0.037 -10000 0 -10000 0 0
JUP 0.026 0.009 -10000 0 -10000 0 0
PIK3R1 0.028 0.009 -10000 0 -10000 0 0
mol:DAG 0.011 0.038 -10000 0 -10000 0 0
CDH1 0.018 0.06 -10000 0 -0.38 9 9
RhoA/GDP 0.029 0.06 0.23 6 -0.25 1 7
establishment of polarity of embryonic epithelium 0.02 0.064 0.2 3 -0.31 5 8
SRC 0.024 0.01 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
EGFR 0.017 0.057 -10000 0 -0.38 8 8
CASR -0.004 0.06 0.21 1 -0.3 2 3
RhoA/GTP 0.024 0.044 -10000 0 -10000 0 0
AKT2 0.027 0.057 0.2 9 -0.24 1 10
actin cable formation 0.016 0.073 0.2 10 -0.34 6 16
apoptosis -0.031 0.068 0.27 2 -0.23 12 14
CTNNA1 0.029 0.008 -10000 0 -10000 0 0
mol:GDP 0.009 0.05 0.24 1 -0.28 1 2
PIP5K1A 0.017 0.067 0.16 1 -0.32 6 7
PLCG1 0.011 0.038 -10000 0 -10000 0 0
Rac1/GTP 0.033 0.076 0.21 2 -0.31 7 9
homophilic cell adhesion 0.001 0.004 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.042 0.045 -9999 0 -0.23 9 9
E-cadherin/beta catenin 0.031 0.046 -9999 0 -0.27 9 9
CTNNB1 0.027 0.006 -9999 0 -10000 0 0
JUP 0.026 0.008 -9999 0 -10000 0 0
CDH1 0.018 0.06 -9999 0 -0.38 9 9
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.02 0.013 -10000 0 -10000 0 0
TRAF2/ASK1 0.035 0.01 -10000 0 -10000 0 0
ATM 0.026 0.02 -10000 0 -0.35 1 1
MAP2K3 -0.01 0.098 0.21 2 -0.34 17 19
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.001 0.086 0.22 2 -0.39 7 9
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.025 0.028 -10000 0 -0.37 2 2
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.028 0.004 -10000 0 -10000 0 0
GADD45B 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 0.026 0.008 -10000 0 -10000 0 0
MAP3K6 0.027 0.006 -10000 0 -10000 0 0
MAP3K7 0.027 0.006 -10000 0 -10000 0 0
MAP3K4 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.039 0.011 -10000 0 -10000 0 0
TAK1/TAB family -0.001 0.016 -10000 0 -0.13 1 1
RAC1/OSM/MEKK3 0.048 0.017 -10000 0 -10000 0 0
TRAF2 0.027 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.006 0.084 -10000 0 -0.32 7 7
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.047 0.16 -10000 0 -0.38 73 73
CCM2 0.026 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.012 0.099 -10000 0 -0.22 73 73
MAPK11 0.026 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.003 0.097 -10000 0 -0.2 71 71
OSM/MEKK3 0.038 0.012 -10000 0 -10000 0 0
TAOK1 0.014 0.009 -10000 0 -10000 0 0
TAOK2 0.014 0.009 -10000 0 -0.14 1 1
TAOK3 0.014 0.009 -10000 0 -0.14 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
MAP3K10 0.027 0.006 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.024 0.015 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.057 0.028 -10000 0 -0.2 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.049 0.16 0.26 1 -0.4 35 36
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.006 -10000 0 -10000 0 0
AKT2 0.027 0.006 -10000 0 -10000 0 0
STXBP4 0.028 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.067 0.16 0.26 2 -0.42 42 44
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.028 0.004 -10000 0 -10000 0 0
TBC1D4 0.009 0.03 -10000 0 -0.24 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.005 -10000 0 -10000 0 0
YWHAB 0.022 0.011 -10000 0 -10000 0 0
SNARE/Synip 0.052 0.017 -10000 0 -10000 0 0
YWHAG 0.026 0.007 -10000 0 -10000 0 0
ASIP 0.016 0.053 -10000 0 -0.35 8 8
PRKCI 0.024 0.027 -10000 0 -0.35 2 2
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.028 0.002 -10000 0 -10000 0 0
GYS1 0.012 0.02 0.24 3 -10000 0 3
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
TRIP10 0.027 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.015 0.05 -10000 0 -0.29 3 3
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 -0.075 0.18 0.26 2 -0.47 42 44
STX4 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.02 0.007 -10000 0 -10000 0 0
SFN 0.015 0.067 -10000 0 -0.37 12 12
LNPEP 0.026 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.031 0.018 -10000 0 -0.28 1 1
VEGFR1 homodimer/NRP1 0.012 0.015 -10000 0 -0.27 1 1
mol:DAG 0.011 0.041 0.19 9 -10000 0 9
VEGFR1 homodimer/NRP1/VEGFR 121 0.026 0.016 -10000 0 -10000 0 0
CaM/Ca2+ 0.024 0.042 -10000 0 -10000 0 0
HIF1A 0.032 0.012 -10000 0 -0.18 1 1
GAB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.019 0.059 0.32 4 -10000 0 4
PLCG1 0.011 0.041 0.2 9 -10000 0 9
NOS3 0.029 0.079 0.3 11 -0.44 2 13
CBL 0.027 0.006 -10000 0 -10000 0 0
mol:NO 0.03 0.086 0.3 13 -0.42 3 16
FLT1 0.016 0.018 -10000 0 -0.32 1 1
PGF 0.015 0.067 -10000 0 -0.35 13 13
VEGFR1 homodimer/NRP2/VEGFR121 0.041 0.026 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
eNOS/Hsp90 0.043 0.092 0.3 13 -0.39 5 18
endothelial cell proliferation 0.022 0.079 0.32 10 -10000 0 10
mol:Ca2+ 0.01 0.041 0.19 9 -10000 0 9
MAPK3 -0.008 0.037 0.17 9 -10000 0 9
MAPK1 -0.008 0.037 0.17 9 -10000 0 9
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
PLGF homodimer 0.015 0.067 -10000 0 -0.35 13 13
PRKACA 0.027 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.024 0.033 -10000 0 -0.35 3 3
VEGFA homodimer 0.025 0.02 -10000 0 -0.35 1 1
VEGFR1 homodimer/VEGFA homodimer 0.029 0.018 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.01 0.035 0.16 9 -10000 0 9
PI3K 0.046 0.049 -10000 0 -10000 0 0
PRKCA -0.007 0.038 0.18 8 -10000 0 8
PRKCB -0.014 0.051 0.18 8 -10000 0 8
VEGFR1 homodimer/PLGF homodimer 0.024 0.044 -10000 0 -0.28 1 1
VEGFA 0.025 0.02 -10000 0 -0.35 1 1
VEGFB 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 0.011 0.041 0.19 9 -10000 0 9
RASA1 0.02 0.039 0.2 17 -0.25 1 18
NRP2 0.027 0.019 -10000 0 -0.35 1 1
VEGFR1 homodimer 0.016 0.018 -10000 0 -0.32 1 1
VEGFB homodimer 0.028 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.038 0.086 0.28 11 -0.41 3 14
PTPN11 0.028 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.048 -10000 0 -0.24 1 1
mol:L-citrulline 0.03 0.086 0.3 13 -0.42 3 16
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.052 0.029 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.041 0.023 -10000 0 -10000 0 0
CD2AP 0.026 0.007 -10000 0 -10000 0 0
PI3K/GAB1 0.06 0.056 -10000 0 -10000 0 0
PDPK1 0.02 0.061 0.34 3 -10000 0 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.042 0.023 -10000 0 -10000 0 0
mol:NADP 0.03 0.086 0.3 13 -0.42 3 16
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
ubiquitin-dependent protein catabolic process 0.05 0.028 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.03 0.022 -10000 0 -0.28 1 1
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.025 0.033 0.36 3 -10000 0 3
PI3K Class IB/PDE3B 0.025 0.033 -10000 0 -0.36 3 3
PDE3B 0.025 0.033 -10000 0 -0.36 3 3
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.083 0.21 17 -0.35 4 21
ERC1 0.026 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.032 0.032 -10000 0 -0.25 4 4
NFKBIA 0.015 0.024 0.21 6 -10000 0 6
BIRC2 0.027 0.006 -10000 0 -10000 0 0
IKBKB 0.025 0.009 -10000 0 -10000 0 0
RIPK2 0.024 0.01 -10000 0 -10000 0 0
IKBKG 0.032 0.03 -10000 0 -10000 0 0
IKK complex/A20 0.039 0.093 0.26 1 -0.4 5 6
NEMO/A20/RIP2 0.024 0.01 -10000 0 -10000 0 0
XPO1 0.028 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.036 0.088 0.26 2 -0.38 10 12
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.037 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.036 0.079 -10000 0 -0.39 5 5
BCL10/MALT1/TRAF6 0.049 0.02 -10000 0 -10000 0 0
NOD2 0.022 0.043 -10000 0 -0.36 5 5
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.025 0.009 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.01 -10000 0 -10000 0 0
ATM 0.026 0.02 -10000 0 -0.35 1 1
TNF/TNFR1A 0.025 0.059 -10000 0 -0.25 17 17
TRAF6 0.027 0.005 -10000 0 -10000 0 0
PRKCA 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.006 -10000 0 -10000 0 0
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
TNF 0.01 0.08 -10000 0 -0.36 18 18
NF kappa B1 p50/RelA 0.058 0.019 -10000 0 -10000 0 0
BCL10 0.028 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.024 0.21 6 -10000 0 6
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
IKK complex 0.042 0.087 0.27 2 -0.42 5 7
CYLD 0.027 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.051 0.086 0.26 2 -0.41 4 6
a4b1 and a4b7 Integrin signaling

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.026 0.02 -9999 0 -0.35 1 1
ITGB7 0.026 0.021 -9999 0 -0.38 1 1
ITGA4 0.025 0.033 -9999 0 -0.35 3 3
alpha4/beta7 Integrin 0.036 0.03 -9999 0 -0.25 4 4
alpha4/beta1 Integrin 0.036 0.03 -9999 0 -0.25 4 4
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.019 0.035 -10000 0 -10000 0 0
regulation of axonogenesis -0.009 0.024 0.24 3 -10000 0 3
myoblast fusion -0.022 0.035 0.31 2 -10000 0 2
mol:GTP 0.018 0.026 -10000 0 -0.15 7 7
regulation of calcium-dependent cell-cell adhesion -0.043 0.048 0.21 8 -10000 0 8
ARF1/GTP 0.033 0.026 -10000 0 -10000 0 0
mol:GM1 0.008 0.019 -10000 0 -10000 0 0
mol:Choline 0.008 0.018 -10000 0 -0.19 1 1
lamellipodium assembly 0.011 0.05 -10000 0 -0.34 6 6
MAPK3 0.021 0.023 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.044 0.049 -10000 0 -0.21 8 8
ARF1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.022 0.036 -10000 0 -0.31 2 2
ARF1/GDP 0.026 0.045 -10000 0 -0.28 3 3
ARF6 0.033 0.014 -10000 0 -10000 0 0
RAB11A 0.027 0.005 -10000 0 -10000 0 0
TIAM1 0.017 0.062 -10000 0 -0.37 10 10
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.023 -10000 0 -10000 0 0
actin filament bundle formation -0.03 0.044 0.27 3 -10000 0 3
KALRN 0.012 0.03 -10000 0 -0.23 4 4
RAB11FIP3/RAB11A 0.038 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.03 0.044 -10000 0 -0.27 3 3
NME1 0.028 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.045 -10000 0 -0.28 3 3
substrate adhesion-dependent cell spreading 0.018 0.026 -10000 0 -0.15 7 7
cortical actin cytoskeleton organization 0.011 0.05 -10000 0 -0.34 6 6
RAC1 0.026 0.008 -10000 0 -10000 0 0
liver development 0.018 0.026 -10000 0 -0.15 7 7
ARF6/GTP 0.018 0.026 -10000 0 -0.15 7 7
RhoA/GTP 0.033 0.026 -10000 0 -10000 0 0
mol:GDP 0.012 0.034 -10000 0 -0.24 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.047 0.028 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
PLD1 0.016 0.024 -10000 0 -0.22 1 1
RAB11FIP3 0.027 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.011 0.05 -10000 0 -0.34 6 6
ruffle organization 0.009 0.024 -10000 0 -0.24 3 3
regulation of epithelial cell migration 0.018 0.026 -10000 0 -0.15 7 7
PLD2 0.017 0.02 -10000 0 -10000 0 0
PIP5K1A 0.009 0.024 -10000 0 -0.24 3 3
mol:Phosphatidic acid 0.008 0.018 -10000 0 -0.19 1 1
Rac1/GTP 0.011 0.05 -10000 0 -0.34 6 6
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.035 0.033 -10000 0 -0.25 5 5
AKT1 0.055 0.077 0.31 16 -10000 0 16
PTK2B 0.023 0.047 -10000 0 -10000 0 0
VEGFR2 homodimer/Frs2 0.034 0.012 -10000 0 -10000 0 0
CAV1 0.024 0.033 -10000 0 -0.35 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.045 0.024 -10000 0 -10000 0 0
endothelial cell proliferation 0.066 0.1 0.27 50 -10000 0 50
mol:Ca2+ 0.02 0.027 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.055 0.031 -10000 0 -10000 0 0
RP11-342D11.1 0.01 0.02 -10000 0 -10000 0 0
CDH5 0.027 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.061 0.03 -10000 0 -0.19 1 1
SHC1 0.027 0.005 -10000 0 -10000 0 0
SHC2 0.021 0.05 -10000 0 -0.38 6 6
HRAS/GDP 0.043 0.025 -10000 0 -10000 0 0
SH2D2A 0.026 0.019 -10000 0 -0.35 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.052 0.094 0.27 3 -0.45 5 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.046 0.025 -10000 0 -10000 0 0
VEGFR1 homodimer 0.025 0.02 -10000 0 -0.35 1 1
SHC/GRB2/SOS1 0.07 0.035 -10000 0 -10000 0 0
GRB10 0.021 0.03 -10000 0 -10000 0 0
PTPN11 0.028 0.004 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.065 0.036 -10000 0 -10000 0 0
HRAS 0.026 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.019 0.047 -10000 0 -0.29 2 2
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.053 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.027 0.006 -10000 0 -10000 0 0
Nck/Pak 0.039 0.011 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.047 0.022 -10000 0 -10000 0 0
mol:GDP 0.056 0.029 -10000 0 -10000 0 0
mol:NADP 0.048 0.1 0.28 18 -0.43 6 24
eNOS/Hsp90 0.058 0.1 0.28 18 -0.42 5 23
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
mol:IP3 0.02 0.027 -10000 0 -10000 0 0
HIF1A/ARNT 0.039 0.011 -10000 0 -10000 0 0
SHB 0.026 0.007 -10000 0 -10000 0 0
VEGFA 0.026 0.02 -10000 0 -0.35 1 1
VEGFC 0.025 0.021 -10000 0 -0.38 1 1
FAK1/Vinculin 0.055 0.073 0.28 7 -10000 0 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.055 0.039 -10000 0 -10000 0 0
PTPN6 0.026 0.02 -10000 0 -0.35 1 1
EPAS1 0.034 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0.048 0.1 0.28 18 -0.43 6 24
ITGAV 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.056 0.03 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.05 0.025 -10000 0 -10000 0 0
VEGFR2/3 heterodimer 0.035 0.01 -10000 0 -10000 0 0
VEGFB 0.028 0.004 -10000 0 -10000 0 0
MAPK11 0.016 0.051 0.24 3 -10000 0 3
VEGFR2 homodimer 0.021 0.004 -10000 0 -10000 0 0
FLT1 0.025 0.02 -10000 0 -0.35 1 1
NEDD4 0.028 0.006 -10000 0 -10000 0 0
MAPK3 0.031 0.083 0.33 14 -10000 0 14
MAPK1 0.03 0.081 0.32 14 -10000 0 14
VEGFA145/NRP2 0.037 0.024 -10000 0 -0.24 2 2
VEGFR1/2 heterodimer 0.033 0.016 -10000 0 -10000 0 0
KDR 0.021 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.049 0.027 -10000 0 -10000 0 0
SRC 0.024 0.01 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.039 0.088 0.32 18 -10000 0 18
PI3K 0.039 0.042 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.047 0.023 -10000 0 -10000 0 0
FES 0.02 0.033 -10000 0 -10000 0 0
GAB1 0.034 0.027 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.042 0.026 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
SOS1 0.028 0.003 -10000 0 -10000 0 0
ARNT 0.027 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.055 0.097 0.29 15 -0.4 5 20
VEGFR2 homodimer/VEGFA homodimer/Yes 0.046 0.023 -10000 0 -10000 0 0
PI3K/GAB1 0.046 0.052 0.28 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.065 0.037 -10000 0 -10000 0 0
PRKACA 0.027 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.047 0.021 -10000 0 -10000 0 0
HSP90AA1 0.025 0.027 -10000 0 -0.35 2 2
CDC42 0.023 0.025 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.046 0.025 -10000 0 -10000 0 0
PTK2 0.028 0.047 0.24 5 -10000 0 5
EDG1 0.01 0.02 -10000 0 -10000 0 0
mol:DAG 0.02 0.027 -10000 0 -10000 0 0
CaM/Ca2+ 0.035 0.035 -10000 0 -10000 0 0
MAP2K3 0.017 0.044 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.055 0.046 -10000 0 -10000 0 0
PLCG1 0.02 0.027 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.051 0.033 -10000 0 -10000 0 0
IQGAP1 0.026 0.007 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.047 0.022 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.045 0.026 -10000 0 -10000 0 0
cell migration 0.06 0.078 0.28 18 -10000 0 18
mol:PI-3-4-5-P3 0.039 0.041 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.028 0.026 -10000 0 -10000 0 0
mol:NO 0.048 0.1 0.28 18 -0.43 6 24
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.026 0.016 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.039 0.027 -10000 0 -10000 0 0
VHL 0.028 0.004 -10000 0 -10000 0 0
ITGB3 0.023 0.042 -10000 0 -0.36 5 5
NOS3 0.048 0.11 0.29 17 -0.49 6 23
VEGFR2 homodimer/VEGFA homodimer/Sck 0.043 0.036 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCA 0.016 0.037 -10000 0 -10000 0 0
PRKCB 0.007 0.052 -10000 0 -10000 0 0
VCL 0.026 0.007 -10000 0 -10000 0 0
VEGFA165/NRP1 0.029 0.022 -10000 0 -10000 0 0
VEGFR1/2 heterodimer/VEGFA homodimer 0.046 0.023 -10000 0 -10000 0 0
VEGFA165/NRP2 0.037 0.024 -10000 0 -0.24 2 2
MAPKKK cascade 0.032 0.031 -10000 0 -10000 0 0
NRP2 0.027 0.019 -10000 0 -0.35 1 1
VEGFC homodimer 0.025 0.021 -10000 0 -0.38 1 1
NCK1 0.027 0.005 -10000 0 -10000 0 0
ROCK1 0.027 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.058 0.073 0.28 6 -10000 0 6
MAP3K13 0.02 0.029 -10000 0 -10000 0 0
PDPK1 0.034 0.049 0.25 8 -10000 0 8
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.062 0.028 -9999 0 -0.19 1 1
HDAC3 0.027 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.034 0.038 -9999 0 -0.27 6 6
GATA1/HDAC5 0.034 0.038 -9999 0 -0.27 6 6
GATA2/HDAC5 0.036 0.035 -9999 0 -0.27 5 5
HDAC5/BCL6/BCoR 0.052 0.016 -9999 0 -10000 0 0
HDAC9 0.008 0.084 -9999 0 -0.38 18 18
Glucocorticoid receptor/Hsp90/HDAC6 0.047 0.039 -9999 0 -0.22 7 7
HDAC4/ANKRA2 0.038 0.013 -9999 0 -10000 0 0
HDAC5/YWHAB 0.033 0.017 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.005 -9999 0 -10000 0 0
GATA2 0.022 0.045 -9999 0 -0.38 5 5
HDAC4/RFXANK 0.039 0.01 -9999 0 -10000 0 0
BCOR 0.028 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.026 0.007 -9999 0 -10000 0 0
HDAC5 0.028 0.004 -9999 0 -10000 0 0
GNB1/GNG2 0.038 0.018 -9999 0 -0.25 1 1
Histones 0.017 0.054 -9999 0 -0.27 2 2
ADRBK1 0.027 0.006 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
XPO1 0.028 0.003 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.012 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.012 -9999 0 -10000 0 0
HDAC7 0.027 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.013 -9999 0 -10000 0 0
TUBA1B 0.028 0.004 -9999 0 -10000 0 0
HDAC6 0.028 0.004 -9999 0 -10000 0 0
HDAC5/RFXANK 0.04 0.009 -9999 0 -10000 0 0
CAMK4 0.016 0.063 -9999 0 -0.38 10 10
Tubulin/HDAC6 0.051 0.022 -9999 0 -0.23 1 1
SUMO1 0.028 0.003 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.022 0.011 -9999 0 -10000 0 0
GATA1 0.02 0.049 -9999 0 -0.38 6 6
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.008 -9999 0 -10000 0 0
NR3C1 0.022 0.045 -9999 0 -0.38 5 5
SUMO1/HDAC4 0.036 0.035 -9999 0 -10000 0 0
SRF 0.026 0.008 -9999 0 -10000 0 0
HDAC4/YWHAB 0.032 0.018 -9999 0 -10000 0 0
Tubulin 0.038 0.019 -9999 0 -0.27 1 1
HDAC4/14-3-3 E 0.037 0.013 -9999 0 -10000 0 0
GNB1 0.026 0.007 -9999 0 -10000 0 0
RANGAP1 0.027 0.005 -9999 0 -10000 0 0
BCL6/BCoR 0.039 0.011 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.051 0.018 -9999 0 -10000 0 0
HDAC4/SRF 0.04 0.047 -9999 0 -0.23 10 10
HDAC4/ER alpha 0.027 0.059 -9999 0 -0.27 15 15
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.017 0.054 -9999 0 -0.27 2 2
cell motility 0.051 0.022 -9999 0 -0.23 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.038 0.012 -9999 0 -10000 0 0
BCL6 0.027 0.006 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.027 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.038 0.022 -9999 0 -0.25 2 2
ESR1 0.012 0.077 -9999 0 -0.38 15 15
HDAC6/HDAC11 0.04 0.008 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.035 -9999 0 -10000 0 0
NPC 0.016 0.002 -9999 0 -10000 0 0
MEF2C 0.026 0.008 -9999 0 -10000 0 0
RAN 0.027 0.005 -9999 0 -10000 0 0
HDAC4/MEF2C 0.07 0.032 -9999 0 -10000 0 0
GNG2 0.027 0.019 -9999 0 -0.35 1 1
NCOR2 0.027 0.005 -9999 0 -10000 0 0
TUBB2A 0.025 0.021 -9999 0 -0.38 1 1
HDAC11 0.028 0.004 -9999 0 -10000 0 0
HSP90AA1 0.025 0.027 -9999 0 -0.35 2 2
RANBP2 0.028 0.003 -9999 0 -10000 0 0
ANKRA2 0.026 0.007 -9999 0 -10000 0 0
RFXANK 0.027 0.005 -9999 0 -10000 0 0
nuclear import -0.027 0.017 -9999 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.033 0.017 -10000 0 -10000 0 0
ATM 0.026 0.02 -10000 0 -0.35 1 1
UBE2D3 0.027 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.009 -10000 0 -10000 0 0
ATR 0.027 0.006 -10000 0 -10000 0 0
UBE2L3 0.027 0.006 -10000 0 -10000 0 0
FANCD2 0.016 0.025 -10000 0 -10000 0 0
protein ubiquitination 0.051 0.054 -10000 0 -10000 0 0
XRCC5 0.028 0.004 -10000 0 -10000 0 0
XRCC6 0.027 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.046 0.023 -10000 0 -10000 0 0
MRE11A 0.027 0.005 -10000 0 -10000 0 0
DNA-PK 0.048 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.022 0.06 -10000 0 -0.36 5 5
FANCF 0.027 0.005 -10000 0 -10000 0 0
BRCA1 0.027 0.019 -10000 0 -0.35 1 1
CCNE1 0.011 0.071 -10000 0 -0.35 15 15
CDK2/Cyclin E1 0.025 0.053 -10000 0 -0.25 14 14
FANCG 0.026 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.039 0.016 -10000 0 -0.25 1 1
FANCE 0.027 0.005 -10000 0 -10000 0 0
FANCC 0.027 0.006 -10000 0 -10000 0 0
NBN 0.025 0.01 -10000 0 -10000 0 0
FANCA 0.019 0.053 -10000 0 -0.35 8 8
DNA repair 0.028 0.066 0.24 11 -10000 0 11
BRCA1/BARD1/ubiquitin 0.039 0.016 -10000 0 -0.25 1 1
BARD1/DNA-PK 0.06 0.027 -10000 0 -10000 0 0
FANCL 0.027 0.019 -10000 0 -0.35 1 1
mRNA polyadenylation -0.033 0.017 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.043 -10000 0 -0.26 1 1
BRCA1/BACH1/BARD1/TopBP1 0.052 0.02 -10000 0 -0.21 1 1
BRCA1/BARD1/P53 0.062 0.028 -10000 0 -0.19 1 1
BARD1/CSTF1/BRCA1 0.044 0.027 -10000 0 -0.21 1 1
BRCA1/BACH1 0.027 0.019 -10000 0 -0.35 1 1
BARD1 0.028 0.004 -10000 0 -10000 0 0
PCNA 0.024 0.021 -10000 0 -0.35 1 1
BRCA1/BARD1/UbcH5C 0.053 0.019 -10000 0 -0.21 1 1
BRCA1/BARD1/UbcH7 0.052 0.02 -10000 0 -0.21 1 1
BRCA1/BARD1/RAD51/PCNA 0.06 0.034 -10000 0 -0.36 1 1
BARD1/DNA-PK/P53 0.066 0.035 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.039 0.016 -10000 0 -0.25 1 1
BRCA1/BARD1/CTIP 0.038 0.024 -10000 0 -0.19 2 2
FA complex 0.024 0.031 -10000 0 -0.25 1 1
BARD1/EWS 0.039 0.01 -10000 0 -10000 0 0
RBBP8 0.011 0.014 -10000 0 -0.25 1 1
TP53 0.026 0.008 -10000 0 -10000 0 0
TOPBP1 0.027 0.005 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.059 0.028 0.19 1 -10000 0 1
BRCA1/BARD1 0.056 0.057 -10000 0 -10000 0 0
CSTF1 0.023 0.011 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.02 0.003 -10000 0 -10000 0 0
CDK2 0.027 0.006 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.027 0.005 -10000 0 -10000 0 0
RAD50 0.026 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.039 0.016 -10000 0 -0.25 1 1
EWSR1 0.027 0.006 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.025 0.022 -10000 0 -0.38 1 1
positive regulation of NF-kappaB transcription factor activity 0.03 0.037 -10000 0 -0.27 5 5
MAP2K4 0.025 0.035 -10000 0 -0.29 1 1
IKBKB 0.025 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.024 0.021 -10000 0 -0.35 1 1
TNFRSF10A 0.025 0.009 -10000 0 -10000 0 0
SMPD1 0.011 0.012 -10000 0 -0.16 1 1
IKBKG 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.021 0.04 -10000 0 -0.38 4 4
TRAIL/TRAILR2 0.032 0.026 -10000 0 -0.26 2 2
TRAIL/TRAILR3 0.028 0.042 -10000 0 -0.25 8 8
TRAIL/TRAILR1 0.033 0.022 -10000 0 -0.27 1 1
TRAIL/TRAILR4 0.03 0.037 -10000 0 -0.27 5 5
TRAIL/TRAILR1/DAP3/GTP 0.042 0.025 -10000 0 -0.21 1 1
IKK complex 0.015 0.045 -10000 0 -0.34 1 1
RIPK1 0.026 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.004 -10000 0 -10000 0 0
MAPK3 0.012 0.015 -10000 0 -0.27 1 1
MAP3K1 0.024 0.035 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.021 0.04 -10000 0 -0.38 4 4
TRADD 0.027 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.025 0.009 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.022 0.019 -10000 0 -10000 0 0
CFLAR 0.028 0.003 -10000 0 -10000 0 0
MAPK1 0.011 0.015 -10000 0 -0.27 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.058 0.041 -10000 0 -0.2 1 1
mol:ceramide 0.011 0.012 -10000 0 -0.16 1 1
FADD 0.026 0.007 -10000 0 -10000 0 0
MAPK8 0.025 0.047 0.2 1 -0.32 2 3
TRAF2 0.027 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.016 0.056 -10000 0 -0.35 9 9
CHUK 0.027 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.043 0.028 -10000 0 -0.23 1 1
DAP3 0.027 0.005 -10000 0 -10000 0 0
CASP10 0.024 0.051 0.2 3 -0.25 1 4
JNK cascade 0.03 0.037 -10000 0 -0.27 5 5
TRAIL (trimer) 0.025 0.022 -10000 0 -0.38 1 1
TNFRSF10C 0.016 0.056 -10000 0 -0.35 9 9
TRAIL/TRAILR1/DAP3/GTP/FADD 0.049 0.032 -10000 0 -0.2 1 1
TRAIL/TRAILR2/FADD 0.042 0.031 -10000 0 -0.22 2 2
cell death 0.011 0.012 -10000 0 -0.16 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.019 -10000 0 -0.19 1 1
TRAILR2 (trimer) 0.024 0.021 -10000 0 -0.35 1 1
CASP8 0.012 0.036 -10000 0 -0.61 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.057 0.042 -10000 0 -0.2 1 1
HIF-2-alpha transcription factor network

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
MMP14 0.025 0.11 -10000 0 -0.64 8 8
oxygen homeostasis 0.001 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.007 -10000 0 -10000 0 0
TCEB1 0.024 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.049 0.069 -10000 0 -10000 0 0
EPO 0.035 0.13 -10000 0 -0.54 1 1
FIH (dimer) 0.025 0.02 -10000 0 -10000 0 0
APEX1 0.024 0.023 -10000 0 -10000 0 0
SERPINE1 0.008 0.16 -10000 0 -0.51 2 2
FLT1 0.024 0.11 -10000 0 -0.55 10 10
ADORA2A 0.025 0.14 0.37 4 -0.55 1 5
germ cell development 0.02 0.14 -10000 0 -0.5 2 2
SLC11A2 0.027 0.14 -10000 0 -0.51 1 1
BHLHE40 0.029 0.14 -10000 0 -0.51 1 1
HIF1AN 0.025 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.037 0.1 0.25 1 -10000 0 1
ETS1 0.036 0.009 -10000 0 -10000 0 0
CITED2 0.02 0.12 -10000 0 -0.68 9 9
KDR 0.024 0.11 -10000 0 -0.57 8 8
PGK1 0.028 0.13 -10000 0 -0.51 1 1
SIRT1 0.027 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.052 0.16 -10000 0 -0.58 1 1
EPAS1 0.019 0.06 -10000 0 -0.3 3 3
SP1 0.031 0.009 -10000 0 -10000 0 0
ABCG2 0.019 0.15 -10000 0 -0.52 6 6
EFNA1 0.029 0.14 -10000 0 -0.51 1 1
FXN 0.025 0.13 0.35 3 -0.54 1 4
POU5F1 0.02 0.15 -10000 0 -0.52 2 2
neuron apoptosis -0.05 0.16 0.56 1 -10000 0 1
EP300 0.027 0.005 -10000 0 -10000 0 0
EGLN3 0.025 0.028 -10000 0 -0.39 1 1
EGLN2 0.025 0.019 -10000 0 -10000 0 0
EGLN1 0.025 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.046 0.023 -10000 0 -10000 0 0
VHL 0.028 0.004 -10000 0 -10000 0 0
ARNT 0.024 0.022 -10000 0 -10000 0 0
SLC2A1 0.015 0.15 0.37 4 -0.51 4 8
TWIST1 0.019 0.14 0.35 3 -10000 0 3
ELK1 0.031 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.043 0.1 -10000 0 -10000 0 0
VEGFA 0.03 0.13 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.043 0.071 -10000 0 -0.27 4 4
Ran/GTP/Exportin 1/HDAC1 -0.008 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.078 -10000 0 -0.32 6 6
SUMO1 0.028 0.003 -10000 0 -10000 0 0
ZFPM1 0.026 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.005 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.05 0.059 -10000 0 -0.29 1 1
YY1/LSF 0.017 0.055 -10000 0 -0.21 11 11
SMG5 0.027 0.005 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.018 0.036 -10000 0 -0.3 1 1
I kappa B alpha/HDAC1 0.027 0.046 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA 0.02 0.047 0.28 1 -0.36 2 3
HDAC1/Smad7 0.045 0.024 -10000 0 -10000 0 0
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
HDAC3/TR2 0.026 0.052 -10000 0 -0.31 1 1
NuRD/MBD3 Complex 0.028 0.032 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.017 0.082 0.2 3 -0.33 10 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.022 0.045 -10000 0 -0.38 5 5
GATA1 0.02 0.049 -10000 0 -0.38 6 6
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.019 0.073 -10000 0 -0.36 7 7
RBBP7 0.027 0.005 -10000 0 -10000 0 0
NPC 0.016 0.002 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
NFKBIA 0.016 0.027 -10000 0 -10000 0 0
KAT2B 0.024 0.041 -10000 0 -0.38 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.024 0.02 -10000 0 -0.28 1 1
SIN3 complex 0.061 0.027 -10000 0 -10000 0 0
SMURF1 0.025 0.009 -10000 0 -10000 0 0
CHD3 0.026 0.007 -10000 0 -10000 0 0
SAP30 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.008 -10000 0 -10000 0 0
YY1/HDAC3 0.013 0.054 -10000 0 -0.34 3 3
YY1/HDAC2 0.017 0.056 -10000 0 -0.28 2 2
YY1/HDAC1 0.018 0.056 -10000 0 -0.22 8 8
NuRD/MBD2 Complex (MeCP1) 0.024 0.036 -10000 0 -10000 0 0
PPARG 0.013 0.057 -10000 0 -0.28 8 8
HDAC8/hEST1B 0.052 0.016 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.025 0.051 -10000 0 -0.31 1 1
MBD3L2 0.018 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.023 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.017 0.079 -10000 0 -0.35 10 10
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.016 0.032 -10000 0 -0.36 1 1
HDAC2 0.027 0.005 -10000 0 -10000 0 0
YY1 0.016 0.025 -10000 0 -0.22 4 4
HDAC8 0.027 0.005 -10000 0 -10000 0 0
SMAD7 0.025 0.009 -10000 0 -10000 0 0
NCOR2 0.027 0.005 -10000 0 -10000 0 0
MXD1 0.028 0.003 -10000 0 -10000 0 0
STAT3 0.02 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.032 0.055 -10000 0 -0.24 2 2
YY1/SAP30/HDAC1 0.031 0.056 -10000 0 -0.25 2 2
EP300 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.02 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.027 -10000 0 -10000 0 0
histone deacetylation 0.021 0.046 -10000 0 -0.24 5 5
STAT3 (dimer non-phopshorylated)/HDAC3 0.021 0.037 -10000 0 -0.38 1 1
nuclear export -0.052 0.016 -10000 0 -10000 0 0
PRKACA 0.027 0.005 -10000 0 -10000 0 0
GATAD2B 0.027 0.005 -10000 0 -10000 0 0
GATAD2A 0.027 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.022 0.058 -10000 0 -0.28 2 2
GATA1/HDAC1 0.034 0.038 -10000 0 -0.27 6 6
GATA1/HDAC3 0.021 0.058 -10000 0 -0.3 2 2
CHD4 0.027 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.025 0.059 -10000 0 -0.25 17 17
SIN3/HDAC complex/Mad/Max 0.025 0.047 -10000 0 -0.41 2 2
NuRD Complex 0.014 0.081 -10000 0 -0.36 9 9
positive regulation of chromatin silencing 0.048 0.057 -10000 0 -0.28 1 1
SIN3B 0.027 0.005 -10000 0 -10000 0 0
MTA2 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.028 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.036 0.034 -10000 0 -10000 0 0
HDAC complex 0.066 0.021 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.039 -10000 0 -0.27 6 6
FKBP25/HDAC1/HDAC2 0.053 0.015 -10000 0 -10000 0 0
TNF 0.01 0.08 -10000 0 -0.36 18 18
negative regulation of cell growth 0.024 0.052 -10000 0 -0.3 5 5
NuRD/MBD2/PRMT5 Complex 0.024 0.036 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.035 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.006 0.067 -10000 0 -0.29 11 11
SIN3/HDAC complex/NCoR1 0.012 0.059 -10000 0 -0.31 6 6
TFCP2 0.027 0.005 -10000 0 -10000 0 0
NR2C1 0.028 0.004 -10000 0 -10000 0 0
MBD3 0.026 0.007 -10000 0 -10000 0 0
MBD2 0.024 0.01 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.027 0.006 -9999 0 -10000 0 0
Rac1/GDP 0.025 0.011 -9999 0 -10000 0 0
DOCK1 0.027 0.006 -9999 0 -10000 0 0
ITGA4 0.025 0.033 -9999 0 -0.35 3 3
RAC1 0.026 0.008 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.036 0.03 -9999 0 -0.25 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.026 0.008 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.031 -9999 0 -0.21 4 4
alpha4/beta7 Integrin/Paxillin 0.041 0.027 -9999 0 -0.19 4 4
lamellipodium assembly 0.006 0.092 -9999 0 -0.37 18 18
PIK3CA 0.026 0.007 -9999 0 -10000 0 0
PI3K 0.036 0.014 -9999 0 -10000 0 0
ARF6 0.027 0.006 -9999 0 -10000 0 0
TLN1 0.026 0.008 -9999 0 -10000 0 0
PXN 0.013 0.003 -9999 0 -10000 0 0
PIK3R1 0.026 0.008 -9999 0 -10000 0 0
ARF6/GTP 0.05 0.031 -9999 0 -10000 0 0
cell adhesion 0.048 0.032 -9999 0 -10000 0 0
CRKL/CBL 0.038 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.027 -9999 0 -0.19 4 4
ITGB1 0.026 0.02 -9999 0 -0.35 1 1
ITGB7 0.026 0.021 -9999 0 -0.38 1 1
ARF6/GDP 0.025 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.051 0.037 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 0.048 0.021 -9999 0 -10000 0 0
VCAM1 0.025 0.033 -9999 0 -0.35 3 3
alpha4/beta1 Integrin/Paxillin/Talin 0.05 0.033 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.053 0.031 -9999 0 -10000 0 0
BCAR1 0.027 0.006 -9999 0 -10000 0 0
mol:GDP -0.051 0.031 -9999 0 -10000 0 0
CBL 0.027 0.006 -9999 0 -10000 0 0
PRKACA 0.027 0.005 -9999 0 -10000 0 0
GIT1 0.028 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.05 0.033 -9999 0 -10000 0 0
Rac1/GTP 0.005 0.1 -9999 0 -0.41 18 18
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.038 0.012 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.027 0.011 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.052 0.22 5 -0.3 1 6
NFKBIA 0.024 0.041 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.026 0.011 -10000 0 -10000 0 0
ARRB2 0.013 0.005 -10000 0 -10000 0 0
REL 0.028 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.026 0.011 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.019 0.008 -10000 0 -10000 0 0
PIK3R1 0.026 0.008 -10000 0 -10000 0 0
NFKB1 0.012 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.021 0.041 -10000 0 -0.31 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.035 0.054 0.2 5 -0.29 2 7
SRC 0.024 0.01 -10000 0 -10000 0 0
PI3K 0.036 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.021 0.041 -10000 0 -0.31 1 1
IKBKB 0.025 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.006 -10000 0 -10000 0 0
SYK 0.026 0.021 -10000 0 -0.38 1 1
I kappa B alpha/PIK3R1 0.034 0.052 0.21 4 -0.26 2 6
cell death 0.032 0.05 0.18 3 -0.28 2 5
NF kappa B1 p105/c-Rel 0.027 0.011 -10000 0 -10000 0 0
LCK 0.017 0.062 -10000 0 -0.35 11 11
BCL3 0.027 0.007 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.026 0.049 0.15 54 -10000 0 54
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0.032 0.17 7 -0.17 1 8
AP2 0.037 0.013 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.034 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.008 -10000 0 -10000 0 0
CD4 0.025 0.027 -10000 0 -0.35 2 2
CLTA 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.011 -10000 0 -10000 0 0
ARF1/GTP 0.032 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.009 0.006 -10000 0 -10000 0 0
mol:Choline 0.007 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.007 -10000 0 -10000 0 0
DDEF1 0.006 0.012 -10000 0 -10000 0 0
ARF1/GDP 0.005 0.01 -10000 0 -10000 0 0
AP2M1 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.032 0.018 -10000 0 -10000 0 0
ARFIP2 0.022 0.015 -10000 0 -10000 0 0
COPA 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.038 0.14 4 -0.19 4 8
ARF1/GTP/ARHGAP10 0.018 0.007 -10000 0 -10000 0 0
GGA3 0.027 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.026 0.012 -10000 0 -10000 0 0
AP2A1 0.027 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.023 -10000 0 -0.2 3 3
ARF1/GDP/Membrin 0.026 0.016 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.033 0.013 -10000 0 -10000 0 0
CYTH2 0.028 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.036 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 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 0.021 0.025 -10000 0 -10000 0 0
PLD2 0.007 0.012 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.003 -10000 0 -10000 0 0
PIP5K1A 0.008 0.011 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.019 0.023 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.011 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.003 -10000 0 -10000 0 0
GOSR2 0.013 0.008 -10000 0 -10000 0 0
USO1 0.011 0.028 -10000 0 -0.31 3 3
GBF1 0.009 0.036 -10000 0 -0.31 5 5
ARF1/GTP/Arfaptin 2 0.037 0.012 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.048 0.027 -10000 0 -0.21 2 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.024 0.01 -10000 0 -10000 0 0
SMAD2 0.011 0.038 0.19 2 -10000 0 2
SMAD3 0.025 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.022 0.086 -10000 0 -0.42 12 12
SMAD4/Ubc9/PIASy 0.045 0.023 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.047 0.046 -10000 0 -10000 0 0
PPM1A 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.017 0.033 -10000 0 -0.23 1 1
MAP3K1 0.026 0.008 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.035 0.015 -10000 0 -10000 0 0
MAPK3 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.027 0.006 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
CTDSP1 0.028 0.004 -10000 0 -10000 0 0
CTDSP2 0.027 0.006 -10000 0 -10000 0 0
CTDSPL 0.027 0.005 -10000 0 -10000 0 0
KPNB1 0.028 0.002 -10000 0 -10000 0 0
TGFBRAP1 0.028 0.004 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
NUP153 0.027 0.006 -10000 0 -10000 0 0
KPNA2 0.027 0.019 -10000 0 -0.35 1 1
PIAS4 0.026 0.007 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.049 0.025 -10000 0 -10000 0 0
CLOCK 0.029 0.006 -10000 0 -10000 0 0
TIMELESS/CRY2 0.037 0.022 -10000 0 -10000 0 0
DEC1/BMAL1 0.034 0.022 -10000 0 -0.26 2 2
ATR 0.027 0.006 -10000 0 -10000 0 0
NR1D1 0.019 0.014 -10000 0 -10000 0 0
ARNTL 0.028 0.021 -10000 0 -0.38 1 1
TIMELESS 0.021 0.012 -10000 0 -10000 0 0
NPAS2 0.029 0.005 -10000 0 -10000 0 0
CRY2 0.027 0.006 -10000 0 -10000 0 0
mol:CO -0.008 0.004 0.074 1 -10000 0 1
CHEK1 0.026 0.02 -10000 0 -0.35 1 1
mol:HEME 0.008 0.004 -10000 0 -0.074 1 1
PER1 0.018 0.057 -10000 0 -0.38 8 8
BMAL/CLOCK/NPAS2 0.062 0.023 -10000 0 -0.22 1 1
BMAL1/CLOCK 0.028 0.053 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.049 0.025 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.05 0.025 -10000 0 -10000 0 0
mol:NADPH 0.008 0.004 -10000 0 -0.074 1 1
PER1/TIMELESS 0.033 0.035 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.019 -10000 0 -0.35 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.005 0.011 -10000 0 -10000 0 0
MDM2/SUMO1 0.035 0.036 -10000 0 -10000 0 0
HDAC4 0.027 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.005 0.01 -10000 0 -10000 0 0
SUMO1 0.028 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.012 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.009 0.009 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.036 0.035 -10000 0 -10000 0 0
SUMO1/HDAC1 0.036 0.034 -10000 0 -10000 0 0
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.059 0.033 -10000 0 -0.19 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.014 0.005 -10000 0 -10000 0 0
Ran/GTP 0.025 0.03 -10000 0 -0.16 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.025 0.027 -10000 0 -0.35 2 2
UBE2I 0.026 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.034 0.19 4 -10000 0 4
NPC 0.016 0.002 -10000 0 -10000 0 0
PIAS2 0.025 0.009 -10000 0 -10000 0 0
PIAS1 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 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 0.039 0.01 -9999 0 -10000 0 0
FBXW11 0.027 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.006 -9999 0 -10000 0 0
CHUK 0.027 0.006 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.072 0.032 -9999 0 -10000 0 0
NFKB1 0.027 0.005 -9999 0 -10000 0 0
MAP3K14 0.028 0.004 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.038 0.018 -9999 0 -0.25 1 1
RELB 0.026 0.02 -9999 0 -0.35 1 1
NFKB2 0.027 0.006 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.034 0.016 -9999 0 -0.2 1 1
regulation of B cell activation 0.034 0.016 -9999 0 -0.2 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 413 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZQ.A9CR TCGA.ZA.A8F6 TCGA.VQ.AA6K TCGA.VQ.AA6J
109_MAP3K5 0.031 0.031 0.078 0.0026
47_PPARGC1A 0.028 0.028 0.028 0.028
105_BMP4 0.028 0.028 0.028 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 0.028 0 0.028
105_BMP2 0.028 0.028 0.028 0.028
131_RELN/VLDLR -0.38 0.073 0.073 -0.38
30_TGFB1/TGF beta receptor Type II 0.028 0.028 0.032 0.031
84_STAT5B -0.04 0.0014 0.038 0.053
84_STAT5A -0.04 0.0014 0.038 0.053
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/STAD-TP/22315237/STAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/STAD-TP/22507290/GDAC_Gistic2Report_22533882/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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