PARADIGM pathway analysis of mRNA expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1D21WZ5
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 mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1D21WZ5
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 54 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
Signaling mediated by p38-alpha and p38-beta 247
Signaling events mediated by Stem cell factor receptor (c-Kit) 217
Endothelins 150
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 147
EGFR-dependent Endothelin signaling events 147
Class IB PI3K non-lipid kinase events 126
IGF1 pathway 121
FOXM1 transcription factor network 109
Arf6 signaling events 106
Nongenotropic Androgen signaling 93
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 526 . 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 ( 526 ).

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
Signaling mediated by p38-alpha and p38-beta 0.4696 247 10869 44 -0.61 0.034 1000 -1000 -0.009 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.4125 217 16984 78 -1 0.32 1000 -1000 -0.028 -1000
Endothelins 0.2852 150 14422 96 -0.81 0.17 1000 -1000 -0.023 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2795 147 10032 68 -0.88 0.45 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 0.2795 147 3090 21 -0.31 0.048 1000 -1000 -0.032 -1000
Class IB PI3K non-lipid kinase events 0.2395 126 378 3 -0.11 -1000 1000 -1000 -0.024 -1000
IGF1 pathway 0.2300 121 6930 57 -0.26 0.098 1000 -1000 -0.025 -1000
FOXM1 transcription factor network 0.2072 109 5604 51 -0.14 0.68 1000 -1000 0.014 -1000
Arf6 signaling events 0.2015 106 6611 62 -0.31 0.082 1000 -1000 -0.004 -1000
Nongenotropic Androgen signaling 0.1768 93 4865 52 -0.57 0.3 1000 -1000 -0.02 -1000
Signaling events mediated by PTP1B 0.1521 80 6123 76 -0.37 0.19 1000 -1000 -0.037 -1000
Glucocorticoid receptor regulatory network 0.1483 78 8965 114 -0.95 0.29 1000 -1000 -0.052 -1000
S1P1 pathway 0.1483 78 2813 36 -0.62 0.046 1000 -1000 -0.022 -1000
Calcium signaling in the CD4+ TCR pathway 0.1407 74 2298 31 -0.35 0.041 1000 -1000 -0.026 -1000
HIF-1-alpha transcription factor network 0.1388 73 5552 76 -0.4 0.066 1000 -1000 -0.005 -1000
PDGFR-alpha signaling pathway 0.1350 71 3125 44 -0.7 0.063 1000 -1000 -0.024 -1000
BMP receptor signaling 0.1293 68 5574 81 -0.4 0.11 1000 -1000 -0.026 -1000
Ephrin B reverse signaling 0.1293 68 3301 48 -0.18 0.06 1000 -1000 -0.028 -1000
Ras signaling in the CD4+ TCR pathway 0.1103 58 987 17 -0.2 0.033 1000 -1000 -0.009 -1000
IL6-mediated signaling events 0.1046 55 4157 75 -0.37 0.073 1000 -1000 -0.02 -1000
Plasma membrane estrogen receptor signaling 0.1027 54 4673 86 -0.25 0.18 1000 -1000 -0.053 -1000
FAS signaling pathway (CD95) 0.1008 53 2518 47 -0.88 0.06 1000 -1000 -0.023 -1000
Integrins in angiogenesis 0.1008 53 4473 84 -0.39 0.13 1000 -1000 -0.028 -1000
EPHB forward signaling 0.1008 53 4509 85 -0.18 0.14 1000 -1000 -0.055 -1000
IL4-mediated signaling events 0.0970 51 4686 91 -0.51 0.14 1000 -1000 -0.077 -1000
PLK1 signaling events 0.0932 49 4205 85 -0.035 0.17 1000 -1000 -0.028 -1000
Visual signal transduction: Rods 0.0894 47 2489 52 -0.43 0.074 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 0.0875 46 4482 97 -0.36 0.041 1000 -1000 -0.039 -1000
IL23-mediated signaling events 0.0875 46 2795 60 -0.79 0.065 1000 -1000 -0.003 -1000
Aurora B signaling 0.0856 45 3035 67 -0.38 0.24 1000 -1000 -0.028 -1000
IL12-mediated signaling events 0.0760 40 3508 87 -0.83 0.088 1000 -1000 -0.04 -1000
Glypican 1 network 0.0760 40 1955 48 -0.39 0.07 1000 -1000 -0.02 -1000
p75(NTR)-mediated signaling 0.0741 39 4875 125 -0.13 0.094 1000 -1000 -0.038 -1000
Nectin adhesion pathway 0.0741 39 2511 63 -0.076 0.054 1000 -1000 -0.027 -1000
S1P5 pathway 0.0741 39 675 17 -0.17 0.065 1000 -1000 -0.006 -1000
Insulin Pathway 0.0741 39 2890 74 -0.28 0.091 1000 -1000 -0.03 -1000
Signaling events mediated by the Hedgehog family 0.0722 38 2023 52 -0.14 0.068 1000 -1000 -0.021 -1000
TCGA08_retinoblastoma 0.0722 38 305 8 -0.022 0.058 1000 -1000 -0.01 -1000
S1P4 pathway 0.0703 37 937 25 -0.17 0.045 1000 -1000 -0.008 -1000
E-cadherin signaling in keratinocytes 0.0684 36 1555 43 -0.27 0.036 1000 -1000 -0.023 -1000
Presenilin action in Notch and Wnt signaling 0.0665 35 2181 61 -0.38 0.11 1000 -1000 -0.028 -1000
LPA receptor mediated events 0.0665 35 3610 102 -0.36 0.095 1000 -1000 -0.052 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0665 35 2613 74 -0.27 0.074 1000 -1000 -0.061 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0646 34 2902 85 -0.54 0.043 1000 -1000 -0.042 -1000
TCR signaling in naïve CD8+ T cells 0.0589 31 2963 93 -0.039 0.081 1000 -1000 -0.036 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0589 31 3758 120 -0.25 0.12 1000 -1000 -0.039 -1000
IL27-mediated signaling events 0.0570 30 1574 51 -0.37 0.068 1000 -1000 -0.05 -1000
ErbB2/ErbB3 signaling events 0.0551 29 1940 65 -0.35 0.047 1000 -1000 -0.047 -1000
Signaling events regulated by Ret tyrosine kinase 0.0551 29 2457 82 -0.1 0.12 1000 -1000 -0.052 -1000
Syndecan-3-mediated signaling events 0.0551 29 1033 35 -0.36 0.076 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 0.0551 29 765 26 -0.27 0.042 1000 -1000 -0.019 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0532 28 1504 52 -0.38 0.11 1000 -1000 -0.013 -1000
Canonical Wnt signaling pathway 0.0513 27 1393 51 -0.38 0.16 1000 -1000 -0.036 -1000
S1P3 pathway 0.0513 27 1151 42 -0.17 0.062 1000 -1000 -0.023 -1000
Regulation of nuclear SMAD2/3 signaling 0.0475 25 3524 136 -0.37 0.075 1000 -1000 -0.041 -1000
FOXA2 and FOXA3 transcription factor networks 0.0475 25 1169 46 -0.75 0.051 1000 -1000 -0.014 -1000
mTOR signaling pathway 0.0475 25 1358 53 -0.051 0.044 1000 -1000 -0.03 -1000
amb2 Integrin signaling 0.0475 25 2100 82 -0.52 0.13 1000 -1000 -0.021 -1000
Ceramide signaling pathway 0.0475 25 1911 76 -0.25 0.083 1000 -1000 -0.016 -1000
IL1-mediated signaling events 0.0456 24 1498 62 -0.049 0.068 1000 -1000 -0.025 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0456 24 2120 88 -0.39 0.13 1000 -1000 -0.056 -1000
ErbB4 signaling events 0.0437 23 1639 69 -0.36 0.14 1000 -1000 -0.029 -1000
Syndecan-2-mediated signaling events 0.0437 23 1633 69 -0.32 0.13 1000 -1000 -0.023 -1000
Reelin signaling pathway 0.0437 23 1340 56 -0.056 0.082 1000 -1000 -0.018 -1000
HIF-2-alpha transcription factor network 0.0437 23 990 43 -0.23 0.26 1000 -1000 -0.085 -1000
Coregulation of Androgen receptor activity 0.0418 22 1724 76 -0.23 0.054 1000 -1000 -0.002 -1000
Osteopontin-mediated events 0.0399 21 817 38 -0.35 0.13 1000 -1000 -0.014 -1000
Thromboxane A2 receptor signaling 0.0399 21 2263 105 -0.27 0.067 1000 -1000 -0.036 -1000
Syndecan-1-mediated signaling events 0.0380 20 700 34 -0.041 0.11 1000 -1000 -0.018 -1000
Regulation of p38-alpha and p38-beta 0.0380 20 1127 54 -0.31 0.071 1000 -1000 -0.041 -1000
Regulation of Telomerase 0.0380 20 2060 102 -0.35 0.087 1000 -1000 -0.012 -1000
Syndecan-4-mediated signaling events 0.0380 20 1399 67 -0.39 0.15 1000 -1000 -0.026 -1000
Regulation of Androgen receptor activity 0.0380 20 1459 70 -0.43 0.079 1000 -1000 -0.025 -1000
Noncanonical Wnt signaling pathway 0.0342 18 474 26 -0.016 0.04 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 0.0342 18 1077 58 -0.12 0.049 1000 -1000 -0.027 -1000
Signaling events mediated by PRL 0.0323 17 592 34 -0.31 0.051 1000 -1000 -0.019 -1000
Wnt signaling 0.0304 16 118 7 -0.016 0.04 1000 -1000 -0.009 -1000
Hedgehog signaling events mediated by Gli proteins 0.0285 15 1004 65 -0.17 0.077 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0285 15 696 45 -0.006 0.059 1000 -1000 -0.02 -1000
E-cadherin signaling in the nascent adherens junction 0.0285 15 1152 76 -0.038 0.06 1000 -1000 -0.048 -1000
E-cadherin signaling events 0.0285 15 77 5 0.007 0.035 1000 -1000 0.016 -1000
Caspase cascade in apoptosis 0.0266 14 1068 74 -0.16 0.049 1000 -1000 -0.021 -1000
Cellular roles of Anthrax toxin 0.0266 14 553 39 -0.063 0.038 1000 -1000 -0.018 -1000
IFN-gamma pathway 0.0266 14 963 68 -0.02 0.1 1000 -1000 -0.025 -1000
PLK2 and PLK4 events 0.0247 13 41 3 0.016 0.055 1000 -1000 0.003 -1000
Arf6 downstream pathway 0.0247 13 559 43 -0.091 0.093 1000 -1000 -0.038 -1000
Class I PI3K signaling events mediated by Akt 0.0228 12 879 68 -0.15 0.062 1000 -1000 -0.023 -1000
ceramide signaling pathway 0.0228 12 627 49 -0.069 0.053 1000 -1000 -0.027 -1000
BCR signaling pathway 0.0228 12 1225 99 -0.15 0.092 1000 -1000 -0.044 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0209 11 329 28 -0.17 0.054 1000 -1000 -0.011 -1000
FoxO family signaling 0.0209 11 718 64 0 0.15 1000 -1000 -0.014 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0190 10 557 54 -0.04 0.083 1000 -1000 -0.019 -1000
EPO signaling pathway 0.0190 10 586 55 -0.089 0.069 1000 -1000 -0.015 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0190 10 1320 125 -0.38 0.075 1000 -1000 -0.033 -1000
Arf6 trafficking events 0.0190 10 730 71 -0.26 0.056 1000 -1000 -0.029 -1000
JNK signaling in the CD4+ TCR pathway 0.0171 9 163 17 -0.04 0.09 1000 -1000 -0.013 -1000
VEGFR1 specific signals 0.0171 9 521 56 -0.38 0.076 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class III 0.0152 8 330 40 -0.061 0.062 1000 -1000 -0.032 -1000
TRAIL signaling pathway 0.0152 8 404 48 -0.001 0.047 1000 -1000 -0.022 -1000
Signaling mediated by p38-gamma and p38-delta 0.0152 8 124 15 -0.005 0.034 1000 -1000 -0.029 -1000
Signaling events mediated by HDAC Class II 0.0133 7 566 75 -0.059 0.067 1000 -1000 -0.013 -1000
Circadian rhythm pathway 0.0133 7 171 22 -0.021 0.11 1000 -1000 -0.026 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0133 7 596 83 -0.069 0.066 1000 -1000 -0.011 -1000
Retinoic acid receptors-mediated signaling 0.0133 7 435 58 -0.053 0.08 1000 -1000 -0.018 -1000
p38 MAPK signaling pathway 0.0133 7 315 44 -0.014 0.067 1000 -1000 -0.012 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0114 6 249 37 -0.02 0.085 1000 -1000 -0.017 -1000
Paxillin-dependent events mediated by a4b1 0.0114 6 233 36 -0.071 0.076 1000 -1000 -0.031 -1000
Visual signal transduction: Cones 0.0095 5 192 38 0 0.07 1000 -1000 0 -1000
Insulin-mediated glucose transport 0.0095 5 189 32 -0.099 0.053 1000 -1000 -0.014 -1000
Class I PI3K signaling events 0.0095 5 404 73 -0.009 0.059 1000 -1000 -0.023 -1000
PDGFR-beta signaling pathway 0.0095 5 543 97 -0.032 0.081 1000 -1000 -0.041 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0076 4 162 34 -0.048 0.084 1000 -1000 -0.028 -1000
Canonical NF-kappaB pathway 0.0076 4 156 39 0 0.073 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class I 0.0076 4 468 104 -0.21 0.082 1000 -1000 -0.035 -1000
Atypical NF-kappaB pathway 0.0076 4 137 31 -0.02 0.048 1000 -1000 -0.007 -1000
IL2 signaling events mediated by STAT5 0.0076 4 105 22 -0.019 0.081 1000 -1000 -0.01 -1000
Aurora A signaling 0.0057 3 199 60 0 0.12 1000 -1000 -0.011 -1000
TCGA08_p53 0.0057 3 21 7 -0.009 0.028 1000 -1000 -0.006 -1000
Effects of Botulinum toxin 0.0057 3 81 26 0 0.07 1000 -1000 0 -1000
LPA4-mediated signaling events 0.0038 2 29 12 -0.01 0.036 1000 -1000 -0.017 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 23 23 -0.007 0.066 1000 -1000 -0.014 -1000
BARD1 signaling events 0.0019 1 75 57 -0.075 0.12 1000 -1000 -0.042 -1000
Ephrin A reverse signaling 0.0019 1 7 7 0 0.044 1000 -1000 0 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0019 1 65 33 0 0.077 1000 -1000 -0.014 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.034 0.054 1000 -1000 0.021 -1000
Aurora C signaling 0.0000 0 4 7 0 0.079 1000 -1000 -0.013 -1000
Glypican 2 network 0.0000 0 0 4 0 0.032 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 25 27 0 0.078 1000 -1000 -0.023 -1000
Rapid glucocorticoid signaling 0.0000 0 16 20 0 0.043 1000 -1000 -0.001 -1000
Arf1 pathway 0.0000 0 51 54 -0.001 0.062 1000 -1000 -0.012 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.095 1000 -1000 0 -1000
Total NA 4345 264860 7203 -30 -990 131000 -131000 -3.1 -131000
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.61 0.54 0.4 4 -1 306 310
MKNK1 0.034 0.006 -10000 0 -10000 0 0
MAPK14 -0.2 0.2 -10000 0 -0.35 306 306
ATF2/c-Jun -0.26 0.32 -10000 0 -0.69 142 142
MAPK11 -0.19 0.2 -10000 0 -0.36 286 286
MITF -0.24 0.23 -10000 0 -0.42 307 307
MAPKAPK5 -0.23 0.22 -10000 0 -0.41 308 308
KRT8 -0.22 0.22 -10000 0 -0.41 274 274
MAPKAPK3 0.034 0.012 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.015 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.31 0.32 -10000 0 -0.54 309 309
CEBPB -0.22 0.23 0.3 1 -0.41 283 284
SLC9A1 -0.23 0.23 -10000 0 -0.42 304 304
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.24 0.24 -10000 0 -0.42 306 306
p38alpha-beta/MNK1 -0.25 0.28 -10000 0 -0.45 306 306
JUN -0.26 0.31 -10000 0 -0.68 142 142
PPARGC1A -0.28 0.29 0.28 1 -0.48 314 315
USF1 -0.21 0.22 0.33 4 -0.39 285 289
RAB5/GDP/GDI1 -0.17 0.17 -10000 0 -0.31 301 301
NOS2 -0.24 0.22 -10000 0 -0.41 308 308
DDIT3 -0.23 0.22 -10000 0 -0.41 303 303
RAB5A 0.034 0.005 -10000 0 -10000 0 0
HSPB1 -0.19 0.18 -10000 0 -0.34 271 271
p38alpha-beta/HBP1 -0.25 0.28 -10000 0 -0.45 306 306
CREB1 -0.25 0.24 -10000 0 -0.43 305 305
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.23 0.24 -10000 0 -0.41 293 293
RPS6KA4 -0.23 0.23 -10000 0 -0.41 304 304
PLA2G4A -0.36 0.27 -10000 0 -0.52 356 356
GDI1 -0.23 0.22 -10000 0 -0.4 308 308
TP53 -0.31 0.29 -10000 0 -0.54 297 297
RPS6KA5 -0.25 0.23 -10000 0 -0.42 315 315
ESR1 -0.29 0.27 0.32 1 -0.46 310 311
HBP1 0.034 0.005 -10000 0 -10000 0 0
MEF2C -0.26 0.26 -10000 0 -0.44 312 312
MEF2A -0.23 0.23 0.3 1 -0.41 302 303
EIF4EBP1 -0.25 0.25 -10000 0 -0.44 300 300
KRT19 -0.21 0.23 0.33 1 -0.39 298 299
ELK4 -0.21 0.22 0.33 2 -0.39 288 290
ATF6 -0.21 0.22 0.33 4 -0.39 295 299
ATF1 -0.25 0.24 -10000 0 -0.43 307 307
p38alpha-beta/MAPKAPK2 -0.22 0.24 -10000 0 -0.42 288 288
p38alpha-beta/MAPKAPK3 -0.25 0.28 -10000 0 -0.45 305 305
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.3 0.16 -10000 0 -0.38 364 364
CRKL -0.32 0.17 -10000 0 -0.4 378 378
HRAS -0.23 0.15 -10000 0 -0.37 97 97
mol:PIP3 -0.28 0.17 -10000 0 -0.39 296 296
SPRED1 0.031 0.037 -10000 0 -0.54 2 2
SPRED2 0.034 0.005 -10000 0 -10000 0 0
GAB1 -0.33 0.18 -10000 0 -0.42 394 394
FOXO3 -0.27 0.16 -10000 0 -0.38 269 269
AKT1 -0.3 0.18 -10000 0 -0.39 329 329
BAD -0.28 0.16 -10000 0 -0.38 256 256
megakaryocyte differentiation -0.32 0.17 -10000 0 -0.41 398 398
GSK3B -0.28 0.16 -10000 0 -0.38 264 264
RAF1 -0.19 0.13 -10000 0 -0.32 51 51
SHC1 0.028 0.014 -10000 0 -10000 0 0
STAT3 -0.33 0.18 -10000 0 -0.42 396 396
STAT1 -0.81 0.43 -10000 0 -1 407 407
HRAS/SPRED1 -0.19 0.14 -10000 0 -0.34 33 33
cell proliferation -0.33 0.17 -10000 0 -0.41 398 398
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
TEC 0.034 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.32 0.18 -10000 0 -0.4 396 396
HRAS/SPRED2 -0.19 0.14 -10000 0 -0.32 53 53
LYN/TEC/p62DOK -0.29 0.18 -10000 0 -0.4 326 326
MAPK3 -0.13 0.097 -10000 0 -0.3 10 10
STAP1 -0.32 0.18 -10000 0 -0.41 393 393
GRAP2 0.035 0.019 -10000 0 -10000 0 0
JAK2 -0.68 0.37 -10000 0 -0.85 407 407
STAT1 (dimer) -0.79 0.42 -10000 0 -0.99 407 407
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.29 0.19 -10000 0 -0.4 328 328
actin filament polymerization -0.33 0.17 -10000 0 -0.41 401 401
LYN 0.03 0.015 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.47 0.26 -10000 0 -0.58 408 408
PIK3R1 -0.021 0.17 -10000 0 -0.54 47 47
CBL/CRKL/GRB2 -0.28 0.17 -10000 0 -0.38 344 344
PI3K -0.32 0.2 -10000 0 -0.42 362 362
PTEN 0.03 0.045 -10000 0 -0.54 3 3
SCF/KIT/EPO/EPOR -0.95 0.51 -10000 0 -1.2 403 403
MAPK8 -0.33 0.18 -10000 0 -0.42 398 398
STAT3 (dimer) -0.33 0.17 -10000 0 -0.41 396 396
positive regulation of transcription -0.11 0.083 -10000 0 -0.25 7 7
mol:GDP -0.24 0.16 -10000 0 -0.36 226 226
PIK3C2B -0.31 0.18 -10000 0 -0.42 320 320
CBL/CRKL -0.3 0.16 -10000 0 -0.39 374 374
FER -0.33 0.18 -10000 0 -0.42 399 399
SH2B3 -0.34 0.17 -10000 0 -0.42 400 400
PDPK1 -0.25 0.17 -10000 0 -0.37 261 261
SNAI2 -0.34 0.2 -10000 0 -0.46 358 358
positive regulation of cell proliferation -0.59 0.3 -10000 0 -0.73 409 409
KITLG -0.011 0.069 -10000 0 -0.56 2 2
cell motility -0.59 0.3 -10000 0 -0.73 409 409
PTPN6 0.05 0.021 -10000 0 -10000 0 0
EPOR -0.23 0.19 -10000 0 -1.1 12 12
STAT5A (dimer) -0.48 0.26 -10000 0 -0.6 410 410
SOCS1 0.032 0.012 -10000 0 -10000 0 0
cell migration 0.32 0.17 0.41 394 -10000 0 394
SOS1 0.034 0.004 -10000 0 -10000 0 0
EPO 0.01 0.064 -10000 0 -10000 0 0
VAV1 0.038 0.025 -10000 0 -10000 0 0
GRB10 -0.34 0.18 -10000 0 -0.42 399 399
PTPN11 0.047 0.009 -10000 0 -10000 0 0
SCF/KIT -0.35 0.19 -10000 0 -0.44 401 401
GO:0007205 0.018 0.009 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.28 18 18
CBL 0.031 0.011 -10000 0 -10000 0 0
KIT -1 0.53 -10000 0 -1.3 403 403
MAP2K2 -0.15 0.11 -10000 0 -0.29 13 13
SHC/Grb2/SOS1 -0.28 0.18 -10000 0 -0.4 285 285
STAT5A -0.5 0.26 -10000 0 -0.61 410 410
GRB2 0.034 0.018 -10000 0 -10000 0 0
response to radiation -0.34 0.2 0.29 1 -0.45 357 358
SHC/GRAP2 0.04 0.026 -10000 0 -10000 0 0
PTPRO -0.33 0.18 -10000 0 -0.42 398 398
SH2B2 -0.33 0.18 -10000 0 -0.42 401 401
DOK1 0.036 0.016 -10000 0 -10000 0 0
MATK -0.33 0.18 -10000 0 -0.42 394 394
CREBBP -0.081 0.072 -10000 0 -10000 0 0
BCL2 -0.43 0.51 -10000 0 -1.4 109 109
Endothelins

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
AKT1 -0.1 0.17 -10000 0 -0.35 142 142
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.17 0.29 -10000 0 -0.74 74 74
EDN1 -0.16 0.25 -10000 0 -0.54 154 154
EDN3 -0.39 0.25 -10000 0 -0.54 376 376
EDN2 0.098 0.078 -10000 0 -0.54 1 1
HRAS/GDP -0.25 0.23 -10000 0 -0.46 227 227
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.18 -10000 0 -0.38 121 121
ADCY4 -0.083 0.15 0.34 1 -0.3 143 144
ADCY5 -0.081 0.15 -10000 0 -0.3 141 141
ADCY6 -0.081 0.15 0.34 1 -0.3 144 145
ADCY7 -0.077 0.15 0.34 1 -0.29 139 140
ADCY1 -0.08 0.15 -10000 0 -0.3 141 141
ADCY2 -0.082 0.16 0.34 1 -0.3 144 145
ADCY3 -0.082 0.15 -10000 0 -0.3 145 145
ADCY8 -0.068 0.13 -10000 0 -0.29 107 107
ADCY9 -0.074 0.14 -10000 0 -0.3 125 125
arachidonic acid secretion -0.52 0.34 -10000 0 -0.7 364 364
ETB receptor/Endothelin-1/Gq/GTP -0.21 0.21 -10000 0 -0.37 273 273
GNAO1 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.092 0.16 -10000 0 -0.32 143 143
ETA receptor/Endothelin-1/Gs/GTP -0.088 0.15 -10000 0 -0.31 146 146
mol:GTP -0.007 0.008 -10000 0 -10000 0 0
COL3A1 -0.099 0.17 -10000 0 -0.35 140 140
EDNRB -0.21 0.28 -10000 0 -0.54 224 224
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.099 0.17 -10000 0 -0.34 141 141
CYSLTR1 -0.1 0.18 0.38 2 -0.36 113 115
SLC9A1 -0.068 0.12 -10000 0 -0.25 88 88
mol:GDP -0.27 0.25 -10000 0 -0.48 244 244
SLC9A3 -0.39 0.39 -10000 0 -0.7 263 263
RAF1 -0.35 0.27 -10000 0 -0.52 327 327
JUN -0.25 0.43 -10000 0 -1 111 111
JAK2 -0.099 0.17 -10000 0 -0.35 144 144
mol:IP3 -0.21 0.22 -10000 0 -0.43 190 190
ETA receptor/Endothelin-1 -0.12 0.2 -10000 0 -0.4 148 148
PLCB1 -0.048 0.2 -10000 0 -0.55 70 70
PLCB2 0.024 0.014 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.29 0.19 -10000 0 -0.4 380 380
FOS -0.68 0.43 -10000 0 -0.96 365 365
Gai/GDP -0.19 0.35 -10000 0 -0.95 81 81
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.26 -10000 0 -0.53 203 203
BCAR1 0.03 0.013 -10000 0 -10000 0 0
PRKCB1 -0.21 0.21 -10000 0 -0.42 198 198
GNAQ -0.009 0.009 -10000 0 -10000 0 0
GNAZ 0.026 0.062 -10000 0 -0.54 6 6
GNAL 0.03 0.044 -10000 0 -0.54 3 3
Gs family/GDP -0.24 0.23 -10000 0 -0.44 231 231
ETA receptor/Endothelin-1/Gq/GTP -0.096 0.15 -10000 0 -0.31 129 129
MAPK14 -0.22 0.22 -10000 0 -0.42 229 229
TRPC6 -0.18 0.31 -10000 0 -0.8 72 72
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.23 -10000 0 -0.43 251 251
ETB receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.33 230 230
ETB receptor/Endothelin-3 -0.42 0.27 -10000 0 -0.53 415 415
ETB receptor/Endothelin-1 -0.26 0.28 -10000 0 -0.48 297 297
MAPK3 -0.6 0.39 -10000 0 -0.84 367 367
MAPK1 -0.62 0.41 -10000 0 -0.86 368 368
Rac1/GDP -0.25 0.23 -10000 0 -0.46 231 231
cAMP biosynthetic process -0.031 0.15 0.37 5 -0.33 36 41
MAPK8 -0.18 0.3 -10000 0 -0.65 117 117
SRC 0.033 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.28 0.29 -10000 0 -0.55 231 231
p130Cas/CRK/Src/PYK2 -0.27 0.29 -10000 0 -0.57 198 198
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.25 0.23 -10000 0 -0.46 227 227
COL1A2 -0.23 0.27 0.42 1 -0.53 164 165
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.072 0.077 0.26 3 -0.34 4 7
mol:DAG -0.21 0.22 -10000 0 -0.44 190 190
MAP2K2 -0.47 0.32 -10000 0 -0.64 369 369
MAP2K1 -0.47 0.32 0.36 1 -0.64 370 371
EDNRA 0.006 0.057 -10000 0 -0.44 3 3
positive regulation of muscle contraction -0.091 0.14 -10000 0 -0.31 138 138
Gq family/GDP -0.21 0.22 -10000 0 -0.45 177 177
HRAS/GTP -0.26 0.24 -10000 0 -0.45 254 254
PRKCH -0.21 0.21 -10000 0 -0.44 187 187
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA -0.19 0.21 -10000 0 -0.44 164 164
PRKCB -0.21 0.21 -10000 0 -0.42 200 200
PRKCE -0.21 0.21 -10000 0 -0.44 185 185
PRKCD -0.21 0.21 -10000 0 -0.44 184 184
PRKCG -0.21 0.21 0.3 1 -0.44 183 184
regulation of vascular smooth muscle contraction -0.81 0.51 -10000 0 -1.1 365 365
PRKCQ -0.2 0.21 -10000 0 -0.45 171 171
PLA2G4A -0.59 0.4 -10000 0 -0.8 363 363
GNA14 0.027 0.073 -10000 0 -0.55 4 4
GNA15 0.021 0.031 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.024 -10000 0 -10000 0 0
Rac1/GTP -0.092 0.16 -10000 0 -0.32 145 145
MMP1 0.17 0.15 0.4 84 -10000 0 84
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.047 0.03 0.21 4 -10000 0 4
NFATC2 -0.083 0.23 0.51 1 -0.55 55 56
NFATC3 -0.15 0.17 0.31 1 -0.32 225 226
CD40LG -0.67 0.53 0.78 4 -1 334 338
ITCH -0.064 0.14 -10000 0 -0.52 1 1
CBLB -0.067 0.14 -10000 0 -0.86 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.31 0.74 7 -0.69 73 80
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.077 0.17 -10000 0 -0.3 190 190
T cell anergy -0.13 0.21 0.33 1 -0.4 182 183
TLE4 -0.066 0.2 -10000 0 -0.61 35 35
Jun/NFAT1-c-4/p21SNFT -0.58 0.55 0.71 4 -0.97 311 315
AP-1/NFAT1-c-4 -0.8 0.68 0.92 5 -1.2 333 338
IKZF1 -0.045 0.17 0.46 10 -0.46 28 38
T-helper 2 cell differentiation -0.12 0.28 0.52 1 -0.78 46 47
AP-1/NFAT1 -0.3 0.3 0.53 6 -0.51 294 300
CALM1 -0.036 0.11 -10000 0 -0.31 1 1
EGR2 -0.8 0.76 0.77 2 -1.5 252 254
EGR3 -0.88 0.76 0.75 2 -1.4 319 321
NFAT1/FOXP3 -0.031 0.18 0.46 8 -0.4 47 55
EGR1 -0.43 0.23 -10000 0 -0.54 415 415
JUN -0.067 0.22 0.26 1 -0.54 89 90
EGR4 0.001 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.089 -10000 0 -0.17 190 190
GBP3 -0.079 0.24 0.44 1 -0.74 44 45
FOSL1 0.034 0.011 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.54 0.53 0.67 3 -0.92 306 309
DGKA -0.052 0.16 0.46 1 -0.46 28 29
CREM 0.033 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.75 0.55 -10000 0 -1.1 344 344
CTLA4 -0.023 0.16 0.42 15 -0.39 27 42
NFAT1-c-4 (dimer)/EGR1 -0.77 0.57 -10000 0 -1.1 352 352
NFAT1-c-4 (dimer)/EGR4 -0.56 0.52 0.67 1 -0.93 311 312
FOS -0.35 0.27 0.25 1 -0.54 345 346
IFNG -0.097 0.3 0.58 6 -0.81 43 49
T cell activation -0.39 0.34 0.68 3 -0.72 189 192
MAF -0.007 0.14 -10000 0 -0.54 33 33
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.45 0.41 0.75 296 -0.7 2 298
TNF -0.67 0.48 -10000 0 -0.97 347 347
FASLG -0.88 0.79 0.85 3 -1.4 329 332
TBX21 0.028 0.15 0.28 12 -0.54 30 42
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.043 0.035 0.24 4 -10000 0 4
PTPN1 -0.048 0.16 -10000 0 -0.46 27 27
NFAT1-c-4/ICER1 -0.55 0.53 0.61 1 -0.94 308 309
GATA3 0.036 0.16 -10000 0 -0.54 33 33
T-helper 1 cell differentiation -0.095 0.3 0.58 6 -0.79 43 49
IL2RA -0.25 0.31 0.74 6 -0.64 95 101
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.051 0.16 -10000 0 -0.46 27 27
E2F1 0.056 0.049 0.25 1 -10000 0 1
PPARG -0.38 0.26 -10000 0 -0.54 367 367
SLC3A2 -0.05 0.16 -10000 0 -0.44 35 35
IRF4 0.039 0.028 -10000 0 -10000 0 0
PTGS2 -0.77 0.57 0.73 4 -1.1 351 355
CSF2 -0.67 0.53 0.78 4 -1 334 338
JunB/Fra1/NFAT1-c-4 -0.53 0.52 0.6 2 -0.9 313 315
IL4 -0.12 0.3 -10000 0 -0.82 46 46
IL5 -0.68 0.52 0.73 4 -1 334 338
IL2 -0.39 0.35 0.68 3 -0.74 185 188
IL3 -0.088 0.16 -10000 0 -0.9 14 14
RNF128 -0.21 0.33 -10000 0 -0.63 191 191
NFATC1 -0.45 0.41 0.7 2 -0.75 295 297
CDK4 0.28 0.28 0.63 57 -10000 0 57
PTPRK -0.085 0.24 -10000 0 -0.68 54 54
IL8 -0.66 0.53 0.73 5 -1 328 333
POU2F1 0.034 0.015 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.034 0.013 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EGF/EGFR -0.3 0.26 -10000 0 -0.43 365 365
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.19 0.21 -10000 0 -0.36 268 268
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.032 0.038 0.18 2 -0.54 2 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.15 0.27 -10000 0 -0.54 163 163
EGF/EGFR dimer/SHC -0.23 0.23 -10000 0 -0.41 289 289
mol:GDP -0.19 0.21 -10000 0 -0.36 268 268
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.14 0.26 -10000 0 -0.54 153 153
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
HRAS/GTP -0.18 0.19 -10000 0 -0.34 264 264
SHC1 0.028 0.014 -10000 0 -10000 0 0
HRAS/GDP -0.18 0.2 -10000 0 -0.34 264 264
FRAP1 -0.2 0.17 -10000 0 -0.35 267 267
EGF/EGFR dimer -0.31 0.26 -10000 0 -0.46 356 356
SOS1 0.034 0.004 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.088 0.2 -10000 0 -0.39 160 160
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.11 0.25 0.54 126 -10000 0 126
PI3K Class IB/PDE3B -0.11 0.25 -10000 0 -0.54 126 126
PDE3B -0.11 0.25 -10000 0 -0.54 126 126
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.035 0.007 -10000 0 -10000 0 0
PTK2 0.027 0.014 -10000 0 -10000 0 0
CRKL -0.16 0.2 -10000 0 -0.34 256 256
GRB2/SOS1/SHC 0.052 0.033 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
IRS1/Crk -0.16 0.21 -10000 0 -0.34 259 259
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.21 -10000 0 -0.36 223 223
AKT1 -0.16 0.19 0.23 1 -0.35 216 217
BAD -0.15 0.18 0.22 1 -0.44 96 97
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.17 0.2 -10000 0 -0.34 259 259
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.21 -10000 0 -0.34 258 258
RAF1 -0.12 0.18 -10000 0 -0.46 65 65
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.22 -10000 0 -0.33 237 237
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.17 0.23 -10000 0 -0.37 259 259
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.18 0.23 1 -0.44 95 96
GNB2L1 0.034 0.005 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.099 0.15 -10000 0 -0.4 59 59
PXN 0.034 0.004 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.18 -10000 0 -0.32 170 170
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.07 0.18 -10000 0 -0.3 163 163
IGF-1R heterotetramer -0.048 0.14 -10000 0 -0.64 21 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.34 257 257
Crk/p130 Cas/Paxillin -0.13 0.21 -10000 0 -0.33 237 237
IGF1R -0.048 0.14 -10000 0 -0.64 21 21
IGF1 -0.26 0.3 -10000 0 -0.57 253 253
IRS2/Crk -0.22 0.26 -10000 0 -0.42 275 275
PI3K -0.15 0.24 -10000 0 -0.37 245 245
apoptosis 0.098 0.16 0.38 69 -0.31 1 70
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
PRKCD -0.18 0.23 -10000 0 -0.39 243 243
RAF1/14-3-3 E -0.096 0.17 -10000 0 -0.42 45 45
BAD/14-3-3 -0.1 0.17 0.32 1 -0.41 69 70
PRKCZ -0.16 0.19 0.22 1 -0.34 225 226
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.17 -10000 0 -0.4 77 77
PTPN1 0.037 0.03 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.19 0.23 -10000 0 -0.41 250 250
BCAR1 0.029 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.095 0.19 -10000 0 -0.33 184 184
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.15 0.21 -10000 0 -0.34 257 257
GRB10 0.03 0.051 -10000 0 -0.54 4 4
PTPN11 -0.16 0.2 -10000 0 -0.34 258 258
IRS1 -0.18 0.22 -10000 0 -0.36 259 259
IRS2 -0.23 0.26 -10000 0 -0.43 280 280
IGF-1R heterotetramer/IGF1 -0.2 0.26 -10000 0 -0.45 251 251
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDPK1 -0.16 0.21 -10000 0 -0.36 226 226
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKD1 -0.22 0.28 -10000 0 -0.46 256 256
SHC1 0.028 0.014 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.55 0.46 1.1 118 -1.1 2 120
PLK1 0.22 0.19 0.61 45 -10000 0 45
BIRC5 0.36 0.24 0.65 136 -0.66 3 139
HSPA1B 0.55 0.46 1.1 142 -0.96 3 145
MAP2K1 0.16 0.12 0.33 131 -10000 0 131
BRCA2 0.58 0.49 1.1 140 -1.1 2 142
FOXM1 0.59 0.6 1.3 146 -1.3 3 149
XRCC1 0.55 0.46 1.1 124 -1.1 2 126
FOXM1B/p19 0.073 0.29 0.93 7 -1.1 3 10
Cyclin D1/CDK4 0.47 0.46 1 107 -0.95 7 114
CDC2 0.6 0.51 1.2 144 -1 3 147
TGFA 0.43 0.52 1 127 -0.94 20 147
SKP2 0.55 0.47 1.1 120 -1.1 2 122
CCNE1 0.086 0.063 0.23 30 -10000 0 30
CKS1B 0.55 0.46 1.1 142 -0.96 3 145
RB1 0.26 0.34 0.72 122 -0.78 8 130
FOXM1C/SP1 0.49 0.45 0.98 114 -1 7 121
AURKB 0.2 0.31 0.65 59 -0.81 22 81
CENPF 0.67 0.52 1.2 182 -1.3 1 183
CDK4 0.09 0.059 0.25 5 -10000 0 5
MYC 0.3 0.44 0.94 86 -0.88 10 96
CHEK2 0.16 0.13 0.33 132 -10000 0 132
ONECUT1 0.49 0.48 1 133 -0.91 6 139
CDKN2A -0.014 0.077 -10000 0 -0.23 14 14
LAMA4 0.54 0.48 1.1 118 -1.1 4 122
FOXM1B/HNF6 0.49 0.5 1.1 115 -1.1 6 121
FOS -0.14 0.65 1.1 48 -1 73 121
SP1 0.032 0.032 -10000 0 -0.2 6 6
CDC25B 0.56 0.47 1.1 128 -1.1 2 130
response to radiation 0.11 0.092 0.24 118 -10000 0 118
CENPB 0.55 0.46 1.1 122 -1.1 2 124
CENPA 0.62 0.5 1.2 154 -1.1 2 156
NEK2 0.68 0.52 1.2 172 -1.2 1 173
HIST1H2BA 0.55 0.46 1.1 118 -1.1 2 120
CCNA2 0.11 0.076 0.22 129 -10000 0 129
EP300 0.032 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.58 0.51 1.2 128 -1.3 2 130
CCNB2 0.61 0.5 1.2 150 -1.1 2 152
CCNB1 0.62 0.53 1.2 142 -1.1 2 144
ETV5 0.52 0.52 1.1 119 -1.2 10 129
ESR1 0.36 0.61 1.2 102 -1 13 115
CCND1 0.48 0.51 1.1 134 -0.96 8 142
GSK3A 0.14 0.1 0.29 95 -10000 0 95
Cyclin A-E1/CDK1-2 0.2 0.13 0.37 137 -10000 0 137
CDK2 0.069 0.035 0.23 6 -10000 0 6
G2/M transition of mitotic cell cycle 0.14 0.11 0.27 164 -10000 0 164
FOXM1B/Cbp/p300 0.31 0.38 0.86 32 -1 3 35
GAS1 0.26 0.71 1.1 103 -1.1 55 158
MMP2 0.54 0.48 1.1 126 -1.2 6 132
RB1/FOXM1C 0.44 0.46 0.97 126 -1 6 132
CREBBP 0.032 0.01 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.018 0.018 -10000 0 -0.34 1 1
ARNO/beta Arrestin1-2 -0.11 0.14 -10000 0 -0.26 245 245
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EPHA2 0.026 0.062 -10000 0 -0.54 6 6
USP6 0.032 0.018 -10000 0 -10000 0 0
IQSEC1 0.033 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.31 0.26 -10000 0 -0.46 356 356
ARRB2 0.016 0.029 -10000 0 -0.33 3 3
mol:GTP 0.012 0.028 0.12 23 -10000 0 23
ARRB1 0.03 0.027 -10000 0 -0.54 1 1
FBXO8 0.033 0.007 -10000 0 -10000 0 0
TSHR 0.03 0.044 -10000 0 -0.54 3 3
EGF -0.15 0.27 -10000 0 -0.54 163 163
somatostatin receptor activity 0 0 -10000 0 -0.001 220 220
ARAP2 0 0 -10000 0 0 246 246
mol:GDP -0.14 0.14 -10000 0 -0.28 184 184
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 221 221
ITGA2B 0.034 0.012 0.18 2 -10000 0 2
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.059 -10000 0 -0.32 6 6
ADAP1 0 0 -10000 0 0 135 135
KIF13B 0.027 0.029 -10000 0 -0.54 1 1
HGF/MET 0.006 0.13 -10000 0 -0.4 51 51
PXN 0.034 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.14 0.12 -10000 0 -0.26 215 215
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.26 0.24 -10000 0 -0.41 347 347
ADRB2 -0.26 0.29 -10000 0 -0.54 264 264
receptor agonist activity 0 0 -10000 0 0 210 210
actin filament binding 0 0 -10000 0 0 257 257
SRC 0.033 0.008 -10000 0 -10000 0 0
ITGB3 0.035 0.019 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -0.001 150 150
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 155 155
ARF6/GDP -0.03 0.083 0.18 1 -0.26 29 30
ARF6/GDP/GULP/ACAP1 -0.16 0.18 -10000 0 -0.35 198 198
alphaIIb/beta3 Integrin/paxillin/GIT1 0.082 0.031 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 0 1 1
ACAP2 0 0 -10000 0 0 244 244
LHCGR/beta Arrestin2 0.022 0.048 -10000 0 -0.46 3 3
EFNA1 0.028 0.015 -10000 0 -10000 0 0
HGF 0.035 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 211 211
CYTH2 -0.002 0.002 -10000 0 -0.004 247 247
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 148 148
endosomal lumen acidification 0 0 0 6 0 151 157
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.071 0.22 -10000 0 -0.54 94 94
GNAQ/ARNO -0.003 0.003 -10000 0 -0.007 139 139
mol:Phosphatidic acid 0 0 -10000 0 0 244 244
PIP3-E 0 0 -10000 0 0 297 297
MET -0.022 0.17 -10000 0 -0.54 50 50
GNA14 0.043 0.068 0.18 50 -0.54 4 54
GNA15 0.036 0.019 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 193 193
GNA11 0.033 0.006 -10000 0 -10000 0 0
LHCGR 0.032 0.046 -10000 0 -0.54 3 3
AGTR1 -0.18 0.3 -10000 0 -0.54 208 208
desensitization of G-protein coupled receptor protein signaling pathway 0.022 0.048 -10000 0 -0.46 3 3
IPCEF1/ARNO -0.21 0.18 -10000 0 -0.32 353 353
alphaIIb/beta3 Integrin 0.05 0.018 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.011 0.13 -10000 0 -0.32 66 66
regulation of S phase of mitotic cell cycle -0.045 0.13 -10000 0 -0.3 92 92
GNAO1 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
SHBG/T-DHT 0.021 0.008 -10000 0 -10000 0 0
PELP1 0.029 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.014 0.14 6 -10000 0 6
MAP2K1 -0.11 0.11 -10000 0 -0.36 61 61
T-DHT/AR -0.033 0.14 -10000 0 -0.4 67 67
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.003 -10000 0 -0.007 350 350
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.033 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
mol:GDP -0.079 0.16 -10000 0 -0.38 101 101
cell proliferation -0.29 0.21 -10000 0 -0.44 317 317
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
FOS -0.57 0.37 -10000 0 -0.8 365 365
mol:Ca2+ -0.037 0.037 -10000 0 -0.075 231 231
MAPK3 -0.2 0.16 -10000 0 -0.44 87 87
MAPK1 -0.16 0.16 -10000 0 -0.4 81 81
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.003 0.002 -10000 0 -0.005 336 336
cAMP biosynthetic process 0.017 0.027 -10000 0 -10000 0 0
GNG2 0.033 0.026 -10000 0 -0.54 1 1
potassium channel inhibitor activity -0.003 0.002 -10000 0 -0.005 336 336
HRAS/GTP -0.059 0.12 -10000 0 -0.33 64 64
actin cytoskeleton reorganization 0.015 0.094 -10000 0 -0.28 43 43
SRC 0.031 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.005 336 336
PI3K 0.007 0.11 -10000 0 -0.34 44 44
apoptosis 0.3 0.22 0.43 349 -10000 0 349
T-DHT/AR/PELP1 -0.014 0.13 -10000 0 -0.35 67 67
HRAS/GDP -0.069 0.17 -10000 0 -0.42 77 77
CREB1 -0.32 0.23 -10000 0 -0.46 349 349
RAC1-CDC42/GTP 0.025 0.099 -10000 0 -0.29 43 43
AR -0.042 0.2 0.18 1 -0.55 66 67
GNB1 0.034 0.011 -10000 0 -10000 0 0
RAF1 -0.085 0.11 -10000 0 -0.34 61 61
RAC1-CDC42/GDP -0.032 0.17 -10000 0 -0.44 66 66
T-DHT/AR/PELP1/Src -0.005 0.13 -10000 0 -0.33 65 65
MAP2K2 -0.11 0.11 -10000 0 -0.36 60 60
T-DHT/AR/PELP1/Src/PI3K -0.045 0.13 -10000 0 -0.3 92 92
GNAZ 0.025 0.062 -10000 0 -0.54 6 6
SHBG 0.031 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.11 0.19 -10000 0 -0.48 75 75
mol:T-DHT -0.001 0.002 -10000 0 -0.005 75 75
RAC1 0.034 0.005 -10000 0 -10000 0 0
GNRH1 -0.002 0.059 0.14 1 -0.4 11 12
Gi family/GTP -0.1 0.14 -10000 0 -0.26 187 187
CDC42 0.033 0.008 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.034 0.005 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.24 0.21 -10000 0 -0.4 260 260
PTP1B/AKT1 -0.16 0.15 0.25 1 -0.3 216 217
FYN 0.03 0.037 -10000 0 -0.54 2 2
p210 bcr-abl/PTP1B -0.19 0.16 0.25 1 -0.31 266 267
EGFR -0.29 0.28 -10000 0 -0.56 269 269
EGF/EGFR -0.36 0.26 -10000 0 -0.5 358 358
CSF1 0.034 0.008 -10000 0 -10000 0 0
AKT1 0.035 0.017 -10000 0 -10000 0 0
INSR 0.034 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.16 0.17 0.34 1 -0.32 208 209
Insulin Receptor/Insulin -0.11 0.14 -10000 0 -0.39 37 37
HCK 0.036 0.022 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
TYK2 -0.18 0.16 0.44 1 -0.32 218 219
EGF -0.18 0.26 -10000 0 -0.56 163 163
YES1 0.032 0.027 -10000 0 -0.54 1 1
CAV1 -0.37 0.23 -10000 0 -0.49 367 367
TXN 0.028 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.2 0.18 -10000 0 -0.35 221 221
cell migration 0.19 0.16 0.31 266 -0.25 1 267
STAT3 0.032 0.007 -10000 0 -10000 0 0
PRLR 0.074 0.064 -10000 0 -10000 0 0
ITGA2B 0.032 0.011 -10000 0 -10000 0 0
CSF1R 0.034 0.005 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.082 0.049 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.18 0.16 0.24 1 -0.31 241 242
Crk/p130 Cas -0.17 0.16 -10000 0 -0.31 214 214
DOK1 -0.15 0.15 0.27 1 -0.37 79 80
JAK2 -0.082 0.15 -10000 0 -0.52 33 33
Jak2/Leptin Receptor/Leptin -0.25 0.2 -10000 0 -0.44 227 227
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
PTPN1 -0.19 0.16 0.25 1 -0.32 266 267
LYN 0.03 0.015 -10000 0 -10000 0 0
CDH2 0.057 0.056 -10000 0 -10000 0 0
SRC -0.05 0.12 -10000 0 -0.66 14 14
ITGB3 0.033 0.018 -10000 0 -10000 0 0
CAT1/PTP1B -0.15 0.18 0.36 1 -0.43 92 93
CAPN1 0.031 0.014 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -10000 0 0
PI3K -0.12 0.16 -10000 0 -0.43 60 60
mol:H2O2 -0.005 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.22 0.19 -10000 0 -0.4 211 211
negative regulation of transcription -0.081 0.14 -10000 0 -0.52 33 33
FCGR2A 0.031 0.025 -10000 0 -10000 0 0
FER 0.027 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.045 0.017 -10000 0 -10000 0 0
BLK 0.039 0.044 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.052 0.03 -10000 0 -10000 0 0
RHOA 0.03 0.007 -10000 0 -10000 0 0
LEPR -0.33 0.28 -10000 0 -0.54 321 321
BCAR1 0.029 0.013 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.034 0.018 -10000 0 -10000 0 0
mol:NADPH -0.006 0.004 -10000 0 -10000 0 0
TRPV6 -0.006 0.15 0.42 2 -0.41 40 42
PRL 0.037 0.009 -10000 0 -10000 0 0
SOCS3 0 0.25 -10000 0 -1.3 17 17
SPRY2 -0.32 0.28 -10000 0 -0.55 304 304
Insulin Receptor/Insulin/IRS1 0.015 0.13 -10000 0 -0.35 59 59
CSF1/CSF1R -0.17 0.16 -10000 0 -0.31 213 213
Ras protein signal transduction 0.088 0.18 0.67 36 -10000 0 36
IRS1 -0.034 0.18 -10000 0 -0.54 60 60
INS 0.033 0.007 -10000 0 -10000 0 0
LEP -0.23 0.29 -10000 0 -0.54 237 237
STAT5B -0.14 0.16 0.24 1 -0.36 102 103
STAT5A -0.14 0.16 0.26 1 -0.36 104 105
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.18 0.16 0.24 1 -0.31 243 244
CSN2 0.078 0.06 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
LAT -0.036 0.081 -10000 0 -0.63 4 4
YBX1 0.044 0.028 -10000 0 -10000 0 0
LCK 0.048 0.044 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
NOX4 0.051 0.055 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.11 0.11 0.52 5 -10000 0 5
SMARCC2 0.034 0.004 -10000 0 -10000 0 0
SMARCC1 0.035 0.02 -10000 0 -10000 0 0
TBX21 -0.12 0.22 0.41 1 -0.84 31 32
SUMO2 0.002 0.025 -10000 0 -10000 0 0
STAT1 (dimer) 0.072 0.069 0.28 25 -10000 0 25
FKBP4 0.037 0.026 -10000 0 -10000 0 0
FKBP5 0.025 0.082 -10000 0 -0.54 10 10
GR alpha/HSP90/FKBP51/HSP90 0.13 0.14 0.34 36 -0.36 4 40
PRL -0.06 0.11 -10000 0 -0.42 1 1
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.53 173 -10000 0 173
RELA -0.092 0.11 0.32 1 -0.29 20 21
FGG 0.24 0.23 0.46 205 -10000 0 205
GR beta/TIF2 0.11 0.14 0.32 69 -0.35 3 72
IFNG -0.39 0.34 -10000 0 -0.73 193 193
apoptosis -0.25 0.18 -10000 0 -0.57 32 32
CREB1 0.058 0.041 -10000 0 -10000 0 0
histone acetylation 0.035 0.14 0.41 34 -0.33 9 43
BGLAP -0.094 0.14 -10000 0 -0.55 3 3
GR/PKAc 0.15 0.14 0.35 45 -0.31 3 48
NF kappa B1 p50/RelA -0.16 0.19 0.47 3 -0.36 96 99
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.23 146 -10000 0 146
GATA3 0.043 0.16 -10000 0 -0.54 33 33
AKT1 0.028 0.024 -10000 0 -10000 0 0
CSF2 -0.008 0.11 0.4 1 -10000 0 1
GSK3B 0.002 0.027 -10000 0 -10000 0 0
NR1I3 -0.19 0.16 -10000 0 -0.59 5 5
CSN2 0.19 0.19 0.39 161 -10000 0 161
BRG1/BAF155/BAF170/BAF60A 0.084 0.028 -10000 0 -10000 0 0
NFATC1 0.038 0.038 -10000 0 -0.54 2 2
POU2F1 0.034 0.015 -10000 0 -10000 0 0
CDKN1A 0.022 0.12 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.011 0.006 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.14 0.14 0.36 24 -0.4 2 26
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.66 0.33 -10000 0 -0.8 426 426
JUN -0.21 0.24 0.38 2 -0.5 153 155
IL4 -0.12 0.15 -10000 0 -0.51 10 10
CDK5R1 0.028 0.014 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.35 0.24 -10000 0 -0.5 324 324
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.14 0.36 29 -0.35 3 32
cortisol/GR alpha (monomer) 0.29 0.31 0.58 225 -10000 0 225
NCOA2 0.028 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.42 0.26 -10000 0 -0.58 359 359
AP-1/NFAT1-c-4 -0.58 0.41 -10000 0 -0.83 340 340
AFP -0.18 0.2 -10000 0 -0.64 13 13
SUV420H1 0.031 0.01 -10000 0 -10000 0 0
IRF1 0.21 0.18 0.43 109 -10000 0 109
TP53 0.046 0.034 -10000 0 -0.51 1 1
PPP5C 0.036 0.017 -10000 0 -10000 0 0
KRT17 -0.9 0.65 -10000 0 -1.4 324 324
KRT14 -0.83 0.63 -10000 0 -1.3 325 325
TBP 0.039 0.012 -10000 0 -10000 0 0
CREBBP 0.18 0.14 0.3 280 -10000 0 280
HDAC1 0.029 0.012 -10000 0 -10000 0 0
HDAC2 0.029 0.022 -10000 0 -10000 0 0
AP-1 -0.58 0.41 -10000 0 -0.83 341 341
MAPK14 0.014 0.021 -10000 0 -10000 0 0
MAPK10 -0.009 0.082 -10000 0 -0.55 10 10
MAPK11 0 0.025 -10000 0 -10000 0 0
KRT5 -0.95 0.63 -10000 0 -1.4 352 352
interleukin-1 receptor activity -0.003 0.006 -10000 0 -10000 0 0
NCOA1 0.037 0.027 -10000 0 -0.54 1 1
STAT1 0.072 0.069 0.28 25 -10000 0 25
CGA -0.085 0.16 -10000 0 -0.51 7 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.19 0.35 163 -0.37 2 165
MAPK3 0.002 0.024 -10000 0 -10000 0 0
MAPK1 0.013 0.021 -10000 0 -10000 0 0
ICAM1 -0.25 0.25 0.59 2 -0.57 96 98
NFKB1 -0.095 0.11 0.32 1 -0.27 19 20
MAPK8 -0.15 0.19 0.57 1 -0.38 116 117
MAPK9 0.014 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.19 -10000 0 -0.6 32 32
BAX 0.028 0.075 -10000 0 -10000 0 0
POMC -0.14 0.19 -10000 0 -0.85 7 7
EP300 0.18 0.14 0.29 287 -10000 0 287
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.52 184 -10000 0 184
proteasomal ubiquitin-dependent protein catabolic process 0.091 0.11 0.32 56 -10000 0 56
SGK1 0.23 0.17 0.36 301 -0.43 1 302
IL13 -0.3 0.25 0.49 1 -0.65 78 79
IL6 -0.75 0.48 0.61 1 -1 376 377
PRKACG 0.033 0.026 -10000 0 -0.54 1 1
IL5 -0.24 0.21 -10000 0 -0.75 15 15
IL2 -0.42 0.32 -10000 0 -0.7 249 249
CDK5 0.032 0.024 -10000 0 -10000 0 0
PRKACB 0.035 0.083 -10000 0 -0.54 8 8
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
IL8 -0.24 0.26 0.59 2 -0.59 82 84
CDK5R1/CDK5 0.038 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.094 0.18 0.43 3 -0.43 24 27
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.51 208 -10000 0 208
SMARCA4 0.035 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.16 0.34 187 -10000 0 187
NF kappa B1 p50/RelA/Cbp -0.003 0.19 0.48 26 -0.35 5 31
JUN (dimer) -0.21 0.24 0.38 2 -0.49 153 155
YWHAH 0.033 0.014 -10000 0 -10000 0 0
VIPR1 -0.11 0.17 -10000 0 -0.52 31 31
NR3C1 0.19 0.2 0.4 165 -0.44 5 170
NR4A1 0.014 0.12 -10000 0 -0.55 24 24
TIF2/SUV420H1 0.039 0.023 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.18 -10000 0 -0.57 32 32
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.53 212 -10000 0 212
PBX1 0.043 0.042 -10000 0 -10000 0 0
POU1F1 0.038 0.026 -10000 0 -0.54 1 1
SELE -0.26 0.35 0.59 2 -0.83 83 85
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.16 0.34 184 -10000 0 184
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.51 208 -10000 0 208
mol:cortisol 0.18 0.17 0.33 238 -10000 0 238
MMP1 -0.023 0.34 -10000 0 -0.94 52 52
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.051 0.038 -10000 0 -10000 0 0
PDGFRB 0.03 0.007 -10000 0 -10000 0 0
SPHK1 -0.042 0.14 -10000 0 -0.9 11 11
mol:S1P -0.044 0.14 0.3 1 -0.82 11 12
S1P1/S1P/Gi -0.28 0.29 0.33 5 -0.49 310 315
GNAO1 0.003 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.25 0.26 0.34 5 -0.45 293 298
PLCG1 -0.27 0.27 0.33 6 -0.46 301 307
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.03 0.007 -10000 0 -10000 0 0
GNAI2 0.004 0.029 -10000 0 -10000 0 0
GNAI3 0.006 0.029 -10000 0 -10000 0 0
GNAI1 -0.19 0.27 -10000 0 -0.56 183 183
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.004 0.04 -10000 0 -10000 0 0
S1P1/S1P -0.064 0.13 0.29 7 -0.66 11 18
negative regulation of cAMP metabolic process -0.28 0.28 0.33 5 -0.47 309 314
MAPK3 -0.37 0.35 0.34 9 -0.63 314 323
calcium-dependent phospholipase C activity -0.005 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
KDR 0.029 0.011 -10000 0 -10000 0 0
PLCB2 -0.054 0.12 0.34 3 -0.57 11 14
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.064 0.1 -10000 0 -0.54 11 11
receptor internalization -0.064 0.12 0.24 6 -0.6 11 17
PTGS2 -0.62 0.53 0.43 4 -1 315 319
Rac1/GTP -0.064 0.1 -10000 0 -0.54 11 11
RHOA 0.033 0.007 -10000 0 -10000 0 0
VEGFA 0.046 0.048 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.28 0.28 0.33 5 -0.47 309 314
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.001 0.066 -10000 0 -0.56 6 6
MAPK1 -0.4 0.38 0.37 5 -0.67 317 322
S1P1/S1P/PDGFB-D/PDGFRB -0.08 0.14 0.32 7 -0.62 11 18
ABCC1 0.032 0.023 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.008 0.057 0.26 9 -0.34 2 11
NFATC2 0.009 0.054 0.25 10 -0.34 1 11
NFATC3 0.012 0.051 0.26 9 -10000 0 9
CD40LG -0.22 0.29 0.6 15 -0.51 191 206
PTGS2 -0.32 0.36 0.57 15 -0.62 266 281
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.031 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.031 -10000 0 -10000 0 0
CALM1 0.033 0.018 -10000 0 -10000 0 0
JUN -0.066 0.22 -10000 0 -0.54 89 89
mol:Ca2+ -0.003 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.012 -10000 0 -10000 0 0
FOSL1 0.034 0.011 -10000 0 -10000 0 0
CREM 0.033 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.033 0.17 0.45 15 -0.35 58 73
FOS -0.35 0.27 -10000 0 -0.54 345 345
IFNG -0.2 0.31 0.66 16 -0.51 185 201
AP-1/NFAT1-c-4 -0.25 0.34 0.71 11 -0.59 199 210
FASLG -0.19 0.29 0.64 17 -0.48 182 199
NFAT1-c-4/ICER1 0.015 0.097 0.4 9 -0.31 2 11
IL2RA -0.21 0.3 0.73 10 -0.51 187 197
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.22 0.3 0.61 16 -0.51 192 208
JunB/Fra1/NFAT1-c-4 0.041 0.11 0.43 10 -0.3 5 15
IL4 -0.22 0.29 0.65 10 -0.51 192 202
IL2 -0.009 0.14 -10000 0 -0.97 11 11
IL3 -0.009 0.13 -10000 0 -0.7 16 16
FKBP1A 0.034 0.011 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.033 0.015 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.058 0.4 0.7 6 -0.72 81 87
HDAC7 0.007 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.001 0.37 0.82 4 -0.7 50 54
SMAD4 0.034 0.008 -10000 0 -10000 0 0
ID2 -0.007 0.43 -10000 0 -0.71 83 83
AP1 -0.33 0.27 -10000 0 -0.48 353 353
ABCG2 -0.021 0.44 -10000 0 -0.73 89 89
HIF1A 0.021 0.13 0.32 4 -0.34 10 14
TFF3 -0.056 0.44 -10000 0 -0.73 95 95
GATA2 0.021 0.049 -10000 0 -10000 0 0
AKT1 0.019 0.13 0.33 3 -0.21 9 12
response to hypoxia -0.006 0.11 0.25 13 -0.16 68 81
MCL1 -0.035 0.4 -10000 0 -0.72 78 78
NDRG1 -0.024 0.4 0.81 2 -0.72 75 77
SERPINE1 0.004 0.44 0.83 9 -0.71 83 92
FECH -0.01 0.42 -10000 0 -0.72 82 82
FURIN -0.002 0.43 -10000 0 -0.72 82 82
NCOA2 0.035 0.023 -10000 0 -10000 0 0
EP300 0.031 0.17 0.44 15 -0.29 35 50
HMOX1 0.001 0.44 0.82 8 -0.71 84 92
BHLHE40 -0.058 0.4 0.7 6 -0.72 81 87
BHLHE41 -0.058 0.4 0.7 6 -0.72 81 87
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.041 0.16 -10000 0 -0.33 3 3
ENG 0.043 0.14 0.46 1 -0.39 1 2
JUN -0.074 0.22 -10000 0 -0.55 89 89
RORA -0.015 0.43 -10000 0 -0.72 88 88
ABCB1 -0.3 0.47 -10000 0 -0.94 164 164
TFRC -0.001 0.43 0.84 6 -0.72 81 87
CXCR4 0.002 0.43 0.79 5 -0.71 83 88
TF -0.014 0.44 0.75 1 -0.74 87 88
CITED2 -0.013 0.43 -10000 0 -0.72 85 85
HIF1A/ARNT -0.074 0.44 0.89 4 -0.83 73 77
LDHA -0.01 0.13 -10000 0 -0.73 13 13
ETS1 -0.01 0.43 0.77 1 -0.71 84 85
PGK1 -0.001 0.43 0.83 3 -0.71 84 87
NOS2 -0.058 0.4 0.7 6 -0.72 81 87
ITGB2 -0.001 0.43 0.81 8 -0.71 83 91
ALDOA -0.003 0.42 -10000 0 -0.73 77 77
Cbp/p300/CITED2 -0.019 0.43 0.81 2 -0.8 64 66
FOS -0.36 0.27 -10000 0 -0.55 345 345
HK2 -0.004 0.43 -10000 0 -0.72 81 81
SP1 -0.018 0.093 -10000 0 -0.2 61 61
GCK 0.06 0.22 0.67 3 -0.52 2 5
HK1 -0.003 0.43 0.75 1 -0.71 84 85
NPM1 -0.006 0.43 -10000 0 -0.71 85 85
EGLN1 -0.028 0.4 -10000 0 -0.73 76 76
CREB1 0.04 0.01 -10000 0 -10000 0 0
PGM1 -0.008 0.43 0.75 1 -0.72 82 83
SMAD3 0.034 0.01 -10000 0 -10000 0 0
EDN1 -0.4 0.6 0.62 1 -1.2 163 164
IGFBP1 -0.005 0.43 -10000 0 -0.72 82 82
VEGFA 0.062 0.36 0.79 20 -0.61 45 65
HIF1A/JAB1 0.039 0.1 0.31 5 -0.41 4 9
CP -0.069 0.51 0.81 9 -0.79 122 131
CXCL12 -0.095 0.48 0.75 1 -0.78 124 125
COPS5 0.033 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4 0.048 0.022 -10000 0 -0.17 3 3
BNIP3 -0.008 0.43 0.84 1 -0.7 89 90
EGLN3 0.013 0.44 0.82 13 -0.71 82 95
CA9 0.007 0.44 0.83 7 -0.71 85 92
TERT -0.019 0.42 -10000 0 -0.71 83 83
ENO1 -0.005 0.43 -10000 0 -0.71 85 85
PFKL -0.006 0.43 -10000 0 -0.72 82 82
NCOA1 0.035 0.027 -10000 0 -0.54 1 1
ADM -0.11 0.5 -10000 0 -0.77 138 138
ARNT 0.019 0.098 -10000 0 -10000 0 0
HNF4A 0.036 0.009 -10000 0 -10000 0 0
ADFP -0.058 0.4 0.7 6 -0.72 81 87
SLC2A1 0.063 0.36 0.82 14 -0.6 49 63
LEP -0.15 0.48 -10000 0 -0.8 134 134
HIF1A/ARNT/Cbp/p300 -0.024 0.37 0.81 2 -0.72 51 53
EPO 0.066 0.32 0.81 10 -0.68 15 25
CREBBP 0.038 0.16 0.45 14 -0.31 10 24
HIF1A/ARNT/Cbp/p300/HDAC7 -0.015 0.35 0.78 6 -0.7 47 53
PFKFB3 -0.013 0.42 0.75 1 -0.71 86 87
NT5E -0.012 0.44 0.75 1 -0.73 87 88
PDGFR-alpha signaling pathway

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.09 0.18 -10000 0 -0.58 61 61
PDGF/PDGFRA/CRKL -0.052 0.14 -10000 0 -0.4 64 64
positive regulation of JUN kinase activity 0.016 0.12 -10000 0 -0.32 45 45
CRKL 0.032 0.009 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.053 0.14 -10000 0 -0.42 62 62
AP1 -0.7 0.45 -10000 0 -0.97 366 366
mol:IP3 -0.085 0.14 -10000 0 -0.45 57 57
PLCG1 -0.085 0.14 -10000 0 -0.45 57 57
PDGF/PDGFRA/alphaV Integrin -0.053 0.14 -10000 0 -0.41 65 65
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.085 0.14 -10000 0 -0.45 57 57
CAV3 0.032 0.037 -10000 0 -0.54 2 2
CAV1 -0.38 0.26 -10000 0 -0.54 364 364
SHC/Grb2/SOS1 0.017 0.12 -10000 0 -0.32 45 45
PDGF/PDGFRA/Shf -0.051 0.14 -10000 0 -0.4 64 64
FOS -0.69 0.44 -10000 0 -0.95 366 366
JUN -0.13 0.16 -10000 0 -0.46 87 87
oligodendrocyte development -0.053 0.14 -10000 0 -0.41 65 65
GRB2 0.034 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:DAG -0.085 0.14 -10000 0 -0.45 57 57
PDGF/PDGFRA -0.09 0.18 -10000 0 -0.58 61 61
actin cytoskeleton reorganization -0.05 0.14 -10000 0 -0.39 65 65
SRF 0.031 0.014 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
PI3K -0.029 0.18 -10000 0 -0.42 83 83
PDGF/PDGFRA/Crk/C3G 0.002 0.13 -10000 0 -0.36 61 61
JAK1 -0.064 0.13 -10000 0 -0.4 63 63
ELK1/SRF -0.058 0.12 0.33 1 -0.36 58 59
SHB 0.036 0.018 -10000 0 -10000 0 0
SHF 0.034 0.013 -10000 0 -10000 0 0
CSNK2A1 0.063 0.025 -10000 0 -10000 0 0
GO:0007205 -0.092 0.14 -10000 0 -0.46 62 62
SOS1 0.034 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.016 0.12 -10000 0 -0.32 45 45
PDGF/PDGFRA/SHB -0.05 0.14 -10000 0 -0.39 65 65
PDGF/PDGFRA/Caveolin-1 -0.33 0.24 -10000 0 -0.46 376 376
ITGAV 0.034 0.027 -10000 0 -0.54 1 1
ELK1 -0.11 0.13 0.23 2 -0.44 60 62
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.053 0.14 -10000 0 -0.41 64 64
JAK-STAT cascade -0.064 0.13 -10000 0 -0.4 63 63
cell proliferation -0.051 0.14 -10000 0 -0.4 64 64
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.11 0.079 -10000 0 -0.3 3 3
SMAD6-7/SMURF1 0.064 0.02 -10000 0 -10000 0 0
NOG 0.031 0.03 -10000 0 -0.54 1 1
SMAD9 -0.081 0.23 -10000 0 -0.67 60 60
SMAD4 0.033 0.008 -10000 0 -10000 0 0
SMAD5 -0.098 0.19 -10000 0 -0.42 86 86
BMP7/USAG1 -0.24 0.2 -10000 0 -0.39 310 310
SMAD5/SKI -0.087 0.19 -10000 0 -0.42 78 78
SMAD1 0.005 0.09 -10000 0 -0.44 10 10
BMP2 -0.23 0.29 -10000 0 -0.54 230 230
SMAD1/SMAD1/SMAD4 0.03 0.087 -10000 0 -0.43 6 6
BMPR1A 0.031 0.044 -10000 0 -0.54 3 3
BMPR1B 0.088 0.071 -10000 0 -10000 0 0
BMPR1A-1B/BAMBI 0.082 0.13 0.26 24 -0.3 38 62
AHSG 0.034 0.006 -10000 0 -10000 0 0
CER1 0.033 0.011 -10000 0 -10000 0 0
BMP2-4/CER1 -0.16 0.23 -10000 0 -0.38 261 261
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.097 0.18 -10000 0 -0.4 83 83
BMP2-4 (homodimer) -0.21 0.25 -10000 0 -0.43 277 277
RGMB 0.033 0.007 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.02 0.19 -10000 0 -0.28 168 168
RGMA -0.052 0.2 -10000 0 -0.54 76 76
SMURF1 0.034 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.18 -10000 0 -0.39 106 106
BMP2-4/USAG1 -0.4 0.26 -10000 0 -0.51 411 411
SMAD6/SMURF1/SMAD5 -0.089 0.19 -10000 0 -0.43 76 76
SOSTDC1 -0.37 0.26 -10000 0 -0.54 359 359
BMP7/BMPR2/BMPR1A-1B 0.11 0.072 -10000 0 -0.31 3 3
SKI 0.033 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) -0.16 0.27 -10000 0 -0.54 168 168
HFE2 0.027 0.039 -10000 0 -0.54 2 2
ZFYVE16 0.033 0.007 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
BMP2-4/CHRD -0.17 0.23 -10000 0 -0.38 262 262
SMAD5/SMAD5/SMAD4 -0.089 0.19 -10000 0 -0.43 75 75
MAPK1 0.032 0.009 -10000 0 -10000 0 0
TAK1/TAB family -0.082 0.17 -10000 0 -0.36 96 96
BMP7 (homodimer) 0.043 0.043 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
BMP6/FETUA -0.098 0.21 -10000 0 -0.39 171 171
SMAD1/SKI 0.015 0.096 -10000 0 -0.41 10 10
SMAD6 0.033 0.007 -10000 0 -10000 0 0
CTDSP2 0.034 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA -0.17 0.23 -10000 0 -0.38 262 262
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.048 0.046 -10000 0 -10000 0 0
BMPR2 (homodimer) 0.034 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.06 0.037 -10000 0 -0.34 2 2
BMPR1A-1B (homodimer) 0.084 0.064 -10000 0 -0.4 3 3
CHRDL1 -0.3 0.28 -10000 0 -0.54 300 300
ENDOFIN/SMAD1 0.015 0.097 -10000 0 -0.41 11 11
SMAD6-7/SMURF1/SMAD1 0.048 0.1 -10000 0 -0.48 6 6
SMAD6/SMURF1 0.034 0.005 -10000 0 -10000 0 0
BAMBI 0.018 0.16 -10000 0 -0.54 36 36
SMURF2 0.031 0.013 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.36 0.31 -10000 0 -0.54 356 356
BMP2-4/GREM1 -0.16 0.24 0.26 2 -0.37 266 268
SMAD7 0.033 0.007 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.074 0.23 -10000 0 -0.63 64 64
SMAD1/SMAD6 0.015 0.098 -10000 0 -0.42 11 11
TAK1/SMAD6 0.047 0.015 -10000 0 -10000 0 0
BMP7 0.043 0.043 -10000 0 -10000 0 0
BMP6 -0.16 0.27 -10000 0 -0.54 168 168
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.098 0.18 -10000 0 -0.4 100 100
PPM1A 0.034 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.012 0.093 -10000 0 -0.46 8 8
SMAD7/SMURF1 0.048 0.012 -10000 0 -10000 0 0
CTDSPL 0.031 0.036 -10000 0 -0.54 2 2
PPP1CA 0.034 0.021 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
PPP1R15A 0.032 0.036 -10000 0 -0.54 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.099 0.19 -10000 0 -0.4 95 95
CHRD 0.036 0.021 -10000 0 -10000 0 0
BMPR2 0.034 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.12 0.21 -10000 0 -0.45 109 109
BMP4 -0.04 0.2 -10000 0 -0.54 67 67
FST 0.032 0.039 -10000 0 -0.54 2 2
BMP2-4/NOG -0.16 0.22 -10000 0 -0.38 246 246
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.11 0.075 -10000 0 -0.3 3 3
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.058 0.18 1 -0.54 5 6
EPHB2 0.042 0.037 -10000 0 -10000 0 0
EFNB1 0.016 0.027 -10000 0 -0.4 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.048 0.18 -10000 0 -0.28 180 180
Ephrin B2/EPHB1-2 -0.074 0.19 -10000 0 -0.31 189 189
neuron projection morphogenesis -0.06 0.16 -10000 0 -0.27 180 180
Ephrin B1/EPHB1-2/Tiam1 -0.059 0.18 -10000 0 -0.3 180 180
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.057 0.18 -10000 0 -0.57 56 56
YES1 -0.069 0.26 -10000 0 -0.8 56 56
Ephrin B1/EPHB1-2/NCK2 -0.06 0.18 -10000 0 -0.3 181 181
PI3K -0.045 0.22 -10000 0 -0.48 92 92
mol:GDP -0.06 0.18 -10000 0 -0.3 180 180
ITGA2B 0.034 0.012 0.18 2 -10000 0 2
endothelial cell proliferation 0.038 0.046 -10000 0 -0.31 7 7
FYN -0.072 0.26 -10000 0 -0.79 56 56
MAP3K7 -0.058 0.19 -10000 0 -0.6 56 56
FGR -0.065 0.26 -10000 0 -0.79 56 56
TIAM1 0.035 0.012 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RGS3 0.034 0.005 -10000 0 -10000 0 0
cell adhesion -0.046 0.2 -10000 0 -0.54 59 59
LYN -0.065 0.25 -10000 0 -0.78 56 56
Ephrin B1/EPHB1-2/Src Family Kinases -0.071 0.24 -10000 0 -0.74 57 57
Ephrin B1/EPHB1-2 -0.061 0.21 -10000 0 -0.64 56 56
SRC -0.064 0.26 -10000 0 -0.78 57 57
ITGB3 0.035 0.019 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 190 190
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
RAC1 0.034 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.039 0.046 -10000 0 -0.31 7 7
alphaIIb/beta3 Integrin 0.05 0.018 -10000 0 -10000 0 0
BLK -0.076 0.26 -10000 0 -0.8 56 56
HCK -0.065 0.25 -10000 0 -0.78 56 56
regulation of stress fiber formation 0.06 0.18 0.3 181 -10000 0 181
MAPK8 -0.056 0.18 -10000 0 -0.55 56 56
Ephrin B1/EPHB1-2/RGS3 -0.06 0.18 -10000 0 -0.3 182 182
endothelial cell migration -0.051 0.17 0.26 1 -0.51 58 59
NCK2 0.035 0.007 -10000 0 -10000 0 0
PTPN13 -0.026 0.2 -10000 0 -0.65 46 46
regulation of focal adhesion formation 0.06 0.18 0.3 181 -10000 0 181
chemotaxis 0.06 0.18 0.3 182 -10000 0 182
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.054 0.17 -10000 0 -0.28 180 180
angiogenesis -0.061 0.2 -10000 0 -0.64 56 56
LCK -0.061 0.26 -10000 0 -0.78 57 57
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.2 0.19 -9999 0 -0.41 88 88
MAP3K8 -0.047 0.19 -9999 0 -0.55 65 65
FOS -0.098 0.12 -9999 0 -0.37 26 26
PRKCA -0.006 0.028 -9999 0 -10000 0 0
PTPN7 -0.002 0.044 -9999 0 -10000 0 0
HRAS 0.032 0.013 -9999 0 -10000 0 0
PRKCB -0.013 0.009 -9999 0 -0.018 361 361
NRAS 0.033 0.016 -9999 0 -10000 0 0
RAS family/GTP 0.032 0.036 -9999 0 -10000 0 0
MAPK3 -0.029 0.075 -9999 0 -0.61 3 3
MAP2K1 -0.054 0.089 -9999 0 -0.28 41 41
ELK1 -0.015 0.037 -9999 0 -10000 0 0
BRAF -0.016 0.037 -9999 0 -0.25 6 6
mol:GTP -0.004 0.003 -9999 0 -0.006 364 364
MAPK1 -0.052 0.12 -9999 0 -0.46 28 28
RAF1 -0.017 0.035 -9999 0 -0.25 5 5
KRAS 0.033 0.019 -9999 0 -10000 0 0
IL6-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
BCL2L1 -0.025 0.3 0.66 3 -0.72 33 36
CRP -0.001 0.31 0.74 4 -0.73 30 34
cell cycle arrest -0.053 0.34 0.64 7 -0.74 55 62
TIMP1 -0.014 0.28 0.67 8 -0.63 31 39
IL6ST 0.038 0.084 -10000 0 -0.54 9 9
Rac1/GDP -0.089 0.22 0.42 7 -0.44 79 86
AP1 -0.16 0.24 0.48 5 -0.53 90 95
GAB2 0.033 0.016 -10000 0 -10000 0 0
TNFSF11 -0.007 0.32 0.69 7 -0.71 32 39
HSP90B1 0.043 0.14 -10000 0 -0.95 6 6
GAB1 0.035 0.027 -10000 0 -0.54 1 1
MAPK14 -0.13 0.2 0.32 1 -0.54 62 63
AKT1 0.032 0.099 0.34 1 -0.45 9 10
FOXO1 0.005 0.14 0.33 1 -0.45 18 19
MAP2K6 -0.12 0.2 0.35 3 -0.46 86 89
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.057 0.24 0.48 8 -0.48 66 74
MITF -0.11 0.21 0.36 5 -0.43 96 101
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.006 -10000 0 -10000 0 0
A2M -0.16 0.49 -10000 0 -1.3 74 74
CEBPB 0.038 0.03 -10000 0 -0.54 1 1
GRB2/SOS1/GAB family/SHP2 -0.002 0.14 0.36 2 -0.47 22 24
STAT3 -0.072 0.36 0.65 6 -0.8 56 62
STAT1 0.032 0.14 -10000 0 -0.84 9 9
CEBPD -0.081 0.44 0.67 4 -1 72 76
PIK3CA 0.034 0.009 -10000 0 -10000 0 0
PI3K 0.007 0.13 -10000 0 -0.4 44 44
JUN -0.066 0.22 -10000 0 -0.54 89 89
PIAS3/MITF -0.1 0.2 0.37 1 -0.43 77 78
MAPK11 -0.13 0.2 0.32 1 -0.53 62 63
STAT3 (dimer)/FOXO1 -0.086 0.33 0.6 8 -0.67 71 79
GRB2/SOS1/GAB family -0.083 0.18 0.37 2 -0.43 50 52
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.19 0.3 5 -0.41 101 106
GRB2 0.036 0.019 -10000 0 -10000 0 0
JAK2 0.033 0.011 -10000 0 -10000 0 0
LBP 0.008 0.28 0.73 5 -0.67 17 22
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
JAK1 0.038 0.013 -10000 0 -10000 0 0
MYC -0.015 0.38 0.73 8 -0.96 43 51
FGG -0.026 0.3 0.69 3 -0.72 34 37
macrophage differentiation -0.053 0.34 0.64 7 -0.74 55 62
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.19 -10000 0 -0.3 263 263
JUNB -0.031 0.3 0.64 3 -0.71 36 39
FOS -0.35 0.27 -10000 0 -0.54 345 345
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.37 8 -0.44 101 109
STAT1/PIAS1 -0.073 0.23 0.43 7 -0.45 73 80
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.1 -10000 0 -0.44 12 12
STAT3 (dimer) -0.069 0.35 0.66 6 -0.8 54 60
PRKCD -0.035 0.26 0.52 10 -0.54 55 65
IL6R 0.03 0.031 -10000 0 -0.55 1 1
SOCS3 -0.15 0.24 -10000 0 -0.89 29 29
gp130 (dimer)/JAK1/JAK1/LMO4 0.073 0.12 0.3 4 -0.32 31 35
Rac1/GTP -0.077 0.23 0.43 9 -0.44 81 90
HCK 0.037 0.022 -10000 0 -10000 0 0
MAPKKK cascade 0.021 0.16 0.4 1 -0.56 25 26
bone resorption -0.003 0.3 0.69 7 -0.67 32 39
IRF1 -0.024 0.3 0.67 6 -0.7 35 41
mol:GDP -0.1 0.21 0.39 9 -0.43 90 99
SOS1 0.038 0.009 -10000 0 -10000 0 0
VAV1 -0.1 0.22 0.4 9 -0.44 90 99
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.2 -10000 0 -0.57 63 63
PTPN11 0.021 0.093 -10000 0 -0.81 5 5
IL6/IL6RA -0.23 0.2 -10000 0 -0.39 297 297
gp130 (dimer)/TYK2/TYK2/LMO4 0.067 0.11 0.28 1 -0.33 27 28
gp130 (dimer)/JAK2/JAK2/LMO4 0.063 0.11 0.28 1 -0.32 30 31
IL6 -0.37 0.27 0.22 1 -0.53 366 367
PIAS3 0.028 0.013 -10000 0 -10000 0 0
PTPRE 0.004 0.043 -10000 0 -0.52 1 1
PIAS1 0.033 0.007 -10000 0 -10000 0 0
RAC1 0.036 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.14 0.17 0.29 3 -0.37 101 104
LMO4 0.03 0.12 0.24 4 -0.54 21 25
STAT3 (dimer)/PIAS3 -0.067 0.32 0.62 4 -0.72 58 62
MCL1 0.067 0.12 0.52 2 -0.71 1 3
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.008 0.16 -10000 0 -0.3 103 103
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.57 72 72
AKT1 -0.19 0.37 -10000 0 -0.79 133 133
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.19 0.38 -10000 0 -0.8 134 134
mol:Ca2+ -0.03 0.12 0.26 3 -0.43 17 20
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
E2/ER alpha (dimer)/Striatin -0.019 0.17 -10000 0 -0.34 105 105
SHC1 0.028 0.014 -10000 0 -10000 0 0
apoptosis 0.18 0.35 0.75 133 -10000 0 133
RhoA/GTP -0.024 0.11 -10000 0 -0.27 81 81
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.13 0.23 0.31 1 -0.45 134 135
regulation of stress fiber formation 0.014 0.12 -10000 0 -0.25 18 18
E2/ERA-ERB (dimer) -0.022 0.17 -10000 0 -0.34 106 106
KRAS 0.035 0.019 -10000 0 -10000 0 0
G13/GTP -0.019 0.15 -10000 0 -0.31 99 99
pseudopodium formation -0.014 0.12 0.25 18 -10000 0 18
E2/ER alpha (dimer)/PELP1 -0.025 0.17 -10000 0 -0.34 106 106
GRB2 0.034 0.018 -10000 0 -10000 0 0
GNG2 0.033 0.026 -10000 0 -0.54 1 1
GNAO1 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.25 -10000 0 -0.5 139 139
E2/ER beta (dimer) 0.025 0.005 -10000 0 -10000 0 0
mol:GDP -0.047 0.18 0.23 10 -0.41 89 99
mol:NADP -0.14 0.25 -10000 0 -0.5 139 139
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.033 0.12 0.26 3 -0.44 17 20
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
PLCB1 -0.034 0.13 -10000 0 -0.33 45 45
PLCB2 0.003 0.087 -10000 0 -0.48 7 7
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
mol:L-citrulline -0.14 0.25 -10000 0 -0.5 139 139
RHOA 0.033 0.007 -10000 0 -10000 0 0
Gai/GDP -0.14 0.28 -10000 0 -0.73 79 79
JNK cascade 0.024 0.005 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
ESR2 0.033 0.007 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.059 0.25 -10000 0 -0.54 106 106
Gq family/GDP/Gbeta gamma 0.009 0.16 -10000 0 -0.84 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.031 0.14 -10000 0 -0.58 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.21 0.31 1 -0.45 107 108
GNAZ 0.026 0.062 -10000 0 -0.54 6 6
E2/ER alpha (dimer) -0.045 0.18 -10000 0 -0.39 110 110
STRN 0.034 0.028 -10000 0 -0.54 1 1
GNAL 0.03 0.044 -10000 0 -0.54 3 3
PELP1 0.031 0.01 -10000 0 -10000 0 0
MAPK11 0.017 0.006 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
HBEGF -0.11 0.23 0.37 7 -0.56 56 63
cAMP biosynthetic process -0.02 0.13 -10000 0 -0.28 102 102
SRC -0.14 0.23 0.31 4 -0.59 60 64
PI3K 0.005 0.13 -10000 0 -0.4 44 44
GNB1 0.034 0.011 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.021 0.18 -10000 0 -0.37 86 86
SOS1 0.034 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.43 207 207
Gs family/GTP -0.012 0.14 -10000 0 -0.28 102 102
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.061 0.025 -10000 0 -10000 0 0
vasodilation -0.14 0.24 -10000 0 -0.48 139 139
mol:DAG -0.033 0.12 0.26 3 -0.44 17 20
Gs family/GDP/Gbeta gamma -0.041 0.16 -10000 0 -0.36 82 82
MSN -0.016 0.12 0.26 18 -10000 0 18
Gq family/GTP 0.003 0.092 -10000 0 -0.45 9 9
mol:PI-3-4-5-P3 -0.18 0.36 -10000 0 -0.77 134 134
NRAS 0.036 0.016 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.14 0.24 0.48 139 -10000 0 139
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
RhoA/GDP -0.028 0.19 -10000 0 -0.39 87 87
NOS3 -0.15 0.26 -10000 0 -0.54 138 138
GNA11 0.034 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.13 0.27 -10000 0 -0.56 133 133
E2/ER alpha (dimer)/PELP1/Src -0.14 0.23 0.32 2 -0.46 138 140
ruffle organization -0.014 0.12 0.25 18 -10000 0 18
ROCK2 -0.014 0.13 0.35 6 -10000 0 6
GNA14 0.044 0.068 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MMP9 -0.097 0.22 0.4 7 -0.55 53 60
MMP2 -0.14 0.22 0.3 5 -0.55 60 65
FAS signaling pathway (CD95)

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
SPTAN1 0.017 0.089 0.21 71 -10000 0 71
RFC1 0.017 0.084 0.21 63 -10000 0 63
PRKDC 0.038 0.11 0.23 104 -10000 0 104
RIPK1 0.041 0.009 -10000 0 -10000 0 0
CASP7 -0.042 0.12 -10000 0 -0.76 10 10
FASLG/FAS/FADD/FAF1 -0.024 0.091 0.26 9 -0.31 17 26
MAP2K4 -0.18 0.19 -10000 0 -0.42 112 112
mol:ceramide -0.075 0.12 0.27 1 -0.36 37 38
GSN -0.059 0.17 0.22 54 -0.34 107 161
FASLG/FAS/FADD/FAF1/Caspase 8 -0.032 0.097 0.32 3 -0.32 16 19
FAS -0.047 0.14 -10000 0 -0.56 33 33
BID -0.022 0.021 -10000 0 -10000 0 0
MAP3K1 -0.093 0.14 0.28 1 -0.47 25 26
MAP3K7 0.026 0.01 -10000 0 -10000 0 0
RB1 0.018 0.081 0.21 65 -10000 0 65
CFLAR 0.04 0.026 -10000 0 -0.52 1 1
HGF/MET -0.009 0.16 -10000 0 -0.36 89 89
ARHGDIB 0.019 0.089 0.22 70 -10000 0 70
FADD -0.008 0.028 -10000 0 -10000 0 0
actin filament polymerization 0.057 0.17 0.34 108 -0.22 55 163
NFKB1 -0.1 0.13 -10000 0 -0.65 9 9
MAPK8 -0.32 0.25 -10000 0 -0.45 371 371
DFFA 0.016 0.083 0.21 63 -10000 0 63
DNA fragmentation during apoptosis 0.019 0.088 0.21 53 -10000 0 53
FAS/FADD/MET -0.029 0.15 -10000 0 -0.39 65 65
CFLAR/RIP1 0.06 0.027 -10000 0 -0.37 1 1
FAIM3 0.035 0.03 -10000 0 -10000 0 0
FAF1 -0.016 0.033 -10000 0 -10000 0 0
PARP1 0.023 0.097 0.24 63 -10000 0 63
DFFB 0.015 0.084 0.21 53 -10000 0 53
CHUK -0.11 0.12 -10000 0 -0.61 9 9
FASLG 0.001 0.061 -10000 0 -0.55 1 1
FAS/FADD -0.033 0.1 -10000 0 -0.41 29 29
HGF 0.035 0.01 -10000 0 -10000 0 0
LMNA 0.022 0.098 0.42 14 -10000 0 14
CASP6 0.017 0.085 0.22 29 -10000 0 29
CASP10 -0.012 0.029 -10000 0 -10000 0 0
CASP3 0.02 0.1 0.26 66 -0.23 4 70
PTPN13 -0.018 0.16 -10000 0 -0.54 46 46
CASP8 -0.027 0.022 -10000 0 -10000 0 0
IL6 -0.88 0.56 -10000 0 -1.2 380 380
MET -0.022 0.17 -10000 0 -0.54 50 50
ICAD/CAD 0.01 0.074 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.076 0.13 0.27 1 -0.36 37 38
activation of caspase activity by cytochrome c -0.022 0.021 -10000 0 -10000 0 0
PAK2 0.016 0.094 0.25 32 -10000 0 32
BCL2 -0.068 0.22 -10000 0 -0.54 91 91
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.06 0.035 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.24 0.18 -10000 0 -0.34 370 370
PTK2 -0.046 0.12 0.38 3 -0.48 7 10
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
PI4KB 0.028 0.014 -10000 0 -10000 0 0
MFGE8 0.007 0.13 -10000 0 -0.54 25 25
SRC 0.033 0.008 -10000 0 -10000 0 0
CDKN1B -0.1 0.13 -10000 0 -0.57 28 28
VEGFA 0.05 0.047 -10000 0 -10000 0 0
ILK -0.088 0.095 -10000 0 -0.47 16 16
ROCK1 0.034 0.006 -10000 0 -10000 0 0
AKT1 -0.082 0.089 -10000 0 -0.45 15 15
PTK2B 0.027 0.05 0.32 4 -0.3 1 5
alphaV/beta3 Integrin/JAM-A -0.16 0.17 -10000 0 -0.3 276 276
CBL 0.031 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.065 0.03 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.25 -10000 0 -0.38 258 258
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.038 0.062 -10000 0 -0.34 6 6
alphaV/beta3 Integrin/Syndecan-1 0.09 0.052 0.26 3 -0.34 1 4
PI4KA 0.032 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.3 0.25 -10000 0 -0.49 274 274
PI4 Kinase 0.038 0.022 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.1 0.068 -10000 0 -0.34 4 4
RPS6KB1 -0.28 0.23 0.6 1 -0.51 204 205
TLN1 0.034 0.006 -10000 0 -10000 0 0
MAPK3 -0.36 0.29 -10000 0 -0.56 332 332
GPR124 0.008 0.1 -10000 0 -0.54 17 17
MAPK1 -0.38 0.29 -10000 0 -0.56 347 347
PXN 0.034 0.004 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
alphaV/beta3 Integrin/Tumstatin 0.066 0.029 -10000 0 -0.34 1 1
cell adhesion 0.034 0.093 -10000 0 -0.3 32 32
ANGPTL3 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.073 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
TGFBR2 -0.004 0.14 -10000 0 -0.54 34 34
ITGB3 0.035 0.019 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
RAC1 0.034 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.04 0.08 -10000 0 -0.34 18 18
apoptosis 0.033 0.027 -10000 0 -0.54 1 1
CD47 0.023 0.08 -10000 0 -0.54 10 10
alphaV/beta3 Integrin/CD47 0.057 0.064 -10000 0 -0.34 11 11
VCL 0.034 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.057 0.095 0.26 2 -0.34 23 25
CSF1 0.034 0.008 -10000 0 -10000 0 0
PIK3C2A -0.084 0.09 -10000 0 -0.46 13 13
PI4 Kinase/Pyk2 -0.15 0.13 -10000 0 -0.27 243 243
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.09 0.045 -10000 0 -0.32 1 1
FAK1/Vinculin -0.033 0.11 0.39 3 -0.37 8 11
alphaV beta3/Integrin/ppsTEM5 0.04 0.081 -10000 0 -0.34 18 18
RHOA 0.033 0.007 -10000 0 -10000 0 0
VTN 0.033 0.011 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
F11R -0.23 0.2 -10000 0 -0.4 299 299
alphaV/beta3 Integrin/Lactadherin 0.047 0.09 0.26 1 -0.34 23 24
alphaV/beta3 Integrin/TGFBR2 0.04 0.1 0.26 1 -0.34 33 34
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.07 0.041 -10000 0 -0.32 1 1
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.062 0.028 -10000 0 -0.31 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.068 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.057 0.048 0.29 1 -0.3 1 2
SDC1 0.073 0.065 -10000 0 -10000 0 0
VAV3 0.013 0.071 -10000 0 -0.3 19 19
PTPN11 0.034 0.004 -10000 0 -10000 0 0
IRS1 -0.034 0.18 -10000 0 -0.54 60 60
FAK1/Paxillin -0.033 0.11 0.37 4 -0.38 7 11
cell migration -0.033 0.1 0.35 4 -0.35 7 11
ITGAV 0.034 0.027 -10000 0 -0.54 1 1
PI3K -0.17 0.18 -10000 0 -0.31 273 273
SPP1 0.091 0.087 -10000 0 -0.54 3 3
KDR 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.034 0.027 -10000 0 -0.54 1 1
COL4A3 0.034 0.006 -10000 0 -10000 0 0
angiogenesis -0.37 0.28 0.31 1 -0.56 326 327
Rac1/GTP 0.031 0.068 -10000 0 -0.28 18 18
EDIL3 0.024 0.13 -10000 0 -0.54 22 22
cell proliferation 0.039 0.1 0.25 1 -0.34 33 34
EPHB forward signaling

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
Ephrin A5/EPHB2 0.048 0.033 0.23 2 -0.34 1 3
cell-cell adhesion 0.1 0.12 0.27 176 -10000 0 176
Ephrin B/EPHB2/RasGAP 0.081 0.067 -10000 0 -0.3 7 7
ITSN1 0.034 0.005 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.044 0.027 -10000 0 -0.34 2 2
Ephrin B1/EPHB1 -0.098 0.19 -10000 0 -0.34 189 189
HRAS/GDP -0.081 0.16 -10000 0 -0.37 47 47
Ephrin B/EPHB1/GRB7 -0.055 0.18 -10000 0 -0.31 158 158
Endophilin/SYNJ1 0.018 0.049 0.26 1 -0.28 7 8
KRAS 0.035 0.019 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.056 0.19 -10000 0 -0.31 175 175
endothelial cell migration 0.027 0.11 -10000 0 -0.3 47 47
GRB2 0.034 0.018 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.009 0.064 0.3 5 -0.28 5 10
HRAS 0.034 0.013 -10000 0 -10000 0 0
RRAS 0.017 0.049 0.26 1 -0.28 7 8
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.092 0.16 0.36 2 -0.29 188 190
lamellipodium assembly -0.1 0.12 -10000 0 -0.27 176 176
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.062 0.15 -10000 0 -0.42 36 36
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
EPHB2 0.043 0.038 -10000 0 -10000 0 0
EPHB3 0.035 0.016 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 190 190
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
mol:GDP -0.08 0.14 -10000 0 -0.39 45 45
Ephrin B/EPHB2 0.068 0.059 -10000 0 -0.3 7 7
Ephrin B/EPHB3 0.062 0.054 -10000 0 -0.3 7 7
JNK cascade -0.089 0.16 0.39 5 -0.3 181 186
Ephrin B/EPHB1 -0.069 0.18 -10000 0 -0.3 188 188
RAP1/GDP -0.058 0.14 -10000 0 -0.36 40 40
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EFNB3 0.031 0.011 -10000 0 -10000 0 0
EFNB1 0.032 0.036 -10000 0 -0.54 2 2
Ephrin B2/EPHB1-2 -0.075 0.19 -10000 0 -0.32 189 189
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.06 0.17 -10000 0 -0.35 43 43
Rap1/GTP -0.074 0.14 -10000 0 -0.27 157 157
axon guidance 0.047 0.033 0.23 2 -0.34 1 3
MAPK3 -0.047 0.14 0.26 1 -0.39 30 31
MAPK1 -0.054 0.14 -10000 0 -0.38 32 32
Rac1/GDP -0.072 0.14 -10000 0 -0.37 44 44
actin cytoskeleton reorganization -0.076 0.12 -10000 0 -0.32 29 29
CDC42/GDP -0.071 0.14 -10000 0 -0.36 45 45
PI3K 0.032 0.12 -10000 0 -0.3 47 47
EFNA5 0.033 0.029 -10000 0 -0.54 1 1
Ephrin B2/EPHB4 0.039 0.046 -10000 0 -0.31 7 7
Ephrin B/EPHB2/Intersectin/N-WASP 0.019 0.068 -10000 0 -0.29 8 8
CDC42 0.033 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.076 0.14 -10000 0 -0.27 135 135
PTK2 0.14 0.27 0.67 101 -10000 0 101
MAP4K4 -0.09 0.16 0.39 5 -0.3 181 186
SRC 0.033 0.008 -10000 0 -10000 0 0
KALRN 0.034 0.006 -10000 0 -10000 0 0
Intersectin/N-WASP 0.049 0.022 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.053 0.14 0.45 5 -0.34 14 19
MAP2K1 -0.059 0.14 -10000 0 -0.4 32 32
WASL 0.033 0.026 -10000 0 -0.54 1 1
Ephrin B1/EPHB1-2/NCK1 -0.061 0.2 -10000 0 -0.31 189 189
cell migration -0.063 0.17 0.33 3 -0.43 36 39
NRAS 0.036 0.016 -10000 0 -10000 0 0
SYNJ1 0.018 0.05 0.26 1 -0.28 7 8
PXN 0.034 0.004 -10000 0 -10000 0 0
TF -0.014 0.068 0.25 1 -0.28 22 23
HRAS/GTP -0.06 0.17 -10000 0 -0.28 177 177
Ephrin B1/EPHB1-2 -0.072 0.19 -10000 0 -0.31 189 189
cell adhesion mediated by integrin -0.008 0.048 0.27 7 -0.2 10 17
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.06 0.18 -10000 0 -0.29 179 179
RAC1-CDC42/GTP -0.087 0.14 -10000 0 -0.27 175 175
RASA1 0.034 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.061 0.14 -10000 0 -0.36 43 43
ruffle organization -0.094 0.14 0.41 3 -0.47 8 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
receptor internalization -0.006 0.049 0.25 1 -0.27 7 8
Ephrin B/EPHB2/KALRN 0.082 0.067 -10000 0 -0.3 7 7
ROCK1 0.024 0.037 -10000 0 -0.31 2 2
RAS family/GDP -0.084 0.095 -10000 0 -0.32 27 27
Rac1/GTP -0.088 0.14 -10000 0 -0.28 176 176
Ephrin B/EPHB1/Src/Paxillin -0.087 0.16 -10000 0 -0.29 178 178
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.62 0.93 3 -1.2 88 91
STAT6 (cleaved dimer) -0.23 0.54 -10000 0 -1.1 106 106
IGHG1 0.027 0.3 0.63 15 -1.1 3 18
IGHG3 -0.15 0.58 0.78 3 -1.1 105 108
AKT1 -0.026 0.35 0.62 2 -0.75 31 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.029 0.28 0.57 6 -0.86 13 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.024 0.37 0.64 6 -0.78 36 42
THY1 -0.14 0.62 1 5 -1.2 89 94
MYB -0.006 0.16 -10000 0 -0.54 40 40
HMGA1 0.037 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.003 0.4 0.73 13 -0.7 38 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0 0.34 0.63 6 -0.82 18 24
SP1 0.057 0.044 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.007 0.057 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.16 0.59 0.84 1 -1.1 103 104
SOCS1 -0.06 0.41 0.7 2 -0.72 80 82
SOCS3 -0.016 0.39 0.69 1 -1.2 19 20
FCER2 -0.14 0.52 0.87 6 -0.89 74 80
PARP14 0.042 0.032 -10000 0 -10000 0 0
CCL17 -0.12 0.64 1 10 -1.2 90 100
GRB2 0.034 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.03 0.29 0.58 11 -0.71 13 24
T cell proliferation -0.18 0.62 -10000 0 -1.2 101 101
IL4R/JAK1 -0.15 0.61 -10000 0 -1.2 94 94
EGR2 -0.51 0.86 1 2 -1.3 232 234
JAK2 0.03 0.089 0.26 3 -10000 0 3
JAK3 0.035 0.019 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.036 0.046 -10000 0 -10000 0 0
COL1A2 0.037 0.31 0.7 4 -1.2 10 14
CCL26 -0.14 0.62 1.1 5 -1.2 91 96
IL4R -0.14 0.68 1.1 7 -1.2 93 100
PTPN6 0.016 0.044 -10000 0 -10000 0 0
IL13RA2 -0.15 0.63 0.96 4 -1.2 95 99
IL13RA1 0.032 0.091 -10000 0 -10000 0 0
IRF4 0.064 0.21 0.75 2 -0.82 3 5
ARG1 0.048 0.26 0.72 4 -1.2 4 8
CBL -0.014 0.36 0.66 6 -0.66 39 45
GTF3A 0.1 0.065 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL13RA1/JAK2 0.05 0.13 0.36 5 -10000 0 5
IRF4/BCL6 0.029 0.21 -10000 0 -0.76 5 5
CD40LG 0.048 0.033 0.31 2 -10000 0 2
MAPK14 -0.013 0.38 0.67 4 -0.78 29 33
mitosis -0.02 0.34 0.61 3 -0.7 31 34
STAT6 -0.15 0.75 1.2 15 -1.3 102 117
SPI1 0.044 0.033 -10000 0 -0.24 1 1
RPS6KB1 -0.003 0.33 0.63 6 -0.7 26 32
STAT6 (dimer) -0.15 0.76 1.2 15 -1.3 102 117
STAT6 (dimer)/PARP14 -0.17 0.64 -10000 0 -1.2 103 103
mast cell activation -0.006 0.026 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.016 0.36 0.62 7 -0.76 36 43
FRAP1 -0.026 0.35 0.65 1 -0.75 31 32
LTA -0.14 0.62 0.93 3 -1.2 89 92
FES 0.031 0.037 -10000 0 -0.54 2 2
T-helper 1 cell differentiation 0.14 0.73 1.3 102 -1.1 15 117
CCL11 -0.1 0.61 0.9 4 -1.1 88 92
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.011 0.34 0.62 7 -0.87 17 24
IL2RG 0.045 0.042 0.22 10 -10000 0 10
IL10 -0.1 0.62 1.1 7 -1.2 81 88
IRS1 -0.034 0.18 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 117 117
IL4 0.045 0.3 0.79 7 -1.1 12 19
IL5 -0.14 0.62 1 4 -1.2 87 91
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.06 0.55 0.96 15 -0.87 91 106
COL1A1 0.12 0.4 0.76 38 -1 21 59
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.16 0.62 -10000 0 -1.2 86 86
IL2R gamma/JAK3 0.063 0.039 -10000 0 -10000 0 0
TFF3 -0.27 0.73 0.96 1 -1.3 123 124
ALOX15 -0.14 0.62 0.93 3 -1.2 90 93
MYBL1 0.048 0.054 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.092 0.53 0.82 6 -0.92 93 99
SHC1 0.028 0.014 -10000 0 -10000 0 0
CEBPB 0.035 0.034 -10000 0 -0.39 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.043 0.36 0.61 6 -0.7 44 50
mol:PI-3-4-5-P3 -0.025 0.36 0.65 1 -0.75 31 32
PI3K -0.032 0.37 0.66 1 -0.81 31 32
DOK2 0.026 0.039 -10000 0 -0.54 2 2
ETS1 0.002 0.059 0.19 2 -0.35 2 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.039 0.28 0.56 11 -0.68 11 22
ITGB3 -0.14 0.62 0.96 4 -1.2 90 94
PIGR -0.4 0.84 1 11 -1.3 202 213
IGHE -0.043 0.1 0.18 12 -0.28 20 32
MAPKKK cascade 0.04 0.27 0.56 11 -0.67 11 22
BCL6 -0.025 0.17 -10000 0 -0.54 51 51
OPRM1 -0.14 0.62 0.93 3 -1.2 91 94
RETNLB -0.14 0.62 0.93 3 -1.2 91 94
SELP -0.29 0.82 0.98 12 -1.4 154 166
AICDA -0.14 0.59 0.94 1 -1.1 89 90
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.035 0.043 0.12 4 -0.11 45 49
BUB1B 0.093 0.063 0.16 148 -10000 0 148
PLK1 0.046 0.035 0.11 65 -0.084 1 66
PLK1S1 0.023 0.019 0.057 59 -10000 0 59
KIF2A 0.038 0.037 0.27 4 -10000 0 4
regulation of mitotic centrosome separation 0.046 0.035 0.11 65 -10000 0 65
GOLGA2 0.034 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.1 0.062 0.17 202 -10000 0 202
WEE1 0.049 0.079 0.22 2 -0.31 18 20
cytokinesis 0.13 0.081 0.21 167 -0.39 1 168
PP2A-alpha B56 0.14 0.11 -10000 0 -0.47 5 5
AURKA 0.051 0.04 0.12 25 -0.16 2 27
PICH/PLK1 0.13 0.094 0.24 176 -10000 0 176
CENPE 0.083 0.066 0.16 188 -10000 0 188
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.039 0.037 0.27 4 -10000 0 4
PPP2CA 0.034 0.006 -10000 0 -10000 0 0
FZR1 0.034 0.009 -10000 0 -10000 0 0
TPX2 0.081 0.038 0.13 59 -10000 0 59
PAK1 0.043 0.044 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.006 -10000 0 -10000 0 0
CLSPN 0.044 0.053 0.14 22 -0.2 12 34
GORASP1 0.034 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 40 -10000 0 40
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.023 0.019 0.057 59 -10000 0 59
G2 phase of mitotic cell cycle 0.001 0.003 0.016 7 -10000 0 7
STAG2 0.034 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.021 0.093 -10000 0 -0.5 15 15
spindle elongation 0.046 0.035 0.11 65 -10000 0 65
ODF2 0.037 0.015 -10000 0 -10000 0 0
BUB1 0.12 0.12 -10000 0 -0.5 6 6
TPT1 0.014 0.059 0.13 1 -0.17 42 43
CDC25C 0.084 0.065 0.17 6 -0.21 10 16
CDC25B 0.048 0.041 -10000 0 -10000 0 0
SGOL1 0.035 0.043 0.11 45 -0.12 4 49
RHOA 0.033 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.091 0.067 0.24 26 -0.21 1 27
CDC14B -0.001 0.065 -10000 0 -0.4 13 13
CDC20 0.083 0.069 -10000 0 -10000 0 0
PLK1/PBIP1 0.073 0.054 0.14 181 -10000 0 181
mitosis -0.001 0.003 0.033 2 -10000 0 2
FBXO5 0.038 0.044 0.16 20 -10000 0 20
CDC2 0.005 0.004 0.016 31 -10000 0 31
NDC80 0.11 0.074 -10000 0 -10000 0 0
metaphase plate congression 0.027 0.057 -10000 0 -0.21 25 25
ERCC6L 0.12 0.094 0.24 168 -10000 0 168
NLP/gamma Tubulin 0.025 0.024 0.089 8 -0.094 2 10
microtubule cytoskeleton organization 0.014 0.059 0.13 1 -0.17 42 43
G2/M transition DNA damage checkpoint 0 0.003 0.013 13 -10000 0 13
PPP1R12A 0.035 0.006 -10000 0 -10000 0 0
interphase 0 0.003 0.013 13 -10000 0 13
PLK1/PRC1-2 0.17 0.098 0.26 238 -10000 0 238
GRASP65/GM130/RAB1/GTP/PLK1 0.083 0.033 -10000 0 -10000 0 0
RAB1A 0.034 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.04 0.032 0.092 85 -10000 0 85
mitotic prometaphase 0.001 0.005 0.021 26 -10000 0 26
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.045 -10000 0 -10000 0 0
microtubule-based process 0.12 0.065 0.17 306 -10000 0 306
Golgi organization 0.046 0.035 0.11 65 -10000 0 65
Cohesin/SA2 0.055 0.027 0.16 2 -10000 0 2
PPP1CB/MYPT1 0.051 0.01 -10000 0 -10000 0 0
KIF20A 0.13 0.071 -10000 0 -10000 0 0
APC/C/CDC20 0.094 0.066 0.18 151 -10000 0 151
PPP2R1A 0.034 0.005 -10000 0 -10000 0 0
chromosome segregation 0.072 0.054 0.13 181 -10000 0 181
PRC1 0.1 0.074 -10000 0 -10000 0 0
ECT2 0.072 0.073 0.2 93 -10000 0 93
C13orf34 0.039 0.031 0.092 66 -10000 0 66
NUDC 0.027 0.058 -10000 0 -0.21 25 25
regulation of attachment of spindle microtubules to kinetochore 0.093 0.063 0.16 148 -10000 0 148
spindle assembly 0.035 0.029 0.098 28 -10000 0 28
spindle stabilization 0.023 0.019 0.057 59 -10000 0 59
APC/C/HCDH1 0.022 0.059 -10000 0 -0.34 13 13
MKLP2/PLK1 0.12 0.065 0.17 306 -10000 0 306
CCNB1 0.088 0.07 -10000 0 -10000 0 0
PPP1CB 0.035 0.004 -10000 0 -10000 0 0
BTRC 0.037 0.021 -10000 0 -10000 0 0
ROCK2 0.04 0.049 0.21 1 -0.33 4 5
TUBG1 0.027 0.039 0.13 1 -0.16 14 15
G2/M transition of mitotic cell cycle 0.061 0.063 0.21 25 -0.21 1 26
MLF1IP 0.071 0.065 0.14 247 -10000 0 247
INCENP 0.047 0.04 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.033 0.007 -10000 0 -10000 0 0
GNAT1/GTP 0.024 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.058 0.041 -10000 0 -0.34 1 1
PDE6G/GNAT1/GTP 0.043 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.033 0.007 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.09 0.17 -10000 0 -0.29 206 206
mol:Na + -0.088 0.17 -10000 0 -0.28 216 216
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.05 0.1 -10000 0 -0.32 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.082 0.18 -10000 0 -0.29 216 216
CNGB1 0.03 0.012 -10000 0 -10000 0 0
RDH5 -0.43 0.23 -10000 0 -0.54 412 412
SAG 0.056 0.06 -10000 0 -0.54 1 1
mol:Ca2+ -0.12 0.15 0.36 6 -0.5 7 13
Na + (4 Units) -0.089 0.16 -10000 0 -0.28 145 145
RGS9 0.002 0.13 -10000 0 -0.54 27 27
GNB1/GNGT1 0.071 0.046 0.26 1 -10000 0 1
GNAT1/GDP 0.058 0.092 -10000 0 -0.27 28 28
GUCY2D 0.031 0.011 -10000 0 -10000 0 0
GNGT1 0.067 0.061 -10000 0 -10000 0 0
GUCY2F 0.033 0.038 -10000 0 -0.54 2 2
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.026 0.052 -10000 0 -0.3 11 11
mol:11-cis-retinal -0.43 0.23 -10000 0 -0.54 412 412
mol:cGMP 0.056 0.073 -10000 0 -0.34 13 13
GNB1 0.034 0.011 -10000 0 -10000 0 0
Rhodopsin -0.31 0.18 -10000 0 -0.4 407 407
SLC24A1 0.033 0.007 -10000 0 -10000 0 0
CNGA1 -0.21 0.29 -10000 0 -0.54 219 219
Metarhodopsin II 0.022 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.067 0.072 -10000 0 -0.34 12 12
RGS9BP 0.055 0.065 -10000 0 -0.54 2 2
Metarhodopsin II/Transducin 0.037 0.038 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.055 0.064 -10000 0 -0.34 12 12
PDE6A/B 0.038 0.071 -10000 0 -0.38 13 13
mol:Pi 0.049 0.1 -10000 0 -0.32 28 28
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.079 0.043 -10000 0 -10000 0 0
PDE6B 0.021 0.089 -10000 0 -0.54 12 12
PDE6A 0.034 0.009 -10000 0 -10000 0 0
PDE6G 0.034 0.014 -10000 0 -10000 0 0
RHO 0.034 0.005 -10000 0 -10000 0 0
PDE6 0.067 0.11 -10000 0 -0.3 25 25
GUCA1A 0.024 0.076 -10000 0 -0.54 9 9
GC2/GCAP Family 0.074 0.076 -10000 0 -0.36 13 13
GUCA1C 0.031 0.046 -10000 0 -0.54 3 3
GUCA1B 0.033 0.027 -10000 0 -0.54 1 1
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A -0.034 0.18 -10000 0 -0.54 60 60
LAT2 -0.029 0.13 -10000 0 -0.35 50 50
AP1 -0.19 0.23 -10000 0 -0.47 149 149
mol:PIP3 0.004 0.2 0.37 20 -0.47 33 53
IKBKB 0.021 0.14 0.3 39 -0.27 34 73
AKT1 -0.008 0.2 0.34 73 -0.46 30 103
IKBKG 0.004 0.13 0.28 19 -0.27 37 56
MS4A2 -0.056 0.21 -10000 0 -0.53 83 83
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
MAP3K1 0.01 0.15 0.34 14 -0.41 24 38
mol:Ca2+ 0.012 0.16 0.32 26 -0.35 31 57
LYN 0.032 0.018 -10000 0 -10000 0 0
CBLB -0.029 0.13 -10000 0 -0.36 45 45
SHC1 0.028 0.014 -10000 0 -10000 0 0
RasGAP/p62DOK -0.09 0.18 -10000 0 -0.31 204 204
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.013 0.2 0.35 62 -0.35 85 147
PTPN13 -0.038 0.19 -10000 0 -0.65 19 19
PTPN11 0.033 0.021 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.002 0.16 0.36 22 -0.35 28 50
SYK 0.041 0.027 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.04 0.15 -10000 0 -0.42 49 49
LAT -0.026 0.12 0.21 2 -0.35 46 48
PAK2 0.008 0.16 0.35 14 -0.43 26 40
NFATC2 -0.011 0.057 -10000 0 -0.69 1 1
HRAS 0.004 0.16 0.3 12 -0.45 28 40
GAB2 0.03 0.012 -10000 0 -10000 0 0
PLA2G1B 0.01 0.11 -10000 0 -0.83 7 7
Fc epsilon R1 -0.036 0.19 -10000 0 -0.41 95 95
Antigen/IgE/Fc epsilon R1 -0.031 0.18 -10000 0 -0.37 95 95
mol:GDP -0.023 0.15 0.28 2 -0.45 29 31
JUN -0.067 0.22 -10000 0 -0.54 89 89
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
FOS -0.36 0.27 -10000 0 -0.54 345 345
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.025 0.13 -10000 0 -0.35 54 54
CHUK 0.003 0.13 0.28 20 -0.27 38 58
KLRG1 -0.024 0.12 -10000 0 -0.31 47 47
VAV1 -0.029 0.13 0.21 2 -0.34 50 52
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.028 0.12 -10000 0 -0.34 50 50
negative regulation of mast cell degranulation -0.027 0.11 -10000 0 -0.29 47 47
BTK -0.023 0.15 -10000 0 -0.49 25 25
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.046 0.17 -10000 0 -0.36 93 93
GAB2/PI3K/SHP2 -0.062 0.15 -10000 0 -0.38 69 69
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.032 0.13 -10000 0 -0.35 53 53
RAF1 0.009 0.12 -10000 0 -0.9 7 7
Fc epsilon R1/FcgammaRIIB/SHIP -0.018 0.18 -10000 0 -0.36 95 95
FCER1G 0.032 0.021 -10000 0 -10000 0 0
FCER1A -0.045 0.19 -10000 0 -0.55 64 64
Antigen/IgE/Fc epsilon R1/Fyn -0.02 0.17 -10000 0 -0.35 93 93
MAPK3 0.011 0.11 -10000 0 -0.86 7 7
MAPK1 0.005 0.11 -10000 0 -0.82 7 7
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.018 0.2 -10000 0 -0.6 37 37
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
NF-kappa-B/RelA 0.012 0.082 0.19 11 -0.18 20 31
actin cytoskeleton reorganization -0.013 0.18 -10000 0 -0.66 14 14
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.013 0.17 -10000 0 -0.46 37 37
FER -0.028 0.13 -10000 0 -0.35 48 48
RELA 0.033 0.007 -10000 0 -10000 0 0
ITK -0.002 0.069 -10000 0 -0.34 14 14
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG1 -0.001 0.17 0.3 8 -0.45 29 37
cytokine secretion -0.006 0.047 -10000 0 -10000 0 0
SPHK1 -0.027 0.12 -10000 0 -0.34 46 46
PTK2 -0.016 0.18 -10000 0 -0.7 14 14
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.039 0.17 -10000 0 -0.43 52 52
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.03 0.22 0.36 16 -0.5 54 70
MAP2K2 0.005 0.11 -10000 0 -0.84 7 7
MAP2K1 0.005 0.11 -10000 0 -0.84 7 7
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.012 0.11 0.24 1 -0.36 23 24
MAP2K4 -0.08 0.32 -10000 0 -0.85 74 74
Fc epsilon R1/FcgammaRIIB -0.019 0.19 -10000 0 -0.38 95 95
mol:Choline -0.013 0.2 0.34 62 -0.34 85 147
SHC/Grb2/SOS1 0.01 0.14 -10000 0 -0.4 24 24
FYN 0.03 0.037 -10000 0 -0.54 2 2
DOK1 0.036 0.016 -10000 0 -10000 0 0
PXN -0.015 0.17 -10000 0 -0.66 12 12
HCLS1 -0.027 0.13 0.21 1 -0.35 46 47
PRKCB -0.004 0.16 0.31 21 -0.35 46 67
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
IGHE 0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.027 0.11 -10000 0 -0.3 47 47
LCP2 0.037 0.023 -10000 0 -10000 0 0
PLA2G4A -0.15 0.2 -10000 0 -0.34 221 221
RASA1 0.034 0.011 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.013 0.2 0.34 62 -0.34 85 147
IKK complex 0.023 0.12 0.28 37 -0.22 19 56
WIPF1 0.037 0.022 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.28 0.52 1 5 -1.3 55 60
IL23A -0.24 0.47 1.1 6 -1.1 42 48
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.46 0.76 2 -1 56 58
positive regulation of T cell mediated cytotoxicity -0.27 0.52 1.1 8 -1.1 57 65
ITGA3 -0.23 0.46 0.98 5 -1 47 52
IL17F -0.18 0.34 0.68 11 -0.67 64 75
IL12B 0.007 0.082 0.31 6 -10000 0 6
STAT1 (dimer) -0.25 0.49 0.91 5 -1.1 56 61
CD4 -0.24 0.46 0.99 4 -1 51 55
IL23 -0.24 0.45 0.95 5 -1 42 47
IL23R -0.019 0.21 0.81 3 -1.1 10 13
IL1B -0.25 0.48 1.1 6 -1.1 46 52
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.46 0.96 6 -1 50 56
TYK2 0.004 0.059 0.27 2 -10000 0 2
STAT4 0.028 0.069 -10000 0 -0.54 7 7
STAT3 0.034 0.007 -10000 0 -10000 0 0
IL18RAP -0.006 0.16 -10000 0 -0.54 42 42
IL12RB1 0.004 0.06 0.26 3 -10000 0 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.01 0.073 0.29 3 -10000 0 3
IL23R/JAK2 -0.023 0.22 0.69 3 -1 10 13
positive regulation of chronic inflammatory response -0.27 0.52 1.1 8 -1.1 57 65
natural killer cell activation 0.001 0.014 0.08 2 -0.061 6 8
JAK2 0.004 0.076 0.31 5 -10000 0 5
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
NFKB1 0.034 0.009 -10000 0 -10000 0 0
RELA 0.033 0.01 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.22 0.44 0.94 5 -0.99 42 47
ALOX12B -0.24 0.46 0.95 5 -1 52 57
CXCL1 -0.64 0.73 1.1 6 -1.2 291 297
T cell proliferation -0.27 0.52 1.1 8 -1.1 57 65
NFKBIA 0.033 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.3 0.65 12 -0.54 41 53
PI3K -0.28 0.47 0.82 1 -1 70 71
IFNG 0.022 0.074 0.18 63 -0.12 5 68
STAT3 (dimer) -0.26 0.45 0.8 1 -0.99 69 70
IL18R1 0.04 0.03 0.2 2 -0.54 1 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.33 0.78 10 -0.76 26 36
IL18/IL18R 0.065 0.14 0.28 27 -0.34 42 69
macrophage activation -0.013 0.028 0.077 19 -10000 0 19
TNF -0.24 0.48 1.1 5 -1.1 46 51
STAT3/STAT4 -0.26 0.47 0.78 3 -1.1 59 62
STAT4 (dimer) -0.27 0.49 0.86 6 -1.1 61 67
IL18 0.048 0.046 -10000 0 -10000 0 0
IL19 -0.2 0.46 0.96 6 -1 38 44
STAT5A (dimer) -0.27 0.48 0.88 4 -1.1 57 61
STAT1 0.059 0.055 -10000 0 -10000 0 0
SOCS3 0.019 0.087 -10000 0 -0.54 12 12
CXCL9 -0.22 0.5 1.1 7 -1.1 52 59
MPO -0.23 0.46 1.1 3 -1 43 46
positive regulation of humoral immune response -0.27 0.52 1.1 8 -1.1 57 65
IL23/IL23R/JAK2/TYK2 -0.28 0.53 1.1 8 -1.2 57 65
IL6 -0.79 0.67 0.93 6 -1.2 360 366
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
IL2 0.049 0.039 0.25 1 -0.52 1 2
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.014 0.08 2 -0.061 6 8
CD3E -0.24 0.46 0.98 5 -1 52 57
keratinocyte proliferation -0.27 0.52 1.1 8 -1.1 57 65
NOS2 -0.24 0.46 0.88 8 -0.98 58 66
Aurora B 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
Condensin I complex 0.05 0.078 0.25 33 -10000 0 33
STMN1 0.054 0.083 0.28 45 -10000 0 45
Aurora B/RasGAP/Survivin 0.11 0.077 0.26 3 -10000 0 3
Chromosomal passenger complex/Cul3 protein complex -0.072 0.13 0.23 9 -0.32 29 38
BIRC5 0.12 0.076 0.19 10 -10000 0 10
DES -0.011 0.13 -10000 0 -0.56 24 24
Aurora C/Aurora B/INCENP 0.076 0.052 -10000 0 -10000 0 0
Aurora B/TACC1 0.026 0.088 -10000 0 -0.31 26 26
Aurora B/PP2A 0.058 0.042 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.02 0.022 0.14 3 -10000 0 3
mitotic metaphase/anaphase transition -0.003 0.004 -10000 0 -10000 0 0
NDC80 0.1 0.1 0.28 86 -10000 0 86
Cul3 protein complex -0.23 0.18 -10000 0 -0.34 366 366
KIF2C 0.14 0.1 0.23 236 -10000 0 236
PEBP1 0.039 0.026 -10000 0 -0.54 1 1
KIF20A 0.12 0.07 0.19 38 -10000 0 38
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.057 0.041 -10000 0 -10000 0 0
SEPT1 0.035 0.023 -10000 0 -10000 0 0
SMC2 0.04 0.03 -10000 0 -10000 0 0
SMC4 0.046 0.042 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.063 0.16 0.31 11 -0.41 34 45
PSMA3 0.034 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.005 -10000 0 -10000 0 0
H3F3B 0.031 0.037 -10000 0 -10000 0 0
AURKB 0.051 0.054 0.2 1 -10000 0 1
AURKC 0.036 0.019 -10000 0 -10000 0 0
CDCA8 0.11 0.075 -10000 0 -10000 0 0
cytokinesis 0.18 0.15 0.35 202 -10000 0 202
Aurora B/Septin1 0.18 0.15 0.38 133 -10000 0 133
AURKA 0.078 0.068 -10000 0 -10000 0 0
INCENP 0.053 0.041 -10000 0 -10000 0 0
KLHL13 -0.38 0.26 -10000 0 -0.54 371 371
BUB1 0.15 0.054 0.21 2 -10000 0 2
hSgo1/Aurora B/Survivin 0.13 0.099 0.27 130 -10000 0 130
EVI5 0.036 0.026 -10000 0 -0.53 1 1
RhoA/GTP 0.22 0.14 0.35 211 -10000 0 211
SGOL1 0.073 0.065 -10000 0 -10000 0 0
CENPA 0.14 0.12 0.28 188 -10000 0 188
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.058 0.042 -10000 0 -10000 0 0
NCAPD2 0.035 0.021 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.059 0.042 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
NCAPH 0.079 0.068 -10000 0 -10000 0 0
NPM1 0.028 0.1 -10000 0 -0.75 3 3
RASA1 0.034 0.011 -10000 0 -10000 0 0
KLHL9 0.032 0.009 -10000 0 -10000 0 0
mitotic prometaphase 0.005 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.042 -10000 0 -10000 0 0
PPP1CC 0.034 0.004 -10000 0 -10000 0 0
Centraspindlin 0.24 0.15 0.37 245 -10000 0 245
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
NSUN2 0.028 0.093 0.26 1 -0.33 14 15
MYLK -0.071 0.17 -10000 0 -0.34 139 139
KIF23 0.12 0.075 -10000 0 -10000 0 0
VIM -0.006 0.13 -10000 0 -0.39 47 47
RACGAP1 0.081 0.066 0.19 57 -10000 0 57
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.025 0.11 -10000 0 -0.44 15 15
Chromosomal passenger complex 0.17 0.13 0.28 248 -10000 0 248
Chromosomal passenger complex/EVI5 0.15 0.11 0.34 47 -10000 0 47
TACC1 0.001 0.12 -10000 0 -0.54 24 24
PPP2R5D 0.034 0.006 -10000 0 -10000 0 0
CUL3 0.032 0.036 -10000 0 -0.54 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.012 0.094 0.36 7 -0.32 7 14
TBX21 -0.13 0.37 0.71 6 -1.2 41 47
B2M 0.038 0.013 -10000 0 -10000 0 0
TYK2 0.018 0.036 -10000 0 -10000 0 0
IL12RB1 0.018 0.035 -10000 0 -10000 0 0
GADD45B -0.069 0.28 0.61 7 -0.75 46 53
IL12RB2 0.037 0.072 0.26 6 -0.55 1 7
GADD45G -0.059 0.26 0.69 3 -0.74 34 37
natural killer cell activation -0.008 0.022 0.089 9 -0.042 47 56
RELB 0.037 0.02 -10000 0 -10000 0 0
RELA 0.033 0.007 -10000 0 -10000 0 0
IL18 0.045 0.046 0.22 8 -10000 0 8
IL2RA 0.041 0.035 -10000 0 -10000 0 0
IFNG 0.063 0.066 -10000 0 -0.54 1 1
STAT3 (dimer) -0.061 0.24 0.56 10 -0.58 49 59
HLA-DRB5 -0.016 0.012 -10000 0 -0.026 274 274
FASLG -0.06 0.26 0.72 7 -0.71 27 34
NF kappa B2 p52/RelB -0.08 0.25 0.53 6 -0.59 62 68
CD4 -0.006 0.031 -10000 0 -10000 0 0
SOCS1 0.032 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.014 0.015 0.029 20 -0.027 231 251
CD3D 0.003 0.05 -10000 0 -10000 0 0
CD3E -0.001 0.033 -10000 0 -10000 0 0
CD3G 0.004 0.081 0.2 12 -0.55 5 17
IL12Rbeta2/JAK2 0.028 0.075 0.3 7 -0.41 1 8
CCL3 -0.085 0.25 0.66 3 -0.63 47 50
CCL4 -0.085 0.25 0.7 2 -0.78 20 22
HLA-A 0.005 0.009 0.027 70 -10000 0 70
IL18/IL18R 0.059 0.14 0.37 16 -0.36 42 58
NOS2 -0.085 0.26 0.59 9 -0.58 69 78
IL12/IL12R/TYK2/JAK2/SPHK2 0.01 0.098 0.35 8 -0.33 7 15
IL1R1 -0.17 0.43 0.7 2 -1.2 63 65
IL4 0.038 0.03 -10000 0 -10000 0 0
JAK2 0.017 0.037 0.25 1 -10000 0 1
EntrezGene:6957 -0.011 0.013 0.027 20 -0.023 218 238
TCR/CD3/MHC I/CD8 -0.006 0.14 0.33 21 -0.4 21 42
RAB7A -0.043 0.24 0.67 2 -0.71 24 26
lysosomal transport -0.039 0.23 0.63 4 -0.68 24 28
FOS -0.83 0.6 0.56 1 -1.2 367 368
STAT4 (dimer) -0.032 0.27 0.61 10 -0.65 46 56
STAT5A (dimer) -0.06 0.26 0.57 8 -0.59 59 67
GZMA -0.091 0.24 0.56 8 -0.57 69 77
GZMB -0.09 0.26 0.69 7 -0.65 47 54
HLX 0.026 0.038 -10000 0 -0.54 2 2
LCK -0.084 0.27 0.67 10 -0.62 63 73
TCR/CD3/MHC II/CD4 -0.12 0.16 0.24 9 -0.36 89 98
IL2/IL2R 0.088 0.056 0.38 4 -0.32 1 5
MAPK14 -0.057 0.28 0.63 8 -0.73 45 53
CCR5 -0.066 0.28 0.7 10 -0.73 42 52
IL1B 0.015 0.07 0.26 1 -0.55 5 6
STAT6 -0.038 0.18 0.39 7 -0.65 27 34
STAT4 0.028 0.069 -10000 0 -0.54 7 7
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.059 0.055 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
NFKB2 0.035 0.012 -10000 0 -10000 0 0
IL12B 0.017 0.046 0.25 2 -10000 0 2
CD8A 0.005 0.009 0.027 70 -10000 0 70
CD8B 0.043 0.027 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.012 0.094 0.31 7 -0.36 7 14
IL2RB 0.035 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.026 0.26 0.6 11 -0.61 44 55
IL2RG 0.044 0.035 -10000 0 -10000 0 0
IL12 0.008 0.088 0.29 3 -0.41 11 14
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
CD247 -0.003 0.11 0.21 8 -0.55 15 23
IL2 0.033 0.027 -10000 0 -0.54 1 1
SPHK2 0.034 0.005 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.093 0.24 1 -0.56 11 12
IL12/IL12R/TYK2/JAK2 -0.099 0.27 0.66 9 -0.64 66 75
MAP2K3 -0.069 0.29 0.62 8 -0.74 51 59
RIPK2 0.029 0.022 -10000 0 -10000 0 0
MAP2K6 -0.06 0.27 0.62 8 -0.71 45 53
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.018 0.014 -10000 0 -0.029 298 298
IL18RAP -0.009 0.16 0.22 2 -0.55 42 44
IL12Rbeta1/TYK2 0.03 0.047 -10000 0 -10000 0 0
EOMES 0.04 0.1 -10000 0 -0.62 3 3
STAT1 (dimer) -0.011 0.26 0.67 15 -0.6 38 53
T cell proliferation -0.03 0.22 0.52 11 -0.54 43 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.038 0.031 0.2 2 -0.55 1 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.02 0.23 0.52 2 -0.61 40 42
ATF2 -0.054 0.26 0.59 8 -0.68 45 53
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.18 -10000 0 -0.35 322 322
fibroblast growth factor receptor signaling pathway -0.22 0.18 -10000 0 -0.35 322 322
LAMA1 0.033 0.01 -10000 0 -10000 0 0
PRNP 0.017 0.094 -10000 0 -0.54 14 14
GPC1/SLIT2 -0.009 0.15 -10000 0 -0.4 63 63
SMAD2 -0.001 0.084 0.28 1 -0.31 32 33
GPC1/PrPc/Cu2+ 0.033 0.064 -10000 0 -0.34 14 14
GPC1/Laminin alpha1 0.048 0.017 -10000 0 -10000 0 0
TDGF1 0.033 0.007 -10000 0 -10000 0 0
CRIPTO/GPC1 0.049 0.015 -10000 0 -10000 0 0
APP/GPC1 0.045 0.048 -10000 0 -0.4 5 5
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.019 0.019 -10000 0 -0.34 1 1
FLT1 0.032 0.013 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.04 0.1 -10000 0 -0.34 34 34
SERPINC1 0.032 0.024 0.18 10 -10000 0 10
FYN 0.018 0.025 -10000 0 -0.34 2 2
FGR 0.02 0.01 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.025 0.086 0.29 2 -0.38 9 11
SLIT2 -0.038 0.19 -10000 0 -0.54 63 63
GPC1/NRG -0.001 0.12 -10000 0 -0.4 40 40
NRG1 -0.017 0.15 -10000 0 -0.54 40 40
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.07 0.039 -10000 0 -10000 0 0
LYN 0.018 0.013 -10000 0 -10000 0 0
mol:Spermine 0.01 0.01 -10000 0 -10000 0 0
cell growth -0.22 0.18 -10000 0 -0.35 322 322
BMP signaling pathway -0.034 0.013 -10000 0 -10000 0 0
SRC 0.019 0.009 -10000 0 -10000 0 0
TGFBR1 0.036 0.016 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.031 0.2 -10000 0 -0.54 64 64
GPC1 0.034 0.013 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.036 0.016 -10000 0 -10000 0 0
VEGFA 0.05 0.047 -10000 0 -10000 0 0
BLK 0.025 0.032 -10000 0 -10000 0 0
HCK 0.022 0.018 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
FGFR1 0.018 0.076 -10000 0 -0.54 9 9
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
TGFBR2 -0.004 0.14 -10000 0 -0.54 34 34
cell death 0.045 0.048 -10000 0 -0.4 5 5
ATIII/GPC1 0.044 0.026 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.004 0.15 -10000 0 -0.37 74 74
LCK 0.031 0.033 -10000 0 -10000 0 0
neuron differentiation -0.001 0.12 -10000 0 -0.4 40 40
PrPc/Cu2+ 0.013 0.069 -10000 0 -0.4 14 14
APP 0.029 0.06 -10000 0 -0.54 5 5
TGFBR2 (dimer) -0.004 0.14 -10000 0 -0.54 34 34
p75(NTR)-mediated 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
Sortilin/TRAF6 0.049 0.012 -10000 0 -10000 0 0
Necdin/E2F1 -0.045 0.18 -10000 0 -0.38 113 113
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.002 0.15 -10000 0 -0.31 89 89
NGF (dimer)/p75(NTR)/BEX1 -0.006 0.14 -10000 0 -0.33 76 76
NT-4/5 (dimer)/p75(NTR) -0.041 0.15 -10000 0 -0.38 80 80
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 -0.033 0.16 0.33 3 -0.32 97 100
IKBKG 0.034 0.004 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
MGDIs/NGR/p75(NTR)/LINGO1 0.013 0.15 -10000 0 -0.33 72 72
FURIN 0.037 0.023 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.001 0.15 -10000 0 -0.34 75 75
LINGO1 0.056 0.053 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.034 0.029 -10000 0 -10000 0 0
proBDNF (dimer) 0.038 0.047 -10000 0 -0.54 2 2
NTRK1 0.031 0.022 -10000 0 -10000 0 0
RTN4R 0.04 0.035 -10000 0 -10000 0 0
neuron apoptosis -0.013 0.16 0.37 4 -0.47 15 19
IRAK1 0.036 0.015 -10000 0 -10000 0 0
SHC1 -0.026 0.11 -10000 0 -0.34 54 54
ARHGDIA 0.033 0.01 -10000 0 -10000 0 0
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
Gamma Secretase 0.076 0.054 -10000 0 -0.3 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.007 0.14 -10000 0 -0.32 83 83
MAGEH1 0.019 0.094 -10000 0 -0.54 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.079 0.2 -10000 0 -0.37 153 153
Mammalian IAPs/DIABLO 0.046 0.078 -10000 0 -0.31 17 17
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.044 0.036 -10000 0 -10000 0 0
APP 0.029 0.06 -10000 0 -0.54 5 5
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.01 0.12 -10000 0 -0.29 74 74
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.037 0.11 0.21 29 -0.27 74 103
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.016 0.095 -10000 0 -0.25 58 58
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.018 0.14 -10000 0 -0.34 76 76
NCSTN 0.028 0.014 -10000 0 -10000 0 0
mol:GTP -0.018 0.15 -10000 0 -0.35 79 79
PSENEN 0.035 0.015 -10000 0 -10000 0 0
mol:ceramide -0.021 0.13 -10000 0 -0.31 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.078 -10000 0 -0.21 57 57
p75(NTR)/beta APP -0.025 0.16 -10000 0 -0.41 76 76
BEX1 0.054 0.05 -10000 0 -10000 0 0
mol:GDP -0.053 0.12 -10000 0 -0.34 76 76
NGF (dimer) 0.004 0.13 -10000 0 -0.31 65 65
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.028 0.15 -10000 0 -0.31 70 70
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RAC1/GTP -0.014 0.12 -10000 0 -0.29 75 75
MYD88 0.034 0.011 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.018 0.15 -10000 0 -0.35 79 79
RHOB 0.033 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.058 0.035 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.25 -10000 0 -0.54 134 134
TP53 -0.027 0.13 0.35 8 -0.29 71 79
PRDM4 -0.018 0.13 -10000 0 -0.31 74 74
BDNF (dimer) 0.056 0.17 -10000 0 -0.31 70 70
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
SORT1 0.034 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.14 -10000 0 -0.31 89 89
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0 0.13 -10000 0 -0.31 74 74
RHOC 0.034 0.005 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.028 0.14 0.3 6 -0.33 72 78
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 -0.021 0.13 -10000 0 -0.31 74 74
APH1B 0.033 0.027 -10000 0 -0.54 1 1
APH1A 0.032 0.028 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.017 0.14 -10000 0 -0.34 74 74
PSEN1 0.033 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.13 0.24 -10000 0 -0.44 173 173
MAPK8 -0.024 0.14 0.29 8 -0.32 68 76
MAPK9 -0.024 0.13 0.28 6 -0.32 68 74
APAF1 0.034 0.003 -10000 0 -10000 0 0
NTF3 -0.12 0.26 -10000 0 -0.54 134 134
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.1 0.24 -10000 0 -0.54 118 118
RAC1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.009 0.14 -10000 0 -0.3 73 73
p75 CTF/Sortilin/TRAF6/NRIF 0.08 0.027 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.018 0.15 -10000 0 -0.35 79 79
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.027 0.14 -10000 0 -0.3 74 74
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.017 0.14 -10000 0 -0.31 75 75
PRKACB 0.035 0.083 -10000 0 -0.54 8 8
proBDNF (dimer)/p75 ECD 0.052 0.037 -10000 0 -0.4 2 2
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.017 0.11 -10000 0 -0.54 17 17
BIRC2 0.031 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.16 -10000 0 -0.39 100 100
BAD -0.025 0.15 0.38 9 -0.33 68 77
RIPK2 0.029 0.022 -10000 0 -10000 0 0
NGFR -0.055 0.2 -10000 0 -0.54 76 76
CYCS -0.009 0.13 0.26 7 -0.29 72 79
ADAM17 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.003 0.12 -10000 0 -0.31 62 62
BCL2L11 -0.024 0.15 0.39 9 -0.33 68 77
BDNF (dimer)/p75(NTR) -0.021 0.16 -10000 0 -0.39 77 77
PI3K -0.03 0.16 -10000 0 -0.34 100 100
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0 0.13 -10000 0 -0.31 74 74
NDNL2 0.033 0.008 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.041 0.15 -10000 0 -0.38 80 80
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.006 0.13 -10000 0 -0.3 74 74
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.027 0.13 -10000 0 -0.33 74 74
SQSTM1 0.034 0.009 -10000 0 -10000 0 0
NGFRAP1 0.01 0.12 -10000 0 -0.54 22 22
CASP3 -0.022 0.14 0.37 9 -0.31 70 79
E2F1 0.051 0.048 -10000 0 -10000 0 0
CASP9 0.033 0.008 -10000 0 -10000 0 0
IKK complex 0.03 0.086 -10000 0 -0.3 1 1
NGF (dimer)/TRKA 0.023 0.016 -10000 0 -10000 0 0
MMP7 -0.041 0.19 -10000 0 -0.54 64 64
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.012 0.13 -10000 0 -0.3 73 73
MMP3 0.094 0.099 -10000 0 -0.54 5 5
APAF-1/Caspase 9 -0.033 0.1 -10000 0 -0.26 64 64
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
PTK2 -0.053 0.18 -10000 0 -0.44 70 70
positive regulation of JNK cascade -0.026 0.15 -10000 0 -0.32 89 89
CDC42/GDP -0.02 0.21 0.44 1 -0.42 93 94
Rac1/GDP -0.02 0.2 -10000 0 -0.42 90 90
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
CDC42/GTP -0.025 0.19 -10000 0 -0.39 88 88
nectin-3/I-afadin -0.024 0.17 -10000 0 -0.39 85 85
RAPGEF1 -0.044 0.2 0.47 1 -0.45 85 86
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.057 0.22 -10000 0 -0.51 86 86
PDGFB-D/PDGFRB 0.034 0.005 -10000 0 -10000 0 0
TLN1 -0.039 0.12 0.2 4 -0.48 22 26
Rap1/GTP -0.03 0.15 -10000 0 -0.33 80 80
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.042 -10000 0 -0.31 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.39 85 85
PVR 0.035 0.015 -10000 0 -10000 0 0
Necl-5(dimer) 0.035 0.015 -10000 0 -10000 0 0
mol:GDP -0.047 0.24 0.45 1 -0.51 93 94
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K -0.005 0.18 -10000 0 -0.34 106 106
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
positive regulation of lamellipodium assembly -0.021 0.16 -10000 0 -0.33 90 90
PVRL1 0.031 0.014 -10000 0 -10000 0 0
PVRL3 -0.052 0.21 -10000 0 -0.54 77 77
PVRL2 0.039 0.027 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
CDH1 0.007 0.12 -10000 0 -0.54 22 22
CLDN1 -0.003 0.16 -10000 0 -0.54 41 41
JAM-A/CLDN1 -0.007 0.17 -10000 0 -0.35 83 83
SRC -0.076 0.24 -10000 0 -0.56 90 90
ITGB3 0.035 0.019 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
FARP2 -0.047 0.24 0.45 1 -0.52 89 90
RAC1 0.034 0.005 -10000 0 -10000 0 0
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.001 0.15 -10000 0 -0.35 79 79
nectin-1/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
nectin-2/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
RAC1/GTP/IQGAP1/filamentous actin 0.044 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.005 0.15 -10000 0 -0.35 79 79
CDC42/GTP/IQGAP1/filamentous actin 0.043 0.014 -10000 0 -10000 0 0
F11R 0.028 0.017 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.026 0.15 -10000 0 -0.32 89 89
alphaV/beta3 Integrin/Talin -0.006 0.13 0.3 1 -0.48 19 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
nectin-2(dimer)/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
PIP5K1C -0.037 0.13 -10000 0 -0.5 23 23
VAV2 -0.044 0.24 0.45 1 -0.52 86 87
RAP1/GDP -0.015 0.19 0.42 1 -0.39 84 85
ITGAV 0.034 0.027 -10000 0 -0.54 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.001 0.15 -10000 0 -0.33 83 83
nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.39 85 85
Rac1/GTP -0.023 0.19 -10000 0 -0.4 87 87
PTPRM -0.035 0.14 -10000 0 -0.3 83 83
E-cadherin/beta catenin/alpha catenin 0.053 0.1 -10000 0 -0.29 26 26
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.033 0.008 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.065 0.14 0.31 59 -10000 0 59
GNAI2 0.033 0.01 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.012 -10000 0 -10000 0 0
RhoA/GTP -0.066 0.14 -10000 0 -0.32 59 59
negative regulation of cAMP metabolic process -0.079 0.14 -10000 0 -0.25 184 184
GNAZ 0.026 0.062 -10000 0 -0.54 6 6
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.079 0.14 -10000 0 -0.25 184 184
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.16 0.2 -10000 0 -0.32 278 278
TC10/GTP -0.13 0.16 -10000 0 -0.28 271 271
Insulin Receptor/Insulin/IRS1/Shp2 0.04 0.14 -10000 0 -0.32 59 59
HRAS 0.034 0.013 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.001 0.19 -10000 0 -0.54 51 51
FOXO3 -0.032 0.16 -10000 0 -0.6 35 35
AKT1 -0.045 0.16 0.32 8 -0.45 22 30
INSR 0.039 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.091 0.072 0.36 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.03 0.051 -10000 0 -0.54 4 4
SORBS1 -0.28 0.29 -10000 0 -0.54 277 277
CRK 0.031 0.01 -10000 0 -10000 0 0
PTPN1 0.02 0.053 0.28 19 -10000 0 19
CAV1 -0.23 0.18 -10000 0 -0.33 366 366
CBL/APS/CAP/Crk-II/C3G -0.13 0.18 -10000 0 -0.3 275 275
Insulin Receptor/Insulin/IRS1/NCK2 0.042 0.13 -10000 0 -0.32 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.15 -10000 0 -0.3 93 93
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.02 0.095 0.35 1 -0.4 6 7
RPS6KB1 -0.039 0.14 0.31 8 -0.4 21 29
PARD6A 0.031 0.019 -10000 0 -10000 0 0
CBL 0.031 0.011 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.055 -10000 0 -0.56 4 4
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.15 -10000 0 -0.42 20 20
HRAS/GTP -0.009 0.078 -10000 0 -0.26 39 39
Insulin Receptor 0.039 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.039 0.12 -10000 0 -0.3 41 41
PRKCI 0.012 0.087 -10000 0 -0.51 8 8
Insulin Receptor/Insulin/GRB14/PDK1 -0.044 0.16 -10000 0 -0.32 104 104
SHC1 0.028 0.014 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.058 0.052 -10000 0 -0.47 4 4
PI3K 0.008 0.15 -10000 0 -0.3 92 92
NCK2 0.035 0.007 -10000 0 -10000 0 0
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
mol:H2O2 0.001 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
AKT2 -0.047 0.16 0.32 7 -0.44 22 29
PRKCZ -0.006 0.082 -10000 0 -0.42 14 14
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.01 0.091 -10000 0 -0.28 46 46
F2RL2 0.046 0.065 -10000 0 -0.54 3 3
TRIP10 0.033 0.026 -10000 0 -0.54 1 1
Insulin Receptor/Insulin/Shc 0.056 0.035 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.044 0.026 -10000 0 -0.34 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.078 0.055 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
RASA1 0.034 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.14 0.18 -10000 0 -0.31 277 277
TC10/GDP 0.024 0.019 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.07 0.056 -10000 0 -0.32 4 4
INPP5D -0.037 0.095 -10000 0 -0.3 59 59
SOS1 0.034 0.004 -10000 0 -10000 0 0
SGK1 -0.009 0.012 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
IRS1 -0.034 0.18 -10000 0 -0.54 60 60
p62DOK/RasGAP 0.059 0.053 -10000 0 -0.48 4 4
INS 0.039 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.036 0.095 -10000 0 -0.29 59 59
GRB2 0.034 0.018 -10000 0 -10000 0 0
EIF4EBP1 -0.043 0.14 0.31 5 -0.4 21 26
PTPRA 0.038 0.013 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.044 0.026 -10000 0 -0.34 2 2
PDPK1 0.032 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0 0.088 -10000 0 -0.33 5 5
Insulin Receptor/Insulin/IRS1 0.023 0.13 -10000 0 -0.32 59 59
Insulin Receptor/Insulin/IRS3 0.057 0.024 -10000 0 -10000 0 0
Par3/Par6 0.073 0.058 -10000 0 -0.29 5 5
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.044 0.24 0.59 2 -0.56 74 76
IHH 0.021 0.074 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 -0.068 0.15 -10000 0 -0.31 128 128
LRPAP1 0.033 0.008 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.068 0.15 0.31 128 -10000 0 128
SMO/beta Arrestin2 -0.001 0.18 0.41 2 -0.48 28 30
SMO -0.016 0.18 0.44 2 -0.5 29 31
AKT1 -0.02 0.19 0.31 1 -0.59 37 38
ARRB2 0.031 0.01 -10000 0 -10000 0 0
BOC -0.091 0.24 -10000 0 -0.54 111 111
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
heart looping -0.015 0.18 0.44 2 -0.49 29 31
STIL 0.041 0.15 0.39 16 -0.34 7 23
DHH N/PTCH2 0.05 0.01 -10000 0 -10000 0 0
DHH N/PTCH1 0.006 0.16 0.38 2 -0.44 23 25
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DHH 0.034 0.004 -10000 0 -10000 0 0
PTHLH -0.11 0.39 0.66 2 -0.9 94 96
determination of left/right symmetry -0.015 0.18 0.44 2 -0.49 29 31
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
skeletal system development -0.11 0.39 0.66 2 -0.89 94 96
IHH N/Hhip 0.038 0.052 -10000 0 -10000 0 0
DHH N/Hhip 0.05 0.011 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.015 0.18 0.44 2 -0.49 29 31
pancreas development 0.034 0.011 -10000 0 -10000 0 0
HHAT 0.024 0.059 -10000 0 -0.54 5 5
PI3K 0.005 0.13 -10000 0 -0.4 44 44
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.14 0.27 -10000 0 -0.54 158 158
somite specification -0.015 0.18 0.44 2 -0.49 29 31
SHH Np/Cholesterol/PTCH1 -0.009 0.12 -10000 0 -0.38 8 8
SHH Np/Cholesterol/PTCH2 0.024 0.037 -10000 0 -0.31 5 5
SHH Np/Cholesterol/Megalin -0.055 0.14 -10000 0 -0.32 110 110
SHH 0.011 0.043 -10000 0 -0.4 5 5
catabolic process -0.009 0.17 0.46 2 -0.36 82 84
SMO/Vitamin D3 0.01 0.17 0.41 15 -0.46 12 27
SHH Np/Cholesterol/Hhip 0.025 0.038 -10000 0 -0.31 5 5
LRP2 -0.12 0.25 -10000 0 -0.54 136 136
receptor-mediated endocytosis -0.061 0.2 0.35 8 -0.51 37 45
SHH Np/Cholesterol/BOC -0.038 0.13 -10000 0 -0.31 87 87
SHH Np/Cholesterol/CDO 0.02 0.049 -10000 0 -0.35 7 7
mesenchymal cell differentiation -0.025 0.038 0.31 5 -10000 0 5
mol:Vitamin D3 0.027 0.16 0.41 16 -0.38 8 24
IHH N/PTCH2 0.038 0.051 -10000 0 -10000 0 0
CDON 0.027 0.045 -10000 0 -0.54 3 3
IHH N/PTCH1 0 0.18 0.46 2 -0.36 84 86
Megalin/LRPAP1 -0.071 0.2 -10000 0 -0.4 137 137
PTCH2 0.034 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.014 0.034 -10000 0 -0.31 5 5
PTCH1 -0.009 0.17 0.46 2 -0.36 82 84
HHIP 0.034 0.011 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.035 0.033 0.19 11 -10000 0 11
CDKN2C -0.022 0.15 -10000 0 -0.52 41 41
CDKN2A 0.058 0.055 -10000 0 -10000 0 0
CCND2 -0.008 0.06 0.17 28 -0.19 16 44
RB1 0.005 0.071 0.21 13 -0.2 31 44
CDK4 -0.004 0.073 0.21 36 -0.21 13 49
CDK6 -0.005 0.072 0.21 33 -0.22 16 49
G1/S progression 0.003 0.086 0.21 53 -0.22 14 67
S1P4 pathway

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:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.03 0.012 -9999 0 -10000 0 0
CDC42/GTP -0.066 0.14 -9999 0 -0.32 56 56
PLCG1 -0.072 0.13 -9999 0 -0.24 168 168
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.033 0.01 -9999 0 -10000 0 0
GNAI3 0.034 0.005 -9999 0 -10000 0 0
G12/G13 0.045 0.017 -9999 0 -10000 0 0
cell migration -0.066 0.14 -9999 0 -0.32 56 56
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.068 0.13 -9999 0 -0.34 46 46
MAPK1 -0.075 0.13 -9999 0 -0.33 54 54
S1P/S1P5/Gi -0.079 0.14 -9999 0 -0.25 184 184
GNAI1 -0.17 0.28 -9999 0 -0.54 183 183
CDC42/GDP 0.024 0.006 -9999 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -9999 0 -10000 0 0
RHOA 0.034 0.051 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.079 0.14 -9999 0 -0.25 184 184
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.026 0.062 -9999 0 -0.54 6 6
S1P/S1P4/G12/G13 0.039 0.015 -9999 0 -10000 0 0
GNA12 0.034 0.005 -9999 0 -10000 0 0
GNA13 0.031 0.01 -9999 0 -10000 0 0
CDC42 0.033 0.008 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.023 0.12 -10000 0 -0.33 42 42
adherens junction organization -0.024 0.13 -10000 0 -0.42 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 0.32 2 -0.38 99 101
FMN1 -0.024 0.12 -10000 0 -0.38 25 25
mol:IP3 -0.023 0.099 -10000 0 -0.28 44 44
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.022 0.12 -10000 0 -0.4 25 25
CTNNB1 0.03 0.051 -10000 0 -0.54 4 4
AKT1 -0.019 0.11 -10000 0 -0.35 16 16
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.027 0.18 -10000 0 -0.53 38 38
CTNND1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.02 0.11 0.26 1 -0.4 20 21
VASP -0.019 0.12 0.24 1 -0.39 22 23
ZYX -0.025 0.12 -10000 0 -0.4 23 23
JUB -0.024 0.12 -10000 0 -0.38 25 25
EGFR(dimer) -0.16 0.2 -10000 0 -0.42 110 110
E-cadherin/beta catenin-gamma catenin 0.036 0.09 -10000 0 -0.32 25 25
mol:PI-3-4-5-P3 -0.006 0.12 -10000 0 -0.35 21 21
PIK3CA 0.032 0.01 -10000 0 -10000 0 0
PI3K -0.006 0.13 -10000 0 -0.35 21 21
FYN -0.023 0.11 0.24 1 -0.38 22 23
mol:Ca2+ -0.022 0.098 -10000 0 -0.28 44 44
JUP 0.033 0.009 -10000 0 -10000 0 0
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
mol:DAG -0.023 0.099 -10000 0 -0.28 44 44
CDH1 0.007 0.12 -10000 0 -0.54 22 22
RhoA/GDP -0.14 0.18 0.32 2 -0.38 97 99
establishment of polarity of embryonic epithelium -0.019 0.12 0.24 1 -0.39 22 23
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
CASR -0.021 0.098 0.23 3 -0.31 16 19
RhoA/GTP -0.005 0.1 -10000 0 -0.3 16 16
AKT2 -0.02 0.11 -10000 0 -0.36 16 16
actin cable formation -0.019 0.12 0.26 2 -0.38 22 24
apoptosis 0.017 0.12 0.31 49 -0.26 4 53
CTNNA1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP -0.16 0.18 -10000 0 -0.4 99 99
PIP5K1A -0.021 0.11 -10000 0 -0.41 20 20
PLCG1 -0.024 0.1 -10000 0 -0.29 44 44
Rac1/GTP -0.14 0.19 -10000 0 -0.4 104 104
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.037 0.085 -10000 0 -0.41 14 14
HDAC1 0.023 0.028 -10000 0 -10000 0 0
AES 0.033 0.008 -10000 0 -10000 0 0
FBXW11 0.034 0.006 -10000 0 -10000 0 0
DTX1 0.031 0.044 -10000 0 -0.54 3 3
LRP6/FZD1 0.047 0.024 -10000 0 -0.4 1 1
TLE1 0.016 0.098 -10000 0 -0.55 15 15
AP1 -0.22 0.19 -10000 0 -0.34 335 335
NCSTN 0.028 0.014 -10000 0 -10000 0 0
ADAM10 0.034 0.013 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.14 -10000 0 -0.68 11 11
NICD/RBPSUH 0.055 0.092 -10000 0 -0.41 14 14
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
NOTCH1 0.02 0.072 -10000 0 -0.42 12 12
PSENEN 0.035 0.015 -10000 0 -10000 0 0
KREMEN2 0.11 0.076 -10000 0 -10000 0 0
DKK1 0.007 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.009 0.092 -10000 0 -0.43 8 8
APH1B 0.033 0.027 -10000 0 -0.54 1 1
APH1A 0.032 0.028 -10000 0 -10000 0 0
AXIN1 0.015 0.07 -10000 0 -0.6 4 4
CtBP/CBP/TCF1/TLE1/AES 0.001 0.079 0.28 3 -0.39 6 9
PSEN1 0.033 0.007 -10000 0 -10000 0 0
FOS -0.36 0.27 -10000 0 -0.54 345 345
JUN -0.067 0.22 -10000 0 -0.54 89 89
MAP3K7 0.03 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.09 -10000 0 -0.46 8 8
MAPK3 0.032 0.01 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.07 -10000 0 -0.31 3 3
HNF1A 0.034 0.013 -10000 0 -10000 0 0
CTBP1 0.032 0.009 -10000 0 -10000 0 0
MYC -0.052 0.32 -10000 0 -1.3 31 31
NKD1 0.032 0.021 -10000 0 -10000 0 0
FZD1 0.033 0.026 -10000 0 -0.54 1 1
NOTCH1 precursor/Deltex homolog 1 0.055 0.095 -10000 0 -0.41 14 14
apoptosis -0.22 0.19 -10000 0 -0.34 335 335
Delta 1/NOTCHprecursor 0.053 0.092 -10000 0 -0.41 14 14
DLL1 0.032 0.009 -10000 0 -10000 0 0
PPARD 0.024 0.1 -10000 0 -0.79 7 7
Gamma Secretase 0.077 0.054 -10000 0 -0.3 1 1
APC 0.005 0.1 -10000 0 -0.49 16 16
DVL1 -0.039 0.095 -10000 0 -0.44 15 15
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.081 0.13 -10000 0 -0.29 42 42
LRP6 0.033 0.008 -10000 0 -10000 0 0
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
NLK 0.015 0.025 -10000 0 -10000 0 0
CCND1 0.036 0.23 -10000 0 -1.3 12 12
WNT1 0.034 0.005 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.018 0.12 0.34 2 -0.48 13 15
DKK2 0.031 0.054 -10000 0 -0.54 4 4
NOTCH1 precursor/DVL1 -0.014 0.12 -10000 0 -0.66 11 11
GSK3B 0.034 0.009 -10000 0 -10000 0 0
FRAT1 0.034 0.008 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.037 0.087 -10000 0 -0.41 14 14
PPP2R5D -0.002 0.063 -10000 0 -0.4 8 8
MAPK1 0.032 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.2 0.17 -10000 0 -0.31 355 355
RBPJ 0.033 0.008 -10000 0 -10000 0 0
CREBBP 0.034 0.016 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.047 0.035 -10000 0 -0.3 3 3
NF kappa B1 p50/RelA/I kappa B alpha 0.058 0.059 0.28 3 -0.26 1 4
AP1 -0.21 0.19 -10000 0 -0.33 345 345
mol:PIP3 -0.15 0.16 -10000 0 -0.28 277 277
AKT1 0.005 0.091 -10000 0 -0.33 7 7
PTK2B -0.015 0.08 -10000 0 -0.18 86 86
RHOA 0.01 0.066 -10000 0 -0.26 20 20
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.057 0.19 43 -0.27 1 44
MAGI3 0.041 0.042 -10000 0 -0.54 1 1
RELA 0.033 0.007 -10000 0 -10000 0 0
apoptosis 0.017 0.022 -10000 0 -0.19 5 5
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.013 0.078 0.25 3 -0.28 6 9
NF kappa B1 p50/RelA 0.02 0.04 0.16 2 -0.31 1 3
endothelial cell migration 0.017 0.053 0.27 2 -0.47 5 7
ADCY4 -0.047 0.095 -10000 0 -0.23 45 45
ADCY5 -0.045 0.093 -10000 0 -0.22 41 41
ADCY6 -0.045 0.093 -10000 0 -0.22 42 42
ADCY7 -0.037 0.09 -10000 0 -0.27 19 19
ADCY1 -0.045 0.093 -10000 0 -0.22 42 42
ADCY2 -0.047 0.097 0.18 1 -0.23 47 48
ADCY3 -0.045 0.093 -10000 0 -0.22 41 41
ADCY8 -0.04 0.087 -10000 0 -0.23 30 30
ADCY9 -0.042 0.09 -10000 0 -0.23 35 35
GSK3B -0.014 0.079 0.24 5 -0.22 17 22
arachidonic acid secretion -0.052 0.1 -10000 0 -0.24 59 59
GNG2 0.033 0.026 -10000 0 -0.54 1 1
TRIP6 0.024 0.02 -10000 0 -0.39 1 1
GNAO1 0.019 0.021 -10000 0 -0.26 2 2
HRAS 0.034 0.013 -10000 0 -10000 0 0
NFKBIA 0.027 0.06 0.26 3 -0.24 3 6
GAB1 0.033 0.027 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.047 0.12 -10000 0 -0.84 9 9
JUN -0.067 0.22 -10000 0 -0.54 89 89
LPA/LPA2/NHERF2 0.024 0.016 -10000 0 -0.13 1 1
TIAM1 0.028 0.14 -10000 0 -0.98 9 9
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.026 0.055 0.19 43 -10000 0 43
PLCB3 0.036 0.049 0.19 40 -10000 0 40
FOS -0.36 0.27 -10000 0 -0.54 345 345
positive regulation of mitosis -0.052 0.1 -10000 0 -0.24 59 59
LPA/LPA1-2-3 0.007 0.02 -10000 0 -0.18 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
stress fiber formation 0.015 0.06 -10000 0 -0.28 8 8
GNAZ 0.016 0.044 0.15 2 -0.28 10 12
EGFR/PI3K-beta/Gab1 -0.15 0.17 -10000 0 -0.3 277 277
positive regulation of dendritic cell cytokine production 0.007 0.019 -10000 0 -0.18 5 5
LPA/LPA2/MAGI-3 0.029 0.03 -10000 0 -0.2 3 3
ARHGEF1 0.038 0.056 -10000 0 -0.22 2 2
GNAI2 0.02 0.025 0.15 2 -0.21 5 7
GNAI3 0.021 0.023 -10000 0 -0.22 4 4
GNAI1 -0.1 0.17 -10000 0 -0.34 184 184
LPA/LPA3 0.002 0.01 -10000 0 -0.093 5 5
LPA/LPA2 0.002 0.01 -10000 0 -0.092 5 5
LPA/LPA1 0.007 0.025 -10000 0 -0.24 5 5
HB-EGF/EGFR -0.12 0.2 -10000 0 -0.31 250 250
HBEGF 0.066 0.076 -10000 0 -0.4 4 4
mol:DAG 0.026 0.055 0.19 43 -10000 0 43
cAMP biosynthetic process -0.055 0.1 -10000 0 -0.28 26 26
NFKB1 0.034 0.005 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
GNB1 0.034 0.011 -10000 0 -10000 0 0
LYN 0.04 0.068 0.26 19 -0.28 1 20
GNAQ 0.003 0.009 0.056 2 -0.074 5 7
LPAR2 0 0 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 0.003 0.016 0.074 2 -0.14 5 7
IL8 -0.19 0.22 0.37 8 -0.4 230 238
PTK2 0.02 0.021 -10000 0 -0.16 4 4
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
CASP3 0.017 0.022 -10000 0 -0.19 5 5
EGFR -0.27 0.29 -10000 0 -0.54 269 269
PLCG1 0.017 0.018 -10000 0 -0.1 3 3
PLD2 0.023 0.025 -10000 0 -0.2 5 5
G12/G13 0.045 0.03 -10000 0 -0.23 2 2
PI3K-beta -0.009 0.088 -10000 0 -0.37 8 8
cell migration 0.027 0.047 -10000 0 -0.25 9 9
SLC9A3R2 0.033 0.015 -10000 0 -10000 0 0
PXN 0.015 0.061 -10000 0 -0.29 8 8
HRAS/GTP -0.053 0.1 -10000 0 -0.25 59 59
RAC1 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.095 0.074 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
PRKCD 0.024 0.058 0.21 8 -0.26 1 9
Gi(beta/gamma) -0.049 0.11 -10000 0 -0.26 54 54
mol:LPA 0.003 0.016 0.074 2 -0.14 5 7
TRIP6/p130 Cas/FAK1/Paxillin 0.03 0.052 -10000 0 -0.24 3 3
MAPKKK cascade -0.052 0.1 -10000 0 -0.24 59 59
contractile ring contraction involved in cytokinesis 0.009 0.068 -10000 0 -0.26 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.021 0.039 0.1 49 -0.26 5 54
GNA15 0.017 0.014 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MAPT -0.014 0.079 0.25 3 -0.29 6 9
GNA11 0.015 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.048 0.13 -10000 0 -0.89 9 9
MMP2 0.017 0.053 0.27 2 -0.47 5 7
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.091 -10000 0 -0.26 46 46
epithelial cell differentiation 0.04 0.086 -10000 0 -0.29 25 25
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
ENAH -0.008 0.071 0.28 5 -0.32 1 6
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EPHA2 0.026 0.062 -10000 0 -0.54 6 6
MYO6 0.001 0.074 -10000 0 -0.28 25 25
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
ABI1/Sra1/Nap1 0.074 0.035 -10000 0 -10000 0 0
AQP5 -0.14 0.24 -10000 0 -0.49 148 148
CTNND1 0.033 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.072 -10000 0 -0.28 25 25
regulation of calcium-dependent cell-cell adhesion -0.023 0.1 -10000 0 -0.29 62 62
EGF -0.15 0.27 -10000 0 -0.54 163 163
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
AQP3 -0.051 0.18 -10000 0 -0.49 61 61
cortical microtubule organization 0.04 0.086 -10000 0 -0.29 25 25
GO:0000145 -0.021 0.064 -10000 0 -0.27 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.089 -10000 0 -0.3 25 25
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GDP -0.029 0.059 -10000 0 -0.38 2 2
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.059 -10000 0 -0.32 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.001 0.07 -10000 0 -0.42 1 1
PVRL2 0.039 0.027 -10000 0 -10000 0 0
ZYX -0.002 0.073 -10000 0 -0.28 26 26
ARF6/GTP 0.063 0.061 -10000 0 -0.3 6 6
CDH1 0.007 0.12 -10000 0 -0.54 22 22
EGFR/EGFR/EGF/EGF -0.23 0.2 -10000 0 -0.35 354 354
RhoA/GDP 0.041 0.084 -10000 0 -0.28 25 25
actin cytoskeleton organization -0.021 0.068 -10000 0 -0.28 24 24
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
GIT1 0.032 0.011 -10000 0 -10000 0 0
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
DIAPH1 0.058 0.12 -10000 0 -0.56 7 7
Wnt receptor signaling pathway -0.04 0.086 0.29 25 -10000 0 25
RHOA 0.033 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.029 0.059 -10000 0 -0.38 2 2
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
VCL -0.021 0.069 -10000 0 -0.28 24 24
EFNA1 0.028 0.015 -10000 0 -10000 0 0
LPP -0.023 0.066 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.023 0.084 -10000 0 -0.29 26 26
SEC6/SEC8 -0.007 0.068 -10000 0 -0.36 1 1
MGAT3 -0.023 0.11 -10000 0 -0.29 61 61
HGF/MET 0.005 0.13 -10000 0 -0.29 73 73
HGF 0.035 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.092 -10000 0 -0.26 46 46
actin cable formation 0.053 0.11 0.35 14 -0.29 1 15
KIAA1543 -0.021 0.065 -10000 0 -0.27 25 25
KIFC3 0.001 0.07 -10000 0 -0.28 25 25
NCK1 0.034 0.005 -10000 0 -10000 0 0
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ACTN1 -0.001 0.073 -10000 0 -0.28 25 25
NCK1/GIT1 0.047 0.016 -10000 0 -10000 0 0
mol:GDP 0.04 0.086 -10000 0 -0.29 25 25
EXOC4 0.034 0.006 -10000 0 -10000 0 0
STX4 -0.001 0.072 -10000 0 -0.28 25 25
PIP5K1C -0.001 0.073 -10000 0 -0.28 25 25
LIMA1 0.013 0.11 -10000 0 -0.54 19 19
ABI1 0.033 0.007 -10000 0 -10000 0 0
ROCK1 0.012 0.1 0.3 11 -0.34 2 13
adherens junction assembly -0.03 0.13 0.3 1 -0.67 12 13
IGF-1R heterotetramer/IGF1 -0.13 0.18 -10000 0 -0.3 248 248
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
MET -0.022 0.17 -10000 0 -0.54 50 50
PLEKHA7 -0.001 0.073 -10000 0 -0.28 25 25
mol:GTP 0.056 0.058 -10000 0 -0.31 6 6
establishment of epithelial cell apical/basal polarity -0.012 0.087 0.36 5 -0.35 1 6
cortical actin cytoskeleton stabilization -0.01 0.091 -10000 0 -0.26 46 46
regulation of cell-cell adhesion -0.021 0.068 -10000 0 -0.28 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.092 -10000 0 -0.26 46 46
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.005 0.13 -10000 0 -0.39 50 50
CRKL 0 0.12 0.37 1 -0.39 17 18
mol:PIP3 0.005 0.062 0.49 3 -0.8 1 4
AKT1 0.018 0.08 0.36 8 -0.7 1 9
PTK2B 0.028 0.014 -10000 0 -10000 0 0
RAPGEF1 -0.001 0.11 0.31 2 -0.42 11 13
RANBP10 0.03 0.012 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.023 0.12 -10000 0 -0.34 50 50
MAP3K5 -0.011 0.13 0.37 1 -0.41 24 25
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.12 -10000 0 -0.31 51 51
AP1 -0.29 0.24 -10000 0 -0.43 347 347
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
apoptosis -0.54 0.38 -10000 0 -0.77 367 367
STAT3 (dimer) -0.007 0.11 -10000 0 -0.42 16 16
GAB1/CRKL/SHP2/PI3K 0.012 0.15 -10000 0 -0.44 16 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.015 0.11 0.36 1 -0.37 17 18
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.033 0.008 -10000 0 -10000 0 0
PTEN 0.029 0.045 -10000 0 -0.54 3 3
ELK1 -0.019 0.085 0.27 13 -0.22 1 14
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.007 0.065 -10000 0 -0.21 12 12
PAK1 0.043 0.098 0.38 13 -0.67 1 14
HGF/MET/RANBP10 0.022 0.12 -10000 0 -0.34 50 50
HRAS -0.032 0.2 -10000 0 -0.58 57 57
DOCK1 -0.003 0.11 0.43 2 -0.42 11 13
GAB1 -0.003 0.12 -10000 0 -0.38 22 22
CRK -0.002 0.11 0.37 1 -0.39 17 18
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.18 -10000 0 -0.54 55 55
JUN -0.067 0.22 -10000 0 -0.54 89 89
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.012 0.087 -10000 0 -0.27 51 51
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
cell morphogenesis -0.016 0.15 0.4 7 -0.44 18 25
GRB2/SHC 0.02 0.082 -10000 0 -0.25 32 32
FOS -0.36 0.27 -10000 0 -0.54 345 345
GLMN 0.005 0.004 -10000 0 -10000 0 0
cell motility -0.019 0.085 0.27 13 -0.22 1 14
HGF/MET/MUC20 0.008 0.12 -10000 0 -0.34 51 51
cell migration 0.019 0.081 -10000 0 -0.25 32 32
GRB2 0.034 0.018 -10000 0 -10000 0 0
CBL 0.031 0.011 -10000 0 -10000 0 0
MET/RANBP10 0.001 0.13 -10000 0 -0.39 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.011 0.098 -10000 0 -0.29 41 41
MET/MUC20 -0.017 0.12 -10000 0 -0.39 52 52
RAP1B 0.005 0.11 0.36 3 -0.4 10 13
RAP1A -0.002 0.11 0.33 1 -0.4 10 11
HGF/MET/RANBP9 0.027 0.12 -10000 0 -0.34 48 48
RAF1 -0.024 0.19 -10000 0 -0.56 56 56
STAT3 -0.006 0.11 -10000 0 -0.43 16 16
cell proliferation 0.023 0.15 0.34 8 -0.38 37 45
RPS6KB1 0.002 0.061 -10000 0 -0.35 8 8
MAPK3 -0.037 0.082 0.62 3 -10000 0 3
MAPK1 -0.004 0.17 0.64 30 -10000 0 30
RANBP9 0.034 0.009 -10000 0 -10000 0 0
MAPK8 -0.002 0.13 0.45 1 -0.39 20 21
SRC -0.006 0.097 -10000 0 -0.37 14 14
PI3K -0.009 0.13 -10000 0 -0.28 86 86
MET/Glomulin -0.012 0.11 -10000 0 -0.35 50 50
SOS1 0.034 0.004 -10000 0 -10000 0 0
MAP2K1 -0.02 0.18 0.48 1 -0.52 56 57
MET -0.022 0.17 -10000 0 -0.54 50 50
MAP4K1 0.004 0.12 0.39 1 -0.41 19 20
PTK2 0.027 0.014 -10000 0 -10000 0 0
MAP2K2 -0.021 0.18 0.48 1 -0.52 55 56
BAD 0.015 0.075 0.35 5 -0.67 1 6
MAP2K4 -0.01 0.12 0.35 1 -0.38 24 25
SHP2/GRB2/SOS1/GAB1 0.02 0.14 -10000 0 -0.36 52 52
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PXN 0.034 0.004 -10000 0 -10000 0 0
SH3KBP1 0.033 0.027 0.18 1 -0.54 1 2
HGS -0.015 0.078 -10000 0 -0.25 49 49
PLCgamma1/PKC 0.024 0.006 -10000 0 -10000 0 0
HGF 0.035 0.01 -10000 0 -10000 0 0
RASA1 0.034 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
PTPRJ 0.035 0.017 0.18 6 -10000 0 6
NCK/PLCgamma1 0.026 0.094 -10000 0 -0.24 48 48
PDPK1 0.02 0.084 0.41 5 -0.74 1 6
HGF/MET/SHIP 0.008 0.12 -10000 0 -0.34 51 51
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.084 0.16 0.32 68 -0.34 18 86
FYN 0.055 0.16 0.35 37 -0.38 23 60
LAT/GRAP2/SLP76 0.066 0.16 0.41 27 -0.35 18 45
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 0.054 0.16 0.34 51 -0.3 33 84
B2M 0.037 0.011 -10000 0 -10000 0 0
IKBKG 0.032 0.069 0.18 49 -0.12 3 52
MAP3K8 -0.039 0.19 -10000 0 -0.54 65 65
mol:Ca2+ -0.011 0.017 -10000 0 -0.09 12 12
integrin-mediated signaling pathway 0.038 0.023 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.047 0.18 0.46 23 -0.4 32 55
TRPV6 0.012 0.22 1.3 10 -0.54 17 27
CD28 0.028 0.084 0.19 3 -0.54 10 13
SHC1 0.066 0.18 0.33 81 -0.35 42 123
receptor internalization 0.02 0.18 0.33 29 -0.39 68 97
PRF1 0.033 0.16 0.53 9 -0.74 7 16
KRAS 0.035 0.019 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
COT/AKT1 0.032 0.16 0.34 41 -0.3 40 81
LAT 0.049 0.16 0.34 43 -0.35 41 84
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.04 0.036 0.22 1 -10000 0 1
CD3E 0.034 0.016 0.22 1 -10000 0 1
CD3G 0.039 0.073 0.2 11 -0.54 5 16
RASGRP2 0.008 0.048 0.16 10 -0.16 27 37
RASGRP1 0.059 0.15 0.43 28 -0.34 14 42
HLA-A 0.003 0.006 0.041 5 -10000 0 5
RASSF5 0.03 0.023 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.038 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.063 0.094 0.25 54 -0.12 3 57
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.009 0.048 -10000 0 -0.17 22 22
PRKCA 0.039 0.099 0.32 24 -0.22 7 31
GRAP2 0.034 0.019 -10000 0 -10000 0 0
mol:IP3 0.003 0.09 0.28 10 -0.27 20 30
EntrezGene:6957 0.003 0.005 0.043 1 -10000 0 1
TCR/CD3/MHC I/CD8 0.008 0.12 0.27 27 -0.31 46 73
ORAI1 -0.019 0.17 -10000 0 -1.1 10 10
CSK 0.039 0.15 0.37 22 -0.33 44 66
B7 family/CD28 0.081 0.17 0.48 22 -0.45 13 35
CHUK 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.035 0.17 0.35 28 -0.35 54 82
PTPN6 0.037 0.15 0.35 26 -0.33 43 69
VAV1 0.039 0.16 0.4 23 -0.34 43 66
Monovalent TCR/CD3 0.023 0.1 0.28 21 -0.37 21 42
CBL 0.031 0.011 -10000 0 -10000 0 0
LCK 0.056 0.15 0.36 32 -0.36 20 52
PAG1 0.056 0.16 0.37 32 -0.34 41 73
RAP1A 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.034 0.16 0.34 28 -0.34 53 81
CD80 0.045 0.038 -10000 0 -10000 0 0
CD86 0.036 0.013 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 0.01 0.066 -10000 0 -0.2 22 22
HRAS 0.034 0.013 -10000 0 -10000 0 0
GO:0035030 0.04 0.14 0.36 27 -0.38 14 41
CD8A 0.003 0.006 0.042 5 -10000 0 5
CD8B 0.041 0.025 0.21 4 -10000 0 4
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDK1/PKC theta 0.064 0.18 0.41 53 -0.35 27 80
CSK/PAG1 0.057 0.16 0.35 33 -0.34 30 63
SOS1 0.034 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.03 0.012 -10000 0 -10000 0 0
GRAP2/SLP76 0.06 0.16 0.43 20 -0.35 32 52
STIM1 0.004 0.1 1.2 3 -10000 0 3
RAS family/GTP 0.072 0.1 0.27 50 -0.18 11 61
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.017 0.19 0.33 28 -0.4 68 96
mol:DAG -0.016 0.068 0.13 2 -0.23 26 28
RAP1A/GDP 0.034 0.048 0.14 44 -10000 0 44
PLCG1 0.032 0.008 -10000 0 -10000 0 0
CD247 0.023 0.11 0.2 10 -0.54 15 25
cytotoxic T cell degranulation 0.034 0.16 0.52 9 -0.68 8 17
RAP1A/GTP 0.002 0.015 -10000 0 -0.06 26 26
mol:PI-3-4-5-P3 0.049 0.16 0.43 26 -0.35 31 57
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.023 0.12 0.32 10 -0.38 12 22
NRAS 0.036 0.016 -10000 0 -10000 0 0
ZAP70 0.039 0.024 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.042 0.13 0.3 12 -0.36 15 27
MALT1 0.033 0.01 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.033 0.022 0.19 5 -10000 0 5
CARD11 0.039 0.027 -10000 0 -10000 0 0
PRKCB -0.013 0.051 0.14 5 -0.17 28 33
PRKCE 0.043 0.1 0.31 28 -0.22 9 37
PRKCQ 0.053 0.18 0.46 27 -0.37 31 58
LCP2 0.037 0.023 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.054 0.14 0.33 51 -0.27 30 81
IKK complex 0.053 0.088 0.23 63 -10000 0 63
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.025 0.13 0.28 47 -0.24 31 78
PDPK1 0.058 0.16 0.37 53 -0.3 27 80
TCR/CD3/MHC I/CD8/Fyn 0.006 0.16 0.37 15 -0.4 48 63
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.032 0.009 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.027 0.096 -10000 0 -0.27 18 18
NT3 (dimer)/TRKC -0.082 0.21 -10000 0 -0.4 150 150
NT3 (dimer)/TRKB -0.25 0.29 -10000 0 -0.48 279 279
SHC/Grb2/SOS1/GAB1/PI3K 0.003 0.074 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
NTRK1 0.031 0.022 -10000 0 -10000 0 0
NTRK2 -0.23 0.29 -10000 0 -0.54 237 237
NTRK3 0.015 0.1 -10000 0 -0.54 16 16
NT-4/5 (dimer)/TRKB -0.17 0.24 -10000 0 -0.41 224 224
neuron apoptosis 0.12 0.21 0.46 102 -10000 0 102
SHC 2-3/Grb2 -0.13 0.23 -10000 0 -0.51 102 102
SHC1 0.028 0.014 -10000 0 -10000 0 0
SHC2 -0.14 0.24 -10000 0 -0.56 102 102
SHC3 -0.12 0.21 -10000 0 -0.49 93 93
STAT3 (dimer) 0.055 0.077 -10000 0 -0.36 10 10
NT3 (dimer)/TRKA -0.086 0.2 -10000 0 -0.38 138 138
RIN/GDP 0.005 0.11 0.27 5 -0.28 19 24
GIPC1 0.034 0.01 -10000 0 -10000 0 0
KRAS 0.035 0.019 -10000 0 -10000 0 0
DNAJA3 -0.055 0.13 -10000 0 -0.35 71 71
RIN/GTP 0.024 0.019 -10000 0 -0.4 1 1
CCND1 0.015 0.12 -10000 0 -0.78 10 10
MAGED1 0.044 0.036 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.052 0.033 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.041 0.027 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.033 0.068 -10000 0 -0.33 14 14
ELMO1 0.034 0.005 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.041 0.032 -10000 0 -0.34 3 3
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
DOCK1 0.03 0.044 -10000 0 -0.54 3 3
GAB2 0.03 0.012 -10000 0 -10000 0 0
RIT2 0.032 0.026 -10000 0 -0.54 1 1
RIT1 0.028 0.013 -10000 0 -10000 0 0
FRS2 0.032 0.029 -10000 0 -0.54 1 1
DNM1 0.034 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.034 0.15 -10000 0 -0.36 66 66
mol:GDP -0.01 0.15 0.33 6 -0.4 24 30
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.025 0.004 -10000 0 -10000 0 0
RIT1/GDP -0.006 0.098 0.25 2 -0.28 17 19
TIAM1 0.035 0.012 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
BDNF (dimer)/TRKB -0.12 0.2 -10000 0 -0.34 234 234
KIDINS220/CRKL/C3G 0.047 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.04 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2 0.064 0.028 -10000 0 -0.34 1 1
SHC/GRB2/SOS1/GAB1 0.064 0.043 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.01 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.25 -10000 0 -0.54 134 134
RAP1/GDP 0.001 0.09 -10000 0 -0.24 18 18
KIDINS220/CRKL 0.032 0.009 -10000 0 -10000 0 0
BDNF (dimer) 0.038 0.047 -10000 0 -0.54 2 2
ubiquitin-dependent protein catabolic process 0.03 0.059 -10000 0 -0.32 11 11
Schwann cell development -0.037 0.032 -10000 0 -10000 0 0
EHD4 0.033 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.076 0.038 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.026 0.067 -10000 0 -0.3 6 6
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.22 -10000 0 -0.35 270 270
ABL1 0.034 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
Rap1/GTP -0.042 0.12 -10000 0 -0.44 24 24
STAT3 0.055 0.077 -10000 0 -0.36 10 10
axon guidance -0.17 0.2 -10000 0 -0.34 270 270
MAPK3 0.046 0.064 0.28 3 -10000 0 3
MAPK1 0.05 0.067 0.28 4 -10000 0 4
CDC42/GDP 0.005 0.11 0.28 6 -0.28 19 25
NTF3 -0.12 0.26 -10000 0 -0.54 134 134
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.039 0.022 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
FRS3 0.034 0.006 -10000 0 -10000 0 0
FAIM 0.034 0.006 -10000 0 -10000 0 0
GAB1 0.033 0.027 -10000 0 -0.54 1 1
RASGRF1 -0.053 0.14 -10000 0 -0.35 77 77
SOS1 0.034 0.004 -10000 0 -10000 0 0
MCF2L -0.083 0.17 -10000 0 -0.35 140 140
RGS19 0.034 0.022 -10000 0 -10000 0 0
CDC42 0.033 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.1 0.36 1 -0.43 5 6
Rac1/GDP 0.006 0.11 0.27 6 -0.28 19 25
NGF (dimer)/TRKA/GRIT 0.021 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.026 0.22 0.42 1 -0.75 26 27
NGF (dimer)/TRKA/NEDD4-2 0.03 0.059 -10000 0 -0.32 11 11
MAP2K1 0.061 0.084 0.36 11 -10000 0 11
NGFR -0.055 0.2 -10000 0 -0.54 76 76
NGF (dimer)/TRKA/GIPC/GAIP 0.025 0.025 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0 0.086 -10000 0 -0.26 40 40
FRS2 family/SHP2/GRB2/SOS1 0.087 0.044 -10000 0 -0.3 1 1
NRAS 0.036 0.016 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.017 0.071 -10000 0 -0.56 4 4
RASA1 0.034 0.011 -10000 0 -10000 0 0
TRKA/c-Abl 0.043 0.024 -10000 0 -10000 0 0
SQSTM1 0.034 0.009 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.098 0.2 -10000 0 -0.31 232 232
NGF (dimer)/TRKA/p62/Atypical PKCs 0.05 0.029 -10000 0 -10000 0 0
MATK 0.039 0.028 -10000 0 -10000 0 0
NEDD4L 0.019 0.091 -10000 0 -0.54 13 13
RAS family/GDP -0.034 0.058 -10000 0 -0.22 17 17
NGF (dimer)/TRKA -0.06 0.14 -10000 0 -0.36 82 82
Rac1/GTP -0.05 0.098 -10000 0 -0.28 40 40
FRS2 family/SHP2/CRK family 0.081 0.047 -10000 0 -0.3 1 1
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.042 0.009 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.01 0.22 0.7 24 -0.52 8 32
IL27/IL27R/JAK1 0.029 0.28 0.71 12 -1.1 19 31
TBX21 0.023 0.26 0.55 36 -0.59 39 75
IL12B 0.042 0.027 -10000 0 -10000 0 0
IL12A 0.005 0.061 0.15 3 -0.4 11 14
IL6ST 0.034 0.079 0.24 1 -0.54 8 9
IL27RA/JAK1 0.002 0.24 0.53 3 -1.2 18 21
IL27 -0.02 0.18 0.33 1 -0.54 52 53
TYK2 0.043 0.026 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.19 0.14 -10000 0 -0.78 2 2
T-helper 2 cell differentiation -0.01 0.22 0.7 24 -0.52 8 32
T cell proliferation during immune response -0.01 0.22 0.7 24 -0.52 8 32
MAPKKK cascade 0.01 0.22 0.52 8 -0.7 24 32
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT2 0.034 0.004 -10000 0 -10000 0 0
STAT1 0.061 0.057 0.21 4 -10000 0 4
IL12RB1 0.037 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.049 0.25 0.55 47 -0.64 22 69
IL27/IL27R/JAK2/TYK2 0.009 0.22 0.53 8 -0.72 24 32
positive regulation of T cell mediated cytotoxicity 0.01 0.22 0.52 8 -0.7 24 32
STAT1 (dimer) 0.034 0.32 0.8 22 -1 21 43
JAK2 0.038 0.022 0.24 1 -10000 0 1
JAK1 0.036 0.013 0.18 1 -10000 0 1
STAT2 (dimer) 0.025 0.21 0.5 6 -0.68 23 29
T cell proliferation -0.18 0.25 0.5 5 -0.6 74 79
IL12/IL12R/TYK2/JAK2 0.068 0.19 0.55 1 -0.79 12 13
IL17A -0.19 0.14 -10000 0 -0.78 2 2
mast cell activation -0.01 0.22 0.7 24 -0.52 8 32
IFNG 0.033 0.065 0.14 101 -0.11 7 108
T cell differentiation 0 0.009 0.019 27 -0.024 19 46
STAT3 (dimer) 0.024 0.21 0.5 6 -0.7 22 28
STAT5A (dimer) 0.024 0.21 0.5 6 -0.66 25 31
STAT4 (dimer) 0.021 0.21 0.5 6 -0.68 24 30
STAT4 0.028 0.069 -10000 0 -0.54 7 7
T cell activation -0.005 0.028 0.12 17 -0.12 9 26
IL27R/JAK2/TYK2 0.052 0.24 0.59 2 -1.1 18 20
GATA3 -0.013 0.37 0.73 12 -1.3 33 45
IL18 0.019 0.036 0.14 41 -10000 0 41
positive regulation of mast cell cytokine production 0.025 0.2 0.49 6 -0.68 22 28
IL27/EBI3 0.015 0.14 0.3 5 -0.39 51 56
IL27RA -0.016 0.25 0.54 4 -1.3 18 22
IL6 -0.37 0.26 -10000 0 -0.54 366 366
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
monocyte differentiation 0.002 0.003 -10000 0 -10000 0 0
IL2 -0.008 0.11 0.47 18 -1.2 1 19
IL1B 0.009 0.044 0.14 10 -0.4 5 15
EBI3 0.041 0.026 0.23 2 -10000 0 2
TNF 0.013 0.02 0.14 13 -10000 0 13
ErbB2/ErbB3 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
USP8 -0.005 0.015 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.1 -10000 0 -0.3 8 8
NFATC4 -0.025 0.084 0.28 7 -0.25 2 9
ERBB2IP 0.034 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.033 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis -0.035 0.086 -10000 0 -0.3 26 26
JUN -0.055 0.072 -10000 0 -10000 0 0
HRAS 0.033 0.013 -10000 0 -10000 0 0
DOCK7 -0.035 0.089 0.26 2 -0.29 26 28
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.018 0.096 -10000 0 -0.31 24 24
AKT1 0.007 0.016 0.14 5 -10000 0 5
BAD -0.004 0.014 -10000 0 -10000 0 0
MAPK10 -0.019 0.073 0.21 11 -0.25 7 18
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.036 0.092 -10000 0 -0.32 26 26
RAF1 -0.037 0.096 -10000 0 -0.34 6 6
ErbB2/ErbB3/neuregulin 2 -0.18 0.17 -10000 0 -0.33 274 274
STAT3 0.01 0.16 -10000 0 -0.84 18 18
cell migration -0.011 0.074 0.26 8 -0.26 3 11
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.26 0.28 -10000 0 -0.67 112 112
FOS -0.33 0.26 -10000 0 -0.5 365 365
NRAS 0.035 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.035 0.086 -10000 0 -0.3 26 26
MAPK3 -0.16 0.21 -10000 0 -0.52 83 83
MAPK1 -0.18 0.24 -10000 0 -0.56 104 104
JAK2 -0.032 0.088 0.26 2 -0.29 26 28
NF2 0.004 0.062 -10000 0 -0.69 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.079 -10000 0 -0.28 23 23
NRG1 -0.018 0.15 -10000 0 -0.55 40 40
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
MAPK8 -0.038 0.1 -10000 0 -0.29 29 29
MAPK9 -0.016 0.067 0.2 12 -10000 0 12
ERBB2 -0.022 0.013 -10000 0 -10000 0 0
ERBB3 0.037 0.025 -10000 0 -10000 0 0
SHC1 0.027 0.013 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.019 0.027 -10000 0 -0.18 2 2
STAT3 (dimer) 0.011 0.16 -10000 0 -0.82 18 18
RNF41 -0.008 0.014 -10000 0 -10000 0 0
FRAP1 -0.002 0.013 0.11 6 -10000 0 6
RAC1-CDC42/GTP -0.036 0.059 -10000 0 -0.22 26 26
ErbB2/ErbB2/HSP90 (dimer) -0.007 0.023 -10000 0 -10000 0 0
CHRNA1 -0.12 0.16 -10000 0 -0.43 33 33
myelination -0.018 0.092 0.32 9 -10000 0 9
PPP3CB -0.033 0.084 0.25 2 -0.27 25 27
KRAS 0.034 0.019 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.034 0.1 -10000 0 -0.26 16 16
NRG2 -0.35 0.27 -10000 0 -0.54 339 339
mol:GDP 0 0.079 -10000 0 -0.28 23 23
SOS1 0.033 0.004 -10000 0 -10000 0 0
MAP2K2 -0.053 0.1 -10000 0 -0.35 11 11
SRC 0.033 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.033 0.09 0.27 2 -0.29 26 28
MAP2K1 -0.17 0.22 -10000 0 -0.6 54 54
heart morphogenesis -0.035 0.086 -10000 0 -0.3 26 26
RAS family/GDP 0.029 0.11 -10000 0 -0.29 6 6
GRB2 0.033 0.018 -10000 0 -10000 0 0
PRKACA 0.006 0.075 -10000 0 -0.68 6 6
CHRNE -0.005 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.016 -10000 0 -0.14 5 5
nervous system development -0.035 0.086 -10000 0 -0.3 26 26
CDC42 0.033 0.008 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.029 0.079 -10000 0 -0.49 7 7
Crk/p130 Cas/Paxillin -0.082 0.14 -10000 0 -0.38 69 69
JUN -0.001 0.15 0.28 3 -0.42 21 24
HRAS 0.034 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.11 0.17 -10000 0 -0.29 60 60
RAP1A 0.034 0.005 -10000 0 -10000 0 0
FRS2 0.032 0.029 -10000 0 -0.54 1 1
RAP1A/GDP 0.025 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.12 0.17 0.35 3 -0.3 56 59
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.056 0.14 0.24 1 -0.31 60 61
RHOA 0.033 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.077 0.15 -10000 0 -0.28 45 45
GRB7 0.029 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.12 0.17 -10000 0 -0.3 56 56
MAPKKK cascade 0.059 0.14 0.25 8 -0.29 41 49
BCAR1 0.029 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.017 0.2 -10000 0 -0.38 92 92
lamellipodium assembly -0.042 0.16 -10000 0 -0.35 72 72
RET51/GFRalpha1/GDNF/SHC 0.094 0.16 -10000 0 -0.3 44 44
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.046 0.13 -10000 0 -0.31 45 45
RET9/GFRalpha1/GDNF/Shank3 0.05 0.14 -10000 0 -0.31 60 60
MAPK3 0.042 0.13 0.28 9 -0.28 44 53
DOK1 0.036 0.016 -10000 0 -10000 0 0
DOK6 0.032 0.049 -10000 0 -0.54 3 3
PXN 0.034 0.004 -10000 0 -10000 0 0
neurite development 0.043 0.12 0.33 1 -0.33 2 3
DOK5 0.012 0.11 -10000 0 -0.54 18 18
GFRA1 0.031 0.22 -10000 0 -0.54 63 63
MAPK8 0.054 0.12 0.27 4 -0.37 8 12
HRAS/GTP 0.094 0.16 0.3 4 -0.32 42 46
tube development 0.056 0.14 0.31 12 -0.3 57 69
MAPK1 0.044 0.13 0.28 9 -0.28 44 53
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.021 0.11 -10000 0 -0.26 57 57
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
PDLIM7 0.034 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.11 0.17 0.35 2 -0.28 56 58
SHC1 0.028 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.092 0.17 -10000 0 -0.3 58 58
RET51/GFRalpha1/GDNF/Dok5 0.088 0.18 -10000 0 -0.3 63 63
PRKCA 0.031 0.013 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
CREB1 0.044 0.12 0.24 1 -0.28 32 33
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.019 0.097 -10000 0 -0.25 40 40
RET51/GFRalpha1/GDNF/Grb7 0.1 0.16 -10000 0 -0.3 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.073 -10000 0 -10000 0 0
DOK4 0.03 0.012 -10000 0 -10000 0 0
JNK cascade -0.001 0.15 0.28 3 -0.41 21 24
RET9/GFRalpha1/GDNF/FRS2 0.051 0.14 0.24 1 -0.31 60 61
SHANK3 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.034 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.019 0.099 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.055 0.13 0.26 7 -0.26 44 51
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.062 0.13 0.24 4 -0.27 45 49
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.048 0.12 0.24 6 -0.26 32 38
PI3K -0.04 0.25 0.35 2 -0.55 72 74
SOS1 0.034 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.059 0.14 -10000 0 -0.3 57 57
GRB10 0.03 0.051 -10000 0 -0.54 4 4
activation of MAPKK activity 0.055 0.12 0.24 10 -0.34 3 13
RET51/GFRalpha1/GDNF/FRS2 0.1 0.17 0.35 1 -0.3 58 59
GAB1 0.033 0.027 -10000 0 -0.54 1 1
IRS1 -0.034 0.18 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 117 117
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.048 0.12 0.24 6 -0.33 4 10
RET51/GFRalpha1/GDNF/PKC alpha 0.099 0.17 -10000 0 -0.3 55 55
GRB2 0.034 0.018 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GDNF 0.034 0.009 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.073 0.23 -10000 0 -0.38 85 85
Rac1/GTP -0.032 0.2 0.25 2 -0.43 72 74
RET9/GFRalpha1/GDNF 0.039 0.15 -10000 0 -0.34 60 60
GFRalpha1/GDNF 0.04 0.17 -10000 0 -0.4 60 60
Syndecan-3-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
CTTN 0.028 0.014 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.13 0.17 -9999 0 -0.56 19 19
Syndecan-3/Neurocan 0.043 0.1 -9999 0 -0.47 16 16
POMC 0.035 0.031 -9999 0 -0.54 1 1
EGFR -0.27 0.29 -9999 0 -0.54 269 269
Syndecan-3/EGFR -0.12 0.18 -9999 0 -0.3 195 195
AGRP 0.03 0.015 -9999 0 -10000 0 0
NCSTN 0.028 0.014 -9999 0 -10000 0 0
PSENEN 0.035 0.015 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.033 0.027 -9999 0 -0.54 1 1
APH1A 0.032 0.028 -9999 0 -10000 0 0
NCAN 0.039 0.028 -9999 0 -10000 0 0
long-term memory 0.04 0.096 -9999 0 -0.45 13 13
Syndecan-3/IL8 0.049 0.11 -9999 0 -0.46 16 16
PSEN1 0.033 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.04 0.022 -9999 0 -10000 0 0
FYN 0.03 0.037 -9999 0 -0.54 2 2
limb bud formation -0.001 0.089 -9999 0 -0.48 16 16
MC4R 0.034 0.013 -9999 0 -10000 0 0
SRC 0.033 0.008 -9999 0 -10000 0 0
PTN -0.36 0.27 -9999 0 -0.54 354 354
FGFR/FGF/Syndecan-3 -0.001 0.09 -9999 0 -0.49 16 16
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.55 19 19
Syndecan-3/AgRP 0.034 0.1 -9999 0 -0.47 16 16
Syndecan-3/AgRP/MC4R 0.049 0.1 -9999 0 -0.46 15 15
Fyn/Cortactin 0.037 0.031 -9999 0 -0.4 1 1
SDC3 -0.001 0.091 -9999 0 -0.49 16 16
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.048 0.11 -9999 0 -0.46 16 16
IL8 0.048 0.053 -9999 0 -0.54 1 1
Syndecan-3/Fyn/Cortactin 0.042 0.098 -9999 0 -0.46 13 13
Syndecan-3/CASK -0.003 0.087 -9999 0 -0.47 16 16
alpha-MSH/MC4R 0.05 0.027 -9999 0 -0.4 1 1
Gamma Secretase 0.076 0.054 -9999 0 -0.3 1 1
TCGA08_rtk_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
PDGFRA -0.035 0.19 -10000 0 -0.54 61 61
HRAS 0.034 0.013 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
AKT -0.018 0.12 0.34 5 -0.26 37 42
FOXO3 0.032 0.01 -10000 0 -10000 0 0
AKT1 0.035 0.017 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 48 48
AKT3 0.029 0.019 -10000 0 -10000 0 0
FOXO4 0.035 0.002 -10000 0 -10000 0 0
MET -0.022 0.17 -10000 0 -0.54 50 50
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
NRAS 0.036 0.016 -10000 0 -10000 0 0
PIK3CG 0.037 0.022 -10000 0 -10000 0 0
PIK3R3 0.042 0.035 -10000 0 -10000 0 0
PIK3R2 0.036 0.017 -10000 0 -10000 0 0
NF1 0.032 0.009 -10000 0 -10000 0 0
RAS -0.076 0.14 0.23 1 -0.33 85 86
ERBB2 0.028 0.029 -10000 0 -0.54 1 1
proliferation/survival/translation -0.017 0.1 0.3 28 -0.3 1 29
PI3K -0.068 0.16 0.29 9 -0.31 104 113
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
KRAS 0.035 0.019 -10000 0 -10000 0 0
FOXO 0.035 0.08 0.29 8 -0.18 8 16
AKT2 0.034 0.005 -10000 0 -10000 0 0
PTEN 0.029 0.045 -10000 0 -0.54 3 3
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.037 0.11 1 1 -10000 0 1
VDR 0.032 0.037 0.18 1 -0.54 2 3
FAM120B 0.032 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.063 0.076 0.29 13 -10000 0 13
RXRs/LXRs/DNA/Oxysterols 0.089 0.089 -10000 0 -0.37 2 2
MED1 0.029 0.013 -10000 0 -10000 0 0
mol:9cRA 0.01 0.014 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.031 0.13 -10000 0 -0.27 101 101
RXRs/NUR77 0.071 0.093 -10000 0 -0.3 18 18
RXRs/PPAR -0.15 0.14 -10000 0 -0.26 262 262
NCOR2 0.034 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RARs/VDR/DNA/Vit D3 0.016 0.13 -10000 0 -0.3 72 72
RARA 0.031 0.013 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 0.18 1 -0.54 2 3
RARs/RARs/DNA/9cRA 0.007 0.12 -10000 0 -0.29 72 72
RARG 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 0.062 0.17 0.56 51 -10000 0 51
RARs/THRs/DNA/SMRT -0.03 0.13 -10000 0 -0.27 100 100
THRA -0.001 0.13 -10000 0 -0.54 28 28
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.076 0.069 -10000 0 -0.3 4 4
NR1H4 0.035 0.01 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.11 0.088 -10000 0 -0.28 5 5
NR1H2 0.043 0.015 -10000 0 -10000 0 0
NR1H3 0.043 0.031 -10000 0 -0.54 1 1
RXRs/VDR/DNA/Vit D3 0.078 0.062 -10000 0 -0.29 4 4
NR4A1 0.007 0.12 -10000 0 -0.54 24 24
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.056 0.059 -10000 0 -0.28 1 1
RXRG 0.032 0.055 -10000 0 -0.54 4 4
RXR alpha/CCPG 0.052 0.02 -10000 0 -10000 0 0
RXRA 0.042 0.015 -10000 0 -10000 0 0
RXRB 0.044 0.016 -10000 0 -10000 0 0
THRB 0.028 0.057 -10000 0 -0.54 5 5
PPARG -0.38 0.26 -10000 0 -0.54 367 367
PPARD 0.034 0.01 -10000 0 -10000 0 0
TNF 0.083 0.088 -10000 0 -10000 0 0
mol:Oxysterols 0.009 0.013 -10000 0 -10000 0 0
cholesterol transport 0.089 0.088 -10000 0 -0.37 2 2
PPARA 0.031 0.027 -10000 0 -0.54 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.054 0.21 -10000 0 -0.54 78 78
RXRs/NUR77/BCL2 -0.027 0.12 -10000 0 -0.26 78 78
SREBF1 0.083 0.1 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.076 0.069 -10000 0 -0.3 4 4
ABCA1 0.077 0.1 -10000 0 -1 2 2
RARs/THRs 0.006 0.16 -10000 0 -0.31 98 98
RXRs/FXR 0.085 0.065 -10000 0 -0.31 4 4
BCL2 -0.069 0.22 -10000 0 -0.54 91 91
Canonical Wnt signaling pathway

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
HDAC1 0.027 0.042 0.26 5 -10000 0 5
AES 0.026 0.036 0.22 4 -10000 0 4
FBXW11 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.048 0.024 -10000 0 -0.4 1 1
SMAD4 0.033 0.008 -10000 0 -10000 0 0
DKK2 0.031 0.054 -10000 0 -0.54 4 4
TLE1 0.01 0.1 0.24 4 -0.55 15 19
MACF1 0.035 0.006 -10000 0 -10000 0 0
CTNNB1 0.15 0.11 0.34 33 -0.41 3 36
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
beta catenin/RanBP3 0.042 0.15 0.5 40 -0.4 3 43
KREMEN2 0.11 0.076 -10000 0 -10000 0 0
DKK1 0.007 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.16 0.1 0.35 29 -0.38 3 32
FZD1 0.034 0.026 -10000 0 -0.54 1 1
AXIN2 0.026 0.28 0.65 45 -1.2 13 58
AXIN1 0.033 0.01 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.07 0.086 -10000 0 -0.53 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.093 0.15 0.41 4 -0.6 12 16
Axin1/APC/GSK3 0.065 0.058 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.062 0.076 0.37 1 -0.55 1 2
HNF1A 0.028 0.042 0.26 6 -10000 0 6
CTBP1 0.025 0.038 0.25 4 -10000 0 4
MYC 0.096 0.44 0.64 109 -1.3 29 138
RANBP3 0.034 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.07 -10000 0 -0.31 3 3
NKD1 0.032 0.021 -10000 0 -10000 0 0
TCF4 0.019 0.076 0.24 5 -0.53 7 12
TCF3 0.027 0.043 0.27 5 -10000 0 5
WNT1/LRP6/FZD1/Axin1 0.077 0.039 -10000 0 -0.32 1 1
Ran/GTP 0.025 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.001 0.21 0.55 32 -0.6 10 42
LEF1 0.054 0.068 0.27 8 -10000 0 8
DVL1 0.08 0.057 0.25 3 -10000 0 3
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.098 0.17 0.34 3 -0.59 15 18
DKK1/LRP6/Kremen 2 0.082 0.13 0.26 1 -0.29 42 43
LRP6 0.033 0.009 -10000 0 -10000 0 0
CSNK1A1 0.027 0.042 0.26 5 -10000 0 5
NLK 0.036 0.032 -10000 0 -10000 0 0
CCND1 0.12 0.38 0.75 93 -1.2 14 107
WNT1 0.035 0.005 -10000 0 -10000 0 0
GSK3A 0.035 0.005 -10000 0 -10000 0 0
GSK3B 0.034 0.009 -10000 0 -10000 0 0
FRAT1 0.035 0.008 -10000 0 -10000 0 0
PPP2R5D 0.056 0.058 -10000 0 -0.39 3 3
APC 0.038 0.062 0.38 4 -0.3 1 5
WNT1/LRP6/FZD1 0.16 0.1 0.23 342 -0.3 1 343
CREBBP 0.024 0.037 0.26 3 -10000 0 3
S1P3 pathway

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
PDGFRB 0.034 0.005 -10000 0 -10000 0 0
mol:S1P 0.001 0.003 0.03 6 -10000 0 6
S1P1/S1P/Gi -0.089 0.16 -10000 0 -0.28 188 188
GNAO1 0.031 0.013 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.042 0.016 -10000 0 -10000 0 0
AKT1 -0.01 0.11 -10000 0 -0.49 18 18
AKT3 -0.014 0.12 0.44 1 -0.56 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.005 -10000 0 -10000 0 0
GNAI2 0.035 0.011 -10000 0 -10000 0 0
GNAI3 0.035 0.007 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.002 0.004 0.035 6 -10000 0 6
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.069 0.14 0.24 2 -0.34 56 58
MAPK3 -0.06 0.13 0.23 1 -0.34 45 46
MAPK1 -0.067 0.13 0.23 1 -0.33 53 54
JAK2 -0.061 0.14 0.33 1 -0.34 60 61
CXCR4 -0.062 0.14 0.24 2 -0.33 51 53
FLT1 0.035 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC -0.064 0.13 0.31 2 -0.33 52 54
S1P/S1P3/Gi -0.069 0.14 0.24 2 -0.34 56 58
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.057 0.14 -10000 0 -0.32 55 55
VEGFA 0.053 0.047 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.073 0.14 -10000 0 -0.25 184 184
VEGFR1 homodimer/VEGFA homodimer 0.062 0.04 0.27 1 -10000 0 1
RHOA 0.033 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.026 0.037 -10000 0 -0.27 5 5
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.063 -10000 0 -0.54 6 6
G12/G13 0.045 0.017 -10000 0 -10000 0 0
GNA14 0.044 0.068 0.18 50 -0.54 4 54
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.058 0.14 -10000 0 -0.32 55 55
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.036 0.016 -10000 0 -10000 0 0
HSPA8 0.03 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.071 0.19 0.33 1 -0.4 106 107
AKT1 0.038 0.02 -10000 0 -10000 0 0
GSC -0.096 0.4 -10000 0 -1.3 45 45
NKX2-5 -0.002 0.016 -10000 0 -10000 0 0
muscle cell differentiation 0.004 0.13 0.49 17 -10000 0 17
SMAD2-3/SMAD4/SP1 0.054 0.12 -10000 0 -0.32 11 11
SMAD4 -0.026 0.08 -10000 0 -0.26 19 19
CBFB 0.03 0.014 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.16 0.2 -10000 0 -0.34 275 275
SMAD3/SMAD4/VDR 0.054 0.093 -10000 0 -0.38 4 4
MYC -0.006 0.12 -10000 0 -0.55 25 25
CDKN2B -0.05 0.2 -10000 0 -0.71 23 23
AP1 -0.26 0.29 -10000 0 -0.67 124 124
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.11 -10000 0 -0.4 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.01 0.11 0.26 1 -0.35 25 26
SP3 0.035 0.008 -10000 0 -10000 0 0
CREB1 0.034 0.006 -10000 0 -10000 0 0
FOXH1 0.018 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.043 0.14 -10000 0 -0.39 51 51
GATA3 0.039 0.16 -10000 0 -0.53 33 33
SKI/SIN3/HDAC complex/NCoR1 0.017 0.084 -10000 0 -0.39 14 14
MEF2C/TIF2 0.002 0.15 0.34 1 -0.54 26 27
endothelial cell migration -0.059 0.11 0.59 5 -10000 0 5
MAX 0.025 0.024 -10000 0 -10000 0 0
RBBP7 0.037 0.022 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
RUNX2 0.036 0.019 -10000 0 -10000 0 0
RUNX3 -0.006 0.15 -10000 0 -0.54 36 36
RUNX1 0.017 0.098 -10000 0 -0.54 15 15
CTBP1 0.033 0.008 -10000 0 -10000 0 0
NR3C1 -0.019 0.16 -10000 0 -0.55 40 40
VDR 0.032 0.037 0.18 1 -0.54 2 3
CDKN1A 0.005 0.11 -10000 0 -0.93 4 4
KAT2B 0.001 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.027 0.11 -10000 0 -0.34 24 24
DCP1A 0.033 0.008 -10000 0 -10000 0 0
SKI 0.033 0.007 -10000 0 -10000 0 0
SERPINE1 0.059 0.11 -10000 0 -0.59 5 5
SMAD3/SMAD4/ATF2 0.01 0.09 -10000 0 -0.26 13 13
SMAD3/SMAD4/ATF3 -0.086 0.2 -10000 0 -0.41 131 131
SAP30 0.033 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.056 0.043 -10000 0 -10000 0 0
JUN -0.26 0.28 -10000 0 -0.69 116 116
SMAD3/SMAD4/IRF7 0.022 0.092 -10000 0 -0.26 13 13
TFE3 0.03 0.045 -10000 0 -0.15 19 19
COL1A2 0.073 0.13 0.41 8 -0.71 5 13
mesenchymal cell differentiation -0.011 0.091 0.26 14 -10000 0 14
DLX1 0.043 0.036 -10000 0 -10000 0 0
TCF3 0.035 0.017 -10000 0 -10000 0 0
FOS -0.37 0.28 -10000 0 -0.56 345 345
SMAD3/SMAD4/Max -0.016 0.088 -10000 0 -0.27 10 10
Cbp/p300/SNIP1 0.062 0.028 -10000 0 -10000 0 0
ZBTB17 0.028 0.021 -10000 0 -10000 0 0
LAMC1 -0.036 0.15 -10000 0 -0.6 28 28
TGIF2/HDAC complex/SMAD3/SMAD4 0.011 0.089 -10000 0 -0.26 14 14
IRF7 0.04 0.024 0.22 1 -10000 0 1
ESR1 -0.069 0.25 -10000 0 -0.55 106 106
HNF4A 0.033 0.008 -10000 0 -10000 0 0
MEF2C 0.007 0.17 0.42 7 -0.55 30 37
SMAD2-3/SMAD4 0.01 0.11 -10000 0 -0.3 21 21
Cbp/p300/Src-1 0.063 0.035 -10000 0 -0.32 1 1
IGHV3OR16-13 -0.005 0.066 -10000 0 -0.44 9 9
TGIF2/HDAC complex 0.033 0.01 -10000 0 -10000 0 0
CREBBP 0.033 0.013 -10000 0 -10000 0 0
SKIL 0.045 0.042 -10000 0 -10000 0 0
HDAC1 0.033 0.006 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
SNIP1 0.033 0.006 -10000 0 -10000 0 0
GCN5L2 0.003 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.12 -10000 0 -0.36 32 32
MSG1/HSC70 -0.21 0.22 -10000 0 -0.4 296 296
SMAD2 0.02 0.053 -10000 0 -0.21 2 2
SMAD3 -0.014 0.063 -10000 0 -0.21 7 7
SMAD3/E2F4-5/DP1/p107/SMAD4 0.006 0.069 -10000 0 -0.3 7 7
SMAD2/SMAD2/SMAD4 0.017 0.057 0.22 7 -0.21 4 11
NCOR1 0.031 0.011 -10000 0 -10000 0 0
NCOA2 0.028 0.015 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
MYOD/E2A 0.049 0.035 -10000 0 -0.4 2 2
SMAD2-3/SMAD4/SP1/MIZ-1 0.075 0.12 -10000 0 -0.33 6 6
IFNB1 -0.011 0.072 0.33 2 -0.29 1 3
SMAD3/SMAD4/MEF2C 0.015 0.18 -10000 0 -0.57 30 30
CITED1 -0.3 0.29 -10000 0 -0.54 296 296
SMAD2-3/SMAD4/ARC105 0.025 0.11 -10000 0 -0.29 14 14
RBL1 0.04 0.032 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.002 0.11 -10000 0 -0.4 18 18
RUNX1-3/PEBPB2 0.02 0.13 -10000 0 -0.35 49 49
SMAD7 -0.18 0.22 -10000 0 -0.52 84 84
MYC/MIZ-1 0.008 0.098 -10000 0 -0.41 25 25
SMAD3/SMAD4 0.039 0.097 0.33 13 -0.39 2 15
IL10 -0.005 0.11 0.4 1 -0.38 23 24
PIASy/HDAC complex 0.027 0.028 -10000 0 -10000 0 0
PIAS3 0.029 0.014 -10000 0 -10000 0 0
CDK2 0.04 0.024 0.22 1 -10000 0 1
IL5 -0.002 0.12 0.4 1 -0.37 24 25
CDK4 0.037 0.011 -10000 0 -10000 0 0
PIAS4 0.027 0.028 -10000 0 -10000 0 0
ATF3 -0.12 0.25 -10000 0 -0.54 128 128
SMAD3/SMAD4/SP1 0.039 0.1 -10000 0 -0.29 11 11
FOXG1 0.042 0.037 -10000 0 -10000 0 0
FOXO3 0.021 0.02 -10000 0 -10000 0 0
FOXO1 -0.018 0.12 -10000 0 -0.39 48 48
FOXO4 0.022 0.019 -10000 0 -10000 0 0
heart looping 0.007 0.17 0.42 7 -0.55 30 37
CEBPB 0.032 0.028 -10000 0 -0.54 1 1
SMAD3/SMAD4/DLX1 0.018 0.092 -10000 0 -0.26 11 11
MYOD1 0.034 0.041 -10000 0 -0.54 2 2
SMAD3/SMAD4/HNF4 0.012 0.089 -10000 0 -0.26 14 14
SMAD3/SMAD4/GATA3 0.027 0.15 -10000 0 -0.4 33 33
SnoN/SIN3/HDAC complex/NCoR1 0.045 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.007 0.15 -10000 0 -0.36 46 46
SMAD3/SMAD4/SP1-3 0.062 0.1 -10000 0 -0.33 4 4
MED15 0.032 0.009 -10000 0 -10000 0 0
SP1 0.047 0.023 -10000 0 -10000 0 0
SIN3B 0.035 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.024 0.12 -10000 0 -0.35 31 31
ITGB5 -0.001 0.083 -10000 0 -0.53 2 2
TGIF/SIN3/HDAC complex/CtBP 0.025 0.069 -10000 0 -0.35 10 10
SMAD3/SMAD4/AR -0.037 0.16 -10000 0 -0.37 78 78
AR -0.039 0.19 0.18 2 -0.54 66 68
negative regulation of cell growth -0.022 0.12 -10000 0 -0.38 22 22
SMAD3/SMAD4/MYOD 0.01 0.094 -10000 0 -0.27 16 16
E2F5 0.036 0.036 -10000 0 -10000 0 0
E2F4 0.03 0.012 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.051 0.1 -10000 0 -0.34 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.11 -10000 0 -0.35 25 25
TFDP1 0.033 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.25 0.3 -10000 0 -0.69 120 120
SMAD3/SMAD4/RUNX2 0.012 0.091 -10000 0 -0.26 14 14
TGIF2 0.033 0.01 -10000 0 -10000 0 0
TGIF1 0.032 0.027 -10000 0 -0.54 1 1
ATF2 0.034 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.014 0.18 -10000 0 -0.76 3 3
PCK1 -0.75 0.54 -10000 0 -1 387 387
HNF4A 0.028 0.2 0.72 1 -0.75 3 4
KCNJ11 0.033 0.24 0.79 2 -0.76 3 5
AKT1 0.008 0.15 -10000 0 -0.47 5 5
response to starvation 0.005 0.002 -10000 0 -10000 0 0
DLK1 0.022 0.22 0.87 1 -0.82 3 4
NKX2-1 0.015 0.11 0.45 1 -0.36 3 4
ACADM 0.01 0.21 -10000 0 -0.86 8 8
TAT -0.062 0.2 -10000 0 -0.72 16 16
CEBPB 0.034 0.028 -10000 0 -0.54 1 1
CEBPA 0.036 0.045 -10000 0 -0.54 3 3
TTR -0.034 0.26 0.59 1 -0.65 44 45
PKLR 0.03 0.19 -10000 0 -0.79 2 2
APOA1 0.015 0.22 0.72 1 -0.89 3 4
CPT1C 0.023 0.2 0.71 1 -0.76 3 4
ALAS1 0.028 0.14 -10000 0 -10000 0 0
TFRC -0.021 0.2 0.67 3 -0.55 1 4
FOXF1 0.031 0.02 -10000 0 -10000 0 0
NF1 0.038 0.01 -10000 0 -10000 0 0
HNF1A (dimer) 0.051 0.022 -10000 0 -10000 0 0
CPT1A 0.022 0.2 0.66 5 -0.7 3 8
HMGCS1 0.018 0.2 0.74 2 -0.76 3 5
NR3C1 0 0.16 -10000 0 -0.52 42 42
CPT1B 0.013 0.19 -10000 0 -0.76 3 3
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.015 -10000 0 -10000 0 0
GCK 0.018 0.19 -10000 0 -0.76 3 3
CREB1 -0.18 0.14 -10000 0 -0.27 325 325
IGFBP1 0.012 0.14 -10000 0 -0.83 2 2
PDX1 0.039 0.16 -10000 0 -1.1 2 2
UCP2 0.02 0.2 0.62 2 -0.7 3 5
ALDOB 0.017 0.22 -10000 0 -0.82 3 3
AFP -0.05 0.14 0.39 1 -0.42 1 2
BDH1 0.019 0.19 0.67 2 -0.76 3 5
HADH 0.013 0.23 -10000 0 -0.94 5 5
F2 0.032 0.22 -10000 0 -0.82 3 3
HNF1A 0.051 0.022 -10000 0 -10000 0 0
G6PC -0.097 0.12 -10000 0 -10000 0 0
SLC2A2 0.043 0.16 -10000 0 -0.84 2 2
INS 0.023 0.014 0.25 1 -10000 0 1
FOXA1 0.002 0.23 0.32 7 -0.53 74 81
FOXA3 -0.11 0.14 -10000 0 -0.29 66 66
FOXA2 0.023 0.27 0.75 1 -0.92 3 4
ABCC8 -0.07 0.42 0.9 1 -0.93 86 87
ALB -0.052 0.15 0.39 1 -0.47 15 16
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.034 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.049 0.13 0.26 1 -0.3 93 94
FRAP1 -0.012 0.11 0.33 1 -0.5 18 19
AKT1 -0.039 0.12 0.2 2 -0.29 69 71
INSR 0.034 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.044 0.011 -10000 0 -10000 0 0
mol:GTP -0.001 0.12 0.26 2 -0.28 33 35
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.056 -10000 0 -0.22 9 9
TSC2 0.032 0.01 -10000 0 -10000 0 0
RHEB/GDP -0.013 0.092 -10000 0 -0.26 31 31
TSC1 0.034 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.018 0.13 -10000 0 -0.33 72 72
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.006 0.073 -10000 0 -0.26 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.034 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.007 0.11 0.31 3 -0.33 22 25
MAP3K5 -0.018 0.097 0.2 6 -0.29 51 57
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
apoptosis -0.018 0.097 0.2 6 -0.29 51 57
mol:LY294002 0 0.001 0.001 1 -0.002 61 62
EIF4B -0.006 0.097 0.28 4 -0.32 15 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.099 0.25 1 -0.3 14 15
eIF4E/eIF4G1/eIF4A1 -0.001 0.068 -10000 0 -0.32 14 14
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.025 0.15 -10000 0 -0.31 104 104
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.076 0.26 9 -0.21 11 20
FKBP1A 0.034 0.012 -10000 0 -10000 0 0
RHEB/GTP 0.007 0.1 0.25 1 -0.26 31 32
mol:Amino Acids 0 0.001 0.001 1 -0.002 61 62
FKBP12/Rapamycin 0.025 0.009 -10000 0 -10000 0 0
PDPK1 -0.051 0.12 0.19 7 -0.29 88 95
EIF4E 0.034 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.038 0.21 -10000 0 -0.57 61 61
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.05 -10000 0 -10000 0 0
TSC1/TSC2 0 0.12 0.28 2 -0.3 33 35
tumor necrosis factor receptor activity 0 0.001 0.002 61 -0.001 1 62
RPS6 0.032 0.026 -10000 0 -0.54 1 1
PPP5C 0.036 0.017 -10000 0 -10000 0 0
EIF4G1 0.034 0.006 -10000 0 -10000 0 0
IRS1 -0.04 0.13 -10000 0 -0.35 73 73
INS 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.029 0.044 -10000 0 -0.54 3 3
PDK2 -0.046 0.12 0.2 4 -0.29 73 77
EIF4EBP1 -0.029 0.24 -10000 0 -1 27 27
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PPP2R5D -0.01 0.1 0.34 3 -0.44 18 21
peptide biosynthetic process 0.02 0.017 -10000 0 -10000 0 0
RHEB 0.034 0.009 0.18 1 -10000 0 1
EIF4A1 0.031 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 16 -0.003 6 22
EEF2 0.02 0.018 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.012 0.23 -10000 0 -0.97 27 27
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.021 0.078 -10000 0 -0.28 5 5
alphaM/beta2 Integrin/GPIbA -0.016 0.079 0.27 3 -10000 0 3
alphaM/beta2 Integrin/proMMP-9 0.043 0.098 0.26 15 -10000 0 15
PLAUR 0.068 0.062 -10000 0 -10000 0 0
HMGB1 -0.029 0.045 -10000 0 -0.23 2 2
alphaM/beta2 Integrin/Talin -0.019 0.073 -10000 0 -10000 0 0
AGER -0.034 0.05 -10000 0 -0.59 1 1
RAP1A 0.034 0.005 -10000 0 -10000 0 0
SELPLG 0.034 0.028 -10000 0 -0.54 1 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.14 -10000 0 -0.38 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.095 0.074 -10000 0 -10000 0 0
CYR61 -0.13 0.26 -10000 0 -0.54 143 143
TLN1 0.034 0.006 -10000 0 -10000 0 0
Rap1/GTP 0.062 0.084 -10000 0 -0.34 6 6
RHOA 0.033 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.1 0.24 -10000 0 -0.54 117 117
MYH2 0.064 0.092 0.35 2 -0.5 4 6
MST1R 0.043 0.038 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.013 0.068 -10000 0 -10000 0 0
APOB 0.034 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.028 0.039 -10000 0 -0.54 2 2
JAM3 -0.008 0.14 -10000 0 -0.54 34 34
GP1BA 0.036 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.032 0.1 -10000 0 -0.36 21 21
alphaM/beta2 Integrin 0.049 0.082 0.27 1 -0.38 7 8
JAM3 homodimer -0.008 0.14 -10000 0 -0.54 34 34
ICAM2 0.021 0.076 -10000 0 -0.54 9 9
ICAM1 0.04 0.029 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor 0.047 0.086 0.27 1 -0.38 8 9
cell adhesion -0.016 0.078 0.27 3 -10000 0 3
NFKB1 -0.22 0.19 0.4 1 -0.36 297 298
THY1 0.034 0.025 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
Lipoprotein(a) 0.043 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.063 0.13 -10000 0 -0.33 75 75
IL6 -0.52 0.36 0.38 1 -0.74 375 376
ITGB2 -0.022 0.063 0.2 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.033 0.11 0.31 9 -10000 0 9
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.2 -10000 0 -0.42 124 124
JAM2 -0.12 0.25 -10000 0 -0.54 133 133
alphaM/beta2 Integrin/ICAM1 0.009 0.092 0.3 1 -10000 0 1
alphaM/beta2 Integrin/uPA/Plg 0.011 0.091 -10000 0 -0.36 1 1
RhoA/GTP 0.045 0.1 -10000 0 -0.44 10 10
positive regulation of phagocytosis 0.038 0.081 0.3 2 -0.36 1 3
Ron/MSP 0.056 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.035 0.11 0.32 9 -10000 0 9
alphaM/beta2 Integrin/uPAR 0.01 0.096 0.26 12 -10000 0 12
PLAU 0.057 0.053 -10000 0 -10000 0 0
PLAT -0.066 0.21 -10000 0 -0.54 85 85
actin filament polymerization 0.065 0.096 0.34 6 -0.44 5 11
MST1 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.01 0.072 -10000 0 -10000 0 0
TNF -0.21 0.18 0.41 3 -0.6 6 9
RAP1B 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.086 -10000 0 -10000 0 0
fibrinolysis 0.01 0.089 -10000 0 -0.36 1 1
HCK 0.036 0.022 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation 0.047 0.086 0.27 1 -0.38 8 9
VTN 0.033 0.011 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.11 0.17 -10000 0 -0.38 128 128
LPA 0.032 0.009 -10000 0 -10000 0 0
LRP1 0.034 0.005 -10000 0 -10000 0 0
cell migration 0.03 0.091 0.27 2 -0.36 2 4
FN1 0.13 0.068 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.017 0.075 -10000 0 -10000 0 0
MPO 0.032 0.016 -10000 0 -10000 0 0
KNG1 0.034 0.006 -10000 0 -10000 0 0
RAP1/GDP 0.044 0.012 -10000 0 -10000 0 0
ROCK1 0.064 0.11 0.28 6 -0.43 9 15
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
CTGF 0.012 0.11 -10000 0 -0.54 19 19
alphaM/beta2 Integrin/Hck -0.017 0.077 0.29 2 -10000 0 2
ITGAM -0.028 0.044 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.073 0.16 -10000 0 -0.36 100 100
HP 0.03 0.012 -10000 0 -10000 0 0
leukocyte adhesion -0.17 0.2 -10000 0 -0.47 120 120
SELP -0.1 0.24 -10000 0 -0.54 117 117
Ceramide signaling 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
SPHK2 -0.021 0.12 -10000 0 -0.4 46 46
MAP4K4 0.005 0.082 -10000 0 -0.32 13 13
BAG4 0.028 0.016 0.18 1 -10000 0 1
PKC zeta/ceramide -0.013 0.067 0.14 5 -0.27 9 14
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.017 0.11 -10000 0 -0.54 17 17
BAX 0.008 0.049 -10000 0 -0.35 5 5
RIPK1 0.034 0.006 -10000 0 -10000 0 0
AKT1 0.009 0.075 0.72 5 -10000 0 5
BAD -0.013 0.07 0.17 5 -0.28 8 13
SMPD1 0.019 0.063 0.26 5 -0.26 9 14
RB1 -0.012 0.067 0.16 3 -0.27 9 12
FADD/Caspase 8 0.033 0.12 0.29 11 -0.4 9 20
MAP2K4 -0.013 0.07 0.18 2 -0.31 8 10
NSMAF 0.028 0.028 -10000 0 -0.54 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.007 0.075 0.23 9 -0.35 4 13
EGF -0.15 0.27 -10000 0 -0.54 163 163
mol:ceramide -0.012 0.074 0.16 35 -0.27 10 45
MADD 0.034 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.023 0.12 -10000 0 -0.41 47 47
ASAH1 0.027 0.042 -10000 0 -0.54 2 2
negative regulation of cell cycle -0.014 0.068 0.16 3 -0.28 8 11
cell proliferation -0.1 0.14 -10000 0 -0.26 192 192
BID -0.014 0.19 -10000 0 -0.67 35 35
MAP3K1 -0.011 0.073 0.15 12 -0.26 12 24
EIF2A -0.005 0.072 0.25 10 -0.25 5 15
TRADD 0.03 0.012 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
MAPK3 -0.002 0.073 0.26 6 -0.31 5 11
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.007 0.079 0.26 6 -0.35 4 10
Cathepsin D/ceramide 0.011 0.08 0.18 4 -0.25 9 13
FADD 0.03 0.1 0.28 2 -0.42 4 6
KSR1 -0.007 0.073 0.19 10 -0.28 7 17
MAPK8 -0.008 0.07 -10000 0 -0.26 11 11
PRKRA -0.012 0.071 0.17 4 -0.28 8 12
PDGFA -0.018 0.16 -10000 0 -0.54 46 46
TRAF2 0.035 0.012 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.012 0.074 0.16 35 -0.28 9 44
CTSD 0.047 0.043 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.048 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.11 0.15 -10000 0 -0.28 192 192
PRKCD 0.035 0.017 0.18 6 -10000 0 6
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.023 0.12 -10000 0 -0.41 47 47
RelA/NF kappa B1 0.048 0.012 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.034 0.03 -10000 0 -0.54 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.009 0.09 -10000 0 -0.32 19 19
TNFR1A/BAG4/TNF-alpha 0.053 0.035 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.021 0.12 -10000 0 -0.4 46 46
MAP2K1 -0.007 0.074 0.28 5 -0.34 4 9
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.033 0.007 -10000 0 -10000 0 0
CYCS 0.027 0.082 0.21 30 -0.25 6 36
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.023 -10000 0 -10000 0 0
EIF2AK2 -0.008 0.069 0.2 6 -0.28 6 12
TNF-alpha/TNFR1A/FAN 0.057 0.037 -10000 0 -0.33 1 1
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.1 -10000 0 -0.43 17 17
MAP2K2 -0.007 0.074 0.28 5 -0.33 4 9
SMPD3 -0.001 0.12 0.24 3 -0.3 55 58
TNF 0.038 0.023 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.022 -10000 0 -0.4 1 1
mol:PHOSPHOCHOLINE 0.083 0.12 0.23 192 -0.22 3 195
NF kappa B1/RelA/I kappa B alpha 0.073 0.033 -10000 0 -0.3 1 1
AIFM1 0.026 0.082 0.23 23 -0.24 7 30
BCL2 -0.069 0.22 -10000 0 -0.54 91 91
IL1-mediated signaling events

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
UBC13/UEV1A 0.025 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.033 0.013 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.1 -10000 0 -0.36 22 22
IRAK/TOLLIP 0.039 0.014 -10000 0 -10000 0 0
IKBKB 0.029 0.013 -10000 0 -10000 0 0
IKBKG 0.034 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.055 0.044 0.26 1 -0.4 3 4
IL1A 0.036 0.016 -10000 0 -10000 0 0
IL1B -0.018 0.12 -10000 0 -0.42 42 42
IRAK/TRAF6/p62/Atypical PKCs 0.065 0.027 -10000 0 -10000 0 0
IL1R2 0.038 0.055 -10000 0 -0.54 3 3
IL1R1 -0.031 0.18 -10000 0 -0.54 58 58
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.031 0.14 -10000 0 -0.42 34 34
TOLLIP 0.033 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.039 0.068 0.3 1 -0.35 1 2
JUN -0.049 0.1 0.33 1 -0.27 82 83
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.025 0.2 -10000 0 -0.37 113 113
IL1 alpha/IL1R1/IL1RAP/MYD88 0.04 0.13 -10000 0 -0.31 58 58
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.052 0.13 -10000 0 -0.3 57 57
IL1 beta fragment/IL1R1/IL1RAP -0.023 0.16 -10000 0 -0.35 92 92
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.009 0.053 0.34 1 -0.27 11 12
IRAK1 0.019 0.011 -10000 0 -10000 0 0
IL1RN/IL1R1 0.014 0.15 -10000 0 -0.39 58 58
IRAK4 0.034 0.005 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.022 0.14 -10000 0 -0.41 35 35
CHUK 0.034 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.023 0.16 -10000 0 -0.35 92 92
IL1 beta/IL1R2 0.007 0.12 -10000 0 -0.36 45 45
IRAK/TRAF6/TAK1/TAB1/TAB2 0.046 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.034 0.18 -10000 0 -0.36 96 96
IRAK3 0.035 0.033 -10000 0 -0.54 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.008 0.16 -10000 0 -0.32 91 91
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.1 -10000 0 -0.27 56 56
IL1 alpha/IL1R1/IL1RAP 0.022 0.13 -10000 0 -0.34 58 58
RELA 0.033 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.034 0.009 -10000 0 -10000 0 0
MYD88 0.034 0.011 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.054 0.028 -10000 0 -10000 0 0
IL1RAP 0.034 0.006 -10000 0 -10000 0 0
UBE2N 0.034 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.023 0.13 -10000 0 -0.29 83 83
CASP1 -0.014 0.15 -10000 0 -0.54 39 39
IL1RN/IL1R2 0.068 0.056 0.26 6 -0.4 3 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.006 0.16 -10000 0 -0.34 92 92
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.13 -10000 0 -0.35 60 60
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL1RN 0.054 0.05 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.046 0.016 -10000 0 -10000 0 0
MAP2K6 0.016 0.055 0.36 2 -0.28 10 12
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.008 0.23 -10000 0 -0.9 24 24
NCK1/PAK1/Dok-R -0.034 0.093 -10000 0 -0.41 24 24
NCK1/Dok-R 0.019 0.24 -10000 0 -1 23 23
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.04 0.23 14 -10000 0 14
RELA 0.033 0.007 -10000 0 -10000 0 0
SHC1 0.029 0.014 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
F2 0.018 0.048 0.28 13 -10000 0 13
TNIP2 0.034 0.013 -10000 0 -10000 0 0
NF kappa B/RelA 0.043 0.23 -10000 0 -0.94 23 23
FN1 0.13 0.068 -10000 0 -10000 0 0
PLD2 -0.002 0.23 -10000 0 -1 23 23
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB14 0.001 0.19 -10000 0 -0.54 51 51
ELK1 0.006 0.21 -10000 0 -0.93 23 23
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.043 0.046 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.098 0.25 -10000 0 -0.96 23 23
CDKN1A -0.002 0.19 -10000 0 -0.66 21 21
ITGA5 0.035 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.018 0.24 -10000 0 -1 23 23
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:NO 0.017 0.18 -10000 0 -0.65 24 24
PLG -0.002 0.23 -10000 0 -1 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0 0.21 -10000 0 -0.84 24 24
GRB2 0.034 0.018 -10000 0 -10000 0 0
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
ANGPT2 -0.073 0.23 -10000 0 -0.67 33 33
BMX -0.16 0.28 -10000 0 -1.3 23 23
ANGPT1 -0.012 0.21 -10000 0 -1.2 14 14
tube development -0.01 0.2 -10000 0 -0.72 21 21
ANGPT4 0.032 0.007 -10000 0 -10000 0 0
response to hypoxia -0.001 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0 0.27 -10000 0 -1.1 23 23
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
STAT5A (dimer) 0 0.23 -10000 0 -0.84 21 21
mol:L-citrulline 0.017 0.18 -10000 0 -0.65 24 24
AGTR1 -0.18 0.3 -10000 0 -0.54 208 208
MAPK14 -0.002 0.26 -10000 0 -1 26 26
Tie2/SHP2 0.002 0.21 -10000 0 -1 15 15
TEK -0.002 0.22 -10000 0 -1.1 15 15
RPS6KB1 0.021 0.23 -10000 0 -0.86 24 24
Angiotensin II/AT1 -0.13 0.22 -10000 0 -0.39 210 210
Tie2/Ang1/GRB2 0.013 0.24 -10000 0 -1.1 23 23
MAPK3 0.006 0.22 -10000 0 -0.93 23 23
MAPK1 -0.002 0.21 -10000 0 -0.95 23 23
Tie2/Ang1/GRB7 0.005 0.24 -10000 0 -1 23 23
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.003 0.23 -10000 0 -1 23 23
PI3K -0.004 0.26 -10000 0 -1 24 24
FES -0.008 0.26 -10000 0 -1.1 26 26
Crk/Dok-R 0.019 0.23 -10000 0 -1 23 23
Tie2/Ang1/ABIN2 0.014 0.24 -10000 0 -1.1 23 23
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.014 0.21 -10000 0 -0.79 24 24
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.034 0.23 -10000 0 -0.82 24 24
Tie2/Ang2 -0.026 0.25 -10000 0 -1 21 21
Tie2/Ang1 0.002 0.25 -10000 0 -1.1 23 23
FOXO1 0.007 0.22 -10000 0 -0.81 25 25
ELF1 0.036 0.027 -10000 0 -10000 0 0
ELF2 0.003 0.23 -10000 0 -1 23 23
mol:Choline 0 0.22 -10000 0 -0.98 23 23
cell migration -0.015 0.054 -10000 0 -0.23 24 24
FYN -0.016 0.22 -10000 0 -0.84 21 21
DOK2 0.026 0.039 -10000 0 -0.54 2 2
negative regulation of cell cycle 0.003 0.17 -10000 0 -0.59 21 21
ETS1 0.031 0.056 -10000 0 -0.29 11 11
PXN 0.038 0.2 -10000 0 -0.68 24 24
ITGB1 0.034 0.006 -10000 0 -10000 0 0
NOS3 0.013 0.2 -10000 0 -0.74 24 24
RAC1 0.034 0.005 -10000 0 -10000 0 0
TNF 0.038 0.054 0.26 1 -0.25 14 15
MAPKKK cascade 0 0.22 -10000 0 -0.98 23 23
RASA1 0.034 0.011 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.005 0.24 -10000 0 -1 22 22
NCK1 0.034 0.005 -10000 0 -10000 0 0
vasculogenesis 0.02 0.16 -10000 0 -0.58 24 24
mol:Phosphatidic acid 0 0.22 -10000 0 -0.98 23 23
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.017 0.18 -10000 0 -0.65 24 24
Rac1/GTP 0.015 0.21 -10000 0 -0.8 24 24
MMP2 -0.002 0.24 -10000 0 -1 23 23
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.035 0.11 -10000 0 -0.36 5 5
epithelial cell differentiation 0.088 0.092 -10000 0 -10000 0 0
ITCH 0.047 0.025 -10000 0 -10000 0 0
WWP1 0.049 0.15 0.52 29 -10000 0 29
FYN 0.03 0.037 -10000 0 -0.54 2 2
EGFR -0.27 0.29 -10000 0 -0.54 269 269
PRL 0.034 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis 0.029 0.12 0.38 10 -0.47 1 11
PTPRZ1 -0.36 0.27 -10000 0 -0.54 353 353
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.017 0.1 -10000 0 -0.4 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.012 0.11 -10000 0 -0.42 6 6
ADAM17 0.047 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4 0.031 0.13 0.43 25 -0.4 3 28
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.035 0.11 0.35 1 -0.36 3 4
NCOR1 0.031 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.005 0.11 -10000 0 -0.4 6 6
GRIN2B -0.014 0.11 0.41 1 -0.41 4 5
ErbB4/ErbB2/betacellulin 0.029 0.099 -10000 0 -0.37 3 3
STAT1 0.059 0.055 -10000 0 -10000 0 0
HBEGF 0.029 0.051 -10000 0 -0.54 4 4
PRLR 0.071 0.064 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.005 0.15 -10000 0 -0.46 22 22
axon guidance 0.12 0.14 0.47 28 -10000 0 28
NEDD4 0.04 0.06 -10000 0 -0.52 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.074 0.047 -10000 0 -10000 0 0
CBFA2T3 -0.022 0.17 -10000 0 -0.54 47 47
ErbB4/ErbB2/HBEGF 0.037 0.088 -10000 0 -10000 0 0
MAPK3 0.029 0.12 0.4 6 -0.48 1 7
STAT1 (dimer) 0.055 0.11 0.41 4 -0.36 3 7
MAPK1 0.035 0.12 0.42 9 -0.48 1 10
JAK2 0.033 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.003 0.11 -10000 0 -0.4 5 5
NRG1 -0.013 0.11 -10000 0 -0.4 38 38
NRG3 0.035 0.043 -10000 0 -0.54 2 2
NRG2 -0.35 0.27 -10000 0 -0.54 339 339
NRG4 0.035 0.012 -10000 0 -10000 0 0
heart development 0.12 0.14 0.47 28 -10000 0 28
neural crest cell migration 0.004 0.11 -10000 0 -0.4 5 5
ERBB2 0.021 0.029 0.3 1 -0.37 1 2
WWOX/E4ICDs 0.026 0.1 0.4 2 -0.36 3 5
SHC1 0.028 0.014 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.13 0.16 -10000 0 -0.37 18 18
apoptosis -0.037 0.1 0.41 1 -0.35 3 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.18 0.17 -10000 0 -0.43 45 45
ErbB4/ErbB2/epiregulin 0.048 0.096 0.36 4 -10000 0 4
ErbB4/ErbB4/betacellulin/betacellulin 0.022 0.13 -10000 0 -0.4 9 9
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.087 0.12 0.38 9 -10000 0 9
MDM2 0.028 0.11 0.45 5 -10000 0 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.1 -10000 0 -0.38 5 5
STAT5A 0.11 0.13 0.42 26 -10000 0 26
ErbB4/EGFR/neuregulin 1 beta -0.15 0.18 -10000 0 -0.49 46 46
DLG4 0.031 0.011 -10000 0 -10000 0 0
GRB2/SHC 0.039 0.026 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.024 0.091 -10000 0 -0.33 3 3
STAT5A (dimer) 0.14 0.12 0.44 10 -10000 0 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.13 0.12 0.42 20 -10000 0 20
LRIG1 0.014 0.1 -10000 0 -0.54 17 17
EREG 0.045 0.049 -10000 0 -0.54 1 1
BTC 0.011 0.12 -10000 0 -0.54 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.11 0.14 0.47 28 -10000 0 28
ERBB4 0.031 0.13 0.43 25 -0.4 3 28
STAT5B 0.033 0.01 -10000 0 -10000 0 0
YAP1 0 0.12 0.26 6 -0.39 37 43
GRB2 0.034 0.018 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.039 0.084 -10000 0 -10000 0 0
glial cell differentiation -0.023 0.09 0.33 3 -10000 0 3
WWOX 0.034 0.031 -10000 0 -10000 0 0
cell proliferation 0.055 0.14 0.45 11 -0.43 4 15
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.071 0.094 0.23 3 -0.32 16 19
EPHB2 0.043 0.038 -10000 0 -10000 0 0
Syndecan-2/TACI 0.016 0.066 -10000 0 -0.33 16 16
LAMA1 0.033 0.01 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.058 0.17 -10000 0 -0.32 134 134
HRAS 0.034 0.013 -10000 0 -10000 0 0
Syndecan-2/CASK -0.001 0.06 -10000 0 -0.33 16 16
ITGA5 0.035 0.008 -10000 0 -10000 0 0
BAX -0.001 0.064 0.49 2 -10000 0 2
EPB41 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.059 -10000 0 -0.3 16 16
LAMA3 -0.15 0.27 -10000 0 -0.54 161 161
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.32 0.28 -10000 0 -0.54 318 318
Syndecan-2/MMP2 0.014 0.073 -10000 0 -0.36 16 16
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.08 -10000 0 -0.36 19 19
dendrite morphogenesis 0.022 0.07 -10000 0 -0.33 16 16
Syndecan-2/GM-CSF 0.021 0.068 -10000 0 -0.33 16 16
determination of left/right symmetry 0 0.071 -10000 0 -0.39 16 16
Syndecan-2/PKC delta 0.018 0.066 -10000 0 -0.33 16 16
GNB2L1 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.041 0.093 0.26 4 -0.3 16 20
MAPK1 0.047 0.097 0.24 6 -0.3 16 22
Syndecan-2/RACK1 0.031 0.062 -10000 0 -0.28 16 16
NF1 0.032 0.009 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0 0.071 -10000 0 -0.39 16 16
ITGA2 0.014 0.1 -10000 0 -0.54 17 17
MAPK8 0.002 0.067 0.4 2 -0.33 17 19
Syndecan-2/alpha2/beta1 Integrin 0.035 0.091 -10000 0 -0.33 23 23
Syndecan-2/Kininogen 0.017 0.065 -10000 0 -0.33 16 16
ITGB1 0.034 0.006 -10000 0 -10000 0 0
SRC 0.043 0.089 0.3 6 -0.28 15 21
Syndecan-2/CASK/Protein 4.1 0.015 0.059 -10000 0 -0.3 16 16
extracellular matrix organization 0.018 0.065 -10000 0 -0.33 16 16
actin cytoskeleton reorganization 0.071 0.094 0.23 3 -0.32 16 19
Syndecan-2/Caveolin-2/Ras -0.15 0.18 -10000 0 -0.32 237 237
Syndecan-2/Laminin alpha3 -0.082 0.17 -10000 0 -0.35 134 134
Syndecan-2/RasGAP 0.042 0.066 -10000 0 -0.27 16 16
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
PRKCD 0.035 0.017 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.071 -10000 0 -0.33 16 16
GO:0007205 0.003 0.005 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.028 0.058 -10000 0 -0.27 15 15
RHOA 0.033 0.007 -10000 0 -10000 0 0
SDCBP 0.029 0.028 -10000 0 -0.54 1 1
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
RASA1 0.034 0.011 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.08 -10000 0 -0.36 19 19
Syndecan-2/Synbindin 0.015 0.065 -10000 0 -0.33 16 16
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CASP3 0.042 0.095 0.24 8 -0.3 16 24
FN1 0.13 0.068 -10000 0 -10000 0 0
Syndecan-2/IL8 0.025 0.074 0.23 1 -0.33 16 17
SDC2 0 0.071 -10000 0 -0.39 16 16
KNG1 0.034 0.006 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.016 0.065 -10000 0 -0.33 16 16
TRAPPC4 0.031 0.011 -10000 0 -10000 0 0
CSF2 0.039 0.028 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.018 0.066 -10000 0 -0.33 16 16
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.06 -10000 0 -0.3 16 16
Syndecan-2/Ezrin 0.015 0.059 -10000 0 -0.3 16 16
PRKACA 0.045 0.096 0.23 4 -0.3 16 20
angiogenesis 0.025 0.074 0.23 1 -0.33 16 17
MMP2 0.028 0.039 -10000 0 -0.54 2 2
IL8 0.048 0.053 -10000 0 -0.54 1 1
calcineurin-NFAT signaling pathway 0.016 0.065 -10000 0 -0.33 16 16
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.05 0.023 -10000 0 -10000 0 0
VLDLR -0.04 0.19 -10000 0 -0.54 65 65
CRKL 0.032 0.009 -10000 0 -10000 0 0
LRPAP1 0.033 0.008 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
ITGA3 0.03 0.028 -10000 0 -0.54 1 1
RELN/VLDLR/Fyn -0.011 0.16 -10000 0 -0.36 82 82
MAPK8IP1/MKK7/MAP3K11/JNK1 0.078 0.049 -10000 0 -0.3 1 1
AKT1 -0.056 0.14 -10000 0 -0.3 108 108
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
DAB1 0.033 0.007 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.069 0.084 0.24 1 -0.29 20 21
LRPAP1/LRP8 0.073 0.048 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.074 0.089 -10000 0 -0.28 22 22
DAB1/alpha3/beta1 Integrin 0.018 0.13 -10000 0 -0.3 58 58
long-term memory 0.08 0.11 -10000 0 -0.32 20 20
DAB1/LIS1 0.034 0.15 -10000 0 -0.3 64 64
DAB1/CRLK/C3G 0.017 0.14 -10000 0 -0.3 64 64
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DAB1/NCK2 0.039 0.15 -10000 0 -0.31 64 64
ARHGEF2 0.03 0.022 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.032 0.012 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
RELN 0.012 0.11 -10000 0 -0.54 20 20
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RELN/LRP8/Fyn 0.066 0.095 -10000 0 -0.32 22 22
GRIN2A/RELN/LRP8/DAB1/Fyn 0.082 0.095 -10000 0 -0.3 14 14
MAPK8 0.033 0.026 -10000 0 -0.54 1 1
RELN/VLDLR/DAB1 -0.005 0.15 -10000 0 -0.33 80 80
ITGB1 0.034 0.006 -10000 0 -10000 0 0
MAP1B -0.037 0.16 0.28 9 -0.34 93 102
RELN/LRP8 0.069 0.091 0.26 1 -0.32 20 21
GRIN2B/RELN/LRP8/DAB1/Fyn 0.078 0.11 -10000 0 -0.33 23 23
PI3K 0.005 0.13 -10000 0 -0.4 44 44
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.043 0.027 -10000 0 -0.4 1 1
RAP1A -0.026 0.13 0.37 6 -0.48 5 11
PAFAH1B1 0.032 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.034 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.047 0.015 -10000 0 -10000 0 0
GRIN2B 0.021 0.085 -10000 0 -0.54 11 11
NCK2 0.035 0.007 -10000 0 -10000 0 0
neuron differentiation 0.048 0.069 0.24 3 -0.54 1 4
neuron adhesion -0.008 0.14 0.4 8 -0.46 4 12
LRP8 0.072 0.065 -10000 0 -10000 0 0
GSK3B -0.05 0.14 -10000 0 -0.5 24 24
RELN/VLDLR/DAB1/Fyn 0.004 0.15 -10000 0 -0.31 82 82
MAP3K11 0.033 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.055 0.16 -10000 0 -0.31 114 114
CDK5 0.037 0.024 -10000 0 -10000 0 0
MAPT 0.016 0.13 0.82 11 -0.49 3 14
neuron migration -0.028 0.15 0.38 4 -0.38 36 40
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.046 0.068 -10000 0 -0.55 1 1
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 80 80
HIF-2-alpha transcription factor network

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
MMP14 0.037 0.1 0.47 2 -0.67 4 6
oxygen homeostasis 0.025 0.029 0.2 3 -10000 0 3
TCEB2 0.032 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.13 0.14 0.44 24 -0.32 5 29
EPO 0.22 0.24 0.68 54 -0.52 1 55
FIH (dimer) 0.056 0.03 0.24 1 -10000 0 1
APEX1 0.058 0.037 0.23 2 -10000 0 2
SERPINE1 0.26 0.24 0.71 43 -0.51 3 46
FLT1 -0.014 0.17 -10000 0 -0.68 21 21
ADORA2A 0.26 0.25 0.66 68 -0.5 3 71
germ cell development 0.24 0.23 0.68 37 -0.52 2 39
SLC11A2 0.25 0.24 0.7 39 -0.51 3 42
BHLHE40 0.18 0.23 0.67 35 -0.49 4 39
HIF1AN 0.056 0.03 0.24 1 -10000 0 1
HIF2A/ARNT/SIRT1 0.17 0.19 0.54 44 -0.4 2 46
ETS1 0.041 0.034 -10000 0 -0.54 1 1
CITED2 0.005 0.15 -10000 0 -0.88 11 11
KDR -0.006 0.15 -10000 0 -0.67 16 16
PGK1 0.26 0.24 0.7 41 -0.51 3 44
SIRT1 0.036 0.008 -10000 0 -10000 0 0
response to hypoxia 0.002 0.006 -10000 0 -10000 0 0
HIF2A/ARNT 0.23 0.26 0.76 27 -0.56 4 31
EPAS1 0.16 0.17 0.46 60 -0.33 8 68
SP1 0.047 0.028 -10000 0 -10000 0 0
ABCG2 0.24 0.26 0.69 37 -0.62 10 47
EFNA1 0.18 0.22 0.66 21 -0.51 3 24
FXN 0.24 0.23 0.67 44 -0.51 2 46
POU5F1 0.25 0.23 0.69 36 -0.5 3 39
neuron apoptosis -0.23 0.26 0.54 4 -0.75 27 31
EP300 0.032 0.009 -10000 0 -10000 0 0
EGLN3 0.08 0.074 0.26 17 -0.54 1 18
EGLN2 0.06 0.035 0.26 2 -10000 0 2
EGLN1 0.045 0.034 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.054 0.033 -10000 0 -10000 0 0
VHL 0.036 0.018 0.18 7 -10000 0 7
ARNT 0.045 0.038 -10000 0 -10000 0 0
SLC2A1 0.25 0.24 0.67 53 -0.5 3 56
TWIST1 0.21 0.28 0.64 51 -0.55 29 80
ELK1 0.04 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.15 0.18 0.54 23 -0.4 2 25
VEGFA 0.25 0.24 0.73 41 -0.53 2 43
CREBBP 0.032 0.01 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.029 0.064 -10000 0 -0.54 6 6
SVIL 0.022 0.084 -10000 0 -0.54 11 11
ZNF318 0.03 0.009 -10000 0 -10000 0 0
JMJD2C 0.007 0.01 0.12 4 -10000 0 4
T-DHT/AR/Ubc9 -0.037 0.14 -10000 0 -0.31 81 81
CARM1 0.035 0.014 0.18 4 -10000 0 4
PRDX1 0.035 0.015 -10000 0 -10000 0 0
PELP1 0.031 0.01 -10000 0 -10000 0 0
CTNNB1 0.03 0.052 -10000 0 -0.54 4 4
AKT1 0.034 0.017 -10000 0 -10000 0 0
PTK2B 0.028 0.014 -10000 0 -10000 0 0
MED1 0.028 0.013 -10000 0 -10000 0 0
MAK 0.037 0.032 -10000 0 -10000 0 0
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.036 0.008 -10000 0 -10000 0 0
GSN -0.11 0.25 -10000 0 -0.54 132 132
NCOA2 0.029 0.015 -10000 0 -10000 0 0
NCOA6 0.035 0.008 -10000 0 -10000 0 0
DNA-PK 0.054 0.03 -10000 0 -10000 0 0
NCOA4 0.033 0.026 -10000 0 -0.54 1 1
PIAS3 0.029 0.014 -10000 0 -10000 0 0
cell proliferation -0.001 0.07 -10000 0 -0.47 6 6
XRCC5 0.033 0.006 -10000 0 -10000 0 0
UBE3A 0.035 0.009 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.052 0.13 -10000 0 -0.31 87 87
FHL2 -0.11 0.32 -10000 0 -0.98 58 58
RANBP9 0.035 0.01 -10000 0 -10000 0 0
JMJD1A -0.027 0.061 -10000 0 -0.14 122 122
CDK6 0.028 0.063 -10000 0 -0.54 6 6
TGFB1I1 0.03 0.045 -10000 0 -0.54 3 3
T-DHT/AR/CyclinD1 -0.036 0.15 -10000 0 -0.36 75 75
XRCC6 0.032 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.057 0.17 -10000 0 -0.36 86 86
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
CTDSP2 0.032 0.008 -10000 0 -10000 0 0
BRCA1 0.037 0.022 -10000 0 -10000 0 0
TCF4 0.024 0.067 -10000 0 -0.54 7 7
CDKN2A 0.052 0.055 -10000 0 -10000 0 0
SRF 0.02 0.058 -10000 0 -10000 0 0
NKX3-1 -0.072 0.11 -10000 0 -0.22 174 174
KLK3 0.015 0.056 -10000 0 -10000 0 0
TMF1 0.033 0.007 -10000 0 -10000 0 0
HNRNPA1 0.033 0.006 -10000 0 -10000 0 0
AOF2 0.001 0.002 0.02 4 -10000 0 4
APPL1 0.016 0.014 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.04 0.14 -10000 0 -0.32 81 81
AR -0.069 0.2 -10000 0 -0.56 66 66
UBA3 0 0.001 -10000 0 -10000 0 0
PATZ1 0.031 0.01 -10000 0 -10000 0 0
PAWR 0.034 0.03 -10000 0 -0.54 1 1
PRKDC 0.031 0.019 -10000 0 -10000 0 0
PA2G4 0.033 0.006 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.032 0.13 -10000 0 -0.29 78 78
RPS6KA3 0.034 0.037 -10000 0 -0.54 2 2
T-DHT/AR/ARA70 -0.039 0.14 -10000 0 -0.31 83 83
LATS2 0.021 0.076 -10000 0 -0.54 9 9
T-DHT/AR/PRX1 -0.034 0.13 -10000 0 -0.29 82 82
Cyclin D3/CDK11 p58 0.025 0.005 -10000 0 -10000 0 0
VAV3 0.03 0.12 -10000 0 -0.54 19 19
KLK2 -0.018 0.069 -10000 0 -0.42 1 1
CASP8 0.034 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.02 0.13 -10000 0 -0.29 69 69
TMPRSS2 -0.23 0.42 -10000 0 -0.97 122 122
CCND1 0.024 0.088 -10000 0 -0.54 10 10
PIAS1 0.035 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.035 0.049 1 -0.071 141 142
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.038 0.016 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.043 0.14 -10000 0 -0.32 87 87
CMTM2 0.03 0.012 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.053 -10000 0 -10000 0 0
CCND3 0.033 0.006 -10000 0 -10000 0 0
TGIF1 0.03 0.027 -10000 0 -0.54 1 1
FKBP4 0.038 0.026 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer 0.098 0.076 0.32 5 -0.28 4 9
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.1 0.37 13 -10000 0 13
alphaV/beta3 Integrin/Osteopontin/Src 0.1 0.072 0.26 2 -0.39 4 6
AP1 -0.14 0.22 0.49 1 -0.46 91 92
ILK 0.076 0.072 0.36 2 -0.3 4 6
bone resorption 0.06 0.07 -10000 0 -10000 0 0
PTK2B 0.028 0.014 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.09 -10000 0 -0.28 4 4
ITGAV 0.04 0.029 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.047 0.031 -10000 0 -0.4 2 2
alphaV/beta3 Integrin/Osteopontin 0.12 0.078 0.32 3 -0.33 4 7
MAP3K1 0.078 0.077 0.31 8 -0.3 5 13
JUN -0.066 0.22 -10000 0 -0.54 89 89
MAPK3 0.078 0.094 0.34 16 -0.28 3 19
MAPK1 0.077 0.091 0.33 13 -0.28 4 17
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.063 0.076 0.3 8 -0.29 6 14
ITGB3 0.041 0.021 -10000 0 -10000 0 0
NFKBIA 0.076 0.097 0.35 20 -10000 0 20
FOS -0.35 0.27 -10000 0 -0.54 345 345
CD44 0.033 0.028 -10000 0 -0.54 1 1
CHUK 0.034 0.005 -10000 0 -10000 0 0
PLAU 0.084 0.15 0.51 6 -0.54 1 7
NF kappa B1 p50/RelA 0.13 0.1 0.41 14 -10000 0 14
BCAR1 0.029 0.013 -10000 0 -10000 0 0
RELA 0.033 0.007 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.061 0.033 -10000 0 -0.39 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.078 0.073 0.31 8 -0.3 4 12
VAV3 0.062 0.094 0.31 10 -0.29 11 21
MAP3K14 0.086 0.082 0.31 8 -0.3 4 12
ROCK2 0.033 0.026 -10000 0 -0.54 1 1
SPP1 0.096 0.088 -10000 0 -0.54 3 3
RAC1 0.034 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.072 0.086 0.31 4 -0.27 10 14
MMP2 -0.14 0.17 0.47 1 -0.41 73 74
Thromboxane A2 receptor signaling

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
TGM2 0.046 0.042 -10000 0 -10000 0 0
GNB1/GNG2 -0.019 0.054 -10000 0 -0.18 47 47
AKT1 0.059 0.13 0.45 14 -0.32 7 21
EGF -0.15 0.27 -10000 0 -0.54 163 163
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.03 0.053 0.26 2 -10000 0 2
mol:Ca2+ 0.06 0.16 0.61 9 -0.32 19 28
LYN 0.027 0.052 0.26 3 -10000 0 3
RhoA/GTP 0.025 0.067 0.21 9 -0.14 3 12
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK 0.058 0.17 0.61 10 -0.34 43 53
GNG2 0.033 0.026 -10000 0 -0.54 1 1
ARRB2 0.031 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.014 0.12 -10000 0 -0.63 14 14
G beta5/gamma2 -0.014 0.075 -10000 0 -0.24 45 45
PRKCH 0.053 0.17 0.62 9 -0.35 45 54
DNM1 0.034 0.008 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.015 0.029 -10000 0 -0.53 1 1
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
PTGDR 0.031 0.06 -10000 0 -0.54 5 5
G12 family/GTP 0.005 0.11 -10000 0 -0.3 42 42
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
ADRBK2 0.03 0.037 -10000 0 -0.54 2 2
RhoA/GTP/ROCK1 0.045 0.012 -10000 0 -10000 0 0
mol:GDP -0.042 0.12 0.38 13 -0.46 9 22
mol:NADP 0.034 0.006 -10000 0 -10000 0 0
RAB11A 0.033 0.007 -10000 0 -10000 0 0
PRKG1 0.034 0.006 -10000 0 -10000 0 0
mol:IP3 0.059 0.18 0.64 9 -0.37 43 52
cell morphogenesis 0.044 0.012 -10000 0 -10000 0 0
PLCB2 0.052 0.22 0.7 8 -0.5 45 53
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.031 0.054 0.25 3 -10000 0 3
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.03 0.055 0.26 2 -10000 0 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
PTGIR 0.034 0.005 -10000 0 -10000 0 0
PRKCB1 0.055 0.18 0.63 9 -0.37 45 54
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.034 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.054 0.22 0.72 8 -0.51 46 54
LCK 0.039 0.061 0.26 5 -10000 0 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.044 0.041 -10000 0 -0.23 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.1 -10000 0 -0.42 21 21
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.041 0.042 -10000 0 -0.23 5 5
MAPK14 0.052 0.13 0.5 11 -0.25 8 19
TGM2/GTP 0.056 0.2 0.7 8 -0.41 36 44
MAPK11 0.051 0.13 0.49 12 -0.25 8 20
ARHGEF1 0.047 0.11 0.36 15 -0.2 6 21
GNAI2 0.033 0.01 -10000 0 -10000 0 0
JNK cascade 0.06 0.18 0.65 9 -0.38 45 54
RAB11/GDP 0.032 0.01 -10000 0 -10000 0 0
ICAM1 0.058 0.15 0.52 13 -0.28 37 50
cAMP biosynthetic process 0.055 0.17 0.6 9 -0.34 36 45
Gq family/GTP/EBP50 0.034 0.048 -10000 0 -0.22 6 6
actin cytoskeleton reorganization 0.044 0.012 -10000 0 -10000 0 0
SRC 0.028 0.053 0.26 2 -10000 0 2
GNB5 0.032 0.026 -10000 0 -0.54 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.11 0.26 3 -0.29 44 47
VCAM1 0.054 0.16 0.55 11 -0.31 45 56
TP beta/Gq family/GDP/G beta5/gamma2 0.014 0.12 -10000 0 -0.63 14 14
platelet activation 0.063 0.16 0.58 11 -0.32 14 25
PGI2/IP 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.031 -10000 0 -0.26 5 5
Gq family/GDP/G beta5/gamma2 0.016 0.11 -10000 0 -0.55 14 14
TXA2/TP beta/beta Arrestin2 -0.003 0.061 -10000 0 -0.39 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.013 0.031 -10000 0 -0.25 5 5
mol:DAG 0.058 0.2 0.69 8 -0.42 45 53
EGFR -0.27 0.29 -10000 0 -0.54 269 269
TXA2/TP alpha 0.058 0.21 0.7 8 -0.47 39 47
Gq family/GTP 0.01 0.052 0.22 1 -0.22 18 19
YES1 0.03 0.057 0.26 2 -0.42 1 3
GNAI2/GTP 0.031 0.04 -10000 0 -0.24 2 2
PGD2/DP 0.023 0.044 -10000 0 -0.4 5 5
SLC9A3R1 0.059 0.058 -10000 0 -10000 0 0
FYN 0.027 0.055 0.27 1 -0.29 2 3
mol:NO 0.034 0.006 -10000 0 -10000 0 0
GNA15 0.036 0.019 -10000 0 -10000 0 0
PGK/cGMP 0.045 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.011 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.067 0.056 0.29 1 -0.34 1 2
NOS3 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.064 0.18 0.6 10 -0.35 40 50
PRKCB 0.054 0.17 0.61 9 -0.35 46 55
PRKCE 0.055 0.17 0.6 10 -0.35 44 54
PRKCD 0.054 0.18 0.63 9 -0.38 46 55
PRKCG 0.056 0.18 0.66 8 -0.38 45 53
muscle contraction 0.055 0.21 0.71 8 -0.47 46 54
PRKCZ 0.057 0.17 0.59 10 -0.34 45 55
ARR3 0.035 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.045 0.048 -10000 0 -0.26 2 2
PRKCQ 0.06 0.18 0.59 12 -0.35 45 57
MAPKKK cascade 0.055 0.2 0.68 8 -0.44 44 52
SELE 0.049 0.18 0.54 12 -0.38 48 60
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.048 0.29 1 -0.34 1 2
ROCK1 0.034 0.006 -10000 0 -10000 0 0
GNA14 0.044 0.068 0.18 50 -0.54 4 54
chemotaxis 0.05 0.25 0.75 8 -0.59 49 57
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.026 0.004 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CCL5 0.029 0.06 -10000 0 -0.54 5 5
SDCBP 0.029 0.028 -10000 0 -0.54 1 1
FGFR/FGF2/Syndecan-1 0.087 0.14 0.32 31 -0.35 6 37
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 0.069 0.14 0.28 16 -0.34 8 24
Syndecan-1/Syntenin 0.072 0.14 0.29 23 -0.34 9 32
MAPK3 0.071 0.13 0.28 27 -0.34 6 33
HGF/MET 0.006 0.13 -10000 0 -0.4 51 51
TGFB1/TGF beta receptor Type II 0.034 0.008 -10000 0 -10000 0 0
BSG 0.034 0.015 -10000 0 -10000 0 0
keratinocyte migration 0.069 0.13 0.28 16 -0.34 8 24
Syndecan-1/RANTES 0.075 0.15 0.3 30 -0.37 10 40
Syndecan-1/CD147 0.091 0.15 0.35 11 -0.35 6 17
Syndecan-1/Syntenin/PIP2 0.067 0.13 0.27 23 -0.32 9 32
LAMA5 0.032 0.012 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.065 0.13 0.27 23 -0.32 9 32
MMP7 -0.041 0.19 -10000 0 -0.54 64 64
HGF 0.035 0.01 -10000 0 -10000 0 0
Syndecan-1/CASK 0.059 0.13 0.25 26 -0.33 9 35
Syndecan-1/HGF/MET 0.062 0.18 0.33 9 -0.38 30 39
regulation of cell adhesion 0.061 0.12 0.3 9 -0.33 5 14
HPSE 0.046 0.04 -10000 0 -10000 0 0
positive regulation of cell migration 0.087 0.14 0.32 31 -0.35 6 37
SDC1 0.086 0.13 0.3 28 -0.35 3 31
Syndecan-1/Collagen 0.087 0.14 0.32 31 -0.35 6 37
PPIB 0.034 0.009 -10000 0 -10000 0 0
MET -0.022 0.17 -10000 0 -0.54 50 50
PRKACA 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.095 0.074 -10000 0 -10000 0 0
MAPK1 0.071 0.13 0.28 23 -0.34 5 28
homophilic cell adhesion 0.085 0.14 0.32 31 -0.35 6 37
MMP1 0.11 0.077 -10000 0 -10000 0 0
Regulation of 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
RIP1/MEKK3 0.041 0.016 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.034 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.021 0.081 -10000 0 -0.54 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.03 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.11 0.12 -10000 0 -0.23 239 239
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.032 0.027 -10000 0 -0.54 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
MAP3K12 0.034 0.005 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.041 0.095 -10000 0 -0.31 41 41
PRKG1 0.034 0.006 -10000 0 -10000 0 0
DUSP8 0.033 0.007 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.012 0.12 -10000 0 -0.33 32 32
apoptosis -0.039 0.091 -10000 0 -0.3 41 41
RAL/GTP 0.045 0.01 -10000 0 -10000 0 0
LYN 0.03 0.015 -10000 0 -10000 0 0
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
PAK1 0.043 0.046 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.071 0.036 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -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 0.034 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.044 0.012 -10000 0 -10000 0 0
MAPK11 0.001 0.13 0.38 2 -0.37 30 32
BLK 0.039 0.044 -10000 0 -10000 0 0
HCK 0.036 0.022 -10000 0 -10000 0 0
MAP2K3 0.031 0.01 -10000 0 -10000 0 0
DUSP16 0.033 0.012 -10000 0 -10000 0 0
DUSP10 0.028 0.032 -10000 0 -0.54 1 1
TRAF6/MEKK3 0.038 0.016 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.13 0.36 2 -0.35 35 37
positive regulation of innate immune response 0 0.16 0.59 1 -0.42 36 37
LCK 0.048 0.044 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.014 0.16 0.58 1 -0.41 32 33
p38alpha-beta/MKP5 0.009 0.15 0.58 1 -0.42 30 31
PGK/cGMP 0.025 0.004 -10000 0 -10000 0 0
PAK2 0.033 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.085 0.2 -10000 0 -0.42 73 73
CDC42 0.033 0.008 -10000 0 -10000 0 0
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.005 -10000 0 -10000 0 0
PAK3 -0.31 0.28 -10000 0 -0.54 309 309
Regulation of Telomerase

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
Telomerase catalytic core complex 0.003 0.18 -10000 0 -0.75 11 11
RAD9A 0.032 0.01 -10000 0 -10000 0 0
AP1 -0.31 0.26 -10000 0 -0.48 345 345
IFNAR2 0.039 0.012 -10000 0 -10000 0 0
AKT1 -0.005 0.12 -10000 0 -0.4 12 12
ER alpha/Oestrogen -0.042 0.19 -10000 0 -0.39 110 110
NFX1/SIN3/HDAC complex 0.035 0.074 -10000 0 -0.35 12 12
EGF -0.15 0.27 -10000 0 -0.54 163 163
SMG5 0.03 0.017 -10000 0 -10000 0 0
SMG6 0.031 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.056 0.025 -10000 0 -10000 0 0
TERT/c-Abl 0.011 0.17 -10000 0 -0.78 8 8
SAP18 0.033 0.01 -10000 0 -10000 0 0
MRN complex 0.049 0.033 -10000 0 -10000 0 0
WT1 0.087 0.07 -10000 0 -10000 0 0
WRN 0.028 0.015 -10000 0 -10000 0 0
SP1 0.041 0.016 -10000 0 -10000 0 0
SP3 0.036 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.012 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.03 0.16 -10000 0 -0.7 8 8
Mad/Max 0.055 0.017 -10000 0 -10000 0 0
TERT -0.004 0.18 -10000 0 -0.84 9 9
CCND1 0.035 0.26 0.57 9 -1 14 23
MAX 0.035 0.01 -10000 0 -10000 0 0
RBBP7 0.039 0.022 -10000 0 -10000 0 0
RBBP4 0.035 0.006 -10000 0 -10000 0 0
TERF2 0.027 0.028 -10000 0 -0.49 1 1
PTGES3 0.033 0.026 -10000 0 -0.54 1 1
SIN3A 0.035 0.006 -10000 0 -10000 0 0
Telomerase/911 0.039 0.06 -10000 0 -0.45 2 2
CDKN1B 0.043 0.11 0.31 1 -0.61 10 11
RAD1 0.034 0.009 -10000 0 -10000 0 0
XRCC5 0.034 0.005 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
SAP30 0.035 0.009 -10000 0 -10000 0 0
TRF2/PARP2 0.043 0.028 -10000 0 -0.39 1 1
UBE3A 0.035 0.009 -10000 0 -10000 0 0
JUN -0.065 0.22 -10000 0 -0.54 89 89
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.029 0.012 -10000 0 -10000 0 0
FOS -0.35 0.27 -10000 0 -0.54 345 345
IFN-gamma/IRF1 0.082 0.083 0.28 9 -0.32 10 19
PARP2 0.034 0.006 -10000 0 -10000 0 0
BLM 0.074 0.066 -10000 0 -10000 0 0
Telomerase 0.004 0.095 -10000 0 -0.72 4 4
IRF1 0.045 0.048 0.2 2 -0.18 9 11
ESR1 -0.058 0.25 -10000 0 -0.54 106 106
KU/TER 0.047 0.014 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.033 -10000 0 -0.29 1 1
ubiquitin-dependent protein catabolic process 0.043 0.069 -10000 0 -0.37 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.044 0.07 -10000 0 -0.38 6 6
HDAC1 0.035 0.006 -10000 0 -10000 0 0
HDAC2 0.039 0.021 -10000 0 -10000 0 0
ATM 0.017 0.021 0.21 1 -10000 0 1
SMAD3 0.01 0.017 -10000 0 -10000 0 0
ABL1 0.034 0.005 -10000 0 -10000 0 0
MXD1 0.037 0.009 -10000 0 -10000 0 0
MRE11A 0.031 0.011 -10000 0 -10000 0 0
HUS1 0.035 0.01 -10000 0 -10000 0 0
RPS6KB1 0.03 0.012 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.026 0.18 -10000 0 -0.74 11 11
NR2F2 0.008 0.094 -10000 0 -0.55 13 13
MAPK3 0.019 0.022 -10000 0 -0.4 1 1
MAPK1 0.019 0.022 -10000 0 -0.4 1 1
TGFB1/TGF beta receptor Type II 0.033 0.008 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
HNRNPC 0.034 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.017 0.021 0.21 1 -10000 0 1
NBN 0.028 0.016 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.31 0.26 -10000 0 -0.46 351 351
MYC -0.001 0.12 -10000 0 -0.54 25 25
IL2 0.04 0.031 -10000 0 -0.54 1 1
KU 0.047 0.014 -10000 0 -10000 0 0
RAD50 0.034 0.006 -10000 0 -10000 0 0
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
TGFB1 0.033 0.008 -10000 0 -10000 0 0
TRF2/BLM 0.066 0.056 -10000 0 -0.39 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.024 0.18 -10000 0 -0.78 8 8
SP1/HDAC2 0.061 0.032 -10000 0 -10000 0 0
PINX1 0.027 0.014 -10000 0 -10000 0 0
Telomerase/EST1A 0.024 0.16 -10000 0 -0.7 8 8
Smad3/Myc 0.006 0.081 -10000 0 -0.34 25 25
911 complex 0.062 0.025 0.26 1 -10000 0 1
IFNG 0.065 0.073 -10000 0 -0.54 1 1
Telomerase/PinX1 0.012 0.16 -10000 0 -0.7 8 8
Telomerase/AKT1/mTOR/p70S6K 0.022 0.12 -10000 0 -0.51 14 14
SIN3B 0.036 0.014 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.03 0.15 -10000 0 -0.72 7 7
response to DNA damage stimulus -0.001 0.03 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.061 0.052 -10000 0 -0.31 1 1
TRF2/WRN 0.036 0.03 -10000 0 -0.39 1 1
Telomerase/hnRNP C1/C2 0.03 0.16 -10000 0 -0.73 7 7
E2F1 0.055 0.049 -10000 0 -10000 0 0
ZNFX1 0.034 0.017 -10000 0 -10000 0 0
PIF1 0.039 0.028 -10000 0 -10000 0 0
NCL 0.034 0.006 -10000 0 -10000 0 0
DKC1 0.035 0.012 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Syndecan-4-mediated 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
PTK2 0.12 0.11 0.29 3 -0.63 4 7
Syndecan-4/Syndesmos 0.13 0.12 0.41 3 -0.72 4 7
positive regulation of JNK cascade 0.062 0.18 0.41 1 -0.66 6 7
Syndecan-4/ADAM12 0.15 0.13 0.41 5 -0.76 4 9
CCL5 0.029 0.06 -10000 0 -0.54 5 5
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DNM2 0.034 0.005 -10000 0 -10000 0 0
ITGA5 0.035 0.008 -10000 0 -10000 0 0
SDCBP 0.029 0.028 -10000 0 -0.54 1 1
PLG 0.013 0.04 -10000 0 -0.54 1 1
ADAM12 0.057 0.061 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.032 0.012 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha 0.008 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.13 0.12 0.42 1 -0.76 4 5
Syndecan-4/CXCL12/CXCR4 0.065 0.19 0.42 1 -0.72 6 7
Syndecan-4/Laminin alpha3 0.054 0.16 0.42 2 -0.75 5 7
MDK 0.044 0.037 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.061 0.18 0.41 1 -0.62 7 8
Syndecan-4/Midkine 0.14 0.12 0.41 3 -0.71 4 7
FZD7 -0.13 0.26 -10000 0 -0.54 145 145
Syndecan-4/FGFR1/FGF -0.065 0.16 0.4 1 -0.56 11 12
THBS1 0.038 0.025 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.14 0.12 0.41 2 -0.72 4 6
positive regulation of MAPKKK cascade 0.062 0.18 0.41 1 -0.66 6 7
Syndecan-4/TACI 0.13 0.12 0.42 2 -0.76 4 6
CXCR4 0.044 0.038 -10000 0 -10000 0 0
cell adhesion 0.092 0.071 0.27 50 -10000 0 50
Syndecan-4/Dynamin 0.14 0.12 0.42 1 -0.76 4 5
Syndecan-4/TSP1 0.14 0.12 0.43 3 -0.76 4 7
Syndecan-4/GIPC 0.14 0.12 0.42 3 -0.76 4 7
Syndecan-4/RANTES 0.13 0.13 0.41 1 -0.76 4 5
ITGB1 0.034 0.006 -10000 0 -10000 0 0
LAMA1 0.033 0.01 -10000 0 -10000 0 0
LAMA3 -0.15 0.27 -10000 0 -0.54 161 161
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.031 0.22 0.7 50 -10000 0 50
Syndecan-4/alpha-Actinin 0.14 0.12 0.42 1 -0.76 4 5
TFPI -0.19 0.28 -10000 0 -0.54 199 199
F2 0.039 0.02 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.044 0.15 0.38 2 -0.72 5 7
ACTN1 0.033 0.007 -10000 0 -10000 0 0
TNC 0.037 0.036 -10000 0 -0.54 1 1
Syndecan-4/CXCL12 0.055 0.19 0.42 1 -0.66 8 9
FGF6 0.03 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
CXCL12 -0.14 0.26 -10000 0 -0.54 152 152
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
FGFR1 0.018 0.076 -10000 0 -0.54 9 9
Syndecan-4/PI-4-5-P2 0.097 0.12 -10000 0 -0.76 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.075 0.21 4 -10000 0 4
cell migration -0.013 0.008 -10000 0 -10000 0 0
PRKCD 0.017 0.035 0.18 2 -10000 0 2
vasculogenesis 0.14 0.12 0.43 3 -0.72 4 7
SDC4 0.11 0.12 -10000 0 -0.81 4 4
Syndecan-4/Tenascin C 0.14 0.12 0.42 2 -0.76 4 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.12 0.12 0.41 1 -0.76 4 5
MMP9 0.094 0.078 0.2 2 -10000 0 2
Rac1/GTP 0.093 0.072 0.27 50 -10000 0 50
cytoskeleton organization 0.13 0.12 0.4 3 -0.69 4 7
GIPC1 0.034 0.01 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.035 0.19 0.4 2 -0.62 9 11
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.017 0.004 -10000 0 -10000 0 0
SMARCC1 0.016 0.052 -10000 0 -0.68 1 1
REL 0.037 0.024 -10000 0 -10000 0 0
HDAC7 -0.051 0.12 0.33 1 -0.33 41 42
JUN -0.066 0.22 -10000 0 -0.54 89 89
EP300 0.033 0.009 -10000 0 -10000 0 0
KAT2B 0 0 0.003 3 -10000 0 3
KAT5 0 0 -10000 0 -0.003 1 1
MAPK14 -0.003 0.063 -10000 0 -0.41 10 10
FOXO1 -0.023 0.17 -10000 0 -0.54 48 48
T-DHT/AR -0.025 0.14 0.36 1 -0.35 40 41
MAP2K6 0.009 0.084 -10000 0 -0.55 10 10
BRM/BAF57 0.046 0.018 -10000 0 -10000 0 0
MAP2K4 0.018 0.027 -10000 0 -10000 0 0
SMARCA2 0.033 0.009 -10000 0 -10000 0 0
PDE9A -0.059 0.26 -10000 0 -1 31 31
NCOA2 0.029 0.015 -10000 0 -10000 0 0
CEBPA 0.03 0.044 -10000 0 -0.54 3 3
EHMT2 0.035 0.005 -10000 0 -10000 0 0
cell proliferation 0.036 0.15 0.43 13 -0.42 4 17
NR0B1 -0.094 0.25 -10000 0 -0.54 120 120
EGR1 -0.43 0.22 -10000 0 -0.54 415 415
RXRs/9cRA 0.051 0.043 -10000 0 -0.31 4 4
AR/RACK1/Src 0.003 0.099 0.34 5 -0.32 8 13
AR/GR -0.04 0.14 -10000 0 -0.29 90 90
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
PKN1 0.035 0.011 -10000 0 -10000 0 0
RCHY1 0.029 0.051 -10000 0 -0.54 4 4
epidermal growth factor receptor activity 0 0.001 0.009 4 -10000 0 4
MAPK8 0.003 0.032 -10000 0 -0.43 1 1
T-DHT/AR/TIF2/CARM1 0.007 0.094 0.35 1 -0.35 7 8
SRC -0.009 0.075 0.47 1 -0.33 7 8
NR3C1 -0.011 0.16 -10000 0 -0.54 40 40
KLK3 -0.042 0.099 0.45 1 -0.41 3 4
APPBP2 0.018 0.027 -10000 0 -10000 0 0
TRIM24 0.035 0.013 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.036 0.072 -10000 0 -0.35 11 11
TMPRSS2 -0.22 0.45 -10000 0 -1 124 124
RXRG 0.025 0.053 -10000 0 -0.54 4 4
mol:9cRA 0 0 0.003 4 -10000 0 4
RXRA 0.034 0.006 -10000 0 -10000 0 0
RXRB 0.034 0.005 -10000 0 -10000 0 0
CARM1 0.035 0.014 0.18 4 -10000 0 4
NR2C2 0.035 0.015 -10000 0 -10000 0 0
KLK2 0.013 0.077 0.35 2 -10000 0 2
AR -0.025 0.1 -10000 0 -0.27 63 63
SENP1 0.034 0.004 -10000 0 -10000 0 0
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
MDM2 0.032 0.011 -10000 0 -10000 0 0
SRY -0.001 0.002 -10000 0 -0.025 4 4
GATA2 0.042 0.033 -10000 0 -10000 0 0
MYST2 0 0.001 -10000 0 -0.006 4 4
HOXB13 0.079 0.07 0.2 2 -10000 0 2
T-DHT/AR/RACK1/Src 0 0.1 0.35 5 -0.33 9 14
positive regulation of transcription 0.042 0.033 -10000 0 -10000 0 0
DNAJA1 0.019 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.032 -10000 0 -0.32 4 4
NCOA1 0.042 0.033 -10000 0 -0.57 1 1
SPDEF -0.019 0.17 -10000 0 -0.54 50 50
T-DHT/AR/TIF2 0.017 0.08 0.41 2 -0.3 5 7
T-DHT/AR/Hsp90 -0.011 0.098 0.39 2 -0.36 11 13
GSK3B 0.033 0.01 -10000 0 -10000 0 0
NR2C1 0.033 0.026 -10000 0 -0.54 1 1
mol:T-DHT -0.019 0.071 0.22 14 -0.35 10 24
SIRT1 0.034 0.005 -10000 0 -10000 0 0
ZMIZ2 0.032 0.008 -10000 0 -10000 0 0
POU2F1 0.003 0.065 -10000 0 -0.19 1 1
T-DHT/AR/DAX-1 -0.073 0.17 0.39 2 -0.34 113 115
CREBBP 0.032 0.01 -10000 0 -10000 0 0
SMARCE1 0.033 0.009 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.03 0.027 -10000 0 -0.54 1 1
GNB1/GNG2 0.025 0.15 -10000 0 -0.44 27 27
mol:DAG 0.006 0.13 -10000 0 -0.4 27 27
PLCG1 0.005 0.13 -10000 0 -0.42 27 27
YES1 -0.002 0.14 0.25 1 -0.48 24 25
FZD3 0.014 0.091 -10000 0 -0.54 13 13
FZD6 0.007 0.11 -10000 0 -0.54 18 18
G protein 0.036 0.15 0.34 5 -0.42 26 31
MAP3K7 -0.005 0.11 0.25 1 -0.36 23 24
mol:Ca2+ 0.006 0.13 -10000 0 -0.39 27 27
mol:IP3 0.006 0.13 -10000 0 -0.4 27 27
NLK 0.003 0.13 -10000 0 -0.8 13 13
GNB1 0.034 0.011 -10000 0 -10000 0 0
CAMK2A 0 0.12 0.26 1 -0.38 26 27
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.13 -10000 0 -0.38 45 45
CSNK1A1 0.034 0.005 -10000 0 -10000 0 0
GNAS -0.005 0.13 0.25 1 -0.45 24 25
GO:0007205 0 0.13 0.26 1 -0.41 26 27
WNT6 0.033 0.04 0.18 6 -0.54 2 8
WNT4 0.04 0.034 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.016 0.14 -10000 0 -0.43 24 24
GNG2 0.033 0.026 -10000 0 -0.54 1 1
WNT5A 0.01 0.13 -10000 0 -0.54 25 25
WNT11 0.024 0.079 -10000 0 -0.54 9 9
CDC42 -0.003 0.13 0.24 1 -0.46 22 23
IL2 signaling events mediated by PI3K

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
BCL2L1 0.02 0.093 -10000 0 -0.48 1 1
UGCG 0.029 0.12 -10000 0 -0.65 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0 0.18 0.33 1 -0.4 43 44
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.03 0.11 -10000 0 -0.64 11 11
mol:DAG 0.003 0.11 -10000 0 -0.82 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.22 0.35 1 -0.42 73 74
FRAP1 -0.036 0.24 0.38 1 -0.47 84 85
FOXO3 0.005 0.18 0.37 4 -0.51 30 34
AKT1 0.002 0.2 0.39 1 -0.54 32 33
GAB2 0.028 0.014 -10000 0 -10000 0 0
SMPD1 0.008 0.12 -10000 0 -0.65 15 15
SGMS1 0.018 0.082 -10000 0 -0.57 8 8
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 -0.028 0.097 -10000 0 -0.34 44 44
CALM1 0.034 0.006 -10000 0 -10000 0 0
cell proliferation 0.049 0.12 0.42 1 -0.5 8 9
EIF3A 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
RPS6KB1 0.001 0.13 -10000 0 -0.83 8 8
mol:sphingomyelin 0.003 0.11 -10000 0 -0.82 8 8
natural killer cell activation -0.002 0.005 -10000 0 -0.02 3 3
JAK3 0.033 0.009 -10000 0 -10000 0 0
PIK3R1 -0.021 0.17 -10000 0 -0.54 47 47
JAK1 0.033 0.01 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MYC 0.022 0.27 0.54 1 -0.92 31 32
MYB -0.047 0.34 0.45 1 -1.2 42 43
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.027 0.13 0.32 1 -0.37 15 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.035 0.13 -10000 0 -0.71 9 9
mol:PI-3-4-5-P3 0.029 0.13 0.32 1 -0.37 14 15
Rac1/GDP -0.011 0.095 -10000 0 -0.31 44 44
T cell proliferation 0.028 0.12 0.3 1 -0.35 14 15
SHC1 0.026 0.016 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.029 0.094 25 -0.068 41 66
PRKCZ 0.026 0.12 0.31 1 -0.36 14 15
NF kappa B1 p50/RelA -0.01 0.22 0.37 1 -0.5 44 45
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.022 0.097 0.3 1 -0.38 9 10
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
RELA 0.033 0.007 -10000 0 -10000 0 0
IL2RA 0.039 0.035 -10000 0 -10000 0 0
IL2RB 0.035 0.023 -10000 0 -10000 0 0
TERT 0.032 0.028 -10000 0 -0.54 1 1
E2F1 0.014 0.14 0.31 2 -0.4 46 48
SOS1 0.032 0.01 -10000 0 -10000 0 0
RPS6 0.032 0.026 -10000 0 -0.54 1 1
mol:cAMP -0.002 0.014 0.032 41 -0.05 24 65
PTPN11 0.031 0.011 -10000 0 -10000 0 0
IL2RG 0.043 0.037 -10000 0 -10000 0 0
actin cytoskeleton organization 0.028 0.12 0.3 1 -0.35 14 15
GRB2 0.032 0.02 -10000 0 -10000 0 0
IL2 0.032 0.029 -10000 0 -0.54 1 1
PIK3CA 0.032 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.1 -10000 0 -0.29 44 44
LCK 0.047 0.046 -10000 0 -10000 0 0
BCL2 -0.12 0.38 0.52 1 -0.84 104 105
Signaling events mediated by PRL

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
CCNE1 0.059 0.056 -10000 0 -10000 0 0
mol:Halofuginone 0.003 0.004 -10000 0 -10000 0 0
ITGA1 0.031 0.037 -10000 0 -0.54 2 2
CDKN1A -0.081 0.1 -10000 0 -0.52 18 18
PRL-3/alpha Tubulin 0.042 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.043 -10000 0 -10000 0 0
AGT 0.043 0.049 0.18 56 -10000 0 56
CCNA2 -0.18 0.12 -10000 0 -10000 0 0
TUBA1B 0.035 0.012 0.18 3 -10000 0 3
EGR1 -0.31 0.16 -10000 0 -0.39 414 414
CDK2/Cyclin E1 -0.042 0.11 -10000 0 -0.44 20 20
MAPK3 0.015 0.019 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.051 0.018 -10000 0 -10000 0 0
MAPK1 0.015 0.018 -10000 0 -10000 0 0
PTP4A1 -0.22 0.13 -10000 0 -10000 0 0
PTP4A3 0.03 0.025 -10000 0 -10000 0 0
PTP4A2 0.037 0.021 -10000 0 -10000 0 0
ITGB1 0.015 0.018 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1 -0.057 0.075 -10000 0 -0.51 6 6
Rab GGTase beta/Rab GGTase alpha 0.049 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.21 0.12 -10000 0 -10000 0 0
RABGGTA 0.034 0.006 -10000 0 -10000 0 0
BCAR1 -0.019 0.017 -10000 0 -10000 0 0
RHOC -0.059 0.084 -10000 0 -0.52 9 9
RHOA -0.064 0.1 -10000 0 -0.54 15 15
cell motility -0.085 0.096 -10000 0 -0.39 25 25
PRL-1/alpha Tubulin -0.21 0.12 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.04 0.034 -10000 0 -0.4 1 1
ROCK1 -0.082 0.095 -10000 0 -0.39 23 23
RABGGTB 0.034 0.006 -10000 0 -10000 0 0
CDK2 0.037 0.021 -10000 0 -10000 0 0
mitosis -0.22 0.13 -10000 0 -10000 0 0
ATF5 0.034 0.011 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.016 0.13 -10000 0 -0.38 45 45
FZD6 0.007 0.11 -10000 0 -0.54 18 18
WNT6 0.033 0.04 0.18 6 -0.54 2 8
WNT4 0.04 0.034 -10000 0 -10000 0 0
FZD3 0.014 0.091 -10000 0 -0.54 13 13
WNT5A 0.01 0.13 -10000 0 -0.54 25 25
WNT11 0.024 0.079 -10000 0 -0.54 9 9
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.034 0.006 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
GNB1/GNG2 0.048 0.088 -10000 0 -0.34 23 23
forebrain development -0.041 0.2 -10000 0 -0.58 45 45
GNAO1 0.031 0.012 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.029 0.092 -10000 0 -0.4 22 22
SMO 0.012 0.12 0.18 7 -0.54 22 29
ARRB2 0.032 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.03 0.11 -10000 0 -0.52 8 8
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.009 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.077 0.032 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
XPO1 0.037 0.006 -10000 0 -10000 0 0
GLI1/Su(fu) -0.03 0.19 -10000 0 -0.67 25 25
SAP30 0.033 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 0.18 7 -0.54 22 29
MIM/GLI2A 0.032 0.029 0.31 1 -10000 0 1
IFT88 0.031 0.027 -10000 0 -0.54 1 1
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GLI2 0.017 0.084 -10000 0 -0.37 14 14
GLI3 0.017 0.11 0.3 1 -0.51 10 11
CSNK1D 0.033 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.009 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.031 0.027 -10000 0 -0.54 1 1
GNG2 0.033 0.026 -10000 0 -0.54 1 1
Gi family/GTP -0.082 0.16 -10000 0 -0.36 73 73
SIN3B 0.035 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.026 0.11 -10000 0 -0.47 12 12
GLI2/Su(fu) 0.02 0.1 -10000 0 -0.46 12 12
FOXA2 0.017 0.12 -10000 0 -0.72 10 10
neural tube patterning -0.041 0.2 -10000 0 -0.58 45 45
SPOP 0.031 0.011 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.064 -10000 0 -0.35 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
CSNK1G2 0.033 0.007 -10000 0 -10000 0 0
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
MTSS1 0.033 0.029 0.31 1 -10000 0 1
embryonic limb morphogenesis -0.041 0.2 -10000 0 -0.58 45 45
SUFU 0.019 0.049 -10000 0 -0.38 1 1
LGALS3 -0.029 0.18 -10000 0 -0.54 56 56
catabolic process 0.038 0.14 -10000 0 -0.58 13 13
GLI3A/CBP 0.004 0.11 -10000 0 -0.35 47 47
KIF3A 0.034 0.006 -10000 0 -10000 0 0
GLI1 -0.043 0.2 -10000 0 -0.59 45 45
RAB23 0.035 0.014 -10000 0 -10000 0 0
CSNK1A1 0.034 0.005 -10000 0 -10000 0 0
IFT172 0.033 0.026 -10000 0 -0.54 1 1
RBBP7 0.037 0.022 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.008 0.13 -10000 0 -0.32 59 59
GNAZ 0.026 0.062 -10000 0 -0.54 6 6
RBBP4 0.033 0.006 -10000 0 -10000 0 0
CSNK1G1 0.033 0.007 -10000 0 -10000 0 0
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.029 0.089 -10000 0 -0.46 9 9
STK36 0.035 0.026 -10000 0 -0.54 1 1
Gi family/GNB1/GNG2/GDP -0.08 0.16 -10000 0 -0.39 68 68
PTCH1 -0.036 0.18 -10000 0 -0.73 15 15
MIM/GLI1 -0.022 0.18 -10000 0 -0.6 30 30
CREBBP 0.004 0.11 -10000 0 -0.35 47 47
Su(fu)/SIN3/HDAC complex 0.016 0.1 -10000 0 -0.49 14 14
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.028 0.016 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.047 0.14 -10000 0 -0.44 17 17
NEF 0.011 0.022 -10000 0 -10000 0 0
NFKBIA 0.029 0.036 -10000 0 -0.35 1 1
BIRC3 0.009 0.14 0.38 1 -0.5 25 26
CYCS 0.033 0.13 0.28 18 -0.44 14 32
RIPK1 0.034 0.006 -10000 0 -10000 0 0
CD247 0.029 0.11 0.24 17 -0.55 15 32
MAP2K7 0.039 0.18 0.34 4 -0.67 19 23
protein ubiquitination 0.016 0.12 0.37 2 -0.39 15 17
CRADD 0.034 0.005 -10000 0 -10000 0 0
DAXX 0.034 0.008 -10000 0 -10000 0 0
FAS -0.003 0.14 -10000 0 -0.54 33 33
BID 0.03 0.13 0.25 8 -0.43 17 25
NF-kappa-B/RelA/I kappa B alpha 0.059 0.086 -10000 0 -0.3 16 16
TRADD 0.03 0.012 -10000 0 -10000 0 0
MAP3K5 0.003 0.13 -10000 0 -0.54 26 26
CFLAR 0.033 0.026 -10000 0 -0.54 1 1
FADD 0.028 0.015 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.059 0.087 -10000 0 -0.3 16 16
MAPK8 0.038 0.17 0.43 3 -0.63 18 21
APAF1 0.034 0.003 -10000 0 -10000 0 0
TRAF1 0.035 0.015 -10000 0 -10000 0 0
TRAF2 0.035 0.012 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.035 0.14 0.26 7 -0.33 38 45
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.14 -10000 0 -0.49 17 17
CHUK 0.014 0.12 0.38 2 -0.43 15 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.12 -10000 0 -0.33 41 41
TCRz/NEF 0.032 0.093 0.24 17 -0.41 15 32
TNF 0.038 0.023 -10000 0 -10000 0 0
FASLG 0.036 0.11 0.31 42 -0.37 15 57
NFKB1 0.03 0.034 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.053 0.035 -10000 0 -10000 0 0
CASP6 0.052 0.15 -10000 0 -0.55 15 15
CASP7 0.02 0.19 0.4 15 -0.48 40 55
RELA 0.03 0.033 -10000 0 -10000 0 0
CASP2 0.034 0.006 -10000 0 -10000 0 0
CASP3 0.017 0.19 0.4 16 -0.47 42 58
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.023 -10000 0 -10000 0 0
CASP8 0.034 0.005 -10000 0 -10000 0 0
CASP9 0.033 0.008 -10000 0 -10000 0 0
MAP3K14 0.016 0.13 0.36 1 -0.45 17 18
APAF-1/Caspase 9 0.019 0.13 0.25 2 -0.38 26 28
BCL2 -0.006 0.18 0.48 5 -0.55 22 27
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.036 0.15 -10000 0 -0.45 35 35
KLHL20 0.042 0.11 0.3 42 -0.26 14 56
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
Rac1/GDP 0.003 0.12 0.32 6 -0.35 6 12
ENAH -0.03 0.14 -10000 0 -0.45 31 31
AP1M1 0.034 0.005 -10000 0 -10000 0 0
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
CDC42/GTP 0.009 0.075 -10000 0 -0.29 2 2
ABI1/Sra1/Nap1 -0.015 0.04 -10000 0 -0.18 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.095 -10000 0 -0.31 25 25
RAPGEF1 -0.029 0.14 0.34 1 -0.4 37 38
CTNND1 0.034 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.03 0.16 -10000 0 -0.45 47 47
CRK -0.026 0.14 0.35 1 -0.43 38 39
E-cadherin/gamma catenin/alpha catenin 0.037 0.089 -10000 0 -0.34 21 21
alphaE/beta7 Integrin 0.046 0.016 -10000 0 -10000 0 0
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.042 -10000 0 -0.31 3 3
DLG1 -0.038 0.16 -10000 0 -0.45 40 40
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.061 -10000 0 -0.22 6 6
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GTP/NME1/Tiam1 0.058 0.025 -10000 0 -10000 0 0
PI3K -0.022 0.08 -10000 0 -0.29 5 5
ARF6 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.021 0.095 -10000 0 -0.4 21 21
TIAM1 0.035 0.012 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.047 0.089 -10000 0 -0.3 25 25
AKT1 -0.007 0.056 -10000 0 -0.2 1 1
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
CDH1 0.007 0.12 -10000 0 -0.54 22 22
RhoA/GDP 0.002 0.12 0.33 4 -0.35 6 10
actin cytoskeleton organization 0.037 0.093 0.25 44 -0.19 12 56
CDC42/GDP 0.001 0.12 0.33 4 -0.35 6 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.005 0.066 -10000 0 -0.25 23 23
ITGB7 0.034 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.051 0.095 -10000 0 -0.31 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin 0.032 0.082 -10000 0 -0.29 26 26
mol:GDP -0.017 0.12 0.33 4 -0.35 25 29
CDC42/GTP/IQGAP1 0.043 0.014 -10000 0 -10000 0 0
JUP 0.032 0.009 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.008 0.12 0.34 3 -0.37 5 8
RAC1/GTP/IQGAP1 0.044 0.011 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.049 0.012 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
CDC42 0.033 0.008 -10000 0 -10000 0 0
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.016 0.067 0.22 20 -0.22 11 31
NME1 0.031 0.011 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.036 0.16 -10000 0 -0.46 39 39
regulation of cell-cell adhesion -0.001 0.061 -10000 0 -0.26 2 2
WASF2 0.02 0.043 0.12 32 -0.12 2 34
Rap1/GTP 0.013 0.087 0.28 1 -0.33 2 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.092 -10000 0 -0.3 21 21
CCND1 0.017 0.079 0.24 20 -0.28 11 31
VAV2 -0.018 0.19 0.41 1 -0.66 16 17
RAP1/GDP 0.012 0.1 0.31 3 -0.35 4 7
adherens junction assembly -0.034 0.15 -10000 0 -0.44 39 39
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.033 0.007 -10000 0 -10000 0 0
PIP5K1C 0.034 0.009 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.045 0.088 -10000 0 -0.29 24 24
E-cadherin/beta catenin -0.006 0.089 -10000 0 -0.34 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.036 0.16 -10000 0 -0.45 41 41
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.14 0.28 59 -0.42 17 76
E-cadherin/beta catenin/alpha catenin 0.036 0.095 -10000 0 -0.34 26 26
ITGAE 0.031 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.031 0.17 -10000 0 -0.46 47 47
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.035 0.094 -9999 0 -0.34 25 25
E-cadherin/beta catenin 0.019 0.1 -9999 0 -0.4 26 26
CTNNB1 0.029 0.052 -9999 0 -0.54 4 4
JUP 0.032 0.009 -9999 0 -10000 0 0
CDH1 0.007 0.12 -9999 0 -0.54 22 22
Caspase cascade in apoptosis

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
TOP1 0.033 0.085 0.29 2 -0.4 9 11
ACTA1 0.006 0.082 0.24 3 -0.44 2 5
NUMA1 0.027 0.083 0.29 2 -0.37 9 11
SPTAN1 0.02 0.069 0.3 6 -0.48 1 7
LIMK1 0.033 0.074 0.28 12 -0.48 1 13
BIRC3 0.017 0.11 -10000 0 -0.54 17 17
BIRC2 0.031 0.011 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.24 8 -0.34 1 9
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 -10000 0 -0.001 35 35
PTK2 0.029 0.095 0.28 3 -0.45 10 13
DIABLO 0.034 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0.02 0.068 0.3 6 -0.48 1 7
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
GSN -0.054 0.14 0.35 1 -0.29 89 90
MADD 0.034 0.005 -10000 0 -10000 0 0
TFAP2A 0.039 0.1 -10000 0 -0.65 9 9
BID 0.013 0.025 0.16 9 -0.2 1 10
MAP3K1 0.012 0.094 -10000 0 -0.37 24 24
TRADD 0.03 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.024 0.069 0.3 5 -0.48 1 6
CASP9 0.033 0.008 -10000 0 -10000 0 0
DNA repair -0.034 0.059 0.32 3 -0.21 12 15
neuron apoptosis 0.007 0.15 -10000 0 -0.68 20 20
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.024 0.075 0.32 1 -0.46 2 3
APAF1 0.034 0.003 -10000 0 -10000 0 0
CASP6 0.021 0.14 -10000 0 -0.85 12 12
TRAF2 0.035 0.012 -10000 0 -10000 0 0
ICAD/CAD 0.017 0.062 0.28 2 -0.47 1 3
CASP7 0.015 0.082 0.27 19 -0.34 3 22
KRT18 0.036 0.096 -10000 0 -0.73 6 6
apoptosis 0.011 0.1 0.29 2 -0.45 9 11
DFFA 0.02 0.065 0.28 3 -0.48 1 4
DFFB 0.02 0.064 0.28 3 -0.48 1 4
PARP1 0.034 0.059 0.21 11 -0.33 3 14
actin filament polymerization 0.017 0.13 0.3 13 -0.29 10 23
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.023 0.044 0.22 6 -0.23 3 9
SATB1 -0.012 0.16 -10000 0 -0.78 14 14
SLK 0.019 0.067 0.28 3 -0.38 2 5
p15 BID/BAX 0.026 0.051 -10000 0 -0.31 3 3
CASP2 0.005 0.084 0.24 6 -0.3 16 22
JNK cascade -0.012 0.093 0.37 24 -10000 0 24
CASP3 0.024 0.07 0.31 3 -0.51 1 4
LMNB2 0.018 0.13 0.35 2 -0.51 21 23
RIPK1 0.034 0.006 -10000 0 -10000 0 0
CASP4 0.025 0.057 -10000 0 -0.54 5 5
Mammalian IAPs/DIABLO 0.046 0.078 -10000 0 -0.31 17 17
negative regulation of DNA binding 0.039 0.1 -10000 0 -0.64 9 9
stress fiber formation 0.019 0.066 0.28 3 -0.37 2 5
GZMB 0.022 0.046 0.29 7 -0.4 2 9
CASP1 -0.017 0.12 -10000 0 -0.4 42 42
LMNB1 0.042 0.13 0.32 4 -0.55 14 18
APP 0.007 0.15 -10000 0 -0.69 20 20
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to stress 0 0 0.001 16 -0.001 25 41
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM 0.014 0.11 0.31 2 -0.45 10 12
LMNA 0.023 0.083 0.34 2 -0.36 9 11
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.087 -10000 0 -0.32 17 17
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.027 0.068 0.27 5 -0.41 1 6
APAF-1/Caspase 9 0.017 0.12 -10000 0 -0.6 16 16
nuclear fragmentation during apoptosis 0.027 0.082 0.28 2 -0.36 9 11
CFL2 -0.017 0.13 0.3 10 -0.28 37 47
GAS2 -0.16 0.15 0.3 5 -0.28 248 253
positive regulation of apoptosis 0.036 0.12 0.33 3 -0.48 17 20
PRF1 0.037 0.022 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.035 0.031 -10000 0 -0.54 1 1
ANTXR2 0.022 0.08 -10000 0 -0.54 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.073 11 11
monocyte activation 0.012 0.088 -10000 0 -0.35 27 27
MAP2K2 0.005 0.094 -10000 0 -0.57 13 13
MAP2K1 -0.005 0.01 -10000 0 -10000 0 0
MAP2K7 -0.005 0.01 -10000 0 -10000 0 0
MAP2K6 -0.01 0.042 0.081 2 -0.3 10 12
CYAA -0.01 0.042 -10000 0 -0.29 11 11
MAP2K4 -0.005 0.012 -10000 0 -0.18 1 1
IL1B -0.012 0.05 0.24 1 -0.3 8 9
Channel 0.036 0.053 -10000 0 -0.31 11 11
NLRP1 -0.007 0.028 -10000 0 -0.27 5 5
CALM1 0.034 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.002 0.075 -10000 0 -0.4 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.073 11 -10000 0 11
MAPK3 -0.005 0.01 -10000 0 -10000 0 0
MAPK1 -0.005 0.01 -10000 0 -10000 0 0
PGR -0.063 0.14 0.085 112 -0.29 143 255
PA/Cellular Receptors 0.038 0.058 -10000 0 -0.34 11 11
apoptosis -0.002 0.01 -10000 0 -0.073 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.036 0.05 -10000 0 -0.29 11 11
macrophage activation -0.006 0.01 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
VCAM1 0.011 0.088 -10000 0 -0.35 27 27
platelet activation 0.002 0.075 -10000 0 -0.4 16 16
MAPKKK cascade -0.003 0.029 0.12 3 -0.15 3 6
IL18 0 0.039 0.14 1 -0.25 3 4
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.073 11 11
LEF -0.002 0.01 -10000 0 -0.073 11 11
CASP1 -0.006 0.032 -10000 0 -0.16 14 14
mol:cAMP 0.002 0.075 -10000 0 -0.41 16 16
necrosis -0.002 0.01 -10000 0 -0.073 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.036 0.05 -10000 0 -0.29 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.086 0.075 0.29 3 -0.28 5 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.032 0.009 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.1 0.11 0.4 35 -0.25 3 38
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.063 0.055 -10000 0 -0.24 10 10
antigen processing and presentation of peptide antigen via MHC class I -0.003 0.096 0.16 4 -0.28 36 40
CaM/Ca2+ 0.084 0.071 0.28 1 -0.27 5 6
RAP1A 0.034 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.076 0.088 0.3 29 -0.27 4 33
AKT1 0.02 0.11 0.31 11 -0.29 33 44
MAP2K1 0.029 0.075 0.31 5 -0.26 6 11
MAP3K11 0.045 0.071 0.32 5 -0.27 5 10
IFNGR1 0.031 0.058 -10000 0 -0.54 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.047 0.087 -10000 0 -0.41 8 8
Rap1/GTP 0.018 0.035 -10000 0 -0.23 5 5
CRKL/C3G 0.047 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.093 0.076 -10000 0 -0.3 5 5
CEBPB 0.058 0.14 0.4 9 -0.49 9 18
STAT3 0.033 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.091 0.11 -10000 0 -0.7 5 5
STAT1 0.061 0.092 0.29 34 -0.27 4 38
CALM1 0.034 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.061 0.064 -10000 0 -0.55 1 1
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.076 0.089 0.3 28 -0.26 4 32
CEBPB/PTGES2/Cbp/p300 0.04 0.085 0.29 3 -0.37 5 8
mol:Ca2+ 0.081 0.072 0.3 1 -0.28 5 6
MAPK3 0.044 0.12 -10000 0 -0.63 9 9
STAT1 (dimer) 0.021 0.15 0.32 3 -0.39 35 38
MAPK1 0.012 0.2 0.39 1 -0.7 33 34
JAK2 0.035 0.016 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.036 0.014 -10000 0 -10000 0 0
CAMK2D 0.03 0.052 -10000 0 -0.54 4 4
DAPK1 0.059 0.11 0.41 12 -0.35 4 16
SMAD7 0.023 0.071 0.22 9 -0.19 5 14
CBL/CRKL/C3G 0.068 0.069 0.33 4 -0.26 5 9
PI3K 0.048 0.12 -10000 0 -0.3 33 33
IFNG 0.061 0.064 -10000 0 -0.55 1 1
apoptosis 0.05 0.11 0.38 11 -0.46 7 18
CAMK2G 0.034 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.033 0.007 -10000 0 -10000 0 0
CAMK2A 0.034 0.005 -10000 0 -10000 0 0
CAMK2B 0.039 0.069 -10000 0 -0.54 5 5
FRAP1 0.004 0.1 0.29 12 -0.27 32 44
PRKCD 0.02 0.11 0.32 12 -0.29 31 43
RAP1B 0.033 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.003 0.096 0.16 4 -0.28 36 40
PTPN2 0.033 0.007 -10000 0 -10000 0 0
EP300 0.034 0.009 -10000 0 -10000 0 0
IRF1 0.067 0.11 0.39 37 -10000 0 37
STAT1 (dimer)/PIASy 0.074 0.09 0.3 27 -0.26 4 31
SOCS1 0.019 0.1 -10000 0 -1 5 5
mol:GDP 0.063 0.065 0.31 4 -0.25 5 9
CASP1 0.006 0.11 0.25 8 -0.27 56 64
PTGES2 0.034 0.005 -10000 0 -10000 0 0
IRF9 0.052 0.068 0.26 17 -10000 0 17
mol:PI-3-4-5-P3 0.031 0.1 -10000 0 -0.29 35 35
RAP1/GDP 0.052 0.052 -10000 0 -0.23 1 1
CBL 0.043 0.069 0.31 5 -0.27 5 10
MAP3K1 0.047 0.072 0.3 6 -0.27 6 12
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PIAS4 0.035 0.016 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.003 0.096 0.16 4 -0.28 36 40
PTPN11 0.045 0.072 0.27 11 -0.28 5 16
CREBBP 0.033 0.011 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.016 0.1 0.18 8 -0.54 17 25
PLK4 0.055 0.052 -10000 0 -10000 0 0
regulation of centriole replication 0.023 0.086 -10000 0 -0.38 16 16
Arf6 downstream 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
PLAUR 0.098 0.13 0.37 21 -10000 0 21
regulation of axonogenesis -0.022 0.05 0.2 13 -10000 0 13
myoblast fusion -0.066 0.073 -10000 0 -0.24 11 11
mol:GTP 0.048 0.044 -10000 0 -0.16 2 2
regulation of calcium-dependent cell-cell adhesion -0.091 0.066 -10000 0 -0.25 7 7
ARF1/GTP 0.053 0.044 -10000 0 -10000 0 0
mol:GM1 0.033 0.039 -10000 0 -10000 0 0
mol:Choline 0.017 0.076 -10000 0 -0.31 20 20
lamellipodium assembly 0.056 0.078 0.25 7 -0.33 1 8
MAPK3 0.071 0.077 0.21 117 -10000 0 117
ARF6/GTP/NME1/Tiam1 0.093 0.067 0.25 7 -10000 0 7
ARF1 0.028 0.014 -10000 0 -10000 0 0
ARF6/GDP 0.066 0.073 0.24 11 -10000 0 11
ARF1/GDP 0.058 0.069 -10000 0 -10000 0 0
ARF6 0.055 0.025 -10000 0 -10000 0 0
RAB11A 0.033 0.007 -10000 0 -10000 0 0
TIAM1 0.04 0.014 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.072 0.078 0.21 119 -10000 0 119
actin filament bundle formation -0.075 0.063 0.19 1 -0.23 7 8
KALRN 0.042 0.055 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.045 0.017 -10000 0 -10000 0 0
RhoA/GDP 0.076 0.064 0.23 7 -0.19 1 8
NME1 0.036 0.015 -10000 0 -10000 0 0
Rac1/GDP 0.078 0.062 0.23 7 -10000 0 7
substrate adhesion-dependent cell spreading 0.048 0.044 -10000 0 -0.16 2 2
cortical actin cytoskeleton organization 0.056 0.078 0.25 7 -0.33 1 8
RAC1 0.034 0.005 -10000 0 -10000 0 0
liver development 0.048 0.044 -10000 0 -0.16 2 2
ARF6/GTP 0.048 0.044 -10000 0 -0.16 2 2
RhoA/GTP 0.062 0.041 -10000 0 -10000 0 0
mol:GDP 0.051 0.076 0.2 100 -0.2 1 101
ARF6/GTP/RAB11FIP3/RAB11A 0.075 0.044 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
PLD1 0.029 0.086 -10000 0 -0.35 20 20
RAB11FIP3 0.032 0.01 -10000 0 -10000 0 0
tube morphogenesis 0.056 0.078 0.25 7 -0.33 1 8
ruffle organization 0.022 0.05 -10000 0 -0.2 13 13
regulation of epithelial cell migration 0.048 0.044 -10000 0 -0.16 2 2
PLD2 0.042 0.045 -10000 0 -0.36 1 1
PIP5K1A 0.022 0.05 -10000 0 -0.2 13 13
mol:Phosphatidic acid 0.017 0.076 -10000 0 -0.31 20 20
Rac1/GTP 0.056 0.078 0.25 7 -0.33 1 8
Class I PI3K signaling events mediated by Akt

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 0.017 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.042 0.028 -10000 0 -10000 0 0
CDKN1B 0.018 0.071 0.3 4 -0.35 7 11
CDKN1A 0.02 0.067 0.28 2 -0.34 9 11
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
FOXO3 0.023 0.061 0.28 1 -0.36 6 7
AKT1 0.022 0.064 -10000 0 -0.33 13 13
BAD 0.033 0.007 -10000 0 -10000 0 0
AKT3 0.015 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.019 0.062 -10000 0 -0.34 9 9
AKT1/ASK1 0.033 0.095 -10000 0 -0.34 10 10
BAD/YWHAZ 0.051 0.033 -10000 0 -10000 0 0
RICTOR 0.034 0.006 -10000 0 -10000 0 0
RAF1 0.034 0.006 -10000 0 -10000 0 0
JNK cascade -0.032 0.092 0.27 27 -10000 0 27
TSC1 0.021 0.056 -10000 0 -0.36 6 6
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
AKT1/RAF1 0.055 0.077 0.3 2 -0.34 9 11
EP300 0.032 0.009 -10000 0 -10000 0 0
mol:GDP 0.022 0.063 -10000 0 -0.32 13 13
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.027 0.08 0.28 21 -0.34 9 30
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.003 0.048 0.25 2 -0.32 10 12
MAP3K5 0.003 0.13 -10000 0 -0.54 26 26
MAPKAP1 0.034 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.041 0.079 0.28 9 -0.28 2 11
YWHAH 0.033 0.014 -10000 0 -10000 0 0
AKT1S1 0.023 0.068 -10000 0 -0.34 9 9
CASP9 0.022 0.046 -10000 0 -0.3 4 4
YWHAB 0.033 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.049 0.083 0.32 4 -0.33 8 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.023 0.062 -10000 0 -0.32 9 9
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.054 -10000 0 -0.33 9 9
CHUK 0.02 0.061 -10000 0 -0.34 8 8
BAD/BCL-XL 0.058 0.073 0.3 2 -0.33 8 10
mTORC2 0.042 0.01 -10000 0 -10000 0 0
AKT2 0.017 0.006 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.043 0.11 0.37 4 -0.4 12 16
PDPK1 0.032 0.01 -10000 0 -10000 0 0
MDM2 0.024 0.071 0.28 4 -0.34 9 13
MAPKKK cascade -0.055 0.075 0.34 9 -0.3 2 11
MDM2/Cbp/p300 0.062 0.081 0.36 2 -0.33 7 9
TSC1/TSC2 0.025 0.079 0.28 22 -0.33 9 31
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.077 0.33 3 -0.31 9 12
glucose import -0.15 0.15 0.21 1 -0.31 240 241
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.055 0.18 3 -0.3 4 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 0.21 1 -0.31 240 241
GSK3A 0.021 0.065 -10000 0 -0.34 9 9
FOXO1 -0.004 0.095 -10000 0 -0.43 9 9
GSK3B 0.021 0.063 0.28 1 -0.34 8 9
SFN 0.032 0.04 -10000 0 -0.54 2 2
G1/S transition of mitotic cell cycle 0.032 0.076 0.33 2 -0.34 9 11
p27Kip1/14-3-3 family 0.031 0.044 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
KPNA1 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
RHEB 0.034 0.009 -10000 0 -10000 0 0
CREBBP 0.032 0.01 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.002 0.13 0.28 1 -0.46 21 22
BAG4 0.028 0.016 0.18 1 -10000 0 1
BAD 0.007 0.047 0.2 2 -0.18 6 8
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.017 0.11 -10000 0 -0.54 17 17
BAX 0.008 0.052 0.26 3 -0.18 8 11
EnzymeConsortium:3.1.4.12 0.003 0.032 0.09 4 -0.098 19 23
IKBKB 0.014 0.13 0.29 5 -0.43 16 21
MAP2K2 0.012 0.06 0.24 7 -0.24 1 8
MAP2K1 0.013 0.061 0.24 9 -0.24 1 10
SMPD1 0.004 0.04 0.2 1 -0.17 10 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.032 0.15 0.31 12 -0.44 20 32
MAP2K4 0.008 0.052 0.2 3 -0.25 5 8
protein ubiquitination 0.004 0.13 0.36 3 -0.43 20 23
EnzymeConsortium:2.7.1.37 0.012 0.063 0.24 10 -0.24 2 12
response to UV 0 0.001 0.003 11 -0.002 1 12
RAF1 0.012 0.061 0.21 19 -0.23 2 21
CRADD 0.034 0.005 -10000 0 -10000 0 0
mol:ceramide 0.008 0.05 0.16 3 -0.15 19 22
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.015 -10000 0 -10000 0 0
MADD 0.034 0.006 -10000 0 -10000 0 0
MAP3K1 0.008 0.054 0.2 2 -0.21 10 12
TRADD 0.03 0.012 -10000 0 -10000 0 0
RELA/p50 0.033 0.007 -10000 0 -10000 0 0
MAPK3 0.015 0.061 0.24 9 -0.24 1 10
MAPK1 0.011 0.07 0.24 9 -0.24 4 13
p50/RELA/I-kappa-B-alpha 0.047 0.017 -10000 0 -10000 0 0
FADD 0.028 0.14 0.3 9 -0.45 18 27
KSR1 0.012 0.057 0.2 15 -0.18 7 22
MAPK8 0.005 0.057 0.26 4 -0.24 5 9
TRAF2 0.035 0.012 -10000 0 -10000 0 0
response to radiation 0 0 0.003 2 -10000 0 2
CHUK -0.005 0.12 -10000 0 -0.45 19 19
TNF R/SODD 0.038 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.025 0.069 0.18 22 -0.18 7 29
IKBKG -0.005 0.12 0.45 1 -0.43 21 22
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.001 0.14 -10000 0 -0.45 24 24
RELA 0.033 0.007 -10000 0 -10000 0 0
RIPK1 0.034 0.006 -10000 0 -10000 0 0
AIFM1 0.025 0.069 0.19 18 -0.18 7 25
TNF/TNF R/SODD 0.053 0.035 -10000 0 -10000 0 0
TNFRSF1A 0.033 0.009 -10000 0 -10000 0 0
response to heat 0 0 0.003 2 -10000 0 2
CASP8 0.009 0.15 -10000 0 -0.66 23 23
NSMAF 0.017 0.13 0.28 4 -0.44 19 23
response to hydrogen peroxide 0 0.001 0.003 11 -0.002 1 12
BCL2 -0.069 0.22 -10000 0 -0.54 91 91
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.015 0.15 0.39 4 -0.36 22 26
IKBKB 0.049 0.09 0.35 7 -0.36 2 9
AKT1 0.061 0.11 0.31 45 -0.25 2 47
IKBKG 0.055 0.076 0.35 5 -0.29 3 8
CALM1 0.032 0.085 0.28 8 -0.37 7 15
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
MAP3K1 0.066 0.14 0.4 6 -0.49 12 18
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.032 0.09 0.28 8 -0.38 8 16
DOK1 0.036 0.016 -10000 0 -10000 0 0
AP-1 -0.073 0.11 0.32 1 -0.24 66 67
LYN 0.03 0.015 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
BCR complex 0.042 0.07 0.26 3 -0.4 10 13
CD22 0.015 0.088 0.29 4 -0.45 11 15
CAMK2G 0.03 0.083 0.26 11 -0.37 6 17
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.024 0.043 -10000 0 -0.27 6 6
GO:0007205 0.032 0.091 0.28 8 -0.38 8 16
SYK 0.039 0.026 -10000 0 -10000 0 0
ELK1 0.033 0.089 0.28 8 -0.37 8 16
NFATC1 0.062 0.11 0.32 10 -0.41 8 18
B-cell antigen/BCR complex 0.042 0.07 0.26 3 -0.4 10 13
PAG1/CSK 0.042 0.028 0.26 1 -10000 0 1
NFKBIB 0.041 0.055 0.21 8 -0.14 5 13
HRAS 0.043 0.093 0.26 15 -0.35 8 23
NFKBIA 0.041 0.054 0.21 8 -0.14 1 9
NF-kappa-B/RelA/I kappa B beta 0.045 0.05 0.22 7 -10000 0 7
RasGAP/Csk 0.066 0.079 0.35 2 -0.39 6 8
mol:GDP 0.032 0.088 0.28 8 -0.35 9 17
PTEN 0.029 0.045 -10000 0 -0.54 3 3
CD79B 0.02 0.081 -10000 0 -0.54 10 10
NF-kappa-B/RelA/I kappa B alpha 0.045 0.05 0.22 7 -10000 0 7
GRB2 0.034 0.018 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.048 0.15 0.39 8 -0.47 15 23
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.031 0.088 0.29 7 -0.38 8 15
CSK 0.034 0.011 -10000 0 -10000 0 0
FOS -0.15 0.14 0.27 1 -0.36 59 60
CHUK 0.053 0.083 0.36 5 -0.33 6 11
IBTK 0.033 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.054 0.089 0.32 2 -0.36 6 8
PTPN6 0.031 0.1 0.32 7 -0.55 6 13
RELA 0.033 0.007 -10000 0 -10000 0 0
BCL2A1 0.041 0.044 0.21 7 -10000 0 7
VAV2 0.043 0.11 0.32 4 -0.57 6 10
ubiquitin-dependent protein catabolic process 0.044 0.054 0.21 8 -0.13 8 16
BTK 0.017 0.091 -10000 0 -0.97 4 4
CD19 0.022 0.093 0.32 4 -0.43 11 15
MAP4K1 0.037 0.021 -10000 0 -10000 0 0
CD72 0.063 0.059 -10000 0 -10000 0 0
PAG1 0.031 0.025 -10000 0 -10000 0 0
MAPK14 0.064 0.12 0.39 8 -0.42 12 20
SH3BP5 0.018 0.094 -10000 0 -0.54 14 14
PIK3AP1 0.03 0.094 0.33 6 -0.44 7 13
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.048 0.094 0.28 10 -0.44 7 17
RAF1 0.042 0.089 0.26 14 -0.34 7 21
RasGAP/p62DOK/SHIP 0.055 0.071 0.3 1 -0.37 6 7
CD79A 0.042 0.034 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.071 0.11 0.32 1 -0.24 61 62
RASA1 0.034 0.011 -10000 0 -10000 0 0
MAPK3 0.049 0.091 0.27 19 -0.34 4 23
MAPK1 0.039 0.083 0.28 7 -0.34 4 11
CD72/SHP1 0.092 0.12 0.36 20 -0.52 6 26
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.063 0.13 0.38 9 -0.42 12 21
actin cytoskeleton organization 0.07 0.11 0.32 18 -0.49 6 24
NF-kappa-B/RelA 0.09 0.092 0.37 7 -10000 0 7
Calcineurin 0.044 0.09 0.28 1 -0.34 8 9
PI3K -0.003 0.073 -10000 0 -0.4 7 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.033 0.093 0.3 9 -0.41 9 18
SOS1 0.034 0.004 -10000 0 -10000 0 0
Bam32/HPK1 0.062 0.16 -10000 0 -0.64 16 16
DAPP1 0.028 0.16 -10000 0 -0.71 17 17
cytokine secretion 0.061 0.11 0.31 12 -0.38 8 20
mol:DAG 0.031 0.088 0.29 7 -0.38 8 15
PLCG2 0.022 0.073 -10000 0 -0.54 8 8
MAP2K1 0.04 0.086 0.26 8 -0.37 4 12
B-cell antigen/BCR complex/FcgammaRIIB 0.047 0.074 0.35 1 -0.43 7 8
mol:PI-3-4-5-P3 0.027 0.091 0.27 14 -0.3 5 19
ETS1 0.027 0.079 0.26 12 -0.34 7 19
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.076 0.077 0.44 1 -0.3 8 9
B-cell antigen/BCR complex/LYN 0.016 0.084 -10000 0 -0.47 11 11
MALT1 0.033 0.01 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.061 0.11 0.32 15 -0.52 6 21
B-cell antigen/BCR complex/LYN/SYK 0.044 0.1 0.36 3 -0.53 6 9
CARD11 0.035 0.092 0.28 12 -0.37 8 20
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
PPP3CA 0.03 0.051 -10000 0 -0.54 4 4
BCL10 0.033 0.007 -10000 0 -10000 0 0
IKK complex 0.044 0.057 0.19 26 -0.14 1 27
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDPK1 0.035 0.085 0.25 29 -0.22 4 33
PPP3CB 0.034 0.004 -10000 0 -10000 0 0
PPP3CC 0.024 0.046 -10000 0 -0.54 3 3
POU2F2 0.035 0.039 0.24 5 -10000 0 5
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.034 0.005 -10000 0 -10000 0 0
SPHK1 0.034 0.059 -10000 0 -0.54 4 4
GNAI2 0.033 0.01 -10000 0 -10000 0 0
mol:S1P 0.02 0.033 0.2 2 -0.26 4 6
GNAO1 0.03 0.012 -10000 0 -10000 0 0
mol:Sphinganine-1-P 0.018 0.045 -10000 0 -0.4 4 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.054 0.041 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.011 0.031 -10000 0 -0.24 4 4
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
S1P/S1P5/G12 0.042 0.04 -10000 0 -0.22 4 4
S1P/S1P3/Gq 0.037 0.053 -10000 0 -0.29 6 6
S1P/S1P4/Gi -0.066 0.15 -10000 0 -0.34 58 58
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.062 -10000 0 -0.54 6 6
GNA14 0.044 0.068 0.18 50 -0.54 4 54
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.034 0.006 -10000 0 -10000 0 0
ABCC1 0.035 0.024 -10000 0 -10000 0 0
FoxO family 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
G6PC 0.003 0.097 -10000 0 -10000 0 0
PLK1 0.13 0.22 0.6 19 -0.63 11 30
CDKN1B 0.099 0.18 0.52 4 -0.45 15 19
FOXO3 0.11 0.23 0.54 23 -0.63 16 39
KAT2B 0.019 0.031 0.085 36 -0.058 10 46
FOXO1/SIRT1 0.006 0.1 -10000 0 -0.32 9 9
CAT 0.055 0.36 0.76 4 -1.1 39 43
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
AKT1 0.053 0.045 -10000 0 -10000 0 0
FOXO1 0.002 0.11 -10000 0 -0.33 10 10
MAPK10 0.024 0.058 0.24 2 -0.29 10 12
mol:GTP 0 0.004 -10000 0 -10000 0 0
FOXO4 0.044 0.12 0.4 3 -0.39 7 10
response to oxidative stress 0.022 0.032 0.09 37 -0.063 8 45
FOXO3A/SIRT1 0.086 0.2 0.46 15 -0.57 17 32
XPO1 0.034 0.005 -10000 0 -10000 0 0
EP300 0.035 0.009 -10000 0 -10000 0 0
BCL2L11 0.057 0.081 -10000 0 -0.82 3 3
FOXO1/SKP2 0.017 0.1 -10000 0 -0.31 9 9
mol:GDP 0.022 0.032 0.09 37 -0.063 8 45
RAN 0.035 0.005 -10000 0 -10000 0 0
GADD45A 0.082 0.21 -10000 0 -0.8 15 15
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.035 0.15 -10000 0 -0.52 21 21
MST1 0.047 0.042 -10000 0 -10000 0 0
CSNK1D 0.033 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.024 0.14 -10000 0 -0.51 20 20
YWHAB 0.033 0.008 -10000 0 -10000 0 0
MAPK8 0.029 0.04 0.24 2 -0.27 1 3
MAPK9 0.029 0.038 0.24 2 -10000 0 2
YWHAG 0.034 0.008 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
SIRT1 0.022 0.023 -10000 0 -10000 0 0
SOD2 0.095 0.2 0.56 9 -0.55 12 21
RBL2 0.036 0.32 -10000 0 -0.84 38 38
RAL/GDP 0.058 0.035 -10000 0 -10000 0 0
CHUK 0.048 0.042 -10000 0 -10000 0 0
Ran/GTP 0.024 0.014 -10000 0 -10000 0 0
CSNK1G2 0.033 0.007 -10000 0 -10000 0 0
RAL/GTP 0.057 0.042 -10000 0 -10000 0 0
CSNK1G1 0.033 0.007 -10000 0 -10000 0 0
FASLG 0.075 0.12 -10000 0 -1.4 1 1
SKP2 0.036 0.019 -10000 0 -10000 0 0
USP7 0.032 0.01 -10000 0 -10000 0 0
IKBKB 0.041 0.041 -10000 0 -10000 0 0
CCNB1 0.15 0.24 0.6 19 -0.84 4 23
FOXO1-3a-4/beta catenin 0.096 0.22 0.56 7 -0.41 29 36
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.1 -10000 0 -0.3 9 9
CSNK1A1 0.034 0.005 -10000 0 -10000 0 0
SGK1 0.019 0.031 0.085 36 -0.058 10 46
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.02 -10000 0 -10000 0 0
ZFAND5 0.044 0.11 0.44 2 -0.38 1 3
SFN 0.032 0.04 -10000 0 -0.54 2 2
CDK2 0.04 0.022 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.054 0.13 -10000 0 -0.48 15 15
CREBBP 0.034 0.011 -10000 0 -10000 0 0
FBXO32 0.12 0.35 0.64 27 -1.1 26 53
BCL6 0.017 0.4 -10000 0 -1.1 54 54
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.006 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.034 0.006 -10000 0 -10000 0 0
VLDLR -0.04 0.19 -10000 0 -0.54 65 65
LRPAP1 0.033 0.008 -10000 0 -10000 0 0
NUDC 0.033 0.008 -10000 0 -10000 0 0
RELN/LRP8 0.069 0.091 0.26 1 -0.32 20 21
CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
KATNA1 0.032 0.009 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.029 0.079 0.28 3 -0.29 20 23
IQGAP1/CaM 0.047 0.014 -10000 0 -10000 0 0
DAB1 0.033 0.007 -10000 0 -10000 0 0
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
PLA2G7 0.044 0.098 -10000 0 -0.54 10 10
CALM1 0.034 0.006 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.073 0.048 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.035 0.007 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.011 0.004 -10000 0 -10000 0 0
CDK5R2 0.034 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.008 0.16 -10000 0 -0.36 80 80
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.042 0.078 0.38 2 -0.32 2 4
MAP1B -0.021 0.089 -10000 0 -0.29 49 49
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 0.035 0.073 0.27 3 -0.28 13 16
RELN 0.012 0.11 -10000 0 -0.54 20 20
PAFAH/LIS1 0.041 0.067 -10000 0 -0.34 10 10
LIS1/CLIP170 0.034 0.014 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.034 0.069 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.008 0.13 -10000 0 -0.3 52 52
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.025 0.073 0.32 4 -0.33 2 6
LIS1/IQGAP1 0.033 0.014 -10000 0 -10000 0 0
RHOA 0.016 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.015 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.083 0.069 -10000 0 -10000 0 0
PAFAH1B2 0.031 0.011 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.006 0.075 -10000 0 -0.36 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.048 0.087 0.36 3 -0.31 2 5
LRP8 0.072 0.065 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.035 0.081 0.38 2 -0.32 2 4
P39/CDK5 0.036 0.072 0.27 2 -0.28 13 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.013 -10000 0 -10000 0 0
CDK5 0.006 0.075 0.28 2 -0.3 13 15
PPP2R5D 0.034 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.03 0.012 -10000 0 -10000 0 0
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.002 0.14 -10000 0 -0.32 80 80
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 80 80
CDC42 0.016 0.007 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.14 -10000 0 -10000 0 0
CRKL 0.016 0.068 0.3 5 -10000 0 5
mol:DAG 0.026 0.075 -10000 0 -0.26 1 1
HRAS 0.049 0.087 0.32 12 -10000 0 12
MAPK8 0.048 0.075 0.26 15 -0.32 1 16
RAP1A 0.017 0.069 0.3 5 -10000 0 5
GAB1 0.018 0.067 0.32 3 -10000 0 3
MAPK14 0.049 0.074 0.27 13 -10000 0 13
EPO 0.047 0.052 -10000 0 -10000 0 0
PLCG1 0.026 0.076 -10000 0 -0.27 1 1
EPOR/TRPC2/IP3 Receptors 0.029 0.024 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.054 0.079 -10000 0 -0.35 11 11
GAB1/SHC/GRB2/SOS1 0.045 0.066 0.31 2 -10000 0 2
EPO/EPOR (dimer) 0.054 0.047 -10000 0 -10000 0 0
IRS2 -0.051 0.14 0.3 2 -0.32 90 92
STAT1 0.044 0.12 -10000 0 -0.36 1 1
STAT5B 0.03 0.1 -10000 0 -10000 0 0
cell proliferation 0.026 0.08 0.26 16 -0.3 1 17
GAB1/SHIP/PIK3R1/SHP2/SHC 0.003 0.087 -10000 0 -0.29 6 6
TEC 0.017 0.066 0.3 2 -10000 0 2
SOCS3 0.019 0.087 -10000 0 -0.54 12 12
STAT1 (dimer) 0.043 0.11 -10000 0 -0.35 1 1
JAK2 0.032 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
EPO/EPOR (dimer)/JAK2 0.069 0.091 -10000 0 -10000 0 0
EPO/EPOR 0.054 0.047 -10000 0 -10000 0 0
LYN 0.022 0.026 -10000 0 -10000 0 0
TEC/VAV2 0.033 0.072 0.29 3 -10000 0 3
elevation of cytosolic calcium ion concentration 0.029 0.024 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.055 0.058 -10000 0 -10000 0 0
mol:IP3 0.026 0.075 -10000 0 -0.26 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.068 0.15 -10000 0 -0.31 120 120
SH2B3 0.034 0.016 -10000 0 -10000 0 0
NFKB1 0.048 0.073 0.27 13 -10000 0 13
EPO/EPOR (dimer)/JAK2/SOCS3 0.024 0.055 -10000 0 -0.27 10 10
PTPN6 0.011 0.061 -10000 0 -10000 0 0
TEC/VAV2/GRB2 0.045 0.075 0.3 2 -10000 0 2
EPOR 0.029 0.024 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.042 0.067 0.31 2 -10000 0 2
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG2 0.022 0.073 -10000 0 -0.54 8 8
CRKL/CBL/C3G 0.038 0.077 0.3 3 -10000 0 3
VAV2 0.019 0.07 0.31 5 -10000 0 5
CBL 0.015 0.068 0.3 5 -10000 0 5
SHC/Grb2/SOS1 0.03 0.059 -10000 0 -10000 0 0
STAT5A 0.029 0.1 -10000 0 -0.29 2 2
GRB2 0.034 0.018 -10000 0 -10000 0 0
STAT5 (dimer) 0.027 0.15 -10000 0 -0.33 52 52
LYN/PLCgamma2 0.029 0.061 0.25 1 -0.35 10 11
PTPN11 0.034 0.004 -10000 0 -10000 0 0
BTK 0.022 0.072 0.32 4 -10000 0 4
BCL2 -0.089 0.36 -10000 0 -0.82 98 98
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
AKT1 0.026 0.14 0.4 2 -0.47 13 15
PTK2B 0.015 0.085 0.36 2 -0.43 1 3
VEGFR2 homodimer/Frs2 0.022 0.086 -10000 0 -0.33 27 27
CAV1 -0.38 0.26 -10000 0 -0.54 364 364
CALM1 0.034 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.049 0.091 -10000 0 -0.3 22 22
endothelial cell proliferation 0.052 0.13 0.4 9 -0.44 8 17
mol:Ca2+ 0.021 0.091 0.37 1 -0.5 4 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.069 0.093 -10000 0 -0.44 1 1
RP11-342D11.1 0.003 0.087 0.27 1 -0.54 4 5
CDH5 0.03 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.071 0.059 -10000 0 -0.28 3 3
SHC1 0.028 0.014 -10000 0 -10000 0 0
SHC2 0.006 0.12 -10000 0 -0.54 24 24
HRAS/GDP 0.031 0.083 -10000 0 -0.45 4 4
SH2D2A 0.044 0.048 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.057 0.12 -10000 0 -0.48 11 11
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.05 0.095 -10000 0 -0.31 19 19
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.057 0.1 -10000 0 -0.48 4 4
GRB10 0.018 0.11 -10000 0 -0.61 7 7
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
PAK1 0.043 0.046 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.068 0.1 -10000 0 -0.43 1 1
HRAS 0.034 0.013 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.028 0.081 -10000 0 -0.37 7 7
HIF1A 0.031 0.054 -10000 0 -0.54 4 4
FRS2 0.032 0.029 -10000 0 -0.54 1 1
oxygen and reactive oxygen species metabolic process 0.067 0.091 -10000 0 -0.44 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.034 0.006 -10000 0 -10000 0 0
Nck/Pak 0.053 0.037 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.045 0.095 -10000 0 -0.31 26 26
mol:GDP 0.043 0.092 -10000 0 -0.47 4 4
mol:NADP 0.033 0.11 0.59 1 -0.45 10 11
eNOS/Hsp90 0.047 0.11 0.58 1 -0.43 10 11
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.021 0.092 0.37 1 -0.5 4 5
HIF1A/ARNT 0.038 0.042 -10000 0 -0.4 3 3
SHB 0.036 0.018 -10000 0 -10000 0 0
VEGFA 0.051 0.048 -10000 0 -10000 0 0
VEGFC 0.021 0.084 -10000 0 -0.54 11 11
FAK1/Vinculin 0.041 0.11 0.37 1 -0.42 3 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.068 0.097 -10000 0 -0.44 1 1
PTPN6 0.034 0.016 -10000 0 -10000 0 0
EPAS1 0.011 0.13 -10000 0 -0.54 28 28
mol:L-citrulline 0.033 0.11 0.59 1 -0.45 10 11
ITGAV 0.034 0.027 -10000 0 -0.54 1 1
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.063 0.094 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.05 0.11 -10000 0 -0.46 7 7
VEGFR2/3 heterodimer 0.023 0.087 -10000 0 -0.33 28 28
VEGFB 0.034 0.006 -10000 0 -10000 0 0
MAPK11 0.003 0.1 -10000 0 -0.48 7 7
VEGFR2 homodimer 0.004 0.096 -10000 0 -0.39 28 28
FLT1 0.032 0.013 -10000 0 -10000 0 0
NEDD4 0.028 0.058 -10000 0 -0.54 5 5
MAPK3 0.017 0.093 0.37 1 -0.45 4 5
MAPK1 0.013 0.093 0.34 2 -0.45 4 6
VEGFA145/NRP2 0.061 0.038 0.26 1 -10000 0 1
VEGFR1/2 heterodimer 0.021 0.087 -10000 0 -0.33 28 28
KDR 0.004 0.096 -10000 0 -0.39 28 28
VEGFA165/NRP1/VEGFR2 homodimer 0.054 0.1 -10000 0 -0.54 4 4
SRC 0.033 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.019 0.097 0.37 2 -0.46 4 6
PI3K 0.019 0.12 -10000 0 -0.5 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.051 0.092 -10000 0 -0.31 24 24
FES 0.019 0.096 -10000 0 -0.55 4 4
GAB1 0.041 0.1 0.36 1 -0.45 3 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.089 -10000 0 -0.31 21 21
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
SOS1 0.034 0.004 -10000 0 -10000 0 0
ARNT 0.028 0.014 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.13 0.16 -10000 0 -0.45 40 40
VEGFR2 homodimer/VEGFA homodimer/Yes 0.049 0.093 -10000 0 -0.31 24 24
PI3K/GAB1 0.03 0.14 0.39 2 -0.46 13 15
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.075 0.096 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.032 0.1 -10000 0 -0.32 38 38
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
CDC42 0.02 0.097 0.37 1 -0.55 4 5
actin cytoskeleton reorganization 0.049 0.095 -10000 0 -0.31 19 19
PTK2 0.023 0.09 -10000 0 -0.44 3 3
EDG1 0.003 0.087 0.27 1 -0.54 4 5
mol:DAG 0.021 0.092 0.37 1 -0.5 4 5
CaM/Ca2+ 0.034 0.088 -10000 0 -0.47 4 4
MAP2K3 0.004 0.087 -10000 0 -0.53 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.047 0.12 -10000 0 -0.63 7 7
PLCG1 0.021 0.092 0.37 1 -0.51 4 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.069 0.094 0.37 1 -0.34 3 4
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
YES1 0.032 0.027 -10000 0 -0.54 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.052 0.092 -10000 0 -0.31 24 24
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.049 0.092 -10000 0 -0.31 23 23
cell migration 0.044 0.11 0.35 1 -0.47 2 3
mol:PI-3-4-5-P3 0.019 0.11 -10000 0 -0.46 8 8
FYN 0.03 0.037 -10000 0 -0.54 2 2
VEGFB/NRP1 0.023 0.089 -10000 0 -0.51 4 4
mol:NO 0.033 0.11 0.59 1 -0.45 10 11
PXN 0.034 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.013 0.073 -10000 0 -0.44 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.039 0.11 -10000 0 -0.62 7 7
VHL 0.036 0.018 -10000 0 -10000 0 0
ITGB3 0.035 0.019 -10000 0 -10000 0 0
NOS3 0.032 0.12 0.6 1 -0.51 10 11
VEGFR2 homodimer/VEGFA homodimer/Sck 0.033 0.12 -10000 0 -0.32 38 38
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.007 0.08 0.37 1 -0.43 4 5
PRKCB 0.006 0.084 0.36 1 -0.47 4 5
VCL 0.034 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.027 0.094 -10000 0 -0.54 4 4
VEGFR1/2 heterodimer/VEGFA homodimer 0.047 0.092 -10000 0 -0.31 24 24
VEGFA165/NRP2 0.061 0.038 0.26 1 -10000 0 1
MAPKKK cascade 0.062 0.12 0.38 6 -0.55 6 12
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFC homodimer 0.021 0.084 -10000 0 -0.54 11 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
ROCK1 0.034 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.042 0.11 0.44 2 -0.42 3 5
MAP3K13 0.018 0.095 -10000 0 -0.55 4 4
PDPK1 0.006 0.098 -10000 0 -0.42 8 8
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.26 0.28 -10000 0 -0.54 254 254
CLTC 0.033 0.056 -10000 0 -0.42 3 3
calcium ion-dependent exocytosis 0.016 0.043 -10000 0 -0.37 2 2
Dynamin 2/GTP 0.03 0.013 -10000 0 -10000 0 0
EXOC4 0.034 0.006 -10000 0 -10000 0 0
CD59 0.021 0.044 -10000 0 -0.28 4 4
CPE -0.041 0.13 -10000 0 -0.34 83 83
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
membrane fusion 0.012 0.035 -10000 0 -0.35 1 1
CTNND1 0.031 0.054 0.37 1 -10000 0 1
DNM2 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.046 0.23 2 -0.29 3 5
TSHR 0.015 0.028 -10000 0 -0.34 3 3
INS 0.008 0.099 -10000 0 -0.5 18 18
BIN1 0.034 0.005 -10000 0 -10000 0 0
mol:Choline 0.012 0.035 -10000 0 -0.35 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.006 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.03 0.012 -10000 0 -10000 0 0
JUP 0.022 0.036 -10000 0 -0.29 2 2
ASAP2/amphiphysin II 0.043 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.004 -10000 0 -10000 0 0
CDH1 0.008 0.066 -10000 0 -0.38 4 4
clathrin-independent pinocytosis 0.025 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.03 0.038 -10000 0 -0.54 2 2
positive regulation of endocytosis 0.025 0.004 -10000 0 -10000 0 0
EXOC2 0.041 0.033 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.053 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.031 0.011 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.044 0.082 0.35 5 -10000 0 5
positive regulation of phagocytosis 0.017 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.041 0.029 -10000 0 -0.34 2 2
ACAP1 0.011 0.035 -10000 0 -0.19 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.027 0.04 -10000 0 -0.29 2 2
clathrin heavy chain/ACAP1 0.03 0.068 0.3 3 -0.32 6 9
JIP4/KLC1 0.056 0.025 -10000 0 -10000 0 0
EXOC1 0.034 0.005 -10000 0 -10000 0 0
exocyst 0.036 0.053 -10000 0 -0.33 4 4
RALA/GTP 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.016 -10000 0 -10000 0 0
receptor recycling 0.025 0.004 -10000 0 -10000 0 0
CTNNA1 0.032 0.055 0.37 1 -10000 0 1
NME1 0.016 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0.037 0.065 0.29 2 -0.42 3 5
IL2RA 0.027 0.047 -10000 0 -0.36 3 3
VAMP3 0.017 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.1 0.13 -10000 0 -0.24 203 203
EXOC6 0.034 0.027 0.18 2 -0.54 1 3
PLD1 0.005 0.062 -10000 0 -0.28 21 21
PLD2 0.016 0.016 -10000 0 -0.27 1 1
EXOC5 0.034 0.006 -10000 0 -10000 0 0
PIP5K1C 0.019 0.038 0.2 2 -0.42 1 3
SDC1 0.037 0.051 -10000 0 -0.36 3 3
ARF6/GDP 0.028 0.011 -10000 0 -10000 0 0
EXOC7 0.032 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.047 0.085 -10000 0 -0.36 5 5
mol:Phosphatidic acid 0.012 0.035 -10000 0 -0.35 1 1
endocytosis -0.041 0.009 -10000 0 -10000 0 0
SCAMP2 0.034 0.006 -10000 0 -10000 0 0
ADRB2 -0.11 0.15 -10000 0 -0.31 50 50
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.034 0.014 -10000 0 -10000 0 0
KLC1 0.033 0.007 -10000 0 -10000 0 0
AVPR2 0.032 0.068 0.27 3 -0.38 4 7
RALA 0.034 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.04 0.084 0.34 2 -0.38 3 5
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.08 0.055 0.4 6 -10000 0 6
MAP4K1 0.037 0.021 -10000 0 -10000 0 0
MAP3K8 -0.039 0.19 -10000 0 -0.54 65 65
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.035 0.012 -10000 0 -10000 0 0
CRKL 0.032 0.009 -10000 0 -10000 0 0
MAP3K1 0.031 0.058 0.3 3 -0.28 5 8
JUN -0.04 0.13 -10000 0 -0.38 30 30
MAP3K7 0.029 0.051 0.27 3 -0.27 3 6
GRAP2 0.035 0.019 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
MAP2K4 0.002 0.1 0.28 3 -0.34 21 24
LAT 0.036 0.025 -10000 0 -10000 0 0
LCP2 0.037 0.023 -10000 0 -10000 0 0
MAPK8 0.011 0.081 -10000 0 -0.58 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.037 0.06 0.26 6 -0.29 4 10
LAT/GRAP2/SLP76/HPK1/HIP-55 0.09 0.059 0.4 6 -10000 0 6
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.038 0.039 -10000 0 -0.33 4 4
VEGFR1 homodimer/NRP1 0.016 0.034 -10000 0 -0.33 4 4
mol:DAG 0.02 0.042 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.043 0.044 -10000 0 -0.3 3 3
CaM/Ca2+ 0.038 0.041 -10000 0 -10000 0 0
HIF1A 0.039 0.055 -10000 0 -0.54 4 4
GAB1 0.033 0.027 -10000 0 -0.54 1 1
AKT1 -0.007 0.1 -10000 0 -0.36 4 4
PLCG1 0.02 0.042 -10000 0 -10000 0 0
NOS3 0.021 0.084 -10000 0 -0.49 5 5
CBL 0.031 0.011 -10000 0 -10000 0 0
mol:NO 0.021 0.09 -10000 0 -0.48 6 6
FLT1 0.022 0.043 -10000 0 -0.39 4 4
PGF 0.034 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.062 0.051 -10000 0 -0.31 3 3
CALM1 0.034 0.006 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
eNOS/Hsp90 0.037 0.092 -10000 0 -0.47 6 6
endothelial cell proliferation 0.028 0.07 0.4 2 -10000 0 2
mol:Ca2+ 0.02 0.042 -10000 0 -10000 0 0
MAPK3 -0.005 0.035 -10000 0 -10000 0 0
MAPK1 -0.006 0.037 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
PLGF homodimer 0.034 0.011 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.38 0.26 -10000 0 -0.54 364 364
VEGFA homodimer 0.05 0.047 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.047 0.049 -10000 0 -0.33 3 3
platelet activating factor biosynthetic process 0.021 0.074 0.34 2 -10000 0 2
PI3K 0.038 0.11 -10000 0 -0.56 1 1
PRKCA -0.003 0.041 0.26 1 -10000 0 1
PRKCB -0.002 0.04 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.038 0.039 -10000 0 -0.33 4 4
VEGFA 0.05 0.047 -10000 0 -10000 0 0
VEGFB 0.034 0.006 -10000 0 -10000 0 0
mol:IP3 0.02 0.042 -10000 0 -10000 0 0
RASA1 0.021 0.043 -10000 0 -0.3 4 4
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer 0.022 0.042 -10000 0 -0.39 4 4
VEGFB homodimer 0.033 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.16 0.16 -10000 0 -0.51 20 20
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.11 -10000 0 -0.55 1 1
mol:L-citrulline 0.021 0.09 -10000 0 -0.48 6 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.076 0.059 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.062 0.05 -10000 0 -0.31 3 3
CD2AP 0.034 0.009 -10000 0 -10000 0 0
PI3K/GAB1 0.048 0.12 -10000 0 -0.54 1 1
PDPK1 0 0.095 -10000 0 -0.36 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.062 0.05 -10000 0 -0.31 3 3
mol:NADP 0.021 0.09 -10000 0 -0.48 6 6
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.073 0.058 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.039 0.04 -10000 0 -0.33 4 4
Signaling events mediated by HDAC Class III

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
EP300 0.032 0.009 -10000 0 -10000 0 0
HDAC4 0.033 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.008 -10000 0 -0.13 1 1
CDKN1A -0.01 0.043 -10000 0 -0.66 2 2
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
FOXO3 -0.006 0.004 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 48 48
FOXO4 0.018 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
TAT 0.029 0.05 -10000 0 -0.54 3 3
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0.03 0.14 8 -0.4 2 10
PPARGC1A -0.023 0.17 -10000 0 -0.54 51 51
FHL2 -0.026 0.18 -10000 0 -0.54 55 55
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.045 0.016 -10000 0 -10000 0 0
HIST2H4A -0.005 0.008 0.13 1 -10000 0 1
SIRT1/FOXO3a 0.022 0.03 0.19 1 -0.2 1 2
SIRT1 0.03 0.012 0.22 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.054 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.051 0.052 -10000 0 -0.23 2 2
apoptosis -0.061 0.022 -10000 0 -10000 0 0
SIRT1/PGC1A 0.004 0.12 -10000 0 -0.33 53 53
p53/SIRT1 0.037 0.024 0.42 1 -10000 0 1
SIRT1/FOXO4 0.033 0.044 -10000 0 -0.23 2 2
FOXO1/FHL2/SIRT1 -0.019 0.16 -10000 0 -0.34 91 91
HIST1H1E 0.04 0.041 -10000 0 -10000 0 0
SIRT1/p300 0.045 0.016 -10000 0 -10000 0 0
muscle cell differentiation -0.019 0.026 0.34 2 -10000 0 2
TP53 0.028 0.017 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.062 0.022 -10000 0 -10000 0 0
CREBBP 0.032 0.01 -10000 0 -10000 0 0
MEF2D 0.029 0.013 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.04 0.042 -10000 0 -0.4 3 3
ACSS2 0.014 0.007 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.019 0.026 -10000 0 -0.34 2 2
TRAIL signaling pathway

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
TNFSF10 0.012 0.11 -10000 0 -0.54 19 19
positive regulation of NF-kappaB transcription factor activity 0.023 0.085 -10000 0 -0.39 19 19
MAP2K4 0.016 0.085 -10000 0 -0.4 12 12
IKBKB 0.029 0.013 -10000 0 -10000 0 0
TNFRSF10B 0.028 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.028 0.018 -10000 0 -10000 0 0
SMPD1 0.005 0.057 -10000 0 -0.27 18 18
IKBKG 0.034 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.014 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.023 0.086 -10000 0 -0.4 19 19
TRAIL/TRAILR3 0.023 0.086 -10000 0 -0.4 19 19
TRAIL/TRAILR1 0.023 0.085 -10000 0 -0.39 19 19
TRAIL/TRAILR4 0.023 0.085 -10000 0 -0.4 19 19
TRAIL/TRAILR1/DAP3/GTP 0.032 0.067 -10000 0 -0.3 14 14
IKK complex 0.025 0.073 -10000 0 -0.4 6 6
RIPK1 0.034 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.01 -10000 0 -10000 0 0
MAPK3 0.001 0.076 -10000 0 -0.4 18 18
MAP3K1 0.017 0.098 -10000 0 -0.47 13 13
TRAILR4 (trimer) 0.027 0.014 -10000 0 -10000 0 0
TRADD 0.03 0.012 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.028 0.018 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.081 -10000 0 -0.4 12 12
CFLAR 0.033 0.026 -10000 0 -0.54 1 1
MAPK1 0.001 0.076 -10000 0 -0.4 18 18
TRAIL/TRAILR1/FADD/TRADD/RIP 0.047 0.079 -10000 0 -0.29 13 13
mol:ceramide 0.005 0.057 -10000 0 -0.26 18 18
FADD 0.028 0.015 -10000 0 -10000 0 0
MAPK8 0.001 0.1 -10000 0 -0.4 16 16
TRAF2 0.035 0.012 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.028 0.017 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.034 0.073 -10000 0 -0.33 14 14
DAP3 0.028 0.013 -10000 0 -10000 0 0
CASP10 0.024 0.077 0.34 3 -0.34 5 8
JNK cascade 0.023 0.085 -10000 0 -0.39 19 19
TRAIL (trimer) 0.012 0.11 -10000 0 -0.54 19 19
TNFRSF10C 0.028 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.036 0.065 -10000 0 -0.28 10 10
TRAIL/TRAILR2/FADD 0.033 0.074 -10000 0 -0.34 14 14
cell death 0.005 0.056 -10000 0 -0.26 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.081 -10000 0 -0.4 12 12
TRAILR2 (trimer) 0.028 0.016 -10000 0 -10000 0 0
CASP8 0.019 0.057 -10000 0 -0.58 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.047 0.08 -10000 0 -0.29 14 14
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.005 0.029 0.35 1 -0.34 1 2
SNTA1 0.032 0.026 -10000 0 -0.54 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.012 0.057 0.33 6 -0.34 1 7
MAPK12 -0.005 0.044 0.19 2 -0.29 10 12
CCND1 0.01 0.076 0.2 2 -0.43 11 13
p38 gamma/SNTA1 0.033 0.071 0.38 1 -0.28 10 11
MAP2K3 0.031 0.01 -10000 0 -10000 0 0
PKN1 0.034 0.011 -10000 0 -10000 0 0
G2/M transition checkpoint 0.01 0.071 0.21 39 -0.29 10 49
MAP2K6 -0.002 0.046 -10000 0 -0.33 10 10
MAPT 0.013 0.073 0.28 8 -0.31 10 18
MAPK13 0.018 0.027 -10000 0 -0.4 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.073 0.038 -10000 0 -0.32 1 1
HDAC3 0.034 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.009 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.049 0.011 -10000 0 -10000 0 0
GATA1/HDAC5 0.049 0.012 -10000 0 -10000 0 0
GATA2/HDAC5 0.054 0.026 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.024 0.12 -10000 0 -0.34 50 50
HDAC9 0.035 0.016 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.11 -10000 0 -0.34 40 40
HDAC4/ANKRA2 0.046 0.032 -10000 0 -0.4 2 2
HDAC5/YWHAB 0.046 0.015 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.02 -10000 0 -0.17 3 3
GATA2 0.042 0.033 -10000 0 -10000 0 0
HDAC4/RFXANK 0.049 0.012 -10000 0 -10000 0 0
BCOR 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.031 0.028 -10000 0 -0.54 1 1
HDAC5 0.033 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.048 0.024 -10000 0 -0.4 1 1
Histones 0.024 0.051 -10000 0 -0.28 4 4
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
HDAC4 0.033 0.007 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.045 0.033 -10000 0 -0.32 3 3
HDAC4/Ubc9 0.045 0.017 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.045 0.019 -10000 0 -0.17 1 1
TUBA1B 0.035 0.012 0.18 3 -10000 0 3
HDAC6 0.034 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.048 0.013 -10000 0 -10000 0 0
CAMK4 0.035 0.017 0.18 6 -10000 0 6
Tubulin/HDAC6 0.06 0.057 -10000 0 -0.34 9 9
SUMO1 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.033 0.008 -10000 0 -10000 0 0
GATA1 0.034 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NR3C1 -0.011 0.16 -10000 0 -0.54 40 40
SUMO1/HDAC4 0.051 0.051 -10000 0 -0.25 3 3
SRF 0.034 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.047 0.015 -10000 0 -10000 0 0
Tubulin 0.042 0.06 -10000 0 -0.4 9 9
HDAC4/14-3-3 E 0.045 0.019 -10000 0 -10000 0 0
GNB1 0.034 0.011 -10000 0 -10000 0 0
RANGAP1 0.038 0.03 -10000 0 -10000 0 0
BCL6/BCoR 0.005 0.13 -10000 0 -0.4 50 50
HDAC4/HDAC3/SMRT (N-CoR2) 0.066 0.018 -10000 0 -10000 0 0
HDAC4/SRF 0.066 0.022 -10000 0 -10000 0 0
HDAC4/ER alpha -0.028 0.2 -10000 0 -0.4 106 106
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.051 -10000 0 -0.28 4 4
cell motility 0.059 0.056 -10000 0 -0.34 9 9
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
HDAC7/HDAC3 0.025 0.004 -10000 0 -10000 0 0
BCL6 -0.024 0.17 -10000 0 -0.54 51 51
HDAC4/CaMK II delta B 0.033 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.049 0.011 -10000 0 -10000 0 0
ESR1 -0.059 0.25 -10000 0 -0.54 106 106
HDAC6/HDAC11 0.053 0.019 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.051 0.05 -10000 0 -0.26 3 3
NPC 0.02 0.002 -10000 0 -10000 0 0
MEF2C 0.005 0.12 -10000 0 -0.54 25 25
RAN 0.034 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.067 0.092 -10000 0 -0.3 24 24
GNG2 0.033 0.026 -10000 0 -0.54 1 1
NCOR2 0.034 0.005 -10000 0 -10000 0 0
TUBB2A 0.024 0.076 -10000 0 -0.54 9 9
HDAC11 0.038 0.025 -10000 0 -10000 0 0
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
ANKRA2 0.031 0.037 -10000 0 -0.54 2 2
RFXANK 0.034 0.005 -10000 0 -10000 0 0
nuclear import -0.038 0.021 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.1 0.085 -10000 0 -10000 0 0
CLOCK 0.039 0.009 -10000 0 -10000 0 0
TIMELESS/CRY2 0.069 0.069 -10000 0 -10000 0 0
DEC1/BMAL1 0.052 0.025 -10000 0 -0.4 1 1
ATR 0.034 0.006 -10000 0 -10000 0 0
NR1D1 0.04 0.052 -10000 0 -10000 0 0
ARNTL 0.037 0.028 -10000 0 -0.54 1 1
TIMELESS 0.059 0.089 -10000 0 -10000 0 0
NPAS2 0.042 0.02 -10000 0 -10000 0 0
CRY2 0.034 0.005 -10000 0 -10000 0 0
mol:CO -0.021 0.03 -10000 0 -0.11 54 54
CHEK1 0.087 0.075 -10000 0 -10000 0 0
mol:HEME 0.021 0.03 0.11 54 -10000 0 54
PER1 0.024 0.063 -10000 0 -0.54 6 6
BMAL/CLOCK/NPAS2 0.089 0.044 -10000 0 -0.34 1 1
BMAL1/CLOCK 0.058 0.073 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.1 0.085 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.11 0.086 -10000 0 -10000 0 0
mol:NADPH 0.021 0.03 0.11 54 -10000 0 54
PER1/TIMELESS 0.059 0.073 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.035 0.01 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.034 0.006 -10000 0 -10000 0 0
NFATC1 0.043 0.087 0.35 3 -0.39 6 9
NFATC2 0.004 0.073 0.29 1 -0.24 16 17
NFATC3 0.013 0.008 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.031 0.062 0.26 1 -0.26 7 8
Exportin 1/Ran/NUP214 0.066 0.017 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.055 0.065 -10000 0 -0.26 2 2
BCL2/BAX -0.033 0.17 -10000 0 -0.38 98 98
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.012 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.012 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
BAD 0.033 0.007 -10000 0 -10000 0 0
CABIN1/MEF2D 0.038 0.06 -10000 0 -0.26 6 6
Calcineurin A alpha-beta B1/BCL2 -0.069 0.22 -10000 0 -0.54 91 91
FKBP8 0.034 0.009 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.038 0.059 0.26 6 -10000 0 6
KPNB1 0.032 0.009 -10000 0 -10000 0 0
KPNA2 0.059 0.06 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
MAP3K8 -0.04 0.19 -10000 0 -0.54 65 65
NFAT4/CK1 alpha 0.029 0.038 -10000 0 -0.33 1 1
MEF2D/NFAT1/Cbp/p300 0.034 0.1 -10000 0 -0.31 16 16
CABIN1 0.031 0.061 0.26 1 -0.27 7 8
CALM1 0.033 0.008 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
CAMK4 0.035 0.017 0.18 6 -10000 0 6
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.01 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.053 0.04 -10000 0 -0.4 2 2
YWHAB 0.033 0.008 -10000 0 -10000 0 0
MAPK8 0.032 0.026 -10000 0 -0.54 1 1
MAPK9 0.034 0.009 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
FKBP1A 0.034 0.011 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.045 0.098 0.32 1 -0.41 7 8
PRKCH 0.029 0.051 -10000 0 -0.54 4 4
CABIN1/Cbp/p300 0.042 0.024 -10000 0 -10000 0 0
CASP3 0.033 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.015 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.009 -10000 0 -10000 0 0
apoptosis -0.002 0.058 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.047 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.01 0.063 -10000 0 -10000 0 0
BAD/BCL-XL 0.048 0.013 -10000 0 -10000 0 0
PRKCD 0.035 0.017 0.18 6 -10000 0 6
NUP214 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0.002 -10000 0 -10000 0 0
PRKCA 0.031 0.013 -10000 0 -10000 0 0
PRKCG 0.034 0.006 -10000 0 -10000 0 0
PRKCQ 0.039 0.03 -10000 0 -10000 0 0
FKBP38/BCL2 -0.033 0.17 -10000 0 -0.38 95 95
EP300 0.03 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
NFATc/JNK1 0.057 0.087 0.34 1 -0.38 6 7
CaM/Ca2+/FKBP38 0.043 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSNK1A1 0.016 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.044 0.018 -10000 0 -10000 0 0
NFATc/ERK1 0.054 0.085 0.34 1 -0.38 5 6
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.066 0.063 -10000 0 -0.26 2 2
NR4A1 0.024 0.14 -10000 0 -0.5 22 22
GSK3B 0.034 0.01 -10000 0 -10000 0 0
positive T cell selection 0.013 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.007 0.06 -10000 0 -0.26 6 6
RCH1/ KPNB1 0.063 0.047 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
AKAP5 0.04 0.051 -10000 0 -0.54 2 2
MEF2D 0.028 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
NFATc/p38 alpha 0.058 0.086 0.34 1 -0.37 6 7
CREBBP 0.03 0.015 -10000 0 -10000 0 0
BCL2 -0.069 0.22 -10000 0 -0.54 91 91
Retinoic acid receptors-mediated signaling

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
HDAC1 0.034 0.006 -10000 0 -10000 0 0
HDAC3 0.034 0.006 -10000 0 -10000 0 0
VDR 0.032 0.037 0.18 1 -0.54 2 3
Cbp/p300/PCAF 0.04 0.017 -10000 0 -10000 0 0
EP300 0.032 0.009 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.001 0.088 0.19 1 -0.29 18 19
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.006 0.11 0.21 21 -0.26 54 75
RAR alpha/9cRA/Cyclin H 0.077 0.064 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.1 -10000 0 -0.24 54 54
CDC2 0 0.003 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.046 0.046 -10000 0 -0.44 1 1
NCOR2 0.034 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RXRs/RARs/NRIP1/9cRA 0.024 0.12 0.38 1 -0.52 10 11
NCOA2 0.028 0.015 -10000 0 -10000 0 0
NCOA3 0.032 0.009 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 0.18 1 -0.54 2 3
RARG 0.035 0.007 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.046 0.009 -10000 0 -10000 0 0
MAPK3 0.032 0.013 -10000 0 -10000 0 0
MAPK1 0.032 0.009 -10000 0 -10000 0 0
MAPK8 0.033 0.027 -10000 0 -0.54 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.068 0.067 -10000 0 -0.36 1 1
RARA 0.022 0.023 0.2 1 -0.23 1 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.001 0.091 -10000 0 -0.23 45 45
PRKCA 0.033 0.019 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.027 0.13 0.43 3 -0.53 10 13
RXRG 0.021 0.033 -10000 0 -0.32 3 3
RXRA 0.04 0.054 -10000 0 -0.28 3 3
RXRB 0.027 0.019 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RBP1 0.007 0.13 -10000 0 -0.54 26 26
CRBP1/9-cic-RA 0.005 0.094 -10000 0 -0.4 26 26
RARB -0.053 0.21 -10000 0 -0.54 78 78
PRKCG 0.035 0.015 -10000 0 -10000 0 0
MNAT1 0.034 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.011 0.11 -10000 0 -0.44 5 5
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.029 0.1 -10000 0 -0.41 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.095 0.25 6 -0.31 10 16
RXRs/RARs/NRIP1/9cRA/HDAC3 0.027 0.13 0.43 3 -0.55 10 13
positive regulation of DNA binding 0.06 0.055 -10000 0 -0.27 1 1
NRIP1 0.02 0.19 0.56 2 -1.1 9 11
RXRs/RARs 0.029 0.12 0.36 4 -0.46 10 14
RXRs/RXRs/DNA/9cRA 0.026 0.056 -10000 0 -0.37 1 1
PRKACA 0.034 0.005 -10000 0 -10000 0 0
CDK7 0.033 0.007 -10000 0 -10000 0 0
TFIIH 0.066 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.08 0.05 -10000 0 -10000 0 0
CCNH 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.032 0.01 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.063 0.023 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.008 0.07 -10000 0 -0.28 26 26
TRAF2/ASK1 0.022 0.087 -10000 0 -0.29 34 34
ATM 0.03 0.012 -10000 0 -10000 0 0
MAP2K3 -0.014 0.14 0.29 1 -0.39 34 35
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.013 0.13 0.28 1 -0.36 42 43
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.036 0.017 -10000 0 -10000 0 0
TXN 0.01 0.006 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
GADD45A 0.025 0.072 -10000 0 -0.54 8 8
GADD45B 0.032 0.037 -10000 0 -0.54 2 2
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
MAP3K6 0.033 0.008 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
MAP3K4 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.021 0.1 -10000 0 -0.34 34 34
TAK1/TAB family -0.002 0.021 -10000 0 -0.21 1 1
RAC1/OSM/MEKK3 0.057 0.023 -10000 0 -10000 0 0
TRAF2 0.035 0.012 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.009 0.12 -10000 0 -0.34 23 23
TRAF6 0.009 0.002 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.039 0.069 -10000 0 -0.54 5 5
CCM2 0.034 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.047 0.046 -10000 0 -0.34 5 5
MAPK11 0.032 0.009 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.042 0.094 -10000 0 -0.3 31 31
OSM/MEKK3 0.045 0.018 -10000 0 -10000 0 0
TAOK1 0.017 0.013 -10000 0 -10000 0 0
TAOK2 0.015 0.008 -10000 0 -10000 0 0
TAOK3 0.016 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.003 0.13 -10000 0 -0.54 26 26
MAP3K10 0.033 0.039 -10000 0 -0.54 2 2
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TRX/ASK1 0.009 0.082 -10000 0 -0.32 28 28
GADD45/MTK1/MTK1 0.067 0.059 -10000 0 -0.29 10 10
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.027 0.026 -10000 0 -10000 0 0
CRKL 0.032 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DOCK1 0.03 0.044 -10000 0 -0.54 3 3
ITGA4 0.04 0.029 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.085 0.033 -10000 0 -10000 0 0
EPO 0.054 0.05 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.054 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.053 0.023 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.063 0.037 -10000 0 -10000 0 0
lamellipodium assembly -0.004 0.11 -10000 0 -0.32 45 45
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
ARF6 0.034 0.005 -10000 0 -10000 0 0
JAK2 0.043 0.034 -10000 0 -10000 0 0
PXN 0.034 0.004 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
MADCAM1 0.034 0.013 -10000 0 -10000 0 0
cell adhesion 0.082 0.032 -10000 0 -10000 0 0
CRKL/CBL 0.044 0.019 -10000 0 -10000 0 0
ITGB1 0.034 0.006 -10000 0 -10000 0 0
SRC 0.021 0.062 0.38 1 -0.31 11 12
ITGB7 0.034 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.062 0.067 0.26 4 -0.34 11 15
p130Cas/Crk/Dock1 0.04 0.071 0.37 1 -0.28 14 15
VCAM1 0.024 0.086 -10000 0 -0.54 11 11
RHOA 0.033 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.082 0.035 -10000 0 -10000 0 0
BCAR1 -0.007 0.059 0.39 1 -0.29 11 12
EPOR 0.034 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.031 0.011 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.12 -10000 0 -0.33 45 45
Paxillin-dependent events mediated by a4b1

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
CRKL 0.032 0.009 -9999 0 -10000 0 0
Rac1/GDP 0.03 0.012 -9999 0 -10000 0 0
DOCK1 0.03 0.044 -9999 0 -0.54 3 3
ITGA4 0.04 0.029 -9999 0 -10000 0 0
RAC1 0.034 0.005 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.054 0.022 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.031 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.07 0.025 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.059 0.023 -9999 0 -10000 0 0
lamellipodium assembly -0.031 0.16 -9999 0 -0.44 57 57
PIK3CA 0.033 0.008 -9999 0 -10000 0 0
PI3K 0.005 0.13 -9999 0 -0.4 44 44
ARF6 0.034 0.005 -9999 0 -10000 0 0
TLN1 0.034 0.006 -9999 0 -10000 0 0
PXN 0.017 0.003 -9999 0 -10000 0 0
PIK3R1 -0.02 0.17 -9999 0 -0.54 47 47
ARF6/GTP 0.069 0.032 -9999 0 -10000 0 0
cell adhesion 0.074 0.029 -9999 0 -10000 0 0
CRKL/CBL 0.044 0.019 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.058 0.024 -9999 0 -10000 0 0
ITGB1 0.034 0.006 -9999 0 -10000 0 0
ITGB7 0.034 0.004 -9999 0 -10000 0 0
ARF6/GDP 0.03 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.07 0.064 -9999 0 -0.3 11 11
p130Cas/Crk/Dock1 0.053 0.043 -9999 0 -0.34 3 3
VCAM1 0.024 0.086 -9999 0 -0.54 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.076 0.03 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.073 0.033 -9999 0 -10000 0 0
BCAR1 0.029 0.013 -9999 0 -10000 0 0
mol:GDP -0.071 0.032 -9999 0 -10000 0 0
CBL 0.031 0.011 -9999 0 -10000 0 0
PRKACA 0.034 0.005 -9999 0 -10000 0 0
GIT1 0.032 0.011 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.076 0.03 -9999 0 -10000 0 0
Rac1/GTP -0.037 0.18 -9999 0 -0.49 57 57
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.048 0.037 -10000 0 -0.29 3 3
RGS9BP 0.055 0.065 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.043 0.042 0.23 1 -0.34 2 3
mol:ADP 0.008 0.019 0.14 1 -0.4 1 2
GNAT2 0.031 0.045 -10000 0 -0.54 3 3
RGS9-1/Gbeta5/R9AP 0.05 0.1 -10000 0 -0.32 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.041 0.038 -10000 0 -0.34 4 4
GRK7 0.033 0.027 -10000 0 -0.54 1 1
CNGB3 0.033 0.03 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.026 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.056 0.075 0.28 8 -0.31 2 10
Cone PDE6 0.07 0.1 -10000 0 -0.3 21 21
Cone Metarhodopsin II 0.021 0.015 -10000 0 -0.31 1 1
Na + (4 Units) 0.056 0.046 -10000 0 -0.31 2 2
GNAT2/GDP 0.057 0.096 -10000 0 -0.28 30 30
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.02 0.044 -10000 0 -0.31 5 5
Cone Transducin 0.052 0.04 -10000 0 -0.31 3 3
SLC24A2 0.033 0.01 -10000 0 -10000 0 0
GNB3/GNGT2 0.043 0.02 -10000 0 -10000 0 0
GNB3 0.033 0.011 -10000 0 -10000 0 0
GNAT2/GTP 0.022 0.034 -10000 0 -0.34 4 4
CNGA3 0.042 0.052 -10000 0 -0.54 2 2
ARR3 0.035 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.044 0.042 0.23 1 -0.34 2 3
mol:Pi 0.049 0.1 -10000 0 -0.32 28 28
Cone CNG Channel 0.063 0.062 -10000 0 -0.28 7 7
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.033 0.01 -10000 0 -10000 0 0
RGS9 0.002 0.13 -10000 0 -0.54 27 27
PDE6C 0.034 0.028 -10000 0 -0.54 1 1
GNGT2 0.031 0.011 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.033 0.03 -10000 0 -0.54 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.075 0.14 0.38 1 -0.29 37 38
CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.035 0.017 -10000 0 -10000 0 0
AKT2 0.034 0.005 -10000 0 -10000 0 0
STXBP4 0.031 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.09 0.13 0.41 1 -0.28 58 59
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.006 0.07 -10000 0 -0.4 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
YWHAB 0.033 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.053 0.031 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
GYS1 0.017 0.021 0.26 3 -10000 0 3
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.033 0.026 -10000 0 -0.54 1 1
TC10/GTP/CIP4/Exocyst 0.044 0.026 -10000 0 -0.34 2 2
AS160/14-3-3 0.025 0.077 -10000 0 -0.37 8 8
VAMP2 0.031 0.011 -10000 0 -10000 0 0
SLC2A4 -0.099 0.14 0.42 1 -0.3 60 61
STX4 0.032 0.01 -10000 0 -10000 0 0
GSK3B 0.028 0.014 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
LNPEP 0.035 0.016 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.006 0.05 0.24 7 -10000 0 7
DAPP1 0.034 0.11 0.29 6 -0.32 20 26
Src family/SYK family/BLNK-LAT/BTK-ITK 0.045 0.14 0.38 9 -0.48 15 24
mol:DAG 0.042 0.09 0.26 35 -10000 0 35
HRAS 0.036 0.014 -10000 0 -10000 0 0
RAP1A 0.036 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.047 0.078 -10000 0 -0.33 8 8
PLCG2 0.022 0.073 -10000 0 -0.54 8 8
PLCG1 0.033 0.008 -10000 0 -10000 0 0
ARF5 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.009 0.041 0.25 4 -10000 0 4
ARF1/GTP 0.002 0.039 0.24 7 -10000 0 7
RHOA 0.033 0.007 -10000 0 -10000 0 0
YES1 0.032 0.027 -10000 0 -0.54 1 1
RAP1A/GTP -0.003 0.053 0.25 9 -10000 0 9
ADAP1 -0.008 0.039 0.22 6 -10000 0 6
ARAP3 -0.009 0.041 0.25 4 -10000 0 4
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PREX1 0.055 0.08 -10000 0 -0.54 4 4
ARHGEF6 0.014 0.11 -10000 0 -0.54 18 18
ARHGEF7 0.031 0.012 -10000 0 -10000 0 0
ARF1 0.028 0.014 -10000 0 -10000 0 0
NRAS 0.037 0.017 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
ARF6 0.034 0.005 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.061 0.22 22 -10000 0 22
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.035 0.012 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
mol:IP3 0.03 0.074 0.22 36 -0.17 1 37
LYN 0.03 0.015 -10000 0 -10000 0 0
ARF1/GDP 0.038 0.075 0.26 1 -0.34 7 8
RhoA/GDP 0.051 0.06 0.32 4 -10000 0 4
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.036 0.08 0.3 8 -0.33 3 11
SRC 0.033 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.005 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PTEN 0.028 0.044 -10000 0 -0.52 3 3
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.006 0.051 0.25 8 -10000 0 8
RhoA/GTP -0.006 0.05 0.26 5 -10000 0 5
Src family/SYK family/BLNK-LAT 0.044 0.091 0.3 11 -0.37 6 17
BLK 0.039 0.044 -10000 0 -10000 0 0
PDPK1 0.032 0.01 -10000 0 -10000 0 0
CYTH1 -0.008 0.039 0.22 6 -10000 0 6
HCK 0.036 0.022 -10000 0 -10000 0 0
CYTH3 -0.008 0.039 0.22 6 -10000 0 6
CYTH2 -0.008 0.039 0.22 6 -10000 0 6
KRAS 0.036 0.018 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.014 0.031 0.26 1 -10000 0 1
SGK1 0.016 0.034 0.27 1 -10000 0 1
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.031 0.077 0.26 1 -0.34 8 9
SOS1 0.034 0.004 -10000 0 -10000 0 0
SYK 0.039 0.026 -10000 0 -10000 0 0
ARF6/GDP 0.031 0.057 0.29 6 -10000 0 6
mol:PI-3-4-5-P3 -0.008 0.043 0.25 6 -10000 0 6
ARAP3/RAP1A/GTP -0.003 0.054 0.25 9 -10000 0 9
VAV1 0.038 0.025 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.008 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.056 0.044 0.29 2 -10000 0 2
PLEKHA1 -0.007 0.021 -10000 0 -0.34 2 2
Rac1/GDP 0.048 0.078 -10000 0 -0.34 7 7
LAT 0.036 0.025 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.082 -10000 0 -0.31 20 20
ITK -0.004 0.053 0.26 5 -0.29 2 7
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.044 0.11 0.3 30 -0.25 3 33
LCK 0.048 0.044 -10000 0 -10000 0 0
BTK -0.003 0.05 0.26 5 -10000 0 5
PDGFR-beta signaling pathway

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.04 0.084 0.3 2 -0.34 7 9
PDGFB-D/PDGFRB/SLAP 0.041 0.027 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.041 0.017 -10000 0 -10000 0 0
AKT1 0.027 0.12 0.39 15 -10000 0 15
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.047 0.094 0.35 3 -0.37 8 11
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
FGR 0.01 0.1 -10000 0 -0.45 17 17
mol:Ca2+ 0.037 0.092 0.34 3 -0.39 9 12
MYC 0.048 0.23 0.42 10 -0.78 29 39
SHC1 0.028 0.014 -10000 0 -10000 0 0
HRAS/GDP 0.049 0.046 0.27 1 -10000 0 1
LRP1/PDGFRB/PDGFB 0.065 0.023 -10000 0 -10000 0 0
GRB10 0.03 0.051 -10000 0 -0.54 4 4
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0.037 0.092 0.34 3 -0.4 9 12
PTEN 0.029 0.045 -10000 0 -0.54 3 3
GRB2 0.034 0.018 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.05 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.047 0.041 -10000 0 -0.4 4 4
cell cycle arrest 0.04 0.027 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
HIF1A 0.021 0.12 0.37 15 -0.33 1 16
GAB1 0.04 0.099 0.33 4 -0.41 7 11
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.038 0.094 0.38 4 -0.35 6 10
PDGFB-D/PDGFRB 0.06 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.049 0.018 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.031 0.078 -10000 0 -0.37 4 4
positive regulation of MAPKKK cascade 0.05 0.01 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.037 0.093 0.34 3 -0.4 9 12
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.033 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.043 0.02 -10000 0 -10000 0 0
SHB 0.036 0.018 -10000 0 -10000 0 0
BLK -0.032 0.17 -10000 0 -0.43 53 53
PTPN2 0.034 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.049 0.013 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
VAV2 0.039 0.11 0.37 3 -0.42 10 13
CBL 0.031 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.05 0.015 -10000 0 -10000 0 0
LCK 0.025 0.096 -10000 0 -0.54 8 8
PDGFRB 0.035 0.008 -10000 0 -10000 0 0
ACP1 0.034 0.006 -10000 0 -10000 0 0
HCK 0.026 0.071 -10000 0 -0.61 3 3
ABL1 0.033 0.096 0.35 3 -0.39 9 12
PDGFB-D/PDGFRB/CBL 0.035 0.11 0.35 1 -0.43 13 14
PTPN1 0.037 0.03 -10000 0 -10000 0 0
SNX15 0.033 0.007 -10000 0 -10000 0 0
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.059 0.055 -10000 0 -10000 0 0
cell proliferation 0.052 0.21 0.4 14 -0.68 29 43
SLA 0.029 0.025 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.051 0.059 0.45 2 -10000 0 2
SRC 0.021 0.06 -10000 0 -0.62 2 2
PI3K -0.011 0.066 -10000 0 -0.27 19 19
PDGFB-D/PDGFRB/GRB7/SHC 0.047 0.034 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.048 0.096 0.35 3 -0.38 8 11
LYN 0.022 0.056 -10000 0 -0.41 3 3
LRP1 0.034 0.005 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
STAT5B 0.033 0.01 -10000 0 -10000 0 0
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
NCK1-2/p130 Cas 0.076 0.053 -10000 0 -10000 0 0
SPHK1 0.035 0.06 -10000 0 -0.55 4 4
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.037 0.093 0.34 3 -0.4 9 12
PLCG1 0.037 0.094 0.34 3 -0.41 9 12
NHERF/PDGFRB 0.075 0.05 -10000 0 -10000 0 0
YES1 0.011 0.11 -10000 0 -0.58 12 12
cell migration 0.074 0.05 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.067 0.056 -10000 0 -10000 0 0
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
SLC9A3R1 0.059 0.058 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.081 0.068 -10000 0 -0.31 3 3
FYN 0.005 0.11 -10000 0 -0.44 19 19
DOK1 0.037 0.051 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.009 -10000 0 -10000 0 0
PDGFB 0.034 0.016 -10000 0 -10000 0 0
RAC1 0.025 0.16 0.38 2 -0.51 27 29
PRKCD 0.037 0.054 0.33 2 -10000 0 2
FER 0.036 0.053 0.39 1 -10000 0 1
MAPKKK cascade 0.049 0.098 0.35 17 -10000 0 17
RASA1 0.036 0.053 0.39 1 -10000 0 1
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.035 0.007 -10000 0 -10000 0 0
p62DOK/Csk 0.055 0.045 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.05 0.019 -10000 0 -0.17 1 1
chemotaxis 0.033 0.095 0.35 3 -0.38 9 12
STAT1-3-5/STAT1-3-5 0.08 0.049 -10000 0 -0.29 1 1
Bovine Papilomavirus E5/PDGFRB 0.026 0.007 -10000 0 -10000 0 0
PTPRJ 0.035 0.017 0.18 6 -10000 0 6
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.048 0.032 -10000 0 -10000 0 0
KIRREL 0.032 0.017 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.048 0.032 -10000 0 -10000 0 0
PLCG1 0.033 0.008 -10000 0 -10000 0 0
ARRB2 0.031 0.01 -10000 0 -10000 0 0
WASL 0.033 0.026 -10000 0 -0.54 1 1
Nephrin/NEPH1/podocin/CD2AP 0.071 0.047 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.032 0.027 -10000 0 -0.24 1 1
FYN 0.064 0.094 0.28 67 -0.24 2 69
mol:Ca2+ 0.066 0.047 -10000 0 -10000 0 0
mol:DAG 0.067 0.048 -10000 0 -10000 0 0
NPHS2 0.033 0.017 -10000 0 -10000 0 0
mol:IP3 0.067 0.048 -10000 0 -10000 0 0
regulation of endocytosis 0.054 0.044 -10000 0 -0.22 2 2
Nephrin/NEPH1/podocin/Cholesterol 0.056 0.038 -10000 0 -10000 0 0
establishment of cell polarity 0.048 0.032 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.084 0.053 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.056 0.046 -10000 0 -0.23 2 2
NPHS1 0.049 0.031 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.056 0.043 -10000 0 -0.24 2 2
TJP1 0.032 0.027 -10000 0 -0.54 1 1
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.035 0.007 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.069 0.049 -10000 0 -10000 0 0
CD2AP 0.034 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.069 0.05 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.056 0.11 0.3 61 -0.3 12 73
cytoskeleton organization 0.034 0.056 0.28 10 -10000 0 10
Nephrin/NEPH1 0.04 0.027 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.058 0.042 -10000 0 -0.36 1 1
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.035 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.063 0.12 0.36 4 -0.34 9 13
ERC1 0.033 0.013 -10000 0 -10000 0 0
RIP2/NOD2 0.053 0.051 0.26 3 -10000 0 3
NFKBIA 0.016 0.027 -10000 0 -0.32 1 1
BIRC2 0.031 0.011 -10000 0 -10000 0 0
IKBKB 0.029 0.013 -10000 0 -10000 0 0
RIPK2 0.029 0.022 -10000 0 -10000 0 0
IKBKG 0.021 0.13 -10000 0 -0.39 41 41
IKK complex/A20 0.042 0.15 -10000 0 -0.42 20 20
NEMO/A20/RIP2 0.029 0.022 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.032 0.15 -10000 0 -0.43 25 25
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.045 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.13 -10000 0 -0.43 16 16
BCL10/MALT1/TRAF6 0.064 0.021 -10000 0 -10000 0 0
NOD2 0.06 0.062 -10000 0 -10000 0 0
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.035 0.009 -10000 0 -10000 0 0
MALT1 0.033 0.01 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.045 0.017 -10000 0 -10000 0 0
ATM 0.03 0.012 -10000 0 -10000 0 0
TNF/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PRKCA 0.031 0.013 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
UBE2D3 0.034 0.005 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.073 0.025 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.027 -10000 0 -0.32 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
IKK complex 0.034 0.14 -10000 0 -0.43 21 21
CYLD 0.03 0.012 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.036 0.14 -10000 0 -0.43 15 15
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.077 0.054 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.009 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.064 -10000 0 -0.31 1 1
SUMO1 0.034 0.005 -10000 0 -10000 0 0
ZFPM1 0.029 0.015 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.02 -10000 0 -0.17 3 3
FKBP3 0.034 0.005 -10000 0 -10000 0 0
Histones 0.077 0.047 -10000 0 -10000 0 0
YY1/LSF 0.031 0.056 -10000 0 -0.26 8 8
SMG5 0.03 0.017 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.031 0.026 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.043 0.042 -10000 0 -0.25 1 1
SAP18 0.032 0.009 -10000 0 -10000 0 0
RELA 0.028 0.043 -10000 0 -0.23 8 8
HDAC1/Smad7 0.065 0.019 -10000 0 -10000 0 0
RANGAP1 0.038 0.03 -10000 0 -10000 0 0
HDAC3/TR2 0.045 0.039 -10000 0 -0.29 1 1
NuRD/MBD3 Complex 0.039 0.06 -10000 0 -0.32 5 5
NF kappa B1 p50/RelA 0.041 0.069 0.4 1 -0.33 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.042 0.033 -10000 0 -10000 0 0
GATA1 0.034 0.003 -10000 0 -10000 0 0
Mad/Max 0.049 0.013 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.028 0.093 -10000 0 -0.36 14 14
RBBP7 0.038 0.022 -10000 0 -10000 0 0
NPC 0.02 0.002 -10000 0 -10000 0 0
RBBP4 0.034 0.006 -10000 0 -10000 0 0
MAX 0.033 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.006 -10000 0 -10000 0 0
NFKBIA 0.028 0.019 -10000 0 -0.27 1 1
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.028 0.052 -10000 0 -0.3 4 4
SIN3 complex 0.078 0.032 -10000 0 -10000 0 0
SMURF1 0.034 0.005 -10000 0 -10000 0 0
CHD3 0.032 0.016 -10000 0 -10000 0 0
SAP30 0.034 0.009 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.031 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.031 0.05 -10000 0 -0.36 2 2
YY1/HDAC2 0.034 0.046 -10000 0 -0.23 5 5
YY1/HDAC1 0.034 0.049 -10000 0 -0.24 6 6
NuRD/MBD2 Complex (MeCP1) 0.039 0.056 -10000 0 -0.25 4 4
PPARG -0.21 0.16 -10000 0 -0.31 338 338
HDAC8/hEST1B 0.058 0.029 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.045 0.036 -10000 0 -10000 0 0
MBD3L2 0.033 0.026 -10000 0 -0.54 1 1
ubiquitin-dependent protein catabolic process 0.064 0.019 -10000 0 -10000 0 0
CREBBP 0.032 0.01 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.04 0.082 -10000 0 -0.35 9 9
HDAC1 0.034 0.006 -10000 0 -10000 0 0
HDAC3 0.03 0.013 -10000 0 -10000 0 0
HDAC2 0.034 0.017 -10000 0 -10000 0 0
YY1 0.017 0.008 -10000 0 -10000 0 0
HDAC8 0.035 0.002 -10000 0 -10000 0 0
SMAD7 0.033 0.007 -10000 0 -10000 0 0
NCOR2 0.034 0.005 -10000 0 -10000 0 0
MXD1 0.035 0.007 -10000 0 -10000 0 0
STAT3 0.024 0.011 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.049 0.057 -10000 0 -0.25 6 6
YY1/SAP30/HDAC1 0.05 0.053 -10000 0 -0.25 2 2
EP300 0.032 0.009 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.024 0.011 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.019 -10000 0 -0.27 1 1
histone deacetylation 0.038 0.059 -10000 0 -0.28 5 5
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.042 -10000 0 -10000 0 0
nuclear export -0.057 0.028 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.013 -10000 0 -10000 0 0
GATAD2A 0.037 0.022 -10000 0 -10000 0 0
GATA2/HDAC3 0.05 0.043 -10000 0 -10000 0 0
GATA1/HDAC1 0.05 0.01 -10000 0 -10000 0 0
GATA1/HDAC3 0.046 0.036 -10000 0 -10000 0 0
CHD4 0.032 0.009 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.029 0.062 -10000 0 -0.45 3 3
NuRD Complex 0.04 0.077 -10000 0 -0.33 6 6
positive regulation of chromatin silencing 0.073 0.045 -10000 0 -10000 0 0
SIN3B 0.035 0.014 -10000 0 -10000 0 0
MTA2 0.034 0.006 -10000 0 -10000 0 0
SIN3A 0.034 0.006 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.053 0.05 -10000 0 -0.25 3 3
HDAC complex 0.082 0.031 -10000 0 -10000 0 0
GATA1/Fog1 0.043 0.02 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.063 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
negative regulation of cell growth 0.026 0.071 -10000 0 -0.41 7 7
NuRD/MBD2/PRMT5 Complex 0.039 0.056 -10000 0 -0.25 4 4
Ran/GTP/Exportin 1 0.051 0.05 -10000 0 -0.26 3 3
NF kappa B/RelA/I kappa B alpha 0.031 0.049 -10000 0 -0.32 1 1
SIN3/HDAC complex/NCoR1 0.021 0.065 -10000 0 -0.32 10 10
TFCP2 0.032 0.036 -10000 0 -0.54 2 2
NR2C1 0.033 0.026 -10000 0 -0.54 1 1
MBD3 0.033 0.007 -10000 0 -10000 0 0
MBD2 0.034 0.011 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.049 0.015 -10000 0 -10000 0 0
FBXW11 0.034 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.033 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.051 -10000 0 -0.26 1 1
NFKBIA 0.033 0.036 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.031 0.016 -10000 0 -10000 0 0
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.038 0.023 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.032 0.018 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.016 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0.015 0.26 1 -10000 0 1
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
NFKB1 0.014 0.007 -10000 0 -10000 0 0
RELA 0.033 0.007 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.039 0.05 -10000 0 -0.22 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.042 0.056 -10000 0 -0.29 1 1
SRC 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
NF kappa B1 p50/RelA 0.039 0.05 -10000 0 -0.22 3 3
IKBKB 0.029 0.013 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -10000 0 0
SYK 0.039 0.026 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.018 0.1 -10000 0 -0.28 36 36
cell death 0.041 0.054 -10000 0 -0.28 1 1
NF kappa B1 p105/c-Rel 0.033 0.022 -10000 0 -10000 0 0
LCK 0.048 0.044 -10000 0 -10000 0 0
BCL3 0.035 0.014 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.03 0.012 -10000 0 -10000 0 0
ELF1 0.045 0.029 -10000 0 -10000 0 0
CCNA2 0.081 0.069 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
JAK3 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
JAK1 0.034 0.007 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.065 0.11 0.31 8 -0.36 8 16
SHC1 0.028 0.014 -10000 0 -10000 0 0
SP1 0.036 0.048 -10000 0 -0.35 8 8
IL2RA 0.036 0.057 -10000 0 -10000 0 0
IL2RB 0.036 0.022 -10000 0 -10000 0 0
SOS1 0.035 0.004 -10000 0 -10000 0 0
IL2RG 0.044 0.035 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.048 0.15 0.4 2 -0.76 11 13
PTPN11 0.035 0.004 -10000 0 -10000 0 0
CCND2 0.01 0.1 -10000 0 -0.74 9 9
LCK 0.049 0.044 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
IL2 0.034 0.027 -10000 0 -0.54 1 1
CDK6 0.028 0.063 -10000 0 -0.54 6 6
CCND3 0.066 0.11 0.46 4 -0.45 1 5
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.046 0.055 -10000 0 -0.29 8 8
BIRC5 0.12 0.074 -10000 0 -10000 0 0
NFKBIA 0.023 0.041 0.27 5 -10000 0 5
CPEB1 0.02 0.092 -10000 0 -0.54 13 13
AKT1 0.023 0.041 0.3 3 -10000 0 3
NDEL1 0.031 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.04 0.034 -10000 0 -10000 0 0
NDEL1/TACC3 0.095 0.066 -10000 0 -10000 0 0
GADD45A 0.025 0.072 -10000 0 -0.54 8 8
GSK3B 0.004 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.056 0.049 -10000 0 -10000 0 0
MDM2 0.033 0.01 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.11 0.059 -10000 0 -10000 0 0
TP53 0.022 0.058 -10000 0 -10000 0 0
DLG7 0.023 0.032 -10000 0 -10000 0 0
AURKAIP1 0.034 0.013 0.18 3 -10000 0 3
ARHGEF7 0.031 0.012 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.1 0.07 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.04 0.034 -10000 0 -10000 0 0
AURKA 0.032 0.041 -10000 0 -10000 0 0
AURKB 0.044 0.053 -10000 0 -10000 0 0
CDC25B 0.035 0.046 -10000 0 -10000 0 0
G2/M transition checkpoint 0.016 0.027 -10000 0 -10000 0 0
mRNA polyadenylation 0.031 0.059 -10000 0 -0.28 13 13
Aurora A/CPEB 0.031 0.059 -10000 0 -0.28 13 13
Aurora A/TACC1/TRAP/chTOG 0.054 0.089 -10000 0 -0.29 19 19
BRCA1 0.036 0.022 -10000 0 -10000 0 0
centrosome duplication 0.056 0.049 -10000 0 -10000 0 0
regulation of centrosome cycle 0.092 0.065 -10000 0 -10000 0 0
spindle assembly 0.052 0.087 -10000 0 -0.29 19 19
TDRD7 0.034 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.072 0.28 1 -10000 0 1
CENPA 0.061 0.056 0.16 63 -0.23 1 64
Aurora A/PP2A 0.052 0.036 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.029 0.037 0.27 1 -10000 0 1
negative regulation of DNA binding 0.022 0.058 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.044 0.02 -10000 0 -10000 0 0
RASA1 0.034 0.011 -10000 0 -10000 0 0
Ajuba/Aurora A 0.016 0.028 -10000 0 -10000 0 0
mitotic prometaphase 0.006 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.041 -10000 0 -10000 0 0
TACC1 0.001 0.12 -10000 0 -0.54 24 24
TACC3 0.096 0.074 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.069 0.037 -10000 0 -10000 0 0
Aurora A/RasGAP 0.051 0.036 -10000 0 -10000 0 0
OAZ1 0.033 0.007 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.004 0.027 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.059 0.043 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.11 0.058 -10000 0 -10000 0 0
PPP2R5D 0.034 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.11 0.062 0.25 5 -10000 0 5
PAK1 0.043 0.046 -10000 0 -10000 0 0
CKAP5 0.035 0.015 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.028 0.046 -10000 0 -10000 0 0
TP53 -0.002 0.055 -10000 0 -0.26 1 1
Senescence -0.005 0.06 -10000 0 -0.26 1 1
Apoptosis -0.005 0.06 -10000 0 -0.26 1 1
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.067 0.3 18 -10000 0 18
MDM4 0.028 0.017 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.012 0.019 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.054 0.029 -10000 0 -10000 0 0
STXBP1 0.034 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.023 0.031 -10000 0 -0.16 1 1
RAB3GAP2/RIMS1/UNC13B 0.058 0.038 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.042 0.036 -10000 0 -10000 0 0
mol:ACh 0 0.032 0.09 14 -0.12 11 25
RAB3GAP2 0.028 0.014 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.041 0.055 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.023 0.031 -10000 0 -0.16 1 1
UNC13B 0.035 0.014 -10000 0 -10000 0 0
CHRNA1 0.035 0.01 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.052 0.077 0.18 11 -0.33 9 20
SNAP25 0.007 0.035 0.093 21 -0.3 5 26
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 0.07 0.1 -10000 0 -0.54 8 8
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.033 0.015 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.041 0.055 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.01 0.033 -10000 0 -0.34 5 5
ADCY5 -0.005 0.021 -10000 0 -0.34 1 1
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.003 0.018 -10000 0 -10000 0 0
ADCY1 -0.006 0.009 -10000 0 -10000 0 0
ADCY2 -0.009 0.042 -10000 0 -0.34 7 7
ADCY3 -0.006 0.007 -10000 0 -10000 0 0
ADCY8 -0.003 0.015 -10000 0 -10000 0 0
PRKCE 0.009 0.001 -10000 0 -10000 0 0
ADCY9 -0.004 0.015 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.036 0.07 0.24 16 -10000 0 16
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.033 0.008 -10000 0 -10000 0 0
SMAD2 -0.007 0.05 -10000 0 -0.25 8 8
SMAD3 0.028 0.045 0.29 2 -10000 0 2
SMAD3/SMAD4 0.058 0.065 -10000 0 -0.46 3 3
SMAD4/Ubc9/PIASy 0.059 0.03 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.066 0.073 -10000 0 -0.32 1 1
PPM1A 0.034 0.006 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.01 0.056 -10000 0 -0.3 3 3
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
TRAP-1/SMAD4 0.047 0.019 -10000 0 -0.17 2 2
MAPK3 0.032 0.01 -10000 0 -10000 0 0
MAPK1 0.032 0.009 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
CTDSP2 0.034 0.006 -10000 0 -10000 0 0
CTDSPL 0.031 0.036 -10000 0 -0.54 2 2
KPNB1 0.032 0.009 -10000 0 -10000 0 0
TGFBRAP1 0.034 0.004 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
NUP153 0.034 0.006 -10000 0 -10000 0 0
KPNA2 0.059 0.06 -10000 0 -10000 0 0
PIAS4 0.035 0.016 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.048 0.022 -10000 0 -10000 0 0
ATM 0.03 0.012 -10000 0 -10000 0 0
UBE2D3 0.034 0.005 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
ATR 0.034 0.006 -10000 0 -10000 0 0
UBE2L3 0.032 0.009 -10000 0 -10000 0 0
FANCD2 0.025 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.089 0.058 -10000 0 -10000 0 0
XRCC5 0.034 0.005 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.049 0.033 -10000 0 -10000 0 0
MRE11A 0.031 0.011 -10000 0 -10000 0 0
DNA-PK 0.056 0.031 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.028 0.1 -10000 0 -0.58 6 6
FANCF 0.034 0.006 -10000 0 -10000 0 0
BRCA1 0.036 0.022 -10000 0 -10000 0 0
CCNE1 0.059 0.056 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.068 0.047 0.26 8 -10000 0 8
FANCG 0.034 0.009 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.052 0.025 -10000 0 -10000 0 0
FANCE 0.033 0.027 -10000 0 -0.54 1 1
FANCC 0.036 0.016 -10000 0 -10000 0 0
NBN 0.028 0.016 -10000 0 -10000 0 0
FANCA 0.061 0.064 -10000 0 -10000 0 0
DNA repair 0.075 0.1 0.35 6 -0.41 2 8
BRCA1/BARD1/ubiquitin 0.052 0.025 -10000 0 -10000 0 0
BARD1/DNA-PK 0.072 0.04 -10000 0 -10000 0 0
FANCL 0.034 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.048 0.022 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.025 0.073 -10000 0 -0.31 3 3
BRCA1/BACH1/BARD1/TopBP1 0.068 0.029 0.26 1 -10000 0 1
BRCA1/BARD1/P53 0.078 0.039 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.063 0.032 -10000 0 -10000 0 0
BRCA1/BACH1 0.036 0.022 -10000 0 -10000 0 0
BARD1 0.037 0.022 0.18 12 -10000 0 12
PCNA 0.038 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.069 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.066 0.03 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.12 0.071 0.27 30 -10000 0 30
BARD1/DNA-PK/P53 0.077 0.05 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.052 0.025 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.048 0.039 -10000 0 -0.31 2 2
FA complex 0.043 0.053 -10000 0 -0.3 2 2
BARD1/EWS 0.05 0.02 -10000 0 -10000 0 0
RBBP8 0.014 0.028 -10000 0 -0.4 2 2
TP53 0.031 0.014 -10000 0 -10000 0 0
TOPBP1 0.035 0.012 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.075 0.037 -10000 0 -10000 0 0
BRCA1/BARD1 0.097 0.063 -10000 0 -10000 0 0
CSTF1 0.032 0.01 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.027 0.016 -10000 0 -10000 0 0
CDK2 0.037 0.021 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.074 -10000 0 -10000 0 0
RAD50 0.034 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.052 0.025 -10000 0 -10000 0 0
EWSR1 0.032 0.009 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.043 0.022 -9999 0 -0.34 1 1
EFNA5 0.033 0.029 -9999 0 -0.54 1 1
FYN 0.017 0.031 -9999 0 -0.31 3 3
neuron projection morphogenesis 0.043 0.022 -9999 0 -0.34 1 1
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.044 0.022 -9999 0 -0.34 1 1
EPHA5 0.034 0.005 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.034 0.004 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.032 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
HIF1A/p53 0.045 0.06 -10000 0 -0.27 7 7
HIF1A 0.029 0.049 -10000 0 -0.27 6 6
COPS5 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.071 0.05 -10000 0 -10000 0 0
FIH (dimer) 0.034 0.005 -10000 0 -10000 0 0
CDKN2A 0.053 0.054 -10000 0 -10000 0 0
ARNT/IPAS 0.04 0.021 -10000 0 -10000 0 0
HIF1AN 0.034 0.005 -10000 0 -10000 0 0
GNB2L1 0.034 0.005 -10000 0 -10000 0 0
HIF1A/ARNT 0.033 0.056 -10000 0 -0.28 7 7
CUL2 0.034 0.009 -10000 0 -10000 0 0
OS9 0.034 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.053 0.03 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.049 0.059 -10000 0 -0.28 7 7
PHD1-3/OS9 0.077 0.06 -10000 0 -0.32 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.058 0.064 -10000 0 -0.27 6 6
VHL 0.036 0.018 0.18 7 -10000 0 7
HSP90AA1 0.033 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.039 0.059 -10000 0 -0.28 6 6
EGLN3 0.06 0.064 -10000 0 -0.54 1 1
EGLN2 0.036 0.017 -10000 0 -10000 0 0
EGLN1 0.028 0.014 -10000 0 -10000 0 0
TP53 0.031 0.014 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.044 0.066 -10000 0 -0.46 7 7
ARNT 0.028 0.014 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.032 0.009 -10000 0 -10000 0 0
HIF1A/p19ARF 0.059 0.069 0.26 4 -0.27 6 10
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.034 0.006 -9999 0 -9999 0 0
ITGB7 0.034 0.004 -9999 0 -9999 0 0
ITGA4 0.04 0.029 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.054 0.022 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.053 0.023 -9999 0 -9999 0 0
Aurora C signaling

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
INCENP 0.045 0.04 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.079 0.055 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.017 0.032 -9999 0 -0.31 4 4
AURKB 0.057 0.058 -9999 0 -10000 0 0
AURKC 0.036 0.019 -9999 0 -10000 0 0
Glypican 2 network

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
MDK 0.044 0.037 -9999 0 -9999 0 0
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine 0.032 0.026 -9999 0 -9999 0 0
neuron projection morphogenesis 0.032 0.026 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.013 -10000 0 -10000 0 0
MDM2/SUMO1 0.049 0.052 -10000 0 -0.25 3 3
HDAC4 0.033 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.014 -10000 0 -10000 0 0
SUMO1 0.034 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.016 0.026 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.034 -10000 0 -0.27 3 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.051 0.051 -10000 0 -0.25 3 3
SUMO1/HDAC1 0.053 0.05 -10000 0 -0.25 3 3
RANGAP1 0.038 0.03 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.078 0.031 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.018 0.02 -10000 0 -0.17 3 3
Ran/GTP 0.036 0.046 -10000 0 -0.26 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.01 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.05 0.26 2 -0.26 3 5
NPC 0.02 0.002 -10000 0 -10000 0 0
PIAS2 0.033 0.007 -10000 0 -10000 0 0
PIAS1 0.033 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.053 0.036 -10000 0 -0.29 4 4
MAPK9 0.009 0.005 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.01 0.017 -10000 0 -10000 0 0
GNB1/GNG2 0.043 0.021 -10000 0 -0.34 1 1
GNB1 0.034 0.011 -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 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.019 0.025 -10000 0 -0.31 3 3
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 0.001 0.006 0.08 3 -10000 0 3
GNAL 0.03 0.044 -10000 0 -0.54 3 3
GNG2 0.033 0.026 -10000 0 -0.54 1 1
CRH 0.031 0.024 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.016 -10000 0 -0.34 1 1
MAPK11 0.009 0.003 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0.016 0.037 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.035 0.051 -10000 0 -0.19 2 2
AP2 0.049 0.017 0.26 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.044 0.015 -10000 0 -10000 0 0
CLTB 0.033 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.019 -10000 0 -10000 0 0
CD4 0.032 0.009 -10000 0 -10000 0 0
CLTA 0.034 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.009 0.008 0.14 2 -10000 0 2
mol:PI-4-5-P2 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP 0.015 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.012 0.022 0.18 5 -10000 0 5
mol:Choline 0.008 0.02 -10000 0 -0.2 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.029 0.015 -10000 0 -10000 0 0
DDEF1 0.007 0.02 -10000 0 -0.2 1 1
ARF1/GDP 0.001 0.024 -10000 0 -0.15 1 1
AP2M1 0.034 0.009 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.008 -10000 0 -10000 0 0
Rac/GTP 0.028 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.034 0.025 -10000 0 -10000 0 0
ARFIP2 0.021 0.026 -10000 0 -10000 0 0
COPA 0.028 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.017 0.031 -10000 0 -0.21 2 2
ARF1/GTP/ARHGAP10 0.018 0.01 -10000 0 -10000 0 0
GGA3 0.032 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.017 0.039 -10000 0 -0.24 7 7
AP2A1 0.034 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.032 -10000 0 -0.23 5 5
ARF1/GDP/Membrin 0.019 0.048 -10000 0 -0.24 12 12
Arfaptin 2/Rac/GDP 0.041 0.016 -10000 0 -10000 0 0
CYTH2 -0.001 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.034 0.021 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -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 0.025 0.032 -10000 0 -10000 0 0
PLD2 0.008 0.02 -10000 0 -0.2 1 1
ARF-GAP1/v-SNARE 0.009 0.008 0.14 2 -10000 0 2
PIP5K1A 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP/Membrin/GBF1/p115 0.016 0.023 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.02 -10000 0 -0.2 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.008 0.14 2 -10000 0 2
GOSR2 0.013 0.018 -10000 0 -0.26 1 1
USO1 0.012 0.024 -10000 0 -0.31 2 2
GBF1 0.013 0.02 -10000 0 -0.31 1 1
ARF1/GTP/Arfaptin 2 0.036 0.022 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.062 0.026 -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 0.048 0.015 -10000 0 -9999 0 0
FBXW11 0.034 0.006 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -9999 0 0
CHUK 0.034 0.005 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.095 0.035 -10000 0 -9999 0 0
NFKB1 0.034 0.005 -10000 0 -9999 0 0
MAP3K14 0.033 0.007 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.051 0.017 -10000 0 -9999 0 0
RELB 0.037 0.02 -10000 0 -9999 0 0
NFKB2 0.035 0.012 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.047 0.018 0.23 1 -9999 0 1
regulation of B cell activation 0.047 0.017 0.23 1 -9999 0 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 513 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.E2.A1BD TCGA.E2.A1BC TCGA.E2.A1B6 TCGA.E2.A1B5
109_MAP3K5 0.04 0.04 0.094 0.094
47_PPARGC1A 0.035 0.035 0.035 0.18
105_BMP4 0.035 0.035 0.035 0.035
105_BMP6 0.035 0.035 0.035 0.035
105_BMP7 0.035 0.035 0.035 0.035
105_BMP2 0.035 0.035 0.035 0.035
131_RELN/VLDLR 0.089 0.089 -0.31 0.18
30_TGFB1/TGF beta receptor Type II 0.034 0.034 0.034 0.034
84_STAT5B -0.21 -0.0031 -0.03 -0.21
84_STAT5A -0.21 -0.0031 -0.03 -0.21
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/22230819/GDAC_MergeDataFiles_12183094/BRCA-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/22506563/GDAC_Gistic2Report_22529547/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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