PARADIGM pathway analysis of mRNA expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1HX1B5S
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1HX1B5S
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 52 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 249
Signaling events mediated by Stem cell factor receptor (c-Kit) 225
Endothelins 154
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 148
EGFR-dependent Endothelin signaling events 146
Class IB PI3K non-lipid kinase events 126
IGF1 pathway 122
FOXM1 transcription factor network 118
Arf6 signaling events 112
Nongenotropic Androgen signaling 94
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 0.4734 249 10986 44 -0.6 0.034 1000 -1000 -0.005 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.4278 225 17619 78 -1 0.32 1000 -1000 -0.026 -1000
Endothelins 0.2928 154 14823 96 -0.81 0.17 1000 -1000 -0.028 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2814 148 10109 68 -0.88 0.45 1000 -1000 -0.055 -1000
EGFR-dependent Endothelin signaling events 0.2776 146 3066 21 -0.31 0.048 1000 -1000 -0.039 -1000
Class IB PI3K non-lipid kinase events 0.2395 126 378 3 -0.11 -1000 1000 -1000 -0.023 -1000
IGF1 pathway 0.2319 122 7001 57 -0.27 0.11 1000 -1000 -0.021 -1000
FOXM1 transcription factor network 0.2243 118 6046 51 -0.12 0.71 1000 -1000 0.012 -1000
Arf6 signaling events 0.2129 112 6950 62 -0.31 0.081 1000 -1000 0 -1000
Nongenotropic Androgen signaling 0.1787 94 4930 52 -0.57 0.3 1000 -1000 -0.021 -1000
Glucocorticoid receptor regulatory network 0.1540 81 9311 114 -0.95 0.29 1000 -1000 -0.047 -1000
S1P1 pathway 0.1464 77 2774 36 -0.62 0.046 1000 -1000 -0.025 -1000
Signaling events mediated by PTP1B 0.1445 76 5781 76 -0.37 0.19 1000 -1000 -0.04 -1000
Calcium signaling in the CD4+ TCR pathway 0.1388 73 2274 31 -0.35 0.039 1000 -1000 -0.034 -1000
HIF-1-alpha transcription factor network 0.1369 72 5472 76 -0.4 0.071 1000 -1000 -0.022 -1000
PDGFR-alpha signaling pathway 0.1331 70 3121 44 -0.7 0.063 1000 -1000 -0.021 -1000
Ephrin B reverse signaling 0.1312 69 3344 48 -0.18 0.061 1000 -1000 -0.033 -1000
BMP receptor signaling 0.1293 68 5580 81 -0.4 0.11 1000 -1000 -0.027 -1000
Ras signaling in the CD4+ TCR pathway 0.1255 66 1128 17 -0.2 0.033 1000 -1000 -0.006 -1000
Plasma membrane estrogen receptor signaling 0.1084 57 4915 86 -0.25 0.17 1000 -1000 -0.051 -1000
FAS signaling pathway (CD95) 0.1065 56 2654 47 -0.88 0.06 1000 -1000 -0.025 -1000
IL6-mediated signaling events 0.1027 54 4062 75 -0.37 0.073 1000 -1000 -0.026 -1000
IL23-mediated signaling events 0.0989 52 3143 60 -0.79 0.065 1000 -1000 -0.003 -1000
IL4-mediated signaling events 0.0970 51 4714 91 -0.51 0.14 1000 -1000 -0.1 -1000
EPHB forward signaling 0.0970 51 4367 85 -0.18 0.15 1000 -1000 -0.057 -1000
Integrins in angiogenesis 0.0951 50 4200 84 -0.39 0.13 1000 -1000 -0.025 -1000
Visual signal transduction: Rods 0.0932 49 2555 52 -0.43 0.074 1000 -1000 -0.018 -1000
Aurora B signaling 0.0932 49 3314 67 -0.38 0.24 1000 -1000 -0.031 -1000
E-cadherin signaling in keratinocytes 0.0913 48 2085 43 -0.27 0.035 1000 -1000 -0.015 -1000
PLK1 signaling events 0.0856 45 3901 85 -0.036 0.17 1000 -1000 -0.025 -1000
Glypican 1 network 0.0798 42 2027 48 -0.39 0.07 1000 -1000 -0.025 -1000
Fc-epsilon receptor I signaling in mast cells 0.0779 41 4060 97 -0.35 0.04 1000 -1000 -0.043 -1000
Signaling events mediated by the Hedgehog family 0.0741 39 2048 52 -0.14 0.068 1000 -1000 -0.019 -1000
p75(NTR)-mediated signaling 0.0741 39 4891 125 -0.13 0.094 1000 -1000 -0.034 -1000
S1P5 pathway 0.0741 39 675 17 -0.17 0.067 1000 -1000 -0.002 -1000
Insulin Pathway 0.0741 39 2907 74 -0.28 0.092 1000 -1000 -0.035 -1000
Nectin adhesion pathway 0.0703 37 2379 63 -0.075 0.054 1000 -1000 -0.029 -1000
TCGA08_retinoblastoma 0.0703 37 302 8 -0.022 0.057 1000 -1000 -0.006 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0684 36 2726 74 -0.27 0.074 1000 -1000 -0.055 -1000
Presenilin action in Notch and Wnt signaling 0.0665 35 2180 61 -0.38 0.11 1000 -1000 -0.036 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0627 33 2845 85 -0.54 0.044 1000 -1000 -0.024 -1000
S1P4 pathway 0.0627 33 833 25 -0.17 0.045 1000 -1000 -0.011 -1000
LPA receptor mediated events 0.0608 32 3284 102 -0.35 0.095 1000 -1000 -0.077 -1000
Signaling events regulated by Ret tyrosine kinase 0.0589 31 2553 82 -0.1 0.11 1000 -1000 -0.051 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0589 31 3800 120 -0.24 0.12 1000 -1000 -0.041 -1000
Regulation of nuclear SMAD2/3 signaling 0.0570 30 4110 136 -0.37 0.075 1000 -1000 -0.039 -1000
TCGA08_p53 0.0570 30 213 7 -0.009 0.028 1000 -1000 -0.002 -1000
IL27-mediated signaling events 0.0570 30 1541 51 -0.37 0.067 1000 -1000 -0.043 -1000
ErbB2/ErbB3 signaling events 0.0551 29 1947 65 -0.35 0.047 1000 -1000 -0.034 -1000
Syndecan-3-mediated signaling events 0.0551 29 1030 35 -0.37 0.075 1000 -1000 -0.019 -1000
TCR signaling in naïve CD8+ T cells 0.0551 29 2772 93 -0.04 0.082 1000 -1000 -0.039 -1000
TCGA08_rtk_signaling 0.0551 29 770 26 -0.27 0.042 1000 -1000 -0.023 -1000
Syndecan-2-mediated signaling events 0.0494 26 1830 69 -0.32 0.13 1000 -1000 -0.011 -1000
FOXA2 and FOXA3 transcription factor networks 0.0494 26 1202 46 -0.74 0.051 1000 -1000 -0.013 -1000
HIF-2-alpha transcription factor network 0.0494 26 1132 43 -0.22 0.26 1000 -1000 -0.087 -1000
Osteopontin-mediated events 0.0475 25 977 38 -0.35 0.14 1000 -1000 -0.011 -1000
mTOR signaling pathway 0.0475 25 1376 53 -0.051 0.044 1000 -1000 -0.032 -1000
amb2 Integrin signaling 0.0475 25 2094 82 -0.52 0.13 1000 -1000 -0.018 -1000
IL12-mediated signaling events 0.0456 24 2139 87 -0.83 0.088 1000 -1000 -0.041 -1000
ErbB4 signaling events 0.0456 24 1681 69 -0.36 0.14 1000 -1000 -0.033 -1000
Ceramide signaling pathway 0.0456 24 1831 76 -0.25 0.083 1000 -1000 -0.021 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0456 24 2119 88 -0.39 0.13 1000 -1000 -0.056 -1000
Thromboxane A2 receptor signaling 0.0437 23 2448 105 -0.27 0.066 1000 -1000 -0.032 -1000
Reelin signaling pathway 0.0437 23 1342 56 -0.055 0.084 1000 -1000 -0.018 -1000
IL1-mediated signaling events 0.0437 23 1427 62 -0.05 0.068 1000 -1000 -0.025 -1000
Canonical Wnt signaling pathway 0.0437 23 1189 51 -0.38 0.16 1000 -1000 -0.028 -1000
S1P3 pathway 0.0437 23 992 42 -0.17 0.063 1000 -1000 -0.017 -1000
Coregulation of Androgen receptor activity 0.0418 22 1672 76 -0.23 0.053 1000 -1000 -0.009 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0418 22 1191 52 -0.38 0.1 1000 -1000 -0.015 -1000
Regulation of Telomerase 0.0399 21 2235 102 -0.35 0.087 1000 -1000 -0.013 -1000
Regulation of p38-alpha and p38-beta 0.0380 20 1107 54 -0.32 0.071 1000 -1000 -0.041 -1000
Syndecan-4-mediated signaling events 0.0380 20 1406 67 -0.39 0.15 1000 -1000 -0.026 -1000
Regulation of Androgen receptor activity 0.0380 20 1454 70 -0.43 0.079 1000 -1000 -0.033 -1000
Noncanonical Wnt signaling pathway 0.0342 18 474 26 -0.017 0.04 1000 -1000 -0.022 -1000
Signaling mediated by p38-gamma and p38-delta 0.0342 18 273 15 -0.006 0.034 1000 -1000 -0.026 -1000
Syndecan-1-mediated signaling events 0.0323 17 591 34 -0.042 0.12 1000 -1000 -0.016 -1000
IL2 signaling events mediated by PI3K 0.0304 16 966 58 -0.12 0.05 1000 -1000 -0.031 -1000
Wnt signaling 0.0304 16 114 7 -0.017 0.04 1000 -1000 -0.008 -1000
E-cadherin signaling in the nascent adherens junction 0.0304 16 1275 76 -0.042 0.059 1000 -1000 -0.049 -1000
Hedgehog signaling events mediated by Gli proteins 0.0285 15 1004 65 -0.17 0.077 1000 -1000 -0.027 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0285 15 704 45 -0.006 0.06 1000 -1000 -0.033 -1000
Signaling events mediated by PRL 0.0285 15 531 34 -0.31 0.051 1000 -1000 -0.023 -1000
E-cadherin signaling events 0.0285 15 77 5 0.006 0.035 1000 -1000 0.02 -1000
Caspase cascade in apoptosis 0.0266 14 1052 74 -0.16 0.049 1000 -1000 -0.033 -1000
IFN-gamma pathway 0.0266 14 986 68 -0.02 0.1 1000 -1000 -0.035 -1000
Cellular roles of Anthrax toxin 0.0228 12 498 39 -0.063 0.038 1000 -1000 -0.018 -1000
Class I PI3K signaling events mediated by Akt 0.0228 12 832 68 -0.15 0.06 1000 -1000 -0.023 -1000
ceramide signaling pathway 0.0228 12 626 49 -0.07 0.053 1000 -1000 -0.022 -1000
BCR signaling pathway 0.0228 12 1245 99 -0.15 0.094 1000 -1000 -0.039 -1000
PLK2 and PLK4 events 0.0209 11 33 3 0.016 0.055 1000 -1000 0.004 -1000
FoxO family signaling 0.0209 11 729 64 0 0.15 1000 -1000 -0.015 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0190 10 284 28 -0.17 0.054 1000 -1000 -0.007 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0190 10 576 54 -0.041 0.083 1000 -1000 -0.02 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0190 10 1290 125 -0.38 0.075 1000 -1000 -0.038 -1000
JNK signaling in the CD4+ TCR pathway 0.0171 9 165 17 -0.04 0.09 1000 -1000 -0.017 -1000
EPO signaling pathway 0.0171 9 537 55 -0.09 0.069 1000 -1000 -0.017 -1000
VEGFR1 specific signals 0.0171 9 517 56 -0.38 0.076 1000 -1000 -0.029 -1000
Signaling events mediated by HDAC Class III 0.0152 8 321 40 -0.061 0.062 1000 -1000 -0.037 -1000
TRAIL signaling pathway 0.0152 8 414 48 -0.002 0.046 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class II 0.0133 7 563 75 -0.058 0.067 1000 -1000 -0.029 -1000
Circadian rhythm pathway 0.0133 7 173 22 -0.021 0.1 1000 -1000 -0.009 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0133 7 607 83 -0.07 0.066 1000 -1000 -0.018 -1000
Arf6 trafficking events 0.0133 7 513 71 -0.25 0.056 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0114 6 234 37 -0.02 0.085 1000 -1000 -0.015 -1000
Paxillin-dependent events mediated by a4b1 0.0114 6 244 36 -0.07 0.076 1000 -1000 -0.027 -1000
PDGFR-beta signaling pathway 0.0114 6 606 97 -0.035 0.08 1000 -1000 -0.035 -1000
p38 MAPK signaling pathway 0.0114 6 293 44 -0.016 0.066 1000 -1000 -0.015 -1000
Visual signal transduction: Cones 0.0095 5 191 38 0 0.07 1000 -1000 0 -1000
Insulin-mediated glucose transport 0.0095 5 171 32 -0.099 0.053 1000 -1000 -0.015 -1000
Retinoic acid receptors-mediated signaling 0.0095 5 345 58 -0.055 0.08 1000 -1000 -0.016 -1000
Class I PI3K signaling events 0.0095 5 380 73 -0.008 0.059 1000 -1000 -0.027 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0076 4 169 34 -0.047 0.083 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class I 0.0076 4 495 104 -0.21 0.082 1000 -1000 -0.034 -1000
Atypical NF-kappaB pathway 0.0076 4 148 31 -0.02 0.048 1000 -1000 -0.007 -1000
IL2 signaling events mediated by STAT5 0.0076 4 105 22 -0.019 0.082 1000 -1000 -0.018 -1000
Canonical NF-kappaB pathway 0.0057 3 144 39 0 0.073 1000 -1000 -0.022 -1000
Aurora A signaling 0.0057 3 198 60 0 0.12 1000 -1000 -0.009 -1000
Arf6 downstream pathway 0.0057 3 154 43 -0.09 0.092 1000 -1000 -0.028 -1000
Aurora C signaling 0.0057 3 23 7 0 0.078 1000 -1000 -0.012 -1000
LPA4-mediated signaling events 0.0038 2 30 12 -0.01 0.035 1000 -1000 -0.018 -1000
Effects of Botulinum toxin 0.0038 2 72 26 0 0.071 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 26 23 -0.007 0.064 1000 -1000 -0.015 -1000
Ephrin A reverse signaling 0.0019 1 7 7 0 0.044 1000 -1000 0 -1000
Rapid glucocorticoid signaling 0.0019 1 25 20 0 0.043 1000 -1000 0 -1000
Arf1 pathway 0.0019 1 65 54 -0.001 0.062 1000 -1000 -0.011 -1000
BARD1 signaling events 0.0000 0 46 57 -0.075 0.13 1000 -1000 -0.038 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.034 0.054 1000 -1000 0.02 -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 26 27 0 0.078 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0000 0 31 33 0 0.076 1000 -1000 -0.016 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 0 0.095 1000 -1000 0 -1000
Total NA 4387 265541 7203 -30 -990 131000 -131000 -3.2 -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 -0.6 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 -0.36 306 306
ATF2/c-Jun -0.26 0.32 -10000 0 -0.65 156 156
MAPK11 -0.19 0.2 -10000 0 -0.36 286 286
MITF -0.24 0.23 -10000 0 -0.42 308 308
MAPKAPK5 -0.23 0.22 -10000 0 -0.41 308 308
KRT8 -0.22 0.22 -10000 0 -0.39 304 304
MAPKAPK3 0.034 0.012 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.016 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.31 0.32 -10000 0 -0.55 309 309
CEBPB -0.22 0.23 0.3 1 -0.41 283 284
SLC9A1 -0.24 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 -0.45 308 308
JUN -0.26 0.31 -10000 0 -0.65 156 156
PPARGC1A -0.28 0.29 0.29 1 -0.48 314 315
USF1 -0.21 0.22 0.33 4 -0.39 292 296
RAB5/GDP/GDI1 -0.17 0.18 -10000 0 -0.31 300 300
NOS2 -0.24 0.22 -10000 0 -0.41 308 308
DDIT3 -0.23 0.22 -10000 0 -0.41 306 306
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 -0.45 304 304
CREB1 -0.25 0.24 -10000 0 -0.43 305 305
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.24 0.24 0.38 1 -0.42 293 294
RPS6KA4 -0.23 0.23 -10000 0 -0.42 304 304
PLA2G4A -0.36 0.27 -10000 0 -0.52 356 356
GDI1 -0.23 0.22 -10000 0 -0.41 307 307
TP53 -0.31 0.3 -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 -0.43 357 358
HBP1 0.034 0.005 -10000 0 -10000 0 0
MEF2C -0.26 0.26 -10000 0 -0.44 313 313
MEF2A -0.23 0.23 0.3 1 -0.41 304 305
EIF4EBP1 -0.25 0.25 -10000 0 -0.44 299 299
KRT19 -0.22 0.23 0.33 1 -0.39 298 299
ELK4 -0.21 0.22 0.33 2 -0.4 288 290
ATF6 -0.22 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 -0.42 285 285
p38alpha-beta/MAPKAPK3 -0.25 0.28 -10000 0 -0.45 308 308
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 -0.38 382 382
CRKL -0.32 0.17 -10000 0 -0.4 389 389
HRAS -0.23 0.15 -10000 0 -0.35 217 217
mol:PIP3 -0.27 0.18 -10000 0 -0.39 299 299
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 -0.42 402 402
FOXO3 -0.27 0.16 -10000 0 -0.37 317 317
AKT1 -0.3 0.18 -10000 0 -0.39 362 362
BAD -0.28 0.16 -10000 0 -0.37 320 320
megakaryocyte differentiation -0.32 0.17 -10000 0 -0.41 402 402
GSK3B -0.28 0.16 -10000 0 -0.37 325 325
RAF1 -0.19 0.13 -10000 0 -0.32 53 53
SHC1 0.028 0.014 -10000 0 -10000 0 0
STAT3 -0.33 0.18 -10000 0 -0.42 401 401
STAT1 -0.81 0.43 -10000 0 -1 419 419
HRAS/SPRED1 -0.19 0.14 -10000 0 -0.34 33 33
cell proliferation -0.33 0.17 -10000 0 -0.41 404 404
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
TEC 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.32 0.18 -10000 0 -0.4 399 399
HRAS/SPRED2 -0.19 0.14 -10000 0 -0.32 54 54
LYN/TEC/p62DOK -0.29 0.18 -10000 0 -0.4 334 334
MAPK3 -0.13 0.098 -10000 0 -0.3 9 9
STAP1 -0.32 0.18 -10000 0 -0.41 404 404
GRAP2 0.034 0.019 -10000 0 -10000 0 0
JAK2 -0.68 0.37 -10000 0 -0.85 408 408
STAT1 (dimer) -0.79 0.42 -10000 0 -0.97 419 419
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.28 0.19 -10000 0 -0.4 325 325
actin filament polymerization -0.33 0.17 -10000 0 -0.41 405 405
LYN 0.03 0.015 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.47 0.26 -10000 0 -0.58 410 410
PIK3R1 -0.021 0.17 -10000 0 -0.55 47 47
CBL/CRKL/GRB2 -0.28 0.17 -10000 0 -0.38 344 344
PI3K -0.32 0.2 -10000 0 -0.42 384 384
PTEN 0.026 0.067 -10000 0 -0.54 7 7
SCF/KIT/EPO/EPOR -0.95 0.51 -10000 0 -1.2 403 403
MAPK8 -0.33 0.18 -10000 0 -0.42 404 404
STAT3 (dimer) -0.33 0.17 -10000 0 -0.41 401 401
positive regulation of transcription -0.11 0.083 -10000 0 -0.25 7 7
mol:GDP -0.24 0.16 -10000 0 -0.36 215 215
PIK3C2B -0.3 0.18 -10000 0 -0.42 328 328
CBL/CRKL -0.3 0.16 -10000 0 -0.38 388 388
FER -0.33 0.18 -10000 0 -0.42 401 401
SH2B3 -0.33 0.18 -10000 0 -0.42 404 404
PDPK1 -0.24 0.17 -10000 0 -0.36 282 282
SNAI2 -0.34 0.2 -10000 0 -0.45 374 374
positive regulation of cell proliferation -0.59 0.3 -10000 0 -0.73 409 409
KITLG -0.011 0.07 -10000 0 -0.56 2 2
cell motility -0.59 0.3 -10000 0 -0.73 409 409
PTPN6 0.05 0.021 0.2 4 -10000 0 4
EPOR -0.23 0.19 -10000 0 -1 14 14
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 0.41 399 -10000 0 399
SOS1 0.034 0.004 -10000 0 -10000 0 0
EPO 0.01 0.065 -10000 0 -10000 0 0
VAV1 0.038 0.025 -10000 0 -10000 0 0
GRB10 -0.34 0.18 -10000 0 -0.42 402 402
PTPN11 0.047 0.009 -10000 0 -10000 0 0
SCF/KIT -0.35 0.19 -10000 0 -0.44 405 405
GO:0007205 0.018 0.009 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.28 17 17
CBL 0.031 0.011 -10000 0 -10000 0 0
KIT -1 0.53 -10000 0 -1.3 404 404
MAP2K2 -0.15 0.11 -10000 0 -0.28 16 16
SHC/Grb2/SOS1 -0.27 0.18 -10000 0 -0.4 279 279
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 0.27 3 -0.44 374 377
SHC/GRAP2 0.039 0.026 -10000 0 -10000 0 0
PTPRO -0.33 0.18 -10000 0 -0.42 402 402
SH2B2 -0.33 0.18 -10000 0 -0.42 405 405
DOK1 0.036 0.016 -10000 0 -10000 0 0
MATK -0.33 0.18 -10000 0 -0.42 399 399
CREBBP -0.082 0.075 -10000 0 -0.19 63 63
BCL2 -0.43 0.51 -10000 0 -1.4 110 110
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 -0.34 146 146
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.17 0.29 -10000 0 -0.72 78 78
EDN1 -0.16 0.25 -10000 0 -0.54 153 153
EDN3 -0.39 0.25 -10000 0 -0.54 376 376
EDN2 0.098 0.079 -10000 0 -0.54 1 1
HRAS/GDP -0.25 0.23 -10000 0 -0.46 231 231
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.18 -10000 0 -0.38 126 126
ADCY4 -0.083 0.15 0.34 2 -0.3 145 147
ADCY5 -0.081 0.15 0.35 1 -0.3 141 142
ADCY6 -0.08 0.15 0.34 2 -0.3 142 144
ADCY7 -0.077 0.15 0.34 2 -0.3 138 140
ADCY1 -0.08 0.15 0.35 1 -0.3 142 143
ADCY2 -0.082 0.16 0.34 2 -0.3 144 146
ADCY3 -0.081 0.15 0.35 1 -0.3 144 145
ADCY8 -0.067 0.14 0.35 1 -0.3 107 108
ADCY9 -0.075 0.14 -10000 0 -0.3 125 125
arachidonic acid secretion -0.52 0.34 -10000 0 -0.69 377 377
ETB receptor/Endothelin-1/Gq/GTP -0.21 0.21 -10000 0 -0.36 291 291
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 -0.32 147 147
ETA receptor/Endothelin-1/Gs/GTP -0.088 0.15 -10000 0 -0.31 148 148
mol:GTP -0.007 0.008 -10000 0 -10000 0 0
COL3A1 -0.1 0.17 -10000 0 -0.35 140 140
EDNRB -0.21 0.29 -10000 0 -0.54 224 224
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.099 0.17 -10000 0 -0.35 141 141
CYSLTR1 -0.1 0.18 0.38 2 -0.35 142 144
SLC9A1 -0.068 0.12 -10000 0 -0.23 141 141
mol:GDP -0.27 0.25 -10000 0 -0.48 242 242
SLC9A3 -0.39 0.39 -10000 0 -0.7 264 264
RAF1 -0.35 0.27 -10000 0 -0.51 330 330
JUN -0.25 0.43 -10000 0 -1 115 115
JAK2 -0.1 0.17 -10000 0 -0.35 145 145
mol:IP3 -0.21 0.22 -10000 0 -0.43 198 198
ETA receptor/Endothelin-1 -0.12 0.2 -10000 0 -0.4 149 149
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 -0.4 378 378
FOS -0.68 0.43 -10000 0 -0.96 365 365
Gai/GDP -0.2 0.36 -10000 0 -0.94 84 84
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.26 -10000 0 -0.53 204 204
BCAR1 0.029 0.013 -10000 0 -10000 0 0
PRKCB1 -0.21 0.21 -10000 0 -0.41 209 209
GNAQ -0.009 0.009 -10000 0 -10000 0 0
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
GNAL 0.03 0.045 -10000 0 -0.54 3 3
Gs family/GDP -0.24 0.22 -10000 0 -0.44 230 230
ETA receptor/Endothelin-1/Gq/GTP -0.097 0.15 -10000 0 -0.31 132 132
MAPK14 -0.22 0.22 -10000 0 -0.41 245 245
TRPC6 -0.18 0.31 -10000 0 -0.78 76 76
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 -0.41 271 271
ETB receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.32 244 244
ETB receptor/Endothelin-3 -0.42 0.27 -10000 0 -0.53 418 418
ETB receptor/Endothelin-1 -0.26 0.28 -10000 0 -0.48 297 297
MAPK3 -0.61 0.39 -10000 0 -0.84 367 367
MAPK1 -0.62 0.41 -10000 0 -0.86 369 369
Rac1/GDP -0.25 0.23 -10000 0 -0.46 232 232
cAMP biosynthetic process -0.03 0.15 0.38 6 -0.34 30 36
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 -0.5 266 266
p130Cas/CRK/Src/PYK2 -0.27 0.29 -10000 0 -0.57 199 199
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.25 0.23 -10000 0 -0.46 231 231
COL1A2 -0.22 0.27 0.43 1 -0.48 221 222
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.071 0.077 0.26 3 -0.35 4 7
mol:DAG -0.21 0.22 -10000 0 -0.43 198 198
MAP2K2 -0.47 0.32 -10000 0 -0.64 371 371
MAP2K1 -0.47 0.32 0.36 1 -0.64 371 372
EDNRA 0.006 0.057 -10000 0 -0.44 3 3
positive regulation of muscle contraction -0.091 0.14 -10000 0 -0.31 141 141
Gq family/GDP -0.21 0.22 -10000 0 -0.44 188 188
HRAS/GTP -0.26 0.24 -10000 0 -0.45 257 257
PRKCH -0.21 0.21 -10000 0 -0.44 188 188
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA -0.2 0.21 -10000 0 -0.43 172 172
PRKCB -0.21 0.21 -10000 0 -0.41 210 210
PRKCE -0.21 0.21 -10000 0 -0.44 182 182
PRKCD -0.21 0.21 -10000 0 -0.44 185 185
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 -0.43 187 187
PLA2G4A -0.59 0.4 -10000 0 -0.78 377 377
GNA14 0.026 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 -0.32 147 147
MMP1 0.17 0.15 0.41 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 0.031 0.22 1 -10000 0 1
NFATC2 -0.081 0.23 0.48 4 -0.55 56 60
NFATC3 -0.15 0.17 0.32 1 -0.32 214 215
CD40LG -0.67 0.53 0.79 4 -1 332 336
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 -0.24 0.31 0.75 7 -0.68 76 83
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 -10000 0 -0.4 179 179
TLE4 -0.065 0.2 -10000 0 -0.56 44 44
Jun/NFAT1-c-4/p21SNFT -0.58 0.55 0.72 4 -0.97 310 314
AP-1/NFAT1-c-4 -0.8 0.68 0.92 5 -1.2 329 334
IKZF1 -0.045 0.17 0.46 10 -0.44 34 44
T-helper 2 cell differentiation -0.12 0.28 0.52 1 -0.75 50 51
AP-1/NFAT1 -0.3 0.3 0.53 6 -0.5 310 316
CALM1 -0.036 0.11 -10000 0 -0.31 1 1
EGR2 -0.8 0.76 0.73 3 -1.5 260 263
EGR3 -0.88 0.76 0.76 2 -1.4 320 322
NFAT1/FOXP3 -0.03 0.18 0.45 10 -0.4 48 58
EGR1 -0.43 0.23 -10000 0 -0.54 414 414
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 -0.078 0.24 0.44 2 -0.64 58 60
FOSL1 0.035 0.01 0.18 2 -10000 0 2
NFAT1-c-4/MAF/IRF4 -0.54 0.53 0.67 3 -0.92 304 307
DGKA -0.051 0.16 0.47 1 -0.42 38 39
CREM 0.033 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.76 0.55 -10000 0 -1.1 344 344
CTLA4 -0.023 0.16 0.43 15 -0.39 26 41
NFAT1-c-4 (dimer)/EGR1 -0.78 0.57 -10000 0 -1.1 351 351
NFAT1-c-4 (dimer)/EGR4 -0.56 0.52 0.68 1 -0.93 311 312
FOS -0.35 0.27 0.26 1 -0.54 344 345
IFNG -0.095 0.3 0.55 9 -0.71 59 68
T cell activation -0.38 0.34 0.69 3 -0.72 187 190
MAF -0.008 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 0.82 223 -0.71 2 225
TNF -0.67 0.48 -10000 0 -0.98 342 342
FASLG -0.88 0.78 0.86 3 -1.4 329 332
TBX21 0.029 0.15 0.29 12 -0.54 30 42
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.043 0.036 0.23 10 -10000 0 10
PTPN1 -0.047 0.16 0.42 1 -0.43 36 37
NFAT1-c-4/ICER1 -0.55 0.53 -10000 0 -0.94 305 305
GATA3 0.036 0.16 -10000 0 -0.54 33 33
T-helper 1 cell differentiation -0.094 0.3 0.55 9 -0.69 59 68
IL2RA -0.25 0.31 0.74 6 -0.58 135 141
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.05 0.16 -10000 0 -0.42 41 41
E2F1 0.056 0.049 0.24 2 -10000 0 2
PPARG -0.38 0.26 -10000 0 -0.54 368 368
SLC3A2 -0.049 0.16 -10000 0 -0.4 48 48
IRF4 0.039 0.028 -10000 0 -10000 0 0
PTGS2 -0.77 0.57 0.73 4 -1.1 350 354
CSF2 -0.67 0.53 0.79 4 -1 329 333
JunB/Fra1/NFAT1-c-4 -0.53 0.52 -10000 0 -0.91 303 303
IL4 -0.12 0.29 0.53 1 -0.81 46 47
IL5 -0.68 0.52 0.73 4 -1 331 335
IL2 -0.39 0.35 0.69 3 -0.74 184 187
IL3 -0.087 0.15 -10000 0 -0.91 13 13
RNF128 -0.21 0.33 -10000 0 -0.63 191 191
NFATC1 -0.45 0.41 0.71 2 -0.82 223 225
CDK4 0.28 0.28 0.56 133 -0.7 1 134
PTPRK -0.087 0.24 -10000 0 -0.66 59 59
IL8 -0.66 0.53 0.74 5 -1 327 332
POU2F1 0.033 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 -0.44 365 365
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.19 0.21 -10000 0 -0.36 264 264
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 -0.41 287 287
mol:GDP -0.19 0.21 -10000 0 -0.36 264 264
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 -0.34 261 261
SHC1 0.028 0.014 -10000 0 -10000 0 0
HRAS/GDP -0.18 0.2 -10000 0 -0.35 261 261
FRAP1 -0.2 0.17 -10000 0 -0.35 264 264
EGF/EGFR dimer -0.31 0.26 -10000 0 -0.47 351 351
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 0.015 -10000 0 -10000 0 0
CRKL -0.16 0.2 -10000 0 -0.35 243 243
GRB2/SOS1/SHC 0.052 0.034 -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 -0.35 220 221
BAD -0.16 0.18 0.22 1 -0.34 204 205
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 -0.35 246 246
RAF1 -0.12 0.18 -10000 0 -0.46 76 76
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.22 -10000 0 -0.34 220 220
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 -0.35 199 200
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.099 0.16 0.33 1 -0.39 66 67
PXN 0.034 0.003 -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 -0.33 159 159
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.07 0.18 -10000 0 -0.3 159 159
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 -0.35 245 245
Crk/p130 Cas/Paxillin -0.13 0.21 -10000 0 -0.33 238 238
IGF1R -0.048 0.14 -10000 0 -0.64 21 21
IGF1 -0.27 0.3 -10000 0 -0.57 253 253
IRS2/Crk -0.22 0.26 -10000 0 -0.42 267 267
PI3K -0.15 0.24 -10000 0 -0.37 244 244
apoptosis 0.11 0.15 0.38 73 -0.31 1 74
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
PRKCD -0.18 0.23 -10000 0 -0.4 226 226
RAF1/14-3-3 E -0.097 0.17 0.34 1 -0.4 72 73
BAD/14-3-3 -0.12 0.16 0.32 1 -0.4 73 74
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 -0.41 244 244
BCAR1 0.029 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.095 0.19 -10000 0 -0.33 178 178
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 -0.35 245 245
GRB10 0.03 0.051 -10000 0 -0.54 4 4
PTPN11 -0.17 0.2 -10000 0 -0.35 246 246
IRS1 -0.18 0.22 -10000 0 -0.37 259 259
IRS2 -0.23 0.26 -10000 0 -0.43 278 278
IGF-1R heterotetramer/IGF1 -0.2 0.26 -10000 0 -0.45 247 247
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDPK1 -0.16 0.21 -10000 0 -0.36 225 225
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKD1 -0.22 0.28 -10000 0 -0.52 193 193
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 0.57 0.46 1.1 126 -1 2 128
PLK1 0.23 0.2 0.66 35 -10000 0 35
BIRC5 0.37 0.25 0.67 137 -0.66 3 140
HSPA1B 0.57 0.46 1.1 148 -0.95 3 151
MAP2K1 0.17 0.13 0.34 129 -10000 0 129
BRCA2 0.6 0.49 1.2 145 -1 2 147
FOXM1 0.62 0.61 1.3 162 -1.2 3 165
XRCC1 0.57 0.46 1.1 133 -1 2 135
FOXM1B/p19 0.079 0.3 0.92 9 -1.1 3 12
Cyclin D1/CDK4 0.49 0.46 1 118 -0.87 10 128
CDC2 0.63 0.52 1.2 158 -1 3 161
TGFA 0.45 0.52 1 132 -0.93 20 152
SKP2 0.58 0.47 1.1 131 -1 2 133
CCNE1 0.087 0.064 0.22 76 -10000 0 76
CKS1B 0.62 0.5 1.2 161 -0.94 3 164
RB1 0.28 0.35 0.73 133 -0.73 9 142
FOXM1C/SP1 0.51 0.45 0.99 118 -1 7 125
AURKB 0.2 0.31 0.66 63 -0.84 21 84
CENPF 0.7 0.53 1.2 200 -1 2 202
CDK4 0.093 0.061 0.24 19 -10000 0 19
MYC 0.32 0.44 0.96 88 -0.87 10 98
CHEK2 0.17 0.13 0.36 104 -10000 0 104
ONECUT1 0.5 0.49 1 147 -0.9 6 153
CDKN2A -0.017 0.078 -10000 0 -0.22 21 21
LAMA4 0.57 0.48 1.1 134 -1.1 4 138
FOXM1B/HNF6 0.5 0.5 1.1 128 -1 7 135
FOS -0.12 0.65 1.1 51 -0.99 82 133
SP1 0.031 0.033 -10000 0 -0.21 5 5
CDC25B 0.58 0.47 1.1 142 -0.94 3 145
response to radiation 0.12 0.094 0.24 135 -10000 0 135
CENPB 0.57 0.46 1.1 138 -0.94 3 141
CENPA 0.64 0.51 1.2 165 -1 2 167
NEK2 0.71 0.52 1.2 190 -1.2 1 191
HIST1H2BA 0.57 0.46 1.1 134 -1 2 136
CCNA2 0.11 0.077 0.23 101 -10000 0 101
EP300 0.032 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.61 0.52 1.2 138 -1.1 3 141
CCNB2 0.63 0.51 1.2 153 -1 2 155
CCNB1 0.64 0.54 1.3 156 -1 3 159
ETV5 0.54 0.52 1.1 135 -1.1 12 147
ESR1 0.38 0.61 1.1 120 -0.95 17 137
CCND1 0.51 0.51 1.1 152 -0.9 10 162
GSK3A 0.15 0.1 0.31 80 -10000 0 80
Cyclin A-E1/CDK1-2 0.21 0.13 0.37 152 -10000 0 152
CDK2 0.071 0.036 0.23 9 -10000 0 9
G2/M transition of mitotic cell cycle 0.14 0.12 0.27 179 -10000 0 179
FOXM1B/Cbp/p300 0.31 0.38 0.86 28 -1 3 31
GAS1 0.28 0.71 1.1 116 -1 63 179
MMP2 0.56 0.48 1.1 129 -1.2 6 135
RB1/FOXM1C 0.46 0.46 0.98 140 -0.93 8 148
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
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 -0.26 246 246
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 0.017 -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 -0.47 351 351
ARRB2 0.015 0.029 -10000 0 -0.33 3 3
mol:GTP 0.012 0.028 0.12 24 -10000 0 24
ARRB1 0.03 0.028 -10000 0 -0.54 1 1
FBXO8 0.033 0.007 -10000 0 -10000 0 0
TSHR 0.03 0.045 -10000 0 -0.54 3 3
EGF -0.15 0.27 -10000 0 -0.54 163 163
somatostatin receptor activity 0 0 -10000 0 -0.001 243 243
ARAP2 0 0 -10000 0 0 259 259
mol:GDP -0.14 0.14 -10000 0 -0.27 214 214
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 255 255
ITGA2B 0.034 0.012 -10000 0 -10000 0 0
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.059 -10000 0 -0.32 6 6
ADAP1 0 0 -10000 0 0 158 158
KIF13B 0.027 0.029 -10000 0 -0.54 1 1
HGF/MET 0.006 0.13 -10000 0 -0.4 50 50
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.14 0.12 -10000 0 -0.25 244 244
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.26 0.24 -10000 0 -0.41 348 348
ADRB2 -0.26 0.29 -10000 0 -0.54 263 263
receptor agonist activity 0 0 -10000 0 0 225 225
actin filament binding 0 0 -10000 0 0 264 264
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 -0.001 194 194
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 165 165
ARF6/GDP -0.03 0.085 0.27 1 -0.27 28 29
ARF6/GDP/GULP/ACAP1 -0.16 0.18 -10000 0 -0.34 209 209
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.031 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 0 3 3
ACAP2 0 0 -10000 0 0 254 254
LHCGR/beta Arrestin2 0.021 0.048 -10000 0 -0.47 3 3
EFNA1 0.028 0.016 -10000 0 -10000 0 0
HGF 0.035 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 224 224
CYTH2 -0.002 0.002 -10000 0 -0.004 262 262
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 157 157
endosomal lumen acidification 0 0 0.001 5 0 163 168
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 -0.007 160 160
mol:Phosphatidic acid 0 0 -10000 0 0 254 254
PIP3-E 0 0 -10000 0 0 348 348
MET -0.022 0.17 -10000 0 -0.54 50 50
GNA14 0.043 0.068 -10000 0 -0.54 4 4
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 -0.001 209 209
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 -0.54 207 207
desensitization of G-protein coupled receptor protein signaling pathway 0.021 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 0.019 -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 -0.046 0.13 -10000 0 -0.3 91 91
GNAO1 0.029 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 -0.12 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 -0.007 363 363
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 -0.39 96 96
cell proliferation -0.3 0.21 -10000 0 -0.43 325 325
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 0.038 -10000 0 -0.075 231 231
MAPK3 -0.21 0.16 -10000 0 -0.37 164 164
MAPK1 -0.16 0.16 -10000 0 -0.59 35 35
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.003 0.002 -10000 0 -0.004 337 337
cAMP biosynthetic process 0.018 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 -0.004 337 337
HRAS/GTP -0.059 0.12 -10000 0 -0.33 64 64
actin cytoskeleton reorganization 0.015 0.095 -10000 0 -0.28 44 44
SRC 0.031 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.004 337 337
PI3K 0.007 0.11 -10000 0 -0.31 51 51
apoptosis 0.3 0.22 0.43 358 -10000 0 358
T-DHT/AR/PELP1 -0.014 0.13 -10000 0 -0.35 66 66
HRAS/GDP -0.069 0.17 -10000 0 -0.45 68 68
CREB1 -0.32 0.23 -10000 0 -0.46 358 358
RAC1-CDC42/GTP 0.025 0.1 -10000 0 -0.29 44 44
AR -0.042 0.2 -10000 0 -0.55 66 66
GNB1 0.034 0.012 -10000 0 -10000 0 0
RAF1 -0.086 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 -0.004 0.13 -10000 0 -0.33 65 65
MAP2K2 -0.12 0.11 -10000 0 -0.36 61 61
T-DHT/AR/PELP1/Src/PI3K -0.046 0.13 -10000 0 -0.3 91 91
GNAZ 0.025 0.062 -10000 0 -0.54 6 6
SHBG 0.03 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.11 0.19 -10000 0 -0.48 76 76
mol:T-DHT -0.001 0.002 -10000 0 -0.004 76 76
RAC1 0.034 0.005 -10000 0 -10000 0 0
GNRH1 -0.001 0.056 -10000 0 -0.4 10 10
Gi family/GTP -0.1 0.14 -10000 0 -0.26 187 187
CDC42 0.033 0.008 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
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 -0.82 32 33
SUMO2 0.001 0.025 -10000 0 -10000 0 0
STAT1 (dimer) 0.072 0.069 0.29 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 0.35 31 -0.36 4 35
PRL -0.061 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.53 171 -10000 0 171
RELA -0.095 0.12 0.28 3 -0.26 31 34
FGG 0.23 0.23 0.46 206 -10000 0 206
GR beta/TIF2 0.11 0.14 0.31 82 -0.36 3 85
IFNG -0.39 0.34 0.47 4 -0.67 249 253
apoptosis -0.25 0.18 -10000 0 -0.57 29 29
CREB1 0.058 0.042 -10000 0 -10000 0 0
histone acetylation 0.036 0.14 0.4 37 -0.32 9 46
BGLAP -0.092 0.14 -10000 0 -0.53 4 4
GR/PKAc 0.15 0.14 0.35 44 -0.31 3 47
NF kappa B1 p50/RelA -0.16 0.2 0.48 3 -0.33 159 162
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.22 175 -10000 0 175
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 -10000 0 -10000 0 0
GSK3B 0.001 0.027 -10000 0 -10000 0 0
NR1I3 -0.19 0.17 -10000 0 -0.62 3 3
CSN2 0.19 0.19 0.38 182 -10000 0 182
BRG1/BAF155/BAF170/BAF60A 0.084 0.027 -10000 0 -10000 0 0
NFATC1 0.037 0.038 -10000 0 -0.54 2 2
POU2F1 0.033 0.015 -10000 0 -10000 0 0
CDKN1A 0.021 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 -0.65 0.33 -10000 0 -0.8 426 426
JUN -0.21 0.24 0.38 2 -0.48 172 174
IL4 -0.12 0.15 -10000 0 -0.5 11 11
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 -0.5 327 327
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.14 0.36 27 -0.4 2 29
cortisol/GR alpha (monomer) 0.29 0.31 0.59 214 -10000 0 214
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 -0.57 361 361
AP-1/NFAT1-c-4 -0.58 0.41 -10000 0 -0.82 346 346
AFP -0.18 0.2 -10000 0 -0.64 13 13
SUV420H1 0.032 0.01 -10000 0 -10000 0 0
IRF1 0.21 0.18 0.48 67 -10000 0 67
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 0.15 0.3 288 -0.29 1 289
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 -0.83 346 346
MAPK14 0.011 0.023 -10000 0 -10000 0 0
MAPK10 -0.011 0.082 -10000 0 -0.55 10 10
MAPK11 0 0.026 -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 0.073 0.069 0.29 25 -10000 0 25
CGA -0.084 0.16 -10000 0 -0.54 5 5
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.19 0.36 133 -10000 0 133
MAPK3 0 0.024 -10000 0 -10000 0 0
MAPK1 0.01 0.023 -10000 0 -10000 0 0
ICAM1 -0.26 0.25 0.51 4 -0.52 160 164
NFKB1 -0.095 0.11 0.28 3 -0.25 30 33
MAPK8 -0.15 0.19 0.57 1 -0.36 155 156
MAPK9 0.01 0.024 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.19 -10000 0 -0.59 33 33
BAX 0.027 0.077 -10000 0 -10000 0 0
POMC -0.14 0.19 -10000 0 -1.2 3 3
EP300 0.18 0.14 0.29 274 -10000 0 274
cortisol/GR alpha (dimer)/p53 0.23 0.26 0.52 181 -10000 0 181
proteasomal ubiquitin-dependent protein catabolic process 0.091 0.11 0.33 52 -10000 0 52
SGK1 0.23 0.17 0.36 299 -0.43 1 300
IL13 -0.29 0.25 0.5 1 -0.62 98 99
IL6 -0.75 0.48 0.62 1 -1 376 377
PRKACG 0.033 0.026 -10000 0 -0.54 1 1
IL5 -0.24 0.21 -10000 0 -0.71 20 20
IL2 -0.42 0.32 -10000 0 -0.71 237 237
CDK5 0.032 0.024 -10000 0 -10000 0 0
PRKACB 0.035 0.083 -10000 0 -0.54 8 8
HSP90AA1 0.034 0.006 -10000 0 -10000 0 0
IL8 -0.24 0.26 0.5 5 -0.52 153 158
CDK5R1/CDK5 0.037 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.096 0.18 0.43 3 -0.38 33 36
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 0.34 160 -10000 0 160
NF kappa B1 p50/RelA/Cbp -0.004 0.2 0.45 36 -0.34 6 42
JUN (dimer) -0.21 0.24 0.38 2 -0.48 171 173
YWHAH 0.033 0.014 -10000 0 -10000 0 0
VIPR1 -0.11 0.16 -10000 0 -0.54 26 26
NR3C1 0.19 0.2 0.4 167 -0.45 5 172
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 29 29
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 0.52 4 -0.7 129 133
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.16 0.35 157 -10000 0 157
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.51 208 -10000 0 208
mol:cortisol 0.18 0.17 0.33 232 -10000 0 232
MMP1 -0.023 0.35 -10000 0 -0.94 53 53
S1P1 pathway

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
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 -0.045 0.14 0.3 1 -0.82 11 12
S1P1/S1P/Gi -0.29 0.29 0.33 5 -0.5 301 306
GNAO1 0.003 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.25 0.26 0.41 3 -0.45 290 293
PLCG1 -0.27 0.27 0.33 6 -0.47 294 300
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.03 0.007 -10000 0 -10000 0 0
GNAI2 0.004 0.03 -10000 0 -10000 0 0
GNAI3 0.005 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 -0.066 0.13 0.29 7 -0.66 11 18
negative regulation of cAMP metabolic process -0.28 0.28 0.33 5 -0.48 305 310
MAPK3 -0.37 0.35 0.36 7 -0.64 309 316
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 -0.056 0.12 0.34 4 -0.57 11 15
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.065 0.1 -10000 0 -0.54 11 11
receptor internalization -0.064 0.12 0.24 5 -0.6 11 16
PTGS2 -0.62 0.53 0.43 4 -1 314 318
Rac1/GTP -0.064 0.1 -10000 0 -0.54 11 11
RHOA 0.033 0.008 -10000 0 -10000 0 0
VEGFA 0.046 0.049 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.28 0.28 0.33 5 -0.48 305 310
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.002 0.067 -10000 0 -0.56 6 6
MAPK1 -0.4 0.38 0.37 5 -0.68 314 319
S1P1/S1P/PDGFB-D/PDGFRB -0.08 0.14 0.34 8 -0.62 11 19
ABCC1 0.032 0.023 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.034 0.006 -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 -0.3 211 212
FYN 0.03 0.037 -10000 0 -0.54 2 2
p210 bcr-abl/PTP1B -0.19 0.16 0.25 1 -0.32 247 248
EGFR -0.29 0.28 -10000 0 -0.56 269 269
EGF/EGFR -0.36 0.26 -10000 0 -0.5 356 356
CSF1 0.034 0.008 0.18 1 -10000 0 1
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 -0.32 193 194
Insulin Receptor/Insulin -0.11 0.13 -10000 0 -0.39 33 33
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 -0.32 212 213
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 -0.5 363 363
TXN 0.028 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.19 0.18 -10000 0 -0.41 130 130
cell migration 0.19 0.16 0.32 247 -0.25 1 248
STAT3 0.032 0.007 -10000 0 -10000 0 0
PRLR 0.075 0.064 -10000 0 -10000 0 0
ITGA2B 0.032 0.011 -10000 0 -10000 0 0
CSF1R 0.034 0.006 -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 -0.17 0.16 -10000 0 -0.31 221 221
Crk/p130 Cas -0.17 0.16 -10000 0 -0.31 209 209
DOK1 -0.15 0.14 0.27 1 -0.37 77 78
JAK2 -0.081 0.15 -10000 0 -0.53 32 32
Jak2/Leptin Receptor/Leptin -0.25 0.2 -10000 0 -0.45 203 203
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
PTPN1 -0.19 0.16 0.25 1 -0.32 251 252
LYN 0.03 0.015 -10000 0 -10000 0 0
CDH2 0.058 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 -0.14 0.18 0.65 1 -0.44 83 84
CAPN1 0.032 0.014 0.18 4 -10000 0 4
CSK 0.034 0.011 -10000 0 -10000 0 0
PI3K -0.12 0.16 -10000 0 -0.42 59 59
mol:H2O2 -0.005 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.22 0.19 -10000 0 -0.41 191 191
negative regulation of transcription -0.08 0.14 -10000 0 -0.52 32 32
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 0.018 -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 0.008 -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 -0.005 0.15 0.57 2 -0.4 39 41
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 -0.32 162 162
Ras protein signal transduction 0.091 0.18 0.67 39 -10000 0 39
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
INS 0.033 0.007 -10000 0 -10000 0 0
LEP -0.24 0.29 -10000 0 -0.55 237 237
STAT5B -0.14 0.16 0.26 1 -0.36 100 101
STAT5A -0.14 0.16 0.26 1 -0.36 101 102
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.18 0.16 -10000 0 -0.32 216 216
CSN2 0.078 0.062 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
LAT -0.035 0.077 -10000 0 -0.64 3 3
YBX1 0.044 0.028 -10000 0 -10000 0 0
LCK 0.048 0.045 -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
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 0.058 0.26 9 -0.34 2 11
NFATC2 0.009 0.055 0.26 9 -0.34 1 10
NFATC3 0.012 0.052 0.26 9 -10000 0 9
CD40LG -0.22 0.29 0.69 10 -0.51 187 197
PTGS2 -0.32 0.36 0.58 15 -0.62 264 279
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.032 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.032 -10000 0 -10000 0 0
CALM1 0.033 0.018 -10000 0 -10000 0 0
JUN -0.066 0.22 0.19 1 -0.54 89 90
mol:Ca2+ -0.003 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.012 0.12 2 -10000 0 2
FOSL1 0.035 0.01 0.18 2 -10000 0 2
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 -0.54 344 344
IFNG -0.2 0.31 0.64 18 -0.51 185 203
AP-1/NFAT1-c-4 -0.25 0.34 0.71 11 -0.59 193 204
FASLG -0.19 0.29 0.67 15 -0.49 178 193
NFAT1-c-4/ICER1 0.015 0.098 0.41 9 -0.34 1 10
IL2RA -0.21 0.3 0.63 16 -0.51 184 200
FKBP12/FK506 0.025 0.008 0.13 2 -10000 0 2
CSF2 -0.22 0.3 0.7 11 -0.51 188 199
JunB/Fra1/NFAT1-c-4 0.039 0.11 0.41 9 -0.3 5 14
IL4 -0.22 0.29 0.58 15 -0.51 188 203
IL2 -0.009 0.14 -10000 0 -0.97 11 11
IL3 -0.008 0.13 -10000 0 -0.74 13 13
FKBP1A 0.034 0.012 0.18 2 -10000 0 2
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 0.005 0.43 0.81 1 -0.71 82 83
HDAC7 0.007 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.002 0.37 0.79 8 -0.7 50 58
SMAD4 0.033 0.027 -10000 0 -0.54 1 1
ID2 0.002 0.43 -10000 0 -0.72 79 79
AP1 -0.33 0.27 -10000 0 -0.48 363 363
ABCG2 -0.014 0.44 -10000 0 -0.73 85 85
HIF1A 0.023 0.13 0.32 4 -0.33 11 15
TFF3 -0.049 0.44 -10000 0 -0.73 93 93
GATA2 0.021 0.049 -10000 0 -10000 0 0
AKT1 0.02 0.13 0.33 5 -0.19 25 30
response to hypoxia -0.004 0.11 0.24 18 -0.16 73 91
MCL1 -0.029 0.39 -10000 0 -0.72 74 74
NDRG1 -0.017 0.4 0.89 1 -0.72 73 74
SERPINE1 0.013 0.44 0.84 9 -0.72 78 87
FECH -0.002 0.42 -10000 0 -0.71 81 81
FURIN 0.006 0.43 -10000 0 -0.72 80 80
NCOA2 0.035 0.024 -10000 0 -10000 0 0
EP300 0.033 0.18 0.45 17 -0.29 36 53
HMOX1 0.009 0.44 0.83 7 -0.7 84 91
BHLHE40 -0.052 0.4 0.72 5 -0.72 78 83
BHLHE41 -0.052 0.4 0.72 5 -0.72 78 83
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.042 0.16 -10000 0 -0.44 2 2
ENG 0.045 0.14 0.43 3 -0.41 2 5
JUN -0.075 0.22 -10000 0 -0.55 89 89
RORA -0.005 0.43 -10000 0 -0.72 86 86
ABCB1 -0.29 0.47 -10000 0 -0.94 163 163
TFRC 0.007 0.43 0.86 6 -0.72 79 85
CXCR4 0.011 0.43 0.81 4 -0.71 80 84
TF -0.006 0.44 -10000 0 -0.74 82 82
CITED2 -0.005 0.43 -10000 0 -0.72 82 82
HIF1A/ARNT -0.07 0.44 0.9 4 -0.84 68 72
LDHA -0.011 0.13 -10000 0 -0.74 13 13
ETS1 -0.001 0.43 0.78 1 -0.72 81 82
PGK1 0.007 0.43 0.83 4 -0.71 83 87
NOS2 -0.052 0.4 0.72 5 -0.72 78 83
ITGB2 0.008 0.43 0.82 8 -0.73 76 84
ALDOA 0.004 0.42 -10000 0 -0.73 75 75
Cbp/p300/CITED2 -0.013 0.43 0.8 3 -0.78 67 70
FOS -0.36 0.27 -10000 0 -0.55 344 344
HK2 0.004 0.43 -10000 0 -0.71 81 81
SP1 -0.018 0.094 -10000 0 -0.22 45 45
GCK 0.065 0.22 0.68 3 -0.52 2 5
HK1 0.005 0.43 -10000 0 -0.73 77 77
NPM1 0.001 0.43 0.76 1 -0.7 85 86
EGLN1 -0.024 0.4 -10000 0 -0.72 77 77
CREB1 0.04 0.01 -10000 0 -10000 0 0
PGM1 0.001 0.43 -10000 0 -0.72 80 80
SMAD3 0.034 0.01 -10000 0 -10000 0 0
EDN1 -0.4 0.6 0.62 1 -1.2 163 164
IGFBP1 0.003 0.43 -10000 0 -0.73 78 78
VEGFA 0.069 0.37 0.8 21 -0.61 44 65
HIF1A/JAB1 0.04 0.1 0.31 6 -0.41 4 10
CP -0.061 0.51 0.84 7 -0.78 122 129
CXCL12 -0.086 0.48 -10000 0 -0.8 116 116
COPS5 0.033 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4 0.048 0.028 -10000 0 -0.4 1 1
BNIP3 0 0.43 0.86 1 -0.72 80 81
EGLN3 0.021 0.44 0.84 12 -0.72 79 91
CA9 0.015 0.44 0.84 8 -0.71 82 90
TERT -0.011 0.42 -10000 0 -0.72 79 79
ENO1 0.003 0.43 -10000 0 -0.73 76 76
PFKL 0.002 0.43 -10000 0 -0.71 81 81
NCOA1 0.035 0.027 -10000 0 -0.54 1 1
ADM -0.1 0.5 -10000 0 -0.77 135 135
ARNT 0.02 0.098 -10000 0 -10000 0 0
HNF4A 0.036 0.009 -10000 0 -10000 0 0
ADFP -0.052 0.4 0.72 5 -0.72 78 83
SLC2A1 0.068 0.36 0.81 15 -0.59 50 65
LEP -0.14 0.48 -10000 0 -0.79 133 133
HIF1A/ARNT/Cbp/p300 -0.02 0.36 0.79 6 -0.7 53 59
EPO 0.071 0.32 0.79 13 -0.65 19 32
CREBBP 0.04 0.16 0.44 18 -0.26 18 36
HIF1A/ARNT/Cbp/p300/HDAC7 -0.013 0.35 0.78 7 -0.68 50 57
PFKFB3 -0.005 0.42 -10000 0 -0.7 84 84
NT5E -0.004 0.44 -10000 0 -0.73 83 83
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 -0.054 0.14 -10000 0 -0.41 63 63
positive regulation of JUN kinase activity 0.015 0.12 -10000 0 -0.32 45 45
CRKL 0.033 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.055 0.14 -10000 0 -0.41 65 65
AP1 -0.7 0.45 -10000 0 -0.97 366 366
mol:IP3 -0.086 0.14 -10000 0 -0.45 57 57
PLCG1 -0.086 0.14 -10000 0 -0.45 57 57
PDGF/PDGFRA/alphaV Integrin -0.055 0.14 -10000 0 -0.41 64 64
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 0.031 0.037 -10000 0 -0.54 2 2
CAV1 -0.38 0.26 -10000 0 -0.54 365 365
SHC/Grb2/SOS1 0.016 0.12 -10000 0 -0.33 45 45
PDGF/PDGFRA/Shf -0.053 0.14 -10000 0 -0.41 63 63
FOS -0.69 0.44 -10000 0 -0.95 366 366
JUN -0.13 0.16 -10000 0 -0.46 86 86
oligodendrocyte development -0.055 0.14 -10000 0 -0.41 64 64
GRB2 0.034 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:DAG -0.086 0.14 -10000 0 -0.45 57 57
PDGF/PDGFRA -0.09 0.18 -10000 0 -0.58 61 61
actin cytoskeleton reorganization -0.052 0.14 -10000 0 -0.4 64 64
SRF 0.031 0.014 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
PI3K -0.028 0.18 -10000 0 -0.41 85 85
PDGF/PDGFRA/Crk/C3G 0.002 0.14 -10000 0 -0.36 61 61
JAK1 -0.065 0.13 -10000 0 -0.4 63 63
ELK1/SRF -0.066 0.12 0.33 2 -0.36 56 58
SHB 0.036 0.018 -10000 0 -10000 0 0
SHF 0.034 0.013 -10000 0 -10000 0 0
CSNK2A1 0.063 0.026 -10000 0 -10000 0 0
GO:0007205 -0.093 0.14 -10000 0 -0.46 62 62
SOS1 0.034 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.015 0.12 -10000 0 -0.32 45 45
PDGF/PDGFRA/SHB -0.052 0.14 -10000 0 -0.4 64 64
PDGF/PDGFRA/Caveolin-1 -0.34 0.24 -10000 0 -0.46 375 375
ITGAV 0.033 0.028 -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 -0.054 0.14 -10000 0 -0.41 64 64
JAK-STAT cascade -0.065 0.13 -10000 0 -0.4 63 63
cell proliferation -0.053 0.14 -10000 0 -0.4 63 63
Ephrin B reverse 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
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EPHB2 0.042 0.037 -10000 0 -10000 0 0
EFNB1 0.015 0.028 -10000 0 -0.4 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.049 0.18 -10000 0 -0.28 180 180
Ephrin B2/EPHB1-2 -0.076 0.19 -10000 0 -0.31 191 191
neuron projection morphogenesis -0.061 0.16 -10000 0 -0.27 180 180
Ephrin B1/EPHB1-2/Tiam1 -0.06 0.18 -10000 0 -0.3 186 186
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.058 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 -0.3 186 186
PI3K -0.045 0.22 -10000 0 -0.48 92 92
mol:GDP -0.06 0.18 -10000 0 -0.29 186 186
ITGA2B 0.034 0.012 -10000 0 -10000 0 0
endothelial cell proliferation 0.038 0.045 -10000 0 -0.31 7 7
FYN -0.072 0.26 -10000 0 -0.8 56 56
MAP3K7 -0.059 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 -0.047 0.2 -10000 0 -0.56 56 56
LYN -0.066 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 -0.062 0.21 -10000 0 -0.65 56 56
SRC -0.065 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 -0.54 192 192
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
RAC1 0.034 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.31 7 7
alphaIIb/beta3 Integrin 0.05 0.019 -10000 0 -10000 0 0
BLK -0.078 0.26 -10000 0 -0.8 56 56
HCK -0.065 0.25 -10000 0 -0.79 56 56
regulation of stress fiber formation 0.061 0.18 0.29 188 -10000 0 188
MAPK8 -0.056 0.18 -10000 0 -0.55 56 56
Ephrin B1/EPHB1-2/RGS3 -0.061 0.18 -10000 0 -0.3 189 189
endothelial cell migration -0.05 0.17 0.27 2 -0.51 58 60
NCK2 0.035 0.007 -10000 0 -10000 0 0
PTPN13 -0.025 0.19 -10000 0 -0.65 45 45
regulation of focal adhesion formation 0.061 0.18 0.29 188 -10000 0 188
chemotaxis 0.061 0.18 0.29 189 -10000 0 189
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
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.11 0.08 -9999 0 -0.3 3 3
SMAD6-7/SMURF1 0.064 0.021 -9999 0 -10000 0 0
NOG 0.031 0.031 -9999 0 -0.54 1 1
SMAD9 -0.086 0.24 -9999 0 -0.69 60 60
SMAD4 0.032 0.027 -9999 0 -0.54 1 1
SMAD5 -0.1 0.19 -9999 0 -0.44 79 79
BMP7/USAG1 -0.24 0.2 -9999 0 -0.39 310 310
SMAD5/SKI -0.093 0.19 -9999 0 -0.44 74 74
SMAD1 0.004 0.094 -9999 0 -0.48 10 10
BMP2 -0.23 0.29 -9999 0 -0.54 230 230
SMAD1/SMAD1/SMAD4 0.029 0.091 -9999 0 -0.45 7 7
BMPR1A 0.031 0.044 -9999 0 -0.54 3 3
BMPR1B 0.088 0.071 -9999 0 -10000 0 0
BMPR1A-1B/BAMBI 0.081 0.13 -9999 0 -0.3 38 38
AHSG 0.033 0.007 -9999 0 -10000 0 0
CER1 0.033 0.011 -9999 0 -10000 0 0
BMP2-4/CER1 -0.17 0.23 -9999 0 -0.38 261 261
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.18 -9999 0 -0.39 96 96
BMP2-4 (homodimer) -0.21 0.25 -9999 0 -0.43 277 277
RGMB 0.033 0.007 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.019 0.19 -9999 0 -0.28 167 167
RGMA -0.053 0.2 -9999 0 -0.54 76 76
SMURF1 0.034 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.18 -9999 0 -0.4 111 111
BMP2-4/USAG1 -0.4 0.27 -9999 0 -0.51 408 408
SMAD6/SMURF1/SMAD5 -0.095 0.19 -9999 0 -0.44 76 76
SOSTDC1 -0.37 0.26 -9999 0 -0.54 359 359
BMP7/BMPR2/BMPR1A-1B 0.11 0.073 -9999 0 -0.32 3 3
SKI 0.033 0.007 -9999 0 -10000 0 0
BMP6 (homodimer) -0.15 0.27 -9999 0 -0.54 167 167
HFE2 0.031 0.038 -9999 0 -0.54 2 2
ZFYVE16 0.033 0.007 -9999 0 -10000 0 0
MAP3K7 0.032 0.009 -9999 0 -10000 0 0
BMP2-4/CHRD -0.17 0.23 -9999 0 -0.38 261 261
SMAD5/SMAD5/SMAD4 -0.096 0.19 -9999 0 -0.45 72 72
MAPK1 0.032 0.009 -9999 0 -10000 0 0
TAK1/TAB family -0.09 0.17 -9999 0 -0.36 100 100
BMP7 (homodimer) 0.043 0.043 -9999 0 -10000 0 0
NUP214 0.034 0.005 -9999 0 -10000 0 0
BMP6/FETUA -0.097 0.21 -9999 0 -0.39 170 170
SMAD1/SKI 0.015 0.099 -9999 0 -0.45 10 10
SMAD6 0.033 0.007 -9999 0 -10000 0 0
CTDSP2 0.034 0.006 -9999 0 -10000 0 0
BMP2-4/FETUA -0.17 0.23 -9999 0 -0.38 261 261
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.048 0.046 -9999 0 -10000 0 0
BMPR2 (homodimer) 0.034 0.005 -9999 0 -10000 0 0
GADD34/PP1CA 0.06 0.038 -9999 0 -0.34 2 2
BMPR1A-1B (homodimer) 0.084 0.064 -9999 0 -0.4 3 3
CHRDL1 -0.3 0.28 -9999 0 -0.54 301 301
ENDOFIN/SMAD1 0.014 0.1 -9999 0 -0.46 10 10
SMAD6-7/SMURF1/SMAD1 0.047 0.1 -9999 0 -0.5 7 7
SMAD6/SMURF1 0.034 0.005 -9999 0 -10000 0 0
BAMBI 0.017 0.16 -9999 0 -0.54 36 36
SMURF2 0.031 0.013 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.36 0.31 -9999 0 -0.54 355 355
BMP2-4/GREM1 -0.16 0.24 -9999 0 -0.37 266 266
SMAD7 0.033 0.007 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.077 0.23 -9999 0 -0.64 63 63
SMAD1/SMAD6 0.014 0.1 -9999 0 -0.46 10 10
TAK1/SMAD6 0.047 0.015 -9999 0 -10000 0 0
BMP7 0.043 0.043 -9999 0 -10000 0 0
BMP6 -0.15 0.27 -9999 0 -0.54 167 167
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.11 0.19 -9999 0 -0.4 111 111
PPM1A 0.033 0.006 -9999 0 -10000 0 0
SMAD1/SMURF2 0.011 0.097 -9999 0 -0.5 8 8
SMAD7/SMURF1 0.048 0.013 -9999 0 -10000 0 0
CTDSPL 0.031 0.037 -9999 0 -0.54 2 2
PPP1CA 0.034 0.021 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.005 -9999 0 -10000 0 0
PPP1R15A 0.032 0.036 -9999 0 -0.54 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.18 -9999 0 -0.38 113 113
CHRD 0.036 0.021 -9999 0 -10000 0 0
BMPR2 0.034 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.21 -9999 0 -0.45 113 113
BMP4 -0.04 0.2 -9999 0 -0.54 67 67
FST 0.032 0.04 -9999 0 -0.54 2 2
BMP2-4/NOG -0.16 0.22 -9999 0 -0.38 246 246
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.11 0.075 -9999 0 -0.3 3 3
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 -10000 0 -0.35 219 219
MAP3K8 -0.047 0.19 -10000 0 -0.55 65 65
FOS -0.099 0.12 -10000 0 -0.37 27 27
PRKCA -0.006 0.028 -10000 0 -10000 0 0
PTPN7 -0.002 0.044 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
PRKCB -0.013 0.009 -10000 0 -0.018 364 364
NRAS 0.033 0.016 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.038 -10000 0 -10000 0 0
MAPK3 -0.029 0.075 -10000 0 -0.61 3 3
MAP2K1 -0.056 0.089 -10000 0 -0.28 42 42
ELK1 -0.015 0.037 0.18 1 -10000 0 1
BRAF -0.017 0.039 -10000 0 -0.25 7 7
mol:GTP -0.004 0.003 -10000 0 -0.006 365 365
MAPK1 -0.053 0.12 -10000 0 -0.46 29 29
RAF1 -0.017 0.037 -10000 0 -0.25 6 6
KRAS 0.033 0.019 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.009 0.16 -10000 0 -0.3 104 104
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.44 156 156
AKT1 -0.18 0.37 -10000 0 -0.78 135 135
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.38 -10000 0 -0.8 132 132
mol:Ca2+ -0.032 0.12 0.26 3 -0.31 47 50
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
E2/ER alpha (dimer)/Striatin -0.018 0.17 0.23 1 -0.33 108 109
SHC1 0.028 0.014 -10000 0 -10000 0 0
apoptosis 0.17 0.35 0.74 135 -10000 0 135
RhoA/GTP -0.024 0.12 -10000 0 -0.27 81 81
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.14 0.23 0.31 1 -0.45 138 139
regulation of stress fiber formation 0.016 0.12 -10000 0 -0.32 5 5
E2/ERA-ERB (dimer) -0.021 0.17 -10000 0 -0.33 110 110
KRAS 0.035 0.019 -10000 0 -10000 0 0
G13/GTP -0.018 0.15 -10000 0 -0.31 99 99
pseudopodium formation -0.016 0.12 0.32 5 -10000 0 5
E2/ER alpha (dimer)/PELP1 -0.024 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 -0.5 140 140
E2/ER beta (dimer) 0.024 0.005 -10000 0 -10000 0 0
mol:GDP -0.045 0.18 0.23 12 -0.39 105 117
mol:NADP -0.14 0.25 -10000 0 -0.5 140 140
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.035 0.12 0.26 3 -0.32 46 49
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
PLCB1 -0.036 0.13 -10000 0 -0.32 52 52
PLCB2 0.002 0.087 -10000 0 -0.46 8 8
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
mol:L-citrulline -0.14 0.25 -10000 0 -0.5 140 140
RHOA 0.033 0.008 -10000 0 -10000 0 0
Gai/GDP -0.15 0.28 -10000 0 -0.73 80 80
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 -0.058 0.26 -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 -0.03 0.14 -10000 0 -0.58 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.21 0.31 1 -0.45 109 110
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
E2/ER alpha (dimer) -0.044 0.18 -10000 0 -0.39 110 110
STRN 0.034 0.027 -10000 0 -0.54 1 1
GNAL 0.03 0.045 -10000 0 -0.54 3 3
PELP1 0.031 0.011 -10000 0 -10000 0 0
MAPK11 0.016 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 -0.55 59 66
cAMP biosynthetic process -0.02 0.13 -10000 0 -0.28 102 102
SRC -0.14 0.23 0.31 4 -0.55 72 76
PI3K 0.005 0.13 -10000 0 -0.37 51 51
GNB1 0.034 0.012 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.18 -10000 0 -0.37 89 89
SOS1 0.034 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.43 212 212
Gs family/GTP -0.011 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 -0.48 141 141
mol:DAG -0.035 0.12 0.26 3 -0.32 46 49
Gs family/GDP/Gbeta gamma -0.041 0.16 -10000 0 -0.35 90 90
MSN -0.018 0.12 0.33 5 -10000 0 5
Gq family/GTP 0.003 0.093 -10000 0 -0.43 10 10
mol:PI-3-4-5-P3 -0.18 0.36 -10000 0 -0.76 132 132
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 0.48 141 -10000 0 141
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
RhoA/GDP -0.026 0.19 0.24 12 -0.37 105 117
NOS3 -0.15 0.26 -10000 0 -0.53 140 140
GNA11 0.034 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.13 0.27 -10000 0 -0.56 131 131
E2/ER alpha (dimer)/PELP1/Src -0.14 0.24 0.33 1 -0.46 140 141
ruffle organization -0.016 0.12 0.32 5 -10000 0 5
ROCK2 -0.016 0.13 0.42 3 -10000 0 3
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 -0.098 0.22 0.4 7 -0.54 57 64
MMP2 -0.14 0.22 0.3 5 -0.54 62 67
FAS signaling pathway (CD95)

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
SPTAN1 0.02 0.092 0.21 83 -10000 0 83
RFC1 0.019 0.088 0.21 65 -10000 0 65
PRKDC 0.04 0.11 0.24 74 -10000 0 74
RIPK1 0.041 0.009 -10000 0 -10000 0 0
CASP7 -0.041 0.11 -10000 0 -0.75 9 9
FASLG/FAS/FADD/FAF1 -0.024 0.091 0.26 9 -0.31 17 26
MAP2K4 -0.18 0.19 -10000 0 -0.45 89 89
mol:ceramide -0.076 0.12 0.27 1 -0.37 32 33
GSN -0.058 0.17 0.21 66 -0.34 107 173
FASLG/FAS/FADD/FAF1/Caspase 8 -0.033 0.097 0.32 3 -0.33 14 17
FAS -0.047 0.14 -10000 0 -0.56 33 33
BID -0.022 0.022 -10000 0 -10000 0 0
MAP3K1 -0.093 0.14 0.28 1 -0.46 24 25
MAP3K7 0.025 0.01 -10000 0 -10000 0 0
RB1 0.02 0.086 0.21 71 -10000 0 71
CFLAR 0.04 0.026 -10000 0 -0.52 1 1
HGF/MET -0.009 0.16 -10000 0 -0.36 88 88
ARHGDIB 0.022 0.092 0.22 68 -10000 0 68
FADD -0.008 0.028 -10000 0 -10000 0 0
actin filament polymerization 0.058 0.17 0.34 108 -0.21 66 174
NFKB1 -0.1 0.13 -10000 0 -0.67 10 10
MAPK8 -0.32 0.25 -10000 0 -0.46 358 358
DFFA 0.019 0.088 0.21 68 -10000 0 68
DNA fragmentation during apoptosis 0.019 0.089 0.21 81 -10000 0 81
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 0.024 0.098 0.23 77 -10000 0 77
DFFB 0.018 0.089 0.21 80 -10000 0 80
CHUK -0.11 0.12 -10000 0 -0.63 10 10
FASLG 0.001 0.061 -10000 0 -0.55 1 1
FAS/FADD -0.033 0.1 -10000 0 -0.38 33 33
HGF 0.035 0.01 -10000 0 -10000 0 0
LMNA 0.021 0.099 0.42 14 -10000 0 14
CASP6 0.02 0.089 0.21 67 -10000 0 67
CASP10 -0.013 0.03 -10000 0 -10000 0 0
CASP3 0.019 0.1 0.26 66 -0.22 17 83
PTPN13 -0.017 0.16 -10000 0 -0.54 45 45
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 0.075 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.077 0.13 0.27 1 -0.38 32 33
activation of caspase activity by cytochrome c -0.022 0.022 -10000 0 -10000 0 0
PAK2 0.016 0.097 0.23 73 -0.2 5 78
BCL2 -0.068 0.22 -10000 0 -0.54 91 91
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.023 0.3 0.72 4 -0.72 32 36
CRP 0.002 0.32 0.7 9 -0.73 30 39
cell cycle arrest -0.051 0.34 0.66 8 -0.74 54 62
TIMP1 -0.012 0.28 0.66 11 -0.63 30 41
IL6ST 0.038 0.084 -10000 0 -0.54 9 9
Rac1/GDP -0.088 0.22 0.42 7 -0.44 79 86
AP1 -0.16 0.24 0.49 4 -0.55 75 79
GAB2 0.033 0.016 -10000 0 -10000 0 0
TNFSF11 -0.005 0.32 0.7 8 -0.74 26 34
HSP90B1 0.044 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 59 60
AKT1 0.032 0.093 0.34 1 -0.4 8 9
FOXO1 0.006 0.13 0.32 3 -0.42 20 23
MAP2K6 -0.12 0.2 0.36 3 -0.49 70 73
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.055 0.24 0.48 10 -0.48 68 78
MITF -0.11 0.21 0.34 7 -0.43 94 101
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.005 -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 -0.001 0.14 0.36 2 -0.48 21 23
STAT3 -0.071 0.36 0.66 8 -0.81 54 62
STAT1 0.035 0.12 -10000 0 -0.85 7 7
CEBPD -0.079 0.44 0.71 5 -1 72 77
PIK3CA 0.034 0.009 -10000 0 -10000 0 0
PI3K 0.007 0.13 -10000 0 -0.37 51 51
JUN -0.067 0.22 -10000 0 -0.54 89 89
PIAS3/MITF -0.1 0.2 0.38 2 -0.44 77 79
MAPK11 -0.13 0.2 -10000 0 -0.57 52 52
STAT3 (dimer)/FOXO1 -0.086 0.33 0.58 11 -0.67 70 81
GRB2/SOS1/GAB family -0.082 0.18 0.37 2 -0.45 43 45
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.19 0.32 4 -0.42 97 101
GRB2 0.036 0.019 -10000 0 -10000 0 0
JAK2 0.033 0.011 -10000 0 -10000 0 0
LBP 0.01 0.28 0.67 13 -0.65 19 32
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
JAK1 0.038 0.013 -10000 0 -10000 0 0
MYC -0.012 0.38 0.71 12 -0.94 45 57
FGG -0.024 0.3 0.69 4 -0.71 34 38
macrophage differentiation -0.051 0.34 0.66 8 -0.74 54 62
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.19 -10000 0 -0.32 221 221
JUNB -0.03 0.3 0.64 4 -0.74 31 35
FOS -0.35 0.27 -10000 0 -0.54 344 344
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.37 8 -0.44 99 107
STAT1/PIAS1 -0.072 0.23 0.42 10 -0.44 74 84
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.097 -10000 0 -0.4 11 11
STAT3 (dimer) -0.069 0.36 0.66 8 -0.8 54 62
PRKCD -0.032 0.27 0.54 13 -0.54 55 68
IL6R 0.03 0.031 -10000 0 -0.55 1 1
SOCS3 -0.15 0.24 -10000 0 -0.97 24 24
gp130 (dimer)/JAK1/JAK1/LMO4 0.073 0.12 0.3 4 -0.32 30 34
Rac1/GTP -0.077 0.23 0.43 10 -0.46 76 86
HCK 0.037 0.023 -10000 0 -10000 0 0
MAPKKK cascade 0.022 0.16 0.41 1 -0.57 23 24
bone resorption -0.001 0.31 0.68 10 -0.69 27 37
IRF1 -0.022 0.31 0.68 7 -0.71 33 40
mol:GDP -0.1 0.21 0.4 9 -0.44 87 96
SOS1 0.038 0.009 -10000 0 -10000 0 0
VAV1 -0.1 0.22 0.4 9 -0.44 88 97
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.2 -10000 0 -0.6 54 54
PTPN11 0.021 0.093 -10000 0 -0.81 5 5
IL6/IL6RA -0.23 0.2 -10000 0 -0.39 294 294
gp130 (dimer)/TYK2/TYK2/LMO4 0.068 0.11 0.29 1 -0.33 27 28
gp130 (dimer)/JAK2/JAK2/LMO4 0.063 0.11 0.29 1 -0.32 30 31
IL6 -0.37 0.27 0.23 1 -0.54 366 367
PIAS3 0.033 0.008 -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 -0.37 100 103
LMO4 0.029 0.12 0.24 4 -0.54 21 25
STAT3 (dimer)/PIAS3 -0.064 0.33 0.61 7 -0.72 59 66
MCL1 0.071 0.12 0.52 2 -10000 0 2
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.28 0.53 0.98 6 -1.2 63 69
IL23A -0.24 0.48 1.1 7 -1 50 57
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 0.76 2 -1 64 66
positive regulation of T cell mediated cytotoxicity -0.27 0.53 1 10 -1.1 64 74
ITGA3 -0.23 0.47 0.96 6 -1 55 61
IL17F -0.18 0.35 0.68 11 -0.66 69 80
IL12B 0.007 0.083 0.32 6 -10000 0 6
STAT1 (dimer) -0.25 0.5 0.85 8 -1.1 64 72
CD4 -0.24 0.47 0.96 5 -1 54 59
IL23 -0.24 0.46 0.91 7 -1 49 56
IL23R -0.018 0.21 0.75 4 -1.1 10 14
IL1B -0.25 0.49 1 8 -1.1 57 65
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.47 0.92 9 -0.99 54 63
TYK2 0.004 0.06 0.27 3 -10000 0 3
STAT4 0.028 0.069 -10000 0 -0.54 7 7
STAT3 0.033 0.007 -10000 0 -10000 0 0
IL18RAP -0.006 0.16 -10000 0 -0.54 42 42
IL12RB1 0.004 0.06 0.27 3 -10000 0 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.009 0.074 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 0.53 1 10 -1.1 64 74
natural killer cell activation 0.001 0.015 0.08 2 -0.062 6 8
JAK2 0.004 0.077 0.32 4 -10000 0 4
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
NFKB1 0.034 0.009 -10000 0 -10000 0 0
RELA 0.034 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.23 0.44 0.88 8 -0.95 51 59
ALOX12B -0.24 0.46 0.96 5 -1 55 60
CXCL1 -0.64 0.73 1 8 -1.2 295 303
T cell proliferation -0.27 0.53 1 10 -1.1 64 74
NFKBIA 0.033 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.3 0.63 15 -0.53 52 67
PI3K -0.28 0.47 0.76 3 -1 81 84
IFNG 0.022 0.074 0.18 65 -0.12 6 71
STAT3 (dimer) -0.26 0.46 0.75 3 -0.96 77 80
IL18R1 0.04 0.03 -10000 0 -0.54 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.34 0.77 11 -0.69 38 49
IL18/IL18R 0.065 0.14 0.29 24 -0.34 42 66
macrophage activation -0.013 0.029 0.077 20 -0.045 13 33
TNF -0.25 0.48 1.1 6 -1 57 63
STAT3/STAT4 -0.26 0.48 0.77 4 -1 65 69
STAT4 (dimer) -0.27 0.5 0.86 6 -1.1 68 74
IL18 0.048 0.046 0.2 27 -10000 0 27
IL19 -0.2 0.47 0.92 10 -0.99 53 63
STAT5A (dimer) -0.27 0.49 0.86 5 -1.1 66 71
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 54 61
MPO -0.23 0.47 1 5 -0.98 59 64
positive regulation of humoral immune response -0.27 0.53 1 10 -1.1 64 74
IL23/IL23R/JAK2/TYK2 -0.28 0.54 1 10 -1.2 63 73
IL6 -0.79 0.67 0.94 6 -1.2 363 369
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 0.015 0.08 2 -0.062 6 8
CD3E -0.24 0.46 0.92 7 -0.99 60 67
keratinocyte proliferation -0.27 0.53 1 10 -1.1 64 74
NOS2 -0.24 0.46 0.89 8 -0.94 70 78
IL4-mediated signaling events

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
BCL2L1 -0.14 0.62 0.93 3 -1.2 91 94
STAT6 (cleaved dimer) -0.23 0.54 -10000 0 -1.1 105 105
IGHG1 0.027 0.3 0.63 16 -0.66 8 24
IGHG3 -0.15 0.59 0.8 1 -1.1 106 107
AKT1 -0.025 0.35 0.66 1 -0.76 30 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.029 0.29 0.67 1 -0.86 13 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.023 0.37 0.65 2 -0.78 34 36
THY1 -0.14 0.63 1 5 -1.2 91 96
MYB -0.006 0.16 -10000 0 -0.54 40 40
HMGA1 0.037 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.002 0.4 0.74 12 -0.66 51 63
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.002 0.34 0.63 6 -0.82 17 23
SP1 0.057 0.045 -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 -1.1 104 105
SOCS1 -0.06 0.41 0.77 1 -0.72 80 81
SOCS3 -0.015 0.39 -10000 0 -1.2 19 19
FCER2 -0.14 0.52 0.9 3 -0.91 67 70
PARP14 0.042 0.032 -10000 0 -10000 0 0
CCL17 -0.12 0.64 1 10 -1.2 93 103
GRB2 0.034 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.031 0.29 0.59 8 -0.71 13 21
T cell proliferation -0.18 0.62 -10000 0 -1.2 103 103
IL4R/JAK1 -0.15 0.61 -10000 0 -1.2 95 95
EGR2 -0.51 0.86 1 2 -1.3 247 249
JAK2 0.03 0.09 0.27 1 -10000 0 1
JAK3 0.035 0.019 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.036 0.047 -10000 0 -10000 0 0
COL1A2 0.039 0.31 0.69 5 -1.2 9 14
CCL26 -0.14 0.63 1.1 5 -1.1 98 103
IL4R -0.14 0.69 1.2 6 -1.2 93 99
PTPN6 0.016 0.044 0.2 3 -10000 0 3
IL13RA2 -0.15 0.63 1 2 -1.2 99 101
IL13RA1 0.032 0.092 0.27 1 -10000 0 1
IRF4 0.065 0.21 0.68 4 -0.68 7 11
ARG1 0.049 0.27 0.72 4 -1.2 4 8
CBL -0.013 0.37 0.66 5 -0.63 50 55
GTF3A 0.1 0.066 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL13RA1/JAK2 0.051 0.13 0.36 5 -10000 0 5
IRF4/BCL6 0.029 0.21 0.53 1 -0.66 9 10
CD40LG 0.049 0.033 0.31 2 -10000 0 2
MAPK14 -0.013 0.38 0.68 4 -0.7 43 47
mitosis -0.019 0.34 0.65 1 -0.7 30 31
STAT6 -0.15 0.76 1.2 13 -1.3 102 115
SPI1 0.044 0.033 -10000 0 -0.24 1 1
RPS6KB1 -0.002 0.33 0.65 5 -0.71 24 29
STAT6 (dimer) -0.15 0.76 1.2 13 -1.3 102 115
STAT6 (dimer)/PARP14 -0.17 0.65 -10000 0 -1.2 104 104
mast cell activation -0.006 0.027 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.017 0.36 0.64 4 -0.76 36 40
FRAP1 -0.025 0.35 0.66 1 -0.76 30 31
LTA -0.14 0.62 0.96 1 -1.2 89 90
FES 0.031 0.037 -10000 0 -0.54 2 2
T-helper 1 cell differentiation 0.14 0.74 1.3 103 -1.2 13 116
CCL11 -0.1 0.61 0.9 4 -1.1 90 94
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.011 0.34 0.63 3 -0.89 16 19
IL2RG 0.045 0.042 0.22 10 -10000 0 10
IL10 -0.1 0.63 1.1 9 -1.2 82 91
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 117 117
IL4 0.046 0.31 0.79 7 -1 14 21
IL5 -0.14 0.62 1 3 -1.2 89 92
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.059 0.55 0.99 13 -0.88 91 104
COL1A1 0.12 0.4 0.8 28 -1 20 48
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 87 87
IL2R gamma/JAK3 0.063 0.04 -10000 0 -10000 0 0
TFF3 -0.27 0.73 0.93 3 -1.3 134 137
ALOX15 -0.14 0.62 0.96 1 -1.2 91 92
MYBL1 0.048 0.054 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.093 0.54 0.82 6 -0.92 96 102
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 -0.041 0.36 0.62 5 -0.7 43 48
mol:PI-3-4-5-P3 -0.024 0.35 0.66 1 -0.76 30 31
PI3K -0.031 0.37 0.66 1 -0.82 30 31
DOK2 0.025 0.039 -10000 0 -0.54 2 2
ETS1 0.002 0.06 0.19 2 -0.51 1 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.04 0.28 0.57 8 -0.68 11 19
ITGB3 -0.14 0.62 1 2 -1.2 92 94
PIGR -0.39 0.84 1.1 9 -1.3 204 213
IGHE -0.043 0.1 0.2 6 -0.29 17 23
MAPKKK cascade 0.041 0.28 0.57 8 -0.67 11 19
BCL6 -0.026 0.17 -10000 0 -0.54 51 51
OPRM1 -0.14 0.62 0.93 3 -1.2 92 95
RETNLB -0.14 0.62 0.96 1 -1.2 91 92
SELP -0.29 0.82 1 7 -1.4 152 159
AICDA -0.14 0.59 0.94 1 -1.1 96 97
EPHB forward signaling

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
Ephrin A5/EPHB2 0.048 0.033 0.23 2 -0.34 1 3
cell-cell adhesion 0.11 0.12 0.27 177 -10000 0 177
Ephrin B/EPHB2/RasGAP 0.08 0.068 -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 -0.1 0.19 -10000 0 -0.34 194 194
HRAS/GDP -0.083 0.16 -10000 0 -0.38 50 50
Ephrin B/EPHB1/GRB7 -0.056 0.18 -10000 0 -0.31 159 159
Endophilin/SYNJ1 0.018 0.051 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 0.026 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 0.008 0.065 0.32 5 -0.29 5 10
HRAS 0.034 0.013 -10000 0 -10000 0 0
RRAS 0.018 0.049 0.26 1 -0.28 6 7
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.095 0.16 0.36 2 -0.29 190 192
lamellipodium assembly -0.11 0.12 -10000 0 -0.27 177 177
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.063 0.15 -10000 0 -0.29 124 124
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
EPHB2 0.042 0.037 -10000 0 -10000 0 0
EPHB3 0.035 0.016 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 192 192
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
mol:GDP -0.084 0.14 -10000 0 -0.39 48 48
Ephrin B/EPHB2 0.067 0.059 -10000 0 -0.3 7 7
Ephrin B/EPHB3 0.061 0.055 -10000 0 -0.3 7 7
JNK cascade -0.091 0.16 0.42 4 -0.3 183 187
Ephrin B/EPHB1 -0.071 0.18 -10000 0 -0.3 190 190
RAP1/GDP -0.062 0.14 -10000 0 -0.36 43 43
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 -0.077 0.19 -10000 0 -0.32 191 191
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.063 0.17 -10000 0 -0.34 46 46
Rap1/GTP -0.075 0.15 -10000 0 -0.27 159 159
axon guidance 0.047 0.033 0.23 2 -0.34 1 3
MAPK3 -0.047 0.14 0.26 1 -0.38 33 34
MAPK1 -0.054 0.14 -10000 0 -0.38 35 35
Rac1/GDP -0.076 0.14 -10000 0 -0.37 47 47
actin cytoskeleton reorganization -0.078 0.12 -10000 0 -0.31 32 32
CDC42/GDP -0.075 0.14 -10000 0 -0.37 46 46
PI3K 0.032 0.12 -10000 0 -0.31 47 47
EFNA5 0.033 0.029 -10000 0 -0.54 1 1
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.31 7 7
Ephrin B/EPHB2/Intersectin/N-WASP 0.018 0.068 -10000 0 -0.38 3 3
CDC42 0.033 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.077 0.14 -10000 0 -0.46 7 7
PTK2 0.15 0.27 0.67 106 -10000 0 106
MAP4K4 -0.092 0.16 0.42 4 -0.3 183 187
SRC 0.033 0.008 -10000 0 -10000 0 0
KALRN 0.034 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.049 0.022 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.057 0.13 0.34 4 -0.35 13 17
MAP2K1 -0.06 0.14 -10000 0 -0.39 35 35
WASL 0.033 0.026 -10000 0 -0.54 1 1
Ephrin B1/EPHB1-2/NCK1 -0.062 0.2 -10000 0 -0.32 191 191
cell migration -0.066 0.17 0.31 4 -0.43 38 42
NRAS 0.036 0.016 -10000 0 -10000 0 0
SYNJ1 0.018 0.051 0.26 1 -0.28 7 8
PXN 0.034 0.003 -10000 0 -10000 0 0
TF -0.014 0.069 0.25 1 -0.28 22 23
HRAS/GTP -0.062 0.17 -10000 0 -0.28 178 178
Ephrin B1/EPHB1-2 -0.073 0.19 -10000 0 -0.31 191 191
cell adhesion mediated by integrin -0.009 0.049 0.26 7 -0.2 12 19
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.062 0.18 -10000 0 -0.29 181 181
RAC1-CDC42/GTP -0.088 0.14 -10000 0 -0.27 141 141
RASA1 0.034 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.064 0.15 -10000 0 -0.36 44 44
ruffle organization -0.096 0.14 0.44 3 -0.47 8 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
receptor internalization -0.006 0.051 0.25 1 -0.27 7 8
Ephrin B/EPHB2/KALRN 0.082 0.067 -10000 0 -0.3 7 7
ROCK1 0.025 0.039 -10000 0 -0.31 2 2
RAS family/GDP -0.086 0.095 -10000 0 -0.31 30 30
Rac1/GTP -0.089 0.15 -10000 0 -0.28 177 177
Ephrin B/EPHB1/Src/Paxillin -0.088 0.16 -10000 0 -0.41 48 48
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.06 0.035 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.23 0.18 -10000 0 -0.34 368 368
PTK2 -0.047 0.12 0.4 2 -0.47 7 9
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 -0.56 28 28
VEGFA 0.05 0.047 -10000 0 -10000 0 0
ILK -0.087 0.096 -10000 0 -0.47 16 16
ROCK1 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.082 0.088 -10000 0 -0.45 15 15
PTK2B 0.027 0.05 0.31 5 -0.3 1 6
alphaV/beta3 Integrin/JAM-A -0.16 0.17 -10000 0 -0.3 274 274
CBL 0.031 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.064 0.031 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.25 -10000 0 -0.39 252 252
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.038 0.061 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Syndecan-1 0.09 0.053 0.26 3 -0.34 1 4
PI4KA 0.033 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.3 0.25 -10000 0 -0.5 272 272
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 0.26 8 -0.34 4 12
RPS6KB1 -0.28 0.23 0.59 1 -0.51 204 205
TLN1 0.034 0.006 -10000 0 -10000 0 0
MAPK3 -0.36 0.29 -10000 0 -0.56 329 329
GPR124 0.008 0.1 -10000 0 -0.54 17 17
MAPK1 -0.38 0.29 -10000 0 -0.56 343 343
PXN 0.034 0.003 -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 -0.003 0.14 -10000 0 -0.54 33 33
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 0.096 0.26 2 -0.34 23 25
CSF1 0.034 0.008 0.18 1 -10000 0 1
PIK3C2A -0.084 0.091 -10000 0 -0.46 13 13
PI4 Kinase/Pyk2 -0.15 0.13 -10000 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.089 0.045 -10000 0 -0.32 1 1
FAK1/Vinculin -0.033 0.11 0.41 2 -0.38 7 9
alphaV beta3/Integrin/ppsTEM5 0.04 0.081 -10000 0 -0.34 18 18
RHOA 0.033 0.008 -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 -0.4 297 297
alphaV/beta3 Integrin/Lactadherin 0.047 0.091 0.26 1 -0.34 23 24
alphaV/beta3 Integrin/TGFBR2 0.04 0.1 0.26 1 -0.34 32 33
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.069 0.042 -10000 0 -0.32 1 1
HSP90AA1 0.034 0.006 -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 0.069 -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 0.19 -10000 0 -0.54 60 60
FAK1/Paxillin -0.032 0.12 0.38 3 -0.38 7 10
cell migration -0.033 0.1 0.4 2 -0.36 6 8
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PI3K -0.17 0.18 -10000 0 -0.31 269 269
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 0.033 0.027 -10000 0 -0.54 1 1
COL4A3 0.034 0.006 -10000 0 -10000 0 0
angiogenesis -0.37 0.28 -10000 0 -0.56 322 322
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 32 33
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 0.006 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.058 0.041 -10000 0 -0.34 1 1
PDE6G/GNAT1/GTP 0.042 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 -0.091 0.17 -10000 0 -0.29 206 206
mol:Na + -0.09 0.17 -10000 0 -0.28 218 218
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.05 0.099 -10000 0 -0.32 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.084 0.19 -10000 0 -0.29 218 218
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 -0.51 7 13
Na + (4 Units) -0.091 0.16 -10000 0 -0.28 192 192
RGS9 0.003 0.13 -10000 0 -0.54 26 26
GNB1/GNGT1 0.071 0.046 0.26 1 -10000 0 1
GNAT1/GDP 0.058 0.091 -10000 0 -0.27 27 27
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) 0.025 0.052 -10000 0 -0.3 11 11
mol:11-cis-retinal -0.43 0.23 -10000 0 -0.54 412 412
mol:cGMP 0.055 0.073 -10000 0 -0.34 13 13
GNB1 0.034 0.012 -10000 0 -10000 0 0
Rhodopsin -0.31 0.18 -10000 0 -0.4 409 409
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 0.066 -10000 0 -0.54 2 2
Metarhodopsin II/Transducin 0.036 0.038 -10000 0 -0.18 6 6
GCAP Family/Ca ++ 0.055 0.064 -10000 0 -0.34 12 12
PDE6A/B 0.038 0.071 -10000 0 -0.37 14 14
mol:Pi 0.049 0.098 -10000 0 -0.32 27 27
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.079 0.043 0.24 1 -10000 0 1
PDE6B 0.021 0.089 -10000 0 -0.54 12 12
PDE6A 0.034 0.009 -10000 0 -10000 0 0
PDE6G 0.033 0.014 0.18 3 -10000 0 3
RHO 0.034 0.005 -10000 0 -10000 0 0
PDE6 0.066 0.11 -10000 0 -0.28 31 31
GUCA1A 0.024 0.077 -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
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.049 0.078 0.25 33 -10000 0 33
STMN1 0.054 0.084 0.29 45 -10000 0 45
Aurora B/RasGAP/Survivin 0.11 0.077 0.26 2 -10000 0 2
Chromosomal passenger complex/Cul3 protein complex -0.071 0.13 0.21 27 -0.23 139 166
BIRC5 0.12 0.077 0.2 5 -10000 0 5
DES -0.013 0.13 -10000 0 -0.56 25 25
Aurora C/Aurora B/INCENP 0.076 0.053 0.24 4 -10000 0 4
Aurora B/TACC1 0.025 0.087 -10000 0 -0.32 24 24
Aurora B/PP2A 0.058 0.042 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.022 0.14 3 -10000 0 3
mitotic metaphase/anaphase transition -0.002 0.005 -10000 0 -10000 0 0
NDC80 0.1 0.1 0.29 84 -10000 0 84
Cul3 protein complex -0.23 0.18 -10000 0 -0.35 365 365
KIF2C 0.14 0.1 0.23 256 -10000 0 256
PEBP1 0.039 0.027 -10000 0 -0.54 1 1
KIF20A 0.12 0.071 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.057 0.042 -10000 0 -10000 0 0
SEPT1 0.035 0.024 -10000 0 -10000 0 0
SMC2 0.04 0.031 -10000 0 -10000 0 0
SMC4 0.046 0.042 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.061 0.17 0.31 13 -0.42 35 48
PSMA3 0.033 0.007 -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 0.05 0.054 0.2 1 -10000 0 1
AURKC 0.036 0.019 -10000 0 -10000 0 0
CDCA8 0.11 0.075 0.19 240 -10000 0 240
cytokinesis 0.18 0.15 0.35 201 -10000 0 201
Aurora B/Septin1 0.18 0.15 0.38 133 -10000 0 133
AURKA 0.078 0.069 -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 0.16 0.054 0.21 3 -10000 0 3
hSgo1/Aurora B/Survivin 0.13 0.1 0.29 85 -10000 0 85
EVI5 0.036 0.026 -10000 0 -0.53 1 1
RhoA/GTP 0.22 0.14 0.35 230 -10000 0 230
SGOL1 0.074 0.065 -10000 0 -10000 0 0
CENPA 0.14 0.12 0.28 180 -10000 0 180
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 0.008 -10000 0 -10000 0 0
NCAPH 0.079 0.068 -10000 0 -10000 0 0
NPM1 0.026 0.11 -10000 0 -0.42 13 13
RASA1 0.034 0.012 -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 0.057 0.042 -10000 0 -10000 0 0
PPP1CC 0.034 0.004 -10000 0 -10000 0 0
Centraspindlin 0.24 0.15 0.37 258 -10000 0 258
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
NSUN2 0.027 0.094 0.27 1 -0.75 2 3
MYLK -0.071 0.17 -10000 0 -0.34 139 139
KIF23 0.12 0.075 0.2 2 -10000 0 2
VIM -0.007 0.13 -10000 0 -0.39 47 47
RACGAP1 0.082 0.067 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.025 0.11 -10000 0 -0.38 21 21
Chromosomal passenger complex 0.16 0.13 0.28 252 -10000 0 252
Chromosomal passenger complex/EVI5 0.14 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
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.026 0.12 0.24 1 -0.33 49 50
adherens junction organization -0.026 0.13 0.23 1 -0.41 27 28
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 0.32 2 -0.38 104 106
FMN1 -0.026 0.12 -10000 0 -0.31 54 54
mol:IP3 -0.025 0.1 -10000 0 -0.29 46 46
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.024 0.12 -10000 0 -0.32 54 54
CTNNB1 0.03 0.051 -10000 0 -0.54 4 4
AKT1 -0.021 0.11 -10000 0 -0.29 52 52
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.029 0.18 -10000 0 -0.52 39 39
CTNND1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.021 0.11 0.26 1 -0.33 38 39
VASP -0.022 0.12 0.24 1 -0.39 24 25
ZYX -0.027 0.12 -10000 0 -0.38 26 26
JUB -0.026 0.12 -10000 0 -0.31 54 54
EGFR(dimer) -0.16 0.2 -10000 0 -0.42 118 118
E-cadherin/beta catenin-gamma catenin 0.035 0.091 -10000 0 -0.32 25 25
mol:PI-3-4-5-P3 -0.008 0.13 -10000 0 -0.3 54 54
PIK3CA 0.032 0.011 -10000 0 -10000 0 0
PI3K -0.008 0.13 -10000 0 -0.3 53 53
FYN -0.025 0.11 -10000 0 -0.38 24 24
mol:Ca2+ -0.024 0.1 -10000 0 -0.28 46 46
JUP 0.034 0.011 -10000 0 -10000 0 0
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
mol:DAG -0.025 0.1 -10000 0 -0.29 46 46
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP -0.14 0.18 0.32 2 -0.38 104 106
establishment of polarity of embryonic epithelium -0.021 0.12 0.24 1 -0.38 24 25
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RHOA 0.033 0.008 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
CASR -0.024 0.1 0.24 2 -0.27 45 47
RhoA/GTP -0.007 0.1 -10000 0 -0.26 45 45
AKT2 -0.023 0.11 -10000 0 -0.29 50 50
actin cable formation -0.021 0.12 0.25 3 -0.38 24 27
apoptosis 0.019 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 -0.32 251 251
PIP5K1A -0.022 0.11 -10000 0 -0.33 38 38
PLCG1 -0.026 0.1 -10000 0 -0.29 46 46
Rac1/GTP -0.14 0.19 -10000 0 -0.39 116 116
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
PLK1 signaling events

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.036 0.043 0.12 4 -0.12 35 39
BUB1B 0.094 0.063 0.16 163 -0.14 1 164
PLK1 0.046 0.035 0.11 54 -10000 0 54
PLK1S1 0.023 0.019 0.06 48 -10000 0 48
KIF2A 0.038 0.037 0.28 4 -10000 0 4
regulation of mitotic centrosome separation 0.046 0.035 0.11 54 -10000 0 54
GOLGA2 0.034 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.1 0.062 0.17 198 -10000 0 198
WEE1 0.05 0.077 0.23 2 -0.31 16 18
cytokinesis 0.13 0.082 0.22 106 -0.39 1 107
PP2A-alpha B56 0.14 0.11 -10000 0 -0.47 5 5
AURKA 0.051 0.04 0.14 10 -0.16 2 12
PICH/PLK1 0.13 0.095 0.24 176 -10000 0 176
CENPE 0.084 0.067 0.17 114 -10000 0 114
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 0.039 0.14 31 -10000 0 31
PAK1 0.043 0.045 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
CLSPN 0.044 0.054 0.15 11 -0.2 12 23
GORASP1 0.033 0.007 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 41 -10000 0 41
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.023 0.019 0.06 48 -10000 0 48
G2 phase of mitotic cell cycle 0.001 0.003 0.016 8 -10000 0 8
STAG2 0.034 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.02 0.094 -10000 0 -0.49 16 16
spindle elongation 0.046 0.035 0.11 54 -10000 0 54
ODF2 0.037 0.015 -10000 0 -10000 0 0
BUB1 0.12 0.12 -10000 0 -0.48 8 8
TPT1 0.014 0.059 0.14 1 -0.16 45 46
CDC25C 0.084 0.067 0.18 1 -0.22 9 10
CDC25B 0.048 0.041 -10000 0 -10000 0 0
SGOL1 0.036 0.043 0.12 35 -0.12 4 39
RHOA 0.033 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 0.091 0.067 0.24 26 -0.2 2 28
CDC14B -0.001 0.065 -10000 0 -0.4 13 13
CDC20 0.083 0.07 -10000 0 -10000 0 0
PLK1/PBIP1 0.074 0.055 0.13 201 -10000 0 201
mitosis -0.001 0.003 0.033 2 -10000 0 2
FBXO5 0.038 0.044 0.17 20 -10000 0 20
CDC2 0.005 0.004 0.016 31 -10000 0 31
NDC80 0.11 0.075 -10000 0 -10000 0 0
metaphase plate congression 0.027 0.058 0.18 1 -0.21 26 27
ERCC6L 0.12 0.094 0.24 168 -10000 0 168
NLP/gamma Tubulin 0.025 0.024 0.09 11 -0.094 2 13
microtubule cytoskeleton organization 0.014 0.059 0.14 1 -0.16 45 46
G2/M transition DNA damage checkpoint 0 0.003 0.012 13 -10000 0 13
PPP1R12A 0.035 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.012 13 -10000 0 13
PLK1/PRC1-2 0.17 0.099 0.27 224 -10000 0 224
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 0.033 0.098 64 -10000 0 64
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 0.066 0.18 262 -10000 0 262
Golgi organization 0.046 0.035 0.11 54 -10000 0 54
Cohesin/SA2 0.055 0.026 0.15 1 -10000 0 1
PPP1CB/MYPT1 0.051 0.01 -10000 0 -10000 0 0
KIF20A 0.13 0.071 -10000 0 -10000 0 0
APC/C/CDC20 0.093 0.066 0.18 147 -10000 0 147
PPP2R1A 0.034 0.006 -10000 0 -10000 0 0
chromosome segregation 0.073 0.054 0.13 201 -10000 0 201
PRC1 0.1 0.074 -10000 0 -10000 0 0
ECT2 0.072 0.074 0.19 117 -10000 0 117
C13orf34 0.039 0.031 0.094 62 -10000 0 62
NUDC 0.027 0.058 0.19 1 -0.21 26 27
regulation of attachment of spindle microtubules to kinetochore 0.094 0.063 0.16 163 -0.14 1 164
spindle assembly 0.036 0.029 0.1 24 -10000 0 24
spindle stabilization 0.023 0.019 0.06 48 -10000 0 48
APC/C/HCDH1 0.022 0.059 -10000 0 -0.34 13 13
MKLP2/PLK1 0.12 0.066 0.18 262 -10000 0 262
CCNB1 0.088 0.071 -10000 0 -10000 0 0
PPP1CB 0.035 0.004 -10000 0 -10000 0 0
BTRC 0.037 0.022 0.18 11 -10000 0 11
ROCK2 0.04 0.051 0.23 1 -0.31 5 6
TUBG1 0.027 0.039 0.13 2 -0.16 16 18
G2/M transition of mitotic cell cycle 0.061 0.063 0.21 26 -0.21 1 27
MLF1IP 0.071 0.066 0.14 247 -10000 0 247
INCENP 0.048 0.04 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.18 -10000 0 -0.35 325 325
fibroblast growth factor receptor signaling pathway -0.22 0.18 -10000 0 -0.35 325 325
LAMA1 0.033 0.011 -10000 0 -10000 0 0
PRNP 0.017 0.094 -10000 0 -0.54 14 14
GPC1/SLIT2 -0.009 0.15 -10000 0 -0.39 68 68
SMAD2 0 0.083 0.28 1 -0.31 31 32
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 0.048 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 0.041 0.1 -10000 0 -0.34 33 33
SERPINC1 0.032 0.025 -10000 0 -10000 0 0
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 0.024 0.085 0.29 2 -0.37 9 11
SLIT2 -0.039 0.19 -10000 0 -0.54 64 64
GPC1/NRG -0.002 0.13 -10000 0 -0.34 60 60
NRG1 -0.019 0.16 -10000 0 -0.54 43 43
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 -0.35 325 325
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 0.017 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.03 0.2 0.18 30 -0.54 63 93
GPC1 0.034 0.013 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.036 0.017 -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 -0.003 0.14 -10000 0 -0.54 33 33
cell death 0.045 0.048 -10000 0 -0.4 5 5
ATIII/GPC1 0.044 0.027 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.004 0.15 -10000 0 -0.37 73 73
LCK 0.031 0.034 -10000 0 -10000 0 0
neuron differentiation -0.002 0.13 -10000 0 -0.34 60 60
PrPc/Cu2+ 0.013 0.069 -10000 0 -0.4 14 14
APP 0.03 0.06 -10000 0 -0.54 5 5
TGFBR2 (dimer) -0.003 0.14 -10000 0 -0.54 33 33
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A -0.036 0.19 -10000 0 -0.54 61 61
LAT2 -0.029 0.13 -10000 0 -0.42 28 28
AP1 -0.19 0.23 -10000 0 -0.48 133 133
mol:PIP3 0.006 0.2 0.34 31 -0.48 30 61
IKBKB 0.022 0.14 0.28 51 -0.27 33 84
AKT1 -0.006 0.21 0.34 76 -0.46 30 106
IKBKG 0.004 0.13 0.26 28 -0.27 34 62
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 0.011 0.15 0.37 10 -0.41 23 33
mol:Ca2+ 0.013 0.16 0.3 34 -0.36 29 63
LYN 0.032 0.018 -10000 0 -10000 0 0
CBLB -0.029 0.13 -10000 0 -0.37 42 42
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 -0.012 0.2 0.34 66 -0.35 84 150
PTPN13 -0.037 0.19 -10000 0 -0.65 20 20
PTPN11 0.033 0.022 -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 20 -0.35 28 48
SYK 0.04 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 47 47
LAT -0.026 0.12 -10000 0 -0.42 25 25
PAK2 0.009 0.16 0.38 9 -0.45 22 31
NFATC2 -0.012 0.057 -10000 0 -0.69 1 1
HRAS 0.005 0.16 0.32 8 -0.46 25 33
GAB2 0.03 0.012 -10000 0 -10000 0 0
PLA2G1B 0.008 0.11 -10000 0 -0.83 8 8
Fc epsilon R1 -0.037 0.19 -10000 0 -0.41 95 95
Antigen/IgE/Fc epsilon R1 -0.031 0.18 -10000 0 -0.38 95 95
mol:GDP -0.023 0.15 0.29 1 -0.47 25 26
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 -0.35 0.27 -10000 0 -0.54 344 344
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.026 0.13 -10000 0 -0.37 45 45
CHUK 0.004 0.13 0.26 28 -0.27 37 65
KLRG1 -0.024 0.12 -10000 0 -0.41 22 22
VAV1 -0.029 0.13 -10000 0 -0.42 26 26
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.028 0.12 -10000 0 -0.42 26 26
negative regulation of mast cell degranulation -0.028 0.11 -10000 0 -0.39 22 22
BTK -0.024 0.15 -10000 0 -0.5 23 23
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.047 0.17 -10000 0 -0.42 65 65
GAB2/PI3K/SHP2 -0.063 0.15 -10000 0 -0.38 68 68
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.032 0.13 -10000 0 -0.47 28 28
RAF1 0.006 0.12 -10000 0 -0.9 8 8
Fc epsilon R1/FcgammaRIIB/SHIP -0.019 0.18 -10000 0 -0.36 95 95
FCER1G 0.031 0.021 -10000 0 -10000 0 0
FCER1A -0.045 0.19 -10000 0 -0.55 64 64
Antigen/IgE/Fc epsilon R1/Fyn -0.021 0.17 -10000 0 -0.35 93 93
MAPK3 0.008 0.12 -10000 0 -0.85 8 8
MAPK1 0.002 0.12 -10000 0 -0.84 8 8
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.018 0.2 -10000 0 -0.62 33 33
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
NF-kappa-B/RelA 0.014 0.083 0.18 15 -0.18 21 36
actin cytoskeleton reorganization -0.013 0.18 -10000 0 -0.65 15 15
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.012 0.17 -10000 0 -0.45 37 37
FER -0.028 0.13 -10000 0 -0.42 26 26
RELA 0.034 0.005 -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 0.32 5 -0.47 26 31
cytokine secretion -0.001 0.051 -10000 0 -10000 0 0
SPHK1 -0.026 0.12 -10000 0 -0.42 26 26
PTK2 -0.015 0.18 -10000 0 -0.71 14 14
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.04 0.16 -10000 0 -0.44 49 49
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.03 0.22 0.34 23 -0.5 52 75
MAP2K2 0.003 0.11 -10000 0 -0.84 8 8
MAP2K1 0.003 0.12 -10000 0 -0.84 8 8
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.013 0.11 -10000 0 -0.38 20 20
MAP2K4 -0.079 0.32 -10000 0 -0.87 72 72
Fc epsilon R1/FcgammaRIIB -0.019 0.19 -10000 0 -0.38 95 95
mol:Choline -0.011 0.2 0.34 66 -0.34 84 150
SHC/Grb2/SOS1 0.01 0.14 -10000 0 -0.44 18 18
FYN 0.03 0.037 -10000 0 -0.54 2 2
DOK1 0.036 0.016 -10000 0 -10000 0 0
PXN -0.014 0.17 -10000 0 -0.67 12 12
HCLS1 -0.028 0.13 -10000 0 -0.42 26 26
PRKCB -0.003 0.16 0.3 27 -0.35 43 70
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
IGHE 0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.028 0.11 -10000 0 -0.39 22 22
LCP2 0.037 0.023 -10000 0 -10000 0 0
PLA2G4A -0.16 0.2 -10000 0 -0.45 101 101
RASA1 0.034 0.012 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.011 0.2 0.34 66 -0.34 84 150
IKK complex 0.024 0.12 0.27 38 -0.22 17 55
WIPF1 0.037 0.022 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.045 0.24 0.59 2 -0.56 74 76
IHH 0.021 0.075 -10000 0 -0.2 1 1
SHH Np/Cholesterol/GAS1 -0.068 0.15 -10000 0 -0.31 128 128
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.068 0.15 0.31 128 -10000 0 128
SMO/beta Arrestin2 -0.002 0.19 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 -0.58 39 40
ARRB2 0.031 0.011 -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 -0.5 29 31
STIL 0.042 0.15 0.39 17 -0.34 7 24
DHH N/PTCH2 0.049 0.01 -10000 0 -10000 0 0
DHH N/PTCH1 0.006 0.16 0.38 2 -0.42 25 27
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 0.52 6 -0.9 94 100
determination of left/right symmetry -0.015 0.18 0.44 2 -0.5 29 31
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
skeletal system development -0.11 0.39 0.52 6 -0.89 94 100
IHH N/Hhip 0.038 0.053 -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 -0.5 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 -0.37 51 51
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 -0.5 29 31
SHH Np/Cholesterol/PTCH1 -0.01 0.12 -10000 0 -0.37 9 9
SHH Np/Cholesterol/PTCH2 0.024 0.037 -10000 0 -0.31 5 5
SHH Np/Cholesterol/Megalin -0.056 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 0.47 2 -0.36 82 84
SMO/Vitamin D3 0.01 0.17 0.41 16 -0.45 13 29
SHH Np/Cholesterol/Hhip 0.025 0.038 -10000 0 -0.31 5 5
LRP2 -0.12 0.26 -10000 0 -0.54 136 136
receptor-mediated endocytosis -0.062 0.2 0.35 9 -0.51 37 46
SHH Np/Cholesterol/BOC -0.038 0.13 -10000 0 -0.31 86 86
SHH Np/Cholesterol/CDO 0.019 0.049 -10000 0 -0.35 7 7
mesenchymal cell differentiation -0.024 0.038 0.31 5 -10000 0 5
mol:Vitamin D3 0.027 0.16 0.41 17 -0.37 9 26
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 0.47 2 -0.36 83 85
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 0.18 0.47 2 -0.36 82 84
HHIP 0.034 0.011 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.049 0.012 -10000 0 -10000 0 0
Necdin/E2F1 -0.045 0.18 -10000 0 -0.38 111 111
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.003 0.15 -10000 0 -0.31 89 89
NGF (dimer)/p75(NTR)/BEX1 -0.005 0.14 -10000 0 -0.33 75 75
NT-4/5 (dimer)/p75(NTR) -0.04 0.15 -10000 0 -0.38 79 79
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 -0.032 0.16 0.34 3 -0.32 98 101
IKBKG 0.034 0.003 -10000 0 -10000 0 0
BDNF 0.038 0.048 -10000 0 -0.54 2 2
MGDIs/NGR/p75(NTR)/LINGO1 0.014 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 0.033 0.03 -10000 0 -0.28 1 1
proBDNF (dimer) 0.038 0.048 -10000 0 -0.54 2 2
NTRK1 0.03 0.022 -10000 0 -10000 0 0
RTN4R 0.04 0.035 -10000 0 -10000 0 0
neuron apoptosis -0.013 0.16 0.51 2 -0.48 15 17
IRAK1 0.036 0.015 -10000 0 -10000 0 0
SHC1 -0.024 0.11 -10000 0 -0.34 51 51
ARHGDIA 0.033 0.011 -10000 0 -10000 0 0
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
Gamma Secretase 0.075 0.054 -10000 0 -0.3 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.007 0.14 -10000 0 -0.33 82 82
MAGEH1 0.019 0.094 -10000 0 -0.54 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.078 0.2 -10000 0 -0.37 150 150
Mammalian IAPs/DIABLO 0.045 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 0.03 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 73 73
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.037 0.11 0.21 30 -0.27 74 104
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.016 0.094 -10000 0 -0.26 56 56
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.017 0.14 -10000 0 -0.34 75 75
NCSTN 0.028 0.014 -10000 0 -10000 0 0
mol:GTP -0.017 0.15 -10000 0 -0.35 78 78
PSENEN 0.035 0.015 -10000 0 -10000 0 0
mol:ceramide -0.021 0.13 0.19 30 -0.31 74 104
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.077 -10000 0 -0.21 56 56
p75(NTR)/beta APP -0.025 0.16 -10000 0 -0.4 77 77
BEX1 0.054 0.05 -10000 0 -10000 0 0
mol:GDP -0.053 0.12 -10000 0 -0.34 75 75
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 -0.013 0.12 -10000 0 -0.28 77 77
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 -0.017 0.15 -10000 0 -0.36 78 78
RHOB 0.032 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.008 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.058 0.036 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.26 -10000 0 -0.54 134 134
TP53 -0.028 0.13 0.37 8 -0.29 59 67
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 0.001 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 -0.029 0.14 0.31 5 -0.33 67 72
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 -0.022 0.13 0.19 30 -0.31 74 104
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 -0.33 78 78
PSEN1 0.033 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.048 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.13 0.23 -10000 0 -0.44 172 172
MAPK8 -0.025 0.14 0.3 7 -0.33 65 72
MAPK9 -0.025 0.13 0.28 6 -0.32 64 70
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 -0.099 0.24 -10000 0 -0.54 117 117
RAC1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.009 0.14 -10000 0 -0.29 77 77
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 78 78
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.027 0.14 -10000 0 -0.3 71 71
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 -0.4 99 99
BAD -0.026 0.15 0.41 8 -0.33 65 73
RIPK2 0.029 0.022 -10000 0 -10000 0 0
NGFR -0.054 0.2 -10000 0 -0.54 75 75
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 61 61
BCL2L11 -0.025 0.15 0.4 9 -0.33 65 74
BDNF (dimer)/p75(NTR) -0.02 0.16 -10000 0 -0.38 80 80
PI3K -0.03 0.16 -10000 0 -0.34 99 99
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0 0.13 -10000 0 -0.31 74 74
NDNL2 0.033 0.007 -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) -0.04 0.15 -10000 0 -0.38 79 79
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.006 0.13 -10000 0 -0.31 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 -0.023 0.14 0.39 9 -0.31 66 75
E2F1 0.05 0.048 -10000 0 -10000 0 0
CASP9 0.033 0.008 -10000 0 -10000 0 0
IKK complex 0.03 0.084 -10000 0 -0.3 1 1
NGF (dimer)/TRKA 0.022 0.016 -10000 0 -10000 0 0
MMP7 -0.042 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 0.1 -10000 0 -0.54 5 5
APAF-1/Caspase 9 -0.033 0.1 -10000 0 -0.26 72 72
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 0.067 0.14 0.32 58 -10000 0 58
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 -0.068 0.14 -10000 0 -0.32 58 58
negative regulation of cAMP metabolic process -0.08 0.14 -10000 0 -0.25 185 185
GNAZ 0.026 0.063 -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 -0.081 0.14 -10000 0 -0.25 185 185
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
RHOA 0.033 0.008 -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 -0.32 281 281
TC10/GTP -0.13 0.16 -10000 0 -0.28 274 274
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 0.19 -10000 0 -0.54 52 52
FOXO3 -0.031 0.16 -10000 0 -0.6 33 33
AKT1 -0.046 0.16 0.33 8 -0.45 22 30
INSR 0.039 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.092 0.073 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 -0.54 279 279
CRK 0.031 0.01 -10000 0 -10000 0 0
PTPN1 0.019 0.054 0.28 19 -10000 0 19
CAV1 -0.24 0.18 -10000 0 -0.33 368 368
CBL/APS/CAP/Crk-II/C3G -0.13 0.18 -10000 0 -0.3 278 278
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 0.018 0.096 0.36 1 -0.4 6 7
RPS6KB1 -0.04 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 -0.55 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 37 37
Insulin Receptor 0.039 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.038 0.12 -10000 0 -0.3 41 41
PRKCI 0.01 0.087 -10000 0 -0.5 8 8
Insulin Receptor/Insulin/GRB14/PDK1 -0.045 0.16 -10000 0 -0.32 108 108
SHC1 0.028 0.014 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.059 0.052 -10000 0 -0.47 4 4
PI3K 0.008 0.16 -10000 0 -0.3 93 93
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 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
AKT2 -0.048 0.16 0.33 7 -0.44 22 29
PRKCZ -0.007 0.084 -10000 0 -0.41 15 15
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.01 0.091 -10000 0 -0.28 46 46
F2RL2 0.046 0.066 -10000 0 -0.54 3 3
TRIP10 0.033 0.026 -10000 0 -0.54 1 1
Insulin Receptor/Insulin/Shc 0.056 0.036 -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 0.076 0.055 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
RASA1 0.034 0.012 -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 -0.31 279 279
TC10/GDP 0.024 0.019 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.069 0.057 -10000 0 -0.32 4 4
INPP5D -0.037 0.096 -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 0.19 -10000 0 -0.54 60 60
p62DOK/RasGAP 0.059 0.053 -10000 0 -0.47 4 4
INS 0.039 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.037 0.095 -10000 0 -0.29 59 59
GRB2 0.034 0.018 -10000 0 -10000 0 0
EIF4EBP1 -0.044 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 0.087 -10000 0 -0.35 4 4
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 -0.3 5 5
Nectin adhesion pathway

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
PDGFRB 0.034 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
PTK2 -0.053 0.17 -10000 0 -0.44 67 67
positive regulation of JNK cascade -0.025 0.15 -10000 0 -0.32 75 75
CDC42/GDP -0.019 0.2 -10000 0 -0.43 85 85
Rac1/GDP -0.018 0.2 -10000 0 -0.42 86 86
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 -0.023 0.18 -10000 0 -0.4 72 72
nectin-3/I-afadin -0.024 0.17 -10000 0 -0.39 85 85
RAPGEF1 -0.043 0.2 0.47 1 -0.46 79 80
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.22 -10000 0 -0.52 81 81
PDGFB-D/PDGFRB 0.034 0.006 -10000 0 -10000 0 0
TLN1 -0.038 0.11 0.2 3 -0.46 21 24
Rap1/GTP -0.03 0.14 -10000 0 -0.33 76 76
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.041 -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 -0.045 0.24 0.49 1 -0.52 87 88
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K -0.004 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 -0.02 0.16 -10000 0 -0.33 84 84
PVRL1 0.031 0.015 -10000 0 -10000 0 0
PVRL3 -0.053 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 0.006 0.12 -10000 0 -0.54 22 22
CLDN1 -0.003 0.16 -10000 0 -0.54 41 41
JAM-A/CLDN1 -0.008 0.17 -10000 0 -0.35 82 82
SRC -0.075 0.24 -10000 0 -0.56 85 85
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 -0.045 0.24 0.48 1 -0.54 74 75
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 0.013 -10000 0 -10000 0 0
F11R 0.028 0.017 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.025 0.15 -10000 0 -0.32 75 75
alphaV/beta3 Integrin/Talin -0.005 0.12 0.3 1 -0.46 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 -0.036 0.12 -10000 0 -0.47 23 23
VAV2 -0.042 0.24 0.48 1 -0.54 75 76
RAP1/GDP -0.014 0.19 -10000 0 -0.4 80 80
ITGAV 0.033 0.028 -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 -0.34 79 79
nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.39 85 85
Rac1/GTP -0.022 0.19 -10000 0 -0.4 84 84
PTPRM -0.034 0.13 -10000 0 -0.29 84 84
E-cadherin/beta catenin/alpha catenin 0.052 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
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 -10000 0 -10000 0 0
CDKN2C -0.022 0.15 -10000 0 -0.52 41 41
CDKN2A 0.057 0.055 0.2 7 -10000 0 7
CCND2 -0.007 0.06 0.17 28 -0.19 16 44
RB1 0.005 0.072 0.22 14 -0.2 31 45
CDK4 -0.003 0.073 0.21 35 -0.21 13 48
CDK6 -0.005 0.073 0.21 33 -0.22 16 49
G1/S progression 0.002 0.087 0.21 53 -0.23 15 68
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.011 0.091 -10000 0 -0.26 46 46
epithelial cell differentiation 0.04 0.086 -10000 0 -0.29 26 26
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
ENAH -0.008 0.071 0.28 5 -0.3 2 7
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EPHA2 0.026 0.062 -10000 0 -0.54 6 6
MYO6 0 0.074 -10000 0 -0.28 25 25
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
ABI1/Sra1/Nap1 0.074 0.036 -10000 0 -10000 0 0
AQP5 -0.14 0.24 -10000 0 -0.49 151 151
CTNND1 0.033 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.072 -10000 0 -0.28 25 25
regulation of calcium-dependent cell-cell adhesion -0.024 0.1 -10000 0 -0.29 63 63
EGF -0.15 0.27 -10000 0 -0.54 163 163
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
AQP3 -0.054 0.18 -10000 0 -0.49 63 63
cortical microtubule organization 0.04 0.086 -10000 0 -0.29 26 26
GO:0000145 -0.022 0.064 -10000 0 -0.27 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.089 -10000 0 -0.29 26 26
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GDP -0.029 0.058 -10000 0 -0.27 24 24
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.059 -10000 0 -0.32 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.002 0.069 -10000 0 -0.42 1 1
PVRL2 0.039 0.027 -10000 0 -10000 0 0
ZYX -0.003 0.073 -10000 0 -0.28 26 26
ARF6/GTP 0.062 0.062 -10000 0 -0.3 6 6
CDH1 0.006 0.12 -10000 0 -0.54 22 22
EGFR/EGFR/EGF/EGF -0.23 0.2 -10000 0 -0.35 356 356
RhoA/GDP 0.04 0.085 -10000 0 -0.28 25 25
actin cytoskeleton organization -0.022 0.067 -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 26 -10000 0 26
RHOA 0.033 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.058 -10000 0 -0.27 24 24
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
VCL -0.022 0.069 -10000 0 -0.28 24 24
EFNA1 0.028 0.016 -10000 0 -10000 0 0
LPP -0.024 0.065 -10000 0 -0.28 25 25
Ephrin A1/EPHA2 0.023 0.083 -10000 0 -0.29 25 25
SEC6/SEC8 -0.007 0.068 -10000 0 -0.27 26 26
MGAT3 -0.024 0.11 -10000 0 -0.29 63 63
HGF/MET 0.004 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 -0.011 0.092 -10000 0 -0.26 46 46
actin cable formation 0.054 0.11 0.36 15 -0.29 1 16
KIAA1543 -0.022 0.065 -10000 0 -0.27 25 25
KIFC3 0 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 -0.002 0.072 -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 26 26
EXOC4 0.034 0.006 -10000 0 -10000 0 0
STX4 -0.002 0.071 -10000 0 -0.28 25 25
PIP5K1C -0.002 0.072 -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 0.013 0.1 0.3 12 -0.34 2 14
adherens junction assembly -0.031 0.13 0.3 1 -0.63 12 13
IGF-1R heterotetramer/IGF1 -0.13 0.18 -10000 0 -0.3 250 250
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 -0.002 0.072 -10000 0 -0.28 25 25
mol:GTP 0.055 0.058 -10000 0 -0.31 6 6
establishment of epithelial cell apical/basal polarity -0.013 0.087 0.36 5 -0.35 1 6
cortical actin cytoskeleton stabilization -0.011 0.091 -10000 0 -0.26 46 46
regulation of cell-cell adhesion -0.022 0.067 -10000 0 -0.28 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.011 0.092 -10000 0 -0.26 46 46
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.085 -10000 0 -0.49 3 3
HDAC1 0.023 0.028 -10000 0 -10000 0 0
AES 0.033 0.008 -10000 0 -10000 0 0
FBXW11 0.033 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 -0.34 333 333
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 0.02 0.14 -10000 0 -0.69 10 10
NICD/RBPSUH 0.056 0.093 -10000 0 -0.49 3 3
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
NOTCH1 0.019 0.072 -10000 0 -0.62 1 1
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 0.095 0.29 1 -0.43 9 10
APH1B 0.033 0.027 -10000 0 -0.54 1 1
APH1A 0.032 0.029 -10000 0 -10000 0 0
AXIN1 0.016 0.07 -10000 0 -0.6 4 4
CtBP/CBP/TCF1/TLE1/AES 0.001 0.08 0.28 3 -0.36 8 11
PSEN1 0.033 0.007 -10000 0 -10000 0 0
FOS -0.35 0.27 -10000 0 -0.54 344 344
JUN -0.067 0.22 -10000 0 -0.54 89 89
MAP3K7 0.03 0.011 -10000 0 -10000 0 0
CTNNB1 -0.003 0.092 0.29 1 -0.45 9 10
MAPK3 0.032 0.009 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.071 0.26 2 -0.31 3 5
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 0.031 0.021 -10000 0 -10000 0 0
FZD1 0.033 0.026 -10000 0 -0.54 1 1
NOTCH1 precursor/Deltex homolog 1 0.056 0.095 -10000 0 -0.49 3 3
apoptosis -0.22 0.19 -10000 0 -0.34 333 333
Delta 1/NOTCHprecursor 0.054 0.092 -10000 0 -0.49 3 3
DLL1 0.032 0.009 -10000 0 -10000 0 0
PPARD 0.024 0.11 -10000 0 -0.8 7 7
Gamma Secretase 0.075 0.055 -10000 0 -0.3 1 1
APC 0.006 0.1 -10000 0 -0.57 11 11
DVL1 -0.04 0.096 -10000 0 -0.36 30 30
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.082 0.13 0.26 50 -0.29 41 91
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 0.037 0.23 -10000 0 -1.3 12 12
WNT1 0.034 0.005 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.019 0.12 0.34 2 -0.48 13 15
DKK2 0.031 0.054 -10000 0 -0.54 4 4
NOTCH1 precursor/DVL1 -0.015 0.12 -10000 0 -0.65 12 12
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.034 0.008 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.036 0.087 -10000 0 -0.49 3 3
PPP2R5D -0.003 0.065 -10000 0 -0.39 9 9
MAPK1 0.032 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.2 0.18 -10000 0 -0.32 356 356
RBPJ 0.033 0.008 -10000 0 -10000 0 0
CREBBP 0.033 0.03 -10000 0 -0.55 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.005 0.13 -10000 0 -0.38 52 52
CRKL 0 0.12 0.37 1 -0.38 18 19
mol:PIP3 0.007 0.075 0.49 7 -0.87 1 8
AKT1 0.019 0.086 0.39 10 -0.76 1 11
PTK2B 0.027 0.014 -10000 0 -10000 0 0
RAPGEF1 -0.002 0.11 0.35 1 -0.43 10 11
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 -0.012 0.13 0.35 2 -0.41 25 27
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.12 -10000 0 -0.32 51 51
AP1 -0.29 0.24 -10000 0 -0.43 350 350
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 17 17
GAB1/CRKL/SHP2/PI3K 0.011 0.15 -10000 0 -0.44 16 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.014 0.11 0.36 1 -0.42 10 11
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 0.026 0.067 -10000 0 -0.54 7 7
ELK1 -0.019 0.085 0.29 9 -10000 0 9
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.007 0.065 -10000 0 -0.26 5 5
PAK1 0.044 0.1 0.4 14 -0.73 1 15
HGF/MET/RANBP10 0.022 0.12 -10000 0 -0.34 50 50
HRAS -0.032 0.2 -10000 0 -0.58 58 58
DOCK1 -0.003 0.11 0.43 2 -0.44 10 12
GAB1 -0.003 0.12 -10000 0 -0.38 23 23
CRK -0.003 0.11 0.37 1 -0.38 18 19
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.18 -10000 0 -0.53 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 -0.017 0.15 0.42 5 -0.44 19 24
GRB2/SHC 0.02 0.082 -10000 0 -0.25 31 31
FOS -0.35 0.27 -10000 0 -0.54 344 344
GLMN 0.004 0.004 -10000 0 -10000 0 0
cell motility -0.019 0.085 0.28 9 -10000 0 9
HGF/MET/MUC20 0.008 0.12 -10000 0 -0.34 50 50
cell migration 0.019 0.08 -10000 0 -0.24 31 31
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 -0.012 0.098 -10000 0 -0.38 15 15
MET/MUC20 -0.017 0.13 -10000 0 -0.39 52 52
RAP1B 0.003 0.11 0.32 2 -0.41 9 11
RAP1A -0.003 0.11 0.51 1 -0.41 9 10
HGF/MET/RANBP9 0.027 0.12 -10000 0 -0.34 48 48
RAF1 -0.025 0.19 -10000 0 -0.55 58 58
STAT3 -0.007 0.11 -10000 0 -0.42 17 17
cell proliferation 0.025 0.15 0.34 10 -0.39 31 41
RPS6KB1 0.002 0.061 -10000 0 -0.33 9 9
MAPK3 -0.037 0.081 0.62 3 -10000 0 3
MAPK1 -0.003 0.18 0.66 29 -10000 0 29
RANBP9 0.034 0.009 -10000 0 -10000 0 0
MAPK8 -0.003 0.13 0.45 1 -0.43 12 13
SRC -0.006 0.098 -10000 0 -0.37 15 15
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 -0.021 0.18 0.48 1 -0.52 56 57
MET -0.022 0.17 -10000 0 -0.54 50 50
MAP4K1 0.002 0.12 0.39 1 -0.42 17 18
PTK2 0.027 0.015 -10000 0 -10000 0 0
MAP2K2 -0.022 0.18 0.48 1 -0.52 57 58
BAD 0.016 0.08 0.38 7 -0.73 1 8
MAP2K4 -0.012 0.12 0.33 2 -0.39 22 24
SHP2/GRB2/SOS1/GAB1 0.02 0.14 -10000 0 -0.36 51 51
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.033 0.027 -10000 0 -0.54 1 1
HGS -0.014 0.077 -10000 0 -0.25 44 44
PLCgamma1/PKC 0.024 0.006 -10000 0 -10000 0 0
HGF 0.035 0.01 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
PTPRJ 0.035 0.017 -10000 0 -10000 0 0
NCK/PLCgamma1 0.026 0.094 -10000 0 -0.24 48 48
PDPK1 0.022 0.092 0.47 7 -0.81 1 8
HGF/MET/SHIP 0.008 0.12 -10000 0 -0.34 50 50
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.03 0.012 -9999 0 -10000 0 0
CDC42/GTP -0.068 0.14 -9999 0 -0.32 58 58
PLCG1 -0.074 0.13 -9999 0 -0.34 54 54
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 -0.068 0.14 -9999 0 -0.32 58 58
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.07 0.13 -9999 0 -0.34 48 48
MAPK1 -0.077 0.13 -9999 0 -0.34 56 56
S1P/S1P5/Gi -0.081 0.14 -9999 0 -0.25 185 185
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 -0.081 0.14 -9999 0 -0.25 185 185
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.026 0.063 -9999 0 -0.54 6 6
S1P/S1P4/G12/G13 0.039 0.014 -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
LPA receptor mediated events

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.047 0.035 -10000 0 -0.25 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.059 0.061 0.28 3 -0.26 1 4
AP1 -0.21 0.19 -10000 0 -0.33 344 344
mol:PIP3 -0.15 0.16 -10000 0 -0.29 277 277
AKT1 0.005 0.092 -10000 0 -0.33 7 7
PTK2B -0.016 0.081 -10000 0 -0.18 89 89
RHOA 0.009 0.067 -10000 0 -0.28 17 17
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.058 0.19 44 -0.27 1 45
MAGI3 0.041 0.042 -10000 0 -0.54 1 1
RELA 0.034 0.005 -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 -0.015 0.079 0.23 5 -0.28 6 11
NF kappa B1 p50/RelA 0.02 0.04 -10000 0 -0.31 1 1
endothelial cell migration 0.016 0.053 0.27 2 -0.47 5 7
ADCY4 -0.048 0.096 -10000 0 -0.23 43 43
ADCY5 -0.046 0.094 -10000 0 -0.29 12 12
ADCY6 -0.046 0.093 -10000 0 -0.29 12 12
ADCY7 -0.037 0.091 -10000 0 -0.3 13 13
ADCY1 -0.046 0.093 -10000 0 -0.28 14 14
ADCY2 -0.049 0.1 -10000 0 -0.32 18 18
ADCY3 -0.046 0.093 -10000 0 -0.29 12 12
ADCY8 -0.04 0.087 -10000 0 -0.31 10 10
ADCY9 -0.042 0.09 -10000 0 -0.3 11 11
GSK3B -0.016 0.079 0.25 4 -0.22 17 21
arachidonic acid secretion -0.053 0.1 -10000 0 -0.28 32 32
GNG2 0.032 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 0.026 0.061 0.26 3 -0.25 3 6
GAB1 0.033 0.027 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.049 0.11 -10000 0 -0.84 8 8
JUN -0.067 0.22 -10000 0 -0.54 89 89
LPA/LPA2/NHERF2 0.024 0.017 -10000 0 -0.11 3 3
TIAM1 0.03 0.13 -10000 0 -0.98 8 8
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.026 0.056 0.19 44 -10000 0 44
PLCB3 0.036 0.05 0.19 41 -10000 0 41
FOS -0.35 0.27 -10000 0 -0.54 344 344
positive regulation of mitosis -0.053 0.1 -10000 0 -0.28 32 32
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 0.059 -10000 0 -0.27 7 7
GNAZ 0.015 0.044 -10000 0 -0.28 10 10
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 -10000 0 -0.21 5 5
GNAI3 0.02 0.023 -10000 0 -0.22 4 4
GNAI1 -0.11 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 -0.093 5 5
LPA/LPA1 0.007 0.026 -10000 0 -0.25 5 5
HB-EGF/EGFR -0.12 0.2 -10000 0 -0.31 250 250
HBEGF 0.067 0.077 -10000 0 -0.4 4 4
mol:DAG 0.026 0.056 0.19 44 -10000 0 44
cAMP biosynthetic process -0.056 0.1 0.24 1 -0.29 23 24
NFKB1 0.034 0.005 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
GNB1 0.034 0.012 -10000 0 -10000 0 0
LYN 0.04 0.069 0.26 19 -0.28 1 20
GNAQ 0.003 0.009 0.057 2 -0.075 5 7
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 0.003 0.016 0.075 2 -0.15 5 7
IL8 -0.19 0.22 0.34 14 -0.39 253 267
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 0.022 0.025 -10000 0 -0.2 5 5
G12/G13 0.045 0.03 -10000 0 -0.23 2 2
PI3K-beta -0.01 0.089 -10000 0 -0.27 35 35
cell migration 0.027 0.045 -10000 0 -0.25 7 7
SLC9A3R2 0.032 0.015 0.18 3 -10000 0 3
PXN 0.015 0.059 -10000 0 -0.28 7 7
HRAS/GTP -0.054 0.1 -10000 0 -0.28 32 32
RAC1 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.095 0.075 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
PRKCD 0.024 0.059 0.2 12 -0.26 1 13
Gi(beta/gamma) -0.051 0.11 -10000 0 -0.31 30 30
mol:LPA 0.003 0.016 0.075 2 -0.15 5 7
TRIP6/p130 Cas/FAK1/Paxillin 0.03 0.052 -10000 0 -0.24 3 3
MAPKKK cascade -0.053 0.1 -10000 0 -0.28 32 32
contractile ring contraction involved in cytokinesis 0.008 0.068 -10000 0 -0.27 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.021 0.039 -10000 0 -0.31 4 4
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 -0.016 0.08 0.23 5 -0.29 6 11
GNA11 0.015 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.05 0.12 -10000 0 -0.9 8 8
MMP2 0.016 0.053 0.27 2 -0.47 5 7
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.028 0.081 -10000 0 -0.49 7 7
Crk/p130 Cas/Paxillin -0.082 0.14 -10000 0 -0.38 71 71
JUN -0.002 0.15 0.26 6 -0.35 38 44
HRAS 0.034 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.11 0.17 -10000 0 -0.3 62 62
RAP1A 0.034 0.005 -10000 0 -10000 0 0
FRS2 0.033 0.029 -10000 0 -0.54 1 1
RAP1A/GDP 0.025 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.11 0.17 0.35 3 -0.3 58 61
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 0.055 0.14 0.24 1 -0.31 61 62
RHOA 0.033 0.008 -10000 0 -10000 0 0
RAP1A/GTP 0.076 0.15 -10000 0 -0.27 60 60
GRB7 0.029 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.11 0.17 -10000 0 -0.3 59 59
MAPKKK cascade 0.057 0.14 0.25 8 -0.29 42 50
BCAR1 0.029 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.016 0.2 -10000 0 -0.38 93 93
lamellipodium assembly -0.043 0.16 -10000 0 -0.34 77 77
RET51/GFRalpha1/GDNF/SHC 0.092 0.16 -10000 0 -0.3 45 45
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.044 0.13 -10000 0 -0.31 46 46
RET9/GFRalpha1/GDNF/Shank3 0.05 0.14 -10000 0 -0.31 62 62
MAPK3 0.043 0.13 0.27 9 -0.28 46 55
DOK1 0.036 0.016 -10000 0 -10000 0 0
DOK6 0.032 0.049 0.18 10 -0.54 3 13
PXN 0.034 0.003 -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 0.029 0.23 -10000 0 -0.54 65 65
MAPK8 0.054 0.12 0.27 4 -0.37 8 12
HRAS/GTP 0.093 0.16 0.31 4 -0.3 56 60
tube development 0.056 0.14 0.31 13 -0.3 58 71
MAPK1 0.045 0.13 0.28 9 -0.28 46 55
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.02 0.11 -10000 0 -0.26 59 59
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 58 60
SHC1 0.028 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.09 0.17 -10000 0 -0.3 60 60
RET51/GFRalpha1/GDNF/Dok5 0.088 0.18 -10000 0 -0.3 65 65
PRKCA 0.031 0.013 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
CREB1 0.043 0.12 -10000 0 -0.46 3 3
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.018 0.097 -10000 0 -0.25 41 41
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 0.26 6 -0.34 38 44
RET9/GFRalpha1/GDNF/FRS2 0.05 0.15 0.24 1 -0.31 63 64
SHANK3 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.034 0.012 -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 0.054 0.13 0.26 7 -0.26 46 53
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.061 0.13 0.25 4 -0.27 47 51
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.048 0.12 0.25 6 -0.38 3 9
PI3K -0.038 0.26 0.31 8 -0.53 77 85
SOS1 0.034 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.058 0.14 -10000 0 -0.3 58 58
GRB10 0.03 0.051 -10000 0 -0.54 4 4
activation of MAPKK activity 0.057 0.12 0.26 7 -0.34 3 10
RET51/GFRalpha1/GDNF/FRS2 0.1 0.17 0.35 1 -0.3 61 62
GAB1 0.033 0.027 -10000 0 -0.54 1 1
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 117 117
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.047 0.12 0.25 6 -0.33 4 10
RET51/GFRalpha1/GDNF/PKC alpha 0.098 0.17 -10000 0 -0.3 57 57
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 0.072 0.23 -10000 0 -0.38 87 87
Rac1/GTP -0.032 0.2 0.25 3 -0.42 74 77
RET9/GFRalpha1/GDNF 0.038 0.15 -10000 0 -0.33 66 66
GFRalpha1/GDNF 0.04 0.17 -10000 0 -0.38 66 66
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.033 0.008 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.027 0.096 -10000 0 -0.27 17 17
NT3 (dimer)/TRKC -0.082 0.21 -10000 0 -0.41 142 142
NT3 (dimer)/TRKB -0.24 0.29 -10000 0 -0.48 279 279
SHC/Grb2/SOS1/GAB1/PI3K 0.002 0.074 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
BDNF 0.038 0.048 -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 0.03 0.022 -10000 0 -10000 0 0
NTRK2 -0.23 0.29 -10000 0 -0.54 236 236
NTRK3 0.015 0.1 -10000 0 -0.54 16 16
NT-4/5 (dimer)/TRKB -0.17 0.23 -10000 0 -0.37 262 262
neuron apoptosis 0.12 0.21 0.45 111 -10000 0 111
SHC 2-3/Grb2 -0.13 0.23 -10000 0 -0.49 111 111
SHC1 0.028 0.014 -10000 0 -10000 0 0
SHC2 -0.14 0.24 -10000 0 -0.53 116 116
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 -0.084 0.2 -10000 0 -0.38 133 133
RIN/GDP 0.006 0.11 0.26 4 -0.29 15 19
GIPC1 0.034 0.011 -10000 0 -10000 0 0
KRAS 0.035 0.019 -10000 0 -10000 0 0
DNAJA3 -0.054 0.13 -10000 0 -0.34 72 72
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 0.034 -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 0.032 0.069 -10000 0 -0.4 10 10
ELMO1 0.034 0.004 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.042 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 0.014 -10000 0 -10000 0 0
FRS2 0.033 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 -0.33 80 80
mol:GDP -0.008 0.15 0.34 5 -0.43 18 23
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.025 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.005 0.096 0.24 1 -0.29 14 15
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 -0.34 233 233
KIDINS220/CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.039 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2 0.064 0.028 -10000 0 -0.34 1 1
SHC/GRB2/SOS1/GAB1 0.063 0.043 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.01 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.26 -10000 0 -0.54 134 134
RAP1/GDP 0.003 0.091 -10000 0 -0.25 14 14
KIDINS220/CRKL 0.032 0.008 -10000 0 -10000 0 0
BDNF (dimer) 0.038 0.048 -10000 0 -0.54 2 2
ubiquitin-dependent protein catabolic process 0.029 0.059 -10000 0 -0.34 10 10
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 0.039 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.026 0.068 -10000 0 -0.3 7 7
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 -0.35 269 269
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 -0.041 0.12 -10000 0 -0.43 24 24
STAT3 0.055 0.077 -10000 0 -0.36 10 10
axon guidance -0.17 0.2 -10000 0 -0.34 269 269
MAPK3 0.048 0.066 0.28 3 -10000 0 3
MAPK1 0.052 0.069 0.28 4 -10000 0 4
CDC42/GDP 0.006 0.11 0.26 5 -0.29 15 20
NTF3 -0.12 0.26 -10000 0 -0.54 134 134
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.022 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.37 51 51
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 -0.34 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 0.048 0.1 0.36 1 -0.43 5 6
Rac1/GDP 0.007 0.11 0.26 6 -0.28 17 23
NGF (dimer)/TRKA/GRIT 0.02 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.025 0.22 0.42 1 -0.73 28 29
NGF (dimer)/TRKA/NEDD4-2 0.03 0.059 -10000 0 -0.34 10 10
MAP2K1 0.064 0.087 0.36 13 -10000 0 13
NGFR -0.054 0.2 -10000 0 -0.54 75 75
NGF (dimer)/TRKA/GIPC/GAIP 0.024 0.026 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0 0.085 -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 0.012 -10000 0 -10000 0 0
TRKA/c-Abl 0.042 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 -0.31 231 231
NGF (dimer)/TRKA/p62/Atypical PKCs 0.049 0.03 -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 -0.033 0.057 -10000 0 -0.22 16 16
NGF (dimer)/TRKA -0.059 0.14 -10000 0 -0.36 81 81
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
Regulation of nuclear SMAD2/3 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
EP300 0.036 0.016 -10000 0 -10000 0 0
HSPA8 0.03 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.073 0.19 0.33 1 -0.4 107 108
AKT1 0.038 0.02 -10000 0 -10000 0 0
GSC -0.095 0.4 -10000 0 -1.3 46 46
NKX2-5 0.046 0.05 -10000 0 -10000 0 0
muscle cell differentiation 0 0.12 0.47 17 -10000 0 17
SMAD2-3/SMAD4/SP1 0.053 0.12 -10000 0 -0.33 10 10
SMAD4 -0.028 0.084 -10000 0 -0.29 18 18
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 0.052 0.095 -10000 0 -0.35 6 6
MYC -0.006 0.12 -10000 0 -0.55 25 25
CDKN2B -0.049 0.2 -10000 0 -0.76 19 19
AP1 -0.26 0.29 -10000 0 -0.42 325 325
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.11 -10000 0 -0.39 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.01 0.11 -10000 0 -0.36 22 22
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 -0.18 2 2
SMAD3/SMAD4/GR -0.045 0.14 -10000 0 -0.39 51 51
GATA3 0.039 0.16 -10000 0 -0.53 33 33
SKI/SIN3/HDAC complex/NCoR1 0.016 0.084 -10000 0 -0.36 16 16
MEF2C/TIF2 0.009 0.15 0.34 1 -0.54 24 25
endothelial cell migration -0.058 0.11 0.6 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 0.018 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 -10000 0 -0.54 2 2
CDKN1A 0.004 0.11 -10000 0 -1.1 3 3
KAT2B 0.001 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.025 0.11 -10000 0 -0.32 32 32
DCP1A 0.033 0.008 -10000 0 -10000 0 0
SKI 0.033 0.007 -10000 0 -10000 0 0
SERPINE1 0.058 0.11 -10000 0 -0.61 5 5
SMAD3/SMAD4/ATF2 0.005 0.092 -10000 0 -0.28 11 11
SMAD3/SMAD4/ATF3 -0.09 0.2 -10000 0 -0.41 132 132
SAP30 0.033 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.063 0.04 -10000 0 -10000 0 0
JUN -0.26 0.28 0.29 1 -0.42 307 308
SMAD3/SMAD4/IRF7 0.022 0.094 -10000 0 -0.29 9 9
TFE3 0.03 0.045 -10000 0 -0.18 7 7
COL1A2 0.075 0.13 0.42 8 -0.71 5 13
mesenchymal cell differentiation -0.006 0.093 0.27 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 -0.56 344 344
SMAD3/SMAD4/Max -0.018 0.089 -10000 0 -0.29 9 9
Cbp/p300/SNIP1 0.061 0.033 -10000 0 -0.32 1 1
ZBTB17 0.027 0.022 -10000 0 -10000 0 0
LAMC1 -0.039 0.15 -10000 0 -0.6 28 28
TGIF2/HDAC complex/SMAD3/SMAD4 0.005 0.091 -10000 0 -0.29 9 9
IRF7 0.04 0.024 0.22 1 -10000 0 1
ESR1 -0.068 0.25 0.23 3 -0.55 106 109
HNF4A 0.033 0.008 -10000 0 -10000 0 0
MEF2C 0.016 0.17 0.42 9 -0.55 28 37
SMAD2-3/SMAD4 0.009 0.11 -10000 0 -0.3 22 22
Cbp/p300/Src-1 0.062 0.039 -10000 0 -0.32 2 2
IGHV3OR16-13 -0.007 0.071 -10000 0 -0.45 10 10
TGIF2/HDAC complex 0.033 0.01 -10000 0 -10000 0 0
CREBBP 0.032 0.027 -10000 0 -0.52 1 1
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 0.007 -10000 0 -10000 0 0
GCN5L2 0.003 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.13 -10000 0 -0.37 31 31
MSG1/HSC70 -0.21 0.22 -10000 0 -0.4 297 297
SMAD2 0.02 0.053 -10000 0 -0.2 3 3
SMAD3 -0.015 0.063 -10000 0 -0.21 6 6
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.069 -10000 0 -0.32 5 5
SMAD2/SMAD2/SMAD4 0.01 0.053 0.22 6 -0.26 3 9
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 0.074 0.12 -10000 0 -0.33 7 7
IFNB1 -0.012 0.072 0.32 3 -0.3 1 4
SMAD3/SMAD4/MEF2C 0.024 0.18 0.41 1 -0.56 29 30
CITED1 -0.3 0.29 -10000 0 -0.54 296 296
SMAD2-3/SMAD4/ARC105 0.025 0.11 -10000 0 -0.3 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 -0.42 14 14
RUNX1-3/PEBPB2 0.02 0.13 -10000 0 -0.35 49 49
SMAD7 -0.18 0.22 -10000 0 -0.49 113 113
MYC/MIZ-1 0.008 0.098 -10000 0 -0.41 25 25
SMAD3/SMAD4 0.032 0.098 0.32 10 -0.38 3 13
IL10 -0.006 0.12 0.4 1 -0.39 22 23
PIASy/HDAC complex 0.026 0.028 -10000 0 -10000 0 0
PIAS3 0.034 0.009 -10000 0 -10000 0 0
CDK2 0.04 0.024 0.21 2 -10000 0 2
IL5 -0.002 0.12 0.4 1 -0.38 24 25
CDK4 0.036 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 -0.31 9 9
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 0.02 -10000 0 -10000 0 0
heart looping 0.017 0.17 0.42 9 -0.55 28 37
CEBPB 0.031 0.029 -10000 0 -0.54 1 1
SMAD3/SMAD4/DLX1 0.013 0.094 -10000 0 -0.29 7 7
MYOD1 0.034 0.041 -10000 0 -0.54 2 2
SMAD3/SMAD4/HNF4 0.006 0.091 -10000 0 -0.26 15 15
SMAD3/SMAD4/GATA3 0.027 0.15 -10000 0 -0.41 32 32
SnoN/SIN3/HDAC complex/NCoR1 0.045 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.006 0.15 -10000 0 -0.36 48 48
SMAD3/SMAD4/SP1-3 0.061 0.11 -10000 0 -0.34 4 4
MED15 0.033 0.008 -10000 0 -10000 0 0
SP1 0.047 0.024 -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 0.044 0.12 -10000 0 -0.36 26 26
ITGB5 -0.003 0.084 0.34 1 -0.53 2 3
TGIF/SIN3/HDAC complex/CtBP 0.023 0.071 -10000 0 -0.33 12 12
SMAD3/SMAD4/AR -0.044 0.16 -10000 0 -0.39 72 72
AR -0.039 0.19 -10000 0 -0.54 66 66
negative regulation of cell growth -0.022 0.12 -10000 0 -0.38 21 21
SMAD3/SMAD4/MYOD 0.005 0.096 -10000 0 -0.28 17 17
E2F5 0.036 0.037 -10000 0 -10000 0 0
E2F4 0.03 0.012 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.049 0.11 -10000 0 -0.35 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.11 -10000 0 -0.36 22 22
TFDP1 0.033 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.25 0.3 -10000 0 -0.42 323 323
SMAD3/SMAD4/RUNX2 0.006 0.093 -10000 0 -0.27 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
TCGA08_p53

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
CDKN2A 0.027 0.046 0.14 77 -10000 0 77
TP53 -0.003 0.057 -10000 0 -0.19 39 39
Senescence -0.006 0.062 -10000 0 -0.19 39 39
Apoptosis -0.006 0.062 -10000 0 -0.19 39 39
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.068 0.3 19 -10000 0 19
MDM4 0.028 0.017 -10000 0 -10000 0 0
IL27-mediated signaling events

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.011 0.22 0.73 22 -0.53 8 30
IL27/IL27R/JAK1 0.032 0.28 0.7 13 -1 19 32
TBX21 0.024 0.26 0.62 25 -0.6 38 63
IL12B 0.042 0.027 -10000 0 -10000 0 0
IL12A 0.005 0.061 0.14 6 -0.4 11 17
IL6ST 0.034 0.08 0.24 1 -0.54 8 9
IL27RA/JAK1 0.003 0.24 0.53 3 -1.2 18 21
IL27 -0.019 0.18 0.33 1 -0.54 51 52
TYK2 0.043 0.026 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.19 0.14 -10000 0 -0.53 7 7
T-helper 2 cell differentiation -0.011 0.22 0.73 22 -0.53 8 30
T cell proliferation during immune response -0.011 0.22 0.73 22 -0.53 8 30
MAPKKK cascade 0.011 0.22 0.53 8 -0.73 22 30
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 0.23 1 -10000 0 1
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 0.56 45 -0.63 23 68
IL27/IL27R/JAK2/TYK2 0.011 0.22 0.55 7 -0.74 22 29
positive regulation of T cell mediated cytotoxicity 0.011 0.22 0.53 8 -0.73 22 30
STAT1 (dimer) 0.038 0.33 0.8 23 -1 22 45
JAK2 0.039 0.023 0.24 1 -10000 0 1
JAK1 0.036 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.026 0.21 0.52 5 -0.7 22 27
T cell proliferation -0.18 0.25 0.6 3 -0.59 74 77
IL12/IL12R/TYK2/JAK2 0.067 0.2 0.53 2 -0.8 13 15
IL17A -0.19 0.14 -10000 0 -0.54 7 7
mast cell activation -0.011 0.22 0.73 22 -0.53 8 30
IFNG 0.034 0.066 0.14 101 -0.11 9 110
T cell differentiation 0 0.009 0.02 27 -0.024 19 46
STAT3 (dimer) 0.024 0.21 0.54 4 -0.71 21 25
STAT5A (dimer) 0.023 0.21 0.54 4 -0.68 23 27
STAT4 (dimer) 0.022 0.21 0.53 5 -0.71 22 27
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 0.25 0.56 3 -1.1 18 21
GATA3 -0.013 0.37 0.71 13 -1.3 33 46
IL18 0.019 0.036 0.14 41 -10000 0 41
positive regulation of mast cell cytokine production 0.024 0.2 0.54 4 -0.69 21 25
IL27/EBI3 0.016 0.14 0.34 3 -0.39 50 53
IL27RA -0.016 0.25 0.55 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 -0.009 0.12 0.47 16 -1.2 1 17
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 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
USP8 -0.005 0.015 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.1 -10000 0 -0.3 8 8
NFATC4 -0.029 0.081 0.27 4 -10000 0 4
ERBB2IP 0.034 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.034 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.036 0.087 -10000 0 -0.3 29 29
JUN -0.055 0.071 -10000 0 -10000 0 0
HRAS 0.033 0.013 -10000 0 -10000 0 0
DOCK7 -0.037 0.089 0.26 2 -0.29 27 29
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.098 -10000 0 -0.3 25 25
AKT1 0.007 0.016 0.14 6 -10000 0 6
BAD -0.005 0.014 -10000 0 -10000 0 0
MAPK10 -0.023 0.07 0.26 4 -0.26 7 11
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.038 0.093 -10000 0 -0.32 28 28
RAF1 -0.038 0.095 -10000 0 -0.32 9 9
ErbB2/ErbB3/neuregulin 2 -0.18 0.17 -10000 0 -0.33 274 274
STAT3 0.011 0.16 -10000 0 -0.84 18 18
cell migration -0.014 0.074 0.32 6 -0.26 3 9
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.26 0.28 -10000 0 -0.66 118 118
FOS -0.33 0.26 -10000 0 -0.5 365 365
NRAS 0.035 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.087 -10000 0 -0.3 29 29
MAPK3 -0.16 0.21 -10000 0 -0.51 86 86
MAPK1 -0.18 0.24 -10000 0 -0.56 104 104
JAK2 -0.033 0.089 0.26 2 -0.29 27 29
NF2 0.003 0.069 -10000 0 -0.68 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.08 -10000 0 -0.28 22 22
NRG1 -0.02 0.16 -10000 0 -0.55 43 43
GRB2/SOS1 0.047 0.019 -10000 0 -10000 0 0
MAPK8 -0.039 0.1 -10000 0 -0.29 31 31
MAPK9 -0.02 0.064 0.26 3 -10000 0 3
ERBB2 -0.022 0.013 -10000 0 -10000 0 0
ERBB3 0.037 0.025 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.02 0.027 -10000 0 -0.18 2 2
STAT3 (dimer) 0.012 0.16 -10000 0 -0.82 18 18
RNF41 -0.009 0.014 -10000 0 -10000 0 0
FRAP1 -0.002 0.013 0.11 6 -10000 0 6
RAC1-CDC42/GTP -0.037 0.06 -10000 0 -0.22 27 27
ErbB2/ErbB2/HSP90 (dimer) -0.008 0.023 -10000 0 -10000 0 0
CHRNA1 -0.12 0.16 -10000 0 -0.42 41 41
myelination -0.021 0.09 0.32 7 -10000 0 7
PPP3CB -0.034 0.085 0.25 2 -0.27 26 28
KRAS 0.034 0.019 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.035 0.1 -10000 0 -0.32 2 2
NRG2 -0.35 0.27 -10000 0 -0.54 339 339
mol:GDP 0 0.08 -10000 0 -0.28 22 22
SOS1 0.033 0.004 -10000 0 -10000 0 0
MAP2K2 -0.054 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 -0.034 0.091 0.27 2 -0.29 27 29
MAP2K1 -0.17 0.22 -10000 0 -0.6 53 53
heart morphogenesis -0.036 0.087 -10000 0 -0.3 29 29
RAS family/GDP 0.029 0.11 -10000 0 -0.29 6 6
GRB2 0.033 0.018 -10000 0 -10000 0 0
PRKACA 0.005 0.082 -10000 0 -0.68 7 7
CHRNE -0.005 0.018 -10000 0 -10000 0 0
HSP90AA1 0.034 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.016 -10000 0 -0.14 6 6
nervous system development -0.036 0.087 -10000 0 -0.3 29 29
CDC42 0.033 0.008 -10000 0 -10000 0 0
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 0.013 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.13 0.17 -9999 0 -0.56 19 19
Syndecan-3/Neurocan 0.044 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 -0.3 192 192
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 0.042 0.096 -9999 0 -0.45 13 13
Syndecan-3/IL8 0.049 0.11 -9999 0 -0.47 16 16
PSEN1 0.033 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.04 0.021 -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 -0.37 0.27 -9999 0 -0.54 355 355
FGFR/FGF/Syndecan-3 -0.001 0.09 -9999 0 -0.49 16 16
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.56 18 18
Syndecan-3/AgRP 0.035 0.1 -9999 0 -0.47 16 16
Syndecan-3/AgRP/MC4R 0.05 0.1 -9999 0 -0.46 15 15
Fyn/Cortactin 0.038 0.031 -9999 0 -0.4 1 1
SDC3 -0.002 0.091 -9999 0 -0.49 16 16
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.049 0.11 -9999 0 -0.46 16 16
IL8 0.048 0.053 -9999 0 -0.54 1 1
Syndecan-3/Fyn/Cortactin 0.043 0.099 -9999 0 -0.46 13 13
Syndecan-3/CASK -0.003 0.087 -9999 0 -0.47 16 16
alpha-MSH/MC4R 0.049 0.027 -9999 0 -0.4 1 1
Gamma Secretase 0.075 0.054 -9999 0 -0.3 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.089 0.16 0.34 69 -0.4 11 80
FYN 0.062 0.16 0.41 25 -0.4 18 43
LAT/GRAP2/SLP76 0.071 0.16 0.41 30 -0.39 13 43
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 0.059 0.16 0.36 53 -0.31 31 84
B2M 0.037 0.011 -10000 0 -10000 0 0
IKBKG 0.034 0.071 0.19 51 -10000 0 51
MAP3K8 -0.04 0.19 -10000 0 -0.54 65 65
mol:Ca2+ -0.011 0.017 0.032 9 -0.09 12 21
integrin-mediated signaling pathway 0.037 0.023 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.053 0.18 0.47 25 -0.4 32 57
TRPV6 0.013 0.22 1.3 10 -0.54 17 27
CD28 0.028 0.085 -10000 0 -0.55 10 10
SHC1 0.072 0.18 0.34 77 -0.41 21 98
receptor internalization 0.024 0.19 0.36 26 -0.39 65 91
PRF1 0.037 0.17 0.55 9 -0.79 6 15
KRAS 0.035 0.019 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
COT/AKT1 0.036 0.16 0.33 49 -0.3 42 91
LAT 0.055 0.17 0.4 30 -0.41 21 51
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.04 0.037 0.21 8 -10000 0 8
CD3E 0.034 0.016 0.22 1 -10000 0 1
CD3G 0.039 0.073 -10000 0 -0.54 5 5
RASGRP2 0.008 0.05 0.17 10 -0.16 29 39
RASGRP1 0.065 0.16 0.42 34 -0.33 15 49
HLA-A 0.041 0.025 -10000 0 -10000 0 0
RASSF5 0.03 0.024 -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 0.067 0.098 0.22 91 -0.13 2 93
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.01 0.048 -10000 0 -0.18 17 17
PRKCA 0.041 0.1 0.31 28 -0.21 7 35
GRAP2 0.034 0.019 -10000 0 -10000 0 0
mol:IP3 0.002 0.091 0.29 10 -0.32 11 21
EntrezGene:6957 0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.025 0.13 0.32 20 -0.3 48 68
ORAI1 -0.02 0.17 -10000 0 -1.1 10 10
CSK 0.046 0.16 0.4 20 -0.4 21 41
B7 family/CD28 0.082 0.17 0.48 23 -0.44 13 36
CHUK 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.042 0.17 0.4 22 -0.37 45 67
PTPN6 0.044 0.16 0.37 25 -0.4 20 45
VAV1 0.044 0.16 0.43 20 -0.4 23 43
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 0.063 0.16 0.39 31 -0.41 14 45
PAG1 0.062 0.17 0.39 30 -0.41 19 49
RAP1A 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.04 0.17 0.38 24 -0.36 43 67
CD80 0.045 0.038 0.18 37 -10000 0 37
CD86 0.036 0.013 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 0.009 0.067 -10000 0 -0.21 17 17
HRAS 0.034 0.013 -10000 0 -10000 0 0
GO:0035030 0.042 0.14 0.39 25 -0.38 14 39
CD8A 0.003 0.006 0.048 1 -10000 0 1
CD8B 0.041 0.026 -10000 0 -10000 0 0
PTPRC 0.035 0.036 -10000 0 -10000 0 0
PDK1/PKC theta 0.07 0.19 0.42 55 -0.36 25 80
CSK/PAG1 0.065 0.16 0.39 29 -0.44 13 42
SOS1 0.034 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.057 0.025 -10000 0 -10000 0 0
GRAP2/SLP76 0.066 0.17 0.46 19 -0.4 19 38
STIM1 0.004 0.1 1.2 3 -10000 0 3
RAS family/GTP 0.077 0.11 0.28 55 -0.18 10 65
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.021 0.19 0.36 26 -0.41 65 91
mol:DAG -0.016 0.068 0.13 3 -0.28 13 16
RAP1A/GDP 0.035 0.048 0.13 54 -10000 0 54
PLCG1 0.032 0.008 -10000 0 -10000 0 0
CD247 0.023 0.11 -10000 0 -0.55 15 15
cytotoxic T cell degranulation 0.038 0.16 0.53 10 -0.75 6 16
RAP1A/GTP 0.002 0.016 -10000 0 -0.06 28 28
mol:PI-3-4-5-P3 0.055 0.17 0.44 28 -0.35 30 58
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.024 0.12 0.34 9 -0.4 11 20
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 0.046 0.13 0.3 13 -0.4 12 25
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 0.18 17 -10000 0 17
PRKCB -0.013 0.051 0.15 5 -0.2 14 19
PRKCE 0.046 0.11 0.3 33 -0.21 10 43
PRKCQ 0.06 0.18 0.48 28 -0.38 29 57
LCP2 0.036 0.023 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.059 0.15 0.34 53 -0.27 30 83
IKK complex 0.056 0.094 0.23 75 -10000 0 75
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.029 0.14 0.28 49 -0.25 29 78
PDPK1 0.063 0.16 0.38 55 -0.3 27 82
TCR/CD3/MHC I/CD8/Fyn 0.014 0.17 0.38 16 -0.41 44 60
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.38 5 -0.26 40 45
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 -0.078 0.14 0.24 1 -0.33 87 88
ERBB2 0.028 0.029 -10000 0 -0.54 1 1
proliferation/survival/translation -0.016 0.099 0.29 26 -0.3 2 28
PI3K -0.068 0.16 0.32 9 -0.31 103 112
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
KRAS 0.035 0.019 -10000 0 -10000 0 0
FOXO 0.035 0.082 0.34 6 -0.18 8 14
AKT2 0.034 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.067 -10000 0 -0.54 7 7
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.071 0.094 0.23 3 -0.32 16 19
EPHB2 0.042 0.037 -10000 0 -10000 0 0
Syndecan-2/TACI 0.016 0.066 -10000 0 -0.33 16 16
LAMA1 0.033 0.011 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.058 0.17 -10000 0 -0.32 135 135
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 0.063 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 0.013 0.073 -10000 0 -0.37 16 16
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.081 -10000 0 -0.36 19 19
dendrite morphogenesis 0.022 0.071 -10000 0 -0.33 16 16
Syndecan-2/GM-CSF 0.02 0.068 -10000 0 -0.33 16 16
determination of left/right symmetry 0 0.071 0.14 3 -0.39 16 19
Syndecan-2/PKC delta 0.017 0.066 -10000 0 -0.33 16 16
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
MAPK3 0.043 0.094 0.26 5 -0.3 16 21
MAPK1 0.048 0.098 0.25 7 -0.3 16 23
Syndecan-2/RACK1 0.03 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 0.14 3 -0.39 16 19
ITGA2 0.014 0.1 -10000 0 -0.54 17 17
MAPK8 0.001 0.067 0.34 3 -0.33 17 20
Syndecan-2/alpha2/beta1 Integrin 0.034 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 0.09 0.3 6 -0.28 15 21
Syndecan-2/CASK/Protein 4.1 0.015 0.06 -10000 0 -0.3 16 16
extracellular matrix organization 0.017 0.065 -10000 0 -0.33 16 16
actin cytoskeleton reorganization 0.07 0.094 0.23 3 -0.32 16 19
Syndecan-2/Caveolin-2/Ras -0.15 0.18 -10000 0 -0.32 236 236
Syndecan-2/Laminin alpha3 -0.083 0.17 -10000 0 -0.34 134 134
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 0.018 -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 0.027 0.058 -10000 0 -0.27 15 15
RHOA 0.033 0.008 -10000 0 -10000 0 0
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.081 -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 0.043 0.096 0.2 95 -0.3 16 111
FN1 0.13 0.069 -10000 0 -10000 0 0
Syndecan-2/IL8 0.024 0.074 0.23 1 -0.33 16 17
SDC2 0 0.071 0.14 3 -0.39 16 19
KNG1 0.033 0.007 -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 0.017 0.066 -10000 0 -0.33 16 16
Syndecan-2/Syntenin/PI-4-5-P2 0.015 0.06 -10000 0 -0.3 16 16
Syndecan-2/Ezrin 0.015 0.059 -10000 0 -0.3 16 16
PRKACA 0.044 0.097 0.2 102 -0.3 16 118
angiogenesis 0.024 0.073 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
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.017 0.18 -10000 0 -0.75 3 3
PCK1 -0.74 0.54 -10000 0 -1 387 387
HNF4A 0.033 0.2 0.71 2 -0.75 3 5
KCNJ11 0.039 0.24 0.8 2 -0.76 3 5
AKT1 0.012 0.15 -10000 0 -0.46 5 5
response to starvation 0.005 0.002 -10000 0 -10000 0 0
DLK1 0.027 0.22 0.88 1 -0.81 3 4
NKX2-1 0.034 0.12 0.65 1 -10000 0 1
ACADM 0.016 0.21 -10000 0 -0.86 8 8
TAT -0.058 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 -10000 0 -0.67 35 35
PKLR 0.035 0.19 -10000 0 -0.79 2 2
APOA1 0.021 0.22 -10000 0 -0.88 3 3
CPT1C 0.028 0.2 0.71 1 -0.76 3 4
ALAS1 0.031 0.14 -10000 0 -0.48 2 2
TFRC -0.018 0.2 0.68 3 -0.55 1 4
FOXF1 0.025 0.021 -10000 0 -10000 0 0
NF1 0.038 0.01 -10000 0 -10000 0 0
HNF1A (dimer) 0.05 0.022 -10000 0 -0.22 1 1
CPT1A 0.026 0.21 0.72 3 -0.7 3 6
HMGCS1 0.022 0.2 0.75 2 -0.76 3 5
NR3C1 0 0.16 -10000 0 -0.51 43 43
CPT1B 0.018 0.19 -10000 0 -0.75 3 3
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.015 -10000 0 -10000 0 0
GCK 0.023 0.19 -10000 0 -0.76 3 3
CREB1 -0.18 0.14 -10000 0 -0.26 371 371
IGFBP1 0.015 0.14 -10000 0 -0.66 4 4
PDX1 0.043 0.16 -10000 0 -0.9 3 3
UCP2 0.027 0.2 0.66 2 -0.7 3 5
ALDOB 0.022 0.22 -10000 0 -0.81 3 3
AFP -0.051 0.14 0.39 1 -0.42 1 2
BDH1 0.025 0.19 0.68 2 -0.76 3 5
HADH 0.018 0.23 -10000 0 -0.93 5 5
F2 0.037 0.22 -10000 0 -0.82 3 3
HNF1A 0.051 0.022 -10000 0 -0.22 1 1
G6PC -0.098 0.12 -10000 0 -0.46 1 1
SLC2A2 0.047 0.16 -10000 0 -0.84 2 2
INS 0.022 0.015 0.25 1 -10000 0 1
FOXA1 -0.003 0.23 0.39 3 -0.53 73 76
FOXA3 -0.11 0.14 -10000 0 -0.29 66 66
FOXA2 0.031 0.27 -10000 0 -0.92 3 3
ABCC8 -0.065 0.43 0.91 1 -0.93 85 86
ALB -0.054 0.15 0.39 1 -0.47 15 16
HIF-2-alpha transcription factor network

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
MMP14 0.037 0.1 0.47 3 -0.63 5 8
oxygen homeostasis 0.026 0.03 0.21 3 -10000 0 3
TCEB2 0.032 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.014 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.13 0.14 0.44 25 -0.32 5 30
EPO 0.22 0.25 0.68 58 -0.52 1 59
FIH (dimer) 0.056 0.031 0.25 1 -10000 0 1
APEX1 0.058 0.038 0.24 1 -10000 0 1
SERPINE1 0.26 0.24 0.71 45 -0.5 4 49
FLT1 -0.015 0.17 -10000 0 -0.68 21 21
ADORA2A 0.26 0.25 0.66 76 -0.48 4 80
germ cell development 0.25 0.23 0.69 39 -0.49 3 42
SLC11A2 0.26 0.24 0.7 41 -0.5 4 45
BHLHE40 0.18 0.23 0.62 54 -0.49 4 58
HIF1AN 0.056 0.031 0.25 1 -10000 0 1
HIF2A/ARNT/SIRT1 0.17 0.19 0.54 44 -0.36 5 49
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 44 -0.49 4 48
SIRT1 0.036 0.008 -10000 0 -10000 0 0
response to hypoxia 0.003 0.006 -10000 0 -10000 0 0
HIF2A/ARNT 0.23 0.26 0.74 33 -0.56 4 37
EPAS1 0.16 0.18 0.47 66 -0.32 10 76
SP1 0.047 0.029 -10000 0 -10000 0 0
ABCG2 0.24 0.26 0.7 39 -0.62 10 49
EFNA1 0.18 0.22 0.66 21 -0.5 4 25
FXN 0.25 0.24 0.64 60 -0.48 3 63
POU5F1 0.25 0.24 0.69 39 -0.51 3 42
neuron apoptosis -0.22 0.26 0.54 4 -0.73 34 38
EP300 0.032 0.009 -10000 0 -10000 0 0
EGLN3 0.08 0.075 0.24 34 -0.54 1 35
EGLN2 0.06 0.036 0.24 3 -10000 0 3
EGLN1 0.045 0.034 0.25 1 -10000 0 1
VHL/Elongin B/Elongin C 0.053 0.033 -10000 0 -10000 0 0
VHL 0.036 0.018 0.18 7 -10000 0 7
ARNT 0.045 0.039 -10000 0 -10000 0 0
SLC2A1 0.25 0.24 0.66 55 -0.48 4 59
TWIST1 0.21 0.29 0.63 63 -0.54 32 95
ELK1 0.04 0.019 -10000 0 -0.13 1 1
HIF2A/ARNT/Cbp/p300 0.14 0.18 0.55 22 -0.36 5 27
VEGFA 0.26 0.25 0.72 46 -0.5 4 50
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Osteopontin-mediated events

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
IKK alpha homodimer 0.099 0.078 0.3 8 -0.29 4 12
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.1 0.37 16 -10000 0 16
alphaV/beta3 Integrin/Osteopontin/Src 0.099 0.073 0.26 2 -0.39 4 6
AP1 -0.14 0.22 0.49 1 -0.46 90 91
ILK 0.077 0.073 0.36 2 -0.3 4 6
bone resorption 0.059 0.07 -10000 0 -10000 0 0
PTK2B 0.027 0.014 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.09 0.33 1 -0.28 4 5
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 0.079 0.32 3 -0.33 4 7
MAP3K1 0.078 0.079 0.3 12 -0.3 5 17
JUN -0.066 0.22 -10000 0 -0.54 89 89
MAPK3 0.079 0.096 0.31 30 -0.28 3 33
MAPK1 0.078 0.093 0.28 48 -0.28 4 52
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.064 0.077 0.29 12 -0.29 6 18
ITGB3 0.041 0.021 -10000 0 -10000 0 0
NFKBIA 0.077 0.1 0.32 34 -10000 0 34
FOS -0.35 0.27 -10000 0 -0.54 344 344
CD44 0.033 0.028 -10000 0 -0.54 1 1
CHUK 0.034 0.005 -10000 0 -10000 0 0
PLAU 0.085 0.15 0.49 11 -0.53 1 12
NF kappa B1 p50/RelA 0.14 0.1 0.42 16 -10000 0 16
BCAR1 0.029 0.013 -10000 0 -10000 0 0
RELA 0.034 0.005 -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 0.079 0.075 0.31 9 -0.3 4 13
VAV3 0.063 0.096 0.3 15 -0.29 11 26
MAP3K14 0.086 0.083 0.3 15 -0.3 4 19
ROCK2 0.033 0.026 -10000 0 -0.54 1 1
SPP1 0.096 0.088 0.2 57 -0.54 3 60
RAC1 0.034 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.072 0.088 0.28 11 -0.27 10 21
MMP2 -0.13 0.17 0.47 1 -0.41 73 74
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 -0.048 0.13 0.26 3 -0.3 95 98
FRAP1 -0.014 0.11 0.34 1 -0.48 19 20
AKT1 -0.04 0.12 0.28 3 -0.29 71 74
INSR 0.034 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.044 0.011 -10000 0 -10000 0 0
mol:GTP -0.003 0.12 0.27 3 -0.28 36 39
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.057 -10000 0 -0.22 9 9
TSC2 0.032 0.01 -10000 0 -10000 0 0
RHEB/GDP -0.013 0.094 -10000 0 -0.26 32 32
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 0.004 0.072 -10000 0 -0.25 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.034 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.009 0.1 0.3 4 -0.32 26 30
MAP3K5 -0.018 0.097 0.2 6 -0.29 51 57
PIK3R1 -0.02 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 2 -0.002 61 63
EIF4B -0.008 0.096 0.29 4 -0.32 15 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.098 -10000 0 -0.3 15 15
eIF4E/eIF4G1/eIF4A1 -0.003 0.069 -10000 0 -0.3 18 18
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.026 0.15 -10000 0 -0.31 104 104
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.076 0.26 9 -0.21 12 21
FKBP1A 0.034 0.012 0.18 2 -10000 0 2
RHEB/GTP 0.005 0.11 0.26 2 -0.32 11 13
mol:Amino Acids 0 0.001 0.001 2 -0.002 61 63
FKBP12/Rapamycin 0.025 0.009 0.13 2 -10000 0 2
PDPK1 -0.051 0.12 0.24 5 -0.29 90 95
EIF4E 0.034 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.04 0.21 -10000 0 -0.57 61 61
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.008 0.051 -10000 0 -10000 0 0
TSC1/TSC2 -0.002 0.12 0.29 3 -0.3 35 38
tumor necrosis factor receptor activity 0 0.001 0.002 61 -0.001 2 63
RPS6 0.032 0.027 -10000 0 -0.54 1 1
PPP5C 0.036 0.017 -10000 0 -10000 0 0
EIF4G1 0.033 0.007 -10000 0 -10000 0 0
IRS1 -0.041 0.13 -10000 0 -0.35 73 73
INS 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.067 -10000 0 -0.54 7 7
PDK2 -0.046 0.12 0.25 4 -0.3 73 77
EIF4EBP1 -0.033 0.25 -10000 0 -1 29 29
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PPP2R5D -0.012 0.1 0.32 4 -0.44 18 22
peptide biosynthetic process 0.02 0.016 -10000 0 -10000 0 0
RHEB 0.034 0.009 -10000 0 -10000 0 0
EIF4A1 0.031 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.005 10 -0.003 6 16
EEF2 0.02 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.016 0.24 -10000 0 -0.97 29 29
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 -0.022 0.077 -10000 0 -0.4 2 2
alphaM/beta2 Integrin/GPIbA -0.016 0.079 0.27 3 -10000 0 3
alphaM/beta2 Integrin/proMMP-9 0.042 0.098 0.3 2 -10000 0 2
PLAUR 0.068 0.062 -10000 0 -10000 0 0
HMGB1 -0.03 0.045 -10000 0 -0.23 2 2
alphaM/beta2 Integrin/Talin -0.02 0.072 -10000 0 -10000 0 0
AGER -0.035 0.051 -10000 0 -0.38 2 2
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 -0.37 8 8
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 0.061 0.087 -10000 0 -0.34 8 8
RHOA 0.033 0.008 -10000 0 -10000 0 0
P-selectin oligomer -0.1 0.24 -10000 0 -0.54 116 116
MYH2 0.064 0.093 0.29 5 -0.5 4 9
MST1R 0.043 0.038 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.013 0.067 -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 -0.033 0.099 -10000 0 -0.38 19 19
alphaM/beta2 Integrin 0.048 0.083 0.24 3 -0.36 8 11
JAM3 homodimer -0.008 0.14 -10000 0 -0.54 34 34
ICAM2 0.021 0.076 -10000 0 -0.54 9 9
ICAM1 0.039 0.029 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor 0.046 0.087 0.24 3 -0.35 10 13
cell adhesion -0.016 0.078 0.27 3 -10000 0 3
NFKB1 -0.22 0.2 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 -0.34 73 73
IL6 -0.52 0.36 0.38 1 -0.74 374 375
ITGB2 -0.022 0.063 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.032 0.11 0.31 8 -10000 0 8
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.2 -10000 0 -0.42 123 123
JAM2 -0.12 0.25 -10000 0 -0.54 132 132
alphaM/beta2 Integrin/ICAM1 0.008 0.092 0.3 1 -10000 0 1
alphaM/beta2 Integrin/uPA/Plg 0.01 0.091 -10000 0 -0.36 1 1
RhoA/GTP 0.043 0.1 -10000 0 -0.4 13 13
positive regulation of phagocytosis 0.036 0.083 0.29 3 -0.39 2 5
Ron/MSP 0.056 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.033 0.11 0.32 8 -10000 0 8
alphaM/beta2 Integrin/uPAR 0.009 0.095 0.3 1 -10000 0 1
PLAU 0.057 0.053 -10000 0 -10000 0 0
PLAT -0.064 0.21 -10000 0 -0.54 82 82
actin filament polymerization 0.064 0.097 0.3 10 -0.44 5 15
MST1 0.033 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.011 0.071 -10000 0 -10000 0 0
TNF -0.21 0.18 0.42 3 -0.6 7 10
RAP1B 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.003 0.085 -10000 0 -10000 0 0
fibrinolysis 0.009 0.089 -10000 0 -0.36 1 1
HCK 0.036 0.022 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation 0.046 0.087 0.24 3 -0.35 10 13
VTN 0.033 0.011 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.11 0.17 -10000 0 -0.37 137 137
LPA 0.032 0.009 -10000 0 -10000 0 0
LRP1 0.034 0.004 -10000 0 -10000 0 0
cell migration 0.029 0.091 0.27 2 -0.36 2 4
FN1 0.13 0.069 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.017 0.075 -10000 0 -10000 0 0
MPO 0.031 0.016 -10000 0 -10000 0 0
KNG1 0.033 0.007 -10000 0 -10000 0 0
RAP1/GDP 0.044 0.012 -10000 0 -10000 0 0
ROCK1 0.063 0.11 0.27 9 -0.42 10 19
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
CTGF 0.011 0.11 -10000 0 -0.54 19 19
alphaM/beta2 Integrin/Hck -0.018 0.076 0.3 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 99 99
HP 0.029 0.012 -10000 0 -10000 0 0
leukocyte adhesion -0.17 0.2 -10000 0 -0.47 117 117
SELP -0.1 0.24 -10000 0 -0.54 116 116
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.011 0.096 0.34 9 -0.31 9 18
TBX21 -0.13 0.37 0.74 5 -1.2 37 42
B2M 0.039 0.013 0.2 1 -10000 0 1
TYK2 0.017 0.036 -10000 0 -10000 0 0
IL12RB1 0.017 0.036 -10000 0 -10000 0 0
GADD45B -0.071 0.28 0.7 2 -0.79 39 41
IL12RB2 0.03 0.076 0.25 8 -0.55 1 9
GADD45G -0.061 0.26 0.7 3 -0.74 34 37
natural killer cell activation -0.008 0.022 0.16 1 -10000 0 1
RELB 0.037 0.02 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL18 0.045 0.046 0.22 13 -10000 0 13
IL2RA 0.041 0.035 -10000 0 -10000 0 0
IFNG 0.063 0.066 0.18 109 -0.54 1 110
STAT3 (dimer) -0.062 0.24 0.6 8 -0.63 39 47
HLA-DRB5 -0.008 0.032 -10000 0 -10000 0 0
FASLG -0.062 0.26 0.73 7 -0.81 17 24
NF kappa B2 p52/RelB -0.082 0.25 0.56 4 -0.6 60 64
CD4 -0.007 0.031 -10000 0 -10000 0 0
SOCS1 0.032 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.014 0.015 -10000 0 -10000 0 0
CD3D 0.003 0.05 0.21 5 -10000 0 5
CD3E -0.001 0.034 0.21 1 -10000 0 1
CD3G 0.004 0.081 -10000 0 -0.56 5 5
IL12Rbeta2/JAK2 0.028 0.075 0.3 7 -0.41 1 8
CCL3 -0.087 0.25 0.79 1 -0.81 18 19
CCL4 -0.087 0.25 0.79 1 -0.84 15 16
HLA-A 0.043 0.026 -10000 0 -10000 0 0
IL18/IL18R 0.059 0.14 0.38 15 -0.36 42 57
NOS2 -0.086 0.26 0.61 8 -0.6 62 70
IL12/IL12R/TYK2/JAK2/SPHK2 0.009 0.099 0.34 9 -0.32 9 18
IL1R1 -0.17 0.43 0.79 1 -1.2 62 63
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 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.002 0.15 0.34 21 -0.46 13 34
RAB7A -0.045 0.24 0.68 2 -0.71 24 26
lysosomal transport -0.041 0.24 0.64 4 -0.67 24 28
FOS -0.83 0.6 0.57 1 -1.2 367 368
STAT4 (dimer) -0.033 0.27 0.63 9 -0.69 38 47
STAT5A (dimer) -0.061 0.26 0.59 7 -0.61 54 61
GZMA -0.093 0.25 0.58 7 -0.59 62 69
GZMB -0.091 0.26 0.71 6 -0.86 19 25
HLX 0.025 0.038 -10000 0 -0.54 2 2
LCK -0.085 0.27 0.7 9 -0.64 56 65
TCR/CD3/MHC II/CD4 -0.12 0.16 0.27 6 -0.42 66 72
IL2/IL2R 0.088 0.056 0.38 4 -0.32 1 5
MAPK14 -0.059 0.28 0.64 8 -0.75 42 50
CCR5 -0.068 0.28 0.71 10 -0.74 40 50
IL1B 0.014 0.071 0.26 1 -0.55 5 6
STAT6 -0.039 0.18 0.38 8 -0.66 27 35
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 0.01 0.048 0.26 2 -10000 0 2
CD8A 0.005 0.009 -10000 0 -10000 0 0
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 -0.011 0.096 0.3 9 -0.34 9 18
IL2RB 0.035 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.26 0.61 10 -0.64 37 47
IL2RG 0.044 0.035 -10000 0 -10000 0 0
IL12 0.008 0.089 0.28 4 -0.41 11 15
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
CD247 -0.003 0.11 -10000 0 -0.55 15 15
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 0.22 3 -0.56 11 14
IL12/IL12R/TYK2/JAK2 -0.1 0.28 0.7 7 -0.66 60 67
MAP2K3 -0.071 0.29 0.63 8 -0.75 51 59
RIPK2 0.029 0.022 -10000 0 -10000 0 0
MAP2K6 -0.062 0.27 0.63 8 -0.71 45 53
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.012 0.034 -10000 0 -10000 0 0
IL18RAP -0.009 0.16 -10000 0 -0.55 42 42
IL12Rbeta1/TYK2 0.029 0.047 -10000 0 -10000 0 0
EOMES 0.041 0.1 -10000 0 -0.61 3 3
STAT1 (dimer) -0.012 0.26 0.68 15 -0.66 27 42
T cell proliferation -0.031 0.22 0.54 9 -0.55 39 48
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.038 0.031 -10000 0 -0.56 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.23 0.52 2 -0.61 39 41
ATF2 -0.056 0.26 0.6 8 -0.69 42 50
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.035 0.11 -10000 0 -0.37 4 4
epithelial cell differentiation 0.087 0.091 -10000 0 -10000 0 0
ITCH 0.047 0.026 -10000 0 -10000 0 0
WWP1 0.051 0.15 0.53 30 -10000 0 30
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 0.027 0.12 0.37 11 -0.47 1 12
PTPRZ1 -0.36 0.27 -10000 0 -0.54 353 353
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.016 0.1 -10000 0 -0.4 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.012 0.11 -10000 0 -0.41 7 7
ADAM17 0.047 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4 0.031 0.13 0.43 25 -0.4 2 27
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.036 0.11 0.35 1 -0.36 2 3
NCOR1 0.031 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.004 0.11 -10000 0 -0.4 6 6
GRIN2B -0.017 0.11 -10000 0 -0.41 4 4
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 0.065 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.006 0.14 -10000 0 -0.46 22 22
axon guidance 0.12 0.14 0.46 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 -0.023 0.17 -10000 0 -0.54 47 47
ErbB4/ErbB2/HBEGF 0.039 0.088 -10000 0 -10000 0 0
MAPK3 0.029 0.12 0.37 8 -0.48 1 9
STAT1 (dimer) 0.055 0.11 0.4 5 -0.36 2 7
MAPK1 0.034 0.12 0.39 11 -0.48 1 12
JAK2 0.033 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.003 0.11 -10000 0 -0.41 5 5
NRG1 -0.015 0.12 -10000 0 -0.4 41 41
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 0.46 28 -10000 0 28
neural crest cell migration 0.003 0.11 -10000 0 -0.4 5 5
ERBB2 0.021 0.028 0.3 1 -0.37 1 2
WWOX/E4ICDs 0.027 0.1 0.4 2 -0.36 2 4
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 0.096 -10000 0 -0.33 11 11
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.19 0.17 -10000 0 -0.44 44 44
ErbB4/ErbB2/epiregulin 0.048 0.095 0.36 4 -10000 0 4
ErbB4/ErbB4/betacellulin/betacellulin 0.02 0.13 -10000 0 -0.41 8 8
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.088 0.12 0.38 9 -10000 0 9
MDM2 0.028 0.12 0.35 28 -0.36 2 30
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.002 0.1 -10000 0 -0.38 5 5
STAT5A 0.11 0.12 0.41 29 -10000 0 29
ErbB4/EGFR/neuregulin 1 beta -0.15 0.18 -10000 0 -0.49 48 48
DLG4 0.031 0.011 -10000 0 -10000 0 0
GRB2/SHC 0.039 0.026 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.023 0.09 -10000 0 -0.33 2 2
STAT5A (dimer) 0.14 0.12 0.44 9 -10000 0 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.13 0.12 0.41 25 -10000 0 25
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 0.46 28 -10000 0 28
ERBB4 0.031 0.13 0.43 25 -0.4 2 27
STAT5B 0.033 0.01 -10000 0 -10000 0 0
YAP1 -0.001 0.12 0.26 7 -0.38 39 46
GRB2 0.034 0.018 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.04 0.084 -10000 0 -10000 0 0
glial cell differentiation -0.023 0.09 0.33 2 -10000 0 2
WWOX 0.034 0.03 -10000 0 -10000 0 0
cell proliferation 0.052 0.14 0.42 9 -0.43 4 13
Ceramide signaling pathway

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
SPHK2 -0.021 0.12 -10000 0 -0.4 46 46
MAP4K4 0.003 0.084 -10000 0 -0.39 7 7
BAG4 0.028 0.016 -10000 0 -10000 0 0
PKC zeta/ceramide -0.012 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 0.076 0.72 5 -10000 0 5
BAD -0.013 0.07 0.17 5 -0.28 8 13
SMPD1 0.019 0.063 0.23 7 -0.25 10 17
RB1 -0.013 0.068 0.16 3 -0.28 8 11
FADD/Caspase 8 0.032 0.12 0.29 10 -0.42 8 18
MAP2K4 -0.013 0.07 0.19 1 -0.35 6 7
NSMAF 0.028 0.028 -10000 0 -0.54 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.007 0.074 0.22 10 -0.35 4 14
EGF -0.15 0.27 -10000 0 -0.54 163 163
mol:ceramide -0.012 0.074 0.16 35 -0.28 9 44
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 -0.024 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 -0.11 0.14 -10000 0 -0.27 166 166
BID -0.015 0.19 -10000 0 -0.68 34 34
MAP3K1 -0.011 0.073 0.18 2 -0.28 10 12
EIF2A -0.005 0.073 0.25 11 -0.25 5 16
TRADD 0.03 0.012 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
MAPK3 -0.003 0.072 0.27 5 -0.32 5 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.008 0.078 0.27 5 -0.36 4 9
Cathepsin D/ceramide 0.011 0.08 0.18 4 -0.25 9 13
FADD 0.029 0.1 0.28 2 -0.41 5 7
KSR1 -0.006 0.074 0.19 10 -0.3 6 16
MAPK8 -0.008 0.07 -10000 0 -0.27 10 10
PRKRA -0.012 0.071 0.17 4 -0.27 9 13
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 0.049 0.011 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.11 0.15 -10000 0 -0.29 165 165
PRKCD 0.035 0.018 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.024 0.12 -10000 0 -0.41 47 47
RelA/NF kappa B1 0.049 0.011 -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 0.008 0.091 -10000 0 -0.32 20 20
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 -0.008 0.072 0.29 4 -0.34 4 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.027 0.082 0.21 28 -0.22 8 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 0.07 0.21 7 -0.3 5 12
TNF-alpha/TNFR1A/FAN 0.057 0.036 -10000 0 -0.33 1 1
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.022 0.094 -10000 0 -0.43 13 13
MAP2K2 -0.007 0.073 0.29 4 -0.33 4 8
SMPD3 -0.001 0.12 0.24 3 -0.3 56 59
TNF 0.038 0.023 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.021 -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 0.075 0.032 -10000 0 -0.3 1 1
AIFM1 0.026 0.082 0.21 30 -0.24 7 37
BCL2 -0.07 0.22 -10000 0 -0.54 91 91
Angiopoietin receptor Tie2-mediated signaling

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
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 0.018 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 0.034 0.005 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
F2 0.018 0.047 0.27 13 -10000 0 13
TNIP2 0.034 0.014 -10000 0 -10000 0 0
NF kappa B/RelA 0.043 0.23 -10000 0 -0.94 23 23
FN1 0.13 0.069 -10000 0 -10000 0 0
PLD2 -0.003 0.23 -10000 0 -1 23 23
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB14 0 0.19 -10000 0 -0.54 52 52
ELK1 0.006 0.22 -10000 0 -0.94 23 23
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.044 0.046 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.097 0.25 -10000 0 -0.96 23 23
CDKN1A -0.003 0.19 -10000 0 -0.68 19 19
ITGA5 0.035 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.017 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 -0.004 0.23 -10000 0 -1 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.002 0.21 -10000 0 -0.84 24 24
GRB2 0.034 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
ANGPT2 -0.074 0.23 -10000 0 -0.65 37 37
BMX -0.16 0.28 -10000 0 -1.3 23 23
ANGPT1 -0.013 0.21 -10000 0 -1.2 14 14
tube development -0.012 0.2 -10000 0 -0.73 21 21
ANGPT4 0.032 0.008 -10000 0 -10000 0 0
response to hypoxia -0.001 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.001 0.28 -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) -0.001 0.23 -10000 0 -0.85 21 21
mol:L-citrulline 0.017 0.18 -10000 0 -0.65 24 24
AGTR1 -0.18 0.3 -10000 0 -0.54 207 207
MAPK14 -0.002 0.26 -10000 0 -1 26 26
Tie2/SHP2 0.002 0.21 -10000 0 -1 15 15
TEK -0.004 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 -0.39 209 209
Tie2/Ang1/GRB2 0.012 0.24 -10000 0 -1.1 23 23
MAPK3 0.006 0.22 -10000 0 -0.93 23 23
MAPK1 -0.004 0.22 -10000 0 -0.96 23 23
Tie2/Ang1/GRB7 0.005 0.24 -10000 0 -1.1 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 -0.009 0.26 -10000 0 -1.1 25 25
Crk/Dok-R 0.018 0.24 -10000 0 -1 23 23
Tie2/Ang1/ABIN2 0.013 0.25 -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 -0.8 24 24
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.035 0.23 -10000 0 -0.82 24 24
Tie2/Ang2 -0.027 0.26 -10000 0 -1 21 21
Tie2/Ang1 0.001 0.25 -10000 0 -1.1 23 23
FOXO1 0.007 0.22 -10000 0 -0.82 25 25
ELF1 0.036 0.027 -10000 0 -10000 0 0
ELF2 0.002 0.23 -10000 0 -1 23 23
mol:Choline -0.001 0.22 -10000 0 -0.99 23 23
cell migration -0.015 0.054 -10000 0 -0.23 24 24
FYN -0.018 0.22 -10000 0 -0.84 21 21
DOK2 0.025 0.039 -10000 0 -0.54 2 2
negative regulation of cell cycle 0.002 0.18 -10000 0 -0.6 20 20
ETS1 0.031 0.056 -10000 0 -0.29 11 11
PXN 0.039 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 -0.24 14 15
MAPKKK cascade -0.001 0.22 -10000 0 -0.99 23 23
RASA1 0.034 0.012 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.004 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 -0.001 0.22 -10000 0 -0.99 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 -0.003 0.24 -10000 0 -1 23 23
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.046 0.042 -10000 0 -10000 0 0
GNB1/GNG2 -0.019 0.054 -10000 0 -0.18 48 48
AKT1 0.06 0.13 0.4 20 -0.28 12 32
EGF -0.15 0.27 -10000 0 -0.54 163 163
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.029 0.053 0.26 2 -0.23 1 3
mol:Ca2+ 0.061 0.16 0.48 18 -0.3 37 55
LYN 0.027 0.052 0.26 3 -10000 0 3
RhoA/GTP 0.025 0.067 0.2 13 -0.14 6 19
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK 0.058 0.17 0.5 17 -0.34 44 61
GNG2 0.033 0.026 -10000 0 -0.54 1 1
ARRB2 0.031 0.011 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.013 0.12 -10000 0 -0.6 15 15
G beta5/gamma2 -0.014 0.075 -10000 0 -0.24 45 45
PRKCH 0.053 0.18 0.6 10 -0.36 45 55
DNM1 0.034 0.008 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.015 0.03 -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 0.13 0.37 14 -0.46 9 23
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 0.06 0.19 0.62 10 -0.37 45 55
cell morphogenesis 0.044 0.012 -10000 0 -10000 0 0
PLCB2 0.052 0.23 0.71 8 -0.5 45 53
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.031 0.055 0.25 4 -10000 0 4
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.03 0.056 0.26 2 -0.23 1 3
RHOA 0.033 0.008 -10000 0 -10000 0 0
PTGIR 0.034 0.005 -10000 0 -10000 0 0
PRKCB1 0.056 0.18 0.61 10 -0.37 45 55
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 0.23 0.73 8 -0.51 46 54
LCK 0.038 0.061 0.25 6 -10000 0 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.044 0.042 -10000 0 -10000 0 0
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 0.04 0.042 -10000 0 -10000 0 0
MAPK14 0.052 0.13 0.4 21 -0.23 35 56
TGM2/GTP 0.056 0.2 0.65 10 -0.41 37 47
MAPK11 0.051 0.13 0.4 21 -0.24 15 36
ARHGEF1 0.047 0.11 0.36 17 -0.19 12 29
GNAI2 0.033 0.01 -10000 0 -10000 0 0
JNK cascade 0.06 0.19 0.56 14 -0.38 46 60
RAB11/GDP 0.031 0.01 -10000 0 -10000 0 0
ICAM1 0.058 0.15 0.46 20 -0.28 41 61
cAMP biosynthetic process 0.055 0.17 0.58 10 -0.34 37 47
Gq family/GTP/EBP50 0.034 0.048 0.16 2 -0.22 6 8
actin cytoskeleton reorganization 0.044 0.012 -10000 0 -10000 0 0
SRC 0.027 0.054 0.26 2 -0.23 1 3
GNB5 0.032 0.026 -10000 0 -0.54 1 1
GNB1 0.034 0.012 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.11 0.26 3 -0.28 45 48
VCAM1 0.054 0.16 0.46 19 -0.31 46 65
TP beta/Gq family/GDP/G beta5/gamma2 0.013 0.12 -10000 0 -0.6 15 15
platelet activation 0.064 0.16 0.47 21 -0.3 35 56
PGI2/IP 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.031 -10000 0 -0.27 5 5
Gq family/GDP/G beta5/gamma2 0.015 0.11 -10000 0 -0.49 17 17
TXA2/TP beta/beta Arrestin2 -0.004 0.062 -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 0.63 10 -0.42 45 55
EGFR -0.27 0.29 -10000 0 -0.54 269 269
TXA2/TP alpha 0.058 0.21 0.71 8 -0.47 38 46
Gq family/GTP 0.01 0.052 0.22 1 -0.22 18 19
YES1 0.029 0.058 0.26 2 -0.43 1 3
GNAI2/GTP 0.03 0.04 -10000 0 -0.23 5 5
PGD2/DP 0.023 0.044 -10000 0 -0.4 5 5
SLC9A3R1 0.059 0.059 -10000 0 -10000 0 0
FYN 0.026 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 0.066 0.056 -10000 0 -0.35 1 1
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 0.57 12 -0.35 40 52
PRKCB 0.054 0.17 0.53 13 -0.35 46 59
PRKCE 0.055 0.17 0.56 12 -0.36 44 56
PRKCD 0.054 0.18 0.61 10 -0.38 45 55
PRKCG 0.057 0.18 0.59 11 -0.38 45 56
muscle contraction 0.055 0.22 0.69 9 -0.47 46 55
PRKCZ 0.057 0.17 0.48 18 -0.34 46 64
ARR3 0.035 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.044 0.049 -10000 0 -0.25 6 6
PRKCQ 0.06 0.18 0.5 20 -0.35 45 65
MAPKKK cascade 0.055 0.2 0.69 8 -0.44 44 52
SELE 0.05 0.18 0.46 20 -0.38 49 69
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.049 0.29 1 -0.35 1 2
ROCK1 0.034 0.005 -10000 0 -10000 0 0
GNA14 0.044 0.068 -10000 0 -0.54 4 4
chemotaxis 0.05 0.25 0.76 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
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 0.049 0.023 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 65 65
CRKL 0.033 0.008 -10000 0 -10000 0 0
LRPAP1 0.033 0.007 -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 -0.055 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 0.034 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.071 0.084 0.24 2 -0.29 20 22
LRPAP1/LRP8 0.073 0.048 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.076 0.089 -10000 0 -0.28 22 22
DAB1/alpha3/beta1 Integrin 0.019 0.13 -10000 0 -0.3 58 58
long-term memory 0.081 0.11 -10000 0 -0.33 20 20
DAB1/LIS1 0.034 0.15 -10000 0 -0.31 64 64
DAB1/CRLK/C3G 0.02 0.14 -10000 0 -0.3 64 64
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DAB1/NCK2 0.04 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 0.084 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 8 -0.34 93 101
RELN/LRP8 0.07 0.091 0.26 1 -0.32 20 21
GRIN2B/RELN/LRP8/DAB1/Fyn 0.08 0.11 -10000 0 -0.33 23 23
PI3K 0.005 0.13 -10000 0 -0.37 51 51
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.043 0.027 -10000 0 -0.4 1 1
RAP1A -0.029 0.12 0.35 3 -0.48 5 8
PAFAH1B1 0.032 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.034 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.047 0.014 -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 0.05 0.069 0.24 3 -0.55 1 4
neuron adhesion -0.011 0.13 0.38 5 -0.46 4 9
LRP8 0.072 0.065 -10000 0 -10000 0 0
GSK3B -0.051 0.14 -10000 0 -0.5 24 24
RELN/VLDLR/DAB1/Fyn 0.005 0.15 -10000 0 -0.31 82 82
MAP3K11 0.034 0.005 -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 0.012 0.11 0.78 9 -0.5 3 12
neuron migration -0.027 0.15 0.33 7 -0.38 36 43
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.068 -10000 0 -0.55 1 1
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 80 80
IL1-mediated signaling events

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
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 -0.38 20 20
IRAK/TOLLIP 0.04 0.018 -10000 0 -10000 0 0
IKBKB 0.029 0.013 -10000 0 -10000 0 0
IKBKG 0.034 0.003 -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 -0.017 0.12 -10000 0 -0.42 41 41
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 33 33
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 0.038 0.068 -10000 0 -0.35 1 1
JUN -0.05 0.1 0.33 1 -0.27 83 84
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.025 0.2 -10000 0 -0.37 112 112
IL1 alpha/IL1R1/IL1RAP/MYD88 0.04 0.13 -10000 0 -0.32 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 -0.024 0.16 -10000 0 -0.35 91 91
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.01 0.052 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 -0.37 51 51
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 -0.024 0.16 -10000 0 -0.35 91 91
IL1 beta/IL1R2 0.007 0.12 -10000 0 -0.36 44 44
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 98 98
IRAK3 0.035 0.033 -10000 0 -0.54 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.008 0.16 -10000 0 -0.33 88 88
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 0.034 0.005 -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 0.033 0.006 -10000 0 -10000 0 0
UBE2N 0.034 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.023 0.12 -10000 0 -0.4 18 18
CASP1 -0.013 0.15 -10000 0 -0.54 38 38
IL1RN/IL1R2 0.068 0.057 0.26 6 -0.4 3 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.006 0.16 -10000 0 -0.34 89 89
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.13 -10000 0 -0.34 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 0.015 0.055 0.36 2 -0.28 10 12
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.043 0.24 8 -10000 0 8
AES 0.026 0.036 0.22 4 -10000 0 4
FBXW11 0.033 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 0.032 0.027 -10000 0 -0.54 1 1
DKK2 0.031 0.054 -10000 0 -0.54 4 4
TLE1 0.01 0.1 0.23 5 -0.55 15 20
MACF1 0.035 0.006 -10000 0 -10000 0 0
CTNNB1 0.15 0.11 0.35 30 -0.41 3 33
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
beta catenin/RanBP3 0.042 0.15 0.51 39 -0.4 3 42
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 0.34 29 -0.38 3 32
FZD1 0.034 0.026 -10000 0 -0.54 1 1
AXIN2 0.03 0.29 0.67 44 -1.2 12 56
AXIN1 0.032 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 -0.54 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.091 0.15 0.41 4 -0.59 13 17
Axin1/APC/GSK3 0.064 0.058 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.06 0.075 0.36 1 -0.43 2 3
HNF1A 0.027 0.041 0.25 6 -10000 0 6
CTBP1 0.025 0.038 0.24 4 -10000 0 4
MYC 0.099 0.44 0.62 132 -1.3 29 161
RANBP3 0.034 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.071 0.25 2 -0.31 3 5
NKD1 0.032 0.021 -10000 0 -10000 0 0
TCF4 0.019 0.076 0.24 5 -0.54 7 12
TCF3 0.027 0.042 0.26 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 0.21 0.55 32 -0.54 13 45
LEF1 0.054 0.068 0.26 10 -10000 0 10
DVL1 0.079 0.058 0.25 3 -10000 0 3
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.098 0.17 0.34 2 -0.59 15 17
DKK1/LRP6/Kremen 2 0.082 0.13 0.26 50 -0.29 41 91
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 0.76 90 -1.3 13 103
WNT1 0.035 0.005 -10000 0 -10000 0 0
GSK3A 0.035 0.005 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.035 0.008 -10000 0 -10000 0 0
PPP2R5D 0.055 0.058 -10000 0 -0.39 3 3
APC 0.038 0.063 0.38 5 -0.3 1 6
WNT1/LRP6/FZD1 0.16 0.1 0.26 62 -0.3 1 63
CREBBP 0.023 0.044 0.25 3 -0.55 1 4
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.006 -10000 0 -10000 0 0
mol:S1P 0.001 0.003 0.031 6 -10000 0 6
S1P1/S1P/Gi -0.091 0.16 -10000 0 -0.28 186 186
GNAO1 0.031 0.013 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.042 0.016 -10000 0 -10000 0 0
AKT1 -0.011 0.11 -10000 0 -0.5 17 17
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 0.006 -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 0.036 6 -10000 0 6
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.07 0.14 0.24 2 -0.34 58 60
MAPK3 -0.061 0.13 0.23 1 -0.34 47 48
MAPK1 -0.068 0.14 0.23 1 -0.33 55 56
JAK2 -0.062 0.15 0.33 1 -0.34 62 63
CXCR4 -0.064 0.14 0.25 2 -0.33 54 56
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 -0.066 0.13 0.32 2 -0.33 54 56
S1P/S1P3/Gi -0.071 0.15 0.24 2 -0.34 58 60
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.059 0.14 -10000 0 -0.32 57 57
VEGFA 0.053 0.048 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.075 0.14 -10000 0 -0.35 58 58
VEGFR1 homodimer/VEGFA homodimer 0.063 0.04 0.27 1 -10000 0 1
RHOA 0.033 0.008 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.026 0.038 -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 -10000 0 -0.54 4 4
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 -0.06 0.14 -10000 0 -0.32 58 58
Coregulation of Androgen receptor activity

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
NRIP1 0.029 0.064 -10000 0 -0.54 6 6
SVIL 0.022 0.084 -10000 0 -0.54 11 11
ZNF318 0.031 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 -0.35 65 65
CARM1 0.035 0.014 -10000 0 -10000 0 0
PRDX1 0.035 0.015 -10000 0 -10000 0 0
PELP1 0.031 0.011 -10000 0 -10000 0 0
CTNNB1 0.03 0.052 -10000 0 -0.54 4 4
AKT1 0.034 0.018 -10000 0 -10000 0 0
PTK2B 0.028 0.014 -10000 0 -10000 0 0
MED1 0.029 0.012 -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 0.028 0.015 -10000 0 -10000 0 0
NCOA6 0.034 0.008 -10000 0 -10000 0 0
DNA-PK 0.053 0.031 -10000 0 -10000 0 0
NCOA4 0.033 0.026 -10000 0 -0.54 1 1
PIAS3 0.034 0.008 -10000 0 -10000 0 0
cell proliferation 0.001 0.066 -10000 0 -0.45 5 5
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 -0.99 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 0.064 -10000 0 -0.54 6 6
TGFB1I1 0.029 0.045 -10000 0 -0.54 3 3
T-DHT/AR/CyclinD1 -0.037 0.15 -10000 0 -0.38 68 68
XRCC6 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.057 0.17 -10000 0 -0.36 82 82
CTDSP1 0.034 0.006 -10000 0 -10000 0 0
CTDSP2 0.031 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 0.059 -10000 0 -10000 0 0
NKX3-1 -0.072 0.11 -10000 0 -0.22 173 173
KLK3 0.012 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 3 -10000 0 3
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 0.035 0.03 -10000 0 -0.54 1 1
PRKDC 0.031 0.019 -10000 0 -10000 0 0
PA2G4 0.033 0.007 -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 -0.32 81 81
LATS2 0.021 0.076 -10000 0 -0.54 9 9
T-DHT/AR/PRX1 -0.034 0.13 -10000 0 -0.29 80 80
Cyclin D3/CDK11 p58 0.025 0.004 -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 0.033 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.019 0.13 -10000 0 -0.32 55 55
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 0.029 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 0.034 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
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.038 0.11 1 1 -10000 0 1
VDR 0.032 0.037 -10000 0 -0.54 2 2
FAM120B 0.032 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.062 0.077 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.09 0.09 -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 -0.032 0.13 -10000 0 -0.5 12 12
RXRs/NUR77 0.07 0.094 -10000 0 -0.3 18 18
RXRs/PPAR -0.15 0.14 -10000 0 -0.39 44 44
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RARs/VDR/DNA/Vit D3 0.014 0.14 -10000 0 -0.3 75 75
RARA 0.031 0.012 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 -10000 0 -0.54 2 2
RARs/RARs/DNA/9cRA 0.006 0.13 -10000 0 -0.29 75 75
RARG 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 0.063 0.17 0.56 52 -10000 0 52
RARs/THRs/DNA/SMRT -0.031 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 0.075 0.07 -10000 0 -0.3 4 4
NR1H4 0.035 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.1 0.089 -10000 0 -0.28 5 5
NR1H2 0.043 0.016 -10000 0 -10000 0 0
NR1H3 0.043 0.031 -10000 0 -0.54 1 1
RXRs/VDR/DNA/Vit D3 0.077 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 0.057 0.058 -10000 0 -10000 0 0
RXRG 0.031 0.056 -10000 0 -0.54 4 4
RXR alpha/CCPG 0.052 0.02 -10000 0 -10000 0 0
RXRA 0.042 0.016 -10000 0 -10000 0 0
RXRB 0.044 0.017 -10000 0 -10000 0 0
THRB 0.028 0.057 -10000 0 -0.54 5 5
PPARG -0.38 0.26 -10000 0 -0.54 368 368
PPARD 0.034 0.01 -10000 0 -10000 0 0
TNF 0.083 0.09 -10000 0 -10000 0 0
mol:Oxysterols 0.009 0.013 -10000 0 -10000 0 0
cholesterol transport 0.089 0.089 -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 -0.057 0.21 -10000 0 -0.54 80 80
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 0.07 -10000 0 -0.3 4 4
ABCA1 0.077 0.11 -10000 0 -1 2 2
RARs/THRs 0.005 0.16 -10000 0 -0.32 98 98
RXRs/FXR 0.085 0.066 -10000 0 -0.31 4 4
BCL2 -0.07 0.22 -10000 0 -0.54 91 91
Regulation of Telomerase

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
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 0.27 -10000 0 -0.46 362 362
IFNAR2 0.038 0.012 -10000 0 -10000 0 0
AKT1 -0.004 0.12 0.23 1 -0.21 103 104
ER alpha/Oestrogen -0.041 0.19 -10000 0 -0.39 110 110
NFX1/SIN3/HDAC complex 0.035 0.073 -10000 0 -0.34 12 12
EGF -0.15 0.27 -10000 0 -0.54 163 163
SMG5 0.029 0.018 -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 -0.69 11 11
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 0.2 8 -10000 0 8
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 0.013 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.03 0.16 -10000 0 -0.62 11 11
Mad/Max 0.055 0.018 -10000 0 -10000 0 0
TERT -0.005 0.18 -10000 0 -0.78 11 11
CCND1 0.036 0.26 0.57 9 -1.1 13 22
MAX 0.035 0.01 -10000 0 -10000 0 0
RBBP7 0.039 0.022 -10000 0 -10000 0 0
RBBP4 0.034 0.007 -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 0.041 0.058 -10000 0 -0.45 2 2
CDKN1B 0.042 0.11 0.28 2 -0.61 10 12
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 0.01 -10000 0 -10000 0 0
TRF2/PARP2 0.042 0.029 -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 -0.54 344 344
IFN-gamma/IRF1 0.082 0.084 0.27 29 -0.32 10 39
PARP2 0.034 0.006 -10000 0 -10000 0 0
BLM 0.074 0.067 -10000 0 -10000 0 0
Telomerase 0.005 0.093 -10000 0 -0.72 4 4
IRF1 0.045 0.048 -10000 0 -0.18 9 9
ESR1 -0.056 0.26 -10000 0 -0.54 106 106
KU/TER 0.047 0.014 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.033 -10000 0 -0.29 1 1
ubiquitin-dependent protein catabolic process 0.043 0.068 -10000 0 -0.36 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.043 0.069 -10000 0 -0.36 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 0.009 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 0.18 2 -10000 0 2
RPS6KB1 0.03 0.012 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.026 0.19 -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 0.009 -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 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.31 0.26 -10000 0 -0.46 352 352
MYC -0.002 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 0.034 0.006 -10000 0 -10000 0 0
TGFB1 0.033 0.009 -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 0.025 0.18 -10000 0 -0.7 11 11
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 -0.62 11 11
Smad3/Myc 0.005 0.081 -10000 0 -0.34 25 25
911 complex 0.062 0.026 0.26 1 -10000 0 1
IFNG 0.065 0.073 0.2 7 -0.22 9 16
Telomerase/PinX1 0.013 0.16 -10000 0 -0.62 11 11
Telomerase/AKT1/mTOR/p70S6K 0.022 0.12 0.3 1 -0.5 14 15
SIN3B 0.036 0.014 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.029 0.15 -10000 0 -0.65 9 9
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 -0.63 10 10
E2F1 0.055 0.049 -10000 0 -10000 0 0
ZNFX1 0.033 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 0.01 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
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 -0.23 241 241
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 0.004 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.041 0.094 -10000 0 -0.31 41 41
PRKG1 0.034 0.005 -10000 0 -10000 0 0
DUSP8 0.033 0.007 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.011 0.12 -10000 0 -0.33 31 31
apoptosis -0.039 0.09 -10000 0 -0.29 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 0.044 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 0.62 1 -0.39 25 26
BLK 0.039 0.044 -10000 0 -10000 0 0
HCK 0.036 0.022 -10000 0 -10000 0 0
MAP2K3 0.031 0.011 -10000 0 -10000 0 0
DUSP16 0.033 0.012 -10000 0 -10000 0 0
DUSP10 0.028 0.033 -10000 0 -0.54 1 1
TRAF6/MEKK3 0.038 0.015 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.005 0.13 0.56 1 -0.35 36 37
positive regulation of innate immune response 0 0.16 0.7 1 -0.42 32 33
LCK 0.048 0.045 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.015 0.16 0.68 1 -0.42 29 30
p38alpha-beta/MKP5 0.009 0.15 0.68 1 -0.42 27 28
PGK/cGMP 0.025 0.004 -10000 0 -10000 0 0
PAK2 0.033 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.086 0.2 -10000 0 -0.43 67 67
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 -0.32 0.28 -10000 0 -0.54 310 310
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 0.12 0.3 2 -0.63 4 6
Syndecan-4/Syndesmos 0.13 0.12 0.41 3 -0.72 4 7
positive regulation of JNK cascade 0.063 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 0.028 0.028 -10000 0 -0.54 1 1
PLG 0.012 0.04 -10000 0 -0.54 1 1
ADAM12 0.057 0.062 -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 0.43 1 -0.72 4 5
Syndecan-4/CXCL12/CXCR4 0.066 0.2 0.43 1 -0.72 6 7
Syndecan-4/Laminin alpha3 0.055 0.16 0.42 2 -0.75 5 7
MDK 0.044 0.038 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.062 0.17 0.41 1 -0.66 6 7
Syndecan-4/Midkine 0.14 0.12 0.38 7 -0.7 4 11
FZD7 -0.13 0.26 -10000 0 -0.54 145 145
Syndecan-4/FGFR1/FGF -0.066 0.16 0.4 1 -0.51 15 16
THBS1 0.038 0.025 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.14 0.12 0.39 3 -0.72 4 7
positive regulation of MAPKKK cascade 0.063 0.18 0.41 1 -0.66 6 7
Syndecan-4/TACI 0.13 0.12 0.4 3 -0.76 4 7
CXCR4 0.044 0.038 -10000 0 -10000 0 0
cell adhesion 0.091 0.071 0.27 50 -10000 0 50
Syndecan-4/Dynamin 0.14 0.12 0.43 1 -0.76 4 5
Syndecan-4/TSP1 0.14 0.12 0.42 4 -0.76 4 8
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 0.011 -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 0.03 0.22 0.71 49 -10000 0 49
Syndecan-4/alpha-Actinin 0.14 0.12 0.43 1 -0.76 4 5
TFPI -0.19 0.28 -10000 0 -0.54 197 197
F2 0.039 0.021 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.045 0.15 0.38 2 -0.69 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 0.056 0.19 0.43 1 -0.66 8 9
FGF6 0.03 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.008 -10000 0 -10000 0 0
CXCL12 -0.14 0.26 -10000 0 -0.54 151 151
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 0.31 1 -0.76 4 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.076 0.21 3 -10000 0 3
cell migration -0.013 0.009 -10000 0 -10000 0 0
PRKCD 0.016 0.035 -10000 0 -10000 0 0
vasculogenesis 0.14 0.12 0.41 4 -0.72 4 8
SDC4 0.11 0.12 0.34 2 -0.81 4 6
Syndecan-4/Tenascin C 0.14 0.12 0.4 3 -0.76 4 7
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 0.095 0.079 -10000 0 -10000 0 0
Rac1/GTP 0.092 0.072 0.27 49 -10000 0 49
cytoskeleton organization 0.13 0.12 0.39 4 -0.69 4 8
GIPC1 0.034 0.011 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.037 0.19 0.38 4 -0.62 9 13
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 0.054 -10000 0 -0.68 1 1
REL 0.037 0.024 -10000 0 -10000 0 0
HDAC7 -0.052 0.12 0.32 1 -0.33 42 43
JUN -0.067 0.22 -10000 0 -0.54 89 89
EP300 0.032 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 -0.026 0.14 0.36 1 -0.35 41 42
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 30 30
NCOA2 0.029 0.015 -10000 0 -10000 0 0
CEBPA 0.03 0.044 -10000 0 -0.54 3 3
EHMT2 0.035 0.004 -10000 0 -10000 0 0
cell proliferation 0.036 0.15 0.43 14 -0.42 4 18
NR0B1 -0.094 0.25 -10000 0 -0.54 120 120
EGR1 -0.43 0.23 -10000 0 -0.54 414 414
RXRs/9cRA 0.051 0.043 -10000 0 -0.31 4 4
AR/RACK1/Src 0.002 0.1 0.34 5 -0.34 8 13
AR/GR -0.041 0.14 -10000 0 -0.29 92 92
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 -0.37 6 7
SRC -0.011 0.073 -10000 0 -0.33 8 8
NR3C1 -0.011 0.16 -10000 0 -0.54 40 40
KLK3 -0.042 0.098 0.45 1 -10000 0 1
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 -1 123 123
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 -10000 0 -10000 0 0
NR2C2 0.035 0.015 -10000 0 -10000 0 0
KLK2 0.013 0.078 0.38 1 -10000 0 1
AR -0.025 0.11 -10000 0 -0.27 62 62
SENP1 0.034 0.004 -10000 0 -10000 0 0
HSP90AA1 0.034 0.006 -10000 0 -10000 0 0
MDM2 0.032 0.011 -10000 0 -10000 0 0
SRY -0.001 0.002 -10000 0 -0.026 4 4
GATA2 0.042 0.034 -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 0.36 5 -0.34 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 0.019 0.032 -10000 0 -0.33 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 0.38 2 -0.3 5 7
T-DHT/AR/Hsp90 -0.011 0.098 0.36 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 -0.018 0.073 0.22 16 -0.36 10 26
SIRT1 0.034 0.006 -10000 0 -10000 0 0
ZMIZ2 0.032 0.008 -10000 0 -10000 0 0
POU2F1 0.003 0.065 -10000 0 -0.18 7 7
T-DHT/AR/DAX-1 -0.072 0.17 0.36 2 -0.34 107 109
CREBBP 0.031 0.027 -10000 0 -0.54 1 1
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 0.024 0.15 -10000 0 -0.45 27 27
mol:DAG 0.005 0.13 0.32 1 -0.41 27 28
PLCG1 0.005 0.13 0.32 1 -0.42 27 28
YES1 -0.003 0.14 0.25 1 -0.48 24 25
FZD3 0.014 0.091 -10000 0 -0.54 13 13
FZD6 0.006 0.11 -10000 0 -0.54 18 18
G protein 0.035 0.15 0.35 4 -0.42 26 30
MAP3K7 -0.005 0.11 0.25 2 -0.36 25 27
mol:Ca2+ 0.005 0.13 0.31 1 -0.4 27 28
mol:IP3 0.005 0.13 0.32 1 -0.41 27 28
NLK 0.004 0.13 -10000 0 -0.8 12 12
GNB1 0.034 0.012 -10000 0 -10000 0 0
CAMK2A 0 0.12 0.27 3 -0.38 27 30
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.017 0.13 -10000 0 -0.38 45 45
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
GNAS -0.006 0.13 0.25 1 -0.46 24 25
GO:0007205 0 0.13 0.28 3 -0.41 27 30
WNT6 0.033 0.04 -10000 0 -0.54 2 2
WNT4 0.04 0.034 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.015 0.14 -10000 0 -0.46 20 20
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 -10000 0 -0.47 22 22
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.006 0.029 0.36 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 0.011 0.058 0.33 6 -0.34 1 7
MAPK12 0.008 0.086 0.21 40 -0.28 23 63
CCND1 0.008 0.085 0.21 2 -0.49 11 13
p38 gamma/SNTA1 0.027 0.086 0.39 1 -0.26 22 23
MAP2K3 0.031 0.011 -10000 0 -10000 0 0
PKN1 0.034 0.01 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.086 0.21 40 -0.28 23 63
MAP2K6 0.014 0.097 0.25 43 -0.3 24 67
MAPT 0.012 0.067 0.28 7 -0.26 9 16
MAPK13 0.017 0.028 -10000 0 -0.4 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.062 -10000 0 -0.33 17 17
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CCL5 0.029 0.06 -10000 0 -0.54 5 5
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
FGFR/FGF2/Syndecan-1 0.087 0.14 0.32 31 -0.35 7 38
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 0.32 5 -0.36 7 12
Syndecan-1/Syntenin 0.07 0.14 0.33 9 -0.37 6 15
MAPK3 0.071 0.13 0.33 10 -0.33 7 17
HGF/MET 0.006 0.13 -10000 0 -0.4 50 50
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 0.14 0.32 5 -0.36 7 12
Syndecan-1/RANTES 0.075 0.15 0.31 23 -0.39 9 32
Syndecan-1/CD147 0.092 0.15 0.36 10 -0.35 7 17
Syndecan-1/Syntenin/PIP2 0.065 0.13 0.32 8 -0.36 6 14
LAMA5 0.032 0.012 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.064 0.13 0.31 8 -0.35 6 14
MMP7 -0.042 0.19 -10000 0 -0.54 64 64
HGF 0.035 0.01 -10000 0 -10000 0 0
Syndecan-1/CASK 0.058 0.13 0.26 24 -0.33 10 34
Syndecan-1/HGF/MET 0.062 0.18 0.34 9 -0.38 31 40
regulation of cell adhesion 0.061 0.12 0.31 8 -0.33 6 14
HPSE 0.045 0.041 -10000 0 -10000 0 0
positive regulation of cell migration 0.087 0.14 0.32 31 -0.35 7 38
SDC1 0.086 0.13 0.31 28 -0.35 3 31
Syndecan-1/Collagen 0.087 0.14 0.32 31 -0.35 7 38
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 0.32 11 -0.34 6 17
homophilic cell adhesion 0.085 0.14 0.32 31 -0.35 7 38
MMP1 0.12 0.077 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.02 0.093 -10000 0 -0.46 2 2
UGCG 0.029 0.11 -10000 0 -0.64 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0.001 0.18 0.33 1 -0.42 35 36
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.03 0.11 -10000 0 -0.64 11 11
mol:DAG 0.005 0.1 -10000 0 -0.85 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.019 0.22 0.35 1 -0.51 40 41
FRAP1 -0.035 0.24 0.38 1 -0.58 43 44
FOXO3 0.006 0.18 0.38 3 -0.6 19 22
AKT1 0.003 0.2 0.39 1 -0.55 31 32
GAB2 0.028 0.014 -10000 0 -10000 0 0
SMPD1 0.009 0.12 -10000 0 -0.65 15 15
SGMS1 0.019 0.082 -10000 0 -0.61 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.028 0.097 -10000 0 -0.33 45 45
CALM1 0.034 0.006 -10000 0 -10000 0 0
cell proliferation 0.05 0.12 0.42 1 -0.53 7 8
EIF3A 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.37 51 51
RPS6KB1 0.001 0.13 -10000 0 -0.83 8 8
mol:sphingomyelin 0.005 0.1 -10000 0 -0.85 7 7
natural killer cell activation -0.002 0.005 -10000 0 -0.028 1 1
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 0.023 0.27 0.48 2 -0.92 31 33
MYB -0.047 0.34 -10000 0 -1.2 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.028 0.13 0.33 1 -0.38 14 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.035 0.13 -10000 0 -0.71 9 9
mol:PI-3-4-5-P3 0.03 0.13 0.32 1 -0.38 12 13
Rac1/GDP -0.011 0.096 -10000 0 -0.31 44 44
T cell proliferation 0.028 0.12 0.31 1 -0.36 12 13
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 0.027 0.12 0.31 1 -0.37 12 13
NF kappa B1 p50/RelA -0.008 0.22 0.37 1 -0.51 39 40
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.022 0.097 0.3 1 -0.38 9 10
HSP90AA1 0.034 0.006 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL2RA 0.039 0.035 -10000 0 -10000 0 0
IL2RB 0.035 0.024 -10000 0 -10000 0 0
TERT 0.032 0.028 -10000 0 -0.54 1 1
E2F1 0.014 0.14 0.34 1 -0.4 44 45
SOS1 0.032 0.009 -10000 0 -10000 0 0
RPS6 0.032 0.027 -10000 0 -0.54 1 1
mol:cAMP -0.002 0.014 0.032 41 -0.051 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 0.31 1 -0.36 12 13
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 0.048 0.046 -10000 0 -10000 0 0
BCL2 -0.12 0.38 0.52 1 -0.84 102 103
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.017 0.13 -10000 0 -0.38 45 45
FZD6 0.006 0.11 -10000 0 -0.54 18 18
WNT6 0.033 0.04 -10000 0 -0.54 2 2
WNT4 0.04 0.034 -10000 0 -10000 0 0
FZD3 0.014 0.091 0.18 2 -0.54 13 15
WNT5A 0.01 0.13 -10000 0 -0.54 25 25
WNT11 0.024 0.079 -10000 0 -0.54 9 9
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.038 0.15 -10000 0 -0.43 44 44
KLHL20 0.042 0.12 0.31 40 -0.26 13 53
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
Rac1/GDP 0 0.12 0.34 4 -0.3 25 29
ENAH -0.033 0.14 -10000 0 -0.43 37 37
AP1M1 0.034 0.006 -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 0.008 0.075 -10000 0 -0.29 2 2
ABI1/Sra1/Nap1 -0.016 0.04 -10000 0 -0.18 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.049 0.095 -10000 0 -0.31 26 26
RAPGEF1 -0.031 0.14 0.34 1 -0.4 38 39
CTNND1 0.033 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.033 0.16 -10000 0 -0.44 50 50
CRK -0.028 0.14 0.35 1 -0.42 44 45
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 0.055 0.042 -10000 0 -0.31 3 3
DLG1 -0.042 0.16 -10000 0 -0.44 48 48
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.061 -10000 0 -0.2 14 14
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 0.081 -10000 0 -0.26 13 13
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 -0.33 31 31
TIAM1 0.035 0.012 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.046 0.089 -10000 0 -0.29 26 26
AKT1 -0.007 0.057 -10000 0 -0.18 2 2
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
CDH1 0.007 0.12 -10000 0 -0.54 22 22
RhoA/GDP -0.001 0.12 0.33 4 -0.3 25 29
actin cytoskeleton organization 0.037 0.093 0.26 42 -0.2 10 52
CDC42/GDP -0.002 0.12 0.33 4 -0.35 6 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.004 0.067 -10000 0 -0.25 24 24
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 0.05 0.096 -10000 0 -0.31 26 26
E-cadherin/Ca2+/beta catenin/alpha catenin 0.032 0.082 -10000 0 -0.29 26 26
mol:GDP -0.02 0.12 0.33 4 -0.34 30 34
CDC42/GTP/IQGAP1 0.043 0.013 -10000 0 -10000 0 0
JUP 0.033 0.01 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.006 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 0.008 -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 0.068 0.22 20 -0.23 11 31
NME1 0.031 0.011 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.039 0.16 -10000 0 -0.44 47 47
regulation of cell-cell adhesion -0.001 0.061 -10000 0 -0.26 2 2
WASF2 0.02 0.044 0.12 31 -0.13 1 32
Rap1/GTP 0.011 0.087 0.28 1 -0.31 3 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.059 0.093 -10000 0 -0.3 21 21
CCND1 0.017 0.08 0.25 19 -0.28 11 30
VAV2 -0.021 0.19 0.42 1 -0.67 16 17
RAP1/GDP 0.009 0.1 0.31 3 -0.35 4 7
adherens junction assembly -0.036 0.16 -10000 0 -0.43 47 47
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 0.044 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 -0.04 0.16 -10000 0 -0.43 49 49
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.15 0.28 60 -0.43 16 76
E-cadherin/beta catenin/alpha catenin 0.036 0.096 -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 -0.034 0.17 -10000 0 -0.45 50 50
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 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 -0.044 0.2 -10000 0 -0.58 46 46
GNAO1 0.03 0.012 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.029 0.093 -10000 0 -0.4 22 22
SMO 0.012 0.12 -10000 0 -0.54 22 22
ARRB2 0.032 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.03 0.11 0.32 1 -0.5 8 9
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -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) -0.034 0.19 -10000 0 -0.66 27 27
SAP30 0.033 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 -10000 0 -0.54 22 22
MIM/GLI2A 0.032 0.029 0.32 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 0.016 0.084 -10000 0 -0.37 14 14
GLI3 0.017 0.11 0.34 1 -0.49 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 -0.083 0.16 -10000 0 -0.37 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) 0.025 0.11 -10000 0 -0.47 12 12
GLI2/Su(fu) 0.019 0.11 -10000 0 -0.49 10 10
FOXA2 0.016 0.12 -10000 0 -0.72 10 10
neural tube patterning -0.044 0.2 -10000 0 -0.58 46 46
SPOP 0.031 0.011 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.064 -10000 0 -0.35 1 1
GNB1 0.034 0.012 -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 0.032 0.029 0.32 1 -10000 0 1
embryonic limb morphogenesis -0.044 0.2 -10000 0 -0.58 46 46
SUFU 0.019 0.049 -10000 0 -0.38 1 1
LGALS3 -0.03 0.18 -10000 0 -0.54 56 56
catabolic process 0.037 0.13 0.35 1 -0.6 12 13
GLI3A/CBP 0.002 0.12 -10000 0 -0.36 49 49
KIF3A 0.033 0.006 -10000 0 -10000 0 0
GLI1 -0.046 0.21 -10000 0 -0.6 46 46
RAB23 0.035 0.014 -10000 0 -10000 0 0
CSNK1A1 0.034 0.006 -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 -0.01 0.13 -10000 0 -0.33 58 58
GNAZ 0.026 0.063 -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 0.028 0.088 -10000 0 -0.46 9 9
STK36 0.035 0.026 -10000 0 -0.54 1 1
Gi family/GNB1/GNG2/GDP -0.083 0.17 -10000 0 -0.4 70 70
PTCH1 -0.039 0.18 -10000 0 -0.72 16 16
MIM/GLI1 -0.026 0.18 -10000 0 -0.6 31 31
CREBBP 0.002 0.12 -10000 0 -0.36 49 49
Su(fu)/SIN3/HDAC complex 0.016 0.1 0.22 1 -0.46 15 16
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
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 0.037 -10000 0 -0.35 1 1
BIRC3 0.008 0.14 0.38 1 -0.5 25 26
CYCS 0.034 0.13 0.28 19 -0.44 14 33
RIPK1 0.034 0.006 -10000 0 -10000 0 0
CD247 0.029 0.11 0.24 17 -0.55 15 32
MAP2K7 0.038 0.19 0.34 4 -0.71 18 22
protein ubiquitination 0.015 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 9 -0.45 16 25
NF-kappa-B/RelA/I kappa B alpha 0.06 0.087 -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 0.06 0.087 -10000 0 -0.31 16 16
MAPK8 0.037 0.17 0.43 3 -0.64 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 0.27 8 -0.33 38 46
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.14 -10000 0 -0.49 17 17
CHUK 0.013 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 42 42
TCRz/NEF 0.031 0.093 0.25 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 0.035 -10000 0 -0.17 1 1
TNFR1A/BAG4/TNF-alpha 0.053 0.035 -10000 0 -10000 0 0
CASP6 0.052 0.15 -10000 0 -0.56 13 13
CASP7 0.02 0.19 0.39 18 -0.47 42 60
RELA 0.03 0.033 -10000 0 -0.17 1 1
CASP2 0.034 0.006 -10000 0 -10000 0 0
CASP3 0.016 0.19 0.4 17 -0.47 43 60
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 0.015 0.13 0.36 1 -0.46 17 18
APAF-1/Caspase 9 0.02 0.13 0.26 2 -0.38 25 27
BCL2 -0.006 0.18 0.48 5 -0.56 22 27
Signaling events mediated by PRL

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
CCNE1 0.059 0.057 -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 -0.53 17 17
PRL-3/alpha Tubulin 0.042 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.042 -10000 0 -10000 0 0
AGT 0.042 0.049 -10000 0 -10000 0 0
CCNA2 -0.18 0.12 -10000 0 -10000 0 0
TUBA1B 0.035 0.012 -10000 0 -10000 0 0
EGR1 -0.31 0.16 -10000 0 -0.39 412 412
CDK2/Cyclin E1 -0.042 0.11 -10000 0 -0.45 18 18
MAPK3 0.015 0.018 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.051 0.018 -10000 0 -10000 0 0
MAPK1 0.014 0.017 -10000 0 -10000 0 0
PTP4A1 -0.22 0.13 -10000 0 -10000 0 0
PTP4A3 0.029 0.024 -10000 0 -10000 0 0
PTP4A2 0.037 0.021 -10000 0 -10000 0 0
ITGB1 0.015 0.017 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1 -0.057 0.075 -10000 0 -0.48 7 7
Rab GGTase beta/Rab GGTase alpha 0.049 0.012 -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 -0.018 0.017 -10000 0 -10000 0 0
RHOC -0.059 0.084 -10000 0 -0.52 9 9
RHOA -0.065 0.1 -10000 0 -0.54 16 16
cell motility -0.084 0.095 0.27 1 -0.39 24 25
PRL-1/alpha Tubulin -0.21 0.12 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.039 0.034 -10000 0 -0.4 1 1
ROCK1 -0.083 0.095 0.27 1 -0.4 23 24
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
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.035 0.094 -9999 0 -0.34 25 25
E-cadherin/beta catenin 0.018 0.1 -9999 0 -0.4 26 26
CTNNB1 0.029 0.052 -9999 0 -0.54 4 4
JUP 0.033 0.01 -9999 0 -10000 0 0
CDH1 0.006 0.12 -9999 0 -0.54 22 22
Caspase cascade in apoptosis

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
TOP1 0.034 0.076 0.32 1 -0.34 9 10
ACTA1 0.007 0.083 0.24 3 -0.34 4 7
NUMA1 0.026 0.084 0.29 2 -0.37 9 11
SPTAN1 0.02 0.068 0.3 5 -0.48 1 6
LIMK1 0.033 0.074 0.28 11 -0.48 1 12
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 38 38
PTK2 0.029 0.095 0.29 2 -0.47 9 11
DIABLO 0.034 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0.02 0.068 0.3 5 -0.48 1 6
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 90 91
MADD 0.034 0.005 -10000 0 -10000 0 0
TFAP2A 0.04 0.099 -10000 0 -0.65 8 8
BID 0.013 0.025 0.16 9 -0.2 1 10
MAP3K1 0.011 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 0.07 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 -0.2 18 21
neuron apoptosis 0.008 0.15 -10000 0 -0.68 20 20
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.023 0.076 0.32 1 -0.36 4 5
APAF1 0.035 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 0.31 1 -0.47 1 2
CASP7 0.016 0.082 0.25 27 -0.29 5 32
KRT18 0.036 0.096 -10000 0 -0.73 6 6
apoptosis 0.012 0.11 0.31 2 -0.44 9 11
DFFA 0.02 0.065 0.28 3 -0.48 1 4
DFFB 0.02 0.065 0.28 3 -0.48 1 4
PARP1 0.034 0.059 0.2 18 -0.33 3 21
actin filament polymerization 0.016 0.13 0.3 13 -0.3 9 22
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.023 0.045 0.21 8 -0.23 3 11
SATB1 -0.012 0.16 -10000 0 -0.81 13 13
SLK 0.02 0.068 0.29 4 -0.38 2 6
p15 BID/BAX 0.026 0.052 -10000 0 -0.31 3 3
CASP2 0.004 0.085 0.28 2 -0.31 14 16
JNK cascade -0.011 0.094 0.37 24 -10000 0 24
CASP3 0.024 0.07 0.31 3 -0.37 2 5
LMNB2 0.019 0.13 0.35 2 -0.56 17 19
RIPK1 0.034 0.006 -10000 0 -10000 0 0
CASP4 0.025 0.058 -10000 0 -0.54 5 5
Mammalian IAPs/DIABLO 0.045 0.078 -10000 0 -0.31 17 17
negative regulation of DNA binding 0.041 0.097 -10000 0 -0.64 8 8
stress fiber formation 0.02 0.068 0.29 4 -0.37 2 6
GZMB 0.022 0.046 0.29 7 -0.4 2 9
CASP1 -0.017 0.12 -10000 0 -0.4 41 41
LMNB1 0.042 0.13 0.39 2 -0.59 12 14
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 21 -0.001 27 48
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM 0.015 0.11 0.34 1 -0.46 9 10
LMNA 0.022 0.083 0.34 2 -0.38 8 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.088 -10000 0 -0.31 18 18
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.027 0.069 0.28 4 -0.41 1 5
APAF-1/Caspase 9 0.017 0.12 -10000 0 -0.6 16 16
nuclear fragmentation during apoptosis 0.026 0.083 0.28 2 -0.36 9 11
CFL2 -0.017 0.13 0.31 8 -0.31 13 21
GAS2 -0.16 0.15 0.3 5 -0.28 246 251
positive regulation of apoptosis 0.036 0.12 0.38 2 -0.49 16 18
PRF1 0.037 0.023 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.087 0.075 0.31 1 -0.28 5 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.033 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.1 0.11 0.41 35 -10000 0 35
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.063 0.055 -10000 0 -0.34 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.004 0.097 0.17 4 -0.28 38 42
CaM/Ca2+ 0.085 0.071 -10000 0 -0.27 5 5
RAP1A 0.034 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.076 0.09 0.3 31 -0.27 5 36
AKT1 0.019 0.11 0.32 11 -0.29 32 43
MAP2K1 0.027 0.075 0.27 9 -0.26 5 14
MAP3K11 0.044 0.071 0.31 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 0.046 0.09 -10000 0 -0.44 7 7
Rap1/GTP 0.018 0.035 -10000 0 -10000 0 0
CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.095 0.076 -10000 0 -0.3 5 5
CEBPB 0.057 0.14 0.39 13 -0.59 5 18
STAT3 0.033 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.092 0.1 -10000 0 -0.7 5 5
STAT1 0.06 0.094 0.29 34 -0.27 5 39
CALM1 0.034 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.061 0.064 0.18 9 -0.55 1 10
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.075 0.09 0.31 27 -0.26 5 32
CEBPB/PTGES2/Cbp/p300 0.039 0.086 0.3 3 -0.37 5 8
mol:Ca2+ 0.082 0.072 0.3 1 -0.28 5 6
MAPK3 0.043 0.12 -10000 0 -0.63 9 9
STAT1 (dimer) 0.02 0.15 0.3 4 -0.39 37 41
MAPK1 0.01 0.2 -10000 0 -0.71 33 33
JAK2 0.036 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 0.058 0.11 0.38 19 -0.35 4 23
SMAD7 0.022 0.071 0.23 8 -0.17 10 18
CBL/CRKL/C3G 0.07 0.07 0.33 4 -10000 0 4
PI3K 0.049 0.12 -10000 0 -0.31 33 33
IFNG 0.061 0.064 0.18 9 -0.55 1 10
apoptosis 0.049 0.12 0.38 12 -0.47 8 20
CAMK2G 0.034 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.033 0.007 -10000 0 -10000 0 0
CAMK2A 0.034 0.006 -10000 0 -10000 0 0
CAMK2B 0.039 0.069 -10000 0 -0.54 5 5
FRAP1 0.003 0.1 0.31 11 -0.28 32 43
PRKCD 0.018 0.11 0.34 11 -0.29 29 40
RAP1B 0.033 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.004 0.097 0.17 4 -0.28 38 42
PTPN2 0.033 0.007 -10000 0 -10000 0 0
EP300 0.033 0.01 -10000 0 -10000 0 0
IRF1 0.066 0.12 0.39 42 -10000 0 42
STAT1 (dimer)/PIASy 0.073 0.091 0.31 27 -0.26 5 32
SOCS1 0.018 0.1 -10000 0 -1 5 5
mol:GDP 0.064 0.066 0.3 4 -10000 0 4
CASP1 0.005 0.11 0.26 11 -0.27 57 68
PTGES2 0.034 0.005 -10000 0 -10000 0 0
IRF9 0.052 0.069 0.27 18 -10000 0 18
mol:PI-3-4-5-P3 0.031 0.1 -10000 0 -0.3 33 33
RAP1/GDP 0.051 0.052 -10000 0 -10000 0 0
CBL 0.042 0.069 0.31 5 -0.27 5 10
MAP3K1 0.046 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 -0.004 0.097 0.17 4 -0.28 38 42
PTPN11 0.045 0.073 0.28 11 -0.28 5 16
CREBBP 0.032 0.027 -10000 0 -0.54 1 1
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
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 0.013 0.085 -10000 0 -0.35 25 25
MAP2K2 0.005 0.093 -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 0.086 1 -0.3 10 11
CYAA -0.011 0.043 -10000 0 -0.29 11 11
MAP2K4 -0.005 0.012 -10000 0 -0.18 1 1
IL1B -0.013 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 0.11 3 -0.29 143 146
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 0.007 0.049 0.18 37 -10000 0 37
TNF 0.038 0.023 -10000 0 -10000 0 0
VCAM1 0.012 0.086 -10000 0 -0.35 25 25
platelet activation 0.002 0.075 -10000 0 -0.4 16 16
MAPKKK cascade -0.003 0.03 0.12 3 -0.14 5 8
IL18 -0.001 0.039 -10000 0 -0.25 3 3
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 0.033 -10000 0 -0.11 35 35
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
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 0.016 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.041 0.028 -10000 0 -10000 0 0
CDKN1B 0.018 0.07 0.32 2 -0.35 7 9
CDKN1A 0.02 0.066 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 0.062 0.28 1 -0.36 6 7
AKT1 0.022 0.064 -10000 0 -0.36 9 9
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 -0.35 9 9
BAD/YWHAZ 0.05 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 -0.031 0.092 0.34 9 -10000 0 9
TSC1 0.02 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 -0.35 9 9
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.026 0.08 0.28 22 -0.34 9 31
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.002 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 -0.27 3 12
YWHAH 0.033 0.014 -10000 0 -10000 0 0
AKT1S1 0.023 0.068 -10000 0 -0.34 9 9
CASP9 0.021 0.046 -10000 0 -0.3 4 4
YWHAB 0.033 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.049 0.084 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 0.022 0.062 -10000 0 -0.36 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.056 -10000 0 -0.33 10 10
CHUK 0.02 0.061 -10000 0 -0.35 8 8
BAD/BCL-XL 0.056 0.074 0.3 2 -0.38 4 6
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 0.07 0.28 4 -0.34 9 13
MAPKKK cascade -0.054 0.075 0.34 9 -0.3 2 11
MDM2/Cbp/p300 0.06 0.082 0.36 2 -0.33 7 9
TSC1/TSC2 0.025 0.08 0.28 23 -0.33 9 32
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.078 0.35 2 -0.32 7 9
glucose import -0.15 0.15 0.21 1 -0.31 237 238
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.055 -10000 0 -0.42 2 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 0.21 1 -0.31 237 238
GSK3A 0.021 0.065 -10000 0 -0.34 9 9
FOXO1 -0.006 0.096 -10000 0 -0.43 9 9
GSK3B 0.021 0.062 0.28 1 -0.35 8 9
SFN 0.032 0.04 -10000 0 -0.54 2 2
G1/S transition of mitotic cell cycle 0.031 0.075 0.39 1 -0.34 9 10
p27Kip1/14-3-3 family 0.03 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 0.034 0.006 -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 0.03 0.027 -10000 0 -0.54 1 1
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 -0.004 0.13 0.28 1 -0.46 21 22
BAG4 0.028 0.016 -10000 0 -10000 0 0
BAD 0.007 0.047 0.18 3 -0.18 6 9
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 20 24
IKBKB 0.013 0.13 0.35 1 -0.46 14 15
MAP2K2 0.011 0.06 0.23 10 -0.24 1 11
MAP2K1 0.012 0.061 0.23 12 -0.24 1 13
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 0.14 0.32 8 -0.44 20 28
MAP2K4 0.007 0.052 0.2 3 -0.24 5 8
protein ubiquitination 0.003 0.13 0.36 3 -0.44 20 23
EnzymeConsortium:2.7.1.37 0.01 0.063 0.24 11 -0.24 2 13
response to UV 0 0.001 0.003 13 -0.002 1 14
RAF1 0.011 0.061 0.21 20 -0.23 2 22
CRADD 0.034 0.005 -10000 0 -10000 0 0
mol:ceramide 0.008 0.05 0.16 3 -0.15 20 23
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.014 -10000 0 -10000 0 0
MADD 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.054 0.2 2 -0.24 7 9
TRADD 0.03 0.012 -10000 0 -10000 0 0
RELA/p50 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.061 0.23 11 -0.24 1 12
MAPK1 0.01 0.069 0.23 12 -0.24 4 16
p50/RELA/I-kappa-B-alpha 0.048 0.016 -10000 0 -10000 0 0
FADD 0.027 0.14 0.3 8 -0.46 18 26
KSR1 0.012 0.057 0.2 15 -0.18 7 22
MAPK8 0.004 0.057 0.25 5 -0.24 5 10
TRAF2 0.035 0.012 -10000 0 -10000 0 0
response to radiation 0 0 0.003 2 -10000 0 2
CHUK -0.007 0.12 -10000 0 -0.46 18 18
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 0.07 0.18 23 -0.17 9 32
IKBKG -0.006 0.13 0.45 1 -0.46 18 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.002 0.14 -10000 0 -0.48 21 21
RELA 0.034 0.005 -10000 0 -10000 0 0
RIPK1 0.034 0.006 -10000 0 -10000 0 0
AIFM1 0.024 0.07 0.18 19 -0.18 8 27
TNF/TNF R/SODD 0.053 0.035 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to heat 0 0 0.003 2 -10000 0 2
CASP8 0.017 0.13 -10000 0 -0.65 17 17
NSMAF 0.015 0.14 0.28 5 -0.45 19 24
response to hydrogen peroxide 0 0.001 0.003 13 -0.002 1 14
BCL2 -0.07 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 5 -0.35 24 29
IKBKB 0.049 0.093 0.37 7 -0.35 2 9
AKT1 0.061 0.12 0.31 47 -0.24 3 50
IKBKG 0.056 0.078 0.38 5 -0.33 1 6
CALM1 0.031 0.087 0.28 8 -0.39 6 14
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
MAP3K1 0.067 0.14 0.4 6 -0.49 12 18
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.032 0.091 0.29 7 -0.39 7 14
DOK1 0.036 0.016 -10000 0 -10000 0 0
AP-1 -0.074 0.11 0.33 1 -0.24 74 75
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 0.089 0.3 4 -0.45 11 15
CAMK2G 0.03 0.085 0.27 1 -0.37 6 7
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.023 0.044 -10000 0 -10000 0 0
GO:0007205 0.032 0.093 0.29 7 -0.4 7 14
SYK 0.039 0.027 -10000 0 -10000 0 0
ELK1 0.033 0.091 0.28 8 -0.4 6 14
NFATC1 0.064 0.11 0.31 12 -0.41 8 20
B-cell antigen/BCR complex 0.042 0.07 0.26 3 -0.4 10 13
PAG1/CSK 0.043 0.028 0.26 1 -10000 0 1
NFKBIB 0.042 0.055 0.22 8 -0.14 5 13
HRAS 0.044 0.094 0.27 13 -0.36 7 20
NFKBIA 0.043 0.054 0.22 8 -0.13 3 11
NF-kappa-B/RelA/I kappa B beta 0.046 0.05 0.22 8 -10000 0 8
RasGAP/Csk 0.065 0.08 0.35 2 -0.39 6 8
mol:GDP 0.032 0.089 0.28 7 -0.38 7 14
PTEN 0.026 0.067 -10000 0 -0.54 7 7
CD79B 0.02 0.081 -10000 0 -0.54 10 10
NF-kappa-B/RelA/I kappa B alpha 0.046 0.05 0.22 8 -10000 0 8
GRB2 0.034 0.018 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.049 0.15 0.39 8 -0.47 16 24
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.031 0.091 0.3 6 -0.42 6 12
CSK 0.034 0.011 -10000 0 -10000 0 0
FOS -0.15 0.14 0.28 1 -0.37 57 58
CHUK 0.053 0.085 0.38 5 -0.31 7 12
IBTK 0.033 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.053 0.09 0.3 4 -0.37 5 9
PTPN6 0.031 0.1 0.3 8 -0.55 6 14
RELA 0.034 0.005 -10000 0 -10000 0 0
BCL2A1 0.042 0.045 0.22 8 -10000 0 8
VAV2 0.044 0.11 0.32 5 -0.57 6 11
ubiquitin-dependent protein catabolic process 0.045 0.055 0.22 8 -0.13 7 15
BTK 0.017 0.091 -10000 0 -0.96 4 4
CD19 0.022 0.093 0.3 5 -0.43 11 16
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 0.13 0.4 8 -0.42 12 20
SH3BP5 0.018 0.094 -10000 0 -0.54 14 14
PIK3AP1 0.029 0.096 0.33 6 -0.41 9 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.047 0.095 0.32 4 -0.44 7 11
RAF1 0.042 0.09 0.26 12 -0.4 4 16
RasGAP/p62DOK/SHIP 0.054 0.071 0.3 1 -0.37 6 7
CD79A 0.042 0.034 0.18 29 -10000 0 29
re-entry into mitotic cell cycle -0.072 0.11 0.32 1 -0.24 68 69
RASA1 0.034 0.012 -10000 0 -10000 0 0
MAPK3 0.048 0.091 0.27 19 -0.34 4 23
MAPK1 0.038 0.083 0.3 5 -0.34 4 9
CD72/SHP1 0.094 0.12 0.36 20 -0.52 6 26
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.064 0.13 0.38 9 -0.42 12 21
actin cytoskeleton organization 0.071 0.11 0.32 18 -0.49 6 24
NF-kappa-B/RelA 0.091 0.091 0.39 7 -0.23 1 8
Calcineurin 0.042 0.091 -10000 0 -0.38 5 5
PI3K -0.003 0.074 -10000 0 -0.4 7 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.032 0.095 0.32 6 -0.42 10 16
SOS1 0.034 0.004 -10000 0 -10000 0 0
Bam32/HPK1 0.063 0.16 -10000 0 -0.63 18 18
DAPP1 0.028 0.17 -10000 0 -0.7 19 19
cytokine secretion 0.063 0.11 0.3 15 -0.38 8 23
mol:DAG 0.031 0.091 0.3 6 -0.42 6 12
PLCG2 0.021 0.073 -10000 0 -0.54 8 8
MAP2K1 0.039 0.087 0.27 6 -0.37 4 10
B-cell antigen/BCR complex/FcgammaRIIB 0.046 0.074 0.29 3 -0.43 7 10
mol:PI-3-4-5-P3 0.031 0.1 0.3 22 -0.3 6 28
ETS1 0.027 0.081 0.3 3 -0.36 5 8
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.075 0.079 0.44 1 -0.3 9 10
B-cell antigen/BCR complex/LYN 0.015 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 0.062 0.11 0.32 16 -0.52 6 22
B-cell antigen/BCR complex/LYN/SYK 0.043 0.1 0.36 3 -0.53 6 9
CARD11 0.034 0.094 0.29 11 -0.4 6 17
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 0.045 0.06 0.2 25 -0.14 1 26
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDPK1 0.039 0.097 0.27 35 -0.22 4 39
PPP3CB 0.034 0.005 -10000 0 -10000 0 0
PPP3CC 0.024 0.046 -10000 0 -0.54 3 3
POU2F2 0.036 0.041 0.25 5 -10000 0 5
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.016 0.1 -9999 0 -0.54 17 17
PLK4 0.055 0.052 -9999 0 -10000 0 0
regulation of centriole replication 0.023 0.086 -9999 0 -0.38 16 16
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 0.098 -10000 0 -10000 0 0
PLK1 0.13 0.22 0.62 18 -0.86 4 22
CDKN1B 0.099 0.18 0.51 5 -0.45 15 20
FOXO3 0.11 0.23 0.56 20 -0.62 16 36
KAT2B 0.02 0.031 0.086 37 -0.056 12 49
FOXO1/SIRT1 0.006 0.1 -10000 0 -0.33 9 9
CAT 0.055 0.36 0.77 4 -1.1 39 43
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
AKT1 0.053 0.046 0.23 1 -10000 0 1
FOXO1 0.001 0.11 -10000 0 -0.35 10 10
MAPK10 0.024 0.059 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 -0.38 9 12
response to oxidative stress 0.023 0.033 0.092 37 -0.063 8 45
FOXO3A/SIRT1 0.086 0.2 0.48 15 -0.6 15 30
XPO1 0.034 0.005 -10000 0 -10000 0 0
EP300 0.035 0.01 -10000 0 -10000 0 0
BCL2L11 0.057 0.082 -10000 0 -0.82 3 3
FOXO1/SKP2 0.016 0.1 -10000 0 -0.31 10 10
mol:GDP 0.023 0.033 0.091 37 -0.063 8 45
RAN 0.035 0.005 -10000 0 -10000 0 0
GADD45A 0.082 0.21 -10000 0 -0.78 16 16
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 0.023 0.14 -10000 0 -0.48 25 25
YWHAB 0.033 0.008 -10000 0 -10000 0 0
MAPK8 0.029 0.041 0.24 2 -0.27 1 3
MAPK9 0.029 0.039 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 0.096 0.2 0.57 8 -0.55 12 20
RBL2 0.037 0.32 -10000 0 -0.85 37 37
RAL/GDP 0.058 0.036 -10000 0 -10000 0 0
CHUK 0.048 0.043 -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 0.018 -10000 0 -10000 0 0
USP7 0.032 0.011 -10000 0 -10000 0 0
IKBKB 0.041 0.041 -10000 0 -10000 0 0
CCNB1 0.15 0.24 0.61 20 -0.67 8 28
FOXO1-3a-4/beta catenin 0.094 0.22 0.55 8 -0.41 32 40
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.1 -10000 0 -0.3 10 10
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
SGK1 0.02 0.031 0.086 37 -0.056 12 49
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 -10000 0 2
SFN 0.032 0.04 -10000 0 -0.54 2 2
CDK2 0.04 0.022 0.19 1 -10000 0 1
FOXO3A/14-3-3 0.053 0.13 -10000 0 -0.48 15 15
CREBBP 0.032 0.027 -10000 0 -0.54 1 1
FBXO32 0.12 0.35 0.66 25 -1.1 26 51
BCL6 0.019 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
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.005 -10000 0 -10000 0 0
SPHK1 0.034 0.06 -10000 0 -0.54 4 4
GNAI2 0.033 0.01 -10000 0 -10000 0 0
mol:S1P 0.02 0.034 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 -0.21 3 3
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 -0.067 0.15 0.27 1 -0.34 59 60
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
GNA14 0.044 0.068 -10000 0 -0.54 4 4
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 0.023 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.034 0.006 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 65 65
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
NUDC 0.033 0.008 -10000 0 -10000 0 0
RELN/LRP8 0.07 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 0.08 0.32 3 -0.29 20 23
IQGAP1/CaM 0.047 0.014 -10000 0 -10000 0 0
DAB1 0.034 0.006 -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 -0.007 0.16 -10000 0 -0.36 80 80
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.041 0.079 0.35 4 -0.32 2 6
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 0.074 0.27 3 -0.28 13 16
RELN 0.012 0.11 -10000 0 -0.54 20 20
PAFAH/LIS1 0.04 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 0.032 0.07 -10000 0 -0.28 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.008 0.13 -10000 0 -0.3 54 54
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.025 0.075 0.31 6 -0.27 14 20
LIS1/IQGAP1 0.032 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 0.03 0.012 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.005 0.075 -10000 0 -0.36 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.047 0.088 0.39 3 -0.31 2 5
LRP8 0.072 0.065 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.034 0.083 0.42 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 0.014 -10000 0 -10000 0 0
CDK5 0.006 0.076 0.28 2 -0.3 13 15
PPP2R5D 0.034 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.029 0.012 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.002 0.15 -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
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 0.13 -10000 0 -0.48 12 12
PTK2B 0.015 0.083 0.36 2 -0.43 1 3
VEGFR2 homodimer/Frs2 0.022 0.087 -10000 0 -0.33 27 27
CAV1 -0.38 0.26 -10000 0 -0.54 365 365
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 0.051 0.13 0.39 9 -0.44 8 17
mol:Ca2+ 0.02 0.091 0.37 1 -0.5 4 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.069 0.093 -10000 0 -0.33 4 4
RP11-342D11.1 0.002 0.087 -10000 0 -0.54 4 4
CDH5 0.03 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.069 0.059 -10000 0 -0.29 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 0.081 -10000 0 -0.41 4 4
SH2D2A 0.044 0.049 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.055 0.12 -10000 0 -0.48 11 11
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.049 0.096 -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 -0.44 4 4
GRB10 0.017 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 0.044 0.046 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.067 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 -0.38 7 7
HIF1A 0.031 0.054 -10000 0 -0.54 4 4
FRS2 0.033 0.029 -10000 0 -0.54 1 1
oxygen and reactive oxygen species metabolic process 0.066 0.091 -10000 0 -0.33 4 4
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 25 25
mol:GDP 0.043 0.09 -10000 0 -0.43 4 4
mol:NADP 0.031 0.11 0.59 1 -0.45 10 11
eNOS/Hsp90 0.045 0.11 0.58 1 -0.44 9 10
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.02 0.092 0.37 1 -0.5 4 5
HIF1A/ARNT 0.037 0.043 -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 0.04 0.11 0.37 1 -0.41 4 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.033 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.068 0.096 -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 0.031 0.11 0.59 1 -0.45 10 11
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.063 0.093 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.05 0.11 -10000 0 -0.58 4 4
VEGFR2/3 heterodimer 0.023 0.087 -10000 0 -0.34 28 28
VEGFB 0.033 0.007 -10000 0 -10000 0 0
MAPK11 0.002 0.1 -10000 0 -0.48 7 7
VEGFR2 homodimer 0.003 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 0.016 0.093 0.37 1 -0.45 4 5
MAPK1 0.012 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 -0.34 28 28
KDR 0.003 0.096 -10000 0 -0.39 28 28
VEGFA165/NRP1/VEGFR2 homodimer 0.053 0.1 -10000 0 -0.54 4 4
SRC 0.033 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.017 0.097 0.37 2 -0.46 4 6
PI3K 0.018 0.12 -10000 0 -0.5 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.051 0.092 -10000 0 -0.31 24 24
FES 0.018 0.096 -10000 0 -0.56 4 4
GAB1 0.042 0.1 0.36 1 -0.46 2 3
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 0.027 0.014 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.13 0.16 -10000 0 -0.45 41 41
VEGFR2 homodimer/VEGFA homodimer/Yes 0.049 0.093 -10000 0 -0.34 5 5
PI3K/GAB1 0.03 0.14 0.39 2 -0.45 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 37 37
HSP90AA1 0.034 0.006 -10000 0 -10000 0 0
CDC42 0.018 0.096 -10000 0 -0.56 4 4
actin cytoskeleton reorganization 0.049 0.095 -10000 0 -0.31 19 19
PTK2 0.023 0.089 -10000 0 -0.44 3 3
EDG1 0.002 0.087 -10000 0 -0.54 4 4
mol:DAG 0.02 0.092 0.37 1 -0.5 4 5
CaM/Ca2+ 0.033 0.088 -10000 0 -0.47 4 4
MAP2K3 0.002 0.086 -10000 0 -0.53 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.047 0.12 -10000 0 -0.63 7 7
PLCG1 0.02 0.092 0.37 1 -0.51 4 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.068 0.094 0.37 1 -0.44 1 2
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 0.093 -10000 0 -0.31 24 24
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.049 0.092 -10000 0 -0.31 23 23
cell migration 0.043 0.1 -10000 0 -0.47 2 2
mol:PI-3-4-5-P3 0.019 0.11 -10000 0 -0.47 8 8
FYN 0.03 0.037 -10000 0 -0.54 2 2
VEGFB/NRP1 0.022 0.089 -10000 0 -0.52 4 4
mol:NO 0.031 0.11 0.59 1 -0.45 10 11
PXN 0.034 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.013 0.071 -10000 0 -0.41 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.038 0.11 -10000 0 -0.63 7 7
VHL 0.036 0.018 -10000 0 -10000 0 0
ITGB3 0.035 0.019 -10000 0 -10000 0 0
NOS3 0.03 0.12 0.6 1 -0.51 10 11
VEGFR2 homodimer/VEGFA homodimer/Sck 0.033 0.12 -10000 0 -0.32 36 36
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.006 0.08 0.37 1 -0.44 4 5
PRKCB 0.005 0.084 0.36 1 -0.48 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 0.093 -10000 0 -0.31 21 21
VEGFA165/NRP2 0.061 0.038 0.26 1 -10000 0 1
MAPKKK cascade 0.063 0.12 0.38 7 -0.56 5 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 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.11 0.44 2 -0.41 4 6
MAP3K13 0.017 0.095 -10000 0 -0.56 4 4
PDPK1 0.005 0.098 -10000 0 -0.42 8 8
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.04 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 0.033 0.008 -10000 0 -10000 0 0
MAP3K1 0.03 0.059 0.3 3 -0.3 4 7
JUN -0.04 0.13 0.43 1 -0.36 37 38
MAP3K7 0.028 0.053 0.27 3 -0.27 3 6
GRAP2 0.034 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 -0.35 19 22
LAT 0.036 0.025 -10000 0 -10000 0 0
LCP2 0.037 0.023 -10000 0 -10000 0 0
MAPK8 0.011 0.08 -10000 0 -0.58 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.036 0.061 0.3 3 -0.29 4 7
LAT/GRAP2/SLP76/HPK1/HIP-55 0.09 0.06 0.4 6 -10000 0 6
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.023 0.14 -10000 0 -10000 0 0
CRKL 0.015 0.067 0.3 3 -10000 0 3
mol:DAG 0.035 0.079 -10000 0 -10000 0 0
HRAS 0.051 0.089 0.33 12 -10000 0 12
MAPK8 0.048 0.075 0.27 13 -0.32 1 14
RAP1A 0.016 0.067 0.3 3 -10000 0 3
GAB1 0.017 0.066 0.3 2 -10000 0 2
MAPK14 0.048 0.074 0.27 13 -10000 0 13
EPO 0.047 0.052 -10000 0 -10000 0 0
PLCG1 0.026 0.075 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.028 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 0.043 0.065 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.053 0.048 -10000 0 -10000 0 0
IRS2 -0.052 0.14 -10000 0 -0.32 90 90
STAT1 0.043 0.12 -10000 0 -0.36 2 2
STAT5B 0.03 0.099 -10000 0 -10000 0 0
cell proliferation 0.026 0.081 0.26 16 -0.3 1 17
GAB1/SHIP/PIK3R1/SHP2/SHC 0.002 0.088 -10000 0 -0.27 12 12
TEC 0.016 0.067 0.3 3 -10000 0 3
SOCS3 0.019 0.087 -10000 0 -0.54 12 12
STAT1 (dimer) 0.043 0.11 -10000 0 -0.35 2 2
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 0.053 0.048 -10000 0 -10000 0 0
LYN 0.022 0.026 -10000 0 -10000 0 0
TEC/VAV2 0.033 0.073 0.29 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.028 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 0.035 0.079 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.068 0.15 -10000 0 -0.31 123 123
SH2B3 0.033 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 0.01 0.06 -10000 0 -10000 0 0
TEC/VAV2/GRB2 0.046 0.076 -10000 0 -10000 0 0
EPOR 0.028 0.024 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.066 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG2 0.021 0.073 -10000 0 -0.54 8 8
CRKL/CBL/C3G 0.039 0.077 0.3 3 -10000 0 3
VAV2 0.018 0.068 0.3 4 -10000 0 4
CBL 0.014 0.066 0.3 3 -10000 0 3
SHC/Grb2/SOS1 0.03 0.059 -10000 0 -10000 0 0
STAT5A 0.029 0.1 -10000 0 -0.32 1 1
GRB2 0.034 0.018 -10000 0 -10000 0 0
STAT5 (dimer) 0.026 0.15 -10000 0 -0.37 15 15
LYN/PLCgamma2 0.029 0.061 0.25 1 -0.4 8 9
PTPN11 0.034 0.004 -10000 0 -10000 0 0
BTK 0.021 0.071 0.3 3 -10000 0 3
BCL2 -0.09 0.36 -10000 0 -0.82 98 98
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 0.037 0.039 -10000 0 -0.34 4 4
VEGFR1 homodimer/NRP1 0.015 0.034 -10000 0 -0.33 4 4
mol:DAG 0.02 0.043 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.042 0.045 -10000 0 -0.3 3 3
CaM/Ca2+ 0.038 0.042 -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 0.043 -10000 0 -10000 0 0
NOS3 0.019 0.088 -10000 0 -0.49 6 6
CBL 0.031 0.011 -10000 0 -10000 0 0
mol:NO 0.019 0.094 -10000 0 -0.48 7 7
FLT1 0.021 0.043 -10000 0 -0.39 4 4
PGF 0.034 0.012 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.062 0.051 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
eNOS/Hsp90 0.036 0.095 -10000 0 -0.46 7 7
endothelial cell proliferation 0.027 0.072 0.37 3 -10000 0 3
mol:Ca2+ 0.02 0.043 -10000 0 -10000 0 0
MAPK3 -0.005 0.036 -10000 0 -10000 0 0
MAPK1 -0.006 0.038 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
PLGF homodimer 0.034 0.012 -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 -0.54 365 365
VEGFA homodimer 0.05 0.047 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.047 0.049 -10000 0 -0.34 3 3
platelet activating factor biosynthetic process 0.02 0.075 0.34 3 -10000 0 3
PI3K 0.038 0.11 -10000 0 -0.56 1 1
PRKCA -0.004 0.041 -10000 0 -10000 0 0
PRKCB -0.002 0.041 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.038 0.039 -10000 0 -0.34 4 4
VEGFA 0.05 0.047 -10000 0 -10000 0 0
VEGFB 0.033 0.007 -10000 0 -10000 0 0
mol:IP3 0.02 0.043 -10000 0 -10000 0 0
RASA1 0.021 0.044 -10000 0 -10000 0 0
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer 0.021 0.043 -10000 0 -0.39 4 4
VEGFB homodimer 0.033 0.007 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.16 0.16 -10000 0 -0.5 22 22
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 0.019 0.094 -10000 0 -0.48 7 7
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 -10000 0 0
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 -10000 0 0
mol:NADP 0.019 0.094 -10000 0 -0.48 7 7
HSP90AA1 0.034 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.073 0.058 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.038 0.04 -10000 0 -0.34 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 -10000 0 0
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 0.017 0.015 -10000 0 -0.28 1 1
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 -10000 0 -0.4 2 2
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 0.044 0.016 -10000 0 -10000 0 0
HIST2H4A -0.005 0.008 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.022 0.032 -10000 0 -0.21 2 2
SIRT1 0.03 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.053 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.051 0.054 -10000 0 -0.23 3 3
apoptosis -0.061 0.023 -10000 0 -10000 0 0
SIRT1/PGC1A 0.004 0.12 -10000 0 -0.34 50 50
p53/SIRT1 0.036 0.025 0.42 1 -10000 0 1
SIRT1/FOXO4 0.032 0.045 -10000 0 -0.23 3 3
FOXO1/FHL2/SIRT1 -0.019 0.16 -10000 0 -0.34 91 91
HIST1H1E 0.039 0.043 -10000 0 -0.28 1 1
SIRT1/p300 0.044 0.016 -10000 0 -10000 0 0
muscle cell differentiation -0.018 0.026 0.34 2 -10000 0 2
TP53 0.028 0.017 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.062 0.023 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
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 0.008 -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 -0.4 19 19
MAP2K4 0.015 0.085 -10000 0 -0.4 12 12
IKBKB 0.029 0.013 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.028 0.018 0.18 3 -10000 0 3
SMPD1 0.004 0.057 -10000 0 -0.27 18 18
IKBKG 0.034 0.003 -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 -0.38 20 20
TRAIL/TRAILR1 0.023 0.085 -10000 0 -0.37 21 21
TRAIL/TRAILR4 0.023 0.085 -10000 0 -0.4 19 19
TRAIL/TRAILR1/DAP3/GTP 0.031 0.067 -10000 0 -0.3 14 14
IKK complex 0.024 0.074 -10000 0 -0.42 5 5
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 0.078 -10000 0 -0.4 19 19
MAP3K1 0.016 0.1 -10000 0 -0.46 14 14
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 0.18 3 -10000 0 3
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 0.046 0.079 -10000 0 -0.3 13 13
mol:ceramide 0.004 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 17 17
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 0.033 0.073 -10000 0 -0.33 14 14
DAP3 0.028 0.014 -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 -0.4 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 0.035 0.065 -10000 0 -0.29 10 10
TRAIL/TRAILR2/FADD 0.033 0.074 -10000 0 -0.34 14 14
cell death 0.004 0.056 -10000 0 -0.26 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.002 0.081 -10000 0 -0.4 12 12
TRAILR2 (trimer) 0.027 0.016 -10000 0 -10000 0 0
CASP8 0.021 0.052 -10000 0 -0.62 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.046 0.08 -10000 0 -0.3 14 14
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.073 0.039 -9999 0 -0.32 1 1
HDAC3 0.034 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.049 0.011 -9999 0 -10000 0 0
GATA1/HDAC5 0.049 0.012 -9999 0 -10000 0 0
GATA2/HDAC5 0.054 0.027 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.024 0.12 -9999 0 -0.34 50 50
HDAC9 0.036 0.017 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.11 -9999 0 -0.34 40 40
HDAC4/ANKRA2 0.046 0.032 -9999 0 -0.32 3 3
HDAC5/YWHAB 0.046 0.015 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.022 -9999 0 -0.17 4 4
GATA2 0.042 0.034 -9999 0 -10000 0 0
HDAC4/RFXANK 0.048 0.012 -9999 0 -10000 0 0
BCOR 0.034 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.031 0.028 -9999 0 -0.54 1 1
HDAC5 0.033 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.048 0.025 -9999 0 -0.4 1 1
Histones 0.024 0.051 -9999 0 -0.28 4 4
ADRBK1 0.032 0.01 -9999 0 -10000 0 0
HDAC4 0.033 0.007 -9999 0 -10000 0 0
XPO1 0.034 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.045 0.033 -9999 0 -0.32 3 3
HDAC4/Ubc9 0.045 0.017 -9999 0 -10000 0 0
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.045 0.019 -9999 0 -10000 0 0
TUBA1B 0.035 0.012 -9999 0 -10000 0 0
HDAC6 0.034 0.003 -9999 0 -10000 0 0
HDAC5/RFXANK 0.048 0.013 -9999 0 -10000 0 0
CAMK4 0.035 0.017 -9999 0 -10000 0 0
Tubulin/HDAC6 0.06 0.057 -9999 0 -0.34 9 9
SUMO1 0.034 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.033 0.008 -9999 0 -10000 0 0
GATA1 0.034 0.003 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.031 0.01 -9999 0 -10000 0 0
NR3C1 -0.011 0.16 -9999 0 -0.54 40 40
SUMO1/HDAC4 0.051 0.051 -9999 0 -0.25 3 3
SRF 0.034 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.047 0.015 -9999 0 -10000 0 0
Tubulin 0.042 0.061 -9999 0 -0.4 9 9
HDAC4/14-3-3 E 0.045 0.019 -9999 0 -0.17 1 1
GNB1 0.034 0.012 -9999 0 -10000 0 0
RANGAP1 0.038 0.03 -9999 0 -10000 0 0
BCL6/BCoR 0.004 0.13 -9999 0 -0.4 50 50
HDAC4/HDAC3/SMRT (N-CoR2) 0.066 0.018 -9999 0 -10000 0 0
HDAC4/SRF 0.065 0.022 -9999 0 -10000 0 0
HDAC4/ER alpha -0.027 0.2 -9999 0 -0.39 110 110
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.051 -9999 0 -0.28 4 4
cell motility 0.059 0.056 -9999 0 -0.34 9 9
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.031 0.01 -9999 0 -10000 0 0
HDAC7/HDAC3 0.025 0.004 -9999 0 -10000 0 0
BCL6 -0.024 0.17 -9999 0 -0.54 51 51
HDAC4/CaMK II delta B 0.033 0.007 -9999 0 -10000 0 0
Hsp90/HDAC6 0.049 0.01 -9999 0 -10000 0 0
ESR1 -0.058 0.26 -9999 0 -0.54 106 106
HDAC6/HDAC11 0.052 0.02 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.051 0.05 -9999 0 -0.26 3 3
NPC 0.02 0.002 -9999 0 -10000 0 0
MEF2C 0.005 0.12 -9999 0 -0.54 25 25
RAN 0.034 0.005 -9999 0 -10000 0 0
HDAC4/MEF2C 0.067 0.092 -9999 0 -0.3 24 24
GNG2 0.033 0.026 -9999 0 -0.54 1 1
NCOR2 0.034 0.004 -9999 0 -10000 0 0
TUBB2A 0.024 0.076 -9999 0 -0.54 9 9
HDAC11 0.038 0.025 -9999 0 -10000 0 0
HSP90AA1 0.034 0.006 -9999 0 -10000 0 0
RANBP2 0.034 0.004 -9999 0 -10000 0 0
ANKRA2 0.031 0.037 -9999 0 -0.54 2 2
RFXANK 0.034 0.005 -9999 0 -10000 0 0
nuclear import -0.038 0.021 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.1 0.086 -10000 0 -10000 0 0
CLOCK 0.039 0.01 -10000 0 -10000 0 0
TIMELESS/CRY2 0.069 0.07 -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 0.053 -10000 0 -10000 0 0
ARNTL 0.037 0.028 -10000 0 -0.54 1 1
TIMELESS 0.059 0.091 -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 0.088 0.045 -10000 0 -0.34 1 1
BMAL1/CLOCK 0.056 0.073 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.1 0.086 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.1 0.087 -10000 0 -10000 0 0
mol:NADPH 0.021 0.03 0.11 54 -10000 0 54
PER1/TIMELESS 0.059 0.074 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.035 0.01 0.18 2 -10000 0 2
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.033 0.007 -10000 0 -10000 0 0
NFATC1 0.042 0.087 0.38 2 -0.39 6 8
NFATC2 0.002 0.074 0.29 1 -0.25 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 0.063 0.26 1 -0.27 6 7
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 0.054 0.065 -10000 0 -0.26 2 2
BCL2/BAX -0.034 0.17 -10000 0 -0.4 91 91
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 0.006 -10000 0 -10000 0 0
BAD 0.033 0.007 -10000 0 -10000 0 0
CABIN1/MEF2D 0.038 0.061 -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 -0.037 0.06 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 -0.32 1 1
MEF2D/NFAT1/Cbp/p300 0.032 0.1 -10000 0 -0.31 19 19
CABIN1 0.031 0.062 0.26 1 -0.28 6 7
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 -10000 0 -10000 0 0
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.009 -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 0.012 0.18 2 -10000 0 2
NFAT1-c-4/YWHAQ 0.043 0.1 0.32 1 -0.42 7 8
PRKCH 0.029 0.051 -10000 0 -0.54 4 4
CABIN1/Cbp/p300 0.041 0.031 -10000 0 -0.4 1 1
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 -0.003 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 0.064 -10000 0 -10000 0 0
BAD/BCL-XL 0.047 0.014 -10000 0 -10000 0 0
PRKCD 0.035 0.018 -10000 0 -10000 0 0
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 -0.4 88 88
EP300 0.03 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.056 0.087 0.34 1 -0.37 6 7
CaM/Ca2+/FKBP38 0.043 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.008 0.13 2 -10000 0 2
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 0.086 0.34 1 -0.4 4 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.065 0.064 -10000 0 -10000 0 0
NR4A1 0.024 0.14 -10000 0 -0.48 25 25
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 0.006 0.062 -10000 0 -0.31 5 5
RCH1/ KPNB1 0.062 0.047 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
PRKACA 0.034 0.006 -10000 0 -10000 0 0
AKAP5 0.04 0.051 0.18 32 -0.54 2 34
MEF2D 0.027 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 0.057 0.086 0.34 1 -0.37 6 7
CREBBP 0.029 0.029 -10000 0 -0.54 1 1
BCL2 -0.07 0.22 -10000 0 -0.54 91 91
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.25 0.28 -10000 0 -0.54 251 251
CLTC 0.034 0.056 0.27 1 -0.42 3 4
calcium ion-dependent exocytosis 0.016 0.044 0.21 1 -0.37 2 3
Dynamin 2/GTP 0.03 0.013 -10000 0 -10000 0 0
EXOC4 0.034 0.006 -10000 0 -10000 0 0
CD59 0.02 0.044 -10000 0 -0.34 2 2
CPE -0.041 0.13 -10000 0 -0.34 84 84
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 0.056 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 0.25 1 -0.29 3 4
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+ 0.029 0.013 -10000 0 -10000 0 0
JUP 0.022 0.036 -10000 0 -0.29 2 2
ASAP2/amphiphysin II 0.042 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.004 -10000 0 -10000 0 0
CDH1 0.007 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 -0.36 3 3
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 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.026 0.04 -10000 0 -0.29 2 2
clathrin heavy chain/ACAP1 0.03 0.069 0.29 4 -0.32 6 10
JIP4/KLC1 0.056 0.024 -10000 0 -10000 0 0
EXOC1 0.034 0.005 -10000 0 -10000 0 0
exocyst 0.036 0.053 -10000 0 -0.36 3 3
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 0.056 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 -0.34 17 17
EXOC6 0.034 0.027 -10000 0 -0.54 1 1
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 -10000 0 -0.42 1 1
SDC1 0.037 0.052 0.24 1 -0.36 3 4
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 0.033 0.006 -10000 0 -10000 0 0
ADRB2 -0.11 0.15 -10000 0 -0.34 30 30
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.037 0.024 -10000 0 -10000 0 0
KLC1 0.034 0.006 -10000 0 -10000 0 0
AVPR2 0.033 0.069 0.29 2 -0.38 4 6
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
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.027 0.026 -10000 0 -10000 0 0
CRKL 0.033 0.008 -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 -0.003 0.11 -10000 0 -0.32 42 42
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.37 51 51
ARF6 0.034 0.005 -10000 0 -10000 0 0
JAK2 0.043 0.034 -10000 0 -10000 0 0
PXN 0.034 0.003 -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 0.018 -10000 0 -10000 0 0
ITGB1 0.034 0.006 -10000 0 -10000 0 0
SRC 0.021 0.064 0.38 2 -0.31 11 13
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 0.039 0.069 0.37 1 -0.28 13 14
VCAM1 0.023 0.086 -10000 0 -0.54 11 11
RHOA 0.033 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.082 0.035 -10000 0 -10000 0 0
BCAR1 -0.007 0.062 0.39 2 -0.3 11 13
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 0.11 -10000 0 -0.36 25 25
Paxillin-dependent events mediated by a4b1

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
CRKL 0.033 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.03 0.013 -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 -0.032 0.16 -9999 0 -0.44 59 59
PIK3CA 0.033 0.008 -9999 0 -10000 0 0
PI3K 0.005 0.13 -9999 0 -0.37 51 51
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 0.068 0.033 -9999 0 -10000 0 0
cell adhesion 0.073 0.029 -9999 0 -10000 0 0
CRKL/CBL 0.044 0.018 -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 0.069 0.064 -9999 0 -0.3 11 11
p130Cas/Crk/Dock1 0.052 0.044 -9999 0 -0.34 3 3
VCAM1 0.023 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 0.034 -9999 0 -10000 0 0
BCAR1 0.029 0.013 -9999 0 -10000 0 0
mol:GDP -0.07 0.033 -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 59 59
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.039 0.085 0.29 4 -0.32 9 13
PDGFB-D/PDGFRB/SLAP 0.04 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.041 0.017 -10000 0 -10000 0 0
AKT1 0.025 0.12 0.38 15 -10000 0 15
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.046 0.094 0.33 4 -0.35 10 14
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
FGR 0.009 0.1 -10000 0 -0.45 17 17
mol:Ca2+ 0.036 0.092 0.34 3 -0.38 11 14
MYC 0.048 0.23 0.42 12 -0.78 29 41
SHC1 0.028 0.014 -10000 0 -10000 0 0
HRAS/GDP 0.048 0.045 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 0.036 0.093 0.34 3 -0.38 11 14
PTEN 0.026 0.067 -10000 0 -0.54 7 7
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 0.019 0.11 0.36 14 -0.34 1 15
GAB1 0.039 0.1 0.33 4 -0.4 8 12
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.037 0.096 0.38 4 -0.34 7 11
PDGFB-D/PDGFRB 0.061 0.036 -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 -0.17 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.03 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 0.036 0.093 0.34 3 -0.38 11 14
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 -0.035 0.17 -10000 0 -0.4 73 73
PTPN2 0.034 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.05 0.012 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
VAV2 0.038 0.12 0.37 3 -0.42 11 14
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 0.009 -10000 0 -10000 0 0
ACP1 0.034 0.006 -10000 0 -10000 0 0
HCK 0.024 0.075 -10000 0 -0.62 4 4
ABL1 0.032 0.096 0.33 4 -0.39 8 12
PDGFB-D/PDGFRB/CBL 0.033 0.11 0.35 1 -0.43 13 14
PTPN1 0.037 0.03 -10000 0 -10000 0 0
SNX15 0.034 0.005 -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 15 -0.68 29 44
SLA 0.029 0.025 0.18 9 -10000 0 9
actin cytoskeleton reorganization 0.05 0.06 0.42 3 -10000 0 3
SRC 0.021 0.06 -10000 0 -0.62 2 2
PI3K -0.011 0.067 -10000 0 -0.27 21 21
PDGFB-D/PDGFRB/GRB7/SHC 0.046 0.034 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.046 0.096 0.34 4 -0.36 10 14
LYN 0.021 0.055 -10000 0 -0.44 2 2
LRP1 0.034 0.004 -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 0.075 0.054 -10000 0 -10000 0 0
SPHK1 0.034 0.06 -10000 0 -0.55 4 4
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.036 0.093 0.34 3 -0.38 11 14
PLCG1 0.036 0.095 0.34 3 -0.39 11 14
NHERF/PDGFRB 0.074 0.051 -10000 0 -10000 0 0
YES1 0.009 0.11 -10000 0 -0.57 14 14
cell migration 0.073 0.05 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.067 0.056 -10000 0 -10000 0 0
SLC9A3R2 0.032 0.015 0.18 3 -10000 0 3
SLC9A3R1 0.059 0.059 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.08 0.071 -10000 0 -0.31 4 4
FYN 0.006 0.1 -10000 0 -0.47 12 12
DOK1 0.036 0.049 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.009 -10000 0 -10000 0 0
PDGFB 0.033 0.016 -10000 0 -10000 0 0
RAC1 0.024 0.16 0.37 3 -0.52 27 30
PRKCD 0.036 0.054 0.33 2 -10000 0 2
FER 0.035 0.052 0.39 1 -10000 0 1
MAPKKK cascade 0.05 0.1 0.34 24 -10000 0 24
RASA1 0.035 0.052 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 0.053 0.044 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.05 0.019 -10000 0 -10000 0 0
chemotaxis 0.032 0.095 0.33 4 -0.38 8 12
STAT1-3-5/STAT1-3-5 0.08 0.049 -10000 0 -0.29 1 1
Bovine Papilomavirus E5/PDGFRB 0.025 0.007 -10000 0 -10000 0 0
PTPRJ 0.035 0.017 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.008 0.07 -10000 0 -0.28 26 26
TRAF2/ASK1 0.022 0.087 -10000 0 -0.34 26 26
ATM 0.03 0.012 -10000 0 -10000 0 0
MAP2K3 -0.016 0.14 0.29 1 -0.41 31 32
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.13 0.27 2 -0.38 35 37
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.036 0.018 -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 -0.37 30 30
TAK1/TAB family -0.002 0.021 -10000 0 -0.21 1 1
RAC1/OSM/MEKK3 0.058 0.023 -10000 0 -10000 0 0
TRAF2 0.035 0.012 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.008 0.12 -10000 0 -0.34 22 22
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 0.017 -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 0.066 0.059 -10000 0 -0.29 10 10
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 0.066 -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 0.099 -10000 0 -0.32 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.041 0.039 -10000 0 -0.34 4 4
GRK7 0.033 0.027 -10000 0 -0.54 1 1
CNGB3 0.032 0.03 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.026 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.057 0.075 0.28 8 -0.31 2 10
Cone PDE6 0.07 0.1 -10000 0 -0.28 25 25
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 0.095 -10000 0 -0.28 29 29
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.021 0.045 -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 0.043 0.053 -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 0.098 -10000 0 -0.32 27 27
Cone CNG Channel 0.063 0.062 -10000 0 -0.29 6 6
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.033 0.01 -10000 0 -10000 0 0
RGS9 0.003 0.13 -10000 0 -0.54 26 26
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 0.4 1 -0.3 31 32
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 0.44 1 -0.29 53 54
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 0.032 -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 0.25 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 0.078 -10000 0 -0.37 8 8
VAMP2 0.031 0.011 -10000 0 -10000 0 0
SLC2A4 -0.099 0.14 0.45 1 -0.31 53 54
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
Retinoic acid receptors-mediated signaling

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.006 -10000 0 -10000 0 0
HDAC3 0.034 0.006 -10000 0 -10000 0 0
VDR 0.032 0.037 -10000 0 -0.54 2 2
Cbp/p300/PCAF 0.039 0.024 -10000 0 -0.34 1 1
EP300 0.032 0.009 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0 0.09 -10000 0 -0.3 18 18
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.008 0.12 0.27 4 -0.26 53 57
RAR alpha/9cRA/Cyclin H 0.077 0.065 -10000 0 -0.29 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.001 0.1 -10000 0 -0.35 16 16
CDC2 0 0.003 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.045 0.047 -10000 0 -0.45 1 1
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RXRs/RARs/NRIP1/9cRA 0.022 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 -10000 0 -0.54 2 2
RARG 0.035 0.008 -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 0.028 -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 0.021 0.025 0.2 1 -0.21 2 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.092 -10000 0 -0.35 13 13
PRKCA 0.033 0.019 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.027 0.13 0.49 2 -0.54 9 11
RXRG 0.021 0.033 -10000 0 -0.32 3 3
RXRA 0.039 0.054 0.23 1 -0.26 4 5
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 -0.055 0.21 -10000 0 -0.54 80 80
PRKCG 0.035 0.015 -10000 0 -10000 0 0
MNAT1 0.033 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.009 0.11 -10000 0 -0.46 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.026 0.11 -10000 0 -0.41 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.096 0.25 6 -0.31 11 17
RXRs/RARs/NRIP1/9cRA/HDAC3 0.027 0.13 0.47 2 -0.56 9 11
positive regulation of DNA binding 0.06 0.055 -10000 0 -0.27 2 2
NRIP1 0.019 0.18 0.57 2 -1.1 9 11
RXRs/RARs 0.029 0.12 0.37 3 -0.49 7 10
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 0.03 0.027 -10000 0 -0.54 1 1
RAR gamma2/9cRA 0.063 0.023 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.006 0.052 0.24 10 -10000 0 10
DAPP1 0.033 0.11 0.31 7 -0.31 20 27
Src family/SYK family/BLNK-LAT/BTK-ITK 0.043 0.14 0.37 11 -0.46 16 27
mol:DAG 0.04 0.095 0.28 31 -0.2 1 32
HRAS 0.035 0.013 -10000 0 -10000 0 0
RAP1A 0.035 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.047 0.078 -10000 0 -0.39 5 5
PLCG2 0.021 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 -0.007 0.054 0.32 6 -10000 0 6
ARF1/GTP 0.003 0.047 0.28 8 -10000 0 8
RHOA 0.033 0.008 -10000 0 -10000 0 0
YES1 0.032 0.027 -10000 0 -0.54 1 1
RAP1A/GTP -0.004 0.053 0.24 10 -10000 0 10
ADAP1 -0.007 0.05 0.3 6 -10000 0 6
ARAP3 -0.007 0.053 0.32 6 -10000 0 6
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 0.013 -10000 0 -10000 0 0
ARF1 0.027 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+ 0.024 0.06 0.22 19 -0.16 1 20
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 0.025 0.068 0.24 17 -0.23 1 18
LYN 0.03 0.015 -10000 0 -10000 0 0
ARF1/GDP 0.037 0.076 0.43 1 -0.39 5 6
RhoA/GDP 0.05 0.058 0.28 5 -10000 0 5
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 0.035 0.083 0.39 5 -0.35 3 8
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 0.024 0.065 -10000 0 -0.52 7 7
HSP90AA1 0.034 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.059 0.28 11 -10000 0 11
RhoA/GTP -0.006 0.056 0.33 5 -10000 0 5
Src family/SYK family/BLNK-LAT 0.043 0.091 0.31 11 -0.36 6 17
BLK 0.039 0.044 -10000 0 -10000 0 0
PDPK1 0.032 0.01 -10000 0 -10000 0 0
CYTH1 -0.007 0.05 0.3 6 -10000 0 6
HCK 0.036 0.022 -10000 0 -10000 0 0
CYTH3 -0.007 0.05 0.3 6 -10000 0 6
CYTH2 -0.007 0.05 0.3 6 -10000 0 6
KRAS 0.035 0.019 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.015 0.035 0.3 2 -10000 0 2
SGK1 0.019 0.043 0.34 3 -10000 0 3
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.031 0.078 0.45 1 -0.36 7 8
SOS1 0.034 0.004 -10000 0 -10000 0 0
SYK 0.039 0.027 -10000 0 -10000 0 0
ARF6/GDP 0.032 0.063 0.32 8 -10000 0 8
mol:PI-3-4-5-P3 -0.006 0.057 0.3 10 -10000 0 10
ARAP3/RAP1A/GTP -0.004 0.053 0.24 10 -10000 0 10
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 0.053 0.04 0.29 2 -10000 0 2
PLEKHA1 -0.008 0.021 -10000 0 -0.34 2 2
Rac1/GDP 0.048 0.078 -10000 0 -0.39 5 5
LAT 0.036 0.025 -10000 0 -10000 0 0
Rac1/GTP 0.027 0.083 -10000 0 -0.38 7 7
ITK -0.004 0.058 0.32 5 -0.29 2 7
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.04 0.1 0.3 24 -0.28 1 25
LCK 0.048 0.045 -10000 0 -10000 0 0
BTK -0.002 0.057 0.31 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 -0.047 0.032 -10000 0 -10000 0 0
KIRREL 0.032 0.018 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.047 0.032 -10000 0 -10000 0 0
PLCG1 0.033 0.008 -10000 0 -10000 0 0
ARRB2 0.031 0.011 -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 0.031 0.027 -10000 0 -0.24 1 1
FYN 0.065 0.096 0.29 70 -0.24 2 72
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 0.053 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 0.047 0.032 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.083 0.053 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.056 0.045 -10000 0 -0.23 1 1
NPHS1 0.049 0.032 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.056 0.043 -10000 0 -0.24 2 2
TJP1 0.032 0.026 -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 0.068 0.049 -10000 0 -10000 0 0
CD2AP 0.034 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.068 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 0.12 0.3 66 -0.31 13 79
cytoskeleton organization 0.034 0.056 0.27 9 -10000 0 9
Nephrin/NEPH1 0.04 0.026 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.058 0.042 -10000 0 -0.37 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.076 0.054 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.01 0.002 -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 0.017 0.022 -10000 0 -0.17 4 4
FKBP3 0.034 0.006 -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 0.029 0.018 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.031 0.025 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.042 0.043 -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 7 7
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 0.061 -10000 0 -0.31 6 6
NF kappa B1 p50/RelA 0.042 0.068 0.4 1 -0.33 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.042 0.034 -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 0.029 0.093 -10000 0 -0.36 13 13
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 0.033 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 0.027 0.054 -10000 0 -0.29 5 5
SIN3 complex 0.078 0.032 -10000 0 -10000 0 0
SMURF1 0.034 0.005 -10000 0 -10000 0 0
CHD3 0.031 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 0.032 0.048 -10000 0 -0.36 1 1
YY1/HDAC2 0.034 0.047 -10000 0 -0.23 5 5
YY1/HDAC1 0.034 0.05 -10000 0 -0.24 6 6
NuRD/MBD2 Complex (MeCP1) 0.039 0.058 -10000 0 -0.25 5 5
PPARG -0.21 0.16 -10000 0 -0.31 341 341
HDAC8/hEST1B 0.057 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 0.037 -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 0.03 0.027 -10000 0 -0.54 1 1
NuRD/MBD3/MBD3L2 Complex 0.041 0.08 -10000 0 -0.34 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 0.016 0.015 -10000 0 -0.28 1 1
HDAC8 0.035 0.002 -10000 0 -10000 0 0
SMAD7 0.033 0.007 -10000 0 -10000 0 0
NCOR2 0.034 0.004 -10000 0 -10000 0 0
MXD1 0.035 0.008 -10000 0 -10000 0 0
STAT3 0.023 0.019 -10000 0 -0.33 1 1
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 0.048 0.058 -10000 0 -0.25 7 7
YY1/SAP30/HDAC1 0.049 0.053 -10000 0 -0.26 2 2
EP300 0.032 0.009 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.023 0.019 -10000 0 -0.32 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.019 -10000 0 -0.27 1 1
histone deacetylation 0.038 0.061 -10000 0 -0.27 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.042 -10000 0 -10000 0 0
nuclear export -0.057 0.029 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.014 -10000 0 -10000 0 0
GATAD2A 0.037 0.022 -10000 0 -10000 0 0
GATA2/HDAC3 0.05 0.044 -10000 0 -10000 0 0
GATA1/HDAC1 0.05 0.01 -10000 0 -10000 0 0
GATA1/HDAC3 0.046 0.037 -10000 0 -10000 0 0
CHD4 0.033 0.008 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.028 0.064 -10000 0 -0.31 11 11
NuRD Complex 0.04 0.075 -10000 0 -0.31 6 6
positive regulation of chromatin silencing 0.073 0.046 -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 0.052 0.05 -10000 0 -0.25 3 3
HDAC complex 0.082 0.031 -10000 0 -10000 0 0
GATA1/Fog1 0.042 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 0.025 0.071 -10000 0 -0.32 14 14
NuRD/MBD2/PRMT5 Complex 0.039 0.058 -10000 0 -0.25 5 5
Ran/GTP/Exportin 1 0.051 0.05 -10000 0 -0.26 3 3
NF kappa B/RelA/I kappa B alpha 0.031 0.048 -10000 0 -0.32 1 1
SIN3/HDAC complex/NCoR1 0.02 0.064 -10000 0 -0.3 11 11
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 0.012 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.05 0.014 -10000 0 -10000 0 0
FBXW11 0.033 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 0.043 0.052 -10000 0 -0.26 1 1
NFKBIA 0.033 0.037 -10000 0 -0.28 1 1
MAPK14 0.034 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.03 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 0.034 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.04 0.05 -10000 0 -0.22 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.041 0.057 -10000 0 -0.29 2 2
SRC 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.37 51 51
NF kappa B1 p50/RelA 0.04 0.051 -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 0.027 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.017 0.1 -10000 0 -0.28 37 37
cell death 0.039 0.055 -10000 0 -0.28 2 2
NF kappa B1 p105/c-Rel 0.033 0.022 -10000 0 -10000 0 0
LCK 0.048 0.045 -10000 0 -10000 0 0
BCL3 0.035 0.014 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.03 0.012 -10000 0 -10000 0 0
ELF1 0.045 0.03 -10000 0 -10000 0 0
CCNA2 0.082 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 7 -0.38 7 14
SHC1 0.028 0.014 -10000 0 -10000 0 0
SP1 0.036 0.049 -10000 0 -0.36 8 8
IL2RA 0.036 0.058 -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 0.37 3 -0.73 12 15
PTPN11 0.035 0.004 -10000 0 -10000 0 0
CCND2 0.009 0.1 -10000 0 -0.77 9 9
LCK 0.049 0.045 -10000 0 -10000 0 0
GRB2 0.034 0.019 -10000 0 -10000 0 0
IL2 0.033 0.027 -10000 0 -0.54 1 1
CDK6 0.028 0.064 -10000 0 -0.54 6 6
CCND3 0.067 0.11 0.49 4 -0.45 1 5
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.035 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 0.065 0.12 0.35 6 -0.34 8 14
ERC1 0.033 0.013 -10000 0 -10000 0 0
RIP2/NOD2 0.053 0.051 0.26 3 -10000 0 3
NFKBIA 0.014 0.022 -10000 0 -0.33 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 0.02 0.13 -10000 0 -0.46 22 22
IKK complex/A20 0.04 0.15 -10000 0 -0.44 18 18
NEMO/A20/RIP2 0.029 0.022 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.031 0.15 0.37 1 -0.44 25 26
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 0.025 0.13 -10000 0 -0.43 17 17
BCL10/MALT1/TRAF6 0.064 0.021 -10000 0 -10000 0 0
NOD2 0.059 0.062 -10000 0 -10000 0 0
NFKB1 0.036 0.008 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
MALT1 0.033 0.01 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.045 0.018 -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 0.024 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.022 -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 0.033 0.14 -10000 0 -0.43 22 22
CYLD 0.03 0.012 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.036 0.14 -10000 0 -0.42 20 20
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 0.075 -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 0.31 3 -10000 0 3
NDEL1 0.031 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.041 0.035 -10000 0 -10000 0 0
NDEL1/TACC3 0.094 0.066 0.26 2 -10000 0 2
GADD45A 0.025 0.072 -10000 0 -0.54 8 8
GSK3B 0.003 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.056 0.05 -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 0.06 -10000 0 -10000 0 0
TP53 0.022 0.059 -10000 0 -10000 0 0
DLG7 0.023 0.033 -10000 0 -10000 0 0
AURKAIP1 0.034 0.013 -10000 0 -10000 0 0
ARHGEF7 0.031 0.013 -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 0.27 2 -10000 0 2
G2/M transition of mitotic cell cycle 0.04 0.035 -10000 0 -10000 0 0
AURKA 0.033 0.042 -10000 0 -10000 0 0
AURKB 0.044 0.055 -10000 0 -10000 0 0
CDC25B 0.035 0.047 -10000 0 -10000 0 0
G2/M transition checkpoint 0.016 0.028 -10000 0 -10000 0 0
mRNA polyadenylation 0.031 0.059 -10000 0 -0.28 13 13
Aurora A/CPEB 0.031 0.06 -10000 0 -0.28 13 13
Aurora A/TACC1/TRAP/chTOG 0.053 0.089 -10000 0 -0.29 18 18
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 0.091 0.065 0.25 1 -10000 0 1
spindle assembly 0.051 0.087 -10000 0 -0.29 18 18
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 0.057 0.16 64 -0.23 1 65
Aurora A/PP2A 0.052 0.037 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.028 0.036 0.27 1 -10000 0 1
negative regulation of DNA binding 0.022 0.059 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.02 -10000 0 -10000 0 0
RASA1 0.034 0.012 -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 0.033 0.042 -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 0.068 0.037 -10000 0 -10000 0 0
Aurora A/RasGAP 0.051 0.037 -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 0.003 0.027 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.059 0.044 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.11 0.059 -10000 0 -10000 0 0
PPP2R5D 0.034 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.063 0.25 3 -10000 0 3
PAK1 0.044 0.046 -10000 0 -10000 0 0
CKAP5 0.035 0.015 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.1 0.13 0.42 8 -10000 0 8
regulation of axonogenesis -0.022 0.05 0.24 1 -10000 0 1
myoblast fusion -0.065 0.074 -10000 0 -0.25 9 9
mol:GTP 0.048 0.045 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.09 0.066 -10000 0 -10000 0 0
ARF1/GTP 0.053 0.044 -10000 0 -10000 0 0
mol:GM1 0.033 0.04 -10000 0 -10000 0 0
mol:Choline 0.017 0.076 -10000 0 -0.32 20 20
lamellipodium assembly 0.056 0.079 0.25 8 -0.33 1 9
MAPK3 0.071 0.078 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.092 0.067 -10000 0 -10000 0 0
ARF1 0.027 0.014 -10000 0 -10000 0 0
ARF6/GDP 0.065 0.074 0.25 9 -10000 0 9
ARF1/GDP 0.057 0.07 -10000 0 -10000 0 0
ARF6 0.054 0.026 -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 0.073 0.08 0.22 23 -10000 0 23
actin filament bundle formation -0.075 0.064 -10000 0 -10000 0 0
KALRN 0.042 0.056 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.045 0.017 -10000 0 -10000 0 0
RhoA/GDP 0.076 0.065 -10000 0 -10000 0 0
NME1 0.035 0.015 -10000 0 -10000 0 0
Rac1/GDP 0.078 0.064 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.048 0.045 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.056 0.08 0.25 8 -0.33 1 9
RAC1 0.034 0.005 -10000 0 -10000 0 0
liver development 0.048 0.045 -10000 0 -10000 0 0
ARF6/GTP 0.048 0.045 -10000 0 -10000 0 0
RhoA/GTP 0.062 0.041 -10000 0 -10000 0 0
mol:GDP 0.052 0.077 0.22 5 -10000 0 5
ARF6/GTP/RAB11FIP3/RAB11A 0.075 0.044 -10000 0 -10000 0 0
RHOA 0.033 0.008 -10000 0 -10000 0 0
PLD1 0.029 0.087 -10000 0 -0.35 20 20
RAB11FIP3 0.031 0.01 -10000 0 -10000 0 0
tube morphogenesis 0.056 0.079 0.25 8 -0.33 1 9
ruffle organization 0.022 0.05 -10000 0 -0.24 1 1
regulation of epithelial cell migration 0.048 0.045 -10000 0 -10000 0 0
PLD2 0.042 0.045 -10000 0 -0.36 1 1
PIP5K1A 0.022 0.05 -10000 0 -0.24 1 1
mol:Phosphatidic acid 0.017 0.076 -10000 0 -0.32 20 20
Rac1/GTP 0.056 0.08 0.25 8 -0.33 1 9
Aurora C signaling

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.045 0.041 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.078 0.055 0.24 19 -10000 0 19
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.017 0.032 -10000 0 -0.31 4 4
AURKB 0.057 0.059 -10000 0 -10000 0 0
AURKC 0.036 0.019 -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 -0.006 0.022 -10000 0 -0.34 1 1
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.003 0.019 -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 -0.007 0.007 -10000 0 -10000 0 0
ADCY8 -0.004 0.015 -10000 0 -10000 0 0
PRKCE 0.009 0.001 -10000 0 -10000 0 0
ADCY9 -0.004 0.016 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.035 0.07 0.23 17 -10000 0 17
Effects of Botulinum toxin

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
STX1A 0.012 0.019 0.14 12 -10000 0 12
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 0.022 0.031 -10000 0 -0.16 1 1
RAB3GAP2/RIMS1/UNC13B 0.057 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 0.092 13 -0.12 11 24
RAB3GAP2 0.028 0.014 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.041 0.056 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.022 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 0.053 0.078 0.18 12 -0.33 9 21
SNAP25 0.007 0.035 -10000 0 -0.3 5 5
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 0.071 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 0.056 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
SMAD2 -0.007 0.052 -10000 0 -0.25 9 9
SMAD3 0.027 0.045 0.29 2 -10000 0 2
SMAD3/SMAD4 0.058 0.065 -10000 0 -0.46 3 3
SMAD4/Ubc9/PIASy 0.058 0.034 -10000 0 -0.34 1 1
SMAD2/SMAD2/SMAD4 0.064 0.075 -10000 0 -0.32 1 1
PPM1A 0.033 0.006 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.009 0.059 -10000 0 -0.3 4 4
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
TRAP-1/SMAD4 0.047 0.025 -10000 0 -0.4 1 1
MAPK3 0.032 0.009 -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 0.037 -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 0.033 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
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 0.03 -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
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.14 9 -10000 0 9
GNB1/GNG2 0.043 0.022 -10000 0 -0.34 1 1
GNB1 0.034 0.012 -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 0.045 -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 0.002 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0.015 0.036 0.17 1 -10000 0 1
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.035 0.052 0.15 1 -0.17 4 5
AP2 0.049 0.017 0.26 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.043 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 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.008 0.14 2 -10000 0 2
mol:PI-4-5-P2 0.008 0.02 -10000 0 -0.19 1 1
ARF1/GTP 0.015 0.014 -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 0.028 0.015 -10000 0 -10000 0 0
DDEF1 0.007 0.02 -10000 0 -0.2 1 1
ARF1/GDP 0.001 0.022 -10000 0 -0.11 5 5
AP2M1 0.034 0.009 0.18 1 -10000 0 1
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.008 -10000 0 -10000 0 0
Rac/GTP 0.029 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.033 0.024 -10000 0 -10000 0 0
ARFIP2 0.02 0.027 -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 0.016 0.032 -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 0.016 0.041 -10000 0 -0.23 9 9
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 0.018 0.049 -10000 0 -0.24 14 14
Arfaptin 2/Rac/GDP 0.041 0.016 -10000 0 -10000 0 0
CYTH2 -0.001 0.002 -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 0.033 -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 0.008 0.02 -10000 0 -0.19 1 1
ARF1/GTP/Membrin/GBF1/p115 0.015 0.024 -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 0.011 0.028 -10000 0 -0.31 3 3
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
BARD1 signaling events

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
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 0.033 0.008 -10000 0 -10000 0 0
FANCD2 0.024 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.089 0.059 0.33 1 -10000 0 1
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 0.026 0.11 -10000 0 -0.48 11 11
FANCF 0.034 0.006 -10000 0 -10000 0 0
BRCA1 0.036 0.022 -10000 0 -10000 0 0
CCNE1 0.059 0.057 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.068 0.047 0.26 8 -10000 0 8
FANCG 0.034 0.011 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.053 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 0.065 -10000 0 -10000 0 0
DNA repair 0.074 0.1 0.33 9 -0.38 3 12
BRCA1/BARD1/ubiquitin 0.053 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 0.024 0.073 -10000 0 -0.31 3 3
BRCA1/BACH1/BARD1/TopBP1 0.069 0.028 0.26 1 -10000 0 1
BRCA1/BARD1/P53 0.078 0.039 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.064 0.032 -10000 0 -10000 0 0
BRCA1/BACH1 0.036 0.021 -10000 0 -10000 0 0
BARD1 0.037 0.023 -10000 0 -10000 0 0
PCNA 0.037 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.069 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.067 0.029 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.13 0.071 0.35 2 -10000 0 2
BARD1/DNA-PK/P53 0.076 0.051 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.053 0.025 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.049 0.039 -10000 0 -0.32 2 2
FA complex 0.043 0.054 -10000 0 -0.3 2 2
BARD1/EWS 0.05 0.02 -10000 0 -10000 0 0
RBBP8 0.013 0.028 -10000 0 -0.4 2 2
TP53 0.031 0.015 -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 0.098 0.064 0.35 1 -10000 0 1
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 0.053 0.025 -10000 0 -10000 0 0
EWSR1 0.032 0.009 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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
Glypican 2 network

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
MDK 0.044 0.038 -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 S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.014 -10000 0 -10000 0 0
MDM2/SUMO1 0.049 0.053 -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 0.035 -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 0.052 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 0.017 0.022 -10000 0 -0.17 4 4
Ran/GTP 0.036 0.047 -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
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
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 0.014 -10000 0 -10000 0 0
HIF1A/p53 0.046 0.06 -10000 0 -0.31 2 2
HIF1A 0.03 0.05 -10000 0 -0.28 5 5
COPS5 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.07 0.051 -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 0.022 -10000 0 -10000 0 0
HIF1AN 0.034 0.005 -10000 0 -10000 0 0
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.033 0.056 -10000 0 -0.28 7 7
CUL2 0.034 0.006 -10000 0 -10000 0 0
OS9 0.034 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.053 0.031 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.05 0.059 -10000 0 -0.31 2 2
PHD1-3/OS9 0.076 0.06 -10000 0 -0.32 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.058 0.065 -10000 0 -0.32 1 1
VHL 0.036 0.018 -10000 0 -10000 0 0
HSP90AA1 0.034 0.006 -10000 0 -10000 0 0
HIF1A/JAB1 0.04 0.059 -10000 0 -0.31 2 2
EGLN3 0.06 0.064 -10000 0 -0.54 1 1
EGLN2 0.035 0.017 -10000 0 -10000 0 0
EGLN1 0.027 0.014 -10000 0 -10000 0 0
TP53 0.031 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.043 0.069 -10000 0 -0.47 7 7
ARNT 0.027 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 0.068 0.27 2 -0.27 1 3
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 -0.16 1 1
FBXW11 0.033 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
NF kappa B2 p100/RelB 0.095 0.036 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAP3K14 0.033 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelB 0.051 0.017 -10000 0 -10000 0 0
RELB 0.037 0.02 -10000 0 -10000 0 0
NFKB2 0.035 0.012 -10000 0 -10000 0 0
NF kappa B2 p52/RelB 0.047 0.018 0.23 1 -10000 0 1
regulation of B cell activation 0.047 0.017 0.23 1 -10000 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 0.039 0.039 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 -0.32 0.18
30_TGFB1/TGF beta receptor Type II 0.034 0.034 0.034 0.034
84_STAT5B -0.21 -0.0033 -0.03 -0.21
84_STAT5A -0.21 -0.0033 -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/5948102/GDAC_MergeDataFiles_3799172/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/6154449/Gistic2_Analysis_6154752/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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