PARADIGM pathway analysis of mRNASeq expression data
Brain Lower Grade Glioma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C11C1VHM
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C11C1VHM
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 63 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
IL23-mediated signaling events 115
Ephrin A reverse signaling 111
TCGA08_retinoblastoma 88
FOXM1 transcription factor network 86
IL12-mediated signaling events 83
Aurora B signaling 78
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 71
Effects of Botulinum toxin 69
Syndecan-1-mediated signaling events 68
E-cadherin signaling events 68
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 463 . 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 ( 463 ).

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
IL23-mediated signaling events 0.2484 115 6913 60 -0.7 0.014 1000 -1000 -0.14 -1000
Ephrin A reverse signaling 0.2397 111 780 7 -0.14 0 1000 -1000 -0.024 -1000
TCGA08_retinoblastoma 0.1901 88 704 8 -0.1 0.077 1000 -1000 -0.011 -1000
FOXM1 transcription factor network 0.1857 86 4421 51 -0.42 0.027 1000 -1000 -0.18 -1000
IL12-mediated signaling events 0.1793 83 7231 87 -0.57 0.12 1000 -1000 -0.12 -1000
Aurora B signaling 0.1685 78 5275 67 -0.35 0.014 1000 -1000 -0.073 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1533 71 4836 68 -0.48 0.22 1000 -1000 -0.11 -1000
Effects of Botulinum toxin 0.1490 69 1804 26 -0.2 0.014 1000 -1000 -0.061 -1000
Syndecan-1-mediated signaling events 0.1469 68 2329 34 -0.23 0.014 1000 -1000 -0.053 -1000
E-cadherin signaling events 0.1469 68 343 5 -0.12 0.014 1000 -1000 -0.046 -1000
TCR signaling in naïve CD8+ T cells 0.1425 66 6149 93 -0.22 0.072 1000 -1000 -0.077 -1000
IL4-mediated signaling events 0.1382 64 5869 91 -0.61 0.44 1000 -1000 -0.12 -1000
Signaling events mediated by the Hedgehog family 0.1339 62 3249 52 -0.19 0.16 1000 -1000 -0.074 -1000
Glypican 2 network 0.1166 54 218 4 -0.065 -0.018 1000 -1000 -0.028 -1000
Syndecan-4-mediated signaling events 0.1123 52 3536 67 -0.19 0.038 1000 -1000 -0.095 -1000
Thromboxane A2 receptor signaling 0.1102 51 5435 105 -0.22 0.061 1000 -1000 -0.058 -1000
Signaling events regulated by Ret tyrosine kinase 0.1058 49 4048 82 -0.18 0.014 1000 -1000 -0.076 -1000
Signaling mediated by p38-alpha and p38-beta 0.1058 49 2197 44 -0.14 0.014 1000 -1000 -0.046 -1000
a4b1 and a4b7 Integrin signaling 0.1037 48 244 5 -0.081 -0.034 1000 -1000 -0.033 -1000
amb2 Integrin signaling 0.0994 46 3792 82 -0.24 0.014 1000 -1000 -0.077 -1000
Endothelins 0.0972 45 4329 96 -0.2 0.014 1000 -1000 -0.076 -1000
Caspase cascade in apoptosis 0.0950 44 3318 74 -0.19 0.05 1000 -1000 -0.043 -1000
Glypican 1 network 0.0929 43 2070 48 -0.17 0.03 1000 -1000 -0.049 -1000
Visual signal transduction: Cones 0.0907 42 1608 38 -0.16 0.017 1000 -1000 -0.061 -1000
FOXA2 and FOXA3 transcription factor networks 0.0907 42 1966 46 -0.27 0.02 1000 -1000 -0.059 -1000
Reelin signaling pathway 0.0907 42 2378 56 -0.29 0.014 1000 -1000 -0.082 -1000
Visual signal transduction: Rods 0.0907 42 2187 52 -0.21 0.014 1000 -1000 -0.079 -1000
HIF-1-alpha transcription factor network 0.0886 41 3137 76 -0.19 0.09 1000 -1000 -0.079 -1000
EGFR-dependent Endothelin signaling events 0.0886 41 871 21 -0.11 0.014 1000 -1000 -0.063 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0864 40 3452 85 -0.14 0.014 1000 -1000 -0.066 -1000
Calcium signaling in the CD4+ TCR pathway 0.0864 40 1270 31 -0.18 0.014 1000 -1000 -0.076 -1000
p75(NTR)-mediated signaling 0.0842 39 4973 125 -0.16 0.014 1000 -1000 -0.085 -1000
Aurora C signaling 0.0842 39 277 7 -0.17 0 1000 -1000 -0.039 -1000
PDGFR-alpha signaling pathway 0.0842 39 1735 44 -0.17 0.028 1000 -1000 -0.051 -1000
Arf6 signaling events 0.0821 38 2364 62 -0.21 0.014 1000 -1000 -0.056 -1000
IL1-mediated signaling events 0.0821 38 2368 62 -0.19 0.065 1000 -1000 -0.083 -1000
Ras signaling in the CD4+ TCR pathway 0.0821 38 647 17 -0.13 0.021 1000 -1000 -0.038 -1000
Glucocorticoid receptor regulatory network 0.0799 37 4295 114 -0.45 0.25 1000 -1000 -0.06 -1000
PLK1 signaling events 0.0778 36 3068 85 -0.18 0.042 1000 -1000 -0.044 -1000
Osteopontin-mediated events 0.0756 35 1334 38 -0.13 0.016 1000 -1000 -0.096 -1000
IL6-mediated signaling events 0.0756 35 2625 75 -0.16 0.065 1000 -1000 -0.067 -1000
LPA receptor mediated events 0.0713 33 3446 102 -0.19 0.018 1000 -1000 -0.079 -1000
PLK2 and PLK4 events 0.0691 32 98 3 -0.017 -0.012 1000 -1000 -0.012 -1000
TCGA08_p53 0.0691 32 225 7 -0.078 0.05 1000 -1000 -0.013 -1000
Nongenotropic Androgen signaling 0.0691 32 1698 52 -0.1 0.033 1000 -1000 -0.05 -1000
BCR signaling pathway 0.0691 32 3259 99 -0.18 0.03 1000 -1000 -0.087 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0648 30 1146 37 -0.14 0.014 1000 -1000 -0.051 -1000
BMP receptor signaling 0.0626 29 2413 81 -0.18 0.05 1000 -1000 -0.084 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0605 28 1458 52 -0.19 0.026 1000 -1000 -0.057 -1000
Fc-epsilon receptor I signaling in mast cells 0.0583 27 2620 97 -0.19 0.041 1000 -1000 -0.074 -1000
Retinoic acid receptors-mediated signaling 0.0583 27 1592 58 -0.19 0.016 1000 -1000 -0.067 -1000
ErbB2/ErbB3 signaling events 0.0562 26 1722 65 -0.17 0.023 1000 -1000 -0.06 -1000
Coregulation of Androgen receptor activity 0.0562 26 2011 76 -0.14 0.028 1000 -1000 -0.037 -1000
FAS signaling pathway (CD95) 0.0562 26 1222 47 -0.16 0.016 1000 -1000 -0.043 -1000
Wnt signaling 0.0562 26 186 7 -0.036 -0.017 1000 -1000 -0.029 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0562 26 2306 88 -0.18 0.019 1000 -1000 -0.12 -1000
Rapid glucocorticoid signaling 0.0562 26 538 20 -0.18 0.014 1000 -1000 -0.033 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0562 26 3130 120 -0.21 0.13 1000 -1000 -0.067 -1000
LPA4-mediated signaling events 0.0540 25 308 12 -0.055 0.014 1000 -1000 -0.018 -1000
Regulation of nuclear SMAD2/3 signaling 0.0540 25 3484 136 -0.22 0.22 1000 -1000 -0.059 -1000
Syndecan-2-mediated signaling events 0.0540 25 1781 69 -0.17 0.037 1000 -1000 -0.047 -1000
S1P5 pathway 0.0540 25 437 17 -0.14 0.057 1000 -1000 -0.05 -1000
IL2 signaling events mediated by STAT5 0.0540 25 567 22 -0.098 0.019 1000 -1000 -0.042 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0497 23 783 34 -0.063 0.014 1000 -1000 -0.063 -1000
JNK signaling in the CD4+ TCR pathway 0.0497 23 394 17 -0.079 0.014 1000 -1000 -0.059 -1000
Cellular roles of Anthrax toxin 0.0475 22 860 39 -0.16 0.019 1000 -1000 -0.026 -1000
Presenilin action in Notch and Wnt signaling 0.0475 22 1372 61 -0.28 0.032 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class III 0.0475 22 911 40 -0.12 0.1 1000 -1000 -0.04 -1000
IL27-mediated signaling events 0.0475 22 1122 51 -0.16 0.019 1000 -1000 -0.073 -1000
Signaling events mediated by PTP1B 0.0454 21 1644 76 -0.16 0.02 1000 -1000 -0.071 -1000
IL2 signaling events mediated by PI3K 0.0454 21 1256 58 -0.096 0.033 1000 -1000 -0.076 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0432 20 1109 54 -0.16 0.029 1000 -1000 -0.094 -1000
Noncanonical Wnt signaling pathway 0.0432 20 539 26 -0.12 0.014 1000 -1000 -0.065 -1000
Integrins in angiogenesis 0.0432 20 1753 84 -0.095 0.014 1000 -1000 -0.082 -1000
Canonical Wnt signaling pathway 0.0432 20 1022 51 -0.28 0.1 1000 -1000 -0.056 -1000
Paxillin-dependent events mediated by a4b1 0.0410 19 709 36 -0.14 0.033 1000 -1000 -0.059 -1000
E-cadherin signaling in the nascent adherens junction 0.0410 19 1516 76 -0.12 0.014 1000 -1000 -0.077 -1000
ErbB4 signaling events 0.0389 18 1297 69 -0.16 0.043 1000 -1000 -0.083 -1000
Ceramide signaling pathway 0.0389 18 1391 76 -0.16 0.023 1000 -1000 -0.063 -1000
S1P1 pathway 0.0389 18 665 36 -0.099 0.014 1000 -1000 -0.048 -1000
TCGA08_rtk_signaling 0.0389 18 485 26 -0.14 0.029 1000 -1000 -0.02 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0389 18 1474 78 -0.065 0.04 1000 -1000 -0.067 -1000
Ephrin B reverse signaling 0.0367 17 853 48 -0.11 0.082 1000 -1000 -0.066 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0346 16 473 28 -0.14 0.024 1000 -1000 -0.04 -1000
Aurora A signaling 0.0346 16 995 60 -0.14 0.033 1000 -1000 -0.058 -1000
TRAIL signaling pathway 0.0346 16 772 48 -0.046 0.031 1000 -1000 -0.066 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0346 16 1367 83 -0.19 0.053 1000 -1000 -0.069 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0346 16 762 45 -0.16 0.03 1000 -1000 -0.075 -1000
E-cadherin signaling in keratinocytes 0.0346 16 696 43 -0.12 0.026 1000 -1000 -0.062 -1000
S1P4 pathway 0.0324 15 389 25 -0.14 0.029 1000 -1000 -0.05 -1000
Signaling mediated by p38-gamma and p38-delta 0.0302 14 221 15 -0.023 0.027 1000 -1000 -0.024 -1000
Syndecan-3-mediated signaling events 0.0302 14 511 35 -0.17 0.014 1000 -1000 -0.061 -1000
EPHB forward signaling 0.0302 14 1212 85 -0.11 0.037 1000 -1000 -0.087 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0302 14 1105 74 -0.16 0.063 1000 -1000 -0.087 -1000
Regulation of Telomerase 0.0302 14 1477 102 -0.14 0.046 1000 -1000 -0.099 -1000
Insulin-mediated glucose transport 0.0281 13 432 32 -0.12 0.035 1000 -1000 -0.067 -1000
Regulation of p38-alpha and p38-beta 0.0281 13 730 54 -0.11 0.014 1000 -1000 -0.054 -1000
Plasma membrane estrogen receptor signaling 0.0281 13 1171 86 -0.056 0.031 1000 -1000 -0.076 -1000
BARD1 signaling events 0.0259 12 732 57 -0.053 0.029 1000 -1000 -0.057 -1000
ceramide signaling pathway 0.0259 12 589 49 -0.16 0.021 1000 -1000 -0.038 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0259 12 420 33 -0.11 0.042 1000 -1000 -0.062 -1000
Regulation of Androgen receptor activity 0.0238 11 820 70 -0.14 0.033 1000 -1000 -0.06 -1000
EPO signaling pathway 0.0216 10 594 55 -0.12 0.057 1000 -1000 -0.083 -1000
Nectin adhesion pathway 0.0216 10 653 63 -0.12 0.048 1000 -1000 -0.073 -1000
Class I PI3K signaling events 0.0216 10 773 73 -0.11 0.029 1000 -1000 -0.064 -1000
p38 MAPK signaling pathway 0.0216 10 472 44 -0.075 0.021 1000 -1000 -0.059 -1000
Canonical NF-kappaB pathway 0.0194 9 364 39 -0.16 0.087 1000 -1000 -0.074 -1000
IFN-gamma pathway 0.0194 9 629 68 -0.23 0.062 1000 -1000 -0.086 -1000
Atypical NF-kappaB pathway 0.0194 9 283 31 -0.089 0.029 1000 -1000 -0.04 -1000
S1P3 pathway 0.0194 9 396 42 -0.034 0.029 1000 -1000 -0.04 -1000
Class IB PI3K non-lipid kinase events 0.0194 9 27 3 -0.003 0.003 1000 -1000 -0.018 -1000
Circadian rhythm pathway 0.0173 8 186 22 -0.016 0.033 1000 -1000 -0.044 -1000
HIF-2-alpha transcription factor network 0.0173 8 347 43 -0.1 0.1 1000 -1000 -0.073 -1000
Signaling events mediated by PRL 0.0173 8 303 34 -0.061 0.022 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 0.0151 7 750 104 -0.16 0.06 1000 -1000 -0.062 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0151 7 945 125 -0.074 0.078 1000 -1000 -0.085 -1000
VEGFR1 specific signals 0.0151 7 421 56 -0.091 0.042 1000 -1000 -0.067 -1000
Hedgehog signaling events mediated by Gli proteins 0.0130 6 404 65 -0.042 0.064 1000 -1000 -0.06 -1000
Arf6 downstream pathway 0.0130 6 269 43 -0.027 0.027 1000 -1000 -0.033 -1000
Insulin Pathway 0.0130 6 505 74 -0.18 0.038 1000 -1000 -0.081 -1000
PDGFR-beta signaling pathway 0.0130 6 582 97 -0.058 0.065 1000 -1000 -0.075 -1000
Signaling events mediated by HDAC Class II 0.0108 5 443 75 -0.17 0.04 1000 -1000 -0.057 -1000
FoxO family signaling 0.0108 5 347 64 -0.12 0.12 1000 -1000 -0.074 -1000
Arf6 trafficking events 0.0108 5 388 71 -0.12 0.048 1000 -1000 -0.07 -1000
IGF1 pathway 0.0086 4 260 57 -0.05 0.054 1000 -1000 -0.085 -1000
Class I PI3K signaling events mediated by Akt 0.0065 3 255 68 -0.12 0.055 1000 -1000 -0.051 -1000
Alternative NF-kappaB pathway 0.0043 2 28 13 -0.006 0.014 1000 -1000 -0.058 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0022 1 43 23 -0.013 0.051 1000 -1000 -0.064 -1000
mTOR signaling pathway 0.0022 1 65 53 -0.006 0.037 1000 -1000 -0.056 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 19 27 -0.004 0.037 1000 -1000 -0.052 -1000
Arf1 pathway 0.0000 0 20 54 -0.005 0.037 1000 -1000 -0.04 -1000
Total NA 3671 202092 7203 -20 5.6 131000 -131000 -8.3 -131000
IL23-mediated signaling events

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
CCL2 -0.61 0.56 -10000 0 -1.2 190 190
IL23A -0.62 0.56 -10000 0 -1.2 185 185
NF kappa B1 p50/RelA/I kappa B alpha -0.59 0.52 -10000 0 -1.1 188 188
positive regulation of T cell mediated cytotoxicity -0.65 0.63 -10000 0 -1.3 192 192
ITGA3 -0.56 0.53 -10000 0 -1.1 175 175
IL17F -0.36 0.33 -10000 0 -0.72 161 161
IL12B -0.022 0.058 -10000 0 -0.55 4 4
STAT1 (dimer) -0.62 0.6 -10000 0 -1.2 191 191
CD4 -0.55 0.51 -10000 0 -1.1 174 174
IL23 -0.6 0.53 -10000 0 -1.2 186 186
IL23R -0.084 0.085 -10000 0 -0.52 1 1
IL1B -0.66 0.61 -10000 0 -1.3 202 202
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.55 0.51 -10000 0 -1.1 176 176
TYK2 -0.001 0.018 -10000 0 -10000 0 0
STAT4 -0.16 0.26 -10000 0 -0.54 148 148
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.081 0.21 -10000 0 -0.55 78 78
IL12RB1 -0.047 0.16 -10000 0 -0.6 36 36
PIK3CA 0.014 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.038 0.12 -10000 0 -0.44 36 36
IL23R/JAK2 -0.095 0.1 -10000 0 -0.51 1 1
positive regulation of chronic inflammatory response -0.65 0.63 -10000 0 -1.3 192 192
natural killer cell activation 0.008 0.007 0.047 1 -10000 0 1
JAK2 0.008 0.018 -10000 0 -10000 0 0
PIK3R1 0.014 0 -10000 0 -10000 0 0
NFKB1 0.011 0.003 -10000 0 -10000 0 0
RELA 0.011 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.57 0.5 -10000 0 -1.1 188 188
ALOX12B -0.62 0.57 -10000 0 -1.3 169 169
CXCL1 -0.61 0.56 -10000 0 -1.2 192 192
T cell proliferation -0.65 0.63 -10000 0 -1.3 192 192
NFKBIA 0.011 0.003 -10000 0 -10000 0 0
IL17A -0.27 0.26 -10000 0 -0.57 119 119
PI3K -0.6 0.53 -10000 0 -1.1 194 194
IFNG -0.024 0.031 -10000 0 -0.098 17 17
STAT3 (dimer) -0.57 0.49 -10000 0 -1.1 188 188
IL18R1 -0.054 0.18 -10000 0 -0.55 57 57
IL23/IL23R/JAK2/TYK2/SOCS3 -0.33 0.3 -10000 0 -0.67 132 132
IL18/IL18R -0.1 0.21 -10000 0 -0.44 105 105
macrophage activation -0.028 0.018 -10000 0 -0.044 174 174
TNF -0.65 0.61 -10000 0 -1.3 193 193
STAT3/STAT4 -0.67 0.54 -10000 0 -1.2 217 217
STAT4 (dimer) -0.68 0.6 -10000 0 -1.2 209 209
IL18 -0.029 0.15 -10000 0 -0.55 36 36
IL19 -0.55 0.51 -10000 0 -1.1 156 156
STAT5A (dimer) -0.62 0.59 -10000 0 -1.2 187 187
STAT1 -0.002 0.09 -10000 0 -0.5 15 15
SOCS3 -0.12 0.24 -10000 0 -0.53 116 116
CXCL9 -0.64 0.57 -10000 0 -1.2 200 200
MPO -0.64 0.57 -10000 0 -1.2 201 201
positive regulation of humoral immune response -0.65 0.63 -10000 0 -1.3 192 192
IL23/IL23R/JAK2/TYK2 -0.7 0.74 -10000 0 -1.4 192 192
IL6 -0.62 0.57 -10000 0 -1.2 193 193
STAT5A 0 0.093 -10000 0 -0.6 11 11
IL2 0.006 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.007 0.047 1 -10000 0 1
CD3E -0.63 0.57 -10000 0 -1.2 180 180
keratinocyte proliferation -0.65 0.63 -10000 0 -1.3 192 192
NOS2 -0.57 0.53 -10000 0 -1.1 178 178
Ephrin A reverse signaling

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
MAPKKK cascade -0.14 0.22 -9999 0 -0.45 146 146
EFNA5 -0.083 0.22 -9999 0 -0.56 79 79
FYN -0.11 0.22 -9999 0 -0.4 146 146
neuron projection morphogenesis -0.14 0.22 -9999 0 -0.45 146 146
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.14 0.22 -9999 0 -0.45 146 146
EPHA5 -0.13 0.25 -9999 0 -0.56 117 117
TCGA08_retinoblastoma

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
CDKN2B -0.062 0.19 -10000 0 -0.55 62 62
CDKN2C -0.021 0.13 -10000 0 -0.44 41 41
CDKN2A -0.1 0.23 -10000 0 -0.55 96 96
CCND2 0.065 0.14 0.3 101 -0.14 2 103
RB1 -0.07 0.15 -10000 0 -0.32 96 96
CDK4 0.077 0.16 0.34 97 -10000 0 97
CDK6 0.069 0.16 0.33 99 -0.17 13 112
G1/S progression 0.057 0.16 0.32 97 -10000 0 97
FOXM1 transcription factor network

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
NFATC3 -0.22 0.65 -10000 0 -1.2 113 113
PLK1 -0.006 0.2 -10000 0 -1.5 4 4
BIRC5 -0.23 0.55 -10000 0 -1.5 69 69
HSPA1B -0.24 0.66 -10000 0 -1.2 119 119
MAP2K1 0.023 0.052 -10000 0 -0.54 1 1
BRCA2 -0.24 0.68 -10000 0 -1.3 122 122
FOXM1 -0.38 0.95 -10000 0 -1.8 121 121
XRCC1 -0.22 0.65 -10000 0 -1.2 112 112
FOXM1B/p19 -0.39 0.57 0.43 4 -1.3 122 126
Cyclin D1/CDK4 -0.21 0.6 -10000 0 -1.1 117 117
CDC2 -0.24 0.69 -10000 0 -1.3 120 120
TGFA -0.19 0.59 -10000 0 -1.1 118 118
SKP2 -0.22 0.66 -10000 0 -1.2 117 117
CCNE1 0.013 0.036 -10000 0 -0.51 2 2
CKS1B -0.22 0.65 -10000 0 -1.2 112 112
RB1 -0.18 0.28 -10000 0 -0.76 60 60
FOXM1C/SP1 -0.3 0.76 -10000 0 -1.5 120 120
AURKB -0.28 0.59 -10000 0 -1.5 87 87
CENPF -0.26 0.7 -10000 0 -1.3 117 117
CDK4 0.003 0.088 -10000 0 -0.5 13 13
MYC -0.19 0.58 -10000 0 -1 116 116
CHEK2 0.009 0.11 -10000 0 -0.57 13 13
ONECUT1 -0.23 0.64 -10000 0 -1.2 120 120
CDKN2A -0.11 0.24 -10000 0 -0.58 96 96
LAMA4 -0.22 0.65 -10000 0 -1.2 116 116
FOXM1B/HNF6 -0.32 0.79 -10000 0 -1.5 122 122
FOS -0.31 0.7 -10000 0 -1.2 154 154
SP1 0.015 0.006 -10000 0 -10000 0 0
CDC25B -0.22 0.65 -10000 0 -1.2 111 111
response to radiation 0.007 0.042 -10000 0 -10000 0 0
CENPB -0.22 0.65 -10000 0 -1.2 113 113
CENPA -0.27 0.71 -10000 0 -1.3 123 123
NEK2 -0.29 0.73 -10000 0 -1.3 131 131
HIST1H2BA -0.23 0.65 -10000 0 -1.2 112 112
CCNA2 -0.058 0.19 -10000 0 -0.55 61 61
EP300 0.009 0.057 -10000 0 -0.61 4 4
CCNB1/CDK1 -0.3 0.78 -10000 0 -1.5 113 113
CCNB2 -0.28 0.74 -10000 0 -1.4 128 128
CCNB1 -0.25 0.7 -10000 0 -1.3 111 111
ETV5 -0.25 0.66 -10000 0 -1.2 120 120
ESR1 -0.24 0.66 -10000 0 -1.2 123 123
CCND1 -0.21 0.62 -10000 0 -1.1 117 117
GSK3A 0.027 0.036 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.018 0.17 -10000 0 -0.4 64 64
CDK2 -0.001 0.095 -10000 0 -0.55 13 13
G2/M transition of mitotic cell cycle 0.007 0.049 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.42 0.59 -10000 0 -1.3 126 126
GAS1 -0.23 0.66 -10000 0 -1.2 113 113
MMP2 -0.23 0.66 -10000 0 -1.2 112 112
RB1/FOXM1C -0.23 0.65 -10000 0 -1.2 119 119
CREBBP 0.014 0 -10000 0 -10000 0 0
IL12-mediated 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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.12 0.17 -10000 0 -0.4 80 80
TBX21 -0.49 0.5 -10000 0 -1 180 180
B2M 0.009 0.053 -10000 0 -0.5 5 5
TYK2 0.001 0.018 -10000 0 -10000 0 0
IL12RB1 -0.045 0.16 -10000 0 -0.59 36 36
GADD45B -0.36 0.39 -10000 0 -0.81 148 148
IL12RB2 -0.13 0.24 -10000 0 -0.56 113 113
GADD45G -0.38 0.41 -10000 0 -0.93 114 114
natural killer cell activation -0.017 0.023 -10000 0 -10000 0 0
RELB 0.009 0.055 -10000 0 -0.52 5 5
RELA 0.014 0 -10000 0 -10000 0 0
IL18 -0.033 0.16 -10000 0 -0.56 36 36
IL2RA -0.065 0.18 -10000 0 -0.51 65 65
IFNG -0.001 0.047 -10000 0 -0.5 4 4
STAT3 (dimer) -0.37 0.36 -10000 0 -0.74 187 187
HLA-DRB5 -0.13 0.24 -10000 0 -0.55 115 115
FASLG -0.46 0.47 -10000 0 -0.94 187 187
NF kappa B2 p52/RelB -0.47 0.43 -10000 0 -0.87 210 210
CD4 0.004 0.066 -10000 0 -0.53 7 7
SOCS1 -0.032 0.15 -10000 0 -0.52 40 40
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D -0.12 0.23 -10000 0 -0.54 108 108
CD3E -0.14 0.25 -10000 0 -0.55 127 127
CD3G -0.031 0.14 -10000 0 -0.5 35 35
IL12Rbeta2/JAK2 -0.1 0.18 -10000 0 -0.41 113 113
CCL3 -0.57 0.58 -10000 0 -1.2 197 197
CCL4 -0.57 0.59 -10000 0 -1.2 198 198
HLA-A 0.004 0.071 -10000 0 -0.5 9 9
IL18/IL18R -0.097 0.23 -10000 0 -0.43 131 131
NOS2 -0.43 0.45 -10000 0 -0.93 162 162
IL12/IL12R/TYK2/JAK2/SPHK2 -0.11 0.15 -10000 0 -0.41 51 51
IL1R1 -0.47 0.49 -10000 0 -1 172 172
IL4 0.019 0.023 -10000 0 -10000 0 0
JAK2 0.001 0.018 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.25 -10000 0 -0.57 87 87
RAB7A -0.29 0.32 -10000 0 -0.71 111 111
lysosomal transport -0.28 0.3 -10000 0 -0.67 114 114
FOS -0.36 0.45 -10000 0 -0.91 143 143
STAT4 (dimer) -0.43 0.41 -10000 0 -0.86 184 184
STAT5A (dimer) -0.48 0.44 -10000 0 -0.88 212 212
GZMA -0.53 0.54 -10000 0 -1.1 190 190
GZMB -0.52 0.53 -10000 0 -1.1 189 189
HLX -0.002 0.093 -10000 0 -0.53 14 14
LCK -0.53 0.53 -10000 0 -1 215 215
TCR/CD3/MHC II/CD4 -0.17 0.25 -10000 0 -0.51 131 131
IL2/IL2R -0.13 0.21 -10000 0 -0.47 101 101
MAPK14 -0.36 0.39 -10000 0 -0.81 155 155
CCR5 -0.42 0.45 -10000 0 -1 121 121
IL1B -0.19 0.28 -10000 0 -0.57 157 157
STAT6 -0.11 0.12 -10000 0 -0.36 2 2
STAT4 -0.16 0.26 -10000 0 -0.54 148 148
STAT3 0.014 0 -10000 0 -10000 0 0
STAT1 -0.002 0.09 -10000 0 -0.5 15 15
NFKB1 0.014 0 -10000 0 -10000 0 0
NFKB2 0.011 0.047 -10000 0 -0.57 3 3
IL12B -0.015 0.054 -10000 0 -0.54 4 4
CD8A -0.079 0.21 -10000 0 -0.56 76 76
CD8B -0.035 0.16 -10000 0 -0.57 39 39
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.12 0.16 0.39 80 -10000 0 80
IL2RB -0.099 0.22 -10000 0 -0.54 94 94
proteasomal ubiquitin-dependent protein catabolic process -0.39 0.36 -10000 0 -0.77 184 184
IL2RG -0.043 0.17 -10000 0 -0.53 49 49
IL12 -0.032 0.11 -10000 0 -0.46 27 27
STAT5A 0 0.093 -10000 0 -0.6 11 11
CD247 -0.02 0.13 -10000 0 -0.53 28 28
IL2 0.001 0.003 -10000 0 -10000 0 0
SPHK2 0.014 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.03 0.14 -10000 0 -0.62 23 23
IL12/IL12R/TYK2/JAK2 -0.53 0.57 -10000 0 -1 211 211
MAP2K3 -0.37 0.4 -10000 0 -0.81 158 158
RIPK2 0.014 0 -10000 0 -10000 0 0
MAP2K6 -0.37 0.4 -10000 0 -0.81 162 162
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.097 0.22 -10000 0 -0.55 91 91
IL18RAP -0.086 0.22 -10000 0 -0.56 78 78
IL12Rbeta1/TYK2 -0.035 0.12 -10000 0 -0.44 36 36
EOMES -0.01 0.16 -10000 0 -0.46 31 31
STAT1 (dimer) -0.37 0.35 -10000 0 -0.74 180 180
T cell proliferation -0.32 0.29 -10000 0 -0.63 170 170
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.058 0.19 -10000 0 -0.56 57 57
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.37 0.29 -10000 0 -0.69 173 173
ATF2 -0.34 0.36 -10000 0 -0.76 142 142
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.13 0.26 -9999 0 -0.55 114 114
STMN1 -0.11 0.2 -9999 0 -0.41 147 147
Aurora B/RasGAP/Survivin -0.18 0.29 -9999 0 -0.58 150 150
Chromosomal passenger complex/Cul3 protein complex -0.097 0.2 -9999 0 -0.43 104 104
BIRC5 -0.15 0.27 -9999 0 -0.58 127 127
DES -0.35 0.47 -9999 0 -0.95 151 151
Aurora C/Aurora B/INCENP -0.11 0.17 -9999 0 -0.34 145 145
Aurora B/TACC1 -0.1 0.17 -9999 0 -0.34 146 146
Aurora B/PP2A -0.12 0.2 -9999 0 -0.4 146 146
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.031 0.076 -9999 0 -0.17 88 88
mitotic metaphase/anaphase transition 0 0.006 -9999 0 -10000 0 0
NDC80 -0.2 0.32 -9999 0 -0.61 167 167
Cul3 protein complex -0.009 0.056 -9999 0 -0.37 11 11
KIF2C -0.14 0.29 -9999 0 -0.47 149 149
PEBP1 0.007 0.042 -9999 0 -0.62 2 2
KIF20A -0.18 0.27 -9999 0 -0.56 154 154
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.12 0.2 -9999 0 -0.4 146 146
SEPT1 0.009 0.055 -9999 0 -0.52 5 5
SMC2 0.014 0 -9999 0 -10000 0 0
SMC4 -0.015 0.12 -9999 0 -0.5 27 27
NSUN2/NPM1/Nucleolin -0.17 0.34 -9999 0 -0.84 87 87
PSMA3 0.014 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B -0.081 0.16 -9999 0 -0.3 146 146
AURKB -0.17 0.28 -9999 0 -0.58 146 146
AURKC -0.02 0.13 -9999 0 -0.52 30 30
CDCA8 -0.058 0.18 -9999 0 -0.54 58 58
cytokinesis -0.28 0.41 -9999 0 -0.82 152 152
Aurora B/Septin1 -0.26 0.39 -9999 0 -0.78 150 150
AURKA -0.015 0.12 -9999 0 -0.5 26 26
INCENP 0.009 0.009 -9999 0 -10000 0 0
KLHL13 0.012 0.041 -9999 0 -0.61 2 2
BUB1 -0.12 0.24 -9999 0 -0.56 108 108
hSgo1/Aurora B/Survivin -0.24 0.36 -9999 0 -0.7 162 162
EVI5 0.013 0.003 -9999 0 -10000 0 0
RhoA/GTP -0.25 0.36 -9999 0 -0.74 148 148
SGOL1 -0.12 0.24 -9999 0 -0.55 114 114
CENPA -0.18 0.32 -9999 0 -0.57 154 154
NCAPG -0.14 0.26 -9999 0 -0.56 128 128
Aurora B/HC8 Proteasome -0.12 0.2 -9999 0 -0.4 146 146
NCAPD2 0.01 0.047 -9999 0 -0.5 4 4
Aurora B/PP1-gamma -0.12 0.2 -9999 0 -0.4 146 146
RHOA 0.014 0 -9999 0 -10000 0 0
NCAPH -0.066 0.2 -9999 0 -0.55 66 66
NPM1 -0.14 0.24 -9999 0 -0.62 87 87
RASA1 0.014 0 -9999 0 -10000 0 0
KLHL9 0.002 0.086 -9999 0 -0.61 9 9
mitotic prometaphase -0.006 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.12 0.2 -9999 0 -0.4 146 146
PPP1CC 0.014 0 -9999 0 -10000 0 0
Centraspindlin -0.28 0.41 -9999 0 -0.8 154 154
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.14 0.24 -9999 0 -0.62 87 87
MYLK -0.089 0.16 -9999 0 -0.3 155 155
KIF23 -0.12 0.24 -9999 0 -0.56 107 107
VIM -0.17 0.24 -9999 0 -0.45 196 196
RACGAP1 0.003 0.061 -9999 0 -0.52 6 6
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.14 0.24 -9999 0 -0.62 87 87
Chromosomal passenger complex -0.22 0.39 -9999 0 -0.7 153 153
Chromosomal passenger complex/EVI5 -0.18 0.32 -9999 0 -0.64 136 136
TACC1 0.014 0 -9999 0 -10000 0 0
PPP2R5D 0.014 0 -9999 0 -10000 0 0
CUL3 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.014 0.1 -10000 0 -0.58 11 11
NFATC2 -0.13 0.31 -10000 0 -0.74 71 71
NFATC3 -0.048 0.11 -10000 0 -0.31 10 10
CD40LG -0.38 0.48 -10000 0 -1 142 142
ITCH -0.03 0.12 -10000 0 -0.53 3 3
CBLB -0.031 0.13 -10000 0 -0.61 4 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.34 0.4 -10000 0 -0.94 102 102
JUNB -0.036 0.16 -10000 0 -0.52 43 43
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.084 0.13 -10000 0 -0.3 82 82
T cell anergy -0.094 0.2 -10000 0 -0.44 85 85
TLE4 -0.082 0.26 -10000 0 -0.68 51 51
Jun/NFAT1-c-4/p21SNFT -0.35 0.44 -10000 0 -0.98 120 120
AP-1/NFAT1-c-4 -0.46 0.57 -10000 0 -1.2 139 139
IKZF1 -0.094 0.28 -10000 0 -0.76 52 52
T-helper 2 cell differentiation -0.18 0.29 -10000 0 -0.75 65 65
AP-1/NFAT1 -0.17 0.26 -10000 0 -0.56 113 113
CALM1 -0.025 0.09 -10000 0 -0.7 2 2
EGR2 -0.29 0.53 -10000 0 -1.2 80 80
EGR3 -0.33 0.58 -10000 0 -1.2 113 113
NFAT1/FOXP3 -0.12 0.26 -10000 0 -0.68 59 59
EGR1 -0.11 0.23 -10000 0 -0.55 99 99
JUN -0.004 0.079 -10000 0 -0.52 10 10
EGR4 -0.2 0.28 -10000 0 -0.56 172 172
mol:Ca2+ -0.04 0.084 -10000 0 -0.3 1 1
GBP3 -0.16 0.36 -10000 0 -0.83 88 88
FOSL1 -0.095 0.22 -10000 0 -0.54 91 91
NFAT1-c-4/MAF/IRF4 -0.32 0.43 -10000 0 -0.96 116 116
DGKA -0.074 0.23 -10000 0 -0.67 39 39
CREM 0.012 0.037 -10000 0 -0.55 2 2
NFAT1-c-4/PPARG -0.33 0.44 -10000 0 -0.97 119 119
CTLA4 -0.12 0.3 -10000 0 -0.7 79 79
NFAT1-c-4 (dimer)/EGR1 -0.38 0.51 -10000 0 -1 139 139
NFAT1-c-4 (dimer)/EGR4 -0.43 0.48 -10000 0 -1 145 145
FOS -0.1 0.23 -10000 0 -0.57 87 87
IFNG -0.17 0.24 -10000 0 -0.75 41 41
T cell activation -0.17 0.28 -10000 0 -0.73 53 53
MAF 0.01 0.05 -10000 0 -0.61 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.22 0.4 0.83 99 -10000 0 99
TNF -0.48 0.5 -10000 0 -1 178 178
FASLG -0.34 0.55 -10000 0 -1.2 107 107
TBX21 -0.046 0.18 -10000 0 -0.54 51 51
BATF3 -0.036 0.16 -10000 0 -0.54 42 42
PRKCQ -0.01 0.12 -10000 0 -0.59 18 18
PTPN1 -0.074 0.23 -10000 0 -0.64 44 44
NFAT1-c-4/ICER1 -0.32 0.44 -10000 0 -0.97 113 113
GATA3 -0.11 0.23 -10000 0 -0.54 100 100
T-helper 1 cell differentiation -0.16 0.24 -10000 0 -0.73 42 42
IL2RA -0.3 0.34 -10000 0 -0.82 98 98
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.075 0.23 -10000 0 -0.66 40 40
E2F1 -0.011 0.13 -10000 0 -0.52 26 26
PPARG -0.014 0.13 -10000 0 -0.58 22 22
SLC3A2 -0.074 0.23 -10000 0 -0.65 42 42
IRF4 -0.048 0.18 -10000 0 -0.55 51 51
PTGS2 -0.41 0.52 -10000 0 -1.1 145 145
CSF2 -0.37 0.47 -10000 0 -1 131 131
JunB/Fra1/NFAT1-c-4 -0.37 0.46 -10000 0 -0.96 134 134
IL4 -0.19 0.31 -10000 0 -0.81 61 61
IL5 -0.37 0.47 -10000 0 -1 134 134
IL2 -0.17 0.29 -10000 0 -0.76 49 49
IL3 -0.066 0.072 -10000 0 -0.96 1 1
RNF128 -0.15 0.3 -10000 0 -0.56 150 150
NFATC1 -0.22 0.41 -10000 0 -0.84 99 99
CDK4 0.13 0.24 0.64 27 -0.6 1 28
PTPRK -0.075 0.24 -10000 0 -0.66 42 42
IL8 -0.44 0.52 -10000 0 -1.1 157 157
POU2F1 0.013 0.029 -10000 0 -0.61 1 1
Effects of Botulinum toxin

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
STX1A -0.052 0.14 -9999 0 -0.37 78 78
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.091 0.17 -9999 0 -0.41 103 103
STXBP1 -0.014 0.12 -9999 0 -0.5 25 25
ACh/CHRNA1 -0.13 0.17 -9999 0 -0.38 144 144
RAB3GAP2/RIMS1/UNC13B -0.075 0.14 -9999 0 -0.34 103 103
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.11 0.24 -9999 0 -0.56 103 103
mol:ACh -0.038 0.069 -9999 0 -0.14 147 147
RAB3GAP2 0.014 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.14 0.21 -9999 0 -0.46 113 113
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.13 0.17 -9999 0 -0.38 144 144
UNC13B 0.013 0.029 -9999 0 -0.61 1 1
CHRNA1 -0.16 0.26 -9999 0 -0.54 143 143
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.16 0.21 -9999 0 -0.42 179 179
SNAP25 -0.075 0.13 -9999 0 -0.25 149 149
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.2 0.28 -9999 0 -0.55 179 179
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.05 0.16 -9999 0 -0.38 80 80
STX1A/SNAP25 fragment 1/VAMP2 -0.14 0.21 -9999 0 -0.46 113 113
Syndecan-1-mediated 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
TGFB1 0.004 0.081 -9999 0 -0.61 8 8
CCL5 -0.093 0.22 -9999 0 -0.55 89 89
SDCBP 0.014 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.14 0.19 -9999 0 -0.42 101 101
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.12 0.18 -9999 0 -0.46 74 74
Syndecan-1/Syntenin -0.12 0.18 -9999 0 -0.45 72 72
MAPK3 -0.098 0.17 -9999 0 -0.48 41 41
HGF/MET -0.17 0.23 -9999 0 -0.44 177 177
TGFB1/TGF beta receptor Type II 0.004 0.081 -9999 0 -0.61 8 8
BSG 0.014 0 -9999 0 -10000 0 0
keratinocyte migration -0.12 0.18 -9999 0 -0.45 74 74
Syndecan-1/RANTES -0.18 0.22 -9999 0 -0.47 131 131
Syndecan-1/CD147 -0.11 0.18 -9999 0 -0.43 72 72
Syndecan-1/Syntenin/PIP2 -0.13 0.17 -9999 0 -0.44 72 72
LAMA5 0.012 0.037 -9999 0 -0.55 2 2
positive regulation of cell-cell adhesion -0.14 0.16 -9999 0 -0.43 72 72
MMP7 -0.15 0.26 -9999 0 -0.55 136 136
HGF -0.078 0.2 -9999 0 -0.52 80 80
Syndecan-1/CASK -0.13 0.18 -9999 0 -0.4 100 100
Syndecan-1/HGF/MET -0.23 0.25 -9999 0 -0.52 162 162
regulation of cell adhesion -0.088 0.16 -9999 0 -0.46 41 41
HPSE -0.057 0.19 -9999 0 -0.57 56 56
positive regulation of cell migration -0.14 0.19 -9999 0 -0.42 101 101
SDC1 -0.14 0.19 -9999 0 -0.42 101 101
Syndecan-1/Collagen -0.14 0.19 -9999 0 -0.42 101 101
PPIB 0.014 0 -9999 0 -10000 0 0
MET -0.14 0.25 -9999 0 -0.55 129 129
PRKACA 0.014 0 -9999 0 -10000 0 0
MMP9 -0.15 0.25 -9999 0 -0.53 136 136
MAPK1 -0.098 0.17 -9999 0 -0.48 41 41
homophilic cell adhesion -0.14 0.19 -9999 0 -0.41 101 101
MMP1 -0.048 0.16 -9999 0 -0.5 51 51
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.084 0.15 -9999 0 -0.34 115 115
E-cadherin/beta catenin -0.092 0.17 -9999 0 -0.39 109 109
CTNNB1 0.014 0 -9999 0 -10000 0 0
JUP 0.001 0.087 -9999 0 -0.58 10 10
CDH1 -0.12 0.24 -9999 0 -0.55 109 109
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.14 0.19 -10000 0 -0.46 99 99
FYN -0.15 0.27 -10000 0 -0.54 122 122
LAT/GRAP2/SLP76 -0.18 0.22 -10000 0 -0.5 118 118
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.11 0.19 -10000 0 -0.39 116 116
B2M 0.006 0.054 -10000 0 -0.51 5 5
IKBKG -0.036 0.046 -10000 0 -0.14 26 26
MAP3K8 -0.006 0.1 -10000 0 -0.51 18 18
mol:Ca2+ -0.027 0.043 -10000 0 -0.11 91 91
integrin-mediated signaling pathway -0.011 0.06 -10000 0 -0.34 15 15
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.16 0.27 -10000 0 -0.55 122 122
TRPV6 -0.12 0.24 -10000 0 -0.57 99 99
CD28 -0.079 0.21 -10000 0 -0.55 75 75
SHC1 -0.15 0.27 -10000 0 -0.54 118 118
receptor internalization -0.13 0.24 -10000 0 -0.5 107 107
PRF1 -0.18 0.37 -10000 0 -0.97 68 68
KRAS 0.013 0.024 -10000 0 -0.5 1 1
GRB2 0.013 0.024 -10000 0 -0.5 1 1
COT/AKT1 -0.087 0.16 -10000 0 -0.34 97 97
LAT -0.17 0.27 -10000 0 -0.54 127 127
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.12 0.23 -10000 0 -0.54 108 108
CD3E -0.14 0.25 -10000 0 -0.55 127 127
CD3G -0.031 0.14 -10000 0 -0.5 35 35
RASGRP2 -0.007 0.025 -10000 0 -0.19 2 2
RASGRP1 -0.12 0.2 -10000 0 -0.4 120 120
HLA-A 0.001 0.071 -10000 0 -0.5 9 9
RASSF5 -0.004 0.1 -10000 0 -0.56 15 15
RAP1A/GTP/RAPL -0.011 0.06 -10000 0 -0.34 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.018 0.063 -10000 0 -0.12 50 50
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.066 0.081 -10000 0 -0.22 65 65
PRKCA -0.083 0.11 -10000 0 -0.25 91 91
GRAP2 -0.051 0.18 -10000 0 -0.54 54 54
mol:IP3 -0.11 0.19 0.2 55 -0.39 107 162
EntrezGene:6957 -0.002 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.22 -10000 0 -0.46 106 106
ORAI1 0.072 0.13 0.31 98 -10000 0 98
CSK -0.16 0.27 -10000 0 -0.55 119 119
B7 family/CD28 -0.22 0.28 -10000 0 -0.61 123 123
CHUK 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.18 0.3 -10000 0 -0.59 128 128
PTPN6 -0.16 0.28 -10000 0 -0.56 124 124
VAV1 -0.17 0.28 -10000 0 -0.56 123 123
Monovalent TCR/CD3 -0.12 0.2 -10000 0 -0.37 156 156
CBL 0.014 0 -10000 0 -10000 0 0
LCK -0.18 0.3 -10000 0 -0.56 141 141
PAG1 -0.16 0.27 -10000 0 -0.55 119 119
RAP1A 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.18 0.3 -10000 0 -0.6 123 123
CD80 -0.047 0.17 -10000 0 -0.52 51 51
CD86 -0.027 0.15 -10000 0 -0.57 32 32
PDK1/CARD11/BCL10/MALT1 -0.081 0.099 -10000 0 -0.26 74 74
HRAS 0.014 0 -10000 0 -10000 0 0
GO:0035030 -0.16 0.25 -10000 0 -0.52 118 118
CD8A -0.081 0.21 -10000 0 -0.56 76 76
CD8B -0.038 0.16 -10000 0 -0.58 39 39
PTPRC -0.044 0.17 -10000 0 -0.55 47 47
PDK1/PKC theta -0.13 0.23 -10000 0 -0.48 113 113
CSK/PAG1 -0.15 0.26 -10000 0 -0.54 112 112
SOS1 0.014 0 -10000 0 -10000 0 0
peptide-MHC class I 0.003 0.073 -10000 0 -0.44 11 11
GRAP2/SLP76 -0.19 0.26 -10000 0 -0.56 125 125
STIM1 0.039 0.063 -10000 0 -10000 0 0
RAS family/GTP -0.025 0.084 -10000 0 -0.17 30 30
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.26 -10000 0 -0.53 107 107
mol:DAG -0.12 0.16 -10000 0 -0.35 113 113
RAP1A/GDP -0.006 0.027 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
CD247 -0.02 0.13 -10000 0 -0.53 28 28
cytotoxic T cell degranulation -0.17 0.35 -10000 0 -0.88 72 72
RAP1A/GTP -0.004 0.006 -10000 0 -0.067 2 2
mol:PI-3-4-5-P3 -0.14 0.22 -10000 0 -0.45 120 120
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.15 0.24 0.23 40 -0.5 109 149
NRAS 0.014 0 -10000 0 -10000 0 0
ZAP70 -0.053 0.18 -10000 0 -0.54 56 56
GRB2/SOS1 -0.001 0.016 -10000 0 -0.35 1 1
LAT/GRAP2/SLP76/VAV1 -0.17 0.22 -10000 0 -0.49 121 121
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.029 -10000 0 -0.61 1 1
CD8 heterodimer -0.086 0.21 -10000 0 -0.47 98 98
CARD11 -0.01 0.12 -10000 0 -0.58 19 19
PRKCB -0.11 0.12 -10000 0 -0.27 118 118
PRKCE -0.086 0.11 -10000 0 -0.26 91 91
PRKCQ -0.16 0.26 -10000 0 -0.53 120 120
LCP2 -0.003 0.094 -10000 0 -0.5 16 16
BCL10 0.014 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.092 0.16 -10000 0 -0.33 114 114
IKK complex -0.012 0.062 -10000 0 -0.11 26 26
RAS family/GDP -0.007 0.009 -10000 0 -10000 0 0
MAP3K14 -0.058 0.13 -10000 0 -0.27 71 71
PDPK1 -0.1 0.18 -10000 0 -0.37 109 109
TCR/CD3/MHC I/CD8/Fyn -0.18 0.31 -10000 0 -0.61 131 131
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.4 0.44 -10000 0 -1.1 81 81
STAT6 (cleaved dimer) -0.48 0.44 -10000 0 -0.99 161 161
IGHG1 -0.16 0.21 -10000 0 -0.57 37 37
IGHG3 -0.39 0.42 -10000 0 -0.94 129 129
AKT1 -0.24 0.29 -10000 0 -0.74 71 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.78 67 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.27 -10000 0 -0.69 60 60
THY1 -0.41 0.46 -10000 0 -1.1 98 98
MYB -0.062 0.19 -10000 0 -0.55 62 62
HMGA1 0.011 0.044 -10000 0 -0.53 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.33 0.35 -10000 0 -0.76 134 134
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.27 -10000 0 -0.68 63 63
SP1 0.021 0.01 -10000 0 -10000 0 0
INPP5D 0.008 0.058 -10000 0 -0.54 5 5
SOCS5 0.028 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.46 -10000 0 -1 146 146
SOCS1 -0.3 0.33 -10000 0 -0.76 109 109
SOCS3 -0.36 0.42 -10000 0 -0.94 124 124
FCER2 -0.43 0.45 -10000 0 -1.1 106 106
PARP14 -0.002 0.087 -10000 0 -0.53 12 12
CCL17 -0.41 0.45 -10000 0 -1.1 102 102
GRB2 0.013 0.024 -10000 0 -0.5 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.23 -10000 0 -0.62 52 52
T cell proliferation -0.41 0.46 -10000 0 -1.1 111 111
IL4R/JAK1 -0.4 0.44 -10000 0 -1.1 97 97
EGR2 -0.51 0.54 -10000 0 -1.3 116 116
JAK2 -0.003 0.027 -10000 0 -10000 0 0
JAK3 -0.06 0.19 -10000 0 -0.54 62 62
PIK3R1 0.014 0 -10000 0 -10000 0 0
JAK1 0.005 0.012 -10000 0 -10000 0 0
COL1A2 -0.16 0.25 -10000 0 -0.73 44 44
CCL26 -0.41 0.45 -10000 0 -1.1 88 88
IL4R -0.42 0.47 -10000 0 -1.1 93 93
PTPN6 0.007 0.098 -10000 0 -0.54 14 14
IL13RA2 -0.61 0.59 -10000 0 -1.2 183 183
IL13RA1 -0.012 0.077 -10000 0 -0.64 6 6
IRF4 -0.19 0.35 -10000 0 -1.1 45 45
ARG1 -0.13 0.24 -10000 0 -0.81 29 29
CBL -0.3 0.33 -10000 0 -0.74 123 123
GTF3A 0.009 0.034 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.012 0.066 -10000 0 -0.47 6 6
IRF4/BCL6 -0.16 0.32 -10000 0 -1 43 43
CD40LG -0.038 0.15 -10000 0 -0.5 44 44
MAPK14 -0.33 0.36 -10000 0 -0.8 127 127
mitosis -0.23 0.28 -10000 0 -0.7 71 71
STAT6 -0.45 0.51 -10000 0 -1.1 119 119
SPI1 -0.004 0.11 -10000 0 -0.55 17 17
RPS6KB1 -0.22 0.27 -10000 0 -0.68 65 65
STAT6 (dimer) -0.45 0.51 -10000 0 -1.1 119 119
STAT6 (dimer)/PARP14 -0.44 0.48 -10000 0 -1.1 124 124
mast cell activation 0.011 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.32 -10000 0 -0.8 82 82
FRAP1 -0.24 0.29 -10000 0 -0.74 71 71
LTA -0.43 0.49 -10000 0 -1.2 95 95
FES 0.01 0.05 -10000 0 -0.52 4 4
T-helper 1 cell differentiation 0.44 0.5 1.1 119 -10000 0 119
CCL11 -0.39 0.42 -10000 0 -1 88 88
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.25 0.31 -10000 0 -0.79 70 70
IL2RG -0.044 0.17 -10000 0 -0.53 49 49
IL10 -0.5 0.57 -10000 0 -1.2 136 136
IRS1 0.013 0.029 -10000 0 -0.61 1 1
IRS2 0.013 0.029 -10000 0 -0.61 1 1
IL4 -0.097 0.12 -10000 0 -10000 0 0
IL5 -0.4 0.44 -10000 0 -1.1 84 84
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.33 0.36 -10000 0 -0.83 94 94
COL1A1 -0.36 0.51 -10000 0 -1.1 112 112
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.4 0.45 -10000 0 -1.1 82 82
IL2R gamma/JAK3 -0.077 0.2 -10000 0 -0.45 93 93
TFF3 -0.42 0.46 -10000 0 -1.1 104 104
ALOX15 -0.41 0.45 -10000 0 -1.1 84 84
MYBL1 0.01 0.047 -10000 0 -0.5 4 4
T-helper 2 cell differentiation -0.36 0.38 -10000 0 -0.86 120 120
SHC1 0.009 0.053 -10000 0 -0.5 5 5
CEBPB -0.003 0.11 -10000 0 -0.58 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.26 -10000 0 -0.67 59 59
mol:PI-3-4-5-P3 -0.24 0.3 -10000 0 -0.74 71 71
PI3K -0.26 0.31 -10000 0 -0.8 71 71
DOK2 -0.074 0.2 -10000 0 -0.54 74 74
ETS1 0.017 0.073 -10000 0 -0.52 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.22 -10000 0 -0.6 50 50
ITGB3 -0.44 0.5 -10000 0 -1.2 106 106
PIGR -0.51 0.57 -10000 0 -1.3 120 120
IGHE 0.021 0.063 -10000 0 -0.26 11 11
MAPKKK cascade -0.17 0.22 -10000 0 -0.59 50 50
BCL6 0.016 0.006 -10000 0 -10000 0 0
OPRM1 -0.42 0.45 -10000 0 -1.1 107 107
RETNLB -0.4 0.44 -10000 0 -1.1 88 88
SELP -0.41 0.45 -10000 0 -1.1 88 88
AICDA -0.39 0.43 -10000 0 -1.1 84 84
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.097 0.29 -10000 0 -0.72 56 56
IHH -0.011 0.081 -10000 0 -0.52 6 6
SHH Np/Cholesterol/GAS1 -0.091 0.16 -10000 0 -0.32 131 131
LRPAP1 0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.09 0.15 0.32 131 -10000 0 131
SMO/beta Arrestin2 -0.033 0.18 -10000 0 -0.74 14 14
SMO -0.043 0.19 -10000 0 -0.73 17 17
AKT1 0.005 0.082 -10000 0 -0.32 2 2
ARRB2 0.014 0 -10000 0 -10000 0 0
BOC 0.007 0.066 -10000 0 -0.57 6 6
ADRBK1 0.014 0 -10000 0 -10000 0 0
heart looping -0.042 0.18 -10000 0 -0.71 17 17
STIL -0.092 0.22 -10000 0 -0.55 63 63
DHH N/PTCH2 -0.062 0.15 -10000 0 -0.41 70 70
DHH N/PTCH1 -0.068 0.2 -10000 0 -0.62 26 26
PIK3CA 0.014 0 -10000 0 -10000 0 0
DHH -0.05 0.18 -10000 0 -0.56 52 52
PTHLH -0.11 0.34 -10000 0 -0.94 54 54
determination of left/right symmetry -0.042 0.18 -10000 0 -0.71 17 17
PIK3R1 0.014 0 -10000 0 -10000 0 0
skeletal system development -0.11 0.34 -10000 0 -0.92 54 54
IHH N/Hhip -0.12 0.21 -10000 0 -0.45 128 128
DHH N/Hhip -0.15 0.22 -10000 0 -0.44 160 160
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.042 0.18 -10000 0 -0.71 17 17
pancreas development -0.14 0.26 -10000 0 -0.56 125 125
HHAT -0.006 0.11 -10000 0 -0.59 16 16
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.017 0.12 -10000 0 -0.5 28 28
somite specification -0.042 0.18 -10000 0 -0.71 17 17
SHH Np/Cholesterol/PTCH1 -0.093 0.22 -10000 0 -0.56 53 53
SHH Np/Cholesterol/PTCH2 -0.088 0.15 -10000 0 -0.32 129 129
SHH Np/Cholesterol/Megalin -0.18 0.21 -10000 0 -0.37 232 232
SHH -0.082 0.19 -10000 0 -0.42 111 111
catabolic process -0.043 0.18 -10000 0 -0.63 21 21
SMO/Vitamin D3 -0.083 0.22 -10000 0 -0.6 44 44
SHH Np/Cholesterol/Hhip -0.16 0.21 -10000 0 -0.36 199 199
LRP2 -0.19 0.28 -10000 0 -0.56 166 166
receptor-mediated endocytosis -0.18 0.22 -10000 0 -0.59 75 75
SHH Np/Cholesterol/BOC -0.079 0.15 -10000 0 -0.32 114 114
SHH Np/Cholesterol/CDO -0.094 0.16 -10000 0 -0.33 132 132
mesenchymal cell differentiation 0.16 0.21 0.36 199 -10000 0 199
mol:Vitamin D3 -0.09 0.22 -10000 0 -0.57 52 52
IHH N/PTCH2 -0.011 0.11 -10000 0 -0.46 23 23
CDON -0.021 0.14 -10000 0 -0.57 28 28
IHH N/PTCH1 -0.043 0.19 -10000 0 -0.64 21 21
Megalin/LRPAP1 -0.14 0.19 -10000 0 -0.4 166 166
PTCH2 -0.011 0.12 -10000 0 -0.57 20 20
SHH Np/Cholesterol -0.077 0.14 -10000 0 -0.32 111 111
PTCH1 -0.043 0.19 -10000 0 -0.63 21 21
HHIP -0.14 0.26 -10000 0 -0.56 125 125
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.048 0.18 -9999 0 -0.55 51 51
GPC2 -0.018 0.14 -9999 0 -0.58 25 25
GPC2/Midkine -0.065 0.16 -9999 0 -0.42 71 71
neuron projection morphogenesis -0.065 0.16 -9999 0 -0.42 71 71
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.001 0.056 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.24 -9999 0 -0.56 92 92
positive regulation of JNK cascade -0.15 0.22 -9999 0 -0.52 100 100
Syndecan-4/ADAM12 -0.18 0.27 -9999 0 -0.58 111 111
CCL5 -0.093 0.22 -9999 0 -0.55 89 89
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
ITGA5 -0.013 0.12 -9999 0 -0.51 24 24
SDCBP 0.014 0 -9999 0 -10000 0 0
PLG 0.001 0.04 -9999 0 -0.48 3 3
ADAM12 -0.078 0.2 -9999 0 -0.52 81 81
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.031 0.043 -9999 0 -0.18 1 1
Syndecan-4/Laminin alpha1 -0.17 0.27 -9999 0 -0.6 104 104
Syndecan-4/CXCL12/CXCR4 -0.14 0.25 -9999 0 -0.55 100 100
Syndecan-4/Laminin alpha3 -0.16 0.26 -9999 0 -0.59 100 100
MDK -0.048 0.18 -9999 0 -0.55 51 51
Syndecan-4/FZD7 -0.16 0.28 -9999 0 -0.61 102 102
Syndecan-4/Midkine -0.16 0.26 -9999 0 -0.59 99 99
FZD7 -0.047 0.18 -9999 0 -0.59 47 47
Syndecan-4/FGFR1/FGF -0.15 0.21 -9999 0 -0.52 93 93
THBS1 -0.092 0.22 -9999 0 -0.53 91 91
integrin-mediated signaling pathway -0.16 0.26 -9999 0 -0.58 103 103
positive regulation of MAPKKK cascade -0.15 0.22 -9999 0 -0.52 100 100
Syndecan-4/TACI -0.14 0.24 -9999 0 -0.57 93 93
CXCR4 -0.013 0.12 -9999 0 -0.54 23 23
cell adhesion 0.02 0.055 -9999 0 -0.26 11 11
Syndecan-4/Dynamin -0.13 0.24 -9999 0 -0.56 92 92
Syndecan-4/TSP1 -0.18 0.26 -9999 0 -0.58 112 112
Syndecan-4/GIPC -0.14 0.24 -9999 0 -0.56 92 92
Syndecan-4/RANTES -0.19 0.26 -9999 0 -0.6 105 105
ITGB1 0.012 0.033 -9999 0 -0.5 2 2
LAMA1 -0.058 0.2 -9999 0 -0.58 56 56
LAMA3 -0.041 0.17 -9999 0 -0.56 45 45
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.038 0.054 -9999 0 -0.55 1 1
Syndecan-4/alpha-Actinin -0.15 0.26 -9999 0 -0.57 103 103
TFPI -0.09 0.22 -9999 0 -0.54 88 88
F2 -0.008 0.066 -9999 0 -0.49 8 8
alpha5/beta1 Integrin -0.02 0.085 -9999 0 -0.37 25 25
positive regulation of cell adhesion -0.18 0.28 -9999 0 -0.6 116 116
ACTN1 -0.02 0.13 -9999 0 -0.5 31 31
TNC -0.054 0.18 -9999 0 -0.55 56 56
Syndecan-4/CXCL12 -0.14 0.24 -9999 0 -0.56 95 95
FGF6 0.001 0.003 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CXCL12 0.003 0.078 -9999 0 -0.55 9 9
TNFRSF13B -0.004 0.069 -9999 0 -0.5 9 9
FGF2 0.011 0.047 -9999 0 -0.57 3 3
FGFR1 0.012 0.041 -9999 0 -0.61 2 2
Syndecan-4/PI-4-5-P2 -0.14 0.24 -9999 0 -0.57 92 92
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0 0.096 -9999 0 -0.49 17 17
cell migration -0.007 0.018 -9999 0 -10000 0 0
PRKCD -0.011 0.13 -9999 0 -0.58 22 22
vasculogenesis -0.18 0.25 -9999 0 -0.56 112 112
SDC4 -0.15 0.26 -9999 0 -0.6 92 92
Syndecan-4/Tenascin C -0.17 0.27 -9999 0 -0.61 103 103
Syndecan-4/PI-4-5-P2/PKC alpha -0.025 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.24 -9999 0 -0.56 92 92
MMP9 -0.15 0.25 -9999 0 -0.53 136 136
Rac1/GTP 0.02 0.057 -9999 0 -0.27 11 11
cytoskeleton organization -0.13 0.23 -9999 0 -0.54 92 92
GIPC1 0.013 0.024 -9999 0 -0.5 1 1
Syndecan-4/TFPI -0.18 0.26 -9999 0 -0.6 98 98
Thromboxane A2 receptor signaling

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
TGM2 0.008 0.047 -10000 0 -0.5 4 4
GNB1/GNG2 -0.081 0.081 -10000 0 -0.19 142 142
AKT1 -0.063 0.12 -10000 0 -0.23 34 34
EGF -0.047 0.18 -10000 0 -0.56 49 49
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.016 0.073 -10000 0 -0.32 4 4
mol:Ca2+ -0.1 0.16 -10000 0 -0.3 141 141
LYN 0.013 0.084 -10000 0 -0.33 10 10
RhoA/GTP -0.053 0.053 -10000 0 -0.15 3 3
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.12 0.18 -10000 0 -0.35 143 143
GNG2 0.009 0.058 -10000 0 -0.61 4 4
ARRB2 0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.008 0.1 -10000 0 -0.38 23 23
G beta5/gamma2 -0.1 0.1 -10000 0 -0.24 113 113
PRKCH -0.12 0.18 -10000 0 -0.34 132 132
DNM1 -0.11 0.23 -10000 0 -0.53 106 106
TXA2/TP beta/beta Arrestin3 -0.045 0.076 -10000 0 -0.25 31 31
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.043 0.16 -10000 0 -0.51 50 50
G12 family/GTP -0.13 0.13 -10000 0 -0.3 141 141
ADRBK1 0.014 0 -10000 0 -10000 0 0
ADRBK2 0.009 0.055 -10000 0 -0.58 4 4
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.061 0.11 0.31 29 -10000 0 29
mol:NADP 0.002 0.081 -10000 0 -0.54 10 10
RAB11A 0.014 0 -10000 0 -10000 0 0
PRKG1 -0.041 0.17 -10000 0 -0.59 42 42
mol:IP3 -0.13 0.19 -10000 0 -0.38 141 141
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.18 0.25 -10000 0 -0.51 141 141
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK -0.042 0.12 -10000 0 -0.34 18 18
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.007 0.093 -10000 0 -0.35 13 13
RHOA 0.014 0 -10000 0 -10000 0 0
PTGIR -0.016 0.13 -10000 0 -0.53 26 26
PRKCB1 -0.13 0.19 -10000 0 -0.37 142 142
GNAQ 0.014 0 -10000 0 -10000 0 0
mol:L-citrulline 0.002 0.081 -10000 0 -0.54 10 10
TXA2/TXA2-R family -0.19 0.26 -10000 0 -0.53 143 143
LCK -0.029 0.12 -10000 0 -0.34 24 24
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.027 0.069 -10000 0 -0.33 9 9
TXA2-R family/G12 family/GDP/G beta/gamma 0.023 0.047 -10000 0 -0.76 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.025 0.066 -10000 0 -0.38 4 4
MAPK14 -0.074 0.13 -10000 0 -0.24 93 93
TGM2/GTP -0.15 0.21 -10000 0 -0.42 143 143
MAPK11 -0.076 0.13 -10000 0 -0.24 136 136
ARHGEF1 -0.056 0.097 -10000 0 -0.2 18 18
GNAI2 0.014 0 -10000 0 -10000 0 0
JNK cascade -0.14 0.2 -10000 0 -0.39 143 143
RAB11/GDP 0.015 0.001 -10000 0 -10000 0 0
ICAM1 -0.1 0.16 -10000 0 -0.3 149 149
cAMP biosynthetic process -0.13 0.18 -10000 0 -0.35 145 145
Gq family/GTP/EBP50 0.006 0.085 -10000 0 -0.29 25 25
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.017 0.071 -10000 0 -0.32 4 4
GNB5 0.014 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
EGF/EGFR -0.026 0.11 -10000 0 -0.31 26 26
VCAM1 -0.13 0.19 -10000 0 -0.37 147 147
TP beta/Gq family/GDP/G beta5/gamma2 0.008 0.1 -10000 0 -0.38 23 23
platelet activation -0.098 0.17 -10000 0 -0.3 141 141
PGI2/IP -0.018 0.09 -10000 0 -0.39 26 26
PRKACA -0.012 0.084 -10000 0 -0.3 18 18
Gq family/GDP/G beta5/gamma2 0.006 0.096 -10000 0 -0.35 24 24
TXA2/TP beta/beta Arrestin2 -0.069 0.15 -10000 0 -0.54 36 36
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.007 0.089 -10000 0 -0.3 24 24
mol:DAG -0.15 0.21 -10000 0 -0.41 142 142
EGFR -0.083 0.22 -10000 0 -0.56 79 79
TXA2/TP alpha -0.18 0.24 -10000 0 -0.48 145 145
Gq family/GTP -0.017 0.071 -10000 0 -0.24 38 38
YES1 0.016 0.075 -10000 0 -0.32 4 4
GNAI2/GTP -0.025 0.064 -10000 0 -0.36 5 5
PGD2/DP -0.037 0.12 -10000 0 -0.37 50 50
SLC9A3R1 0.01 0.05 -10000 0 -0.61 3 3
FYN 0.017 0.071 -10000 0 -0.32 4 4
mol:NO 0.002 0.081 -10000 0 -0.54 10 10
GNA15 -0.01 0.12 -10000 0 -0.58 19 19
PGK/cGMP -0.04 0.12 -10000 0 -0.36 51 51
RhoA/GDP 0.015 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.027 0.076 -10000 0 -0.43 6 6
NOS3 0.002 0.081 -10000 0 -0.54 10 10
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.12 0.18 -10000 0 -0.34 133 133
PRKCB -0.14 0.2 -10000 0 -0.38 152 152
PRKCE -0.12 0.18 -10000 0 -0.35 134 134
PRKCD -0.14 0.2 -10000 0 -0.39 142 142
PRKCG -0.18 0.22 -10000 0 -0.43 164 164
muscle contraction -0.18 0.25 -10000 0 -0.49 146 146
PRKCZ -0.13 0.19 -10000 0 -0.35 151 151
ARR3 0.002 0.024 -10000 0 -0.5 1 1
TXA2/TP beta -0.028 0.073 -10000 0 -0.4 5 5
PRKCQ -0.12 0.18 -10000 0 -0.35 148 148
MAPKKK cascade -0.16 0.23 -10000 0 -0.45 145 145
SELE -0.13 0.18 -10000 0 -0.34 158 158
TP beta/GNAI2/GDP/G beta/gamma -0.025 0.069 -10000 0 -0.38 5 5
ROCK1 0.014 0 -10000 0 -10000 0 0
GNA14 -0.018 0.13 -10000 0 -0.58 25 25
chemotaxis -0.22 0.3 -10000 0 -0.61 144 144
GNA12 0.013 0.029 -10000 0 -0.61 1 1
GNA13 0.014 0 -10000 0 -10000 0 0
GNA11 0.005 0.076 -10000 0 -0.61 7 7
Rac1/GTP 0.003 0.005 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.038 0.051 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.092 0.14 -9999 0 -0.43 44 44
JUN -0.079 0.2 -9999 0 -0.54 49 49
HRAS 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.16 0.22 -9999 0 -0.45 127 127
RAP1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.012 0.037 -9999 0 -0.55 2 2
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.16 0.22 -9999 0 -0.45 126 126
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.095 0.18 -9999 0 -0.37 120 120
RHOA 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.21 -9999 0 -0.64 48 48
GRB7 -0.031 0.14 -9999 0 -0.5 38 38
RET51/GFRalpha1/GDNF -0.16 0.22 -9999 0 -0.45 126 126
MAPKKK cascade -0.13 0.18 -9999 0 -0.58 44 44
BCAR1 0.013 0.029 -9999 0 -0.61 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.091 0.17 -9999 0 -0.36 116 116
lamellipodium assembly -0.086 0.13 -9999 0 -0.4 43 43
RET51/GFRalpha1/GDNF/SHC -0.16 0.23 -9999 0 -0.46 126 126
PIK3CA 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.093 0.18 -9999 0 -0.37 116 116
RET9/GFRalpha1/GDNF/Shank3 -0.096 0.18 -9999 0 -0.36 122 122
MAPK3 -0.11 0.22 -9999 0 -0.6 48 48
DOK1 0.013 0.029 -9999 0 -0.61 1 1
DOK6 -0.048 0.18 -9999 0 -0.59 48 48
PXN 0.014 0 -9999 0 -10000 0 0
neurite development -0.1 0.22 -9999 0 -0.57 58 58
DOK5 0.001 0.09 -9999 0 -0.61 10 10
GFRA1 -0.073 0.21 -9999 0 -0.57 69 69
MAPK8 -0.087 0.2 -9999 0 -0.56 48 48
HRAS/GTP -0.14 0.21 -9999 0 -0.43 126 126
tube development -0.089 0.16 -9999 0 -0.39 84 84
MAPK1 -0.11 0.22 -9999 0 -0.6 48 48
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.042 0.15 -9999 0 -0.32 83 83
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
PDLIM7 0.006 0.066 -9999 0 -0.5 8 8
RET51/GFRalpha1/GDNF/Dok6 -0.18 0.26 -9999 0 -0.75 58 58
SHC1 0.009 0.053 -9999 0 -0.5 5 5
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.23 -9999 0 -0.46 135 135
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.23 -9999 0 -0.46 133 133
PRKCA 0.013 0.029 -9999 0 -0.61 1 1
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.069 0.18 -9999 0 -0.5 51 51
PIK3R1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.044 0.15 -9999 0 -0.34 83 83
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.24 -9999 0 -0.49 128 128
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.24 -9999 0 -0.56 107 107
DOK4 -0.008 0.12 -9999 0 -0.61 17 17
JNK cascade -0.077 0.19 -9999 0 -0.52 49 49
RET9/GFRalpha1/GDNF/FRS2 -0.092 0.17 -9999 0 -0.37 116 116
SHANK3 0.004 0.074 -9999 0 -0.52 9 9
RASA1 0.014 0 -9999 0 -10000 0 0
NCK1 0.013 0.029 -9999 0 -0.61 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.043 0.15 -9999 0 -0.33 83 83
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.094 0.21 -9999 0 -0.55 49 49
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.094 0.21 -9999 0 -0.37 126 126
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.098 0.22 -9999 0 -0.64 42 42
PI3K -0.09 0.24 -9999 0 -0.58 58 58
SOS1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.089 0.16 -9999 0 -0.39 84 84
GRB10 0.012 0.037 -9999 0 -0.55 2 2
activation of MAPKK activity -0.088 0.2 -9999 0 -0.48 71 71
RET51/GFRalpha1/GDNF/FRS2 -0.16 0.22 -9999 0 -0.45 126 126
GAB1 0.012 0.037 -9999 0 -0.55 2 2
IRS1 0.013 0.029 -9999 0 -0.61 1 1
IRS2 0.013 0.029 -9999 0 -0.61 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.099 0.22 -9999 0 -0.66 41 41
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.22 -9999 0 -0.45 126 126
GRB2 0.013 0.024 -9999 0 -0.5 1 1
PRKACA 0.014 0 -9999 0 -10000 0 0
GDNF -0.07 0.21 -9999 0 -0.59 64 64
RAC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.16 0.22 -9999 0 -0.45 126 126
Rac1/GTP -0.1 0.16 -9999 0 -0.49 43 43
RET9/GFRalpha1/GDNF -0.1 0.19 -9999 0 -0.41 115 115
GFRalpha1/GDNF -0.12 0.22 -9999 0 -0.47 115 115
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.14 0.37 -9999 0 -1 57 57
MKNK1 0.009 0.057 -9999 0 -0.61 4 4
MAPK14 -0.038 0.12 -9999 0 -0.36 7 7
ATF2/c-Jun -0.024 0.14 -9999 0 -0.56 16 16
MAPK11 -0.044 0.14 -9999 0 -0.31 73 73
MITF -0.038 0.16 -9999 0 -0.35 75 75
MAPKAPK5 -0.036 0.15 -9999 0 -0.34 73 73
KRT8 -0.11 0.22 -9999 0 -0.42 118 118
MAPKAPK3 0.012 0.041 -9999 0 -0.61 2 2
MAPKAPK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.059 0.19 -9999 0 -0.44 73 73
CEBPB -0.049 0.18 -9999 0 -0.39 81 81
SLC9A1 -0.037 0.16 -9999 0 -0.36 73 73
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.039 0.17 -9999 0 -0.35 82 82
p38alpha-beta/MNK1 -0.036 0.16 -9999 0 -0.57 12 12
JUN -0.024 0.14 -9999 0 -0.56 16 16
PPARGC1A -0.054 0.19 -9999 0 -0.4 82 82
USF1 -0.036 0.15 -9999 0 -0.34 73 73
RAB5/GDP/GDI1 -0.05 0.092 -9999 0 -0.39 8 8
NOS2 -0.082 0.28 -9999 0 -1 26 26
DDIT3 -0.04 0.16 -9999 0 -0.35 74 74
RAB5A 0.014 0 -9999 0 -10000 0 0
HSPB1 -0.037 0.15 -9999 0 -0.46 20 20
p38alpha-beta/HBP1 -0.033 0.15 -9999 0 -0.55 8 8
CREB1 -0.037 0.16 -9999 0 -0.37 71 71
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.025 0.14 -9999 0 -0.54 10 10
RPS6KA4 -0.036 0.15 -9999 0 -0.34 73 73
PLA2G4A -0.043 0.17 -9999 0 -0.6 21 21
GDI1 -0.036 0.15 -9999 0 -0.34 73 73
TP53 -0.057 0.19 -9999 0 -0.43 80 80
RPS6KA5 -0.043 0.16 -9999 0 -0.36 80 80
ESR1 -0.052 0.17 -9999 0 -0.37 86 86
HBP1 0.014 0 -9999 0 -10000 0 0
MEF2C -0.047 0.16 -9999 0 -0.36 80 80
MEF2A -0.037 0.16 -9999 0 -0.35 73 73
EIF4EBP1 -0.04 0.16 -9999 0 -0.37 72 72
KRT19 -0.098 0.21 -9999 0 -0.4 119 119
ELK4 -0.036 0.15 -9999 0 -0.34 73 73
ATF6 -0.036 0.15 -9999 0 -0.34 73 73
ATF1 -0.037 0.16 -9999 0 -0.36 75 75
p38alpha-beta/MAPKAPK2 -0.033 0.15 -9999 0 -0.34 73 73
p38alpha-beta/MAPKAPK3 -0.035 0.16 -9999 0 -0.51 12 12
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.012 0.033 -9999 0 -0.5 2 2
ITGB7 -0.034 0.16 -9999 0 -0.55 40 40
ITGA4 -0.056 0.19 -9999 0 -0.54 58 58
alpha4/beta7 Integrin -0.081 0.18 -9999 0 -0.44 86 86
alpha4/beta1 Integrin -0.05 0.13 -9999 0 -0.4 58 58
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.083 0.18 -9999 0 -0.49 65 65
alphaM/beta2 Integrin/GPIbA -0.079 0.17 -9999 0 -0.47 66 66
alphaM/beta2 Integrin/proMMP-9 -0.16 0.22 -9999 0 -0.41 170 170
PLAUR -0.024 0.14 -9999 0 -0.5 34 34
HMGB1 -0.001 0.022 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.067 0.16 -9999 0 -0.5 51 51
AGER -0.026 0.12 -9999 0 -0.61 18 18
RAP1A 0.014 0 -9999 0 -10000 0 0
SELPLG -0.019 0.14 -9999 0 -0.6 25 25
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.14 0.19 -9999 0 -0.58 48 48
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.15 0.25 -9999 0 -0.53 136 136
CYR61 -0.11 0.24 -9999 0 -0.56 99 99
TLN1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP -0.091 0.13 -9999 0 -0.42 41 41
RHOA 0.014 0 -9999 0 -10000 0 0
P-selectin oligomer -0.03 0.14 -9999 0 -0.49 37 37
MYH2 -0.088 0.15 -9999 0 -0.42 40 40
MST1R 0.005 0.074 -9999 0 -0.59 7 7
leukocyte activation during inflammatory response -0.12 0.19 -9999 0 -0.45 82 82
APOB -0.076 0.21 -9999 0 -0.56 73 73
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.013 0.12 -9999 0 -0.54 23 23
JAM3 0.014 0 -9999 0 -10000 0 0
GP1BA -0.005 0.11 -9999 0 -0.59 15 15
alphaM/beta2 Integrin/CTGF -0.089 0.19 -9999 0 -0.48 70 70
alphaM/beta2 Integrin -0.1 0.17 -9999 0 -0.42 65 65
JAM3 homodimer 0.014 0 -9999 0 -10000 0 0
ICAM2 0.013 0.024 -9999 0 -0.5 1 1
ICAM1 -0.029 0.15 -9999 0 -0.52 38 38
phagocytosis triggered by activation of immune response cell surface activating receptor -0.099 0.17 -9999 0 -0.42 65 65
cell adhesion -0.078 0.17 -9999 0 -0.47 66 66
NFKB1 -0.16 0.27 -9999 0 -0.65 74 74
THY1 -0.003 0.1 -9999 0 -0.57 14 14
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.073 0.14 -9999 0 -0.33 102 102
alphaM/beta2 Integrin/LRP/tPA -0.087 0.18 -9999 0 -0.46 62 62
IL6 -0.22 0.35 -9999 0 -0.8 94 94
ITGB2 -0.048 0.16 -9999 0 -0.58 36 36
elevation of cytosolic calcium ion concentration -0.11 0.21 -9999 0 -0.52 76 76
alphaM/beta2 Integrin/JAM2/JAM3 -0.055 0.15 -9999 0 -0.47 47 47
JAM2 0.013 0.029 -9999 0 -0.61 1 1
alphaM/beta2 Integrin/ICAM1 -0.096 0.18 -9999 0 -0.53 45 45
alphaM/beta2 Integrin/uPA/Plg -0.1 0.19 -9999 0 -0.45 84 84
RhoA/GTP -0.091 0.16 -9999 0 -0.42 50 50
positive regulation of phagocytosis -0.11 0.19 -9999 0 -0.6 44 44
Ron/MSP -0.037 0.12 -9999 0 -0.42 41 41
alphaM/beta2 Integrin/uPAR/uPA -0.11 0.21 -9999 0 -0.52 76 76
alphaM/beta2 Integrin/uPAR -0.089 0.19 -9999 0 -0.48 74 74
PLAU -0.061 0.19 -9999 0 -0.52 66 66
PLAT -0.049 0.17 -9999 0 -0.5 57 57
actin filament polymerization -0.085 0.15 -9999 0 -0.4 42 42
MST1 -0.029 0.16 -9999 0 -0.58 34 34
alphaM/beta2 Integrin/lipoprotein(a) -0.12 0.19 -9999 0 -0.45 82 82
TNF -0.24 0.36 -9999 0 -0.81 105 105
RAP1B 0.013 0.024 -9999 0 -0.5 1 1
alphaM/beta2 Integrin/uPA -0.11 0.2 -9999 0 -0.48 87 87
fibrinolysis -0.1 0.19 -9999 0 -0.45 84 84
HCK -0.01 0.11 -9999 0 -0.55 20 20
dendritic cell antigen processing and presentation -0.099 0.17 -9999 0 -0.42 65 65
VTN -0.012 0.12 -9999 0 -0.56 21 21
alphaM/beta2 Integrin/CYR61 -0.14 0.23 -9999 0 -0.47 123 123
LPA -0.024 0.13 -9999 0 -0.5 31 31
LRP1 0.014 0 -9999 0 -10000 0 0
cell migration -0.15 0.22 -9999 0 -0.47 108 108
FN1 -0.004 0.096 -9999 0 -0.5 17 17
alphaM/beta2 Integrin/Thy1 -0.077 0.17 -9999 0 -0.49 61 61
MPO -0.13 0.25 -9999 0 -0.55 115 115
KNG1 -0.019 0.11 -9999 0 -0.5 22 22
RAP1/GDP -0.001 0.014 -9999 0 -0.29 1 1
ROCK1 -0.078 0.15 -9999 0 -0.43 32 32
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.04 -9999 0 -0.5 3 3
CTGF -0.024 0.14 -9999 0 -0.54 32 32
alphaM/beta2 Integrin/Hck -0.08 0.21 -9999 0 -0.58 54 54
ITGAM -0.047 0.16 -9999 0 -0.62 34 34
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.095 0.22 -9999 0 -0.58 58 58
HP -0.1 0.23 -9999 0 -0.54 100 100
leukocyte adhesion -0.11 0.18 -9999 0 -0.57 45 45
SELP -0.03 0.14 -9999 0 -0.5 37 37
Endothelins

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
AKT1 -0.095 0.22 -10000 0 -0.57 47 47
PTK2B -0.011 0.11 -10000 0 -0.5 23 23
mol:Ca2+ -0.059 0.23 -10000 0 -0.76 28 28
EDN1 -0.082 0.19 -10000 0 -0.5 55 55
EDN3 -0.017 0.14 -10000 0 -0.6 24 24
EDN2 -0.013 0.094 -10000 0 -0.5 17 17
HRAS/GDP -0.094 0.21 -10000 0 -0.53 51 51
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.053 0.16 -10000 0 -0.41 44 44
ADCY4 -0.11 0.23 -10000 0 -0.52 81 81
ADCY5 -0.12 0.25 -10000 0 -0.57 80 80
ADCY6 -0.1 0.22 -10000 0 -0.51 77 77
ADCY7 -0.1 0.22 -10000 0 -0.51 77 77
ADCY1 -0.16 0.25 -10000 0 -0.54 109 109
ADCY2 -0.11 0.24 -10000 0 -0.53 83 83
ADCY3 -0.1 0.22 -10000 0 -0.51 77 77
ADCY8 -0.14 0.26 -10000 0 -0.54 103 103
ADCY9 -0.1 0.22 -10000 0 -0.52 77 77
arachidonic acid secretion -0.093 0.22 -10000 0 -0.52 64 64
ETB receptor/Endothelin-1/Gq/GTP -0.046 0.16 -10000 0 -0.45 37 37
GNAO1 0.006 0.07 -10000 0 -0.61 6 6
HRAS 0.013 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.097 0.21 0.26 21 -0.55 45 66
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.23 0.25 20 -0.54 80 100
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.2 0.33 -10000 0 -0.62 151 151
EDNRB -0.044 0.18 -10000 0 -0.6 43 43
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.12 0.26 -10000 0 -0.68 56 56
CYSLTR1 -0.11 0.25 -10000 0 -0.66 50 50
SLC9A1 -0.068 0.1 -10000 0 -0.32 30 30
mol:GDP -0.11 0.23 -10000 0 -0.54 64 64
SLC9A3 -0.093 0.26 -10000 0 -0.69 56 56
RAF1 -0.11 0.23 -10000 0 -0.54 63 63
JUN -0.043 0.19 -10000 0 -0.6 24 24
JAK2 -0.095 0.22 -10000 0 -0.57 47 47
mol:IP3 -0.06 0.18 -10000 0 -0.49 38 38
ETA receptor/Endothelin-1 -0.14 0.25 0.3 21 -0.58 67 88
PLCB1 -0.011 0.12 -10000 0 -0.61 18 18
PLCB2 -0.011 0.12 -10000 0 -0.58 18 18
ETA receptor/Endothelin-3 -0.074 0.16 -10000 0 -0.49 50 50
FOS -0.14 0.33 -10000 0 -0.85 66 66
Gai/GDP 0.001 0.13 -10000 0 -1 6 6
CRK 0.014 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.12 0.25 -10000 0 -0.56 79 79
BCAR1 0.013 0.029 -10000 0 -0.61 1 1
PRKCB1 -0.059 0.17 -10000 0 -0.47 39 39
GNAQ 0.014 0.007 -10000 0 -10000 0 0
GNAZ 0.013 0.029 -10000 0 -0.61 1 1
GNAL -0.051 0.19 -10000 0 -0.6 49 49
Gs family/GDP -0.15 0.21 -10000 0 -0.52 86 86
ETA receptor/Endothelin-1/Gq/GTP -0.053 0.15 -10000 0 -0.39 44 44
MAPK14 -0.038 0.16 -10000 0 -0.53 24 24
TRPC6 -0.063 0.25 -10000 0 -0.84 26 26
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.008 0.12 -10000 0 -0.61 17 17
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.049 0.17 -10000 0 -0.48 34 34
ETB receptor/Endothelin-2 -0.044 0.15 -10000 0 -0.42 59 59
ETB receptor/Endothelin-3 -0.048 0.17 -10000 0 -0.47 61 61
ETB receptor/Endothelin-1 -0.097 0.2 -10000 0 -0.52 62 62
MAPK3 -0.13 0.3 -10000 0 -0.75 69 69
MAPK1 -0.13 0.3 -10000 0 -0.74 70 70
Rac1/GDP -0.094 0.21 -10000 0 -0.53 51 51
cAMP biosynthetic process -0.12 0.24 -10000 0 -0.53 89 89
MAPK8 -0.058 0.21 -10000 0 -0.63 31 31
SRC 0.014 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.023 0.13 -10000 0 -0.4 28 28
p130Cas/CRK/Src/PYK2 -0.098 0.23 -10000 0 -0.58 52 52
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.094 0.21 -10000 0 -0.54 50 50
COL1A2 -0.13 0.29 -10000 0 -0.69 74 74
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.067 0.14 -10000 0 -0.45 44 44
mol:DAG -0.06 0.18 -10000 0 -0.5 37 37
MAP2K2 -0.12 0.25 -10000 0 -0.59 71 71
MAP2K1 -0.12 0.25 -10000 0 -0.6 69 69
EDNRA -0.067 0.18 -10000 0 -0.52 41 41
positive regulation of muscle contraction -0.073 0.19 -10000 0 -0.51 45 45
Gq family/GDP -0.12 0.2 -10000 0 -0.57 50 50
HRAS/GTP -0.1 0.22 -10000 0 -0.51 63 63
PRKCH -0.051 0.17 -10000 0 -0.52 28 28
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.051 0.17 -10000 0 -0.5 32 32
PRKCB -0.09 0.2 -10000 0 -0.5 57 57
PRKCE -0.056 0.18 -10000 0 -0.49 36 36
PRKCD -0.066 0.2 -10000 0 -0.56 41 41
PRKCG -0.15 0.23 -10000 0 -0.5 94 94
regulation of vascular smooth muscle contraction -0.16 0.38 -10000 0 -1 63 63
PRKCQ -0.062 0.19 -10000 0 -0.52 43 43
PLA2G4A -0.1 0.24 -10000 0 -0.57 64 64
GNA14 -0.018 0.13 -10000 0 -0.58 25 25
GNA15 -0.011 0.12 -10000 0 -0.58 19 19
GNA12 0.013 0.029 -10000 0 -0.61 1 1
GNA11 0.004 0.076 -10000 0 -0.61 7 7
Rac1/GTP -0.096 0.2 0.26 21 -0.54 45 66
MMP1 0.013 0.17 -10000 0 -0.42 43 43
Caspase cascade in apoptosis

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
TOP1 -0.051 0.16 0.2 2 -0.33 90 92
ACTA1 -0.074 0.19 0.25 1 -0.41 93 94
NUMA1 -0.051 0.16 0.21 1 -0.34 87 88
SPTAN1 -0.063 0.19 0.25 3 -0.41 87 90
LIMK1 -0.063 0.19 0.25 3 -0.41 87 90
BIRC3 -0.035 0.16 -10000 0 -0.56 40 40
BIRC2 0.014 0 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
CASP10 -0.092 0.21 -10000 0 -0.4 132 132
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
PTK2 -0.051 0.16 0.21 1 -0.34 87 88
DIABLO 0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.062 0.19 0.25 3 -0.4 87 90
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
GSN -0.07 0.19 0.25 1 -0.41 90 91
MADD 0.014 0 -10000 0 -10000 0 0
TFAP2A -0.19 0.3 -10000 0 -0.66 125 125
BID -0.044 0.12 -10000 0 -0.24 98 98
MAP3K1 -0.016 0.071 -10000 0 -0.22 6 6
TRADD 0.013 0.029 -10000 0 -0.61 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.007 0.02 -10000 0 -0.35 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.065 0.19 0.25 3 -0.41 88 91
CASP9 0.013 0.024 -10000 0 -0.5 1 1
DNA repair 0.004 0.063 -10000 0 -0.19 19 19
neuron apoptosis 0.005 0.048 -10000 0 -0.43 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.055 0.18 0.24 2 -0.4 81 83
APAF1 0.014 0 -10000 0 -10000 0 0
CASP6 -0.033 0.12 -10000 0 -0.68 5 5
TRAF2 0.014 0 -10000 0 -10000 0 0
ICAD/CAD -0.053 0.18 -10000 0 -0.4 79 79
CASP7 0.02 0.079 0.27 35 -10000 0 35
KRT18 -0.085 0.2 -10000 0 -0.6 57 57
apoptosis -0.077 0.19 0.26 1 -0.42 70 71
DFFA -0.063 0.19 0.25 3 -0.41 85 88
DFFB -0.063 0.19 0.25 3 -0.41 86 89
PARP1 -0.004 0.063 0.19 19 -10000 0 19
actin filament polymerization 0.05 0.18 0.38 81 -0.25 1 82
TNF -0.16 0.26 -10000 0 -0.55 142 142
CYCS -0.027 0.084 -10000 0 -0.21 38 38
SATB1 -0.028 0.12 -10000 0 -0.55 9 9
SLK -0.064 0.19 0.25 3 -0.41 86 89
p15 BID/BAX -0.032 0.1 -10000 0 -0.32 19 19
CASP2 -0.018 0.11 -10000 0 -0.39 12 12
JNK cascade 0.016 0.071 0.22 6 -10000 0 6
CASP3 -0.075 0.2 0.25 4 -0.43 91 95
LMNB2 -0.015 0.096 -10000 0 -0.4 9 9
RIPK1 0.014 0 -10000 0 -10000 0 0
CASP4 -0.016 0.12 -10000 0 -0.5 27 27
Mammalian IAPs/DIABLO -0.025 0.083 -10000 0 -0.33 23 23
negative regulation of DNA binding -0.19 0.3 -10000 0 -0.65 125 125
stress fiber formation -0.063 0.19 0.25 3 -0.4 86 89
GZMB -0.12 0.24 -10000 0 -0.48 132 132
CASP1 -0.009 0.094 -10000 0 -0.31 39 39
LMNB1 -0.023 0.11 -10000 0 -0.39 16 16
APP 0.005 0.048 -10000 0 -0.43 1 1
TNFRSF1A 0.003 0.079 -10000 0 -0.56 9 9
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0 0.069 -10000 0 -0.36 16 16
VIM -0.083 0.19 0.23 8 -0.4 92 100
LMNA -0.015 0.095 -10000 0 -0.39 9 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.028 0.12 -10000 0 -0.38 17 17
LRDD 0.007 0.068 -10000 0 -0.59 6 6
SREBF1 -0.074 0.19 0.25 2 -0.4 95 97
APAF-1/Caspase 9 -0.007 0.044 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.05 0.15 0.21 1 -0.33 87 88
CFL2 -0.052 0.18 0.25 1 -0.39 81 82
GAS2 -0.073 0.2 0.25 2 -0.41 93 95
positive regulation of apoptosis -0.015 0.1 -10000 0 -0.36 13 13
PRF1 -0.07 0.2 -10000 0 -0.55 69 69
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.006 0.049 -10000 0 -0.44 4 4
fibroblast growth factor receptor signaling pathway -0.006 0.049 -10000 0 -0.43 4 4
LAMA1 -0.058 0.2 -10000 0 -0.58 56 56
PRNP 0.013 0.029 -10000 0 -0.61 1 1
GPC1/SLIT2 -0.097 0.17 -10000 0 -0.39 115 115
SMAD2 0.03 0.048 -10000 0 -0.42 2 2
GPC1/PrPc/Cu2+ -0.003 0.032 -10000 0 -0.31 5 5
GPC1/Laminin alpha1 -0.053 0.14 -10000 0 -0.43 58 58
TDGF1 -0.081 0.22 -10000 0 -0.58 74 74
CRIPTO/GPC1 -0.07 0.16 -10000 0 -0.43 75 75
APP/GPC1 -0.003 0.032 -10000 0 -0.35 4 4
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.035 0.15 -10000 0 -0.37 76 76
FLT1 0.013 0.029 -10000 0 -0.61 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.007 0.048 -10000 0 -0.32 10 10
SERPINC1 -0.003 0.087 -10000 0 -0.5 14 14
FYN -0.032 0.15 -10000 0 -0.36 75 75
FGR -0.034 0.15 -10000 0 -0.36 78 78
positive regulation of MAPKKK cascade -0.078 0.2 -10000 0 -0.48 67 67
SLIT2 -0.12 0.24 -10000 0 -0.55 112 112
GPC1/NRG -0.13 0.19 -10000 0 -0.41 148 148
NRG1 -0.17 0.27 -10000 0 -0.57 146 146
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.016 0.068 -10000 0 -0.3 25 25
LYN -0.039 0.15 -10000 0 -0.39 58 58
mol:Spermine 0.009 0.034 -10000 0 -0.36 4 4
cell growth -0.006 0.049 -10000 0 -0.43 4 4
BMP signaling pathway -0.01 0.047 0.49 4 -10000 0 4
SRC -0.032 0.15 -10000 0 -0.36 75 75
TGFBR1 0.012 0.037 -10000 0 -0.55 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.085 0.2 -10000 0 -0.51 81 81
GPC1 0.01 0.047 -10000 0 -0.5 4 4
TGFBR1 (dimer) 0.012 0.037 -10000 0 -0.55 2 2
VEGFA -0.009 0.11 -10000 0 -0.5 21 21
BLK -0.11 0.2 -10000 0 -0.35 165 165
HCK -0.047 0.17 -10000 0 -0.37 89 89
FGF2 0.011 0.047 -10000 0 -0.57 3 3
FGFR1 0.012 0.041 -10000 0 -0.61 2 2
VEGFR1 homodimer 0.013 0.029 -10000 0 -0.61 1 1
TGFBR2 0.009 0.053 -10000 0 -0.5 5 5
cell death -0.003 0.032 -10000 0 -0.34 4 4
ATIII/GPC1 -0.013 0.067 -10000 0 -0.35 18 18
PLA2G2A/GPC1 -0.066 0.14 -10000 0 -0.37 82 82
LCK -0.095 0.2 -10000 0 -0.38 142 142
neuron differentiation -0.13 0.19 -10000 0 -0.41 148 148
PrPc/Cu2+ -0.001 0.021 -10000 0 -0.45 1 1
APP 0.014 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.009 0.053 -10000 0 -0.49 5 5
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.038 0.1 -9999 0 -0.32 43 43
RGS9BP 0.002 0.084 -9999 0 -0.6 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.011 0.037 -9999 0 -0.55 2 2
mol:Na + -0.1 0.15 -9999 0 -0.32 146 146
mol:ADP 0.017 0.044 -9999 0 -0.36 6 6
GNAT2 0.009 0.034 -9999 0 -0.5 2 2
RGS9-1/Gbeta5/R9AP -0.04 0.12 -9999 0 -0.4 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.013 0.062 -9999 0 -0.31 19 19
GRK7 0.008 0.047 -9999 0 -0.5 4 4
CNGB3 -0.011 0.098 -9999 0 -0.5 18 18
Cone Metarhodopsin II/X-Arrestin -0.001 0.017 -9999 0 -0.36 1 1
mol:Ca2+ -0.14 0.2 -9999 0 -0.35 210 210
Cone PDE6 -0.045 0.12 -9999 0 -0.36 33 33
Cone Metarhodopsin II -0.004 0.032 -9999 0 -0.28 6 6
Na + (4 Units) -0.16 0.19 -9999 0 -0.35 210 210
GNAT2/GDP -0.035 0.11 -9999 0 -0.34 43 43
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.003 0.066 -9999 0 -0.27 24 24
Cone Transducin -0.041 0.11 -9999 0 -0.34 43 43
SLC24A2 -0.11 0.24 -9999 0 -0.56 103 103
GNB3/GNGT2 -0.052 0.14 -9999 0 -0.41 58 58
GNB3 -0.031 0.16 -9999 0 -0.58 35 35
GNAT2/GTP -0.002 0.023 -9999 0 -0.36 2 2
CNGA3 -0.14 0.25 -9999 0 -0.54 129 129
ARR3 0.002 0.024 -9999 0 -0.5 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.1 0.15 -9999 0 -0.33 146 146
mol:Pi -0.04 0.12 -9999 0 -0.4 43 43
Cone CNG Channel -0.092 0.14 -9999 0 -0.38 37 37
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.11 0.24 -9999 0 -0.56 103 103
RGS9 -0.042 0.18 -9999 0 -0.59 43 43
PDE6C 0.002 0.052 -9999 0 -0.5 5 5
GNGT2 -0.014 0.13 -9999 0 -0.56 23 23
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.01 0.098 -9999 0 -0.5 18 18
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.18 0.38 -10000 0 -0.96 57 57
PCK1 -0.25 0.44 -10000 0 -1.1 75 75
HNF4A -0.21 0.42 -10000 0 -1.1 59 59
KCNJ11 -0.25 0.51 -10000 0 -1.2 78 78
AKT1 -0.077 0.17 -10000 0 -0.42 21 21
response to starvation -0.003 0.023 -10000 0 -10000 0 0
DLK1 -0.25 0.45 -10000 0 -1 91 91
NKX2-1 -0.076 0.22 -10000 0 -0.67 23 23
ACADM -0.18 0.38 -10000 0 -0.96 56 56
TAT -0.23 0.42 -10000 0 -1.1 59 59
CEBPB -0.005 0.11 -10000 0 -0.58 15 15
CEBPA -0.016 0.13 -10000 0 -0.58 24 24
TTR -0.16 0.28 -10000 0 -0.78 45 45
PKLR -0.19 0.4 -10000 0 -0.94 66 66
APOA1 -0.24 0.48 -10000 0 -1.2 61 61
CPT1C -0.18 0.39 -10000 0 -0.96 59 59
ALAS1 -0.063 0.2 -10000 0 -0.88 2 2
TFRC -0.17 0.32 -10000 0 -0.78 53 53
FOXF1 -0.005 0.094 -10000 0 -0.52 14 14
NF1 0.02 0.041 -10000 0 -0.6 2 2
HNF1A (dimer) 0.011 0.041 -10000 0 -0.67 1 1
CPT1A -0.18 0.39 -10000 0 -0.98 57 57
HMGCS1 -0.18 0.38 -10000 0 -0.97 56 56
NR3C1 -0.023 0.076 -10000 0 -0.3 1 1
CPT1B -0.2 0.41 -10000 0 -0.97 70 70
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.01 0.025 -10000 0 -10000 0 0
GCK -0.25 0.48 -10000 0 -1 98 98
CREB1 -0.004 0.055 -10000 0 -10000 0 0
IGFBP1 -0.26 0.51 -10000 0 -1.3 78 78
PDX1 -0.08 0.21 -10000 0 -0.72 8 8
UCP2 -0.2 0.42 -10000 0 -0.96 77 77
ALDOB -0.19 0.43 -10000 0 -1 67 67
AFP -0.093 0.18 -10000 0 -0.58 28 28
BDH1 -0.21 0.44 -10000 0 -1.1 73 73
HADH -0.18 0.4 -10000 0 -0.98 60 60
F2 -0.21 0.42 -10000 0 -1.1 49 49
HNF1A 0.011 0.041 -10000 0 -0.67 1 1
G6PC -0.072 0.22 -10000 0 -0.79 23 23
SLC2A2 -0.092 0.22 -10000 0 -0.57 20 20
INS 0.014 0.089 0.24 7 -0.56 4 11
FOXA1 -0.053 0.17 -10000 0 -0.53 43 43
FOXA3 -0.13 0.24 -10000 0 -0.56 91 91
FOXA2 -0.22 0.46 -10000 0 -1 75 75
ABCC8 -0.27 0.53 -10000 0 -1.2 85 85
ALB -0.13 0.3 -10000 0 -1.1 34 34
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.024 0.099 -9999 0 -0.44 25 25
VLDLR -0.003 0.1 -9999 0 -0.57 14 14
CRKL 0.014 0 -9999 0 -10000 0 0
LRPAP1 0.014 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
ITGA3 -0.011 0.11 -9999 0 -0.51 22 22
RELN/VLDLR/Fyn -0.098 0.16 -9999 0 -0.34 132 132
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.01 0.053 -9999 0 -10000 0 0
AKT1 -0.067 0.15 -9999 0 -0.48 24 24
MAP2K7 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
DAB1 -0.087 0.22 -9999 0 -0.58 79 79
RELN/LRP8/DAB1 -0.13 0.18 -9999 0 -0.39 120 120
LRPAP1/LRP8 -0.001 0.02 -9999 0 -0.44 1 1
RELN/LRP8/DAB1/Fyn -0.12 0.17 -9999 0 -0.36 120 120
DAB1/alpha3/beta1 Integrin -0.13 0.17 -9999 0 -0.54 43 43
long-term memory -0.29 0.29 -9999 0 -0.65 151 151
DAB1/LIS1 -0.12 0.16 -9999 0 -0.55 31 31
DAB1/CRLK/C3G -0.11 0.16 -9999 0 -0.53 31 31
PIK3CA 0.014 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.12 0.17 -9999 0 -0.55 31 31
ARHGEF2 0.013 0.029 -9999 0 -0.61 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.17 0.27 -9999 0 -0.56 147 147
CDK5R1 -0.019 0.14 -9999 0 -0.6 25 25
RELN -0.14 0.25 -9999 0 -0.56 122 122
PIK3R1 0.014 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.088 0.15 -9999 0 -0.33 122 122
GRIN2A/RELN/LRP8/DAB1/Fyn -0.21 0.24 -9999 0 -0.61 93 93
MAPK8 0.001 0.09 -9999 0 -0.61 10 10
RELN/VLDLR/DAB1 -0.14 0.19 -9999 0 -0.4 127 127
ITGB1 0.012 0.033 -9999 0 -0.5 2 2
MAP1B -0.1 0.19 -9999 0 -0.57 31 31
RELN/LRP8 -0.088 0.15 -9999 0 -0.37 69 69
GRIN2B/RELN/LRP8/DAB1/Fyn -0.22 0.24 -9999 0 -0.6 95 95
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.018 0.082 -9999 0 -0.37 23 23
RAP1A -0.068 0.17 -9999 0 -0.49 31 31
PAFAH1B1 0.014 0 -9999 0 -10000 0 0
MAPK8IP1 0.009 0.057 -9999 0 -0.61 4 4
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.19 0.27 -9999 0 -0.55 165 165
NCK2 0.014 0 -9999 0 -10000 0 0
neuron differentiation -0.039 0.14 -9999 0 -0.43 26 26
neuron adhesion -0.062 0.18 -9999 0 -0.48 36 36
LRP8 0.013 0.029 -9999 0 -0.61 1 1
GSK3B -0.055 0.15 -9999 0 -0.46 23 23
RELN/VLDLR/DAB1/Fyn -0.13 0.18 -9999 0 -0.37 127 127
MAP3K11 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.08 0.16 -9999 0 -0.31 127 127
CDK5 0.014 0 -9999 0 -10000 0 0
MAPT 0.01 0.084 -9999 0 -0.55 9 9
neuron migration -0.065 0.19 -9999 0 -0.52 33 33
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.039 0.14 -9999 0 -0.43 26 26
RELN/VLDLR -0.087 0.14 -9999 0 -0.34 79 79
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 + 0.014 0 -9999 0 -10000 0 0
GNAT1/GTP -0.023 0.089 -9999 0 -0.36 30 30
Metarhodopsin II/Arrestin -0.033 0.1 -9999 0 -0.33 47 47
PDE6G/GNAT1/GTP -0.048 0.12 -9999 0 -0.34 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.022 0.13 -9999 0 -0.5 30 30
GRK1 0.011 0.037 -9999 0 -0.55 2 2
CNG Channel -0.2 0.2 -9999 0 -0.55 75 75
mol:Na + -0.2 0.2 -9999 0 -0.52 92 92
mol:ADP 0.011 0.037 -9999 0 -0.55 2 2
RGS9-1/Gbeta5/R9AP -0.04 0.12 -9999 0 -0.4 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.21 0.21 -9999 0 -0.54 92 92
CNGB1 -0.18 0.26 -9999 0 -0.53 166 166
RDH5 -0.018 0.12 -9999 0 -0.5 29 29
SAG 0.003 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.17 0.21 -9999 0 -0.5 92 92
Na + (4 Units) -0.19 0.19 -9999 0 -0.49 92 92
RGS9 -0.042 0.18 -9999 0 -0.59 43 43
GNB1/GNGT1 -0.001 0.016 -9999 0 -0.35 1 1
GNAT1/GDP -0.049 0.12 -9999 0 -0.34 45 45
GUCY2D -0.007 0.09 -9999 0 -0.5 15 15
GNGT1 -0.001 0.023 -9999 0 -0.5 1 1
GUCY2F 0.005 0.047 -9999 0 -0.5 4 4
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.067 0.16 -9999 0 -0.37 70 70
mol:11-cis-retinal -0.018 0.12 -9999 0 -0.5 29 29
mol:cGMP -0.091 0.17 -9999 0 -0.38 88 88
GNB1 0.014 0 -9999 0 -10000 0 0
Rhodopsin -0.06 0.14 -9999 0 -0.37 75 75
SLC24A1 0.014 0 -9999 0 -10000 0 0
CNGA1 -0.054 0.19 -9999 0 -0.57 54 54
Metarhodopsin II -0.031 0.09 -9999 0 -0.29 49 49
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.11 0.18 -9999 0 -0.41 90 90
RGS9BP 0.002 0.084 -9999 0 -0.6 9 9
Metarhodopsin II/Transducin -0.014 0.079 -9999 0 -0.3 17 17
GCAP Family/Ca ++ -0.1 0.17 -9999 0 -0.35 137 137
PDE6A/B -0.074 0.16 -9999 0 -0.4 85 85
mol:Pi -0.04 0.12 -9999 0 -0.4 43 43
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.018 0.07 -9999 0 -0.28 30 30
PDE6B -0.037 0.16 -9999 0 -0.55 42 42
PDE6A -0.043 0.17 -9999 0 -0.54 47 47
PDE6G -0.034 0.16 -9999 0 -0.57 38 38
RHO -0.044 0.16 -9999 0 -0.53 47 47
PDE6 -0.1 0.17 -9999 0 -0.58 29 29
GUCA1A -0.14 0.25 -9999 0 -0.55 127 127
GC2/GCAP Family -0.1 0.17 -9999 0 -0.4 83 83
GUCA1C -0.013 0.091 -9999 0 -0.5 16 16
GUCA1B -0.007 0.11 -9999 0 -0.6 16 16
HIF-1-alpha transcription factor network

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
PKM2 -0.017 0.49 -9999 0 -1.1 52 52
HDAC7 0.017 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.14 0.33 -9999 0 -0.86 54 54
SMAD4 0.016 0.003 -9999 0 -10000 0 0
ID2 -0.017 0.49 -9999 0 -1.1 52 52
AP1 -0.065 0.18 -9999 0 -0.43 88 88
ABCG2 -0.018 0.49 -9999 0 -1.1 52 52
HIF1A 0.025 0.09 -9999 0 -0.56 1 1
TFF3 -0.056 0.51 -9999 0 -1.1 61 61
GATA2 -0.006 0.11 -9999 0 -0.58 16 16
AKT1 0.019 0.1 -9999 0 -10000 0 0
response to hypoxia 0.001 0.11 -9999 0 -0.23 19 19
MCL1 -0.017 0.49 -9999 0 -1.1 52 52
NDRG1 -0.021 0.5 -9999 0 -1.1 53 53
SERPINE1 -0.092 0.55 -9999 0 -1.1 75 75
FECH -0.017 0.49 -9999 0 -1.1 52 52
FURIN -0.017 0.49 -9999 0 -1.1 52 52
NCOA2 -0.023 0.15 -9999 0 -0.61 29 29
EP300 0.034 0.18 -9999 0 -0.34 32 32
HMOX1 -0.027 0.51 -9999 0 -1.1 55 55
BHLHE40 -0.026 0.51 -9999 0 -1.1 56 56
BHLHE41 -0.024 0.51 -9999 0 -1.1 55 55
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.013 0.059 -9999 0 -0.38 6 6
ENG 0.09 0.13 -9999 0 -0.52 7 7
JUN 0.003 0.076 -9999 0 -0.51 10 10
RORA -0.017 0.49 -9999 0 -1 53 53
ABCB1 -0.04 0.096 -9999 0 -1.1 2 2
TFRC -0.023 0.5 -9999 0 -1.1 55 55
CXCR4 -0.029 0.51 -9999 0 -1.1 57 57
TF -0.048 0.53 -9999 0 -1.1 58 58
CITED2 -0.018 0.49 -9999 0 -1.1 52 52
HIF1A/ARNT -0.19 0.51 -9999 0 -1.2 58 58
LDHA -0.031 0.094 -9999 0 -0.68 6 6
ETS1 -0.021 0.5 -9999 0 -1.1 54 54
PGK1 -0.017 0.49 -9999 0 -1.1 52 52
NOS2 -0.043 0.52 -9999 0 -1.1 60 60
ITGB2 -0.037 0.52 -9999 0 -1.1 58 58
ALDOA -0.017 0.49 -9999 0 -1.1 52 52
Cbp/p300/CITED2 -0.086 0.5 -9999 0 -1.1 54 54
FOS -0.093 0.22 -9999 0 -0.56 87 87
HK2 -0.03 0.51 -9999 0 -1.1 56 56
SP1 0.024 0.005 -9999 0 -10000 0 0
GCK -0.068 0.48 -9999 0 -1.1 63 63
HK1 -0.017 0.49 -9999 0 -1.1 52 52
NPM1 -0.017 0.49 -9999 0 -1.1 52 52
EGLN1 -0.017 0.49 -9999 0 -1.1 52 52
CREB1 0.023 0.003 -9999 0 -10000 0 0
PGM1 -0.017 0.49 -9999 0 -1.1 52 52
SMAD3 0.016 0.003 -9999 0 -10000 0 0
EDN1 -0.047 0.33 -9999 0 -1 28 28
IGFBP1 -0.078 0.53 -9999 0 -1.1 65 65
VEGFA 0.017 0.41 -9999 0 -0.85 43 43
HIF1A/JAB1 -0.007 0.031 -9999 0 -0.41 1 1
CP -0.1 0.55 -9999 0 -1.1 72 72
CXCL12 -0.021 0.5 -9999 0 -1.1 53 53
COPS5 0.016 0.003 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
BNIP3 -0.018 0.49 -9999 0 -1.1 52 52
EGLN3 -0.02 0.5 -9999 0 -1.1 52 52
CA9 -0.053 0.53 -9999 0 -1.1 59 59
TERT -0.084 0.51 -9999 0 -1.1 69 69
ENO1 -0.017 0.49 -9999 0 -1.1 52 52
PFKL -0.017 0.49 -9999 0 -1.1 52 52
NCOA1 0.015 0.001 -9999 0 -10000 0 0
ADM -0.053 0.52 -9999 0 -1.1 61 61
ARNT 0.015 0.089 -9999 0 -0.66 1 1
HNF4A -0.043 0.14 -9999 0 -0.49 37 37
ADFP -0.066 0.47 -9999 0 -1 55 55
SLC2A1 0.025 0.39 -9999 0 -0.79 41 41
LEP -0.053 0.48 -9999 0 -1.1 52 52
HIF1A/ARNT/Cbp/p300 -0.15 0.35 -9999 0 -0.86 61 61
EPO 0.027 0.36 -9999 0 -0.83 28 28
CREBBP 0.037 0.17 -9999 0 -0.33 27 27
HIF1A/ARNT/Cbp/p300/HDAC7 -0.14 0.34 -9999 0 -0.89 53 53
PFKFB3 -0.018 0.49 -9999 0 -1.1 52 52
NT5E -0.026 0.5 -9999 0 -1.1 57 57
EGFR-dependent Endothelin signaling events

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.014 0 -9999 0 -10000 0 0
EGFR -0.083 0.22 -9999 0 -0.56 79 79
EGF/EGFR -0.11 0.17 -9999 0 -0.37 103 103
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.078 0.14 -9999 0 -0.35 76 76
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.021 0.14 -9999 0 -0.56 29 29
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.047 0.18 -9999 0 -0.56 49 49
EGF/EGFR dimer/SHC -0.094 0.17 -9999 0 -0.37 117 117
mol:GDP -0.077 0.14 -9999 0 -0.35 76 76
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.037 0.16 -9999 0 -0.53 43 43
GRB2/SOS1 -0.001 0.016 -9999 0 -0.35 1 1
HRAS/GTP -0.07 0.13 -9999 0 -0.5 16 16
SHC1 0.009 0.053 -9999 0 -0.5 5 5
HRAS/GDP -0.071 0.13 -9999 0 -0.51 16 16
FRAP1 -0.044 0.15 -9999 0 -0.34 76 76
EGF/EGFR dimer -0.11 0.2 -9999 0 -0.44 115 115
SOS1 0.014 0 -9999 0 -10000 0 0
GRB2 0.013 0.024 -9999 0 -0.5 1 1
ETA receptor/Endothelin-1 -0.06 0.15 -9999 0 -0.4 69 69
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.11 0.18 -10000 0 -0.39 129 129
CRKL -0.045 0.13 -10000 0 -0.5 10 10
mol:PIP3 -0.018 0.026 0.53 1 -10000 0 1
AKT1 0.003 0.024 0.37 1 -0.34 1 2
PTK2B -0.011 0.11 -10000 0 -0.5 23 23
RAPGEF1 -0.035 0.13 -10000 0 -0.46 10 10
RANBP10 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.14 0.19 -10000 0 -0.37 177 177
MAP3K5 -0.038 0.14 -10000 0 -0.42 21 21
HGF/MET/CIN85/CBL/ENDOPHILINS -0.13 0.17 -10000 0 -0.4 95 95
AP1 -0.088 0.17 -10000 0 -0.41 88 88
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.009 0.053 -10000 0 -0.5 5 5
apoptosis -0.097 0.24 -10000 0 -0.77 50 50
STAT3 (dimer) -0.048 0.14 -10000 0 -0.42 15 15
GAB1/CRKL/SHP2/PI3K -0.058 0.097 -10000 0 -0.45 9 9
INPP5D 0.008 0.058 -10000 0 -0.54 5 5
CBL/CRK -0.035 0.13 -10000 0 -0.46 10 10
PTPN11 0.014 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
PTEN 0.013 0.029 -10000 0 -0.61 1 1
ELK1 -0.057 0.092 -10000 0 -0.2 129 129
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.049 0.077 -10000 0 -0.34 10 10
PAK1 -0.015 0.081 0.35 1 -0.31 6 7
HGF/MET/RANBP10 -0.14 0.19 -10000 0 -0.37 177 177
HRAS -0.1 0.24 -10000 0 -0.65 61 61
DOCK1 -0.037 0.13 -10000 0 -0.46 10 10
GAB1 -0.056 0.14 -10000 0 -0.3 84 84
CRK -0.045 0.13 -10000 0 -0.29 66 66
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.13 0.22 -10000 0 -0.6 72 72
JUN 0.003 0.076 -10000 0 -0.51 10 10
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.074 0.13 -10000 0 -0.29 95 95
PIK3R1 0.014 0 -10000 0 -10000 0 0
cell morphogenesis -0.018 0.14 -10000 0 -0.45 10 10
GRB2/SHC -0.052 0.12 -10000 0 -0.45 14 14
FOS -0.093 0.22 -10000 0 -0.56 87 87
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.057 0.092 -10000 0 -0.2 129 129
HGF/MET/MUC20 -0.14 0.2 -10000 0 -0.38 177 177
cell migration -0.051 0.12 -10000 0 -0.44 14 14
GRB2 0.013 0.024 -10000 0 -0.5 1 1
CBL 0.014 0 -10000 0 -10000 0 0
MET/RANBP10 -0.11 0.18 -10000 0 -0.39 129 129
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.061 0.14 -10000 0 -0.36 33 33
MET/MUC20 -0.11 0.18 -10000 0 -0.4 129 129
RAP1B -0.025 0.12 -10000 0 -0.43 10 10
RAP1A -0.025 0.12 -10000 0 -0.44 9 9
HGF/MET/RANBP9 -0.14 0.19 -10000 0 -0.37 177 177
RAF1 -0.089 0.22 -10000 0 -0.61 60 60
STAT3 -0.049 0.14 -10000 0 -0.42 15 15
cell proliferation -0.062 0.18 -10000 0 -0.4 81 81
RPS6KB1 -0.02 0.05 -10000 0 -0.24 1 1
MAPK3 -0.058 0.083 -10000 0 -10000 0 0
MAPK1 -0.058 0.083 -10000 0 -0.21 2 2
RANBP9 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.02 0.14 -10000 0 -0.44 21 21
SRC -0.048 0.13 -10000 0 -0.42 15 15
PI3K -0.049 0.12 -10000 0 -0.27 60 60
MET/Glomulin -0.088 0.16 -10000 0 -0.35 129 129
SOS1 0.014 0 -10000 0 -10000 0 0
MAP2K1 -0.075 0.21 -10000 0 -0.55 60 60
MET -0.14 0.25 -10000 0 -0.55 129 129
MAP4K1 -0.046 0.14 -10000 0 -0.44 19 19
PTK2 0.014 0 -10000 0 -10000 0 0
MAP2K2 -0.074 0.21 -10000 0 -0.55 60 60
BAD 0.011 0.022 0.35 1 -0.31 1 2
MAP2K4 -0.027 0.13 -10000 0 -0.43 17 17
SHP2/GRB2/SOS1/GAB1 -0.088 0.14 -10000 0 -0.39 61 61
INPPL1 0.014 0 -10000 0 -10000 0 0
PXN 0.014 0 -10000 0 -10000 0 0
SH3KBP1 0.014 0 -10000 0 -10000 0 0
HGS -0.06 0.12 -10000 0 -0.28 83 83
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.078 0.2 -10000 0 -0.52 80 80
RASA1 0.014 0 -10000 0 -10000 0 0
NCK1 0.013 0.029 -10000 0 -0.61 1 1
PTPRJ 0.012 0.037 -10000 0 -0.55 2 2
NCK/PLCgamma1 -0.049 0.12 -10000 0 -0.26 83 83
PDPK1 -0.007 0.027 0.42 1 -0.37 1 2
HGF/MET/SHIP -0.14 0.2 -10000 0 -0.38 178 178
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.009 0.093 -9999 0 -0.38 25 25
NFATC2 -0.041 0.13 -9999 0 -0.36 66 66
NFATC3 0.011 0.034 -9999 0 -0.35 2 2
CD40LG -0.15 0.29 -9999 0 -0.64 88 88
PTGS2 -0.18 0.32 -9999 0 -0.67 111 111
JUNB -0.036 0.16 -9999 0 -0.52 43 43
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.029 -9999 0 -0.41 2 2
CaM/Ca2+ -0.006 0.029 -9999 0 -0.41 2 2
CALM1 0.01 0.038 -9999 0 -0.56 2 2
JUN 0.001 0.077 -9999 0 -0.51 10 10
mol:Ca2+ -0.005 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.003 -9999 0 -10000 0 0
FOSL1 -0.095 0.22 -9999 0 -0.54 91 91
CREM 0.012 0.037 -9999 0 -0.55 2 2
Jun/NFAT1-c-4/p21SNFT -0.12 0.18 -9999 0 -0.51 57 57
FOS -0.096 0.23 -9999 0 -0.56 87 87
IFNG -0.14 0.26 -9999 0 -0.59 80 80
AP-1/NFAT1-c-4 -0.16 0.32 -9999 0 -0.67 93 93
FASLG -0.15 0.29 -9999 0 -0.61 93 93
NFAT1-c-4/ICER1 -0.055 0.15 -9999 0 -0.45 32 32
IL2RA -0.16 0.3 -9999 0 -0.63 100 100
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.14 0.26 -9999 0 -0.59 75 75
JunB/Fra1/NFAT1-c-4 -0.14 0.2 -9999 0 -0.49 86 86
IL4 -0.14 0.26 -9999 0 -0.58 79 79
IL2 -0.008 0.015 -9999 0 -10000 0 0
IL3 -0.019 0.045 -9999 0 -0.89 1 1
FKBP1A 0.014 0 -9999 0 -10000 0 0
BATF3 -0.036 0.16 -9999 0 -0.54 42 42
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.029 -9999 0 -0.61 1 1
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.002 0.029 -10000 0 -0.44 2 2
Necdin/E2F1 -0.051 0.14 -10000 0 -0.42 56 56
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.082 0.14 -10000 0 -0.56 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.18 -10000 0 -0.38 139 139
NT-4/5 (dimer)/p75(NTR) -0.071 0.16 -10000 0 -0.41 81 81
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.049 0.16 -10000 0 -0.56 11 11
IKBKG 0.014 0 -10000 0 -10000 0 0
BDNF -0.08 0.2 -10000 0 -0.51 83 83
MGDIs/NGR/p75(NTR)/LINGO1 -0.097 0.19 -10000 0 -0.4 113 113
FURIN 0.014 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.1 0.17 -10000 0 -0.35 134 134
LINGO1 -0.019 0.14 -10000 0 -0.61 25 25
Sortilin/TRAF6/NRIF -0.001 0.016 -10000 0 -10000 0 0
proBDNF (dimer) -0.08 0.2 -10000 0 -0.51 83 83
NTRK1 -0.008 0.11 -10000 0 -0.53 19 19
RTN4R -0.036 0.17 -10000 0 -0.57 40 40
neuron apoptosis -0.068 0.18 -10000 0 -0.48 39 39
IRAK1 0.014 0 -10000 0 -10000 0 0
SHC1 -0.08 0.19 -10000 0 -0.36 130 130
ARHGDIA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.094 0.16 -10000 0 -0.36 90 90
MAGEH1 0.005 0.076 -10000 0 -0.61 7 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.11 0.18 -10000 0 -0.4 107 107
Mammalian IAPs/DIABLO -0.025 0.083 -10000 0 -0.33 23 23
proNGF (dimer) -0.074 0.21 -10000 0 -0.57 69 69
MAGED1 0.014 0 -10000 0 -10000 0 0
APP 0.014 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.093 -10000 0 -0.5 16 16
ZNF274 0.014 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.057 0.16 -10000 0 -0.34 82 82
NGF -0.074 0.21 -10000 0 -0.58 69 69
cell cycle arrest -0.078 0.14 -10000 0 -0.32 83 83
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.034 0.13 -10000 0 -0.43 14 14
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.06 0.13 -10000 0 -0.34 82 82
NCSTN 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.099 0.17 -10000 0 -0.4 85 85
PSENEN 0.014 0 -10000 0 -10000 0 0
mol:ceramide -0.062 0.17 -10000 0 -0.36 83 83
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.024 0.12 -10000 0 -0.39 18 18
p75(NTR)/beta APP -0.058 0.14 -10000 0 -0.39 69 69
BEX1 -0.01 0.12 -10000 0 -0.61 18 18
mol:GDP -0.087 0.18 -10000 0 -0.37 127 127
NGF (dimer) -0.14 0.18 -10000 0 -0.39 116 116
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.087 0.17 -10000 0 -0.41 75 75
PIK3R1 0.014 0 -10000 0 -10000 0 0
RAC1/GTP -0.085 0.15 -10000 0 -0.31 127 127
MYD88 0.008 0.062 -10000 0 -0.58 5 5
CHUK 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.1 0.17 -10000 0 -0.4 85 85
RHOB 0.011 0.041 -10000 0 -0.5 3 3
RHOA 0.014 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.02 0.084 -10000 0 -0.36 26 26
NT3 (dimer) -0.008 0.092 -10000 0 -0.49 16 16
TP53 -0.051 0.17 -10000 0 -0.52 26 26
PRDM4 -0.062 0.17 -10000 0 -0.36 83 83
BDNF (dimer) -0.16 0.2 -10000 0 -0.36 210 210
PIK3CA 0.014 0 -10000 0 -10000 0 0
SORT1 0.013 0.029 -10000 0 -0.61 1 1
activation of caspase activity -0.081 0.14 -10000 0 -0.56 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.09 0.15 -10000 0 -0.36 84 84
RHOC 0.012 0.037 -10000 0 -0.55 2 2
XIAP 0.014 0 -10000 0 -10000 0 0
MAPK10 -0.047 0.17 -10000 0 -0.48 29 29
DIABLO 0.014 0 -10000 0 -10000 0 0
SMPD2 -0.062 0.17 -10000 0 -0.36 83 83
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.1 0.17 -10000 0 -0.36 128 128
PSEN1 0.014 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.016 -10000 0 -0.35 1 1
NT3 (dimer)/p75(NTR) -0.071 0.16 -10000 0 -0.41 80 80
MAPK8 -0.05 0.17 -10000 0 -0.47 29 29
MAPK9 -0.045 0.17 -10000 0 -0.48 25 25
APAF1 0.014 0 -10000 0 -10000 0 0
NTF3 -0.008 0.092 -10000 0 -0.5 16 16
NTF4 -0.012 0.093 -10000 0 -0.5 16 16
NDN -0.029 0.16 -10000 0 -0.61 32 32
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.076 0.13 -10000 0 -0.51 12 12
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.046 -10000 0 -0.38 6 6
RhoA-B-C/GTP -0.099 0.17 -10000 0 -0.4 85 85
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.084 0.14 -10000 0 -0.39 53 53
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.091 0.16 -10000 0 -0.42 53 53
PRKACB 0.014 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.069 0.15 -10000 0 -0.37 86 86
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.035 0.16 -10000 0 -0.56 40 40
BIRC2 0.014 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.093 0.16 0.21 5 -0.38 89 94
BAD -0.039 0.16 -10000 0 -0.46 27 27
RIPK2 0.014 0 -10000 0 -10000 0 0
NGFR -0.07 0.2 -10000 0 -0.55 69 69
CYCS -0.05 0.16 -10000 0 -0.54 12 12
ADAM17 0.008 0.064 -10000 0 -0.61 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.089 0.15 -10000 0 -0.36 83 83
BCL2L11 -0.04 0.17 -10000 0 -0.46 27 27
BDNF (dimer)/p75(NTR) -0.12 0.2 -10000 0 -0.42 133 133
PI3K -0.088 0.15 -10000 0 -0.36 82 82
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.089 0.15 -10000 0 -0.36 83 83
NDNL2 0.014 0 -10000 0 -10000 0 0
YWHAE 0.014 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.12 0.2 -10000 0 -0.43 127 127
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.089 0.15 -10000 0 -0.36 83 83
TRAF6 0.013 0.029 -10000 0 -0.61 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.017 0.13 -10000 0 -0.57 25 25
PLG -0.001 0.04 -10000 0 -0.5 3 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.098 0.19 -10000 0 -0.39 101 101
SQSTM1 0.014 0 -10000 0 -10000 0 0
NGFRAP1 0.014 0 -10000 0 -10000 0 0
CASP3 -0.034 0.16 -10000 0 -0.42 27 27
E2F1 -0.015 0.12 -10000 0 -0.52 26 26
CASP9 0.013 0.024 -10000 0 -0.5 1 1
IKK complex -0.071 0.13 -10000 0 -0.52 15 15
NGF (dimer)/TRKA -0.077 0.17 -10000 0 -0.42 84 84
MMP7 -0.15 0.26 -10000 0 -0.55 136 136
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.082 0.14 -10000 0 -0.54 12 12
MMP3 -0.038 0.15 -10000 0 -0.5 42 42
APAF-1/Caspase 9 -0.072 0.12 -10000 0 -0.45 23 23
Aurora C signaling

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.014 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.11 0.16 -9999 0 -0.36 100 100
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.033 0.046 -9999 0 -0.25 1 1
AURKB -0.17 0.27 -9999 0 -0.56 146 146
AURKC -0.02 0.13 -9999 0 -0.52 30 30
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.065 0.2 -9999 0 -0.59 58 58
PDGF/PDGFRA/CRKL -0.051 0.14 -9999 0 -0.41 58 58
positive regulation of JUN kinase activity -0.041 0.11 -9999 0 -0.33 47 47
CRKL 0.014 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.063 0.15 -9999 0 -0.43 67 67
AP1 -0.17 0.32 -9999 0 -0.9 65 65
mol:IP3 -0.037 0.15 -9999 0 -0.43 58 58
PLCG1 -0.037 0.15 -9999 0 -0.43 58 58
PDGF/PDGFRA/alphaV Integrin -0.052 0.14 -9999 0 -0.42 58 58
RAPGEF1 0.014 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ -0.037 0.15 -9999 0 -0.43 58 58
CAV3 -0.007 0.083 -9999 0 -0.5 13 13
CAV1 -0.048 0.17 -9999 0 -0.5 56 56
SHC/Grb2/SOS1 -0.041 0.11 -9999 0 -0.34 47 47
PDGF/PDGFRA/Shf -0.055 0.15 -9999 0 -0.43 59 59
FOS -0.13 0.34 -9999 0 -0.89 65 65
JUN -0.02 0.062 -9999 0 -0.41 10 10
oligodendrocyte development -0.052 0.14 -9999 0 -0.42 58 58
GRB2 0.013 0.024 -9999 0 -0.5 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:DAG -0.037 0.15 -9999 0 -0.43 58 58
PDGF/PDGFRA -0.065 0.2 -9999 0 -0.59 58 58
actin cytoskeleton reorganization -0.051 0.14 -9999 0 -0.41 58 58
SRF 0.028 0.01 -9999 0 -10000 0 0
SHC1 0.009 0.053 -9999 0 -0.5 5 5
PI3K -0.043 0.11 -9999 0 -0.34 58 58
PDGF/PDGFRA/Crk/C3G -0.043 0.11 -9999 0 -0.34 58 58
JAK1 -0.032 0.14 -9999 0 -0.41 58 58
ELK1/SRF -0.002 0.11 -9999 0 -0.32 47 47
SHB 0.014 0 -9999 0 -10000 0 0
SHF 0.009 0.057 -9999 0 -0.61 4 4
CSNK2A1 0.014 0.022 -9999 0 -10000 0 0
GO:0007205 -0.039 0.16 -9999 0 -0.44 58 58
SOS1 0.014 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.041 0.11 -9999 0 -0.33 47 47
PDGF/PDGFRA/SHB -0.051 0.14 -9999 0 -0.41 58 58
PDGF/PDGFRA/Caveolin-1 -0.094 0.18 -9999 0 -0.41 105 105
ITGAV 0.013 0.029 -9999 0 -0.61 1 1
ELK1 -0.029 0.14 -9999 0 -0.4 51 51
PIK3CA 0.014 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.051 0.14 -9999 0 -0.41 58 58
JAK-STAT cascade -0.031 0.14 -9999 0 -0.41 58 58
cell proliferation -0.055 0.15 -9999 0 -0.43 59 59
Arf6 signaling events

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.021 0.083 -9999 0 -0.35 28 28
ARNO/beta Arrestin1-2 -0.024 0.088 -9999 0 -0.55 7 7
EGFR -0.083 0.22 -9999 0 -0.56 79 79
EPHA2 -0.019 0.13 -9999 0 -0.5 30 30
USP6 0.006 0.066 -9999 0 -0.5 8 8
IQSEC1 0.005 0.07 -9999 0 -0.52 8 8
EGFR/EGFR/EGF/EGF -0.11 0.2 -9999 0 -0.44 115 115
ARRB2 0.01 0.035 -9999 0 -10000 0 0
mol:GTP 0.005 0.046 -9999 0 -0.17 21 21
ARRB1 -0.002 0.099 -9999 0 -0.61 12 12
FBXO8 0.013 0.029 -9999 0 -0.61 1 1
TSHR -0.21 0.28 -9999 0 -0.55 182 182
EGF -0.047 0.18 -9999 0 -0.56 49 49
somatostatin receptor activity 0 0 -9999 0 -0.001 69 69
ARAP2 -0.004 0.11 -9999 0 -0.61 14 14
mol:GDP -0.073 0.12 -9999 0 -0.29 78 78
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 32 32
ITGA2B -0.046 0.18 -9999 0 -0.58 47 47
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.019 0.069 -9999 0 -0.41 3 3
ADAP1 -0.021 0.14 -9999 0 -0.57 28 28
KIF13B 0.014 0 -9999 0 -10000 0 0
HGF/MET -0.17 0.23 -9999 0 -0.44 177 177
PXN 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.065 0.12 -9999 0 -0.29 62 62
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.096 0.17 -9999 0 -0.37 120 120
ADRB2 -0.019 0.14 -9999 0 -0.6 25 25
receptor agonist activity 0 0 -9999 0 0 72 72
actin filament binding 0 0 -9999 0 -0.001 73 73
SRC 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.055 0.18 -9999 0 -0.52 60 60
GNAQ 0.014 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 51 51
ARF6/GDP -0.006 0.1 -9999 0 -0.38 16 16
ARF6/GDP/GULP/ACAP1 -0.11 0.17 -9999 0 -0.42 76 76
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.066 0.14 -9999 0 -0.37 51 51
ACAP1 -0.032 0.15 -9999 0 -0.51 41 41
ACAP2 0.013 0.029 -9999 0 -0.61 1 1
LHCGR/beta Arrestin2 0.003 0.048 -9999 0 -0.29 12 12
EFNA1 0.011 0.041 -9999 0 -0.5 3 3
HGF -0.078 0.2 -9999 0 -0.52 80 80
CYTH3 0.012 0 -9999 0 -10000 0 0
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.013 0.029 -9999 0 -0.61 1 1
fibronectin binding 0 0 -9999 0 0 59 59
endosomal lumen acidification 0 0 -9999 0 0 73 73
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.053 0.19 -9999 0 -0.58 52 52
GNAQ/ARNO 0.014 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 37 37
MET -0.14 0.25 -9999 0 -0.55 129 129
GNA14 -0.018 0.13 -9999 0 -0.58 25 25
GNA15 -0.01 0.12 -9999 0 -0.58 19 19
GIT1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 53 53
GNA11 0.005 0.076 -9999 0 -0.61 7 7
LHCGR -0.004 0.08 -9999 0 -0.5 12 12
AGTR1 -0.038 0.16 -9999 0 -0.56 42 42
desensitization of G-protein coupled receptor protein signaling pathway 0.003 0.048 -9999 0 -0.29 12 12
IPCEF1/ARNO -0.058 0.14 -9999 0 -0.49 14 14
alphaIIb/beta3 Integrin -0.089 0.18 -9999 0 -0.42 98 98
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.001 0.023 -9999 0 -0.35 2 2
PRKCZ -0.017 0.13 -9999 0 -0.57 25 25
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0.024 -9999 0 -0.5 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.08 0.12 -9999 0 -0.42 25 25
IRAK/TOLLIP 0.031 0.019 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
IKBKG 0.014 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.17 0.22 -9999 0 -0.42 188 188
IL1A -0.098 0.23 -9999 0 -0.55 92 92
IL1B -0.14 0.22 -9999 0 -0.41 172 172
IRAK/TRAF6/p62/Atypical PKCs -0.014 0.059 -9999 0 -0.43 1 1
IL1R2 -0.13 0.24 -9999 0 -0.54 116 116
IL1R1 -0.035 0.16 -9999 0 -0.54 41 41
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.048 0.12 -9999 0 -0.45 17 17
TOLLIP 0.014 0 -9999 0 -10000 0 0
TICAM2 0.001 0.089 -9999 0 -0.6 10 10
MAP3K3 0.014 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.065 0.033 -9999 0 -10000 0 0
JUN 0.036 0.067 -9999 0 -0.48 3 3
MAP3K7 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.14 0.18 -9999 0 -0.56 41 41
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.11 0.17 -9999 0 -0.39 83 83
PIK3R1 0.014 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.1 0.16 -9999 0 -0.36 83 83
IL1 beta fragment/IL1R1/IL1RAP -0.14 0.22 -9999 0 -0.43 114 114
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0.035 0.056 -9999 0 -0.56 1 1
IRAK1 0.025 0.021 -9999 0 -0.28 2 2
IL1RN/IL1R1 -0.12 0.2 -9999 0 -0.41 134 134
IRAK4 0.013 0.024 -9999 0 -0.5 1 1
PRKCI 0.014 0 -9999 0 -10000 0 0
TRAF6 0.013 0.029 -9999 0 -0.61 1 1
PI3K 0 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.067 0.15 -9999 0 -0.44 31 31
CHUK 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.14 0.22 -9999 0 -0.43 114 114
IL1 beta/IL1R2 -0.19 0.23 -9999 0 -0.39 241 241
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.019 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.12 0.16 -9999 0 -0.5 41 41
IRAK3 0.008 0.062 -9999 0 -0.58 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.15 0.18 -9999 0 -0.56 48 48
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.046 0.14 -9999 0 -0.38 24 24
IL1 alpha/IL1R1/IL1RAP -0.12 0.18 -9999 0 -0.36 157 157
RELA 0.014 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.014 0 -9999 0 -10000 0 0
MYD88 0.008 0.062 -9999 0 -0.58 5 5
IRAK/TRAF6/MEKK3 0.038 0.024 -9999 0 -0.31 1 1
IL1RAP -0.04 0.16 -9999 0 -0.52 47 47
UBE2N 0.014 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.12 0.15 -9999 0 -0.46 48 48
CASP1 -0.017 0.13 -9999 0 -0.54 26 26
IL1RN/IL1R2 -0.18 0.24 -9999 0 -0.46 179 179
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.13 0.21 -9999 0 -0.41 116 116
TMEM189-UBE2V1 0.006 0.034 -9999 0 -0.5 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.026 0.13 -9999 0 -0.39 23 23
PIK3CA 0.014 0 -9999 0 -10000 0 0
IL1RN -0.11 0.23 -9999 0 -0.54 106 106
TRAF6/TAK1/TAB1/TAB2 -0.002 0.02 -9999 0 -0.3 1 1
MAP2K6 0.035 0.027 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.097 0.22 -9999 0 -0.5 75 75
MAP3K8 -0.008 0.1 -9999 0 -0.51 18 18
FOS -0.087 0.2 -9999 0 -0.49 73 73
PRKCA 0.011 0.029 -9999 0 -0.61 1 1
PTPN7 -0.13 0.25 -9999 0 -0.55 114 114
HRAS 0.014 0.001 -9999 0 -10000 0 0
PRKCB -0.066 0.19 -9999 0 -0.53 67 67
NRAS 0.014 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.021 0.019 -9999 0 -10000 0 0
MAPK3 -0.071 0.17 -9999 0 -0.46 66 66
MAP2K1 -0.017 0.14 -9999 0 -0.49 23 23
ELK1 0.013 0.007 -9999 0 -10000 0 0
BRAF -0.054 0.14 -9999 0 -0.45 37 37
mol:GTP -0.001 0.002 -9999 0 -0.005 84 84
MAPK1 -0.071 0.17 -9999 0 -0.46 66 66
RAF1 -0.039 0.11 -9999 0 -0.46 22 22
KRAS 0.013 0.024 -9999 0 -0.5 1 1
Glucocorticoid receptor regulatory network

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
PCK2 0.022 0.1 -10000 0 -0.9 3 3
SMARCC2 0.015 0.011 -10000 0 -10000 0 0
SMARCC1 0.015 0.011 -10000 0 -10000 0 0
TBX21 -0.12 0.25 -10000 0 -0.71 58 58
SUMO2 0.014 0.014 -10000 0 -10000 0 0
STAT1 (dimer) -0.001 0.11 -10000 0 -0.59 15 15
FKBP4 0.014 0 -10000 0 -10000 0 0
FKBP5 -0.094 0.23 -10000 0 -0.57 86 86
GR alpha/HSP90/FKBP51/HSP90 0.021 0.17 0.29 24 -0.33 40 64
PRL -0.051 0.098 -10000 0 -0.61 2 2
cortisol/GR alpha (dimer)/TIF2 0.19 0.25 0.52 113 -0.46 3 116
RELA -0.068 0.098 -10000 0 -0.29 4 4
FGG 0.17 0.17 0.47 51 -0.48 2 53
GR beta/TIF2 0.071 0.16 0.3 41 -0.4 28 69
IFNG -0.24 0.22 -10000 0 -0.62 66 66
apoptosis 0 0.2 0.62 20 -0.67 1 21
CREB1 0.013 0.024 -10000 0 -10000 0 0
histone acetylation -0.048 0.13 -10000 0 -0.38 36 36
BGLAP -0.053 0.13 -10000 0 -0.53 13 13
GR/PKAc 0.091 0.097 0.3 24 -10000 0 24
NF kappa B1 p50/RelA -0.12 0.18 -10000 0 -0.44 59 59
SMARCD1 0.015 0.011 -10000 0 -10000 0 0
MDM2 0.084 0.08 0.25 43 -10000 0 43
GATA3 -0.1 0.23 -10000 0 -0.54 100 100
AKT1 0.002 0.017 -10000 0 -10000 0 0
CSF2 -0.067 0.1 -10000 0 -0.49 4 4
GSK3B 0.014 0.014 -10000 0 -10000 0 0
NR1I3 0.038 0.19 0.61 18 -0.72 2 20
CSN2 0.15 0.13 0.41 31 -10000 0 31
BRG1/BAF155/BAF170/BAF60A 0.039 0.037 -10000 0 -10000 0 0
NFATC1 -0.015 0.13 -10000 0 -0.58 24 24
POU2F1 0.014 0.03 -10000 0 -0.61 1 1
CDKN1A -0.069 0.32 -10000 0 -1.4 21 21
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.012 -10000 0 -10000 0 0
SFN -0.12 0.23 -10000 0 -0.53 109 109
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.044 0.19 0.29 13 -0.43 40 53
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.036 0.31 0.58 18 -0.82 42 60
JUN -0.17 0.19 -10000 0 -0.49 72 72
IL4 -0.086 0.15 -10000 0 -0.55 25 25
CDK5R1 -0.02 0.14 -10000 0 -0.6 25 25
PRKACA 0.014 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.2 0.2 1 -0.48 109 110
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.03 0.15 0.3 19 -0.33 12 31
cortisol/GR alpha (monomer) 0.25 0.26 0.6 123 -10000 0 123
NCOA2 -0.025 0.15 -10000 0 -0.61 29 29
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.14 0.23 -10000 0 -0.6 87 87
AP-1/NFAT1-c-4 -0.32 0.31 -10000 0 -0.68 139 139
AFP -0.13 0.18 -10000 0 -0.69 11 11
SUV420H1 0.014 0 -10000 0 -10000 0 0
IRF1 0.12 0.15 0.44 20 -0.47 4 24
TP53 -0.016 0.16 -10000 0 -0.53 32 32
PPP5C 0.014 0 -10000 0 -10000 0 0
KRT17 -0.45 0.49 -10000 0 -0.99 173 173
KRT14 -0.14 0.18 -10000 0 -0.55 39 39
TBP 0.023 0.019 -10000 0 -10000 0 0
CREBBP 0.033 0.06 -10000 0 -10000 0 0
HDAC1 0.004 0.051 -10000 0 -0.61 3 3
HDAC2 0.014 0.001 -10000 0 -10000 0 0
AP-1 -0.32 0.31 -10000 0 -0.69 140 140
MAPK14 0.013 0.012 -10000 0 -10000 0 0
MAPK10 0.008 0.059 -10000 0 -0.61 4 4
MAPK11 0.008 0.059 -10000 0 -0.6 4 4
KRT5 -0.42 0.46 -10000 0 -0.94 161 161
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.017 0.01 -10000 0 -10000 0 0
STAT1 -0.001 0.11 -10000 0 -0.59 15 15
CGA -0.073 0.13 -10000 0 -0.52 7 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.086 0.11 0.35 20 -10000 0 20
MAPK3 0.013 0.013 -10000 0 -10000 0 0
MAPK1 0.013 0.012 -10000 0 -10000 0 0
ICAM1 -0.21 0.28 -10000 0 -0.74 71 71
NFKB1 -0.068 0.098 -10000 0 -0.31 2 2
MAPK8 -0.14 0.17 -10000 0 -0.48 55 55
MAPK9 0.013 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.003 0.2 0.62 20 -0.71 1 21
BAX -0.002 0.11 -10000 0 -10000 0 0
POMC -0.14 0.25 -10000 0 -1.1 18 18
EP300 0.027 0.084 -10000 0 -0.6 4 4
cortisol/GR alpha (dimer)/p53 0.19 0.23 0.51 105 -0.54 2 107
proteasomal ubiquitin-dependent protein catabolic process 0.06 0.07 0.24 24 -10000 0 24
SGK1 0.057 0.24 -10000 0 -1.4 11 11
IL13 -0.24 0.24 -10000 0 -0.67 68 68
IL6 -0.31 0.4 -10000 0 -0.86 132 132
PRKACG 0.005 0.047 -10000 0 -0.5 4 4
IL5 -0.21 0.2 -10000 0 -0.66 26 26
IL2 -0.24 0.22 -10000 0 -0.62 62 62
CDK5 0.014 0.007 -10000 0 -10000 0 0
PRKACB 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
IL8 -0.34 0.42 -10000 0 -0.88 144 144
CDK5R1/CDK5 -0.018 0.1 -10000 0 -0.44 25 25
NF kappa B1 p50/RelA/PKAc -0.061 0.13 -10000 0 -0.42 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.22 0.2 0.49 119 -10000 0 119
SMARCA4 0.015 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.14 0.37 58 -0.36 1 59
NF kappa B1 p50/RelA/Cbp -0.058 0.16 -10000 0 -0.51 8 8
JUN (dimer) -0.17 0.19 -10000 0 -0.49 72 72
YWHAH -0.01 0.11 -10000 0 -0.5 22 22
VIPR1 -0.13 0.28 -10000 0 -0.74 69 69
NR3C1 0.15 0.15 0.42 70 -10000 0 70
NR4A1 -0.025 0.15 -10000 0 -0.5 39 39
TIF2/SUV420H1 -0.028 0.11 -10000 0 -0.44 29 29
MAPKKK cascade 0 0.2 0.62 20 -0.67 1 21
cortisol/GR alpha (dimer)/Src-1 0.22 0.22 0.51 125 -10000 0 125
PBX1 0.014 0.03 -10000 0 -0.61 1 1
POU1F1 0.004 0.025 -10000 0 -0.5 1 1
SELE -0.3 0.38 -10000 0 -0.88 105 105
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.14 0.38 57 -0.36 1 58
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.22 0.2 0.49 119 -10000 0 119
mol:cortisol 0.14 0.16 0.33 129 -10000 0 129
MMP1 -0.12 0.16 -10000 0 -0.54 41 41
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.042 0.098 0.2 114 -10000 0 114
BUB1B -0.062 0.15 -10000 0 -0.31 114 114
PLK1 -0.001 0.044 -10000 0 -0.13 29 29
PLK1S1 0.006 0.023 -10000 0 -0.13 1 1
KIF2A 0.006 0.05 -10000 0 -0.31 5 5
regulation of mitotic centrosome separation -0.001 0.044 -10000 0 -0.13 29 29
GOLGA2 0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.14 0.24 -10000 0 -0.44 166 166
WEE1 -0.007 0.089 -10000 0 -0.37 18 18
cytokinesis -0.11 0.21 -10000 0 -0.42 128 128
PP2A-alpha B56 -0.064 0.23 -10000 0 -0.66 56 56
AURKA 0.001 0.042 -10000 0 -0.16 22 22
PICH/PLK1 -0.031 0.16 -10000 0 -0.43 57 57
CENPE -0.043 0.14 -10000 0 -0.33 80 80
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.006 0.049 -10000 0 -0.3 5 5
PPP2CA 0.014 0 -10000 0 -10000 0 0
FZR1 0.014 0 -10000 0 -10000 0 0
TPX2 -0.021 0.082 -10000 0 -0.2 67 67
PAK1 -0.036 0.15 -10000 0 -0.5 45 45
SPC24 -0.13 0.25 -10000 0 -0.54 122 122
FBXW11 0.014 0 -10000 0 -10000 0 0
CLSPN -0.036 0.1 -10000 0 -0.23 91 91
GORASP1 0.014 0 -10000 0 -10000 0 0
metaphase 0 0.004 -10000 0 -0.014 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0 0.023 -10000 0 -0.066 28 28
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.011 3 3
STAG2 0.014 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.004 0.011 -10000 0 -10000 0 0
spindle elongation -0.001 0.044 -10000 0 -0.13 29 29
ODF2 0.013 0.003 -10000 0 -10000 0 0
BUB1 -0.1 0.24 -10000 0 -0.73 56 56
TPT1 0.006 0.023 -10000 0 -0.12 2 2
CDC25C -0.052 0.14 -10000 0 -0.3 93 93
CDC25B 0.014 0.004 -10000 0 -10000 0 0
SGOL1 -0.042 0.098 -10000 0 -0.2 114 114
RHOA 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.028 0.089 -10000 0 -0.34 27 27
CDC14B 0.012 0.001 -10000 0 -10000 0 0
CDC20 -0.1 0.23 -10000 0 -0.55 98 98
PLK1/PBIP1 -0.051 0.12 -10000 0 -0.33 66 66
mitosis 0.001 0.005 0.022 7 -0.022 1 8
FBXO5 0.004 0.052 -10000 0 -0.29 8 8
CDC2 0 0.004 -10000 0 -0.014 28 28
NDC80 -0.14 0.25 -10000 0 -0.56 122 122
metaphase plate congression 0.005 0.027 -10000 0 -0.15 2 2
ERCC6L -0.056 0.14 -10000 0 -0.44 49 49
NLP/gamma Tubulin 0.003 0.025 -10000 0 -0.11 3 3
microtubule cytoskeleton organization 0.006 0.023 -10000 0 -0.12 2 2
G2/M transition DNA damage checkpoint 0 0.002 0.01 4 -10000 0 4
PPP1R12A 0.014 0.001 -10000 0 -10000 0 0
interphase 0 0.002 0.01 4 -10000 0 4
PLK1/PRC1-2 -0.095 0.19 -10000 0 -0.35 154 154
GRASP65/GM130/RAB1/GTP/PLK1 -0.005 0.024 -10000 0 -10000 0 0
RAB1A 0.014 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.037 -10000 0 -0.21 2 2
mitotic prometaphase -0.001 0.002 -10000 0 -0.01 9 9
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.062 -10000 0 -10000 0 0
microtubule-based process -0.098 0.17 -10000 0 -0.34 154 154
Golgi organization -0.001 0.044 -10000 0 -0.13 29 29
Cohesin/SA2 -0.012 0.03 -10000 0 -0.22 2 2
PPP1CB/MYPT1 0.004 0.009 -10000 0 -10000 0 0
KIF20A -0.18 0.27 -10000 0 -0.56 154 154
APC/C/CDC20 -0.058 0.15 -10000 0 -0.34 98 98
PPP2R1A 0.014 0 -10000 0 -10000 0 0
chromosome segregation -0.05 0.12 -10000 0 -0.33 66 66
PRC1 -0.007 0.1 -10000 0 -0.5 19 19
ECT2 -0.003 0.082 -10000 0 -0.36 20 20
C13orf34 0.006 0.037 -10000 0 -0.21 2 2
NUDC 0.005 0.027 -10000 0 -0.15 2 2
regulation of attachment of spindle microtubules to kinetochore -0.061 0.15 -10000 0 -0.3 114 114
spindle assembly 0.002 0.036 -10000 0 -0.1 24 24
spindle stabilization 0.006 0.023 -10000 0 -0.13 1 1
APC/C/HCDH1 0.02 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 -0.099 0.17 -10000 0 -0.34 154 154
CCNB1 -0.018 0.12 -10000 0 -0.5 29 29
PPP1CB 0.014 0.001 -10000 0 -10000 0 0
BTRC 0.014 0 -10000 0 -10000 0 0
ROCK2 -0.002 0.085 -10000 0 -0.42 16 16
TUBG1 0.006 0.023 -10000 0 -0.13 1 1
G2/M transition of mitotic cell cycle -0.03 0.087 -10000 0 -0.33 27 27
MLF1IP -0.047 0.15 -10000 0 -0.41 66 66
INCENP 0.012 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.037 0.17 -9999 0 -0.5 26 26
NF kappa B1 p50/RelA/I kappa B alpha -0.013 0.16 -9999 0 -0.5 19 19
alphaV/beta3 Integrin/Osteopontin/Src -0.067 0.15 -9999 0 -0.39 80 80
AP1 -0.078 0.23 -9999 0 -0.6 41 41
ILK -0.046 0.17 -9999 0 -0.52 25 25
bone resorption -0.078 0.24 -9999 0 -0.55 69 69
PTK2B -0.011 0.11 -9999 0 -0.5 23 23
PYK2/p130Cas -0.096 0.16 -9999 0 -0.52 41 41
ITGAV 0.016 0.029 -9999 0 -0.6 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.066 0.16 -9999 0 -0.42 73 73
alphaV/beta3 Integrin/Osteopontin -0.095 0.17 -9999 0 -0.4 90 90
MAP3K1 -0.05 0.18 -9999 0 -0.5 30 30
JUN 0.003 0.076 -9999 0 -0.51 10 10
MAPK3 -0.039 0.18 -9999 0 -0.52 27 27
MAPK1 -0.039 0.18 -9999 0 -0.52 27 27
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.044 0.18 -9999 0 -0.5 33 33
ITGB3 -0.053 0.18 -9999 0 -0.52 60 60
NFKBIA -0.03 0.18 -9999 0 -0.5 27 27
FOS -0.093 0.22 -9999 0 -0.56 87 87
CD44 -0.061 0.2 -9999 0 -0.56 60 60
CHUK 0.014 0 -9999 0 -10000 0 0
PLAU -0.07 0.28 -9999 0 -0.85 33 33
NF kappa B1 p50/RelA -0.076 0.13 -9999 0 -0.52 19 19
BCAR1 0.013 0.029 -9999 0 -0.61 1 1
RELA 0.014 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.049 0.13 -9999 0 -0.37 61 61
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.061 0.2 -9999 0 -0.43 80 80
VAV3 -0.12 0.23 -9999 0 -0.57 63 63
MAP3K14 -0.048 0.18 -9999 0 -0.45 41 41
ROCK2 -0.006 0.11 -9999 0 -0.61 15 15
SPP1 -0.078 0.21 -9999 0 -0.54 79 79
RAC1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.19 -9999 0 -0.53 62 62
MMP2 -0.066 0.21 -9999 0 -0.61 31 31
IL6-mediated signaling events

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
BCL2L1 -0.04 0.23 -10000 0 -0.7 16 16
CRP -0.048 0.23 -10000 0 -0.64 25 25
cell cycle arrest -0.061 0.26 -10000 0 -0.66 41 41
TIMP1 -0.091 0.28 -10000 0 -0.63 62 62
IL6ST -0.024 0.15 -10000 0 -0.6 28 28
Rac1/GDP -0.072 0.2 -10000 0 -0.44 76 76
AP1 -0.018 0.14 -10000 0 -0.48 13 13
GAB2 0.014 0.029 -10000 0 -0.61 1 1
TNFSF11 -0.049 0.24 -10000 0 -0.67 23 23
HSP90B1 0.004 0.16 -10000 0 -0.93 12 12
GAB1 0.013 0.037 -10000 0 -0.55 2 2
MAPK14 -0.1 0.24 -10000 0 -0.49 101 101
AKT1 0.06 0.028 -10000 0 -0.46 1 1
FOXO1 0.064 0.036 -10000 0 -0.43 1 1
MAP2K6 -0.091 0.21 0.27 1 -0.42 94 95
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.059 0.22 -10000 0 -0.48 62 62
MITF -0.071 0.19 0.28 1 -0.42 73 74
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.014 0 -10000 0 -10000 0 0
A2M 0.018 0.076 -10000 0 -1.4 1 1
CEBPB 0.004 0.11 -10000 0 -0.58 15 15
GRB2/SOS1/GAB family/SHP2 0.002 0.081 -10000 0 -0.83 1 1
STAT3 -0.065 0.27 -10000 0 -0.69 43 43
STAT1 -0.008 0.036 -10000 0 -10000 0 0
CEBPD -0.083 0.33 -10000 0 -0.9 47 47
PIK3CA 0.016 0 -10000 0 -10000 0 0
PI3K 0.025 0.001 -10000 0 -10000 0 0
JUN 0.003 0.076 -10000 0 -0.51 10 10
PIAS3/MITF -0.06 0.18 -10000 0 -0.41 64 64
MAPK11 -0.11 0.24 -10000 0 -0.49 102 102
STAT3 (dimer)/FOXO1 0.011 0.22 -10000 0 -0.58 16 16
GRB2/SOS1/GAB family -0.075 0.13 -10000 0 -0.47 29 29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.069 0.18 -10000 0 -0.41 64 64
GRB2 0.014 0.024 -10000 0 -0.5 1 1
JAK2 0.014 0 -10000 0 -10000 0 0
LBP -0.038 0.23 -10000 0 -0.62 32 32
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.012 0.009 -10000 0 -10000 0 0
MYC -0.071 0.31 -10000 0 -0.88 40 40
FGG -0.049 0.24 -10000 0 -0.67 21 21
macrophage differentiation -0.061 0.26 -10000 0 -0.66 41 41
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.18 -10000 0 -0.42 74 74
JUNB -0.062 0.28 -10000 0 -0.75 39 39
FOS -0.093 0.22 -10000 0 -0.56 87 87
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.082 0.2 0.3 1 -0.42 80 81
STAT1/PIAS1 -0.059 0.18 0.29 1 -0.43 57 58
GRB2/SOS1/GAB family/SHP2/PI3K 0.046 0.031 -10000 0 -0.49 1 1
STAT3 (dimer) -0.063 0.27 -10000 0 -0.69 41 41
PRKCD -0.062 0.26 -10000 0 -0.57 63 63
IL6R -0.013 0.12 -10000 0 -0.58 20 20
SOCS3 -0.16 0.36 -10000 0 -0.75 93 93
gp130 (dimer)/JAK1/JAK1/LMO4 0.003 0.097 -10000 0 -0.36 28 28
Rac1/GTP -0.075 0.21 -10000 0 -0.45 75 75
HCK -0.01 0.11 -10000 0 -0.55 20 20
MAPKKK cascade 0.025 0.07 -10000 0 -0.92 1 1
bone resorption -0.045 0.23 -10000 0 -0.62 24 24
IRF1 -0.048 0.25 -10000 0 -0.66 30 30
mol:GDP -0.084 0.21 0.28 1 -0.44 86 87
SOS1 0.015 0.002 -10000 0 -10000 0 0
VAV1 -0.086 0.21 0.28 1 -0.44 86 87
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.23 -10000 0 -0.47 102 102
PTPN11 -0.002 0.017 -10000 0 -10000 0 0
IL6/IL6RA -0.11 0.21 -10000 0 -0.43 137 137
gp130 (dimer)/TYK2/TYK2/LMO4 0 0.095 -10000 0 -0.36 28 28
gp130 (dimer)/JAK2/JAK2/LMO4 0 0.095 -10000 0 -0.36 28 28
IL6 -0.14 0.25 -10000 0 -0.55 128 128
PIAS3 0.014 0 -10000 0 -10000 0 0
PTPRE 0.013 0.034 -10000 0 -0.62 1 1
PIAS1 0.009 0.057 -10000 0 -0.61 4 4
RAC1 0.015 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.07 0.16 0.27 1 -0.34 86 87
LMO4 0.013 0.012 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.21 0.35 1 -0.65 40 41
MCL1 0.065 0.026 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.051 0.12 -9999 0 -0.34 47 47
NF kappa B1 p50/RelA/I kappa B alpha -0.043 0.091 -9999 0 -0.46 9 9
AP1 -0.12 0.17 -9999 0 -0.48 52 52
mol:PIP3 -0.1 0.15 -9999 0 -0.48 38 38
AKT1 0.018 0.099 -9999 0 -0.4 2 2
PTK2B -0.021 0.11 -9999 0 -0.33 34 34
RHOA 0.007 0.065 -9999 0 -0.32 7 7
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.002 0.092 -9999 0 -0.37 10 10
MAGI3 0.002 0.086 -9999 0 -0.61 9 9
RELA 0.014 0 -9999 0 -10000 0 0
apoptosis -0.043 0.13 -9999 0 -0.34 52 52
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.11 -9999 0 -0.34 22 22
NF kappa B1 p50/RelA -0.071 0.13 -9999 0 -0.53 19 19
endothelial cell migration -0.045 0.18 -9999 0 -0.44 65 65
ADCY4 -0.023 0.15 -9999 0 -0.42 50 50
ADCY5 -0.029 0.16 -9999 0 -0.41 59 59
ADCY6 -0.021 0.15 -9999 0 -0.41 49 49
ADCY7 -0.021 0.15 -9999 0 -0.41 49 49
ADCY1 -0.05 0.17 -9999 0 -0.44 58 58
ADCY2 -0.027 0.16 -9999 0 -0.43 53 53
ADCY3 -0.021 0.15 -9999 0 -0.41 49 49
ADCY8 -0.046 0.19 -9999 0 -0.5 55 55
ADCY9 -0.021 0.15 -9999 0 -0.42 49 49
GSK3B -0.012 0.11 -9999 0 -0.34 22 22
arachidonic acid secretion -0.013 0.14 -9999 0 -0.38 49 49
GNG2 0.009 0.057 -9999 0 -0.61 4 4
TRIP6 0.008 0.067 -9999 0 -0.38 5 5
GNAO1 -0.034 0.14 -9999 0 -0.35 73 73
HRAS 0.014 0 -9999 0 -10000 0 0
NFKBIA -0.013 0.13 -9999 0 -0.44 20 20
GAB1 0.012 0.037 -9999 0 -0.55 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.004 0.087 -9999 0 -1 3 3
JUN 0.003 0.076 -9999 0 -0.51 10 10
LPA/LPA2/NHERF2 -0.015 0.062 -9999 0 -0.33 16 16
TIAM1 -0.007 0.11 -9999 0 -1.3 3 3
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.002 0.093 -9999 0 -0.38 10 10
PLCB3 0.016 0.061 -9999 0 -0.29 16 16
FOS -0.093 0.22 -9999 0 -0.56 87 87
positive regulation of mitosis -0.013 0.14 -9999 0 -0.38 49 49
LPA/LPA1-2-3 -0.083 0.15 -9999 0 -0.39 58 58
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.013 0.029 -9999 0 -0.61 1 1
stress fiber formation -0.024 0.12 -9999 0 -0.34 34 34
GNAZ -0.03 0.14 -9999 0 -0.34 69 69
EGFR/PI3K-beta/Gab1 -0.1 0.16 -9999 0 -0.5 38 38
positive regulation of dendritic cell cytokine production -0.083 0.15 -9999 0 -0.38 58 58
LPA/LPA2/MAGI-3 -0.021 0.08 -9999 0 -0.37 22 22
ARHGEF1 -0.01 0.12 -9999 0 -0.56 3 3
GNAI2 -0.03 0.14 -9999 0 -0.34 68 68
GNAI3 -0.03 0.14 -9999 0 -0.34 68 68
GNAI1 -0.044 0.15 -9999 0 -0.35 85 85
LPA/LPA3 -0.04 0.11 -9999 0 -0.37 46 46
LPA/LPA2 -0.017 0.072 -9999 0 -0.41 14 14
LPA/LPA1 -0.067 0.15 -9999 0 -0.38 81 81
HB-EGF/EGFR -0.14 0.21 -9999 0 -0.38 185 185
HBEGF -0.1 0.19 -9999 0 -0.39 140 140
mol:DAG 0.002 0.093 -9999 0 -0.38 10 10
cAMP biosynthetic process -0.025 0.16 -9999 0 -0.42 49 49
NFKB1 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN -0.018 0.14 -9999 0 -0.48 19 19
GNAQ -0.011 0.088 -9999 0 -0.33 15 15
LPAR2 -0.003 0.099 -9999 0 -0.56 14 14
LPAR3 -0.043 0.15 -9999 0 -0.5 46 46
LPAR1 -0.065 0.2 -9999 0 -0.57 60 60
IL8 -0.19 0.23 -9999 0 -0.46 160 160
PTK2 -0.048 0.15 -9999 0 -0.35 58 58
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.043 0.13 -9999 0 -0.34 52 52
EGFR -0.084 0.22 -9999 0 -0.56 79 79
PLCG1 -0.013 0.095 -9999 0 -0.31 22 22
PLD2 -0.048 0.15 -9999 0 -0.35 58 58
G12/G13 -0.049 0.11 -9999 0 -0.34 44 44
PI3K-beta -0.039 0.086 -9999 0 -0.39 9 9
cell migration -0.027 0.056 -9999 0 -0.24 9 9
SLC9A3R2 0.012 0.033 -9999 0 -0.5 2 2
PXN -0.024 0.13 -9999 0 -0.35 34 34
HRAS/GTP -0.014 0.15 -9999 0 -0.39 49 49
RAC1 0.014 0 -9999 0 -10000 0 0
MMP9 -0.15 0.25 -9999 0 -0.53 136 136
PRKCE 0.002 0.082 -9999 0 -0.52 11 11
PRKCD -0.006 0.12 -9999 0 -0.4 21 21
Gi(beta/gamma) -0.016 0.15 -9999 0 -0.38 50 50
mol:LPA -0.004 0.037 -9999 0 -0.2 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.067 0.13 -9999 0 -0.46 20 20
MAPKKK cascade -0.013 0.14 -9999 0 -0.38 49 49
contractile ring contraction involved in cytokinesis 0.007 0.065 -9999 0 -0.31 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.028 0.11 -9999 0 -0.32 34 34
GNA15 -0.024 0.11 -9999 0 -0.32 32 32
GNA12 0.013 0.029 -9999 0 -0.6 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
MAPT -0.009 0.11 -9999 0 -0.36 22 22
GNA11 -0.016 0.099 -9999 0 -0.35 22 22
Rac1/GTP -0.004 0.096 -9999 0 -1.1 3 3
MMP2 -0.046 0.18 -9999 0 -0.44 65 65
PLK2 and PLK4 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
PLK2 -0.017 0.12 -9999 0 -0.52 27 27
PLK4 -0.012 0.11 -9999 0 -0.51 23 23
regulation of centriole replication -0.016 0.12 -9999 0 -0.37 48 48
TCGA08_p53

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
CDKN2A -0.078 0.18 -10000 0 -0.43 96 96
TP53 -0.035 0.093 0.19 3 -0.44 13 16
Senescence -0.035 0.092 0.19 3 -0.44 13 16
Apoptosis -0.035 0.092 0.19 3 -0.44 13 16
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.05 0.1 0.27 70 -0.26 2 72
MDM4 0.004 0.07 -10000 0 -0.5 9 9
Nongenotropic Androgen 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
PTK2 0.013 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.062 0.13 -10000 0 -0.32 95 95
regulation of S phase of mitotic cell cycle -0.017 0.1 -10000 0 -0.26 66 66
GNAO1 0.006 0.07 -10000 0 -0.61 6 6
HRAS 0.014 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.004 0.046 -10000 0 -0.37 7 7
PELP1 0.014 0.001 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.021 0.13 -10000 0 -0.37 21 21
T-DHT/AR -0.083 0.17 -10000 0 -0.43 91 91
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.006 83 83
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.12 -10000 0 -0.61 17 17
mol:GDP -0.076 0.16 -10000 0 -0.46 66 66
cell proliferation -0.034 0.18 -10000 0 -0.42 55 55
PIK3CA 0.014 0 -10000 0 -10000 0 0
FOS -0.08 0.28 -10000 0 -0.76 57 57
mol:Ca2+ -0.011 0.02 -10000 0 -0.062 35 35
MAPK3 -0.027 0.15 -10000 0 -0.47 21 21
MAPK1 -0.012 0.09 -10000 0 -0.27 17 17
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.004 87 87
cAMP biosynthetic process 0.005 0.047 -10000 0 -0.34 7 7
GNG2 0.009 0.057 -10000 0 -0.61 4 4
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 87 87
HRAS/GTP -0.058 0.11 -10000 0 -0.3 72 72
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.014 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 87 87
PI3K 0.001 0.005 -10000 0 -10000 0 0
apoptosis 0.033 0.17 0.42 55 -10000 0 55
T-DHT/AR/PELP1 -0.069 0.14 -10000 0 -0.36 91 91
HRAS/GDP -0.07 0.15 -10000 0 -0.43 66 66
CREB1 -0.038 0.18 -10000 0 -0.45 55 55
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.1 0.24 -10000 0 -0.58 91 91
GNB1 0.014 0 -10000 0 -10000 0 0
RAF1 -0.026 0.13 -10000 0 -0.34 21 21
RAC1-CDC42/GDP -0.065 0.15 -10000 0 -0.41 66 66
T-DHT/AR/PELP1/Src -0.061 0.13 -10000 0 -0.32 91 91
MAP2K2 -0.021 0.13 -10000 0 -0.35 21 21
T-DHT/AR/PELP1/Src/PI3K -0.017 0.11 -10000 0 -0.26 66 66
GNAZ 0.013 0.029 -10000 0 -0.61 1 1
SHBG 0.005 0.074 -10000 0 -0.59 7 7
Gi family/GNB1/GNG2/GDP 0.018 0.083 -10000 0 -0.47 7 7
mol:T-DHT 0 0.001 -10000 0 -0.003 61 61
RAC1 0.014 0 -10000 0 -10000 0 0
GNRH1 0.003 0.065 -10000 0 -0.41 11 11
Gi family/GTP -0.015 0.085 -10000 0 -0.36 7 7
CDC42 0.014 0 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.042 0.14 -10000 0 -0.37 49 49
IKBKB -0.014 0.079 -10000 0 -0.27 12 12
AKT1 -0.054 0.1 -10000 0 -0.25 43 43
IKBKG -0.012 0.084 -10000 0 -0.27 19 19
CALM1 -0.057 0.15 -10000 0 -0.41 52 52
PIK3CA 0.014 0 -10000 0 -10000 0 0
MAP3K1 -0.069 0.19 -10000 0 -0.52 48 48
MAP3K7 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.067 0.16 0.21 3 -0.43 53 56
DOK1 0.013 0.029 -10000 0 -0.61 1 1
AP-1 -0.035 0.1 -10000 0 -0.26 32 32
LYN 0.003 0.078 -10000 0 -0.52 10 10
BLNK -0.055 0.19 -10000 0 -0.59 53 53
SHC1 0.009 0.053 -10000 0 -0.5 5 5
BCR complex -0.085 0.19 -10000 0 -0.46 87 87
CD22 -0.18 0.22 -10000 0 -0.56 81 81
CAMK2G -0.046 0.14 -10000 0 -0.47 28 28
CSNK2A1 0.014 0 -10000 0 -10000 0 0
INPP5D 0.008 0.058 -10000 0 -0.54 5 5
SHC/GRB2/SOS1 -0.096 0.17 -10000 0 -0.56 39 39
GO:0007205 -0.068 0.16 0.21 2 -0.44 53 55
SYK -0.012 0.12 -10000 0 -0.57 21 21
ELK1 -0.057 0.15 -10000 0 -0.41 52 52
NFATC1 -0.065 0.18 -10000 0 -0.47 54 54
B-cell antigen/BCR complex -0.085 0.19 -10000 0 -0.46 87 87
PAG1/CSK -0.001 0.02 -10000 0 -0.44 1 1
NFKBIB 0.006 0.029 -10000 0 -10000 0 0
HRAS -0.051 0.16 -10000 0 -0.43 45 45
NFKBIA 0.006 0.029 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.012 0.024 -10000 0 -10000 0 0
RasGAP/Csk -0.14 0.2 -10000 0 -0.56 51 51
mol:GDP -0.063 0.16 0.22 3 -0.42 53 56
PTEN 0.013 0.029 -10000 0 -0.61 1 1
CD79B -0.056 0.19 -10000 0 -0.55 58 58
NF-kappa-B/RelA/I kappa B alpha 0.012 0.024 -10000 0 -10000 0 0
GRB2 0.013 0.024 -10000 0 -0.5 1 1
PI3K/BCAP/CD19 -0.094 0.2 -10000 0 -0.5 67 67
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.069 0.17 0.22 3 -0.44 53 56
CSK 0.014 0 -10000 0 -10000 0 0
FOS -0.096 0.18 -10000 0 -0.52 41 41
CHUK -0.012 0.084 -10000 0 -0.28 16 16
IBTK 0.014 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.066 0.14 -10000 0 -0.53 30 30
PTPN6 -0.18 0.22 -10000 0 -0.56 78 78
RELA 0.014 0 -10000 0 -10000 0 0
BCL2A1 -0.006 0.046 -10000 0 -0.1 32 32
VAV2 -0.12 0.19 -10000 0 -0.59 48 48
ubiquitin-dependent protein catabolic process 0.011 0.028 -10000 0 -10000 0 0
BTK -0.036 0.19 0.37 1 -1.1 13 14
CD19 -0.12 0.2 -10000 0 -0.57 56 56
MAP4K1 -0.021 0.14 -10000 0 -0.59 27 27
CD72 -0.013 0.12 -10000 0 -0.51 24 24
PAG1 0.013 0.029 -10000 0 -0.61 1 1
MAPK14 -0.051 0.16 -10000 0 -0.44 47 47
SH3BP5 0.008 0.062 -10000 0 -0.58 5 5
PIK3AP1 -0.067 0.19 0.24 3 -0.48 58 61
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.067 0.22 -10000 0 -0.56 55 55
RAF1 -0.04 0.15 -10000 0 -0.46 30 30
RasGAP/p62DOK/SHIP -0.13 0.19 -10000 0 -0.55 52 52
CD79A -0.042 0.17 -10000 0 -0.54 47 47
re-entry into mitotic cell cycle -0.036 0.1 -10000 0 -0.26 31 31
RASA1 0.014 0 -10000 0 -10000 0 0
MAPK3 -0.018 0.13 -10000 0 -0.42 21 21
MAPK1 -0.018 0.13 -10000 0 -0.42 21 21
CD72/SHP1 -0.15 0.23 -10000 0 -0.58 72 72
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.056 0.17 -10000 0 -0.44 49 49
actin cytoskeleton organization -0.071 0.18 -10000 0 -0.5 47 47
NF-kappa-B/RelA 0.03 0.045 -10000 0 -10000 0 0
Calcineurin -0.059 0.12 -10000 0 -0.46 26 26
PI3K -0.14 0.18 -10000 0 -0.49 68 68
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.083 0.18 0.25 3 -0.48 53 56
SOS1 0.014 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.12 0.28 -10000 0 -0.79 57 57
DAPP1 -0.14 0.3 -10000 0 -0.9 52 52
cytokine secretion -0.06 0.17 -10000 0 -0.44 54 54
mol:DAG -0.069 0.17 0.22 3 -0.44 53 56
PLCG2 0.001 0.086 -10000 0 -0.55 11 11
MAP2K1 -0.029 0.14 -10000 0 -0.46 23 23
B-cell antigen/BCR complex/FcgammaRIIB -0.16 0.23 -10000 0 -0.48 131 131
mol:PI-3-4-5-P3 -0.1 0.12 -10000 0 -0.36 55 55
ETS1 -0.038 0.14 -10000 0 -0.44 28 28
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.11 0.2 -10000 0 -0.65 37 37
B-cell antigen/BCR complex/LYN -0.11 0.2 -10000 0 -0.53 61 61
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.029 -10000 0 -0.61 1 1
RAC1 -0.077 0.19 -10000 0 -0.54 47 47
B-cell antigen/BCR complex/LYN/SYK -0.18 0.24 -10000 0 -0.61 77 77
CARD11 -0.068 0.19 -10000 0 -0.49 56 56
FCGR2B -0.15 0.26 -10000 0 -0.55 134 134
PPP3CA 0.012 0.033 -10000 0 -0.5 2 2
BCL10 0.014 0 -10000 0 -10000 0 0
IKK complex 0.001 0.037 -10000 0 -0.12 1 1
PTPRC -0.042 0.17 -10000 0 -0.54 47 47
PDPK1 -0.054 0.099 -10000 0 -0.25 41 41
PPP3CB 0.011 0.041 -10000 0 -0.5 3 3
PPP3CC 0.014 0 -10000 0 -10000 0 0
POU2F2 0.013 0.024 -10000 0 -0.1 5 5
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.033 0.15 -9999 0 -0.38 56 56
CRKL 0.014 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.01 0.05 -9999 0 -0.61 3 3
ITGA4 -0.056 0.19 -9999 0 -0.54 58 58
alpha4/beta7 Integrin/MAdCAM1 -0.13 0.18 -9999 0 -0.42 96 96
EPO -0.009 0.1 -9999 0 -0.5 19 19
alpha4/beta7 Integrin -0.081 0.18 -9999 0 -0.44 86 86
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.05 0.13 -9999 0 -0.4 58 58
EPO/EPOR (dimer) -0.016 0.076 -9999 0 -0.37 20 20
lamellipodium assembly 0.01 0.017 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
JAK2 -0.002 0.094 -9999 0 -0.28 32 32
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
MADCAM1 -0.12 0.24 -9999 0 -0.55 113 113
cell adhesion -0.13 0.18 -9999 0 -0.41 96 96
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.012 0.033 -9999 0 -0.5 2 2
SRC -0.094 0.18 -9999 0 -0.36 114 114
ITGB7 -0.034 0.16 -9999 0 -0.55 40 40
RAC1 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.13 0.19 -9999 0 -0.37 167 167
p130Cas/Crk/Dock1 -0.059 0.16 -9999 0 -0.51 17 17
VCAM1 -0.14 0.26 -9999 0 -0.57 124 124
RHOA 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.036 0.098 -9999 0 -0.34 27 27
BCAR1 -0.079 0.17 -9999 0 -0.56 16 16
EPOR 0.012 0.033 -9999 0 -0.5 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP 0.01 0.018 -9999 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.061 0.13 -9999 0 -0.57 9 9
SMAD6-7/SMURF1 -0.004 0.039 -9999 0 -0.34 6 6
NOG -0.066 0.21 -9999 0 -0.59 61 61
SMAD9 -0.029 0.17 -9999 0 -0.58 32 32
SMAD4 0.014 0 -9999 0 -10000 0 0
SMAD5 -0.002 0.12 -9999 0 -0.48 16 16
BMP7/USAG1 -0.092 0.17 -9999 0 -0.38 111 111
SMAD5/SKI 0.006 0.12 -9999 0 -0.46 15 15
SMAD1 0.044 0.031 -9999 0 -0.32 1 1
BMP2 -0.082 0.22 -9999 0 -0.61 72 72
SMAD1/SMAD1/SMAD4 -0.004 0.027 -9999 0 -10000 0 0
BMPR1A 0.014 0 -9999 0 -10000 0 0
BMPR1B -0.025 0.15 -9999 0 -0.61 29 29
BMPR1A-1B/BAMBI -0.028 0.1 -9999 0 -0.4 33 33
AHSG -0.073 0.21 -9999 0 -0.56 70 70
CER1 -0.015 0.1 -9999 0 -0.5 20 20
BMP2-4/CER1 -0.086 0.2 -9999 0 -0.48 84 84
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.016 0.16 -9999 0 -0.48 34 34
BMP2-4 (homodimer) -0.087 0.21 -9999 0 -0.53 76 76
RGMB 0.003 0.079 -9999 0 -0.56 9 9
BMP6/BMPR2/BMPR1A-1B -0.029 0.095 -9999 0 -0.35 32 32
RGMA -0.002 0.097 -9999 0 -0.6 12 12
SMURF1 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.023 0.15 -9999 0 -0.47 34 34
BMP2-4/USAG1 -0.14 0.23 -9999 0 -0.44 153 153
SMAD6/SMURF1/SMAD5 0.006 0.12 -9999 0 -0.46 15 15
SOSTDC1 -0.11 0.23 -9999 0 -0.53 106 106
BMP7/BMPR2/BMPR1A-1B -0.025 0.086 -9999 0 -0.33 35 35
SKI 0.014 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.003 0.096 -9999 0 -0.52 15 15
HFE2 0.003 0.062 -9999 0 -0.5 7 7
ZFYVE16 0.014 0 -9999 0 -10000 0 0
MAP3K7 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.077 0.18 -9999 0 -0.45 79 79
SMAD5/SMAD5/SMAD4 0.006 0.12 -9999 0 -0.46 15 15
MAPK1 0.014 0 -9999 0 -10000 0 0
TAK1/TAB family -0.049 0.11 -9999 0 -0.4 33 33
BMP7 (homodimer) 0.006 0.07 -9999 0 -0.61 6 6
NUP214 0.014 0 -9999 0 -10000 0 0
BMP6/FETUA -0.072 0.16 -9999 0 -0.41 81 81
SMAD1/SKI 0.05 0.029 -9999 0 -10000 0 0
SMAD6 0.007 0.066 -9999 0 -0.57 6 6
CTDSP2 0.01 0.047 -9999 0 -0.5 4 4
BMP2-4/FETUA -0.12 0.22 -9999 0 -0.44 131 131
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.17 0.27 -9999 0 -0.56 150 150
BMPR2 (homodimer) 0.014 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.006 0.041 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.028 0.11 -9999 0 -0.44 29 29
CHRDL1 -0.079 0.22 -9999 0 -0.59 72 72
ENDOFIN/SMAD1 0.05 0.029 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.004 0.031 -9999 0 -10000 0 0
SMAD6/SMURF1 0.014 0 -9999 0 -10000 0 0
BAMBI 0.005 0.07 -9999 0 -0.52 8 8
SMURF2 0.012 0.041 -9999 0 -0.61 2 2
BMP2-4/CHRDL1 -0.13 0.22 -9999 0 -0.43 138 138
BMP2-4/GREM1 -0.18 0.24 -9999 0 -0.42 197 197
SMAD7 0.014 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.02 0.16 -9999 0 -0.54 32 32
SMAD1/SMAD6 0.05 0.029 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.006 0.07 -9999 0 -0.61 6 6
BMP6 -0.003 0.096 -9999 0 -0.52 15 15
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.016 0.14 -9999 0 -0.43 34 34
PPM1A 0.014 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.049 0.037 -9999 0 -0.33 1 1
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0.029 -9999 0 -0.61 1 1
PPP1CA 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
PPP1R15A 0.003 0.074 -9999 0 -0.5 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.054 0.19 -9999 0 -0.49 50 50
CHRD 0.009 0.057 -9999 0 -0.61 4 4
BMPR2 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.032 0.17 -9999 0 -0.51 34 34
BMP4 -0.016 0.13 -9999 0 -0.6 23 23
FST -0.067 0.2 -9999 0 -0.55 67 67
BMP2-4/NOG -0.12 0.26 -9999 0 -0.56 98 98
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.023 0.079 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.002 0.17 -9999 0 -1.3 8 8
VDR -0.069 0.2 -9999 0 -0.54 69 69
FAM120B 0.014 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.049 0.16 -9999 0 -0.47 28 28
RXRs/LXRs/DNA/Oxysterols -0.078 0.22 -9999 0 -0.46 86 86
MED1 0.014 0 -9999 0 -10000 0 0
mol:9cRA -0.009 0.024 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.026 0.059 -9999 0 -10000 0 0
RXRs/NUR77 -0.038 0.15 -9999 0 -0.38 57 57
RXRs/PPAR -0.016 0.12 -9999 0 -0.37 29 29
NCOR2 0.014 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.059 0.14 -9999 0 -0.4 69 69
RARs/VDR/DNA/Vit D3 -0.043 0.1 -9999 0 -0.32 33 33
RARA 0.014 0 -9999 0 -10000 0 0
NCOA1 0.014 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.069 0.2 -9999 0 -0.54 69 69
RARs/RARs/DNA/9cRA 0.014 0.037 -9999 0 -0.31 5 5
RARG 0.013 0.024 -9999 0 -0.5 1 1
RPS6KB1 0.02 0.067 -9999 0 -0.4 8 8
RARs/THRs/DNA/SMRT 0.026 0.059 -9999 0 -0.25 15 15
THRA 0.01 0.05 -9999 0 -0.61 3 3
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.059 0.14 -9999 0 -0.4 69 69
RXRs/PPAR/9cRA/PGJ2/DNA -0.037 0.14 -9999 0 -0.36 54 54
NR1H4 -0.13 0.24 -9999 0 -0.54 119 119
RXRs/LXRs/DNA -0.025 0.15 -9999 0 -0.45 21 21
NR1H2 0.011 0.017 -9999 0 -10000 0 0
NR1H3 0.009 0.02 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.061 0.17 -9999 0 -0.38 79 79
NR4A1 -0.023 0.14 -9999 0 -0.52 32 32
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.068 0.14 -9999 0 -0.38 47 47
RXRG -0.065 0.2 -9999 0 -0.6 57 57
RXR alpha/CCPG 0.017 0.013 -9999 0 -10000 0 0
RXRA 0.011 0.017 -9999 0 -10000 0 0
RXRB 0.009 0.02 -9999 0 -10000 0 0
THRB -0.013 0.12 -9999 0 -0.53 23 23
PPARG -0.014 0.13 -9999 0 -0.58 22 22
PPARD 0.014 0 -9999 0 -10000 0 0
TNF -0.19 0.42 -9999 0 -1.1 74 74
mol:Oxysterols -0.007 0.022 -9999 0 -10000 0 0
cholesterol transport -0.077 0.22 -9999 0 -0.46 86 86
PPARA 0.014 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.009 0.057 -9999 0 -0.61 4 4
RXRs/NUR77/BCL2 -0.025 0.13 -9999 0 -0.32 58 58
SREBF1 -0.082 0.27 -9999 0 -0.92 28 28
RXRs/RXRs/DNA/9cRA -0.037 0.14 -9999 0 -0.36 54 54
ABCA1 -0.084 0.28 -9999 0 -0.89 32 32
RARs/THRs -0.017 0.066 -9999 0 -0.3 15 15
RXRs/FXR -0.097 0.19 -9999 0 -0.4 97 97
BCL2 0.005 0.076 -9999 0 -0.61 7 7
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.024 -9999 0 -0.5 1 1
LAT2 -0.05 0.17 -9999 0 -0.59 29 29
AP1 -0.1 0.17 -9999 0 -0.56 40 40
mol:PIP3 -0.063 0.2 -9999 0 -0.57 36 36
IKBKB -0.03 0.11 -9999 0 -0.3 27 27
AKT1 -0.032 0.14 -9999 0 -0.42 17 17
IKBKG -0.03 0.11 -9999 0 -0.29 30 30
MS4A2 -0.026 0.12 -9999 0 -0.5 26 26
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.001 -9999 0 -10000 0 0
MAP3K1 -0.015 0.15 -9999 0 -0.53 25 25
mol:Ca2+ -0.043 0.15 -9999 0 -0.41 36 36
LYN 0.002 0.079 -9999 0 -0.53 10 10
CBLB -0.037 0.13 -9999 0 -0.49 21 21
SHC1 0.009 0.053 -9999 0 -0.5 5 5
RasGAP/p62DOK -0.019 0.072 -9999 0 -0.29 30 30
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.008 0.058 -9999 0 -0.54 5 5
PLD2 -0.069 0.16 -9999 0 -0.35 70 70
PTPN13 -0.028 0.14 -9999 0 -0.55 17 17
PTPN11 0.011 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.001 0.12 -9999 0 -0.33 15 15
SYK -0.014 0.13 -9999 0 -0.59 21 21
GRB2 0.013 0.024 -9999 0 -0.5 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.17 -9999 0 -0.57 36 36
LAT -0.054 0.15 -9999 0 -0.41 45 45
PAK2 -0.025 0.17 -9999 0 -0.6 26 26
NFATC2 -0.097 0.18 -9999 0 -0.54 55 55
HRAS -0.037 0.19 -9999 0 -0.66 28 28
GAB2 0.013 0.029 -9999 0 -0.61 1 1
PLA2G1B 0.041 0.023 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.18 -9999 0 -0.36 161 161
Antigen/IgE/Fc epsilon R1 -0.11 0.17 -9999 0 -0.34 133 133
mol:GDP -0.046 0.2 -9999 0 -0.7 29 29
JUN 0.003 0.076 -9999 0 -0.51 10 10
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
FOS -0.093 0.22 -9999 0 -0.56 87 87
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.062 0.13 -9999 0 -0.46 27 27
CHUK -0.03 0.11 -9999 0 -0.3 28 28
KLRG1 -0.041 0.13 -9999 0 -0.5 19 19
VAV1 -0.053 0.18 -9999 0 -0.62 30 30
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.035 0.13 -9999 0 -0.51 19 19
negative regulation of mast cell degranulation -0.032 0.14 -9999 0 -0.51 20 20
BTK -0.069 0.19 -9999 0 -0.74 25 25
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.19 -9999 0 -0.54 44 44
GAB2/PI3K/SHP2 -0.08 0.12 -9999 0 -0.47 17 17
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.054 0.15 -9999 0 -0.53 24 24
RAF1 0.03 0.026 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.18 0.22 -9999 0 -0.49 107 107
FCER1G -0.021 0.14 -9999 0 -0.58 27 27
FCER1A -0.14 0.25 -9999 0 -0.54 127 127
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.15 -9999 0 -0.36 78 78
MAPK3 0.039 0.023 -9999 0 -10000 0 0
MAPK1 0.039 0.023 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0 0.1 -9999 0 -0.59 10 10
DUSP1 -0.02 0.14 -9999 0 -0.54 29 29
NF-kappa-B/RelA -0.033 0.049 -9999 0 -0.23 1 1
actin cytoskeleton reorganization -0.033 0.13 -9999 0 -0.53 16 16
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.067 0.16 -9999 0 -0.63 26 26
FER -0.048 0.15 -9999 0 -0.44 36 36
RELA 0.014 0 -9999 0 -10000 0 0
ITK -0.069 0.12 -9999 0 -0.35 56 56
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG1 -0.044 0.2 -9999 0 -0.69 29 29
cytokine secretion -0.024 0.036 -9999 0 -10000 0 0
SPHK1 -0.057 0.16 -9999 0 -0.47 37 37
PTK2 -0.035 0.14 -9999 0 -0.55 16 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.18 -9999 0 -0.66 31 31
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.05 0.19 -9999 0 -0.57 29 29
MAP2K2 0.036 0.023 -9999 0 -10000 0 0
MAP2K1 0.035 0.026 -9999 0 -10000 0 0
MAP2K7 0.014 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.047 0.12 -9999 0 -0.48 19 19
MAP2K4 0.02 0.014 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.19 0.23 -9999 0 -0.47 147 147
mol:Choline -0.068 0.16 -9999 0 -0.34 70 70
SHC/Grb2/SOS1 -0.057 0.11 -9999 0 -0.51 17 17
FYN 0.014 0 -9999 0 -10000 0 0
DOK1 0.013 0.029 -9999 0 -0.61 1 1
PXN -0.024 0.13 -9999 0 -0.5 16 16
HCLS1 -0.053 0.17 -9999 0 -0.55 32 32
PRKCB -0.053 0.14 -9999 0 -0.38 42 42
FCGR2B -0.15 0.26 -9999 0 -0.55 134 134
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.033 0.14 -9999 0 -0.52 20 20
LCP2 -0.004 0.095 -9999 0 -0.5 16 16
PLA2G4A -0.052 0.16 -9999 0 -0.46 38 38
RASA1 0.014 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.068 0.16 -9999 0 -0.34 70 70
IKK complex -0.008 0.086 -9999 0 -0.23 17 17
WIPF1 0.014 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.01 0.05 -10000 0 -0.61 3 3
HDAC3 0.014 0 -10000 0 -10000 0 0
VDR -0.069 0.2 -10000 0 -0.54 69 69
Cbp/p300/PCAF -0.004 0.036 -10000 0 -0.35 5 5
EP300 0.009 0.057 -10000 0 -0.61 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.066 -10000 0 -0.4 5 5
KAT2B 0.013 0.024 -10000 0 -0.5 1 1
MAPK14 0.014 0 -10000 0 -10000 0 0
AKT1 0.009 0.072 0.23 7 -0.32 4 11
RAR alpha/9cRA/Cyclin H -0.051 0.085 -10000 0 -0.92 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.06 -10000 0 -0.34 5 5
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.062 0.1 -10000 0 -0.55 10 10
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.059 0.14 -10000 0 -0.4 69 69
RXRs/RARs/NRIP1/9cRA -0.058 0.2 -10000 0 -0.47 64 64
NCOA2 -0.025 0.15 -10000 0 -0.61 29 29
NCOA3 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.069 0.2 -10000 0 -0.54 69 69
RARG 0.014 0.024 -10000 0 -0.49 1 1
RAR gamma1/9cRA -0.001 0.014 -10000 0 -0.29 1 1
MAPK3 0.015 0 -10000 0 -10000 0 0
MAPK1 0.014 0 -10000 0 -10000 0 0
MAPK8 0.002 0.09 -10000 0 -0.61 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.15 0.22 -10000 0 -0.57 81 81
RARA -0.05 0.12 -10000 0 -0.26 85 85
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.003 0.1 -10000 0 -0.39 16 16
PRKCA 0.016 0.029 -10000 0 -0.61 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.071 0.2 -10000 0 -0.47 76 76
RXRG -0.12 0.22 -10000 0 -0.46 105 105
RXRA -0.034 0.11 -10000 0 -0.85 1 1
RXRB -0.075 0.15 -10000 0 -0.35 76 76
VDR/Vit D3/DNA -0.059 0.14 -10000 0 -0.4 69 69
RBP1 -0.076 0.2 -10000 0 -0.51 80 80
CRBP1/9-cic-RA -0.063 0.14 -10000 0 -0.37 80 80
RARB 0.011 0.058 -10000 0 -0.61 4 4
PRKCG -0.19 0.27 -10000 0 -0.54 171 171
MNAT1 0.013 0.024 -10000 0 -0.5 1 1
RAR alpha/RXRs -0.061 0.21 -10000 0 -0.51 64 64
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.045 0.17 -10000 0 -0.4 64 64
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.097 -10000 0 -0.41 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.071 0.2 -10000 0 -0.47 76 76
positive regulation of DNA binding -0.049 0.08 -10000 0 -0.82 1 1
NRIP1 -0.062 0.18 -10000 0 -0.59 24 24
RXRs/RARs -0.078 0.2 -10000 0 -0.48 76 76
RXRs/RXRs/DNA/9cRA -0.12 0.2 -10000 0 -0.53 76 76
PRKACA 0.014 0 -10000 0 -10000 0 0
CDK7 0.014 0 -10000 0 -10000 0 0
TFIIH -0.001 0.013 -10000 0 -0.28 1 1
RAR alpha/9cRA -0.036 0.064 -10000 0 -0.81 1 1
CCNH 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.013 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.018 0.006 -9999 0 -10000 0 0
RAS family/GTP -0.072 0.16 -9999 0 -0.54 23 23
NFATC4 -0.062 0.14 -9999 0 -0.38 30 30
ERBB2IP 0.015 0.029 -9999 0 -0.6 1 1
HSP90 (dimer) 0.014 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.092 0.16 -9999 0 -0.49 23 23
JUN -0.022 0.1 -9999 0 -0.37 19 19
HRAS 0.014 0.001 -9999 0 -10000 0 0
DOCK7 -0.086 0.16 -9999 0 -0.48 27 27
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.14 0.18 -9999 0 -0.38 127 127
AKT1 0.011 0.004 -9999 0 -10000 0 0
BAD 0.02 0.003 -9999 0 -10000 0 0
MAPK10 -0.049 0.077 -9999 0 -0.24 26 26
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.097 0.17 -9999 0 -0.53 23 23
RAF1 -0.064 0.16 -9999 0 -0.52 23 23
ErbB2/ErbB3/neuregulin 2 -0.047 0.12 -9999 0 -0.36 51 51
STAT3 0.004 0.005 -9999 0 -10000 0 0
cell migration -0.021 0.095 -9999 0 -0.24 19 19
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.15 0.27 -9999 0 -0.61 85 85
FOS -0.12 0.22 -9999 0 -0.42 128 128
NRAS 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.092 0.16 -9999 0 -0.49 23 23
MAPK3 -0.12 0.23 -9999 0 -0.51 75 75
MAPK1 -0.12 0.23 -9999 0 -0.51 75 75
JAK2 -0.082 0.15 -9999 0 -0.46 23 23
NF2 -0.003 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.094 0.18 -9999 0 -0.34 126 126
NRG1 -0.17 0.27 -9999 0 -0.57 146 146
GRB2/SOS1 -0.001 0.016 -9999 0 -0.35 1 1
MAPK8 -0.077 0.15 -9999 0 -0.41 27 27
MAPK9 -0.047 0.074 -9999 0 -0.23 25 25
ERBB2 -0.006 0.045 -9999 0 -0.37 7 7
ERBB3 -0.063 0.2 -9999 0 -0.58 58 58
SHC1 0.008 0.053 -9999 0 -0.5 5 5
RAC1 0.014 0 -9999 0 -10000 0 0
apoptosis -0.001 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0.01 0.009 -9999 0 -10000 0 0
RNF41 0.023 0.009 -9999 0 -10000 0 0
FRAP1 0.009 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.074 0.1 -9999 0 -0.33 25 25
ErbB2/ErbB2/HSP90 (dimer) -0.005 0.037 -9999 0 -0.3 7 7
CHRNA1 -0.14 0.26 -9999 0 -0.58 92 92
myelination -0.054 0.13 -9999 0 -0.36 29 29
PPP3CB -0.077 0.14 -9999 0 -0.42 25 25
KRAS 0.013 0.024 -9999 0 -0.5 1 1
RAC1-CDC42/GDP -0.067 0.16 -9999 0 -0.54 24 24
NRG2 0.012 0.041 -9999 0 -0.61 2 2
mol:GDP -0.093 0.18 -9999 0 -0.34 126 126
SOS1 0.014 0.001 -9999 0 -10000 0 0
MAP2K2 -0.062 0.16 -9999 0 -0.55 17 17
SRC 0.014 0 -9999 0 -10000 0 0
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.081 0.15 -9999 0 -0.46 23 23
MAP2K1 -0.13 0.22 -9999 0 -0.52 64 64
heart morphogenesis -0.092 0.16 -9999 0 -0.49 23 23
RAS family/GDP -0.07 0.16 -9999 0 -0.54 23 23
GRB2 0.013 0.024 -9999 0 -0.5 1 1
PRKACA -0.007 0.009 -9999 0 -10000 0 0
CHRNE 0.001 0.046 -9999 0 -0.19 21 21
HSP90AA1 0.014 0 -9999 0 -10000 0 0
activation of caspase activity -0.011 0.004 -9999 0 -10000 0 0
nervous system development -0.092 0.16 -9999 0 -0.49 23 23
CDC42 0.014 0 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.014 0.004 -9999 0 -10000 0 0
SVIL -0.01 0.11 -9999 0 -0.5 21 21
ZNF318 0.018 0.017 -9999 0 -10000 0 0
JMJD2C -0.002 0.02 -9999 0 -0.077 27 27
T-DHT/AR/Ubc9 -0.066 0.16 -9999 0 -0.38 91 91
CARM1 0.014 0.001 -9999 0 -10000 0 0
PRDX1 -0.014 0.13 -9999 0 -0.61 21 21
PELP1 0.015 0.003 -9999 0 -10000 0 0
CTNNB1 0.014 0.004 -9999 0 -10000 0 0
AKT1 0.015 0.004 -9999 0 -10000 0 0
PTK2B -0.012 0.11 -9999 0 -0.5 23 23
MED1 0.015 0.005 -9999 0 -10000 0 0
MAK -0.037 0.16 -9999 0 -0.5 49 49
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 -0.001 0.095 -9999 0 -0.61 11 11
GSN 0.002 0.083 -9999 0 -0.58 9 9
NCOA2 -0.025 0.15 -9999 0 -0.61 29 29
NCOA6 0.014 0.004 -9999 0 -10000 0 0
DNA-PK 0.007 0.024 -9999 0 -10000 0 0
NCOA4 0.014 0.001 -9999 0 -10000 0 0
PIAS3 0.014 0.004 -9999 0 -10000 0 0
cell proliferation -0.043 0.1 -9999 0 -0.36 26 26
XRCC5 0.015 0.004 -9999 0 -10000 0 0
UBE3A 0.012 0.009 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.078 0.18 -9999 0 -0.39 102 102
FHL2 -0.05 0.22 -9999 0 -0.68 38 38
RANBP9 0.014 0.004 -9999 0 -10000 0 0
JMJD1A -0.01 0.055 -9999 0 -0.11 95 95
CDK6 -0.035 0.16 -9999 0 -0.54 41 41
TGFB1I1 0.004 0.074 -9999 0 -0.55 8 8
T-DHT/AR/CyclinD1 -0.086 0.19 -9999 0 -0.4 106 106
XRCC6 0.015 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.074 0.18 -9999 0 -0.39 99 99
CTDSP1 0.013 0.004 -9999 0 -10000 0 0
CTDSP2 0.012 0.049 -9999 0 -0.5 4 4
BRCA1 0.009 0.047 -9999 0 -0.5 4 4
TCF4 0.015 0.03 -9999 0 -0.61 1 1
CDKN2A -0.11 0.24 -9999 0 -0.57 96 96
SRF 0.017 0.028 -9999 0 -10000 0 0
NKX3-1 -0.062 0.18 -9999 0 -0.9 14 14
KLK3 -0.014 0.11 -9999 0 -10000 0 0
TMF1 0.014 0.003 -9999 0 -10000 0 0
HNRNPA1 0.016 0.006 -9999 0 -10000 0 0
AOF2 -0.002 0.007 -9999 0 -10000 0 0
APPL1 0.028 0.01 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.076 0.17 -9999 0 -0.38 103 103
AR -0.11 0.24 -9999 0 -0.59 91 91
UBA3 0.013 0.004 -9999 0 -10000 0 0
PATZ1 0.016 0.006 -9999 0 -10000 0 0
PAWR -0.028 0.14 -9999 0 -0.53 35 35
PRKDC 0.015 0.004 -9999 0 -10000 0 0
PA2G4 0.016 0.007 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.059 0.15 -9999 0 -0.34 92 92
RPS6KA3 0.012 0.029 -9999 0 -0.61 1 1
T-DHT/AR/ARA70 -0.067 0.16 -9999 0 -0.38 91 91
LATS2 -0.002 0.096 -9999 0 -0.52 15 15
T-DHT/AR/PRX1 -0.074 0.17 -9999 0 -0.38 102 102
Cyclin D3/CDK11 p58 0 0.017 -9999 0 -0.36 1 1
VAV3 -0.12 0.23 -9999 0 -0.53 113 113
KLK2 -0.062 0.11 -9999 0 -0.44 28 28
CASP8 -0.003 0.094 -9999 0 -0.5 16 16
T-DHT/AR/TIF2/CARM1 -0.073 0.18 -9999 0 -0.39 95 95
TMPRSS2 -0.14 0.32 -9999 0 -0.89 56 56
CCND1 -0.017 0.13 -9999 0 -0.54 26 26
PIAS1 0.007 0.058 -9999 0 -0.61 4 4
mol:T-DHT -0.011 0.032 -9999 0 -0.08 54 54
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.011 0.015 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.096 0.19 -9999 0 -0.39 121 121
CMTM2 -0.008 0.11 -9999 0 -0.56 18 18
SNURF -0.005 0.11 -9999 0 -0.59 15 15
ZMIZ1 0.006 0.027 -9999 0 -10000 0 0
CCND3 0.013 0.024 -9999 0 -0.5 1 1
TGIF1 -0.006 0.11 -9999 0 -0.54 18 18
FKBP4 0.014 0.004 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.009 0.06 0.28 7 -10000 0 7
RFC1 0.009 0.06 0.28 7 -10000 0 7
PRKDC 0.009 0.06 0.23 19 -10000 0 19
RIPK1 0.016 0.004 -10000 0 -10000 0 0
CASP7 -0.005 0.076 0.25 14 -0.33 5 19
FASLG/FAS/FADD/FAF1 -0.011 0.092 0.23 19 -0.32 16 35
MAP2K4 -0.009 0.12 -10000 0 -0.36 15 15
mol:ceramide -0.008 0.1 -10000 0 -0.39 11 11
GSN 0.002 0.07 0.25 5 -0.34 7 12
FASLG/FAS/FADD/FAF1/Caspase 8 -0.005 0.097 0.21 2 -0.32 18 20
FAS -0.011 0.11 -10000 0 -0.56 18 18
BID 0.006 0.084 0.3 17 -0.29 16 33
MAP3K1 0.007 0.094 0.22 13 -0.28 12 25
MAP3K7 0.012 0.006 -10000 0 -10000 0 0
RB1 0.008 0.062 0.28 7 -0.37 1 8
CFLAR 0.015 0.023 -10000 0 -0.48 1 1
HGF/MET -0.15 0.2 -10000 0 -0.38 179 179
ARHGDIB 0.007 0.067 0.23 19 -0.37 3 22
FADD 0.011 0.007 -10000 0 -10000 0 0
actin filament polymerization -0.002 0.07 0.34 7 -0.25 5 12
NFKB1 -0.043 0.07 -10000 0 -10000 0 0
MAPK8 -0.035 0.18 -10000 0 -0.43 54 54
DFFA 0.009 0.06 0.28 7 -10000 0 7
DNA fragmentation during apoptosis 0.009 0.06 0.28 7 -10000 0 7
FAS/FADD/MET -0.1 0.17 -10000 0 -0.35 138 138
CFLAR/RIP1 0.013 0.018 -10000 0 -0.32 1 1
FAIM3 -0.032 0.16 -10000 0 -0.55 39 39
FAF1 0.01 0.03 -10000 0 -0.61 1 1
PARP1 0.008 0.061 0.23 19 -0.29 1 20
DFFB 0.009 0.06 0.28 7 -10000 0 7
CHUK -0.036 0.06 -10000 0 -10000 0 0
FASLG -0.033 0.14 -10000 0 -0.5 35 35
FAS/FADD 0 0.084 -10000 0 -0.41 18 18
HGF -0.078 0.2 -10000 0 -0.52 80 80
LMNA 0.005 0.065 0.25 7 -0.3 6 13
CASP6 0.006 0.069 0.22 23 -0.36 4 27
CASP10 0.01 0.025 -10000 0 -0.51 1 1
CASP3 0.01 0.071 0.26 23 -0.2 6 29
PTPN13 0.005 0.074 -10000 0 -0.59 7 7
CASP8 0.012 0.11 0.32 34 -0.34 16 50
IL6 -0.16 0.4 -10000 0 -1.2 51 51
MET -0.14 0.25 -10000 0 -0.55 129 129
ICAD/CAD 0.009 0.056 0.26 7 -10000 0 7
FASLG/FAS/FADD/FAF1/Caspase 10 -0.009 0.1 -10000 0 -0.4 11 11
activation of caspase activity by cytochrome c 0.006 0.084 0.3 17 -0.29 16 33
PAK2 0.009 0.06 0.28 7 -10000 0 7
BCL2 0.005 0.076 -10000 0 -0.61 7 7
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.034 0.14 -9999 0 -0.43 24 24
FZD6 -0.013 0.12 -9999 0 -0.5 25 25
WNT6 -0.036 0.16 -9999 0 -0.54 42 42
WNT4 -0.035 0.16 -9999 0 -0.53 42 42
FZD3 0.01 0.05 -9999 0 -0.61 3 3
WNT5A -0.018 0.13 -9999 0 -0.58 25 25
WNT11 -0.017 0.13 -9999 0 -0.56 25 25
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.077 0.27 -10000 0 -0.89 28 28
NCK1/PAK1/Dok-R -0.094 0.13 -10000 0 -0.41 42 42
NCK1/Dok-R -0.1 0.3 -10000 0 -1.1 28 28
PIK3CA 0.014 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.012 0.059 0.21 23 -10000 0 23
RELA 0.014 0 -10000 0 -10000 0 0
SHC1 0.008 0.053 -10000 0 -0.5 5 5
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.011 0.087 0.25 10 -0.49 7 17
TNIP2 0.014 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.095 0.25 -10000 0 -1 27 27
FN1 -0.004 0.096 -10000 0 -0.5 17 17
PLD2 -0.07 0.3 -10000 0 -1.1 27 27
PTPN11 0.014 0 -10000 0 -10000 0 0
GRB14 -0.18 0.27 -10000 0 -0.54 164 164
ELK1 -0.047 0.27 -10000 0 -1 27 27
GRB7 -0.031 0.14 -10000 0 -0.5 38 38
PAK1 -0.036 0.16 -10000 0 -0.51 45 45
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.28 -10000 0 -1 32 32
CDKN1A -0.1 0.29 -10000 0 -0.71 62 62
ITGA5 -0.013 0.12 -10000 0 -0.51 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.1 0.3 -10000 0 -1.1 28 28
CRK 0.014 0 -10000 0 -10000 0 0
mol:NO -0.052 0.22 -10000 0 -0.65 29 29
PLG -0.079 0.3 -10000 0 -1.1 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.069 0.25 -10000 0 -0.88 26 26
GRB2 0.013 0.024 -10000 0 -0.5 1 1
PIK3R1 0.014 0.002 -10000 0 -10000 0 0
ANGPT2 -0.11 0.29 -10000 0 -0.84 46 46
BMX -0.1 0.3 -10000 0 -1.1 28 28
ANGPT1 -0.12 0.33 -10000 0 -1.1 33 33
tube development -0.081 0.26 -10000 0 -0.68 49 49
ANGPT4 -0.055 0.18 -10000 0 -0.55 56 56
response to hypoxia -0.007 0.02 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.17 0.34 -10000 0 -1.3 29 29
alpha5/beta1 Integrin -0.02 0.085 -10000 0 -0.37 25 25
FGF2 0.011 0.047 -10000 0 -0.57 3 3
STAT5A (dimer) -0.11 0.31 -10000 0 -0.8 52 52
mol:L-citrulline -0.052 0.22 -10000 0 -0.65 29 29
AGTR1 -0.038 0.16 -10000 0 -0.56 42 42
MAPK14 -0.077 0.29 -10000 0 -1.1 26 26
Tie2/SHP2 -0.036 0.15 -10000 0 -1.2 6 6
TEK -0.016 0.18 -10000 0 -1.3 6 6
RPS6KB1 -0.063 0.25 -10000 0 -0.87 26 26
Angiotensin II/AT1 -0.029 0.12 -10000 0 -0.41 42 42
Tie2/Ang1/GRB2 -0.073 0.31 -10000 0 -1.2 27 27
MAPK3 -0.054 0.27 -10000 0 -1 27 27
MAPK1 -0.054 0.27 -10000 0 -1 27 27
Tie2/Ang1/GRB7 -0.096 0.31 -10000 0 -1.2 27 27
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.076 0.3 -10000 0 -1.2 27 27
PI3K -0.084 0.29 -10000 0 -1.1 26 26
FES -0.077 0.29 -10000 0 -1.1 26 26
Crk/Dok-R -0.1 0.3 -10000 0 -1.1 28 28
Tie2/Ang1/ABIN2 -0.073 0.31 -10000 0 -1.2 27 27
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.068 0.25 -10000 0 -0.79 28 28
STAT5A -0.001 0.093 -10000 0 -0.6 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.063 0.25 -10000 0 -0.87 26 26
Tie2/Ang2 -0.12 0.34 -10000 0 -0.95 48 48
Tie2/Ang1 -0.085 0.32 -10000 0 -1.2 27 27
FOXO1 -0.076 0.27 -10000 0 -0.77 35 35
ELF1 0.019 0.034 -10000 0 -0.65 1 1
ELF2 -0.074 0.29 -10000 0 -1.1 27 27
mol:Choline -0.064 0.28 -10000 0 -1.1 27 27
cell migration -0.053 0.072 -10000 0 -0.23 35 35
FYN -0.095 0.29 -10000 0 -0.78 48 48
DOK2 -0.074 0.2 -10000 0 -0.54 74 74
negative regulation of cell cycle -0.089 0.26 -10000 0 -0.63 63 63
ETS1 -0.006 0.094 -10000 0 -0.58 8 8
PXN -0.043 0.22 -10000 0 -0.71 26 26
ITGB1 0.012 0.033 -10000 0 -0.5 2 2
NOS3 -0.062 0.24 -10000 0 -0.75 28 28
RAC1 0.014 0 -10000 0 -10000 0 0
TNF -0.17 0.27 -10000 0 -0.57 142 142
MAPKKK cascade -0.064 0.28 -10000 0 -1.1 27 27
RASA1 0.014 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.078 0.31 -10000 0 -1.2 27 27
NCK1 0.013 0.029 -10000 0 -0.61 1 1
vasculogenesis -0.045 0.2 -10000 0 -0.58 29 29
mol:Phosphatidic acid -0.064 0.28 -10000 0 -1.1 27 27
mol:Angiotensin II -0.001 0.008 -10000 0 -10000 0 0
mol:NADP -0.052 0.22 -10000 0 -0.65 29 29
Rac1/GTP -0.11 0.2 -10000 0 -0.81 26 26
MMP2 -0.084 0.3 -10000 0 -1.1 27 27
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.036 0.1 -10000 0 -0.33 51 51
MAPK9 0.01 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.13 0.2 -10000 0 -0.4 159 159
GNB1/GNG2 -0.003 0.035 -10000 0 -0.38 4 4
GNB1 0.014 0 -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 0.01 0 -10000 0 -10000 0 0
Gs family/GTP -0.037 0.11 -10000 0 -0.35 49 49
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 0.009 0.027 0.089 49 -10000 0 49
GNAL -0.051 0.19 -10000 0 -0.6 49 49
GNG2 0.009 0.057 -10000 0 -0.61 4 4
CRH -0.18 0.27 -10000 0 -0.55 159 159
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.055 -10000 0 -0.37 10 10
MAPK11 0.006 0.035 -10000 0 -0.37 4 4
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.014 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.029 0.04 -10000 0 -0.52 1 1
NT3 (dimer)/TRKC -0.016 0.081 -10000 0 -0.4 18 18
NT3 (dimer)/TRKB -0.079 0.16 -10000 0 -0.38 96 96
SHC/Grb2/SOS1/GAB1/PI3K 0.038 0.03 -10000 0 -0.45 1 1
RAPGEF1 0.014 0 -10000 0 -10000 0 0
BDNF -0.08 0.2 -10000 0 -0.51 83 83
PIK3CA 0.014 0 -10000 0 -10000 0 0
DYNLT1 0.012 0.041 -10000 0 -0.61 2 2
NTRK1 -0.008 0.11 -10000 0 -0.53 19 19
NTRK2 -0.021 0.14 -10000 0 -0.61 26 26
NTRK3 0.009 0.057 -10000 0 -0.61 4 4
NT-4/5 (dimer)/TRKB -0.08 0.16 -10000 0 -0.38 97 97
neuron apoptosis 0.13 0.17 0.42 89 -10000 0 89
SHC 2-3/Grb2 -0.14 0.19 -10000 0 -0.46 89 89
SHC1 0.009 0.053 -10000 0 -0.5 5 5
SHC2 -0.075 0.12 -10000 0 -0.42 29 29
SHC3 -0.17 0.24 -10000 0 -0.56 99 99
STAT3 (dimer) 0.007 0.069 -10000 0 -0.35 11 11
NT3 (dimer)/TRKA -0.071 0.15 -10000 0 -0.36 92 92
RIN/GDP -0.037 0.12 -10000 0 -0.27 19 19
GIPC1 0.013 0.024 -10000 0 -0.5 1 1
KRAS 0.013 0.024 -10000 0 -0.5 1 1
DNAJA3 -0.073 0.13 -10000 0 -0.37 44 44
RIN/GTP -0.16 0.2 -10000 0 -0.41 179 179
CCND1 -0.001 0.15 -10000 0 -0.6 26 26
MAGED1 0.014 0 -10000 0 -10000 0 0
PTPN11 0.014 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.093 -10000 0 -0.5 16 16
SHC/GRB2/SOS1 -0.004 0.032 -10000 0 -0.28 6 6
GRB2 0.013 0.024 -10000 0 -0.5 1 1
NGF (dimer)/TRKA/MATK -0.12 0.2 -10000 0 -0.45 96 96
TRKA/NEDD4-2 -0.026 0.099 -10000 0 -0.39 31 31
ELMO1 0.001 0.09 -10000 0 -0.61 10 10
RhoG/GTP/ELMO1/DOCK1 -0.011 0.062 -10000 0 -0.38 13 13
NGF -0.074 0.21 -10000 0 -0.58 69 69
HRAS 0.014 0 -10000 0 -10000 0 0
DOCK1 0.01 0.05 -10000 0 -0.61 3 3
GAB2 0.013 0.029 -10000 0 -0.61 1 1
RIT2 -0.21 0.28 -10000 0 -0.56 179 179
RIT1 0.014 0 -10000 0 -10000 0 0
FRS2 0.012 0.037 -10000 0 -0.55 2 2
DNM1 -0.11 0.23 -10000 0 -0.53 106 106
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.077 0.13 -10000 0 -0.36 54 54
mol:GDP 0.045 0.069 -10000 0 -0.46 2 2
NGF (dimer) -0.074 0.21 -10000 0 -0.57 69 69
RhoG/GDP -0.01 0.065 -10000 0 -0.45 10 10
RIT1/GDP 0.041 0.05 -10000 0 -0.29 2 2
TIAM1 0.013 0.029 -10000 0 -0.61 1 1
PIK3R1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.077 0.14 -10000 0 -0.33 108 108
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.004 0.036 -10000 0 -0.35 5 5
FRS2 family/SHP2 -0.001 0.022 -10000 0 -0.32 2 2
SHC/GRB2/SOS1/GAB1 -0.004 0.039 -10000 0 -0.58 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.008 0.092 -10000 0 -0.49 16 16
RAP1/GDP -0.006 0.024 -10000 0 -0.26 1 1
KIDINS220/CRKL 0.014 0 -10000 0 -10000 0 0
BDNF (dimer) -0.08 0.2 -10000 0 -0.51 83 83
ubiquitin-dependent protein catabolic process -0.072 0.15 -10000 0 -0.37 91 91
Schwann cell development -0.021 0.028 -10000 0 -10000 0 0
EHD4 0.009 0.053 -10000 0 -0.5 5 5
FRS2 family/GRB2/SOS1 -0.002 0.022 -10000 0 -0.33 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.044 0.017 -10000 0 -10000 0 0
RAP1B 0.013 0.024 -10000 0 -0.5 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.063 0.12 -10000 0 -0.49 17 17
ABL1 0.014 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 -0.001 0.016 -10000 0 -0.35 1 1
Rap1/GTP -0.023 0.045 -10000 0 -10000 0 0
STAT3 0.007 0.069 -10000 0 -0.35 11 11
axon guidance -0.061 0.12 -10000 0 -0.47 17 17
MAPK3 -0.085 0.19 -10000 0 -0.4 96 96
MAPK1 -0.085 0.19 -10000 0 -0.4 96 96
CDC42/GDP 0.041 0.05 -10000 0 -0.29 2 2
NTF3 -0.008 0.092 -10000 0 -0.5 16 16
NTF4 -0.012 0.093 -10000 0 -0.5 16 16
NGF (dimer)/TRKA/FAIM -0.066 0.14 -10000 0 -0.39 61 61
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0.014 0 -10000 0 -10000 0 0
FAIM 0.01 0.05 -10000 0 -0.61 3 3
GAB1 0.012 0.037 -10000 0 -0.55 2 2
RASGRF1 -0.12 0.17 -10000 0 -0.39 101 101
SOS1 0.014 0 -10000 0 -10000 0 0
MCF2L 0.013 0.075 -10000 0 -0.33 19 19
RGS19 0.014 0 -10000 0 -10000 0 0
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP 0.013 0.076 -10000 0 -10000 0 0
Rac1/GDP 0.041 0.05 -10000 0 -0.29 2 2
NGF (dimer)/TRKA/GRIT -0.066 0.14 -10000 0 -0.36 84 84
neuron projection morphogenesis -0.041 0.14 -10000 0 -0.51 9 9
NGF (dimer)/TRKA/NEDD4-2 -0.073 0.16 -10000 0 -0.37 91 91
MAP2K1 0.038 0.042 -10000 0 -0.55 1 1
NGFR -0.07 0.2 -10000 0 -0.55 69 69
NGF (dimer)/TRKA/GIPC/GAIP -0.054 0.14 -10000 0 -0.45 25 25
RAS family/GTP/PI3K 0.034 0.008 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.002 0.02 -10000 0 -0.3 1 1
NRAS 0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.016 -10000 0 -0.35 1 1
PRKCI 0.014 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.017 0.13 -10000 0 -0.57 25 25
MAPKKK cascade -0.089 0.21 -10000 0 -0.62 59 59
RASA1 0.014 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.015 0.075 -10000 0 -0.38 19 19
SQSTM1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.067 0.13 -10000 0 -0.37 41 41
NGF (dimer)/TRKA/p62/Atypical PKCs -0.067 0.14 -10000 0 -0.64 8 8
MATK -0.091 0.22 -10000 0 -0.56 85 85
NEDD4L -0.001 0.092 -10000 0 -0.54 13 13
RAS family/GDP -0.005 0.022 -10000 0 -0.26 1 1
NGF (dimer)/TRKA -0.079 0.14 -10000 0 -0.32 91 91
Rac1/GTP -0.067 0.098 -10000 0 -0.33 30 30
FRS2 family/SHP2/CRK family -0.001 0.017 -10000 0 -0.3 1 1
LPA4-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
ADCY4 0.007 0.07 -9999 0 -0.32 20 20
ADCY5 -0.002 0.097 -9999 0 -0.38 27 27
ADCY6 0.014 0.052 -9999 0 -0.32 11 11
ADCY7 0.014 0.052 -9999 0 -0.32 11 11
ADCY1 -0.055 0.16 -9999 0 -0.36 93 93
ADCY2 0.003 0.086 -9999 0 -0.36 23 23
ADCY3 0.014 0.052 -9999 0 -0.32 11 11
ADCY8 -0.035 0.14 -9999 0 -0.36 68 68
PRKCE 0.003 0.061 -9999 0 -0.38 11 11
ADCY9 0.012 0.06 -9999 0 -0.34 12 12
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.01 0.1 -9999 0 -0.36 21 21
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.009 0.06 -10000 0 -0.6 4 4
HSPA8 0.013 0.029 -10000 0 -0.61 1 1
SMAD3/SMAD4/ER alpha -0.027 0.11 0.22 3 -0.4 23 26
AKT1 0.008 0.024 -10000 0 -10000 0 0
GSC -0.16 0.48 -10000 0 -1.4 58 58
NKX2-5 -0.095 0.21 -10000 0 -0.51 93 93
muscle cell differentiation 0.15 0.19 0.48 88 -10000 0 88
SMAD2-3/SMAD4/SP1 -0.005 0.11 -10000 0 -0.43 8 8
SMAD4 -0.016 0.066 -10000 0 -0.34 2 2
CBFB 0.014 0 -10000 0 -10000 0 0
SAP18 0.014 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.021 0.11 -10000 0 -0.34 40 40
SMAD3/SMAD4/VDR -0.037 0.12 -10000 0 -0.37 22 22
MYC -0.011 0.14 -10000 0 -0.56 25 25
CDKN2B -0.13 0.45 -10000 0 -1.4 50 50
AP1 -0.028 0.16 -10000 0 -0.5 26 26
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.045 0.055 -10000 0 -0.4 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.008 0.13 -10000 0 -0.38 26 26
SP3 0.017 0.007 -10000 0 -10000 0 0
CREB1 0.014 0 -10000 0 -10000 0 0
FOXH1 -0.017 0.11 -10000 0 -0.58 15 15
SMAD3/SMAD4/GR -0.009 0.062 -10000 0 -0.36 2 2
GATA3 -0.13 0.24 -10000 0 -0.57 100 100
SKI/SIN3/HDAC complex/NCoR1 0.047 0.031 -10000 0 -10000 0 0
MEF2C/TIF2 -0.078 0.19 -10000 0 -0.52 40 40
endothelial cell migration 0.22 0.48 1.3 72 -10000 0 72
MAX 0.023 0.019 -10000 0 -10000 0 0
RBBP7 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.014 0.002 -10000 0 -10000 0 0
RUNX2 -0.006 0.1 -10000 0 -0.53 17 17
RUNX3 -0.035 0.16 -10000 0 -0.56 40 40
RUNX1 -0.055 0.18 -10000 0 -0.54 58 58
CTBP1 0.014 0 -10000 0 -10000 0 0
NR3C1 0.023 0.019 -10000 0 -10000 0 0
VDR -0.069 0.2 -10000 0 -0.54 69 69
CDKN1A -0.052 0.29 -10000 0 -1.2 22 22
KAT2B 0.013 0.024 -10000 0 -0.5 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.027 0.12 -10000 0 -0.38 25 25
DCP1A 0.014 0 -10000 0 -10000 0 0
SKI 0.014 0.002 -10000 0 -10000 0 0
SERPINE1 -0.22 0.49 -10000 0 -1.3 69 69
SMAD3/SMAD4/ATF2 -0.025 0.078 -10000 0 -0.4 11 11
SMAD3/SMAD4/ATF3 -0.051 0.12 -10000 0 -0.39 45 45
SAP30 0.013 0.029 -10000 0 -0.61 1 1
Cbp/p300/PIAS3 0.013 0.057 0.21 1 -0.36 4 5
JUN -0.023 0.16 -10000 0 -0.51 24 24
SMAD3/SMAD4/IRF7 -0.034 0.099 -10000 0 -0.42 18 18
TFE3 0.008 0.029 -10000 0 -10000 0 0
COL1A2 -0.043 0.16 -10000 0 -0.46 51 51
mesenchymal cell differentiation 0.03 0.09 0.4 17 -10000 0 17
DLX1 -0.16 0.26 -10000 0 -0.55 141 141
TCF3 0.012 0.041 -10000 0 -0.61 2 2
FOS -0.09 0.23 -10000 0 -0.56 87 87
SMAD3/SMAD4/Max -0.009 0.062 -10000 0 -0.36 2 2
Cbp/p300/SNIP1 0.006 0.04 -10000 0 -0.36 4 4
ZBTB17 0.019 0.019 -10000 0 -10000 0 0
LAMC1 0.001 0.11 -10000 0 -0.5 16 16
TGIF2/HDAC complex/SMAD3/SMAD4 -0.023 0.08 -10000 0 -0.45 9 9
IRF7 -0.012 0.12 -10000 0 -0.53 22 22
ESR1 -0.014 0.13 -10000 0 -0.55 24 24
HNF4A -0.033 0.14 -10000 0 -0.5 37 37
MEF2C -0.065 0.18 -10000 0 -0.53 30 30
SMAD2-3/SMAD4 -0.034 0.073 -10000 0 -0.37 6 6
Cbp/p300/Src-1 0.01 0.046 -10000 0 -0.36 4 4
IGHV3OR16-13 -0.015 0.033 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.005 0.074 -10000 0 -0.59 7 7
CREBBP 0.014 0.012 -10000 0 -10000 0 0
SKIL 0.005 0.076 -10000 0 -0.61 7 7
HDAC1 0.01 0.05 -10000 0 -0.61 3 3
HDAC2 0.014 0.002 -10000 0 -10000 0 0
SNIP1 0.014 0.005 -10000 0 -10000 0 0
GCN5L2 -0.001 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.011 0.083 -10000 0 -0.4 5 5
MSG1/HSC70 -0.03 0.12 -10000 0 -0.38 46 46
SMAD2 -0.003 0.047 -10000 0 -10000 0 0
SMAD3 -0.005 0.056 -10000 0 -0.26 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.075 -10000 0 -0.3 13 13
SMAD2/SMAD2/SMAD4 -0.003 0.033 -10000 0 -10000 0 0
NCOR1 0.013 0.029 -10000 0 -0.61 1 1
NCOA2 -0.025 0.15 -10000 0 -0.61 29 29
NCOA1 0.014 0 -10000 0 -10000 0 0
MYOD/E2A -0.14 0.19 -10000 0 -0.4 160 160
SMAD2-3/SMAD4/SP1/MIZ-1 0.006 0.11 -10000 0 -0.45 6 6
IFNB1 -0.008 0.1 -10000 0 -0.46 9 9
SMAD3/SMAD4/MEF2C -0.069 0.18 -10000 0 -0.52 31 31
CITED1 -0.039 0.16 -10000 0 -0.53 45 45
SMAD2-3/SMAD4/ARC105 -0.012 0.072 -10000 0 -0.35 4 4
RBL1 -0.008 0.11 -10000 0 -0.58 17 17
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.027 0.19 -10000 0 -0.54 51 51
RUNX1-3/PEBPB2 -0.068 0.15 -10000 0 -0.36 88 88
SMAD7 -0.009 0.14 -10000 0 -0.57 7 7
MYC/MIZ-1 -0.004 0.1 -10000 0 -0.4 24 24
SMAD3/SMAD4 -0.043 0.19 0.3 39 -0.42 60 99
IL10 -0.15 0.29 -10000 0 -0.61 108 108
PIASy/HDAC complex 0.016 0.013 -10000 0 -10000 0 0
PIAS3 0.014 0.007 -10000 0 -10000 0 0
CDK2 -0.001 0.092 -10000 0 -0.54 13 13
IL5 -0.085 0.19 -10000 0 -0.51 40 40
CDK4 0.001 0.086 -10000 0 -0.5 13 13
PIAS4 0.016 0.013 -10000 0 -10000 0 0
ATF3 -0.039 0.16 -10000 0 -0.53 46 46
SMAD3/SMAD4/SP1 -0.017 0.097 -10000 0 -0.42 7 7
FOXG1 -0.019 0.14 -10000 0 -0.6 26 26
FOXO3 0.017 0.032 -10000 0 -10000 0 0
FOXO1 0.014 0.047 -10000 0 -0.42 3 3
FOXO4 0.016 0.04 -10000 0 -0.52 1 1
heart looping -0.064 0.18 -10000 0 -0.52 30 30
CEBPB -0.008 0.11 -10000 0 -0.59 15 15
SMAD3/SMAD4/DLX1 -0.12 0.18 -10000 0 -0.39 119 119
MYOD1 -0.18 0.27 -10000 0 -0.56 158 158
SMAD3/SMAD4/HNF4 -0.045 0.1 -10000 0 -0.35 30 30
SMAD3/SMAD4/GATA3 -0.13 0.19 -10000 0 -0.46 82 82
SnoN/SIN3/HDAC complex/NCoR1 0.005 0.076 -10000 0 -0.61 7 7
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.065 0.15 -10000 0 -0.4 53 53
SMAD3/SMAD4/SP1-3 0.011 0.097 -10000 0 -0.46 4 4
MED15 0.014 0 -10000 0 -10000 0 0
SP1 0.005 0.04 -10000 0 -10000 0 0
SIN3B 0.014 0.002 -10000 0 -10000 0 0
SIN3A 0.014 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.074 0.17 -10000 0 -0.43 37 37
ITGB5 0.022 0.1 -10000 0 -0.68 4 4
TGIF/SIN3/HDAC complex/CtBP 0.045 0.042 -10000 0 -0.45 1 1
SMAD3/SMAD4/AR -0.09 0.16 -10000 0 -0.39 87 87
AR -0.1 0.24 -10000 0 -0.58 91 91
negative regulation of cell growth -0.007 0.12 -10000 0 -0.41 21 21
SMAD3/SMAD4/MYOD -0.14 0.18 -10000 0 -0.38 145 145
E2F5 0.01 0.05 -10000 0 -0.61 3 3
E2F4 0.014 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.008 0.1 -10000 0 -0.34 14 14
SMAD2-3/SMAD4/FOXO1-3a-4 -0.009 0.13 -10000 0 -0.37 40 40
TFDP1 0.013 0.029 -10000 0 -0.61 1 1
SMAD3/SMAD4/AP1 -0.028 0.16 -10000 0 -0.52 24 24
SMAD3/SMAD4/RUNX2 -0.03 0.09 -10000 0 -0.4 17 17
TGIF2 0.005 0.074 -10000 0 -0.59 7 7
TGIF1 -0.007 0.11 -10000 0 -0.54 18 18
ATF2 0.002 0.086 -10000 0 -0.61 9 9
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.002 0.092 -9999 0 -0.32 34 34
EPHB2 0.001 0.083 -9999 0 -0.53 11 11
Syndecan-2/TACI -0.008 0.082 -9999 0 -0.33 26 26
LAMA1 -0.058 0.2 -9999 0 -0.58 56 56
Syndecan-2/alpha2 ITGB1 -0.027 0.15 -9999 0 -0.4 48 48
HRAS 0.014 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.013 0.067 -9999 0 -0.34 18 18
ITGA5 -0.013 0.12 -9999 0 -0.51 24 24
BAX 0.024 0.081 -9999 0 -10000 0 0
EPB41 0.011 0.047 -9999 0 -0.57 3 3
positive regulation of cell-cell adhesion -0.012 0.059 -9999 0 -0.3 18 18
LAMA3 -0.041 0.17 -9999 0 -0.56 45 45
EZR 0.005 0.076 -9999 0 -0.61 7 7
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.014 0.12 -9999 0 -0.5 25 25
Syndecan-2/MMP2 -0.004 0.1 -9999 0 -0.34 40 40
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.036 0.12 -9999 0 -0.39 43 43
dendrite morphogenesis 0.005 0.09 -9999 0 -0.35 27 27
Syndecan-2/GM-CSF -0.012 0.067 -9999 0 -0.34 18 18
determination of left/right symmetry 0.006 0.082 -9999 0 -0.4 18 18
Syndecan-2/PKC delta -0.005 0.12 -9999 0 -0.41 34 34
GNB2L1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.014 0.064 -9999 0 -0.33 11 11
MAPK1 0.014 0.064 -9999 0 -0.3 18 18
Syndecan-2/RACK1 -0.01 0.054 -9999 0 -0.31 11 11
NF1 0.012 0.041 -9999 0 -0.61 2 2
FGFR/FGF/Syndecan-2 0.006 0.082 -9999 0 -0.4 18 18
ITGA2 -0.036 0.16 -9999 0 -0.55 41 41
MAPK8 0.015 0.09 -9999 0 -0.34 28 28
Syndecan-2/alpha2/beta1 Integrin -0.037 0.17 -9999 0 -0.38 67 67
Syndecan-2/Kininogen -0.019 0.091 -9999 0 -0.31 40 40
ITGB1 0.012 0.033 -9999 0 -0.5 2 2
SRC 0.029 0.058 -9999 0 -0.28 11 11
Syndecan-2/CASK/Protein 4.1 -0.013 0.07 -9999 0 -0.34 19 19
extracellular matrix organization 0.006 0.089 -9999 0 -0.36 25 25
actin cytoskeleton reorganization 0.002 0.091 -9999 0 -0.32 34 34
Syndecan-2/Caveolin-2/Ras 0.006 0.093 -9999 0 -0.29 41 41
Syndecan-2/Laminin alpha3 -0.021 0.13 -9999 0 -0.36 58 58
Syndecan-2/RasGAP -0.01 0.05 -9999 0 -0.29 11 11
alpha5/beta1 Integrin -0.02 0.085 -9999 0 -0.37 25 25
PRKCD -0.015 0.13 -9999 0 -0.61 22 22
Syndecan-2 dimer 0.005 0.09 -9999 0 -0.35 27 27
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.037 0.057 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
SDCBP 0.014 0 -9999 0 -10000 0 0
TNFRSF13B -0.004 0.069 -9999 0 -0.5 9 9
RASA1 0.014 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.036 0.12 -9999 0 -0.39 43 43
Syndecan-2/Synbindin 0.013 0.07 -9999 0 -0.33 18 18
TGFB1 0.004 0.081 -9999 0 -0.61 8 8
CASP3 0.006 0.11 -9999 0 -0.4 27 27
FN1 -0.004 0.096 -9999 0 -0.5 17 17
Syndecan-2/IL8 -0.099 0.18 -9999 0 -0.33 162 162
SDC2 0.006 0.083 -9999 0 -0.4 18 18
KNG1 -0.019 0.11 -9999 0 -0.5 22 22
Syndecan-2/Neurofibromin 0.012 0.077 -9999 0 -0.35 19 19
TRAPPC4 0.014 0 -9999 0 -10000 0 0
CSF2 0.001 0.003 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.006 0.089 -9999 0 -0.36 25 25
Syndecan-2/Syntenin/PI-4-5-P2 -0.011 0.059 -9999 0 -0.3 18 18
Syndecan-2/Ezrin 0.017 0.088 -9999 0 -0.42 14 14
PRKACA 0.022 0.071 -9999 0 -0.34 13 13
angiogenesis -0.099 0.18 -9999 0 -0.33 162 162
MMP2 -0.013 0.12 -9999 0 -0.54 23 23
IL8 -0.17 0.26 -9999 0 -0.54 151 151
calcineurin-NFAT signaling pathway -0.008 0.082 -9999 0 -0.33 26 26
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.057 0.11 0.51 10 -10000 0 10
GNAI2 0.014 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.091 0.15 -10000 0 -0.34 123 123
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.006 0.07 -10000 0 -0.61 6 6
RhoA/GTP -0.058 0.11 -10000 0 -0.52 10 10
negative regulation of cAMP metabolic process -0.038 0.14 -10000 0 -0.29 73 73
GNAZ 0.013 0.029 -10000 0 -0.61 1 1
GNAI3 0.014 0 -10000 0 -10000 0 0
GNA12 0.013 0.029 -10000 0 -0.61 1 1
S1PR5 -0.14 0.26 -10000 0 -0.56 123 123
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.038 0.14 -10000 0 -0.3 73 73
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.008 0.12 -10000 0 -0.61 17 17
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0.029 -9999 0 -0.61 1 1
ELF1 -0.017 0.095 -9999 0 -0.37 12 12
CCNA2 -0.058 0.19 -9999 0 -0.54 61 61
PIK3CA 0.015 0.001 -9999 0 -10000 0 0
JAK3 -0.059 0.19 -9999 0 -0.54 62 62
PIK3R1 0.015 0.001 -9999 0 -10000 0 0
JAK1 0.015 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.03 0.16 -9999 0 -0.44 27 27
SHC1 0.01 0.053 -9999 0 -0.5 5 5
SP1 0.016 0.046 -9999 0 -0.35 4 4
IL2RA -0.046 0.19 -9999 0 -0.49 66 66
IL2RB -0.098 0.22 -9999 0 -0.54 94 94
SOS1 0.015 0.001 -9999 0 -10000 0 0
IL2RG -0.042 0.17 -9999 0 -0.53 49 49
G1/S transition of mitotic cell cycle -0.038 0.19 -9999 0 -0.52 42 42
PTPN11 0.015 0.001 -9999 0 -10000 0 0
CCND2 0.019 0.099 -9999 0 -0.56 12 12
LCK -0.088 0.22 -9999 0 -0.54 85 85
GRB2 0.014 0.024 -9999 0 -0.49 1 1
IL2 0.001 0.003 -9999 0 -10000 0 0
CDK6 -0.035 0.16 -9999 0 -0.54 41 41
CCND3 -0.016 0.14 -9999 0 -0.49 5 5
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.062 0.15 0.4 72 -10000 0 72
KIRREL -0.033 0.16 -10000 0 -0.61 33 33
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.063 0.15 -10000 0 -0.4 72 72
PLCG1 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
WASL 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.045 0.11 -10000 0 -0.34 34 34
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.003 0.094 -10000 0 -0.46 4 4
FYN -0.023 0.11 -10000 0 -0.33 34 34
mol:Ca2+ -0.045 0.11 -10000 0 -0.34 34 34
mol:DAG -0.045 0.11 -10000 0 -0.34 34 34
NPHS2 -0.006 0.041 -10000 0 -0.55 2 2
mol:IP3 -0.045 0.11 -10000 0 -0.34 34 34
regulation of endocytosis -0.017 0.1 -10000 0 -0.37 8 8
Nephrin/NEPH1/podocin/Cholesterol -0.047 0.11 -10000 0 -0.35 34 34
establishment of cell polarity -0.062 0.15 -10000 0 -0.4 72 72
Nephrin/NEPH1/podocin/NCK1-2 -0.041 0.099 -10000 0 -0.55 4 4
Nephrin/NEPH1/beta Arrestin2 -0.013 0.1 -10000 0 -0.38 8 8
NPHS1 -0.038 0.15 -10000 0 -0.5 42 42
Nephrin/NEPH1/podocin -0.027 0.11 -10000 0 -0.33 34 34
TJP1 0.014 0 -10000 0 -10000 0 0
NCK1 0.013 0.029 -10000 0 -0.61 1 1
NCK2 0.014 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.045 0.11 -10000 0 -0.34 34 34
CD2AP 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.046 0.11 -10000 0 -0.34 34 34
GRB2 0.013 0.024 -10000 0 -0.5 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.041 0.13 -10000 0 -0.34 47 47
cytoskeleton organization -0.003 0.11 -10000 0 -0.46 6 6
Nephrin/NEPH1 -0.044 0.11 -10000 0 -0.28 72 72
Nephrin/NEPH1/ZO-1 -0.048 0.12 -10000 0 -0.37 33 33
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.079 0.15 -9999 0 -0.38 77 77
MAP4K1 -0.021 0.14 -9999 0 -0.59 27 27
MAP3K8 -0.006 0.1 -9999 0 -0.51 18 18
PRKCB -0.065 0.19 -9999 0 -0.53 67 67
DBNL 0.014 0 -9999 0 -10000 0 0
CRKL 0.014 0 -9999 0 -10000 0 0
MAP3K1 -0.007 0.11 -9999 0 -0.45 7 7
JUN -0.029 0.16 -9999 0 -0.58 31 31
MAP3K7 -0.004 0.11 -9999 0 -0.45 7 7
GRAP2 -0.051 0.18 -9999 0 -0.54 54 54
CRK 0.014 0 -9999 0 -10000 0 0
MAP2K4 0 0.11 -9999 0 -0.42 10 10
LAT -0.022 0.14 -9999 0 -0.6 27 27
LCP2 -0.004 0.094 -9999 0 -0.5 16 16
MAPK8 -0.033 0.17 -9999 0 -0.61 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.014 0.12 -9999 0 -0.48 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.073 0.14 -9999 0 -0.55 16 16
Cellular roles of Anthrax toxin

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
ANTXR1 0.008 0.064 -10000 0 -0.61 5 5
ANTXR2 0.001 0.084 -10000 0 -0.51 12 12
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.067 17 17
monocyte activation -0.16 0.26 -10000 0 -0.52 132 132
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.003 0.018 -10000 0 -0.33 1 1
MAP2K7 -0.002 0.01 -10000 0 -10000 0 0
MAP2K6 -0.003 0.018 -10000 0 -0.33 1 1
CYAA 0.006 0.056 -10000 0 -0.28 17 17
MAP2K4 -0.003 0.023 -10000 0 -0.33 2 2
IL1B -0.085 0.14 -10000 0 -0.28 157 157
Channel -0.011 0.056 -10000 0 -0.3 17 17
NLRP1 -0.003 0.024 -10000 0 -0.33 2 2
CALM1 0.012 0.037 -10000 0 -0.55 2 2
negative regulation of phagocytosis -0.004 0.03 -10000 0 -0.55 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.067 17 -10000 0 17
MAPK3 -0.002 0.01 -10000 0 -10000 0 0
MAPK1 -0.002 0.01 -10000 0 -10000 0 0
PGR -0.032 0.096 -10000 0 -0.34 42 42
PA/Cellular Receptors -0.012 0.062 -10000 0 -0.33 17 17
apoptosis -0.002 0.013 -10000 0 -0.067 17 17
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.007 0.055 -10000 0 -0.27 17 17
macrophage activation 0.019 0.012 -10000 0 -10000 0 0
TNF -0.16 0.26 -10000 0 -0.55 142 142
VCAM1 -0.16 0.26 -10000 0 -0.53 132 132
platelet activation -0.004 0.03 -10000 0 -0.55 1 1
MAPKKK cascade -0.015 0.018 0.18 2 -10000 0 2
IL18 -0.009 0.089 -10000 0 -0.3 36 36
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.067 17 17
LEF -0.002 0.013 -10000 0 -0.067 17 17
CASP1 -0.005 0.024 -10000 0 -0.28 2 2
mol:cAMP -0.004 0.03 -10000 0 -0.55 1 1
necrosis -0.002 0.013 -10000 0 -0.067 17 17
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.007 0.056 -10000 0 -0.28 17 17
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.043 0.15 -10000 0 -0.73 15 15
HDAC1 0.009 0.05 -10000 0 -0.6 3 3
AES 0.014 0.004 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
DTX1 0.002 0.084 -10000 0 -0.6 9 9
LRP6/FZD1 -0.004 0.039 -10000 0 -0.35 6 6
TLE1 0.013 0.029 -10000 0 -0.61 1 1
AP1 -0.026 0.12 -10000 0 -0.29 61 61
NCSTN 0.014 0 -10000 0 -10000 0 0
ADAM10 0.002 0.086 -10000 0 -0.61 9 9
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.027 0.073 -10000 0 -10000 0 0
NICD/RBPSUH -0.019 0.11 -10000 0 -0.6 15 15
WIF1 -0.28 0.28 -10000 0 -0.55 244 244
NOTCH1 -0.021 0.11 -10000 0 -0.64 15 15
PSENEN 0.014 0 -10000 0 -10000 0 0
KREMEN2 -0.053 0.18 -10000 0 -0.54 56 56
DKK1 -0.12 0.24 -10000 0 -0.54 109 109
beta catenin/beta TrCP1 0.015 0.043 0.33 2 -10000 0 2
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
AXIN1 0 0.043 0.23 3 -0.23 5 8
CtBP/CBP/TCF1/TLE1/AES 0.032 0.05 0.29 4 -10000 0 4
PSEN1 0.014 0 -10000 0 -10000 0 0
FOS -0.093 0.22 -10000 0 -0.56 87 87
JUN 0.003 0.076 -10000 0 -0.51 10 10
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
CTNNB1 0.008 0.046 0.31 3 -10000 0 3
MAPK3 0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.18 -10000 0 -0.36 143 143
HNF1A 0.013 0.029 -10000 0 -0.61 1 1
CTBP1 0.014 0.004 -10000 0 -10000 0 0
MYC -0.045 0.3 -10000 0 -1.4 22 22
NKD1 0.001 0.087 -10000 0 -0.56 11 11
FZD1 0.009 0.053 -10000 0 -0.5 5 5
NOTCH1 precursor/Deltex homolog 1 -0.024 0.12 -10000 0 -0.62 15 15
apoptosis -0.026 0.12 -10000 0 -0.29 61 61
Delta 1/NOTCHprecursor -0.042 0.15 -10000 0 -0.72 15 15
DLL1 -0.035 0.17 -10000 0 -0.61 37 37
PPARD 0.02 0.027 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.002 0.062 0.23 3 -0.35 6 9
DVL1 -0.021 0.025 -10000 0 -10000 0 0
CSNK2A1 0.014 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.42 74 74
LRP6 0.013 0.024 -10000 0 -0.5 1 1
CSNK1A1 0.014 0.004 -10000 0 -10000 0 0
NLK 0.017 0.016 -10000 0 -10000 0 0
CCND1 -0.024 0.23 -10000 0 -1.4 11 11
WNT1 -0.023 0.13 -10000 0 -0.5 31 31
Axin1/APC/beta catenin 0.017 0.061 0.33 3 -0.41 2 5
DKK2 -0.11 0.23 -10000 0 -0.55 103 103
NOTCH1 precursor/DVL1 -0.019 0.1 -10000 0 -0.57 15 15
GSK3B 0.014 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.047 -10000 0 -0.57 3 3
NOTCH/Deltex homolog 1 -0.025 0.12 -10000 0 -0.63 15 15
PPP2R5D -0.006 0.043 0.26 11 -10000 0 11
MAPK1 0.014 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.17 0.17 -10000 0 -0.38 126 126
RBPJ 0.013 0.024 -10000 0 -0.5 1 1
CREBBP 0.017 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.009 0.057 -10000 0 -0.61 4 4
HDAC4 0.014 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.028 0.039 0.35 3 -10000 0 3
CDKN1A -0.057 0.18 -10000 0 -0.49 57 57
KAT2B 0.013 0.024 -10000 0 -0.5 1 1
BAX 0.014 0 -10000 0 -10000 0 0
FOXO3 0.004 0.043 0.46 4 -10000 0 4
FOXO1 0.011 0.047 -10000 0 -0.57 3 3
FOXO4 0.022 0.033 -10000 0 -0.3 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
TAT -0.082 0.21 -10000 0 -0.54 80 80
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.12 0.2 -10000 0 -0.4 158 158
PPARGC1A -0.012 0.12 -10000 0 -0.59 20 20
FHL2 -0.031 0.15 -10000 0 -0.53 38 38
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.013 0.037 -10000 0 -10000 0 0
HIST2H4A 0.028 0.039 -10000 0 -0.35 3 3
SIRT1/FOXO3a 0.014 0.041 0.3 4 -10000 0 4
SIRT1 0.017 0.047 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.012 0.039 -10000 0 -0.28 1 1
SIRT1/Histone H1b 0.002 0.066 -10000 0 -0.26 13 13
apoptosis -0.013 0.036 -10000 0 -10000 0 0
SIRT1/PGC1A -0.004 0.083 -10000 0 -0.36 20 20
p53/SIRT1 0.025 0.13 0.4 19 -0.44 12 31
SIRT1/FOXO4 0.012 0.048 -10000 0 -0.25 4 4
FOXO1/FHL2/SIRT1 -0.014 0.09 -10000 0 -0.29 36 36
HIST1H1E 0.008 0.067 -10000 0 -0.31 14 14
SIRT1/p300 0.009 0.056 -10000 0 -0.44 4 4
muscle cell differentiation 0.1 0.17 0.33 157 -10000 0 157
TP53 -0.001 0.11 -10000 0 -0.58 14 14
KU70/SIRT1/BAX 0.013 0.036 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
MEF2D 0.013 0.024 -10000 0 -0.5 1 1
HIV-1 Tat/SIRT1 -0.056 0.15 -10000 0 -0.38 79 79
ACSS2 0.03 0.025 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.1 0.17 -10000 0 -0.33 157 157
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.004 0.081 -10000 0 -0.61 8 8
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.001 0.099 0.45 5 -10000 0 5
IL27/IL27R/JAK1 -0.033 0.15 -10000 0 -0.57 6 6
TBX21 -0.057 0.22 -10000 0 -0.56 39 39
IL12B 0 0.047 -10000 0 -0.5 4 4
IL12A -0.01 0.098 -10000 0 -0.44 23 23
IL6ST -0.023 0.15 -10000 0 -0.61 28 28
IL27RA/JAK1 0.019 0.037 -10000 0 -10000 0 0
IL27 -0.017 0.11 -10000 0 -0.49 25 25
TYK2 0.015 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.06 0.12 -10000 0 -0.73 2 2
T-helper 2 cell differentiation 0.001 0.099 0.45 5 -10000 0 5
T cell proliferation during immune response 0.001 0.099 0.45 5 -10000 0 5
MAPKKK cascade -0.001 0.099 -10000 0 -0.45 5 5
STAT3 0.014 0 -10000 0 -10000 0 0
STAT2 0.01 0.047 -10000 0 -0.5 4 4
STAT1 -0.003 0.091 -10000 0 -0.5 15 15
IL12RB1 -0.031 0.16 -10000 0 -0.56 36 36
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.087 0.24 -10000 0 -0.54 55 55
IL27/IL27R/JAK2/TYK2 -0.001 0.1 -10000 0 -0.45 5 5
positive regulation of T cell mediated cytotoxicity -0.001 0.099 -10000 0 -0.45 5 5
STAT1 (dimer) -0.062 0.24 0.52 24 -0.66 16 40
JAK2 0.015 0.004 -10000 0 -10000 0 0
JAK1 0.014 0.004 -10000 0 -10000 0 0
STAT2 (dimer) 0.005 0.099 -10000 0 -0.42 5 5
T cell proliferation -0.071 0.16 -10000 0 -0.5 16 16
IL12/IL12R/TYK2/JAK2 -0.003 0.091 -10000 0 -0.57 4 4
IL17A -0.06 0.12 -10000 0 -0.73 2 2
mast cell activation 0.001 0.099 0.45 5 -10000 0 5
IFNG 0.002 0.02 -10000 0 -0.092 3 3
T cell differentiation -0.004 0.005 -10000 0 -0.022 3 3
STAT3 (dimer) 0.007 0.094 -10000 0 -0.42 5 5
STAT5A (dimer) -0.001 0.11 -10000 0 -0.48 10 10
STAT4 (dimer) -0.085 0.17 -10000 0 -0.48 21 21
STAT4 -0.16 0.26 -10000 0 -0.54 148 148
T cell activation -0.009 0.007 0.062 3 -10000 0 3
IL27R/JAK2/TYK2 -0.009 0.086 -10000 0 -10000 0 0
GATA3 -0.15 0.4 -10000 0 -1.4 43 43
IL18 -0.02 0.11 -10000 0 -0.41 36 36
positive regulation of mast cell cytokine production 0.007 0.093 -10000 0 -0.42 5 5
IL27/EBI3 -0.02 0.12 -10000 0 -0.4 41 41
IL27RA 0.014 0.036 -10000 0 -10000 0 0
IL6 -0.14 0.25 -10000 0 -0.54 128 128
STAT5A 0 0.093 -10000 0 -0.6 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.001 0.021 -10000 0 -10000 0 0
IL1B -0.13 0.2 -10000 0 -0.4 157 157
EBI3 -0.012 0.12 -10000 0 -0.58 19 19
TNF -0.11 0.19 -10000 0 -0.4 142 142
Signaling events mediated by PTP1B

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
PDGFRB 0.011 0.041 -10000 0 -0.5 3 3
Jak2/Leptin Receptor -0.01 0.11 0.2 18 -0.45 12 30
PTP1B/AKT1 -0.006 0.088 -10000 0 -0.35 9 9
FYN 0.014 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.015 0.097 -10000 0 -0.3 24 24
EGFR -0.084 0.22 -10000 0 -0.56 79 79
EGF/EGFR -0.095 0.16 -10000 0 -0.4 82 82
CSF1 -0.007 0.11 -10000 0 -0.61 16 16
AKT1 0.014 0.002 -10000 0 -10000 0 0
INSR 0.014 0.002 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.007 0.095 -10000 0 -0.35 13 13
Insulin Receptor/Insulin -0.026 0.061 -10000 0 -0.32 8 8
HCK -0.01 0.11 -10000 0 -0.55 20 20
CRK 0.014 0 -10000 0 -10000 0 0
TYK2 -0.006 0.093 -10000 0 -0.34 11 11
EGF -0.048 0.18 -10000 0 -0.57 49 49
YES1 0.01 0.05 -10000 0 -0.61 3 3
CAV1 -0.029 0.12 -10000 0 -0.35 32 32
TXN 0.012 0.025 -10000 0 -0.5 1 1
PTP1B/IRS1/GRB2 -0.003 0.089 -10000 0 -0.34 10 10
cell migration 0.015 0.097 0.3 24 -10000 0 24
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.021 0.14 -10000 0 -0.56 30 30
ITGA2B -0.047 0.18 -10000 0 -0.58 47 47
CSF1R -0.022 0.14 -10000 0 -0.58 28 28
Prolactin Receptor/Prolactin -0.019 0.11 -10000 0 -0.41 32 32
FGR 0.011 0.041 -10000 0 -0.5 3 3
PTP1B/p130 Cas -0.007 0.093 -10000 0 -0.33 14 14
Crk/p130 Cas -0.003 0.088 -10000 0 -0.35 9 9
DOK1 0.003 0.089 -10000 0 -0.34 10 10
JAK2 0.001 0.089 -10000 0 -0.35 13 13
Jak2/Leptin Receptor/Leptin -0.12 0.19 -10000 0 -0.43 105 105
PIK3R1 0.014 0 -10000 0 -10000 0 0
PTPN1 -0.015 0.098 -10000 0 -0.3 24 24
LYN 0.003 0.078 -10000 0 -0.52 10 10
CDH2 0.013 0.029 -10000 0 -0.61 1 1
SRC 0.012 0.039 -10000 0 -10000 0 0
ITGB3 -0.056 0.18 -10000 0 -0.52 60 60
CAT1/PTP1B -0.064 0.15 -10000 0 -0.4 47 47
CAPN1 0.014 0.029 -10000 0 -0.61 1 1
CSK 0.014 0 -10000 0 -10000 0 0
PI3K -0.019 0.053 -10000 0 -0.36 2 2
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.12 0.19 -10000 0 -0.44 104 104
negative regulation of transcription 0.001 0.088 -10000 0 -0.35 13 13
FCGR2A -0.032 0.16 -10000 0 -0.55 38 38
FER -0.011 0.12 -10000 0 -0.62 18 18
alphaIIb/beta3 Integrin -0.086 0.18 -10000 0 -0.42 98 98
BLK -0.11 0.22 -10000 0 -0.52 104 104
Insulin Receptor/Insulin/Shc -0.005 0.045 -10000 0 -0.32 8 8
RHOA 0.015 0.002 -10000 0 -10000 0 0
LEPR -0.001 0.096 -10000 0 -0.54 14 14
BCAR1 0.013 0.029 -10000 0 -0.61 1 1
p210 bcr-abl/Grb2 0.013 0.024 -10000 0 -0.49 1 1
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.075 0.16 -10000 0 -0.44 49 49
PRL 0.002 0.033 -10000 0 -0.49 2 2
SOCS3 -0.16 0.36 -10000 0 -1.4 32 32
SPRY2 0.005 0.069 -10000 0 -0.51 8 8
Insulin Receptor/Insulin/IRS1 -0.002 0.037 -10000 0 -0.35 5 5
CSF1/CSF1R -0.031 0.14 -10000 0 -0.46 30 30
Ras protein signal transduction 0.02 0.036 -10000 0 -0.4 1 1
IRS1 0.013 0.029 -10000 0 -0.61 1 1
INS -0.004 0.054 -10000 0 -0.58 4 4
LEP -0.002 0.057 -10000 0 -0.5 6 6
STAT5B -0.003 0.088 -10000 0 -0.3 15 15
STAT5A -0.007 0.093 -10000 0 -0.31 17 17
GRB2 0.013 0.024 -10000 0 -0.5 1 1
PDGFB-D/PDGFRB -0.008 0.097 -10000 0 -0.35 15 15
CSN2 -0.001 0.043 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
LAT -0.041 0.16 -10000 0 -0.49 44 44
YBX1 0.02 0.041 -10000 0 -0.59 2 2
LCK -0.089 0.22 -10000 0 -0.55 85 85
SHC1 0.009 0.053 -10000 0 -0.5 5 5
NOX4 -0.072 0.2 -10000 0 -0.53 73 73
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.042 0.16 -10000 0 -0.56 4 4
UGCG -0.02 0.13 -10000 0 -0.65 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT -0.04 0.16 -10000 0 -0.41 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.019 0.12 -10000 0 -0.62 17 17
mol:DAG -0.004 0.045 -10000 0 -0.98 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.073 0.13 -10000 0 -0.46 26 26
FRAP1 -0.031 0.18 -10000 0 -0.5 31 31
FOXO3 -0.023 0.17 -10000 0 -0.45 34 34
AKT1 -0.035 0.18 -10000 0 -0.47 42 42
GAB2 0.013 0.029 -10000 0 -0.61 1 1
SMPD1 0.003 0.037 -10000 0 -10000 0 0
SGMS1 0.002 0.048 -10000 0 -0.67 1 1
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 0.023 0.007 -10000 0 -10000 0 0
CALM1 0.012 0.037 -10000 0 -0.55 2 2
cell proliferation -0.015 0.11 -10000 0 -0.3 29 29
EIF3A 0.014 0 -10000 0 -10000 0 0
PI3K 0.024 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.003 0.063 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.045 -10000 0 -0.98 1 1
natural killer cell activation 0 0.002 -10000 0 -0.012 10 10
JAK3 -0.057 0.19 -10000 0 -0.53 62 62
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.017 0.003 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
MYC -0.045 0.25 -10000 0 -0.91 26 26
MYB -0.087 0.34 -10000 0 -0.98 48 48
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.042 0.17 -10000 0 -0.4 57 57
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.014 0.06 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.04 0.17 -10000 0 -0.4 57 57
Rac1/GDP 0.029 0.008 -10000 0 -10000 0 0
T cell proliferation -0.042 0.18 -10000 0 -0.49 37 37
SHC1 0.009 0.053 -10000 0 -0.5 5 5
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.02 -10000 0 -0.05 62 62
PRKCZ -0.045 0.19 -10000 0 -0.51 38 38
NF kappa B1 p50/RelA -0.067 0.13 -10000 0 -0.46 23 23
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.056 0.18 -10000 0 -0.44 57 57
HSP90AA1 0.014 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
IL2RA -0.064 0.18 -10000 0 -0.51 65 65
IL2RB -0.096 0.22 -10000 0 -0.54 94 94
TERT -0.082 0.21 -10000 0 -0.57 72 72
E2F1 -0.029 0.15 -10000 0 -0.42 50 50
SOS1 0.014 0.004 -10000 0 -10000 0 0
RPS6 0.013 0.024 -10000 0 -0.5 1 1
mol:cAMP 0 0.01 0.024 62 -10000 0 62
PTPN11 0.014 0.004 -10000 0 -10000 0 0
IL2RG -0.041 0.17 -10000 0 -0.53 49 49
actin cytoskeleton organization -0.042 0.18 -10000 0 -0.49 37 37
GRB2 0.013 0.024 -10000 0 -0.49 1 1
IL2 0.003 0.004 -10000 0 -10000 0 0
PIK3CA 0.016 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.033 0.016 -10000 0 -10000 0 0
LCK -0.086 0.22 -10000 0 -0.54 85 85
BCL2 -0.018 0.18 -10000 0 -0.71 13 13
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.014 0 -9999 0 -10000 0 0
VLDLR -0.003 0.1 -9999 0 -0.57 14 14
LRPAP1 0.014 0 -9999 0 -10000 0 0
NUDC 0.014 0 -9999 0 -10000 0 0
RELN/LRP8 -0.088 0.15 -9999 0 -0.37 69 69
CaM/Ca2+ -0.002 0.027 -9999 0 -0.4 2 2
KATNA1 0.014 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.05 0.15 -9999 0 -0.33 69 69
IQGAP1/CaM -0.007 0.05 -9999 0 -0.38 8 8
DAB1 -0.087 0.22 -9999 0 -0.58 79 79
IQGAP1 0.007 0.062 -9999 0 -0.53 6 6
PLA2G7 -0.044 0.18 -9999 0 -0.57 46 46
CALM1 0.012 0.037 -9999 0 -0.55 2 2
DYNLT1 0.012 0.041 -9999 0 -0.61 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.02 -9999 0 -0.44 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0.029 -9999 0 -0.61 1 1
CDK5R1 -0.019 0.14 -9999 0 -0.6 25 25
LIS1/Poliovirus Protein 3A 0.019 0 -9999 0 -10000 0 0
CDK5R2 -0.11 0.24 -9999 0 -0.58 94 94
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.21 -9999 0 -0.44 127 127
YWHAE 0.014 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.068 0.2 -9999 0 -0.56 38 38
MAP1B -0.001 0.017 -9999 0 -0.32 1 1
RAC1 -0.002 0.015 -9999 0 -10000 0 0
p35/CDK5 -0.045 0.16 -9999 0 -0.59 13 13
RELN -0.14 0.25 -9999 0 -0.56 122 122
PAFAH/LIS1 -0.007 0.11 -9999 0 -0.34 46 46
LIS1/CLIP170 0.029 0.018 -9999 0 -0.37 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.08 0.13 -9999 0 -0.45 35 35
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.081 0.2 -9999 0 -0.68 27 27
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.082 0.21 -9999 0 -0.61 38 38
LIS1/IQGAP1 0.025 0.039 -9999 0 -0.31 6 6
RHOA -0.002 0.015 -9999 0 -10000 0 0
PAFAH1B1 0.025 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0 -9999 0 -10000 0 0
PAFAH1B2 -0.003 0.1 -9999 0 -0.61 13 13
MAP1B/LIS1/Dynein heavy chain 0.027 0.012 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.1 0.16 -9999 0 -0.54 38 38
LRP8 0.013 0.029 -9999 0 -0.61 1 1
NDEL1/Katanin 60 -0.068 0.2 -9999 0 -0.56 38 38
P39/CDK5 -0.09 0.19 -9999 0 -0.55 36 36
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.029 0 -9999 0 -10000 0 0
CDK5 -0.037 0.14 -9999 0 -0.61 1 1
PPP2R5D 0.014 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.001 0.015 -9999 0 -0.32 1 1
CSNK2A1 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.1 0.19 -9999 0 -0.57 30 30
RELN/VLDLR -0.087 0.14 -9999 0 -0.34 79 79
CDC42 -0.002 0.015 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.066 0.2 -9999 0 -0.56 64 64
GNB1/GNG2 -0.018 0.13 -9999 0 -0.43 21 21
mol:DAG -0.007 0.12 -9999 0 -0.44 12 12
PLCG1 -0.008 0.13 -9999 0 -0.46 12 12
YES1 -0.025 0.14 -9999 0 -0.45 23 23
FZD3 0.01 0.05 -9999 0 -0.61 3 3
FZD6 -0.013 0.12 -9999 0 -0.5 25 25
G protein -0.008 0.13 -9999 0 -0.46 12 12
MAP3K7 -0.1 0.16 -9999 0 -0.42 44 44
mol:Ca2+ -0.007 0.12 -9999 0 -0.43 12 12
mol:IP3 -0.007 0.12 -9999 0 -0.44 12 12
NLK -0.006 0.012 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.18 -9999 0 -0.46 47 47
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.034 0.14 -9999 0 -0.43 24 24
CSNK1A1 0.014 0 -9999 0 -10000 0 0
GNAS -0.023 0.13 -9999 0 -0.42 21 21
GO:0007205 -0.007 0.12 -9999 0 -0.44 11 11
WNT6 -0.036 0.16 -9999 0 -0.54 42 42
WNT4 -0.035 0.16 -9999 0 -0.53 42 42
NFAT1/CK1 alpha -0.082 0.14 -9999 0 -0.46 35 35
GNG2 0.009 0.057 -9999 0 -0.61 4 4
WNT5A -0.018 0.13 -9999 0 -0.58 25 25
WNT11 -0.017 0.13 -9999 0 -0.56 25 25
CDC42 -0.016 0.13 -9999 0 -0.42 23 23
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.021 0.089 -9999 0 -0.38 26 26
alphaV beta3 Integrin -0.042 0.11 -9999 0 -0.38 18 18
PTK2 -0.014 0.15 -9999 0 -0.47 23 23
IGF1R 0.013 0.024 -9999 0 -0.5 1 1
PI4KB 0.014 0 -9999 0 -10000 0 0
MFGE8 0.01 0.05 -9999 0 -0.61 3 3
SRC 0.014 0 -9999 0 -10000 0 0
CDKN1B -0.031 0.093 -9999 0 -0.5 14 14
VEGFA -0.009 0.11 -9999 0 -0.5 21 21
ILK -0.031 0.093 -9999 0 -0.5 14 14
ROCK1 0.014 0 -9999 0 -10000 0 0
AKT1 0.006 0.096 -9999 0 -0.46 14 14
PTK2B -0.023 0.14 -9999 0 -0.41 34 34
alphaV/beta3 Integrin/JAM-A -0.017 0.13 -9999 0 -0.53 8 8
CBL 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.041 0.11 -9999 0 -0.31 61 61
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.013 0.061 -9999 0 -0.33 13 13
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.009 0.089 -9999 0 -0.38 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.065 0.15 -9999 0 -0.36 84 84
PI4KA 0.006 0.066 -9999 0 -0.5 8 8
IGF-1R heterotetramer/IGF1/IRS1 -0.048 0.12 -9999 0 -0.48 16 16
PI4 Kinase -0.006 0.045 -9999 0 -0.35 8 8
PIK3CA 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.095 0.17 -9999 0 -0.38 117 117
RPS6KB1 0.007 0.13 -9999 0 -0.45 16 16
TLN1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.001 0.13 -9999 0 -0.45 21 21
GPR124 0.01 0.047 -9999 0 -0.5 4 4
MAPK1 0.001 0.13 -9999 0 -0.45 21 21
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.086 0.16 -9999 0 -0.35 114 114
cell adhesion -0.035 0.09 -9999 0 -0.35 16 16
ANGPTL3 0.006 0.007 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.017 0.074 -9999 0 -0.31 26 26
IGF-1R heterotetramer 0.013 0.024 -9999 0 -0.49 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.009 0.053 -9999 0 -0.5 5 5
ITGB3 -0.055 0.18 -9999 0 -0.52 60 60
IGF1 -0.008 0.11 -9999 0 -0.57 18 18
RAC1 0.014 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.042 0.11 -9999 0 -0.31 63 63
apoptosis 0.013 0.029 -9999 0 -0.6 1 1
CD47 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.04 0.1 -9999 0 -0.37 16 16
VCL 0.006 0.068 -9999 0 -0.54 7 7
alphaV/beta3 Integrin/Del1 -0.084 0.17 -9999 0 -0.37 105 105
CSF1 -0.007 0.11 -9999 0 -0.61 16 16
PIK3C2A -0.033 0.1 -9999 0 -0.52 15 15
PI4 Kinase/Pyk2 -0.061 0.12 -9999 0 -0.43 30 30
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.051 0.13 -9999 0 -0.43 34 34
FAK1/Vinculin -0.005 0.13 -9999 0 -0.42 18 18
alphaV beta3/Integrin/ppsTEM5 -0.043 0.11 -9999 0 -0.31 63 63
RHOA 0.014 0 -9999 0 -10000 0 0
VTN -0.012 0.12 -9999 0 -0.56 21 21
BCAR1 0.013 0.029 -9999 0 -0.61 1 1
FGF2 0.011 0.047 -9999 0 -0.57 3 3
F11R 0.013 0.069 -9999 0 -0.36 15 15
alphaV/beta3 Integrin/Lactadherin -0.043 0.11 -9999 0 -0.31 64 64
alphaV/beta3 Integrin/TGFBR2 -0.043 0.11 -9999 0 -0.4 19 19
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.013 0.063 -9999 0 -0.33 18 18
HSP90AA1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.036 0.094 -9999 0 -0.28 61 61
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.004 0.096 -9999 0 -0.5 17 17
alphaV/beta3 Integrin/Pyk2 -0.023 0.14 -9999 0 -0.41 34 34
SDC1 -0.031 0.15 -9999 0 -0.51 40 40
VAV3 -0.04 0.14 -9999 0 -0.56 6 6
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.013 0.029 -9999 0 -0.61 1 1
FAK1/Paxillin -0.002 0.13 -9999 0 -0.38 18 18
cell migration 0.006 0.12 -9999 0 -0.43 9 9
ITGAV 0.013 0.029 -9999 0 -0.61 1 1
PI3K -0.045 0.1 -9999 0 -0.48 8 8
SPP1 -0.082 0.21 -9999 0 -0.55 79 79
KDR 0.006 0.066 -9999 0 -0.53 7 7
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.029 -9999 0 -0.61 1 1
COL4A3 -0.067 0.2 -9999 0 -0.53 69 69
angiogenesis 0.003 0.14 -9999 0 -0.46 21 21
Rac1/GTP -0.064 0.11 -9999 0 -0.51 6 6
EDIL3 -0.061 0.2 -9999 0 -0.59 58 58
cell proliferation -0.043 0.11 -9999 0 -0.4 19 19
Canonical Wnt signaling pathway

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.055 -10000 0 -0.59 3 3
AES 0.007 0.023 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.003 0.039 -10000 0 -0.34 6 6
SMAD4 0.014 0 -10000 0 -10000 0 0
DKK2 -0.11 0.23 -10000 0 -0.55 103 103
TLE1 0.006 0.037 -10000 0 -0.61 1 1
MACF1 0.015 0 -10000 0 -10000 0 0
CTNNB1 0.063 0.085 -10000 0 -10000 0 0
WIF1 -0.28 0.28 -10000 0 -0.55 244 244
beta catenin/RanBP3 0.022 0.11 0.41 30 -10000 0 30
KREMEN2 -0.053 0.18 -10000 0 -0.54 56 56
DKK1 -0.12 0.24 -10000 0 -0.54 109 109
beta catenin/beta TrCP1 0.069 0.08 -10000 0 -10000 0 0
FZD1 0.009 0.053 -10000 0 -0.49 5 5
AXIN2 -0.001 0.098 -10000 0 -0.77 4 4
AXIN1 0.015 0.001 -10000 0 -10000 0 0
RAN 0.014 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.025 0.037 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.093 0.053 0.3 3 -10000 0 3
Axin1/APC/GSK3 0.008 0.036 0.25 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.055 0.065 -10000 0 -10000 0 0
HNF1A 0.006 0.038 0.2 1 -0.61 1 2
CTBP1 0.007 0.025 -10000 0 -10000 0 0
MYC -0.057 0.32 -10000 0 -1.4 22 22
RANBP3 0.014 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.18 -10000 0 -0.36 143 143
NKD1 0 0.087 -10000 0 -0.56 11 11
TCF4 0.006 0.036 -10000 0 -0.56 1 1
TCF3 0.005 0.043 -10000 0 -0.54 2 2
WNT1/LRP6/FZD1/Axin1 -0.019 0.069 -10000 0 -0.51 1 1
Ran/GTP 0.002 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.036 0.13 0.5 29 -10000 0 29
LEF1 0.002 0.057 -10000 0 -0.5 5 5
DVL1 0.061 0.048 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.088 0.079 -10000 0 -0.44 2 2
DKK1/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.42 74 74
LRP6 0.014 0.024 -10000 0 -0.5 1 1
CSNK1A1 0.009 0.026 -10000 0 -10000 0 0
NLK 0.012 0.035 -10000 0 -0.52 2 2
CCND1 -0.037 0.25 -10000 0 -1.4 12 12
WNT1 -0.022 0.13 -10000 0 -0.49 31 31
GSK3A 0.015 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.047 -10000 0 -0.57 3 3
PPP2R5D 0.042 0.046 0.29 11 -10000 0 11
APC 0.022 0.075 -10000 0 -0.47 1 1
WNT1/LRP6/FZD1 0.1 0.1 0.24 101 -10000 0 101
CREBBP 0.007 0.025 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.014 0 -10000 0 -10000 0 0
Rac1/GDP 0.007 0.017 -10000 0 -10000 0 0
DOCK1 0.01 0.05 -10000 0 -0.61 3 3
ITGA4 -0.056 0.19 -10000 0 -0.54 58 58
RAC1 0.014 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.081 0.18 -10000 0 -0.44 86 86
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.041 0.11 -10000 0 -0.33 58 58
alpha4/beta7 Integrin/Paxillin -0.03 0.14 -10000 0 -0.37 55 55
lamellipodium assembly 0.005 0.034 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
ARF6 0.014 0 -10000 0 -10000 0 0
TLN1 0.014 0 -10000 0 -10000 0 0
PXN 0.025 0 -10000 0 -10000 0 0
PIK3R1 0.014 0 -10000 0 -10000 0 0
ARF6/GTP -0.03 0.08 -10000 0 -0.43 2 2
cell adhesion -0.033 0.089 -10000 0 -0.31 27 27
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.004 0.11 -10000 0 -0.34 27 27
ITGB1 0.012 0.033 -10000 0 -0.5 2 2
ITGB7 -0.034 0.16 -10000 0 -0.55 40 40
ARF6/GDP 0.007 0.017 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.08 0.17 -10000 0 -0.34 114 114
p130Cas/Crk/Dock1 -0.003 0.034 -10000 0 -0.37 4 4
VCAM1 -0.14 0.26 -10000 0 -0.57 124 124
alpha4/beta1 Integrin/Paxillin/Talin 0.005 0.1 -10000 0 -0.31 27 27
alpha4/beta1 Integrin/Paxillin/GIT1 0.005 0.1 -10000 0 -0.31 27 27
BCAR1 0.013 0.029 -10000 0 -0.61 1 1
mol:GDP 0.033 0.089 0.31 27 -10000 0 27
CBL 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0 -10000 0 -10000 0 0
GIT1 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.005 0.1 -10000 0 -0.31 27 27
Rac1/GTP 0.006 0.036 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.033 0.17 -9999 0 -0.47 53 53
KLHL20 -0.026 0.056 -9999 0 -0.27 8 8
CYFIP2 0.008 0.058 -9999 0 -0.54 5 5
Rac1/GDP 0.01 0.11 -9999 0 -10000 0 0
ENAH -0.034 0.17 -9999 0 -0.47 53 53
AP1M1 0.014 0 -9999 0 -10000 0 0
RAP1B 0.013 0.024 -9999 0 -0.5 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.035 0.068 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.017 0.039 -9999 0 -0.18 9 9
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.092 0.16 -9999 0 -0.39 67 67
RAPGEF1 -0.012 0.15 -9999 0 -0.39 53 53
CTNND1 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.073 0.16 -9999 0 -0.49 53 53
CRK -0.023 0.16 -9999 0 -0.43 53 53
E-cadherin/gamma catenin/alpha catenin -0.084 0.15 -9999 0 -0.34 115 115
alphaE/beta7 Integrin -0.034 0.11 -9999 0 -0.39 40 40
IQGAP1 0.007 0.062 -9999 0 -0.53 6 6
NCKAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.02 -9999 0 -0.3 2 2
DLG1 -0.034 0.17 -9999 0 -0.46 54 54
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.025 0.049 -9999 0 -10000 0 0
MLLT4 0.013 0.029 -9999 0 -0.61 1 1
ARF6/GTP/NME1/Tiam1 0 0.016 -9999 0 -0.34 1 1
PI3K -0.032 0.062 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.1 0.18 -9999 0 -0.41 115 115
TIAM1 0.013 0.029 -9999 0 -0.61 1 1
E-cadherin(dimer)/Ca2+ -0.063 0.12 -9999 0 -0.31 53 53
AKT1 -0.018 0.035 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
CDH1 -0.12 0.24 -9999 0 -0.55 109 109
RhoA/GDP 0.009 0.11 -9999 0 -10000 0 0
actin cytoskeleton organization -0.019 0.041 -9999 0 -0.2 8 8
CDC42/GDP 0.009 0.11 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.032 0.11 -9999 0 -0.28 58 58
ITGB7 -0.034 0.16 -9999 0 -0.55 40 40
RAC1 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.067 0.12 -9999 0 -0.33 53 53
E-cadherin/Ca2+/beta catenin/alpha catenin -0.065 0.12 -9999 0 -0.32 53 53
mol:GDP 0 0.13 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 -0.004 0.037 -9999 0 -0.32 6 6
JUP 0.001 0.087 -9999 0 -0.58 10 10
p120 catenin/RhoA/GDP -0.042 0.087 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 -0.004 0.037 -9999 0 -0.32 6 6
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.064 -9999 0 -0.21 26 26
NME1 0.014 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.033 0.17 -9999 0 -0.47 53 53
regulation of cell-cell adhesion -0.031 0.06 -9999 0 -10000 0 0
WASF2 -0.008 0.02 -9999 0 -10000 0 0
Rap1/GTP -0.041 0.078 -9999 0 -0.33 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.091 0.16 -9999 0 -0.53 24 24
CCND1 0.011 0.078 -9999 0 -0.27 26 26
VAV2 -0.017 0.16 -9999 0 -0.46 8 8
RAP1/GDP -0.039 0.082 -9999 0 -10000 0 0
adherens junction assembly -0.032 0.16 -9999 0 -0.45 53 53
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.052 0.17 -9999 0 -0.56 19 19
E-cadherin/beta catenin -0.067 0.13 -9999 0 -0.39 53 53
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.035 0.17 -9999 0 -0.47 53 53
PIK3CA 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.042 0.091 -9999 0 -0.47 8 8
E-cadherin/beta catenin/alpha catenin -0.076 0.14 -9999 0 -0.37 53 53
ITGAE 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.075 0.16 -9999 0 -0.5 53 53
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.017 0.069 -10000 0 -0.37 3 3
epithelial cell differentiation -0.044 0.091 -10000 0 -0.48 7 7
ITCH 0.019 0.013 -10000 0 -10000 0 0
WWP1 0.025 0.05 -10000 0 -10000 0 0
FYN 0.014 0 -10000 0 -10000 0 0
EGFR -0.083 0.22 -10000 0 -0.56 79 79
PRL 0 0.033 -10000 0 -0.5 2 2
neuron projection morphogenesis -0.032 0.15 -10000 0 -0.47 7 7
PTPRZ1 0.003 0.083 -10000 0 -0.58 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.091 0.13 -10000 0 -0.45 16 16
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.078 0.17 -10000 0 -0.34 107 107
ADAM17 0.012 0.065 -10000 0 -0.6 5 5
ErbB4/ErbB4 0.022 0.064 -10000 0 -0.42 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.006 0.13 -10000 0 -0.4 38 38
NCOR1 0.013 0.029 -10000 0 -0.61 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.066 0.16 -10000 0 -0.38 23 23
GRIN2B -0.16 0.21 -10000 0 -0.52 73 73
ErbB4/ErbB2/betacellulin -0.033 0.14 -10000 0 -0.42 19 19
STAT1 -0.002 0.09 -10000 0 -0.5 15 15
HBEGF 0.003 0.074 -10000 0 -0.5 10 10
PRLR -0.023 0.14 -10000 0 -0.57 30 30
E4ICDs/ETO2 0.018 0.07 -10000 0 -0.36 7 7
axon guidance -0.015 0.079 -10000 0 -0.38 1 1
NEDD4 0.007 0.079 -10000 0 -0.54 9 9
Prolactin receptor/Prolactin receptor/Prolactin -0.028 0.1 -10000 0 -0.41 32 32
CBFA2T3 0.005 0.074 -10000 0 -0.59 7 7
ErbB4/ErbB2/HBEGF 0.023 0.076 -10000 0 -0.37 7 7
MAPK3 -0.042 0.15 -10000 0 -0.46 11 11
STAT1 (dimer) 0.014 0.077 -10000 0 -0.4 4 4
MAPK1 -0.042 0.15 -10000 0 -0.46 11 11
JAK2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.071 0.16 -10000 0 -0.39 27 27
NRG1 -0.12 0.21 -10000 0 -0.41 150 150
NRG3 -0.035 0.17 -10000 0 -0.61 37 37
NRG2 0.012 0.041 -10000 0 -0.61 2 2
NRG4 -0.05 0.18 -10000 0 -0.53 54 54
heart development -0.015 0.079 -10000 0 -0.38 1 1
neural crest cell migration -0.07 0.16 -10000 0 -0.39 27 27
ERBB2 0.017 0.068 -10000 0 -0.38 13 13
WWOX/E4ICDs 0.024 0.054 -10000 0 -0.36 1 1
SHC1 0.009 0.053 -10000 0 -0.5 5 5
ErbB4/EGFR/neuregulin 4 -0.089 0.15 -10000 0 -0.48 34 34
apoptosis 0.043 0.12 0.42 38 -10000 0 38
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.022 0.063 -10000 0 -0.45 3 3
ErbB4/ErbB2/epiregulin 0.006 0.085 -10000 0 -0.4 6 6
ErbB4/ErbB4/betacellulin/betacellulin -0.043 0.15 -10000 0 -0.37 56 56
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.031 0.08 -10000 0 -0.48 4 4
MDM2 0.027 0.058 -10000 0 -0.36 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.097 0.14 -10000 0 -0.4 13 13
STAT5A -0.014 0.094 -10000 0 -0.43 8 8
ErbB4/EGFR/neuregulin 1 beta -0.12 0.2 -10000 0 -0.51 54 54
DLG4 0.003 0.074 -10000 0 -0.5 10 10
GRB2/SHC -0.004 0.039 -10000 0 -0.35 6 6
E4ICDs/TAB2/NCoR1 -0.013 0.043 -10000 0 -0.4 2 2
STAT5A (dimer) -0.047 0.097 -10000 0 -0.54 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.073 -10000 0 -0.35 1 1
LRIG1 -0.004 0.11 -10000 0 -0.61 14 14
EREG -0.013 0.11 -10000 0 -0.5 22 22
BTC -0.091 0.22 -10000 0 -0.56 83 83
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.016 0.079 -10000 0 -0.38 1 1
ERBB4 0.022 0.064 -10000 0 -0.42 1 1
STAT5B 0.014 0 -10000 0 -10000 0 0
YAP1 -0.035 0.13 -10000 0 -0.6 23 23
GRB2 0.013 0.024 -10000 0 -0.5 1 1
ErbB4/ErbB2/neuregulin 4 -0.008 0.12 -10000 0 -0.39 16 16
glial cell differentiation 0.013 0.043 0.4 2 -10000 0 2
WWOX 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.11 0.19 -10000 0 -0.51 41 41
Ceramide signaling pathway

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
SPHK2 -0.007 0.11 -10000 0 -0.35 40 40
MAP4K4 -0.023 0.12 -10000 0 -0.46 16 16
BAG4 0.001 0.09 -10000 0 -0.61 10 10
PKC zeta/ceramide -0.014 0.076 0.16 1 -0.28 24 25
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.035 0.16 -10000 0 -0.56 40 40
BAX 0.006 0.025 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AKT1 0.022 0.014 -10000 0 -10000 0 0
BAD 0.004 0.048 0.17 7 -10000 0 7
SMPD1 -0.027 0.09 -10000 0 -0.2 69 69
RB1 0.003 0.052 0.17 7 -0.41 1 8
FADD/Caspase 8 -0.014 0.12 -10000 0 -0.42 19 19
MAP2K4 0.008 0.055 -10000 0 -0.26 6 6
NSMAF 0.014 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.012 0.045 -10000 0 -10000 0 0
EGF -0.047 0.18 -10000 0 -0.56 49 49
mol:ceramide -0.006 0.052 0.17 7 -10000 0 7
MADD 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.007 0.11 -10000 0 -0.35 40 40
ASAH1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.003 0.051 0.16 7 -0.41 1 8
cell proliferation 0 0.092 -10000 0 -0.43 13 13
BID -0.011 0.092 -10000 0 -0.38 11 11
MAP3K1 0.001 0.055 0.17 5 -0.27 5 10
EIF2A 0.016 0.057 -10000 0 -0.33 4 4
TRADD 0.013 0.029 -10000 0 -0.61 1 1
CRADD 0.014 0 -10000 0 -10000 0 0
MAPK3 0.023 0.043 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.043 -10000 0 -10000 0 0
Cathepsin D/ceramide 0.002 0.046 0.16 6 -10000 0 6
FADD -0.023 0.12 -10000 0 -0.46 16 16
KSR1 0.004 0.048 0.17 7 -10000 0 7
MAPK8 -0.002 0.073 -10000 0 -0.28 14 14
PRKRA 0.004 0.048 0.17 7 -10000 0 7
PDGFA -0.03 0.14 -10000 0 -0.5 40 40
TRAF2 0.014 0 -10000 0 -10000 0 0
IGF1 -0.008 0.11 -10000 0 -0.57 18 18
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.006 0.052 0.17 7 -10000 0 7
CTSD 0.013 0.024 -10000 0 -0.5 1 1
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.001 0.1 -10000 0 -0.47 13 13
PRKCD -0.015 0.13 -10000 0 -0.61 22 22
PRKCZ -0.017 0.13 -10000 0 -0.57 25 25
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.007 0.11 -10000 0 -0.35 40 40
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.027 0.15 -10000 0 -0.53 35 35
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.033 0.13 -10000 0 -0.5 16 16
TNFR1A/BAG4/TNF-alpha -0.11 0.17 -10000 0 -0.34 154 154
mol:Sphingosine-1-phosphate -0.007 0.11 -10000 0 -0.35 40 40
MAP2K1 0.019 0.045 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
CYCS 0.008 0.039 0.19 4 -10000 0 4
TNFRSF1A 0.003 0.079 -10000 0 -0.56 9 9
NFKB1 0.014 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.017 0.087 -10000 0 -0.44 18 18
EIF2AK2 0.008 0.059 -10000 0 -0.32 6 6
TNF-alpha/TNFR1A/FAN -0.1 0.16 -10000 0 -0.33 149 149
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.004 0.083 -10000 0 -0.31 11 11
MAP2K2 0.019 0.044 -10000 0 -10000 0 0
SMPD3 -0.048 0.13 -10000 0 -0.26 98 98
TNF -0.16 0.26 -10000 0 -0.55 142 142
PKC zeta/PAR4 -0.05 0.14 -10000 0 -0.41 56 56
mol:PHOSPHOCHOLINE 0.005 0.076 0.21 39 -10000 0 39
NF kappa B1/RelA/I kappa B alpha -0.034 0.095 -10000 0 -0.55 4 4
AIFM1 0.008 0.039 0.19 4 -10000 0 4
BCL2 0.005 0.076 -10000 0 -0.61 7 7
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.021 0.089 -9999 0 -0.38 26 26
PDGFRB 0.01 0.042 -9999 0 -0.5 3 3
SPHK1 -0.041 0.14 -9999 0 -0.75 16 16
mol:S1P -0.041 0.12 -9999 0 -0.6 19 19
S1P1/S1P/Gi -0.023 0.16 -9999 0 -0.37 56 56
GNAO1 0.004 0.071 -9999 0 -0.61 6 6
PDGFB-D/PDGFRB/PLCgamma1 -0.011 0.15 -9999 0 -0.55 11 11
PLCG1 -0.015 0.15 -9999 0 -0.57 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.042 -9999 0 -0.5 3 3
GNAI2 0.012 0.007 -9999 0 -10000 0 0
GNAI3 0.012 0.007 -9999 0 -10000 0 0
GNAI1 -0.01 0.12 -9999 0 -0.61 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.003 0.08 -9999 0 -0.32 26 26
S1P1/S1P -0.051 0.11 -9999 0 -0.43 28 28
negative regulation of cAMP metabolic process -0.021 0.15 -9999 0 -0.36 56 56
MAPK3 -0.039 0.21 -9999 0 -0.54 52 52
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.005 0.067 -9999 0 -0.53 7 7
PLCB2 -0.017 0.14 -9999 0 -0.42 31 31
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.042 0.094 -9999 0 -0.37 26 26
receptor internalization -0.048 0.1 -9999 0 -0.38 32 32
PTGS2 -0.099 0.35 -9999 0 -1 52 52
Rac1/GTP -0.042 0.094 -9999 0 -0.37 26 26
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFA -0.01 0.11 -9999 0 -0.5 21 21
negative regulation of T cell proliferation -0.021 0.15 -9999 0 -0.36 56 56
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.03 -9999 0 -0.62 1 1
MAPK1 -0.039 0.21 -9999 0 -0.54 52 52
S1P1/S1P/PDGFB-D/PDGFRB -0.011 0.13 -9999 0 -0.42 27 27
ABCC1 0.009 0.048 -9999 0 -0.5 4 4
TCGA08_rtk_signaling

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
PDGFRA -0.061 0.2 -10000 0 -0.59 58 58
HRAS 0.014 0 -10000 0 -10000 0 0
EGFR -0.083 0.22 -10000 0 -0.56 79 79
AKT 0.022 0.042 -10000 0 -0.37 3 3
FOXO3 0.014 0 -10000 0 -10000 0 0
AKT1 0.014 0 -10000 0 -10000 0 0
FOXO1 0.011 0.047 -10000 0 -0.57 3 3
AKT3 0.009 0.057 -10000 0 -0.61 4 4
FOXO4 0.013 0.029 -10000 0 -0.61 1 1
MET -0.14 0.25 -10000 0 -0.55 129 129
PIK3CA 0.014 0 -10000 0 -10000 0 0
PIK3CB 0.014 0 -10000 0 -10000 0 0
NRAS 0.014 0 -10000 0 -10000 0 0
PIK3CG -0.063 0.19 -10000 0 -0.54 65 65
PIK3R3 0.012 0.033 -10000 0 -0.5 2 2
PIK3R2 0.014 0 -10000 0 -10000 0 0
NF1 0.012 0.041 -10000 0 -0.61 2 2
RAS -0.053 0.11 0.23 1 -0.29 48 49
ERBB2 0.006 0.066 -10000 0 -0.5 8 8
proliferation/survival/translation -0.01 0.052 0.2 9 -0.15 1 10
PI3K -0.045 0.11 -10000 0 -0.25 70 70
PIK3R1 0.014 0 -10000 0 -10000 0 0
KRAS 0.013 0.024 -10000 0 -0.5 1 1
FOXO 0.029 0.03 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
PTEN 0.013 0.029 -10000 0 -0.61 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.01 0.12 -10000 0 -0.41 19 19
CRKL 0.02 0.11 -10000 0 -0.41 20 20
HRAS 0 0.14 -10000 0 -0.48 13 13
mol:PIP3 0.002 0.1 -10000 0 -0.38 21 21
SPRED1 0.014 0 -10000 0 -10000 0 0
SPRED2 0.011 0.041 -10000 0 -0.5 3 3
GAB1 0.012 0.12 -10000 0 -0.44 20 20
FOXO3 0.025 0.1 -10000 0 -0.37 18 18
AKT1 0.017 0.11 -10000 0 -0.4 19 19
BAD 0.025 0.1 -10000 0 -0.37 18 18
megakaryocyte differentiation 0.003 0.13 -10000 0 -0.39 33 33
GSK3B 0.025 0.1 -10000 0 -0.37 18 18
RAF1 0.012 0.12 -10000 0 -0.39 12 12
SHC1 0.009 0.053 -10000 0 -0.5 5 5
STAT3 0.013 0.12 -10000 0 -0.43 20 20
STAT1 0.002 0.24 -10000 0 -0.93 25 25
HRAS/SPRED1 0.009 0.12 -10000 0 -0.39 12 12
cell proliferation 0.007 0.13 -10000 0 -0.44 23 23
PIK3CA 0.014 0 -10000 0 -10000 0 0
TEC -0.007 0.11 -10000 0 -0.55 17 17
RPS6KB1 0.013 0.12 -10000 0 -0.37 29 29
HRAS/SPRED2 0.008 0.12 -10000 0 -0.39 14 14
LYN/TEC/p62DOK -0.04 0.12 -10000 0 -0.45 27 27
MAPK3 0.024 0.091 -10000 0 -0.3 5 5
STAP1 -0.005 0.14 -10000 0 -0.43 29 29
GRAP2 -0.051 0.18 -10000 0 -0.54 54 54
JAK2 -0.052 0.18 -10000 0 -0.79 22 22
STAT1 (dimer) 0.003 0.24 -10000 0 -0.91 25 25
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.058 0.13 -10000 0 -0.46 29 29
actin filament polymerization 0.006 0.12 -10000 0 -0.43 20 20
LYN 0.003 0.078 -10000 0 -0.52 10 10
STAP1/STAT5A (dimer) -0.005 0.18 -10000 0 -0.62 28 28
PIK3R1 0.014 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.03 0.1 -10000 0 -0.37 18 18
PI3K 0.022 0.11 -10000 0 -0.4 19 19
PTEN 0.013 0.029 -10000 0 -0.61 1 1
SCF/KIT/EPO/EPOR -0.007 0.28 -10000 0 -1.2 20 20
MAPK8 0.006 0.13 -10000 0 -0.45 23 23
STAT3 (dimer) 0.013 0.11 -10000 0 -0.42 20 20
positive regulation of transcription 0.025 0.079 -10000 0 -0.24 5 5
mol:GDP -0.065 0.13 0.22 1 -0.48 20 21
PIK3C2B 0.008 0.12 -10000 0 -0.41 24 24
CBL/CRKL 0.027 0.11 -10000 0 -0.39 18 18
FER 0.001 0.14 -10000 0 -0.44 33 33
SH2B3 0.012 0.12 -10000 0 -0.43 20 20
PDPK1 0.01 0.1 -10000 0 -0.36 20 20
SNAI2 -0.005 0.14 -10000 0 -0.42 30 30
positive regulation of cell proliferation 0.009 0.19 -10000 0 -0.7 25 25
KITLG 0.003 0.1 -10000 0 -0.61 12 12
cell motility 0.009 0.19 -10000 0 -0.7 25 25
PTPN6 -0.013 0.096 -10000 0 -0.55 14 14
EPOR 0.038 0.081 -10000 0 -10000 0 0
STAT5A (dimer) 0.007 0.17 -10000 0 -0.61 25 25
SOCS1 -0.032 0.15 -10000 0 -0.52 40 40
cell migration 0.04 0.17 0.38 63 -10000 0 63
SOS1 0.014 0 -10000 0 -10000 0 0
EPO -0.007 0.1 -10000 0 -0.5 19 19
VAV1 -0.021 0.14 -10000 0 -0.57 28 28
GRB10 0.012 0.12 -10000 0 -0.42 21 21
PTPN11 0.013 0.005 -10000 0 -10000 0 0
SCF/KIT 0.005 0.12 0.23 7 -0.4 29 36
GO:0007205 -0.002 0.006 -10000 0 -10000 0 0
MAP2K1 0.021 0.099 -10000 0 -0.32 6 6
CBL 0.014 0 -10000 0 -10000 0 0
KIT -0.01 0.28 -10000 0 -1.3 19 19
MAP2K2 0.021 0.099 -10000 0 -0.33 5 5
SHC/Grb2/SOS1 -0.028 0.094 -10000 0 -0.4 19 19
STAT5A 0.006 0.17 -10000 0 -0.63 25 25
GRB2 0.013 0.024 -10000 0 -0.5 1 1
response to radiation -0.004 0.13 -10000 0 -0.41 30 30
SHC/GRAP2 -0.049 0.13 -10000 0 -0.4 57 57
PTPRO 0.003 0.13 -10000 0 -0.4 33 33
SH2B2 0.005 0.12 -10000 0 -0.44 20 20
DOK1 0.013 0.029 -10000 0 -0.61 1 1
MATK -0.041 0.17 -10000 0 -0.39 63 63
CREBBP 0.039 0.012 -10000 0 -10000 0 0
BCL2 0.023 0.18 -10000 0 -1.4 7 7
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0 0.086 -10000 0 -0.52 12 12
EPHB2 0.001 0.083 -10000 0 -0.53 11 11
EFNB1 -0.07 0.18 -10000 0 -0.38 107 107
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.082 0.15 -10000 0 -0.59 18 18
Ephrin B2/EPHB1-2 -0.036 0.12 -10000 0 -0.38 41 41
neuron projection morphogenesis -0.079 0.14 -10000 0 -0.56 18 18
Ephrin B1/EPHB1-2/Tiam1 -0.06 0.18 -10000 0 -0.62 19 19
DNM1 -0.11 0.23 -10000 0 -0.53 106 106
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.01 0.088 -10000 0 -0.73 6 6
YES1 -0.01 0.12 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/NCK2 -0.059 0.18 -10000 0 -0.63 18 18
PI3K 0.012 0.087 -10000 0 -0.74 6 6
mol:GDP -0.081 0.16 -10000 0 -0.62 19 19
ITGA2B -0.046 0.18 -10000 0 -0.58 47 47
endothelial cell proliferation -0.008 0.05 -10000 0 -0.31 12 12
FYN -0.009 0.11 -10000 0 -0.96 6 6
MAP3K7 -0.008 0.089 -10000 0 -0.78 6 6
FGR -0.009 0.11 -10000 0 -0.95 6 6
TIAM1 0.013 0.029 -10000 0 -0.61 1 1
PIK3R1 0.014 0 -10000 0 -10000 0 0
RGS3 0.011 0.041 -10000 0 -0.5 3 3
cell adhesion -0.038 0.16 -10000 0 -0.62 15 15
LYN -0.011 0.11 -10000 0 -0.96 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.013 0.1 -10000 0 -0.92 6 6
Ephrin B1/EPHB1-2 -0.015 0.096 -10000 0 -0.84 6 6
SRC -0.009 0.11 -10000 0 -0.95 6 6
ITGB3 -0.055 0.18 -10000 0 -0.52 60 60
EPHB1 -0.037 0.17 -10000 0 -0.61 38 38
EPHB4 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.006 0.051 -10000 0 -0.32 12 12
alphaIIb/beta3 Integrin -0.089 0.18 -10000 0 -0.42 98 98
BLK -0.029 0.12 -10000 0 -0.99 6 6
HCK -0.014 0.12 -10000 0 -1 6 6
regulation of stress fiber formation 0.081 0.16 0.62 18 -10000 0 18
MAPK8 0.01 0.099 -10000 0 -0.73 6 6
Ephrin B1/EPHB1-2/RGS3 -0.061 0.18 -10000 0 -0.62 20 20
endothelial cell migration -0.01 0.087 -10000 0 -0.62 7 7
NCK2 0.014 0 -10000 0 -10000 0 0
PTPN13 0.002 0.088 -10000 0 -0.7 7 7
regulation of focal adhesion formation 0.081 0.16 0.62 18 -10000 0 18
chemotaxis 0.082 0.16 0.61 20 -10000 0 20
PIK3CA 0.014 0 -10000 0 -10000 0 0
Rac1/GTP -0.081 0.14 -10000 0 -0.58 18 18
angiogenesis -0.015 0.095 -10000 0 -0.83 6 6
LCK -0.028 0.12 -10000 0 -0.98 6 6
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.014 0 -9999 0 -10000 0 0
SPHK1 -0.028 0.15 -9999 0 -0.55 35 35
GNAI2 0.014 0 -9999 0 -10000 0 0
mol:S1P 0.005 0.071 -9999 0 -0.3 18 18
GNAO1 0.006 0.07 -9999 0 -0.61 6 6
mol:Sphinganine-1-P -0.006 0.11 -9999 0 -0.39 35 35
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.024 0.073 -9999 0 -0.52 4 4
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.02 -9999 0 -0.44 1 1
S1PR3 -0.036 0.16 -9999 0 -0.52 44 44
S1PR2 0.008 0.062 -9999 0 -0.58 5 5
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.015 0.055 -9999 0 -0.26 18 18
S1PR5 -0.14 0.26 -9999 0 -0.56 123 123
S1PR4 0.001 0.083 -9999 0 -0.5 12 12
GNAI1 -0.008 0.12 -9999 0 -0.61 17 17
S1P/S1P5/G12 -0.066 0.16 -9999 0 -0.35 76 76
S1P/S1P3/Gq -0.012 0.12 -9999 0 -0.46 15 15
S1P/S1P4/Gi 0.022 0.076 -9999 0 -0.38 7 7
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ 0.013 0.029 -9999 0 -0.61 1 1
GNA14 -0.018 0.13 -9999 0 -0.58 25 25
GNA15 -0.01 0.12 -9999 0 -0.58 19 19
GNA12 0.013 0.029 -9999 0 -0.61 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.005 0.076 -9999 0 -0.61 7 7
ABCC1 0.01 0.047 -9999 0 -0.5 4 4
Aurora A signaling

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
Aurora A/GADD45A 0.006 0.094 -9999 0 -0.32 27 27
BIRC5 -0.14 0.26 -9999 0 -0.56 127 127
NFKBIA 0.03 0.048 -9999 0 -0.29 1 1
CPEB1 0.001 0.09 -9999 0 -0.61 10 10
AKT1 0.03 0.048 -9999 0 -0.29 1 1
NDEL1 0.014 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.002 0.053 -9999 0 -0.34 5 5
NDEL1/TACC3 -0.012 0.089 -9999 0 -0.38 17 17
GADD45A -0.018 0.12 -9999 0 -0.5 29 29
GSK3B 0.018 0.014 -9999 0 -10000 0 0
PAK1/Aurora A -0.005 0.1 -9999 0 -0.3 33 33
MDM2 0.012 0.033 -9999 0 -0.5 2 2
JUB -0.014 0.13 -9999 0 -0.58 22 22
TPX2 -0.039 0.15 -9999 0 -0.38 73 73
TP53 0.021 0.063 -9999 0 -0.3 10 10
DLG7 0.019 0.048 -9999 0 -0.3 1 1
AURKAIP1 0.013 0.024 -9999 0 -0.5 1 1
ARHGEF7 0.014 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.01 0.096 -9999 0 -0.4 17 17
G2/M transition of mitotic cell cycle 0.002 0.053 -9999 0 -0.34 5 5
AURKA 0.024 0.06 -9999 0 -0.35 1 1
AURKB -0.086 0.14 -9999 0 -0.3 112 112
CDC25B 0.025 0.047 -9999 0 -0.28 1 1
G2/M transition checkpoint -0.011 0.074 -9999 0 -0.29 21 21
mRNA polyadenylation -0.003 0.067 -9999 0 -0.35 11 11
Aurora A/CPEB -0.003 0.067 -9999 0 -0.35 11 11
Aurora A/TACC1/TRAP/chTOG 0.012 0.047 -9999 0 -10000 0 0
BRCA1 0.01 0.047 -9999 0 -0.5 4 4
centrosome duplication -0.005 0.1 -9999 0 -0.3 33 33
regulation of centrosome cycle -0.021 0.082 -9999 0 -0.37 17 17
spindle assembly 0.005 0.043 -9999 0 -0.3 1 1
TDRD7 0.012 0.041 -9999 0 -0.61 2 2
Aurora A/RasGAP/Survivin -0.074 0.13 -9999 0 -0.33 55 55
CENPA -0.059 0.13 -9999 0 -0.33 70 70
Aurora A/PP2A 0.026 0.046 -9999 0 -0.29 1 1
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.033 0.044 -9999 0 -0.27 1 1
negative regulation of DNA binding 0.021 0.063 -9999 0 -0.28 13 13
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.011 0.075 -9999 0 -0.3 21 21
mitotic prometaphase 0.023 0.038 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.06 -9999 0 -0.35 1 1
TACC1 0.014 0 -9999 0 -10000 0 0
TACC3 -0.022 0.13 -9999 0 -0.5 33 33
Aurora A/Antizyme1 0.01 0.045 -9999 0 -10000 0 0
Aurora A/RasGAP 0.026 0.046 -9999 0 -0.29 1 1
OAZ1 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.018 0.014 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.028 0.087 -9999 0 -0.29 45 45
Importin alpha/Importin beta/TPX2 -0.039 0.15 -9999 0 -0.38 73 73
PPP2R5D 0.014 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.015 0.14 -9999 0 -0.37 41 41
PAK1 -0.036 0.16 -9999 0 -0.51 45 45
CKAP5 0.014 0 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.016 0.13 -10000 0 -0.54 25 25
positive regulation of NF-kappaB transcription factor activity -0.032 0.11 -10000 0 -0.38 40 40
MAP2K4 0.03 0.066 -10000 0 -0.36 3 3
IKBKB 0.014 0 -10000 0 -10000 0 0
TNFRSF10B 0.009 0.055 -10000 0 -0.58 4 4
TNFRSF10A -0.022 0.14 -10000 0 -0.56 29 29
SMPD1 0.01 0.051 -10000 0 -0.23 13 13
IKBKG 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.003 0.093 -10000 0 -0.51 15 15
TRAIL/TRAILR2 -0.024 0.099 -10000 0 -0.4 28 28
TRAIL/TRAILR3 -0.045 0.14 -10000 0 -0.42 50 50
TRAIL/TRAILR1 -0.046 0.13 -10000 0 -0.42 51 51
TRAIL/TRAILR4 -0.033 0.11 -10000 0 -0.38 40 40
TRAIL/TRAILR1/DAP3/GTP -0.035 0.1 -10000 0 -0.32 51 51
IKK complex -0.01 0.031 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.003 0.094 -10000 0 -0.39 25 25
MAP3K1 0.024 0.065 -10000 0 -0.34 2 2
TRAILR4 (trimer) -0.003 0.093 -10000 0 -0.51 15 15
TRADD 0.013 0.029 -10000 0 -0.61 1 1
TRAILR1 (trimer) -0.022 0.14 -10000 0 -0.56 29 29
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.014 0.081 -10000 0 -0.28 3 3
CFLAR 0.013 0.024 -10000 0 -0.5 1 1
MAPK1 0.003 0.094 -10000 0 -0.39 25 25
TRAIL/TRAILR1/FADD/TRADD/RIP -0.032 0.091 -10000 0 -0.32 33 33
mol:ceramide 0.01 0.05 -10000 0 -0.23 13 13
FADD 0.014 0 -10000 0 -10000 0 0
MAPK8 0.031 0.082 -10000 0 -0.39 5 5
TRAF2 0.014 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.022 0.14 -10000 0 -0.54 30 30
CHUK 0.014 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.038 0.11 -10000 0 -0.35 51 51
DAP3 0.014 0 -10000 0 -10000 0 0
CASP10 -0.021 0.09 0.28 1 -0.39 14 15
JNK cascade -0.032 0.11 -10000 0 -0.38 40 40
TRAIL (trimer) -0.016 0.13 -10000 0 -0.54 25 25
TNFRSF10C -0.022 0.14 -10000 0 -0.54 30 30
TRAIL/TRAILR1/DAP3/GTP/FADD -0.032 0.093 -10000 0 -0.32 32 32
TRAIL/TRAILR2/FADD -0.02 0.082 -10000 0 -0.34 28 28
cell death 0.01 0.05 -10000 0 -0.23 13 13
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.027 0.061 -10000 0 -0.52 1 1
TRAILR2 (trimer) 0.009 0.055 -10000 0 -0.58 4 4
CASP8 -0.003 0.053 -10000 0 -0.81 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.017 0.068 -10000 0 -0.62 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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 0.013 0.024 -10000 0 -0.5 1 1
NFATC1 0.031 0.094 -10000 0 -0.45 2 2
NFATC2 0.01 0.077 -10000 0 -0.28 15 15
NFATC3 0.005 0.087 -10000 0 -0.41 17 17
YWHAE 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.064 0.18 -10000 0 -0.53 37 37
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.15 0.2 -10000 0 -0.5 77 77
BCL2/BAX -0.007 0.054 -10000 0 -0.44 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.028 -10000 0 -0.41 2 2
CaM/Ca2+ 0.01 0.028 -10000 0 -0.41 2 2
BAX 0.014 0 -10000 0 -10000 0 0
MAPK14 0.014 0.004 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.054 0.17 -10000 0 -0.51 37 37
Calcineurin A alpha-beta B1/BCL2 0.005 0.076 -10000 0 -0.61 7 7
FKBP8 0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.053 0.17 0.5 37 -10000 0 37
KPNB1 0.014 0 -10000 0 -10000 0 0
KPNA2 0.012 0.033 -10000 0 -0.5 2 2
XPO1 0.014 0 -10000 0 -10000 0 0
SFN -0.12 0.23 -10000 0 -0.53 109 109
MAP3K8 -0.006 0.1 -10000 0 -0.51 18 18
NFAT4/CK1 alpha -0.015 0.06 -10000 0 -0.41 3 3
MEF2D/NFAT1/Cbp/p300 0.025 0.11 -10000 0 -0.42 14 14
CABIN1 -0.065 0.18 -10000 0 -0.54 37 37
CALM1 0.012 0.038 -10000 0 -0.56 2 2
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.009 0.053 -10000 0 -0.5 5 5
CAMK4 -0.17 0.28 -10000 0 -0.58 145 145
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.014 0 -10000 0 -10000 0 0
YWHAH -0.01 0.11 -10000 0 -0.5 22 22
Calcineurin A alpha-beta B1/AKAP79/PKA -0.032 0.1 -10000 0 -0.35 42 42
YWHAB 0.014 0 -10000 0 -10000 0 0
MAPK8 0.001 0.09 -10000 0 -0.61 10 10
MAPK9 0.014 0 -10000 0 -10000 0 0
YWHAG 0.001 0.081 -10000 0 -0.5 12 12
FKBP1A 0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.039 0.1 -10000 0 -0.45 5 5
PRKCH 0.014 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.003 0.041 -10000 0 -0.44 4 4
CASP3 0.013 0.024 -10000 0 -0.5 1 1
PIM1 0.008 0.058 -10000 0 -0.5 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.003 -10000 0 -10000 0 0
apoptosis -0.002 0.022 -10000 0 -0.34 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.078 -10000 0 -0.31 4 4
PRKCB -0.065 0.19 -10000 0 -0.53 67 67
PRKCE 0.001 0.083 -10000 0 -0.53 11 11
JNK2/NFAT4 0.013 0.079 -10000 0 -0.37 17 17
BAD/BCL-XL -0.001 0.016 -10000 0 -0.35 1 1
PRKCD -0.015 0.13 -10000 0 -0.61 22 22
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.017 0.13 -10000 0 -0.57 25 25
PRKCA 0.013 0.029 -10000 0 -0.61 1 1
PRKCG -0.19 0.27 -10000 0 -0.55 171 171
PRKCQ -0.009 0.12 -10000 0 -0.6 18 18
FKBP38/BCL2 -0.007 0.054 -10000 0 -0.44 7 7
EP300 0.009 0.057 -10000 0 -0.61 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.099 -10000 0 -0.5 1 1
CaM/Ca2+/FKBP38 0.001 0.024 -10000 0 -0.34 2 2
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.02 0.025 -10000 0 -0.34 2 2
CaM/Ca2+/CAMK IV -0.11 0.17 -10000 0 -0.36 146 146
NFATc/ERK1 0.038 0.089 -10000 0 -0.5 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.15 0.19 -10000 0 -0.5 77 77
NR4A1 0.016 0.15 -10000 0 -0.47 36 36
GSK3B 0.014 0.004 -10000 0 -10000 0 0
positive T cell selection 0.005 0.087 -10000 0 -0.41 17 17
NFAT1/CK1 alpha -0.02 0.05 -10000 0 -0.36 4 4
RCH1/ KPNB1 -0.001 0.023 -10000 0 -0.35 2 2
YWHAQ 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0.004 -10000 0 -10000 0 0
AKAP5 -0.032 0.15 -10000 0 -0.5 42 42
MEF2D 0.013 0.024 -10000 0 -0.49 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.036 0.09 -10000 0 -0.42 2 2
CREBBP 0.014 0.002 -10000 0 -10000 0 0
BCL2 0.005 0.076 -10000 0 -0.61 7 7
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.001 0.09 -9999 0 -0.61 10 10
Caspase 8 (4 units) -0.013 0.086 -9999 0 -0.36 15 15
NEF -0.006 0.034 -9999 0 -10000 0 0
NFKBIA 0.009 0.03 -9999 0 -10000 0 0
BIRC3 -0.002 0.17 -9999 0 -0.55 40 40
CYCS 0.022 0.088 -9999 0 -0.32 13 13
RIPK1 0.014 0 -9999 0 -10000 0 0
CD247 -0.026 0.15 -9999 0 -0.61 28 28
MAP2K7 0.016 0.076 -9999 0 -0.32 2 2
protein ubiquitination 0.017 0.094 -9999 0 -0.41 6 6
CRADD 0.014 0 -9999 0 -10000 0 0
DAXX 0.014 0 -9999 0 -10000 0 0
FAS -0.008 0.11 -9999 0 -0.56 18 18
BID 0.014 0.092 -9999 0 -0.33 15 15
NF-kappa-B/RelA/I kappa B alpha -0.022 0.073 -9999 0 -10000 0 0
TRADD 0.013 0.029 -9999 0 -0.61 1 1
MAP3K5 0.009 0.057 -9999 0 -0.61 4 4
CFLAR 0.013 0.024 -9999 0 -0.5 1 1
FADD 0.014 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.022 0.073 -9999 0 -10000 0 0
MAPK8 0.017 0.085 -9999 0 -0.52 1 1
APAF1 0.014 0 -9999 0 -10000 0 0
TRAF1 0.002 0.084 -9999 0 -0.6 9 9
TRAF2 0.014 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.006 0.095 -9999 0 -0.3 27 27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.12 -9999 0 -0.54 7 7
CHUK 0.017 0.1 -9999 0 -0.46 6 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.021 0.074 -9999 0 -0.32 17 17
TCRz/NEF -0.041 0.13 -9999 0 -0.41 46 46
TNF -0.16 0.26 -9999 0 -0.55 142 142
FASLG -0.032 0.18 -9999 0 -0.53 46 46
NFKB1 0.009 0.03 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.11 0.17 -9999 0 -0.34 154 154
CASP6 -0.021 0.07 -9999 0 -0.58 3 3
CASP7 0.03 0.16 -9999 0 -0.51 32 32
RELA 0.009 0.03 -9999 0 -10000 0 0
CASP2 0.014 0 -9999 0 -10000 0 0
CASP3 0.03 0.16 -9999 0 -0.51 32 32
TNFRSF1A 0.003 0.079 -9999 0 -0.56 9 9
TNFR1A/BAG4 -0.017 0.087 -9999 0 -0.44 18 18
CASP8 -0.004 0.094 -9999 0 -0.5 16 16
CASP9 0.013 0.024 -9999 0 -0.5 1 1
MAP3K14 0.008 0.11 -9999 0 -0.49 7 7
APAF-1/Caspase 9 -0.041 0.11 -9999 0 -0.4 34 34
BCL2 0.02 0.089 -9999 0 -0.49 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.021 0.069 -10000 0 -0.39 3 3
adherens junction organization -0.03 0.12 -10000 0 -0.4 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.018 0.12 -10000 0 -0.36 15 15
FMN1 -0.062 0.16 -10000 0 -0.52 20 20
mol:IP3 0.011 0.069 -10000 0 -0.41 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.015 0.11 -10000 0 -0.28 58 58
CTNNB1 0.016 0.004 -10000 0 -10000 0 0
AKT1 0.014 0.079 -10000 0 -0.44 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.03 0.16 -10000 0 -0.42 54 54
CTNND1 0.015 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.005 0.11 -10000 0 -0.53 4 4
VASP -0.006 0.11 -10000 0 -0.54 4 4
ZYX -0.011 0.11 -10000 0 -0.53 5 5
JUB -0.02 0.13 -10000 0 -0.36 22 22
EGFR(dimer) -0.055 0.15 -10000 0 -0.34 57 57
E-cadherin/beta catenin-gamma catenin -0.082 0.15 -10000 0 -0.33 115 115
mol:PI-3-4-5-P3 -0.03 0.064 -10000 0 -0.43 4 4
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
PI3K -0.031 0.066 -10000 0 -0.44 4 4
FYN 0.021 0.068 -10000 0 -0.33 3 3
mol:Ca2+ 0.011 0.068 -10000 0 -0.4 3 3
JUP 0.003 0.087 -10000 0 -0.58 10 10
PIK3R1 0.015 0.001 -10000 0 -10000 0 0
mol:DAG 0.011 0.069 -10000 0 -0.41 3 3
CDH1 -0.12 0.24 -10000 0 -0.55 109 109
RhoA/GDP -0.018 0.12 -10000 0 -0.36 15 15
establishment of polarity of embryonic epithelium -0.006 0.11 -10000 0 -0.53 4 4
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
EGFR -0.083 0.22 -10000 0 -0.56 79 79
CASR 0.009 0.076 -10000 0 -0.37 3 3
RhoA/GTP -0.02 0.045 -10000 0 -0.36 3 3
AKT2 0.014 0.079 -10000 0 -0.4 4 4
actin cable formation -0.053 0.15 -10000 0 -0.49 21 21
apoptosis 0.026 0.057 0.39 4 -10000 0 4
CTNNA1 0.015 0.002 -10000 0 -10000 0 0
mol:GDP -0.028 0.13 -10000 0 -0.39 15 15
PIP5K1A -0.006 0.11 -10000 0 -0.54 4 4
PLCG1 -0.024 0.053 -10000 0 -0.42 3 3
Rac1/GTP -0.077 0.12 -10000 0 -0.4 23 23
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.006 0.07 -9999 0 -0.61 6 6
CDC42/GTP -0.013 0.055 -9999 0 -0.4 4 4
PLCG1 0.029 0.067 -9999 0 -0.42 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.02 -9999 0 -0.44 1 1
cell migration -0.013 0.054 -9999 0 -0.4 4 4
S1PR5 -0.14 0.26 -9999 0 -0.56 123 123
S1PR4 0.001 0.083 -9999 0 -0.5 12 12
MAPK3 0.029 0.067 -9999 0 -0.42 4 4
MAPK1 0.029 0.067 -9999 0 -0.42 4 4
S1P/S1P5/Gi -0.038 0.14 -9999 0 -0.3 73 73
GNAI1 -0.008 0.12 -9999 0 -0.61 17 17
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.091 0.15 -9999 0 -0.34 123 123
RHOA 0.027 0.046 -9999 0 -0.31 2 2
S1P/S1P4/Gi 0.021 0.071 -9999 0 -0.35 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.029 -9999 0 -0.61 1 1
S1P/S1P4/G12/G13 -0.008 0.045 -9999 0 -0.34 2 2
GNA12 0.013 0.029 -9999 0 -0.61 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.006 0.095 -9999 0 -0.33 34 34
SNTA1 -0.023 0.14 -9999 0 -0.58 29 29
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.005 0.098 -9999 0 -0.33 36 36
MAPK12 0.027 0.047 -9999 0 -0.34 6 6
CCND1 0.007 0.073 -9999 0 -0.4 12 12
p38 gamma/SNTA1 0.013 0.09 -9999 0 -0.31 28 28
MAP2K3 0.012 0.033 -9999 0 -0.5 2 2
PKN1 0.014 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.027 0.047 -9999 0 -0.34 6 6
MAP2K6 0.023 0.033 -9999 0 -0.33 2 2
MAPT 0.01 0.087 -9999 0 -0.31 24 24
MAPK13 -0.006 0.11 -9999 0 -0.39 34 34
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0.032 -9999 0 -0.22 8 8
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.014 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.005 0.045 -9999 0 -0.84 1 1
Syndecan-3/Neurocan -0.02 0.082 -9999 0 -0.91 1 1
POMC -0.006 0.11 -9999 0 -0.55 17 17
EGFR -0.083 0.22 -9999 0 -0.56 79 79
Syndecan-3/EGFR -0.048 0.11 -9999 0 -0.91 1 1
AGRP 0.006 0.047 -9999 0 -0.5 4 4
NCSTN 0.014 0 -9999 0 -10000 0 0
PSENEN 0.014 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
NCAN -0.024 0.15 -9999 0 -0.6 29 29
long-term memory -0.002 0.027 -9999 0 -0.56 1 1
Syndecan-3/IL8 -0.086 0.13 -9999 0 -0.61 1 1
PSEN1 0.014 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
limb bud formation -0.002 0.03 -9999 0 -0.63 1 1
MC4R -0.11 0.24 -9999 0 -0.57 98 98
SRC 0.014 0 -9999 0 -10000 0 0
PTN 0.006 0.064 -9999 0 -0.51 7 7
FGFR/FGF/Syndecan-3 -0.002 0.031 -9999 0 -0.64 1 1
neuron projection morphogenesis -0.02 0.08 -9999 0 -0.72 2 2
Syndecan-3/AgRP -0.004 0.036 -9999 0 -0.61 1 1
Syndecan-3/AgRP/MC4R -0.06 0.12 -9999 0 -0.6 3 3
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.002 0.031 -9999 0 -0.64 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.085 0.12 -9999 0 -0.6 1 1
IL8 -0.17 0.26 -9999 0 -0.54 151 151
Syndecan-3/Fyn/Cortactin -0.002 0.028 -9999 0 -0.58 1 1
Syndecan-3/CASK -0.002 0.029 -9999 0 -0.61 1 1
alpha-MSH/MC4R -0.1 0.19 -9999 0 -0.43 109 109
Gamma Secretase 0 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.065 0.14 -10000 0 -0.35 85 85
cell-cell adhesion 0.037 0.1 0.49 14 -10000 0 14
Ephrin B/EPHB2/RasGAP -0.022 0.084 -10000 0 -0.55 5 5
ITSN1 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
SHC1 0.009 0.053 -10000 0 -0.5 5 5
Ephrin B1/EPHB3 -0.003 0.03 -10000 0 -0.29 5 5
Ephrin B1/EPHB1 -0.033 0.11 -10000 0 -0.38 40 40
HRAS/GDP -0.033 0.1 -10000 0 -0.48 12 12
Ephrin B/EPHB1/GRB7 -0.06 0.14 -10000 0 -0.61 17 17
Endophilin/SYNJ1 0.017 0.091 -10000 0 -0.5 6 6
KRAS 0.013 0.024 -10000 0 -0.5 1 1
Ephrin B/EPHB1/Src -0.041 0.12 -10000 0 -0.58 11 11
endothelial cell migration -0.006 0.04 -10000 0 -0.3 3 3
GRB2 0.013 0.024 -10000 0 -0.5 1 1
GRB7 -0.031 0.14 -10000 0 -0.5 38 38
PAK1 -0.007 0.14 -10000 0 -0.48 19 19
HRAS 0.014 0 -10000 0 -10000 0 0
RRAS 0.018 0.09 -10000 0 -0.52 5 5
DNM1 -0.11 0.23 -10000 0 -0.53 106 106
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.002 0.13 -10000 0 -0.56 11 11
lamellipodium assembly -0.037 0.1 -10000 0 -0.49 14 14
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.006 0.12 -10000 0 -0.5 12 12
PIK3R1 0.014 0 -10000 0 -10000 0 0
EPHB2 0.001 0.083 -10000 0 -0.53 11 11
EPHB3 0.012 0.033 -10000 0 -0.5 2 2
EPHB1 -0.037 0.17 -10000 0 -0.61 38 38
EPHB4 0.014 0 -10000 0 -10000 0 0
mol:GDP -0.032 0.096 -10000 0 -0.44 15 15
Ephrin B/EPHB2 -0.023 0.086 -10000 0 -0.39 16 16
Ephrin B/EPHB3 -0.018 0.072 -10000 0 -0.35 13 13
JNK cascade 0.006 0.12 -10000 0 -0.62 5 5
Ephrin B/EPHB1 -0.042 0.12 -10000 0 -0.38 46 46
RAP1/GDP -0.028 0.082 -10000 0 -0.4 11 11
EFNB2 0 0.086 -10000 0 -0.52 12 12
EFNB3 -0.003 0.1 -10000 0 -0.57 14 14
EFNB1 0.011 0.041 -10000 0 -0.5 3 3
Ephrin B2/EPHB1-2 -0.041 0.12 -10000 0 -0.38 41 41
RAP1B 0.013 0.024 -10000 0 -0.5 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.038 0.11 -10000 0 -0.52 14 14
Rap1/GTP -0.037 0.1 -10000 0 -0.49 14 14
axon guidance -0.065 0.14 -10000 0 -0.35 85 85
MAPK3 0.022 0.11 -10000 0 -0.43 13 13
MAPK1 0.022 0.11 -10000 0 -0.43 13 13
Rac1/GDP 0.019 0.1 -10000 0 -0.43 11 11
actin cytoskeleton reorganization -0.028 0.08 -10000 0 -0.39 12 12
CDC42/GDP 0.019 0.1 -10000 0 -0.43 11 11
PI3K -0.006 0.04 -10000 0 -0.31 3 3
EFNA5 -0.083 0.22 -10000 0 -0.56 79 79
Ephrin B2/EPHB4 -0.008 0.05 -10000 0 -0.31 12 12
Ephrin B/EPHB2/Intersectin/N-WASP 0.023 0.072 -10000 0 -0.41 5 5
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.036 0.1 -10000 0 -0.48 14 14
PTK2 0.009 0.027 -10000 0 -10000 0 0
MAP4K4 0.006 0.12 -10000 0 -0.64 5 5
SRC 0.014 0 -10000 0 -10000 0 0
KALRN -0.001 0.087 -10000 0 -0.5 14 14
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.018 0.12 -10000 0 -0.44 8 8
MAP2K1 0.014 0.11 -10000 0 -0.46 13 13
WASL 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.036 0.11 -10000 0 -0.36 40 40
cell migration 0.017 0.12 -10000 0 -0.49 13 13
NRAS 0.014 0 -10000 0 -10000 0 0
SYNJ1 0.017 0.093 -10000 0 -0.51 6 6
PXN 0.014 0 -10000 0 -10000 0 0
TF -0.01 0.14 -10000 0 -0.57 13 13
HRAS/GTP -0.04 0.11 -10000 0 -0.53 14 14
Ephrin B1/EPHB1-2 -0.036 0.11 -10000 0 -0.37 39 39
cell adhesion mediated by integrin 0.012 0.071 0.32 15 -10000 0 15
RAC1 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.043 0.12 -10000 0 -0.57 14 14
RAC1-CDC42/GTP -0.037 0.11 -10000 0 -0.5 15 15
RASA1 0.014 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.027 0.082 -10000 0 -0.41 10 10
ruffle organization 0.023 0.13 -10000 0 -0.49 14 14
NCK1 0.013 0.029 -10000 0 -0.61 1 1
receptor internalization -0.038 0.15 -10000 0 -0.6 11 11
Ephrin B/EPHB2/KALRN -0.029 0.092 -10000 0 -0.54 6 6
ROCK1 0.025 0.029 -10000 0 -0.26 5 5
RAS family/GDP -0.026 0.076 -10000 0 -0.43 7 7
Rac1/GTP -0.039 0.11 -10000 0 -0.52 14 14
Ephrin B/EPHB1/Src/Paxillin 0.003 0.11 -10000 0 -0.48 11 11
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.024 0.11 -10000 0 -0.46 1 1
epithelial cell differentiation -0.063 0.12 -10000 0 -0.3 53 53
CYFIP2 0.008 0.058 -10000 0 -0.54 5 5
ENAH 0.009 0.1 -10000 0 -0.37 1 1
EGFR -0.083 0.22 -10000 0 -0.56 79 79
EPHA2 -0.019 0.13 -10000 0 -0.5 30 30
MYO6 -0.026 0.12 -10000 0 -10000 0 0
CTNNB1 0.014 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.003 0.033 -10000 0 -0.32 5 5
AQP5 -0.14 0.19 -10000 0 -0.52 68 68
CTNND1 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.026 0.12 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.032 0.13 -10000 0 -0.55 2 2
EGF -0.047 0.18 -10000 0 -0.56 49 49
NCKAP1 0.014 0 -10000 0 -10000 0 0
AQP3 -0.078 0.13 -10000 0 -0.54 19 19
cortical microtubule organization -0.063 0.12 -10000 0 -0.3 53 53
GO:0000145 -0.024 0.12 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.063 0.12 -10000 0 -0.31 53 53
MLLT4 0.013 0.029 -10000 0 -0.61 1 1
ARF6/GDP -0.058 0.097 -10000 0 -0.41 9 9
ARF6 0.014 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.019 0.069 -10000 0 -0.41 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.026 0.12 -10000 0 -0.38 2 2
PVRL2 0.012 0.037 -10000 0 -0.55 2 2
ZYX -0.031 0.13 -10000 0 -0.53 1 1
ARF6/GTP -0.017 0.062 -10000 0 -0.38 3 3
CDH1 -0.12 0.24 -10000 0 -0.55 109 109
EGFR/EGFR/EGF/EGF -0.12 0.17 -10000 0 -0.53 40 40
RhoA/GDP -0.058 0.1 -10000 0 -10000 0 0
actin cytoskeleton organization -0.021 0.12 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.013 0.024 -10000 0 -0.49 1 1
GIT1 0.014 0 -10000 0 -10000 0 0
IGF1R 0.013 0.024 -10000 0 -0.5 1 1
IGF1 -0.008 0.11 -10000 0 -0.57 18 18
DIAPH1 0 0.045 -10000 0 -0.64 2 2
Wnt receptor signaling pathway 0.063 0.12 0.3 53 -10000 0 53
RHOA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP -0.058 0.098 -10000 0 -0.41 9 9
CTNNA1 0.014 0 -10000 0 -10000 0 0
VCL -0.022 0.12 -10000 0 -10000 0 0
EFNA1 0.011 0.041 -10000 0 -0.5 3 3
LPP -0.04 0.14 -10000 0 -0.44 5 5
Ephrin A1/EPHA2 -0.07 0.12 -10000 0 -0.47 8 8
SEC6/SEC8 -0.05 0.094 -10000 0 -0.48 3 3
MGAT3 -0.033 0.13 -10000 0 -0.56 2 2
HGF/MET -0.16 0.18 -10000 0 -0.52 59 59
HGF -0.078 0.2 -10000 0 -0.52 80 80
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.024 0.11 -10000 0 -0.46 1 1
actin cable formation 0.021 0.1 -10000 0 -0.32 3 3
KIAA1543 -0.062 0.17 -10000 0 -0.56 22 22
KIFC3 -0.027 0.13 -10000 0 -0.6 1 1
NCK1 0.013 0.029 -10000 0 -0.61 1 1
EXOC3 0.014 0 -10000 0 -10000 0 0
ACTN1 -0.043 0.14 -10000 0 -0.47 5 5
NCK1/GIT1 -0.001 0.02 -10000 0 -0.44 1 1
mol:GDP -0.063 0.12 -10000 0 -0.3 53 53
EXOC4 0.014 0 -10000 0 -10000 0 0
STX4 -0.026 0.12 -10000 0 -10000 0 0
PIP5K1C -0.026 0.12 -10000 0 -10000 0 0
LIMA1 0.004 0.081 -10000 0 -0.61 8 8
ABI1 0.014 0 -10000 0 -10000 0 0
ROCK1 -0.001 0.12 -10000 0 -0.38 5 5
adherens junction assembly -0.042 0.17 -10000 0 -0.52 22 22
IGF-1R heterotetramer/IGF1 -0.065 0.12 -10000 0 -0.56 6 6
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.033 -10000 0 -0.41 3 3
MET -0.14 0.25 -10000 0 -0.55 129 129
PLEKHA7 -0.035 0.14 -10000 0 -0.57 5 5
mol:GTP -0.019 0.069 -10000 0 -0.41 3 3
establishment of epithelial cell apical/basal polarity 0.006 0.12 -10000 0 -0.46 3 3
cortical actin cytoskeleton stabilization -0.024 0.11 -10000 0 -0.46 1 1
regulation of cell-cell adhesion -0.021 0.12 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.024 0.11 -10000 0 -0.46 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.13 0.38 -9999 0 -1.1 52 52
RAD9A 0.014 0 -9999 0 -10000 0 0
AP1 -0.066 0.18 -9999 0 -0.43 88 88
IFNAR2 0.013 0.007 -9999 0 -10000 0 0
AKT1 0.001 0.051 -9999 0 -0.28 2 2
ER alpha/Oestrogen -0.012 0.093 -9999 0 -0.41 24 24
NFX1/SIN3/HDAC complex 0.041 0.029 -9999 0 -10000 0 0
EGF -0.048 0.18 -9999 0 -0.56 49 49
SMG5 0.014 0 -9999 0 -10000 0 0
SMG6 0.014 0 -9999 0 -10000 0 0
SP3/HDAC2 0.019 0.012 -9999 0 -10000 0 0
TERT/c-Abl -0.13 0.34 -9999 0 -1 51 51
SAP18 0.013 0.004 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.038 0.14 -9999 0 -0.5 40 40
WRN 0.01 0.05 -9999 0 -0.61 3 3
SP1 0.013 0.009 -9999 0 -10000 0 0
SP3 0.012 0.006 -9999 0 -10000 0 0
TERF2IP 0.014 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.13 0.29 -9999 0 -0.91 51 51
Mad/Max 0.019 0.01 -9999 0 -10000 0 0
TERT -0.14 0.41 -9999 0 -1.2 51 51
CCND1 -0.12 0.36 -9999 0 -1 59 59
MAX 0.013 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.004 -9999 0 -10000 0 0
RBBP4 0.013 0.004 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.014 0 -9999 0 -10000 0 0
SIN3A 0.013 0.004 -9999 0 -10000 0 0
Telomerase/911 0.033 0.039 -9999 0 -10000 0 0
CDKN1B 0.013 0.074 -9999 0 -0.55 1 1
RAD1 0.014 0 -9999 0 -10000 0 0
XRCC5 0.014 0 -9999 0 -10000 0 0
XRCC6 0.014 0 -9999 0 -10000 0 0
SAP30 0.012 0.029 -9999 0 -0.61 1 1
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.012 0.006 -9999 0 -10000 0 0
JUN 0.002 0.076 -9999 0 -0.51 10 10
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.007 -9999 0 -10000 0 0
FOS -0.095 0.22 -9999 0 -0.56 87 87
IFN-gamma/IRF1 -0.012 0.084 -9999 0 -0.35 26 26
PARP2 0.014 0 -9999 0 -10000 0 0
BLM -0.053 0.18 -9999 0 -0.54 56 56
Telomerase -0.038 0.1 -9999 0 -0.4 25 25
IRF1 -0.008 0.11 -9999 0 -0.49 23 23
ESR1 -0.016 0.13 -9999 0 -0.55 24 24
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0.022 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.031 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.046 0.031 -9999 0 -10000 0 0
HDAC1 0.009 0.05 -9999 0 -0.61 3 3
HDAC2 0.012 0.009 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.019 0.061 -9999 0 -0.44 8 8
ABL1 0.014 0 -9999 0 -10000 0 0
MXD1 0.013 0.006 -9999 0 -10000 0 0
MRE11A 0.014 0 -9999 0 -10000 0 0
HUS1 0.013 0.024 -9999 0 -0.5 1 1
RPS6KB1 0.014 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.32 -9999 0 -1 51 51
NR2F2 -0.011 0.12 -9999 0 -0.52 24 24
MAPK3 0.011 0.008 -9999 0 -10000 0 0
MAPK1 0.011 0.008 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.004 0.081 -9999 0 -0.6 8 8
NFKB1 0.014 0 -9999 0 -10000 0 0
HNRNPC 0.014 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.014 0 -9999 0 -10000 0 0
EGFR -0.084 0.22 -9999 0 -0.56 79 79
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.096 0.21 -9999 0 -0.44 115 115
MYC -0.02 0.14 -9999 0 -0.59 25 25
IL2 -0.003 0.014 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
TGFB1 0.004 0.081 -9999 0 -0.6 8 8
TRF2/BLM -0.043 0.12 -9999 0 -0.36 56 56
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.1 0.35 -9999 0 -1 51 51
SP1/HDAC2 0.019 0.017 -9999 0 -10000 0 0
PINX1 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.13 0.29 -9999 0 -0.91 51 51
Smad3/Myc 0.003 0.1 -9999 0 -0.37 32 32
911 complex -0.001 0.013 -9999 0 -0.28 1 1
IFNG 0.003 0.047 -9999 0 -0.49 4 4
Telomerase/PinX1 -0.13 0.29 -9999 0 -0.91 51 51
Telomerase/AKT1/mTOR/p70S6K 0.01 0.074 -9999 0 -10000 0 0
SIN3B 0.013 0.004 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.13 0.29 -9999 0 -0.91 51 51
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN -0.003 0.033 -9999 0 -0.41 3 3
Telomerase/hnRNP C1/C2 -0.13 0.29 -9999 0 -0.91 51 51
E2F1 -0.017 0.12 -9999 0 -0.52 26 26
ZNFX1 0.013 0.004 -9999 0 -10000 0 0
PIF1 -0.052 0.18 -9999 0 -0.55 55 55
NCL 0.014 0 -9999 0 -10000 0 0
DKC1 0.014 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.036 0.098 0.17 2 -0.41 17 19
CaM/Ca2+ -0.002 0.027 -10000 0 -0.4 2 2
AKT1 0.014 0 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
STXBP4 0.013 0.029 -10000 0 -0.61 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.023 0.14 0.25 53 -0.46 16 69
YWHAZ 0.014 0 -10000 0 -10000 0 0
CALM1 0.012 0.037 -10000 0 -0.55 2 2
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.025 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH -0.01 0.11 -10000 0 -0.5 22 22
YWHAB 0.014 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.017 -10000 0 -0.37 1 1
YWHAG 0.001 0.081 -10000 0 -0.5 12 12
ASIP -0.096 0.23 -10000 0 -0.57 87 87
PRKCI 0.014 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ -0.002 0.027 -10000 0 -0.4 2 2
RHOQ 0.014 0 -10000 0 -10000 0 0
GYS1 0.035 0 -10000 0 -10000 0 0
PRKCZ -0.017 0.13 -10000 0 -0.57 25 25
TRIP10 0.006 0.07 -10000 0 -0.56 7 7
TC10/GTP/CIP4/Exocyst -0.005 0.042 -10000 0 -0.34 7 7
AS160/14-3-3 0.002 0.089 -10000 0 -0.38 3 3
VAMP2 0.014 0 -10000 0 -10000 0 0
SLC2A4 0.022 0.15 0.28 28 -0.52 16 44
STX4 0.014 0 -10000 0 -10000 0 0
GSK3B 0.029 0 -10000 0 -10000 0 0
SFN -0.12 0.23 -10000 0 -0.53 109 109
LNPEP -0.013 0.13 -10000 0 -0.61 20 20
YWHAE 0.014 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.013 0.029 -9999 0 -0.61 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.012 0.033 -9999 0 -0.5 2 2
RAC1-CDC42/GTP/PAK family -0.031 0.1 -9999 0 -0.22 92 92
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.01 0.05 -9999 0 -0.61 3 3
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
MAP3K12 0.014 0 -9999 0 -10000 0 0
FGR 0.011 0.041 -9999 0 -0.5 3 3
p38 alpha/TAB1 -0.027 0.058 -9999 0 -0.32 8 8
PRKG1 -0.04 0.17 -9999 0 -0.59 42 42
DUSP8 0 0.089 -9999 0 -0.54 12 12
PGK/cGMP/p38 alpha -0.046 0.092 -9999 0 -0.29 42 42
apoptosis -0.026 0.056 -9999 0 -0.32 7 7
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.003 0.078 -9999 0 -0.52 10 10
DUSP1 -0.02 0.14 -9999 0 -0.54 29 29
PAK1 -0.036 0.16 -9999 0 -0.51 45 45
SRC 0.014 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.016 -9999 0 -10000 0 0
TRAF6 0.013 0.029 -9999 0 -0.61 1 1
RAC1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.014 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.005 0.1 -9999 0 -0.37 12 12
BLK -0.11 0.22 -9999 0 -0.52 104 104
HCK -0.01 0.11 -9999 0 -0.55 20 20
MAP2K3 0.012 0.033 -9999 0 -0.5 2 2
DUSP16 0.014 0 -9999 0 -10000 0 0
DUSP10 -0.007 0.11 -9999 0 -0.56 17 17
TRAF6/MEKK3 -0.001 0.016 -9999 0 -0.34 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.007 0.083 -9999 0 -0.33 9 9
positive regulation of innate immune response 0 0.11 -9999 0 -0.42 10 10
LCK -0.089 0.22 -9999 0 -0.55 85 85
p38alpha-beta/MKP7 0.007 0.11 -9999 0 -0.44 7 7
p38alpha-beta/MKP5 -0.002 0.12 -9999 0 -0.41 13 13
PGK/cGMP -0.039 0.12 -9999 0 -0.44 42 42
PAK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.008 0.12 -9999 0 -0.43 11 11
CDC42 0.014 0 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
PAK3 -0.11 0.24 -9999 0 -0.57 100 100
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.027 0.086 -10000 0 -0.32 29 29
ER alpha/Gai/GDP/Gbeta gamma 0.022 0.099 -10000 0 -0.4 17 17
AKT1 0.016 0.13 -10000 0 -0.75 12 12
PIK3CA 0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.014 0.13 -10000 0 -0.76 12 12
mol:Ca2+ -0.013 0.14 -10000 0 -0.47 25 25
IGF1R 0.013 0.024 -10000 0 -0.5 1 1
E2/ER alpha (dimer)/Striatin -0.034 0.11 -10000 0 -0.36 44 44
SHC1 0.009 0.053 -10000 0 -0.5 5 5
apoptosis -0.017 0.12 0.72 12 -10000 0 12
RhoA/GTP -0.012 0.052 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.023 0.082 -10000 0 -0.4 18 18
regulation of stress fiber formation -0.016 0.1 0.4 9 -10000 0 9
E2/ERA-ERB (dimer) -0.029 0.1 -10000 0 -0.36 38 38
KRAS 0.013 0.024 -10000 0 -0.5 1 1
G13/GTP -0.016 0.068 -10000 0 -0.3 24 24
pseudopodium formation 0.016 0.1 -10000 0 -0.4 9 9
E2/ER alpha (dimer)/PELP1 -0.017 0.075 -10000 0 -0.34 24 24
GRB2 0.013 0.024 -10000 0 -0.5 1 1
GNG2 0.009 0.057 -10000 0 -0.61 4 4
GNAO1 0.006 0.07 -10000 0 -0.61 6 6
HRAS 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.024 0.1 -10000 0 -0.46 13 13
E2/ER beta (dimer) -0.015 0.077 -10000 0 -0.42 16 16
mol:GDP -0.025 0.087 -10000 0 -0.36 25 25
mol:NADP 0.024 0.1 -10000 0 -0.46 13 13
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.014 0.15 -10000 0 -0.49 25 25
IGF-1R heterotetramer 0.013 0.024 -10000 0 -0.49 1 1
PLCB1 -0.011 0.13 -10000 0 -0.46 21 21
PLCB2 -0.011 0.14 -10000 0 -0.51 23 23
IGF1 -0.008 0.11 -10000 0 -0.57 18 18
mol:L-citrulline 0.024 0.1 -10000 0 -0.46 13 13
RHOA 0.014 0 -10000 0 -10000 0 0
Gai/GDP -0.018 0.096 -10000 0 -0.76 6 6
JNK cascade -0.015 0.077 -10000 0 -0.42 16 16
BCAR1 0.013 0.029 -10000 0 -0.61 1 1
ESR2 -0.006 0.11 -10000 0 -0.57 16 16
GNAQ 0.014 0 -10000 0 -10000 0 0
ESR1 -0.015 0.13 -10000 0 -0.55 24 24
Gq family/GDP/Gbeta gamma 0.007 0.12 -10000 0 -0.45 23 23
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.031 0.058 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.025 0.087 -10000 0 -0.42 18 18
GNAZ 0.013 0.029 -10000 0 -0.61 1 1
E2/ER alpha (dimer) -0.021 0.09 -10000 0 -0.4 24 24
STRN -0.014 0.13 -10000 0 -0.6 21 21
GNAL -0.051 0.19 -10000 0 -0.6 49 49
PELP1 0.014 0 -10000 0 -10000 0 0
MAPK11 0.005 0.077 -10000 0 -0.36 20 20
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.008 0.12 -10000 0 -0.61 17 17
HBEGF -0.01 0.12 -10000 0 -0.49 9 9
cAMP biosynthetic process -0.055 0.12 -10000 0 -0.31 81 81
SRC 0.03 0.095 -10000 0 -0.49 5 5
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.023 0.077 -10000 0 -0.35 14 14
SOS1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.027 0.081 -10000 0 -0.36 17 17
Gs family/GTP -0.056 0.13 -10000 0 -0.32 81 81
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.012 -10000 0 -10000 0 0
vasodilation 0.024 0.1 -10000 0 -0.44 13 13
mol:DAG -0.014 0.15 -10000 0 -0.49 25 25
Gs family/GDP/Gbeta gamma -0.046 0.1 -10000 0 -0.38 20 20
MSN 0.015 0.11 -10000 0 -0.44 9 9
Gq family/GTP -0.008 0.12 -10000 0 -0.49 19 19
mol:PI-3-4-5-P3 0.015 0.12 -10000 0 -0.73 12 12
NRAS 0.014 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.024 0.1 0.44 13 -10000 0 13
GRB2/SOS1 -0.001 0.016 -10000 0 -0.35 1 1
RhoA/GDP -0.023 0.08 -10000 0 -0.34 25 25
NOS3 0.023 0.11 -10000 0 -0.48 13 13
GNA11 0.005 0.076 -10000 0 -0.61 7 7
MAPKKK cascade 0.022 0.13 -10000 0 -0.54 16 16
E2/ER alpha (dimer)/PELP1/Src -0.024 0.085 -10000 0 -0.42 17 17
ruffle organization 0.016 0.1 -10000 0 -0.4 9 9
ROCK2 0.03 0.083 -10000 0 -0.53 2 2
GNA14 -0.018 0.13 -10000 0 -0.58 25 25
GNA15 -0.01 0.12 -10000 0 -0.58 19 19
GNA13 0.014 0 -10000 0 -10000 0 0
MMP9 -0.041 0.15 -10000 0 -0.46 17 17
MMP2 0.024 0.11 -10000 0 -0.5 7 7
BARD1 signaling events

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
BARD1/CSTF1 -0.022 0.096 -10000 0 -0.43 24 24
ATM 0.014 0 -10000 0 -10000 0 0
UBE2D3 0.014 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
ATR 0.014 0 -10000 0 -10000 0 0
UBE2L3 0.014 0 -10000 0 -10000 0 0
FANCD2 0.016 0.057 -10000 0 -0.35 5 5
protein ubiquitination -0.025 0.094 -10000 0 -0.35 30 30
XRCC5 0.014 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.014 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.014 0.058 -10000 0 -0.39 7 7
FANCF 0.014 0 -10000 0 -10000 0 0
BRCA1 0.01 0.047 -10000 0 -0.5 4 4
CCNE1 0.012 0.033 -10000 0 -0.5 2 2
CDK2/Cyclin E1 -0.012 0.07 -10000 0 -0.4 14 14
FANCG 0.013 0.024 -10000 0 -0.5 1 1
BRCA1/BACH1/BARD1 -0.025 0.1 -10000 0 -0.43 27 27
FANCE 0.014 0 -10000 0 -10000 0 0
FANCC 0.011 0.044 -10000 0 -0.53 3 3
NBN 0.014 0 -10000 0 -10000 0 0
FANCA -0.029 0.15 -10000 0 -0.52 37 37
DNA repair 0.017 0.15 -10000 0 -0.53 15 15
BRCA1/BARD1/ubiquitin -0.025 0.1 -10000 0 -0.43 27 27
BARD1/DNA-PK -0.017 0.071 -10000 0 -0.33 22 22
FANCL 0.014 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.022 0.096 0.43 24 -10000 0 24
BRCA1/BARD1/CTIP/M/R/N Complex 0.029 0.067 -10000 0 -0.37 2 2
BRCA1/BACH1/BARD1/TopBP1 -0.021 0.086 -10000 0 -0.36 27 27
BRCA1/BARD1/P53 -0.029 0.097 -10000 0 -0.35 34 34
BARD1/CSTF1/BRCA1 -0.021 0.086 -10000 0 -0.36 27 27
BRCA1/BACH1 0.01 0.047 -10000 0 -0.49 4 4
BARD1 -0.017 0.14 -10000 0 -0.6 24 24
PCNA 0.012 0.033 -10000 0 -0.5 2 2
BRCA1/BARD1/UbcH5C -0.021 0.086 -10000 0 -0.36 27 27
BRCA1/BARD1/UbcH7 -0.021 0.086 -10000 0 -0.36 27 27
BRCA1/BARD1/RAD51/PCNA -0.053 0.13 -10000 0 -0.39 38 38
BARD1/DNA-PK/P53 -0.024 0.086 -10000 0 -0.62 2 2
BRCA1/BARD1/Ubiquitin -0.025 0.1 -10000 0 -0.43 27 27
BRCA1/BARD1/CTIP 0.014 0.093 -10000 0 -0.36 23 23
FA complex 0.028 0.059 -10000 0 -10000 0 0
BARD1/EWS -0.022 0.096 -10000 0 -0.43 24 24
RBBP8 0.023 0.03 -10000 0 -0.35 3 3
TP53 -0.004 0.1 -10000 0 -0.6 14 14
TOPBP1 0.014 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.028 0.097 0.35 34 -10000 0 34
BRCA1/BARD1 -0.026 0.095 -10000 0 -0.35 30 30
CSTF1 0.014 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.023 0.098 -10000 0 -0.44 24 24
CDK2 -0.001 0.092 -10000 0 -0.54 13 13
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.052 0.18 -10000 0 -0.52 57 57
RAD50 0.014 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.025 0.1 -10000 0 -0.43 27 27
EWSR1 0.014 0 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.017 0.12 -10000 0 -0.47 16 16
BAG4 0.001 0.09 -10000 0 -0.61 10 10
BAD 0.008 0.045 -10000 0 -0.2 1 1
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.035 0.16 -10000 0 -0.56 40 40
BAX 0.008 0.045 -10000 0 -0.2 1 1
EnzymeConsortium:3.1.4.12 -0.003 0.033 -10000 0 -0.1 16 16
IKBKB -0.007 0.12 -10000 0 -0.43 16 16
MAP2K2 0.018 0.049 -10000 0 -10000 0 0
MAP2K1 0.018 0.051 -10000 0 -0.31 1 1
SMPD1 0.003 0.033 -10000 0 -0.14 1 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.44 17 17
MAP2K4 0.011 0.054 -10000 0 -0.29 3 3
protein ubiquitination -0.006 0.12 -10000 0 -0.44 16 16
EnzymeConsortium:2.7.1.37 0.019 0.057 -10000 0 -0.3 1 1
response to UV 0 0.001 -10000 0 -0.002 2 2
RAF1 0.013 0.049 -10000 0 -10000 0 0
CRADD 0.015 0 -10000 0 -10000 0 0
mol:ceramide 0 0.047 -10000 0 -0.16 11 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.015 0 -10000 0 -10000 0 0
MAP3K1 0.005 0.053 -10000 0 -0.24 6 6
TRADD 0.013 0.029 -10000 0 -0.61 1 1
RELA/p50 0.014 0 -10000 0 -10000 0 0
MAPK3 0.021 0.05 -10000 0 -10000 0 0
MAPK1 0.021 0.05 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD -0.016 0.12 -10000 0 -0.47 16 16
KSR1 0.007 0.048 -10000 0 -0.21 1 1
MAPK8 0.013 0.067 -10000 0 -0.29 7 7
TRAF2 0.014 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.007 0.12 -10000 0 -0.43 16 16
TNF R/SODD -0.015 0.087 -10000 0 -0.44 18 18
TNF -0.16 0.26 -10000 0 -0.55 142 142
CYCS 0.012 0.044 0.15 3 -0.17 2 5
IKBKG -0.007 0.12 -10000 0 -0.43 16 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.026 0.13 -10000 0 -0.5 16 16
RELA 0.014 0 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AIFM1 0.012 0.044 0.15 3 -0.19 1 4
TNF/TNF R/SODD -0.11 0.17 -10000 0 -0.34 154 154
TNFRSF1A 0.003 0.079 -10000 0 -0.56 9 9
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.053 -10000 0 -0.72 1 1
NSMAF -0.016 0.12 -10000 0 -0.46 16 16
response to hydrogen peroxide 0 0.001 -10000 0 -0.002 2 2
BCL2 0.005 0.076 -10000 0 -0.61 7 7
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.24 -9999 0 -0.57 96 96
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.014 0 -9999 0 -10000 0 0
TCEB1 0.014 0 -9999 0 -10000 0 0
HIF1A/p53 0.023 0.056 -9999 0 -0.28 13 13
HIF1A 0.024 0.021 -9999 0 -0.2 1 1
COPS5 0.014 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.014 0 -9999 0 -10000 0 0
CDKN2A -0.11 0.24 -9999 0 -0.58 96 96
ARNT/IPAS -0.085 0.17 -9999 0 -0.4 97 97
HIF1AN 0.014 0 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.032 0.025 -9999 0 -0.31 1 1
CUL2 0.014 0 -9999 0 -10000 0 0
OS9 0.004 0.07 -9999 0 -0.5 9 9
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.032 0.02 -9999 0 -10000 0 0
PHD1-3/OS9 -0.01 0.054 -9999 0 -0.33 8 8
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.01 -9999 0 -10000 0 0
VHL 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.032 0.02 -9999 0 -10000 0 0
EGLN3 0.004 0.081 -9999 0 -0.61 8 8
EGLN2 0.014 0 -9999 0 -10000 0 0
EGLN1 0.014 0 -9999 0 -10000 0 0
TP53 -0.004 0.1 -9999 0 -0.6 14 14
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.042 0.005 -9999 0 -10000 0 0
ARNT 0.013 0.024 -9999 0 -0.5 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.014 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.029 0.12 -9999 0 -0.29 76 76
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.037 -9999 0 -0.44 3 3
SMARCC1 0.01 0.013 -9999 0 -10000 0 0
REL -0.022 0.14 -9999 0 -0.58 29 29
HDAC7 0.023 0.1 -9999 0 -0.45 1 1
JUN 0.002 0.076 -9999 0 -0.51 10 10
EP300 0.009 0.057 -9999 0 -0.61 4 4
KAT2B 0.013 0.024 -9999 0 -0.5 1 1
KAT5 0.014 0 -9999 0 -10000 0 0
MAPK14 0.023 0.025 -9999 0 -0.44 1 1
FOXO1 0.01 0.047 -9999 0 -0.57 3 3
T-DHT/AR 0.019 0.11 -9999 0 -0.4 7 7
MAP2K6 0.012 0.029 -9999 0 -0.6 1 1
BRM/BAF57 0.004 0.023 -9999 0 -0.44 1 1
MAP2K4 0.012 0.034 -9999 0 -0.5 2 2
SMARCA2 0.012 0.029 -9999 0 -0.61 1 1
PDE9A -0.025 0.11 -9999 0 -0.77 5 5
NCOA2 -0.025 0.15 -9999 0 -0.61 29 29
CEBPA -0.016 0.13 -9999 0 -0.57 24 24
EHMT2 0.013 0.004 -9999 0 -10000 0 0
cell proliferation 0.033 0.13 -9999 0 -0.46 8 8
NR0B1 -0.097 0.23 -9999 0 -0.56 89 89
EGR1 -0.11 0.23 -9999 0 -0.54 99 99
RXRs/9cRA -0.035 0.11 -9999 0 -0.33 57 57
AR/RACK1/Src -0.008 0.075 -9999 0 -0.38 8 8
AR/GR -0.012 0.11 -9999 0 -0.39 15 15
GNB2L1 0.014 0.001 -9999 0 -10000 0 0
PKN1 0.014 0 -9999 0 -10000 0 0
RCHY1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.012 0.073 -9999 0 -0.43 12 12
T-DHT/AR/TIF2/CARM1 0.002 0.13 -9999 0 -0.66 10 10
SRC 0.031 0.061 -9999 0 -0.31 1 1
NR3C1 0.014 0 -9999 0 -10000 0 0
KLK3 -0.042 0.14 -9999 0 -0.47 20 20
APPBP2 0.014 0.005 -9999 0 -10000 0 0
TRIM24 0.012 0.024 -9999 0 -0.5 1 1
T-DHT/AR/TIP60 0.015 0.082 -9999 0 -0.42 7 7
TMPRSS2 -0.14 0.32 -9999 0 -1.1 41 41
RXRG -0.061 0.2 -9999 0 -0.6 57 57
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.014 0.001 -9999 0 -10000 0 0
RXRB 0.014 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.001 -9999 0 -10000 0 0
NR2C2 0.005 0.076 -9999 0 -0.61 7 7
KLK2 -0.002 0.14 -9999 0 -0.47 18 18
AR -0.02 0.13 -9999 0 -0.41 18 18
SENP1 0.014 0.001 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
MDM2 0.013 0.034 -9999 0 -0.5 2 2
SRY -0.019 0.11 -9999 0 -0.49 22 22
GATA2 -0.006 0.11 -9999 0 -0.58 16 16
MYST2 0.014 0.001 -9999 0 -10000 0 0
HOXB13 -0.052 0.16 -9999 0 -0.5 53 53
T-DHT/AR/RACK1/Src 0.022 0.082 -9999 0 -0.39 7 7
positive regulation of transcription -0.006 0.11 -9999 0 -0.58 16 16
DNAJA1 0.014 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.025 -9999 0 -0.25 3 3
NCOA1 0.018 0.005 -9999 0 -10000 0 0
SPDEF -0.045 0.17 -9999 0 -0.55 48 48
T-DHT/AR/TIF2 0.018 0.12 -9999 0 -0.62 10 10
T-DHT/AR/Hsp90 0.015 0.082 -9999 0 -0.42 7 7
GSK3B 0.014 0.004 -9999 0 -10000 0 0
NR2C1 0.015 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.025 0.065 -9999 0 -0.32 12 12
SIRT1 0.014 0 -9999 0 -10000 0 0
ZMIZ2 0.015 0.005 -9999 0 -10000 0 0
POU2F1 0.024 0.033 -9999 0 -0.6 1 1
T-DHT/AR/DAX-1 -0.045 0.15 -9999 0 -0.41 33 33
CREBBP 0.014 0 -9999 0 -10000 0 0
SMARCE1 0.014 0.003 -9999 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.06 0.1 -9999 0 -0.66 4 4
CRKL 0.035 0.076 -9999 0 -0.47 4 4
mol:DAG 0.039 0.082 -9999 0 -0.48 5 5
HRAS 0.057 0.078 -9999 0 -0.62 2 2
MAPK8 0.014 0.099 -9999 0 -0.41 14 14
RAP1A 0.035 0.076 -9999 0 -0.47 4 4
GAB1 0.034 0.083 -9999 0 -0.54 4 4
MAPK14 0.022 0.078 -9999 0 -0.41 5 5
EPO -0.006 0.1 -9999 0 -0.5 19 19
PLCG1 0.039 0.084 -9999 0 -0.49 5 5
EPOR/TRPC2/IP3 Receptors 0.014 0.035 -9999 0 -0.5 2 2
RAPGEF1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.069 0.17 -9999 0 -0.34 128 128
GAB1/SHC/GRB2/SOS1 -0.016 0.066 -9999 0 -0.52 4 4
EPO/EPOR (dimer) 0.009 0.081 -9999 0 -0.36 20 20
IRS2 0.035 0.082 -9999 0 -0.54 4 4
STAT1 0.042 0.1 -9999 0 -0.5 8 8
STAT5B 0.044 0.087 -9999 0 -0.56 4 4
cell proliferation 0.023 0.093 -9999 0 -0.46 7 7
GAB1/SHIP/PIK3R1/SHP2/SHC -0.017 0.071 -9999 0 -0.44 8 8
TEC 0.024 0.099 -9999 0 -0.44 10 10
SOCS3 -0.12 0.24 -9999 0 -0.53 116 116
STAT1 (dimer) 0.042 0.1 -9999 0 -0.49 8 8
JAK2 0.015 0.007 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.041 0.083 -9999 0 -0.5 4 4
EPO/EPOR 0.009 0.081 -9999 0 -0.36 20 20
LYN 0.005 0.078 -9999 0 -0.52 10 10
TEC/VAV2 0.033 0.097 -9999 0 -0.42 10 10
elevation of cytosolic calcium ion concentration 0.014 0.035 -9999 0 -0.5 2 2
SHC1 0.009 0.053 -9999 0 -0.5 5 5
EPO/EPOR (dimer)/LYN 0.02 0.088 -9999 0 -0.36 14 14
mol:IP3 0.039 0.082 -9999 0 -0.48 5 5
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.007 0.078 -9999 0 -0.45 9 9
SH2B3 0.013 0.034 -9999 0 -0.49 2 2
NFKB1 0.022 0.078 -9999 0 -0.41 5 5
EPO/EPOR (dimer)/JAK2/SOCS3 -0.043 0.078 -9999 0 -0.27 14 14
PTPN6 0.027 0.079 -9999 0 -0.5 4 4
TEC/VAV2/GRB2 0.039 0.095 -9999 0 -0.42 9 9
EPOR 0.014 0.035 -9999 0 -0.5 2 2
INPP5D 0.008 0.058 -9999 0 -0.54 5 5
mol:GDP -0.016 0.067 -9999 0 -0.49 5 5
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG2 0.001 0.086 -9999 0 -0.55 11 11
CRKL/CBL/C3G 0.049 0.072 -9999 0 -0.43 4 4
VAV2 0.035 0.076 -9999 0 -0.47 4 4
CBL 0.035 0.076 -9999 0 -0.47 4 4
SHC/Grb2/SOS1 -0.016 0.064 -9999 0 -0.46 5 5
STAT5A 0.035 0.12 -9999 0 -0.6 9 9
GRB2 0.013 0.024 -9999 0 -0.5 1 1
STAT5 (dimer) 0.055 0.12 -9999 0 -0.6 9 9
LYN/PLCgamma2 0.005 0.096 -9999 0 -0.48 16 16
PTPN11 0.014 0 -9999 0 -10000 0 0
BTK 0.023 0.11 -9999 0 -0.5 13 13
BCL2 0.052 0.15 -9999 0 -0.93 8 8
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.041 -9999 0 -0.5 3 3
alphaV beta3 Integrin -0.049 0.13 -9999 0 -0.37 61 61
PTK2 -0.033 0.11 -9999 0 -0.54 17 17
positive regulation of JNK cascade -0.009 0.048 -9999 0 -0.33 9 9
CDC42/GDP 0.046 0.079 -9999 0 -0.45 9 9
Rac1/GDP 0.048 0.078 -9999 0 -0.45 9 9
RAP1B 0.013 0.024 -9999 0 -0.5 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.011 0.06 -9999 0 -0.41 9 9
nectin-3/I-afadin -0.009 0.061 -9999 0 -0.44 9 9
RAPGEF1 0.039 0.088 -9999 0 -0.52 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.032 0.1 -9999 0 -0.6 9 9
PDGFB-D/PDGFRB 0.011 0.041 -9999 0 -0.49 3 3
TLN1 0.032 0.037 -9999 0 -0.35 2 2
Rap1/GTP -0.01 0.052 -9999 0 -0.35 9 9
IQGAP1 0.007 0.062 -9999 0 -0.53 6 6
Rap1/GTP/I-afadin -0.001 0.02 -9999 0 -0.3 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.009 0.061 -9999 0 -0.44 9 9
PVR 0.014 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.014 0 -9999 0 -10000 0 0
mol:GDP 0.043 0.096 -9999 0 -0.57 9 9
MLLT4 0.013 0.029 -9999 0 -0.61 1 1
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K -0.007 0.049 -9999 0 -0.55 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.016 0.083 -9999 0 -0.44 17 17
positive regulation of lamellipodium assembly -0.01 0.051 -9999 0 -0.35 9 9
PVRL1 -0.007 0.11 -9999 0 -0.61 16 16
PVRL3 0.004 0.081 -9999 0 -0.61 8 8
PVRL2 0.012 0.037 -9999 0 -0.55 2 2
PIK3R1 0.014 0 -9999 0 -10000 0 0
CDH1 -0.12 0.24 -9999 0 -0.55 109 109
CLDN1 -0.015 0.12 -9999 0 -0.54 25 25
JAM-A/CLDN1 -0.028 0.092 -9999 0 -0.36 22 22
SRC -0.021 0.1 -9999 0 -0.69 9 9
ITGB3 -0.055 0.18 -9999 0 -0.52 60 60
nectin-1(dimer)/I-afadin/I-afadin -0.016 0.083 -9999 0 -0.44 17 17
FARP2 0.037 0.093 -9999 0 -0.56 9 9
RAC1 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.007 0.051 -9999 0 -0.37 9 9
nectin-1/I-afadin -0.016 0.083 -9999 0 -0.44 17 17
nectin-2/I-afadin -0.003 0.033 -9999 0 -0.41 3 3
RAC1/GTP/IQGAP1/filamentous actin -0.004 0.037 -9999 0 -0.32 6 6
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.02 0.089 -9999 0 -0.4 23 23
CDC42/GTP/IQGAP1/filamentous actin -0.004 0.037 -9999 0 -0.32 6 6
F11R 0.001 0.083 -9999 0 -0.5 12 12
positive regulation of filopodium formation -0.009 0.048 -9999 0 -0.33 9 9
alphaV/beta3 Integrin/Talin 0.01 0.1 -9999 0 -0.46 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.033 -9999 0 -0.41 3 3
nectin-2(dimer)/I-afadin/I-afadin -0.003 0.033 -9999 0 -0.41 3 3
PIP5K1C 0.024 0.039 -9999 0 -0.38 2 2
VAV2 0.036 0.094 -9999 0 -0.57 9 9
RAP1/GDP -0.011 0.06 -9999 0 -0.42 9 9
ITGAV 0.013 0.029 -9999 0 -0.61 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.009 0.055 -9999 0 -0.37 10 10
nectin-3(dimer)/I-afadin/I-afadin -0.009 0.061 -9999 0 -0.44 9 9
Rac1/GTP -0.011 0.062 -9999 0 -0.43 9 9
PTPRM 0.016 0.043 -9999 0 -0.26 10 10
E-cadherin/beta catenin/alpha catenin -0.069 0.13 -9999 0 -0.6 8 8
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.013 0.047 -9999 0 -10000 0 0
DAPP1 -0.037 0.15 -9999 0 -0.42 36 36
Src family/SYK family/BLNK-LAT/BTK-ITK -0.088 0.22 -9999 0 -0.53 61 61
mol:DAG -0.027 0.11 -9999 0 -0.29 24 24
HRAS 0.014 0.003 -9999 0 -10000 0 0
RAP1A 0.014 0.003 -9999 0 -10000 0 0
ARF5/GDP 0.029 0.059 -9999 0 -0.29 6 6
PLCG2 0.001 0.086 -9999 0 -0.55 11 11
PLCG1 0.014 0 -9999 0 -10000 0 0
ARF5 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.015 0.054 -9999 0 -10000 0 0
ARF1/GTP -0.012 0.044 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
YES1 0.01 0.05 -9999 0 -0.61 3 3
RAP1A/GTP -0.015 0.053 -9999 0 -10000 0 0
ADAP1 -0.03 0.09 -9999 0 -0.48 9 9
ARAP3 -0.015 0.054 -9999 0 -10000 0 0
INPPL1 0.014 0 -9999 0 -10000 0 0
PREX1 0.001 0.09 -9999 0 -0.61 10 10
ARHGEF6 0.008 0.064 -9999 0 -0.61 5 5
ARHGEF7 0.014 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
NRAS 0.014 0.003 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
FGR 0.011 0.041 -9999 0 -0.5 3 3
mol:Ca2+ -0.004 0.058 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.013 0.029 -9999 0 -0.61 1 1
ZAP70 -0.053 0.18 -9999 0 -0.54 56 56
mol:IP3 -0.01 0.077 -9999 0 -0.22 9 9
LYN 0.003 0.078 -9999 0 -0.52 10 10
ARF1/GDP 0.029 0.059 -9999 0 -0.29 6 6
RhoA/GDP -0.015 0.045 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.017 -9999 0 -0.37 1 1
BLNK -0.055 0.19 -9999 0 -0.59 53 53
actin cytoskeleton reorganization 0.043 0.078 -9999 0 -0.38 5 5
SRC 0.014 0 -9999 0 -10000 0 0
PLEKHA2 0.029 0.036 -9999 0 -0.32 5 5
RAC1 0.014 0 -9999 0 -10000 0 0
PTEN 0.001 0.029 -9999 0 -0.58 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.013 0.047 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.049 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.082 0.21 -9999 0 -0.53 53 53
BLK -0.11 0.22 -9999 0 -0.52 104 104
PDPK1 0.013 0.029 -9999 0 -0.61 1 1
CYTH1 -0.014 0.049 -9999 0 -10000 0 0
HCK -0.01 0.11 -9999 0 -0.55 20 20
CYTH3 -0.014 0.049 -9999 0 -10000 0 0
CYTH2 -0.014 0.049 -9999 0 -10000 0 0
KRAS 0.013 0.024 -9999 0 -0.49 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.027 0.084 -9999 0 -0.46 11 11
SGK1 -0.02 0.079 -9999 0 -0.5 11 11
INPP5D 0.008 0.058 -9999 0 -0.54 5 5
mol:GDP 0.022 0.061 -9999 0 -0.31 6 6
SOS1 0.014 0 -9999 0 -10000 0 0
SYK -0.012 0.12 -9999 0 -0.57 21 21
ARF6/GDP -0.015 0.045 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.015 0.054 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.015 0.054 -9999 0 -10000 0 0
VAV1 -0.021 0.14 -9999 0 -0.57 28 28
mol:PI-3-4-P2 0.021 0.043 -9999 0 -0.38 5 5
RAS family/GTP/PI3K Class I 0.017 0.063 -9999 0 -10000 0 0
PLEKHA1 0.025 0.051 -9999 0 -0.3 11 11
Rac1/GDP 0.029 0.059 -9999 0 -0.29 6 6
LAT -0.022 0.14 -9999 0 -0.6 27 27
Rac1/GTP 0.023 0.09 -9999 0 -0.46 10 10
ITK -0.066 0.12 -9999 0 -0.43 20 20
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.044 0.14 -9999 0 -0.39 32 32
LCK -0.089 0.22 -9999 0 -0.55 85 85
BTK -0.024 0.07 -9999 0 -0.43 1 1
p38 MAPK 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
TRAF6/ASK1 0.012 0.034 -10000 0 -0.31 5 5
TRAF2/ASK1 -0.003 0.035 -10000 0 -0.38 4 4
ATM 0.014 0 -10000 0 -10000 0 0
MAP2K3 0.021 0.052 -10000 0 -0.31 2 2
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.021 0.068 -10000 0 -0.45 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.032 0.16 -10000 0 -0.55 38 38
TXN 0.009 0.01 -10000 0 -0.21 1 1
CALM1 0.012 0.037 -10000 0 -0.55 2 2
GADD45A -0.018 0.12 -10000 0 -0.5 29 29
GADD45B -0.027 0.14 -10000 0 -0.53 35 35
MAP3K1 0.009 0.053 -10000 0 -0.5 5 5
MAP3K6 0.007 0.062 -10000 0 -0.5 7 7
MAP3K7 0.014 0 -10000 0 -10000 0 0
MAP3K4 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.009 0.058 -10000 0 -0.38 11 11
TAK1/TAB family 0.001 0.019 0.19 4 -0.18 1 5
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0.014 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.007 0.024 -10000 0 -10000 0 0
TRAF6 0.009 0.018 -10000 0 -0.37 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.075 0.21 -10000 0 -0.55 73 73
CCM2 0.014 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.054 0.13 -10000 0 -0.34 73 73
MAPK11 0.009 0.057 -10000 0 -0.61 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.051 0.12 -10000 0 -0.32 74 74
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 -0.014 0.11 -10000 0 -0.36 40 40
TAOK2 0.019 0 -10000 0 -10000 0 0
TAOK3 0.019 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.014 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.057 -10000 0 -0.61 4 4
MAP3K10 0.006 0.066 -10000 0 -0.5 8 8
MAP3K3 0.014 0 -10000 0 -10000 0 0
TRX/ASK1 0.014 0.04 -10000 0 -0.41 4 4
GADD45/MTK1/MTK1 -0.057 0.13 -10000 0 -0.38 43 43
Canonical NF-kappaB 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
FBXW11 0.018 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.087 0.032 -9999 0 -10000 0 0
ERC1 0.013 0.024 -9999 0 -0.5 1 1
RIP2/NOD2 -0.022 0.091 -9999 0 -0.38 27 27
NFKBIA 0.051 0 -9999 0 -10000 0 0
BIRC2 0.014 0 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
RIPK2 0.014 0 -9999 0 -10000 0 0
IKBKG -0.008 0.034 -9999 0 -10000 0 0
IKK complex/A20 -0.072 0.1 -9999 0 -0.45 6 6
NEMO/A20/RIP2 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
NEMO/ATM 0.047 0.043 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.006 0.026 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.001 0.017 -9999 0 -0.37 1 1
NOD2 -0.018 0.13 -9999 0 -0.54 27 27
NFKB1 0.018 0 -9999 0 -10000 0 0
RELA 0.018 0 -9999 0 -10000 0 0
MALT1 0.014 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.13 0.19 -9999 0 -0.4 149 149
TRAF6 0.013 0.029 -9999 0 -0.61 1 1
PRKCA 0.013 0.029 -9999 0 -0.61 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
UBE2D3 0.014 0 -9999 0 -10000 0 0
TNF -0.16 0.26 -9999 0 -0.55 142 142
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.051 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.018 0 -9999 0 -10000 0 0
TNFRSF1A 0.003 0.079 -9999 0 -0.56 9 9
IKK complex 0.053 0.042 -9999 0 -10000 0 0
CYLD 0.014 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.006 0.028 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.029 -9999 0 -0.3 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.045 0.095 -9999 0 -0.43 11 11
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.003 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.055 0.08 -9999 0 -0.32 21 21
CaM/Ca2+ -0.003 0.025 -9999 0 -0.29 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.034 0.064 -9999 0 -0.33 6 6
AKT1 0.054 0.024 -9999 0 -10000 0 0
MAP2K1 0.048 0.041 -9999 0 -10000 0 0
MAP3K11 0.042 0.027 -9999 0 -0.28 1 1
IFNGR1 0.016 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.14 0.2 -9999 0 -0.47 93 93
Rap1/GTP -0.001 0.014 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0 0.023 -9999 0 -10000 0 0
CEBPB 0.062 0.11 -9999 0 -0.5 10 10
STAT3 0.014 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.005 0.18 -9999 0 -1.1 9 9
STAT1 0.035 0.064 -9999 0 -0.33 6 6
CALM1 0.012 0.037 -9999 0 -0.55 2 2
IFN-gamma (dimer) 0.002 0.046 -9999 0 -0.49 4 4
PIK3CA 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.039 0.068 -9999 0 -0.39 1 1
CEBPB/PTGES2/Cbp/p300 -0.015 0.059 -9999 0 -0.36 7 7
mol:Ca2+ -0.002 0.021 -9999 0 -0.29 1 1
MAPK3 0.056 0.049 -9999 0 -10000 0 0
STAT1 (dimer) -0.073 0.11 -9999 0 -0.47 21 21
MAPK1 0.056 0.049 -9999 0 -10000 0 0
JAK2 0.016 0.002 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.016 0.002 -9999 0 -10000 0 0
CAMK2D 0.013 0.029 -9999 0 -0.61 1 1
DAPK1 0.052 0.13 -9999 0 -0.63 15 15
SMAD7 0.007 0.067 -9999 0 -0.19 4 4
CBL/CRKL/C3G 0.001 0.019 -9999 0 -10000 0 0
PI3K -0.002 0.018 -9999 0 -10000 0 0
IFNG 0.002 0.046 -9999 0 -0.49 4 4
apoptosis 0.032 0.094 -9999 0 -0.45 15 15
CAMK2G 0.013 0.029 -9999 0 -0.61 1 1
STAT3 (dimer) 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.23 0.28 -9999 0 -0.55 205 205
CAMK2B -0.075 0.21 -9999 0 -0.55 73 73
FRAP1 0.052 0.023 -9999 0 -10000 0 0
PRKCD 0.041 0.071 -9999 0 -10000 0 0
RAP1B 0.013 0.024 -9999 0 -0.5 1 1
negative regulation of cell growth -0.055 0.08 -9999 0 -0.32 21 21
PTPN2 0.014 0 -9999 0 -10000 0 0
EP300 0.009 0.058 -9999 0 -0.61 4 4
IRF1 0.034 0.14 -9999 0 -0.53 19 19
STAT1 (dimer)/PIASy 0.041 0.064 -9999 0 -0.39 1 1
SOCS1 -0.049 0.2 -9999 0 -1 13 13
mol:GDP -0.001 0.016 -9999 0 -10000 0 0
CASP1 -0.003 0.091 -9999 0 -0.29 26 26
PTGES2 0.014 0 -9999 0 -10000 0 0
IRF9 0.051 0.049 -9999 0 -0.24 5 5
mol:PI-3-4-5-P3 -0.002 0.017 -9999 0 -10000 0 0
RAP1/GDP -0.001 0.015 -9999 0 -10000 0 0
CBL 0.042 0.026 -9999 0 -10000 0 0
MAP3K1 0.04 0.039 -9999 0 -10000 0 0
PIAS1 0.009 0.057 -9999 0 -0.61 4 4
PIAS4 0.014 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.055 0.08 -9999 0 -0.32 21 21
PTPN11 0.035 0.027 -9999 0 -0.29 1 1
CREBBP 0.015 0.001 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA -0.01 0.057 -9999 0 -0.35 13 13
FBXW11 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.006 0.091 -9999 0 -0.37 21 21
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.083 -9999 0 -0.5 2 2
NFKBIA -0.012 0.094 -9999 0 -0.23 55 55
MAPK14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.029 0 -9999 0 -10000 0 0
ARRB2 0.019 0 -9999 0 -10000 0 0
REL -0.023 0.14 -9999 0 -0.58 29 29
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.052 -9999 0 -0.28 13 13
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.029 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
NFKB1 0.025 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.004 0.09 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.018 0.081 -9999 0 -0.49 2 2
SRC 0.014 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.09 -9999 0 -0.45 2 2
IKBKB 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
SYK -0.012 0.12 -9999 0 -0.57 21 21
I kappa B alpha/PIK3R1 -0.003 0.088 -9999 0 -0.55 2 2
cell death 0.017 0.078 -9999 0 -0.47 2 2
NF kappa B1 p105/c-Rel 0.006 0.091 -9999 0 -0.37 21 21
LCK -0.089 0.22 -9999 0 -0.55 85 85
BCL3 0 0.084 -9999 0 -0.5 13 13
S1P3 pathway

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
PDGFRB 0.011 0.041 -9999 0 -0.5 3 3
mol:S1P 0.002 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.023 0.07 -9999 0 -0.29 19 19
GNAO1 0.008 0.071 -9999 0 -0.61 6 6
S1P/S1P3/G12/G13 0.002 0.093 -9999 0 -0.28 44 44
AKT1 -0.008 0.033 -9999 0 -0.34 1 1
AKT3 0.027 0.14 -9999 0 -1.1 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.041 -9999 0 -0.49 3 3
GNAI2 0.016 0.002 -9999 0 -10000 0 0
GNAI3 0.016 0.002 -9999 0 -10000 0 0
GNAI1 -0.007 0.12 -9999 0 -0.61 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.034 0.16 -9999 0 -0.52 44 44
S1PR2 0.008 0.062 -9999 0 -0.58 5 5
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.017 0.099 -9999 0 -0.48 9 9
MAPK3 0.025 0.095 -9999 0 -0.45 9 9
MAPK1 0.025 0.095 -9999 0 -0.45 9 9
JAK2 0.021 0.1 -9999 0 -0.43 11 11
CXCR4 0.01 0.12 -9999 0 -0.37 24 24
FLT1 0.016 0.03 -9999 0 -0.62 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.025 0.095 -9999 0 -0.45 9 9
S1P/S1P3/Gi 0.017 0.1 -9999 0 -0.49 9 9
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.022 0.077 -9999 0 -0.44 9 9
VEGFA -0.006 0.11 -9999 0 -0.49 21 21
S1P/S1P2/Gi 0.029 0.078 -9999 0 -0.46 6 6
VEGFR1 homodimer/VEGFA homodimer 0.013 0.081 -9999 0 -0.35 22 22
RHOA 0.014 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.012 0.11 -9999 0 -0.3 47 47
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ 0.015 0.029 -9999 0 -0.61 1 1
G12/G13 -0.001 0.02 -9999 0 -0.44 1 1
GNA14 -0.018 0.13 -9999 0 -0.58 25 25
GNA15 -0.01 0.12 -9999 0 -0.58 19 19
GNA12 0.013 0.029 -9999 0 -0.61 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.005 0.076 -9999 0 -0.61 7 7
Rac1/GTP -0.022 0.077 -9999 0 -0.44 9 9
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.003 0.082 0.58 9 -10000 0 9
PI3K Class IB/PDE3B 0.003 0.082 -10000 0 -0.58 9 9
PDE3B 0.003 0.083 -10000 0 -0.58 9 9
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.032 0.089 -10000 0 -0.55 6 6
CLOCK -0.016 0.14 -10000 0 -0.6 25 25
TIMELESS/CRY2 0.025 0.085 -10000 0 -0.65 1 1
DEC1/BMAL1 -0.006 0.06 -10000 0 -0.35 14 14
ATR 0.014 0 -10000 0 -10000 0 0
NR1D1 0.027 0.11 -10000 0 -1.4 2 2
ARNTL 0.014 0.042 -10000 0 -0.5 3 3
TIMELESS 0.025 0.083 -10000 0 -10000 0 0
NPAS2 0.006 0.082 -10000 0 -0.57 9 9
CRY2 0.009 0.057 -10000 0 -0.61 4 4
mol:CO -0.012 0.019 0.081 15 -10000 0 15
CHEK1 0.008 0.058 -10000 0 -0.5 6 6
mol:HEME 0.012 0.019 -10000 0 -0.081 15 15
PER1 0.001 0.09 -10000 0 -0.61 10 10
BMAL/CLOCK/NPAS2 0.014 0.11 -10000 0 -0.37 32 32
BMAL1/CLOCK 0.017 0.13 -10000 0 -0.71 5 5
S phase of mitotic cell cycle 0.032 0.089 -10000 0 -0.55 6 6
TIMELESS/CHEK1/ATR 0.033 0.09 -10000 0 -0.55 6 6
mol:NADPH 0.012 0.019 -10000 0 -0.081 15 15
PER1/TIMELESS 0.021 0.093 -10000 0 -0.65 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.003 0.077 -10000 0 -0.5 11 11
HIF-2-alpha transcription factor network

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
MMP14 -0.052 0.22 -10000 0 -0.9 22 22
oxygen homeostasis 0.008 0.018 -10000 0 -10000 0 0
TCEB2 0.014 0 -10000 0 -10000 0 0
TCEB1 0.014 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.005 0.049 -10000 0 -0.33 4 4
EPO 0.095 0.24 -10000 0 -0.7 14 14
FIH (dimer) 0.022 0.017 -10000 0 -10000 0 0
APEX1 0.021 0.017 -10000 0 -10000 0 0
SERPINE1 0.014 0.34 -10000 0 -0.73 32 32
FLT1 -0.003 0.1 -10000 0 -0.95 4 4
ADORA2A 0.095 0.24 -10000 0 -0.72 13 13
germ cell development 0.078 0.26 -10000 0 -0.71 18 18
SLC11A2 0.097 0.24 -10000 0 -0.73 13 13
BHLHE40 0.086 0.26 -10000 0 -0.78 18 18
HIF1AN 0.022 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.024 0.088 -10000 0 -0.45 9 9
ETS1 0.021 0.077 -10000 0 -0.56 8 8
CITED2 0.002 0.039 -10000 0 -0.45 1 1
KDR -0.009 0.12 -10000 0 -0.75 10 10
PGK1 0.097 0.24 -10000 0 -0.73 13 13
SIRT1 0.015 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.1 0.28 -10000 0 -0.89 14 14
EPAS1 0.07 0.12 -10000 0 -0.38 6 6
SP1 0.019 0.017 -10000 0 -10000 0 0
ABCG2 0.096 0.25 -10000 0 -0.78 13 13
EFNA1 0.096 0.24 -10000 0 -0.73 14 14
FXN 0.096 0.24 -10000 0 -0.72 13 13
POU5F1 0.077 0.27 -10000 0 -0.74 19 19
neuron apoptosis -0.1 0.27 0.84 14 -10000 0 14
EP300 0.009 0.057 -10000 0 -0.61 4 4
EGLN3 0.011 0.084 -10000 0 -0.61 8 8
EGLN2 0.022 0.017 -10000 0 -10000 0 0
EGLN1 0.022 0.017 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.014 0 -10000 0 -10000 0 0
ARNT 0.02 0.031 -10000 0 -0.52 1 1
SLC2A1 0.095 0.24 -10000 0 -0.73 13 13
TWIST1 0.069 0.28 -10000 0 -0.76 23 23
ELK1 0.023 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.024 0.089 -10000 0 -0.45 9 9
VEGFA 0.088 0.26 -10000 0 -0.78 17 17
CREBBP 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.012 0.033 -10000 0 -0.5 2 2
mol:Halofuginone 0.005 0.011 -10000 0 -0.23 1 1
ITGA1 -0.009 0.11 -10000 0 -0.52 20 20
CDKN1A -0.024 0.12 -10000 0 -0.41 24 24
PRL-3/alpha Tubulin -0.003 0.032 -10000 0 -0.35 4 4
mol:Ca2+ -0.017 0.089 0.23 2 -0.44 19 21
AGT -0.011 0.12 -10000 0 -0.6 19 19
CCNA2 -0.057 0.16 -10000 0 -0.53 14 14
TUBA1B 0.014 0 -10000 0 -10000 0 0
EGR1 -0.061 0.17 -10000 0 -0.38 100 100
CDK2/Cyclin E1 -0.014 0.12 -10000 0 -0.41 23 23
MAPK3 0.022 0.034 -10000 0 -0.35 4 4
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.034 -10000 0 -0.35 4 4
PTP4A1 -0.028 0.14 -10000 0 -0.96 1 1
PTP4A3 0.01 0.047 -10000 0 -0.5 4 4
PTP4A2 0.014 0 -10000 0 -10000 0 0
ITGB1 0.02 0.042 -10000 0 -0.35 6 6
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.005 0.062 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.023 0.13 -10000 0 -0.91 1 1
RABGGTA 0.014 0 -10000 0 -10000 0 0
BCAR1 0.001 0.03 0.23 4 -0.46 1 5
RHOC 0.004 0.064 -10000 0 -0.33 2 2
RHOA 0.005 0.062 -10000 0 -0.28 1 1
cell motility 0.008 0.066 -10000 0 -0.3 1 1
PRL-1/alpha Tubulin -0.019 0.13 -10000 0 -0.91 1 1
PRL-3/alpha1 Integrin -0.019 0.084 -10000 0 -0.38 23 23
ROCK1 0.008 0.066 -10000 0 -0.3 1 1
RABGGTB 0.014 0 -10000 0 -10000 0 0
CDK2 -0.001 0.092 -10000 0 -0.54 13 13
mitosis -0.028 0.14 -10000 0 -0.95 1 1
ATF5 0.007 0.062 -10000 0 -0.5 7 7
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.087 0.14 -10000 0 -0.36 71 71
Ran/GTP/Exportin 1/HDAC1 -0.002 0.022 -10000 0 -0.27 3 3
NF kappa B1 p50/RelA/I kappa B alpha -0.035 0.14 -10000 0 -0.52 2 2
SUMO1 0.014 0 -10000 0 -10000 0 0
ZFPM1 0.013 0.029 -10000 0 -0.61 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -10000 0 -10000 0 0
FKBP3 0.014 0 -10000 0 -10000 0 0
Histones -0.039 0.066 -10000 0 -0.44 3 3
YY1/LSF 0.031 0.032 -10000 0 -0.35 1 1
SMG5 0.014 0 -10000 0 -10000 0 0
RAN 0.014 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.042 0.12 -10000 0 -0.45 2 2
I kappa B alpha/HDAC1 -0.024 0.094 -10000 0 -0.39 5 5
SAP18 0.014 0 -10000 0 -10000 0 0
RELA -0.032 0.11 -10000 0 -0.25 71 71
HDAC1/Smad7 -0.002 0.03 -10000 0 -0.37 3 3
RANGAP1 0.014 0 -10000 0 -10000 0 0
HDAC3/TR2 -0.022 0.087 -10000 0 -0.3 2 2
NuRD/MBD3 Complex 0.051 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.1 -10000 0 -0.35 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.006 0.11 -10000 0 -0.58 16 16
GATA1 0.004 0.058 -10000 0 -0.5 6 6
Mad/Max 0 0 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.06 0.027 -10000 0 -10000 0 0
RBBP7 0.014 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
RBBP4 0.014 0 -10000 0 -10000 0 0
MAX 0.014 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
NFKBIA -0.033 0.098 -10000 0 -0.34 2 2
KAT2B 0.013 0.024 -10000 0 -0.5 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.046 0.023 -10000 0 -10000 0 0
SIN3 complex -0.001 0.015 -10000 0 -0.33 1 1
SMURF1 0.014 0 -10000 0 -10000 0 0
CHD3 0.013 0.029 -10000 0 -0.61 1 1
SAP30 0.013 0.029 -10000 0 -0.61 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.013 0.029 -10000 0 -0.61 1 1
YY1/HDAC3 -0.007 0.085 -10000 0 -0.3 3 3
YY1/HDAC2 0.032 0.026 -10000 0 -0.24 4 4
YY1/HDAC1 0.029 0.04 -10000 0 -0.29 7 7
NuRD/MBD2 Complex (MeCP1) 0.051 0.02 -10000 0 -10000 0 0
PPARG -0.092 0.14 -10000 0 -0.36 82 82
HDAC8/hEST1B -0.001 0.017 -10000 0 -0.37 1 1
UBE2I 0.014 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -10000 0 -10000 0 0
TNFRSF1A 0.003 0.079 -10000 0 -0.56 9 9
HDAC3/SMRT (N-CoR2) -0.022 0.087 -10000 0 -0.3 2 2
MBD3L2 0 0.001 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.029 -10000 0 -0.37 3 3
CREBBP 0.014 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.055 0.021 -10000 0 -10000 0 0
HDAC1 0.01 0.05 -10000 0 -0.61 3 3
HDAC3 -0.033 0.098 -10000 0 -0.34 2 2
HDAC2 0.014 0 -10000 0 -10000 0 0
YY1 0.031 0.031 -10000 0 -0.29 4 4
HDAC8 0.013 0.029 -10000 0 -0.61 1 1
SMAD7 0.014 0 -10000 0 -10000 0 0
NCOR2 0.014 0 -10000 0 -10000 0 0
MXD1 0.014 0 -10000 0 -10000 0 0
STAT3 0.025 0.035 -10000 0 -0.35 4 4
NFKB1 0.014 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.014 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.035 0.041 -10000 0 -0.32 4 4
YY1/SAP30/HDAC1 0.035 0.041 -10000 0 -0.32 4 4
EP300 0.009 0.057 -10000 0 -0.61 4 4
STAT3 (dimer non-phopshorylated) 0.025 0.035 -10000 0 -0.35 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.033 0.098 -10000 0 -0.34 2 2
histone deacetylation 0.051 0.02 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.011 0.086 -10000 0 -0.36 2 2
nuclear export 0.001 0.017 0.37 1 -10000 0 1
PRKACA 0.014 0 -10000 0 -10000 0 0
GATAD2B 0.014 0 -10000 0 -10000 0 0
GATAD2A 0.014 0 -10000 0 -10000 0 0
GATA2/HDAC3 -0.033 0.11 -10000 0 -0.39 13 13
GATA1/HDAC1 -0.007 0.053 -10000 0 -0.38 9 9
GATA1/HDAC3 -0.033 0.089 -10000 0 -0.35 3 3
CHD4 0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.13 0.19 -10000 0 -0.4 149 149
SIN3/HDAC complex/Mad/Max 0.051 0.02 -10000 0 -10000 0 0
NuRD Complex 0.06 0.021 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.038 0.065 -10000 0 -0.44 3 3
SIN3B 0.014 0 -10000 0 -10000 0 0
MTA2 0.014 0 -10000 0 -10000 0 0
SIN3A 0.014 0 -10000 0 -10000 0 0
XPO1 0.014 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.031 0.027 -10000 0 -0.3 3 3
HDAC complex -0.002 0.026 -10000 0 -0.33 3 3
GATA1/Fog1 -0.005 0.044 -10000 0 -0.36 7 7
FKBP25/HDAC1/HDAC2 -0.002 0.03 -10000 0 -0.37 3 3
TNF -0.16 0.26 -10000 0 -0.55 142 142
negative regulation of cell growth 0.051 0.02 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.051 0.02 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.045 0.14 -10000 0 -0.34 71 71
SIN3/HDAC complex/NCoR1 0.048 0.022 -10000 0 -10000 0 0
TFCP2 0.013 0.029 -10000 0 -0.61 1 1
NR2C1 0.014 0 -10000 0 -10000 0 0
MBD3 0.014 0 -10000 0 -10000 0 0
MBD2 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.049 0.13 -9999 0 -0.37 61 61
AKT1 0.077 0.079 -9999 0 -0.58 2 2
PTK2B -0.003 0.15 -9999 0 -0.5 20 20
VEGFR2 homodimer/Frs2 0.031 0.074 -9999 0 -0.47 8 8
CAV1 -0.048 0.17 -9999 0 -0.5 56 56
CALM1 0.012 0.037 -9999 0 -0.55 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.019 0.082 -9999 0 -0.67 4 4
endothelial cell proliferation 0.062 0.1 -9999 0 -0.47 4 4
mol:Ca2+ 0.038 0.094 -9999 0 -0.6 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.019 0.084 -9999 0 -0.64 5 5
RP11-342D11.1 0.028 0.093 -9999 0 -0.61 4 4
CDH5 0.011 0.041 -9999 0 -0.5 3 3
VEGFA homodimer -0.012 0.053 -9999 0 -10000 0 0
SHC1 0.009 0.053 -9999 0 -0.5 5 5
SHC2 0.013 0.029 -9999 0 -0.61 1 1
HRAS/GDP -0.019 0.074 -9999 0 -0.53 5 5
SH2D2A -0.074 0.2 -9999 0 -0.54 73 73
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.022 0.073 -9999 0 -0.48 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.06 0.14 -9999 0 -0.6 12 12
VEGFR1 homodimer 0.013 0.029 -9999 0 -0.61 1 1
SHC/GRB2/SOS1 -0.021 0.083 -9999 0 -0.52 8 8
GRB10 0.037 0.1 -9999 0 -0.57 6 6
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB2 0.013 0.024 -9999 0 -0.5 1 1
PAK1 -0.036 0.16 -9999 0 -0.51 45 45
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.019 0.088 -9999 0 -0.71 5 5
HRAS 0.014 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.026 0.081 -9999 0 -0.4 4 4
HIF1A 0.013 0.024 -9999 0 -0.5 1 1
FRS2 0.012 0.037 -9999 0 -0.55 2 2
oxygen and reactive oxygen species metabolic process -0.019 0.083 -9999 0 -0.64 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.004 0.076 -9999 0 -0.53 9 9
Nck/Pak -0.036 0.11 -9999 0 -0.36 46 46
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.018 0.081 -9999 0 -0.67 4 4
mol:GDP -0.021 0.08 -9999 0 -0.51 8 8
mol:NADP 0.062 0.084 -9999 0 -0.41 7 7
eNOS/Hsp90 0.066 0.08 -9999 0 -0.42 4 4
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.095 -9999 0 -0.61 4 4
HIF1A/ARNT -0.001 0.023 -9999 0 -0.35 2 2
SHB 0.014 0 -9999 0 -10000 0 0
VEGFA -0.006 0.11 -9999 0 -0.49 21 21
VEGFC -0.002 0.095 -9999 0 -0.54 14 14
FAK1/Vinculin 0.034 0.12 -9999 0 -0.64 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.048 0.12 -9999 0 -0.52 19 19
PTPN6 -0.003 0.099 -9999 0 -0.56 14 14
EPAS1 0.02 0.053 -9999 0 -0.63 2 2
mol:L-citrulline 0.062 0.084 -9999 0 -0.41 7 7
ITGAV 0.013 0.029 -9999 0 -0.61 1 1
PIK3CA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.018 0.078 -9999 0 -0.63 4 4
VEGFR2 homodimer/VEGFA homodimer -0.023 0.088 -9999 0 -0.66 4 4
VEGFR2/3 heterodimer 0.026 0.094 -9999 0 -0.55 9 9
VEGFB 0.014 0 -9999 0 -10000 0 0
MAPK11 0.039 0.099 -9999 0 -0.6 5 5
VEGFR2 homodimer 0.031 0.08 -9999 0 -0.56 7 7
FLT1 0.013 0.029 -9999 0 -0.61 1 1
NEDD4 0.006 0.077 -9999 0 -0.54 9 9
MAPK3 0.03 0.1 -9999 0 -0.51 5 5
MAPK1 0.03 0.1 -9999 0 -0.51 5 5
VEGFA145/NRP2 -0.023 0.09 -9999 0 -0.37 28 28
VEGFR1/2 heterodimer 0.031 0.073 -9999 0 -0.47 8 8
KDR 0.031 0.08 -9999 0 -0.56 7 7
VEGFA165/NRP1/VEGFR2 homodimer 0.031 0.1 -9999 0 -0.57 5 5
SRC 0.014 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.032 0.1 -9999 0 -0.53 5 5
PI3K 0.064 0.09 -9999 0 -0.6 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.018 0.082 -9999 0 -0.67 4 4
FES 0.036 0.1 -9999 0 -0.59 5 5
GAB1 -0.017 0.077 -9999 0 -0.63 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.018 0.081 -9999 0 -0.67 4 4
CTNNB1 0.014 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
ARNT 0.013 0.024 -9999 0 -0.5 1 1
eNOS/Caveolin-1 0.04 0.12 -9999 0 -0.48 6 6
VEGFR2 homodimer/VEGFA homodimer/Yes -0.02 0.084 -9999 0 -0.67 4 4
PI3K/GAB1 0.078 0.083 -9999 0 -0.55 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.036 0.093 -9999 0 -0.6 5 5
PRKACA 0.014 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.02 0.096 -9999 0 -0.69 6 6
HSP90AA1 0.014 0 -9999 0 -10000 0 0
CDC42 0.038 0.096 -9999 0 -0.62 4 4
actin cytoskeleton reorganization -0.06 0.13 -9999 0 -0.59 12 12
PTK2 0.031 0.12 -9999 0 -0.62 5 5
EDG1 0.028 0.093 -9999 0 -0.61 4 4
mol:DAG 0.038 0.095 -9999 0 -0.61 4 4
CaM/Ca2+ -0.019 0.072 -9999 0 -0.56 4 4
MAP2K3 0.038 0.11 -9999 0 -0.59 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.037 0.1 -9999 0 -0.59 6 6
PLCG1 0.038 0.096 -9999 0 -0.62 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.016 0.075 -9999 0 -0.63 4 4
IQGAP1 0.007 0.062 -9999 0 -0.53 6 6
YES1 0.01 0.05 -9999 0 -0.61 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.018 0.081 -9999 0 -0.67 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.026 0.096 -9999 0 -0.62 6 6
cell migration 0.059 0.12 -9999 0 -0.62 6 6
mol:PI-3-4-5-P3 0.062 0.085 -9999 0 -0.55 3 3
FYN 0.014 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.035 0.089 -9999 0 -0.57 4 4
mol:NO 0.062 0.084 -9999 0 -0.41 7 7
PXN 0.014 0 -9999 0 -10000 0 0
HRAS/GTP -0.019 0.074 -9999 0 -0.53 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.037 0.1 -9999 0 -0.59 6 6
VHL 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.055 0.18 -9999 0 -0.52 60 60
NOS3 0.063 0.091 -9999 0 -0.46 7 7
VEGFR2 homodimer/VEGFA homodimer/Sck -0.018 0.085 -9999 0 -0.66 5 5
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.045 0.091 -9999 0 -0.56 4 4
PRKCB 0.005 0.14 -9999 0 -0.51 16 16
VCL 0.006 0.068 -9999 0 -0.54 7 7
VEGFA165/NRP1 0.028 0.094 -9999 0 -0.61 4 4
VEGFR1/2 heterodimer/VEGFA homodimer -0.018 0.082 -9999 0 -0.67 4 4
VEGFA165/NRP2 -0.023 0.09 -9999 0 -0.37 28 28
MAPKKK cascade 0.059 0.098 -9999 0 -0.57 5 5
NRP2 0.004 0.078 -9999 0 -0.58 8 8
VEGFC homodimer -0.002 0.094 -9999 0 -0.53 14 14
NCK1 0.013 0.029 -9999 0 -0.61 1 1
ROCK1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.037 0.11 -9999 0 -0.61 4 4
MAP3K13 0.031 0.11 -9999 0 -0.6 5 5
PDPK1 0.068 0.079 -9999 0 -0.55 2 2
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.034 0.038 -9999 0 -0.74 1 1
VEGFR1 homodimer/NRP1 0.023 0.038 -9999 0 -0.74 1 1
mol:DAG -0.018 0.13 -9999 0 -0.67 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.013 0.062 -9999 0 -0.69 1 1
CaM/Ca2+ -0.01 0.13 -9999 0 -0.59 2 2
HIF1A 0.021 0.029 -9999 0 -0.41 2 2
GAB1 0.012 0.037 -9999 0 -0.55 2 2
AKT1 0.008 0.12 -9999 0 -0.58 1 1
PLCG1 -0.018 0.13 -9999 0 -0.67 1 1
NOS3 0.008 0.13 -9999 0 -0.49 3 3
CBL 0.014 0 -9999 0 -10000 0 0
mol:NO 0.009 0.12 -9999 0 -0.47 3 3
FLT1 0.032 0.044 -9999 0 -0.84 1 1
PGF -0.091 0.22 -9999 0 -0.56 84 84
VEGFR1 homodimer/NRP2/VEGFR121 0.022 0.083 -9999 0 -0.59 2 2
CALM1 0.012 0.037 -9999 0 -0.55 2 2
PIK3CA 0.014 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.016 0.12 -9999 0 -0.5 2 2
endothelial cell proliferation -0.032 0.16 -9999 0 -0.53 16 16
mol:Ca2+ -0.018 0.13 -9999 0 -0.66 1 1
MAPK3 0.001 0.12 -9999 0 -0.58 1 1
MAPK1 0.001 0.12 -9999 0 -0.58 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
PLGF homodimer -0.091 0.22 -9999 0 -0.56 84 84
PRKACA 0.014 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.048 0.17 -9999 0 -0.5 56 56
VEGFA homodimer -0.009 0.11 -9999 0 -0.49 21 21
VEGFR1 homodimer/VEGFA homodimer 0.02 0.075 -9999 0 -0.74 1 1
platelet activating factor biosynthetic process 0.009 0.12 -9999 0 -0.56 1 1
PI3K -0.05 0.11 -9999 0 -0.64 1 1
PRKCA -0.008 0.12 -9999 0 -0.62 1 1
PRKCB -0.05 0.16 -9999 0 -0.56 15 15
VEGFR1 homodimer/PLGF homodimer -0.033 0.15 -9999 0 -0.37 53 53
VEGFA -0.009 0.11 -9999 0 -0.5 21 21
VEGFB 0.014 0 -9999 0 -10000 0 0
mol:IP3 -0.018 0.13 -9999 0 -0.67 1 1
RASA1 0.042 0.036 -9999 0 -0.67 1 1
NRP2 0.004 0.078 -9999 0 -0.58 8 8
VEGFR1 homodimer 0.031 0.044 -9999 0 -0.83 1 1
VEGFB homodimer 0.014 0 -9999 0 -10000 0 0
NCK1 0.013 0.029 -9999 0 -0.61 1 1
eNOS/Caveolin-1 -0.013 0.14 -9999 0 -0.48 7 7
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.049 0.11 -9999 0 -0.63 1 1
mol:L-citrulline 0.009 0.12 -9999 0 -0.47 3 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.012 0.055 -9999 0 -0.64 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.071 -9999 0 -0.68 1 1
CD2AP 0.014 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.047 0.099 -9999 0 -0.6 1 1
PDPK1 -0.001 0.12 -9999 0 -0.59 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.069 -9999 0 -0.68 1 1
mol:NADP 0.009 0.12 -9999 0 -0.47 3 3
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.012 0.054 -9999 0 -0.63 1 1
VEGFR1 homodimer/NRP2 0.027 0.062 -9999 0 -0.42 7 7
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.01 0.05 -9999 0 -0.61 3 3
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.008 0.054 -9999 0 -0.37 10 10
forebrain development -0.005 0.16 -9999 0 -0.44 37 37
GNAO1 0.006 0.071 -9999 0 -0.61 6 6
SMO/beta Arrestin2 0.016 0.053 -9999 0 -0.44 6 6
SMO 0.006 0.07 -9999 0 -0.61 6 6
ARRB2 0.014 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.04 0.069 -9999 0 -0.61 1 1
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.014 0 -9999 0 -10000 0 0
GNAI2 0.014 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.003 0.02 -9999 0 -0.33 1 1
GNAI1 -0.008 0.12 -9999 0 -0.61 17 17
XPO1 0.016 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.042 0.1 -9999 0 -0.52 11 11
SAP30 0.013 0.029 -9999 0 -0.61 1 1
mol:GDP 0.006 0.07 -9999 0 -0.6 6 6
MIM/GLI2A 0.01 0.063 -9999 0 -0.59 5 5
IFT88 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0.002 -9999 0 -10000 0 0
GLI2 0.044 0.036 -9999 0 -10000 0 0
GLI3 0.034 0.072 -9999 0 -0.64 1 1
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0 -9999 0 -10000 0 0
GNG2 0.009 0.057 -9999 0 -0.61 4 4
Gi family/GTP 0.022 0.074 -9999 0 -0.3 13 13
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.054 0.054 -9999 0 -0.44 1 1
GLI2/Su(fu) 0.056 0.046 -9999 0 -10000 0 0
FOXA2 -0.04 0.14 -9999 0 -0.7 9 9
neural tube patterning -0.005 0.16 -9999 0 -0.44 37 37
SPOP 0.014 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.029 0.042 -9999 0 -0.32 4 4
GNB1 0.014 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
CSNK1G3 0.014 0 -9999 0 -10000 0 0
MTSS1 0.01 0.063 -9999 0 -0.59 5 5
embryonic limb morphogenesis -0.005 0.16 -9999 0 -0.44 37 37
SUFU 0.028 0.029 -9999 0 -10000 0 0
LGALS3 -0.024 0.14 -9999 0 -0.5 34 34
catabolic process 0.064 0.065 -9999 0 -0.5 1 1
GLI3A/CBP -0.017 0.11 -9999 0 -0.35 29 29
KIF3A 0.013 0.029 -9999 0 -0.61 1 1
GLI1 -0.006 0.16 -9999 0 -0.45 37 37
RAB23 0.013 0.029 -9999 0 -0.61 1 1
CSNK1A1 0.014 0 -9999 0 -10000 0 0
IFT172 0.01 0.05 -9999 0 -0.61 3 3
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.011 0.082 -9999 0 -0.43 3 3
GNAZ 0.013 0.029 -9999 0 -0.61 1 1
RBBP4 0.014 0.001 -9999 0 -10000 0 0
CSNK1G1 0.013 0.024 -9999 0 -0.5 1 1
PIAS1 0.009 0.057 -9999 0 -0.61 4 4
PRKACA 0.014 0 -9999 0 -10000 0 0
GLI2/SPOP 0.048 0.033 -9999 0 -10000 0 0
STK36 0.015 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.028 0.076 -9999 0 -0.47 4 4
PTCH1 -0.006 0.19 -9999 0 -0.96 11 11
MIM/GLI1 -0.007 0.18 -9999 0 -0.55 23 23
CREBBP -0.017 0.1 -9999 0 -0.35 29 29
Su(fu)/SIN3/HDAC complex 0.053 0.026 -9999 0 -0.29 1 1
Arf6 downstream pathway

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
PLAUR 0.014 0.13 -10000 0 -1.1 2 2
regulation of axonogenesis -0.005 0.07 0.22 31 -10000 0 31
myoblast fusion -0.003 0.062 0.41 2 -10000 0 2
mol:GTP -0.011 0.036 -10000 0 -0.23 2 2
regulation of calcium-dependent cell-cell adhesion -0.027 0.042 0.35 1 -10000 0 1
ARF1/GTP -0.006 0.023 -10000 0 -10000 0 0
mol:GM1 0.004 0.03 -10000 0 -0.18 2 2
mol:Choline -0.006 0.1 -10000 0 -0.33 39 39
lamellipodium assembly -0.017 0.057 -10000 0 -0.45 2 2
MAPK3 0.017 0.057 -10000 0 -0.34 2 2
ARF6/GTP/NME1/Tiam1 0.027 0.043 -10000 0 -0.35 1 1
ARF1 0.014 0 -10000 0 -10000 0 0
ARF6/GDP 0.003 0.062 -10000 0 -0.42 2 2
ARF1/GDP 0.013 0.057 -10000 0 -0.38 2 2
ARF6 0.007 0.021 -10000 0 -10000 0 0
RAB11A 0.014 0 -10000 0 -10000 0 0
TIAM1 0.014 0.029 -10000 0 -0.61 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.057 -10000 0 -0.34 2 2
actin filament bundle formation -0.012 0.057 0.38 2 -10000 0 2
KALRN -0.018 0.057 -10000 0 -0.24 16 16
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP 0.012 0.057 -10000 0 -0.38 2 2
NME1 0.015 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.012 0.057 -10000 0 -0.38 2 2
substrate adhesion-dependent cell spreading -0.011 0.036 -10000 0 -0.23 2 2
cortical actin cytoskeleton organization -0.017 0.058 -10000 0 -0.45 2 2
RAC1 0.014 0 -10000 0 -10000 0 0
liver development -0.011 0.036 -10000 0 -0.23 2 2
ARF6/GTP -0.011 0.036 -10000 0 -0.23 2 2
RhoA/GTP -0.006 0.023 -10000 0 -10000 0 0
mol:GDP -0.017 0.057 -10000 0 -0.42 2 2
ARF6/GTP/RAB11FIP3/RAB11A -0.004 0.017 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
PLD1 -0.02 0.12 -10000 0 -0.39 39 39
RAB11FIP3 0.014 0 -10000 0 -10000 0 0
tube morphogenesis -0.017 0.057 -10000 0 -0.45 2 2
ruffle organization 0.005 0.07 -10000 0 -0.22 31 31
regulation of epithelial cell migration -0.011 0.036 -10000 0 -0.23 2 2
PLD2 0.015 0.03 -10000 0 -10000 0 0
PIP5K1A 0.005 0.07 -10000 0 -0.22 31 31
mol:Phosphatidic acid -0.006 0.1 -10000 0 -0.33 39 39
Rac1/GTP -0.017 0.058 -10000 0 -0.45 2 2
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.012 0.058 -9999 0 -0.59 1 1
TC10/GTP -0.009 0.051 -9999 0 -0.57 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.003 0.031 -9999 0 -0.31 4 4
HRAS 0.014 0 -9999 0 -10000 0 0
APS homodimer -0.001 0.094 -9999 0 -0.58 12 12
GRB14 -0.18 0.27 -9999 0 -0.54 164 164
FOXO3 -0.025 0.091 -9999 0 -0.59 11 11
AKT1 -0.039 0.13 -9999 0 -0.44 4 4
INSR 0.016 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.037 0.027 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.012 0.037 -9999 0 -0.55 2 2
SORBS1 0.009 0.057 -9999 0 -0.61 4 4
CRK 0.014 0 -9999 0 -10000 0 0
PTPN1 0.036 0.027 -9999 0 -10000 0 0
CAV1 -0.006 0.099 -9999 0 -0.43 6 6
CBL/APS/CAP/Crk-II/C3G -0.01 0.057 -9999 0 -0.62 1 1
Insulin Receptor/Insulin/IRS1/NCK2 -0.003 0.031 -9999 0 -0.31 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.026 -9999 0 -0.29 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.033 -9999 0 -10000 0 0
RPS6KB1 -0.027 0.12 -9999 0 -0.4 4 4
PARD6A 0.014 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.001 0.039 -9999 0 -0.83 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.064 0.091 -9999 0 -0.41 4 4
HRAS/GTP -0.007 0.039 -9999 0 -0.43 1 1
Insulin Receptor 0.016 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.006 0.038 -9999 0 -0.31 1 1
PRKCI -0.023 0.057 -9999 0 -0.56 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.082 0.11 -9999 0 -0.48 4 4
SHC1 0.009 0.053 -9999 0 -0.5 5 5
negative regulation of MAPKKK cascade -0.001 0.037 -9999 0 -0.51 2 2
PI3K -0.003 0.026 -9999 0 -0.3 1 1
NCK2 0.014 0 -9999 0 -10000 0 0
RHOQ 0.014 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 -0.039 0.13 -9999 0 -0.44 4 4
PRKCZ -0.046 0.12 -9999 0 -0.6 20 20
SH2B2 -0.001 0.095 -9999 0 -0.58 12 12
SHC/SHIP 0.029 0.053 -9999 0 -0.35 4 4
F2RL2 -0.098 0.22 -9999 0 -0.52 97 97
TRIP10 0.006 0.07 -9999 0 -0.56 7 7
Insulin Receptor/Insulin/Shc -0.005 0.039 -9999 0 -0.28 8 8
TC10/GTP/CIP4/Exocyst -0.005 0.042 -9999 0 -0.34 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.005 0.035 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
RASA1 0.014 0 -9999 0 -10000 0 0
NCK1 0.013 0.029 -9999 0 -0.61 1 1
CBL/APS/CAP/Crk-II -0.011 0.061 -9999 0 -0.36 12 12
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.007 0.042 -9999 0 -0.31 4 4
INPP5D 0.024 0.048 -9999 0 -0.34 6 6
SOS1 0.014 0 -9999 0 -10000 0 0
SGK1 -0.026 0.14 -9999 0 -0.89 11 11
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.013 0.029 -9999 0 -0.61 1 1
p62DOK/RasGAP -0.001 0.037 -9999 0 -0.52 2 2
INS -0.001 0.054 -9999 0 -0.57 4 4
mol:PI-3-4-P2 0.024 0.047 -9999 0 -0.34 6 6
GRB2 0.013 0.024 -9999 0 -0.5 1 1
EIF4EBP1 -0.034 0.13 -9999 0 -0.43 12 12
PTPRA 0.016 0.002 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 -0.005 0.042 -9999 0 -0.34 7 7
PDPK1 0.013 0.029 -9999 0 -0.61 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.033 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.032 -9999 0 -0.32 4 4
Insulin Receptor/Insulin/IRS3 -0.004 0.038 -9999 0 -0.41 4 4
Par3/Par6 -0.056 0.11 -9999 0 -0.32 28 28
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.02 0.075 -9999 0 -0.37 10 10
PDGFB-D/PDGFRB/SLAP -0.017 0.1 -9999 0 -0.4 30 30
PDGFB-D/PDGFRB/APS/CBL -0.01 0.064 -9999 0 -0.37 12 12
AKT1 0.06 0.036 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.008 0.087 -9999 0 -0.37 10 10
PIK3CA 0.014 0 -9999 0 -10000 0 0
FGR 0.001 0.029 -9999 0 -10000 0 0
mol:Ca2+ 0.018 0.042 -9999 0 -10000 0 0
MYC -0.002 0.19 -9999 0 -0.81 22 22
SHC1 0.009 0.053 -9999 0 -0.5 5 5
HRAS/GDP 0.019 0.028 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.001 0.023 -9999 0 -0.28 1 1
GRB10 0.012 0.037 -9999 0 -0.55 2 2
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 0.018 0.042 -9999 0 -10000 0 0
PTEN 0.013 0.029 -9999 0 -0.61 1 1
GRB2 0.013 0.024 -9999 0 -0.5 1 1
GRB7 -0.031 0.14 -9999 0 -0.5 38 38
PDGFB-D/PDGFRB/SHP2 0.007 0.03 -9999 0 -0.34 3 3
PDGFB-D/PDGFRB/GRB10 0.006 0.04 -9999 0 -0.36 5 5
cell cycle arrest -0.02 0.1 -9999 0 -0.4 30 30
HRAS 0.014 0 -9999 0 -10000 0 0
HIF1A 0.065 0.035 -9999 0 -10000 0 0
GAB1 0.005 0.074 -9999 0 -0.39 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.009 0.075 -9999 0 -0.39 3 3
PDGFB-D/PDGFRB 0.011 0.03 -9999 0 -0.29 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.007 0.03 -9999 0 -0.34 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.026 0.087 -9999 0 -0.42 11 11
positive regulation of MAPKKK cascade 0.005 0.03 -9999 0 -0.34 3 3
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:IP3 0.018 0.043 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.014 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.021 0.1 -9999 0 -0.36 40 40
SHB 0.014 0 -9999 0 -10000 0 0
BLK -0.054 0.13 -9999 0 -0.54 27 27
PTPN2 0.014 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.007 0.03 -9999 0 -0.34 3 3
BCAR1 0.013 0.029 -9999 0 -0.61 1 1
VAV2 0.006 0.089 -9999 0 -0.39 7 7
CBL 0.014 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.006 0.04 -9999 0 -0.36 5 5
LCK -0.058 0.15 -9999 0 -0.53 40 40
PDGFRB 0.011 0.041 -9999 0 -0.5 3 3
ACP1 0.014 0 -9999 0 -10000 0 0
HCK -0.011 0.097 -9999 0 -0.62 10 10
ABL1 0.007 0.063 -9999 0 -0.32 4 4
PDGFB-D/PDGFRB/CBL 0.005 0.071 -9999 0 -0.4 2 2
PTPN1 0.014 0.003 -9999 0 -10000 0 0
SNX15 0.014 0 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
STAT1 -0.002 0.09 -9999 0 -0.5 15 15
cell proliferation 0.002 0.17 -9999 0 -0.7 22 22
SLA -0.02 0.14 -9999 0 -0.55 28 28
actin cytoskeleton reorganization 0.048 0.034 -9999 0 -10000 0 0
SRC 0.002 0.026 -9999 0 -10000 0 0
PI3K -0.004 0.03 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.027 0.093 -9999 0 -0.69 2 2
SH2B2 -0.001 0.095 -9999 0 -0.58 12 12
PLCgamma1/SPHK1 0.008 0.089 -9999 0 -0.38 10 10
LYN -0.002 0.053 -9999 0 -0.64 2 2
LRP1 0.014 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
STAT5B 0.014 0 -9999 0 -10000 0 0
STAT5A 0 0.093 -9999 0 -0.6 11 11
NCK1-2/p130 Cas 0.004 0.031 -9999 0 -10000 0 0
SPHK1 -0.028 0.15 -9999 0 -0.55 35 35
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.018 0.043 -9999 0 -10000 0 0
PLCG1 0.019 0.043 -9999 0 -10000 0 0
NHERF/PDGFRB -0.004 0.042 -9999 0 -0.33 6 6
YES1 -0.001 0.053 -9999 0 -0.56 3 3
cell migration -0.005 0.042 -9999 0 -0.33 6 6
SHC/Grb2/SOS1 0.002 0.041 -9999 0 -0.46 2 2
SLC9A3R2 0.012 0.033 -9999 0 -0.5 2 2
SLC9A3R1 0.01 0.05 -9999 0 -0.61 3 3
NHERF1-2/PDGFRB/PTEN 0.001 0.043 -9999 0 -0.33 4 4
FYN 0.003 0.027 -9999 0 -10000 0 0
DOK1 0.032 0.03 -9999 0 -0.34 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.014 0 -9999 0 -10000 0 0
RAC1 0.01 0.12 -9999 0 -0.43 23 23
PRKCD 0.016 0.082 -9999 0 -0.34 22 22
FER 0.019 0.075 -9999 0 -0.33 18 18
MAPKKK cascade -0.004 0.036 -9999 0 -0.45 2 2
RASA1 0.034 0.025 -9999 0 -10000 0 0
NCK1 0.013 0.029 -9999 0 -0.61 1 1
NCK2 0.014 0 -9999 0 -10000 0 0
p62DOK/Csk 0.022 0.033 -9999 0 -0.3 1 1
PDGFB-D/PDGFRB/SHB 0.007 0.03 -9999 0 -0.34 3 3
chemotaxis 0.007 0.062 -9999 0 -0.31 4 4
STAT1-3-5/STAT1-3-5 -0.014 0.057 -9999 0 -0.44 1 1
Bovine Papilomavirus E5/PDGFRB 0.007 0.03 -9999 0 -0.36 3 3
PTPRJ 0.012 0.037 -9999 0 -0.55 2 2
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.003 0.03 -9999 0 -0.33 4 4
HDAC3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.004 0.039 -9999 0 -0.35 6 6
GATA1/HDAC5 -0.004 0.039 -9999 0 -0.35 6 6
GATA2/HDAC5 -0.014 0.076 -9999 0 -0.42 16 16
HDAC5/BCL6/BCoR -0.001 0.013 -9999 0 -0.28 1 1
HDAC9 0.001 0.087 -9999 0 -0.56 11 11
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -9999 0 -10000 0 0
GATA2 -0.006 0.11 -9999 0 -0.58 16 16
HDAC4/RFXANK -0.001 0.016 -9999 0 -0.35 1 1
BCOR 0.013 0.024 -9999 0 -0.5 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0 -9999 0 -10000 0 0
HDAC5 0.014 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.004 0.041 -9999 0 -0.44 4 4
Histones 0.04 0.031 -9999 0 -10000 0 0
ADRBK1 0.014 0 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.014 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.014 0 -9999 0 -10000 0 0
HDAC6 0.014 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.016 -9999 0 -0.35 1 1
CAMK4 -0.17 0.28 -9999 0 -0.58 145 145
Tubulin/HDAC6 -0.001 0.017 -9999 0 -0.37 1 1
SUMO1 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
GATA1 0.004 0.058 -9999 0 -0.5 6 6
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.034 0 -9999 0 -10000 0 0
SRF 0.014 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.001 0.02 -9999 0 -0.44 1 1
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.016 -9999 0 -0.35 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.11 0.16 -9999 0 -0.35 145 145
HDAC4/ER alpha -0.02 0.088 -9999 0 -0.39 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.04 0.031 -9999 0 -10000 0 0
cell motility -0.001 0.017 -9999 0 -0.37 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.014 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.014 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.015 0.13 -9999 0 -0.55 24 24
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.008 0.11 -9999 0 -0.51 20 20
RAN 0.014 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.01 0.047 -9999 0 -0.3 2 2
GNG2 0.009 0.057 -9999 0 -0.61 4 4
NCOR2 0.014 0 -9999 0 -10000 0 0
TUBB2A 0.013 0.029 -9999 0 -0.61 1 1
HDAC11 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
ANKRA2 0.014 0 -9999 0 -10000 0 0
RFXANK 0.013 0.024 -9999 0 -0.5 1 1
nuclear import -0.032 0 -9999 0 -10000 0 0
FoxO family 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
G6PC 0.012 0.17 -9999 0 -1.4 5 5
PLK1 0.05 0.22 -9999 0 -1.1 7 7
CDKN1B 0.1 0.12 -9999 0 -10000 0 0
FOXO3 0.065 0.16 -9999 0 -0.59 6 6
KAT2B 0.022 0.027 -9999 0 -0.48 1 1
FOXO1/SIRT1 -0.005 0.07 -9999 0 -0.41 5 5
CAT 0.068 0.16 -9999 0 -0.92 2 2
CTNNB1 0.014 0 -9999 0 -10000 0 0
AKT1 0.025 0.017 -9999 0 -10000 0 0
FOXO1 0.026 0.085 -9999 0 -0.35 12 12
MAPK10 0.038 0.036 -9999 0 -0.32 4 4
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
FOXO4 0.097 0.065 -9999 0 -10000 0 0
response to oxidative stress 0.011 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.014 0.14 -9999 0 -0.54 6 6
XPO1 0.015 0.001 -9999 0 -10000 0 0
EP300 0.01 0.058 -9999 0 -0.61 4 4
BCL2L11 0.031 0.1 -9999 0 -1.4 2 2
FOXO1/SKP2 0.024 0.093 -9999 0 -0.41 12 12
mol:GDP 0.011 0.02 -9999 0 -10000 0 0
RAN 0.016 0.001 -9999 0 -10000 0 0
GADD45A 0.082 0.14 -9999 0 -1 1 1
YWHAQ 0.014 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.042 0.073 -9999 0 -0.31 1 1
MST1 -0.021 0.16 -9999 0 -0.57 34 34
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.1 -9999 0 -0.52 1 1
YWHAB 0.014 0 -9999 0 -10000 0 0
MAPK8 0.034 0.054 -9999 0 -0.31 10 10
MAPK9 0.041 0.014 -9999 0 -10000 0 0
YWHAG 0.001 0.081 -9999 0 -0.5 12 12
YWHAE 0.014 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
SIRT1 0.01 0.011 -9999 0 -10000 0 0
SOD2 0.095 0.16 -9999 0 -0.74 2 2
RBL2 0.087 0.12 -9999 0 -10000 0 0
RAL/GDP 0.03 0.017 -9999 0 -10000 0 0
CHUK 0.023 0.014 -9999 0 -10000 0 0
Ran/GTP 0.014 0.005 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
RAL/GTP 0.038 0.019 -9999 0 -10000 0 0
CSNK1G1 0.013 0.024 -9999 0 -0.5 1 1
FASLG 0.001 0.11 -9999 0 -0.36 35 35
SKP2 0.004 0.076 -9999 0 -0.56 8 8
USP7 0.016 0.001 -9999 0 -10000 0 0
IKBKB 0.023 0.014 -9999 0 -10000 0 0
CCNB1 0.058 0.18 -9999 0 -0.73 3 3
FOXO1-3a-4/beta catenin 0.12 0.13 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.092 -9999 0 -0.41 12 12
CSNK1A1 0.014 0 -9999 0 -10000 0 0
SGK1 0.007 0.099 -9999 0 -0.59 12 12
CSNK1G3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.009 -9999 0 -10000 0 0
ZFAND5 0.099 0.058 -9999 0 -10000 0 0
SFN -0.12 0.23 -9999 0 -0.53 109 109
CDK2 -0.001 0.092 -9999 0 -0.54 13 13
FOXO3A/14-3-3 0.022 0.094 -9999 0 -0.44 1 1
CREBBP 0.014 0.013 -9999 0 -10000 0 0
FBXO32 0.057 0.19 -9999 0 -1.1 4 4
BCL6 0.087 0.12 -9999 0 -10000 0 0
RALB 0.016 0.001 -9999 0 -10000 0 0
RALA 0.016 0.001 -9999 0 -10000 0 0
YWHAH -0.01 0.11 -9999 0 -0.5 22 22
Arf6 trafficking events

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
SLC2A4 -0.067 0.2 -9999 0 -0.56 65 65
CLTC 0.031 0.015 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.016 0.046 -9999 0 -10000 0 0
Dynamin 2/GTP 0 0 -9999 0 -10000 0 0
EXOC4 0.014 0 -9999 0 -10000 0 0
CD59 0.026 0.021 -9999 0 -10000 0 0
CPE 0.005 0.076 -9999 0 -0.37 18 18
CTNNB1 0.014 0 -9999 0 -10000 0 0
membrane fusion 0.015 0.049 -9999 0 -10000 0 0
CTNND1 0.035 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.026 -9999 0 -10000 0 0
TSHR -0.12 0.18 -9999 0 -0.34 182 182
INS 0.007 0.044 -9999 0 -0.52 3 3
BIN1 0.014 0 -9999 0 -10000 0 0
mol:Choline 0.015 0.049 -9999 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.021 0 -9999 0 -10000 0 0
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0.021 0.043 -9999 0 -0.3 4 4
ASAP2/amphiphysin II 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 -0.019 0.09 -9999 0 -0.3 11 11
clathrin-independent pinocytosis 0 0 -9999 0 -10000 0 0
MAPK8IP3 0.014 0 -9999 0 -10000 0 0
positive regulation of endocytosis 0 0 -9999 0 -10000 0 0
EXOC2 0.014 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.048 0.006 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.026 0.051 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.021 0 -9999 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -9999 0 -10000 0 0
ACAP1 0.013 0.043 -9999 0 -0.29 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 -0.02 0.085 -9999 0 -0.3 4 4
clathrin heavy chain/ACAP1 0.032 0.03 -9999 0 -10000 0 0
JIP4/KLC1 0 0 -9999 0 -10000 0 0
EXOC1 0.014 0 -9999 0 -10000 0 0
exocyst 0.048 0.006 -9999 0 -10000 0 0
RALA/GTP 0 0 -9999 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -9999 0 -10000 0 0
receptor recycling 0 0 -9999 0 -10000 0 0
CTNNA1 0.035 0 -9999 0 -10000 0 0
NME1 0.021 0 -9999 0 -10000 0 0
clathrin coat assembly 0.031 0.015 -9999 0 -10000 0 0
IL2RA 0.002 0.06 -9999 0 -10000 0 0
VAMP3 0.021 0 -9999 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.038 0.086 -9999 0 -0.28 39 39
EXOC6 0.014 0 -9999 0 -10000 0 0
PLD1 -0.021 0.073 -9999 0 -0.29 31 31
PLD2 0 0 -9999 0 -10000 0 0
EXOC5 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.029 0.026 -9999 0 -10000 0 0
SDC1 0.012 0.049 -9999 0 -10000 0 0
ARF6/GDP 0.02 0 -9999 0 -10000 0 0
EXOC7 0.013 0.024 -9999 0 -0.5 1 1
E-cadherin/beta catenin -0.027 0.053 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.015 0.049 -9999 0 -10000 0 0
endocytosis 0 0 -9999 0 -10000 0 0
SCAMP2 0.014 0 -9999 0 -10000 0 0
ADRB2 0.021 0.077 -9999 0 -0.3 24 24
EXOC3 0.014 0 -9999 0 -10000 0 0
ASAP2 0.014 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0.028 0 -9999 0 -10000 0 0
KLC1 0.014 0 -9999 0 -10000 0 0
AVPR2 0.026 0.056 -9999 0 -0.26 5 5
RALA 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.045 -9999 0 -10000 0 0
IGF1 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
NCK2 0.014 0 -9999 0 -10000 0 0
PTK2 0.014 0 -9999 0 -10000 0 0
CRKL 0.018 0.058 -9999 0 -0.3 12 12
GRB2/SOS1/SHC -0.004 0.032 -9999 0 -0.28 6 6
HRAS 0.014 0 -9999 0 -10000 0 0
IRS1/Crk 0.018 0.058 -9999 0 -0.3 12 12
IGF-1R heterotetramer/IGF1/PTP1B -0.013 0.062 -9999 0 -0.34 12 12
AKT1 0.039 0.053 -9999 0 -10000 0 0
BAD 0.046 0.05 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.018 0.058 -9999 0 -0.3 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.017 0.058 -9999 0 -0.3 12 12
RAF1 0.05 0.05 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.025 0.057 -9999 0 -0.28 12 12
YWHAZ 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.009 0.063 -9999 0 -0.32 13 13
PIK3CA 0.014 0 -9999 0 -10000 0 0
RPS6KB1 0.039 0.053 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.043 0.044 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 -0.001 0.016 -9999 0 -0.35 1 1
HRAS/GTP -0.011 0.049 -9999 0 -0.36 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.013 0.057 -9999 0 -0.44 2 2
IGF-1R heterotetramer 0.011 0.027 -9999 0 -0.48 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.018 0.058 -9999 0 -0.3 12 12
Crk/p130 Cas/Paxillin -0.01 0.046 -9999 0 -10000 0 0
IGF1R 0.011 0.027 -9999 0 -0.48 1 1
IGF1 -0.008 0.11 -9999 0 -0.57 18 18
IRS2/Crk 0.025 0.06 -9999 0 -0.48 1 1
PI3K 0.026 0.055 -9999 0 -0.27 12 12
apoptosis -0.05 0.045 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.016 0.12 -9999 0 -0.56 12 12
RAF1/14-3-3 E 0.054 0.045 -9999 0 -10000 0 0
BAD/14-3-3 0.052 0.047 -9999 0 -10000 0 0
PRKCZ 0.023 0.085 -9999 0 -0.44 2 2
Crk/p130 Cas/Paxillin/FAK1 -0.007 0.034 -9999 0 -10000 0 0
PTPN1 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.024 0.075 -9999 0 -0.4 12 12
BCAR1 0.013 0.029 -9999 0 -0.61 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.015 0.065 -9999 0 -0.44 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
IRS1/NCK2 0.018 0.058 -9999 0 -0.3 12 12
GRB10 0.012 0.037 -9999 0 -0.55 2 2
PTPN11 0.018 0.058 -9999 0 -0.3 12 12
IRS1 0.009 0.063 -9999 0 -0.32 13 13
IRS2 0.017 0.063 -9999 0 -0.31 13 13
IGF-1R heterotetramer/IGF1 0.002 0.086 -9999 0 -0.41 19 19
GRB2 0.013 0.024 -9999 0 -0.5 1 1
PDPK1 0.032 0.055 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKD1 0.032 0.072 -9999 0 -0.38 12 12
SHC1 0.009 0.053 -9999 0 -0.5 5 5
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0.017 -10000 0 -0.35 1 1
BAD/BCL-XL/YWHAZ 0.036 0.013 -10000 0 -10000 0 0
CDKN1B 0.041 0.006 -10000 0 -10000 0 0
CDKN1A 0.007 0.093 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
FOXO3 0.041 0.006 -10000 0 -10000 0 0
AKT1 0 0.005 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
AKT3 0.015 0.051 -10000 0 -0.49 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.04 0.016 -10000 0 -10000 0 0
AKT1/ASK1 -0.003 0.029 -10000 0 -0.31 4 4
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.014 0 -10000 0 -10000 0 0
RAF1 0.014 0 -10000 0 -10000 0 0
JNK cascade 0.003 0.028 0.3 4 -10000 0 4
TSC1 0.041 0.006 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
AKT1/RAF1 0.041 0.006 -10000 0 -10000 0 0
EP300 0.009 0.057 -10000 0 -0.61 4 4
mol:GDP 0.034 0.007 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.041 0.006 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.026 0.015 -10000 0 -0.3 1 1
MAP3K5 0.009 0.057 -10000 0 -0.61 4 4
MAPKAP1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.06 0.28 1 -10000 0 1
YWHAH -0.01 0.11 -10000 0 -0.5 22 22
AKT1S1 0.041 0.006 -10000 0 -10000 0 0
CASP9 0.041 0.013 -10000 0 -10000 0 0
YWHAB 0.014 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.048 0.006 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.017 -10000 0 -0.37 1 1
YWHAE 0.014 0 -10000 0 -10000 0 0
SRC 0.014 0 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.028 0.075 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.002 -10000 0 -10000 0 0
CHUK 0.041 0.006 -10000 0 -10000 0 0
BAD/BCL-XL 0.055 0.013 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.018 0.018 -10000 0 -0.36 1 1
FOXO1-3a-4/14-3-3 family 0.03 0.065 -10000 0 -0.29 1 1
PDPK1 0.013 0.029 -10000 0 -0.61 1 1
MDM2 0.04 0.018 -10000 0 -10000 0 0
MAPKKK cascade -0.04 0.006 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.035 -10000 0 -0.38 1 1
TSC1/TSC2 0.048 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.028 -10000 0 -0.36 1 1
glucose import -0.013 0.12 -10000 0 -0.32 40 40
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.035 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.013 0.12 -10000 0 -0.33 40 40
GSK3A 0.041 0.006 -10000 0 -10000 0 0
FOXO1 0.039 0.025 -10000 0 -10000 0 0
GSK3B 0.041 0.006 -10000 0 -10000 0 0
SFN -0.12 0.23 -10000 0 -0.53 109 109
G1/S transition of mitotic cell cycle 0.048 0.006 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.006 0.087 -10000 0 -0.39 3 3
PRKACA 0.014 0 -10000 0 -10000 0 0
KPNA1 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
YWHAG 0.001 0.081 -10000 0 -0.5 12 12
RHEB 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.004 0.037 -9999 0 -0.48 1 1
NFKB1 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.004 0.038 -9999 0 -0.36 5 5
RELB 0.009 0.055 -9999 0 -0.52 5 5
NFKB2 0.011 0.047 -9999 0 -0.57 3 3
NF kappa B2 p52/RelB -0.006 0.046 -9999 0 -0.37 7 7
regulation of B cell activation -0.006 0.046 -9999 0 -0.37 7 7
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.014 0 -9999 0 -10000 0 0
SMAD2 0.016 0.018 -9999 0 -0.25 1 1
SMAD3 0.044 0.019 -9999 0 -10000 0 0
SMAD3/SMAD4 0.051 0.01 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.015 -9999 0 -10000 0 0
PPM1A 0.014 0 -9999 0 -10000 0 0
CALM1 0.012 0.037 -9999 0 -0.55 2 2
SMAD2/SMAD4 0.023 0.016 -9999 0 -10000 0 0
MAP3K1 0.009 0.053 -9999 0 -0.5 5 5
TRAP-1/SMAD4 -0.013 0.075 -9999 0 -0.44 14 14
MAPK3 0.014 0 -9999 0 -10000 0 0
MAPK1 0.014 0 -9999 0 -10000 0 0
NUP214 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.01 0.047 -9999 0 -0.5 4 4
CTDSPL 0.013 0.029 -9999 0 -0.61 1 1
KPNB1 0.014 0 -9999 0 -10000 0 0
TGFBRAP1 -0.004 0.11 -9999 0 -0.61 14 14
UBE2I 0.014 0 -9999 0 -10000 0 0
NUP153 0.014 0 -9999 0 -10000 0 0
KPNA2 0.012 0.033 -9999 0 -0.5 2 2
PIAS4 0.014 0 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.009 0.057 -10000 0 -0.61 4 4
mol:PIP3 0 0.019 0.29 1 -0.29 1 2
FRAP1 0.017 0.008 -10000 0 -10000 0 0
AKT1 0.031 0.02 0.23 1 -10000 0 1
INSR 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.033 -10000 0 -0.36 4 4
mol:GTP -0.001 0.011 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.003 -10000 0 -10000 0 0
TSC2 0.014 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.01 -10000 0 -10000 0 0
TSC1 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.017 0.017 -10000 0 -0.36 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.014 0 -10000 0 -10000 0 0
RPS6KB1 0.031 0.013 -10000 0 -10000 0 0
MAP3K5 0.008 0.037 -10000 0 -0.39 4 4
PIK3R1 0.014 0 -10000 0 -10000 0 0
apoptosis 0.008 0.037 -10000 0 -0.39 4 4
mol:LY294002 0 0 -10000 0 -0.002 1 1
EIF4B 0.037 0.012 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.01 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.002 0.017 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.026 0.016 -10000 0 -0.32 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.035 0.01 0.17 1 -10000 0 1
FKBP1A 0.015 0 -10000 0 -10000 0 0
RHEB/GTP -0.001 0.01 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.002 1 1
FKBP12/Rapamycin 0.011 0.001 -10000 0 -10000 0 0
PDPK1 -0.001 0.021 0.24 1 -0.28 2 3
EIF4E 0.014 0 -10000 0 -10000 0 0
ASK1/PP5C 0.019 0.059 -10000 0 -0.61 4 4
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.001 0.012 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.002 1 -10000 0 1
RPS6 0.013 0.024 -10000 0 -0.5 1 1
PPP5C 0.014 0 -10000 0 -10000 0 0
EIF4G1 0.014 0 -10000 0 -10000 0 0
IRS1 0.009 0.019 -10000 0 -0.39 1 1
INS -0.005 0.054 -10000 0 -0.58 4 4
PTEN 0.012 0.029 -10000 0 -0.6 1 1
PDK2 -0.001 0.021 0.24 1 -0.28 2 3
EIF4EBP1 -0.006 0.14 -10000 0 -1.1 7 7
PIK3CA 0.014 0 -10000 0 -10000 0 0
PPP2R5D 0.024 0.007 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.031 -10000 0 -0.31 4 4
RHEB 0.014 0 -10000 0 -10000 0 0
EIF4A1 0.014 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -10000 0 1
EEF2 0.016 0.031 -10000 0 -0.31 4 4
eIF4E/4E-BP1 0.003 0.13 -10000 0 -1 7 7
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.01 0.05 -9999 0 -0.61 3 3
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.032 0.017 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.002 0.02 -9999 0 -0.25 3 3
SUMO1 0.014 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.032 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.034 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.031 0.027 -9999 0 -0.3 3 3
RANGAP1 0.014 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.004 0.034 -9999 0 -0.33 4 4
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.024 0 -9999 0 -10000 0 0
Ran/GTP 0.03 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.012 0.033 -9999 0 -0.5 2 2
UBE2I 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.014 0 -9999 0 -10000 0 0
PIAS1 0.009 0.057 -9999 0 -0.61 4 4
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 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
coatomer protein complex 0 0.01 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.023 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.028 0 -9999 0 -10000 0 0
CD4 0.006 0.066 -9999 0 -0.53 7 7
CLTA 0.014 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.012 0.017 -9999 0 -0.36 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.03 0.012 -9999 0 -0.22 1 1
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.015 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP -0.001 0.011 -9999 0 -0.24 1 1
AP2M1 0.014 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.019 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.027 0.013 -9999 0 -0.24 1 1
ARFIP2 0.012 0 -9999 0 -10000 0 0
COPA 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.029 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.03 0.007 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.02 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.037 0.022 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.012 0.017 -9999 0 -0.36 1 1
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.012 0.017 -9999 0 -0.36 1 1
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.038 -9999 0 -0.31 7 7
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 463 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.VW.A7QS TCGA.TQ.A7RW TCGA.TQ.A7RV TCGA.TQ.A7RU
109_MAP3K5 -0.16 0.06 -0.16 -0.22
47_PPARGC1A 0.014 0.014 0.014 0.014
105_BMP4 0.014 0.014 0.014 0.014
105_BMP6 0.014 0.014 0.014 0.014
105_BMP7 0.014 0.014 0.014 0.014
105_BMP2 0.014 0.014 0.014 0.014
131_RELN/VLDLR -0.59 0 0 -0.33
30_TGFB1/TGF beta receptor Type II 0.014 0.014 0.014 0.014
84_STAT5B -0.03 0.12 0.052 -0.08
84_STAT5A -0.18 0.12 0.052 -0.08
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LGG-TP/8100485/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

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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