PARADIGM pathway analysis of mRNASeq expression data
Brain Lower Grade Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1KD1XBH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1KD1XBH
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 69 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
Ephrin A reverse signaling 132
IL23-mediated signaling events 128
FOXM1 transcription factor network 104
TCGA08_retinoblastoma 95
IL12-mediated signaling events 94
Aurora B signaling 86
Effects of Botulinum toxin 78
E-cadherin signaling events 78
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 74
TCR signaling in naïve CD8+ T cells 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 516 . 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 ( 516 ).

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
Ephrin A reverse signaling 0.2558 132 924 7 -0.15 0 1000 -1000 -0.029 -1000
IL23-mediated signaling events 0.2481 128 7699 60 -0.68 0.014 1000 -1000 -0.13 -1000
FOXM1 transcription factor network 0.2016 104 5313 51 -0.41 0.025 1000 -1000 -0.14 -1000
TCGA08_retinoblastoma 0.1841 95 764 8 -0.097 0.075 1000 -1000 -0.023 -1000
IL12-mediated signaling events 0.1822 94 8187 87 -0.56 0.12 1000 -1000 -0.11 -1000
Aurora B signaling 0.1667 86 5811 67 -0.34 0.014 1000 -1000 -0.06 -1000
Effects of Botulinum toxin 0.1512 78 2046 26 -0.2 0.014 1000 -1000 -0.058 -1000
E-cadherin signaling events 0.1512 78 392 5 -0.12 0.014 1000 -1000 -0.038 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1434 74 5098 68 -0.48 0.23 1000 -1000 -0.12 -1000
TCR signaling in naïve CD8+ T cells 0.1318 68 6368 93 -0.21 0.067 1000 -1000 -0.074 -1000
Syndecan-1-mediated signaling events 0.1298 67 2309 34 -0.23 0.014 1000 -1000 -0.053 -1000
Signaling events mediated by the Hedgehog family 0.1298 67 3529 52 -0.19 0.15 1000 -1000 -0.073 -1000
Syndecan-4-mediated signaling events 0.1163 60 4033 67 -0.18 0.037 1000 -1000 -0.078 -1000
Thromboxane A2 receptor signaling 0.1143 59 6235 105 -0.21 0.057 1000 -1000 -0.063 -1000
IL4-mediated signaling events 0.1124 58 5300 91 -0.61 0.44 1000 -1000 -0.15 -1000
Glypican 2 network 0.1085 56 224 4 -0.059 -0.015 1000 -1000 -0.033 -1000
amb2 Integrin signaling 0.1047 54 4443 82 -0.23 0.014 1000 -1000 -0.075 -1000
Reelin signaling pathway 0.1047 54 3069 56 -0.28 0.014 1000 -1000 -0.067 -1000
Aurora C signaling 0.1027 53 371 7 -0.16 0 1000 -1000 -0.041 -1000
a4b1 and a4b7 Integrin signaling 0.1008 52 264 5 -0.077 -0.034 1000 -1000 -0.033 -1000
Signaling events regulated by Ret tyrosine kinase 0.0988 51 4233 82 -0.18 0.014 1000 -1000 -0.08 -1000
Endothelins 0.0988 51 4962 96 -0.19 0.014 1000 -1000 -0.071 -1000
Signaling mediated by p38-alpha and p38-beta 0.0950 49 2161 44 -0.15 0.014 1000 -1000 -0.047 -1000
Visual signal transduction: Cones 0.0930 48 1857 38 -0.15 0.017 1000 -1000 -0.055 -1000
FOXA2 and FOXA3 transcription factor networks 0.0930 48 2229 46 -0.27 0.02 1000 -1000 -0.051 -1000
Glypican 1 network 0.0930 48 2308 48 -0.17 0.03 1000 -1000 -0.045 -1000
Caspase cascade in apoptosis 0.0911 47 3496 74 -0.19 0.043 1000 -1000 -0.043 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0872 45 3856 85 -0.15 0.014 1000 -1000 -0.07 -1000
PDGFR-alpha signaling pathway 0.0833 43 1908 44 -0.17 0.028 1000 -1000 -0.062 -1000
Calcium signaling in the CD4+ TCR pathway 0.0814 42 1321 31 -0.18 0.014 1000 -1000 -0.077 -1000
Visual signal transduction: Rods 0.0814 42 2206 52 -0.2 0.014 1000 -1000 -0.077 -1000
Arf6 signaling events 0.0795 41 2555 62 -0.2 0.014 1000 -1000 -0.057 -1000
Ras signaling in the CD4+ TCR pathway 0.0795 41 707 17 -0.12 0.023 1000 -1000 -0.043 -1000
HIF-1-alpha transcription factor network 0.0775 40 3060 76 -0.19 0.087 1000 -1000 -0.11 -1000
PLK1 signaling events 0.0775 40 3416 85 -0.17 0.041 1000 -1000 -0.039 -1000
Osteopontin-mediated events 0.0756 39 1490 38 -0.13 0.016 1000 -1000 -0.088 -1000
p75(NTR)-mediated signaling 0.0756 39 4897 125 -0.16 0.014 1000 -1000 -0.089 -1000
Glucocorticoid receptor regulatory network 0.0756 39 4474 114 -0.43 0.23 1000 -1000 -0.068 -1000
PLK2 and PLK4 events 0.0736 38 115 3 -0.018 -0.012 1000 -1000 -0.014 -1000
IL1-mediated signaling events 0.0736 38 2378 62 -0.19 0.064 1000 -1000 -0.088 -1000
TCGA08_p53 0.0717 37 259 7 -0.074 0.048 1000 -1000 -0.017 -1000
LPA receptor mediated events 0.0717 37 3869 102 -0.18 0.019 1000 -1000 -0.073 -1000
BCR signaling pathway 0.0717 37 3688 99 -0.17 0.03 1000 -1000 -0.08 -1000
Nongenotropic Androgen signaling 0.0698 36 1889 52 -0.1 0.038 1000 -1000 -0.06 -1000
Wnt signaling 0.0698 36 252 7 -0.033 -0.013 1000 -1000 -0.015 -1000
EGFR-dependent Endothelin signaling events 0.0678 35 741 21 -0.11 0.014 1000 -1000 -0.07 -1000
BMP receptor signaling 0.0659 34 2810 81 -0.18 0.05 1000 -1000 -0.082 -1000
Fc-epsilon receptor I signaling in mast cells 0.0640 33 3250 97 -0.19 0.039 1000 -1000 -0.071 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0640 33 1222 37 -0.14 0.014 1000 -1000 -0.048 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0640 33 2925 88 -0.18 0.019 1000 -1000 -0.1 -1000
Retinoic acid receptors-mediated signaling 0.0620 32 1860 58 -0.19 0.016 1000 -1000 -0.065 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0601 31 1637 52 -0.19 0.027 1000 -1000 -0.051 -1000
Rapid glucocorticoid signaling 0.0601 31 629 20 -0.18 0.014 1000 -1000 -0.038 -1000
ErbB2/ErbB3 signaling events 0.0562 29 1912 65 -0.17 0.023 1000 -1000 -0.061 -1000
Coregulation of Androgen receptor activity 0.0562 29 2263 76 -0.14 0.027 1000 -1000 -0.042 -1000
Syndecan-2-mediated signaling events 0.0562 29 2057 69 -0.16 0.034 1000 -1000 -0.053 -1000
IL6-mediated signaling events 0.0562 29 2236 75 -0.15 0.064 1000 -1000 -0.089 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0543 28 1516 54 -0.16 0.029 1000 -1000 -0.094 -1000
JNK signaling in the CD4+ TCR pathway 0.0543 28 487 17 -0.072 0.014 1000 -1000 -0.056 -1000
FAS signaling pathway (CD95) 0.0543 28 1337 47 -0.15 0.016 1000 -1000 -0.04 -1000
LPA4-mediated signaling events 0.0523 27 327 12 -0.053 0.014 1000 -1000 -0.019 -1000
Presenilin action in Notch and Wnt signaling 0.0523 27 1658 61 -0.28 0.031 1000 -1000 -0.064 -1000
S1P5 pathway 0.0523 27 466 17 -0.13 0.053 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.0523 27 606 22 -0.094 0.019 1000 -1000 -0.046 -1000
Regulation of nuclear SMAD2/3 signaling 0.0504 26 3643 136 -0.22 0.22 1000 -1000 -0.068 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0504 26 886 34 -0.063 0.014 1000 -1000 -0.059 -1000
Ephrin B reverse signaling 0.0504 26 1269 48 -0.1 0.078 1000 -1000 -0.055 -1000
E-cadherin signaling in the nascent adherens junction 0.0504 26 2032 76 -0.12 0.014 1000 -1000 -0.074 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0504 26 3124 120 -0.21 0.13 1000 -1000 -0.071 -1000
Noncanonical Wnt signaling pathway 0.0484 25 675 26 -0.11 0.014 1000 -1000 -0.047 -1000
Syndecan-3-mediated signaling events 0.0465 24 862 35 -0.16 0.014 1000 -1000 -0.05 -1000
Integrins in angiogenesis 0.0465 24 2050 84 -0.093 0.014 1000 -1000 -0.082 -1000
Canonical Wnt signaling pathway 0.0465 24 1236 51 -0.28 0.098 1000 -1000 -0.058 -1000
IL27-mediated signaling events 0.0465 24 1246 51 -0.16 0.018 1000 -1000 -0.081 -1000
Cellular roles of Anthrax toxin 0.0446 23 924 39 -0.16 0.019 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 0.0446 23 1790 76 -0.14 0.02 1000 -1000 -0.065 -1000
IL2 signaling events mediated by PI3K 0.0446 23 1350 58 -0.095 0.032 1000 -1000 -0.079 -1000
Signaling events mediated by HDAC Class III 0.0407 21 842 40 -0.12 0.1 1000 -1000 -0.04 -1000
Paxillin-dependent events mediated by a4b1 0.0388 20 739 36 -0.14 0.031 1000 -1000 -0.065 -1000
TCGA08_rtk_signaling 0.0388 20 536 26 -0.15 0.028 1000 -1000 -0.021 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0388 20 1540 74 -0.16 0.063 1000 -1000 -0.083 -1000
Ceramide signaling pathway 0.0368 19 1511 76 -0.15 0.022 1000 -1000 -0.057 -1000
S1P1 pathway 0.0368 19 694 36 -0.1 0.014 1000 -1000 -0.052 -1000
ErbB4 signaling events 0.0349 18 1282 69 -0.15 0.041 1000 -1000 -0.074 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0349 18 511 28 -0.13 0.024 1000 -1000 -0.031 -1000
Aurora A signaling 0.0349 18 1087 60 -0.14 0.032 1000 -1000 -0.06 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0349 18 1542 83 -0.19 0.053 1000 -1000 -0.061 -1000
EPHB forward signaling 0.0349 18 1574 85 -0.1 0.035 1000 -1000 -0.082 -1000
E-cadherin signaling in keratinocytes 0.0349 18 814 43 -0.12 0.026 1000 -1000 -0.06 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0329 17 788 45 -0.15 0.032 1000 -1000 -0.078 -1000
S1P4 pathway 0.0329 17 428 25 -0.13 0.03 1000 -1000 -0.051 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0329 17 1366 78 -0.062 0.04 1000 -1000 -0.077 -1000
TRAIL signaling pathway 0.0310 16 792 48 -0.046 0.03 1000 -1000 -0.064 -1000
Signaling mediated by p38-gamma and p38-delta 0.0310 16 245 15 -0.026 0.027 1000 -1000 -0.023 -1000
Regulation of Telomerase 0.0310 16 1681 102 -0.14 0.045 1000 -1000 -0.094 -1000
BARD1 signaling events 0.0291 15 860 57 -0.053 0.03 1000 -1000 -0.058 -1000
Insulin-mediated glucose transport 0.0271 14 477 32 -0.11 0.034 1000 -1000 -0.06 -1000
Regulation of p38-alpha and p38-beta 0.0271 14 800 54 -0.11 0.014 1000 -1000 -0.053 -1000
Plasma membrane estrogen receptor signaling 0.0271 14 1285 86 -0.058 0.033 1000 -1000 -0.072 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0271 14 464 33 -0.1 0.041 1000 -1000 -0.061 -1000
ceramide signaling pathway 0.0252 13 673 49 -0.15 0.02 1000 -1000 -0.042 -1000
Regulation of Androgen receptor activity 0.0252 13 919 70 -0.13 0.031 1000 -1000 -0.062 -1000
p38 MAPK signaling pathway 0.0233 12 556 44 -0.072 0.02 1000 -1000 -0.061 -1000
EPO signaling pathway 0.0213 11 635 55 -0.11 0.057 1000 -1000 -0.083 -1000
Nectin adhesion pathway 0.0213 11 735 63 -0.12 0.048 1000 -1000 -0.063 -1000
Class I PI3K signaling events 0.0213 11 818 73 -0.1 0.03 1000 -1000 -0.067 -1000
Canonical NF-kappaB pathway 0.0194 10 404 39 -0.15 0.086 1000 -1000 -0.074 -1000
IFN-gamma pathway 0.0194 10 685 68 -0.23 0.058 1000 -1000 -0.084 -1000
Signaling events mediated by PRL 0.0194 10 347 34 -0.063 0.021 1000 -1000 -0.033 -1000
Circadian rhythm pathway 0.0174 9 207 22 -0.018 0.033 1000 -1000 -0.034 -1000
S1P3 pathway 0.0174 9 383 42 -0.032 0.031 1000 -1000 -0.041 -1000
Class IB PI3K non-lipid kinase events 0.0174 9 27 3 -0.004 0.004 1000 -1000 -0.01 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0155 8 1090 125 -0.073 0.075 1000 -1000 -0.085 -1000
VEGFR1 specific signals 0.0155 8 495 56 -0.092 0.04 1000 -1000 -0.071 -1000
HIF-2-alpha transcription factor network 0.0136 7 335 43 -0.098 0.099 1000 -1000 -0.08 -1000
Signaling events mediated by HDAC Class I 0.0136 7 751 104 -0.15 0.058 1000 -1000 -0.068 -1000
Atypical NF-kappaB pathway 0.0136 7 236 31 -0.081 0.029 1000 -1000 -0.04 -1000
Insulin Pathway 0.0136 7 556 74 -0.18 0.038 1000 -1000 -0.08 -1000
Signaling events mediated by HDAC Class II 0.0116 6 501 75 -0.18 0.038 1000 -1000 -0.062 -1000
Hedgehog signaling events mediated by Gli proteins 0.0116 6 446 65 -0.042 0.064 1000 -1000 -0.064 -1000
FoxO family signaling 0.0116 6 423 64 -0.11 0.12 1000 -1000 -0.048 -1000
PDGFR-beta signaling pathway 0.0116 6 645 97 -0.054 0.063 1000 -1000 -0.078 -1000
Arf6 trafficking events 0.0097 5 424 71 -0.11 0.047 1000 -1000 -0.064 -1000
IGF1 pathway 0.0097 5 329 57 -0.049 0.053 1000 -1000 -0.082 -1000
Arf6 downstream pathway 0.0078 4 197 43 -0.027 0.028 1000 -1000 -0.034 -1000
Class I PI3K signaling events mediated by Akt 0.0078 4 337 68 -0.11 0.054 1000 -1000 -0.055 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0039 2 52 23 -0.014 0.05 1000 -1000 -0.055 -1000
Alternative NF-kappaB pathway 0.0039 2 28 13 -0.005 0.014 1000 -1000 -0.059 -1000
mTOR signaling pathway 0.0019 1 88 53 -0.005 0.036 1000 -1000 -0.055 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 20 27 -0.004 0.036 1000 -1000 -0.052 -1000
Arf1 pathway 0.0000 0 26 54 -0.004 0.037 1000 -1000 -0.038 -1000
Total NA 4075 222217 7203 -20 5.5 131000 -131000 -8.1 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.15 0.22 -9999 0 -0.44 173 173
EFNA5 -0.085 0.22 -9999 0 -0.55 91 91
FYN -0.11 0.22 -9999 0 -0.39 173 173
neuron projection morphogenesis -0.15 0.22 -9999 0 -0.44 173 173
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.15 0.22 -9999 0 -0.44 173 173
EPHA5 -0.14 0.25 -9999 0 -0.55 141 141
IL23-mediated signaling events

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
CCL2 -0.58 0.56 -10000 0 -1.2 212 212
IL23A -0.6 0.56 -10000 0 -1.2 198 198
NF kappa B1 p50/RelA/I kappa B alpha -0.57 0.51 -10000 0 -1.1 209 209
positive regulation of T cell mediated cytotoxicity -0.62 0.62 -10000 0 -1.2 212 212
ITGA3 -0.55 0.52 -10000 0 -1.1 184 184
IL17F -0.35 0.33 -10000 0 -0.71 185 185
IL12B -0.023 0.064 -10000 0 -0.54 6 6
STAT1 (dimer) -0.6 0.59 -10000 0 -1.2 210 210
CD4 -0.53 0.5 -10000 0 -1.1 193 193
IL23 -0.58 0.53 -10000 0 -1.2 199 199
IL23R -0.082 0.084 -10000 0 -0.51 1 1
IL1B -0.64 0.61 -10000 0 -1.3 216 216
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.53 0.5 -10000 0 -1.1 185 185
TYK2 -0.001 0.018 -10000 0 -10000 0 0
STAT4 -0.16 0.26 -10000 0 -0.53 166 166
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.077 0.21 -10000 0 -0.54 85 85
IL12RB1 -0.047 0.16 -10000 0 -0.59 41 41
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
IL12Rbeta1/TYK2 -0.038 0.12 -10000 0 -0.44 41 41
IL23R/JAK2 -0.092 0.1 -10000 0 -0.5 1 1
positive regulation of chronic inflammatory response -0.62 0.62 -10000 0 -1.2 212 212
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 -0.55 0.5 -10000 0 -1.1 199 199
ALOX12B -0.6 0.56 -10000 0 -1.2 218 218
CXCL1 -0.59 0.55 -10000 0 -1.2 204 204
T cell proliferation -0.62 0.62 -10000 0 -1.2 212 212
NFKBIA 0.011 0.003 -10000 0 -10000 0 0
IL17A -0.26 0.26 -10000 0 -0.56 150 150
PI3K -0.58 0.52 -10000 0 -1.1 219 219
IFNG -0.023 0.031 -10000 0 -0.098 19 19
STAT3 (dimer) -0.55 0.48 -10000 0 -1.1 208 208
IL18R1 -0.049 0.18 -10000 0 -0.54 60 60
IL23/IL23R/JAK2/TYK2/SOCS3 -0.32 0.3 -10000 0 -0.63 174 174
IL18/IL18R -0.092 0.21 -10000 0 -0.43 111 111
macrophage activation -0.027 0.018 -10000 0 -0.044 185 185
TNF -0.63 0.6 -10000 0 -1.3 206 206
STAT3/STAT4 -0.64 0.53 -10000 0 -1.1 244 244
STAT4 (dimer) -0.66 0.59 -10000 0 -1.2 237 237
IL18 -0.029 0.15 -10000 0 -0.54 41 41
IL19 -0.53 0.5 -10000 0 -1.1 191 191
STAT5A (dimer) -0.6 0.59 -10000 0 -1.2 209 209
STAT1 -0.001 0.087 -10000 0 -0.49 16 16
SOCS3 -0.11 0.23 -10000 0 -0.52 124 124
CXCL9 -0.62 0.56 -10000 0 -1.2 221 221
MPO -0.62 0.56 -10000 0 -1.2 218 218
positive regulation of humoral immune response -0.62 0.62 -10000 0 -1.2 212 212
IL23/IL23R/JAK2/TYK2 -0.68 0.72 -10000 0 -1.4 212 212
IL6 -0.6 0.56 -10000 0 -1.2 211 211
STAT5A 0.001 0.088 -10000 0 -0.59 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 -0.61 0.56 -10000 0 -1.2 216 216
keratinocyte proliferation -0.62 0.62 -10000 0 -1.2 212 212
NOS2 -0.55 0.53 -10000 0 -1.1 200 200
FOXM1 transcription factor network

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
NFATC3 -0.21 0.64 -10000 0 -1.2 134 134
PLK1 -0.006 0.2 -10000 0 -0.57 39 39
BIRC5 -0.22 0.54 -10000 0 -1 136 136
HSPA1B -0.23 0.66 -10000 0 -1.2 144 144
MAP2K1 0.022 0.056 -10000 0 -0.54 2 2
BRCA2 -0.23 0.67 -10000 0 -1.2 141 141
FOXM1 -0.36 0.92 -10000 0 -1.7 143 143
XRCC1 -0.21 0.64 -10000 0 -1.2 134 134
FOXM1B/p19 -0.38 0.56 0.41 12 -1.2 145 157
Cyclin D1/CDK4 -0.2 0.6 -10000 0 -1.1 143 143
CDC2 -0.23 0.68 -10000 0 -1.2 143 143
TGFA -0.18 0.58 -10000 0 -1 140 140
SKP2 -0.22 0.65 -10000 0 -1.2 136 136
CCNE1 0.012 0.041 -10000 0 -0.5 3 3
CKS1B -0.21 0.64 -10000 0 -1.2 134 134
RB1 -0.17 0.27 -10000 0 -0.73 65 65
FOXM1C/SP1 -0.29 0.75 -10000 0 -1.4 145 145
AURKB -0.27 0.57 -10000 0 -1.5 91 91
CENPF -0.24 0.7 -10000 0 -1.3 137 137
CDK4 0.002 0.091 -10000 0 -0.5 16 16
MYC -0.18 0.57 -10000 0 -1 138 138
CHEK2 0.007 0.11 -10000 0 -0.56 16 16
ONECUT1 -0.22 0.63 -10000 0 -1.1 145 145
CDKN2A -0.1 0.23 -10000 0 -0.56 104 104
LAMA4 -0.21 0.64 -10000 0 -1.2 136 136
FOXM1B/HNF6 -0.3 0.78 -10000 0 -1.4 145 145
FOS -0.3 0.7 -10000 0 -1.2 174 174
SP1 0.014 0.006 -10000 0 -10000 0 0
CDC25B -0.21 0.64 -10000 0 -1.2 134 134
response to radiation 0.008 0.041 -10000 0 -10000 0 0
CENPB -0.21 0.64 -10000 0 -1.2 135 135
CENPA -0.26 0.7 -10000 0 -1.3 143 143
NEK2 -0.28 0.72 -10000 0 -1.3 151 151
HIST1H2BA -0.22 0.64 -10000 0 -1.2 132 132
CCNA2 -0.054 0.19 -10000 0 -0.54 66 66
EP300 0.009 0.053 -10000 0 -0.59 4 4
CCNB1/CDK1 -0.29 0.77 -10000 0 -1.4 143 143
CCNB2 -0.28 0.74 -10000 0 -1.4 148 148
CCNB1 -0.24 0.69 -10000 0 -1.2 143 143
ETV5 -0.23 0.65 -10000 0 -1.2 140 140
ESR1 -0.23 0.65 -10000 0 -1.2 145 145
CCND1 -0.2 0.61 -10000 0 -1.1 145 145
GSK3A 0.025 0.036 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.015 0.16 -10000 0 -0.39 69 69
CDK2 0.001 0.089 -10000 0 -0.54 13 13
G2/M transition of mitotic cell cycle 0.008 0.049 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.41 0.58 -10000 0 -1.3 147 147
GAS1 -0.22 0.65 -10000 0 -1.2 135 135
MMP2 -0.22 0.65 -10000 0 -1.2 136 136
RB1/FOXM1C -0.22 0.64 -10000 0 -1.2 143 143
CREBBP 0.014 0 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.06 0.19 -10000 0 -0.54 69 69
CDKN2C -0.022 0.13 -10000 0 -0.44 46 46
CDKN2A -0.097 0.22 -10000 0 -0.54 104 104
CCND2 0.064 0.14 0.3 109 -0.14 2 111
RB1 -0.068 0.15 -10000 0 -0.32 105 105
CDK4 0.075 0.15 0.34 107 -10000 0 107
CDK6 0.068 0.16 0.34 102 -0.16 15 117
G1/S progression 0.055 0.15 0.32 105 -10000 0 105
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 -0.39 96 96
TBX21 -0.47 0.5 -10000 0 -1 204 204
B2M 0.009 0.05 -10000 0 -0.49 5 5
TYK2 0.001 0.019 -10000 0 -10000 0 0
IL12RB1 -0.045 0.16 -10000 0 -0.58 41 41
GADD45B -0.35 0.39 -10000 0 -0.8 163 163
IL12RB2 -0.13 0.24 -10000 0 -0.54 126 126
GADD45G -0.36 0.41 -10000 0 -0.85 160 160
natural killer cell activation -0.016 0.023 -10000 0 -10000 0 0
RELB 0.009 0.052 -10000 0 -0.51 5 5
RELA 0.014 0 -10000 0 -10000 0 0
IL18 -0.033 0.15 -10000 0 -0.56 41 41
IL2RA -0.063 0.18 -10000 0 -0.5 73 73
IFNG -0.002 0.049 -10000 0 -0.49 5 5
STAT3 (dimer) -0.36 0.36 -10000 0 -0.74 205 205
HLA-DRB5 -0.13 0.24 -10000 0 -0.54 130 130
FASLG -0.44 0.46 -10000 0 -0.94 202 202
NF kappa B2 p52/RelB -0.46 0.43 -10000 0 -0.87 225 225
CD4 0.005 0.062 -10000 0 -0.52 7 7
SOCS1 -0.031 0.15 -10000 0 -0.51 45 45
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D -0.11 0.23 -10000 0 -0.53 115 115
CD3E -0.13 0.24 -10000 0 -0.54 137 137
CD3G -0.034 0.14 -10000 0 -0.5 43 43
IL12Rbeta2/JAK2 -0.097 0.18 -10000 0 -0.4 126 126
CCL3 -0.56 0.58 -10000 0 -1.1 219 219
CCL4 -0.56 0.59 -10000 0 -1.2 206 206
HLA-A 0.005 0.07 -10000 0 -0.49 10 10
IL18/IL18R -0.091 0.22 -10000 0 -0.42 141 141
NOS2 -0.41 0.45 -10000 0 -0.9 187 187
IL12/IL12R/TYK2/JAK2/SPHK2 -0.1 0.15 -10000 0 -0.37 83 83
IL1R1 -0.45 0.48 -10000 0 -1 183 183
IL4 0.019 0.023 -10000 0 -10000 0 0
JAK2 0.001 0.019 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.23 -10000 0 -0.55 88 88
RAB7A -0.28 0.32 -10000 0 -0.7 129 129
lysosomal transport -0.27 0.3 -10000 0 -0.66 129 129
FOS -0.36 0.46 -10000 0 -1 134 134
STAT4 (dimer) -0.42 0.41 -10000 0 -0.82 216 216
STAT5A (dimer) -0.46 0.44 -10000 0 -0.88 229 229
GZMA -0.52 0.54 -10000 0 -1.1 203 203
GZMB -0.5 0.52 -10000 0 -1.1 205 205
HLX -0.002 0.092 -10000 0 -0.52 16 16
LCK -0.51 0.53 -10000 0 -1 231 231
TCR/CD3/MHC II/CD4 -0.16 0.25 -10000 0 -0.5 142 142
IL2/IL2R -0.12 0.21 -10000 0 -0.47 104 104
MAPK14 -0.35 0.39 -10000 0 -0.79 180 180
CCR5 -0.4 0.45 -10000 0 -0.9 181 181
IL1B -0.19 0.27 -10000 0 -0.56 174 174
STAT6 -0.11 0.12 -10000 0 -0.24 87 87
STAT4 -0.16 0.26 -10000 0 -0.53 166 166
STAT3 0.014 0 -10000 0 -10000 0 0
STAT1 -0.001 0.087 -10000 0 -0.49 16 16
NFKB1 0.014 0 -10000 0 -10000 0 0
NFKB2 0.011 0.044 -10000 0 -0.56 3 3
IL12B -0.016 0.06 -10000 0 -0.53 6 6
CD8A -0.077 0.21 -10000 0 -0.55 85 85
CD8B -0.032 0.16 -10000 0 -0.56 42 42
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.12 0.17 0.39 96 -10000 0 96
IL2RB -0.095 0.22 -10000 0 -0.53 103 103
proteasomal ubiquitin-dependent protein catabolic process -0.38 0.36 -10000 0 -0.75 214 214
IL2RG -0.041 0.16 -10000 0 -0.52 53 53
IL12 -0.035 0.11 -10000 0 -0.44 35 35
STAT5A 0.001 0.088 -10000 0 -0.59 11 11
CD247 -0.02 0.13 -10000 0 -0.52 31 31
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 -0.032 0.14 -10000 0 -0.6 29 29
IL12/IL12R/TYK2/JAK2 -0.52 0.57 -10000 0 -1 230 230
MAP2K3 -0.36 0.4 -10000 0 -0.78 190 190
RIPK2 0.014 0 -10000 0 -10000 0 0
MAP2K6 -0.36 0.4 -10000 0 -0.78 189 189
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.09 0.22 -10000 0 -0.54 96 96
IL18RAP -0.081 0.21 -10000 0 -0.55 85 85
IL12Rbeta1/TYK2 -0.034 0.12 -10000 0 -0.43 41 41
EOMES -0.002 0.13 -10000 0 -1.3 1 1
STAT1 (dimer) -0.36 0.35 -10000 0 -0.72 204 204
T cell proliferation -0.31 0.29 -10000 0 -0.61 196 196
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.053 0.18 -10000 0 -0.55 60 60
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.36 0.29 -10000 0 -0.67 202 202
ATF2 -0.33 0.36 -10000 0 -0.74 172 172
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 -0.56 116 116
STMN1 -0.1 0.2 -9999 0 -0.4 158 158
Aurora B/RasGAP/Survivin -0.17 0.28 -9999 0 -0.55 171 171
Chromosomal passenger complex/Cul3 protein complex -0.093 0.2 -9999 0 -0.4 127 127
BIRC5 -0.14 0.26 -9999 0 -0.57 138 138
DES -0.34 0.45 -9999 0 -0.92 167 167
Aurora C/Aurora B/INCENP -0.1 0.17 -9999 0 -0.33 173 173
Aurora B/TACC1 -0.094 0.16 -9999 0 -0.33 157 157
Aurora B/PP2A -0.11 0.19 -9999 0 -0.4 157 157
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.028 0.074 -9999 0 -0.17 92 92
mitotic metaphase/anaphase transition 0 0.006 -9999 0 -10000 0 0
NDC80 -0.2 0.32 -9999 0 -0.6 182 182
Cul3 protein complex -0.008 0.052 -9999 0 -0.36 11 11
KIF2C -0.13 0.27 -9999 0 -0.44 170 170
PEBP1 0.005 0.055 -9999 0 -0.61 4 4
KIF20A -0.17 0.27 -9999 0 -0.55 169 169
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.11 0.19 -9999 0 -0.4 157 157
SEPT1 0.009 0.052 -9999 0 -0.51 5 5
SMC2 0.014 0 -9999 0 -10000 0 0
SMC4 -0.015 0.12 -9999 0 -0.49 30 30
NSUN2/NPM1/Nucleolin -0.16 0.32 -9999 0 -0.83 91 91
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 -0.075 0.15 -9999 0 -0.29 157 157
AURKB -0.16 0.27 -9999 0 -0.56 157 157
AURKC -0.021 0.13 -9999 0 -0.52 34 34
CDCA8 -0.062 0.19 -9999 0 -0.53 70 70
cytokinesis -0.27 0.4 -9999 0 -0.78 172 172
Aurora B/Septin1 -0.24 0.38 -9999 0 -0.75 166 166
AURKA -0.015 0.12 -9999 0 -0.5 29 29
INCENP 0.008 0.029 -9999 0 -0.62 1 1
KLHL13 0.012 0.038 -9999 0 -0.59 2 2
BUB1 -0.11 0.24 -9999 0 -0.55 119 119
hSgo1/Aurora B/Survivin -0.23 0.35 -9999 0 -0.66 186 186
EVI5 0.013 0.003 -9999 0 -10000 0 0
RhoA/GTP -0.24 0.35 -9999 0 -0.7 167 167
SGOL1 -0.12 0.24 -9999 0 -0.54 127 127
CENPA -0.17 0.32 -9999 0 -0.57 165 165
NCAPG -0.14 0.25 -9999 0 -0.55 142 142
Aurora B/HC8 Proteasome -0.11 0.19 -9999 0 -0.4 157 157
NCAPD2 0.009 0.049 -9999 0 -0.49 5 5
Aurora B/PP1-gamma -0.11 0.19 -9999 0 -0.4 157 157
RHOA 0.014 0 -9999 0 -10000 0 0
NCAPH -0.065 0.19 -9999 0 -0.54 74 74
NPM1 -0.13 0.24 -9999 0 -0.62 91 91
RASA1 0.014 0 -9999 0 -10000 0 0
KLHL9 0.004 0.079 -9999 0 -0.59 9 9
mitotic prometaphase -0.006 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.11 0.19 -9999 0 -0.39 157 157
PPP1CC 0.014 0 -9999 0 -10000 0 0
Centraspindlin -0.26 0.39 -9999 0 -0.76 174 174
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.13 0.24 -9999 0 -0.62 91 91
MYLK -0.086 0.16 -9999 0 -0.3 171 171
KIF23 -0.11 0.23 -9999 0 -0.54 113 113
VIM -0.16 0.24 -9999 0 -0.43 214 214
RACGAP1 0.004 0.057 -9999 0 -0.52 6 6
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.13 0.24 -9999 0 -0.62 91 91
Chromosomal passenger complex -0.21 0.38 -9999 0 -0.68 171 171
Chromosomal passenger complex/EVI5 -0.18 0.31 -9999 0 -0.6 161 161
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
Effects of Botulinum toxin

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
STX1A -0.049 0.14 -9999 0 -0.36 85 85
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.093 0.17 -9999 0 -0.4 120 120
STXBP1 -0.014 0.12 -9999 0 -0.5 28 28
ACh/CHRNA1 -0.13 0.17 -9999 0 -0.37 162 162
RAB3GAP2/RIMS1/UNC13B -0.077 0.14 -9999 0 -0.33 120 120
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 -0.12 0.24 -9999 0 -0.56 120 120
mol:ACh -0.038 0.068 -9999 0 -0.13 171 171
RAB3GAP2 0.014 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.14 0.2 -9999 0 -0.45 130 130
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.13 0.17 -9999 0 -0.37 162 162
UNC13B 0.013 0.027 -9999 0 -0.59 1 1
CHRNA1 -0.16 0.26 -9999 0 -0.53 162 162
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.16 0.21 -9999 0 -0.41 200 200
SNAP25 -0.075 0.13 -9999 0 -0.25 168 168
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.2 0.27 -9999 0 -0.54 200 200
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.047 0.16 -9999 0 -0.38 87 87
STX1A/SNAP25 fragment 1/VAMP2 -0.14 0.2 -9999 0 -0.45 130 130
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.083 0.15 -9999 0 -0.32 132 132
E-cadherin/beta catenin -0.093 0.17 -9999 0 -0.38 125 125
CTNNB1 0.014 0 -9999 0 -10000 0 0
JUP 0.003 0.081 -9999 0 -0.57 10 10
CDH1 -0.12 0.24 -9999 0 -0.54 125 125
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.012 0.1 -10000 0 -0.57 12 12
NFATC2 -0.13 0.3 -10000 0 -0.75 74 74
NFATC3 -0.049 0.11 -10000 0 -0.31 12 12
CD40LG -0.38 0.49 -10000 0 -1.1 147 147
ITCH -0.031 0.12 -10000 0 -0.52 3 3
CBLB -0.033 0.13 -10000 0 -0.6 4 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.4 -10000 0 -0.98 106 106
JUNB -0.031 0.15 -10000 0 -0.52 44 44
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.084 0.12 -10000 0 -0.3 90 90
T cell anergy -0.096 0.19 -10000 0 -0.43 96 96
TLE4 -0.08 0.25 -10000 0 -0.7 47 47
Jun/NFAT1-c-4/p21SNFT -0.36 0.46 -10000 0 -1 131 131
AP-1/NFAT1-c-4 -0.46 0.6 -10000 0 -1.3 145 145
IKZF1 -0.091 0.28 -10000 0 -0.75 55 55
T-helper 2 cell differentiation -0.18 0.3 -10000 0 -0.78 66 66
AP-1/NFAT1 -0.17 0.26 -10000 0 -0.59 106 106
CALM1 -0.026 0.088 -10000 0 -0.55 3 3
EGR2 -0.31 0.57 -10000 0 -1.4 83 83
EGR3 -0.34 0.6 -10000 0 -1.2 124 124
NFAT1/FOXP3 -0.12 0.25 -10000 0 -0.66 66 66
EGR1 -0.11 0.23 -10000 0 -0.54 114 114
JUN -0.003 0.077 -10000 0 -0.51 11 11
EGR4 -0.19 0.27 -10000 0 -0.55 187 187
mol:Ca2+ -0.041 0.083 -10000 0 -0.3 1 1
GBP3 -0.16 0.35 -10000 0 -0.79 99 99
FOSL1 -0.093 0.22 -10000 0 -0.53 101 101
NFAT1-c-4/MAF/IRF4 -0.33 0.45 -10000 0 -1 121 121
DGKA -0.073 0.23 -10000 0 -0.64 46 46
CREM 0.012 0.035 -10000 0 -0.54 2 2
NFAT1-c-4/PPARG -0.34 0.46 -10000 0 -1 127 127
CTLA4 -0.12 0.29 -10000 0 -0.7 84 84
NFAT1-c-4 (dimer)/EGR1 -0.38 0.53 -10000 0 -1.1 143 143
NFAT1-c-4 (dimer)/EGR4 -0.43 0.49 -10000 0 -1.1 146 146
FOS -0.1 0.23 -10000 0 -0.56 101 101
IFNG -0.17 0.24 -10000 0 -0.73 51 51
T cell activation -0.17 0.29 -10000 0 -0.8 45 45
MAF 0.011 0.046 -10000 0 -0.59 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.23 0.42 0.98 85 -10000 0 85
TNF -0.48 0.51 -10000 0 -1.1 180 180
FASLG -0.35 0.57 -10000 0 -1.3 117 117
TBX21 -0.044 0.17 -10000 0 -0.53 56 56
BATF3 -0.034 0.16 -10000 0 -0.53 45 45
PRKCQ -0.005 0.11 -10000 0 -0.58 17 17
PTPN1 -0.073 0.23 -10000 0 -0.65 44 44
NFAT1-c-4/ICER1 -0.32 0.46 -10000 0 -1 126 126
GATA3 -0.11 0.23 -10000 0 -0.54 115 115
T-helper 1 cell differentiation -0.16 0.25 -10000 0 -0.72 51 51
IL2RA -0.3 0.34 -10000 0 -0.86 99 99
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.074 0.23 -10000 0 -0.65 44 44
E2F1 -0.01 0.12 -10000 0 -0.52 28 28
PPARG -0.014 0.12 -10000 0 -0.56 25 25
SLC3A2 -0.073 0.23 -10000 0 -0.63 48 48
IRF4 -0.043 0.17 -10000 0 -0.54 53 53
PTGS2 -0.41 0.53 -10000 0 -1.1 153 153
CSF2 -0.37 0.48 -10000 0 -1 142 142
JunB/Fra1/NFAT1-c-4 -0.37 0.47 -10000 0 -1 139 139
IL4 -0.19 0.31 -10000 0 -0.86 57 57
IL5 -0.37 0.48 -10000 0 -1 142 142
IL2 -0.17 0.29 -10000 0 -0.84 40 40
IL3 -0.064 0.064 -10000 0 -0.55 1 1
RNF128 -0.15 0.29 -10000 0 -0.55 172 172
NFATC1 -0.23 0.43 -10000 0 -0.99 84 84
CDK4 0.13 0.24 0.68 27 -0.59 1 28
PTPRK -0.075 0.23 -10000 0 -0.67 44 44
IL8 -0.43 0.53 -10000 0 -1.1 166 166
POU2F1 0.013 0.027 -10000 0 -0.59 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.14 0.18 -10000 0 -0.45 104 104
FYN -0.14 0.27 -10000 0 -0.54 126 126
LAT/GRAP2/SLP76 -0.16 0.22 -10000 0 -0.49 124 124
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.1 0.19 -10000 0 -0.39 116 116
B2M 0.007 0.051 -10000 0 -0.5 5 5
IKBKG -0.034 0.046 -10000 0 -0.15 19 19
MAP3K8 -0.005 0.099 -10000 0 -0.51 19 19
mol:Ca2+ -0.025 0.042 -10000 0 -0.11 98 98
integrin-mediated signaling pathway -0.01 0.058 -10000 0 -0.33 16 16
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.15 0.26 -10000 0 -0.55 124 124
TRPV6 -0.11 0.23 -10000 0 -0.56 105 105
CD28 -0.075 0.2 -10000 0 -0.54 81 81
SHC1 -0.14 0.26 -10000 0 -0.54 123 123
receptor internalization -0.13 0.23 -10000 0 -0.49 114 114
PRF1 -0.17 0.36 -10000 0 -0.96 69 69
KRAS 0.013 0.022 -10000 0 -0.49 1 1
GRB2 0.013 0.022 -10000 0 -0.49 1 1
COT/AKT1 -0.081 0.16 -10000 0 -0.33 106 106
LAT -0.16 0.26 -10000 0 -0.53 130 130
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.11 0.23 -10000 0 -0.53 115 115
CD3E -0.13 0.25 -10000 0 -0.54 137 137
CD3G -0.034 0.14 -10000 0 -0.5 43 43
RASGRP2 -0.006 0.025 -10000 0 -0.18 3 3
RASGRP1 -0.11 0.2 -10000 0 -0.4 117 117
HLA-A 0.002 0.071 -10000 0 -0.5 10 10
RASSF5 -0.003 0.098 -10000 0 -0.55 16 16
RAP1A/GTP/RAPL -0.01 0.058 -10000 0 -0.33 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.015 0.062 -10000 0 -0.12 48 48
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.063 0.08 -10000 0 -0.23 51 51
PRKCA -0.078 0.1 -10000 0 -0.26 84 84
GRAP2 -0.047 0.17 -10000 0 -0.53 58 58
mol:IP3 -0.1 0.19 0.21 50 -0.39 106 156
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.11 0.21 -10000 0 -0.44 116 116
ORAI1 0.067 0.12 0.31 104 -0.36 1 105
CSK -0.15 0.26 -10000 0 -0.54 122 122
B7 family/CD28 -0.21 0.27 -10000 0 -0.59 139 139
CHUK 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.17 0.29 -10000 0 -0.58 138 138
PTPN6 -0.15 0.27 -10000 0 -0.55 131 131
VAV1 -0.16 0.27 -10000 0 -0.56 130 130
Monovalent TCR/CD3 -0.11 0.19 -10000 0 -0.36 170 170
CBL 0.014 0 -10000 0 -10000 0 0
LCK -0.17 0.29 -10000 0 -0.56 146 146
PAG1 -0.15 0.26 -10000 0 -0.54 125 125
RAP1A 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.17 0.29 -10000 0 -0.59 132 132
CD80 -0.046 0.16 -10000 0 -0.51 56 56
CD86 -0.027 0.15 -10000 0 -0.56 36 36
PDK1/CARD11/BCL10/MALT1 -0.077 0.097 -10000 0 -0.27 65 65
HRAS 0.014 0 -10000 0 -10000 0 0
GO:0035030 -0.15 0.25 -10000 0 -0.5 132 132
CD8A -0.08 0.21 -10000 0 -0.55 85 85
CD8B -0.035 0.16 -10000 0 -0.56 42 42
PTPRC -0.042 0.17 -10000 0 -0.54 51 51
PDK1/PKC theta -0.12 0.23 -10000 0 -0.48 110 110
CSK/PAG1 -0.14 0.26 -10000 0 -0.54 112 112
SOS1 0.014 0 -10000 0 -10000 0 0
peptide-MHC class I 0.004 0.071 -10000 0 -0.43 12 12
GRAP2/SLP76 -0.18 0.25 -10000 0 -0.55 129 129
STIM1 0.037 0.061 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.083 -10000 0 -0.18 20 20
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.13 0.25 -10000 0 -0.52 114 114
mol:DAG -0.11 0.15 -10000 0 -0.35 114 114
RAP1A/GDP -0.005 0.027 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
CD247 -0.019 0.13 -10000 0 -0.52 31 31
cytotoxic T cell degranulation -0.16 0.34 -10000 0 -0.9 69 69
RAP1A/GTP -0.004 0.007 -10000 0 -0.067 2 2
mol:PI-3-4-5-P3 -0.13 0.22 -10000 0 -0.45 122 122
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.14 0.23 0.24 41 -0.5 111 152
NRAS 0.014 0 -10000 0 -10000 0 0
ZAP70 -0.046 0.17 -10000 0 -0.53 57 57
GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
LAT/GRAP2/SLP76/VAV1 -0.16 0.21 -10000 0 -0.49 122 122
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.027 -10000 0 -0.59 1 1
CD8 heterodimer -0.083 0.2 -10000 0 -0.46 108 108
CARD11 -0.009 0.11 -10000 0 -0.57 20 20
PRKCB -0.1 0.12 -10000 0 -0.27 118 118
PRKCE -0.082 0.11 -10000 0 -0.26 94 94
PRKCQ -0.15 0.25 -10000 0 -0.53 123 123
LCP2 -0.001 0.086 -10000 0 -0.5 15 15
BCL10 0.014 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.087 0.16 -10000 0 -0.33 114 114
IKK complex -0.01 0.062 -10000 0 -0.11 22 22
RAS family/GDP -0.007 0.009 -10000 0 -10000 0 0
MAP3K14 -0.054 0.13 -10000 0 -0.27 78 78
PDPK1 -0.096 0.18 -10000 0 -0.38 106 106
TCR/CD3/MHC I/CD8/Fyn -0.17 0.3 -10000 0 -0.58 146 146
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.004 0.079 -9999 0 -0.59 9 9
CCL5 -0.086 0.21 -9999 0 -0.53 94 94
SDCBP 0.014 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.13 0.19 -9999 0 -0.48 75 75
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 -0.45 76 76
Syndecan-1/Syntenin -0.12 0.18 -9999 0 -0.45 75 75
MAPK3 -0.095 0.16 -9999 0 -0.47 43 43
HGF/MET -0.17 0.22 -9999 0 -0.43 204 204
TGFB1/TGF beta receptor Type II 0.004 0.079 -9999 0 -0.59 9 9
BSG 0.014 0 -9999 0 -10000 0 0
keratinocyte migration -0.12 0.18 -9999 0 -0.44 77 77
Syndecan-1/RANTES -0.17 0.22 -9999 0 -0.48 122 122
Syndecan-1/CD147 -0.11 0.17 -9999 0 -0.43 75 75
Syndecan-1/Syntenin/PIP2 -0.12 0.16 -9999 0 -0.43 75 75
LAMA5 0.012 0.035 -9999 0 -0.54 2 2
positive regulation of cell-cell adhesion -0.13 0.15 -9999 0 -0.42 75 75
MMP7 -0.16 0.26 -9999 0 -0.54 155 155
HGF -0.079 0.2 -9999 0 -0.51 91 91
Syndecan-1/CASK -0.13 0.18 -9999 0 -0.46 75 75
Syndecan-1/HGF/MET -0.23 0.25 -9999 0 -0.51 181 181
regulation of cell adhesion -0.084 0.16 -9999 0 -0.45 43 43
HPSE -0.052 0.18 -9999 0 -0.56 59 59
positive regulation of cell migration -0.13 0.19 -9999 0 -0.48 75 75
SDC1 -0.14 0.19 -9999 0 -0.48 75 75
Syndecan-1/Collagen -0.13 0.19 -9999 0 -0.48 75 75
PPIB 0.014 0 -9999 0 -10000 0 0
MET -0.15 0.25 -9999 0 -0.54 151 151
PRKACA 0.014 0 -9999 0 -10000 0 0
MMP9 -0.14 0.24 -9999 0 -0.52 144 144
MAPK1 -0.095 0.16 -9999 0 -0.47 43 43
homophilic cell adhesion -0.13 0.18 -9999 0 -0.47 75 75
MMP1 -0.047 0.16 -9999 0 -0.49 56 56
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.1 0.29 -10000 0 -0.72 65 65
IHH -0.014 0.086 -10000 0 -0.51 9 9
SHH Np/Cholesterol/GAS1 -0.069 0.16 -10000 0 -0.32 143 143
LRPAP1 0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.086 0.15 0.31 143 -10000 0 143
SMO/beta Arrestin2 -0.036 0.17 -10000 0 -0.7 16 16
SMO -0.046 0.18 -10000 0 -0.68 20 20
AKT1 0.002 0.083 -10000 0 -0.31 6 6
ARRB2 0.014 0 -10000 0 -10000 0 0
BOC 0.008 0.062 -10000 0 -0.56 6 6
ADRBK1 0.014 0 -10000 0 -10000 0 0
heart looping -0.045 0.18 -10000 0 -0.61 24 24
STIL -0.092 0.22 -10000 0 -0.52 74 74
DHH N/PTCH2 -0.058 0.14 -10000 0 -0.4 74 74
DHH N/PTCH1 -0.069 0.19 -10000 0 -0.54 37 37
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
DHH -0.047 0.17 -10000 0 -0.54 56 56
PTHLH -0.11 0.34 -10000 0 -0.92 63 63
determination of left/right symmetry -0.045 0.18 -10000 0 -0.61 24 24
PIK3R1 0.014 0 -10000 0 -10000 0 0
skeletal system development -0.11 0.34 -10000 0 -0.91 63 63
IHH N/Hhip -0.12 0.21 -10000 0 -0.45 143 143
DHH N/Hhip -0.15 0.21 -10000 0 -0.42 180 180
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.045 0.18 -10000 0 -0.61 24 24
pancreas development -0.14 0.25 -10000 0 -0.55 142 142
HHAT -0.006 0.11 -10000 0 -0.58 18 18
PI3K -0.001 0.019 -10000 0 -0.43 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.014 0.12 -10000 0 -0.5 28 28
somite specification -0.045 0.18 -10000 0 -0.61 24 24
SHH Np/Cholesterol/PTCH1 -0.093 0.21 -10000 0 -0.54 64 64
SHH Np/Cholesterol/PTCH2 -0.067 0.16 -10000 0 -0.31 142 142
SHH Np/Cholesterol/Megalin -0.17 0.22 -10000 0 -0.36 259 259
SHH -0.079 0.19 -10000 0 -0.41 123 123
catabolic process -0.047 0.18 -10000 0 -0.6 26 26
SMO/Vitamin D3 -0.084 0.22 -10000 0 -0.56 54 54
SHH Np/Cholesterol/Hhip -0.14 0.21 -10000 0 -0.42 137 137
LRP2 -0.19 0.27 -10000 0 -0.55 187 187
receptor-mediated endocytosis -0.18 0.22 -10000 0 -0.56 93 93
SHH Np/Cholesterol/BOC -0.057 0.15 -10000 0 -0.31 126 126
SHH Np/Cholesterol/CDO -0.075 0.17 -10000 0 -0.33 148 148
mesenchymal cell differentiation 0.15 0.2 0.41 137 -10000 0 137
mol:Vitamin D3 -0.091 0.22 -10000 0 -0.54 64 64
IHH N/PTCH2 -0.011 0.11 -10000 0 -0.45 25 25
CDON -0.025 0.14 -10000 0 -0.56 35 35
IHH N/PTCH1 -0.047 0.18 -10000 0 -0.6 26 26
Megalin/LRPAP1 -0.14 0.19 -10000 0 -0.39 187 187
PTCH2 -0.009 0.11 -10000 0 -0.56 21 21
SHH Np/Cholesterol -0.075 0.14 -10000 0 -0.32 123 123
PTCH1 -0.047 0.18 -10000 0 -0.6 26 26
HHIP -0.14 0.25 -10000 0 -0.55 142 142
Syndecan-4-mediated signaling events

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0 0.055 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.24 -9999 0 -0.56 100 100
positive regulation of JNK cascade -0.14 0.22 -9999 0 -0.52 108 108
Syndecan-4/ADAM12 -0.17 0.26 -9999 0 -0.54 147 147
CCL5 -0.086 0.21 -9999 0 -0.53 94 94
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
ITGA5 -0.01 0.11 -9999 0 -0.5 24 24
SDCBP 0.014 0 -9999 0 -10000 0 0
PLG 0.001 0.043 -9999 0 -0.48 4 4
ADAM12 -0.07 0.19 -9999 0 -0.5 84 84
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 -0.03 0.043 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.16 0.27 -9999 0 -0.59 119 119
Syndecan-4/CXCL12/CXCR4 -0.13 0.25 -9999 0 -0.55 108 108
Syndecan-4/Laminin alpha3 -0.15 0.26 -9999 0 -0.58 114 114
MDK -0.042 0.17 -9999 0 -0.54 52 52
Syndecan-4/FZD7 -0.16 0.28 -9999 0 -0.6 114 114
Syndecan-4/Midkine -0.16 0.26 -9999 0 -0.56 120 120
FZD7 -0.048 0.18 -9999 0 -0.58 54 54
Syndecan-4/FGFR1/FGF -0.14 0.2 -9999 0 -0.51 102 102
THBS1 -0.09 0.21 -9999 0 -0.51 102 102
integrin-mediated signaling pathway -0.15 0.26 -9999 0 -0.56 121 121
positive regulation of MAPKKK cascade -0.14 0.22 -9999 0 -0.52 108 108
Syndecan-4/TACI -0.14 0.24 -9999 0 -0.56 105 105
CXCR4 -0.013 0.12 -9999 0 -0.54 25 25
cell adhesion 0.021 0.052 -9999 0 -0.26 11 11
Syndecan-4/Dynamin -0.13 0.24 -9999 0 -0.56 100 100
Syndecan-4/TSP1 -0.18 0.26 -9999 0 -0.54 148 148
Syndecan-4/GIPC -0.13 0.24 -9999 0 -0.56 100 100
Syndecan-4/RANTES -0.18 0.26 -9999 0 -0.56 131 131
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
LAMA1 -0.063 0.2 -9999 0 -0.57 68 68
LAMA3 -0.041 0.17 -9999 0 -0.54 51 51
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.037 0.053 -9999 0 -0.53 1 1
Syndecan-4/alpha-Actinin -0.14 0.25 -9999 0 -0.55 120 120
TFPI -0.091 0.21 -9999 0 -0.52 101 101
F2 -0.008 0.069 -9999 0 -0.49 10 10
alpha5/beta1 Integrin -0.017 0.079 -9999 0 -0.36 25 25
positive regulation of cell adhesion -0.18 0.28 -9999 0 -0.59 131 131
ACTN1 -0.021 0.13 -9999 0 -0.5 36 36
TNC -0.049 0.18 -9999 0 -0.54 59 59
Syndecan-4/CXCL12 -0.13 0.24 -9999 0 -0.55 105 105
FGF6 0.001 0.003 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CXCL12 0.003 0.077 -9999 0 -0.54 10 10
TNFRSF13B -0.005 0.072 -9999 0 -0.49 11 11
FGF2 0.011 0.044 -9999 0 -0.56 3 3
FGFR1 0.013 0.027 -9999 0 -0.59 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.24 -9999 0 -0.55 106 106
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0 0.092 -9999 0 -0.48 18 18
cell migration -0.007 0.018 -9999 0 -10000 0 0
PRKCD -0.013 0.13 -9999 0 -0.57 27 27
vasculogenesis -0.17 0.25 -9999 0 -0.52 148 148
SDC4 -0.14 0.25 -9999 0 -0.58 106 106
Syndecan-4/Tenascin C -0.16 0.27 -9999 0 -0.58 121 121
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.24 -9999 0 -0.56 100 100
MMP9 -0.14 0.24 -9999 0 -0.52 144 144
Rac1/GTP 0.021 0.053 -9999 0 -0.26 11 11
cytoskeleton organization -0.12 0.23 -9999 0 -0.53 100 100
GIPC1 0.013 0.022 -9999 0 -0.49 1 1
Syndecan-4/TFPI -0.18 0.26 -9999 0 -0.57 122 122
Thromboxane A2 receptor signaling

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
TGM2 0.008 0.049 -10000 0 -0.49 5 5
GNB1/GNG2 -0.079 0.08 -10000 0 -0.19 153 153
AKT1 -0.06 0.12 -10000 0 -0.21 108 108
EGF -0.05 0.18 -10000 0 -0.56 58 58
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.018 0.07 -10000 0 -0.35 2 2
mol:Ca2+ -0.1 0.16 -10000 0 -0.3 159 159
LYN 0.014 0.079 -10000 0 -0.34 7 7
RhoA/GTP -0.051 0.053 -10000 0 -0.13 52 52
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.12 0.18 -10000 0 -0.35 156 156
GNG2 0.009 0.053 -10000 0 -0.59 4 4
ARRB2 0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.01 0.098 -10000 0 -0.39 24 24
G beta5/gamma2 -0.098 0.1 -10000 0 -0.24 151 151
PRKCH -0.11 0.18 -10000 0 -0.34 154 154
DNM1 -0.1 0.22 -10000 0 -0.52 112 112
TXA2/TP beta/beta Arrestin3 -0.041 0.072 -10000 0 -0.24 30 30
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.039 0.16 -10000 0 -0.5 52 52
G12 family/GTP -0.13 0.13 -10000 0 -0.3 157 157
ADRBK1 0.014 0 -10000 0 -10000 0 0
ADRBK2 0.01 0.051 -10000 0 -0.57 4 4
RhoA/GTP/ROCK1 0.004 0.008 -10000 0 -10000 0 0
mol:GDP 0.057 0.11 0.29 32 -10000 0 32
mol:NADP 0.005 0.071 -10000 0 -0.52 9 9
RAB11A 0.014 0 -10000 0 -10000 0 0
PRKG1 -0.039 0.17 -10000 0 -0.58 46 46
mol:IP3 -0.13 0.19 -10000 0 -0.37 158 158
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.18 0.25 -10000 0 -0.5 156 156
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.038 0.11 -10000 0 -0.35 13 13
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.01 0.088 -10000 0 -0.36 10 10
RHOA 0.014 0 -10000 0 -10000 0 0
PTGIR -0.015 0.12 -10000 0 -0.52 28 28
PRKCB1 -0.12 0.19 -10000 0 -0.36 162 162
GNAQ 0.014 0 -10000 0 -10000 0 0
mol:L-citrulline 0.005 0.071 -10000 0 -0.52 9 9
TXA2/TXA2-R family -0.18 0.26 -10000 0 -0.52 164 164
LCK -0.023 0.12 -10000 0 -0.36 15 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.025 0.066 -10000 0 -0.37 5 5
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.044 -10000 0 -0.75 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.023 0.063 -10000 0 -0.38 4 4
MAPK14 -0.071 0.13 -10000 0 -0.23 145 145
TGM2/GTP -0.14 0.21 -10000 0 -0.42 159 159
MAPK11 -0.074 0.13 -10000 0 -0.24 153 153
ARHGEF1 -0.053 0.097 -10000 0 -0.18 100 100
GNAI2 0.014 0 -10000 0 -10000 0 0
JNK cascade -0.13 0.2 -10000 0 -0.38 165 165
RAB11/GDP 0.015 0.001 -10000 0 -10000 0 0
ICAM1 -0.099 0.16 -10000 0 -0.29 163 163
cAMP biosynthetic process -0.12 0.18 -10000 0 -0.35 162 162
Gq family/GTP/EBP50 0.007 0.083 -10000 0 -0.29 27 27
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.019 0.068 -10000 0 -0.35 2 2
GNB5 0.014 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
EGF/EGFR -0.024 0.11 -10000 0 -0.35 16 16
VCAM1 -0.13 0.19 -10000 0 -0.37 160 160
TP beta/Gq family/GDP/G beta5/gamma2 0.01 0.098 -10000 0 -0.39 24 24
platelet activation -0.094 0.17 -10000 0 -0.3 155 155
PGI2/IP -0.016 0.087 -10000 0 -0.38 28 28
PRKACA -0.01 0.08 -10000 0 -0.29 18 18
Gq family/GDP/G beta5/gamma2 0.009 0.093 -10000 0 -0.36 25 25
TXA2/TP beta/beta Arrestin2 -0.062 0.14 -10000 0 -0.53 35 35
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.005 0.085 -10000 0 -0.31 18 18
mol:DAG -0.14 0.21 -10000 0 -0.41 157 157
EGFR -0.083 0.21 -10000 0 -0.55 89 89
TXA2/TP alpha -0.17 0.24 -10000 0 -0.48 161 161
Gq family/GTP -0.015 0.068 -10000 0 -0.24 38 38
YES1 0.017 0.072 -10000 0 -0.35 2 2
GNAI2/GTP -0.023 0.061 -10000 0 -0.35 5 5
PGD2/DP -0.033 0.11 -10000 0 -0.36 52 52
SLC9A3R1 0.009 0.053 -10000 0 -0.59 4 4
FYN 0.019 0.068 -10000 0 -0.35 2 2
mol:NO 0.005 0.071 -10000 0 -0.52 9 9
GNA15 -0.007 0.11 -10000 0 -0.57 19 19
PGK/cGMP -0.037 0.11 -10000 0 -0.36 54 54
RhoA/GDP 0.015 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.023 0.074 -10000 0 -0.42 6 6
NOS3 0.005 0.071 -10000 0 -0.52 9 9
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.11 0.18 -10000 0 -0.34 150 150
PRKCB -0.14 0.2 -10000 0 -0.38 169 169
PRKCE -0.11 0.18 -10000 0 -0.34 154 154
PRKCD -0.13 0.2 -10000 0 -0.39 159 159
PRKCG -0.17 0.22 -10000 0 -0.42 190 190
muscle contraction -0.17 0.25 -10000 0 -0.48 166 166
PRKCZ -0.12 0.19 -10000 0 -0.35 166 166
ARR3 0.002 0.022 -10000 0 -0.49 1 1
TXA2/TP beta -0.025 0.069 -10000 0 -0.39 5 5
PRKCQ -0.12 0.18 -10000 0 -0.35 163 163
MAPKKK cascade -0.16 0.23 -10000 0 -0.44 161 161
SELE -0.12 0.18 -10000 0 -0.33 181 181
TP beta/GNAI2/GDP/G beta/gamma -0.021 0.067 -10000 0 -0.37 5 5
ROCK1 0.014 0 -10000 0 -10000 0 0
GNA14 -0.014 0.12 -10000 0 -0.56 25 25
chemotaxis -0.21 0.3 -10000 0 -0.59 168 168
GNA12 0.013 0.027 -10000 0 -0.59 1 1
GNA13 0.014 0 -10000 0 -10000 0 0
GNA11 0.004 0.079 -10000 0 -0.59 9 9
Rac1/GTP 0.004 0.005 -10000 0 -10000 0 0
IL4-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
BCL2L1 -0.39 0.43 -10000 0 -1.1 80 80
STAT6 (cleaved dimer) -0.47 0.43 -10000 0 -1 144 144
IGHG1 -0.16 0.21 -10000 0 -0.69 25 25
IGHG3 -0.39 0.41 -10000 0 -1 111 111
AKT1 -0.24 0.29 -10000 0 -0.77 64 64
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.84 59 59
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.26 -10000 0 -0.72 50 50
THY1 -0.41 0.46 -10000 0 -1.2 81 81
MYB -0.065 0.2 -10000 0 -0.54 73 73
HMGA1 0.01 0.047 -10000 0 -0.52 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.34 -10000 0 -0.83 106 106
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.27 -10000 0 -0.74 50 50
SP1 0.02 0.01 -10000 0 -10000 0 0
INPP5D 0.008 0.06 -10000 0 -0.54 6 6
SOCS5 0.027 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.45 0.45 -10000 0 -1.1 128 128
SOCS1 -0.3 0.33 -10000 0 -0.82 77 77
SOCS3 -0.35 0.41 -10000 0 -0.99 110 110
FCER2 -0.42 0.44 -10000 0 -1.1 104 104
PARP14 -0.002 0.084 -10000 0 -0.52 13 13
CCL17 -0.4 0.44 -10000 0 -1.1 85 85
GRB2 0.013 0.022 -10000 0 -0.49 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.23 -10000 0 -0.66 46 46
T cell proliferation -0.41 0.45 -10000 0 -1.1 96 96
IL4R/JAK1 -0.4 0.43 -10000 0 -1.1 84 84
EGR2 -0.52 0.55 -10000 0 -1.3 116 116
JAK2 -0.004 0.027 -10000 0 -10000 0 0
JAK3 -0.058 0.18 -10000 0 -0.53 68 68
PIK3R1 0.014 0 -10000 0 -10000 0 0
JAK1 0.005 0.012 -10000 0 -10000 0 0
COL1A2 -0.16 0.24 -10000 0 -0.75 39 39
CCL26 -0.4 0.44 -10000 0 -1.1 82 82
IL4R -0.42 0.46 -10000 0 -1.2 83 83
PTPN6 0.007 0.099 -10000 0 -0.54 16 16
IL13RA2 -0.61 0.58 -10000 0 -1.3 179 179
IL13RA1 -0.015 0.084 -10000 0 -0.61 9 9
IRF4 -0.18 0.33 -10000 0 -1.2 40 40
ARG1 -0.13 0.23 -10000 0 -0.9 24 24
CBL -0.3 0.32 -10000 0 -0.8 96 96
GTF3A 0.009 0.033 -10000 0 -10000 0 0
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
IL13RA1/JAK2 -0.015 0.07 -10000 0 -0.45 9 9
IRF4/BCL6 -0.15 0.31 -10000 0 -1.1 38 38
CD40LG -0.035 0.15 -10000 0 -0.5 46 46
MAPK14 -0.32 0.35 -10000 0 -0.83 115 115
mitosis -0.23 0.27 -10000 0 -0.73 63 63
STAT6 -0.45 0.5 -10000 0 -1.2 99 99
SPI1 -0.004 0.11 -10000 0 -0.54 19 19
RPS6KB1 -0.21 0.26 -10000 0 -0.7 60 60
STAT6 (dimer) -0.45 0.5 -10000 0 -1.2 99 99
STAT6 (dimer)/PARP14 -0.43 0.47 -10000 0 -1.2 101 101
mast cell activation 0.011 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.27 0.32 -10000 0 -0.83 78 78
FRAP1 -0.24 0.29 -10000 0 -0.77 64 64
LTA -0.43 0.49 -10000 0 -1.2 92 92
FES 0.01 0.047 -10000 0 -0.52 4 4
T-helper 1 cell differentiation 0.44 0.48 1.2 99 -10000 0 99
CCL11 -0.39 0.42 -10000 0 -1.1 88 88
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.25 0.3 -10000 0 -0.83 66 66
IL2RG -0.041 0.16 -10000 0 -0.52 53 53
IL10 -0.5 0.56 -10000 0 -1.3 126 126
IRS1 0.014 0 -10000 0 -10000 0 0
IRS2 0.012 0.035 -10000 0 -0.54 2 2
IL4 -0.097 0.11 -10000 0 -10000 0 0
IL5 -0.4 0.43 -10000 0 -1.1 75 75
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.33 0.35 -10000 0 -0.86 83 83
COL1A1 -0.35 0.5 -10000 0 -1.4 83 83
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.44 -10000 0 -1.2 70 70
IL2R gamma/JAK3 -0.073 0.19 -10000 0 -0.44 101 101
TFF3 -0.41 0.45 -10000 0 -1.2 82 82
ALOX15 -0.4 0.44 -10000 0 -1.1 91 91
MYBL1 0.01 0.044 -10000 0 -0.49 4 4
T-helper 2 cell differentiation -0.36 0.37 -10000 0 -0.9 105 105
SHC1 0.009 0.049 -10000 0 -0.49 5 5
CEBPB -0.003 0.11 -10000 0 -0.57 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.26 -10000 0 -0.7 52 52
mol:PI-3-4-5-P3 -0.24 0.29 -10000 0 -0.77 64 64
PI3K -0.25 0.31 -10000 0 -0.84 63 63
DOK2 -0.07 0.2 -10000 0 -0.53 80 80
ETS1 0.014 0.08 -10000 0 -0.52 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.17 0.22 -10000 0 -0.63 45 45
ITGB3 -0.43 0.48 -10000 0 -1.2 102 102
PIGR -0.5 0.55 -10000 0 -1.4 111 111
IGHE 0.021 0.062 -10000 0 -0.26 12 12
MAPKKK cascade -0.17 0.22 -10000 0 -0.61 45 45
BCL6 0.016 0.006 -10000 0 -10000 0 0
OPRM1 -0.41 0.44 -10000 0 -1.1 82 82
RETNLB -0.4 0.43 -10000 0 -1.1 82 82
SELP -0.41 0.44 -10000 0 -1.2 78 78
AICDA -0.38 0.42 -10000 0 -1.1 86 86
Glypican 2 network

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
MDK -0.042 0.17 -9999 0 -0.54 52 52
GPC2 -0.015 0.13 -9999 0 -0.57 26 26
GPC2/Midkine -0.059 0.15 -9999 0 -0.42 73 73
neuron projection morphogenesis -0.059 0.15 -9999 0 -0.42 73 73
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.077 0.17 -9999 0 -0.45 78 78
alphaM/beta2 Integrin/GPIbA -0.073 0.16 -9999 0 -0.45 72 72
alphaM/beta2 Integrin/proMMP-9 -0.15 0.21 -9999 0 -0.4 182 182
PLAUR -0.02 0.13 -9999 0 -0.5 35 35
HMGB1 -0.001 0.022 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.062 0.16 -9999 0 -0.48 56 56
AGER -0.029 0.13 -9999 0 -0.6 24 24
RAP1A 0.014 0 -9999 0 -10000 0 0
SELPLG -0.023 0.14 -9999 0 -0.58 32 32
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.18 -9999 0 -0.46 85 85
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.14 0.24 -9999 0 -0.52 144 144
CYR61 -0.099 0.23 -9999 0 -0.55 104 104
TLN1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP -0.088 0.13 -9999 0 -0.39 51 51
RHOA 0.014 0 -9999 0 -10000 0 0
P-selectin oligomer -0.027 0.13 -9999 0 -0.49 38 38
MYH2 -0.085 0.15 -9999 0 -0.39 61 61
MST1R 0.006 0.069 -9999 0 -0.58 7 7
leukocyte activation during inflammatory response -0.11 0.18 -9999 0 -0.39 116 116
APOB -0.074 0.2 -9999 0 -0.55 80 80
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.012 0.12 -9999 0 -0.54 25 25
JAM3 0.014 0 -9999 0 -10000 0 0
GP1BA -0.004 0.1 -9999 0 -0.57 16 16
alphaM/beta2 Integrin/CTGF -0.086 0.18 -9999 0 -0.44 89 89
alphaM/beta2 Integrin -0.096 0.16 -9999 0 -0.42 70 70
JAM3 homodimer 0.014 0 -9999 0 -10000 0 0
ICAM2 0.013 0.022 -9999 0 -0.49 1 1
ICAM1 -0.026 0.14 -9999 0 -0.51 40 40
phagocytosis triggered by activation of immune response cell surface activating receptor -0.095 0.16 -9999 0 -0.41 70 70
cell adhesion -0.073 0.16 -9999 0 -0.45 72 72
NFKB1 -0.16 0.26 -9999 0 -0.63 80 80
THY1 -0.004 0.1 -9999 0 -0.56 16 16
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.07 0.14 -9999 0 -0.33 109 109
alphaM/beta2 Integrin/LRP/tPA -0.082 0.17 -9999 0 -0.46 64 64
IL6 -0.21 0.33 -9999 0 -0.77 98 98
ITGB2 -0.044 0.15 -9999 0 -0.57 38 38
elevation of cytosolic calcium ion concentration -0.11 0.2 -9999 0 -0.45 107 107
alphaM/beta2 Integrin/JAM2/JAM3 -0.051 0.14 -9999 0 -0.44 53 53
JAM2 0.013 0.027 -9999 0 -0.59 1 1
alphaM/beta2 Integrin/ICAM1 -0.087 0.18 -9999 0 -0.48 55 55
alphaM/beta2 Integrin/uPA/Plg -0.096 0.18 -9999 0 -0.42 96 96
RhoA/GTP -0.088 0.16 -9999 0 -0.4 61 61
positive regulation of phagocytosis -0.1 0.18 -9999 0 -0.51 61 61
Ron/MSP -0.034 0.11 -9999 0 -0.41 42 42
alphaM/beta2 Integrin/uPAR/uPA -0.11 0.2 -9999 0 -0.45 107 107
alphaM/beta2 Integrin/uPAR -0.082 0.18 -9999 0 -0.45 83 83
PLAU -0.059 0.18 -9999 0 -0.51 73 73
PLAT -0.049 0.17 -9999 0 -0.49 64 64
actin filament polymerization -0.082 0.15 -9999 0 -0.38 61 61
MST1 -0.026 0.15 -9999 0 -0.57 35 35
alphaM/beta2 Integrin/lipoprotein(a) -0.11 0.18 -9999 0 -0.4 116 116
TNF -0.23 0.36 -9999 0 -0.78 119 119
RAP1B 0.013 0.022 -9999 0 -0.49 1 1
alphaM/beta2 Integrin/uPA -0.1 0.19 -9999 0 -0.42 116 116
fibrinolysis -0.095 0.18 -9999 0 -0.42 96 96
HCK -0.007 0.11 -9999 0 -0.54 20 20
dendritic cell antigen processing and presentation -0.095 0.16 -9999 0 -0.41 70 70
VTN -0.008 0.11 -9999 0 -0.56 20 20
alphaM/beta2 Integrin/CYR61 -0.13 0.22 -9999 0 -0.45 137 137
LPA -0.021 0.12 -9999 0 -0.49 32 32
LRP1 0.014 0 -9999 0 -10000 0 0
cell migration -0.13 0.22 -9999 0 -0.42 145 145
FN1 -0.003 0.092 -9999 0 -0.49 18 18
alphaM/beta2 Integrin/Thy1 -0.073 0.17 -9999 0 -0.46 71 71
MPO -0.12 0.24 -9999 0 -0.54 127 127
KNG1 -0.019 0.1 -9999 0 -0.49 24 24
RAP1/GDP -0.001 0.013 -9999 0 -0.29 1 1
ROCK1 -0.076 0.15 -9999 0 -0.39 54 54
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.002 0.043 -9999 0 -0.49 4 4
CTGF -0.027 0.15 -9999 0 -0.54 39 39
alphaM/beta2 Integrin/Hck -0.073 0.19 -9999 0 -0.55 59 59
ITGAM -0.044 0.16 -9999 0 -0.6 36 36
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.09 0.21 -9999 0 -0.5 81 81
HP -0.11 0.23 -9999 0 -0.53 116 116
leukocyte adhesion -0.11 0.17 -9999 0 -0.54 51 51
SELP -0.027 0.13 -9999 0 -0.49 38 38
Reelin signaling pathway

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
CDK5R1/CDK5 -0.026 0.1 -9999 0 -0.43 31 31
VLDLR -0.007 0.11 -9999 0 -0.57 19 19
CRKL 0.013 0.022 -9999 0 -0.49 1 1
LRPAP1 0.014 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
ITGA3 -0.009 0.11 -9999 0 -0.5 23 23
RELN/VLDLR/Fyn -0.1 0.16 -9999 0 -0.34 153 153
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.011 0.055 -9999 0 -10000 0 0
AKT1 -0.072 0.16 -9999 0 -0.44 38 38
MAP2K7 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
DAB1 -0.089 0.22 -9999 0 -0.56 92 92
RELN/LRP8/DAB1 -0.14 0.18 -9999 0 -0.34 203 203
LRPAP1/LRP8 -0.002 0.027 -9999 0 -0.43 2 2
RELN/LRP8/DAB1/Fyn -0.12 0.17 -9999 0 -0.36 139 139
DAB1/alpha3/beta1 Integrin -0.13 0.18 -9999 0 -0.54 51 51
long-term memory -0.28 0.28 -9999 0 -0.64 164 164
DAB1/LIS1 -0.12 0.17 -9999 0 -0.54 39 39
DAB1/CRLK/C3G -0.12 0.16 -9999 0 -0.53 39 39
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
DAB1/NCK2 -0.12 0.17 -9999 0 -0.55 39 39
ARHGEF2 0.013 0.027 -9999 0 -0.59 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.16 0.26 -9999 0 -0.55 158 158
CDK5R1 -0.022 0.14 -9999 0 -0.59 31 31
RELN -0.14 0.25 -9999 0 -0.55 140 140
PIK3R1 0.014 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.089 0.15 -9999 0 -0.32 141 141
GRIN2A/RELN/LRP8/DAB1/Fyn -0.2 0.23 -9999 0 -0.58 108 108
MAPK8 -0.002 0.099 -9999 0 -0.59 14 14
RELN/VLDLR/DAB1 -0.14 0.19 -9999 0 -0.35 212 212
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
MAP1B -0.11 0.2 -9999 0 -0.37 141 141
RELN/LRP8 -0.089 0.15 -9999 0 -0.32 141 141
GRIN2B/RELN/LRP8/DAB1/Fyn -0.22 0.23 -9999 0 -0.58 111 111
PI3K -0.001 0.019 -9999 0 -0.43 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.017 0.078 -9999 0 -0.36 24 24
RAP1A -0.072 0.18 -9999 0 -0.49 39 39
PAFAH1B1 0.014 0 -9999 0 -10000 0 0
MAPK8IP1 0.009 0.053 -9999 0 -0.59 4 4
CRLK/C3G -0.001 0.015 -9999 0 -0.34 1 1
GRIN2B -0.18 0.26 -9999 0 -0.54 180 180
NCK2 0.014 0 -9999 0 -10000 0 0
neuron differentiation -0.043 0.14 -9999 0 -0.42 34 34
neuron adhesion -0.065 0.18 -9999 0 -0.49 44 44
LRP8 0.012 0.038 -9999 0 -0.59 2 2
GSK3B -0.061 0.15 -9999 0 -0.47 30 30
RELN/VLDLR/DAB1/Fyn -0.13 0.18 -9999 0 -0.37 148 148
MAP3K11 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.085 0.17 -9999 0 -0.31 148 148
CDK5 0.014 0 -9999 0 -10000 0 0
MAPT 0.011 0.082 -9999 0 -0.54 10 10
neuron migration -0.07 0.19 -9999 0 -0.51 43 43
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.043 0.14 -9999 0 -0.42 34 34
RELN/VLDLR -0.09 0.14 -9999 0 -0.34 93 93
Aurora C 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
INCENP 0.013 0.027 -9999 0 -0.59 1 1
Aurora C/Aurora B/INCENP -0.11 0.16 -9999 0 -0.31 178 178
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.031 0.045 -9999 0 -0.25 1 1
AURKB -0.16 0.26 -9999 0 -0.55 157 157
AURKC -0.021 0.13 -9999 0 -0.52 34 34
a4b1 and a4b7 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
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
ITGB7 -0.034 0.16 -9999 0 -0.54 45 45
ITGA4 -0.052 0.18 -9999 0 -0.53 62 62
alpha4/beta7 Integrin -0.077 0.17 -9999 0 -0.43 93 93
alpha4/beta1 Integrin -0.047 0.13 -9999 0 -0.39 62 62
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.038 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.092 0.14 -9999 0 -0.42 49 49
JUN -0.08 0.2 -9999 0 -0.52 59 59
HRAS 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.16 0.22 -9999 0 -0.44 145 145
RAP1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.012 0.035 -9999 0 -0.54 2 2
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.16 0.22 -9999 0 -0.44 144 144
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 0.17 -9999 0 -0.4 95 95
RHOA 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.14 0.2 -9999 0 -0.61 55 55
GRB7 -0.032 0.14 -9999 0 -0.49 43 43
RET51/GFRalpha1/GDNF -0.15 0.22 -9999 0 -0.43 144 144
MAPKKK cascade -0.12 0.18 -9999 0 -0.56 51 51
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.09 0.17 -9999 0 -0.39 95 95
lamellipodium assembly -0.086 0.13 -9999 0 -0.39 49 49
RET51/GFRalpha1/GDNF/SHC -0.16 0.22 -9999 0 -0.44 144 144
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
RET9/GFRalpha1/GDNF/SHC -0.093 0.17 -9999 0 -0.4 95 95
RET9/GFRalpha1/GDNF/Shank3 -0.095 0.17 -9999 0 -0.36 138 138
MAPK3 -0.11 0.21 -9999 0 -0.57 55 55
DOK1 0.012 0.035 -9999 0 -0.54 2 2
DOK6 -0.05 0.18 -9999 0 -0.58 56 56
PXN 0.014 0 -9999 0 -10000 0 0
neurite development -0.1 0.22 -9999 0 -0.53 72 72
DOK5 0.001 0.088 -9999 0 -0.59 11 11
GFRA1 -0.071 0.2 -9999 0 -0.56 77 77
MAPK8 -0.087 0.2 -9999 0 -0.57 51 51
HRAS/GTP -0.14 0.2 -9999 0 -0.64 49 49
tube development -0.088 0.16 -9999 0 -0.37 97 97
MAPK1 -0.11 0.21 -9999 0 -0.57 55 55
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.042 0.15 -9999 0 -0.32 95 95
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
PDLIM7 0.005 0.066 -9999 0 -0.49 9 9
RET51/GFRalpha1/GDNF/Dok6 -0.17 0.26 -9999 0 -0.73 67 67
SHC1 0.009 0.049 -9999 0 -0.49 5 5
RET51/GFRalpha1/GDNF/Dok4 -0.16 0.23 -9999 0 -0.45 151 151
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.44 152 152
PRKCA 0.013 0.027 -9999 0 -0.59 1 1
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.069 0.18 -9999 0 -0.48 57 57
PIK3R1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.044 0.15 -9999 0 -0.34 81 81
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.24 -9999 0 -0.47 147 147
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.11 0.24 -9999 0 -0.55 117 117
DOK4 -0.005 0.1 -9999 0 -0.59 16 16
JNK cascade -0.078 0.19 -9999 0 -0.51 59 59
RET9/GFRalpha1/GDNF/FRS2 -0.091 0.17 -9999 0 -0.4 95 95
SHANK3 0.004 0.073 -9999 0 -0.51 10 10
RASA1 0.014 0 -9999 0 -10000 0 0
NCK1 0.013 0.027 -9999 0 -0.59 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.043 0.15 -9999 0 -0.32 95 95
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.092 0.2 -9999 0 -0.6 45 45
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.092 0.2 -9999 0 -0.58 47 47
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.096 0.21 -9999 0 -0.62 47 47
PI3K -0.09 0.23 -9999 0 -0.63 50 50
SOS1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.088 0.16 -9999 0 -0.37 97 97
GRB10 0.011 0.044 -9999 0 -0.56 3 3
activation of MAPKK activity -0.087 0.2 -9999 0 -0.46 83 83
RET51/GFRalpha1/GDNF/FRS2 -0.16 0.22 -9999 0 -0.44 144 144
GAB1 0.012 0.035 -9999 0 -0.54 2 2
IRS1 0.014 0 -9999 0 -10000 0 0
IRS2 0.012 0.035 -9999 0 -0.54 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.097 0.21 -9999 0 -0.64 46 46
RET51/GFRalpha1/GDNF/PKC alpha -0.15 0.22 -9999 0 -0.44 144 144
GRB2 0.013 0.022 -9999 0 -0.49 1 1
PRKACA 0.014 0 -9999 0 -10000 0 0
GDNF -0.071 0.21 -9999 0 -0.57 74 74
RAC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.15 0.22 -9999 0 -0.43 144 144
Rac1/GTP -0.1 0.15 -9999 0 -0.48 49 49
RET9/GFRalpha1/GDNF -0.1 0.18 -9999 0 -0.4 131 131
GFRalpha1/GDNF -0.12 0.21 -9999 0 -0.46 131 131
Endothelins

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
AKT1 -0.092 0.21 -10000 0 -0.56 51 51
PTK2B -0.009 0.11 -10000 0 -0.49 24 24
mol:Ca2+ -0.062 0.24 -10000 0 -0.72 41 41
EDN1 -0.08 0.18 -10000 0 -0.47 70 70
EDN3 -0.017 0.13 -10000 0 -0.58 27 27
EDN2 -0.017 0.1 -10000 0 -0.49 23 23
HRAS/GDP -0.093 0.21 -10000 0 -0.54 54 54
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.051 0.16 -10000 0 -0.42 48 48
ADCY4 -0.11 0.23 -10000 0 -0.52 90 90
ADCY5 -0.12 0.24 -10000 0 -0.56 89 89
ADCY6 -0.1 0.22 -10000 0 -0.51 86 86
ADCY7 -0.1 0.22 -10000 0 -0.51 86 86
ADCY1 -0.16 0.25 -10000 0 -0.54 119 119
ADCY2 -0.11 0.23 -10000 0 -0.53 92 92
ADCY3 -0.1 0.22 -10000 0 -0.51 86 86
ADCY8 -0.14 0.25 -10000 0 -0.54 113 113
ADCY9 -0.11 0.22 -10000 0 -0.51 88 88
arachidonic acid secretion -0.095 0.22 -10000 0 -0.52 73 73
ETB receptor/Endothelin-1/Gq/GTP -0.045 0.16 -10000 0 -0.4 57 57
GNAO1 0.008 0.059 -10000 0 -0.59 5 5
HRAS 0.013 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.094 0.2 0.26 21 -0.53 49 70
ETA receptor/Endothelin-1/Gs/GTP -0.13 0.23 0.24 20 -0.54 86 106
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.19 0.32 -10000 0 -0.62 156 156
EDNRB -0.045 0.18 -10000 0 -0.59 49 49
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.11 0.26 -10000 0 -0.69 58 58
CYSLTR1 -0.1 0.24 -10000 0 -0.66 54 54
SLC9A1 -0.066 0.099 -10000 0 -0.31 35 35
mol:GDP -0.11 0.22 -10000 0 -0.53 72 72
SLC9A3 -0.095 0.27 -10000 0 -0.66 74 74
RAF1 -0.11 0.23 -10000 0 -0.52 78 78
JUN -0.045 0.2 -10000 0 -0.7 18 18
JAK2 -0.092 0.21 -10000 0 -0.56 51 51
mol:IP3 -0.058 0.18 -10000 0 -0.5 43 43
ETA receptor/Endothelin-1 -0.13 0.24 0.3 21 -0.56 73 94
PLCB1 -0.01 0.11 -10000 0 -0.59 19 19
PLCB2 -0.009 0.11 -10000 0 -0.57 19 19
ETA receptor/Endothelin-3 -0.072 0.16 -10000 0 -0.46 59 59
FOS -0.15 0.33 -10000 0 -0.86 75 75
Gai/GDP 0.006 0.11 -10000 0 -0.97 5 5
CRK 0.014 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.12 0.25 -10000 0 -0.56 87 87
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
PRKCB1 -0.057 0.17 -10000 0 -0.47 44 44
GNAQ 0.013 0.007 -10000 0 -10000 0 0
GNAZ 0.014 0 -10000 0 -10000 0 0
GNAL -0.058 0.2 -10000 0 -0.59 62 62
Gs family/GDP -0.15 0.21 -10000 0 -0.52 98 98
ETA receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.39 51 51
MAPK14 -0.037 0.16 -10000 0 -0.54 27 27
TRPC6 -0.066 0.25 -10000 0 -0.79 38 38
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.1 -10000 0 -0.59 16 16
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.047 0.17 -10000 0 -0.44 50 50
ETB receptor/Endothelin-2 -0.047 0.15 -10000 0 -0.41 71 71
ETB receptor/Endothelin-3 -0.047 0.17 -10000 0 -0.46 69 69
ETB receptor/Endothelin-1 -0.096 0.19 -10000 0 -0.46 92 92
MAPK3 -0.14 0.3 -10000 0 -0.75 80 80
MAPK1 -0.14 0.3 -10000 0 -0.75 80 80
Rac1/GDP -0.092 0.21 -10000 0 -0.54 55 55
cAMP biosynthetic process -0.12 0.24 -10000 0 -0.54 96 96
MAPK8 -0.06 0.22 -10000 0 -0.64 42 42
SRC 0.014 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.02 0.12 -10000 0 -0.35 35 35
p130Cas/CRK/Src/PYK2 -0.097 0.23 -10000 0 -0.57 58 58
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.092 0.21 -10000 0 -0.51 64 64
COL1A2 -0.13 0.28 -10000 0 -0.68 80 80
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.069 0.14 -10000 0 -0.42 56 56
mol:DAG -0.058 0.18 -10000 0 -0.5 43 43
MAP2K2 -0.12 0.25 -10000 0 -0.6 81 81
MAP2K1 -0.12 0.26 -10000 0 -0.6 82 82
EDNRA -0.066 0.17 -10000 0 -0.48 52 52
positive regulation of muscle contraction -0.071 0.19 -10000 0 -0.5 48 48
Gq family/GDP -0.12 0.2 -10000 0 -0.55 60 60
HRAS/GTP -0.1 0.21 -10000 0 -0.52 67 67
PRKCH -0.049 0.17 -10000 0 -0.5 37 37
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.05 0.18 -10000 0 -0.51 37 37
PRKCB -0.087 0.2 -10000 0 -0.49 64 64
PRKCE -0.054 0.18 -10000 0 -0.49 42 42
PRKCD -0.065 0.2 -10000 0 -0.55 50 50
PRKCG -0.15 0.23 -10000 0 -0.47 124 124
regulation of vascular smooth muscle contraction -0.17 0.38 -10000 0 -1 72 72
PRKCQ -0.058 0.19 -10000 0 -0.51 48 48
PLA2G4A -0.1 0.24 -10000 0 -0.57 73 73
GNA14 -0.014 0.12 -10000 0 -0.56 25 25
GNA15 -0.008 0.11 -10000 0 -0.57 19 19
GNA12 0.013 0.027 -10000 0 -0.59 1 1
GNA11 0.003 0.08 -10000 0 -0.59 9 9
Rac1/GTP -0.093 0.2 0.26 21 -0.53 48 69
MMP1 0.013 0.16 -10000 0 -0.4 50 50
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.38 -9999 0 -1 67 67
MKNK1 0.009 0.053 -9999 0 -0.59 4 4
MAPK14 -0.037 0.12 -9999 0 -0.36 7 7
ATF2/c-Jun -0.028 0.14 -9999 0 -0.57 17 17
MAPK11 -0.049 0.15 -9999 0 -0.55 16 16
MITF -0.041 0.16 -9999 0 -0.47 16 16
MAPKAPK5 -0.039 0.16 -9999 0 -0.35 85 85
KRT8 -0.11 0.22 -9999 0 -0.45 100 100
MAPKAPK3 0.012 0.038 -9999 0 -0.59 2 2
MAPKAPK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.062 0.19 -9999 0 -0.44 88 88
CEBPB -0.052 0.18 -9999 0 -0.39 93 93
SLC9A1 -0.04 0.16 -9999 0 -0.35 85 85
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.044 0.17 -9999 0 -0.47 25 25
p38alpha-beta/MNK1 -0.038 0.16 -9999 0 -0.55 14 14
JUN -0.027 0.14 -9999 0 -0.57 17 17
PPARGC1A -0.056 0.18 -9999 0 -0.39 94 94
USF1 -0.039 0.16 -9999 0 -0.35 85 85
RAB5/GDP/GDI1 -0.051 0.095 -9999 0 -0.38 10 10
NOS2 -0.082 0.28 -9999 0 -1 27 27
DDIT3 -0.044 0.16 -9999 0 -0.35 89 89
RAB5A 0.014 0 -9999 0 -10000 0 0
HSPB1 -0.042 0.15 -9999 0 -0.47 20 20
p38alpha-beta/HBP1 -0.035 0.16 -9999 0 -0.54 10 10
CREB1 -0.041 0.17 -9999 0 -0.37 87 87
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.027 0.14 -9999 0 -0.56 10 10
RPS6KA4 -0.039 0.16 -9999 0 -0.34 88 88
PLA2G4A -0.046 0.17 -9999 0 -0.61 22 22
GDI1 -0.039 0.16 -9999 0 -0.34 88 88
TP53 -0.06 0.2 -9999 0 -0.43 95 95
RPS6KA5 -0.047 0.17 -9999 0 -0.36 92 92
ESR1 -0.054 0.17 -9999 0 -0.37 100 100
HBP1 0.014 0 -9999 0 -10000 0 0
MEF2C -0.049 0.16 -9999 0 -0.36 96 96
MEF2A -0.04 0.16 -9999 0 -0.56 10 10
EIF4EBP1 -0.044 0.17 -9999 0 -0.37 88 88
KRT19 -0.1 0.22 -9999 0 -0.41 132 132
ELK4 -0.039 0.16 -9999 0 -0.35 85 85
ATF6 -0.039 0.16 -9999 0 -0.34 88 88
ATF1 -0.041 0.17 -9999 0 -0.37 87 87
p38alpha-beta/MAPKAPK2 -0.035 0.16 -9999 0 -0.54 10 10
p38alpha-beta/MAPKAPK3 -0.037 0.16 -9999 0 -0.53 12 12
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 -0.041 0.11 -9999 0 -0.3 71 71
RGS9BP 0.002 0.085 -9999 0 -0.57 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.012 0.022 -9999 0 -0.49 1 1
mol:Na + -0.1 0.15 -9999 0 -0.32 162 162
mol:ADP 0.017 0.042 -9999 0 -0.34 7 7
GNAT2 0.01 0.032 -9999 0 -0.49 2 2
RGS9-1/Gbeta5/R9AP -0.038 0.12 -9999 0 -0.38 47 47
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.014 0.064 -9999 0 -0.3 24 24
GRK7 0.006 0.054 -9999 0 -0.49 6 6
CNGB3 -0.01 0.094 -9999 0 -0.49 19 19
Cone Metarhodopsin II/X-Arrestin -0.001 0.015 -9999 0 -0.35 1 1
mol:Ca2+ -0.14 0.2 -9999 0 -0.34 234 234
Cone PDE6 -0.044 0.11 -9999 0 -0.43 15 15
Cone Metarhodopsin II -0.004 0.03 -9999 0 -0.26 7 7
Na + (4 Units) -0.15 0.19 -9999 0 -0.34 234 234
GNAT2/GDP -0.033 0.1 -9999 0 -0.33 47 47
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.002 0.067 -9999 0 -0.26 29 29
Cone Transducin -0.044 0.11 -9999 0 -0.32 71 71
SLC24A2 -0.11 0.24 -9999 0 -0.55 115 115
GNB3/GNGT2 -0.056 0.14 -9999 0 -0.42 70 70
GNB3 -0.035 0.16 -9999 0 -0.58 43 43
GNAT2/GTP -0.001 0.022 -9999 0 -0.35 2 2
CNGA3 -0.14 0.24 -9999 0 -0.53 144 144
ARR3 0.002 0.022 -9999 0 -0.49 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.1 0.15 -9999 0 -0.32 162 162
mol:Pi -0.038 0.12 -9999 0 -0.38 47 47
Cone CNG Channel -0.091 0.14 -9999 0 -0.34 67 67
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.11 0.24 -9999 0 -0.55 115 115
RGS9 -0.039 0.17 -9999 0 -0.58 46 46
PDE6C 0.002 0.049 -9999 0 -0.49 5 5
GNGT2 -0.018 0.13 -9999 0 -0.55 29 29
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.013 0.1 -9999 0 -0.49 23 23
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 0.39 -10000 0 -1 61 61
PCK1 -0.24 0.43 -10000 0 -1 83 83
HNF4A -0.21 0.43 -10000 0 -1.1 71 71
KCNJ11 -0.25 0.51 -10000 0 -1.2 90 90
AKT1 -0.076 0.16 -10000 0 -0.41 32 32
response to starvation -0.002 0.023 -10000 0 -10000 0 0
DLK1 -0.25 0.46 -10000 0 -1 99 99
NKX2-1 -0.076 0.22 -10000 0 -0.8 14 14
ACADM -0.18 0.39 -10000 0 -0.95 70 70
TAT -0.23 0.42 -10000 0 -1 80 80
CEBPB -0.005 0.1 -10000 0 -0.57 17 17
CEBPA -0.015 0.13 -10000 0 -0.56 27 27
TTR -0.15 0.28 -10000 0 -0.86 37 37
PKLR -0.19 0.4 -10000 0 -0.95 76 76
APOA1 -0.24 0.48 -10000 0 -1.2 70 70
CPT1C -0.18 0.39 -10000 0 -1 61 61
ALAS1 -0.062 0.2 -10000 0 -0.83 2 2
TFRC -0.17 0.31 -10000 0 -0.76 60 60
FOXF1 -0.005 0.094 -10000 0 -0.51 16 16
NF1 0.02 0.038 -10000 0 -0.59 2 2
HNF1A (dimer) 0.012 0.039 -10000 0 -0.65 1 1
CPT1A -0.18 0.39 -10000 0 -0.98 67 67
HMGCS1 -0.18 0.39 -10000 0 -0.94 75 75
NR3C1 -0.023 0.077 -10000 0 -0.3 1 1
CPT1B -0.2 0.41 -10000 0 -0.99 77 77
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.01 0.024 -10000 0 -10000 0 0
GCK -0.25 0.48 -10000 0 -1 110 110
CREB1 -0.003 0.054 -10000 0 -10000 0 0
IGFBP1 -0.26 0.5 -10000 0 -1.3 85 85
PDX1 -0.079 0.21 -10000 0 -0.7 10 10
UCP2 -0.2 0.42 -10000 0 -1 78 78
ALDOB -0.2 0.44 -10000 0 -1.1 72 72
AFP -0.09 0.17 -10000 0 -0.55 34 34
BDH1 -0.22 0.45 -10000 0 -1.1 81 81
HADH -0.18 0.41 -10000 0 -0.98 73 73
F2 -0.21 0.43 -10000 0 -1.1 61 61
HNF1A 0.012 0.039 -10000 0 -0.66 1 1
G6PC -0.067 0.21 -10000 0 -0.76 23 23
SLC2A2 -0.093 0.22 -10000 0 -0.72 7 7
INS 0.013 0.091 0.24 13 -0.56 5 18
FOXA1 -0.054 0.17 -10000 0 -0.5 54 54
FOXA3 -0.12 0.23 -10000 0 -0.53 105 105
FOXA2 -0.22 0.47 -10000 0 -1.1 83 83
ABCC8 -0.27 0.53 -10000 0 -1.2 94 94
ALB -0.13 0.3 -10000 0 -0.9 51 51
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.005 0.043 -10000 0 -0.35 7 7
fibroblast growth factor receptor signaling pathway -0.005 0.043 -10000 0 -0.35 7 7
LAMA1 -0.063 0.2 -10000 0 -0.57 68 68
PRNP 0.014 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.095 0.17 -10000 0 -0.38 128 128
SMAD2 0.03 0.044 -10000 0 -0.41 2 2
GPC1/PrPc/Cu2+ -0.002 0.025 -10000 0 -0.29 4 4
GPC1/Laminin alpha1 -0.057 0.14 -10000 0 -0.42 70 70
TDGF1 -0.077 0.21 -10000 0 -0.57 81 81
CRIPTO/GPC1 -0.066 0.15 -10000 0 -0.42 82 82
APP/GPC1 -0.003 0.03 -10000 0 -0.34 4 4
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.032 0.15 -10000 0 -0.35 84 84
FLT1 0.013 0.027 -10000 0 -0.59 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.006 0.045 -10000 0 -0.46 2 2
SERPINC1 -0.005 0.09 -10000 0 -0.49 17 17
FYN -0.029 0.14 -10000 0 -0.34 82 82
FGR -0.031 0.14 -10000 0 -0.34 85 85
positive regulation of MAPKKK cascade -0.071 0.19 -10000 0 -0.47 67 67
SLIT2 -0.12 0.24 -10000 0 -0.54 125 125
GPC1/NRG -0.13 0.19 -10000 0 -0.4 166 166
NRG1 -0.17 0.27 -10000 0 -0.55 164 164
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.015 0.065 -10000 0 -0.29 26 26
LYN -0.036 0.15 -10000 0 -0.35 90 90
mol:Spermine 0.01 0.032 -10000 0 -0.35 4 4
cell growth -0.005 0.043 -10000 0 -0.35 7 7
BMP signaling pathway -0.01 0.044 0.49 4 -10000 0 4
SRC -0.029 0.14 -10000 0 -0.34 82 82
TGFBR1 0.012 0.035 -10000 0 -0.54 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.087 0.2 -10000 0 -0.51 92 92
GPC1 0.01 0.044 -10000 0 -0.49 4 4
TGFBR1 (dimer) 0.012 0.035 -10000 0 -0.54 2 2
VEGFA -0.007 0.1 -10000 0 -0.49 22 22
BLK -0.1 0.19 -10000 0 -0.35 180 180
HCK -0.042 0.16 -10000 0 -0.36 96 96
FGF2 0.011 0.044 -10000 0 -0.56 3 3
FGFR1 0.013 0.027 -10000 0 -0.59 1 1
VEGFR1 homodimer 0.013 0.027 -10000 0 -0.59 1 1
TGFBR2 0.009 0.049 -10000 0 -0.49 5 5
cell death -0.003 0.03 -10000 0 -0.34 4 4
ATIII/GPC1 -0.014 0.067 -10000 0 -0.34 21 21
PLA2G2A/GPC1 -0.066 0.14 -10000 0 -0.37 93 93
LCK -0.087 0.19 -10000 0 -0.37 152 152
neuron differentiation -0.13 0.19 -10000 0 -0.4 166 166
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.014 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.009 0.049 -10000 0 -0.49 5 5
Caspase cascade in apoptosis

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
TOP1 -0.044 0.15 0.21 1 -0.32 90 91
ACTA1 -0.065 0.18 0.25 1 -0.39 98 99
NUMA1 -0.044 0.15 0.21 1 -0.32 91 92
SPTAN1 -0.055 0.18 0.25 3 -0.39 90 93
LIMK1 -0.055 0.18 0.25 3 -0.39 91 94
BIRC3 -0.033 0.16 -10000 0 -0.55 43 43
BIRC2 0.014 0 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
CASP10 -0.083 0.2 -10000 0 -0.39 140 140
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
PTK2 -0.044 0.15 0.21 1 -0.32 90 91
DIABLO 0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.054 0.18 0.25 3 -0.39 90 93
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
GSN -0.063 0.18 0.25 1 -0.39 97 98
MADD 0.014 0 -10000 0 -10000 0 0
TFAP2A -0.19 0.3 -10000 0 -0.65 138 138
BID -0.039 0.11 -10000 0 -0.24 103 103
MAP3K1 -0.014 0.068 -10000 0 -0.22 6 6
TRADD 0.013 0.027 -10000 0 -0.59 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.007 0.019 -10000 0 -0.34 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.057 0.18 0.25 3 -0.4 90 93
CASP9 0.013 0.022 -10000 0 -0.49 1 1
DNA repair 0.003 0.061 -10000 0 -0.2 18 18
neuron apoptosis 0.006 0.045 -10000 0 -0.42 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.047 0.17 0.23 2 -0.37 89 91
APAF1 0.014 0 -10000 0 -10000 0 0
CASP6 -0.028 0.12 -10000 0 -0.73 4 4
TRAF2 0.014 0 -10000 0 -10000 0 0
ICAD/CAD -0.046 0.17 0.24 3 -0.38 85 88
CASP7 0.019 0.076 0.27 38 -10000 0 38
KRT18 -0.09 0.21 -10000 0 -0.61 67 67
apoptosis -0.069 0.18 0.26 1 -0.38 95 96
DFFA -0.055 0.18 0.25 3 -0.39 91 94
DFFB -0.055 0.18 0.25 3 -0.39 91 94
PARP1 -0.003 0.061 0.2 18 -10000 0 18
actin filament polymerization 0.043 0.17 0.36 85 -0.24 1 86
TNF -0.15 0.26 -10000 0 -0.54 156 156
CYCS -0.023 0.08 -10000 0 -0.21 35 35
SATB1 -0.024 0.12 -10000 0 -0.56 8 8
SLK -0.056 0.18 0.25 3 -0.39 92 95
p15 BID/BAX -0.027 0.099 -10000 0 -0.32 17 17
CASP2 -0.018 0.11 -10000 0 -0.42 12 12
JNK cascade 0.014 0.068 0.22 6 -10000 0 6
CASP3 -0.066 0.19 0.26 3 -0.41 95 98
LMNB2 -0.013 0.093 -10000 0 -0.4 9 9
RIPK1 0.014 0 -10000 0 -10000 0 0
CASP4 -0.013 0.11 -10000 0 -0.5 27 27
Mammalian IAPs/DIABLO -0.024 0.08 -10000 0 -0.32 25 25
negative regulation of DNA binding -0.18 0.3 -10000 0 -0.64 138 138
stress fiber formation -0.055 0.18 0.25 3 -0.38 92 95
GZMB -0.11 0.22 -10000 0 -0.46 140 140
CASP1 -0.007 0.09 -10000 0 -0.36 27 27
LMNB1 -0.022 0.1 -10000 0 -0.39 17 17
APP 0.006 0.045 -10000 0 -0.42 1 1
TNFRSF1A 0.001 0.085 -10000 0 -0.55 12 12
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.064 -10000 0 -0.36 16 16
VIM -0.075 0.18 0.26 1 -0.38 96 97
LMNA -0.013 0.093 -10000 0 -0.39 9 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.028 0.12 -10000 0 -0.4 18 18
LRDD 0.006 0.069 -10000 0 -0.58 7 7
SREBF1 -0.065 0.18 0.24 2 -0.39 99 101
APAF-1/Caspase 9 -0.006 0.042 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.043 0.14 0.2 2 -0.32 91 93
CFL2 -0.044 0.17 0.25 1 -0.37 85 86
GAS2 -0.064 0.18 0.24 2 -0.4 96 98
positive regulation of apoptosis -0.014 0.097 -10000 0 -0.4 10 10
PRF1 -0.062 0.19 -10000 0 -0.54 71 71
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.11 0.17 -10000 0 -0.38 151 151
CRKL -0.046 0.13 -10000 0 -0.48 10 10
mol:PIP3 -0.018 0.024 0.52 1 -10000 0 1
AKT1 0.003 0.027 0.37 1 -0.34 2 3
PTK2B -0.009 0.11 -10000 0 -0.49 24 24
RAPGEF1 -0.036 0.12 -10000 0 -0.44 10 10
RANBP10 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
HGF/MET/SHIP2 -0.14 0.19 -10000 0 -0.36 204 204
MAP3K5 -0.04 0.13 -10000 0 -0.44 20 20
HGF/MET/CIN85/CBL/ENDOPHILINS -0.13 0.17 -10000 0 -0.39 110 110
AP1 -0.09 0.17 -10000 0 -0.4 102 102
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.009 0.049 -10000 0 -0.49 5 5
apoptosis -0.1 0.25 -10000 0 -0.78 56 56
STAT3 (dimer) -0.05 0.13 -10000 0 -0.42 15 15
GAB1/CRKL/SHP2/PI3K -0.059 0.094 -10000 0 -0.42 10 10
INPP5D 0.008 0.06 -10000 0 -0.54 6 6
CBL/CRK -0.036 0.12 -10000 0 -0.44 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 0.027 -10000 0 -0.59 1 1
ELK1 -0.059 0.092 -10000 0 -0.2 151 151
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.049 0.071 -10000 0 -0.31 10 10
PAK1 -0.015 0.08 0.34 1 -0.31 8 9
HGF/MET/RANBP10 -0.14 0.19 -10000 0 -0.36 204 204
HRAS -0.1 0.23 -10000 0 -0.64 68 68
DOCK1 -0.039 0.12 -10000 0 -0.44 10 10
GAB1 -0.057 0.13 -10000 0 -0.31 73 73
CRK -0.046 0.13 -10000 0 -0.48 10 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.13 0.22 -10000 0 -0.59 81 81
JUN 0.003 0.074 -10000 0 -0.5 11 11
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.075 0.13 -10000 0 -0.28 110 110
PIK3R1 0.014 0 -10000 0 -10000 0 0
cell morphogenesis -0.021 0.14 -10000 0 -0.45 10 10
GRB2/SHC -0.052 0.12 -10000 0 -0.42 14 14
FOS -0.096 0.22 -10000 0 -0.55 101 101
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.059 0.092 -10000 0 -0.2 151 151
HGF/MET/MUC20 -0.15 0.2 -10000 0 -0.37 204 204
cell migration -0.052 0.12 -10000 0 -0.41 14 14
GRB2 0.013 0.022 -10000 0 -0.49 1 1
CBL 0.014 0 -10000 0 -10000 0 0
MET/RANBP10 -0.11 0.17 -10000 0 -0.38 151 151
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.062 0.14 -10000 0 -0.28 127 127
MET/MUC20 -0.11 0.18 -10000 0 -0.39 151 151
RAP1B -0.027 0.12 -10000 0 -0.42 9 9
RAP1A -0.026 0.12 -10000 0 -0.42 9 9
HGF/MET/RANBP9 -0.14 0.19 -10000 0 -0.36 204 204
RAF1 -0.091 0.22 -10000 0 -0.59 68 68
STAT3 -0.051 0.13 -10000 0 -0.42 15 15
cell proliferation -0.063 0.18 -10000 0 -0.39 90 90
RPS6KB1 -0.02 0.049 -10000 0 -10000 0 0
MAPK3 -0.059 0.083 -10000 0 -10000 0 0
MAPK1 -0.059 0.083 -10000 0 -10000 0 0
RANBP9 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.025 0.14 -10000 0 -0.44 26 26
SRC -0.05 0.13 -10000 0 -0.42 15 15
PI3K -0.05 0.11 -10000 0 -0.26 68 68
MET/Glomulin -0.09 0.16 -10000 0 -0.34 151 151
SOS1 0.014 0 -10000 0 -10000 0 0
MAP2K1 -0.077 0.2 -10000 0 -0.54 67 67
MET -0.15 0.25 -10000 0 -0.54 151 151
MAP4K1 -0.047 0.14 -10000 0 -0.44 18 18
PTK2 0.014 0 -10000 0 -10000 0 0
MAP2K2 -0.076 0.2 -10000 0 -0.54 67 67
BAD 0.01 0.025 0.34 1 -0.31 2 3
MAP2K4 -0.03 0.13 -10000 0 -0.42 19 19
SHP2/GRB2/SOS1/GAB1 -0.089 0.14 -10000 0 -0.38 68 68
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 -0.061 0.12 -10000 0 -0.27 96 96
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.079 0.2 -10000 0 -0.51 91 91
RASA1 0.014 0 -10000 0 -10000 0 0
NCK1 0.013 0.027 -10000 0 -0.59 1 1
PTPRJ 0.013 0.022 -10000 0 -0.49 1 1
NCK/PLCgamma1 -0.05 0.12 -10000 0 -0.42 10 10
PDPK1 -0.007 0.03 0.41 1 -0.37 2 3
HGF/MET/SHIP -0.15 0.2 -10000 0 -0.37 206 206
PDGFR-alpha signaling pathway

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
PDGFRA -0.062 0.2 -9999 0 -0.58 63 63
PDGF/PDGFRA/CRKL -0.05 0.14 -9999 0 -0.41 64 64
positive regulation of JUN kinase activity -0.039 0.1 -9999 0 -0.32 53 53
CRKL 0.013 0.022 -9999 0 -0.49 1 1
PDGF/PDGFRA/Caveolin-3 -0.057 0.15 -9999 0 -0.42 74 74
AP1 -0.17 0.32 -9999 0 -0.9 74 74
mol:IP3 -0.036 0.15 -9999 0 -0.42 63 63
PLCG1 -0.036 0.15 -9999 0 -0.42 63 63
PDGF/PDGFRA/alphaV Integrin -0.05 0.14 -9999 0 -0.41 63 63
RAPGEF1 0.014 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ -0.036 0.15 -9999 0 -0.42 63 63
CAV3 -0.007 0.084 -9999 0 -0.49 15 15
CAV1 -0.05 0.17 -9999 0 -0.49 65 65
SHC/Grb2/SOS1 -0.037 0.11 -9999 0 -0.32 53 53
PDGF/PDGFRA/Shf -0.052 0.14 -9999 0 -0.42 64 64
FOS -0.14 0.34 -9999 0 -0.89 74 74
JUN -0.02 0.061 -9999 0 -0.4 11 11
oligodendrocyte development -0.05 0.14 -9999 0 -0.41 63 63
GRB2 0.013 0.022 -9999 0 -0.49 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:DAG -0.036 0.15 -9999 0 -0.42 63 63
PDGF/PDGFRA -0.062 0.2 -9999 0 -0.58 63 63
actin cytoskeleton reorganization -0.049 0.13 -9999 0 -0.41 63 63
SRF 0.028 0.01 -9999 0 -10000 0 0
SHC1 0.009 0.049 -9999 0 -0.49 5 5
PI3K -0.042 0.11 -9999 0 -0.34 64 64
PDGF/PDGFRA/Crk/C3G -0.041 0.11 -9999 0 -0.34 57 57
JAK1 -0.03 0.14 -9999 0 -0.41 63 63
ELK1/SRF -0.001 0.11 -9999 0 -0.31 53 53
SHB 0.014 0 -9999 0 -10000 0 0
SHF 0.009 0.053 -9999 0 -0.59 4 4
CSNK2A1 0.014 0.022 -9999 0 -10000 0 0
GO:0007205 -0.037 0.15 -9999 0 -0.44 63 63
SOS1 0.014 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.039 0.1 -9999 0 -0.32 53 53
PDGF/PDGFRA/SHB -0.049 0.13 -9999 0 -0.41 63 63
PDGF/PDGFRA/Caveolin-1 -0.093 0.18 -9999 0 -0.41 118 118
ITGAV 0.013 0.027 -9999 0 -0.59 1 1
ELK1 -0.029 0.14 -9999 0 -0.39 57 57
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
PDGF/PDGFRA/Crk -0.049 0.13 -9999 0 -0.41 63 63
JAK-STAT cascade -0.03 0.14 -9999 0 -0.41 63 63
cell proliferation -0.052 0.14 -9999 0 -0.42 64 64
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.011 0.096 -9999 0 -0.37 32 32
NFATC2 -0.041 0.13 -9999 0 -0.36 76 76
NFATC3 0.012 0.032 -9999 0 -0.34 2 2
CD40LG -0.15 0.29 -9999 0 -0.65 94 94
PTGS2 -0.18 0.32 -9999 0 -0.69 113 113
JUNB -0.031 0.15 -9999 0 -0.52 44 44
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.027 -9999 0 -0.41 2 2
CaM/Ca2+ -0.005 0.027 -9999 0 -0.41 2 2
CALM1 0.01 0.036 -9999 0 -0.55 2 2
JUN 0.001 0.075 -9999 0 -0.5 11 11
mol:Ca2+ -0.005 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.003 -9999 0 -10000 0 0
FOSL1 -0.093 0.22 -9999 0 -0.53 101 101
CREM 0.012 0.035 -9999 0 -0.54 2 2
Jun/NFAT1-c-4/p21SNFT -0.12 0.18 -9999 0 -0.51 63 63
FOS -0.099 0.23 -9999 0 -0.56 101 101
IFNG -0.13 0.27 -9999 0 -0.62 79 79
AP-1/NFAT1-c-4 -0.16 0.32 -9999 0 -0.71 93 93
FASLG -0.14 0.28 -9999 0 -0.64 91 91
NFAT1-c-4/ICER1 -0.056 0.15 -9999 0 -0.44 41 41
IL2RA -0.16 0.3 -9999 0 -0.67 91 91
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.14 0.26 -9999 0 -0.63 70 70
JunB/Fra1/NFAT1-c-4 -0.14 0.2 -9999 0 -0.5 87 87
IL4 -0.13 0.26 -9999 0 -0.61 77 77
IL2 -0.008 0.015 -9999 0 -10000 0 0
IL3 -0.018 0.038 -9999 0 -0.75 1 1
FKBP1A 0.014 0 -9999 0 -10000 0 0
BATF3 -0.034 0.16 -9999 0 -0.53 45 45
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.027 -9999 0 -0.59 1 1
Visual signal transduction: Rods

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
mol:K + 0.014 0 -9999 0 -10000 0 0
GNAT1/GTP -0.021 0.085 -9999 0 -0.36 31 31
Metarhodopsin II/Arrestin -0.03 0.095 -9999 0 -0.32 49 49
PDE6G/GNAT1/GTP -0.045 0.12 -9999 0 -0.33 70 70
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.019 0.12 -9999 0 -0.5 31 31
GRK1 0.012 0.022 -9999 0 -0.49 1 1
CNG Channel -0.19 0.2 -9999 0 -0.55 82 82
mol:Na + -0.2 0.2 -9999 0 -0.52 102 102
mol:ADP 0.012 0.022 -9999 0 -0.49 1 1
RGS9-1/Gbeta5/R9AP -0.038 0.12 -9999 0 -0.38 47 47
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.2 0.21 -9999 0 -0.54 102 102
CNGB1 -0.18 0.26 -9999 0 -0.53 181 181
RDH5 -0.018 0.12 -9999 0 -0.5 33 33
SAG 0.002 0.022 -9999 0 -0.49 1 1
mol:Ca2+ -0.17 0.21 -9999 0 -0.5 102 102
Na + (4 Units) -0.18 0.18 -9999 0 -0.48 102 102
RGS9 -0.039 0.17 -9999 0 -0.58 46 46
GNB1/GNGT1 -0.001 0.021 -9999 0 -0.34 2 2
GNAT1/GDP -0.046 0.11 -9999 0 -0.48 8 8
GUCY2D -0.006 0.087 -9999 0 -0.49 16 16
GNGT1 -0.001 0.031 -9999 0 -0.49 2 2
GUCY2F 0.005 0.049 -9999 0 -0.49 5 5
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.061 0.16 -9999 0 -0.49 27 27
mol:11-cis-retinal -0.018 0.12 -9999 0 -0.5 33 33
mol:cGMP -0.082 0.17 -9999 0 -0.47 41 41
GNB1 0.014 0 -9999 0 -10000 0 0
Rhodopsin -0.057 0.13 -9999 0 -0.36 81 81
SLC24A1 0.014 0 -9999 0 -10000 0 0
CNGA1 -0.057 0.19 -9999 0 -0.56 64 64
Metarhodopsin II -0.027 0.083 -9999 0 -0.28 50 50
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.11 0.17 -9999 0 -0.4 104 104
RGS9BP 0.002 0.085 -9999 0 -0.57 11 11
Metarhodopsin II/Transducin -0.011 0.073 -9999 0 -0.3 14 14
GCAP Family/Ca ++ -0.1 0.17 -9999 0 -0.37 109 109
PDE6A/B -0.069 0.16 -9999 0 -0.4 90 90
mol:Pi -0.038 0.12 -9999 0 -0.38 47 47
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.017 0.067 -9999 0 -0.27 31 31
PDE6B -0.034 0.16 -9999 0 -0.54 45 45
PDE6A -0.039 0.16 -9999 0 -0.53 50 50
PDE6G -0.032 0.16 -9999 0 -0.56 42 42
RHO -0.039 0.16 -9999 0 -0.52 49 49
PDE6 -0.095 0.16 -9999 0 -0.56 31 31
GUCA1A -0.14 0.25 -9999 0 -0.54 141 141
GC2/GCAP Family -0.1 0.16 -9999 0 -0.38 96 96
GUCA1C -0.013 0.091 -9999 0 -0.49 18 18
GUCA1B -0.007 0.11 -9999 0 -0.59 18 18
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.021 0.082 -9999 0 -0.34 32 32
ARNO/beta Arrestin1-2 -0.024 0.084 -9999 0 -0.53 7 7
EGFR -0.083 0.21 -9999 0 -0.55 89 89
EPHA2 -0.015 0.12 -9999 0 -0.5 30 30
USP6 0.004 0.069 -9999 0 -0.49 10 10
IQSEC1 0.005 0.069 -9999 0 -0.51 9 9
EGFR/EGFR/EGF/EGF -0.11 0.2 -9999 0 -0.43 132 132
ARRB2 0.009 0.037 -9999 0 -10000 0 0
mol:GTP 0.004 0.045 -9999 0 -0.16 24 24
ARRB1 -0.003 0.1 -9999 0 -0.59 15 15
FBXO8 0.013 0.027 -9999 0 -0.59 1 1
TSHR -0.2 0.27 -9999 0 -0.54 196 196
EGF -0.05 0.18 -9999 0 -0.56 58 58
somatostatin receptor activity 0 0 -9999 0 -0.001 72 72
ARAP2 -0.008 0.11 -9999 0 -0.59 19 19
mol:GDP -0.071 0.12 -9999 0 -0.29 76 76
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 34 34
ITGA2B -0.043 0.17 -9999 0 -0.57 50 50
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.017 0.066 -9999 0 -0.4 3 3
ADAP1 -0.021 0.14 -9999 0 -0.55 32 32
KIF13B 0.014 0 -9999 0 -10000 0 0
HGF/MET -0.17 0.23 -9999 0 -0.43 204 204
PXN 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.063 0.12 -9999 0 -0.28 66 66
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.097 0.17 -9999 0 -0.41 92 92
ADRB2 -0.015 0.13 -9999 0 -0.59 25 25
receptor agonist activity 0 0 -9999 0 0 79 79
actin filament binding 0 0 -9999 0 -0.001 76 76
SRC 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.052 0.18 -9999 0 -0.51 65 65
GNAQ 0.014 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 48 48
ARF6/GDP -0.007 0.1 -9999 0 -0.38 18 18
ARF6/GDP/GULP/ACAP1 -0.11 0.16 -9999 0 -0.41 83 83
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.062 0.13 -9999 0 -0.35 54 54
ACAP1 -0.03 0.14 -9999 0 -0.5 44 44
ACAP2 0.013 0.027 -9999 0 -0.59 1 1
LHCGR/beta Arrestin2 0.002 0.052 -9999 0 -0.28 16 16
EFNA1 0.01 0.044 -9999 0 -0.49 4 4
HGF -0.079 0.2 -9999 0 -0.51 91 91
CYTH3 0.012 0 -9999 0 -10000 0 0
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.013 0.027 -9999 0 -0.59 1 1
fibronectin binding 0 0 -9999 0 0 69 69
endosomal lumen acidification 0 0 -9999 0 0 78 78
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.05 0.18 -9999 0 -0.57 57 57
GNAQ/ARNO 0.014 0.008 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 38 38
MET -0.15 0.25 -9999 0 -0.54 151 151
GNA14 -0.014 0.12 -9999 0 -0.56 25 25
GNA15 -0.007 0.11 -9999 0 -0.57 19 19
GIT1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 56 56
GNA11 0.004 0.08 -9999 0 -0.59 9 9
LHCGR -0.007 0.087 -9999 0 -0.49 16 16
AGTR1 -0.033 0.16 -9999 0 -0.55 43 43
desensitization of G-protein coupled receptor protein signaling pathway 0.002 0.051 -9999 0 -0.28 16 16
IPCEF1/ARNO -0.057 0.14 -9999 0 -0.48 15 15
alphaIIb/beta3 Integrin -0.084 0.17 -9999 0 -0.41 107 107
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.1 0.23 -9999 0 -0.53 79 79
MAP3K8 -0.007 0.099 -9999 0 -0.51 19 19
FOS -0.09 0.21 -9999 0 -0.51 81 81
PRKCA 0.011 0.028 -9999 0 -0.6 1 1
PTPN7 -0.12 0.24 -9999 0 -0.55 127 127
HRAS 0.014 0.001 -9999 0 -10000 0 0
PRKCB -0.064 0.19 -9999 0 -0.52 73 73
NRAS 0.014 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.023 0.017 -9999 0 -10000 0 0
MAPK3 -0.073 0.18 -9999 0 -0.48 70 70
MAP2K1 -0.016 0.12 -9999 0 -0.47 25 25
ELK1 0.012 0.007 -9999 0 -10000 0 0
BRAF -0.051 0.12 -9999 0 -0.44 41 41
mol:GTP -0.001 0.002 -9999 0 -0.005 95 95
MAPK1 -0.073 0.18 -9999 0 -0.48 70 70
RAF1 -0.037 0.1 -9999 0 -0.43 25 25
KRAS 0.013 0.022 -9999 0 -0.49 1 1
HIF-1-alpha transcription factor network

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
PKM2 -0.018 0.49 -9999 0 -1.1 49 49
HDAC7 0.017 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.14 0.33 -9999 0 -0.9 53 53
SMAD4 0.016 0.004 -9999 0 -10000 0 0
ID2 -0.019 0.49 -9999 0 -1.1 48 48
AP1 -0.066 0.18 -9999 0 -0.42 102 102
ABCG2 -0.019 0.49 -9999 0 -1.1 49 49
HIF1A 0.024 0.093 -9999 0 -0.62 2 2
TFF3 -0.059 0.5 -9999 0 -1.1 56 56
GATA2 -0.003 0.1 -9999 0 -0.56 16 16
AKT1 0.018 0.1 -9999 0 -10000 0 0
response to hypoxia 0.001 0.11 -9999 0 -0.24 13 13
MCL1 -0.018 0.49 -9999 0 -1.1 49 49
NDRG1 -0.023 0.49 -9999 0 -1.1 50 50
SERPINE1 -0.093 0.54 -9999 0 -1.1 74 74
FECH -0.018 0.49 -9999 0 -1.1 49 49
FURIN -0.018 0.49 -9999 0 -1.1 49 49
NCOA2 -0.025 0.15 -9999 0 -0.59 35 35
EP300 0.033 0.18 -9999 0 -0.35 34 34
HMOX1 -0.028 0.5 -9999 0 -1.1 52 52
BHLHE40 -0.026 0.5 -9999 0 -1.1 52 52
BHLHE41 -0.026 0.5 -9999 0 -1.1 53 53
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.013 0.059 -9999 0 -0.4 6 6
ENG 0.087 0.13 -9999 0 -0.54 6 6
JUN 0.003 0.075 -9999 0 -0.5 11 11
RORA -0.019 0.49 -9999 0 -1.1 51 51
ABCB1 -0.039 0.093 -9999 0 -1.1 2 2
TFRC -0.024 0.5 -9999 0 -1.1 54 54
CXCR4 -0.03 0.5 -9999 0 -1.2 52 52
TF -0.051 0.53 -9999 0 -1.2 61 61
CITED2 -0.019 0.49 -9999 0 -1.1 48 48
HIF1A/ARNT -0.19 0.49 -9999 0 -1.3 57 57
LDHA -0.03 0.09 -9999 0 -0.67 6 6
ETS1 -0.024 0.49 -9999 0 -1.1 51 51
PGK1 -0.018 0.49 -9999 0 -1.1 48 48
NOS2 -0.042 0.51 -9999 0 -1.2 54 54
ITGB2 -0.037 0.51 -9999 0 -1.2 54 54
ALDOA -0.018 0.49 -9999 0 -1.1 48 48
Cbp/p300/CITED2 -0.088 0.5 -9999 0 -1.2 52 52
FOS -0.096 0.22 -9999 0 -0.55 101 101
HK2 -0.03 0.5 -9999 0 -1.1 54 54
SP1 0.024 0.005 -9999 0 -10000 0 0
GCK -0.066 0.47 -9999 0 -1.1 69 69
HK1 -0.018 0.49 -9999 0 -1.1 48 48
NPM1 -0.018 0.49 -9999 0 -1.1 49 49
EGLN1 -0.018 0.49 -9999 0 -1.1 49 49
CREB1 0.023 0.003 -9999 0 -10000 0 0
PGM1 -0.018 0.49 -9999 0 -1.1 48 48
SMAD3 0.016 0.004 -9999 0 -10000 0 0
EDN1 -0.045 0.32 -9999 0 -0.81 46 46
IGFBP1 -0.076 0.52 -9999 0 -1.1 63 63
VEGFA 0.016 0.41 -9999 0 -0.91 37 37
HIF1A/JAB1 -0.008 0.037 -9999 0 -0.46 2 2
CP -0.1 0.55 -9999 0 -1.2 73 73
CXCL12 -0.023 0.49 -9999 0 -1.1 52 52
COPS5 0.015 0.003 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.004 -9999 0 -10000 0 0
BNIP3 -0.019 0.49 -9999 0 -1.1 49 49
EGLN3 -0.024 0.5 -9999 0 -1.1 53 53
CA9 -0.054 0.52 -9999 0 -1.2 58 58
TERT -0.085 0.51 -9999 0 -1.1 64 64
ENO1 -0.018 0.49 -9999 0 -1.1 48 48
PFKL -0.018 0.49 -9999 0 -1.1 49 49
NCOA1 0.015 0.001 -9999 0 -10000 0 0
ADM -0.053 0.52 -9999 0 -1.1 61 61
ARNT 0.014 0.087 -9999 0 -0.65 1 1
HNF4A -0.043 0.14 -9999 0 -0.49 42 42
ADFP -0.069 0.47 -9999 0 -1.1 55 55
SLC2A1 0.024 0.39 -9999 0 -0.88 29 29
LEP -0.054 0.48 -9999 0 -1.1 51 51
HIF1A/ARNT/Cbp/p300 -0.15 0.35 -9999 0 -0.92 56 56
EPO 0.024 0.36 -9999 0 -0.92 22 22
CREBBP 0.036 0.17 -9999 0 -0.33 31 31
HIF1A/ARNT/Cbp/p300/HDAC7 -0.14 0.34 -9999 0 -0.92 54 54
PFKFB3 -0.02 0.49 -9999 0 -1.1 49 49
NT5E -0.026 0.5 -9999 0 -1.1 51 51
PLK1 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
regulation of centriole-centriole cohesion 0.041 0.095 0.2 127 -10000 0 127
BUB1B -0.058 0.14 -10000 0 -0.3 124 124
PLK1 -0.001 0.043 -10000 0 -0.13 27 27
PLK1S1 0.006 0.022 -10000 0 -0.11 2 2
KIF2A 0.006 0.048 -10000 0 -0.3 5 5
regulation of mitotic centrosome separation -0.001 0.043 -10000 0 -0.13 27 27
GOLGA2 0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.13 0.24 -10000 0 -0.43 182 182
WEE1 -0.007 0.088 -10000 0 -0.34 23 23
cytokinesis -0.11 0.21 -10000 0 -0.42 139 139
PP2A-alpha B56 -0.062 0.23 -10000 0 -0.67 60 60
AURKA 0.001 0.041 -10000 0 -0.15 23 23
PICH/PLK1 -0.031 0.16 -10000 0 -0.41 69 69
CENPE -0.045 0.14 -10000 0 -0.32 94 94
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.006 0.047 -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 -0.019 0.08 -10000 0 -0.21 63 63
PAK1 -0.035 0.15 -10000 0 -0.5 49 49
SPC24 -0.12 0.24 -10000 0 -0.53 128 128
FBXW11 0.014 0 -10000 0 -10000 0 0
CLSPN -0.037 0.11 -10000 0 -0.25 85 85
GORASP1 0.014 0 -10000 0 -10000 0 0
metaphase 0 0.004 0.009 4 -0.013 38 42
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0 0.022 -10000 0 -0.067 25 25
G2 phase of mitotic cell cycle 0 0.002 0.009 1 -0.009 17 18
STAG2 0.014 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.01 -10000 0 -10000 0 0
spindle elongation -0.001 0.043 -10000 0 -0.13 27 27
ODF2 0.013 0.003 -10000 0 -10000 0 0
BUB1 -0.1 0.24 -10000 0 -0.74 60 60
TPT1 0.006 0.022 -10000 0 -0.13 1 1
CDC25C -0.048 0.13 -10000 0 -0.3 95 95
CDC25B 0.014 0.003 -10000 0 -10000 0 0
SGOL1 -0.041 0.096 -10000 0 -0.2 127 127
RHOA 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.029 0.089 -10000 0 -0.3 44 44
CDC14B 0.012 0.001 -10000 0 -10000 0 0
CDC20 -0.1 0.23 -10000 0 -0.54 112 112
PLK1/PBIP1 -0.047 0.11 -10000 0 -0.32 70 70
mitosis 0.001 0.005 0.021 9 -0.022 1 10
FBXO5 0.004 0.05 -10000 0 -0.28 8 8
CDC2 0 0.004 -10000 0 -0.012 55 55
NDC80 -0.13 0.25 -10000 0 -0.55 136 136
metaphase plate congression 0.005 0.026 -10000 0 -0.14 2 2
ERCC6L -0.056 0.14 -10000 0 -0.4 68 68
NLP/gamma Tubulin 0.003 0.025 -10000 0 -0.11 3 3
microtubule cytoskeleton organization 0.006 0.022 -10000 0 -0.13 1 1
G2/M transition DNA damage checkpoint 0 0.002 0.01 5 -10000 0 5
PPP1R12A 0.013 0.027 -10000 0 -0.59 1 1
interphase 0 0.002 0.01 5 -10000 0 5
PLK1/PRC1-2 -0.091 0.18 -10000 0 -0.34 169 169
GRASP65/GM130/RAB1/GTP/PLK1 -0.005 0.023 -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 0.036 -10000 0 -0.2 2 2
mitotic prometaphase -0.001 0.002 -10000 0 -0.01 10 10
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.061 -10000 0 -10000 0 0
microtubule-based process -0.094 0.17 -10000 0 -0.33 169 169
Golgi organization -0.001 0.043 -10000 0 -0.13 27 27
Cohesin/SA2 -0.012 0.029 -10000 0 -0.22 2 2
PPP1CB/MYPT1 0.003 0.021 -10000 0 -0.43 1 1
KIF20A -0.17 0.26 -10000 0 -0.55 169 169
APC/C/CDC20 -0.058 0.15 -10000 0 -0.33 112 112
PPP2R1A 0.014 0 -10000 0 -10000 0 0
chromosome segregation -0.047 0.11 -10000 0 -0.32 70 70
PRC1 -0.006 0.1 -10000 0 -0.49 21 21
ECT2 -0.002 0.079 -10000 0 -0.35 21 21
C13orf34 0.006 0.036 -10000 0 -0.21 2 2
NUDC 0.005 0.026 -10000 0 -0.14 2 2
regulation of attachment of spindle microtubules to kinetochore -0.058 0.14 -10000 0 -0.3 124 124
spindle assembly 0.002 0.035 -10000 0 -0.1 25 25
spindle stabilization 0.006 0.022 -10000 0 -0.11 2 2
APC/C/HCDH1 0.02 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 -0.094 0.17 -10000 0 -0.33 169 169
CCNB1 -0.019 0.13 -10000 0 -0.49 34 34
PPP1CB 0.014 0.001 -10000 0 -10000 0 0
BTRC 0.014 0 -10000 0 -10000 0 0
ROCK2 -0.006 0.095 -10000 0 -0.44 21 21
TUBG1 0.006 0.022 -10000 0 -0.11 2 2
G2/M transition of mitotic cell cycle -0.031 0.086 -10000 0 -0.29 44 44
MLF1IP -0.043 0.14 -10000 0 -0.4 70 70
INCENP 0.011 0.027 -10000 0 -0.6 1 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.035 0.16 -9999 0 -0.49 25 25
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.16 -9999 0 -0.46 24 24
alphaV/beta3 Integrin/Osteopontin/Src -0.067 0.14 -9999 0 -0.38 91 91
AP1 -0.08 0.22 -9999 0 -0.59 47 47
ILK -0.044 0.17 -9999 0 -0.51 24 24
bone resorption -0.077 0.23 -9999 0 -0.53 79 79
PTK2B -0.009 0.11 -9999 0 -0.49 24 24
PYK2/p130Cas -0.093 0.16 -9999 0 -0.5 43 43
ITGAV 0.016 0.027 -9999 0 -0.58 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.067 0.16 -9999 0 -0.42 83 83
alphaV/beta3 Integrin/Osteopontin -0.093 0.16 -9999 0 -0.39 101 101
MAP3K1 -0.049 0.17 -9999 0 -0.48 34 34
JUN 0.003 0.074 -9999 0 -0.5 11 11
MAPK3 -0.037 0.17 -9999 0 -0.44 43 43
MAPK1 -0.037 0.17 -9999 0 -0.44 43 43
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.045 0.18 -9999 0 -0.48 38 38
ITGB3 -0.049 0.18 -9999 0 -0.51 65 65
NFKBIA -0.028 0.17 -9999 0 -0.48 28 28
FOS -0.095 0.22 -9999 0 -0.55 101 101
CD44 -0.057 0.19 -9999 0 -0.55 65 65
CHUK 0.014 0 -9999 0 -10000 0 0
PLAU -0.067 0.27 -9999 0 -0.73 51 51
NF kappa B1 p50/RelA -0.074 0.13 -9999 0 -0.47 25 25
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
RELA 0.014 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.047 0.12 -9999 0 -0.36 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.06 0.19 -9999 0 -0.53 47 47
VAV3 -0.12 0.23 -9999 0 -0.57 71 71
MAP3K14 -0.046 0.17 -9999 0 -0.43 44 44
ROCK2 -0.011 0.12 -9999 0 -0.59 21 21
SPP1 -0.079 0.21 -9999 0 -0.53 90 90
RAC1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.19 -9999 0 -0.52 69 69
MMP2 -0.067 0.21 -9999 0 -0.6 35 35
p75(NTR)-mediated signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.002 0.027 -9999 0 -0.43 2 2
Necdin/E2F1 -0.049 0.14 -9999 0 -0.41 62 62
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.077 0.14 -9999 0 -0.55 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.18 -9999 0 -0.37 147 147
NT-4/5 (dimer)/p75(NTR) -0.066 0.15 -9999 0 -0.4 85 85
IKBKB 0.014 0 -9999 0 -10000 0 0
AKT1 -0.045 0.16 -9999 0 -0.55 16 16
IKBKG 0.014 0 -9999 0 -10000 0 0
BDNF -0.08 0.2 -9999 0 -0.51 93 93
MGDIs/NGR/p75(NTR)/LINGO1 -0.093 0.18 -9999 0 -0.44 81 81
FURIN 0.014 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.098 0.16 -9999 0 -0.43 56 56
LINGO1 -0.019 0.14 -9999 0 -0.59 28 28
Sortilin/TRAF6/NRIF -0.001 0.015 -9999 0 -10000 0 0
proBDNF (dimer) -0.079 0.2 -9999 0 -0.5 93 93
NTRK1 -0.008 0.11 -9999 0 -0.52 22 22
RTN4R -0.036 0.16 -9999 0 -0.56 45 45
neuron apoptosis -0.062 0.17 -9999 0 -0.52 28 28
IRAK1 0.014 0 -9999 0 -10000 0 0
SHC1 -0.074 0.18 -9999 0 -0.4 88 88
ARHGDIA 0.014 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.089 0.16 -9999 0 -0.37 91 91
MAGEH1 0.004 0.079 -9999 0 -0.59 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.11 0.18 -9999 0 -0.4 109 109
Mammalian IAPs/DIABLO -0.024 0.08 -9999 0 -0.32 25 25
proNGF (dimer) -0.071 0.2 -9999 0 -0.56 77 77
MAGED1 0.014 0 -9999 0 -10000 0 0
APP 0.014 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.011 0.09 -9999 0 -0.5 17 17
ZNF274 0.014 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.052 0.15 -9999 0 -0.34 82 82
NGF -0.071 0.2 -9999 0 -0.56 77 77
cell cycle arrest -0.074 0.14 -9999 0 -0.53 16 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.032 0.13 -9999 0 -0.44 19 19
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.056 0.13 -9999 0 -0.33 86 86
NCSTN 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.093 0.17 -9999 0 -0.36 135 135
PSENEN 0.014 0 -9999 0 -10000 0 0
mol:ceramide -0.056 0.16 -9999 0 -0.36 83 83
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.02 0.12 -9999 0 -0.4 20 20
p75(NTR)/beta APP -0.054 0.14 -9999 0 -0.38 73 73
BEX1 -0.007 0.11 -9999 0 -0.59 18 18
mol:GDP -0.081 0.18 -9999 0 -0.37 135 135
NGF (dimer) -0.13 0.18 -9999 0 -0.38 127 127
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.083 0.16 -9999 0 -0.4 81 81
PIK3R1 0.014 0 -9999 0 -10000 0 0
RAC1/GTP -0.08 0.14 -9999 0 -0.35 85 85
MYD88 0.004 0.077 -9999 0 -0.57 9 9
CHUK 0.014 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.094 0.17 -9999 0 -0.36 135 135
RHOB 0.011 0.038 -9999 0 -0.49 3 3
RHOA 0.014 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.02 0.082 -9999 0 -0.36 28 28
NT3 (dimer) -0.008 0.092 -9999 0 -0.49 18 18
TP53 -0.048 0.16 -9999 0 -0.51 25 25
PRDM4 -0.057 0.16 -9999 0 -0.36 83 83
BDNF (dimer) -0.16 0.2 -9999 0 -0.44 124 124
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
SORT1 0.013 0.027 -9999 0 -0.59 1 1
activation of caspase activity -0.076 0.14 -9999 0 -0.54 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.085 0.15 -9999 0 -0.37 84 84
RHOC 0.011 0.041 -9999 0 -0.52 3 3
XIAP 0.014 0 -9999 0 -10000 0 0
MAPK10 -0.042 0.16 -9999 0 -0.48 29 29
DIABLO 0.014 0 -9999 0 -10000 0 0
SMPD2 -0.057 0.16 -9999 0 -0.36 83 83
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.094 0.17 -9999 0 -0.4 86 86
PSEN1 0.014 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.015 -9999 0 -0.34 1 1
NT3 (dimer)/p75(NTR) -0.066 0.15 -9999 0 -0.39 87 87
MAPK8 -0.046 0.17 -9999 0 -0.46 33 33
MAPK9 -0.04 0.16 -9999 0 -0.48 26 26
APAF1 0.014 0 -9999 0 -10000 0 0
NTF3 -0.008 0.092 -9999 0 -0.49 18 18
NTF4 -0.011 0.09 -9999 0 -0.5 17 17
NDN -0.028 0.16 -9999 0 -0.59 36 36
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.072 0.13 -9999 0 -0.52 16 16
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.044 -9999 0 -0.36 7 7
RhoA-B-C/GTP -0.093 0.16 -9999 0 -0.36 135 135
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.08 0.14 -9999 0 -0.52 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.087 0.15 -9999 0 -0.39 56 56
PRKACB 0.014 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.069 0.15 -9999 0 -0.37 96 96
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.033 0.16 -9999 0 -0.55 43 43
BIRC2 0.014 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.089 0.16 -9999 0 -0.38 89 89
BAD -0.035 0.16 -9999 0 -0.46 27 27
RIPK2 0.014 0 -9999 0 -10000 0 0
NGFR -0.064 0.19 -9999 0 -0.54 73 73
CYCS -0.045 0.16 -9999 0 -0.55 15 15
ADAM17 0.007 0.065 -9999 0 -0.59 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.084 0.15 -9999 0 -0.37 83 83
BCL2L11 -0.035 0.16 -9999 0 -0.46 27 27
BDNF (dimer)/p75(NTR) -0.12 0.19 -9999 0 -0.4 149 149
PI3K -0.084 0.15 -9999 0 -0.37 82 82
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.084 0.15 -9999 0 -0.37 83 83
NDNL2 0.014 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKCI 0.014 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.2 -9999 0 -0.43 135 135
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.084 0.15 -9999 0 -0.37 83 83
TRAF6 0.013 0.027 -9999 0 -0.59 1 1
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCZ -0.015 0.13 -9999 0 -0.55 27 27
PLG -0.002 0.043 -9999 0 -0.49 4 4
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.091 0.19 -9999 0 -0.46 62 62
SQSTM1 0.014 0 -9999 0 -10000 0 0
NGFRAP1 0.014 0 -9999 0 -10000 0 0
CASP3 -0.03 0.15 -9999 0 -0.42 27 27
E2F1 -0.014 0.12 -9999 0 -0.51 28 28
CASP9 0.013 0.022 -9999 0 -0.49 1 1
IKK complex -0.066 0.12 -9999 0 -0.5 19 19
NGF (dimer)/TRKA -0.075 0.16 -9999 0 -0.4 95 95
MMP7 -0.16 0.26 -9999 0 -0.54 155 155
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.078 0.14 -9999 0 -0.54 17 17
MMP3 -0.036 0.14 -9999 0 -0.49 46 46
APAF-1/Caspase 9 -0.068 0.11 -9999 0 -0.45 21 21
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 0.021 0.099 -10000 0 -0.88 3 3
SMARCC2 0.015 0.011 -10000 0 -10000 0 0
SMARCC1 0.015 0.011 -10000 0 -10000 0 0
TBX21 -0.11 0.25 -10000 0 -0.68 65 65
SUMO2 0.013 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0 0.11 -10000 0 -0.58 16 16
FKBP4 0.014 0 -10000 0 -10000 0 0
FKBP5 -0.086 0.22 -10000 0 -0.56 90 90
GR alpha/HSP90/FKBP51/HSP90 0.022 0.16 0.29 26 -0.32 48 74
PRL -0.046 0.094 -10000 0 -0.52 3 3
cortisol/GR alpha (dimer)/TIF2 0.18 0.24 0.52 111 -0.42 10 121
RELA -0.063 0.097 -10000 0 -0.26 15 15
FGG 0.16 0.17 0.46 53 -0.48 2 55
GR beta/TIF2 0.063 0.16 0.32 31 -0.4 34 65
IFNG -0.23 0.22 -10000 0 -0.6 70 70
apoptosis -0.009 0.2 0.61 20 -0.7 2 22
CREB1 0.013 0.023 -10000 0 -10000 0 0
histone acetylation -0.045 0.12 -10000 0 -0.38 33 33
BGLAP -0.047 0.12 -10000 0 -0.66 6 6
GR/PKAc 0.087 0.093 0.28 35 -10000 0 35
NF kappa B1 p50/RelA -0.11 0.18 -10000 0 -0.42 72 72
SMARCD1 0.015 0.011 -10000 0 -10000 0 0
MDM2 0.079 0.078 0.25 38 -10000 0 38
GATA3 -0.1 0.23 -10000 0 -0.53 115 115
AKT1 0.002 0.016 -10000 0 -10000 0 0
CSF2 -0.062 0.099 -10000 0 -0.5 3 3
GSK3B 0.012 0.03 -10000 0 -0.6 1 1
NR1I3 0.028 0.19 0.63 16 -0.68 3 19
CSN2 0.14 0.13 0.4 29 -10000 0 29
BRG1/BAF155/BAF170/BAF60A 0.039 0.038 -10000 0 -0.29 1 1
NFATC1 -0.019 0.14 -10000 0 -0.57 31 31
POU2F1 0.013 0.028 -10000 0 -0.59 1 1
CDKN1A -0.06 0.31 -10000 0 -1.5 20 20
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.012 -10000 0 -10000 0 0
SFN -0.11 0.23 -10000 0 -0.53 119 119
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.04 0.19 0.28 14 -0.4 46 60
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.052 0.32 0.58 18 -0.8 55 73
JUN -0.16 0.19 -10000 0 -0.5 71 71
IL4 -0.082 0.15 -10000 0 -0.56 24 24
CDK5R1 -0.023 0.14 -10000 0 -0.59 31 31
PRKACA 0.014 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.2 -10000 0 -0.48 116 116
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.031 0.15 0.29 22 -0.32 16 38
cortisol/GR alpha (monomer) 0.23 0.26 0.6 121 -10000 0 121
NCOA2 -0.027 0.15 -10000 0 -0.59 35 35
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.14 0.23 -10000 0 -0.59 101 101
AP-1/NFAT1-c-4 -0.31 0.31 -10000 0 -0.71 133 133
AFP -0.12 0.18 -10000 0 -0.68 17 17
SUV420H1 0.014 0 -10000 0 -10000 0 0
IRF1 0.11 0.15 0.46 14 -0.46 6 20
TP53 -0.013 0.15 -10000 0 -0.53 33 33
PPP5C 0.014 0 -10000 0 -10000 0 0
KRT17 -0.43 0.48 -10000 0 -1.1 151 151
KRT14 -0.13 0.18 -10000 0 -0.55 40 40
TBP 0.023 0.016 -10000 0 -10000 0 0
CREBBP 0.031 0.061 -10000 0 -10000 0 0
HDAC1 0.004 0.054 -10000 0 -0.59 4 4
HDAC2 0.014 0.001 -10000 0 -10000 0 0
AP-1 -0.31 0.31 -10000 0 -0.72 134 134
MAPK14 0.013 0.011 -10000 0 -10000 0 0
MAPK10 0.008 0.055 -10000 0 -0.6 4 4
MAPK11 0.003 0.081 -10000 0 -0.59 9 9
KRT5 -0.4 0.45 -10000 0 -0.98 153 153
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.017 0.009 -10000 0 -10000 0 0
STAT1 0 0.11 -10000 0 -0.59 16 16
CGA -0.065 0.12 -10000 0 -0.51 5 5
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.081 0.11 0.34 22 -10000 0 22
MAPK3 0.013 0.012 -10000 0 -10000 0 0
MAPK1 0.013 0.011 -10000 0 -10000 0 0
ICAM1 -0.2 0.27 -10000 0 -0.69 83 83
NFKB1 -0.063 0.097 -10000 0 -0.29 5 5
MAPK8 -0.14 0.17 -10000 0 -0.42 91 91
MAPK9 0.013 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.013 0.2 0.62 20 -0.65 3 23
BAX 0.001 0.11 -10000 0 -0.49 2 2
POMC -0.13 0.24 -10000 0 -1.3 13 13
EP300 0.026 0.08 -10000 0 -0.57 4 4
cortisol/GR alpha (dimer)/p53 0.18 0.23 0.5 110 -0.49 3 113
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.069 0.25 19 -10000 0 19
SGK1 0.05 0.25 -10000 0 -1.4 14 14
IL13 -0.23 0.24 -10000 0 -0.71 57 57
IL6 -0.28 0.38 -10000 0 -0.82 140 140
PRKACG 0.005 0.044 -10000 0 -0.49 4 4
IL5 -0.2 0.19 -10000 0 -0.72 19 19
IL2 -0.23 0.21 -10000 0 -0.68 38 38
CDK5 0.014 0.006 -10000 0 -10000 0 0
PRKACB 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
IL8 -0.32 0.41 -10000 0 -0.89 147 147
CDK5R1/CDK5 -0.021 0.1 -10000 0 -0.43 31 31
NF kappa B1 p50/RelA/PKAc -0.056 0.13 -10000 0 -0.36 18 18
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.2 0.2 0.49 116 -10000 0 116
SMARCA4 0.015 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.13 0.37 56 -0.34 4 60
NF kappa B1 p50/RelA/Cbp -0.053 0.16 -10000 0 -0.47 16 16
JUN (dimer) -0.16 0.19 -10000 0 -0.5 70 70
YWHAH -0.01 0.11 -10000 0 -0.49 25 25
VIPR1 -0.12 0.26 -10000 0 -0.73 69 69
NR3C1 0.14 0.14 0.42 64 -10000 0 64
NR4A1 -0.019 0.14 -10000 0 -0.5 39 39
TIF2/SUV420H1 -0.029 0.11 -10000 0 -0.43 35 35
MAPKKK cascade -0.009 0.2 0.61 20 -0.7 2 22
cortisol/GR alpha (dimer)/Src-1 0.21 0.21 0.52 119 -10000 0 119
PBX1 0.013 0.028 -10000 0 -0.59 1 1
POU1F1 0.004 0.024 -10000 0 -0.49 1 1
SELE -0.28 0.36 -10000 0 -0.77 142 142
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.14 0.37 56 -0.35 4 60
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.2 0.2 0.49 116 -10000 0 116
mol:cortisol 0.12 0.15 0.34 119 -10000 0 119
MMP1 -0.12 0.16 -10000 0 -0.53 46 46
PLK2 and PLK4 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
PLK2 -0.018 0.12 -9999 0 -0.5 32 32
PLK4 -0.012 0.11 -9999 0 -0.5 26 26
regulation of centriole replication -0.018 0.12 -9999 0 -0.36 57 57
IL1-mediated signaling 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
UBC13/UEV1A -0.003 0.03 -10000 0 -0.34 4 4
PRKCZ -0.015 0.13 -10000 0 -0.55 27 27
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.013 0.022 -10000 0 -0.49 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.078 0.12 -10000 0 -0.39 31 31
IRAK/TOLLIP 0.03 0.024 -10000 0 -10000 0 0
IKBKB 0.014 0 -10000 0 -10000 0 0
IKBKG 0.014 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.16 0.21 -10000 0 -0.41 207 207
IL1A -0.093 0.22 -10000 0 -0.54 99 99
IL1B -0.13 0.21 -10000 0 -0.4 190 190
IRAK/TRAF6/p62/Atypical PKCs -0.014 0.057 -10000 0 -0.42 1 1
IL1R2 -0.12 0.24 -10000 0 -0.53 128 128
IL1R1 -0.032 0.15 -10000 0 -0.52 45 45
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.045 0.12 0.21 1 -0.41 21 22
TOLLIP 0.014 0 -10000 0 -10000 0 0
TICAM2 0 0.089 -10000 0 -0.58 12 12
MAP3K3 0.014 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.064 0.033 -10000 0 -10000 0 0
JUN 0.034 0.07 -10000 0 -0.45 4 4
MAP3K7 0.014 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.14 0.17 -10000 0 -0.54 49 49
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.11 0.17 -10000 0 -0.4 87 87
PIK3R1 0.014 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.099 0.16 -10000 0 -0.52 31 31
IL1 beta fragment/IL1R1/IL1RAP -0.14 0.21 -10000 0 -0.43 119 119
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 0.032 0.059 -10000 0 -0.54 1 1
IRAK1 0.023 0.027 -10000 0 -0.28 4 4
IL1RN/IL1R1 -0.12 0.2 -10000 0 -0.42 144 144
IRAK4 0.013 0.022 -10000 0 -0.49 1 1
PRKCI 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.027 -10000 0 -0.59 1 1
PI3K -0.001 0.019 -10000 0 -0.43 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.063 0.14 -10000 0 -0.41 36 36
CHUK 0.014 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.14 0.21 -10000 0 -0.43 119 119
IL1 beta/IL1R2 -0.19 0.23 -10000 0 -0.38 266 266
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.12 0.15 -10000 0 -0.48 49 49
IRAK3 0.008 0.062 -10000 0 -0.56 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.14 0.18 -10000 0 -0.54 56 56
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.043 0.14 -10000 0 -0.41 24 24
IL1 alpha/IL1R1/IL1RAP -0.12 0.18 -10000 0 -0.44 83 83
RELA 0.014 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.014 0 -10000 0 -10000 0 0
MYD88 0.004 0.077 -10000 0 -0.57 9 9
IRAK/TRAF6/MEKK3 0.037 0.027 -10000 0 -0.3 1 1
IL1RAP -0.036 0.15 -10000 0 -0.51 50 50
UBE2N 0.014 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.11 0.15 -10000 0 -0.48 41 41
CASP1 -0.015 0.12 -10000 0 -0.53 28 28
IL1RN/IL1R2 -0.18 0.24 -10000 0 -0.45 201 201
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.13 0.21 -10000 0 -0.57 52 52
TMEM189-UBE2V1 0.004 0.044 -10000 0 -0.49 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.023 0.12 -10000 0 -0.41 23 23
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
IL1RN -0.11 0.23 -10000 0 -0.53 119 119
TRAF6/TAK1/TAB1/TAB2 -0.002 0.023 -10000 0 -0.3 1 1
MAP2K6 0.033 0.029 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.074 0.17 -10000 0 -0.42 104 104
TP53 -0.034 0.089 -10000 0 -0.43 14 14
Senescence -0.034 0.089 -10000 0 -0.43 14 14
Apoptosis -0.034 0.089 -10000 0 -0.43 14 14
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.048 0.1 0.25 102 -0.26 2 104
MDM4 0.005 0.066 -10000 0 -0.49 9 9
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 55 55
NF kappa B1 p50/RelA/I kappa B alpha -0.041 0.089 -9999 0 -0.38 17 17
AP1 -0.12 0.17 -9999 0 -0.52 50 50
mol:PIP3 -0.098 0.15 -9999 0 -0.46 44 44
AKT1 0.018 0.099 -9999 0 -0.34 10 10
PTK2B -0.018 0.1 -9999 0 -0.31 34 34
RHOA 0.008 0.063 -9999 0 -0.32 7 7
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.086 -9999 0 -0.37 9 9
MAGI3 0.002 0.084 -9999 0 -0.59 10 10
RELA 0.014 0 -9999 0 -10000 0 0
apoptosis -0.043 0.13 -9999 0 -0.34 61 61
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.006 0.1 -9999 0 -0.32 28 28
NF kappa B1 p50/RelA -0.069 0.13 -9999 0 -0.46 33 33
endothelial cell migration -0.045 0.18 -9999 0 -0.44 73 73
ADCY4 -0.022 0.15 -9999 0 -0.41 57 57
ADCY5 -0.027 0.16 -9999 0 -0.42 64 64
ADCY6 -0.02 0.15 -9999 0 -0.41 56 56
ADCY7 -0.02 0.15 -9999 0 -0.41 56 56
ADCY1 -0.048 0.17 -9999 0 -0.43 65 65
ADCY2 -0.026 0.16 -9999 0 -0.42 60 60
ADCY3 -0.02 0.15 -9999 0 -0.41 56 56
ADCY8 -0.043 0.18 -9999 0 -0.48 63 63
ADCY9 -0.021 0.15 -9999 0 -0.42 56 56
GSK3B -0.01 0.1 -9999 0 -0.32 25 25
arachidonic acid secretion -0.012 0.14 -9999 0 -0.38 56 56
GNG2 0.009 0.053 -9999 0 -0.59 4 4
TRIP6 0.009 0.065 -9999 0 -0.4 5 5
GNAO1 -0.034 0.14 -9999 0 -0.35 81 81
HRAS 0.014 0 -9999 0 -10000 0 0
NFKBIA -0.011 0.12 -9999 0 -0.4 27 27
GAB1 0.012 0.035 -9999 0 -0.54 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.082 -9999 0 -1 3 3
JUN 0.003 0.074 -9999 0 -0.5 11 11
LPA/LPA2/NHERF2 -0.011 0.054 -9999 0 -0.33 13 13
TIAM1 -0.006 0.11 -9999 0 -1.3 3 3
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.005 0.088 -9999 0 -0.38 9 9
PLCB3 0.019 0.053 -9999 0 -0.29 13 13
FOS -0.096 0.22 -9999 0 -0.55 101 101
positive regulation of mitosis -0.012 0.14 -9999 0 -0.38 56 56
LPA/LPA1-2-3 -0.08 0.14 -9999 0 -0.38 68 68
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
stress fiber formation -0.021 0.12 -9999 0 -0.34 34 34
GNAZ -0.03 0.14 -9999 0 -0.34 77 77
EGFR/PI3K-beta/Gab1 -0.1 0.15 -9999 0 -0.48 44 44
positive regulation of dendritic cell cytokine production -0.08 0.14 -9999 0 -0.37 68 68
LPA/LPA2/MAGI-3 -0.017 0.07 -9999 0 -0.35 21 21
ARHGEF1 -0.01 0.12 -9999 0 -0.31 52 52
GNAI2 -0.03 0.14 -9999 0 -0.34 77 77
GNAI3 -0.03 0.14 -9999 0 -0.34 77 77
GNAI1 -0.042 0.15 -9999 0 -0.35 93 93
LPA/LPA3 -0.038 0.11 -9999 0 -0.36 50 50
LPA/LPA2 -0.013 0.062 -9999 0 -0.41 11 11
LPA/LPA1 -0.067 0.15 -9999 0 -0.38 90 90
HB-EGF/EGFR -0.13 0.21 -9999 0 -0.37 201 201
HBEGF -0.092 0.19 -9999 0 -0.38 148 148
mol:DAG 0.005 0.088 -9999 0 -0.38 9 9
cAMP biosynthetic process -0.024 0.16 -9999 0 -0.42 56 56
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 -0.015 0.13 -9999 0 -0.42 28 28
GNAQ -0.008 0.084 -9999 0 -0.32 17 17
LPAR2 0.002 0.084 -9999 0 -0.56 11 11
LPAR3 -0.042 0.15 -9999 0 -0.49 50 50
LPAR1 -0.066 0.2 -9999 0 -0.57 69 69
IL8 -0.18 0.23 -9999 0 -0.48 158 158
PTK2 -0.045 0.15 -9999 0 -0.34 68 68
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.043 0.13 -9999 0 -0.34 61 61
EGFR -0.083 0.21 -9999 0 -0.55 89 89
PLCG1 -0.009 0.09 -9999 0 -0.3 23 23
PLD2 -0.046 0.15 -9999 0 -0.36 58 58
G12/G13 -0.05 0.11 -9999 0 -0.34 52 52
PI3K-beta -0.039 0.086 -9999 0 -0.38 12 12
cell migration -0.026 0.055 -9999 0 -0.26 5 5
SLC9A3R2 0.012 0.031 -9999 0 -0.49 2 2
PXN -0.022 0.12 -9999 0 -0.34 34 34
HRAS/GTP -0.013 0.15 -9999 0 -0.39 56 56
RAC1 0.014 0 -9999 0 -10000 0 0
MMP9 -0.14 0.24 -9999 0 -0.52 144 144
PRKCE 0.003 0.077 -9999 0 -0.52 11 11
PRKCD -0.003 0.11 -9999 0 -0.39 22 22
Gi(beta/gamma) -0.015 0.14 -9999 0 -0.38 57 57
mol:LPA -0.003 0.035 -9999 0 -0.19 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.065 0.12 -9999 0 -0.43 25 25
MAPKKK cascade -0.012 0.14 -9999 0 -0.38 56 56
contractile ring contraction involved in cytokinesis 0.008 0.062 -9999 0 -0.31 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.022 0.1 -9999 0 -0.32 35 35
GNA15 -0.019 0.099 -9999 0 -0.32 33 33
GNA12 0.013 0.027 -9999 0 -0.59 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
MAPT -0.007 0.11 -9999 0 -0.34 25 25
GNA11 -0.014 0.094 -9999 0 -0.32 26 26
Rac1/GTP -0.003 0.09 -9999 0 -1.1 3 3
MMP2 -0.045 0.18 -9999 0 -0.44 73 73
BCR signaling pathway

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
JUN -0.037 0.14 -10000 0 -0.36 50 50
IKBKB -0.012 0.078 -10000 0 -0.26 17 17
AKT1 -0.05 0.1 -10000 0 -0.25 50 50
IKBKG -0.01 0.082 -10000 0 -0.27 20 20
CALM1 -0.055 0.15 -10000 0 -0.41 56 56
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
MAP3K1 -0.061 0.18 -10000 0 -0.49 55 55
MAP3K7 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.065 0.16 0.21 2 -0.44 57 59
DOK1 0.012 0.035 -10000 0 -0.54 2 2
AP-1 -0.034 0.099 0.18 2 -0.25 38 40
LYN 0.004 0.072 -10000 0 -0.51 10 10
BLNK -0.056 0.19 -10000 0 -0.58 61 61
SHC1 0.009 0.049 -10000 0 -0.49 5 5
BCR complex -0.076 0.18 -10000 0 -0.44 91 91
CD22 -0.17 0.21 -10000 0 -0.51 99 99
CAMK2G -0.044 0.14 -10000 0 -0.45 35 35
CSNK2A1 0.014 0 -10000 0 -10000 0 0
INPP5D 0.008 0.06 -10000 0 -0.54 6 6
SHC/GRB2/SOS1 -0.091 0.17 -10000 0 -0.55 43 43
GO:0007205 -0.066 0.16 0.21 2 -0.44 57 59
SYK -0.013 0.12 -10000 0 -0.57 24 24
ELK1 -0.055 0.15 -10000 0 -0.41 57 57
NFATC1 -0.061 0.17 -10000 0 -0.45 62 62
B-cell antigen/BCR complex -0.076 0.18 -10000 0 -0.44 91 91
PAG1/CSK -0.001 0.019 -10000 0 -0.43 1 1
NFKBIB 0.006 0.029 0.081 2 -10000 0 2
HRAS -0.049 0.16 -10000 0 -0.48 38 38
NFKBIA 0.007 0.028 0.081 2 -10000 0 2
NF-kappa-B/RelA/I kappa B beta 0.013 0.023 -10000 0 -10000 0 0
RasGAP/Csk -0.12 0.18 -10000 0 -0.55 51 51
mol:GDP -0.062 0.16 -10000 0 -0.42 57 57
PTEN 0.013 0.027 -10000 0 -0.59 1 1
CD79B -0.047 0.17 -10000 0 -0.53 58 58
NF-kappa-B/RelA/I kappa B alpha 0.013 0.023 -10000 0 -10000 0 0
GRB2 0.013 0.022 -10000 0 -0.49 1 1
PI3K/BCAP/CD19 -0.086 0.19 -10000 0 -0.48 74 74
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.067 0.16 0.21 2 -0.45 57 59
CSK 0.014 0 -10000 0 -10000 0 0
FOS -0.095 0.18 -10000 0 -0.5 54 54
CHUK -0.01 0.082 -10000 0 -0.28 18 18
IBTK 0.014 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.064 0.14 -10000 0 -0.51 35 35
PTPN6 -0.16 0.21 -10000 0 -0.52 95 95
RELA 0.014 0 -10000 0 -10000 0 0
BCL2A1 -0.006 0.045 -10000 0 -0.1 40 40
VAV2 -0.11 0.18 -10000 0 -0.52 60 60
ubiquitin-dependent protein catabolic process 0.011 0.028 0.085 2 -10000 0 2
BTK -0.041 0.2 0.36 1 -1.1 17 18
CD19 -0.11 0.18 -10000 0 -0.48 75 75
MAP4K1 -0.018 0.13 -10000 0 -0.58 28 28
CD72 -0.008 0.11 -10000 0 -0.51 22 22
PAG1 0.013 0.027 -10000 0 -0.59 1 1
MAPK14 -0.044 0.16 -10000 0 -0.42 49 49
SH3BP5 0.01 0.051 -10000 0 -0.57 4 4
PIK3AP1 -0.064 0.18 0.24 2 -0.48 64 66
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.065 0.22 -10000 0 -0.54 64 64
RAF1 -0.038 0.15 -10000 0 -0.48 31 31
RasGAP/p62DOK/SHIP -0.12 0.18 -10000 0 -0.54 53 53
CD79A -0.04 0.16 -10000 0 -0.54 50 50
re-entry into mitotic cell cycle -0.034 0.099 0.18 2 -0.26 38 40
RASA1 0.014 0 -10000 0 -10000 0 0
MAPK3 -0.017 0.12 -10000 0 -0.41 25 25
MAPK1 -0.017 0.12 -10000 0 -0.41 25 25
CD72/SHP1 -0.14 0.22 -10000 0 -0.53 89 89
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.051 0.16 -10000 0 -0.42 58 58
actin cytoskeleton organization -0.062 0.17 -10000 0 -0.48 48 48
NF-kappa-B/RelA 0.03 0.045 0.16 2 -10000 0 2
Calcineurin -0.057 0.12 -10000 0 -0.44 31 31
PI3K -0.13 0.18 -10000 0 -0.47 82 82
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.081 0.17 0.24 2 -0.49 57 59
SOS1 0.014 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.11 0.27 -10000 0 -0.79 58 58
DAPP1 -0.14 0.29 -10000 0 -0.88 55 55
cytokine secretion -0.056 0.16 -10000 0 -0.42 62 62
mol:DAG -0.067 0.16 0.21 2 -0.45 57 59
PLCG2 0 0.088 -10000 0 -0.55 13 13
MAP2K1 -0.028 0.14 -10000 0 -0.45 28 28
B-cell antigen/BCR complex/FcgammaRIIB -0.15 0.22 -10000 0 -0.41 185 185
mol:PI-3-4-5-P3 -0.1 0.12 -10000 0 -0.35 65 65
ETS1 -0.038 0.14 -10000 0 -0.43 33 33
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.1 0.2 -10000 0 -0.63 41 41
B-cell antigen/BCR complex/LYN -0.1 0.18 -10000 0 -0.47 76 76
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.027 -10000 0 -0.59 1 1
RAC1 -0.067 0.18 -10000 0 -0.52 47 47
B-cell antigen/BCR complex/LYN/SYK -0.17 0.23 -10000 0 -0.56 96 96
CARD11 -0.066 0.18 -10000 0 -0.49 60 60
FCGR2B -0.13 0.24 -10000 0 -0.53 138 138
PPP3CA 0.012 0.031 -10000 0 -0.49 2 2
BCL10 0.014 0 -10000 0 -10000 0 0
IKK complex 0.002 0.036 -10000 0 -0.12 1 1
PTPRC -0.04 0.17 -10000 0 -0.54 51 51
PDPK1 -0.05 0.098 -10000 0 -0.25 46 46
PPP3CB 0.011 0.038 -10000 0 -0.49 3 3
PPP3CC 0.014 0 -10000 0 -10000 0 0
POU2F2 0.013 0.024 -10000 0 -0.099 7 7
Nongenotropic Androgen signaling

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.012 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.062 0.13 -10000 0 -0.33 76 76
regulation of S phase of mitotic cell cycle -0.019 0.11 -10000 0 -0.26 72 72
GNAO1 0.008 0.059 -10000 0 -0.59 5 5
HRAS 0.014 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.007 0.055 -10000 0 -0.36 12 12
PELP1 0.014 0.001 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.024 0.13 -10000 0 -0.37 24 24
T-DHT/AR -0.084 0.17 -10000 0 -0.41 107 107
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.006 97 97
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.1 -10000 0 -0.59 16 16
mol:GDP -0.077 0.16 -10000 0 -0.46 72 72
cell proliferation -0.038 0.18 -10000 0 -0.42 63 63
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
FOS -0.086 0.28 -10000 0 -0.78 63 63
mol:Ca2+ -0.01 0.019 -10000 0 -0.067 17 17
MAPK3 -0.03 0.15 -10000 0 -0.47 24 24
MAPK1 -0.014 0.09 -10000 0 -0.27 20 20
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.004 101 101
cAMP biosynthetic process 0.002 0.055 -10000 0 -0.33 12 12
GNG2 0.009 0.053 -10000 0 -0.59 4 4
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 101 101
HRAS/GTP -0.059 0.11 -10000 0 -0.3 76 76
actin cytoskeleton reorganization -0.001 0.012 -10000 0 -0.28 1 1
SRC 0.014 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 101 101
PI3K 0.001 0.017 -10000 0 -0.37 1 1
apoptosis 0.038 0.17 0.42 63 -10000 0 63
T-DHT/AR/PELP1 -0.07 0.14 -10000 0 -0.34 107 107
HRAS/GDP -0.071 0.15 -10000 0 -0.43 72 72
CREB1 -0.042 0.18 -10000 0 -0.45 63 63
RAC1-CDC42/GTP -0.001 0.013 -10000 0 -0.28 1 1
AR -0.1 0.23 -10000 0 -0.56 107 107
GNB1 0.014 0 -10000 0 -10000 0 0
RAF1 -0.029 0.12 -10000 0 -0.34 24 24
RAC1-CDC42/GDP -0.065 0.14 -10000 0 -0.4 72 72
T-DHT/AR/PELP1/Src -0.062 0.13 -10000 0 -0.31 107 107
MAP2K2 -0.023 0.12 -10000 0 -0.34 24 24
T-DHT/AR/PELP1/Src/PI3K -0.019 0.11 -10000 0 -0.26 72 72
GNAZ 0.014 0 -10000 0 -10000 0 0
SHBG 0 0.089 -10000 0 -0.58 12 12
Gi family/GNB1/GNG2/GDP 0.021 0.074 -10000 0 -0.45 6 6
mol:T-DHT 0 0.001 -10000 0 -0.003 73 73
RAC1 0.014 0 -10000 0 -10000 0 0
GNRH1 0.001 0.067 -10000 0 -0.4 14 14
Gi family/GTP -0.013 0.08 -10000 0 -0.36 6 6
CDC42 0.014 0 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.03 0.13 -9999 0 -0.3 76 76
FZD6 -0.014 0.12 -9999 0 -0.49 29 29
WNT6 -0.033 0.16 -9999 0 -0.53 45 45
WNT4 -0.033 0.15 -9999 0 -0.52 46 46
FZD3 0.011 0.046 -9999 0 -0.59 3 3
WNT5A -0.013 0.12 -9999 0 -0.56 24 24
WNT11 -0.017 0.13 -9999 0 -0.54 29 29
EGFR-dependent Endothelin signaling events

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
HRAS 0.014 0 -9999 0 -10000 0 0
EGFR -0.083 0.21 -9999 0 -0.55 89 89
EGF/EGFR -0.11 0.17 -9999 0 -0.36 119 119
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.078 0.14 -9999 0 -0.53 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.021 0.14 -9999 0 -0.54 33 33
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.05 0.18 -9999 0 -0.56 58 58
EGF/EGFR dimer/SHC -0.095 0.17 -9999 0 -0.4 92 92
mol:GDP -0.077 0.14 -9999 0 -0.52 17 17
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.036 0.16 -9999 0 -0.52 48 48
GRB2/SOS1 -0.001 0.015 -9999 0 -0.34 1 1
HRAS/GTP -0.07 0.13 -9999 0 -0.48 17 17
SHC1 0.009 0.049 -9999 0 -0.49 5 5
HRAS/GDP -0.071 0.13 -9999 0 -0.49 17 17
FRAP1 -0.045 0.15 -9999 0 -0.5 17 17
EGF/EGFR dimer -0.11 0.2 -9999 0 -0.43 132 132
SOS1 0.014 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -0.49 1 1
ETA receptor/Endothelin-1 -0.059 0.14 -9999 0 -0.39 78 78
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.059 0.12 -9999 0 -0.32 73 73
SMAD6-7/SMURF1 -0.004 0.036 -9999 0 -0.33 6 6
NOG -0.064 0.2 -9999 0 -0.58 68 68
SMAD9 -0.029 0.16 -9999 0 -0.56 37 37
SMAD4 0.014 0 -9999 0 -10000 0 0
SMAD5 -0.001 0.12 -9999 0 -0.48 17 17
BMP7/USAG1 -0.092 0.16 -9999 0 -0.38 126 126
SMAD5/SKI 0.007 0.12 -9999 0 -0.45 17 17
SMAD1 0.044 0.029 -9999 0 -0.32 1 1
BMP2 -0.079 0.22 -9999 0 -0.59 79 79
SMAD1/SMAD1/SMAD4 -0.003 0.025 -9999 0 -10000 0 0
BMPR1A 0.014 0 -9999 0 -10000 0 0
BMPR1B -0.022 0.14 -9999 0 -0.59 31 31
BMPR1A-1B/BAMBI -0.027 0.1 -9999 0 -0.39 35 35
AHSG -0.078 0.21 -9999 0 -0.55 83 83
CER1 -0.013 0.098 -9999 0 -0.49 21 21
BMP2-4/CER1 -0.082 0.19 -9999 0 -0.45 94 94
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.014 0.16 -9999 0 -0.46 40 40
BMP2-4 (homodimer) -0.083 0.2 -9999 0 -0.51 84 84
RGMB 0.004 0.074 -9999 0 -0.55 9 9
BMP6/BMPR2/BMPR1A-1B -0.028 0.092 -9999 0 -0.33 36 36
RGMA -0.002 0.096 -9999 0 -0.58 14 14
SMURF1 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.021 0.15 -9999 0 -0.46 37 37
BMP2-4/USAG1 -0.14 0.22 -9999 0 -0.42 172 172
SMAD6/SMURF1/SMAD5 0.007 0.12 -9999 0 -0.46 16 16
SOSTDC1 -0.11 0.23 -9999 0 -0.52 120 120
BMP7/BMPR2/BMPR1A-1B -0.023 0.083 -9999 0 -0.32 38 38
SKI 0.014 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.004 0.097 -9999 0 -0.52 17 17
HFE2 0.002 0.066 -9999 0 -0.49 9 9
ZFYVE16 0.014 0 -9999 0 -10000 0 0
MAP3K7 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.075 0.17 -9999 0 -0.43 90 90
SMAD5/SMAD5/SMAD4 0.007 0.12 -9999 0 -0.45 17 17
MAPK1 0.014 0 -9999 0 -10000 0 0
TAK1/TAB family -0.047 0.11 -9999 0 -0.4 34 34
BMP7 (homodimer) 0.006 0.07 -9999 0 -0.59 7 7
NUP214 0.014 0 -9999 0 -10000 0 0
BMP6/FETUA -0.075 0.16 -9999 0 -0.41 95 95
SMAD1/SKI 0.05 0.028 -9999 0 -10000 0 0
SMAD6 0.008 0.062 -9999 0 -0.56 6 6
CTDSP2 0.01 0.044 -9999 0 -0.49 4 4
BMP2-4/FETUA -0.12 0.21 -9999 0 -0.42 150 150
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.17 0.27 -9999 0 -0.55 168 168
BMPR2 (homodimer) 0.014 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.005 0.037 -9999 0 -0.28 9 9
BMPR1A-1B (homodimer) -0.026 0.1 -9999 0 -0.43 31 31
CHRDL1 -0.077 0.21 -9999 0 -0.57 80 80
ENDOFIN/SMAD1 0.05 0.028 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.029 -9999 0 -10000 0 0
SMAD6/SMURF1 0.014 0 -9999 0 -10000 0 0
BAMBI 0.005 0.069 -9999 0 -0.51 9 9
SMURF2 0.012 0.038 -9999 0 -0.59 2 2
BMP2-4/CHRDL1 -0.12 0.21 -9999 0 -0.42 153 153
BMP2-4/GREM1 -0.18 0.23 -9999 0 -0.41 221 221
SMAD7 0.014 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.02 0.16 -9999 0 -0.52 37 37
SMAD1/SMAD6 0.05 0.028 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.006 0.07 -9999 0 -0.59 7 7
BMP6 -0.004 0.097 -9999 0 -0.53 17 17
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.014 0.14 -9999 0 -0.42 37 37
PPM1A 0.014 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.049 0.035 -9999 0 -0.32 1 1
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0.027 -9999 0 -0.59 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 0.005 0.066 -9999 0 -0.49 9 9
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.052 0.18 -9999 0 -0.48 54 54
CHRD 0.006 0.07 -9999 0 -0.59 7 7
BMPR2 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.16 -9999 0 -0.5 37 37
BMP4 -0.014 0.13 -9999 0 -0.58 24 24
FST -0.067 0.2 -9999 0 -0.54 76 76
BMP2-4/NOG -0.11 0.25 -9999 0 -0.54 109 109
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.021 0.076 -9999 0 -0.29 38 38
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.022 -9999 0 -0.49 1 1
LAT2 -0.052 0.18 -9999 0 -0.56 36 36
AP1 -0.11 0.18 -9999 0 -0.53 57 57
mol:PIP3 -0.063 0.2 -9999 0 -0.56 42 42
IKBKB -0.029 0.11 -9999 0 -0.28 41 41
AKT1 -0.034 0.14 -9999 0 -0.42 23 23
IKBKG -0.029 0.11 -9999 0 -0.28 36 36
MS4A2 -0.022 0.11 -9999 0 -0.49 25 25
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
MAP3K1 -0.018 0.15 -9999 0 -0.52 31 31
mol:Ca2+ -0.043 0.15 -9999 0 -0.41 41 41
LYN 0.003 0.074 -9999 0 -0.52 10 10
CBLB -0.039 0.14 -9999 0 -0.45 30 30
SHC1 0.009 0.049 -9999 0 -0.49 5 5
RasGAP/p62DOK -0.019 0.071 -9999 0 -0.28 34 34
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.008 0.06 -9999 0 -0.54 6 6
PLD2 -0.07 0.16 -9999 0 -0.34 88 88
PTPN13 -0.03 0.14 -9999 0 -0.56 20 20
PTPN11 0.011 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.003 0.12 -9999 0 -0.34 20 20
SYK -0.014 0.13 -9999 0 -0.58 24 24
GRB2 0.013 0.022 -9999 0 -0.49 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.17 -9999 0 -0.58 40 40
LAT -0.054 0.15 -9999 0 -0.42 48 48
PAK2 -0.027 0.17 -9999 0 -0.61 30 30
NFATC2 -0.099 0.19 -9999 0 -0.55 63 63
HRAS -0.04 0.19 -9999 0 -0.66 33 33
GAB2 0.013 0.027 -9999 0 -0.59 1 1
PLA2G1B 0.039 0.024 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.18 -9999 0 -0.36 178 178
Antigen/IgE/Fc epsilon R1 -0.11 0.17 -9999 0 -0.33 178 178
mol:GDP -0.049 0.2 -9999 0 -0.67 37 37
JUN 0.003 0.074 -9999 0 -0.5 11 11
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
FOS -0.096 0.22 -9999 0 -0.55 101 101
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.064 0.14 -9999 0 -0.43 37 37
CHUK -0.029 0.11 -9999 0 -0.28 38 38
KLRG1 -0.042 0.14 -9999 0 -0.5 24 24
VAV1 -0.054 0.18 -9999 0 -0.61 35 35
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.037 0.14 -9999 0 -0.52 22 22
negative regulation of mast cell degranulation -0.035 0.14 -9999 0 -0.52 24 24
BTK -0.072 0.2 -9999 0 -0.7 34 34
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.19 -9999 0 -0.38 114 114
GAB2/PI3K/SHP2 -0.081 0.13 -9999 0 -0.46 23 23
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.056 0.16 -9999 0 -0.42 46 46
RAF1 0.029 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.17 0.22 -9999 0 -0.44 157 157
FCER1G -0.02 0.14 -9999 0 -0.57 30 30
FCER1A -0.14 0.25 -9999 0 -0.54 148 148
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.16 -9999 0 -0.36 95 95
MAPK3 0.038 0.023 -9999 0 -10000 0 0
MAPK1 0.038 0.023 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.004 0.11 -9999 0 -0.59 14 14
DUSP1 -0.02 0.13 -9999 0 -0.53 32 32
NF-kappa-B/RelA -0.033 0.049 -9999 0 -0.23 1 1
actin cytoskeleton reorganization -0.035 0.13 -9999 0 -0.53 20 20
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.069 0.16 -9999 0 -0.63 30 30
FER -0.051 0.15 -9999 0 -0.42 49 49
RELA 0.014 0 -9999 0 -10000 0 0
ITK -0.067 0.12 -9999 0 -0.34 59 59
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG1 -0.047 0.21 -9999 0 -0.67 36 36
cytokine secretion -0.024 0.036 -9999 0 -10000 0 0
SPHK1 -0.059 0.16 -9999 0 -0.46 46 46
PTK2 -0.037 0.14 -9999 0 -0.56 20 20
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.19 -9999 0 -0.6 42 42
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.051 0.19 -9999 0 -0.54 39 39
MAP2K2 0.035 0.022 -9999 0 -10000 0 0
MAP2K1 0.033 0.028 -9999 0 -10000 0 0
MAP2K7 0.014 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.047 0.13 -9999 0 -0.48 23 23
MAP2K4 0.02 0.014 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.19 0.22 -9999 0 -0.46 163 163
mol:Choline -0.069 0.16 -9999 0 -0.34 88 88
SHC/Grb2/SOS1 -0.059 0.11 -9999 0 -0.5 22 22
FYN 0.014 0 -9999 0 -10000 0 0
DOK1 0.012 0.035 -9999 0 -0.54 2 2
PXN -0.026 0.13 -9999 0 -0.51 20 20
HCLS1 -0.055 0.17 -9999 0 -0.54 40 40
PRKCB -0.052 0.14 -9999 0 -0.37 53 53
FCGR2B -0.13 0.24 -9999 0 -0.53 138 138
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.035 0.14 -9999 0 -0.53 24 24
LCP2 -0.001 0.086 -9999 0 -0.5 15 15
PLA2G4A -0.054 0.16 -9999 0 -0.45 46 46
RASA1 0.014 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.069 0.16 -9999 0 -0.34 88 88
IKK complex -0.008 0.086 -9999 0 -0.22 21 21
WIPF1 0.014 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.03 0.14 -9999 0 -0.38 58 58
CRKL 0.013 0.022 -9999 0 -0.49 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.009 0.053 -9999 0 -0.59 4 4
ITGA4 -0.052 0.18 -9999 0 -0.53 62 62
alpha4/beta7 Integrin/MAdCAM1 -0.12 0.18 -9999 0 -0.4 99 99
EPO -0.007 0.098 -9999 0 -0.5 20 20
alpha4/beta7 Integrin -0.077 0.17 -9999 0 -0.43 93 93
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.047 0.13 -9999 0 -0.39 62 62
EPO/EPOR (dimer) -0.014 0.071 -9999 0 -0.36 20 20
lamellipodium assembly 0.009 0.022 -9999 0 -10000 0 0
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
PI3K -0.001 0.019 -9999 0 -0.43 1 1
ARF6 0.014 0 -9999 0 -10000 0 0
JAK2 0 0.09 -9999 0 -0.28 33 33
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
MADCAM1 -0.11 0.23 -9999 0 -0.53 120 120
cell adhesion -0.12 0.17 -9999 0 -0.4 99 99
CRKL/CBL -0.001 0.015 -9999 0 -0.34 1 1
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
SRC -0.087 0.18 -9999 0 -0.35 124 124
ITGB7 -0.034 0.16 -9999 0 -0.54 45 45
RAC1 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.12 0.18 -9999 0 -0.35 182 182
p130Cas/Crk/Dock1 -0.054 0.16 -9999 0 -0.5 17 17
VCAM1 -0.14 0.25 -9999 0 -0.56 134 134
RHOA 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.034 0.094 -9999 0 -0.33 28 28
BCAR1 -0.073 0.17 -9999 0 -0.55 15 15
EPOR 0.013 0.022 -9999 0 -0.49 1 1
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 0.009 0.022 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.085 0.28 -10000 0 -0.88 39 39
NCK1/PAK1/Dok-R -0.095 0.13 -10000 0 -0.41 52 52
NCK1/Dok-R -0.11 0.32 -10000 0 -1.1 38 38
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
mol:beta2-estradiol 0.015 0.064 0.22 30 -10000 0 30
RELA 0.014 0 -10000 0 -10000 0 0
SHC1 0.009 0.049 -10000 0 -0.49 5 5
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.013 0.089 0.25 17 -0.47 8 25
TNIP2 0.014 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.11 0.26 -10000 0 -1 37 37
FN1 -0.003 0.092 -10000 0 -0.49 18 18
PLD2 -0.084 0.31 -10000 0 -1.1 37 37
PTPN11 0.014 0 -10000 0 -10000 0 0
GRB14 -0.18 0.26 -10000 0 -0.53 186 186
ELK1 -0.061 0.28 -10000 0 -0.99 37 37
GRB7 -0.032 0.14 -10000 0 -0.49 43 43
PAK1 -0.035 0.15 -10000 0 -0.5 49 49
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.29 -10000 0 -1 42 42
CDKN1A -0.1 0.28 -10000 0 -0.68 73 73
ITGA5 -0.01 0.11 -10000 0 -0.5 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.11 0.32 -10000 0 -1.1 38 38
CRK 0.014 0 -10000 0 -10000 0 0
mol:NO -0.057 0.22 -10000 0 -0.64 40 40
PLG -0.093 0.31 -10000 0 -1.1 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.077 0.26 -10000 0 -0.85 38 38
GRB2 0.013 0.022 -10000 0 -0.49 1 1
PIK3R1 0.014 0.002 -10000 0 -10000 0 0
ANGPT2 -0.11 0.28 -10000 0 -0.78 55 55
BMX -0.11 0.32 -10000 0 -1.1 39 39
ANGPT1 -0.13 0.34 -10000 0 -1.2 41 41
tube development -0.083 0.26 -10000 0 -0.66 61 61
ANGPT4 -0.05 0.18 -10000 0 -0.54 58 58
response to hypoxia -0.008 0.021 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.18 0.36 -10000 0 -1.2 44 44
alpha5/beta1 Integrin -0.017 0.079 -10000 0 -0.36 25 25
FGF2 0.011 0.044 -10000 0 -0.56 3 3
STAT5A (dimer) -0.11 0.31 -10000 0 -0.76 70 70
mol:L-citrulline -0.057 0.22 -10000 0 -0.64 40 40
AGTR1 -0.034 0.16 -10000 0 -0.55 43 43
MAPK14 -0.089 0.31 -10000 0 -1.1 37 37
Tie2/SHP2 -0.041 0.16 -10000 0 -1.2 8 8
TEK -0.023 0.19 -10000 0 -1.3 8 8
RPS6KB1 -0.072 0.26 -10000 0 -0.85 37 37
Angiotensin II/AT1 -0.025 0.12 -10000 0 -0.4 43 43
Tie2/Ang1/GRB2 -0.087 0.32 -10000 0 -1.2 37 37
MAPK3 -0.068 0.29 -10000 0 -1 37 37
MAPK1 -0.068 0.29 -10000 0 -1 37 37
Tie2/Ang1/GRB7 -0.11 0.33 -10000 0 -1.1 40 40
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.091 0.32 -10000 0 -1.1 37 37
PI3K -0.094 0.31 -10000 0 -1 37 37
FES -0.089 0.31 -10000 0 -1.1 37 37
Crk/Dok-R -0.11 0.32 -10000 0 -1.1 38 38
Tie2/Ang1/ABIN2 -0.087 0.32 -10000 0 -1.2 37 37
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.075 0.26 -10000 0 -0.77 41 41
STAT5A 0.001 0.088 -10000 0 -0.59 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.072 0.26 -10000 0 -0.85 37 37
Tie2/Ang2 -0.12 0.34 -10000 0 -0.9 61 61
Tie2/Ang1 -0.099 0.34 -10000 0 -1.2 37 37
FOXO1 -0.082 0.27 -10000 0 -0.73 56 56
ELF1 0.019 0.032 -10000 0 -0.64 1 1
ELF2 -0.088 0.31 -10000 0 -1.1 37 37
mol:Choline -0.078 0.3 -10000 0 -1.1 37 37
cell migration -0.054 0.073 -10000 0 -0.24 40 40
FYN -0.097 0.29 -10000 0 -0.75 61 61
DOK2 -0.07 0.2 -10000 0 -0.53 80 80
negative regulation of cell cycle -0.088 0.26 -10000 0 -0.61 73 73
ETS1 -0.011 0.1 -10000 0 -0.59 11 11
PXN -0.05 0.23 -10000 0 -0.7 37 37
ITGB1 0.012 0.031 -10000 0 -0.49 2 2
NOS3 -0.068 0.25 -10000 0 -0.73 40 40
RAC1 0.014 0 -10000 0 -10000 0 0
TNF -0.17 0.27 -10000 0 -0.56 156 156
MAPKKK cascade -0.078 0.3 -10000 0 -1.1 37 37
RASA1 0.014 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.091 0.33 -10000 0 -1.2 37 37
NCK1 0.013 0.027 -10000 0 -0.59 1 1
vasculogenesis -0.049 0.2 -10000 0 -0.57 41 41
mol:Phosphatidic acid -0.078 0.3 -10000 0 -1.1 37 37
mol:Angiotensin II -0.001 0.008 -10000 0 -10000 0 0
mol:NADP -0.057 0.22 -10000 0 -0.64 40 40
Rac1/GTP -0.12 0.22 -10000 0 -0.79 37 37
MMP2 -0.097 0.32 -10000 0 -1.1 38 38
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 0.009 0.053 -10000 0 -0.59 4 4
HDAC3 0.014 0 -10000 0 -10000 0 0
VDR -0.065 0.19 -10000 0 -0.53 74 74
Cbp/p300/PCAF -0.003 0.034 -10000 0 -0.34 5 5
EP300 0.009 0.053 -10000 0 -0.59 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.064 -10000 0 -0.4 5 5
KAT2B 0.013 0.022 -10000 0 -0.49 1 1
MAPK14 0.014 0 -10000 0 -10000 0 0
AKT1 0.008 0.07 0.22 7 -0.34 3 10
RAR alpha/9cRA/Cyclin H -0.053 0.087 -10000 0 -0.74 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.058 -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 -0.065 0.11 -10000 0 -0.53 14 14
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.056 0.14 -10000 0 -0.39 74 74
RXRs/RARs/NRIP1/9cRA -0.061 0.2 -10000 0 -0.46 77 77
NCOA2 -0.027 0.15 -10000 0 -0.59 35 35
NCOA3 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.064 0.19 -10000 0 -0.53 74 74
RARG 0.014 0.022 -10000 0 -0.49 1 1
RAR gamma1/9cRA -0.001 0.013 -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 -0.001 0.099 -10000 0 -0.59 14 14
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.15 0.22 -10000 0 -0.55 95 95
RARA -0.053 0.12 -10000 0 -0.26 102 102
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.005 0.097 -10000 0 -0.37 18 18
PRKCA 0.016 0.027 -10000 0 -0.59 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.074 0.2 -10000 0 -0.46 90 90
RXRG -0.13 0.22 -10000 0 -0.44 124 124
RXRA -0.037 0.11 -10000 0 -0.7 2 2
RXRB -0.076 0.15 -10000 0 -0.35 90 90
VDR/Vit D3/DNA -0.056 0.14 -10000 0 -0.39 74 74
RBP1 -0.075 0.2 -10000 0 -0.5 89 89
CRBP1/9-cic-RA -0.062 0.14 -10000 0 -0.36 89 89
RARB 0.013 0.046 -10000 0 -0.59 3 3
PRKCG -0.19 0.27 -10000 0 -0.54 193 193
MNAT1 0.013 0.022 -10000 0 -0.49 1 1
RAR alpha/RXRs -0.064 0.21 -10000 0 -0.47 90 90
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.049 0.17 -10000 0 -0.38 90 90
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.097 -10000 0 -0.41 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.074 0.2 -10000 0 -0.46 90 90
positive regulation of DNA binding -0.051 0.082 -10000 0 -0.67 2 2
NRIP1 -0.065 0.18 -10000 0 -0.58 27 27
RXRs/RARs -0.081 0.2 -10000 0 -0.47 90 90
RXRs/RXRs/DNA/9cRA -0.12 0.2 -10000 0 -0.52 90 90
PRKACA 0.014 0 -10000 0 -10000 0 0
CDK7 0.014 0 -10000 0 -10000 0 0
TFIIH -0.001 0.012 -10000 0 -0.28 1 1
RAR alpha/9cRA -0.038 0.065 -10000 0 -0.6 2 2
CCNH 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.012 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.002 0.17 -9999 0 -1.3 9 9
VDR -0.065 0.19 -9999 0 -0.53 74 74
FAM120B 0.014 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.048 0.16 -9999 0 -0.45 31 31
RXRs/LXRs/DNA/Oxysterols -0.075 0.22 -9999 0 -0.45 97 97
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 0.027 0.056 -9999 0 -0.25 15 15
RXRs/NUR77 -0.035 0.14 -9999 0 -0.36 67 67
RXRs/PPAR -0.017 0.12 -9999 0 -0.36 31 31
NCOR2 0.014 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.056 0.14 -9999 0 -0.39 74 74
RARs/VDR/DNA/Vit D3 -0.039 0.097 -9999 0 -0.31 35 35
RARA 0.014 0 -9999 0 -10000 0 0
NCOA1 0.014 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.064 0.19 -9999 0 -0.53 74 74
RARs/RARs/DNA/9cRA 0.017 0.032 -9999 0 -0.3 4 4
RARG 0.013 0.022 -9999 0 -0.49 1 1
RPS6KB1 0.02 0.067 -9999 0 -0.4 9 9
RARs/THRs/DNA/SMRT 0.027 0.056 -9999 0 -0.25 15 15
THRA 0.011 0.046 -9999 0 -0.59 3 3
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.056 0.14 -9999 0 -0.39 74 74
RXRs/PPAR/9cRA/PGJ2/DNA -0.036 0.13 -9999 0 -0.35 60 60
NR1H4 -0.12 0.24 -9999 0 -0.53 129 129
RXRs/LXRs/DNA -0.024 0.14 -9999 0 -0.43 23 23
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 -0.058 0.16 -9999 0 -0.37 89 89
NR4A1 -0.017 0.13 -9999 0 -0.51 31 31
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.066 0.14 -9999 0 -0.34 69 69
RXRG -0.065 0.2 -9999 0 -0.59 65 65
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 -0.012 0.12 -9999 0 -0.53 25 25
PPARG -0.014 0.12 -9999 0 -0.56 25 25
PPARD 0.014 0 -9999 0 -10000 0 0
TNF -0.19 0.42 -9999 0 -1 84 84
mol:Oxysterols -0.007 0.022 -9999 0 -10000 0 0
cholesterol transport -0.074 0.21 -9999 0 -0.44 97 97
PPARA 0.014 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.011 0.046 -9999 0 -0.59 3 3
RXRs/NUR77/BCL2 -0.024 0.12 -9999 0 -0.31 68 68
SREBF1 -0.079 0.26 -9999 0 -0.91 29 29
RXRs/RXRs/DNA/9cRA -0.036 0.13 -9999 0 -0.35 60 60
ABCA1 -0.079 0.26 -9999 0 -0.87 32 32
RARs/THRs -0.016 0.062 -9999 0 -0.29 15 15
RXRs/FXR -0.093 0.19 -9999 0 -0.39 112 112
BCL2 0.005 0.075 -9999 0 -0.59 8 8
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.039 0.11 -10000 0 -0.32 62 62
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.13 0.19 -10000 0 -0.39 175 175
GNB1/GNG2 -0.003 0.032 -10000 0 -0.37 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 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.041 0.11 -10000 0 -0.34 62 62
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 0.01 0.028 0.087 62 -10000 0 62
GNAL -0.058 0.2 -10000 0 -0.59 62 62
GNG2 0.009 0.053 -10000 0 -0.59 4 4
CRH -0.18 0.26 -10000 0 -0.54 175 175
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.061 -10000 0 -0.36 14 14
MAPK11 0.003 0.049 -10000 0 -0.36 9 9
ErbB2/ErbB3 signaling events

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.018 0.006 -9999 0 -10000 0 0
RAS family/GTP -0.07 0.15 -9999 0 -0.51 25 25
NFATC4 -0.06 0.13 -9999 0 -0.37 35 35
ERBB2IP 0.015 0.027 -9999 0 -0.59 1 1
HSP90 (dimer) 0.014 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.089 0.15 -9999 0 -0.47 27 27
JUN -0.02 0.1 -9999 0 -0.36 19 19
HRAS 0.014 0.001 -9999 0 -10000 0 0
DOCK7 -0.082 0.15 -9999 0 -0.46 30 30
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.12 0.18 -9999 0 -0.37 141 141
AKT1 0.01 0.004 -9999 0 -10000 0 0
BAD 0.02 0.003 -9999 0 -10000 0 0
MAPK10 -0.043 0.079 -9999 0 -0.26 17 17
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.094 0.17 -9999 0 -0.51 27 27
RAF1 -0.063 0.15 -9999 0 -0.49 25 25
ErbB2/ErbB3/neuregulin 2 -0.043 0.12 -9999 0 -0.33 68 68
STAT3 0.004 0.005 -9999 0 -10000 0 0
cell migration -0.02 0.094 -9999 0 -0.24 22 22
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.15 0.27 -9999 0 -0.62 90 90
FOS -0.12 0.22 -9999 0 -0.45 110 110
NRAS 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.089 0.15 -9999 0 -0.47 27 27
MAPK3 -0.12 0.22 -9999 0 -0.51 84 84
MAPK1 -0.12 0.22 -9999 0 -0.51 84 84
JAK2 -0.079 0.15 -9999 0 -0.44 27 27
NF2 -0.003 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.09 0.18 -9999 0 -0.33 140 140
NRG1 -0.17 0.27 -9999 0 -0.56 164 164
GRB2/SOS1 0.008 0.019 -9999 0 -0.34 1 1
MAPK8 -0.076 0.15 -9999 0 -0.35 55 55
MAPK9 -0.041 0.076 -9999 0 -0.23 26 26
ERBB2 -0.006 0.047 -9999 0 -0.38 8 8
ERBB3 -0.058 0.19 -9999 0 -0.57 62 62
SHC1 0.009 0.049 -9999 0 -0.49 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 -0.071 0.097 -9999 0 -0.33 26 26
ErbB2/ErbB2/HSP90 (dimer) -0.005 0.038 -9999 0 -0.31 8 8
CHRNA1 -0.14 0.26 -9999 0 -0.59 98 98
myelination -0.053 0.13 -9999 0 -0.36 35 35
PPP3CB -0.075 0.14 -9999 0 -0.41 28 28
KRAS 0.013 0.022 -9999 0 -0.49 1 1
RAC1-CDC42/GDP -0.063 0.16 -9999 0 -0.51 26 26
NRG2 0.012 0.038 -9999 0 -0.59 2 2
mol:GDP -0.09 0.17 -9999 0 -0.33 140 140
SOS1 0.014 0.001 -9999 0 -10000 0 0
MAP2K2 -0.06 0.15 -9999 0 -0.47 25 25
SRC 0.014 0 -9999 0 -10000 0 0
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.079 0.15 -9999 0 -0.44 27 27
MAP2K1 -0.13 0.22 -9999 0 -0.51 75 75
heart morphogenesis -0.089 0.15 -9999 0 -0.47 27 27
RAS family/GDP -0.067 0.15 -9999 0 -0.51 25 25
GRB2 0.013 0.022 -9999 0 -0.49 1 1
PRKACA -0.007 0.009 -9999 0 -10000 0 0
CHRNE 0.002 0.044 -9999 0 -0.19 21 21
HSP90AA1 0.014 0 -9999 0 -10000 0 0
activation of caspase activity -0.01 0.004 -9999 0 -10000 0 0
nervous system development -0.089 0.15 -9999 0 -0.47 27 27
CDC42 0.014 0 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.013 0.004 -9999 0 -10000 0 0
SVIL -0.011 0.11 -9999 0 -0.5 24 24
ZNF318 0.019 0.018 -9999 0 -10000 0 0
JMJD2C -0.003 0.021 -9999 0 -0.077 35 35
T-DHT/AR/Ubc9 -0.068 0.16 -9999 0 -0.36 107 107
CARM1 0.014 0.001 -9999 0 -10000 0 0
PRDX1 -0.014 0.13 -9999 0 -0.59 24 24
PELP1 0.015 0.003 -9999 0 -10000 0 0
CTNNB1 0.013 0.004 -9999 0 -10000 0 0
AKT1 0.015 0.005 -9999 0 -10000 0 0
PTK2B -0.01 0.11 -9999 0 -0.49 24 24
MED1 0.015 0.005 -9999 0 -10000 0 0
MAK -0.034 0.16 -9999 0 -0.5 53 53
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 -0.002 0.096 -9999 0 -0.6 13 13
GSN 0 0.089 -9999 0 -0.58 12 12
NCOA2 -0.027 0.15 -9999 0 -0.59 35 35
NCOA6 0.013 0.004 -9999 0 -10000 0 0
DNA-PK 0.008 0.025 -9999 0 -10000 0 0
NCOA4 0.014 0.001 -9999 0 -10000 0 0
PIAS3 0.013 0.004 -9999 0 -10000 0 0
cell proliferation -0.042 0.11 -9999 0 -0.46 16 16
XRCC5 0.015 0.004 -9999 0 -10000 0 0
UBE3A 0.012 0.009 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.081 0.18 -9999 0 -0.38 120 120
FHL2 -0.048 0.21 -9999 0 -0.8 26 26
RANBP9 0.013 0.004 -9999 0 -10000 0 0
JMJD1A -0.009 0.053 -9999 0 -0.11 97 97
CDK6 -0.033 0.16 -9999 0 -0.54 44 44
TGFB1I1 0.003 0.075 -9999 0 -0.53 10 10
T-DHT/AR/CyclinD1 -0.087 0.18 -9999 0 -0.39 125 125
XRCC6 0.015 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.076 0.18 -9999 0 -0.38 116 116
CTDSP1 0.013 0.004 -9999 0 -10000 0 0
CTDSP2 0.013 0.046 -9999 0 -0.49 4 4
BRCA1 0.009 0.044 -9999 0 -0.49 4 4
TCF4 0.015 0.028 -9999 0 -0.59 1 1
CDKN2A -0.1 0.23 -9999 0 -0.56 104 104
SRF 0.016 0.028 -9999 0 -10000 0 0
NKX3-1 -0.059 0.18 -9999 0 -1 12 12
KLK3 -0.018 0.11 -9999 0 -10000 0 0
TMF1 0.012 0.027 -9999 0 -0.59 1 1
HNRNPA1 0.016 0.006 -9999 0 -10000 0 0
AOF2 -0.002 0.008 -9999 0 -10000 0 0
APPL1 0.027 0.01 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.076 0.17 -9999 0 -0.37 119 119
AR -0.12 0.24 -9999 0 -0.57 107 107
UBA3 0.013 0.004 -9999 0 -10000 0 0
PATZ1 0.016 0.006 -9999 0 -10000 0 0
PAWR -0.034 0.15 -9999 0 -0.53 45 45
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 -0.061 0.15 -9999 0 -0.33 108 108
RPS6KA3 0.012 0.027 -9999 0 -0.59 1 1
T-DHT/AR/ARA70 -0.068 0.16 -9999 0 -0.36 107 107
LATS2 -0.001 0.094 -9999 0 -0.52 16 16
T-DHT/AR/PRX1 -0.075 0.17 -9999 0 -0.36 119 119
Cyclin D3/CDK11 p58 0 0.016 -9999 0 -0.35 1 1
VAV3 -0.12 0.23 -9999 0 -0.52 127 127
KLK2 -0.065 0.12 -9999 0 -0.44 36 36
CASP8 -0.001 0.089 -9999 0 -0.5 16 16
T-DHT/AR/TIF2/CARM1 -0.076 0.18 -9999 0 -0.38 108 108
TMPRSS2 -0.14 0.31 -9999 0 -0.88 62 62
CCND1 -0.017 0.13 -9999 0 -0.53 29 29
PIAS1 0.007 0.054 -9999 0 -0.59 4 4
mol:T-DHT -0.011 0.031 -9999 0 -0.081 52 52
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.01 0.015 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.096 0.19 -9999 0 -0.38 139 139
CMTM2 -0.007 0.11 -9999 0 -0.56 19 19
SNURF -0.008 0.11 -9999 0 -0.58 19 19
ZMIZ1 0.006 0.026 -9999 0 -10000 0 0
CCND3 0.013 0.022 -9999 0 -0.49 1 1
TGIF1 -0.007 0.11 -9999 0 -0.53 21 21
FKBP4 0.013 0.004 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0 0.093 -9999 0 -0.32 40 40
EPHB2 0 0.087 -9999 0 -0.52 14 14
Syndecan-2/TACI -0.011 0.086 -9999 0 -0.33 33 33
LAMA1 -0.063 0.2 -9999 0 -0.57 68 68
Syndecan-2/alpha2 ITGB1 -0.027 0.15 -9999 0 -0.38 55 55
HRAS 0.014 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.015 0.071 -9999 0 -0.34 23 23
ITGA5 -0.01 0.11 -9999 0 -0.5 24 24
BAX 0.02 0.087 -9999 0 -10000 0 0
EPB41 0.011 0.044 -9999 0 -0.56 3 3
positive regulation of cell-cell adhesion -0.013 0.062 -9999 0 -0.3 23 23
LAMA3 -0.041 0.17 -9999 0 -0.54 51 51
EZR 0.004 0.079 -9999 0 -0.59 9 9
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.015 0.12 -9999 0 -0.5 30 30
Syndecan-2/MMP2 -0.006 0.1 -9999 0 -0.33 47 47
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.034 0.11 -9999 0 -0.38 46 46
dendrite morphogenesis 0.002 0.096 -9999 0 -0.35 34 34
Syndecan-2/GM-CSF -0.014 0.071 -9999 0 -0.34 23 23
determination of left/right symmetry 0.003 0.088 -9999 0 -0.4 23 23
Syndecan-2/PKC delta -0.009 0.12 -9999 0 -0.4 43 43
GNB2L1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.012 0.068 -9999 0 -0.32 16 16
MAPK1 0.012 0.068 -9999 0 -0.3 23 23
Syndecan-2/RACK1 -0.012 0.058 -9999 0 -0.3 16 16
NF1 0.012 0.038 -9999 0 -0.59 2 2
FGFR/FGF/Syndecan-2 0.003 0.088 -9999 0 -0.4 23 23
ITGA2 -0.033 0.16 -9999 0 -0.54 44 44
MAPK8 0.011 0.097 -9999 0 -0.34 37 37
Syndecan-2/alpha2/beta1 Integrin -0.039 0.17 -9999 0 -0.38 79 79
Syndecan-2/Kininogen -0.02 0.093 -9999 0 -0.31 47 47
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
SRC 0.027 0.061 -9999 0 -0.28 16 16
Syndecan-2/CASK/Protein 4.1 -0.015 0.071 -9999 0 -0.33 24 24
extracellular matrix organization 0.004 0.093 -9999 0 -0.36 30 30
actin cytoskeleton reorganization 0 0.093 -9999 0 -0.32 40 40
Syndecan-2/Caveolin-2/Ras 0.003 0.096 -9999 0 -0.34 20 20
Syndecan-2/Laminin alpha3 -0.023 0.13 -9999 0 -0.35 69 69
Syndecan-2/RasGAP -0.011 0.053 -9999 0 -0.28 16 16
alpha5/beta1 Integrin -0.017 0.079 -9999 0 -0.36 25 25
PRKCD -0.018 0.14 -9999 0 -0.59 27 27
Syndecan-2 dimer 0.002 0.096 -9999 0 -0.35 34 34
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.034 0.06 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
SDCBP 0.014 0 -9999 0 -10000 0 0
TNFRSF13B -0.005 0.072 -9999 0 -0.49 11 11
RASA1 0.014 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.034 0.11 -9999 0 -0.38 46 46
Syndecan-2/Synbindin 0.011 0.074 -9999 0 -0.33 23 23
TGFB1 0.004 0.079 -9999 0 -0.59 9 9
CASP3 0.002 0.12 -9999 0 -0.38 37 37
FN1 -0.003 0.092 -9999 0 -0.49 18 18
Syndecan-2/IL8 -0.095 0.18 -9999 0 -0.33 176 176
SDC2 0.003 0.088 -9999 0 -0.4 23 23
KNG1 -0.019 0.1 -9999 0 -0.49 24 24
Syndecan-2/Neurofibromin 0.009 0.08 -9999 0 -0.35 24 24
TRAPPC4 0.014 0 -9999 0 -10000 0 0
CSF2 0.001 0.003 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.004 0.094 -9999 0 -0.36 30 30
Syndecan-2/Syntenin/PI-4-5-P2 -0.013 0.063 -9999 0 -0.3 23 23
Syndecan-2/Ezrin 0.014 0.093 -9999 0 -0.4 20 20
PRKACA 0.019 0.073 -9999 0 -0.33 18 18
angiogenesis -0.095 0.18 -9999 0 -0.33 176 176
MMP2 -0.012 0.12 -9999 0 -0.54 25 25
IL8 -0.16 0.26 -9999 0 -0.53 162 162
calcineurin-NFAT signaling pathway -0.011 0.085 -9999 0 -0.33 33 33
IL6-mediated signaling events

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
BCL2L1 -0.036 0.23 -10000 0 -0.72 16 16
CRP -0.043 0.23 -10000 0 -0.73 15 15
cell cycle arrest -0.056 0.26 -10000 0 -0.7 36 36
TIMP1 -0.08 0.27 -10000 0 -0.67 46 46
IL6ST -0.029 0.15 -10000 0 -0.59 36 36
Rac1/GDP -0.068 0.2 -10000 0 -0.5 50 50
AP1 -0.018 0.14 -10000 0 -0.48 13 13
GAB2 0.014 0.027 -10000 0 -0.59 1 1
TNFSF11 -0.044 0.24 -10000 0 -0.71 19 19
HSP90B1 0.006 0.16 -10000 0 -0.92 13 13
GAB1 0.013 0.035 -10000 0 -0.54 2 2
MAPK14 -0.097 0.23 -10000 0 -0.52 85 85
AKT1 0.058 0.03 -10000 0 -0.45 1 1
FOXO1 0.063 0.036 -10000 0 -0.42 1 1
MAP2K6 -0.085 0.2 -10000 0 -0.48 69 69
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.054 0.21 -10000 0 -0.56 38 38
MITF -0.066 0.19 0.27 1 -0.46 57 58
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 0.071 -10000 0 -1.4 1 1
CEBPB 0.004 0.11 -10000 0 -0.57 17 17
GRB2/SOS1/GAB family/SHP2 0.004 0.078 -10000 0 -0.82 1 1
STAT3 -0.06 0.27 -10000 0 -0.74 36 36
STAT1 -0.008 0.035 -10000 0 -10000 0 0
CEBPD -0.078 0.33 -10000 0 -0.97 43 43
PIK3CA 0.015 0.027 -10000 0 -0.59 1 1
PI3K 0.023 0.02 -10000 0 -0.43 1 1
JUN 0.003 0.074 -10000 0 -0.5 11 11
PIAS3/MITF -0.056 0.18 -10000 0 -0.48 40 40
MAPK11 -0.1 0.24 -10000 0 -0.52 88 88
STAT3 (dimer)/FOXO1 0.015 0.21 -10000 0 -0.6 15 15
GRB2/SOS1/GAB family -0.072 0.12 -10000 0 -0.46 29 29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.065 0.17 -10000 0 -0.46 49 49
GRB2 0.014 0.022 -10000 0 -0.49 1 1
JAK2 0.014 0 -10000 0 -10000 0 0
LBP -0.034 0.23 -10000 0 -0.67 24 24
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.012 0.009 -10000 0 -10000 0 0
MYC -0.064 0.3 -10000 0 -0.95 35 35
FGG -0.044 0.24 -10000 0 -0.71 19 19
macrophage differentiation -0.056 0.26 -10000 0 -0.7 36 36
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.17 -10000 0 -0.44 66 66
JUNB -0.056 0.27 -10000 0 -0.83 30 30
FOS -0.096 0.22 -10000 0 -0.55 101 101
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.077 0.19 0.29 1 -0.44 74 75
STAT1/PIAS1 -0.054 0.18 0.29 1 -0.44 54 55
GRB2/SOS1/GAB family/SHP2/PI3K 0.045 0.032 -10000 0 -0.38 2 2
STAT3 (dimer) -0.059 0.27 -10000 0 -0.74 36 36
PRKCD -0.058 0.25 -10000 0 -0.63 47 47
IL6R -0.014 0.12 -10000 0 -0.57 24 24
SOCS3 -0.15 0.34 -10000 0 -1 48 48
gp130 (dimer)/JAK1/JAK1/LMO4 0 0.1 -10000 0 -0.35 36 36
Rac1/GTP -0.069 0.2 -10000 0 -0.51 50 50
HCK -0.007 0.11 -10000 0 -0.54 20 20
MAPKKK cascade 0.025 0.068 -10000 0 -0.91 1 1
bone resorption -0.04 0.23 -10000 0 -0.67 20 20
IRF1 -0.044 0.24 -10000 0 -0.73 20 20
mol:GDP -0.079 0.2 0.28 1 -0.46 75 76
SOS1 0.015 0.002 -10000 0 -10000 0 0
VAV1 -0.081 0.2 -10000 0 -0.47 75 75
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.23 -10000 0 -0.56 60 60
PTPN11 -0.002 0.017 -10000 0 -10000 0 0
IL6/IL6RA -0.1 0.2 -10000 0 -0.41 150 150
gp130 (dimer)/TYK2/TYK2/LMO4 -0.002 0.099 -10000 0 -0.35 36 36
gp130 (dimer)/JAK2/JAK2/LMO4 -0.002 0.099 -10000 0 -0.35 36 36
IL6 -0.13 0.24 -10000 0 -0.53 137 137
PIAS3 0.014 0 -10000 0 -10000 0 0
PTPRE 0.012 0.032 -10000 0 -0.6 1 1
PIAS1 0.009 0.053 -10000 0 -0.59 4 4
RAC1 0.015 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.067 0.16 0.26 1 -0.43 48 49
LMO4 0.014 0.012 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.21 -10000 0 -0.7 34 34
MCL1 0.064 0.027 -10000 0 -0.4 1 1
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.014 0 -9999 0 -10000 0 0
VLDLR -0.007 0.11 -9999 0 -0.57 19 19
LRPAP1 0.014 0 -9999 0 -10000 0 0
NUDC 0.014 0 -9999 0 -10000 0 0
RELN/LRP8 -0.089 0.15 -9999 0 -0.32 141 141
CaM/Ca2+ -0.002 0.025 -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 -0.052 0.15 -9999 0 -0.32 79 79
IQGAP1/CaM -0.009 0.057 -9999 0 -0.38 12 12
DAB1 -0.089 0.22 -9999 0 -0.56 92 92
IQGAP1 0.004 0.075 -9999 0 -0.53 10 10
PLA2G7 -0.039 0.17 -9999 0 -0.55 48 48
CALM1 0.012 0.035 -9999 0 -0.54 2 2
DYNLT1 0.012 0.038 -9999 0 -0.59 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.002 0.027 -9999 0 -0.43 2 2
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.014 0 -9999 0 -10000 0 0
CDK5R1 -0.022 0.14 -9999 0 -0.59 31 31
LIS1/Poliovirus Protein 3A 0.018 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.23 -9999 0 -0.57 104 104
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.21 -9999 0 -0.39 212 212
YWHAE 0.014 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.07 0.19 -9999 0 -0.54 43 43
MAP1B -0.001 0.016 -9999 0 -0.31 1 1
RAC1 -0.003 0.019 -9999 0 -10000 0 0
p35/CDK5 -0.048 0.16 -9999 0 -0.57 16 16
RELN -0.14 0.25 -9999 0 -0.55 140 140
PAFAH/LIS1 -0.004 0.1 -9999 0 -0.33 48 48
LIS1/CLIP170 0.029 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.08 0.13 -9999 0 -0.44 39 39
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.085 0.2 -9999 0 -0.64 34 34
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.083 0.2 -9999 0 -0.59 43 43
LIS1/IQGAP1 0.022 0.047 -9999 0 -0.31 10 10
RHOA -0.003 0.019 -9999 0 -10000 0 0
PAFAH1B1 0.025 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0 -9999 0 -10000 0 0
PAFAH1B2 -0.005 0.1 -9999 0 -0.59 16 16
MAP1B/LIS1/Dynein heavy chain 0.027 0.011 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.1 0.16 -9999 0 -0.52 42 42
LRP8 0.012 0.038 -9999 0 -0.59 2 2
NDEL1/Katanin 60 -0.07 0.19 -9999 0 -0.54 43 43
P39/CDK5 -0.089 0.19 -9999 0 -0.53 41 41
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.029 0 -9999 0 -10000 0 0
CDK5 -0.039 0.14 -9999 0 -0.59 1 1
PPP2R5D 0.014 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.1 0.2 -9999 0 -0.36 148 148
RELN/VLDLR -0.09 0.14 -9999 0 -0.34 93 93
CDC42 -0.003 0.019 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.072 0.15 -9999 0 -0.37 80 80
MAP4K1 -0.018 0.13 -9999 0 -0.58 28 28
MAP3K8 -0.005 0.099 -9999 0 -0.51 19 19
PRKCB -0.062 0.19 -9999 0 -0.52 73 73
DBNL 0.014 0 -9999 0 -10000 0 0
CRKL 0.013 0.022 -9999 0 -0.49 1 1
MAP3K1 -0.004 0.11 -9999 0 -0.43 8 8
JUN -0.03 0.16 -9999 0 -0.56 37 37
MAP3K7 -0.001 0.1 -9999 0 -0.44 7 7
GRAP2 -0.048 0.17 -9999 0 -0.53 58 58
CRK 0.014 0 -9999 0 -10000 0 0
MAP2K4 0.003 0.11 -9999 0 -0.41 11 11
LAT -0.017 0.13 -9999 0 -0.59 27 27
LCP2 -0.001 0.086 -9999 0 -0.5 15 15
MAPK8 -0.034 0.16 -9999 0 -0.59 36 36
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.01 0.11 -9999 0 -0.47 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.066 0.14 -9999 0 -0.34 80 80
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.057 0.27 8 -10000 0 8
RFC1 0.008 0.057 0.22 21 -10000 0 21
PRKDC 0.008 0.057 0.27 8 -10000 0 8
RIPK1 0.016 0.003 -10000 0 -10000 0 0
CASP7 -0.004 0.071 0.25 14 -0.38 3 17
FASLG/FAS/FADD/FAF1 -0.009 0.085 0.22 19 -0.31 15 34
MAP2K4 -0.003 0.12 -10000 0 -0.36 15 15
mol:ceramide -0.003 0.096 -10000 0 -0.39 11 11
GSN 0 0.072 0.21 19 -0.34 10 29
FASLG/FAS/FADD/FAF1/Caspase 8 -0.001 0.09 0.21 2 -0.32 18 20
FAS -0.008 0.1 -10000 0 -0.55 18 18
BID 0.005 0.079 0.3 17 -0.3 12 29
MAP3K1 0.009 0.09 0.22 14 -0.3 7 21
MAP3K7 0.012 0.004 -10000 0 -10000 0 0
RB1 0.008 0.059 0.22 21 -0.36 1 22
CFLAR 0.015 0.022 -10000 0 -0.47 1 1
HGF/MET -0.15 0.2 -10000 0 -0.37 208 208
ARHGDIB 0.006 0.063 0.27 8 -0.36 3 11
FADD 0.011 0.007 -10000 0 -10000 0 0
actin filament polymerization 0 0.071 0.34 10 -0.25 6 16
NFKB1 -0.039 0.067 -10000 0 -10000 0 0
MAPK8 -0.028 0.17 -10000 0 -0.42 54 54
DFFA 0.008 0.057 0.22 23 -10000 0 23
DNA fragmentation during apoptosis 0.008 0.057 0.22 21 -10000 0 21
FAS/FADD/MET -0.1 0.16 -10000 0 -0.34 158 158
CFLAR/RIP1 0.014 0.017 -10000 0 -0.32 1 1
FAIM3 -0.027 0.15 -10000 0 -0.54 39 39
FAF1 0.01 0.027 -10000 0 -0.59 1 1
PARP1 0.008 0.059 0.27 8 -0.28 1 9
DFFB 0.008 0.057 0.22 21 -10000 0 21
CHUK -0.033 0.057 -10000 0 -10000 0 0
FASLG -0.026 0.12 -10000 0 -0.5 33 33
FAS/FADD 0.002 0.077 -10000 0 -0.4 18 18
HGF -0.079 0.2 -10000 0 -0.51 91 91
LMNA 0.006 0.061 0.25 8 -0.35 3 11
CASP6 0.007 0.064 0.22 21 -0.38 3 24
CASP10 0.01 0.024 -10000 0 -0.5 1 1
CASP3 0.01 0.068 0.26 24 -10000 0 24
PTPN13 0.006 0.069 -10000 0 -0.58 7 7
CASP8 0.01 0.1 0.31 34 -0.34 15 49
IL6 -0.14 0.38 -10000 0 -1.2 48 48
MET -0.15 0.25 -10000 0 -0.54 151 151
ICAD/CAD 0.009 0.053 0.25 8 -10000 0 8
FASLG/FAS/FADD/FAF1/Caspase 10 -0.003 0.097 -10000 0 -0.39 11 11
activation of caspase activity by cytochrome c 0.005 0.079 0.3 17 -0.3 12 29
PAK2 0.008 0.057 0.27 8 -10000 0 8
BCL2 0.005 0.075 -10000 0 -0.59 8 8
LPA4-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
ADCY4 0.008 0.066 -9999 0 -0.31 21 21
ADCY5 0 0.091 -9999 0 -0.37 28 28
ADCY6 0.014 0.048 -9999 0 -0.31 11 11
ADCY7 0.014 0.048 -9999 0 -0.31 11 11
ADCY1 -0.053 0.15 -9999 0 -0.35 103 103
ADCY2 0.004 0.081 -9999 0 -0.36 24 24
ADCY3 0.014 0.048 -9999 0 -0.31 11 11
ADCY8 -0.03 0.13 -9999 0 -0.36 71 71
PRKCE 0.004 0.056 -9999 0 -0.38 11 11
ADCY9 0.012 0.06 -9999 0 -0.34 14 14
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.008 0.098 -9999 0 -0.35 22 22
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.044 0.15 -10000 0 -0.72 19 19
HDAC1 0.008 0.054 -10000 0 -0.59 4 4
AES 0.014 0.004 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
DTX1 0.004 0.078 -10000 0 -0.58 9 9
LRP6/FZD1 -0.005 0.04 -10000 0 -0.34 7 7
TLE1 0.012 0.038 -10000 0 -0.6 2 2
AP1 -0.029 0.12 -10000 0 -0.3 70 70
NCSTN 0.014 0 -10000 0 -10000 0 0
ADAM10 0 0.092 -10000 0 -0.59 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.027 0.072 -10000 0 -10000 0 0
NICD/RBPSUH -0.02 0.11 -10000 0 -0.59 19 19
WIF1 -0.28 0.28 -10000 0 -0.54 271 271
NOTCH1 -0.023 0.12 -10000 0 -0.63 19 19
PSENEN 0.014 0 -10000 0 -10000 0 0
KREMEN2 -0.052 0.18 -10000 0 -0.53 63 63
DKK1 -0.12 0.24 -10000 0 -0.53 123 123
beta catenin/beta TrCP1 0.017 0.046 0.33 3 -10000 0 3
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
AXIN1 -0.001 0.045 0.23 4 -0.26 2 6
CtBP/CBP/TCF1/TLE1/AES 0.031 0.051 0.28 4 -10000 0 4
PSEN1 0.014 0 -10000 0 -10000 0 0
FOS -0.096 0.22 -10000 0 -0.55 101 101
JUN 0.003 0.074 -10000 0 -0.5 11 11
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
CTNNB1 0.009 0.049 0.32 4 -10000 0 4
MAPK3 0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 163 163
HNF1A 0.013 0.027 -10000 0 -0.59 1 1
CTBP1 0.014 0.004 -10000 0 -10000 0 0
MYC -0.04 0.29 -10000 0 -1.4 22 22
NKD1 -0.004 0.099 -10000 0 -0.54 17 17
FZD1 0.008 0.054 -10000 0 -0.49 6 6
NOTCH1 precursor/Deltex homolog 1 -0.025 0.12 -10000 0 -0.6 19 19
apoptosis -0.029 0.12 -10000 0 -0.29 70 70
Delta 1/NOTCHprecursor -0.042 0.15 -10000 0 -0.71 19 19
DLL1 -0.033 0.16 -10000 0 -0.59 40 40
PPARD 0.02 0.027 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.002 0.061 0.23 4 -0.28 12 16
DVL1 -0.021 0.024 -10000 0 -10000 0 0
CSNK2A1 0.014 0.003 -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 -0.34 168 168
LRP6 0.013 0.022 -10000 0 -0.49 1 1
CSNK1A1 0.014 0.003 -10000 0 -10000 0 0
NLK 0.016 0.015 -10000 0 -10000 0 0
CCND1 -0.021 0.22 -10000 0 -1.3 12 12
WNT1 -0.022 0.12 -10000 0 -0.49 34 34
Axin1/APC/beta catenin 0.018 0.061 0.31 4 -0.41 2 6
DKK2 -0.11 0.23 -10000 0 -0.54 117 117
NOTCH1 precursor/DVL1 -0.021 0.11 -10000 0 -0.56 19 19
GSK3B 0.013 0.027 -10000 0 -0.59 1 1
FRAT1 0.01 0.049 -10000 0 -0.54 4 4
NOTCH/Deltex homolog 1 -0.027 0.12 -10000 0 -0.62 19 19
PPP2R5D -0.003 0.049 0.25 17 -10000 0 17
MAPK1 0.014 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.15 0.18 -10000 0 -0.37 139 139
RBPJ 0.013 0.022 -10000 0 -0.49 1 1
CREBBP 0.017 0.005 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.053 0.099 0.52 8 -10000 0 8
GNAI2 0.014 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.087 0.15 -10000 0 -0.34 134 134
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.008 0.059 -10000 0 -0.59 5 5
RhoA/GTP -0.053 0.1 -10000 0 -0.53 8 8
negative regulation of cAMP metabolic process -0.034 0.13 -10000 0 -0.28 80 80
GNAZ 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNA12 0.013 0.027 -10000 0 -0.59 1 1
S1PR5 -0.13 0.25 -10000 0 -0.55 134 134
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.034 0.13 -10000 0 -0.28 80 80
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.1 -10000 0 -0.59 16 16
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0.027 -9999 0 -0.59 1 1
ELF1 -0.016 0.091 -9999 0 -0.37 9 9
CCNA2 -0.055 0.18 -9999 0 -0.53 66 66
PIK3CA 0.014 0.027 -9999 0 -0.59 1 1
JAK3 -0.056 0.18 -9999 0 -0.53 68 68
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 -0.025 0.16 -9999 0 -0.47 20 20
SHC1 0.01 0.049 -9999 0 -0.49 5 5
SP1 0.016 0.044 -9999 0 -0.34 4 4
IL2RA -0.043 0.18 -9999 0 -0.46 74 74
IL2RB -0.094 0.22 -9999 0 -0.53 103 103
SOS1 0.015 0.001 -9999 0 -10000 0 0
IL2RG -0.04 0.16 -9999 0 -0.52 53 53
G1/S transition of mitotic cell cycle -0.034 0.18 -9999 0 -0.49 50 50
PTPN11 0.015 0.001 -9999 0 -10000 0 0
CCND2 0.019 0.095 -9999 0 -0.54 13 13
LCK -0.08 0.21 -9999 0 -0.53 89 89
GRB2 0.014 0.022 -9999 0 -0.49 1 1
IL2 0.001 0.003 -9999 0 -10000 0 0
CDK6 -0.033 0.16 -9999 0 -0.54 44 44
CCND3 -0.012 0.14 -9999 0 -0.5 5 5
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.01 0.056 -10000 0 -0.59 4 4
HSPA8 0.013 0.027 -10000 0 -0.59 1 1
SMAD3/SMAD4/ER alpha -0.026 0.1 0.21 2 -0.39 25 27
AKT1 0.008 0.023 -10000 0 -10000 0 0
GSC -0.17 0.49 -10000 0 -1.4 70 70
NKX2-5 -0.092 0.2 -10000 0 -0.5 102 102
muscle cell differentiation 0.15 0.19 0.49 89 -10000 0 89
SMAD2-3/SMAD4/SP1 -0.007 0.11 -10000 0 -0.48 5 5
SMAD4 -0.017 0.066 -10000 0 -0.31 3 3
CBFB 0.014 0 -10000 0 -10000 0 0
SAP18 0.014 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.023 0.11 -10000 0 -0.33 47 47
SMAD3/SMAD4/VDR -0.034 0.12 -10000 0 -0.38 18 18
MYC -0.009 0.13 -10000 0 -0.55 26 26
CDKN2B -0.13 0.45 -10000 0 -1.4 56 56
AP1 -0.03 0.16 -10000 0 -0.6 18 18
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.043 0.063 -10000 0 -0.54 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.012 0.14 -10000 0 -0.39 31 31
SP3 0.016 0.008 -10000 0 -10000 0 0
CREB1 0.014 0 -10000 0 -10000 0 0
FOXH1 -0.016 0.1 -10000 0 -0.56 16 16
SMAD3/SMAD4/GR -0.01 0.062 -10000 0 -0.36 2 2
GATA3 -0.13 0.24 -10000 0 -0.56 115 115
SKI/SIN3/HDAC complex/NCoR1 0.045 0.036 -10000 0 -0.36 1 1
MEF2C/TIF2 -0.076 0.18 -10000 0 -0.51 42 42
endothelial cell migration 0.22 0.48 1.4 72 -10000 0 72
MAX 0.023 0.019 -10000 0 -10000 0 0
RBBP7 0.014 0.003 -10000 0 -10000 0 0
RBBP4 0.013 0.027 -10000 0 -0.59 1 1
RUNX2 -0.005 0.1 -10000 0 -0.53 18 18
RUNX3 -0.03 0.15 -10000 0 -0.55 40 40
RUNX1 -0.053 0.18 -10000 0 -0.53 64 64
CTBP1 0.014 0 -10000 0 -10000 0 0
NR3C1 0.023 0.019 -10000 0 -10000 0 0
VDR -0.065 0.19 -10000 0 -0.53 74 74
CDKN1A -0.045 0.28 -10000 0 -1.3 21 21
KAT2B 0.013 0.023 -10000 0 -0.49 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.027 0.12 -10000 0 -0.37 26 26
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 -1.4 72 72
SMAD3/SMAD4/ATF2 -0.028 0.081 -10000 0 -0.38 15 15
SMAD3/SMAD4/ATF3 -0.05 0.12 -10000 0 -0.39 47 47
SAP30 0.013 0.027 -10000 0 -0.6 1 1
Cbp/p300/PIAS3 0.015 0.057 -10000 0 -0.36 4 4
JUN -0.024 0.16 -10000 0 -0.6 17 17
SMAD3/SMAD4/IRF7 -0.033 0.097 -10000 0 -0.41 20 20
TFE3 0.008 0.029 -10000 0 -10000 0 0
COL1A2 -0.044 0.16 -10000 0 -0.46 56 56
mesenchymal cell differentiation 0.03 0.09 0.41 18 -10000 0 18
DLX1 -0.16 0.26 -10000 0 -0.54 161 161
TCF3 0.012 0.038 -10000 0 -0.59 2 2
FOS -0.093 0.23 -10000 0 -0.55 101 101
SMAD3/SMAD4/Max -0.01 0.062 -10000 0 -0.36 2 2
Cbp/p300/SNIP1 0.007 0.039 -10000 0 -0.36 4 4
ZBTB17 0.019 0.019 -10000 0 -10000 0 0
LAMC1 0.001 0.11 -10000 0 -0.49 18 18
TGIF2/HDAC complex/SMAD3/SMAD4 -0.023 0.073 -10000 0 -0.43 8 8
IRF7 -0.01 0.11 -10000 0 -0.52 23 23
ESR1 -0.013 0.12 -10000 0 -0.54 26 26
HNF4A -0.034 0.14 -10000 0 -0.49 42 42
MEF2C -0.063 0.17 -10000 0 -0.51 32 32
SMAD2-3/SMAD4 -0.035 0.073 -10000 0 -0.36 8 8
Cbp/p300/Src-1 0.01 0.045 -10000 0 -0.36 4 4
IGHV3OR16-13 -0.015 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.007 0.063 -10000 0 -0.57 6 6
CREBBP 0.015 0.012 -10000 0 -10000 0 0
SKIL 0.006 0.07 -10000 0 -0.59 7 7
HDAC1 0.009 0.053 -10000 0 -0.59 4 4
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 -0.009 0.083 -10000 0 -0.4 5 5
MSG1/HSC70 -0.022 0.12 -10000 0 -0.37 55 55
SMAD2 -0.004 0.047 -10000 0 -10000 0 0
SMAD3 -0.005 0.056 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.009 0.073 -10000 0 -0.33 7 7
SMAD2/SMAD2/SMAD4 -0.003 0.033 -10000 0 -10000 0 0
NCOR1 0.012 0.038 -10000 0 -0.59 2 2
NCOA2 -0.027 0.15 -10000 0 -0.59 35 35
NCOA1 0.014 0 -10000 0 -10000 0 0
MYOD/E2A -0.14 0.19 -10000 0 -0.39 180 180
SMAD2-3/SMAD4/SP1/MIZ-1 0.004 0.11 -10000 0 -0.47 5 5
IFNB1 -0.007 0.1 -10000 0 -0.48 10 10
SMAD3/SMAD4/MEF2C -0.067 0.18 -10000 0 -0.55 24 24
CITED1 -0.043 0.17 -10000 0 -0.53 54 54
SMAD2-3/SMAD4/ARC105 -0.011 0.074 -10000 0 -0.37 3 3
RBL1 -0.007 0.11 -10000 0 -0.57 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.027 0.19 -10000 0 -0.53 56 56
RUNX1-3/PEBPB2 -0.063 0.14 -10000 0 -0.4 54 54
SMAD7 -0.012 0.15 -10000 0 -0.6 6 6
MYC/MIZ-1 -0.002 0.1 -10000 0 -0.39 24 24
SMAD3/SMAD4 -0.041 0.19 0.31 38 -0.42 62 100
IL10 -0.14 0.28 -10000 0 -0.6 115 115
PIASy/HDAC complex 0.016 0.014 -10000 0 -10000 0 0
PIAS3 0.013 0.007 -10000 0 -10000 0 0
CDK2 0.001 0.086 -10000 0 -0.53 13 13
IL5 -0.085 0.19 -10000 0 -0.52 40 40
CDK4 -0.001 0.089 -10000 0 -0.49 16 16
PIAS4 0.016 0.013 -10000 0 -10000 0 0
ATF3 -0.038 0.16 -10000 0 -0.51 51 51
SMAD3/SMAD4/SP1 -0.009 0.1 -10000 0 -0.46 5 5
FOXG1 -0.025 0.15 -10000 0 -0.59 34 34
FOXO3 0.017 0.032 -10000 0 -10000 0 0
FOXO1 0.014 0.045 -10000 0 -0.42 3 3
FOXO4 0.016 0.039 -10000 0 -0.51 1 1
heart looping -0.062 0.17 -10000 0 -0.51 32 32
CEBPB -0.008 0.11 -10000 0 -0.57 17 17
SMAD3/SMAD4/DLX1 -0.12 0.17 -10000 0 -0.38 136 136
MYOD1 -0.18 0.27 -10000 0 -0.55 178 178
SMAD3/SMAD4/HNF4 -0.045 0.1 -10000 0 -0.36 30 30
SMAD3/SMAD4/GATA3 -0.13 0.19 -10000 0 -0.47 79 79
SnoN/SIN3/HDAC complex/NCoR1 0.006 0.07 -10000 0 -0.59 7 7
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.061 0.14 -10000 0 -0.46 32 32
SMAD3/SMAD4/SP1-3 0.009 0.098 -10000 0 -0.44 5 5
MED15 0.014 0 -10000 0 -10000 0 0
SP1 0.005 0.041 -10000 0 -10000 0 0
SIN3B 0.014 0.003 -10000 0 -10000 0 0
SIN3A 0.014 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.073 0.16 -10000 0 -0.43 37 37
ITGB5 0.02 0.11 -10000 0 -0.66 6 6
TGIF/SIN3/HDAC complex/CtBP 0.043 0.043 -10000 0 -0.44 1 1
SMAD3/SMAD4/AR -0.092 0.16 -10000 0 -0.39 94 94
AR -0.1 0.23 -10000 0 -0.56 107 107
negative regulation of cell growth -0.007 0.12 -10000 0 -0.42 21 21
SMAD3/SMAD4/MYOD -0.14 0.18 -10000 0 -0.4 128 128
E2F5 0.011 0.046 -10000 0 -0.59 3 3
E2F4 0.014 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.007 0.097 -10000 0 -0.35 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 -0.01 0.13 -10000 0 -0.37 39 39
TFDP1 0.013 0.027 -10000 0 -0.59 1 1
SMAD3/SMAD4/AP1 -0.03 0.16 -10000 0 -0.62 17 17
SMAD3/SMAD4/RUNX2 -0.03 0.091 -10000 0 -0.42 17 17
TGIF2 0.007 0.063 -10000 0 -0.58 6 6
TGIF1 -0.008 0.11 -10000 0 -0.53 21 21
ATF2 -0.001 0.095 -10000 0 -0.59 13 13
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.063 0.15 0.4 81 -10000 0 81
KIRREL -0.037 0.16 -10000 0 -0.59 41 41
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.063 0.15 -10000 0 -0.4 81 81
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 -0.046 0.11 -10000 0 -0.34 42 42
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.004 0.096 -10000 0 -0.34 13 13
FYN -0.024 0.11 -10000 0 -0.32 42 42
mol:Ca2+ -0.045 0.11 -10000 0 -0.33 42 42
mol:DAG -0.045 0.11 -10000 0 -0.34 42 42
NPHS2 -0.006 0.039 -10000 0 -0.54 2 2
mol:IP3 -0.045 0.11 -10000 0 -0.34 42 42
regulation of endocytosis -0.015 0.1 -10000 0 -0.5 4 4
Nephrin/NEPH1/podocin/Cholesterol -0.047 0.11 -10000 0 -0.35 42 42
establishment of cell polarity -0.063 0.15 -10000 0 -0.4 81 81
Nephrin/NEPH1/podocin/NCK1-2 -0.041 0.099 -10000 0 -0.53 5 5
Nephrin/NEPH1/beta Arrestin2 -0.014 0.1 -10000 0 -0.5 4 4
NPHS1 -0.035 0.14 -10000 0 -0.49 44 44
Nephrin/NEPH1/podocin -0.027 0.11 -10000 0 -0.32 42 42
TJP1 0.014 0 -10000 0 -10000 0 0
NCK1 0.013 0.027 -10000 0 -0.59 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 -0.046 0.11 -10000 0 -0.34 42 42
CD2AP 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.046 0.11 -10000 0 -0.34 42 42
GRB2 0.013 0.022 -10000 0 -0.49 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.043 0.13 -10000 0 -0.34 55 55
cytoskeleton organization -0.004 0.11 -10000 0 -0.39 13 13
Nephrin/NEPH1 -0.045 0.11 -10000 0 -0.33 41 41
Nephrin/NEPH1/ZO-1 -0.049 0.12 -10000 0 -0.36 41 41
Ephrin B reverse 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
EFNB2 0.002 0.08 -10000 0 -0.52 12 12
EPHB2 -0.001 0.087 -10000 0 -0.52 14 14
EFNB1 -0.063 0.17 -10000 0 -0.37 113 113
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.077 0.14 -10000 0 -0.58 20 20
Ephrin B2/EPHB1-2 -0.034 0.12 -10000 0 -0.34 61 61
neuron projection morphogenesis -0.074 0.14 -10000 0 -0.55 20 20
Ephrin B1/EPHB1-2/Tiam1 -0.055 0.17 -10000 0 -0.39 69 69
DNM1 -0.1 0.22 -10000 0 -0.52 112 112
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.011 0.082 -10000 0 -0.72 6 6
YES1 -0.009 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/NCK2 -0.054 0.17 -10000 0 -0.38 69 69
PI3K 0.012 0.083 -10000 0 -0.67 7 7
mol:GDP -0.077 0.16 -10000 0 -0.38 69 69
ITGA2B -0.043 0.17 -10000 0 -0.57 50 50
endothelial cell proliferation -0.005 0.048 -10000 0 -0.31 12 12
FYN -0.008 0.1 -10000 0 -0.94 6 6
MAP3K7 -0.007 0.083 -10000 0 -0.76 6 6
FGR -0.008 0.1 -10000 0 -0.94 6 6
TIAM1 0.013 0.027 -10000 0 -0.59 1 1
PIK3R1 0.014 0 -10000 0 -10000 0 0
RGS3 0.011 0.038 -10000 0 -0.49 3 3
cell adhesion -0.033 0.14 -10000 0 -0.59 14 14
LYN -0.009 0.1 -10000 0 -0.94 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.011 0.098 -10000 0 -0.91 6 6
Ephrin B1/EPHB1-2 -0.013 0.089 -10000 0 -0.83 6 6
SRC -0.007 0.1 -10000 0 -0.94 6 6
ITGB3 -0.052 0.18 -10000 0 -0.51 65 65
EPHB1 -0.036 0.17 -10000 0 -0.6 42 42
EPHB4 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.004 0.048 -10000 0 -0.31 12 12
alphaIIb/beta3 Integrin -0.084 0.17 -10000 0 -0.41 107 107
BLK -0.027 0.11 -10000 0 -0.98 6 6
HCK -0.012 0.11 -10000 0 -1 6 6
regulation of stress fiber formation 0.076 0.16 0.38 69 -10000 0 69
MAPK8 0.01 0.096 -10000 0 -0.72 6 6
Ephrin B1/EPHB1-2/RGS3 -0.055 0.17 -10000 0 -0.39 69 69
endothelial cell migration -0.008 0.082 -10000 0 -0.54 9 9
NCK2 0.014 0 -10000 0 -10000 0 0
PTPN13 0.003 0.082 -10000 0 -0.68 7 7
regulation of focal adhesion formation 0.076 0.16 0.38 69 -10000 0 69
chemotaxis 0.078 0.16 0.38 69 -10000 0 69
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
Rac1/GTP -0.076 0.14 -10000 0 -0.57 20 20
angiogenesis -0.013 0.089 -10000 0 -0.82 6 6
LCK -0.026 0.11 -10000 0 -0.96 6 6
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.035 0.16 -9999 0 -0.46 60 60
KLHL20 -0.026 0.056 -9999 0 -0.27 9 9
CYFIP2 0.008 0.06 -9999 0 -0.54 6 6
Rac1/GDP 0.008 0.11 -9999 0 -10000 0 0
ENAH -0.035 0.16 -9999 0 -0.46 60 60
AP1M1 0.014 0 -9999 0 -10000 0 0
RAP1B 0.013 0.022 -9999 0 -0.49 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.035 0.066 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.017 0.038 -9999 0 -0.18 10 10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.092 0.15 -9999 0 -0.38 74 74
RAPGEF1 -0.014 0.14 -9999 0 -0.39 60 60
CTNND1 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.073 0.16 -9999 0 -0.48 60 60
CRK -0.024 0.16 -9999 0 -0.43 60 60
E-cadherin/gamma catenin/alpha catenin -0.083 0.15 -9999 0 -0.32 132 132
alphaE/beta7 Integrin -0.033 0.11 -9999 0 -0.38 45 45
IQGAP1 0.004 0.075 -9999 0 -0.53 10 10
NCKAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.018 -9999 0 -0.29 2 2
DLG1 -0.035 0.16 -9999 0 -0.46 61 61
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.026 0.048 -9999 0 -10000 0 0
MLLT4 0.013 0.027 -9999 0 -0.59 1 1
ARF6/GTP/NME1/Tiam1 0 0.015 -9999 0 -0.33 1 1
PI3K -0.032 0.061 -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 -0.39 132 132
TIAM1 0.013 0.027 -9999 0 -0.59 1 1
E-cadherin(dimer)/Ca2+ -0.064 0.11 -9999 0 -0.3 60 60
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 -0.54 125 125
RhoA/GDP 0.008 0.11 -9999 0 -10000 0 0
actin cytoskeleton organization -0.02 0.041 -9999 0 -0.19 9 9
CDC42/GDP 0.008 0.11 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.032 0.11 -9999 0 -0.27 66 66
ITGB7 -0.034 0.16 -9999 0 -0.54 45 45
RAC1 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.041 0.14 -9999 0 -0.32 60 60
E-cadherin/Ca2+/beta catenin/alpha catenin -0.066 0.12 -9999 0 -0.27 125 125
mol:GDP -0.002 0.12 -9999 0 -0.32 8 8
CDC42/GTP/IQGAP1 -0.006 0.044 -9999 0 -0.32 10 10
JUP 0.003 0.081 -9999 0 -0.57 10 10
p120 catenin/RhoA/GDP -0.042 0.086 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 -0.006 0.044 -9999 0 -0.32 10 10
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 0.01 0.063 -9999 0 -0.21 29 29
NME1 0.014 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.035 0.16 -9999 0 -0.46 60 60
regulation of cell-cell adhesion -0.032 0.059 -9999 0 -10000 0 0
WASF2 -0.008 0.02 -9999 0 -10000 0 0
Rap1/GTP -0.041 0.077 -9999 0 -0.32 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.09 0.15 -9999 0 -0.36 80 80
CCND1 0.011 0.077 -9999 0 -0.26 29 29
VAV2 -0.018 0.15 -9999 0 -0.42 60 60
RAP1/GDP -0.039 0.081 -9999 0 -0.3 1 1
adherens junction assembly -0.033 0.16 -9999 0 -0.44 60 60
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 -0.051 0.16 -9999 0 -0.55 19 19
E-cadherin/beta catenin -0.067 0.13 -9999 0 -0.28 125 125
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.036 0.16 -9999 0 -0.46 60 60
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
Rac1/GTP -0.042 0.089 -9999 0 -0.45 9 9
E-cadherin/beta catenin/alpha catenin -0.077 0.14 -9999 0 -0.32 125 125
ITGAE 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.075 0.16 -9999 0 -0.49 60 60
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.013 0.022 -10000 0 -0.49 1 1
RAS family/GTP/Tiam1 0.029 0.038 -10000 0 -0.51 1 1
NT3 (dimer)/TRKC -0.015 0.078 -10000 0 -0.39 20 20
NT3 (dimer)/TRKB -0.074 0.15 -10000 0 -0.42 65 65
SHC/Grb2/SOS1/GAB1/PI3K 0.037 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 93 93
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
DYNLT1 0.012 0.038 -10000 0 -0.59 2 2
NTRK1 -0.008 0.11 -10000 0 -0.52 22 22
NTRK2 -0.018 0.14 -10000 0 -0.59 27 27
NTRK3 0.009 0.053 -10000 0 -0.59 4 4
NT-4/5 (dimer)/TRKB -0.073 0.16 -10000 0 -0.39 84 84
neuron apoptosis 0.13 0.16 0.49 55 -10000 0 55
SHC 2-3/Grb2 -0.12 0.2 -10000 0 -0.54 55 55
SHC1 0.009 0.049 -10000 0 -0.49 5 5
SHC2 -0.07 0.11 -10000 0 -0.41 28 28
SHC3 -0.16 0.23 -10000 0 -0.56 106 106
STAT3 (dimer) 0.007 0.067 -10000 0 -0.34 11 11
NT3 (dimer)/TRKA -0.068 0.14 -10000 0 -0.41 49 49
RIN/GDP -0.039 0.11 -10000 0 -0.28 13 13
GIPC1 0.013 0.022 -10000 0 -0.49 1 1
KRAS 0.013 0.022 -10000 0 -0.49 1 1
DNAJA3 -0.069 0.12 -10000 0 -0.38 46 46
RIN/GTP -0.16 0.2 -10000 0 -0.4 206 206
CCND1 0 0.15 -10000 0 -0.57 29 29
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) -0.011 0.09 -10000 0 -0.5 17 17
SHC/GRB2/SOS1 -0.003 0.03 -10000 0 -0.28 6 6
GRB2 0.013 0.022 -10000 0 -0.49 1 1
NGF (dimer)/TRKA/MATK -0.12 0.19 -10000 0 -0.38 167 167
TRKA/NEDD4-2 -0.026 0.097 -10000 0 -0.38 35 35
ELMO1 0.001 0.088 -10000 0 -0.59 11 11
RhoG/GTP/ELMO1/DOCK1 -0.011 0.062 -10000 0 -0.37 15 15
NGF -0.071 0.2 -10000 0 -0.56 77 77
HRAS 0.014 0 -10000 0 -10000 0 0
DOCK1 0.009 0.053 -10000 0 -0.59 4 4
GAB2 0.013 0.027 -10000 0 -0.59 1 1
RIT2 -0.21 0.28 -10000 0 -0.55 206 206
RIT1 0.014 0 -10000 0 -10000 0 0
FRS2 0.012 0.035 -10000 0 -0.54 2 2
DNM1 -0.1 0.22 -10000 0 -0.52 112 112
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 -0.073 0.13 -10000 0 -0.37 57 57
mol:GDP 0.045 0.066 -10000 0 -0.46 2 2
NGF (dimer) -0.071 0.2 -10000 0 -0.56 77 77
RhoG/GDP -0.009 0.063 -10000 0 -0.44 11 11
RIT1/GDP 0.041 0.048 -10000 0 -0.29 2 2
TIAM1 0.013 0.027 -10000 0 -0.59 1 1
PIK3R1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.075 0.14 -10000 0 -0.39 43 43
KIDINS220/CRKL/C3G -0.001 0.015 -10000 0 -0.34 1 1
SHC/RasGAP -0.003 0.033 -10000 0 -0.34 5 5
FRS2 family/SHP2 -0.001 0.02 -10000 0 -0.32 2 2
SHC/GRB2/SOS1/GAB1 -0.004 0.036 -10000 0 -0.57 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.008 0.092 -10000 0 -0.49 18 18
RAP1/GDP -0.005 0.022 -10000 0 -0.26 1 1
KIDINS220/CRKL 0.013 0.022 -10000 0 -0.49 1 1
BDNF (dimer) -0.079 0.2 -10000 0 -0.5 93 93
ubiquitin-dependent protein catabolic process -0.07 0.14 -10000 0 -0.39 64 64
Schwann cell development -0.02 0.027 -10000 0 -10000 0 0
EHD4 0.007 0.058 -10000 0 -0.49 7 7
FRS2 family/GRB2/SOS1 -0.002 0.021 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.043 0.018 -10000 0 -10000 0 0
RAP1B 0.013 0.022 -10000 0 -0.49 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.061 0.12 -10000 0 -0.48 18 18
ABL1 0.014 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
Rap1/GTP -0.022 0.044 -10000 0 -10000 0 0
STAT3 0.007 0.067 -10000 0 -0.34 11 11
axon guidance -0.059 0.11 -10000 0 -0.46 18 18
MAPK3 -0.085 0.19 -10000 0 -0.39 107 107
MAPK1 -0.085 0.19 -10000 0 -0.39 107 107
CDC42/GDP 0.041 0.048 -10000 0 -0.29 2 2
NTF3 -0.008 0.092 -10000 0 -0.49 18 18
NTF4 -0.011 0.09 -10000 0 -0.5 17 17
NGF (dimer)/TRKA/FAIM -0.065 0.14 -10000 0 -0.34 98 98
PI3K -0.001 0.019 -10000 0 -0.43 1 1
FRS3 0.014 0 -10000 0 -10000 0 0
FAIM 0.009 0.053 -10000 0 -0.59 4 4
GAB1 0.012 0.035 -10000 0 -0.54 2 2
RASGRF1 -0.12 0.17 -10000 0 -0.38 108 108
SOS1 0.014 0 -10000 0 -10000 0 0
MCF2L 0.013 0.072 -10000 0 -0.32 21 21
RGS19 0.014 0 -10000 0 -10000 0 0
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP 0.014 0.074 -10000 0 -10000 0 0
Rac1/GDP 0.041 0.048 -10000 0 -0.29 2 2
NGF (dimer)/TRKA/GRIT -0.064 0.14 -10000 0 -0.35 95 95
neuron projection morphogenesis -0.036 0.13 -10000 0 -0.51 10 10
NGF (dimer)/TRKA/NEDD4-2 -0.07 0.15 -10000 0 -0.39 64 64
MAP2K1 0.038 0.041 -10000 0 -0.53 1 1
NGFR -0.064 0.19 -10000 0 -0.54 73 73
NGF (dimer)/TRKA/GIPC/GAIP -0.049 0.14 -10000 0 -0.43 24 24
RAS family/GTP/PI3K 0.033 0.015 -10000 0 -0.26 1 1
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.019 -10000 0 -10000 0 0
NRAS 0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 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 -0.015 0.13 -10000 0 -0.55 27 27
MAPKKK cascade -0.084 0.2 -10000 0 -0.61 60 60
RASA1 0.014 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.016 0.074 -10000 0 -0.36 22 22
SQSTM1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.064 0.12 -10000 0 -0.36 43 43
NGF (dimer)/TRKA/p62/Atypical PKCs -0.064 0.13 -10000 0 -0.6 10 10
MATK -0.093 0.22 -10000 0 -0.55 98 98
NEDD4L 0 0.088 -10000 0 -0.53 14 14
RAS family/GDP -0.004 0.021 -10000 0 -0.26 1 1
NGF (dimer)/TRKA -0.074 0.13 -10000 0 -0.4 46 46
Rac1/GTP -0.064 0.095 -10000 0 -0.33 31 31
FRS2 family/SHP2/CRK family -0.001 0.019 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.067 0.2 -9999 0 -0.55 74 74
GNB1/GNG2 -0.014 0.12 -9999 0 -0.42 20 20
mol:DAG -0.004 0.12 -9999 0 -0.38 20 20
PLCG1 -0.004 0.12 -9999 0 -0.39 20 20
YES1 -0.022 0.13 -9999 0 -0.43 23 23
FZD3 0.011 0.046 -9999 0 -0.59 3 3
FZD6 -0.014 0.12 -9999 0 -0.49 29 29
G protein -0.005 0.12 -9999 0 -0.39 20 20
MAP3K7 -0.098 0.16 -9999 0 -0.41 44 44
mol:Ca2+ -0.003 0.11 -9999 0 -0.37 20 20
mol:IP3 -0.004 0.12 -9999 0 -0.38 20 20
NLK -0.004 0.011 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.11 0.17 -9999 0 -0.41 60 60
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.03 0.13 -9999 0 -0.3 76 76
CSNK1A1 0.014 0 -9999 0 -10000 0 0
GNAS -0.019 0.12 -9999 0 -0.41 20 20
GO:0007205 -0.003 0.11 -9999 0 -0.38 19 19
WNT6 -0.033 0.16 -9999 0 -0.53 45 45
WNT4 -0.033 0.15 -9999 0 -0.52 46 46
NFAT1/CK1 alpha -0.037 0.16 -9999 0 -0.45 37 37
GNG2 0.009 0.053 -9999 0 -0.59 4 4
WNT5A -0.013 0.12 -9999 0 -0.56 24 24
WNT11 -0.017 0.13 -9999 0 -0.54 29 29
CDC42 -0.012 0.12 -9999 0 -0.41 22 22
Syndecan-3-mediated signaling events

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
CTTN 0.014 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.004 0.043 -9999 0 -0.82 1 1
Syndecan-3/Neurocan -0.021 0.082 -9999 0 -0.32 31 31
POMC -0.005 0.1 -9999 0 -0.54 18 18
EGFR -0.083 0.21 -9999 0 -0.55 89 89
Syndecan-3/EGFR -0.047 0.1 -9999 0 -0.3 50 50
AGRP 0.005 0.049 -9999 0 -0.49 5 5
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 -0.026 0.15 -9999 0 -0.58 35 35
long-term memory -0.002 0.026 -9999 0 -0.56 1 1
Syndecan-3/IL8 -0.082 0.12 -9999 0 -0.3 68 68
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 0.029 -9999 0 -0.62 1 1
MC4R -0.11 0.24 -9999 0 -0.56 112 112
SRC 0.014 0 -9999 0 -10000 0 0
PTN 0.007 0.062 -9999 0 -0.52 7 7
FGFR/FGF/Syndecan-3 -0.002 0.029 -9999 0 -0.63 1 1
neuron projection morphogenesis -0.021 0.08 -9999 0 -0.57 4 4
Syndecan-3/AgRP -0.004 0.036 -9999 0 -0.29 6 6
Syndecan-3/AgRP/MC4R -0.06 0.12 -9999 0 -0.29 77 77
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.002 0.03 -9999 0 -0.64 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.081 0.12 -9999 0 -0.3 68 68
IL8 -0.16 0.26 -9999 0 -0.53 162 162
Syndecan-3/Fyn/Cortactin -0.002 0.026 -9999 0 -0.57 1 1
Syndecan-3/CASK -0.002 0.028 -9999 0 -0.61 1 1
alpha-MSH/MC4R -0.1 0.18 -9999 0 -0.42 123 123
Gamma Secretase 0 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.021 0.087 -9999 0 -0.37 29 29
alphaV beta3 Integrin -0.04 0.1 -9999 0 -0.31 67 67
PTK2 -0.012 0.15 -9999 0 -0.46 23 23
IGF1R 0.013 0.022 -9999 0 -0.49 1 1
PI4KB 0.014 0 -9999 0 -10000 0 0
MFGE8 0.01 0.051 -9999 0 -0.57 4 4
SRC 0.014 0 -9999 0 -10000 0 0
CDKN1B -0.028 0.089 -9999 0 -0.49 15 15
VEGFA -0.007 0.1 -9999 0 -0.49 22 22
ILK -0.028 0.089 -9999 0 -0.49 15 15
ROCK1 0.014 0 -9999 0 -10000 0 0
AKT1 0.008 0.092 -9999 0 -0.45 15 15
PTK2B -0.02 0.14 -9999 0 -0.5 20 20
alphaV/beta3 Integrin/JAM-A -0.012 0.13 -9999 0 -0.53 9 9
CBL 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.039 0.1 -9999 0 -0.3 67 67
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.012 0.058 -9999 0 -0.32 14 14
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.011 0.085 -9999 0 -0.37 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.063 0.14 -9999 0 -0.45 40 40
PI4KA 0.005 0.066 -9999 0 -0.49 9 9
IGF-1R heterotetramer/IGF1/IRS1 -0.045 0.11 -9999 0 -0.47 19 19
PI4 Kinase -0.006 0.045 -9999 0 -0.34 9 9
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
alphaV/beta3 Integrin/Osteopontin -0.093 0.16 -9999 0 -0.36 133 133
RPS6KB1 0.01 0.12 -9999 0 -0.44 19 19
TLN1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.006 0.12 -9999 0 -0.44 23 23
GPR124 0.01 0.044 -9999 0 -0.49 4 4
MAPK1 0.006 0.12 -9999 0 -0.44 23 23
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 -0.34 129 129
cell adhesion -0.033 0.085 -9999 0 -0.33 15 15
ANGPTL3 0.005 0.023 -9999 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.017 0.072 -9999 0 -0.31 29 29
IGF-1R heterotetramer 0.013 0.022 -9999 0 -0.49 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.009 0.049 -9999 0 -0.49 5 5
ITGB3 -0.052 0.18 -9999 0 -0.51 65 65
IGF1 -0.008 0.11 -9999 0 -0.56 20 20
RAC1 0.014 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.04 0.1 -9999 0 -0.3 68 68
apoptosis 0.013 0.027 -9999 0 -0.59 1 1
CD47 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.038 0.099 -9999 0 -0.3 66 66
VCL 0.008 0.058 -9999 0 -0.52 6 6
alphaV/beta3 Integrin/Del1 -0.083 0.16 -9999 0 -0.35 122 122
CSF1 -0.006 0.11 -9999 0 -0.59 17 17
PIK3C2A -0.031 0.097 -9999 0 -0.5 17 17
PI4 Kinase/Pyk2 -0.057 0.12 -9999 0 -0.43 32 32
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.049 0.12 -9999 0 -0.43 35 35
FAK1/Vinculin -0.003 0.13 -9999 0 -0.39 19 19
alphaV beta3/Integrin/ppsTEM5 -0.04 0.1 -9999 0 -0.3 68 68
RHOA 0.014 0 -9999 0 -10000 0 0
VTN -0.008 0.11 -9999 0 -0.56 20 20
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
FGF2 0.011 0.044 -9999 0 -0.56 3 3
F11R 0.014 0.065 -9999 0 -0.36 15 15
alphaV/beta3 Integrin/Lactadherin -0.04 0.1 -9999 0 -0.3 70 70
alphaV/beta3 Integrin/TGFBR2 -0.04 0.11 -9999 0 -0.31 68 68
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.012 0.06 -9999 0 -0.32 19 19
HSP90AA1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.034 0.09 -9999 0 -0.27 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.003 0.092 -9999 0 -0.49 18 18
alphaV/beta3 Integrin/Pyk2 -0.02 0.14 -9999 0 -0.42 32 32
SDC1 -0.031 0.15 -9999 0 -0.51 44 44
VAV3 -0.039 0.14 -9999 0 -0.55 6 6
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0 0.12 -9999 0 -0.37 18 18
cell migration 0.008 0.12 -9999 0 -0.37 14 14
ITGAV 0.013 0.027 -9999 0 -0.59 1 1
PI3K -0.042 0.097 -9999 0 -0.47 9 9
SPP1 -0.082 0.21 -9999 0 -0.54 90 90
KDR 0.005 0.071 -9999 0 -0.52 9 9
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.027 -9999 0 -0.59 1 1
COL4A3 -0.071 0.2 -9999 0 -0.52 82 82
angiogenesis 0.008 0.13 -9999 0 -0.46 20 20
Rac1/GTP -0.062 0.11 -9999 0 -0.5 6 6
EDIL3 -0.065 0.2 -9999 0 -0.57 69 69
cell proliferation -0.04 0.11 -9999 0 -0.31 68 68
Canonical 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
HDAC1 0.003 0.058 -10000 0 -0.58 4 4
AES 0.011 0.022 -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 -0.001 0.04 -10000 0 -0.34 7 7
SMAD4 0.014 0 -10000 0 -10000 0 0
DKK2 -0.11 0.23 -10000 0 -0.54 117 117
TLE1 0.008 0.044 -10000 0 -0.6 2 2
MACF1 0.015 0 -10000 0 -10000 0 0
CTNNB1 0.062 0.082 -10000 0 -10000 0 0
WIF1 -0.28 0.28 -10000 0 -0.54 271 271
beta catenin/RanBP3 0.021 0.11 0.39 33 -10000 0 33
KREMEN2 -0.052 0.18 -10000 0 -0.53 63 63
DKK1 -0.12 0.24 -10000 0 -0.53 123 123
beta catenin/beta TrCP1 0.067 0.077 -10000 0 -10000 0 0
FZD1 0.009 0.054 -10000 0 -0.49 6 6
AXIN2 -0.002 0.11 -10000 0 -0.9 5 5
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 0.023 0.044 -10000 0 -0.56 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.091 0.052 0.29 3 -10000 0 3
Axin1/APC/GSK3 0.008 0.037 0.28 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.054 0.065 -10000 0 -10000 0 0
HNF1A 0.006 0.036 -10000 0 -0.6 1 1
CTBP1 0.007 0.024 -10000 0 -10000 0 0
MYC -0.052 0.31 -10000 0 -1.5 22 22
RANBP3 0.014 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 163 163
NKD1 -0.004 0.099 -10000 0 -0.54 17 17
TCF4 0.006 0.034 -10000 0 -0.55 1 1
TCF3 0.005 0.04 -10000 0 -0.53 2 2
WNT1/LRP6/FZD1/Axin1 -0.017 0.068 -10000 0 -0.5 1 1
Ran/GTP 0.002 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.034 0.13 0.49 31 -10000 0 31
LEF1 0.002 0.054 -10000 0 -0.49 5 5
DVL1 0.061 0.047 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.087 0.078 -10000 0 -0.44 2 2
DKK1/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 168 168
LRP6 0.014 0.022 -10000 0 -0.49 1 1
CSNK1A1 0.009 0.026 -10000 0 -10000 0 0
NLK 0.012 0.033 -10000 0 -0.51 2 2
CCND1 -0.034 0.24 -10000 0 -1.4 12 12
WNT1 -0.021 0.12 -10000 0 -0.49 34 34
GSK3A 0.015 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.027 -10000 0 -0.59 1 1
FRAT1 0.01 0.049 -10000 0 -0.54 4 4
PPP2R5D 0.043 0.049 0.27 17 -10000 0 17
APC 0.022 0.073 -10000 0 -0.38 2 2
WNT1/LRP6/FZD1 0.098 0.1 0.24 113 -10000 0 113
CREBBP 0.007 0.024 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.004 0.08 -10000 0 -0.59 9 9
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.004 0.1 0.44 6 -10000 0 6
IL27/IL27R/JAK1 -0.034 0.15 -10000 0 -0.68 2 2
TBX21 -0.057 0.21 -10000 0 -0.55 41 41
IL12B -0.002 0.054 -10000 0 -0.49 6 6
IL12A -0.012 0.1 -10000 0 -0.42 29 29
IL6ST -0.028 0.16 -10000 0 -0.6 36 36
IL27RA/JAK1 0.018 0.035 -10000 0 -10000 0 0
IL27 -0.015 0.11 -10000 0 -0.49 27 27
TYK2 0.015 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.055 0.12 -10000 0 -0.72 2 2
T-helper 2 cell differentiation 0.004 0.1 0.44 6 -10000 0 6
T cell proliferation during immune response 0.004 0.1 0.44 6 -10000 0 6
MAPKKK cascade -0.004 0.1 -10000 0 -0.44 6 6
STAT3 0.014 0 -10000 0 -10000 0 0
STAT2 0.01 0.044 -10000 0 -0.49 4 4
STAT1 -0.002 0.088 -10000 0 -0.49 16 16
IL12RB1 -0.031 0.16 -10000 0 -0.56 41 41
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.087 0.24 -10000 0 -0.54 56 56
IL27/IL27R/JAK2/TYK2 -0.004 0.1 -10000 0 -0.44 6 6
positive regulation of T cell mediated cytotoxicity -0.004 0.1 -10000 0 -0.44 6 6
STAT1 (dimer) -0.059 0.24 0.52 27 -0.69 14 41
JAK2 0.015 0.004 -10000 0 -10000 0 0
JAK1 0.014 0.004 -10000 0 -10000 0 0
STAT2 (dimer) 0.002 0.1 -10000 0 -0.41 6 6
T cell proliferation -0.068 0.16 -10000 0 -0.48 19 19
IL12/IL12R/TYK2/JAK2 -0.005 0.091 -10000 0 -0.56 4 4
IL17A -0.055 0.12 -10000 0 -0.72 2 2
mast cell activation 0.004 0.1 0.44 6 -10000 0 6
IFNG 0.001 0.02 -10000 0 -0.091 4 4
T cell differentiation -0.004 0.005 -10000 0 -0.022 4 4
STAT3 (dimer) 0.004 0.096 -10000 0 -0.41 6 6
STAT5A (dimer) -0.003 0.11 -10000 0 -0.46 11 11
STAT4 (dimer) -0.086 0.17 -10000 0 -0.48 25 25
STAT4 -0.16 0.26 -10000 0 -0.53 166 166
T cell activation -0.009 0.007 0.061 3 -10000 0 3
IL27R/JAK2/TYK2 -0.011 0.087 -10000 0 -10000 0 0
GATA3 -0.16 0.41 -10000 0 -1.4 51 51
IL18 -0.02 0.11 -10000 0 -0.4 41 41
positive regulation of mast cell cytokine production 0.004 0.095 -10000 0 -0.41 6 6
IL27/EBI3 -0.02 0.12 -10000 0 -0.4 46 46
IL27RA 0.014 0.034 -10000 0 -10000 0 0
IL6 -0.13 0.24 -10000 0 -0.52 137 137
STAT5A 0.001 0.088 -10000 0 -0.59 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.001 0.02 -10000 0 -10000 0 0
IL1B -0.12 0.19 -10000 0 -0.39 174 174
EBI3 -0.012 0.12 -10000 0 -0.57 22 22
TNF -0.11 0.19 -10000 0 -0.39 156 156
Cellular roles of Anthrax toxin

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
ANTXR1 0.008 0.059 -10000 0 -0.59 5 5
ANTXR2 0.002 0.079 -10000 0 -0.51 12 12
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.012 -10000 0 -0.066 17 17
monocyte activation -0.16 0.25 -10000 0 -0.52 140 140
MAP2K2 -0.001 0.004 -10000 0 -10000 0 0
MAP2K1 -0.003 0.02 -10000 0 -0.29 2 2
MAP2K7 -0.002 0.009 -10000 0 -10000 0 0
MAP2K6 -0.002 0.017 -10000 0 -0.32 1 1
CYAA 0.007 0.052 -10000 0 -0.27 17 17
MAP2K4 -0.003 0.022 -10000 0 -0.32 2 2
IL1B -0.082 0.14 -10000 0 -0.28 174 174
Channel -0.01 0.052 -10000 0 -0.29 17 17
NLRP1 -0.003 0.022 -10000 0 -0.32 2 2
CALM1 0.012 0.035 -10000 0 -0.54 2 2
negative regulation of phagocytosis -0.004 0.028 -10000 0 -0.54 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.012 0.066 17 -10000 0 17
MAPK3 -0.002 0.009 -10000 0 -10000 0 0
MAPK1 -0.002 0.009 -10000 0 -10000 0 0
PGR -0.034 0.099 -10000 0 -0.32 53 53
PA/Cellular Receptors -0.011 0.058 -10000 0 -0.32 17 17
apoptosis -0.002 0.012 -10000 0 -0.066 17 17
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.009 0.051 -10000 0 -0.26 17 17
macrophage activation 0.019 0.011 -10000 0 -10000 0 0
TNF -0.15 0.26 -10000 0 -0.54 156 156
VCAM1 -0.16 0.26 -10000 0 -0.53 140 140
platelet activation -0.004 0.028 -10000 0 -0.54 1 1
MAPKKK cascade -0.015 0.017 0.18 2 -10000 0 2
IL18 -0.009 0.088 -10000 0 -0.29 41 41
negative regulation of macrophage activation -0.002 0.012 -10000 0 -0.066 17 17
LEF -0.002 0.012 -10000 0 -0.066 17 17
CASP1 -0.004 0.022 -10000 0 -0.27 2 2
mol:cAMP -0.004 0.028 -10000 0 -0.55 1 1
necrosis -0.002 0.012 -10000 0 -0.066 17 17
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.008 0.052 -10000 0 -0.27 17 17
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.011 0.038 -10000 0 -0.49 3 3
Jak2/Leptin Receptor -0.009 0.1 0.2 20 -0.35 21 41
PTP1B/AKT1 -0.005 0.084 -10000 0 -0.31 12 12
FYN 0.014 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.014 0.093 -10000 0 -0.28 26 26
EGFR -0.084 0.22 -10000 0 -0.55 89 89
EGF/EGFR -0.095 0.16 -10000 0 -0.38 97 97
CSF1 -0.006 0.11 -10000 0 -0.59 17 17
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 0.09 -10000 0 -0.31 17 17
Insulin Receptor/Insulin -0.025 0.059 -10000 0 -0.31 8 8
HCK -0.007 0.11 -10000 0 -0.54 20 20
CRK 0.014 0 -10000 0 -10000 0 0
TYK2 -0.005 0.088 -10000 0 -0.32 13 13
EGF -0.052 0.18 -10000 0 -0.56 58 58
YES1 0.009 0.053 -10000 0 -0.59 4 4
CAV1 -0.03 0.12 -10000 0 -0.33 36 36
TXN 0.011 0.023 -10000 0 -0.5 1 1
PTP1B/IRS1/GRB2 -0.001 0.084 -10000 0 -0.34 9 9
cell migration 0.014 0.093 0.28 26 -10000 0 26
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.018 0.14 -10000 0 -0.56 31 31
ITGA2B -0.043 0.17 -10000 0 -0.57 50 50
CSF1R -0.022 0.14 -10000 0 -0.57 32 32
Prolactin Receptor/Prolactin -0.018 0.1 -10000 0 -0.4 34 34
FGR 0.011 0.038 -10000 0 -0.49 3 3
PTP1B/p130 Cas -0.007 0.089 -10000 0 -0.32 14 14
Crk/p130 Cas -0.002 0.084 -10000 0 -0.33 10 10
DOK1 0.003 0.084 -10000 0 -0.33 9 9
JAK2 0.001 0.084 -10000 0 -0.34 13 13
Jak2/Leptin Receptor/Leptin -0.11 0.18 -10000 0 -0.42 110 110
PIK3R1 0.014 0 -10000 0 -10000 0 0
PTPN1 -0.014 0.093 -10000 0 -0.29 26 26
LYN 0.004 0.073 -10000 0 -0.51 10 10
CDH2 0.013 0.027 -10000 0 -0.59 1 1
SRC 0.012 0.037 -10000 0 -10000 0 0
ITGB3 -0.052 0.18 -10000 0 -0.51 65 65
CAT1/PTP1B -0.058 0.15 -10000 0 -0.4 45 45
CAPN1 0.014 0.027 -10000 0 -0.6 1 1
CSK 0.014 0 -10000 0 -10000 0 0
PI3K -0.018 0.053 -10000 0 -0.35 2 2
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.11 0.18 -10000 0 -0.43 108 108
negative regulation of transcription 0.002 0.083 -10000 0 -0.34 13 13
FCGR2A -0.031 0.15 -10000 0 -0.54 42 42
FER -0.013 0.12 -10000 0 -0.6 22 22
alphaIIb/beta3 Integrin -0.081 0.17 -10000 0 -0.41 107 107
BLK -0.1 0.22 -10000 0 -0.52 113 113
Insulin Receptor/Insulin/Shc -0.003 0.045 -10000 0 -0.32 10 10
RHOA 0.015 0.002 -10000 0 -10000 0 0
LEPR 0.001 0.089 -10000 0 -0.53 14 14
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
p210 bcr-abl/Grb2 0.013 0.022 -10000 0 -0.49 1 1
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.068 0.16 -10000 0 -0.43 49 49
PRL 0.001 0.038 -10000 0 -0.48 3 3
SOCS3 -0.14 0.34 -10000 0 -1.4 32 32
SPRY2 0.006 0.064 -10000 0 -0.5 8 8
Insulin Receptor/Insulin/IRS1 0 0.035 -10000 0 -0.34 5 5
CSF1/CSF1R -0.029 0.14 -10000 0 -0.4 45 45
Ras protein signal transduction 0.019 0.034 -10000 0 -0.4 1 1
IRS1 0.014 0 -10000 0 -10000 0 0
INS -0.005 0.056 -10000 0 -0.57 5 5
LEP -0.002 0.058 -10000 0 -0.49 7 7
STAT5B -0.003 0.084 -10000 0 -0.28 17 17
STAT5A -0.006 0.088 -10000 0 -0.29 19 19
GRB2 0.013 0.022 -10000 0 -0.49 1 1
PDGFB-D/PDGFRB -0.008 0.091 -10000 0 -0.33 15 15
CSN2 -0.001 0.042 -10000 0 -10000 0 0
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
LAT -0.037 0.15 -10000 0 -0.48 46 46
YBX1 0.02 0.038 -10000 0 -0.58 2 2
LCK -0.081 0.21 -10000 0 -0.54 89 89
SHC1 0.009 0.049 -10000 0 -0.49 5 5
NOX4 -0.065 0.19 -10000 0 -0.52 76 76
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.037 0.16 -10000 0 -0.53 14 14
UGCG -0.022 0.14 -10000 0 -0.65 21 21
AKT1/mTOR/p70S6K/Hsp90/TERT -0.039 0.16 -10000 0 -0.41 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.021 0.13 -10000 0 -0.64 21 21
mol:DAG -0.004 0.043 -10000 0 -0.97 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.069 0.12 -10000 0 -0.45 28 28
FRAP1 -0.027 0.18 -10000 0 -0.53 27 27
FOXO3 -0.019 0.17 -10000 0 -0.51 22 22
AKT1 -0.03 0.18 -10000 0 -0.46 43 43
GAB2 0.013 0.027 -10000 0 -0.6 1 1
SMPD1 0.004 0.036 -10000 0 -10000 0 0
SGMS1 0.003 0.046 -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 0.022 0.018 -10000 0 -0.36 1 1
CALM1 0.012 0.035 -10000 0 -0.54 2 2
cell proliferation -0.015 0.11 -10000 0 -0.3 44 44
EIF3A 0.014 0 -10000 0 -10000 0 0
PI3K 0.024 0.021 -10000 0 -0.43 1 1
RPS6KB1 -0.004 0.065 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.043 -10000 0 -0.97 1 1
natural killer cell activation 0 0.002 -10000 0 -0.012 11 11
JAK3 -0.055 0.18 -10000 0 -0.52 68 68
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
MYC -0.04 0.24 -10000 0 -0.93 26 26
MYB -0.095 0.35 -10000 0 -1 56 56
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.037 0.17 -10000 0 -0.42 50 50
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.013 0.061 -10000 0 -0.28 1 1
mol:PI-3-4-5-P3 -0.035 0.16 -10000 0 -0.4 50 50
Rac1/GDP 0.028 0.017 -10000 0 -0.32 1 1
T cell proliferation -0.037 0.18 -10000 0 -0.5 36 36
SHC1 0.009 0.05 -10000 0 -0.49 5 5
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.02 -10000 0 -0.05 73 73
PRKCZ -0.039 0.18 -10000 0 -0.52 36 36
NF kappa B1 p50/RelA -0.062 0.12 -10000 0 -0.47 22 22
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.05 0.17 -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 -0.063 0.18 -10000 0 -0.5 73 73
IL2RB -0.092 0.22 -10000 0 -0.53 103 103
TERT -0.082 0.21 -10000 0 -0.56 81 81
E2F1 -0.032 0.15 -10000 0 -0.43 56 56
SOS1 0.014 0.004 -10000 0 -10000 0 0
RPS6 0.013 0.022 -10000 0 -0.49 1 1
mol:cAMP 0.001 0.01 0.024 73 -10000 0 73
PTPN11 0.014 0.004 -10000 0 -10000 0 0
IL2RG -0.039 0.16 -10000 0 -0.52 53 53
actin cytoskeleton organization -0.037 0.18 -10000 0 -0.5 36 36
GRB2 0.013 0.022 -10000 0 -0.49 1 1
IL2 0.003 0.004 -10000 0 -10000 0 0
PIK3CA 0.015 0.027 -10000 0 -0.59 1 1
Rac1/GTP 0.032 0.022 -10000 0 -0.3 1 1
LCK -0.078 0.21 -10000 0 -0.53 89 89
BCL2 -0.015 0.18 -10000 0 -0.63 19 19
Signaling events mediated by HDAC Class III

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
EP300 0.009 0.053 -10000 0 -0.59 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 -0.027 0.037 0.34 3 -10000 0 3
CDKN1A -0.052 0.17 -10000 0 -0.48 60 60
KAT2B 0.013 0.022 -10000 0 -0.49 1 1
BAX 0.014 0 -10000 0 -10000 0 0
FOXO3 0.004 0.04 0.45 4 -10000 0 4
FOXO1 0.011 0.044 -10000 0 -0.56 3 3
FOXO4 0.022 0.031 -10000 0 -0.29 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
TAT -0.08 0.21 -10000 0 -0.54 88 88
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.12 0.2 -10000 0 -0.39 178 178
PPARGC1A -0.011 0.12 -10000 0 -0.57 22 22
FHL2 -0.032 0.15 -10000 0 -0.52 45 45
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.012 0.035 -10000 0 -10000 0 0
HIST2H4A 0.027 0.037 -10000 0 -0.34 3 3
SIRT1/FOXO3a 0.013 0.039 0.29 4 -10000 0 4
SIRT1 0.016 0.045 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.011 0.039 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.002 0.069 -10000 0 -0.26 19 19
apoptosis -0.012 0.034 -10000 0 -10000 0 0
SIRT1/PGC1A -0.004 0.08 -10000 0 -0.35 22 22
p53/SIRT1 0.023 0.12 0.4 19 -0.43 13 32
SIRT1/FOXO4 0.011 0.046 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.015 0.089 -10000 0 -0.32 14 14
HIST1H1E 0.003 0.073 -10000 0 -0.3 20 20
SIRT1/p300 0.009 0.052 -10000 0 -0.43 4 4
muscle cell differentiation 0.1 0.16 0.36 103 -10000 0 103
TP53 -0.002 0.11 -10000 0 -0.57 15 15
KU70/SIRT1/BAX 0.012 0.035 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
MEF2D 0.012 0.031 -10000 0 -0.49 2 2
HIV-1 Tat/SIRT1 -0.054 0.15 -10000 0 -0.38 88 88
ACSS2 0.029 0.024 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.1 0.16 -10000 0 -0.36 103 103
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0.022 -10000 0 -0.49 1 1
Rac1/GDP 0.006 0.017 -10000 0 -10000 0 0
DOCK1 0.009 0.053 -10000 0 -0.59 4 4
ITGA4 -0.052 0.18 -10000 0 -0.53 62 62
RAC1 0.014 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.077 0.17 -10000 0 -0.43 93 93
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.039 0.11 -10000 0 -0.32 62 62
alpha4/beta7 Integrin/Paxillin -0.028 0.14 -10000 0 -0.37 57 57
lamellipodium assembly 0.004 0.038 -10000 0 -0.37 1 1
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
PI3K -0.001 0.019 -10000 0 -0.43 1 1
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 -0.028 0.077 -10000 0 -0.43 2 2
cell adhesion -0.031 0.085 -10000 0 -0.46 2 2
CRKL/CBL -0.001 0.015 -10000 0 -0.34 1 1
alpha4/beta1 Integrin/Paxillin -0.002 0.1 -10000 0 -0.33 28 28
ITGB1 0.012 0.031 -10000 0 -0.49 2 2
ITGB7 -0.034 0.16 -10000 0 -0.54 45 45
ARF6/GDP 0.006 0.017 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.074 0.17 -10000 0 -0.32 124 124
p130Cas/Crk/Dock1 -0.003 0.035 -10000 0 -0.36 5 5
VCAM1 -0.14 0.25 -10000 0 -0.56 134 134
alpha4/beta1 Integrin/Paxillin/Talin 0.007 0.1 -10000 0 -0.3 28 28
alpha4/beta1 Integrin/Paxillin/GIT1 0.007 0.1 -10000 0 -0.3 28 28
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
mol:GDP 0.031 0.085 0.3 28 -10000 0 28
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 0.007 0.1 -10000 0 -0.3 28 28
Rac1/GTP 0.004 0.041 -10000 0 -0.41 1 1
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.058 0.19 -10000 0 -0.58 63 63
HRAS 0.014 0 -10000 0 -10000 0 0
EGFR -0.083 0.21 -10000 0 -0.55 89 89
AKT 0.02 0.045 -10000 0 -0.38 4 4
FOXO3 0.014 0 -10000 0 -10000 0 0
AKT1 0.014 0 -10000 0 -10000 0 0
FOXO1 0.011 0.044 -10000 0 -0.56 3 3
AKT3 0.008 0.059 -10000 0 -0.59 5 5
FOXO4 0.013 0.027 -10000 0 -0.59 1 1
MET -0.15 0.25 -10000 0 -0.54 151 151
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
PIK3CB 0.014 0 -10000 0 -10000 0 0
NRAS 0.014 0 -10000 0 -10000 0 0
PIK3CG -0.059 0.19 -10000 0 -0.53 69 69
PIK3R3 0.011 0.041 -10000 0 -0.52 3 3
PIK3R2 0.014 0 -10000 0 -10000 0 0
NF1 0.012 0.038 -10000 0 -0.59 2 2
RAS -0.054 0.11 0.22 1 -0.3 49 50
ERBB2 0.005 0.068 -10000 0 -0.5 9 9
proliferation/survival/translation -0.008 0.051 0.22 7 -10000 0 7
PI3K -0.046 0.11 -10000 0 -0.25 77 77
PIK3R1 0.014 0 -10000 0 -10000 0 0
KRAS 0.013 0.022 -10000 0 -0.49 1 1
FOXO 0.028 0.03 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
PTEN 0.013 0.027 -10000 0 -0.59 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.025 0.11 -10000 0 -0.26 68 68
epithelial cell differentiation -0.063 0.11 -10000 0 -0.3 60 60
CYFIP2 0.008 0.06 -10000 0 -0.54 6 6
ENAH 0.009 0.1 -10000 0 -0.36 1 1
EGFR -0.083 0.21 -10000 0 -0.55 89 89
EPHA2 -0.015 0.12 -10000 0 -0.5 30 30
MYO6 -0.027 0.12 -10000 0 -10000 0 0
CTNNB1 0.014 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.004 0.034 -10000 0 -0.36 3 3
AQP5 -0.14 0.18 -10000 0 -0.51 75 75
CTNND1 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.027 0.12 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.033 0.13 -10000 0 -0.53 3 3
EGF -0.05 0.18 -10000 0 -0.56 58 58
NCKAP1 0.014 0 -10000 0 -10000 0 0
AQP3 -0.076 0.13 -10000 0 -0.51 19 19
cortical microtubule organization -0.063 0.11 -10000 0 -0.3 60 60
GO:0000145 -0.025 0.12 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.064 0.11 -10000 0 -0.3 60 60
MLLT4 0.013 0.027 -10000 0 -0.59 1 1
ARF6/GDP -0.057 0.095 -10000 0 -0.4 10 10
ARF6 0.014 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.017 0.066 -10000 0 -0.4 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.028 0.12 -10000 0 -0.35 11 11
PVRL2 0.012 0.035 -10000 0 -0.54 2 2
ZYX -0.032 0.12 -10000 0 -0.52 1 1
ARF6/GTP -0.015 0.059 -10000 0 -0.53 1 1
CDH1 -0.12 0.24 -10000 0 -0.54 125 125
EGFR/EGFR/EGF/EGF -0.13 0.17 -10000 0 -0.52 47 47
RhoA/GDP -0.058 0.1 -10000 0 -10000 0 0
actin cytoskeleton organization -0.021 0.12 -10000 0 -0.54 1 1
IGF-1R heterotetramer 0.013 0.022 -10000 0 -0.49 1 1
GIT1 0.014 0 -10000 0 -10000 0 0
IGF1R 0.013 0.022 -10000 0 -0.49 1 1
IGF1 -0.008 0.11 -10000 0 -0.56 20 20
DIAPH1 -0.001 0.052 -10000 0 -0.65 3 3
Wnt receptor signaling pathway 0.063 0.11 0.3 60 -10000 0 60
RHOA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP -0.057 0.096 -10000 0 -0.4 10 10
CTNNA1 0.014 0 -10000 0 -10000 0 0
VCL -0.022 0.12 -10000 0 -0.56 1 1
EFNA1 0.01 0.044 -10000 0 -0.49 4 4
LPP -0.042 0.14 -10000 0 -0.45 10 10
Ephrin A1/EPHA2 -0.069 0.11 -10000 0 -0.46 9 9
SEC6/SEC8 -0.05 0.092 -10000 0 -0.47 3 3
MGAT3 -0.033 0.13 -10000 0 -0.54 3 3
HGF/MET -0.16 0.18 -10000 0 -0.51 73 73
HGF -0.079 0.2 -10000 0 -0.51 91 91
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.025 0.11 -10000 0 -0.26 68 68
actin cable formation 0.02 0.1 -10000 0 -0.32 3 3
KIAA1543 -0.063 0.17 -10000 0 -0.55 25 25
KIFC3 -0.028 0.12 -10000 0 -0.58 1 1
NCK1 0.013 0.027 -10000 0 -0.59 1 1
EXOC3 0.014 0 -10000 0 -10000 0 0
ACTN1 -0.045 0.14 -10000 0 -0.47 8 8
NCK1/GIT1 -0.001 0.019 -10000 0 -0.43 1 1
mol:GDP -0.063 0.11 -10000 0 -0.3 60 60
EXOC4 0.014 0 -10000 0 -10000 0 0
STX4 -0.027 0.12 -10000 0 -10000 0 0
PIP5K1C -0.027 0.12 -10000 0 -10000 0 0
LIMA1 0.004 0.079 -10000 0 -0.59 9 9
ABI1 0.014 0 -10000 0 -10000 0 0
ROCK1 -0.001 0.11 -10000 0 -0.37 5 5
adherens junction assembly -0.043 0.17 -10000 0 -0.52 25 25
IGF-1R heterotetramer/IGF1 -0.065 0.12 -10000 0 -0.54 8 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.031 -10000 0 -0.4 3 3
MET -0.15 0.25 -10000 0 -0.54 151 151
PLEKHA7 -0.037 0.14 -10000 0 -0.56 6 6
mol:GTP -0.017 0.065 -10000 0 -0.4 3 3
establishment of epithelial cell apical/basal polarity 0.004 0.11 -10000 0 -0.45 3 3
cortical actin cytoskeleton stabilization -0.025 0.11 -10000 0 -0.26 68 68
regulation of cell-cell adhesion -0.021 0.12 -10000 0 -0.54 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.025 0.11 -10000 0 -0.26 68 68
Ceramide signaling pathway

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.007 0.1 -10000 0 -0.34 45 45
MAP4K4 -0.022 0.12 -10000 0 -0.45 18 18
BAG4 -0.001 0.095 -10000 0 -0.59 13 13
PKC zeta/ceramide -0.013 0.074 0.15 6 -0.27 26 32
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.033 0.16 -10000 0 -0.55 43 43
BAX 0.006 0.026 -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 0.003 0.048 0.16 10 -10000 0 10
SMPD1 -0.026 0.089 -10000 0 -0.27 12 12
RB1 0.003 0.051 0.16 10 -0.4 1 11
FADD/Caspase 8 -0.012 0.12 -10000 0 -0.48 14 14
MAP2K4 0.007 0.057 -10000 0 -0.26 8 8
NSMAF 0.014 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.011 0.046 -10000 0 -10000 0 0
EGF -0.05 0.18 -10000 0 -0.56 58 58
mol:ceramide -0.006 0.052 0.15 40 -10000 0 40
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 0.1 -10000 0 -0.34 45 45
ASAH1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.002 0.051 0.16 13 -0.4 1 14
cell proliferation -0.002 0.093 -10000 0 -0.33 31 31
BID -0.01 0.091 -10000 0 -0.41 9 9
MAP3K1 0 0.058 0.16 13 -0.27 7 20
EIF2A 0.015 0.052 -10000 0 -0.28 5 5
TRADD 0.013 0.027 -10000 0 -0.59 1 1
CRADD 0.014 0 -10000 0 -10000 0 0
MAPK3 0.022 0.044 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.044 -10000 0 -10000 0 0
Cathepsin D/ceramide 0.002 0.046 0.15 9 -10000 0 9
FADD -0.021 0.12 -10000 0 -0.46 17 17
KSR1 0.003 0.048 0.16 10 -10000 0 10
MAPK8 -0.003 0.073 0.16 2 -0.25 26 28
PRKRA 0.003 0.048 0.14 38 -10000 0 38
PDGFA -0.03 0.14 -10000 0 -0.49 45 45
TRAF2 0.014 0 -10000 0 -10000 0 0
IGF1 -0.008 0.11 -10000 0 -0.56 20 20
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.006 0.052 0.15 40 -10000 0 40
CTSD 0.013 0.022 -10000 0 -0.49 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 -0.36 31 31
PRKCD -0.018 0.14 -10000 0 -0.59 27 27
PRKCZ -0.015 0.13 -10000 0 -0.55 27 27
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.007 0.1 -10000 0 -0.34 45 45
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.033 0.16 -10000 0 -0.53 45 45
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.032 0.13 -10000 0 -0.5 17 17
TNFR1A/BAG4/TNF-alpha -0.11 0.17 -10000 0 -0.34 171 171
mol:Sphingosine-1-phosphate -0.007 0.1 -10000 0 -0.34 45 45
MAP2K1 0.018 0.046 -10000 0 -0.23 2 2
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 0.001 0.085 -10000 0 -0.55 12 12
NFKB1 0.014 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.02 0.093 -10000 0 -0.44 23 23
EIF2AK2 0.008 0.055 0.16 10 -0.3 5 15
TNF-alpha/TNFR1A/FAN -0.1 0.15 -10000 0 -0.37 77 77
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.002 0.081 -10000 0 -0.44 3 3
MAP2K2 0.019 0.044 -10000 0 -10000 0 0
SMPD3 -0.047 0.13 -10000 0 -0.37 41 41
TNF -0.15 0.26 -10000 0 -0.54 156 156
PKC zeta/PAR4 -0.053 0.14 -10000 0 -0.4 68 68
mol:PHOSPHOCHOLINE 0.007 0.077 0.21 49 -10000 0 49
NF kappa B1/RelA/I kappa B alpha -0.035 0.095 -10000 0 -0.54 4 4
AIFM1 0.008 0.039 0.19 4 -10000 0 4
BCL2 0.005 0.075 -10000 0 -0.59 8 8
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.004 0.092 -9999 0 -0.37 29 29
PDGFRB 0.01 0.039 -9999 0 -0.5 3 3
SPHK1 -0.041 0.14 -9999 0 -0.75 18 18
mol:S1P -0.041 0.12 -9999 0 -0.61 21 21
S1P1/S1P/Gi -0.021 0.15 -9999 0 -0.36 61 61
GNAO1 0.007 0.06 -9999 0 -0.6 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.009 0.14 -9999 0 -0.53 11 11
PLCG1 -0.014 0.15 -9999 0 -0.54 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.039 -9999 0 -0.5 3 3
GNAI2 0.012 0.006 -9999 0 -10000 0 0
GNAI3 0.012 0.006 -9999 0 -10000 0 0
GNAI1 -0.007 0.11 -9999 0 -0.6 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.003 0.078 -9999 0 -0.31 29 29
S1P1/S1P -0.051 0.11 -9999 0 -0.45 28 28
negative regulation of cAMP metabolic process -0.019 0.15 -9999 0 -0.35 61 61
MAPK3 -0.038 0.21 -9999 0 -0.53 61 61
calcium-dependent phospholipase C activity -0.001 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.004 0.071 -9999 0 -0.53 9 9
PLCB2 -0.016 0.13 -9999 0 -0.46 25 25
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.042 0.094 -9999 0 -0.41 22 22
receptor internalization -0.048 0.1 -9999 0 -0.42 28 28
PTGS2 -0.1 0.36 -9999 0 -1 61 61
Rac1/GTP -0.042 0.094 -9999 0 -0.41 22 22
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFA -0.008 0.1 -9999 0 -0.49 22 22
negative regulation of T cell proliferation -0.019 0.15 -9999 0 -0.35 61 61
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.012 0.006 -9999 0 -10000 0 0
MAPK1 -0.038 0.21 -9999 0 -0.53 61 61
S1P1/S1P/PDGFB-D/PDGFRB -0.011 0.13 -9999 0 -0.46 22 22
ABCC1 0.01 0.045 -9999 0 -0.49 4 4
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.017 0.068 -10000 0 -0.36 3 3
epithelial cell differentiation -0.042 0.086 -10000 0 -0.46 8 8
ITCH 0.019 0.013 -10000 0 -10000 0 0
WWP1 0.024 0.05 -10000 0 -10000 0 0
FYN 0.014 0 -10000 0 -10000 0 0
EGFR -0.083 0.21 -10000 0 -0.55 89 89
PRL -0.001 0.038 -10000 0 -0.49 3 3
neuron projection morphogenesis -0.031 0.15 -10000 0 -0.46 12 12
PTPRZ1 0.005 0.072 -10000 0 -0.57 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.089 0.13 -10000 0 -0.52 12 12
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.078 0.17 -10000 0 -0.42 27 27
ADAM17 0.011 0.066 -10000 0 -0.59 6 6
ErbB4/ErbB4 0.02 0.064 -10000 0 -0.41 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.004 0.12 -10000 0 -0.38 39 39
NCOR1 0.012 0.038 -10000 0 -0.59 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.065 0.16 -10000 0 -0.43 16 16
GRIN2B -0.15 0.21 -10000 0 -0.5 82 82
ErbB4/ErbB2/betacellulin -0.031 0.14 -10000 0 -0.43 19 19
STAT1 -0.001 0.087 -10000 0 -0.49 16 16
HBEGF 0.004 0.069 -10000 0 -0.49 10 10
PRLR -0.02 0.14 -10000 0 -0.56 31 31
E4ICDs/ETO2 0.018 0.07 -10000 0 -0.37 8 8
axon guidance -0.016 0.078 -10000 0 -0.36 2 2
NEDD4 0.007 0.08 -10000 0 -0.52 11 11
Prolactin receptor/Prolactin receptor/Prolactin -0.026 0.1 -10000 0 -0.4 34 34
CBFA2T3 0.006 0.07 -10000 0 -0.59 7 7
ErbB4/ErbB2/HBEGF 0.022 0.075 -10000 0 -0.36 8 8
MAPK3 -0.041 0.15 -10000 0 -0.48 12 12
STAT1 (dimer) 0.014 0.075 -10000 0 -0.39 4 4
MAPK1 -0.041 0.15 -10000 0 -0.48 12 12
JAK2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.07 0.16 -10000 0 -0.45 20 20
NRG1 -0.11 0.21 -10000 0 -0.41 167 167
NRG3 -0.031 0.16 -10000 0 -0.59 38 38
NRG2 0.012 0.038 -10000 0 -0.59 2 2
NRG4 -0.046 0.17 -10000 0 -0.52 58 58
heart development -0.016 0.078 -10000 0 -0.36 2 2
neural crest cell migration -0.069 0.16 -10000 0 -0.44 20 20
ERBB2 0.016 0.069 -10000 0 -0.38 15 15
WWOX/E4ICDs 0.023 0.054 -10000 0 -0.36 1 1
SHC1 0.009 0.049 -10000 0 -0.49 5 5
ErbB4/EGFR/neuregulin 4 -0.057 0.16 -10000 0 -0.47 35 35
apoptosis 0.041 0.11 0.41 39 -10000 0 39
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.021 0.061 -10000 0 -0.44 3 3
ErbB4/ErbB2/epiregulin 0.005 0.086 -10000 0 -0.4 8 8
ErbB4/ErbB4/betacellulin/betacellulin -0.04 0.14 -10000 0 -0.36 63 63
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.03 0.076 -10000 0 -0.47 4 4
MDM2 0.026 0.058 -10000 0 -0.36 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.096 0.14 -10000 0 -0.42 16 16
STAT5A -0.013 0.091 -10000 0 -0.41 9 9
ErbB4/EGFR/neuregulin 1 beta -0.12 0.2 -10000 0 -0.53 53 53
DLG4 0.004 0.069 -10000 0 -0.49 10 10
GRB2/SHC -0.004 0.037 -10000 0 -0.34 6 6
E4ICDs/TAB2/NCoR1 -0.014 0.049 -10000 0 -0.55 2 2
STAT5A (dimer) -0.044 0.092 -10000 0 -0.51 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.073 -10000 0 -10000 0 0
LRIG1 -0.002 0.099 -10000 0 -0.59 14 14
EREG -0.013 0.1 -10000 0 -0.49 24 24
BTC -0.086 0.22 -10000 0 -0.56 88 88
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.016 0.078 -10000 0 -0.36 2 2
ERBB4 0.02 0.064 -10000 0 -0.42 1 1
STAT5B 0.014 0 -10000 0 -10000 0 0
YAP1 -0.036 0.13 -10000 0 -0.58 28 28
GRB2 0.013 0.022 -10000 0 -0.49 1 1
ErbB4/ErbB2/neuregulin 4 -0.007 0.11 -10000 0 -0.42 12 12
glial cell differentiation 0.014 0.048 0.54 2 -10000 0 2
WWOX 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.1 0.19 -10000 0 -0.53 44 44
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.014 0 -9999 0 -10000 0 0
SPHK1 -0.028 0.15 -9999 0 -0.54 40 40
GNAI2 0.014 0 -9999 0 -10000 0 0
mol:S1P 0.005 0.07 -9999 0 -0.3 20 20
GNAO1 0.008 0.059 -9999 0 -0.59 5 5
mol:Sphinganine-1-P -0.007 0.11 -9999 0 -0.38 40 40
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.024 0.071 -9999 0 -0.5 4 4
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.019 -9999 0 -0.43 1 1
S1PR3 -0.034 0.15 -9999 0 -0.52 47 47
S1PR2 0.008 0.062 -9999 0 -0.56 6 6
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.015 0.055 -9999 0 -0.26 20 20
S1PR5 -0.13 0.25 -9999 0 -0.55 134 134
S1PR4 0 0.086 -9999 0 -0.51 14 14
GNAI1 -0.005 0.1 -9999 0 -0.59 16 16
S1P/S1P5/G12 -0.063 0.16 -9999 0 -0.34 84 84
S1P/S1P3/Gq -0.009 0.12 -9999 0 -0.46 16 16
S1P/S1P4/Gi 0.024 0.07 -9999 0 -0.37 6 6
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ 0.014 0 -9999 0 -10000 0 0
GNA14 -0.014 0.12 -9999 0 -0.56 25 25
GNA15 -0.007 0.11 -9999 0 -0.57 19 19
GNA12 0.013 0.027 -9999 0 -0.59 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.004 0.079 -9999 0 -0.59 9 9
ABCC1 0.01 0.044 -9999 0 -0.49 4 4
Aurora A signaling

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
Aurora A/GADD45A 0.005 0.095 -9999 0 -0.32 30 30
BIRC5 -0.14 0.25 -9999 0 -0.55 138 138
NFKBIA 0.029 0.049 -9999 0 -0.28 2 2
CPEB1 -0.002 0.099 -9999 0 -0.59 14 14
AKT1 0.029 0.049 -9999 0 -0.28 2 2
NDEL1 0.014 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.002 0.052 -9999 0 -0.39 3 3
NDEL1/TACC3 -0.013 0.092 -9999 0 -0.37 20 20
GADD45A -0.018 0.12 -9999 0 -0.49 33 33
GSK3B 0.017 0.03 -9999 0 -0.6 1 1
PAK1/Aurora A -0.005 0.1 -9999 0 -0.3 38 38
MDM2 0.012 0.031 -9999 0 -0.49 2 2
JUB -0.013 0.12 -9999 0 -0.57 24 24
TPX2 -0.037 0.15 -9999 0 -0.38 80 80
TP53 0.021 0.062 -9999 0 -0.28 14 14
DLG7 0.018 0.049 -9999 0 -0.29 2 2
AURKAIP1 0.013 0.022 -9999 0 -0.49 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 0.009 0.1 -9999 0 -0.39 20 20
G2/M transition of mitotic cell cycle 0.002 0.052 -9999 0 -0.38 3 3
AURKA 0.023 0.061 -9999 0 -0.34 2 2
AURKB -0.082 0.13 -9999 0 -0.29 126 126
CDC25B 0.024 0.048 -9999 0 -0.27 2 2
G2/M transition checkpoint -0.011 0.073 -9999 0 -0.29 24 24
mRNA polyadenylation -0.005 0.073 -9999 0 -0.37 14 14
Aurora A/CPEB -0.005 0.074 -9999 0 -0.37 14 14
Aurora A/TACC1/TRAP/chTOG 0.011 0.047 -9999 0 -10000 0 0
BRCA1 0.01 0.044 -9999 0 -0.49 4 4
centrosome duplication -0.005 0.1 -9999 0 -0.3 38 38
regulation of centrosome cycle -0.024 0.084 -9999 0 -0.36 20 20
spindle assembly 0.005 0.043 -9999 0 -10000 0 0
TDRD7 0.012 0.038 -9999 0 -0.59 2 2
Aurora A/RasGAP/Survivin -0.071 0.12 -9999 0 -0.36 28 28
CENPA -0.056 0.13 -9999 0 -0.32 77 77
Aurora A/PP2A 0.025 0.047 -9999 0 -0.28 2 2
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.032 0.045 -9999 0 -0.26 2 2
negative regulation of DNA binding 0.021 0.062 -9999 0 -0.28 14 14
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 0.074 -9999 0 -0.29 24 24
mitotic prometaphase 0.022 0.037 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.061 -9999 0 -0.34 2 2
TACC1 0.014 0 -9999 0 -10000 0 0
TACC3 -0.027 0.14 -9999 0 -0.5 42 42
Aurora A/Antizyme1 0.032 0.044 -9999 0 -10000 0 0
Aurora A/RasGAP 0.025 0.047 -9999 0 -0.28 2 2
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 -0.027 0.085 -9999 0 -0.29 49 49
Importin alpha/Importin beta/TPX2 -0.037 0.15 -9999 0 -0.38 80 80
PPP2R5D 0.014 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.014 0.13 -9999 0 -0.36 43 43
PAK1 -0.035 0.15 -9999 0 -0.5 49 49
CKAP5 0.014 0 -9999 0 -10000 0 0
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 0.022 -10000 0 -0.49 1 1
NFATC1 0.029 0.095 -10000 0 -0.44 2 2
NFATC2 0.009 0.078 -10000 0 -0.26 19 19
NFATC3 0.006 0.082 -10000 0 -0.4 17 17
YWHAE 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.064 0.18 -10000 0 -0.52 42 42
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.15 0.19 -10000 0 -0.48 91 91
BCL2/BAX -0.007 0.053 -10000 0 -0.43 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.026 -10000 0 -0.4 2 2
CaM/Ca2+ 0.01 0.026 -10000 0 -0.4 2 2
BAX 0.014 0 -10000 0 -10000 0 0
MAPK14 0.014 0.003 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.054 0.17 -10000 0 -0.49 43 43
Calcineurin A alpha-beta B1/BCL2 0.005 0.075 -10000 0 -0.59 8 8
FKBP8 0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.053 0.16 0.48 43 -10000 0 43
KPNB1 0.014 0 -10000 0 -10000 0 0
KPNA2 0.012 0.031 -10000 0 -0.49 2 2
XPO1 0.014 0 -10000 0 -10000 0 0
SFN -0.11 0.23 -10000 0 -0.53 119 119
MAP3K8 -0.005 0.1 -10000 0 -0.51 19 19
NFAT4/CK1 alpha -0.015 0.057 -10000 0 -0.4 3 3
MEF2D/NFAT1/Cbp/p300 0.025 0.11 -10000 0 -0.43 13 13
CABIN1 -0.065 0.18 -10000 0 -0.53 42 42
CALM1 0.012 0.035 -10000 0 -0.54 2 2
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.007 0.058 -10000 0 -0.49 7 7
CAMK4 -0.18 0.27 -10000 0 -0.57 168 168
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 -0.49 25 25
Calcineurin A alpha-beta B1/AKAP79/PKA -0.014 0.11 -10000 0 -0.35 48 48
YWHAB 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.003 0.099 -10000 0 -0.59 14 14
MAPK9 0.014 0 -10000 0 -10000 0 0
YWHAG 0.002 0.079 -10000 0 -0.49 13 13
FKBP1A 0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.037 0.1 -10000 0 -0.43 5 5
PRKCH 0.014 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.003 0.038 -10000 0 -0.43 4 4
CASP3 0.013 0.022 -10000 0 -0.49 1 1
PIM1 0.008 0.054 -10000 0 -0.49 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.003 -10000 0 -10000 0 0
apoptosis -0.002 0.021 -10000 0 -0.34 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.077 -10000 0 -0.31 4 4
PRKCB -0.062 0.19 -10000 0 -0.52 73 73
PRKCE 0.003 0.077 -10000 0 -0.52 11 11
JNK2/NFAT4 0.014 0.075 -10000 0 -0.36 17 17
BAD/BCL-XL -0.001 0.015 -10000 0 -0.34 1 1
PRKCD -0.018 0.14 -10000 0 -0.59 27 27
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.016 0.13 -10000 0 -0.55 27 27
PRKCA 0.013 0.027 -10000 0 -0.59 1 1
PRKCG -0.19 0.27 -10000 0 -0.54 193 193
PRKCQ -0.005 0.11 -10000 0 -0.58 17 17
FKBP38/BCL2 -0.007 0.053 -10000 0 -0.43 8 8
EP300 0.01 0.053 -10000 0 -0.59 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 0.026 0.1 -10000 0 -0.42 4 4
CaM/Ca2+/FKBP38 0.018 0.023 -10000 0 -0.33 2 2
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.02 0.023 -10000 0 -0.33 2 2
CaM/Ca2+/CAMK IV -0.1 0.17 -10000 0 -0.35 169 169
NFATc/ERK1 0.036 0.091 -10000 0 -0.41 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.15 0.19 -10000 0 -0.48 91 91
NR4A1 0.018 0.14 -10000 0 -0.47 34 34
GSK3B 0.013 0.027 -10000 0 -0.59 1 1
positive T cell selection 0.006 0.082 -10000 0 -0.4 17 17
NFAT1/CK1 alpha -0.02 0.05 -10000 0 -0.34 5 5
RCH1/ KPNB1 -0.001 0.021 -10000 0 -0.34 2 2
YWHAQ 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0.003 -10000 0 -10000 0 0
AKAP5 -0.033 0.15 -10000 0 -0.5 48 48
MEF2D 0.012 0.032 -10000 0 -0.5 2 2
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.034 0.091 -10000 0 -0.41 2 2
CREBBP 0.014 0.002 -10000 0 -10000 0 0
BCL2 0.005 0.075 -10000 0 -0.59 8 8
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.067 0.14 -10000 0 -0.35 99 99
cell-cell adhesion 0.035 0.099 0.47 14 -10000 0 14
Ephrin B/EPHB2/RasGAP -0.022 0.08 -10000 0 -0.54 5 5
ITSN1 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
SHC1 0.009 0.049 -10000 0 -0.49 5 5
Ephrin B1/EPHB3 -0.003 0.028 -10000 0 -0.29 5 5
Ephrin B1/EPHB1 -0.031 0.1 -10000 0 -0.37 44 44
HRAS/GDP -0.031 0.094 -10000 0 -0.47 12 12
Ephrin B/EPHB1/GRB7 -0.058 0.14 -10000 0 -0.4 51 51
Endophilin/SYNJ1 0.017 0.088 -10000 0 -0.34 19 19
KRAS 0.013 0.022 -10000 0 -0.49 1 1
Ephrin B/EPHB1/Src -0.039 0.11 -10000 0 -0.35 51 51
endothelial cell migration -0.006 0.039 -10000 0 -0.3 4 4
GRB2 0.013 0.022 -10000 0 -0.49 1 1
GRB7 -0.032 0.14 -10000 0 -0.49 43 43
PAK1 -0.007 0.13 -10000 0 -0.47 20 20
HRAS 0.014 0 -10000 0 -10000 0 0
RRAS 0.017 0.088 -10000 0 -0.34 18 18
DNM1 -0.1 0.22 -10000 0 -0.52 112 112
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.001 0.12 -10000 0 -0.54 11 11
lamellipodium assembly -0.035 0.099 -10000 0 -0.47 14 14
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.11 -10000 0 -0.5 12 12
PIK3R1 0.014 0 -10000 0 -10000 0 0
EPHB2 0 0.087 -10000 0 -0.52 14 14
EPHB3 0.012 0.031 -10000 0 -0.49 2 2
EPHB1 -0.035 0.17 -10000 0 -0.59 42 42
EPHB4 0.014 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.091 -10000 0 -0.43 15 15
Ephrin B/EPHB2 -0.022 0.082 -10000 0 -0.37 18 18
Ephrin B/EPHB3 -0.016 0.068 -10000 0 -0.33 14 14
JNK cascade 0.006 0.11 -10000 0 -0.32 45 45
Ephrin B/EPHB1 -0.04 0.12 -10000 0 -0.36 51 51
RAP1/GDP -0.026 0.078 -10000 0 -0.4 11 11
EFNB2 0.002 0.08 -10000 0 -0.52 12 12
EFNB3 -0.003 0.098 -10000 0 -0.56 15 15
EFNB1 0.011 0.038 -10000 0 -0.49 3 3
Ephrin B2/EPHB1-2 -0.04 0.12 -10000 0 -0.34 61 61
RAP1B 0.013 0.022 -10000 0 -0.49 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.037 0.11 -10000 0 -0.51 14 14
Rap1/GTP -0.035 0.1 -10000 0 -0.48 14 14
axon guidance -0.066 0.14 -10000 0 -0.35 99 99
MAPK3 0.022 0.1 -10000 0 -0.43 13 13
MAPK1 0.022 0.1 -10000 0 -0.43 13 13
Rac1/GDP 0.02 0.099 -10000 0 -0.42 11 11
actin cytoskeleton reorganization -0.027 0.076 -10000 0 -0.38 12 12
CDC42/GDP 0.02 0.099 -10000 0 -0.42 11 11
PI3K -0.006 0.039 -10000 0 -0.3 4 4
EFNA5 -0.085 0.22 -10000 0 -0.55 91 91
Ephrin B2/EPHB4 -0.007 0.047 -10000 0 -0.31 12 12
Ephrin B/EPHB2/Intersectin/N-WASP 0.023 0.07 -10000 0 -0.41 5 5
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.034 0.097 -10000 0 -0.46 14 14
PTK2 0.009 0.026 -10000 0 -10000 0 0
MAP4K4 0.006 0.11 -10000 0 -0.33 45 45
SRC 0.014 0 -10000 0 -10000 0 0
KALRN -0.003 0.092 -10000 0 -0.5 17 17
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.018 0.12 -10000 0 -0.42 9 9
MAP2K1 0.015 0.11 -10000 0 -0.46 13 13
WASL 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.035 0.11 -10000 0 -0.35 45 45
cell migration 0.017 0.12 -10000 0 -0.48 13 13
NRAS 0.014 0 -10000 0 -10000 0 0
SYNJ1 0.017 0.089 -10000 0 -0.35 19 19
PXN 0.014 0 -10000 0 -10000 0 0
TF -0.011 0.14 -10000 0 -0.55 15 15
HRAS/GTP -0.038 0.11 -10000 0 -0.51 14 14
Ephrin B1/EPHB1-2 -0.035 0.11 -10000 0 -0.34 54 54
cell adhesion mediated by integrin 0.01 0.067 0.28 24 -10000 0 24
RAC1 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.041 0.12 -10000 0 -0.55 14 14
RAC1-CDC42/GTP -0.035 0.1 -10000 0 -0.48 15 15
RASA1 0.014 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.026 0.077 -10000 0 -0.4 10 10
ruffle organization 0.023 0.12 -10000 0 -0.48 14 14
NCK1 0.013 0.027 -10000 0 -0.59 1 1
receptor internalization -0.033 0.14 -10000 0 -0.58 11 11
Ephrin B/EPHB2/KALRN -0.029 0.09 -10000 0 -0.53 6 6
ROCK1 0.025 0.027 -10000 0 -0.25 5 5
RAS family/GDP -0.025 0.072 -10000 0 -0.43 6 6
Rac1/GTP -0.037 0.11 -10000 0 -0.51 14 14
Ephrin B/EPHB1/Src/Paxillin 0.004 0.11 -10000 0 -0.3 51 51
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 0.019 0.066 -10000 0 -0.35 3 3
adherens junction organization -0.03 0.12 -10000 0 -0.35 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.12 -10000 0 -0.36 17 17
FMN1 -0.06 0.15 -10000 0 -0.36 59 59
mol:IP3 0.01 0.067 -10000 0 -0.4 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.015 0.11 -10000 0 -0.27 66 66
CTNNB1 0.016 0.004 -10000 0 -10000 0 0
AKT1 0.013 0.076 -10000 0 -0.38 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.03 0.15 -10000 0 -0.41 61 61
CTNND1 0.014 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.006 0.1 -10000 0 -0.5 3 3
VASP -0.007 0.1 -10000 0 -0.52 3 3
ZYX -0.011 0.11 -10000 0 -0.5 4 4
JUB -0.02 0.12 -10000 0 -0.36 23 23
EGFR(dimer) -0.055 0.15 -10000 0 -0.33 64 64
E-cadherin/beta catenin-gamma catenin -0.081 0.14 -10000 0 -0.32 132 132
mol:PI-3-4-5-P3 -0.03 0.061 -10000 0 -0.37 4 4
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
PI3K -0.03 0.062 -10000 0 -0.38 4 4
FYN 0.021 0.066 -10000 0 -0.32 2 2
mol:Ca2+ 0.01 0.066 -10000 0 -0.34 3 3
JUP 0.005 0.081 -10000 0 -0.57 10 10
PIK3R1 0.015 0.001 -10000 0 -10000 0 0
mol:DAG 0.01 0.067 -10000 0 -0.4 2 2
CDH1 -0.12 0.24 -10000 0 -0.54 125 125
RhoA/GDP -0.019 0.12 -10000 0 -0.36 17 17
establishment of polarity of embryonic epithelium -0.006 0.1 -10000 0 -0.5 3 3
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 0.21 -10000 0 -0.55 89 89
CASR 0.009 0.073 -10000 0 -0.31 5 5
RhoA/GTP -0.02 0.042 -10000 0 -0.35 2 2
AKT2 0.013 0.076 -10000 0 -0.38 3 3
actin cable formation -0.051 0.15 -10000 0 -0.48 25 25
apoptosis 0.026 0.054 0.34 4 -10000 0 4
CTNNA1 0.014 0.002 -10000 0 -10000 0 0
mol:GDP -0.029 0.12 -10000 0 -0.4 17 17
PIP5K1A -0.006 0.1 -10000 0 -0.52 3 3
PLCG1 0.01 0.068 -10000 0 -0.41 2 2
Rac1/GTP -0.076 0.12 -10000 0 -0.39 26 26
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 -0.001 0.095 -9999 0 -0.59 13 13
Caspase 8 (4 units) -0.011 0.082 -9999 0 -0.36 15 15
NEF -0.004 0.03 -9999 0 -10000 0 0
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 0 0.16 -9999 0 -0.54 43 43
CYCS 0.024 0.084 -9999 0 -0.32 12 12
RIPK1 0.014 0 -9999 0 -10000 0 0
CD247 -0.024 0.15 -9999 0 -0.6 31 31
MAP2K7 0.017 0.074 -9999 0 -0.32 2 2
protein ubiquitination 0.017 0.093 -9999 0 -0.4 7 7
CRADD 0.014 0 -9999 0 -10000 0 0
DAXX 0.014 0 -9999 0 -10000 0 0
FAS -0.005 0.1 -9999 0 -0.54 18 18
BID 0.016 0.087 -9999 0 -0.35 12 12
NF-kappa-B/RelA/I kappa B alpha -0.021 0.071 -9999 0 -10000 0 0
TRADD 0.013 0.027 -9999 0 -0.59 1 1
MAP3K5 0.006 0.07 -9999 0 -0.59 7 7
CFLAR 0.013 0.022 -9999 0 -0.49 1 1
FADD 0.014 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.071 -9999 0 -10000 0 0
MAPK8 0.017 0.085 -9999 0 -0.51 1 1
APAF1 0.014 0 -9999 0 -10000 0 0
TRAF1 0.004 0.078 -9999 0 -0.58 9 9
TRAF2 0.014 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.009 0.09 -9999 0 -0.36 14 14
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.11 -9999 0 -0.53 8 8
CHUK 0.016 0.099 -9999 0 -0.44 7 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.02 0.072 -9999 0 -0.47 2 2
TCRz/NEF -0.038 0.13 -9999 0 -0.42 46 46
TNF -0.15 0.26 -9999 0 -0.54 156 156
FASLG -0.026 0.17 -9999 0 -0.53 46 46
NFKB1 0.009 0.029 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.11 0.17 -9999 0 -0.34 171 171
CASP6 -0.019 0.067 -9999 0 -0.58 3 3
CASP7 0.032 0.16 -9999 0 -0.51 33 33
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.014 0 -9999 0 -10000 0 0
CASP3 0.032 0.16 -9999 0 -0.51 33 33
TNFRSF1A 0.001 0.085 -9999 0 -0.55 12 12
TNFR1A/BAG4 -0.02 0.093 -9999 0 -0.44 23 23
CASP8 -0.002 0.089 -9999 0 -0.5 16 16
CASP9 0.013 0.022 -9999 0 -0.49 1 1
MAP3K14 0.008 0.11 -9999 0 -0.48 8 8
APAF-1/Caspase 9 -0.038 0.11 -9999 0 -0.4 35 35
BCL2 0.019 0.089 -9999 0 -0.48 2 2
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.008 0.059 -9999 0 -0.59 5 5
CDC42/GTP -0.012 0.049 -9999 0 -0.39 3 3
PLCG1 0.03 0.061 -9999 0 -0.4 3 3
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 0.019 -9999 0 -0.43 1 1
cell migration -0.011 0.048 -9999 0 -0.38 3 3
S1PR5 -0.13 0.25 -9999 0 -0.55 134 134
S1PR4 0 0.086 -9999 0 -0.51 14 14
MAPK3 0.03 0.061 -9999 0 -0.4 3 3
MAPK1 0.03 0.061 -9999 0 -0.4 3 3
S1P/S1P5/Gi -0.034 0.13 -9999 0 -0.28 80 80
GNAI1 -0.005 0.1 -9999 0 -0.59 16 16
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.087 0.15 -9999 0 -0.34 134 134
RHOA 0.026 0.047 -9999 0 -0.3 4 4
S1P/S1P4/Gi 0.023 0.064 -9999 0 -0.31 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.014 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.008 0.046 -9999 0 -0.27 15 15
GNA12 0.013 0.027 -9999 0 -0.59 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.011 0.12 -10000 0 -0.42 19 19
CRKL 0.02 0.11 -10000 0 -0.43 19 19
HRAS 0.002 0.14 -10000 0 -0.49 13 13
mol:PIP3 0.003 0.1 -10000 0 -0.39 21 21
SPRED1 0.014 0 -10000 0 -10000 0 0
SPRED2 0.011 0.038 -10000 0 -0.49 3 3
GAB1 0.013 0.12 -10000 0 -0.45 20 20
FOXO3 0.025 0.1 -10000 0 -0.38 18 18
AKT1 0.017 0.11 -10000 0 -0.4 20 20
BAD 0.025 0.1 -10000 0 -0.38 18 18
megakaryocyte differentiation 0.006 0.12 -10000 0 -0.44 23 23
GSK3B 0.024 0.1 -10000 0 -0.39 18 18
RAF1 0.014 0.12 -10000 0 -0.38 13 13
SHC1 0.009 0.049 -10000 0 -0.49 5 5
STAT3 0.014 0.11 -10000 0 -0.44 20 20
STAT1 0.004 0.24 -10000 0 -1 22 22
HRAS/SPRED1 0.011 0.12 -10000 0 -0.38 13 13
cell proliferation 0.006 0.13 -10000 0 -0.46 24 24
PIK3CA 0.013 0.027 -10000 0 -0.6 1 1
TEC -0.004 0.1 -10000 0 -0.54 17 17
RPS6KB1 0.014 0.11 -10000 0 -0.43 20 20
HRAS/SPRED2 0.009 0.12 -10000 0 -0.38 15 15
LYN/TEC/p62DOK -0.038 0.11 -10000 0 -0.45 28 28
MAPK3 0.025 0.089 -10000 0 -0.3 5 5
STAP1 -0.004 0.13 -10000 0 -0.47 25 25
GRAP2 -0.048 0.17 -10000 0 -0.53 58 58
JAK2 -0.05 0.18 -10000 0 -0.84 20 20
STAT1 (dimer) 0.006 0.23 -10000 0 -0.98 22 22
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.056 0.13 -10000 0 -0.48 28 28
actin filament polymerization 0.006 0.12 -10000 0 -0.44 20 20
LYN 0.004 0.073 -10000 0 -0.51 10 10
STAP1/STAT5A (dimer) -0.004 0.18 -10000 0 -0.6 30 30
PIK3R1 0.014 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.029 0.1 -10000 0 -0.38 18 18
PI3K 0.022 0.11 -10000 0 -0.42 19 19
PTEN 0.013 0.027 -10000 0 -0.59 1 1
SCF/KIT/EPO/EPOR -0.004 0.28 -10000 0 -1.3 20 20
MAPK8 0.005 0.13 -10000 0 -0.47 24 24
STAT3 (dimer) 0.014 0.11 -10000 0 -0.43 20 20
positive regulation of transcription 0.026 0.077 -10000 0 -0.24 4 4
mol:GDP -0.062 0.12 0.22 2 -0.48 21 23
PIK3C2B 0.01 0.12 -10000 0 -0.43 22 22
CBL/CRKL 0.027 0.11 -10000 0 -0.4 18 18
FER 0.001 0.14 -10000 0 -0.51 24 24
SH2B3 0.013 0.11 -10000 0 -0.44 20 20
PDPK1 0.01 0.1 -10000 0 -0.39 19 19
SNAI2 -0.006 0.14 -10000 0 -0.46 27 27
positive regulation of cell proliferation 0.01 0.18 -10000 0 -0.72 24 24
KITLG 0.004 0.093 -10000 0 -0.6 12 12
cell motility 0.01 0.18 -10000 0 -0.72 24 24
PTPN6 -0.012 0.097 -10000 0 -0.55 16 16
EPOR 0.038 0.078 -10000 0 -10000 0 0
STAT5A (dimer) 0.008 0.16 -10000 0 -0.62 25 25
SOCS1 -0.031 0.15 -10000 0 -0.51 45 45
cell migration 0.04 0.16 0.46 34 -10000 0 34
SOS1 0.014 0 -10000 0 -10000 0 0
EPO -0.006 0.099 -10000 0 -0.5 20 20
VAV1 -0.019 0.14 -10000 0 -0.56 30 30
GRB10 0.012 0.12 -10000 0 -0.44 20 20
PTPN11 0.013 0.005 -10000 0 -10000 0 0
SCF/KIT 0.006 0.12 -10000 0 -0.46 20 20
GO:0007205 -0.002 0.006 -10000 0 -10000 0 0
MAP2K1 0.022 0.097 -10000 0 -0.33 5 5
CBL 0.014 0 -10000 0 -10000 0 0
KIT -0.009 0.27 -10000 0 -1.3 20 20
MAP2K2 0.022 0.097 -10000 0 -0.33 5 5
SHC/Grb2/SOS1 -0.028 0.092 -10000 0 -0.42 18 18
STAT5A 0.007 0.17 -10000 0 -0.64 25 25
GRB2 0.013 0.022 -10000 0 -0.49 1 1
response to radiation -0.006 0.13 -10000 0 -0.45 27 27
SHC/GRAP2 -0.046 0.13 -10000 0 -0.39 61 61
PTPRO 0.005 0.13 -10000 0 -0.45 23 23
SH2B2 0.006 0.12 -10000 0 -0.45 20 20
DOK1 0.012 0.035 -10000 0 -0.54 2 2
MATK -0.041 0.16 -10000 0 -0.48 34 34
CREBBP 0.039 0.012 -10000 0 -10000 0 0
BCL2 0.022 0.18 -10000 0 -1.3 8 8
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.012 0.12 -10000 0 -0.54 25 25
positive regulation of NF-kappaB transcription factor activity -0.029 0.099 -10000 0 -0.37 40 40
MAP2K4 0.03 0.063 -10000 0 -0.35 3 3
IKBKB 0.014 0 -10000 0 -10000 0 0
TNFRSF10B 0.01 0.051 -10000 0 -0.57 4 4
TNFRSF10A -0.026 0.15 -10000 0 -0.56 36 36
SMPD1 0.011 0.047 -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 -0.001 0.087 -10000 0 -0.5 15 15
TRAIL/TRAILR2 -0.021 0.092 -10000 0 -0.4 28 28
TRAIL/TRAILR3 -0.041 0.13 -10000 0 -0.41 52 52
TRAIL/TRAILR1 -0.046 0.13 -10000 0 -0.41 58 58
TRAIL/TRAILR4 -0.029 0.1 -10000 0 -0.37 40 40
TRAIL/TRAILR1/DAP3/GTP -0.035 0.1 -10000 0 -0.31 58 58
IKK complex -0.01 0.029 -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 0.005 0.087 -10000 0 -0.38 25 25
MAP3K1 0.024 0.063 -10000 0 -0.34 2 2
TRAILR4 (trimer) -0.001 0.087 -10000 0 -0.5 15 15
TRADD 0.013 0.027 -10000 0 -0.59 1 1
TRAILR1 (trimer) -0.026 0.15 -10000 0 -0.56 36 36
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.013 0.081 -10000 0 -0.28 3 3
CFLAR 0.013 0.022 -10000 0 -0.49 1 1
MAPK1 0.005 0.087 -10000 0 -0.38 25 25
TRAIL/TRAILR1/FADD/TRADD/RIP -0.032 0.09 -10000 0 -0.47 3 3
mol:ceramide 0.011 0.047 -10000 0 -0.23 13 13
FADD 0.014 0 -10000 0 -10000 0 0
MAPK8 0.029 0.082 -10000 0 -0.36 8 8
TRAF2 0.014 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.02 0.13 -10000 0 -0.53 32 32
CHUK 0.014 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.038 0.11 -10000 0 -0.34 58 58
DAP3 0.014 0 -10000 0 -10000 0 0
CASP10 -0.021 0.086 0.27 1 -0.38 14 15
JNK cascade -0.029 0.099 -10000 0 -0.37 40 40
TRAIL (trimer) -0.012 0.12 -10000 0 -0.53 25 25
TNFRSF10C -0.02 0.13 -10000 0 -0.53 32 32
TRAIL/TRAILR1/DAP3/GTP/FADD -0.032 0.092 -10000 0 -0.31 38 38
TRAIL/TRAILR2/FADD -0.018 0.077 -10000 0 -0.33 28 28
cell death 0.011 0.047 -10000 0 -0.23 13 13
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.028 0.057 -10000 0 -0.52 1 1
TRAILR2 (trimer) 0.01 0.051 -10000 0 -0.57 4 4
CASP8 -0.003 0.049 -10000 0 -0.8 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.015 0.063 -10000 0 -0.6 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.007 0.091 -9999 0 -0.32 37 37
SNTA1 -0.026 0.15 -9999 0 -0.57 36 36
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.006 0.094 -9999 0 -0.32 39 39
MAPK12 0.027 0.044 -9999 0 -0.33 6 6
CCND1 0.008 0.069 -9999 0 -0.42 11 11
p38 gamma/SNTA1 0.011 0.09 -9999 0 -0.3 34 34
MAP2K3 0.011 0.038 -9999 0 -0.49 3 3
PKN1 0.014 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.026 0.044 -9999 0 -0.33 6 6
MAP2K6 0.022 0.031 -9999 0 -0.32 2 2
MAPT 0.011 0.084 -9999 0 -0.31 25 25
MAPK13 -0.004 0.11 -9999 0 -0.38 37 37
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0.031 -9999 0 -0.22 9 9
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 60 60
RAD9A 0.014 0 -9999 0 -10000 0 0
AP1 -0.068 0.18 -9999 0 -0.42 102 102
IFNAR2 0.013 0.006 -9999 0 -10000 0 0
AKT1 0.001 0.049 -9999 0 -0.28 2 2
ER alpha/Oestrogen -0.011 0.089 -9999 0 -0.4 26 26
NFX1/SIN3/HDAC complex 0.04 0.032 -9999 0 -10000 0 0
EGF -0.051 0.18 -9999 0 -0.56 58 58
SMG5 0.013 0.022 -9999 0 -0.49 1 1
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 59 59
SAP18 0.013 0.004 -9999 0 -10000 0 0
MRN complex -0.001 0.016 -9999 0 -0.36 1 1
WT1 -0.038 0.14 -9999 0 -0.49 45 45
WRN 0.009 0.053 -9999 0 -0.59 4 4
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 -0.9 58 58
Mad/Max 0.019 0.009 -9999 0 -10000 0 0
TERT -0.14 0.4 -9999 0 -1.2 59 59
CCND1 -0.12 0.36 -9999 0 -1 66 66
MAX 0.012 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.004 -9999 0 -10000 0 0
RBBP4 0.012 0.027 -9999 0 -0.6 1 1
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 0.032 0.039 -9999 0 -10000 0 0
CDKN1B 0.012 0.076 -9999 0 -0.53 2 2
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 0.027 -9999 0 -0.59 1 1
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.012 0.005 -9999 0 -10000 0 0
JUN 0.002 0.074 -9999 0 -0.5 11 11
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.007 -9999 0 -10000 0 0
FOS -0.097 0.22 -9999 0 -0.55 101 101
IFN-gamma/IRF1 -0.011 0.087 -9999 0 -0.35 30 30
PARP2 0.014 0 -9999 0 -10000 0 0
BLM -0.051 0.18 -9999 0 -0.53 62 62
Telomerase -0.037 0.1 -9999 0 -0.4 29 29
IRF1 -0.009 0.11 -9999 0 -0.48 27 27
ESR1 -0.015 0.12 -9999 0 -0.54 26 26
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0.022 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.033 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.045 0.034 -9999 0 -10000 0 0
HDAC1 0.008 0.053 -9999 0 -0.59 4 4
HDAC2 0.012 0.009 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.019 0.059 -9999 0 -0.42 9 9
ABL1 0.014 0 -9999 0 -10000 0 0
MXD1 0.012 0.006 -9999 0 -10000 0 0
MRE11A 0.014 0 -9999 0 -10000 0 0
HUS1 0.013 0.022 -9999 0 -0.49 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 58 58
NR2F2 -0.009 0.12 -9999 0 -0.51 25 25
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 0.079 -9999 0 -0.59 9 9
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 0.21 -9999 0 -0.55 89 89
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.097 0.2 -9999 0 -0.44 132 132
MYC -0.017 0.13 -9999 0 -0.58 26 26
IL2 -0.003 0.014 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0.027 -9999 0 -0.59 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
TGFB1 0.004 0.079 -9999 0 -0.59 9 9
TRF2/BLM -0.042 0.11 -9999 0 -0.35 62 62
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.35 -9999 0 -1 59 59
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 -0.9 58 58
Smad3/Myc 0.005 0.098 -9999 0 -0.36 34 34
911 complex -0.001 0.012 -9999 0 -0.28 1 1
IFNG 0.003 0.049 -9999 0 -0.49 5 5
Telomerase/PinX1 -0.13 0.29 -9999 0 -0.9 58 58
Telomerase/AKT1/mTOR/p70S6K 0.009 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 58 58
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.001 0.012 -9999 0 -10000 0 0
TRF2/WRN -0.003 0.035 -9999 0 -0.4 4 4
Telomerase/hnRNP C1/C2 -0.13 0.29 -9999 0 -0.9 58 58
E2F1 -0.016 0.12 -9999 0 -0.52 28 28
ZNFX1 0.013 0.004 -9999 0 -10000 0 0
PIF1 -0.052 0.18 -9999 0 -0.54 62 62
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
BARD1 signaling events

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
BARD1/CSTF1 -0.025 0.1 -10000 0 -0.42 31 31
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 0.015 0.057 -10000 0 -0.34 6 6
protein ubiquitination -0.026 0.093 -10000 0 -0.58 5 5
XRCC5 0.014 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
M/R/N Complex -0.001 0.016 -10000 0 -0.36 1 1
MRE11A 0.014 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.013 0.054 -10000 0 -0.39 6 6
FANCF 0.014 0 -10000 0 -10000 0 0
BRCA1 0.01 0.044 -10000 0 -0.49 4 4
CCNE1 0.011 0.038 -10000 0 -0.49 3 3
CDK2/Cyclin E1 -0.011 0.067 -10000 0 -0.39 15 15
FANCG 0.013 0.022 -10000 0 -0.49 1 1
BRCA1/BACH1/BARD1 -0.028 0.11 -10000 0 -0.42 34 34
FANCE 0.014 0 -10000 0 -10000 0 0
FANCC 0.011 0.041 -10000 0 -0.52 3 3
NBN 0.014 0 -10000 0 -10000 0 0
FANCA -0.027 0.14 -10000 0 -0.51 40 40
DNA repair 0.017 0.15 -10000 0 -0.51 16 16
BRCA1/BARD1/ubiquitin -0.028 0.11 -10000 0 -0.42 34 34
BARD1/DNA-PK -0.019 0.074 -10000 0 -0.32 29 29
FANCL 0.014 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.025 0.1 0.42 31 -10000 0 31
BRCA1/BARD1/CTIP/M/R/N Complex 0.025 0.075 -10000 0 -0.47 3 3
BRCA1/BACH1/BARD1/TopBP1 -0.024 0.092 -10000 0 -0.36 34 34
BRCA1/BARD1/P53 -0.03 0.097 -10000 0 -0.34 42 42
BARD1/CSTF1/BRCA1 -0.023 0.089 -10000 0 -0.35 34 34
BRCA1/BACH1 0.01 0.044 -10000 0 -0.49 4 4
BARD1 -0.022 0.14 -10000 0 -0.59 31 31
PCNA 0.012 0.031 -10000 0 -0.49 2 2
BRCA1/BARD1/UbcH5C -0.023 0.089 -10000 0 -0.35 34 34
BRCA1/BARD1/UbcH7 -0.023 0.089 -10000 0 -0.36 30 30
BRCA1/BARD1/RAD51/PCNA -0.053 0.12 -10000 0 -0.38 45 45
BARD1/DNA-PK/P53 -0.026 0.086 -10000 0 -0.31 41 41
BRCA1/BARD1/Ubiquitin -0.028 0.11 -10000 0 -0.42 34 34
BRCA1/BARD1/CTIP 0.012 0.094 -10000 0 -0.34 30 30
FA complex 0.028 0.057 -10000 0 -10000 0 0
BARD1/EWS -0.025 0.1 -10000 0 -0.42 31 31
RBBP8 0.023 0.028 -10000 0 -0.34 3 3
TP53 -0.003 0.1 -10000 0 -0.59 15 15
TOPBP1 0.013 0.027 -10000 0 -0.59 1 1
G1/S transition of mitotic cell cycle 0.03 0.096 0.34 42 -10000 0 42
BRCA1/BARD1 -0.027 0.094 -10000 0 -0.59 5 5
CSTF1 0.014 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.026 0.1 -10000 0 -0.43 31 31
CDK2 0 0.086 -10000 0 -0.53 13 13
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.048 0.17 -10000 0 -0.51 61 61
RAD50 0.013 0.027 -10000 0 -0.59 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.028 0.11 -10000 0 -0.42 34 34
EWSR1 0.014 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.034 0.093 0.18 2 -0.4 17 19
CaM/Ca2+ -0.002 0.025 -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 0.027 -10000 0 -0.59 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.027 0.14 0.25 60 -0.46 16 76
YWHAZ 0.014 0 -10000 0 -10000 0 0
CALM1 0.012 0.035 -10000 0 -0.54 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 -0.49 25 25
YWHAB 0.014 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.016 -10000 0 -0.36 1 1
YWHAG 0.002 0.079 -10000 0 -0.49 13 13
ASIP -0.096 0.22 -10000 0 -0.55 99 99
PRKCI 0.014 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ -0.002 0.025 -10000 0 -0.4 2 2
RHOQ 0.014 0 -10000 0 -10000 0 0
GYS1 0.034 0.014 -10000 0 -0.29 1 1
PRKCZ -0.015 0.13 -10000 0 -0.55 27 27
TRIP10 0.007 0.065 -10000 0 -0.55 7 7
TC10/GTP/CIP4/Exocyst -0.005 0.039 -10000 0 -0.33 7 7
AS160/14-3-3 0.003 0.087 -10000 0 -0.37 3 3
VAMP2 0.014 0 -10000 0 -10000 0 0
SLC2A4 0.025 0.15 0.28 34 -0.52 16 50
STX4 0.014 0 -10000 0 -10000 0 0
GSK3B 0.028 0.016 -10000 0 -0.34 1 1
SFN -0.11 0.23 -10000 0 -0.53 119 119
LNPEP -0.012 0.12 -10000 0 -0.59 22 22
YWHAE 0.014 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
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 0.027 -9999 0 -0.59 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.012 0.031 -9999 0 -0.49 2 2
RAC1-CDC42/GTP/PAK family -0.032 0.1 -9999 0 -0.22 106 106
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.009 0.053 -9999 0 -0.59 4 4
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 0.038 -9999 0 -0.49 3 3
p38 alpha/TAB1 -0.025 0.057 -9999 0 -0.31 9 9
PRKG1 -0.039 0.17 -9999 0 -0.58 46 46
DUSP8 0.001 0.083 -9999 0 -0.53 12 12
PGK/cGMP/p38 alpha -0.044 0.09 -9999 0 -0.28 48 48
apoptosis -0.024 0.055 -9999 0 -0.31 8 8
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.004 0.073 -9999 0 -0.51 10 10
DUSP1 -0.02 0.13 -9999 0 -0.53 32 32
PAK1 -0.035 0.15 -9999 0 -0.5 49 49
SRC 0.014 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.002 0.021 -9999 0 -10000 0 0
TRAF6 0.013 0.027 -9999 0 -0.59 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 0.013 0.022 -9999 0 -0.49 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.004 0.1 -9999 0 -0.38 12 12
BLK -0.1 0.22 -9999 0 -0.52 113 113
HCK -0.007 0.11 -9999 0 -0.54 20 20
MAP2K3 0.011 0.038 -9999 0 -0.49 3 3
DUSP16 0.014 0 -9999 0 -10000 0 0
DUSP10 -0.004 0.1 -9999 0 -0.55 17 17
TRAF6/MEKK3 -0.001 0.015 -9999 0 -0.33 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.008 0.081 -9999 0 -0.34 8 8
positive regulation of innate immune response 0.001 0.11 -9999 0 -0.42 11 11
LCK -0.081 0.21 -9999 0 -0.54 89 89
p38alpha-beta/MKP7 0.008 0.1 -9999 0 -0.43 8 8
p38alpha-beta/MKP5 0 0.11 -9999 0 -0.43 12 12
PGK/cGMP -0.038 0.12 -9999 0 -0.42 46 46
PAK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.007 0.12 -9999 0 -0.42 13 13
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 -0.56 115 115
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.025 0.082 -10000 0 -0.31 31 31
ER alpha/Gai/GDP/Gbeta gamma 0.026 0.088 -10000 0 -0.38 16 16
AKT1 0.017 0.12 -10000 0 -0.72 13 13
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.015 0.12 -10000 0 -0.73 13 13
mol:Ca2+ -0.008 0.14 -10000 0 -0.49 25 25
IGF1R 0.013 0.022 -10000 0 -0.49 1 1
E2/ER alpha (dimer)/Striatin -0.035 0.11 -10000 0 -0.35 51 51
SHC1 0.009 0.049 -10000 0 -0.49 5 5
apoptosis -0.017 0.12 0.69 13 -10000 0 13
RhoA/GTP -0.011 0.049 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.02 0.074 -10000 0 -0.38 17 17
regulation of stress fiber formation -0.015 0.099 0.4 9 -10000 0 9
E2/ERA-ERB (dimer) -0.028 0.097 -10000 0 -0.35 42 42
KRAS 0.013 0.022 -10000 0 -0.49 1 1
G13/GTP -0.015 0.065 -10000 0 -0.29 26 26
pseudopodium formation 0.015 0.099 -10000 0 -0.4 9 9
E2/ER alpha (dimer)/PELP1 -0.016 0.071 -10000 0 -0.32 26 26
GRB2 0.013 0.022 -10000 0 -0.49 1 1
GNG2 0.009 0.053 -10000 0 -0.59 4 4
GNAO1 0.008 0.059 -10000 0 -0.59 5 5
HRAS 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.027 0.096 -10000 0 -0.45 12 12
E2/ER beta (dimer) -0.014 0.076 -10000 0 -0.41 18 18
mol:GDP -0.024 0.083 -10000 0 -0.35 27 27
mol:NADP 0.027 0.096 -10000 0 -0.45 12 12
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.01 0.14 -10000 0 -0.52 25 25
IGF-1R heterotetramer 0.013 0.022 -10000 0 -0.49 1 1
PLCB1 -0.007 0.13 -10000 0 -0.49 21 21
PLCB2 -0.007 0.14 -10000 0 -0.53 23 23
IGF1 -0.008 0.11 -10000 0 -0.56 20 20
mol:L-citrulline 0.027 0.096 -10000 0 -0.45 12 12
RHOA 0.014 0 -10000 0 -10000 0 0
Gai/GDP -0.013 0.077 -10000 0 -0.7 5 5
JNK cascade -0.014 0.076 -10000 0 -0.41 18 18
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
ESR2 -0.006 0.11 -10000 0 -0.56 18 18
GNAQ 0.014 0 -10000 0 -10000 0 0
ESR1 -0.014 0.12 -10000 0 -0.54 26 26
Gq family/GDP/Gbeta gamma 0.01 0.12 -10000 0 -0.45 24 24
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.032 0.054 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.021 0.078 -10000 0 -0.41 17 17
GNAZ 0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.02 0.086 -10000 0 -0.39 26 26
STRN -0.016 0.13 -10000 0 -0.59 26 26
GNAL -0.058 0.2 -10000 0 -0.59 62 62
PELP1 0.014 0 -10000 0 -10000 0 0
MAPK11 0.001 0.083 -10000 0 -0.35 27 27
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.1 -10000 0 -0.59 16 16
HBEGF -0.004 0.12 -10000 0 -0.48 8 8
cAMP biosynthetic process -0.057 0.12 -10000 0 -0.3 97 97
SRC 0.033 0.084 -10000 0 -0.35 16 16
PI3K -0.001 0.019 -10000 0 -0.43 1 1
GNB1 0.014 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.022 0.074 -10000 0 -0.34 14 14
SOS1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.024 0.074 -10000 0 -0.34 17 17
Gs family/GTP -0.058 0.12 -10000 0 -0.31 97 97
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0.011 -10000 0 -10000 0 0
vasodilation 0.027 0.093 -10000 0 -0.43 12 12
mol:DAG -0.01 0.14 -10000 0 -0.52 25 25
Gs family/GDP/Gbeta gamma -0.047 0.1 -10000 0 -0.38 21 21
MSN 0.014 0.1 -10000 0 -0.43 9 9
Gq family/GTP -0.005 0.12 -10000 0 -0.5 19 19
mol:PI-3-4-5-P3 0.016 0.12 -10000 0 -0.7 13 13
NRAS 0.014 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.027 0.093 0.43 12 -10000 0 12
GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
RhoA/GDP -0.022 0.077 -10000 0 -0.33 27 27
NOS3 0.026 0.099 -10000 0 -0.47 12 12
GNA11 0.004 0.079 -10000 0 -0.59 9 9
MAPKKK cascade 0.023 0.13 -10000 0 -0.41 36 36
E2/ER alpha (dimer)/PELP1/Src -0.021 0.076 -10000 0 -0.41 16 16
ruffle organization 0.015 0.099 -10000 0 -0.4 9 9
ROCK2 0.027 0.083 -10000 0 -0.51 2 2
GNA14 -0.014 0.12 -10000 0 -0.56 25 25
GNA15 -0.007 0.11 -10000 0 -0.57 19 19
GNA13 0.014 0 -10000 0 -10000 0 0
MMP9 -0.032 0.14 -10000 0 -0.44 16 16
MMP2 0.027 0.1 -10000 0 -0.48 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.099 0.23 -9999 0 -0.55 103 103
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 0.021 0.056 -9999 0 -0.27 14 14
HIF1A 0.023 0.025 -9999 0 -0.24 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 -0.1 0.23 -9999 0 -0.56 104 104
ARNT/IPAS -0.08 0.16 -9999 0 -0.4 104 104
HIF1AN 0.014 0 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.03 0.028 -9999 0 -0.3 1 1
CUL2 0.014 0 -9999 0 -10000 0 0
OS9 0.003 0.073 -9999 0 -0.49 11 11
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.03 0.024 -9999 0 -10000 0 0
PHD1-3/OS9 -0.013 0.06 -9999 0 -0.32 13 13
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.014 -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 0.03 0.024 -9999 0 -10000 0 0
EGLN3 -0.001 0.095 -9999 0 -0.59 13 13
EGLN2 0.014 0 -9999 0 -10000 0 0
EGLN1 0.014 0 -9999 0 -10000 0 0
TP53 -0.003 0.1 -9999 0 -0.59 15 15
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.041 0.006 -9999 0 -10000 0 0
ARNT 0.013 0.022 -9999 0 -0.49 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.014 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.028 0.12 -9999 0 -0.28 84 84
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.017 0.13 -10000 0 -0.5 17 17
BAG4 -0.001 0.095 -10000 0 -0.59 13 13
BAD 0.008 0.045 -10000 0 -0.19 2 2
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.033 0.16 -10000 0 -0.55 43 43
BAX 0.008 0.045 -10000 0 -0.19 2 2
EnzymeConsortium:3.1.4.12 -0.003 0.033 -10000 0 -0.1 17 17
IKBKB -0.007 0.12 -10000 0 -0.46 17 17
MAP2K2 0.018 0.049 -10000 0 -10000 0 0
MAP2K1 0.017 0.052 -10000 0 -0.3 2 2
SMPD1 0.003 0.033 -10000 0 -0.14 2 2
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.46 18 18
MAP2K4 0.011 0.055 -10000 0 -0.28 3 3
protein ubiquitination -0.006 0.12 -10000 0 -0.46 17 17
EnzymeConsortium:2.7.1.37 0.019 0.057 -10000 0 -0.29 1 1
response to UV 0 0.001 -10000 0 -0.002 4 4
RAF1 0.013 0.049 -10000 0 -0.2 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0 0.047 -10000 0 -0.16 12 12
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.005 0.053 -10000 0 -0.22 9 9
TRADD 0.013 0.027 -10000 0 -0.59 1 1
RELA/p50 0.014 0 -10000 0 -10000 0 0
MAPK3 0.02 0.05 -10000 0 -10000 0 0
MAPK1 0.02 0.05 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD -0.016 0.13 -10000 0 -0.5 17 17
KSR1 0.007 0.047 -10000 0 -0.2 2 2
MAPK8 0.01 0.069 -10000 0 -0.26 17 17
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 -0.46 17 17
TNF R/SODD -0.018 0.094 -10000 0 -0.44 23 23
TNF -0.15 0.26 -10000 0 -0.54 156 156
CYCS 0.011 0.044 0.14 4 -0.19 2 6
IKBKG -0.007 0.12 -10000 0 -0.46 17 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.025 0.13 -10000 0 -0.53 17 17
RELA 0.014 0 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AIFM1 0.011 0.044 0.14 4 -0.19 2 6
TNF/TNF R/SODD -0.11 0.17 -10000 0 -0.34 171 171
TNFRSF1A 0.001 0.085 -10000 0 -0.55 12 12
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.051 -10000 0 -0.72 1 1
NSMAF -0.016 0.12 -10000 0 -0.49 17 17
response to hydrogen peroxide 0 0.001 -10000 0 -0.002 4 4
BCL2 0.005 0.075 -10000 0 -0.59 8 8
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 0.021 0.04 -9999 0 -0.43 4 4
SMARCC1 0.009 0.013 -9999 0 -10000 0 0
REL -0.017 0.13 -9999 0 -0.56 29 29
HDAC7 0.021 0.1 -9999 0 -0.52 2 2
JUN 0.002 0.074 -9999 0 -0.5 11 11
EP300 0.009 0.053 -9999 0 -0.59 4 4
KAT2B 0.013 0.022 -9999 0 -0.49 1 1
KAT5 0.014 0 -9999 0 -10000 0 0
MAPK14 0.023 0.023 -9999 0 -0.42 1 1
FOXO1 0.011 0.044 -9999 0 -0.56 3 3
T-DHT/AR 0.017 0.11 -9999 0 -0.43 7 7
MAP2K6 0.012 0.027 -9999 0 -0.59 1 1
BRM/BAF57 0.004 0.021 -9999 0 -0.43 1 1
MAP2K4 0.012 0.032 -9999 0 -0.5 2 2
SMARCA2 0.012 0.027 -9999 0 -0.59 1 1
PDE9A -0.022 0.1 -9999 0 -0.81 5 5
NCOA2 -0.028 0.15 -9999 0 -0.59 35 35
CEBPA -0.016 0.13 -9999 0 -0.56 27 27
EHMT2 0.013 0.004 -9999 0 -10000 0 0
cell proliferation 0.031 0.12 -9999 0 -0.44 11 11
NR0B1 -0.099 0.23 -9999 0 -0.55 103 103
EGR1 -0.11 0.23 -9999 0 -0.54 114 114
RXRs/9cRA -0.035 0.11 -9999 0 -0.32 65 65
AR/RACK1/Src -0.011 0.079 -9999 0 -0.39 9 9
AR/GR -0.015 0.12 -9999 0 -0.4 16 16
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 0.01 0.078 -9999 0 -0.42 16 16
T-DHT/AR/TIF2/CARM1 -0.002 0.14 -9999 0 -0.65 13 13
SRC 0.028 0.064 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
KLK3 -0.045 0.14 -9999 0 -0.51 9 9
APPBP2 0.014 0.005 -9999 0 -10000 0 0
TRIM24 0.012 0.022 -9999 0 -0.49 1 1
T-DHT/AR/TIP60 0.012 0.086 -9999 0 -0.44 7 7
TMPRSS2 -0.13 0.32 -9999 0 -1.1 45 45
RXRG -0.061 0.2 -9999 0 -0.58 65 65
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 0.002 0.084 -9999 0 -0.59 10 10
KLK2 -0.008 0.15 -9999 0 -0.47 24 24
AR -0.023 0.13 -9999 0 -0.42 20 20
SENP1 0.014 0.001 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
MDM2 0.013 0.032 -9999 0 -0.49 2 2
SRY -0.021 0.11 -9999 0 -0.49 27 27
GATA2 -0.004 0.1 -9999 0 -0.56 16 16
MYST2 0.014 0.001 -9999 0 -10000 0 0
HOXB13 -0.053 0.16 -9999 0 -0.5 60 60
T-DHT/AR/RACK1/Src 0.018 0.086 -9999 0 -0.42 7 7
positive regulation of transcription -0.004 0.1 -9999 0 -0.56 16 16
DNAJA1 0.014 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.026 -9999 0 -0.24 4 4
NCOA1 0.017 0.005 -9999 0 -10000 0 0
SPDEF -0.044 0.17 -9999 0 -0.54 53 53
T-DHT/AR/TIF2 0.015 0.12 -9999 0 -0.58 13 13
T-DHT/AR/Hsp90 0.012 0.086 -9999 0 -0.44 7 7
GSK3B 0.013 0.027 -9999 0 -0.59 1 1
NR2C1 0.014 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.023 0.068 -9999 0 -0.32 16 16
SIRT1 0.014 0 -9999 0 -10000 0 0
ZMIZ2 0.015 0.005 -9999 0 -10000 0 0
POU2F1 0.024 0.031 -9999 0 -0.59 1 1
T-DHT/AR/DAX-1 -0.049 0.15 -9999 0 -0.42 34 34
CREBBP 0.014 0 -9999 0 -10000 0 0
SMARCE1 0.013 0.003 -9999 0 -10000 0 0
p38 MAPK 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
TRAF6/ASK1 0.01 0.04 -10000 0 -0.31 8 8
TRAF2/ASK1 -0.005 0.042 -10000 0 -0.37 7 7
ATM 0.014 0 -10000 0 -10000 0 0
MAP2K3 0.02 0.054 -10000 0 -0.3 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.019 0.071 -10000 0 -0.41 7 7
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.031 0.15 -10000 0 -0.54 42 42
TXN 0.009 0.01 -10000 0 -0.21 1 1
CALM1 0.012 0.035 -10000 0 -0.54 2 2
GADD45A -0.018 0.12 -10000 0 -0.49 33 33
GADD45B -0.026 0.14 -10000 0 -0.52 39 39
MAP3K1 0.007 0.058 -10000 0 -0.49 7 7
MAP3K6 0.007 0.058 -10000 0 -0.49 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 -0.01 0.063 -10000 0 -0.38 14 14
TAK1/TAB family 0.003 0.025 0.18 9 -0.17 1 10
RAC1/OSM/MEKK3 0 0.011 -10000 0 -0.25 1 1
TRAF2 0.014 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.008 0.027 -10000 0 -10000 0 0
TRAF6 0.009 0.016 -10000 0 -0.36 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.072 0.2 -10000 0 -0.54 80 80
CCM2 0.013 0.022 -10000 0 -0.49 1 1
CaM/Ca2+/CAMKIIB -0.052 0.12 -10000 0 -0.34 80 80
MAPK11 0.004 0.079 -10000 0 -0.59 9 9
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.05 0.12 -10000 0 -0.31 83 83
OSM/MEKK3 -0.001 0.015 -10000 0 -0.34 1 1
TAOK1 -0.015 0.11 -10000 0 -0.35 47 47
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 0.006 0.07 -10000 0 -0.59 7 7
MAP3K10 0.005 0.066 -10000 0 -0.49 9 9
MAP3K3 0.014 0 -10000 0 -10000 0 0
TRX/ASK1 0.012 0.047 -10000 0 -0.38 7 7
GADD45/MTK1/MTK1 -0.056 0.13 -10000 0 -0.38 50 50
EPO signaling 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
BCL2L1 0.06 0.098 -9999 0 -0.65 4 4
CRKL 0.035 0.073 -9999 0 -0.46 4 4
mol:DAG 0.04 0.078 -9999 0 -0.41 8 8
HRAS 0.057 0.074 -9999 0 -0.61 2 2
MAPK8 0.014 0.098 -9999 0 -0.37 23 23
RAP1A 0.035 0.073 -9999 0 -0.46 4 4
GAB1 0.034 0.079 -9999 0 -0.53 4 4
MAPK14 0.024 0.073 -9999 0 -0.4 5 5
EPO -0.004 0.099 -9999 0 -0.5 20 20
PLCG1 0.04 0.08 -9999 0 -0.42 8 8
EPOR/TRPC2/IP3 Receptors 0.015 0.024 -9999 0 -0.51 1 1
RAPGEF1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.062 0.16 -9999 0 -0.33 136 136
GAB1/SHC/GRB2/SOS1 -0.015 0.062 -9999 0 -0.47 5 5
EPO/EPOR (dimer) 0.01 0.076 -9999 0 -0.36 20 20
IRS2 0.034 0.079 -9999 0 -0.53 4 4
STAT1 0.043 0.097 -9999 0 -0.5 8 8
STAT5B 0.045 0.083 -9999 0 -0.56 4 4
cell proliferation 0.022 0.092 -9999 0 -0.44 9 9
GAB1/SHIP/PIK3R1/SHP2/SHC -0.016 0.067 -9999 0 -0.47 6 6
TEC 0.026 0.094 -9999 0 -0.44 10 10
SOCS3 -0.11 0.23 -9999 0 -0.52 124 124
STAT1 (dimer) 0.043 0.095 -9999 0 -0.48 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 0.042 0.08 -9999 0 -0.49 4 4
EPO/EPOR 0.01 0.076 -9999 0 -0.36 20 20
LYN 0.006 0.073 -9999 0 -0.51 10 10
TEC/VAV2 0.035 0.092 -9999 0 -0.42 10 10
elevation of cytosolic calcium ion concentration 0.015 0.024 -9999 0 -0.51 1 1
SHC1 0.009 0.049 -9999 0 -0.49 5 5
EPO/EPOR (dimer)/LYN 0.022 0.083 -9999 0 -0.36 14 14
mol:IP3 0.04 0.078 -9999 0 -0.41 8 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.084 -9999 0 -0.44 9 9
SH2B3 0.013 0.032 -9999 0 -0.48 2 2
NFKB1 0.024 0.073 -9999 0 -0.37 7 7
EPO/EPOR (dimer)/JAK2/SOCS3 -0.039 0.075 -9999 0 -0.28 10 10
PTPN6 0.028 0.076 -9999 0 -0.49 4 4
TEC/VAV2/GRB2 0.04 0.09 -9999 0 -0.41 9 9
EPOR 0.015 0.024 -9999 0 -0.52 1 1
INPP5D 0.008 0.06 -9999 0 -0.54 6 6
mol:GDP -0.015 0.063 -9999 0 -0.48 5 5
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG2 0 0.088 -9999 0 -0.55 13 13
CRKL/CBL/C3G 0.049 0.07 -9999 0 -0.42 4 4
VAV2 0.035 0.073 -9999 0 -0.46 4 4
CBL 0.035 0.073 -9999 0 -0.46 4 4
SHC/Grb2/SOS1 -0.015 0.061 -9999 0 -0.45 5 5
STAT5A 0.037 0.11 -9999 0 -0.59 10 10
GRB2 0.013 0.022 -9999 0 -0.49 1 1
STAT5 (dimer) 0.056 0.12 -9999 0 -0.57 10 10
LYN/PLCgamma2 0.005 0.093 -9999 0 -0.47 18 18
PTPN11 0.014 0 -9999 0 -10000 0 0
BTK 0.023 0.11 -9999 0 -0.49 15 15
BCL2 0.052 0.15 -9999 0 -0.92 9 9
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.038 -9999 0 -0.49 3 3
alphaV beta3 Integrin -0.046 0.12 -9999 0 -0.36 66 66
PTK2 -0.03 0.099 -9999 0 -0.48 19 19
positive regulation of JNK cascade -0.009 0.045 -9999 0 -0.31 10 10
CDC42/GDP 0.046 0.073 -9999 0 -0.41 10 10
Rac1/GDP 0.048 0.073 -9999 0 -0.41 10 10
RAP1B 0.013 0.022 -9999 0 -0.49 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.055 -9999 0 -0.38 10 10
nectin-3/I-afadin -0.008 0.059 -9999 0 -0.43 10 10
RAPGEF1 0.04 0.081 -9999 0 -0.46 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.033 0.09 -9999 0 -0.53 10 10
PDGFB-D/PDGFRB 0.011 0.038 -9999 0 -0.49 3 3
TLN1 0.032 0.029 -9999 0 -10000 0 0
Rap1/GTP -0.009 0.048 -9999 0 -0.32 10 10
IQGAP1 0.004 0.075 -9999 0 -0.53 10 10
Rap1/GTP/I-afadin -0.001 0.018 -9999 0 -0.29 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.008 0.059 -9999 0 -0.43 10 10
PVR 0.014 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.014 0 -9999 0 -10000 0 0
mol:GDP 0.044 0.087 -9999 0 -0.51 10 10
MLLT4 0.013 0.027 -9999 0 -0.59 1 1
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
PI3K -0.008 0.049 -9999 0 -0.32 10 10
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.014 0.076 -9999 0 -0.43 17 17
positive regulation of lamellipodium assembly -0.009 0.047 -9999 0 -0.32 10 10
PVRL1 -0.005 0.1 -9999 0 -0.59 16 16
PVRL3 0.004 0.079 -9999 0 -0.59 9 9
PVRL2 0.012 0.035 -9999 0 -0.54 2 2
PIK3R1 0.014 0 -9999 0 -10000 0 0
CDH1 -0.12 0.24 -9999 0 -0.54 125 125
CLDN1 -0.019 0.13 -9999 0 -0.53 31 31
JAM-A/CLDN1 -0.029 0.091 -9999 0 -0.35 27 27
SRC -0.019 0.087 -9999 0 -0.6 10 10
ITGB3 -0.052 0.18 -9999 0 -0.51 65 65
nectin-1(dimer)/I-afadin/I-afadin -0.014 0.076 -9999 0 -0.43 17 17
FARP2 0.037 0.085 -9999 0 -0.5 10 10
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 0.049 -9999 0 -0.36 10 10
nectin-1/I-afadin -0.014 0.076 -9999 0 -0.43 17 17
nectin-2/I-afadin -0.002 0.031 -9999 0 -0.4 3 3
RAC1/GTP/IQGAP1/filamentous actin -0.006 0.044 -9999 0 -0.32 10 10
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.018 0.081 -9999 0 -0.37 25 25
CDC42/GTP/IQGAP1/filamentous actin -0.006 0.044 -9999 0 -0.32 10 10
F11R 0.002 0.077 -9999 0 -0.5 12 12
positive regulation of filopodium formation -0.009 0.045 -9999 0 -0.31 10 10
alphaV/beta3 Integrin/Talin 0.013 0.094 -9999 0 -0.4 4 4
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.031 -9999 0 -0.4 3 3
nectin-2(dimer)/I-afadin/I-afadin -0.002 0.031 -9999 0 -0.4 3 3
PIP5K1C 0.025 0.031 -9999 0 -10000 0 0
VAV2 0.037 0.086 -9999 0 -0.51 10 10
RAP1/GDP -0.011 0.055 -9999 0 -0.38 10 10
ITGAV 0.013 0.027 -9999 0 -0.59 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.008 0.053 -9999 0 -0.35 12 12
nectin-3(dimer)/I-afadin/I-afadin -0.008 0.059 -9999 0 -0.43 10 10
Rac1/GTP -0.01 0.057 -9999 0 -0.39 10 10
PTPRM 0.017 0.034 -9999 0 -0.22 11 11
E-cadherin/beta catenin/alpha catenin -0.068 0.12 -9999 0 -0.59 9 9
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 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
ARF5/GTP -0.012 0.045 -9999 0 -10000 0 0
DAPP1 -0.033 0.14 -9999 0 -0.48 26 26
Src family/SYK family/BLNK-LAT/BTK-ITK -0.081 0.22 -9999 0 -0.53 66 66
mol:DAG -0.024 0.1 -9999 0 -0.29 26 26
HRAS 0.014 0.003 -9999 0 -10000 0 0
RAP1A 0.014 0.003 -9999 0 -10000 0 0
ARF5/GDP 0.03 0.057 -9999 0 -0.29 6 6
PLCG2 0 0.088 -9999 0 -0.55 13 13
PLCG1 0.014 0 -9999 0 -10000 0 0
ARF5 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.014 0.051 -9999 0 -10000 0 0
ARF1/GTP -0.011 0.042 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
YES1 0.009 0.053 -9999 0 -0.59 4 4
RAP1A/GTP -0.014 0.05 -9999 0 -10000 0 0
ADAP1 -0.028 0.085 -9999 0 -0.47 8 8
ARAP3 -0.014 0.051 -9999 0 -10000 0 0
INPPL1 0.014 0 -9999 0 -10000 0 0
PREX1 0.002 0.084 -9999 0 -0.59 10 10
ARHGEF6 0.008 0.059 -9999 0 -0.59 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 0.038 -9999 0 -0.49 3 3
mol:Ca2+ -0.003 0.057 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.013 0.027 -9999 0 -0.59 1 1
ZAP70 -0.046 0.17 -9999 0 -0.53 57 57
mol:IP3 -0.008 0.076 -9999 0 -0.22 9 9
LYN 0.004 0.073 -9999 0 -0.51 10 10
ARF1/GDP 0.03 0.057 -9999 0 -0.29 6 6
RhoA/GDP -0.014 0.043 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.022 -9999 0 -0.36 2 2
BLNK -0.056 0.19 -9999 0 -0.58 61 61
actin cytoskeleton reorganization 0.044 0.074 -9999 0 -0.38 5 5
SRC 0.014 0 -9999 0 -10000 0 0
PLEKHA2 0.028 0.038 -9999 0 -0.32 6 6
RAC1 0.014 0 -9999 0 -10000 0 0
PTEN 0.001 0.027 -9999 0 -0.57 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.012 0.045 -9999 0 -10000 0 0
RhoA/GTP -0.013 0.047 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.075 0.2 -9999 0 -0.51 58 58
BLK -0.1 0.22 -9999 0 -0.52 113 113
PDPK1 0.012 0.038 -9999 0 -0.59 2 2
CYTH1 -0.013 0.047 -9999 0 -10000 0 0
HCK -0.007 0.11 -9999 0 -0.54 20 20
CYTH3 -0.013 0.047 -9999 0 -10000 0 0
CYTH2 -0.013 0.047 -9999 0 -10000 0 0
KRAS 0.013 0.022 -9999 0 -0.49 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.025 0.087 -9999 0 -0.45 14 14
SGK1 -0.021 0.083 -9999 0 -0.49 14 14
INPP5D 0.008 0.06 -9999 0 -0.54 6 6
mol:GDP 0.023 0.059 -9999 0 -0.31 6 6
SOS1 0.014 0 -9999 0 -10000 0 0
SYK -0.013 0.12 -9999 0 -0.57 24 24
ARF6/GDP -0.014 0.043 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.051 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.014 0.051 -9999 0 -10000 0 0
VAV1 -0.019 0.14 -9999 0 -0.56 30 30
mol:PI-3-4-P2 0.02 0.044 -9999 0 -0.38 6 6
RAS family/GTP/PI3K Class I 0.018 0.06 -9999 0 -10000 0 0
PLEKHA1 0.024 0.05 -9999 0 -0.3 12 12
Rac1/GDP 0.03 0.057 -9999 0 -0.29 6 6
LAT -0.017 0.13 -9999 0 -0.59 27 27
Rac1/GTP 0.024 0.085 -9999 0 -0.45 10 10
ITK -0.063 0.12 -9999 0 -0.42 20 20
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.04 0.14 -9999 0 -0.39 34 34
LCK -0.081 0.21 -9999 0 -0.54 89 89
BTK -0.024 0.069 -9999 0 -0.42 1 1
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 0.086 0.03 -9999 0 -10000 0 0
ERC1 0.013 0.022 -9999 0 -0.49 1 1
RIP2/NOD2 -0.022 0.088 -9999 0 -0.37 30 30
NFKBIA 0.05 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 -0.007 0.032 -9999 0 -10000 0 0
IKK complex/A20 -0.071 0.1 -9999 0 -0.45 7 7
NEMO/A20/RIP2 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
NEMO/ATM 0.046 0.041 -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 -0.005 0.024 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.001 0.016 -9999 0 -0.36 1 1
NOD2 -0.017 0.13 -9999 0 -0.53 30 30
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 -0.12 0.18 -9999 0 -0.39 165 165
TRAF6 0.013 0.027 -9999 0 -0.59 1 1
PRKCA 0.013 0.027 -9999 0 -0.59 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
UBE2D3 0.014 0 -9999 0 -10000 0 0
TNF -0.15 0.26 -9999 0 -0.54 156 156
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 0.05 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.018 0 -9999 0 -10000 0 0
TNFRSF1A 0.001 0.085 -9999 0 -0.55 12 12
IKK complex 0.053 0.04 -9999 0 -10000 0 0
CYLD 0.014 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.006 0.026 -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 0.034 0.029 -9999 0 -0.29 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.013 0.022 -9999 0 -0.49 1 1
STAT1 (dimer)/Cbp/p300 0.044 0.095 -9999 0 -0.43 12 12
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 0.077 -9999 0 -0.32 21 21
CaM/Ca2+ -0.003 0.025 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.034 0.062 -9999 0 -0.33 6 6
AKT1 0.052 0.028 -9999 0 -10000 0 0
MAP2K1 0.046 0.045 -9999 0 -10000 0 0
MAP3K11 0.041 0.028 -9999 0 -10000 0 0
IFNGR1 0.016 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.14 0.19 -9999 0 -0.46 106 106
Rap1/GTP -0.002 0.016 -9999 0 -10000 0 0
CRKL/C3G -0.001 0.015 -9999 0 -0.34 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0 0.024 -9999 0 -10000 0 0
CEBPB 0.058 0.11 -9999 0 -0.48 14 14
STAT3 0.014 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.001 0.17 -9999 0 -1.1 9 9
STAT1 0.034 0.062 -9999 0 -0.33 6 6
CALM1 0.012 0.035 -9999 0 -0.54 2 2
IFN-gamma (dimer) 0.001 0.048 -9999 0 -0.49 5 5
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
STAT1 (dimer)/PIAS1 0.038 0.065 -9999 0 -0.38 1 1
CEBPB/PTGES2/Cbp/p300 -0.015 0.061 -9999 0 -0.36 9 9
mol:Ca2+ 0.022 0.03 -9999 0 -0.29 1 1
MAPK3 0.053 0.051 -9999 0 -10000 0 0
STAT1 (dimer) -0.072 0.11 -9999 0 -0.46 21 21
MAPK1 0.053 0.051 -9999 0 -10000 0 0
JAK2 0.016 0.003 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.016 0.003 -9999 0 -10000 0 0
CAMK2D 0.013 0.027 -9999 0 -0.59 1 1
DAPK1 0.049 0.13 -9999 0 -0.63 18 18
SMAD7 0.005 0.065 -9999 0 -0.19 4 4
CBL/CRKL/C3G 0.037 0.033 -9999 0 -10000 0 0
PI3K -0.002 0.021 -9999 0 -10000 0 0
IFNG 0.001 0.049 -9999 0 -0.49 5 5
apoptosis 0.03 0.097 -9999 0 -0.45 18 18
CAMK2G 0.013 0.027 -9999 0 -0.59 1 1
STAT3 (dimer) 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.23 0.28 -9999 0 -0.54 230 230
CAMK2B -0.072 0.2 -9999 0 -0.54 80 80
FRAP1 0.05 0.027 -9999 0 -10000 0 0
PRKCD 0.038 0.073 -9999 0 -10000 0 0
RAP1B 0.013 0.022 -9999 0 -0.49 1 1
negative regulation of cell growth -0.055 0.077 -9999 0 -0.32 21 21
PTPN2 0.014 0 -9999 0 -10000 0 0
EP300 0.01 0.053 -9999 0 -0.59 4 4
IRF1 0.032 0.14 -9999 0 -0.58 18 18
STAT1 (dimer)/PIASy 0.04 0.062 -9999 0 -0.39 1 1
SOCS1 -0.047 0.2 -9999 0 -1.4 8 8
mol:GDP -0.001 0.019 -9999 0 -10000 0 0
CASP1 -0.004 0.089 -9999 0 -0.28 28 28
PTGES2 0.014 0 -9999 0 -10000 0 0
IRF9 0.05 0.047 -9999 0 -0.24 4 4
mol:PI-3-4-5-P3 -0.002 0.021 -9999 0 -10000 0 0
RAP1/GDP -0.002 0.017 -9999 0 -10000 0 0
CBL 0.041 0.027 -9999 0 -10000 0 0
MAP3K1 0.038 0.042 -9999 0 -10000 0 0
PIAS1 0.009 0.053 -9999 0 -0.59 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 0.077 -9999 0 -0.32 21 21
PTPN11 0.034 0.028 -9999 0 -0.29 1 1
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
Signaling events mediated by PRL

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.011 0.038 -10000 0 -0.49 3 3
mol:Halofuginone 0.005 0.01 -10000 0 -0.23 1 1
ITGA1 -0.012 0.12 -10000 0 -0.52 25 25
CDKN1A -0.023 0.11 -10000 0 -0.44 21 21
PRL-3/alpha Tubulin -0.003 0.033 -10000 0 -0.34 5 5
mol:Ca2+ -0.02 0.095 0.23 3 -0.43 25 28
AGT -0.015 0.13 -10000 0 -0.58 25 25
CCNA2 -0.056 0.16 -10000 0 -0.52 15 15
TUBA1B 0.014 0 -10000 0 -10000 0 0
EGR1 -0.063 0.17 -10000 0 -0.38 115 115
CDK2/Cyclin E1 -0.013 0.12 -10000 0 -0.42 22 22
MAPK3 0.021 0.036 -10000 0 -0.34 5 5
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.036 -10000 0 -0.34 5 5
PTP4A1 -0.03 0.14 -10000 0 -0.95 1 1
PTP4A3 0.009 0.049 -10000 0 -0.49 5 5
PTP4A2 0.014 0 -10000 0 -10000 0 0
ITGB1 0.02 0.042 -10000 0 -0.34 7 7
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.004 0.061 -10000 0 -0.27 1 1
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.024 0.13 -10000 0 -0.9 1 1
RABGGTA 0.014 0 -10000 0 -10000 0 0
BCAR1 0.001 0.03 0.23 5 -0.44 1 6
RHOC 0.003 0.064 -10000 0 -0.33 2 2
RHOA 0.004 0.061 -10000 0 -0.27 1 1
cell motility 0.006 0.066 -10000 0 -0.3 1 1
PRL-1/alpha Tubulin -0.021 0.13 -10000 0 -0.9 1 1
PRL-3/alpha1 Integrin -0.021 0.088 -10000 0 -0.38 29 29
ROCK1 0.006 0.066 -10000 0 -0.3 1 1
RABGGTB 0.014 0 -10000 0 -10000 0 0
CDK2 0 0.086 -10000 0 -0.53 13 13
mitosis -0.03 0.14 -10000 0 -0.94 1 1
ATF5 0.007 0.058 -10000 0 -0.49 7 7
Circadian rhythm 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
chromatin modification 0.032 0.085 -10000 0 -0.54 6 6
CLOCK -0.018 0.14 -10000 0 -0.59 30 30
TIMELESS/CRY2 0.025 0.082 -10000 0 -0.64 1 1
DEC1/BMAL1 0.008 0.059 -10000 0 -0.34 14 14
ATR 0.014 0 -10000 0 -10000 0 0
NR1D1 0.025 0.12 -10000 0 -1.4 3 3
ARNTL 0.014 0.039 -10000 0 -0.5 3 3
TIMELESS 0.025 0.08 -10000 0 -0.45 1 1
NPAS2 0.006 0.079 -10000 0 -0.55 10 10
CRY2 0.008 0.059 -10000 0 -0.59 5 5
mol:CO -0.012 0.019 0.084 16 -10000 0 16
CHEK1 0.008 0.054 -10000 0 -0.49 6 6
mol:HEME 0.012 0.019 -10000 0 -0.084 16 16
PER1 0.004 0.079 -10000 0 -0.59 9 9
BMAL/CLOCK/NPAS2 0.013 0.11 -10000 0 -0.35 42 42
BMAL1/CLOCK 0.016 0.13 -10000 0 -0.73 6 6
S phase of mitotic cell cycle 0.032 0.085 -10000 0 -0.54 6 6
TIMELESS/CHEK1/ATR 0.033 0.086 -10000 0 -0.55 6 6
mol:NADPH 0.012 0.019 -10000 0 -0.084 16 16
PER1/TIMELESS 0.022 0.084 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.002 0.072 -10000 0 -0.49 11 11
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.038 -9999 0 -0.49 3 3
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.026 0.06 -9999 0 -0.27 17 17
GNAO1 0.01 0.06 -9999 0 -0.6 5 5
S1P/S1P3/G12/G13 0.003 0.09 -9999 0 -0.28 47 47
AKT1 0.027 0.04 -9999 0 -0.3 2 2
AKT3 0.027 0.14 -9999 0 -1.3 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.038 -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 -0.003 0.11 -9999 0 -0.59 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.032 0.15 -9999 0 -0.51 47 47
S1PR2 0.008 0.062 -9999 0 -0.56 6 6
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.019 0.092 -9999 0 -0.49 7 7
MAPK3 0.027 0.088 -9999 0 -0.46 7 7
MAPK1 0.027 0.088 -9999 0 -0.46 7 7
JAK2 0.024 0.096 -9999 0 -0.42 11 11
CXCR4 0.013 0.11 -9999 0 -0.44 14 14
FLT1 0.016 0.028 -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 0.027 0.088 -9999 0 -0.46 7 7
S1P/S1P3/Gi 0.019 0.093 -9999 0 -0.49 7 7
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.02 0.07 -9999 0 -0.44 7 7
VEGFA -0.004 0.1 -9999 0 -0.49 22 22
S1P/S1P2/Gi 0.031 0.069 -9999 0 -0.36 8 8
VEGFR1 homodimer/VEGFA homodimer 0.013 0.077 -9999 0 -0.34 23 23
RHOA 0.014 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.009 0.11 -9999 0 -0.3 49 49
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ 0.016 0.002 -9999 0 -10000 0 0
G12/G13 -0.001 0.019 -9999 0 -0.43 1 1
GNA14 -0.014 0.12 -9999 0 -0.56 25 25
GNA15 -0.007 0.11 -9999 0 -0.57 19 19
GNA12 0.013 0.027 -9999 0 -0.59 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.004 0.079 -9999 0 -0.59 9 9
Rac1/GTP -0.02 0.07 -9999 0 -0.44 7 7
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.004 0.076 0.57 9 -10000 0 9
PI3K Class IB/PDE3B 0.004 0.077 -10000 0 -0.57 9 9
PDE3B 0.004 0.077 -10000 0 -0.57 9 9
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.046 0.12 -9999 0 -0.36 66 66
AKT1 0.074 0.085 -9999 0 -0.64 3 3
PTK2B -0.001 0.14 -9999 0 -0.48 23 23
VEGFR2 homodimer/Frs2 0.029 0.073 -9999 0 -0.62 4 4
CAV1 -0.05 0.17 -9999 0 -0.49 65 65
CALM1 0.012 0.035 -9999 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.018 0.08 -9999 0 -0.61 5 5
endothelial cell proliferation 0.061 0.1 -9999 0 -0.49 4 4
mol:Ca2+ 0.036 0.092 -9999 0 -0.55 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.021 0.083 -9999 0 -0.6 6 6
RP11-342D11.1 0.027 0.092 -9999 0 -0.56 5 5
CDH5 0.011 0.038 -9999 0 -0.49 3 3
VEGFA homodimer -0.012 0.052 -9999 0 -0.32 1 1
SHC1 0.009 0.049 -9999 0 -0.49 5 5
SHC2 0.013 0.027 -9999 0 -0.59 1 1
HRAS/GDP -0.019 0.072 -9999 0 -0.49 6 6
SH2D2A -0.073 0.2 -9999 0 -0.54 81 81
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.022 0.07 -9999 0 -0.47 6 6
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.059 0.14 -9999 0 -0.59 15 15
VEGFR1 homodimer 0.013 0.027 -9999 0 -0.59 1 1
SHC/GRB2/SOS1 -0.021 0.08 -9999 0 -0.5 9 9
GRB10 0.035 0.1 -9999 0 -0.55 8 8
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -0.49 1 1
PAK1 -0.035 0.15 -9999 0 -0.5 49 49
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.021 0.088 -9999 0 -0.62 7 7
HRAS 0.014 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.078 -9999 0 -0.37 5 5
HIF1A 0.012 0.035 -9999 0 -0.54 2 2
FRS2 0.012 0.035 -9999 0 -0.54 2 2
oxygen and reactive oxygen species metabolic process -0.021 0.082 -9999 0 -0.59 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.005 0.071 -9999 0 -0.52 9 9
Nck/Pak -0.034 0.1 -9999 0 -0.35 50 50
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.017 0.079 -9999 0 -0.61 5 5
mol:GDP -0.021 0.078 -9999 0 -0.48 9 9
mol:NADP 0.061 0.081 -9999 0 -0.41 7 7
eNOS/Hsp90 0.065 0.077 -9999 0 -0.4 5 5
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:IP3 0.036 0.093 -9999 0 -0.56 5 5
HIF1A/ARNT -0.002 0.028 -9999 0 -0.37 3 3
SHB 0.014 0 -9999 0 -10000 0 0
VEGFA -0.005 0.1 -9999 0 -0.48 22 22
VEGFC -0.004 0.098 -9999 0 -0.52 18 18
FAK1/Vinculin 0.035 0.11 -9999 0 -0.62 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 -0.046 0.12 -9999 0 -0.5 22 22
PTPN6 -0.003 0.099 -9999 0 -0.55 16 16
EPAS1 0.02 0.038 -9999 0 -0.34 3 3
mol:L-citrulline 0.061 0.081 -9999 0 -0.41 7 7
ITGAV 0.013 0.027 -9999 0 -0.59 1 1
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.018 0.075 -9999 0 -0.58 5 5
VEGFR2 homodimer/VEGFA homodimer -0.023 0.086 -9999 0 -0.61 5 5
VEGFR2/3 heterodimer 0.025 0.091 -9999 0 -0.52 11 11
VEGFB 0.013 0.022 -9999 0 -0.49 1 1
MAPK11 0.035 0.099 -9999 0 -0.54 7 7
VEGFR2 homodimer 0.029 0.08 -9999 0 -0.54 9 9
FLT1 0.013 0.027 -9999 0 -0.59 1 1
NEDD4 0.005 0.078 -9999 0 -0.52 11 11
MAPK3 0.029 0.098 -9999 0 -0.46 7 7
MAPK1 0.029 0.098 -9999 0 -0.46 7 7
VEGFA145/NRP2 -0.022 0.089 -9999 0 -0.37 31 31
VEGFR1/2 heterodimer 0.03 0.072 -9999 0 -0.53 6 6
KDR 0.029 0.081 -9999 0 -0.54 9 9
VEGFA165/NRP1/VEGFR2 homodimer 0.029 0.1 -9999 0 -0.53 6 6
SRC 0.014 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.031 0.099 -9999 0 -0.48 7 7
PI3K 0.061 0.092 -9999 0 -0.67 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.018 0.08 -9999 0 -0.61 5 5
FES 0.034 0.098 -9999 0 -0.55 6 6
GAB1 -0.017 0.074 -9999 0 -0.63 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.017 0.079 -9999 0 -0.61 5 5
CTNNB1 0.014 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
ARNT 0.013 0.022 -9999 0 -0.49 1 1
eNOS/Caveolin-1 0.038 0.11 -9999 0 -0.44 8 8
VEGFR2 homodimer/VEGFA homodimer/Yes -0.019 0.084 -9999 0 -0.6 6 6
PI3K/GAB1 0.075 0.085 -9999 0 -0.55 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.035 0.09 -9999 0 -0.55 6 6
PRKACA 0.014 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.019 0.094 -9999 0 -0.64 7 7
HSP90AA1 0.014 0 -9999 0 -10000 0 0
CDC42 0.036 0.094 -9999 0 -0.57 5 5
actin cytoskeleton reorganization -0.059 0.13 -9999 0 -0.58 15 15
PTK2 0.031 0.11 -9999 0 -0.58 6 6
EDG1 0.027 0.092 -9999 0 -0.56 5 5
mol:DAG 0.036 0.093 -9999 0 -0.56 5 5
CaM/Ca2+ -0.02 0.071 -9999 0 -0.51 5 5
MAP2K3 0.034 0.11 -9999 0 -0.55 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.035 0.1 -9999 0 -0.56 8 8
PLCG1 0.036 0.094 -9999 0 -0.57 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.016 0.072 -9999 0 -0.58 5 5
IQGAP1 0.004 0.075 -9999 0 -0.53 10 10
YES1 0.009 0.053 -9999 0 -0.59 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.017 0.079 -9999 0 -0.61 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.026 0.094 -9999 0 -0.59 7 7
cell migration 0.058 0.11 -9999 0 -0.56 7 7
mol:PI-3-4-5-P3 0.06 0.087 -9999 0 -0.61 3 3
FYN 0.014 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.033 0.088 -9999 0 -0.52 5 5
mol:NO 0.061 0.081 -9999 0 -0.41 7 7
PXN 0.014 0 -9999 0 -10000 0 0
HRAS/GTP -0.019 0.072 -9999 0 -0.49 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.035 0.1 -9999 0 -0.56 8 8
VHL 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.052 0.18 -9999 0 -0.51 65 65
NOS3 0.062 0.088 -9999 0 -0.46 7 7
VEGFR2 homodimer/VEGFA homodimer/Sck -0.018 0.082 -9999 0 -0.61 6 6
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.043 0.089 -9999 0 -0.52 5 5
PRKCB 0.005 0.14 -9999 0 -0.5 18 18
VCL 0.008 0.058 -9999 0 -0.52 6 6
VEGFA165/NRP1 0.027 0.093 -9999 0 -0.56 5 5
VEGFR1/2 heterodimer/VEGFA homodimer -0.018 0.08 -9999 0 -0.61 5 5
VEGFA165/NRP2 -0.022 0.089 -9999 0 -0.37 31 31
MAPKKK cascade 0.057 0.098 -9999 0 -0.52 7 7
NRP2 0.003 0.08 -9999 0 -0.56 10 10
VEGFC homodimer -0.004 0.098 -9999 0 -0.52 18 18
NCK1 0.013 0.027 -9999 0 -0.59 1 1
ROCK1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.038 0.1 -9999 0 -0.57 5 5
MAP3K13 0.028 0.11 -9999 0 -0.56 6 6
PDPK1 0.065 0.085 -9999 0 -0.61 3 3
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.032 0.042 -9999 0 -0.53 2 2
VEGFR1 homodimer/NRP1 0.022 0.039 -9999 0 -0.54 2 2
mol:DAG -0.019 0.13 -9999 0 -0.66 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.013 0.06 -9999 0 -0.49 2 2
CaM/Ca2+ -0.012 0.12 -9999 0 -0.57 2 2
HIF1A 0.02 0.038 -9999 0 -0.46 3 3
GAB1 0.012 0.035 -9999 0 -0.54 2 2
AKT1 0.005 0.13 -9999 0 -0.71 2 2
PLCG1 -0.02 0.13 -9999 0 -0.66 1 1
NOS3 0.007 0.13 -9999 0 -0.47 4 4
CBL 0.014 0 -9999 0 -10000 0 0
mol:NO 0.008 0.12 -9999 0 -0.45 4 4
FLT1 0.03 0.045 -9999 0 -0.62 2 2
PGF -0.092 0.22 -9999 0 -0.55 96 96
VEGFR1 homodimer/NRP2/VEGFR121 0.021 0.082 -9999 0 -0.58 2 2
CALM1 0.012 0.035 -9999 0 -0.54 2 2
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
eNOS/Hsp90 0.015 0.12 -9999 0 -0.45 3 3
endothelial cell proliferation -0.033 0.16 -9999 0 -0.52 16 16
mol:Ca2+ -0.019 0.13 -9999 0 -0.65 1 1
MAPK3 -0.001 0.12 -9999 0 -0.57 1 1
MAPK1 -0.001 0.12 -9999 0 -0.57 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
PLGF homodimer -0.091 0.22 -9999 0 -0.55 96 96
PRKACA 0.014 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.05 0.17 -9999 0 -0.49 65 65
VEGFA homodimer -0.007 0.1 -9999 0 -0.49 22 22
VEGFR1 homodimer/VEGFA homodimer 0.02 0.073 -9999 0 -0.53 2 2
platelet activating factor biosynthetic process 0.007 0.11 -9999 0 -0.55 1 1
PI3K -0.011 0.13 -9999 0 -0.61 2 2
PRKCA -0.01 0.12 -9999 0 -0.61 1 1
PRKCB -0.049 0.16 -9999 0 -0.55 16 16
VEGFR1 homodimer/PLGF homodimer -0.034 0.14 -9999 0 -0.36 61 61
VEGFA -0.007 0.1 -9999 0 -0.49 22 22
VEGFB 0.013 0.022 -9999 0 -0.49 1 1
mol:IP3 -0.019 0.13 -9999 0 -0.66 1 1
RASA1 0.04 0.039 -9999 0 -0.66 1 1
NRP2 0.003 0.08 -9999 0 -0.56 10 10
VEGFR1 homodimer 0.03 0.045 -9999 0 -0.62 2 2
VEGFB homodimer 0.013 0.022 -9999 0 -0.49 1 1
NCK1 0.013 0.027 -9999 0 -0.59 1 1
eNOS/Caveolin-1 -0.014 0.14 -9999 0 -0.47 13 13
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.05 0.11 -9999 0 -0.6 2 2
mol:L-citrulline 0.008 0.12 -9999 0 -0.45 4 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.035 0.063 -9999 0 -0.63 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.069 -9999 0 -0.67 1 1
CD2AP 0.014 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.048 0.1 -9999 0 -0.57 2 2
PDPK1 -0.003 0.12 -9999 0 -0.71 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.067 -9999 0 -0.67 1 1
mol:NADP 0.008 0.12 -9999 0 -0.45 4 4
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.011 0.053 -9999 0 -0.62 1 1
VEGFR1 homodimer/NRP2 0.026 0.064 -9999 0 -0.39 9 9
HIF-2-alpha transcription factor network

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
MMP14 -0.05 0.21 -10000 0 -1.1 17 17
oxygen homeostasis 0.007 0.017 -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 0.048 -10000 0 -0.32 2 2
EPO 0.092 0.23 -10000 0 -0.72 14 14
FIH (dimer) 0.021 0.017 -10000 0 -10000 0 0
APEX1 0.02 0.017 -10000 0 -10000 0 0
SERPINE1 0.01 0.33 -10000 0 -0.75 27 27
FLT1 -0.004 0.1 -10000 0 -0.84 6 6
ADORA2A 0.091 0.23 -10000 0 -0.72 13 13
germ cell development 0.075 0.25 -10000 0 -0.7 19 19
SLC11A2 0.093 0.23 -10000 0 -0.73 13 13
BHLHE40 0.084 0.25 -10000 0 -0.79 17 17
HIF1AN 0.021 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.024 0.085 -10000 0 -0.44 8 8
ETS1 0.018 0.084 -10000 0 -0.55 11 11
CITED2 0.003 0.037 -10000 0 -0.44 1 1
KDR -0.012 0.13 -10000 0 -0.86 9 9
PGK1 0.093 0.23 -10000 0 -0.75 12 12
SIRT1 0.015 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.099 0.27 -10000 0 -0.91 13 13
EPAS1 0.066 0.11 -10000 0 -0.35 7 7
SP1 0.019 0.017 -10000 0 -10000 0 0
ABCG2 0.092 0.24 -10000 0 -0.8 12 12
EFNA1 0.092 0.24 -10000 0 -0.76 13 13
FXN 0.092 0.23 -10000 0 -0.72 13 13
POU5F1 0.074 0.26 -10000 0 -0.74 19 19
neuron apoptosis -0.098 0.26 0.86 13 -10000 0 13
EP300 0.009 0.053 -10000 0 -0.59 4 4
EGLN3 0.006 0.098 -10000 0 -0.59 13 13
EGLN2 0.021 0.017 -10000 0 -10000 0 0
EGLN1 0.021 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 0.019 0.029 -10000 0 -0.52 1 1
SLC2A1 0.091 0.23 -10000 0 -0.78 10 10
TWIST1 0.065 0.28 -10000 0 -0.75 25 25
ELK1 0.023 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.023 0.085 -10000 0 -0.44 8 8
VEGFA 0.085 0.25 -10000 0 -0.81 15 15
CREBBP 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.085 0.13 -10000 0 -0.35 77 77
Ran/GTP/Exportin 1/HDAC1 -0.002 0.023 -10000 0 -0.26 4 4
NF kappa B1 p50/RelA/I kappa B alpha -0.034 0.14 -10000 0 -0.51 3 3
SUMO1 0.014 0 -10000 0 -10000 0 0
ZFPM1 0.013 0.027 -10000 0 -0.59 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -10000 0 -10000 0 0
FKBP3 0.014 0 -10000 0 -10000 0 0
Histones -0.005 0.087 -10000 0 -0.44 4 4
YY1/LSF 0.031 0.029 -10000 0 -0.34 1 1
SMG5 0.013 0.022 -10000 0 -0.49 1 1
RAN 0.014 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.041 0.12 -10000 0 -0.44 3 3
I kappa B alpha/HDAC1 -0.024 0.094 -10000 0 -0.46 4 4
SAP18 0.014 0 -10000 0 -10000 0 0
RELA -0.031 0.11 -10000 0 -0.38 6 6
HDAC1/Smad7 -0.003 0.031 -10000 0 -0.36 4 4
RANGAP1 0.014 0 -10000 0 -10000 0 0
HDAC3/TR2 -0.021 0.086 -10000 0 -0.29 3 3
NuRD/MBD3 Complex 0.05 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.1 -10000 0 -0.35 6 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.004 0.1 -10000 0 -0.56 16 16
GATA1 0.004 0.058 -10000 0 -0.49 7 7
Mad/Max 0 0 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.058 0.029 -10000 0 -10000 0 0
RBBP7 0.014 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
RBBP4 0.013 0.027 -10000 0 -0.59 1 1
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 0.097 -10000 0 -0.33 3 3
KAT2B 0.013 0.022 -10000 0 -0.49 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.045 0.026 -10000 0 -10000 0 0
SIN3 complex -0.001 0.014 -10000 0 -0.32 1 1
SMURF1 0.014 0 -10000 0 -10000 0 0
CHD3 0.013 0.027 -10000 0 -0.59 1 1
SAP30 0.013 0.027 -10000 0 -0.59 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.012 0.038 -10000 0 -0.59 2 2
YY1/HDAC3 -0.007 0.084 -10000 0 -0.31 3 3
YY1/HDAC2 0.032 0.025 -10000 0 -10000 0 0
YY1/HDAC1 0.029 0.041 -10000 0 -0.34 4 4
NuRD/MBD2 Complex (MeCP1) 0.05 0.023 -10000 0 -10000 0 0
PPARG -0.091 0.14 -10000 0 -0.36 79 79
HDAC8/hEST1B -0.001 0.02 -10000 0 -0.32 2 2
UBE2I 0.014 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -10000 0 -10000 0 0
TNFRSF1A 0.001 0.085 -10000 0 -0.55 12 12
HDAC3/SMRT (N-CoR2) -0.021 0.086 -10000 0 -10000 0 0
MBD3L2 0 0.001 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.003 0.031 -10000 0 -0.36 4 4
CREBBP 0.014 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.024 -10000 0 -10000 0 0
HDAC1 0.009 0.053 -10000 0 -0.59 4 4
HDAC3 -0.033 0.097 -10000 0 -0.33 3 3
HDAC2 0.014 0 -10000 0 -10000 0 0
YY1 0.03 0.029 -10000 0 -0.28 4 4
HDAC8 0.013 0.027 -10000 0 -0.59 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 0.033 -10000 0 -0.34 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 0.04 -10000 0 -0.31 5 5
YY1/SAP30/HDAC1 0.035 0.04 -10000 0 -0.31 5 5
EP300 0.009 0.053 -10000 0 -0.59 4 4
STAT3 (dimer non-phopshorylated) 0.025 0.032 -10000 0 -0.34 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.032 0.096 -10000 0 -0.33 3 3
histone deacetylation 0.05 0.023 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.01 0.085 -10000 0 -0.36 3 3
nuclear export 0.001 0.02 0.32 2 -10000 0 2
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 -0.031 0.1 -10000 0 -0.36 14 14
GATA1/HDAC1 -0.008 0.054 -10000 0 -0.37 11 11
GATA1/HDAC3 -0.032 0.089 -10000 0 -0.41 2 2
CHD4 0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.12 0.18 -10000 0 -0.39 165 165
SIN3/HDAC complex/Mad/Max 0.05 0.023 -10000 0 -10000 0 0
NuRD Complex 0.058 0.024 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.038 0.066 -10000 0 -0.43 4 4
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 0.028 -10000 0 -0.29 4 4
HDAC complex -0.003 0.031 -10000 0 -0.32 5 5
GATA1/Fog1 -0.005 0.044 -10000 0 -0.35 8 8
FKBP25/HDAC1/HDAC2 -0.003 0.031 -10000 0 -0.36 4 4
TNF -0.15 0.26 -10000 0 -0.54 156 156
negative regulation of cell growth 0.05 0.023 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.05 0.023 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.044 0.14 -10000 0 -0.33 80 80
SIN3/HDAC complex/NCoR1 0.047 0.03 -10000 0 -0.39 1 1
TFCP2 0.013 0.027 -10000 0 -0.59 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
Atypical NF-kappaB pathway

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
BCL3/RelA -0.008 0.051 -9999 0 -0.34 12 12
FBXW11 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.009 0.083 -9999 0 -0.36 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.08 -9999 0 -0.5 2 2
NFKBIA -0.01 0.09 -9999 0 -0.35 6 6
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 -0.018 0.13 -9999 0 -0.56 29 29
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.046 -9999 0 -0.28 12 12
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.029 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
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 -0.002 0.087 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.019 0.079 -9999 0 -0.48 2 2
SRC 0.014 0 -9999 0 -10000 0 0
PI3K -0.001 0.019 -9999 0 -0.43 1 1
NF kappa B1 p50/RelA -0.002 0.087 -9999 0 -0.44 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 -0.013 0.12 -9999 0 -0.57 24 24
I kappa B alpha/PIK3R1 -0.002 0.085 -9999 0 -0.54 2 2
cell death 0.018 0.076 -9999 0 -0.46 2 2
NF kappa B1 p105/c-Rel 0.009 0.083 -9999 0 -0.36 19 19
LCK -0.081 0.21 -9999 0 -0.54 89 89
BCL3 0.002 0.076 -9999 0 -0.49 12 12
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.011 0.054 -9999 0 -0.57 1 1
TC10/GTP -0.008 0.048 -9999 0 -0.55 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.003 0.027 -9999 0 -0.29 4 4
HRAS 0.014 0 -9999 0 -10000 0 0
APS homodimer -0.001 0.094 -9999 0 -0.56 14 14
GRB14 -0.18 0.26 -9999 0 -0.53 186 186
FOXO3 -0.027 0.096 -9999 0 -0.59 14 14
AKT1 -0.04 0.13 -9999 0 -0.45 4 4
INSR 0.016 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.036 0.028 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.011 0.044 -9999 0 -0.56 3 3
SORBS1 0.011 0.046 -9999 0 -0.59 3 3
CRK 0.014 0 -9999 0 -10000 0 0
PTPN1 0.035 0.028 -9999 0 -10000 0 0
CAV1 -0.007 0.096 -9999 0 -0.37 6 6
CBL/APS/CAP/Crk-II/C3G -0.009 0.053 -9999 0 -0.32 12 12
Insulin Receptor/Insulin/IRS1/NCK2 -0.003 0.027 -9999 0 -0.29 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.026 -9999 0 -0.28 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.032 -9999 0 -10000 0 0
RPS6KB1 -0.029 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 0.038 -9999 0 -0.82 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.064 0.088 -9999 0 -0.39 5 5
HRAS/GTP -0.006 0.037 -9999 0 -0.42 1 1
Insulin Receptor 0.016 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.005 0.035 -9999 0 -10000 0 0
PRKCI -0.022 0.053 -9999 0 -0.55 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.082 0.11 -9999 0 -0.48 4 4
SHC1 0.009 0.049 -9999 0 -0.49 5 5
negative regulation of MAPKKK cascade -0.001 0.035 -9999 0 -0.7 1 1
PI3K -0.003 0.027 -9999 0 -0.29 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 -0.04 0.13 -9999 0 -0.45 4 4
PRKCZ -0.043 0.12 -9999 0 -0.59 20 20
SH2B2 -0.001 0.094 -9999 0 -0.56 14 14
SHC/SHIP 0.029 0.05 -9999 0 -0.49 1 1
F2RL2 -0.095 0.21 -9999 0 -0.51 107 107
TRIP10 0.007 0.065 -9999 0 -0.55 7 7
Insulin Receptor/Insulin/Shc -0.005 0.038 -9999 0 -0.28 9 9
TC10/GTP/CIP4/Exocyst -0.005 0.039 -9999 0 -0.33 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 0.027 -9999 0 -0.59 1 1
CBL/APS/CAP/Crk-II -0.01 0.057 -9999 0 -0.34 12 12
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.007 0.044 -9999 0 -0.31 6 6
INPP5D 0.023 0.046 -9999 0 -0.36 4 4
SOS1 0.014 0 -9999 0 -10000 0 0
SGK1 -0.029 0.14 -9999 0 -0.88 14 14
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.014 0 -9999 0 -10000 0 0
p62DOK/RasGAP -0.001 0.036 -9999 0 -0.71 1 1
INS -0.002 0.056 -9999 0 -0.57 5 5
mol:PI-3-4-P2 0.023 0.046 -9999 0 -0.36 4 4
GRB2 0.013 0.022 -9999 0 -0.49 1 1
EIF4EBP1 -0.035 0.13 -9999 0 -0.42 12 12
PTPRA 0.016 0.003 -9999 0 -10000 0 0
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
TC10/GTP/CIP4 -0.005 0.039 -9999 0 -0.33 7 7
PDPK1 0.012 0.038 -9999 0 -0.59 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.031 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.028 -9999 0 -0.3 4 4
Insulin Receptor/Insulin/IRS3 -0.004 0.04 -9999 0 -0.41 5 5
Par3/Par6 -0.054 0.1 -9999 0 -0.31 29 29
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.002 0.028 -9999 0 -0.32 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 -0.005 0.039 -9999 0 -0.34 7 7
GATA1/HDAC5 -0.005 0.039 -9999 0 -0.34 7 7
GATA2/HDAC5 -0.012 0.07 -9999 0 -0.4 16 16
HDAC5/BCL6/BCoR -0.001 0.012 -9999 0 -0.28 1 1
HDAC9 -0.002 0.094 -9999 0 -0.55 15 15
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 -0.004 0.1 -9999 0 -0.56 16 16
HDAC4/RFXANK -0.001 0.015 -9999 0 -0.34 1 1
BCOR 0.013 0.022 -9999 0 -0.49 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 -0.003 0.038 -9999 0 -0.43 4 4
Histones 0.038 0.036 -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 0.015 -9999 0 -0.34 1 1
CAMK4 -0.18 0.27 -9999 0 -0.57 168 168
Tubulin/HDAC6 -0.001 0.016 -9999 0 -0.36 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 -0.49 7 7
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 0.033 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 0.019 -9999 0 -0.43 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 0.015 -9999 0 -0.34 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.11 0.16 -9999 0 -0.34 168 168
HDAC4/ER alpha -0.019 0.084 -9999 0 -0.38 26 26
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.038 0.036 -9999 0 -10000 0 0
cell motility -0.001 0.016 -9999 0 -0.36 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 -0.014 0.12 -9999 0 -0.54 26 26
HDAC6/HDAC11 -0.001 0.019 -9999 0 -0.43 1 1
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.007 0.1 -9999 0 -0.5 21 21
RAN 0.014 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.009 0.045 -9999 0 -10000 0 0
GNG2 0.009 0.053 -9999 0 -0.59 4 4
NCOR2 0.014 0 -9999 0 -10000 0 0
TUBB2A 0.013 0.027 -9999 0 -0.59 1 1
HDAC11 0.013 0.027 -9999 0 -0.59 1 1
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 0.022 -9999 0 -0.49 1 1
nuclear import -0.032 0 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.009 0.053 -9999 0 -0.59 4 4
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.008 0.052 -9999 0 -0.36 11 11
forebrain development -0.005 0.15 -9999 0 -0.43 43 43
GNAO1 0.008 0.06 -9999 0 -0.6 5 5
SMO/beta Arrestin2 0.016 0.053 -9999 0 -0.43 7 7
SMO 0.006 0.07 -9999 0 -0.59 7 7
ARRB2 0.014 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.04 0.067 -9999 0 -0.6 1 1
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.013 0.027 -9999 0 -0.59 1 1
GNAI2 0.014 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.004 0.019 -9999 0 -0.32 1 1
GNAI1 -0.005 0.1 -9999 0 -0.59 16 16
XPO1 0.015 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.042 0.11 -9999 0 -0.55 11 11
SAP30 0.013 0.027 -9999 0 -0.59 1 1
mol:GDP 0.006 0.07 -9999 0 -0.59 7 7
MIM/GLI2A 0.01 0.059 -9999 0 -0.58 5 5
IFT88 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0.003 -9999 0 -10000 0 0
GLI2 0.043 0.036 -9999 0 -10000 0 0
GLI3 0.034 0.07 -9999 0 -0.48 2 2
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 0.053 -9999 0 -0.59 4 4
Gi family/GTP 0.025 0.067 -9999 0 -0.28 15 15
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.052 0.058 -9999 0 -0.46 2 2
GLI2/Su(fu) 0.053 0.057 -9999 0 -0.77 1 1
FOXA2 -0.039 0.13 -9999 0 -0.99 4 4
neural tube patterning -0.005 0.15 -9999 0 -0.43 43 43
SPOP 0.014 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.051 -9999 0 -0.39 5 5
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 0.059 -9999 0 -0.58 5 5
embryonic limb morphogenesis -0.005 0.15 -9999 0 -0.43 43 43
SUFU 0.026 0.045 -9999 0 -0.78 1 1
LGALS3 -0.026 0.14 -9999 0 -0.5 41 41
catabolic process 0.064 0.064 -9999 0 -0.49 1 1
GLI3A/CBP -0.017 0.1 -9999 0 -0.34 32 32
KIF3A 0.013 0.027 -9999 0 -0.59 1 1
GLI1 -0.006 0.16 -9999 0 -0.44 42 42
RAB23 0.013 0.027 -9999 0 -0.59 1 1
CSNK1A1 0.014 0 -9999 0 -10000 0 0
IFT172 0.011 0.046 -9999 0 -0.59 3 3
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.008 0.089 -9999 0 -0.46 5 5
GNAZ 0.014 0.003 -9999 0 -10000 0 0
RBBP4 0.013 0.027 -9999 0 -0.59 1 1
CSNK1G1 0.013 0.022 -9999 0 -0.49 1 1
PIAS1 0.009 0.053 -9999 0 -0.59 4 4
PRKACA 0.014 0 -9999 0 -10000 0 0
GLI2/SPOP 0.047 0.034 -9999 0 -10000 0 0
STK36 0.014 0.027 -9999 0 -0.59 1 1
Gi family/GNB1/GNG2/GDP 0.031 0.069 -9999 0 -0.48 3 3
PTCH1 -0.006 0.19 -9999 0 -0.83 15 15
MIM/GLI1 -0.007 0.17 -9999 0 -0.59 17 17
CREBBP -0.017 0.1 -9999 0 -0.34 32 32
Su(fu)/SIN3/HDAC complex 0.051 0.03 -9999 0 -0.28 1 1
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.015 0.16 -9999 0 -1.3 5 5
PLK1 0.048 0.22 -9999 0 -0.96 11 11
CDKN1B 0.098 0.11 -9999 0 -10000 0 0
FOXO3 0.063 0.16 -9999 0 -0.55 11 11
KAT2B 0.022 0.026 -9999 0 -0.47 1 1
FOXO1/SIRT1 -0.003 0.067 -9999 0 -0.41 5 5
CAT 0.066 0.16 -9999 0 -0.61 9 9
CTNNB1 0.014 0 -9999 0 -10000 0 0
AKT1 0.025 0.017 -9999 0 -10000 0 0
FOXO1 0.028 0.08 -9999 0 -0.35 11 11
MAPK10 0.037 0.034 -9999 0 -0.31 4 4
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
FOXO4 0.094 0.068 -9999 0 -0.49 1 1
response to oxidative stress 0.01 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.01 0.14 -9999 0 -0.52 10 10
XPO1 0.015 0.001 -9999 0 -10000 0 0
EP300 0.011 0.054 -9999 0 -0.59 4 4
BCL2L11 0.028 0.11 -9999 0 -1.4 3 3
FOXO1/SKP2 0.026 0.086 -9999 0 -0.39 12 12
mol:GDP 0.01 0.02 -9999 0 -10000 0 0
RAN 0.016 0.001 -9999 0 -10000 0 0
GADD45A 0.078 0.14 -9999 0 -0.48 12 12
YWHAQ 0.014 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.043 0.071 -9999 0 -10000 0 0
MST1 -0.017 0.15 -9999 0 -0.57 35 35
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 -0.38 3 3
YWHAB 0.014 0 -9999 0 -10000 0 0
MAPK8 0.032 0.058 -9999 0 -0.3 14 14
MAPK9 0.04 0.014 -9999 0 -10000 0 0
YWHAG 0.002 0.079 -9999 0 -0.49 13 13
YWHAE 0.014 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
SIRT1 0.009 0.011 -9999 0 -10000 0 0
SOD2 0.093 0.16 -9999 0 -0.56 6 6
RBL2 0.083 0.13 -9999 0 -1.2 1 1
RAL/GDP 0.029 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 0.037 0.019 -9999 0 -10000 0 0
CSNK1G1 0.013 0.022 -9999 0 -0.49 1 1
FASLG 0.005 0.099 -9999 0 -0.4 8 8
SKP2 0.005 0.07 -9999 0 -0.55 8 8
USP7 0.016 0.001 -9999 0 -10000 0 0
IKBKB 0.023 0.014 -9999 0 -10000 0 0
CCNB1 0.056 0.18 -9999 0 -0.51 31 31
FOXO1-3a-4/beta catenin 0.12 0.13 -9999 0 -0.38 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.086 -9999 0 -0.39 12 12
CSNK1A1 0.014 0 -9999 0 -10000 0 0
SGK1 0.005 0.1 -9999 0 -0.58 15 15
CSNK1G3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.009 -9999 0 -10000 0 0
ZFAND5 0.096 0.061 -9999 0 -0.39 1 1
SFN -0.11 0.23 -9999 0 -0.53 119 119
CDK2 0.001 0.086 -9999 0 -0.53 13 13
FOXO3A/14-3-3 0.022 0.093 -9999 0 -0.35 3 3
CREBBP 0.014 0.012 -9999 0 -10000 0 0
FBXO32 0.054 0.19 -9999 0 -0.7 13 13
BCL6 0.085 0.12 -9999 0 -0.42 1 1
RALB 0.015 0.001 -9999 0 -10000 0 0
RALA 0.015 0.001 -9999 0 -10000 0 0
YWHAH -0.01 0.11 -9999 0 -0.49 25 25
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.015 0.077 -9999 0 -0.38 8 8
PDGFB-D/PDGFRB/SLAP -0.006 0.1 -9999 0 -0.4 32 32
PDGFB-D/PDGFRB/APS/CBL -0.006 0.063 -9999 0 -0.35 16 16
AKT1 0.058 0.037 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.009 0.086 -9999 0 -0.38 8 8
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
FGR 0.001 0.028 -9999 0 -10000 0 0
mol:Ca2+ 0.019 0.041 -9999 0 -10000 0 0
MYC 0.001 0.18 -9999 0 -0.82 22 22
SHC1 0.009 0.049 -9999 0 -0.49 5 5
HRAS/GDP 0.037 0.021 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.003 0.024 -9999 0 -10000 0 0
GRB10 0.011 0.044 -9999 0 -0.56 3 3
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 0.019 0.041 -9999 0 -10000 0 0
PTEN 0.013 0.027 -9999 0 -0.59 1 1
GRB2 0.013 0.022 -9999 0 -0.49 1 1
GRB7 -0.032 0.14 -9999 0 -0.49 43 43
PDGFB-D/PDGFRB/SHP2 0.017 0.028 -9999 0 -0.34 3 3
PDGFB-D/PDGFRB/GRB10 0.015 0.043 -9999 0 -0.37 6 6
cell cycle arrest -0.006 0.1 -9999 0 -0.39 32 32
HRAS 0.014 0 -9999 0 -10000 0 0
HIF1A 0.063 0.041 -9999 0 -0.44 1 1
GAB1 0.007 0.072 -9999 0 -0.38 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.01 0.074 -9999 0 -0.37 4 4
PDGFB-D/PDGFRB 0.011 0.028 -9999 0 -0.29 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.017 0.028 -9999 0 -0.34 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.025 0.085 -9999 0 -0.44 9 9
positive regulation of MAPKKK cascade 0.017 0.028 -9999 0 -0.34 3 3
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:IP3 0.019 0.042 -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 -0.015 0.1 -9999 0 -0.35 45 45
SHB 0.014 0 -9999 0 -10000 0 0
BLK -0.054 0.14 -9999 0 -0.55 31 31
PTPN2 0.014 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.017 0.028 -9999 0 -0.34 3 3
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
VAV2 0.008 0.087 -9999 0 -0.43 4 4
CBL 0.014 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.017 0.032 -9999 0 -0.34 4 4
LCK -0.053 0.15 -9999 0 -0.53 40 40
PDGFRB 0.011 0.039 -9999 0 -0.49 3 3
ACP1 0.014 0 -9999 0 -10000 0 0
HCK -0.01 0.091 -9999 0 -0.61 10 10
ABL1 0.008 0.062 -9999 0 -0.38 1 1
PDGFB-D/PDGFRB/CBL 0.007 0.07 -9999 0 -0.39 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 -0.001 0.087 -9999 0 -0.49 16 16
cell proliferation 0.006 0.16 -9999 0 -0.72 22 22
SLA -0.018 0.13 -9999 0 -0.54 30 30
actin cytoskeleton reorganization 0.048 0.032 -9999 0 -10000 0 0
SRC 0.003 0.026 -9999 0 -10000 0 0
PI3K -0.005 0.031 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.023 0.092 -9999 0 -0.31 32 32
SH2B2 -0.001 0.094 -9999 0 -0.56 14 14
PLCgamma1/SPHK1 0.009 0.088 -9999 0 -0.39 8 8
LYN -0.001 0.051 -9999 0 -0.63 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 0.001 0.088 -9999 0 -0.59 11 11
NCK1-2/p130 Cas 0.008 0.031 -9999 0 -10000 0 0
SPHK1 -0.028 0.15 -9999 0 -0.54 40 40
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.019 0.042 -9999 0 -10000 0 0
PLCG1 0.019 0.042 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.043 -9999 0 -0.32 9 9
YES1 -0.002 0.056 -9999 0 -0.55 4 4
cell migration -0.004 0.042 -9999 0 -0.31 9 9
SHC/Grb2/SOS1 0.006 0.041 -9999 0 -0.45 2 2
SLC9A3R2 0.012 0.031 -9999 0 -0.49 2 2
SLC9A3R1 0.009 0.053 -9999 0 -0.59 4 4
NHERF1-2/PDGFRB/PTEN 0.006 0.044 -9999 0 -0.32 5 5
FYN 0.003 0.026 -9999 0 -10000 0 0
DOK1 0.032 0.03 -9999 0 -0.33 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.014 0 -9999 0 -10000 0 0
RAC1 0.013 0.12 -9999 0 -0.44 24 24
PRKCD 0.015 0.083 -9999 0 -0.33 27 27
FER 0.018 0.075 -9999 0 -0.32 21 21
MAPKKK cascade -0.004 0.034 -9999 0 -0.45 2 2
RASA1 0.033 0.023 -9999 0 -10000 0 0
NCK1 0.013 0.027 -9999 0 -0.59 1 1
NCK2 0.014 0 -9999 0 -10000 0 0
p62DOK/Csk 0.04 0.027 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.017 0.028 -9999 0 -0.34 3 3
chemotaxis 0.008 0.061 -9999 0 -0.34 2 2
STAT1-3-5/STAT1-3-5 -0.013 0.052 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.008 0.028 -9999 0 -0.35 3 3
PTPRJ 0.013 0.022 -9999 0 -0.49 1 1
Arf6 trafficking events

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
SLC2A4 -0.062 0.19 -10000 0 -0.55 69 69
CLTC 0.031 0.015 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.015 0.046 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0 -10000 0 -10000 0 0
EXOC4 0.014 0 -10000 0 -10000 0 0
CD59 0.025 0.022 -10000 0 -10000 0 0
CPE 0.007 0.07 -10000 0 -0.36 18 18
CTNNB1 0.014 0 -10000 0 -10000 0 0
membrane fusion 0.014 0.049 -10000 0 -10000 0 0
CTNND1 0.035 0 -10000 0 -10000 0 0
DNM2 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.025 -10000 0 -10000 0 0
TSHR -0.11 0.17 -10000 0 -0.33 196 196
INS 0.006 0.048 -10000 0 -0.52 4 4
BIN1 0.013 0.027 -10000 0 -0.59 1 1
mol:Choline 0.014 0.049 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.021 0.04 -10000 0 -0.29 4 4
ASAP2/amphiphysin II -0.001 0.014 -10000 0 -0.33 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 -0.02 0.089 -10000 0 -0.29 13 13
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.014 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.014 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.047 0.005 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.014 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.026 0.051 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.012 0.044 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.022 0.087 -10000 0 -0.29 6 6
clathrin heavy chain/ACAP1 0.031 0.03 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.014 0 -10000 0 -10000 0 0
exocyst 0.047 0.006 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.035 0 -10000 0 -10000 0 0
NME1 0.021 0 -10000 0 -10000 0 0
clathrin coat assembly 0.031 0.015 -10000 0 -10000 0 0
IL2RA 0.002 0.058 -10000 0 -0.29 1 1
VAMP3 0.021 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.036 0.083 -10000 0 -0.27 42 42
EXOC6 0.014 0 -10000 0 -10000 0 0
PLD1 -0.021 0.072 -10000 0 -0.28 34 34
PLD2 -0.001 0.012 -10000 0 -0.28 1 1
EXOC5 0.014 0 -10000 0 -10000 0 0
PIP5K1C 0.028 0.026 -10000 0 -10000 0 0
SDC1 0.012 0.049 -10000 0 -10000 0 0
ARF6/GDP 0.02 0 -10000 0 -10000 0 0
EXOC7 0.013 0.022 -10000 0 -0.49 1 1
E-cadherin/beta catenin -0.027 0.052 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.014 0.049 -10000 0 -10000 0 0
endocytosis 0.001 0.014 0.32 1 -10000 0 1
SCAMP2 0.014 0 -10000 0 -10000 0 0
ADRB2 0.022 0.071 -10000 0 -0.29 24 24
EXOC3 0.014 0 -10000 0 -10000 0 0
ASAP2 0.014 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0 -10000 0 -10000 0 0
KLC1 0.014 0 -10000 0 -10000 0 0
AVPR2 0.025 0.055 -10000 0 -0.26 6 6
RALA 0.014 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.045 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.014 0 -10000 0 -10000 0 0
PTK2 0.014 0 -10000 0 -10000 0 0
CRKL 0.018 0.057 -10000 0 -0.29 14 14
GRB2/SOS1/SHC -0.003 0.03 -10000 0 -0.28 6 6
HRAS 0.014 0 -10000 0 -10000 0 0
IRS1/Crk 0.018 0.056 -10000 0 -0.29 14 14
IGF-1R heterotetramer/IGF1/PTP1B -0.012 0.061 -10000 0 -0.34 14 14
AKT1 0.038 0.057 -10000 0 -0.54 1 1
BAD 0.044 0.054 -10000 0 -0.5 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.018 0.056 -10000 0 -0.29 14 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.018 0.056 -10000 0 -0.29 14 14
RAF1 0.048 0.054 -10000 0 -0.52 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.025 0.055 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.009 0.061 -10000 0 -0.32 14 14
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
RPS6KB1 0.038 0.057 -10000 0 -0.54 1 1
GNB2L1 0.014 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.041 0.048 -10000 0 -0.44 1 1
PXN 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.014 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
HRAS/GTP -0.01 0.047 -10000 0 -0.36 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.012 0.055 -10000 0 -0.43 2 2
IGF-1R heterotetramer 0.011 0.025 -10000 0 -0.48 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.018 0.057 -10000 0 -0.29 14 14
Crk/p130 Cas/Paxillin -0.009 0.045 -10000 0 -10000 0 0
IGF1R 0.011 0.025 -10000 0 -0.48 1 1
IGF1 -0.008 0.11 -10000 0 -0.56 20 20
IRS2/Crk 0.025 0.058 -10000 0 -0.47 1 1
PI3K 0.025 0.055 -10000 0 -0.27 15 15
apoptosis -0.049 0.048 0.42 1 -10000 0 1
HRAS/GDP 0 0 -10000 0 -10000 0 0
PRKCD 0.015 0.12 -10000 0 -0.39 33 33
RAF1/14-3-3 E 0.053 0.049 -10000 0 -0.44 1 1
BAD/14-3-3 0.051 0.051 -10000 0 -0.45 1 1
PRKCZ 0.023 0.085 -10000 0 -0.46 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.008 0.038 -10000 0 -0.44 1 1
PTPN1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.024 0.075 -10000 0 -0.4 14 14
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.015 0.065 -10000 0 -0.31 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.014 0 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.056 -10000 0 -0.29 14 14
GRB10 0.011 0.044 -10000 0 -0.56 3 3
PTPN11 0.018 0.056 -10000 0 -0.29 14 14
IRS1 0.01 0.061 -10000 0 -0.32 14 14
IRS2 0.017 0.061 -10000 0 -0.3 16 16
IGF-1R heterotetramer/IGF1 0.002 0.085 -10000 0 -0.41 21 21
GRB2 0.013 0.022 -10000 0 -0.49 1 1
PDPK1 0.031 0.059 -10000 0 -0.57 1 1
YWHAE 0.014 0 -10000 0 -10000 0 0
PRKD1 0.031 0.071 -10000 0 -0.37 14 14
SHC1 0.009 0.049 -10000 0 -0.49 5 5
Arf6 downstream 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
PLAUR 0.016 0.12 -10000 0 -1.1 2 2
regulation of axonogenesis -0.005 0.069 -10000 0 -10000 0 0
myoblast fusion -0.004 0.06 0.41 2 -10000 0 2
mol:GTP -0.01 0.034 -10000 0 -0.23 2 2
regulation of calcium-dependent cell-cell adhesion -0.027 0.04 0.34 1 -10000 0 1
ARF1/GTP -0.006 0.022 -10000 0 -10000 0 0
mol:GM1 0.004 0.028 -10000 0 -0.17 2 2
mol:Choline -0.006 0.1 -10000 0 -0.32 45 45
lamellipodium assembly -0.016 0.055 -10000 0 -0.45 2 2
MAPK3 0.018 0.054 -10000 0 -0.33 2 2
ARF6/GTP/NME1/Tiam1 0.028 0.041 -10000 0 -0.34 1 1
ARF1 0.014 0 -10000 0 -10000 0 0
ARF6/GDP 0.004 0.06 -10000 0 -0.41 2 2
ARF1/GDP 0.013 0.055 -10000 0 -0.37 2 2
ARF6 0.008 0.02 -10000 0 -10000 0 0
RAB11A 0.014 0 -10000 0 -10000 0 0
TIAM1 0.014 0.027 -10000 0 -0.59 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.054 -10000 0 -0.33 2 2
actin filament bundle formation -0.013 0.055 0.37 2 -10000 0 2
KALRN -0.018 0.058 -10000 0 -0.24 19 19
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.055 -10000 0 -0.38 2 2
NME1 0.015 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.055 -10000 0 -0.38 2 2
substrate adhesion-dependent cell spreading -0.01 0.034 -10000 0 -0.23 2 2
cortical actin cytoskeleton organization -0.016 0.055 -10000 0 -0.45 2 2
RAC1 0.014 0 -10000 0 -10000 0 0
liver development -0.01 0.034 -10000 0 -0.23 2 2
ARF6/GTP -0.01 0.034 -10000 0 -0.23 2 2
RhoA/GTP -0.006 0.022 -10000 0 -10000 0 0
mol:GDP -0.016 0.054 -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 -0.019 0.11 -10000 0 -0.38 44 44
RAB11FIP3 0.014 0 -10000 0 -10000 0 0
tube morphogenesis -0.016 0.055 -10000 0 -0.45 2 2
ruffle organization 0.005 0.069 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.01 0.034 -10000 0 -0.23 2 2
PLD2 0.015 0.034 -10000 0 -0.4 1 1
PIP5K1A 0.005 0.069 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.006 0.1 -10000 0 -0.32 45 45
Rac1/GTP -0.016 0.055 -10000 0 -0.45 2 2
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 0.016 -10000 0 -0.34 1 1
BAD/BCL-XL/YWHAZ 0.036 0.012 -10000 0 -10000 0 0
CDKN1B 0.04 0.009 -10000 0 -10000 0 0
CDKN1A 0.008 0.088 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
FOXO3 0.04 0.009 -10000 0 -10000 0 0
AKT1 0 0.007 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
AKT3 0.013 0.061 -10000 0 -0.56 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.04 0.016 -10000 0 -10000 0 0
AKT1/ASK1 0.034 0.038 -10000 0 -0.4 1 1
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 0.004 0.033 0.38 1 -10000 0 1
TSC1 0.04 0.009 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
AKT1/RAF1 0.04 0.009 -10000 0 -10000 0 0
EP300 0.009 0.053 -10000 0 -0.59 4 4
mol:GDP 0.033 0.009 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.04 0.009 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.025 0.02 -10000 0 -0.3 2 2
MAP3K5 0.006 0.07 -10000 0 -0.59 7 7
MAPKAP1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.059 0.27 1 -10000 0 1
YWHAH -0.01 0.11 -10000 0 -0.49 25 25
AKT1S1 0.04 0.009 -10000 0 -10000 0 0
CASP9 0.04 0.014 -10000 0 -10000 0 0
YWHAB 0.014 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.047 0.008 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.022 -10000 0 -0.36 2 2
YWHAE 0.014 0 -10000 0 -10000 0 0
SRC 0.014 0 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.026 0.072 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.003 -10000 0 -10000 0 0
CHUK 0.04 0.009 -10000 0 -10000 0 0
BAD/BCL-XL 0.054 0.013 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.017 0.023 -10000 0 -0.35 2 2
FOXO1-3a-4/14-3-3 family 0.03 0.064 -10000 0 -0.29 1 1
PDPK1 0.012 0.038 -10000 0 -0.59 2 2
MDM2 0.039 0.018 -10000 0 -10000 0 0
MAPKKK cascade -0.039 0.008 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.05 0.035 -10000 0 -0.37 2 2
TSC1/TSC2 0.047 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.034 -10000 0 -0.35 2 2
glucose import -0.011 0.11 -10000 0 -0.29 71 71
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.034 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.11 -10000 0 -0.29 71 71
GSK3A 0.04 0.009 -10000 0 -10000 0 0
FOXO1 0.038 0.024 -10000 0 -10000 0 0
GSK3B 0.04 0.021 -10000 0 -0.41 1 1
SFN -0.11 0.23 -10000 0 -0.53 119 119
G1/S transition of mitotic cell cycle 0.046 0.02 -10000 0 -0.39 1 1
p27Kip1/14-3-3 family 0.006 0.085 -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 0.002 0.079 -10000 0 -0.49 13 13
RHEB 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.014 0 -9999 0 -10000 0 0
SMAD2 0.016 0.017 -9999 0 -0.25 1 1
SMAD3 0.044 0.018 -9999 0 -10000 0 0
SMAD3/SMAD4 0.05 0.01 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.014 -9999 0 -10000 0 0
PPM1A 0.014 0 -9999 0 -10000 0 0
CALM1 0.012 0.035 -9999 0 -0.54 2 2
SMAD2/SMAD4 0.023 0.015 -9999 0 -0.22 1 1
MAP3K1 0.007 0.058 -9999 0 -0.49 7 7
TRAP-1/SMAD4 -0.014 0.076 -9999 0 -0.43 17 17
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 0.044 -9999 0 -0.49 4 4
CTDSPL 0.013 0.027 -9999 0 -0.59 1 1
KPNB1 0.014 0 -9999 0 -10000 0 0
TGFBRAP1 -0.006 0.11 -9999 0 -0.59 17 17
UBE2I 0.014 0 -9999 0 -10000 0 0
NUP153 0.014 0 -9999 0 -10000 0 0
KPNA2 0.012 0.031 -9999 0 -0.49 2 2
PIAS4 0.014 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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
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 0.034 -9999 0 -0.47 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 -0.003 0.035 -9999 0 -0.36 5 5
RELB 0.009 0.052 -9999 0 -0.51 5 5
NFKB2 0.011 0.044 -9999 0 -0.56 3 3
NF kappa B2 p52/RelB -0.005 0.043 -9999 0 -0.36 7 7
regulation of B cell activation -0.005 0.043 -9999 0 -0.36 7 7
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 0.053 -10000 0 -0.59 4 4
mol:PIP3 0 0.018 0.29 1 -0.31 1 2
FRAP1 0.016 0.01 -10000 0 -10000 0 0
AKT1 0.03 0.026 0.23 1 -0.46 1 2
INSR 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.035 -10000 0 -0.35 5 5
mol:GTP -0.001 0.018 -10000 0 -0.37 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.007 -10000 0 -10000 0 0
TSC2 0.014 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.016 -10000 0 -0.34 1 1
TSC1 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.001 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.014 0 -10000 0 -10000 0 0
RPS6KB1 0.03 0.017 0.18 1 -0.28 1 2
MAP3K5 0.006 0.046 -10000 0 -0.39 7 7
PIK3R1 0.014 0 -10000 0 -10000 0 0
apoptosis 0.006 0.046 -10000 0 -0.39 7 7
mol:LY294002 0 0 0.001 1 -10000 0 1
EIF4B 0.036 0.016 -10000 0 -0.24 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.013 -10000 0 -0.22 1 1
eIF4E/eIF4G1/eIF4A1 -0.002 0.016 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.026 0.015 -10000 0 -0.31 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.034 0.014 0.17 1 -0.2 1 2
FKBP1A 0.014 0 -10000 0 -10000 0 0
RHEB/GTP -0.001 0.016 -10000 0 -0.34 1 1
mol:Amino Acids 0 0 0.001 1 -10000 0 1
FKBP12/Rapamycin 0.011 0.001 -10000 0 -10000 0 0
PDPK1 -0.001 0.03 0.24 1 -0.42 2 3
EIF4E 0.014 0 -10000 0 -10000 0 0
ASK1/PP5C 0.015 0.073 -10000 0 -0.6 7 7
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.001 0.019 -10000 0 -0.4 1 1
tumor necrosis factor receptor activity 0 0 -10000 0 -0.001 1 1
RPS6 0.013 0.022 -10000 0 -0.49 1 1
PPP5C 0.014 0 -10000 0 -10000 0 0
EIF4G1 0.014 0 -10000 0 -10000 0 0
IRS1 0.009 0.001 -10000 0 -10000 0 0
INS -0.005 0.056 -10000 0 -0.57 5 5
PTEN 0.012 0.027 -10000 0 -0.59 1 1
PDK2 -0.001 0.021 0.24 1 -0.28 2 3
EIF4EBP1 -0.004 0.13 -10000 0 -1.1 7 7
PIK3CA 0.013 0.027 -10000 0 -0.6 1 1
PPP2R5D 0.023 0.009 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.032 -10000 0 -0.31 5 5
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 -0.003 1 2
EEF2 0.016 0.032 -10000 0 -0.31 5 5
eIF4E/4E-BP1 0.005 0.12 -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 0.009 0.053 -9999 0 -0.59 4 4
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.032 0.016 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.002 0.021 -9999 0 -10000 0 0
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 0.031 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 0.033 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.031 0.028 -9999 0 -0.29 4 4
RANGAP1 0.014 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.004 0.034 -9999 0 -0.32 5 5
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.024 0 -9999 0 -10000 0 0
Ran/GTP 0.029 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.012 0.031 -9999 0 -0.49 2 2
UBE2I 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.013 0.027 -9999 0 -0.59 1 1
PIAS1 0.009 0.053 -9999 0 -0.59 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 0.009 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0.005 -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 0.001 -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 0.007 0.062 -9999 0 -0.52 7 7
CLTA 0.014 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.012 0.016 -9999 0 -0.35 1 1
mol:PI-4-5-P2 0 0.008 -9999 0 -10000 0 0
ARF1/GTP 0 0.004 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0.011 -9999 0 -0.22 1 1
mol:Choline 0 0.009 -9999 0 -0.2 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 0 0.009 -9999 0 -0.2 1 1
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 0.018 0 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.027 0.012 -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 0.028 0.003 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.002 -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 0.004 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.001 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.001 -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 0.02 -9999 0 -0.21 2 2
PLD2 0 0.009 -9999 0 -0.2 1 1
ARF-GAP1/v-SNARE 0.012 0.016 -9999 0 -0.35 1 1
PIP5K1A 0 0.009 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0.004 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0.009 -9999 0 -0.2 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.012 0.016 -9999 0 -0.35 1 1
GOSR2 0 0.004 -9999 0 -10000 0 0
USO1 0 0.004 -9999 0 -10000 0 0
GBF1 0 0.004 -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 -0.004 0.035 -9999 0 -0.3 7 7
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 516 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WY.A85E TCGA.WY.A85D TCGA.WY.A85C TCGA.WY.A85B
109_MAP3K5 0.059 -0.21 0.059 -0.21
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 0 -0.32 0
30_TGFB1/TGF beta receptor Type II 0.014 0.014 0.017 0.014
84_STAT5B 0.011 0.049 0.049 0.049
84_STAT5A 0.011 0.049 0.049 0.049
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/22309339/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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