PARADIGM pathway analysis of mRNASeq expression and copy number data
Thyroid Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1610ZS5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1610ZS5
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 34 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 247
Signaling events mediated by Stem cell factor receptor (c-Kit) 171
Signaling events regulated by Ret tyrosine kinase 144
Reelin signaling pathway 122
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 112
Wnt signaling 102
PDGFR-alpha signaling pathway 94
FOXA2 and FOXA3 transcription factor networks 91
Noncanonical Wnt signaling pathway 89
Nongenotropic Androgen signaling 88
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 501 . 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 ( 501 ).

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 0.4930 247 1732 7 -0.42 0 1000 -1000 -0.005 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3413 171 13374 78 -0.75 0.24 1000 -1000 -0.038 -1000
Signaling events regulated by Ret tyrosine kinase 0.2874 144 11818 82 -0.37 0.027 1000 -1000 -0.061 -1000
Reelin signaling pathway 0.2435 122 6849 56 -0.46 0.061 1000 -1000 -0.047 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2236 112 7636 68 -0.73 0.35 1000 -1000 -0.074 -1000
Wnt signaling 0.2036 102 718 7 -0.33 0.014 1000 -1000 -0.021 -1000
PDGFR-alpha signaling pathway 0.1876 94 4164 44 -0.4 0.043 1000 -1000 -0.034 -1000
FOXA2 and FOXA3 transcription factor networks 0.1816 91 4227 46 -0.84 0.031 1000 -1000 -0.066 -1000
Noncanonical Wnt signaling pathway 0.1776 89 2314 26 -0.33 0.027 1000 -1000 -0.042 -1000
Nongenotropic Androgen signaling 0.1756 88 4598 52 -0.26 0.19 1000 -1000 -0.032 -1000
Signaling events mediated by the Hedgehog family 0.1517 76 3971 52 -0.29 0.14 1000 -1000 -0.039 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1337 67 2292 34 -0.1 0.027 1000 -1000 -0.042 -1000
Calcium signaling in the CD4+ TCR pathway 0.1317 66 2074 31 -0.36 0.027 1000 -1000 -0.05 -1000
IGF1 pathway 0.1297 65 3731 57 -0.14 0.063 1000 -1000 -0.042 -1000
Endothelins 0.1257 63 6118 96 -0.32 0.029 1000 -1000 -0.046 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1238 62 3365 54 -0.46 0.039 1000 -1000 -0.065 -1000
IL4-mediated signaling events 0.1238 62 5688 91 -1.2 0.57 1000 -1000 -0.076 -1000
Glypican 1 network 0.1238 62 3016 48 -0.3 0.052 1000 -1000 -0.028 -1000
HIF-1-alpha transcription factor network 0.1138 57 4368 76 -0.49 0.041 1000 -1000 -0.062 -1000
Ephrin B reverse signaling 0.1058 53 2567 48 -0.24 0.12 1000 -1000 -0.041 -1000
IL23-mediated signaling events 0.1038 52 3136 60 -0.26 0.027 1000 -1000 -0.04 -1000
Coregulation of Androgen receptor activity 0.1018 51 3880 76 -0.68 0.076 1000 -1000 -0.017 -1000
Glucocorticoid receptor regulatory network 0.0978 49 5646 114 -0.45 0.26 1000 -1000 -0.053 -1000
BMP receptor signaling 0.0958 48 3966 81 -0.45 0.052 1000 -1000 -0.051 -1000
TCR signaling in naïve CD8+ T cells 0.0958 48 4494 93 -0.16 0.046 1000 -1000 -0.048 -1000
Arf6 signaling events 0.0918 46 2856 62 -0.26 0.061 1000 -1000 -0.036 -1000
EPHB forward signaling 0.0898 45 3867 85 -0.24 0.11 1000 -1000 -0.075 -1000
IL12-mediated signaling events 0.0818 41 3600 87 -0.36 0.029 1000 -1000 -0.068 -1000
Signaling mediated by p38-alpha and p38-beta 0.0778 39 1757 44 -0.22 0.027 1000 -1000 -0.028 -1000
Thromboxane A2 receptor signaling 0.0719 36 3849 105 -0.16 0.047 1000 -1000 -0.046 -1000
IL6-mediated signaling events 0.0639 32 2414 75 -0.15 0.054 1000 -1000 -0.038 -1000
Hedgehog signaling events mediated by Gli proteins 0.0619 31 2078 65 -0.58 0.064 1000 -1000 -0.045 -1000
EGFR-dependent Endothelin signaling events 0.0619 31 666 21 -0.076 0.038 1000 -1000 -0.048 -1000
Ras signaling in the CD4+ TCR pathway 0.0599 30 518 17 -0.1 0.041 1000 -1000 -0.022 -1000
Osteopontin-mediated events 0.0499 25 963 38 -0.15 0.043 1000 -1000 -0.04 -1000
Regulation of p38-alpha and p38-beta 0.0499 25 1393 54 -0.36 0.065 1000 -1000 -0.05 -1000
Regulation of Androgen receptor activity 0.0499 25 1800 70 -0.45 0.036 1000 -1000 -0.061 -1000
ErbB2/ErbB3 signaling events 0.0479 24 1594 65 -0.17 0.037 1000 -1000 -0.052 -1000
Syndecan-1-mediated signaling events 0.0479 24 830 34 -0.079 0.027 1000 -1000 -0.048 -1000
FAS signaling pathway (CD95) 0.0479 24 1167 47 -0.2 0.042 1000 -1000 -0.03 -1000
Plasma membrane estrogen receptor signaling 0.0479 24 2130 86 -0.14 0.049 1000 -1000 -0.059 -1000
BCR signaling pathway 0.0459 23 2306 99 -0.1 0.048 1000 -1000 -0.057 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0439 22 1897 85 -0.22 0.14 1000 -1000 -0.045 -1000
Syndecan-4-mediated signaling events 0.0439 22 1512 67 -0.16 0.039 1000 -1000 -0.051 -1000
IFN-gamma pathway 0.0419 21 1430 68 -0.17 0.035 1000 -1000 -0.055 -1000
LPA receptor mediated events 0.0419 21 2193 102 -0.15 0.035 1000 -1000 -0.069 -1000
Ceramide signaling pathway 0.0399 20 1549 76 -0.15 0.075 1000 -1000 -0.033 -1000
Signaling events mediated by PRL 0.0399 20 685 34 -0.087 0.04 1000 -1000 -0.04 -1000
Fc-epsilon receptor I signaling in mast cells 0.0379 19 1904 97 -0.15 0.044 1000 -1000 -0.055 -1000
Integrins in angiogenesis 0.0359 18 1515 84 -0.14 0.056 1000 -1000 -0.045 -1000
IL27-mediated signaling events 0.0359 18 943 51 -0.11 0.045 1000 -1000 -0.058 -1000
Insulin Pathway 0.0359 18 1339 74 -0.054 0.065 1000 -1000 -0.045 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0359 18 1649 88 -0.26 0.039 1000 -1000 -0.062 -1000
ceramide signaling pathway 0.0339 17 862 49 -0.055 0.039 1000 -1000 -0.034 -1000
Signaling events mediated by PTP1B 0.0319 16 1274 76 -0.19 0.039 1000 -1000 -0.033 -1000
amb2 Integrin signaling 0.0319 16 1345 82 -0.19 0.035 1000 -1000 -0.032 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0319 16 848 52 -0.18 0.057 1000 -1000 -0.037 -1000
mTOR signaling pathway 0.0299 15 799 53 -0.042 0.03 1000 -1000 -0.04 -1000
VEGFR1 specific signals 0.0299 15 881 56 -0.045 0.058 1000 -1000 -0.051 -1000
FOXM1 transcription factor network 0.0299 15 791 51 -0.22 0.052 1000 -1000 -0.069 -1000
LPA4-mediated signaling events 0.0279 14 178 12 -0.054 0.004 1000 -1000 -0.023 -1000
Regulation of nuclear SMAD2/3 signaling 0.0279 14 1984 136 -0.26 0.053 1000 -1000 -0.03 -1000
Visual signal transduction: Cones 0.0279 14 550 38 -0.043 0.042 1000 -1000 -0.017 -1000
JNK signaling in the CD4+ TCR pathway 0.0279 14 247 17 -0.084 0.026 1000 -1000 -0.032 -1000
p75(NTR)-mediated signaling 0.0279 14 1791 125 -0.28 0.071 1000 -1000 -0.064 -1000
Caspase cascade in apoptosis 0.0259 13 975 74 -0.056 0.046 1000 -1000 -0.043 -1000
Nectin adhesion pathway 0.0259 13 866 63 -0.11 0.073 1000 -1000 -0.048 -1000
Signaling events mediated by HDAC Class III 0.0259 13 557 40 -0.28 0.046 1000 -1000 -0.02 -1000
IL1-mediated signaling events 0.0259 13 838 62 -0.077 0.062 1000 -1000 -0.044 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0259 13 587 45 -0.056 0.076 1000 -1000 -0.051 -1000
Rapid glucocorticoid signaling 0.0259 13 266 20 -0.061 0.034 1000 -1000 -0.01 -1000
Presenilin action in Notch and Wnt signaling 0.0240 12 755 61 -0.15 0.07 1000 -1000 -0.051 -1000
IL2 signaling events mediated by PI3K 0.0240 12 751 58 -0.059 0.048 1000 -1000 -0.033 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0240 12 1542 120 -0.24 0.074 1000 -1000 -0.054 -1000
Cellular roles of Anthrax toxin 0.0220 11 458 39 -0.056 0.027 1000 -1000 -0.025 -1000
Syndecan-3-mediated signaling events 0.0220 11 393 35 -0.11 0.07 1000 -1000 -0.031 -1000
Visual signal transduction: Rods 0.0220 11 596 52 -0.073 0.046 1000 -1000 -0.03 -1000
ErbB4 signaling events 0.0200 10 738 69 -0.052 0.037 1000 -1000 -0.055 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0200 10 300 28 -0.14 0.056 1000 -1000 -0.022 -1000
Syndecan-2-mediated signaling events 0.0200 10 704 69 -0.16 0.05 1000 -1000 -0.032 -1000
S1P1 pathway 0.0200 10 379 36 -0.054 0.027 1000 -1000 -0.036 -1000
TCGA08_rtk_signaling 0.0200 10 261 26 -0.18 0.045 1000 -1000 -0.008 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0200 10 748 74 -0.13 0.068 1000 -1000 -0.069 -1000
BARD1 signaling events 0.0180 9 544 57 -0.04 0.051 1000 -1000 -0.05 -1000
TCGA08_p53 0.0180 9 67 7 -0.025 0.025 1000 -1000 -0.008 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0160 8 668 83 -0.17 0.05 1000 -1000 -0.035 -1000
Retinoic acid receptors-mediated signaling 0.0160 8 506 58 -0.037 0.054 1000 -1000 -0.049 -1000
Class I PI3K signaling events 0.0160 8 594 73 -0.19 0.05 1000 -1000 -0.038 -1000
Regulation of Telomerase 0.0160 8 866 102 -0.19 0.071 1000 -1000 -0.041 -1000
S1P3 pathway 0.0160 8 363 42 -0.14 0.048 1000 -1000 -0.039 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0140 7 246 33 -0.11 0.055 1000 -1000 -0.04 -1000
Class IB PI3K non-lipid kinase events 0.0140 7 21 3 -0.015 0.015 1000 -1000 -0.005 -1000
a4b1 and a4b7 Integrin signaling 0.0120 6 32 5 0.004 0.034 1000 -1000 -0.001 -1000
PLK1 signaling events 0.0120 6 538 85 -0.006 0.049 1000 -1000 -0.038 -1000
IL2 signaling events mediated by STAT5 0.0120 6 134 22 -0.033 0.033 1000 -1000 -0.043 -1000
TCGA08_retinoblastoma 0.0120 6 54 8 -0.035 0.031 1000 -1000 -0.003 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0100 5 656 125 -0.008 0.07 1000 -1000 -0.053 -1000
PDGFR-beta signaling pathway 0.0100 5 494 97 -0.15 0.079 1000 -1000 -0.053 -1000
Aurora B signaling 0.0100 5 384 67 -0.32 0.1 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 0.0080 4 150 32 -0.085 0.05 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 0.0080 4 291 68 -0.085 0.05 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class I 0.0080 4 510 104 -0.056 0.063 1000 -1000 -0.029 -1000
Atypical NF-kappaB pathway 0.0080 4 128 31 -0.018 0.04 1000 -1000 -0.027 -1000
Canonical Wnt signaling pathway 0.0080 4 226 51 -0.037 0.065 1000 -1000 -0.051 -1000
Effects of Botulinum toxin 0.0080 4 125 26 -0.067 0.048 1000 -1000 -0.015 -1000
S1P4 pathway 0.0080 4 122 25 -0.003 0.047 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0060 3 71 23 -0.016 0.049 1000 -1000 -0.028 -1000
Canonical NF-kappaB pathway 0.0060 3 149 39 -0.056 0.061 1000 -1000 -0.035 -1000
Circadian rhythm pathway 0.0060 3 81 22 -0.017 0.04 1000 -1000 -0.032 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0060 3 137 37 0 0.063 1000 -1000 -0.034 -1000
S1P5 pathway 0.0060 3 56 17 -0.007 0.032 1000 -1000 -0.018 -1000
HIF-2-alpha transcription factor network 0.0060 3 132 43 -0.16 0.16 1000 -1000 -0.048 -1000
FoxO family signaling 0.0060 3 245 64 -0.085 0.1 1000 -1000 -0.058 -1000
Signaling mediated by p38-gamma and p38-delta 0.0060 3 53 15 -0.005 0.027 1000 -1000 -0.029 -1000
E-cadherin signaling in keratinocytes 0.0060 3 146 43 -0.03 0.051 1000 -1000 -0.038 -1000
p38 MAPK signaling pathway 0.0060 3 168 44 -0.032 0.049 1000 -1000 -0.026 -1000
Aurora A signaling 0.0040 2 128 60 -0.025 0.055 1000 -1000 -0.025 -1000
EPO signaling pathway 0.0040 2 162 55 -0.015 0.059 1000 -1000 -0.033 -1000
TRAIL signaling pathway 0.0040 2 109 48 -0.014 0.074 1000 -1000 -0.041 -1000
Paxillin-dependent events mediated by a4b1 0.0040 2 98 36 -0.053 0.055 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class II 0.0020 1 87 75 -0.036 0.074 1000 -1000 -0.03 -1000
E-cadherin signaling in the nascent adherens junction 0.0020 1 135 76 -0.059 0.066 1000 -1000 -0.067 -1000
Arf6 trafficking events 0.0020 1 84 71 -0.048 0.05 1000 -1000 -0.039 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.016 0.027 1000 -1000 -0.015 -1000
Arf6 downstream pathway 0.0000 0 9 43 -0.061 0.045 1000 -1000 -0.032 -1000
Aurora C signaling 0.0000 0 4 7 -0.007 0.046 1000 -1000 -0.016 -1000
Glypican 2 network 0.0000 0 3 4 -0.02 0.016 1000 -1000 0.002 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 14 27 0 0.066 1000 -1000 -0.037 -1000
E-cadherin signaling events 0.0000 0 0 5 0.026 0.051 1000 -1000 0.002 -1000
Arf1 pathway 0.0000 0 24 54 -0.001 0.052 1000 -1000 -0.022 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.072 1000 -1000 -0.003 -1000
Total NA 3450 199224 7203 -22 8.1 131000 -131000 -5.1 -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 -0.32 0.26 -9999 0 -0.48 339 339
EFNA5 -0.071 0.24 -9999 0 -0.67 69 69
FYN -0.3 0.24 -9999 0 -0.45 333 333
neuron projection morphogenesis -0.32 0.26 -9999 0 -0.48 339 339
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.32 0.26 -9999 0 -0.48 339 339
EPHA5 -0.42 0.33 -9999 0 -0.67 313 313
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.22 0.21 0.38 1 -0.39 279 280
CRKL -0.23 0.22 -10000 0 -0.41 285 285
HRAS -0.2 0.19 -10000 0 -0.36 231 231
mol:PIP3 -0.2 0.2 -10000 0 -0.39 259 259
SPRED1 0.027 0.004 -10000 0 -10000 0 0
SPRED2 0.025 0.032 -10000 0 -0.67 1 1
GAB1 -0.24 0.24 -10000 0 -0.44 286 286
FOXO3 -0.19 0.21 0.37 2 -0.37 272 274
AKT1 -0.21 0.22 0.29 2 -0.39 278 280
BAD -0.19 0.2 0.28 2 -0.37 270 272
megakaryocyte differentiation -0.24 0.23 -10000 0 -0.43 295 295
GSK3B -0.19 0.21 0.32 2 -0.37 271 273
RAF1 -0.16 0.16 0.35 1 -0.34 86 87
SHC1 0.025 0.008 -10000 0 -10000 0 0
STAT3 -0.24 0.23 -10000 0 -0.44 281 281
STAT1 -0.6 0.56 -10000 0 -1.1 289 289
HRAS/SPRED1 -0.16 0.16 -10000 0 -0.34 91 91
cell proliferation -0.24 0.24 -10000 0 -0.44 289 289
PIK3CA 0.022 0.055 -10000 0 -0.68 3 3
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.23 -10000 0 -0.42 286 286
HRAS/SPRED2 -0.16 0.16 -10000 0 -0.35 72 72
LYN/TEC/p62DOK -0.21 0.24 -10000 0 -0.41 284 284
MAPK3 -0.11 0.12 0.26 5 -0.29 19 24
STAP1 -0.25 0.24 -10000 0 -0.44 287 287
GRAP2 -0.02 0.15 -10000 0 -0.56 33 33
JAK2 -0.5 0.48 -10000 0 -0.89 289 289
STAT1 (dimer) -0.58 0.54 -10000 0 -1 289 289
mol:Gleevec 0.008 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.21 0.24 -10000 0 -0.42 269 269
actin filament polymerization -0.24 0.23 -10000 0 -0.43 284 284
LYN 0.027 0.005 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.32 0.35 1 -0.61 287 288
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.19 0.21 -10000 0 -0.38 270 270
PI3K -0.21 0.24 -10000 0 -0.41 283 283
PTEN 0.026 0.018 -10000 0 -0.36 1 1
SCF/KIT/EPO/EPOR -0.71 0.66 -10000 0 -1.3 287 287
MAPK8 -0.25 0.24 -10000 0 -0.44 289 289
STAT3 (dimer) -0.23 0.23 -10000 0 -0.43 280 280
positive regulation of transcription -0.086 0.11 0.3 7 -0.24 18 25
mol:GDP -0.2 0.2 -10000 0 -0.38 240 240
PIK3C2B -0.23 0.23 -10000 0 -0.43 279 279
CBL/CRKL -0.21 0.22 -10000 0 -0.39 283 283
FER -0.24 0.24 -10000 0 -0.44 285 285
SH2B3 -0.24 0.23 -10000 0 -0.44 287 287
PDPK1 -0.19 0.2 0.3 3 -0.36 253 256
SNAI2 -0.24 0.24 -10000 0 -0.44 286 286
positive regulation of cell proliferation -0.42 0.4 -10000 0 -0.74 289 289
KITLG -0.018 0.094 -10000 0 -0.71 8 8
cell motility -0.42 0.4 -10000 0 -0.74 289 289
PTPN6 0.039 0.014 -10000 0 -10000 0 0
EPOR -0.16 0.19 -10000 0 -0.87 9 9
STAT5A (dimer) -0.34 0.33 -10000 0 -0.61 287 287
SOCS1 0.023 0.035 -10000 0 -0.67 1 1
cell migration 0.24 0.23 0.43 281 -10000 0 281
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO -0.008 0.031 -10000 0 -10000 0 0
VAV1 0.011 0.061 -10000 0 -0.57 3 3
GRB10 -0.24 0.23 -10000 0 -0.44 284 284
PTPN11 0.034 0.033 -10000 0 -0.66 1 1
SCF/KIT -0.25 0.25 -10000 0 -0.46 287 287
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.13 0.13 0.27 3 -0.3 30 33
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.75 0.68 -10000 0 -1.3 287 287
MAP2K2 -0.12 0.13 0.28 2 -0.31 25 27
SHC/Grb2/SOS1 -0.2 0.23 -10000 0 -0.42 249 249
STAT5A -0.35 0.34 -10000 0 -0.63 287 287
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.24 0.24 -10000 0 -0.43 286 286
SHC/GRAP2 -0.001 0.11 -10000 0 -0.39 33 33
PTPRO -0.25 0.23 -10000 0 -0.44 295 295
SH2B2 -0.24 0.23 -10000 0 -0.44 284 284
DOK1 0.027 0.005 -10000 0 -10000 0 0
MATK -0.24 0.23 -10000 0 -0.44 280 280
CREBBP -0.043 0.077 -10000 0 -10000 0 0
BCL2 -0.22 0.4 -10000 0 -1.5 42 42
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.061 0.097 -10000 0 -0.67 6 6
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 254 254
JUN -0.26 0.26 -10000 0 -0.56 165 165
HRAS 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.26 0.29 -10000 0 -0.49 287 287
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.26 0.29 -10000 0 -0.49 290 290
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.2 0.22 -10000 0 -0.41 265 265
RHOA 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.26 -10000 0 -0.44 285 285
GRB7 0.001 0.056 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.26 0.29 -10000 0 -0.49 283 283
MAPKKK cascade -0.23 0.24 -10000 0 -0.42 282 282
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.25 0.27 -10000 0 -0.46 289 289
lamellipodium assembly -0.19 0.18 -10000 0 -0.35 258 258
RET51/GFRalpha1/GDNF/SHC -0.26 0.29 -10000 0 -0.49 277 277
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
RET9/GFRalpha1/GDNF/SHC -0.2 0.22 -10000 0 -0.39 271 271
RET9/GFRalpha1/GDNF/Shank3 -0.21 0.21 -10000 0 -0.4 276 276
MAPK3 -0.24 0.23 -10000 0 -0.42 282 282
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.083 0.26 -10000 0 -0.67 78 78
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.26 0.25 -10000 0 -0.53 168 168
DOK5 -0.067 0.24 -10000 0 -0.67 67 67
GFRA1 -0.37 0.34 -10000 0 -0.67 281 281
MAPK8 -0.2 0.2 -10000 0 -0.36 242 242
HRAS/GTP -0.26 0.28 -10000 0 -0.47 289 289
tube development -0.19 0.2 -10000 0 -0.38 258 258
MAPK1 -0.24 0.23 0.32 3 -0.42 284 287
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 258 258
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PDLIM7 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.3 0.34 -10000 0 -0.54 300 300
SHC1 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.26 0.29 -10000 0 -0.49 289 289
RET51/GFRalpha1/GDNF/Dok5 -0.31 0.34 -10000 0 -0.55 303 303
PRKCA 0.002 0.13 -10000 0 -0.67 17 17
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
CREB1 -0.19 0.21 -10000 0 -0.38 254 254
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.14 0.16 -10000 0 -0.29 242 242
RET51/GFRalpha1/GDNF/Grb7 -0.27 0.29 -10000 0 -0.49 287 287
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.1 0.26 -10000 0 -0.66 85 85
DOK4 0.026 0.009 -10000 0 -10000 0 0
JNK cascade -0.25 0.25 -10000 0 -0.56 156 156
RET9/GFRalpha1/GDNF/FRS2 -0.2 0.22 -10000 0 -0.4 272 272
SHANK3 0.02 0.013 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 243 243
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.35 286 286
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.21 -10000 0 -0.35 291 291
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.4 276 276
PI3K -0.3 0.29 -10000 0 -0.55 260 260
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.19 0.21 -10000 0 -0.38 258 258
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.32 267 267
RET51/GFRalpha1/GDNF/FRS2 -0.26 0.29 -10000 0 -0.49 290 290
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.26 -10000 0 -0.4 274 274
RET51/GFRalpha1/GDNF/PKC alpha -0.27 0.3 -10000 0 -0.5 288 288
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GDNF -0.007 0.024 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.31 0.32 -10000 0 -0.54 304 304
Rac1/GTP -0.23 0.22 -10000 0 -0.42 258 258
RET9/GFRalpha1/GDNF -0.23 0.23 -10000 0 -0.44 279 279
GFRalpha1/GDNF -0.27 0.27 -10000 0 -0.5 279 279
Reelin signaling pathway

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
CDK5R1/CDK5 0.037 0.015 -10000 0 -10000 0 0
VLDLR -0.004 0.14 -10000 0 -0.66 21 21
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ITGA3 0.025 0.015 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.3 0.23 -10000 0 -0.45 351 351
MAPK8IP1/MKK7/MAP3K11/JNK1 0.061 0.067 -10000 0 -0.38 9 9
AKT1 -0.2 0.15 -10000 0 -0.3 336 336
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.023 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.28 0.22 -10000 0 -0.42 340 340
LRPAP1/LRP8 0.017 0.11 -10000 0 -0.51 20 20
RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 339 339
DAB1/alpha3/beta1 Integrin -0.25 0.21 -10000 0 -0.39 311 311
long-term memory -0.26 0.23 -10000 0 -0.4 339 339
DAB1/LIS1 -0.26 0.22 -10000 0 -0.4 331 331
DAB1/CRLK/C3G -0.25 0.21 -10000 0 -0.39 288 288
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DAB1/NCK2 -0.26 0.22 -10000 0 -0.4 338 338
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.001 0.12 -10000 0 -0.67 16 16
CDK5R1 0.025 0.014 -10000 0 -10000 0 0
RELN -0.46 0.32 -10000 0 -0.67 343 343
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.3 0.24 -10000 0 -0.45 347 347
GRIN2A/RELN/LRP8/DAB1/Fyn -0.27 0.24 -10000 0 -0.42 339 339
MAPK8 0.013 0.095 -10000 0 -0.64 10 10
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.42 342 342
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.41 341 341
RELN/LRP8 -0.3 0.24 -10000 0 -0.46 339 339
GRIN2B/RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.41 339 339
PI3K 0.036 0.043 -10000 0 -0.51 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.015 -10000 0 -10000 0 0
RAP1A -0.24 0.2 0.49 3 -0.67 25 28
PAFAH1B1 0.026 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.019 -10000 0 -10000 0 0
GRIN2B -0.005 0.02 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
neuron differentiation -0.14 0.13 -10000 0 -0.43 37 37
neuron adhesion -0.22 0.21 0.44 10 -0.64 25 35
LRP8 -0.002 0.14 -10000 0 -0.67 20 20
GSK3B -0.19 0.14 -10000 0 -0.43 31 31
RELN/VLDLR/DAB1/Fyn -0.26 0.21 -10000 0 -0.4 340 340
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.31 340 340
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.052 0.17 0.82 20 -0.61 3 23
neuron migration -0.26 0.19 -10000 0 -0.41 171 171
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.43 37 37
RELN/VLDLR -0.29 0.24 -10000 0 -0.43 342 342
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.011 0.11 -10000 0 -0.41 20 20
NFATC2 -0.23 0.33 -10000 0 -0.72 126 126
NFATC3 -0.083 0.14 -10000 0 -0.29 96 96
CD40LG -0.63 0.55 -10000 0 -1.1 275 275
ITCH 0.038 0.016 -10000 0 -10000 0 0
CBLB 0.039 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.46 0.52 -10000 0 -1.2 132 132
JUNB 0.02 0.057 -10000 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.042 0.018 -10000 0 -0.32 1 1
T cell anergy 0.007 0.073 0.4 5 -0.47 1 6
TLE4 -0.22 0.36 -10000 0 -0.8 110 110
Jun/NFAT1-c-4/p21SNFT -0.56 0.58 -10000 0 -1.1 238 238
AP-1/NFAT1-c-4 -0.72 0.73 -10000 0 -1.3 263 263
IKZF1 -0.17 0.28 -10000 0 -0.67 80 80
T-helper 2 cell differentiation -0.28 0.33 -10000 0 -0.85 96 96
AP-1/NFAT1 -0.32 0.41 -10000 0 -0.73 209 209
CALM1 0.038 0.012 -10000 0 -0.19 1 1
EGR2 -0.73 0.78 -10000 0 -1.5 237 237
EGR3 -0.53 0.68 -10000 0 -1.5 135 135
NFAT1/FOXP3 -0.17 0.28 -10000 0 -0.58 131 131
EGR1 -0.12 0.28 -10000 0 -0.68 101 101
JUN -0.14 0.28 -10000 0 -0.67 108 108
EGR4 -0.016 0.15 -10000 0 -0.66 24 24
mol:Ca2+ 0.012 0.009 -10000 0 -10000 0 0
GBP3 -0.16 0.26 -10000 0 -0.59 101 101
FOSL1 0.005 0.055 -10000 0 -0.36 1 1
NFAT1-c-4/MAF/IRF4 -0.49 0.55 -10000 0 -0.99 241 241
DGKA -0.16 0.25 -10000 0 -0.6 84 84
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.5 0.55 -10000 0 -1 242 242
CTLA4 -0.2 0.31 -10000 0 -0.7 104 104
NFAT1-c-4 (dimer)/EGR1 -0.56 0.63 -10000 0 -1.1 235 235
NFAT1-c-4 (dimer)/EGR4 -0.52 0.55 -10000 0 -1 242 242
FOS -0.16 0.3 -10000 0 -0.68 125 125
IFNG -0.38 0.5 -10000 0 -1.1 127 127
T cell activation -0.39 0.39 0.42 1 -0.83 185 186
MAF 0.026 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.35 0.4 0.73 229 -10000 0 229
TNF -0.55 0.54 -10000 0 -1 256 256
FASLG -0.7 0.75 -10000 0 -1.4 249 249
TBX21 -0.02 0.15 -10000 0 -0.69 22 22
BATF3 0.018 0.043 -10000 0 -0.67 1 1
PRKCQ 0.017 0.074 -10000 0 -0.62 6 6
PTPN1 -0.16 0.25 -10000 0 -0.63 76 76
NFAT1-c-4/ICER1 -0.49 0.54 -10000 0 -1 238 238
GATA3 -0.007 0.15 -10000 0 -0.64 25 25
T-helper 1 cell differentiation -0.36 0.48 -10000 0 -1.1 127 127
IL2RA -0.42 0.46 -10000 0 -1.1 132 132
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.16 0.25 -10000 0 -0.62 77 77
E2F1 -0.013 0.07 -10000 0 -10000 0 0
PPARG 0.016 0.083 -10000 0 -0.67 7 7
SLC3A2 -0.16 0.25 -10000 0 -0.62 76 76
IRF4 -0.048 0.18 -10000 0 -0.66 37 37
PTGS2 -0.61 0.54 0.51 1 -1.1 258 259
CSF2 -0.62 0.52 -10000 0 -1.1 262 262
JunB/Fra1/NFAT1-c-4 -0.46 0.53 -10000 0 -0.97 233 233
IL4 -0.3 0.35 -10000 0 -0.92 92 92
IL5 -0.6 0.52 -10000 0 -1 261 261
IL2 -0.4 0.4 0.42 1 -0.85 184 185
IL3 -0.071 0.089 -10000 0 -0.86 2 2
RNF128 0.035 0.037 -10000 0 -0.75 1 1
NFATC1 -0.35 0.41 -10000 0 -0.74 229 229
CDK4 0.24 0.25 0.58 100 -10000 0 100
PTPRK -0.16 0.25 -10000 0 -0.56 108 108
IL8 -0.61 0.53 0.51 1 -1 264 265
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.23 0.24 -9999 0 -0.4 301 301
FZD6 0.027 0.005 -9999 0 -10000 0 0
WNT6 0.02 0.027 -9999 0 -10000 0 0
WNT4 -0.19 0.32 -9999 0 -0.67 156 156
FZD3 0.027 0.005 -9999 0 -10000 0 0
WNT5A 0.014 0.094 -9999 0 -0.67 9 9
WNT11 -0.33 0.35 -9999 0 -0.67 252 252
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.2 0.32 -10000 0 -0.69 149 149
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.5 148 148
positive regulation of JUN kinase activity -0.072 0.2 -10000 0 -0.4 129 129
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.14 0.24 -10000 0 -0.52 147 147
AP1 -0.4 0.54 -10000 0 -1.2 135 135
mol:IP3 -0.16 0.24 -10000 0 -0.53 147 147
PLCG1 -0.16 0.24 -10000 0 -0.53 147 147
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.51 149 149
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.52 147 147
CAV3 -0.011 0.019 -10000 0 -10000 0 0
CAV1 0.014 0.094 -10000 0 -0.67 9 9
SHC/Grb2/SOS1 -0.072 0.2 -10000 0 -0.4 129 129
PDGF/PDGFRA/Shf -0.14 0.24 -10000 0 -0.51 148 148
FOS -0.39 0.52 0.31 1 -1.2 135 136
JUN -0.15 0.22 -10000 0 -0.57 106 106
oligodendrocyte development -0.14 0.25 -10000 0 -0.51 149 149
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.53 147 147
PDGF/PDGFRA -0.2 0.32 -10000 0 -0.69 149 149
actin cytoskeleton reorganization -0.13 0.24 -10000 0 -0.5 148 148
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
PI3K -0.095 0.22 -10000 0 -0.43 148 148
PDGF/PDGFRA/Crk/C3G -0.094 0.22 -10000 0 -0.43 140 140
JAK1 -0.15 0.24 -10000 0 -0.51 148 148
ELK1/SRF -0.12 0.19 0.32 1 -0.41 141 142
SHB 0.025 0.007 -10000 0 -10000 0 0
SHF 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.043 0.024 -10000 0 -10000 0 0
GO:0007205 -0.17 0.25 -10000 0 -0.54 148 148
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.072 0.2 -10000 0 -0.4 129 129
PDGF/PDGFRA/SHB -0.14 0.24 -10000 0 -0.5 148 148
PDGF/PDGFRA/Caveolin-1 -0.14 0.26 -10000 0 -0.52 150 150
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
ELK1 -0.16 0.22 -10000 0 -0.49 145 145
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PDGF/PDGFRA/Crk -0.13 0.24 -10000 0 -0.5 146 146
JAK-STAT cascade -0.15 0.24 -10000 0 -0.51 148 148
cell proliferation -0.13 0.24 -10000 0 -0.51 148 148
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.47 0.49 -10000 0 -0.97 204 204
PCK1 -0.3 0.44 -10000 0 -1.4 59 59
HNF4A -0.61 0.6 -10000 0 -1.2 234 234
KCNJ11 -0.45 0.47 -10000 0 -1 171 171
AKT1 -0.065 0.14 -10000 0 -0.45 12 12
response to starvation -0.018 0.042 -10000 0 -0.49 2 2
DLK1 -0.45 0.47 -10000 0 -0.99 179 179
NKX2-1 -0.18 0.19 0.29 1 -0.39 176 177
ACADM -0.47 0.48 -10000 0 -0.94 217 217
TAT -0.18 0.2 -10000 0 -0.69 1 1
CEBPB 0.027 0.005 -10000 0 -10000 0 0
CEBPA 0.019 0.07 -10000 0 -0.67 5 5
TTR -0.14 0.22 0.68 6 -0.76 21 27
PKLR -0.46 0.48 -10000 0 -0.96 203 203
APOA1 -0.84 0.83 -10000 0 -1.7 234 234
CPT1C -0.47 0.49 -10000 0 -0.97 210 210
ALAS1 -0.16 0.19 -10000 0 -0.63 1 1
TFRC -0.23 0.27 -10000 0 -0.88 18 18
FOXF1 0.02 0.063 -10000 0 -0.67 4 4
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.028 0.008 -10000 0 -10000 0 0
CPT1A -0.47 0.48 -10000 0 -1 192 192
HMGCS1 -0.47 0.48 -10000 0 -1 168 168
NR3C1 0.031 0.012 -10000 0 -10000 0 0
CPT1B -0.47 0.48 -10000 0 -0.96 209 209
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
GCK -0.59 0.62 -10000 0 -1.2 220 220
CREB1 0.009 0.066 -10000 0 -0.24 16 16
IGFBP1 -0.16 0.18 -10000 0 -10000 0 0
PDX1 -0.18 0.19 -10000 0 -0.61 3 3
UCP2 -0.47 0.48 -10000 0 -1 192 192
ALDOB -0.44 0.47 -10000 0 -1 170 170
AFP -0.017 0.085 -10000 0 -10000 0 0
BDH1 -0.47 0.48 -10000 0 -1 189 189
HADH -0.44 0.47 -10000 0 -1 170 170
F2 -0.58 0.58 -10000 0 -1.2 215 215
HNF1A 0.028 0.008 -10000 0 -10000 0 0
G6PC -0.001 0.067 -10000 0 -10000 0 0
SLC2A2 -0.22 0.23 -10000 0 -0.56 1 1
INS -0.025 0.053 -10000 0 -0.68 3 3
FOXA1 -0.009 0.096 -10000 0 -0.32 28 28
FOXA3 -0.027 0.12 -10000 0 -0.39 18 18
FOXA2 -0.5 0.54 -10000 0 -1.1 194 194
ABCC8 -0.7 0.66 -10000 0 -1.3 251 251
ALB -0.058 0.27 -10000 0 -1.1 30 30
Noncanonical Wnt signaling pathway

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
NFATC2 -0.092 0.26 -10000 0 -0.67 84 84
GNB1/GNG2 -0.2 0.23 -10000 0 -0.53 115 115
mol:DAG -0.19 0.2 -10000 0 -0.49 112 112
PLCG1 -0.19 0.21 -10000 0 -0.51 112 112
YES1 -0.22 0.22 -10000 0 -0.53 121 121
FZD3 0.027 0.005 -10000 0 -10000 0 0
FZD6 0.027 0.005 -10000 0 -10000 0 0
G protein -0.19 0.22 -10000 0 -0.51 112 112
MAP3K7 -0.16 0.17 0.28 2 -0.42 109 111
mol:Ca2+ -0.18 0.2 -10000 0 -0.47 112 112
mol:IP3 -0.19 0.2 -10000 0 -0.49 112 112
NLK 0 0.054 -10000 0 -0.81 2 2
GNB1 0.026 0.006 -10000 0 -10000 0 0
CAMK2A -0.17 0.19 0.29 2 -0.45 110 112
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.23 0.24 -10000 0 -0.4 301 301
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.22 0.22 -10000 0 -0.53 121 121
GO:0007205 -0.18 0.2 -10000 0 -0.48 112 112
WNT6 0.02 0.027 -10000 0 -10000 0 0
WNT4 -0.19 0.32 -10000 0 -0.67 156 156
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.55 141 141
GNG2 0.025 0.032 -10000 0 -0.67 1 1
WNT5A 0.014 0.094 -10000 0 -0.67 9 9
WNT11 -0.33 0.35 -10000 0 -0.67 252 252
CDC42 -0.2 0.21 -10000 0 -0.51 116 116
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.14 0.22 -10000 0 -0.4 199 199
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.29 200 200
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.009 0.061 -10000 0 -0.44 9 9
PELP1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.2 0.45 5 -0.37 195 200
T-DHT/AR -0.2 0.26 -10000 0 -0.5 206 206
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.005 128 128
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.68 1 1
mol:GDP -0.21 0.26 -10000 0 -0.52 203 203
cell proliferation -0.2 0.26 0.46 11 -0.51 149 160
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
FOS -0.26 0.37 0.45 9 -0.79 145 154
mol:Ca2+ -0.026 0.029 -10000 0 -0.066 105 105
MAPK3 -0.16 0.24 0.5 12 -0.49 99 111
MAPK1 -0.18 0.22 0.31 4 -0.42 173 177
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 128 128
cAMP biosynthetic process 0.016 0.071 0.26 10 -0.41 9 19
GNG2 0.025 0.032 -10000 0 -0.67 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 128 128
HRAS/GTP -0.14 0.2 -10000 0 -0.38 195 195
actin cytoskeleton reorganization 0.037 0.033 -10000 0 -0.36 3 3
SRC 0.026 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 128 128
PI3K 0.033 0.038 -10000 0 -0.44 3 3
apoptosis 0.19 0.25 0.51 151 -0.41 7 158
T-DHT/AR/PELP1 -0.16 0.23 -10000 0 -0.44 204 204
HRAS/GDP -0.2 0.26 -10000 0 -0.5 202 202
CREB1 -0.21 0.27 0.42 7 -0.56 151 158
RAC1-CDC42/GTP 0.047 0.035 -10000 0 -0.37 3 3
AR -0.26 0.34 -10000 0 -0.67 206 206
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.5 6 -0.38 195 201
RAC1-CDC42/GDP -0.17 0.26 -10000 0 -0.48 201 201
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.41 195 195
MAP2K2 -0.14 0.19 0.43 2 -0.37 191 193
T-DHT/AR/PELP1/Src/PI3K -0.1 0.16 -10000 0 -0.3 200 200
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.013 0.094 -10000 0 -0.67 9 9
Gi family/GNB1/GNG2/GDP -0.032 0.099 -10000 0 -0.46 16 16
mol:T-DHT 0 0.003 0.001 59 -0.005 67 126
RAC1 0.026 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.033 -10000 0 -0.51 2 2
Gi family/GTP -0.087 0.11 -10000 0 -0.3 48 48
CDC42 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.087 0.21 -10000 0 -0.62 30 30
IHH -0.15 0.31 -10000 0 -0.7 119 119
SHH Np/Cholesterol/GAS1 -0.053 0.16 -10000 0 -0.4 84 84
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.053 0.16 0.39 84 -10000 0 84
SMO/beta Arrestin2 -0.073 0.2 -10000 0 -0.52 16 16
SMO -0.094 0.21 -10000 0 -0.44 113 113
AKT1 -0.015 0.1 -10000 0 -0.61 2 2
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.016 0.088 -10000 0 -0.67 8 8
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.093 0.2 -10000 0 -0.43 113 113
STIL -0.064 0.16 -10000 0 -0.49 14 14
DHH N/PTCH2 -0.05 0.2 -10000 0 -0.51 80 80
DHH N/PTCH1 -0.075 0.19 -10000 0 -0.38 120 120
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DHH 0.021 0.063 -10000 0 -0.67 4 4
PTHLH -0.14 0.31 -10000 0 -1 32 32
determination of left/right symmetry -0.093 0.2 -10000 0 -0.43 113 113
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
skeletal system development -0.13 0.3 -10000 0 -1 32 32
IHH N/Hhip -0.29 0.33 -10000 0 -0.59 258 258
DHH N/Hhip -0.17 0.27 -10000 0 -0.51 190 190
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.093 0.2 -10000 0 -0.43 113 113
pancreas development -0.25 0.33 -10000 0 -0.67 189 189
HHAT 0.024 0.032 -10000 0 -0.67 1 1
PI3K 0.036 0.043 -10000 0 -0.51 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.1 0.26 -10000 0 -0.63 95 95
somite specification -0.093 0.2 -10000 0 -0.43 113 113
SHH Np/Cholesterol/PTCH1 -0.069 0.16 -10000 0 -0.5 13 13
SHH Np/Cholesterol/PTCH2 -0.043 0.15 -10000 0 -0.38 79 79
SHH Np/Cholesterol/Megalin -0.081 0.18 -10000 0 -0.38 126 126
SHH -0.005 0.029 -10000 0 -0.51 1 1
catabolic process -0.092 0.2 -10000 0 -0.42 124 124
SMO/Vitamin D3 -0.074 0.18 -10000 0 -0.55 12 12
SHH Np/Cholesterol/Hhip -0.14 0.2 -10000 0 -0.39 189 189
LRP2 -0.16 0.3 -10000 0 -0.66 131 131
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.6 41 41
SHH Np/Cholesterol/BOC 0.014 0.056 -10000 0 -0.37 9 9
SHH Np/Cholesterol/CDO -0.095 0.18 -10000 0 -0.38 145 145
mesenchymal cell differentiation 0.14 0.2 0.39 189 -10000 0 189
mol:Vitamin D3 -0.063 0.17 -10000 0 -0.5 13 13
IHH N/PTCH2 -0.17 0.29 -10000 0 -0.53 176 176
CDON -0.18 0.32 -10000 0 -0.67 146 146
IHH N/PTCH1 -0.09 0.21 -10000 0 -0.42 124 124
Megalin/LRPAP1 -0.1 0.24 -10000 0 -0.5 131 131
PTCH2 -0.084 0.26 -10000 0 -0.67 79 79
SHH Np/Cholesterol 0.009 0.023 -10000 0 -0.4 1 1
PTCH1 -0.093 0.2 -10000 0 -0.42 124 124
HHIP -0.25 0.33 -10000 0 -0.67 189 189
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.1 0.25 0.53 115 -10000 0 115
KIRREL -0.046 0.2 -10000 0 -0.69 41 41
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.1 0.25 -10000 0 -0.54 111 111
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.057 0.21 -10000 0 -0.44 105 105
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.058 0.16 -10000 0 -0.35 103 103
FYN -0.063 0.2 0.28 26 -0.41 105 131
mol:Ca2+ -0.056 0.2 -10000 0 -0.43 104 104
mol:DAG -0.056 0.2 -10000 0 -0.43 104 104
NPHS2 -0.005 0.054 -10000 0 -0.74 1 1
mol:IP3 -0.056 0.2 -10000 0 -0.43 104 104
regulation of endocytosis -0.05 0.18 -10000 0 -0.39 103 103
Nephrin/NEPH1/podocin/Cholesterol -0.068 0.2 -10000 0 -0.43 106 106
establishment of cell polarity -0.1 0.25 -10000 0 -0.53 115 115
Nephrin/NEPH1/podocin/NCK1-2 -0.04 0.2 -10000 0 -0.4 105 105
Nephrin/NEPH1/beta Arrestin2 -0.05 0.18 -10000 0 -0.39 103 103
NPHS1 -0.1 0.26 -10000 0 -0.68 84 84
Nephrin/NEPH1/podocin -0.061 0.19 -10000 0 -0.41 106 106
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.055 0.2 -10000 0 -0.44 104 104
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.055 0.2 -10000 0 -0.44 102 102
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.078 0.2 0.28 21 -0.41 107 128
cytoskeleton organization -0.082 0.2 -10000 0 -0.45 102 102
Nephrin/NEPH1 -0.072 0.19 -10000 0 -0.41 109 109
Nephrin/NEPH1/ZO-1 -0.069 0.21 -10000 0 -0.46 106 106
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.01 0.068 -9999 0 -0.45 9 9
NFATC2 -0.08 0.17 -9999 0 -0.45 84 84
NFATC3 -0.002 0.031 -9999 0 -10000 0 0
CD40LG -0.34 0.37 -9999 0 -0.76 184 184
PTGS2 -0.31 0.35 -9999 0 -0.73 171 171
JUNB 0.02 0.057 -9999 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.024 -9999 0 -10000 0 0
CaM/Ca2+ 0.007 0.024 -9999 0 -10000 0 0
CALM1 0.017 0.021 -9999 0 -10000 0 0
JUN -0.14 0.29 -9999 0 -0.67 108 108
mol:Ca2+ -0.008 0.02 -9999 0 -0.18 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.011 -9999 0 -10000 0 0
FOSL1 0.005 0.055 -9999 0 -0.36 1 1
CREM 0.027 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.18 0.25 -9999 0 -0.47 163 163
FOS -0.16 0.3 -9999 0 -0.68 125 125
IFNG -0.34 0.36 -9999 0 -0.75 185 185
AP-1/NFAT1-c-4 -0.36 0.45 -9999 0 -0.86 176 176
FASLG -0.32 0.35 -9999 0 -0.73 171 171
NFAT1-c-4/ICER1 -0.08 0.17 -9999 0 -0.41 91 91
IL2RA -0.32 0.34 -9999 0 -0.72 170 170
FKBP12/FK506 0.02 0.004 -9999 0 -10000 0 0
CSF2 -0.33 0.32 -9999 0 -0.7 172 172
JunB/Fra1/NFAT1-c-4 -0.071 0.18 -9999 0 -0.4 86 86
IL4 -0.31 0.32 -9999 0 -0.69 166 166
IL2 0.003 0.071 -9999 0 -1 2 2
IL3 -0.009 0.054 -9999 0 -0.92 1 1
FKBP1A 0.027 0.005 -9999 0 -10000 0 0
BATF3 0.018 0.043 -9999 0 -0.67 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.025 0.01 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.1 0.18 -10000 0 -0.36 151 151
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.011 -10000 0 -10000 0 0
IRS1/Crk -0.091 0.19 -10000 0 -0.36 148 148
IGF-1R heterotetramer/IGF1/PTP1B -0.064 0.2 -10000 0 -0.43 107 107
AKT1 -0.089 0.17 -10000 0 -0.36 106 106
BAD -0.087 0.16 -10000 0 -0.34 106 106
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.097 0.18 -10000 0 -0.36 148 148
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.088 0.19 -10000 0 -0.37 152 152
RAF1 -0.068 0.15 0.39 1 -0.54 17 18
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.062 0.19 -10000 0 -0.35 145 145
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.096 0.21 -10000 0 -0.39 153 153
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
RPS6KB1 -0.088 0.17 -10000 0 -0.36 103 103
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.14 0.32 6 -0.45 16 22
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.07 0.16 -10000 0 -0.35 99 99
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.028 0.17 -10000 0 -0.35 97 97
IGF-1R heterotetramer -0.008 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.077 0.2 -10000 0 -0.36 152 152
Crk/p130 Cas/Paxillin -0.056 0.19 -10000 0 -0.34 147 147
IGF1R -0.008 0.058 -10000 0 -10000 0 0
IGF1 -0.14 0.29 -10000 0 -0.69 108 108
IRS2/Crk -0.085 0.18 -10000 0 -0.35 146 146
PI3K -0.065 0.2 -10000 0 -0.35 152 152
apoptosis 0.063 0.15 0.5 15 -0.32 2 17
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
PRKCD -0.09 0.2 -10000 0 -0.45 107 107
RAF1/14-3-3 E -0.044 0.14 0.33 3 -0.46 17 20
BAD/14-3-3 -0.067 0.16 0.35 3 -0.54 15 18
PRKCZ -0.087 0.17 0.25 1 -0.36 105 106
Crk/p130 Cas/Paxillin/FAK1 -0.057 0.16 -10000 0 -0.54 15 15
PTPN1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.093 0.21 -10000 0 -0.47 108 108
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.042 0.18 -10000 0 -0.38 104 104
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.087 0.19 -10000 0 -0.36 152 152
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.098 0.19 -10000 0 -0.36 152 152
IRS1 -0.11 0.2 -10000 0 -0.39 153 153
IRS2 -0.098 0.18 -10000 0 -0.36 152 152
IGF-1R heterotetramer/IGF1 -0.1 0.23 -10000 0 -0.54 108 108
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDPK1 -0.089 0.18 -10000 0 -0.34 149 149
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKD1 -0.09 0.19 -10000 0 -0.45 107 107
SHC1 0.025 0.008 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.03 0.094 -10000 0 -0.45 9 9
PTK2B 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.47 1 -0.68 71 72
EDN1 -0.004 0.099 -10000 0 -0.56 8 8
EDN3 -0.31 0.35 -10000 0 -0.67 236 236
EDN2 0.011 0.082 -10000 0 -0.67 6 6
HRAS/GDP -0.11 0.23 0.45 3 -0.49 91 94
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.15 -10000 0 -0.34 87 87
ADCY4 -0.071 0.15 0.35 1 -0.41 66 67
ADCY5 -0.12 0.2 0.35 1 -0.45 112 113
ADCY6 -0.069 0.15 0.35 1 -0.4 65 66
ADCY7 -0.068 0.15 0.35 1 -0.4 65 66
ADCY1 -0.072 0.15 0.35 1 -0.42 67 68
ADCY2 -0.1 0.18 -10000 0 -0.44 92 92
ADCY3 -0.07 0.15 0.35 1 -0.4 69 70
ADCY8 -0.1 0.16 0.35 1 -0.44 69 70
ADCY9 -0.068 0.15 0.35 1 -0.4 65 66
arachidonic acid secretion -0.19 0.32 0.36 11 -0.6 153 164
ETB receptor/Endothelin-1/Gq/GTP -0.084 0.18 -10000 0 -0.37 122 122
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.029 0.11 -10000 0 -0.4 8 8
ETA receptor/Endothelin-1/Gs/GTP -0.028 0.18 -10000 0 -0.42 70 70
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.036 0.1 -10000 0 -0.48 9 9
EDNRB 0.015 0.079 -10000 0 -0.68 6 6
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.07 0.15 -10000 0 -0.6 23 23
CYSLTR1 -0.038 0.13 -10000 0 -0.67 15 15
SLC9A1 0 0.055 -10000 0 -0.27 9 9
mol:GDP -0.12 0.24 0.44 4 -0.51 94 98
SLC9A3 -0.055 0.21 0.37 1 -0.71 34 35
RAF1 -0.16 0.28 0.44 3 -0.55 138 141
JUN -0.29 0.49 0.46 1 -1.1 128 129
JAK2 -0.031 0.098 -10000 0 -0.44 13 13
mol:IP3 -0.1 0.2 -10000 0 -0.42 118 118
ETA receptor/Endothelin-1 0.011 0.13 -10000 0 -0.46 17 17
PLCB1 0.024 0.032 -10000 0 -0.68 1 1
PLCB2 0.02 0.025 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.24 0.28 -10000 0 -0.52 237 237
FOS -0.27 0.44 0.4 7 -0.98 131 138
Gai/GDP -0.011 0.15 -10000 0 -0.65 22 22
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.19 -10000 0 -0.48 59 59
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.2 -10000 0 -0.41 120 120
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.061 0.23 -10000 0 -0.66 64 64
Gs family/GDP -0.15 0.25 0.28 1 -0.53 115 116
ETA receptor/Endothelin-1/Gq/GTP -0.09 0.18 -10000 0 -0.37 113 113
MAPK14 -0.071 0.15 -10000 0 -0.35 79 79
TRPC6 -0.16 0.3 0.47 1 -0.73 69 70
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.073 0.16 -10000 0 -0.36 88 88
ETB receptor/Endothelin-2 0.02 0.087 -10000 0 -0.51 12 12
ETB receptor/Endothelin-3 -0.23 0.28 -10000 0 -0.51 239 239
ETB receptor/Endothelin-1 0.014 0.1 -10000 0 -0.55 11 11
MAPK3 -0.24 0.41 0.38 9 -0.85 137 146
MAPK1 -0.29 0.44 0.6 1 -0.96 136 137
Rac1/GDP -0.11 0.22 0.37 1 -0.48 87 88
cAMP biosynthetic process -0.076 0.18 0.47 10 -0.45 62 72
MAPK8 -0.19 0.36 0.48 1 -0.72 110 111
SRC 0.026 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.003 0.076 -10000 0 -0.34 12 12
p130Cas/CRK/Src/PYK2 -0.15 0.29 0.44 7 -0.55 129 136
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 0.37 1 -0.48 87 88
COL1A2 -0.007 0.11 -10000 0 -0.59 7 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.012 0.085 -10000 0 -0.53 7 7
mol:DAG -0.1 0.2 -10000 0 -0.42 118 118
MAP2K2 -0.19 0.34 0.39 12 -0.67 138 150
MAP2K1 -0.2 0.34 0.43 3 -0.68 143 146
EDNRA 0.001 0.073 -10000 0 -0.37 5 5
positive regulation of muscle contraction -0.024 0.08 -10000 0 -0.41 6 6
Gq family/GDP -0.15 0.28 0.38 1 -0.55 129 130
HRAS/GTP -0.14 0.24 0.48 2 -0.51 107 109
PRKCH -0.11 0.2 -10000 0 -0.45 93 93
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.22 -10000 0 -0.47 101 101
PRKCB -0.11 0.2 -10000 0 -0.45 98 98
PRKCE -0.11 0.2 -10000 0 -0.46 94 94
PRKCD -0.11 0.2 -10000 0 -0.45 93 93
PRKCG -0.1 0.2 -10000 0 -0.45 89 89
regulation of vascular smooth muscle contraction -0.32 0.52 0.65 2 -1.2 130 132
PRKCQ -0.11 0.2 -10000 0 -0.45 96 96
PLA2G4A -0.21 0.35 0.37 10 -0.67 153 163
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
GNA15 0.007 0.052 -10000 0 -0.67 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA11 0.008 0.085 -10000 0 -0.64 8 8
Rac1/GTP 0.029 0.11 -10000 0 -0.4 8 8
MMP1 -0.035 0.08 0.62 2 -10000 0 2
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR -0.004 0.14 -10000 0 -0.66 21 21
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.3 0.24 -10000 0 -0.46 339 339
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.28 0.21 -10000 0 -0.42 335 335
IQGAP1/CaM 0.039 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.023 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.062 0.23 -10000 0 -0.67 63 63
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.017 0.11 -10000 0 -0.51 20 20
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.025 0.014 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.003 -10000 0 -10000 0 0
CDK5R2 0.001 0.023 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.31 0.23 -10000 0 -0.46 342 342
YWHAE 0.026 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.19 0.42 3 -0.59 17 20
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.017 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.24 0.19 -10000 0 -0.38 323 323
RELN -0.46 0.32 -10000 0 -0.67 343 343
PAFAH/LIS1 -0.027 0.15 -10000 0 -0.43 63 63
LIS1/CLIP170 0.031 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -10000 0 -0.48 16 16
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.17 -10000 0 -0.46 50 50
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.23 0.18 0.64 1 -0.58 22 23
LIS1/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
RHOA 0.017 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.016 -10000 0 -10000 0 0
PAFAH1B2 0.016 0.084 -10000 0 -0.64 8 8
MAP1B/LIS1/Dynein heavy chain 0.031 0.012 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.18 0.32 2 -0.57 17 19
LRP8 -0.002 0.14 -10000 0 -0.67 20 20
NDEL1/Katanin 60 -0.21 0.18 0.33 2 -0.58 18 20
P39/CDK5 -0.25 0.19 -10000 0 -0.38 332 332
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.031 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.19 -10000 0 -0.39 335 335
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.26 0.21 -10000 0 -0.4 331 331
RELN/VLDLR -0.29 0.24 -10000 0 -0.43 342 342
CDC42 0.017 0.005 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.52 0.4 -10000 0 -1.1 89 89
STAT6 (cleaved dimer) -0.53 0.41 -10000 0 -0.95 176 176
IGHG1 -0.18 0.13 -10000 0 -0.41 6 6
IGHG3 -0.51 0.38 -10000 0 -0.9 175 175
AKT1 -0.27 0.28 0.62 2 -0.82 60 62
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.23 0.29 -10000 0 -1 48 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.31 0.3 -10000 0 -0.77 95 95
THY1 -0.52 0.4 -10000 0 -1.1 82 82
MYB 0.01 0.1 -10000 0 -0.65 11 11
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.35 0.31 -10000 0 -0.78 104 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.28 -10000 0 -0.89 51 51
SP1 0.03 0.012 -10000 0 -10000 0 0
INPP5D 0.019 0.034 -10000 0 -10000 0 0
SOCS5 0.041 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.52 0.41 -10000 0 -1 133 133
SOCS1 -0.36 0.26 -10000 0 -0.72 78 78
SOCS3 -0.32 0.33 0.6 2 -1 56 58
FCER2 -0.56 0.46 -10000 0 -0.97 213 213
PARP14 0.026 0.009 -10000 0 -10000 0 0
CCL17 -0.55 0.42 -10000 0 -1.1 108 108
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.2 -10000 0 -0.7 40 40
T cell proliferation -0.51 0.41 -10000 0 -1.1 103 103
IL4R/JAK1 -0.52 0.4 -10000 0 -1.1 92 92
EGR2 -0.86 0.68 -10000 0 -1.5 238 238
JAK2 -0.033 0.041 -10000 0 -0.39 2 2
JAK3 -0.012 0.067 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.003 0.021 -10000 0 -10000 0 0
COL1A2 -0.16 0.15 -10000 0 -1.2 3 3
CCL26 -0.52 0.4 -10000 0 -1.1 95 95
IL4R -0.55 0.43 -10000 0 -1.2 91 91
PTPN6 0.04 0.012 -10000 0 -10000 0 0
IL13RA2 -0.62 0.53 -10000 0 -1.4 125 125
IL13RA1 -0.031 0.033 -10000 0 -10000 0 0
IRF4 -0.31 0.5 -10000 0 -1.1 109 109
ARG1 -0.13 0.13 -10000 0 -0.73 4 4
CBL -0.33 0.29 -10000 0 -0.8 82 82
GTF3A 0.024 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
IL13RA1/JAK2 -0.038 0.047 -10000 0 -0.25 1 1
IRF4/BCL6 -0.28 0.46 -10000 0 -1 109 109
CD40LG -0.081 0.24 -10000 0 -0.64 77 77
MAPK14 -0.34 0.32 -10000 0 -0.88 81 81
mitosis -0.26 0.26 0.62 2 -0.77 61 63
STAT6 -0.58 0.48 -10000 0 -1.1 145 145
SPI1 0.022 0.035 -10000 0 -10000 0 0
RPS6KB1 -0.25 0.25 0.71 3 -0.72 57 60
STAT6 (dimer) -0.59 0.48 -10000 0 -1.1 145 145
STAT6 (dimer)/PARP14 -0.55 0.44 -10000 0 -1.1 139 139
mast cell activation 0.015 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.3 -10000 0 -0.97 54 54
FRAP1 -0.28 0.28 0.62 2 -0.82 61 63
LTA -0.53 0.4 -10000 0 -1.1 87 87
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.57 0.46 1.1 151 -10000 0 151
CCL11 -0.5 0.38 -10000 0 -1 105 105
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.3 -10000 0 -0.91 61 61
IL2RG -0.01 0.14 -10000 0 -0.62 21 21
IL10 -0.53 0.42 -10000 0 -1.2 85 85
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.09 -10000 0 -10000 0 0
IL5 -0.52 0.4 -10000 0 -1.1 91 91
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.45 0.35 -10000 0 -0.91 111 111
COL1A1 -0.22 0.24 -10000 0 -1 26 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.52 0.42 -10000 0 -1.2 71 71
IL2R gamma/JAK3 -0.021 0.12 -10000 0 -0.48 20 20
TFF3 -1.2 0.58 -10000 0 -1.4 402 402
ALOX15 -0.52 0.4 -10000 0 -1.1 88 88
MYBL1 0.026 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.45 0.35 -10000 0 -0.9 110 110
SHC1 0.025 0.008 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.28 0.28 -10000 0 -0.88 50 50
mol:PI-3-4-5-P3 -0.28 0.28 0.62 2 -0.83 60 62
PI3K -0.29 0.3 0.67 1 -0.9 60 61
DOK2 0.019 0.052 -10000 0 -0.67 2 2
ETS1 0.039 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.69 34 34
ITGB3 -0.53 0.43 -10000 0 -1.2 95 95
PIGR -0.55 0.45 -10000 0 -1.2 100 100
IGHE 0.047 0.044 0.24 9 -10000 0 9
MAPKKK cascade -0.2 0.19 0.59 1 -0.68 34 35
BCL6 0.026 0.032 -10000 0 -0.67 1 1
OPRM1 -0.53 0.4 -10000 0 -1.1 92 92
RETNLB -0.53 0.4 -10000 0 -1.1 86 86
SELP -0.52 0.41 -10000 0 -1.2 84 84
AICDA -0.51 0.38 -10000 0 -1.1 77 77
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.052 0.025 -9999 0 -0.44 1 1
fibroblast growth factor receptor signaling pathway 0.052 0.025 -9999 0 -0.44 1 1
LAMA1 -0.021 0.18 -9999 0 -0.66 34 34
PRNP 0.025 0.032 -9999 0 -0.67 1 1
GPC1/SLIT2 -0.042 0.19 -9999 0 -0.5 74 74
SMAD2 0.016 0.038 -9999 0 -0.4 3 3
GPC1/PrPc/Cu2+ 0.034 0.023 -9999 0 -0.44 1 1
GPC1/Laminin alpha1 0.002 0.14 -9999 0 -0.5 34 34
TDGF1 -0.27 0.34 -9999 0 -0.67 212 212
CRIPTO/GPC1 -0.19 0.27 -9999 0 -0.5 212 212
APP/GPC1 0.038 0.011 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.17 0.22 -9999 0 -0.44 210 210
FLT1 0.024 0.032 -9999 0 -0.67 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.047 0.042 -9999 0 -0.43 3 3
SERPINC1 0.019 0.023 -9999 0 -10000 0 0
FYN -0.17 0.23 -9999 0 -0.44 210 210
FGR -0.17 0.22 -9999 0 -0.43 210 210
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.52 204 204
SLIT2 -0.077 0.25 -9999 0 -0.67 74 74
GPC1/NRG -0.008 0.15 -9999 0 -0.5 43 43
NRG1 -0.033 0.19 -9999 0 -0.66 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.053 -9999 0 -0.57 3 3
LYN -0.17 0.22 -9999 0 -0.44 208 208
mol:Spermine 0.009 0.004 -9999 0 -10000 0 0
cell growth 0.052 0.025 -9999 0 -0.44 1 1
BMP signaling pathway -0.026 0.009 -9999 0 -10000 0 0
SRC -0.17 0.22 -9999 0 -0.44 209 209
TGFBR1 0.021 0.025 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.18 0.3 -9999 0 -0.67 132 132
GPC1 0.026 0.009 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.021 0.025 -9999 0 -10000 0 0
VEGFA 0.023 0.054 -9999 0 -0.67 3 3
BLK -0.3 0.3 -9999 0 -0.54 281 281
HCK -0.18 0.22 -9999 0 -0.44 210 210
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.025 0.032 -9999 0 -0.67 1 1
VEGFR1 homodimer 0.024 0.032 -9999 0 -0.67 1 1
TGFBR2 0.023 0.054 -9999 0 -0.67 3 3
cell death 0.038 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.034 0.02 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.24 -9999 0 -0.51 131 131
LCK -0.18 0.22 -9999 0 -0.44 215 215
neuron differentiation -0.008 0.15 -9999 0 -0.49 43 43
PrPc/Cu2+ 0.019 0.024 -9999 0 -0.51 1 1
APP 0.026 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.023 0.054 -9999 0 -0.67 3 3
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.21 0.33 -10000 0 -0.79 63 63
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.24 0.4 -10000 0 -0.81 110 110
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.2 0.35 0.62 3 -0.83 52 55
AP1 -0.19 0.37 -10000 0 -0.72 149 149
ABCG2 -0.2 0.35 0.61 1 -0.84 54 55
HIF1A -0.021 0.073 -10000 0 -0.35 1 1
TFF3 -0.49 0.43 0.62 3 -0.91 181 184
GATA2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.054 0.11 -10000 0 -0.28 11 11
response to hypoxia -0.071 0.11 -10000 0 -0.23 95 95
MCL1 -0.19 0.34 0.61 3 -0.83 50 53
NDRG1 -0.2 0.34 0.6 2 -0.82 53 55
SERPINE1 -0.2 0.34 0.61 1 -0.84 50 51
FECH -0.2 0.35 0.61 4 -0.82 54 58
FURIN -0.2 0.35 0.61 4 -0.82 55 59
NCOA2 -0.036 0.2 -10000 0 -0.67 45 45
EP300 -0.1 0.18 -10000 0 -0.35 157 157
HMOX1 -0.21 0.33 0.62 2 -0.83 52 54
BHLHE40 -0.2 0.35 0.62 2 -0.82 56 58
BHLHE41 -0.2 0.35 0.61 1 -0.83 52 53
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.029 0.1 -10000 0 -10000 0 0
ENG 0.01 0.091 0.47 3 -10000 0 3
JUN -0.12 0.29 -10000 0 -0.67 107 107
RORA -0.2 0.35 0.61 4 -0.84 53 57
ABCB1 -0.052 0.16 -10000 0 -1.2 8 8
TFRC -0.2 0.35 0.62 2 -0.84 54 56
CXCR4 -0.2 0.35 0.62 3 -0.82 53 56
TF -0.24 0.4 0.62 2 -0.92 82 84
CITED2 -0.22 0.39 0.61 3 -0.92 67 70
HIF1A/ARNT -0.22 0.38 -10000 0 -0.91 54 54
LDHA -0.033 0.11 -10000 0 -0.7 8 8
ETS1 -0.2 0.35 0.62 3 -0.82 53 56
PGK1 -0.2 0.34 0.61 1 -0.83 52 53
NOS2 -0.2 0.35 0.61 2 -0.83 52 54
ITGB2 -0.2 0.35 0.62 3 -0.83 53 56
ALDOA -0.2 0.34 0.61 1 -0.82 53 54
Cbp/p300/CITED2 -0.3 0.46 -10000 0 -0.98 116 116
FOS -0.15 0.3 -10000 0 -0.67 125 125
HK2 -0.2 0.35 0.62 3 -0.82 55 58
SP1 0.032 0.017 -10000 0 -10000 0 0
GCK -0.4 0.64 -10000 0 -1.4 137 137
HK1 -0.2 0.35 0.62 3 -0.82 55 58
NPM1 -0.2 0.34 0.61 1 -0.83 51 52
EGLN1 -0.19 0.34 0.61 3 -0.83 50 53
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.2 0.35 0.61 3 -0.82 55 58
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.19 0.29 0.5 1 -0.7 74 75
IGFBP1 -0.2 0.34 0.61 1 -0.83 52 53
VEGFA -0.2 0.35 -10000 0 -0.71 102 102
HIF1A/JAB1 0.003 0.058 -10000 0 -10000 0 0
CP -0.32 0.46 0.62 2 -0.92 140 142
CXCL12 -0.24 0.4 0.62 3 -0.93 76 79
COPS5 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.008 -10000 0 -10000 0 0
BNIP3 -0.2 0.35 0.62 3 -0.82 54 57
EGLN3 -0.21 0.35 -10000 0 -0.84 58 58
CA9 -0.2 0.35 0.6 2 -0.82 59 61
TERT -0.2 0.34 0.6 1 -0.83 51 52
ENO1 -0.2 0.35 0.61 3 -0.82 55 58
PFKL -0.2 0.35 0.62 3 -0.83 52 55
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.21 0.36 0.62 3 -0.83 57 60
ARNT -0.015 0.071 -10000 0 -0.31 2 2
HNF4A -0.015 0.058 -10000 0 -0.22 4 4
ADFP -0.21 0.33 -10000 0 -0.79 63 63
SLC2A1 -0.2 0.35 -10000 0 -0.71 99 99
LEP -0.2 0.34 0.61 1 -0.84 51 52
HIF1A/ARNT/Cbp/p300 -0.26 0.41 -10000 0 -0.83 117 117
EPO -0.14 0.28 -10000 0 -0.89 23 23
CREBBP -0.081 0.17 -10000 0 -0.33 133 133
HIF1A/ARNT/Cbp/p300/HDAC7 -0.23 0.4 -10000 0 -0.82 107 107
PFKFB3 -0.2 0.35 0.62 3 -0.82 55 58
NT5E -0.2 0.36 0.61 3 -0.83 56 59
Ephrin B reverse 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
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EPHB2 0.021 0.055 -10000 0 -0.68 3 3
EFNB1 -0.002 0.085 -10000 0 -0.49 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.11 0.22 -10000 0 -0.4 184 184
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.4 181 181
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.38 184 184
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.23 -10000 0 -0.42 186 186
DNM1 0.004 0.11 -10000 0 -0.63 15 15
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.002 0.094 0.41 1 -0.65 8 9
YES1 0.004 0.11 -10000 0 -0.89 7 7
Ephrin B1/EPHB1-2/NCK2 -0.12 0.22 -10000 0 -0.39 185 185
PI3K 0.024 0.11 -10000 0 -0.83 7 7
mol:GDP -0.13 0.23 -10000 0 -0.42 186 186
ITGA2B -0.041 0.2 -10000 0 -0.67 48 48
endothelial cell proliferation 0.033 0.01 -10000 0 -10000 0 0
FYN 0.003 0.11 -10000 0 -0.86 8 8
MAP3K7 -0.011 0.088 -10000 0 -0.68 8 8
FGR 0.002 0.11 -10000 0 -0.85 8 8
TIAM1 -0.059 0.081 -10000 0 -0.67 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.027 0.16 -10000 0 -0.43 57 57
LYN 0.003 0.11 -10000 0 -0.86 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.006 0.1 -10000 0 -0.81 8 8
Ephrin B1/EPHB1-2 -0.01 0.092 -10000 0 -0.77 7 7
SRC 0.002 0.11 -10000 0 -0.85 8 8
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
EPHB1 -0.24 0.34 -10000 0 -0.67 188 188
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.025 0.18 -10000 0 -0.53 55 55
BLK -0.049 0.14 -10000 0 -0.92 8 8
HCK 0.002 0.11 -10000 0 -0.85 8 8
regulation of stress fiber formation 0.12 0.21 0.38 185 -10000 0 185
MAPK8 -0.006 0.12 0.36 5 -0.67 12 17
Ephrin B1/EPHB1-2/RGS3 -0.12 0.21 -10000 0 -0.38 185 185
endothelial cell migration -0.006 0.083 0.4 2 -0.62 7 9
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTPN13 0.024 0.091 -10000 0 -0.79 6 6
regulation of focal adhesion formation 0.12 0.21 0.38 185 -10000 0 185
chemotaxis 0.12 0.21 0.38 185 -10000 0 185
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
Rac1/GTP -0.12 0.22 -10000 0 -0.39 184 184
angiogenesis -0.011 0.094 -10000 0 -0.73 8 8
LCK 0 0.12 -10000 0 -0.9 8 8
IL23-mediated signaling events

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
CCL2 -0.18 0.53 -10000 0 -1.3 77 77
IL23A -0.2 0.54 -10000 0 -1.2 96 96
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.54 -10000 0 -1.2 83 83
positive regulation of T cell mediated cytotoxicity -0.22 0.61 -10000 0 -1.3 92 92
ITGA3 -0.17 0.5 -10000 0 -1.2 76 76
IL17F -0.094 0.33 0.64 2 -0.74 76 78
IL12B 0.003 0.097 -10000 0 -0.7 7 7
STAT1 (dimer) -0.2 0.58 -10000 0 -1.3 89 89
CD4 -0.17 0.49 -10000 0 -1.2 76 76
IL23 -0.19 0.52 -10000 0 -1.2 95 95
IL23R 0.006 0.1 -10000 0 -0.82 2 2
IL1B -0.21 0.56 -10000 0 -1.3 85 85
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.16 0.5 -10000 0 -1.2 75 75
TYK2 0.016 0.035 -10000 0 -10000 0 0
STAT4 0.004 0.099 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP -0.012 0.15 -10000 0 -0.68 23 23
IL12RB1 -0.004 0.089 -10000 0 -0.66 6 6
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
IL12Rbeta1/TYK2 0.011 0.078 -10000 0 -0.51 6 6
IL23R/JAK2 0.013 0.13 -10000 0 -0.72 2 2
positive regulation of chronic inflammatory response -0.22 0.61 -10000 0 -1.3 92 92
natural killer cell activation 0.001 0.009 -10000 0 -0.046 2 2
JAK2 0.016 0.051 -10000 0 -0.38 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.49 -10000 0 -1.1 96 96
ALOX12B -0.17 0.49 -10000 0 -1.2 78 78
CXCL1 -0.18 0.52 -10000 0 -1.2 83 83
T cell proliferation -0.22 0.61 -10000 0 -1.3 92 92
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.051 0.26 -10000 0 -0.57 67 67
PI3K -0.18 0.55 -10000 0 -1.2 84 84
IFNG -0.015 0.053 0.12 1 -0.13 67 68
STAT3 (dimer) -0.16 0.51 -10000 0 -1.2 79 79
IL18R1 -0.002 0.096 -10000 0 -0.59 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.089 0.34 -10000 0 -0.79 66 66
IL18/IL18R -0.004 0.15 -10000 0 -0.48 37 37
macrophage activation -0.008 0.021 -10000 0 -0.044 97 97
TNF -0.24 0.6 -10000 0 -1.4 94 94
STAT3/STAT4 -0.19 0.55 -10000 0 -1.2 86 86
STAT4 (dimer) -0.21 0.58 -10000 0 -1.3 90 90
IL18 -0.009 0.11 -10000 0 -0.65 11 11
IL19 -0.16 0.5 -10000 0 -1.2 73 73
STAT5A (dimer) -0.2 0.57 -10000 0 -1.3 88 88
STAT1 0.023 0.023 -10000 0 -10000 0 0
SOCS3 -0.001 0.13 -10000 0 -0.67 19 19
CXCL9 -0.26 0.62 -10000 0 -1.4 109 109
MPO -0.17 0.5 -10000 0 -1.2 81 81
positive regulation of humoral immune response -0.22 0.61 -10000 0 -1.3 92 92
IL23/IL23R/JAK2/TYK2 -0.26 0.74 -10000 0 -1.6 92 92
IL6 -0.26 0.62 -10000 0 -1.3 112 112
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.003 0.03 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 -10000 0 -0.046 2 2
CD3E -0.2 0.55 -10000 0 -1.3 85 85
keratinocyte proliferation -0.22 0.61 -10000 0 -1.3 92 92
NOS2 -0.17 0.49 -10000 0 -1.2 75 75
Coregulation of Androgen receptor activity

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
NRIP1 -0.006 0.053 -10000 0 -10000 0 0
SVIL -0.003 0.048 -10000 0 -10000 0 0
ZNF318 0.076 0.087 0.22 56 -0.67 1 57
JMJD2C -0.066 0.067 -10000 0 -0.12 285 285
T-DHT/AR/Ubc9 -0.23 0.24 -10000 0 -0.49 209 209
CARM1 0.023 0.009 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.032 0.013 -10000 0 -10000 0 0
CTNNB1 0.002 0.04 -10000 0 -10000 0 0
AKT1 0.038 0.021 -10000 0 -10000 0 0
PTK2B 0.007 0.032 -10000 0 -10000 0 0
MED1 0.037 0.021 -10000 0 -10000 0 0
MAK 0.067 0.12 0.26 3 -0.65 7 10
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.006 0.064 -10000 0 -0.67 2 2
GSN -0.001 0.045 -10000 0 -10000 0 0
NCOA2 -0.039 0.2 -10000 0 -0.68 45 45
NCOA6 -0.003 0.054 -10000 0 -0.67 1 1
DNA-PK 0.074 0.078 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.038 -10000 0 -10000 0 0
cell proliferation -0.003 0.15 -10000 0 -0.81 10 10
XRCC5 0.037 0.018 -10000 0 -10000 0 0
UBE3A -0.012 0.063 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.25 0.26 -10000 0 -0.52 217 217
FHL2 -0.13 0.33 -10000 0 -1.1 43 43
RANBP9 -0.001 0.046 -10000 0 -10000 0 0
JMJD1A -0.006 0.032 -10000 0 -0.13 30 30
CDK6 0.023 0.055 -10000 0 -0.67 3 3
TGFB1I1 -0.003 0.047 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.24 -10000 0 -0.49 218 218
XRCC6 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.26 -10000 0 -0.53 234 234
CTDSP1 0.012 0.023 -10000 0 -10000 0 0
CTDSP2 0.058 0.052 -10000 0 -10000 0 0
BRCA1 -0.003 0.047 -10000 0 -10000 0 0
TCF4 0.048 0.035 -10000 0 -10000 0 0
CDKN2A 0.003 0.083 -10000 0 -10000 0 0
SRF 0.035 0.051 -10000 0 -10000 0 0
NKX3-1 -0.12 0.1 -10000 0 -0.21 240 240
KLK3 -0.39 0.65 -10000 0 -1.4 142 142
TMF1 0.017 0.046 -10000 0 -0.67 2 2
HNRNPA1 0.044 0.029 -10000 0 -10000 0 0
AOF2 -0.02 0.033 -10000 0 -0.072 142 142
APPL1 0.042 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.22 0.24 -10000 0 -0.48 208 208
AR -0.31 0.34 -10000 0 -0.71 206 206
UBA3 0.013 0.023 -10000 0 -10000 0 0
PATZ1 0.033 0.031 -10000 0 -10000 0 0
PAWR 0.02 0.015 -10000 0 -10000 0 0
PRKDC 0.037 0.018 -10000 0 -10000 0 0
PA2G4 0.049 0.037 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.22 -10000 0 -0.46 203 203
RPS6KA3 -0.003 0.046 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.5 206 206
LATS2 0.041 0.043 -10000 0 -0.67 1 1
T-DHT/AR/PRX1 -0.2 0.22 -10000 0 -0.44 204 204
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.005 0.084 -10000 0 -0.68 6 6
KLK2 -0.68 0.55 -10000 0 -1.1 291 291
CASP8 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.53 209 209
TMPRSS2 -0.16 0.27 -10000 0 -1.1 33 33
CCND1 0.013 0.031 -10000 0 -10000 0 0
PIAS1 -0.012 0.063 -10000 0 -10000 0 0
mol:T-DHT -0.034 0.04 -10000 0 -0.079 184 184
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.031 0.09 -10000 0 -0.22 1 1
T-DHT/AR/CDK6 -0.23 0.24 -10000 0 -0.49 208 208
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF -0.015 0.16 -10000 0 -0.65 29 29
ZMIZ1 -0.025 0.057 -10000 0 -0.67 1 1
CCND3 0.028 0.004 -10000 0 -10000 0 0
TGIF1 0.044 0.029 -10000 0 -10000 0 0
FKBP4 -0.002 0.046 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.084 0.087 0.36 1 -10000 0 1
SMARCC2 0.026 0.018 -10000 0 -10000 0 0
SMARCC1 0.026 0.018 -10000 0 -10000 0 0
TBX21 -0.12 0.24 0.32 2 -0.66 55 57
SUMO2 0.024 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.024 -10000 0 -10000 0 0
FKBP4 0.027 0.005 -10000 0 -10000 0 0
FKBP5 0.019 0.072 -10000 0 -0.62 6 6
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.33 51 -0.42 4 55
PRL -0.062 0.1 -10000 0 -0.4 1 1
cortisol/GR alpha (dimer)/TIF2 0.18 0.29 0.54 144 -0.46 20 164
RELA -0.026 0.098 -10000 0 -0.28 21 21
FGG 0.16 0.2 0.47 104 -10000 0 104
GR beta/TIF2 0.073 0.2 0.33 69 -0.45 45 114
IFNG -0.36 0.48 -10000 0 -1.2 106 106
apoptosis -0.015 0.23 0.5 36 -0.52 21 57
CREB1 0.026 0.014 -10000 0 -10000 0 0
histone acetylation -0.074 0.16 -10000 0 -0.43 57 57
BGLAP -0.077 0.13 -10000 0 -0.49 12 12
GR/PKAc 0.11 0.1 0.36 25 -0.34 1 26
NF kappa B1 p50/RelA -0.044 0.17 -10000 0 -0.46 37 37
SMARCD1 0.026 0.018 -10000 0 -10000 0 0
MDM2 0.085 0.097 0.24 102 -10000 0 102
GATA3 -0.004 0.15 -10000 0 -0.64 25 25
AKT1 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.12 0.14 -10000 0 -0.56 17 17
GSK3B 0.025 0.018 -10000 0 -10000 0 0
NR1I3 0.003 0.23 0.51 33 -0.58 10 43
CSN2 0.13 0.16 0.4 87 -10000 0 87
BRG1/BAF155/BAF170/BAF60A 0.063 0.054 -10000 0 -0.31 7 7
NFATC1 0.016 0.094 -10000 0 -0.67 9 9
POU2F1 0.026 0.01 -10000 0 -10000 0 0
CDKN1A 0.026 0.034 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.013 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.67 15 15
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.14 0.34 45 -0.37 12 57
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.4 0.48 27 -0.83 103 130
JUN -0.24 0.27 -10000 0 -0.56 171 171
IL4 -0.1 0.16 -10000 0 -0.64 20 20
CDK5R1 0.025 0.015 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.31 -10000 0 -0.66 154 154
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.36 32 -0.38 4 36
cortisol/GR alpha (monomer) 0.26 0.3 0.63 156 -10000 0 156
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.3 -10000 0 -0.69 126 126
AP-1/NFAT1-c-4 -0.38 0.41 -10000 0 -0.75 233 233
AFP -0.17 0.21 -10000 0 -0.64 33 33
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.45 49 -10000 0 49
TP53 0.041 0.015 -10000 0 -10000 0 0
PPP5C 0.025 0.008 -10000 0 -10000 0 0
KRT17 -0.29 0.34 -10000 0 -0.72 136 136
KRT14 -0.085 0.12 -10000 0 -0.49 6 6
TBP 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.036 0.046 -10000 0 -0.26 10 10
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.005 -10000 0 -10000 0 0
AP-1 -0.38 0.41 -10000 0 -0.75 233 233
MAPK14 0.027 0.016 -10000 0 -10000 0 0
MAPK10 0.025 0.035 -10000 0 -0.68 1 1
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.37 0.49 -10000 0 -1 144 144
interleukin-1 receptor activity 0.003 0.003 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.024 -10000 0 -10000 0 0
CGA -0.095 0.14 -10000 0 -0.52 14 14
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.094 0.12 0.35 35 -10000 0 35
MAPK3 0.025 0.016 -10000 0 -10000 0 0
MAPK1 0.02 0.017 -10000 0 -10000 0 0
ICAM1 -0.16 0.24 -10000 0 -0.64 73 73
NFKB1 -0.025 0.096 -10000 0 -0.28 14 14
MAPK8 -0.14 0.18 -10000 0 -0.44 95 95
MAPK9 0.027 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.02 0.24 0.5 33 -0.55 21 54
BAX 0.04 0.093 0.85 5 -10000 0 5
POMC -0.45 0.63 -10000 0 -1.4 131 131
EP300 0.027 0.044 -10000 0 -0.26 8 8
cortisol/GR alpha (dimer)/p53 0.23 0.25 0.55 151 -10000 0 151
proteasomal ubiquitin-dependent protein catabolic process 0.08 0.13 0.33 85 -10000 0 85
SGK1 0.013 0.21 0.51 1 -1.3 10 11
IL13 -0.21 0.25 -10000 0 -0.7 61 61
IL6 -0.28 0.48 -10000 0 -1.1 110 110
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.18 0.2 -10000 0 -0.65 43 43
IL2 -0.25 0.28 -10000 0 -0.6 146 146
CDK5 0.027 0.008 -10000 0 -10000 0 0
PRKACB 0.025 0.032 -10000 0 -0.67 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.29 -10000 0 -0.67 86 86
CDK5R1/CDK5 0.038 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.002 0.14 -10000 0 -0.4 18 18
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.52 154 -10000 0 154
SMARCA4 0.025 0.018 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.37 105 -0.44 1 106
NF kappa B1 p50/RelA/Cbp -0.006 0.16 -10000 0 -0.43 23 23
JUN (dimer) -0.24 0.27 -10000 0 -0.56 171 171
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.22 0.36 -10000 0 -0.88 102 102
NR3C1 0.16 0.19 0.44 113 -10000 0 113
NR4A1 -0.26 0.36 -10000 0 -0.66 211 211
TIF2/SUV420H1 -0.011 0.16 -10000 0 -0.51 45 45
MAPKKK cascade -0.015 0.23 0.5 36 -0.52 21 57
cortisol/GR alpha (dimer)/Src-1 0.23 0.25 0.55 147 -10000 0 147
PBX1 0.025 0.032 -10000 0 -0.67 1 1
POU1F1 0.005 0.022 -10000 0 -10000 0 0
SELE -0.25 0.45 -10000 0 -1.1 88 88
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.37 102 -0.44 1 103
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.52 154 -10000 0 154
mol:cortisol 0.14 0.19 0.37 157 -10000 0 157
MMP1 -0.1 0.14 -10000 0 -0.87 10 10
BMP receptor signaling

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.16 0.3 -10000 0 -0.48 211 211
SMAD6-7/SMURF1 0.052 0.014 -10000 0 -10000 0 0
NOG -0.02 0.17 -10000 0 -0.67 30 30
SMAD9 -0.18 0.27 -10000 0 -0.54 169 169
SMAD4 0.027 0.004 -10000 0 -10000 0 0
SMAD5 -0.084 0.17 -10000 0 -0.44 31 31
BMP7/USAG1 -0.24 0.27 -10000 0 -0.51 250 250
SMAD5/SKI -0.069 0.17 0.31 3 -0.43 31 34
SMAD1 -0.037 0.094 -10000 0 -0.66 1 1
BMP2 0.001 0.13 -10000 0 -0.67 18 18
SMAD1/SMAD1/SMAD4 -0.022 0.085 -10000 0 -0.53 1 1
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.21 0.33 -10000 0 -0.67 164 164
BMPR1A-1B/BAMBI -0.11 0.24 -10000 0 -0.44 164 164
AHSG -0.005 0.042 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.014 0.12 -10000 0 -0.44 29 29
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.066 0.16 -10000 0 -0.54 29 29
BMP2-4 (homodimer) 0.006 0.13 -10000 0 -0.51 29 29
RGMB 0.026 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.088 0.22 -10000 0 -0.4 163 163
RGMA 0.001 0.13 -10000 0 -0.66 19 19
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.079 0.16 -10000 0 -0.46 34 34
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.46 263 263
SMAD6/SMURF1/SMAD5 -0.068 0.17 0.32 1 -0.43 27 28
SOSTDC1 -0.33 0.35 -10000 0 -0.67 250 250
BMP7/BMPR2/BMPR1A-1B -0.088 0.22 -10000 0 -0.4 161 161
SKI 0.026 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.026 0.014 -10000 0 -10000 0 0
HFE2 -0.003 0.022 -10000 0 -10000 0 0
ZFYVE16 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.015 0.14 -10000 0 -0.45 38 38
SMAD5/SMAD5/SMAD4 -0.067 0.17 0.31 3 -0.42 31 34
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.054 0.15 -10000 0 -0.42 29 29
BMP7 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.026 0.034 -10000 0 -10000 0 0
SMAD1/SKI -0.027 0.1 0.34 1 -0.48 2 3
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.022 0.12 -10000 0 -0.45 29 29
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.66 114 114
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.046 0.047 -10000 0 -0.44 4 4
BMPR1A-1B (homodimer) -0.14 0.26 -10000 0 -0.51 164 164
CHRDL1 -0.45 0.32 -10000 0 -0.66 341 341
ENDOFIN/SMAD1 -0.029 0.098 -10000 0 -0.62 1 1
SMAD6-7/SMURF1/SMAD1 -0.013 0.1 -10000 0 -0.58 1 1
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.019 0.052 -10000 0 -0.67 2 2
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.25 -10000 0 -0.46 332 332
BMP2-4/GREM1 -0.079 0.24 -10000 0 -0.47 125 125
SMAD7 0.027 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.17 0.26 -10000 0 -0.52 162 162
SMAD1/SMAD6 -0.028 0.096 -10000 0 -0.62 1 1
TAK1/SMAD6 0.039 0.01 -10000 0 -10000 0 0
BMP7 0.027 0.005 -10000 0 -10000 0 0
BMP6 0.026 0.014 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.058 0.13 -10000 0 -0.4 31 31
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.026 0.097 0.31 1 -0.48 2 3
SMAD7/SMURF1 0.038 0.01 -10000 0 -10000 0 0
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.02 0.063 -10000 0 -0.67 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.26 -10000 0 -0.64 88 88
CHRD 0.013 0.099 -10000 0 -0.67 10 10
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.08 0.16 -10000 0 -0.49 32 32
BMP4 0.008 0.11 -10000 0 -0.65 12 12
FST -0.14 0.29 -10000 0 -0.67 112 112
BMP2-4/NOG -0.006 0.16 -10000 0 -0.44 58 58
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.073 0.21 -10000 0 -0.38 158 158
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.057 0.24 0.29 20 -0.6 70 90
FYN -0.1 0.32 0.46 1 -0.78 74 75
LAT/GRAP2/SLP76 -0.084 0.25 -10000 0 -0.63 76 76
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.062 0.21 0.56 9 -0.48 75 84
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.016 0.057 0.14 3 -0.16 34 37
MAP3K8 0.018 0.079 -10000 0 -0.63 7 7
mol:Ca2+ -0.03 0.042 0.092 5 -0.11 102 107
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.3 0.51 4 -0.73 78 82
TRPV6 -0.1 0.35 0.99 20 -0.68 103 123
CD28 -0.014 0.15 -10000 0 -0.65 25 25
SHC1 -0.1 0.32 0.3 21 -0.79 73 94
receptor internalization -0.13 0.34 -10000 0 -0.8 86 86
PRF1 -0.11 0.33 -10000 0 -0.88 64 64
KRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.046 0.16 0.44 5 -0.38 77 82
LAT -0.11 0.31 0.3 4 -0.79 75 79
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.048 0.21 -10000 0 -0.64 52 52
CD3E -0.03 0.19 -10000 0 -0.63 42 42
CD3G -0.096 0.26 -10000 0 -0.65 88 88
RASGRP2 -0.004 0.033 0.094 3 -0.18 12 15
RASGRP1 -0.051 0.22 0.56 11 -0.47 75 86
HLA-A 0 0.006 0.063 2 -10000 0 2
RASSF5 0.025 0.008 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.14 0.35 29 -0.13 38 67
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.048 0.085 -10000 0 -0.25 60 60
PRKCA -0.035 0.12 -10000 0 -0.29 73 73
GRAP2 -0.02 0.15 -10000 0 -0.56 33 33
mol:IP3 -0.033 0.21 0.26 72 -0.45 72 144
EntrezGene:6957 0 0.005 0.045 2 -10000 0 2
TCR/CD3/MHC I/CD8 -0.13 0.35 -10000 0 -0.88 73 73
ORAI1 0.046 0.21 0.7 2 -0.78 16 18
CSK -0.11 0.32 -10000 0 -0.81 74 74
B7 family/CD28 -0.11 0.35 -10000 0 -0.79 82 82
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.38 -10000 0 -0.91 82 82
PTPN6 -0.12 0.32 0.24 1 -0.82 74 75
VAV1 -0.11 0.31 0.31 1 -0.79 74 75
Monovalent TCR/CD3 -0.11 0.31 -10000 0 -0.61 107 107
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK -0.11 0.33 -10000 0 -0.82 74 74
PAG1 -0.11 0.32 -10000 0 -0.82 74 74
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.14 0.38 -10000 0 -0.92 80 80
CD80 -0.043 0.21 -10000 0 -0.67 49 49
CD86 0.013 0.077 -10000 0 -0.68 5 5
PDK1/CARD11/BCL10/MALT1 -0.042 0.11 -10000 0 -0.29 61 61
HRAS 0.026 0.011 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.6 90 90
CD8A -0.025 0.18 -10000 0 -0.66 38 38
CD8B -0.052 0.22 -10000 0 -0.65 55 55
PTPRC -0.009 0.14 -10000 0 -0.68 20 20
PDK1/PKC theta -0.076 0.26 0.61 12 -0.59 75 87
CSK/PAG1 -0.11 0.31 -10000 0 -0.79 74 74
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.012 -10000 0 -10000 0 0
GRAP2/SLP76 -0.1 0.3 -10000 0 -0.76 76 76
STIM1 0.019 0.16 1.2 2 -0.9 9 11
RAS family/GTP 0.008 0.098 0.23 25 -0.19 42 67
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.38 -10000 0 -0.88 86 86
mol:DAG -0.059 0.16 0.15 5 -0.4 74 79
RAP1A/GDP 0.008 0.059 0.19 17 -0.066 11 28
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 -0.001 0.13 -10000 0 -0.68 17 17
cytotoxic T cell degranulation -0.1 0.31 -10000 0 -0.8 70 70
RAP1A/GTP -0.001 0.012 -10000 0 -0.067 11 11
mol:PI-3-4-5-P3 -0.083 0.24 0.54 8 -0.58 78 86
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.051 0.26 0.28 65 -0.59 74 139
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 0 0.13 -10000 0 -0.66 17 17
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.082 0.24 -10000 0 -0.59 76 76
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
CD8 heterodimer -0.057 0.24 -10000 0 -0.6 73 73
CARD11 -0.019 0.12 -10000 0 -0.67 11 11
PRKCB -0.032 0.12 -10000 0 -0.3 67 67
PRKCE -0.031 0.12 -10000 0 -0.28 71 71
PRKCQ -0.095 0.29 0.59 9 -0.69 75 84
LCP2 0.024 0.021 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.049 0.18 0.54 9 -0.4 75 84
IKK complex 0.018 0.13 0.41 23 -0.13 13 36
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.035 0.12 0.27 4 -0.29 64 68
PDPK1 -0.059 0.2 0.53 11 -0.45 76 87
TCR/CD3/MHC I/CD8/Fyn -0.16 0.41 -10000 0 -1 80 80
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.035 0.009 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.017 0.15 -10000 0 -0.71 12 12
EGFR 0.019 0.07 -10000 0 -0.67 5 5
EPHA2 0.026 0.013 -10000 0 -10000 0 0
USP6 0.025 0.014 -10000 0 -10000 0 0
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.045 0.2 -10000 0 -0.5 76 76
ARRB2 -0.037 0.13 -10000 0 -0.39 62 62
mol:GTP 0.024 0.037 0.17 20 -10000 0 20
ARRB1 0.025 0.032 -10000 0 -0.67 1 1
FBXO8 0.027 0.004 -10000 0 -10000 0 0
TSHR 0.024 0.045 -10000 0 -0.68 2 2
EGF -0.076 0.25 -10000 0 -0.67 72 72
somatostatin receptor activity 0 0.001 0.002 14 -0.001 145 159
ARAP2 0.025 0.036 -10000 0 -0.52 2 2
mol:GDP -0.11 0.14 0.27 5 -0.3 121 126
mol:PI-3-4-5-P3 0 0 0.002 11 -0.001 71 82
ITGA2B -0.041 0.2 -10000 0 -0.67 48 48
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.025 -10000 0 -10000 0 0
ADAP1 0.026 0.006 -10000 0 -10000 0 0
KIF13B 0.027 0.005 -10000 0 -10000 0 0
HGF/MET -0.078 0.19 -10000 0 -0.52 70 70
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.16 0.51 8 -0.29 151 159
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.022 0.18 -10000 0 -0.44 76 76
ADRB2 0.011 0.1 -10000 0 -0.67 11 11
receptor agonist activity 0 0 0.001 19 0 153 172
actin filament binding 0 0 0.002 15 -0.001 146 161
SRC 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
GNAQ 0.025 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.004 17 -0.001 90 107
ARF6/GDP -0.006 0.088 0.25 2 -0.42 9 11
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.42 112 112
alphaIIb/beta3 Integrin/paxillin/GIT1 0.011 0.16 -10000 0 -0.42 55 55
ACAP1 0.019 0.045 -10000 0 -0.52 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.053 0.19 -10000 0 -0.56 62 62
EFNA1 0.025 0.008 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 70 70
CYTH3 0.006 0.033 -10000 0 -0.51 2 2
CYTH2 -0.008 0.15 -10000 0 -0.94 13 13
NCK1 0.027 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 23 0 113 136
endosomal lumen acidification 0 0 0.002 6 -0.001 146 152
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 -0.093 0.26 -10000 0 -0.65 88 88
GNAQ/ARNO 0.005 0.14 -10000 0 -0.86 13 13
mol:Phosphatidic acid 0 0 0.001 12 -10000 0 12
PIP3-E 0 0 0.001 10 0 17 27
MET -0.03 0.074 -10000 0 -10000 0 0
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
GNA15 0.013 0.05 -10000 0 -0.67 1 1
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.003 15 -0.001 123 138
GNA11 0.014 0.084 -10000 0 -0.64 8 8
LHCGR -0.078 0.23 -10000 0 -0.67 62 62
AGTR1 -0.26 0.34 -10000 0 -0.67 201 201
desensitization of G-protein coupled receptor protein signaling pathway -0.052 0.19 -10000 0 -0.56 62 62
IPCEF1/ARNO -0.035 0.18 -10000 0 -0.75 13 13
alphaIIb/beta3 Integrin -0.025 0.18 -10000 0 -0.53 55 55
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.034 0.17 -10000 0 -0.44 71 71
cell-cell adhesion 0.11 0.16 0.32 164 -10000 0 164
Ephrin B/EPHB2/RasGAP 0.065 0.06 -10000 0 -0.38 7 7
ITSN1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
SHC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.026 0.048 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.23 -10000 0 -0.43 186 186
HRAS/GDP -0.079 0.16 -10000 0 -0.36 12 12
Ephrin B/EPHB1/GRB7 -0.099 0.23 -10000 0 -0.4 178 178
Endophilin/SYNJ1 0.023 0.073 0.44 6 -0.35 7 13
KRAS 0.027 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.096 0.22 -10000 0 -0.38 179 179
endothelial cell migration 0.052 0.037 -10000 0 -0.37 3 3
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.056 -10000 0 -10000 0 0
PAK1 0.024 0.075 0.47 5 -0.35 7 12
HRAS 0.026 0.011 -10000 0 -10000 0 0
RRAS 0.02 0.067 0.44 4 -0.36 6 10
DNM1 0.005 0.12 -10000 0 -0.62 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.12 0.19 -10000 0 -0.37 178 178
lamellipodium assembly -0.11 0.16 -10000 0 -0.32 164 164
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.085 0.16 -10000 0 -0.3 161 161
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
EPHB2 0.022 0.055 -10000 0 -0.67 3 3
EPHB3 -0.067 0.075 -10000 0 -10000 0 0
EPHB1 -0.24 0.34 -10000 0 -0.67 188 188
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.071 0.13 -10000 0 -0.38 13 13
Ephrin B/EPHB2 0.051 0.056 -10000 0 -0.38 7 7
Ephrin B/EPHB3 0.057 0.055 -10000 0 -0.43 4 4
JNK cascade -0.12 0.19 -10000 0 -0.38 176 176
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.38 180 180
RAP1/GDP -0.046 0.14 -10000 0 -0.37 5 5
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EFNB3 0.015 0.068 -10000 0 -0.67 4 4
EFNB1 0.026 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.4 181 181
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.084 0.18 -10000 0 -0.38 20 20
Rap1/GTP -0.1 0.17 -10000 0 -0.44 7 7
axon guidance -0.034 0.17 -10000 0 -0.44 71 71
MAPK3 -0.081 0.14 -10000 0 -0.46 9 9
MAPK1 -0.079 0.13 -10000 0 -0.43 11 11
Rac1/GDP -0.057 0.13 -10000 0 -0.38 5 5
actin cytoskeleton reorganization -0.079 0.12 -10000 0 -0.34 3 3
CDC42/GDP -0.054 0.14 0.4 2 -0.38 5 7
PI3K 0.057 0.039 -10000 0 -0.38 3 3
EFNA5 -0.071 0.24 -10000 0 -0.67 69 69
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.044 -10000 0 -0.36 3 3
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.16 -10000 0 -0.42 7 7
PTK2 0.043 0.098 0.67 10 -10000 0 10
MAP4K4 -0.12 0.19 -10000 0 -0.38 176 176
SRC 0.026 0.008 -10000 0 -10000 0 0
KALRN 0.027 0.003 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.076 0.14 0.32 5 -10000 0 5
MAP2K1 -0.082 0.15 -10000 0 -0.4 17 17
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.11 0.22 -10000 0 -0.4 176 176
cell migration -0.083 0.18 0.58 4 -0.48 13 17
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.074 0.45 6 -0.36 7 13
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.024 0.13 0.47 3 -0.37 52 55
HRAS/GTP -0.092 0.19 -10000 0 -0.34 173 173
Ephrin B1/EPHB1-2 -0.12 0.22 -10000 0 -0.39 187 187
cell adhesion mediated by integrin -0.007 0.073 0.39 4 -0.37 8 12
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.096 0.2 -10000 0 -0.36 176 176
RAC1-CDC42/GTP -0.14 0.16 -10000 0 -0.37 131 131
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.048 0.14 -10000 0 -0.37 5 5
ruffle organization -0.1 0.18 0.58 6 -0.48 1 7
NCK1 0.027 0.003 -10000 0 -10000 0 0
receptor internalization 0.002 0.085 0.41 3 -0.37 17 20
Ephrin B/EPHB2/KALRN 0.065 0.06 -10000 0 -0.38 7 7
ROCK1 -0.025 0.044 -10000 0 -10000 0 0
RAS family/GDP -0.073 0.1 -10000 0 -0.34 2 2
Rac1/GTP -0.11 0.17 -10000 0 -0.34 164 164
Ephrin B/EPHB1/Src/Paxillin -0.091 0.16 -10000 0 -0.3 181 181
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.029 0.14 -10000 0 -0.37 44 44
TBX21 -0.12 0.43 -10000 0 -1.1 62 62
B2M 0.023 0.018 -10000 0 -10000 0 0
TYK2 0.019 0.03 -10000 0 -10000 0 0
IL12RB1 0 0.088 -10000 0 -0.64 6 6
GADD45B -0.096 0.39 -10000 0 -1 61 61
IL12RB2 -0.003 0.13 -10000 0 -0.66 17 17
GADD45G -0.092 0.36 -10000 0 -0.95 53 53
natural killer cell activation 0.001 0.02 0.047 10 -0.04 36 46
RELB 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 -0.003 0.11 -10000 0 -0.66 11 11
IL2RA -0.017 0.16 -10000 0 -0.64 28 28
IFNG -0.073 0.23 -10000 0 -0.67 62 62
STAT3 (dimer) -0.081 0.32 -10000 0 -0.78 64 64
HLA-DRB5 -0.005 0.01 -10000 0 -0.022 105 105
FASLG -0.14 0.46 -10000 0 -1.2 64 64
NF kappa B2 p52/RelB -0.1 0.39 -10000 0 -0.94 67 67
CD4 0.011 0.036 -10000 0 -10000 0 0
SOCS1 0.023 0.035 -10000 0 -0.67 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -0.029 139 139
CD3D -0.061 0.2 -10000 0 -0.64 52 52
CD3E -0.043 0.18 -10000 0 -0.62 42 42
CD3G -0.11 0.26 -10000 0 -0.66 88 88
IL12Rbeta2/JAK2 0.012 0.11 -10000 0 -0.47 19 19
CCL3 -0.12 0.42 -10000 0 -1.2 55 55
CCL4 -0.15 0.49 -10000 0 -1.3 63 63
HLA-A -0.001 0.01 -10000 0 -0.036 30 30
IL18/IL18R 0.027 0.16 -10000 0 -0.48 37 37
NOS2 -0.088 0.36 -10000 0 -1 47 47
IL12/IL12R/TYK2/JAK2/SPHK2 -0.029 0.14 -10000 0 -0.38 40 40
IL1R1 -0.1 0.38 -10000 0 -1 53 53
IL4 0 0.034 -10000 0 -10000 0 0
JAK2 0.018 0.04 -10000 0 -0.38 2 2
EntrezGene:6957 -0.006 0.014 -10000 0 -0.027 132 132
TCR/CD3/MHC I/CD8 -0.21 0.49 -10000 0 -1.1 96 96
RAB7A -0.057 0.3 -10000 0 -0.76 53 53
lysosomal transport -0.051 0.29 -10000 0 -0.71 53 53
FOS -0.36 0.61 -10000 0 -1.2 163 163
STAT4 (dimer) -0.085 0.36 -10000 0 -0.84 70 70
STAT5A (dimer) -0.14 0.41 -10000 0 -0.95 79 79
GZMA -0.12 0.4 -10000 0 -1.2 50 50
GZMB -0.11 0.39 -10000 0 -1.1 49 49
HLX 0.022 0.025 -10000 0 -10000 0 0
LCK -0.13 0.43 -10000 0 -1.1 65 65
TCR/CD3/MHC II/CD4 -0.14 0.26 -10000 0 -0.42 163 163
IL2/IL2R -0.007 0.17 -10000 0 -0.55 37 37
MAPK14 -0.085 0.37 0.46 1 -0.89 67 68
CCR5 -0.095 0.4 -10000 0 -1.2 42 42
IL1B -0.025 0.18 -10000 0 -0.71 32 32
STAT6 -0.007 0.11 -10000 0 -0.36 10 10
STAT4 0.004 0.099 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B 0.004 0.09 -10000 0 -0.68 7 7
CD8A -0.028 0.18 -10000 0 -0.66 38 38
CD8B -0.055 0.21 -10000 0 -0.65 55 55
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.029 0.14 0.37 44 -10000 0 44
IL2RB 0.004 0.09 -10000 0 -0.58 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.072 0.33 -10000 0 -0.76 70 70
IL2RG -0.012 0.14 -10000 0 -0.63 21 21
IL12 -0.037 0.18 -10000 0 -0.53 58 58
STAT5A 0.026 0.007 -10000 0 -10000 0 0
CD247 -0.013 0.13 -10000 0 -0.68 17 17
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.055 0.22 -10000 0 -0.68 53 53
IL12/IL12R/TYK2/JAK2 -0.14 0.51 -10000 0 -1.2 67 67
MAP2K3 -0.086 0.37 -10000 0 -0.9 64 64
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.093 0.38 -10000 0 -0.89 69 69
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.005 0.011 -10000 0 -0.026 114 114
IL18RAP -0.006 0.15 -10000 0 -0.68 23 23
IL12Rbeta1/TYK2 0.019 0.076 -10000 0 -0.49 6 6
EOMES -0.13 0.4 -10000 0 -1.3 49 49
STAT1 (dimer) -0.12 0.36 -10000 0 -0.8 87 87
T cell proliferation -0.051 0.27 -10000 0 -0.62 65 65
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.096 -10000 0 -0.58 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.068 0.28 -10000 0 -0.66 70 70
ATF2 -0.088 0.34 0.44 1 -0.79 71 72
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.083 0.32 -10000 0 -1.2 39 39
MKNK1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.016 0.11 -10000 0 -0.35 33 33
ATF2/c-Jun -0.2 0.36 -10000 0 -0.79 123 123
MAPK11 -0.011 0.095 -10000 0 -0.35 27 27
MITF -0.022 0.12 -10000 0 -0.42 36 36
MAPKAPK5 -0.018 0.11 -10000 0 -0.41 32 32
KRT8 -0.018 0.11 -10000 0 -0.41 32 32
MAPKAPK3 0.027 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.027 0.15 -10000 0 -0.49 36 36
CEBPB -0.02 0.12 -10000 0 -0.41 34 34
SLC9A1 -0.022 0.12 -10000 0 -0.41 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.074 0.19 -10000 0 -0.44 80 80
p38alpha-beta/MNK1 -0.009 0.13 -10000 0 -0.41 32 32
JUN -0.2 0.35 -10000 0 -0.79 123 123
PPARGC1A -0.22 0.25 -10000 0 -0.45 254 254
USF1 -0.023 0.12 -10000 0 -0.41 37 37
RAB5/GDP/GDI1 -0.034 0.1 -10000 0 -0.32 34 34
NOS2 -0.027 0.12 -10000 0 -0.53 6 6
DDIT3 -0.019 0.11 -10000 0 -0.41 32 32
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.015 0.092 0.37 2 -0.34 30 32
p38alpha-beta/HBP1 -0.005 0.12 -10000 0 -0.42 26 26
CREB1 -0.054 0.16 -10000 0 -0.47 41 41
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.024 0.1 -10000 0 -0.38 25 25
RPS6KA4 -0.02 0.12 -10000 0 -0.42 34 34
PLA2G4A -0.05 0.16 -10000 0 -0.48 49 49
GDI1 -0.018 0.12 -10000 0 -0.43 31 31
TP53 -0.031 0.13 -10000 0 -0.5 31 31
RPS6KA5 -0.062 0.18 -10000 0 -0.45 77 77
ESR1 -0.049 0.19 -10000 0 -0.54 50 50
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.019 0.12 -10000 0 -0.41 33 33
MEF2A -0.024 0.12 -10000 0 -0.42 38 38
EIF4EBP1 -0.053 0.15 -10000 0 -0.46 42 42
KRT19 -0.051 0.16 -10000 0 -0.49 44 44
ELK4 -0.023 0.12 -10000 0 -0.41 37 37
ATF6 -0.023 0.12 -10000 0 -0.41 37 37
ATF1 -0.052 0.15 -10000 0 -0.47 39 39
p38alpha-beta/MAPKAPK2 -0.01 0.12 -10000 0 -0.41 32 32
p38alpha-beta/MAPKAPK3 -0.009 0.13 -10000 0 -0.42 32 32
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.005 0.053 -10000 0 -10000 0 0
GNB1/GNG2 -0.032 0.065 -10000 0 -0.19 67 67
AKT1 0.014 0.13 0.41 23 -0.23 5 28
EGF -0.076 0.25 -10000 0 -0.67 72 72
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.02 0.086 0.36 14 -0.5 2 16
mol:Ca2+ -0.014 0.15 0.4 16 -0.3 68 84
LYN 0.02 0.085 0.36 13 -0.5 2 15
RhoA/GTP -0.008 0.054 -10000 0 -0.15 2 2
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.015 0.17 0.43 19 -0.34 67 86
GNG2 0.025 0.032 -10000 0 -0.68 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.59 12 13
G beta5/gamma2 -0.042 0.089 -10000 0 -0.25 67 67
PRKCH -0.021 0.17 0.44 15 -0.36 68 83
DNM1 0.005 0.12 -10000 0 -0.62 16 16
TXA2/TP beta/beta Arrestin3 -0.009 0.12 -10000 0 -0.49 24 24
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.002 0.14 -10000 0 -0.67 20 20
G12 family/GTP -0.033 0.12 -10000 0 -0.31 65 65
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.007 -10000 0 -10000 0 0
mol:GDP 0.047 0.14 0.39 37 -0.35 7 44
mol:NADP 0.026 0.006 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.67 136 136
mol:IP3 -0.024 0.18 0.45 14 -0.38 68 82
cell morphogenesis 0.036 0.007 -10000 0 -10000 0 0
PLCB2 -0.045 0.22 0.45 12 -0.52 68 80
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.077 0.17 0.36 10 -0.33 140 150
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.015 0.081 0.35 11 -0.5 2 13
RHOA 0.027 0.003 -10000 0 -10000 0 0
PTGIR 0.02 0.063 -10000 0 -0.68 4 4
PRKCB1 -0.024 0.17 0.43 14 -0.38 68 82
GNAQ 0.025 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.042 0.23 0.49 14 -0.54 68 82
LCK 0.016 0.098 0.36 14 -0.53 5 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.027 0.081 -10000 0 -0.68 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.033 -10000 0 -0.36 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.032 0.081 -10000 0 -0.67 2 2
MAPK14 -0.003 0.12 0.35 21 -0.23 61 82
TGM2/GTP -0.041 0.18 0.34 6 -0.43 63 69
MAPK11 -0.006 0.13 0.38 20 -0.23 50 70
ARHGEF1 -0.014 0.073 0.17 1 -0.19 37 38
GNAI2 0.027 0.003 -10000 0 -10000 0 0
JNK cascade -0.021 0.18 0.43 19 -0.39 68 87
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.013 0.14 0.38 19 -0.29 69 88
cAMP biosynthetic process -0.025 0.17 0.43 16 -0.36 63 79
Gq family/GTP/EBP50 -0.046 0.12 0.24 2 -0.23 120 122
actin cytoskeleton reorganization 0.036 0.007 -10000 0 -10000 0 0
SRC 0.018 0.08 0.35 11 -0.5 2 13
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.019 0.13 0.43 17 -0.29 14 31
VCAM1 -0.01 0.15 0.37 19 -0.3 69 88
TP beta/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.59 12 13
platelet activation -0.002 0.17 0.45 24 -0.3 64 88
PGI2/IP 0.015 0.048 -10000 0 -0.51 4 4
PRKACA 0.005 0.079 -10000 0 -0.35 21 21
Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.28 1 -0.54 13 14
TXA2/TP beta/beta Arrestin2 0.006 0.1 -10000 0 -0.54 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.001 0.079 -10000 0 -0.35 19 19
mol:DAG -0.029 0.19 0.45 14 -0.43 68 82
EGFR 0.019 0.07 -10000 0 -0.67 5 5
TXA2/TP alpha -0.041 0.22 0.52 13 -0.49 63 76
Gq family/GTP -0.066 0.13 0.22 2 -0.28 123 125
YES1 0.022 0.088 0.37 15 -0.5 2 17
GNAI2/GTP 0.009 0.069 -10000 0 -0.6 2 2
PGD2/DP -0.002 0.1 -10000 0 -0.51 20 20
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.024 0.089 0.36 17 -0.5 2 19
mol:NO 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.013 0.05 -10000 0 -0.67 1 1
PGK/cGMP -0.092 0.21 -10000 0 -0.43 135 135
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.091 -10000 0 -0.48 6 6
NOS3 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.024 0.18 0.44 17 -0.38 70 87
PRKCB -0.023 0.18 0.44 17 -0.37 67 84
PRKCE -0.027 0.16 0.37 12 -0.37 69 81
PRKCD -0.025 0.17 0.43 13 -0.38 68 81
PRKCG -0.024 0.18 0.44 15 -0.39 66 81
muscle contraction -0.034 0.22 0.5 15 -0.49 68 83
PRKCZ -0.014 0.17 0.43 19 -0.34 65 84
ARR3 -0.002 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.016 0.08 -10000 0 -0.32 18 18
PRKCQ -0.024 0.17 0.41 14 -0.36 69 83
MAPKKK cascade -0.034 0.21 0.46 16 -0.46 68 84
SELE -0.027 0.18 0.37 19 -0.42 69 88
TP beta/GNAI2/GDP/G beta/gamma 0.039 0.089 -10000 0 -0.8 2 2
ROCK1 0.027 0.005 -10000 0 -10000 0 0
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
chemotaxis -0.049 0.26 0.58 10 -0.61 69 79
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.084 -10000 0 -0.64 8 8
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.003 0.19 0.6 5 -0.59 18 23
CRP 0.005 0.2 0.58 9 -0.6 18 27
cell cycle arrest -0.011 0.2 0.49 6 -0.64 26 32
TIMP1 -0.037 0.22 0.6 3 -0.67 25 28
IL6ST -0.065 0.24 -10000 0 -0.67 66 66
Rac1/GDP -0.043 0.2 0.31 1 -0.53 45 46
AP1 -0.11 0.27 -10000 0 -0.6 92 92
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.009 0.19 0.63 4 -0.6 17 21
HSP90B1 0.043 0.052 -10000 0 -0.64 1 1
GAB1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 -0.082 0.24 -10000 0 -0.71 46 46
AKT1 0.04 0.06 -10000 0 -0.98 1 1
FOXO1 0.04 0.058 -10000 0 -0.91 1 1
MAP2K6 -0.074 0.23 0.25 1 -0.61 52 53
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.029 0.19 0.34 5 -0.54 37 42
MITF -0.063 0.21 -10000 0 -0.56 47 47
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.008 -10000 0 -10000 0 0
A2M 0.026 0.07 -10000 0 -1.1 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.009 0.093 -10000 0 -0.49 6 6
STAT3 -0.021 0.21 0.51 4 -0.68 26 30
STAT1 0.01 0.097 -10000 0 -0.92 5 5
CEBPD 0 0.19 0.5 7 -0.56 25 32
PIK3CA 0.024 0.055 -10000 0 -0.67 3 3
PI3K 0.038 0.043 -10000 0 -0.51 3 3
JUN -0.12 0.29 -10000 0 -0.67 107 107
PIAS3/MITF -0.048 0.2 -10000 0 -0.57 40 40
MAPK11 -0.084 0.23 -10000 0 -0.72 43 43
STAT3 (dimer)/FOXO1 0.018 0.16 0.38 1 -0.52 19 20
GRB2/SOS1/GAB family -0.025 0.2 -10000 0 -0.61 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.068 0.21 -10000 0 -0.37 128 128
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.025 -10000 0 -0.36 2 2
LBP 0.008 0.18 0.59 8 -0.51 15 23
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.013 -10000 0 -10000 0 0
MYC -0.013 0.24 0.52 7 -0.78 28 35
FGG -0.006 0.19 0.68 3 -0.6 19 22
macrophage differentiation -0.011 0.2 0.49 6 -0.64 26 32
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.065 0.25 -10000 0 -0.46 129 129
JUNB -0.001 0.21 0.6 3 -0.68 20 23
FOS -0.15 0.3 -10000 0 -0.67 125 125
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.062 0.22 -10000 0 -0.41 108 108
STAT1/PIAS1 -0.034 0.2 -10000 0 -0.51 46 46
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.062 -10000 0 -0.55 3 3
STAT3 (dimer) -0.015 0.21 0.55 3 -0.67 26 29
PRKCD -0.017 0.19 0.4 7 -0.56 29 36
IL6R 0.003 0.12 -10000 0 -0.67 16 16
SOCS3 -0.095 0.31 0.43 2 -0.95 43 45
gp130 (dimer)/JAK1/JAK1/LMO4 -0.006 0.17 -10000 0 -0.44 64 64
Rac1/GTP -0.04 0.2 -10000 0 -0.55 42 42
HCK 0.016 0.039 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.1 -10000 0 -0.61 5 5
bone resorption -0.008 0.18 0.63 4 -0.56 19 23
IRF1 0.003 0.19 0.61 7 -0.59 17 24
mol:GDP -0.061 0.2 0.25 1 -0.54 50 51
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.062 0.2 0.25 1 -0.55 50 51
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.078 0.24 -10000 0 -0.71 48 48
PTPN11 0.014 0.074 -10000 0 -0.87 3 3
IL6/IL6RA -0.07 0.22 -10000 0 -0.52 92 92
gp130 (dimer)/TYK2/TYK2/LMO4 -0.009 0.16 -10000 0 -0.41 66 66
gp130 (dimer)/JAK2/JAK2/LMO4 -0.012 0.17 -10000 0 -0.43 66 66
IL6 -0.095 0.26 -10000 0 -0.68 81 81
PIAS3 0.026 0.007 -10000 0 -10000 0 0
PTPRE -0.025 0.078 -10000 0 -0.68 1 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.069 0.21 -10000 0 -0.38 126 126
LMO4 0.028 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.017 0.21 -10000 0 -0.68 25 25
MCL1 0.054 0.072 -10000 0 -0.82 1 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.045 0.042 -10000 0 -0.82 1 1
forebrain development -0.3 0.28 0.41 2 -0.59 181 183
GNAO1 0.002 0.12 -10000 0 -0.67 15 15
SMO/beta Arrestin2 0.015 0.036 -10000 0 -0.51 1 1
SMO 0.015 0.034 -10000 0 -0.67 1 1
ARRB2 0.021 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.036 0.075 -10000 0 -0.37 3 3
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.003 -10000 0 -10000 0 0
GNAI2 0.025 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.033 -10000 0 -0.4 1 1
GNAI1 0.023 0.032 -10000 0 -0.68 1 1
XPO1 0.016 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.21 0.21 -10000 0 -0.49 135 135
SAP30 0.026 0.032 -10000 0 -0.67 1 1
mol:GDP 0.015 0.034 -10000 0 -0.67 1 1
MIM/GLI2A -0.031 0.067 -10000 0 -10000 0 0
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.025 0.006 -10000 0 -10000 0 0
GLI2 0 0.079 0.28 2 -0.38 7 9
GLI3 0.027 0.078 0.28 3 -0.36 5 8
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.67 1 1
Gi family/GTP -0.016 0.069 -10000 0 -0.3 17 17
SIN3B 0.026 0.008 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.067 -10000 0 -0.48 2 2
GLI2/Su(fu) 0.01 0.075 -10000 0 -0.49 3 3
FOXA2 -0.58 0.62 -10000 0 -1.2 242 242
neural tube patterning -0.3 0.28 0.41 2 -0.59 181 183
SPOP 0.026 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.035 0.03 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
MTSS1 -0.031 0.067 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.41 2 -0.59 181 183
SUFU 0.019 0.016 -10000 0 -0.24 1 1
LGALS3 -0.023 0.077 -10000 0 -0.67 1 1
catabolic process 0.032 0.1 -10000 0 -0.49 5 5
GLI3A/CBP -0.17 0.2 -10000 0 -0.38 245 245
KIF3A 0.026 0.006 -10000 0 -10000 0 0
GLI1 -0.3 0.28 0.41 2 -0.61 180 182
RAB23 0.022 0.063 -10000 0 -0.67 4 4
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.019 0.052 -10000 0 -0.33 2 2
GNAZ 0.018 0.012 -10000 0 -10000 0 0
RBBP4 0.025 0.045 -10000 0 -0.67 2 2
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GLI2/SPOP 0.011 0.081 -10000 0 -0.36 7 7
STK36 0.016 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.054 -10000 0 -0.34 4 4
PTCH1 -0.27 0.26 0.58 2 -0.59 133 135
MIM/GLI1 -0.42 0.37 -10000 0 -0.72 249 249
CREBBP -0.17 0.2 -10000 0 -0.38 245 245
Su(fu)/SIN3/HDAC complex 0.036 0.068 -10000 0 -0.53 5 5
EGFR-dependent Endothelin signaling events

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
HRAS 0.026 0.011 -9999 0 -10000 0 0
EGFR 0.019 0.07 -9999 0 -0.67 5 5
EGF/EGFR -0.017 0.15 -9999 0 -0.37 78 78
EGF/EGFR dimer/SHC/GRB2/SOS1 0.003 0.16 -9999 0 -0.38 70 70
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.024 0.035 -9999 0 -0.67 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.076 0.25 -9999 0 -0.67 72 72
EGF/EGFR dimer/SHC -0.025 0.18 -9999 0 -0.44 73 73
mol:GDP -0.002 0.16 -9999 0 -0.38 70 70
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.019 0.071 -9999 0 -0.67 5 5
GRB2/SOS1 0.038 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.014 0.14 -9999 0 -0.35 70 70
SHC1 0.025 0.008 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.15 -9999 0 -0.36 70 70
FRAP1 -0.052 0.13 -9999 0 -0.36 70 70
EGF/EGFR dimer -0.045 0.2 -9999 0 -0.5 76 76
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.032 0.062 -9999 0 -0.51 6 6
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.1 0.22 -10000 0 -0.42 132 132
MAP3K8 0.015 0.079 -10000 0 -0.63 7 7
FOS -0.075 0.17 0.3 2 -0.44 59 61
PRKCA -0.008 0.13 -10000 0 -0.68 17 17
PTPN7 -0.023 0.13 -10000 0 -0.67 18 18
HRAS 0.025 0.011 -10000 0 -10000 0 0
PRKCB -0.003 0.081 -10000 0 -0.68 5 5
NRAS 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.022 -10000 0 -10000 0 0
MAPK3 -0.012 0.12 -10000 0 -0.47 22 22
MAP2K1 -0.015 0.13 -10000 0 -0.53 22 22
ELK1 0.013 0.025 -10000 0 -10000 0 0
BRAF -0.011 0.11 -10000 0 -0.52 21 21
mol:GTP -0.002 0.004 -10000 0 -0.007 128 128
MAPK1 -0.1 0.2 -10000 0 -0.5 64 64
RAF1 -0.011 0.11 -10000 0 -0.52 21 21
KRAS 0.026 0.005 -10000 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer 0.001 0.11 -10000 0 -0.38 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.11 0.35 3 -0.51 2 5
alphaV/beta3 Integrin/Osteopontin/Src -0.003 0.12 -10000 0 -0.5 25 25
AP1 -0.14 0.3 -10000 0 -0.7 89 89
ILK -0.006 0.11 -10000 0 -0.4 30 30
bone resorption -0.007 0.13 -10000 0 -0.54 7 7
PTK2B 0.027 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.043 0.11 -10000 0 -0.37 31 31
ITGAV 0.026 0.045 -10000 0 -0.67 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.013 0.12 -10000 0 -0.5 24 24
alphaV/beta3 Integrin/Osteopontin 0.027 0.13 -10000 0 -0.44 31 31
MAP3K1 -0.007 0.11 -10000 0 -0.4 31 31
JUN -0.12 0.29 -10000 0 -0.67 107 107
MAPK3 -0.022 0.099 -10000 0 -0.37 31 31
MAPK1 -0.023 0.095 -10000 0 -0.37 30 30
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.018 0.12 -10000 0 -0.4 37 37
ITGB3 0.013 0.1 -10000 0 -0.64 11 11
NFKBIA -0.018 0.094 -10000 0 -0.37 29 29
FOS -0.15 0.3 -10000 0 -0.67 125 125
CD44 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.039 0.11 0.52 3 -0.61 1 4
NF kappa B1 p50/RelA 0.022 0.1 -10000 0 -0.51 2 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.028 0.088 -10000 0 -0.54 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.007 0.11 -10000 0 -0.4 31 31
VAV3 -0.015 0.12 0.4 1 -0.39 35 36
MAP3K14 -0.013 0.11 -10000 0 -0.4 31 31
ROCK2 -0.006 0.15 -10000 0 -0.66 24 24
SPP1 -0.028 0.15 -10000 0 -0.67 23 23
RAC1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.11 -10000 0 -0.36 34 34
MMP2 -0.13 0.24 -10000 0 -0.56 91 91
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.099 -10000 0 -0.67 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 256 256
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.015 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.044 0.068 -10000 0 -0.28 10 10
PRKG1 -0.16 0.31 -10000 0 -0.67 136 136
DUSP8 0.019 0.065 -10000 0 -0.67 4 4
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.37 132 132
apoptosis -0.042 0.065 -10000 0 -0.27 10 10
RAL/GTP 0.036 0.008 -10000 0 -10000 0 0
LYN 0.027 0.005 -10000 0 -10000 0 0
DUSP1 -0.084 0.26 -10000 0 -0.67 78 78
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.065 0.02 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.01 -10000 0 -10000 0 0
MAPK11 -0.054 0.16 0.44 16 -0.33 30 46
BLK -0.19 0.31 -10000 0 -0.67 148 148
HCK 0.017 0.039 -10000 0 -10000 0 0
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.023 0.034 -10000 0 -0.67 1 1
TRAF6/MEKK3 0.031 0.029 -10000 0 -0.4 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.011 0.12 0.38 16 -0.32 8 24
positive regulation of innate immune response -0.043 0.17 0.46 19 -0.47 8 27
LCK 0.012 0.082 -10000 0 -0.67 6 6
p38alpha-beta/MKP7 -0.045 0.14 0.34 9 -0.46 7 16
p38alpha-beta/MKP5 -0.037 0.15 0.46 12 -0.45 7 19
PGK/cGMP -0.12 0.23 -10000 0 -0.5 136 136
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.097 0.18 0.31 4 -0.46 47 51
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.027 0.005 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
PAK3 -0.36 0.34 -10000 0 -0.66 279 279
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.013 -10000 0 -10000 0 0
SMARCC1 0.011 0.013 -10000 0 -10000 0 0
REL -0.012 0.17 -10000 0 -0.66 32 32
HDAC7 -0.07 0.12 -10000 0 -0.53 16 16
JUN -0.12 0.29 -10000 0 -0.67 107 107
EP300 0.02 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.015 0.075 -10000 0 -0.52 10 10
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.068 0.13 -10000 0 -0.53 19 19
MAP2K6 0.004 0.1 -10000 0 -0.68 10 10
BRM/BAF57 0.017 0.033 -10000 0 -10000 0 0
MAP2K4 0.019 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.022 -10000 0 -10000 0 0
PDE9A 0.015 0.066 -10000 0 -0.59 1 1
NCOA2 -0.043 0.2 -10000 0 -0.68 45 45
CEBPA 0.019 0.07 -10000 0 -0.67 5 5
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.082 0.2 0.57 20 -0.49 20 40
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.13 0.28 -10000 0 -0.68 101 101
RXRs/9cRA 0.017 0.072 -10000 0 -0.4 4 4
AR/RACK1/Src -0.13 0.15 0.33 2 -0.56 18 20
AR/GR -0.12 0.18 0.28 2 -0.34 149 151
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.007 -10000 0 -0.011 179 179
MAPK8 -0.014 0.071 -10000 0 -0.52 9 9
T-DHT/AR/TIF2/CARM1 -0.13 0.19 0.34 3 -0.58 47 50
SRC -0.044 0.088 0.24 1 -0.46 16 17
NR3C1 0.026 0.006 -10000 0 -10000 0 0
KLK3 -0.36 0.55 0.38 2 -1.2 143 145
APPBP2 0.024 0.012 -10000 0 -10000 0 0
TRIM24 0.013 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.07 0.13 0.32 7 -0.57 16 23
TMPRSS2 -0.043 0.28 -10000 0 -1.1 30 30
RXRG -0.11 0.076 -10000 0 -0.67 4 4
mol:9cRA -0.002 0.003 -10000 0 -0.011 10 10
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.009 -10000 0 -10000 0 0
NR2C2 0.012 0.099 -10000 0 -0.68 10 10
KLK2 -0.45 0.38 0.34 2 -0.77 287 289
AR -0.14 0.18 -10000 0 -0.35 198 198
SENP1 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.036 0.016 -10000 0 -10000 0 0
SRY 0.009 0.015 0.031 142 -10000 0 142
GATA2 0.027 0.008 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.011 0.034 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.1 0.13 0.33 4 -0.57 16 20
positive regulation of transcription 0.027 0.008 -10000 0 -10000 0 0
DNAJA1 0.024 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.018 0.022 -10000 0 -10000 0 0
SPDEF -0.003 0.049 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.092 0.15 0.28 2 -0.45 48 50
T-DHT/AR/Hsp90 -0.071 0.13 0.33 7 -0.56 16 23
GSK3B 0.025 0.007 -10000 0 -10000 0 0
NR2C1 0.028 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.038 0.092 0.26 1 -0.49 16 17
SIRT1 0.025 0.032 -10000 0 -0.67 1 1
ZMIZ2 0.036 0.017 -10000 0 -10000 0 0
POU2F1 0.032 0.036 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.075 0.13 0.32 6 -0.57 16 22
CREBBP 0.026 0.006 -10000 0 -10000 0 0
SMARCE1 0.012 0.022 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.005 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.005 0.12 -10000 0 -0.37 18 18
NFATC4 -0.018 0.087 0.28 4 -0.29 9 13
ERBB2IP 0.027 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.014 0.11 -10000 0 -0.35 39 39
JUN -0.005 0.094 0.34 10 -0.4 1 11
HRAS 0.025 0.011 -10000 0 -10000 0 0
DOCK7 -0.024 0.1 -10000 0 -0.34 38 38
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.004 0.12 -10000 0 -0.4 41 41
AKT1 0.007 0.006 -10000 0 -10000 0 0
BAD 0.005 0.004 -10000 0 -10000 0 0
MAPK10 -0.008 0.065 0.25 4 -0.3 2 6
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.015 0.12 -10000 0 -0.38 39 39
RAF1 -0.011 0.12 0.32 9 -0.39 18 27
ErbB2/ErbB3/neuregulin 2 -0.025 0.14 -10000 0 -0.41 60 60
STAT3 0.028 0.069 -10000 0 -0.84 3 3
cell migration 0.007 0.11 0.39 20 -0.28 4 24
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.15 0.32 0.35 1 -0.68 117 118
FOS -0.12 0.26 0.35 6 -0.5 152 158
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.11 -10000 0 -0.35 39 39
MAPK3 -0.077 0.24 0.38 3 -0.52 87 90
MAPK1 -0.17 0.3 0.36 1 -0.64 119 120
JAK2 -0.024 0.098 -10000 0 -0.34 38 38
NF2 -0.011 0.11 -10000 0 -0.62 16 16
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.011 0.11 -10000 0 -0.34 41 41
NRG1 -0.034 0.19 -10000 0 -0.66 43 43
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
MAPK8 -0.019 0.11 -10000 0 -0.33 46 46
MAPK9 -0.009 0.062 0.23 3 -10000 0 3
ERBB2 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.016 0.079 -10000 0 -0.63 7 7
SHC1 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.001 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.067 -10000 0 -0.82 3 3
RNF41 0 0.008 -10000 0 -10000 0 0
FRAP1 0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.017 0.076 -10000 0 -0.25 37 37
ErbB2/ErbB2/HSP90 (dimer) 0.014 0.013 -10000 0 -10000 0 0
CHRNA1 -0.075 0.19 0.33 1 -0.4 99 100
myelination -0.008 0.14 0.52 17 -0.31 1 18
PPP3CB -0.021 0.094 -10000 0 -0.32 37 37
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.021 0.1 -10000 0 -0.3 40 40
NRG2 -0.052 0.22 -10000 0 -0.67 54 54
mol:GDP -0.011 0.11 -10000 0 -0.34 41 41
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.026 0.12 0.31 5 -0.38 20 25
SRC 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP 0 0.003 -10000 0 -10000 0 0
PTPN11 -0.022 0.1 0.25 1 -0.34 39 40
MAP2K1 -0.073 0.23 0.36 1 -0.58 37 38
heart morphogenesis -0.014 0.11 -10000 0 -0.35 39 39
RAS family/GDP 0.017 0.11 -10000 0 -0.38 14 14
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA -0.011 0.12 -10000 0 -0.65 18 18
CHRNE 0.008 0.037 0.18 12 -0.23 1 13
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.006 -10000 0 -10000 0 0
nervous system development -0.014 0.11 -10000 0 -0.35 39 39
CDC42 0.027 0.005 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CCL5 -0.016 0.16 -10000 0 -0.67 28 28
SDCBP 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.039 0.13 -10000 0 -0.41 42 42
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.033 0.14 -10000 0 -0.48 29 29
Syndecan-1/Syntenin -0.031 0.14 0.25 1 -0.53 23 24
MAPK3 -0.031 0.12 -10000 0 -0.51 19 19
HGF/MET -0.078 0.19 -10000 0 -0.52 70 70
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
BSG 0.025 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.033 0.14 -10000 0 -0.47 29 29
Syndecan-1/RANTES -0.051 0.19 -10000 0 -0.56 47 47
Syndecan-1/CD147 -0.016 0.14 -10000 0 -0.52 22 22
Syndecan-1/Syntenin/PIP2 -0.031 0.14 -10000 0 -0.52 23 23
LAMA5 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.031 0.13 -10000 0 -0.5 23 23
MMP7 -0.079 0.16 -10000 0 -0.66 26 26
HGF -0.073 0.24 -10000 0 -0.67 70 70
Syndecan-1/CASK -0.046 0.13 -10000 0 -0.41 45 45
Syndecan-1/HGF/MET -0.076 0.2 -10000 0 -0.5 73 73
regulation of cell adhesion -0.033 0.11 -10000 0 -0.49 19 19
HPSE 0.01 0.094 -10000 0 -0.64 9 9
positive regulation of cell migration -0.039 0.13 -10000 0 -0.41 42 42
SDC1 -0.039 0.13 -10000 0 -0.42 42 42
Syndecan-1/Collagen -0.039 0.13 -10000 0 -0.41 42 42
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET -0.029 0.074 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
MAPK1 -0.032 0.12 -10000 0 -0.5 21 21
homophilic cell adhesion -0.039 0.13 -10000 0 -0.4 43 43
MMP1 -0.045 0.075 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.013 0.062 0.24 32 -10000 0 32
RFC1 0.015 0.064 0.24 35 -10000 0 35
PRKDC 0.017 0.071 0.26 37 -10000 0 37
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.003 0.095 -10000 0 -0.74 6 6
FASLG/FAS/FADD/FAF1 -0.015 0.096 0.24 5 -0.34 33 38
MAP2K4 -0.027 0.16 0.32 2 -0.49 26 28
mol:ceramide -0.02 0.13 -10000 0 -0.43 35 35
GSN 0.013 0.062 0.24 32 -10000 0 32
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.12 -10000 0 -0.43 33 33
FAS 0.02 0.018 -10000 0 -10000 0 0
BID -0.017 0.036 0.26 4 -10000 0 4
MAP3K1 -0.008 0.12 0.27 3 -0.41 18 21
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
RB1 0.014 0.066 0.25 33 -10000 0 33
CFLAR 0.028 0.006 -10000 0 -10000 0 0
HGF/MET -0.02 0.19 -10000 0 -0.47 73 73
ARHGDIB 0.016 0.069 0.25 38 -10000 0 38
FADD 0.02 0.018 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.062 -10000 0 -0.24 32 32
NFKB1 -0.015 0.098 -10000 0 -0.57 3 3
MAPK8 -0.063 0.22 0.4 2 -0.47 93 95
DFFA 0.015 0.065 0.24 36 -10000 0 36
DNA fragmentation during apoptosis 0.015 0.065 0.24 36 -10000 0 36
FAS/FADD/MET 0.039 0.044 -10000 0 -10000 0 0
CFLAR/RIP1 0.042 0.01 -10000 0 -10000 0 0
FAIM3 0.016 0.061 -10000 0 -0.67 3 3
FAF1 0.019 0.02 -10000 0 -10000 0 0
PARP1 0.019 0.082 0.29 36 -10000 0 36
DFFB 0.015 0.065 0.24 36 -10000 0 36
CHUK -0.015 0.089 -10000 0 -0.62 2 2
FASLG -0.034 0.18 -10000 0 -0.68 33 33
FAS/FADD 0.029 0.026 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 70 70
LMNA 0.014 0.07 0.26 28 -10000 0 28
CASP6 0.015 0.064 0.24 35 -10000 0 35
CASP10 0.02 0.018 -10000 0 -10000 0 0
CASP3 0.019 0.08 0.3 37 -10000 0 37
PTPN13 0.019 0.077 -10000 0 -0.67 6 6
CASP8 -0.012 0.034 0.4 3 -10000 0 3
IL6 -0.2 0.5 -10000 0 -1.3 91 91
MET -0.029 0.074 -10000 0 -10000 0 0
ICAD/CAD 0.014 0.06 0.23 27 -10000 0 27
FASLG/FAS/FADD/FAF1/Caspase 10 -0.02 0.14 -10000 0 -0.43 35 35
activation of caspase activity by cytochrome c -0.017 0.036 0.26 4 -10000 0 4
PAK2 0.015 0.065 0.24 36 -10000 0 36
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
Plasma membrane estrogen receptor signaling

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.04 0.1 -10000 0 -0.41 22 22
ER alpha/Gai/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.54 22 22
AKT1 -0.012 0.2 -10000 0 -0.78 28 28
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.008 0.2 -10000 0 -0.81 27 27
mol:Ca2+ -0.098 0.19 -10000 0 -0.43 120 120
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.019 0.15 -10000 0 -0.46 49 49
SHC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.01 0.18 0.74 28 -10000 0 28
RhoA/GTP 0.006 0.071 -10000 0 -0.34 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.005 0.13 -10000 0 -0.54 20 20
regulation of stress fiber formation 0.009 0.088 0.36 5 -0.28 1 6
E2/ERA-ERB (dimer) 0.007 0.11 -10000 0 -0.45 23 23
KRAS 0.027 0.005 -10000 0 -10000 0 0
G13/GTP 0.01 0.085 -10000 0 -0.37 21 21
pseudopodium formation -0.009 0.088 0.28 1 -0.36 5 6
E2/ER alpha (dimer)/PELP1 0.01 0.093 -10000 0 -0.41 21 21
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.67 1 1
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.01 0.15 0.47 7 -0.59 22 29
E2/ER beta (dimer) 0.017 0.041 -10000 0 -0.51 3 3
mol:GDP 0.003 0.11 -10000 0 -0.47 23 23
mol:NADP 0.01 0.15 0.47 7 -0.59 22 29
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.1 0.2 -10000 0 -0.44 120 120
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.1 0.21 -10000 0 -0.45 121 121
PLCB2 -0.1 0.21 -10000 0 -0.46 121 121
IGF1 -0.13 0.29 -10000 0 -0.67 108 108
mol:L-citrulline 0.01 0.15 0.47 7 -0.59 22 29
RHOA 0.027 0.003 -10000 0 -10000 0 0
Gai/GDP 0.005 0.14 -10000 0 -0.67 20 20
JNK cascade 0.017 0.041 -10000 0 -0.51 3 3
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.023 0.055 -10000 0 -0.67 3 3
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.014 0.15 -10000 0 -0.65 23 23
Gq family/GDP/Gbeta gamma -0.059 0.19 -10000 0 -0.65 28 28
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.097 -10000 0 -0.64 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.003 0.13 -10000 0 -0.55 19 19
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.01 0.11 -10000 0 -0.49 23 23
STRN -0.016 0.17 -10000 0 -0.66 31 31
GNAL -0.061 0.23 -10000 0 -0.66 64 64
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.01 0.035 -10000 0 -0.43 3 3
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
HBEGF -0.019 0.14 0.41 2 -0.55 20 22
cAMP biosynthetic process -0.041 0.16 -10000 0 -0.38 78 78
SRC -0.004 0.13 -10000 0 -0.61 13 13
PI3K 0.036 0.043 -10000 0 -0.51 3 3
GNB1 0.026 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.031 0.11 -10000 0 -0.46 19 19
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.069 0.16 -10000 0 -0.5 30 30
Gs family/GTP -0.036 0.16 -10000 0 -0.39 78 78
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.015 -10000 0 -10000 0 0
vasodilation 0.011 0.15 0.46 7 -0.56 22 29
mol:DAG -0.1 0.2 -10000 0 -0.44 120 120
Gs family/GDP/Gbeta gamma -0.026 0.14 -10000 0 -0.45 23 23
MSN -0.011 0.094 0.29 1 -0.39 5 6
Gq family/GTP -0.1 0.22 -10000 0 -0.48 122 122
mol:PI-3-4-5-P3 -0.006 0.19 -10000 0 -0.77 27 27
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.011 0.15 0.56 22 -0.46 7 29
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.11 -10000 0 -0.44 23 23
NOS3 0.004 0.15 0.49 2 -0.63 22 24
GNA11 0.015 0.084 -10000 0 -0.64 8 8
MAPKKK cascade -0.015 0.18 0.37 1 -0.59 29 30
E2/ER alpha (dimer)/PELP1/Src 0.001 0.14 -10000 0 -0.57 20 20
ruffle organization -0.009 0.088 0.28 1 -0.36 5 6
ROCK2 -0.004 0.11 0.36 5 -0.36 19 24
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
GNA15 0.013 0.05 -10000 0 -0.67 1 1
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.034 0.16 -10000 0 -0.58 25 25
MMP2 -0.004 0.13 0.34 1 -0.59 14 15
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.067 0.18 0.43 10 -0.42 44 54
IKBKB 0.01 0.12 0.48 16 -0.32 7 23
AKT1 -0.001 0.17 0.55 25 -0.24 15 40
IKBKG -0.001 0.13 0.47 15 -0.32 18 33
CALM1 -0.022 0.093 0.39 3 -0.4 8 11
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
MAP3K1 -0.015 0.17 0.45 12 -0.53 21 33
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.093 0.32 2 -0.4 9 11
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.058 0.15 0.5 12 -0.27 96 108
LYN 0.027 0.005 -10000 0 -10000 0 0
BLNK 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
BCR complex -0.072 0.18 -10000 0 -0.5 67 67
CD22 -0.07 0.18 -10000 0 -0.42 83 83
CAMK2G -0.019 0.09 0.34 4 -0.37 8 12
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.034 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.04 0.12 -10000 0 -0.34 56 56
GO:0007205 -0.025 0.095 0.32 2 -0.42 9 11
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.019 0.093 0.31 4 -0.42 7 11
NFATC1 -0.04 0.14 0.36 6 -0.44 23 29
B-cell antigen/BCR complex -0.072 0.18 -10000 0 -0.5 67 67
PAG1/CSK 0.038 0.027 -10000 0 -0.51 1 1
NFKBIB 0.019 0.044 0.19 13 -0.13 6 19
HRAS -0.017 0.099 0.35 5 -0.34 9 14
NFKBIA 0.019 0.044 0.19 13 -0.12 8 21
NF-kappa-B/RelA/I kappa B beta 0.024 0.04 0.2 12 -10000 0 12
RasGAP/Csk -0.028 0.18 -10000 0 -0.4 74 74
mol:GDP -0.023 0.093 0.29 2 -0.4 10 12
PTEN 0.026 0.018 -10000 0 -0.36 1 1
CD79B 0.006 0.052 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.024 0.04 0.2 12 -10000 0 12
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.038 0.16 0.44 4 -0.48 20 24
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.024 0.092 0.32 2 -0.4 8 10
CSK 0.027 0.008 -10000 0 -10000 0 0
FOS -0.098 0.18 0.47 8 -0.37 126 134
CHUK 0.007 0.1 0.42 14 -0.33 8 22
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.013 0.11 -10000 0 -0.45 11 11
PTPN6 -0.065 0.16 -10000 0 -0.49 41 41
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.014 0.036 0.16 6 -0.12 11 17
VAV2 -0.057 0.16 -10000 0 -0.63 16 16
ubiquitin-dependent protein catabolic process 0.022 0.043 0.19 13 -0.12 6 19
BTK -0.038 0.24 -10000 0 -0.98 30 30
CD19 -0.062 0.16 -10000 0 -0.4 68 68
MAP4K1 0.008 0.079 -10000 0 -0.67 5 5
CD72 0.024 0.016 -10000 0 -10000 0 0
PAG1 0.025 0.032 -10000 0 -0.67 1 1
MAPK14 -0.008 0.15 0.42 14 -0.46 20 34
SH3BP5 0.027 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.017 0.094 -10000 0 -0.45 8 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.049 0.18 -10000 0 -0.42 79 79
RAF1 -0.015 0.097 0.34 7 -0.39 4 11
RasGAP/p62DOK/SHIP -0.008 0.17 -10000 0 -0.39 74 74
CD79A -0.1 0.23 -10000 0 -0.66 68 68
re-entry into mitotic cell cycle -0.057 0.15 0.5 12 -0.26 97 109
RASA1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.004 0.1 0.4 14 -0.4 2 16
MAPK1 -0.01 0.09 0.38 8 -0.39 2 10
CD72/SHP1 -0.047 0.17 0.31 1 -0.53 27 28
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.014 0.16 0.46 13 -0.49 21 34
actin cytoskeleton organization -0.045 0.14 0.34 2 -0.52 16 18
NF-kappa-B/RelA 0.048 0.073 0.34 13 -0.22 1 14
Calcineurin 0.008 0.091 -10000 0 -0.41 4 4
PI3K -0.063 0.14 -10000 0 -0.45 25 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.019 0.098 -10000 0 -0.44 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.025 0.22 -10000 0 -0.91 21 21
DAPP1 -0.045 0.25 -10000 0 -1.1 20 20
cytokine secretion -0.037 0.13 0.36 6 -0.41 23 29
mol:DAG -0.024 0.092 0.32 2 -0.4 8 10
PLCG2 0.026 0.006 -10000 0 -10000 0 0
MAP2K1 -0.013 0.092 0.34 6 -0.45 2 8
B-cell antigen/BCR complex/FcgammaRIIB -0.057 0.19 -10000 0 -0.44 83 83
mol:PI-3-4-5-P3 -0.053 0.099 -10000 0 -0.36 16 16
ETS1 -0.015 0.086 0.34 5 -0.39 5 10
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.013 0.16 -10000 0 -0.38 64 64
B-cell antigen/BCR complex/LYN -0.05 0.17 -10000 0 -0.42 69 69
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
RAC1 -0.049 0.15 0.36 1 -0.56 16 17
B-cell antigen/BCR complex/LYN/SYK -0.04 0.19 -10000 0 -0.45 66 66
CARD11 -0.036 0.12 0.34 5 -0.44 18 23
FCGR2B -0.009 0.15 -10000 0 -0.67 24 24
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.019 0.095 0.43 18 -0.13 6 24
PTPRC -0.008 0.14 -10000 0 -0.67 20 20
PDPK1 -0.029 0.087 0.23 11 -0.25 17 28
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.027 0.005 -10000 0 -10000 0 0
POU2F2 0.019 0.033 0.16 14 -10000 0 14
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.005 0.058 -10000 0 -10000 0 0
CRKL -0.013 0.091 0.36 2 -0.42 1 3
mol:PIP3 -0.002 0.017 0.34 1 -10000 0 1
AKT1 0.003 0.056 0.37 2 -0.45 3 5
PTK2B 0.027 0.005 -10000 0 -10000 0 0
RAPGEF1 0.002 0.1 0.4 9 -0.4 1 10
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
HGF/MET/SHIP2 -0.015 0.18 -10000 0 -0.46 68 68
MAP3K5 0.011 0.12 0.44 13 -0.4 6 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.002 0.17 -10000 0 -0.42 66 66
AP1 -0.18 0.33 -10000 0 -0.65 149 149
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis -0.22 0.4 0.38 1 -0.81 150 151
STAT3 (dimer) -0.019 0.1 -10000 0 -0.52 1 1
GAB1/CRKL/SHP2/PI3K 0.027 0.11 0.34 1 -0.5 3 4
INPP5D 0.019 0.034 -10000 0 -10000 0 0
CBL/CRK 0.016 0.11 0.5 7 -0.41 1 8
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
ELK1 0.035 0.14 0.42 29 -0.26 2 31
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.068 -10000 0 -0.24 5 5
PAK1 0.006 0.058 0.35 5 -0.4 2 7
HGF/MET/RANBP10 -0.015 0.18 -10000 0 -0.45 70 70
HRAS -0.02 0.13 -10000 0 -0.55 3 3
DOCK1 0.001 0.11 0.42 10 -0.4 4 14
GAB1 -0.011 0.097 0.26 1 -0.35 4 5
CRK -0.006 0.098 0.37 2 -0.43 1 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.044 0.19 -10000 0 -0.51 70 70
JUN -0.12 0.29 -10000 0 -0.67 107 107
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.031 0.086 -10000 0 -0.24 68 68
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.007 0.13 0.45 7 -0.51 3 10
GRB2/SHC 0.004 0.085 -10000 0 -0.28 1 1
FOS -0.15 0.3 -10000 0 -0.67 125 125
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.035 0.14 0.42 29 -0.26 2 31
HGF/MET/MUC20 -0.065 0.16 -10000 0 -0.45 70 70
cell migration 0.004 0.084 -10000 0 -0.27 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.005 0.057 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.016 0.11 -10000 0 -0.3 64 64
MET/MUC20 -0.017 0.048 -10000 0 -10000 0 0
RAP1B 0.012 0.13 0.54 13 -0.37 1 14
RAP1A 0.009 0.11 0.39 12 -0.37 1 13
HGF/MET/RANBP9 -0.014 0.18 -10000 0 -0.45 70 70
RAF1 -0.018 0.12 -10000 0 -0.46 3 3
STAT3 -0.02 0.11 -10000 0 -0.52 1 1
cell proliferation -0.023 0.15 -10000 0 -0.39 60 60
RPS6KB1 0 0.034 -10000 0 -0.22 2 2
MAPK3 -0.022 0.1 0.52 12 -10000 0 12
MAPK1 0.14 0.29 0.61 134 -10000 0 134
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.024 0.17 0.55 20 -0.6 9 29
SRC -0.021 0.1 -10000 0 -0.3 25 25
PI3K 0.003 0.094 -10000 0 -0.25 29 29
MET/Glomulin -0.007 0.045 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.01 0.13 0.37 4 -0.46 2 6
MET -0.029 0.074 -10000 0 -10000 0 0
MAP4K1 0.007 0.12 0.46 8 -0.43 6 14
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.006 0.12 0.43 2 -0.44 1 3
BAD 0.006 0.058 0.35 5 -0.4 2 7
MAP2K4 0.021 0.14 0.5 20 -0.4 4 24
SHP2/GRB2/SOS1/GAB1 0.018 0.098 -10000 0 -0.36 1 1
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.026 0.007 -10000 0 -10000 0 0
HGS -0.028 0.077 -10000 0 -0.22 65 65
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 70 70
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.003 0.099 -10000 0 -0.24 67 67
PDPK1 -0.001 0.048 -10000 0 -0.48 3 3
HGF/MET/SHIP -0.018 0.18 -10000 0 -0.46 70 70
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.01 0.1 -10000 0 -0.81 6 6
Syndecan-4/Syndesmos -0.041 0.16 -10000 0 -0.54 42 42
positive regulation of JNK cascade -0.054 0.19 -10000 0 -0.56 44 44
Syndecan-4/ADAM12 -0.053 0.16 -10000 0 -0.55 42 42
CCL5 -0.016 0.16 -10000 0 -0.67 28 28
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
DNM2 0.025 0.008 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
PLG 0.007 0.031 -10000 0 -10000 0 0
ADAM12 -0.011 0.067 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.058 0.03 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.063 0.18 -10000 0 -0.58 41 41
Syndecan-4/CXCL12/CXCR4 -0.057 0.2 -10000 0 -0.6 44 44
Syndecan-4/Laminin alpha3 -0.052 0.17 -10000 0 -0.57 40 40
MDK -0.02 0.076 -10000 0 -0.67 1 1
Syndecan-4/FZD7 -0.041 0.16 -10000 0 -0.55 42 42
Syndecan-4/Midkine -0.053 0.16 -10000 0 -0.56 41 41
FZD7 0.022 0.051 -10000 0 -0.52 4 4
Syndecan-4/FGFR1/FGF -0.014 0.16 -10000 0 -0.51 40 40
THBS1 0.012 0.046 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.059 0.16 -10000 0 -0.55 42 42
positive regulation of MAPKKK cascade -0.054 0.19 -10000 0 -0.56 44 44
Syndecan-4/TACI -0.13 0.21 -10000 0 -0.62 40 40
CXCR4 0.026 0.013 -10000 0 -10000 0 0
cell adhesion -0.009 0.066 0.2 5 -0.31 17 22
Syndecan-4/Dynamin -0.041 0.16 -10000 0 -0.55 41 41
Syndecan-4/TSP1 -0.045 0.16 -10000 0 -0.55 42 42
Syndecan-4/GIPC -0.041 0.16 -10000 0 -0.55 41 41
Syndecan-4/RANTES -0.061 0.2 -10000 0 -0.66 42 42
ITGB1 0.027 0.004 -10000 0 -10000 0 0
LAMA1 -0.021 0.18 -10000 0 -0.66 34 34
LAMA3 -0.001 0.13 -10000 0 -0.67 16 16
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.019 0.19 0.76 21 -0.62 17 38
Syndecan-4/alpha-Actinin -0.04 0.16 -10000 0 -0.55 41 41
TFPI -0.012 0.16 -10000 0 -0.66 28 28
F2 0.01 0.03 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.075 0.18 -10000 0 -0.58 41 41
ACTN1 0.027 0.008 -10000 0 -10000 0 0
TNC -0.033 0.096 -10000 0 -0.67 5 5
Syndecan-4/CXCL12 -0.077 0.2 -10000 0 -0.62 44 44
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
CXCL12 -0.047 0.22 -10000 0 -0.67 53 53
TNFRSF13B -0.16 0.29 -10000 0 -0.67 121 121
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.025 0.032 -10000 0 -0.67 1 1
Syndecan-4/PI-4-5-P2 -0.051 0.16 -10000 0 -0.55 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.086 0.07 -10000 0 -0.22 2 2
cell migration -0.027 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.022 -10000 0 -10000 0 0
vasculogenesis -0.043 0.16 -10000 0 -0.53 42 42
SDC4 -0.051 0.16 -10000 0 -0.58 42 42
Syndecan-4/Tenascin C -0.061 0.17 -10000 0 -0.58 42 42
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.023 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.04 0.16 -10000 0 -0.55 42 42
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
Rac1/GTP -0.009 0.068 0.2 5 -0.32 17 22
cytoskeleton organization -0.039 0.15 -10000 0 -0.52 42 42
GIPC1 0.025 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.059 0.18 -10000 0 -0.57 43 43
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.009 0.14 -10000 0 -0.36 62 62
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.001 0.12 -10000 0 -0.44 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.053 -10000 0 -0.29 1 1
antigen processing and presentation of peptide antigen via MHC class I 0.008 0.072 -10000 0 -0.24 4 4
CaM/Ca2+ 0.013 0.14 -10000 0 -0.33 62 62
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.013 0.13 -10000 0 -0.34 62 62
AKT1 -0.017 0.12 0.38 5 -0.38 7 12
MAP2K1 -0.025 0.12 0.29 2 -0.32 59 61
MAP3K11 -0.022 0.13 0.3 5 -0.34 62 67
IFNGR1 0.02 0.026 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.017 0.074 -10000 0 -0.44 2 2
Rap1/GTP -0.02 0.095 -10000 0 -0.36 1 1
CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.016 0.15 -10000 0 -0.37 61 61
CEBPB -0.059 0.19 0.52 6 -0.56 29 35
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.016 0.16 -10000 0 -0.71 6 6
STAT1 -0.023 0.13 0.3 5 -0.34 62 67
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.066 0.23 -10000 0 -0.67 62 62
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
STAT1 (dimer)/PIAS1 -0.006 0.13 0.3 4 -0.33 58 62
CEBPB/PTGES2/Cbp/p300 -0.024 0.12 -10000 0 -0.39 14 14
mol:Ca2+ 0.006 0.14 -10000 0 -0.35 62 62
MAPK3 -0.009 0.12 -10000 0 -0.65 4 4
STAT1 (dimer) 0.017 0.098 -10000 0 -0.34 3 3
MAPK1 -0.17 0.31 0.44 1 -0.67 122 123
JAK2 0.017 0.036 -10000 0 -0.38 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.02 0.025 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 -0.041 0.18 0.48 9 -0.6 27 36
SMAD7 0.018 0.065 0.33 9 -10000 0 9
CBL/CRKL/C3G -0.009 0.12 0.3 2 -0.36 5 7
PI3K 0.011 0.14 -10000 0 -0.34 62 62
IFNG -0.067 0.23 -10000 0 -0.68 62 62
apoptosis -0.038 0.15 0.56 4 -0.46 36 40
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A 0.011 0.035 -10000 0 -10000 0 0
CAMK2B 0.019 0.07 -10000 0 -0.67 5 5
FRAP1 -0.024 0.11 0.37 5 -0.35 7 12
PRKCD -0.013 0.13 0.42 9 -0.38 7 16
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.008 0.072 -10000 0 -0.24 4 4
PTPN2 0.027 0.004 -10000 0 -10000 0 0
EP300 0.02 0.013 -10000 0 -10000 0 0
IRF1 -0.015 0.086 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.012 0.12 0.3 2 -0.32 55 57
SOCS1 0.018 0.12 -10000 0 -1 6 6
mol:GDP -0.01 0.11 0.28 2 -0.34 5 7
CASP1 0.016 0.064 0.35 6 -0.32 2 8
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.058 0.35 1 -10000 0 1
mol:PI-3-4-5-P3 -0.002 0.13 -10000 0 -0.33 62 62
RAP1/GDP -0.006 0.1 -10000 0 -0.36 1 1
CBL -0.022 0.13 0.29 6 -0.34 62 68
MAP3K1 -0.023 0.12 0.3 2 -0.34 60 62
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.008 0.072 -10000 0 -0.24 4 4
PTPN11 -0.026 0.13 -10000 0 -0.36 62 62
CREBBP 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.019 0.12 -10000 0 -0.42 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.087 0.42 1 -10000 0 1
AP1 -0.15 0.3 -10000 0 -0.55 157 157
mol:PIP3 -0.011 0.091 -10000 0 -0.35 30 30
AKT1 0.032 0.097 0.34 4 -0.57 2 6
PTK2B -0.009 0.085 0.26 1 -0.36 12 13
RHOA 0.014 0.042 0.25 1 -10000 0 1
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.072 0.27 8 -10000 0 8
MAGI3 0.025 0.032 -10000 0 -0.67 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.008 0.1 -10000 0 -0.35 36 36
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0 0.099 0.35 11 -0.37 9 20
NF kappa B1 p50/RelA -0.019 0.1 -10000 0 -0.43 9 9
endothelial cell migration -0.015 0.15 -10000 0 -0.52 33 33
ADCY4 -0.029 0.14 -10000 0 -0.52 35 35
ADCY5 -0.054 0.16 -10000 0 -0.54 39 39
ADCY6 -0.029 0.14 -10000 0 -0.52 35 35
ADCY7 -0.029 0.15 -10000 0 -0.52 35 35
ADCY1 -0.031 0.15 -10000 0 -0.51 37 37
ADCY2 -0.049 0.17 -10000 0 -0.54 39 39
ADCY3 -0.029 0.15 -10000 0 -0.53 34 34
ADCY8 -0.037 0.15 -10000 0 -0.52 36 36
ADCY9 -0.029 0.15 -10000 0 -0.52 35 35
GSK3B -0.007 0.084 0.37 2 -0.34 12 14
arachidonic acid secretion -0.029 0.14 -10000 0 -0.43 48 48
GNG2 0.025 0.032 -10000 0 -0.67 1 1
TRIP6 0.024 0.01 -10000 0 -10000 0 0
GNAO1 -0.024 0.15 -10000 0 -0.47 46 46
HRAS 0.026 0.011 -10000 0 -10000 0 0
NFKBIA -0.005 0.095 0.46 5 -0.49 1 6
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.18 -10000 0 -0.79 22 22
JUN -0.12 0.29 -10000 0 -0.67 107 107
LPA/LPA2/NHERF2 0.035 0.017 -10000 0 -10000 0 0
TIAM1 0 0.21 -10000 0 -0.93 23 23
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.012 0.065 0.32 1 -10000 0 1
PLCB3 0.027 0.034 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
positive regulation of mitosis -0.029 0.14 -10000 0 -0.43 48 48
LPA/LPA1-2-3 0.019 0.12 -10000 0 -0.41 29 29
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation 0.002 0.1 0.45 2 -0.39 12 14
GNAZ -0.015 0.12 -10000 0 -0.44 33 33
EGFR/PI3K-beta/Gab1 -0.001 0.099 -10000 0 -0.36 30 30
positive regulation of dendritic cell cytokine production 0.018 0.11 -10000 0 -0.4 29 29
LPA/LPA2/MAGI-3 0.035 0.027 -10000 0 -0.45 1 1
ARHGEF1 0.006 0.1 0.36 3 -0.39 23 26
GNAI2 -0.012 0.12 -10000 0 -0.45 33 33
GNAI3 -0.011 0.12 -10000 0 -0.42 37 37
GNAI1 -0.011 0.12 -10000 0 -0.44 34 34
LPA/LPA3 0.015 0.025 -10000 0 -10000 0 0
LPA/LPA2 0.02 0.013 -10000 0 -10000 0 0
LPA/LPA1 -0.015 0.14 -10000 0 -0.47 40 40
HB-EGF/EGFR -0.022 0.14 -10000 0 -0.44 44 44
HBEGF -0.038 0.14 -10000 0 -0.49 42 42
mol:DAG -0.012 0.065 0.32 1 -10000 0 1
cAMP biosynthetic process -0.035 0.17 0.42 10 -0.46 49 59
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.007 0.091 0.36 6 -0.49 1 7
GNAQ 0.016 0.015 -10000 0 -10000 0 0
LPAR2 0.025 0.008 -10000 0 -10000 0 0
LPAR3 0.013 0.034 -10000 0 -10000 0 0
LPAR1 -0.022 0.18 -10000 0 -0.62 38 38
IL8 -0.084 0.17 0.36 1 -0.47 40 41
PTK2 -0.002 0.1 -10000 0 -0.4 25 25
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
CASP3 -0.008 0.1 -10000 0 -0.36 36 36
EGFR 0.019 0.07 -10000 0 -0.67 5 5
PLCG1 -0.013 0.064 -10000 0 -0.28 4 4
PLD2 -0.002 0.1 -10000 0 -0.39 24 24
G12/G13 0.022 0.12 -10000 0 -0.4 32 32
PI3K-beta 0.006 0.087 -10000 0 -0.68 2 2
cell migration 0.019 0.072 -10000 0 -0.27 9 9
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN 0 0.098 0.27 1 -0.4 12 13
HRAS/GTP -0.028 0.15 -10000 0 -0.45 47 47
RAC1 0.026 0.006 -10000 0 -10000 0 0
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
PRKCE 0.02 0.07 -10000 0 -0.68 5 5
PRKCD -0.008 0.085 0.37 7 -10000 0 7
Gi(beta/gamma) -0.023 0.14 -10000 0 -0.51 33 33
mol:LPA 0.002 0.017 -10000 0 -0.19 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.019 0.11 -10000 0 -0.42 15 15
MAPKKK cascade -0.029 0.14 -10000 0 -0.43 48 48
contractile ring contraction involved in cytokinesis 0.017 0.047 0.27 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.068 0.15 -10000 0 -0.35 109 109
GNA15 0.013 0.027 -10000 0 -0.36 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.003 0.094 0.33 8 -0.38 9 17
GNA11 0.012 0.046 -10000 0 -0.33 8 8
Rac1/GTP 0.014 0.19 -10000 0 -0.84 21 21
MMP2 -0.015 0.15 -10000 0 -0.53 33 33
Ceramide signaling pathway

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
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.014 0.12 -10000 0 -0.49 16 16
BAG4 0.025 0.032 -10000 0 -0.67 1 1
PKC zeta/ceramide -0.02 0.097 -10000 0 -0.28 37 37
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX -0.013 0.075 -10000 0 -0.34 20 20
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.028 0.14 0.79 16 -10000 0 16
BAD -0.033 0.088 0.18 1 -0.39 16 17
SMPD1 -0.011 0.089 0.27 6 -0.23 61 67
RB1 -0.033 0.09 0.19 1 -0.38 19 20
FADD/Caspase 8 -0.005 0.12 -10000 0 -0.52 13 13
MAP2K4 -0.02 0.072 0.21 2 -0.37 8 10
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.024 0.083 -10000 0 -0.41 12 12
EGF -0.076 0.25 -10000 0 -0.67 72 72
mol:ceramide -0.038 0.098 -10000 0 -0.3 39 39
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.016 0.024 -10000 0 -0.51 1 1
ASAH1 0.025 0.032 -10000 0 -0.67 1 1
negative regulation of cell cycle -0.033 0.089 0.19 1 -0.37 19 20
cell proliferation -0.059 0.15 -10000 0 -0.33 104 104
BID -0.15 0.28 -10000 0 -0.6 127 127
MAP3K1 -0.028 0.079 0.19 1 -0.28 27 28
EIF2A -0.03 0.078 -10000 0 -0.45 10 10
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.014 0.07 -10000 0 -0.35 10 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.043 0.086 -10000 0 -0.38 13 13
Cathepsin D/ceramide -0.019 0.093 -10000 0 -0.27 37 37
FADD -0.013 0.12 -10000 0 -0.5 15 15
KSR1 -0.027 0.087 0.18 7 -0.43 13 20
MAPK8 -0.019 0.091 -10000 0 -0.37 20 20
PRKRA -0.035 0.091 -10000 0 -0.36 21 21
PDGFA 0.026 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.67 108 108
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.037 0.097 -10000 0 -0.29 39 39
CTSD 0.026 0.009 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.063 0.16 -10000 0 -0.35 104 104
PRKCD 0.027 0.003 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.016 0.024 -10000 0 -0.51 1 1
RelA/NF kappa B1 0.039 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.12 -10000 0 -0.47 19 19
TNFR1A/BAG4/TNF-alpha -0.003 0.16 -10000 0 -0.44 57 57
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.023 0.078 -10000 0 -0.38 12 12
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS -0.006 0.072 0.17 25 -0.24 18 43
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.51 1 1
EIF2AK2 -0.032 0.084 -10000 0 -0.47 11 11
TNF-alpha/TNFR1A/FAN -0.002 0.16 -10000 0 -0.44 56 56
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.088 -10000 0 -0.48 7 7
MAP2K2 -0.015 0.068 -10000 0 -0.4 6 6
SMPD3 -0.016 0.1 -10000 0 -0.26 65 65
TNF -0.056 0.22 -10000 0 -0.67 56 56
PKC zeta/PAR4 0.038 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.016 0.11 0.25 70 -0.25 17 87
NF kappa B1/RelA/I kappa B alpha 0.075 0.024 -10000 0 -10000 0 0
AIFM1 -0.01 0.082 0.17 25 -0.28 22 47
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
Signaling events mediated by PRL

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
CCNE1 0.025 0.007 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.017 0.083 -10000 0 -0.67 7 7
CDKN1A -0.007 0.071 -10000 0 -0.61 1 1
PRL-3/alpha Tubulin 0.028 0.035 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.082 0.24 5 -0.52 11 16
AGT 0.003 0.11 -10000 0 -0.67 11 11
CCNA2 -0.067 0.15 -10000 0 -0.37 100 100
TUBA1B 0.027 0.005 -10000 0 -10000 0 0
EGR1 -0.087 0.21 -10000 0 -0.5 101 101
CDK2/Cyclin E1 0.018 0.077 -10000 0 -0.54 1 1
MAPK3 0.008 0.027 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.04 0.007 -10000 0 -10000 0 0
MAPK1 0.007 0.023 -10000 0 -10000 0 0
PTP4A1 -0.07 0.16 -10000 0 -0.39 101 101
PTP4A3 0.013 0.043 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.008 0.028 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 -0.011 0.082 -10000 0 -0.37 8 8
Rab GGTase beta/Rab GGTase alpha 0.039 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.054 0.16 -10000 0 -0.37 99 99
RABGGTA 0.027 0.005 -10000 0 -10000 0 0
BCAR1 -0.012 0.014 -10000 0 -10000 0 0
RHOC -0.011 0.083 -10000 0 -0.4 7 7
RHOA -0.011 0.081 -10000 0 -0.61 2 2
cell motility -0.004 0.096 0.3 5 -0.4 7 12
PRL-1/alpha Tubulin -0.05 0.16 -10000 0 -0.36 101 101
PRL-3/alpha1 Integrin 0.02 0.074 -10000 0 -0.52 7 7
ROCK1 -0.005 0.093 0.3 3 -0.4 7 10
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.005 -10000 0 -10000 0 0
mitosis -0.07 0.16 -10000 0 -0.39 101 101
ATF5 0.02 0.029 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.009 -10000 0 -10000 0 0
LAT2 -0.003 0.066 -10000 0 -0.29 1 1
AP1 -0.12 0.26 -10000 0 -0.55 107 107
mol:PIP3 0.027 0.17 0.61 21 -0.41 12 33
IKBKB 0.039 0.17 0.58 28 -0.27 6 34
AKT1 -0.007 0.12 0.32 26 -0.43 8 34
IKBKG 0.041 0.17 0.62 28 -0.26 7 35
MS4A2 -0.015 0.064 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
MAP3K1 0.023 0.11 0.44 13 -0.4 7 20
mol:Ca2+ 0.033 0.16 0.52 29 -0.32 11 40
LYN 0.027 0.011 -10000 0 -10000 0 0
CBLB -0.001 0.063 -10000 0 -0.27 1 1
SHC1 0.025 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK -0.021 0.16 -10000 0 -0.4 78 78
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.034 -10000 0 -10000 0 0
PLD2 -0.009 0.13 0.32 34 -0.37 30 64
PTPN13 0.012 0.13 0.53 1 -0.63 13 14
PTPN11 0.023 0.036 -10000 0 -0.7 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.031 0.16 0.62 21 -0.37 6 27
SYK 0.025 0.012 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.001 0.11 -10000 0 -0.37 28 28
LAT -0.004 0.069 -10000 0 -0.33 4 4
PAK2 0.017 0.1 0.32 8 -0.42 9 17
NFATC2 -0.11 0.23 -10000 0 -0.61 84 84
HRAS 0.012 0.099 0.24 2 -0.43 10 12
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.006 0.096 -10000 0 -0.68 7 7
Fc epsilon R1 0.005 0.13 -10000 0 -0.45 32 32
Antigen/IgE/Fc epsilon R1 0.009 0.12 -10000 0 -0.41 32 32
mol:GDP 0.003 0.11 -10000 0 -0.46 14 14
JUN -0.12 0.29 -10000 0 -0.67 107 107
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.003 0.069 -10000 0 -0.26 8 8
CHUK 0.036 0.16 0.58 26 -0.26 7 33
KLRG1 -0.007 0.077 -10000 0 -0.31 13 13
VAV1 -0.005 0.073 0.21 1 -0.36 6 7
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.001 0.063 -10000 0 -10000 0 0
negative regulation of mast cell degranulation 0.006 0.08 -10000 0 -0.3 10 10
BTK -0.006 0.12 -10000 0 -0.53 18 18
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.15 -10000 0 -0.47 41 41
GAB2/PI3K/SHP2 -0.029 0.098 -10000 0 -0.38 29 29
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.072 -10000 0 -0.27 28 28
RAF1 0.014 0.085 -10000 0 -0.85 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.019 0.17 -10000 0 -0.5 42 42
FCER1G 0.018 0.035 -10000 0 -10000 0 0
FCER1A -0.033 0.18 -10000 0 -0.68 33 33
Antigen/IgE/Fc epsilon R1/Fyn 0.025 0.12 -10000 0 -0.38 32 32
MAPK3 0.019 0.091 -10000 0 -0.7 6 6
MAPK1 -0.014 0.11 -10000 0 -0.72 7 7
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.001 0.18 -10000 0 -0.63 31 31
DUSP1 -0.084 0.26 -10000 0 -0.67 78 78
NF-kappa-B/RelA 0.015 0.048 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.014 0.13 0.37 1 -0.71 10 11
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.098 -10000 0 -0.47 7 7
FER -0.004 0.071 -10000 0 -0.38 4 4
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.042 0.15 -10000 0 -0.47 54 54
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.011 0.12 0.4 8 -0.51 10 18
cytokine secretion 0.005 0.03 -10000 0 -10000 0 0
SPHK1 -0.001 0.065 0.27 1 -0.28 2 3
PTK2 0.014 0.13 0.37 1 -0.75 10 11
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.006 0.11 -10000 0 -0.38 27 27
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.035 0.18 0.64 21 -0.41 11 32
MAP2K2 0.019 0.09 -10000 0 -0.79 4 4
MAP2K1 0.01 0.083 -10000 0 -0.76 5 5
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 -0.001 0.082 -10000 0 -0.34 10 10
MAP2K4 -0.005 0.19 -10000 0 -0.84 24 24
Fc epsilon R1/FcgammaRIIB 0.007 0.18 -10000 0 -0.53 42 42
mol:Choline -0.009 0.13 0.32 34 -0.37 30 64
SHC/Grb2/SOS1 0.037 0.076 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.018 0.13 0.46 3 -0.67 10 13
HCLS1 -0.002 0.064 -10000 0 -0.28 2 2
PRKCB 0.036 0.18 0.62 26 -0.34 12 38
FCGR2B -0.009 0.15 -10000 0 -0.67 24 24
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.006 0.082 -10000 0 -0.31 10 10
LCP2 0.024 0.021 -10000 0 -10000 0 0
PLA2G4A -0.023 0.12 -10000 0 -0.42 31 31
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.13 0.32 34 -0.37 30 64
IKK complex 0.044 0.18 0.61 30 -0.21 2 32
WIPF1 0.027 0.005 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.07 -10000 0 -0.58 6 6
alphaV beta3 Integrin 0.039 0.081 -10000 0 -0.48 11 11
PTK2 0.013 0.14 0.41 11 -0.5 11 22
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.009 0.05 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
CDKN1B -0.027 0.16 -10000 0 -0.54 45 45
VEGFA 0.023 0.054 -10000 0 -0.67 3 3
ILK -0.027 0.16 -10000 0 -0.53 46 46
ROCK1 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.029 0.15 -10000 0 -0.5 45 45
PTK2B 0.012 0.09 0.36 1 -0.42 16 17
alphaV/beta3 Integrin/JAM-A 0.007 0.14 -10000 0 -0.4 51 51
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.036 0.08 -10000 0 -0.46 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.088 0.24 -10000 0 -0.44 152 152
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.001 0.092 -10000 0 -0.41 5 5
alphaV/beta3 Integrin/Syndecan-1 0.04 0.081 -10000 0 -0.48 11 11
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.093 0.23 -10000 0 -0.43 152 152
PI4 Kinase 0.028 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
alphaV/beta3 Integrin/Osteopontin 0.02 0.13 -10000 0 -0.43 35 35
RPS6KB1 -0.14 0.19 0.42 2 -0.4 152 154
TLN1 0.025 0.007 -10000 0 -10000 0 0
MAPK3 -0.051 0.13 -10000 0 -0.64 12 12
GPR124 0.027 0.005 -10000 0 -10000 0 0
MAPK1 -0.06 0.14 -10000 0 -0.57 20 20
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.12 -10000 0 -0.52 20 20
cell adhesion 0.03 0.078 -10000 0 -0.46 10 10
ANGPTL3 0.007 0.024 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.064 -10000 0 -0.5 6 6
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
TGFBR2 0.023 0.054 -10000 0 -0.67 3 3
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
IGF1 -0.13 0.29 -10000 0 -0.67 108 108
RAC1 0.026 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.039 0.081 -10000 0 -0.47 11 11
apoptosis 0.024 0.044 -10000 0 -0.67 2 2
CD47 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.04 0.081 -10000 0 -0.48 11 11
VCL 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.032 0.1 -10000 0 -0.48 18 18
CSF1 0.015 0.088 -10000 0 -0.67 8 8
PIK3C2A -0.028 0.17 -10000 0 -0.53 47 47
PI4 Kinase/Pyk2 -0.014 0.12 -10000 0 -0.36 42 42
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.097 -10000 0 -0.45 16 16
FAK1/Vinculin 0.024 0.12 0.39 9 -0.41 9 18
alphaV beta3/Integrin/ppsTEM5 0.04 0.081 -10000 0 -0.48 11 11
RHOA 0.027 0.003 -10000 0 -10000 0 0
VTN -0.038 0.2 -10000 0 -0.67 44 44
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 0.027 0.004 -10000 0 -10000 0 0
F11R 0.016 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.041 0.082 -10000 0 -0.48 11 11
alphaV/beta3 Integrin/TGFBR2 0.037 0.086 -10000 0 -0.44 14 14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.056 0.072 -10000 0 -0.44 9 9
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.036 0.075 -10000 0 -0.44 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.085 0.069 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.034 0.089 -10000 0 -0.42 16 16
SDC1 0.026 0.015 -10000 0 -10000 0 0
VAV3 0.009 0.08 -10000 0 -0.43 14 14
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
FAK1/Paxillin 0.022 0.12 0.35 8 -0.41 9 17
cell migration 0.018 0.11 0.34 6 -0.41 6 12
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
PI3K 0.016 0.14 -10000 0 -0.38 52 52
SPP1 -0.031 0.15 -10000 0 -0.67 23 23
KDR 0.021 0.063 -10000 0 -0.67 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.045 -10000 0 -0.67 2 2
COL4A3 0.008 0.11 -10000 0 -0.63 14 14
angiogenesis -0.054 0.15 -10000 0 -0.52 32 32
Rac1/GTP 0.021 0.075 -10000 0 -0.4 14 14
EDIL3 0.005 0.095 -10000 0 -0.67 8 8
cell proliferation 0.037 0.086 -10000 0 -0.44 14 14
IL27-mediated signaling events

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
TGFB1 0.026 0.017 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.045 0.13 0.47 16 -10000 0 16
IL27/IL27R/JAK1 -0.015 0.17 -10000 0 -0.48 12 12
TBX21 -0.066 0.18 0.39 6 -0.57 29 35
IL12B 0.004 0.085 -10000 0 -0.68 7 7
IL12A -0.049 0.16 -10000 0 -0.5 53 53
IL6ST -0.072 0.24 -10000 0 -0.68 66 66
IL27RA/JAK1 0.02 0.054 0.55 1 -10000 0 1
IL27 0.011 0.028 -10000 0 -10000 0 0
TYK2 0.019 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.04 0.13 -10000 0 -0.49 3 3
T-helper 2 cell differentiation 0.045 0.13 0.47 16 -10000 0 16
T cell proliferation during immune response 0.045 0.13 0.47 16 -10000 0 16
MAPKKK cascade -0.045 0.13 -10000 0 -0.47 16 16
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
IL12RB1 0.004 0.082 -10000 0 -0.62 6 6
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.057 0.19 0.48 13 -0.56 25 38
IL27/IL27R/JAK2/TYK2 -0.046 0.13 -10000 0 -0.47 16 16
positive regulation of T cell mediated cytotoxicity -0.045 0.13 -10000 0 -0.47 16 16
STAT1 (dimer) -0.026 0.22 0.52 12 -0.6 17 29
JAK2 0.019 0.031 -10000 0 -0.36 2 2
JAK1 0.027 0.008 -10000 0 -10000 0 0
STAT2 (dimer) -0.033 0.14 -10000 0 -0.46 15 15
T cell proliferation -0.11 0.19 -10000 0 -0.45 87 87
IL12/IL12R/TYK2/JAK2 -0.073 0.24 -10000 0 -0.84 30 30
IL17A -0.04 0.13 -10000 0 -0.49 3 3
mast cell activation 0.045 0.13 0.47 16 -10000 0 16
IFNG -0.016 0.051 0.092 5 -0.13 69 74
T cell differentiation -0.004 0.008 0.014 1 -0.022 65 66
STAT3 (dimer) -0.032 0.14 -10000 0 -0.45 15 15
STAT5A (dimer) -0.032 0.14 -10000 0 -0.46 14 14
STAT4 (dimer) -0.039 0.15 0.32 1 -0.44 24 25
STAT4 0.004 0.099 -10000 0 -0.59 11 11
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.025 0.15 -10000 0 -0.45 15 15
GATA3 -0.058 0.3 -10000 0 -1.4 25 25
IL18 -0.012 0.077 -10000 0 -0.49 11 11
positive regulation of mast cell cytokine production -0.032 0.13 -10000 0 -0.44 15 15
IL27/EBI3 -0.031 0.06 -10000 0 -0.26 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.096 0.26 -10000 0 -0.67 81 81
STAT5A 0.026 0.007 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -0.023 2 2
IL2 -0.011 0.018 -10000 0 -10000 0 0
IL1B -0.027 0.13 -10000 0 -0.51 32 32
EBI3 -0.052 0.075 -10000 0 -0.37 1 1
TNF -0.053 0.16 -10000 0 -0.51 56 56
Insulin Pathway

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
CBL/APS/CAP -0.004 0.14 -10000 0 -0.37 62 62
TC10/GTP 0.041 0.042 -10000 0 -0.35 4 4
Insulin Receptor/Insulin/IRS1/Shp2 0 0.16 -10000 0 -0.42 60 60
HRAS 0.026 0.011 -10000 0 -10000 0 0
APS homodimer 0.024 0.033 -10000 0 -0.67 1 1
GRB14 0.006 0.12 -10000 0 -0.67 15 15
FOXO3 0.002 0.12 -10000 0 -0.65 14 14
AKT1 -0.028 0.14 0.34 6 -0.34 70 76
INSR 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.05 0.036 -10000 0 -0.34 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.006 -10000 0 -10000 0 0
SORBS1 0.021 0.063 -10000 0 -0.67 4 4
CRK 0.026 0.007 -10000 0 -10000 0 0
PTPN1 0.016 0.039 -10000 0 -0.34 2 2
CAV1 -0.035 0.14 -10000 0 -0.38 68 68
CBL/APS/CAP/Crk-II/C3G 0.065 0.052 -10000 0 -0.38 4 4
Insulin Receptor/Insulin/IRS1/NCK2 0.002 0.16 -10000 0 -0.41 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.14 -10000 0 -0.37 62 62
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.007 0.1 -10000 0 -0.45 7 7
RPS6KB1 -0.032 0.12 0.3 3 -0.32 63 66
PARD6A 0.026 0.006 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.036 -10000 0 -0.52 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.011 0.13 -10000 0 -0.33 65 65
HRAS/GTP -0.024 0.11 -10000 0 -0.34 46 46
Insulin Receptor 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.015 0.14 -10000 0 -0.39 47 47
PRKCI 0.012 0.075 -10000 0 -0.49 5 5
Insulin Receptor/Insulin/GRB14/PDK1 -0.026 0.14 -10000 0 -0.36 71 71
SHC1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.045 0.046 -10000 0 -0.43 2 2
PI3K 0.004 0.15 -10000 0 -0.38 62 62
NCK2 0.027 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
AKT2 -0.03 0.14 0.38 7 -0.34 70 77
PRKCZ 0.013 0.074 -10000 0 -0.51 5 5
SH2B2 0.024 0.033 -10000 0 -0.67 1 1
SHC/SHIP -0.013 0.13 0.3 1 -0.37 50 51
F2RL2 -0.018 0.085 -10000 0 -0.67 3 3
TRIP10 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.039 0.037 -10000 0 -0.37 3 3
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.062 0.041 -10000 0 -0.34 2 2
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.059 0.049 -10000 0 -0.4 4 4
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.053 0.041 -10000 0 -0.37 3 3
INPP5D -0.031 0.14 0.31 1 -0.39 60 61
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.013 0.15 -10000 0 -0.83 15 15
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
p62DOK/RasGAP 0.046 0.046 -10000 0 -0.44 2 2
INS 0.015 0.054 -10000 0 -0.67 3 3
mol:PI-3-4-P2 -0.031 0.14 0.31 1 -0.38 60 61
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.032 0.12 0.36 3 -0.32 61 64
PTPRA 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
TC10/GTP/CIP4 0.034 0.011 -10000 0 -10000 0 0
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.009 0.1 -10000 0 -0.3 47 47
Insulin Receptor/Insulin/IRS1 -0.012 0.15 -10000 0 -0.41 60 60
Insulin Receptor/Insulin/IRS3 0.03 0.043 -10000 0 -0.5 3 3
Par3/Par6 0.058 0.039 -10000 0 -0.38 2 2
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.012 0.2 -10000 0 -0.94 20 20
NCK1/PAK1/Dok-R -0.028 0.088 -10000 0 -0.43 20 20
NCK1/Dok-R -0.003 0.25 -10000 0 -1.1 21 21
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
mol:beta2-estradiol 0 0.045 0.23 18 -10000 0 18
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
Rac/GDP 0.02 0.004 -10000 0 -10000 0 0
F2 -0.012 0.056 0.27 13 -10000 0 13
TNIP2 0.027 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.011 0.23 -10000 0 -1.1 20 20
FN1 -0.085 0.069 -10000 0 -10000 0 0
PLD2 -0.024 0.25 -10000 0 -1.2 20 20
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GRB14 0.006 0.12 -10000 0 -0.67 15 15
ELK1 -0.024 0.22 -10000 0 -1 20 20
GRB7 0.001 0.056 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.007 0.25 -10000 0 -1.1 20 20
CDKN1A -0.022 0.16 0.49 4 -0.63 20 24
ITGA5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.004 0.25 -10000 0 -1.1 21 21
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:NO 0.011 0.17 0.57 8 -0.67 20 28
PLG -0.031 0.25 -10000 0 -1.2 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.011 0.19 -10000 0 -0.89 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 0.42 1 -0.78 17 18
BMX -0.034 0.26 -10000 0 -1.2 20 20
ANGPT1 -0.043 0.26 -10000 0 -1.3 18 18
tube development -0.037 0.17 0.46 3 -0.73 20 23
ANGPT4 -0.034 0.2 -10000 0 -0.67 42 42
response to hypoxia -0.004 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.027 0.27 -10000 0 -1.2 20 20
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.037 0.19 -10000 0 -0.83 20 20
mol:L-citrulline 0.011 0.17 0.57 8 -0.67 20 28
AGTR1 -0.26 0.34 -10000 0 -0.67 201 201
MAPK14 -0.026 0.25 -10000 0 -1.2 20 20
Tie2/SHP2 -0.003 0.18 -10000 0 -1.2 8 8
TEK 0.005 0.19 -10000 0 -1.4 8 8
RPS6KB1 -0.006 0.2 0.51 2 -0.89 20 22
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.5 201 201
Tie2/Ang1/GRB2 -0.016 0.26 -10000 0 -1.2 20 20
MAPK3 -0.02 0.22 -10000 0 -1.1 20 20
MAPK1 -0.029 0.22 -10000 0 -1.1 20 20
Tie2/Ang1/GRB7 -0.016 0.26 -10000 0 -1.2 20 20
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.032 0.26 -10000 0 -1.2 20 20
PI3K -0.02 0.23 -10000 0 -1.1 20 20
FES -0.027 0.25 -10000 0 -1.2 20 20
Crk/Dok-R -0.003 0.25 -10000 0 -1.1 21 21
Tie2/Ang1/ABIN2 -0.015 0.26 -10000 0 -1.2 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.003 0.19 0.5 4 -0.83 20 24
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.01 0.2 0.48 1 -0.9 20 21
Tie2/Ang2 -0.056 0.22 -10000 0 -1 20 20
Tie2/Ang1 -0.027 0.28 -10000 0 -1.3 20 20
FOXO1 0 0.19 0.56 4 -0.84 20 24
ELF1 0.028 0.053 -10000 0 -0.59 3 3
ELF2 -0.023 0.24 -10000 0 -1.2 20 20
mol:Choline -0.021 0.23 -10000 0 -1.1 20 20
cell migration -0.014 0.055 -10000 0 -0.24 20 20
FYN -0.046 0.19 0.53 1 -0.84 20 21
DOK2 0.019 0.052 -10000 0 -0.67 2 2
negative regulation of cell cycle -0.019 0.15 0.45 6 -0.57 20 26
ETS1 0.026 0.047 -10000 0 -0.24 13 13
PXN 0.003 0.18 0.59 5 -0.73 20 25
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.004 0.19 0.58 7 -0.78 20 27
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF -0.056 0.23 -10000 0 -0.59 71 71
MAPKKK cascade -0.021 0.23 -10000 0 -1.1 20 20
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.017 0.26 -10000 0 -1.2 20 20
NCK1 0.027 0.003 -10000 0 -10000 0 0
vasculogenesis 0.014 0.16 0.52 10 -0.6 20 30
mol:Phosphatidic acid -0.021 0.23 -10000 0 -1.1 20 20
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.011 0.17 0.57 8 -0.67 20 28
Rac1/GTP -0.004 0.18 -10000 0 -0.83 20 20
MMP2 -0.029 0.26 -10000 0 -1.2 20 20
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.015 0.12 -10000 0 -0.44 20 20
BAG4 0.025 0.032 -10000 0 -0.67 1 1
BAD 0.007 0.065 0.34 9 -10000 0 9
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX 0.013 0.07 0.25 23 -10000 0 23
EnzymeConsortium:3.1.4.12 0.002 0.039 0.16 10 -0.1 17 27
IKBKB -0.013 0.12 0.29 1 -0.45 15 16
MAP2K2 0.018 0.094 0.34 23 -0.3 2 25
MAP2K1 0.011 0.083 0.32 19 -0.3 2 21
SMPD1 0.005 0.045 0.24 7 -0.13 4 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.45 20 20
MAP2K4 0.017 0.096 0.35 26 -10000 0 26
protein ubiquitination -0.011 0.12 0.32 4 -0.43 18 22
EnzymeConsortium:2.7.1.37 0.018 0.11 0.38 25 -0.31 2 27
response to UV 0 0.002 0.006 27 -0.002 3 30
RAF1 0.012 0.085 0.31 21 -0.32 2 23
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.005 0.059 0.22 12 -0.15 16 28
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.008 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.076 0.31 18 -0.16 10 28
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.018 0.088 0.34 19 -0.29 2 21
MAPK1 -0.005 0.09 0.33 16 -0.27 4 20
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD -0.014 0.12 -10000 0 -0.44 19 19
KSR1 0.01 0.08 0.28 23 -0.33 2 25
MAPK8 0.011 0.11 0.38 22 -0.35 9 31
TRAF2 0.025 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 13 -10000 0 13
CHUK -0.014 0.12 0.33 1 -0.42 20 21
TNF R/SODD 0.038 0.026 -10000 0 -0.51 1 1
TNF -0.055 0.22 -10000 0 -0.68 56 56
CYCS 0.02 0.08 0.26 25 -0.18 1 26
IKBKG -0.012 0.12 0.32 2 -0.42 18 20
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.015 0.13 -10000 0 -0.41 29 29
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.018 0.079 0.25 25 -0.18 2 27
TNF/TNF R/SODD -0.003 0.16 -10000 0 -0.44 57 57
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 13 -10000 0 13
CASP8 0.009 0.13 -10000 0 -0.72 14 14
NSMAF -0.014 0.12 -10000 0 -0.44 19 19
response to hydrogen peroxide 0 0.002 0.006 27 -0.002 3 30
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
Jak2/Leptin Receptor -0.006 0.12 0.26 4 -0.37 31 35
PTP1B/AKT1 0.006 0.071 0.32 2 -0.28 6 8
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0 0.082 0.31 11 -0.28 9 20
EGFR 0.013 0.072 -10000 0 -0.68 5 5
EGF/EGFR -0.035 0.16 0.24 1 -0.39 74 75
CSF1 0.015 0.088 -10000 0 -0.67 8 8
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.026 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.004 0.11 0.32 6 -0.32 21 27
Insulin Receptor/Insulin 0.015 0.072 -10000 0 -0.35 4 4
HCK 0.017 0.039 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0.008 0.093 0.31 21 -0.29 5 26
EGF -0.076 0.25 -10000 0 -0.67 72 72
YES1 0.027 0.005 -10000 0 -10000 0 0
CAV1 -0.004 0.11 0.4 12 -0.32 10 22
TXN 0.024 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.029 0.14 -10000 0 -0.38 57 57
cell migration 0 0.082 0.28 9 -0.31 11 20
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.014 0.16 -10000 0 -0.67 25 25
ITGA2B -0.042 0.21 -10000 0 -0.67 48 48
CSF1R 0.024 0.035 -10000 0 -0.67 1 1
Prolactin Receptor/Prolactin 0.001 0.12 -10000 0 -0.51 25 25
FGR 0.025 0.015 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.006 0.073 0.28 3 -0.27 8 11
Crk/p130 Cas 0.013 0.071 -10000 0 -0.29 4 4
DOK1 0.012 0.087 0.36 12 -0.32 4 16
JAK2 -0.012 0.12 0.31 7 -0.37 35 42
Jak2/Leptin Receptor/Leptin -0.007 0.13 -10000 0 -0.49 20 20
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
PTPN1 0 0.083 0.31 11 -0.28 9 20
LYN 0.027 0.005 -10000 0 -10000 0 0
CDH2 -0.073 0.12 -10000 0 -0.63 14 14
SRC 0.023 0.057 0.32 1 -0.39 5 6
ITGB3 0.01 0.1 -10000 0 -0.65 11 11
CAT1/PTP1B -0.06 0.16 0.4 14 -0.36 45 59
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.008 -10000 0 -10000 0 0
PI3K 0.021 0.082 -10000 0 -0.42 6 6
mol:H2O2 -0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.007 0.13 -10000 0 -0.52 19 19
negative regulation of transcription -0.01 0.12 0.31 7 -0.36 35 42
FCGR2A 0.017 0.045 -10000 0 -0.67 1 1
FER 0.021 0.055 -10000 0 -0.68 3 3
alphaIIb/beta3 Integrin -0.026 0.18 -10000 0 -0.53 55 55
BLK -0.19 0.31 -10000 0 -0.67 148 148
Insulin Receptor/Insulin/Shc 0.039 0.04 -10000 0 -0.42 3 3
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.021 0.06 -10000 0 -0.54 5 5
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.005 -10000 0 -10000 0 0
TRPV6 -0.09 0.18 0.38 3 -0.47 42 45
PRL -0.006 0.019 -10000 0 -10000 0 0
SOCS3 -0.038 0.3 -10000 0 -1.3 26 26
SPRY2 0.022 0.046 -10000 0 -0.68 2 2
Insulin Receptor/Insulin/IRS1 -0.016 0.16 -10000 0 -0.45 60 60
CSF1/CSF1R 0.008 0.095 0.28 1 -0.46 10 11
Ras protein signal transduction 0.026 0.11 0.46 26 -10000 0 26
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
INS 0.007 0.055 -10000 0 -0.67 3 3
LEP 0.009 0.033 -10000 0 -10000 0 0
STAT5B 0.001 0.091 0.29 11 -0.28 14 25
STAT5A 0.001 0.091 0.29 11 -0.28 14 25
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.073 0.28 1 -0.3 9 10
CSN2 0.001 0.062 0.81 1 -10000 0 1
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
LAT 0.02 0.073 0.32 1 -0.45 8 9
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.012 0.082 -10000 0 -0.67 6 6
SHC1 0.025 0.008 -10000 0 -10000 0 0
NOX4 -0.041 0.077 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.01 0.1 -10000 0 -0.52 11 11
alphaM/beta2 Integrin/GPIbA 0.001 0.12 -10000 0 -0.49 18 18
alphaM/beta2 Integrin/proMMP-9 -0.023 0.17 -10000 0 -0.5 44 44
PLAUR -0.023 0.071 -10000 0 -10000 0 0
HMGB1 0.009 0.035 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.015 0.085 -10000 0 -0.57 5 5
AGER -0.037 0.18 -10000 0 -0.7 32 32
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.016 0.039 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.19 -10000 0 -0.47 55 55
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
CYR61 -0.18 0.32 -10000 0 -0.67 144 144
TLN1 0.025 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.087 -10000 0 -0.37 9 9
RHOA 0.027 0.003 -10000 0 -10000 0 0
P-selectin oligomer 0.015 0.078 -10000 0 -0.67 6 6
MYH2 -0.031 0.097 -10000 0 -0.41 9 9
MST1R 0.02 0.065 -10000 0 -0.67 4 4
leukocyte activation during inflammatory response 0.014 0.081 -10000 0 -0.49 5 5
APOB 0.006 0.04 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.017 0.079 -10000 0 -0.63 7 7
JAM3 0.027 0.005 -10000 0 -10000 0 0
GP1BA 0.002 0.12 -10000 0 -0.63 15 15
alphaM/beta2 Integrin/CTGF -0.051 0.19 -10000 0 -0.47 76 76
alphaM/beta2 Integrin -0.024 0.089 -10000 0 -0.35 16 16
JAM3 homodimer 0.027 0.005 -10000 0 -10000 0 0
ICAM2 0.026 0.007 -10000 0 -10000 0 0
ICAM1 -0.011 0.065 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.024 0.089 -10000 0 -0.37 14 14
cell adhesion 0.001 0.12 -10000 0 -0.49 18 18
NFKB1 -0.11 0.26 0.33 1 -0.5 129 130
THY1 0.026 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.021 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.026 0.095 -10000 0 -0.48 9 9
IL6 -0.19 0.38 -10000 0 -0.96 88 88
ITGB2 -0.001 0.058 -10000 0 -0.46 2 2
elevation of cytosolic calcium ion concentration -0.02 0.11 -10000 0 -0.52 5 5
alphaM/beta2 Integrin/JAM2/JAM3 0.026 0.094 -10000 0 -0.47 9 9
JAM2 0.021 0.063 -10000 0 -0.67 4 4
alphaM/beta2 Integrin/ICAM1 0.034 0.1 -10000 0 -0.52 8 8
alphaM/beta2 Integrin/uPA/Plg 0.009 0.098 -10000 0 -0.52 5 5
RhoA/GTP -0.026 0.1 -10000 0 -0.36 19 19
positive regulation of phagocytosis -0.007 0.096 -10000 0 -0.49 7 7
Ron/MSP 0.034 0.056 -10000 0 -0.51 5 5
alphaM/beta2 Integrin/uPAR/uPA -0.02 0.11 -10000 0 -0.52 5 5
alphaM/beta2 Integrin/uPAR 0.007 0.094 -10000 0 -0.55 5 5
PLAU -0.045 0.077 -10000 0 -10000 0 0
PLAT 0.02 0.058 -10000 0 -0.67 3 3
actin filament polymerization -0.029 0.095 -10000 0 -0.4 9 9
MST1 0.026 0.032 -10000 0 -0.67 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.018 0.083 -10000 0 -0.5 5 5
TNF -0.16 0.35 -10000 0 -0.92 73 73
RAP1B 0.027 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.099 -10000 0 -0.51 6 6
fibrinolysis 0.008 0.097 -10000 0 -0.52 5 5
HCK 0.017 0.039 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.024 0.089 -10000 0 -0.37 14 14
VTN -0.038 0.2 -10000 0 -0.67 44 44
alphaM/beta2 Integrin/CYR61 -0.12 0.23 -10000 0 -0.47 146 146
LPA -0.005 0.026 -10000 0 -10000 0 0
LRP1 0.025 0.032 -10000 0 -0.67 1 1
cell migration -0.031 0.16 -10000 0 -0.49 45 45
FN1 -0.085 0.069 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.016 0.086 -10000 0 -0.56 5 5
MPO 0.012 0.078 -10000 0 -0.67 6 6
KNG1 -0.005 0.038 -10000 0 -10000 0 0
RAP1/GDP 0.035 0.009 -10000 0 -10000 0 0
ROCK1 -0.024 0.098 -10000 0 -0.43 7 7
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.014 0.02 -10000 0 -10000 0 0
CTGF -0.078 0.25 -10000 0 -0.66 76 76
alphaM/beta2 Integrin/Hck 0.011 0.092 -10000 0 -0.51 6 6
ITGAM -0.005 0.081 -10000 0 -0.62 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.02 0.1 -10000 0 -0.52 10 10
HP -0.023 0.098 -10000 0 -0.67 6 6
leukocyte adhesion -0.025 0.16 -10000 0 -0.46 35 35
SELP 0.015 0.078 -10000 0 -0.67 6 6
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.04 0.12 0.89 7 -10000 0 7
VDR 0.026 0.009 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.006 0.11 -10000 0 -0.41 8 8
RXRs/LXRs/DNA/Oxysterols -0.01 0.15 -10000 0 -0.42 51 51
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA -0.001 0.018 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.02 0.069 -10000 0 -0.3 21 21
RXRs/NUR77 -0.091 0.24 -10000 0 -0.45 136 136
RXRs/PPAR -0.021 0.081 -10000 0 -0.38 11 11
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.049 0.074 -10000 0 -0.39 13 13
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.009 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.032 0.071 -10000 0 -0.37 14 14
RARG 0.027 0.005 -10000 0 -10000 0 0
RPS6KB1 0.051 0.12 0.56 27 -10000 0 27
RARs/THRs/DNA/SMRT 0.021 0.069 -10000 0 -0.3 21 21
THRA 0.026 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.036 0.097 -10000 0 -0.44 5 5
NR1H4 -0.004 0.022 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.057 0.12 -10000 0 -0.5 4 4
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.023 0.026 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.048 0.08 -10000 0 -0.45 3 3
NR4A1 -0.18 0.32 -10000 0 -0.67 146 146
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.003 0.054 -10000 0 -0.31 3 3
RXRG -0.11 0.077 -10000 0 -0.7 4 4
RXR alpha/CCPG 0.032 0.025 -10000 0 -10000 0 0
RXRA 0.021 0.025 -10000 0 -10000 0 0
RXRB 0.023 0.026 -10000 0 -10000 0 0
THRB 0.014 0.095 -10000 0 -0.64 10 10
PPARG 0.016 0.083 -10000 0 -0.67 7 7
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.097 0.37 -10000 0 -1.1 57 57
mol:Oxysterols 0 0.016 -10000 0 -10000 0 0
cholesterol transport -0.009 0.15 -10000 0 -0.42 51 51
PPARA 0.02 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.007 0.12 -10000 0 -0.67 14 14
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.34 157 157
SREBF1 -0.011 0.14 -10000 0 -0.53 7 7
RXRs/RXRs/DNA/9cRA 0.037 0.097 -10000 0 -0.44 5 5
ABCA1 -0.01 0.14 -10000 0 -0.59 4 4
RARs/THRs 0.056 0.098 -10000 0 -0.4 20 20
RXRs/FXR 0.047 0.085 -10000 0 -0.48 3 3
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.03 0.11 -10000 0 -0.33 58 58
FRAP1 0.01 0.047 0.33 4 -0.42 1 5
AKT1 -0.026 0.096 -10000 0 -0.28 55 55
INSR 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.024 0.037 -10000 0 -0.43 3 3
mol:GTP 0.004 0.089 -10000 0 -0.42 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.007 0.036 -10000 0 -0.24 1 1
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.074 -10000 0 -0.39 3 3
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.023 0.13 -10000 0 -0.38 59 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.044 -10000 0 -0.27 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.019 0.098 0.37 20 -0.37 3 23
MAP3K5 0.006 0.028 0.18 1 -0.22 6 7
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.029 0.18 1 -0.21 7 8
mol:LY294002 0 0.001 0.001 1 -0.002 72 73
EIF4B 0.024 0.11 0.46 21 -0.32 3 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.069 0.35 5 -0.31 3 8
eIF4E/eIF4G1/eIF4A1 0.016 0.024 -10000 0 -0.25 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.007 0.13 -10000 0 -0.36 59 59
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.047 0.28 3 -0.24 2 5
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.012 0.08 -10000 0 -0.38 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 72 73
FKBP12/Rapamycin 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.032 0.11 -10000 0 -0.32 57 57
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.026 0.074 -10000 0 -0.5 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.006 0.096 0.28 1 -0.46 3 4
tumor necrosis factor receptor activity 0 0.001 0.002 72 -0.001 1 73
RPS6 0.025 0.008 -10000 0 -10000 0 0
PPP5C 0.025 0.008 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.042 0.14 -10000 0 -0.37 67 67
INS -0.02 0.051 -10000 0 -0.67 3 3
PTEN 0.025 0.018 -10000 0 -0.36 1 1
PDK2 -0.029 0.1 0.22 3 -0.31 55 58
EIF4EBP1 0.016 0.096 -10000 0 -0.93 5 5
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PPP2R5D 0.02 0.074 0.38 14 -0.38 1 15
peptide biosynthetic process 0.011 0.034 -10000 0 -0.39 3 3
RHEB 0.026 0.006 -10000 0 -10000 0 0
EIF4A1 0.026 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.002 0.009 19 -0.003 3 22
EEF2 0.011 0.034 -10000 0 -0.39 3 3
eIF4E/4E-BP1 0.03 0.088 -10000 0 -0.83 5 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.04 -10000 0 -0.82 1 1
VEGFR1 homodimer/NRP1 0.015 0.038 -10000 0 -0.82 1 1
mol:DAG -0.022 0.13 -10000 0 -0.4 51 51
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.059 -10000 0 -0.64 3 3
CaM/Ca2+ -0.006 0.13 -10000 0 -0.38 51 51
HIF1A 0.033 0.019 -10000 0 -0.37 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.02 0.14 -10000 0 -0.7 4 4
PLCG1 -0.022 0.13 -10000 0 -0.4 51 51
NOS3 -0.012 0.12 -10000 0 -0.53 3 3
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:NO -0.007 0.12 0.47 3 -0.5 3 6
FLT1 0.02 0.042 -10000 0 -0.91 1 1
PGF -0.045 0.21 -10000 0 -0.67 51 51
VEGFR1 homodimer/NRP2/VEGFR121 0.045 0.062 -10000 0 -0.64 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
eNOS/Hsp90 0.005 0.12 -10000 0 -0.74 1 1
endothelial cell proliferation -0.037 0.15 0.36 2 -0.43 49 51
mol:Ca2+ -0.022 0.13 -10000 0 -0.4 51 51
MAPK3 -0.038 0.13 0.36 2 -0.99 1 3
MAPK1 -0.042 0.13 -10000 0 -0.41 12 12
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.044 0.21 -10000 0 -0.67 51 51
PRKACA 0.025 0.008 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.014 0.094 -10000 0 -0.67 9 9
VEGFA homodimer 0.023 0.054 -10000 0 -0.67 3 3
VEGFR1 homodimer/VEGFA homodimer 0.031 0.063 -10000 0 -0.68 3 3
platelet activating factor biosynthetic process -0.041 0.12 -10000 0 -0.96 1 1
PI3K 0.015 0.14 -10000 0 -0.39 52 52
PRKCA -0.039 0.14 -10000 0 -0.38 65 65
PRKCB -0.034 0.13 -10000 0 -0.38 54 54
VEGFR1 homodimer/PLGF homodimer -0.014 0.15 -10000 0 -0.44 51 51
VEGFA 0.023 0.054 -10000 0 -0.67 3 3
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.022 0.13 -10000 0 -0.4 51 51
RASA1 0.02 0.038 -10000 0 -0.76 1 1
NRP2 0.014 0.043 -10000 0 -10000 0 0
VEGFR1 homodimer 0.02 0.042 -10000 0 -0.91 1 1
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.002 0.14 0.55 4 -0.62 4 8
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
mol:PI-3-4-5-P3 0.013 0.14 -10000 0 -0.38 52 52
mol:L-citrulline -0.007 0.12 0.47 3 -0.5 3 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.062 -10000 0 -0.61 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.061 -10000 0 -0.64 3 3
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.025 0.14 -10000 0 -0.37 52 52
PDPK1 -0.017 0.13 0.34 3 -0.38 47 50
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.074 -10000 0 -0.75 3 3
mol:NADP -0.007 0.12 0.47 3 -0.5 3 6
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.06 -10000 0 -0.6 3 3
VEGFR1 homodimer/NRP2 0.026 0.047 -10000 0 -0.82 1 1
FOXM1 transcription factor network

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
NFATC3 -0.017 0.31 0.78 2 -0.92 12 14
PLK1 0.029 0.095 -10000 0 -0.82 5 5
BIRC5 0.025 0.1 -10000 0 -0.93 4 4
HSPA1B -0.023 0.31 -10000 0 -0.92 12 12
MAP2K1 0.025 0.045 -10000 0 -10000 0 0
BRCA2 -0.025 0.32 0.79 1 -0.97 16 17
FOXM1 -0.048 0.34 -10000 0 -0.95 23 23
XRCC1 -0.014 0.31 -10000 0 -0.89 13 13
FOXM1B/p19 -0.047 0.33 -10000 0 -0.87 29 29
Cyclin D1/CDK4 0 0.29 -10000 0 -0.83 11 11
CDC2 -0.026 0.32 0.61 1 -0.85 23 24
TGFA -0.014 0.29 -10000 0 -0.8 14 14
SKP2 -0.019 0.32 0.78 2 -0.92 19 21
CCNE1 0.027 0.01 -10000 0 -10000 0 0
CKS1B -0.023 0.31 -10000 0 -0.82 23 23
RB1 0.026 0.19 -10000 0 -0.72 7 7
FOXM1C/SP1 -0.029 0.33 -10000 0 -0.92 23 23
AURKB 0.009 0.13 -10000 0 -0.83 9 9
CENPF -0.012 0.31 0.78 1 -0.91 12 13
CDK4 0.027 0.019 -10000 0 -10000 0 0
MYC -0.029 0.31 -10000 0 -0.86 23 23
CHEK2 0.02 0.04 -10000 0 -10000 0 0
ONECUT1 -0.012 0.3 -10000 0 -0.82 17 17
CDKN2A -0.033 0.073 -10000 0 -10000 0 0
LAMA4 -0.023 0.31 -10000 0 -0.91 13 13
FOXM1B/HNF6 -0.019 0.32 -10000 0 -0.93 17 17
FOS -0.22 0.59 0.78 2 -1.2 129 131
SP1 0.027 0.009 -10000 0 -10000 0 0
CDC25B -0.018 0.31 0.79 1 -0.93 11 12
response to radiation 0.006 0.026 -10000 0 -10000 0 0
CENPB -0.018 0.31 0.79 1 -0.92 12 13
CENPA -0.032 0.32 -10000 0 -0.89 22 22
NEK2 -0.012 0.31 0.78 1 -0.93 11 12
HIST1H2BA -0.029 0.31 -10000 0 -0.91 13 13
CCNA2 0.026 0.022 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.034 0.33 -10000 0 -0.96 18 18
CCNB2 -0.025 0.31 -10000 0 -0.92 12 12
CCNB1 -0.024 0.32 0.66 2 -0.89 18 20
ETV5 -0.023 0.31 -10000 0 -0.86 17 17
ESR1 -0.059 0.38 -10000 0 -1.1 28 28
CCND1 -0.006 0.29 0.58 1 -0.84 12 13
GSK3A 0.022 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.052 0.043 -10000 0 -10000 0 0
CDK2 0.028 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.009 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.036 0.31 -10000 0 -0.87 21 21
GAS1 -0.17 0.55 0.79 1 -1.2 99 100
MMP2 -0.024 0.34 0.78 2 -1.1 14 16
RB1/FOXM1C -0.005 0.29 -10000 0 -0.89 11 11
CREBBP 0.026 0.006 -10000 0 -10000 0 0
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 0.002 0.044 -10000 0 -0.44 5 5
ADCY5 -0.054 0.15 -10000 0 -0.44 66 66
ADCY6 0.002 0.044 -10000 0 -0.44 5 5
ADCY7 0.002 0.044 -10000 0 -0.44 5 5
ADCY1 -0.002 0.065 -10000 0 -0.49 8 8
ADCY2 -0.038 0.13 -10000 0 -0.44 46 46
ADCY3 0.002 0.044 -10000 0 -0.44 5 5
ADCY8 -0.05 0.054 -10000 0 -0.49 5 5
PRKCE 0.004 0.052 -10000 0 -0.51 5 5
ADCY9 0.002 0.044 -10000 0 -0.44 5 5
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.035 0.096 0.34 7 -0.36 16 23
Regulation of nuclear SMAD2/3 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
EP300 0.025 0.025 0.37 1 -10000 0 1
HSPA8 0.02 0.057 -10000 0 -0.6 4 4
SMAD3/SMAD4/ER alpha -0.002 0.13 -10000 0 -0.48 21 21
AKT1 0.026 0.007 -10000 0 -10000 0 0
GSC -0.17 0.49 -10000 0 -1.4 67 67
NKX2-5 0.002 0.002 -10000 0 -10000 0 0
muscle cell differentiation -0.012 0.081 0.38 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.037 0.096 -10000 0 -0.31 1 1
SMAD4 -0.006 0.071 -10000 0 -0.26 1 1
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.034 0.072 -10000 0 -0.44 3 3
SMAD3/SMAD4/VDR 0.048 0.074 -10000 0 -10000 0 0
MYC 0.012 0.1 -10000 0 -0.65 12 12
CDKN2B -0.021 0.11 -10000 0 -0.47 3 3
AP1 -0.19 0.41 -10000 0 -0.76 150 150
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.029 0.063 -10000 0 -0.51 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.01 0.035 -10000 0 -10000 0 0
SP3 0.029 0.005 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 0.005 0.053 -10000 0 -0.23 1 1
SMAD3/SMAD4/GR 0.021 0.079 -10000 0 -10000 0 0
GATA3 -0.01 0.15 -10000 0 -0.63 25 25
SKI/SIN3/HDAC complex/NCoR1 0.028 0.041 -10000 0 -0.65 1 1
MEF2C/TIF2 -0.026 0.15 0.32 3 -0.4 42 45
endothelial cell migration -0.022 0.079 1.3 1 -10000 0 1
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.007 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.67 2 2
RUNX2 -0.015 0.08 -10000 0 -0.67 2 2
RUNX3 0.009 0.1 -10000 0 -0.67 11 11
RUNX1 -0.04 0.076 -10000 0 -10000 0 0
CTBP1 0.027 0.004 -10000 0 -10000 0 0
NR3C1 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.009 -10000 0 -10000 0 0
CDKN1A 0.019 0.047 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.014 0.12 -10000 0 -0.29 37 37
DCP1A 0.027 0.003 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 0.022 0.079 -10000 0 -1.3 1 1
SMAD3/SMAD4/ATF2 0.003 0.13 -10000 0 -0.46 23 23
SMAD3/SMAD4/ATF3 -0.079 0.24 -10000 0 -0.51 109 109
SAP30 0.025 0.032 -10000 0 -0.68 1 1
Cbp/p300/PIAS3 0.048 0.044 -10000 0 -10000 0 0
JUN -0.2 0.4 0.3 1 -0.76 150 151
SMAD3/SMAD4/IRF7 0.025 0.08 -10000 0 -10000 0 0
TFE3 0.03 0.009 -10000 0 -10000 0 0
COL1A2 0.026 0.064 -10000 0 -1.1 1 1
mesenchymal cell differentiation -0.014 0.097 0.34 5 -10000 0 5
DLX1 -0.009 0.15 -10000 0 -0.65 26 26
TCF3 0.025 0.008 -10000 0 -10000 0 0
FOS -0.17 0.33 -10000 0 -0.73 125 125
SMAD3/SMAD4/Max 0.02 0.08 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.042 0.036 -10000 0 -0.42 1 1
ZBTB17 0.028 0.006 -10000 0 -10000 0 0
LAMC1 0.012 0.06 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.022 0.08 -10000 0 -0.25 3 3
IRF7 0.027 0.01 -10000 0 -10000 0 0
ESR1 -0.015 0.15 -10000 0 -0.65 23 23
HNF4A -0.009 0.024 -10000 0 -10000 0 0
MEF2C -0.006 0.1 0.38 4 -0.88 1 5
SMAD2-3/SMAD4 0.012 0.095 -10000 0 -0.29 2 2
Cbp/p300/Src-1 0.046 0.035 -10000 0 -10000 0 0
IGHV3OR16-13 0.001 0.034 -10000 0 -0.34 3 3
TGIF2/HDAC complex 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.029 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.032 -10000 0 -0.67 1 1
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
SNIP1 0.024 0.032 -10000 0 -0.67 1 1
GCN5L2 0.004 0.013 0.2 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.03 0.08 -10000 0 -0.27 1 1
MSG1/HSC70 -0.068 0.07 -10000 0 -0.47 8 8
SMAD2 0.012 0.047 -10000 0 -10000 0 0
SMAD3 0.005 0.06 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.067 -10000 0 -0.34 9 9
SMAD2/SMAD2/SMAD4 0.004 0.036 0.23 3 -10000 0 3
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.046 0.094 -10000 0 -10000 0 0
IFNB1 0 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.01 0.11 -10000 0 -0.61 2 2
CITED1 -0.1 0.081 -10000 0 -0.61 5 5
SMAD2-3/SMAD4/ARC105 0.013 0.085 -10000 0 -10000 0 0
RBL1 0.014 0.094 -10000 0 -0.67 9 9
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.012 0.035 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.043 0.077 -10000 0 -0.43 11 11
SMAD7 -0.087 0.25 -10000 0 -0.52 106 106
MYC/MIZ-1 0.028 0.083 -10000 0 -0.49 12 12
SMAD3/SMAD4 0.022 0.11 0.3 26 -0.52 1 27
IL10 -0.03 0.15 -10000 0 -0.52 35 35
PIASy/HDAC complex 0.018 0.02 -10000 0 -10000 0 0
PIAS3 0.027 0.008 -10000 0 -10000 0 0
CDK2 0.03 0.011 -10000 0 -10000 0 0
IL5 -0.022 0.11 -10000 0 -0.4 24 24
CDK4 0.031 0.011 -10000 0 -10000 0 0
PIAS4 0.018 0.02 -10000 0 -10000 0 0
ATF3 -0.13 0.29 -10000 0 -0.67 110 110
SMAD3/SMAD4/SP1 0.033 0.083 -10000 0 -0.29 1 1
FOXG1 0.007 0.043 -10000 0 -0.68 1 1
FOXO3 0.015 0.008 -10000 0 -10000 0 0
FOXO1 0.014 0.009 -10000 0 -10000 0 0
FOXO4 0.014 0.008 -10000 0 -10000 0 0
heart looping -0.006 0.1 0.38 4 -0.86 1 5
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.003 0.14 -10000 0 -0.49 24 24
MYOD1 -0.013 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.016 0.081 -10000 0 -0.26 4 4
SMAD3/SMAD4/GATA3 0 0.14 -10000 0 -0.41 35 35
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.032 -10000 0 -0.67 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.028 0.12 -10000 0 -0.48 10 10
SMAD3/SMAD4/SP1-3 0.053 0.081 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.03 0.015 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.022 0.11 -10000 0 -0.28 23 23
ITGB5 0.015 0.06 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.031 0.034 -10000 0 -0.49 1 1
SMAD3/SMAD4/AR -0.18 0.26 -10000 0 -0.48 200 200
AR -0.26 0.34 -10000 0 -0.66 206 206
negative regulation of cell growth -0.022 0.12 -10000 0 -0.36 12 12
SMAD3/SMAD4/MYOD 0.016 0.08 -10000 0 -10000 0 0
E2F5 0.025 0.032 -10000 0 -0.67 1 1
E2F4 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.027 0.096 -10000 0 -0.33 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.036 -10000 0 -10000 0 0
TFDP1 0.025 0.018 -10000 0 -0.36 1 1
SMAD3/SMAD4/AP1 -0.18 0.43 -10000 0 -0.78 150 150
SMAD3/SMAD4/RUNX2 0.015 0.097 -10000 0 -0.34 5 5
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.005 -10000 0 -10000 0 0
ATF2 -0.002 0.14 -10000 0 -0.66 21 21
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.074 -9999 0 -0.38 15 15
RGS9BP -0.015 0.16 -9999 0 -0.66 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.038 0.2 -9999 0 -0.65 46 46
mol:Na + 0.017 0.034 -9999 0 -10000 0 0
mol:ADP -0.043 0.15 -9999 0 -0.5 45 45
GNAT2 0.016 0.02 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.022 0.18 -9999 0 -0.45 71 71
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.01 -9999 0 -10000 0 0
GRK7 0.005 0.022 -9999 0 -10000 0 0
CNGB3 -0.008 0.017 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.01 0.029 -9999 0 -10000 0 0
Cone PDE6 -0.003 0.16 -9999 0 -0.4 70 70
Cone Metarhodopsin II -0.01 0.12 -9999 0 -0.4 45 45
Na + (4 Units) 0.022 0.039 -9999 0 -10000 0 0
GNAT2/GDP -0.008 0.16 -9999 0 -0.39 68 68
GNB5 0.027 0.004 -9999 0 -10000 0 0
mol:GMP (4 units) -0.003 0.022 -9999 0 -10000 0 0
Cone Transducin 0.033 0.079 -9999 0 -0.4 15 15
SLC24A2 -0.008 0.031 -9999 0 -10000 0 0
GNB3/GNGT2 0.021 0.094 -9999 0 -0.51 15 15
GNB3 0.007 0.12 -9999 0 -0.67 14 14
GNAT2/GTP 0.017 0.008 -9999 0 -10000 0 0
CNGA3 0.007 0.052 -9999 0 -10000 0 0
ARR3 -0.002 0.02 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.017 0.034 -9999 0 -10000 0 0
mol:Pi -0.022 0.18 -9999 0 -0.45 71 71
Cone CNG Channel 0.042 0.034 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.008 0.031 -9999 0 -10000 0 0
RGS9 -0.039 0.2 -9999 0 -0.67 45 45
PDE6C -0.005 0.02 -9999 0 -10000 0 0
GNGT2 0.023 0.035 -9999 0 -0.67 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.003 0.02 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.018 0.12 -10000 0 -0.45 25 25
MAP4K1 0.008 0.079 -10000 0 -0.67 5 5
MAP3K8 0.018 0.079 -10000 0 -0.63 7 7
PRKCB 0.007 0.08 -10000 0 -0.67 5 5
DBNL 0.026 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 0.002 0.081 -10000 0 -0.41 9 9
JUN -0.084 0.21 0.37 1 -0.51 56 57
MAP3K7 0.002 0.081 -10000 0 -0.41 9 9
GRAP2 -0.02 0.15 -10000 0 -0.56 33 33
CRK 0.026 0.007 -10000 0 -10000 0 0
MAP2K4 -0.003 0.097 0.34 3 -0.37 17 20
LAT 0.021 0.058 -10000 0 -0.6 4 4
LCP2 0.024 0.021 -10000 0 -10000 0 0
MAPK8 -0.007 0.15 -10000 0 -0.62 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.085 -10000 0 -0.34 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55 0.026 0.12 -10000 0 -0.44 23 23
p75(NTR)-mediated 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
Sortilin/TRAF6 0.037 0.036 -10000 0 -0.51 2 2
Necdin/E2F1 -0.002 0.078 -10000 0 -0.55 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.057 0.091 -10000 0 -0.4 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.25 -10000 0 -0.44 227 227
NT-4/5 (dimer)/p75(NTR) -0.012 0.14 -10000 0 -0.52 30 30
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.005 0.097 0.36 1 -0.4 19 20
IKBKG 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.008 0.1 -10000 0 -0.67 11 11
MGDIs/NGR/p75(NTR)/LINGO1 0.022 0.092 -10000 0 -0.45 16 16
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.026 0.11 -10000 0 -0.42 27 27
LINGO1 0.02 0.032 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.028 -10000 0 -0.35 2 2
proBDNF (dimer) 0.008 0.1 -10000 0 -0.67 11 11
NTRK1 0.01 0.031 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.13 0.46 10 -0.56 3 13
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.006 0.09 -10000 0 -0.46 15 15
ARHGDIA 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.092 -10000 0 -0.43 16 16
MAGEH1 0.026 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.045 0.1 -10000 0 -0.42 20 20
Mammalian IAPs/DIABLO 0.046 0.094 -10000 0 -0.39 20 20
proNGF (dimer) 0.021 0.056 -10000 0 -0.67 3 3
MAGED1 0.026 0.007 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.12 -10000 0 -0.65 15 15
ZNF274 0.025 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.012 0.085 -10000 0 -0.4 16 16
NGF 0.022 0.056 -10000 0 -0.67 3 3
cell cycle arrest 0.057 0.14 0.46 16 -0.38 16 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.069 -10000 0 -0.32 18 18
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.018 0.13 -10000 0 -0.45 32 32
NCSTN 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0.034 0.097 -10000 0 -0.46 17 17
PSENEN 0.026 0.007 -10000 0 -10000 0 0
mol:ceramide 0.003 0.092 -10000 0 -0.42 16 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.019 0.059 -10000 0 -0.38 4 4
p75(NTR)/beta APP 0.005 0.1 -10000 0 -0.51 16 16
BEX1 -0.28 0.35 -10000 0 -0.67 218 218
mol:GDP -0.018 0.088 -10000 0 -0.44 18 18
NGF (dimer) 0.036 0.11 -10000 0 -0.41 27 27
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.034 0.09 -10000 0 -0.41 16 16
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.03 0.083 -10000 0 -0.4 16 16
MYD88 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.034 0.098 -10000 0 -0.46 17 17
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.004 0.055 -10000 0 -10000 0 0
NT3 (dimer) -0.016 0.15 -10000 0 -0.67 25 25
TP53 -0.003 0.099 0.35 1 -0.36 25 26
PRDM4 0.001 0.09 -10000 0 -0.42 16 16
BDNF (dimer) -0.011 0.14 -10000 0 -0.44 34 34
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.051 0.088 -10000 0 -0.4 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.047 0.097 -10000 0 -0.43 18 18
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
MAPK10 0.015 0.11 0.34 16 -0.4 14 30
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 0.003 0.092 -10000 0 -0.42 16 16
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.035 0.095 -10000 0 -0.46 16 16
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.026 -10000 0 -0.51 1 1
NT3 (dimer)/p75(NTR) -0.026 0.15 -10000 0 -0.51 40 40
MAPK8 0.01 0.12 0.35 14 -0.41 15 29
MAPK9 0.011 0.1 0.34 10 -0.39 13 23
APAF1 0.025 0.032 -10000 0 -0.67 1 1
NTF3 -0.017 0.16 -10000 0 -0.67 25 25
NTF4 0.002 0.12 -10000 0 -0.65 15 15
NDN 0.02 0.07 -10000 0 -0.67 5 5
RAC1/GDP 0.02 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.085 -10000 0 -0.38 17 17
p75 CTF/Sortilin/TRAF6/NRIF 0.06 0.052 -10000 0 -0.52 3 3
RhoA-B-C/GTP 0.033 0.097 -10000 0 -0.46 17 17
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.11 -10000 0 -0.38 26 26
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.039 0.11 -10000 0 -0.4 27 27
PRKACB 0.025 0.032 -10000 0 -0.67 1 1
proBDNF (dimer)/p75 ECD 0.023 0.089 -10000 0 -0.51 13 13
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.071 0.14 0.48 12 -0.43 12 24
BAD 0.027 0.14 0.44 25 -0.4 15 40
RIPK2 0.027 0.005 -10000 0 -10000 0 0
NGFR -0.016 0.13 -10000 0 -0.67 16 16
CYCS 0.008 0.1 0.36 12 -0.4 16 28
ADAM17 0.024 0.045 -10000 0 -0.67 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.046 0.097 -10000 0 -0.43 18 18
BCL2L11 0.027 0.14 0.44 25 -0.4 15 40
BDNF (dimer)/p75(NTR) -0.009 0.13 -10000 0 -0.51 27 27
PI3K 0.046 0.099 -10000 0 -0.43 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.049 0.092 -10000 0 -0.43 16 16
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.002 0.11 -10000 0 -0.51 18 18
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.047 0.092 -10000 0 -0.43 16 16
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
PLG -0.014 0.02 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.005 0.099 -10000 0 -0.4 26 26
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.026 0.007 -10000 0 -10000 0 0
CASP3 0.031 0.14 0.44 26 -0.37 15 41
E2F1 -0.019 0.07 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.051 0.074 -10000 0 -0.46 3 3
NGF (dimer)/TRKA 0.027 0.05 -10000 0 -0.51 3 3
MMP7 -0.079 0.16 -10000 0 -0.66 26 26
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.096 -10000 0 -0.4 18 18
MMP3 -0.018 0.049 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.014 0.095 -10000 0 -0.58 5 5
Caspase cascade in apoptosis

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
TOP1 0.02 0.088 0.32 5 -0.42 12 17
ACTA1 0.008 0.1 0.34 6 -0.48 12 18
NUMA1 0.016 0.097 0.3 4 -0.48 13 17
SPTAN1 0.006 0.1 0.37 5 -0.49 11 16
LIMK1 0.012 0.11 0.45 8 -0.51 10 18
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
CASP10 -0.011 0.089 -10000 0 -0.54 12 12
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
PTK2 0.014 0.099 0.39 2 -0.46 14 16
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.006 0.1 0.35 6 -0.48 11 17
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN 0.006 0.1 0.37 5 -0.48 12 17
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.042 0.22 -10000 0 -0.61 62 62
BID -0.012 0.061 -10000 0 -0.32 12 12
MAP3K1 0.018 0.042 0.27 3 -10000 0 3
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.026 -10000 0 -0.51 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.11 0.45 8 -0.51 10 18
CASP9 0.027 0.006 -10000 0 -10000 0 0
DNA repair -0.017 0.063 0.42 4 -0.21 19 23
neuron apoptosis 0.009 0.11 -10000 0 -0.55 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.016 0.11 0.35 4 -0.51 13 17
APAF1 0.025 0.032 -10000 0 -0.67 1 1
CASP6 0.02 0.086 0.39 1 -0.59 4 5
TRAF2 0.025 0.009 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.11 0.4 14 -0.5 10 24
CASP7 0.007 0.097 0.31 22 -0.45 8 30
KRT18 0.021 0.04 -10000 0 -0.44 2 2
apoptosis 0.016 0.1 0.48 4 -0.46 11 15
DFFA 0.008 0.1 0.36 6 -0.49 11 17
DFFB 0.009 0.1 0.36 6 -0.49 11 17
PARP1 0.017 0.064 0.21 19 -0.43 4 23
actin filament polymerization -0.017 0.12 0.47 10 -0.54 11 21
TNF -0.056 0.22 -10000 0 -0.67 56 56
CYCS -0.001 0.048 0.24 3 -0.22 10 13
SATB1 0.02 0.085 0.52 2 -0.55 4 6
SLK 0.004 0.1 0.46 3 -0.48 13 16
p15 BID/BAX -0.011 0.07 -10000 0 -0.34 8 8
CASP2 -0.014 0.1 0.21 4 -0.37 18 22
JNK cascade -0.018 0.041 -10000 0 -0.27 3 3
CASP3 0.005 0.1 0.38 4 -0.5 12 16
LMNB2 0.006 0.11 0.36 9 -0.41 12 21
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.046 0.094 -10000 0 -0.4 20 20
negative regulation of DNA binding -0.041 0.22 -10000 0 -0.6 62 62
stress fiber formation 0.004 0.1 0.46 3 -0.47 13 16
GZMB -0.007 0.1 -10000 0 -0.61 12 12
CASP1 0.015 0.026 -10000 0 -0.39 2 2
LMNB1 0.02 0.087 0.33 11 -0.3 3 14
APP 0.009 0.11 -10000 0 -0.56 15 15
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0.001 -10000 0 -10000 0 0
CASP8 0.009 0.002 -10000 0 -10000 0 0
VIM 0.017 0.095 0.45 3 -0.46 10 13
LMNA 0.015 0.097 0.35 11 -0.4 6 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.013 0.11 -10000 0 -0.28 59 59
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.014 0.11 0.43 9 -0.53 9 18
APAF-1/Caspase 9 0.013 0.063 -10000 0 -0.55 4 4
nuclear fragmentation during apoptosis 0.016 0.096 0.29 5 -0.47 13 18
CFL2 0.017 0.12 0.54 11 -0.49 10 21
GAS2 0.002 0.1 0.36 4 -0.47 14 18
positive regulation of apoptosis 0.016 0.1 0.36 9 -0.36 9 18
PRF1 0.015 0.089 -10000 0 -0.68 8 8
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
alphaV beta3 Integrin 0.025 0.089 -10000 0 -0.52 12 12
PTK2 0.008 0.15 -10000 0 -0.55 27 27
positive regulation of JNK cascade 0.013 0.099 -10000 0 -0.33 32 32
CDC42/GDP 0.029 0.14 0.44 1 -0.44 34 35
Rac1/GDP 0.029 0.14 -10000 0 -0.45 30 30
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.022 0.12 -10000 0 -0.4 32 32
nectin-3/I-afadin 0.007 0.13 -10000 0 -0.51 30 30
RAPGEF1 0.011 0.14 0.35 2 -0.51 29 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.008 0.16 -10000 0 -0.58 30 30
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
TLN1 -0.005 0.061 -10000 0 -0.79 1 1
Rap1/GTP 0.01 0.097 -10000 0 -0.36 29 29
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.007 0.13 -10000 0 -0.51 30 30
PVR 0.026 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.015 0.17 0.47 1 -0.55 36 37
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PI3K 0.049 0.12 -10000 0 -0.42 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.037 0.02 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.008 0.11 -10000 0 -0.35 30 30
PVRL1 0.023 0.025 -10000 0 -10000 0 0
PVRL3 -0.016 0.17 -10000 0 -0.66 31 31
PVRL2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.11 0.095 -10000 0 -0.61 10 10
JAM-A/CLDN1 0.037 0.13 -10000 0 -0.42 35 35
SRC 0.004 0.17 -10000 0 -0.64 31 31
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
nectin-1(dimer)/I-afadin/I-afadin 0.037 0.02 -10000 0 -10000 0 0
FARP2 0.018 0.16 -10000 0 -0.54 35 35
RAC1 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.022 0.12 -10000 0 -0.44 30 30
nectin-1/I-afadin 0.037 0.02 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.024 0.12 -10000 0 -0.44 30 30
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.025 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.013 0.099 -10000 0 -0.33 32 32
alphaV/beta3 Integrin/Talin 0.023 0.11 -10000 0 -0.55 11 11
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
PIP5K1C -0.003 0.066 -10000 0 -0.83 1 1
VAV2 -0.002 0.19 0.37 1 -0.59 34 35
RAP1/GDP 0.033 0.13 0.28 2 -0.42 31 33
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.022 0.12 -10000 0 -0.44 30 30
nectin-3(dimer)/I-afadin/I-afadin 0.007 0.13 -10000 0 -0.51 30 30
Rac1/GTP 0.014 0.14 -10000 0 -0.44 30 30
PTPRM 0 0.073 -10000 0 -0.27 29 29
E-cadherin/beta catenin/alpha catenin 0.073 0.027 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.012 -10000 0 -10000 0 0
HDAC4 0.027 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.024 0.51 1 -10000 0 1
CDKN1A -0.006 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
FOXO3 -0.004 0.007 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
TAT 0.011 0.025 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.01 -10000 0 -10000 0 0
PPARGC1A -0.28 0.35 -10000 0 -0.67 220 220
FHL2 -0.028 0.19 -10000 0 -0.67 39 39
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.026 0.03 -10000 0 -0.51 1 1
HIST2H4A 0.013 0.024 -10000 0 -0.51 1 1
SIRT1/FOXO3a 0.039 0.053 -10000 0 -0.43 1 1
SIRT1 0.022 0.032 -10000 0 -0.68 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.046 0.028 -10000 0 -0.44 1 1
SIRT1/Histone H1b -0.006 0.07 -10000 0 -0.3 12 12
apoptosis -0.036 0.033 0.44 1 -10000 0 1
SIRT1/PGC1A -0.18 0.24 -10000 0 -0.44 220 220
p53/SIRT1 0.028 0.027 -10000 0 -0.51 1 1
SIRT1/FOXO4 -0.004 0.064 -10000 0 -0.31 4 4
FOXO1/FHL2/SIRT1 0.009 0.12 -10000 0 -0.4 40 40
HIST1H1E 0.008 0.047 -10000 0 -0.34 8 8
SIRT1/p300 0.026 0.03 -10000 0 -0.51 1 1
muscle cell differentiation -0.029 0.028 0.44 1 -10000 0 1
TP53 0.023 0.006 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.033 -10000 0 -0.44 1 1
CREBBP 0.026 0.006 -10000 0 -10000 0 0
MEF2D 0.025 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.029 -10000 0 -0.51 1 1
ACSS2 0.014 0.024 -10000 0 -0.51 1 1
SIRT1/PCAF/MYOD 0.029 0.028 -10000 0 -0.45 1 1
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.02 0.004 -9999 0 -10000 0 0
PRKCZ 0.026 0.006 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.016 0.06 -9999 0 -0.38 2 2
IRAK/TOLLIP 0.03 0.011 -9999 0 -10000 0 0
IKBKB 0.027 0.005 -9999 0 -10000 0 0
IKBKG 0.025 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.054 0.21 -9999 0 -0.53 73 73
IL1A -0.029 0.18 -9999 0 -0.67 37 37
IL1B -0.02 0.13 -9999 0 -0.51 33 33
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.037 -9999 0 -0.36 2 2
IL1R2 -0.044 0.19 -9999 0 -0.66 42 42
IL1R1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.049 -9999 0 -10000 0 0
TOLLIP 0.027 0.005 -9999 0 -10000 0 0
TICAM2 0.019 0.07 -9999 0 -0.67 5 5
MAP3K3 0.026 0.007 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.038 0.059 -9999 0 -10000 0 0
JUN -0.077 0.16 -9999 0 -0.37 111 111
MAP3K7 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.042 0.12 -9999 0 -0.38 32 32
IL1 alpha/IL1R1/IL1RAP/MYD88 0.036 0.13 -9999 0 -0.41 36 36
PIK3R1 0.027 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.12 -9999 0 -0.39 36 36
IL1 beta fragment/IL1R1/IL1RAP 0.018 0.12 -9999 0 -0.42 32 32
NFKB1 0.027 0.004 -9999 0 -10000 0 0
MAPK8 -0.003 0.086 -9999 0 -0.44 16 16
IRAK1 0.016 0.005 -9999 0 -10000 0 0
IL1RN/IL1R1 0.01 0.087 -9999 0 -0.48 11 11
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.003 -9999 0 -10000 0 0
TRAF6 0.024 0.045 -9999 0 -0.67 2 2
PI3K 0.036 0.043 -9999 0 -0.51 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.015 0.066 -9999 0 -0.38 3 3
CHUK 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.018 0.12 -9999 0 -0.42 32 32
IL1 beta/IL1R2 -0.042 0.18 -9999 0 -0.48 66 66
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.028 -9999 0 -0.36 2 2
NF kappa B1 p50/RelA 0.029 0.11 -9999 0 -0.36 32 32
IRAK3 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.04 0.12 -9999 0 -0.39 34 34
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.084 -9999 0 -0.29 36 36
IL1 alpha/IL1R1/IL1RAP 0.02 0.13 -9999 0 -0.44 36 36
RELA 0.027 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.026 0.006 -9999 0 -10000 0 0
MYD88 0.027 0.003 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.043 0.032 -9999 0 -0.38 2 2
IL1RAP -0.013 0.068 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 0.009 0.1 -9999 0 -0.38 11 11
CASP1 0.022 0.047 -9999 0 -0.67 2 2
IL1RN/IL1R2 -0.042 0.17 -9999 0 -0.54 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.032 0.12 -9999 0 -0.4 32 32
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.07 -9999 0 -0.36 2 2
PIK3CA 0.023 0.054 -9999 0 -0.67 3 3
IL1RN -0.011 0.11 -9999 0 -0.65 11 11
TRAF6/TAK1/TAB1/TAB2 0.037 0.027 -9999 0 -0.37 2 2
MAP2K6 0.01 0.06 -9999 0 -0.36 12 12
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.032 -10000 0 -0.67 1 1
Caspase 8 (4 units) 0.023 0.09 -10000 0 -0.44 5 5
NEF -0.014 0.067 -10000 0 -0.25 29 29
NFKBIA 0.021 0.032 -10000 0 -10000 0 0
BIRC3 -0.004 0.15 -10000 0 -0.65 23 23
CYCS -0.008 0.093 -10000 0 -0.37 10 10
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CD247 -0.014 0.15 -10000 0 -0.77 17 17
MAP2K7 -0.001 0.16 -10000 0 -0.61 24 24
protein ubiquitination 0.009 0.099 0.36 6 -0.35 5 11
CRADD 0.027 0.005 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.027 0.005 -10000 0 -10000 0 0
BID -0.01 0.098 0.22 1 -0.33 25 26
NF-kappa-B/RelA/I kappa B alpha 0.043 0.079 -10000 0 -0.33 18 18
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.079 -10000 0 -0.33 18 18
MAPK8 -0.005 0.16 0.35 1 -0.58 24 25
APAF1 0.025 0.032 -10000 0 -0.67 1 1
TRAF1 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.001 0.098 -10000 0 -0.32 35 35
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.37 19 19
CHUK 0.005 0.098 0.28 3 -0.38 5 8
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.076 0.029 -10000 0 -0.38 1 1
TCRz/NEF -0.022 0.15 -10000 0 -0.45 46 46
TNF -0.056 0.22 -10000 0 -0.67 56 56
FASLG -0.048 0.23 -10000 0 -0.77 41 41
NFKB1 0.021 0.033 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.003 0.16 -10000 0 -0.44 57 57
CASP6 0.039 0.096 -10000 0 -0.66 5 5
CASP7 0.01 0.15 0.39 2 -0.57 26 28
RELA 0.021 0.033 -10000 0 -10000 0 0
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.01 0.15 0.35 1 -0.56 26 27
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.51 1 1
CASP8 0.027 0.005 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
MAP3K14 0.003 0.1 -10000 0 -0.4 7 7
APAF-1/Caspase 9 -0.002 0.12 -10000 0 -0.48 22 22
BCL2 -0.027 0.16 0.34 1 -0.56 24 25
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.007 0.14 -10000 0 -0.37 62 62
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.022 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.023 -10000 0 -0.44 1 1
GNB1 0.026 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.035 0.14 -10000 0 -0.39 64 64
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 0.012 0.032 0.096 64 -10000 0 64
GNAL -0.061 0.23 -10000 0 -0.66 64 64
GNG2 0.025 0.032 -10000 0 -0.67 1 1
CRH 0 0.039 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.055 -10000 0 -0.38 10 10
MAPK11 0.006 0.004 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.006 0.14 -10000 0 -0.69 11 11
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.024 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.045 -10000 0 -0.67 2 2
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.055 -10000 0 -0.68 3 3
AP1 -0.13 0.24 -10000 0 -0.49 139 139
NCSTN 0.026 0.007 -10000 0 -10000 0 0
ADAM10 0.011 0.1 -10000 0 -0.67 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.029 0.075 -10000 0 -0.55 4 4
NICD/RBPSUH 0.006 0.13 -10000 0 -0.64 11 11
WIF1 -0.015 0.047 -10000 0 -10000 0 0
NOTCH1 -0.003 0.13 -10000 0 -0.69 10 10
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 0.016 0.037 -10000 0 -10000 0 0
DKK1 -0.001 0.07 -10000 0 -0.67 2 2
beta catenin/beta TrCP1 0.046 0.048 0.29 2 -10000 0 2
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.007 -10000 0 -10000 0 0
AXIN1 -0.006 0.082 0.38 1 -0.55 4 5
CtBP/CBP/TCF1/TLE1/AES 0.019 0.031 -10000 0 -0.29 3 3
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
JUN -0.12 0.29 -10000 0 -0.67 107 107
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.038 0.063 0.31 11 -10000 0 11
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.096 -10000 0 -0.44 19 19
HNF1A 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC -0.017 0.25 -10000 0 -1.2 19 19
NKD1 0.006 0.11 -10000 0 -0.68 13 13
FZD1 0.026 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.006 0.14 -10000 0 -0.64 13 13
apoptosis -0.13 0.24 -10000 0 -0.48 139 139
Delta 1/NOTCHprecursor 0.006 0.14 -10000 0 -0.67 11 11
DLL1 0.025 0.032 -10000 0 -0.67 1 1
PPARD 0.022 0.081 -10000 0 -0.84 4 4
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
APC 0 0.074 0.33 2 -0.55 3 5
DVL1 0.025 0.01 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.048 0.044 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.014 0.007 -10000 0 -10000 0 0
CCND1 0.01 0.13 -10000 0 -0.85 10 10
WNT1 0.018 0.022 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.045 0.095 0.42 12 -0.61 1 13
DKK2 -0.004 0.14 -10000 0 -0.66 20 20
NOTCH1 precursor/DVL1 0.013 0.12 -10000 0 -0.59 11 11
GSK3B 0.027 0.003 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.006 0.14 -10000 0 -0.66 13 13
PPP2R5D 0.027 0.062 0.33 13 -0.38 3 16
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.064 0.018 -10000 0 -10000 0 0
RBPJ 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.61 8 8
UGCG -0.059 0.22 -10000 0 -0.64 58 58
AKT1/mTOR/p70S6K/Hsp90/TERT 0.013 0.14 0.42 5 -0.41 22 27
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.059 0.22 -10000 0 -0.62 60 60
mol:DAG -0.009 0.12 -10000 0 -0.77 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.17 -10000 0 -0.43 50 50
FRAP1 -0.017 0.2 0.44 2 -0.5 51 53
FOXO3 -0.003 0.17 0.44 2 -0.61 22 24
AKT1 -0.008 0.18 -10000 0 -0.66 23 23
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 0.01 0.085 -10000 0 -0.77 5 5
SGMS1 0.002 0.11 -10000 0 -0.64 12 12
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 0.007 0.036 -10000 0 -0.45 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.03 0.19 0.33 5 -0.52 42 47
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.044 -10000 0 -0.51 3 3
RPS6KB1 0.016 0.067 -10000 0 -0.82 2 2
mol:sphingomyelin -0.009 0.12 -10000 0 -0.77 12 12
natural killer cell activation 0 0.002 -10000 0 -0.012 4 4
JAK3 -0.01 0.066 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.029 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC -0.006 0.21 0.47 4 -0.92 18 22
MYB 0.002 0.19 -10000 0 -1.2 11 11
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.005 0.15 -10000 0 -0.55 23 23
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.043 0.067 -10000 0 -0.74 2 2
mol:PI-3-4-5-P3 -0.004 0.14 -10000 0 -0.53 23 23
Rac1/GDP 0.023 0.036 -10000 0 -0.41 3 3
T cell proliferation -0.004 0.13 -10000 0 -0.52 20 20
SHC1 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.01 -10000 0 -0.066 11 11
PRKCZ -0.005 0.14 -10000 0 -0.54 20 20
NF kappa B1 p50/RelA 0.01 0.17 -10000 0 -0.5 28 28
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.11 -10000 0 -0.49 16 16
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.017 0.16 -10000 0 -0.64 28 28
IL2RB 0.005 0.09 -10000 0 -0.58 10 10
TERT -0.006 0.023 -10000 0 -10000 0 0
E2F1 0.022 0.07 -10000 0 -0.43 11 11
SOS1 0.027 0.005 -10000 0 -10000 0 0
RPS6 0.025 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 11 -10000 0 11
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
IL2RG -0.01 0.14 -10000 0 -0.63 21 21
actin cytoskeleton organization -0.004 0.13 -10000 0 -0.52 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.018 0.013 -10000 0 -10000 0 0
PIK3CA 0.025 0.055 -10000 0 -0.68 3 3
Rac1/GTP 0.048 0.042 -10000 0 -0.39 3 3
LCK 0.014 0.082 -10000 0 -0.67 6 6
BCL2 -0.042 0.27 0.47 4 -0.79 51 55
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.003 0.065 -10000 0 -0.38 2 2
NT3 (dimer)/TRKC -0.022 0.14 -10000 0 -0.5 37 37
NT3 (dimer)/TRKB 0.005 0.14 -10000 0 -0.44 44 44
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.028 -10000 0 -0.29 3 3
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.008 0.1 -10000 0 -0.67 11 11
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.01 0.031 -10000 0 -10000 0 0
NTRK2 0.019 0.065 -10000 0 -0.61 5 5
NTRK3 -0.013 0.12 -10000 0 -0.65 13 13
NT-4/5 (dimer)/TRKB 0.013 0.13 -10000 0 -0.45 34 34
neuron apoptosis -0.011 0.11 0.38 18 -10000 0 18
SHC 2-3/Grb2 0.011 0.12 -10000 0 -0.42 18 18
SHC1 0.025 0.008 -10000 0 -10000 0 0
SHC2 0.001 0.1 -10000 0 -0.55 10 10
SHC3 -0.005 0.12 -10000 0 -0.42 28 28
STAT3 (dimer) 0.03 0.015 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.003 0.14 -10000 0 -0.45 37 37
RIN/GDP -0.005 0.078 0.3 7 -0.27 3 10
GIPC1 0.025 0.008 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
DNAJA3 -0.005 0.071 -10000 0 -0.38 15 15
RIN/GTP 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.02 0.018 -10000 0 -10000 0 0
MAGED1 0.026 0.007 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.12 -10000 0 -0.65 15 15
SHC/GRB2/SOS1 0.048 0.02 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.038 0.064 -10000 0 -0.44 7 7
TRKA/NEDD4-2 0.031 0.024 -10000 0 -10000 0 0
ELMO1 -0.24 0.34 -10000 0 -0.67 190 190
RhoG/GTP/ELMO1/DOCK1 -0.15 0.24 -10000 0 -0.44 190 190
NGF 0.022 0.056 -10000 0 -0.67 3 3
HRAS 0.026 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.054 -10000 0 -0.67 3 3
GAB2 0.027 0.005 -10000 0 -10000 0 0
RIT2 -0.009 0.016 -10000 0 -10000 0 0
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
DNM1 0.005 0.12 -10000 0 -0.62 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.19 -10000 0 -0.35 189 189
mol:GDP -0.014 0.1 0.35 8 -0.4 4 12
NGF (dimer) 0.021 0.056 -10000 0 -0.67 3 3
RhoG/GDP -0.18 0.26 -10000 0 -0.51 190 190
RIT1/GDP -0.003 0.076 0.3 7 -0.27 3 10
TIAM1 -0.059 0.081 -10000 0 -0.67 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.036 0.087 -10000 0 -0.45 15 15
KIDINS220/CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.053 0.025 -10000 0 -0.44 1 1
SHC/GRB2/SOS1/GAB1 0.061 0.026 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.006 -10000 0 -10000 0 0
NT3 (dimer) -0.016 0.15 -10000 0 -0.67 25 25
RAP1/GDP -0.005 0.057 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.008 0.1 -10000 0 -0.67 11 11
ubiquitin-dependent protein catabolic process 0.045 0.043 -10000 0 -0.44 3 3
Schwann cell development -0.031 0.028 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.037 -10000 0 -0.28 1 1
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.12 -10000 0 -0.35 45 45
ABL1 0.025 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.1 -10000 0 -0.49 7 7
STAT3 0.03 0.015 -10000 0 -10000 0 0
axon guidance -0.016 0.11 -10000 0 -0.34 46 46
MAPK3 0.018 0.069 -10000 0 -0.4 7 7
MAPK1 0.01 0.063 -10000 0 -0.4 7 7
CDC42/GDP -0.001 0.078 0.3 7 -0.27 3 10
NTF3 -0.017 0.16 -10000 0 -0.67 25 25
NTF4 0.002 0.12 -10000 0 -0.65 15 15
NGF (dimer)/TRKA/FAIM 0.046 0.043 -10000 0 -0.44 3 3
PI3K 0.036 0.043 -10000 0 -0.51 3 3
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.027 0.003 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.043 0.083 -10000 0 -0.4 19 19
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.028 0.12 -10000 0 -0.44 36 36
RGS19 0.026 0.009 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.07 -10000 0 -0.59 1 1
Rac1/GDP -0.005 0.067 0.22 1 -0.26 2 3
NGF (dimer)/TRKA/GRIT 0.025 0.043 -10000 0 -0.44 3 3
neuron projection morphogenesis 0.024 0.088 -10000 0 -0.7 2 2
NGF (dimer)/TRKA/NEDD4-2 0.045 0.043 -10000 0 -0.44 3 3
MAP2K1 0.04 0.058 0.36 4 -10000 0 4
NGFR -0.016 0.13 -10000 0 -0.67 16 16
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.07 -10000 0 -0.34 15 15
RAS family/GTP/PI3K 0.027 0.027 -10000 0 -0.3 3 3
FRS2 family/SHP2/GRB2/SOS1 0.074 0.032 -10000 0 -0.38 1 1
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade 0.021 0.074 -10000 0 -0.54 6 6
RASA1 0.027 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.03 0.025 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.047 0.083 -10000 0 -0.41 14 14
NGF (dimer)/TRKA/p62/Atypical PKCs 0.068 0.046 -10000 0 -0.38 3 3
MATK 0.015 0.069 -10000 0 -0.61 5 5
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.003 0.077 -10000 0 -0.39 16 16
Rac1/GTP -0.11 0.12 -10000 0 -0.32 46 46
FRS2 family/SHP2/CRK family 0.057 0.043 -10000 0 -0.38 1 1
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 0.014 0.091 -10000 0 -0.61 10 10
ANTXR2 0.023 0.054 -10000 0 -0.67 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.082 13 13
monocyte activation -0.035 0.16 -10000 0 -0.44 62 62
MAP2K2 -0.008 0.11 -10000 0 -0.54 22 22
MAP2K1 -0.001 0.012 -10000 0 -10000 0 0
MAP2K7 -0.001 0.012 -10000 0 -10000 0 0
MAP2K6 -0.009 0.056 0.11 1 -0.39 10 11
CYAA -0.007 0.057 -10000 0 -0.38 11 11
MAP2K4 -0.001 0.012 -10000 0 -10000 0 0
IL1B -0.021 0.094 0.18 1 -0.35 34 35
Channel 0.024 0.066 -10000 0 -0.37 13 13
NLRP1 -0.002 0.027 0.11 1 -0.38 2 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.011 0.028 -10000 0 -0.51 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.082 13 -10000 0 13
MAPK3 -0.001 0.012 -10000 0 -10000 0 0
MAPK1 -0.001 0.012 -10000 0 -10000 0 0
PGR -0.012 0.055 -10000 0 -0.32 13 13
PA/Cellular Receptors 0.025 0.072 -10000 0 -0.4 13 13
apoptosis -0.002 0.013 -10000 0 -0.082 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.024 0.062 -10000 0 -0.35 13 13
macrophage activation -0.001 0.011 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.67 56 56
VCAM1 -0.036 0.16 -10000 0 -0.44 62 62
platelet activation 0.011 0.028 -10000 0 -0.51 1 1
MAPKKK cascade -0.003 0.029 0.17 2 -0.13 8 10
IL18 -0.009 0.06 -10000 0 -0.33 13 13
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.082 13 13
LEF -0.002 0.013 -10000 0 -0.082 13 13
CASP1 0.001 0.018 -10000 0 -0.097 14 14
mol:cAMP 0.011 0.029 -10000 0 -0.52 1 1
necrosis -0.002 0.013 -10000 0 -0.082 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.024 0.063 -10000 0 -0.35 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.026 0.12 -9999 0 -0.34 36 36
Syndecan-3/Neurocan 0.004 0.095 -9999 0 -0.36 28 28
POMC -0.11 0.28 -9999 0 -0.66 101 101
EGFR 0.019 0.07 -9999 0 -0.67 5 5
Syndecan-3/EGFR 0.027 0.044 -9999 0 -0.33 6 6
AGRP 0.003 0.035 -9999 0 -10000 0 0
NCSTN 0.025 0.007 -9999 0 -10000 0 0
PSENEN 0.026 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.026 0.17 -9999 0 -0.66 34 34
long-term memory 0.051 0.029 -9999 0 -10000 0 0
Syndecan-3/IL8 0.029 0.066 -9999 0 -0.36 11 11
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.039 0.01 -9999 0 -10000 0 0
FYN 0.027 0.004 -9999 0 -10000 0 0
limb bud formation 0.015 0.006 -9999 0 -10000 0 0
MC4R 0 0.028 -9999 0 -10000 0 0
SRC 0.026 0.008 -9999 0 -10000 0 0
PTN -0.038 0.2 -9999 0 -0.67 45 45
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.023 0.13 -9999 0 -0.45 3 3
Syndecan-3/AgRP 0.031 0.023 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.045 0.03 -9999 0 -10000 0 0
Fyn/Cortactin 0.039 0.008 -9999 0 -10000 0 0
SDC3 0.015 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.029 0.065 -9999 0 -0.36 11 11
IL8 -0.026 0.12 -9999 0 -0.67 11 11
Syndecan-3/Fyn/Cortactin 0.052 0.03 -9999 0 -10000 0 0
Syndecan-3/CASK 0.011 0.023 -9999 0 -0.3 1 1
alpha-MSH/MC4R -0.077 0.22 -9999 0 -0.5 100 100
Gamma Secretase 0.07 0.03 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.009 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.026 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.02 0.049 -10000 0 -0.44 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.001 0.023 -10000 0 -10000 0 0
GRK1 -0.038 0.2 -10000 0 -0.65 46 46
CNG Channel 0.036 0.061 -10000 0 -0.38 8 8
mol:Na + 0.028 0.072 -10000 0 -0.39 10 10
mol:ADP -0.038 0.2 -10000 0 -0.65 46 46
RGS9-1/Gbeta5/R9AP -0.022 0.18 -10000 0 -0.45 71 71
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.041 0.075 -10000 0 -0.4 10 10
CNGB1 0.016 0.034 -10000 0 -10000 0 0
RDH5 -0.073 0.074 -10000 0 -10000 0 0
SAG -0.009 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.1 0.5 11 -0.38 9 20
Na + (4 Units) 0.021 0.067 -10000 0 -0.37 10 10
RGS9 -0.039 0.2 -10000 0 -0.67 45 45
GNB1/GNGT1 0.029 0.014 -10000 0 -10000 0 0
GNAT1/GDP -0.01 0.16 -10000 0 -0.39 70 70
GUCY2D 0.013 0.077 -10000 0 -0.62 6 6
GNGT1 -0.015 0.014 -10000 0 -10000 0 0
GUCY2F -0.013 0.01 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.014 0.044 -10000 0 -0.38 3 3
mol:11-cis-retinal -0.072 0.073 -10000 0 -10000 0 0
mol:cGMP 0.032 0.057 -10000 0 -0.4 6 6
GNB1 0.026 0.006 -10000 0 -10000 0 0
Rhodopsin -0.043 0.057 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.017 0.078 -10000 0 -0.67 6 6
Metarhodopsin II -0.009 0.12 -10000 0 -0.4 44 44
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.045 0.065 -10000 0 -0.41 8 8
RGS9BP -0.015 0.16 -10000 0 -0.66 29 29
Metarhodopsin II/Transducin 0.013 0.007 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.038 0.038 -10000 0 -0.41 3 3
PDE6A/B 0.031 0.028 -10000 0 -10000 0 0
mol:Pi -0.022 0.18 -10000 0 -0.45 71 71
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.037 0.016 -10000 0 -10000 0 0
PDE6B 0.027 0.004 -10000 0 -10000 0 0
PDE6A 0.012 0.037 -10000 0 -10000 0 0
PDE6G 0.01 0.072 -10000 0 -0.67 4 4
RHO 0.006 0.023 -10000 0 -10000 0 0
PDE6 0.004 0.17 -10000 0 -0.39 71 71
GUCA1A 0.005 0.025 -10000 0 -10000 0 0
GC2/GCAP Family 0.046 0.037 -10000 0 -0.42 2 2
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.023 0.055 -10000 0 -0.67 3 3
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.002 0.086 -10000 0 -0.41 1 1
epithelial cell differentiation -0.004 0.098 -10000 0 -0.41 7 7
ITCH 0.037 0.019 -10000 0 -10000 0 0
WWP1 -0.009 0.07 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
PRL -0.012 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.018 0.11 0.34 3 -0.48 5 8
PTPRZ1 0.002 0.1 -10000 0 -0.67 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.002 0.13 -10000 0 -0.51 6 6
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.037 0.13 -10000 0 -0.42 42 42
ADAM17 0.033 0.049 -10000 0 -0.67 2 2
ErbB4/ErbB4 -0.015 0.088 -10000 0 -0.46 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.14 -10000 0 -0.45 33 33
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.025 0.13 -10000 0 -0.4 41 41
GRIN2B -0.034 0.12 -10000 0 -0.51 8 8
ErbB4/ErbB2/betacellulin 0 0.11 -10000 0 -0.5 14 14
STAT1 0.023 0.023 -10000 0 -10000 0 0
HBEGF 0.018 0.035 -10000 0 -10000 0 0
PRLR -0.015 0.15 -10000 0 -0.67 25 25
E4ICDs/ETO2 -0.002 0.086 -10000 0 -0.48 2 2
axon guidance -0.006 0.071 -10000 0 -0.47 1 1
NEDD4 0.034 0.048 -10000 0 -0.66 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.001 0.12 -10000 0 -0.51 25 25
CBFA2T3 0.024 0.034 -10000 0 -0.67 1 1
ErbB4/ErbB2/HBEGF 0.01 0.073 -10000 0 -0.45 2 2
MAPK3 -0.013 0.12 -10000 0 -0.48 6 6
STAT1 (dimer) -0.001 0.086 -10000 0 -0.41 1 1
MAPK1 -0.016 0.11 -10000 0 -0.5 5 5
JAK2 0.024 0.025 -10000 0 -0.36 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.03 0.12 -10000 0 -0.4 38 38
NRG1 -0.025 0.15 -10000 0 -0.52 43 43
NRG3 -0.021 0.17 -10000 0 -0.65 35 35
NRG2 -0.052 0.22 -10000 0 -0.67 54 54
NRG4 0.021 0.021 -10000 0 -10000 0 0
heart development -0.006 0.071 -10000 0 -0.47 1 1
neural crest cell migration -0.03 0.12 -10000 0 -0.39 38 38
ERBB2 0.019 0.035 -10000 0 -0.5 2 2
WWOX/E4ICDs -0.003 0.089 -10000 0 -0.78 1 1
SHC1 0.025 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.008 0.097 -10000 0 -0.49 5 5
apoptosis 0.022 0.13 0.41 32 -10000 0 32
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.049 0.16 -10000 0 -0.44 56 56
ErbB4/ErbB2/epiregulin 0.01 0.085 -10000 0 -0.42 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.015 0.12 -10000 0 -0.52 16 16
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.12 -10000 0 -0.37 24 24
MDM2 -0.013 0.078 -10000 0 -0.41 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.021 0.13 -10000 0 -0.4 41 41
STAT5A -0.001 0.072 -10000 0 -0.45 1 1
ErbB4/EGFR/neuregulin 1 beta -0.027 0.14 -10000 0 -0.41 44 44
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.002 0.076 -10000 0 -0.38 1 1
STAT5A (dimer) 0.005 0.11 -10000 0 -0.45 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.073 -10000 0 -0.45 1 1
LRIG1 0.017 0.084 -10000 0 -0.64 8 8
EREG -0.052 0.072 -10000 0 -10000 0 0
BTC 0.004 0.12 -10000 0 -0.67 16 16
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.006 0.07 -10000 0 -0.48 1 1
ERBB4 -0.015 0.088 -10000 0 -0.46 1 1
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 0.005 0.066 -10000 0 -0.47 8 8
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.01 0.072 -10000 0 -0.43 2 2
glial cell differentiation 0.002 0.076 0.38 1 -10000 0 1
WWOX 0.025 0.032 -10000 0 -0.67 1 1
cell proliferation -0.024 0.14 -10000 0 -0.59 8 8
Sphingosine 1-phosphate (S1P) pathway

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.025 0.007 -9999 0 -10000 0 0
SPHK1 0.022 0.024 -9999 0 -10000 0 0
GNAI2 0.027 0.003 -9999 0 -10000 0 0
mol:S1P 0.017 0.008 -9999 0 -10000 0 0
GNAO1 0.004 0.12 -9999 0 -0.67 15 15
mol:Sphinganine-1-P 0.014 0.015 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.056 0.028 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
S1PR3 0.025 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.018 -9999 0 -0.2 2 2
S1PR5 0.023 0.034 -9999 0 -0.67 1 1
S1PR4 0.023 0.02 -9999 0 -10000 0 0
GNAI1 0.025 0.032 -9999 0 -0.67 1 1
S1P/S1P5/G12 0.043 0.031 -9999 0 -0.38 1 1
S1P/S1P3/Gq -0.056 0.16 -9999 0 -0.3 134 134
S1P/S1P4/Gi 0.003 0.079 -9999 0 -0.32 17 17
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.14 0.29 -9999 0 -0.64 120 120
GNA15 0.013 0.05 -9999 0 -0.67 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.015 0.084 -9999 0 -0.64 8 8
ABCC1 0.026 0.006 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.038 0.06 -10000 0 -0.4 6 6
EPHB2 0.022 0.055 -10000 0 -0.67 3 3
Syndecan-2/TACI -0.089 0.2 -10000 0 -0.44 121 121
LAMA1 -0.021 0.18 -10000 0 -0.66 34 34
Syndecan-2/alpha2 ITGB1 0.042 0.092 -10000 0 -0.38 19 19
HRAS 0.026 0.011 -10000 0 -10000 0 0
Syndecan-2/CASK 0.007 0.043 -10000 0 -0.33 7 7
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.003 0.065 -10000 0 -0.46 1 1
EPB41 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.041 -10000 0 -0.39 4 4
LAMA3 -0.001 0.13 -10000 0 -0.67 16 16
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.045 -10000 0 -0.67 2 2
Syndecan-2/MMP2 0.021 0.071 -10000 0 -0.48 9 9
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.008 0.059 -10000 0 -10000 0 0
dendrite morphogenesis 0.023 0.057 -10000 0 -0.43 7 7
Syndecan-2/GM-CSF -0.035 0.057 -10000 0 -0.45 4 4
determination of left/right symmetry 0.01 0.05 -10000 0 -0.39 7 7
Syndecan-2/PKC delta 0.026 0.045 -10000 0 -0.43 4 4
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.032 0.049 -10000 0 -0.41 4 4
MAPK1 -0.026 0.048 -10000 0 -0.41 4 4
Syndecan-2/RACK1 0.038 0.041 -10000 0 -0.38 4 4
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.05 -10000 0 -0.39 7 7
ITGA2 -0.034 0.075 -10000 0 -10000 0 0
MAPK8 0.004 0.074 -10000 0 -0.42 14 14
Syndecan-2/alpha2/beta1 Integrin 0.032 0.12 -10000 0 -0.42 32 32
Syndecan-2/Kininogen 0.016 0.05 -10000 0 -0.44 4 4
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.022 0.045 0.35 1 -0.36 4 5
Syndecan-2/CASK/Protein 4.1 0.023 0.041 -10000 0 -0.4 4 4
extracellular matrix organization 0.024 0.044 -10000 0 -0.43 4 4
actin cytoskeleton reorganization -0.038 0.059 -10000 0 -0.4 6 6
Syndecan-2/Caveolin-2/Ras 0.039 0.05 -10000 0 -0.39 6 6
Syndecan-2/Laminin alpha3 0.009 0.094 -10000 0 -0.43 20 20
Syndecan-2/RasGAP 0.05 0.042 -10000 0 -0.36 4 4
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.003 -10000 0 -10000 0 0
Syndecan-2 dimer 0.023 0.058 -10000 0 -0.43 7 7
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.042 -10000 0 -0.35 4 4
RHOA 0.027 0.003 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
TNFRSF13B -0.16 0.29 -10000 0 -0.67 121 121
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.008 0.059 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.044 -10000 0 -0.43 4 4
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CASP3 0.018 0.044 -10000 0 -0.4 4 4
FN1 -0.085 0.069 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.005 0.087 -10000 0 -0.4 18 18
SDC2 0.01 0.05 -10000 0 -0.39 7 7
KNG1 -0.005 0.038 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.043 -10000 0 -0.43 4 4
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 -0.082 0.067 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.024 0.044 -10000 0 -0.43 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.041 -10000 0 -0.4 4 4
Syndecan-2/Ezrin 0.042 0.043 -10000 0 -0.4 4 4
PRKACA 0.017 0.041 -10000 0 -0.4 4 4
angiogenesis -0.005 0.087 -10000 0 -0.39 18 18
MMP2 0.017 0.079 -10000 0 -0.63 7 7
IL8 -0.026 0.12 -10000 0 -0.67 11 11
calcineurin-NFAT signaling pathway -0.089 0.2 -10000 0 -0.44 121 121
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.03 0.071 -10000 0 -0.57 6 6
PDGFRB 0.025 0.032 -10000 0 -0.68 1 1
SPHK1 0.01 0.059 -10000 0 -0.86 2 2
mol:S1P 0.008 0.057 -10000 0 -0.79 2 2
S1P1/S1P/Gi -0.007 0.12 -10000 0 -0.4 39 39
GNAO1 0.002 0.12 -10000 0 -0.68 15 15
PDGFB-D/PDGFRB/PLCgamma1 -0.005 0.12 -10000 0 -0.38 30 30
PLCG1 -0.007 0.12 -10000 0 -0.39 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.68 1 1
GNAI2 0.025 0.012 -10000 0 -10000 0 0
GNAI3 0.025 0.013 -10000 0 -10000 0 0
GNAI1 0.023 0.033 -10000 0 -0.68 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.058 -10000 0 -0.5 6 6
S1P1/S1P 0.004 0.07 -10000 0 -0.45 7 7
negative regulation of cAMP metabolic process -0.006 0.12 -10000 0 -0.39 39 39
MAPK3 -0.019 0.16 -10000 0 -0.58 33 33
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.021 0.063 -10000 0 -0.68 4 4
PLCB2 0.014 0.077 0.4 5 -0.4 7 12
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.01 0.06 -10000 0 -0.38 7 7
receptor internalization 0.004 0.065 -10000 0 -0.42 7 7
PTGS2 -0.054 0.29 0.64 3 -0.98 41 44
Rac1/GTP 0.011 0.059 -10000 0 -0.38 7 7
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFA 0.023 0.055 -10000 0 -0.67 3 3
negative regulation of T cell proliferation -0.006 0.12 -10000 0 -0.39 39 39
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.015 -10000 0 -10000 0 0
MAPK1 -0.02 0.17 -10000 0 -0.6 34 34
S1P1/S1P/PDGFB-D/PDGFRB 0.012 0.08 -10000 0 -0.44 8 8
ABCC1 0.026 0.006 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.18 0.32 -10000 0 -0.67 150 150
HRAS 0.026 0.011 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
AKT 0.015 0.084 0.32 10 -10000 0 10
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.025 0.008 -10000 0 -10000 0 0
FOXO4 0.026 0.007 -10000 0 -10000 0 0
MET -0.029 0.074 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.005 0.12 -10000 0 -0.67 14 14
PIK3R3 0.027 0.005 -10000 0 -10000 0 0
PIK3R2 0.025 0.008 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.031 0.087 -10000 0 -0.2 41 41
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.038 0.06 0.32 7 -0.2 1 8
PI3K -0.016 0.099 0.39 8 -0.25 13 21
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
FOXO 0.045 0.059 0.31 8 -10000 0 8
AKT2 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.029 0.009 -10000 0 -10000 0 0
epithelial cell differentiation 0.055 0.016 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
ENAH 0.022 0.078 0.46 11 -10000 0 11
EGFR 0.019 0.07 -10000 0 -0.67 5 5
EPHA2 0.026 0.013 -10000 0 -10000 0 0
MYO6 0.031 0.065 0.42 11 -10000 0 11
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.013 -10000 0 -10000 0 0
AQP5 0.001 0.11 -10000 0 -0.53 19 19
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.046 0.38 7 -10000 0 7
regulation of calcium-dependent cell-cell adhesion -0.011 0.054 0.39 5 -10000 0 5
EGF -0.076 0.25 -10000 0 -0.67 72 72
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.041 0.17 -10000 0 -0.53 49 49
cortical microtubule organization 0.055 0.016 -10000 0 -10000 0 0
GO:0000145 0.012 0.046 0.37 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.061 0.017 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.013 0.031 -10000 0 -10000 0 0
PVRL2 0.026 0.007 -10000 0 -10000 0 0
ZYX 0.021 0.021 -10000 0 -10000 0 0
ARF6/GTP 0.067 0.028 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.011 0.14 -10000 0 -0.36 74 74
RhoA/GDP 0.057 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization 0.021 0.05 0.38 8 -10000 0 8
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.027 0.004 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.67 108 108
DIAPH1 0.05 0.05 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.055 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.004 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL 0.021 0.051 0.39 8 -10000 0 8
EFNA1 0.025 0.008 -10000 0 -10000 0 0
LPP 0.011 0.06 0.35 4 -0.36 8 12
Ephrin A1/EPHA2 0.047 0.019 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 -0.011 0.055 0.4 5 -10000 0 5
HGF/MET -0.006 0.14 -10000 0 -0.38 64 64
HGF -0.073 0.24 -10000 0 -0.67 70 70
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.029 0.009 -10000 0 -10000 0 0
actin cable formation 0.068 0.13 0.48 31 -0.33 1 32
KIAA1543 0.013 0.052 0.37 8 -0.35 1 9
KIFC3 0.021 0.023 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ACTN1 0.024 0.038 0.36 4 -10000 0 4
NCK1/GIT1 0.038 0.01 -10000 0 -10000 0 0
mol:GDP 0.055 0.016 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.021 0.023 -10000 0 -10000 0 0
PIP5K1C 0.024 0.047 0.38 7 -10000 0 7
LIMA1 0.027 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.045 0.1 0.44 22 -10000 0 22
adherens junction assembly 0.027 0.085 0.46 12 -0.56 1 13
IGF-1R heterotetramer/IGF1 -0.036 0.16 -10000 0 -0.36 102 102
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
MET -0.029 0.074 -10000 0 -10000 0 0
PLEKHA7 0.026 0.052 0.38 8 -0.37 1 9
mol:GTP 0.059 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.033 0.067 0.48 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.029 0.009 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.021 0.05 0.38 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.029 0.009 -10000 0 -10000 0 0
BARD1 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
BARD1/CSTF1 0.012 0.12 -10000 0 -0.47 27 27
ATM 0.025 0.032 -10000 0 -0.67 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.027 0.005 -10000 0 -10000 0 0
ATR 0.026 0.032 -10000 0 -0.67 1 1
UBE2L3 0.02 0.012 -10000 0 -10000 0 0
FANCD2 0.023 0.026 -10000 0 -0.38 2 2
protein ubiquitination 0.044 0.096 -10000 0 -0.38 21 21
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.051 0.034 -10000 0 -0.44 2 2
MRE11A 0.024 0.045 -10000 0 -0.67 2 2
DNA-PK 0.04 0.026 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.008 0.12 -10000 0 -0.49 23 23
FANCF 0.027 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
CCNE1 0.025 0.007 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.037 0.012 -10000 0 -10000 0 0
FANCG 0.025 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.011 0.12 -10000 0 -0.46 27 27
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.025 0.008 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
FANCA 0.02 0.031 -10000 0 -10000 0 0
DNA repair 0.018 0.09 0.41 2 -0.49 4 6
BRCA1/BARD1/ubiquitin 0.011 0.12 -10000 0 -0.46 27 27
BARD1/DNA-PK 0.028 0.1 -10000 0 -0.4 23 23
FANCL 0.027 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.011 0.12 0.47 27 -10000 0 27
BRCA1/BARD1/CTIP/M/R/N Complex 0.014 0.075 -10000 0 -0.48 1 1
BRCA1/BACH1/BARD1/TopBP1 0.028 0.1 -10000 0 -0.42 24 24
BRCA1/BARD1/P53 0.042 0.1 -10000 0 -0.4 22 22
BARD1/CSTF1/BRCA1 0.028 0.1 -10000 0 -0.44 21 21
BRCA1/BACH1 0.026 0.007 -10000 0 -10000 0 0
BARD1 -0.011 0.15 -10000 0 -0.63 28 28
PCNA 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.028 0.1 -10000 0 -0.44 21 21
BRCA1/BARD1/UbcH7 0.017 0.1 -10000 0 -0.43 22 22
BRCA1/BARD1/RAD51/PCNA 0.043 0.1 -10000 0 -0.41 21 21
BARD1/DNA-PK/P53 0.037 0.098 -10000 0 -0.38 21 21
BRCA1/BARD1/Ubiquitin 0.011 0.12 -10000 0 -0.46 27 27
BRCA1/BARD1/CTIP 0.023 0.096 -10000 0 -0.4 22 22
FA complex 0.028 0.033 -10000 0 -10000 0 0
BARD1/EWS 0.002 0.12 -10000 0 -0.48 26 26
RBBP8 0.016 0.024 -10000 0 -0.51 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
TOPBP1 0.027 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.04 0.099 0.4 22 -10000 0 22
BRCA1/BARD1 0.05 0.099 -10000 0 -0.38 21 21
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.008 0.12 -10000 0 -0.47 28 28
CDK2 0.027 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.011 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.011 0.12 -10000 0 -0.46 27 27
EWSR1 0.02 0.012 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.025 0.043 -10000 0 -10000 0 0
TP53 -0.009 0.039 -10000 0 -0.18 22 22
Senescence -0.009 0.038 -10000 0 -0.18 22 22
Apoptosis -0.009 0.038 -10000 0 -0.18 22 22
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.011 0.025 0.35 1 -10000 0 1
MDM4 0.025 0.008 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.037 0.094 0.46 9 -0.38 9 18
NFATC2 -0.022 0.097 0.28 9 -0.27 31 40
NFATC3 0.018 0.011 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.007 0.086 0.28 1 -0.4 10 11
Exportin 1/Ran/NUP214 0.047 0.018 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.004 0.098 -10000 0 -0.44 9 9
BCL2/BAX -0.003 0.14 -10000 0 -0.48 38 38
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.02 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
MAPK14 0.025 0.005 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.006 0.091 0.4 2 -0.39 10 12
Calcineurin A alpha-beta B1/BCL2 -0.026 0.18 -10000 0 -0.66 38 38
FKBP8 0.025 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.006 0.09 0.38 10 -0.39 2 12
KPNB1 0.026 0.007 -10000 0 -10000 0 0
KPNA2 0.026 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.67 15 15
MAP3K8 0.016 0.079 -10000 0 -0.63 7 7
NFAT4/CK1 alpha 0.019 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.073 0.17 -10000 0 -0.34 109 109
CABIN1 -0.007 0.084 0.28 1 -0.4 9 10
CALM1 0.023 0.009 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.027 0.005 -10000 0 -10000 0 0
CAMK4 0.013 0.085 -10000 0 -0.67 7 7
mol:Ca2+ -0.004 0.009 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.011 0.095 -10000 0 -0.64 10 10
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.022 0.086 0.37 2 -0.47 3 5
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.013 0.031 -10000 0 -10000 0 0
CASP3 0.025 0.005 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.012 -10000 0 -10000 0 0
apoptosis 0.009 0.044 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.054 -10000 0 -0.32 5 5
PRKCB 0.007 0.08 -10000 0 -0.67 5 5
PRKCE 0.02 0.07 -10000 0 -0.67 5 5
JNK2/NFAT4 0.031 0.026 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.003 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.007 -10000 0 -10000 0 0
PRKCA 0.002 0.13 -10000 0 -0.67 17 17
PRKCG 0.005 0.023 -10000 0 -10000 0 0
PRKCQ 0.019 0.072 -10000 0 -0.62 6 6
FKBP38/BCL2 -0.003 0.14 -10000 0 -0.48 38 38
EP300 0.01 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.039 0.1 0.41 7 -0.38 11 18
CaM/Ca2+/FKBP38 0.019 0.025 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.013 0.062 -10000 0 -0.45 7 7
NFATc/ERK1 0.044 0.08 0.44 3 -0.41 4 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.008 0.1 -10000 0 -0.45 9 9
NR4A1 -0.17 0.29 -10000 0 -0.61 148 148
GSK3B 0.024 0.007 -10000 0 -10000 0 0
positive T cell selection 0.018 0.011 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.023 0.072 -10000 0 -0.31 10 10
RCH1/ KPNB1 0.038 0.01 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.023 0.008 -10000 0 -10000 0 0
AKAP5 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.014 0.021 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.05 0.093 0.43 10 -0.41 4 14
CREBBP 0.013 0.022 -10000 0 -10000 0 0
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
Retinoic acid receptors-mediated signaling

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.009 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.026 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.07 -10000 0 -0.31 10 10
KAT2B 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.014 0.083 0.25 14 -0.36 14 28
RAR alpha/9cRA/Cyclin H 0.035 0.097 -10000 0 -0.38 18 18
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.066 0.25 1 -0.35 8 9
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.011 0.097 -10000 0 -0.57 10 10
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.003 0.13 -10000 0 -0.55 21 21
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
NCOA3 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.009 -10000 0 -10000 0 0
RARG 0.027 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.011 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.014 0.095 -10000 0 -0.64 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.12 -10000 0 -0.54 18 18
RARA 0.005 0.075 -10000 0 -0.31 24 24
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.015 0.13 -10000 0 -0.48 25 25
PRKCA 0.004 0.13 -10000 0 -0.67 17 17
RXRs/RARs/NRIP1/9cRA/HDAC1 0.011 0.14 0.4 4 -0.54 23 27
RXRG -0.028 0.079 -10000 0 -0.4 21 21
RXRA 0.007 0.075 -10000 0 -0.31 21 21
RXRB 0.009 0.074 -10000 0 -0.38 17 17
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RBP1 0.013 0.094 -10000 0 -0.67 9 9
CRBP1/9-cic-RA 0.01 0.071 -10000 0 -0.51 9 9
RARB 0.009 0.12 -10000 0 -0.67 14 14
PRKCG 0.022 0.014 -10000 0 -10000 0 0
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.006 0.13 -10000 0 -0.58 21 21
RXRs/RARs/SMRT(N-CoR2)/9cRA 0 0.12 -10000 0 -0.49 21 21
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.09 0.36 3 -0.42 11 14
RXRs/RARs/NRIP1/9cRA/HDAC3 0.012 0.14 0.42 5 -0.54 22 27
positive regulation of DNA binding 0.023 0.088 -10000 0 -0.36 19 19
NRIP1 0.012 0.13 0.5 1 -0.72 5 6
RXRs/RARs 0.005 0.13 -10000 0 -0.54 23 23
RXRs/RXRs/DNA/9cRA -0.011 0.12 -10000 0 -0.55 19 19
PRKACA 0.025 0.008 -10000 0 -10000 0 0
CDK7 0.027 0.005 -10000 0 -10000 0 0
TFIIH 0.054 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.047 0.068 -10000 0 -0.42 3 3
CCNH 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.05 0.018 -10000 0 -10000 0 0
Class I PI3K signaling events

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.026 0.046 0.29 10 -0.35 1 11
DAPP1 -0.037 0.13 0.33 4 -0.47 12 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.052 0.17 0.29 7 -0.48 27 34
mol:DAG -0.016 0.095 0.35 11 -0.25 14 25
HRAS 0.027 0.012 -10000 0 -10000 0 0
RAP1A 0.028 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.035 0.064 0.35 1 -0.35 4 5
PLCG2 0.026 0.006 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARF5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.048 0.3 10 -10000 0 10
ARF1/GTP 0.004 0.017 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
ADAP1 0 0.045 0.29 10 -10000 0 10
ARAP3 0 0.047 0.3 10 -10000 0 10
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PREX1 0.027 0.005 -10000 0 -10000 0 0
ARHGEF6 0.025 0.019 -10000 0 -0.36 1 1
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
ARF1 0.025 0.008 -10000 0 -10000 0 0
NRAS 0.028 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.065 0.3 10 -10000 0 10
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.059 0.081 -10000 0 -0.67 1 1
ZAP70 0 0.13 -10000 0 -0.66 17 17
mol:IP3 -0.013 0.069 0.24 12 -0.21 4 16
LYN 0.027 0.005 -10000 0 -10000 0 0
ARF1/GDP 0.034 0.073 0.32 6 -0.35 6 12
RhoA/GDP 0.039 0.044 0.35 2 -10000 0 2
PDK1/Src/Hsp90 0.05 0.034 -10000 0 -0.44 2 2
BLNK 0.027 0.004 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.076 0.4 10 -10000 0 10
SRC 0.026 0.008 -10000 0 -10000 0 0
PLEKHA2 0.005 0.016 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.021 -10000 0 -0.34 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.039 0.29 9 -10000 0 9
RhoA/GTP 0.025 0.042 0.3 9 -10000 0 9
Src family/SYK family/BLNK-LAT -0.045 0.14 -10000 0 -0.44 24 24
BLK -0.19 0.31 -10000 0 -0.67 148 148
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
CYTH1 0.002 0.054 0.31 12 -10000 0 12
HCK 0.017 0.039 -10000 0 -10000 0 0
CYTH3 -0.002 0.049 0.29 10 -0.36 1 11
CYTH2 0.003 0.057 0.31 14 -10000 0 14
KRAS 0.028 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.017 0.089 -10000 0 -0.54 10 10
SGK1 0.018 0.098 -10000 0 -0.59 10 10
INPP5D 0.019 0.034 -10000 0 -10000 0 0
mol:GDP 0.026 0.08 0.3 12 -0.33 8 20
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.03 0.051 0.29 8 -10000 0 8
mol:PI-3-4-5-P3 -0.007 0.015 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
VAV1 0.011 0.061 -10000 0 -0.57 3 3
mol:PI-3-4-P2 0.012 0.021 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.029 0.33 1 -10000 0 1
PLEKHA1 0.005 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.034 0.065 0.35 1 -0.34 5 6
LAT 0.021 0.058 -10000 0 -0.6 4 4
Rac1/GTP 0.017 0.059 0.27 1 -0.48 3 4
ITK -0.039 0.12 0.28 9 -0.36 48 57
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.38 9 -0.36 15 24
LCK 0.012 0.082 -10000 0 -0.67 6 6
BTK -0.005 0.067 0.3 13 -0.36 6 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.002 0.099 0.49 5 -10000 0 5
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.19 0.37 -10000 0 -0.72 149 149
IFNAR2 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.008 0.053 -10000 0 -0.24 20 20
ER alpha/Oestrogen -0.009 0.11 -10000 0 -0.48 23 23
NFX1/SIN3/HDAC complex 0.032 0.036 -10000 0 -0.49 1 1
EGF -0.075 0.24 -10000 0 -0.67 72 72
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.026 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.003 0.081 0.47 1 -10000 0 1
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.051 0.034 -10000 0 -0.44 2 2
WT1 0.007 0.048 -10000 0 -10000 0 0
WRN 0.025 0.032 -10000 0 -0.67 1 1
SP1 0.028 0.006 -10000 0 -10000 0 0
SP3 0.027 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.012 0.081 -10000 0 -10000 0 0
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
TERT -0.002 0.1 0.5 5 -10000 0 5
CCND1 0.001 0.1 0.53 6 -10000 0 6
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.007 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.67 2 2
TERF2 0.024 0.009 -10000 0 -10000 0 0
PTGES3 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
Telomerase/911 0.027 0.057 -10000 0 -10000 0 0
CDKN1B -0.029 0.15 -10000 0 -0.42 57 57
RAD1 0.026 0.006 -10000 0 -10000 0 0
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
SAP30 0.026 0.032 -10000 0 -0.67 1 1
TRF2/PARP2 0.038 0.011 -10000 0 -10000 0 0
UBE3A 0.028 0.004 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.67 107 107
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.003 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
IFN-gamma/IRF1 -0.023 0.18 -10000 0 -0.48 62 62
PARP2 0.027 0.005 -10000 0 -10000 0 0
BLM 0.027 0.008 -10000 0 -10000 0 0
Telomerase 0.016 0.1 0.27 1 -0.48 12 13
IRF1 0.03 0.009 -10000 0 -10000 0 0
ESR1 -0.013 0.15 -10000 0 -0.65 23 23
KU/TER 0.029 0.019 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.025 -10000 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.038 0.039 -10000 0 -0.33 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.04 -10000 0 -0.34 3 3
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
ATM 0.009 0.023 -10000 0 -0.48 1 1
SMAD3 0.015 0.011 -10000 0 -10000 0 0
ABL1 0.025 0.008 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
MRE11A 0.024 0.045 -10000 0 -0.67 2 2
HUS1 0.026 0.006 -10000 0 -10000 0 0
RPS6KB1 0.026 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.017 0.08 -10000 0 -10000 0 0
NR2F2 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.013 -10000 0 -10000 0 0
MAPK1 0.002 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.023 -10000 0 -0.48 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.02 0.07 -10000 0 -0.67 5 5
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.044 0.2 -10000 0 -0.5 76 76
MYC 0.011 0.1 -10000 0 -0.65 12 12
IL2 0.02 0.009 -10000 0 -10000 0 0
KU 0.029 0.019 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.017 -10000 0 -10000 0 0
TRF2/BLM 0.038 0.012 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.002 0.084 0.5 2 -10000 0 2
SP1/HDAC2 0.042 0.01 -10000 0 -10000 0 0
PINX1 0.027 0.005 -10000 0 -10000 0 0
Telomerase/EST1A 0.012 0.08 -10000 0 -10000 0 0
Smad3/Myc 0.018 0.068 -10000 0 -0.42 11 11
911 complex 0.052 0.015 -10000 0 -10000 0 0
IFNG -0.062 0.23 -10000 0 -0.67 62 62
Telomerase/PinX1 0.011 0.081 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.015 0.061 0.37 1 -0.42 2 3
SIN3B 0.026 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.01 0.078 -10000 0 -10000 0 0
response to DNA damage stimulus 0.003 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.071 0.036 -10000 0 -0.38 2 2
TRF2/WRN 0.037 0.026 -10000 0 -0.48 1 1
Telomerase/hnRNP C1/C2 0.012 0.082 -10000 0 -10000 0 0
E2F1 -0.018 0.071 -10000 0 -10000 0 0
ZNFX1 0.027 0.005 -10000 0 -10000 0 0
PIF1 0.017 0.078 -10000 0 -0.67 6 6
NCL 0.027 0.005 -10000 0 -10000 0 0
DKC1 0.025 0.008 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -9999 0 -0.67 1 1
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.053 -9999 0 -0.26 16 16
GNAO1 0.005 0.12 -9999 0 -0.67 15 15
S1P/S1P3/G12/G13 0.048 0.02 -9999 0 -10000 0 0
AKT1 0.023 0.041 -9999 0 -0.35 3 3
AKT3 0.019 0.067 -9999 0 -0.51 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -9999 0 -0.67 1 1
GNAI2 0.029 0.004 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.032 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.026 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.07 -9999 0 -0.3 15 15
MAPK3 0.003 0.065 -9999 0 -0.4 3 3
MAPK1 0.014 0.058 -9999 0 -0.38 3 3
JAK2 0.006 0.067 -9999 0 -0.4 3 3
CXCR4 0.003 0.064 -9999 0 -0.4 3 3
FLT1 0.027 0.032 -9999 0 -0.67 1 1
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.02 0.004 -9999 0 -10000 0 0
SRC 0.003 0.063 -9999 0 -0.34 3 3
S1P/S1P3/Gi 0.006 0.07 -9999 0 -0.3 15 15
RAC1 0.026 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.01 0.073 -9999 0 -0.38 3 3
VEGFA 0.025 0.055 -9999 0 -0.67 3 3
S1P/S1P2/Gi 0.004 0.074 -9999 0 -0.32 16 16
VEGFR1 homodimer/VEGFA homodimer 0.04 0.057 -9999 0 -0.64 3 3
RHOA 0.027 0.003 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.057 0.15 -9999 0 -0.31 122 122
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.021 0.013 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
GNA14 -0.14 0.29 -9999 0 -0.64 120 120
GNA15 0.013 0.05 -9999 0 -0.67 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.015 0.084 -9999 0 -0.64 8 8
Rac1/GTP 0.01 0.072 -9999 0 -0.38 3 3
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.28 -10000 0 -0.67 97 97
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.014 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.033 0.039 0.35 1 -10000 0 1
HIF1A 0.009 0.024 -10000 0 -10000 0 0
COPS5 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.054 0.052 -10000 0 -0.39 3 3
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.032 0.074 -10000 0 -10000 0 0
ARNT/IPAS -0.067 0.21 -10000 0 -0.49 97 97
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.032 0.048 0.31 7 -10000 0 7
CUL2 0.027 0.004 -10000 0 -10000 0 0
OS9 0.027 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.033 0.038 0.28 1 -10000 0 1
PHD1-3/OS9 0.05 0.073 -10000 0 -0.4 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.055 0.039 -10000 0 -10000 0 0
VHL 0.023 0.054 -10000 0 -0.67 3 3
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.036 0.047 0.34 4 -10000 0 4
EGLN3 0.006 0.1 -10000 0 -0.67 10 10
EGLN2 0.026 0.007 -10000 0 -10000 0 0
EGLN1 0.024 0.032 -10000 0 -0.67 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.026 0.075 -10000 0 -0.57 6 6
ARNT 0.025 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.037 0.052 0.33 5 -10000 0 5
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.015 0.08 0.63 7 -10000 0 7
PI3K Class IB/PDE3B 0.015 0.08 -10000 0 -0.63 7 7
PDE3B 0.015 0.08 -10000 0 -0.63 7 7
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.004 0.11 -9999 0 -0.65 12 12
ITGA4 0.02 0.058 -9999 0 -0.67 3 3
alpha4/beta7 Integrin 0.016 0.095 -9999 0 -0.51 14 14
alpha4/beta1 Integrin 0.034 0.046 -9999 0 -0.51 3 3
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.006 0.016 0.12 1 -0.13 3 4
BUB1B 0.014 0.031 0.18 10 -0.15 1 11
PLK1 0.012 0.03 0.16 13 -0.1 1 14
PLK1S1 0.015 0.026 0.18 9 -10000 0 9
KIF2A 0.018 0.067 0.32 20 -0.39 1 21
regulation of mitotic centrosome separation 0.012 0.03 0.16 13 -0.1 1 14
GOLGA2 0.025 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.033 0.036 -10000 0 -10000 0 0
WEE1 0.022 0.046 0.29 5 -0.34 2 7
cytokinesis 0.011 0.062 0.27 8 -0.26 2 10
PP2A-alpha B56 0.048 0.095 -10000 0 -0.55 9 9
AURKA 0.014 0.023 0.17 7 -10000 0 7
PICH/PLK1 0.02 0.015 -10000 0 -10000 0 0
CENPE 0.01 0.051 0.26 10 -0.39 3 13
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.067 0.32 20 -0.38 1 21
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.025 0.008 -10000 0 -10000 0 0
TPX2 0.015 0.027 0.17 11 -10000 0 11
PAK1 0.026 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.037 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN 0.012 0.029 0.14 1 -0.29 3 4
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.023 27 -10000 0 27
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.018 0.095 14 -0.05 1 15
G2 phase of mitotic cell cycle 0 0.004 0.02 12 -10000 0 12
STAG2 0.026 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.024 0.03 -10000 0 -0.41 2 2
spindle elongation 0.012 0.03 0.16 13 -0.1 1 14
ODF2 0.025 0.008 -10000 0 -10000 0 0
BUB1 0.022 0.099 -10000 0 -0.56 13 13
TPT1 0.004 0.045 0.14 4 -0.18 24 28
CDC25C 0.019 0.025 0.2 5 -10000 0 5
CDC25B 0.027 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.016 0.13 3 -0.12 1 4
RHOA 0.027 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.015 -10000 0 -10000 0 0
CDC14B 0.003 0.045 -10000 0 -0.38 6 6
CDC20 0.025 0.019 -10000 0 -10000 0 0
PLK1/PBIP1 0.01 0.019 0.14 3 -10000 0 3
mitosis -0.001 0.003 0.019 4 -10000 0 4
FBXO5 0.013 0.037 0.21 9 -0.34 1 10
CDC2 0.002 0.001 0.01 1 -10000 0 1
NDC80 0.009 0.049 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.025 0.14 1 -0.24 3 4
ERCC6L 0.025 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.011 0.027 0.14 15 -10000 0 15
microtubule cytoskeleton organization 0.004 0.045 0.14 4 -0.18 24 28
G2/M transition DNA damage checkpoint 0 0.004 0.019 15 -10000 0 15
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.004 0.019 15 -10000 0 15
PLK1/PRC1-2 0.038 0.027 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.049 0.021 -10000 0 -10000 0 0
RAB1A 0.027 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.009 0.027 0.14 14 -10000 0 14
mitotic prometaphase 0 0.004 0.027 7 -10000 0 7
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.026 -10000 0 -10000 0 0
microtubule-based process 0.013 0.031 -10000 0 -10000 0 0
Golgi organization 0.012 0.03 0.16 13 -0.1 1 14
Cohesin/SA2 0.021 0.02 0.18 3 -10000 0 3
PPP1CB/MYPT1 0.04 0.009 -10000 0 -10000 0 0
KIF20A 0.005 0.054 -10000 0 -10000 0 0
APC/C/CDC20 0.025 0.024 0.18 2 -10000 0 2
PPP2R1A 0.025 0.007 -10000 0 -10000 0 0
chromosome segregation 0.01 0.019 0.14 3 -10000 0 3
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.01 0.041 0.22 8 -0.4 2 10
C13orf34 0.01 0.026 0.14 13 -0.081 1 14
NUDC 0.014 0.025 0.14 1 -0.24 3 4
regulation of attachment of spindle microtubules to kinetochore 0.014 0.031 0.18 10 -0.14 1 11
spindle assembly 0.014 0.037 0.17 18 -10000 0 18
spindle stabilization 0.015 0.026 0.18 9 -10000 0 9
APC/C/HCDH1 0.019 0.041 -10000 0 -0.32 6 6
MKLP2/PLK1 0.013 0.032 -10000 0 -10000 0 0
CCNB1 0.028 0.006 -10000 0 -10000 0 0
PPP1CB 0.027 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 -0.006 0.11 0.22 2 -0.41 32 34
TUBG1 0.015 0.028 0.18 9 -0.16 2 11
G2/M transition of mitotic cell cycle 0.013 0.01 -10000 0 -10000 0 0
MLF1IP 0.007 0.012 -10000 0 -10000 0 0
INCENP 0.024 0.045 -10000 0 -0.68 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.005 -10000 0 -10000 0 0
ELF1 0.004 0.1 -10000 0 -0.39 29 29
CCNA2 0.025 0.02 -10000 0 -10000 0 0
PIK3CA 0.024 0.054 -10000 0 -0.67 3 3
JAK3 -0.012 0.066 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.003 0.13 -10000 0 -0.59 16 16
SHC1 0.026 0.008 -10000 0 -10000 0 0
SP1 0.033 0.006 -10000 0 -10000 0 0
IL2RA -0.033 0.21 -10000 0 -0.87 28 28
IL2RB 0.004 0.09 -10000 0 -0.58 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
IL2RG -0.011 0.14 -10000 0 -0.63 21 21
G1/S transition of mitotic cell cycle 0.03 0.063 0.42 5 -0.5 3 8
PTPN11 0.026 0.032 -10000 0 -0.67 1 1
CCND2 0.024 0.005 -10000 0 -10000 0 0
LCK 0.013 0.082 -10000 0 -0.67 6 6
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
CDK6 0.022 0.055 -10000 0 -0.67 3 3
CCND3 0.007 0.12 -10000 0 -0.59 9 9
TCGA08_retinoblastoma

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
CDKN2B -0.035 0.077 -10000 0 -10000 0 0
CDKN2C 0.031 0.02 -10000 0 -10000 0 0
CDKN2A -0.032 0.077 -10000 0 -10000 0 0
CCND2 0.011 0.024 -10000 0 -10000 0 0
RB1 -0.016 0.049 0.32 2 -0.24 14 16
CDK4 0.015 0.042 0.26 10 -10000 0 10
CDK6 0.017 0.044 0.26 10 -0.16 1 11
G1/S progression 0.017 0.051 0.24 15 -0.32 2 17
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.025 0.089 -10000 0 -0.52 12 12
AKT1 0.04 0.09 0.37 3 -0.58 7 10
PTK2B 0.017 0.11 0.35 1 -0.8 5 6
VEGFR2 homodimer/Frs2 0.032 0.083 -10000 0 -0.88 4 4
CAV1 0.014 0.094 -10000 0 -0.67 9 9
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.047 0.094 -10000 0 -0.74 6 6
endothelial cell proliferation 0.054 0.14 0.57 19 -0.55 6 25
mol:Ca2+ 0.023 0.09 -10000 0 -0.64 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.061 0.092 -10000 0 -0.77 5 5
RP11-342D11.1 0.012 0.089 -10000 0 -0.64 7 7
CDH5 0.026 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.059 0.058 -10000 0 -0.49 4 4
SHC1 0.025 0.008 -10000 0 -10000 0 0
SHC2 0.021 0.055 -10000 0 -0.67 3 3
HRAS/GDP 0.04 0.079 -10000 0 -0.64 5 5
SH2D2A -0.008 0.14 -10000 0 -0.67 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.058 0.095 -10000 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.025 0.13 -10000 0 -0.46 27 27
VEGFR1 homodimer 0.024 0.032 -10000 0 -0.67 1 1
SHC/GRB2/SOS1 0.066 0.095 -10000 0 -0.81 4 4
GRB10 0.024 0.089 -10000 0 -0.86 4 4
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.07 0.092 -10000 0 -0.84 4 4
HRAS 0.026 0.011 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.028 0.065 -10000 0 -0.44 5 5
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.059 0.089 -10000 0 -0.75 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.018 0.077 -10000 0 -0.67 6 6
Nck/Pak 0.039 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.048 0.094 -10000 0 -0.74 6 6
mol:GDP 0.052 0.086 -10000 0 -0.76 4 4
mol:NADP 0.041 0.097 0.46 7 -0.48 6 13
eNOS/Hsp90 0.044 0.079 -10000 0 -0.5 4 4
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.093 -10000 0 -0.66 7 7
HIF1A/ARNT 0.037 0.012 -10000 0 -10000 0 0
SHB 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.025 0.054 -10000 0 -0.67 3 3
VEGFC 0.026 0.032 -10000 0 -0.67 1 1
FAK1/Vinculin 0.04 0.1 0.33 1 -0.69 6 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.12 -10000 0 -0.52 16 16
PTPN6 0.027 0.005 -10000 0 -10000 0 0
EPAS1 0.031 0.056 -10000 0 -0.53 4 4
mol:L-citrulline 0.041 0.097 0.46 7 -0.48 6 13
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.059 0.092 -10000 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer 0.05 0.11 -10000 0 -0.73 7 7
VEGFR2/3 heterodimer 0.027 0.11 -10000 0 -0.84 7 7
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.006 0.098 0.38 1 -0.7 7 8
VEGFR2 homodimer 0.019 0.09 -10000 0 -0.97 4 4
FLT1 0.024 0.032 -10000 0 -0.67 1 1
NEDD4 0.026 0.045 -10000 0 -0.67 2 2
MAPK3 0.002 0.091 0.38 1 -0.73 5 6
MAPK1 -0.003 0.091 0.38 1 -0.74 5 6
VEGFA145/NRP2 0.027 0.054 -10000 0 -0.51 3 3
VEGFR1/2 heterodimer 0.03 0.093 -10000 0 -0.96 4 4
KDR 0.019 0.091 -10000 0 -0.98 4 4
VEGFA165/NRP1/VEGFR2 homodimer 0.054 0.099 -10000 0 -0.67 7 7
SRC 0.026 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.011 0.11 0.38 11 -0.76 5 16
PI3K 0.042 0.098 -10000 0 -0.78 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.048 0.094 -10000 0 -0.74 6 6
FES 0.024 0.096 -10000 0 -0.73 6 6
GAB1 0.03 0.093 -10000 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.095 -10000 0 -0.74 6 6
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.04 0.09 0.4 1 -0.54 5 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.047 0.095 -10000 0 -0.74 6 6
PI3K/GAB1 0.051 0.085 -10000 0 -0.62 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.07 0.092 -10000 0 -0.68 6 6
PRKACA 0.025 0.008 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.11 -10000 0 -0.74 8 8
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.096 -10000 0 -0.68 7 7
actin cytoskeleton reorganization 0.025 0.13 -10000 0 -0.46 27 27
PTK2 0.025 0.1 0.32 1 -0.75 6 7
EDG1 0.012 0.089 -10000 0 -0.64 7 7
mol:DAG 0.023 0.093 -10000 0 -0.66 7 7
CaM/Ca2+ 0.036 0.086 -10000 0 -0.6 7 7
MAP2K3 0.009 0.1 0.37 1 -0.9 4 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.1 -10000 0 -0.94 4 4
PLCG1 0.023 0.096 -10000 0 -0.68 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.058 0.093 -10000 0 -0.7 6 6
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.046 0.1 -10000 0 -0.79 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.047 0.094 -10000 0 -0.74 6 6
cell migration 0.047 0.084 0.34 1 -0.66 4 5
mol:PI-3-4-5-P3 0.042 0.086 -10000 0 -0.68 5 5
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.028 0.085 -10000 0 -0.61 7 7
mol:NO 0.041 0.097 0.46 7 -0.48 6 13
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.075 -10000 0 -0.64 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.044 0.1 -10000 0 -0.94 4 4
VHL 0.023 0.054 -10000 0 -0.67 3 3
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
NOS3 0.04 0.1 0.47 7 -0.55 6 13
VEGFR2 homodimer/VEGFA homodimer/Sck 0.041 0.1 -10000 0 -0.65 8 8
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.003 0.12 0.36 1 -0.48 19 20
PRKCB 0.007 0.094 0.36 1 -0.56 9 10
VCL 0.027 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.03 0.095 -10000 0 -0.67 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.044 0.1 -10000 0 -0.78 6 6
VEGFA165/NRP2 0.027 0.054 -10000 0 -0.51 3 3
MAPKKK cascade 0.054 0.091 0.36 2 -0.71 4 6
NRP2 0.014 0.043 -10000 0 -10000 0 0
VEGFC homodimer 0.025 0.032 -10000 0 -0.67 1 1
NCK1 0.027 0.003 -10000 0 -10000 0 0
ROCK1 0.027 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.1 -10000 0 -0.69 6 6
MAP3K13 0.016 0.12 -10000 0 -0.53 15 15
PDPK1 0.028 0.081 -10000 0 -0.67 5 5
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.025 0.052 0.31 1 -0.67 1 2
PDGFB-D/PDGFRB/SLAP 0.038 0.027 -10000 0 -0.51 1 1
PDGFB-D/PDGFRB/APS/CBL 0.051 0.034 -10000 0 -0.43 2 2
AKT1 0.03 0.087 0.5 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.029 0.054 0.34 1 -0.71 1 2
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
FGR 0.018 0.045 0.36 1 -0.54 2 3
mol:Ca2+ 0.034 0.082 0.41 13 -0.74 1 14
MYC 0.03 0.18 0.57 19 -0.77 14 33
SHC1 0.025 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.025 -10000 0 -0.38 1 1
LRP1/PDGFRB/PDGFB 0.038 0.04 -10000 0 -0.44 2 2
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GO:0007205 0.034 0.083 0.41 13 -0.76 1 14
PTEN 0.026 0.018 -10000 0 -0.36 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.056 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.037 0.036 -10000 0 -0.51 2 2
PDGFB-D/PDGFRB/GRB10 0.038 0.027 -10000 0 -0.51 1 1
cell cycle arrest 0.037 0.027 -10000 0 -0.51 1 1
HRAS 0.026 0.011 -10000 0 -10000 0 0
HIF1A 0.024 0.084 0.48 11 -10000 0 11
GAB1 0.029 0.094 0.45 11 -0.56 2 13
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.034 0.11 0.51 15 -0.7 1 16
PDGFB-D/PDGFRB 0.054 0.029 -10000 0 -0.46 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.027 -10000 0 -0.51 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.033 0.053 -10000 0 -0.67 1 1
positive regulation of MAPKKK cascade 0.037 0.036 -10000 0 -0.51 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0.034 0.083 0.41 13 -0.76 1 14
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.017 0.052 -10000 0 -0.57 1 1
SHB 0.025 0.007 -10000 0 -10000 0 0
BLK -0.15 0.26 -10000 0 -0.56 144 144
PTPN2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.038 0.026 -10000 0 -0.49 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.034 0.11 0.49 14 -0.57 3 17
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.027 -10000 0 -0.51 1 1
LCK 0.011 0.08 -10000 0 -0.65 6 6
PDGFRB 0.026 0.033 -10000 0 -0.68 1 1
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK 0.024 0.031 -10000 0 -0.44 1 1
ABL1 0.026 0.097 0.42 14 -0.59 2 16
PDGFB-D/PDGFRB/CBL 0.023 0.083 0.45 4 -0.64 2 6
PTPN1 0.028 0.005 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
cell proliferation 0.032 0.17 0.54 20 -0.68 14 34
SLA 0.026 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.027 -10000 0 -0.37 1 1
SRC 0.019 0.035 -10000 0 -0.4 2 2
PI3K 0.012 0.034 -10000 0 -0.35 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.049 0.028 -10000 0 -0.31 1 1
SH2B2 0.024 0.033 -10000 0 -0.67 1 1
PLCgamma1/SPHK1 0.029 0.055 0.34 1 -0.74 1 2
LYN 0.018 0.035 -10000 0 -0.44 2 2
LRP1 0.025 0.032 -10000 0 -0.67 1 1
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.079 0.032 -10000 0 -0.38 1 1
SPHK1 0.023 0.023 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.034 0.083 0.41 13 -0.76 1 14
PLCG1 0.034 0.084 0.44 11 -0.79 1 12
NHERF/PDGFRB 0.05 0.028 -10000 0 -0.44 1 1
YES1 0.015 0.056 0.37 1 -0.51 4 5
cell migration 0.05 0.028 -10000 0 -0.44 1 1
SHC/Grb2/SOS1 0.072 0.035 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.033 -10000 0 -0.4 1 1
FYN 0.016 0.05 -10000 0 -0.44 4 4
DOK1 0.024 0.029 -10000 0 -0.41 1 1
HRAS/GTP 0.019 0.008 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.039 0.14 0.54 20 -0.46 12 32
PRKCD 0.024 0.031 -10000 0 -0.42 1 1
FER 0.02 0.043 -10000 0 -0.42 4 4
MAPKKK cascade 0.016 0.056 0.37 1 -10000 0 1
RASA1 0.023 0.028 -10000 0 -0.42 1 1
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.03 -10000 0 -0.38 1 1
PDGFB-D/PDGFRB/SHB 0.036 0.028 -10000 0 -0.51 1 1
chemotaxis 0.026 0.095 0.42 14 -0.56 2 16
STAT1-3-5/STAT1-3-5 0.064 0.029 -10000 0 -0.37 1 1
Bovine Papilomavirus E5/PDGFRB 0.019 0.025 -10000 0 -0.52 1 1
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.017 0.041 -10000 0 -0.26 1 1
STMN1 0.001 0.042 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.053 0.051 -10000 0 -0.44 1 1
Chromosomal passenger complex/Cul3 protein complex 0.014 0.05 -10000 0 -0.25 11 11
BIRC5 0.017 0.048 -10000 0 -0.68 1 1
DES -0.32 0.3 -10000 0 -0.57 289 289
Aurora C/Aurora B/INCENP 0.054 0.044 -10000 0 -0.45 2 2
Aurora B/TACC1 0.029 0.043 -10000 0 -0.5 1 1
Aurora B/PP2A 0.02 0.05 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.007 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.008 0.06 -10000 0 -10000 0 0
Cul3 protein complex 0.038 0.072 -10000 0 -0.44 10 10
KIF2C 0.015 0.028 -10000 0 -0.47 1 1
PEBP1 0.027 0.006 -10000 0 -10000 0 0
KIF20A 0.004 0.054 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.02 0.05 -10000 0 -10000 0 0
SEPT1 0.024 0.021 -10000 0 -10000 0 0
SMC2 0.025 0.008 -10000 0 -10000 0 0
SMC4 0.027 0.003 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.017 0.079 0.28 2 -0.54 8 10
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.011 0.017 -10000 0 -10000 0 0
AURKB 0.001 0.066 -10000 0 -10000 0 0
AURKC 0.02 0.03 -10000 0 -10000 0 0
CDCA8 0.027 0.016 -10000 0 -10000 0 0
cytokinesis -0.018 0.054 -10000 0 -0.36 4 4
Aurora B/Septin1 0.045 0.066 -10000 0 -0.36 3 3
AURKA 0.026 0.005 -10000 0 -10000 0 0
INCENP 0.026 0.046 -10000 0 -0.68 2 2
KLHL13 0.006 0.1 -10000 0 -0.62 12 12
BUB1 -0.028 0.079 -10000 0 -0.68 1 1
hSgo1/Aurora B/Survivin 0.048 0.055 -10000 0 -0.4 1 1
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.05 0.047 -10000 0 -10000 0 0
SGOL1 0.021 0.029 -10000 0 -10000 0 0
CENPA 0.018 0.041 0.2 2 -0.22 6 8
NCAPG 0.013 0.045 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.02 0.05 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.019 0.05 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
NCAPH 0.005 0.054 -10000 0 -10000 0 0
NPM1 0.012 0.041 -10000 0 -0.3 7 7
RASA1 0.027 0.005 -10000 0 -10000 0 0
KLHL9 0.025 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.05 -10000 0 -10000 0 0
PPP1CC 0.027 0.005 -10000 0 -10000 0 0
Centraspindlin 0.043 0.048 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 0.011 0.043 -10000 0 -0.31 4 4
MYLK 0.01 0.025 -10000 0 -0.41 1 1
KIF23 0.021 0.034 -10000 0 -10000 0 0
VIM 0 0.04 -10000 0 -10000 0 0
RACGAP1 0.028 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.006 0.072 -10000 0 -0.47 7 7
Chromosomal passenger complex 0.015 0.036 -10000 0 -0.26 3 3
Chromosomal passenger complex/EVI5 0.1 0.069 -10000 0 -0.42 3 3
TACC1 0.025 0.032 -10000 0 -0.67 1 1
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.03 0.1 -10000 0 -0.5 7 7
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.026 0.007 -10000 0 -10000 0 0
STXBP4 0.024 0.032 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.024 0.1 0.33 7 -0.47 7 14
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.053 0.18 -10000 0 -0.49 67 67
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.05 0.027 -10000 0 -0.44 1 1
YWHAG 0.026 0.006 -10000 0 -10000 0 0
ASIP 0.005 0.05 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.017 0.012 0.25 1 -10000 0 1
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
TRIP10 0.025 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
AS160/14-3-3 -0.035 0.094 -10000 0 -0.35 15 15
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.022 0.11 0.33 6 -0.53 7 13
STX4 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.024 0.008 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.67 15 15
LNPEP 0.004 0.12 -10000 0 -0.67 16 16
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.016 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.044 0.016 -10000 0 -10000 0 0
CDKN1B 0.022 0.024 -10000 0 -10000 0 0
CDKN1A 0.021 0.025 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.005 -10000 0 -10000 0 0
FOXO3 0.022 0.024 -10000 0 -10000 0 0
AKT1 0.022 0.023 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.014 0.026 -10000 0 -0.39 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.022 0.026 -10000 0 -10000 0 0
AKT1/ASK1 0.038 0.036 -10000 0 -0.33 1 1
BAD/YWHAZ 0.05 0.018 -10000 0 -10000 0 0
RICTOR 0.025 0.032 -10000 0 -0.67 1 1
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.036 0.035 0.32 1 -10000 0 1
TSC1 0.021 0.025 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.041 0.035 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
mol:GDP 0.022 0.023 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.022 0.023 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.046 0.15 -10000 0 -0.43 64 64
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
MAPKAP1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.075 0.4 4 -0.32 8 12
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.027 0.038 -10000 0 -10000 0 0
CASP9 0.024 0.031 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.048 0.36 6 -10000 0 6
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.034 -10000 0 -0.44 2 2
YWHAE 0.026 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.029 -10000 0 -0.36 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.011 -10000 0 -10000 0 0
CHUK 0.022 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.046 0.034 -10000 0 -10000 0 0
mTORC2 0.03 0.023 -10000 0 -0.4 1 1
AKT2 0.014 0.026 -10000 0 -0.39 2 2
FOXO1-3a-4/14-3-3 family 0.02 0.079 0.37 8 -0.37 2 10
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
MDM2 0.023 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.041 0.035 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.034 -10000 0 -10000 0 0
TSC1/TSC2 0.023 0.039 0.44 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.033 -10000 0 -10000 0 0
glucose import -0.057 0.16 0.21 5 -0.42 78 83
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.029 0.24 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.059 0.16 -10000 0 -0.42 78 78
GSK3A 0.026 0.037 -10000 0 -10000 0 0
FOXO1 0.021 0.025 -10000 0 -10000 0 0
GSK3B 0.022 0.024 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.67 15 15
G1/S transition of mitotic cell cycle 0.029 0.044 0.32 2 -10000 0 2
p27Kip1/14-3-3 family 0.015 0.054 -10000 0 -0.34 5 5
PRKACA 0.025 0.008 -10000 0 -10000 0 0
KPNA1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.006 0.16 -10000 0 -0.44 56 56
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.018 0.14 -10000 0 -0.38 55 55
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.026 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.036 0.083 -10000 0 -10000 0 0
YY1/LSF 0.006 0.065 -10000 0 -0.43 4 4
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.007 0.11 -10000 0 -0.31 54 54
I kappa B alpha/HDAC1 0.011 0.08 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA -0.016 0.11 -10000 0 -0.32 56 56
HDAC1/Smad7 0.052 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.012 0.08 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.031 0.037 -10000 0 -0.44 2 2
NF kappa B1 p50/RelA -0.024 0.12 0.32 1 -0.43 15 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.027 0.008 -10000 0 -10000 0 0
GATA1 0.012 0.021 -10000 0 -10000 0 0
Mad/Max 0.039 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.035 0.067 -10000 0 -0.49 5 5
RBBP7 0.026 0.007 -10000 0 -10000 0 0
NPC 0.016 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.67 2 2
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NFKBIA -0.003 0.083 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.034 -10000 0 -0.55 1 1
SIN3 complex 0.061 0.032 -10000 0 -0.4 1 1
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.026 0.007 -10000 0 -10000 0 0
SAP30 0.026 0.032 -10000 0 -0.67 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.007 -10000 0 -10000 0 0
YY1/HDAC3 -0.008 0.079 -10000 0 -10000 0 0
YY1/HDAC2 0.009 0.054 -10000 0 -0.28 1 1
YY1/HDAC1 0.009 0.054 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.032 0.031 -10000 0 -0.4 1 1
PPARG -0.021 0.14 -10000 0 -0.39 60 60
HDAC8/hEST1B 0.046 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.012 0.08 -10000 0 -10000 0 0
MBD3L2 -0.015 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.015 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.036 0.061 -10000 0 -0.45 4 4
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 -0.003 0.083 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.019 0.012 -10000 0 -10000 0 0
HDAC8 0.026 0.007 -10000 0 -10000 0 0
SMAD7 0.027 0.004 -10000 0 -10000 0 0
NCOR2 0.027 0.005 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.018 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.019 0.066 -10000 0 -0.4 4 4
YY1/SAP30/HDAC1 0.021 0.058 -10000 0 -0.31 1 1
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.082 -10000 0 -10000 0 0
histone deacetylation 0.038 0.034 -10000 0 -0.39 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.003 0.074 -10000 0 -0.3 1 1
nuclear export -0.046 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GATAD2B 0.025 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.008 -10000 0 -10000 0 0
GATA2/HDAC3 0.012 0.08 -10000 0 -10000 0 0
GATA1/HDAC1 0.035 0.013 -10000 0 -10000 0 0
GATA1/HDAC3 0.009 0.079 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.024 0.17 -10000 0 -0.51 56 56
SIN3/HDAC complex/Mad/Max 0.032 0.034 -10000 0 -0.49 1 1
NuRD Complex 0.042 0.052 -10000 0 -0.49 2 2
positive regulation of chromatin silencing 0.034 0.081 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.014 0.057 -10000 0 -0.27 2 2
HDAC complex 0.063 0.036 -10000 0 -0.4 2 2
GATA1/Fog1 0.034 0.014 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.053 0.014 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.67 56 56
negative regulation of cell growth 0.036 0.035 -10000 0 -0.48 1 1
NuRD/MBD2/PRMT5 Complex 0.032 0.031 -10000 0 -0.4 1 1
Ran/GTP/Exportin 1 0.017 0.052 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.03 0.14 -10000 0 -0.4 56 56
SIN3/HDAC complex/NCoR1 0.031 0.044 -10000 0 -0.45 2 2
TFCP2 0.021 0.063 -10000 0 -0.67 4 4
NR2C1 0.027 0.005 -10000 0 -10000 0 0
MBD3 0.025 0.008 -10000 0 -10000 0 0
MBD2 0.027 0.004 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.037 0.013 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.003 0.11 -10000 0 -0.44 30 30
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.038 -10000 0 -10000 0 0
NFKBIA 0.014 0.029 -10000 0 -0.24 5 5
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.032 0.008 -10000 0 -10000 0 0
ARRB2 0.016 0.005 -10000 0 -10000 0 0
REL -0.018 0.17 -10000 0 -0.66 32 32
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
NF kappa B1 p50 dimer 0.025 0.023 0.25 5 -10000 0 5
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.017 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.02 0.038 -10000 0 -0.31 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.04 0.039 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.043 -10000 0 -0.51 3 3
NF kappa B1 p50/RelA 0.021 0.038 -10000 0 -0.31 5 5
IKBKB 0.027 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.038 -10000 0 -0.23 4 4
cell death 0.038 0.038 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.003 0.11 -10000 0 -0.44 30 30
LCK 0.012 0.082 -10000 0 -0.67 6 6
BCL3 0.025 0.01 -10000 0 -10000 0 0
Canonical Wnt 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
HDAC1 0.027 0.022 0.25 1 -10000 0 1
AES 0.025 0.018 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
SMAD4 0.027 0.004 -10000 0 -10000 0 0
DKK2 -0.004 0.14 -10000 0 -0.66 20 20
TLE1 0.021 0.056 -10000 0 -0.66 3 3
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.048 0.088 0.46 16 -10000 0 16
WIF1 -0.015 0.047 -10000 0 -10000 0 0
beta catenin/RanBP3 0.03 0.084 0.38 24 -10000 0 24
KREMEN2 0.016 0.037 -10000 0 -10000 0 0
DKK1 -0.001 0.07 -10000 0 -0.67 2 2
beta catenin/beta TrCP1 0.048 0.045 0.38 2 -10000 0 2
FZD1 0.027 0.006 -10000 0 -10000 0 0
AXIN2 -0.029 0.3 0.62 12 -1.4 18 30
AXIN1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.03 0.066 -10000 0 -0.51 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.094 0.3 1 -0.55 4 5
Axin1/APC/GSK3 0.034 0.045 0.34 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.034 0.029 0.32 1 -10000 0 1
HNF1A 0.027 0.02 0.23 1 -10000 0 1
CTBP1 0.027 0.02 0.24 1 -10000 0 1
MYC -0.037 0.24 0.53 6 -1.4 14 20
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.096 -10000 0 -0.44 19 19
NKD1 0.007 0.11 -10000 0 -0.67 13 13
TCF4 0.027 0.019 0.22 1 -10000 0 1
TCF3 0.025 0.02 0.23 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.065 0.02 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.021 0.12 0.49 22 -10000 0 22
LEF1 0.022 0.049 0.22 1 -0.63 2 3
DVL1 0.028 0.016 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.039 0.11 -10000 0 -0.52 9 9
DKK1/LRP6/Kremen 2 0.049 0.044 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.019 -10000 0 -10000 0 0
NLK 0.026 0.008 -10000 0 -10000 0 0
CCND1 -0.011 0.082 0.58 2 -0.69 2 4
WNT1 0.022 0.018 -10000 0 -10000 0 0
GSK3A 0.026 0.008 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
PPP2R5D 0.031 0.058 0.33 13 -0.32 2 15
APC 0.022 0.039 0.36 3 -0.39 1 4
WNT1/LRP6/FZD1 0.032 0.021 -10000 0 -10000 0 0
CREBBP 0.027 0.02 0.23 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.013 -10000 0 -10000 0 0
STXBP1 0.025 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.009 0.044 -10000 0 -0.24 4 4
RAB3GAP2/RIMS1/UNC13B 0.048 0.02 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.021 0.018 -10000 0 -10000 0 0
mol:ACh 0.002 0.044 0.14 20 -0.14 22 42
RAB3GAP2 0.025 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.031 0.055 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.009 0.044 -10000 0 -0.24 4 4
UNC13B 0.025 0.008 -10000 0 -10000 0 0
CHRNA1 0.008 0.052 -10000 0 -0.67 1 1
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.041 0.11 -10000 0 -0.48 25 25
SNAP25 -0.015 0.075 -10000 0 -0.34 25 25
VAMP2 0.006 0.001 -10000 0 -10000 0 0
SYT1 -0.067 0.16 -10000 0 -0.67 24 24
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.009 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.031 0.055 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
CDC42/GTP 0.008 0.074 -10000 0 -0.31 14 14
PLCG1 -0.002 0.067 -10000 0 -0.32 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.011 -10000 0 -10000 0 0
cell migration 0.007 0.073 -10000 0 -0.3 14 14
S1PR5 0.023 0.034 -10000 0 -0.67 1 1
S1PR4 0.023 0.02 -10000 0 -10000 0 0
MAPK3 -0.003 0.068 -10000 0 -0.5 3 3
MAPK1 0.009 0.06 -10000 0 -0.32 14 14
S1P/S1P5/Gi -0.001 0.074 -10000 0 -0.33 16 16
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.025 -10000 0 -0.44 1 1
RHOA 0.035 0.07 0.41 12 -10000 0 12
S1P/S1P4/Gi 0 0.073 -10000 0 -0.32 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.047 0.018 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.027 0.004 -9999 0 -10000 0 0
SMAD2 -0.016 0.044 -9999 0 -0.24 1 1
SMAD3 0.021 0.016 -9999 0 -10000 0 0
SMAD3/SMAD4 0.032 0.05 -9999 0 -0.41 5 5
SMAD4/Ubc9/PIASy 0.049 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.027 0.064 -9999 0 -0.42 1 1
PPM1A 0.027 0.005 -9999 0 -10000 0 0
CALM1 0.027 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.004 0.055 -9999 0 -0.43 1 1
MAP3K1 0.027 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.006 0.13 -9999 0 -0.49 31 31
MAPK3 0.026 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.012 -9999 0 -10000 0 0
NUP214 0.025 0.008 -9999 0 -10000 0 0
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.027 0.005 -9999 0 -10000 0 0
CTDSPL 0.027 0.003 -9999 0 -10000 0 0
KPNB1 0.026 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.016 0.17 -9999 0 -0.66 31 31
UBE2I 0.026 0.007 -9999 0 -10000 0 0
NUP153 0.026 0.032 -9999 0 -0.67 1 1
KPNA2 0.026 0.007 -9999 0 -10000 0 0
PIAS4 0.025 0.008 -9999 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.064 0.38 1 -10000 0 1
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.021 0.053 -10000 0 -0.51 2 2
NFKBIA 0.022 0.014 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.027 0.005 -10000 0 -10000 0 0
RIPK2 0.027 0.005 -10000 0 -10000 0 0
IKBKG 0.034 0.025 -10000 0 -10000 0 0
IKK complex/A20 0.017 0.14 -10000 0 -0.48 5 5
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.035 0.072 -10000 0 -0.56 1 1
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.046 0.065 -10000 0 -0.38 1 1
BCL10/MALT1/TRAF6 0.051 0.034 -10000 0 -0.44 2 2
NOD2 0.003 0.067 -10000 0 -0.67 2 2
NFKB1 0.03 0.004 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.027 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.008 -10000 0 -10000 0 0
ATM 0.025 0.032 -10000 0 -0.67 1 1
TNF/TNFR1A -0.024 0.17 -10000 0 -0.51 56 56
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
PRKCA 0.002 0.13 -10000 0 -0.67 17 17
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.67 56 56
NF kappa B1 p50/RelA 0.061 0.016 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.013 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.05 0.07 -10000 0 -0.4 1 1
CYLD 0.026 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.045 0.098 -10000 0 -0.47 2 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.039 0.042 -9999 0 -0.45 1 1
CLOCK -0.017 0.17 -9999 0 -0.67 32 32
TIMELESS/CRY2 0.026 0.036 -9999 0 -10000 0 0
DEC1/BMAL1 0.016 0.039 -9999 0 -10000 0 0
ATR 0.026 0.032 -9999 0 -0.67 1 1
NR1D1 -0.001 0.042 -9999 0 -10000 0 0
ARNTL 0.01 0.049 -9999 0 -10000 0 0
TIMELESS 0.01 0.032 -9999 0 -10000 0 0
NPAS2 0.027 0.019 -9999 0 -0.36 1 1
CRY2 0.027 0.005 -9999 0 -10000 0 0
mol:CO -0.004 0.009 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.004 0.009 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.023 0.13 -9999 0 -0.44 32 32
BMAL1/CLOCK -0.005 0.11 -9999 0 -0.44 13 13
S phase of mitotic cell cycle 0.039 0.042 -9999 0 -0.45 1 1
TIMELESS/CHEK1/ATR 0.04 0.043 -9999 0 -10000 0 0
mol:NADPH 0.004 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.026 0.034 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.012 0.013 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.07 -9999 0 -0.38 14 14
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.02 0.004 -9999 0 -10000 0 0
DOCK1 0.023 0.054 -9999 0 -0.67 3 3
ITGA4 0.02 0.058 -9999 0 -0.67 3 3
alpha4/beta7 Integrin/MAdCAM1 0.044 0.089 -9999 0 -0.41 16 16
EPO 0.004 0.027 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.016 0.095 -9999 0 -0.51 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.046 -9999 0 -0.51 3 3
EPO/EPOR (dimer) 0.03 0.021 -9999 0 -10000 0 0
lamellipodium assembly 0.02 0.037 -9999 0 -0.4 3 3
PIK3CA 0.023 0.054 -9999 0 -0.67 3 3
PI3K 0.036 0.043 -9999 0 -0.51 3 3
ARF6 0.027 0.005 -9999 0 -10000 0 0
JAK2 0.022 0.045 -9999 0 -0.51 3 3
PXN 0.027 0.005 -9999 0 -10000 0 0
PIK3R1 0.027 0.005 -9999 0 -10000 0 0
MADCAM1 0.004 0.064 -9999 0 -0.67 3 3
cell adhesion 0.043 0.088 -9999 0 -0.4 16 16
CRKL/CBL 0.029 0.019 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
SRC 0.016 0.065 -9999 0 -0.45 7 7
ITGB7 0.004 0.11 -9999 0 -0.65 12 12
RAC1 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.068 -9999 0 -0.49 7 7
p130Cas/Crk/Dock1 0.035 0.065 -9999 0 -0.37 10 10
VCAM1 0.018 0.071 -9999 0 -0.67 5 5
RHOA 0.027 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.038 -9999 0 -0.4 2 2
BCAR1 0.008 0.061 -9999 0 -0.43 7 7
EPOR 0.024 0.017 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.027 0.005 -9999 0 -10000 0 0
GIT1 0.026 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.02 0.038 -9999 0 -0.41 3 3
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.074 0.47 3 -10000 0 3
GNAI2 0.027 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.025 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
RhoA/GTP 0.007 0.075 -10000 0 -0.48 3 3
negative regulation of cAMP metabolic process -0.001 0.074 -10000 0 -0.32 16 16
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
S1PR5 0.023 0.034 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.074 -10000 0 -0.33 16 16
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
HIF-2-alpha transcription factor network

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
MMP14 0.015 0.034 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.014 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.087 -10000 0 -0.54 3 3
EPO 0.12 0.11 -10000 0 -0.91 1 1
FIH (dimer) 0.037 0.012 -10000 0 -10000 0 0
APEX1 0.035 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.12 -10000 0 -0.67 3 3
FLT1 -0.002 0.12 -10000 0 -0.72 8 8
ADORA2A 0.1 0.12 0.43 1 -0.72 2 3
germ cell development 0.13 0.11 -10000 0 -0.71 2 2
SLC11A2 0.12 0.11 -10000 0 -0.75 2 2
BHLHE40 0.13 0.11 -10000 0 -0.75 2 2
HIF1AN 0.037 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.096 -10000 0 -0.66 2 2
ETS1 0.038 0.015 -10000 0 -10000 0 0
CITED2 -0.036 0.31 -10000 0 -1.1 39 39
KDR 0.004 0.13 -10000 0 -1 6 6
PGK1 0.12 0.11 -10000 0 -0.75 2 2
SIRT1 0.026 0.032 -10000 0 -0.67 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.14 -10000 0 -0.95 2 2
EPAS1 0.061 0.069 -10000 0 -0.46 2 2
SP1 0.032 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.13 -10000 0 -0.78 4 4
EFNA1 0.13 0.11 -10000 0 -0.75 2 2
FXN 0.12 0.12 0.51 2 -0.72 2 4
POU5F1 0.13 0.11 -10000 0 -0.75 2 2
neuron apoptosis -0.16 0.13 0.89 2 -10000 0 2
EP300 0.02 0.012 -10000 0 -10000 0 0
EGLN3 0.016 0.1 -10000 0 -0.66 10 10
EGLN2 0.035 0.014 -10000 0 -10000 0 0
EGLN1 0.034 0.035 -10000 0 -0.68 1 1
VHL/Elongin B/Elongin C 0.05 0.042 -10000 0 -0.46 3 3
VHL 0.023 0.054 -10000 0 -0.67 3 3
ARNT 0.034 0.015 -10000 0 -10000 0 0
SLC2A1 0.14 0.12 0.47 6 -0.72 2 8
TWIST1 0.12 0.14 0.44 2 -0.57 8 10
ELK1 0.022 0.036 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.089 0.098 -10000 0 -0.63 1 1
VEGFA 0.12 0.12 -10000 0 -0.7 4 4
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.025 0.11 0.66 10 -10000 0 10
PLK1 0.07 0.12 0.6 2 -0.71 1 3
CDKN1B 0.074 0.09 0.47 3 -0.4 1 4
FOXO3 0.067 0.11 -10000 0 -0.63 4 4
KAT2B 0.032 0.019 -10000 0 -10000 0 0
FOXO1/SIRT1 0.019 0.056 0.42 2 -0.4 1 3
CAT 0.063 0.13 -10000 0 -1.4 2 2
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.034 0.02 -10000 0 -10000 0 0
FOXO1 0.017 0.08 0.44 11 -10000 0 11
MAPK10 0.033 0.032 0.2 10 -0.41 1 11
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.069 0.085 0.49 9 -0.51 3 12
response to oxidative stress 0.01 0.012 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.087 0.087 -10000 0 -0.79 2 2
XPO1 0.027 0.005 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
BCL2L11 0.027 0.099 -10000 0 -0.66 8 8
FOXO1/SKP2 0.016 0.055 -10000 0 -0.44 3 3
mol:GDP 0.01 0.012 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.1 0.091 0.46 6 -0.54 4 10
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0 0.1 -10000 0 -0.48 7 7
MST1 0.031 0.036 -10000 0 -0.66 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.008 0.11 -10000 0 -0.56 9 9
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.027 0.062 -10000 0 -0.39 9 9
MAPK9 0.031 0.018 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
SIRT1 0.026 0.037 -10000 0 -0.67 1 1
SOD2 0.1 0.1 0.56 10 -0.62 2 12
RBL2 0.078 0.15 0.57 1 -1 5 6
RAL/GDP 0.046 0.015 -10000 0 -10000 0 0
CHUK 0.032 0.019 -10000 0 -10000 0 0
Ran/GTP 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
RAL/GTP 0.05 0.016 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.07 0.38 -10000 0 -1.4 39 39
SKP2 0.022 0.055 -10000 0 -0.67 3 3
USP7 0.028 0.006 -10000 0 -10000 0 0
IKBKB 0.032 0.02 -10000 0 -10000 0 0
CCNB1 0.07 0.11 0.6 2 -0.63 2 4
FOXO1-3a-4/beta catenin 0.1 0.099 0.44 7 -0.42 4 11
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.055 -10000 0 -0.43 3 3
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
SGK1 0.018 0.1 -10000 0 -0.67 10 10
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.041 0.01 -10000 0 -10000 0 0
ZFAND5 0.077 0.11 0.6 13 -0.44 2 15
SFN -0.085 0.13 -10000 0 -0.67 15 15
CDK2 0.027 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.009 0.099 -10000 0 -0.47 10 10
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FBXO32 0.067 0.11 0.59 1 -0.71 1 2
BCL6 0.084 0.12 0.57 1 -0.82 4 5
RALB 0.028 0.005 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.009 0.003 -10000 0 -10000 0 0
SNTA1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.009 0.004 -10000 0 -10000 0 0
MAPK12 -0.004 0.053 -10000 0 -0.39 9 9
CCND1 0.004 0.037 -10000 0 -0.33 4 4
p38 gamma/SNTA1 0.018 0.065 -10000 0 -0.38 10 10
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
G2/M transition checkpoint -0.005 0.056 -10000 0 -0.39 10 10
MAP2K6 -0.003 0.062 -10000 0 -0.44 10 10
MAPT 0.009 0.052 0.32 7 -0.37 3 10
MAPK13 0.016 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.008 0.002 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.028 0.041 0.29 3 -0.38 3 6
adherens junction organization 0.021 0.04 0.25 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.036 0.052 -10000 0 -0.36 7 7
FMN1 0.008 0.082 -10000 0 -0.35 24 24
mol:IP3 0.028 0.032 -10000 0 -0.33 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.022 -10000 0 -10000 0 0
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.035 0.25 1 -0.32 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.036 0.028 -10000 0 -10000 0 0
CTNND1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.032 -10000 0 -0.38 2 2
VASP 0.025 0.018 -10000 0 -10000 0 0
ZYX 0.026 0.021 -10000 0 -10000 0 0
JUB 0.025 0.02 -10000 0 -10000 0 0
EGFR(dimer) 0.039 0.048 -10000 0 -0.36 5 5
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.048 0.038 0.25 1 -0.34 3 4
PIK3CA 0.025 0.055 -10000 0 -0.68 3 3
PI3K 0.05 0.039 0.26 1 -0.35 3 4
FYN 0.026 0.036 0.29 3 -0.29 3 6
mol:Ca2+ 0.027 0.032 -10000 0 -0.32 3 3
JUP 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:DAG 0.028 0.032 -10000 0 -0.33 3 3
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.037 0.053 -10000 0 -0.36 7 7
establishment of polarity of embryonic epithelium 0.025 0.018 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
CASR 0.018 0.031 -10000 0 -0.32 3 3
RhoA/GTP 0.039 0.032 -10000 0 -0.3 3 3
AKT2 0.031 0.033 -10000 0 -0.32 3 3
actin cable formation 0.006 0.078 -10000 0 -0.34 23 23
apoptosis -0.03 0.043 0.36 3 -0.32 4 7
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.022 0.052 -10000 0 -0.38 7 7
PIP5K1A 0.023 0.033 -10000 0 -0.39 2 2
PLCG1 0.028 0.033 -10000 0 -0.34 3 3
Rac1/GTP 0.048 0.047 -10000 0 -0.33 5 5
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.03 -10000 0 -0.32 3 3
TRAF2/ASK1 0.032 0.024 -10000 0 -0.44 1 1
ATM 0.025 0.032 -10000 0 -0.67 1 1
MAP2K3 0.036 0.094 0.42 15 -0.38 3 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.095 0.34 14 -0.4 7 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.084 -10000 0 -0.67 7 7
TXN 0.008 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.006 0.11 -10000 0 -0.61 15 15
MAP3K1 0.027 0.005 -10000 0 -10000 0 0
MAP3K6 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.026 -10000 0 -0.51 1 1
TAK1/TAB family 0.011 0.033 -10000 0 -0.19 3 3
RAC1/OSM/MEKK3 0.049 0.015 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.036 0.055 -10000 0 -0.33 2 2
TRAF6 0.007 0.026 -10000 0 -0.4 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.019 0.07 -10000 0 -0.67 5 5
CCM2 0.026 0.011 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.031 0.048 -10000 0 -0.44 5 5
MAPK11 0.02 0.013 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.045 0.056 -10000 0 -0.48 5 5
OSM/MEKK3 0.037 0.014 -10000 0 -10000 0 0
TAOK1 -0.032 0.13 -10000 0 -0.4 57 57
TAOK2 0.015 0.019 -10000 0 -0.39 1 1
TAOK3 0.016 0.019 -10000 0 -0.39 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
MAP3K10 0.026 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.037 -10000 0 -0.43 1 1
GADD45/MTK1/MTK1 0.038 0.091 -10000 0 -0.4 18 18
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.03 0.025 -10000 0 -10000 0 0
BIRC5 0.015 0.047 -10000 0 -0.67 1 1
NFKBIA 0.015 0.022 0.25 3 -10000 0 3
CPEB1 -0.025 0.18 -10000 0 -0.65 38 38
AKT1 0.015 0.024 0.25 4 -10000 0 4
NDEL1 0.026 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.027 0.021 -10000 0 -10000 0 0
NDEL1/TACC3 0.044 0.024 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.03 0.025 -10000 0 -10000 0 0
MDM2 0.027 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.028 -10000 0 -10000 0 0
TP53 0.026 0.012 -10000 0 -10000 0 0
DLG7 0.013 0.011 -10000 0 -10000 0 0
AURKAIP1 0.026 0.011 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.047 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.027 0.021 -10000 0 -10000 0 0
AURKA 0.021 0.016 -10000 0 -10000 0 0
AURKB 0.012 0.023 -10000 0 -0.16 3 3
CDC25B 0.021 0.012 -10000 0 -10000 0 0
G2/M transition checkpoint 0.01 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.003 0.11 -10000 0 -0.4 34 34
Aurora A/CPEB -0.003 0.11 -10000 0 -0.4 34 34
Aurora A/TACC1/TRAP/chTOG 0.055 0.038 -10000 0 -0.38 1 1
BRCA1 0.026 0.007 -10000 0 -10000 0 0
centrosome duplication 0.03 0.024 -10000 0 -10000 0 0
regulation of centrosome cycle 0.043 0.023 -10000 0 -10000 0 0
spindle assembly 0.053 0.038 -10000 0 -0.37 1 1
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.055 0.033 -10000 0 -0.36 1 1
CENPA 0.015 0.033 -10000 0 -0.25 7 7
Aurora A/PP2A 0.03 0.024 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.022 0.02 -10000 0 -10000 0 0
negative regulation of DNA binding 0.026 0.012 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.01 0.019 -10000 0 -10000 0 0
mitotic prometaphase -0.004 0.011 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.016 -10000 0 -10000 0 0
TACC1 0.025 0.032 -10000 0 -0.67 1 1
TACC3 0.026 0.011 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.046 0.02 -10000 0 -10000 0 0
Aurora A/RasGAP 0.03 0.024 -10000 0 -10000 0 0
OAZ1 0.025 0.008 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.01 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.018 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.008 0.028 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.018 0.031 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
EPO signaling 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
BCL2L1 0.031 0.099 -10000 0 -10000 0 0
CRKL 0.014 0.048 0.46 3 -10000 0 3
mol:DAG 0.028 0.048 -10000 0 -10000 0 0
HRAS 0.034 0.064 0.35 6 -10000 0 6
MAPK8 0.013 0.069 -10000 0 -0.44 9 9
RAP1A 0.023 0.063 0.49 5 -10000 0 5
GAB1 0.021 0.054 0.46 3 -10000 0 3
MAPK14 0.021 0.033 -10000 0 -10000 0 0
EPO 0.018 0.023 -10000 0 -10000 0 0
PLCG1 0.028 0.048 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.023 0.022 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.027 0.093 -10000 0 -0.41 19 19
GAB1/SHC/GRB2/SOS1 0.047 0.045 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.03 0.028 -10000 0 -10000 0 0
IRS2 0.02 0.055 0.5 3 -10000 0 3
STAT1 0.029 0.072 -10000 0 -10000 0 0
STAT5B 0.027 0.061 -10000 0 -10000 0 0
cell proliferation 0.012 0.077 0.34 7 -0.41 9 16
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.042 -10000 0 -0.41 1 1
TEC 0.021 0.054 0.46 3 -10000 0 3
SOCS3 -0.001 0.13 -10000 0 -0.67 19 19
STAT1 (dimer) 0.029 0.071 -10000 0 -10000 0 0
JAK2 0.026 0.027 -10000 0 -0.34 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.059 0.054 -10000 0 -10000 0 0
EPO/EPOR 0.03 0.028 -10000 0 -10000 0 0
LYN 0.025 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.032 0.042 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.023 0.022 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.049 0.032 -10000 0 -10000 0 0
mol:IP3 0.028 0.048 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.047 -10000 0 -10000 0 0
SH2B3 0.028 0.008 -10000 0 -10000 0 0
NFKB1 0.021 0.033 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0.002 0.057 -10000 0 -0.26 18 18
PTPN6 0.022 0.048 0.31 1 -10000 0 1
TEC/VAV2/GRB2 0.042 0.045 -10000 0 -10000 0 0
EPOR 0.023 0.022 -10000 0 -10000 0 0
INPP5D 0.019 0.034 -10000 0 -10000 0 0
mol:GDP 0.046 0.045 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG2 0.026 0.006 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.03 0.043 -10000 0 -10000 0 0
VAV2 0.023 0.059 0.47 5 -10000 0 5
CBL 0.022 0.056 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.035 0.039 -10000 0 -10000 0 0
STAT5A 0.027 0.061 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.097 -10000 0 -0.42 1 1
LYN/PLCgamma2 0.039 0.011 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
BTK 0.01 0.059 -10000 0 -0.36 6 6
BCL2 -0.015 0.26 -10000 0 -0.9 37 37
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.023 0.055 -10000 0 -0.67 3 3
positive regulation of NF-kappaB transcription factor activity 0.036 0.043 -10000 0 -0.51 3 3
MAP2K4 0.027 0.046 -10000 0 -0.44 1 1
IKBKB 0.027 0.005 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.005 -10000 0 -10000 0 0
TNFRSF10A 0.023 0.055 -10000 0 -0.67 3 3
SMPD1 0.015 0.03 -10000 0 -0.34 3 3
IKBKG 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.036 0.043 -10000 0 -0.51 3 3
TRAIL/TRAILR3 0.004 0.067 -10000 0 -0.51 3 3
TRAIL/TRAILR1 0.033 0.061 -10000 0 -0.51 6 6
TRAIL/TRAILR4 0.036 0.043 -10000 0 -0.51 3 3
TRAIL/TRAILR1/DAP3/GTP 0.042 0.052 -10000 0 -0.4 6 6
IKK complex 0.025 0.051 -10000 0 -0.4 2 2
RIPK1 0.027 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.006 -10000 0 -10000 0 0
MAPK3 0.013 0.041 -10000 0 -0.51 3 3
MAP3K1 0.027 0.047 -10000 0 -0.37 4 4
TRAILR4 (trimer) 0.027 0.005 -10000 0 -10000 0 0
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.054 -10000 0 -0.67 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.043 -10000 0 -0.33 6 6
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.01 0.041 -10000 0 -0.5 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.071 0.054 -10000 0 -0.38 6 6
mol:ceramide 0.015 0.03 -10000 0 -0.34 3 3
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.016 0.071 0.28 1 -0.36 10 11
TRAF2 0.025 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.068 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.047 0.055 -10000 0 -0.44 6 6
DAP3 0.025 0.008 -10000 0 -10000 0 0
CASP10 0.01 0.04 -10000 0 -0.43 3 3
JNK cascade 0.036 0.043 -10000 0 -0.51 3 3
TRAIL (trimer) 0.023 0.055 -10000 0 -0.67 3 3
TNFRSF10C -0.014 0.068 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.053 0.052 -10000 0 -0.38 6 6
TRAIL/TRAILR2/FADD 0.05 0.04 -10000 0 -0.43 3 3
cell death 0.015 0.03 -10000 0 -0.34 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.035 -10000 0 -0.37 3 3
TRAILR2 (trimer) 0.027 0.005 -10000 0 -10000 0 0
CASP8 0.011 0.032 -10000 0 -0.58 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.074 0.041 -10000 0 -0.38 3 3
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.054 -10000 0 -0.67 3 3
ITGA4 0.02 0.058 -10000 0 -0.67 3 3
RAC1 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.016 0.095 -10000 0 -0.51 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.042 -10000 0 -0.44 3 3
alpha4/beta7 Integrin/Paxillin 0.032 0.077 -10000 0 -0.41 14 14
lamellipodium assembly 0.025 0.063 -10000 0 -0.53 5 5
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PI3K 0.036 0.043 -10000 0 -0.51 3 3
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.025 0.007 -10000 0 -10000 0 0
PXN 0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.053 0.035 -10000 0 -0.35 2 2
cell adhesion 0.051 0.04 -10000 0 -0.37 3 3
CRKL/CBL 0.029 0.019 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.042 0.038 -10000 0 -0.4 3 3
ITGB1 0.027 0.004 -10000 0 -10000 0 0
ITGB7 0.004 0.11 -10000 0 -0.65 12 12
ARF6/GDP 0.024 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.064 -10000 0 -0.43 7 7
p130Cas/Crk/Dock1 0.048 0.041 -10000 0 -0.44 3 3
VCAM1 0.018 0.071 -10000 0 -0.67 5 5
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.041 -10000 0 -0.37 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.037 -10000 0 -0.38 2 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.053 0.036 0.38 2 -10000 0 2
CBL 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.052 0.041 -10000 0 -0.37 3 3
Rac1/GTP 0.026 0.071 -10000 0 -0.61 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.063 0.03 -9999 0 -0.39 1 1
HDAC3 0.026 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -9999 0 -10000 0 0
GATA1/HDAC5 0.034 0.013 -9999 0 -10000 0 0
GATA2/HDAC5 0.038 0.011 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.049 0.028 -9999 0 -0.44 1 1
HDAC9 0.012 0.045 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.016 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.039 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.038 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -9999 0 -10000 0 0
GATA2 0.027 0.008 -9999 0 -10000 0 0
HDAC4/RFXANK 0.037 0.014 -9999 0 -10000 0 0
BCOR 0.026 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.02 0.013 -9999 0 -10000 0 0
HDAC5 0.026 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.027 -9999 0 -0.51 1 1
Histones 0.008 0.048 -9999 0 -10000 0 0
ADRBK1 0.027 0.005 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.011 -9999 0 -10000 0 0
HDAC7 0.027 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
TUBA1B 0.027 0.005 -9999 0 -10000 0 0
HDAC6 0.026 0.007 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.015 -9999 0 -10000 0 0
CAMK4 0.013 0.085 -9999 0 -0.67 7 7
Tubulin/HDAC6 0.047 0.048 -9999 0 -0.4 5 5
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.027 0.005 -9999 0 -10000 0 0
GATA1 0.012 0.021 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.007 -9999 0 -10000 0 0
NR3C1 0.026 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.29 1 1
SRF 0.027 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.039 0.009 -9999 0 -10000 0 0
Tubulin 0.034 0.055 -9999 0 -0.51 5 5
HDAC4/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
GNB1 0.026 0.006 -9999 0 -10000 0 0
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
BCL6/BCoR 0.037 0.027 -9999 0 -0.51 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.046 0.06 -9999 0 -0.44 7 7
HDAC4/ER alpha 0.008 0.11 -9999 0 -0.51 21 21
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.008 0.048 -9999 0 -10000 0 0
cell motility 0.046 0.048 -9999 0 -0.4 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -9999 0 -10000 0 0
BCL6 0.026 0.032 -9999 0 -0.67 1 1
HDAC4/CaMK II delta B 0.027 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.012 -9999 0 -10000 0 0
ESR1 -0.014 0.15 -9999 0 -0.65 23 23
HDAC6/HDAC11 0.038 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.052 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
MEF2C 0.025 0.032 -9999 0 -0.67 1 1
RAN 0.027 0.005 -9999 0 -10000 0 0
HDAC4/MEF2C 0.074 0.031 -9999 0 -0.38 1 1
GNG2 0.025 0.032 -9999 0 -0.67 1 1
NCOR2 0.027 0.005 -9999 0 -10000 0 0
TUBB2A 0.02 0.07 -9999 0 -0.67 5 5
HDAC11 0.027 0.004 -9999 0 -10000 0 0
HSP90AA1 0.027 0.005 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
ANKRA2 0.027 0.005 -9999 0 -10000 0 0
RFXANK 0.025 0.012 -9999 0 -10000 0 0
nuclear import -0.036 0.011 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.03 0.029 -10000 0 -10000 0 0
KLHL20 0.013 0.051 0.2 1 -10000 0 1
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.039 0.042 0.26 1 -10000 0 1
ENAH 0.028 0.027 -10000 0 -10000 0 0
AP1M1 0.025 0.008 -10000 0 -10000 0 0
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.035 0.016 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.032 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.055 0.072 -10000 0 -0.4 11 11
RAPGEF1 0.026 0.033 -10000 0 -10000 0 0
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.033 0.034 -10000 0 -10000 0 0
CRK 0.026 0.026 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.051 0.016 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.021 0.084 -10000 0 -0.51 11 11
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
DLG1 0.029 0.033 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.016 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.053 0.03 -10000 0 -0.4 1 1
PI3K 0.017 0.022 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.011 -10000 0 -10000 0 0
TIAM1 -0.059 0.081 -10000 0 -0.67 1 1
E-cadherin(dimer)/Ca2+ 0.061 0.017 -10000 0 -10000 0 0
AKT1 0.018 0.021 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.046 0.067 0.44 7 -10000 0 7
actin cytoskeleton organization 0.012 0.041 0.19 3 -10000 0 3
CDC42/GDP 0.046 0.075 0.48 9 -10000 0 9
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.008 -10000 0 -10000 0 0
ITGB7 0.004 0.11 -10000 0 -0.65 12 12
RAC1 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.066 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.012 -10000 0 -10000 0 0
mol:GDP 0.036 0.081 0.54 8 -10000 0 8
CDC42/GTP/IQGAP1 0.036 0.008 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.046 0.043 0.26 1 -10000 0 1
RAC1/GTP/IQGAP1 0.035 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.037 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.037 0.2 5 -10000 0 5
NME1 0.026 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.029 0.033 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.025 0.011 -10000 0 -10000 0 0
WASF2 0.007 0.022 -10000 0 -10000 0 0
Rap1/GTP 0.042 0.027 0.24 2 -10000 0 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.064 0.072 -10000 0 -0.38 11 11
CCND1 0.012 0.04 0.19 4 -10000 0 4
VAV2 0.006 0.14 -10000 0 -0.53 27 27
RAP1/GDP 0.048 0.039 0.3 5 -10000 0 5
adherens junction assembly 0.029 0.032 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.025 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.053 0.067 -10000 0 -0.37 11 11
E-cadherin/beta catenin 0.015 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.03 0.029 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
Rac1/GTP -0.006 0.076 -10000 0 -0.32 1 1
E-cadherin/beta catenin/alpha catenin 0.053 0.014 -10000 0 -10000 0 0
ITGAE 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.034 -10000 0 -10000 0 0
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 -0.003 0.14 -10000 0 -0.66 20 20
CLTC 0.029 0.022 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.019 0.015 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0.01 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
CD59 0.022 0.011 -10000 0 -10000 0 0
CPE 0.011 0.05 -10000 0 -0.44 6 6
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.02 0.013 -10000 0 -10000 0 0
CTNND1 0.022 0.037 0.36 3 -10000 0 3
DNM2 0.025 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.031 0.24 1 -10000 0 1
TSHR 0.015 0.029 -10000 0 -0.44 2 2
INS 0.007 0.073 -10000 0 -0.48 10 10
BIN1 0.027 0.005 -10000 0 -10000 0 0
mol:Choline 0.02 0.013 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.01 -10000 0 -10000 0 0
JUP 0.021 0.01 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.05 0.023 -10000 0 -0.4 1 1
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.021 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.009 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.033 0.014 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.047 0.025 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.01 -10000 0 -10000 0 0
ACAP1 0.024 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.01 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.029 0.024 -10000 0 -10000 0 0
JIP4/KLC1 0.049 0.014 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.033 0.014 -10000 0 -10000 0 0
RALA/GTP 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 0.02 0.029 0.36 1 -10000 0 1
NME1 0.016 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.032 0.036 0.34 3 -10000 0 3
IL2RA 0.008 0.055 -10000 0 -10000 0 0
VAMP3 0.016 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.024 0.071 -10000 0 -0.32 19 19
EXOC6 0.027 0.005 -10000 0 -10000 0 0
PLD1 0.018 0.005 -10000 0 -10000 0 0
PLD2 0.018 0.006 -10000 0 -10000 0 0
EXOC5 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.012 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.007 -10000 0 -10000 0 0
EXOC7 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.049 0.026 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.02 0.013 -10000 0 -10000 0 0
endocytosis -0.048 0.023 0.4 1 -10000 0 1
SCAMP2 0.027 0.004 -10000 0 -10000 0 0
ADRB2 0.03 0.084 0.43 9 -10000 0 9
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ASAP2 0.025 0.032 -10000 0 -0.67 1 1
Dynamin 2/GDP 0.03 0.011 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 0.029 0.082 0.46 7 -10000 0 7
RALA 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.026 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.025 0.018 -9999 0 -9999 0 0
PLK4 0.027 0.004 -9999 0 -9999 0 0
regulation of centriole replication 0.016 0.011 -9999 0 -9999 0 0
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 -0.004 0.042 -10000 0 -10000 0 0
regulation of axonogenesis -0.011 0.021 0.27 2 -10000 0 2
myoblast fusion -0.01 0.028 -10000 0 -10000 0 0
mol:GTP 0.008 0.019 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.024 0.063 0.41 1 -10000 0 1
ARF1/GTP 0.03 0.014 -10000 0 -10000 0 0
mol:GM1 0.004 0.012 -10000 0 -10000 0 0
mol:Choline 0.008 0.014 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.027 -10000 0 -10000 0 0
MAPK3 0.008 0.027 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.024 0.064 -10000 0 -0.42 1 1
ARF1 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.01 0.028 -10000 0 -10000 0 0
ARF1/GDP 0.02 0.03 -10000 0 -10000 0 0
ARF6 0.03 0.009 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 -0.061 0.082 -10000 0 -0.67 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.025 -10000 0 -10000 0 0
actin filament bundle formation -0.023 0.03 -10000 0 -10000 0 0
KALRN 0.009 0.021 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.03 -10000 0 -10000 0 0
NME1 0.026 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.027 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.008 0.019 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.015 0.027 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
liver development 0.008 0.019 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.019 -10000 0 -10000 0 0
RhoA/GTP 0.031 0.012 -10000 0 -10000 0 0
mol:GDP 0.008 0.021 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.045 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
PLD1 0.012 0.018 -10000 0 -10000 0 0
RAB11FIP3 0.026 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.015 0.027 -10000 0 -10000 0 0
ruffle organization 0.011 0.021 -10000 0 -0.27 2 2
regulation of epithelial cell migration 0.008 0.019 -10000 0 -10000 0 0
PLD2 0.012 0.017 -10000 0 -10000 0 0
PIP5K1A 0.011 0.021 -10000 0 -0.27 2 2
mol:Phosphatidic acid 0.008 0.014 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.027 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.045 -9999 0 -0.67 2 2
Aurora C/Aurora B/INCENP 0.046 0.041 -9999 0 -0.45 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.014 -9999 0 -10000 0 0
AURKB -0.007 0.063 -9999 0 -10000 0 0
AURKC 0.02 0.03 -9999 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.02 0.076 -9999 0 -0.67 1 1
GPC2 0.016 0.038 -9999 0 -10000 0 0
GPC2/Midkine -0.004 0.061 -9999 0 -0.3 1 1
neuron projection morphogenesis -0.004 0.061 -9999 0 -0.3 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.001 0.014 -9999 0 -10000 0 0
MDM2/SUMO1 0.015 0.054 -9999 0 -0.22 1 1
HDAC4 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.001 0.013 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.007 0.035 -9999 0 -0.24 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.012 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.29 1 1
SUMO1/HDAC1 0.014 0.057 -9999 0 -0.27 2 2
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.066 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.009 -9999 0 -10000 0 0
Ran/GTP 0.006 0.048 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.046 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
PIAS2 0.027 0.004 -9999 0 -10000 0 0
PIAS1 0.027 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.039 0.009 -9999 0 -9999 0 0
CTNNB1 0.027 0.003 -9999 0 -9999 0 0
JUP 0.026 0.007 -9999 0 -9999 0 0
CDH1 0.026 0.006 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.017 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.025 0.034 0.2 2 -0.17 2 4
AP2 0.038 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.036 0.011 -10000 0 -10000 0 0
CLTB 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.009 -10000 0 -10000 0 0
CD4 0.021 0.03 -10000 0 -10000 0 0
CLTA 0.025 0.007 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.024 -10000 0 -0.37 2 2
ARF1/GTP 0.028 0.02 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.015 0.007 -10000 0 -10000 0 0
mol:Choline 0.006 0.024 -10000 0 -0.37 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.026 0.009 -10000 0 -10000 0 0
DDEF1 0.007 0.028 -10000 0 -0.37 2 2
ARF1/GDP 0.005 0.017 -10000 0 -10000 0 0
AP2M1 0.027 0.003 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.015 -10000 0 -10000 0 0
ARFIP2 0.022 0.013 -10000 0 -10000 0 0
COPA 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.033 -10000 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.018 0.007 -10000 0 -10000 0 0
GGA3 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.022 -10000 0 -0.28 1 1
AP2A1 0.025 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.009 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.026 0.024 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.034 0.011 -10000 0 -10000 0 0
CYTH2 0.028 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.02 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.025 0.025 -10000 0 -10000 0 0
PLD2 0.006 0.024 -10000 0 -0.37 2 2
ARF-GAP1/v-SNARE 0.009 0.002 -10000 0 -10000 0 0
PIP5K1A 0.006 0.024 -10000 0 -0.37 2 2
ARF1/GTP/Membrin/GBF1/p115 0.023 0.02 -10000 0 -0.19 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.024 -10000 0 -0.37 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.014 0.013 -10000 0 -10000 0 0
USO1 0.014 0.013 -10000 0 -10000 0 0
GBF1 0.013 0.024 -10000 0 -0.3 2 2
ARF1/GTP/Arfaptin 2 0.035 0.014 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.052 0.017 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.038 0.011 -9999 0 -9999 0 0
FBXW11 0.026 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.072 0.027 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -9999 0 0
RELB 0.026 0.007 -9999 0 -9999 0 0
NFKB2 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 497 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QD.A8IV TCGA.MK.A84Z TCGA.MK.A4N9 TCGA.MK.A4N7
109_MAP3K5 -0.065 0.053 -0.2 0.025
47_PPARGC1A 0.028 0 -0.67 -0.67
105_BMP4 0.028 0.028 0.028 -0.13
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 0.028 0.028 0.028
105_BMP2 0.028 0.028 0.028 0.028
131_RELN/VLDLR 0.064 -0.22 -0.4 -0.4
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.027
84_STAT5B 0.04 0.053 0.04 -0.05
84_STAT5A 0.04 0.053 0.04 -0.05
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/22319926/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/THCA-TP/22489308/GDAC_Gistic2Report_22489313/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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