PARADIGM pathway analysis of mRNA expression and copy number data
Colon Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1251GGV
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 31 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
TCGA08_retinoblastoma 86
Signaling events mediated by Stem cell factor receptor (c-Kit) 45
Fc-epsilon receptor I signaling in mast cells 36
BCR signaling pathway 35
HIF-1-alpha transcription factor network 31
IGF1 pathway 28
FAS signaling pathway (CD95) 23
Syndecan-1-mediated signaling events 21
Visual signal transduction: Rods 20
Arf6 signaling events 15
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 153 . 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 ( 153 ).

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
TCGA08_retinoblastoma 0.5621 86 693 8 -0.37 0.2 1000 -1000 -0.006 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2941 45 3583 78 -0.99 0.26 1000 -1000 -0.054 -1000
Fc-epsilon receptor I signaling in mast cells 0.2353 36 3553 97 -0.33 0.042 1000 -1000 -0.082 -1000
BCR signaling pathway 0.2288 35 3526 99 -0.36 0.035 1000 -1000 -0.057 -1000
HIF-1-alpha transcription factor network 0.2026 31 2375 76 -0.75 0.041 1000 -1000 -0.082 -1000
IGF1 pathway 0.1830 28 1631 57 -0.3 0.096 1000 -1000 -0.045 -1000
FAS signaling pathway (CD95) 0.1503 23 1127 47 -0.17 0.11 1000 -1000 -0.03 -1000
Syndecan-1-mediated signaling events 0.1373 21 731 34 -0.3 0.034 1000 -1000 -0.04 -1000
Visual signal transduction: Rods 0.1307 20 1075 52 -0.41 0.07 1000 -1000 -0.031 -1000
Arf6 signaling events 0.0980 15 954 62 -0.14 0.082 1000 -1000 -0.02 -1000
HIF-2-alpha transcription factor network 0.0915 14 607 43 -0.56 0.33 1000 -1000 -0.045 -1000
Wnt signaling 0.0915 14 100 7 -0.048 0.034 1000 -1000 -0.023 -1000
EGFR-dependent Endothelin signaling events 0.0915 14 312 21 -0.11 0.049 1000 -1000 -0.046 -1000
Syndecan-2-mediated signaling events 0.0784 12 867 69 -0.3 0.056 1000 -1000 -0.027 -1000
BMP receptor signaling 0.0784 12 995 81 -0.23 0.067 1000 -1000 -0.055 -1000
Reelin signaling pathway 0.0784 12 687 56 -0.27 0.093 1000 -1000 -0.042 -1000
TRAIL signaling pathway 0.0784 12 618 48 -0.11 0.035 1000 -1000 -0.045 -1000
Endothelins 0.0784 12 1223 96 -0.42 0.091 1000 -1000 -0.047 -1000
IL6-mediated signaling events 0.0784 12 910 75 -0.29 0.069 1000 -1000 -0.058 -1000
FOXA2 and FOXA3 transcription factor networks 0.0719 11 509 46 -0.73 0.039 1000 -1000 -0.098 -1000
Glypican 1 network 0.0719 11 566 48 -0.23 0.053 1000 -1000 -0.03 -1000
TCGA08_p53 0.0719 11 82 7 -0.062 0.033 1000 -1000 -0.006 -1000
IL12-mediated signaling events 0.0654 10 956 87 -0.38 0.069 1000 -1000 -0.065 -1000
IL4-mediated signaling events 0.0654 10 953 91 -0.53 0.33 1000 -1000 -0.12 -1000
IL1-mediated signaling events 0.0654 10 620 62 -0.24 0.065 1000 -1000 -0.043 -1000
Signaling events mediated by PRL 0.0654 10 368 34 -0.061 0.097 1000 -1000 -0.033 -1000
FOXM1 transcription factor network 0.0654 10 520 51 -0.34 0.034 1000 -1000 -0.11 -1000
Visual signal transduction: Cones 0.0588 9 366 38 -0.11 0.056 1000 -1000 -0.008 -1000
Syndecan-3-mediated signaling events 0.0588 9 335 35 -0.3 0.061 1000 -1000 -0.032 -1000
PLK2 and PLK4 events 0.0523 8 26 3 -0.001 0.02 1000 -1000 -0.008 -1000
Ceramide signaling pathway 0.0523 8 646 76 -0.29 0.078 1000 -1000 -0.039 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0458 7 418 54 -0.27 0.042 1000 -1000 -0.051 -1000
Signaling events mediated by the Hedgehog family 0.0458 7 410 52 -0.078 0.057 1000 -1000 -0.037 -1000
Thromboxane A2 receptor signaling 0.0458 7 823 105 -0.35 0.081 1000 -1000 -0.048 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0458 7 612 85 -0.12 0.069 1000 -1000 -0.05 -1000
p75(NTR)-mediated signaling 0.0458 7 875 125 -0.3 0.079 1000 -1000 -0.058 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0458 7 413 52 -0.42 0.11 1000 -1000 -0.05 -1000
IL2 signaling events mediated by PI3K 0.0458 7 462 58 -0.54 0.042 1000 -1000 -0.039 -1000
Canonical Wnt signaling pathway 0.0458 7 384 51 -0.22 0.17 1000 -1000 -0.055 -1000
Regulation of nuclear SMAD2/3 signaling 0.0392 6 926 136 -1.2 0.1 1000 -1000 -0.049 -1000
Osteopontin-mediated events 0.0392 6 257 38 -0.22 0.048 1000 -1000 -0.053 -1000
Presenilin action in Notch and Wnt signaling 0.0392 6 419 61 -0.22 0.12 1000 -1000 -0.044 -1000
PDGFR-alpha signaling pathway 0.0392 6 269 44 -0.034 0.075 1000 -1000 -0.036 -1000
amb2 Integrin signaling 0.0392 6 515 82 -0.24 0.049 1000 -1000 -0.038 -1000
Glucocorticoid receptor regulatory network 0.0392 6 767 114 -0.31 0.23 1000 -1000 -0.057 -1000
Ephrin B reverse signaling 0.0392 6 291 48 -0.085 0.049 1000 -1000 -0.031 -1000
TCR signaling in naïve CD8+ T cells 0.0392 6 629 93 -0.068 0.049 1000 -1000 -0.051 -1000
Glypican 2 network 0.0392 6 24 4 0 0.012 1000 -1000 0 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0392 6 504 74 -0.29 0.067 1000 -1000 -0.062 -1000
Noncanonical Wnt signaling pathway 0.0327 5 135 26 -0.048 0.034 1000 -1000 -0.044 -1000
a4b1 and a4b7 Integrin signaling 0.0327 5 25 5 0.001 0.043 1000 -1000 0.007 -1000
Signaling events mediated by PTP1B 0.0327 5 391 76 -0.28 0.056 1000 -1000 -0.06 -1000
EPO signaling pathway 0.0327 5 282 55 -0.48 0.035 1000 -1000 -0.037 -1000
PLK1 signaling events 0.0327 5 497 85 -0.096 0.069 1000 -1000 -0.042 -1000
Nectin adhesion pathway 0.0327 5 329 63 -0.3 0.085 1000 -1000 -0.049 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0327 5 188 37 -0.12 0.076 1000 -1000 -0.028 -1000
Integrins in angiogenesis 0.0327 5 480 84 -0.29 0.085 1000 -1000 -0.048 -1000
Calcium signaling in the CD4+ TCR pathway 0.0327 5 156 31 -0.15 0.04 1000 -1000 -0.051 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0327 5 392 68 -0.37 0.06 1000 -1000 -0.085 -1000
IL23-mediated signaling events 0.0327 5 350 60 -0.28 0.034 1000 -1000 -0.094 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0327 5 181 33 -0.11 0.079 1000 -1000 -0.041 -1000
Regulation of Androgen receptor activity 0.0327 5 418 70 -0.52 0.063 1000 -1000 -0.069 -1000
Aurora B signaling 0.0327 5 364 67 -0.13 0.047 1000 -1000 -0.043 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0261 4 125 28 -0.027 0.044 1000 -1000 -0.021 -1000
Cellular roles of Anthrax toxin 0.0261 4 191 39 -0.051 0.034 1000 -1000 -0.026 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0261 4 217 45 -0.097 0.062 1000 -1000 -0.047 -1000
EPHB forward signaling 0.0261 4 351 85 -0.086 0.11 1000 -1000 -0.066 -1000
Regulation of p38-alpha and p38-beta 0.0261 4 243 54 -0.079 0.064 1000 -1000 -0.056 -1000
IL27-mediated signaling events 0.0261 4 249 51 -0.15 0.034 1000 -1000 -0.062 -1000
TCGA08_rtk_signaling 0.0261 4 119 26 -0.12 0.068 1000 -1000 -0.01 -1000
Class I PI3K signaling events 0.0261 4 307 73 -0.24 0.061 1000 -1000 -0.047 -1000
Syndecan-4-mediated signaling events 0.0261 4 302 67 -0.36 0.1 1000 -1000 -0.043 -1000
Plasma membrane estrogen receptor signaling 0.0261 4 395 86 -0.29 0.1 1000 -1000 -0.061 -1000
VEGFR1 specific signals 0.0261 4 279 56 -0.004 0.1 1000 -1000 -0.044 -1000
ErbB4 signaling events 0.0196 3 209 69 -0.2 0.099 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class III 0.0196 3 151 40 -0.2 0.064 1000 -1000 -0.023 -1000
ceramide signaling pathway 0.0196 3 195 49 -0.17 0.061 1000 -1000 -0.048 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0196 3 313 83 -0.17 0.093 1000 -1000 -0.034 -1000
FoxO family signaling 0.0196 3 201 64 -0.18 0.062 1000 -1000 -0.063 -1000
Signaling mediated by p38-gamma and p38-delta 0.0196 3 56 15 -0.029 0.034 1000 -1000 -0.028 -1000
Signaling mediated by p38-alpha and p38-beta 0.0196 3 135 44 -0.16 0.034 1000 -1000 -0.031 -1000
Effects of Botulinum toxin 0.0196 3 78 26 -0.019 0.065 1000 -1000 -0.012 -1000
Nongenotropic Androgen signaling 0.0196 3 160 52 -0.038 0.079 1000 -1000 -0.031 -1000
Arf6 trafficking events 0.0196 3 273 71 -0.098 0.055 1000 -1000 -0.029 -1000
Regulation of Telomerase 0.0196 3 359 102 -0.14 0.08 1000 -1000 -0.039 -1000
S1P3 pathway 0.0196 3 137 42 -0.026 0.05 1000 -1000 -0.039 -1000
Ras signaling in the CD4+ TCR pathway 0.0196 3 66 17 0 0.057 1000 -1000 -0.019 -1000
Caspase cascade in apoptosis 0.0131 2 184 74 -0.08 0.05 1000 -1000 -0.045 -1000
Coregulation of Androgen receptor activity 0.0131 2 172 76 -0.083 0.067 1000 -1000 -0.034 -1000
Canonical NF-kappaB pathway 0.0131 2 92 39 -0.022 0.076 1000 -1000 -0.031 -1000
BARD1 signaling events 0.0131 2 140 57 -0.055 0.07 1000 -1000 -0.051 -1000
JNK signaling in the CD4+ TCR pathway 0.0131 2 35 17 -0.006 0.076 1000 -1000 -0.031 -1000
Aurora A signaling 0.0131 2 123 60 -0.011 0.086 1000 -1000 -0.013 -1000
Arf6 downstream pathway 0.0131 2 126 43 -0.05 0.051 1000 -1000 -0.034 -1000
mTOR signaling pathway 0.0131 2 144 53 -0.067 0.047 1000 -1000 -0.041 -1000
IFN-gamma pathway 0.0131 2 172 68 -0.044 0.058 1000 -1000 -0.054 -1000
Class I PI3K signaling events mediated by Akt 0.0131 2 202 68 -0.057 0.081 1000 -1000 -0.041 -1000
S1P1 pathway 0.0131 2 102 36 -0.037 0.035 1000 -1000 -0.053 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0131 2 270 125 -0.03 0.12 1000 -1000 -0.048 -1000
LPA receptor mediated events 0.0131 2 213 102 -0.1 0.051 1000 -1000 -0.07 -1000
E-cadherin signaling in the nascent adherens junction 0.0131 2 227 76 -0.031 0.099 1000 -1000 -0.063 -1000
Insulin Pathway 0.0131 2 164 74 -0.033 0.1 1000 -1000 -0.037 -1000
S1P4 pathway 0.0131 2 57 25 -0.027 0.044 1000 -1000 -0.026 -1000
E-cadherin signaling events 0.0131 2 14 5 0.019 0.054 1000 -1000 0.012 -1000
LPA4-mediated signaling events 0.0065 1 14 12 -0.005 0.03 1000 -1000 -0.021 -1000
ErbB2/ErbB3 signaling events 0.0065 1 67 65 -0.009 0.062 1000 -1000 -0.071 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0065 1 26 23 0.011 0.045 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class II 0.0065 1 75 75 -0.023 0.067 1000 -1000 -0.028 -1000
Ephrin A reverse signaling 0.0065 1 13 7 0 0.038 1000 -1000 -0.007 -1000
Hedgehog signaling events mediated by Gli proteins 0.0065 1 124 65 -0.051 0.078 1000 -1000 -0.053 -1000
Insulin-mediated glucose transport 0.0065 1 35 32 -0.03 0.054 1000 -1000 -0.025 -1000
S1P5 pathway 0.0065 1 27 17 -0.027 0.035 1000 -1000 -0.016 -1000
Retinoic acid receptors-mediated signaling 0.0065 1 82 58 -0.011 0.067 1000 -1000 -0.042 -1000
Paxillin-dependent events mediated by a4b1 0.0065 1 65 36 -0.068 0.072 1000 -1000 -0.036 -1000
IL2 signaling events mediated by STAT5 0.0065 1 34 22 -0.019 0.074 1000 -1000 -0.045 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0065 1 129 88 -0.092 0.12 1000 -1000 -0.072 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0065 1 141 120 -0.026 0.093 1000 -1000 -0.05 -1000
PDGFR-beta signaling pathway 0.0065 1 175 97 -0.1 0.1 1000 -1000 -0.05 -1000
E-cadherin signaling in keratinocytes 0.0065 1 43 43 -0.054 0.1 1000 -1000 -0.031 -1000
Arf1 pathway 0.0065 1 103 54 0 0.081 1000 -1000 -0.016 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0000 0 17 34 -0.047 0.094 1000 -1000 -0.036 -1000
Circadian rhythm pathway 0.0000 0 19 22 -0.01 0.078 1000 -1000 -0.047 -1000
Aurora C signaling 0.0000 0 3 7 0 0.048 1000 -1000 -0.023 -1000
Signaling events regulated by Ret tyrosine kinase 0.0000 0 43 82 0 0.073 1000 -1000 -0.066 -1000
Signaling events mediated by HDAC Class I 0.0000 0 65 104 -0.065 0.082 1000 -1000 -0.031 -1000
Atypical NF-kappaB pathway 0.0000 0 2 31 0 0.069 1000 -1000 -0.026 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 5 27 0 0.06 1000 -1000 -0.039 -1000
Rapid glucocorticoid signaling 0.0000 0 3 20 0 0.039 1000 -1000 -0.004 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.034 0.034 1000 -1000 -0.009 -1000
p38 MAPK signaling pathway 0.0000 0 16 44 -0.001 0.069 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 0 0.091 1000 -1000 0 -1000
Total NA 890 53577 7203 -22 9.6 131000 -131000 -5.4 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.37 0.21 -10000 0 -0.48 114 114
CDKN2C 0.04 0.051 -10000 0 -0.48 1 1
CDKN2A -0.085 0.17 -10000 0 -0.32 48 48
CCND2 0.18 0.093 0.23 114 -10000 0 114
RB1 -0.16 0.1 0.2 1 -0.23 91 92
CDK4 0.19 0.093 0.23 114 -10000 0 114
CDK6 0.2 0.1 0.25 114 -10000 0 114
G1/S progression 0.17 0.11 0.23 94 -0.26 2 96
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 -0.24 0.2 0.28 1 -0.42 69 70
CRKL -0.26 0.2 -10000 0 -0.44 70 70
HRAS -0.2 0.19 -10000 0 -0.38 62 62
mol:PIP3 -0.23 0.19 -10000 0 -0.41 64 64
SPRED1 0.027 0.041 -10000 0 -0.32 2 2
SPRED2 0.035 0 -10000 0 -10000 0 0
GAB1 -0.27 0.22 -10000 0 -0.46 71 71
FOXO3 -0.25 0.22 -10000 0 -0.44 68 68
AKT1 -0.27 0.24 -10000 0 -0.47 70 70
BAD -0.25 0.22 -10000 0 -0.44 68 68
megakaryocyte differentiation -0.28 0.21 -10000 0 -0.46 75 75
GSK3B -0.25 0.22 -10000 0 -0.44 67 67
RAF1 -0.17 0.15 -10000 0 -0.32 45 45
SHC1 0.033 0.006 -10000 0 -10000 0 0
STAT3 -0.26 0.22 -10000 0 -0.46 70 70
STAT1 -0.72 0.56 -10000 0 -1.1 93 93
HRAS/SPRED1 -0.17 0.16 -10000 0 -0.33 36 36
cell proliferation -0.26 0.21 -10000 0 -0.45 71 71
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
TEC 0.034 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.27 0.23 -10000 0 -0.47 72 72
HRAS/SPRED2 -0.17 0.16 -10000 0 -0.32 44 44
LYN/TEC/p62DOK -0.23 0.22 -10000 0 -0.43 62 62
MAPK3 -0.12 0.11 -10000 0 -0.28 11 11
STAP1 -0.38 0.27 -10000 0 -0.57 87 87
GRAP2 0.032 0.009 -10000 0 -10000 0 0
JAK2 -0.55 0.44 -10000 0 -0.92 75 75
STAT1 (dimer) -0.7 0.54 -10000 0 -1 100 100
mol:Gleevec 0.011 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.25 0.24 -10000 0 -0.46 71 71
actin filament polymerization -0.26 0.21 -10000 0 -0.45 71 71
LYN 0.03 0.012 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.48 0.33 -10000 0 -0.73 86 86
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.22 0.2 -10000 0 -0.41 66 66
PI3K -0.24 0.23 -10000 0 -0.44 70 70
PTEN 0.025 0.064 -10000 0 -0.51 2 2
SCF/KIT/EPO/EPOR -0.78 0.68 -10000 0 -1.5 70 70
MAPK8 -0.27 0.21 -10000 0 -0.46 71 71
STAT3 (dimer) -0.26 0.21 -10000 0 -0.45 70 70
positive regulation of transcription -0.099 0.091 -10000 0 -0.23 11 11
mol:GDP -0.22 0.2 -10000 0 -0.4 68 68
PIK3C2B -0.26 0.22 -10000 0 -0.46 71 71
CBL/CRKL -0.24 0.2 -10000 0 -0.42 69 69
FER -0.27 0.21 -10000 0 -0.46 70 70
SH2B3 -0.27 0.21 -10000 0 -0.46 71 71
PDPK1 -0.21 0.18 -10000 0 -0.38 64 64
SNAI2 -0.26 0.21 -10000 0 -0.45 69 69
positive regulation of cell proliferation -0.48 0.36 -10000 0 -0.79 74 74
KITLG -0.02 0.061 -10000 0 -0.45 2 2
cell motility -0.48 0.36 -10000 0 -0.79 74 74
PTPN6 0.048 0.013 -10000 0 -10000 0 0
EPOR -0.19 0.19 -10000 0 -1.1 2 2
STAT5A (dimer) -0.38 0.29 -10000 0 -0.64 72 72
SOCS1 0.034 0.003 -10000 0 -10000 0 0
cell migration 0.26 0.21 0.45 71 -10000 0 71
SOS1 0.035 0 -10000 0 -10000 0 0
EPO -0.007 0.037 -10000 0 -0.33 1 1
VAV1 -0.003 0.14 -10000 0 -0.51 10 10
GRB10 -0.26 0.21 -10000 0 -0.45 71 71
PTPN11 0.043 0.031 -10000 0 -0.32 1 1
SCF/KIT -0.28 0.23 -10000 0 -0.48 71 71
GO:0007205 0.015 0.01 -10000 0 -10000 0 0
MAP2K1 -0.13 0.12 -10000 0 -0.3 12 12
CBL 0.034 0.006 -10000 0 -10000 0 0
KIT -0.74 0.71 -10000 0 -1.5 70 70
MAP2K2 -0.13 0.12 -10000 0 -0.3 12 12
SHC/Grb2/SOS1 -0.23 0.22 -10000 0 -0.44 67 67
STAT5A -0.39 0.3 -10000 0 -0.66 72 72
GRB2 0.033 0.007 -10000 0 -10000 0 0
response to radiation -0.25 0.21 -10000 0 -0.44 69 69
SHC/GRAP2 0.046 0.016 -10000 0 -10000 0 0
PTPRO -0.28 0.22 -10000 0 -0.47 75 75
SH2B2 -0.27 0.21 -10000 0 -0.46 71 71
DOK1 0.032 0.029 -10000 0 -0.32 1 1
MATK -0.26 0.21 -10000 0 -0.46 71 71
CREBBP -0.071 0.083 -10000 0 -10000 0 0
BCL2 -0.99 0.75 -10000 0 -1.6 91 91
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.033 0.18 -10000 0 -0.51 18 18
LAT2 -0.21 0.21 -10000 0 -0.38 80 80
AP1 -0.26 0.3 -10000 0 -0.56 57 57
mol:PIP3 -0.27 0.25 0.28 1 -0.52 61 62
IKBKB -0.13 0.15 0.2 7 -0.27 58 65
AKT1 -0.2 0.18 0.31 1 -0.42 49 50
IKBKG -0.14 0.14 0.22 1 -0.28 60 61
MS4A2 -0.28 0.27 -10000 0 -0.51 83 83
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
MAP3K1 -0.21 0.21 -10000 0 -0.44 58 58
mol:Ca2+ -0.2 0.19 0.25 1 -0.38 61 62
LYN 0.026 0.013 -10000 0 -10000 0 0
CBLB -0.21 0.2 -10000 0 -0.37 80 80
SHC1 0.033 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.041 0.09 -10000 0 -0.29 10 10
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.23 0.22 0.34 1 -0.43 68 69
PTPN13 -0.25 0.24 -10000 0 -0.58 25 25
PTPN11 0.007 0.042 -10000 0 -0.34 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.16 0.15 -10000 0 -0.33 49 49
SYK 0.03 0.008 -10000 0 -10000 0 0
GRB2 0.032 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.26 0.27 -10000 0 -0.49 77 77
LAT -0.21 0.21 -10000 0 -0.38 81 81
PAK2 -0.24 0.24 -10000 0 -0.49 58 58
NFATC2 -0.061 0.066 -10000 0 -10000 0 0
HRAS -0.26 0.26 -10000 0 -0.52 61 61
GAB2 0.034 0.005 -10000 0 -10000 0 0
PLA2G1B 0.03 0.16 -10000 0 -0.91 4 4
Fc epsilon R1 -0.28 0.27 -10000 0 -0.46 94 94
Antigen/IgE/Fc epsilon R1 -0.25 0.25 -10000 0 -0.42 94 94
mol:GDP -0.28 0.29 -10000 0 -0.56 62 62
JUN 0.022 0.064 -10000 0 -0.32 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.032 0.005 -10000 0 -10000 0 0
FOS 0.003 0.11 -10000 0 -0.46 8 8
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.22 0.22 -10000 0 -0.39 82 82
CHUK -0.14 0.14 0.22 1 -0.28 61 62
KLRG1 -0.19 0.19 -10000 0 -0.38 62 62
VAV1 -0.23 0.22 -10000 0 -0.4 82 82
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.21 0.21 -10000 0 -0.38 80 80
negative regulation of mast cell degranulation -0.18 0.18 -10000 0 -0.37 57 57
BTK -0.29 0.33 -10000 0 -0.62 59 59
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.33 0.33 -10000 0 -0.62 72 72
GAB2/PI3K/SHP2 -0.22 0.2 -10000 0 -0.43 55 55
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.23 0.22 -10000 0 -0.48 57 57
RAF1 0.032 0.18 -10000 0 -1 4 4
Fc epsilon R1/FcgammaRIIB/SHIP -0.28 0.3 -10000 0 -0.47 96 96
FCER1G 0.042 0.013 -10000 0 -10000 0 0
FCER1A -0.23 0.28 -10000 0 -0.52 68 68
Antigen/IgE/Fc epsilon R1/Fyn -0.23 0.24 -10000 0 -0.4 94 94
MAPK3 0.03 0.16 -10000 0 -0.91 4 4
MAPK1 0.024 0.17 -10000 0 -0.94 4 4
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.19 0.35 -10000 0 -0.83 30 30
DUSP1 0.001 0.13 -10000 0 -0.51 9 9
NF-kappa-B/RelA -0.076 0.097 -10000 0 -0.19 6 6
actin cytoskeleton reorganization -0.22 0.22 -10000 0 -0.59 9 9
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.22 0.24 -10000 0 -0.48 58 58
FER -0.22 0.21 -10000 0 -0.38 80 80
RELA 0.034 0.006 -10000 0 -10000 0 0
ITK -0.046 0.061 -10000 0 -0.34 2 2
SOS1 0.035 0 -10000 0 -10000 0 0
PLCG1 -0.23 0.29 0.28 1 -0.52 59 60
cytokine secretion -0.061 0.062 -10000 0 -10000 0 0
SPHK1 -0.23 0.21 -10000 0 -0.39 83 83
PTK2 -0.23 0.23 -10000 0 -0.67 7 7
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.27 0.29 0.22 3 -0.49 82 85
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.28 0.27 0.29 1 -0.54 63 64
MAP2K2 0.025 0.16 -10000 0 -0.92 4 4
MAP2K1 0.024 0.17 -10000 0 -0.95 4 4
MAP2K7 0.034 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.16 0.18 -10000 0 -0.36 55 55
MAP2K4 -0.2 0.43 -10000 0 -0.96 35 35
Fc epsilon R1/FcgammaRIIB -0.3 0.32 -10000 0 -0.5 96 96
mol:Choline -0.23 0.21 0.34 1 -0.42 68 69
SHC/Grb2/SOS1 -0.18 0.22 -10000 0 -0.41 55 55
FYN 0.031 0.029 -10000 0 -0.32 1 1
DOK1 0.032 0.029 -10000 0 -0.32 1 1
PXN -0.21 0.22 -10000 0 -0.61 7 7
HCLS1 -0.22 0.22 -10000 0 -0.39 81 81
PRKCB -0.2 0.19 0.25 1 -0.38 63 64
FCGR2B -0.078 0.22 -10000 0 -0.51 30 30
IGHE -0.007 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.18 0.18 -10000 0 -0.38 57 57
LCP2 0.025 0.061 -10000 0 -0.38 3 3
PLA2G4A -0.27 0.24 -10000 0 -0.44 86 86
RASA1 0.031 0.029 -10000 0 -0.32 1 1
mol:Phosphatidic acid -0.23 0.21 0.34 1 -0.42 68 69
IKK complex -0.093 0.12 0.19 6 -0.22 24 30
WIPF1 0.034 0.003 -10000 0 -10000 0 0
BCR 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
JUN -0.2 0.26 -10000 0 -0.5 54 54
IKBKB -0.089 0.13 -10000 0 -0.31 8 8
AKT1 -0.11 0.14 -10000 0 -0.27 47 47
IKBKG -0.098 0.14 -10000 0 -0.3 13 13
CALM1 -0.28 0.32 -10000 0 -0.59 66 66
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
MAP3K1 -0.24 0.36 -10000 0 -0.66 55 55
MAP3K7 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.3 0.35 -10000 0 -0.63 67 67
DOK1 0.032 0.029 -10000 0 -0.32 1 1
AP-1 -0.13 0.14 -10000 0 -0.29 53 53
LYN 0.03 0.012 -10000 0 -10000 0 0
BLNK 0.017 0.089 -10000 0 -0.51 4 4
SHC1 0.033 0.006 -10000 0 -10000 0 0
BCR complex -0.24 0.3 -10000 0 -0.53 71 71
CD22 -0.27 0.38 -10000 0 -0.76 50 50
CAMK2G -0.26 0.29 -10000 0 -0.54 66 66
CSNK2A1 0.027 0.015 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.15 0.21 -10000 0 -0.44 40 40
GO:0007205 -0.31 0.36 -10000 0 -0.65 67 67
SYK 0.034 0.006 -10000 0 -10000 0 0
ELK1 -0.29 0.33 -10000 0 -0.6 67 67
NFATC1 -0.29 0.35 -10000 0 -0.67 60 60
B-cell antigen/BCR complex -0.24 0.3 -10000 0 -0.53 71 71
PAG1/CSK -0.09 0.19 -10000 0 -0.37 46 46
NFKBIB -0.015 0.055 -10000 0 -0.14 5 5
HRAS -0.24 0.28 0.23 1 -0.54 62 63
NFKBIA -0.013 0.053 -10000 0 -0.13 5 5
NF-kappa-B/RelA/I kappa B beta -0.004 0.047 -10000 0 -10000 0 0
RasGAP/Csk -0.2 0.31 -10000 0 -0.48 73 73
mol:GDP -0.29 0.34 -10000 0 -0.61 67 67
PTEN 0.025 0.064 -10000 0 -0.51 2 2
CD79B -0.12 0.24 -10000 0 -0.51 42 42
NF-kappa-B/RelA/I kappa B alpha -0.003 0.046 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.29 0.34 -10000 0 -0.65 64 64
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 -0.31 0.37 -10000 0 -0.66 67 67
CSK 0.032 0.009 -10000 0 -10000 0 0
FOS -0.28 0.3 -10000 0 -0.57 66 66
CHUK -0.11 0.15 -10000 0 -0.33 22 22
IBTK 0.034 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.22 0.28 -10000 0 -0.52 61 61
PTPN6 -0.26 0.36 -10000 0 -0.71 50 50
RELA 0.034 0.006 -10000 0 -10000 0 0
BCL2A1 -0.002 0.033 -10000 0 -10000 0 0
VAV2 -0.35 0.44 -10000 0 -0.84 60 60
ubiquitin-dependent protein catabolic process -0.01 0.054 -10000 0 -0.14 5 5
BTK -0.17 0.45 -10000 0 -1.2 23 23
CD19 -0.35 0.45 -10000 0 -0.83 62 62
MAP4K1 0.033 0.006 -10000 0 -10000 0 0
CD72 0.029 0.041 -10000 0 -0.32 2 2
PAG1 -0.14 0.25 -10000 0 -0.51 46 46
MAPK14 -0.2 0.29 -10000 0 -0.55 53 53
SH3BP5 0.034 0.006 -10000 0 -10000 0 0
PIK3AP1 -0.31 0.37 -10000 0 -0.68 63 63
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.36 0.42 -10000 0 -0.77 65 65
RAF1 -0.22 0.26 -10000 0 -0.5 62 62
RasGAP/p62DOK/SHIP -0.2 0.3 -10000 0 -0.46 75 75
CD79A -0.22 0.27 -10000 0 -0.51 69 69
re-entry into mitotic cell cycle -0.13 0.14 -10000 0 -0.29 53 53
RASA1 0.031 0.029 -10000 0 -0.32 1 1
MAPK3 -0.19 0.22 -10000 0 -0.43 55 55
MAPK1 -0.18 0.21 -10000 0 -0.44 50 50
CD72/SHP1 -0.22 0.34 -10000 0 -0.67 49 49
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.2 0.29 -10000 0 -0.55 54 54
actin cytoskeleton organization -0.26 0.36 0.28 3 -0.66 60 63
NF-kappa-B/RelA -0.001 0.089 -10000 0 -0.22 1 1
Calcineurin -0.22 0.28 -10000 0 -0.5 63 63
PI3K -0.23 0.28 -10000 0 -0.55 60 60
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.33 0.39 -10000 0 -0.7 66 66
SOS1 0.035 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.26 0.4 -10000 0 -0.81 46 46
DAPP1 -0.32 0.46 -10000 0 -0.94 47 47
cytokine secretion -0.26 0.32 -10000 0 -0.61 60 60
mol:DAG -0.31 0.37 -10000 0 -0.66 67 67
PLCG2 -0.24 0.27 -10000 0 -0.51 74 74
MAP2K1 -0.21 0.24 -10000 0 -0.46 60 60
B-cell antigen/BCR complex/FcgammaRIIB -0.25 0.34 -10000 0 -0.54 74 74
mol:PI-3-4-5-P3 -0.15 0.19 -10000 0 -0.37 57 57
ETS1 -0.23 0.26 -10000 0 -0.5 63 63
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.15 0.25 -10000 0 -0.4 69 69
B-cell antigen/BCR complex/LYN -0.29 0.41 -10000 0 -0.8 51 51
MALT1 0.024 0.016 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 -0.29 0.4 0.28 3 -0.73 60 63
B-cell antigen/BCR complex/LYN/SYK -0.23 0.36 -10000 0 -0.69 49 49
CARD11 -0.28 0.34 -10000 0 -0.62 64 64
FCGR2B -0.078 0.22 -10000 0 -0.51 30 30
PPP3CA 0.034 0.005 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
IKK complex -0.028 0.057 0.12 1 -0.13 2 3
PTPRC 0.018 0.089 -10000 0 -0.51 4 4
PDPK1 -0.1 0.13 0.16 1 -0.26 50 51
PPP3CB 0.034 0.006 -10000 0 -10000 0 0
PPP3CC 0.023 0.047 -10000 0 -0.51 1 1
POU2F2 0 0.033 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.53 0.37 -9999 0 -0.96 46 46
HDAC7 -0.001 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.43 0.29 -9999 0 -0.82 29 29
SMAD4 0.024 0.017 -9999 0 -10000 0 0
ID2 -0.53 0.37 -9999 0 -0.96 46 46
AP1 0.008 0.1 -9999 0 -0.3 12 12
ABCG2 -0.75 0.38 -9999 0 -1 81 81
HIF1A -0.081 0.068 -9999 0 -0.45 1 1
TFF3 -0.54 0.37 -9999 0 -0.96 47 47
GATA2 0.032 0.017 -9999 0 -10000 0 0
AKT1 -0.076 0.062 -9999 0 -10000 0 0
response to hypoxia -0.093 0.048 -9999 0 -0.23 1 1
MCL1 -0.53 0.36 -9999 0 -0.95 46 46
NDRG1 -0.56 0.4 -9999 0 -1 49 49
SERPINE1 -0.56 0.37 -9999 0 -0.96 50 50
FECH -0.53 0.37 -9999 0 -0.96 45 45
FURIN -0.53 0.36 -9999 0 -0.95 46 46
NCOA2 0.031 0.012 -9999 0 -10000 0 0
EP300 -0.09 0.088 -9999 0 -0.38 2 2
HMOX1 -0.56 0.4 -9999 0 -1 50 50
BHLHE40 -0.54 0.35 -9999 0 -0.94 48 48
BHLHE41 -0.54 0.35 -9999 0 -0.94 48 48
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.095 0.097 -9999 0 -10000 0 0
ENG -0.094 0.078 -9999 0 -10000 0 0
JUN 0.019 0.064 -9999 0 -0.31 5 5
RORA -0.54 0.37 -9999 0 -0.97 46 46
ABCB1 -0.59 0.6 -9999 0 -1.3 64 64
TFRC -0.53 0.37 -9999 0 -0.95 47 47
CXCR4 -0.54 0.37 -9999 0 -0.96 47 47
TF -0.53 0.36 -9999 0 -0.95 46 46
CITED2 -0.53 0.36 -9999 0 -0.95 47 47
HIF1A/ARNT -0.6 0.41 -9999 0 -1.1 47 47
LDHA -0.055 0.14 -9999 0 -0.93 3 3
ETS1 -0.53 0.36 -9999 0 -0.96 46 46
PGK1 -0.54 0.36 -9999 0 -0.95 48 48
NOS2 -0.54 0.35 -9999 0 -0.94 48 48
ITGB2 -0.53 0.37 -9999 0 -0.96 46 46
ALDOA -0.53 0.36 -9999 0 -0.96 45 45
Cbp/p300/CITED2 -0.53 0.37 -9999 0 -0.99 42 42
FOS 0.001 0.11 -9999 0 -0.46 8 8
HK2 -0.53 0.36 -9999 0 -0.95 47 47
SP1 -0.019 0.071 -9999 0 -10000 0 0
GCK -0.1 0.12 -9999 0 -10000 0 0
HK1 -0.53 0.36 -9999 0 -0.94 47 47
NPM1 -0.53 0.36 -9999 0 -0.95 46 46
EGLN1 -0.53 0.36 -9999 0 -0.95 46 46
CREB1 0.041 0.001 -9999 0 -10000 0 0
PGM1 -0.56 0.38 -9999 0 -0.99 49 49
SMAD3 0.033 0.009 -9999 0 -10000 0 0
EDN1 -0.15 0.3 -9999 0 -1.3 8 8
IGFBP1 -0.53 0.37 -9999 0 -0.96 47 47
VEGFA -0.39 0.27 -9999 0 -0.75 29 29
HIF1A/JAB1 -0.042 0.052 -9999 0 -0.32 1 1
CP -0.57 0.4 -9999 0 -1 53 53
CXCL12 -0.7 0.41 -9999 0 -1 78 78
COPS5 0.031 0.012 -9999 0 -10000 0 0
SMAD3/SMAD4 0.034 0.03 -9999 0 -10000 0 0
BNIP3 -0.55 0.38 -9999 0 -0.98 48 48
EGLN3 -0.6 0.41 -9999 0 -1 58 58
CA9 -0.59 0.36 -9999 0 -0.97 53 53
TERT -0.53 0.36 -9999 0 -0.95 46 46
ENO1 -0.53 0.36 -9999 0 -0.95 47 47
PFKL -0.53 0.36 -9999 0 -0.96 45 45
NCOA1 0.027 0.063 -9999 0 -0.51 2 2
ADM -0.53 0.37 -9999 0 -0.96 46 46
ARNT -0.089 0.056 -9999 0 -10000 0 0
HNF4A 0.013 0.064 -9999 0 -0.51 2 2
ADFP -0.54 0.35 -9999 0 -0.94 48 48
SLC2A1 -0.4 0.26 -9999 0 -0.76 27 27
LEP -0.53 0.36 -9999 0 -0.95 47 47
HIF1A/ARNT/Cbp/p300 -0.44 0.29 -9999 0 -0.84 30 30
EPO -0.29 0.23 -9999 0 -0.83 12 12
CREBBP -0.086 0.081 -9999 0 -0.27 6 6
HIF1A/ARNT/Cbp/p300/HDAC7 -0.44 0.29 -9999 0 -0.84 30 30
PFKFB3 -0.54 0.37 -9999 0 -0.95 49 49
NT5E -0.54 0.37 -9999 0 -0.98 46 46
IGF1 pathway

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
NCK2 0.035 0 -10000 0 -10000 0 0
PTK2 0.028 0.013 -10000 0 -10000 0 0
CRKL -0.15 0.14 -10000 0 -0.27 85 85
GRB2/SOS1/SHC 0.065 0.019 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
IRS1/Crk -0.14 0.15 -10000 0 -0.27 85 85
IGF-1R heterotetramer/IGF1/PTP1B -0.09 0.14 -10000 0 -0.3 42 42
AKT1 -0.13 0.12 -10000 0 -0.34 3 3
BAD -0.12 0.11 -10000 0 -0.32 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.15 0.14 -10000 0 -0.27 85 85
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.16 -10000 0 -0.27 85 85
RAF1 -0.12 0.14 -10000 0 -0.58 4 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.16 -10000 0 -0.26 82 82
YWHAZ 0.029 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.17 -10000 0 -0.29 85 85
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.13 0.12 -10000 0 -0.34 3 3
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.083 0.12 -10000 0 -0.46 3 3
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.14 -10000 0 -0.34 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.093 0.16 -10000 0 -0.28 3 3
IGF-1R heterotetramer -0.03 0.056 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.13 0.16 -10000 0 -0.27 85 85
Crk/p130 Cas/Paxillin -0.11 0.16 -10000 0 -0.35 4 4
IGF1R -0.03 0.056 -10000 0 -10000 0 0
IGF1 -0.3 0.28 -10000 0 -0.52 86 86
IRS2/Crk -0.097 0.13 -10000 0 -0.26 56 56
PI3K -0.12 0.16 -10000 0 -0.26 83 83
apoptosis 0.096 0.11 0.29 3 -10000 0 3
HRAS/GDP 0.025 0.004 -10000 0 -10000 0 0
PRKCD -0.2 0.19 -10000 0 -0.36 81 81
RAF1/14-3-3 E -0.096 0.13 -10000 0 -0.49 4 4
BAD/14-3-3 -0.1 0.11 -10000 0 -0.3 3 3
PRKCZ -0.13 0.12 -10000 0 -0.34 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.094 0.12 -10000 0 -0.31 3 3
PTPN1 0.019 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.2 0.2 -10000 0 -0.37 86 86
BCAR1 0.034 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.12 0.16 -10000 0 -0.27 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.035 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.14 0.15 -10000 0 -0.27 85 85
GRB10 0.015 0.075 -10000 0 -0.32 7 7
PTPN11 -0.15 0.15 -10000 0 -0.27 85 85
IRS1 -0.16 0.15 -10000 0 -0.29 85 85
IRS2 -0.097 0.14 -10000 0 -0.27 56 56
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.39 85 85
GRB2 0.033 0.007 -10000 0 -10000 0 0
PDPK1 -0.13 0.13 -10000 0 -0.36 3 3
YWHAE 0.027 0.014 -10000 0 -10000 0 0
PRKD1 -0.2 0.19 -10000 0 -0.36 81 81
SHC1 0.033 0.006 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.089 0.1 0.21 48 -10000 0 48
RFC1 0.086 0.1 0.21 47 -10000 0 47
PRKDC 0.1 0.13 0.25 50 -10000 0 50
RIPK1 0.036 0.004 -10000 0 -10000 0 0
CASP7 -0.11 0.27 -10000 0 -0.73 22 22
FASLG/FAS/FADD/FAF1 -0.046 0.16 -10000 0 -0.35 25 25
MAP2K4 -0.1 0.18 -10000 0 -0.46 23 23
mol:ceramide -0.08 0.16 -10000 0 -0.38 28 28
GSN 0.054 0.14 0.21 46 -0.3 4 50
FASLG/FAS/FADD/FAF1/Caspase 8 -0.057 0.16 -10000 0 -0.38 25 25
FAS -0.02 0.15 -10000 0 -0.51 13 13
BID -0.025 0.035 -10000 0 -0.25 1 1
MAP3K1 -0.062 0.19 -10000 0 -0.53 16 16
MAP3K7 0.032 0.005 -10000 0 -10000 0 0
RB1 0.11 0.15 0.28 52 -10000 0 52
CFLAR 0.037 0.002 -10000 0 -10000 0 0
HGF/MET -0.1 0.16 -10000 0 -0.35 27 27
ARHGDIB 0.088 0.1 0.21 47 -10000 0 47
FADD 0.03 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.052 0.14 0.29 4 -0.21 46 50
NFKB1 -0.042 0.14 -10000 0 -1 3 3
MAPK8 -0.12 0.17 -10000 0 -0.47 20 20
DFFA 0.084 0.1 0.21 46 -10000 0 46
DNA fragmentation during apoptosis 0.084 0.11 0.21 47 -10000 0 47
FAS/FADD/MET -0.084 0.15 -10000 0 -0.36 14 14
CFLAR/RIP1 0.054 0.006 -10000 0 -10000 0 0
FAIM3 0.032 0.03 -10000 0 -0.32 1 1
FAF1 0.027 0.008 -10000 0 -10000 0 0
PARP1 0.088 0.1 0.21 47 -10000 0 47
DFFB 0.081 0.11 0.21 45 -10000 0 45
CHUK -0.038 0.14 -10000 0 -0.93 3 3
FASLG -0.054 0.19 -10000 0 -0.51 22 22
FAS/FADD 0.003 0.12 -10000 0 -0.37 13 13
HGF 0.033 0.008 -10000 0 -10000 0 0
LMNA 0.077 0.092 0.21 1 -10000 0 1
CASP6 0.088 0.1 0.21 47 -10000 0 47
CASP10 0.027 0.045 -10000 0 -0.51 1 1
CASP3 0.11 0.12 0.26 47 -10000 0 47
PTPN13 -0.08 0.17 -10000 0 -0.33 46 46
CASP8 -0.022 0.013 -10000 0 -10000 0 0
IL6 -0.11 0.16 -10000 0 -0.98 3 3
MET -0.12 0.17 -10000 0 -0.32 66 66
ICAD/CAD 0.065 0.097 0.22 3 -10000 0 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.081 0.16 -10000 0 -0.39 28 28
activation of caspase activity by cytochrome c -0.025 0.035 -10000 0 -0.25 1 1
PAK2 0.091 0.11 0.22 48 -10000 0 48
BCL2 -0.17 0.25 -10000 0 -0.51 51 51
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.034 0.006 -10000 0 -10000 0 0
CCL5 -0.068 0.21 -10000 0 -0.51 27 27
SDCBP 0.03 0.012 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.11 0.4 1 -0.31 22 23
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 -0.085 0.098 -10000 0 -0.36 8 8
Syndecan-1/Syntenin -0.096 0.1 0.36 1 -0.36 9 10
MAPK3 -0.1 0.098 0.34 1 -0.31 10 11
HGF/MET -0.072 0.13 -10000 0 -0.22 66 66
TGFB1/TGF beta receptor Type II 0.034 0.006 -10000 0 -10000 0 0
BSG 0.033 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.085 0.097 -10000 0 -0.36 8 8
Syndecan-1/RANTES -0.15 0.15 0.36 1 -0.4 32 33
Syndecan-1/CD147 -0.1 0.1 0.36 1 -0.34 9 10
Syndecan-1/Syntenin/PIP2 -0.094 0.099 0.33 1 -0.34 9 10
LAMA5 0.004 0.068 -10000 0 -0.32 6 6
positive regulation of cell-cell adhesion -0.092 0.097 0.33 1 -0.34 9 10
MMP7 -0.3 0.076 -10000 0 -0.32 139 139
HGF 0.033 0.008 -10000 0 -10000 0 0
Syndecan-1/CASK -0.11 0.096 -10000 0 -0.3 23 23
Syndecan-1/HGF/MET -0.16 0.12 -10000 0 -0.39 16 16
regulation of cell adhesion -0.098 0.097 0.32 1 -0.34 2 3
HPSE -0.041 0.19 -10000 0 -0.51 20 20
positive regulation of cell migration -0.11 0.11 0.4 1 -0.31 22 23
SDC1 -0.11 0.11 0.4 1 -0.31 22 23
Syndecan-1/Collagen -0.11 0.11 0.4 1 -0.31 22 23
PPIB 0.025 0.05 -10000 0 -0.32 3 3
MET -0.12 0.17 -10000 0 -0.32 66 66
PRKACA 0.034 0.006 -10000 0 -10000 0 0
MMP9 0.005 0.071 -10000 0 -0.35 5 5
MAPK1 -0.1 0.098 0.34 1 -0.32 9 10
homophilic cell adhesion -0.11 0.11 0.4 1 -0.3 22 23
MMP1 -0.28 0.1 -10000 0 -0.32 132 132
Visual signal transduction: Rods

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
mol:K + 0.032 0.008 -10000 0 -10000 0 0
GNAT1/GTP 0.025 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin -0.24 0.14 -10000 0 -0.31 117 117
PDE6G/GNAT1/GTP 0.044 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.034 0.005 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.23 0.2 -10000 0 -0.33 106 106
mol:Na + -0.11 0.15 -10000 0 -0.37 3 3
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.055 0.17 -10000 0 -0.32 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.11 0.16 -10000 0 -0.38 3 3
CNGB1 0.035 0 -10000 0 -10000 0 0
RDH5 -0.12 0.25 -10000 0 -0.51 42 42
SAG -0.41 0.21 -10000 0 -0.51 118 118
mol:Ca2+ -0.12 0.14 0.34 2 -0.36 3 5
Na + (4 Units) -0.11 0.14 -10000 0 -0.36 3 3
RGS9 -0.11 0.24 -10000 0 -0.51 39 39
GNB1/GNGT1 -0.05 0.12 -10000 0 -0.22 50 50
GNAT1/GDP -0.035 0.15 -10000 0 -0.27 39 39
GUCY2D 0.027 0.014 -10000 0 -10000 0 0
GNGT1 -0.094 0.17 -10000 0 -0.32 53 53
GUCY2F 0.027 0.063 -10000 0 -0.51 2 2
GNB5 0.023 0.057 -10000 0 -0.32 4 4
mol:GMP (4 units) -0.1 0.15 -10000 0 -0.27 68 68
mol:11-cis-retinal -0.12 0.25 -10000 0 -0.51 42 42
mol:cGMP 0.048 0.067 -10000 0 -0.27 3 3
GNB1 0.032 0.009 -10000 0 -10000 0 0
Rhodopsin -0.071 0.19 -10000 0 -0.37 42 42
SLC24A1 0.032 0.008 -10000 0 -10000 0 0
CNGA1 -0.26 0.27 -10000 0 -0.51 78 78
Metarhodopsin II 0.022 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.059 0.06 -10000 0 -0.29 1 1
RGS9BP 0.021 0.064 -10000 0 -0.32 5 5
Metarhodopsin II/Transducin -0.006 0.056 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.055 0.048 -10000 0 -0.29 1 1
PDE6A/B -0.15 0.21 -10000 0 -0.37 68 68
mol:Pi -0.055 0.17 -10000 0 -0.32 39 39
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.023 0.1 -10000 0 -10000 0 0
PDE6B 0.033 0.008 -10000 0 -10000 0 0
PDE6A -0.22 0.27 -10000 0 -0.51 68 68
PDE6G 0.033 0.007 -10000 0 -10000 0 0
RHO 0.034 0.004 -10000 0 -10000 0 0
PDE6 -0.16 0.22 -10000 0 -0.48 29 29
GUCA1A 0.034 0.006 -10000 0 -10000 0 0
GC2/GCAP Family 0.07 0.068 -10000 0 -0.29 3 3
GUCA1C 0.026 0.06 -10000 0 -0.38 3 3
GUCA1B 0.029 0.041 -10000 0 -0.32 2 2
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.014 0.04 -10000 0 -0.31 2 2
ARNO/beta Arrestin1-2 -0.062 0.13 -10000 0 -0.24 50 50
EGFR 0.02 0.077 -10000 0 -0.51 3 3
EPHA2 0.015 0.075 -10000 0 -0.32 7 7
USP6 0.027 0.014 -10000 0 -10000 0 0
IQSEC1 0.033 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.066 0.17 -10000 0 -0.37 29 29
ARRB2 0.016 0.013 -10000 0 -10000 0 0
mol:GTP 0.006 0.022 0.12 3 -10000 0 3
ARRB1 0.023 0.077 -10000 0 -0.51 3 3
FBXO8 0.032 0.008 -10000 0 -10000 0 0
TSHR 0.03 0.012 -10000 0 -10000 0 0
EGF -0.11 0.22 -10000 0 -0.44 44 44
somatostatin receptor activity 0 0 0.001 5 -0.001 24 29
ARAP2 0 0 0 6 0 20 26
mol:GDP -0.071 0.11 0.16 2 -0.26 25 27
mol:PI-3-4-5-P3 0 0 0 5 -0.001 24 29
ITGA2B 0.033 0.007 -10000 0 -10000 0 0
ARF6 0.031 0.011 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.06 -10000 0 -10000 0 0
ADAP1 0 0 0 3 0 6 9
KIF13B 0.02 0.064 -10000 0 -0.51 2 2
HGF/MET -0.073 0.13 -10000 0 -0.22 66 66
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.066 0.12 0.21 3 -0.24 26 29
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.041 0.16 -10000 0 -0.32 28 28
ADRB2 -0.14 0.25 -10000 0 -0.51 47 47
receptor agonist activity 0 0 0 5 0 22 27
actin filament binding 0 0 0 5 0 28 33
SRC 0.019 0.017 -10000 0 -10000 0 0
ITGB3 0.033 0.007 -10000 0 -10000 0 0
GNAQ 0 0 0.001 6 -0.001 14 20
EFA6/PI-4-5-P2 0 0.001 0.001 7 -0.001 13 20
ARF6/GDP -0.046 0.12 0.2 1 -0.33 16 17
ARF6/GDP/GULP/ACAP1 -0.069 0.14 -10000 0 -0.32 23 23
alphaIIb/beta3 Integrin/paxillin/GIT1 0.082 0.024 -10000 0 -10000 0 0
ACAP1 0 0 0 1 -10000 0 1
ACAP2 0 0 0 5 0 16 21
LHCGR/beta Arrestin2 0.016 0.036 -10000 0 -10000 0 0
EFNA1 0.033 0.006 -10000 0 -10000 0 0
HGF 0.033 0.008 -10000 0 -10000 0 0
CYTH3 0 0 0.001 6 -0.001 23 29
CYTH2 -0.001 0.002 -10000 0 -0.004 28 28
NCK1 0.034 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0 5 0 19 24
endosomal lumen acidification 0 0 0 10 0 12 22
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.013 0.15 -10000 0 -0.5 13 13
GNAQ/ARNO -0.001 0.004 0.008 6 -0.006 12 18
mol:Phosphatidic acid 0 0 0 5 0 16 21
PIP3-E 0 0 0 2 0 30 32
MET -0.12 0.17 -10000 0 -0.32 66 66
GNA14 0.011 0.11 -10000 0 -0.51 6 6
GNA15 0.024 0.057 -10000 0 -0.32 4 4
GIT1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 6 -0.001 19 25
GNA11 0 0.13 -10000 0 -0.51 9 9
LHCGR 0.032 0.029 -10000 0 -0.32 1 1
AGTR1 -0.083 0.22 -10000 0 -0.5 32 32
desensitization of G-protein coupled receptor protein signaling pathway 0.016 0.036 -10000 0 -10000 0 0
IPCEF1/ARNO -0.039 0.11 -10000 0 -0.24 29 29
alphaIIb/beta3 Integrin 0.049 0.01 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.072 0.22 -10000 0 -0.73 13 13
oxygen homeostasis -0.013 0.009 -10000 0 -10000 0 0
TCEB2 0.034 0.005 -10000 0 -10000 0 0
TCEB1 0.03 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.12 0.14 -10000 0 -0.41 12 12
EPO -0.26 0.17 -10000 0 -0.57 11 11
FIH (dimer) 0.003 0.026 -10000 0 -10000 0 0
APEX1 -0.001 0.029 -10000 0 -10000 0 0
SERPINE1 -0.32 0.22 -10000 0 -0.64 31 31
FLT1 -0.03 0.13 -10000 0 -0.88 2 2
ADORA2A -0.29 0.19 -10000 0 -0.6 19 19
germ cell development -0.29 0.19 -10000 0 -0.59 19 19
SLC11A2 -0.31 0.2 -10000 0 -0.6 29 29
BHLHE40 -0.3 0.2 -10000 0 -0.56 34 34
HIF1AN 0.003 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.2 0.15 -10000 0 -0.42 24 24
ETS1 0.039 0.036 -10000 0 -0.31 1 1
CITED2 -0.015 0.14 -10000 0 -0.94 3 3
KDR -0.02 0.16 -10000 0 -0.91 4 4
PGK1 -0.3 0.2 -10000 0 -0.61 22 22
SIRT1 0.034 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.33 0.23 -10000 0 -0.64 32 32
EPAS1 -0.16 0.14 -10000 0 -0.35 41 41
SP1 0.036 0.019 -10000 0 -10000 0 0
ABCG2 -0.56 0.25 -10000 0 -0.7 93 93
EFNA1 -0.3 0.19 -10000 0 -0.62 19 19
FXN -0.29 0.19 -10000 0 -0.6 19 19
POU5F1 -0.3 0.2 -10000 0 -0.62 19 19
neuron apoptosis 0.33 0.22 0.63 32 -10000 0 32
EP300 0.032 0.009 -10000 0 -10000 0 0
EGLN3 -0.14 0.23 -10000 0 -0.52 38 38
EGLN2 0.007 0.026 -10000 0 -10000 0 0
EGLN1 0.004 0.026 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.057 0.027 -10000 0 -10000 0 0
VHL 0.033 0.006 -10000 0 -10000 0 0
ARNT 0.001 0.03 -10000 0 -10000 0 0
SLC2A1 -0.3 0.2 -10000 0 -0.62 26 26
TWIST1 -0.3 0.21 -10000 0 -0.63 27 27
ELK1 0.041 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.2 0.15 -10000 0 -0.47 13 13
VEGFA -0.31 0.2 -10000 0 -0.61 24 24
CREBBP 0.034 0.005 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.043 0.11 -9999 0 -0.33 11 11
FZD6 0.02 0.058 -9999 0 -0.32 4 4
WNT6 0.034 0.003 -9999 0 -10000 0 0
WNT4 -0.001 0.13 -9999 0 -0.49 9 9
FZD3 -0.048 0.14 -9999 0 -0.32 31 31
WNT5A -0.007 0.11 -9999 0 -0.32 17 17
WNT11 -0.033 0.14 -9999 0 -0.32 28 28
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.006 -9999 0 -10000 0 0
EGFR 0.02 0.077 -9999 0 -0.51 3 3
EGF/EGFR -0.085 0.16 -9999 0 -0.32 37 37
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.011 0.15 -9999 0 -0.27 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.057 0.15 -9999 0 -0.32 38 38
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.22 -9999 0 -0.44 44 44
EGF/EGFR dimer/SHC -0.04 0.15 -9999 0 -0.31 28 28
mol:GDP -0.015 0.14 -9999 0 -0.27 27 27
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.005 0.12 -9999 0 -0.51 8 8
GRB2/SOS1 0.049 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.026 0.13 -9999 0 -10000 0 0
SHC1 0.033 0.006 -9999 0 -10000 0 0
HRAS/GDP -0.013 0.14 -9999 0 -10000 0 0
FRAP1 -0.068 0.1 -9999 0 -0.26 27 27
EGF/EGFR dimer -0.066 0.17 -9999 0 -0.37 29 29
SOS1 0.035 0 -9999 0 -10000 0 0
GRB2 0.033 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.04 0.14 -9999 0 -0.25 44 44
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.001 0.076 -10000 0 -0.17 23 23
EPHB2 0.023 0.061 -10000 0 -0.38 3 3
Syndecan-2/TACI 0.025 0.02 -10000 0 -10000 0 0
LAMA1 0.026 0.015 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.02 0.098 -10000 0 -0.29 1 1
HRAS 0.034 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.011 0.008 -10000 0 -10000 0 0
ITGA5 0.027 0.05 -10000 0 -0.32 3 3
BAX 0.009 0.02 -10000 0 -10000 0 0
EPB41 0.031 0.01 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.028 0.015 -10000 0 -10000 0 0
LAMA3 0.021 0.042 -10000 0 -0.32 2 2
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.016 0.075 -10000 0 -0.32 7 7
Syndecan-2/MMP2 0.03 0.024 -10000 0 -0.17 1 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.046 0.13 -10000 0 -0.22 52 52
dendrite morphogenesis 0.024 0.04 -10000 0 -0.31 1 1
Syndecan-2/GM-CSF -0.066 0.11 -10000 0 -0.17 70 70
determination of left/right symmetry 0.014 0.01 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.031 0.017 -10000 0 -10000 0 0
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
MAPK3 -0.047 0.13 0.2 16 -0.3 3 19
MAPK1 -0.041 0.12 0.2 16 -10000 0 16
Syndecan-2/RACK1 0.044 0.024 -10000 0 -10000 0 0
NF1 0.033 0.008 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.01 -10000 0 -10000 0 0
ITGA2 -0.09 0.17 -10000 0 -0.32 52 52
MAPK8 0.014 0.014 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.016 0.098 -10000 0 -0.29 1 1
Syndecan-2/Kininogen 0.022 0.058 -10000 0 -0.31 4 4
ITGB1 0.032 0.029 -10000 0 -0.32 1 1
SRC 0.022 0.04 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.027 0.017 -10000 0 -10000 0 0
extracellular matrix organization 0.031 0.017 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.001 0.076 -10000 0 -0.17 23 23
Syndecan-2/Caveolin-2/Ras 0.035 0.05 -10000 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.021 0.03 -10000 0 -0.17 2 2
Syndecan-2/RasGAP 0.056 0.034 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.043 0.044 -10000 0 -0.22 4 4
PRKCD 0.034 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.024 0.04 -10000 0 -0.31 1 1
GO:0007205 0.003 0.005 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.03 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
SDCBP 0.03 0.012 -10000 0 -10000 0 0
TNFRSF13B 0.023 0.047 -10000 0 -0.51 1 1
RASA1 0.031 0.029 -10000 0 -0.32 1 1
alpha2/beta1 Integrin -0.046 0.13 -10000 0 -0.22 52 52
Syndecan-2/Synbindin 0.031 0.017 -10000 0 -10000 0 0
TGFB1 0.034 0.006 -10000 0 -10000 0 0
CASP3 0.047 0.064 0.2 21 -10000 0 21
FN1 -0.023 0.13 -10000 0 -0.32 24 24
Syndecan-2/IL8 -0.12 0.1 -10000 0 -0.17 119 119
SDC2 0.014 0.01 -10000 0 -10000 0 0
KNG1 0.019 0.089 -10000 0 -0.51 4 4
Syndecan-2/Neurofibromin 0.03 0.018 -10000 0 -10000 0 0
TRAPPC4 0.034 0.006 -10000 0 -10000 0 0
CSF2 -0.15 0.18 -10000 0 -0.32 78 78
Syndecan-2/TGFB1 0.031 0.017 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.029 0.015 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.029 0.015 -10000 0 -10000 0 0
PRKACA 0.048 0.065 0.2 22 -10000 0 22
angiogenesis -0.12 0.1 -10000 0 -0.17 119 119
MMP2 0.032 0.029 -10000 0 -0.32 1 1
IL8 -0.3 0.074 -10000 0 -0.32 139 139
calcineurin-NFAT signaling pathway 0.025 0.02 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.027 0.12 -9999 0 -10000 0 0
SMAD6-7/SMURF1 0.044 0.038 -9999 0 -10000 0 0
NOG 0.033 0.007 -9999 0 -10000 0 0
SMAD9 -0.082 0.21 -9999 0 -0.52 25 25
SMAD4 0.023 0.016 -9999 0 -10000 0 0
SMAD5 -0.1 0.16 -9999 0 -0.49 12 12
BMP7/USAG1 -0.15 0.19 -9999 0 -0.36 56 56
SMAD5/SKI -0.096 0.16 -9999 0 -0.49 10 10
SMAD1 -0.019 0.1 -9999 0 -0.49 4 4
BMP2 -0.041 0.18 -9999 0 -0.51 18 18
SMAD1/SMAD1/SMAD4 0.009 0.09 -9999 0 -0.43 3 3
BMPR1A 0.032 0.009 -9999 0 -10000 0 0
BMPR1B 0.031 0.029 -9999 0 -0.32 1 1
BMPR1A-1B/BAMBI 0.031 0.085 -9999 0 -10000 0 0
AHSG 0.034 0.004 -9999 0 -10000 0 0
CER1 0.031 0.029 -9999 0 -0.32 1 1
BMP2-4/CER1 -0.064 0.17 -9999 0 -0.38 23 23
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.023 0.12 -9999 0 -0.38 7 7
BMP2-4 (homodimer) -0.086 0.18 -9999 0 -0.32 48 48
RGMB 0.024 0.057 -9999 0 -0.32 4 4
BMP6/BMPR2/BMPR1A-1B -0.097 0.18 -9999 0 -0.29 69 69
RGMA 0.025 0.064 -9999 0 -0.51 2 2
SMURF1 0.033 0.008 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.032 0.11 -9999 0 -0.33 8 8
BMP2-4/USAG1 -0.18 0.23 -9999 0 -0.41 63 63
SMAD6/SMURF1/SMAD5 -0.096 0.15 -9999 0 -0.48 10 10
SOSTDC1 -0.18 0.26 -9999 0 -0.51 58 58
BMP7/BMPR2/BMPR1A-1B -0.021 0.092 -9999 0 -10000 0 0
SKI 0.032 0.009 -9999 0 -10000 0 0
BMP6 (homodimer) -0.23 0.27 -9999 0 -0.51 70 70
HFE2 0.034 0.005 -9999 0 -10000 0 0
ZFYVE16 0.034 0.006 -9999 0 -10000 0 0
MAP3K7 0.034 0.005 -9999 0 -10000 0 0
BMP2-4/CHRD -0.061 0.16 -9999 0 -0.38 22 22
SMAD5/SMAD5/SMAD4 -0.089 0.16 -9999 0 -0.48 10 10
MAPK1 0.032 0.008 -9999 0 -10000 0 0
TAK1/TAB family -0.021 0.11 -9999 0 -0.31 4 4
BMP7 (homodimer) -0.072 0.14 -9999 0 -0.31 38 38
NUP214 0.034 0.005 -9999 0 -10000 0 0
BMP6/FETUA -0.15 0.21 -9999 0 -0.37 68 68
SMAD1/SKI -0.011 0.1 -9999 0 -0.51 3 3
SMAD6 0.028 0.041 -9999 0 -0.32 2 2
CTDSP2 0.027 0.063 -9999 0 -0.51 2 2
BMP2-4/FETUA -0.061 0.16 -9999 0 -0.38 22 22
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.005 0.092 -9999 0 -0.32 11 11
BMPR2 (homodimer) 0.035 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.067 0.015 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) 0.045 0.026 -9999 0 -0.22 1 1
CHRDL1 0.028 0.053 -9999 0 -0.41 2 2
ENDOFIN/SMAD1 -0.01 0.1 -9999 0 -0.51 3 3
SMAD6-7/SMURF1/SMAD1 0.016 0.1 -9999 0 -0.48 3 3
SMAD6/SMURF1 0.033 0.008 -9999 0 -10000 0 0
BAMBI -0.014 0.12 -9999 0 -0.32 20 20
SMURF2 0.007 0.092 -9999 0 -0.32 11 11
BMP2-4/CHRDL1 -0.067 0.17 -9999 0 -0.38 24 24
BMP2-4/GREM1 -0.078 0.18 -9999 0 -0.4 24 24
SMAD7 0.024 0.016 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.081 0.22 -9999 0 -0.48 27 27
SMAD1/SMAD6 -0.012 0.1 -9999 0 -0.51 3 3
TAK1/SMAD6 0.047 0.014 -9999 0 -10000 0 0
BMP7 -0.072 0.14 -9999 0 -0.32 38 38
BMP6 -0.23 0.27 -9999 0 -0.51 70 70
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.038 0.13 -9999 0 -0.39 10 10
PPM1A 0.03 0.011 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.02 0.11 -9999 0 -0.55 3 3
SMAD7/SMURF1 0.033 0.024 -9999 0 -10000 0 0
CTDSPL 0.03 0.045 -9999 0 -0.51 1 1
PPP1CA 0.034 0.006 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.003 -9999 0 -10000 0 0
PPP1R15A 0.034 0.004 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.026 0.11 -9999 0 -0.36 5 5
CHRD 0.034 0.004 -9999 0 -10000 0 0
BMPR2 0.035 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.029 0.12 -9999 0 -0.35 8 8
BMP4 -0.081 0.17 -9999 0 -0.33 45 45
FST 0.034 0.004 -9999 0 -10000 0 0
BMP2-4/NOG -0.062 0.16 -9999 0 -0.38 23 23
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.026 0.12 -9999 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.045 0.026 -10000 0 -0.22 1 1
VLDLR -0.081 0.22 -10000 0 -0.5 31 31
CRKL 0.032 0.008 -10000 0 -10000 0 0
LRPAP1 0.033 0.008 -10000 0 -10000 0 0
FYN 0.031 0.029 -10000 0 -0.32 1 1
ITGA3 0.031 0.03 -10000 0 -0.32 1 1
RELN/VLDLR/Fyn -0.016 0.15 -10000 0 -0.32 28 28
MAPK8IP1/MKK7/MAP3K11/JNK1 0.093 0.035 -10000 0 -10000 0 0
AKT1 -0.024 0.094 -10000 0 -10000 0 0
MAP2K7 0.034 0.003 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
DAB1 0.033 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.12 0.082 -10000 0 -0.19 2 2
LRPAP1/LRP8 -0.18 0.091 -10000 0 -0.22 120 120
RELN/LRP8/DAB1/Fyn -0.11 0.081 -10000 0 -10000 0 0
DAB1/alpha3/beta1 Integrin -0.16 0.13 -10000 0 -0.38 26 26
long-term memory -0.13 0.1 -10000 0 -0.31 1 1
DAB1/LIS1 -0.16 0.13 -10000 0 -0.39 25 25
DAB1/CRLK/C3G -0.16 0.13 -10000 0 -0.38 24 24
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
DAB1/NCK2 -0.16 0.14 -10000 0 -0.39 26 26
ARHGEF2 0.031 0.029 -10000 0 -0.32 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.034 0.003 -10000 0 -10000 0 0
CDK5R1 0.033 0.007 -10000 0 -10000 0 0
RELN 0.032 0.008 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.14 0.089 -10000 0 -0.23 1 1
GRIN2A/RELN/LRP8/DAB1/Fyn -0.11 0.09 -10000 0 -10000 0 0
MAPK8 0.033 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.011 0.14 -10000 0 -0.28 28 28
ITGB1 0.032 0.029 -10000 0 -0.32 1 1
MAP1B -0.15 0.12 -10000 0 -0.38 26 26
RELN/LRP8 -0.14 0.09 -10000 0 -0.22 2 2
GRIN2B/RELN/LRP8/DAB1/Fyn -0.13 0.11 -10000 0 -0.3 20 20
PI3K 0.05 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.045 0.033 -10000 0 -0.22 2 2
RAP1A -0.15 0.12 -10000 0 -0.36 24 24
PAFAH1B1 0.027 0.014 -10000 0 -10000 0 0
MAPK8IP1 0.031 0.029 -10000 0 -0.32 1 1
CRLK/C3G 0.047 0.014 -10000 0 -10000 0 0
GRIN2B -0.023 0.13 -10000 0 -0.32 24 24
NCK2 0.035 0 -10000 0 -10000 0 0
neuron differentiation -0.021 0.054 -10000 0 -0.35 2 2
neuron adhesion -0.14 0.12 -10000 0 -0.35 24 24
LRP8 -0.27 0.12 -10000 0 -0.32 126 126
GSK3B -0.023 0.093 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/Fyn 0.001 0.14 -10000 0 -0.27 28 28
MAP3K11 0.034 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.022 0.11 -10000 0 -0.24 27 27
CDK5 0.031 0.03 -10000 0 -0.32 1 1
MAPT 0.017 0.11 0.79 3 -10000 0 3
neuron migration -0.12 0.12 -10000 0 -0.34 26 26
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.022 0.055 -10000 0 -0.36 2 2
RELN/VLDLR -0.18 0.14 -10000 0 -0.4 32 32
TRAIL signaling pathway

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
TNFSF10 -0.029 0.18 -9999 0 -0.51 17 17
positive regulation of NF-kappaB transcription factor activity -0.014 0.13 -9999 0 -0.34 20 20
MAP2K4 -0.015 0.1 -9999 0 -0.44 4 4
IKBKB 0.03 0.012 -9999 0 -10000 0 0
TNFRSF10B -0.031 0.13 -9999 0 -0.32 24 24
TNFRSF10A -0.014 0.11 -9999 0 -0.32 17 17
SMPD1 -0.11 0.2 -9999 0 -0.41 39 39
IKBKG 0.034 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.02 0.051 -9999 0 -0.32 3 3
TRAIL/TRAILR2 -0.048 0.16 -9999 0 -0.32 35 35
TRAIL/TRAILR3 -0.038 0.15 -9999 0 -0.3 33 33
TRAIL/TRAILR1 -0.036 0.16 -9999 0 -0.32 30 30
TRAIL/TRAILR4 -0.014 0.13 -9999 0 -0.34 20 20
TRAIL/TRAILR1/DAP3/GTP -0.012 0.13 -9999 0 -0.32 17 17
IKK complex -0.009 0.092 -9999 0 -0.53 2 2
RIPK1 0.034 0.003 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.025 0.005 -9999 0 -10000 0 0
MAPK3 -0.03 0.14 -9999 0 -0.39 18 18
MAP3K1 -0.013 0.12 -9999 0 -0.37 9 9
TRAILR4 (trimer) 0.02 0.05 -9999 0 -0.31 3 3
TRADD 0.035 0 -9999 0 -10000 0 0
TRAILR1 (trimer) -0.014 0.11 -9999 0 -0.31 17 17
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.014 0.11 -9999 0 -0.36 9 9
CFLAR 0.035 0 -9999 0 -10000 0 0
MAPK1 -0.021 0.12 -9999 0 -0.37 15 15
TRAIL/TRAILR1/FADD/TRADD/RIP 0.012 0.14 -9999 0 -0.3 17 17
mol:ceramide -0.11 0.2 -9999 0 -0.41 39 39
FADD 0.034 0.005 -9999 0 -10000 0 0
MAPK8 -0.017 0.1 -9999 0 -0.42 4 4
TRAF2 0.034 0.005 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.11 -9999 0 -0.31 17 17
CHUK 0.032 0.008 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.015 0.14 -9999 0 -0.34 17 17
DAP3 0.033 0.006 -9999 0 -10000 0 0
CASP10 -0.049 0.13 -9999 0 -0.43 12 12
JNK cascade -0.014 0.13 -9999 0 -0.34 20 20
TRAIL (trimer) -0.029 0.17 -9999 0 -0.51 17 17
TNFRSF10C -0.014 0.11 -9999 0 -0.32 17 17
TRAIL/TRAILR1/DAP3/GTP/FADD 0 0.13 -9999 0 -0.3 17 17
TRAIL/TRAILR2/FADD -0.025 0.15 -9999 0 -0.36 17 17
cell death -0.11 0.2 -9999 0 -0.4 39 39
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.018 0.11 -9999 0 -0.33 12 12
TRAILR2 (trimer) -0.031 0.13 -9999 0 -0.31 24 24
CASP8 0.031 0.034 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.002 0.14 -9999 0 -0.31 17 17
Endothelins

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
AKT1 -0.02 0.15 -10000 0 -0.36 10 10
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0.015 0.18 -10000 0 -0.72 3 3
EDN1 0.036 0.15 -10000 0 -0.51 8 8
EDN3 -0.18 0.25 -10000 0 -0.51 52 52
EDN2 -0.38 0.23 -10000 0 -0.51 111 111
HRAS/GDP 0.009 0.18 0.31 2 -0.49 8 10
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.006 0.14 -10000 0 -0.38 9 9
ADCY4 -0.024 0.11 -10000 0 -0.35 4 4
ADCY5 -0.025 0.11 -10000 0 -0.38 3 3
ADCY6 -0.023 0.11 -10000 0 -0.34 2 2
ADCY7 -0.025 0.11 -10000 0 -0.35 4 4
ADCY1 -0.022 0.11 -10000 0 -0.35 4 4
ADCY2 -0.025 0.11 -10000 0 -0.35 4 4
ADCY3 -0.034 0.12 -10000 0 -0.32 6 6
ADCY8 -0.027 0.11 -10000 0 -0.35 4 4
ADCY9 -0.024 0.11 -10000 0 -0.38 3 3
arachidonic acid secretion -0.056 0.22 0.29 1 -0.54 16 17
ETB receptor/Endothelin-1/Gq/GTP -0.04 0.16 -10000 0 -0.36 21 21
GNAO1 0.035 0 -10000 0 -10000 0 0
HRAS 0.033 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.09 0.18 -10000 0 -0.39 4 4
ETA receptor/Endothelin-1/Gs/GTP 0.059 0.17 -10000 0 -0.32 8 8
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
COL3A1 -0.021 0.15 -10000 0 -0.48 4 4
EDNRB -0.046 0.17 -10000 0 -0.52 16 16
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.016 0.13 -10000 0 -0.36 9 9
CYSLTR1 -0.021 0.16 -10000 0 -0.48 4 4
SLC9A1 0.002 0.093 -10000 0 -0.27 4 4
mol:GDP -0.006 0.18 0.31 2 -0.49 10 12
SLC9A3 -0.42 0.32 -10000 0 -0.73 53 53
RAF1 -0.027 0.19 0.3 2 -0.55 10 12
JUN 0.013 0.17 -10000 0 -0.67 2 2
JAK2 -0.023 0.15 -10000 0 -0.36 11 11
mol:IP3 -0.018 0.17 0.24 4 -0.46 10 14
ETA receptor/Endothelin-1 0.091 0.22 -10000 0 -0.42 10 10
PLCB1 -0.042 0.14 -10000 0 -0.32 28 28
PLCB2 0.032 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.15 0.21 -10000 0 -0.42 52 52
FOS -0.065 0.3 -10000 0 -0.9 14 14
Gai/GDP 0.014 0.14 -10000 0 -0.79 3 3
CRK 0.028 0.014 -10000 0 -10000 0 0
mol:Ca ++ -0.031 0.19 -10000 0 -0.54 10 10
BCAR1 0.034 0.004 -10000 0 -10000 0 0
PRKCB1 -0.015 0.16 0.22 6 -0.44 10 16
GNAQ 0.001 0.004 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
GNAL 0.026 0.015 -10000 0 -10000 0 0
Gs family/GDP -0.003 0.17 0.27 1 -0.45 9 10
ETA receptor/Endothelin-1/Gq/GTP -0.005 0.14 -10000 0 -0.36 11 11
MAPK14 -0.038 0.14 -10000 0 -0.4 12 12
TRPC6 0.013 0.18 -10000 0 -0.76 3 3
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
GNAI3 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.027 0.17 -10000 0 -0.51 16 16
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.037 0.14 -10000 0 -0.41 13 13
ETB receptor/Endothelin-2 -0.25 0.2 -10000 0 -0.42 78 78
ETB receptor/Endothelin-3 -0.15 0.22 -10000 0 -0.45 48 48
ETB receptor/Endothelin-1 -0.025 0.18 -10000 0 -0.42 20 20
MAPK3 -0.046 0.25 -10000 0 -0.72 14 14
MAPK1 -0.054 0.26 -10000 0 -0.73 15 15
Rac1/GDP -0.005 0.17 0.29 1 -0.49 8 9
cAMP biosynthetic process 0.002 0.1 -10000 0 -0.31 2 2
MAPK8 0.013 0.18 -10000 0 -0.59 7 7
SRC 0.019 0.017 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.015 0.13 -10000 0 -0.35 11 11
p130Cas/CRK/Src/PYK2 0.017 0.2 0.33 5 -0.53 7 12
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.005 0.17 0.29 1 -0.52 7 8
COL1A2 -0.015 0.22 -10000 0 -0.63 7 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.31 0.2 -10000 0 -0.41 115 115
mol:DAG -0.018 0.17 0.24 4 -0.46 10 14
MAP2K2 -0.035 0.21 0.32 1 -0.56 13 14
MAP2K1 -0.038 0.22 0.32 1 -0.62 12 13
EDNRA -0.026 0.18 -10000 0 -0.32 38 38
positive regulation of muscle contraction 0.003 0.14 0.27 8 -0.39 3 11
Gq family/GDP -0.01 0.17 -10000 0 -0.47 11 11
HRAS/GTP -0.019 0.18 0.28 1 -0.47 11 12
PRKCH -0.016 0.16 0.23 1 -0.46 9 10
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCA -0.009 0.17 0.28 6 -0.47 9 15
PRKCB -0.017 0.16 0.22 5 -0.44 10 15
PRKCE -0.015 0.16 -10000 0 -0.48 8 8
PRKCD -0.013 0.16 0.23 1 -0.46 8 9
PRKCG -0.017 0.16 0.24 5 -0.47 9 14
regulation of vascular smooth muscle contraction -0.08 0.34 -10000 0 -1.1 14 14
PRKCQ -0.017 0.16 0.23 3 -0.46 8 11
PLA2G4A -0.063 0.23 0.3 1 -0.59 16 17
GNA14 0.012 0.11 -10000 0 -0.52 6 6
GNA15 0.025 0.057 -10000 0 -0.31 4 4
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.001 0.13 -10000 0 -0.51 9 9
Rac1/GTP 0.09 0.18 -10000 0 -0.39 4 4
MMP1 -0.22 0.097 0.41 1 -10000 0 1
IL6-mediated signaling events

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
BCL2L1 -0.067 0.14 -10000 0 -10000 0 0
CRP -0.12 0.14 -10000 0 -0.65 1 1
cell cycle arrest -0.14 0.15 -10000 0 -0.76 1 1
TIMP1 -0.16 0.15 -10000 0 -0.94 1 1
IL6ST 0.032 0.01 -10000 0 -10000 0 0
Rac1/GDP -0.18 0.16 -10000 0 -0.42 23 23
AP1 0.011 0.13 -10000 0 -0.55 3 3
GAB2 0.038 0.01 -10000 0 -10000 0 0
TNFSF11 -0.11 0.17 -10000 0 -0.74 1 1
HSP90B1 0.012 0.043 -10000 0 -10000 0 0
GAB1 0.032 0.046 -10000 0 -0.51 1 1
MAPK14 -0.17 0.16 -10000 0 -0.5 13 13
AKT1 0.041 0.048 -10000 0 -10000 0 0
FOXO1 0.069 0.092 -10000 0 -10000 0 0
MAP2K6 -0.19 0.17 -10000 0 -0.44 23 23
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
MAP2K4 -0.18 0.15 -10000 0 -0.46 15 15
MITF -0.18 0.15 -10000 0 -0.34 39 39
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.006 -10000 0 -10000 0 0
A2M -0.18 0.52 -10000 0 -1.4 22 22
CEBPB 0.019 0.035 -10000 0 -0.31 1 1
GRB2/SOS1/GAB family/SHP2 -0.007 0.099 0.29 1 -0.49 2 3
STAT3 -0.15 0.15 -10000 0 -0.8 1 1
STAT1 0.006 0.022 -10000 0 -10000 0 0
CEBPD -0.11 0.14 -10000 0 -0.65 1 1
PIK3CA 0.035 0.004 -10000 0 -10000 0 0
PI3K 0.051 0.01 -10000 0 -10000 0 0
JUN 0.021 0.064 -10000 0 -0.32 5 5
PIAS3/MITF -0.17 0.15 -10000 0 -0.36 24 24
MAPK11 -0.17 0.17 -10000 0 -0.51 13 13
STAT3 (dimer)/FOXO1 -0.088 0.16 -10000 0 -0.6 1 1
GRB2/SOS1/GAB family -0.096 0.18 0.29 1 -0.43 9 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.16 -10000 0 -0.37 36 36
GRB2 0.035 0.009 -10000 0 -10000 0 0
JAK2 0.026 0.05 -10000 0 -0.32 3 3
LBP -0.017 0.14 -10000 0 -0.5 1 1
PIK3R1 0.035 0.005 -10000 0 -10000 0 0
JAK1 0.031 0.012 -10000 0 -10000 0 0
MYC -0.14 0.17 -10000 0 -0.74 1 1
FGG -0.13 0.13 -10000 0 -0.64 1 1
macrophage differentiation -0.14 0.15 -10000 0 -0.76 1 1
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.22 0.18 -10000 0 -0.36 74 74
JUNB -0.13 0.14 -10000 0 -0.71 1 1
FOS 0.003 0.11 -10000 0 -0.46 8 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.19 0.16 -10000 0 -0.34 54 54
STAT1/PIAS1 -0.14 0.13 -10000 0 -0.38 9 9
GRB2/SOS1/GAB family/SHP2/PI3K 0.048 0.045 -10000 0 -10000 0 0
STAT3 (dimer) -0.14 0.15 -10000 0 -0.79 1 1
PRKCD -0.17 0.17 0.37 1 -0.5 9 10
IL6R -0.28 0.27 -10000 0 -0.51 83 83
SOCS3 -0.16 0.17 -10000 0 -0.64 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.049 0.06 -10000 0 -0.29 1 1
Rac1/GTP -0.18 0.16 -10000 0 -0.43 21 21
HCK -0.002 0.11 -10000 0 -0.51 6 6
MAPKKK cascade 0.03 0.11 -10000 0 -0.56 2 2
bone resorption -0.1 0.17 -10000 0 -0.7 1 1
IRF1 -0.14 0.15 -10000 0 -0.86 2 2
mol:GDP -0.19 0.17 -10000 0 -0.39 37 37
SOS1 0.038 0.009 -10000 0 -10000 0 0
VAV1 -0.2 0.17 -10000 0 -0.4 38 38
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.26 0.22 -10000 0 -0.49 47 47
PTPN11 0.009 0.076 -10000 0 -0.88 1 1
IL6/IL6RA -0.29 0.2 -10000 0 -0.38 111 111
gp130 (dimer)/TYK2/TYK2/LMO4 0.051 0.058 -10000 0 -0.29 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 0.049 0.073 -10000 0 -0.33 4 4
IL6 -0.16 0.17 -10000 0 -0.32 78 78
PIAS3 0.031 0.029 -10000 0 -0.32 1 1
PTPRE 0.033 0.03 -10000 0 -0.3 1 1
PIAS1 0.032 0.008 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.17 0.15 -10000 0 -0.31 63 63
LMO4 0.016 0.078 -10000 0 -0.35 6 6
STAT3 (dimer)/PIAS3 -0.14 0.15 -10000 0 -0.77 1 1
MCL1 0.044 0.061 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.097 0.27 -10000 0 -0.84 10 10
PCK1 -0.73 0.66 -10000 0 -1.3 87 87
HNF4A -0.073 0.32 0.59 5 -1.3 4 9
KCNJ11 -0.086 0.29 -10000 0 -0.98 6 6
AKT1 -0.037 0.14 -10000 0 -0.45 2 2
response to starvation -0.013 0.028 -10000 0 -0.22 1 1
DLK1 -0.08 0.29 -10000 0 -0.98 6 6
NKX2-1 0.011 0.19 -10000 0 -10000 0 0
ACADM -0.1 0.3 -10000 0 -0.9 11 11
TAT -0.13 0.22 -10000 0 -0.88 5 5
CEBPB -0.007 0.038 -10000 0 -0.32 1 1
CEBPA -0.004 0.043 -10000 0 -10000 0 0
TTR -0.71 0.67 -10000 0 -1.3 79 79
PKLR -0.099 0.28 -10000 0 -0.85 10 10
APOA1 -0.086 0.36 -10000 0 -1.3 7 7
CPT1C -0.1 0.28 -10000 0 -0.9 8 8
ALAS1 -0.03 0.16 -10000 0 -0.71 1 1
TFRC -0.13 0.29 -10000 0 -1.2 4 4
FOXF1 0.021 0.08 -10000 0 -0.51 3 3
NF1 0.039 0.009 -10000 0 -10000 0 0
HNF1A (dimer) 0.035 0.038 -10000 0 -10000 0 0
CPT1A -0.1 0.29 -10000 0 -0.96 8 8
HMGCS1 -0.096 0.28 0.59 1 -0.84 9 10
NR3C1 -0.013 0.16 -10000 0 -0.5 13 13
CPT1B -0.097 0.27 -10000 0 -0.86 9 9
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.036 0.024 -10000 0 -10000 0 0
GCK -0.086 0.28 -10000 0 -0.86 9 9
CREB1 -0.12 0.14 -10000 0 -0.26 61 61
IGFBP1 -0.062 0.17 -10000 0 -0.62 3 3
PDX1 -0.015 0.14 -10000 0 -10000 0 0
UCP2 -0.095 0.27 -10000 0 -0.86 9 9
ALDOB -0.12 0.37 -10000 0 -1.2 11 11
AFP -0.13 0.14 -10000 0 -0.48 7 7
BDH1 -0.1 0.31 -10000 0 -0.98 9 9
HADH -0.089 0.29 -10000 0 -0.98 6 6
F2 -0.072 0.33 -10000 0 -1.2 5 5
HNF1A 0.035 0.038 -10000 0 -10000 0 0
G6PC -0.078 0.18 -10000 0 -1.4 1 1
SLC2A2 -0.04 0.2 -10000 0 -1.1 1 1
INS 0.028 0.021 -10000 0 -10000 0 0
FOXA1 -0.097 0.2 -10000 0 -0.51 28 28
FOXA3 -0.14 0.17 -10000 0 -0.34 37 37
FOXA2 -0.1 0.33 -10000 0 -1 8 8
ABCC8 -0.13 0.36 -10000 0 -1.1 12 12
ALB -0.13 0.14 -10000 0 -0.44 12 12
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.059 -10000 0 -10000 0 0
fibroblast growth factor receptor signaling pathway 0.046 0.058 -10000 0 -10000 0 0
LAMA1 0.026 0.015 -10000 0 -10000 0 0
PRNP 0.026 0.015 -10000 0 -10000 0 0
GPC1/SLIT2 -0.17 0.2 -10000 0 -0.36 77 77
SMAD2 0.014 0.038 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.026 0.046 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.025 0.058 -10000 0 -0.22 7 7
TDGF1 -0.19 0.17 -10000 0 -0.32 92 92
CRIPTO/GPC1 -0.13 0.14 -10000 0 -0.23 95 95
APP/GPC1 0.034 0.058 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.11 0.1 -10000 0 -0.33 7 7
FLT1 0 0.087 -10000 0 -0.32 10 10
GPC1/TGFB/TGFBR1/TGFBR2 0.053 0.055 -10000 0 -10000 0 0
SERPINC1 0.031 0.029 -10000 0 -0.32 1 1
FYN -0.11 0.11 -10000 0 -0.33 7 7
FGR -0.11 0.1 -10000 0 -0.33 7 7
positive regulation of MAPKKK cascade -0.02 0.12 0.29 2 -0.35 6 8
SLIT2 -0.23 0.27 -10000 0 -0.51 71 71
GPC1/NRG 0.029 0.057 -10000 0 -0.22 5 5
NRG1 0.028 0.013 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.011 0.09 -10000 0 -0.34 2 2
LYN -0.098 0.11 -10000 0 -0.33 7 7
mol:Spermine 0 0.048 -10000 0 -0.21 7 7
cell growth 0.046 0.058 -10000 0 -10000 0 0
BMP signaling pathway -0.017 0.075 0.31 7 -10000 0 7
SRC -0.052 0.097 -10000 0 -0.32 5 5
TGFBR1 0.034 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.061 0.19 -10000 0 -0.43 29 29
GPC1 0.017 0.075 -10000 0 -0.32 7 7
TGFBR1 (dimer) 0.034 0.006 -10000 0 -10000 0 0
VEGFA -0.002 0.11 -10000 0 -0.32 15 15
BLK -0.15 0.15 -10000 0 -0.39 25 25
HCK -0.068 0.12 -10000 0 -0.37 11 11
FGF2 0.031 0.029 -10000 0 -0.32 1 1
FGFR1 0.03 0.012 -10000 0 -10000 0 0
VEGFR1 homodimer 0 0.087 -10000 0 -0.31 10 10
TGFBR2 0.034 0.005 -10000 0 -10000 0 0
cell death 0.034 0.058 -10000 0 -10000 0 0
ATIII/GPC1 0.034 0.061 -10000 0 -0.22 8 8
PLA2G2A/GPC1 -0.039 0.15 -10000 0 -0.31 33 33
LCK -0.12 0.1 -10000 0 -0.33 7 7
neuron differentiation 0.029 0.057 -10000 0 -0.22 5 5
PrPc/Cu2+ 0.019 0.011 -10000 0 -10000 0 0
APP 0.032 0.009 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.034 0.005 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.062 0.11 0.22 1 -0.21 48 49
TP53 -0.028 0.066 -10000 0 -0.25 10 10
Senescence -0.029 0.067 -10000 0 -0.24 11 11
Apoptosis -0.029 0.067 -10000 0 -0.24 11 11
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.031 0.057 0.29 1 -10000 0 1
MDM4 0.033 0.006 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.009 0.087 -10000 0 -0.31 1 1
TBX21 -0.38 0.66 -10000 0 -1.3 45 45
B2M 0.014 0.099 -10000 0 -0.51 5 5
TYK2 0.016 0.039 -10000 0 -10000 0 0
IL12RB1 0.016 0.039 -10000 0 -10000 0 0
GADD45B -0.14 0.36 -10000 0 -0.92 19 19
IL12RB2 0.013 0.051 -10000 0 -0.36 1 1
GADD45G -0.14 0.35 -10000 0 -0.89 19 19
natural killer cell activation -0.006 0.023 -10000 0 -10000 0 0
RELB 0.034 0.004 -10000 0 -10000 0 0
RELA 0.034 0.006 -10000 0 -10000 0 0
IL18 -0.018 0.16 -10000 0 -0.5 14 14
IL2RA 0.022 0.064 -10000 0 -0.32 5 5
IFNG -0.045 0.15 -10000 0 -0.32 33 33
STAT3 (dimer) -0.12 0.32 -10000 0 -0.71 25 25
HLA-DRB5 0.01 0.11 -10000 0 -0.51 6 6
FASLG -0.24 0.55 -10000 0 -1.3 27 27
NF kappa B2 p52/RelB -0.14 0.37 -10000 0 -0.8 27 27
CD4 0.032 0.013 -10000 0 -10000 0 0
SOCS1 0.034 0.003 -10000 0 -10000 0 0
EntrezGene:6955 0.001 0.006 -10000 0 -10000 0 0
CD3D 0.014 0.1 -10000 0 -0.51 5 5
CD3E 0.033 0.014 -10000 0 -10000 0 0
CD3G 0.012 0.1 -10000 0 -0.48 6 6
IL12Rbeta2/JAK2 0.019 0.07 -10000 0 -0.23 3 3
CCL3 -0.15 0.36 -10000 0 -0.88 20 20
CCL4 -0.15 0.38 -10000 0 -0.92 20 20
HLA-A 0.021 0.089 -10000 0 -0.51 4 4
IL18/IL18R -0.033 0.21 -10000 0 -0.36 38 38
NOS2 -0.16 0.37 -10000 0 -0.74 34 34
IL12/IL12R/TYK2/JAK2/SPHK2 0.006 0.089 -10000 0 -0.31 1 1
IL1R1 -0.16 0.38 -10000 0 -0.9 22 22
IL4 0.04 0.025 -10000 0 -10000 0 0
JAK2 0.008 0.06 -10000 0 -0.3 3 3
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.004 0.16 -10000 0 -0.59 7 7
RAB7A -0.12 0.32 -10000 0 -0.76 19 19
lysosomal transport -0.11 0.3 -10000 0 -0.72 19 19
FOS -0.19 0.48 -10000 0 -1.2 25 25
STAT4 (dimer) -0.13 0.36 -10000 0 -0.81 23 23
STAT5A (dimer) -0.15 0.36 -10000 0 -0.8 27 27
GZMA -0.15 0.36 -10000 0 -0.78 28 28
GZMB -0.15 0.36 -10000 0 -0.89 20 20
HLX 0.033 0.006 -10000 0 -10000 0 0
LCK -0.16 0.38 -10000 0 -0.86 27 27
TCR/CD3/MHC II/CD4 -0.015 0.19 -10000 0 -0.72 8 8
IL2/IL2R 0.069 0.06 -10000 0 -0.29 1 1
MAPK14 -0.15 0.39 -10000 0 -0.89 24 24
CCR5 -0.2 0.49 -10000 0 -1.2 23 23
IL1B -0.093 0.16 -10000 0 -0.31 47 47
STAT6 -0.017 0.1 -10000 0 -10000 0 0
STAT4 0.031 0.045 -10000 0 -0.51 1 1
STAT3 0.034 0.006 -10000 0 -10000 0 0
STAT1 0.001 0.1 -10000 0 -0.32 14 14
NFKB1 0.034 0.005 -10000 0 -10000 0 0
NFKB2 0.03 0.03 -10000 0 -0.32 1 1
IL12B 0.015 0.048 -10000 0 -0.3 1 1
CD8A 0.001 0.002 -10000 0 -10000 0 0
CD8B 0.036 0.002 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.009 0.086 0.31 1 -10000 0 1
IL2RB 0.032 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.11 0.33 -10000 0 -0.74 23 23
IL2RG 0.031 0.045 -10000 0 -0.51 1 1
IL12 0.017 0.074 -10000 0 -0.24 2 2
STAT5A 0.033 0.006 -10000 0 -10000 0 0
CD247 0.007 0.12 -10000 0 -0.51 7 7
IL2 0.034 0.005 -10000 0 -10000 0 0
SPHK2 0.03 0.045 -10000 0 -0.51 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.072 -10000 0 -0.32 5 5
IL12/IL12R/TYK2/JAK2 -0.17 0.41 -10000 0 -0.9 28 28
MAP2K3 -0.17 0.42 -10000 0 -0.96 24 24
RIPK2 -0.012 0.11 -10000 0 -0.32 17 17
MAP2K6 -0.16 0.39 -10000 0 -0.93 22 22
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.017 0.089 -10000 0 -0.51 4 4
IL18RAP -0.074 0.22 -10000 0 -0.52 29 29
IL12Rbeta1/TYK2 0.026 0.054 -10000 0 -10000 0 0
EOMES 0.02 0.097 -10000 0 -0.63 2 2
STAT1 (dimer) -0.12 0.3 -10000 0 -0.7 23 23
T cell proliferation -0.1 0.27 -10000 0 -0.62 22 22
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.031 0.047 -10000 0 -0.52 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.32 -10000 0 -0.68 24 24
ATF2 -0.14 0.36 -10000 0 -0.84 22 22
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.23 0.45 -10000 0 -1.1 16 16
STAT6 (cleaved dimer) -0.34 0.45 -10000 0 -1.1 26 26
IGHG1 -0.082 0.17 -10000 0 -10000 0 0
IGHG3 -0.29 0.42 -10000 0 -1.1 22 22
AKT1 -0.14 0.26 -10000 0 -0.85 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.21 -10000 0 -0.77 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.24 -10000 0 -0.96 3 3
THY1 -0.31 0.44 -10000 0 -1.1 20 20
MYB 0.03 0.045 -10000 0 -0.51 1 1
HMGA1 0.034 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.23 0.32 -10000 0 -0.84 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.24 -10000 0 -0.93 3 3
SP1 0.024 0.034 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.049 0.025 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.33 0.46 -10000 0 -1.1 25 25
SOCS1 -0.22 0.31 -10000 0 -0.74 18 18
SOCS3 -0.2 0.27 -10000 0 -0.78 8 8
FCER2 -0.26 0.4 -10000 0 -1.2 11 11
PARP14 0.03 0.041 -10000 0 -0.31 2 2
CCL17 -0.31 0.44 -10000 0 -1.2 18 18
GRB2 0.033 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.18 -10000 0 -0.57 3 3
T cell proliferation -0.29 0.44 -10000 0 -1.1 20 20
IL4R/JAK1 -0.3 0.44 -10000 0 -1.1 20 20
EGR2 -0.32 0.49 -10000 0 -1.3 17 17
JAK2 -0.014 0.07 -10000 0 -0.35 3 3
JAK3 0.02 0.034 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
JAK1 0.01 0.029 -10000 0 -10000 0 0
COL1A2 -0.097 0.17 -10000 0 -10000 0 0
CCL26 -0.31 0.44 -10000 0 -1.2 18 18
IL4R -0.32 0.46 -10000 0 -1.2 19 19
PTPN6 0.04 0.015 -10000 0 -10000 0 0
IL13RA2 -0.33 0.44 -10000 0 -1.1 21 21
IL13RA1 -0.006 0.051 -10000 0 -10000 0 0
IRF4 -0.37 0.64 -10000 0 -1.4 37 37
ARG1 -0.017 0.16 -10000 0 -10000 0 0
CBL -0.22 0.3 -10000 0 -0.8 15 15
GTF3A -0.098 0.15 -10000 0 -0.36 34 34
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.008 0.08 -10000 0 -0.3 2 2
IRF4/BCL6 -0.34 0.6 -10000 0 -1.3 37 37
CD40LG -0.001 0.08 -10000 0 -0.51 1 1
MAPK14 -0.21 0.3 -10000 0 -0.8 15 15
mitosis -0.13 0.24 -10000 0 -0.79 4 4
STAT6 -0.33 0.49 -10000 0 -1.2 22 22
SPI1 0.037 0.018 -10000 0 -10000 0 0
RPS6KB1 -0.13 0.24 -10000 0 -0.81 3 3
STAT6 (dimer) -0.33 0.49 -10000 0 -1.2 22 22
STAT6 (dimer)/PARP14 -0.31 0.47 -10000 0 -1.2 22 22
mast cell activation 0.008 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.25 -10000 0 -0.77 7 7
FRAP1 -0.14 0.26 -10000 0 -0.84 4 4
LTA -0.3 0.43 -10000 0 -1.1 18 18
FES 0.028 0.046 -10000 0 -0.51 1 1
T-helper 1 cell differentiation 0.33 0.48 1.2 22 -10000 0 22
CCL11 -0.41 0.6 -10000 0 -1.4 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.25 -10000 0 -0.8 5 5
IL2RG 0.017 0.057 -10000 0 -0.54 1 1
IL10 -0.3 0.43 -10000 0 -1.1 19 19
IRS1 0.027 0.05 -10000 0 -0.32 3 3
IRS2 0.024 0.016 -10000 0 -10000 0 0
IL4 -0.048 0.12 -10000 0 -10000 0 0
IL5 -0.31 0.44 -10000 0 -1.1 19 19
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.23 0.35 -10000 0 -0.86 18 18
COL1A1 -0.21 0.23 -10000 0 -1.1 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.3 0.45 -10000 0 -1.2 18 18
IL2R gamma/JAK3 0.026 0.062 -10000 0 -0.44 1 1
TFF3 -0.32 0.47 -10000 0 -1.2 19 19
ALOX15 -0.3 0.44 -10000 0 -1.2 19 19
MYBL1 0.025 0.042 -10000 0 -0.32 2 2
T-helper 2 cell differentiation -0.24 0.36 -10000 0 -0.87 21 21
SHC1 0.033 0.006 -10000 0 -10000 0 0
CEBPB 0.017 0.035 -10000 0 -0.31 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.24 -10000 0 -1.1 2 2
mol:PI-3-4-5-P3 -0.14 0.26 -10000 0 -0.84 4 4
PI3K -0.15 0.27 -10000 0 -0.92 4 4
DOK2 0.023 0.047 -10000 0 -0.51 1 1
ETS1 0.038 0.032 -10000 0 -0.28 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.1 0.18 -10000 0 -0.58 4 4
ITGB3 -0.3 0.43 -10000 0 -1.2 17 17
PIGR -0.33 0.51 -10000 0 -1.3 22 22
IGHE 0.07 0.072 0.18 14 -10000 0 14
MAPKKK cascade -0.099 0.18 -10000 0 -0.57 4 4
BCL6 0.031 0.029 -10000 0 -0.32 1 1
OPRM1 -0.3 0.43 -10000 0 -1.1 20 20
RETNLB -0.53 0.7 -10000 0 -1.5 47 47
SELP -0.37 0.57 -10000 0 -1.4 27 27
AICDA -0.32 0.46 -10000 0 -1.2 22 22
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.025 0.004 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.034 0.006 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.062 -9999 0 -10000 0 0
IRAK/TOLLIP 0.039 0.01 -9999 0 -10000 0 0
IKBKB 0.03 0.012 -9999 0 -10000 0 0
IKBKG 0.034 0.004 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.24 0.19 -9999 0 -0.43 57 57
IL1A -0.15 0.17 -9999 0 -0.32 78 78
IL1B -0.081 0.14 -9999 0 -0.25 54 54
IRAK/TRAF6/p62/Atypical PKCs 0.065 0.028 -9999 0 -10000 0 0
IL1R2 -0.18 0.27 -9999 0 -0.51 57 57
IL1R1 0.027 0.063 -9999 0 -0.51 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.062 -9999 0 -10000 0 0
TOLLIP 0.034 0.006 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.033 0.008 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.023 0.003 -9999 0 -10000 0 0
IKK complex/ELKS 0.041 0.057 -9999 0 -10000 0 0
JUN -0.023 0.063 -9999 0 -10000 0 0
MAP3K7 0.034 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.016 0.14 -9999 0 -0.3 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.053 0.13 -9999 0 -0.33 6 6
PIK3R1 0.034 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.041 0.14 -9999 0 -0.31 6 6
IL1 beta fragment/IL1R1/IL1RAP -0.043 0.13 -9999 0 -0.3 16 16
NFKB1 0.034 0.005 -9999 0 -10000 0 0
MAPK8 -0.007 0.068 -9999 0 -0.24 10 10
IRAK1 0.02 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.062 0.14 -9999 0 -0.22 61 61
IRAK4 0.034 0.003 -9999 0 -10000 0 0
PRKCI 0.032 0.029 -9999 0 -0.32 1 1
TRAF6 0.033 0.006 -9999 0 -10000 0 0
PI3K 0.05 0.009 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.01 0.072 -9999 0 -10000 0 0
CHUK 0.032 0.008 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.043 0.13 -9999 0 -0.3 16 16
IL1 beta/IL1R2 -0.18 0.19 -9999 0 -0.36 60 60
IRAK/TRAF6/TAK1/TAB1/TAB2 0.048 0.014 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.12 -9999 0 -0.37 1 1
IRAK3 0.025 0.057 -9999 0 -0.32 4 4
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.028 0.13 -9999 0 -0.28 15 15
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.018 0.067 -9999 0 -0.29 3 3
IL1 alpha/IL1R1/IL1RAP -0.071 0.14 -9999 0 -0.36 6 6
RELA 0.034 0.006 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.034 0.004 -9999 0 -10000 0 0
MYD88 0.034 0.005 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.057 0.022 -9999 0 -10000 0 0
IL1RAP 0.025 0.057 -9999 0 -0.32 4 4
UBE2N 0.034 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 -0.038 0.1 -9999 0 -0.34 1 1
CASP1 -0.002 0.13 -9999 0 -0.47 10 10
IL1RN/IL1R2 -0.21 0.18 -9999 0 -0.4 57 57
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.028 0.14 -9999 0 -0.29 15 15
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.071 -9999 0 -0.34 4 4
PIK3CA 0.034 0.004 -9999 0 -10000 0 0
IL1RN -0.11 0.17 -9999 0 -0.32 59 59
TRAF6/TAK1/TAB1/TAB2 0.048 0.012 -9999 0 -10000 0 0
MAP2K6 0.001 0.073 -9999 0 -0.25 11 11
Signaling events mediated by PRL

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
CCNE1 0.019 0.069 -10000 0 -0.32 6 6
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 0.032 0.029 -10000 0 -0.32 1 1
CDKN1A 0.012 0.049 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.017 0.11 -10000 0 -0.22 32 32
mol:Ca2+ -0.056 0.12 0.38 1 -0.25 22 23
AGT -0.061 0.16 -10000 0 -0.32 39 39
CCNA2 0.057 0.11 -10000 0 -10000 0 0
TUBA1B 0.032 0.029 -10000 0 -0.32 1 1
EGR1 0.011 0.048 -10000 0 -0.2 7 7
CDK2/Cyclin E1 0.051 0.11 -10000 0 -10000 0 0
MAPK3 -0.006 0.14 0.24 19 -0.22 32 51
PRL-2 /Rab GGTase beta 0.048 0.013 -10000 0 -10000 0 0
MAPK1 -0.005 0.13 0.24 18 -0.21 31 49
PTP4A1 0.004 0.024 -10000 0 -10000 0 0
PTP4A3 -0.046 0.14 -10000 0 -0.32 31 31
PTP4A2 0.032 0.008 -10000 0 -10000 0 0
ITGB1 -0.004 0.13 0.24 19 -0.22 32 51
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1 0.02 0.045 -10000 0 -0.3 1 1
Rab GGTase beta/Rab GGTase alpha 0.045 0.017 -10000 0 -10000 0 0
PRL-1/ATF-5 0.097 0.09 0.37 1 -10000 0 1
RABGGTA 0.031 0.01 -10000 0 -10000 0 0
BCAR1 0.012 0.057 -10000 0 -10000 0 0
RHOC 0.014 0.071 -10000 0 -0.41 1 1
RHOA 0.021 0.051 -10000 0 -10000 0 0
cell motility 0.048 0.11 0.26 11 -0.44 1 12
PRL-1/alpha Tubulin 0.097 0.092 0.37 1 -10000 0 1
PRL-3/alpha1 Integrin -0.014 0.11 -10000 0 -0.22 31 31
ROCK1 0.048 0.1 0.26 10 -0.44 1 11
RABGGTB 0.033 0.007 -10000 0 -10000 0 0
CDK2 -0.011 0.12 -10000 0 -0.32 19 19
mitosis 0.004 0.024 -10000 0 -10000 0 0
ATF5 0.034 0.004 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.23 0.33 -9999 0 -1 7 7
PLK1 0.005 0.15 -9999 0 -0.99 3 3
BIRC5 -0.04 0.23 -9999 0 -1.2 5 5
HSPA1B -0.23 0.33 -9999 0 -0.92 13 13
MAP2K1 0.002 0.041 -9999 0 -10000 0 0
BRCA2 -0.2 0.35 -9999 0 -1 8 8
FOXM1 -0.26 0.38 -9999 0 -1.1 13 13
XRCC1 -0.22 0.33 -9999 0 -1 7 7
FOXM1B/p19 -0.28 0.36 -9999 0 -0.98 18 18
Cyclin D1/CDK4 -0.23 0.32 -9999 0 -0.91 11 11
CDC2 -0.24 0.34 -9999 0 -0.97 13 13
TGFA -0.22 0.32 -9999 0 -0.93 10 10
SKP2 -0.23 0.34 -9999 0 -0.99 9 9
CCNE1 0.016 0.071 -9999 0 -0.32 6 6
CKS1B -0.22 0.34 -9999 0 -0.99 9 9
RB1 -0.081 0.17 -9999 0 -0.98 1 1
FOXM1C/SP1 -0.27 0.38 -9999 0 -1.1 14 14
AURKB -0.18 0.42 -9999 0 -1 29 29
CENPF -0.22 0.34 -9999 0 -1 7 7
CDK4 -0.006 0.098 -9999 0 -0.32 12 12
MYC -0.26 0.32 -9999 0 -0.88 17 17
CHEK2 0.002 0.04 -9999 0 -10000 0 0
ONECUT1 -0.23 0.33 -9999 0 -0.92 13 13
CDKN2A -0.083 0.16 -9999 0 -0.32 48 48
LAMA4 -0.22 0.33 -9999 0 -0.98 9 9
FOXM1B/HNF6 -0.25 0.37 -9999 0 -1.1 13 13
FOS -0.28 0.42 -9999 0 -1.2 17 17
SP1 0.031 0.013 -9999 0 -10000 0 0
CDC25B -0.23 0.34 -9999 0 -0.99 9 9
response to radiation -0.012 0.021 -9999 0 -10000 0 0
CENPB -0.2 0.32 -9999 0 -0.96 8 8
CENPA -0.24 0.35 -9999 0 -1 10 10
NEK2 -0.26 0.35 -9999 0 -1 11 11
HIST1H2BA -0.23 0.33 -9999 0 -0.98 9 9
CCNA2 -0.022 0.13 -9999 0 -0.32 22 22
EP300 0.032 0.009 -9999 0 -10000 0 0
CCNB1/CDK1 -0.26 0.37 -9999 0 -1.1 11 11
CCNB2 -0.22 0.33 -9999 0 -0.98 9 9
CCNB1 -0.24 0.35 -9999 0 -1 11 11
ETV5 -0.24 0.33 -9999 0 -1 8 8
ESR1 -0.23 0.35 -9999 0 -1.2 7 7
CCND1 -0.23 0.32 -9999 0 -0.89 13 13
GSK3A 0.004 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.022 0.13 -9999 0 -0.39 7 7
CDK2 -0.014 0.12 -9999 0 -0.32 19 19
G2/M transition of mitotic cell cycle -0.014 0.025 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.22 0.36 -9999 0 -1 12 12
GAS1 -0.34 0.49 -9999 0 -1.3 23 23
MMP2 -0.23 0.33 -9999 0 -0.96 10 10
RB1/FOXM1C -0.21 0.32 -9999 0 -0.97 9 9
CREBBP 0.034 0.005 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.052 0.031 -10000 0 -10000 0 0
RGS9BP 0.021 0.064 -10000 0 -0.32 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + -0.031 0.14 -10000 0 -0.31 25 25
mol:ADP 0.009 0.019 -10000 0 -0.21 1 1
GNAT2 0.028 0.041 -10000 0 -0.32 2 2
RGS9-1/Gbeta5/R9AP -0.055 0.17 -10000 0 -0.32 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.041 0.028 -10000 0 -0.18 2 2
GRK7 0.032 0.029 -10000 0 -0.32 1 1
CNGB3 0.019 0.057 -10000 0 -0.32 4 4
Cone Metarhodopsin II/X-Arrestin 0.026 0 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.14 -10000 0 -0.28 24 24
Cone PDE6 -0.023 0.16 -10000 0 -0.27 38 38
Cone Metarhodopsin II 0.021 0.015 -10000 0 -0.16 1 1
Na + (4 Units) -0.013 0.13 -10000 0 -0.28 24 24
GNAT2/GDP -0.039 0.15 -10000 0 -0.27 39 39
GNB5 0.023 0.057 -10000 0 -0.32 4 4
mol:GMP (4 units) 0.019 0.026 0.19 1 -10000 0 1
Cone Transducin 0.056 0.033 -10000 0 -10000 0 0
SLC24A2 0.034 0.006 -10000 0 -10000 0 0
GNB3/GNGT2 0.047 0.014 -10000 0 -10000 0 0
GNB3 0.034 0.006 -10000 0 -10000 0 0
GNAT2/GTP 0.021 0.028 -10000 0 -0.21 2 2
CNGA3 -0.07 0.21 -10000 0 -0.51 28 28
ARR3 0.035 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.031 0.14 -10000 0 -0.31 25 25
mol:Pi -0.055 0.17 -10000 0 -0.32 39 39
Cone CNG Channel -0.005 0.13 -10000 0 -0.26 23 23
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.034 0.006 -10000 0 -10000 0 0
RGS9 -0.11 0.24 -10000 0 -0.51 39 39
PDE6C 0.032 0.009 -10000 0 -10000 0 0
GNGT2 0.033 0.007 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.034 0.004 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.034 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.056 0.15 -9999 0 -0.5 5 5
Syndecan-3/Neurocan 0.013 0.1 -9999 0 -0.37 9 9
POMC 0.031 0.045 -9999 0 -0.51 1 1
EGFR 0.02 0.077 -9999 0 -0.51 3 3
Syndecan-3/EGFR 0.005 0.11 -9999 0 -0.36 9 9
AGRP 0.035 0 -9999 0 -10000 0 0
NCSTN 0.033 0.006 -9999 0 -10000 0 0
PSENEN 0.033 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.03 0.03 -9999 0 -0.32 1 1
APH1A 0.007 0.12 -9999 0 -0.51 7 7
NCAN 0.034 0.004 -9999 0 -10000 0 0
long-term memory 0.028 0.1 -9999 0 -0.35 9 9
Syndecan-3/IL8 -0.14 0.11 -9999 0 -0.49 10 10
PSEN1 0.031 0.011 -9999 0 -10000 0 0
Src/Cortactin 0.028 0.026 -9999 0 -10000 0 0
FYN 0.031 0.029 -9999 0 -0.32 1 1
limb bud formation -0.009 0.097 -9999 0 -0.38 9 9
MC4R 0.024 0.016 -9999 0 -10000 0 0
SRC 0.019 0.017 -9999 0 -10000 0 0
PTN -0.17 0.26 -9999 0 -0.51 55 55
FGFR/FGF/Syndecan-3 -0.009 0.097 -9999 0 -0.38 9 9
neuron projection morphogenesis -0.023 0.17 -9999 0 -0.49 5 5
Syndecan-3/AgRP 0.013 0.1 -9999 0 -0.37 9 9
Syndecan-3/AgRP/MC4R 0.019 0.1 -9999 0 -0.34 9 9
Fyn/Cortactin 0.047 0.024 -9999 0 -0.22 1 1
SDC3 -0.01 0.098 -9999 0 -0.39 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.14 0.11 -9999 0 -0.48 10 10
IL8 -0.3 0.074 -9999 0 -0.32 139 139
Syndecan-3/Fyn/Cortactin 0.029 0.11 -9999 0 -0.36 9 9
Syndecan-3/CASK -0.012 0.095 -9999 0 -0.37 9 9
alpha-MSH/MC4R 0.033 0.04 -9999 0 -0.35 1 1
Gamma Secretase 0.061 0.087 -9999 0 -0.27 6 6
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.017 0.075 -9999 0 -0.32 7 7
PLK4 0.02 0.069 -9999 0 -0.32 6 6
regulation of centriole replication -0.001 0.067 -9999 0 -0.22 13 13
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.008 0.064 -10000 0 -0.37 4 4
MAP4K4 0.016 0.072 -10000 0 -0.34 3 3
BAG4 0.03 0.011 -10000 0 -10000 0 0
PKC zeta/ceramide -0.038 0.068 0.15 1 -0.2 15 16
NFKBIA 0.031 0.011 -10000 0 -10000 0 0
BIRC3 0.013 0.097 -10000 0 -0.44 6 6
BAX -0.005 0.045 -10000 0 -0.39 1 1
RIPK1 0.034 0.003 -10000 0 -10000 0 0
AKT1 0.006 0.012 -10000 0 -10000 0 0
BAD -0.038 0.069 0.16 1 -0.2 15 16
SMPD1 -0.029 0.12 -10000 0 -0.26 28 28
RB1 0.018 0.098 0.18 26 -0.2 6 32
FADD/Caspase 8 0.035 0.052 -10000 0 -10000 0 0
MAP2K4 -0.033 0.067 0.17 1 -0.23 6 7
NSMAF 0.03 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.03 0.072 0.19 2 -0.22 6 8
EGF -0.11 0.22 -10000 0 -0.44 44 44
mol:ceramide -0.041 0.073 0.16 3 -0.21 15 18
MADD 0.034 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.007 0.055 -10000 0 -0.37 3 3
ASAH1 0.027 0.014 -10000 0 -10000 0 0
negative regulation of cell cycle 0.017 0.098 0.18 26 -0.2 6 32
cell proliferation -0.14 0.13 -10000 0 -0.3 28 28
BID -0.012 0.18 -10000 0 -0.7 9 9
MAP3K1 -0.038 0.069 0.16 1 -0.2 15 16
EIF2A -0.051 0.074 -10000 0 -0.22 4 4
TRADD 0.035 0 -10000 0 -10000 0 0
CRADD 0.03 0.045 -10000 0 -0.51 1 1
MAPK3 -0.025 0.069 0.19 1 -0.23 1 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.031 0.072 -10000 0 -0.27 2 2
Cathepsin D/ceramide -0.03 0.087 0.18 1 -0.22 16 17
FADD 0.026 0.044 -10000 0 -10000 0 0
KSR1 -0.034 0.073 0.17 3 -0.2 14 17
MAPK8 -0.033 0.071 0.17 1 -0.22 8 9
PRKRA -0.039 0.068 0.16 1 -0.2 15 16
PDGFA 0.02 0.077 -10000 0 -0.51 3 3
TRAF2 0.034 0.005 -10000 0 -10000 0 0
IGF1 -0.29 0.27 -10000 0 -0.51 86 86
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.04 0.073 0.16 3 -0.21 15 18
CTSD 0.026 0.063 -10000 0 -0.51 2 2
regulation of nitric oxide biosynthetic process 0.049 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.15 0.14 -10000 0 -0.32 28 28
PRKCD 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.007 0.055 -10000 0 -0.37 3 3
RelA/NF kappa B1 0.05 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.034 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.03 0.06 -10000 0 -0.3 3 3
TNFR1A/BAG4/TNF-alpha 0.06 0.025 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.008 0.064 -10000 0 -0.37 4 4
MAP2K1 -0.029 0.068 -10000 0 -0.24 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.006 -10000 0 -10000 0 0
CYCS 0.078 0.077 0.16 30 -10000 0 30
TNFRSF1A 0.033 0.006 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.044 0.018 -10000 0 -10000 0 0
EIF2AK2 -0.04 0.067 -10000 0 -0.22 7 7
TNF-alpha/TNFR1A/FAN 0.058 0.026 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.037 0.08 -10000 0 -0.4 4 4
MAP2K2 -0.03 0.069 -10000 0 -0.24 1 1
SMPD3 0.02 0.078 -10000 0 -0.32 6 6
TNF 0.034 0.003 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.045 0.1 0.23 28 -10000 0 28
NF kappa B1/RelA/I kappa B alpha 0.07 0.029 -10000 0 -10000 0 0
AIFM1 0.071 0.082 0.17 32 -10000 0 32
BCL2 -0.17 0.25 -10000 0 -0.51 51 51
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.012 -9999 0 -10000 0 0
VLDLR -0.081 0.22 -9999 0 -0.5 31 31
LRPAP1 0.033 0.008 -9999 0 -10000 0 0
NUDC 0.031 0.011 -9999 0 -10000 0 0
RELN/LRP8 -0.14 0.09 -9999 0 -0.22 2 2
CaM/Ca2+ 0.022 0.009 -9999 0 -10000 0 0
KATNA1 0.034 0.006 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.12 0.075 -9999 0 -10000 0 0
IQGAP1/CaM 0.042 0.02 -9999 0 -10000 0 0
DAB1 0.033 0.006 -9999 0 -10000 0 0
IQGAP1 0.032 0.009 -9999 0 -10000 0 0
PLA2G7 0.008 0.12 -9999 0 -0.51 7 7
CALM1 0.03 0.012 -9999 0 -10000 0 0
DYNLT1 0.034 0.006 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.18 0.091 -9999 0 -0.22 120 120
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.034 0.003 -9999 0 -10000 0 0
CDK5R1 0.033 0.007 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.007 -9999 0 -10000 0 0
CDK5R2 0.034 0.003 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.015 0.15 -9999 0 -0.31 28 28
YWHAE 0.027 0.014 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.09 0.087 -9999 0 -10000 0 0
MAP1B 0.007 0.004 -9999 0 -10000 0 0
RAC1 0.013 0.011 -9999 0 -10000 0 0
p35/CDK5 -0.11 0.068 -9999 0 -10000 0 0
RELN 0.032 0.008 -9999 0 -10000 0 0
PAFAH/LIS1 0.011 0.072 -9999 0 -0.3 7 7
LIS1/CLIP170 0.026 0.02 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.064 0.071 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.028 0.13 -9999 0 -0.27 27 27
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.094 0.082 -9999 0 -10000 0 0
LIS1/IQGAP1 0.026 0.02 -9999 0 -10000 0 0
RHOA 0.014 0.011 -9999 0 -10000 0 0
PAFAH1B1 0.013 0.01 -9999 0 -10000 0 0
PAFAH1B3 0.005 0.096 -9999 0 -0.32 12 12
PAFAH1B2 0.034 0.006 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.038 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.089 0.087 -9999 0 -10000 0 0
LRP8 -0.27 0.12 -9999 0 -0.32 126 126
NDEL1/Katanin 60 -0.093 0.088 -9999 0 -10000 0 0
P39/CDK5 -0.11 0.068 -9999 0 -10000 0 0
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.02 -9999 0 -10000 0 0
CDK5 -0.12 0.063 -9999 0 -10000 0 0
PPP2R5D 0.034 0.006 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.017 -9999 0 -10000 0 0
CSNK2A1 0.027 0.015 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0 0.14 -9999 0 -0.27 26 26
RELN/VLDLR -0.18 0.14 -9999 0 -0.4 32 32
CDC42 0.014 0.011 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 0.027 0.09 -10000 0 -0.71 1 1
IHH 0.035 0.062 -10000 0 -0.62 1 1
SHH Np/Cholesterol/GAS1 -0.054 0.15 -10000 0 -0.32 30 30
LRPAP1 0.033 0.008 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.054 0.15 0.32 30 -10000 0 30
SMO/beta Arrestin2 0.038 0.085 -10000 0 -0.53 1 1
SMO 0.027 0.07 -10000 0 -0.56 1 1
AKT1 0.014 0.11 -10000 0 -0.38 2 2
ARRB2 0.027 0.014 -10000 0 -10000 0 0
BOC 0.034 0.004 -10000 0 -10000 0 0
ADRBK1 0.034 0.006 -10000 0 -10000 0 0
heart looping 0.027 0.069 -10000 0 -0.55 1 1
STIL -0.011 0.12 -10000 0 -0.36 7 7
DHH N/PTCH2 0.05 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.046 0.068 -10000 0 -0.49 1 1
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
DHH 0.034 0.003 -10000 0 -10000 0 0
PTHLH 0.026 0.096 -10000 0 -0.86 1 1
determination of left/right symmetry 0.027 0.069 -10000 0 -0.55 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
skeletal system development 0.026 0.095 -10000 0 -0.86 1 1
IHH N/Hhip -0.044 0.19 -10000 0 -0.41 30 30
DHH N/Hhip -0.037 0.17 -10000 0 -0.37 30 30
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.027 0.069 -10000 0 -0.55 1 1
pancreas development -0.078 0.22 -10000 0 -0.51 30 30
HHAT -0.015 0.16 -10000 0 -0.51 13 13
PI3K 0.05 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.07 0.2 -10000 0 -0.45 31 31
somite specification 0.027 0.069 -10000 0 -0.55 1 1
SHH Np/Cholesterol/PTCH1 0.008 0.099 -10000 0 -0.37 3 3
SHH Np/Cholesterol/PTCH2 0.003 0.093 -10000 0 -0.28 13 13
SHH Np/Cholesterol/Megalin 0.004 0.093 -10000 0 -0.28 13 13
SHH -0.016 0.11 0.24 1 -0.36 14 15
catabolic process 0.031 0.07 -10000 0 -0.54 1 1
SMO/Vitamin D3 0.011 0.1 -10000 0 -0.38 3 3
SHH Np/Cholesterol/Hhip -0.057 0.16 -10000 0 -0.32 36 36
LRP2 0.034 0.003 -10000 0 -10000 0 0
receptor-mediated endocytosis 0.007 0.099 -10000 0 -0.39 2 2
SHH Np/Cholesterol/BOC 0.005 0.09 -10000 0 -0.28 12 12
SHH Np/Cholesterol/CDO 0.003 0.093 -10000 0 -0.28 13 13
mesenchymal cell differentiation 0.057 0.16 0.32 36 -10000 0 36
mol:Vitamin D3 0.016 0.11 -10000 0 -0.37 3 3
IHH N/PTCH2 0.05 0.039 -10000 0 -0.39 1 1
CDON 0.034 0.006 -10000 0 -10000 0 0
IHH N/PTCH1 0.039 0.073 -10000 0 -0.55 1 1
Megalin/LRPAP1 0.048 0.012 -10000 0 -10000 0 0
PTCH2 0.034 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.009 0.088 -10000 0 -0.28 13 13
PTCH1 0.031 0.07 -10000 0 -0.55 1 1
HHIP -0.078 0.22 -10000 0 -0.51 30 30
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.005 0.068 -10000 0 -0.32 6 6
GNB1/GNG2 -0.058 0.053 -10000 0 -0.18 6 6
AKT1 -0.039 0.11 -10000 0 -0.31 8 8
EGF -0.11 0.22 -10000 0 -0.44 44 44
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.12 0.087 -10000 0 -0.27 3 3
mol:Ca2+ -0.039 0.11 -10000 0 -0.32 5 5
LYN -0.11 0.092 -10000 0 -0.27 3 3
RhoA/GTP -0.013 0.049 -10000 0 -0.14 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.041 0.11 -10000 0 -0.36 4 4
GNG2 0.031 0.011 -10000 0 -10000 0 0
ARRB2 0.027 0.014 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.081 0.17 -10000 0 -0.51 16 16
G beta5/gamma2 -0.073 0.071 -10000 0 -0.25 6 6
PRKCH -0.048 0.12 -10000 0 -0.41 5 5
DNM1 0.024 0.061 -10000 0 -0.34 4 4
TXA2/TP beta/beta Arrestin3 -0.007 0.03 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.35 0.25 -10000 0 -0.51 101 101
G12 family/GTP -0.042 0.096 -10000 0 -0.32 3 3
ADRBK1 0.034 0.006 -10000 0 -10000 0 0
ADRBK2 0.032 0.009 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.019 -10000 0 -10000 0 0
mol:GDP 0.081 0.1 0.34 10 -10000 0 10
mol:NADP 0.031 0.029 -10000 0 -0.32 1 1
RAB11A 0.032 0.008 -10000 0 -10000 0 0
PRKG1 0.034 0.006 -10000 0 -10000 0 0
mol:IP3 -0.051 0.13 -10000 0 -0.4 6 6
cell morphogenesis 0.036 0.019 -10000 0 -10000 0 0
PLCB2 -0.07 0.17 -10000 0 -0.55 6 6
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.15 0.11 -10000 0 -0.37 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.082 0.1 -10000 0 -0.37 5 5
RHOA 0.034 0.005 -10000 0 -10000 0 0
PTGIR 0.034 0.005 -10000 0 -10000 0 0
PRKCB1 -0.046 0.12 -10000 0 -0.38 6 6
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.031 0.029 -10000 0 -0.32 1 1
TXA2/TXA2-R family -0.066 0.16 -10000 0 -0.54 5 5
LCK -0.12 0.087 -10000 0 -0.28 3 3
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.15 0.11 -10000 0 -0.3 4 4
TXA2-R family/G12 family/GDP/G beta/gamma -0.053 0.14 -10000 0 -0.57 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.15 0.11 -10000 0 -0.29 4 4
MAPK14 -0.026 0.082 -10000 0 -0.25 3 3
TGM2/GTP -0.056 0.14 -10000 0 -0.44 4 4
MAPK11 -0.027 0.082 -10000 0 -0.24 4 4
ARHGEF1 -0.014 0.072 -10000 0 -0.2 2 2
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
JNK cascade -0.048 0.12 -10000 0 -0.4 5 5
RAB11/GDP 0.033 0.009 -10000 0 -10000 0 0
ICAM1 -0.031 0.097 -10000 0 -0.29 4 4
cAMP biosynthetic process -0.051 0.12 -10000 0 -0.38 4 4
Gq family/GTP/EBP50 -0.006 0.08 -10000 0 -0.22 16 16
actin cytoskeleton reorganization 0.036 0.019 -10000 0 -10000 0 0
SRC -0.071 0.092 -10000 0 -0.28 1 1
GNB5 0.023 0.057 -10000 0 -0.32 4 4
GNB1 0.032 0.009 -10000 0 -10000 0 0
EGF/EGFR -0.093 0.11 0.2 1 -0.31 12 13
VCAM1 -0.032 0.1 -10000 0 -0.41 4 4
TP beta/Gq family/GDP/G beta5/gamma2 -0.081 0.17 -10000 0 -0.51 16 16
platelet activation -0.038 0.11 -10000 0 -0.33 3 3
PGI2/IP 0.025 0.004 -10000 0 -10000 0 0
PRKACA -0.18 0.12 -10000 0 -0.26 98 98
Gq family/GDP/G beta5/gamma2 -0.091 0.16 -10000 0 -0.48 17 17
TXA2/TP beta/beta Arrestin2 -0.039 0.072 -10000 0 -0.42 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.17 0.11 -10000 0 -0.24 96 96
mol:DAG -0.054 0.14 -10000 0 -0.43 6 6
EGFR 0.02 0.077 -10000 0 -0.51 3 3
TXA2/TP alpha -0.068 0.16 -10000 0 -0.53 4 4
Gq family/GTP -0.011 0.082 0.23 1 -0.21 18 19
YES1 -0.12 0.09 -10000 0 -0.27 2 2
GNAI2/GTP -0.14 0.099 -10000 0 -0.29 5 5
PGD2/DP -0.26 0.16 -10000 0 -0.37 101 101
SLC9A3R1 0.029 0.045 -10000 0 -0.51 1 1
FYN -0.12 0.086 -10000 0 -0.27 3 3
mol:NO 0.031 0.029 -10000 0 -0.32 1 1
GNA15 0.024 0.057 -10000 0 -0.32 4 4
PGK/cGMP 0.042 0.022 -10000 0 -0.18 1 1
RhoA/GDP 0.035 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.1 0.11 -10000 0 -0.33 4 4
NOS3 0.031 0.03 -10000 0 -0.32 1 1
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCA -0.042 0.12 -10000 0 -0.36 5 5
PRKCB -0.044 0.12 -10000 0 -0.36 6 6
PRKCE -0.044 0.12 -10000 0 -0.38 4 4
PRKCD -0.046 0.12 -10000 0 -0.39 5 5
PRKCG -0.047 0.13 -10000 0 -0.4 5 5
muscle contraction -0.059 0.15 -10000 0 -0.5 5 5
PRKCZ -0.043 0.11 -10000 0 -0.35 5 5
ARR3 0.035 0 -10000 0 -10000 0 0
TXA2/TP beta -0.15 0.11 -10000 0 -0.31 4 4
PRKCQ -0.047 0.12 -10000 0 -0.36 6 6
MAPKKK cascade -0.061 0.15 -10000 0 -0.47 6 6
SELE -0.044 0.11 -10000 0 -0.31 6 6
TP beta/GNAI2/GDP/G beta/gamma -0.14 0.12 -10000 0 -0.31 5 5
ROCK1 0.027 0.014 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.51 6 6
chemotaxis -0.063 0.16 -10000 0 -0.64 4 4
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.033 0.007 -10000 0 -10000 0 0
GNA11 0 0.13 -10000 0 -0.51 9 9
Rac1/GTP 0.023 0.007 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.072 0.13 -10000 0 -0.22 66 66
CRKL 0.021 0.098 -10000 0 -0.47 3 3
mol:PIP3 0.004 0.061 0.45 2 -10000 0 2
AKT1 0.001 0.046 0.31 2 -10000 0 2
PTK2B 0.027 0.014 -10000 0 -10000 0 0
RAPGEF1 0.022 0.096 0.3 1 -0.45 3 4
RANBP10 0.035 0 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.047 0.12 -10000 0 -10000 0 0
MAP3K5 0.034 0.097 -10000 0 -0.56 2 2
HGF/MET/CIN85/CBL/ENDOPHILINS -0.038 0.13 -10000 0 -0.39 4 4
AP1 -0.034 0.11 -10000 0 -0.32 10 10
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
apoptosis -0.1 0.3 -10000 0 -0.76 23 23
STAT3 (dimer) 0.015 0.061 0.23 2 -10000 0 2
GAB1/CRKL/SHP2/PI3K 0.069 0.096 -10000 0 -0.49 2 2
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.04 0.098 -10000 0 -0.51 2 2
PTPN11 0.032 0.029 -10000 0 -0.32 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.019 0.017 -10000 0 -10000 0 0
PTEN 0.025 0.064 -10000 0 -0.51 2 2
ELK1 -0.043 0.11 0.29 6 -10000 0 6
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.049 -10000 0 -0.34 1 1
PAK1 0 0.043 0.28 2 -10000 0 2
HGF/MET/RANBP10 -0.047 0.12 -10000 0 -10000 0 0
HRAS 0.018 0.07 -10000 0 -0.4 1 1
DOCK1 0.019 0.097 -10000 0 -0.45 3 3
GAB1 0.011 0.094 -10000 0 -0.5 3 3
CRK 0.02 0.097 -10000 0 -0.47 3 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.052 -10000 0 -10000 0 0
JUN 0.022 0.064 -10000 0 -0.32 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.046 0.057 -10000 0 -0.22 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.059 0.099 0.28 5 -10000 0 5
GRB2/SHC -0.019 0.077 -10000 0 -10000 0 0
FOS 0.003 0.11 -10000 0 -0.46 8 8
GLMN 0.002 0.013 -10000 0 -0.16 1 1
cell motility -0.043 0.11 0.28 6 -10000 0 6
HGF/MET/MUC20 -0.058 0.11 -10000 0 -0.18 66 66
cell migration -0.02 0.076 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
CBL 0.034 0.006 -10000 0 -10000 0 0
MET/RANBP10 -0.072 0.13 -10000 0 -0.22 66 66
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.013 0.061 -10000 0 -0.28 1 1
MET/MUC20 -0.084 0.12 -10000 0 -0.21 66 66
RAP1B 0.023 0.093 0.29 1 -0.48 2 3
RAP1A 0.019 0.09 0.29 1 -0.48 2 3
HGF/MET/RANBP9 -0.047 0.12 -10000 0 -10000 0 0
RAF1 0.017 0.066 -10000 0 -0.39 1 1
STAT3 0.015 0.061 0.23 2 -10000 0 2
cell proliferation 0.033 0.073 -10000 0 -10000 0 0
RPS6KB1 -0.02 0.058 0.14 1 -0.32 3 4
MAPK3 -0.057 0.12 0.7 2 -10000 0 2
MAPK1 -0.023 0.2 0.66 9 -10000 0 9
RANBP9 0.034 0.003 -10000 0 -10000 0 0
MAPK8 0.038 0.1 -10000 0 -0.5 2 2
SRC 0.019 0.068 -10000 0 -10000 0 0
PI3K -0.021 0.078 -10000 0 -10000 0 0
MET/Glomulin -0.098 0.11 -10000 0 -0.21 69 69
SOS1 0.035 0 -10000 0 -10000 0 0
MAP2K1 0.018 0.066 -10000 0 -10000 0 0
MET -0.12 0.17 -10000 0 -0.32 66 66
MAP4K1 0.034 0.11 -10000 0 -0.62 2 2
PTK2 0.028 0.013 -10000 0 -10000 0 0
MAP2K2 0.018 0.066 -10000 0 -10000 0 0
BAD 0 0.043 0.28 2 -10000 0 2
MAP2K4 0.023 0.089 -10000 0 -0.51 2 2
SHP2/GRB2/SOS1/GAB1 0.036 0.098 -10000 0 -0.48 2 2
INPPL1 0.034 0.005 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.019 0.089 -10000 0 -0.51 4 4
HGS -0.041 0.055 -10000 0 -0.2 1 1
PLCgamma1/PKC 0.014 0.013 -10000 0 -10000 0 0
HGF 0.033 0.008 -10000 0 -10000 0 0
RASA1 0.031 0.029 -10000 0 -0.32 1 1
NCK1 0.034 0.004 -10000 0 -10000 0 0
PTPRJ 0.034 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 0.006 0.056 -10000 0 -10000 0 0
PDPK1 0.001 0.052 0.35 2 -10000 0 2
HGF/MET/SHIP -0.058 0.11 -10000 0 -0.18 66 66
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.045 0.037 -10000 0 -0.37 1 1
Necdin/E2F1 -0.026 0.13 -10000 0 -0.37 15 15
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.054 0.059 -10000 0 -0.27 3 3
NGF (dimer)/p75(NTR)/BEX1 0.042 0.031 -10000 0 -0.31 1 1
NT-4/5 (dimer)/p75(NTR) 0.025 0.005 -10000 0 -10000 0 0
IKBKB 0.03 0.012 -10000 0 -10000 0 0
AKT1 0.022 0.021 -10000 0 -10000 0 0
IKBKG 0.034 0.004 -10000 0 -10000 0 0
BDNF 0.007 0.092 -10000 0 -0.32 11 11
MGDIs/NGR/p75(NTR)/LINGO1 0.041 0.074 -10000 0 -0.34 1 1
FURIN 0.032 0.009 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.043 0.073 -10000 0 -0.32 1 1
LINGO1 0.025 0.05 -10000 0 -0.32 3 3
Sortilin/TRAF6/NRIF 0.02 0.069 -10000 0 -10000 0 0
proBDNF (dimer) 0.007 0.092 -10000 0 -0.31 11 11
NTRK1 0.033 0.006 -10000 0 -10000 0 0
RTN4R 0.009 0.088 -10000 0 -0.32 10 10
neuron apoptosis 0.016 0.081 -10000 0 -0.37 1 1
IRAK1 0.034 0.004 -10000 0 -10000 0 0
SHC1 0.019 0.005 -10000 0 -10000 0 0
ARHGDIA 0.033 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.025 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.061 0.087 -10000 0 -0.27 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.042 0.081 -10000 0 -0.29 8 8
MAGEH1 0.008 0.12 -10000 0 -0.51 7 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.003 0.13 -10000 0 -0.3 23 23
Mammalian IAPs/DIABLO 0.05 0.065 -10000 0 -0.29 4 4
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.032 0.029 -10000 0 -0.32 1 1
APP 0.032 0.009 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.034 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.046 0.012 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.006 0.036 0.21 2 -0.28 1 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.032 0.047 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.044 0.011 -10000 0 -10000 0 0
NCSTN 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.095 0.17 -10000 0 -0.31 55 55
PSENEN 0.033 0.007 -10000 0 -10000 0 0
mol:ceramide 0.021 0.033 0.19 2 -0.28 1 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.028 0.043 -10000 0 -10000 0 0
p75(NTR)/beta APP 0.047 0.014 -10000 0 -10000 0 0
BEX1 0.031 0.045 -10000 0 -0.51 1 1
mol:GDP 0.005 0.001 -10000 0 -10000 0 0
NGF (dimer) -0.15 0.051 -10000 0 -0.21 2 2
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.057 0.075 -10000 0 -0.31 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.036 0.014 -10000 0 -10000 0 0
MYD88 0.034 0.005 -10000 0 -10000 0 0
CHUK 0.032 0.008 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.095 0.17 -10000 0 -0.31 55 55
RHOB 0.011 0.088 -10000 0 -0.32 10 10
RHOA 0.034 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.022 0.043 -10000 0 -0.22 3 3
NT3 (dimer) 0.031 0.029 -10000 0 -0.31 1 1
TP53 -0.002 0.053 -10000 0 -10000 0 0
PRDM4 0.022 0.033 0.19 2 -0.28 1 3
BDNF (dimer) -0.3 0.066 -10000 0 -0.32 129 129
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
SORT1 0.029 0.045 -10000 0 -0.51 1 1
activation of caspase activity 0.048 0.056 -10000 0 -0.27 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.058 0.035 -10000 0 -0.29 1 1
RHOC 0.033 0.008 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.018 0.071 0.24 2 -10000 0 2
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 0.022 0.033 0.19 2 -0.28 1 3
APH1B 0.03 0.03 -10000 0 -0.32 1 1
APH1A 0.007 0.12 -10000 0 -0.51 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.04 0.032 -10000 0 -0.31 1 1
PSEN1 0.031 0.011 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.015 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.046 0.025 -10000 0 -0.22 1 1
MAPK8 0.021 0.063 0.24 1 -10000 0 1
MAPK9 0.022 0.063 0.24 1 -10000 0 1
APAF1 0.034 0.003 -10000 0 -10000 0 0
NTF3 0.031 0.029 -10000 0 -0.32 1 1
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.054 0.2 -10000 0 -0.51 23 23
RAC1/GDP 0.023 0.008 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.067 0.16 -10000 0 -0.38 3 3
p75 CTF/Sortilin/TRAF6/NRIF 0.079 0.039 -10000 0 -0.29 1 1
RhoA-B-C/GTP -0.095 0.17 -10000 0 -0.31 55 55
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.072 0.076 -10000 0 -0.27 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.06 0.074 -10000 0 -0.29 1 1
PRKACB -0.17 0.26 -10000 0 -0.51 55 55
proBDNF (dimer)/p75 ECD 0.03 0.071 -10000 0 -0.22 11 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.013 0.097 -10000 0 -0.44 6 6
BIRC2 0.033 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.12 0.14 -10000 0 -0.38 18 18
BAD 0.017 0.069 0.23 1 -10000 0 1
RIPK2 -0.012 0.11 -10000 0 -0.32 17 17
NGFR 0.033 0.007 -10000 0 -10000 0 0
CYCS 0.015 0.04 -10000 0 -0.27 2 2
ADAM17 0.035 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.026 0.073 -10000 0 -10000 0 0
BCL2L11 0.018 0.069 0.23 1 -10000 0 1
BDNF (dimer)/p75(NTR) 0.028 0.071 -10000 0 -10000 0 0
PI3K 0.062 0.018 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.053 0.041 -10000 0 -0.29 1 1
NDNL2 0.029 0.03 -10000 0 -0.32 1 1
YWHAE 0.027 0.014 -10000 0 -10000 0 0
PRKCI 0.032 0.029 -10000 0 -0.32 1 1
NGF (dimer)/p75(NTR) 0.025 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.057 0.038 -10000 0 -0.29 1 1
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.034 0.006 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.015 0.05 -10000 0 -0.31 1 1
SQSTM1 0.034 0.004 -10000 0 -10000 0 0
NGFRAP1 0.027 0.063 -10000 0 -0.51 2 2
CASP3 0.015 0.068 -10000 0 -10000 0 0
E2F1 0.015 0.042 -10000 0 -0.32 2 2
CASP9 0.031 0.01 -10000 0 -10000 0 0
IKK complex 0.057 0.045 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0.025 0.005 -10000 0 -10000 0 0
MMP7 -0.3 0.076 -10000 0 -0.32 139 139
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.071 0.038 -10000 0 -0.27 1 1
MMP3 -0.29 0.092 -10000 0 -0.32 135 135
APAF-1/Caspase 9 0.006 0.053 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.057 -10000 0 -10000 0 0
VDR 0.012 0.11 -10000 0 -0.51 6 6
FAM120B 0.034 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.056 0.031 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.066 0.034 -10000 0 -10000 0 0
MED1 0.033 0.008 -10000 0 -10000 0 0
mol:9cRA 0.006 0.002 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.024 0.073 -10000 0 -0.46 1 1
RXRs/NUR77 0.093 0.034 -10000 0 -10000 0 0
RXRs/PPAR 0.029 0.065 -10000 0 -10000 0 0
NCOR2 0.034 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0.078 -10000 0 -0.37 6 6
RARs/VDR/DNA/Vit D3 0.057 0.076 -10000 0 -0.27 6 6
RARA 0.032 0.009 -10000 0 -10000 0 0
NCOA1 0.027 0.063 -10000 0 -0.51 2 2
VDR/VDR/DNA 0.012 0.11 -10000 0 -0.51 6 6
RARs/RARs/DNA/9cRA 0.056 0.031 -10000 0 -10000 0 0
RARG 0.03 0.041 -10000 0 -0.32 2 2
RPS6KB1 0.02 0.074 0.53 3 -10000 0 3
RARs/THRs/DNA/SMRT 0.027 0.061 -10000 0 -10000 0 0
THRA 0.032 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.009 0.078 -10000 0 -0.37 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.078 0.024 -10000 0 -10000 0 0
NR1H4 -0.42 0.2 -10000 0 -0.51 121 121
RXRs/LXRs/DNA 0.11 0.051 -10000 0 -10000 0 0
NR1H2 0.04 0.005 -10000 0 -10000 0 0
NR1H3 0.036 0.045 -10000 0 -0.5 1 1
RXRs/VDR/DNA/Vit D3 0.073 0.073 -10000 0 -0.26 6 6
NR4A1 0.032 0.029 -10000 0 -0.32 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.18 0.1 -10000 0 -0.32 7 7
RXRG 0.038 0.007 -10000 0 -10000 0 0
RXR alpha/CCPG 0.053 0.011 -10000 0 -10000 0 0
RXRA 0.039 0.006 -10000 0 -10000 0 0
RXRB 0.04 0.005 -10000 0 -10000 0 0
THRB 0.004 0.12 -10000 0 -0.51 8 8
PPARG 0.004 0.12 -10000 0 -0.51 8 8
PPARD 0.035 0 -10000 0 -10000 0 0
TNF 0.058 0.032 -10000 0 -10000 0 0
mol:Oxysterols 0.005 0.002 -10000 0 -10000 0 0
cholesterol transport 0.066 0.033 -10000 0 -10000 0 0
PPARA 0.028 0.046 -10000 0 -0.51 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.034 0.005 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.092 0.12 -10000 0 -0.23 48 48
SREBF1 0.047 0.036 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.079 0.024 -10000 0 -10000 0 0
ABCA1 0.057 0.031 -10000 0 -10000 0 0
RARs/THRs 0.073 0.088 -10000 0 -0.27 7 7
RXRs/FXR -0.21 0.14 -10000 0 -0.28 116 116
BCL2 -0.17 0.25 -10000 0 -0.51 51 51
IL2 signaling events mediated by PI3K

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
BCL2L1 0.078 0.095 -10000 0 -10000 0 0
UGCG -0.014 0.1 -10000 0 -0.83 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT -0.19 0.21 -10000 0 -0.54 24 24
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.014 0.098 -10000 0 -0.81 2 2
mol:DAG 0.042 0.12 -10000 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.25 0.22 -10000 0 -0.46 65 65
FRAP1 -0.29 0.26 -10000 0 -0.52 67 67
FOXO3 -0.16 0.17 -10000 0 -0.44 18 18
AKT1 -0.18 0.18 -10000 0 -0.44 26 26
GAB2 0.028 0.006 -10000 0 -10000 0 0
SMPD1 -0.17 0.33 -10000 0 -0.78 32 32
SGMS1 -0.011 0.079 -10000 0 -0.64 2 2
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 -0.01 0.013 -10000 0 -10000 0 0
CALM1 0.03 0.012 -10000 0 -10000 0 0
cell proliferation -0.027 0.11 -10000 0 -0.53 3 3
EIF3A 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.04 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.024 0.17 -10000 0 -1 4 4
mol:sphingomyelin 0.042 0.12 -10000 0 -0.64 2 2
natural killer cell activation -0.007 0.005 -10000 0 -0.016 8 8
JAK3 0.03 0.007 -10000 0 -10000 0 0
PIK3R1 0.029 0.008 -10000 0 -10000 0 0
JAK1 0.029 0.008 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MYC -0.16 0.17 -10000 0 -0.47 13 13
MYB 0.019 0.12 -10000 0 -1.3 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.081 0.12 -10000 0 -0.41 6 6
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.16 -10000 0 -0.92 4 4
mol:PI-3-4-5-P3 -0.08 0.11 -10000 0 -0.4 6 6
Rac1/GDP 0.01 0.022 -10000 0 -10000 0 0
T cell proliferation -0.076 0.11 -10000 0 -0.39 5 5
SHC1 0.028 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.006 -10000 0 -0.066 1 1
PRKCZ -0.078 0.11 -10000 0 -0.4 5 5
NF kappa B1 p50/RelA -0.25 0.23 -10000 0 -0.47 60 60
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.023 0.05 -10000 0 -0.41 1 1
HSP90AA1 0.03 0.012 -10000 0 -10000 0 0
RELA 0.034 0.006 -10000 0 -10000 0 0
IL2RA 0.016 0.063 -10000 0 -0.32 5 5
IL2RB 0.028 0.01 -10000 0 -10000 0 0
TERT 0.033 0.008 -10000 0 -10000 0 0
E2F1 0.019 0.062 -10000 0 -0.43 1 1
SOS1 0.029 0.004 -10000 0 -10000 0 0
RPS6 0.034 0.006 -10000 0 -10000 0 0
mol:cAMP -0.002 0.003 0.031 1 -10000 0 1
PTPN11 0.025 0.029 -10000 0 -0.32 1 1
IL2RG 0.026 0.045 -10000 0 -0.51 1 1
actin cytoskeleton organization -0.076 0.11 -10000 0 -0.39 5 5
GRB2 0.028 0.007 -10000 0 -10000 0 0
IL2 0.029 0.008 -10000 0 -10000 0 0
PIK3CA 0.029 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.009 0.035 -10000 0 -10000 0 0
LCK 0.025 0.03 -10000 0 -0.32 1 1
BCL2 -0.54 0.44 -10000 0 -0.89 88 88
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.055 0.025 -10000 0 -10000 0 0
AES 0.053 0.02 -10000 0 -10000 0 0
FBXW11 0.034 0.004 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.047 0.014 -10000 0 -10000 0 0
SMAD4 0.023 0.016 -10000 0 -10000 0 0
DKK2 -0.12 0.17 -10000 0 -0.32 65 65
TLE1 0.052 0.019 -10000 0 -10000 0 0
MACF1 0.034 0.006 -10000 0 -10000 0 0
CTNNB1 0.062 0.065 -10000 0 -10000 0 0
WIF1 -0.03 0.14 -10000 0 -0.32 27 27
beta catenin/RanBP3 0.17 0.12 0.33 33 -10000 0 33
KREMEN2 -0.023 0.13 -10000 0 -0.32 24 24
DKK1 -0.043 0.14 -10000 0 -0.32 32 32
beta catenin/beta TrCP1 0.079 0.064 -10000 0 -10000 0 0
FZD1 0.033 0.008 -10000 0 -10000 0 0
AXIN2 -0.15 0.18 -10000 0 -1.6 1 1
AXIN1 0.035 0.005 -10000 0 -10000 0 0
RAN 0.035 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.056 0.064 -10000 0 -0.5 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.003 0.17 -10000 0 -0.63 5 5
Axin1/APC/GSK3 0.07 0.062 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.053 0.063 -10000 0 -10000 0 0
HNF1A 0.054 0.018 -10000 0 -10000 0 0
CTBP1 0.052 0.022 -10000 0 -10000 0 0
MYC -0.044 0.24 0.56 9 -10000 0 9
RANBP3 0.035 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.07 0.15 -10000 0 -0.34 14 14
NKD1 -0.22 0.16 -10000 0 -0.32 106 106
TCF4 0.038 0.031 -10000 0 -10000 0 0
TCF3 0.052 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.081 0.028 -10000 0 -10000 0 0
Ran/GTP 0.027 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.13 0.14 0.4 13 -0.44 1 14
LEF1 -0.021 0.15 -10000 0 -0.3 32 32
DVL1 0.053 0.065 -10000 0 -0.47 1 1
CSNK2A1 0.027 0.015 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.009 0.1 -10000 0 -0.52 3 3
DKK1/LRP6/Kremen 2 -0.024 0.13 -10000 0 -0.33 9 9
LRP6 0.034 0.005 -10000 0 -10000 0 0
CSNK1A1 0.058 0.022 -10000 0 -10000 0 0
NLK 0.029 0.009 -10000 0 -10000 0 0
CCND1 -0.084 0.1 -10000 0 -10000 0 0
WNT1 0.034 0.003 -10000 0 -10000 0 0
GSK3A 0.034 0.005 -10000 0 -10000 0 0
GSK3B 0.034 0.004 -10000 0 -10000 0 0
FRAT1 0.028 0.045 -10000 0 -0.51 1 1
PPP2R5D 0.13 0.075 0.24 7 -10000 0 7
APC 0.032 0.058 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.05 0.047 -10000 0 -10000 0 0
CREBBP 0.053 0.019 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.045 0.017 -10000 0 -10000 0 0
HSPA8 0.03 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.002 0.084 -10000 0 -0.38 2 2
AKT1 -0.055 0.056 -10000 0 -10000 0 0
GSC -0.061 0.16 -10000 0 -0.64 2 2
NKX2-5 0.023 0.043 -10000 0 -0.31 1 1
muscle cell differentiation 0.098 0.16 0.56 7 -10000 0 7
SMAD2-3/SMAD4/SP1 -0.097 0.11 -10000 0 -0.34 2 2
SMAD4 -0.02 0.045 -10000 0 -10000 0 0
CBFB 0.027 0.05 -10000 0 -0.32 3 3
SAP18 0.024 0.015 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.053 0.093 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.052 0.1 -10000 0 -10000 0 0
MYC -0.048 0.14 -10000 0 -0.19 63 63
CDKN2B -1.2 0.58 -10000 0 -1.4 119 119
AP1 -0.011 0.098 -10000 0 -0.35 4 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.039 0.14 -10000 0 -0.4 14 14
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.32 0.22 -10000 0 -0.45 93 93
SP3 0.036 0.003 -10000 0 -10000 0 0
CREB1 0.035 0 -10000 0 -10000 0 0
FOXH1 0.02 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.035 0.12 -10000 0 -0.37 13 13
GATA3 0.031 0.031 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.02 0.074 -10000 0 -0.46 1 1
MEF2C/TIF2 -0.045 0.15 -10000 0 -0.52 11 11
endothelial cell migration -0.014 0.11 -10000 0 -10000 0 0
MAX 0.033 0.014 -10000 0 -10000 0 0
RBBP7 0.033 0.003 -10000 0 -10000 0 0
RBBP4 0.031 0.008 -10000 0 -10000 0 0
RUNX2 0.034 0.004 -10000 0 -10000 0 0
RUNX3 0.004 0.11 -10000 0 -0.46 8 8
RUNX1 -0.071 0.16 -10000 0 -0.32 43 43
CTBP1 0.033 0.008 -10000 0 -10000 0 0
NR3C1 -0.012 0.16 -10000 0 -0.51 13 13
VDR 0.012 0.11 -10000 0 -0.51 6 6
CDKN1A -0.062 0.18 -10000 0 -1.5 2 2
KAT2B 0.004 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.034 0.072 -10000 0 -10000 0 0
DCP1A 0.034 0.005 -10000 0 -10000 0 0
SKI 0.031 0.009 -10000 0 -10000 0 0
SERPINE1 0.014 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.008 0.062 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.015 0.072 -10000 0 -0.3 1 1
SAP30 0.031 0.008 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.095 0.051 -10000 0 -10000 0 0
JUN -0.027 0.09 -10000 0 -0.35 4 4
SMAD3/SMAD4/IRF7 0.002 0.061 -10000 0 -10000 0 0
TFE3 0.036 0.007 -10000 0 -10000 0 0
COL1A2 -0.034 0.1 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.008 0.061 -10000 0 -10000 0 0
DLX1 0.03 0.041 -10000 0 -0.32 2 2
TCF3 0.033 0.007 -10000 0 -10000 0 0
FOS -0.001 0.12 -10000 0 -0.48 8 8
SMAD3/SMAD4/Max -0.003 0.067 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.073 0.027 -10000 0 -10000 0 0
ZBTB17 0.075 0.036 -10000 0 -10000 0 0
LAMC1 -0.017 0.039 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.058 -10000 0 -10000 0 0
IRF7 0.037 0.006 -10000 0 -10000 0 0
ESR1 0.027 0.064 -10000 0 -0.51 2 2
HNF4A 0.011 0.064 -10000 0 -0.51 2 2
MEF2C -0.052 0.16 -10000 0 -0.51 13 13
SMAD2-3/SMAD4 -0.066 0.088 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.079 0.055 -10000 0 -0.3 2 2
IGHV3OR16-13 -0.006 0.027 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0.057 -10000 0 -0.31 4 4
CREBBP 0.044 0.011 -10000 0 -10000 0 0
SKIL 0.025 0.057 -10000 0 -0.32 4 4
HDAC1 0.031 0.008 -10000 0 -10000 0 0
HDAC2 0.032 0.006 -10000 0 -10000 0 0
SNIP1 0.031 0.006 -10000 0 -10000 0 0
GCN5L2 0.012 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.002 0.059 -10000 0 -10000 0 0
MSG1/HSC70 0.01 0.088 -10000 0 -0.22 19 19
SMAD2 -0.039 0.053 -10000 0 -10000 0 0
SMAD3 -0.024 0.042 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.011 0.066 -10000 0 -0.32 1 1
SMAD2/SMAD2/SMAD4 -0.059 0.074 -10000 0 -0.2 19 19
NCOR1 0.025 0.014 -10000 0 -10000 0 0
NCOA2 0.03 0.012 -10000 0 -10000 0 0
NCOA1 0.027 0.063 -10000 0 -0.51 2 2
MYOD/E2A 0.046 0.025 -10000 0 -0.22 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 -0.095 0.11 -10000 0 -0.32 2 2
IFNB1 -0.015 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.063 0.17 -10000 0 -0.53 12 12
CITED1 -0.012 0.12 -10000 0 -0.32 19 19
SMAD2-3/SMAD4/ARC105 -0.053 0.085 -10000 0 -10000 0 0
RBL1 0.012 0.05 -10000 0 -0.32 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.39 0.27 -10000 0 -0.56 98 98
RUNX1-3/PEBPB2 -0.032 0.13 -10000 0 -0.34 6 6
SMAD7 -0.068 0.14 -10000 0 -0.47 6 6
MYC/MIZ-1 0.1 0.12 -10000 0 -0.22 8 8
SMAD3/SMAD4 0.057 0.12 0.33 2 -10000 0 2
IL10 -0.014 0.054 -10000 0 -10000 0 0
PIASy/HDAC complex 0.006 0.026 -10000 0 -10000 0 0
PIAS3 0.036 0.03 -10000 0 -0.32 1 1
CDK2 -0.002 0.12 -10000 0 -0.31 19 19
IL5 -0.025 0.085 -10000 0 -0.33 3 3
CDK4 0.017 0.096 -10000 0 -0.3 12 12
PIAS4 0.007 0.026 -10000 0 -10000 0 0
ATF3 0.022 0.064 -10000 0 -0.32 5 5
SMAD3/SMAD4/SP1 -0.047 0.083 -10000 0 -0.33 1 1
FOXG1 -0.015 0.12 -10000 0 -0.32 19 19
FOXO3 -0.075 0.064 -10000 0 -10000 0 0
FOXO1 -0.06 0.088 -10000 0 -0.46 4 4
FOXO4 -0.073 0.063 -10000 0 -10000 0 0
heart looping -0.052 0.16 -10000 0 -0.5 13 13
CEBPB -0.018 0.042 -10000 0 -0.37 1 1
SMAD3/SMAD4/DLX1 -0.011 0.067 -10000 0 -0.26 1 1
MYOD1 0.031 0.029 -10000 0 -0.32 1 1
SMAD3/SMAD4/HNF4 -0.002 0.056 -10000 0 -0.31 2 2
SMAD3/SMAD4/GATA3 0.001 0.074 -10000 0 -10000 0 0
SnoN/SIN3/HDAC complex/NCoR1 0.024 0.057 -10000 0 -0.31 4 4
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.051 0.12 -10000 0 -0.36 4 4
SMAD3/SMAD4/SP1-3 -0.031 0.081 -10000 0 -10000 0 0
MED15 0.032 0.008 -10000 0 -10000 0 0
SP1 -0.029 0.039 -10000 0 -10000 0 0
SIN3B 0.033 0.005 -10000 0 -10000 0 0
SIN3A 0.031 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.034 0.096 -10000 0 -0.32 8 8
ITGB5 -0.043 0.055 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.024 0.081 -10000 0 -0.49 2 2
SMAD3/SMAD4/AR -0.009 0.065 -10000 0 -0.26 1 1
AR 0.032 0.029 -10000 0 -0.32 1 1
negative regulation of cell growth -0.029 0.091 -10000 0 -0.35 4 4
SMAD3/SMAD4/MYOD -0.008 0.064 -10000 0 -10000 0 0
E2F5 -0.062 0.15 -10000 0 -0.32 38 38
E2F4 0.035 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.022 0.074 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.33 0.24 -10000 0 -0.46 107 107
TFDP1 0.017 0.051 -10000 0 -0.32 3 3
SMAD3/SMAD4/AP1 -0.005 0.1 -10000 0 -0.35 4 4
SMAD3/SMAD4/RUNX2 -0.008 0.062 -10000 0 -10000 0 0
TGIF2 0.01 0.057 -10000 0 -0.32 4 4
TGIF1 -0.015 0.11 -10000 0 -0.32 17 17
ATF2 0.034 0.003 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.1 0.096 -9999 0 -0.32 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.098 0.11 -9999 0 -0.37 1 1
alphaV/beta3 Integrin/Osteopontin/Src -0.14 0.12 -9999 0 -0.23 48 48
AP1 -0.1 0.11 -9999 0 -0.41 1 1
ILK -0.1 0.094 -9999 0 -0.32 1 1
bone resorption -0.088 0.093 -9999 0 -10000 0 0
PTK2B 0.027 0.014 -9999 0 -10000 0 0
PYK2/p130Cas -0.08 0.1 -9999 0 -0.3 1 1
ITGAV 0.033 0.03 -9999 0 -0.32 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.037 0.057 -9999 0 -0.22 7 7
alphaV/beta3 Integrin/Osteopontin -0.11 0.11 -9999 0 -0.36 1 1
MAP3K1 -0.1 0.094 -9999 0 -0.33 1 1
JUN 0.022 0.063 -9999 0 -0.31 5 5
MAPK3 -0.12 0.1 -9999 0 -0.4 3 3
MAPK1 -0.11 0.097 -9999 0 -0.35 1 1
Rac1/GDP 0.023 0.008 -9999 0 -10000 0 0
NFKB1 0.034 0.005 -9999 0 -10000 0 0
MAPK8 -0.096 0.088 -9999 0 -0.31 1 1
ITGB3 0.034 0.008 -9999 0 -10000 0 0
NFKBIA -0.1 0.094 -9999 0 -0.33 2 2
FOS 0.003 0.11 -9999 0 -0.46 8 8
CD44 0.017 0.075 -9999 0 -0.32 7 7
CHUK 0.032 0.008 -9999 0 -10000 0 0
PLAU -0.14 0.15 -9999 0 -0.62 1 1
NF kappa B1 p50/RelA -0.1 0.12 -9999 0 -0.44 1 1
BCAR1 0.034 0.004 -9999 0 -10000 0 0
RELA 0.034 0.006 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.048 0.026 -9999 0 -0.22 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.1 0.094 -9999 0 -0.33 1 1
VAV3 -0.15 0.15 -9999 0 -0.42 28 28
MAP3K14 -0.11 0.096 -9999 0 -0.34 1 1
ROCK2 0.035 0 -9999 0 -10000 0 0
SPP1 -0.22 0.16 -9999 0 -0.32 106 106
RAC1 0.031 0.01 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.14 -9999 0 -0.39 27 27
MMP2 -0.097 0.085 -9999 0 -0.41 1 1
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.03 0.11 -10000 0 -0.37 7 7
HDAC1 0.038 0.012 -10000 0 -10000 0 0
AES 0.035 0.007 -10000 0 -10000 0 0
FBXW11 0.034 0.004 -10000 0 -10000 0 0
DTX1 0.034 0.004 -10000 0 -10000 0 0
LRP6/FZD1 0.047 0.014 -10000 0 -10000 0 0
TLE1 0.035 0.006 -10000 0 -10000 0 0
AP1 -0.083 0.11 -10000 0 -0.28 24 24
NCSTN 0.033 0.006 -10000 0 -10000 0 0
ADAM10 0.032 0.009 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.001 0.094 -10000 0 -0.67 2 2
NICD/RBPSUH 0.026 0.11 -10000 0 -0.36 7 7
WIF1 -0.03 0.14 -10000 0 -0.32 27 27
NOTCH1 0.004 0.11 -10000 0 -0.38 11 11
PSENEN 0.033 0.007 -10000 0 -10000 0 0
KREMEN2 -0.024 0.13 -10000 0 -0.32 24 24
DKK1 -0.043 0.14 -10000 0 -0.32 32 32
beta catenin/beta TrCP1 0.078 0.07 -10000 0 -10000 0 0
APH1B 0.03 0.03 -10000 0 -0.32 1 1
APH1A 0.007 0.12 -10000 0 -0.51 7 7
AXIN1 -0.021 0.075 -10000 0 -0.66 1 1
CtBP/CBP/TCF1/TLE1/AES 0.057 0.04 -10000 0 -10000 0 0
PSEN1 0.03 0.011 -10000 0 -10000 0 0
FOS 0.003 0.11 -10000 0 -0.46 8 8
JUN 0.022 0.064 -10000 0 -0.32 5 5
MAP3K7 0.037 0.006 -10000 0 -10000 0 0
CTNNB1 0.061 0.072 0.25 1 -10000 0 1
MAPK3 0.027 0.063 -10000 0 -0.51 2 2
DKK2/LRP6/Kremen 2 -0.071 0.15 -10000 0 -0.34 14 14
HNF1A 0.036 0.004 -10000 0 -10000 0 0
CTBP1 0.034 0.009 -10000 0 -10000 0 0
MYC -0.088 0.11 -10000 0 -10000 0 0
NKD1 -0.22 0.16 -10000 0 -0.31 106 106
FZD1 0.032 0.008 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.027 0.11 -10000 0 -0.37 2 2
apoptosis -0.083 0.1 -10000 0 -0.28 24 24
Delta 1/NOTCHprecursor 0.027 0.11 -10000 0 -0.36 7 7
DLL1 0.034 0.005 -10000 0 -10000 0 0
PPARD 0.023 0.02 -10000 0 -10000 0 0
Gamma Secretase 0.06 0.087 -10000 0 -0.27 6 6
APC -0.037 0.1 -10000 0 -0.4 8 8
DVL1 0.012 0.079 -10000 0 -0.58 2 2
CSNK2A1 0.026 0.014 -10000 0 -10000 0 0
MAP3K7IP1 0.003 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.024 0.13 -10000 0 -0.33 9 9
LRP6 0.034 0.005 -10000 0 -10000 0 0
CSNK1A1 0.033 0.004 -10000 0 -10000 0 0
NLK 0.026 0.011 -10000 0 -10000 0 0
CCND1 -0.026 0.14 -10000 0 -0.83 3 3
WNT1 0.034 0.003 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.015 0.12 0.28 1 -0.45 3 4
DKK2 -0.12 0.17 -10000 0 -0.32 65 65
NOTCH1 precursor/DVL1 0.012 0.15 -10000 0 -0.53 7 7
GSK3B 0.035 0.004 -10000 0 -10000 0 0
FRAT1 0.03 0.046 -10000 0 -0.51 1 1
NOTCH/Deltex homolog 1 0.031 0.11 -10000 0 -0.37 2 2
PPP2R5D 0.12 0.073 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.039 0.093 -10000 0 -10000 0 0
RBPJ 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.029 0.007 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.022 0.08 -10000 0 -0.51 3 3
PDGF/PDGFRA/CRKL 0.041 0.06 -10000 0 -0.36 3 3
positive regulation of JUN kinase activity 0.073 0.056 -10000 0 -0.27 3 3
CRKL 0.032 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.043 0.059 -10000 0 -0.36 3 3
AP1 -0.018 0.2 -10000 0 -0.75 7 7
mol:IP3 0.022 0.077 0.22 12 -0.37 2 14
PLCG1 0.022 0.077 0.22 12 -0.37 2 14
PDGF/PDGFRA/alphaV Integrin 0.042 0.063 -10000 0 -0.32 4 4
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
CRK 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.077 0.22 12 -0.37 2 14
CAV3 0.033 0.006 -10000 0 -10000 0 0
CAV1 0.026 0.05 -10000 0 -0.32 3 3
SHC/Grb2/SOS1 0.075 0.057 -10000 0 -0.27 3 3
PDGF/PDGFRA/Shf -0.008 0.12 -10000 0 -0.24 28 28
FOS -0.034 0.18 0.32 3 -0.74 7 10
JUN -0.015 0.043 -10000 0 -0.23 3 3
oligodendrocyte development 0.042 0.063 -10000 0 -0.32 4 4
GRB2 0.033 0.007 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:DAG 0.022 0.077 0.22 12 -0.37 2 14
PDGF/PDGFRA 0.022 0.08 -10000 0 -0.51 3 3
actin cytoskeleton reorganization 0.037 0.069 -10000 0 -0.28 6 6
SRF 0.011 0.014 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.063 0.048 -10000 0 -0.3 2 2
PDGF/PDGFRA/Crk/C3G 0.047 0.06 -10000 0 -0.3 3 3
JAK1 0.013 0.055 -10000 0 -0.36 3 3
ELK1/SRF 0.036 0.073 -10000 0 -0.29 2 2
SHB 0.027 0.05 -10000 0 -0.32 3 3
SHF -0.03 0.13 -10000 0 -0.32 26 26
CSNK2A1 0.019 0.023 -10000 0 -10000 0 0
GO:0007205 0.019 0.084 0.25 12 -0.39 2 14
SOS1 0.035 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.073 0.056 -10000 0 -0.27 3 3
PDGF/PDGFRA/SHB 0.038 0.069 -10000 0 -0.28 6 6
PDGF/PDGFRA/Caveolin-1 0.036 0.07 -10000 0 -0.29 6 6
ITGAV 0.032 0.029 -10000 0 -0.32 1 1
ELK1 0.036 0.096 0.22 25 -0.34 2 27
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.033 0.061 -10000 0 -0.36 3 3
JAK-STAT cascade 0.013 0.055 -10000 0 -0.36 3 3
cell proliferation -0.008 0.12 -10000 0 -0.24 28 28
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.028 0.079 -9999 0 -0.31 5 5
alphaM/beta2 Integrin/GPIbA 0.024 0.073 -9999 0 -0.33 4 4
alphaM/beta2 Integrin/proMMP-9 0.016 0.06 -9999 0 -0.25 2 2
PLAUR 0.034 0.005 -9999 0 -10000 0 0
HMGB1 -0.002 0.026 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.03 0.077 -9999 0 -0.34 4 4
AGER -0.002 0.034 -9999 0 -10000 0 0
RAP1A 0.033 0.008 -9999 0 -10000 0 0
SELPLG 0.019 0.089 -9999 0 -0.51 4 4
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.017 0.081 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 0.005 0.071 -9999 0 -0.35 5 5
CYR61 -0.001 0.1 -9999 0 -0.32 14 14
TLN1 0.034 0.005 -9999 0 -10000 0 0
Rap1/GTP 0.018 0.1 -9999 0 -0.49 3 3
RHOA 0.034 0.005 -9999 0 -10000 0 0
P-selectin oligomer -0.023 0.16 -9999 0 -0.51 15 15
MYH2 -0.007 0.1 -9999 0 -0.48 4 4
MST1R 0.034 0.005 -9999 0 -10000 0 0
leukocyte activation during inflammatory response 0.044 0.068 -9999 0 -0.29 4 4
APOB 0.032 0.029 -9999 0 -0.32 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.032 0.029 -9999 0 -0.32 1 1
JAM3 0.033 0.007 -9999 0 -10000 0 0
GP1BA 0.027 0.014 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.027 0.079 -9999 0 -0.31 5 5
alphaM/beta2 Integrin -0.005 0.11 -9999 0 -0.5 4 4
JAM3 homodimer 0.033 0.007 -9999 0 -10000 0 0
ICAM2 0.027 0.054 -9999 0 -0.41 2 2
ICAM1 0.014 0.079 -9999 0 -0.32 8 8
phagocytosis triggered by activation of immune response cell surface activating receptor -0.004 0.11 -9999 0 -0.5 4 4
cell adhesion 0.024 0.073 -9999 0 -0.33 4 4
NFKB1 -0.012 0.13 -9999 0 -10000 0 0
THY1 -0.015 0.12 -9999 0 -0.32 20 20
RhoA/GDP 0.025 0.004 -9999 0 -10000 0 0
Lipoprotein(a) 0.044 0.02 -9999 0 -0.18 1 1
alphaM/beta2 Integrin/LRP/tPA 0.045 0.076 -9999 0 -0.3 4 4
IL6 -0.07 0.16 -9999 0 -10000 0 0
ITGB2 -0.009 0.067 -9999 0 -0.5 2 2
elevation of cytosolic calcium ion concentration -0.034 0.13 -9999 0 -0.31 4 4
alphaM/beta2 Integrin/JAM2/JAM3 -0.13 0.19 -9999 0 -0.31 70 70
JAM2 -0.24 0.27 -9999 0 -0.51 72 72
alphaM/beta2 Integrin/ICAM1 0.04 0.11 -9999 0 -0.3 6 6
alphaM/beta2 Integrin/uPA/Plg -0.032 0.13 -9999 0 -0.31 4 4
RhoA/GTP -0.003 0.1 -9999 0 -0.53 3 3
positive regulation of phagocytosis -0.008 0.094 -9999 0 -0.39 3 3
Ron/MSP 0.034 0.064 -9999 0 -0.22 9 9
alphaM/beta2 Integrin/uPAR/uPA -0.033 0.13 -9999 0 -0.31 4 4
alphaM/beta2 Integrin/uPAR 0.029 0.077 -9999 0 -0.34 4 4
PLAU -0.093 0.17 -9999 0 -0.32 53 53
PLAT 0.024 0.054 -9999 0 -0.41 2 2
actin filament polymerization -0.006 0.099 -9999 0 -0.46 4 4
MST1 0.012 0.084 -9999 0 -0.32 9 9
alphaM/beta2 Integrin/lipoprotein(a) 0.049 0.071 -9999 0 -0.29 4 4
TNF -0.013 0.12 -9999 0 -10000 0 0
RAP1B 0.034 0.003 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.052 0.13 -9999 0 -0.3 7 7
fibrinolysis -0.033 0.13 -9999 0 -0.31 4 4
HCK -0.002 0.11 -9999 0 -0.51 6 6
dendritic cell antigen processing and presentation -0.004 0.11 -9999 0 -0.5 4 4
VTN 0.033 0.008 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.009 0.1 -9999 0 -0.24 17 17
LPA 0.034 0.006 -9999 0 -10000 0 0
LRP1 0.034 0.003 -9999 0 -10000 0 0
cell migration 0.012 0.059 -9999 0 -0.3 2 2
FN1 -0.023 0.13 -9999 0 -0.32 24 24
alphaM/beta2 Integrin/Thy1 0 0.11 -9999 0 -0.27 11 11
MPO 0.009 0.088 -9999 0 -0.32 10 10
KNG1 0.019 0.089 -9999 0 -0.51 4 4
RAP1/GDP 0.044 0.011 -9999 0 -10000 0 0
ROCK1 -0.001 0.097 -9999 0 -0.48 3 3
ELA2 0 0 -9999 0 -10000 0 0
PLG 0.034 0.006 -9999 0 -10000 0 0
CTGF 0.031 0.029 -9999 0 -0.32 1 1
alphaM/beta2 Integrin/Hck 0.007 0.083 -9999 0 -0.31 7 7
ITGAM -0.009 0.069 -9999 0 -0.52 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.012 0.15 -9999 0 -0.34 19 19
HP 0.034 0.004 -9999 0 -10000 0 0
leukocyte adhesion -0.14 0.14 -9999 0 -0.39 8 8
SELP -0.023 0.16 -9999 0 -0.51 15 15
Glucocorticoid receptor regulatory network

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
PCK2 0.054 0.099 -10000 0 -0.76 1 1
SMARCC2 0.034 0.003 -10000 0 -10000 0 0
SMARCC1 0.027 0.05 -10000 0 -0.32 3 3
TBX21 -0.3 0.38 -10000 0 -0.87 43 43
SUMO2 0.033 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.007 0.1 -10000 0 -0.31 14 14
FKBP4 0.033 0.006 -10000 0 -10000 0 0
FKBP5 0.034 0.003 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.093 0.13 0.31 4 -0.32 5 9
PRL -0.035 0.096 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.2 0.22 0.52 29 -10000 0 29
RELA -0.09 0.055 -10000 0 -10000 0 0
FGG 0.13 0.17 0.44 14 -10000 0 14
GR beta/TIF2 0.092 0.13 0.3 11 -0.34 6 17
IFNG -0.15 0.18 -10000 0 -0.6 7 7
apoptosis 0.053 0.1 0.52 1 -0.44 1 2
CREB1 0.043 0 -10000 0 -10000 0 0
histone acetylation -0.055 0.096 -10000 0 -0.33 3 3
BGLAP -0.052 0.1 -10000 0 -0.38 1 1
GR/PKAc -0.028 0.22 0.32 3 -0.34 20 23
NF kappa B1 p50/RelA -0.15 0.092 -10000 0 -0.36 5 5
SMARCD1 0.034 0.003 -10000 0 -10000 0 0
MDM2 0.078 0.064 0.22 13 -10000 0 13
GATA3 0.039 0.026 -10000 0 -10000 0 0
AKT1 0.026 0.02 0.24 1 -10000 0 1
CSF2 -0.12 0.13 -10000 0 -0.53 1 1
GSK3B 0.035 0.006 -10000 0 -10000 0 0
NR1I3 0.056 0.1 0.5 1 -10000 0 1
CSN2 0.1 0.14 0.36 10 -10000 0 10
BRG1/BAF155/BAF170/BAF60A 0.08 0.039 -10000 0 -10000 0 0
NFATC1 0.027 0.034 -10000 0 -0.3 1 1
POU2F1 0.039 0.011 -10000 0 -10000 0 0
CDKN1A -0.033 0.21 -10000 0 -1.7 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.005 -10000 0 -10000 0 0
SFN 0.027 0.046 -10000 0 -0.51 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.095 0.13 0.32 3 -0.29 5 8
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.042 0.1 0.48 1 -10000 0 1
JUN -0.1 0.12 -10000 0 -0.4 7 7
IL4 -0.049 0.097 -10000 0 -0.46 1 1
CDK5R1 0.033 0.007 -10000 0 -10000 0 0
PRKACA 0.034 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.017 0.13 -10000 0 -0.32 10 10
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.13 0.32 3 -0.29 5 8
cortisol/GR alpha (monomer) 0.23 0.26 0.58 34 -10000 0 34
NCOA2 0.03 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.031 0.12 -10000 0 -0.48 8 8
AP-1/NFAT1-c-4 -0.14 0.14 -10000 0 -0.56 4 4
AFP -0.068 0.098 -10000 0 -10000 0 0
SUV420H1 0.034 0.006 -10000 0 -10000 0 0
IRF1 0.11 0.16 0.42 3 -1 1 4
TP53 0.026 0.074 -10000 0 -0.31 6 6
PPP5C 0.034 0.005 -10000 0 -10000 0 0
KRT17 -0.13 0.16 -10000 0 -0.6 5 5
KRT14 -0.068 0.099 -10000 0 -10000 0 0
TBP 0.042 0.006 -10000 0 -10000 0 0
CREBBP 0.036 0.015 -10000 0 -10000 0 0
HDAC1 0.031 0.016 -10000 0 -10000 0 0
HDAC2 0.043 0.012 -10000 0 -10000 0 0
AP-1 -0.14 0.14 -10000 0 -0.54 5 5
MAPK14 0.035 0.004 -10000 0 -10000 0 0
MAPK10 0.024 0.07 -10000 0 -0.44 3 3
MAPK11 0.03 0.03 -10000 0 -0.31 1 1
KRT5 -0.12 0.15 -10000 0 -0.59 2 2
interleukin-1 receptor activity 0.009 0.01 -10000 0 -10000 0 0
NCOA1 0.028 0.065 -10000 0 -0.51 2 2
STAT1 0.007 0.1 -10000 0 -0.31 14 14
CGA -0.055 0.1 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.083 0.14 0.35 11 -10000 0 11
MAPK3 0.027 0.064 -10000 0 -0.51 2 2
MAPK1 0.033 0.009 -10000 0 -10000 0 0
ICAM1 -0.18 0.16 -10000 0 -0.59 6 6
NFKB1 -0.09 0.055 -10000 0 -0.24 1 1
MAPK8 -0.1 0.13 -10000 0 -0.38 12 12
MAPK9 0.034 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.053 0.1 0.53 1 -0.46 1 2
BAX -0.012 0.083 -10000 0 -10000 0 0
POMC -0.085 0.16 -10000 0 -1.3 1 1
EP300 0.036 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.18 0.22 0.54 23 -10000 0 23
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.087 0.31 11 -10000 0 11
SGK1 0.036 0.06 -10000 0 -10000 0 0
IL13 -0.094 0.13 -10000 0 -0.49 1 1
IL6 -0.24 0.2 -10000 0 -0.53 22 22
PRKACG 0.034 0.005 -10000 0 -10000 0 0
IL5 -0.09 0.13 -10000 0 -10000 0 0
IL2 -0.12 0.15 -10000 0 -0.53 5 5
CDK5 0.031 0.03 -10000 0 -0.32 1 1
PRKACB -0.17 0.26 -10000 0 -0.51 55 55
HSP90AA1 0.03 0.012 -10000 0 -10000 0 0
IL8 -0.31 0.15 -10000 0 -0.58 18 18
CDK5R1/CDK5 0.046 0.026 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA/PKAc -0.2 0.16 -10000 0 -0.41 39 39
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.51 23 -10000 0 23
SMARCA4 0.034 0.004 -10000 0 -10000 0 0
chromatin remodeling 0.12 0.13 0.34 16 -10000 0 16
NF kappa B1 p50/RelA/Cbp -0.1 0.075 -10000 0 -0.34 1 1
JUN (dimer) -0.1 0.12 -10000 0 -0.39 7 7
YWHAH 0.032 0.009 -10000 0 -10000 0 0
VIPR1 -0.16 0.28 -10000 0 -0.85 18 18
NR3C1 0.12 0.2 0.41 17 -0.44 11 28
NR4A1 0.033 0.068 -10000 0 -0.51 2 2
TIF2/SUV420H1 0.043 0.019 -10000 0 -10000 0 0
MAPKKK cascade 0.053 0.1 0.52 1 -0.44 1 2
cortisol/GR alpha (dimer)/Src-1 0.22 0.23 0.52 33 -0.46 1 34
PBX1 0.024 0.09 -10000 0 -0.5 4 4
POU1F1 0.036 0.046 -10000 0 -0.5 1 1
SELE -0.21 0.2 -10000 0 -0.56 20 20
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.12 0.13 0.34 16 -10000 0 16
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.51 23 -10000 0 23
mol:cortisol 0.13 0.12 0.31 34 -10000 0 34
MMP1 -0.22 0.13 -10000 0 -0.87 3 3
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.02 0.047 -10000 0 -0.51 1 1
EPHB2 0.022 0.061 -10000 0 -0.38 3 3
EFNB1 0.013 0.042 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.001 0.11 -10000 0 -0.28 3 3
Ephrin B2/EPHB1-2 -0.015 0.092 -10000 0 -0.29 2 2
neuron projection morphogenesis -0.015 0.095 -10000 0 -0.26 4 4
Ephrin B1/EPHB1-2/Tiam1 -0.013 0.12 -10000 0 -0.29 5 5
DNM1 0.024 0.061 -10000 0 -0.34 4 4
cell-cell signaling -0.001 0.005 -10000 0 -10000 0 0
MAP2K4 -0.013 0.074 -10000 0 -0.42 4 4
YES1 -0.029 0.12 -10000 0 -0.68 4 4
Ephrin B1/EPHB1-2/NCK2 -0.012 0.12 -10000 0 -0.29 5 5
PI3K 0.02 0.089 -10000 0 -0.38 5 5
mol:GDP -0.015 0.11 -10000 0 -0.29 5 5
ITGA2B 0.033 0.007 -10000 0 -10000 0 0
endothelial cell proliferation -0.004 0.08 -10000 0 -0.18 22 22
FYN -0.02 0.12 -10000 0 -0.65 5 5
MAP3K7 -0.019 0.077 -10000 0 -0.45 4 4
FGR -0.014 0.099 -10000 0 -0.65 3 3
TIAM1 0.033 0.008 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
RGS3 0.034 0.005 -10000 0 -10000 0 0
cell adhesion 0.015 0.076 -10000 0 -0.37 3 3
LYN -0.015 0.11 -10000 0 -0.66 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.017 0.1 -10000 0 -0.59 4 4
Ephrin B1/EPHB1-2 -0.017 0.066 -10000 0 -0.53 2 2
SRC -0.016 0.11 -10000 0 -0.63 4 4
ITGB3 0.033 0.007 -10000 0 -10000 0 0
EPHB1 -0.085 0.16 -10000 0 -0.31 50 50
EPHB4 -0.032 0.14 -10000 0 -0.32 27 27
RAC1 0.031 0.01 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.003 0.08 -10000 0 -0.18 22 22
alphaIIb/beta3 Integrin 0.049 0.01 -10000 0 -10000 0 0
BLK -0.041 0.12 -10000 0 -0.7 3 3
HCK -0.017 0.091 -10000 0 -0.7 2 2
regulation of stress fiber formation 0.014 0.12 0.29 5 -10000 0 5
MAPK8 -0.011 0.071 -10000 0 -0.43 3 3
Ephrin B1/EPHB1-2/RGS3 -0.013 0.12 -10000 0 -0.29 5 5
endothelial cell migration 0.015 0.14 0.38 5 -0.47 3 8
NCK2 0.035 0 -10000 0 -10000 0 0
PTPN13 -0.075 0.16 -10000 0 -0.3 46 46
regulation of focal adhesion formation 0.014 0.12 0.29 5 -10000 0 5
chemotaxis 0.015 0.11 0.29 5 -10000 0 5
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.009 0.1 -10000 0 -0.27 4 4
angiogenesis -0.016 0.065 -10000 0 -0.53 2 2
LCK -0.017 0.11 -10000 0 -0.66 4 4
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.013 0.15 0.29 3 -0.49 8 11
FYN -0.033 0.18 -10000 0 -0.57 10 10
LAT/GRAP2/SLP76 0.003 0.15 -10000 0 -0.5 8 8
IKBKB 0.03 0.012 -10000 0 -10000 0 0
AKT1 -0.024 0.14 -10000 0 -0.39 13 13
B2M 0.013 0.1 -10000 0 -0.52 5 5
IKBKG 0.003 0.049 0.12 2 -0.14 2 4
MAP3K8 0.001 0.1 -10000 0 -0.32 14 14
mol:Ca2+ -0.009 0.016 0.09 1 -0.084 2 3
integrin-mediated signaling pathway 0.042 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.035 0.19 -10000 0 -0.57 12 12
TRPV6 0.049 0.26 1.2 7 -10000 0 7
CD28 -0.033 0.18 -10000 0 -0.51 18 18
SHC1 -0.02 0.18 0.3 3 -0.58 9 12
receptor internalization -0.021 0.19 -10000 0 -0.55 13 13
PRF1 -0.011 0.2 -10000 0 -0.76 7 7
KRAS 0.034 0.003 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.017 0.12 -10000 0 -0.34 12 12
LAT -0.025 0.17 -10000 0 -0.58 9 9
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.016 0.1 -10000 0 -0.52 5 5
CD3E 0.034 0.006 -10000 0 -10000 0 0
CD3G 0.013 0.1 -10000 0 -0.48 6 6
RASGRP2 0.005 0.035 -10000 0 -0.14 6 6
RASGRP1 0.003 0.14 -10000 0 -0.42 9 9
HLA-A 0.02 0.09 -10000 0 -0.52 4 4
RASSF5 0.033 0.006 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.043 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.026 0.06 0.15 4 -0.13 4 8
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.022 0.061 -10000 0 -0.22 8 8
PRKCA 0.026 0.098 0.17 11 -0.26 6 17
GRAP2 0.032 0.009 -10000 0 -10000 0 0
mol:IP3 -0.021 0.11 -10000 0 -0.36 10 10
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.009 0.16 -10000 0 -0.53 9 9
ORAI1 -0.042 0.22 -10000 0 -1 7 7
CSK -0.025 0.17 -10000 0 -0.53 11 11
B7 family/CD28 -0.019 0.23 -10000 0 -0.62 13 13
CHUK 0.032 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.028 0.2 -10000 0 -0.58 12 12
PTPN6 -0.025 0.18 -10000 0 -0.63 8 8
VAV1 -0.039 0.2 -10000 0 -0.66 10 10
Monovalent TCR/CD3 -0.007 0.15 -10000 0 -0.49 10 10
CBL 0.034 0.006 -10000 0 -10000 0 0
LCK -0.034 0.18 -10000 0 -0.58 10 10
PAG1 -0.068 0.21 -10000 0 -0.58 12 12
RAP1A 0.033 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.028 0.2 -10000 0 -0.62 11 11
CD80 0.027 0.05 -10000 0 -0.32 3 3
CD86 0.008 0.12 -10000 0 -0.51 7 7
PDK1/CARD11/BCL10/MALT1 -0.014 0.082 -10000 0 -0.27 8 8
HRAS 0.034 0.006 -10000 0 -10000 0 0
GO:0035030 -0.042 0.18 -10000 0 -0.52 13 13
CD8A 0.001 0.002 -10000 0 -10000 0 0
CD8B 0.035 0.003 -10000 0 -10000 0 0
PTPRC 0.018 0.09 -10000 0 -0.51 4 4
PDK1/PKC theta -0.016 0.16 -10000 0 -0.5 10 10
CSK/PAG1 -0.061 0.2 -10000 0 -0.57 11 11
SOS1 0.035 0 -10000 0 -10000 0 0
peptide-MHC class I 0.022 0.12 -10000 0 -0.52 6 6
GRAP2/SLP76 0.002 0.18 -10000 0 -0.6 8 8
STIM1 0 0.11 1.2 1 -10000 0 1
RAS family/GTP 0.031 0.07 0.19 2 -0.19 3 5
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.025 0.21 -10000 0 -0.59 13 13
mol:DAG -0.033 0.089 -10000 0 -0.33 10 10
RAP1A/GDP 0.017 0.029 0.087 2 -10000 0 2
PLCG1 0.019 0.017 -10000 0 -10000 0 0
CD247 0.008 0.12 -10000 0 -0.51 7 7
cytotoxic T cell degranulation -0.01 0.19 -10000 0 -0.73 7 7
RAP1A/GTP 0.002 0.013 -10000 0 -0.064 3 3
mol:PI-3-4-5-P3 -0.025 0.16 -10000 0 -0.46 12 12
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.023 0.14 -10000 0 -0.46 10 10
NRAS 0.028 0.041 -10000 0 -0.32 2 2
ZAP70 0.035 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.016 0.16 -10000 0 -0.52 10 10
MALT1 0.024 0.016 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.025 0.008 -10000 0 -10000 0 0
CARD11 0.005 0.092 -10000 0 -0.32 11 11
PRKCB -0.021 0.065 -10000 0 -0.23 10 10
PRKCE 0.029 0.099 0.17 11 -0.26 6 17
PRKCQ -0.02 0.18 -10000 0 -0.57 10 10
LCP2 0.026 0.06 -10000 0 -0.38 3 3
BCL10 0.033 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression -0.018 0.12 -10000 0 -0.33 13 13
IKK complex 0.036 0.066 0.13 34 -0.11 2 36
RAS family/GDP -0.001 0.011 -10000 0 -0.058 1 1
MAP3K14 -0.013 0.096 0.19 1 -0.26 12 13
PDPK1 -0.018 0.13 -10000 0 -0.4 10 10
TCR/CD3/MHC I/CD8/Fyn -0.026 0.19 -10000 0 -0.63 9 9
Glypican 2 network

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
MDK 0.014 0.079 -9999 0 -0.32 8 8
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.012 0.055 -9999 0 -0.21 8 8
neuron projection morphogenesis 0.012 0.054 -9999 0 -0.21 8 8
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.001 0.1 -10000 0 -0.25 18 18
epithelial cell differentiation 0.06 0.06 -10000 0 -0.27 4 4
CYFIP2 0.023 0.077 -10000 0 -0.51 3 3
ENAH -0.011 0.049 -10000 0 -10000 0 0
EGFR 0.02 0.077 -10000 0 -0.51 3 3
EPHA2 0.015 0.075 -10000 0 -0.32 7 7
MYO6 0.012 0.047 -10000 0 -0.26 4 4
CTNNB1 0.031 0.029 -10000 0 -0.32 1 1
ABI1/Sra1/Nap1 0.059 0.059 -10000 0 -0.32 3 3
AQP5 0.008 0.049 -10000 0 -10000 0 0
CTNND1 0.034 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.012 0.047 -10000 0 -0.25 4 4
regulation of calcium-dependent cell-cell adhesion 0.001 0.067 -10000 0 -0.26 9 9
EGF -0.11 0.22 -10000 0 -0.44 44 44
NCKAP1 0.032 0.029 -10000 0 -0.32 1 1
AQP3 0.01 0.051 -10000 0 -10000 0 0
cortical microtubule organization 0.06 0.06 -10000 0 -0.27 4 4
GO:0000145 -0.011 0.041 -10000 0 -0.24 4 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.067 0.062 -10000 0 -0.27 4 4
MLLT4 0.034 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.007 0.056 -10000 0 -0.35 2 2
ARF6 0.031 0.011 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.06 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.006 0.042 -10000 0 -10000 0 0
PVRL2 0.034 0.004 -10000 0 -10000 0 0
ZYX 0.01 0.049 -10000 0 -0.26 4 4
ARF6/GTP 0.063 0.063 -10000 0 -10000 0 0
CDH1 0.019 0.089 -10000 0 -0.51 4 4
EGFR/EGFR/EGF/EGF -0.033 0.14 -10000 0 -0.49 1 1
RhoA/GDP 0.063 0.059 -10000 0 -0.26 4 4
actin cytoskeleton organization 0.005 0.045 -10000 0 -0.25 4 4
IGF-1R heterotetramer 0.032 0.008 -10000 0 -10000 0 0
GIT1 0.033 0.008 -10000 0 -10000 0 0
IGF1R 0.032 0.008 -10000 0 -10000 0 0
IGF1 -0.29 0.27 -10000 0 -0.51 86 86
DIAPH1 0.05 0.13 -10000 0 -0.66 3 3
Wnt receptor signaling pathway -0.06 0.06 0.27 4 -10000 0 4
RHOA 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.006 0.056 -10000 0 -0.35 2 2
CTNNA1 0.034 0.004 -10000 0 -10000 0 0
VCL 0.005 0.046 -10000 0 -0.26 4 4
EFNA1 0.033 0.006 -10000 0 -10000 0 0
LPP 0.001 0.044 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.04 0.076 -10000 0 -0.38 2 2
SEC6/SEC8 0.01 0.044 -10000 0 -10000 0 0
MGAT3 0.001 0.068 -10000 0 -0.26 9 9
HGF/MET -0.039 0.11 -10000 0 -0.29 3 3
HGF 0.033 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.001 0.1 -10000 0 -0.26 18 18
actin cable formation 0.015 0.071 0.27 3 -0.3 1 4
KIAA1543 -0.012 0.041 -10000 0 -0.25 4 4
KIFC3 0.012 0.049 -10000 0 -0.26 4 4
NCK1 0.034 0.004 -10000 0 -10000 0 0
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ACTN1 0.01 0.047 -10000 0 -0.26 4 4
NCK1/GIT1 0.048 0.013 -10000 0 -10000 0 0
mol:GDP 0.06 0.06 -10000 0 -0.27 4 4
EXOC4 0.033 0.007 -10000 0 -10000 0 0
STX4 0.012 0.047 -10000 0 -0.26 4 4
PIP5K1C 0.012 0.047 -10000 0 -0.26 4 4
LIMA1 -0.022 0.16 -10000 0 -0.51 15 15
ABI1 0.034 0.004 -10000 0 -10000 0 0
ROCK1 0.006 0.065 0.31 1 -0.31 2 3
adherens junction assembly 0.007 0.05 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.13 0.16 -10000 0 -0.26 84 84
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.05 0.009 -10000 0 -10000 0 0
MET -0.12 0.17 -10000 0 -0.32 66 66
PLEKHA7 0.012 0.047 -10000 0 -0.26 4 4
mol:GTP 0.059 0.059 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.024 0.068 0.34 1 -10000 0 1
cortical actin cytoskeleton stabilization -0.001 0.1 -10000 0 -0.25 18 18
regulation of cell-cell adhesion 0.005 0.045 -10000 0 -0.25 4 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.001 0.1 -10000 0 -0.26 18 18
Noncanonical Wnt signaling pathway

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
NFATC2 0.019 0.017 -10000 0 -10000 0 0
GNB1/GNG2 -0.026 0.11 -10000 0 -0.34 4 4
mol:DAG -0.021 0.077 -10000 0 -0.32 1 1
PLCG1 -0.021 0.079 -10000 0 -0.33 1 1
YES1 -0.027 0.091 -10000 0 -0.3 7 7
FZD3 -0.048 0.14 -10000 0 -0.32 31 31
FZD6 0.02 0.058 -10000 0 -0.32 4 4
G protein 0.033 0.13 0.3 4 -0.33 1 5
MAP3K7 -0.015 0.071 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.076 -10000 0 -0.31 1 1
mol:IP3 -0.021 0.077 -10000 0 -0.32 1 1
NLK -0.013 0.14 -10000 0 -0.76 5 5
GNB1 0.032 0.009 -10000 0 -10000 0 0
CAMK2A -0.018 0.073 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.043 0.11 -10000 0 -0.33 11 11
CSNK1A1 0.034 0.004 -10000 0 -10000 0 0
GNAS -0.005 0.095 0.24 1 -0.3 7 8
GO:0007205 -0.022 0.074 -10000 0 -0.31 1 1
WNT6 0.034 0.003 -10000 0 -10000 0 0
WNT4 -0.001 0.13 -10000 0 -0.49 9 9
NFAT1/CK1 alpha -0.015 0.085 -10000 0 -10000 0 0
GNG2 0.031 0.011 -10000 0 -10000 0 0
WNT5A -0.007 0.11 -10000 0 -0.32 17 17
WNT11 -0.033 0.14 -10000 0 -0.32 28 28
CDC42 -0.028 0.082 -10000 0 -0.34 1 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.032 0.029 -9999 0 -0.32 1 1
ITGB7 0.001 0.13 -9999 0 -0.51 9 9
ITGA4 0.027 0.063 -9999 0 -0.51 2 2
alpha4/beta7 Integrin 0.02 0.12 -9999 0 -0.4 10 10
alpha4/beta1 Integrin 0.043 0.054 -9999 0 -0.32 3 3
Signaling events mediated by PTP1B

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
PDGFRB 0.034 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.042 0.086 -10000 0 -0.56 1 1
PTP1B/AKT1 0.008 0.089 -10000 0 -0.35 3 3
FYN 0.031 0.029 -10000 0 -0.32 1 1
p210 bcr-abl/PTP1B 0.002 0.095 0.24 1 -0.32 5 6
EGFR 0.011 0.079 -10000 0 -0.52 3 3
EGF/EGFR -0.036 0.16 -10000 0 -0.32 22 22
CSF1 0.033 0.007 -10000 0 -10000 0 0
AKT1 0.031 0.012 -10000 0 -10000 0 0
INSR 0.023 0.078 -10000 0 -0.51 3 3
PTP1B/N-cadherin 0 0.09 0.23 1 -0.34 3 4
Insulin Receptor/Insulin 0.031 0.1 -10000 0 -0.38 4 4
HCK -0.002 0.11 -10000 0 -0.51 6 6
CRK 0.027 0.014 -10000 0 -10000 0 0
TYK2 0.003 0.095 0.25 3 -0.35 3 6
EGF -0.11 0.23 -10000 0 -0.44 44 44
YES1 0.027 0.014 -10000 0 -10000 0 0
CAV1 0.012 0.12 0.26 4 -0.33 3 7
TXN 0.032 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.024 0.1 -10000 0 -0.34 3 3
cell migration -0.002 0.095 0.32 5 -0.24 1 6
STAT3 0.034 0.006 -10000 0 -10000 0 0
PRLR 0.034 0.03 -10000 0 -0.31 1 1
ITGA2B 0.032 0.007 -10000 0 -10000 0 0
CSF1R 0.034 0.004 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.053 0.035 -10000 0 -0.21 2 2
FGR 0.031 0.01 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.011 0.097 0.23 1 -0.35 3 4
Crk/p130 Cas 0.015 0.094 -10000 0 -0.34 3 3
DOK1 0.01 0.091 -10000 0 -0.33 4 4
JAK2 0.028 0.089 -10000 0 -0.4 3 3
Jak2/Leptin Receptor/Leptin 0.022 0.11 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
PTPN1 0.002 0.096 0.24 1 -0.32 5 6
LYN 0.03 0.012 -10000 0 -10000 0 0
CDH2 0.017 0.054 -10000 0 -0.34 3 3
SRC 0.022 0.087 -10000 0 -0.36 3 3
ITGB3 0.032 0.007 -10000 0 -10000 0 0
CAT1/PTP1B 0.018 0.18 0.27 12 -0.54 7 19
CAPN1 0.032 0.006 -10000 0 -10000 0 0
CSK 0.032 0.009 -10000 0 -10000 0 0
PI3K 0.045 0.099 -10000 0 -0.38 3 3
mol:H2O2 -0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.1 -10000 0 -10000 0 0
negative regulation of transcription 0.028 0.088 -10000 0 -0.39 3 3
FCGR2A 0.009 0.088 -10000 0 -0.32 10 10
FER 0.02 0.063 -10000 0 -0.32 5 5
alphaIIb/beta3 Integrin 0.046 0.01 -10000 0 -10000 0 0
BLK -0.033 0.17 -10000 0 -0.51 16 16
Insulin Receptor/Insulin/Shc 0.056 0.057 -10000 0 -0.32 3 3
RHOA 0.033 0.005 -10000 0 -10000 0 0
LEPR 0.033 0.007 -10000 0 -10000 0 0
BCAR1 0.034 0.004 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.007 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.035 0.22 -10000 0 -0.55 15 15
PRL 0.036 0.029 -10000 0 -0.31 1 1
SOCS3 -0.024 0.2 -10000 0 -1.1 5 5
SPRY2 0.017 0.055 -10000 0 -0.42 2 2
Insulin Receptor/Insulin/IRS1 0.053 0.066 -10000 0 -0.32 3 3
CSF1/CSF1R 0.028 0.1 0.24 1 -0.33 3 4
Ras protein signal transduction 0.001 0.062 0.46 2 -10000 0 2
IRS1 0.027 0.05 -10000 0 -0.32 3 3
INS 0.033 0.008 -10000 0 -10000 0 0
LEP 0.025 0.064 -10000 0 -0.51 2 2
STAT5B 0.018 0.093 0.22 1 -0.34 4 5
STAT5A 0.018 0.093 0.22 1 -0.34 4 5
GRB2 0.033 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.098 0.23 1 -0.35 3 4
CSN2 0.027 0.043 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
LAT 0.026 0.078 -10000 0 -0.53 2 2
YBX1 0.043 0.01 -10000 0 -10000 0 0
LCK 0.03 0.03 -10000 0 -0.32 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
NOX4 -0.28 0.11 -10000 0 -0.32 130 130
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.11 0.15 -10000 0 -10000 0 0
CRKL -0.03 0.074 -10000 0 -10000 0 0
mol:DAG -0.013 0.064 -10000 0 -10000 0 0
HRAS -0.022 0.078 -10000 0 -0.31 1 1
MAPK8 0.023 0.075 -10000 0 -10000 0 0
RAP1A -0.031 0.074 -10000 0 -10000 0 0
GAB1 -0.032 0.079 -10000 0 -0.36 1 1
MAPK14 0.024 0.077 -10000 0 -10000 0 0
EPO 0.011 0.039 -10000 0 -0.33 1 1
PLCG1 -0.015 0.064 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.014 0.027 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.025 0.07 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 -0.01 0.091 -10000 0 -0.33 1 1
EPO/EPOR (dimer) 0.014 0.044 -10000 0 -0.23 1 1
IRS2 -0.019 0.064 -10000 0 -10000 0 0
STAT1 -0.079 0.13 -10000 0 -0.36 6 6
STAT5B -0.049 0.11 -10000 0 -10000 0 0
cell proliferation 0.02 0.075 0.2 5 -10000 0 5
GAB1/SHIP/PIK3R1/SHP2/SHC -0.023 0.075 -10000 0 -0.32 1 1
TEC -0.032 0.074 -10000 0 -10000 0 0
SOCS3 0.009 0.088 -10000 0 -0.32 10 10
STAT1 (dimer) -0.078 0.13 -10000 0 -0.36 6 6
JAK2 0.021 0.051 -10000 0 -0.32 3 3
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.015 0.097 -10000 0 -10000 0 0
EPO/EPOR 0.014 0.044 -10000 0 -0.23 1 1
LYN 0.01 0.025 -10000 0 -10000 0 0
TEC/VAV2 -0.03 0.081 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.014 0.027 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.008 0.055 -10000 0 -10000 0 0
mol:IP3 -0.013 0.064 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.012 0.066 -10000 0 -10000 0 0
SH2B3 0.028 0.015 -10000 0 -10000 0 0
NFKB1 0.023 0.076 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0.01 0.037 -10000 0 -10000 0 0
PTPN6 -0.034 0.075 -10000 0 -10000 0 0
TEC/VAV2/GRB2 -0.021 0.089 -10000 0 -10000 0 0
EPOR 0.014 0.027 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.092 -10000 0 -0.34 1 1
SOS1 0.035 0 -10000 0 -10000 0 0
PLCG2 -0.24 0.27 -10000 0 -0.51 74 74
CRKL/CBL/C3G -0.015 0.086 -10000 0 -10000 0 0
VAV2 -0.037 0.078 -10000 0 -10000 0 0
CBL -0.031 0.074 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.021 0.076 -10000 0 -10000 0 0
STAT5A -0.049 0.11 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
STAT5 (dimer) -0.1 0.17 -10000 0 -0.35 2 2
LYN/PLCgamma2 -0.15 0.2 -10000 0 -0.37 63 63
PTPN11 0.032 0.029 -10000 0 -0.32 1 1
BTK -0.07 0.12 -10000 0 -0.33 16 16
BCL2 -0.48 0.44 -10000 0 -0.83 88 88
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.008 0.028 0.13 2 -0.12 1 3
BUB1B -0.01 0.065 -10000 0 -0.16 1 1
PLK1 0.019 0.033 0.08 2 -0.095 1 3
PLK1S1 0.008 0.017 0.043 1 -10000 0 1
KIF2A 0.016 0.028 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.019 0.033 0.079 2 -0.095 1 3
GOLGA2 0.034 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.026 0.034 -10000 0 -0.18 1 1
WEE1 0.015 0.076 -10000 0 -0.42 3 3
cytokinesis 0.016 0.055 -10000 0 -10000 0 0
PP2A-alpha B56 0.033 0.13 -10000 0 -0.63 5 5
AURKA 0.028 0.032 0.11 1 -10000 0 1
PICH/PLK1 -0.072 0.14 0.19 7 -0.28 29 36
CENPE 0.011 0.042 -10000 0 -0.16 4 4
RhoA/GTP 0.025 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.016 0.028 -10000 0 -10000 0 0
PPP2CA 0.034 0.004 -10000 0 -10000 0 0
FZR1 0.033 0.006 -10000 0 -10000 0 0
TPX2 0.044 0.051 0.13 22 -10000 0 22
PAK1 0.034 0.005 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.004 -10000 0 -10000 0 0
CLSPN 0.011 0.052 -10000 0 -0.22 6 6
GORASP1 0.034 0.005 -10000 0 -10000 0 0
metaphase 0 0.003 0.018 2 -0.011 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.008 0.017 0.043 1 -10000 0 1
G2 phase of mitotic cell cycle 0.001 0.004 0.019 3 -10000 0 3
STAG2 0.03 0.041 -10000 0 -0.32 2 2
GRASP65/GM130/RAB1/GTP 0.007 0.088 -10000 0 -0.58 3 3
spindle elongation 0.019 0.033 0.079 2 -0.095 1 3
ODF2 0.036 0.006 -10000 0 -10000 0 0
BUB1 -0.01 0.13 -10000 0 -0.68 5 5
TPT1 0.028 0.041 -10000 0 -0.19 2 2
CDC25C 0.018 0.037 -10000 0 -0.24 2 2
CDC25B -0.096 0.16 -10000 0 -0.32 51 51
SGOL1 0.008 0.028 0.12 1 -0.13 2 3
RHOA 0.034 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 -0.029 0.092 -10000 0 -0.22 8 8
CDC14B 0.011 0.003 -10000 0 -10000 0 0
CDC20 0.024 0.057 -10000 0 -0.32 4 4
PLK1/PBIP1 0.005 0.048 -10000 0 -0.15 8 8
mitosis -0.002 0.003 -10000 0 -10000 0 0
FBXO5 0.002 0.046 -10000 0 -0.14 5 5
CDC2 -0.001 0.006 0.011 13 -0.013 5 18
NDC80 0.024 0.032 -10000 0 -0.32 1 1
metaphase plate congression -0.003 0.08 -10000 0 -0.22 16 16
ERCC6L -0.068 0.13 0.18 7 -0.28 22 29
NLP/gamma Tubulin 0.009 0.019 0.087 1 -10000 0 1
microtubule cytoskeleton organization 0.028 0.041 -10000 0 -0.19 2 2
G2/M transition DNA damage checkpoint 0 0.003 0.018 3 -10000 0 3
PPP1R12A 0.035 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.018 3 -10000 0 3
PLK1/PRC1-2 0.031 0.079 -10000 0 -0.24 5 5
GRASP65/GM130/RAB1/GTP/PLK1 0.069 0.029 -10000 0 -10000 0 0
RAB1A 0.035 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.025 0.034 0.076 23 -10000 0 23
mitotic prometaphase 0.001 0.006 0.019 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.055 -10000 0 -0.39 2 2
microtubule-based process 0.02 0.067 -10000 0 -0.17 11 11
Golgi organization 0.019 0.033 0.079 2 -0.095 1 3
Cohesin/SA2 0.033 0.031 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.051 0.008 -10000 0 -10000 0 0
KIF20A -0.002 0.11 -10000 0 -0.32 15 15
APC/C/CDC20 0.033 0.043 -10000 0 -0.17 3 3
PPP2R1A 0.034 0.004 -10000 0 -10000 0 0
chromosome segregation 0.005 0.048 -10000 0 -0.15 8 8
PRC1 0.023 0.057 -10000 0 -0.32 4 4
ECT2 -0.083 0.087 0.23 1 -0.16 45 46
C13orf34 0.019 0.029 0.07 4 -10000 0 4
NUDC -0.003 0.081 -10000 0 -0.23 16 16
regulation of attachment of spindle microtubules to kinetochore -0.01 0.065 -10000 0 -0.16 1 1
spindle assembly 0.014 0.027 0.13 1 -10000 0 1
spindle stabilization 0.008 0.017 0.043 1 -10000 0 1
APC/C/HCDH1 0.032 0.009 -10000 0 -10000 0 0
MKLP2/PLK1 0.02 0.067 -10000 0 -0.17 11 11
CCNB1 -0.028 0.13 -10000 0 -0.31 26 26
PPP1CB 0.035 0.001 -10000 0 -10000 0 0
BTRC 0.032 0.008 -10000 0 -10000 0 0
ROCK2 0.029 0.031 -10000 0 -10000 0 0
TUBG1 0.017 0.023 0.1 1 -0.16 1 2
G2/M transition of mitotic cell cycle -0.025 0.1 0.17 14 -0.22 7 21
MLF1IP -0.009 0.063 -10000 0 -0.22 12 12
INCENP 0.029 0.041 -10000 0 -0.32 2 2
Nectin adhesion pathway

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 0.034 0.004 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.047 0.024 -9999 0 -0.22 1 1
PTK2 0.006 0.11 -9999 0 -0.39 9 9
positive regulation of JNK cascade 0.021 0.1 -9999 0 -0.31 5 5
CDC42/GDP 0.055 0.14 -9999 0 -0.4 5 5
Rac1/GDP 0.05 0.14 -9999 0 -0.39 5 5
RAP1B 0.034 0.003 -9999 0 -10000 0 0
RAP1A 0.033 0.008 -9999 0 -10000 0 0
CTNNB1 0.031 0.029 -9999 0 -0.32 1 1
CDC42/GTP 0.044 0.13 -9999 0 -0.38 5 5
nectin-3/I-afadin 0.023 0.1 -9999 0 -0.37 9 9
RAPGEF1 0.023 0.13 -9999 0 -0.43 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.009 0.14 -9999 0 -0.46 9 9
PDGFB-D/PDGFRB 0.034 0.004 -9999 0 -10000 0 0
TLN1 -0.004 0.051 -9999 0 -0.38 1 1
Rap1/GTP 0.016 0.096 -9999 0 -0.32 4 4
IQGAP1 0.032 0.009 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.061 0.018 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.023 0.1 -9999 0 -0.37 9 9
PVR 0.034 0.004 -9999 0 -10000 0 0
Necl-5(dimer) 0.034 0.004 -9999 0 -10000 0 0
mol:GDP 0.043 0.16 -9999 0 -0.47 6 6
MLLT4 0.034 0.006 -9999 0 -10000 0 0
PIK3CA 0.034 0.004 -9999 0 -10000 0 0
PI3K 0.074 0.091 -9999 0 -0.27 9 9
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.049 0.01 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly 0.024 0.11 -9999 0 -0.3 5 5
PVRL1 0.034 0.006 -9999 0 -10000 0 0
PVRL3 0.001 0.13 -9999 0 -0.51 9 9
PVRL2 0.034 0.004 -9999 0 -10000 0 0
PIK3R1 0.034 0.005 -9999 0 -10000 0 0
CDH1 0.019 0.089 -9999 0 -0.51 4 4
CLDN1 -0.3 0.067 -9999 0 -0.32 140 140
JAM-A/CLDN1 -0.16 0.082 -9999 0 -0.41 9 9
SRC -0.008 0.14 -9999 0 -0.5 9 9
ITGB3 0.033 0.007 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.049 0.01 -9999 0 -10000 0 0
FARP2 0.042 0.16 -9999 0 -0.68 1 1
RAC1 0.031 0.01 -9999 0 -10000 0 0
CTNNA1 0.034 0.004 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.043 0.093 -9999 0 -0.32 9 9
nectin-1/I-afadin 0.049 0.01 -9999 0 -10000 0 0
nectin-2/I-afadin 0.05 0.009 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.039 0.017 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.043 0.093 -9999 0 -0.32 9 9
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.017 -9999 0 -10000 0 0
F11R 0.033 0.006 -9999 0 -10000 0 0
positive regulation of filopodium formation 0.021 0.1 -9999 0 -0.31 5 5
alphaV/beta3 Integrin/Talin 0.004 0.085 -9999 0 -0.36 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.05 0.009 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.05 0.009 -9999 0 -10000 0 0
PIP5K1C -0.002 0.055 -9999 0 -0.41 1 1
VAV2 0.036 0.17 -9999 0 -0.47 4 4
RAP1/GDP 0.06 0.13 -9999 0 -0.37 4 4
ITGAV 0.032 0.029 -9999 0 -0.32 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.043 0.093 -9999 0 -0.32 9 9
nectin-3(dimer)/I-afadin/I-afadin 0.023 0.1 -9999 0 -0.37 9 9
Rac1/GTP 0.032 0.13 -9999 0 -0.37 4 4
PTPRM 0.001 0.061 -9999 0 -0.22 9 9
E-cadherin/beta catenin/alpha catenin 0.085 0.067 -9999 0 -0.26 4 4
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.031 0.01 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.006 0.083 -9999 0 -0.3 9 9
CRKL 0.032 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.008 -9999 0 -10000 0 0
DOCK1 0.026 0.063 -9999 0 -0.51 2 2
ITGA4 0.027 0.063 -9999 0 -0.51 2 2
alpha4/beta7 Integrin/MAdCAM1 -0.041 0.2 -9999 0 -0.32 44 44
EPO 0.03 0.03 -9999 0 -0.32 1 1
alpha4/beta7 Integrin 0.02 0.12 -9999 0 -0.4 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.014 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.043 0.054 -9999 0 -0.32 3 3
EPO/EPOR (dimer) 0.046 0.026 -9999 0 -0.22 1 1
lamellipodium assembly 0.004 0.098 -9999 0 -0.56 1 1
PIK3CA 0.034 0.004 -9999 0 -10000 0 0
PI3K 0.05 0.009 -9999 0 -10000 0 0
ARF6 0.031 0.011 -9999 0 -10000 0 0
JAK2 0.028 0.041 -9999 0 -10000 0 0
PXN 0.034 0.003 -9999 0 -10000 0 0
PIK3R1 0.034 0.005 -9999 0 -10000 0 0
MADCAM1 -0.12 0.24 -9999 0 -0.51 40 40
cell adhesion -0.043 0.19 -9999 0 -0.32 44 44
CRKL/CBL 0.048 0.013 -9999 0 -10000 0 0
ITGB1 0.032 0.029 -9999 0 -0.32 1 1
SRC 0.003 0.056 -9999 0 -0.31 4 4
ITGB7 0.001 0.13 -9999 0 -0.51 9 9
RAC1 0.031 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.049 0.086 -9999 0 -0.37 5 5
p130Cas/Crk/Dock1 0.057 0.091 -9999 0 -0.31 1 1
VCAM1 0.018 0.089 -9999 0 -0.51 4 4
RHOA 0.034 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.076 0.052 -9999 0 -0.29 2 2
BCAR1 -0.003 0.051 -9999 0 -0.29 4 4
EPOR 0.034 0.005 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.034 0.006 -9999 0 -10000 0 0
GIT1 0.033 0.008 -9999 0 -10000 0 0
Rac1/GTP 0.004 0.1 -9999 0 -0.58 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.021 0.081 -10000 0 -0.21 15 15
alphaV beta3 Integrin 0.062 0.033 -10000 0 -10000 0 0
PTK2 0.068 0.096 0.35 2 -10000 0 2
IGF1R 0.032 0.008 -10000 0 -10000 0 0
PI4KB 0.033 0.006 -10000 0 -10000 0 0
MFGE8 0.032 0.009 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
CDKN1B 0.032 0.014 -10000 0 -10000 0 0
VEGFA -0.002 0.11 -10000 0 -0.32 15 15
ILK 0.032 0.014 -10000 0 -10000 0 0
ROCK1 0.027 0.014 -10000 0 -10000 0 0
AKT1 0.023 0.014 -10000 0 -10000 0 0
PTK2B 0.007 0.053 -10000 0 -10000 0 0
alphaV/beta3 Integrin/JAM-A 0.073 0.041 -10000 0 -10000 0 0
CBL 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.063 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.19 -10000 0 -0.29 85 85
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.024 0.059 -10000 0 -0.35 2 2
alphaV/beta3 Integrin/Syndecan-1 0.065 0.025 -10000 0 -10000 0 0
PI4KA 0.032 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.17 -10000 0 -0.4 16 16
PI4 Kinase 0.047 0.015 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.11 0.11 -10000 0 -0.26 3 3
RPS6KB1 -0.16 0.14 -10000 0 -0.38 16 16
TLN1 0.034 0.005 -10000 0 -10000 0 0
MAPK3 -0.042 0.11 -10000 0 -0.44 6 6
GPR124 0.025 0.042 -10000 0 -0.32 2 2
MAPK1 -0.042 0.11 -10000 0 -0.44 7 7
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.061 0.038 -10000 0 -10000 0 0
cell adhesion 0.055 0.03 -10000 0 -10000 0 0
ANGPTL3 0.033 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.024 0.062 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
TGFBR2 0.034 0.005 -10000 0 -10000 0 0
ITGB3 0.033 0.007 -10000 0 -10000 0 0
IGF1 -0.29 0.27 -10000 0 -0.51 86 86
RAC1 0.031 0.01 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.052 0.042 -10000 0 -10000 0 0
apoptosis 0.032 0.029 -10000 0 -0.31 1 1
CD47 0.034 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.064 0.026 -10000 0 -10000 0 0
VCL 0.034 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.022 0.12 -10000 0 -0.32 16 16
CSF1 0.033 0.007 -10000 0 -10000 0 0
PIK3C2A 0.027 0.028 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.023 0.059 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.056 0.077 -10000 0 -10000 0 0
FAK1/Vinculin 0.079 0.093 0.3 4 -10000 0 4
alphaV beta3/Integrin/ppsTEM5 0.053 0.043 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
VTN 0.033 0.008 -10000 0 -10000 0 0
BCAR1 0.034 0.004 -10000 0 -10000 0 0
FGF2 0.031 0.029 -10000 0 -0.32 1 1
F11R 0.018 0.02 -10000 0 -0.22 1 1
alphaV/beta3 Integrin/Lactadherin 0.06 0.03 -10000 0 -10000 0 0
alphaV/beta3 Integrin/TGFBR2 0.064 0.026 -10000 0 -10000 0 0
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.081 0.03 -10000 0 -10000 0 0
HSP90AA1 0.03 0.012 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.061 0.024 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.023 0.13 -10000 0 -0.32 24 24
alphaV/beta3 Integrin/Pyk2 0.033 0.07 -10000 0 -10000 0 0
SDC1 0.035 0 -10000 0 -10000 0 0
VAV3 -0.04 0.12 -10000 0 -0.28 30 30
PTPN11 0.032 0.029 -10000 0 -0.32 1 1
IRS1 0.027 0.05 -10000 0 -0.32 3 3
FAK1/Paxillin 0.079 0.094 0.3 4 -10000 0 4
cell migration 0.073 0.09 0.27 7 -10000 0 7
ITGAV 0.032 0.029 -10000 0 -0.32 1 1
PI3K 0.085 0.044 -10000 0 -10000 0 0
SPP1 -0.22 0.16 -10000 0 -0.32 106 106
KDR 0.033 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.032 0.029 -10000 0 -0.31 1 1
COL4A3 0.029 0.041 -10000 0 -0.32 2 2
angiogenesis -0.03 0.11 -10000 0 -0.46 6 6
Rac1/GTP -0.022 0.12 -10000 0 -0.38 1 1
EDIL3 -0.026 0.17 -10000 0 -0.51 16 16
cell proliferation 0.063 0.026 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.017 0.039 -9999 0 -0.2 1 1
NFATC2 -0.012 0.028 -9999 0 -10000 0 0
NFATC3 -0.02 0.041 -9999 0 -10000 0 0
CD40LG -0.087 0.2 -9999 0 -0.52 6 6
PTGS2 -0.12 0.24 -9999 0 -0.53 21 21
JUNB 0.024 0.057 -9999 0 -0.32 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.031 -9999 0 -10000 0 0
CaM/Ca2+ -0.007 0.031 -9999 0 -10000 0 0
CALM1 0.011 0.028 -9999 0 -10000 0 0
JUN 0.004 0.066 -9999 0 -0.32 5 5
mol:Ca2+ -0.012 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.012 -9999 0 -10000 0 0
FOSL1 0.005 0.096 -9999 0 -0.32 12 12
CREM 0.034 0.003 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.049 0.11 -9999 0 -0.3 2 2
FOS -0.012 0.11 -9999 0 -0.46 8 8
IFNG -0.11 0.24 -9999 0 -0.53 19 19
AP-1/NFAT1-c-4 -0.1 0.23 -9999 0 -0.47 21 21
FASLG -0.12 0.23 -9999 0 -0.51 16 16
NFAT1-c-4/ICER1 -0.02 0.079 -9999 0 -10000 0 0
IL2RA -0.089 0.21 -9999 0 -0.57 5 5
FKBP12/FK506 0.019 0.011 -9999 0 -10000 0 0
CSF2 -0.15 0.24 -9999 0 -0.52 25 25
JunB/Fra1/NFAT1-c-4 0.002 0.12 -9999 0 -0.35 2 2
IL4 -0.085 0.2 -9999 0 -0.5 5 5
IL2 0 0.14 -9999 0 -0.98 3 3
IL3 0.025 0.086 -9999 0 -0.8 1 1
FKBP1A 0.026 0.015 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.04 0.008 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.037 0.024 -10000 0 -10000 0 0
NFATC2 -0.008 0.12 -10000 0 -10000 0 0
NFATC3 -0.029 0.088 -10000 0 -0.34 2 2
CD40LG -0.26 0.25 -10000 0 -0.76 10 10
ITCH 0.014 0.047 -10000 0 -10000 0 0
CBLB 0.032 0.043 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.16 -10000 0 -0.7 2 2
JUNB 0.024 0.057 -10000 0 -0.32 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.056 -10000 0 -0.28 4 4
T cell anergy 0.039 0.093 -10000 0 -0.42 3 3
TLE4 -0.001 0.077 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.12 0.18 -10000 0 -0.8 2 2
AP-1/NFAT1-c-4 -0.27 0.28 -10000 0 -0.84 9 9
IKZF1 -0.002 0.076 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.07 0.13 -10000 0 -0.83 1 1
AP-1/NFAT1 -0.049 0.12 -10000 0 -0.37 4 4
CALM1 0.034 0.039 -10000 0 -10000 0 0
EGR2 -0.071 0.28 -10000 0 -1.4 5 5
EGR3 -0.056 0.16 -10000 0 -10000 0 0
NFAT1/FOXP3 0.009 0.09 -10000 0 -10000 0 0
EGR1 0.019 0.075 -10000 0 -0.31 7 7
JUN -0.049 0.067 -10000 0 -0.34 5 5
EGR4 0.001 0 -10000 0 -10000 0 0
mol:Ca2+ 0.007 0.029 -10000 0 -10000 0 0
GBP3 -0.062 0.24 -10000 0 -0.75 16 16
FOSL1 0.005 0.096 -10000 0 -0.32 12 12
NFAT1-c-4/MAF/IRF4 -0.2 0.25 -10000 0 -0.92 7 7
DGKA -0.002 0.077 -10000 0 -10000 0 0
CREM 0.034 0.003 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.078 0.18 -10000 0 -0.9 1 1
CTLA4 0.045 0.11 -10000 0 -10000 0 0
NFAT1-c-4 (dimer)/EGR1 -0.065 0.18 -10000 0 -0.89 1 1
NFAT1-c-4 (dimer)/EGR4 -0.067 0.16 -10000 0 -0.89 1 1
FOS -0.061 0.11 -10000 0 -0.49 8 8
IFNG -0.19 0.25 -10000 0 -0.66 19 19
T cell activation -0.049 0.14 -10000 0 -10000 0 0
MAF -0.17 0.26 -10000 0 -0.51 55 55
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.06 0.15 0.64 2 -10000 0 2
TNF -0.064 0.15 -10000 0 -0.81 1 1
FASLG -0.24 0.57 -10000 0 -1.6 22 22
TBX21 -0.14 0.24 -10000 0 -0.51 41 41
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.013 0.064 -10000 0 -0.31 3 3
PTPN1 -0.001 0.077 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 -0.065 0.17 -10000 0 -0.9 1 1
GATA3 0.037 0.005 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.19 0.25 -10000 0 -0.65 19 19
IL2RA -0.12 0.16 -10000 0 -0.73 2 2
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.001 0.074 -10000 0 -10000 0 0
E2F1 0.013 0.046 -10000 0 -0.31 2 2
PPARG 0.004 0.12 -10000 0 -0.51 8 8
SLC3A2 0 0.078 -10000 0 -10000 0 0
IRF4 -0.096 0.23 -10000 0 -0.51 35 35
PTGS2 -0.29 0.28 -10000 0 -0.78 15 15
CSF2 -0.32 0.28 -10000 0 -0.77 19 19
JunB/Fra1/NFAT1-c-4 -0.065 0.18 -10000 0 -0.86 1 1
IL4 -0.072 0.14 -10000 0 -0.87 1 1
IL5 -0.26 0.25 -10000 0 -0.76 11 11
IL2 -0.05 0.14 -10000 0 -10000 0 0
IL3 -0.016 0.091 -10000 0 -0.86 1 1
RNF128 0.017 0.11 -10000 0 -0.6 4 4
NFATC1 -0.06 0.15 -10000 0 -0.64 2 2
CDK4 0.029 0.12 -10000 0 -10000 0 0
PTPRK -0.001 0.075 -10000 0 -10000 0 0
IL8 -0.37 0.26 -10000 0 -0.77 24 24
POU2F1 0.04 0.008 -10000 0 -10000 0 0
IL23-mediated signaling events

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.25 0.36 -10000 0 -1.2 13 13
IL23A -0.28 0.3 -10000 0 -1.2 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.22 0.3 -10000 0 -1.1 6 6
positive regulation of T cell mediated cytotoxicity -0.24 0.31 -10000 0 -1.2 6 6
ITGA3 -0.23 0.29 -10000 0 -1.1 6 6
IL17F -0.15 0.21 -10000 0 -0.7 6 6
IL12B -0.005 0.048 -10000 0 -0.34 1 1
STAT1 (dimer) -0.24 0.32 -10000 0 -1.2 6 6
CD4 -0.21 0.28 -10000 0 -1.1 5 5
IL23 -0.27 0.3 -10000 0 -1.1 6 6
IL23R -0.082 0.29 -10000 0 -1.1 9 9
IL1B -0.27 0.31 -10000 0 -1.2 6 6
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.22 0.3 -10000 0 -1.1 6 6
TYK2 -0.002 0.033 -10000 0 -10000 0 0
STAT4 0.031 0.045 -10000 0 -0.51 1 1
STAT3 0.034 0.006 -10000 0 -10000 0 0
IL18RAP -0.074 0.22 -10000 0 -0.51 29 29
IL12RB1 -0.002 0.033 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.006 0.044 -10000 0 -10000 0 0
IL23R/JAK2 -0.085 0.28 -10000 0 -1.1 8 8
positive regulation of chronic inflammatory response -0.24 0.31 -10000 0 -1.2 6 6
natural killer cell activation 0.005 0.014 0.081 4 -10000 0 4
JAK2 -0.009 0.063 -10000 0 -0.34 3 3
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
NFKB1 0.032 0.005 -10000 0 -10000 0 0
RELA 0.032 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.29 -10000 0 -1 6 6
ALOX12B -0.21 0.28 -10000 0 -1.1 5 5
CXCL1 -0.28 0.3 -10000 0 -1.1 6 6
T cell proliferation -0.24 0.31 -10000 0 -1.2 6 6
NFKBIA 0.029 0.011 -10000 0 -10000 0 0
IL17A -0.12 0.18 -10000 0 -0.56 4 4
PI3K -0.2 0.31 -10000 0 -1.1 6 6
IFNG -0.021 0.041 0.14 3 -0.11 3 6
STAT3 (dimer) -0.18 0.3 -10000 0 -1.1 6 6
IL18R1 0.03 0.045 -10000 0 -0.51 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.14 0.2 -10000 0 -0.78 5 5
IL18/IL18R -0.057 0.19 -10000 0 -0.35 38 38
macrophage activation -0.019 0.015 -10000 0 -0.045 3 3
TNF -0.25 0.3 -10000 0 -1.1 6 6
STAT3/STAT4 -0.21 0.3 -10000 0 -1.1 6 6
STAT4 (dimer) -0.22 0.31 -10000 0 -1.2 6 6
IL18 -0.018 0.16 -10000 0 -0.5 14 14
IL19 -0.21 0.28 -10000 0 -1.1 6 6
STAT5A (dimer) -0.22 0.31 -10000 0 -1.2 6 6
STAT1 0.001 0.1 -10000 0 -0.32 14 14
SOCS3 0.009 0.088 -10000 0 -0.32 10 10
CXCL9 -0.28 0.37 -10000 0 -1.2 14 14
MPO -0.22 0.28 -10000 0 -1.1 5 5
positive regulation of humoral immune response -0.24 0.31 -10000 0 -1.2 6 6
IL23/IL23R/JAK2/TYK2 -0.24 0.32 -10000 0 -1.3 6 6
IL6 -0.26 0.31 -10000 0 -1.2 5 5
STAT5A 0.033 0.006 -10000 0 -10000 0 0
IL2 0.033 0.014 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.014 0.081 4 -10000 0 4
CD3E -0.22 0.28 -10000 0 -1.1 5 5
keratinocyte proliferation -0.24 0.31 -10000 0 -1.2 6 6
NOS2 -0.22 0.28 -10000 0 -1 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.034 0.005 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.034 0.005 -9999 0 -10000 0 0
TCEB1 0.03 0.012 -9999 0 -10000 0 0
HIF1A/p53 -0.013 0.094 -9999 0 -0.33 8 8
HIF1A -0.024 0.091 -9999 0 -0.36 8 8
COPS5 0.03 0.012 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.079 0.044 -9999 0 -10000 0 0
FIH (dimer) 0.032 0.008 -9999 0 -10000 0 0
CDKN2A -0.081 0.16 -9999 0 -0.32 48 48
ARNT/IPAS 0.049 0.012 -9999 0 -10000 0 0
HIF1AN 0.032 0.008 -9999 0 -10000 0 0
GNB2L1 0.034 0.004 -9999 0 -10000 0 0
HIF1A/ARNT -0.02 0.096 -9999 0 -0.34 8 8
CUL2 0.034 0.003 -9999 0 -10000 0 0
OS9 0.034 0.003 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.058 0.026 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.01 0.092 -9999 0 -0.34 8 8
PHD1-3/OS9 -0.029 0.16 -9999 0 -0.29 35 35
HIF1A/RACK1/Elongin B/Elongin C 0.005 0.1 -9999 0 -0.41 4 4
VHL 0.033 0.006 -9999 0 -10000 0 0
HSP90AA1 0.03 0.012 -9999 0 -10000 0 0
HIF1A/JAB1 -0.017 0.094 -9999 0 -0.35 7 7
EGLN3 -0.11 0.24 -9999 0 -0.51 38 38
EGLN2 0.034 0.006 -9999 0 -10000 0 0
EGLN1 0.033 0.008 -9999 0 -10000 0 0
TP53 0.015 0.064 -9999 0 -0.32 5 5
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.026 0.11 -9999 0 -0.55 4 4
ARNT 0.033 0.006 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.032 0.009 -9999 0 -10000 0 0
HIF1A/p19ARF -0.067 0.11 -9999 0 -0.37 8 8
Regulation of Androgen receptor activity

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
HDAC1 0.019 0.006 -10000 0 -10000 0 0
SMARCC1 0.006 0.085 -10000 0 -0.88 1 1
REL 0.034 0 -10000 0 -10000 0 0
HDAC7 -0.098 0.14 -10000 0 -0.44 10 10
JUN 0.022 0.064 -10000 0 -0.32 5 5
EP300 0.032 0.009 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.03 0.11 -10000 0 -0.39 11 11
FOXO1 0.009 0.089 -10000 0 -0.51 4 4
T-DHT/AR -0.081 0.17 -10000 0 -0.47 10 10
MAP2K6 -0.014 0.15 -10000 0 -0.52 11 11
BRM/BAF57 0.048 0.015 -10000 0 -10000 0 0
MAP2K4 0.023 0.016 -10000 0 -10000 0 0
SMARCA2 0.034 0.006 -10000 0 -10000 0 0
PDE9A -0.52 0.58 -10000 0 -1.1 72 72
NCOA2 0.03 0.012 -10000 0 -10000 0 0
CEBPA 0.033 0.007 -10000 0 -10000 0 0
EHMT2 0.035 0.003 -10000 0 -10000 0 0
cell proliferation -0.006 0.18 0.34 2 -0.39 9 11
NR0B1 0.03 0.041 -10000 0 -0.32 2 2
EGR1 0.018 0.075 -10000 0 -0.31 7 7
RXRs/9cRA 0.063 0.017 -10000 0 -10000 0 0
AR/RACK1/Src 0.039 0.14 -10000 0 -0.34 8 8
AR/GR -0.035 0.11 -10000 0 -0.3 13 13
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
PKN1 0.034 0.006 -10000 0 -10000 0 0
RCHY1 0.034 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.024 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.024 0.11 -10000 0 -0.35 8 8
SRC 0.003 0.12 -10000 0 -0.32 8 8
NR3C1 -0.014 0.16 -10000 0 -0.51 13 13
KLK3 -0.061 0.097 -10000 0 -10000 0 0
APPBP2 0.012 0.027 -10000 0 -10000 0 0
TRIM24 0.034 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.055 0.099 -10000 0 -0.35 11 11
TMPRSS2 -0.071 0.18 -10000 0 -0.86 4 4
RXRG 0.034 0.006 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.034 0.005 -10000 0 -10000 0 0
RXRB 0.034 0.004 -10000 0 -10000 0 0
CARM1 0.034 0.005 -10000 0 -10000 0 0
NR2C2 0.034 0.006 -10000 0 -10000 0 0
KLK2 0.024 0.098 -10000 0 -10000 0 0
AR -0.012 0.065 -10000 0 -0.26 3 3
SENP1 0.034 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.012 -10000 0 -10000 0 0
MDM2 0.033 0.003 -10000 0 -10000 0 0
SRY -0.001 0 -10000 0 -10000 0 0
GATA2 0.034 0.004 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.24 0.14 -10000 0 -0.32 116 116
T-DHT/AR/RACK1/Src 0.037 0.14 -10000 0 -0.35 8 8
positive regulation of transcription 0.034 0.004 -10000 0 -10000 0 0
DNAJA1 0.01 0.04 -10000 0 -0.34 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.03 0.075 -10000 0 -0.59 2 2
SPDEF -0.13 0.25 -10000 0 -0.51 44 44
T-DHT/AR/TIF2 -0.006 0.085 -10000 0 -0.42 2 2
T-DHT/AR/Hsp90 -0.04 0.11 -10000 0 -0.37 9 9
GSK3B 0.032 0.005 -10000 0 -10000 0 0
NR2C1 0.024 0.057 -10000 0 -0.32 4 4
mol:T-DHT -0.04 0.091 -10000 0 -0.33 11 11
SIRT1 0.033 0.006 -10000 0 -10000 0 0
ZMIZ2 0.03 0.009 -10000 0 -10000 0 0
POU2F1 -0.023 0.072 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.046 0.11 -10000 0 -0.37 9 9
CREBBP 0.034 0.005 -10000 0 -10000 0 0
SMARCE1 0.033 0.008 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.004 0.057 -9999 0 -0.23 1 1
STMN1 0.012 0.029 -9999 0 -0.22 2 2
Aurora B/RasGAP/Survivin 0.024 0.083 -9999 0 -0.24 1 1
Chromosomal passenger complex/Cul3 protein complex -0.058 0.12 -9999 0 -0.32 14 14
BIRC5 -0.011 0.12 -9999 0 -0.33 18 18
DES -0.13 0.32 -9999 0 -0.69 34 34
Aurora C/Aurora B/INCENP 0.047 0.037 -9999 0 -10000 0 0
Aurora B/TACC1 0.034 0.02 -9999 0 -10000 0 0
Aurora B/PP2A 0.039 0.021 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.01 0.011 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.002 0.004 -9999 0 -10000 0 0
NDC80 0.013 0.022 -9999 0 -0.22 1 1
Cul3 protein complex -0.044 0.17 -9999 0 -0.31 36 36
KIF2C 0 0.051 -9999 0 -0.26 2 2
PEBP1 0.034 0.004 -9999 0 -10000 0 0
KIF20A 0.001 0.11 -9999 0 -0.31 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.038 0.03 -9999 0 -0.22 1 1
SEPT1 0.034 0.003 -9999 0 -10000 0 0
SMC2 0.017 0.075 -9999 0 -0.32 7 7
SMC4 0.034 0.004 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.081 0.22 -9999 0 -0.48 31 31
PSMA3 0.031 0.011 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B 0.016 0.009 -9999 0 -10000 0 0
AURKB 0.027 0.015 -9999 0 -10000 0 0
AURKC 0.034 0.005 -9999 0 -10000 0 0
CDCA8 0.031 0.03 -9999 0 -0.32 1 1
cytokinesis -0.026 0.13 -9999 0 -0.42 9 9
Aurora B/Septin1 -0.023 0.14 -9999 0 -0.44 6 6
AURKA 0.012 0.05 -9999 0 -0.31 3 3
INCENP 0.028 0.041 -9999 0 -0.32 2 2
KLHL13 -0.12 0.24 -9999 0 -0.47 46 46
BUB1 -0.076 0.16 -9999 0 -0.31 47 47
hSgo1/Aurora B/Survivin 0.019 0.084 -9999 0 -0.28 3 3
EVI5 0.033 0.006 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.13 -9999 0 -0.36 6 6
SGOL1 0.024 0.057 -9999 0 -0.32 4 4
CENPA 0.008 0.081 -9999 0 -0.26 3 3
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.039 0.021 -9999 0 -10000 0 0
NCAPD2 0.033 0.007 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.039 0.021 -9999 0 -10000 0 0
RHOA 0.034 0.005 -9999 0 -10000 0 0
NCAPH 0.018 0.075 -9999 0 -0.32 7 7
NPM1 -0.043 0.14 -9999 0 -0.4 6 6
RASA1 0.031 0.029 -9999 0 -0.32 1 1
KLHL9 0.034 0.006 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.021 -9999 0 -10000 0 0
PPP1CC 0.034 0.004 -9999 0 -10000 0 0
Centraspindlin -0.016 0.13 -9999 0 -0.36 8 8
RhoA/GDP 0.025 0.004 -9999 0 -10000 0 0
NSUN2 -0.04 0.14 -9999 0 -0.57 2 2
MYLK -0.011 0.1 -9999 0 -0.39 10 10
KIF23 -0.02 0.13 -9999 0 -0.32 22 22
VIM 0.013 0.033 -9999 0 -0.38 1 1
RACGAP1 0.019 0.07 -9999 0 -0.32 6 6
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.044 0.14 -9999 0 -1 1 1
Chromosomal passenger complex -0.013 0.083 -9999 0 -0.29 6 6
Chromosomal passenger complex/EVI5 0.043 0.092 -9999 0 -0.29 1 1
TACC1 0.03 0.012 -9999 0 -10000 0 0
PPP2R5D 0.034 0.006 -9999 0 -10000 0 0
CUL3 0.034 0.003 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.03 0.045 -10000 0 -0.51 1 1
SPHK1 -0.022 0.13 -10000 0 -0.32 23 23
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
mol:S1P -0.005 0.057 0.17 1 -0.29 2 3
GNAO1 0.035 0 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.02 0.094 -10000 0 -0.23 23 23
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.021 0.06 -10000 0 -0.28 1 1
GNAI3 0.033 0.007 -10000 0 -10000 0 0
G12/G13 0.044 0.018 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.011 0.048 -10000 0 -0.32 1 1
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.027 0.17 -10000 0 -0.51 16 16
S1P/S1P5/G12 0.007 0.054 -10000 0 -0.3 1 1
S1P/S1P3/Gq -0.014 0.11 -10000 0 -0.29 15 15
S1P/S1P4/Gi -0.011 0.11 -10000 0 -0.36 6 6
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.51 6 6
GNA15 0.024 0.057 -10000 0 -0.32 4 4
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.033 0.007 -10000 0 -10000 0 0
GNA11 0 0.13 -10000 0 -0.51 9 9
ABCC1 -0.002 0.11 -10000 0 -0.32 15 15
Cellular roles of Anthrax toxin

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
ANTXR1 0.015 0.08 -10000 0 -0.32 8 8
ANTXR2 0.03 0.045 -10000 0 -0.51 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.068 1 1
monocyte activation -0.001 0.1 -10000 0 -0.33 12 12
MAP2K2 0.005 0.096 -10000 0 -0.57 4 4
MAP2K1 -0.003 0.009 -10000 0 -10000 0 0
MAP2K7 -0.003 0.009 -10000 0 -10000 0 0
MAP2K6 -0.023 0.071 -10000 0 -0.27 11 11
CYAA -0.012 0.039 -10000 0 -0.27 1 1
MAP2K4 -0.002 0.009 -10000 0 -10000 0 0
IL1B -0.051 0.072 -10000 0 -0.15 44 44
Channel 0.03 0.053 -10000 0 -0.28 1 1
NLRP1 -0.004 0.015 -10000 0 -0.15 1 1
CALM1 0.03 0.012 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.041 0.14 -10000 0 -0.39 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.068 1 -10000 0 1
MAPK3 -0.007 0.032 -10000 0 -0.27 2 2
MAPK1 -0.003 0.009 -10000 0 -10000 0 0
PGR -0.003 0.009 -10000 0 -10000 0 0
PA/Cellular Receptors 0.031 0.059 -10000 0 -0.31 1 1
apoptosis -0.002 0.01 -10000 0 -0.068 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.03 0.048 -10000 0 -0.27 1 1
macrophage activation -0.007 0.031 -10000 0 -0.26 2 2
TNF 0.034 0.003 -10000 0 -10000 0 0
VCAM1 -0.002 0.1 -10000 0 -0.34 12 12
platelet activation -0.041 0.14 -10000 0 -0.39 20 20
MAPKKK cascade 0.006 0.024 0.1 1 -10000 0 1
IL18 -0.028 0.078 -10000 0 -0.26 14 14
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.068 1 1
LEF -0.002 0.01 -10000 0 -0.069 1 1
CASP1 -0.004 0.02 -10000 0 -0.078 8 8
mol:cAMP -0.041 0.14 -10000 0 -0.39 20 20
necrosis -0.002 0.01 -10000 0 -0.068 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.03 0.05 -10000 0 -0.27 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.03 0.011 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.002 0.15 -10000 0 -0.4 10 10
NEF -0.019 0.058 -10000 0 -10000 0 0
NFKBIA 0.027 0.029 -10000 0 -10000 0 0
BIRC3 0.009 0.1 -10000 0 -0.56 4 4
CYCS -0.028 0.15 -10000 0 -0.46 9 9
RIPK1 0.034 0.003 -10000 0 -10000 0 0
CD247 -0.019 0.15 -10000 0 -0.62 7 7
MAP2K7 -0.001 0.16 -10000 0 -0.79 3 3
protein ubiquitination 0.035 0.06 -10000 0 -0.31 1 1
CRADD 0.03 0.045 -10000 0 -0.51 1 1
DAXX 0.034 0.004 -10000 0 -10000 0 0
FAS -0.016 0.16 -10000 0 -0.51 13 13
BID -0.039 0.15 0.2 4 -0.33 24 28
NF-kappa-B/RelA/I kappa B alpha 0.055 0.07 -10000 0 -0.28 4 4
TRADD 0.035 0 -10000 0 -10000 0 0
MAP3K5 0.034 0.005 -10000 0 -10000 0 0
CFLAR 0.035 0 -10000 0 -10000 0 0
FADD 0.034 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.055 0.07 -10000 0 -0.28 4 4
MAPK8 0 0.15 -10000 0 -0.71 3 3
APAF1 0.034 0.003 -10000 0 -10000 0 0
TRAF1 0.034 0.005 -10000 0 -10000 0 0
TRAF2 0.034 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.031 0.16 0.21 5 -0.34 24 29
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.042 0.069 -10000 0 -0.38 2 2
CHUK 0.038 0.058 -10000 0 -0.33 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.062 0.11 -10000 0 -0.27 13 13
TCRz/NEF -0.034 0.16 -10000 0 -0.37 24 24
TNF 0.034 0.003 -10000 0 -10000 0 0
FASLG -0.08 0.25 -10000 0 -0.63 24 24
NFKB1 0.031 0.027 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.06 0.025 -10000 0 -10000 0 0
CASP6 0.019 0.14 -10000 0 -0.66 3 3
CASP7 -0.05 0.19 -10000 0 -0.49 14 14
RELA 0.031 0.026 -10000 0 -10000 0 0
CASP2 0.033 0.007 -10000 0 -10000 0 0
CASP3 -0.019 0.16 -10000 0 -0.53 8 8
TNFRSF1A 0.033 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.044 0.018 -10000 0 -10000 0 0
CASP8 0.035 0 -10000 0 -10000 0 0
CASP9 0.031 0.01 -10000 0 -10000 0 0
MAP3K14 0.043 0.067 -10000 0 -0.38 1 1
APAF-1/Caspase 9 -0.012 0.14 -10000 0 -0.41 7 7
BCL2 -0.097 0.16 -10000 0 -0.61 4 4
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.033 0.05 -10000 0 -0.25 4 4
cell-cell adhesion 0.048 0.075 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.052 0.066 -10000 0 -0.26 2 2
ITSN1 0.033 0.007 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.027 0.067 -10000 0 -0.2 11 11
Ephrin B1/EPHB1 -0.031 0.11 -10000 0 -0.18 50 50
HRAS/GDP -0.04 0.11 -10000 0 -0.43 2 2
Ephrin B/EPHB1/GRB7 0.011 0.1 -10000 0 -10000 0 0
Endophilin/SYNJ1 0.061 0.082 -10000 0 -0.25 1 1
KRAS 0.034 0.003 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.016 0.08 -10000 0 -10000 0 0
endothelial cell migration 0.014 0.079 -10000 0 -0.27 1 1
GRB2 0.033 0.007 -10000 0 -10000 0 0
GRB7 0.032 0.009 -10000 0 -10000 0 0
PAK1 0.068 0.085 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
RRAS 0.069 0.086 -10000 0 -0.26 1 1
DNM1 0.024 0.061 -10000 0 -0.34 4 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.008 0.095 -10000 0 -0.31 1 1
lamellipodium assembly -0.048 0.075 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.022 0.057 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
EPHB2 0.023 0.061 -10000 0 -0.38 3 3
EPHB3 0.005 0.1 -10000 0 -0.35 11 11
EPHB1 -0.086 0.17 -10000 0 -0.32 50 50
EPHB4 -0.032 0.14 -10000 0 -0.32 27 27
mol:GDP -0.026 0.11 0.26 2 -0.45 2 4
Ephrin B/EPHB2 0.041 0.054 -10000 0 -0.26 2 2
Ephrin B/EPHB3 0.032 0.069 -10000 0 -0.26 3 3
JNK cascade -0.041 0.1 0.35 2 -0.31 5 7
Ephrin B/EPHB1 -0.002 0.09 -10000 0 -0.26 1 1
RAP1/GDP -0.009 0.13 0.33 2 -0.4 2 4
EFNB2 0.02 0.047 -10000 0 -0.51 1 1
EFNB3 0.027 0.014 -10000 0 -10000 0 0
EFNB1 0.035 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.014 0.093 -10000 0 -0.29 2 2
RAP1B 0.034 0.003 -10000 0 -10000 0 0
RAP1A 0.033 0.008 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.09 -10000 0 -0.31 1 1
Rap1/GTP -0.018 0.072 -10000 0 -10000 0 0
axon guidance 0.033 0.05 -10000 0 -0.24 4 4
MAPK3 0.019 0.063 0.21 1 -10000 0 1
MAPK1 0.022 0.054 0.21 1 -10000 0 1
Rac1/GDP -0.026 0.11 0.3 1 -0.41 2 3
actin cytoskeleton reorganization -0.05 0.075 -10000 0 -0.3 2 2
CDC42/GDP -0.015 0.12 0.33 2 -0.41 2 4
PI3K 0.017 0.083 -10000 0 -0.27 1 1
EFNA5 0.03 0.045 -10000 0 -0.51 1 1
Ephrin B2/EPHB4 -0.003 0.08 -10000 0 -0.18 22 22
Ephrin B/EPHB2/Intersectin/N-WASP 0.019 0.047 -10000 0 -0.26 3 3
CDC42 0.031 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.021 0.068 -10000 0 -10000 0 0
PTK2 0.11 0.22 0.59 25 -10000 0 25
MAP4K4 -0.041 0.1 0.36 2 -0.31 5 7
SRC 0.019 0.017 -10000 0 -10000 0 0
KALRN 0.034 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.044 0.037 -10000 0 -0.37 1 1
neuron projection morphogenesis -0.004 0.12 0.32 8 -10000 0 8
MAP2K1 0.019 0.051 -10000 0 -10000 0 0
WASL 0.029 0.045 -10000 0 -0.51 1 1
Ephrin B1/EPHB1-2/NCK1 -0.007 0.12 -10000 0 -0.3 3 3
cell migration 0.05 0.088 0.23 4 -10000 0 4
NRAS 0.028 0.041 -10000 0 -0.32 2 2
SYNJ1 0.062 0.083 -10000 0 -0.26 1 1
PXN 0.034 0.003 -10000 0 -10000 0 0
TF 0.054 0.083 -10000 0 -10000 0 0
HRAS/GTP -0.005 0.085 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 -0.019 0.11 -10000 0 -0.3 3 3
cell adhesion mediated by integrin -0.061 0.099 0.25 1 -0.21 42 43
RAC1 0.031 0.01 -10000 0 -10000 0 0
mol:GTP -0.005 0.09 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.032 0.078 -10000 0 -0.35 2 2
RASA1 0.031 0.029 -10000 0 -0.32 1 1
RAC1-CDC42/GDP -0.019 0.11 0.3 1 -0.4 2 3
ruffle organization 0 0.14 0.36 7 -10000 0 7
NCK1 0.034 0.004 -10000 0 -10000 0 0
receptor internalization 0.051 0.085 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.053 0.064 -10000 0 -0.27 1 1
ROCK1 0.006 0.054 0.19 1 -0.28 2 3
RAS family/GDP -0.049 0.071 -10000 0 -0.35 1 1
Rac1/GTP -0.046 0.081 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.009 0.041 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.044 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.034 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.008 0.14 -10000 0 -0.51 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.015 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.022 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.014 -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 0.033 0.008 -10000 0 -10000 0 0
FYN 0.031 0.029 -10000 0 -0.32 1 1
MAP3K12 0.034 0.003 -10000 0 -10000 0 0
FGR 0.031 0.01 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.079 0.15 -10000 0 -0.41 19 19
PRKG1 0.034 0.006 -10000 0 -10000 0 0
DUSP8 0.026 0.063 -10000 0 -0.51 2 2
PGK/cGMP/p38 alpha -0.02 0.18 0.2 2 -0.43 16 18
apoptosis -0.075 0.14 -10000 0 -0.4 18 18
RAL/GTP 0.042 0.014 -10000 0 -10000 0 0
LYN 0.03 0.012 -10000 0 -10000 0 0
DUSP1 0.001 0.13 -10000 0 -0.51 9 9
PAK1 0.034 0.005 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.064 0.04 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.01 -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 0.031 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.038 0.018 -10000 0 -10000 0 0
MAPK11 -0.004 0.19 0.3 6 -0.47 11 17
BLK -0.033 0.17 -10000 0 -0.51 16 16
HCK -0.002 0.11 -10000 0 -0.51 6 6
MAP2K3 0.028 0.013 -10000 0 -10000 0 0
DUSP16 0.034 0.005 -10000 0 -10000 0 0
DUSP10 -0.003 0.11 -10000 0 -0.32 15 15
TRAF6/MEKK3 0.041 0.012 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.025 0.21 0.22 10 -0.48 16 26
positive regulation of innate immune response -0.018 0.22 0.32 6 -0.53 14 20
LCK 0.03 0.03 -10000 0 -0.32 1 1
p38alpha-beta/MKP7 -0.005 0.22 0.32 6 -0.52 13 19
p38alpha-beta/MKP5 -0.012 0.22 0.32 6 -0.52 14 20
PGK/cGMP 0.025 0.004 -10000 0 -10000 0 0
PAK2 0.034 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.018 0.24 0.32 6 -0.49 19 25
CDC42 0.031 0.01 -10000 0 -10000 0 0
RALB 0.035 0 -10000 0 -10000 0 0
RALA 0.031 0.01 -10000 0 -10000 0 0
PAK3 0.034 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.04 0.013 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.015 0.083 0.44 1 -10000 0 1
IL27/IL27R/JAK1 -0.015 0.11 -10000 0 -10000 0 0
TBX21 -0.14 0.2 -10000 0 -0.44 39 39
IL12B 0.031 0.029 -10000 0 -0.31 1 1
IL12A 0 0.042 -10000 0 -0.22 5 5
IL6ST 0.029 0.008 -10000 0 -10000 0 0
IL27RA/JAK1 0.01 0.045 -10000 0 -10000 0 0
IL27 -0.001 0.12 -10000 0 -0.48 9 9
TYK2 0.028 0.013 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.006 0.11 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.015 0.083 0.44 1 -10000 0 1
T cell proliferation during immune response 0.015 0.083 0.44 1 -10000 0 1
MAPKKK cascade -0.015 0.083 -10000 0 -0.44 1 1
STAT3 0.034 0.006 -10000 0 -10000 0 0
STAT2 0.034 0.003 -10000 0 -10000 0 0
STAT1 0 0.1 -10000 0 -0.32 14 14
IL12RB1 0.034 0.004 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.082 0.13 -10000 0 -0.45 3 3
IL27/IL27R/JAK2/TYK2 -0.016 0.084 -10000 0 -0.45 1 1
positive regulation of T cell mediated cytotoxicity -0.015 0.083 -10000 0 -0.44 1 1
STAT1 (dimer) -0.078 0.17 -10000 0 -0.59 2 2
JAK2 0.023 0.052 -10000 0 -0.33 3 3
JAK1 0.032 0.007 -10000 0 -10000 0 0
STAT2 (dimer) -0.008 0.092 -10000 0 -0.43 1 1
T cell proliferation -0.08 0.13 -10000 0 -0.42 5 5
IL12/IL12R/TYK2/JAK2 0.01 0.14 -10000 0 -0.75 4 4
IL17A -0.006 0.11 -10000 0 -10000 0 0
mast cell activation 0.015 0.083 0.44 1 -10000 0 1
IFNG -0.002 0.029 -10000 0 -0.086 2 2
T cell differentiation -0.005 0.005 -10000 0 -0.02 1 1
STAT3 (dimer) -0.008 0.092 -10000 0 -0.43 1 1
STAT5A (dimer) -0.009 0.091 -10000 0 -0.43 1 1
STAT4 (dimer) -0.01 0.095 -10000 0 -0.43 1 1
STAT4 0.031 0.045 -10000 0 -0.51 1 1
T cell activation -0.007 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.007 0.072 -10000 0 -10000 0 0
GATA3 0.003 0.023 -10000 0 -10000 0 0
IL18 -0.025 0.11 -10000 0 -0.36 14 14
positive regulation of mast cell cytokine production -0.008 0.09 -10000 0 -0.42 1 1
IL27/EBI3 0.017 0.095 -10000 0 -0.35 9 9
IL27RA 0 0.044 -10000 0 -10000 0 0
IL6 -0.15 0.17 -10000 0 -0.31 78 78
STAT5A 0.033 0.006 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.008 0.017 -10000 0 -10000 0 0
IL1B -0.062 0.11 -10000 0 -0.22 47 47
EBI3 0.029 0.007 -10000 0 -10000 0 0
TNF 0.01 0.001 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA 0.022 0.077 -10000 0 -0.51 3 3
HRAS 0.034 0.006 -10000 0 -10000 0 0
EGFR 0.02 0.077 -10000 0 -0.51 3 3
AKT 0.052 0.068 0.28 4 -10000 0 4
FOXO3 0.034 0.006 -10000 0 -10000 0 0
AKT1 0.03 0.011 -10000 0 -10000 0 0
FOXO1 0.009 0.089 -10000 0 -0.51 4 4
AKT3 0.033 0.008 -10000 0 -10000 0 0
FOXO4 0.035 0 -10000 0 -10000 0 0
MET -0.12 0.17 -10000 0 -0.32 66 66
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
PIK3CB 0.034 0.004 -10000 0 -10000 0 0
NRAS 0.028 0.041 -10000 0 -0.32 2 2
PIK3CG 0.003 0.12 -10000 0 -0.51 8 8
PIK3R3 0.034 0.006 -10000 0 -10000 0 0
PIK3R2 0.034 0.004 -10000 0 -10000 0 0
NF1 0.033 0.008 -10000 0 -10000 0 0
RAS 0.004 0.067 0.22 4 -0.21 3 7
ERBB2 0.032 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.032 0.079 0.28 3 -0.25 1 4
PI3K 0.022 0.081 0.26 7 -0.22 2 9
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
KRAS 0.034 0.003 -10000 0 -10000 0 0
FOXO 0.068 0.069 0.25 7 -10000 0 7
AKT2 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.064 -10000 0 -0.51 2 2
Class I PI3K signaling events

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.019 0.032 0.22 2 -10000 0 2
DAPP1 0.01 0.18 0.25 7 -0.52 9 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.035 0.23 0.31 1 -0.64 12 13
mol:DAG -0.018 0.11 0.2 16 -0.25 6 22
HRAS 0.035 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.061 0.086 -10000 0 -0.29 3 3
PLCG2 -0.24 0.27 -10000 0 -0.51 74 74
PLCG1 0.019 0.017 -10000 0 -10000 0 0
ARF5 0.033 0.008 -10000 0 -10000 0 0
mol:GTP -0.01 0.031 0.19 2 -10000 0 2
ARF1/GTP -0.002 0.027 0.19 2 -10000 0 2
RHOA 0.034 0.005 -10000 0 -10000 0 0
YES1 0.027 0.014 -10000 0 -10000 0 0
RAP1A/GTP 0.018 0.036 0.21 2 -10000 0 2
ADAP1 -0.009 0.03 0.18 2 -10000 0 2
ARAP3 -0.009 0.031 0.19 2 -10000 0 2
INPPL1 0.034 0.005 -10000 0 -10000 0 0
PREX1 0.019 0.017 -10000 0 -10000 0 0
ARHGEF6 0.027 0.063 -10000 0 -0.51 2 2
ARHGEF7 0.024 0.016 -10000 0 -10000 0 0
ARF1 0.033 0.007 -10000 0 -10000 0 0
NRAS 0.029 0.042 -10000 0 -0.32 2 2
FYN 0.031 0.029 -10000 0 -0.32 1 1
ARF6 0.031 0.011 -10000 0 -10000 0 0
FGR 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.063 0.16 4 -10000 0 4
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.033 0.008 -10000 0 -10000 0 0
ZAP70 0.035 0 -10000 0 -10000 0 0
mol:IP3 -0.01 0.082 0.16 16 -0.2 3 19
LYN 0.03 0.012 -10000 0 -10000 0 0
ARF1/GDP 0.058 0.087 -10000 0 -0.29 3 3
RhoA/GDP 0.057 0.063 0.24 4 -10000 0 4
PDK1/Src/Hsp90 0.037 0.035 -10000 0 -10000 0 0
BLNK 0.017 0.089 -10000 0 -0.51 4 4
actin cytoskeleton reorganization 0.053 0.084 0.26 2 -0.34 1 3
SRC 0.019 0.017 -10000 0 -10000 0 0
PLEKHA2 0.004 0.027 0.21 1 -0.18 2 3
RAC1 0.031 0.01 -10000 0 -10000 0 0
PTEN 0.025 0.061 -10000 0 -0.48 2 2
HSP90AA1 0.03 0.012 -10000 0 -10000 0 0
ARF6/GTP 0.018 0.032 0.22 2 -10000 0 2
RhoA/GTP 0.02 0.042 0.23 3 -10000 0 3
Src family/SYK family/BLNK-LAT -0.021 0.12 -10000 0 -0.45 7 7
BLK -0.033 0.17 -10000 0 -0.51 16 16
PDPK1 0.034 0.005 -10000 0 -10000 0 0
CYTH1 -0.009 0.03 0.18 2 -10000 0 2
HCK -0.002 0.11 -10000 0 -0.51 6 6
CYTH3 -0.009 0.03 0.18 2 -10000 0 2
CYTH2 -0.009 0.03 0.18 2 -10000 0 2
KRAS 0.036 0.005 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.032 0.19 1 -10000 0 1
SGK1 0.01 0.032 0.2 1 -10000 0 1
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.049 0.087 0.19 1 -0.31 3 4
SOS1 0.035 0 -10000 0 -10000 0 0
SYK 0.034 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.039 0.059 0.22 4 -10000 0 4
mol:PI-3-4-5-P3 -0.009 0.036 0.24 2 -10000 0 2
ARAP3/RAP1A/GTP 0.018 0.036 0.21 2 -10000 0 2
VAV1 -0.003 0.14 -10000 0 -0.51 10 10
mol:PI-3-4-P2 0.01 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.057 0.047 -10000 0 -10000 0 0
PLEKHA1 0.006 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.057 0.085 -10000 0 -0.29 3 3
LAT 0.031 0.029 -10000 0 -0.32 1 1
Rac1/GTP 0.01 0.062 -10000 0 -0.38 2 2
ITK -0.011 0.024 0.19 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.034 0.14 0.22 15 -0.32 10 25
LCK 0.03 0.03 -10000 0 -0.32 1 1
BTK -0.047 0.096 0.19 2 -0.27 21 23
Syndecan-4-mediated signaling events

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.034 0.051 -10000 0 -10000 0 0
Syndecan-4/Syndesmos 0.1 0.12 -10000 0 -0.43 1 1
positive regulation of JNK cascade -0.07 0.15 -10000 0 -0.57 2 2
Syndecan-4/ADAM12 0.056 0.16 -10000 0 -0.45 3 3
CCL5 -0.068 0.21 -10000 0 -0.51 27 27
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
DNM2 0.034 0.005 -10000 0 -10000 0 0
ITGA5 0.027 0.05 -10000 0 -0.32 3 3
SDCBP 0.03 0.012 -10000 0 -10000 0 0
PLG 0.007 0.03 -10000 0 -10000 0 0
ADAM12 -0.12 0.17 -10000 0 -0.32 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.034 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.023 0.027 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.075 0.11 -10000 0 -0.42 1 1
Syndecan-4/CXCL12/CXCR4 -0.072 0.16 -10000 0 -0.61 2 2
Syndecan-4/Laminin alpha3 0.07 0.11 -10000 0 -0.42 1 1
MDK 0.014 0.079 -10000 0 -0.32 8 8
Syndecan-4/FZD7 0.1 0.12 -10000 0 -0.43 1 1
Syndecan-4/Midkine 0.1 0.12 -10000 0 -0.43 1 1
FZD7 0.02 0.069 -10000 0 -0.32 6 6
Syndecan-4/FGFR1/FGF 0.1 0.12 -10000 0 -10000 0 0
THBS1 0.032 0.009 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.1 0.12 -10000 0 -0.42 1 1
positive regulation of MAPKKK cascade -0.07 0.15 -10000 0 -0.57 2 2
Syndecan-4/TACI 0.076 0.11 -10000 0 -0.42 1 1
CXCR4 0.013 0.084 -10000 0 -0.32 9 9
cell adhesion 0.003 0.05 0.2 2 -10000 0 2
Syndecan-4/Dynamin 0.1 0.12 -10000 0 -0.43 1 1
Syndecan-4/TSP1 0.097 0.12 -10000 0 -0.42 1 1
Syndecan-4/GIPC 0.1 0.12 -10000 0 -0.43 1 1
Syndecan-4/RANTES 0.059 0.14 -10000 0 -0.66 1 1
ITGB1 0.032 0.029 -10000 0 -0.32 1 1
LAMA1 0.026 0.015 -10000 0 -10000 0 0
LAMA3 0.021 0.042 -10000 0 -0.32 2 2
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCA 0.015 0.11 0.67 4 -10000 0 4
Syndecan-4/alpha-Actinin 0.09 0.11 -10000 0 -0.43 1 1
TFPI 0.032 0.029 -10000 0 -0.32 1 1
F2 0.053 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.043 0.044 -10000 0 -0.22 4 4
positive regulation of cell adhesion 0.063 0.11 -10000 0 -10000 0 0
ACTN1 0.03 0.011 -10000 0 -10000 0 0
TNC 0.024 0.057 -10000 0 -0.32 4 4
Syndecan-4/CXCL12 -0.064 0.15 -10000 0 -0.62 2 2
FGF6 0.033 0.007 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
CXCL12 -0.36 0.24 -10000 0 -0.51 105 105
TNFRSF13B 0.023 0.047 -10000 0 -0.51 1 1
FGF2 0.031 0.029 -10000 0 -0.32 1 1
FGFR1 0.03 0.012 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.014 0.072 -10000 0 -0.43 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.05 0.13 -10000 0 -0.33 24 24
cell migration -0.013 0.015 -10000 0 -10000 0 0
PRKCD 0.008 0.03 -10000 0 -10000 0 0
vasculogenesis 0.095 0.11 -10000 0 -0.4 1 1
SDC4 0.019 0.068 -10000 0 -0.45 1 1
Syndecan-4/Tenascin C 0.1 0.12 -10000 0 -0.43 1 1
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.022 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.086 0.11 -10000 0 -10000 0 0
MMP9 0.006 0.071 -10000 0 -0.35 5 5
Rac1/GTP 0.003 0.051 0.21 2 -10000 0 2
cytoskeleton organization 0.1 0.11 -10000 0 -0.42 1 1
GIPC1 0.03 0.045 -10000 0 -0.51 1 1
Syndecan-4/TFPI 0.1 0.12 -10000 0 -0.43 1 1
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.063 0.049 -10000 0 -0.25 2 2
ER alpha/Gai/GDP/Gbeta gamma -0.014 0.16 -10000 0 -0.67 5 5
AKT1 0.018 0.17 -10000 0 -0.78 6 6
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.022 0.17 -10000 0 -0.79 6 6
mol:Ca2+ -0.017 0.13 -10000 0 -0.39 8 8
IGF1R 0.032 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.037 0.049 -10000 0 -0.25 4 4
SHC1 0.033 0.006 -10000 0 -10000 0 0
apoptosis -0.02 0.16 0.74 6 -10000 0 6
RhoA/GTP 0.026 0.037 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.062 0.14 -10000 0 -0.51 3 3
regulation of stress fiber formation -0.01 0.039 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) 0.036 0.043 -10000 0 -0.3 2 2
KRAS 0.034 0.003 -10000 0 -10000 0 0
G13/GTP 0.037 0.039 -10000 0 -0.28 2 2
pseudopodium formation 0.01 0.039 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 0.032 0.044 -10000 0 -0.3 2 2
GRB2 0.033 0.007 -10000 0 -10000 0 0
GNG2 0.031 0.011 -10000 0 -10000 0 0
GNAO1 0.035 0 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.006 0.15 -10000 0 -0.62 5 5
E2/ER beta (dimer) 0.022 0.008 -10000 0 -10000 0 0
mol:GDP 0.013 0.06 -10000 0 -0.38 2 2
mol:NADP 0.006 0.15 -10000 0 -0.62 5 5
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 -0.029 0.12 -10000 0 -0.4 8 8
IGF-1R heterotetramer 0.032 0.008 -10000 0 -10000 0 0
PLCB1 -0.032 0.13 -10000 0 -0.38 11 11
PLCB2 -0.019 0.11 -10000 0 -0.42 7 7
IGF1 -0.29 0.27 -10000 0 -0.51 86 86
mol:L-citrulline 0.006 0.15 -10000 0 -0.62 5 5
RHOA 0.034 0.005 -10000 0 -10000 0 0
Gai/GDP 0.013 0.13 -10000 0 -0.75 3 3
JNK cascade 0.022 0.008 -10000 0 -10000 0 0
BCAR1 0.034 0.004 -10000 0 -10000 0 0
ESR2 0.03 0.011 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 0.026 0.063 -10000 0 -0.51 2 2
Gq family/GDP/Gbeta gamma -0.037 0.18 -10000 0 -0.49 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.038 0.13 -10000 0 -0.69 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.061 0.14 -10000 0 -0.51 3 3
GNAZ 0.032 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.019 0.046 -10000 0 -0.37 2 2
STRN 0.03 0.041 -10000 0 -0.32 2 2
GNAL 0.026 0.015 -10000 0 -10000 0 0
PELP1 0.027 0.014 -10000 0 -10000 0 0
MAPK11 0.016 0.018 -10000 0 -0.18 1 1
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
GNAI3 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.027 0.17 -10000 0 -0.51 16 16
HBEGF 0.1 0.17 0.34 33 -0.55 2 35
cAMP biosynthetic process 0.026 0.035 -10000 0 -0.23 2 2
SRC 0.051 0.13 -10000 0 -0.91 1 1
PI3K 0.05 0.009 -10000 0 -10000 0 0
GNB1 0.032 0.009 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.046 0.065 -10000 0 -0.32 2 2
SOS1 0.035 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.093 0.13 -10000 0 -0.41 10 10
Gs family/GTP 0.034 0.039 -10000 0 -0.24 2 2
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.059 0.031 -10000 0 -10000 0 0
vasodilation 0.008 0.14 -10000 0 -0.58 5 5
mol:DAG -0.029 0.12 -10000 0 -0.4 8 8
Gs family/GDP/Gbeta gamma 0.02 0.054 -10000 0 -0.3 2 2
MSN 0.01 0.041 -10000 0 -10000 0 0
Gq family/GTP -0.015 0.11 -10000 0 -0.32 15 15
mol:PI-3-4-5-P3 0.023 0.17 -10000 0 -0.75 6 6
NRAS 0.028 0.041 -10000 0 -0.32 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.008 0.14 0.58 5 -10000 0 5
GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.067 -10000 0 -0.36 2 2
NOS3 0.005 0.16 -10000 0 -0.66 5 5
GNA11 0 0.13 -10000 0 -0.51 9 9
MAPKKK cascade 0.044 0.15 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src 0.06 0.14 0.28 4 -0.5 4 8
ruffle organization 0.01 0.039 -10000 0 -10000 0 0
ROCK2 0.019 0.043 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.51 6 6
GNA15 0.024 0.057 -10000 0 -0.32 4 4
GNA13 0.033 0.007 -10000 0 -10000 0 0
MMP9 0.084 0.18 0.39 29 -0.69 1 30
MMP2 0.048 0.14 0.29 4 -0.55 3 7
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.011 0.071 -10000 0 -0.39 1 1
VEGFR1 homodimer/NRP1 -0.004 0.064 -10000 0 -0.39 1 1
mol:DAG 0.016 0.083 -10000 0 -0.34 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.003 0.081 -10000 0 -0.42 2 2
CaM/Ca2+ 0.025 0.082 -10000 0 -0.33 2 2
HIF1A 0.024 0.059 -10000 0 -0.45 1 1
GAB1 0.03 0.045 -10000 0 -0.51 1 1
AKT1 0.044 0.095 -10000 0 -10000 0 0
PLCG1 0.016 0.083 -10000 0 -0.35 2 2
NOS3 0.09 0.12 0.31 22 -10000 0 22
CBL 0.034 0.006 -10000 0 -10000 0 0
mol:NO 0.089 0.12 0.31 22 -10000 0 22
FLT1 -0.003 0.077 -10000 0 -0.45 1 1
PGF 0.019 0.064 -10000 0 -0.32 5 5
VEGFR1 homodimer/NRP2/VEGFR121 0.015 0.095 -10000 0 -0.49 2 2
CALM1 0.03 0.012 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 0.1 0.13 0.31 21 -0.38 1 22
endothelial cell proliferation 0.089 0.14 0.34 23 -10000 0 23
mol:Ca2+ 0.016 0.082 -10000 0 -0.34 2 2
MAPK3 0.019 0.1 0.35 5 -0.42 1 6
MAPK1 0.02 0.096 0.35 5 -10000 0 5
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.019 0.064 -10000 0 -0.31 5 5
PRKACA 0.034 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.026 0.05 -10000 0 -0.32 3 3
VEGFA homodimer -0.002 0.11 -10000 0 -0.31 15 15
VEGFR1 homodimer/VEGFA homodimer 0.003 0.09 -10000 0 -0.46 2 2
platelet activating factor biosynthetic process 0.071 0.15 0.34 20 -0.41 1 21
PI3K 0.072 0.1 -10000 0 -0.33 2 2
PRKCA 0.025 0.1 0.37 5 -10000 0 5
PRKCB 0.022 0.1 0.36 5 -0.32 2 7
VEGFR1 homodimer/PLGF homodimer 0.006 0.08 -10000 0 -0.38 2 2
VEGFA -0.002 0.11 -10000 0 -0.32 15 15
VEGFB 0.034 0.006 -10000 0 -10000 0 0
mol:IP3 0.016 0.083 -10000 0 -0.34 2 2
RASA1 0.044 0.11 -10000 0 -0.36 1 1
NRP2 0.032 0.029 -10000 0 -0.32 1 1
VEGFR1 homodimer -0.003 0.077 -10000 0 -0.45 1 1
VEGFB homodimer 0.034 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.096 0.13 0.31 19 -0.4 1 20
PTPN11 0.032 0.029 -10000 0 -0.32 1 1
mol:PI-3-4-5-P3 0.07 0.1 -10000 0 -0.32 2 2
mol:L-citrulline 0.089 0.12 0.31 22 -10000 0 22
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.064 0.11 -10000 0 -0.47 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.016 0.089 -10000 0 -0.42 2 2
CD2AP 0.03 0.045 -10000 0 -0.51 1 1
PI3K/GAB1 0.079 0.11 -10000 0 -10000 0 0
PDPK1 0.044 0.1 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.017 0.09 -10000 0 -0.42 2 2
mol:NADP 0.089 0.12 0.31 22 -10000 0 22
HSP90AA1 0.03 0.012 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.062 0.11 -10000 0 -0.47 1 1
VEGFR1 homodimer/NRP2 0.01 0.078 -10000 0 -0.54 1 1
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.069 0.049 -10000 0 -10000 0 0
epithelial cell differentiation 0.06 0.061 -10000 0 -10000 0 0
ITCH 0.021 0.018 -10000 0 -10000 0 0
WWP1 0.022 0.041 -10000 0 -10000 0 0
FYN 0.031 0.029 -10000 0 -0.32 1 1
EGFR 0.02 0.077 -10000 0 -0.51 3 3
PRL 0.032 0.029 -10000 0 -0.32 1 1
neuron projection morphogenesis 0.051 0.056 0.29 1 -10000 0 1
PTPRZ1 0.008 0.11 -10000 0 -0.48 7 7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.07 0.054 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.045 0.034 -10000 0 -10000 0 0
ADAM17 0.031 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4 0.022 0.026 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.072 0.039 -10000 0 -10000 0 0
NCOR1 0.027 0.015 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.058 0.039 -10000 0 -10000 0 0
GRIN2B 0.021 0.064 -10000 0 -10000 0 0
ErbB4/ErbB2/betacellulin 0.066 0.052 -10000 0 -10000 0 0
STAT1 0.001 0.1 -10000 0 -0.32 14 14
HBEGF 0.027 0.05 -10000 0 -0.32 3 3
PRLR 0.03 0.03 -10000 0 -0.32 1 1
E4ICDs/ETO2 -0.035 0.15 -10000 0 -10000 0 0
axon guidance 0.015 0.045 -10000 0 -10000 0 0
NEDD4 0.015 0.064 -10000 0 -0.32 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.044 0.033 -10000 0 -0.22 2 2
CBFA2T3 -0.16 0.26 -10000 0 -0.51 53 53
ErbB4/ErbB2/HBEGF 0.068 0.046 -10000 0 -10000 0 0
MAPK3 0.046 0.055 -10000 0 -10000 0 0
STAT1 (dimer) 0.057 0.072 -10000 0 -10000 0 0
MAPK1 0.048 0.043 -10000 0 -10000 0 0
JAK2 0.026 0.05 -10000 0 -0.32 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.038 0.035 -10000 0 -10000 0 0
NRG1 0.016 0.008 -10000 0 -10000 0 0
NRG3 0.033 0.007 -10000 0 -10000 0 0
NRG2 0.03 0.045 -10000 0 -0.51 1 1
NRG4 0.015 0.093 -10000 0 -0.47 5 5
heart development 0.015 0.045 -10000 0 -10000 0 0
neural crest cell migration 0.038 0.035 -10000 0 -10000 0 0
ERBB2 0.025 0.037 0.24 4 -10000 0 4
WWOX/E4ICDs 0.073 0.039 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.063 0.077 -10000 0 -10000 0 0
apoptosis -0.059 0.063 0.37 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.071 0.047 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.023 0.1 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.067 0.056 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.099 0.064 -10000 0 -10000 0 0
MDM2 0.02 0.031 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.026 0.026 -10000 0 -10000 0 0
STAT5A 0.037 0.058 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.05 0.055 -10000 0 -10000 0 0
DLG4 0.027 0.014 -10000 0 -10000 0 0
GRB2/SHC 0.047 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.05 0.039 -10000 0 -10000 0 0
STAT5A (dimer) 0.079 0.074 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.06 0.061 -10000 0 -10000 0 0
LRIG1 0.019 0.089 -10000 0 -0.51 4 4
EREG -0.2 0.17 -10000 0 -0.32 94 94
BTC 0.026 0.063 -10000 0 -0.51 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.015 0.045 -10000 0 -10000 0 0
ERBB4 0.022 0.027 -10000 0 -10000 0 0
STAT5B 0.033 0.006 -10000 0 -10000 0 0
YAP1 0.004 0.073 -10000 0 -0.42 4 4
GRB2 0.033 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.059 0.065 -10000 0 -10000 0 0
glial cell differentiation -0.049 0.039 -10000 0 -10000 0 0
WWOX 0.034 0.005 -10000 0 -10000 0 0
cell proliferation 0.044 0.067 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.032 0.009 -10000 0 -10000 0 0
HDAC4 0.034 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.01 0.011 -10000 0 -10000 0 0
CDKN1A -0.009 0.046 -10000 0 -0.55 1 1
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.032 0.029 -10000 0 -0.32 1 1
FOXO3 -0.008 0.004 -10000 0 -10000 0 0
FOXO1 0.009 0.089 -10000 0 -0.51 4 4
FOXO4 0.022 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
TAT 0.034 0.003 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0.019 -10000 0 -0.21 1 1
PPARGC1A -0.2 0.27 -10000 0 -0.51 62 62
FHL2 0.032 0.029 -10000 0 -0.32 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.045 0.016 -10000 0 -10000 0 0
HIST2H4A 0.01 0.011 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.023 0.025 -10000 0 -10000 0 0
SIRT1 0.031 0.013 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.064 0.019 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.029 0.04 -10000 0 -10000 0 0
apoptosis -0.059 0.029 -10000 0 -10000 0 0
SIRT1/PGC1A -0.11 0.18 -10000 0 -0.31 62 62
p53/SIRT1 0.022 0.048 -10000 0 -0.22 5 5
SIRT1/FOXO4 0.031 0.037 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.034 0.068 -10000 0 -0.32 4 4
HIST1H1E 0.02 0.013 -10000 0 -10000 0 0
SIRT1/p300 0.045 0.016 -10000 0 -10000 0 0
muscle cell differentiation -0.02 0.019 0.18 1 -10000 0 1
TP53 0.012 0.063 -10000 0 -0.32 5 5
KU70/SIRT1/BAX 0.06 0.029 -10000 0 -10000 0 0
CREBBP 0.034 0.005 -10000 0 -10000 0 0
MEF2D 0.033 0.006 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.048 0.013 -10000 0 -10000 0 0
ACSS2 0.002 0.055 -10000 0 -0.37 3 3
SIRT1/PCAF/MYOD 0.02 0.019 -10000 0 -0.18 1 1
ceramide signaling pathway

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
MAP4K4 0.019 0.099 -10000 0 -0.48 3 3
BAG4 0.03 0.011 -10000 0 -10000 0 0
BAD -0.004 0.057 -10000 0 -0.19 3 3
NFKBIA 0.031 0.011 -10000 0 -10000 0 0
BIRC3 0.013 0.097 -10000 0 -0.44 6 6
BAX -0.005 0.06 -10000 0 -0.2 4 4
EnzymeConsortium:3.1.4.12 0.01 0.022 -10000 0 -0.099 2 2
IKBKB 0.033 0.1 -10000 0 -0.52 2 2
MAP2K2 0.002 0.057 0.21 3 -10000 0 3
MAP2K1 0.004 0.056 0.21 3 -10000 0 3
SMPD1 -0.034 0.099 -10000 0 -0.22 31 31
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.03 0.095 -10000 0 -0.52 2 2
MAP2K4 -0.001 0.048 -10000 0 -10000 0 0
protein ubiquitination 0.026 0.097 -10000 0 -0.53 2 2
EnzymeConsortium:2.7.1.37 0.005 0.058 0.22 3 -10000 0 3
response to UV 0 0 0.002 3 -10000 0 3
RAF1 0.003 0.06 0.22 3 -10000 0 3
CRADD 0.03 0.045 -10000 0 -0.51 1 1
mol:ceramide -0.004 0.061 -10000 0 -0.21 3 3
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.016 -10000 0 -10000 0 0
MADD 0.034 0.006 -10000 0 -10000 0 0
MAP3K1 -0.004 0.057 -10000 0 -0.19 3 3
TRADD 0.035 0.001 -10000 0 -10000 0 0
RELA/p50 0.034 0.006 -10000 0 -10000 0 0
MAPK3 0.007 0.059 0.21 3 -10000 0 3
MAPK1 0.003 0.065 0.22 2 -0.25 1 3
p50/RELA/I-kappa-B-alpha 0.045 0.017 -10000 0 -10000 0 0
FADD 0.025 0.087 -10000 0 -0.48 2 2
KSR1 0 0.061 0.23 2 -0.19 3 5
MAPK8 -0.003 0.05 -10000 0 -10000 0 0
TRAF2 0.034 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK 0.017 0.093 -10000 0 -0.51 2 2
TNF R/SODD 0.044 0.018 -10000 0 -10000 0 0
TNF 0.034 0.003 -10000 0 -10000 0 0
CYCS 0.061 0.08 0.17 19 -10000 0 19
IKBKG 0.02 0.095 -10000 0 -0.52 2 2
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.027 0.094 -10000 0 -0.45 3 3
RELA 0.034 0.006 -10000 0 -10000 0 0
RIPK1 0.034 0.003 -10000 0 -10000 0 0
AIFM1 0.057 0.077 0.16 12 -10000 0 12
TNF/TNF R/SODD 0.06 0.025 -10000 0 -10000 0 0
TNFRSF1A 0.033 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.029 0.13 -10000 0 -0.74 4 4
NSMAF 0.045 0.11 0.26 3 -0.48 2 5
response to hydrogen peroxide 0 0 0.002 3 -10000 0 3
BCL2 -0.17 0.25 -10000 0 -0.51 51 51
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.02 0.017 -10000 0 -10000 0 0
NFATC1 -0.019 0.14 -10000 0 -0.39 11 11
NFATC2 0.043 0.047 0.16 1 -10000 0 1
NFATC3 0.016 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.004 0.07 -10000 0 -0.26 4 4
Exportin 1/Ran/NUP214 0.069 0.012 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.042 0.075 -10000 0 -10000 0 0
BCL2/BAX -0.14 0.18 -10000 0 -0.37 52 52
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.01 -10000 0 -10000 0 0
BAX 0.032 0.029 -10000 0 -0.32 1 1
MAPK14 0.035 0.003 -10000 0 -10000 0 0
BAD 0.034 0.006 -10000 0 -10000 0 0
CABIN1/MEF2D 0.021 0.073 -10000 0 -0.29 1 1
Calcineurin A alpha-beta B1/BCL2 -0.17 0.25 -10000 0 -0.51 51 51
FKBP8 0.034 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.021 0.072 0.28 1 -10000 0 1
KPNB1 0.024 0.057 -10000 0 -0.32 4 4
KPNA2 0.011 0.084 -10000 0 -0.32 9 9
XPO1 0.035 0 -10000 0 -10000 0 0
SFN 0.027 0.046 -10000 0 -0.51 1 1
MAP3K8 0.001 0.1 -10000 0 -0.31 14 14
NFAT4/CK1 alpha 0.034 0.028 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.093 0.055 -10000 0 -10000 0 0
CABIN1 0.004 0.07 -10000 0 -0.26 4 4
CALM1 0.03 0.012 -10000 0 -10000 0 0
RAN 0.034 0.003 -10000 0 -10000 0 0
MAP3K1 0.034 0.006 -10000 0 -10000 0 0
CAMK4 0.034 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.027 0.063 -10000 0 -0.51 2 2
YWHAH 0.032 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.032 0.071 -10000 0 -0.37 4 4
YWHAB 0.018 0.017 -10000 0 -10000 0 0
MAPK8 0.034 0.006 -10000 0 -10000 0 0
MAPK9 0.034 0.004 -10000 0 -10000 0 0
YWHAG 0.033 0.008 -10000 0 -10000 0 0
FKBP1A 0.026 0.015 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.012 0.14 -10000 0 -0.42 4 4
PRKCH 0.023 0.064 -10000 0 -0.51 2 2
CABIN1/Cbp/p300 0.048 0.014 -10000 0 -10000 0 0
CASP3 0.032 0.009 -10000 0 -10000 0 0
PIM1 0.034 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.01 -10000 0 -10000 0 0
apoptosis -0.015 0.05 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.039 0.048 0.2 1 -10000 0 1
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.03 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.03 0.025 -10000 0 -10000 0 0
PRKCD 0.034 0.005 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.033 0.008 -10000 0 -10000 0 0
PRKCG 0.025 0.057 -10000 0 -0.32 4 4
PRKCQ 0.027 0.05 -10000 0 -0.32 3 3
FKBP38/BCL2 -0.14 0.18 -10000 0 -0.37 51 51
EP300 0.033 0.009 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.015 -10000 0 -10000 0 0
NFATc/JNK1 -0.002 0.14 -10000 0 -0.39 8 8
CaM/Ca2+/FKBP38 0.041 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.011 -10000 0 -10000 0 0
CSNK1A1 0.019 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.04 0.018 -10000 0 -10000 0 0
NFATc/ERK1 -0.007 0.14 -10000 0 -0.4 7 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.042 0.075 -10000 0 -10000 0 0
NR4A1 0.059 0.053 -10000 0 -10000 0 0
GSK3B 0.035 0.004 -10000 0 -10000 0 0
positive T cell selection 0.016 0.006 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.038 0.036 -10000 0 -10000 0 0
RCH1/ KPNB1 0.026 0.084 -10000 0 -0.27 10 10
YWHAQ 0.035 0 -10000 0 -10000 0 0
PRKACA 0.034 0.006 -10000 0 -10000 0 0
AKAP5 0.015 0.089 -10000 0 -0.51 4 4
MEF2D 0.034 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.029 0.013 -10000 0 -10000 0 0
NFATc/p38 alpha -0.004 0.14 -10000 0 -0.39 8 8
CREBBP 0.034 0.005 -10000 0 -10000 0 0
BCL2 -0.17 0.25 -10000 0 -0.51 51 51
FoxO family signaling

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
G6PC 0.025 0.14 -10000 0 -1.4 1 1
PLK1 -0.01 0.18 -10000 0 -0.78 3 3
CDKN1B 0.055 0.14 0.34 1 -0.39 1 2
FOXO3 -0.013 0.2 -10000 0 -0.68 6 6
KAT2B 0 0.018 -10000 0 -0.052 4 4
FOXO1/SIRT1 0.044 0.095 -10000 0 -0.35 3 3
CAT -0.01 0.18 -10000 0 -0.73 3 3
CTNNB1 0.031 0.029 -10000 0 -0.32 1 1
AKT1 0.028 0.031 -10000 0 -10000 0 0
FOXO1 0.033 0.098 -10000 0 -0.37 3 3
MAPK10 0.041 0.064 0.2 12 -0.26 2 14
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.062 0.07 -10000 0 -10000 0 0
response to oxidative stress 0.004 0.018 -10000 0 -0.05 5 5
FOXO3A/SIRT1 0.029 0.17 -10000 0 -0.52 8 8
XPO1 0.035 0 -10000 0 -10000 0 0
EP300 0.034 0.012 -10000 0 -10000 0 0
BCL2L11 0.034 0.034 -10000 0 -10000 0 0
FOXO1/SKP2 0.018 0.11 -10000 0 -0.32 2 2
mol:GDP 0.004 0.018 -10000 0 -0.05 5 5
RAN 0.035 0.003 -10000 0 -10000 0 0
GADD45A 0.048 0.16 -10000 0 -0.62 5 5
YWHAQ 0.035 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.055 0.13 -10000 0 -0.52 3 3
MST1 0.007 0.088 -10000 0 -0.31 9 9
CSNK1D 0.033 0.007 -10000 0 -10000 0 0
CSNK1E 0.032 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.01 0.12 -10000 0 -0.45 3 3
YWHAB 0.018 0.017 -10000 0 -10000 0 0
MAPK8 0.047 0.053 0.2 15 -10000 0 15
MAPK9 0.047 0.053 0.2 15 -10000 0 15
YWHAG 0.033 0.008 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
YWHAZ 0.029 0.013 -10000 0 -10000 0 0
SIRT1 0.038 0.021 -10000 0 -10000 0 0
SOD2 0.047 0.14 -10000 0 -10000 0 0
RBL2 0.035 0.14 -10000 0 -10000 0 0
RAL/GDP 0.047 0.023 -10000 0 -10000 0 0
CHUK 0.027 0.031 -10000 0 -10000 0 0
Ran/GTP 0.029 0.003 -10000 0 -10000 0 0
CSNK1G2 0.033 0.006 -10000 0 -10000 0 0
RAL/GTP 0.05 0.024 -10000 0 -10000 0 0
CSNK1G1 0.032 0.008 -10000 0 -10000 0 0
FASLG -0.18 0.54 -10000 0 -1.5 22 22
SKP2 -0.025 0.13 -10000 0 -0.32 24 24
USP7 0.032 0.045 -10000 0 -0.51 1 1
IKBKB 0.025 0.03 -10000 0 -10000 0 0
CCNB1 -0.027 0.2 -10000 0 -0.86 3 3
FOXO1-3a-4/beta catenin 0.062 0.15 0.34 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.11 -10000 0 -0.32 2 2
CSNK1A1 0.034 0.004 -10000 0 -10000 0 0
SGK1 0 0.018 -10000 0 -0.052 4 4
CSNK1G3 0.034 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.051 0.005 -10000 0 -10000 0 0
ZFAND5 0.059 0.066 -10000 0 -10000 0 0
SFN 0.027 0.046 -10000 0 -0.51 1 1
CDK2 -0.009 0.12 -10000 0 -0.31 19 19
FOXO3A/14-3-3 -0.007 0.12 -10000 0 -0.66 2 2
CREBBP 0.036 0.012 -10000 0 -10000 0 0
FBXO32 -0.029 0.37 -10000 0 -1.4 9 9
BCL6 0.034 0.14 -10000 0 -10000 0 0
RALB 0.036 0.001 -10000 0 -10000 0 0
RALA 0.032 0.011 -10000 0 -10000 0 0
YWHAH 0.032 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.008 0.004 -10000 0 -10000 0 0
SNTA1 0.02 0.017 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.005 0.022 -10000 0 -10000 0 0
MAPK12 -0.027 0.087 0.22 2 -0.28 11 13
CCND1 -0.006 0.045 -10000 0 -10000 0 0
p38 gamma/SNTA1 -0.011 0.083 -10000 0 -0.27 10 10
MAP2K3 0.028 0.013 -10000 0 -10000 0 0
PKN1 0.034 0.006 -10000 0 -10000 0 0
G2/M transition checkpoint -0.029 0.089 0.21 2 -0.28 12 14
MAP2K6 -0.023 0.093 0.24 2 -0.29 12 14
MAPT -0.006 0.055 0.21 1 -0.26 2 3
MAPK13 0.017 0.008 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.004 0.056 -10000 0 -0.28 2 2
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.041 0.12 -10000 0 -10000 0 0
MKNK1 0.034 0.006 -10000 0 -10000 0 0
MAPK14 -0.004 0.07 -10000 0 -10000 0 0
ATF2/c-Jun -0.007 0.071 -10000 0 -0.42 1 1
MAPK11 -0.006 0.071 -10000 0 -0.3 1 1
MITF -0.005 0.065 -10000 0 -10000 0 0
MAPKAPK5 -0.006 0.067 -10000 0 -0.26 1 1
KRT8 -0.009 0.073 -10000 0 -0.3 2 2
MAPKAPK3 0.034 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.033 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.006 0.092 -10000 0 -10000 0 0
CEBPB -0.002 0.051 -10000 0 -10000 0 0
SLC9A1 -0.008 0.065 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.005 0.07 -10000 0 -0.32 1 1
p38alpha-beta/MNK1 0.012 0.084 -10000 0 -10000 0 0
JUN -0.009 0.069 -10000 0 -0.42 1 1
PPARGC1A -0.16 0.19 -10000 0 -0.36 62 62
USF1 -0.011 0.076 -10000 0 -10000 0 0
RAB5/GDP/GDI1 0.006 0.054 -10000 0 -10000 0 0
NOS2 -0.008 0.057 -10000 0 -0.27 1 1
DDIT3 -0.007 0.067 -10000 0 -0.26 1 1
RAB5A 0.034 0.006 -10000 0 -10000 0 0
HSPB1 0.004 0.086 0.29 7 -0.26 1 8
p38alpha-beta/HBP1 0.011 0.083 -10000 0 -10000 0 0
CREB1 -0.001 0.064 -10000 0 -0.36 1 1
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.01 0.056 -10000 0 -10000 0 0
RPS6KA4 -0.003 0.061 -10000 0 -10000 0 0
PLA2G4A -0.082 0.13 -10000 0 -0.3 26 26
GDI1 -0.004 0.065 -10000 0 -0.26 1 1
TP53 -0.023 0.065 -10000 0 -10000 0 0
RPS6KA5 -0.01 0.071 -10000 0 -0.41 1 1
ESR1 -0.009 0.072 -10000 0 -0.3 1 1
HBP1 0.033 0.008 -10000 0 -10000 0 0
MEF2C -0.036 0.12 -10000 0 -0.33 15 15
MEF2A -0.005 0.065 -10000 0 -0.26 1 1
EIF4EBP1 -0.008 0.074 -10000 0 -0.36 2 2
KRT19 -0.014 0.085 -10000 0 -0.34 5 5
ELK4 -0.004 0.068 -10000 0 -0.26 1 1
ATF6 -0.002 0.064 -10000 0 -0.26 1 1
ATF1 -0.001 0.064 -10000 0 -0.36 1 1
p38alpha-beta/MAPKAPK2 0.016 0.082 -10000 0 -10000 0 0
p38alpha-beta/MAPKAPK3 0.012 0.085 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.002 0.048 0.22 1 -0.21 6 7
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.049 0.01 -10000 0 -10000 0 0
STXBP1 0.017 0.075 -10000 0 -0.32 7 7
ACh/CHRNA1 0.022 0.039 -10000 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.065 0.019 -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 0.034 0.005 -10000 0 -10000 0 0
mol:ACh 0.005 0.045 0.1 6 -0.11 5 11
RAB3GAP2 0.033 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.025 0.076 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.022 0.039 -10000 0 -10000 0 0
UNC13B 0.034 0.005 -10000 0 -10000 0 0
CHRNA1 0.034 0.003 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.01 0.081 -10000 0 -0.19 17 17
SNAP25 0.006 0.003 -10000 0 -10000 0 0
VAMP2 0.006 0.003 -10000 0 -10000 0 0
SYT1 -0.019 0.12 -10000 0 -0.32 22 22
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.013 0.062 0.18 1 -0.18 13 14
STX1A/SNAP25 fragment 1/VAMP2 0.025 0.076 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.009 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.054 0.03 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.018 0.019 -10000 0 -10000 0 0
GNAO1 0.035 0 -10000 0 -10000 0 0
HRAS 0.033 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.018 0.01 -10000 0 -10000 0 0
PELP1 0.027 0.014 -10000 0 -10000 0 0
AKT1 0.009 0.004 -10000 0 -10000 0 0
MAP2K1 0.065 0.085 0.22 1 -10000 0 1
T-DHT/AR 0.024 0.02 -10000 0 -0.21 1 1
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 14 14
GNAI2 0.031 0.029 -10000 0 -0.32 1 1
GNAI3 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.027 0.17 -10000 0 -0.51 16 16
mol:GDP 0.007 0.007 -10000 0 -10000 0 0
cell proliferation 0.044 0.14 -10000 0 -0.41 5 5
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
FOS -0.004 0.25 -10000 0 -0.8 12 12
mol:Ca2+ -0.004 0.025 -10000 0 -0.065 16 16
MAPK3 0.058 0.11 0.31 1 -10000 0 1
MAPK1 0.021 0.11 -10000 0 -0.39 5 5
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 14 14
cAMP biosynthetic process 0.003 0.019 -10000 0 -10000 0 0
GNG2 0.031 0.011 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 14 14
HRAS/GTP 0.032 0.037 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.043 0.022 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 14 14
PI3K 0.045 0.008 -10000 0 -10000 0 0
apoptosis -0.038 0.14 0.35 12 -10000 0 12
T-DHT/AR/PELP1 0.036 0.025 -10000 0 -0.16 1 1
HRAS/GDP 0.021 0.022 -10000 0 -10000 0 0
CREB1 0.037 0.14 -10000 0 -0.37 12 12
RAC1-CDC42/GTP 0.054 0.028 -10000 0 -10000 0 0
AR 0.032 0.029 -10000 0 -0.31 1 1
GNB1 0.032 0.009 -10000 0 -10000 0 0
RAF1 0.079 0.085 0.23 1 -10000 0 1
RAC1-CDC42/GDP 0.067 0.046 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0.033 0.033 -10000 0 -10000 0 0
MAP2K2 0.067 0.085 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0.018 0.019 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
SHBG 0.027 0.014 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.094 -10000 0 -0.48 2 2
mol:T-DHT 0 0.001 -10000 0 -0.004 12 12
RAC1 0.031 0.01 -10000 0 -10000 0 0
GNRH1 0.008 0.004 -10000 0 -10000 0 0
Gi family/GTP -0.005 0.088 -10000 0 -0.28 5 5
CDC42 0.031 0.01 -10000 0 -10000 0 0
Arf6 trafficking 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
SLC2A4 -0.014 0.14 -10000 0 -0.51 11 11
CLTC -0.017 0.14 -10000 0 -0.4 15 15
calcium ion-dependent exocytosis -0.016 0.098 -10000 0 -0.32 7 7
Dynamin 2/GTP 0.03 0.021 -10000 0 -10000 0 0
EXOC4 0.033 0.007 -10000 0 -10000 0 0
CD59 -0.014 0.11 -10000 0 -0.36 13 13
CPE -0.007 0.084 -10000 0 -0.28 12 12
CTNNB1 0.031 0.029 -10000 0 -0.32 1 1
membrane fusion 0.004 0.07 -10000 0 -0.34 2 2
CTNND1 0.02 0.028 -10000 0 -10000 0 0
DNM2 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.082 -10000 0 -0.29 5 5
TSHR 0.018 0.007 -10000 0 -10000 0 0
INS 0.008 0.069 -10000 0 -0.54 2 2
BIN1 0.035 0 -10000 0 -10000 0 0
mol:Choline 0.004 0.07 -10000 0 -0.34 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.018 -10000 0 -0.18 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0.03 0.021 -10000 0 -10000 0 0
JUP -0.014 0.11 -10000 0 -0.35 13 13
ASAP2/amphiphysin II 0.039 0.014 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.008 -10000 0 -10000 0 0
CDH1 -0.02 0.12 -10000 0 -0.34 15 15
clathrin-independent pinocytosis 0.023 0.008 -10000 0 -10000 0 0
MAPK8IP3 0.034 0.005 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.008 -10000 0 -10000 0 0
EXOC2 0.034 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.028 0.058 -10000 0 -0.31 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.033 0.008 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.01 0.12 0.33 13 -10000 0 13
positive regulation of phagocytosis 0.017 0.008 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.041 0.015 -10000 0 -10000 0 0
ACAP1 0.003 0.069 -10000 0 -0.28 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.02 0.11 -10000 0 -0.35 13 13
clathrin heavy chain/ACAP1 -0.017 0.12 -10000 0 -0.34 12 12
JIP4/KLC1 0.055 0.025 -10000 0 -10000 0 0
EXOC1 0.033 0.006 -10000 0 -10000 0 0
exocyst 0.034 0.051 -10000 0 -0.31 2 2
RALA/GTP 0.023 0.008 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.04 0.016 -10000 0 -10000 0 0
receptor recycling 0.023 0.008 -10000 0 -10000 0 0
CTNNA1 0.02 0.028 -10000 0 -10000 0 0
NME1 0.016 0.018 -10000 0 -0.18 1 1
clathrin coat assembly -0.016 0.14 -10000 0 -0.39 15 15
IL2RA -0.017 0.11 -10000 0 -0.35 13 13
VAMP3 0.017 0.008 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.025 0.13 -10000 0 -0.35 9 9
EXOC6 0.032 0.008 -10000 0 -10000 0 0
PLD1 -0.03 0.11 -10000 0 -0.3 21 21
PLD2 0.015 0.012 -10000 0 -10000 0 0
EXOC5 0.031 0.011 -10000 0 -10000 0 0
PIP5K1C -0.002 0.074 -10000 0 -0.28 3 3
SDC1 -0.014 0.11 -10000 0 -0.35 13 13
ARF6/GDP 0.029 0.024 0.18 1 -0.18 1 2
EXOC7 0.033 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.011 0.13 -10000 0 -0.35 12 12
mol:Phosphatidic acid 0.004 0.07 -10000 0 -0.34 2 2
endocytosis -0.038 0.013 -10000 0 -10000 0 0
SCAMP2 0.032 0.009 -10000 0 -10000 0 0
ADRB2 -0.098 0.19 -10000 0 -0.49 18 18
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.034 0.022 -10000 0 -10000 0 0
KLC1 0.03 0.012 -10000 0 -10000 0 0
AVPR2 -0.015 0.13 -10000 0 -0.37 15 15
RALA 0.031 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.009 0.12 -10000 0 -0.39 4 4
Regulation of Telomerase

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
Telomerase catalytic core complex 0.011 0.11 -9999 0 -10000 0 0
RAD9A 0.034 0.006 -9999 0 -10000 0 0
AP1 0.012 0.1 -9999 0 -0.3 12 12
IFNAR2 0.034 0.008 -9999 0 -10000 0 0
AKT1 0.023 0.044 -9999 0 -0.44 1 1
ER alpha/Oestrogen 0.02 0.046 -9999 0 -0.37 2 2
NFX1/SIN3/HDAC complex 0.046 0.046 -9999 0 -10000 0 0
EGF -0.11 0.22 -9999 0 -0.44 44 44
SMG5 0.033 0.006 -9999 0 -10000 0 0
SMG6 0.027 0.014 -9999 0 -10000 0 0
SP3/HDAC2 0.051 0.01 -9999 0 -10000 0 0
TERT/c-Abl 0.022 0.11 -9999 0 -10000 0 0
SAP18 0.025 0.016 -9999 0 -10000 0 0
MRN complex 0.056 0.028 -9999 0 -10000 0 0
WT1 -0.14 0.18 -9999 0 -0.32 73 73
WRN 0.028 0.014 -9999 0 -10000 0 0
SP1 0.035 0.005 -9999 0 -10000 0 0
SP3 0.035 0.003 -9999 0 -10000 0 0
TERF2IP 0.034 0.003 -9999 0 -10000 0 0
Telomerase/Nucleolin 0.017 0.13 -9999 0 -10000 0 0
Mad/Max 0.026 0.09 -9999 0 -0.37 7 7
TERT 0.011 0.11 -9999 0 -10000 0 0
CCND1 -0.004 0.12 -9999 0 -10000 0 0
MAX 0.031 0.012 -9999 0 -10000 0 0
RBBP7 0.034 0.003 -9999 0 -10000 0 0
RBBP4 0.033 0.008 -9999 0 -10000 0 0
TERF2 0.032 0.01 -9999 0 -10000 0 0
PTGES3 0.034 0.003 -9999 0 -10000 0 0
SIN3A 0.033 0.008 -9999 0 -10000 0 0
Telomerase/911 0.038 0.057 -9999 0 -0.3 1 1
CDKN1B -0.016 0.09 -9999 0 -0.31 2 2
RAD1 0.023 0.057 -9999 0 -0.32 4 4
XRCC5 0.034 0.003 -9999 0 -10000 0 0
XRCC6 0.032 0.009 -9999 0 -10000 0 0
SAP30 0.032 0.009 -9999 0 -10000 0 0
TRF2/PARP2 0.046 0.017 -9999 0 -10000 0 0
UBE3A 0.032 0.01 -9999 0 -10000 0 0
JUN 0.022 0.064 -9999 0 -0.32 5 5
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.024 0.008 -9999 0 -10000 0 0
FOS 0.004 0.11 -9999 0 -0.46 8 8
IFN-gamma/IRF1 -0.005 0.12 -9999 0 -0.37 2 2
PARP2 0.031 0.01 -9999 0 -10000 0 0
BLM 0.027 0.041 -9999 0 -0.32 2 2
Telomerase -0.019 0.13 -9999 0 -0.57 4 4
IRF1 0.032 0.053 -9999 0 -0.4 2 2
ESR1 0.026 0.063 -9999 0 -0.51 2 2
KU/TER 0.048 0.013 -9999 0 -10000 0 0
ATM/TRF2 0.05 0.01 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.061 -9999 0 -0.3 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.042 0.059 -9999 0 -0.31 1 1
HDAC1 0.033 0.008 -9999 0 -10000 0 0
HDAC2 0.035 0.007 -9999 0 -10000 0 0
ATM 0.013 0.003 -9999 0 -10000 0 0
SMAD3 0.018 0.006 -9999 0 -10000 0 0
ABL1 0.034 0.005 -9999 0 -10000 0 0
MXD1 0.009 0.12 -9999 0 -0.51 7 7
MRE11A 0.033 0.006 -9999 0 -10000 0 0
HUS1 0.031 0.01 -9999 0 -10000 0 0
RPS6KB1 0.033 0.007 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.026 0.12 -9999 0 -0.52 2 2
NR2F2 0.032 0.009 -9999 0 -10000 0 0
MAPK3 0.015 0.046 -9999 0 -0.37 2 2
MAPK1 0.02 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.033 0.006 -9999 0 -10000 0 0
NFKB1 0.034 0.005 -9999 0 -10000 0 0
HNRNPC 0.031 0.01 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.003 -9999 0 -10000 0 0
NBN 0.029 0.013 -9999 0 -10000 0 0
EGFR 0.021 0.078 -9999 0 -0.51 3 3
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.066 0.17 -9999 0 -0.35 32 32
MYC -0.12 0.17 -9999 0 -0.31 63 63
IL2 0.035 0.007 -9999 0 -10000 0 0
KU 0.048 0.013 -9999 0 -10000 0 0
RAD50 0.034 0.004 -9999 0 -10000 0 0
HSP90AA1 0.03 0.012 -9999 0 -10000 0 0
TGFB1 0.033 0.006 -9999 0 -10000 0 0
TRF2/BLM 0.044 0.033 -9999 0 -0.2 2 2
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT 0.033 0.11 -9999 0 -10000 0 0
SP1/HDAC2 0.052 0.013 -9999 0 -10000 0 0
PINX1 0.024 0.032 -9999 0 -0.32 1 1
Telomerase/EST1A 0.007 0.12 -9999 0 -10000 0 0
Smad3/Myc -0.061 0.1 -9999 0 -10000 0 0
911 complex 0.053 0.043 -9999 0 -10000 0 0
IFNG -0.039 0.14 -9999 0 -0.31 33 33
Telomerase/PinX1 0.004 0.12 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K -0.004 0.12 -9999 0 -0.47 4 4
SIN3B 0.034 0.005 -9999 0 -10000 0 0
YWHAE 0.027 0.014 -9999 0 -10000 0 0
Telomerase/EST1B 0.016 0.12 -9999 0 -10000 0 0
response to DNA damage stimulus 0.002 0.021 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.08 0.04 -9999 0 -10000 0 0
TRF2/WRN 0.04 0.021 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.017 0.12 -9999 0 -10000 0 0
E2F1 0.015 0.043 -9999 0 -0.32 2 2
ZNFX1 0.019 0.017 -9999 0 -10000 0 0
PIF1 0.03 0.03 -9999 0 -0.32 </