PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C18P5XJP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C18P5XJP
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 55 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
Class IB PI3K non-lipid kinase events 248
Signaling events mediated by Stem cell factor receptor (c-Kit) 235
Reelin signaling pathway 212
EGFR-dependent Endothelin signaling events 204
Signaling mediated by p38-alpha and p38-beta 201
HIF-1-alpha transcription factor network 178
p75(NTR)-mediated signaling 145
Glucocorticoid receptor regulatory network 144
IL4-mediated signaling events 142
FOXA2 and FOXA3 transcription factor networks 139
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 914 . 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 ( 914 ).

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
Class IB PI3K non-lipid kinase events 0.2713 248 744 3 -0.22 -1000 1000 -1000 -0.022 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2571 235 18337 78 -0.62 0.19 1000 -1000 -0.1 -1000
Reelin signaling pathway 0.2319 212 11915 56 -0.51 0 1000 -1000 -0.095 -1000
EGFR-dependent Endothelin signaling events 0.2232 204 4297 21 -0.35 0 1000 -1000 -0.062 -1000
Signaling mediated by p38-alpha and p38-beta 0.2199 201 8858 44 -0.4 0 1000 -1000 -0.045 -1000
HIF-1-alpha transcription factor network 0.1947 178 13539 76 -0.78 0.018 1000 -1000 -0.083 -1000
p75(NTR)-mediated signaling 0.1586 145 18242 125 -0.42 0 1000 -1000 -0.098 -1000
Glucocorticoid receptor regulatory network 0.1575 144 16440 114 -0.96 0.36 1000 -1000 -0.064 -1000
IL4-mediated signaling events 0.1554 142 12943 91 -1 0.51 1000 -1000 -0.11 -1000
FOXA2 and FOXA3 transcription factor networks 0.1521 139 6422 46 -1.2 0.025 1000 -1000 -0.042 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1411 129 8839 68 -0.53 0.17 1000 -1000 -0.097 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1346 123 6683 54 -0.51 0.022 1000 -1000 -0.084 -1000
Arf6 signaling events 0.1247 114 7095 62 -0.35 0.017 1000 -1000 -0.055 -1000
ErbB2/ErbB3 signaling events 0.1236 113 7382 65 -0.42 0.018 1000 -1000 -0.06 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1225 112 9929 88 -0.36 0.036 1000 -1000 -0.11 -1000
Endothelins 0.1214 111 10681 96 -0.39 0.034 1000 -1000 -0.072 -1000
EPHB forward signaling 0.1214 111 9439 85 -0.35 0.19 1000 -1000 -0.085 -1000
Wnt signaling 0.1204 110 773 7 -0.19 -0.006 1000 -1000 -0.05 -1000
Ephrin B reverse signaling 0.1171 107 5175 48 -0.35 0.2 1000 -1000 -0.073 -1000
FOXM1 transcription factor network 0.1171 107 5486 51 -0.44 0.013 1000 -1000 -0.14 -1000
IGF1 pathway 0.1160 106 6070 57 -0.18 0.079 1000 -1000 -0.08 -1000
IL23-mediated signaling events 0.0985 90 5410 60 -0.47 0.017 1000 -1000 -0.12 -1000
BMP receptor signaling 0.0952 87 7085 81 -0.57 0.025 1000 -1000 -0.087 -1000
Calcium signaling in the CD4+ TCR pathway 0.0930 85 2640 31 -0.35 0.011 1000 -1000 -0.096 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0930 85 10287 120 -0.63 0.25 1000 -1000 -0.077 -1000
ErbB4 signaling events 0.0919 84 5861 69 -0.44 0.061 1000 -1000 -0.082 -1000
Aurora B signaling 0.0919 84 5628 67 -0.33 0.012 1000 -1000 -0.074 -1000
Visual signal transduction: Rods 0.0897 82 4306 52 -0.52 0 1000 -1000 -0.075 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0886 81 6960 85 -0.26 0.011 1000 -1000 -0.066 -1000
Nongenotropic Androgen signaling 0.0886 81 4251 52 -0.24 0.11 1000 -1000 -0.058 -1000
Noncanonical Wnt signaling pathway 0.0875 80 2097 26 -0.19 0 1000 -1000 -0.075 -1000
Syndecan-1-mediated signaling events 0.0864 79 2719 34 -0.21 0 1000 -1000 -0.067 -1000
Glypican 1 network 0.0864 79 3811 48 -0.33 0.03 1000 -1000 -0.052 -1000
Signaling events regulated by Ret tyrosine kinase 0.0864 79 6519 82 -0.17 0 1000 -1000 -0.079 -1000
Aurora C signaling 0.0853 78 546 7 -0.16 0 1000 -1000 -0.042 -1000
Plasma membrane estrogen receptor signaling 0.0810 74 6399 86 -0.2 0.085 1000 -1000 -0.076 -1000
IL6-mediated signaling events 0.0755 69 5189 75 -0.3 0.053 1000 -1000 -0.074 -1000
amb2 Integrin signaling 0.0744 68 5645 82 -0.53 0 1000 -1000 -0.08 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0722 66 3465 52 -0.2 0.031 1000 -1000 -0.064 -1000
Integrins in angiogenesis 0.0722 66 5571 84 -0.34 0 1000 -1000 -0.089 -1000
Signaling events mediated by PTP1B 0.0700 64 4917 76 -0.67 0.068 1000 -1000 -0.071 -1000
Ephrin A reverse signaling 0.0689 63 445 7 -0.081 0 1000 -1000 -0.044 -1000
Syndecan-3-mediated signaling events 0.0656 60 2120 35 -0.36 0 1000 -1000 -0.061 -1000
LPA receptor mediated events 0.0656 60 6191 102 -0.3 0.029 1000 -1000 -0.079 -1000
Fc-epsilon receptor I signaling in mast cells 0.0646 59 5777 97 -0.26 0.028 1000 -1000 -0.078 -1000
Signaling events mediated by the Hedgehog family 0.0613 56 2917 52 -0.22 0.03 1000 -1000 -0.076 -1000
PDGFR-alpha signaling pathway 0.0580 53 2364 44 -0.38 0.019 1000 -1000 -0.055 -1000
S1P1 pathway 0.0580 53 1929 36 -0.33 0.007 1000 -1000 -0.066 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0558 51 1760 34 -0.081 0 1000 -1000 -0.062 -1000
E-cadherin signaling in keratinocytes 0.0558 51 2219 43 -0.3 0.043 1000 -1000 -0.067 -1000
Visual signal transduction: Cones 0.0547 50 1906 38 -0.18 0.006 1000 -1000 -0.056 -1000
TCGA08_rtk_signaling 0.0536 49 1290 26 -0.3 0.027 1000 -1000 -0.028 -1000
Signaling events mediated by PRL 0.0536 49 1690 34 -0.19 0.02 1000 -1000 -0.061 -1000
Presenilin action in Notch and Wnt signaling 0.0514 47 2890 61 -0.44 0.013 1000 -1000 -0.06 -1000
Ras signaling in the CD4+ TCR pathway 0.0503 46 798 17 -0.12 0 1000 -1000 -0.055 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0481 44 3321 74 -0.3 0.07 1000 -1000 -0.092 -1000
Signaling events mediated by HDAC Class III 0.0470 43 1741 40 -0.59 0.029 1000 -1000 -0.046 -1000
Rapid glucocorticoid signaling 0.0470 43 860 20 -0.19 0.027 1000 -1000 -0.042 -1000
FAS signaling pathway (CD95) 0.0460 42 1998 47 -0.48 0.012 1000 -1000 -0.047 -1000
LPA4-mediated signaling events 0.0449 41 492 12 -0.16 0.019 1000 -1000 -0.015 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0438 40 1349 33 -0.57 0 1000 -1000 -0.073 -1000
Nectin adhesion pathway 0.0427 39 2487 63 -0.077 0.008 1000 -1000 -0.076 -1000
Canonical Wnt signaling pathway 0.0416 38 1950 51 -0.44 0.15 1000 -1000 -0.059 -1000
Glypican 2 network 0.0372 34 137 4 -0.034 -0.028 1000 -1000 -0.038 -1000
IL27-mediated signaling events 0.0372 34 1756 51 -0.3 0.023 1000 -1000 -0.079 -1000
IL12-mediated signaling events 0.0361 33 2871 87 -0.37 0.053 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.0361 33 3151 93 -0.17 0.082 1000 -1000 -0.075 -1000
Insulin Pathway 0.0350 32 2437 74 -0.2 0.032 1000 -1000 -0.079 -1000
Regulation of Telomerase 0.0328 30 3110 102 -0.35 0.021 1000 -1000 -0.09 -1000
Syndecan-4-mediated signaling events 0.0328 30 2010 67 -0.33 0.005 1000 -1000 -0.081 -1000
Coregulation of Androgen receptor activity 0.0317 29 2235 76 -0.2 0.035 1000 -1000 -0.051 -1000
PLK1 signaling events 0.0306 28 2438 85 -0.22 0.034 1000 -1000 -0.062 -1000
BCR signaling pathway 0.0295 27 2677 99 -0.14 0.042 1000 -1000 -0.08 -1000
Regulation of Androgen receptor activity 0.0295 27 1911 70 -0.27 0.021 1000 -1000 -0.068 -1000
Regulation of nuclear SMAD2/3 signaling 0.0274 25 3510 136 -0.33 0.051 1000 -1000 -0.079 -1000
Thromboxane A2 receptor signaling 0.0274 25 2682 105 -0.3 0.069 1000 -1000 -0.07 -1000
Regulation of p38-alpha and p38-beta 0.0274 25 1364 54 -0.38 0.027 1000 -1000 -0.072 -1000
Effects of Botulinum toxin 0.0274 25 672 26 -0.1 0 1000 -1000 -0.052 -1000
Osteopontin-mediated events 0.0263 24 931 38 -0.26 0.027 1000 -1000 -0.098 -1000
Arf6 trafficking events 0.0263 24 1757 71 -0.46 0.032 1000 -1000 -0.068 -1000
Syndecan-2-mediated signaling events 0.0230 21 1503 69 -0.2 0.035 1000 -1000 -0.061 -1000
E-cadherin signaling events 0.0186 17 86 5 -0.025 0 1000 -1000 -0.049 -1000
Hedgehog signaling events mediated by Gli proteins 0.0175 16 1083 65 -0.069 0.041 1000 -1000 -0.071 -1000
Class I PI3K signaling events mediated by Akt 0.0175 16 1093 68 -0.27 0.053 1000 -1000 -0.069 -1000
Ceramide signaling pathway 0.0164 15 1161 76 -0.18 0.047 1000 -1000 -0.061 -1000
TRAIL signaling pathway 0.0164 15 745 48 -0.079 0.046 1000 -1000 -0.066 -1000
Signaling mediated by p38-gamma and p38-delta 0.0153 14 217 15 -0.017 0.021 1000 -1000 -0.055 -1000
Caspase cascade in apoptosis 0.0142 13 1019 74 -0.052 0.045 1000 -1000 -0.063 -1000
PLK2 and PLK4 events 0.0142 13 40 3 -0.012 0.013 1000 -1000 -0.022 -1000
Cellular roles of Anthrax toxin 0.0131 12 497 39 -0.14 0.02 1000 -1000 -0.039 -1000
Aurora A signaling 0.0131 12 760 60 -0.2 0.006 1000 -1000 -0.066 -1000
Retinoic acid receptors-mediated signaling 0.0131 12 747 58 -0.11 0.038 1000 -1000 -0.068 -1000
S1P4 pathway 0.0131 12 301 25 -0.042 0 1000 -1000 -0.051 -1000
S1P5 pathway 0.0109 10 181 17 -0.042 0.024 1000 -1000 -0.049 -1000
E-cadherin signaling in the nascent adherens junction 0.0109 10 813 76 -0.025 0.047 1000 -1000 -0.077 -1000
S1P3 pathway 0.0109 10 452 42 -0.032 0.021 1000 -1000 -0.054 -1000
IL1-mediated signaling events 0.0098 9 595 62 -0.038 0.031 1000 -1000 -0.091 -1000
BARD1 signaling events 0.0088 8 488 57 -0.11 0.022 1000 -1000 -0.073 -1000
JNK signaling in the CD4+ TCR pathway 0.0088 8 145 17 -0.019 0.044 1000 -1000 -0.067 -1000
IL2 signaling events mediated by PI3K 0.0088 8 510 58 -0.038 0.064 1000 -1000 -0.068 -1000
Signaling events mediated by HDAC Class II 0.0077 7 552 75 -0.15 0 1000 -1000 -0.063 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0077 7 208 28 -0.042 0.018 1000 -1000 -0.054 -1000
mTOR signaling pathway 0.0077 7 397 53 -0.017 0.027 1000 -1000 -0.056 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0077 7 634 83 -0.071 0.05 1000 -1000 -0.079 -1000
IL2 signaling events mediated by STAT5 0.0077 7 156 22 -0.12 0.066 1000 -1000 -0.041 -1000
TCGA08_retinoblastoma 0.0077 7 57 8 -0.047 0.009 1000 -1000 -0.028 -1000
VEGFR1 specific signals 0.0066 6 377 56 -0.17 0.062 1000 -1000 -0.07 -1000
p38 MAPK signaling pathway 0.0066 6 288 44 -0.074 0.029 1000 -1000 -0.063 -1000
a4b1 and a4b7 Integrin signaling 0.0055 5 29 5 -0.008 -0.002 1000 -1000 -0.036 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0055 5 252 45 -0.026 0.074 1000 -1000 -0.075 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0055 5 638 125 -0.17 0.086 1000 -1000 -0.086 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0044 4 114 23 -0.03 0.041 1000 -1000 -0.074 -1000
HIF-2-alpha transcription factor network 0.0044 4 196 43 -0.16 0.18 1000 -1000 -0.073 -1000
Signaling events mediated by HDAC Class I 0.0044 4 418 104 -0.094 0.045 1000 -1000 -0.065 -1000
PDGFR-beta signaling pathway 0.0044 4 406 97 -0.024 0.055 1000 -1000 -0.076 -1000
EPO signaling pathway 0.0033 3 175 55 -0.036 0.057 1000 -1000 -0.084 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0033 3 115 37 -0.047 0.035 1000 -1000 -0.075 -1000
ceramide signaling pathway 0.0033 3 151 49 -0.027 0.052 1000 -1000 -0.051 -1000
FoxO family signaling 0.0033 3 247 64 -0.044 0.093 1000 -1000 -0.073 -1000
Atypical NF-kappaB pathway 0.0033 3 93 31 -0.018 0.024 1000 -1000 -0.064 -1000
Canonical NF-kappaB pathway 0.0022 2 90 39 -0.02 0.076 1000 -1000 -0.074 -1000
Circadian rhythm pathway 0.0022 2 47 22 -0.018 0.044 1000 -1000 -0.061 -1000
Insulin-mediated glucose transport 0.0022 2 77 32 -0.14 0.031 1000 -1000 -0.057 -1000
IFN-gamma pathway 0.0022 2 194 68 -0.074 0.075 1000 -1000 -0.084 -1000
Class I PI3K signaling events 0.0022 2 214 73 -0.039 0.06 1000 -1000 -0.069 -1000
Arf6 downstream pathway 0.0011 1 54 43 -0.014 0.022 1000 -1000 -0.042 -1000
Paxillin-dependent events mediated by a4b1 0.0011 1 59 36 -0.008 0.022 1000 -1000 -0.067 -1000
TCGA08_p53 0.0000 0 0 7 -0.021 0.015 1000 -1000 -0.024 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 3 27 -0.001 0.028 1000 -1000 -0.057 -1000
Arf1 pathway 0.0000 0 0 54 -0.001 0.025 1000 -1000 -0.043 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 -0.002 0 1000 -1000 -0.059 -1000
Total NA 6577 391415 7203 -32 -990 131000 -131000 -8.8 -131000
Class IB PI3K non-lipid kinase events

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.22 0.37 0.82 248 -10000 0 248
PI3K Class IB/PDE3B -0.22 0.37 -10000 0 -0.82 248 248
PDE3B -0.22 0.37 -10000 0 -0.82 248 248
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 -0.15 0.22 -10000 0 -0.39 416 416
CRKL -0.17 0.23 -10000 0 -0.41 415 415
HRAS -0.16 0.17 -10000 0 -0.55 25 25
mol:PIP3 -0.17 0.21 -10000 0 -0.4 416 416
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.2 0.22 -10000 0 -0.44 417 417
FOXO3 -0.15 0.21 -10000 0 -0.38 415 415
AKT1 -0.16 0.22 -10000 0 -0.41 416 416
BAD -0.15 0.21 -10000 0 -0.37 415 415
megakaryocyte differentiation -0.18 0.24 -10000 0 -0.43 417 417
GSK3B -0.15 0.21 -10000 0 -0.37 415 415
RAF1 -0.091 0.17 -10000 0 -0.46 19 19
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 417 417
STAT1 -0.45 0.56 -10000 0 -1.1 423 423
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.44 22 22
cell proliferation -0.18 0.24 -10000 0 -0.44 417 417
PIK3CA 0 0.009 -10000 0 -10000 0 0
TEC -0.002 0.039 -10000 0 -0.82 2 2
RPS6KB1 -0.18 0.24 -10000 0 -0.44 417 417
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.44 22 22
LYN/TEC/p62DOK -0.19 0.2 -10000 0 -0.4 416 416
MAPK3 -0.054 0.13 -10000 0 -0.32 17 17
STAP1 -0.2 0.24 -10000 0 -0.45 419 419
GRAP2 -0.014 0.1 -10000 0 -0.82 14 14
JAK2 -0.4 0.44 -10000 0 -0.88 419 419
STAT1 (dimer) -0.44 0.55 -10000 0 -1 423 423
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.19 0.2 -10000 0 -0.41 416 416
actin filament polymerization -0.18 0.24 -10000 0 -0.44 417 417
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.33 -10000 0 -0.62 417 417
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.42 25 25
PI3K -0.19 0.2 -10000 0 -0.41 416 416
PTEN -0.002 0.039 -10000 0 -0.82 2 2
SCF/KIT/EPO/EPOR -0.6 0.68 -10000 0 -1.3 415 415
MAPK8 -0.18 0.24 -10000 0 -0.44 417 417
STAT3 (dimer) -0.18 0.24 -10000 0 -0.43 417 417
positive regulation of transcription -0.041 0.11 -10000 0 -0.26 17 17
mol:GDP -0.16 0.18 -10000 0 -0.59 25 25
PIK3C2B -0.18 0.24 -10000 0 -0.44 417 417
CBL/CRKL -0.17 0.19 -10000 0 -0.38 415 415
FER -0.18 0.24 -10000 0 -0.44 420 420
SH2B3 -0.18 0.24 -10000 0 -0.44 417 417
PDPK1 -0.15 0.2 -10000 0 -0.36 415 415
SNAI2 -0.19 0.24 -10000 0 -0.45 418 418
positive regulation of cell proliferation -0.32 0.41 -10000 0 -0.75 423 423
KITLG 0 0.075 -10000 0 -0.85 6 6
cell motility -0.32 0.41 -10000 0 -0.75 423 423
PTPN6 0.015 0.021 -10000 0 -0.27 2 2
EPOR -0.097 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 419 419
SOCS1 -0.003 0.038 -10000 0 -0.34 9 9
cell migration 0.19 0.24 0.45 424 -10000 0 424
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.044 0.11 -10000 0 -0.3 94 94
VAV1 -0.002 0.03 -10000 0 -0.46 3 3
GRB10 -0.18 0.24 -10000 0 -0.44 417 417
PTPN11 0.012 0.013 -10000 0 -10000 0 0
SCF/KIT -0.22 0.24 -10000 0 -0.47 417 417
GO:0007205 0.009 0.013 -10000 0 -10000 0 0
MAP2K1 -0.063 0.14 -10000 0 -0.36 17 17
CBL 0 0 -10000 0 -10000 0 0
KIT -0.62 0.74 -10000 0 -1.4 413 413
MAP2K2 -0.063 0.14 -10000 0 -0.36 17 17
SHC/Grb2/SOS1 -0.19 0.2 -10000 0 -0.4 415 415
STAT5A -0.27 0.35 -10000 0 -0.65 417 417
GRB2 0 0.009 -10000 0 -10000 0 0
response to radiation -0.18 0.24 -10000 0 -0.44 418 418
SHC/GRAP2 -0.01 0.078 -10000 0 -0.63 14 14
PTPRO -0.18 0.24 -10000 0 -0.44 417 417
SH2B2 -0.19 0.24 -10000 0 -0.45 417 417
DOK1 0 0.009 -10000 0 -10000 0 0
MATK -0.19 0.25 -10000 0 -0.46 424 424
CREBBP 0.019 0.018 -10000 0 -10000 0 0
BCL2 -0.13 0.3 -10000 0 -1.6 30 30
Reelin signaling pathway

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
CDK5R1/CDK5 -0.006 0.033 -9999 0 -10000 0 0
VLDLR -0.023 0.14 -9999 0 -0.82 25 25
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.001 0.027 -9999 0 -0.82 1 1
ITGA3 -0.004 0.056 -9999 0 -0.82 4 4
RELN/VLDLR/Fyn -0.35 0.28 -9999 0 -0.56 570 570
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.004 0.038 -9999 0 -0.47 6 6
AKT1 -0.21 0.17 -9999 0 -0.33 570 570
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.067 -9999 0 -0.28 56 56
RELN/LRP8/DAB1 -0.34 0.26 -9999 0 -0.53 565 565
LRPAP1/LRP8 -0.02 0.056 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.32 0.24 -9999 0 -0.5 565 565
DAB1/alpha3/beta1 Integrin -0.29 0.23 -9999 0 -0.46 573 573
long-term memory -0.38 0.31 -9999 0 -0.56 610 610
DAB1/LIS1 -0.3 0.24 -9999 0 -0.48 570 570
DAB1/CRLK/C3G -0.29 0.23 -9999 0 -0.52 223 223
PIK3CA 0 0.009 -9999 0 -10000 0 0
DAB1/NCK2 -0.31 0.24 -9999 0 -0.48 570 570
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.092 0.26 -9999 0 -0.77 109 109
CDK5R1 -0.009 0.048 -9999 0 -0.28 28 28
RELN -0.51 0.4 -9999 0 -0.82 564 564
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
RELN/LRP8/Fyn -0.35 0.27 -9999 0 -0.57 564 564
GRIN2A/RELN/LRP8/DAB1/Fyn -0.36 0.3 -9999 0 -0.56 577 577
MAPK8 -0.003 0.047 -9999 0 -0.82 3 3
RELN/VLDLR/DAB1 -0.34 0.27 -9999 0 -0.53 570 570
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.33 0.26 -9999 0 -0.52 572 572
RELN/LRP8 -0.35 0.27 -9999 0 -0.57 564 564
GRIN2B/RELN/LRP8/DAB1/Fyn -0.35 0.26 -9999 0 -0.53 598 598
PI3K -0.001 0.022 -9999 0 -0.63 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.043 -9999 0 -0.63 4 4
RAP1A -0.27 0.21 -9999 0 -0.55 128 128
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.051 -9999 0 -0.48 8 8
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.066 0.22 -9999 0 -0.81 74 74
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.14 0.11 -9999 0 -0.42 8 8
neuron adhesion -0.25 0.2 -9999 0 -0.52 130 130
LRP8 -0.032 0.089 -9999 0 -0.28 105 105
GSK3B -0.18 0.18 -9999 0 -0.61 20 20
RELN/VLDLR/DAB1/Fyn -0.31 0.25 -9999 0 -0.5 570 570
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.22 0.18 -9999 0 -0.36 570 570
CDK5 -0.002 0.021 -9999 0 -10000 0 0
MAPT -0.043 0.25 -9999 0 -0.75 96 96
neuron migration -0.24 0.24 -9999 0 -0.42 565 565
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.11 -9999 0 -0.43 8 8
RELN/VLDLR -0.34 0.26 -9999 0 -0.53 570 570
EGFR-dependent Endothelin signaling events

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
HRAS -0.001 0.013 -9999 0 -0.28 2 2
EGFR -0.3 0.4 -9999 0 -0.82 331 331
EGF/EGFR -0.29 0.32 -9999 0 -0.57 463 463
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.28 -9999 0 -0.52 453 453
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.16 0.33 -9999 0 -0.82 183 183
EGF/EGFR dimer/SHC -0.3 0.32 -9999 0 -0.61 453 453
mol:GDP -0.26 0.28 -9999 0 -0.52 453 453
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.066 0.22 -9999 0 -0.82 74 74
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.24 0.26 -9999 0 -0.48 453 453
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.24 0.26 -9999 0 -0.48 453 453
FRAP1 -0.25 0.27 -9999 0 -0.5 453 453
EGF/EGFR dimer -0.35 0.37 -9999 0 -0.7 453 453
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.051 0.17 -9999 0 -0.63 73 73
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.4 0.63 -9999 0 -1.3 309 309
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.082 0.15 -9999 0 -0.38 15 15
ATF2/c-Jun -0.056 0.16 -9999 0 -0.91 14 14
MAPK11 -0.084 0.16 -9999 0 -0.3 311 311
MITF -0.093 0.2 -9999 0 -0.36 314 314
MAPKAPK5 -0.09 0.19 -9999 0 -0.35 311 311
KRT8 -0.096 0.19 -9999 0 -0.36 312 312
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.009 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.13 0.24 -9999 0 -0.45 311 311
CEBPB -0.09 0.19 -9999 0 -0.35 311 311
SLC9A1 -0.09 0.19 -9999 0 -0.35 311 311
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.083 0.19 -9999 0 -0.34 311 311
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.54 15 15
JUN -0.055 0.16 -9999 0 -0.9 14 14
PPARGC1A -0.22 0.37 -9999 0 -0.58 385 385
USF1 -0.09 0.19 -9999 0 -0.35 311 311
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.37 15 15
NOS2 -0.093 0.21 -9999 0 -0.77 17 17
DDIT3 -0.09 0.19 -9999 0 -0.35 311 311
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.071 0.16 -9999 0 -0.42 37 37
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.35 311 311
CREB1 -0.094 0.2 -9999 0 -0.37 311 311
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.07 0.17 -9999 0 -0.48 14 14
RPS6KA4 -0.09 0.19 -9999 0 -0.35 311 311
PLA2G4A -0.13 0.27 -9999 0 -0.73 108 108
GDI1 -0.09 0.19 -9999 0 -0.35 311 311
TP53 -0.12 0.24 -9999 0 -0.44 311 311
RPS6KA5 -0.094 0.2 -9999 0 -0.36 318 318
ESR1 -0.17 0.25 -9999 0 -0.42 421 421
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.091 0.19 -9999 0 -0.36 311 311
MEF2A -0.09 0.19 -9999 0 -0.35 311 311
EIF4EBP1 -0.093 0.2 -9999 0 -0.37 311 311
KRT19 -0.1 0.21 -9999 0 -0.38 314 314
ELK4 -0.09 0.19 -9999 0 -0.35 311 311
ATF6 -0.09 0.19 -9999 0 -0.35 311 311
ATF1 -0.094 0.2 -9999 0 -0.37 311 311
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.53 16 16
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.35 311 311
HIF-1-alpha transcription factor network

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
PKM2 -0.42 0.46 -9999 0 -1 249 249
HDAC7 0 0 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.33 0.31 -9999 0 -0.78 199 199
SMAD4 0 0 -9999 0 -10000 0 0
ID2 -0.42 0.46 -9999 0 -0.99 251 251
AP1 -0.2 0.3 -9999 0 -0.65 284 284
ABCG2 -0.44 0.49 -9999 0 -1.1 259 259
HIF1A -0.053 0.062 -9999 0 -10000 0 0
TFF3 -0.49 0.52 -9999 0 -1.1 325 325
GATA2 -0.015 0.13 -9999 0 -0.78 25 25
AKT1 -0.055 0.08 -9999 0 -10000 0 0
response to hypoxia -0.077 0.086 -9999 0 -0.25 33 33
MCL1 -0.42 0.46 -9999 0 -0.99 251 251
NDRG1 -0.42 0.46 -9999 0 -1 247 247
SERPINE1 -0.42 0.46 -9999 0 -1 249 249
FECH -0.42 0.46 -9999 0 -1 249 249
FURIN -0.42 0.46 -9999 0 -0.99 250 250
NCOA2 -0.01 0.11 -9999 0 -0.82 17 17
EP300 -0.056 0.12 -9999 0 -0.36 50 50
HMOX1 -0.42 0.46 -9999 0 -1 249 249
BHLHE40 -0.42 0.46 -9999 0 -1 249 249
BHLHE41 -0.42 0.47 -9999 0 -1 250 250
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.05 0.052 -9999 0 -10000 0 0
ENG -0.039 0.048 -9999 0 -10000 0 0
JUN -0.008 0.082 -9999 0 -0.83 9 9
RORA -0.42 0.46 -9999 0 -0.99 251 251
ABCB1 -0.34 0.55 -9999 0 -1.5 173 173
TFRC -0.42 0.46 -9999 0 -1 249 249
CXCR4 -0.42 0.46 -9999 0 -1 250 250
TF -0.67 0.58 -9999 0 -1.1 497 497
CITED2 -0.42 0.46 -9999 0 -1 249 249
HIF1A/ARNT -0.5 0.51 -9999 0 -1.2 255 255
LDHA -0.05 0.047 -9999 0 -10000 0 0
ETS1 -0.42 0.46 -9999 0 -1 250 250
PGK1 -0.42 0.46 -9999 0 -1 247 247
NOS2 -0.42 0.46 -9999 0 -1 251 251
ITGB2 -0.42 0.46 -9999 0 -1 249 249
ALDOA -0.42 0.46 -9999 0 -1 247 247
Cbp/p300/CITED2 -0.43 0.44 -9999 0 -1 236 236
FOS -0.26 0.38 -9999 0 -0.83 283 283
HK2 -0.42 0.46 -9999 0 -1 251 251
SP1 0.012 0.023 -9999 0 -10000 0 0
GCK -0.15 0.39 -9999 0 -1.6 54 54
HK1 -0.42 0.46 -9999 0 -1 249 249
NPM1 -0.42 0.46 -9999 0 -1 249 249
EGLN1 -0.42 0.46 -9999 0 -1 249 249
CREB1 0.018 0 -9999 0 -10000 0 0
PGM1 -0.42 0.46 -9999 0 -1 249 249
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.2 0.41 -9999 0 -1.2 113 113
IGFBP1 -0.52 0.53 -9999 0 -1.1 329 329
VEGFA -0.25 0.31 -9999 0 -0.75 109 109
HIF1A/JAB1 -0.029 0.026 -9999 0 -10000 0 0
CP -0.53 0.55 -9999 0 -1.1 346 346
CXCL12 -0.44 0.5 -9999 0 -1.1 261 261
COPS5 0.002 0.011 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.42 0.46 -9999 0 -1 249 249
EGLN3 -0.42 0.46 -9999 0 -1 255 255
CA9 -0.46 0.48 -9999 0 -1 264 264
TERT -0.43 0.47 -9999 0 -1 252 252
ENO1 -0.42 0.46 -9999 0 -1 248 248
PFKL -0.42 0.46 -9999 0 -1 244 244
NCOA1 -0.001 0.027 -9999 0 -0.82 1 1
ADM -0.45 0.49 -9999 0 -1.1 271 271
ARNT -0.058 0.053 -9999 0 -10000 0 0
HNF4A -0.001 0.039 -9999 0 -0.37 1 1
ADFP -0.42 0.46 -9999 0 -1 253 253
SLC2A1 -0.25 0.32 -9999 0 -0.76 111 111
LEP -0.78 0.52 -9999 0 -1.1 589 589
HIF1A/ARNT/Cbp/p300 -0.35 0.32 -9999 0 -0.81 200 200
EPO -0.23 0.25 -9999 0 -0.77 23 23
CREBBP -0.056 0.12 -9999 0 -0.36 51 51
HIF1A/ARNT/Cbp/p300/HDAC7 -0.32 0.31 -9999 0 -0.79 184 184
PFKFB3 -0.42 0.46 -9999 0 -1 253 253
NT5E -0.42 0.46 -9999 0 -1 249 249
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.001 0.021 -9999 0 -0.63 1 1
Necdin/E2F1 -0.078 0.15 -9999 0 -0.71 33 33
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.16 0.23 -9999 0 -0.48 305 305
NGF (dimer)/p75(NTR)/BEX1 -0.28 0.33 -9999 0 -0.65 374 374
NT-4/5 (dimer)/p75(NTR) -0.42 0.43 -9999 0 -0.8 483 483
IKBKB -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.16 0.23 -9999 0 -0.47 304 304
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.073 0.23 -9999 0 -0.82 74 74
MGDIs/NGR/p75(NTR)/LINGO1 -0.21 0.26 -9999 0 -0.58 296 296
FURIN -0.001 0.013 -9999 0 -0.28 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.22 0.3 -9999 0 -0.6 337 337
LINGO1 -0.065 0.12 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.001 0.027 -9999 0 -0.82 1 1
proBDNF (dimer) -0.073 0.23 -9999 0 -0.82 74 74
NTRK1 -0.01 0.065 -9999 0 -0.82 3 3
RTN4R -0.009 0.048 -9999 0 -0.28 28 28
neuron apoptosis -0.16 0.28 -9999 0 -0.51 296 296
IRAK1 -0.001 0.016 -9999 0 -0.28 3 3
SHC1 -0.17 0.28 -9999 0 -0.56 303 303
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.016 -9999 0 -0.47 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.17 0.25 -9999 0 -0.51 303 303
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.19 0.27 -9999 0 -0.55 314 314
Mammalian IAPs/DIABLO -0.006 0.048 -9999 0 -0.5 8 8
proNGF (dimer) -0.016 0.11 -9999 0 -0.65 22 22
MAGED1 -0.001 0.013 -9999 0 -0.28 2 2
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.3 0.4 -9999 0 -0.82 338 338
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.16 0.23 -9999 0 -0.48 303 303
NGF -0.016 0.11 -9999 0 -0.65 22 22
cell cycle arrest -0.13 0.25 -9999 0 -0.46 303 303
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.11 0.16 -9999 0 -0.34 303 303
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.37 0.39 -9999 0 -0.7 483 483
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.19 0.27 -9999 0 -0.57 303 303
PSENEN 0 0.009 -9999 0 -0.28 1 1
mol:ceramide -0.17 0.24 -9999 0 -0.51 303 303
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.09 0.13 -9999 0 -0.48 14 14
p75(NTR)/beta APP -0.2 0.3 -9999 0 -0.63 296 296
BEX1 -0.16 0.29 -9999 0 -0.82 127 127
mol:GDP -0.18 0.28 -9999 0 -0.57 303 303
NGF (dimer) -0.085 0.19 -9999 0 -0.52 142 142
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.19 0.24 -9999 0 -0.53 296 296
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
RAC1/GTP -0.16 0.24 -9999 0 -0.49 303 303
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.2 0.28 -9999 0 -0.58 303 303
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.056 0.082 -9999 0 -10000 0 0
NT3 (dimer) -0.14 0.3 -9999 0 -0.82 149 149
TP53 -0.18 0.25 -9999 0 -0.48 337 337
PRDM4 -0.17 0.24 -9999 0 -0.51 303 303
BDNF (dimer) -0.17 0.24 -9999 0 -0.6 192 192
PIK3CA 0 0.009 -9999 0 -10000 0 0
SORT1 -0.001 0.027 -9999 0 -0.82 1 1
activation of caspase activity -0.16 0.23 -9999 0 -0.47 305 305
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.17 0.25 -9999 0 -0.51 303 303
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.17 0.28 -9999 0 -0.51 308 308
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.17 0.24 -9999 0 -0.51 303 303
APH1B -0.001 0.027 -9999 0 -0.82 1 1
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.19 0.27 -9999 0 -0.56 303 303
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.3 0.38 -9999 0 -0.72 383 383
MAPK8 -0.12 0.25 -9999 0 -0.45 296 296
MAPK9 -0.12 0.25 -9999 0 -0.45 296 296
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.14 0.3 -9999 0 -0.82 149 149
NTF4 -0.3 0.4 -9999 0 -0.82 338 338
NDN -0.03 0.15 -9999 0 -0.82 33 33
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.15 0.22 -9999 0 -0.45 303 303
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.016 -9999 0 -0.5 1 1
RhoA-B-C/GTP -0.19 0.27 -9999 0 -0.57 303 303
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.19 0.26 -9999 0 -0.52 337 337
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.2 0.28 -9999 0 -0.55 337 337
PRKACB -0.017 0.077 -9999 0 -0.82 3 3
proBDNF (dimer)/p75 ECD -0.055 0.17 -9999 0 -0.63 74 74
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.082 -9999 0 -0.82 8 8
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.14 0.27 -9999 0 -0.49 303 303
BAD -0.13 0.25 -9999 0 -0.46 298 298
RIPK2 -0.002 0.021 -9999 0 -0.28 5 5
NGFR -0.27 0.39 -9999 0 -0.82 296 296
CYCS -0.16 0.23 -9999 0 -0.48 303 303
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.17 0.24 -9999 0 -0.51 303 303
BCL2L11 -0.13 0.25 -9999 0 -0.46 298 298
BDNF (dimer)/p75(NTR) -0.26 0.34 -9999 0 -0.69 337 337
PI3K -0.17 0.24 -9999 0 -0.51 304 304
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.17 0.25 -9999 0 -0.51 303 303
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0.009 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.22 0.31 -9999 0 -0.65 303 303
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.17 0.25 -9999 0 -0.51 303 303
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.027 -9999 0 -0.82 1 1
PLG -0.001 0.018 -9999 0 -0.28 4 4
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.21 0.28 -9999 0 -0.55 344 344
SQSTM1 -0.001 0.013 -9999 0 -10000 0 0
NGFRAP1 -0.002 0.039 -9999 0 -0.82 2 2
CASP3 -0.12 0.23 -9999 0 -0.43 298 298
E2F1 -0.089 0.13 -9999 0 -0.28 292 292
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.071 0.12 -9999 0 -0.59 19 19
NGF (dimer)/TRKA -0.018 0.093 -9999 0 -0.63 18 18
MMP7 -0.12 0.29 -9999 0 -0.73 155 155
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.16 0.23 -9999 0 -0.48 303 303
MMP3 -0.12 0.16 -9999 0 -0.3 359 359
APAF-1/Caspase 9 -0.12 0.17 -9999 0 -0.68 14 14
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.024 0.078 0.36 2 -10000 0 2
SMARCC2 0.011 0.009 -10000 0 -10000 0 0
SMARCC1 0.011 0.009 -10000 0 -10000 0 0
TBX21 -0.14 0.26 -10000 0 -0.69 103 103
SUMO2 0 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.042 -10000 0 -0.34 1 1
FKBP4 -0.002 0.024 -10000 0 -0.28 7 7
FKBP5 -0.013 0.099 -10000 0 -0.82 13 13
GR alpha/HSP90/FKBP51/HSP90 0.12 0.14 0.33 72 -0.44 15 87
PRL -0.091 0.12 -10000 0 -0.57 1 1
cortisol/GR alpha (dimer)/TIF2 0.29 0.28 0.52 448 -0.61 12 460
RELA -0.041 0.083 -10000 0 -10000 0 0
FGG 0.24 0.22 0.46 359 -0.55 2 361
GR beta/TIF2 0.12 0.16 0.32 163 -0.61 19 182
IFNG -0.44 0.35 -10000 0 -0.76 432 432
apoptosis -0.28 0.3 0.59 3 -0.66 249 252
CREB1 -0.008 0.028 -10000 0 -10000 0 0
histone acetylation 0.022 0.14 0.4 30 -0.4 24 54
BGLAP -0.1 0.15 -10000 0 -0.49 26 26
GR/PKAc 0.12 0.12 0.32 59 -0.52 3 62
NF kappa B1 p50/RelA -0.07 0.15 -10000 0 -0.42 29 29
SMARCD1 0.011 0.009 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.24 290 -10000 0 290
GATA3 -0.028 0.16 -10000 0 -0.58 60 60
AKT1 0 0.004 -10000 0 -10000 0 0
CSF2 -0.041 0.11 -10000 0 -0.58 6 6
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.21 0.27 0.56 3 -0.62 150 153
CSN2 0.2 0.18 0.41 220 -0.56 1 221
BRG1/BAF155/BAF170/BAF60A -0.002 0.03 -10000 0 -0.46 4 4
NFATC1 0.002 0.028 -10000 0 -0.82 1 1
POU2F1 0.007 0.013 -10000 0 -0.28 1 1
CDKN1A 0.046 0.059 -10000 0 -1.5 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.008 0.008 -10000 0 -10000 0 0
SFN -0.016 0.1 -10000 0 -0.54 27 27
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.32 61 -0.4 25 86
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.38 0.44 0.54 3 -0.91 327 330
JUN -0.32 0.29 -10000 0 -0.57 439 439
IL4 -0.13 0.15 -10000 0 -0.5 34 34
CDK5R1 -0.009 0.049 -10000 0 -0.28 28 28
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.44 0.42 -10000 0 -0.75 516 516
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.13 0.34 48 -0.43 9 57
cortisol/GR alpha (monomer) 0.36 0.32 0.62 472 -0.57 2 474
NCOA2 -0.015 0.11 -10000 0 -0.82 17 17
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.3 0.4 -10000 0 -0.89 283 283
AP-1/NFAT1-c-4 -0.68 0.53 -10000 0 -1 596 596
AFP -0.62 0.71 -10000 0 -1.5 335 335
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.2 0.16 0.41 199 -10000 0 199
TP53 0.031 0.018 -10000 0 -0.5 1 1
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.87 0.82 -10000 0 -1.6 462 462
KRT14 -0.87 0.78 -10000 0 -1.6 498 498
TBP 0.019 0.003 -10000 0 -10000 0 0
CREBBP 0.15 0.14 0.3 184 -10000 0 184
HDAC1 0 0.003 -10000 0 -10000 0 0
HDAC2 0.001 0.004 -10000 0 -10000 0 0
AP-1 -0.69 0.54 -10000 0 -1 596 596
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.13 0.3 -10000 0 -0.83 144 144
MAPK11 -0.001 0.04 -10000 0 -0.84 2 2
KRT5 -0.96 0.82 -10000 0 -1.7 504 504
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.007 0.028 -10000 0 -0.82 1 1
STAT1 0.012 0.042 -10000 0 -0.34 1 1
CGA -0.16 0.18 -10000 0 -0.47 126 126
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.21 0.18 0.37 455 -10000 0 455
MAPK3 0 0.004 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
ICAM1 -0.19 0.25 -10000 0 -0.58 178 178
NFKB1 -0.041 0.083 -10000 0 -0.26 3 3
MAPK8 -0.24 0.22 -10000 0 -0.43 406 406
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.3 0.32 0.59 3 -0.7 251 254
BAX 0.048 0.03 -10000 0 -10000 0 0
POMC -0.2 0.31 -10000 0 -0.95 77 77
EP300 0.15 0.14 0.31 131 -10000 0 131
cortisol/GR alpha (dimer)/p53 0.32 0.26 0.54 448 -0.59 1 449
proteasomal ubiquitin-dependent protein catabolic process 0.089 0.079 0.22 90 -10000 0 90
SGK1 0.23 0.2 -10000 0 -1.2 4 4
IL13 -0.32 0.28 -10000 0 -0.67 230 230
IL6 -0.51 0.64 -10000 0 -1.3 343 343
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.28 0.22 -10000 0 -0.5 377 377
IL2 -0.43 0.35 -10000 0 -0.72 477 477
CDK5 -0.001 0.021 -10000 0 -0.29 3 3
PRKACB -0.017 0.077 -10000 0 -0.82 3 3
HSP90AA1 0 0.009 -10000 0 -10000 0 0
IL8 -0.21 0.31 -10000 0 -0.61 245 245
CDK5R1/CDK5 -0.006 0.035 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.06 0.098 -10000 0 -0.6 4 4
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.29 0.24 0.5 448 -0.55 1 449
SMARCA4 0.011 0.013 -10000 0 -0.28 1 1
chromatin remodeling 0.2 0.16 0.37 307 -10000 0 307
NF kappa B1 p50/RelA/Cbp 0.057 0.17 0.35 39 -10000 0 39
JUN (dimer) -0.32 0.29 -10000 0 -0.57 440 440
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.14 0.25 -10000 0 -0.79 76 76
NR3C1 0.2 0.2 0.41 351 -0.55 5 356
NR4A1 -0.065 0.24 -10000 0 -0.76 96 96
TIF2/SUV420H1 -0.012 0.086 -10000 0 -0.63 17 17
MAPKKK cascade -0.28 0.3 0.59 3 -0.66 249 252
cortisol/GR alpha (dimer)/Src-1 0.31 0.26 0.53 454 -0.6 1 455
PBX1 0.005 0.042 -10000 0 -0.82 2 2
POU1F1 0.003 0.012 -10000 0 -0.28 1 1
SELE -0.23 0.36 -10000 0 -0.71 238 238
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.38 303 -10000 0 303
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.29 0.24 0.5 448 -0.55 1 449
mol:cortisol 0.2 0.2 0.36 481 -10000 0 481
MMP1 -0.21 0.1 -10000 0 -10000 0 0
IL4-mediated signaling events

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.46 0.45 -10000 0 -1 264 264
STAT6 (cleaved dimer) -0.5 0.44 -10000 0 -0.92 394 394
IGHG1 -0.16 0.16 -10000 0 -0.34 186 186
IGHG3 -0.45 0.44 -10000 0 -0.89 372 372
AKT1 -0.21 0.24 -10000 0 -0.59 105 105
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.19 -10000 0 -0.56 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.57 148 148
THY1 -0.46 0.45 -10000 0 -1 266 266
MYB -0.014 0.11 -10000 0 -0.82 15 15
HMGA1 -0.011 0.055 -10000 0 -0.28 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.62 246 246
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.23 -10000 0 -0.54 128 128
SP1 0.017 0.005 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.025 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.48 0.43 -10000 0 -0.92 369 369
SOCS1 -0.3 0.3 -10000 0 -0.72 191 191
SOCS3 -0.23 0.26 -10000 0 -0.81 57 57
FCER2 -0.61 0.65 -10000 0 -1.4 331 331
PARP14 0 0.018 -10000 0 -0.29 3 3
CCL17 -0.47 0.45 -10000 0 -1 264 264
GRB2 0 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.19 -10000 0 -0.51 38 38
T cell proliferation -0.46 0.47 -10000 0 -1 279 279
IL4R/JAK1 -0.46 0.45 -10000 0 -1 270 270
EGR2 -0.61 0.63 -10000 0 -1.3 347 347
JAK2 -0.008 0.038 -10000 0 -0.85 1 1
JAK3 0.008 0.038 -10000 0 -0.28 6 6
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
JAK1 0.005 0.011 -10000 0 -10000 0 0
COL1A2 -0.14 0.15 -10000 0 -1.7 1 1
CCL26 -0.46 0.45 -10000 0 -1 256 256
IL4R -0.49 0.48 -10000 0 -1.1 272 272
PTPN6 0.022 0.018 -10000 0 -0.26 2 2
IL13RA2 -0.46 0.46 -10000 0 -1 249 249
IL13RA1 -0.007 0.025 -10000 0 -10000 0 0
IRF4 -0.22 0.47 -10000 0 -1.6 92 92
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.27 -10000 0 -0.62 201 201
GTF3A 0.013 0.016 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.014 0.042 -10000 0 -0.65 1 1
IRF4/BCL6 -0.2 0.42 -10000 0 -1.4 95 95
CD40LG -0.033 0.19 -10000 0 -0.79 49 49
MAPK14 -0.26 0.27 -10000 0 -0.62 198 198
mitosis -0.2 0.23 -10000 0 -0.56 105 105
STAT6 -0.52 0.52 -10000 0 -1.1 360 360
SPI1 0.006 0.026 -10000 0 -0.27 7 7
RPS6KB1 -0.19 0.22 -10000 0 -0.57 78 78
STAT6 (dimer) -0.52 0.52 -10000 0 -1.1 360 360
STAT6 (dimer)/PARP14 -0.51 0.5 -10000 0 -1 376 376
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.23 -10000 0 -0.55 116 116
FRAP1 -0.21 0.24 -10000 0 -0.59 105 105
LTA -0.47 0.45 -10000 0 -1.1 244 244
FES -0.003 0.047 -10000 0 -0.82 3 3
T-helper 1 cell differentiation 0.51 0.51 1 360 -10000 0 360
CCL11 -0.48 0.44 -10000 0 -1 283 283
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.23 -10000 0 -0.55 118 118
IL2RG -0.004 0.084 -10000 0 -0.82 5 5
IL10 -0.46 0.46 -10000 0 -1 257 257
IRS1 -0.033 0.16 -10000 0 -0.82 36 36
IRS2 -0.034 0.16 -10000 0 -0.82 38 38
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.47 0.45 -10000 0 -0.95 336 336
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.36 -10000 0 -0.76 332 332
COL1A1 -0.18 0.16 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.46 -10000 0 -1.1 215 215
IL2R gamma/JAK3 -0.014 0.069 -10000 0 -0.43 19 19
TFF3 -0.56 0.58 -10000 0 -1.2 360 360
ALOX15 -0.55 0.57 -10000 0 -1.2 304 304
MYBL1 -0.044 0.1 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.4 0.37 -10000 0 -0.78 353 353
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.008 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.23 -10000 0 -0.55 132 132
mol:PI-3-4-5-P3 -0.21 0.24 -10000 0 -0.59 105 105
PI3K -0.22 0.25 -10000 0 -0.63 104 104
DOK2 -0.003 0.043 -10000 0 -0.82 2 2
ETS1 0.02 0.04 -10000 0 -0.79 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.18 -10000 0 -0.53 25 25
ITGB3 -0.47 0.48 -10000 0 -1.1 252 252
PIGR -1 0.75 -10000 0 -1.5 598 598
IGHE 0.046 0.039 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.17 -10000 0 -0.52 25 25
BCL6 0.002 0.048 -10000 0 -0.82 3 3
OPRM1 -0.47 0.45 -10000 0 -1 276 276
RETNLB -0.47 0.45 -10000 0 -1 272 272
SELP -0.64 0.68 -10000 0 -1.5 315 315
AICDA -0.45 0.44 -10000 0 -0.98 275 275
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.28 -9999 0 -0.8 93 93
PCK1 -1 0.72 -9999 0 -1.6 562 562
HNF4A -0.25 0.28 -9999 0 -0.87 65 65
KCNJ11 -0.27 0.31 -9999 0 -0.84 129 129
AKT1 -0.15 0.14 -9999 0 -0.39 38 38
response to starvation -0.001 0.006 -9999 0 -10000 0 0
DLK1 -0.5 0.57 -9999 0 -1.2 307 307
NKX2-1 -0.058 0.15 -9999 0 -10000 0 0
ACADM -0.25 0.28 -9999 0 -0.78 114 114
TAT -1.2 0.68 -9999 0 -1.6 670 670
CEBPB 0.003 0.005 -9999 0 -10000 0 0
CEBPA -0.003 0.078 -9999 0 -0.82 8 8
TTR -0.45 0.28 -9999 0 -0.8 242 242
PKLR -0.25 0.28 -9999 0 -0.78 108 108
APOA1 -0.3 0.3 -9999 0 -0.86 109 109
CPT1C -0.24 0.28 -9999 0 -0.79 103 103
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.74 281 281
FOXF1 -0.003 0.053 -9999 0 -0.46 9 9
NF1 0.016 0.028 -9999 0 -0.82 1 1
HNF1A (dimer) 0.003 0.024 -9999 0 -10000 0 0
CPT1A -0.24 0.28 -9999 0 -0.81 90 90
HMGCS1 -0.24 0.28 -9999 0 -0.77 113 113
NR3C1 -0.11 0.12 -9999 0 -0.38 69 69
CPT1B -0.25 0.28 -9999 0 -0.81 94 94
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.006 -9999 0 -10000 0 0
GCK -0.29 0.36 -9999 0 -0.97 138 138
CREB1 -0.057 0.066 -9999 0 -10000 0 0
IGFBP1 -0.47 0.61 -9999 0 -1.5 217 217
PDX1 -0.13 0.14 -9999 0 -10000 0 0
UCP2 -0.24 0.28 -9999 0 -0.82 85 85
ALDOB -0.27 0.3 -9999 0 -0.9 83 83
AFP -0.69 0.62 -9999 0 -0.98 616 616
BDH1 -0.24 0.28 -9999 0 -0.77 114 114
HADH -0.27 0.3 -9999 0 -0.86 91 91
F2 -0.3 0.3 -9999 0 -0.92 73 73
HNF1A 0.003 0.024 -9999 0 -10000 0 0
G6PC -0.2 0.12 -9999 0 -0.68 6 6
SLC2A2 -0.16 0.17 -9999 0 -0.54 4 4
INS 0.025 0.068 -9999 0 -10000 0 0
FOXA1 -0.24 0.28 -9999 0 -0.61 230 230
FOXA3 -0.43 0.23 -9999 0 -0.54 635 635
FOXA2 -0.32 0.34 -9999 0 -0.86 167 167
ABCC8 -0.35 0.44 -9999 0 -1.1 164 164
ALB -0.95 0.65 -9999 0 -1.4 594 594
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.074 0.15 -10000 0 -0.32 241 241
NFATC2 -0.041 0.25 -10000 0 -0.78 80 80
NFATC3 -0.062 0.12 -10000 0 -10000 0 0
CD40LG -0.38 0.58 -10000 0 -1.1 289 289
ITCH 0.012 0.1 -10000 0 -10000 0 0
CBLB 0.012 0.1 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.24 0.34 -10000 0 -1.1 83 83
JUNB 0 0.009 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.037 0.11 -10000 0 -10000 0 0
T cell anergy -0.026 0.17 -10000 0 -0.48 97 97
TLE4 -0.018 0.24 -10000 0 -0.8 59 59
Jun/NFAT1-c-4/p21SNFT -0.3 0.44 -10000 0 -0.93 257 257
AP-1/NFAT1-c-4 -0.53 0.66 -10000 0 -1.3 319 319
IKZF1 -0.007 0.19 -10000 0 -0.62 62 62
T-helper 2 cell differentiation -0.1 0.29 -10000 0 -0.81 90 90
AP-1/NFAT1 -0.23 0.33 -10000 0 -0.66 313 313
CALM1 -0.019 0.055 -10000 0 -10000 0 0
EGR2 -0.3 0.66 -10000 0 -1.5 167 167
EGR3 -0.39 0.74 -10000 0 -1.5 253 253
NFAT1/FOXP3 -0.099 0.2 -10000 0 -0.6 81 81
EGR1 -0.27 0.38 -10000 0 -0.82 295 295
JUN -0.012 0.083 -10000 0 -0.83 9 9
EGR4 -0.019 0.069 -10000 0 -0.28 61 61
mol:Ca2+ -0.022 0.064 -10000 0 -10000 0 0
GBP3 -0.013 0.21 -10000 0 -0.71 60 60
FOSL1 -0.008 0.056 -10000 0 -0.82 2 2
NFAT1-c-4/MAF/IRF4 -0.32 0.47 -10000 0 -0.95 273 273
DGKA -0.006 0.19 -10000 0 -0.65 51 51
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.4 0.53 -10000 0 -1.1 299 299
CTLA4 -0.075 0.22 -10000 0 -0.66 58 58
NFAT1-c-4 (dimer)/EGR1 -0.44 0.58 -10000 0 -1.2 301 301
NFAT1-c-4 (dimer)/EGR4 -0.29 0.46 -10000 0 -0.91 295 295
FOS -0.26 0.38 -10000 0 -0.84 283 283
IFNG -0.14 0.26 -10000 0 -0.85 79 79
T cell activation -0.17 0.35 -10000 0 -0.76 192 192
MAF -0.001 0.027 -10000 0 -0.82 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.17 0.36 0.68 252 -10000 0 252
TNF -0.33 0.53 -10000 0 -1.1 273 273
FASLG -0.36 0.68 -10000 0 -1.3 294 294
TBX21 -0.025 0.17 -10000 0 -0.7 47 47
BATF3 -0.002 0.033 -10000 0 -0.39 5 5
PRKCQ -0.023 0.16 -10000 0 -0.68 47 47
PTPN1 -0.007 0.19 -10000 0 -0.64 58 58
NFAT1-c-4/ICER1 -0.3 0.44 -10000 0 -0.9 294 294
GATA3 -0.036 0.16 -10000 0 -0.58 60 60
T-helper 1 cell differentiation -0.14 0.25 -10000 0 -0.83 79 79
IL2RA -0.23 0.33 -10000 0 -0.92 98 98
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.006 0.19 -10000 0 -0.63 58 58
E2F1 -0.075 0.13 -10000 0 -10000 0 0
PPARG -0.19 0.35 -10000 0 -0.82 209 209
SLC3A2 -0.006 0.19 -10000 0 -0.63 59 59
IRF4 -0.072 0.23 -10000 0 -0.76 87 87
PTGS2 -0.49 0.66 -10000 0 -1.2 386 386
CSF2 -0.37 0.56 -10000 0 -1.1 288 288
JunB/Fra1/NFAT1-c-4 -0.28 0.43 -10000 0 -0.89 261 261
IL4 -0.11 0.3 -10000 0 -0.86 89 89
IL5 -0.37 0.56 -10000 0 -1.1 314 314
IL2 -0.18 0.36 -10000 0 -0.78 189 189
IL3 -0.064 0.066 -10000 0 -10000 0 0
RNF128 -0.058 0.29 -10000 0 -0.88 98 98
NFATC1 -0.17 0.36 -10000 0 -0.69 242 242
CDK4 0.086 0.23 0.6 30 -10000 0 30
PTPRK -0.009 0.2 -10000 0 -0.64 70 70
IL8 -0.38 0.57 -10000 0 -1.1 301 301
POU2F1 0.001 0.01 -10000 0 -0.28 1 1
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.023 0.14 -9999 0 -0.82 25 25
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.35 0.27 -9999 0 -0.57 564 564
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0.009 -9999 0 -0.28 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.32 0.25 -9999 0 -0.51 564 564
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.067 -9999 0 -0.28 56 56
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.015 0.09 -9999 0 -0.82 8 8
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0.009 -9999 0 -0.28 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.02 0.056 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.009 0.048 -9999 0 -0.28 28 28
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.041 0.098 -9999 0 -0.28 133 133
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.36 0.29 -9999 0 -0.57 570 570
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.25 0.2 -9999 0 -0.46 161 161
MAP1B -0.007 0.05 -9999 0 -0.38 16 16
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.28 0.22 -9999 0 -0.45 564 564
RELN -0.51 0.4 -9999 0 -0.82 564 564
PAFAH/LIS1 -0.009 0.056 -9999 0 -0.55 8 8
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.19 0.15 -9999 0 -0.41 23 23
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.21 0.17 -9999 0 -0.37 208 208
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.27 0.21 -9999 0 -0.43 564 564
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 -0.027 0.083 -9999 0 -10000 0 0
PAFAH1B2 -0.002 0.039 -9999 0 -0.82 2 2
MAP1B/LIS1/Dynein heavy chain -0.004 0.032 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.24 0.19 -9999 0 -0.47 88 88
LRP8 -0.032 0.089 -9999 0 -0.28 105 105
NDEL1/Katanin 60 -0.25 0.2 -9999 0 -0.46 162 162
P39/CDK5 -0.29 0.23 -9999 0 -0.47 564 564
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.28 0.25 -9999 0 -0.48 564 564
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.31 0.25 -9999 0 -0.49 570 570
RELN/VLDLR -0.34 0.26 -9999 0 -0.53 570 570
CDC42 0 0 -9999 0 -10000 0 0
Arf6 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
CENTA1/KIF3B -0.004 0.048 -9999 0 -0.68 4 4
ARNO/beta Arrestin1-2 -0.14 0.2 -9999 0 -0.45 223 223
EGFR -0.3 0.4 -9999 0 -0.82 331 331
EPHA2 -0.005 0.067 -9999 0 -0.82 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.35 0.37 -9999 0 -0.7 453 453
ARRB2 -0.063 0.16 -9999 0 -0.45 128 128
mol:GTP 0.017 0.019 -9999 0 -0.16 5 5
ARRB1 -0.002 0.04 -9999 0 -0.64 3 3
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.038 0.17 -9999 0 -0.78 45 45
EGF -0.16 0.33 -9999 0 -0.82 183 183
somatostatin receptor activity 0 0 -9999 0 -0.001 309 309
ARAP2 -0.005 0.067 -9999 0 -0.82 6 6
mol:GDP -0.14 0.18 -9999 0 -0.36 275 275
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 221 221
ITGA2B -0.016 0.076 -9999 0 -0.31 47 47
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.041 -9999 0 -0.5 6 6
ADAP1 -0.004 0.051 -9999 0 -0.82 3 3
KIF13B -0.002 0.039 -9999 0 -0.82 2 2
HGF/MET -0.14 0.29 -9999 0 -0.68 193 193
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.16 -9999 0 -0.32 298 298
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.3 0.32 -9999 0 -0.61 453 453
ADRB2 -0.2 0.36 -9999 0 -0.83 223 223
receptor agonist activity 0 0 -9999 0 0 306 306
actin filament binding 0 0 -9999 0 -0.001 299 299
SRC 0 0.009 -9999 0 -10000 0 0
ITGB3 -0.018 0.12 -9999 0 -0.82 19 19
GNAQ -0.002 0.039 -9999 0 -0.83 2 2
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 279 279
ARF6/GDP -0.016 0.086 -9999 0 -0.42 17 17
ARF6/GDP/GULP/ACAP1 -0.15 0.2 -9999 0 -0.54 149 149
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.018 0.081 -9999 0 -0.5 22 22
ACAP1 -0.017 0.095 -9999 0 -0.4 39 39
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.095 0.24 -9999 0 -0.68 128 128
EFNA1 0 0.009 -9999 0 -10000 0 0
HGF -0.051 0.2 -9999 0 -0.83 57 57
CYTH3 0.011 0 -9999 0 -10000 0 0
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 265 265
endosomal lumen acidification 0 0 -9999 0 -0.001 240 240
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.052 0.2 -9999 0 -0.82 58 58
GNAQ/ARNO 0.003 0.024 -9999 0 -0.48 2 2
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 303 303
MET -0.14 0.31 -9999 0 -0.82 155 155
GNA14 -0.014 0.087 -9999 0 -0.42 30 30
GNA15 -0.003 0.035 -9999 0 -0.36 7 7
GIT1 -0.001 0.018 -9999 0 -0.28 4 4
mol:PI-4-5-P2 0 0 -9999 0 -0.001 298 298
GNA11 -0.002 0.039 -9999 0 -0.83 2 2
LHCGR -0.12 0.29 -9999 0 -0.83 128 128
AGTR1 -0.21 0.34 -9999 0 -0.71 266 266
desensitization of G-protein coupled receptor protein signaling pathway -0.095 0.24 -9999 0 -0.68 128 128
IPCEF1/ARNO -0.24 0.26 -9999 0 -0.49 453 453
alphaIIb/beta3 Integrin -0.024 0.1 -9999 0 -0.64 22 22
ErbB2/ErbB3 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
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.39 19 19
NFATC4 -0.091 0.16 -9999 0 -0.31 153 153
ERBB2IP 0.007 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.009 -9999 0 -10000 0 0
mammary gland morphogenesis -0.15 0.19 -9999 0 -0.41 333 333
JUN -0.019 0.079 -9999 0 -0.37 4 4
HRAS -0.001 0.013 -9999 0 -0.28 2 2
DOCK7 -0.13 0.2 -9999 0 -0.38 333 333
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.23 -9999 0 -0.49 333 333
AKT1 0.007 0.006 -9999 0 -10000 0 0
BAD 0.018 0.004 -9999 0 -10000 0 0
MAPK10 -0.11 0.14 -9999 0 -0.37 145 145
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.21 -9999 0 -0.44 333 333
RAF1 -0.083 0.16 -9999 0 -0.4 14 14
ErbB2/ErbB3/neuregulin 2 -0.27 0.26 -9999 0 -0.53 463 463
STAT3 0 0.004 -9999 0 -10000 0 0
cell migration -0.064 0.13 -9999 0 -0.32 74 74
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.23 -9999 0 -0.52 146 146
FOS -0.17 0.26 -9999 0 -0.54 285 285
NRAS -0.001 0.013 -9999 0 -0.28 2 2
mol:Ca2+ -0.15 0.19 -9999 0 -0.41 333 333
MAPK3 -0.11 0.19 -9999 0 -0.48 59 59
MAPK1 -0.11 0.19 -9999 0 -0.43 146 146
JAK2 -0.13 0.2 -9999 0 -0.38 334 334
NF2 -0.007 0.01 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.14 0.18 -9999 0 -0.37 333 333
NRG1 -0.3 0.4 -9999 0 -0.82 336 336
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.34 334 334
MAPK9 -0.071 0.091 -9999 0 -0.29 1 1
ERBB2 -0.017 0.054 -9999 0 -10000 0 0
ERBB3 -0.002 0.039 -9999 0 -0.83 2 2
SHC1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.016 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.004 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.007 0.005 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.1 0.13 -9999 0 -0.33 21 21
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.042 -9999 0 -10000 0 0
CHRNA1 -0.094 0.16 -9999 0 -0.41 55 55
myelination -0.085 0.16 -9999 0 -0.31 153 153
PPP3CB -0.13 0.17 -9999 0 -0.36 333 333
KRAS 0 0.009 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.31 333 333
NRG2 -0.42 0.41 -9999 0 -0.82 461 461
mol:GDP -0.13 0.18 -9999 0 -0.36 333 333
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.075 0.15 -9999 0 -0.4 14 14
SRC 0 0.009 -9999 0 -10000 0 0
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.38 333 333
MAP2K1 -0.14 0.21 -9999 0 -0.49 145 145
heart morphogenesis -0.15 0.19 -9999 0 -0.41 333 333
RAS family/GDP -0.11 0.14 -9999 0 -0.39 14 14
GRB2 0 0.009 -9999 0 -10000 0 0
PRKACA -0.011 0.014 -9999 0 -10000 0 0
CHRNE 0.007 0.021 -9999 0 -0.18 4 4
HSP90AA1 0 0.009 -9999 0 -10000 0 0
activation of caspase activity -0.007 0.006 -9999 0 -10000 0 0
nervous system development -0.15 0.19 -9999 0 -0.41 333 333
CDC42 0 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.11 0.4 -10000 0 -0.9 181 181
NCK1/PAK1/Dok-R -0.084 0.17 -10000 0 -0.42 181 181
NCK1/Dok-R -0.23 0.46 -10000 0 -1.1 181 181
PIK3CA 0.002 0.011 -10000 0 -10000 0 0
mol:beta2-estradiol 0.034 0.097 0.24 154 -10000 0 154
RELA 0 0 -10000 0 -10000 0 0
SHC1 0 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.036 0.1 0.29 8 -0.3 5 13
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.21 0.42 -10000 0 -1.1 181 181
FN1 -0.12 0.14 -10000 0 -10000 0 0
PLD2 -0.18 0.51 -10000 0 -1.2 181 181
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.23 -10000 0 -0.47 194 194
ELK1 -0.14 0.45 -10000 0 -1 181 181
GRB7 -0.021 0.076 -10000 0 -0.82 1 1
PAK1 -0.006 0.041 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.18 0.48 -10000 0 -1.1 181 181
CDKN1A -0.054 0.27 -10000 0 -0.63 104 104
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.23 0.46 -10000 0 -1.1 181 181
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.057 0.3 -10000 0 -0.66 181 181
PLG -0.18 0.51 -10000 0 -1.2 181 181
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.36 -10000 0 -0.88 181 181
GRB2 0 0.009 -10000 0 -10000 0 0
PIK3R1 0 0.028 -10000 0 -0.82 1 1
ANGPT2 -0.1 0.27 -10000 0 -0.76 89 89
BMX -0.36 0.58 -10000 0 -1.4 181 181
ANGPT1 -0.22 0.56 -10000 0 -1.4 162 162
tube development -0.07 0.3 -10000 0 -0.67 148 148
ANGPT4 -0.27 0.39 -10000 0 -0.83 296 296
response to hypoxia -0.009 0.029 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.26 0.53 -10000 0 -1.3 181 181
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.33 0.41 -10000 0 -0.82 370 370
STAT5A (dimer) -0.085 0.34 -10000 0 -0.78 143 143
mol:L-citrulline -0.057 0.3 -10000 0 -0.66 181 181
AGTR1 -0.2 0.34 -10000 0 -0.7 266 266
MAPK14 -0.17 0.49 -10000 0 -1.1 181 181
Tie2/SHP2 -0.086 0.26 -10000 0 -1.3 35 35
TEK -0.095 0.3 -10000 0 -1.5 35 35
RPS6KB1 -0.1 0.38 -10000 0 -0.87 181 181
Angiotensin II/AT1 -0.16 0.27 -10000 0 -0.64 208 208
Tie2/Ang1/GRB2 -0.24 0.5 -10000 0 -1.2 181 181
MAPK3 -0.15 0.46 -10000 0 -1.1 181 181
MAPK1 -0.15 0.46 -10000 0 -1.1 181 181
Tie2/Ang1/GRB7 -0.24 0.5 -10000 0 -1.2 181 181
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.18 0.51 -10000 0 -1.2 181 181
PI3K -0.14 0.46 -10000 0 -1 181 181
FES -0.16 0.48 -10000 0 -1.1 181 181
Crk/Dok-R -0.23 0.46 -10000 0 -1.1 181 181
Tie2/Ang1/ABIN2 -0.24 0.5 -10000 0 -1.2 181 181
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.088 0.36 -10000 0 -0.8 181 181
STAT5A -0.006 0.072 -10000 0 -0.82 7 7
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.1 0.38 -10000 0 -0.87 181 181
Tie2/Ang2 -0.12 0.4 -10000 0 -0.93 143 143
Tie2/Ang1 -0.21 0.56 -10000 0 -1.3 181 181
FOXO1 -0.085 0.37 -10000 0 -0.81 181 181
ELF1 0.014 0.02 -10000 0 -10000 0 0
ELF2 -0.18 0.5 -10000 0 -1.2 181 181
mol:Choline -0.16 0.48 -10000 0 -1.1 181 181
cell migration -0.035 0.1 -10000 0 -0.25 51 51
FYN -0.086 0.34 -10000 0 -0.77 143 143
DOK2 -0.003 0.043 -10000 0 -0.82 2 2
negative regulation of cell cycle -0.045 0.25 -10000 0 -0.57 105 105
ETS1 -0.023 0.1 -10000 0 -1 2 2
PXN -0.068 0.32 -10000 0 -0.71 181 181
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.074 0.34 -10000 0 -0.75 181 181
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.04 0.15 -10000 0 -0.84 17 17
MAPKKK cascade -0.16 0.48 -10000 0 -1.1 181 181
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.22 0.51 -10000 0 -1.2 181 181
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.045 0.27 -10000 0 -0.58 181 181
mol:Phosphatidic acid -0.16 0.48 -10000 0 -1.1 181 181
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.057 0.3 -10000 0 -0.66 181 181
Rac1/GTP -0.16 0.32 -10000 0 -0.8 181 181
MMP2 -0.18 0.51 -10000 0 -1.2 181 181
Endothelins

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
AKT1 -0.014 0.19 -9999 0 -0.6 75 75
PTK2B 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.024 0.18 -9999 0 -0.93 20 20
EDN1 -0.042 0.25 -9999 0 -0.85 74 74
EDN3 -0.39 0.41 -9999 0 -0.82 429 429
EDN2 -0.074 0.14 -9999 0 -0.82 6 6
HRAS/GDP -0.029 0.2 -9999 0 -0.52 80 80
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.14 -9999 0 -0.42 50 50
ADCY4 -0.15 0.29 -9999 0 -0.58 257 257
ADCY5 -0.28 0.37 -9999 0 -0.63 423 423
ADCY6 -0.14 0.27 -9999 0 -0.55 241 241
ADCY7 -0.14 0.27 -9999 0 -0.55 241 241
ADCY1 -0.15 0.29 -9999 0 -0.58 252 252
ADCY2 -0.17 0.32 -9999 0 -0.62 267 267
ADCY3 -0.14 0.27 -9999 0 -0.55 241 241
ADCY8 -0.14 0.27 -9999 0 -0.56 241 241
ADCY9 -0.14 0.27 -9999 0 -0.55 241 241
arachidonic acid secretion -0.11 0.29 -9999 0 -0.46 306 306
ETB receptor/Endothelin-1/Gq/GTP -0.033 0.17 -9999 0 -0.38 141 141
GNAO1 -0.034 0.14 -9999 0 -0.82 24 24
HRAS -0.001 0.013 -9999 0 -0.28 2 2
ETA receptor/Endothelin-1/G12/GTP 0.034 0.2 -9999 0 -0.56 75 75
ETA receptor/Endothelin-1/Gs/GTP -0.095 0.32 -9999 0 -0.59 241 241
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.023 0.2 -9999 0 -0.6 75 75
EDNRB -0.065 0.24 -9999 0 -0.82 81 81
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.025 0.23 -9999 0 -0.67 86 86
CYSLTR1 -0.023 0.22 -9999 0 -0.66 84 84
SLC9A1 0 0.1 -9999 0 -0.31 74 74
mol:GDP -0.038 0.21 -9999 0 -0.55 85 85
SLC9A3 -0.047 0.27 -9999 0 -0.62 145 145
RAF1 -0.086 0.24 -9999 0 -0.53 137 137
JUN 0.026 0.18 -9999 0 -0.9 21 21
JAK2 -0.015 0.2 -9999 0 -0.6 75 75
mol:IP3 -0.029 0.17 -9999 0 -0.5 62 62
ETA receptor/Endothelin-1 0.03 0.25 -9999 0 -0.68 77 77
PLCB1 -0.053 0.2 -9999 0 -0.83 59 59
PLCB2 -0.001 0.029 -9999 0 -0.83 1 1
ETA receptor/Endothelin-3 -0.29 0.33 -9999 0 -0.64 427 427
FOS -0.26 0.5 -9999 0 -0.99 290 290
Gai/GDP -0.042 0.16 -9999 0 -0.69 35 35
CRK 0 0 -9999 0 -10000 0 0
mol:Ca ++ -0.05 0.24 -9999 0 -0.67 91 91
BCAR1 0.001 0.002 -9999 0 -10000 0 0
PRKCB1 -0.032 0.17 -9999 0 -0.46 72 72
GNAQ 0.007 0.04 -9999 0 -0.83 2 2
GNAZ -0.007 0.077 -9999 0 -0.82 8 8
GNAL -0.19 0.35 -9999 0 -0.82 210 210
Gs family/GDP -0.17 0.26 -9999 0 -0.55 250 250
ETA receptor/Endothelin-1/Gq/GTP 0.015 0.13 -9999 0 -0.39 49 49
MAPK14 -0.03 0.17 -9999 0 -0.47 72 72
TRPC6 0.022 0.19 -9999 0 -1 20 20
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.042 0.18 -9999 0 -0.82 47 47
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.038 0.18 -9999 0 -0.43 111 111
ETB receptor/Endothelin-2 -0.1 0.2 -9999 0 -0.68 86 86
ETB receptor/Endothelin-3 -0.35 0.35 -9999 0 -0.68 469 469
ETB receptor/Endothelin-1 -0.082 0.27 -9999 0 -0.68 145 145
MAPK3 -0.2 0.41 -9999 0 -0.79 291 291
MAPK1 -0.2 0.41 -9999 0 -0.79 291 291
Rac1/GDP -0.03 0.2 -9999 0 -0.52 80 80
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.61 254 254
MAPK8 0.022 0.16 -9999 0 -0.66 29 29
SRC 0 0.009 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.049 0.19 -9999 0 -0.42 133 133
p130Cas/CRK/Src/PYK2 -0.013 0.2 -9999 0 -0.58 60 60
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.03 0.2 -9999 0 -0.52 78 78
COL1A2 -0.054 0.25 -9999 0 -0.68 84 84
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.63 6 6
mol:DAG -0.029 0.17 -9999 0 -0.48 68 68
MAP2K2 -0.14 0.31 -9999 0 -0.56 296 296
MAP2K1 -0.14 0.31 -9999 0 -0.56 296 296
EDNRA 0.026 0.059 -9999 0 -0.31 2 2
positive regulation of muscle contraction -0.013 0.17 -9999 0 -0.52 75 75
Gq family/GDP -0.073 0.16 -9999 0 -0.6 44 44
HRAS/GTP -0.052 0.2 -9999 0 -0.46 117 117
PRKCH -0.023 0.17 -9999 0 -0.52 51 51
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.034 0.19 -9999 0 -0.58 64 64
PRKCB -0.035 0.19 -9999 0 -0.62 48 48
PRKCE -0.023 0.17 -9999 0 -0.52 52 52
PRKCD -0.024 0.17 -9999 0 -0.53 48 48
PRKCG -0.032 0.17 -9999 0 -0.54 50 50
regulation of vascular smooth muscle contraction -0.31 0.57 -9999 0 -1.1 290 290
PRKCQ -0.044 0.21 -9999 0 -0.58 81 81
PLA2G4A -0.12 0.32 -9999 0 -0.51 306 306
GNA14 -0.005 0.089 -9999 0 -0.43 30 30
GNA15 0.006 0.037 -9999 0 -0.36 7 7
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.007 0.039 -9999 0 -0.82 2 2
Rac1/GTP 0.034 0.2 -9999 0 -0.56 75 75
MMP1 -0.12 0.12 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.057 0.16 -10000 0 -0.56 89 89
cell-cell adhesion 0.19 0.22 0.71 63 -10000 0 63
Ephrin B/EPHB2/RasGAP -0.041 0.13 -10000 0 -0.47 77 77
ITSN1 -0.002 0.039 -10000 0 -0.82 2 2
PIK3CA 0 0.009 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.016 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.23 0.27 -10000 0 -0.56 384 384
HRAS/GDP -0.19 0.24 -10000 0 -0.43 402 402
Ephrin B/EPHB1/GRB7 -0.24 0.29 -10000 0 -0.54 403 403
Endophilin/SYNJ1 -0.039 0.12 -10000 0 -0.44 77 77
KRAS 0 0.009 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.24 0.29 -10000 0 -0.53 402 402
endothelial cell migration -0.001 0.016 -10000 0 -0.47 1 1
GRB2 0 0.009 -10000 0 -10000 0 0
GRB7 -0.021 0.076 -10000 0 -0.82 1 1
PAK1 -0.048 0.14 -10000 0 -0.48 85 85
HRAS -0.001 0.013 -10000 0 -0.28 2 2
RRAS -0.039 0.12 -10000 0 -0.44 77 77
DNM1 -0.005 0.062 -10000 0 -0.73 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.22 0.27 -10000 0 -0.51 402 402
lamellipodium assembly -0.19 0.22 -10000 0 -0.71 63 63
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.16 0.19 -10000 0 -0.37 384 384
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
EPHB2 -0.005 0.038 -10000 0 -10000 0 0
EPHB3 -0.003 0.029 -10000 0 -0.28 10 10
EPHB1 -0.35 0.41 -10000 0 -0.82 384 384
EPHB4 0 0.009 -10000 0 -0.28 1 1
mol:GDP -0.17 0.22 -10000 0 -0.66 81 81
Ephrin B/EPHB2 -0.042 0.13 -10000 0 -0.48 77 77
Ephrin B/EPHB3 -0.041 0.13 -10000 0 -0.48 77 77
JNK cascade -0.19 0.22 -10000 0 -0.46 384 384
Ephrin B/EPHB1 -0.24 0.29 -10000 0 -0.54 402 402
RAP1/GDP -0.14 0.18 -10000 0 -0.57 77 77
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.07 0.23 -10000 0 -0.82 77 77
EFNB1 0 0.009 -10000 0 -0.28 1 1
Ephrin B2/EPHB1-2 -0.22 0.25 -10000 0 -0.51 384 384
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.2 0.24 -10000 0 -0.71 80 80
Rap1/GTP -0.19 0.23 -10000 0 -0.73 62 62
axon guidance -0.057 0.16 -10000 0 -0.55 89 89
MAPK3 -0.11 0.19 -10000 0 -0.54 59 59
MAPK1 -0.11 0.19 -10000 0 -0.54 59 59
Rac1/GDP -0.15 0.2 -10000 0 -0.6 78 78
actin cytoskeleton reorganization -0.14 0.17 -10000 0 -0.55 62 62
CDC42/GDP -0.15 0.2 -10000 0 -0.6 78 78
PI3K -0.001 0.016 -10000 0 -0.47 1 1
EFNA5 -0.081 0.24 -10000 0 -0.82 89 89
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.03 0.1 -10000 0 -0.35 77 77
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.18 0.22 -10000 0 -0.7 63 63
PTK2 0.045 0.052 -10000 0 -10000 0 0
MAP4K4 -0.2 0.23 -10000 0 -0.46 384 384
SRC 0 0.009 -10000 0 -10000 0 0
KALRN -0.014 0.11 -10000 0 -0.82 16 16
Intersectin/N-WASP -0.001 0.03 -10000 0 -0.63 2 2
neuron projection morphogenesis -0.15 0.18 -10000 0 -0.56 68 68
MAP2K1 -0.15 0.18 -10000 0 -0.57 60 60
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.21 0.25 -10000 0 -0.5 384 384
cell migration -0.14 0.23 -10000 0 -0.56 82 82
NRAS -0.001 0.013 -10000 0 -0.28 2 2
SYNJ1 -0.039 0.12 -10000 0 -0.44 77 77
PXN 0 0 -10000 0 -10000 0 0
TF -0.26 0.28 -10000 0 -0.48 535 535
HRAS/GTP -0.2 0.24 -10000 0 -0.46 402 402
Ephrin B1/EPHB1-2 -0.22 0.25 -10000 0 -0.51 384 384
cell adhesion mediated by integrin 0.007 0.14 0.44 77 -10000 0 77
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.22 0.26 -10000 0 -0.49 402 402
RAC1-CDC42/GTP -0.19 0.22 -10000 0 -0.72 63 63
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.14 0.18 -10000 0 -0.57 77 77
ruffle organization -0.19 0.23 -10000 0 -0.73 63 63
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.002 0.14 -10000 0 -0.44 78 78
Ephrin B/EPHB2/KALRN -0.049 0.15 -10000 0 -0.51 85 85
ROCK1 -0.001 0.013 -10000 0 -10000 0 0
RAS family/GDP -0.13 0.16 -10000 0 -0.54 60 60
Rac1/GTP -0.2 0.24 -10000 0 -0.78 63 63
Ephrin B/EPHB1/Src/Paxillin -0.17 0.21 -10000 0 -0.38 402 402
Wnt signaling

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.17 0.26 -9999 0 -0.46 332 332
FZD6 -0.006 0.072 -9999 0 -0.82 7 7
WNT6 -0.17 0.33 -9999 0 -0.82 181 181
WNT4 -0.024 0.13 -9999 0 -0.82 20 20
FZD3 -0.009 0.086 -9999 0 -0.82 10 10
WNT5A -0.013 0.094 -9999 0 -0.58 20 20
WNT11 -0.19 0.34 -9999 0 -0.82 203 203
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 -0.004 0.038 -10000 0 -10000 0 0
EFNB1 0.017 0.049 -10000 0 -0.64 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.18 0.22 -10000 0 -0.43 385 385
Ephrin B2/EPHB1-2 -0.21 0.25 -10000 0 -0.5 384 384
neuron projection morphogenesis -0.18 0.21 -10000 0 -0.42 385 385
Ephrin B1/EPHB1-2/Tiam1 -0.2 0.23 -10000 0 -0.47 385 385
DNM1 -0.005 0.062 -10000 0 -0.74 6 6
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.003 0.13 -10000 0 -0.76 25 25
YES1 -0.023 0.16 -10000 0 -1 24 24
Ephrin B1/EPHB1-2/NCK2 -0.2 0.23 -10000 0 -0.47 385 385
PI3K -0.021 0.13 -10000 0 -0.77 25 25
mol:GDP -0.2 0.23 -10000 0 -0.46 385 385
ITGA2B -0.016 0.076 -10000 0 -0.31 47 47
endothelial cell proliferation 0 0.005 -10000 0 -10000 0 0
FYN -0.023 0.16 -10000 0 -1 24 24
MAP3K7 -0.021 0.13 -10000 0 -0.82 24 24
FGR -0.025 0.16 -10000 0 -1 24 24
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.035 0.14 -10000 0 -0.63 44 44
LYN -0.023 0.16 -10000 0 -1 24 24
Ephrin B1/EPHB1-2/Src Family Kinases -0.024 0.15 -10000 0 -0.94 24 24
Ephrin B1/EPHB1-2 -0.028 0.14 -10000 0 -0.89 24 24
SRC -0.025 0.16 -10000 0 -1 24 24
ITGB3 -0.018 0.12 -10000 0 -0.82 19 19
EPHB1 -0.35 0.41 -10000 0 -0.82 384 384
EPHB4 0 0.009 -10000 0 -0.28 1 1
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.024 0.1 -10000 0 -0.64 22 22
BLK -0.025 0.16 -10000 0 -1 24 24
HCK -0.025 0.16 -10000 0 -1 24 24
regulation of stress fiber formation 0.2 0.23 0.46 385 -10000 0 385
MAPK8 0.004 0.13 -10000 0 -0.74 26 26
Ephrin B1/EPHB1-2/RGS3 -0.2 0.23 -10000 0 -0.47 385 385
endothelial cell migration -0.015 0.12 -10000 0 -0.72 24 24
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.015 0.15 -10000 0 -0.94 24 24
regulation of focal adhesion formation 0.2 0.23 0.46 385 -10000 0 385
chemotaxis 0.2 0.23 0.46 385 -10000 0 385
PIK3CA 0 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.18 0.21 -10000 0 -0.42 385 385
angiogenesis -0.027 0.14 -10000 0 -0.88 24 24
LCK -0.027 0.16 -10000 0 -1 24 24
FOXM1 transcription factor network

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
NFATC3 -0.22 0.42 -9999 0 -0.97 99 99
PLK1 -0.079 0.098 -9999 0 -10000 0 0
BIRC5 -0.089 0.094 -9999 0 -10000 0 0
HSPA1B -0.22 0.42 -9999 0 -0.93 120 120
MAP2K1 0.008 0.028 -9999 0 -10000 0 0
BRCA2 -0.22 0.42 -9999 0 -0.94 124 124
FOXM1 -0.27 0.49 -9999 0 -1 191 191
XRCC1 -0.22 0.42 -9999 0 -0.94 113 113
FOXM1B/p19 -0.27 0.4 -9999 0 -0.89 195 195
Cyclin D1/CDK4 -0.21 0.39 -9999 0 -0.88 120 120
CDC2 -0.24 0.44 -9999 0 -0.88 191 191
TGFA -0.21 0.41 -9999 0 -0.9 129 129
SKP2 -0.22 0.42 -9999 0 -0.95 109 109
CCNE1 -0.051 0.12 -9999 0 -0.29 176 176
CKS1B -0.22 0.42 -9999 0 -0.94 120 120
RB1 -0.11 0.12 -9999 0 -1 2 2
FOXM1C/SP1 -0.28 0.43 -9999 0 -0.91 200 200
AURKB -0.071 0.099 -9999 0 -10000 0 0
CENPF -0.25 0.44 -9999 0 -0.98 126 126
CDK4 0.007 0.018 -9999 0 -0.28 2 2
MYC -0.2 0.4 -9999 0 -0.83 156 156
CHEK2 0.007 0.032 -9999 0 -0.3 2 2
ONECUT1 -0.22 0.41 -9999 0 -0.87 153 153
CDKN2A -0.033 0.11 -9999 0 -10000 0 0
LAMA4 -0.22 0.42 -9999 0 -0.94 120 120
FOXM1B/HNF6 -0.25 0.46 -9999 0 -1 153 153
FOS -0.44 0.68 -9999 0 -1.3 300 300
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.22 0.42 -9999 0 -0.93 124 124
response to radiation -0.007 0.029 -9999 0 -10000 0 0
CENPB -0.22 0.42 -9999 0 -0.92 126 126
CENPA -0.25 0.44 -9999 0 -0.9 180 180
NEK2 -0.27 0.43 -9999 0 -0.93 158 158
HIST1H2BA -0.23 0.42 -9999 0 -0.93 127 127
CCNA2 -0.12 0.15 -9999 0 -0.29 389 389
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.26 0.46 -9999 0 -0.98 170 170
CCNB2 -0.25 0.44 -9999 0 -0.98 125 125
CCNB1 -0.24 0.44 -9999 0 -0.92 170 170
ETV5 -0.22 0.42 -9999 0 -0.95 113 113
ESR1 -0.32 0.56 -9999 0 -1.3 185 185
CCND1 -0.21 0.4 -9999 0 -0.88 128 128
GSK3A 0.013 0.02 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.08 0.13 -9999 0 -0.32 11 11
CDK2 0.005 0.008 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.009 0.035 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.31 0.36 -9999 0 -0.87 198 198
GAS1 -0.26 0.48 -9999 0 -1.1 145 145
MMP2 -0.22 0.43 -9999 0 -0.99 108 108
RB1/FOXM1C -0.22 0.42 -9999 0 -0.93 128 128
CREBBP 0 0 -9999 0 -10000 0 0
IGF1 pathway

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
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.12 0.23 -10000 0 -0.51 219 219
GRB2/SOS1/SHC 0 0.004 -10000 0 -10000 0 0
HRAS -0.001 0.013 -10000 0 -0.28 2 2
IRS1/Crk -0.12 0.24 -10000 0 -0.51 219 219
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.24 -10000 0 -0.56 207 207
AKT1 -0.066 0.21 -10000 0 -0.43 207 207
BAD -0.053 0.2 -10000 0 -0.69 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.23 -10000 0 -0.51 219 219
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.24 -10000 0 -0.51 219 219
RAF1 -0.046 0.19 -10000 0 -0.64 33 33
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.22 -10000 0 -0.48 219 219
YWHAZ -0.001 0.016 -10000 0 -0.28 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.26 -10000 0 -0.55 219 219
PIK3CA 0 0.009 -10000 0 -10000 0 0
RPS6KB1 -0.066 0.21 -10000 0 -0.43 207 207
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.039 0.16 -10000 0 -0.52 33 33
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.2 -10000 0 -0.43 208 208
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.2 -10000 0 -0.45 207 207
IGF-1R heterotetramer -0.044 0.14 -10000 0 -0.66 33 33
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.24 -10000 0 -0.51 219 219
Crk/p130 Cas/Paxillin -0.11 0.21 -10000 0 -0.46 207 207
IGF1R -0.044 0.14 -10000 0 -0.66 33 33
IGF1 -0.18 0.35 -10000 0 -0.85 197 197
IRS2/Crk -0.13 0.26 -10000 0 -0.53 230 230
PI3K -0.11 0.22 -10000 0 -0.48 219 219
apoptosis 0.079 0.15 0.56 34 -10000 0 34
HRAS/GDP 0 0.009 -10000 0 -10000 0 0
PRKCD -0.095 0.25 -10000 0 -0.55 207 207
RAF1/14-3-3 E -0.074 0.14 -10000 0 -0.54 31 31
BAD/14-3-3 -0.084 0.16 -10000 0 -0.61 34 34
PRKCZ -0.067 0.21 -10000 0 -0.43 207 207
Crk/p130 Cas/Paxillin/FAK1 -0.083 0.16 -10000 0 -0.64 31 31
PTPN1 -0.003 0.03 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.13 0.25 -10000 0 -0.58 207 207
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.21 -10000 0 -0.49 207 207
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.23 -10000 0 -0.51 219 219
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.12 0.23 -10000 0 -0.51 219 219
IRS1 -0.13 0.25 -10000 0 -0.55 219 219
IRS2 -0.14 0.27 -10000 0 -0.56 230 230
IGF-1R heterotetramer/IGF1 -0.16 0.29 -10000 0 -0.69 207 207
GRB2 0 0.009 -10000 0 -10000 0 0
PDPK1 -0.11 0.21 -10000 0 -0.46 207 207
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.28 -10000 0 -0.59 218 218
SHC1 0 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.17 0.4 -9999 0 -0.95 97 97
IL23A -0.18 0.4 -9999 0 -1 79 79
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.32 -9999 0 -0.87 130 130
positive regulation of T cell mediated cytotoxicity -0.19 0.43 -9999 0 -0.86 208 208
ITGA3 -0.17 0.39 -9999 0 -1 80 80
IL17F -0.1 0.29 -9999 0 -0.63 90 90
IL12B -0.042 0.12 -9999 0 -0.27 176 176
STAT1 (dimer) -0.22 0.38 -9999 0 -0.82 208 208
CD4 -0.16 0.38 -9999 0 -0.91 98 98
IL23 -0.18 0.38 -9999 0 -1 78 78
IL23R -0.013 0.088 -9999 0 -10000 0 0
IL1B -0.18 0.41 -9999 0 -1 101 101
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.17 0.39 -9999 0 -0.95 89 89
TYK2 0.011 0.016 -9999 0 -10000 0 0
STAT4 -0.033 0.16 -9999 0 -0.81 37 37
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.031 0.16 -9999 0 -0.79 36 36
IL12RB1 0 0.064 -9999 0 -0.3 35 35
PIK3CA 0 0.009 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 -0.003 0.048 -9999 0 -0.68 1 1
IL23R/JAK2 -0.011 0.11 -9999 0 -0.66 1 1
positive regulation of chronic inflammatory response -0.19 0.43 -9999 0 -0.86 208 208
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.017 0.036 -9999 0 -0.86 1 1
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
NFKB1 0 0.001 -9999 0 -10000 0 0
RELA 0 0.001 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.38 -9999 0 -0.94 84 84
ALOX12B -0.17 0.39 -9999 0 -0.97 80 80
CXCL1 -0.37 0.65 -9999 0 -1.4 254 254
T cell proliferation -0.19 0.43 -9999 0 -0.86 208 208
NFKBIA 0 0.001 -9999 0 -10000 0 0
IL17A -0.071 0.24 -9999 0 -0.51 69 69
PI3K -0.25 0.33 -9999 0 -0.79 207 207
IFNG -0.005 0.026 -9999 0 -0.09 26 26
STAT3 (dimer) -0.24 0.32 -9999 0 -0.79 164 164
IL18R1 -0.011 0.094 -9999 0 -0.82 12 12
IL23/IL23R/JAK2/TYK2/SOCS3 -0.085 0.24 -9999 0 -0.56 55 55
IL18/IL18R -0.031 0.12 -9999 0 -0.57 44 44
macrophage activation -0.014 0.017 -9999 0 -0.041 113 113
TNF -0.18 0.42 -9999 0 -1.1 84 84
STAT3/STAT4 -0.26 0.36 -9999 0 -0.82 218 218
STAT4 (dimer) -0.24 0.4 -9999 0 -0.86 218 218
IL18 -0.007 0.043 -9999 0 -10000 0 0
IL19 -0.18 0.39 -9999 0 -0.91 108 108
STAT5A (dimer) -0.23 0.38 -9999 0 -0.82 211 211
STAT1 -0.006 0.04 -9999 0 -0.28 19 19
SOCS3 -0.005 0.067 -9999 0 -0.82 6 6
CXCL9 -0.19 0.39 -9999 0 -0.94 108 108
MPO -0.22 0.48 -9999 0 -1.1 148 148
positive regulation of humoral immune response -0.19 0.43 -9999 0 -0.86 208 208
IL23/IL23R/JAK2/TYK2 -0.2 0.45 -9999 0 -0.89 208 208
IL6 -0.47 0.71 -9999 0 -1.4 344 344
STAT5A -0.006 0.072 -9999 0 -0.82 7 7
IL2 0.003 0.029 -9999 0 -0.29 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.18 0.42 -9999 0 -0.97 118 118
keratinocyte proliferation -0.19 0.43 -9999 0 -0.86 208 208
NOS2 -0.17 0.39 -9999 0 -0.89 119 119
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.11 0.21 -9999 0 -0.62 111 111
SMAD6-7/SMURF1 -0.001 0.018 -9999 0 -0.55 1 1
NOG -0.023 0.13 -9999 0 -0.61 35 35
SMAD9 -0.1 0.26 -9999 0 -0.83 87 87
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.079 0.18 -9999 0 -0.48 120 120
BMP7/USAG1 -0.36 0.36 -9999 0 -0.69 471 471
SMAD5/SKI -0.09 0.16 -9999 0 -0.52 80 80
SMAD1 0.025 0.031 -9999 0 -10000 0 0
BMP2 -0.15 0.32 -9999 0 -0.82 164 164
SMAD1/SMAD1/SMAD4 -0.002 0.012 -9999 0 -10000 0 0
BMPR1A -0.001 0.027 -9999 0 -0.82 1 1
BMPR1B -0.14 0.18 -9999 0 -0.31 402 402
BMPR1A-1B/BAMBI -0.092 0.15 -9999 0 -0.62 51 51
AHSG -0.002 0.024 -9999 0 -10000 0 0
CER1 -0.001 0.013 -9999 0 -10000 0 0
BMP2-4/CER1 -0.14 0.26 -9999 0 -0.6 206 206
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.11 0.2 -9999 0 -0.61 87 87
BMP2-4 (homodimer) -0.15 0.29 -9999 0 -0.68 206 206
RGMB -0.001 0.027 -9999 0 -0.82 1 1
BMP6/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.56 96 96
RGMA -0.11 0.28 -9999 0 -0.82 125 125
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.63 90 90
BMP2-4/USAG1 -0.39 0.38 -9999 0 -0.68 528 528
SMAD6/SMURF1/SMAD5 -0.09 0.16 -9999 0 -0.52 80 80
SOSTDC1 -0.4 0.41 -9999 0 -0.82 450 450
BMP7/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.59 89 89
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.067 0.22 -9999 0 -0.81 76 76
HFE2 -0.002 0.024 -9999 0 -10000 0 0
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.009 -9999 0 -10000 0 0
BMP2-4/CHRD -0.15 0.28 -9999 0 -0.64 208 208
SMAD5/SMAD5/SMAD4 -0.09 0.16 -9999 0 -0.52 80 80
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.089 0.17 -9999 0 -0.54 88 88
BMP7 (homodimer) -0.076 0.22 -9999 0 -0.82 71 71
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.054 0.18 -9999 0 -0.64 74 74
SMAD1/SKI -0.005 0.014 -9999 0 -10000 0 0
SMAD6 -0.001 0.027 -9999 0 -0.82 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.14 0.26 -9999 0 -0.6 206 206
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.039 0.12 -9999 0 -0.33 109 109
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.089 0.12 -9999 0 -0.64 24 24
CHRDL1 -0.57 0.38 -9999 0 -0.82 632 632
ENDOFIN/SMAD1 -0.005 0.014 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.015 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.035 0.15 -9999 0 -0.82 27 27
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.5 0.38 -9999 0 -0.7 648 648
BMP2-4/GREM1 -0.15 0.26 -9999 0 -0.61 209 209
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.093 0.24 -9999 0 -0.77 87 87
SMAD1/SMAD6 -0.005 0.014 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.076 0.22 -9999 0 -0.82 71 71
BMP6 -0.067 0.22 -9999 0 -0.81 76 76
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.19 -9999 0 -0.61 87 87
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.005 0.014 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA -0.002 0.021 -9999 0 -0.28 5 5
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.13 0.25 -9999 0 -0.52 180 180
CHRD -0.031 0.13 -9999 0 -0.42 67 67
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.24 -9999 0 -0.55 170 170
BMP4 -0.054 0.2 -9999 0 -0.82 60 60
FST -0.035 0.16 -9999 0 -0.78 41 41
BMP2-4/NOG -0.15 0.27 -9999 0 -0.61 218 218
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.093 0.16 -9999 0 -0.56 89 89
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.01 0.031 -9999 0 -0.54 1 1
NFATC2 -0.028 0.15 -9999 0 -0.58 61 61
NFATC3 0.011 0.025 -9999 0 -10000 0 0
CD40LG -0.24 0.35 -9999 0 -0.73 254 254
PTGS2 -0.35 0.45 -9999 0 -0.87 357 357
JUNB 0 0.009 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.009 -9999 0 -10000 0 0
CALM1 0 0.002 -9999 0 -10000 0 0
JUN -0.008 0.082 -9999 0 -0.83 9 9
mol:Ca2+ -0.006 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -9999 0 -10000 0 0
FOSL1 -0.008 0.056 -9999 0 -0.82 2 2
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.067 0.14 -9999 0 -0.55 50 50
FOS -0.26 0.39 -9999 0 -0.84 283 283
IFNG -0.23 0.34 -9999 0 -0.69 260 260
AP-1/NFAT1-c-4 -0.31 0.38 -9999 0 -0.84 257 257
FASLG -0.23 0.33 -9999 0 -0.69 248 248
NFAT1-c-4/ICER1 -0.048 0.13 -9999 0 -0.49 62 62
IL2RA -0.23 0.34 -9999 0 -0.7 251 251
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.22 0.33 -9999 0 -0.69 249 249
JunB/Fra1/NFAT1-c-4 -0.045 0.12 -9999 0 -0.52 43 43
IL4 -0.21 0.34 -9999 0 -0.69 246 246
IL2 -0.011 0.024 -9999 0 -10000 0 0
IL3 -0.024 0.027 -9999 0 -10000 0 0
FKBP1A 0 0.009 -9999 0 -0.28 1 1
BATF3 -0.002 0.033 -9999 0 -0.39 5 5
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.01 -9999 0 -0.28 1 1
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.11 0.13 -10000 0 -0.34 74 74
NT3 (dimer)/TRKC -0.32 0.38 -10000 0 -0.73 397 397
NT3 (dimer)/TRKB -0.53 0.47 -10000 0 -0.83 583 583
SHC/Grb2/SOS1/GAB1/PI3K 0 0.011 -10000 0 -0.33 1 1
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.073 0.23 -10000 0 -0.82 74 74
PIK3CA 0 0.009 -10000 0 -10000 0 0
DYNLT1 0 0.009 -10000 0 -0.28 1 1
NTRK1 -0.01 0.065 -10000 0 -0.82 3 3
NTRK2 -0.43 0.41 -10000 0 -0.82 476 476
NTRK3 -0.29 0.39 -10000 0 -0.82 319 319
NT-4/5 (dimer)/TRKB -0.63 0.52 -10000 0 -0.92 630 630
neuron apoptosis 0.25 0.25 0.6 263 -10000 0 263
SHC 2-3/Grb2 -0.28 0.28 -10000 0 -0.67 263 263
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.26 0.3 -10000 0 -0.69 249 249
SHC3 -0.26 0.28 -10000 0 -0.67 252 252
STAT3 (dimer) -0.005 0.028 -10000 0 -0.38 3 3
NT3 (dimer)/TRKA -0.27 0.34 -10000 0 -0.64 383 383
RIN/GDP -0.072 0.13 -10000 0 -0.28 57 57
GIPC1 0 0.009 -10000 0 -10000 0 0
KRAS 0 0.009 -10000 0 -10000 0 0
DNAJA3 -0.15 0.21 -10000 0 -0.44 296 296
RIN/GTP 0 0.009 -10000 0 -10000 0 0
CCND1 0.018 0.072 -10000 0 -1 3 3
MAGED1 -0.001 0.013 -10000 0 -0.28 2 2
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.3 0.4 -10000 0 -0.82 338 338
SHC/GRB2/SOS1 0 0.004 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.029 0.11 -10000 0 -0.57 35 35
TRKA/NEDD4-2 -0.007 0.05 -10000 0 -0.63 4 4
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.016 0.11 -10000 0 -0.65 22 22
HRAS -0.001 0.013 -10000 0 -0.28 2 2
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.002 0.026 -10000 0 -10000 0 0
RIT2 -0.001 0.013 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.029 -10000 0 -0.28 10 10
DNM1 -0.005 0.062 -10000 0 -0.73 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.14 0.2 -10000 0 -0.43 296 296
mol:GDP -0.11 0.19 -10000 0 -0.37 207 207
NGF (dimer) -0.016 0.11 -10000 0 -0.65 22 22
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.068 0.13 -10000 0 -0.26 99 99
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
BDNF (dimer)/TRKB -0.33 0.32 -10000 0 -0.6 500 500
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0.004 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.14 0.3 -10000 0 -0.82 149 149
RAP1/GDP -0.077 0.087 -10000 0 -0.25 17 17
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.073 0.23 -10000 0 -0.82 74 74
ubiquitin-dependent protein catabolic process -0.016 0.081 -10000 0 -0.55 19 19
Schwann cell development -0.06 0.045 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0.001 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.46 0.4 -10000 0 -0.88 367 367
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.11 0.1 -10000 0 -10000 0 0
STAT3 -0.005 0.028 -10000 0 -0.38 3 3
axon guidance -0.42 0.37 -10000 0 -0.65 591 591
MAPK3 -0.026 0.1 -10000 0 -0.52 35 35
MAPK1 -0.026 0.1 -10000 0 -0.52 35 35
CDC42/GDP -0.068 0.13 -10000 0 -0.26 99 99
NTF3 -0.14 0.3 -10000 0 -0.82 149 149
NTF4 -0.3 0.4 -10000 0 -0.82 338 338
NGF (dimer)/TRKA/FAIM -0.015 0.079 -10000 0 -0.55 18 18
PI3K -0.001 0.022 -10000 0 -0.63 1 1
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.16 0.22 -10000 0 -0.46 305 305
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.26 0.35 -10000 0 -0.64 398 398
RGS19 -0.001 0.016 -10000 0 -0.28 3 3
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.083 -10000 0 -10000 0 0
Rac1/GDP -0.068 0.13 -10000 0 -0.28 52 52
NGF (dimer)/TRKA/GRIT -0.016 0.081 -10000 0 -0.56 18 18
neuron projection morphogenesis -0.11 0.21 -10000 0 -0.41 294 294
NGF (dimer)/TRKA/NEDD4-2 -0.016 0.081 -10000 0 -0.55 19 19
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.27 0.39 -10000 0 -0.82 296 296
NGF (dimer)/TRKA/GIPC/GAIP -0.01 0.055 -10000 0 -0.35 22 22
RAS family/GTP/PI3K -0.001 0.011 -10000 0 -0.34 1 1
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.01 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.28 2 2
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.027 -10000 0 -0.82 1 1
MAPKKK cascade -0.067 0.12 -10000 0 -0.82 18 18
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.007 0.046 -10000 0 -0.63 3 3
SQSTM1 -0.001 0.013 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.3 0.29 -10000 0 -0.55 500 500
NGF (dimer)/TRKA/p62/Atypical PKCs -0.013 0.068 -10000 0 -0.47 19 19
MATK -0.023 0.12 -10000 0 -0.53 39 39
NEDD4L -0.001 0.027 -10000 0 -0.82 1 1
RAS family/GDP -0.069 0.082 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.16 0.22 -10000 0 -0.47 303 303
Rac1/GTP -0.13 0.14 -10000 0 -0.35 227 227
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.026 0.064 -10000 0 -0.52 2 2
epithelial cell differentiation -0.02 0.055 -10000 0 -0.44 2 2
ITCH 0.009 0.021 -10000 0 -10000 0 0
WWP1 0.007 0.068 -10000 0 -10000 0 0
FYN -0.001 0.027 -10000 0 -0.82 1 1
EGFR -0.3 0.4 -10000 0 -0.82 331 331
PRL -0.003 0.03 -10000 0 -0.28 11 11
neuron projection morphogenesis -0.11 0.22 -10000 0 -0.49 56 56
PTPRZ1 -0.44 0.41 -10000 0 -0.82 479 479
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.17 0.21 -10000 0 -0.54 63 63
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.2 0.25 -10000 0 -0.52 332 332
ADAM17 0.009 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.061 0.14 -10000 0 -0.56 58 58
NCOR1 -0.001 0.027 -10000 0 -0.82 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.19 0.23 -10000 0 -0.49 332 332
GRIN2B -0.2 0.25 -10000 0 -0.49 382 382
ErbB4/ErbB2/betacellulin -0.049 0.12 -10000 0 -0.49 49 49
STAT1 -0.006 0.04 -10000 0 -0.28 19 19
HBEGF -0.002 0.039 -10000 0 -0.82 2 2
PRLR -0.003 0.035 -10000 0 -0.36 7 7
E4ICDs/ETO2 -0.036 0.095 -10000 0 -0.57 17 17
axon guidance 0.044 0.13 -10000 0 -0.39 1 1
NEDD4 0.009 0.021 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.004 0.032 -10000 0 -0.64 1 1
CBFA2T3 -0.017 0.11 -10000 0 -0.72 21 21
ErbB4/ErbB2/HBEGF -0.025 0.052 -10000 0 -0.46 2 2
MAPK3 -0.16 0.2 -10000 0 -0.51 60 60
STAT1 (dimer) -0.028 0.064 -10000 0 -10000 0 0
MAPK1 -0.16 0.2 -10000 0 -0.51 60 60
JAK2 -0.001 0.027 -10000 0 -0.82 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.2 0.23 -10000 0 -0.49 332 332
NRG1 -0.22 0.32 -10000 0 -0.64 332 332
NRG3 -0.059 0.2 -10000 0 -0.82 58 58
NRG2 -0.42 0.41 -10000 0 -0.82 461 461
NRG4 -0.005 0.037 -10000 0 -0.28 16 16
heart development 0.044 0.13 -10000 0 -0.39 1 1
neural crest cell migration -0.19 0.23 -10000 0 -0.49 332 332
ERBB2 0.009 0.057 -10000 0 -10000 0 0
WWOX/E4ICDs -0.025 0.059 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.2 0.22 -10000 0 -0.48 326 326
apoptosis 0.061 0.15 0.54 58 -10000 0 58
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.29 0.25 -10000 0 -0.53 461 461
ErbB4/ErbB2/epiregulin -0.087 0.16 -10000 0 -0.48 108 108
ErbB4/ErbB4/betacellulin/betacellulin -0.053 0.13 -10000 0 -0.53 49 49
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.019 0.057 -10000 0 -0.51 4 4
MDM2 0.009 0.075 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.19 0.24 -10000 0 -0.5 332 332
STAT5A 0.044 0.12 -10000 0 -0.49 4 4
ErbB4/EGFR/neuregulin 1 beta -0.35 0.37 -10000 0 -0.69 455 455
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.056 -10000 0 -0.48 1 1
STAT5A (dimer) -0.02 0.059 -10000 0 -0.48 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.022 0.066 -10000 0 -0.47 3 3
LRIG1 -0.001 0.027 -10000 0 -0.82 1 1
EREG -0.12 0.27 -10000 0 -0.82 108 108
BTC -0.045 0.19 -10000 0 -0.82 49 49
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.044 0.13 -10000 0 -0.39 1 1
ERBB4 -0.031 0.073 -10000 0 -10000 0 0
STAT5B -0.003 0.047 -10000 0 -0.82 3 3
YAP1 -0.01 0.042 -10000 0 -0.66 3 3
GRB2 0 0.009 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.026 0.051 -10000 0 -10000 0 0
glial cell differentiation 0.024 0.056 0.48 1 -10000 0 1
WWOX 0 0.009 -10000 0 -0.28 1 1
cell proliferation -0.12 0.24 -10000 0 -0.56 70 70
Aurora B signaling

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.055 0.054 -9999 0 -10000 0 0
STMN1 -0.1 0.12 -9999 0 -0.35 70 70
Aurora B/RasGAP/Survivin -0.17 0.13 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.15 0.15 -9999 0 -0.35 281 281
BIRC5 -0.2 0.13 -9999 0 -10000 0 0
DES -0.3 0.34 -9999 0 -0.65 437 437
Aurora C/Aurora B/INCENP -0.065 0.072 -9999 0 -0.64 1 1
Aurora B/TACC1 -0.091 0.12 -9999 0 -0.63 25 25
Aurora B/PP2A -0.094 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.007 0.015 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.21 0.16 -9999 0 -0.35 483 483
Cul3 protein complex -0.22 0.27 -9999 0 -0.55 366 366
KIF2C -0.036 0.026 -9999 0 -10000 0 0
PEBP1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.12 -9999 0 -0.28 261 261
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.094 0.091 -9999 0 -10000 0 0
SEPT1 -0.006 0.041 -9999 0 -10000 0 0
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.005 0.035 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.012 0.015 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.002 -9999 0 -10000 0 0
H3F3B -0.031 0.04 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -0.28 416 416
AURKC -0.005 0.043 -9999 0 -0.32 14 14
CDCA8 -0.1 0.14 -9999 0 -0.28 330 330
cytokinesis -0.1 0.068 -9999 0 -10000 0 0
Aurora B/Septin1 -0.087 0.078 -9999 0 -10000 0 0
AURKA -0.14 0.14 -9999 0 -0.28 450 450
INCENP 0.001 0.004 -9999 0 -10000 0 0
KLHL13 -0.33 0.4 -9999 0 -0.82 365 365
BUB1 -0.2 0.13 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.25 0.17 -9999 0 -0.39 481 481
EVI5 0.007 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.093 0.092 -9999 0 -10000 0 0
SGOL1 -0.19 0.13 -9999 0 -0.28 613 613
CENPA -0.049 0.054 -9999 0 -10000 0 0
NCAPG -0.15 0.14 -9999 0 -0.28 497 497
Aurora B/HC8 Proteasome -0.094 0.091 -9999 0 -10000 0 0
NCAPD2 -0.002 0.026 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.094 0.091 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.12 0.14 -9999 0 -0.28 397 397
NPM1 -0.012 0.019 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.002 0.039 -9999 0 -0.82 2 2
mitotic prometaphase -0.006 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.094 0.091 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.11 0.1 -9999 0 -0.34 16 16
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.019 -9999 0 -10000 0 0
MYLK -0.077 0.14 -9999 0 -0.47 96 96
KIF23 -0.092 0.13 -9999 0 -10000 0 0
VIM -0.091 0.1 -9999 0 -0.71 2 2
RACGAP1 -0.013 0.061 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.019 -9999 0 -10000 0 0
Chromosomal passenger complex -0.077 0.063 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.15 0.17 -9999 0 -10000 0 0
TACC1 -0.023 0.14 -9999 0 -0.82 25 25
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.022 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.01 0.038 -9999 0 -0.3 2 2
PDE6G/GNAT1/GTP -0.008 0.034 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.033 -9999 0 -10000 0 0
GRK1 -0.003 0.029 -9999 0 -0.28 10 10
CNG Channel -0.15 0.21 -9999 0 -0.46 276 276
mol:Na + -0.14 0.2 -9999 0 -0.44 271 271
mol:ADP -0.003 0.029 -9999 0 -0.28 10 10
RGS9-1/Gbeta5/R9AP -0.067 0.17 -9999 0 -0.56 97 97
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.14 0.2 -9999 0 -0.45 271 271
CNGB1 -0.014 0.062 -9999 0 -0.28 47 47
RDH5 -0.52 0.4 -9999 0 -0.82 573 573
SAG -0.014 0.061 -9999 0 -0.28 46 46
mol:Ca2+ -0.13 0.19 -9999 0 -0.42 270 270
Na + (4 Units) -0.13 0.18 -9999 0 -0.41 270 270
RGS9 -0.091 0.26 -9999 0 -0.77 107 107
GNB1/GNGT1 -0.028 0.064 -9999 0 -10000 0 0
GNAT1/GDP -0.059 0.15 -9999 0 -0.49 97 97
GUCY2D -0.005 0.049 -9999 0 -0.36 13 13
GNGT1 -0.044 0.1 -9999 0 -0.28 144 144
GUCY2F -0.001 0.013 -9999 0 -0.28 2 2
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.018 0.073 -9999 0 -0.48 19 19
mol:11-cis-retinal -0.52 0.4 -9999 0 -0.82 573 573
mol:cGMP -0.01 0.049 -9999 0 -0.48 7 7
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.4 0.31 -9999 0 -0.64 573 573
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.24 0.38 -9999 0 -0.82 272 272
Metarhodopsin II -0.003 0.021 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.011 0.052 -9999 0 -0.51 7 7
RGS9BP -0.016 0.064 -9999 0 -0.28 51 51
Metarhodopsin II/Transducin -0.008 0.018 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.009 0.046 -9999 0 -0.52 5 5
PDE6A/B -0.017 0.094 -9999 0 -0.64 19 19
mol:Pi -0.067 0.17 -9999 0 -0.56 97 97
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.021 0.047 -9999 0 -10000 0 0
PDE6B -0.017 0.12 -9999 0 -0.8 20 20
PDE6A -0.006 0.042 -9999 0 -0.28 21 21
PDE6G -0.011 0.055 -9999 0 -10000 0 0
RHO -0.004 0.034 -9999 0 -0.28 14 14
PDE6 -0.068 0.16 -9999 0 -0.47 112 112
GUCA1A -0.012 0.058 -9999 0 -10000 0 0
GC2/GCAP Family -0.009 0.046 -9999 0 -0.52 5 5
GUCA1C 0 0.009 -9999 0 -10000 0 0
GUCA1B -0.005 0.061 -9999 0 -0.82 5 5
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.11 0.24 -10000 0 -0.63 154 154
CRKL -0.04 0.16 -10000 0 -0.36 154 154
mol:PIP3 -0.017 0.039 0.81 2 -10000 0 2
AKT1 0.004 0.024 0.5 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.031 0.15 -10000 0 -0.56 18 18
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.13 0.25 -10000 0 -0.59 193 193
MAP3K5 -0.021 0.15 -10000 0 -0.54 20 20
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.23 -10000 0 -0.54 193 193
AP1 -0.2 0.28 -10000 0 -0.61 284 284
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.24 0.37 -10000 0 -0.78 284 284
STAT3 (dimer) -0.073 0.15 -10000 0 -0.34 193 193
GAB1/CRKL/SHP2/PI3K -0.061 0.12 -10000 0 -0.52 19 19
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.066 0.13 -10000 0 -0.56 18 18
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.039 -10000 0 -0.82 2 2
ELK1 -0.044 0.1 -10000 0 -0.28 154 154
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.046 0.095 -10000 0 -0.43 18 18
PAK1 0.009 0.029 0.46 2 -10000 0 2
HGF/MET/RANBP10 -0.13 0.25 -10000 0 -0.59 193 193
HRAS -0.15 0.3 -10000 0 -0.71 193 193
DOCK1 -0.031 0.15 -10000 0 -0.56 18 18
GAB1 -0.051 0.17 -10000 0 -0.36 193 193
CRK -0.04 0.16 -10000 0 -0.36 154 154
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.15 0.31 -10000 0 -0.73 193 193
JUN -0.008 0.081 -10000 0 -0.82 9 9
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.078 0.16 -10000 0 -0.37 193 193
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
cell morphogenesis -0.015 0.17 -10000 0 -0.6 18 18
GRB2/SHC -0.067 0.14 -10000 0 -0.34 154 154
FOS -0.26 0.38 -10000 0 -0.82 283 283
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.044 0.1 -10000 0 -0.28 154 154
HGF/MET/MUC20 -0.13 0.26 -10000 0 -0.6 193 193
cell migration -0.066 0.13 -10000 0 -0.34 154 154
GRB2 0 0.009 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.11 0.24 -10000 0 -0.63 154 154
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.077 0.16 -10000 0 -0.36 193 193
MET/MUC20 -0.11 0.24 -10000 0 -0.64 154 154
RAP1B -0.021 0.14 -10000 0 -0.51 18 18
RAP1A -0.021 0.14 -10000 0 -0.51 18 18
HGF/MET/RANBP9 -0.13 0.25 -10000 0 -0.59 193 193
RAF1 -0.1 0.3 -10000 0 -0.73 154 154
STAT3 -0.073 0.15 -10000 0 -0.35 193 193
cell proliferation -0.061 0.23 -10000 0 -0.5 193 193
RPS6KB1 -0.027 0.053 -10000 0 -10000 0 0
MAPK3 -0.044 0.094 -10000 0 -0.25 154 154
MAPK1 -0.044 0.094 -10000 0 -0.25 154 154
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 0 0.13 -10000 0 -0.43 22 22
SRC -0.071 0.14 -10000 0 -0.63 18 18
PI3K -0.067 0.14 -10000 0 -0.34 155 155
MET/Glomulin -0.098 0.22 -10000 0 -0.58 154 154
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.086 0.27 -10000 0 -0.66 154 154
MET -0.14 0.31 -10000 0 -0.82 155 155
MAP4K1 -0.03 0.15 -10000 0 -0.56 20 20
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.086 0.27 -10000 0 -0.66 154 154
BAD 0.011 0.022 0.46 2 -10000 0 2
MAP2K4 -0.011 0.14 -10000 0 -0.47 21 21
SHP2/GRB2/SOS1/GAB1 -0.098 0.2 -10000 0 -0.52 154 154
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.071 0.14 -10000 0 -0.36 154 154
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.051 0.2 -10000 0 -0.82 57 57
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.068 0.14 -10000 0 -0.34 154 154
PDPK1 -0.006 0.028 0.58 2 -10000 0 2
HGF/MET/SHIP -0.13 0.25 -10000 0 -0.59 193 193
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.062 0.17 -10000 0 -0.51 110 110
regulation of S phase of mitotic cell cycle -0.039 0.11 -10000 0 -0.34 104 104
GNAO1 -0.034 0.14 -10000 0 -0.83 24 24
HRAS -0.001 0.013 -10000 0 -0.28 2 2
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.011 0.001 -10000 0 -10000 0 0
MAP2K1 -0.04 0.16 -10000 0 -0.45 104 104
T-DHT/AR -0.074 0.21 -10000 0 -0.65 104 104
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 283 283
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.042 0.18 -10000 0 -0.83 47 47
mol:GDP -0.071 0.2 -10000 0 -0.63 104 104
cell proliferation -0.1 0.24 -10000 0 -0.57 88 88
PIK3CA 0 0.009 -10000 0 -10000 0 0
FOS -0.24 0.43 -10000 0 -0.87 283 283
mol:Ca2+ -0.016 0.028 -10000 0 -0.078 121 121
MAPK3 -0.073 0.2 -10000 0 -0.62 52 52
MAPK1 -0.047 0.12 -10000 0 -0.31 52 52
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
mol:IP3 -0.001 0.002 -10000 0 -0.005 283 283
cAMP biosynthetic process 0.012 0.024 -10000 0 -10000 0 0
GNG2 -0.006 0.072 -10000 0 -0.82 7 7
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 283 283
HRAS/GTP -0.062 0.15 -10000 0 -0.48 104 104
actin cytoskeleton reorganization -0.001 0.015 -10000 0 -0.45 1 1
SRC 0 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 283 283
PI3K -0.001 0.019 -10000 0 -0.56 1 1
apoptosis 0.11 0.23 0.43 283 -10000 0 283
T-DHT/AR/PELP1 -0.064 0.18 -10000 0 -0.56 104 104
HRAS/GDP -0.068 0.19 -10000 0 -0.59 104 104
CREB1 -0.12 0.25 -10000 0 -0.46 283 283
RAC1-CDC42/GTP -0.001 0.015 -10000 0 -0.45 1 1
AR -0.095 0.26 -10000 0 -0.83 104 104
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.04 0.16 -10000 0 -0.47 104 104
RAC1-CDC42/GDP -0.064 0.18 -10000 0 -0.56 104 104
T-DHT/AR/PELP1/Src -0.059 0.16 -10000 0 -0.52 104 104
MAP2K2 -0.04 0.16 -10000 0 -0.45 104 104
T-DHT/AR/PELP1/Src/PI3K -0.039 0.11 -10000 0 -0.35 104 104
GNAZ -0.007 0.077 -10000 0 -0.82 8 8
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.037 0.1 -10000 0 -0.47 33 33
mol:T-DHT -0.001 0.001 0.002 51 -0.003 231 282
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.004 0.068 -10000 0 -0.64 10 10
Gi family/GTP -0.048 0.1 -10000 0 -0.31 78 78
CDC42 0 0 -10000 0 -10000 0 0
Noncanonical Wnt 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
NFATC2 -0.055 0.21 -9999 0 -0.82 61 61
GNB1/GNG2 -0.15 0.24 -9999 0 -0.71 94 94
mol:DAG -0.13 0.21 -9999 0 -0.62 94 94
PLCG1 -0.14 0.22 -9999 0 -0.66 94 94
YES1 -0.16 0.24 -9999 0 -0.69 100 100
FZD3 -0.009 0.086 -9999 0 -0.82 10 10
FZD6 -0.006 0.072 -9999 0 -0.82 7 7
G protein -0.14 0.22 -9999 0 -0.66 95 95
MAP3K7 -0.074 0.19 -9999 0 -0.5 93 93
mol:Ca2+ -0.13 0.2 -9999 0 -0.6 94 94
mol:IP3 -0.13 0.21 -9999 0 -0.62 94 94
NLK -0.006 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.088 0.21 -9999 0 -0.55 94 94
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.17 0.26 -9999 0 -0.46 332 332
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.16 0.24 -9999 0 -0.69 101 101
GO:0007205 -0.1 0.22 -9999 0 -0.61 94 94
WNT6 -0.17 0.33 -9999 0 -0.82 181 181
WNT4 -0.024 0.13 -9999 0 -0.82 20 20
NFAT1/CK1 alpha -0.16 0.23 -9999 0 -0.64 119 119
GNG2 -0.006 0.072 -9999 0 -0.82 7 7
WNT5A -0.013 0.094 -9999 0 -0.58 20 20
WNT11 -0.19 0.34 -9999 0 -0.82 203 203
CDC42 -0.12 0.24 -9999 0 -0.68 90 90
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0.009 -9999 0 -0.28 1 1
CCL5 -0.014 0.078 -9999 0 -0.36 35 35
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.074 0.11 -9999 0 -0.34 91 91
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.068 0.099 -9999 0 -0.36 37 37
Syndecan-1/Syntenin -0.068 0.099 -9999 0 -0.36 37 37
MAPK3 -0.051 0.09 -9999 0 -0.49 5 5
HGF/MET -0.14 0.29 -9999 0 -0.68 193 193
TGFB1/TGF beta receptor Type II 0 0.009 -9999 0 -0.28 1 1
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.067 0.098 -9999 0 -0.35 37 37
Syndecan-1/RANTES -0.074 0.11 -9999 0 -0.4 40 40
Syndecan-1/CD147 -0.059 0.096 -9999 0 -0.52 5 5
Syndecan-1/Syntenin/PIP2 -0.065 0.095 -9999 0 -0.34 37 37
LAMA5 0 0.009 -9999 0 -0.28 1 1
positive regulation of cell-cell adhesion -0.064 0.094 -9999 0 -0.34 37 37
MMP7 -0.12 0.29 -9999 0 -0.73 155 155
HGF -0.051 0.2 -9999 0 -0.82 57 57
Syndecan-1/CASK -0.07 0.1 -9999 0 -0.33 91 91
Syndecan-1/HGF/MET -0.17 0.26 -9999 0 -0.61 195 195
regulation of cell adhesion -0.037 0.093 -9999 0 -0.5 4 4
HPSE -0.007 0.054 -9999 0 -0.33 20 20
positive regulation of cell migration -0.074 0.11 -9999 0 -0.34 91 91
SDC1 -0.074 0.11 -9999 0 -0.35 91 91
Syndecan-1/Collagen -0.074 0.11 -9999 0 -0.34 91 91
PPIB -0.001 0.016 -9999 0 -0.28 3 3
MET -0.14 0.31 -9999 0 -0.82 155 155
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.28 411 411
MAPK1 -0.051 0.09 -9999 0 -0.49 5 5
homophilic cell adhesion -0.073 0.11 -9999 0 -0.34 91 91
MMP1 -0.21 0.12 -9999 0 -0.28 702 702
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.23 0.28 -10000 0 -0.56 376 376
fibroblast growth factor receptor signaling pathway -0.23 0.27 -10000 0 -0.55 376 376
LAMA1 -0.096 0.26 -10000 0 -0.82 106 106
PRNP -0.011 0.094 -10000 0 -0.82 12 12
GPC1/SLIT2 -0.057 0.18 -10000 0 -0.63 81 81
SMAD2 -0.017 0.089 -10000 0 -0.5 30 30
GPC1/PrPc/Cu2+ -0.008 0.066 -10000 0 -0.56 13 13
GPC1/Laminin alpha1 -0.075 0.2 -10000 0 -0.63 107 107
TDGF1 -0.009 0.086 -10000 0 -0.82 10 10
CRIPTO/GPC1 -0.008 0.07 -10000 0 -0.63 11 11
APP/GPC1 -0.001 0.023 -10000 0 -0.63 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.017 0.066 -10000 0 -0.55 12 12
FLT1 -0.001 0.027 -10000 0 -0.82 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.019 0.098 -10000 0 -0.55 30 30
SERPINC1 -0.013 0.06 -10000 0 -10000 0 0
FYN 0.017 0.066 -10000 0 -0.55 12 12
FGR 0.017 0.066 -10000 0 -0.55 12 12
positive regulation of MAPKKK cascade 0.03 0.077 -10000 0 -0.54 12 12
SLIT2 -0.072 0.23 -10000 0 -0.82 80 80
GPC1/NRG -0.23 0.3 -10000 0 -0.63 333 333
NRG1 -0.3 0.4 -10000 0 -0.82 336 336
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.03 -10000 0 -0.55 2 2
LYN 0.018 0.063 -10000 0 -0.55 11 11
mol:Spermine 0.01 0.024 -10000 0 -0.64 1 1
cell growth -0.23 0.27 -10000 0 -0.55 376 376
BMP signaling pathway 0.002 0.032 0.82 1 -10000 0 1
SRC 0.018 0.063 -10000 0 -0.55 11 11
TGFBR1 0 0.009 -10000 0 -0.28 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.28 0.39 -10000 0 -0.82 306 306
GPC1 -0.002 0.032 -10000 0 -0.82 1 1
TGFBR1 (dimer) 0 0.009 -10000 0 -0.28 1 1
VEGFA -0.003 0.028 -10000 0 -0.28 9 9
BLK -0.006 0.09 -10000 0 -0.58 13 13
HCK 0.016 0.066 -10000 0 -0.55 11 11
FGF2 -0.33 0.4 -10000 0 -0.82 370 370
FGFR1 -0.01 0.087 -10000 0 -0.73 12 12
VEGFR1 homodimer -0.001 0.027 -10000 0 -0.82 1 1
TGFBR2 -0.026 0.14 -10000 0 -0.82 29 29
cell death -0.001 0.023 -10000 0 -0.63 1 1
ATIII/GPC1 -0.01 0.044 -10000 0 -0.64 1 1
PLA2G2A/GPC1 -0.22 0.3 -10000 0 -0.64 306 306
LCK 0.006 0.093 -10000 0 -0.56 22 22
neuron differentiation -0.23 0.3 -10000 0 -0.63 333 333
PrPc/Cu2+ -0.008 0.073 -10000 0 -0.64 12 12
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.026 0.14 -10000 0 -0.82 29 29
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.035 0.051 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.08 0.16 -9999 0 -0.48 76 76
JUN -0.05 0.15 -9999 0 -0.57 21 21
HRAS -0.001 0.013 -9999 0 -0.28 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.21 -9999 0 -0.55 169 169
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.029 -9999 0 -0.28 10 10
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.21 -9999 0 -0.55 169 169
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.1 0.19 -9999 0 -0.52 160 160
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.19 -9999 0 -0.5 166 166
GRB7 -0.021 0.076 -9999 0 -0.82 1 1
RET51/GFRalpha1/GDNF -0.15 0.21 -9999 0 -0.55 169 169
MAPKKK cascade -0.097 0.17 -9999 0 -0.56 41 41
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.24 -9999 0 -0.59 169 169
lamellipodium assembly -0.079 0.15 -9999 0 -0.37 166 166
RET51/GFRalpha1/GDNF/SHC -0.15 0.21 -9999 0 -0.55 169 169
PIK3CA 0 0.009 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.52 160 160
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.52 160 160
MAPK3 -0.12 0.18 -9999 0 -0.47 166 166
DOK1 0 0.009 -9999 0 -10000 0 0
DOK6 -0.01 0.084 -9999 0 -0.82 9 9
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.56 44 44
DOK5 -0.017 0.11 -9999 0 -0.7 22 22
GFRA1 -0.16 0.31 -9999 0 -0.68 215 215
MAPK8 -0.073 0.14 -9999 0 -0.48 29 29
HRAS/GTP -0.1 0.2 -9999 0 -0.51 166 166
tube development -0.096 0.18 -9999 0 -0.48 160 160
MAPK1 -0.12 0.18 -9999 0 -0.47 166 166
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.064 0.13 -9999 0 -0.34 160 160
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.15 0.2 -9999 0 -0.53 171 171
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.21 -9999 0 -0.55 169 169
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.57 182 182
PRKCA -0.02 0.12 -9999 0 -0.78 23 23
HRAS/GDP 0 0.009 -9999 0 -10000 0 0
CREB1 -0.071 0.15 -9999 0 -0.39 160 160
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.064 0.13 -9999 0 -0.34 160 160
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.22 -9999 0 -0.57 171 171
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.16 -9999 0 -0.82 15 15
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.049 0.14 -9999 0 -0.55 21 21
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.52 160 160
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.064 0.13 -9999 0 -0.35 160 160
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.081 0.14 -9999 0 -0.37 166 166
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.081 0.14 -9999 0 -0.46 40 40
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.083 0.15 -9999 0 -0.38 166 166
PI3K -0.13 0.25 -9999 0 -0.6 168 168
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.096 0.18 -9999 0 -0.48 160 160
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.077 0.13 -9999 0 -0.35 160 160
RET51/GFRalpha1/GDNF/FRS2 -0.16 0.21 -9999 0 -0.55 169 169
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.82 36 36
IRS2 -0.034 0.16 -9999 0 -0.82 38 38
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.083 0.15 -9999 0 -0.38 166 166
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.22 -9999 0 -0.56 190 190
GRB2 0 0.009 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.016 0.064 -9999 0 -0.28 51 51
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.25 -9999 0 -0.63 177 177
Rac1/GTP -0.096 0.18 -9999 0 -0.46 166 166
RET9/GFRalpha1/GDNF -0.12 0.21 -9999 0 -0.56 164 164
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.64 164 164
Aurora C signaling

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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.072 0.064 -9999 0 -0.63 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.019 0.017 -9999 0 -10000 0 0
AURKB -0.16 0.14 -9999 0 -0.28 531 531
AURKC -0.005 0.043 -9999 0 -0.32 14 14
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.096 0.18 -10000 0 -0.49 158 158
ER alpha/Gai/GDP/Gbeta gamma -0.089 0.19 -10000 0 -0.48 151 151
AKT1 -0.12 0.3 -10000 0 -0.85 131 131
PIK3CA 0 0.009 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.3 -10000 0 -0.86 131 131
mol:Ca2+ -0.026 0.15 -10000 0 -0.48 68 68
IGF1R -0.022 0.12 -10000 0 -0.61 33 33
E2/ER alpha (dimer)/Striatin -0.1 0.2 -10000 0 -0.56 136 136
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.085 0.3 0.81 131 -10000 0 131
RhoA/GTP -0.07 0.14 -10000 0 -0.42 131 131
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.089 0.21 -10000 0 -0.56 137 137
regulation of stress fiber formation 0.017 0.14 0.52 4 -10000 0 4
E2/ERA-ERB (dimer) -0.11 0.21 -10000 0 -0.56 152 152
KRAS 0 0.009 -10000 0 -10000 0 0
G13/GTP -0.09 0.18 -10000 0 -0.51 131 131
pseudopodium formation -0.017 0.14 -10000 0 -0.52 4 4
E2/ER alpha (dimer)/PELP1 -0.098 0.19 -10000 0 -0.56 131 131
GRB2 0 0.009 -10000 0 -10000 0 0
GNG2 -0.006 0.072 -10000 0 -0.82 7 7
GNAO1 -0.034 0.14 -10000 0 -0.82 24 24
HRAS -0.001 0.013 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.057 0.22 -10000 0 -0.55 138 138
E2/ER beta (dimer) -0.015 0.098 -10000 0 -0.64 22 22
mol:GDP -0.085 0.21 -10000 0 -0.55 152 152
mol:NADP -0.057 0.22 -10000 0 -0.55 138 138
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
mol:IP3 -0.028 0.15 -10000 0 -0.5 68 68
IGF-1R heterotetramer -0.022 0.12 -10000 0 -0.61 33 33
PLCB1 -0.062 0.14 -10000 0 -0.52 67 67
PLCB2 -0.034 0.092 -10000 0 -0.65 12 12
IGF1 -0.18 0.34 -10000 0 -0.82 197 197
mol:L-citrulline -0.057 0.22 -10000 0 -0.55 138 138
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.04 0.16 -10000 0 -0.86 24 24
JNK cascade -0.015 0.098 -10000 0 -0.64 22 22
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.02 0.13 -10000 0 -0.82 22 22
GNAQ -0.002 0.039 -10000 0 -0.82 2 2
ESR1 -0.15 0.29 -10000 0 -0.57 248 248
Gq family/GDP/Gbeta gamma -0.006 0.072 -10000 0 -0.74 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.023 0.13 -10000 0 -0.36 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.089 0.21 -10000 0 -0.56 137 137
GNAZ -0.007 0.077 -10000 0 -0.82 8 8
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.64 131 131
STRN -0.006 0.072 -10000 0 -0.82 7 7
GNAL -0.19 0.35 -10000 0 -0.82 210 210
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.003 0.094 -10000 0 -0.58 23 23
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.042 0.18 -10000 0 -0.82 47 47
HBEGF -0.067 0.19 -10000 0 -0.45 142 142
cAMP biosynthetic process -0.19 0.26 -10000 0 -0.53 319 319
SRC -0.049 0.2 -10000 0 -0.46 140 140
PI3K -0.001 0.022 -10000 0 -0.63 1 1
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.076 0.19 -10000 0 -0.49 143 143
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.52 205 205
Gs family/GTP -0.2 0.27 -10000 0 -0.54 319 319
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.009 -10000 0 -10000 0 0
vasodilation -0.053 0.21 -10000 0 -0.52 138 138
mol:DAG -0.028 0.15 -10000 0 -0.5 68 68
Gs family/GDP/Gbeta gamma -0.16 0.23 -10000 0 -0.52 193 193
MSN -0.02 0.14 -10000 0 -0.58 4 4
Gq family/GTP -0.037 0.096 -10000 0 -0.69 11 11
mol:PI-3-4-5-P3 -0.09 0.3 -10000 0 -0.82 131 131
NRAS -0.001 0.013 -10000 0 -0.28 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.053 0.21 0.52 138 -10000 0 138
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.078 0.2 -10000 0 -0.51 152 152
NOS3 -0.061 0.23 -10000 0 -0.59 137 137
GNA11 -0.002 0.039 -10000 0 -0.82 2 2
MAPKKK cascade -0.059 0.25 -10000 0 -0.65 136 136
E2/ER alpha (dimer)/PELP1/Src -0.094 0.22 -10000 0 -0.59 137 137
ruffle organization -0.017 0.14 -10000 0 -0.52 4 4
ROCK2 -0.068 0.14 -10000 0 -0.39 139 139
GNA14 -0.014 0.087 -10000 0 -0.42 30 30
GNA15 -0.003 0.035 -10000 0 -0.36 7 7
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.093 0.2 -10000 0 -0.49 145 145
MMP2 -0.041 0.19 -10000 0 -0.68 27 27
IL6-mediated signaling events

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
BCL2L1 -0.056 0.22 -9999 0 -0.63 46 46
CRP -0.06 0.22 -9999 0 -0.63 46 46
cell cycle arrest -0.074 0.24 -9999 0 -0.71 53 53
TIMP1 -0.055 0.2 -9999 0 -0.56 48 48
IL6ST -0.059 0.24 -9999 0 -0.82 79 79
Rac1/GDP -0.14 0.2 -9999 0 -0.66 64 64
AP1 -0.14 0.24 -9999 0 -0.5 239 239
GAB2 -0.002 0.026 -9999 0 -10000 0 0
TNFSF11 -0.066 0.22 -9999 0 -0.63 46 46
HSP90B1 0.017 0.047 -9999 0 -10000 0 0
GAB1 0 0.002 -9999 0 -10000 0 0
MAPK14 -0.12 0.24 -9999 0 -0.74 67 67
AKT1 0.04 0.027 -9999 0 -10000 0 0
FOXO1 0.05 0.049 -9999 0 -0.43 8 8
MAP2K6 -0.14 0.25 -9999 0 -0.67 91 91
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.076 0.22 -9999 0 -0.64 61 61
MITF -0.13 0.25 -9999 0 -0.48 169 169
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M 0.015 0.11 -9999 0 -1.5 5 5
CEBPB 0.015 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.052 0.07 -9999 0 -10000 0 0
STAT3 -0.081 0.26 -9999 0 -0.77 54 54
STAT1 -0.012 0.023 -9999 0 -10000 0 0
CEBPD -0.058 0.22 -9999 0 -0.66 46 46
PIK3CA 0.01 0.01 -9999 0 -10000 0 0
PI3K -0.001 0.022 -9999 0 -0.63 1 1
JUN -0.008 0.082 -9999 0 -0.82 9 9
PIAS3/MITF -0.15 0.21 -9999 0 -0.67 66 66
MAPK11 -0.12 0.24 -9999 0 -0.75 67 67
STAT3 (dimer)/FOXO1 -0.024 0.22 -9999 0 -0.57 53 53
GRB2/SOS1/GAB family -0.13 0.19 -9999 0 -0.75 42 42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.15 0.24 -9999 0 -0.44 234 234
GRB2 0 0.009 -9999 0 -10000 0 0
JAK2 -0.001 0.027 -9999 0 -0.82 1 1
LBP -0.23 0.45 -9999 0 -0.96 226 226
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
JAK1 0 0.002 -9999 0 -10000 0 0
MYC -0.07 0.26 -9999 0 -0.8 56 56
FGG -0.065 0.22 -9999 0 -0.63 48 48
macrophage differentiation -0.074 0.24 -9999 0 -0.71 53 53
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.22 0.28 -9999 0 -0.51 398 398
JUNB -0.055 0.21 -9999 0 -0.61 46 46
FOS -0.26 0.38 -9999 0 -0.83 283 283
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.14 0.25 -9999 0 -0.46 231 231
STAT1/PIAS1 -0.14 0.2 -9999 0 -0.57 91 91
GRB2/SOS1/GAB family/SHP2/PI3K 0.001 0.013 -9999 0 -10000 0 0
STAT3 (dimer) -0.076 0.25 -9999 0 -0.75 53 53
PRKCD -0.052 0.22 -9999 0 -0.6 59 59
IL6R -0.022 0.13 -9999 0 -0.82 25 25
SOCS3 -0.12 0.24 -9999 0 -0.79 58 58
gp130 (dimer)/JAK1/JAK1/LMO4 -0.04 0.16 -9999 0 -0.55 82 82
Rac1/GTP -0.14 0.2 -9999 0 -0.64 69 69
HCK -0.004 0.032 -9999 0 -0.28 12 12
MAPKKK cascade -0.001 0.069 -9999 0 -10000 0 0
bone resorption -0.062 0.21 -9999 0 -0.6 47 47
IRF1 -0.057 0.22 -9999 0 -0.62 50 50
mol:GDP -0.12 0.24 -9999 0 -0.47 169 169
SOS1 0 0.002 -9999 0 -10000 0 0
VAV1 -0.12 0.24 -9999 0 -0.48 169 169
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.23 -9999 0 -0.8 63 63
PTPN11 -0.013 0.02 -9999 0 -10000 0 0
IL6/IL6RA -0.25 0.32 -9999 0 -0.65 349 349
gp130 (dimer)/TYK2/TYK2/LMO4 -0.043 0.16 -9999 0 -0.55 82 82
gp130 (dimer)/JAK2/JAK2/LMO4 -0.044 0.16 -9999 0 -0.55 82 82
IL6 -0.3 0.4 -9999 0 -0.82 338 338
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.002 0.028 -9999 0 -0.83 1 1
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.17 0.23 -9999 0 -0.4 397 397
LMO4 0.008 0.054 -9999 0 -0.82 3 3
STAT3 (dimer)/PIAS3 -0.14 0.2 -9999 0 -0.77 53 53
MCL1 0.053 0.016 -9999 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.023 0.061 -9999 0 -0.59 8 8
alphaM/beta2 Integrin/GPIbA -0.025 0.062 -9999 0 -0.57 8 8
alphaM/beta2 Integrin/proMMP-9 -0.081 0.079 -9999 0 -0.42 5 5
PLAUR -0.021 0.073 -9999 0 -0.28 68 68
HMGB1 -0.014 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.018 0.028 -9999 0 -10000 0 0
AGER -0.015 0.044 -9999 0 -0.88 2 2
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG 0 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.076 0.099 -9999 0 -0.72 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.28 411 411
CYR61 -0.046 0.19 -9999 0 -0.82 51 51
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.058 0.11 -9999 0 -0.54 20 20
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.2 0.35 -9999 0 -0.82 217 217
MYH2 -0.07 0.17 -9999 0 -0.43 84 84
MST1R -0.01 0.085 -9999 0 -0.59 16 16
leukocyte activation during inflammatory response -0.32 0.23 -9999 0 -0.49 586 586
APOB -0.53 0.4 -9999 0 -0.82 586 586
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.007 0.077 -9999 0 -0.82 8 8
JAM3 -0.004 0.054 -9999 0 -0.82 4 4
GP1BA -0.013 0.083 -9999 0 -0.82 7 7
alphaM/beta2 Integrin/CTGF -0.025 0.07 -9999 0 -0.61 11 11
alphaM/beta2 Integrin -0.073 0.14 -9999 0 -0.37 84 84
JAM3 homodimer -0.004 0.054 -9999 0 -0.82 4 4
ICAM2 -0.005 0.061 -9999 0 -0.82 5 5
ICAM1 -0.004 0.032 -9999 0 -0.28 12 12
phagocytosis triggered by activation of immune response cell surface activating receptor -0.062 0.14 -9999 0 -0.3 173 173
cell adhesion -0.025 0.062 -9999 0 -0.57 8 8
NFKB1 -0.14 0.18 -9999 0 -0.66 14 14
THY1 -0.002 0.022 -9999 0 -0.28 6 6
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.36 0.27 -9999 0 -0.56 586 586
alphaM/beta2 Integrin/LRP/tPA -0.034 0.11 -9999 0 -0.57 36 36
IL6 -0.32 0.49 -9999 0 -0.96 338 338
ITGB2 -0.017 0.036 -9999 0 -0.31 5 5
elevation of cytosolic calcium ion concentration -0.025 0.048 -9999 0 -0.38 1 1
alphaM/beta2 Integrin/JAM2/JAM3 -0.041 0.13 -9999 0 -0.55 50 50
JAM2 -0.043 0.18 -9999 0 -0.82 48 48
alphaM/beta2 Integrin/ICAM1 -0.022 0.083 -9999 0 -0.54 19 19
alphaM/beta2 Integrin/uPA/Plg -0.02 0.033 -9999 0 -10000 0 0
RhoA/GTP -0.087 0.17 -9999 0 -0.39 183 183
positive regulation of phagocytosis -0.05 0.092 -9999 0 -0.47 17 17
Ron/MSP -0.016 0.1 -9999 0 -0.69 19 19
alphaM/beta2 Integrin/uPAR/uPA -0.025 0.048 -9999 0 -0.38 1 1
alphaM/beta2 Integrin/uPAR -0.028 0.045 -9999 0 -0.42 1 1
PLAU -0.009 0.048 -9999 0 -10000 0 0
PLAT -0.027 0.14 -9999 0 -0.77 32 32
actin filament polymerization -0.067 0.16 -9999 0 -0.4 94 94
MST1 -0.011 0.095 -9999 0 -0.75 14 14
alphaM/beta2 Integrin/lipoprotein(a) -0.33 0.23 -9999 0 -0.5 586 586
TNF -0.093 0.23 -9999 0 -0.97 18 18
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.022 0.037 -9999 0 -10000 0 0
fibrinolysis -0.02 0.033 -9999 0 -10000 0 0
HCK -0.004 0.032 -9999 0 -0.28 12 12
dendritic cell antigen processing and presentation -0.062 0.14 -9999 0 -0.3 173 173
VTN -0.023 0.092 -9999 0 -0.32 67 67
alphaM/beta2 Integrin/CYR61 -0.049 0.14 -9999 0 -0.6 51 51
LPA -0.001 0.018 -9999 0 -0.28 4 4
LRP1 -0.009 0.086 -9999 0 -0.82 10 10
cell migration -0.07 0.081 -9999 0 -0.54 9 9
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.019 0.03 -9999 0 -10000 0 0
MPO -0.057 0.21 -9999 0 -0.81 65 65
KNG1 -0.004 0.032 -9999 0 -0.28 12 12
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.065 0.17 -9999 0 -0.4 109 109
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.018 -9999 0 -0.28 4 4
CTGF -0.011 0.091 -9999 0 -0.74 13 13
alphaM/beta2 Integrin/Hck -0.02 0.034 -9999 0 -10000 0 0
ITGAM -0.015 0.029 -9999 0 -0.34 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.13 0.22 -9999 0 -0.53 217 217
HP -0.16 0.32 -9999 0 -0.74 200 200
leukocyte adhesion -0.075 0.13 -9999 0 -0.6 32 32
SELP -0.2 0.35 -9999 0 -0.82 217 217
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.018 0.031 -9999 0 -10000 0 0
VDR 0 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.041 0.17 -9999 0 -0.32 233 233
RXRs/LXRs/DNA/Oxysterols -0.02 0.15 -9999 0 -0.5 17 17
MED1 -0.007 0.044 -9999 0 -0.28 23 23
mol:9cRA 0.005 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.02 0.086 -9999 0 -0.37 48 48
RXRs/NUR77 -0.17 0.26 -9999 0 -0.53 289 289
RXRs/PPAR -0.14 0.23 -9999 0 -0.39 378 378
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.007 0.051 -9999 0 -0.47 10 10
RARA -0.004 0.033 -9999 0 -10000 0 0
NCOA1 -0.001 0.027 -9999 0 -0.82 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.007 0.051 -9999 0 -0.48 10 10
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.031 0.054 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.019 0.081 -9999 0 -0.35 48 48
THRA -0.001 0.027 -9999 0 -0.82 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.13 0.22 -9999 0 -0.49 232 232
NR1H4 -0.002 0.024 -9999 0 -10000 0 0
RXRs/LXRs/DNA -0.12 0.2 -9999 0 -0.45 232 232
NR1H2 0.016 0.006 -9999 0 -10000 0 0
NR1H3 0.016 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.2 -9999 0 -0.46 232 232
NR4A1 -0.074 0.24 -9999 0 -0.82 82 82
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.048 0.14 -9999 0 -0.28 232 232
RXRG -0.2 0.36 -9999 0 -0.82 232 232
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.016 0.006 -9999 0 -10000 0 0
RXRB 0.015 0.007 -9999 0 -10000 0 0
THRB -0.036 0.17 -9999 0 -0.82 40 40
PPARG -0.19 0.35 -9999 0 -0.82 209 209
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.023 0.2 -9999 0 -1.3 14 14
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.019 0.15 -9999 0 -0.43 28 28
PPARA -0.003 0.047 -9999 0 -0.82 3 3
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.009 0.086 -9999 0 -0.82 10 10
RXRs/NUR77/BCL2 -0.13 0.2 -9999 0 -0.39 306 306
SREBF1 -0.01 0.14 -9999 0 -0.68 5 5
RXRs/RXRs/DNA/9cRA -0.13 0.22 -9999 0 -0.49 232 232
ABCA1 -0.012 0.16 -9999 0 -0.96 8 8
RARs/THRs -0.027 0.11 -9999 0 -0.5 48 48
RXRs/FXR -0.13 0.22 -9999 0 -0.5 232 232
BCL2 -0.027 0.15 -9999 0 -0.82 30 30
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.003 0.034 -9999 0 -0.63 2 2
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.56 377 377
PTK2 -0.088 0.19 -9999 0 -0.67 24 24
IGF1R -0.022 0.12 -9999 0 -0.61 33 33
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.012 0.093 -9999 0 -0.63 17 17
SRC 0 0.009 -9999 0 -10000 0 0
CDKN1B -0.088 0.12 -9999 0 -0.89 8 8
VEGFA -0.003 0.028 -9999 0 -0.28 9 9
ILK -0.085 0.11 -9999 0 -0.78 5 5
ROCK1 0 0 -9999 0 -10000 0 0
AKT1 -0.075 0.098 -9999 0 -0.73 5 5
PTK2B -0.012 0.073 -9999 0 -0.48 20 20
alphaV/beta3 Integrin/JAM-A -0.21 0.25 -9999 0 -0.49 380 380
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.013 0.08 -9999 0 -0.55 19 19
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.26 -9999 0 -0.57 219 219
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.008 0.046 -9999 0 -0.43 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.022 0.087 -9999 0 -0.56 20 20
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.34 0.36 -9999 0 -0.73 337 337
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.049 0.098 -9999 0 -0.57 19 19
RPS6KB1 -0.31 0.33 -9999 0 -0.71 292 292
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.34 0.39 -9999 0 -0.78 377 377
GPR124 -0.007 0.077 -9999 0 -0.82 8 8
MAPK1 -0.34 0.39 -9999 0 -0.78 377 377
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
alphaV/beta3 Integrin/Tumstatin -0.12 0.23 -9999 0 -0.56 192 192
cell adhesion -0.018 0.093 -9999 0 -0.51 29 29
ANGPTL3 -0.002 0.021 -9999 0 -0.28 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.029 -9999 0 -0.55 2 2
IGF-1R heterotetramer -0.022 0.12 -9999 0 -0.61 33 33
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.026 0.14 -9999 0 -0.82 29 29
ITGB3 -0.018 0.12 -9999 0 -0.82 19 19
IGF1 -0.18 0.34 -9999 0 -0.82 197 197
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.017 0.1 -9999 0 -0.61 24 24
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.027 -9999 0 -0.82 1 1
alphaV/beta3 Integrin/CD47 -0.013 0.081 -9999 0 -0.55 20 20
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.034 0.15 -9999 0 -0.69 42 42
CSF1 -0.005 0.067 -9999 0 -0.82 6 6
PIK3C2A -0.085 0.11 -9999 0 -0.78 5 5
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.59 51 51
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.013 0.079 -9999 0 -0.52 20 20
FAK1/Vinculin -0.065 0.15 -9999 0 -0.51 23 23
alphaV beta3/Integrin/ppsTEM5 -0.017 0.1 -9999 0 -0.61 24 24
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.023 0.092 -9999 0 -0.32 67 67
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.33 0.4 -9999 0 -0.82 370 370
F11R -0.24 0.32 -9999 0 -0.63 370 370
alphaV/beta3 Integrin/Lactadherin -0.019 0.1 -9999 0 -0.58 28 28
alphaV/beta3 Integrin/TGFBR2 -0.029 0.14 -9999 0 -0.65 40 40
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.04 -9999 0 -0.5 6 6
HSP90AA1 0 0.009 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.011 0.073 -9999 0 -0.51 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.012 0.074 -9999 0 -0.49 20 20
SDC1 -0.02 0.076 -9999 0 -0.82 1 1
VAV3 -0.008 0.054 -9999 0 -0.46 12 12
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.82 36 36
FAK1/Paxillin -0.065 0.15 -9999 0 -0.51 23 23
cell migration -0.051 0.14 -9999 0 -0.45 23 23
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.22 -9999 0 -0.44 381 381
SPP1 -0.077 0.12 -9999 0 -0.28 254 254
KDR -0.002 0.039 -9999 0 -0.82 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.16 0.32 -9999 0 -0.81 180 180
angiogenesis -0.3 0.39 -9999 0 -0.75 379 379
Rac1/GTP -0.007 0.049 -9999 0 -0.42 12 12
EDIL3 -0.036 0.16 -9999 0 -0.82 35 35
cell proliferation -0.029 0.14 -9999 0 -0.64 40 40
Signaling events mediated by PTP1B

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
PDGFRB -0.002 0.039 -10000 0 -0.82 2 2
Jak2/Leptin Receptor -0.16 0.24 -10000 0 -0.54 234 234
PTP1B/AKT1 -0.067 0.098 -10000 0 -0.32 88 88
FYN -0.001 0.027 -10000 0 -0.82 1 1
p210 bcr-abl/PTP1B -0.068 0.12 -10000 0 -0.37 93 93
EGFR -0.3 0.4 -10000 0 -0.83 331 331
EGF/EGFR -0.3 0.32 -10000 0 -0.59 453 453
CSF1 -0.005 0.067 -10000 0 -0.82 6 6
AKT1 0 0 -10000 0 -10000 0 0
INSR 0 0.009 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.092 0.12 -10000 0 -0.36 92 92
Insulin Receptor/Insulin -0.047 0.072 -10000 0 -0.39 8 8
HCK -0.004 0.032 -10000 0 -0.28 12 12
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.057 0.12 -10000 0 -0.35 90 90
EGF -0.17 0.33 -10000 0 -0.83 183 183
YES1 -0.001 0.027 -10000 0 -0.82 1 1
CAV1 -0.17 0.24 -10000 0 -0.51 235 235
TXN 0 0.013 -10000 0 -0.29 1 1
PTP1B/IRS1/GRB2 -0.084 0.14 -10000 0 -0.5 57 57
cell migration 0.068 0.12 0.37 93 -10000 0 93
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.001 0.036 -10000 0 -0.36 7 7
ITGA2B -0.016 0.076 -10000 0 -0.32 46 46
CSF1R -0.001 0.029 -10000 0 -0.55 2 2
Prolactin Receptor/Prolactin -0.003 0.033 -10000 0 -0.64 1 1
FGR -0.001 0.029 -10000 0 -0.82 1 1
PTP1B/p130 Cas -0.072 0.11 -10000 0 -0.35 89 89
Crk/p130 Cas -0.066 0.1 -10000 0 -0.41 24 24
DOK1 -0.043 0.1 -10000 0 -0.37 26 26
JAK2 -0.039 0.073 -10000 0 -0.33 10 10
Jak2/Leptin Receptor/Leptin -0.38 0.19 -10000 0 -0.51 461 461
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
PTPN1 -0.069 0.12 -10000 0 -0.37 93 93
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.054 0.12 -10000 0 -0.82 2 2
SRC -0.013 0.045 -10000 0 -10000 0 0
ITGB3 -0.018 0.12 -10000 0 -0.83 19 19
CAT1/PTP1B -0.084 0.17 -10000 0 -0.44 81 81
CAPN1 0 0.002 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.037 0.066 -10000 0 -0.45 3 3
mol:H2O2 -0.006 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.33 0.16 -10000 0 -0.45 453 453
negative regulation of transcription -0.039 0.072 -10000 0 -0.33 10 10
FCGR2A 0 0.009 -10000 0 -10000 0 0
FER -0.005 0.068 -10000 0 -0.84 6 6
alphaIIb/beta3 Integrin -0.025 0.1 -10000 0 -0.64 22 22
BLK -0.039 0.1 -10000 0 -0.82 3 3
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0 0.002 -10000 0 -10000 0 0
LEPR -0.2 0.36 -10000 0 -0.83 232 232
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0.009 -10000 0 -10000 0 0
mol:NADPH -0.005 0.005 -10000 0 -10000 0 0
TRPV6 -0.034 0.13 -10000 0 -0.47 17 17
PRL -0.003 0.031 -10000 0 -0.28 11 11
SOCS3 0.015 0.12 -10000 0 -1.5 6 6
SPRY2 -0.092 0.26 -10000 0 -0.84 101 101
Insulin Receptor/Insulin/IRS1 -0.022 0.11 -10000 0 -0.56 36 36
CSF1/CSF1R -0.069 0.11 -10000 0 -0.36 79 79
Ras protein signal transduction 0.036 0.035 -10000 0 -10000 0 0
IRS1 -0.033 0.16 -10000 0 -0.82 36 36
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.67 0.32 -10000 0 -0.83 740 740
STAT5B -0.056 0.1 -10000 0 -0.3 92 92
STAT5A -0.056 0.1 -10000 0 -0.3 94 94
GRB2 0 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.073 0.11 -10000 0 -0.36 91 91
CSN2 0.019 0.03 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -10000 0 0
LAT -0.014 0.053 -10000 0 -0.58 2 2
YBX1 -0.001 0.014 -10000 0 -10000 0 0
LCK -0.018 0.1 -10000 0 -0.43 39 39
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.003 0.038 -10000 0 -0.84 1 1
Ephrin A reverse 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
MAPKKK cascade -0.055 0.17 -9999 0 -0.56 89 89
EFNA5 -0.081 0.24 -9999 0 -0.82 89 89
FYN -0.051 0.15 -9999 0 -0.51 89 89
neuron projection morphogenesis -0.055 0.17 -9999 0 -0.56 89 89
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.055 0.17 -9999 0 -0.56 89 89
EPHA5 -0.001 0.018 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.003 0.028 -9999 0 -0.28 9 9
Syndecan-3/Src/Cortactin -0.19 0.21 -9999 0 -0.43 403 403
Syndecan-3/Neurocan -0.007 0.026 -9999 0 -10000 0 0
POMC -0.024 0.12 -9999 0 -0.48 45 45
EGFR -0.3 0.4 -9999 0 -0.82 331 331
Syndecan-3/EGFR -0.17 0.22 -9999 0 -0.47 326 326
AGRP -0.002 0.026 -9999 0 -10000 0 0
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0.009 -9999 0 -0.28 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.027 -9999 0 -0.82 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.019 0.07 -9999 0 -0.28 61 61
long-term memory -0.001 0.017 -9999 0 -0.44 1 1
Syndecan-3/IL8 -0.016 0.069 -9999 0 -0.47 18 18
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.001 0.027 -9999 0 -0.82 1 1
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.003 0.03 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
PTN -0.36 0.41 -9999 0 -0.82 404 404
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.19 0.21 -9999 0 -0.42 403 403
Syndecan-3/AgRP -0.001 0.01 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.014 -9999 0 -10000 0 0
Fyn/Cortactin -0.002 0.027 -9999 0 -0.63 1 1
SDC3 0 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.016 0.068 -9999 0 -0.46 18 18
IL8 -0.034 0.13 -9999 0 -0.41 77 77
Syndecan-3/Fyn/Cortactin -0.001 0.017 -9999 0 -0.45 1 1
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.02 0.093 -9999 0 -0.62 18 18
Gamma Secretase -0.001 0.016 -9999 0 -0.47 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.014 0.086 -9999 0 -0.56 19 19
NF kappa B1 p50/RelA/I kappa B alpha -0.046 0.12 -9999 0 -0.42 11 11
AP1 -0.2 0.27 -9999 0 -0.5 361 361
mol:PIP3 -0.2 0.25 -9999 0 -0.48 371 371
AKT1 -0.009 0.057 -9999 0 -0.58 3 3
PTK2B 0.015 0.059 -9999 0 -0.31 16 16
RHOA 0.029 0.025 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.01 0.14 -9999 0 -0.37 111 111
MAGI3 -0.001 0.027 -9999 0 -0.82 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.063 0.15 -9999 0 -0.43 128 128
HRAS/GDP 0 0.009 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.019 0.15 -9999 0 -0.43 96 96
NF kappa B1 p50/RelA -0.054 0.14 -9999 0 -0.53 16 16
endothelial cell migration 0.011 0.11 -9999 0 -0.66 22 22
ADCY4 -0.001 0.15 -9999 0 -0.66 29 29
ADCY5 -0.069 0.19 -9999 0 -0.62 59 59
ADCY6 0.009 0.12 -9999 0 -0.63 21 21
ADCY7 0.009 0.12 -9999 0 -0.63 21 21
ADCY1 0.001 0.13 -9999 0 -0.63 25 25
ADCY2 -0.011 0.15 -9999 0 -0.63 34 34
ADCY3 0.009 0.12 -9999 0 -0.63 21 21
ADCY8 0.006 0.12 -9999 0 -0.64 21 21
ADCY9 0.009 0.12 -9999 0 -0.63 21 21
GSK3B 0.022 0.056 -9999 0 -0.36 7 7
arachidonic acid secretion 0.013 0.12 -9999 0 -0.46 42 42
GNG2 -0.006 0.072 -9999 0 -0.82 7 7
TRIP6 -0.001 0.018 -9999 0 -0.53 1 1
GNAO1 -0.006 0.13 -9999 0 -0.55 43 43
HRAS -0.001 0.013 -9999 0 -0.28 2 2
NFKBIA -0.006 0.16 -9999 0 -0.41 111 111
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.031 -9999 0 -0.95 1 1
JUN -0.008 0.081 -9999 0 -0.82 9 9
LPA/LPA2/NHERF2 -0.001 0.012 -9999 0 -10000 0 0
TIAM1 -0.001 0.038 -9999 0 -1.1 1 1
PIK3R1 -0.001 0.027 -9999 0 -0.83 1 1
mol:IP3 -0.01 0.14 -9999 0 -0.37 111 111
PLCB3 -0.001 0.01 -9999 0 -10000 0 0
FOS -0.26 0.38 -9999 0 -0.82 283 283
positive regulation of mitosis 0.013 0.12 -9999 0 -0.46 42 42
LPA/LPA1-2-3 -0.075 0.18 -9999 0 -0.52 121 121
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.1 -9999 0 -0.41 15 15
GNAZ 0.011 0.095 -9999 0 -0.5 29 29
EGFR/PI3K-beta/Gab1 -0.21 0.27 -9999 0 -0.5 371 371
positive regulation of dendritic cell cytokine production -0.074 0.18 -9999 0 -0.51 121 121
LPA/LPA2/MAGI-3 -0.002 0.021 -9999 0 -0.55 1 1
ARHGEF1 -0.009 0.06 -9999 0 -0.46 14 14
GNAI2 0.016 0.076 -9999 0 -0.46 22 22
GNAI3 0.016 0.076 -9999 0 -0.46 22 22
GNAI1 -0.013 0.16 -9999 0 -0.57 62 62
LPA/LPA3 -0.085 0.21 -9999 0 -0.64 111 111
LPA/LPA2 -0.002 0.015 -9999 0 -10000 0 0
LPA/LPA1 -0.013 0.084 -9999 0 -0.54 22 22
HB-EGF/EGFR -0.26 0.27 -9999 0 -0.6 326 326
HBEGF -0.069 0.1 -9999 0 -0.64 3 3
mol:DAG -0.01 0.14 -9999 0 -0.37 111 111
cAMP biosynthetic process -0.01 0.15 -9999 0 -0.57 43 43
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
LYN -0.006 0.16 -9999 0 -0.41 111 111
GNAQ -0.056 0.14 -9999 0 -0.43 113 113
LPAR2 -0.001 0.013 -9999 0 -0.28 2 2
LPAR3 -0.11 0.27 -9999 0 -0.7 145 145
LPAR1 -0.014 0.1 -9999 0 -0.82 14 14
IL8 -0.19 0.23 -9999 0 -0.44 361 361
PTK2 -0.069 0.16 -9999 0 -0.48 121 121
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.063 0.16 -9999 0 -0.43 128 128
EGFR -0.3 0.4 -9999 0 -0.82 331 331
PLCG1 -0.058 0.14 -9999 0 -0.44 112 112
PLD2 -0.069 0.16 -9999 0 -0.48 121 121
G12/G13 -0.01 0.065 -9999 0 -0.49 14 14
PI3K-beta -0.011 0.066 -9999 0 -0.42 20 20
cell migration -0.022 0.055 -9999 0 -0.24 7 7
SLC9A3R2 0 0.009 -9999 0 -10000 0 0
PXN 0.002 0.1 -9999 0 -0.42 15 15
HRAS/GTP -0.032 0.11 -9999 0 -0.47 42 42
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.28 411 411
PRKCE -0.001 0.027 -9999 0 -0.83 1 1
PRKCD -0.002 0.13 -9999 0 -0.35 110 110
Gi(beta/gamma) -0.032 0.12 -9999 0 -0.64 23 23
mol:LPA -0.002 0.02 -9999 0 -0.22 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.057 0.14 -9999 0 -0.54 16 16
MAPKKK cascade 0.013 0.12 -9999 0 -0.46 42 42
contractile ring contraction involved in cytokinesis 0.029 0.025 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.061 0.15 -9999 0 -0.44 117 117
GNA15 -0.056 0.14 -9999 0 -0.43 112 112
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.02 0.15 -9999 0 -0.44 96 96
GNA11 -0.056 0.14 -9999 0 -0.43 113 113
Rac1/GTP 0 0.034 -9999 0 -1 1 1
MMP2 0.01 0.11 -9999 0 -0.67 22 22
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.001 0.027 -9999 0 -0.82 1 1
LAT2 -0.064 0.14 -9999 0 -0.43 75 75
AP1 -0.16 0.22 -9999 0 -0.46 297 297
mol:PIP3 -0.029 0.21 -9999 0 -0.43 182 182
IKBKB 0.001 0.12 -9999 0 -0.32 40 40
AKT1 -0.082 0.17 -9999 0 -0.67 33 33
IKBKG 0.001 0.12 -9999 0 -0.32 40 40
MS4A2 -0.068 0.23 -9999 0 -0.8 78 78
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
MAP3K1 0.007 0.13 -9999 0 -0.45 30 30
mol:Ca2+ -0.014 0.16 -9999 0 -0.32 182 182
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.062 0.14 -9999 0 -0.43 75 75
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.069 0.17 -9999 0 -0.51 124 124
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.1 0.21 -9999 0 -0.5 182 182
PTPN13 -0.031 0.17 -9999 0 -0.55 50 50
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.006 0.15 -9999 0 -0.42 31 31
SYK 0.01 0.01 -9999 0 -0.28 1 1
GRB2 0 0.009 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.088 0.18 -9999 0 -0.44 182 182
LAT -0.064 0.14 -9999 0 -0.43 76 76
PAK2 -0.003 0.14 -9999 0 -0.5 31 31
NFATC2 -0.086 0.23 -9999 0 -0.87 61 61
HRAS -0.013 0.15 -9999 0 -0.41 76 76
GAB2 -0.002 0.026 -9999 0 -10000 0 0
PLA2G1B 0.028 0.018 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.26 -9999 0 -0.62 182 182
Antigen/IgE/Fc epsilon R1 -0.12 0.24 -9999 0 -0.58 182 182
mol:GDP -0.019 0.15 -9999 0 -0.42 76 76
JUN -0.008 0.081 -9999 0 -0.82 9 9
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
FOS -0.26 0.38 -9999 0 -0.82 283 283
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.067 0.15 -9999 0 -0.45 77 77
CHUK 0.001 0.12 -9999 0 -0.32 40 40
KLRG1 -0.062 0.13 -9999 0 -0.4 77 77
VAV1 -0.064 0.14 -9999 0 -0.44 76 76
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.062 0.14 -9999 0 -0.43 75 75
negative regulation of mast cell degranulation -0.057 0.12 -9999 0 -0.51 32 32
BTK -0.061 0.14 -9999 0 -0.42 76 76
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.087 0.2 -9999 0 -0.44 183 183
GAB2/PI3K/SHP2 -0.091 0.19 -9999 0 -0.73 35 35
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.071 0.16 -9999 0 -0.38 143 143
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.23 -9999 0 -0.53 183 183
FCER1G 0.002 0.016 -9999 0 -0.28 2 2
FCER1A -0.12 0.3 -9999 0 -0.84 137 137
Antigen/IgE/Fc epsilon R1/Fyn -0.11 0.23 -9999 0 -0.54 182 182
MAPK3 0.026 0.019 -9999 0 -10000 0 0
MAPK1 0.026 0.019 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.012 0.059 -9999 0 -0.56 4 4
DUSP1 -0.11 0.28 -9999 0 -0.82 124 124
NF-kappa-B/RelA -0.027 0.055 -9999 0 -0.24 1 1
actin cytoskeleton reorganization -0.028 0.15 -9999 0 -0.42 75 75
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.054 0.12 -9999 0 -0.51 33 33
FER -0.065 0.14 -9999 0 -0.44 79 79
RELA 0 0 -9999 0 -10000 0 0
ITK -0.033 0.11 -9999 0 -0.62 29 29
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.017 0.16 -9999 0 -0.43 76 76
cytokine secretion -0.02 0.04 -9999 0 -10000 0 0
SPHK1 -0.065 0.14 -9999 0 -0.44 78 78
PTK2 -0.03 0.16 -9999 0 -0.44 75 75
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.091 0.19 -9999 0 -0.46 182 182
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.024 0.2 -9999 0 -0.48 85 85
MAP2K2 0.022 0.019 -9999 0 -10000 0 0
MAP2K1 0.022 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.058 0.12 -9999 0 -0.52 32 32
MAP2K4 0.016 0.036 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.12 0.24 -9999 0 -0.57 183 183
mol:Choline -0.099 0.21 -9999 0 -0.5 182 182
SHC/Grb2/SOS1 -0.056 0.13 -9999 0 -0.54 30 30
FYN -0.001 0.027 -9999 0 -0.82 1 1
DOK1 0 0.009 -9999 0 -10000 0 0
PXN -0.02 0.15 -9999 0 -0.54 30 30
HCLS1 -0.062 0.14 -9999 0 -0.43 75 75
PRKCB -0.016 0.16 -9999 0 -0.37 90 90
FCGR2B -0.003 0.048 -9999 0 -0.69 4 4
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.058 0.12 -9999 0 -0.52 32 32
LCP2 0 0.009 -9999 0 -0.28 1 1
PLA2G4A -0.11 0.21 -9999 0 -0.52 157 157
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.099 0.21 -9999 0 -0.5 182 182
IKK complex 0.019 0.094 -9999 0 -0.23 38 38
WIPF1 0 0 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.055 0.3 -10000 0 -0.83 109 109
IHH -0.013 0.078 -10000 0 -0.5 3 3
SHH Np/Cholesterol/GAS1 -0.03 0.12 -10000 0 -0.52 49 49
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.03 0.12 0.52 49 -10000 0 49
SMO/beta Arrestin2 -0.077 0.24 -10000 0 -0.86 68 68
SMO -0.054 0.26 -10000 0 -0.92 68 68
AKT1 -0.004 0.096 -10000 0 -0.31 66 66
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.061 0.22 -10000 0 -0.82 68 68
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.035 0.26 -10000 0 -0.9 68 68
STIL -0.04 0.22 -10000 0 -0.73 70 70
DHH N/PTCH2 -0.071 0.21 -10000 0 -0.67 97 97
DHH N/PTCH1 -0.091 0.25 -10000 0 -0.76 97 97
PIK3CA 0 0.009 -10000 0 -10000 0 0
DHH -0.024 0.14 -10000 0 -0.82 26 26
PTHLH -0.083 0.39 -10000 0 -1.1 109 109
determination of left/right symmetry -0.035 0.26 -10000 0 -0.9 68 68
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
skeletal system development -0.08 0.38 -10000 0 -1.1 109 109
IHH N/Hhip -0.01 0.047 -10000 0 -0.68 1 1
DHH N/Hhip -0.021 0.11 -10000 0 -0.65 27 27
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.035 0.26 -10000 0 -0.9 68 68
pancreas development -0.004 0.039 -10000 0 -0.82 1 1
HHAT -0.001 0.027 -10000 0 -0.82 1 1
PI3K -0.001 0.022 -10000 0 -0.63 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.043 0.18 -10000 0 -0.82 48 48
somite specification -0.035 0.26 -10000 0 -0.9 68 68
SHH Np/Cholesterol/PTCH1 -0.072 0.21 -10000 0 -0.78 67 67
SHH Np/Cholesterol/PTCH2 -0.046 0.14 -10000 0 -0.52 78 78
SHH Np/Cholesterol/Megalin -0.14 0.22 -10000 0 -0.51 238 238
SHH 0.01 0.036 -10000 0 -0.64 1 1
catabolic process -0.048 0.26 -10000 0 -0.88 74 74
SMO/Vitamin D3 -0.075 0.23 -10000 0 -0.84 68 68
SHH Np/Cholesterol/Hhip -0.005 0.035 -10000 0 -0.52 2 2
LRP2 -0.22 0.36 -10000 0 -0.78 260 260
receptor-mediated endocytosis -0.15 0.26 -10000 0 -0.84 85 85
SHH Np/Cholesterol/BOC -0.041 0.14 -10000 0 -0.52 69 69
SHH Np/Cholesterol/CDO -0.01 0.063 -10000 0 -0.51 13 13
mesenchymal cell differentiation 0.005 0.035 0.51 2 -10000 0 2
mol:Vitamin D3 -0.031 0.23 -10000 0 -0.79 67 67
IHH N/PTCH2 -0.065 0.2 -10000 0 -0.7 77 77
CDON -0.011 0.094 -10000 0 -0.82 12 12
IHH N/PTCH1 -0.046 0.27 -10000 0 -0.89 74 74
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.63 237 237
PTCH2 -0.07 0.23 -10000 0 -0.82 77 77
SHH Np/Cholesterol -0.003 0.025 -10000 0 -0.52 1 1
PTCH1 -0.049 0.26 -10000 0 -0.89 74 74
HHIP -0.004 0.039 -10000 0 -0.82 1 1
PDGFR-alpha signaling pathway

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.058 0.2 -9999 0 -0.84 56 56
PDGF/PDGFRA/CRKL -0.039 0.15 -9999 0 -0.64 55 55
positive regulation of JUN kinase activity -0.03 0.12 -9999 0 -0.49 55 55
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.042 0.15 -9999 0 -0.64 55 55
AP1 -0.38 0.55 -9999 0 -1.2 283 283
mol:IP3 -0.034 0.16 -9999 0 -0.66 55 55
PLCG1 -0.034 0.16 -9999 0 -0.66 55 55
PDGF/PDGFRA/alphaV Integrin -0.039 0.15 -9999 0 -0.64 55 55
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.16 -9999 0 -0.66 55 55
CAV3 -0.001 0.016 -9999 0 -0.28 3 3
CAV1 -0.17 0.34 -9999 0 -0.82 191 191
SHC/Grb2/SOS1 -0.03 0.12 -9999 0 -0.49 55 55
PDGF/PDGFRA/Shf -0.039 0.16 -9999 0 -0.65 55 55
FOS -0.34 0.56 -9999 0 -1.2 283 283
JUN -0.027 0.074 -9999 0 -0.71 9 9
oligodendrocyte development -0.038 0.15 -9999 0 -0.64 55 55
GRB2 0 0.009 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
mol:DAG -0.034 0.16 -9999 0 -0.66 55 55
PDGF/PDGFRA -0.058 0.2 -9999 0 -0.84 56 56
actin cytoskeleton reorganization -0.039 0.15 -9999 0 -0.64 56 56
SRF 0.016 0.022 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.034 0.13 -9999 0 -0.55 56 56
PDGF/PDGFRA/Crk/C3G -0.033 0.13 -9999 0 -0.55 55 55
JAK1 -0.023 0.16 -9999 0 -0.64 55 55
ELK1/SRF -0.026 0.12 -9999 0 -0.5 55 55
SHB -0.001 0.029 -9999 0 -0.55 2 2
SHF -0.001 0.029 -9999 0 -0.55 2 2
CSNK2A1 0.019 0.027 -9999 0 -10000 0 0
GO:0007205 -0.036 0.17 -9999 0 -0.68 55 55
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.03 0.12 -9999 0 -0.49 55 55
PDGF/PDGFRA/SHB -0.04 0.15 -9999 0 -0.64 56 56
PDGF/PDGFRA/Caveolin-1 -0.17 0.32 -9999 0 -0.74 210 210
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.035 0.16 -9999 0 -0.61 55 55
PIK3CA 0 0.009 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.039 0.15 -9999 0 -0.64 55 55
JAK-STAT cascade -0.023 0.16 -9999 0 -0.63 55 55
cell proliferation -0.039 0.15 -9999 0 -0.64 55 55
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.003 0.035 -9999 0 -0.64 2 2
PDGFRB -0.002 0.039 -9999 0 -0.83 2 2
SPHK1 -0.025 0.059 -9999 0 -1.1 2 2
mol:S1P -0.031 0.061 -9999 0 -0.98 2 2
S1P1/S1P/Gi -0.1 0.23 -9999 0 -0.57 86 86
GNAO1 -0.027 0.15 -9999 0 -0.58 46 46
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.61 57 57
PLCG1 -0.09 0.22 -9999 0 -0.57 76 76
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.039 -9999 0 -0.83 2 2
GNAI2 0.007 0.006 -9999 0 -10000 0 0
GNAI3 0 0.001 -9999 0 -10000 0 0
GNAI1 -0.043 0.18 -9999 0 -0.84 47 47
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.007 0.034 -9999 0 -0.57 2 2
S1P1/S1P -0.044 0.072 -9999 0 -0.68 4 4
negative regulation of cAMP metabolic process -0.098 0.22 -9999 0 -0.38 318 318
MAPK3 -0.16 0.31 -9999 0 -0.58 308 308
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.002 0.039 -9999 0 -0.83 2 2
PLCB2 -0.008 0.084 -9999 0 -0.57 5 5
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.037 0.059 -9999 0 -0.55 4 4
receptor internalization -0.042 0.067 -9999 0 -0.62 4 4
PTGS2 -0.33 0.56 -9999 0 -1.1 308 308
Rac1/GTP -0.037 0.059 -9999 0 -0.55 4 4
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.028 -9999 0 -0.28 9 9
negative regulation of T cell proliferation -0.098 0.22 -9999 0 -0.38 318 318
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.078 -9999 0 -0.83 8 8
MAPK1 -0.16 0.31 -9999 0 -0.58 308 308
S1P1/S1P/PDGFB-D/PDGFRB -0.052 0.084 -9999 0 -0.71 5 5
ABCC1 0 0 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.081 0.19 0.66 76 -10000 0 76
KIRREL -0.069 0.23 -10000 0 -0.83 76 76
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.081 0.19 -10000 0 -0.66 76 76
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.058 0.14 -10000 0 -0.51 76 76
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.034 0.1 -10000 0 -0.37 76 76
FYN -0.054 0.14 -10000 0 -0.49 76 76
mol:Ca2+ -0.058 0.14 -10000 0 -0.5 76 76
mol:DAG -0.058 0.14 -10000 0 -0.51 76 76
NPHS2 -0.008 0.029 -10000 0 -0.28 5 5
mol:IP3 -0.058 0.14 -10000 0 -0.51 76 76
regulation of endocytosis -0.026 0.13 -10000 0 -0.45 76 76
Nephrin/NEPH1/podocin/Cholesterol -0.061 0.14 -10000 0 -0.52 76 76
establishment of cell polarity -0.081 0.19 -10000 0 -0.66 76 76
Nephrin/NEPH1/podocin/NCK1-2 -0.026 0.14 -10000 0 -0.46 76 76
Nephrin/NEPH1/beta Arrestin2 -0.026 0.14 -10000 0 -0.46 76 76
NPHS1 -0.05 0.1 -10000 0 -0.28 150 150
Nephrin/NEPH1/podocin -0.049 0.14 -10000 0 -0.49 76 76
TJP1 -0.001 0.027 -10000 0 -0.82 1 1
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.058 0.14 -10000 0 -0.51 76 76
CD2AP 0 0.009 -10000 0 -0.28 1 1
Nephrin/NEPH1/podocin/GRB2 -0.058 0.14 -10000 0 -0.51 76 76
GRB2 0 0.009 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.061 0.15 -10000 0 -0.51 83 83
cytoskeleton organization -0.044 0.13 -10000 0 -0.47 76 76
Nephrin/NEPH1 -0.058 0.14 -10000 0 -0.5 76 76
Nephrin/NEPH1/ZO-1 -0.064 0.16 -10000 0 -0.55 76 76
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.005 0.031 -10000 0 -0.44 1 1
adherens junction organization 0.031 0.066 -10000 0 -0.31 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.19 -10000 0 -0.39 327 327
FMN1 0.024 0.09 -10000 0 -0.48 16 16
mol:IP3 -0.006 0.032 -10000 0 -0.41 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.057 -10000 0 -0.32 29 29
CTNNB1 0.001 0.004 -10000 0 -10000 0 0
AKT1 -0.007 0.036 -10000 0 -0.4 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.016 0.089 -10000 0 -0.52 28 28
CTNND1 0 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.032 0.06 -10000 0 -0.3 29 29
VASP 0.032 0.061 -10000 0 -10000 0 0
ZYX 0.032 0.061 -10000 0 -10000 0 0
JUB 0.03 0.068 -10000 0 -0.44 4 4
EGFR(dimer) -0.17 0.22 -10000 0 -0.45 327 327
E-cadherin/beta catenin-gamma catenin -0.017 0.093 -10000 0 -0.53 29 29
mol:PI-3-4-5-P3 -0.007 0.04 -10000 0 -0.43 1 1
PIK3CA 0 0.009 -10000 0 -10000 0 0
PI3K -0.007 0.04 -10000 0 -0.44 1 1
FYN 0.043 0.038 -10000 0 -0.37 2 2
mol:Ca2+ -0.006 0.032 -10000 0 -0.4 1 1
JUP -0.001 0.03 -10000 0 -0.82 1 1
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
mol:DAG -0.006 0.032 -10000 0 -0.41 1 1
CDH1 -0.025 0.14 -10000 0 -0.82 28 28
RhoA/GDP -0.14 0.19 -10000 0 -0.39 327 327
establishment of polarity of embryonic epithelium 0.032 0.06 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
EGFR -0.3 0.4 -10000 0 -0.82 331 331
CASR -0.006 0.03 -10000 0 -0.38 1 1
RhoA/GTP -0.005 0.028 -10000 0 -0.37 1 1
AKT2 -0.007 0.036 -10000 0 -0.4 1 1
actin cable formation 0.031 0.088 -10000 0 -0.46 16 16
apoptosis 0.006 0.036 0.42 1 -10000 0 1
CTNNA1 0 0 -10000 0 -10000 0 0
mol:GDP -0.15 0.2 -10000 0 -0.42 327 327
PIP5K1A 0.032 0.061 -10000 0 -0.3 29 29
PLCG1 -0.006 0.033 -10000 0 -0.42 1 1
Rac1/GTP -0.15 0.2 -10000 0 -0.41 327 327
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.007 0.058 -9999 0 -0.48 13 13
RGS9BP -0.016 0.064 -9999 0 -0.28 51 51
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.029 -9999 0 -0.28 10 10
mol:Na + -0.02 0.05 -9999 0 -10000 0 0
mol:ADP 0.006 0.03 -9999 0 -10000 0 0
GNAT2 -0.001 0.016 -9999 0 -0.28 3 3
RGS9-1/Gbeta5/R9AP -0.067 0.17 -9999 0 -0.56 97 97
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.013 -9999 0 -10000 0 0
GRK7 -0.003 0.03 -9999 0 -0.28 11 11
CNGB3 -0.01 0.052 -9999 0 -0.28 33 33
Cone Metarhodopsin II/X-Arrestin -0.001 0.016 -9999 0 -10000 0 0
mol:Ca2+ -0.096 0.077 -9999 0 -10000 0 0
Cone PDE6 -0.058 0.15 -9999 0 -0.48 97 97
Cone Metarhodopsin II -0.003 0.02 -9999 0 -10000 0 0
Na + (4 Units) -0.096 0.076 -9999 0 -10000 0 0
GNAT2/GDP -0.058 0.15 -9999 0 -0.48 97 97
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.005 0.013 -9999 0 -10000 0 0
Cone Transducin -0.008 0.061 -9999 0 -0.51 13 13
SLC24A2 -0.18 0.14 -9999 0 -0.28 574 574
GNB3/GNGT2 -0.009 0.075 -9999 0 -0.63 13 13
GNB3 -0.011 0.095 -9999 0 -0.75 14 14
GNAT2/GTP -0.001 0.011 -9999 0 -10000 0 0
CNGA3 -0.027 0.083 -9999 0 -0.28 90 90
ARR3 -0.002 0.024 -9999 0 -0.28 7 7
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.02 0.051 -9999 0 -10000 0 0
mol:Pi -0.067 0.17 -9999 0 -0.56 97 97
Cone CNG Channel -0.015 0.038 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.18 0.13 -9999 0 -0.28 574 574
RGS9 -0.091 0.26 -9999 0 -0.77 107 107
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.001 0.027 -9999 0 -0.82 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.018 -9999 0 -0.28 4 4
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.05 0.2 -10000 0 -0.82 56 56
HRAS -0.001 0.013 -10000 0 -0.28 2 2
EGFR -0.3 0.4 -10000 0 -0.82 331 331
AKT 0.016 0.074 -10000 0 -0.59 12 12
FOXO3 -0.002 0.039 -10000 0 -0.82 2 2
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.007 0.077 -10000 0 -0.82 8 8
AKT3 -0.011 0.094 -10000 0 -0.82 12 12
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.31 -10000 0 -0.82 155 155
PIK3CA 0 0.009 -10000 0 -10000 0 0
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.28 2 2
PIK3CG -0.009 0.083 -10000 0 -0.82 9 9
PIK3R3 0 0.009 -10000 0 -10000 0 0
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.027 -10000 0 -0.82 1 1
RAS -0.093 0.16 0.26 1 -0.27 353 354
ERBB2 -0.024 0.078 -10000 0 -10000 0 0
proliferation/survival/translation -0.006 0.054 0.28 5 -10000 0 5
PI3K -0.082 0.16 -10000 0 -0.26 338 338
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
KRAS 0 0.009 -10000 0 -10000 0 0
FOXO 0.027 0.024 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.039 -10000 0 -0.82 2 2
Signaling events mediated by PRL

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
CCNE1 -0.054 0.11 -9999 0 -0.28 176 176
mol:Halofuginone 0 0.002 -9999 0 -10000 0 0
ITGA1 -0.002 0.039 -9999 0 -0.82 2 2
CDKN1A -0.06 0.09 -9999 0 -0.87 1 1
PRL-3/alpha Tubulin -0.002 0.018 -9999 0 -10000 0 0
mol:Ca2+ -0.035 0.1 -9999 0 -0.65 14 14
AGT -0.05 0.14 -9999 0 -0.82 14 14
CCNA2 -0.17 0.25 -9999 0 -0.52 295 295
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.19 0.3 -9999 0 -0.63 295 295
CDK2/Cyclin E1 -0.068 0.089 -9999 0 -0.78 1 1
MAPK3 0.02 0.021 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.008 -9999 0 -10000 0 0
MAPK1 0.02 0.021 -9999 0 -10000 0 0
PTP4A1 -0.13 0.25 -9999 0 -0.49 295 295
PTP4A3 -0.003 0.029 -9999 0 -10000 0 0
PTP4A2 -0.001 0.013 -9999 0 -0.28 2 2
ITGB1 0.02 0.021 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
RAC1 -0.059 0.086 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.15 0.21 -9999 0 -0.62 3 3
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0.001 0.009 -9999 0 -10000 0 0
RHOC -0.059 0.086 -9999 0 -10000 0 0
RHOA -0.059 0.086 -9999 0 -10000 0 0
cell motility -0.039 0.11 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.15 0.21 -9999 0 -0.45 295 295
PRL-3/alpha1 Integrin -0.003 0.035 -9999 0 -0.63 2 2
ROCK1 -0.039 0.11 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.13 0.24 -9999 0 -0.48 295 295
ATF5 -0.001 0.018 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.003 0.039 -10000 0 -0.52 5 5
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.001 0.003 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.077 0.24 -10000 0 -0.82 85 85
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
TLE1 -0.007 0.077 -10000 0 -0.83 8 8
AP1 -0.12 0.18 -10000 0 -0.38 287 287
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.001 0.027 -10000 0 -0.82 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.045 -10000 0 -0.34 1 1
NICD/RBPSUH -0.001 0.024 -10000 0 -0.72 1 1
WIF1 -0.44 0.41 -10000 0 -0.81 495 495
NOTCH1 -0.001 0.026 -10000 0 -0.77 1 1
PSENEN 0 0.009 -10000 0 -0.28 1 1
KREMEN2 -0.13 0.14 -10000 0 -0.28 431 431
DKK1 -0.079 0.2 -10000 0 -0.42 172 172
beta catenin/beta TrCP1 -0.011 0.023 -10000 0 -10000 0 0
APH1B -0.001 0.027 -10000 0 -0.82 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.011 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.042 -10000 0 -0.34 8 8
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.26 0.38 -10000 0 -0.82 283 283
JUN -0.008 0.081 -10000 0 -0.82 9 9
MAP3K7 0.001 0.01 -10000 0 -10000 0 0
CTNNB1 -0.004 0.036 0.24 2 -10000 0 2
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.075 0.11 -10000 0 -0.64 19 19
HNF1A -0.001 0.023 -10000 0 -0.28 6 6
CTBP1 0.001 0.003 -10000 0 -10000 0 0
MYC -0.033 0.22 -10000 0 -1.5 20 20
NKD1 -0.01 0.076 -10000 0 -0.43 22 22
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.044 0.14 -10000 0 -0.46 86 86
apoptosis -0.12 0.18 -10000 0 -0.38 287 287
Delta 1/NOTCHprecursor -0.003 0.039 -10000 0 -0.51 5 5
DLL1 -0.004 0.054 -10000 0 -0.82 4 4
PPARD -0.001 0.012 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.016 -10000 0 -0.46 1 1
APC 0.003 0.011 -10000 0 -0.22 1 1
DVL1 -0.04 0.038 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.14 -10000 0 -0.59 47 47
LRP6 -0.001 0.013 -10000 0 -0.28 2 2
CSNK1A1 0 0 -10000 0 -10000 0 0
NLK 0.002 0.01 -10000 0 -10000 0 0
CCND1 -0.011 0.09 -10000 0 -1.5 3 3
WNT1 0 0.009 -10000 0 -0.28 1 1
Axin1/APC/beta catenin 0.009 0.037 -10000 0 -10000 0 0
DKK2 -0.018 0.12 -10000 0 -0.82 19 19
NOTCH1 precursor/DVL1 -0.02 0.028 -10000 0 -0.64 1 1
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 0 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.044 0.14 -10000 0 -0.46 86 86
PPP2R5D -0.016 0.04 0.36 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.27 0.25 -10000 0 -0.5 483 483
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0.003 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.12 0.18 -9999 0 -0.39 285 285
MAP3K8 -0.005 0.062 -9999 0 -0.83 5 5
FOS -0.037 0.13 -9999 0 -0.46 28 28
PRKCA -0.02 0.13 -9999 0 -0.79 23 23
PTPN7 -0.008 0.069 -9999 0 -0.32 16 16
HRAS -0.001 0.013 -9999 0 -0.28 2 2
PRKCB -0.02 0.12 -9999 0 -0.7 21 21
NRAS -0.001 0.013 -9999 0 -0.28 2 2
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.008 0.072 -9999 0 -10000 0 0
MAP2K1 -0.013 0.14 -9999 0 -0.59 39 39
ELK1 -0.003 0.005 -9999 0 -10000 0 0
BRAF -0.031 0.12 -9999 0 -0.6 35 35
mol:GTP -0.002 0.003 -9999 0 -0.006 283 283
MAPK1 -0.008 0.072 -9999 0 -0.26 24 24
RAF1 -0.031 0.12 -9999 0 -0.6 35 35
KRAS 0 0.009 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.011 0.059 -10000 0 -0.34 29 29
epithelial cell differentiation -0.014 0.081 -10000 0 -0.47 28 28
CYFIP2 -0.01 0.061 -10000 0 -0.32 29 29
ENAH 0.055 0.064 -10000 0 -10000 0 0
EGFR -0.3 0.4 -10000 0 -0.82 331 331
EPHA2 -0.005 0.067 -10000 0 -0.82 6 6
MYO6 -0.014 0.078 -10000 0 -0.44 29 29
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.034 -10000 0 -0.55 2 2
AQP5 -0.25 0.3 -10000 0 -0.61 372 372
CTNND1 0 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.075 -10000 0 -0.44 28 28
regulation of calcium-dependent cell-cell adhesion -0.036 0.12 -10000 0 -0.45 73 73
EGF -0.16 0.33 -10000 0 -0.82 183 183
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.041 0.15 -10000 0 -0.6 49 49
cortical microtubule organization -0.014 0.081 -10000 0 -0.47 28 28
GO:0000145 0.024 0.078 -10000 0 -0.42 28 28
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.015 0.082 -10000 0 -0.47 28 28
MLLT4 -0.005 0.061 -10000 0 -0.82 5 5
ARF6/GDP -0.014 0.069 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.041 -10000 0 -0.5 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.035 0.08 -10000 0 -0.41 28 28
PVRL2 -0.001 0.016 -10000 0 -10000 0 0
ZYX -0.014 0.076 -10000 0 -0.44 28 28
ARF6/GTP -0.004 0.038 -10000 0 -0.46 6 6
CDH1 -0.025 0.14 -10000 0 -0.82 28 28
EGFR/EGFR/EGF/EGF -0.25 0.27 -10000 0 -0.49 467 467
RhoA/GDP -0.014 0.076 -10000 0 -0.44 28 28
actin cytoskeleton organization 0.03 0.081 -10000 0 -0.42 29 29
IGF-1R heterotetramer -0.022 0.12 -10000 0 -0.61 33 33
GIT1 -0.001 0.018 -10000 0 -0.28 4 4
IGF1R -0.022 0.12 -10000 0 -0.61 33 33
IGF1 -0.18 0.34 -10000 0 -0.82 197 197
DIAPH1 -0.001 0.033 -10000 0 -0.68 2 2
Wnt receptor signaling pathway 0.014 0.081 0.47 28 -10000 0 28
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.07 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL -0.014 0.075 -10000 0 -0.43 29 29
EFNA1 0 0.009 -10000 0 -10000 0 0
LPP 0.03 0.084 -10000 0 -0.42 31 31
Ephrin A1/EPHA2 -0.016 0.08 -10000 0 -0.42 34 34
SEC6/SEC8 -0.014 0.075 -10000 0 -0.79 1 1
MGAT3 -0.037 0.12 -10000 0 -0.46 73 73
HGF/MET -0.11 0.22 -10000 0 -0.48 213 213
HGF -0.051 0.2 -10000 0 -0.82 57 57
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.011 0.059 -10000 0 -0.34 29 29
actin cable formation 0.07 0.061 -10000 0 -10000 0 0
KIAA1543 0.03 0.092 -10000 0 -0.46 28 28
KIFC3 -0.015 0.079 -10000 0 -0.44 30 30
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.014 0.078 -10000 0 -0.44 29 29
NCK1/GIT1 -0.001 0.012 -10000 0 -10000 0 0
mol:GDP -0.014 0.081 -10000 0 -0.47 28 28
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.014 0.076 -10000 0 -0.44 28 28
PIP5K1C -0.014 0.076 -10000 0 -0.44 28 28
LIMA1 -0.001 0.027 -10000 0 -0.82 1 1
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.012 0.06 -10000 0 -10000 0 0
adherens junction assembly 0.045 0.088 -10000 0 -0.66 4 4
IGF-1R heterotetramer/IGF1 -0.12 0.2 -10000 0 -0.46 231 231
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.048 -10000 0 -0.63 5 5
MET -0.14 0.31 -10000 0 -0.82 155 155
PLEKHA7 -0.015 0.085 -10000 0 -0.48 28 28
mol:GTP -0.004 0.041 -10000 0 -0.5 6 6
establishment of epithelial cell apical/basal polarity -0.013 0.071 -10000 0 -0.74 1 1
cortical actin cytoskeleton stabilization -0.011 0.059 -10000 0 -0.34 29 29
regulation of cell-cell adhesion 0.03 0.081 -10000 0 -0.42 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.011 0.059 -10000 0 -0.34 29 29
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.027 -10000 0 -0.82 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.029 0.069 0.63 1 -10000 0 1
CDKN1A -0.001 0.032 -10000 0 -0.97 1 1
KAT2B 0 0 -10000 0 -10000 0 0
BAX -0.001 0.016 -10000 0 -10000 0 0
FOXO3 -0.001 0.016 -10000 0 -0.34 2 2
FOXO1 -0.007 0.077 -10000 0 -0.82 8 8
FOXO4 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.59 0.37 -10000 0 -0.8 670 670
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0.021 -10000 0 -10000 0 0
PPARGC1A -0.18 0.34 -10000 0 -0.82 195 195
FHL2 -0.005 0.062 -10000 0 -0.82 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.005 -10000 0 -10000 0 0
HIST2H4A -0.029 0.069 -10000 0 -0.64 1 1
SIRT1/FOXO3a 0 0.013 -10000 0 -0.26 2 2
SIRT1 0 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.019 -10000 0 -0.55 1 1
SIRT1/Histone H1b -0.002 0.009 -10000 0 -10000 0 0
apoptosis 0 0.009 -10000 0 -10000 0 0
SIRT1/PGC1A -0.12 0.23 -10000 0 -0.56 195 195
p53/SIRT1 0.001 0.015 0.43 1 -10000 0 1
SIRT1/FOXO4 0 0.006 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.007 0.061 -10000 0 -0.51 13 13
HIST1H1E -0.004 0.012 -10000 0 -10000 0 0
SIRT1/p300 0 0.005 -10000 0 -10000 0 0
muscle cell differentiation 0.001 0.016 -10000 0 -10000 0 0
TP53 0 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.009 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.45 0.28 -10000 0 -0.64 644 644
ACSS2 -0.001 0.022 -10000 0 -0.64 1 1
SIRT1/PCAF/MYOD -0.001 0.016 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.11 0.21 -10000 0 -0.5 211 211
MAPK9 0 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.02 -10000 0 -10000 0 0
GNB1/GNG2 -0.004 0.049 -10000 0 -0.56 7 7
GNB1 0 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
Gs family/GTP -0.12 0.22 -10000 0 -0.52 210 210
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.027 0.049 0.12 210 -10000 0 210
GNAL -0.19 0.35 -10000 0 -0.82 210 210
GNG2 -0.006 0.072 -10000 0 -0.82 7 7
CRH -0.003 0.029 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.002 0.026 -10000 0 -0.46 3 3
MAPK11 -0.001 0.021 -10000 0 -0.46 2 2
FAS signaling pathway (CD95)

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
SPTAN1 0.01 0.052 0.29 30 -10000 0 30
RFC1 0.01 0.052 0.29 30 -10000 0 30
PRKDC 0.009 0.053 0.29 30 -10000 0 30
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.023 0.036 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.015 0.06 0.23 23 -0.4 8 31
MAP2K4 -0.058 0.16 -10000 0 -0.53 12 12
mol:ceramide -0.029 0.11 -10000 0 -0.58 11 11
GSN 0.002 0.081 0.29 29 -0.52 13 42
FASLG/FAS/FADD/FAF1/Caspase 8 -0.028 0.062 0.23 10 -0.47 8 18
FAS -0.003 0.048 -10000 0 -0.84 3 3
BID 0.001 0.005 -10000 0 -10000 0 0
MAP3K1 -0.021 0.092 -10000 0 -0.3 6 6
MAP3K7 0 0.009 -10000 0 -10000 0 0
RB1 0.009 0.055 0.29 29 -0.43 2 31
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.14 0.27 -10000 0 -0.62 204 204
ARHGDIB 0.01 0.052 0.29 30 -10000 0 30
FADD -0.005 0.039 -10000 0 -0.3 16 16
actin filament polymerization -0.002 0.081 0.52 13 -0.29 29 42
NFKB1 -0.077 0.1 -10000 0 -0.29 11 11
MAPK8 -0.12 0.24 -10000 0 -0.43 340 340
DFFA 0.01 0.052 0.29 30 -10000 0 30
DNA fragmentation during apoptosis 0.01 0.052 0.29 30 -10000 0 30
FAS/FADD/MET -0.099 0.22 -10000 0 -0.58 154 154
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.001 0.046 -10000 0 -0.28 24 24
FAF1 0.007 0.006 -10000 0 -10000 0 0
PARP1 0.01 0.052 0.29 30 -10000 0 30
DFFB 0.01 0.052 0.29 30 -10000 0 30
CHUK -0.066 0.088 -10000 0 -0.3 1 1
FASLG -0.01 0.088 -10000 0 -0.36 41 41
FAS/FADD -0.006 0.047 -10000 0 -0.7 3 3
HGF -0.051 0.2 -10000 0 -0.82 57 57
LMNA 0.009 0.047 0.26 30 -10000 0 30
CASP6 0.01 0.052 0.29 30 -10000 0 30
CASP10 -0.003 0.048 -10000 0 -0.84 3 3
CASP3 0.012 0.063 0.35 30 -10000 0 30
PTPN13 -0.022 0.13 -10000 0 -0.82 24 24
CASP8 0.002 0.013 -10000 0 -10000 0 0
IL6 -0.48 0.68 -10000 0 -1.4 338 338
MET -0.14 0.31 -10000 0 -0.82 155 155
ICAD/CAD 0.01 0.048 0.27 30 -10000 0 30
FASLG/FAS/FADD/FAF1/Caspase 10 -0.056 0.093 -10000 0 -0.59 11 11
activation of caspase activity by cytochrome c 0.001 0.005 -10000 0 -10000 0 0
PAK2 0.01 0.051 0.29 30 -10000 0 30
BCL2 -0.023 0.15 -10000 0 -0.82 30 30
LPA4-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
ADCY4 -0.002 0.11 -9999 0 -0.56 35 35
ADCY5 -0.16 0.27 -9999 0 -0.56 289 289
ADCY6 0.019 0.019 -9999 0 -0.56 1 1
ADCY7 0.019 0.019 -9999 0 -0.56 1 1
ADCY1 -0.006 0.094 -9999 0 -0.56 20 20
ADCY2 -0.031 0.16 -9999 0 -0.56 71 71
ADCY3 0.019 0.02 -9999 0 -0.56 1 1
ADCY8 0.009 0.033 -9999 0 -0.56 1 1
PRKCE 0.01 0.022 -9999 0 -0.64 1 1
ADCY9 0.019 0.019 -9999 0 -0.56 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.032 0.1 -9999 0 -0.31 71 71
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 -0.57 0.38 -9999 0 -0.82 637 637
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.003 0.028 -9999 0 -10000 0 0
TCEB1 -0.001 0.016 -9999 0 -10000 0 0
HIF1A/p53 -0.001 0.004 -9999 0 -10000 0 0
HIF1A -0.002 0.006 -9999 0 -10000 0 0
COPS5 0 0.009 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.011 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.045 0.1 -9999 0 -10000 0 0
ARNT/IPAS -0.44 0.29 -9999 0 -0.63 637 637
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.001 0.004 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0.009 -9999 0 -0.28 1 1
RACK1/Elongin B/Elongin C -0.002 0.015 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.005 -9999 0 -10000 0 0
PHD1-3/OS9 -0.01 0.035 -9999 0 -0.5 1 1
HIF1A/RACK1/Elongin B/Elongin C 0 0.01 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -10000 0 0
HIF1A/JAB1 -0.001 0.006 -9999 0 -10000 0 0
EGLN3 -0.022 0.075 -9999 0 -0.28 72 72
EGLN2 -0.001 0.018 -9999 0 -10000 0 0
EGLN1 -0.001 0.027 -9999 0 -0.82 1 1
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0.004 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.017 0.037 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.002 0.039 -9999 0 -0.82 2 2
alphaV beta3 Integrin -0.014 0.091 -9999 0 -0.63 19 19
PTK2 -0.055 0.17 -9999 0 -0.56 86 86
positive regulation of JNK cascade -0.032 0.099 -9999 0 -0.34 86 86
CDC42/GDP 0.006 0.15 -9999 0 -0.46 86 86
Rac1/GDP 0.008 0.15 -9999 0 -0.46 86 86
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.04 0.12 -9999 0 -0.42 86 86
nectin-3/I-afadin -0.062 0.2 -9999 0 -0.66 86 86
RAPGEF1 0 0.17 -9999 0 -0.52 86 86
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.013 0.2 -9999 0 -0.61 86 86
PDGFB-D/PDGFRB -0.002 0.038 -9999 0 -0.82 2 2
TLN1 -0.026 0.09 -9999 0 -0.55 10 10
Rap1/GTP -0.034 0.11 -9999 0 -0.36 86 86
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.037 -9999 0 -0.51 5 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.062 0.2 -9999 0 -0.66 86 86
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP -0.003 0.19 -9999 0 -0.58 86 86
MLLT4 -0.005 0.061 -9999 0 -0.82 5 5
PIK3CA 0 0.009 -9999 0 -10000 0 0
PI3K -0.047 0.15 -9999 0 -0.49 89 89
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.003 0.047 -9999 0 -0.63 5 5
positive regulation of lamellipodium assembly -0.034 0.1 -9999 0 -0.36 86 86
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.077 0.24 -9999 0 -0.82 85 85
PVRL2 -0.001 0.016 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
CDH1 -0.025 0.14 -9999 0 -0.82 28 28
CLDN1 -0.038 0.16 -9999 0 -0.82 34 34
JAM-A/CLDN1 -0.07 0.19 -9999 0 -0.55 112 112
SRC -0.066 0.21 -9999 0 -0.7 86 86
ITGB3 -0.018 0.12 -9999 0 -0.82 19 19
nectin-1(dimer)/I-afadin/I-afadin -0.003 0.047 -9999 0 -0.63 5 5
FARP2 -0.008 0.18 -9999 0 -0.57 86 86
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.054 0.17 -9999 0 -0.57 86 86
nectin-1/I-afadin -0.003 0.047 -9999 0 -0.63 5 5
nectin-2/I-afadin -0.004 0.048 -9999 0 -0.63 5 5
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.054 0.17 -9999 0 -0.57 86 86
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.032 0.099 -9999 0 -0.34 86 86
alphaV/beta3 Integrin/Talin -0.032 0.11 -9999 0 -0.62 23 23
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.048 -9999 0 -0.63 5 5
nectin-2(dimer)/I-afadin/I-afadin -0.004 0.048 -9999 0 -0.63 5 5
PIP5K1C -0.029 0.098 -9999 0 -0.59 10 10
VAV2 -0.01 0.18 -9999 0 -0.58 86 86
RAP1/GDP -0.04 0.12 -9999 0 -0.42 86 86
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.054 0.17 -9999 0 -0.57 86 86
nectin-3(dimer)/I-afadin/I-afadin -0.062 0.2 -9999 0 -0.66 86 86
Rac1/GTP -0.042 0.13 -9999 0 -0.44 86 86
PTPRM -0.032 0.11 -9999 0 -0.33 89 89
E-cadherin/beta catenin/alpha catenin -0.016 0.085 -9999 0 -0.46 32 32
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.017 -10000 0 -10000 0 0
AES 0.003 0.014 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
SMAD4 0 0 -10000 0 -10000 0 0
DKK2 -0.018 0.12 -10000 0 -0.82 19 19
TLE1 -0.004 0.079 -10000 0 -0.83 8 8
MACF1 0 0 -10000 0 -10000 0 0
CTNNB1 0.11 0.088 -10000 0 -10000 0 0
WIF1 -0.44 0.41 -10000 0 -0.81 495 495
beta catenin/RanBP3 0.013 0.074 0.37 35 -10000 0 35
KREMEN2 -0.13 0.14 -10000 0 -0.28 431 431
DKK1 -0.079 0.2 -10000 0 -0.42 172 172
beta catenin/beta TrCP1 0.1 0.085 -10000 0 -10000 0 0
FZD1 0 0 -10000 0 -10000 0 0
AXIN2 -0.01 0.2 -10000 0 -1.6 14 14
AXIN1 0 0.002 -10000 0 -10000 0 0
RAN 0 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.004 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.095 0.074 -10000 0 -0.49 4 4
Axin1/APC/GSK3 0.001 0.015 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.078 0.034 -10000 0 -10000 0 0
HNF1A 0.002 0.026 -10000 0 -0.28 3 3
CTBP1 0.004 0.015 -10000 0 -10000 0 0
MYC -0.019 0.23 -10000 0 -1.6 20 20
RANBP3 0 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.075 0.11 -10000 0 -0.64 19 19
NKD1 -0.01 0.076 -10000 0 -0.43 22 22
TCF4 -0.002 0.068 -10000 0 -0.82 6 6
TCF3 0.004 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.006 -10000 0 -10000 0 0
Ran/GTP 0 0 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.013 0.094 0.44 36 -0.44 1 37
LEF1 -0.034 0.098 -10000 0 -0.28 118 118
DVL1 0.073 0.065 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.1 0.084 -10000 0 -0.53 3 3
DKK1/LRP6/Kremen 2 -0.11 0.14 -10000 0 -0.59 47 47
LRP6 -0.001 0.013 -10000 0 -0.28 2 2
CSNK1A1 0.004 0.017 -10000 0 -10000 0 0
NLK 0 0.009 -10000 0 -10000 0 0
CCND1 0.003 0.1 -10000 0 -1.6 3 3
WNT1 0 0.009 -10000 0 -0.28 1 1
GSK3A 0.003 0.005 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.045 0.047 0.35 7 -10000 0 7
APC 0 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.15 0.14 0.27 483 -10000 0 483
CREBBP 0.004 0.015 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.01 0.052 -9999 0 -10000 0 0
GPC2 -0.034 0.099 -9999 0 -0.29 105 105
GPC2/Midkine -0.028 0.077 -9999 0 -0.4 16 16
neuron projection morphogenesis -0.028 0.077 -9999 0 -0.4 16 16
IL27-mediated signaling events

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.002 0.012 -10000 0 -0.28 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.023 0.11 0.45 21 -10000 0 21
IL27/IL27R/JAK1 -0.056 0.17 -10000 0 -0.68 27 27
TBX21 -0.032 0.21 -10000 0 -0.62 63 63
IL12B -0.048 0.11 -10000 0 -0.28 176 176
IL12A -0.029 0.15 -10000 0 -0.55 63 63
IL6ST -0.067 0.24 -10000 0 -0.83 79 79
IL27RA/JAK1 -0.006 0.065 -10000 0 -1.3 2 2
IL27 -0.023 0.084 -10000 0 -0.29 30 30
TYK2 0.009 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.13 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.023 0.11 0.45 21 -10000 0 21
T cell proliferation during immune response 0.023 0.11 0.45 21 -10000 0 21
MAPKKK cascade -0.023 0.11 -10000 0 -0.45 21 21
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.006 0.04 -10000 0 -0.28 19 19
IL12RB1 -0.011 0.06 -10000 0 -0.3 35 35
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.049 0.23 -10000 0 -0.64 79 79
IL27/IL27R/JAK2/TYK2 -0.023 0.12 -10000 0 -0.46 20 20
positive regulation of T cell mediated cytotoxicity -0.023 0.11 -10000 0 -0.45 21 21
STAT1 (dimer) -0.077 0.22 0.47 19 -0.76 39 58
JAK2 0.003 0.028 -10000 0 -0.83 1 1
JAK1 0 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.035 0.099 -10000 0 -0.53 8 8
T cell proliferation -0.19 0.25 -10000 0 -0.49 343 343
IL12/IL12R/TYK2/JAK2 0.013 0.07 -10000 0 -10000 0 0
IL17A -0.13 0.18 -10000 0 -10000 0 0
mast cell activation 0.023 0.11 0.45 21 -10000 0 21
IFNG 0.001 0.022 -10000 0 -0.076 9 9
T cell differentiation -0.003 0.005 -10000 0 -0.018 27 27
STAT3 (dimer) -0.035 0.099 -10000 0 -0.5 10 10
STAT5A (dimer) -0.038 0.11 -10000 0 -0.53 16 16
STAT4 (dimer) -0.053 0.14 -10000 0 -0.53 46 46
STAT4 -0.033 0.16 -10000 0 -0.81 37 37
T cell activation -0.008 0.008 0.13 2 -10000 0 2
IL27R/JAK2/TYK2 -0.046 0.15 -10000 0 -0.58 35 35
GATA3 -0.042 0.28 -10000 0 -1.5 33 33
IL18 0.006 0.03 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production -0.034 0.098 -10000 0 -0.49 10 10
IL27/EBI3 -0.023 0.081 -10000 0 -0.56 11 11
IL27RA 0 0.071 -10000 0 -1.4 2 2
IL6 -0.3 0.4 -10000 0 -0.82 338 338
STAT5A -0.006 0.072 -10000 0 -0.82 7 7
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.003 0.027 0.48 2 -10000 0 2
IL1B 0.002 0.076 -10000 0 -0.53 16 16
EBI3 -0.005 0.078 -10000 0 -0.63 11 11
TNF -0.003 0.085 -10000 0 -0.64 14 14
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.13 -10000 0 -0.37 74 74
TBX21 -0.009 0.34 -10000 0 -1.3 47 47
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.005 0.066 -10000 0 -0.3 35 35
GADD45B 0.037 0.21 -10000 0 -0.83 25 25
IL12RB2 -0.061 0.2 -10000 0 -0.51 118 118
GADD45G 0.031 0.21 -10000 0 -0.89 21 21
natural killer cell activation 0.007 0.017 -10000 0 -10000 0 0
RELB -0.002 0.024 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL18 0.007 0.045 -10000 0 -10000 0 0
IL2RA -0.029 0.11 -10000 0 -0.36 72 72
IFNG -0.04 0.098 -10000 0 -0.28 131 131
STAT3 (dimer) 0.031 0.21 -10000 0 -0.64 45 45
HLA-DRB5 -0.025 0.095 -10000 0 -0.32 70 70
FASLG 0.014 0.26 -10000 0 -1.1 29 29
NF kappa B2 p52/RelB -0.075 0.19 -10000 0 -0.74 49 49
CD4 0 0 -10000 0 -10000 0 0
SOCS1 -0.003 0.038 -10000 0 -0.34 9 9
EntrezGene:6955 -0.006 0.013 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.5 56 56
CD3E -0.021 0.14 -10000 0 -0.53 50 50
CD3G -0.032 0.16 -10000 0 -0.74 38 38
IL12Rbeta2/JAK2 -0.03 0.16 -10000 0 -0.66 47 47
CCL3 0.018 0.26 -10000 0 -0.93 36 36
CCL4 0.02 0.25 -10000 0 -0.9 33 33
HLA-A 0.009 0.02 -10000 0 -10000 0 0
IL18/IL18R 0.023 0.14 -10000 0 -0.58 44 44
NOS2 0.024 0.24 -10000 0 -0.88 36 36
IL12/IL12R/TYK2/JAK2/SPHK2 -0.002 0.13 -10000 0 -0.36 73 73
IL1R1 0.011 0.28 -10000 0 -1.1 33 33
IL4 -0.005 0.017 -10000 0 -10000 0 0
JAK2 0.016 0.032 -10000 0 -0.84 1 1
EntrezGene:6957 -0.005 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.029 0.25 -10000 0 -1.1 38 38
RAB7A 0.052 0.19 -10000 0 -0.77 16 16
lysosomal transport 0.053 0.18 -10000 0 -0.72 16 16
FOS -0.37 0.67 -10000 0 -1.3 293 293
STAT4 (dimer) 0.027 0.26 -10000 0 -0.89 40 40
STAT5A (dimer) -0.078 0.21 -10000 0 -0.69 61 61
GZMA 0.009 0.28 -10000 0 -1.1 31 31
GZMB -0.002 0.3 -10000 0 -1.2 36 36
HLX -0.001 0.013 -10000 0 -10000 0 0
LCK 0.011 0.28 -10000 0 -0.81 59 59
TCR/CD3/MHC II/CD4 -0.065 0.2 -10000 0 -0.57 68 68
IL2/IL2R -0.028 0.097 -10000 0 -0.47 33 33
MAPK14 0.042 0.22 -10000 0 -0.83 27 27
CCR5 0.031 0.22 -10000 0 -0.85 26 26
IL1B 0.005 0.1 -10000 0 -0.7 16 16
STAT6 0.027 0.085 -10000 0 -0.25 9 9
STAT4 -0.033 0.16 -10000 0 -0.81 37 37
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.006 0.04 -10000 0 -0.28 19 19
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B -0.039 0.12 -10000 0 -0.27 176 176
CD8A -0.001 0.077 -10000 0 -0.38 28 28
CD8B -0.024 0.16 -10000 0 -0.83 30 30
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.003 0.13 0.36 74 -10000 0 74
IL2RB -0.012 0.056 -10000 0 -0.28 38 38
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.24 -10000 0 -0.8 40 40
IL2RG -0.016 0.081 -10000 0 -0.82 5 5
IL12 -0.049 0.17 -10000 0 -0.61 55 55
STAT5A -0.006 0.072 -10000 0 -0.82 7 7
CD247 -0.015 0.13 -10000 0 -0.62 33 33
IL2 -0.002 0.026 -10000 0 -0.28 8 8
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.034 0.2 -10000 0 -0.72 63 63
IL12/IL12R/TYK2/JAK2 0.014 0.28 -10000 0 -0.82 57 57
MAP2K3 0.038 0.22 -10000 0 -0.82 28 28
RIPK2 -0.002 0.021 -10000 0 -0.28 5 5
MAP2K6 0.034 0.22 -10000 0 -0.81 31 31
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.03 -10000 0 -0.47 3 3
IL18RAP -0.018 0.16 -10000 0 -0.8 36 36
IL12Rbeta1/TYK2 0.014 0.051 -10000 0 -0.69 1 1
EOMES -0.021 0.17 -10000 0 -1.5 12 12
STAT1 (dimer) 0.035 0.21 -10000 0 -0.69 34 34
T cell proliferation 0.036 0.19 -10000 0 -0.64 38 38
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.003 0.096 -10000 0 -0.83 12 12
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.058 0.17 -10000 0 -0.75 35 35
ATF2 0.049 0.2 -10000 0 -0.78 25 25
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.034 0.12 -10000 0 -0.62 32 32
FYN 0.016 0.18 -10000 0 -0.77 35 35
LAT/GRAP2/SLP76 -0.027 0.15 -10000 0 -0.66 36 36
IKBKB -0.001 0.013 -10000 0 -10000 0 0
AKT1 0.031 0.12 -10000 0 -0.48 36 36
B2M 0.008 0.006 -10000 0 -10000 0 0
IKBKG -0.008 0.026 -10000 0 -0.19 1 1
MAP3K8 -0.005 0.062 -10000 0 -0.82 5 5
mol:Ca2+ -0.026 0.05 -10000 0 -0.12 184 184
integrin-mediated signaling pathway -0.001 0.026 -10000 0 -0.55 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.023 0.17 -10000 0 -0.74 36 36
TRPV6 -0.17 0.34 -10000 0 -0.8 198 198
CD28 -0.007 0.066 -10000 0 -0.49 13 13
SHC1 0.011 0.18 -10000 0 -0.83 33 33
receptor internalization -0.001 0.2 -10000 0 -0.86 39 39
PRF1 -0.001 0.23 -10000 0 -1.1 30 30
KRAS 0 0.009 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -10000 0 0
COT/AKT1 0.033 0.1 -10000 0 -0.39 35 35
LAT 0.009 0.19 -10000 0 -0.81 36 36
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.5 56 56
CD3E -0.018 0.14 -10000 0 -0.52 50 50
CD3G -0.031 0.16 -10000 0 -0.83 31 31
RASGRP2 -0.006 0.04 -10000 0 -0.18 41 41
RASGRP1 0.038 0.12 -10000 0 -0.48 37 37
HLA-A 0.01 0.019 -10000 0 -10000 0 0
RASSF5 -0.002 0.04 -10000 0 -0.64 3 3
RAP1A/GTP/RAPL -0.001 0.026 -10000 0 -0.56 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.033 0.042 -10000 0 -0.12 34 34
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.047 -10000 0 -0.24 22 22
PRKCA -0.011 0.084 -10000 0 -0.32 46 46
GRAP2 -0.014 0.1 -10000 0 -0.82 14 14
mol:IP3 0.022 0.15 0.27 157 -0.45 35 192
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.006 0.21 -10000 0 -0.95 33 33
ORAI1 0.082 0.16 0.39 184 -10000 0 184
CSK 0.009 0.19 -10000 0 -0.85 33 33
B7 family/CD28 -0.02 0.18 -10000 0 -0.75 39 39
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.22 -10000 0 -1 34 34
PTPN6 0.008 0.19 -10000 0 -0.82 35 35
VAV1 0.011 0.18 -10000 0 -0.81 35 35
Monovalent TCR/CD3 -0.029 0.21 -10000 0 -0.71 54 54
CBL 0 0 -10000 0 -10000 0 0
LCK 0.01 0.19 -10000 0 -0.83 36 36
PAG1 0.008 0.19 -10000 0 -0.84 34 34
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.002 0.22 -10000 0 -0.95 36 36
CD80 -0.08 0.12 -10000 0 -0.28 262 262
CD86 -0.002 0.021 -10000 0 -0.28 3 3
PDK1/CARD11/BCL10/MALT1 -0.017 0.057 -10000 0 -0.28 28 28
HRAS -0.001 0.013 -10000 0 -0.28 2 2
GO:0035030 -0.045 0.13 -10000 0 -0.6 39 39
CD8A -0.004 0.077 -10000 0 -0.38 28 28
CD8B -0.024 0.16 -10000 0 -0.83 30 30
PTPRC -0.009 0.074 -10000 0 -0.83 6 6
PDK1/PKC theta 0.036 0.15 -10000 0 -0.6 38 38
CSK/PAG1 0.014 0.18 -10000 0 -0.81 33 33
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.001 0.011 -10000 0 -10000 0 0
GRAP2/SLP76 -0.034 0.17 -10000 0 -0.79 36 36
STIM1 0.043 0.081 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.053 -10000 0 -0.18 27 27
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.005 0.23 -10000 0 -0.96 39 39
mol:DAG -0.005 0.1 -10000 0 -0.41 36 36
RAP1A/GDP 0.015 0.018 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
CD247 -0.015 0.13 -10000 0 -0.64 31 31
cytotoxic T cell degranulation 0.002 0.21 -10000 0 -1 30 30
RAP1A/GTP -0.003 0.014 -10000 0 -0.068 25 25
mol:PI-3-4-5-P3 0.027 0.14 -10000 0 -0.58 36 36
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.016 0.18 0.29 150 -0.61 36 186
NRAS -0.001 0.013 -10000 0 -0.28 2 2
ZAP70 -0.029 0.13 -10000 0 -0.83 19 19
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.024 0.14 -10000 0 -0.63 36 36
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.033 0.14 -10000 0 -0.6 46 46
CARD11 -0.008 0.055 -10000 0 -0.33 21 21
PRKCB -0.01 0.086 -10000 0 -0.35 38 38
PRKCE -0.005 0.069 -10000 0 -0.28 35 35
PRKCQ 0.026 0.18 -10000 0 -0.7 39 39
LCP2 0 0.009 -10000 0 -0.28 1 1
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.032 0.1 -10000 0 -0.4 36 36
IKK complex 0.042 0.043 -10000 0 -0.12 24 24
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.037 0.079 -10000 0 -0.3 31 31
PDPK1 0.034 0.11 -10000 0 -0.46 34 34
TCR/CD3/MHC I/CD8/Fyn -0.006 0.24 -10000 0 -0.97 42 42
Insulin Pathway

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
CBL/APS/CAP -0.12 0.22 -9999 0 -0.49 228 228
TC10/GTP -0.1 0.18 -9999 0 -0.43 216 216
Insulin Receptor/Insulin/IRS1/Shp2 -0.02 0.1 -9999 0 -0.52 36 36
HRAS -0.001 0.013 -9999 0 -0.28 2 2
APS homodimer -0.011 0.055 -9999 0 -0.28 37 37
GRB14 -0.1 0.23 -9999 0 -0.47 194 194
FOXO3 -0.013 0.062 -9999 0 -0.72 6 6
AKT1 -0.054 0.12 -9999 0 -0.4 77 77
INSR 0 0.009 -9999 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.027 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.2 0.35 -9999 0 -0.82 216 216
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.032 0.031 -9999 0 -10000 0 0
CAV1 -0.12 0.23 -9999 0 -0.53 207 207
CBL/APS/CAP/Crk-II/C3G -0.11 0.2 -9999 0 -0.48 216 216
Insulin Receptor/Insulin/IRS1/NCK2 -0.02 0.1 -9999 0 -0.52 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.089 -9999 0 -0.45 37 37
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.056 -9999 0 -10000 0 0
RPS6KB1 -0.005 0.13 -9999 0 -0.47 7 7
PARD6A -0.001 0.016 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.047 0.11 -9999 0 -0.49 7 7
HRAS/GTP -0.016 0.076 -9999 0 -0.49 2 2
Insulin Receptor 0 0.009 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.019 0.094 -9999 0 -0.48 36 36
PRKCI -0.012 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.059 0.14 -9999 0 -0.43 105 105
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.002 -9999 0 -10000 0 0
PI3K -0.019 0.091 -9999 0 -0.46 37 37
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP 0 0.009 -9999 0 -10000 0 0
AKT2 -0.054 0.12 -9999 0 -0.4 78 78
PRKCZ -0.013 0.038 -9999 0 -0.62 1 1
SH2B2 -0.011 0.055 -9999 0 -0.28 37 37
SHC/SHIP -0.018 0.088 -9999 0 -0.45 36 36
F2RL2 -0.056 0.14 -9999 0 -0.34 151 151
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0.004 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.12 0.22 -9999 0 -0.51 216 216
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.003 -9999 0 -10000 0 0
INPP5D -0.019 0.095 -9999 0 -0.49 36 36
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.008 0.068 -9999 0 -1 4 4
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.82 36 36
p62DOK/RasGAP 0 0.002 -9999 0 -10000 0 0
INS 0.003 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.094 -9999 0 -0.48 36 36
GRB2 0 0.009 -9999 0 -10000 0 0
EIF4EBP1 -0.01 0.14 -9999 0 -0.47 14 14
PTPRA 0 0.001 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.013 0.065 -9999 0 -0.34 36 36
Insulin Receptor/Insulin/IRS1 -0.021 0.1 -9999 0 -0.53 36 36
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.024 0.073 -9999 0 -0.48 17 17
Regulation of Telomerase

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
Telomerase catalytic core complex -0.051 0.11 -9999 0 -0.64 3 3
RAD9A 0 0.009 -9999 0 -0.28 1 1
AP1 -0.2 0.3 -9999 0 -0.65 284 284
IFNAR2 0.009 0.006 -9999 0 -10000 0 0
AKT1 -0.037 0.11 -9999 0 -0.29 131 131
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.64 131 131
NFX1/SIN3/HDAC complex 0 0.001 -9999 0 -10000 0 0
EGF -0.16 0.33 -9999 0 -0.82 183 183
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.064 0.084 -9999 0 -0.6 3 3
SAP18 0 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.14 0.14 -9999 0 -0.28 485 485
WRN 0 0 -9999 0 -10000 0 0
SP1 0.01 0.006 -9999 0 -10000 0 0
SP3 0 0 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.049 0.074 -9999 0 -0.58 2 2
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.052 0.12 -9999 0 -0.66 3 3
CCND1 -0.044 0.13 -9999 0 -1.3 3 3
MAX 0 0 -9999 0 -10000 0 0
RBBP7 -0.002 0.026 -9999 0 -0.28 8 8
RBBP4 0 0 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
Telomerase/911 -0.001 0.004 -9999 0 -10000 0 0
CDKN1B 0.006 0.076 -9999 0 -0.9 3 3
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.018 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0 0 -9999 0 -10000 0 0
JUN -0.008 0.082 -9999 0 -0.82 9 9
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.26 0.38 -9999 0 -0.82 283 283
IFN-gamma/IRF1 -0.025 0.061 -9999 0 -0.35 5 5
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.031 0.087 -9999 0 -0.28 101 101
Telomerase -0.003 0.026 -9999 0 -10000 0 0
IRF1 -0.002 0.019 -9999 0 -0.27 3 3
ESR1 -0.15 0.29 -9999 0 -0.76 149 149
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.002 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC2 0.009 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.007 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0 0.009 -9999 0 -0.28 1 1
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.016 -9999 0 -0.28 3 3
TERT/NF kappa B1/14-3-3 -0.062 0.098 -9999 0 -0.67 3 3
NR2F2 0 0.048 -9999 0 -0.82 3 3
MAPK3 0.014 0.019 -9999 0 -10000 0 0
MAPK1 0.014 0.019 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0 0.009 -9999 0 -0.28 1 1
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.3 0.39 -9999 0 -0.82 331 331
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.35 0.37 -9999 0 -0.7 453 453
MYC -0.014 0.12 -9999 0 -0.82 20 20
IL2 0.004 0.027 -9999 0 -0.28 8 8
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -10000 0 0
TGFB1 0 0.009 -9999 0 -0.28 1 1
TRF2/BLM -0.017 0.049 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.06 0.083 -9999 0 -0.64 2 2
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.049 0.074 -9999 0 -0.58 2 2
Smad3/Myc -0.012 0.08 -9999 0 -0.55 20 20
911 complex 0 0.004 -9999 0 -10000 0 0
IFNG -0.038 0.095 -9999 0 -10000 0 0
Telomerase/PinX1 -0.049 0.074 -9999 0 -0.58 2 2
Telomerase/AKT1/mTOR/p70S6K 0.003 0.054 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.049 0.074 -9999 0 -0.58 2 2
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.049 0.074 -9999 0 -0.58 2 2
E2F1 -0.082 0.14 -9999 0 -0.28 292 292
ZNFX1 0 0 -9999 0 -10000 0 0
PIF1 -0.053 0.11 -9999 0 -0.28 174 174
NCL 0 0 -9999 0 -10000 0 0
DKC1 -0.001 0.013 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0 0.031 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.019 0.033 -9999 0 -0.66 1 1
positive regulation of JNK cascade -0.047 0.11 -9999 0 -0.48 5 5
Syndecan-4/ADAM12 -0.029 0.054 -9999 0 -0.66 1 1
CCL5 -0.014 0.078 -9999 0 -0.36 35 35
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.001 0.02 -9999 0 -0.28 4 4
ADAM12 -0.022 0.081 -9999 0 -0.82 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.001 0.016 -9999 0 -0.28 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.056 0.043 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.071 0.14 -9999 0 -0.54 11 11
Syndecan-4/CXCL12/CXCR4 -0.048 0.11 -9999 0 -0.55 2 2
Syndecan-4/Laminin alpha3 -0.13 0.2 -9999 0 -0.5 149 149
MDK -0.01 0.052 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.028 0.07 -9999 0 -0.54 3 3
Syndecan-4/Midkine -0.022 0.04 -9999 0 -0.66 1 1
FZD7 -0.017 0.12 -9999 0 -0.82 19 19
Syndecan-4/FGFR1/FGF -0.19 0.22 -9999 0 -0.54 54 54
THBS1 -0.001 0.027 -9999 0 -0.82 1 1
integrin-mediated signaling pathway -0.028 0.071 -9999 0 -0.5 12 12
positive regulation of MAPKKK cascade -0.047 0.11 -9999 0 -0.48 5 5
Syndecan-4/TACI -0.03 0.068 -9999 0 -0.53 5 5
CXCR4 -0.008 0.046 -9999 0 -10000 0 0
cell adhesion -0.025 0.055 -9999 0 -0.36 21 21
Syndecan-4/Dynamin -0.019 0.033 -9999 0 -0.66 1 1
Syndecan-4/TSP1 -0.02 0.036 -9999 0 -0.66 1 1
Syndecan-4/GIPC -0.019 0.033 -9999 0 -0.66 1 1
Syndecan-4/RANTES -0.025 0.051 -9999 0 -0.52 5 5
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.096 0.26 -9999 0 -0.82 106 106
LAMA3 -0.2 0.36 -9999 0 -0.82 227 227
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.005 0.12 -9999 0 -0.74 23 23
Syndecan-4/alpha-Actinin -0.02 0.036 -9999 0 -0.56 2 2
TFPI -0.035 0.17 -9999 0 -0.82 39 39
F2 0.001 0.025 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.24 -9999 0 -0.6 100 100
ACTN1 -0.001 0.027 -9999 0 -0.82 1 1
TNC -0.019 0.12 -9999 0 -0.71 24 24
Syndecan-4/CXCL12 -0.052 0.12 -9999 0 -0.48 23 23
FGF6 -0.002 0.039 -9999 0 -0.82 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.06 0.22 -9999 0 -0.82 67 67
TNFRSF13B -0.025 0.12 -9999 0 -0.82 14 14
FGF2 -0.33 0.4 -9999 0 -0.82 370 370
FGFR1 -0.01 0.087 -9999 0 -0.73 12 12
Syndecan-4/PI-4-5-P2 -0.014 0.044 -9999 0 -0.66 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.15 -9999 0 -0.29 202 202
cell migration -0.025 0.019 -9999 0 -10000 0 0
PRKCD 0.004 0.013 -9999 0 -0.27 1 1
vasculogenesis -0.019 0.035 -9999 0 -0.63 1 1
SDC4 -0.014 0.046 -9999 0 -0.7 1 1
Syndecan-4/Tenascin C -0.029 0.074 -9999 0 -0.52 11 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.044 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.019 0.033 -9999 0 -0.66 1 1
MMP9 -0.12 0.14 -9999 0 -0.28 408 408
Rac1/GTP -0.026 0.056 -9999 0 -0.36 21 21
cytoskeleton organization -0.019 0.032 -9999 0 -0.63 1 1
GIPC1 0 0.009 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.038 0.095 -9999 0 -0.52 10 10
Coregulation of Androgen receptor activity

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
NRIP1 -0.004 0.035 -10000 0 -0.82 1 1
SVIL -0.009 0.05 -10000 0 -0.82 3 3
ZNF318 0.024 0.06 -10000 0 -10000 0 0
JMJD2C -0.004 0.043 -10000 0 -0.13 89 89
T-DHT/AR/Ubc9 -0.076 0.18 -10000 0 -0.57 104 104
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.003 0.007 -10000 0 -10000 0 0
PELP1 0.005 0.013 -10000 0 -10000 0 0
CTNNB1 -0.005 0.013 -10000 0 -10000 0 0
AKT1 0.008 0.019 -10000 0 -10000 0 0
PTK2B -0.004 0.011 -10000 0 -10000 0 0
MED1 0.002 0.048 -10000 0 -0.28 19 19
MAK 0.013 0.11 0.28 1 -0.8 10 11
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.01 0.057 -10000 0 -0.82 4 4
GSN -0.015 0.1 -10000 0 -0.82 13 13
NCOA2 -0.015 0.11 -10000 0 -0.83 17 17
NCOA6 -0.002 0.021 -10000 0 -0.28 1 1
DNA-PK 0.023 0.061 -10000 0 -10000 0 0
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 -0.005 0.013 -10000 0 -10000 0 0
cell proliferation -0.006 0.11 -10000 0 -0.87 10 10
XRCC5 0.007 0.016 -10000 0 -10000 0 0
UBE3A -0.007 0.032 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.089 0.21 -10000 0 -0.61 117 117
FHL2 -0.016 0.12 -10000 0 -1.3 5 5
RANBP9 -0.002 0.019 -10000 0 -10000 0 0
JMJD1A -0.012 0.057 -10000 0 -0.14 138 138
CDK6 -0.006 0.078 -10000 0 -0.72 10 10
TGFB1I1 -0.009 0.05 -10000 0 -0.82 3 3
T-DHT/AR/CyclinD1 -0.088 0.19 -10000 0 -0.58 107 107
XRCC6 0.007 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.063 0.21 -10000 0 -0.56 120 120
CTDSP1 0 0 -10000 0 -10000 0 0
CTDSP2 0.016 0.041 -10000 0 -10000 0 0
BRCA1 -0.007 0.023 -10000 0 -0.36 1 1
TCF4 0.007 0.074 -10000 0 -0.82 6 6
CDKN2A -0.036 0.1 -10000 0 -10000 0 0
SRF 0.024 0.02 -10000 0 -10000 0 0
NKX3-1 -0.083 0.2 -10000 0 -1.2 20 20
KLK3 -0.2 0.54 -10000 0 -1.6 121 121
TMF1 0 0 -10000 0 -10000 0 0
HNRNPA1 0.009 0.022 -10000 0 -10000 0 0
AOF2 -0.009 0.025 -10000 0 -0.072 121 121
APPL1 0.035 0.034 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.067 0.19 -10000 0 -0.57 104 104
AR -0.092 0.27 -10000 0 -0.83 105 105
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.009 0.022 -10000 0 -10000 0 0
PAWR -0.001 0.027 -10000 0 -0.82 1 1
PRKDC 0.005 0.024 -10000 0 -10000 0 0
PA2G4 0.012 0.029 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.063 0.17 -10000 0 -0.53 104 104
RPS6KA3 -0.006 0.052 -10000 0 -0.82 3 3
T-DHT/AR/ARA70 -0.08 0.18 -10000 0 -0.57 104 104
LATS2 0.01 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.058 0.18 -10000 0 -0.52 104 104
Cyclin D3/CDK11 p58 0 0.006 -10000 0 -10000 0 0
VAV3 -0.016 0.077 -10000 0 -0.71 8 8
KLK2 -0.12 0.34 -10000 0 -1.2 76 76
CASP8 0.004 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.081 0.18 -10000 0 -0.54 117 117
TMPRSS2 -0.18 0.4 -10000 0 -1.2 119 119
CCND1 -0.016 0.072 -10000 0 -0.33 38 38
PIAS1 -0.007 0.032 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.035 -10000 0 -0.08 166 166
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.014 0.052 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.19 -10000 0 -0.57 112 112
CMTM2 0.003 0.013 -10000 0 -0.28 1 1
SNURF -0.021 0.13 -10000 0 -0.82 23 23
ZMIZ1 0.003 0.032 -10000 0 -0.35 1 1
CCND3 0.001 0.011 -10000 0 -0.28 1 1
TGIF1 0.009 0.022 -10000 0 -10000 0 0
FKBP4 -0.004 0.032 -10000 0 -0.29 7 7
PLK1 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
regulation of centriole-centriole cohesion 0.027 0.027 -9999 0 -10000 0 0
BUB1B -0.037 0.047 -9999 0 -10000 0 0
PLK1 -0.007 0.021 -9999 0 -10000 0 0
PLK1S1 0.001 0.013 -9999 0 -10000 0 0
KIF2A 0.003 0.019 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.007 0.021 -9999 0 -10000 0 0
GOLGA2 0 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.16 0.11 -9999 0 -0.26 462 462
WEE1 -0.001 0.022 -9999 0 -10000 0 0
cytokinesis -0.045 0.047 -9999 0 -0.26 5 5
PP2A-alpha B56 0.034 0.022 -9999 0 -10000 0 0
AURKA 0.003 0.011 -9999 0 -10000 0 0
PICH/PLK1 -0.074 0.092 -9999 0 -0.32 11 11
CENPE -0.051 0.083 -9999 0 -0.2 2 2
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.019 -9999 0 -10000 0 0
PPP2CA 0 0 -9999 0 -10000 0 0
FZR1 0 0 -9999 0 -10000 0 0
TPX2 -0.002 0.013 -9999 0 -10000 0 0
PAK1 -0.006 0.04 -9999 0 -10000 0 0
SPC24 -0.17 0.14 -9999 0 -0.28 562 562
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.002 0.015 -9999 0 -10000 0 0
GORASP1 0 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.004 0.012 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
STAG2 -0.001 0.027 -9999 0 -0.82 1 1
GRASP65/GM130/RAB1/GTP 0.008 0.009 -9999 0 -10000 0 0
spindle elongation -0.007 0.021 -9999 0 -10000 0 0
ODF2 0 0 -9999 0 -10000 0 0
BUB1 0.029 0.019 -9999 0 -10000 0 0
TPT1 0.001 0.013 -9999 0 -10000 0 0
CDC25C -0.002 0.013 -9999 0 -10000 0 0
CDC25B -0.003 0.038 -9999 0 -0.28 17 17
SGOL1 -0.027 0.027 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.021 0.04 -9999 0 -10000 0 0
CDC14B -0.009 0.11 -9999 0 -0.65 27 27
CDC20 -0.15 0.14 -9999 0 -10000 0 0
PLK1/PBIP1 -0.029 0.053 -9999 0 -10000 0 0
mitosis -0.007 0.007 -9999 0 -0.022 2 2
FBXO5 0.001 0.021 -9999 0 -10000 0 0
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.18 0.13 -9999 0 -0.28 592 592
metaphase plate congression -0.002 0.014 -9999 0 -10000 0 0
ERCC6L -0.065 0.084 -9999 0 -10000 0 0
NLP/gamma Tubulin 0 0.012 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.001 0.013 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.14 0.095 -9999 0 -0.27 246 246
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.003 -9999 0 -10000 0 0
RAB1A 0 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.001 0.022 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.049 -9999 0 -0.3 12 12
microtubule-based process -0.11 0.061 -9999 0 -0.2 2 2
Golgi organization -0.007 0.021 -9999 0 -10000 0 0
Cohesin/SA2 -0.008 0.018 -9999 0 -0.48 1 1
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.12 -9999 0 -10000 0 0
APC/C/CDC20 -0.084 0.075 -9999 0 -0.2 2 2
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.029 0.052 -9999 0 -10000 0 0
PRC1 -0.076 0.12 -9999 0 -0.28 248 248
ECT2 -0.003 0.038 -9999 0 -10000 0 0
C13orf34 0.001 0.02 -9999 0 -10000 0 0
NUDC -0.002 0.014 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.037 0.047 -9999 0 -10000 0 0
spindle assembly -0.002 0.018 -9999 0 -10000 0 0
spindle stabilization 0.001 0.013 -9999 0 -10000 0 0
APC/C/HCDH1 -0.017 0.095 -9999 0 -0.56 27 27
MKLP2/PLK1 -0.11 0.061 -9999 0 -0.2 2 2
CCNB1 -0.062 0.12 -9999 0 -0.28 207 207
PPP1CB 0 0 -9999 0 -10000 0 0
BTRC 0 0 -9999 0 -10000 0 0
ROCK2 0.001 0.057 -9999 0 -0.52 10 10
TUBG1 0.001 0.013 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.021 0.039 -9999 0 -10000 0 0
MLF1IP -0.03 0.075 -9999 0 -10000 0 0
INCENP 0 0 -9999 0 -10000 0 0
BCR signaling pathway

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.004 0.11 -10000 0 -0.46 30 30
IKBKB 0.015 0.054 -10000 0 -0.26 3 3
AKT1 0.005 0.08 0.25 1 -0.28 16 17
IKBKG 0.018 0.056 -10000 0 -0.28 3 3
CALM1 -0.012 0.096 -10000 0 -0.46 27 27
PIK3CA 0 0.009 -10000 0 -10000 0 0
MAP3K1 -0.009 0.15 -10000 0 -0.68 27 27
MAP3K7 0 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.1 -10000 0 -0.49 27 27
DOK1 0 0.009 -10000 0 -10000 0 0
AP-1 -0.045 0.11 -10000 0 -0.26 75 75
LYN 0 0 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.08 0.22 -10000 0 -0.67 96 96
CD22 -0.062 0.19 -10000 0 -0.56 85 85
CAMK2G -0.003 0.09 -10000 0 -0.51 15 15
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.049 0.14 -10000 0 -0.81 15 15
GO:0007205 -0.021 0.1 -10000 0 -0.5 27 27
SYK 0 0.009 -10000 0 -0.28 1 1
ELK1 -0.012 0.097 -10000 0 -0.47 27 27
NFATC1 -0.016 0.13 -10000 0 -0.57 28 28
B-cell antigen/BCR complex -0.08 0.22 -10000 0 -0.67 96 96
PAG1/CSK -0.001 0.013 -10000 0 -10000 0 0
NFKBIB 0.015 0.02 -10000 0 -10000 0 0
HRAS -0.009 0.11 -10000 0 -0.49 27 27
NFKBIA 0.015 0.019 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.019 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.059 0.17 -10000 0 -0.55 84 84
mol:GDP -0.021 0.095 -10000 0 -0.47 27 27
PTEN -0.002 0.039 -10000 0 -0.82 2 2
CD79B -0.029 0.14 -10000 0 -0.63 42 42
NF-kappa-B/RelA/I kappa B alpha 0.019 0.016 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.024 0.16 -10000 0 -0.48 82 82
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
mol:IP3 -0.03 0.1 -10000 0 -0.51 27 27
CSK 0 0 -10000 0 -10000 0 0
FOS -0.14 0.23 -10000 0 -0.46 302 302
CHUK 0.018 0.056 -10000 0 -0.24 16 16
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.024 0.081 -10000 0 -0.49 16 16
PTPN6 -0.057 0.17 -10000 0 -0.52 85 85
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.12 1 1
VAV2 -0.07 0.17 -10000 0 -0.84 28 28
ubiquitin-dependent protein catabolic process 0.019 0.019 -10000 0 -10000 0 0
BTK -0.004 0.006 -10000 0 -10000 0 0
CD19 -0.08 0.18 -10000 0 -0.56 82 82
MAP4K1 -0.012 0.064 -10000 0 -0.82 2 2
CD72 -0.008 0.051 -10000 0 -0.3 23 23
PAG1 -0.002 0.021 -10000 0 -10000 0 0
MAPK14 0.002 0.13 -10000 0 -0.55 27 27
SH3BP5 0 0 -10000 0 -10000 0 0
PIK3AP1 -0.012 0.11 -10000 0 -0.55 27 27
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.042 0.14 -10000 0 -0.49 71 71
RAF1 -0.001 0.1 -10000 0 -0.45 27 27
RasGAP/p62DOK/SHIP -0.056 0.16 -10000 0 -0.52 84 84
CD79A -0.082 0.22 -10000 0 -0.57 133 133
re-entry into mitotic cell cycle -0.045 0.11 -10000 0 -0.26 71 71
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.015 0.085 -10000 0 -0.44 15 15
MAPK1 0.015 0.085 -10000 0 -0.44 15 15
CD72/SHP1 -0.054 0.16 -10000 0 -0.7 35 35
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.13 -10000 0 -0.54 30 30
actin cytoskeleton organization -0.025 0.15 -10000 0 -0.67 28 28
NF-kappa-B/RelA 0.042 0.031 -10000 0 -10000 0 0
Calcineurin -0.021 0.074 -10000 0 -0.45 15 15
PI3K -0.055 0.13 -10000 0 -0.55 31 31
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.033 0.11 -10000 0 -0.58 27 27
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.054 0.17 -10000 0 -0.85 31 31
DAPP1 -0.053 0.2 -10000 0 -1 30 30
cytokine secretion -0.014 0.12 -10000 0 -0.52 29 29
mol:DAG -0.03 0.1 -10000 0 -0.51 27 27
PLCG2 -0.001 0.029 -10000 0 -0.55 2 2
MAP2K1 0.007 0.093 -10000 0 -0.5 15 15
B-cell antigen/BCR complex/FcgammaRIIB -0.071 0.2 -10000 0 -0.64 84 84
mol:PI-3-4-5-P3 -0.041 0.091 0.35 1 -0.37 30 31
ETS1 0.004 0.087 -10000 0 -0.47 16 16
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.058 0.17 -10000 0 -0.55 82 82
B-cell antigen/BCR complex/LYN -0.059 0.2 -10000 0 -0.6 82 82
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 -0.029 0.17 -10000 0 -0.74 28 28
B-cell antigen/BCR complex/LYN/SYK -0.058 0.18 -10000 0 -0.57 84 84
CARD11 -0.016 0.1 -10000 0 -0.5 27 27
FCGR2B -0.003 0.048 -10000 0 -0.69 4 4
PPP3CA 0 0.009 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 -10000 0 -10000 0 0
PTPRC -0.009 0.074 -10000 0 -0.82 6 6
PDPK1 -0.026 0.061 0.22 1 -0.28 16 17
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.019 0.013 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.02 0.006 -9999 0 -10000 0 0
SMARCC1 0.004 0.021 -9999 0 -0.58 1 1
REL 0 0.062 -9999 0 -0.82 5 5
HDAC7 0.009 0.13 -9999 0 -0.63 11 11
JUN -0.008 0.081 -9999 0 -0.82 9 9
EP300 0 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0.002 0.004 -9999 0 -10000 0 0
MAPK14 0.004 0.1 -9999 0 -0.64 21 21
FOXO1 -0.007 0.077 -9999 0 -0.83 8 8
T-DHT/AR -0.005 0.14 -9999 0 -0.54 25 25
MAP2K6 -0.019 0.12 -9999 0 -0.81 22 22
BRM/BAF57 -0.001 0.011 -9999 0 -10000 0 0
MAP2K4 0 0.028 -9999 0 -0.83 1 1
SMARCA2 0 0 -9999 0 -10000 0 0
PDE9A -0.094 0.3 -9999 0 -1.2 57 57
NCOA2 -0.015 0.11 -9999 0 -0.82 17 17
CEBPA -0.006 0.077 -9999 0 -0.82 8 8
EHMT2 0 0 -9999 0 -10000 0 0
cell proliferation 0.016 0.14 -9999 0 -0.52 18 18
NR0B1 -0.01 0.051 -9999 0 -0.28 32 32
EGR1 -0.27 0.39 -9999 0 -0.83 295 295
RXRs/9cRA -0.13 0.22 -9999 0 -0.51 232 232
AR/RACK1/Src -0.005 0.11 -9999 0 -0.5 24 24
AR/GR -0.047 0.12 -9999 0 -0.44 37 37
GNB2L1 0.001 0.003 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.017 0.046 -9999 0 -0.64 4 4
T-DHT/AR/TIF2/CARM1 -0.035 0.12 -9999 0 -0.52 38 38
SRC 0.021 0.093 -9999 0 -0.5 24 24
NR3C1 -0.009 0.086 -9999 0 -0.82 10 10
KLK3 -0.22 0.44 -9999 0 -1.2 145 145
APPBP2 -0.001 0.016 -9999 0 -10000 0 0
TRIM24 0 0.009 -9999 0 -0.28 1 1
T-DHT/AR/TIP60 -0.026 0.096 -9999 0 -0.53 24 24
TMPRSS2 -0.17 0.43 -9999 0 -1.3 120 120
RXRG -0.21 0.36 -9999 0 -0.83 232 232
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0 0 -9999 0 -10000 0 0
NR2C2 -0.004 0.054 -9999 0 -0.82 4 4
KLK2 -0.04 0.25 -9999 0 -0.78 87 87
AR -0.023 0.13 -9999 0 -0.34 112 112
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -10000 0 0
MDM2 0.004 0.023 -9999 0 -10000 0 0
SRY 0.004 0.01 -9999 0 -10000 0 0
GATA2 -0.024 0.13 -9999 0 -0.82 23 23
MYST2 0.001 0.01 -9999 0 -0.28 1 1
HOXB13 -0.13 0.14 -9999 0 -0.31 63 63
T-DHT/AR/RACK1/Src -0.026 0.094 -9999 0 -0.51 24 24
positive regulation of transcription -0.024 0.13 -9999 0 -0.82 23 23
DNAJA1 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.013 -9999 0 -10000 0 0
NCOA1 0.011 0.029 -9999 0 -0.85 1 1
SPDEF -0.05 0.2 -9999 0 -0.69 72 72
T-DHT/AR/TIF2 0.021 0.081 -9999 0 -0.53 6 6
T-DHT/AR/Hsp90 -0.032 0.092 -9999 0 -0.53 24 24
GSK3B 0.001 0.004 -9999 0 -10000 0 0
NR2C1 0.002 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.014 0.099 -9999 0 -0.54 24 24
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.006 0.014 -9999 0 -10000 0 0
POU2F1 0.02 0.027 -9999 0 -0.41 1 1
T-DHT/AR/DAX-1 -0.034 0.096 -9999 0 -0.54 24 24
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 -0.001 0.016 -9999 0 -0.3 1 1
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.1 0.21 -10000 0 -0.59 131 131
AKT1 0.013 0.005 -10000 0 -10000 0 0
GSC -0.047 0.32 -10000 0 -1.5 41 41
NKX2-5 -0.039 0.096 -10000 0 -0.27 131 131
muscle cell differentiation 0.005 0.042 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.003 0.03 -10000 0 -10000 0 0
SMAD4 0.013 0.033 -10000 0 -10000 0 0
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.22 0.27 -10000 0 -0.55 365 365
SMAD3/SMAD4/VDR 0.006 0.029 -10000 0 -0.48 1 1
MYC -0.018 0.12 -10000 0 -0.83 20 20
CDKN2B 0.03 0.12 -10000 0 -1.5 5 5
AP1 -0.13 0.22 -10000 0 -0.44 263 263
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.012 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.001 0.039 -10000 0 -0.33 2 2
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.046 0.099 -10000 0 -0.4 4 4
SMAD3/SMAD4/GR -0.008 0.066 -10000 0 -0.6 10 10
GATA3 -0.038 0.16 -10000 0 -0.57 60 60
SKI/SIN3/HDAC complex/NCoR1 0.002 0.012 -10000 0 -10000 0 0
MEF2C/TIF2 -0.037 0.09 -10000 0 -0.54 19 19
endothelial cell migration -0.01 0.036 -10000 0 -10000 0 0
MAX 0.001 0.004 -10000 0 -10000 0 0
RBBP7 -0.002 0.026 -10000 0 -0.28 8 8
RBBP4 0 0 -10000 0 -10000 0 0
RUNX2 -0.004 0.032 -10000 0 -0.28 12 12
RUNX3 -0.004 0.056 -10000 0 -0.82 4 4
RUNX1 -0.001 0.027 -10000 0 -0.82 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.008 0.086 -10000 0 -0.83 10 10
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.05 0.063 -10000 0 -1.4 1 1
KAT2B 0.001 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.02 0.069 -10000 0 -0.42 4 4
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0 -10000 0 -10000 0 0
SERPINE1 0.01 0.036 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.002 0.029 -10000 0 -0.56 1 1
SMAD3/SMAD4/ATF3 -0.088 0.21 -10000 0 -0.59 137 137
SAP30 -0.001 0.018 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.006 0.024 -10000 0 -10000 0 0
JUN -0.089 0.24 -10000 0 -0.46 164 164
SMAD3/SMAD4/IRF7 -0.009 0.057 -10000 0 -10000 0 0
TFE3 0.016 0.007 -10000 0 -10000 0 0
COL1A2 0.029 0.091 -10000 0 -1.2 1 1
mesenchymal cell differentiation 0.003 0.028 -10000 0 -10000 0 0
DLX1 -0.051 0.13 -10000 0 -0.82 9 9
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.24 0.39 -10000 0 -0.82 283 283
SMAD3/SMAD4/Max -0.002 0.023 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0 -10000 0 -10000 0 0
ZBTB17 0 0.005 -10000 0 -10000 0 0
LAMC1 0.042 0.046 -10000 0 -0.81 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.023 -10000 0 -10000 0 0
IRF7 -0.022 0.075 -10000 0 -0.35 17 17
ESR1 -0.15 0.29 -10000 0 -0.57 247 247
HNF4A -0.004 0.033 -10000 0 -10000 0 0
MEF2C 0 0.086 -10000 0 -0.57 3 3
SMAD2-3/SMAD4 -0.002 0.029 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.003 0.024 -10000 0 -0.55 1 1
IGHV3OR16-13 -0.001 0.009 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.002 0.007 -10000 0 -10000 0 0
SKIL -0.003 0.03 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
SNIP1 0 0 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.002 0.025 -10000 0 -10000 0 0
MSG1/HSC70 -0.26 0.31 -10000 0 -0.63 365 365
SMAD2 0.014 0.022 -10000 0 -10000 0 0
SMAD3 0.013 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.006 0.021 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.02 -10000 0 -10000 0 0
NCOR1 -0.001 0.027 -10000 0 -0.83 1 1
NCOA2 -0.015 0.11 -10000 0 -0.82 17 17
NCOA1 -0.001 0.027 -10000 0 -0.82 1 1
MYOD/E2A -0.002 0.019 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.008 0.034 -10000 0 -10000 0 0
IFNB1 0.016 0.08 -10000 0 -0.4 10 10
SMAD3/SMAD4/MEF2C -0.023 0.067 -10000 0 -0.9 1 1
CITED1 -0.33 0.4 -10000 0 -0.81 377 377
SMAD2-3/SMAD4/ARC105 0 0.025 -10000 0 -10000 0 0
RBL1 -0.001 0.013 -10000 0 -0.28 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.021 0.058 -10000 0 -0.49 5 5
RUNX1-3/PEBPB2 -0.003 0.047 -10000 0 -0.67 4 4
SMAD7 -0.082 0.14 -10000 0 -0.56 8 8
MYC/MIZ-1 -0.013 0.094 -10000 0 -0.64 20 20
SMAD3/SMAD4 0.02 0.06 0.27 38 -10000 0 38
IL10 0.016 0.12 -10000 0 -0.53 35 35
PIASy/HDAC complex 0.001 0.003 -10000 0 -10000 0 0
PIAS3 0.001 0.005 -10000 0 -10000 0 0
CDK2 0.002 0.008 -10000 0 -10000 0 0
IL5 0.012 0.12 -10000 0 -0.52 33 33
CDK4 0.001 0.016 -10000 0 -0.28 2 2
PIAS4 0.001 0.003 -10000 0 -10000 0 0
ATF3 -0.12 0.3 -10000 0 -0.82 137 137
SMAD3/SMAD4/SP1 0.001 0.024 -10000 0 -10000 0 0
FOXG1 -0.02 0.071 -10000 0 -0.28 64 64
FOXO3 0.025 0.032 -10000 0 -0.63 2 2
FOXO1 0.02 0.062 -10000 0 -0.63 8 8
FOXO4 0.026 0.007 -10000 0 -10000 0 0
heart looping 0 0.086 -10000 0 -0.57 3 3
CEBPB 0.008 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.028 0.08 -10000 0 -0.59 9 9
MYOD1 -0.003 0.03 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.006 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 -0.024 0.12 -10000 0 -0.59 33 33
SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.03 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.001 0.048 -10000 0 -0.63 4 4
SMAD3/SMAD4/SP1-3 0.004 0.023 -10000 0 -10000 0 0
MED15 0 0 -10000 0 -10000 0 0
SP1 0.018 0.012 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.007 0.084 -10000 0 -0.42 5 5
ITGB5 0.051 0.042 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.067 0.19 -10000 0 -0.59 104 104
AR -0.094 0.26 -10000 0 -0.82 104 104
negative regulation of cell growth -0.027 0.074 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.006 0.029 -10000 0 -10000 0 0
E2F5 -0.006 0.041 -10000 0 -0.28 20 20
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0 0.052 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.042 -10000 0 -0.34 5 5
TFDP1 -0.001 0.018 -10000 0 -0.28 4 4
SMAD3/SMAD4/AP1 -0.13 0.22 -10000 0 -0.48 132 132
SMAD3/SMAD4/RUNX2 -0.003 0.028 -10000 0 -10000 0 0
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.001 0.027 -10000 0 -0.82 1 1
Thromboxane A2 receptor signaling

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
TGM2 0.001 0.036 -10000 0 -10000 0 0
GNB1/GNG2 -0.014 0.046 -10000 0 -0.2 30 30
AKT1 0.052 0.07 -10000 0 -0.2 51 51
EGF -0.16 0.33 -10000 0 -0.82 183 183
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.009 0.049 -10000 0 -0.43 3 3
mol:Ca2+ 0.049 0.096 -10000 0 -0.3 51 51
LYN -0.009 0.045 -10000 0 -0.33 2 2
RhoA/GTP -0.008 0.029 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.055 0.11 -10000 0 -0.34 51 51
GNG2 -0.006 0.072 -10000 0 -0.83 7 7
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.03 0.056 -10000 0 -0.55 6 6
G beta5/gamma2 -0.018 0.061 -10000 0 -0.27 28 28
PRKCH 0.051 0.11 -10000 0 -0.35 51 51
DNM1 -0.005 0.062 -10000 0 -0.73 6 6
TXA2/TP beta/beta Arrestin3 -0.003 0.025 -10000 0 -0.31 5 5
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.027 0.14 -10000 0 -0.72 35 35
G12 family/GTP -0.02 0.071 -10000 0 -0.3 51 51
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.003 0.047 -10000 0 -0.83 3 3
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.039 0.075 0.35 15 -10000 0 15
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.28 2 2
PRKG1 -0.039 0.18 -10000 0 -0.82 43 43
mol:IP3 0.051 0.12 -10000 0 -0.38 51 51
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.049 0.15 -10000 0 -0.51 51 51
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.001 0.061 -10000 0 -0.39 7 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.008 0.046 -10000 0 -0.33 3 3
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.002 0.022 -10000 0 -10000 0 0
PRKCB1 0.048 0.11 -10000 0 -0.37 51 51
GNAQ -0.002 0.039 -10000 0 -0.82 2 2
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.051 0.15 -10000 0 -0.54 51 51
LCK -0.011 0.069 -10000 0 -0.45 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.011 0.054 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.025 0.029 -10000 0 -0.3 3 3
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.01 0.053 -10000 0 -10000 0 0
MAPK14 0.053 0.076 -10000 0 -0.22 51 51
TGM2/GTP 0.051 0.13 -10000 0 -0.42 51 51
MAPK11 0.053 0.079 -10000 0 -0.23 51 51
ARHGEF1 0.04 0.059 -10000 0 -0.19 14 14
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.052 0.12 -10000 0 -0.39 51 51
RAB11/GDP -0.001 0.013 -10000 0 -0.28 2 2
ICAM1 0.048 0.09 -10000 0 -0.28 51 51
cAMP biosynthetic process 0.047 0.11 -10000 0 -0.35 51 51
Gq family/GTP/EBP50 -0.006 0.031 -10000 0 -0.25 13 13
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.009 0.045 -10000 0 -0.33 2 2
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.028 0.1 -10000 0 -0.31 34 34
VCAM1 0.047 0.097 -10000 0 -0.31 51 51
TP beta/Gq family/GDP/G beta5/gamma2 0.03 0.056 -10000 0 -0.55 6 6
platelet activation 0.069 0.1 -10000 0 -0.3 51 51
PGI2/IP -0.001 0.015 -10000 0 -10000 0 0
PRKACA -0.013 0.066 -10000 0 -0.38 28 28
Gq family/GDP/G beta5/gamma2 0.027 0.057 -10000 0 -0.55 6 6
TXA2/TP beta/beta Arrestin2 -0.005 0.049 -10000 0 -0.66 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.012 0.061 -10000 0 -0.36 28 28
mol:DAG 0.05 0.12 -10000 0 -0.42 51 51
EGFR -0.3 0.4 -10000 0 -0.82 331 331
TXA2/TP alpha 0.052 0.14 -10000 0 -0.48 51 51
Gq family/GTP -0.004 0.034 -10000 0 -0.28 13 13
YES1 -0.009 0.047 -10000 0 -0.35 3 3
GNAI2/GTP -0.01 0.052 -10000 0 -0.38 3 3
PGD2/DP -0.021 0.11 -10000 0 -0.64 28 28
SLC9A3R1 -0.024 0.079 -10000 0 -0.28 80 80
FYN -0.009 0.047 -10000 0 -0.35 3 3
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.003 0.035 -10000 0 -0.36 7 7
PGK/cGMP -0.026 0.12 -10000 0 -0.56 43 43
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.011 0.07 -10000 0 -0.54 7 7
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.045 0.12 -10000 0 -0.36 65 65
PRKCB 0.046 0.12 -10000 0 -0.37 61 61
PRKCE 0.052 0.11 -10000 0 -0.34 52 52
PRKCD 0.051 0.11 -10000 0 -0.38 51 51
PRKCG 0.047 0.12 -10000 0 -0.38 51 51
muscle contraction 0.054 0.15 -10000 0 -0.49 51 51
PRKCZ 0.055 0.11 -10000 0 -0.34 52 52
ARR3 -0.002 0.024 -10000 0 -0.28 7 7
TXA2/TP beta -0.011 0.058 -10000 0 -0.43 3 3
PRKCQ 0.04 0.13 -10000 0 -0.37 75 75
MAPKKK cascade 0.048 0.14 -10000 0 -0.46 52 52
SELE 0.04 0.12 -10000 0 -0.42 51 51
TP beta/GNAI2/GDP/G beta/gamma -0.013 0.069 -10000 0 -0.54 7 7
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.014 0.087 -10000 0 -0.42 30 30
chemotaxis 0.05 0.17 -10000 0 -0.62 51 51
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.002 0.039 -10000 0 -0.82 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.019 0.12 -9999 0 -0.8 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.027 -9999 0 -0.82 1 1
RAC1-CDC42/GTP/PAK family -0.13 0.14 -9999 0 -0.28 421 421
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.027 -9999 0 -0.82 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.001 0.027 -9999 0 -0.82 1 1
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.001 0.029 -9999 0 -0.82 1 1
p38 alpha/TAB1 -0.007 0.035 -9999 0 -0.33 3 3
PRKG1 -0.039 0.18 -9999 0 -0.82 43 43
DUSP8 -0.003 0.048 -9999 0 -0.82 3 3
PGK/cGMP/p38 alpha -0.026 0.093 -9999 0 -0.42 45 45
apoptosis -0.007 0.034 -9999 0 -0.32 3 3
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.11 0.28 -9999 0 -0.82 124 124
PAK1 -0.006 0.041 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.005 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0 0.009 -9999 0 -0.28 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.016 0.07 -9999 0 -0.36 17 17
BLK -0.039 0.1 -9999 0 -0.82 3 3
HCK -0.004 0.032 -9999 0 -0.28 12 12
MAP2K3 0 0.009 -9999 0 -0.28 1 1
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.013 -9999 0 -10000 0 0
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.027 0.049 -9999 0 -0.36 3 3
positive regulation of innate immune response 0.022 0.076 -9999 0 -0.37 17 17
LCK -0.018 0.1 -9999 0 -0.43 39 39
p38alpha-beta/MKP7 -0.012 0.056 -9999 0 -0.39 7 7
p38alpha-beta/MKP5 -0.012 0.057 -9999 0 -0.42 4 4
PGK/cGMP -0.03 0.14 -9999 0 -0.64 43 43
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.063 0.14 -9999 0 -0.4 128 128
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.38 0.41 -9999 0 -0.82 421 421
Effects of Botulinum toxin

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
STX1A 0.003 0.039 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.047 0.14 -9999 0 -0.63 40 40
STXBP1 -0.004 0.054 -9999 0 -0.82 4 4
ACh/CHRNA1 -0.063 0.079 -9999 0 -0.27 9 9
RAB3GAP2/RIMS1/UNC13B -0.039 0.12 -9999 0 -0.55 40 40
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.067 0.18 -9999 0 -0.43 142 142
mol:ACh 0 0.032 -9999 0 -0.15 32 32
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.038 0.097 -9999 0 -0.42 44 44
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.062 0.078 -9999 0 -0.27 9 9
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.1 0.13 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.06 0.13 -9999 0 -0.48 52 52
SNAP25 -0.017 0.071 -9999 0 -0.38 32 32
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.089 0.19 -9999 0 -0.37 220 220
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.008 0.046 -9999 0 -0.56 4 4
STX1A/SNAP25 fragment 1/VAMP2 -0.038 0.097 -9999 0 -0.42 44 44
Osteopontin-mediated events

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
IKK alpha homodimer -0.031 0.072 -9999 0 -0.46 19 19
NF kappa B1 p50/RelA/I kappa B alpha -0.018 0.058 -9999 0 -0.48 3 3
alphaV/beta3 Integrin/Osteopontin/Src -0.045 0.073 -9999 0 -10000 0 0
AP1 -0.15 0.21 -9999 0 -0.78 26 26
ILK -0.001 0.096 -9999 0 -0.49 19 19
bone resorption -0.026 0.08 -9999 0 -0.66 6 6
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.011 0.08 -9999 0 -0.44 19 19
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.008 0.067 -9999 0 -0.63 10 10
alphaV/beta3 Integrin/Osteopontin -0.044 0.091 -9999 0 -0.55 19 19
MAP3K1 -0.001 0.097 -9999 0 -0.5 19 19
JUN -0.008 0.081 -9999 0 -0.82 9 9
MAPK3 0.014 0.094 -9999 0 -0.46 19 19
MAPK1 0.014 0.094 -9999 0 -0.46 19 19
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.1 -9999 0 -0.51 20 20
ITGB3 -0.018 0.12 -9999 0 -0.82 19 19
NFKBIA 0.027 0.09 -9999 0 -0.44 19 19
FOS -0.26 0.38 -9999 0 -0.82 283 283
CD44 -0.001 0.016 -9999 0 -0.28 3 3
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.024 0.091 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.017 0.056 -9999 0 -0.46 3 3
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.014 0.089 -9999 0 -0.62 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.003 0.097 -9999 0 -0.5 19 19
VAV3 0.003 0.1 -9999 0 -0.47 25 25
MAP3K14 0.001 0.098 -9999 0 -0.5 19 19
ROCK2 -0.009 0.086 -9999 0 -0.82 10 10
SPP1 -0.075 0.12 -9999 0 -0.27 254 254
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.031 0.074 -9999 0 -0.43 25 25
MMP2 -0.079 0.21 -9999 0 -0.69 26 26
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.46 0.41 -10000 0 -0.82 513 513
CLTC 0.027 0.016 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.017 -10000 0 -10000 0 0
Dynamin 2/GTP -0.006 0.026 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.016 -10000 0 -0.28 1 1
CPE 0.005 0.084 -10000 0 -0.56 20 20
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.001 0.017 -10000 0 -10000 0 0
CTNND1 -0.005 0.023 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.013 -10000 0 -10000 0 0
TSHR -0.009 0.12 -10000 0 -0.56 41 41
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 -0.008 0.082 -10000 0 -0.77 10 10
mol:Choline -0.001 0.017 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.036 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.026 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -0.28 1 1
ASAP2/amphiphysin II -0.006 0.053 -10000 0 -0.51 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.016 0.054 -10000 0 -0.28 28 28
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0.009 -10000 0 -0.28 1 1
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 -0.004 0.033 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.001 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.035 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.005 -10000 0 -10000 0 0
ACAP1 -0.001 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.02 0.014 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.02 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0.001 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 -0.005 0.023 -10000 0 -10000 0 0
NME1 0.01 0.036 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.016 -10000 0 -10000 0 0
IL2RA 0.018 0.043 -10000 0 -0.33 11 11
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.24 0.21 -10000 0 -0.42 513 513
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.002 0.028 -10000 0 -0.35 6 6
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.013 -10000 0 -10000 0 0
SDC1 0.021 0.023 -10000 0 -0.36 1 1
ARF6/GDP -0.007 0.032 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.009 0.036 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.017 -10000 0 -10000 0 0
endocytosis 0.006 0.052 0.5 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.084 0.21 -10000 0 -0.45 223 223
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.027 -10000 0 -0.82 1 1
Dynamin 2/GDP -0.006 0.026 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.16 0.24 -10000 0 -0.45 367 367
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.008 0.031 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.06 0.074 -9999 0 -0.42 6 6
EPHB2 -0.005 0.038 -9999 0 -10000 0 0
Syndecan-2/TACI -0.017 0.079 -9999 0 -0.55 17 17
LAMA1 -0.096 0.26 -9999 0 -0.82 106 106
Syndecan-2/alpha2 ITGB1 -0.13 0.22 -9999 0 -0.49 239 239
HRAS -0.001 0.013 -9999 0 -0.28 2 2
Syndecan-2/CASK -0.003 0.033 -9999 0 -0.55 3 3
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.035 0.048 -9999 0 -0.65 2 2
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.03 -9999 0 -0.5 3 3
LAMA3 -0.2 0.36 -9999 0 -0.82 227 227
EZR -0.001 0.016 -9999 0 -0.28 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.1 0.28 -9999 0 -0.82 116 116
Syndecan-2/MMP2 -0.007 0.072 -9999 0 -0.73 8 8
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.013 0.09 -9999 0 -0.63 19 19
dendrite morphogenesis -0.005 0.037 -9999 0 -0.54 3 3
Syndecan-2/GM-CSF -0.005 0.038 -9999 0 -0.55 3 3
determination of left/right symmetry 0.016 0.039 -9999 0 -0.63 3 3
Syndecan-2/PKC delta -0.003 0.033 -9999 0 -0.55 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.038 -9999 0 -0.5 3 3
MAPK1 0.022 0.038 -9999 0 -0.5 3 3
Syndecan-2/RACK1 -0.002 0.028 -9999 0 -0.47 3 3
NF1 -0.001 0.027 -9999 0 -0.82 1 1
FGFR/FGF/Syndecan-2 0.016 0.039 -9999 0 -0.63 3 3
ITGA2 -0.017 0.12 -9999 0 -0.82 19 19
MAPK8 0.029 0.051 -9999 0 -0.58 6 6
Syndecan-2/alpha2/beta1 Integrin -0.066 0.19 -9999 0 -0.54 112 112
Syndecan-2/Kininogen -0.004 0.036 -9999 0 -0.55 3 3
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.002 0.026 -9999 0 -0.44 3 3
Syndecan-2/CASK/Protein 4.1 -0.002 0.03 -9999 0 -0.5 3 3
extracellular matrix organization -0.003 0.033 -9999 0 -0.54 3 3
actin cytoskeleton reorganization -0.06 0.074 -9999 0 -0.42 6 6
Syndecan-2/Caveolin-2/Ras -0.066 0.17 -9999 0 -0.51 116 116
Syndecan-2/Laminin alpha3 -0.14 0.24 -9999 0 -0.55 230 230
Syndecan-2/RasGAP -0.002 0.027 -9999 0 -0.45 3 3
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0.009 -9999 0 -0.28 1 1
Syndecan-2 dimer -0.005 0.037 -9999 0 -0.55 3 3
GO:0007205 0 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.025 -9999 0 -0.43 3 3
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.025 0.12 -9999 0 -0.82 14 14
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.013 0.09 -9999 0 -0.63 19 19
Syndecan-2/Synbindin -0.002 0.032 -9999 0 -0.55 3 3
TGFB1 0 0.009 -9999 0 -0.28 1 1
CASP3 0.029 0.032 -9999 0 -0.49 3 3
FN1 -0.12 0.14 -9999 0 -10000 0 0
Syndecan-2/IL8 -0.022 0.088 -9999 0 -0.55 21 21
SDC2 0.016 0.04 -9999 0 -0.63 3 3
KNG1 -0.004 0.032 -9999 0 -0.28 12 12
Syndecan-2/Neurofibromin -0.003 0.037 -9999 0 -0.55 4 4
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.006 0.041 -9999 0 -10000 0 0
Syndecan-2/TGFB1 -0.003 0.033 -9999 0 -0.55 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.03 -9999 0 -0.5 3 3
Syndecan-2/Ezrin -0.002 0.03 -9999 0 -0.5 3 3
PRKACA 0.029 0.036 -9999 0 -0.5 4 4
angiogenesis -0.022 0.088 -9999 0 -0.55 21 21
MMP2 -0.007 0.077 -9999 0 -0.82 8 8
IL8 -0.034 0.13 -9999 0 -0.41 77 77
calcineurin-NFAT signaling pathway -0.017 0.079 -9999 0 -0.55 17 17
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.018 0.096 -9999 0 -0.55 29 29
E-cadherin/beta catenin -0.019 0.11 -9999 0 -0.63 28 28
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.002 0.03 -9999 0 -0.82 1 1
CDH1 -0.025 0.14 -9999 0 -0.82 28 28
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.001 0.003 -9999 0 -10000 0 0
HDAC2 0.001 0.004 -9999 0 -10000 0 0
GNB1/GNG2 -0.008 0.071 -9999 0 -0.59 13 13
forebrain development -0.027 0.2 -9999 0 -0.52 113 113
GNAO1 -0.034 0.14 -9999 0 -0.75 28 28
SMO/beta Arrestin2 -0.005 0.056 -9999 0 -0.64 7 7
SMO -0.004 0.073 -9999 0 -0.76 8 8
ARRB2 0.002 0.005 -9999 0 -10000 0 0
GLI3/SPOP -0.003 0.037 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.042 0.18 -9999 0 -0.83 47 47
XPO1 0.011 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.055 0.16 -9999 0 -0.52 68 68
SAP30 0 0.019 -9999 0 -10000 0 0
mol:GDP -0.004 0.073 -9999 0 -0.76 8 8
MIM/GLI2A 0.001 0.029 -9999 0 -0.28 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GLI2 0.041 0.033 -9999 0 -10000 0 0
GLI3 0.038 0.043 -9999 0 -0.31 12 12
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.001 0.003 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.006 0.072 -9999 0 -0.82 7 7
Gi family/GTP -0.025 0.099 -9999 0 -0.32 81 81
SIN3B 0.001 0.004 -9999 0 -10000 0 0
SIN3A 0.001 0.003 -9999 0 -10000 0 0
GLI3/Su(fu) -0.002 0.024 -9999 0 -10000 0 0
GLI2/Su(fu) -0.004 0.034 -9999 0 -0.41 4 4
FOXA2 -0.013 0.033 -9999 0 -10000 0 0
neural tube patterning -0.027 0.2 -9999 0 -0.52 113 113
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.022 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 0.001 0.029 -9999 0 -0.28 9 9
embryonic limb morphogenesis -0.027 0.2 -9999 0 -0.52 113 113
SUFU -0.002 0.025 -9999 0 -0.29 3 3
LGALS3 -0.011 0.094 -9999 0 -0.82 12 12
catabolic process -0.005 0.029 -9999 0 -10000 0 0
GLI3A/CBP -0.026 0.097 -9999 0 -0.38 62 62
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.029 0.21 -9999 0 -0.54 113 113
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.027 -9999 0 -0.82 1 1
RBBP7 -0.002 0.026 -9999 0 -0.28 8 8
Su(fu)/Galectin3 -0.009 0.066 -9999 0 -0.55 12 12
GNAZ -0.007 0.077 -9999 0 -0.82 8 8
RBBP4 0.001 0.003 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.003 0.024 -9999 0 -10000 0 0
STK36 0.011 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.028 0.096 -9999 0 -0.44 20 20
PTCH1 -0.069 0.35 -9999 0 -1.1 77 77
MIM/GLI1 -0.054 0.19 -9999 0 -0.59 65 65
CREBBP -0.026 0.097 -9999 0 -0.38 62 62
Su(fu)/SIN3/HDAC complex 0.006 0.019 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0.006 -10000 0 -10000 0 0
CDKN1B 0.035 0.028 -10000 0 -0.45 3 3
CDKN1A 0.036 0.017 -10000 0 -0.45 1 1
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -10000 0 0
FOXO3 0.036 0.023 -10000 0 -0.45 2 2
AKT1 0 0.001 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
AKT3 -0.006 0.051 -10000 0 -0.45 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.002 -10000 0 -10000 0 0
AKT1/ASK1 -0.001 0.02 -10000 0 -0.44 2 2
BAD/YWHAZ 0 0.008 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.001 0.02 0.42 2 -10000 0 2
TSC1 0.037 0.002 -10000 0 -10000 0 0
YWHAZ -0.001 0.016 -10000 0 -0.28 3 3
AKT1/RAF1 0 0.001 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.037 0.002 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.024 0.019 -10000 0 -0.54 1 1
MAP3K5 -0.002 0.039 -10000 0 -0.82 2 2
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.039 0.023 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.037 0.002 -10000 0 -10000 0 0
CASP9 0.037 0.002 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.001 0.024 -10000 0 -0.42 3 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -10000 0 0
AKT2/p21CIP1 0 0.014 -10000 0 -0.43 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.002 -10000 0 -10000 0 0
BAD/BCL-XL 0 0.002 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.053 0.03 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.036 0.009 -10000 0 -10000 0 0
MAPKKK cascade 0 0.001 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.005 -10000 0 -10000 0 0
TSC1/TSC2 0.043 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.005 -10000 0 -10000 0 0
glucose import -0.26 0.26 -10000 0 -0.5 513 513
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.031 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.27 0.26 -10000 0 -0.5 513 513
GSK3A 0.037 0.002 -10000 0 -10000 0 0
FOXO1 0.032 0.045 -10000 0 -0.45 8 8
GSK3B 0.037 0.002 -10000 0 -10000 0 0
SFN -0.016 0.1 -10000 0 -0.54 27 27
G1/S transition of mitotic cell cycle 0.043 0.002 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.041 0.034 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0.009 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.021 0.022 -10000 0 -0.63 1 1
MAP4K4 -0.006 0.042 -10000 0 -0.71 1 1
BAG4 -0.004 0.04 -10000 0 -0.82 1 1
PKC zeta/ceramide -0.024 0.049 -10000 0 -0.6 1 1
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.082 -10000 0 -0.82 8 8
BAX -0.009 0.022 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.024 0.01 -10000 0 -10000 0 0
BAD -0.023 0.046 0.2 1 -10000 0 1
SMPD1 0.024 0.037 -10000 0 -0.26 14 14
RB1 -0.024 0.051 0.2 1 -0.5 2 3
FADD/Caspase 8 -0.006 0.041 -10000 0 -0.67 1 1
MAP2K4 -0.015 0.046 -10000 0 -0.48 1 1
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.015 0.047 -10000 0 -0.47 1 1
EGF -0.16 0.33 -10000 0 -0.82 183 183
mol:ceramide -0.034 0.049 0.21 1 -10000 0 1
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0.024 -10000 0 -0.63 1 1
ASAH1 -0.001 0.016 -10000 0 -10000 0 0
negative regulation of cell cycle -0.024 0.051 0.2 1 -0.49 2 3
cell proliferation -0.096 0.16 -10000 0 -0.4 197 197
BID 0.022 0.037 -10000 0 -0.4 1 1
MAP3K1 -0.023 0.046 0.2 1 -10000 0 1
EIF2A -0.006 0.042 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.003 0.045 -10000 0 -0.43 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.003 0.045 -10000 0 -0.43 1 1
Cathepsin D/ceramide -0.029 0.05 -10000 0 -0.25 1 1
FADD -0.007 0.045 -10000 0 -0.48 3 3
KSR1 -0.023 0.05 0.2 1 -0.33 3 4
MAPK8 -0.011 0.049 0.2 1 -0.31 5 6
PRKRA -0.023 0.046 0.2 1 -10000 0 1
PDGFA -0.001 0.027 -10000 0 -0.82 1 1
TRAF2 -0.001 0.013 -10000 0 -10000 0 0
IGF1 -0.18 0.34 -10000 0 -0.82 197 197
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.034 0.049 0.21 1 -10000 0 1
CTSD -0.011 0.054 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.1 0.18 -10000 0 -0.43 197 197
PRKCD 0 0.009 -10000 0 -0.28 1 1
PRKCZ -0.001 0.027 -10000 0 -0.82 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.024 -10000 0 -0.63 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.001 0.027 -10000 0 -0.82 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.007 0.046 -10000 0 -0.75 1 1
TNFR1A/BAG4/TNF-alpha -0.013 0.073 -10000 0 -0.55 15 15
mol:Sphingosine-1-phosphate 0.021 0.022 -10000 0 -0.63 1 1
MAP2K1 -0.006 0.045 -10000 0 -0.44 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.008 0.044 0.19 21 -10000 0 21
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.028 -10000 0 -0.63 1 1
EIF2AK2 -0.014 0.044 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.011 0.07 -10000 0 -0.55 14 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.023 -10000 0 -0.33 1 1
MAP2K2 -0.006 0.045 -10000 0 -0.44 1 1
SMPD3 0.024 0.044 -10000 0 -0.28 17 17
TNF -0.018 0.11 -10000 0 -0.82 14 14
PKC zeta/PAR4 -0.001 0.03 -10000 0 -0.63 2 2
mol:PHOSPHOCHOLINE 0.047 0.12 0.28 182 -10000 0 182
NF kappa B1/RelA/I kappa B alpha -0.001 0.022 -10000 0 -0.46 2 2
AIFM1 -0.008 0.044 0.19 21 -10000 0 21
BCL2 -0.027 0.15 -10000 0 -0.82 30 30
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.007 0.073 -10000 0 -0.82 7 7
positive regulation of NF-kappaB transcription factor activity -0.065 0.19 -10000 0 -0.63 94 94
MAP2K4 0.042 0.037 -10000 0 -0.45 1 1
IKBKB -0.001 0.013 -10000 0 -10000 0 0
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.004 0.054 -10000 0 -0.82 4 4
SMPD1 -0.002 0.026 -10000 0 -0.29 7 7
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.079 0.24 -10000 0 -0.82 88 88
TRAIL/TRAILR2 -0.005 0.056 -10000 0 -0.63 7 7
TRAIL/TRAILR3 -0.009 0.072 -10000 0 -0.69 9 9
TRAIL/TRAILR1 -0.008 0.069 -10000 0 -0.63 11 11
TRAIL/TRAILR4 -0.066 0.19 -10000 0 -0.63 94 94
TRAIL/TRAILR1/DAP3/GTP -0.006 0.055 -10000 0 -0.51 11 11
IKK complex -0.002 0.019 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0.006 -10000 0 -10000 0 0
MAPK3 0.017 0.057 -10000 0 -0.63 7 7
MAP3K1 -0.003 0.03 -10000 0 -0.33 7 7
TRAILR4 (trimer) -0.079 0.24 -10000 0 -0.82 88 88
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.004 0.054 -10000 0 -0.82 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.037 -10000 0 -0.34 11 11
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.057 -10000 0 -0.63 7 7
TRAIL/TRAILR1/FADD/TRADD/RIP -0.007 0.053 -10000 0 -0.48 11 11
mol:ceramide -0.002 0.026 -10000 0 -0.29 7 7
FADD -0.005 0.037 -10000 0 -0.28 16 16
MAPK8 0.046 0.045 -10000 0 -0.42 4 4
TRAF2 -0.001 0.013 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.005 0.054 -10000 0 -0.82 3 3
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.009 0.063 -10000 0 -0.56 11 11
DAP3 0 0.009 -10000 0 -10000 0 0
CASP10 0.021 0.11 0.31 83 -0.52 10 93
JNK cascade -0.065 0.19 -10000 0 -0.63 94 94
TRAIL (trimer) -0.007 0.072 -10000 0 -0.82 7 7
TNFRSF10C -0.005 0.054 -10000 0 -0.82 3 3
TRAIL/TRAILR1/DAP3/GTP/FADD -0.008 0.055 -10000 0 -0.48 11 11
TRAIL/TRAILR2/FADD -0.007 0.051 -10000 0 -0.55 7 7
cell death -0.002 0.025 -10000 0 -0.29 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.029 -10000 0 -0.33 7 7
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.014 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.005 0.042 -10000 0 -0.47 7 7
Signaling mediated by p38-gamma and p38-delta

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.03 0.009 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.045 -9999 0 -10000 0 0
MAPK12 0.016 0.088 -9999 0 -0.49 25 25
CCND1 0.015 0.043 -9999 0 -0.22 23 23
p38 gamma/SNTA1 -0.013 0.077 -9999 0 -0.48 21 21
MAP2K3 0 0.009 -9999 0 -0.28 1 1
PKN1 0 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.016 0.087 -9999 0 -0.49 25 25
MAP2K6 0.009 0.089 -9999 0 -0.52 25 25
MAPT -0.017 0.14 -9999 0 -0.41 93 93
MAPK13 0.021 0.011 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.002 0.03 -9999 0 -0.45 4 4
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.005 0.095 -10000 0 -0.47 30 30
ACTA1 -0.017 0.13 -10000 0 -0.66 29 29
NUMA1 0.005 0.095 -10000 0 -0.47 30 30
SPTAN1 -0.004 0.13 -10000 0 -0.64 27 27
LIMK1 -0.004 0.13 -10000 0 -0.64 27 27
BIRC3 -0.01 0.082 -10000 0 -0.82 8 8
BIRC2 0 0 -10000 0 -10000 0 0
BAX -0.001 0.016 -10000 0 -10000 0 0
CASP10 -0.015 0.15 -10000 0 -0.69 31 31
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.005 0.095 -10000 0 -0.47 30 30
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.003 0.12 -10000 0 -0.63 27 27
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.011 0.15 -10000 0 -0.65 36 36
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.011 0.094 -10000 0 -0.7 15 15
BID 0.005 0.062 -10000 0 -0.3 30 30
MAP3K1 0.005 0.039 -10000 0 -0.24 6 6
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.004 0.13 -10000 0 -0.64 27 27
CASP9 0 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.03 0.19 1 -0.22 3 4
neuron apoptosis 0.021 0.014 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.003 0.12 -10000 0 -0.62 27 27
APAF1 0 0 -10000 0 -10000 0 0
CASP6 0.022 0.059 -10000 0 -0.43 4 4
TRAF2 -0.001 0.013 -10000 0 -10000 0 0
ICAD/CAD 0.004 0.12 -10000 0 -0.62 27 27
CASP7 -0.007 0.038 0.37 8 -10000 0 8
KRT18 0.015 0.017 -10000 0 -10000 0 0
apoptosis 0.009 0.11 -10000 0 -0.55 27 27
DFFA -0.004 0.13 -10000 0 -0.64 27 27
DFFB -0.004 0.13 -10000 0 -0.64 27 27
PARP1 0.002 0.03 0.22 3 -0.19 1 4
actin filament polymerization -0.003 0.12 0.59 29 -10000 0 29
TNF -0.018 0.11 -10000 0 -0.82 14 14
CYCS 0.008 0.05 -10000 0 -0.22 28 28
SATB1 0.018 0.099 -10000 0 -0.52 21 21
SLK -0.004 0.13 -10000 0 -0.64 27 27
p15 BID/BAX -0.013 0.049 -10000 0 -0.35 7 7
CASP2 0.042 0.044 -10000 0 -0.46 1 1
JNK cascade -0.005 0.038 0.24 6 -10000 0 6
CASP3 -0.013 0.13 -10000 0 -0.66 30 30
LMNB2 0.039 0.041 -10000 0 -0.36 3 3
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.027 -10000 0 -0.82 1 1
Mammalian IAPs/DIABLO -0.006 0.048 -10000 0 -0.5 8 8
negative regulation of DNA binding 0.011 0.093 -10000 0 -0.69 15 15
stress fiber formation -0.003 0.12 -10000 0 -0.63 27 27
GZMB -0.028 0.16 -10000 0 -0.67 38 38
CASP1 -0.002 0.033 -10000 0 -0.45 5 5
LMNB1 0.044 0.041 -10000 0 -0.36 3 3
APP 0.021 0.014 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.003 0.1 -10000 0 -0.53 27 27
LMNA 0.039 0.041 -10000 0 -0.36 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.006 0.039 -10000 0 -0.5 1 1
LRDD -0.001 0.013 -10000 0 -10000 0 0
SREBF1 -0.006 0.13 -10000 0 -0.65 27 27
APAF-1/Caspase 9 -0.004 0.019 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.006 0.093 -10000 0 -0.46 30 30
CFL2 0.003 0.12 -10000 0 -0.61 29 29
GAS2 -0.052 0.19 -10000 0 -0.54 110 110
positive regulation of apoptosis 0.045 0.041 -10000 0 -0.35 3 3
PRF1 -0.019 0.12 -10000 0 -0.82 18 18
PLK2 and PLK4 events

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0 0 -9999 0 -10000 0 0
PLK4 -0.012 0.057 -9999 0 -0.28 40 40
regulation of centriole replication 0.013 0.04 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0 0.009 -10000 0 -10000 0 0
ANTXR2 -0.008 0.081 -10000 0 -0.82 9 9
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.01 -10000 0 -0.1 9 9
monocyte activation 0.004 0.071 -10000 0 -0.46 21 21
MAP2K2 0 0.004 -10000 0 -10000 0 0
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.001 0.009 -10000 0 -10000 0 0
MAP2K6 -0.012 0.075 -10000 0 -0.5 21 21
CYAA -0.005 0.048 -10000 0 -0.48 9 9
MAP2K4 -0.001 0.018 -10000 0 -0.5 1 1
IL1B 0.008 0.065 -10000 0 -0.36 23 23
Channel -0.005 0.051 -10000 0 -0.52 9 9
NLRP1 -0.007 0.056 -10000 0 -0.51 11 11
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.01 0.1 9 -10000 0 9
MAPK3 -0.001 0.009 -10000 0 -10000 0 0
MAPK1 -0.001 0.009 -10000 0 -10000 0 0
PGR -0.14 0.22 -10000 0 -0.5 253 253
PA/Cellular Receptors -0.006 0.055 -10000 0 -0.56 9 9
apoptosis -0.001 0.01 -10000 0 -0.1 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.005 0.048 -10000 0 -0.48 9 9
macrophage activation 0.02 0.009 -10000 0 -10000 0 0
TNF -0.018 0.11 -10000 0 -0.82 14 14
VCAM1 -0.01 0.069 -10000 0 -0.46 21 21
platelet activation -0.001 0.012 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.022 0.24 2 -10000 0 2
IL18 0.011 0.034 -10000 0 -0.22 11 11
negative regulation of macrophage activation -0.001 0.01 -10000 0 -0.1 9 9
LEF -0.001 0.01 -10000 0 -0.1 9 9
CASP1 -0.004 0.028 -10000 0 -0.24 11 11
mol:cAMP -0.001 0.012 -10000 0 -10000 0 0
necrosis -0.001 0.01 -10000 0 -0.1 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.005 0.048 -10000 0 -0.49 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.026 0.029 -9999 0 -10000 0 0
BIRC5 -0.2 0.12 -9999 0 -10000 0 0
NFKBIA -0.024 0.031 -9999 0 -10000 0 0
CPEB1 -0.16 0.32 -9999 0 -0.82 175 175
AKT1 -0.024 0.031 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.023 0.026 -9999 0 -10000 0 0
NDEL1/TACC3 -0.038 0.057 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.001 0.002 -9999 0 -10000 0 0
PAK1/Aurora A -0.029 0.037 -9999 0 -10000 0 0
MDM2 -0.001 0.018 -9999 0 -10000 0 0
JUB -0.004 0.054 -9999 0 -0.82 4 4
TPX2 -0.11 0.095 -9999 0 -10000 0 0
TP53 -0.011 0.015 -9999 0 -10000 0 0
DLG7 -0.03 0.034 -9999 0 -10000 0 0
AURKAIP1 -0.002 0.021 -9999 0 -0.28 5 5
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.041 0.061 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.023 0.026 -9999 0 -10000 0 0
AURKA -0.038 0.043 -9999 0 -10000 0 0
AURKB -0.003 0.008 -9999 0 -10000 0 0
CDC25B -0.017 0.024 -9999 0 -10000 0 0
G2/M transition checkpoint -0.025 0.041 -9999 0 -0.52 4 4
mRNA polyadenylation -0.12 0.21 -9999 0 -0.55 174 174
Aurora A/CPEB -0.12 0.21 -9999 0 -0.55 174 174
Aurora A/TACC1/TRAP/chTOG -0.027 0.08 -9999 0 -0.5 25 25
BRCA1 -0.001 0.013 -9999 0 -10000 0 0
centrosome duplication -0.029 0.037 -9999 0 -10000 0 0
regulation of centrosome cycle -0.038 0.056 -9999 0 -10000 0 0
spindle assembly -0.027 0.079 -9999 0 -0.49 25 25
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.099 0.065 -9999 0 -10000 0 0
CENPA 0.001 0.01 -9999 0 -10000 0 0
Aurora A/PP2A -0.026 0.029 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.006 0.027 -9999 0 -10000 0 0
negative regulation of DNA binding -0.011 0.015 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.012 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.025 0.042 -9999 0 -0.52 4 4
mitotic prometaphase -0.014 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.038 0.043 -9999 0 -10000 0 0
TACC1 -0.023 0.14 -9999 0 -0.82 25 25
TACC3 -0.043 0.1 -9999 0 -0.28 141 141
Aurora A/Antizyme1 -0.02 0.021 -9999 0 -10000 0 0
Aurora A/RasGAP -0.026 0.029 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.001 0.002 -9999 0 -10000 0 0
GIT1 -0.001 0.018 -9999 0 -0.28 4 4
GIT1/beta-PIX/PAK1 -0.004 0.021 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.11 0.094 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.11 0.082 -9999 0 -10000 0 0
PAK1 -0.006 0.041 -9999 0 -10000 0 0
CKAP5 0 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR 0 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.038 0.035 -10000 0 -0.33 2 2
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.021 0.045 0.24 4 -0.34 8 12
RAR alpha/9cRA/Cyclin H -0.01 0.059 -10000 0 -0.38 21 21
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.035 0.046 -10000 0 -0.33 10 10
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.009 0.053 -10000 0 -0.57 4 4
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.006 0.12 -10000 0 -0.58 23 23
NCOA2 -0.015 0.11 -10000 0 -0.82 17 17
NCOA3 0 0.009 -10000 0 -10000 0 0
NCOA1 -0.001 0.027 -10000 0 -0.82 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0.007 0.006 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 -0.003 0.047 -10000 0 -0.82 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.1 -10000 0 -0.63 21 21
RARA 0.016 0.055 -10000 0 -0.31 24 24
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.03 0.058 -10000 0 -0.28 27 27
PRKCA -0.006 0.13 -10000 0 -0.78 23 23
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.005 0.12 -10000 0 -0.59 25 25
RXRG -0.11 0.22 -10000 0 -0.45 249 249
RXRA 0.024 0.059 -10000 0 -0.33 24 24
RXRB 0.012 0.072 -10000 0 -0.45 21 21
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.022 0.096 -10000 0 -0.34 59 59
CRBP1/9-cic-RA -0.016 0.07 -10000 0 -0.64 7 7
RARB 0.003 0.087 -10000 0 -0.82 10 10
PRKCG -0.001 0.055 -10000 0 -10000 0 0
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.027 0.11 -10000 0 -0.62 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.013 0.1 -10000 0 -0.49 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.049 -10000 0 -0.43 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.005 0.12 -10000 0 -0.59 25 25
positive regulation of DNA binding -0.009 0.056 -10000 0 -0.36 21 21
NRIP1 -0.003 0.12 -10000 0 -0.59 22 22
RXRs/RARs -0.012 0.12 -10000 0 -0.57 26 26
RXRs/RXRs/DNA/9cRA -0.046 0.11 -10000 0 -0.66 21 21
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.005 0.03 -10000 0 -10000 0 0
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.034 0.14 -9999 0 -0.82 24 24
CDC42/GTP -0.026 0.08 -9999 0 -0.32 35 35
PLCG1 -0.027 0.083 -9999 0 -0.52 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.025 0.079 -9999 0 -0.31 35 35
S1PR5 -0.008 0.059 -9999 0 -0.36 19 19
S1PR4 -0.014 0.082 -9999 0 -0.82 6 6
MAPK3 -0.027 0.083 -9999 0 -0.52 4 4
MAPK1 -0.027 0.083 -9999 0 -0.33 35 35
S1P/S1P5/Gi -0.028 0.092 -9999 0 -0.38 34 34
GNAI1 -0.042 0.18 -9999 0 -0.82 47 47
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.037 -9999 0 -0.56 3 3
RHOA -0.006 0.042 -9999 0 -0.47 6 6
S1P/S1P4/Gi -0.03 0.09 -9999 0 -0.36 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.077 -9999 0 -0.82 8 8
S1P/S1P4/G12/G13 -0.007 0.046 -9999 0 -0.51 6 6
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
S1P5 pathway

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.024 0.08 0.52 6 -10000 0 6
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.037 -10000 0 -0.56 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.034 0.14 -10000 0 -0.82 24 24
RhoA/GTP -0.025 0.082 -10000 0 -0.53 6 6
negative regulation of cAMP metabolic process -0.028 0.091 -10000 0 -0.37 34 34
GNAZ -0.007 0.077 -10000 0 -0.82 8 8
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.059 -10000 0 -0.36 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.028 0.092 -10000 0 -0.38 34 34
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.042 0.18 -10000 0 -0.82 47 47
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.019 0.1 -9999 0 -0.6 28 28
KLHL20 -0.009 0.034 -9999 0 -0.25 3 3
CYFIP2 -0.01 0.061 -9999 0 -0.32 29 29
Rac1/GDP 0.047 0.073 -9999 0 -0.45 2 2
ENAH -0.019 0.1 -9999 0 -0.59 28 28
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.052 -9999 0 -0.51 1 1
ABI1/Sra1/Nap1 -0.006 0.024 -9999 0 -0.17 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.019 0.09 -9999 0 -0.5 30 30
RAPGEF1 0.037 0.095 -9999 0 -0.5 28 28
CTNND1 0 0.009 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.019 0.11 -9999 0 -0.62 28 28
CRK 0.028 0.1 -9999 0 -0.55 28 28
E-cadherin/gamma catenin/alpha catenin -0.018 0.096 -9999 0 -0.55 29 29
alphaE/beta7 Integrin -0.005 0.039 -9999 0 -0.63 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.037 -9999 0 -0.51 5 5
DLG1 -0.019 0.1 -9999 0 -0.59 28 28
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.038 -9999 0 -0.34 1 1
MLLT4 -0.005 0.061 -9999 0 -0.82 5 5
ARF6/GTP/NME1/Tiam1 -0.007 0.027 -9999 0 -10000 0 0
PI3K -0.009 0.049 -9999 0 -0.47 1 1
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.02 0.11 -9999 0 -0.63 29 29
TIAM1 -0.001 0.018 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.015 0.082 -9999 0 -0.47 28 28
AKT1 -0.005 0.027 -9999 0 -0.24 1 1
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
CDH1 -0.025 0.14 -9999 0 -0.82 28 28
RhoA/GDP 0.047 0.073 -9999 0 -0.44 2 2
actin cytoskeleton organization -0.006 0.025 -9999 0 -0.18 3 3
CDC42/GDP 0.047 0.073 -9999 0 -0.36 28 28
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.011 0.061 -9999 0 -0.35 29 29
ITGB7 -0.008 0.057 -9999 0 -0.33 23 23
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.015 0.086 -9999 0 -0.5 28 28
E-cadherin/Ca2+/beta catenin/alpha catenin -0.015 0.083 -9999 0 -0.48 28 28
mol:GDP 0.044 0.085 -9999 0 -0.42 28 28
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.002 0.03 -9999 0 -0.82 1 1
p120 catenin/RhoA/GDP -0.011 0.063 -9999 0 -0.55 1 1
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.028 -9999 0 -0.21 6 6
NME1 -0.014 0.062 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.019 0.1 -9999 0 -0.59 29 29
regulation of cell-cell adhesion -0.009 0.046 -9999 0 -0.43 1 1
WASF2 -0.003 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.011 0.06 -9999 0 -0.61 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.085 -9999 0 -0.47 31 31
CCND1 -0.009 0.035 -9999 0 -0.26 6 6
VAV2 0.032 0.1 -9999 0 -0.52 28 28
RAP1/GDP -0.011 0.061 -9999 0 -0.57 1 1
adherens junction assembly -0.018 0.1 -9999 0 -0.57 29 29
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.017 0.081 -9999 0 -0.44 31 31
E-cadherin/beta catenin -0.016 0.087 -9999 0 -0.51 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.019 0.1 -9999 0 -0.59 28 28
PIK3CA 0 0.009 -9999 0 -10000 0 0
Rac1/GTP -0.011 0.055 -9999 0 -0.42 3 3
E-cadherin/beta catenin/alpha catenin -0.017 0.094 -9999 0 -0.55 28 28
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.11 -9999 0 -0.64 28 28
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.002 0.039 -9999 0 -0.82 2 2
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.029 0.097 -9999 0 -0.34 76 76
GNAO1 -0.023 0.14 -9999 0 -0.8 25 25
S1P/S1P3/G12/G13 -0.001 0.012 -9999 0 -10000 0 0
AKT1 -0.01 0.045 -9999 0 -0.68 2 2
AKT3 0.017 0.17 -9999 0 -1.4 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.038 -9999 0 -0.82 2 2
GNAI2 0.011 0.003 -9999 0 -10000 0 0
GNAI3 0.01 0.004 -9999 0 -10000 0 0
GNAI1 -0.032 0.18 -9999 0 -0.83 47 47
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.009 0.029 -9999 0 -0.32 1 1
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.11 -9999 0 -0.39 35 35
MAPK3 0.018 0.1 -9999 0 -0.52 11 11
MAPK1 0.018 0.1 -9999 0 -0.38 31 31
JAK2 0.02 0.1 -9999 0 -0.46 17 17
CXCR4 0.014 0.1 -9999 0 -0.49 16 16
FLT1 0.012 0.028 -9999 0 -0.84 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.017 0.1 -9999 0 -0.52 11 11
S1P/S1P3/Gi 0.009 0.11 -9999 0 -0.4 35 35
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.024 0.085 -9999 0 -0.51 11 11
VEGFA 0.01 0.029 -9999 0 -0.28 9 9
S1P/S1P2/Gi -0.028 0.09 -9999 0 -0.38 34 34
VEGFR1 homodimer/VEGFA homodimer 0.021 0.03 -9999 0 -0.66 1 1
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.006 0.041 -9999 0 -0.34 13 13
GNAQ -0.002 0.039 -9999 0 -0.82 2 2
GNAZ 0.003 0.078 -9999 0 -0.83 8 8
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.014 0.087 -9999 0 -0.42 30 30
GNA15 -0.003 0.035 -9999 0 -0.36 7 7
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.039 -9999 0 -0.82 2 2
Rac1/GTP -0.024 0.085 -9999 0 -0.51 11 11
IL1-mediated signaling events

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.027 -10000 0 -0.82 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.037 -10000 0 -0.43 3 3
IRAK/TOLLIP -0.001 0.009 -10000 0 -10000 0 0
IKBKB -0.001 0.013 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.032 0.12 -10000 0 -0.62 36 36
IL1A -0.005 0.038 -10000 0 -0.28 17 17
IL1B 0.01 0.096 -10000 0 -0.75 13 13
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.016 -10000 0 -0.42 1 1
IL1R2 -0.038 0.16 -10000 0 -0.59 59 59
IL1R1 -0.011 0.094 -10000 0 -0.82 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.058 0.24 25 -0.33 11 36
TOLLIP 0 0.009 -10000 0 -0.28 1 1
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.004 -10000 0 -10000 0 0
JUN 0.031 0.083 -10000 0 -0.4 32 32
MAP3K7 0 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.014 0.09 -10000 0 -0.51 25 25
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.009 0.059 -10000 0 -0.5 12 12
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.054 -10000 0 -0.47 12 12
IL1 beta fragment/IL1R1/IL1RAP -0.016 0.099 -10000 0 -0.58 24 24
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.028 0.073 -10000 0 -0.41 24 24
IRAK1 0.021 0.012 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.017 0.084 -10000 0 -0.63 14 14
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.022 -10000 0 -0.63 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.053 -10000 0 -0.36 14 14
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.016 0.099 -10000 0 -0.58 24 24
IL1 beta/IL1R2 -0.034 0.13 -10000 0 -0.58 47 47
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.013 0.08 -10000 0 -0.9 3 3
IRAK3 -0.026 0.14 -10000 0 -0.81 29 29
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.014 0.089 -10000 0 -0.52 24 24
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.038 -10000 0 -0.33 12 12
IL1 alpha/IL1R1/IL1RAP -0.01 0.065 -10000 0 -0.55 12 12
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 -0.001 0.013 -10000 0 -10000 0 0
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.007 -10000 0 -10000 0 0
IL1RAP 0 0 -10000 0 -10000 0 0
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.011 0.071 -10000 0 -0.8 3 3
CASP1 -0.004 0.054 -10000 0 -0.82 4 4
IL1RN/IL1R2 -0.037 0.13 -10000 0 -0.6 40 40
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.015 0.093 -10000 0 -0.54 24 24
TMEM189-UBE2V1 -0.001 0.013 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.043 -10000 0 -0.38 12 12
PIK3CA 0 0.009 -10000 0 -10000 0 0
IL1RN -0.013 0.066 -10000 0 -0.82 2 2
TRAF6/TAK1/TAB1/TAB2 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.011 0.066 -10000 0 -0.44 21 21
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.005 0.052 -10000 0 -0.63 6 6
ATM 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -10000 0 0
ATR 0 0 -10000 0 -10000 0 0
UBE2L3 0 0 -10000 0 -10000 0 0
FANCD2 -0.001 0.007 -10000 0 -10000 0 0
protein ubiquitination -0.022 0.055 -10000 0 -0.5 6 6
XRCC5 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0 0 -10000 0 -10000 0 0
DNA-PK -0.001 0.009 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.002 0.01 -10000 0 -10000 0 0
FANCF 0 0.009 -10000 0 -0.28 1 1
BRCA1 -0.001 0.013 -10000 0 -10000 0 0
CCNE1 -0.054 0.11 -10000 0 -0.28 176 176
CDK2/Cyclin E1 -0.034 0.069 -10000 0 -10000 0 0
FANCG 0 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.005 0.052 -10000 0 -0.63 6 6
FANCE 0 0 -10000 0 -10000 0 0
FANCC 0 0 -10000 0 -10000 0 0
NBN 0 0 -10000 0 -10000 0 0
FANCA -0.052 0.11 -10000 0 -0.28 171 171
DNA repair 0.012 0.082 -10000 0 -0.49 3 3
BRCA1/BARD1/ubiquitin -0.005 0.052 -10000 0 -0.63 6 6
BARD1/DNA-PK -0.004 0.041 -10000 0 -0.5 6 6
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.005 0.052 0.63 6 -10000 0 6
BRCA1/BARD1/CTIP/M/R/N Complex -0.002 0.026 -10000 0 -0.32 6 6
BRCA1/BACH1/BARD1/TopBP1 -0.004 0.045 -10000 0 -0.55 6 6
BRCA1/BARD1/P53 -0.004 0.041 -10000 0 -0.5 6 6
BARD1/CSTF1/BRCA1 -0.004 0.045 -10000 0 -0.55 6 6
BRCA1/BACH1 -0.001 0.013 -10000 0 -10000 0 0
BARD1 -0.006 0.067 -10000 0 -0.75 7 7
PCNA -0.001 0.016 -10000 0 -0.28 3 3
BRCA1/BARD1/UbcH5C -0.004 0.045 -10000 0 -0.55 6 6
BRCA1/BARD1/UbcH7 -0.004 0.045 -10000 0 -0.55 6 6
BRCA1/BARD1/RAD51/PCNA -0.048 0.07 -10000 0 -0.56 6 6
BARD1/DNA-PK/P53 -0.004 0.038 -10000 0 -0.47 6 6
BRCA1/BARD1/Ubiquitin -0.005 0.052 -10000 0 -0.63 6 6
BRCA1/BARD1/CTIP -0.004 0.041 -10000 0 -0.5 6 6
FA complex -0.004 0.009 -10000 0 -10000 0 0
BARD1/EWS -0.004 0.052 -10000 0 -0.63 6 6
RBBP8 0.022 0.007 -10000 0 -10000 0 0
TP53 0 0 -10000 0 -10000 0 0
TOPBP1 0 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.004 0.04 0.5 6 -10000 0 6
BRCA1/BARD1 -0.022 0.055 -10000 0 -0.51 6 6
CSTF1 0 0.009 -10000 0 -0.28 1 1
BARD1/EWS-Fli1 -0.004 0.052 -10000 0 -0.64 6 6
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.11 0.14 -10000 0 -10000 0 0
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.005 0.052 -10000 0 -0.63 6 6
EWSR1 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.016 0.083 -9999 0 -0.54 19 19
MAP4K1 -0.012 0.064 -9999 0 -0.82 2 2
MAP3K8 -0.005 0.062 -9999 0 -0.82 5 5
PRKCB -0.019 0.11 -9999 0 -0.82 16 16
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 -0.006 0.045 -9999 0 -0.57 2 2
JUN 0.018 0.11 -9999 0 -0.57 28 28
MAP3K7 -0.006 0.045 -9999 0 -0.57 2 2
GRAP2 -0.014 0.1 -9999 0 -0.82 14 14
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.044 0.056 -9999 0 -0.51 4 4
LAT -0.005 0.048 -9999 0 -0.82 2 2
LCP2 0 0.009 -9999 0 -0.28 1 1
MAPK8 0.015 0.1 -9999 0 -0.67 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.007 0.049 -9999 0 -0.37 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.014 0.078 -9999 0 -0.52 17 17
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.049 0.05 -10000 0 -0.48 2 2
UGCG -0.003 0.051 -10000 0 -0.73 4 4
AKT1/mTOR/p70S6K/Hsp90/TERT 0.057 0.084 -10000 0 -0.38 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.021 0.053 -10000 0 -0.72 4 4
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.023 0.081 -10000 0 -0.36 32 32
FRAP1 0.056 0.12 -10000 0 -0.38 53 53
FOXO3 0.064 0.097 -10000 0 -0.38 26 26
AKT1 0.059 0.099 -10000 0 -0.41 24 24
GAB2 -0.002 0.026 -10000 0 -10000 0 0
SMPD1 -0.001 0.012 -10000 0 -10000 0 0
SGMS1 -0.001 0.012 -10000 0 -10000 0 0
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 0.021 0.02 -10000 0 -0.55 1 1
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.038 0.062 -10000 0 -0.27 26 26
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.022 -10000 0 -0.63 1 1
RPS6KB1 0.022 0.03 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 20 20
JAK3 0.008 0.037 -10000 0 -10000 0 0
PIK3R1 0.012 0.028 -10000 0 -0.82 1 1
JAK1 0.013 0.004 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.049 0.18 -10000 0 -0.99 22 22
MYB 0.014 0.17 -10000 0 -1.3 15 15
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.057 0.079 -10000 0 -0.59 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.02 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.057 0.077 -10000 0 -0.57 4 4
Rac1/GDP -0.001 0.017 -10000 0 -0.5 1 1
T cell proliferation 0.062 0.074 -10000 0 -0.49 5 5
SHC1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.009 -10000 0 -0.067 15 15
PRKCZ 0.062 0.076 -10000 0 -0.52 5 5
NF kappa B1 p50/RelA -0.022 0.079 -10000 0 -0.44 8 8
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.016 0.053 -10000 0 -0.54 2 2
HSP90AA1 0 0.009 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.028 0.11 -10000 0 -0.36 72 72
IL2RB 0.001 0.058 -10000 0 -0.28 38 38
TERT -0.038 0.096 -10000 0 -10000 0 0
E2F1 0.025 0.06 -10000 0 -0.44 15 15
SOS1 0 0 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.03 15 -10000 0 15
PTPN11 0 0 -10000 0 -10000 0 0
IL2RG -0.003 0.083 -10000 0 -0.82 5 5
actin cytoskeleton organization 0.062 0.074 -10000 0 -0.49 5 5
GRB2 0 0.009 -10000 0 -10000 0 0
IL2 0.006 0.027 -10000 0 -0.28 8 8
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.03 0.019 -10000 0 -0.48 1 1
LCK -0.006 0.1 -10000 0 -0.43 39 39
BCL2 0.042 0.19 -10000 0 -0.9 32 32
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.004 0.043 -10000 0 -0.5 7 7
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.014 -10000 0 -0.42 1 1
GATA1/HDAC4 -0.003 0.028 -10000 0 -0.63 1 1
GATA1/HDAC5 -0.002 0.019 -10000 0 -10000 0 0
GATA2/HDAC5 -0.018 0.1 -10000 0 -0.63 23 23
HDAC5/BCL6/BCoR -0.002 0.036 -10000 0 -0.55 4 4
HDAC9 -0.009 0.074 -10000 0 -0.82 6 6
Glucocorticoid receptor/Hsp90/HDAC6 -0.006 0.057 -10000 0 -0.55 10 10
HDAC4/ANKRA2 -0.001 0.021 -10000 0 -0.63 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.024 0.13 -10000 0 -0.82 23 23
HDAC4/RFXANK -0.001 0.022 -10000 0 -0.63 1 1
BCOR -0.001 0.027 -10000 0 -0.82 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.005 0.055 -10000 0 -0.63 7 7
Histones -0.002 0.023 -10000 0 -10000 0 0
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.027 -10000 0 -0.82 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.021 -10000 0 -0.63 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0 0.008 -10000 0 -10000 0 0
CAMK4 -0.01 0.053 -10000 0 -0.28 34 34
Tubulin/HDAC6 0 0.006 -10000 0 -10000 0 0
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 -0.003 0.03 -10000 0 -0.28 11 11
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.009 0.086 -10000 0 -0.82 10 10
SUMO1/HDAC4 -0.001 0.015 -10000 0 -0.46 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.021 -10000 0 -0.63 1 1
Tubulin 0 0.008 -10000 0 -10000 0 0
HDAC4/14-3-3 E -0.001 0.021 -10000 0 -0.63 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0 -10000 0 -10000 0 0
BCL6/BCoR -0.003 0.042 -10000 0 -0.63 4 4
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.018 -10000 0 -0.55 1 1
HDAC4/SRF -0.006 0.031 -10000 0 -0.55 1 1
HDAC4/ER alpha -0.11 0.22 -10000 0 -0.63 132 132
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.002 0.023 -10000 0 -10000 0 0
cell motility 0 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.003 0.047 -10000 0 -0.82 3 3
HDAC4/CaMK II delta B -0.001 0.027 -10000 0 -0.82 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.15 0.29 -10000 0 -0.57 248 248
HDAC6/HDAC11 0 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.001 0.027 -10000 0 -0.82 1 1
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.022 -10000 0 -0.47 2 2
GNG2 -0.006 0.072 -10000 0 -0.82 7 7
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.013 -10000 0 -0.28 2 2
HDAC11 -0.001 0.013 -10000 0 -0.28 2 2
HSP90AA1 0 0.009 -10000 0 -10000 0 0
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK -0.001 0.013 -10000 0 -0.28 2 2
nuclear import 0 0.015 0.45 1 -10000 0 1
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 -0.005 0.05 -9999 0 -0.36 14 14
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P -0.001 0.018 -9999 0 -0.37 2 2
GNAO1 -0.034 0.14 -9999 0 -0.82 24 24
mol:Sphinganine-1-P 0.018 0.038 -9999 0 -0.63 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.012 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.003 0.028 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.015 -9999 0 -0.32 2 2
S1PR5 -0.008 0.059 -9999 0 -0.36 19 19
S1PR4 -0.014 0.082 -9999 0 -0.82 6 6
GNAI1 -0.042 0.18 -9999 0 -0.82 47 47
S1P/S1P5/G12 -0.004 0.034 -9999 0 -0.49 3 3
S1P/S1P3/Gq -0.004 0.036 -9999 0 -0.32 3 3
S1P/S1P4/Gi -0.028 0.087 -9999 0 -0.35 37 37
GNAQ -0.002 0.039 -9999 0 -0.82 2 2
GNAZ -0.007 0.077 -9999 0 -0.82 8 8
GNA14 -0.014 0.087 -9999 0 -0.42 30 30
GNA15 -0.003 0.035 -9999 0 -0.36 7 7
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.039 -9999 0 -0.82 2 2
ABCC1 0 0 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.014 0.07 0.33 1 -0.35 36 37
FRAP1 0.012 0.016 -10000 0 -10000 0 0
AKT1 -0.012 0.059 0.24 1 -0.29 36 37
INSR 0 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.009 0.045 -10000 0 -0.37 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.003 0.013 -10000 0 -10000 0 0
TSC2 0 0.001 -10000 0 -10000 0 0
RHEB/GDP -0.008 0.038 -10000 0 -0.33 2 2
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.017 0.083 -10000 0 -0.43 36 36
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.036 -10000 0 -0.27 2 2
MAP3K5 0.009 0.022 -10000 0 -0.45 2 2
PIK3R1 -0.001 0.027 -10000 0 -0.82 1 1
apoptosis 0.009 0.022 -10000 0 -0.45 2 2
mol:LY294002 0 0 0.001 1 -0.002 36 37
EIF4B 0.027 0.033 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.005 0.023 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.001 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.016 0.075 -10000 0 -0.38 37 37
mTOR/RHEB/GTP/Raptor/GBL 0.027 0.024 0.18 1 -0.19 2 3
FKBP1A 0 0.009 -10000 0 -0.28 1 1
RHEB/GTP -0.008 0.037 -10000 0 -0.33 2 2
mol:Amino Acids 0 0 0.001 1 -0.002 36 37
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.012 0.062 0.26 1 -0.32 36 37
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.002 0.03 -10000 0 -0.63 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.01 0.048 -10000 0 -0.4 2 2
tumor necrosis factor receptor activity 0 0 0.002 36 -0.001 1 37
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 -0.01 0.091 -10000 0 -0.46 36 36
INS 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.038 -10000 0 -0.82 2 2
PDK2 -0.014 0.07 0.26 1 -0.34 39 40
EIF4EBP1 0.013 0.014 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -10000 0 0
PPP2R5D 0.019 0.015 -10000 0 -10000 0 0
peptide biosynthetic process 0 0.004 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -0.003 1 3
EEF2 0 0.004 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.049 0.024 -10000 0 -10000 0 0
NFATC2 0.02 0.056 -10000 0 -0.29 6 6
NFATC3 -0.001 0.017 -10000 0 -0.53 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.013 0.094 -10000 0 -0.4 28 28
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.017 0.073 -10000 0 -0.52 11 11
BCL2/BAX -0.021 0.12 -10000 0 -0.64 30 30
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.003 -10000 0 -10000 0 0
BAX -0.001 0.016 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.019 0.081 -10000 0 -0.58 11 11
Calcineurin A alpha-beta B1/BCL2 -0.027 0.15 -10000 0 -0.82 30 30
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.018 0.079 0.57 11 -10000 0 11
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.03 0.087 -10000 0 -0.28 100 100
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.016 0.1 -10000 0 -0.54 27 27
MAP3K8 -0.005 0.062 -10000 0 -0.82 5 5
NFAT4/CK1 alpha 0 0.011 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.036 0.095 -10000 0 -0.47 3 3
CABIN1 0.013 0.095 -10000 0 -0.41 28 28
CALM1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.01 0.053 -10000 0 -0.28 34 34
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.01 0.045 -10000 0 -0.63 1 1
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 -0.003 0.047 -10000 0 -0.82 3 3
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0.009 -10000 0 -0.28 1 1
NFAT1-c-4/YWHAQ -0.002 0.018 -10000 0 -0.42 1 1
PRKCH -0.001 0.027 -10000 0 -0.82 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0 0 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -10000 0 -10000 0 0
apoptosis -0.007 0.036 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.025 -10000 0 -10000 0 0
PRKCB -0.019 0.11 -10000 0 -0.82 16 16
PRKCE -0.001 0.027 -10000 0 -0.82 1 1
JNK2/NFAT4 -0.001 0.016 -10000 0 -0.48 1 1
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0.009 -10000 0 -0.28 1 1
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.027 -10000 0 -0.82 1 1
PRKCA -0.02 0.12 -10000 0 -0.78 23 23
PRKCG -0.011 0.053 -10000 0 -10000 0 0
PRKCQ -0.035 0.16 -10000 0 -0.67 47 47
FKBP38/BCL2 -0.021 0.11 -10000 0 -0.63 30 30
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.049 0.037 -10000 0 -0.4 3 3
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.005 0.027 -10000 0 -10000 0 0
NFATc/ERK1 -0.001 0.015 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.017 0.073 -10000 0 -0.52 11 11
NR4A1 -0.071 0.21 -10000 0 -0.73 82 82
GSK3B 0 0 -10000 0 -10000 0 0
positive T cell selection -0.001 0.017 -10000 0 -0.52 1 1
NFAT1/CK1 alpha -0.012 0.034 -10000 0 -0.3 1 1
RCH1/ KPNB1 -0.019 0.055 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
AKAP5 -0.016 0.069 -10000 0 -0.29 51 51
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.001 0.016 -10000 0 -0.28 3 3
NFATc/p38 alpha 0.05 0.026 -10000 0 -10000 0 0
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.027 0.15 -10000 0 -0.82 30 30
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 -0.002 0.026 -9999 0 -10000 0 0
ELF1 -0.011 0.047 -9999 0 -0.38 11 11
CCNA2 -0.12 0.14 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
JAK3 -0.005 0.035 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
JAK1 0 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.061 0.065 -9999 0 -0.6 4 4
SHC1 0 0 -9999 0 -10000 0 0
SP1 -0.003 0.034 -9999 0 -0.38 7 7
IL2RA 0.004 0.12 -9999 0 -1 11 11
IL2RB -0.012 0.055 -9999 0 -0.28 38 38
SOS1 0 0 -9999 0 -10000 0 0
IL2RG -0.016 0.081 -9999 0 -0.82 5 5
G1/S transition of mitotic cell cycle 0.011 0.11 -9999 0 -0.79 13 13
PTPN11 0 0 -9999 0 -10000 0 0
CCND2 0.021 0.093 -9999 0 -1 7 7
LCK -0.018 0.1 -9999 0 -0.43 39 39
GRB2 0 0.009 -9999 0 -10000 0 0
IL2 -0.002 0.026 -9999 0 -0.28 8 8
CDK6 -0.008 0.078 -9999 0 -0.72 10 10
CCND3 0.066 0.058 -9999 0 -0.62 2 2
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.002 0.06 -10000 0 -0.71 6 6
CDKN2C 0.005 0.041 -10000 0 -0.82 2 2
CDKN2A -0.047 0.11 -10000 0 -10000 0 0
CCND2 0.006 0.029 0.26 6 -0.16 7 13
RB1 -0.007 0.029 0.17 2 -0.26 6 8
CDK4 0.009 0.028 0.26 7 -10000 0 7
CDK6 0.006 0.033 0.28 6 -0.21 7 13
G1/S progression -0.007 0.032 0.26 6 -0.17 2 8
VEGFR1 specific signals

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer -0.001 0.031 -9999 0 -0.93 1 1
VEGFR1 homodimer/NRP1 -0.001 0.031 -9999 0 -0.94 1 1
mol:DAG 0.038 0.034 -9999 0 -0.67 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.031 -9999 0 -0.87 1 1
CaM/Ca2+ -0.001 0.031 -9999 0 -0.63 2 2
HIF1A 0 0.013 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.002 0.032 -9999 0 -0.53 3 3
PLCG1 0.038 0.035 -9999 0 -0.68 2 2
NOS3 0.062 0.031 -9999 0 -0.58 2 2
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.062 0.03 -9999 0 -0.55 2 2
FLT1 0.028 0.035 -9999 0 -1 1 1
PGF -0.001 0.029 -9999 0 -0.55 2 2
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.045 -9999 0 -1.3 1 1
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
eNOS/Hsp90 -0.001 0.026 -9999 0 -0.66 1 1
endothelial cell proliferation 0.037 0.09 -9999 0 -0.88 3 3
mol:Ca2+ 0.038 0.034 -9999 0 -0.66 2 2
MAPK3 0.04 0.083 -9999 0 -0.46 22 22
MAPK1 0.04 0.083 -9999 0 -0.46 22 22
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
PLGF homodimer -0.001 0.029 -9999 0 -0.55 2 2
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.17 0.34 -9999 0 -0.82 191 191
VEGFA homodimer -0.003 0.027 -9999 0 -0.28 9 9
VEGFR1 homodimer/VEGFA homodimer -0.002 0.033 -9999 0 -0.93 1 1
platelet activating factor biosynthetic process 0.047 0.081 -9999 0 -0.44 22 22
PI3K -0.002 0.035 -9999 0 -0.58 3 3
PRKCA 0.033 0.087 -9999 0 -0.5 22 22
PRKCB 0.034 0.081 -9999 0 -0.51 17 17
VEGFR1 homodimer/PLGF homodimer -0.002 0.036 -9999 0 -0.74 2 2
VEGFA -0.003 0.028 -9999 0 -0.28 9 9
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.034 -9999 0 -0.67 2 2
RASA1 0.038 0.03 -9999 0 -0.86 1 1
NRP2 -0.001 0.029 -9999 0 -0.55 2 2
VEGFR1 homodimer 0.028 0.035 -9999 0 -1 1 1
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.082 0.16 -9999 0 -0.92 2 2
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.034 -9999 0 -0.57 3 3
mol:L-citrulline 0.062 0.03 -9999 0 -0.55 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.029 -9999 0 -0.82 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.03 -9999 0 -0.87 1 1
CD2AP 0 0.009 -9999 0 -0.28 1 1
PI3K/GAB1 -0.002 0.033 -9999 0 -0.55 3 3
PDPK1 -0.002 0.032 -9999 0 -0.54 3 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.03 -9999 0 -0.87 1 1
mol:NADP 0.062 0.03 -9999 0 -0.55 2 2
HSP90AA1 0 0.009 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.029 -9999 0 -0.81 1 1
VEGFR1 homodimer/NRP2 -0.002 0.046 -9999 0 -1.4 1 1
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.001 0.023 -10000 0 -0.49 2 2
TRAF2/ASK1 -0.002 0.027 -10000 0 -0.56 2 2
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.027 0.038 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.029 0.056 -10000 0 -0.35 5 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.025 0.079 -10000 0 -10000 0 0
TXN 0 0.004 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A 0 0 -10000 0 -10000 0 0
GADD45B 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
MAP3K6 -0.001 0.027 -10000 0 -0.82 1 1
MAP3K7 0 0.009 -10000 0 -10000 0 0
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.002 0.036 -10000 0 -0.63 3 3
TAK1/TAB family 0 0.01 0.22 2 -10000 0 2
RAC1/OSM/MEKK3 0 0.004 -10000 0 -10000 0 0
TRAF2 -0.001 0.013 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.005 0.017 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.074 0.22 -10000 0 -0.62 108 108
CCM2 0 0.009 -10000 0 -0.28 1 1
CaM/Ca2+/CAMKIIB -0.048 0.15 -10000 0 -0.56 68 68
MAPK11 -0.002 0.039 -10000 0 -0.82 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.044 0.14 -10000 0 -0.51 70 70
OSM/MEKK3 0 0.006 -10000 0 -10000 0 0
TAOK1 -0.01 0.066 -10000 0 -0.45 20 20
TAOK2 0 0 -10000 0 -10000 0 0
TAOK3 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.002 0.039 -10000 0 -0.82 2 2
MAP3K10 0 0.009 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.001 0.026 -10000 0 -0.55 2 2
GADD45/MTK1/MTK1 -0.009 0.029 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.008 0.057 -9999 0 -0.33 23 23
ITGA4 -0.003 0.029 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.44 6 6
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 -0.004 0.04 -9999 0 -0.82 1 1
Caspase 8 (4 units) -0.007 0.044 -9999 0 -1 1 1
NEF -0.004 0.021 -9999 0 -0.22 3 3
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 -0.01 0.08 -9999 0 -0.83 8 8
CYCS 0.042 0.054 -9999 0 -0.96 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.026 0.13 -9999 0 -0.72 27 27
MAP2K7 0.043 0.045 -9999 0 -0.82 1 1
protein ubiquitination 0.065 0.036 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.003 0.047 -9999 0 -0.82 3 3
BID -0.008 0.049 -9999 0 -1.1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.034 -9999 0 -0.34 8 8
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.002 0.039 -9999 0 -0.82 2 2
CFLAR 0 0 -9999 0 -10000 0 0
FADD -0.005 0.037 -9999 0 -0.28 16 16
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.034 -9999 0 -0.34 8 8
MAPK8 0.048 0.05 -9999 0 -0.5 4 4
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.018 -9999 0 -0.28 4 4
TRAF2 -0.001 0.013 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.009 0.053 -9999 0 -0.39 10 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.033 -9999 0 -0.38 2 2
CHUK 0.067 0.037 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.004 0.045 -9999 0 -0.61 4 4
TCRz/NEF -0.024 0.11 -9999 0 -0.57 30 30
TNF -0.018 0.11 -9999 0 -0.82 14 14
FASLG -0.002 0.13 -9999 0 -0.62 30 30
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.073 -9999 0 -0.55 15 15
CASP6 -0.003 0.03 -9999 0 -0.71 1 1
CASP7 0.074 0.075 -9999 0 -0.64 8 8
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.074 0.075 -9999 0 -0.64 8 8
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.028 -9999 0 -0.63 1 1
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.062 0.04 -9999 0 -0.36 1 1
APAF-1/Caspase 9 -0.008 0.054 -9999 0 -0.54 8 8
BCL2 0.039 0.098 -9999 0 -0.44 32 32
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.014 0.091 -9999 0 -0.63 19 19
AKT1 0.085 0.043 -9999 0 -0.69 2 2
PTK2B -0.011 0.075 -9999 0 -0.96 2 2
VEGFR2 homodimer/Frs2 -0.003 0.045 -9999 0 -0.92 2 2
CAV1 -0.17 0.34 -9999 0 -0.82 191 191
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.004 0.042 -9999 0 -0.86 2 2
endothelial cell proliferation 0.086 0.069 -9999 0 -0.64 3 3
mol:Ca2+ 0.054 0.041 -9999 0 -0.77 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.001 0.039 -9999 0 -0.81 2 2
RP11-342D11.1 0.046 0.041 -9999 0 -0.78 2 2
CDH5 -0.005 0.061 -9999 0 -0.82 5 5
VEGFA homodimer -0.001 0.011 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.023 0.14 -9999 0 -0.82 25 25
HRAS/GDP -0.001 0.031 -9999 0 -0.66 2 2
SH2D2A -0.03 0.09 -9999 0 -0.28 98 98
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0 0.032 -9999 0 -0.63 2 2
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.014 0.055 -9999 0 -0.77 3 3
VEGFR1 homodimer -0.001 0.027 -9999 0 -0.82 1 1
SHC/GRB2/SOS1 -0.001 0.036 -9999 0 -0.74 2 2
GRB10 0.054 0.041 -9999 0 -0.77 2 2
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -10000 0 0
PAK1 -0.006 0.041 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.003 0.062 -9999 0 -1.2 2 2
HRAS -0.001 0.013 -9999 0 -0.28 2 2
VEGF/Rho/ROCK1/Integrin Complex -0.006 0.042 -9999 0 -0.52 2 2
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.029 -9999 0 -0.28 10 10
oxygen and reactive oxygen species metabolic process -0.001 0.038 -9999 0 -0.8 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.039 -9999 0 -0.82 2 2
Nck/Pak -0.004 0.026 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.003 0.053 -9999 0 -1.1 2 2
mol:GDP -0.001 0.034 -9999 0 -0.71 2 2
mol:NADP 0.076 0.03 -9999 0 -0.52 2 2
eNOS/Hsp90 0.077 0.028 -9999 0 -0.48 2 2
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
mol:IP3 0.054 0.041 -9999 0 -0.78 2 2
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.029 -9999 0 -0.55 2 2
VEGFA -0.003 0.027 -9999 0 -0.27 9 9
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin -0.007 0.056 -9999 0 -0.89 2 2
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.01 0.081 -9999 0 -0.51 20 20
PTPN6 -0.001 0.013 -9999 0 -0.28 2 2
EPAS1 -0.001 0.018 -9999 0 -0.38 2 2
mol:L-citrulline 0.076 0.03 -9999 0 -0.52 2 2
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0 0.04 -9999 0 -0.81 2 2
VEGFR2 homodimer/VEGFA homodimer -0.001 0.041 -9999 0 -0.85 2 2
VEGFR2/3 heterodimer -0.003 0.058 -9999 0 -0.95 3 3
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.059 0.043 -9999 0 -0.79 2 2
VEGFR2 homodimer 0.033 0.049 -9999 0 -1 2 2
FLT1 -0.001 0.027 -9999 0 -0.82 1 1
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 0.055 0.061 -9999 0 -0.79 3 3
MAPK1 0.055 0.061 -9999 0 -0.79 3 3
VEGFA145/NRP2 -0.003 0.028 -9999 0 -0.63 1 1
VEGFR1/2 heterodimer -0.003 0.055 -9999 0 -1.2 2 2
KDR 0.033 0.05 -9999 0 -1 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.001 0.049 -9999 0 -1 2 2
SRC 0 0.009 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.057 0.061 -9999 0 -0.8 3 3
PI3K -0.003 0.047 -9999 0 -0.9 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.003 0.041 -9999 0 -0.86 2 2
FES 0.053 0.051 -9999 0 -0.59 5 5
GAB1 -0.002 0.045 -9999 0 -0.94 2 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.041 -9999 0 -0.86 2 2
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.009 0.17 -9999 0 -0.54 5 5
VEGFR2 homodimer/VEGFA homodimer/Yes -0.003 0.044 -9999 0 -0.73 3 3
PI3K/GAB1 -0.002 0.038 -9999 0 -0.71 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.002 0.041 -9999 0 -0.78 2 2
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.054 -9999 0 -0.89 3 3
HSP90AA1 0 0.009 -9999 0 -10000 0 0
CDC42 0.055 0.042 -9999 0 -0.8 2 2
actin cytoskeleton reorganization -0.014 0.054 -9999 0 -0.76 3 3
PTK2 0.06 0.071 -9999 0 -0.99 2 2
EDG1 0.046 0.041 -9999 0 -0.78 2 2
mol:DAG 0.054 0.041 -9999 0 -0.78 2 2
CaM/Ca2+ -0.002 0.034 -9999 0 -0.72 2 2
MAP2K3 0.061 0.046 -9999 0 -0.59 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.001 0.039 -9999 0 -0.81 2 2
PLCG1 0.055 0.042 -9999 0 -0.8 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.001 0.042 -9999 0 -0.69 3 3
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.027 -9999 0 -0.82 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.003 0.041 -9999 0 -0.86 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.003 0.041 -9999 0 -0.86 2 2
cell migration 0.084 0.061 -9999 0 -0.78 2 2
mol:PI-3-4-5-P3 -0.002 0.042 -9999 0 -0.8 2 2
FYN -0.001 0.027 -9999 0 -0.82 1 1
VEGFB/NRP1 -0.002 0.035 -9999 0 -0.73 2 2
mol:NO 0.076 0.03 -9999 0 -0.52 2 2
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.031 -9999 0 -0.66 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.001 0.039 -9999 0 -0.81 2 2
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.018 0.12 -9999 0 -0.82 19 19
NOS3 0.078 0.033 -9999 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/Sck -0.016 0.089 -9999 0 -0.51 27 27
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.05 0.087 -9999 0 -0.48 22 22
PRKCB 0.051 0.085 -9999 0 -0.52 16 16
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.001 0.038 -9999 0 -0.78 2 2
VEGFR1/2 heterodimer/VEGFA homodimer -0.003 0.053 -9999 0 -1.1 2 2
VEGFA165/NRP2 -0.003 0.028 -9999 0 -0.63 1 1
MAPKKK cascade 0 0.033 -9999 0 -0.65 2 2
NRP2 -0.001 0.029 -9999 0 -0.55 2 2
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.007 0.056 -9999 0 -0.89 2 2
MAP3K13 0.053 0.048 -9999 0 -0.62 4 4
PDPK1 0.078 0.042 -9999 0 -0.68 2 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0 0 -9999 0 -10000 0 0
SMAD2 0.014 0 -9999 0 -10000 0 0
SMAD3 0.041 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.009 0.026 -9999 0 -10000 0 0
PPM1A 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
MAP3K1 0 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.005 0.055 -9999 0 -0.63 7 7
MAPK3 0 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
NUP214 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
KPNB1 0 0 -9999 0 -10000 0 0
TGFBRAP1 -0.006 0.072 -9999 0 -0.82 7 7
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.009 -9999 0 -10000 0 0
KPNA2 -0.03 0.087 -9999 0 -0.28 100 100
PIAS4 0 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0 0.015 -10000 0 -10000 0 0
oxygen homeostasis 0.013 0.012 -10000 0 -10000 0 0
TCEB2 -0.003 0.028 -10000 0 -10000 0 0
TCEB1 -0.001 0.016 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.003 0.024 -10000 0 -10000 0 0
EPO 0.16 0.14 -10000 0 -0.5 1 1
FIH (dimer) 0.023 0.011 -10000 0 -10000 0 0
APEX1 0.022 0.014 -10000 0 -0.3 1 1
SERPINE1 0.17 0.14 -10000 0 -0.59 1 1
FLT1 -0.001 0.07 -10000 0 -1.4 2 2
ADORA2A 0.15 0.15 -10000 0 -0.54 2 2
germ cell development 0.16 0.14 -10000 0 -0.61 4 4
SLC11A2 0.17 0.14 -10000 0 -0.59 1 1
BHLHE40 0.17 0.14 -10000 0 -0.97 2 2
HIF1AN 0.023 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.019 0.065 -10000 0 -0.38 1 1
ETS1 0.024 0.041 -10000 0 -0.86 2 2
CITED2 0.001 0.01 -10000 0 -10000 0 0
KDR -0.001 0.082 -10000 0 -1.7 2 2
PGK1 0.17 0.14 -10000 0 -0.59 1 1
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.18 0.14 -10000 0 -0.64 2 2
EPAS1 0.098 0.072 -10000 0 -0.41 1 1
SP1 0.018 0.002 -10000 0 -10000 0 0
ABCG2 0.14 0.24 -10000 0 -0.71 57 57
EFNA1 0.17 0.14 -10000 0 -0.59 1 1
FXN 0.16 0.14 -10000 0 -0.57 1 1
POU5F1 0.17 0.14 -10000 0 -0.64 4 4
neuron apoptosis -0.16 0.15 0.62 2 -10000 0 2
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0 0.079 -10000 0 -0.27 72 72
EGLN2 0.022 0.022 -10000 0 -0.29 1 1
EGLN1 0.022 0.03 -10000 0 -0.84 1 1
VHL/Elongin B/Elongin C -0.002 0.015 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.023 0.009 -10000 0 -10000 0 0
SLC2A1 0.16 0.14 -10000 0 -0.55 3 3
TWIST1 0.15 0.19 -10000 0 -0.7 29 29
ELK1 0.018 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.012 0.057 -10000 0 -10000 0 0
VEGFA 0.17 0.14 -10000 0 -0.55 2 2
CREBBP 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.006 0.063 -9999 0 -0.51 14 14
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.052 -9999 0 -0.42 14 14
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.022 -9999 0 -0.28 6 6
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.026 -9999 0 -10000 0 0
YY1/LSF 0 0 -9999 0 -10000 0 0
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.007 0.046 -9999 0 -0.37 14 14
I kappa B alpha/HDAC1 -0.004 0.031 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.006 0.04 -9999 0 -0.32 14 14
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.031 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.005 0.036 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.024 0.13 -9999 0 -0.82 23 23
GATA1 -0.003 0.03 -9999 0 -0.28 11 11
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.004 -9999 0 -10000 0 0
RBBP7 -0.002 0.026 -9999 0 -0.28 8 8
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.005 0.035 -9999 0 -0.28 14 14
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
SIN3 complex 0 0.007 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.018 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.027 -9999 0 -0.82 1 1
YY1/HDAC3 -0.004 0.027 -9999 0 -10000 0 0
YY1/HDAC2 0 0 -9999 0 -10000 0 0
YY1/HDAC1 0 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0 0.001 -9999 0 -10000 0 0
PPARG -0.094 0.17 -9999 0 -0.39 218 218
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.004 0.031 -9999 0 -10000 0 0
MBD3L2 -0.001 0.013 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.002 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.005 0.035 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0 0 -9999 0 -10000 0 0
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0 0 -9999 0 -10000 0 0
NCOR2 0 0 -9999 0 -10000 0 0
MXD1 0 0.009 -9999 0 -0.28 1 1
STAT3 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0 0.007 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.024 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.035 -9999 0 -0.28 14 14
histone deacetylation 0.045 0.003 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.004 0.028 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.018 0.084 -9999 0 -0.5 23 23
GATA1/HDAC1 -0.002 0.019 -9999 0 -10000 0 0
GATA1/HDAC3 -0.006 0.034 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.013 0.081 -9999 0 -0.63 14 14
SIN3/HDAC complex/Mad/Max 0 0.002 -9999 0 -10000 0 0
NuRD Complex 0 0.002 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.025 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.01 -9999 0 -10000 0 0
GATA1/Fog1 -0.003 0.024 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.018 0.11 -9999 0 -0.82 14 14
negative regulation of cell growth 0.045 0.004 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0.001 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.007 0.054 -9999 0 -0.44 14 14
SIN3/HDAC complex/NCoR1 0 0.007 -9999 0 -10000 0 0
TFCP2 0 0 -9999 0 -10000 0 0
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 0 0.009 -9999 0 -0.28 1 1
MBD2 0 0 -9999 0 -10000 0 0
PDGFR-beta signaling pathway

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.004 0.039 -9999 0 -0.54 4 4
PDGFB-D/PDGFRB/SLAP -0.003 0.034 -9999 0 -0.63 2 2
PDGFB-D/PDGFRB/APS/CBL -0.007 0.037 -9999 0 -0.54 2 2
AKT1 -0.007 0.031 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.003 0.04 -9999 0 -0.57 4 4
PIK3CA 0 0.009 -9999 0 -10000 0 0
FGR -0.003 0.035 -9999 0 -0.56 3 3
mol:Ca2+ 0.034 0.038 -9999 0 -0.67 2 2
MYC 0.039 0.14 -9999 0 -0.82 22 22
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.023 -9999 0 -0.44 2 2
LRP1/PDGFRB/PDGFB -0.007 0.07 -9999 0 -0.65 10 10
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.033 0.039 -9999 0 -0.68 2 2
PTEN -0.002 0.039 -9999 0 -0.82 2 2
GRB2 0 0.009 -9999 0 -10000 0 0
GRB7 -0.021 0.076 -9999 0 -0.82 1 1
PDGFB-D/PDGFRB/SHP2 -0.001 0.029 -9999 0 -0.63 2 2
PDGFB-D/PDGFRB/GRB10 -0.001 0.029 -9999 0 -0.63 2 2
cell cycle arrest -0.003 0.034 -9999 0 -0.63 2 2
HRAS -0.001 0.013 -9999 0 -0.28 2 2
HIF1A 0.055 0.043 -9999 0 -10000 0 0
GAB1 0.036 0.047 -9999 0 -0.66 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.04 0.046 -9999 0 -0.6 2 2
PDGFB-D/PDGFRB -0.002 0.03 -9999 0 -0.56 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.029 -9999 0 -0.63 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.044 -9999 0 -0.57 4 4
positive regulation of MAPKKK cascade -0.001 0.029 -9999 0 -0.63 2 2
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
mol:IP3 0.034 0.039 -9999 0 -0.69 2 2
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.015 0.058 -9999 0 -0.63 3 3
SHB -0.001 0.029 -9999 0 -0.55 2 2
BLK -0.001 0.049 -9999 0 -0.63 5 5
PTPN2 0 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.029 -9999 0 -0.63 2 2
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.04 0.055 -9999 0 -0.56 3 3
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.001 0.029 -9999 0 -0.63 2 2
LCK -0.009 0.072 -9999 0 -0.6 13 13
PDGFRB -0.001 0.039 -9999 0 -0.83 2 2
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.002 0.028 -9999 0 -0.52 2 2
ABL1 0.034 0.041 -9999 0 -0.61 2 2
PDGFB-D/PDGFRB/CBL 0.035 0.049 -9999 0 -0.75 2 2
PTPN1 -0.003 0.03 -9999 0 -0.29 1 1
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.006 0.04 -9999 0 -0.28 19 19
cell proliferation 0.04 0.12 -9999 0 -0.71 22 22
SLA -0.002 0.026 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.002 0.025 -9999 0 -0.42 3 3
SRC -0.002 0.027 -9999 0 -0.52 2 2
PI3K -0.009 0.035 -9999 0 -0.4 1 1
PDGFB-D/PDGFRB/GRB7/SHC -0.011 0.046 -9999 0 -0.55 3 3
SH2B2 -0.011 0.055 -9999 0 -0.28 37 37
PLCgamma1/SPHK1 -0.003 0.042 -9999 0 -0.59 4 4
LYN -0.002 0.027 -9999 0 -0.52 2 2
LRP1 -0.009 0.086 -9999 0 -0.82 10 10
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.003 0.047 -9999 0 -0.82 3 3
STAT5A -0.006 0.072 -9999 0 -0.82 7 7
NCK1-2/p130 Cas -0.002 0.022 -9999 0 -0.44 2 2
SPHK1 -0.005 0.05 -9999 0 -0.36 14 14
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.034 0.039 -9999 0 -0.69 2 2
PLCG1 0.034 0.04 -9999 0 -0.71 2 2
NHERF/PDGFRB -0.013 0.046 -9999 0 -0.54 2 2
YES1 -0.003 0.034 -9999 0 -0.55 3 3
cell migration -0.013 0.045 -9999 0 -0.54 2 2
SHC/Grb2/SOS1 -0.002 0.022 -9999 0 -0.44 2 2
SLC9A3R2 0 0.009 -9999 0 -10000 0 0
SLC9A3R1 -0.024 0.079 -9999 0 -0.28 80 80
NHERF1-2/PDGFRB/PTEN -0.012 0.045 -9999 0 -0.5 4 4
FYN -0.003 0.048 -9999 0 -0.91 2 2
DOK1 -0.001 0.027 -9999 0 -0.5 2 2
HRAS/GTP 0 0.009 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.047 0.078 -9999 0 -0.43 22 22
PRKCD 0.003 0.029 -9999 0 -0.5 2 2
FER 0 0.051 -9999 0 -0.5 8 8
MAPKKK cascade -0.002 0.022 -9999 0 -0.43 2 2
RASA1 0.003 0.029 -9999 0 -0.5 2 2
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.024 -9999 0 -0.46 2 2
PDGFB-D/PDGFRB/SHB -0.002 0.037 -9999 0 -0.63 3 3
chemotaxis 0.034 0.04 -9999 0 -0.59 2 2
STAT1-3-5/STAT1-3-5 -0.008 0.054 -9999 0 -0.46 11 11
Bovine Papilomavirus E5/PDGFRB -0.001 0.03 -9999 0 -0.64 2 2
PTPRJ 0 0 -9999 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.058 0.076 -9999 0 -0.53 1 1
CRKL 0.028 0.049 -9999 0 -0.51 1 1
mol:DAG -0.001 0.028 -9999 0 -0.4 1 1
HRAS -0.005 0.021 -9999 0 -0.41 1 1
MAPK8 0.013 0.059 -9999 0 -0.53 3 3
RAP1A 0.028 0.049 -9999 0 -0.51 1 1
GAB1 0.028 0.049 -9999 0 -0.51 1 1
MAPK14 0.014 0.05 -9999 0 -10000 0 0
EPO -0.036 0.11 -9999 0 -0.3 10 10
PLCG1 -0.001 0.028 -9999 0 -0.41 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.01 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.024 0.068 -9999 0 -0.65 6 6
GAB1/SHC/GRB2/SOS1 -0.007 0.023 -9999 0 -0.44 1 1
EPO/EPOR (dimer) -0.029 0.063 -9999 0 -10000 0 0
IRS2 0.008 0.12 -9999 0 -0.49 39 39
STAT1 0.049 0.056 -9999 0 -0.52 1 1
STAT5B -0.004 0.046 -9999 0 -0.45 4 4
cell proliferation 0.022 0.055 -9999 0 -0.49 3 3
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.023 -9999 0 -0.41 1 1
TEC 0.027 0.055 -9999 0 -0.49 3 3
SOCS3 -0.005 0.067 -9999 0 -0.82 6 6
STAT1 (dimer) 0.048 0.056 -9999 0 -0.51 1 1
JAK2 0 0.028 -9999 0 -0.84 1 1
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
EPO/EPOR (dimer)/JAK2 0.054 0.043 -9999 0 -0.54 1 1
EPO/EPOR -0.029 0.063 -9999 0 -10000 0 0
LYN 0.012 0.002 -9999 0 -10000 0 0
TEC/VAV2 -0.012 0.036 -9999 0 -0.47 3 3
elevation of cytosolic calcium ion concentration 0.012 0.01 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.017 0.047 -9999 0 -10000 0 0
mol:IP3 -0.001 0.028 -9999 0 -0.4 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.026 0.091 -9999 0 -0.48 22 22
SH2B3 0.001 0.002 -9999 0 -10000 0 0
NFKB1 0.014 0.05 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.009 0.032 -9999 0 -0.33 7 7
PTPN6 0.021 0.051 -9999 0 -0.53 1 1
TEC/VAV2/GRB2 -0.01 0.033 -9999 0 -0.48 2 2
EPOR 0.012 0.01 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.007 0.023 -9999 0 -0.44 1 1
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.001 0.029 -9999 0 -0.55 2 2
CRKL/CBL/C3G -0.009 0.025 -9999 0 -0.47 1 1
VAV2 0.028 0.049 -9999 0 -0.51 1 1
CBL 0.028 0.049 -9999 0 -0.51 1 1
SHC/Grb2/SOS1 0.005 0.03 -9999 0 -0.47 1 1
STAT5A -0.006 0.058 -9999 0 -0.49 8 8
GRB2 0 0.009 -9999 0 -10000 0 0
STAT5 (dimer) 0.057 0.088 -9999 0 -0.62 4 4
LYN/PLCgamma2 -0.001 0.022 -9999 0 -0.63 1 1
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.027 0.05 -9999 0 -0.51 1 1
BCL2 0.036 0.19 -9999 0 -1 30 30
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.004 0.025 -9999 0 -0.42 2 2
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.029 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 -0.009 0.042 -9999 0 -0.46 3 3
EPO -0.047 0.1 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.44 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.03 0.066 -9999 0 -10000 0 0
lamellipodium assembly 0 0.015 -9999 0 -0.41 1 1
PIK3CA 0 0.009 -9999 0 -10000 0 0
PI3K -0.001 0.022 -9999 0 -0.63 1 1
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.009 0.025 -9999 0 -0.52 1 1
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
MADCAM1 -0.011 0.053 -9999 0 -0.28 35 35
cell adhesion -0.009 0.042 -9999 0 -0.46 3 3
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.006 0.046 -9999 0 -0.5 7 7
ITGB7 -0.008 0.057 -9999 0 -0.33 23 23
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.007 0.051 -9999 0 -0.55 7 7
p130Cas/Crk/Dock1 -0.004 0.037 -9999 0 -10000 0 0
VCAM1 -0.008 0.075 -9999 0 -0.57 13 13
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.035 0.047 -9999 0 -0.46 7 7
EPOR 0 0.009 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.018 -9999 0 -0.28 4 4
Rac1/GTP 0 0.015 -9999 0 -0.42 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.044 0.05 -10000 0 -0.56 1 1
BAG4 -0.004 0.04 -10000 0 -0.82 1 1
BAD 0.032 0.018 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.082 -10000 0 -0.82 8 8
BAX 0.031 0.02 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.014 -10000 0 -0.1 2 2
IKBKB 0.05 0.048 -10000 0 -0.52 1 1
MAP2K2 0.044 0.026 -10000 0 -0.48 1 1
MAP2K1 0.044 0.026 -10000 0 -0.48 1 1
SMPD1 0.02 0.014 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.048 0.052 -10000 0 -0.46 3 3
MAP2K4 0.038 0.024 -10000 0 -0.41 1 1
protein ubiquitination 0.052 0.048 -10000 0 -0.53 1 1
EnzymeConsortium:2.7.1.37 0.049 0.029 -10000 0 -0.51 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.038 0.027 -10000 0 -0.52 1 1
CRADD 0 0 -10000 0 -10000 0 0
mol:ceramide 0.025 0.019 -10000 0 -0.17 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.019 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.046 0.026 -10000 0 -0.47 1 1
MAPK1 0.046 0.026 -10000 0 -0.47 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.042 0.054 -10000 0 -0.48 3 3
KSR1 0.032 0.027 -10000 0 -0.55 1 1
MAPK8 0.042 0.035 -10000 0 -0.42 4 4
TRAF2 -0.001 0.013 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.05 0.047 -10000 0 -0.52 1 1
TNF R/SODD -0.003 0.028 -10000 0 -0.63 1 1
TNF -0.018 0.11 -10000 0 -0.83 14 14
CYCS 0.037 0.026 0.15 25 -10000 0 25
IKBKG 0.05 0.047 -10000 0 -0.52 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.037 0.052 -10000 0 -0.6 1 1
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.026 0.15 25 -10000 0 25
TNF/TNF R/SODD -0.013 0.073 -10000 0 -0.55 15 15
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.027 0.013 -10000 0 -10000 0 0
NSMAF 0.044 0.049 -10000 0 -0.56 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.027 0.15 -10000 0 -0.82 30 30
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.03 0.036 -9999 0 -10000 0 0
PLK1 0.014 0.11 -9999 0 -0.6 1 1
CDKN1B 0.082 0.066 -9999 0 -0.55 3 3
FOXO3 0.045 0.096 -9999 0 -0.51 5 5
KAT2B 0.008 0.012 -9999 0 -10000 0 0
FOXO1/SIRT1 0.007 0.037 -9999 0 -0.33 8 8
CAT 0.048 0.11 -9999 0 -1.1 3 3
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.015 0.011 -9999 0 -10000 0 0
FOXO1 0.032 0.038 -9999 0 -0.37 8 8
MAPK10 -0.044 0.19 -9999 0 -0.47 144 144
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.063 0.087 -9999 0 -10000 0 0
response to oxidative stress 0.005 0.011 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.012 0.058 -9999 0 -0.48 5 5
XPO1 0 0 -9999 0 -10000 0 0
EP300 0.002 0.005 -9999 0 -10000 0 0
BCL2L11 0.029 0.018 -9999 0 -10000 0 0
FOXO1/SKP2 -0.003 0.031 -9999 0 -0.34 1 1
mol:GDP 0.005 0.011 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
GADD45A 0.069 0.058 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.068 0.028 -9999 0 -10000 0 0
MST1 -0.003 0.097 -9999 0 -0.79 13 13
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.001 0.042 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.035 0.03 -9999 0 -0.47 3 3
MAPK9 0.036 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ -0.001 0.016 -9999 0 -0.28 3 3
SIRT1 0.002 0.007 -9999 0 -10000 0 0
SOD2 0.093 0.069 -9999 0 -10000 0 0
RBL2 0.062 0.072 -9999 0 -10000 0 0
RAL/GDP 0.011 0.015 -9999 0 -10000 0 0
CHUK 0.008 0.012 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.029 0.01 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.014 0.13 -9999 0 -1.5 6 6
SKP2 0 0 -9999 0 -10000 0 0
USP7 0 0.001 -9999 0 -10000 0 0
IKBKB 0.008 0.017 -9999 0 -10000 0 0
CCNB1 0.038 0.1 -9999 0 -0.54 3 3
FOXO1-3a-4/beta catenin -0.007 0.034 -9999 0 -0.41 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.031 -9999 0 -0.34 1 1
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.005 0.057 -9999 0 -0.83 4 4
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.067 0.077 -9999 0 -10000 0 0
SFN -0.016 0.1 -9999 0 -0.54 27 27
CDK2 0.002 0.005 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.022 0.051 -9999 0 -10000 0 0
CREBBP 0.002 0.005 -9999 0 -10000 0 0
FBXO32 0.047 0.12 -9999 0 -1.4 3 3
BCL6 0.059 0.1 -9999 0 -1.2 3 3
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0 0.008 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.003 0.041 -9999 0 -0.55 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.025 -9999 0 -10000 0 0
NFKBIA 0.024 0.034 -9999 0 -0.28 11 11
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0.006 -9999 0 -10000 0 0
ARRB2 0 0 -9999 0 -10000 0 0
REL -0.005 0.061 -9999 0 -0.82 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.009 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0 0.008 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
NFKB1 0.022 0.009 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.003 0.03 -9999 0 -0.27 11 11
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.024 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -10000 0 0
PI3K -0.001 0.022 -9999 0 -0.63 1 1
NF kappa B1 p50/RelA -0.004 0.03 -9999 0 -0.28 11 11
IKBKB -0.001 0.013 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0.009 -9999 0 -0.28 1 1
I kappa B alpha/PIK3R1 -0.004 0.032 -9999 0 -0.46 1 1
cell death -0.003 0.023 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.003 0.041 -9999 0 -0.55 5 5
LCK -0.018 0.1 -9999 0 -0.43 39 39
BCL3 -0.001 0.013 -9999 0 -0.28 2 2
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.076 0.034 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.006 0.034 -9999 0 -0.35 1 1
NFKBIA 0.047 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.013 -9999 0 -10000 0 0
RIPK2 -0.002 0.021 -9999 0 -0.28 5 5
IKBKG 0 0.001 -9999 0 -10000 0 0
IKK complex/A20 -0.005 0.05 -9999 0 -10000 0 0
NEMO/A20/RIP2 -0.002 0.021 -9999 0 -0.28 5 5
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM 0 0.002 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.004 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.009 0.048 -9999 0 -0.28 28 28
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.013 0.081 -9999 0 -0.63 14 14
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.02 0.12 -9999 0 -0.78 23 23
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.018 0.11 -9999 0 -0.82 14 14
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex 0.001 0.005 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.06 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.001 0.019 -9999 0 -10000 0 0
CLOCK 0.01 0.055 -9999 0 -0.82 4 4
TIMELESS/CRY2 -0.001 0.008 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.011 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.041 0.013 -9999 0 -10000 0 0
ARNTL 0.014 0.002 -9999 0 -10000 0 0
TIMELESS 0.041 0.016 -9999 0 -10000 0 0
NPAS2 0.009 0.057 -9999 0 -0.59 7 7
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.013 0.003 -9999 0 -10000 0 0
CHEK1 -0.008 0.046 -9999 0 -10000 0 0
mol:HEME 0.013 0.003 -9999 0 -10000 0 0
PER1 -0.018 0.12 -9999 0 -0.82 20 20
BMAL/CLOCK/NPAS2 -0.005 0.051 -9999 0 -0.54 8 8
BMAL1/CLOCK 0.044 0.04 -9999 0 -0.41 4 4
S phase of mitotic cell cycle 0.001 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.001 0.019 -9999 0 -10000 0 0
mol:NADPH 0.013 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.011 0.07 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.001 0.018 -9999 0 -0.28 4 4
Insulin-mediated glucose transport

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.38 14 14
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
STXBP4 -0.001 0.013 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.12 0.15 -9999 0 -0.36 11 11
YWHAZ -0.001 0.016 -9999 0 -0.28 3 3
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.021 0.022 -9999 0 -0.64 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
SNARE/Synip 0 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.002 0.021 -9999 0 -0.28 5 5
PRKCI 0 0.009 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0.031 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.027 -9999 0 -0.82 1 1
TRIP10 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.004 0.031 -9999 0 -10000 0 0
VAMP2 0 0 -9999 0 -10000 0 0
SLC2A4 -0.14 0.16 -9999 0 -0.39 11 11
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
SFN -0.016 0.1 -9999 0 -0.54 27 27
LNPEP -0.004 0.054 -9999 0 -0.82 4 4
YWHAE 0 0 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.012 0.036 -9999 0 -0.45 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.006 0.027 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.001 0.018 -9999 0 -0.55 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.008 0.035 -9999 0 -0.41 1 1
CaM/Ca2+ 0.011 0.032 -9999 0 -0.42 1 1
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.034 -9999 0 -0.42 1 1
AKT1 -0.006 0.022 -9999 0 -10000 0 0
MAP2K1 0.041 0.039 -9999 0 -10000 0 0
MAP3K11 0.03 0.04 -9999 0 -0.42 1 1
IFNGR1 0.001 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.026 0.1 -9999 0 -0.42 22 22
Rap1/GTP -0.004 0.013 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.012 0.035 -9999 0 -0.46 1 1
CEBPB 0.075 0.035 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.01 0.057 -9999 0 -1.3 1 1
STAT1 -0.011 0.034 -9999 0 -0.42 1 1
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.038 0.095 -9999 0 -0.28 2 2
PIK3CA 0 0.009 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.009 0.03 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0 0.009 -9999 0 -10000 0 0
mol:Ca2+ 0.011 0.034 -9999 0 -0.44 1 1
MAPK3 0.054 0.035 -9999 0 -10000 0 0
STAT1 (dimer) -0.003 0.051 -9999 0 -0.61 1 1
MAPK1 0.054 0.035 -9999 0 -10000 0 0
JAK2 0 0.027 -9999 0 -0.82 1 1
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
JAK1 0.001 0.002 -9999 0 -10000 0 0
CAMK2D -0.003 0.047 -9999 0 -0.82 3 3
DAPK1 0.069 0.031 -9999 0 -10000 0 0
SMAD7 0.05 0.036 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.006 0.019 -9999 0 -10000 0 0
PI3K 0.009 0.032 -9999 0 -0.41 2 2
IFNG -0.038 0.095 -9999 0 -0.28 2 2
apoptosis 0.053 0.027 -9999 0 -10000 0 0
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.009 0.048 -9999 0 -0.28 28 28
CAMK2B -0.074 0.22 -9999 0 -0.62 108 108
FRAP1 0.042 0.038 -9999 0 -10000 0 0
PRKCD -0.006 0.023 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.008 0.035 -9999 0 -0.41 1 1
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.064 0.045 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.009 0.032 -9999 0 -0.4 1 1
SOCS1 0.001 0.052 -9999 0 -1.5 1 1
mol:GDP -0.006 0.018 -9999 0 -10000 0 0
CASP1 0.049 0.043 -9999 0 -0.36 4 4
PTGES2 0 0.009 -9999 0 -0.28 1 1
IRF9 0.057 0.018 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.006 0.027 -9999 0 -0.4 2 2
RAP1/GDP -0.004 0.013 -9999 0 -10000 0 0
CBL -0.009 0.025 -9999 0 -0.42 1 1
MAP3K1 0.031 0.04 -9999 0 -0.42 1 1
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.008 0.035 -9999 0 -0.41 1 1
PTPN11 -0.011 0.029 -9999 0 -0.44 1 1
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
Class I PI3K signaling events

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0 0.02 0.3 2 -10000 0 2
DAPP1 0.036 0.053 -10000 0 -0.61 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK 0.047 0.078 -10000 0 -0.57 8 8
mol:DAG 0.053 0.049 0.21 1 -0.26 6 7
HRAS -0.001 0.013 -10000 0 -0.28 2 2
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP -0.002 0.023 -10000 0 -0.3 1 1
PLCG2 -0.001 0.029 -10000 0 -0.55 2 2
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.009 -10000 0 -10000 0 0
mol:GTP 0 0.019 0.27 2 -0.41 1 3
ARF1/GTP 0 0.019 0.28 2 -0.39 1 3
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.027 -10000 0 -0.82 1 1
RAP1A/GTP 0 0.019 -10000 0 -0.41 1 1
ADAP1 -0.002 0.031 -10000 0 -0.42 4 4
ARAP3 0 0.019 0.27 2 -0.41 1 3
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.011 0.058 -10000 0 -0.82 1 1
ARHGEF6 -0.009 0.086 -10000 0 -0.82 10 10
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.28 2 2
FYN -0.001 0.027 -10000 0 -0.82 1 1
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.001 0.029 -10000 0 -0.82 1 1
mol:Ca2+ 0.039 0.028 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
ZAP70 -0.029 0.13 -10000 0 -0.82 19 19
mol:IP3 0.048 0.037 -10000 0 -10000 0 0
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.002 0.023 -10000 0 -0.3 1 1
RhoA/GDP -0.001 0.02 0.28 2 -10000 0 2
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.062 0.029 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -10000 0 0
PLEKHA2 0.03 0.005 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.038 -10000 0 -0.8 2 2
HSP90AA1 0 0.009 -10000 0 -10000 0 0
ARF6/GTP 0 0.019 0.3 2 -10000 0 2
RhoA/GTP 0 0.018 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.01 0.057 -10000 0 -0.53 5 5
BLK -0.039 0.1 -10000 0 -0.82 3 3
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 0 0.018 -10000 0 -10000 0 0
HCK -0.004 0.032 -10000 0 -0.28 12 12
CYTH3 0 0.018 -10000 0 -0.38 1 1
CYTH2 0 0.018 -10000 0 -10000 0 0
KRAS 0 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.003 0.047 -10000 0 -0.55 6 6
SGK1 -0.003 0.047 -10000 0 -0.68 4 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.035 0.029 -10000 0 -0.29 2 2
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0.009 -10000 0 -0.28 1 1
ARF6/GDP -0.001 0.02 0.29 2 -10000 0 2
mol:PI-3-4-5-P3 0 0.023 0.36 2 -0.41 1 3
ARAP3/RAP1A/GTP 0 0.019 -10000 0 -0.41 1 1
VAV1 -0.002 0.03 -10000 0 -0.46 3 3
mol:PI-3-4-P2 0.022 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.001 0.015 -10000 0 -0.41 1 1
PLEKHA1 0.029 0.02 -10000 0 -0.55 1 1
Rac1/GDP -0.002 0.023 -10000 0 -0.3 1 1
LAT -0.005 0.048 -10000 0 -0.82 2 2
Rac1/GTP -0.004 0.041 -10000 0 -0.37 10 10
ITK -0.017 0.081 -10000 0 -0.45 28 28
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.06 0.063 0.24 1 -0.38 6 7
LCK -0.018 0.1 -10000 0 -0.43 39 39
BTK -0.001 0.019 -10000 0 -0.38 1 1
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.029 0.042 -10000 0 -10000 0 0
regulation of axonogenesis 0.003 0.026 0.33 6 -10000 0 6
myoblast fusion 0.007 0.025 -10000 0 -10000 0 0
mol:GTP -0.005 0.014 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.029 -10000 0 -10000 0 0
ARF1/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GM1 0.006 0.013 -10000 0 -10000 0 0
mol:Choline 0.022 0.047 -10000 0 -0.54 6 6
lamellipodium assembly -0.004 0.03 -10000 0 -10000 0 0
MAPK3 0.021 0.023 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.029 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.007 0.025 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.023 -10000 0 -10000 0 0
ARF6 0.007 0.007 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.28 2 2
TIAM1 -0.001 0.018 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.023 -10000 0 -10000 0 0
actin filament bundle formation 0.006 0.02 -10000 0 -10000 0 0
KALRN -0.01 0.067 -10000 0 -0.5 16 16
RAB11FIP3/RAB11A 0 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.02 -10000 0 -10000 0 0
NME1 -0.014 0.061 -10000 0 -10000 0 0
Rac1/GDP -0.006 0.02 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.014 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.004 0.03 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.005 0.014 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GDP -0.005 0.028 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.007 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.012 0.052 -10000 0 -0.61 6 6
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.03 -10000 0 -10000 0 0
ruffle organization -0.003 0.026 -10000 0 -0.33 6 6
regulation of epithelial cell migration -0.005 0.014 -10000 0 -10000 0 0
PLD2 0.016 0.013 -10000 0 -10000 0 0
PIP5K1A -0.003 0.027 -10000 0 -0.33 6 6
mol:Phosphatidic acid 0.022 0.047 -10000 0 -0.54 6 6
Rac1/GTP -0.004 0.03 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.029 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.44 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.014 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.005 0.033 -9999 0 -0.5 2 2
lamellipodium assembly 0 0.017 -9999 0 -0.47 1 1
PIK3CA 0 0.009 -9999 0 -10000 0 0
PI3K -0.001 0.022 -9999 0 -0.63 1 1
ARF6 0 0 -9999 0 -10000 0 0
TLN1 0 0 -9999 0 -10000 0 0
PXN 0.022 0 -9999 0 -10000 0 0
PIK3R1 -0.001 0.027 -9999 0 -0.82 1 1
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
cell adhesion -0.001 0.01 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.012 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.008 0.057 -9999 0 -0.33 23 23
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.005 0.042 -9999 0 -0.47 7 7
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.008 0.075 -9999 0 -0.57 13 13
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.012 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.001 0.012 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.018 -9999 0 -0.28 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.01 -9999 0 -10000 0 0
Rac1/GTP 0 0.019 -9999 0 -0.53 1 1
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.021 0.073 -9999 0 -9999 0 0
TP53 -0.007 0.018 -9999 0 -9999 0 0
Senescence -0.007 0.018 -9999 0 -9999 0 0
Apoptosis -0.007 0.018 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.015 0.037 -9999 0 -9999 0 0
MDM4 0 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.013 -9999 0 -0.39 1 1
MDM2/SUMO1 0 0.007 -9999 0 -10000 0 0
HDAC4 -0.001 0.027 -9999 0 -0.82 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.028 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 -0.001 0.015 -9999 0 -0.46 1 1
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0 0.007 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.018 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.005 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0 -9999 0 -9999 0 0
AP2 0 0 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -9999 0 0
CLTB -0.001 0.013 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.002 -9999 0 -9999 0 0
CD4 0 0 -9999 0 -9999 0 0
CLTA 0 0 -9999 0 -9999 0 0
mol:GTP 0.002 0 -9999 0 -9999 0 0
ARFGAP1 0.01 0.013 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
ARF1/GTP 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0.005 -9999 0 -9999 0 0
mol:Choline 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0 0 -9999 0 -9999 0 0
DDEF1 0 0 -9999 0 -9999 0 0
ARF1/GDP 0 0.007 -9999 0 -9999 0 0
AP2M1 0 0 -9999 0 -9999 0 0
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization 0 0 -9999 0 -9999 0 0
Rac/GTP 0 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.007 -9999 0 -9999 0 0
ARFIP2 0 0 -9999 0 -9999 0 0
COPA 0 0 -9999 0 -9999 0 0
RAC1 0 0 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.025 0.002 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -9999 0 0
GGA3 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -9999 0 0
AP2A1 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.003 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -9999 0 0
CYTH2 0 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -9999 0 0
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0 0 -9999 0 -9999 0 0
mol:Brefeldin A 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0 0.001 -9999 0 -9999 0 0
PLD2 0 0 -9999 0 -9999 0 0
ARF-GAP1/v-SNARE 0.01 0.013 -9999 0 -9999 0 0
PIP5K1A 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -9999 0 0
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0 0 -9999 0 -9999 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0.013 -9999 0 -9999 0 0
GOSR2 0 0 -9999 0 -9999 0 0
USO1 0 0 -9999 0 -9999 0 0
GBF1 0 0 -9999 0 -9999 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -9999 0 0
FBXW11 0 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -9999 0 0
CHUK 0 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB -0.001 0.008 -9999 0 -9999 0 0
NFKB1 0 0 -9999 0 -9999 0 0
MAP3K14 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB -0.001 0.015 -9999 0 -9999 0 0
RELB -0.002 0.024 -9999 0 -9999 0 0
NFKB2 0 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB -0.001 0.013 -9999 0 -9999 0 0
regulation of B cell activation -0.001 0.013 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 914 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.LL.A441 TCGA.LL.A440 TCGA.JL.A3YX TCGA.JL.A3YW
109_MAP3K5 0.042 0.053 0.053 0.053
47_PPARGC1A 0 0 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 0 0 0 0
131_RELN/VLDLR 0 0 0 -0.5
30_TGFB1/TGF beta receptor Type II 0 0 0 0
84_STAT5B 0.021 0.037 -0.077 0.059
84_STAT5A 0.021 0.037 -0.077 0.059
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/3351778/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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