PARADIGM pathway analysis of mRNASeq expression data
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1ZG6R90
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1ZG6R90
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 59 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
HIF-1-alpha transcription factor network 196
VEGFR1 specific signals 188
Endothelins 187
FOXA2 and FOXA3 transcription factor networks 178
Signaling events mediated by VEGFR1 and VEGFR2 158
Syndecan-1-mediated signaling events 142
Syndecan-4-mediated signaling events 140
Angiopoietin receptor Tie2-mediated signaling 131
Nephrin/Neph1 signaling in the kidney podocyte 130
Ephrin A reverse signaling 130
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 889 . 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 ( 889 ).

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
HIF-1-alpha transcription factor network 0.2205 196 14968 76 -0.76 0.026 1000 -1000 -0.13 -1000
VEGFR1 specific signals 0.2115 188 10531 56 -0.4 0.016 1000 -1000 -0.095 -1000
Endothelins 0.2103 187 18031 96 -0.42 0.016 1000 -1000 -0.09 -1000
FOXA2 and FOXA3 transcription factor networks 0.2002 178 8225 46 -0.74 0.025 1000 -1000 -0.075 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1777 158 19773 125 -0.48 0.016 1000 -1000 -0.13 -1000
Syndecan-1-mediated signaling events 0.1597 142 4854 34 -0.29 0.016 1000 -1000 -0.078 -1000
Syndecan-4-mediated signaling events 0.1575 140 9439 67 -0.39 0.087 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1474 131 11552 88 -0.41 0.038 1000 -1000 -0.14 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1462 130 4431 34 -0.25 0.016 1000 -1000 -0.088 -1000
Ephrin A reverse signaling 0.1462 130 910 7 -0.13 0 1000 -1000 -0.048 -1000
IL4-mediated signaling events 0.1462 130 11856 91 -0.79 0.54 1000 -1000 -0.15 -1000
IL23-mediated signaling events 0.1451 129 7755 60 -0.48 0.017 1000 -1000 -0.16 -1000
HIF-2-alpha transcription factor network 0.1440 128 5517 43 -0.44 0.31 1000 -1000 -0.11 -1000
PDGFR-alpha signaling pathway 0.1406 125 5514 44 -0.21 0.032 1000 -1000 -0.091 -1000
S1P1 pathway 0.1327 118 4266 36 -0.32 0.016 1000 -1000 -0.077 -1000
p75(NTR)-mediated signaling 0.1249 111 13898 125 -0.42 0.016 1000 -1000 -0.14 -1000
Signaling events mediated by the Hedgehog family 0.1215 108 5654 52 -0.4 0.15 1000 -1000 -0.1 -1000
LPA4-mediated signaling events 0.1181 105 1270 12 -0.17 0.023 1000 -1000 -0.033 -1000
TCR signaling in naïve CD8+ T cells 0.1102 98 9170 93 -0.23 0.052 1000 -1000 -0.11 -1000
amb2 Integrin signaling 0.1080 96 7952 82 -0.28 0.016 1000 -1000 -0.11 -1000
EGFR-dependent Endothelin signaling events 0.1080 96 2021 21 -0.28 0.016 1000 -1000 -0.098 -1000
IL12-mediated signaling events 0.1069 95 8312 87 -0.34 0.097 1000 -1000 -0.14 -1000
Glypican 2 network 0.1035 92 370 4 -0.081 -0.028 1000 -1000 -0.051 -1000
BMP receptor signaling 0.1024 91 7382 81 -0.4 0.034 1000 -1000 -0.11 -1000
Thromboxane A2 receptor signaling 0.1001 89 9434 105 -0.15 0.054 1000 -1000 -0.096 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0990 88 5993 68 -0.39 0.11 1000 -1000 -0.14 -1000
Integrins in angiogenesis 0.0956 85 7149 84 -0.32 0.026 1000 -1000 -0.14 -1000
Wnt signaling 0.0956 85 597 7 -0.11 -0.072 1000 -1000 -0.042 -1000
Glypican 1 network 0.0889 79 3818 48 -0.29 0.036 1000 -1000 -0.06 -1000
PDGFR-beta signaling pathway 0.0866 77 7472 97 -0.16 0.016 1000 -1000 -0.12 -1000
Class IB PI3K non-lipid kinase events 0.0832 74 222 3 -0.045 -1000 1000 -1000 -0.015 -1000
IL6-mediated signaling events 0.0787 70 5298 75 -0.38 0.064 1000 -1000 -0.11 -1000
Reelin signaling pathway 0.0776 69 3877 56 -0.35 0.016 1000 -1000 -0.11 -1000
Calcium signaling in the CD4+ TCR pathway 0.0765 68 2122 31 -0.27 0.016 1000 -1000 -0.11 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0765 68 8248 120 -0.26 0.18 1000 -1000 -0.1 -1000
Signaling events regulated by Ret tyrosine kinase 0.0709 63 5208 82 -0.21 0.016 1000 -1000 -0.11 -1000
Arf6 signaling events 0.0697 62 3864 62 -0.22 0.016 1000 -1000 -0.082 -1000
Effects of Botulinum toxin 0.0664 59 1544 26 -0.21 0.016 1000 -1000 -0.082 -1000
Signaling mediated by p38-alpha and p38-beta 0.0652 58 2592 44 -0.23 0.016 1000 -1000 -0.066 -1000
TCGA08_retinoblastoma 0.0652 58 464 8 -0.041 0.023 1000 -1000 -0.02 -1000
Visual signal transduction: Rods 0.0652 58 3032 52 -0.17 0.016 1000 -1000 -0.1 -1000
BCR signaling pathway 0.0641 57 5673 99 -0.19 0.042 1000 -1000 -0.12 -1000
Noncanonical Wnt signaling pathway 0.0619 55 1440 26 -0.15 0.016 1000 -1000 -0.12 -1000
Fc-epsilon receptor I signaling in mast cells 0.0619 55 5418 97 -0.2 0.037 1000 -1000 -0.12 -1000
Caspase cascade in apoptosis 0.0607 54 4005 74 -0.1 0.043 1000 -1000 -0.073 -1000
Glucocorticoid receptor regulatory network 0.0607 54 6189 114 -0.45 0.12 1000 -1000 -0.093 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0607 54 2015 37 -0.22 0.016 1000 -1000 -0.077 -1000
S1P3 pathway 0.0607 54 2299 42 -0.3 0.018 1000 -1000 -0.076 -1000
a4b1 and a4b7 Integrin signaling 0.0585 52 263 5 -0.066 0.008 1000 -1000 -0.048 -1000
Ephrin B reverse signaling 0.0585 52 2521 48 -0.13 0.12 1000 -1000 -0.096 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0585 52 4071 78 -0.22 0.069 1000 -1000 -0.11 -1000
E-cadherin signaling events 0.0562 50 251 5 -0.054 0.016 1000 -1000 -0.052 -1000
FOXM1 transcription factor network 0.0551 49 2545 51 -0.16 0.15 1000 -1000 -0.19 -1000
Nongenotropic Androgen signaling 0.0540 48 2512 52 -0.097 0.016 1000 -1000 -0.081 -1000
EPHB forward signaling 0.0529 47 4077 85 -0.14 0.1 1000 -1000 -0.12 -1000
Plasma membrane estrogen receptor signaling 0.0529 47 4075 86 -0.14 0.027 1000 -1000 -0.11 -1000
Visual signal transduction: Cones 0.0517 46 1750 38 -0.12 0.015 1000 -1000 -0.085 -1000
JNK signaling in the CD4+ TCR pathway 0.0517 46 789 17 -0.12 0.016 1000 -1000 -0.1 -1000
IL27-mediated signaling events 0.0517 46 2361 51 -0.19 0.064 1000 -1000 -0.11 -1000
Syndecan-2-mediated signaling events 0.0495 44 3063 69 -0.18 0.042 1000 -1000 -0.082 -1000
LPA receptor mediated events 0.0495 44 4538 102 -0.15 0.021 1000 -1000 -0.12 -1000
EPO signaling pathway 0.0461 41 2255 55 -0.21 0.016 1000 -1000 -0.13 -1000
Osteopontin-mediated events 0.0450 40 1524 38 -0.12 0.016 1000 -1000 -0.14 -1000
Signaling events mediated by PTP1B 0.0450 40 3110 76 -0.15 0.025 1000 -1000 -0.1 -1000
IL2 signaling events mediated by STAT5 0.0450 40 880 22 -0.097 0.017 1000 -1000 -0.052 -1000
Canonical Wnt signaling pathway 0.0439 39 1998 51 -0.16 0.04 1000 -1000 -0.074 -1000
Coregulation of Androgen receptor activity 0.0427 38 2893 76 -0.29 0.034 1000 -1000 -0.063 -1000
IL2 signaling events mediated by PI3K 0.0427 38 2211 58 -0.1 0.035 1000 -1000 -0.1 -1000
ErbB4 signaling events 0.0405 36 2484 69 -0.17 0.088 1000 -1000 -0.11 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0405 36 1981 54 -0.27 0.034 1000 -1000 -0.13 -1000
Cellular roles of Anthrax toxin 0.0405 36 1423 39 -0.1 0.019 1000 -1000 -0.05 -1000
IL1-mediated signaling events 0.0394 35 2175 62 -0.18 0.077 1000 -1000 -0.13 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0382 34 969 28 -0.086 0.016 1000 -1000 -0.079 -1000
Paxillin-dependent events mediated by a4b1 0.0371 33 1203 36 -0.11 0.045 1000 -1000 -0.092 -1000
Ras signaling in the CD4+ TCR pathway 0.0371 33 561 17 -0.037 0.016 1000 -1000 -0.057 -1000
Aurora B signaling 0.0371 33 2276 67 -0.17 0.016 1000 -1000 -0.095 -1000
Presenilin action in Notch and Wnt signaling 0.0360 32 1978 61 -0.11 0.047 1000 -1000 -0.092 -1000
FAS signaling pathway (CD95) 0.0360 32 1506 47 -0.23 0.017 1000 -1000 -0.069 -1000
Signaling mediated by p38-gamma and p38-delta 0.0360 32 483 15 -0.031 0.02 1000 -1000 -0.038 -1000
TRAIL signaling pathway 0.0337 30 1487 48 -0.076 0.028 1000 -1000 -0.1 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0326 29 2158 74 -0.15 0.066 1000 -1000 -0.13 -1000
S1P5 pathway 0.0315 28 476 17 -0.057 0.055 1000 -1000 -0.071 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0304 27 908 33 -0.21 0.032 1000 -1000 -0.085 -1000
Regulation of p38-alpha and p38-beta 0.0292 26 1427 54 -0.14 0.019 1000 -1000 -0.074 -1000
ErbB2/ErbB3 signaling events 0.0270 24 1575 65 -0.1 0.032 1000 -1000 -0.087 -1000
Regulation of nuclear SMAD2/3 signaling 0.0270 24 3295 136 -0.32 0.31 1000 -1000 -0.097 -1000
Nectin adhesion pathway 0.0270 24 1535 63 -0.12 0.055 1000 -1000 -0.11 -1000
Syndecan-3-mediated signaling events 0.0270 24 847 35 -0.16 0.016 1000 -1000 -0.09 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0270 24 1106 45 -0.14 0.042 1000 -1000 -0.12 -1000
Regulation of Androgen receptor activity 0.0270 24 1686 70 -0.3 0.038 1000 -1000 -0.089 -1000
Signaling events mediated by PRL 0.0259 23 790 34 -0.1 0.024 1000 -1000 -0.056 -1000
p38 MAPK signaling pathway 0.0259 23 1014 44 -0.25 0.021 1000 -1000 -0.084 -1000
Insulin-mediated glucose transport 0.0236 21 674 32 -0.23 0.039 1000 -1000 -0.081 -1000
Ceramide signaling pathway 0.0236 21 1616 76 -0.15 0.039 1000 -1000 -0.087 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0236 21 1134 52 -0.12 0.051 1000 -1000 -0.089 -1000
S1P4 pathway 0.0236 21 542 25 -0.052 0.02 1000 -1000 -0.071 -1000
BARD1 signaling events 0.0225 20 1173 57 -0.043 0.055 1000 -1000 -0.098 -1000
Aurora A signaling 0.0225 20 1215 60 -0.2 0.043 1000 -1000 -0.084 -1000
Class I PI3K signaling events 0.0225 20 1501 73 -0.1 0.032 1000 -1000 -0.099 -1000
Regulation of Telomerase 0.0225 20 2118 102 -0.26 0.048 1000 -1000 -0.13 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0214 19 1617 83 -0.23 0.064 1000 -1000 -0.096 -1000
IGF1 pathway 0.0214 19 1139 57 -0.06 0.032 1000 -1000 -0.12 -1000
PLK2 and PLK4 events 0.0202 18 56 3 -0.008 0.014 1000 -1000 -0.034 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0202 18 1565 85 -0.094 0.036 1000 -1000 -0.1 -1000
TCGA08_rtk_signaling 0.0202 18 484 26 -0.18 0.042 1000 -1000 -0.026 -1000
E-cadherin signaling in keratinocytes 0.0202 18 774 43 -0.094 0.035 1000 -1000 -0.089 -1000
IFN-gamma pathway 0.0191 17 1217 68 -0.25 0.05 1000 -1000 -0.12 -1000
TCGA08_p53 0.0191 17 122 7 -0.031 0.023 1000 -1000 -0.023 -1000
E-cadherin signaling in the nascent adherens junction 0.0191 17 1330 76 -0.056 0.047 1000 -1000 -0.11 -1000
FoxO family signaling 0.0180 16 1030 64 -0.31 0.14 1000 -1000 -0.073 -1000
Hedgehog signaling events mediated by Gli proteins 0.0169 15 1010 65 -0.12 0.051 1000 -1000 -0.079 -1000
Insulin Pathway 0.0169 15 1159 74 -0.12 0.042 1000 -1000 -0.12 -1000
Rapid glucocorticoid signaling 0.0169 15 319 20 -0.031 0.016 1000 -1000 -0.05 -1000
Aurora C signaling 0.0157 14 102 7 -0.036 0.001 1000 -1000 -0.06 -1000
PLK1 signaling events 0.0157 14 1236 85 -0.038 0.038 1000 -1000 -0.068 -1000
Signaling events mediated by HDAC Class III 0.0157 14 571 40 -0.071 0.028 1000 -1000 -0.057 -1000
ceramide signaling pathway 0.0157 14 734 49 -0.066 0.037 1000 -1000 -0.052 -1000
Atypical NF-kappaB pathway 0.0157 14 434 31 -0.08 0.033 1000 -1000 -0.057 -1000
Signaling events mediated by HDAC Class II 0.0135 12 920 75 -0.07 0.037 1000 -1000 -0.082 -1000
Retinoic acid receptors-mediated signaling 0.0135 12 721 58 -0.042 0.047 1000 -1000 -0.094 -1000
Circadian rhythm pathway 0.0124 11 248 22 -0.05 0.041 1000 -1000 -0.076 -1000
Class I PI3K signaling events mediated by Akt 0.0101 9 612 68 -0.23 0.06 1000 -1000 -0.087 -1000
Signaling events mediated by HDAC Class I 0.0101 9 946 104 -0.07 0.069 1000 -1000 -0.082 -1000
Canonical NF-kappaB pathway 0.0090 8 330 39 -0.062 0.095 1000 -1000 -0.1 -1000
Arf6 downstream pathway 0.0090 8 374 43 -0.03 0.03 1000 -1000 -0.045 -1000
Arf6 trafficking events 0.0090 8 621 71 -0.071 0.054 1000 -1000 -0.097 -1000
Alternative NF-kappaB pathway 0.0079 7 92 13 -0.021 0.016 1000 -1000 -0.088 -1000
mTOR signaling pathway 0.0067 6 333 53 -0.014 0.036 1000 -1000 -0.078 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0022 2 66 23 -0.018 0.058 1000 -1000 -0.094 -1000
Arf1 pathway 0.0022 2 140 54 -0.016 0.036 1000 -1000 -0.063 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 12 27 -0.001 0.037 1000 -1000 -0.081 -1000
Total NA 6846 404941 7203 -25 -990 131000 -131000 -12 -131000
HIF-1-alpha transcription factor network

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
PKM2 -0.46 0.76 -9999 0 -1.4 277 277
HDAC7 0.015 0.041 -9999 0 -0.85 2 2
HIF1A/ARNT/Cbp/p300/Src-1 -0.41 0.48 -9999 0 -1 292 292
SMAD4 0.018 0.003 -9999 0 -10000 0 0
ID2 -0.46 0.76 -9999 0 -1.4 278 278
AP1 -0.076 0.21 -9999 0 -0.58 123 123
ABCG2 -0.49 0.77 -9999 0 -1.5 285 285
HIF1A -0.043 0.12 -9999 0 -0.81 9 9
TFF3 -0.51 0.8 -9999 0 -1.5 302 302
GATA2 -0.072 0.25 -9999 0 -0.75 103 103
AKT1 -0.032 0.11 -9999 0 -1 1 1
response to hypoxia -0.055 0.12 -9999 0 -10000 0 0
MCL1 -0.46 0.76 -9999 0 -1.4 277 277
NDRG1 -0.47 0.77 -9999 0 -1.5 277 277
SERPINE1 -0.54 0.81 -9999 0 -1.5 301 301
FECH -0.46 0.76 -9999 0 -1.4 276 276
FURIN -0.46 0.76 -9999 0 -1.4 277 277
NCOA2 -0.046 0.21 -9999 0 -0.85 57 57
EP300 -0.015 0.17 -9999 0 -0.42 7 7
HMOX1 -0.49 0.79 -9999 0 -1.5 283 283
BHLHE40 -0.46 0.76 -9999 0 -1.4 276 276
BHLHE41 -0.48 0.78 -9999 0 -1.5 281 281
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.049 0.094 -9999 0 -0.54 14 14
ENG 0.021 0.17 -9999 0 -0.86 11 11
JUN 0.009 0.07 -9999 0 -0.77 7 7
RORA -0.46 0.76 -9999 0 -1.4 279 279
ABCB1 -0.33 0.55 -9999 0 -1.3 190 190
TFRC -0.47 0.76 -9999 0 -1.4 278 278
CXCR4 -0.48 0.78 -9999 0 -1.5 279 279
TF -0.54 0.77 -9999 0 -1.4 301 301
CITED2 -0.46 0.76 -9999 0 -1.4 278 278
HIF1A/ARNT -0.76 1 -9999 0 -2 301 301
LDHA -0.066 0.16 -9999 0 -1.6 9 9
ETS1 -0.47 0.77 -9999 0 -1.4 284 284
PGK1 -0.46 0.76 -9999 0 -1.4 276 276
NOS2 -0.51 0.78 -9999 0 -1.5 292 292
ITGB2 -0.47 0.77 -9999 0 -1.5 279 279
ALDOA -0.46 0.76 -9999 0 -1.4 278 278
Cbp/p300/CITED2 -0.52 0.74 -9999 0 -1.5 288 288
FOS -0.088 0.26 -9999 0 -0.74 120 120
HK2 -0.48 0.78 -9999 0 -1.5 285 285
SP1 0.018 0.029 -9999 0 -10000 0 0
GCK -0.1 0.36 -9999 0 -0.99 46 46
HK1 -0.46 0.76 -9999 0 -1.4 277 277
NPM1 -0.46 0.76 -9999 0 -1.4 277 277
EGLN1 -0.46 0.76 -9999 0 -1.4 278 278
CREB1 0.026 0.003 -9999 0 -10000 0 0
PGM1 -0.46 0.76 -9999 0 -1.4 277 277
SMAD3 0.018 0.003 -9999 0 -10000 0 0
EDN1 -0.22 0.54 -9999 0 -1.4 139 139
IGFBP1 -0.56 0.78 -9999 0 -1.5 305 305
VEGFA -0.4 0.62 -9999 0 -1.2 277 277
HIF1A/JAB1 -0.032 0.071 -9999 0 -0.62 9 9
CP -0.68 0.83 -9999 0 -1.5 372 372
CXCL12 -0.48 0.78 -9999 0 -1.5 282 282
COPS5 0.01 0.014 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
BNIP3 -0.46 0.76 -9999 0 -1.4 278 278
EGLN3 -0.54 0.84 -9999 0 -1.5 319 319
CA9 -0.57 0.85 -9999 0 -1.5 341 341
TERT -0.5 0.76 -9999 0 -1.4 291 291
ENO1 -0.46 0.76 -9999 0 -1.4 277 277
PFKL -0.46 0.76 -9999 0 -1.4 277 277
NCOA1 0.013 0.008 -9999 0 -10000 0 0
ADM -0.51 0.81 -9999 0 -1.5 301 301
ARNT -0.033 0.093 -9999 0 -10000 0 0
HNF4A -0.13 0.32 -9999 0 -0.85 150 150
ADFP -0.5 0.72 -9999 0 -1.4 288 288
SLC2A1 -0.34 0.56 -9999 0 -1.1 233 233
LEP -0.51 0.76 -9999 0 -1.4 304 304
HIF1A/ARNT/Cbp/p300 -0.41 0.52 -9999 0 -1 295 295
EPO -0.35 0.5 -9999 0 -1.1 165 165
CREBBP -0.014 0.17 -9999 0 -0.44 3 3
HIF1A/ARNT/Cbp/p300/HDAC7 -0.48 0.56 -9999 0 -1.2 316 316
PFKFB3 -0.47 0.77 -9999 0 -1.5 277 277
NT5E -0.47 0.77 -9999 0 -1.5 281 281
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.23 0.44 -9999 0 -0.95 243 243
VEGFR1 homodimer/NRP1 -0.26 0.43 -9999 0 -0.95 246 246
mol:DAG -0.35 0.51 -9999 0 -1.1 259 259
VEGFR1 homodimer/NRP1/VEGFR 121 -0.37 0.58 -9999 0 -1.2 270 270
CaM/Ca2+ -0.33 0.49 -9999 0 -1.1 239 239
HIF1A -0.092 0.2 -9999 0 -0.4 241 241
GAB1 0.014 0.041 -9999 0 -0.85 2 2
AKT1 -0.28 0.45 -9999 0 -0.96 242 242
PLCG1 -0.36 0.53 -9999 0 -1.1 259 259
NOS3 -0.3 0.5 -9999 0 -1 243 243
CBL 0.015 0.029 -9999 0 -0.85 1 1
mol:NO -0.27 0.45 -9999 0 -0.95 243 243
FLT1 -0.26 0.49 -9999 0 -1.1 246 246
PGF -0.26 0.37 -9999 0 -0.75 321 321
VEGFR1 homodimer/NRP2/VEGFR121 -0.4 0.63 -9999 0 -1.3 270 270
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
eNOS/Hsp90 -0.25 0.43 -9999 0 -0.9 243 243
endothelial cell proliferation -0.33 0.49 -9999 0 -1 260 260
mol:Ca2+ -0.34 0.5 -9999 0 -1.1 259 259
MAPK3 -0.29 0.45 -9999 0 -0.97 240 240
MAPK1 -0.29 0.45 -9999 0 -0.97 240 240
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
PLGF homodimer -0.26 0.37 -9999 0 -0.75 321 321
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.081 0.27 -9999 0 -0.84 101 101
VEGFA homodimer -0.21 0.38 -9999 0 -0.84 236 236
VEGFR1 homodimer/VEGFA homodimer -0.36 0.63 -9999 0 -1.3 270 270
platelet activating factor biosynthetic process -0.27 0.43 -9999 0 -0.93 240 240
PI3K -0.37 0.49 -9999 0 -1.1 241 241
PRKCA -0.32 0.47 -9999 0 -1 240 240
PRKCB -0.34 0.48 -9999 0 -0.99 277 277
VEGFR1 homodimer/PLGF homodimer -0.4 0.56 -9999 0 -1.2 263 263
VEGFA -0.21 0.38 -9999 0 -0.84 236 236
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.35 0.51 -9999 0 -1.1 259 259
RASA1 -0.21 0.42 -9999 0 -0.89 238 238
NRP2 -0.047 0.22 -9999 0 -0.84 66 66
VEGFR1 homodimer -0.26 0.49 -9999 0 -1 246 246
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.014 0.041 -9999 0 -0.85 2 2
eNOS/Caveolin-1 -0.28 0.48 -9999 0 -0.99 250 250
PTPN11 0.015 0.029 -9999 0 -0.85 1 1
mol:PI-3-4-5-P3 -0.36 0.47 -9999 0 -1.1 241 241
mol:L-citrulline -0.27 0.45 -9999 0 -0.95 243 243
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.35 0.55 -9999 0 -1.2 238 238
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.37 0.58 -9999 0 -1.2 265 265
CD2AP 0.015 0.022 -9999 0 -0.65 1 1
PI3K/GAB1 -0.35 0.45 -9999 0 -1 241 241
PDPK1 -0.3 0.46 -9999 0 -1 241 241
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.37 0.58 -9999 0 -1.2 265 265
mol:NADP -0.27 0.45 -9999 0 -0.95 243 243
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.34 0.53 -9999 0 -1.2 238 238
VEGFR1 homodimer/NRP2 -0.27 0.51 -9999 0 -1.1 249 249
Endothelins

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
AKT1 -0.31 0.56 -10000 0 -1 265 265
PTK2B 0.016 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.26 0.52 -10000 0 -1 257 257
EDN1 -0.14 0.35 -10000 0 -0.87 147 147
EDN3 -0.044 0.18 -10000 0 -0.65 72 72
EDN2 -0.18 0.35 -10000 0 -0.77 226 226
HRAS/GDP -0.2 0.42 -10000 0 -0.83 231 231
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.46 -10000 0 -0.83 264 264
ADCY4 -0.31 0.52 -10000 0 -1.1 248 248
ADCY5 -0.33 0.52 -10000 0 -1 262 262
ADCY6 -0.27 0.47 -10000 0 -0.97 231 231
ADCY7 -0.27 0.47 -10000 0 -0.97 232 232
ADCY1 -0.38 0.57 -10000 0 -1.1 300 300
ADCY2 -0.42 0.5 -10000 0 -0.87 397 397
ADCY3 -0.28 0.49 -10000 0 -1 231 231
ADCY8 -0.41 0.46 -10000 0 -0.88 351 351
ADCY9 -0.27 0.47 -10000 0 -0.98 231 231
arachidonic acid secretion -0.17 0.37 -10000 0 -0.7 237 237
ETB receptor/Endothelin-1/Gq/GTP -0.11 0.28 -10000 0 -0.52 221 221
GNAO1 -0.052 0.22 -10000 0 -0.76 79 79
HRAS 0.011 0.059 -10000 0 -0.77 5 5
ETA receptor/Endothelin-1/G12/GTP -0.28 0.55 0.36 109 -1 263 372
ETA receptor/Endothelin-1/Gs/GTP -0.28 0.53 0.34 109 -0.97 271 380
mol:GTP 0 0.006 -10000 0 -10000 0 0
COL3A1 -0.38 0.64 -10000 0 -1.2 285 285
EDNRB -0.053 0.23 -10000 0 -0.83 72 72
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.42 0.63 -10000 0 -1.2 307 307
CYSLTR1 -0.35 0.62 -10000 0 -1.2 243 243
SLC9A1 -0.12 0.2 0.22 40 -0.42 213 253
mol:GDP -0.23 0.48 -10000 0 -0.9 255 255
SLC9A3 -0.29 0.48 -10000 0 -0.98 236 236
RAF1 -0.2 0.43 -10000 0 -0.85 222 222
JUN -0.18 0.41 -10000 0 -0.85 202 202
JAK2 -0.31 0.56 -10000 0 -1 265 265
mol:IP3 -0.22 0.44 -10000 0 -0.81 256 256
ETA receptor/Endothelin-1 -0.34 0.63 0.42 114 -1.2 270 384
PLCB1 -0.14 0.33 -10000 0 -0.84 160 160
PLCB2 -0.016 0.16 -10000 0 -0.83 32 32
ETA receptor/Endothelin-3 -0.21 0.38 -10000 0 -0.78 248 248
FOS -0.16 0.36 -10000 0 -0.79 157 157
Gai/GDP -0.043 0.26 -10000 0 -1.1 44 44
CRK 0.015 0.022 -10000 0 -0.65 1 1
mol:Ca ++ -0.37 0.64 -10000 0 -1.2 296 296
BCAR1 0.013 0.05 -10000 0 -0.85 3 3
PRKCB1 -0.21 0.41 -10000 0 -0.76 260 260
GNAQ 0.014 0.009 -10000 0 -10000 0 0
GNAZ 0.007 0.085 -10000 0 -0.79 10 10
GNAL -0.006 0.13 -10000 0 -0.72 27 27
Gs family/GDP -0.25 0.36 -10000 0 -0.77 251 251
ETA receptor/Endothelin-1/Gq/GTP -0.22 0.48 -10000 0 -0.86 252 252
MAPK14 -0.13 0.32 -10000 0 -0.7 160 160
TRPC6 -0.29 0.57 -10000 0 -1.1 255 255
GNAI2 0.015 0.029 -10000 0 -0.85 1 1
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.004 0.1 -10000 0 -0.85 12 12
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.15 0.34 -10000 0 -0.63 226 226
ETB receptor/Endothelin-2 -0.2 0.32 -10000 0 -0.66 263 263
ETB receptor/Endothelin-3 -0.087 0.22 -10000 0 -0.59 136 136
ETB receptor/Endothelin-1 -0.16 0.35 -10000 0 -0.77 185 185
MAPK3 -0.18 0.41 -10000 0 -0.86 190 190
MAPK1 -0.18 0.41 -10000 0 -0.86 190 190
Rac1/GDP -0.19 0.42 -10000 0 -0.82 234 234
cAMP biosynthetic process -0.37 0.46 -10000 0 -0.93 309 309
MAPK8 -0.27 0.57 -10000 0 -1.1 239 239
SRC 0.015 0.022 -10000 0 -0.65 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.064 0.22 -10000 0 -0.58 91 91
p130Cas/CRK/Src/PYK2 -0.22 0.46 -10000 0 -0.86 265 265
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.19 0.42 -10000 0 -0.82 232 232
COL1A2 -0.33 0.61 -10000 0 -1.1 265 265
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.32 0.42 -10000 0 -0.76 382 382
mol:DAG -0.22 0.44 -10000 0 -0.82 256 256
MAP2K2 -0.18 0.4 -10000 0 -0.84 195 195
MAP2K1 -0.18 0.4 -10000 0 -0.84 190 190
EDNRA -0.22 0.45 -10000 0 -1 198 198
positive regulation of muscle contraction -0.27 0.5 -10000 0 -1 233 233
Gq family/GDP -0.24 0.39 -10000 0 -0.87 214 214
HRAS/GTP -0.22 0.45 -10000 0 -0.86 248 248
PRKCH -0.22 0.46 -10000 0 -0.9 235 235
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.2 0.41 -10000 0 -0.81 230 230
PRKCB -0.22 0.45 -10000 0 -0.87 236 236
PRKCE -0.2 0.41 -10000 0 -0.81 229 229
PRKCD -0.22 0.43 -10000 0 -0.83 245 245
PRKCG -0.23 0.44 -10000 0 -0.85 243 243
regulation of vascular smooth muscle contraction -0.19 0.43 -10000 0 -0.97 158 158
PRKCQ -0.22 0.44 -10000 0 -0.86 241 241
PLA2G4A -0.19 0.42 -10000 0 -0.8 238 238
GNA14 -0.079 0.27 -10000 0 -0.85 97 97
GNA15 -0.016 0.16 -10000 0 -0.81 33 33
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 -0.012 0.14 -10000 0 -0.75 31 31
Rac1/GTP -0.28 0.54 0.36 109 -1 263 372
MMP1 -0.29 0.61 -10000 0 -1 313 313
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.54 0.59 -10000 0 -1.3 285 285
PCK1 -0.55 0.65 -10000 0 -1.4 251 251
HNF4A -0.71 0.74 -10000 0 -1.5 331 331
KCNJ11 -0.58 0.68 -10000 0 -1.4 284 284
AKT1 -0.16 0.2 -10000 0 -0.5 20 20
response to starvation -0.017 0.041 -10000 0 -10000 0 0
DLK1 -0.56 0.63 -10000 0 -1.4 273 273
NKX2-1 -0.12 0.24 0.68 2 -0.82 5 7
ACADM -0.54 0.59 -10000 0 -1.3 273 273
TAT -0.31 0.32 -10000 0 -0.9 119 119
CEBPB -0.007 0.077 -10000 0 -0.68 10 10
CEBPA -0.032 0.16 -10000 0 -0.78 37 37
TTR -0.38 0.39 -10000 0 -0.94 214 214
PKLR -0.65 0.72 -10000 0 -1.5 325 325
APOA1 -0.64 0.67 -10000 0 -1.4 303 303
CPT1C -0.62 0.65 -10000 0 -1.3 335 335
ALAS1 -0.18 0.22 -10000 0 -1 2 2
TFRC -0.36 0.4 -10000 0 -1 137 137
FOXF1 -0.085 0.27 -10000 0 -0.81 109 109
NF1 0.025 0.003 -10000 0 -10000 0 0
HNF1A (dimer) -0.075 0.24 -10000 0 -0.88 72 72
CPT1A -0.54 0.59 -10000 0 -1.3 273 273
HMGCS1 -0.54 0.59 -10000 0 -1.3 282 282
NR3C1 -0.013 0.083 -10000 0 -0.83 4 4
CPT1B -0.59 0.65 -10000 0 -1.4 297 297
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.016 0.01 -10000 0 -10000 0 0
GCK -0.56 0.61 -10000 0 -1.3 282 282
CREB1 -0.023 0.064 -10000 0 -10000 0 0
IGFBP1 -0.41 0.53 -10000 0 -1.2 228 228
PDX1 -0.26 0.36 -10000 0 -1.1 89 89
UCP2 -0.55 0.61 -10000 0 -1.3 281 281
ALDOB -0.73 0.74 -10000 0 -1.5 365 365
AFP -0.18 0.26 -10000 0 -0.71 116 116
BDH1 -0.62 0.66 -10000 0 -1.3 345 345
HADH -0.54 0.62 -10000 0 -1.3 265 265
F2 -0.74 0.73 -10000 0 -1.5 340 340
HNF1A -0.075 0.25 -10000 0 -0.88 72 72
G6PC -0.43 0.6 -10000 0 -1.3 242 242
SLC2A2 -0.54 0.76 -10000 0 -1.8 208 208
INS 0.021 0.074 -10000 0 -0.59 3 3
FOXA1 -0.15 0.28 -10000 0 -0.7 169 169
FOXA3 -0.2 0.32 -10000 0 -0.73 197 197
FOXA2 -0.64 0.74 -10000 0 -1.5 313 313
ABCC8 -0.56 0.63 -10000 0 -1.4 278 278
ALB -0.28 0.44 -10000 0 -0.98 189 189
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.05 0.17 -9999 0 -0.6 74 74
AKT1 -0.18 0.42 -9999 0 -0.82 255 255
PTK2B -0.31 0.56 -9999 0 -1.2 242 242
VEGFR2 homodimer/Frs2 -0.23 0.46 -9999 0 -1 233 233
CAV1 -0.081 0.27 -9999 0 -0.84 101 101
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.37 0.59 -9999 0 -1.3 233 233
endothelial cell proliferation -0.16 0.39 -9999 0 -0.75 258 258
mol:Ca2+ -0.28 0.54 -9999 0 -1.2 234 234
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.35 0.56 -9999 0 -1.3 233 233
RP11-342D11.1 -0.29 0.54 -9999 0 -1.2 234 234
CDH5 -0.13 0.32 -9999 0 -0.84 148 148
VEGFA homodimer -0.14 0.24 -9999 0 -0.52 236 236
SHC1 0.015 0.022 -9999 0 -0.65 1 1
SHC2 -0.021 0.17 -9999 0 -0.8 40 40
HRAS/GDP -0.27 0.41 -9999 0 -0.94 235 235
SH2D2A -0.073 0.25 -9999 0 -0.76 101 101
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.25 0.38 -9999 0 -0.87 236 236
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.42 0.61 -9999 0 -1.4 238 238
VEGFR1 homodimer -0.22 0.38 -9999 0 -0.84 240 240
SHC/GRB2/SOS1 -0.32 0.5 -9999 0 -1.1 234 234
GRB10 -0.28 0.54 -9999 0 -1.1 235 235
PTPN11 0.015 0.029 -9999 0 -0.85 1 1
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.4 0.64 -9999 0 -1.4 235 235
HRAS 0.012 0.059 -9999 0 -0.77 5 5
VEGF/Rho/ROCK1/Integrin Complex -0.16 0.35 -9999 0 -0.72 222 222
HIF1A 0.008 0.076 -9999 0 -0.74 9 9
FRS2 0.016 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.34 0.54 -9999 0 -1.2 233 233
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.12 0.32 -9999 0 -0.84 144 144
Nck/Pak -0.001 0.031 -9999 0 -0.65 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.38 0.6 -9999 0 -1.3 233 233
mol:GDP -0.3 0.46 -9999 0 -1.1 234 234
mol:NADP -0.14 0.36 -9999 0 -0.71 235 235
eNOS/Hsp90 -0.12 0.33 -9999 0 -0.65 235 235
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
mol:IP3 -0.29 0.56 -9999 0 -1.2 234 234
HIF1A/ARNT -0.006 0.056 -9999 0 -0.56 9 9
SHB 0.015 0.029 -9999 0 -0.85 1 1
VEGFA -0.21 0.38 -9999 0 -0.84 236 236
VEGFC -0.013 0.15 -9999 0 -0.82 31 31
FAK1/Vinculin -0.26 0.53 -9999 0 -1.1 243 243
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.39 0.58 -9999 0 -1.3 242 242
PTPN6 0.014 0.041 -9999 0 -0.85 2 2
EPAS1 -0.11 0.26 -9999 0 -1.2 25 25
mol:L-citrulline -0.14 0.36 -9999 0 -0.71 235 235
ITGAV 0.009 0.074 -9999 0 -0.82 7 7
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.35 0.56 -9999 0 -1.3 233 233
VEGFR2 homodimer/VEGFA homodimer -0.38 0.59 -9999 0 -1.3 234 234
VEGFR2/3 heterodimer -0.31 0.6 -9999 0 -1.3 238 238
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.29 0.56 -9999 0 -1.2 238 238
VEGFR2 homodimer -0.26 0.51 -9999 0 -1.1 242 242
FLT1 -0.22 0.38 -9999 0 -0.84 240 240
NEDD4 -0.001 0.13 -9999 0 -0.84 20 20
MAPK3 -0.24 0.48 -9999 0 -0.99 242 242
MAPK1 -0.24 0.48 -9999 0 -0.99 243 243
VEGFA145/NRP2 -0.21 0.36 -9999 0 -0.75 251 251
VEGFR1/2 heterodimer -0.36 0.66 -9999 0 -1.4 257 257
KDR -0.26 0.52 -9999 0 -1.1 242 242
VEGFA165/NRP1/VEGFR2 homodimer -0.38 0.58 -9999 0 -1.3 240 240
SRC 0.015 0.022 -9999 0 -0.65 1 1
platelet activating factor biosynthetic process -0.25 0.5 -9999 0 -1 242 242
PI3K -0.37 0.55 -9999 0 -1.2 254 254
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.37 0.59 -9999 0 -1.3 233 233
FES -0.31 0.59 -9999 0 -1.3 234 234
GAB1 -0.38 0.57 -9999 0 -1.3 251 251
VEGFR2 homodimer/VEGFA homodimer/Src -0.37 0.59 -9999 0 -1.3 233 233
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.15 0.37 -9999 0 -0.71 244 244
VEGFR2 homodimer/VEGFA homodimer/Yes -0.37 0.59 -9999 0 -1.3 233 233
PI3K/GAB1 -0.18 0.43 -9999 0 -0.85 253 253
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.34 0.54 -9999 0 -1.2 233 233
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.34 0.57 -9999 0 -1.3 235 235
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 -0.3 0.58 -9999 0 -1.2 234 234
actin cytoskeleton reorganization -0.41 0.58 -9999 0 -1.3 238 238
PTK2 -0.31 0.61 -9999 0 -1.3 243 243
EDG1 -0.29 0.54 -9999 0 -1.2 234 234
mol:DAG -0.29 0.56 -9999 0 -1.2 234 234
CaM/Ca2+ -0.3 0.47 -9999 0 -1.1 234 234
MAP2K3 -0.28 0.55 -9999 0 -1.1 237 237
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.36 0.56 -9999 0 -1.3 235 235
PLCG1 -0.3 0.58 -9999 0 -1.2 234 234
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.36 0.56 -9999 0 -1.3 233 233
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.37 0.59 -9999 0 -1.3 233 233
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.37 0.59 -9999 0 -1.3 234 234
cell migration -0.17 0.43 -9999 0 -0.85 243 243
mol:PI-3-4-5-P3 -0.31 0.46 -9999 0 -1 254 254
FYN 0.007 0.086 -9999 0 -0.85 9 9
VEGFB/NRP1 -0.26 0.5 -9999 0 -1.1 234 234
mol:NO -0.14 0.36 -9999 0 -0.71 235 235
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.27 0.42 -9999 0 -0.95 235 235
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.31 0.6 -9999 0 -1.3 235 235
VHL 0.012 0.058 -9999 0 -0.85 4 4
ITGB3 -0.046 0.21 -9999 0 -0.76 71 71
NOS3 -0.18 0.43 -9999 0 -0.86 235 235
VEGFR2 homodimer/VEGFA homodimer/Sck -0.39 0.6 -9999 0 -1.3 239 239
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.25 0.5 -9999 0 -1.1 234 234
PRKCB -0.28 0.51 -9999 0 -1.1 244 244
VCL 0.016 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.31 0.57 -9999 0 -1.2 234 234
VEGFR1/2 heterodimer/VEGFA homodimer -0.48 0.75 -9999 0 -1.7 249 249
VEGFA165/NRP2 -0.21 0.36 -9999 0 -0.75 251 251
MAPKKK cascade -0.28 0.42 -9999 0 -0.96 236 236
NRP2 -0.047 0.22 -9999 0 -0.84 66 66
VEGFC homodimer -0.013 0.15 -9999 0 -0.82 31 31
NCK1 0.014 0.041 -9999 0 -0.85 2 2
ROCK1 0.013 0.05 -9999 0 -0.85 3 3
FAK1/Paxillin -0.26 0.53 -9999 0 -1.1 243 243
MAP3K13 -0.31 0.59 -9999 0 -1.2 237 237
PDPK1 -0.18 0.42 -9999 0 -0.82 254 254
Syndecan-1-mediated signaling events

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
TGFB1 -0.003 0.12 -9999 0 -0.83 20 20
CCL5 -0.071 0.25 -9999 0 -0.75 101 101
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.26 0.31 -9999 0 -0.65 254 254
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 -0.25 0.31 -9999 0 -0.67 222 222
Syndecan-1/Syntenin -0.24 0.3 -9999 0 -0.69 196 196
MAPK3 -0.21 0.27 -9999 0 -0.72 133 133
HGF/MET -0.087 0.21 -9999 0 -0.6 129 129
TGFB1/TGF beta receptor Type II -0.003 0.12 -9999 0 -0.83 20 20
BSG 0.011 0.058 -9999 0 -0.68 6 6
keratinocyte migration -0.24 0.3 -9999 0 -0.65 222 222
Syndecan-1/RANTES -0.29 0.34 -9999 0 -0.74 239 239
Syndecan-1/CD147 -0.23 0.3 -9999 0 -0.66 198 198
Syndecan-1/Syntenin/PIP2 -0.25 0.28 -9999 0 -0.67 196 196
LAMA5 0.009 0.074 -9999 0 -0.82 7 7
positive regulation of cell-cell adhesion -0.24 0.26 -9999 0 -0.65 196 196
MMP7 -0.25 0.37 -9999 0 -0.75 312 312
HGF -0.094 0.28 -9999 0 -0.78 122 122
Syndecan-1/CASK -0.25 0.3 -9999 0 -0.63 251 251
Syndecan-1/HGF/MET -0.29 0.35 -9999 0 -0.81 200 200
regulation of cell adhesion -0.19 0.26 -9999 0 -0.77 93 93
HPSE -0.048 0.22 -9999 0 -0.81 69 69
positive regulation of cell migration -0.26 0.31 -9999 0 -0.65 254 254
SDC1 -0.27 0.32 -9999 0 -0.66 251 251
Syndecan-1/Collagen -0.26 0.31 -9999 0 -0.65 254 254
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.009 0.075 -9999 0 -0.77 8 8
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.15 0.31 -9999 0 -0.73 194 194
MAPK1 -0.21 0.27 -9999 0 -0.71 134 134
homophilic cell adhesion -0.26 0.31 -9999 0 -0.64 254 254
MMP1 -0.27 0.38 -9999 0 -0.77 319 319
Syndecan-4-mediated signaling events

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
PTK2 -0.1 0.24 -9999 0 -0.65 131 131
Syndecan-4/Syndesmos -0.33 0.34 -9999 0 -0.8 234 234
positive regulation of JNK cascade -0.35 0.31 -9999 0 -0.74 281 281
Syndecan-4/ADAM12 -0.39 0.38 -9999 0 -0.83 311 311
CCL5 -0.071 0.25 -9999 0 -0.75 101 101
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.009 0.14 -9999 0 -0.81 27 27
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.27 0.36 -9999 0 -0.72 347 347
ADAM12 -0.11 0.28 -9999 0 -0.71 154 154
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.014 0.037 -9999 0 -0.75 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.085 0.055 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.37 0.36 -9999 0 -0.82 269 269
Syndecan-4/CXCL12/CXCR4 -0.36 0.37 -9999 0 -0.85 256 256
Syndecan-4/Laminin alpha3 -0.36 0.35 -9999 0 -0.79 278 278
MDK -0.051 0.22 -9999 0 -0.76 77 77
Syndecan-4/FZD7 -0.35 0.35 -9999 0 -0.8 257 257
Syndecan-4/Midkine -0.37 0.35 -9999 0 -0.82 265 265
FZD7 -0.017 0.16 -9999 0 -0.77 37 37
Syndecan-4/FGFR1/FGF -0.34 0.3 -9999 0 -0.78 226 226
THBS1 -0.05 0.23 -9999 0 -0.84 69 69
integrin-mediated signaling pathway -0.36 0.34 -9999 0 -0.77 285 285
positive regulation of MAPKKK cascade -0.35 0.31 -9999 0 -0.74 281 281
Syndecan-4/TACI -0.36 0.35 -9999 0 -0.78 288 288
CXCR4 -0.04 0.21 -9999 0 -0.84 58 58
cell adhesion -0.036 0.17 -9999 0 -0.47 99 99
Syndecan-4/Dynamin -0.33 0.34 -9999 0 -0.77 260 260
Syndecan-4/TSP1 -0.37 0.36 -9999 0 -0.8 289 289
Syndecan-4/GIPC -0.33 0.34 -9999 0 -0.8 235 235
Syndecan-4/RANTES -0.37 0.36 -9999 0 -0.82 288 288
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.059 0.24 -9999 0 -0.8 82 82
LAMA3 -0.039 0.19 -9999 0 -0.67 71 71
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.087 0.064 -9999 0 -0.54 2 2
Syndecan-4/alpha-Actinin -0.34 0.34 -9999 0 -0.81 236 236
TFPI -0.1 0.3 -9999 0 -0.84 124 124
F2 -0.21 0.34 -9999 0 -0.72 268 268
alpha5/beta1 Integrin -0.019 0.11 -9999 0 -0.62 27 27
positive regulation of cell adhesion -0.37 0.35 -9999 0 -0.8 285 285
ACTN1 0.005 0.098 -9999 0 -0.83 12 12
TNC -0.08 0.26 -9999 0 -0.75 112 112
Syndecan-4/CXCL12 -0.36 0.36 -9999 0 -0.81 278 278
FGF6 0 0.022 -9999 0 -0.65 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.047 0.22 -9999 0 -0.8 69 69
TNFRSF13B -0.032 0.16 -9999 0 -0.65 58 58
FGF2 -0.033 0.2 -9999 0 -0.84 51 51
FGFR1 0.011 0.062 -9999 0 -0.81 5 5
Syndecan-4/PI-4-5-P2 -0.34 0.34 -9999 0 -0.78 260 260
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.1 0.28 -9999 0 -0.76 137 137
cell migration -0.025 0.021 -9999 0 -10000 0 0
PRKCD -0.024 0.16 -9999 0 -0.65 57 57
vasculogenesis -0.35 0.33 -9999 0 -0.76 289 289
SDC4 -0.37 0.37 -9999 0 -0.85 260 260
Syndecan-4/Tenascin C -0.38 0.37 -9999 0 -0.84 273 273
Syndecan-4/PI-4-5-P2/PKC alpha -0.067 0.043 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.33 0.34 -9999 0 -0.8 234 234
MMP9 -0.15 0.31 -9999 0 -0.73 194 194
Rac1/GTP -0.053 0.18 -9999 0 -0.49 99 99
cytoskeleton organization -0.32 0.32 -9999 0 -0.74 246 246
GIPC1 0.012 0.055 -9999 0 -0.8 4 4
Syndecan-4/TFPI -0.39 0.37 -9999 0 -0.83 300 300
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.22 0.54 -10000 0 -1.1 195 195
NCK1/PAK1/Dok-R -0.14 0.19 -10000 0 -0.47 196 196
NCK1/Dok-R -0.34 0.6 -10000 0 -1.4 189 189
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
mol:beta2-estradiol 0.038 0.099 0.26 107 -10000 0 107
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.014 0.023 -10000 0 -0.65 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.17 0.37 -10000 0 -0.72 258 258
TNIP2 0.014 0.041 -10000 0 -0.85 2 2
NF kappa B/RelA -0.29 0.52 -10000 0 -1.3 183 183
FN1 -0.11 0.29 -10000 0 -0.79 137 137
PLD2 -0.26 0.67 -10000 0 -1.5 187 187
PTPN11 0.015 0.029 -10000 0 -0.85 1 1
GRB14 -0.087 0.25 -10000 0 -0.7 128 128
ELK1 -0.19 0.57 -10000 0 -1.2 188 188
GRB7 -0.002 0.12 -10000 0 -0.76 21 21
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.34 0.58 -10000 0 -1.4 189 189
CDKN1A -0.15 0.41 -10000 0 -0.71 277 277
ITGA5 -0.009 0.14 -10000 0 -0.81 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.34 0.6 -10000 0 -1.4 189 189
CRK 0.015 0.022 -10000 0 -0.65 1 1
mol:NO -0.14 0.41 -10000 0 -0.8 199 199
PLG -0.41 0.65 -10000 0 -1.5 193 193
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.22 0.45 -10000 0 -1 188 188
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.066 -10000 0 -0.78 6 6
ANGPT2 -0.36 0.66 0.47 2 -1.3 269 271
BMX -0.32 0.68 -10000 0 -1.5 188 188
ANGPT1 -0.24 0.66 -10000 0 -1.6 157 157
tube development -0.19 0.46 -10000 0 -0.83 278 278
ANGPT4 -0.054 0.21 -10000 0 -0.73 77 77
response to hypoxia -0.016 0.031 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.33 0.71 -10000 0 -1.6 195 195
alpha5/beta1 Integrin -0.019 0.11 -10000 0 -0.62 27 27
FGF2 -0.031 0.2 -10000 0 -0.84 51 51
STAT5A (dimer) -0.23 0.53 -10000 0 -0.98 278 278
mol:L-citrulline -0.14 0.41 -10000 0 -0.8 199 199
AGTR1 -0.22 0.35 -10000 0 -0.73 275 275
MAPK14 -0.26 0.66 -10000 0 -1.5 183 183
Tie2/SHP2 -0.24 0.51 -10000 0 -1.4 131 131
TEK -0.24 0.6 -10000 0 -1.6 137 137
RPS6KB1 -0.18 0.49 -10000 0 -1.1 189 189
Angiotensin II/AT1 -0.17 0.27 -10000 0 -0.56 275 275
Tie2/Ang1/GRB2 -0.28 0.71 -10000 0 -1.6 182 182
MAPK3 -0.21 0.59 -10000 0 -1.3 188 188
MAPK1 -0.21 0.59 -10000 0 -1.3 187 187
Tie2/Ang1/GRB7 -0.29 0.71 -10000 0 -1.6 184 184
NFKB1 0.015 0.029 -10000 0 -0.85 1 1
MAPK8 -0.26 0.68 -10000 0 -1.5 182 182
PI3K -0.26 0.62 -10000 0 -1.4 189 189
FES -0.27 0.66 -10000 0 -1.5 185 185
Crk/Dok-R -0.34 0.6 -10000 0 -1.4 189 189
Tie2/Ang1/ABIN2 -0.28 0.71 -10000 0 -1.6 183 183
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.18 0.47 -10000 0 -0.97 195 195
STAT5A 0.013 0.05 -10000 0 -0.85 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.18 0.49 -10000 0 -1.1 189 189
Tie2/Ang2 -0.33 0.66 -10000 0 -1.3 278 278
Tie2/Ang1 -0.32 0.8 -10000 0 -1.8 182 182
FOXO1 -0.2 0.5 -10000 0 -1 207 207
ELF1 0.008 0.064 -10000 0 -0.87 3 3
ELF2 -0.26 0.68 -10000 0 -1.5 182 182
mol:Choline -0.23 0.62 -10000 0 -1.4 187 187
cell migration -0.078 0.1 -10000 0 -10000 0 0
FYN -0.24 0.53 -10000 0 -0.98 278 278
DOK2 -0.041 0.21 -10000 0 -0.84 59 59
negative regulation of cell cycle -0.13 0.38 -10000 0 -0.64 277 277
ETS1 -0.054 0.22 -10000 0 -0.91 43 43
PXN -0.13 0.4 -10000 0 -0.82 188 188
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 -0.18 0.47 -10000 0 -0.96 199 199
RAC1 0.016 0 -10000 0 -10000 0 0
TNF -0.098 0.26 -10000 0 -0.77 99 99
MAPKKK cascade -0.23 0.62 -10000 0 -1.4 187 187
RASA1 0.013 0.05 -10000 0 -0.85 3 3
Tie2/Ang1/Shc -0.28 0.71 -10000 0 -1.6 182 182
NCK1 0.014 0.041 -10000 0 -0.85 2 2
vasculogenesis -0.11 0.36 -10000 0 -0.7 199 199
mol:Phosphatidic acid -0.23 0.62 -10000 0 -1.4 187 187
mol:Angiotensin II -0.006 0.015 -10000 0 -10000 0 0
mol:NADP -0.14 0.41 -10000 0 -0.8 199 199
Rac1/GTP -0.26 0.38 -10000 0 -0.96 189 189
MMP2 -0.28 0.68 -10000 0 -1.5 186 186
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.17 0.27 0.6 241 -10000 0 241
KIRREL -0.078 0.25 -10000 0 -0.86 82 82
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.17 0.27 -10000 0 -0.6 241 241
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.016 0 -10000 0 -10000 0 0
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.16 0.25 -10000 0 -0.58 189 189
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.081 0.19 -10000 0 -0.41 188 188
FYN -0.14 0.25 -10000 0 -0.55 193 193
mol:Ca2+ -0.16 0.24 -10000 0 -0.57 188 188
mol:DAG -0.16 0.24 -10000 0 -0.58 188 188
NPHS2 -0.093 0.23 -10000 0 -0.68 113 113
mol:IP3 -0.16 0.24 -10000 0 -0.58 188 188
regulation of endocytosis -0.14 0.22 -10000 0 -0.51 188 188
Nephrin/NEPH1/podocin/Cholesterol -0.17 0.25 -10000 0 -0.59 188 188
establishment of cell polarity -0.17 0.27 -10000 0 -0.6 241 241
Nephrin/NEPH1/podocin/NCK1-2 -0.15 0.23 -10000 0 -0.56 150 150
Nephrin/NEPH1/beta Arrestin2 -0.13 0.23 -10000 0 -0.52 188 188
NPHS1 -0.14 0.29 -10000 0 -0.73 166 166
Nephrin/NEPH1/podocin -0.16 0.24 -10000 0 -0.55 193 193
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.014 0.041 -10000 0 -0.85 2 2
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.16 0.25 -10000 0 -0.58 188 188
CD2AP 0.015 0.022 -10000 0 -0.65 1 1
Nephrin/NEPH1/podocin/GRB2 -0.16 0.25 -10000 0 -0.58 188 188
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.25 0.33 -10000 0 -0.62 333 333
cytoskeleton organization -0.11 0.24 -10000 0 -0.53 167 167
Nephrin/NEPH1 -0.12 0.21 -10000 0 -0.45 241 241
Nephrin/NEPH1/ZO-1 -0.14 0.22 -10000 0 -0.53 186 186
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.12 0.23 -9999 0 -0.54 191 191
EFNA5 -0.13 0.32 -9999 0 -0.79 166 166
FYN -0.091 0.23 -9999 0 -0.56 132 132
neuron projection morphogenesis -0.12 0.23 -9999 0 -0.54 191 191
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.12 0.23 -9999 0 -0.54 191 191
EPHA5 -0.024 0.13 -9999 0 -0.65 39 39
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.47 0.59 -10000 0 -1.3 224 224
STAT6 (cleaved dimer) -0.55 0.58 -10000 0 -1.3 303 303
IGHG1 -0.14 0.2 -10000 0 -0.52 14 14
IGHG3 -0.46 0.56 -10000 0 -1.2 286 286
AKT1 -0.24 0.38 -10000 0 -1 115 115
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.43 -10000 0 -1.2 99 99
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.42 -10000 0 -1.1 105 105
THY1 -0.55 0.7 -10000 0 -1.5 261 261
MYB -0.035 0.19 -10000 0 -0.72 61 61
HMGA1 -0.008 0.13 -10000 0 -0.68 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.53 -10000 0 -1.1 190 190
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.42 -10000 0 -1.1 101 101
SP1 0.023 0.012 -10000 0 -10000 0 0
INPP5D 0.009 0.076 -10000 0 -0.85 7 7
SOCS5 0.026 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.6 -10000 0 -1.3 308 308
SOCS1 -0.3 0.4 -10000 0 -0.85 209 209
SOCS3 -0.27 0.42 -10000 0 -1.1 113 113
FCER2 -0.38 0.5 -10000 0 -1.1 204 204
PARP14 0.016 0.005 -10000 0 -10000 0 0
CCL17 -0.53 0.65 -10000 0 -1.4 265 265
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.34 -10000 0 -1 83 83
T cell proliferation -0.49 0.63 -10000 0 -1.3 247 247
IL4R/JAK1 -0.48 0.6 -10000 0 -1.3 228 228
EGR2 -0.5 0.63 -10000 0 -1.4 240 240
JAK2 0.001 0.045 -10000 0 -0.89 1 1
JAK3 -0.025 0.19 -10000 0 -0.81 48 48
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
JAK1 0.01 0.017 -10000 0 -10000 0 0
COL1A2 -0.24 0.47 -10000 0 -1.3 111 111
CCL26 -0.49 0.61 -10000 0 -1.3 235 235
IL4R -0.52 0.66 -10000 0 -1.4 232 232
PTPN6 0.024 0.043 -10000 0 -0.83 2 2
IL13RA2 -0.6 0.7 -10000 0 -1.4 307 307
IL13RA1 0.002 0.033 -10000 0 -10000 0 0
IRF4 -0.24 0.53 -10000 0 -1.3 135 135
ARG1 -0.1 0.2 -10000 0 -0.9 19 19
CBL -0.3 0.46 -10000 0 -1 162 162
GTF3A 0.021 0.015 -10000 0 -10000 0 0
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
IL13RA1/JAK2 -0.001 0.057 -10000 0 -0.7 1 1
IRF4/BCL6 -0.23 0.47 -10000 0 -1.2 129 129
CD40LG -0.055 0.25 -10000 0 -0.84 81 81
MAPK14 -0.31 0.5 -10000 0 -1.2 148 148
mitosis -0.22 0.35 -10000 0 -0.91 115 115
STAT6 -0.58 0.78 -10000 0 -1.5 277 277
SPI1 0.005 0.11 -10000 0 -0.8 15 15
RPS6KB1 -0.2 0.34 -10000 0 -0.89 105 105
STAT6 (dimer) -0.58 0.79 -10000 0 -1.5 277 277
STAT6 (dimer)/PARP14 -0.52 0.66 -10000 0 -1.4 263 263
mast cell activation 0.01 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.48 -10000 0 -1.2 120 120
FRAP1 -0.24 0.38 -10000 0 -1 115 115
LTA -0.51 0.64 -10000 0 -1.4 236 236
FES 0 0.12 -10000 0 -0.85 17 17
T-helper 1 cell differentiation 0.54 0.71 1.4 278 -10000 0 278
CCL11 -0.53 0.62 -10000 0 -1.3 287 287
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.27 0.46 -10000 0 -1.2 117 117
IL2RG -0.057 0.24 -10000 0 -0.78 85 85
IL10 -0.51 0.63 -10000 0 -1.4 244 244
IRS1 -0.01 0.14 -10000 0 -0.72 31 31
IRS2 -0.019 0.15 -10000 0 -0.66 46 46
IL4 -0.088 0.14 -10000 0 -10000 0 0
IL5 -0.47 0.59 -10000 0 -1.3 221 221
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.35 0.44 -10000 0 -0.91 247 247
COL1A1 -0.25 0.47 -10000 0 -1.2 118 118
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.63 -10000 0 -1.4 215 215
IL2R gamma/JAK3 -0.063 0.26 -10000 0 -0.75 104 104
TFF3 -0.56 0.69 -10000 0 -1.5 269 269
ALOX15 -0.47 0.6 -10000 0 -1.3 235 235
MYBL1 0 0.1 -10000 0 -0.65 21 21
T-helper 2 cell differentiation -0.41 0.52 -10000 0 -1.1 258 258
SHC1 0.015 0.022 -10000 0 -0.65 1 1
CEBPB 0.012 0.074 -10000 0 -0.66 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.25 0.42 -10000 0 -1.1 109 109
mol:PI-3-4-5-P3 -0.24 0.38 -10000 0 -1 115 115
PI3K -0.26 0.43 -10000 0 -1.1 116 116
DOK2 -0.041 0.21 -10000 0 -0.84 59 59
ETS1 -0.01 0.17 -10000 0 -0.81 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.32 -10000 0 -0.97 81 81
ITGB3 -0.51 0.64 -10000 0 -1.4 233 233
PIGR -0.79 0.72 -10000 0 -1.4 430 430
IGHE 0.03 0.062 -10000 0 -10000 0 0
MAPKKK cascade -0.17 0.31 -10000 0 -0.93 82 82
BCL6 0.012 0.058 -10000 0 -0.84 4 4
OPRM1 -0.48 0.59 -10000 0 -1.3 220 220
RETNLB -0.48 0.59 -10000 0 -1.3 235 235
SELP -0.5 0.64 -10000 0 -1.4 238 238
AICDA -0.5 0.61 -10000 0 -1.3 252 252
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.36 0.57 -10000 0 -1.2 197 197
IL23A -0.34 0.56 -10000 0 -1.2 188 188
NF kappa B1 p50/RelA/I kappa B alpha -0.4 0.49 -10000 0 -1.2 216 216
positive regulation of T cell mediated cytotoxicity -0.4 0.64 -10000 0 -1.3 220 220
ITGA3 -0.34 0.55 -10000 0 -1.2 186 186
IL17F -0.2 0.36 -10000 0 -0.76 153 153
IL12B -0.044 0.19 -10000 0 -0.7 67 67
STAT1 (dimer) -0.38 0.6 -10000 0 -1.3 215 215
CD4 -0.33 0.54 -10000 0 -1.2 187 187
IL23 -0.36 0.54 -10000 0 -1.2 191 191
IL23R -0.032 0.13 -10000 0 -0.64 15 15
IL1B -0.36 0.59 -10000 0 -1.3 199 199
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.32 0.53 -10000 0 -1.2 168 168
TYK2 0.011 0.047 -10000 0 -0.88 2 2
STAT4 -0.052 0.23 -10000 0 -0.84 71 71
STAT3 0.016 0.001 -10000 0 -10000 0 0
IL18RAP -0.04 0.21 -10000 0 -0.8 60 60
IL12RB1 -0.042 0.21 -10000 0 -0.84 58 58
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
IL12Rbeta1/TYK2 -0.035 0.17 -10000 0 -0.66 60 60
IL23R/JAK2 -0.037 0.15 -10000 0 -0.63 14 14
positive regulation of chronic inflammatory response -0.4 0.64 -10000 0 -1.3 220 220
natural killer cell activation 0.004 0.011 0.054 18 -10000 0 18
JAK2 0.017 0.042 -10000 0 -0.87 1 1
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
NFKB1 0.014 0.029 -10000 0 -0.85 1 1
RELA 0.015 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.34 0.51 -10000 0 -1.1 193 193
ALOX12B -0.38 0.59 -10000 0 -1.3 208 208
CXCL1 -0.48 0.65 -10000 0 -1.3 271 271
T cell proliferation -0.4 0.64 -10000 0 -1.3 220 220
NFKBIA 0.015 0.004 -10000 0 -10000 0 0
IL17A -0.14 0.3 -10000 0 -0.6 101 101
PI3K -0.41 0.51 -10000 0 -1.2 220 220
IFNG -0.026 0.056 0.12 8 -0.12 141 149
STAT3 (dimer) -0.39 0.47 -10000 0 -1.1 211 211
IL18R1 -0.065 0.25 -10000 0 -0.84 82 82
IL23/IL23R/JAK2/TYK2/SOCS3 -0.2 0.38 -10000 0 -0.95 101 101
IL18/IL18R -0.09 0.27 -10000 0 -0.68 133 133
macrophage activation -0.019 0.018 -10000 0 -0.044 168 168
TNF -0.37 0.6 -10000 0 -1.3 208 208
STAT3/STAT4 -0.42 0.53 -10000 0 -1.2 224 224
STAT4 (dimer) -0.39 0.62 -10000 0 -1.3 223 223
IL18 -0.02 0.16 -10000 0 -0.72 42 42
IL19 -0.33 0.52 -10000 0 -1.1 195 195
STAT5A (dimer) -0.38 0.6 -10000 0 -1.3 213 213
STAT1 0.009 0.074 -10000 0 -0.72 9 9
SOCS3 -0.033 0.19 -10000 0 -0.78 55 55
CXCL9 -0.47 0.66 -10000 0 -1.3 268 268
MPO -0.35 0.55 -10000 0 -1.2 192 192
positive regulation of humoral immune response -0.4 0.64 -10000 0 -1.3 220 220
IL23/IL23R/JAK2/TYK2 -0.45 0.79 -10000 0 -1.5 218 218
IL6 -0.44 0.62 -10000 0 -1.3 250 250
STAT5A 0.013 0.05 -10000 0 -0.85 3 3
IL2 -0.001 0.078 -10000 0 -0.66 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.011 0.054 18 -10000 0 18
CD3E -0.37 0.59 -10000 0 -1.3 179 179
keratinocyte proliferation -0.4 0.64 -10000 0 -1.3 220 220
NOS2 -0.39 0.59 -10000 0 -1.2 230 230
HIF-2-alpha transcription factor network

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
MMP14 -0.039 0.18 -10000 0 -1.2 17 17
oxygen homeostasis -0.002 0.021 -10000 0 -10000 0 0
TCEB2 0.009 0.071 -10000 0 -0.72 8 8
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.14 0.21 -10000 0 -0.52 161 161
EPO -0.31 0.43 -10000 0 -0.82 262 262
FIH (dimer) 0.015 0.019 -10000 0 -10000 0 0
APEX1 0.01 0.019 -10000 0 -10000 0 0
SERPINE1 -0.34 0.55 -10000 0 -1.1 247 247
FLT1 -0.44 0.72 -10000 0 -1.6 244 244
ADORA2A -0.24 0.47 -10000 0 -0.9 232 232
germ cell development -0.28 0.49 -10000 0 -0.93 269 269
SLC11A2 -0.25 0.47 -10000 0 -0.94 221 221
BHLHE40 -0.25 0.48 -10000 0 -0.94 219 219
HIF1AN 0.015 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.22 0.27 -10000 0 -0.64 206 206
ETS1 -0.013 0.18 -10000 0 -0.86 38 38
CITED2 -0.018 0.057 -10000 0 -1.4 1 1
KDR -0.44 0.71 -10000 0 -1.6 239 239
PGK1 -0.25 0.48 -10000 0 -0.94 223 223
SIRT1 0.013 0.029 -10000 0 -0.85 1 1
response to hypoxia -0.004 0.008 -10000 0 -10000 0 0
HIF2A/ARNT -0.34 0.64 -10000 0 -1.2 254 254
EPAS1 -0.12 0.29 -10000 0 -0.55 225 225
SP1 0.026 0.004 -10000 0 -10000 0 0
ABCG2 -0.28 0.5 -10000 0 -0.98 239 239
EFNA1 -0.26 0.48 -10000 0 -0.95 223 223
FXN -0.23 0.47 -10000 0 -0.88 242 242
POU5F1 -0.3 0.52 -10000 0 -0.98 281 281
neuron apoptosis 0.31 0.58 1.1 254 -10000 0 254
EP300 0.014 0.041 -10000 0 -0.85 2 2
EGLN3 -0.22 0.39 -10000 0 -0.87 236 236
EGLN2 0.012 0.051 -10000 0 -0.8 3 3
EGLN1 0.015 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.007 0.062 -10000 0 -0.62 7 7
VHL 0.012 0.058 -10000 0 -0.85 4 4
ARNT 0.01 0.02 -10000 0 -10000 0 0
SLC2A1 -0.26 0.51 -10000 0 -0.98 237 237
TWIST1 -0.27 0.51 -10000 0 -0.96 245 245
ELK1 0.026 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.2 0.27 -10000 0 -0.64 192 192
VEGFA -0.34 0.58 -10000 0 -1.1 285 285
CREBBP 0.016 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.18 0.34 -9999 0 -0.75 228 228
PDGF/PDGFRA/CRKL -0.14 0.25 -9999 0 -0.55 228 228
positive regulation of JUN kinase activity -0.11 0.19 -9999 0 -0.49 116 116
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.15 0.26 -9999 0 -0.57 233 233
AP1 -0.21 0.37 -9999 0 -1.2 78 78
mol:IP3 -0.13 0.27 -9999 0 -0.57 228 228
PLCG1 -0.13 0.27 -9999 0 -0.57 228 228
PDGF/PDGFRA/alphaV Integrin -0.15 0.25 -9999 0 -0.56 232 232
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.015 0.022 -9999 0 -0.65 1 1
mol:Ca2+ -0.13 0.26 -9999 0 -0.57 228 228
CAV3 -0.004 0.073 -9999 0 -0.65 11 11
CAV1 -0.081 0.27 -9999 0 -0.84 101 101
SHC/Grb2/SOS1 -0.11 0.19 -9999 0 -0.5 116 116
PDGF/PDGFRA/Shf -0.15 0.25 -9999 0 -0.56 232 232
FOS -0.16 0.38 -9999 0 -1.2 78 78
JUN -0.019 0.058 -9999 0 -0.63 7 7
oligodendrocyte development -0.15 0.25 -9999 0 -0.56 232 232
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
mol:DAG -0.13 0.27 -9999 0 -0.57 228 228
PDGF/PDGFRA -0.18 0.34 -9999 0 -0.75 228 228
actin cytoskeleton reorganization -0.14 0.25 -9999 0 -0.56 228 228
SRF 0.032 0.01 -9999 0 -10000 0 0
SHC1 0.015 0.022 -9999 0 -0.65 1 1
PI3K -0.13 0.22 -9999 0 -0.54 141 141
PDGF/PDGFRA/Crk/C3G -0.12 0.21 -9999 0 -0.54 133 133
JAK1 -0.12 0.26 -9999 0 -0.55 228 228
ELK1/SRF -0.065 0.2 -9999 0 -0.55 25 25
SHB 0.015 0.029 -9999 0 -0.85 1 1
SHF 0.011 0.066 -9999 0 -0.78 6 6
CSNK2A1 0.017 0.024 -9999 0 -10000 0 0
GO:0007205 -0.12 0.26 -9999 0 -0.56 228 228
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.11 0.19 -9999 0 -0.49 116 116
PDGF/PDGFRA/SHB -0.14 0.25 -9999 0 -0.56 228 228
PDGF/PDGFRA/Caveolin-1 -0.21 0.31 -9999 0 -0.62 307 307
ITGAV 0.009 0.074 -9999 0 -0.82 7 7
ELK1 -0.1 0.24 -9999 0 -0.58 132 132
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
PDGF/PDGFRA/Crk -0.14 0.25 -9999 0 -0.56 228 228
JAK-STAT cascade -0.12 0.26 -9999 0 -0.55 228 228
cell proliferation -0.15 0.25 -9999 0 -0.56 232 232
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.32 0.5 -9999 0 -1 276 276
PDGFRB -0.12 0.31 -9999 0 -0.84 140 140
SPHK1 -0.057 0.15 -9999 0 -0.51 57 57
mol:S1P -0.056 0.14 -9999 0 -0.55 39 39
S1P1/S1P/Gi -0.15 0.34 -9999 0 -0.7 186 186
GNAO1 -0.053 0.22 -9999 0 -0.76 79 79
PDGFB-D/PDGFRB/PLCgamma1 -0.15 0.37 -9999 0 -0.87 155 155
PLCG1 -0.13 0.32 -9999 0 -0.73 148 148
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.12 0.31 -9999 0 -0.84 140 140
GNAI2 0.014 0.03 -9999 0 -0.86 1 1
GNAI3 0.013 0.008 -9999 0 -10000 0 0
GNAI1 0.001 0.1 -9999 0 -0.85 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.27 0.46 -9999 0 -0.92 276 276
S1P1/S1P -0.26 0.38 -9999 0 -0.8 279 279
negative regulation of cAMP metabolic process -0.14 0.32 -9999 0 -0.66 186 186
MAPK3 -0.15 0.35 -9999 0 -0.9 113 113
calcium-dependent phospholipase C activity -0.002 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 -0.22 0.38 -9999 0 -0.84 242 242
PLCB2 -0.2 0.35 -9999 0 -0.71 258 258
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.2 0.29 -9999 0 -0.65 249 249
receptor internalization -0.23 0.34 -9999 0 -0.71 279 279
PTGS2 -0.16 0.38 -9999 0 -1 112 112
Rac1/GTP -0.2 0.29 -9999 0 -0.65 249 249
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.21 0.38 -9999 0 -0.85 236 236
negative regulation of T cell proliferation -0.14 0.32 -9999 0 -0.66 186 186
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.004 0.086 -9999 0 -0.79 10 10
MAPK1 -0.15 0.35 -9999 0 -0.9 113 113
S1P1/S1P/PDGFB-D/PDGFRB -0.27 0.48 -9999 0 -1 244 244
ABCC1 0.014 0.029 -9999 0 -0.86 1 1
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.002 0.038 -9999 0 -0.65 3 3
Necdin/E2F1 -0.063 0.19 -9999 0 -0.65 87 87
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.19 0.31 -9999 0 -0.93 94 94
NGF (dimer)/p75(NTR)/BEX1 -0.37 0.39 -9999 0 -0.66 501 501
NT-4/5 (dimer)/p75(NTR) -0.15 0.28 -9999 0 -0.65 202 202
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.15 0.33 -9999 0 -0.66 219 219
IKBKG 0.013 0.05 -9999 0 -0.85 3 3
BDNF -0.11 0.29 -9999 0 -0.78 140 140
MGDIs/NGR/p75(NTR)/LINGO1 -0.21 0.35 -9999 0 -0.77 215 215
FURIN 0.014 0.041 -9999 0 -0.85 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.18 0.28 -9999 0 -0.63 220 220
LINGO1 -0.14 0.33 -9999 0 -0.82 166 166
Sortilin/TRAF6/NRIF -0.006 0.051 -9999 0 -0.84 1 1
proBDNF (dimer) -0.11 0.29 -9999 0 -0.77 140 140
NTRK1 -0.033 0.18 -9999 0 -0.69 60 60
RTN4R 0.002 0.1 -9999 0 -0.73 17 17
neuron apoptosis -0.14 0.31 -9999 0 -0.76 124 124
IRAK1 0.015 0.029 -9999 0 -0.85 1 1
SHC1 -0.19 0.36 -9999 0 -0.68 278 278
ARHGDIA 0.014 0.041 -9999 0 -0.85 2 2
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.004 0.045 -9999 0 -0.48 8 8
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.2 0.33 -9999 0 -0.72 212 212
MAGEH1 0.011 0.062 -9999 0 -0.81 5 5
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.24 0.39 -9999 0 -0.81 236 236
Mammalian IAPs/DIABLO -0.048 0.14 -9999 0 -0.51 70 70
proNGF (dimer) -0.16 0.34 -9999 0 -0.8 189 189
MAGED1 0.015 0.032 -9999 0 -0.65 2 2
APP 0.014 0.041 -9999 0 -0.85 2 2
NT-4/5 (dimer) -0.031 0.15 -9999 0 -0.65 50 50
ZNF274 0.015 0.029 -9999 0 -0.85 1 1
RhoA/GDP/RHOGDI -0.18 0.31 -9999 0 -0.68 210 210
NGF -0.16 0.34 -9999 0 -0.8 189 189
cell cycle arrest -0.13 0.34 -9999 0 -0.66 211 211
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.1 0.24 -9999 0 -0.48 219 219
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.13 0.25 -9999 0 -0.56 202 202
NCSTN 0.015 0.029 -9999 0 -0.85 1 1
mol:GTP -0.21 0.35 -9999 0 -0.68 277 277
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.16 0.34 -9999 0 -0.71 211 211
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.067 0.2 -9999 0 -0.55 94 94
p75(NTR)/beta APP -0.12 0.25 -9999 0 -0.62 178 178
BEX1 -0.25 0.36 -9999 0 -0.74 311 311
mol:GDP -0.2 0.36 -9999 0 -0.69 277 277
NGF (dimer) -0.42 0.35 -9999 0 -0.73 402 402
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.2 0.33 -9999 0 -0.71 215 215
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
RAC1/GTP -0.19 0.31 -9999 0 -0.6 277 277
MYD88 0.002 0.11 -9999 0 -0.85 14 14
CHUK 0.015 0.029 -9999 0 -0.85 1 1
NGF (dimer)/p75(NTR)/PKA -0.21 0.35 -9999 0 -0.68 277 277
RHOB -0.005 0.13 -9999 0 -0.82 22 22
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.004 0.047 -9999 0 -0.5 8 8
NT3 (dimer) -0.074 0.26 -9999 0 -0.79 99 99
TP53 -0.11 0.26 -9999 0 -0.82 34 34
PRDM4 -0.17 0.34 -9999 0 -0.71 211 211
BDNF (dimer) -0.42 0.35 -9999 0 -0.76 368 368
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
SORT1 0.013 0.05 -9999 0 -0.85 3 3
activation of caspase activity -0.18 0.3 -9999 0 -0.91 94 94
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.2 0.33 -9999 0 -0.72 210 210
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.14 0.29 -9999 0 -0.71 127 127
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.17 0.34 -9999 0 -0.71 211 211
APH1B 0.009 0.076 -9999 0 -0.85 7 7
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.21 0.35 -9999 0 -0.78 210 210
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.022 -9999 0 -0.65 1 1
NT3 (dimer)/p75(NTR) -0.18 0.34 -9999 0 -0.72 226 226
MAPK8 -0.13 0.29 -9999 0 -0.72 121 121
MAPK9 -0.13 0.29 -9999 0 -0.71 119 119
APAF1 0.015 0.029 -9999 0 -0.85 1 1
NTF3 -0.074 0.26 -9999 0 -0.79 99 99
NTF4 -0.031 0.15 -9999 0 -0.65 50 50
NDN -0.062 0.25 -9999 0 -0.84 81 81
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.18 0.3 -9999 0 -0.88 100 100
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.048 -9999 0 -0.51 8 8
RhoA-B-C/GTP -0.21 0.34 -9999 0 -0.67 277 277
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.16 0.24 -9999 0 -0.86 34 34
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.17 0.26 -9999 0 -0.57 220 220
PRKACB 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.095 0.22 -9999 0 -0.59 143 143
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.066 0.25 -9999 0 -0.81 89 89
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.14 0.38 -9999 0 -0.77 185 185
BAD -0.12 0.28 -9999 0 -0.68 122 122
RIPK2 0.015 0.022 -9999 0 -0.65 1 1
NGFR -0.15 0.33 -9999 0 -0.81 177 177
CYCS -0.16 0.33 -9999 0 -0.68 217 217
ADAM17 0.012 0.058 -9999 0 -0.85 4 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.2 0.32 -9999 0 -0.72 209 209
BCL2L11 -0.12 0.28 -9999 0 -0.68 122 122
BDNF (dimer)/p75(NTR) -0.21 0.32 -9999 0 -0.66 287 287
PI3K -0.2 0.33 -9999 0 -0.71 218 218
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.2 0.33 -9999 0 -0.72 210 210
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.015 0.022 -9999 0 -0.65 1 1
NGF (dimer)/p75(NTR) -0.24 0.39 -9999 0 -0.77 277 277
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.2 0.33 -9999 0 -0.72 210 210
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.008 0.082 -9999 0 -0.85 8 8
PLG -0.28 0.36 -9999 0 -0.72 347 347
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.22 0.37 -9999 0 -0.85 176 176
SQSTM1 0.009 0.067 -9999 0 -0.65 9 9
NGFRAP1 0.011 0.065 -9999 0 -0.85 5 5
CASP3 -0.1 0.26 -9999 0 -0.61 119 119
E2F1 0.01 0.066 -9999 0 -0.68 8 8
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.15 0.25 -9999 0 -0.63 158 158
NGF (dimer)/TRKA -0.16 0.28 -9999 0 -0.62 234 234
MMP7 -0.25 0.37 -9999 0 -0.75 312 312
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.19 0.31 -9999 0 -0.93 94 94
MMP3 -0.043 0.17 -9999 0 -0.65 67 67
APAF-1/Caspase 9 -0.17 0.25 -9999 0 -0.7 120 120
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.23 0.34 -10000 0 -0.88 101 101
IHH -0.17 0.32 -10000 0 -0.81 176 176
SHH Np/Cholesterol/GAS1 -0.081 0.19 -10000 0 -0.58 76 76
LRPAP1 0.014 0.041 -10000 0 -0.85 2 2
dorsoventral neural tube patterning 0.081 0.19 0.58 76 -10000 0 76
SMO/beta Arrestin2 -0.15 0.25 -10000 0 -0.66 95 95
SMO -0.16 0.26 -10000 0 -0.64 142 142
AKT1 -0.053 0.13 -10000 0 -0.69 8 8
ARRB2 0.016 0 -10000 0 -10000 0 0
BOC -0.004 0.13 -10000 0 -0.84 21 21
ADRBK1 0.014 0.041 -10000 0 -0.85 2 2
heart looping -0.16 0.26 -10000 0 -0.62 142 142
STIL -0.16 0.25 -10000 0 -0.66 103 103
DHH N/PTCH2 -0.068 0.19 -10000 0 -0.6 101 101
DHH N/PTCH1 -0.17 0.26 -10000 0 -0.66 121 121
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
DHH -0.04 0.2 -10000 0 -0.77 63 63
PTHLH -0.4 0.54 -10000 0 -1.2 215 215
determination of left/right symmetry -0.16 0.26 -10000 0 -0.62 142 142
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
skeletal system development -0.39 0.52 -10000 0 -1.2 215 215
IHH N/Hhip -0.21 0.32 -10000 0 -0.63 292 292
DHH N/Hhip -0.15 0.26 -10000 0 -0.57 227 227
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.16 0.26 -10000 0 -0.62 142 142
pancreas development -0.13 0.29 -10000 0 -0.7 180 180
HHAT 0.009 0.076 -10000 0 -0.85 7 7
PI3K -0.008 0.072 -10000 0 -0.62 12 12
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.011 0.14 -10000 0 -0.71 33 33
somite specification -0.16 0.26 -10000 0 -0.62 142 142
SHH Np/Cholesterol/PTCH1 -0.17 0.26 -10000 0 -0.66 125 125
SHH Np/Cholesterol/PTCH2 -0.088 0.2 -10000 0 -0.57 88 88
SHH Np/Cholesterol/Megalin -0.15 0.28 -10000 0 -0.65 177 177
SHH -0.06 0.22 -10000 0 -0.58 128 128
catabolic process -0.16 0.25 -10000 0 -0.59 151 151
SMO/Vitamin D3 -0.18 0.28 -10000 0 -0.69 127 127
SHH Np/Cholesterol/Hhip -0.15 0.25 -10000 0 -0.64 132 132
LRP2 -0.13 0.32 -10000 0 -0.84 153 153
receptor-mediated endocytosis -0.25 0.29 -10000 0 -0.76 163 163
SHH Np/Cholesterol/BOC -0.078 0.18 -10000 0 -0.48 146 146
SHH Np/Cholesterol/CDO -0.091 0.2 -10000 0 -0.57 99 99
mesenchymal cell differentiation 0.15 0.25 0.63 132 -10000 0 132
mol:Vitamin D3 -0.17 0.27 -10000 0 -0.67 125 125
IHH N/PTCH2 -0.12 0.26 -10000 0 -0.57 208 208
CDON -0.026 0.18 -10000 0 -0.8 46 46
IHH N/PTCH1 -0.16 0.25 -10000 0 -0.6 151 151
Megalin/LRPAP1 -0.11 0.25 -10000 0 -0.65 155 155
PTCH2 -0.021 0.17 -10000 0 -0.78 41 41
SHH Np/Cholesterol -0.068 0.17 -10000 0 -0.47 128 128
PTCH1 -0.16 0.25 -10000 0 -0.6 151 151
HHIP -0.13 0.29 -10000 0 -0.71 180 180
LPA4-mediated signaling events

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
ADCY4 -0.038 0.18 -9999 0 -0.56 96 96
ADCY5 -0.05 0.2 -9999 0 -0.58 110 110
ADCY6 0.023 0.047 -9999 0 -0.74 3 3
ADCY7 0.023 0.047 -9999 0 -0.74 3 3
ADCY1 -0.12 0.25 -9999 0 -0.53 239 239
ADCY2 -0.16 0.26 -9999 0 -0.52 304 304
ADCY3 0.008 0.1 -9999 0 -0.57 26 26
ADCY8 -0.15 0.24 -9999 0 -0.47 316 316
PRKCE 0.012 0.039 -9999 0 -0.66 3 3
ADCY9 0.023 0.04 -9999 0 -0.57 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.17 0.2 -9999 0 -0.5 166 166
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.15 0.26 -10000 0 -0.66 161 161
FYN -0.14 0.4 -10000 0 -0.9 172 172
LAT/GRAP2/SLP76 -0.17 0.31 -10000 0 -0.77 160 160
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.059 0.25 -10000 0 -0.52 168 168
B2M 0.012 0.051 -10000 0 -0.85 3 3
IKBKG -0.035 0.058 -10000 0 -0.19 40 40
MAP3K8 0.012 0.059 -10000 0 -0.77 5 5
mol:Ca2+ -0.024 0.048 -10000 0 -0.13 131 131
integrin-mediated signaling pathway -0.02 0.1 -10000 0 -0.57 31 31
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.12 0.38 -10000 0 -0.83 173 173
TRPV6 -0.095 0.24 -10000 0 -0.67 129 129
CD28 -0.038 0.21 -10000 0 -0.81 58 58
SHC1 -0.14 0.4 -10000 0 -0.9 168 168
receptor internalization -0.18 0.45 -10000 0 -0.95 194 194
PRF1 -0.17 0.47 -10000 0 -1.2 133 133
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.034 0.2 -10000 0 -0.41 151 151
LAT -0.16 0.41 -10000 0 -0.92 174 174
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.11 0.3 -10000 0 -0.8 141 141
CD3E -0.096 0.28 -10000 0 -0.8 123 123
CD3G -0.14 0.32 -10000 0 -0.79 175 175
RASGRP2 -0.003 0.049 -10000 0 -0.19 41 41
RASGRP1 -0.056 0.25 -10000 0 -0.52 158 158
HLA-A 0.012 0.051 -10000 0 -0.86 3 3
RASSF5 -0.014 0.16 -10000 0 -0.84 31 31
RAP1A/GTP/RAPL -0.02 0.1 -10000 0 -0.57 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.078 -10000 0 -0.15 48 48
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.064 0.1 -10000 0 -0.34 49 49
PRKCA -0.066 0.12 -10000 0 -0.32 130 130
GRAP2 -0.039 0.21 -10000 0 -0.85 57 57
mol:IP3 -0.097 0.22 0.27 65 -0.53 143 208
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.23 0.58 -10000 0 -1.2 189 189
ORAI1 0.052 0.13 0.35 125 -0.66 2 127
CSK -0.15 0.41 -10000 0 -0.94 169 169
B7 family/CD28 -0.23 0.4 -10000 0 -0.98 174 174
CHUK 0.015 0.029 -10000 0 -0.85 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.2 0.5 -10000 0 -1.1 194 194
PTPN6 -0.16 0.42 -10000 0 -0.95 173 173
VAV1 -0.15 0.42 -10000 0 -0.94 170 170
Monovalent TCR/CD3 -0.19 0.5 -10000 0 -0.99 192 192
CBL 0.015 0.029 -10000 0 -0.85 1 1
LCK -0.17 0.46 -10000 0 -1 176 176
PAG1 -0.16 0.42 -10000 0 -0.95 173 173
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.2 0.5 -10000 0 -1.1 193 193
CD80 -0.054 0.23 -10000 0 -0.78 78 78
CD86 -0.019 0.17 -10000 0 -0.85 36 36
PDK1/CARD11/BCL10/MALT1 -0.079 0.13 -10000 0 -0.35 110 110
HRAS 0.012 0.059 -10000 0 -0.77 5 5
GO:0035030 -0.12 0.34 -10000 0 -0.75 172 172
CD8A -0.15 0.32 -10000 0 -0.76 188 188
CD8B -0.15 0.32 -10000 0 -0.76 197 197
PTPRC -0.03 0.19 -10000 0 -0.83 47 47
PDK1/PKC theta -0.08 0.31 -10000 0 -0.67 161 161
CSK/PAG1 -0.15 0.41 -10000 0 -0.91 173 173
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I 0.015 0.063 -10000 0 -0.77 5 5
GRAP2/SLP76 -0.19 0.36 -10000 0 -0.89 168 168
STIM1 0.027 0.074 -10000 0 -0.55 4 4
RAS family/GTP 0.012 0.1 -10000 0 -0.2 19 19
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.21 0.52 -10000 0 -1.1 194 194
mol:DAG -0.098 0.18 0.19 2 -0.46 151 153
RAP1A/GDP 0.008 0.034 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.052 0.23 -10000 0 -0.82 73 73
cytotoxic T cell degranulation -0.15 0.43 -10000 0 -1.1 134 134
RAP1A/GTP -0.005 0.015 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.084 0.3 -10000 0 -0.64 172 172
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.14 0.3 0.29 63 -0.72 149 212
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.054 0.23 -10000 0 -0.79 77 77
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.15 0.28 -10000 0 -0.72 155 155
MALT1 0.015 0.029 -10000 0 -0.85 1 1
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.21 0.42 -10000 0 -0.9 225 225
CARD11 -0.052 0.22 -10000 0 -0.74 81 81
PRKCB -0.077 0.15 -10000 0 -0.4 124 124
PRKCE -0.066 0.13 -10000 0 -0.32 124 124
PRKCQ -0.11 0.36 -10000 0 -0.78 172 172
LCP2 -0.028 0.19 -10000 0 -0.84 46 46
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.043 0.21 -10000 0 -0.43 166 166
IKK complex 0.025 0.078 -10000 0 -0.13 44 44
RAS family/GDP -0.006 0.012 -10000 0 -0.098 4 4
MAP3K14 -0.02 0.17 -10000 0 -0.37 115 115
PDPK1 -0.051 0.24 -10000 0 -0.5 157 157
TCR/CD3/MHC I/CD8/Fyn -0.22 0.53 -10000 0 -1.1 200 200
amb2 Integrin signaling

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.088 0.26 -9999 0 -0.74 97 97
alphaM/beta2 Integrin/GPIbA -0.07 0.23 -9999 0 -0.82 65 65
alphaM/beta2 Integrin/proMMP-9 -0.16 0.31 -9999 0 -0.69 164 164
PLAUR -0.01 0.14 -9999 0 -0.72 31 31
HMGB1 0.006 0.021 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.059 0.22 -9999 0 -0.9 50 50
AGER -0.03 0.16 -9999 0 -0.76 41 41
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.005 0.13 -9999 0 -0.85 22 22
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.12 0.26 -9999 0 -0.92 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.15 0.31 -9999 0 -0.73 194 194
CYR61 -0.051 0.22 -9999 0 -0.79 74 74
TLN1 0.015 0.029 -9999 0 -0.85 1 1
Rap1/GTP -0.18 0.23 -9999 0 -0.6 140 140
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.044 0.22 -9999 0 -0.8 65 65
MYH2 -0.23 0.28 -9999 0 -0.64 198 198
MST1R -0.091 0.26 -9999 0 -0.7 133 133
leukocyte activation during inflammatory response -0.22 0.28 -9999 0 -0.63 195 195
APOB -0.26 0.37 -9999 0 -0.74 322 322
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.032 0.18 -9999 0 -0.73 57 57
JAM3 -0.06 0.24 -9999 0 -0.84 79 79
GP1BA -0.002 0.12 -9999 0 -0.79 20 20
alphaM/beta2 Integrin/CTGF -0.074 0.24 -9999 0 -0.86 65 65
alphaM/beta2 Integrin -0.21 0.31 -9999 0 -0.62 205 205
JAM3 homodimer -0.06 0.24 -9999 0 -0.84 79 79
ICAM2 0.009 0.074 -9999 0 -0.82 7 7
ICAM1 -0.028 0.19 -9999 0 -0.84 46 46
phagocytosis triggered by activation of immune response cell surface activating receptor -0.2 0.29 -9999 0 -0.61 205 205
cell adhesion -0.069 0.22 -9999 0 -0.81 65 65
NFKB1 -0.12 0.33 -9999 0 -0.99 71 71
THY1 -0.11 0.3 -9999 0 -0.83 130 130
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.2 0.25 -9999 0 -0.5 364 364
alphaM/beta2 Integrin/LRP/tPA -0.067 0.24 -9999 0 -0.86 63 63
IL6 -0.21 0.43 -9999 0 -1 143 143
ITGB2 -0.031 0.18 -9999 0 -0.85 38 38
elevation of cytosolic calcium ion concentration -0.08 0.26 -9999 0 -0.98 55 55
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.28 -9999 0 -0.71 135 135
JAM2 -0.013 0.15 -9999 0 -0.82 31 31
alphaM/beta2 Integrin/ICAM1 -0.15 0.32 -9999 0 -0.98 80 80
alphaM/beta2 Integrin/uPA/Plg -0.23 0.31 -9999 0 -0.69 176 176
RhoA/GTP -0.24 0.3 -9999 0 -0.68 198 198
positive regulation of phagocytosis -0.16 0.24 -9999 0 -0.83 77 77
Ron/MSP -0.11 0.23 -9999 0 -0.56 174 174
alphaM/beta2 Integrin/uPAR/uPA -0.082 0.27 -9999 0 -1 55 55
alphaM/beta2 Integrin/uPAR -0.073 0.25 -9999 0 -0.89 62 62
PLAU -0.019 0.16 -9999 0 -0.7 43 43
PLAT -0.005 0.13 -9999 0 -0.78 24 24
actin filament polymerization -0.22 0.26 -9999 0 -0.6 202 202
MST1 -0.03 0.18 -9999 0 -0.76 53 53
alphaM/beta2 Integrin/lipoprotein(a) -0.22 0.29 -9999 0 -0.64 195 195
TNF -0.13 0.36 -9999 0 -1 90 90
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.079 0.26 -9999 0 -0.89 64 64
fibrinolysis -0.23 0.3 -9999 0 -0.68 176 176
HCK -0.005 0.13 -9999 0 -0.83 22 22
dendritic cell antigen processing and presentation -0.2 0.29 -9999 0 -0.61 205 205
VTN -0.11 0.27 -9999 0 -0.69 161 161
alphaM/beta2 Integrin/CYR61 -0.1 0.29 -9999 0 -0.85 93 93
LPA -0.034 0.16 -9999 0 -0.65 54 54
LRP1 0.005 0.095 -9999 0 -0.85 11 11
cell migration -0.17 0.32 -9999 0 -0.79 133 133
FN1 -0.11 0.29 -9999 0 -0.79 137 137
alphaM/beta2 Integrin/Thy1 -0.14 0.29 -9999 0 -0.7 168 168
MPO -0.045 0.2 -9999 0 -0.7 75 75
KNG1 -0.18 0.32 -9999 0 -0.71 238 238
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.22 0.28 -9999 0 -0.64 190 190
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.28 0.36 -9999 0 -0.72 347 347
CTGF -0.01 0.14 -9999 0 -0.72 31 31
alphaM/beta2 Integrin/Hck -0.07 0.26 -9999 0 -1 55 55
ITGAM -0.035 0.18 -9999 0 -0.84 42 42
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.095 0.3 -9999 0 -0.9 86 86
HP -0.24 0.35 -9999 0 -0.72 307 307
leukocyte adhesion -0.21 0.35 -9999 0 -0.91 148 148
SELP -0.044 0.22 -9999 0 -0.8 65 65
EGFR-dependent Endothelin signaling events

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0.059 -9999 0 -0.77 5 5
EGFR -0.021 0.17 -9999 0 -0.78 41 41
EGF/EGFR -0.28 0.34 -9999 0 -0.64 341 341
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.1 0.19 -9999 0 -0.53 104 104
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.18 0.36 -9999 0 -0.84 198 198
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.15 0.31 -9999 0 -0.73 196 196
EGF/EGFR dimer/SHC -0.13 0.23 -9999 0 -0.5 223 223
mol:GDP -0.1 0.19 -9999 0 -0.52 104 104
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.12 0.31 -9999 0 -0.81 147 147
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.097 0.18 -9999 0 -0.76 16 16
SHC1 0.015 0.022 -9999 0 -0.65 1 1
HRAS/GDP -0.099 0.18 -9999 0 -0.77 16 16
FRAP1 -0.065 0.2 -9999 0 -0.5 104 104
EGF/EGFR dimer -0.15 0.26 -9999 0 -0.58 222 222
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.24 0.35 -9999 0 -0.71 303 303
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.098 0.24 -10000 0 -0.58 112 112
TBX21 -0.19 0.56 -10000 0 -1.3 147 147
B2M 0.012 0.051 -10000 0 -0.85 3 3
TYK2 0.018 0.047 -10000 0 -0.86 2 2
IL12RB1 -0.034 0.21 -10000 0 -0.84 58 58
GADD45B -0.13 0.45 -10000 0 -1 128 128
IL12RB2 -0.2 0.33 -10000 0 -0.69 275 275
GADD45G -0.16 0.48 -10000 0 -1.1 141 141
natural killer cell activation 0.006 0.027 -10000 0 -10000 0 0
RELB 0.015 0.029 -10000 0 -0.85 1 1
RELA 0.016 0 -10000 0 -10000 0 0
IL18 -0.016 0.16 -10000 0 -0.72 42 42
IL2RA -0.1 0.28 -10000 0 -0.76 137 137
IFNG -0.11 0.27 -10000 0 -0.7 151 151
STAT3 (dimer) -0.13 0.41 -10000 0 -0.89 158 158
HLA-DRB5 -0.059 0.23 -10000 0 -0.77 84 84
FASLG -0.23 0.6 -10000 0 -1.3 175 175
NF kappa B2 p52/RelB -0.27 0.45 -10000 0 -1.1 166 166
CD4 -0.009 0.14 -10000 0 -0.85 25 25
SOCS1 -0.038 0.19 -10000 0 -0.7 68 68
EntrezGene:6955 -0.002 0.011 -10000 0 -10000 0 0
CD3D -0.11 0.3 -10000 0 -0.79 141 141
CD3E -0.097 0.28 -10000 0 -0.79 123 123
CD3G -0.14 0.32 -10000 0 -0.8 175 175
IL12Rbeta2/JAK2 -0.14 0.26 -10000 0 -0.51 276 276
CCL3 -0.2 0.56 -10000 0 -1.2 157 157
CCL4 -0.19 0.56 -10000 0 -1.3 156 156
HLA-A 0.012 0.051 -10000 0 -0.85 3 3
IL18/IL18R -0.05 0.29 -10000 0 -0.69 137 137
NOS2 -0.22 0.59 -10000 0 -1.3 173 173
IL12/IL12R/TYK2/JAK2/SPHK2 -0.077 0.21 -10000 0 -0.55 85 85
IL1R1 -0.18 0.53 -10000 0 -1.2 147 147
IL4 -0.002 0.028 -10000 0 -10000 0 0
JAK2 0.019 0.038 -10000 0 -0.89 1 1
EntrezGene:6957 -0.002 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.34 0.78 -10000 0 -1.5 220 220
RAB7A -0.083 0.37 -10000 0 -0.85 107 107
lysosomal transport -0.074 0.35 -10000 0 -0.78 110 110
FOS -0.21 0.53 -10000 0 -1.2 158 158
STAT4 (dimer) -0.17 0.51 -10000 0 -1.1 160 160
STAT5A (dimer) -0.31 0.48 -10000 0 -1.1 212 212
GZMA -0.21 0.57 -10000 0 -1.3 158 158
GZMB -0.23 0.61 -10000 0 -1.4 168 168
HLX -0.042 0.21 -10000 0 -0.81 62 62
LCK -0.23 0.63 -10000 0 -1.3 182 182
TCR/CD3/MHC II/CD4 -0.2 0.51 -10000 0 -1.1 169 169
IL2/IL2R -0.16 0.33 -10000 0 -0.81 143 143
MAPK14 -0.13 0.47 -10000 0 -1 145 145
CCR5 -0.17 0.51 -10000 0 -1.2 147 147
IL1B -0.039 0.22 -10000 0 -0.8 65 65
STAT6 -0.014 0.14 -10000 0 -10000 0 0
STAT4 -0.052 0.23 -10000 0 -0.84 71 71
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.009 0.074 -10000 0 -0.72 9 9
NFKB1 0.015 0.029 -10000 0 -0.85 1 1
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.032 0.19 -10000 0 -0.69 67 67
CD8A -0.15 0.32 -10000 0 -0.76 188 188
CD8B -0.16 0.32 -10000 0 -0.76 197 197
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.097 0.24 0.57 112 -10000 0 112
IL2RB -0.051 0.23 -10000 0 -0.82 72 72
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.44 -10000 0 -0.94 160 160
IL2RG -0.061 0.24 -10000 0 -0.79 85 85
IL12 -0.022 0.17 -10000 0 -0.53 86 86
STAT5A 0.013 0.05 -10000 0 -0.85 3 3
CD247 -0.054 0.23 -10000 0 -0.82 73 73
IL2 -0.001 0.076 -10000 0 -0.65 12 12
SPHK2 0.013 0.05 -10000 0 -0.85 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.002 0.12 -10000 0 -0.77 19 19
IL12/IL12R/TYK2/JAK2 -0.27 0.77 -10000 0 -1.5 176 176
MAP2K3 -0.14 0.48 -10000 0 -1 152 152
RIPK2 0.015 0.022 -10000 0 -0.65 1 1
MAP2K6 -0.14 0.48 -10000 0 -1 156 156
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.022 0.18 -10000 0 -0.85 39 39
IL18RAP -0.037 0.21 -10000 0 -0.8 60 60
IL12Rbeta1/TYK2 -0.018 0.18 -10000 0 -0.66 60 60
EOMES -0.21 0.52 -10000 0 -1.2 149 149
STAT1 (dimer) -0.17 0.43 -10000 0 -0.89 182 182
T cell proliferation -0.083 0.36 0.53 2 -0.73 151 153
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.061 0.25 -10000 0 -0.85 82 82
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.22 0.32 -10000 0 -0.84 154 154
ATF2 -0.12 0.43 -10000 0 -0.93 137 137
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.051 0.22 -9999 0 -0.76 77 77
GPC2 -0.028 0.18 -9999 0 -0.74 51 51
GPC2/Midkine -0.081 0.21 -9999 0 -0.6 121 121
neuron projection morphogenesis -0.081 0.21 -9999 0 -0.6 121 121
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.36 0.34 -9999 0 -0.8 250 250
SMAD6-7/SMURF1 -0.003 0.042 -9999 0 -0.56 5 5
NOG -0.16 0.32 -9999 0 -0.73 209 209
SMAD9 -0.11 0.23 -9999 0 -0.71 100 100
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.084 0.19 -9999 0 -0.53 59 59
BMP7/USAG1 -0.4 0.36 -9999 0 -0.67 541 541
SMAD5/SKI -0.072 0.18 -9999 0 -0.55 44 44
SMAD1 0.026 0.056 -9999 0 -0.69 2 2
BMP2 -0.015 0.16 -9999 0 -0.84 32 32
SMAD1/SMAD1/SMAD4 -0.004 0.042 -9999 0 -0.84 1 1
BMPR1A 0.015 0.029 -9999 0 -0.85 1 1
BMPR1B -0.25 0.36 -9999 0 -0.73 317 317
BMPR1A-1B/BAMBI -0.21 0.27 -9999 0 -0.52 359 359
AHSG -0.03 0.15 -9999 0 -0.65 50 50
CER1 0 0.058 -9999 0 -0.65 7 7
BMP2-4/CER1 -0.053 0.18 -9999 0 -0.6 78 78
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.07 0.19 -9999 0 -0.6 53 53
BMP2-4 (homodimer) -0.057 0.2 -9999 0 -0.69 73 73
RGMB 0.014 0.039 -9999 0 -0.65 3 3
BMP6/BMPR2/BMPR1A-1B -0.16 0.22 -9999 0 -0.55 150 150
RGMA -0.044 0.22 -9999 0 -0.8 65 65
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.084 0.19 -9999 0 -0.53 75 75
BMP2-4/USAG1 -0.24 0.3 -9999 0 -0.66 200 200
SMAD6/SMURF1/SMAD5 -0.071 0.18 -9999 0 -0.54 42 42
SOSTDC1 -0.3 0.37 -9999 0 -0.73 376 376
BMP7/BMPR2/BMPR1A-1B -0.29 0.3 -9999 0 -0.67 266 266
SKI 0.014 0.041 -9999 0 -0.85 2 2
BMP6 (homodimer) -0.008 0.14 -9999 0 -0.75 28 28
HFE2 -0.016 0.13 -9999 0 -0.65 37 37
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.12 0.27 -9999 0 -0.62 179 179
SMAD5/SMAD5/SMAD4 -0.071 0.18 -9999 0 -0.54 42 42
MAPK1 0.015 0.029 -9999 0 -0.85 1 1
TAK1/TAB family -0.09 0.14 -9999 0 -0.49 56 56
BMP7 (homodimer) -0.24 0.35 -9999 0 -0.71 316 316
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.045 0.15 -9999 0 -0.52 77 77
SMAD1/SKI 0.033 0.059 -9999 0 -0.57 4 4
SMAD6 0.012 0.058 -9999 0 -0.85 4 4
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.072 0.19 -9999 0 -0.63 71 71
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.26 0.37 -9999 0 -0.74 318 318
BMPR2 (homodimer) 0.015 0.029 -9999 0 -0.85 1 1
GADD34/PP1CA -0.002 0.041 -9999 0 -0.82 2 2
BMPR1A-1B (homodimer) -0.2 0.27 -9999 0 -0.55 318 318
CHRDL1 -0.29 0.38 -9999 0 -0.74 358 358
ENDOFIN/SMAD1 0.034 0.054 -9999 0 -0.64 2 2
SMAD6-7/SMURF1/SMAD1 -0.003 0.05 -9999 0 -0.62 4 4
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI -0.052 0.23 -9999 0 -0.8 74 74
SMURF2 0.014 0.037 -9999 0 -0.75 2 2
BMP2-4/CHRDL1 -0.24 0.3 -9999 0 -0.53 399 399
BMP2-4/GREM1 -0.22 0.29 -9999 0 -0.66 191 191
SMAD7 0.015 0.029 -9999 0 -0.85 1 1
SMAD8A/SMAD8A/SMAD4 -0.075 0.23 -9999 0 -0.66 99 99
SMAD1/SMAD6 0.034 0.054 -9999 0 -0.64 2 2
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.24 0.35 -9999 0 -0.71 316 316
BMP6 -0.008 0.14 -9999 0 -0.75 28 28
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.063 0.17 -9999 0 -0.48 70 70
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.033 0.062 -9999 0 -0.86 2 2
SMAD7/SMURF1 -0.001 0.022 -9999 0 -0.65 1 1
CTDSPL 0.015 0.022 -9999 0 -0.65 1 1
PPP1CA 0.014 0.041 -9999 0 -0.85 2 2
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.015 0.029 -9999 0 -0.85 1 1
PPP1R15A 0.015 0.029 -9999 0 -0.85 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.26 -9999 0 -0.63 144 144
CHRD -0.1 0.29 -9999 0 -0.82 127 127
BMPR2 0.015 0.029 -9999 0 -0.85 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.092 0.2 -9999 0 -0.58 72 72
BMP4 -0.03 0.19 -9999 0 -0.81 50 50
FST -0.15 0.31 -9999 0 -0.73 195 195
BMP2-4/NOG -0.16 0.26 -9999 0 -0.52 267 267
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.27 0.28 -9999 0 -0.73 158 158
Thromboxane A2 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
TGM2 -0.052 0.22 -10000 0 -0.82 69 69
GNB1/GNG2 -0.075 0.094 -10000 0 -0.23 154 154
AKT1 -0.02 0.14 -10000 0 -0.29 6 6
EGF -0.15 0.31 -10000 0 -0.73 196 196
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.027 0.2 -10000 0 -0.66 58 58
mol:Ca2+ -0.06 0.2 -10000 0 -0.35 193 193
LYN -0.017 0.18 -10000 0 -0.61 54 54
RhoA/GTP -0.046 0.059 -10000 0 -0.21 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.067 0.22 -10000 0 -0.4 189 189
GNG2 -0.016 0.16 -10000 0 -0.85 33 33
ARRB2 0.016 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.034 0.22 -10000 0 -0.72 62 62
G beta5/gamma2 -0.1 0.13 -10000 0 -0.32 158 158
PRKCH -0.085 0.24 -10000 0 -0.45 192 192
DNM1 -0.1 0.28 -10000 0 -0.76 136 136
TXA2/TP beta/beta Arrestin3 -0.048 0.099 -10000 0 -0.3 98 98
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.053 0.23 -10000 0 -0.83 73 73
G12 family/GTP -0.11 0.15 -10000 0 -0.34 197 197
ADRBK1 0.014 0.041 -10000 0 -0.85 2 2
ADRBK2 0.015 0.029 -10000 0 -0.85 1 1
RhoA/GTP/ROCK1 -0.002 0.033 -10000 0 -0.57 3 3
mol:GDP 0.054 0.19 0.46 110 -10000 0 110
mol:NADP -0.063 0.25 -10000 0 -0.84 82 82
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.14 0.33 -10000 0 -0.84 158 158
mol:IP3 -0.085 0.24 -10000 0 -0.45 201 201
cell morphogenesis -0.002 0.033 -10000 0 -0.57 3 3
PLCB2 -0.14 0.32 -10000 0 -0.63 201 201
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.062 0.22 -10000 0 -0.61 74 74
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.023 0.2 -10000 0 -0.66 55 55
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR -0.038 0.2 -10000 0 -0.8 59 59
PRKCB1 -0.082 0.23 -10000 0 -0.42 235 235
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline -0.063 0.25 -10000 0 -0.84 82 82
TXA2/TXA2-R family -0.13 0.32 -10000 0 -0.59 260 260
LCK -0.055 0.25 -10000 0 -0.67 96 96
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.089 0.23 -10000 0 -0.67 91 91
TXA2-R family/G12 family/GDP/G beta/gamma 0.009 0.084 -10000 0 -0.37 22 22
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.088 0.22 -10000 0 -0.66 91 91
MAPK14 -0.029 0.16 -10000 0 -0.32 19 19
TGM2/GTP -0.11 0.29 -10000 0 -0.55 194 194
MAPK11 -0.032 0.16 -10000 0 -0.37 33 33
ARHGEF1 -0.022 0.12 -10000 0 -0.28 3 3
GNAI2 0.015 0.029 -10000 0 -0.85 1 1
JNK cascade -0.083 0.24 -10000 0 -0.42 256 256
RAB11/GDP 0.016 0.002 -10000 0 -10000 0 0
ICAM1 -0.053 0.19 -10000 0 -0.39 78 78
cAMP biosynthetic process -0.085 0.23 -10000 0 -0.42 207 207
Gq family/GTP/EBP50 -0.018 0.14 -10000 0 -0.43 51 51
actin cytoskeleton reorganization -0.002 0.033 -10000 0 -0.57 3 3
SRC -0.016 0.18 -10000 0 -0.6 51 51
GNB5 0.015 0.029 -10000 0 -0.85 1 1
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.032 0.17 -10000 0 -0.45 80 80
VCAM1 -0.069 0.21 -10000 0 -0.4 192 192
TP beta/Gq family/GDP/G beta5/gamma2 -0.034 0.22 -10000 0 -0.72 62 62
platelet activation -0.042 0.21 -10000 0 -0.35 151 151
PGI2/IP -0.041 0.16 -10000 0 -0.62 59 59
PRKACA -0.037 0.19 -10000 0 -0.54 91 91
Gq family/GDP/G beta5/gamma2 -0.03 0.21 -10000 0 -0.67 66 66
TXA2/TP beta/beta Arrestin2 -0.082 0.2 -10000 0 -0.67 83 83
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.074 0.28 -10000 0 -0.65 133 133
mol:DAG -0.096 0.26 -10000 0 -0.48 235 235
EGFR -0.021 0.17 -10000 0 -0.78 41 41
TXA2/TP alpha -0.13 0.32 -10000 0 -0.6 210 210
Gq family/GTP -0.044 0.12 -10000 0 -0.31 127 127
YES1 -0.016 0.18 -10000 0 -0.6 51 51
GNAI2/GTP -0.078 0.2 -10000 0 -0.74 52 52
PGD2/DP -0.053 0.18 -10000 0 -0.64 73 73
SLC9A3R1 0.005 0.095 -10000 0 -0.85 11 11
FYN -0.019 0.19 -10000 0 -0.63 54 54
mol:NO -0.063 0.25 -10000 0 -0.84 82 82
GNA15 -0.014 0.16 -10000 0 -0.81 33 33
PGK/cGMP -0.15 0.3 -10000 0 -0.68 196 196
RhoA/GDP 0.016 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.13 0.29 -10000 0 -0.94 77 77
NOS3 -0.063 0.25 -10000 0 -0.84 82 82
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.07 0.22 -10000 0 -0.4 178 178
PRKCB -0.084 0.24 -10000 0 -0.45 193 193
PRKCE -0.069 0.22 -10000 0 -0.4 176 176
PRKCD -0.088 0.25 -10000 0 -0.44 244 244
PRKCG -0.095 0.25 -10000 0 -0.47 204 204
muscle contraction -0.12 0.3 -10000 0 -0.55 250 250
PRKCZ -0.066 0.22 -10000 0 -0.39 199 199
ARR3 0.004 0.007 -10000 0 -10000 0 0
TXA2/TP beta -0.091 0.23 -10000 0 -0.73 80 80
PRKCQ -0.087 0.24 -10000 0 -0.45 200 200
MAPKKK cascade -0.12 0.3 -10000 0 -0.56 216 216
SELE -0.078 0.22 -10000 0 -0.4 217 217
TP beta/GNAI2/GDP/G beta/gamma -0.099 0.26 -10000 0 -0.98 57 57
ROCK1 0.013 0.05 -10000 0 -0.85 3 3
GNA14 -0.078 0.27 -10000 0 -0.84 97 97
chemotaxis -0.15 0.35 -10000 0 -0.65 255 255
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.015 0.022 -10000 0 -0.65 1 1
GNA11 -0.011 0.14 -10000 0 -0.75 31 31
Rac1/GTP 0.006 0.007 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.081 0.25 -10000 0 -0.78 96 96
NFATC2 -0.12 0.37 -10000 0 -0.87 139 139
NFATC3 -0.015 0.1 -10000 0 -0.85 1 1
CD40LG -0.28 0.54 -10000 0 -1.2 162 162
ITCH 0.027 0.1 -10000 0 -10000 0 0
CBLB 0.027 0.1 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.39 0.54 -10000 0 -1.3 209 209
JUNB 0.001 0.11 -10000 0 -0.78 17 17
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.035 0.1 -10000 0 -10000 0 0
T cell anergy -0.028 0.18 -10000 0 -0.56 78 78
TLE4 -0.067 0.29 -10000 0 -0.88 65 65
Jun/NFAT1-c-4/p21SNFT -0.27 0.45 -10000 0 -1.3 114 114
AP-1/NFAT1-c-4 -0.34 0.66 -10000 0 -1.5 151 151
IKZF1 -0.097 0.38 -10000 0 -1.1 84 84
T-helper 2 cell differentiation -0.18 0.36 -10000 0 -0.9 131 131
AP-1/NFAT1 -0.18 0.32 -10000 0 -0.83 121 121
CALM1 0.013 0.063 -10000 0 -10000 0 0
EGR2 -0.18 0.51 -10000 0 -1.3 106 106
EGR3 -0.19 0.54 -10000 0 -1.4 97 97
NFAT1/FOXP3 -0.17 0.38 -10000 0 -0.86 151 151
EGR1 -0.072 0.24 -10000 0 -0.74 102 102
JUN 0.005 0.074 -10000 0 -0.77 7 7
EGR4 -0.027 0.15 -10000 0 -0.65 49 49
mol:Ca2+ -0.004 0.069 -10000 0 -10000 0 0
GBP3 -0.13 0.41 -10000 0 -1 118 118
FOSL1 -0.055 0.22 -10000 0 -0.73 84 84
NFAT1-c-4/MAF/IRF4 -0.29 0.47 -10000 0 -1.3 123 123
DGKA -0.086 0.35 -10000 0 -1 77 77
CREM 0.015 0.022 -10000 0 -0.65 1 1
NFAT1-c-4/PPARG -0.24 0.42 -10000 0 -1.2 106 106
CTLA4 -0.2 0.45 -10000 0 -1 166 166
NFAT1-c-4 (dimer)/EGR1 -0.29 0.48 -10000 0 -1.3 137 137
NFAT1-c-4 (dimer)/EGR4 -0.26 0.44 -10000 0 -1.2 118 118
FOS -0.092 0.26 -10000 0 -0.75 120 120
IFNG -0.29 0.45 -10000 0 -1.1 164 164
T cell activation -0.11 0.32 -10000 0 -0.88 78 78
MAF -0.013 0.16 -10000 0 -0.85 30 30
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.11 0.34 0.93 80 -10000 0 80
TNF -0.24 0.48 -10000 0 -1.1 165 165
FASLG -0.31 0.67 -10000 0 -1.6 147 147
TBX21 -0.054 0.22 -10000 0 -0.84 65 65
BATF3 -0.028 0.19 -10000 0 -0.8 48 48
PRKCQ -0.044 0.21 -10000 0 -0.79 62 62
PTPN1 -0.066 0.29 -10000 0 -0.9 62 62
NFAT1-c-4/ICER1 -0.24 0.42 -10000 0 -1.2 106 106
GATA3 -0.12 0.29 -10000 0 -0.72 159 159
T-helper 1 cell differentiation -0.25 0.46 -10000 0 -1 166 166
IL2RA -0.34 0.47 -10000 0 -1.1 189 189
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.065 0.29 -10000 0 -0.83 75 75
E2F1 0.018 0.066 -10000 0 -0.67 8 8
PPARG 0.011 0.066 -10000 0 -0.78 6 6
SLC3A2 -0.07 0.3 -10000 0 -0.87 74 74
IRF4 -0.091 0.27 -10000 0 -0.75 124 124
PTGS2 -0.3 0.55 -10000 0 -1.2 176 176
CSF2 -0.26 0.5 -10000 0 -1.2 152 152
JunB/Fra1/NFAT1-c-4 -0.26 0.44 -10000 0 -1.2 110 110
IL4 -0.19 0.38 -10000 0 -0.97 129 129
IL5 -0.26 0.49 -10000 0 -1.2 145 145
IL2 -0.12 0.32 -10000 0 -0.9 78 78
IL3 -0.055 0.088 -10000 0 -1.2 3 3
RNF128 -0.039 0.29 -10000 0 -0.88 94 94
NFATC1 -0.11 0.35 -10000 0 -0.94 79 79
CDK4 0.085 0.23 0.7 30 -10000 0 30
PTPRK -0.067 0.29 -10000 0 -0.86 72 72
IL8 -0.31 0.54 -10000 0 -1.2 184 184
POU2F1 0.014 0.05 -10000 0 -0.85 3 3
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.32 0.5 -9999 0 -1 276 276
alphaV beta3 Integrin -0.075 0.21 -9999 0 -0.58 115 115
PTK2 -0.25 0.39 -9999 0 -0.79 274 274
IGF1R 0.013 0.05 -9999 0 -0.85 3 3
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 -0.027 0.19 -9999 0 -0.84 45 45
SRC 0.015 0.022 -9999 0 -0.65 1 1
CDKN1B -0.09 0.18 -9999 0 -0.64 49 49
VEGFA -0.21 0.38 -9999 0 -0.84 236 236
ILK -0.09 0.18 -9999 0 -0.64 49 49
ROCK1 0.013 0.05 -9999 0 -0.85 3 3
AKT1 -0.049 0.18 -9999 0 -0.61 46 46
PTK2B -0.25 0.45 -9999 0 -0.87 286 286
alphaV/beta3 Integrin/JAM-A -0.13 0.23 -9999 0 -0.86 39 39
CBL 0.015 0.029 -9999 0 -0.85 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.22 0.27 -9999 0 -0.63 173 173
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.058 0.16 -9999 0 -0.56 51 51
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.18 0.31 -9999 0 -0.64 240 240
alphaV/beta3 Integrin/Syndecan-1 -0.057 0.18 -9999 0 -0.54 94 94
PI4KA 0.015 0.029 -9999 0 -0.85 1 1
IGF-1R heterotetramer/IGF1/IRS1 -0.17 0.29 -9999 0 -0.86 89 89
PI4 Kinase -0.001 0.022 -9999 0 -0.65 1 1
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
alphaV/beta3 Integrin/Osteopontin -0.079 0.21 -9999 0 -0.69 75 75
RPS6KB1 -0.1 0.29 -9999 0 -0.78 89 89
TLN1 0.015 0.029 -9999 0 -0.85 1 1
MAPK3 -0.13 0.27 -9999 0 -0.87 87 87
GPR124 -0.11 0.3 -9999 0 -0.84 129 129
MAPK1 -0.13 0.27 -9999 0 -0.87 86 86
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
alphaV/beta3 Integrin/Tumstatin -0.08 0.21 -9999 0 -0.63 90 90
cell adhesion -0.19 0.26 -9999 0 -0.81 74 74
ANGPTL3 -0.26 0.36 -9999 0 -0.72 334 334
VEGFR2 homodimer/VEGFA homodimer/Src -0.29 0.45 -9999 0 -0.96 262 262
IGF-1R heterotetramer 0.013 0.05 -9999 0 -0.85 3 3
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.012 0.058 -9999 0 -0.85 4 4
ITGB3 -0.046 0.21 -9999 0 -0.76 71 71
IGF1 -0.058 0.22 -9999 0 -0.72 89 89
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.12 0.25 -9999 0 -0.59 184 184
apoptosis 0.009 0.074 -9999 0 -0.82 7 7
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.043 0.15 -9999 0 -0.61 42 42
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.14 0.28 -9999 0 -0.6 217 217
CSF1 0 0.12 -9999 0 -0.82 17 17
PIK3C2A -0.092 0.18 -9999 0 -0.66 51 51
PI4 Kinase/Pyk2 -0.31 0.38 -9999 0 -0.85 264 264
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.31 0.46 -9999 0 -0.93 286 286
FAK1/Vinculin -0.17 0.29 -9999 0 -0.57 261 261
alphaV beta3/Integrin/ppsTEM5 -0.12 0.26 -9999 0 -0.6 184 184
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.11 0.27 -9999 0 -0.69 161 161
BCAR1 0.013 0.05 -9999 0 -0.85 3 3
FGF2 -0.033 0.2 -9999 0 -0.84 51 51
F11R -0.01 0.16 -9999 0 -0.65 51 51
alphaV/beta3 Integrin/Lactadherin -0.071 0.21 -9999 0 -0.66 77 77
alphaV/beta3 Integrin/TGFBR2 -0.046 0.16 -9999 0 -0.62 45 45
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.016 0.095 -9999 0 -0.57 23 23
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.041 0.14 -9999 0 -0.58 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.11 0.29 -9999 0 -0.79 137 137
alphaV/beta3 Integrin/Pyk2 -0.29 0.43 -9999 0 -0.94 240 240
SDC1 -0.006 0.13 -9999 0 -0.73 26 26
VAV3 0.026 0.12 -9999 0 -0.51 37 37
PTPN11 0.015 0.029 -9999 0 -0.85 1 1
IRS1 -0.01 0.14 -9999 0 -0.72 31 31
FAK1/Paxillin -0.17 0.29 -9999 0 -0.57 261 261
cell migration -0.14 0.26 -9999 0 -0.51 239 239
ITGAV 0.009 0.074 -9999 0 -0.82 7 7
PI3K -0.12 0.22 -9999 0 -0.82 42 42
SPP1 -0.042 0.2 -9999 0 -0.75 68 68
KDR -0.22 0.38 -9999 0 -0.84 242 242
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.009 0.074 -9999 0 -0.82 7 7
COL4A3 -0.042 0.21 -9999 0 -0.82 61 61
angiogenesis -0.096 0.29 -9999 0 -0.85 86 86
Rac1/GTP -0.02 0.096 -9999 0 -0.82 3 3
EDIL3 -0.14 0.33 -9999 0 -0.82 171 171
cell proliferation -0.046 0.16 -9999 0 -0.62 45 45
Wnt signaling

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
Noncanonical Wnts/FZD -0.11 0.2 -9999 0 -0.56 81 81
FZD6 0.014 0.043 -9999 0 -0.72 3 3
WNT6 -0.098 0.27 -9999 0 -0.73 134 134
WNT4 -0.089 0.26 -9999 0 -0.72 127 127
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A -0.072 0.23 -9999 0 -0.69 112 112
WNT11 -0.096 0.26 -9999 0 -0.69 140 140
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.039 0.16 -10000 0 -0.61 57 57
fibroblast growth factor receptor signaling pathway -0.039 0.16 -10000 0 -0.61 57 57
LAMA1 -0.059 0.24 -10000 0 -0.8 82 82
PRNP 0.012 0.055 -10000 0 -0.8 4 4
GPC1/SLIT2 -0.12 0.24 -10000 0 -0.56 192 192
SMAD2 0.036 0.06 -10000 0 -0.51 9 9
GPC1/PrPc/Cu2+ -0.007 0.061 -10000 0 -0.52 12 12
GPC1/Laminin alpha1 -0.061 0.19 -10000 0 -0.62 88 88
TDGF1 -0.093 0.24 -10000 0 -0.66 140 140
CRIPTO/GPC1 -0.081 0.18 -10000 0 -0.49 148 148
APP/GPC1 -0.007 0.064 -10000 0 -0.6 10 10
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.041 0.17 -10000 0 -0.56 11 11
FLT1 -0.22 0.38 -10000 0 -0.84 240 240
GPC1/TGFB/TGFBR1/TGFBR2 -0.007 0.061 -10000 0 -0.52 12 12
SERPINC1 -0.029 0.16 -10000 0 -0.66 57 57
FYN -0.047 0.17 -10000 0 -0.42 157 157
FGR -0.06 0.2 -10000 0 -0.46 169 169
positive regulation of MAPKKK cascade -0.066 0.22 -10000 0 -0.7 55 55
SLIT2 -0.14 0.31 -10000 0 -0.74 186 186
GPC1/NRG -0.063 0.19 -10000 0 -0.62 90 90
NRG1 -0.062 0.24 -10000 0 -0.8 85 85
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.29 0.45 -10000 0 -0.94 278 278
LYN -0.044 0.17 -10000 0 -0.42 150 150
mol:Spermine 0.009 0.058 -10000 0 -0.6 8 8
cell growth -0.039 0.16 -10000 0 -0.61 57 57
BMP signaling pathway -0.009 0.075 0.77 8 -10000 0 8
SRC -0.041 0.17 -10000 0 -0.58 12 12
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.081 0.23 -10000 0 -0.66 120 120
GPC1 0.009 0.075 -10000 0 -0.77 8 8
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA -0.21 0.38 -10000 0 -0.84 236 236
BLK -0.1 0.23 -10000 0 -0.59 88 88
HCK -0.055 0.19 -10000 0 -0.44 166 166
FGF2 -0.033 0.2 -10000 0 -0.84 51 51
FGFR1 0.011 0.062 -10000 0 -0.81 5 5
VEGFR1 homodimer -0.22 0.38 -10000 0 -0.84 240 240
TGFBR2 0.012 0.058 -10000 0 -0.85 4 4
cell death -0.007 0.064 -10000 0 -0.6 10 10
ATIII/GPC1 -0.036 0.13 -10000 0 -0.5 65 65
PLA2G2A/GPC1 -0.07 0.17 -10000 0 -0.49 127 127
LCK -0.1 0.25 -10000 0 -0.51 224 224
neuron differentiation -0.063 0.19 -10000 0 -0.62 90 90
PrPc/Cu2+ -0.003 0.042 -10000 0 -0.62 4 4
APP 0.014 0.041 -10000 0 -0.85 2 2
TGFBR2 (dimer) 0.012 0.058 -10000 0 -0.85 4 4
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.13 0.26 -9999 0 -0.68 149 149
PDGFB-D/PDGFRB/SLAP -0.13 0.27 -9999 0 -0.67 169 169
PDGFB-D/PDGFRB/APS/CBL -0.098 0.22 -9999 0 -0.58 147 147
AKT1 -0.005 0.18 -9999 0 -0.72 8 8
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.1 0.3 -9999 0 -0.72 149 149
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
FGR -0.11 0.26 -9999 0 -0.63 152 152
mol:Ca2+ -0.087 0.28 -9999 0 -0.73 134 134
MYC -0.055 0.26 -9999 0 -0.7 78 78
SHC1 0.015 0.022 -9999 0 -0.65 1 1
HRAS/GDP -0.068 0.18 -9999 0 -0.48 79 79
LRP1/PDGFRB/PDGFB -0.098 0.22 -9999 0 -0.59 143 143
GRB10 0.014 0.041 -9999 0 -0.85 2 2
PTPN11 0.015 0.029 -9999 0 -0.85 1 1
GO:0007205 -0.09 0.29 -9999 0 -0.75 134 134
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 -0.002 0.12 -9999 0 -0.76 21 21
PDGFB-D/PDGFRB/SHP2 -0.1 0.24 -9999 0 -0.64 141 141
PDGFB-D/PDGFRB/GRB10 -0.1 0.24 -9999 0 -0.64 142 142
cell cycle arrest -0.13 0.27 -9999 0 -0.67 169 169
HRAS 0.012 0.059 -9999 0 -0.77 5 5
HIF1A 0.005 0.17 -9999 0 -0.64 11 11
GAB1 -0.099 0.3 -9999 0 -0.74 143 143
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.086 0.28 -9999 0 -0.68 141 141
PDGFB-D/PDGFRB -0.084 0.21 -9999 0 -0.57 134 134
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.1 0.24 -9999 0 -0.64 140 140
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.14 0.27 -9999 0 -0.68 150 150
positive regulation of MAPKKK cascade -0.1 0.24 -9999 0 -0.64 141 141
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
mol:IP3 -0.091 0.29 -9999 0 -0.76 134 134
E5 -0.001 0.003 -9999 0 -10000 0 0
CSK 0.014 0.041 -9999 0 -0.84 2 2
PDGFB-D/PDGFRB/GRB7 -0.11 0.25 -9999 0 -0.65 157 157
SHB 0.015 0.029 -9999 0 -0.85 1 1
BLK -0.14 0.26 -9999 0 -0.64 166 166
PTPN2 0.014 0.006 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.1 0.24 -9999 0 -0.64 140 140
BCAR1 0.013 0.05 -9999 0 -0.85 3 3
VAV2 -0.093 0.3 -9999 0 -0.72 144 144
CBL 0.015 0.029 -9999 0 -0.85 1 1
PDGFB-D/PDGFRB/DEP1 -0.1 0.24 -9999 0 -0.64 146 146
LCK -0.16 0.35 -9999 0 -0.78 178 178
PDGFRB -0.12 0.31 -9999 0 -0.84 140 140
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.1 0.26 -9999 0 -0.63 143 143
ABL1 -0.088 0.27 -9999 0 -0.68 140 140
PDGFB-D/PDGFRB/CBL -0.11 0.32 -9999 0 -0.81 139 139
PTPN1 0.013 0.03 -9999 0 -0.85 1 1
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.009 0.074 -9999 0 -0.72 9 9
cell proliferation -0.045 0.23 -9999 0 -0.56 101 101
SLA -0.02 0.17 -9999 0 -0.82 39 39
actin cytoskeleton reorganization -0.021 0.18 -9999 0 -0.87 1 1
SRC -0.085 0.2 -9999 0 -0.56 134 134
PI3K -0.075 0.16 -9999 0 -0.83 7 7
PDGFB-D/PDGFRB/GRB7/SHC -0.099 0.22 -9999 0 -0.56 158 158
SH2B2 0 0.12 -9999 0 -0.82 17 17
PLCgamma1/SPHK1 -0.11 0.32 -9999 0 -0.76 149 149
LYN -0.087 0.21 -9999 0 -0.56 138 138
LRP1 0.005 0.095 -9999 0 -0.85 11 11
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.013 0.05 -9999 0 -0.85 3 3
NCK1-2/p130 Cas -0.071 0.17 -9999 0 -0.93 1 1
SPHK1 -0.062 0.22 -9999 0 -0.69 97 97
EDG1 -0.001 0.005 -9999 0 -10000 0 0
mol:DAG -0.091 0.29 -9999 0 -0.76 134 134
PLCG1 -0.095 0.3 -9999 0 -0.79 134 134
NHERF/PDGFRB -0.097 0.21 -9999 0 -0.57 146 146
YES1 -0.084 0.2 -9999 0 -0.56 134 134
cell migration -0.097 0.21 -9999 0 -0.56 146 146
SHC/Grb2/SOS1 -0.069 0.16 -9999 0 -10000 0 0
SLC9A3R2 0.011 0.063 -9999 0 -0.75 6 6
SLC9A3R1 0.005 0.095 -9999 0 -0.85 11 11
NHERF1-2/PDGFRB/PTEN -0.088 0.19 -9999 0 -0.52 146 146
FYN -0.092 0.23 -9999 0 -0.6 135 135
DOK1 -0.049 0.2 -9999 0 -0.51 140 140
HRAS/GTP -0.003 0.045 -9999 0 -0.59 5 5
PDGFB 0.009 0.076 -9999 0 -0.85 7 7
RAC1 -0.075 0.28 -9999 0 -0.64 154 154
PRKCD -0.071 0.22 -9999 0 -0.53 134 134
FER -0.047 0.2 -9999 0 -0.52 136 136
MAPKKK cascade -0.068 0.16 -9999 0 -10000 0 0
RASA1 -0.047 0.21 -9999 0 -0.52 135 135
NCK1 0.014 0.041 -9999 0 -0.85 2 2
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk -0.066 0.18 -9999 0 -0.47 141 141
PDGFB-D/PDGFRB/SHB -0.1 0.24 -9999 0 -0.64 141 141
chemotaxis -0.083 0.26 -9999 0 -0.65 140 140
STAT1-3-5/STAT1-3-5 -0.072 0.16 -9999 0 -0.76 3 3
Bovine Papilomavirus E5/PDGFRB -0.1 0.24 -9999 0 -0.66 140 140
PTPRJ 0.011 0.063 -9999 0 -0.75 6 6
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.045 0.2 0.71 74 -10000 0 74
PI3K Class IB/PDE3B -0.045 0.2 -10000 0 -0.71 74 74
PDE3B -0.045 0.2 -10000 0 -0.71 74 74
IL6-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
BCL2L1 -0.19 0.29 -9999 0 -0.74 77 77
CRP -0.22 0.33 -9999 0 -0.8 140 140
cell cycle arrest -0.23 0.33 -9999 0 -0.8 133 133
TIMP1 -0.18 0.32 -9999 0 -0.84 98 98
IL6ST -0.082 0.27 -9999 0 -0.85 97 97
Rac1/GDP -0.13 0.26 -9999 0 -0.71 91 91
AP1 -0.04 0.17 -9999 0 -0.61 28 28
GAB2 0.013 0.061 -9999 0 -0.72 6 6
TNFSF11 -0.24 0.34 -9999 0 -0.86 120 120
HSP90B1 -0.001 0.062 -9999 0 -10000 0 0
GAB1 0.015 0.041 -9999 0 -0.85 2 2
MAPK14 -0.1 0.26 -9999 0 -0.73 89 89
AKT1 0.056 0.061 -9999 0 -0.77 2 2
FOXO1 0.061 0.064 -9999 0 -0.99 1 1
MAP2K6 -0.12 0.25 -9999 0 -0.65 103 103
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 -0.14 0.26 -9999 0 -0.72 79 79
MITF -0.12 0.23 -9999 0 -0.6 102 102
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.014 0.041 -9999 0 -0.85 2 2
A2M -0.053 0.36 -9999 0 -1.6 44 44
CEBPB 0.016 0.071 -9999 0 -0.65 10 10
GRB2/SOS1/GAB family/SHP2 -0.017 0.1 -9999 0 -0.7 6 6
STAT3 -0.24 0.35 -9999 0 -0.85 138 138
STAT1 -0.017 0.082 -9999 0 -0.76 7 7
CEBPD -0.19 0.3 -9999 0 -0.77 72 72
PIK3CA 0.012 0.071 -9999 0 -0.85 6 6
PI3K 0.018 0.075 -9999 0 -0.62 12 12
JUN 0.009 0.069 -9999 0 -0.76 7 7
PIAS3/MITF -0.1 0.22 -9999 0 -0.69 61 61
MAPK11 -0.11 0.27 -9999 0 -0.72 101 101
STAT3 (dimer)/FOXO1 -0.14 0.28 -9999 0 -0.72 66 66
GRB2/SOS1/GAB family -0.1 0.19 -9999 0 -0.7 49 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.24 -9999 0 -0.56 132 132
GRB2 0.017 0.003 -9999 0 -10000 0 0
JAK2 0.015 0.029 -9999 0 -0.85 1 1
LBP -0.29 0.39 -9999 0 -0.83 237 237
PIK3R1 0.012 0.066 -9999 0 -0.78 6 6
JAK1 0.015 0.007 -9999 0 -10000 0 0
MYC -0.21 0.34 -9999 0 -0.95 87 87
FGG -0.38 0.47 -9999 0 -1 258 258
macrophage differentiation -0.23 0.33 -9999 0 -0.8 133 133
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.18 0.27 -9999 0 -0.58 197 197
JUNB -0.19 0.3 -9999 0 -0.78 82 82
FOS -0.087 0.26 -9999 0 -0.74 120 120
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.14 0.24 -9999 0 -0.56 141 141
STAT1/PIAS1 -0.13 0.22 -9999 0 -0.57 102 102
GRB2/SOS1/GAB family/SHP2/PI3K 0.033 0.064 -9999 0 -1.2 1 1
STAT3 (dimer) -0.24 0.35 -9999 0 -0.84 134 134
PRKCD -0.16 0.3 -9999 0 -0.78 97 97
IL6R -0.009 0.14 -9999 0 -0.84 25 25
SOCS3 -0.11 0.33 -9999 0 -1 77 77
gp130 (dimer)/JAK1/JAK1/LMO4 -0.045 0.18 -9999 0 -0.56 98 98
Rac1/GTP -0.15 0.26 -9999 0 -0.71 95 95
HCK -0.005 0.13 -9999 0 -0.83 22 22
MAPKKK cascade 0.008 0.097 -9999 0 -0.91 4 4
bone resorption -0.22 0.32 -9999 0 -0.8 121 121
IRF1 -0.19 0.29 -9999 0 -0.76 69 69
mol:GDP -0.14 0.27 -9999 0 -0.7 107 107
SOS1 0.017 0.006 -9999 0 -10000 0 0
VAV1 -0.15 0.27 -9999 0 -0.72 107 107
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.27 -9999 0 -0.71 92 92
PTPN11 -0.011 0.045 -9999 0 -1.2 1 1
IL6/IL6RA -0.16 0.28 -9999 0 -0.57 268 268
gp130 (dimer)/TYK2/TYK2/LMO4 -0.049 0.18 -9999 0 -0.56 100 100
gp130 (dimer)/JAK2/JAK2/LMO4 -0.048 0.18 -9999 0 -0.57 98 98
IL6 -0.2 0.34 -9999 0 -0.74 247 247
PIAS3 0.016 0 -9999 0 -10000 0 0
PTPRE 0.013 0.077 -9999 0 -0.84 7 7
PIAS1 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.22 -9999 0 -0.49 155 155
LMO4 0.011 0.025 -9999 0 -0.63 1 1
STAT3 (dimer)/PIAS3 -0.26 0.28 -9999 0 -0.8 126 126
MCL1 0.064 0.054 -9999 0 -0.88 1 1
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.003 0.041 -9999 0 -0.55 5 5
VLDLR 0.01 0.067 -9999 0 -0.74 7 7
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.014 0.041 -9999 0 -0.85 2 2
FYN 0.007 0.086 -9999 0 -0.85 9 9
ITGA3 -0.009 0.14 -9999 0 -0.75 29 29
RELN/VLDLR/Fyn -0.18 0.24 -9999 0 -0.47 349 349
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.014 0.097 -9999 0 -0.6 18 18
AKT1 -0.082 0.15 -9999 0 -0.46 27 27
MAP2K7 0.014 0.041 -9999 0 -0.85 2 2
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.036 0.17 -9999 0 -0.65 60 60
RELN/LRP8/DAB1 -0.2 0.23 -9999 0 -0.58 140 140
LRPAP1/LRP8 -0.018 0.093 -9999 0 -0.5 32 32
RELN/LRP8/DAB1/Fyn -0.19 0.22 -9999 0 -0.55 148 148
DAB1/alpha3/beta1 Integrin -0.18 0.21 -9999 0 -0.69 47 47
long-term memory -0.35 0.32 -9999 0 -0.8 223 223
DAB1/LIS1 -0.17 0.2 -9999 0 -0.71 30 30
DAB1/CRLK/C3G -0.17 0.2 -9999 0 -0.68 30 30
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
DAB1/NCK2 -0.18 0.2 -9999 0 -0.71 30 30
ARHGEF2 0.014 0.041 -9999 0 -0.85 2 2
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.28 0.38 -9999 0 -0.75 337 337
CDK5R1 0.013 0.048 -9999 0 -0.7 4 4
RELN -0.27 0.36 -9999 0 -0.72 343 343
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
RELN/LRP8/Fyn -0.2 0.24 -9999 0 -0.6 136 136
GRIN2A/RELN/LRP8/DAB1/Fyn -0.34 0.32 -9999 0 -0.68 338 338
MAPK8 0.005 0.095 -9999 0 -0.85 11 11
RELN/VLDLR/DAB1 -0.19 0.23 -9999 0 -0.48 259 259
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.17 0.24 -9999 0 -0.56 151 151
RELN/LRP8 -0.19 0.24 -9999 0 -0.58 130 130
GRIN2B/RELN/LRP8/DAB1/Fyn -0.21 0.24 -9999 0 -0.57 167 167
PI3K -0.008 0.072 -9999 0 -0.62 12 12
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.018 0.1 -9999 0 -0.56 29 29
RAP1A -0.12 0.21 -9999 0 -0.63 30 30
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.007 0.081 -9999 0 -0.75 10 10
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.031 0.16 -9999 0 -0.65 54 54
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.05 0.14 -9999 0 -0.5 28 28
neuron adhesion -0.11 0.22 -9999 0 -0.69 19 19
LRP8 -0.007 0.12 -9999 0 -0.66 30 30
GSK3B -0.068 0.15 -9999 0 -0.51 12 12
RELN/VLDLR/DAB1/Fyn -0.18 0.22 -9999 0 -0.54 146 146
MAP3K11 0.014 0.041 -9999 0 -0.85 2 2
RELN/VLDLR/DAB1/P13K -0.097 0.16 -9999 0 -0.37 148 148
CDK5 0.015 0.029 -9999 0 -0.85 1 1
MAPT -0.061 0.25 -9999 0 -0.78 95 95
neuron migration -0.083 0.2 -9999 0 -0.58 22 22
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.051 0.14 -9999 0 -0.5 28 28
RELN/VLDLR -0.18 0.22 -9999 0 -0.54 133 133
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.004 0.083 -9999 0 -0.61 13 13
NFATC2 -0.056 0.19 -9999 0 -0.58 102 102
NFATC3 0.013 0.042 -9999 0 -0.58 1 1
CD40LG -0.2 0.41 -9999 0 -0.88 169 169
PTGS2 -0.22 0.42 -9999 0 -0.89 189 189
JUNB 0.001 0.11 -9999 0 -0.78 17 17
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.014 -9999 0 -10000 0 0
CaM/Ca2+ -0.007 0.014 -9999 0 -10000 0 0
CALM1 0.013 0.01 -9999 0 -10000 0 0
JUN 0.007 0.071 -9999 0 -0.77 7 7
mol:Ca2+ -0.008 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.003 -9999 0 -10000 0 0
FOSL1 -0.055 0.22 -9999 0 -0.73 84 84
CREM 0.015 0.022 -9999 0 -0.65 1 1
Jun/NFAT1-c-4/p21SNFT -0.15 0.24 -9999 0 -0.72 89 89
FOS -0.09 0.26 -9999 0 -0.75 120 120
IFNG -0.22 0.42 -9999 0 -0.82 231 231
AP-1/NFAT1-c-4 -0.27 0.46 -9999 0 -1 174 174
FASLG -0.22 0.44 -9999 0 -0.88 222 222
NFAT1-c-4/ICER1 -0.094 0.17 -9999 0 -0.59 66 66
IL2RA -0.22 0.42 -9999 0 -0.9 184 184
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.18 0.37 -9999 0 -0.82 144 144
JunB/Fra1/NFAT1-c-4 -0.13 0.22 -9999 0 -0.66 92 92
IL4 -0.18 0.36 -9999 0 -0.79 151 151
IL2 -0.01 0.068 -9999 0 -0.57 12 12
IL3 -0.024 0.07 -9999 0 -1.1 3 3
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.028 0.19 -9999 0 -0.8 48 48
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.014 0.05 -9999 0 -0.85 3 3
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.053 0.11 -10000 0 -0.61 8 8
NT3 (dimer)/TRKC -0.15 0.29 -10000 0 -0.68 195 195
NT3 (dimer)/TRKB -0.26 0.37 -10000 0 -0.66 357 357
SHC/Grb2/SOS1/GAB1/PI3K 0.042 0.046 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.11 0.29 -10000 0 -0.78 140 140
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 -0.033 0.18 -10000 0 -0.69 60 60
NTRK2 -0.16 0.32 -10000 0 -0.76 196 196
NTRK3 -0.099 0.28 -10000 0 -0.76 132 132
NT-4/5 (dimer)/TRKB -0.24 0.32 -10000 0 -0.6 348 348
neuron apoptosis 0.18 0.23 0.56 197 -10000 0 197
SHC 2-3/Grb2 -0.2 0.27 -10000 0 -0.63 196 196
SHC1 0.015 0.022 -10000 0 -0.65 1 1
SHC2 -0.19 0.29 -10000 0 -0.67 182 182
SHC3 -0.18 0.24 -10000 0 -0.57 190 190
STAT3 (dimer) 0.007 0.086 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.19 0.32 -10000 0 -0.62 269 269
RIN/GDP -0.005 0.11 -10000 0 -0.32 10 10
GIPC1 0.012 0.055 -10000 0 -0.8 4 4
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.16 0.25 -10000 0 -0.63 161 161
RIN/GTP -0.002 0.028 -10000 0 -0.49 3 3
CCND1 -0.012 0.23 -10000 0 -1 42 42
MAGED1 0.015 0.032 -10000 0 -0.65 2 2
PTPN11 0.015 0.029 -10000 0 -0.85 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.031 0.15 -10000 0 -0.65 50 50
SHC/GRB2/SOS1 0 0.013 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.18 0.29 -10000 0 -0.58 266 266
TRKA/NEDD4-2 -0.063 0.17 -10000 0 -0.51 109 109
ELMO1 -0.032 0.2 -10000 0 -0.85 49 49
RhoG/GTP/ELMO1/DOCK1 -0.033 0.14 -10000 0 -0.58 50 50
NGF -0.16 0.34 -10000 0 -0.8 189 189
HRAS 0.012 0.059 -10000 0 -0.77 5 5
DOCK1 0.014 0.041 -10000 0 -0.85 2 2
GAB2 0.011 0.06 -10000 0 -0.72 6 6
RIT2 0.001 0.038 -10000 0 -0.65 3 3
RIT1 0.015 0.029 -10000 0 -0.85 1 1
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 -0.1 0.28 -10000 0 -0.76 136 136
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0.022 -10000 0 -0.65 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.18 0.29 -10000 0 -0.69 178 178
mol:GDP -0.014 0.16 -10000 0 -0.5 16 16
NGF (dimer) -0.16 0.34 -10000 0 -0.8 189 189
RhoG/GDP -0.037 0.15 -10000 0 -0.66 49 49
RIT1/GDP 0.002 0.11 -10000 0 -0.33 12 12
TIAM1 0.005 0.098 -10000 0 -0.83 12 12
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
BDNF (dimer)/TRKB -0.19 0.29 -10000 0 -0.56 292 292
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.003 0.041 -10000 0 -0.61 4 4
FRS2 family/SHP2 -0.004 0.042 -10000 0 -0.56 3 3
SHC/GRB2/SOS1/GAB1 -0.002 0.027 -10000 0 -0.51 2 2
RIT1/GTP -0.001 0.022 -10000 0 -0.66 1 1
NT3 (dimer) -0.074 0.26 -10000 0 -0.79 99 99
RAP1/GDP -0.036 0.069 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.11 0.29 -10000 0 -0.77 140 140
ubiquitin-dependent protein catabolic process -0.16 0.26 -10000 0 -0.53 276 276
Schwann cell development -0.042 0.041 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.003 0.034 -10000 0 -0.51 2 2
FRS2 family/SHP2/CRK family/C3G/GAB2 0.048 0.036 -10000 0 -0.5 1 1
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.24 0.31 -10000 0 -0.86 129 129
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.056 0.086 -10000 0 -10000 0 0
STAT3 0.007 0.086 -10000 0 -10000 0 0
axon guidance -0.22 0.29 -10000 0 -0.79 129 129
MAPK3 -0.13 0.29 -10000 0 -0.62 175 175
MAPK1 -0.13 0.29 -10000 0 -0.62 176 176
CDC42/GDP 0.002 0.11 -10000 0 -0.31 14 14
NTF3 -0.074 0.26 -10000 0 -0.79 99 99
NTF4 -0.031 0.15 -10000 0 -0.65 50 50
NGF (dimer)/TRKA/FAIM -0.14 0.25 -10000 0 -0.61 154 154
PI3K -0.008 0.072 -10000 0 -0.62 12 12
FRS3 0.011 0.06 -10000 0 -0.72 6 6
FAIM 0.015 0.032 -10000 0 -0.65 2 2
GAB1 0.014 0.041 -10000 0 -0.85 2 2
RASGRF1 -0.18 0.27 -10000 0 -0.63 191 191
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L -0.1 0.27 -10000 0 -0.65 150 150
RGS19 0.014 0.041 -10000 0 -0.85 2 2
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.098 -10000 0 -0.56 2 2
Rac1/GDP 0.002 0.11 -10000 0 -0.32 11 11
NGF (dimer)/TRKA/GRIT -0.14 0.25 -10000 0 -0.54 234 234
neuron projection morphogenesis -0.12 0.26 -10000 0 -0.68 111 111
NGF (dimer)/TRKA/NEDD4-2 -0.16 0.26 -10000 0 -0.53 276 276
MAP2K1 0.049 0.028 -10000 0 -0.47 2 2
NGFR -0.15 0.33 -10000 0 -0.81 177 177
NGF (dimer)/TRKA/GIPC/GAIP -0.096 0.21 -10000 0 -0.41 227 227
RAS family/GTP/PI3K 0.033 0.053 -10000 0 -0.38 13 13
FRS2 family/SHP2/GRB2/SOS1 -0.003 0.035 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.015 0.022 -10000 0 -0.65 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.008 0.082 -10000 0 -0.85 8 8
MAPKKK cascade -0.16 0.3 -10000 0 -0.77 154 154
RASA1 0.013 0.05 -10000 0 -0.85 3 3
TRKA/c-Abl -0.034 0.13 -10000 0 -0.51 60 60
SQSTM1 0.009 0.067 -10000 0 -0.65 9 9
BDNF (dimer)/TRKB/GIPC -0.17 0.27 -10000 0 -0.61 187 187
NGF (dimer)/TRKA/p62/Atypical PKCs -0.13 0.22 -10000 0 -0.52 162 162
MATK -0.04 0.21 -10000 0 -0.79 62 62
NEDD4L -0.023 0.16 -10000 0 -0.66 52 52
RAS family/GDP -0.033 0.065 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.17 0.27 -10000 0 -0.59 219 219
Rac1/GTP -0.12 0.16 -10000 0 -0.43 135 135
FRS2 family/SHP2/CRK family -0.003 0.042 -10000 0 -0.59 3 3
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.036 0.055 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.15 -9999 0 -0.49 51 51
JUN -0.053 0.19 -9999 0 -0.63 41 41
HRAS 0.012 0.059 -9999 0 -0.77 5 5
RET51/GFRalpha1/GDNF/GRB10 -0.16 0.24 -9999 0 -0.59 151 151
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.16 0.25 -9999 0 -0.6 153 153
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0.029 -9999 0 -0.85 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.022 -9999 0 -0.65 1 1
RET9/GFRalpha1/GDNF/Enigma -0.12 0.21 -9999 0 -0.55 124 124
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.24 -9999 0 -0.58 157 157
GRB7 -0.002 0.12 -9999 0 -0.76 21 21
RET51/GFRalpha1/GDNF -0.16 0.24 -9999 0 -0.59 150 150
MAPKKK cascade -0.13 0.2 -9999 0 -0.7 42 42
BCAR1 0.013 0.05 -9999 0 -0.85 3 3
RET9/GFRalpha1/GDNF/IRS1 -0.13 0.22 -9999 0 -0.57 130 130
lamellipodium assembly -0.093 0.14 -9999 0 -0.45 49 49
RET51/GFRalpha1/GDNF/SHC -0.16 0.24 -9999 0 -0.59 151 151
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
RET9/GFRalpha1/GDNF/SHC -0.12 0.21 -9999 0 -0.54 122 122
RET9/GFRalpha1/GDNF/Shank3 -0.13 0.22 -9999 0 -0.56 132 132
MAPK3 -0.11 0.25 -9999 0 -0.8 46 46
DOK1 0.01 0.071 -9999 0 -0.85 6 6
DOK6 -0.11 0.3 -9999 0 -0.83 128 128
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.11 0.25 -9999 0 -0.71 79 79
DOK5 -0.076 0.25 -9999 0 -0.76 105 105
GFRA1 -0.18 0.34 -9999 0 -0.76 221 221
MAPK8 -0.063 0.19 -9999 0 -0.65 37 37
HRAS/GTP -0.14 0.23 -9999 0 -0.81 39 39
tube development -0.12 0.2 -9999 0 -0.52 132 132
MAPK1 -0.11 0.25 -9999 0 -0.8 46 46
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.047 0.14 -9999 0 -0.51 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.015 0.022 -9999 0 -0.65 1 1
PDLIM7 0.012 0.055 -9999 0 -0.8 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.21 0.31 -9999 0 -0.67 219 219
SHC1 0.015 0.022 -9999 0 -0.65 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.27 -9999 0 -0.64 157 157
RET51/GFRalpha1/GDNF/Dok5 -0.21 0.31 -9999 0 -0.72 179 179
PRKCA 0.015 0.032 -9999 0 -0.65 2 2
HRAS/GDP -0.003 0.045 -9999 0 -0.59 5 5
CREB1 -0.055 0.16 -9999 0 -0.4 128 128
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.049 0.15 -9999 0 -0.36 122 122
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.26 -9999 0 -0.62 156 156
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.052 0.22 -9999 0 -0.72 83 83
DOK4 -0.007 0.14 -9999 0 -0.85 24 24
JNK cascade -0.051 0.18 -9999 0 -0.61 41 41
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.21 -9999 0 -0.54 122 122
SHANK3 0.003 0.1 -9999 0 -0.8 14 14
RASA1 0.013 0.05 -9999 0 -0.85 3 3
NCK1 0.014 0.041 -9999 0 -0.85 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.048 0.14 -9999 0 -0.36 122 122
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.066 0.17 -9999 0 -0.55 30 30
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.071 0.19 -9999 0 -0.63 35 35
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.068 0.18 -9999 0 -0.63 30 30
PI3K -0.096 0.26 -9999 0 -0.6 133 133
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.12 0.2 -9999 0 -0.52 132 132
GRB10 0.014 0.041 -9999 0 -0.85 2 2
activation of MAPKK activity -0.058 0.16 -9999 0 -0.51 26 26
RET51/GFRalpha1/GDNF/FRS2 -0.16 0.24 -9999 0 -0.59 150 150
GAB1 0.014 0.041 -9999 0 -0.85 2 2
IRS1 -0.01 0.14 -9999 0 -0.72 31 31
IRS2 -0.019 0.15 -9999 0 -0.66 46 46
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.07 0.19 -9999 0 -0.64 33 33
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.24 -9999 0 -0.59 150 150
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF -0.005 0.082 -9999 0 -0.65 14 14
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.26 -9999 0 -0.61 161 161
Rac1/GTP -0.11 0.17 -9999 0 -0.56 49 49
RET9/GFRalpha1/GDNF -0.13 0.23 -9999 0 -0.51 229 229
GFRalpha1/GDNF -0.15 0.26 -9999 0 -0.59 229 229
Arf6 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
CENTA1/KIF3B -0.039 0.14 -9999 0 -0.51 68 68
ARNO/beta Arrestin1-2 -0.04 0.11 -9999 0 -0.81 7 7
EGFR -0.021 0.17 -9999 0 -0.78 41 41
EPHA2 0.006 0.094 -9999 0 -0.83 11 11
USP6 0.004 0.09 -9999 0 -0.66 16 16
IQSEC1 0.016 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.15 0.26 -9999 0 -0.58 222 222
ARRB2 -0.011 0.085 -9999 0 -0.29 77 77
mol:GTP 0.014 0.048 -9999 0 -0.33 9 9
ARRB1 0.003 0.11 -9999 0 -0.83 14 14
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR -0.12 0.3 -9999 0 -0.79 152 152
EGF -0.15 0.31 -9999 0 -0.73 196 196
somatostatin receptor activity 0 0 -9999 0 -0.001 115 115
ARAP2 0.011 0.065 -9999 0 -0.85 5 5
mol:GDP -0.086 0.14 -9999 0 -0.35 135 135
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 58 58
ITGA2B -0.058 0.22 -9999 0 -0.73 88 88
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.1 -9999 0 -0.55 28 28
ADAP1 -0.009 0.13 -9999 0 -0.69 31 31
KIF13B -0.023 0.16 -9999 0 -0.65 52 52
HGF/MET -0.087 0.21 -9999 0 -0.6 129 129
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.086 0.14 -9999 0 -0.34 120 120
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.12 0.23 -9999 0 -0.62 104 104
ADRB2 -0.024 0.16 -9999 0 -0.69 50 50
receptor agonist activity 0 0 -9999 0 0 102 102
actin filament binding 0 0 -9999 0 -0.001 119 119
SRC 0.015 0.022 -9999 0 -0.65 1 1
ITGB3 -0.046 0.21 -9999 0 -0.76 71 71
GNAQ 0.016 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 82 82
ARF6/GDP -0.009 0.14 -9999 0 -0.49 45 45
ARF6/GDP/GULP/ACAP1 -0.12 0.19 -9999 0 -0.56 110 110
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.078 0.18 -9999 0 -0.57 76 76
ACAP1 -0.04 0.21 -9999 0 -0.79 62 62
ACAP2 0.015 0.029 -9999 0 -0.85 1 1
LHCGR/beta Arrestin2 -0.031 0.12 -9999 0 -0.42 77 77
EFNA1 0.001 0.12 -9999 0 -0.85 16 16
HGF -0.094 0.28 -9999 0 -0.78 122 122
CYTH3 0.014 0 -9999 0 -10000 0 0
CYTH2 0.007 0.061 -9999 0 -1.3 2 2
NCK1 0.014 0.041 -9999 0 -0.85 2 2
fibronectin binding 0 0 -9999 0 -0.001 109 109
endosomal lumen acidification 0 0 -9999 0 -0.001 127 127
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.028 0.18 -9999 0 -0.79 49 49
GNAQ/ARNO 0.012 0.057 -9999 0 -1.2 2 2
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 17 17
MET 0.009 0.075 -9999 0 -0.77 8 8
GNA14 -0.078 0.27 -9999 0 -0.84 97 97
GNA15 -0.015 0.16 -9999 0 -0.81 33 33
GIT1 0.014 0.041 -9999 0 -0.85 2 2
mol:PI-4-5-P2 0 0 -9999 0 -0.001 91 91
GNA11 -0.011 0.14 -9999 0 -0.75 31 31
LHCGR -0.052 0.18 -9999 0 -0.65 77 77
AGTR1 -0.22 0.35 -9999 0 -0.73 275 275
desensitization of G-protein coupled receptor protein signaling pathway -0.03 0.12 -9999 0 -0.42 77 77
IPCEF1/ARNO -0.087 0.2 -9999 0 -0.51 106 106
alphaIIb/beta3 Integrin -0.099 0.23 -9999 0 -0.6 147 147
Effects of Botulinum toxin

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
STX1A 0.004 0.075 -9999 0 -0.54 16 16
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.054 0.15 -9999 0 -0.48 100 100
STXBP1 0.014 0.037 -9999 0 -0.75 2 2
ACh/CHRNA1 -0.15 0.24 -9999 0 -0.51 264 264
RAB3GAP2/RIMS1/UNC13B -0.046 0.13 -9999 0 -0.67 2 2
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 -0.064 0.21 -9999 0 -0.65 100 100
mol:ACh -0.011 0.057 -9999 0 -0.15 127 127
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.062 0.13 -9999 0 -0.5 43 43
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.15 0.24 -9999 0 -0.51 264 264
UNC13B 0.015 0.022 -9999 0 -0.65 1 1
CHRNA1 -0.21 0.34 -9999 0 -0.73 264 264
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.051 0.17 -9999 0 -0.52 93 93
SNAP25 -0.041 0.13 -9999 0 -0.39 114 114
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.062 0.23 -9999 0 -0.73 93 93
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.013 0.069 -9999 0 -0.46 18 18
STX1A/SNAP25 fragment 1/VAMP2 -0.062 0.13 -9999 0 -0.5 43 43
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.14 0.42 -9999 0 -0.96 145 145
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 -0.039 0.14 -9999 0 -0.47 19 19
ATF2/c-Jun -0.024 0.16 -9999 0 -0.76 20 20
MAPK11 -0.054 0.18 -9999 0 -0.68 34 34
MITF -0.044 0.18 -9999 0 -0.56 43 43
MAPKAPK5 -0.041 0.18 -9999 0 -0.57 38 38
KRT8 -0.045 0.19 -9999 0 -0.59 43 43
MAPKAPK3 0.015 0.029 -9999 0 -0.85 1 1
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.072 0.23 -9999 0 -0.53 140 140
CEBPB -0.045 0.18 -9999 0 -0.56 43 43
SLC9A1 -0.041 0.18 -9999 0 -0.57 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.042 0.2 -9999 0 -0.6 49 49
p38alpha-beta/MNK1 -0.044 0.19 -9999 0 -0.68 35 35
JUN -0.023 0.16 -9999 0 -0.74 20 20
PPARGC1A -0.089 0.23 -9999 0 -0.56 108 108
USF1 -0.041 0.18 -9999 0 -0.4 139 139
RAB5/GDP/GDI1 -0.06 0.11 -9999 0 -0.48 26 26
NOS2 -0.15 0.44 -9999 0 -1.1 130 130
DDIT3 -0.052 0.2 -9999 0 -0.59 52 52
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 -0.027 0.16 -9999 0 -0.55 35 35
p38alpha-beta/HBP1 -0.044 0.19 -9999 0 -0.68 35 35
CREB1 -0.042 0.19 -9999 0 -0.59 42 42
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.03 0.17 -9999 0 -0.62 33 33
RPS6KA4 -0.041 0.18 -9999 0 -0.57 38 38
PLA2G4A -0.056 0.22 -9999 0 -0.68 57 57
GDI1 -0.041 0.18 -9999 0 -0.56 40 40
TP53 -0.06 0.23 -9999 0 -0.52 139 139
RPS6KA5 -0.05 0.2 -9999 0 -0.62 45 45
ESR1 -0.078 0.26 -9999 0 -0.71 77 77
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C -0.071 0.26 -9999 0 -0.76 74 74
MEF2A -0.043 0.18 -9999 0 -0.56 42 42
EIF4EBP1 -0.047 0.2 -9999 0 -0.43 143 143
KRT19 -0.23 0.3 -9999 0 -0.59 280 280
ELK4 -0.042 0.18 -9999 0 -0.56 40 40
ATF6 -0.041 0.18 -9999 0 -0.4 139 139
ATF1 -0.042 0.19 -9999 0 -0.42 140 140
p38alpha-beta/MAPKAPK2 -0.044 0.19 -9999 0 -0.68 35 35
p38alpha-beta/MAPKAPK3 -0.044 0.2 -9999 0 -0.69 35 35
TCGA08_retinoblastoma

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
CDKN2B -0.004 0.12 -10000 0 -0.81 20 20
CDKN2C 0.001 0.13 -10000 0 -0.82 20 20
CDKN2A -0.041 0.21 -10000 0 -0.79 63 63
CCND2 0.015 0.091 0.28 66 -0.18 33 99
RB1 -0.021 0.096 0.2 1 -0.31 64 65
CDK4 0.023 0.099 0.32 64 -10000 0 64
CDK6 0.022 0.1 0.32 66 -0.25 2 68
G1/S progression 0.002 0.1 0.31 64 -0.2 1 65
Visual signal transduction: Rods

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
mol:K + 0.015 0.022 -9999 0 -0.65 1 1
GNAT1/GTP -0.006 0.054 -9999 0 -0.49 11 11
Metarhodopsin II/Arrestin -0.01 0.063 -9999 0 -0.42 21 21
PDE6G/GNAT1/GTP -0.045 0.14 -9999 0 -0.46 88 88
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.003 0.073 -9999 0 -0.65 11 11
GRK1 -0.004 0.073 -9999 0 -0.65 11 11
CNG Channel -0.16 0.27 -9999 0 -0.67 146 146
mol:Na + -0.13 0.22 -9999 0 -0.7 62 62
mol:ADP -0.004 0.073 -9999 0 -0.65 11 11
RGS9-1/Gbeta5/R9AP -0.12 0.23 -9999 0 -0.6 119 119
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.14 0.23 -9999 0 -0.73 62 62
CNGB1 -0.055 0.2 -9999 0 -0.65 87 87
RDH5 -0.1 0.29 -9999 0 -0.81 124 124
SAG 0 0.031 -9999 0 -0.65 2 2
mol:Ca2+ -0.091 0.23 -9999 0 -0.68 62 62
Na + (4 Units) -0.12 0.2 -9999 0 -0.65 62 62
RGS9 -0.12 0.3 -9999 0 -0.76 160 160
GNB1/GNGT1 -0.095 0.22 -9999 0 -0.62 137 137
GNAT1/GDP -0.11 0.2 -9999 0 -0.53 123 123
GUCY2D -0.023 0.15 -9999 0 -0.66 47 47
GNGT1 -0.12 0.3 -9999 0 -0.81 137 137
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.015 0.029 -9999 0 -0.85 1 1
mol:GMP (4 units) -0.056 0.21 -9999 0 -0.6 81 81
mol:11-cis-retinal -0.099 0.29 -9999 0 -0.81 124 124
mol:cGMP -0.05 0.14 -9999 0 -0.57 30 30
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin -0.098 0.23 -9999 0 -0.62 141 141
SLC24A1 0.015 0.022 -9999 0 -0.65 1 1
CNGA1 -0.096 0.27 -9999 0 -0.75 129 129
Metarhodopsin II -0.013 0.071 -9999 0 -0.39 29 29
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.056 0.15 -9999 0 -0.6 30 30
RGS9BP -0.041 0.2 -9999 0 -0.73 68 68
Metarhodopsin II/Transducin -0.041 0.14 -9999 0 -0.37 114 114
GCAP Family/Ca ++ -0.037 0.13 -9999 0 -0.44 75 75
PDE6A/B -0.06 0.19 -9999 0 -0.62 87 87
mol:Pi -0.12 0.23 -9999 0 -0.6 119 119
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.081 0.19 -9999 0 -0.5 146 146
PDE6B -0.045 0.22 -9999 0 -0.84 63 63
PDE6A -0.007 0.11 -9999 0 -0.65 27 27
PDE6G -0.046 0.2 -9999 0 -0.7 77 77
RHO -0.005 0.096 -9999 0 -0.65 19 19
PDE6 -0.17 0.28 -9999 0 -0.88 81 81
GUCA1A -0.009 0.1 -9999 0 -0.65 21 21
GC2/GCAP Family -0.037 0.13 -9999 0 -0.57 26 26
GUCA1C -0.018 0.12 -9999 0 -0.65 31 31
GUCA1B -0.01 0.14 -9999 0 -0.8 28 28
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.038 0.18 -10000 0 -0.47 79 79
IKBKB -0.007 0.095 -10000 0 -0.28 22 22
AKT1 -0.029 0.13 -10000 0 -0.29 52 52
IKBKG -0.006 0.1 -10000 0 -0.32 24 24
CALM1 -0.051 0.18 -10000 0 -0.58 59 59
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
MAP3K1 -0.077 0.25 -10000 0 -0.68 92 92
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.065 0.19 -10000 0 -0.57 73 73
DOK1 0.01 0.071 -10000 0 -0.85 6 6
AP-1 -0.022 0.12 0.21 17 -0.29 57 74
LYN 0.012 0.058 -10000 0 -0.85 4 4
BLNK -0.011 0.14 -10000 0 -0.74 32 32
SHC1 0.015 0.022 -10000 0 -0.65 1 1
BCR complex -0.15 0.29 -10000 0 -0.63 214 214
CD22 -0.16 0.31 -10000 0 -0.81 121 121
CAMK2G -0.038 0.16 -10000 0 -0.6 42 42
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.009 0.076 -10000 0 -0.85 7 7
SHC/GRB2/SOS1 -0.12 0.22 -10000 0 -0.83 52 52
GO:0007205 -0.066 0.19 -10000 0 -0.59 73 73
SYK -0.001 0.12 -10000 0 -0.8 19 19
ELK1 -0.053 0.18 -10000 0 -0.59 59 59
NFATC1 -0.07 0.22 -10000 0 -0.61 80 80
B-cell antigen/BCR complex -0.15 0.29 -10000 0 -0.63 214 214
PAG1/CSK -0.023 0.12 -10000 0 -0.66 31 31
NFKBIB 0.011 0.037 0.099 20 -0.14 1 21
HRAS -0.051 0.19 -10000 0 -0.56 74 74
NFKBIA 0.011 0.037 0.099 20 -0.14 1 21
NF-kappa-B/RelA/I kappa B beta 0.018 0.031 -10000 0 -0.2 1 1
RasGAP/Csk -0.16 0.28 -10000 0 -0.91 64 64
mol:GDP -0.061 0.18 -10000 0 -0.55 73 73
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B -0.049 0.22 -10000 0 -0.81 70 70
NF-kappa-B/RelA/I kappa B alpha 0.018 0.031 -10000 0 -0.2 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.092 0.25 -10000 0 -0.6 107 107
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
mol:IP3 -0.076 0.19 -10000 0 -0.6 73 73
CSK 0.014 0.041 -10000 0 -0.85 2 2
FOS -0.091 0.23 -10000 0 -0.61 101 101
CHUK -0.006 0.1 -10000 0 -0.31 23 23
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.085 0.17 -10000 0 -0.6 65 65
PTPN6 -0.15 0.28 -10000 0 -0.86 92 92
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 0.008 0.048 -10000 0 -0.13 63 63
VAV2 -0.16 0.29 -10000 0 -0.71 159 159
ubiquitin-dependent protein catabolic process 0.016 0.036 0.1 20 -0.13 1 21
BTK -0.044 0.23 0.46 4 -1.3 29 33
CD19 -0.17 0.32 -10000 0 -0.75 170 170
MAP4K1 -0.049 0.22 -10000 0 -0.8 71 71
CD72 -0.016 0.16 -10000 0 -0.74 38 38
PAG1 -0.013 0.15 -10000 0 -0.84 30 30
MAPK14 -0.052 0.21 -10000 0 -0.56 84 84
SH3BP5 -0.05 0.23 -10000 0 -0.84 68 68
PIK3AP1 -0.074 0.24 -10000 0 -0.66 94 94
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.093 0.28 -10000 0 -0.76 90 90
RAF1 -0.038 0.17 -10000 0 -0.61 48 48
RasGAP/p62DOK/SHIP -0.16 0.28 -10000 0 -0.92 66 66
CD79A -0.13 0.3 -10000 0 -0.72 177 177
re-entry into mitotic cell cycle -0.022 0.12 0.21 17 -0.29 59 76
RASA1 0.013 0.05 -10000 0 -0.85 3 3
MAPK3 -0.013 0.14 -10000 0 -0.52 35 35
MAPK1 -0.013 0.14 -10000 0 -0.5 40 40
CD72/SHP1 -0.11 0.29 -10000 0 -0.77 112 112
NFKB1 0.015 0.029 -10000 0 -0.85 1 1
MAPK8 -0.057 0.22 -10000 0 -0.56 92 92
actin cytoskeleton organization -0.091 0.26 -10000 0 -0.68 89 89
NF-kappa-B/RelA 0.042 0.06 0.2 20 -0.26 2 22
Calcineurin -0.056 0.13 -10000 0 -0.54 41 41
PI3K -0.14 0.22 -10000 0 -0.65 78 78
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.081 0.21 0.29 24 -0.65 74 98
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.14 0.35 -10000 0 -0.96 118 118
DAPP1 -0.17 0.37 -10000 0 -1.1 103 103
cytokine secretion -0.063 0.2 -10000 0 -0.55 80 80
mol:DAG -0.076 0.19 -10000 0 -0.6 73 73
PLCG2 -0.054 0.21 -10000 0 -0.68 90 90
MAP2K1 -0.025 0.16 -10000 0 -0.57 41 41
B-cell antigen/BCR complex/FcgammaRIIB -0.19 0.32 -10000 0 -0.74 162 162
mol:PI-3-4-5-P3 -0.099 0.15 -10000 0 -0.43 72 72
ETS1 -0.043 0.18 -10000 0 -0.56 64 64
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.14 0.26 -10000 0 -0.7 112 112
B-cell antigen/BCR complex/LYN -0.14 0.31 -10000 0 -0.85 108 108
MALT1 0.015 0.029 -10000 0 -0.85 1 1
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.1 0.28 -10000 0 -0.75 89 89
B-cell antigen/BCR complex/LYN/SYK -0.16 0.3 -10000 0 -0.87 99 99
CARD11 -0.088 0.23 -10000 0 -0.65 97 97
FCGR2B -0.08 0.26 -10000 0 -0.79 106 106
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.01 0.046 -10000 0 -0.13 2 2
PTPRC -0.028 0.19 -10000 0 -0.82 47 47
PDPK1 -0.031 0.12 -10000 0 -0.29 52 52
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 0.016 0.035 -10000 0 -0.13 28 28
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.081 0.27 -9999 0 -0.83 102 102
GNB1/GNG2 -0.14 0.19 -9999 0 -0.6 83 83
mol:DAG -0.085 0.2 -9999 0 -0.61 50 50
PLCG1 -0.088 0.2 -9999 0 -0.64 50 50
YES1 -0.097 0.19 -9999 0 -0.6 53 53
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.014 0.043 -9999 0 -0.72 3 3
G protein -0.09 0.2 -9999 0 -0.65 50 50
MAP3K7 -0.071 0.18 -9999 0 -0.54 44 44
mol:Ca2+ -0.082 0.19 -9999 0 -0.58 50 50
mol:IP3 -0.085 0.2 -9999 0 -0.61 50 50
NLK -0.004 0.008 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.087 0.2 -9999 0 -0.59 49 49
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.11 0.2 -9999 0 -0.56 81 81
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.097 0.19 -9999 0 -0.6 53 53
GO:0007205 -0.083 0.19 -9999 0 -0.6 50 50
WNT6 -0.098 0.27 -9999 0 -0.73 134 134
WNT4 -0.089 0.26 -9999 0 -0.72 127 127
NFAT1/CK1 alpha -0.15 0.2 -9999 0 -0.63 73 73
GNG2 -0.016 0.16 -9999 0 -0.85 33 33
WNT5A -0.072 0.23 -9999 0 -0.69 112 112
WNT11 -0.096 0.26 -9999 0 -0.69 140 140
CDC42 -0.083 0.18 -9999 0 -0.56 53 53
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.01 0.071 -9999 0 -0.85 6 6
LAT2 -0.067 0.28 -9999 0 -0.86 66 66
AP1 -0.13 0.23 -9999 0 -0.7 98 98
mol:PIP3 -0.068 0.28 -9999 0 -0.76 85 85
IKBKB -0.014 0.15 -9999 0 -0.38 78 78
AKT1 -0.052 0.24 -9999 0 -0.76 52 52
IKBKG -0.015 0.15 -9999 0 -0.38 78 78
MS4A2 -0.11 0.29 -9999 0 -0.8 133 133
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
MAP3K1 -0.022 0.22 -9999 0 -0.63 73 73
mol:Ca2+ -0.038 0.2 -9999 0 -0.51 85 85
LYN 0.011 0.06 -9999 0 -0.88 4 4
CBLB -0.058 0.24 -9999 0 -0.76 64 64
SHC1 0.015 0.022 -9999 0 -0.65 1 1
RasGAP/p62DOK -0.063 0.17 -9999 0 -0.53 102 102
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.009 0.076 -9999 0 -0.85 7 7
PLD2 -0.098 0.28 -9999 0 -0.68 118 118
PTPN13 -0.051 0.24 -9999 0 -0.72 67 67
PTPN11 0.013 0.031 -9999 0 -0.86 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.002 0.18 -9999 0 -0.44 58 58
SYK -0.003 0.12 -9999 0 -0.82 19 19
GRB2 0.016 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.25 -9999 0 -0.78 90 90
LAT -0.079 0.27 -9999 0 -0.79 79 79
PAK2 -0.04 0.25 -9999 0 -0.74 74 74
NFATC2 -0.13 0.28 -9999 0 -0.84 102 102
HRAS -0.06 0.29 -9999 0 -0.85 79 79
GAB2 0.011 0.06 -9999 0 -0.72 6 6
PLA2G1B 0.037 0.033 -9999 0 -0.41 1 1
Fc epsilon R1 -0.16 0.3 -9999 0 -0.67 193 193
Antigen/IgE/Fc epsilon R1 -0.15 0.28 -9999 0 -0.66 167 167
mol:GDP -0.07 0.3 -9999 0 -0.9 78 78
JUN 0.01 0.069 -9999 0 -0.76 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.066 -9999 0 -0.78 6 6
FOS -0.086 0.26 -9999 0 -0.74 120 120
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.11 0.24 -9999 0 -0.58 129 129
CHUK -0.014 0.15 -9999 0 -0.38 77 77
KLRG1 -0.065 0.25 -9999 0 -0.75 71 71
VAV1 -0.079 0.3 -9999 0 -0.9 78 78
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.059 0.24 -9999 0 -0.76 65 65
negative regulation of mast cell degranulation -0.053 0.23 -9999 0 -0.7 72 72
BTK -0.12 0.28 -9999 0 -0.85 81 81
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.12 0.34 -9999 0 -1 84 84
GAB2/PI3K/SHP2 -0.12 0.24 -9999 0 -0.85 57 57
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.063 0.24 -9999 0 -0.77 63 63
RAF1 0.024 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.19 0.35 -9999 0 -0.83 147 147
FCER1G -0.008 0.15 -9999 0 -0.83 27 27
FCER1A -0.091 0.28 -9999 0 -0.8 117 117
Antigen/IgE/Fc epsilon R1/Fyn -0.14 0.27 -9999 0 -0.63 170 170
MAPK3 0.036 0.035 -9999 0 -0.6 1 1
MAPK1 0.037 0.029 -9999 0 -10000 0 0
NFKB1 0.015 0.029 -9999 0 -0.85 1 1
MAPK8 0.008 0.096 -9999 0 -0.59 13 13
DUSP1 -0.081 0.27 -9999 0 -0.84 101 101
NF-kappa-B/RelA -0.038 0.068 -9999 0 -0.29 1 1
actin cytoskeleton reorganization -0.052 0.22 -9999 0 -0.69 64 64
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.11 0.24 -9999 0 -0.82 74 74
FER -0.06 0.24 -9999 0 -0.76 67 67
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.085 0.21 -9999 0 -0.67 91 91
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.065 0.3 -9999 0 -0.89 78 78
cytokine secretion -0.028 0.049 -9999 0 -10000 0 0
SPHK1 -0.099 0.28 -9999 0 -0.76 96 96
PTK2 -0.057 0.24 -9999 0 -0.74 64 64
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.26 -9999 0 -0.83 85 85
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.056 0.26 -9999 0 -0.73 80 80
MAP2K2 0.031 0.041 -9999 0 -0.54 3 3
MAP2K1 0.033 0.024 -9999 0 -10000 0 0
MAP2K7 0.014 0.041 -9999 0 -0.85 2 2
KLRG1/SHP2 -0.095 0.22 -9999 0 -0.71 72 72
MAP2K4 0.021 0.055 -9999 0 -1.1 2 2
Fc epsilon R1/FcgammaRIIB -0.2 0.36 -9999 0 -0.76 198 198
mol:Choline -0.095 0.28 -9999 0 -0.66 119 119
SHC/Grb2/SOS1 -0.089 0.2 -9999 0 -0.75 54 54
FYN 0.007 0.086 -9999 0 -0.85 9 9
DOK1 0.01 0.071 -9999 0 -0.85 6 6
PXN -0.041 0.21 -9999 0 -0.68 59 59
HCLS1 -0.074 0.29 -9999 0 -0.84 77 77
PRKCB -0.043 0.22 -9999 0 -0.56 88 88
FCGR2B -0.08 0.26 -9999 0 -0.79 106 106
IGHE -0.002 0.009 -9999 0 -10000 0 0
KLRG1/SHIP -0.055 0.24 -9999 0 -0.73 72 72
LCP2 -0.029 0.19 -9999 0 -0.85 46 46
PLA2G4A -0.081 0.27 -9999 0 -0.77 85 85
RASA1 0.013 0.05 -9999 0 -0.85 3 3
mol:Phosphatidic acid -0.095 0.28 -9999 0 -0.66 119 119
IKK complex 0.01 0.12 -9999 0 -0.29 41 41
WIPF1 0.016 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.032 0.21 0.28 1 -0.53 109 110
ACTA1 -0.063 0.27 0.3 5 -0.71 109 114
NUMA1 -0.032 0.21 0.28 1 -0.53 108 109
SPTAN1 -0.055 0.27 -10000 0 -0.71 107 107
LIMK1 -0.058 0.27 0.32 1 -0.7 110 111
BIRC3 -0.066 0.25 -10000 0 -0.81 89 89
BIRC2 0.016 0 -10000 0 -10000 0 0
BAX 0.014 0.041 -10000 0 -0.85 2 2
CASP10 -0.085 0.3 -10000 0 -0.69 150 150
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.016 0 -10000 0 -10000 0 0
PTK2 -0.032 0.21 0.28 1 -0.53 108 109
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.053 0.26 -10000 0 -0.69 107 107
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.056 0.27 0.32 1 -0.72 107 108
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.1 0.26 -10000 0 -0.78 81 81
BID -0.022 0.13 -10000 0 -0.32 116 116
MAP3K1 -0.003 0.082 -10000 0 -0.23 41 41
TRADD 0.015 0.029 -10000 0 -0.85 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.001 0.023 -10000 0 -0.65 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.065 0.3 0.32 1 -0.76 111 112
CASP9 0.016 0 -10000 0 -10000 0 0
DNA repair -0.009 0.076 -10000 0 -0.24 44 44
neuron apoptosis 0.021 0.046 -10000 0 -0.58 3 3
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.045 0.26 -10000 0 -0.68 107 107
APAF1 0.015 0.029 -10000 0 -0.85 1 1
CASP6 -0.001 0.13 -10000 0 -0.54 22 22
TRAF2 0.014 0.041 -10000 0 -0.85 2 2
ICAD/CAD -0.045 0.26 -10000 0 -0.68 107 107
CASP7 0.025 0.11 0.34 89 -10000 0 89
KRT18 0.012 0.042 -10000 0 -0.42 2 2
apoptosis -0.052 0.24 0.31 1 -0.61 110 111
DFFA -0.055 0.27 0.32 1 -0.71 107 108
DFFB -0.055 0.27 -10000 0 -0.71 107 107
PARP1 0.009 0.076 0.24 43 -10000 0 43
actin filament polymerization 0.043 0.25 0.64 110 -10000 0 110
TNF -0.062 0.23 -10000 0 -0.75 90 90
CYCS -0.018 0.1 -10000 0 -0.29 57 57
SATB1 0.005 0.13 -10000 0 -0.51 26 26
SLK -0.057 0.27 0.32 1 -0.7 109 110
p15 BID/BAX -0.013 0.12 -10000 0 -0.37 43 43
CASP2 0.016 0.12 -10000 0 -0.5 18 18
JNK cascade 0.003 0.082 0.23 41 -10000 0 41
CASP3 -0.068 0.28 0.32 6 -0.75 109 115
LMNB2 0.019 0.095 -10000 0 -0.42 18 18
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.011 0.065 -10000 0 -0.85 5 5
Mammalian IAPs/DIABLO -0.048 0.14 -10000 0 -0.51 70 70
negative regulation of DNA binding -0.099 0.25 -10000 0 -0.76 82 82
stress fiber formation -0.054 0.26 0.32 1 -0.69 109 110
GZMB -0.1 0.32 -10000 0 -0.77 146 146
CASP1 -0.001 0.12 -10000 0 -0.57 34 34
LMNB1 0.016 0.1 -10000 0 -0.45 24 24
APP 0.021 0.046 -10000 0 -0.59 3 3
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.023 -10000 0 -0.66 1 1
VIM -0.056 0.23 0.31 1 -0.6 108 109
LMNA 0.019 0.1 -10000 0 -0.46 18 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.12 -10000 0 -0.54 18 18
LRDD 0.011 0.066 -10000 0 -0.78 6 6
SREBF1 -0.057 0.27 -10000 0 -0.71 109 109
APAF-1/Caspase 9 0.001 0.052 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.031 0.2 0.28 1 -0.52 109 110
CFL2 -0.046 0.26 -10000 0 -0.66 110 110
GAS2 -0.1 0.28 -10000 0 -0.72 117 117
positive regulation of apoptosis 0.021 0.1 -10000 0 -0.41 22 22
PRF1 -0.048 0.22 -10000 0 -0.81 69 69
Glucocorticoid receptor regulatory network

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
PCK2 -0.002 0.11 0.46 1 -1 4 5
SMARCC2 0.016 0.014 -10000 0 -10000 0 0
SMARCC1 0.016 0.014 -10000 0 -10000 0 0
TBX21 -0.074 0.33 -10000 0 -1.1 67 67
SUMO2 0.014 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.019 0.076 -10000 0 -0.72 9 9
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 -0.066 0.24 -10000 0 -0.74 96 96
GR alpha/HSP90/FKBP51/HSP90 0.002 0.19 0.36 19 -0.51 68 87
PRL -0.014 0.13 -10000 0 -0.74 3 3
cortisol/GR alpha (dimer)/TIF2 0.067 0.31 0.59 104 -0.58 27 131
RELA -0.056 0.1 -10000 0 -10000 0 0
FGG -0.15 0.43 0.56 36 -0.73 247 283
GR beta/TIF2 0.01 0.2 0.38 34 -0.6 61 95
IFNG -0.28 0.41 -10000 0 -0.96 151 151
apoptosis -0.04 0.18 0.62 12 -0.66 14 26
CREB1 0.008 0.046 -10000 0 -10000 0 0
histone acetylation 0.008 0.16 0.41 8 -0.51 40 48
BGLAP 0.002 0.14 -10000 0 -0.69 7 7
GR/PKAc 0.06 0.11 0.37 10 -0.54 1 11
NF kappa B1 p50/RelA -0.1 0.2 -10000 0 -0.54 46 46
SMARCD1 0.016 0.014 -10000 0 -10000 0 0
MDM2 0.045 0.097 0.32 31 -10000 0 31
GATA3 -0.11 0.29 -10000 0 -0.72 159 159
AKT1 0.001 0.033 -10000 0 -0.86 1 1
CSF2 -0.02 0.14 -10000 0 -0.69 7 7
GSK3B 0.014 0.01 -10000 0 -10000 0 0
NR1I3 -0.006 0.18 0.62 10 -0.79 8 18
CSN2 0.046 0.2 0.48 18 -0.56 2 20
BRG1/BAF155/BAF170/BAF60A 0.037 0.053 -10000 0 -0.51 1 1
NFATC1 0.006 0.1 -10000 0 -0.85 13 13
POU2F1 0.014 0.053 -10000 0 -0.85 3 3
CDKN1A 0.034 0.15 -10000 0 -1.7 6 6
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.008 -10000 0 -10000 0 0
SFN -0.23 0.35 -10000 0 -0.72 299 299
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.14 0.28 0.36 7 -0.66 98 105
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.048 0.28 0.6 10 -0.93 50 60
JUN -0.16 0.22 -10000 0 -0.63 71 71
IL4 -0.023 0.16 -10000 0 -0.6 27 27
CDK5R1 0.012 0.049 -10000 0 -0.7 4 4
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.3 0.29 4 -0.69 200 204
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.014 0.18 0.36 19 -0.5 37 56
cortisol/GR alpha (monomer) 0.12 0.34 0.68 129 -0.58 5 134
NCOA2 -0.039 0.21 -10000 0 -0.85 57 57
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.15 0.27 -10000 0 -0.81 120 120
AP-1/NFAT1-c-4 -0.36 0.38 -10000 0 -0.85 239 239
AFP -0.13 0.24 -10000 0 -0.8 48 48
SUV420H1 0.015 0.022 -10000 0 -0.65 1 1
IRF1 0.079 0.16 0.53 19 -0.6 1 20
TP53 0.039 0.058 -10000 0 -0.52 9 9
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.39 0.54 -10000 0 -1.1 261 261
KRT14 -0.11 0.26 -10000 0 -0.77 79 79
TBP 0.028 0.013 -10000 0 -10000 0 0
CREBBP 0.035 0.078 0.36 3 -10000 0 3
HDAC1 0.012 0.01 -10000 0 -10000 0 0
HDAC2 0.016 0.007 -10000 0 -10000 0 0
AP-1 -0.36 0.38 -10000 0 -0.85 243 243
MAPK14 0.014 0.009 -10000 0 -10000 0 0
MAPK10 -0.008 0.13 -10000 0 -0.85 22 22
MAPK11 -0.001 0.11 -10000 0 -0.83 15 15
KRT5 -0.3 0.43 -10000 0 -0.95 196 196
interleukin-1 receptor activity 0 0.007 -10000 0 -10000 0 0
NCOA1 0.019 0.008 -10000 0 -10000 0 0
STAT1 0.019 0.076 -10000 0 -0.73 9 9
CGA -0.041 0.19 -10000 0 -0.73 31 31
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.038 0.14 0.43 24 -0.44 1 25
MAPK3 0.013 0.03 -10000 0 -0.85 1 1
MAPK1 0.013 0.03 -10000 0 -0.85 1 1
ICAM1 -0.16 0.41 -10000 0 -1.3 68 68
NFKB1 -0.057 0.11 -10000 0 -0.96 1 1
MAPK8 -0.11 0.2 -10000 0 -0.56 74 74
MAPK9 0.014 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.045 0.18 0.62 12 -0.7 14 26
BAX 0.04 0.091 -10000 0 -1.7 2 2
POMC -0.12 0.32 -10000 0 -1.2 34 34
EP300 0.033 0.087 0.4 1 -0.79 2 3
cortisol/GR alpha (dimer)/p53 0.12 0.28 0.6 119 -0.73 2 121
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.076 0.26 6 -10000 0 6
SGK1 0.043 0.28 -10000 0 -1.6 23 23
IL13 -0.21 0.31 -10000 0 -0.83 117 117
IL6 -0.3 0.53 -10000 0 -1.1 200 200
PRKACG 0.002 0.032 -10000 0 -0.65 2 2
IL5 -0.18 0.25 -10000 0 -0.84 56 56
IL2 -0.19 0.25 -10000 0 -0.71 79 79
CDK5 0.014 0.029 -10000 0 -0.84 1 1
PRKACB 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.22 0.45 -10000 0 -1 162 162
CDK5R1/CDK5 -0.001 0.043 -10000 0 -0.55 5 5
NF kappa B1 p50/RelA/PKAc -0.047 0.15 -10000 0 -0.59 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.12 0.26 0.58 101 -0.55 2 103
SMARCA4 0.015 0.032 -10000 0 -0.85 1 1
chromatin remodeling 0.084 0.16 0.43 49 -0.5 2 51
NF kappa B1 p50/RelA/Cbp -0.039 0.19 0.45 1 -0.69 12 13
JUN (dimer) -0.16 0.22 -10000 0 -0.63 71 71
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.078 0.29 -10000 0 -0.77 106 106
NR3C1 0.07 0.2 0.52 63 -0.75 4 67
NR4A1 -0.12 0.3 -10000 0 -0.73 166 166
TIF2/SUV420H1 -0.042 0.16 -10000 0 -0.65 58 58
MAPKKK cascade -0.04 0.18 0.62 12 -0.66 14 26
cortisol/GR alpha (dimer)/Src-1 0.12 0.28 0.59 119 -0.64 2 121
PBX1 0.005 0.1 -10000 0 -0.85 13 13
POU1F1 0.007 0.018 -10000 0 -10000 0 0
SELE -0.31 0.57 -10000 0 -1.3 196 196
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.084 0.16 0.43 49 -0.51 2 51
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.12 0.26 0.58 101 -0.55 2 103
mol:cortisol 0.054 0.2 0.41 119 -0.27 11 130
MMP1 -0.45 0.64 -10000 0 -1.3 267 267
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.023 0.19 -9999 0 -0.59 87 87
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.014 0.041 -9999 0 -0.85 2 2
ITGA4 -0.064 0.25 -9999 0 -0.84 83 83
alpha4/beta7 Integrin/MAdCAM1 -0.073 0.18 -9999 0 -0.56 88 88
EPO -0.22 0.34 -9999 0 -0.7 285 285
alpha4/beta7 Integrin -0.066 0.2 -9999 0 -0.66 89 89
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.022 -9999 0 -0.65 1 1
alpha4/beta1 Integrin -0.06 0.19 -9999 0 -0.65 83 83
EPO/EPOR (dimer) -0.17 0.25 -9999 0 -0.52 287 287
lamellipodium assembly 0.001 0.057 -9999 0 -0.49 10 10
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
PI3K -0.008 0.072 -9999 0 -0.62 12 12
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.098 0.19 -9999 0 -0.51 40 40
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
MADCAM1 -0.026 0.16 -9999 0 -0.65 53 53
cell adhesion -0.073 0.18 -9999 0 -0.56 88 88
CRKL/CBL -0.001 0.022 -9999 0 -0.65 1 1
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC -0.083 0.26 -9999 0 -0.58 177 177
ITGB7 0.008 0.082 -9999 0 -0.85 8 8
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.13 0.27 -9999 0 -0.64 177 177
p130Cas/Crk/Dock1 -0.047 0.24 -9999 0 -0.84 30 30
VCAM1 -0.1 0.3 -9999 0 -0.85 123 123
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.048 0.15 -9999 0 -0.52 82 82
BCAR1 -0.069 0.25 -9999 0 -0.54 180 180
EPOR 0.013 0.048 -9999 0 -0.7 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.015 0.029 -9999 0 -0.85 1 1
GIT1 0.014 0.041 -9999 0 -0.85 2 2
Rac1/GTP 0.001 0.059 -9999 0 -0.51 10 10
S1P3 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
PDGFRB -0.12 0.31 -9999 0 -0.84 140 140
mol:S1P 0.002 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.011 0.096 -9999 0 -0.35 23 23
GNAO1 -0.051 0.22 -9999 0 -0.75 79 79
S1P/S1P3/G12/G13 -0.061 0.16 -9999 0 -0.52 92 92
AKT1 -0.13 0.3 -9999 0 -0.78 134 134
AKT3 -0.11 0.31 -9999 0 -0.78 113 113
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.12 0.31 -9999 0 -0.84 140 140
GNAI2 0.017 0.029 -9999 0 -0.85 1 1
GNAI3 0.018 0.002 -9999 0 -10000 0 0
GNAI1 0.006 0.1 -9999 0 -0.85 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.084 0.28 -9999 0 -0.82 109 109
S1PR2 0.012 0.056 -9999 0 -0.73 5 5
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.03 0.2 -9999 0 -0.84 32 32
MAPK3 -0.02 0.2 -9999 0 -0.82 31 31
MAPK1 -0.02 0.2 -9999 0 -0.82 31 31
JAK2 -0.03 0.22 -9999 0 -0.75 50 50
CXCR4 -0.051 0.26 -9999 0 -0.76 74 74
FLT1 -0.21 0.38 -9999 0 -0.84 240 240
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC -0.019 0.2 -9999 0 -0.82 31 31
S1P/S1P3/Gi -0.031 0.21 -9999 0 -0.85 32 32
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.068 0.17 -9999 0 -0.8 30 30
VEGFA -0.21 0.38 -9999 0 -0.84 236 236
S1P/S1P2/Gi 0.014 0.11 -9999 0 -0.39 25 25
VEGFR1 homodimer/VEGFA homodimer -0.3 0.51 -9999 0 -1 272 272
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.072 0.25 -9999 0 -0.52 164 164
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.009 0.085 -9999 0 -0.79 10 10
G12/G13 -0.001 0.016 -9999 0 -0.48 1 1
GNA14 -0.078 0.27 -9999 0 -0.84 97 97
GNA15 -0.014 0.16 -9999 0 -0.81 33 33
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.022 -9999 0 -0.65 1 1
GNA11 -0.011 0.14 -9999 0 -0.75 31 31
Rac1/GTP -0.068 0.17 -9999 0 -0.8 30 30
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.008 0.082 -9999 0 -0.85 8 8
ITGA4 -0.064 0.25 -9999 0 -0.84 83 83
alpha4/beta7 Integrin -0.066 0.2 -9999 0 -0.66 89 89
alpha4/beta1 Integrin -0.06 0.19 -9999 0 -0.65 83 83
Ephrin B reverse signaling

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.02 0.17 -10000 0 -0.85 37 37
EPHB2 -0.025 0.17 -10000 0 -0.72 50 50
EFNB1 -0.065 0.22 -10000 0 -0.58 136 136
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.22 -10000 0 -0.81 40 40
Ephrin B2/EPHB1-2 -0.087 0.2 -10000 0 -0.48 161 161
neuron projection morphogenesis -0.11 0.21 -10000 0 -0.76 40 40
Ephrin B1/EPHB1-2/Tiam1 -0.12 0.24 -10000 0 -0.69 78 78
DNM1 -0.1 0.28 -10000 0 -0.77 136 136
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 0.003 0.14 -10000 0 -0.86 23 23
YES1 -0.027 0.18 -10000 0 -1.1 23 23
Ephrin B1/EPHB1-2/NCK2 -0.12 0.23 -10000 0 -0.58 124 124
PI3K -0.004 0.16 -10000 0 -0.81 31 31
mol:GDP -0.13 0.24 -10000 0 -0.59 129 129
ITGA2B -0.058 0.22 -10000 0 -0.73 88 88
endothelial cell proliferation -0.028 0.12 -10000 0 -0.57 44 44
FYN -0.029 0.18 -10000 0 -1.1 23 23
MAP3K7 -0.024 0.15 -10000 0 -0.91 23 23
FGR -0.032 0.18 -10000 0 -1.1 23 23
TIAM1 0.005 0.098 -10000 0 -0.83 12 12
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
RGS3 0.015 0.032 -10000 0 -0.65 2 2
cell adhesion -0.058 0.23 -10000 0 -0.66 78 78
LYN -0.028 0.18 -10000 0 -1.1 23 23
Ephrin B1/EPHB1-2/Src Family Kinases -0.028 0.17 -10000 0 -1 23 23
Ephrin B1/EPHB1-2 -0.031 0.16 -10000 0 -0.98 23 23
SRC -0.027 0.18 -10000 0 -1.1 23 23
ITGB3 -0.046 0.21 -10000 0 -0.76 71 71
EPHB1 -0.06 0.22 -10000 0 -0.71 93 93
EPHB4 0.009 0.076 -10000 0 -0.85 7 7
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.028 0.12 -10000 0 -0.58 44 44
alphaIIb/beta3 Integrin -0.099 0.23 -10000 0 -0.6 147 147
BLK -0.043 0.18 -10000 0 -1.1 23 23
HCK -0.031 0.18 -10000 0 -1.1 23 23
regulation of stress fiber formation 0.12 0.22 0.57 124 -10000 0 124
MAPK8 0.006 0.15 -10000 0 -0.72 33 33
Ephrin B1/EPHB1-2/RGS3 -0.12 0.23 -10000 0 -0.58 126 126
endothelial cell migration -0.042 0.17 -10000 0 -0.61 65 65
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 -0.015 0.16 -10000 0 -0.96 24 24
regulation of focal adhesion formation 0.12 0.22 0.57 124 -10000 0 124
chemotaxis 0.12 0.22 0.57 126 -10000 0 126
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
Rac1/GTP -0.12 0.22 -10000 0 -0.8 40 40
angiogenesis -0.03 0.16 -10000 0 -0.97 23 23
LCK -0.045 0.19 -10000 0 -1.1 23 23
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.052 0.21 -10000 0 -0.64 67 67
CRKL -0.029 0.16 -10000 0 -0.48 57 57
HRAS -0.038 0.22 -10000 0 -0.68 65 65
mol:PIP3 -0.046 0.15 -10000 0 -0.46 62 62
SPRED1 0.013 0.05 -10000 0 -0.85 3 3
SPRED2 0.014 0.041 -10000 0 -0.85 2 2
GAB1 -0.04 0.16 -10000 0 -0.5 60 60
FOXO3 -0.019 0.14 -10000 0 -0.52 19 19
AKT1 -0.031 0.15 -10000 0 -0.46 56 56
BAD -0.021 0.14 -10000 0 -0.42 60 60
megakaryocyte differentiation -0.074 0.22 -10000 0 -0.59 114 114
GSK3B -0.019 0.14 -10000 0 -0.42 52 52
RAF1 -0.015 0.18 -10000 0 -0.52 57 57
SHC1 0.015 0.022 -10000 0 -0.65 1 1
STAT3 -0.039 0.16 -10000 0 -0.5 55 55
STAT1 -0.098 0.32 -10000 0 -1.1 57 57
HRAS/SPRED1 -0.06 0.16 -10000 0 -0.51 65 65
cell proliferation -0.044 0.17 -10000 0 -0.49 67 67
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.038 0.16 -10000 0 -0.47 68 68
HRAS/SPRED2 -0.06 0.16 -10000 0 -0.51 64 64
LYN/TEC/p62DOK -0.058 0.15 -10000 0 -0.72 18 18
MAPK3 0.008 0.13 -10000 0 -0.38 34 34
STAP1 -0.11 0.25 -10000 0 -0.57 168 168
GRAP2 -0.039 0.21 -10000 0 -0.85 57 57
JAK2 -0.13 0.26 -10000 0 -0.93 60 60
STAT1 (dimer) -0.095 0.32 -10000 0 -1.1 57 57
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.1 0.22 -10000 0 -0.7 73 73
actin filament polymerization -0.047 0.18 -10000 0 -0.53 71 71
LYN 0.012 0.058 -10000 0 -0.85 4 4
STAP1/STAT5A (dimer) -0.11 0.28 -10000 0 -0.67 148 148
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
CBL/CRKL/GRB2 -0.046 0.12 -10000 0 -0.61 12 12
PI3K -0.025 0.16 -10000 0 -0.48 64 64
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.19 0.41 -10000 0 -1.3 73 73
MAPK8 -0.045 0.17 -10000 0 -0.5 67 67
STAT3 (dimer) -0.038 0.16 -10000 0 -0.49 55 55
positive regulation of transcription 0.013 0.11 -10000 0 -0.32 14 14
mol:GDP -0.1 0.22 -10000 0 -0.72 74 74
PIK3C2B -0.042 0.17 -10000 0 -0.52 60 60
CBL/CRKL -0.018 0.15 -10000 0 -0.62 13 13
FER -0.041 0.16 -10000 0 -0.5 59 59
SH2B3 -0.04 0.16 -10000 0 -0.51 57 57
PDPK1 -0.035 0.14 -10000 0 -0.43 62 62
SNAI2 -0.1 0.24 -10000 0 -0.57 139 139
positive regulation of cell proliferation -0.066 0.25 -10000 0 -0.79 61 61
KITLG -0.029 0.18 -10000 0 -0.73 54 54
cell motility -0.066 0.25 -10000 0 -0.79 61 61
PTPN6 0.01 0.042 -10000 0 -0.84 2 2
EPOR 0.007 0.12 -10000 0 -1 3 3
STAT5A (dimer) -0.054 0.21 -10000 0 -0.66 61 61
SOCS1 -0.038 0.19 -10000 0 -0.7 68 68
cell migration 0.069 0.21 0.56 99 -10000 0 99
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.22 0.33 -10000 0 -0.7 285 285
VAV1 -0.026 0.18 -10000 0 -0.83 44 44
GRB10 -0.04 0.16 -10000 0 -0.5 60 60
PTPN11 0.016 0.029 -10000 0 -0.84 1 1
SCF/KIT -0.052 0.17 -10000 0 -0.5 70 70
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 0.003 0.14 -10000 0 -0.42 31 31
CBL 0.015 0.029 -10000 0 -0.85 1 1
KIT -0.1 0.39 -10000 0 -1.5 53 53
MAP2K2 0.002 0.14 -10000 0 -0.42 41 41
SHC/Grb2/SOS1 -0.053 0.14 -10000 0 -0.65 12 12
STAT5A -0.056 0.22 -10000 0 -0.68 61 61
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation -0.097 0.23 -10000 0 -0.55 139 139
SHC/GRAP2 -0.042 0.16 -10000 0 -0.65 58 58
PTPRO -0.076 0.23 -10000 0 -0.61 114 114
SH2B2 -0.048 0.18 -10000 0 -0.54 71 71
DOK1 0.01 0.071 -10000 0 -0.85 6 6
MATK -0.071 0.21 -10000 0 -0.57 99 99
CREBBP 0.038 0.018 -10000 0 -10000 0 0
BCL2 -0.008 0.21 -10000 0 -1.5 14 14
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.048 0.16 -9999 0 -0.51 84 84
E-cadherin/beta catenin -0.052 0.17 -9999 0 -0.57 80 80
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.009 0.076 -9999 0 -0.85 7 7
CDH1 -0.054 0.22 -9999 0 -0.76 80 80
FOXM1 transcription factor network

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
NFATC3 0.15 0.48 -10000 0 -1.2 57 57
PLK1 0.048 0.2 -10000 0 -1.7 6 6
BIRC5 0.01 0.31 -10000 0 -0.94 68 68
HSPA1B 0.15 0.49 -10000 0 -1.2 57 57
MAP2K1 0.06 0.046 -10000 0 -10000 0 0
BRCA2 0.13 0.53 -10000 0 -1.3 77 77
FOXM1 0.11 0.62 -10000 0 -1.6 71 71
XRCC1 0.15 0.48 -10000 0 -1.2 56 56
FOXM1B/p19 -0.16 0.37 0.48 5 -1.2 81 86
Cyclin D1/CDK4 0.1 0.5 -10000 0 -1.1 77 77
CDC2 0.15 0.51 -10000 0 -1.2 66 66
TGFA 0.078 0.55 -10000 0 -1.1 103 103
SKP2 0.15 0.49 -10000 0 -1.2 58 58
CCNE1 0.008 0.11 -10000 0 -0.67 21 21
CKS1B 0.15 0.48 -10000 0 -1.2 56 56
RB1 -0.071 0.16 -10000 0 -0.79 19 19
FOXM1C/SP1 0.12 0.54 -10000 0 -1.3 68 68
AURKB 0.023 0.28 -10000 0 -1.7 17 17
CENPF 0.14 0.52 -10000 0 -1.3 67 67
CDK4 0.031 0.021 -10000 0 -10000 0 0
MYC 0.14 0.48 -10000 0 -1.1 76 76
CHEK2 0.053 0.093 -10000 0 -0.86 7 7
ONECUT1 0.11 0.5 -10000 0 -1.1 69 69
CDKN2A -0.052 0.21 -10000 0 -0.81 63 63
LAMA4 0.075 0.61 -10000 0 -1.3 125 125
FOXM1B/HNF6 0.085 0.6 -10000 0 -1.5 73 73
FOS 0.085 0.58 -10000 0 -1.3 95 95
SP1 0.017 0.004 -10000 0 -10000 0 0
CDC25B 0.15 0.48 -10000 0 -1.2 56 56
response to radiation 0.037 0.044 -10000 0 -10000 0 0
CENPB 0.15 0.48 -10000 0 -1.2 57 57
CENPA 0.14 0.51 -10000 0 -1.3 61 61
NEK2 0.13 0.52 -10000 0 -1.3 70 70
HIST1H2BA 0.15 0.48 -10000 0 -1.2 57 57
CCNA2 0.014 0.087 -10000 0 -0.69 13 13
EP300 0.014 0.041 -10000 0 -0.85 2 2
CCNB1/CDK1 0.13 0.55 -10000 0 -1.4 58 58
CCNB2 0.14 0.51 -10000 0 -1.2 63 63
CCNB1 0.15 0.51 -10000 0 -1.3 58 58
ETV5 0.15 0.48 -10000 0 -1.2 55 55
ESR1 0.11 0.56 -10000 0 -1.3 94 94
CCND1 0.11 0.52 -10000 0 -1.1 80 80
GSK3A 0.055 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.054 0.12 -10000 0 -0.72 8 8
CDK2 0.024 0.012 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.043 0.051 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.15 0.36 -10000 0 -1.2 71 71
GAS1 0.14 0.51 -10000 0 -1.2 63 63
MMP2 0.13 0.53 -10000 0 -1.2 74 74
RB1/FOXM1C 0.12 0.51 -10000 0 -1.2 67 67
CREBBP 0.016 0 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.014 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.087 0.2 -10000 0 -0.54 139 139
regulation of S phase of mitotic cell cycle -0.015 0.14 -10000 0 -0.53 21 21
GNAO1 -0.053 0.22 -10000 0 -0.76 79 79
HRAS 0.011 0.059 -10000 0 -0.77 5 5
SHBG/T-DHT -0.042 0.14 -10000 0 -0.48 78 78
PELP1 0.016 0.001 -10000 0 -10000 0 0
AKT1 0.014 0.023 -10000 0 -0.66 1 1
MAP2K1 -0.013 0.16 -10000 0 -0.56 16 16
T-DHT/AR -0.086 0.22 -10000 0 -0.64 120 120
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 114 114
GNAI2 0.015 0.029 -10000 0 -0.85 1 1
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.004 0.1 -10000 0 -0.85 12 12
mol:GDP -0.085 0.22 -10000 0 -0.67 104 104
cell proliferation -0.016 0.2 -10000 0 -0.67 24 24
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
FOS -0.045 0.26 -10000 0 -0.85 63 63
mol:Ca2+ -0.014 0.028 -10000 0 -0.1 36 36
MAPK3 -0.014 0.18 -10000 0 -0.62 24 24
MAPK1 0.001 0.096 -10000 0 -0.33 18 18
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
mol:IP3 0 0.002 -10000 0 -0.004 120 120
cAMP biosynthetic process -0.027 0.14 -10000 0 -0.45 78 78
GNG2 -0.016 0.16 -10000 0 -0.85 33 33
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 120 120
HRAS/GTP -0.065 0.16 -10000 0 -0.48 106 106
actin cytoskeleton reorganization -0.006 0.05 -10000 0 -0.46 10 10
SRC 0.015 0.022 -10000 0 -0.65 1 1
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 120 120
PI3K -0.007 0.063 -10000 0 -0.55 12 12
apoptosis 0.011 0.16 0.45 62 -10000 0 62
T-DHT/AR/PELP1 -0.073 0.19 -10000 0 -0.55 120 120
HRAS/GDP -0.081 0.21 -10000 0 -0.63 107 107
CREB1 -0.015 0.18 -10000 0 -0.49 62 62
RAC1-CDC42/GTP -0.006 0.051 -10000 0 -0.47 10 10
AR -0.097 0.29 -10000 0 -0.82 120 120
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 -0.022 0.17 -10000 0 -0.56 18 18
RAC1-CDC42/GDP -0.076 0.2 -10000 0 -0.6 104 104
T-DHT/AR/PELP1/Src -0.067 0.18 -10000 0 -0.53 104 104
MAP2K2 -0.015 0.17 -10000 0 -0.61 18 18
T-DHT/AR/PELP1/Src/PI3K -0.016 0.14 -10000 0 -0.54 21 21
GNAZ 0.007 0.085 -10000 0 -0.79 10 10
SHBG -0.049 0.21 -10000 0 -0.72 78 78
Gi family/GNB1/GNG2/GDP -0.006 0.16 -10000 0 -0.56 45 45
mol:T-DHT 0 0.001 0.002 1 -0.003 100 101
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.016 0.14 -10000 0 -0.61 43 43
Gi family/GTP -0.053 0.11 -10000 0 -0.51 22 22
CDC42 0.016 0 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.12 0.23 -10000 0 -0.53 206 206
cell-cell adhesion 0.1 0.19 0.7 45 -10000 0 45
Ephrin B/EPHB2/RasGAP -0.091 0.2 -10000 0 -0.8 25 25
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
SHC1 0.015 0.022 -10000 0 -0.65 1 1
Ephrin B1/EPHB3 -0.057 0.17 -10000 0 -0.54 93 93
Ephrin B1/EPHB1 -0.049 0.14 -10000 0 -0.46 94 94
HRAS/GDP -0.09 0.18 -10000 0 -0.7 39 39
Ephrin B/EPHB1/GRB7 -0.12 0.22 -10000 0 -0.6 115 115
Endophilin/SYNJ1 -0.045 0.2 -10000 0 -0.71 26 26
KRAS 0.016 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.11 0.22 -10000 0 -0.6 100 100
endothelial cell migration -0.03 0.12 -10000 0 -0.49 53 53
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 -0.002 0.12 -10000 0 -0.76 21 21
PAK1 -0.043 0.21 -10000 0 -0.8 25 25
HRAS 0.012 0.059 -10000 0 -0.77 5 5
RRAS -0.047 0.2 -10000 0 -0.54 93 93
DNM1 -0.1 0.28 -10000 0 -0.76 136 136
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.064 0.22 -10000 0 -0.57 100 100
lamellipodium assembly -0.1 0.19 -10000 0 -0.7 45 45
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.024 0.16 -10000 0 -0.59 29 29
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
EPHB2 -0.025 0.17 -10000 0 -0.71 50 50
EPHB3 -0.069 0.25 -10000 0 -0.8 93 93
EPHB1 -0.06 0.22 -10000 0 -0.71 93 93
EPHB4 0.009 0.076 -10000 0 -0.85 7 7
mol:GDP -0.077 0.2 -10000 0 -0.6 70 70
Ephrin B/EPHB2 -0.091 0.2 -10000 0 -0.57 92 92
Ephrin B/EPHB3 -0.12 0.24 -10000 0 -0.62 130 130
JNK cascade -0.019 0.17 -10000 0 -0.53 51 51
Ephrin B/EPHB1 -0.11 0.22 -10000 0 -0.61 100 100
RAP1/GDP -0.063 0.16 -10000 0 -0.64 29 29
EFNB2 -0.02 0.17 -10000 0 -0.85 37 37
EFNB3 -0.075 0.24 -10000 0 -0.72 110 110
EFNB1 0.015 0.029 -10000 0 -0.85 1 1
Ephrin B2/EPHB1-2 -0.088 0.2 -10000 0 -0.48 161 161
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.11 0.2 -10000 0 -0.75 42 42
Rap1/GTP -0.1 0.19 -10000 0 -0.7 43 43
axon guidance -0.12 0.23 -10000 0 -0.53 206 206
MAPK3 -0.002 0.14 -10000 0 -0.64 15 15
MAPK1 -0.002 0.14 -10000 0 -0.64 15 15
Rac1/GDP -0.024 0.19 -10000 0 -0.58 50 50
actin cytoskeleton reorganization -0.076 0.14 -10000 0 -0.54 37 37
CDC42/GDP -0.024 0.19 -10000 0 -0.58 50 50
PI3K -0.03 0.12 -10000 0 -0.5 53 53
EFNA5 -0.13 0.32 -10000 0 -0.79 166 166
Ephrin B2/EPHB4 -0.028 0.12 -10000 0 -0.57 44 44
Ephrin B/EPHB2/Intersectin/N-WASP -0.019 0.15 -10000 0 -0.56 21 21
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.099 0.18 -10000 0 -0.68 45 45
PTK2 0.015 0.036 -10000 0 -10000 0 0
MAP4K4 -0.019 0.17 -10000 0 -0.53 51 51
SRC 0.015 0.022 -10000 0 -0.65 1 1
KALRN 0.004 0.1 -10000 0 -0.82 13 13
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.013 0.18 -10000 0 -0.55 41 41
MAP2K1 -0.012 0.15 -10000 0 -0.6 24 24
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.066 0.16 -10000 0 -0.56 51 51
cell migration -0.006 0.16 -10000 0 -0.62 24 24
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 -0.047 0.2 -10000 0 -0.79 21 21
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.12 0.24 -10000 0 -0.75 45 45
HRAS/GTP -0.11 0.2 -10000 0 -0.76 45 45
Ephrin B1/EPHB1-2 -0.067 0.16 -10000 0 -0.57 49 49
cell adhesion mediated by integrin 0.079 0.19 0.56 88 -10000 0 88
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.12 0.22 -10000 0 -0.83 42 42
RAC1-CDC42/GTP -0.14 0.23 -10000 0 -0.72 77 77
RASA1 0.013 0.05 -10000 0 -0.85 3 3
RAC1-CDC42/GDP -0.063 0.16 -10000 0 -0.64 29 29
ruffle organization -0.046 0.22 -10000 0 -0.72 46 46
NCK1 0.014 0.041 -10000 0 -0.85 2 2
receptor internalization -0.099 0.26 -10000 0 -0.76 67 67
Ephrin B/EPHB2/KALRN -0.096 0.2 -10000 0 -0.57 99 99
ROCK1 -0.024 0.16 -10000 0 -0.53 74 74
RAS family/GDP -0.075 0.14 -10000 0 -0.56 37 37
Rac1/GTP -0.11 0.21 -10000 0 -0.77 45 45
Ephrin B/EPHB1/Src/Paxillin -0.034 0.17 -10000 0 -0.64 29 29
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.063 0.18 -10000 0 -0.59 75 75
ER alpha/Gai/GDP/Gbeta gamma -0.018 0.22 -10000 0 -0.68 64 64
AKT1 -0.021 0.24 -10000 0 -0.95 54 54
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.023 0.25 -10000 0 -0.98 53 53
mol:Ca2+ -0.13 0.32 -10000 0 -0.61 230 230
IGF1R 0.013 0.05 -10000 0 -0.85 3 3
E2/ER alpha (dimer)/Striatin -0.057 0.18 -10000 0 -0.58 88 88
SHC1 0.015 0.022 -10000 0 -0.65 1 1
apoptosis 0.017 0.23 0.89 54 -10000 0 54
RhoA/GTP -0.029 0.1 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.061 0.18 -10000 0 -0.69 50 50
regulation of stress fiber formation -0.026 0.12 0.63 7 -10000 0 7
E2/ERA-ERB (dimer) -0.054 0.16 -10000 0 -0.52 91 91
KRAS 0.016 0 -10000 0 -10000 0 0
G13/GTP -0.033 0.13 -10000 0 -0.5 59 59
pseudopodium formation 0.026 0.12 -10000 0 -0.63 7 7
E2/ER alpha (dimer)/PELP1 -0.036 0.14 -10000 0 -0.55 58 58
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 -0.016 0.16 -10000 0 -0.85 33 33
GNAO1 -0.052 0.22 -10000 0 -0.76 79 79
HRAS 0.012 0.059 -10000 0 -0.77 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.031 0.22 -10000 0 -0.68 74 74
E2/ER beta (dimer) -0.021 0.1 -10000 0 -0.52 37 37
mol:GDP -0.048 0.15 -10000 0 -0.59 55 55
mol:NADP -0.031 0.22 -10000 0 -0.68 74 74
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
mol:IP3 -0.14 0.34 -10000 0 -0.66 230 230
IGF-1R heterotetramer 0.013 0.05 -10000 0 -0.85 3 3
PLCB1 -0.14 0.32 -10000 0 -0.64 227 227
PLCB2 -0.068 0.27 -10000 0 -0.67 126 126
IGF1 -0.058 0.22 -10000 0 -0.72 89 89
mol:L-citrulline -0.031 0.22 -10000 0 -0.68 74 74
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.056 0.19 -10000 0 -0.84 43 43
JNK cascade -0.021 0.1 -10000 0 -0.52 37 37
BCAR1 0.013 0.05 -10000 0 -0.85 3 3
ESR2 -0.013 0.14 -10000 0 -0.68 37 37
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 -0.038 0.21 -10000 0 -0.82 58 58
Gq family/GDP/Gbeta gamma -0.041 0.25 -10000 0 -0.85 61 61
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.023 0.093 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.06 0.18 -10000 0 -0.69 50 50
GNAZ 0.007 0.085 -10000 0 -0.79 10 10
E2/ER alpha (dimer) -0.041 0.16 -10000 0 -0.64 58 58
STRN -0.017 0.17 -10000 0 -0.85 34 34
GNAL -0.006 0.13 -10000 0 -0.72 27 27
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 -0.005 0.12 -10000 0 -0.48 51 51
GNAI2 0.015 0.029 -10000 0 -0.85 1 1
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.004 0.1 -10000 0 -0.85 12 12
HBEGF -0.049 0.23 -10000 0 -0.75 59 59
cAMP biosynthetic process -0.055 0.15 -10000 0 -0.43 114 114
SRC -0.006 0.2 -10000 0 -0.78 38 38
PI3K -0.008 0.072 -10000 0 -0.62 12 12
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.056 0.16 -10000 0 -0.61 53 53
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.07 0.17 -10000 0 -0.65 48 48
Gs family/GTP -0.056 0.15 -10000 0 -0.44 114 114
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.035 -10000 0 -0.52 3 3
vasodilation -0.027 0.21 -10000 0 -0.64 74 74
mol:DAG -0.14 0.34 -10000 0 -0.66 230 230
Gs family/GDP/Gbeta gamma -0.059 0.16 -10000 0 -0.57 55 55
MSN 0.025 0.14 -10000 0 -0.71 7 7
Gq family/GTP -0.1 0.23 -10000 0 -0.66 113 113
mol:PI-3-4-5-P3 -0.02 0.23 -10000 0 -0.91 54 54
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.027 0.21 0.64 74 -10000 0 74
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.044 0.14 -10000 0 -0.54 55 55
NOS3 -0.036 0.24 -10000 0 -0.74 74 74
GNA11 -0.011 0.14 -10000 0 -0.75 31 31
MAPKKK cascade -0.004 0.22 -10000 0 -0.74 58 58
E2/ER alpha (dimer)/PELP1/Src -0.064 0.19 -10000 0 -0.68 63 63
ruffle organization 0.026 0.12 -10000 0 -0.63 7 7
ROCK2 0.016 0.14 -10000 0 -0.81 5 5
GNA14 -0.078 0.27 -10000 0 -0.84 97 97
GNA15 -0.014 0.16 -10000 0 -0.81 33 33
GNA13 0.015 0.022 -10000 0 -0.65 1 1
MMP9 -0.08 0.26 -10000 0 -0.78 63 63
MMP2 -0.019 0.23 -10000 0 -0.8 46 46
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.067 0.16 -9999 0 -0.49 88 88
RGS9BP -0.041 0.2 -9999 0 -0.73 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.004 0.073 -9999 0 -0.65 11 11
mol:Na + -0.036 0.12 -9999 0 -0.42 77 77
mol:ADP 0.004 0.067 -9999 0 -0.48 16 16
GNAT2 0.014 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.12 0.23 -9999 0 -0.6 119 119
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.024 -9999 0 -0.41 3 3
GRK7 0.007 0.05 -9999 0 -0.65 5 5
CNGB3 -0.036 0.16 -9999 0 -0.65 57 57
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.049 0.17 -9999 0 -0.5 92 92
Cone PDE6 -0.11 0.2 -9999 0 -0.53 120 120
Cone Metarhodopsin II -0.007 0.051 -9999 0 -0.38 16 16
Na + (4 Units) -0.056 0.16 -9999 0 -0.5 89 89
GNAT2/GDP -0.11 0.2 -9999 0 -0.52 119 119
GNB5 0.015 0.029 -9999 0 -0.85 1 1
mol:GMP (4 units) 0.014 0.033 -9999 0 -0.37 6 6
Cone Transducin -0.071 0.17 -9999 0 -0.51 88 88
SLC24A2 -0.039 0.16 -9999 0 -0.65 57 57
GNB3/GNGT2 -0.09 0.21 -9999 0 -0.58 137 137
GNB3 -0.076 0.25 -9999 0 -0.73 108 108
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 -0.01 0.097 -9999 0 -0.65 20 20
ARR3 0.004 0.007 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.036 0.12 -9999 0 -0.42 77 77
mol:Pi -0.12 0.23 -9999 0 -0.6 119 119
Cone CNG Channel -0.031 0.099 -9999 0 -0.66 2 2
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.039 0.16 -9999 0 -0.65 57 57
RGS9 -0.12 0.3 -9999 0 -0.76 160 160
PDE6C 0.004 0.039 -9999 0 -0.65 3 3
GNGT2 -0.015 0.16 -9999 0 -0.84 32 32
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.039 -9999 0 -0.65 3 3
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.12 0.32 -9999 0 -0.9 103 103
MAP4K1 -0.049 0.22 -9999 0 -0.8 71 71
MAP3K8 0.012 0.059 -9999 0 -0.77 5 5
PRKCB -0.035 0.2 -9999 0 -0.83 54 54
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.025 0.25 -9999 0 -0.89 56 56
JUN -0.028 0.26 -9999 0 -0.91 63 63
MAP3K7 -0.024 0.25 -9999 0 -0.9 55 55
GRAP2 -0.039 0.21 -9999 0 -0.85 57 57
CRK 0.015 0.022 -9999 0 -0.65 1 1
MAP2K4 -0.014 0.24 -9999 0 -0.86 56 56
LAT -0.022 0.16 -9999 0 -0.72 46 46
LCP2 -0.028 0.19 -9999 0 -0.84 46 46
MAPK8 -0.037 0.27 -9999 0 -0.99 60 60
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.037 0.26 -9999 0 -0.96 55 55
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.11 0.3 -9999 0 -1.1 61 61
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.002 0.13 -10000 0 -0.83 20 20
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.064 0.22 0.83 36 -0.36 3 39
IL27/IL27R/JAK1 -0.12 0.29 -10000 0 -1.1 38 38
TBX21 -0.12 0.28 -10000 0 -0.7 113 113
IL12B -0.041 0.18 -10000 0 -0.68 67 67
IL12A -0.001 0.089 -10000 0 -0.59 19 19
IL6ST -0.082 0.27 -10000 0 -0.86 97 97
IL27RA/JAK1 -0.018 0.21 -10000 0 -1.5 18 18
IL27 -0.012 0.12 -10000 0 -0.66 28 28
TYK2 0.012 0.043 -10000 0 -0.87 2 2
T-helper cell lineage commitment -0.078 0.16 -10000 0 -0.94 6 6
T-helper 2 cell differentiation 0.064 0.22 0.83 36 -0.36 3 39
T cell proliferation during immune response 0.064 0.22 0.83 36 -0.36 3 39
MAPKKK cascade -0.064 0.22 0.36 3 -0.83 36 39
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.008 0.074 -10000 0 -0.72 9 9
IL12RB1 -0.04 0.2 -10000 0 -0.81 58 58
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.19 0.33 -10000 0 -0.71 158 158
IL27/IL27R/JAK2/TYK2 -0.066 0.23 -10000 0 -0.86 36 36
positive regulation of T cell mediated cytotoxicity -0.064 0.22 0.36 3 -0.83 36 39
STAT1 (dimer) -0.17 0.36 0.54 10 -0.99 88 98
JAK2 0.014 0.03 -10000 0 -0.85 1 1
JAK1 0.015 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.053 0.21 -10000 0 -0.85 31 31
T cell proliferation -0.17 0.29 -10000 0 -0.69 126 126
IL12/IL12R/TYK2/JAK2 -0.05 0.18 -10000 0 -0.74 26 26
IL17A -0.078 0.16 -10000 0 -0.94 6 6
mast cell activation 0.064 0.22 0.83 36 -0.36 3 39
IFNG -0.016 0.048 0.099 3 -0.1 163 166
T cell differentiation -0.007 0.009 0.022 4 -0.026 79 83
STAT3 (dimer) -0.053 0.21 -10000 0 -0.86 30 30
STAT5A (dimer) -0.054 0.22 -10000 0 -0.86 32 32
STAT4 (dimer) -0.09 0.28 -10000 0 -0.81 75 75
STAT4 -0.052 0.23 -10000 0 -0.84 71 71
T cell activation -0.009 0.021 0.13 19 -10000 0 19
IL27R/JAK2/TYK2 -0.087 0.26 -10000 0 -1.4 20 20
GATA3 -0.14 0.42 -10000 0 -1.6 60 60
IL18 -0.012 0.12 -10000 0 -0.55 42 42
positive regulation of mast cell cytokine production -0.051 0.2 -10000 0 -0.82 30 30
IL27/EBI3 -0.034 0.16 -10000 0 -0.62 61 61
IL27RA -0.029 0.23 -10000 0 -1.6 18 18
IL6 -0.19 0.34 -10000 0 -0.73 247 247
STAT5A 0.013 0.05 -10000 0 -0.85 3 3
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.008 0.089 0.51 18 -10000 0 18
IL1B -0.032 0.16 -10000 0 -0.61 65 65
EBI3 -0.025 0.17 -10000 0 -0.8 40 40
TNF -0.046 0.18 -10000 0 -0.58 90 90
Syndecan-2-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
Syndecan-2/Fibronectin -0.063 0.22 -9999 0 -0.54 147 147
EPHB2 -0.025 0.17 -9999 0 -0.71 50 50
Syndecan-2/TACI -0.015 0.13 -9999 0 -0.44 73 73
LAMA1 -0.059 0.24 -9999 0 -0.8 82 82
Syndecan-2/alpha2 ITGB1 -0.048 0.14 -9999 0 -0.55 38 38
HRAS 0.012 0.059 -9999 0 -0.77 5 5
Syndecan-2/CASK -0.01 0.072 -9999 0 -0.54 16 16
ITGA5 -0.009 0.14 -9999 0 -0.81 27 27
BAX 0.033 0.12 -9999 0 -1.3 3 3
EPB41 0.014 0.043 -9999 0 -0.72 3 3
positive regulation of cell-cell adhesion -0.009 0.065 -9999 0 -0.48 16 16
LAMA3 -0.039 0.19 -9999 0 -0.67 71 71
EZR 0.015 0.029 -9999 0 -0.85 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.001 0.11 -9999 0 -0.84 16 16
Syndecan-2/MMP2 -0.011 0.15 -9999 0 -0.51 69 69
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.017 0.1 -9999 0 -0.63 24 24
dendrite morphogenesis -0.006 0.14 -9999 0 -0.48 64 64
Syndecan-2/GM-CSF -0.004 0.093 -9999 0 -0.46 33 33
determination of left/right symmetry 0.014 0.086 -9999 0 -0.61 16 16
Syndecan-2/PKC delta -0.007 0.13 -9999 0 -0.45 70 70
GNB2L1 0.016 0 -9999 0 -10000 0 0
MAPK3 0.018 0.092 -9999 0 -0.56 12 12
MAPK1 0.018 0.089 -9999 0 -0.52 13 13
Syndecan-2/RACK1 -0.011 0.074 -9999 0 -0.54 14 14
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.086 -9999 0 -0.61 16 16
ITGA2 -0.007 0.14 -9999 0 -0.82 24 24
MAPK8 0.026 0.11 -9999 0 -0.56 27 27
Syndecan-2/alpha2/beta1 Integrin -0.061 0.17 -9999 0 -0.53 89 89
Syndecan-2/Kininogen -0.12 0.23 -9999 0 -0.47 244 244
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.036 0.078 -9999 0 -0.51 15 15
Syndecan-2/CASK/Protein 4.1 -0.01 0.07 -9999 0 -0.48 19 19
extracellular matrix organization 0.008 0.12 -9999 0 -0.58 33 33
actin cytoskeleton reorganization -0.063 0.22 -9999 0 -0.53 147 147
Syndecan-2/Caveolin-2/Ras -0.02 0.11 -9999 0 -0.57 28 28
Syndecan-2/Laminin alpha3 -0.015 0.14 -9999 0 -0.45 85 85
Syndecan-2/RasGAP -0.012 0.077 -9999 0 -0.52 17 17
alpha5/beta1 Integrin -0.019 0.11 -9999 0 -0.62 27 27
PRKCD -0.027 0.16 -9999 0 -0.65 57 57
Syndecan-2 dimer -0.006 0.14 -9999 0 -0.48 64 64
GO:0007205 0.004 0.006 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.042 0.084 -9999 0 -0.73 4 4
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.032 0.16 -9999 0 -0.65 58 58
RASA1 0.013 0.05 -9999 0 -0.85 3 3
alpha2/beta1 Integrin -0.017 0.1 -9999 0 -0.63 24 24
Syndecan-2/Synbindin 0.021 0.075 -9999 0 -0.53 16 16
TGFB1 -0.003 0.12 -9999 0 -0.83 20 20
CASP3 0.007 0.12 -9999 0 -0.4 69 69
FN1 -0.11 0.29 -9999 0 -0.79 137 137
Syndecan-2/IL8 -0.065 0.2 -9999 0 -0.48 166 166
SDC2 0.014 0.086 -9999 0 -0.61 16 16
KNG1 -0.18 0.32 -9999 0 -0.71 238 238
Syndecan-2/Neurofibromin 0.021 0.075 -9999 0 -0.53 16 16
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.006 0.09 -9999 0 -0.65 17 17
Syndecan-2/TGFB1 0.008 0.12 -9999 0 -0.59 33 33
Syndecan-2/Syntenin/PI-4-5-P2 -0.009 0.065 -9999 0 -0.48 16 16
Syndecan-2/Ezrin -0.009 0.066 -9999 0 -0.52 13 13
PRKACA 0.032 0.069 -9999 0 -0.51 12 12
angiogenesis -0.064 0.2 -9999 0 -0.48 166 166
MMP2 -0.032 0.18 -9999 0 -0.73 57 57
IL8 -0.11 0.28 -9999 0 -0.72 154 154
calcineurin-NFAT signaling pathway -0.015 0.13 -9999 0 -0.44 73 73
LPA receptor mediated events

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.068 0.18 -9999 0 -0.58 86 86
NF kappa B1 p50/RelA/I kappa B alpha -0.041 0.1 -9999 0 -0.61 11 11
AP1 -0.11 0.21 -9999 0 -0.75 40 40
mol:PIP3 -0.067 0.15 -9999 0 -0.63 27 27
AKT1 0.017 0.15 -9999 0 -0.55 22 22
PTK2B 0 0.1 -9999 0 -0.44 19 19
RHOA 0.018 0.066 -9999 0 -0.43 5 5
PIK3CB 0.015 0.022 -9999 0 -0.65 1 1
mol:Ca2+ 0.01 0.12 -9999 0 -0.71 12 12
MAGI3 0.003 0.091 -9999 0 -0.65 17 17
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.02 0.14 -9999 0 -0.46 57 57
HRAS/GDP -0.003 0.045 -9999 0 -0.59 5 5
positive regulation of microtubule depolymerization -0.03 0.18 -9999 0 -0.47 100 100
NF kappa B1 p50/RelA -0.066 0.16 -9999 0 -0.69 30 30
endothelial cell migration -0.051 0.24 -9999 0 -0.68 104 104
ADCY4 -0.058 0.23 -9999 0 -0.66 91 91
ADCY5 -0.06 0.22 -9999 0 -0.64 86 86
ADCY6 -0.028 0.19 -9999 0 -0.6 67 67
ADCY7 -0.028 0.19 -9999 0 -0.6 67 67
ADCY1 -0.091 0.24 -9999 0 -0.68 95 95
ADCY2 -0.1 0.24 -9999 0 -0.66 101 101
ADCY3 -0.036 0.21 -9999 0 -0.66 72 72
ADCY8 -0.091 0.21 -9999 0 -0.63 82 82
ADCY9 -0.028 0.19 -9999 0 -0.6 67 67
GSK3B 0.01 0.1 -9999 0 -0.48 12 12
arachidonic acid secretion -0.029 0.2 -9999 0 -0.58 79 79
GNG2 -0.016 0.16 -9999 0 -0.85 33 33
TRIP6 0.019 0.083 -9999 0 -0.64 11 11
GNAO1 -0.068 0.22 -9999 0 -0.55 140 140
HRAS 0.012 0.059 -9999 0 -0.77 5 5
NFKBIA -0.001 0.14 -9999 0 -0.56 27 27
GAB1 0.014 0.041 -9999 0 -0.85 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.012 0.13 -9999 0 -1 14 14
JUN 0.01 0.069 -9999 0 -0.76 7 7
LPA/LPA2/NHERF2 -0.013 0.072 -9999 0 -0.56 13 13
TIAM1 -0.017 0.16 -9999 0 -1.3 14 14
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
mol:IP3 0.009 0.12 -9999 0 -0.74 12 12
PLCB3 0.021 0.087 -9999 0 -0.67 10 10
FOS -0.086 0.26 -9999 0 -0.74 120 120
positive regulation of mitosis -0.029 0.2 -9999 0 -0.58 79 79
LPA/LPA1-2-3 -0.063 0.16 -9999 0 -0.57 64 64
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.013 0.05 -9999 0 -0.85 3 3
stress fiber formation 0.002 0.12 -9999 0 -0.49 20 20
GNAZ -0.029 0.18 -9999 0 -0.58 71 71
EGFR/PI3K-beta/Gab1 -0.07 0.16 -9999 0 -0.67 27 27
positive regulation of dendritic cell cytokine production -0.062 0.16 -9999 0 -0.56 64 64
LPA/LPA2/MAGI-3 -0.017 0.08 -9999 0 -0.47 24 24
ARHGEF1 -0.002 0.15 -9999 0 -0.51 58 58
GNAI2 -0.023 0.17 -9999 0 -0.58 63 63
GNAI3 -0.023 0.17 -9999 0 -0.57 62 62
GNAI1 -0.031 0.18 -9999 0 -0.59 73 73
LPA/LPA3 -0.019 0.079 -9999 0 -0.48 22 22
LPA/LPA2 -0.012 0.065 -9999 0 -0.64 8 8
LPA/LPA1 -0.064 0.18 -9999 0 -0.6 80 80
HB-EGF/EGFR -0.11 0.25 -9999 0 -0.51 231 231
HBEGF -0.1 0.26 -9999 0 -0.57 199 199
mol:DAG 0.009 0.12 -9999 0 -0.74 12 12
cAMP biosynthetic process -0.072 0.22 -9999 0 -0.62 102 102
NFKB1 0.015 0.029 -9999 0 -0.85 1 1
SRC 0.015 0.022 -9999 0 -0.65 1 1
GNB1 0.016 0.001 -9999 0 -10000 0 0
LYN -0.004 0.16 -9999 0 -0.61 29 29
GNAQ 0.01 0.07 -9999 0 -0.49 8 8
LPAR2 0.008 0.079 -9999 0 -0.82 8 8
LPAR3 -0.008 0.1 -9999 0 -0.65 22 22
LPAR1 -0.048 0.22 -9999 0 -0.83 62 62
IL8 -0.11 0.23 -9999 0 -0.51 144 144
PTK2 -0.019 0.17 -9999 0 -0.53 64 64
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.02 0.14 -9999 0 -0.46 57 57
EGFR -0.022 0.17 -9999 0 -0.78 41 41
PLCG1 -0.007 0.11 -9999 0 -0.44 25 25
PLD2 -0.023 0.17 -9999 0 -0.54 71 71
G12/G13 -0.049 0.14 -9999 0 -0.55 56 56
PI3K-beta -0.055 0.14 -9999 0 -0.61 27 27
cell migration -0.018 0.064 -9999 0 -0.31 5 5
SLC9A3R2 0.011 0.063 -9999 0 -0.75 6 6
PXN 0.002 0.13 -9999 0 -0.5 19 19
HRAS/GTP -0.031 0.21 -9999 0 -0.6 79 79
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.15 0.31 -9999 0 -0.73 194 194
PRKCE 0.013 0.05 -9999 0 -0.85 3 3
PRKCD -0.004 0.15 -9999 0 -0.64 21 21
Gi(beta/gamma) -0.03 0.2 -9999 0 -0.59 80 80
mol:LPA -0.006 0.047 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.046 0.15 -9999 0 -0.73 16 16
MAPKKK cascade -0.029 0.2 -9999 0 -0.58 79 79
contractile ring contraction involved in cytokinesis 0.018 0.065 -9999 0 -0.42 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.041 0.16 -9999 0 -0.46 102 102
GNA15 -0.006 0.12 -9999 0 -0.52 37 37
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.022 -9999 0 -0.65 1 1
MAPT -0.032 0.18 -9999 0 -0.49 100 100
GNA11 -0.004 0.1 -9999 0 -0.48 26 26
Rac1/GTP -0.013 0.14 -9999 0 -1.1 14 14
MMP2 -0.052 0.24 -9999 0 -0.68 104 104
EPO signaling 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
BCL2L1 -0.01 0.17 -10000 0 -0.76 2 2
CRKL -0.056 0.18 -10000 0 -0.73 3 3
mol:DAG -0.048 0.18 -10000 0 -0.47 72 72
HRAS -0.017 0.16 -10000 0 -0.86 2 2
MAPK8 -0.094 0.2 -10000 0 -0.5 85 85
RAP1A -0.056 0.18 -10000 0 -0.73 3 3
GAB1 -0.057 0.18 -10000 0 -0.62 5 5
MAPK14 -0.087 0.2 -10000 0 -0.49 74 74
EPO -0.21 0.33 -10000 0 -0.69 285 285
PLCG1 -0.049 0.18 -10000 0 -0.48 72 72
EPOR/TRPC2/IP3 Receptors 0.006 0.052 -10000 0 -0.72 4 4
RAPGEF1 0.016 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.16 0.24 -10000 0 -0.59 122 122
GAB1/SHC/GRB2/SOS1 -0.081 0.12 -10000 0 -0.92 1 1
EPO/EPOR (dimer) -0.15 0.26 -10000 0 -0.51 287 287
IRS2 -0.074 0.19 -10000 0 -0.68 19 19
STAT1 -0.043 0.19 -10000 0 -0.66 8 8
STAT5B -0.044 0.18 -10000 0 -0.85 3 3
cell proliferation -0.078 0.19 -10000 0 -0.46 85 85
GAB1/SHIP/PIK3R1/SHP2/SHC -0.081 0.12 -10000 0 -0.78 4 4
TEC -0.056 0.18 -10000 0 -0.73 3 3
SOCS3 -0.033 0.19 -10000 0 -0.78 55 55
STAT1 (dimer) -0.042 0.18 -10000 0 -0.63 8 8
JAK2 0.008 0.035 -10000 0 -0.91 1 1
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
EPO/EPOR (dimer)/JAK2 -0.059 0.19 -10000 0 -0.45 75 75
EPO/EPOR -0.15 0.26 -10000 0 -0.51 287 287
LYN 0.014 0.058 -10000 0 -0.85 4 4
TEC/VAV2 -0.044 0.17 -10000 0 -0.81 2 2
elevation of cytosolic calcium ion concentration 0.006 0.052 -10000 0 -0.72 4 4
SHC1 0.015 0.022 -10000 0 -0.65 1 1
EPO/EPOR (dimer)/LYN -0.1 0.22 -10000 0 -0.55 79 79
mol:IP3 -0.048 0.18 -10000 0 -0.47 72 72
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.1 0.16 -10000 0 -0.65 22 22
SH2B3 0.007 0.043 -10000 0 -0.84 2 2
NFKB1 -0.088 0.2 -10000 0 -0.5 74 74
EPO/EPOR (dimer)/JAK2/SOCS3 -0.098 0.14 0.34 1 -0.41 82 83
PTPN6 -0.069 0.18 -10000 0 -0.45 75 75
TEC/VAV2/GRB2 -0.035 0.17 -10000 0 -0.77 2 2
EPOR 0.006 0.052 -10000 0 -0.72 4 4
INPP5D 0.009 0.076 -10000 0 -0.85 7 7
mol:GDP -0.082 0.12 -10000 0 -0.73 2 2
SOS1 0.016 0 -10000 0 -10000 0 0
PLCG2 -0.054 0.21 -10000 0 -0.68 90 90
CRKL/CBL/C3G -0.035 0.17 -10000 0 -0.92 2 2
VAV2 -0.056 0.18 -10000 0 -0.73 3 3
CBL -0.056 0.18 -10000 0 -0.86 3 3
SHC/Grb2/SOS1 -0.087 0.13 -10000 0 -0.77 2 2
STAT5A -0.046 0.19 -10000 0 -0.85 4 4
GRB2 0.016 0 -10000 0 -10000 0 0
STAT5 (dimer) -0.023 0.18 -10000 0 -0.71 7 7
LYN/PLCgamma2 -0.053 0.16 -10000 0 -0.52 90 90
PTPN11 0.015 0.029 -10000 0 -0.85 1 1
BTK -0.073 0.2 -10000 0 -0.59 33 33
BCL2 -0.02 0.21 -10000 0 -1 16 16
Osteopontin-mediated events

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
IKK alpha homodimer -0.021 0.23 -9999 0 -0.77 47 47
NF kappa B1 p50/RelA/I kappa B alpha -0.071 0.19 -9999 0 -0.8 33 33
alphaV/beta3 Integrin/Osteopontin/Src -0.047 0.16 -9999 0 -0.56 74 74
AP1 -0.12 0.24 -9999 0 -0.88 55 55
ILK -0.015 0.21 -9999 0 -0.74 34 34
bone resorption -0.085 0.22 -9999 0 -0.81 44 44
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.072 0.19 -9999 0 -0.82 33 33
ITGAV 0.014 0.074 -9999 0 -0.82 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.045 0.16 -9999 0 -0.6 66 66
alphaV/beta3 Integrin/Osteopontin -0.076 0.21 -9999 0 -0.65 81 81
MAP3K1 -0.017 0.21 -9999 0 -0.61 76 76
JUN 0.01 0.07 -9999 0 -0.76 7 7
MAPK3 -0.017 0.23 -9999 0 -0.81 42 42
MAPK1 -0.017 0.23 -9999 0 -0.81 43 43
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.015 0.029 -9999 0 -0.85 1 1
MAPK8 -0.01 0.21 -9999 0 -0.73 40 40
ITGB3 -0.041 0.21 -9999 0 -0.76 71 71
NFKBIA -0.007 0.24 -9999 0 -0.8 46 46
FOS -0.086 0.26 -9999 0 -0.74 120 120
CD44 -0.016 0.15 -9999 0 -0.75 37 37
CHUK 0.015 0.029 -9999 0 -0.85 1 1
PLAU -0.015 0.28 -9999 0 -0.97 43 43
NF kappa B1 p50/RelA -0.071 0.18 -9999 0 -0.8 28 28
BCAR1 0.013 0.05 -9999 0 -0.85 3 3
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.049 0.17 -9999 0 -0.6 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.027 0.23 -9999 0 -0.64 88 88
VAV3 -0.022 0.23 -9999 0 -0.8 39 39
MAP3K14 -0.031 0.24 -9999 0 -0.65 93 93
ROCK2 -0.012 0.15 -9999 0 -0.85 29 29
SPP1 -0.037 0.2 -9999 0 -0.74 68 68
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.071 0.19 -9999 0 -0.76 34 34
MMP2 -0.036 0.26 -9999 0 -0.74 67 67
Signaling events mediated by PTP1B

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
PDGFRB -0.12 0.31 -10000 0 -0.84 140 140
Jak2/Leptin Receptor -0.046 0.13 -10000 0 -0.51 35 35
PTP1B/AKT1 0.003 0.098 -10000 0 -0.46 17 17
FYN 0.007 0.086 -10000 0 -0.85 9 9
p210 bcr-abl/PTP1B -0.006 0.11 -10000 0 -0.39 40 40
EGFR -0.024 0.17 -10000 0 -0.79 41 41
EGF/EGFR -0.12 0.21 -10000 0 -0.56 126 126
CSF1 0 0.12 -10000 0 -0.82 17 17
AKT1 0.015 0.029 -10000 0 -0.86 1 1
INSR 0.014 0.041 -10000 0 -0.85 2 2
PTP1B/N-cadherin -0.06 0.22 -10000 0 -0.59 119 119
Insulin Receptor/Insulin -0.022 0.071 -10000 0 -0.53 4 4
HCK -0.005 0.13 -10000 0 -0.83 22 22
CRK 0.015 0.022 -10000 0 -0.65 1 1
TYK2 0.003 0.11 -10000 0 -0.45 24 24
EGF -0.15 0.31 -10000 0 -0.73 196 196
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.035 0.16 -10000 0 -0.49 50 50
TXN 0.008 0.059 -10000 0 -0.65 7 7
PTP1B/IRS1/GRB2 -0.003 0.13 -10000 0 -0.54 30 30
cell migration 0.006 0.11 0.39 40 -10000 0 40
STAT3 0.016 0.001 -10000 0 -10000 0 0
PRLR -0.13 0.29 -10000 0 -0.72 172 172
ITGA2B -0.059 0.22 -10000 0 -0.73 88 88
CSF1R -0.009 0.14 -10000 0 -0.82 26 26
Prolactin Receptor/Prolactin -0.11 0.22 -10000 0 -0.54 181 181
FGR -0.012 0.15 -10000 0 -0.83 30 30
PTP1B/p130 Cas 0.002 0.11 -10000 0 -0.47 23 23
Crk/p130 Cas 0.009 0.11 -10000 0 -0.53 15 15
DOK1 -0.036 0.15 -10000 0 -0.41 59 59
JAK2 -0.025 0.13 -10000 0 -0.4 48 48
Jak2/Leptin Receptor/Leptin -0.086 0.18 -10000 0 -0.64 61 61
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
PTPN1 -0.006 0.11 -10000 0 -0.39 40 40
LYN 0.012 0.058 -10000 0 -0.85 4 4
CDH2 -0.092 0.29 -10000 0 -0.85 111 111
SRC 0.018 0.053 -10000 0 -0.56 3 3
ITGB3 -0.047 0.21 -10000 0 -0.76 71 71
CAT1/PTP1B -0.041 0.2 -10000 0 -0.62 62 62
CAPN1 0.014 0.041 -10000 0 -0.86 2 2
CSK 0.014 0.041 -10000 0 -0.85 2 2
PI3K -0.02 0.087 -10000 0 -0.6 9 9
mol:H2O2 -0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.08 0.18 -10000 0 -0.66 58 58
negative regulation of transcription -0.024 0.12 -10000 0 -0.4 49 49
FCGR2A -0.003 0.13 -10000 0 -0.84 20 20
FER 0.01 0.051 -10000 0 -0.86 3 3
alphaIIb/beta3 Integrin -0.098 0.23 -10000 0 -0.6 147 147
BLK -0.081 0.25 -10000 0 -0.72 115 115
Insulin Receptor/Insulin/Shc -0.003 0.038 -10000 0 -0.52 3 3
RHOA 0.016 0.002 -10000 0 -10000 0 0
LEPR 0.002 0.11 -10000 0 -0.82 15 15
BCAR1 0.013 0.05 -10000 0 -0.85 3 3
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.057 0.23 -10000 0 -0.7 65 65
PRL -0.002 0.066 -10000 0 -0.65 9 9
SOCS3 -0.059 0.32 -10000 0 -1.2 55 55
SPRY2 0.011 0.051 -10000 0 -0.86 3 3
Insulin Receptor/Insulin/IRS1 -0.019 0.096 -10000 0 -0.61 13 13
CSF1/CSF1R -0.012 0.16 -10000 0 -0.62 43 43
Ras protein signal transduction 0.02 0.031 -10000 0 -10000 0 0
IRS1 -0.01 0.14 -10000 0 -0.72 31 31
INS -0.001 0.038 -10000 0 -0.65 3 3
LEP -0.058 0.2 -10000 0 -0.65 92 92
STAT5B -0.009 0.11 -10000 0 -0.36 45 45
STAT5A -0.01 0.11 -10000 0 -0.37 45 45
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.076 0.21 -10000 0 -0.5 157 157
CSN2 -0.029 0.071 -10000 0 -10000 0 0
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
LAT -0.012 0.14 -10000 0 -0.6 38 38
YBX1 0.025 0.014 -10000 0 -0.4 1 1
LCK -0.08 0.26 -10000 0 -0.8 104 104
SHC1 0.015 0.022 -10000 0 -0.65 1 1
NOX4 -0.036 0.2 -10000 0 -0.83 52 52
IL2 signaling events mediated by STAT5

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
GAB2 0.012 0.06 -9999 0 -0.72 6 6
ELF1 -0.031 0.14 -9999 0 -0.4 76 76
CCNA2 0.006 0.084 -9999 0 -0.68 13 13
PIK3CA 0.011 0.071 -9999 0 -0.85 6 6
JAK3 -0.029 0.19 -9999 0 -0.83 48 48
PIK3R1 0.012 0.066 -9999 0 -0.78 6 6
JAK1 0.017 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.033 0.3 -9999 0 -0.87 83 83
SHC1 0.016 0.022 -9999 0 -0.65 1 1
SP1 0.003 0.095 -9999 0 -0.38 50 50
IL2RA -0.097 0.33 -9999 0 -0.83 140 140
IL2RB -0.051 0.23 -9999 0 -0.82 72 72
SOS1 0.017 0.001 -9999 0 -10000 0 0
IL2RG -0.06 0.24 -9999 0 -0.79 85 85
G1/S transition of mitotic cell cycle -0.01 0.24 -9999 0 -0.93 54 54
PTPN11 0.016 0.029 -9999 0 -0.85 1 1
CCND2 -0.024 0.26 -9999 0 -1.1 51 51
LCK -0.079 0.26 -9999 0 -0.8 104 104
GRB2 0.017 0.001 -9999 0 -10000 0 0
IL2 0 0.076 -9999 0 -0.65 12 12
CDK6 0.012 0.059 -9999 0 -0.77 5 5
CCND3 -0.008 0.24 -9999 0 -0.74 67 67
Canonical Wnt signaling pathway

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
HDAC1 0.009 0.027 -10000 0 -10000 0 0
AES 0.008 0.038 -10000 0 -0.85 1 1
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.052 0.18 -10000 0 -0.65 71 71
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.11 0.29 -10000 0 -0.75 149 149
TLE1 0.007 0.047 -10000 0 -0.85 2 2
MACF1 0.016 0.001 -10000 0 -10000 0 0
CTNNB1 0.005 0.12 0.32 1 -0.46 19 20
WIF1 -0.023 0.14 -10000 0 -0.65 42 42
beta catenin/RanBP3 0.002 0.14 0.39 52 -0.48 5 57
KREMEN2 -0.031 0.17 -10000 0 -0.67 60 60
DKK1 -0.094 0.27 -10000 0 -0.75 126 126
beta catenin/beta TrCP1 0.015 0.12 0.31 1 -0.44 12 13
FZD1 -0.051 0.23 -10000 0 -0.85 70 70
AXIN2 0.009 0.17 -10000 0 -1 14 14
AXIN1 0.014 0.041 -10000 0 -0.85 2 2
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.042 -10000 0 -0.68 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.067 0.25 -10000 0 -0.69 93 93
Axin1/APC/GSK3 0.002 0.065 0.26 1 -0.56 2 3
Axin1/APC/GSK3/beta catenin/Macf1 0.02 0.15 -10000 0 -0.47 54 54
HNF1A -0.06 0.23 -10000 0 -0.84 72 72
CTBP1 0.01 0.024 -10000 0 -10000 0 0
MYC -0.037 0.35 -10000 0 -1.7 37 37
RANBP3 0.015 0.029 -10000 0 -0.85 1 1
DKK2/LRP6/Kremen 2 -0.11 0.21 -10000 0 -0.58 97 97
NKD1 -0.043 0.2 -10000 0 -0.7 73 73
TCF4 -0.087 0.27 -10000 0 -0.82 102 102
TCF3 0.01 0.023 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.048 0.15 -10000 0 -0.52 74 74
Ran/GTP 0.001 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.056 0.22 0.48 42 -0.64 49 91
LEF1 -0.16 0.32 -10000 0 -0.76 200 200
DVL1 0.01 0.047 -10000 0 -0.37 3 3
CSNK2A1 0.016 0.001 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.075 0.27 -10000 0 -0.78 80 80
DKK1/LRP6/Kremen 2 -0.097 0.2 -10000 0 -0.57 82 82
LRP6 0.015 0.029 -10000 0 -0.85 1 1
CSNK1A1 0.01 0.027 -10000 0 -10000 0 0
NLK 0.016 0.005 -10000 0 -10000 0 0
CCND1 -0.042 0.36 -10000 0 -1.7 40 40
WNT1 0.002 0.09 -10000 0 -0.66 16 16
GSK3A 0.016 0.001 -10000 0 -10000 0 0
GSK3B 0.016 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0.022 -10000 0 -0.65 1 1
PPP2R5D 0.04 0.085 0.31 73 -10000 0 73
APC -0.001 0.16 -10000 0 -0.49 74 74
WNT1/LRP6/FZD1 -0.002 0.12 0.22 33 -0.35 69 102
CREBBP 0.01 0.023 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.064 -9999 0 -0.83 5 5
SVIL 0.012 0.041 -9999 0 -0.85 2 2
ZNF318 0.024 0.043 -9999 0 -0.76 1 1
JMJD2C -0.003 0.025 -9999 0 -0.089 57 57
T-DHT/AR/Ubc9 -0.081 0.22 -9999 0 -0.62 120 120
CARM1 0.015 0.029 -9999 0 -0.85 1 1
PRDX1 0.015 0.032 -9999 0 -0.65 2 2
PELP1 0.018 0.004 -9999 0 -10000 0 0
CTNNB1 0.014 0.006 -9999 0 -10000 0 0
AKT1 0.018 0.03 -9999 0 -0.85 1 1
PTK2B 0.015 0.004 -9999 0 -10000 0 0
MED1 0.017 0.029 -9999 0 -0.83 1 1
MAK -0.004 0.15 -9999 0 -0.7 35 35
response to oxidative stress 0 0.002 -9999 0 -10000 0 0
HIP1 -0.002 0.12 -9999 0 -0.86 16 16
GSN 0.013 0.03 -9999 0 -0.85 1 1
NCOA2 -0.04 0.21 -9999 0 -0.85 57 57
NCOA6 0.014 0.006 -9999 0 -10000 0 0
DNA-PK 0.016 0.042 -9999 0 -10000 0 0
NCOA4 0.015 0.029 -9999 0 -0.85 1 1
PIAS3 0.014 0.006 -9999 0 -10000 0 0
cell proliferation -0.029 0.12 -9999 0 -0.53 34 34
XRCC5 0.019 0.007 -9999 0 -10000 0 0
UBE3A 0.011 0.016 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.26 -9999 0 -0.66 152 152
FHL2 -0.1 0.36 -9999 0 -1.3 66 66
RANBP9 0.014 0.006 -9999 0 -10000 0 0
JMJD1A -0.022 0.066 -9999 0 -0.13 224 224
CDK6 0.012 0.059 -9999 0 -0.77 5 5
TGFB1I1 -0.055 0.23 -9999 0 -0.84 71 71
T-DHT/AR/CyclinD1 -0.11 0.26 -9999 0 -0.63 157 157
XRCC6 0.019 0.007 -9999 0 -10000 0 0
T-DHT/AR -0.1 0.27 -9999 0 -0.66 140 140
CTDSP1 0.013 0.029 -9999 0 -0.85 1 1
CTDSP2 0.023 0.02 -9999 0 -10000 0 0
BRCA1 0.005 0.087 -9999 0 -0.85 9 9
TCF4 -0.076 0.27 -9999 0 -0.83 102 102
CDKN2A -0.039 0.21 -9999 0 -0.81 63 63
SRF 0.021 0.03 -9999 0 -10000 0 0
NKX3-1 -0.095 0.17 -9999 0 -1.2 9 9
KLK3 -0.053 0.19 -9999 0 -0.63 6 6
TMF1 0.011 0.058 -9999 0 -0.85 4 4
HNRNPA1 0.02 0.011 -9999 0 -10000 0 0
AOF2 -0.004 0.013 -9999 0 -10000 0 0
APPL1 0.034 0.029 -9999 0 -0.65 1 1
T-DHT/AR/Caspase 8 -0.085 0.22 -9999 0 -0.62 121 121
AR -0.12 0.3 -9999 0 -0.87 120 120
UBA3 0.013 0.03 -9999 0 -0.86 1 1
PATZ1 0.02 0.011 -9999 0 -10000 0 0
PAWR 0.013 0.041 -9999 0 -0.85 2 2
PRKDC 0.019 0.007 -9999 0 -10000 0 0
PA2G4 0.021 0.013 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.073 0.21 -9999 0 -0.57 122 122
RPS6KA3 0.013 0.031 -9999 0 -0.87 1 1
T-DHT/AR/ARA70 -0.082 0.23 -9999 0 -0.62 121 121
LATS2 0.019 0.03 -9999 0 -0.83 1 1
T-DHT/AR/PRX1 -0.074 0.21 -9999 0 -0.57 121 121
Cyclin D3/CDK11 p58 -0.002 0.028 -9999 0 -0.48 3 3
VAV3 0.001 0.11 -9999 0 -0.85 14 14
KLK2 -0.092 0.19 -9999 0 -0.67 78 78
CASP8 0.016 0.029 -9999 0 -0.83 1 1
T-DHT/AR/TIF2/CARM1 -0.1 0.27 -9999 0 -0.66 147 147
TMPRSS2 -0.29 0.45 -9999 0 -0.91 270 270
CCND1 -0.025 0.18 -9999 0 -0.84 42 42
PIAS1 0.011 0.016 -9999 0 -10000 0 0
mol:T-DHT -0.018 0.044 -9999 0 -0.093 169 169
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.004 0.05 -9999 0 -0.85 2 2
T-DHT/AR/CDK6 -0.086 0.23 -9999 0 -0.63 122 122
CMTM2 -0.017 0.15 -9999 0 -0.7 42 42
SNURF -0.029 0.19 -9999 0 -0.85 45 45
ZMIZ1 0.001 0.047 -9999 0 -0.84 1 1
CCND3 0.014 0.039 -9999 0 -0.65 3 3
TGIF1 0.02 0.011 -9999 0 -10000 0 0
FKBP4 0.014 0.006 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.028 0.28 -10000 0 -0.89 70 70
UGCG -0.017 0.13 -10000 0 -0.82 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT 0.006 0.18 -10000 0 -0.46 84 84
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.001 0.13 -10000 0 -0.8 19 19
mol:DAG -0.003 0.011 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.082 0.19 -10000 0 -0.61 85 85
FRAP1 -0.011 0.28 -10000 0 -0.73 89 89
FOXO3 -0.005 0.27 -10000 0 -0.75 81 81
AKT1 -0.022 0.3 -10000 0 -0.84 84 84
GAB2 0.012 0.061 -10000 0 -0.72 6 6
SMPD1 0 0.043 -10000 0 -10000 0 0
SGMS1 0 0.044 -10000 0 -0.38 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.067 -10000 0 -0.54 12 12
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation 0.01 0.14 -10000 0 -0.41 37 37
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K 0.02 0.076 -10000 0 -0.62 12 12
RPS6KB1 0.015 0.056 -10000 0 -10000 0 0
mol:sphingomyelin -0.003 0.011 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.002 -10000 0 -0.013 10 10
JAK3 -0.026 0.19 -10000 0 -0.83 48 48
PIK3R1 0.014 0.066 -10000 0 -0.78 6 6
JAK1 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.015 0.029 -10000 0 -0.85 1 1
MYC -0.016 0.3 -10000 0 -0.86 79 79
MYB -0.018 0.24 -10000 0 -0.79 62 62
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.038 0.32 -10000 0 -0.81 105 105
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.032 0.054 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.033 0.3 -10000 0 -0.77 105 105
Rac1/GDP 0.027 0.062 -10000 0 -0.52 10 10
T cell proliferation -0.02 0.28 -10000 0 -0.78 82 82
SHC1 0.016 0.023 -10000 0 -0.65 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.016 -10000 0 -0.054 61 61
PRKCZ -0.026 0.3 -10000 0 -0.84 82 82
NF kappa B1 p50/RelA -0.08 0.19 -10000 0 -0.64 72 72
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.047 0.32 -10000 0 -0.91 91 91
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.1 0.28 -10000 0 -0.76 137 137
IL2RB -0.048 0.23 -10000 0 -0.82 72 72
TERT -0.057 0.2 -10000 0 -0.65 87 87
E2F1 0.009 0.099 -10000 0 -0.33 62 62
SOS1 0.017 0.003 -10000 0 -10000 0 0
RPS6 0.015 0.032 -10000 0 -0.65 2 2
mol:cAMP -0.002 0.008 0.026 61 -10000 0 61
PTPN11 0.016 0.029 -10000 0 -0.85 1 1
IL2RG -0.057 0.24 -10000 0 -0.79 85 85
actin cytoskeleton organization -0.02 0.28 -10000 0 -0.78 82 82
GRB2 0.017 0.003 -10000 0 -10000 0 0
IL2 0.002 0.076 -10000 0 -0.65 12 12
PIK3CA 0.014 0.071 -10000 0 -0.85 6 6
Rac1/GTP 0.035 0.061 -10000 0 -0.49 10 10
LCK -0.077 0.27 -10000 0 -0.8 104 104
BCL2 0.007 0.24 -10000 0 -0.64 76 76
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.01 0.11 -10000 0 -0.62 9 9
epithelial cell differentiation -0.082 0.15 -10000 0 -0.6 14 14
ITCH 0.028 0.019 -10000 0 -10000 0 0
WWP1 0 0.086 -10000 0 -0.99 1 1
FYN 0.007 0.086 -10000 0 -0.85 9 9
EGFR -0.021 0.17 -10000 0 -0.78 41 41
PRL -0.002 0.066 -10000 0 -0.65 9 9
neuron projection morphogenesis 0.007 0.16 -10000 0 -0.68 12 12
PTPRZ1 -0.045 0.18 -10000 0 -0.65 74 74
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.061 0.15 -10000 0 -0.66 17 17
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.04 0.18 -10000 0 -0.57 75 75
ADAM17 0.024 0.061 -10000 0 -0.84 4 4
ErbB4/ErbB4 -0.01 0.1 -10000 0 -0.44 12 12
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.049 0.18 -10000 0 -0.58 78 78
NCOR1 0.015 0.029 -10000 0 -0.85 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.068 0.17 -10000 0 -0.55 75 75
GRIN2B -0.047 0.19 -10000 0 -0.6 48 48
ErbB4/ErbB2/betacellulin -0.056 0.14 -10000 0 -0.54 50 50
STAT1 0.009 0.074 -10000 0 -0.72 9 9
HBEGF 0.004 0.094 -10000 0 -0.74 14 14
PRLR -0.13 0.29 -10000 0 -0.72 172 172
E4ICDs/ETO2 -0.016 0.13 -10000 0 -0.63 20 20
axon guidance 0.012 0.09 -10000 0 -0.63 2 2
NEDD4 0.008 0.13 -10000 0 -0.84 20 20
Prolactin receptor/Prolactin receptor/Prolactin -0.11 0.22 -10000 0 -0.54 181 181
CBFA2T3 -0.005 0.13 -10000 0 -0.82 22 22
ErbB4/ErbB2/HBEGF -0.028 0.086 -10000 0 -0.56 14 14
MAPK3 -0.003 0.16 -10000 0 -0.69 11 11
STAT1 (dimer) -0.007 0.1 -10000 0 -0.73 5 5
MAPK1 -0.003 0.16 -10000 0 -0.7 11 11
JAK2 0.015 0.029 -10000 0 -0.85 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.066 0.16 -10000 0 -0.54 73 73
NRG1 -0.029 0.2 -10000 0 -0.61 89 89
NRG3 -0.057 0.24 -10000 0 -0.81 78 78
NRG2 -0.059 0.22 -10000 0 -0.71 92 92
NRG4 -0.074 0.23 -10000 0 -0.67 115 115
heart development 0.012 0.09 -10000 0 -0.63 2 2
neural crest cell migration -0.031 0.17 -10000 0 -0.53 73 73
ERBB2 0.031 0.064 -10000 0 -0.62 8 8
WWOX/E4ICDs -0.003 0.09 -10000 0 -1 1 1
SHC1 0.015 0.022 -10000 0 -0.65 1 1
ErbB4/EGFR/neuregulin 4 -0.1 0.19 -10000 0 -0.67 48 48
apoptosis 0.088 0.17 0.56 70 -10000 0 70
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.049 0.18 -10000 0 -0.54 86 86
ErbB4/ErbB2/epiregulin -0.12 0.18 -10000 0 -0.51 88 88
ErbB4/ErbB4/betacellulin/betacellulin -0.043 0.17 -10000 0 -0.54 67 67
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.1 0.18 -10000 0 -0.6 41 41
MDM2 0.002 0.091 -10000 0 -1 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.061 0.15 -10000 0 -0.54 68 68
STAT5A 0.019 0.091 -10000 0 -0.6 4 4
ErbB4/EGFR/neuregulin 1 beta -0.084 0.19 -10000 0 -0.65 54 54
DLG4 0.005 0.096 -10000 0 -0.82 12 12
GRB2/SHC -0.001 0.016 -10000 0 -0.48 1 1
E4ICDs/TAB2/NCoR1 -0.033 0.07 -10000 0 -0.88 2 2
STAT5A (dimer) -0.087 0.16 -10000 0 -0.67 13 13
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.019 0.083 -10000 0 -0.77 1 1
LRIG1 0.012 0.055 -10000 0 -0.8 4 4
EREG -0.17 0.31 -10000 0 -0.7 228 228
BTC -0.046 0.21 -10000 0 -0.78 69 69
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.012 0.09 -10000 0 -0.64 2 2
ERBB4 -0.01 0.1 -10000 0 -1.1 1 1
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.011 0.033 -10000 0 -0.79 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.07 0.15 -10000 0 -0.54 29 29
glial cell differentiation 0.033 0.069 0.87 2 -10000 0 2
WWOX 0.015 0.022 -10000 0 -0.65 1 1
cell proliferation -0.04 0.21 -10000 0 -0.67 48 48
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -10000 0 -10000 0 0
VLDLR 0.01 0.067 -10000 0 -0.74 7 7
LRPAP1 0.014 0.041 -10000 0 -0.85 2 2
NUDC 0.016 0 -10000 0 -10000 0 0
RELN/LRP8 -0.19 0.24 -10000 0 -0.58 130 130
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
KATNA1 0.016 0.001 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.15 0.23 -10000 0 -0.53 129 129
IQGAP1/CaM 0 0 -10000 0 -10000 0 0
DAB1 -0.036 0.17 -10000 0 -0.65 60 60
IQGAP1 0.016 0 -10000 0 -10000 0 0
PLA2G7 -0.071 0.25 -10000 0 -0.77 99 99
CALM1 0.016 0 -10000 0 -10000 0 0
DYNLT1 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.018 0.093 -10000 0 -0.5 32 32
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.016 0 -10000 0 -10000 0 0
CDK5R1 0.013 0.048 -10000 0 -0.7 4 4
LIS1/Poliovirus Protein 3A 0 0 -10000 0 -10000 0 0
CDK5R2 -0.055 0.2 -10000 0 -0.65 89 89
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.21 0.25 -10000 0 -0.48 389 389
YWHAE 0.016 0 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.1 0.2 -10000 0 -0.61 19 19
MAP1B -0.012 0.067 0.24 2 -0.39 23 25
RAC1 0 0 -10000 0 -10000 0 0
p35/CDK5 -0.11 0.21 -10000 0 -0.71 11 11
RELN -0.27 0.36 -10000 0 -0.72 343 343
PAFAH/LIS1 -0.026 0.17 -10000 0 -0.56 60 60
LIS1/CLIP170 0.034 0 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.1 0.13 -10000 0 -0.53 4 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.087 0.17 -10000 0 -0.65 21 21
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.12 0.21 -10000 0 -0.66 19 19
LIS1/IQGAP1 0.034 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PAFAH1B1 0.029 0 -10000 0 -10000 0 0
PAFAH1B3 0.009 0.071 -10000 0 -0.72 8 8
PAFAH1B2 0.001 0.12 -10000 0 -0.85 16 16
MAP1B/LIS1/Dynein heavy chain 0.024 0.047 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.16 -10000 0 -0.59 17 17
LRP8 -0.007 0.12 -10000 0 -0.66 30 30
NDEL1/Katanin 60 -0.1 0.2 -10000 0 -0.61 19 19
P39/CDK5 -0.15 0.24 -10000 0 -0.7 46 46
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.034 0 -10000 0 -10000 0 0
CDK5 -0.13 0.22 -10000 0 -0.49 129 129
PPP2R5D 0.015 0.032 -10000 0 -0.65 2 2
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.17 0.21 -10000 0 -0.52 138 138
RELN/VLDLR -0.18 0.22 -10000 0 -0.54 133 133
CDC42 0 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.001 0.11 -10000 0 -0.84 16 16
ANTXR2 -0.02 0.17 -10000 0 -0.84 38 38
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.025 -10000 0 -0.11 49 49
monocyte activation -0.09 0.24 -10000 0 -0.56 155 155
MAP2K2 -0.005 0.054 -10000 0 -0.91 3 3
MAP2K1 -0.005 0.021 -10000 0 -10000 0 0
MAP2K7 -0.006 0.032 -10000 0 -0.51 2 2
MAP2K6 -0.011 0.061 -10000 0 -0.52 11 11
CYAA -0.011 0.13 -10000 0 -0.54 49 49
MAP2K4 -0.005 0.021 -10000 0 -10000 0 0
IL1B -0.031 0.16 -10000 0 -0.52 76 76
Channel -0.032 0.14 -10000 0 -0.57 49 49
NLRP1 -0.025 0.11 -10000 0 -0.52 37 37
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.007 0.029 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.025 0.11 49 -10000 0 49
MAPK3 -0.005 0.027 -10000 0 -0.51 1 1
MAPK1 -0.005 0.027 -10000 0 -0.51 1 1
PGR -0.1 0.2 -10000 0 -0.48 191 191
PA/Cellular Receptors -0.034 0.14 -10000 0 -0.62 49 49
apoptosis -0.006 0.025 -10000 0 -0.11 49 49
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.01 0.13 -10000 0 -0.54 49 49
macrophage activation 0.019 0.033 -10000 0 -0.48 2 2
TNF -0.062 0.23 -10000 0 -0.75 90 90
VCAM1 -0.091 0.24 -10000 0 -0.56 155 155
platelet activation -0.007 0.029 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.032 0.21 7 -10000 0 7
IL18 -0.017 0.13 -10000 0 -0.48 55 55
negative regulation of macrophage activation -0.006 0.025 -10000 0 -0.11 49 49
LEF -0.006 0.025 -10000 0 -0.11 49 49
CASP1 -0.02 0.082 -10000 0 -0.32 44 44
mol:cAMP -0.007 0.029 -10000 0 -10000 0 0
necrosis -0.006 0.025 -10000 0 -0.11 49 49
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.03 0.13 -10000 0 -0.55 49 49
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.001 0.023 -10000 0 -0.48 2 2
PRKCZ 0.008 0.082 -10000 0 -0.85 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.016 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.047 0.18 -10000 0 -0.82 29 29
IRAK/TOLLIP 0.034 0.027 -10000 0 -0.52 1 1
IKBKB 0.016 0 -10000 0 -10000 0 0
IKBKG 0.013 0.05 -10000 0 -0.85 3 3
IL1 alpha/IL1R2 -0.15 0.25 -10000 0 -0.55 248 248
IL1A -0.013 0.13 -10000 0 -0.66 36 36
IL1B -0.04 0.23 -10000 0 -0.71 84 84
IRAK/TRAF6/p62/Atypical PKCs -0.008 0.059 -10000 0 -0.89 1 1
IL1R2 -0.17 0.32 -10000 0 -0.72 221 221
IL1R1 -0.005 0.13 -10000 0 -0.84 22 22
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.16 0.25 16 -0.8 21 37
TOLLIP 0.016 0 -10000 0 -10000 0 0
TICAM2 0.008 0.082 -10000 0 -0.85 8 8
MAP3K3 0.016 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.077 0.051 -10000 0 -0.76 2 2
JUN 0.043 0.08 -10000 0 -0.7 1 1
MAP3K7 0.016 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.076 0.23 -10000 0 -1 33 33
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.049 0.17 -10000 0 -0.66 43 43
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.046 0.16 -10000 0 -0.62 43 43
IL1 beta fragment/IL1R1/IL1RAP -0.079 0.23 -10000 0 -0.69 88 88
NFKB1 0.015 0.029 -10000 0 -0.85 1 1
MAPK8 0.038 0.074 -10000 0 -0.44 11 11
IRAK1 0.027 0.029 -10000 0 -0.46 3 3
IL1RN/IL1R1 -0.062 0.18 -10000 0 -0.58 95 95
IRAK4 0.016 0 -10000 0 -10000 0 0
PRKCI 0.015 0.022 -10000 0 -0.65 1 1
TRAF6 0.016 0 -10000 0 -10000 0 0
PI3K -0.008 0.072 -10000 0 -0.62 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.2 -10000 0 -0.92 28 28
CHUK 0.015 0.029 -10000 0 -0.85 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.079 0.23 -10000 0 -0.69 88 88
IL1 beta/IL1R2 -0.17 0.29 -10000 0 -0.55 275 275
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.021 -10000 0 -0.45 1 1
NF kappa B1 p50/RelA -0.067 0.2 -10000 0 -0.91 33 33
IRAK3 -0.017 0.16 -10000 0 -0.83 35 35
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.074 0.22 -10000 0 -1.1 26 26
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.13 -10000 0 -0.63 19 19
IL1 alpha/IL1R1/IL1RAP -0.046 0.15 -10000 0 -0.6 41 41
RELA 0.016 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.009 0.067 -10000 0 -0.65 9 9
MYD88 0.002 0.11 -10000 0 -0.85 14 14
IRAK/TRAF6/MEKK3 0.024 0.031 -10000 0 -0.48 1 1
IL1RAP -0.009 0.14 -10000 0 -0.8 27 27
UBE2N 0.016 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.06 0.17 -10000 0 -0.83 26 26
CASP1 -0.017 0.17 -10000 0 -0.85 34 34
IL1RN/IL1R2 -0.18 0.28 -10000 0 -0.58 270 270
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.081 0.25 -10000 0 -0.71 89 89
TMEM189-UBE2V1 0.005 0.032 -10000 0 -0.65 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.019 0.14 -10000 0 -0.63 27 27
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
IL1RN -0.047 0.21 -10000 0 -0.72 76 76
TRAF6/TAK1/TAB1/TAB2 -0.001 0.015 -10000 0 -10000 0 0
MAP2K6 0.035 0.054 -10000 0 -0.46 8 8
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.013 0.05 -9999 0 -0.85 3 3
SPHK1 -0.061 0.22 -9999 0 -0.69 97 97
GNAI2 0.015 0.029 -9999 0 -0.85 1 1
mol:S1P -0.004 0.1 -9999 0 -0.46 19 19
GNAO1 -0.052 0.22 -9999 0 -0.76 79 79
mol:Sphinganine-1-P -0.031 0.18 -9999 0 -0.52 97 97
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.021 0.075 -9999 0 -0.66 6 6
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.016 -9999 0 -0.48 1 1
S1PR3 -0.086 0.27 -9999 0 -0.82 109 109
S1PR2 0.012 0.056 -9999 0 -0.73 5 5
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.025 0.083 -9999 0 -0.41 19 19
S1PR5 -0.052 0.23 -9999 0 -0.81 73 73
S1PR4 -0.018 0.17 -9999 0 -0.83 36 36
GNAI1 0.004 0.1 -9999 0 -0.85 12 12
S1P/S1P5/G12 -0.06 0.15 -9999 0 -0.56 61 61
S1P/S1P3/Gq -0.072 0.26 -9999 0 -0.58 139 139
S1P/S1P4/Gi -0.01 0.17 -9999 0 -0.62 39 39
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.007 0.085 -9999 0 -0.79 10 10
GNA14 -0.078 0.27 -9999 0 -0.84 97 97
GNA15 -0.014 0.16 -9999 0 -0.81 33 33
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.022 -9999 0 -0.65 1 1
GNA11 -0.011 0.14 -9999 0 -0.75 31 31
ABCC1 0.015 0.029 -9999 0 -0.85 1 1
Paxillin-dependent events mediated by a4b1

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.016 0 -10000 0 -10000 0 0
Rac1/GDP 0.007 0.021 -10000 0 -10000 0 0
DOCK1 0.014 0.041 -10000 0 -0.85 2 2
ITGA4 -0.064 0.25 -10000 0 -0.84 83 83
RAC1 0.016 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.066 0.2 -10000 0 -0.66 89 89
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0.022 -10000 0 -0.65 1 1
alpha4/beta1 Integrin -0.052 0.16 -10000 0 -0.56 83 83
alpha4/beta7 Integrin/Paxillin -0.052 0.16 -10000 0 -0.52 87 87
lamellipodium assembly -0.002 0.071 -10000 0 -0.56 12 12
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
PI3K -0.008 0.072 -10000 0 -0.62 12 12
ARF6 0.016 0 -10000 0 -10000 0 0
TLN1 0.015 0.029 -10000 0 -0.85 1 1
PXN 0.029 0 -10000 0 -10000 0 0
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
ARF6/GTP -0.041 0.13 -10000 0 -0.75 2 2
cell adhesion -0.044 0.14 -10000 0 -0.48 81 81
CRKL/CBL -0.001 0.022 -10000 0 -0.65 1 1
alpha4/beta1 Integrin/Paxillin -0.047 0.15 -10000 0 -0.51 80 80
ITGB1 0.016 0 -10000 0 -10000 0 0
ITGB7 0.008 0.082 -10000 0 -0.85 8 8
ARF6/GDP 0.007 0.021 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.11 0.23 -10000 0 -0.55 177 177
p130Cas/Crk/Dock1 -0.004 0.049 -10000 0 -0.64 5 5
VCAM1 -0.1 0.3 -10000 0 -0.85 123 123
alpha4/beta1 Integrin/Paxillin/Talin -0.045 0.14 -10000 0 -0.48 81 81
alpha4/beta1 Integrin/Paxillin/GIT1 -0.045 0.14 -10000 0 -0.49 82 82
BCAR1 0.013 0.05 -10000 0 -0.85 3 3
mol:GDP 0.045 0.14 0.48 82 -10000 0 82
CBL 0.015 0.029 -10000 0 -0.85 1 1
PRKACA 0.016 0 -10000 0 -10000 0 0
GIT1 0.014 0.041 -10000 0 -0.85 2 2
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.045 0.14 -10000 0 -0.48 81 81
Rac1/GTP -0.003 0.082 -10000 0 -0.64 12 12
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.021 0.23 -9999 0 -0.81 46 46
MAP3K8 0.01 0.059 -9999 0 -0.77 5 5
FOS -0.014 0.21 -9999 0 -0.76 46 46
PRKCA 0.014 0.032 -9999 0 -0.65 2 2
PTPN7 -0.037 0.2 -9999 0 -0.77 61 61
HRAS 0.011 0.059 -9999 0 -0.77 5 5
PRKCB -0.036 0.2 -9999 0 -0.83 54 54
NRAS 0.016 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.003 0.035 -9999 0 -0.52 3 3
MAPK3 -0.01 0.18 -9999 0 -0.74 39 39
MAP2K1 0.011 0.14 -9999 0 -0.54 50 50
ELK1 0.015 0.006 -9999 0 -10000 0 0
BRAF -0.033 0.13 -9999 0 -0.55 49 49
mol:GTP 0 0.002 -9999 0 -0.006 113 113
MAPK1 -0.01 0.18 -9999 0 -0.74 39 39
RAF1 -0.033 0.13 -9999 0 -0.55 49 49
KRAS 0.016 0.001 -9999 0 -10000 0 0
Aurora B 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
Condensin I complex 0.005 0.14 -9999 0 -0.55 38 38
STMN1 -0.007 0.15 -9999 0 -0.56 57 57
Aurora B/RasGAP/Survivin -0.047 0.21 -9999 0 -0.73 65 65
Chromosomal passenger complex/Cul3 protein complex -0.001 0.14 -9999 0 -0.45 57 57
BIRC5 -0.04 0.2 -9999 0 -0.73 68 68
DES -0.17 0.27 -9999 0 -0.67 168 168
Aurora C/Aurora B/INCENP -0.021 0.13 -9999 0 -0.47 42 42
Aurora B/TACC1 -0.02 0.12 -9999 0 -0.47 60 60
Aurora B/PP2A -0.022 0.14 -9999 0 -0.52 59 59
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.01 0.042 -9999 0 -0.21 17 17
mitotic metaphase/anaphase transition 0 0.004 -9999 0 -10000 0 0
NDC80 -0.038 0.21 -9999 0 -0.64 91 91
Cul3 protein complex -0.023 0.11 -9999 0 -0.51 40 40
KIF2C -0.002 0.11 -9999 0 -0.42 45 45
PEBP1 0.015 0.005 -9999 0 -10000 0 0
KIF20A -0.039 0.2 -9999 0 -0.74 64 64
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.023 0.14 -9999 0 -0.54 59 59
SEPT1 0.002 0.1 -9999 0 -0.71 17 17
SMC2 0.015 0.029 -9999 0 -0.85 1 1
SMC4 0.011 0.065 -9999 0 -0.85 5 5
NSUN2/NPM1/Nucleolin 0.004 0.15 -9999 0 -0.93 17 17
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -9999 0 -10000 0 0
H3F3B 0 0.091 -9999 0 -0.34 57 57
AURKB -0.027 0.18 -9999 0 -0.72 57 57
AURKC 0.001 0.1 -9999 0 -0.7 19 19
CDCA8 0.002 0.097 -9999 0 -0.68 18 18
cytokinesis -0.071 0.19 -9999 0 -0.7 60 60
Aurora B/Septin1 -0.045 0.2 -9999 0 -0.73 54 54
AURKA 0.008 0.071 -9999 0 -0.66 10 10
INCENP 0.014 0.042 -9999 0 -0.86 2 2
KLHL13 -0.018 0.16 -9999 0 -0.76 39 39
BUB1 -0.023 0.16 -9999 0 -0.69 49 49
hSgo1/Aurora B/Survivin -0.06 0.23 -9999 0 -0.73 82 82
EVI5 0.016 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.051 0.16 -9999 0 -0.68 44 44
SGOL1 -0.016 0.15 -9999 0 -0.71 39 39
CENPA -0.009 0.15 -9999 0 -0.54 56 56
NCAPG -0.017 0.16 -9999 0 -0.76 38 38
Aurora B/HC8 Proteasome -0.021 0.14 -9999 0 -0.53 57 57
NCAPD2 0.015 0.032 -9999 0 -0.65 2 2
Aurora B/PP1-gamma -0.021 0.14 -9999 0 -0.53 57 57
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.012 0.14 -9999 0 -0.73 33 33
NPM1 -0.022 0.13 -9999 0 -0.78 17 17
RASA1 0.013 0.05 -9999 0 -0.85 3 3
KLHL9 0.014 0.041 -9999 0 -0.85 2 2
mitotic prometaphase -0.001 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.021 0.13 -9999 0 -0.52 57 57
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.057 0.18 -9999 0 -0.74 47 47
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.022 0.13 -9999 0 -0.73 19 19
MYLK -0.035 0.16 -9999 0 -0.46 87 87
KIF23 -0.003 0.12 -9999 0 -0.7 24 24
VIM -0.055 0.24 -9999 0 -0.66 110 110
RACGAP1 0.013 0.039 -9999 0 -0.66 3 3
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.022 0.13 -9999 0 -0.78 17 17
Chromosomal passenger complex -0.013 0.18 -9999 0 -0.55 73 73
Chromosomal passenger complex/EVI5 -0.03 0.22 -9999 0 -0.71 68 68
TACC1 0.012 0.058 -9999 0 -0.85 4 4
PPP2R5D 0.015 0.032 -9999 0 -0.65 2 2
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.078 0.19 -10000 0 -0.52 117 117
HDAC1 0.005 0.014 -10000 0 -10000 0 0
AES 0.015 0.029 -10000 0 -0.85 1 1
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.03 0.19 -10000 0 -0.78 52 52
LRP6/FZD1 -0.052 0.18 -10000 0 -0.65 71 71
TLE1 0.014 0.041 -10000 0 -0.85 2 2
AP1 -0.038 0.15 -10000 0 -0.42 77 77
NCSTN 0.015 0.029 -10000 0 -0.85 1 1
ADAM10 0.006 0.089 -10000 0 -0.83 10 10
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.009 0.13 -10000 0 -0.62 13 13
NICD/RBPSUH -0.009 0.08 -10000 0 -0.78 9 9
WIF1 -0.022 0.14 -10000 0 -0.65 42 42
NOTCH1 -0.01 0.085 -10000 0 -0.83 9 9
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.031 0.17 -10000 0 -0.67 60 60
DKK1 -0.094 0.27 -10000 0 -0.75 126 126
beta catenin/beta TrCP1 0.04 0.06 0.33 1 -10000 0 1
APH1B 0.009 0.076 -10000 0 -0.85 7 7
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 0 0.04 -10000 0 -0.45 3 3
CtBP/CBP/TCF1/TLE1/AES 0.007 0.12 -10000 0 -0.87 2 2
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.086 0.26 -10000 0 -0.74 120 120
JUN 0.01 0.069 -10000 0 -0.76 7 7
MAP3K7 0.015 0.005 -10000 0 -10000 0 0
CTNNB1 0.032 0.064 0.26 14 -10000 0 14
MAPK3 0.015 0.029 -10000 0 -0.85 1 1
DKK2/LRP6/Kremen 2 -0.11 0.21 -10000 0 -0.58 97 97
HNF1A -0.054 0.24 -10000 0 -0.85 72 72
CTBP1 0.016 0.003 -10000 0 -10000 0 0
MYC -0.041 0.33 -10000 0 -1.6 37 37
NKD1 -0.044 0.2 -10000 0 -0.7 73 73
FZD1 -0.052 0.23 -10000 0 -0.85 70 70
NOTCH1 precursor/Deltex homolog 1 -0.033 0.13 -10000 0 -0.54 44 44
apoptosis -0.037 0.15 -10000 0 -0.42 77 77
Delta 1/NOTCHprecursor -0.077 0.19 -10000 0 -0.52 117 117
DLL1 -0.11 0.3 -10000 0 -0.82 137 137
PPARD 0.022 0.084 -10000 0 -1.6 2 2
Gamma Secretase -0.004 0.045 -10000 0 -0.48 8 8
APC 0 0.036 -10000 0 -0.41 2 2
DVL1 -0.009 0.039 -10000 0 -0.54 3 3
CSNK2A1 0.015 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.097 0.2 -10000 0 -0.57 83 83
LRP6 0.015 0.029 -10000 0 -0.85 1 1
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
NLK 0.02 0.013 -10000 0 -10000 0 0
CCND1 -0.046 0.34 -10000 0 -1.6 40 40
WNT1 0.002 0.09 -10000 0 -0.66 16 16
Axin1/APC/beta catenin 0.047 0.059 0.32 1 -0.48 3 4
DKK2 -0.11 0.29 -10000 0 -0.75 149 149
NOTCH1 precursor/DVL1 -0.012 0.076 -10000 0 -0.7 9 9
GSK3B 0.016 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0.023 -10000 0 -0.65 1 1
NOTCH/Deltex homolog 1 -0.034 0.13 -10000 0 -0.54 44 44
PPP2R5D 0.021 0.092 0.32 73 -10000 0 73
MAPK1 0.015 0.029 -10000 0 -0.85 1 1
WNT1/LRP6/FZD1 -0.065 0.16 -10000 0 -0.54 73 73
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.019 0.006 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.01 0.053 0.31 14 -0.33 1 15
RFC1 0.01 0.053 0.31 14 -0.33 1 15
PRKDC 0.01 0.053 0.31 14 -0.33 1 15
RIPK1 0.017 0.005 -10000 0 -10000 0 0
CASP7 -0.019 0.055 0.26 2 -0.56 1 3
FASLG/FAS/FADD/FAF1 -0.057 0.14 0.27 9 -0.4 80 89
MAP2K4 -0.045 0.17 -10000 0 -0.52 45 45
mol:ceramide -0.061 0.2 -10000 0 -0.53 93 93
GSN 0.01 0.056 0.31 14 -0.44 2 16
FASLG/FAS/FADD/FAF1/Caspase 8 -0.05 0.16 -10000 0 -0.49 67 67
FAS -0.013 0.14 -10000 0 -0.85 26 26
BID 0.008 0.057 0.34 20 -0.49 2 22
MAP3K1 -0.011 0.1 0.24 1 -0.35 7 8
MAP3K7 0.012 0.007 -10000 0 -10000 0 0
RB1 0.008 0.065 0.31 14 -0.51 5 19
CFLAR 0.017 0.005 -10000 0 -10000 0 0
HGF/MET -0.089 0.21 -10000 0 -0.6 104 104
ARHGDIB -0.003 0.092 0.31 14 -0.5 21 35
FADD 0.013 0.008 -10000 0 -10000 0 0
actin filament polymerization -0.01 0.056 0.44 2 -0.31 14 16
NFKB1 -0.062 0.095 -10000 0 -0.88 2 2
MAPK8 -0.072 0.22 -10000 0 -0.5 112 112
DFFA 0.01 0.053 0.31 14 -0.33 1 15
DNA fragmentation during apoptosis 0.01 0.052 0.31 14 -0.33 1 15
FAS/FADD/MET -0.021 0.11 -10000 0 -0.57 31 31
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.008 0.14 -10000 0 -0.8 27 27
FAF1 0.012 0.03 -10000 0 -0.85 1 1
PARP1 0.01 0.053 0.31 14 -0.33 1 15
DFFB 0.01 0.053 0.31 14 -0.33 1 15
CHUK -0.053 0.085 -10000 0 -0.92 2 2
FASLG -0.12 0.3 -10000 0 -0.76 153 153
FAS/FADD -0.019 0.11 -10000 0 -0.66 26 26
HGF -0.094 0.28 -10000 0 -0.78 122 122
LMNA 0.008 0.055 0.43 1 -0.51 2 3
CASP6 0.01 0.053 0.31 14 -0.33 1 15
CASP10 0.004 0.087 -10000 0 -0.85 9 9
CASP3 0.012 0.063 0.38 14 -0.38 1 15
PTPN13 -0.007 0.14 -10000 0 -0.84 24 24
CASP8 0.013 0.08 0.44 27 -0.68 1 28
IL6 -0.23 0.48 -10000 0 -1.3 122 122
MET 0.009 0.075 -10000 0 -0.77 8 8
ICAD/CAD 0.01 0.049 0.29 14 -10000 0 14
FASLG/FAS/FADD/FAF1/Caspase 10 -0.062 0.2 -10000 0 -0.54 93 93
activation of caspase activity by cytochrome c 0.008 0.057 0.34 20 -0.48 2 22
PAK2 0.01 0.052 0.31 14 -0.33 1 15
BCL2 0.003 0.11 -10000 0 -0.85 14 14
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.018 0.11 -9999 0 -0.55 31 31
SNTA1 0.003 0.098 -9999 0 -0.71 16 16
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.018 0.11 -9999 0 -0.57 30 30
MAPK12 -0.002 0.14 -9999 0 -0.43 76 76
CCND1 -0.011 0.12 -9999 0 -0.46 45 45
p38 gamma/SNTA1 -0.001 0.14 -9999 0 -0.53 33 33
MAP2K3 0.015 0.029 -9999 0 -0.85 1 1
PKN1 0.014 0.041 -9999 0 -0.85 2 2
G2/M transition checkpoint -0.001 0.14 -9999 0 -0.43 76 76
MAP2K6 0.02 0.076 -9999 0 -0.48 19 19
MAPT -0.031 0.17 -9999 0 -0.43 117 117
MAPK13 0.008 0.12 -9999 0 -0.65 27 27
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.017 0.049 -9999 0 -0.44 10 10
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.045 0.22 -10000 0 -0.84 63 63
positive regulation of NF-kappaB transcription factor activity -0.054 0.19 -10000 0 -0.68 70 70
MAP2K4 0.025 0.12 -10000 0 -0.49 19 19
IKBKB 0.016 0 -10000 0 -10000 0 0
TNFRSF10B 0.014 0.041 -10000 0 -0.85 2 2
TNFRSF10A -0.027 0.19 -10000 0 -0.85 44 44
SMPD1 -0.022 0.079 -10000 0 -0.6 1 1
IKBKG 0.013 0.05 -10000 0 -0.85 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.005 0.098 -10000 0 -0.83 12 12
TRAIL/TRAILR2 -0.048 0.17 -10000 0 -0.65 65 65
TRAIL/TRAILR3 -0.062 0.2 -10000 0 -0.67 82 82
TRAIL/TRAILR1 -0.076 0.24 -10000 0 -0.76 89 89
TRAIL/TRAILR4 -0.054 0.19 -10000 0 -0.68 70 70
TRAIL/TRAILR1/DAP3/GTP -0.062 0.2 -10000 0 -0.62 88 88
IKK complex -0.022 0.078 -10000 0 -0.76 4 4
RIPK1 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 -0.02 0.18 -10000 0 -0.65 64 64
MAP3K1 -0.032 0.11 -10000 0 -0.53 19 19
TRAILR4 (trimer) 0.005 0.098 -10000 0 -0.83 12 12
TRADD 0.015 0.029 -10000 0 -0.85 1 1
TRAILR1 (trimer) -0.027 0.19 -10000 0 -0.85 44 44
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.001 0.15 -10000 0 -0.72 19 19
CFLAR 0.016 0 -10000 0 -10000 0 0
MAPK1 -0.02 0.18 -10000 0 -0.65 64 64
TRAIL/TRAILR1/FADD/TRADD/RIP -0.058 0.18 -10000 0 -0.96 19 19
mol:ceramide 0.002 0.085 -10000 0 -0.3 64 64
FADD 0.016 0 -10000 0 -10000 0 0
MAPK8 0.028 0.13 -10000 0 -0.72 6 6
TRAF2 0.014 0.041 -10000 0 -0.85 2 2
TRAILR3 (trimer) -0.007 0.13 -10000 0 -0.76 26 26
CHUK 0.015 0.029 -10000 0 -0.85 1 1
TRAIL/TRAILR1/FADD -0.067 0.21 -10000 0 -0.67 88 88
DAP3 0.016 0 -10000 0 -10000 0 0
CASP10 -0.054 0.19 0.33 5 -0.68 61 66
JNK cascade -0.054 0.19 -10000 0 -0.68 70 70
TRAIL (trimer) -0.045 0.22 -10000 0 -0.84 63 63
TNFRSF10C -0.007 0.13 -10000 0 -0.76 26 26
TRAIL/TRAILR1/DAP3/GTP/FADD -0.058 0.19 -10000 0 -0.58 88 88
TRAIL/TRAILR2/FADD -0.041 0.15 -10000 0 -0.56 64 64
cell death 0.002 0.085 -10000 0 -0.3 64 64
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.019 0.1 -10000 0 -0.68 1 1
TRAILR2 (trimer) 0.014 0.041 -10000 0 -0.85 2 2
CASP8 0.009 0.056 0.31 1 -1.1 1 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.035 0.12 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.007 0.1 -10000 0 -0.35 53 53
epithelial cell differentiation -0.037 0.12 -10000 0 -0.48 44 44
CYFIP2 0.008 0.078 -10000 0 -0.76 9 9
ENAH 0.045 0.12 -10000 0 -0.51 13 13
EGFR -0.021 0.17 -10000 0 -0.78 41 41
EPHA2 0.006 0.094 -10000 0 -0.83 11 11
MYO6 0.008 0.13 -10000 0 -0.48 45 45
CTNNB1 0.016 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.05 -10000 0 -0.49 9 9
AQP5 -0.057 0.12 -10000 0 -0.58 14 14
CTNND1 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.13 -10000 0 -0.45 46 46
regulation of calcium-dependent cell-cell adhesion -0.1 0.25 -10000 0 -0.53 169 169
EGF -0.15 0.31 -10000 0 -0.73 196 196
NCKAP1 0.016 0 -10000 0 -10000 0 0
AQP3 -0.084 0.21 -10000 0 -0.69 77 77
cortical microtubule organization -0.037 0.12 -10000 0 -0.48 44 44
GO:0000145 0.009 0.12 -10000 0 -0.43 46 46
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.038 0.12 -10000 0 -0.49 44 44
MLLT4 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.041 0.13 -10000 0 -0.74 14 14
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.1 -10000 0 -0.55 28 28
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.02 0.13 -10000 0 -0.58 7 7
PVRL2 0.015 0.029 -10000 0 -0.85 1 1
ZYX 0.007 0.13 -10000 0 -0.46 4 4
ARF6/GTP -0.016 0.092 -10000 0 -0.5 28 28
CDH1 -0.054 0.22 -10000 0 -0.76 80 80
EGFR/EGFR/EGF/EGF -0.13 0.22 -10000 0 -0.73 49 49
RhoA/GDP -0.035 0.11 -10000 0 -10000 0 0
actin cytoskeleton organization 0.017 0.13 -10000 0 -0.84 2 2
IGF-1R heterotetramer 0.013 0.05 -10000 0 -0.85 3 3
GIT1 0.014 0.041 -10000 0 -0.85 2 2
IGF1R 0.013 0.05 -10000 0 -0.85 3 3
IGF1 -0.058 0.22 -10000 0 -0.72 89 89
DIAPH1 -0.007 0.068 -10000 0 -0.89 5 5
Wnt receptor signaling pathway 0.037 0.12 0.48 44 -10000 0 44
RHOA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.041 0.13 -10000 0 -0.73 14 14
CTNNA1 0.016 0 -10000 0 -10000 0 0
VCL 0.017 0.13 -10000 0 -0.88 2 2
EFNA1 0.001 0.12 -10000 0 -0.85 16 16
LPP 0.011 0.14 -10000 0 -0.78 7 7
Ephrin A1/EPHA2 -0.047 0.15 -10000 0 -0.84 14 14
SEC6/SEC8 -0.031 0.099 -10000 0 -10000 0 0
MGAT3 -0.11 0.25 -10000 0 -0.54 169 169
HGF/MET -0.091 0.19 -10000 0 -0.84 24 24
HGF -0.094 0.28 -10000 0 -0.78 122 122
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.007 0.1 -10000 0 -0.35 53 53
actin cable formation 0.066 0.11 -10000 0 -0.44 11 11
KIAA1543 0.007 0.17 -10000 0 -1.1 8 8
KIFC3 -0.006 0.16 -10000 0 -0.5 72 72
NCK1 0.014 0.041 -10000 0 -0.85 2 2
EXOC3 0.015 0.029 -10000 0 -0.85 1 1
ACTN1 0.003 0.14 -10000 0 -0.49 55 55
NCK1/GIT1 -0.003 0.044 -10000 0 -0.65 4 4
mol:GDP -0.037 0.12 -10000 0 -0.48 44 44
EXOC4 0.016 0 -10000 0 -10000 0 0
STX4 0.009 0.13 -10000 0 -0.46 1 1
PIP5K1C 0.008 0.13 -10000 0 -0.46 46 46
LIMA1 0.002 0.096 -10000 0 -0.66 18 18
ABI1 0.016 0 -10000 0 -10000 0 0
ROCK1 -0.036 0.11 -10000 0 -0.62 15 15
adherens junction assembly 0.013 0.19 -10000 0 -0.88 21 21
IGF-1R heterotetramer/IGF1 -0.07 0.17 -10000 0 -0.73 22 22
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.001 0.022 -10000 0 -0.65 1 1
MET 0.009 0.075 -10000 0 -0.77 8 8
PLEKHA7 0.002 0.15 -10000 0 -0.51 51 51
mol:GTP -0.017 0.1 -10000 0 -0.54 28 28
establishment of epithelial cell apical/basal polarity 0.043 0.12 -10000 0 -0.76 1 1
cortical actin cytoskeleton stabilization 0.007 0.1 -10000 0 -0.35 53 53
regulation of cell-cell adhesion 0.017 0.13 -10000 0 -0.84 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.007 0.1 -10000 0 -0.35 53 53
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.055 0.16 0.79 27 -10000 0 27
GNAI2 0.015 0.029 -10000 0 -0.85 1 1
S1P/S1P5/G12 -0.044 0.15 -10000 0 -0.54 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.052 0.22 -10000 0 -0.76 79 79
RhoA/GTP -0.057 0.16 -10000 0 -0.82 27 27
negative regulation of cAMP metabolic process -0.025 0.19 -10000 0 -0.51 87 87
GNAZ 0.007 0.085 -10000 0 -0.79 10 10
GNAI3 0.016 0 -10000 0 -10000 0 0
GNA12 0.016 0 -10000 0 -10000 0 0
S1PR5 -0.052 0.23 -10000 0 -0.81 73 73
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.026 0.19 -10000 0 -0.51 87 87
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
GNAI1 0.004 0.1 -10000 0 -0.85 12 12
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.093 0.27 -9999 0 -0.75 126 126
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.009 0.071 -9999 0 -0.72 8 8
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 0 0.069 -9999 0 -0.38 5 5
HIF1A -0.009 0.071 -9999 0 -0.38 4 4
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.007 0.061 -9999 0 -0.58 9 9
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.043 0.21 -9999 0 -0.81 63 63
ARNT/IPAS -0.08 0.2 -9999 0 -0.57 126 126
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.016 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.001 0.068 -9999 0 -0.36 4 4
CUL2 0.015 0.029 -9999 0 -0.85 1 1
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.004 0.044 -9999 0 -0.56 3 3
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.001 0.068 -9999 0 -0.41 2 2
PHD1-3/OS9 -0.14 0.23 -9999 0 -0.51 237 237
HIF1A/RACK1/Elongin B/Elongin C -0.026 0.057 -9999 0 -0.53 6 6
VHL 0.012 0.058 -9999 0 -0.85 4 4
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.001 0.068 -9999 0 -0.36 4 4
EGLN3 -0.21 0.38 -9999 0 -0.85 236 236
EGLN2 0.013 0.047 -9999 0 -0.78 3 3
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.015 0.029 -9999 0 -0.85 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.032 0.067 -9999 0 -0.68 6 6
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.015 0.022 -9999 0 -0.65 1 1
HIF1A/p19ARF -0.031 0.15 -9999 0 -0.54 59 59
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.006 0.09 -9999 0 -0.79 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.006 0.096 -9999 0 -0.28 74 74
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.007 0.086 -9999 0 -0.85 9 9
MAP3K12 0.011 0.062 -9999 0 -0.81 5 5
FGR -0.012 0.15 -9999 0 -0.83 30 30
p38 alpha/TAB1 -0.034 0.089 -9999 0 -0.42 28 28
PRKG1 -0.14 0.33 -9999 0 -0.84 158 158
DUSP8 -0.014 0.14 -9999 0 -0.68 38 38
PGK/cGMP/p38 alpha -0.1 0.19 -9999 0 -0.46 164 164
apoptosis -0.033 0.085 -9999 0 -0.4 28 28
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.012 0.058 -9999 0 -0.85 4 4
DUSP1 -0.081 0.27 -9999 0 -0.84 101 101
PAK1 0.016 0 -9999 0 -10000 0 0
SRC 0.015 0.022 -9999 0 -0.65 1 1
RAC1/OSM/MEKK3/MKK3 -0.001 0.024 -9999 0 -0.51 2 2
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 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 0.015 0.029 -9999 0 -0.85 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.003 0.16 -9999 0 -0.53 39 39
BLK -0.081 0.25 -9999 0 -0.72 115 115
HCK -0.005 0.13 -9999 0 -0.83 22 22
MAP2K3 0.015 0.029 -9999 0 -0.85 1 1
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.007 0.083 -9999 0 -0.77 10 10
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.016 0.12 -9999 0 -0.45 29 29
positive regulation of innate immune response 0.01 0.16 -9999 0 -0.57 36 36
LCK -0.08 0.26 -9999 0 -0.8 104 104
p38alpha-beta/MKP7 0.019 0.16 -9999 0 -0.6 25 25
p38alpha-beta/MKP5 0.015 0.16 -9999 0 -0.63 29 29
PGK/cGMP -0.12 0.25 -9999 0 -0.66 158 158
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.028 0.22 -9999 0 -0.62 66 66
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.11 0.28 -9999 0 -0.76 139 139
ErbB2/ErbB3 signaling events

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
USP8 0.024 0.029 -10000 0 -0.58 2 2
RAS family/GTP -0.013 0.16 -10000 0 -0.84 19 19
NFATC4 -0.015 0.15 -10000 0 -0.54 25 25
ERBB2IP 0.015 0.029 -10000 0 -0.84 1 1
HSP90 (dimer) 0.016 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.029 0.16 -10000 0 -0.72 18 18
JUN 0.015 0.12 -10000 0 -0.44 30 30
HRAS 0.011 0.059 -10000 0 -0.77 5 5
DOCK7 -0.018 0.16 -10000 0 -0.67 19 19
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.069 0.19 -10000 0 -0.59 92 92
AKT1 0.014 0.023 -10000 0 -0.66 1 1
BAD 0.022 0.049 -10000 0 -0.67 4 4
MAPK10 -0.031 0.082 -10000 0 -0.32 38 38
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.028 0.18 -10000 0 -0.82 18 18
RAF1 0.002 0.16 -10000 0 -0.77 19 19
ErbB2/ErbB3/neuregulin 2 -0.07 0.2 -10000 0 -0.57 94 94
STAT3 0.001 0.009 -10000 0 -10000 0 0
cell migration 0.028 0.093 -10000 0 -0.3 22 22
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.086 0.28 -10000 0 -0.63 120 120
FOS -0.057 0.23 -10000 0 -0.5 92 92
NRAS 0.016 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.16 -10000 0 -0.72 18 18
MAPK3 -0.058 0.24 -10000 0 -0.64 41 41
MAPK1 -0.058 0.23 -10000 0 -0.63 42 42
JAK2 -0.018 0.16 -10000 0 -0.67 19 19
NF2 -0.003 0.02 -10000 0 -0.48 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.022 0.18 -10000 0 -0.49 90 90
NRG1 -0.062 0.24 -10000 0 -0.8 85 85
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 -0.009 0.14 -10000 0 -0.44 30 30
MAPK9 -0.025 0.067 -10000 0 -0.29 18 18
ERBB2 -0.002 0.045 0.47 1 -0.63 4 5
ERBB3 -0.026 0.18 -10000 0 -0.85 42 42
SHC1 0.015 0.022 -10000 0 -0.65 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.005 0.044 0.68 3 -10000 0 3
STAT3 (dimer) 0.001 0.009 -10000 0 -10000 0 0
RNF41 0.032 0.028 -10000 0 -0.53 2 2
FRAP1 0.012 0.02 -10000 0 -0.58 1 1
RAC1-CDC42/GTP -0.036 0.097 -10000 0 -0.43 19 19
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.038 0.31 1 -0.54 4 5
CHRNA1 -0.1 0.29 -10000 0 -0.67 128 128
myelination -0.003 0.15 -10000 0 -0.5 25 25
PPP3CB -0.015 0.15 -10000 0 -0.61 18 18
KRAS 0.016 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.031 0.15 -10000 0 -0.89 17 17
NRG2 -0.059 0.22 -10000 0 -0.71 92 92
mol:GDP -0.022 0.18 -10000 0 -0.48 90 90
SOS1 0.016 0.001 -10000 0 -10000 0 0
MAP2K2 0.005 0.16 -10000 0 -0.74 19 19
SRC 0.015 0.022 -10000 0 -0.65 1 1
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.018 0.16 -10000 0 -0.67 19 19
MAP2K1 -0.051 0.21 -10000 0 -0.63 39 39
heart morphogenesis -0.029 0.16 -10000 0 -0.72 18 18
RAS family/GDP -0.013 0.16 -10000 0 -0.84 19 19
GRB2 0.016 0.001 -10000 0 -10000 0 0
PRKACA -0.003 0.009 -10000 0 -10000 0 0
CHRNE 0.012 0.052 -10000 0 -0.24 30 30
HSP90AA1 0.016 0 -10000 0 -10000 0 0
activation of caspase activity -0.014 0.023 0.66 1 -10000 0 1
nervous system development -0.029 0.16 -10000 0 -0.72 18 18
CDC42 0.016 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.009 0.043 -10000 0 -0.85 2 2
HSPA8 0.016 0.041 -10000 0 -0.84 2 2
SMAD3/SMAD4/ER alpha -0.018 0.16 -10000 0 -0.59 49 49
AKT1 0.018 0.031 -10000 0 -0.84 1 1
GSC 0 0.23 -10000 0 -1.3 20 20
NKX2-5 -0.024 0.14 -10000 0 -0.65 39 39
muscle cell differentiation 0.03 0.09 0.5 9 -10000 0 9
SMAD2-3/SMAD4/SP1 0.048 0.098 -10000 0 -0.44 3 3
SMAD4 0.018 0.045 -10000 0 -10000 0 0
CBFB 0.015 0.029 -10000 0 -0.85 1 1
SAP18 0.017 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.013 0.087 -10000 0 -0.64 5 5
SMAD3/SMAD4/VDR -0.019 0.091 -10000 0 -0.53 2 2
MYC -0.024 0.18 -10000 0 -0.82 40 40
CDKN2B 0.031 0.24 -10000 0 -1.5 19 19
AP1 0.005 0.17 -10000 0 -0.64 21 21
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.069 0.067 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.044 0.077 -10000 0 -0.47 5 5
SP3 0.018 0.041 -10000 0 -0.84 2 2
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.018 0.15 -10000 0 -0.7 41 41
SMAD3/SMAD4/GR 0.004 0.053 -10000 0 -0.47 3 3
GATA3 -0.12 0.29 -10000 0 -0.74 159 159
SKI/SIN3/HDAC complex/NCoR1 0.054 0.055 -10000 0 -0.42 1 1
MEF2C/TIF2 -0.059 0.26 -10000 0 -0.83 65 65
endothelial cell migration 0.31 0.59 1.6 147 -10000 0 147
MAX 0.026 0.022 -10000 0 -10000 0 0
RBBP7 0.017 0.002 -10000 0 -10000 0 0
RBBP4 0.016 0.029 -10000 0 -0.85 1 1
RUNX2 -0.013 0.15 -10000 0 -0.82 31 31
RUNX3 -0.029 0.19 -10000 0 -0.83 48 48
RUNX1 -0.013 0.15 -10000 0 -0.84 30 30
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.023 0.055 -10000 0 -0.73 4 4
VDR -0.028 0.17 -10000 0 -0.66 58 58
CDKN1A 0.059 0.15 -10000 0 -1.5 6 6
KAT2B 0.013 0.029 -10000 0 -0.84 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.023 0.12 -10000 0 -0.54 25 25
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.041 -10000 0 -0.85 2 2
SERPINE1 -0.32 0.6 -10000 0 -1.6 147 147
SMAD3/SMAD4/ATF2 -0.01 0.081 -10000 0 -0.58 14 14
SMAD3/SMAD4/ATF3 -0.044 0.14 -10000 0 -0.57 33 33
SAP30 -0.013 0.16 -10000 0 -0.85 31 31
Cbp/p300/PIAS3 0 0.036 -10000 0 -0.57 2 2
JUN 0.018 0.17 -10000 0 -0.65 19 19
SMAD3/SMAD4/IRF7 -0.009 0.077 -10000 0 -0.6 10 10
TFE3 0.014 0.02 -10000 0 -10000 0 0
COL1A2 -0.11 0.34 -10000 0 -0.9 118 118
mesenchymal cell differentiation 0.021 0.11 0.61 28 -10000 0 28
DLX1 -0.1 0.29 -10000 0 -0.8 131 131
TCF3 0.016 0 -10000 0 -10000 0 0
FOS -0.077 0.26 -10000 0 -0.73 120 120
SMAD3/SMAD4/Max 0.006 0.043 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.001 0.029 -10000 0 -0.57 2 2
ZBTB17 0.011 0.051 -10000 0 -0.85 3 3
LAMC1 0.048 0.055 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.036 -10000 0 -10000 0 0
IRF7 0.006 0.097 -10000 0 -0.78 13 13
ESR1 -0.034 0.2 -10000 0 -0.8 58 58
HNF4A -0.13 0.32 -10000 0 -0.84 150 150
MEF2C -0.007 0.23 -10000 0 -0.82 52 52
SMAD2-3/SMAD4 -0.004 0.043 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.002 0.031 -10000 0 -0.57 2 2
IGHV3OR16-13 -0.009 0.031 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.012 0.009 -10000 0 -10000 0 0
SKIL 0.008 0.085 -10000 0 -0.83 9 9
HDAC1 0.017 0.002 -10000 0 -10000 0 0
HDAC2 0.017 0.002 -10000 0 -10000 0 0
SNIP1 0.018 0.004 -10000 0 -10000 0 0
GCN5L2 -0.006 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0 0.043 -10000 0 -10000 0 0
MSG1/HSC70 -0.008 0.097 -10000 0 -0.5 32 32
SMAD2 0.019 0.027 -10000 0 -10000 0 0
SMAD3 0.019 0.039 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.041 0.061 -10000 0 -0.43 2 2
SMAD2/SMAD2/SMAD4 0.014 0.038 -10000 0 -0.6 1 1
NCOR1 0.016 0.029 -10000 0 -0.85 1 1
NCOA2 -0.039 0.21 -10000 0 -0.85 57 57
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A -0.01 0.069 -10000 0 -0.48 19 19
SMAD2-3/SMAD4/SP1/MIZ-1 0.055 0.1 -10000 0 -0.51 3 3
IFNB1 0.042 0.089 -10000 0 -0.57 10 10
SMAD3/SMAD4/MEF2C -0.003 0.22 -10000 0 -0.79 51 51
CITED1 -0.007 0.12 -10000 0 -0.67 30 30
SMAD2-3/SMAD4/ARC105 0.001 0.047 -10000 0 -0.53 2 2
RBL1 0.006 0.091 -10000 0 -0.85 10 10
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.058 0.11 -10000 0 -0.58 19 19
RUNX1-3/PEBPB2 -0.048 0.18 -10000 0 -0.66 61 61
SMAD7 0.041 0.16 -10000 0 -0.68 12 12
MYC/MIZ-1 -0.028 0.14 -10000 0 -0.63 43 43
SMAD3/SMAD4 -0.085 0.18 0.31 7 -0.48 63 70
IL10 -0.074 0.31 -10000 0 -0.81 92 92
PIASy/HDAC complex 0.021 0.043 -10000 0 -0.85 2 2
PIAS3 0.012 0.008 -10000 0 -10000 0 0
CDK2 0.012 0.008 -10000 0 -10000 0 0
IL5 -0.043 0.22 -10000 0 -0.7 42 42
CDK4 0.012 0.009 -10000 0 -10000 0 0
PIAS4 0.021 0.043 -10000 0 -0.85 2 2
ATF3 -0.052 0.21 -10000 0 -0.7 84 84
SMAD3/SMAD4/SP1 -0.013 0.072 -10000 0 -10000 0 0
FOXG1 -0.016 0.12 -10000 0 -0.65 30 30
FOXO3 0.032 0.028 -10000 0 -0.65 1 1
FOXO1 0.029 0.05 -10000 0 -0.5 7 7
FOXO4 0.032 0.028 -10000 0 -0.65 1 1
heart looping -0.006 0.23 -10000 0 -0.8 52 52
CEBPB 0.01 0.07 -10000 0 -0.65 10 10
SMAD3/SMAD4/DLX1 -0.081 0.2 -10000 0 -0.57 110 110
MYOD1 -0.01 0.095 -10000 0 -0.65 19 19
SMAD3/SMAD4/HNF4 -0.099 0.22 -10000 0 -0.59 150 150
SMAD3/SMAD4/GATA3 -0.1 0.22 -10000 0 -0.66 81 81
SnoN/SIN3/HDAC complex/NCoR1 0.008 0.084 -10000 0 -0.82 9 9
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.039 0.17 -10000 0 -0.67 40 40
SMAD3/SMAD4/SP1-3 0.017 0.081 -10000 0 -0.54 2 2
MED15 0.014 0.041 -10000 0 -0.85 2 2
SP1 0.011 0.053 -10000 0 -10000 0 0
SIN3B 0.015 0.041 -10000 0 -0.85 2 2
SIN3A 0.017 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.016 0.16 -10000 0 -0.64 29 29
ITGB5 0.068 0.081 -10000 0 -0.53 1 1
TGIF/SIN3/HDAC complex/CtBP 0.053 0.051 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.076 0.2 -10000 0 -0.58 110 110
AR -0.097 0.29 -10000 0 -0.82 120 120
negative regulation of cell growth 0.035 0.083 -10000 0 -0.47 2 2
SMAD3/SMAD4/MYOD -0.012 0.07 -10000 0 -0.47 7 7
E2F5 0.01 0.068 -10000 0 -0.82 6 6
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.019 0.099 -10000 0 -0.59 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 0.052 0.079 -10000 0 -0.5 5 5
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.007 0.17 -10000 0 -0.67 19 19
SMAD3/SMAD4/RUNX2 -0.021 0.11 -10000 0 -0.61 28 28
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.002 0.11 -10000 0 -0.85 14 14
Nectin adhesion pathway

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
PDGFRB -0.12 0.31 -9999 0 -0.84 140 140
alphaV beta3 Integrin -0.05 0.17 -9999 0 -0.6 74 74
PTK2 -0.034 0.12 -9999 0 -0.64 25 25
positive regulation of JNK cascade -0.012 0.059 -9999 0 -0.35 25 25
CDC42/GDP 0.053 0.095 -9999 0 -0.48 24 24
Rac1/GDP 0.055 0.094 -9999 0 -0.47 24 24
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.014 0.073 -9999 0 -0.43 25 25
nectin-3/I-afadin -0.018 0.11 -9999 0 -0.65 24 24
RAPGEF1 0.046 0.11 -9999 0 -0.55 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.037 0.12 -9999 0 -0.65 24 24
PDGFB-D/PDGFRB -0.12 0.31 -9999 0 -0.84 140 140
TLN1 0.029 0.08 -9999 0 -0.56 10 10
Rap1/GTP -0.012 0.062 -9999 0 -0.45 6 6
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.018 0.11 -9999 0 -0.65 24 24
PVR 0.015 0.022 -9999 0 -0.65 1 1
Necl-5(dimer) 0.015 0.022 -9999 0 -0.65 1 1
mol:GDP 0.05 0.12 -9999 0 -0.61 24 24
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
PI3K -0.093 0.21 -9999 0 -0.52 155 155
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.005 0.052 -9999 0 -0.54 8 8
positive regulation of lamellipodium assembly -0.012 0.06 -9999 0 -0.37 24 24
PVRL1 0.009 0.071 -9999 0 -0.72 8 8
PVRL3 -0.007 0.14 -9999 0 -0.85 24 24
PVRL2 0.015 0.029 -9999 0 -0.85 1 1
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
CDH1 -0.054 0.22 -9999 0 -0.76 80 80
CLDN1 -0.09 0.27 -9999 0 -0.76 121 121
JAM-A/CLDN1 -0.074 0.18 -9999 0 -0.53 89 89
SRC -0.026 0.12 -9999 0 -0.75 24 24
ITGB3 -0.046 0.21 -9999 0 -0.76 71 71
nectin-1(dimer)/I-afadin/I-afadin -0.005 0.052 -9999 0 -0.54 8 8
FARP2 0.042 0.12 -9999 0 -0.6 25 25
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.016 0.092 -9999 0 -0.56 24 24
nectin-1/I-afadin -0.005 0.052 -9999 0 -0.54 8 8
nectin-2/I-afadin -0.001 0.022 -9999 0 -0.65 1 1
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 -0.019 0.1 -9999 0 -0.58 27 27
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.016 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.012 0.059 -9999 0 -0.35 25 25
alphaV/beta3 Integrin/Talin 0.007 0.16 -9999 0 -0.89 10 10
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.001 0.022 -9999 0 -0.65 1 1
nectin-2(dimer)/I-afadin/I-afadin -0.001 0.022 -9999 0 -0.65 1 1
PIP5K1C 0.021 0.079 -9999 0 -0.55 10 10
VAV2 0.042 0.11 -9999 0 -0.61 24 24
RAP1/GDP -0.014 0.073 -9999 0 -0.44 24 24
ITGAV 0.009 0.074 -9999 0 -0.82 7 7
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.016 0.093 -9999 0 -0.56 25 25
nectin-3(dimer)/I-afadin/I-afadin -0.018 0.11 -9999 0 -0.65 24 24
Rac1/GTP -0.014 0.075 -9999 0 -0.45 24 24
PTPRM -0.013 0.076 -9999 0 -0.38 31 31
E-cadherin/beta catenin/alpha catenin -0.038 0.12 -9999 0 -0.72 4 4
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.016 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.091 0.18 -9999 0 -0.71 13 13
Syndecan-3/Neurocan -0.015 0.081 -9999 0 -0.77 5 5
POMC -0.014 0.15 -9999 0 -0.72 36 36
EGFR -0.021 0.17 -9999 0 -0.78 41 41
Syndecan-3/EGFR -0.025 0.11 -9999 0 -0.54 32 32
AGRP -0.01 0.12 -9999 0 -0.65 28 28
NCSTN 0.015 0.029 -9999 0 -0.85 1 1
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.009 0.076 -9999 0 -0.85 7 7
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.009 0.11 -9999 0 -0.65 27 27
long-term memory -0.009 0.069 -9999 0 -0.54 14 14
Syndecan-3/IL8 -0.072 0.17 -9999 0 -0.52 63 63
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin -0.001 0.016 -9999 0 -0.48 1 1
FYN 0.007 0.086 -9999 0 -0.85 9 9
limb bud formation -0.006 0.06 -9999 0 -0.78 5 5
MC4R -0.007 0.087 -9999 0 -0.65 16 16
SRC 0.015 0.022 -9999 0 -0.65 1 1
PTN -0.16 0.33 -9999 0 -0.77 201 201
FGFR/FGF/Syndecan-3 -0.006 0.061 -9999 0 -0.8 5 5
neuron projection morphogenesis -0.096 0.18 -9999 0 -0.68 21 21
Syndecan-3/AgRP -0.016 0.082 -9999 0 -0.71 6 6
Syndecan-3/AgRP/MC4R -0.021 0.088 -9999 0 -0.68 6 6
Fyn/Cortactin -0.007 0.065 -9999 0 -0.65 9 9
SDC3 -0.006 0.062 -9999 0 -0.81 5 5
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.071 0.16 -9999 0 -0.52 63 63
IL8 -0.11 0.28 -9999 0 -0.72 154 154
Syndecan-3/Fyn/Cortactin -0.01 0.071 -9999 0 -0.55 14 14
Syndecan-3/CASK -0.005 0.059 -9999 0 -0.77 5 5
alpha-MSH/MC4R -0.031 0.13 -9999 0 -0.54 51 51
Gamma Secretase -0.004 0.045 -9999 0 -0.48 8 8
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.011 0.065 -9999 0 -0.85 5 5
Caspase 8 (4 units) -0.044 0.093 -9999 0 -0.49 11 11
NEF -0.02 0.065 -9999 0 -10000 0 0
NFKBIA 0.008 0.038 -9999 0 -10000 0 0
BIRC3 -0.028 0.26 -9999 0 -0.79 90 90
CYCS 0 0.15 -9999 0 -0.6 20 20
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.08 0.28 -9999 0 -0.97 73 73
MAP2K7 0.012 0.12 -9999 0 -0.54 11 11
protein ubiquitination 0.042 0.12 -9999 0 -0.51 23 23
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS -0.009 0.15 -9999 0 -0.85 26 26
BID -0.003 0.13 -9999 0 -0.58 10 10
NF-kappa-B/RelA/I kappa B alpha -0.033 0.099 -9999 0 -0.55 1 1
TRADD 0.015 0.029 -9999 0 -0.85 1 1
MAP3K5 0.014 0.041 -9999 0 -0.85 2 2
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.033 0.1 -9999 0 -0.55 1 1
MAPK8 0.016 0.12 -9999 0 -0.48 19 19
APAF1 0.015 0.029 -9999 0 -0.85 1 1
TRAF1 0.008 0.082 -9999 0 -0.8 9 9
TRAF2 0.014 0.041 -9999 0 -0.85 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.014 0.14 -9999 0 -0.57 10 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.036 0.1 -9999 0 -0.54 5 5
CHUK 0.041 0.13 -9999 0 -0.57 23 23
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.016 0.085 -9999 0 -0.48 29 29
TCRz/NEF -0.11 0.26 -9999 0 -0.73 111 111
TNF -0.062 0.23 -9999 0 -0.75 90 90
FASLG -0.14 0.4 -9999 0 -0.91 169 169
NFKB1 0.007 0.047 -9999 0 -0.84 1 1
TNFR1A/BAG4/TNF-alpha -0.052 0.15 -9999 0 -0.49 95 95
CASP6 -0.027 0.069 -9999 0 -0.52 3 3
CASP7 0.012 0.22 -9999 0 -0.65 74 74
RELA 0.008 0.038 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 0.012 0.22 -9999 0 -0.65 74 74
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.049 -9999 0 -0.65 5 5
CASP8 0.015 0.029 -9999 0 -0.85 1 1
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.032 0.14 -9999 0 -0.67 22 22
APAF-1/Caspase 9 -0.071 0.16 -9999 0 -0.56 78 78
BCL2 0.018 0.13 -9999 0 -0.52 11 11
Regulation of Androgen receptor activity

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
HDAC1 0.028 0.002 -9999 0 -10000 0 0
SMARCC1 0.009 0.013 -9999 0 -10000 0 0
REL -0.01 0.15 -9999 0 -0.83 29 29
HDAC7 0.006 0.15 -9999 0 -0.59 23 23
JUN 0.008 0.069 -9999 0 -0.76 7 7
EP300 0.014 0.041 -9999 0 -0.85 2 2
KAT2B 0.015 0.029 -9999 0 -0.85 1 1
KAT5 0.016 0.001 -9999 0 -10000 0 0
MAPK14 0.016 0.074 -9999 0 -0.62 11 11
FOXO1 0.011 0.055 -9999 0 -0.66 6 6
T-DHT/AR 0 0.16 -9999 0 -0.64 21 21
MAP2K6 0.003 0.092 -9999 0 -0.81 11 11
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.014 0.008 -9999 0 -10000 0 0
SMARCA2 0.014 0.006 -9999 0 -10000 0 0
PDE9A -0.084 0.19 -9999 0 -1.3 8 8
NCOA2 -0.04 0.21 -9999 0 -0.85 57 57
CEBPA -0.016 0.16 -9999 0 -0.77 37 37
EHMT2 0.011 0.05 -9999 0 -0.85 3 3
cell proliferation -0.002 0.19 -9999 0 -0.6 15 15
NR0B1 -0.06 0.2 -9999 0 -0.65 90 90
EGR1 -0.073 0.24 -9999 0 -0.74 102 102
RXRs/9cRA -0.013 0.071 -9999 0 -0.4 21 21
AR/RACK1/Src -0.021 0.11 -9999 0 -0.6 18 18
AR/GR -0.014 0.16 -9999 0 -0.54 44 44
GNB2L1 0.016 0.001 -9999 0 -10000 0 0
PKN1 0.014 0.041 -9999 0 -0.85 2 2
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -9999 0 -10000 0 0
MAPK8 0.016 0.077 -9999 0 -0.66 11 11
T-DHT/AR/TIF2/CARM1 -0.047 0.18 -9999 0 -0.72 39 39
SRC 0.027 0.09 -9999 0 -0.5 19 19
NR3C1 0.012 0.055 -9999 0 -0.8 4 4
KLK3 -0.12 0.26 -9999 0 -0.76 92 92
APPBP2 0.012 0.03 -9999 0 -0.86 1 1
TRIM24 0.014 0.005 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.01 0.12 -9999 0 -0.6 22 22
TMPRSS2 -0.3 0.47 -9999 0 -1.1 194 194
RXRG -0.01 0.11 -9999 0 -0.65 27 27
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0.014 0.041 -9999 0 -0.85 2 2
RXRB 0.015 0.029 -9999 0 -0.85 1 1
CARM1 0.014 0.029 -9999 0 -0.85 1 1
NR2C2 0.007 0.087 -9999 0 -0.85 9 9
KLK2 -0.025 0.2 -9999 0 -0.64 43 43
AR -0.02 0.17 -9999 0 -0.43 104 104
SENP1 0.016 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0.019 0.008 -9999 0 -10000 0 0
SRY 0.004 0.009 -9999 0 -10000 0 0
GATA2 -0.07 0.24 -9999 0 -0.73 103 103
MYST2 0.015 0.029 -9999 0 -0.85 1 1
HOXB13 -0.14 0.28 -9999 0 -0.67 187 187
T-DHT/AR/RACK1/Src 0.016 0.12 -9999 0 -0.62 17 17
positive regulation of transcription -0.07 0.24 -9999 0 -0.73 103 103
DNAJA1 0.013 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.003 -9999 0 -10000 0 0
NCOA1 0.019 0.006 -9999 0 -10000 0 0
SPDEF -0.062 0.21 -9999 0 -0.66 99 99
T-DHT/AR/TIF2 0.017 0.14 -9999 0 -0.64 21 21
T-DHT/AR/Hsp90 0.009 0.12 -9999 0 -0.6 22 22
GSK3B 0.014 0.006 -9999 0 -10000 0 0
NR2C1 0.017 0.002 -9999 0 -10000 0 0
mol:T-DHT 0.02 0.094 -9999 0 -0.52 22 22
SIRT1 0.015 0.029 -9999 0 -0.85 1 1
ZMIZ2 0.017 0.042 -9999 0 -0.85 2 2
POU2F1 0.022 0.055 -9999 0 -0.87 3 3
T-DHT/AR/DAX-1 -0.055 0.16 -9999 0 -0.66 28 28
CREBBP 0.016 0.001 -9999 0 -10000 0 0
SMARCE1 0.014 0.006 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0 0.1 -10000 0 -0.66 21 21
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 -0.08 0.27 -10000 0 -0.85 99 99
CDKN1A 0.017 0.073 -10000 0 -0.44 6 6
PRL-3/alpha Tubulin -0.005 0.056 -10000 0 -0.59 8 8
mol:Ca2+ -0.089 0.23 0.4 6 -0.65 126 132
AGT -0.1 0.3 -10000 0 -0.83 126 126
CCNA2 -0.001 0.15 -10000 0 -0.8 2 2
TUBA1B 0.016 0 -10000 0 -10000 0 0
EGR1 -0.036 0.19 -10000 0 -0.55 102 102
CDK2/Cyclin E1 0.024 0.085 -10000 0 -0.47 4 4
MAPK3 0.023 0.063 -10000 0 -0.59 9 9
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.063 -10000 0 -0.59 9 9
PTP4A1 -0.006 0.15 -10000 0 -0.5 47 47
PTP4A3 0.009 0.075 -10000 0 -0.77 8 8
PTP4A2 0.016 0 -10000 0 -10000 0 0
ITGB1 0.024 0.059 -10000 0 -0.59 8 8
SRC 0.015 0.022 -10000 0 -0.65 1 1
RAC1 0.017 0.072 -10000 0 -0.44 5 5
Rab GGTase beta/Rab GGTase alpha -0.001 0.031 -10000 0 -0.65 2 2
PRL-1/ATF-5 -0.002 0.15 -10000 0 -0.76 3 3
RABGGTA 0.014 0.041 -10000 0 -0.85 2 2
BCAR1 0.001 0.046 0.4 6 -0.53 3 9
RHOC 0.017 0.072 -10000 0 -0.44 5 5
RHOA 0.017 0.072 -10000 0 -0.44 5 5
cell motility 0.021 0.078 -10000 0 -0.44 6 6
PRL-1/alpha Tubulin 0.002 0.14 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.078 0.21 -10000 0 -0.65 107 107
ROCK1 0.021 0.078 -10000 0 -0.45 6 6
RABGGTB 0.016 0 -10000 0 -10000 0 0
CDK2 0.016 0 -10000 0 -10000 0 0
mitosis -0.005 0.15 -10000 0 -0.49 47 47
ATF5 0.008 0.074 -10000 0 -0.65 11 11
p38 MAPK signaling pathway

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
TRAF6/ASK1 -0.001 0.024 -10000 0 -0.5 2 2
TRAF2/ASK1 -0.003 0.038 -10000 0 -0.57 4 4
ATM 0.014 0.041 -10000 0 -0.85 2 2
MAP2K3 0.009 0.073 -10000 0 -0.64 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.015 0.085 -10000 0 -0.61 7 7
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.052 0.2 -10000 0 -0.67 89 89
TXN 0.009 0.027 -10000 0 -0.3 7 7
CALM1 0.016 0 -10000 0 -10000 0 0
GADD45A 0.015 0.022 -10000 0 -0.65 1 1
GADD45B -0.003 0.12 -10000 0 -0.72 23 23
MAP3K1 0.015 0.022 -10000 0 -0.65 1 1
MAP3K6 0.014 0.041 -10000 0 -0.85 2 2
MAP3K7 0.016 0 -10000 0 -10000 0 0
MAP3K4 0.014 0.041 -10000 0 -0.85 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.003 0.044 -10000 0 -0.65 4 4
TAK1/TAB family 0.004 0.028 0.22 15 -10000 0 15
RAC1/OSM/MEKK3 -0.001 0.017 -10000 0 -0.52 1 1
TRAF2 0.014 0.041 -10000 0 -0.85 2 2
RAC1/OSM/MEKK3/MKK3 -0.011 0.039 -10000 0 -0.53 3 3
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.25 0.35 -10000 0 -0.7 326 326
CCM2 0.015 0.029 -10000 0 -0.85 1 1
CaM/Ca2+/CAMKIIB -0.17 0.22 -10000 0 -0.45 326 326
MAPK11 0.002 0.11 -10000 0 -0.84 15 15
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.15 0.2 -10000 0 -0.53 88 88
OSM/MEKK3 -0.001 0.022 -10000 0 -0.65 1 1
TAOK1 -0.011 0.13 -10000 0 -0.49 57 57
TAOK2 0.021 0.023 -10000 0 -0.46 2 2
TAOK3 0.02 0.028 -10000 0 -0.46 3 3
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.014 0.041 -10000 0 -0.85 2 2
MAP3K10 0.013 0.05 -10000 0 -0.85 3 3
MAP3K3 0.016 0 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.039 -10000 0 -0.67 2 2
GADD45/MTK1/MTK1 -0.046 0.14 -10000 0 -0.62 20 20
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.028 0.086 -10000 0 -0.41 23 23
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.015 0.029 -10000 0 -0.85 1 1
AKT2 0.015 0.029 -10000 0 -0.85 1 1
STXBP4 0.015 0.029 -10000 0 -0.85 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.032 0.13 0.3 70 -0.48 13 83
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.026 0.044 -10000 0 -0.51 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.027 -10000 0 -0.56 2 2
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP -0.085 0.25 -10000 0 -0.71 120 120
PRKCI 0.015 0.022 -10000 0 -0.65 1 1
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.039 0.038 -10000 0 -1.1 1 1
PRKCZ 0.008 0.082 -10000 0 -0.85 8 8
TRIP10 0.006 0.091 -10000 0 -0.85 10 10
TC10/GTP/CIP4/Exocyst -0.006 0.061 -10000 0 -0.57 10 10
AS160/14-3-3 -0.017 0.11 -10000 0 -0.43 3 3
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 0.03 0.14 0.3 70 -0.54 13 83
STX4 0.015 0.029 -10000 0 -0.85 1 1
GSK3B 0.032 0.041 -10000 0 -1.2 1 1
SFN -0.23 0.35 -10000 0 -0.72 299 299
LNPEP -0.003 0.13 -10000 0 -0.85 20 20
YWHAE 0.016 0 -10000 0 -10000 0 0
Ceramide signaling 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
SPHK2 0.015 0.094 -10000 0 -0.6 20 20
MAP4K4 0.006 0.14 -10000 0 -0.7 20 20
BAG4 0.011 0.065 -10000 0 -0.85 5 5
PKC zeta/ceramide -0.024 0.067 0.2 1 -0.52 8 9
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.066 0.25 -10000 0 -0.81 89 89
BAX -0.006 0.029 -10000 0 -0.36 2 2
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.027 0.029 -10000 0 -0.78 1 1
BAD -0.02 0.052 -10000 0 -0.36 4 4
SMPD1 0.007 0.082 -10000 0 -0.28 47 47
RB1 -0.02 0.061 -10000 0 -0.56 4 4
FADD/Caspase 8 0.02 0.14 -10000 0 -0.7 18 18
MAP2K4 -0.008 0.047 -10000 0 -0.35 1 1
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.017 0.078 -10000 0 -0.48 16 16
EGF -0.15 0.31 -10000 0 -0.73 196 196
mol:ceramide -0.031 0.052 0.19 8 -10000 0 8
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.013 0.096 -10000 0 -0.56 24 24
ASAH1 0.011 0.059 -10000 0 -0.65 7 7
negative regulation of cell cycle -0.021 0.06 -10000 0 -0.55 4 4
cell proliferation -0.066 0.15 -10000 0 -0.5 75 75
BID 0.003 0.1 -10000 0 -0.48 19 19
MAP3K1 -0.018 0.05 0.21 2 -0.38 1 3
EIF2A 0.002 0.044 -10000 0 -10000 0 0
TRADD 0.015 0.029 -10000 0 -0.85 1 1
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.073 -10000 0 -0.44 16 16
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.002 0.072 -10000 0 -0.43 16 16
Cathepsin D/ceramide -0.021 0.054 -10000 0 -0.37 5 5
FADD 0.007 0.14 -10000 0 -0.72 18 18
KSR1 -0.027 0.082 0.21 2 -0.51 16 18
MAPK8 -0.008 0.061 0.21 1 -0.3 17 18
PRKRA -0.018 0.049 0.22 1 -10000 0 1
PDGFA 0.001 0.11 -10000 0 -0.78 17 17
TRAF2 0.014 0.041 -10000 0 -0.85 2 2
IGF1 -0.058 0.22 -10000 0 -0.72 89 89
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.031 0.052 0.19 8 -10000 0 8
CTSD 0.012 0.056 -10000 0 -0.73 5 5
regulation of nitric oxide biosynthetic process -0.001 0.022 -10000 0 -0.65 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.043 0.18 -10000 0 -0.56 72 72
PRKCD -0.027 0.16 -10000 0 -0.65 57 57
PRKCZ 0.008 0.082 -10000 0 -0.85 8 8
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.013 0.096 -10000 0 -0.56 24 24
RelA/NF kappa B1 -0.001 0.022 -10000 0 -0.65 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.041 -10000 0 -0.85 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.004 0.15 -10000 0 -0.75 19 19
TNFR1A/BAG4/TNF-alpha -0.052 0.15 -10000 0 -0.49 95 95
mol:Sphingosine-1-phosphate 0.015 0.094 -10000 0 -0.6 20 20
MAP2K1 -0.006 0.074 -10000 0 -0.47 13 13
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.011 0.049 0.19 8 -0.25 15 23
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.015 0.029 -10000 0 -0.85 1 1
TNFR1A/BAG4 -0.004 0.049 -10000 0 -0.65 5 5
EIF2AK2 -0.008 0.046 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.049 0.15 -10000 0 -0.48 90 90
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.023 0.087 -10000 0 -0.38 17 17
MAP2K2 -0.008 0.075 -10000 0 -0.46 14 14
SMPD3 0.005 0.093 -10000 0 -0.31 51 51
TNF -0.062 0.23 -10000 0 -0.75 90 90
PKC zeta/PAR4 -0.007 0.073 -10000 0 -0.71 9 9
mol:PHOSPHOCHOLINE 0.039 0.11 0.24 184 -10000 0 184
NF kappa B1/RelA/I kappa B alpha -0.006 0.062 -10000 0 -0.58 9 9
AIFM1 -0.008 0.042 0.19 8 -0.31 3 11
BCL2 0.002 0.11 -10000 0 -0.85 14 14
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.024 0.21 -9999 0 -1.5 18 18
VDR -0.028 0.17 -9999 0 -0.66 58 58
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.042 0.11 -9999 0 -0.59 7 7
RXRs/LXRs/DNA/Oxysterols 0.041 0.14 -9999 0 -0.75 7 7
MED1 0.015 0.029 -9999 0 -0.85 1 1
mol:9cRA 0.004 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.02 0.093 -9999 0 -0.65 2 2
RXRs/NUR77 -0.047 0.2 -9999 0 -0.53 80 80
RXRs/PPAR 0.039 0.067 -9999 0 -0.57 4 4
NCOR2 0.014 0.041 -9999 0 -0.85 2 2
VDR/VDR/Vit D3 -0.033 0.12 -9999 0 -0.5 58 58
RARs/VDR/DNA/Vit D3 -0.03 0.1 -9999 0 -0.53 16 16
RARA 0.013 0.05 -9999 0 -0.85 3 3
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.028 0.17 -9999 0 -0.66 58 58
RARs/RARs/DNA/9cRA -0.007 0.059 -9999 0 -0.5 12 12
RARG 0.013 0.047 -9999 0 -0.78 3 3
RPS6KB1 0 0.067 -9999 0 -0.42 18 18
RARs/THRs/DNA/SMRT 0.019 0.1 -9999 0 -0.88 3 3
THRA 0.014 0.041 -9999 0 -0.85 2 2
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.033 0.12 -9999 0 -0.5 58 58
RXRs/PPAR/9cRA/PGJ2/DNA 0.029 0.095 -9999 0 -0.57 6 6
NR1H4 -0.061 0.24 -9999 0 -0.84 79 79
RXRs/LXRs/DNA 0.051 0.11 -9999 0 -0.66 7 7
NR1H2 0.019 0.044 -9999 0 -0.88 2 2
NR1H3 0.021 0.013 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.008 0.13 -9999 0 -0.56 25 25
NR4A1 -0.12 0.29 -9999 0 -0.73 159 159
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.001 0.13 -9999 0 -0.38 76 76
RXRG -0.005 0.12 -9999 0 -0.65 27 27
RXR alpha/CCPG 0.025 0.035 -9999 0 -0.68 2 2
RXRA 0.019 0.044 -9999 0 -0.88 2 2
RXRB 0.02 0.033 -9999 0 -0.87 1 1
THRB -0.039 0.2 -9999 0 -0.72 66 66
PPARG 0.011 0.066 -9999 0 -0.78 6 6
PPARD 0.014 0.041 -9999 0 -0.85 2 2
TNF -0.012 0.33 -9999 0 -1.2 49 49
mol:Oxysterols 0.004 0.015 -9999 0 -10000 0 0
cholesterol transport 0.041 0.14 -9999 0 -0.73 7 7
PPARA 0.016 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.009 0.076 -9999 0 -0.85 7 7
RXRs/NUR77/BCL2 -0.028 0.14 -9999 0 -0.37 82 82
SREBF1 0.047 0.15 -9999 0 -1.1 5 5
RXRs/RXRs/DNA/9cRA 0.029 0.095 -9999 0 -0.57 6 6
ABCA1 0.046 0.16 -9999 0 -0.96 9 9
RARs/THRs -0.036 0.12 -9999 0 -0.89 2 2
RXRs/FXR -0.013 0.19 -9999 0 -0.56 83 83
BCL2 0.002 0.11 -9999 0 -0.85 14 14
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.052 0.22 -9999 0 -0.76 79 79
CDC42/GTP -0.042 0.13 -9999 0 -0.82 16 16
PLCG1 0.002 0.15 -9999 0 -0.84 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.015 0.029 -9999 0 -0.85 1 1
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.016 -9999 0 -0.48 1 1
cell migration -0.041 0.13 -9999 0 -0.78 16 16
S1PR5 -0.052 0.23 -9999 0 -0.81 73 73
S1PR4 -0.018 0.17 -9999 0 -0.83 36 36
MAPK3 0.001 0.16 -9999 0 -0.84 17 17
MAPK1 0.001 0.16 -9999 0 -0.84 17 17
S1P/S1P5/Gi -0.026 0.19 -9999 0 -0.51 87 87
GNAI1 0.004 0.1 -9999 0 -0.85 12 12
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.044 0.15 -9999 0 -0.54 73 73
RHOA 0.02 0.1 -9999 0 -0.49 32 32
S1P/S1P4/Gi -0.009 0.16 -9999 0 -0.82 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.007 0.085 -9999 0 -0.79 10 10
S1P/S1P4/G12/G13 -0.021 0.1 -9999 0 -0.51 36 36
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.022 -9999 0 -0.65 1 1
CDC42 0.016 0 -9999 0 -10000 0 0
BARD1 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
BARD1/CSTF1 -0.037 0.15 -10000 0 -0.65 51 51
ATM 0.014 0.041 -10000 0 -0.85 2 2
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
ATR 0.015 0.029 -10000 0 -0.85 1 1
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.028 0.053 -10000 0 -0.7 3 3
protein ubiquitination -0.041 0.14 -10000 0 -0.87 6 6
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex -0.003 0.04 -10000 0 -0.56 4 4
MRE11A 0.015 0.029 -10000 0 -0.85 1 1
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.004 0.049 -10000 0 -0.81 2 2
FANCF 0.016 0 -10000 0 -10000 0 0
BRCA1 0.008 0.085 -10000 0 -0.83 9 9
CCNE1 0 0.1 -10000 0 -0.66 21 21
CDK2/Cyclin E1 -0.011 0.074 -10000 0 -0.48 21 21
FANCG 0.015 0.029 -10000 0 -0.85 1 1
BRCA1/BACH1/BARD1 -0.043 0.17 -10000 0 -0.68 57 57
FANCE 0.014 0.037 -10000 0 -0.75 2 2
FANCC 0.014 0.037 -10000 0 -0.75 2 2
NBN 0.015 0.022 -10000 0 -0.65 1 1
FANCA 0.011 0.063 -10000 0 -0.75 6 6
DNA repair 0.055 0.14 -10000 0 -0.74 7 7
BRCA1/BARD1/ubiquitin -0.043 0.17 -10000 0 -0.68 57 57
BARD1/DNA-PK -0.029 0.12 -10000 0 -0.51 51 51
FANCL 0.016 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.037 0.15 0.65 51 -10000 0 51
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.11 -10000 0 -0.81 5 5
BRCA1/BACH1/BARD1/TopBP1 -0.038 0.15 -10000 0 -0.59 57 57
BRCA1/BARD1/P53 -0.035 0.14 -10000 0 -0.54 58 58
BARD1/CSTF1/BRCA1 -0.038 0.15 -10000 0 -0.59 56 56
BRCA1/BACH1 0.008 0.084 -10000 0 -0.82 9 9
BARD1 -0.034 0.2 -10000 0 -0.85 51 51
PCNA 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.038 0.15 -10000 0 -0.59 56 56
BRCA1/BARD1/UbcH7 -0.038 0.15 -10000 0 -0.59 57 57
BRCA1/BARD1/RAD51/PCNA -0.039 0.14 -10000 0 -0.55 57 57
BARD1/DNA-PK/P53 -0.028 0.11 -10000 0 -0.48 52 52
BRCA1/BARD1/Ubiquitin -0.043 0.17 -10000 0 -0.68 57 57
BRCA1/BARD1/CTIP -0.038 0.14 -10000 0 -0.55 59 59
FA complex 0.047 0.047 -10000 0 -1 1 1
BARD1/EWS -0.037 0.15 -10000 0 -0.65 51 51
RBBP8 0.025 0.064 -10000 0 -0.88 4 4
TP53 0.015 0.029 -10000 0 -0.85 1 1
TOPBP1 0.015 0.029 -10000 0 -0.85 1 1
G1/S transition of mitotic cell cycle 0.035 0.14 0.53 58 -10000 0 58
BRCA1/BARD1 -0.041 0.14 -10000 0 -0.89 6 6
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.038 0.15 -10000 0 -0.66 51 51
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.008 0.075 -10000 0 -0.69 10 10
RAD50 0.013 0.05 -10000 0 -0.85 3 3
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.043 0.17 -10000 0 -0.68 57 57
EWSR1 0.016 0 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.031 0.03 -9999 0 -0.4 1 1
BIRC5 -0.04 0.2 -9999 0 -0.71 68 68
NFKBIA 0.037 0.027 -9999 0 -10000 0 0
CPEB1 -0.2 0.34 -9999 0 -0.74 252 252
AKT1 0.036 0.033 -9999 0 -0.56 1 1
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.004 0.055 -9999 0 -0.5 9 9
NDEL1/TACC3 -0.001 0.044 -9999 0 -0.52 5 5
GADD45A 0.015 0.022 -9999 0 -0.65 1 1
GSK3B 0.016 0.007 -9999 0 -10000 0 0
PAK1/Aurora A 0.032 0.026 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
JUB -0.014 0.16 -9999 0 -0.85 31 31
TPX2 0.007 0.11 -9999 0 -0.53 35 35
TP53 0.036 0.026 -9999 0 -0.53 1 1
DLG7 0.024 0.027 -9999 0 -10000 0 0
AURKAIP1 0.013 0.052 -9999 0 -0.75 4 4
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.001 0.047 -9999 0 -0.54 5 5
G2/M transition of mitotic cell cycle -0.004 0.055 -9999 0 -0.5 9 9
AURKA 0.029 0.033 -9999 0 -10000 0 0
AURKB -0.018 0.066 -9999 0 -0.28 45 45
CDC25B -0.005 0.047 -9999 0 -0.41 4 4
G2/M transition checkpoint -0.017 0.099 -9999 0 -0.52 31 31
mRNA polyadenylation -0.12 0.2 -9999 0 -0.44 251 251
Aurora A/CPEB -0.12 0.2 -9999 0 -0.44 251 251
Aurora A/TACC1/TRAP/chTOG -0.001 0.042 -9999 0 -0.47 5 5
BRCA1 0.008 0.085 -9999 0 -0.83 9 9
centrosome duplication 0.031 0.026 -9999 0 -10000 0 0
regulation of centrosome cycle -0.002 0.043 -9999 0 -0.51 5 5
spindle assembly -0.001 0.041 -9999 0 -0.47 5 5
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.034 0.12 -9999 0 -0.53 34 34
CENPA -0.015 0.059 -9999 0 -0.26 37 37
Aurora A/PP2A 0.031 0.033 -9999 0 -0.4 2 2
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.043 0.027 -9999 0 -10000 0 0
negative regulation of DNA binding 0.036 0.026 -9999 0 -0.53 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.031 -9999 0 -0.65 2 2
RASA1 0.013 0.05 -9999 0 -0.85 3 3
Ajuba/Aurora A -0.017 0.1 -9999 0 -0.53 31 31
mitotic prometaphase 0.005 0.019 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.033 -9999 0 -10000 0 0
TACC1 0.012 0.058 -9999 0 -0.85 4 4
TACC3 0.012 0.055 -9999 0 -0.65 6 6
Aurora A/Antizyme1 0 0.04 -9999 0 -0.51 2 2
Aurora A/RasGAP 0.029 0.043 -9999 0 -0.56 3 3
OAZ1 0.015 0.022 -9999 0 -0.65 1 1
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0.007 -9999 0 -10000 0 0
GIT1 0.014 0.041 -9999 0 -0.85 2 2
GIT1/beta-PIX/PAK1 -0.001 0.027 -9999 0 -0.56 2 2
Importin alpha/Importin beta/TPX2 0.007 0.11 -9999 0 -0.53 35 35
PPP2R5D 0.015 0.032 -9999 0 -0.65 2 2
Aurora A/TPX2 0.024 0.096 -9999 0 -0.52 19 19
PAK1 0.016 0 -9999 0 -10000 0 0
CKAP5 0.015 0.029 -9999 0 -0.85 1 1
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.051 0.13 -9999 0 -0.71 2 2
DAPP1 -0.036 0.24 -9999 0 -0.8 61 61
Src family/SYK family/BLNK-LAT/BTK-ITK -0.064 0.3 -9999 0 -0.81 103 103
mol:DAG -0.007 0.14 -9999 0 -0.33 78 78
HRAS 0.01 0.06 -9999 0 -0.77 5 5
RAP1A 0.014 0.008 -9999 0 -10000 0 0
ARF5/GDP 0.021 0.1 -9999 0 -0.46 25 25
PLCG2 -0.054 0.21 -9999 0 -0.68 90 90
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.015 0.029 -9999 0 -0.85 1 1
mol:GTP -0.055 0.14 -9999 0 -0.48 4 4
ARF1/GTP -0.053 0.14 -9999 0 -0.6 3 3
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.054 0.14 -9999 0 -0.48 4 4
ADAP1 -0.063 0.15 -9999 0 -0.75 5 5
ARAP3 -0.055 0.14 -9999 0 -0.43 113 113
INPPL1 0.014 0.041 -9999 0 -0.85 2 2
PREX1 0.002 0.11 -9999 0 -0.85 14 14
ARHGEF6 0.003 0.1 -9999 0 -0.85 13 13
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.014 0.008 -9999 0 -10000 0 0
FYN 0.007 0.086 -9999 0 -0.85 9 9
ARF6 0.016 0 -9999 0 -10000 0 0
FGR -0.012 0.15 -9999 0 -0.83 30 30
mol:Ca2+ 0.012 0.072 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.005 0.098 -9999 0 -0.83 12 12
ZAP70 -0.054 0.23 -9999 0 -0.79 77 77
mol:IP3 0.009 0.098 -9999 0 -10000 0 0
LYN 0.012 0.058 -9999 0 -0.85 4 4
ARF1/GDP 0.021 0.1 -9999 0 -0.45 24 24
RhoA/GDP -0.054 0.13 -9999 0 -0.59 10 10
PDK1/Src/Hsp90 -0.002 0.03 -9999 0 -0.51 3 3
BLNK -0.011 0.14 -9999 0 -0.74 32 32
actin cytoskeleton reorganization 0.011 0.17 -9999 0 -0.62 16 16
SRC 0.015 0.022 -9999 0 -0.65 1 1
PLEKHA2 0.032 0.06 -9999 0 -0.56 9 9
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0.007 0.017 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.051 0.13 -9999 0 -0.75 3 3
RhoA/GTP -0.051 0.13 -9999 0 -0.58 1 1
Src family/SYK family/BLNK-LAT -0.06 0.3 -9999 0 -0.86 84 84
BLK -0.081 0.25 -9999 0 -0.72 115 115
PDPK1 0.014 0.041 -9999 0 -0.85 2 2
CYTH1 -0.051 0.13 -9999 0 -0.58 1 1
HCK -0.005 0.13 -9999 0 -0.83 22 22
CYTH3 -0.051 0.13 -9999 0 -0.58 1 1
CYTH2 -0.052 0.14 -9999 0 -0.77 3 3
KRAS 0.014 0.008 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.04 0.11 -9999 0 -0.6 24 24
SGK1 -0.044 0.13 -9999 0 -0.67 24 24
INPP5D 0.009 0.076 -9999 0 -0.85 7 7
mol:GDP 0.012 0.1 -9999 0 -0.46 28 28
SOS1 0.016 0 -9999 0 -10000 0 0
SYK -0.001 0.12 -9999 0 -0.8 19 19
ARF6/GDP -0.054 0.13 -9999 0 -0.53 18 18
mol:PI-3-4-5-P3 -0.055 0.14 -9999 0 -0.48 4 4
ARAP3/RAP1A/GTP -0.055 0.14 -9999 0 -0.48 4 4
VAV1 -0.026 0.18 -9999 0 -0.83 44 44
mol:PI-3-4-P2 0.022 0.068 -9999 0 -0.65 9 9
RAS family/GTP/PI3K Class I -0.021 0.16 -9999 0 -0.49 4 4
PLEKHA1 0.031 0.063 -9999 0 -0.56 10 10
Rac1/GDP 0.021 0.1 -9999 0 -0.45 24 24
LAT -0.022 0.16 -9999 0 -0.72 46 46
Rac1/GTP 0.017 0.14 -9999 0 -0.7 24 24
ITK -0.1 0.21 -9999 0 -0.86 33 33
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.024 0.19 -9999 0 -0.48 86 86
LCK -0.08 0.26 -9999 0 -0.8 104 104
BTK -0.066 0.16 -9999 0 -0.88 7 7
Regulation of Telomerase

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
Telomerase catalytic core complex -0.087 0.21 -9999 0 -0.68 44 44
RAD9A 0.014 0.043 -9999 0 -0.72 3 3
AP1 -0.07 0.21 -9999 0 -0.57 123 123
IFNAR2 0.01 0.071 -9999 0 -0.85 6 6
AKT1 -0.002 0.089 -9999 0 -0.35 17 17
ER alpha/Oestrogen -0.038 0.16 -9999 0 -0.64 58 58
NFX1/SIN3/HDAC complex 0.041 0.062 -9999 0 -10000 0 0
EGF -0.15 0.31 -9999 0 -0.73 196 196
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.015 0.029 -9999 0 -0.85 1 1
SP3/HDAC2 0.01 0.035 -9999 0 -0.65 2 2
TERT/c-Abl -0.099 0.18 -9999 0 -0.66 35 35
SAP18 0.016 0.002 -9999 0 -10000 0 0
MRN complex -0.003 0.04 -9999 0 -0.56 4 4
WT1 -0.26 0.36 -9999 0 -0.74 317 317
WRN 0.015 0.029 -9999 0 -0.85 1 1
SP1 0.016 0.007 -9999 0 -10000 0 0
SP3 0.013 0.041 -9999 0 -0.85 2 2
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.087 0.16 -9999 0 -0.76 9 9
Mad/Max 0.01 0.027 -9999 0 -0.48 2 2
TERT -0.089 0.22 -9999 0 -0.7 42 42
CCND1 -0.1 0.31 -9999 0 -1.3 43 43
MAX 0.015 0.006 -9999 0 -10000 0 0
RBBP7 0.016 0.003 -9999 0 -10000 0 0
RBBP4 0.015 0.029 -9999 0 -0.85 1 1
TERF2 0 0.005 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0.002 -9999 0 -10000 0 0
Telomerase/911 0.036 0.036 -9999 0 -10000 0 0
CDKN1B -0.035 0.18 -9999 0 -0.55 40 40
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 -0.014 0.16 -9999 0 -0.85 31 31
TRF2/PARP2 0 0.005 -9999 0 -10000 0 0
UBE3A 0.015 0.006 -9999 0 -10000 0 0
JUN 0.009 0.069 -9999 0 -0.76 7 7
E6 -0.001 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.007 -9999 0 -10000 0 0
FOS -0.088 0.26 -9999 0 -0.74 120 120
IFN-gamma/IRF1 -0.086 0.19 -9999 0 -0.51 151 151
PARP2 0.016 0 -9999 0 -10000 0 0
BLM 0.005 0.091 -9999 0 -0.71 14 14
Telomerase -0.002 0.096 -9999 0 -0.53 12 12
IRF1 0.018 0.032 -9999 0 -0.64 2 2
ESR1 -0.039 0.21 -9999 0 -0.82 58 58
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.027 -9999 0 -0.58 2 2
ubiquitin-dependent protein catabolic process 0.048 0.058 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.048 0.059 -9999 0 -10000 0 0
HDAC1 0.016 0.002 -9999 0 -10000 0 0
HDAC2 0.016 0.007 -9999 0 -10000 0 0
ATM -0.001 0.027 -9999 0 -0.58 2 2
SMAD3 0.015 0.099 -9999 0 -0.63 20 20
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.013 0.032 -9999 0 -0.65 2 2
MRE11A 0.015 0.029 -9999 0 -0.85 1 1
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.084 0.18 -9999 0 -0.76 14 14
NR2F2 0.015 0.042 -9999 0 -0.85 2 2
MAPK3 0.013 0.063 -9999 0 -0.49 13 13
MAPK1 0.013 0.063 -9999 0 -0.49 13 13
TGFB1/TGF beta receptor Type II -0.003 0.12 -9999 0 -0.83 20 20
NFKB1 0.015 0.029 -9999 0 -0.85 1 1
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.027 -9999 0 -0.58 2 2
NBN 0.015 0.022 -9999 0 -0.65 1 1
EGFR -0.022 0.17 -9999 0 -0.79 41 41
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.15 0.26 -9999 0 -0.59 222 222
MYC -0.023 0.18 -9999 0 -0.83 40 40
IL2 -0.002 0.077 -9999 0 -0.65 12 12
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0.05 -9999 0 -0.85 3 3
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 -0.003 0.12 -9999 0 -0.83 20 20
TRF2/BLM -0.008 0.062 -9999 0 -0.49 14 14
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.08 0.19 -9999 0 -0.72 20 20
SP1/HDAC2 0.025 0.012 -9999 0 -10000 0 0
PINX1 0.014 0.041 -9999 0 -0.85 2 2
Telomerase/EST1A -0.087 0.16 -9999 0 -0.74 10 10
Smad3/Myc -0.005 0.16 -9999 0 -0.59 55 55
911 complex -0.002 0.027 -9999 0 -0.56 1 1
IFNG -0.1 0.27 -9999 0 -0.69 151 151
Telomerase/PinX1 -0.088 0.16 -9999 0 -0.76 9 9
Telomerase/AKT1/mTOR/p70S6K 0.013 0.07 -9999 0 -10000 0 0
SIN3B 0.014 0.041 -9999 0 -0.85 2 2
YWHAE 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.087 0.16 -9999 0 -0.74 10 10
response to DNA damage stimulus 0.004 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.002 0.033 -9999 0 -0.47 2 2
TRF2/WRN 0 0.021 -9999 0 -0.61 1 1
Telomerase/hnRNP C1/C2 -0.087 0.16 -9999 0 -0.7 13 13
E2F1 0.009 0.066 -9999 0 -0.68 8 8
ZNFX1 0.016 0.002 -9999 0 -10000 0 0
PIF1 -0.023 0.16 -9999 0 -0.7 48 48
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0 -10000 0 -10000 0 0
NFATC1 0.057 0.07 -10000 0 -0.47 3 3
NFATC2 0.014 0.079 -10000 0 -0.37 9 9
NFATC3 0.02 0.058 -10000 0 -0.55 9 9
YWHAE 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.031 0.18 -10000 0 -0.54 68 68
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.087 0.2 -10000 0 -0.72 62 62
BCL2/BAX -0.012 0.087 -10000 0 -0.65 16 16
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.008 -10000 0 -10000 0 0
BAX 0.014 0.041 -10000 0 -0.85 2 2
MAPK14 0.014 0.006 -10000 0 -10000 0 0
BAD 0.012 0.055 -10000 0 -0.8 4 4
CABIN1/MEF2D -0.023 0.17 -10000 0 -0.51 68 68
Calcineurin A alpha-beta B1/BCL2 0.002 0.11 -10000 0 -0.85 14 14
FKBP8 0.014 0.041 -10000 0 -0.85 2 2
activation-induced cell death of T cells 0.022 0.16 0.5 68 -10000 0 68
KPNB1 0.015 0.029 -10000 0 -0.85 1 1
KPNA2 0.013 0.045 -10000 0 -0.65 4 4
XPO1 0.016 0.001 -10000 0 -10000 0 0
SFN -0.23 0.35 -10000 0 -0.72 299 299
MAP3K8 0.009 0.059 -10000 0 -0.77 5 5
NFAT4/CK1 alpha -0.004 0.037 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.062 0.12 -10000 0 -0.49 14 14
CABIN1 -0.032 0.18 -10000 0 -0.55 68 68
CALM1 0.014 0.006 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
MAP3K1 0.015 0.022 -10000 0 -0.65 1 1
CAMK4 -0.05 0.23 -10000 0 -0.84 69 69
mol:Ca2+ -0.002 0.008 -10000 0 -10000 0 0
MAPK3 0.015 0.029 -10000 0 -0.85 1 1
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.037 0.14 -10000 0 -0.55 60 60
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.003 0.096 -10000 0 -0.85 11 11
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.003 0.06 -10000 0 -0.46 6 6
PRKCH -0.04 0.21 -10000 0 -0.85 58 58
CABIN1/Cbp/p300 -0.001 0.031 -10000 0 -0.65 2 2
CASP3 0.014 0.006 -10000 0 -10000 0 0
PIM1 0.011 0.062 -10000 0 -0.68 7 7
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.006 0.055 -10000 0 -0.81 3 3
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.012 0.1 -10000 0 -0.6 2 2
PRKCB -0.035 0.2 -10000 0 -0.83 54 54
PRKCE 0.013 0.05 -10000 0 -0.85 3 3
JNK2/NFAT4 0.028 0.053 -10000 0 -0.49 9 9
BAD/BCL-XL -0.003 0.041 -10000 0 -0.61 4 4
PRKCD -0.027 0.16 -10000 0 -0.65 57 57
NUP214 0.016 0.001 -10000 0 -10000 0 0
PRKCZ 0.006 0.082 -10000 0 -0.85 8 8
PRKCA 0.015 0.032 -10000 0 -0.65 2 2
PRKCG -0.042 0.18 -10000 0 -0.65 68 68
PRKCQ -0.04 0.2 -10000 0 -0.78 62 62
FKBP38/BCL2 -0.012 0.087 -10000 0 -0.65 16 16
EP300 0.013 0.041 -10000 0 -0.85 2 2
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.049 0.088 -10000 0 -0.5 1 1
CaM/Ca2+/FKBP38 -0.001 0.028 -10000 0 -0.59 2 2
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.022 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.044 0.15 -10000 0 -0.57 69 69
NFATc/ERK1 0.064 0.071 -10000 0 -0.62 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.086 0.2 -10000 0 -0.67 72 72
NR4A1 -0.054 0.28 -10000 0 -0.62 160 160
GSK3B 0.014 0.006 -10000 0 -10000 0 0
positive T cell selection 0.02 0.058 -10000 0 -0.54 9 9
NFAT1/CK1 alpha -0.02 0.045 -10000 0 -0.35 1 1
RCH1/ KPNB1 -0.003 0.039 -10000 0 -0.51 5 5
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.014 0.006 -10000 0 -10000 0 0
AKAP5 -0.034 0.19 -10000 0 -0.73 60 60
MEF2D 0.015 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.055 0.072 -10000 0 -0.5 1 1
CREBBP 0.015 0.005 -10000 0 -10000 0 0
BCL2 0.002 0.11 -10000 0 -0.85 14 14
IGF1 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
NCK2 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL -0.017 0.14 -10000 0 -0.52 40 40
GRB2/SOS1/SHC 0 0.013 -10000 0 -10000 0 0
HRAS 0.012 0.059 -10000 0 -0.77 5 5
IRS1/Crk -0.018 0.14 -10000 0 -0.49 50 50
IGF-1R heterotetramer/IGF1/PTP1B -0.047 0.14 -10000 0 -0.55 41 41
AKT1 0.007 0.14 -10000 0 -0.66 16 16
BAD 0.015 0.14 -10000 0 -0.72 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.017 0.14 -10000 0 -0.49 50 50
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.019 0.14 -10000 0 -0.52 41 41
RAF1 0.023 0.13 -10000 0 -0.63 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.044 0.12 -10000 0 -0.68 9 9
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.031 0.15 -10000 0 -0.53 50 50
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
RPS6KB1 0.007 0.14 -10000 0 -0.66 15 15
GNB2L1 0.016 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.02 0.11 -10000 0 -0.52 11 11
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.04 0.11 -10000 0 -0.62 11 11
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.035 0.11 -10000 0 -0.62 4 4
IGF-1R heterotetramer 0.003 0.061 -10000 0 -0.92 3 3
IGF-1R heterotetramer/IGF1/IRS/Nck -0.047 0.13 -10000 0 -0.52 40 40
Crk/p130 Cas/Paxillin -0.043 0.12 -10000 0 -0.66 10 10
IGF1R 0.003 0.061 -10000 0 -0.92 3 3
IGF1 -0.06 0.23 -10000 0 -0.73 89 89
IRS2/Crk -0.026 0.17 -10000 0 -0.54 52 52
PI3K -0.05 0.14 -10000 0 -0.65 19 19
apoptosis -0.024 0.12 0.58 12 -10000 0 12
HRAS/GDP -0.003 0.045 -10000 0 -0.59 5 5
PRKCD -0.013 0.17 -10000 0 -0.55 65 65
RAF1/14-3-3 E 0.032 0.11 -10000 0 -0.54 8 8
BAD/14-3-3 0.024 0.13 -10000 0 -0.64 12 12
PRKCZ 0.003 0.15 -10000 0 -0.66 19 19
Crk/p130 Cas/Paxillin/FAK1 -0.036 0.1 -10000 0 -0.61 12 12
PTPN1 0.015 0.029 -10000 0 -0.85 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0 0.14 -10000 0 -0.58 34 34
BCAR1 0.013 0.05 -10000 0 -0.85 3 3
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.041 0.12 -10000 0 -0.5 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.018 0.14 -10000 0 -0.51 40 40
GRB10 0.014 0.041 -10000 0 -0.85 2 2
PTPN11 -0.017 0.14 -10000 0 -0.52 41 41
IRS1 -0.03 0.15 -10000 0 -0.53 50 50
IRS2 -0.037 0.17 -10000 0 -0.57 52 52
IGF-1R heterotetramer/IGF1 -0.06 0.17 -10000 0 -0.56 91 91
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 -0.004 0.15 -10000 0 -0.65 19 19
YWHAE 0.016 0 -10000 0 -10000 0 0
PRKD1 0.005 0.14 -10000 0 -0.56 41 41
SHC1 0.015 0.022 -10000 0 -0.65 1 1
PLK2 and PLK4 events

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
PLK2 -0.008 0.14 -9999 0 -0.84 25 25
PLK4 0.014 0.039 -9999 0 -0.65 3 3
regulation of centriole replication 0.008 0.12 -9999 0 -0.63 28 28
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.005 0.056 -10000 0 -0.59 8 8
CRKL 0.01 0.11 -10000 0 -0.49 6 6
mol:PIP3 -0.026 0.007 -10000 0 -10000 0 0
AKT1 0 0.031 -10000 0 -0.53 3 3
PTK2B 0.016 0 -10000 0 -10000 0 0
RAPGEF1 0.019 0.1 -10000 0 -0.57 3 3
RANBP10 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
HGF/MET/SHIP2 -0.076 0.18 -10000 0 -0.57 90 90
MAP3K5 0.009 0.14 -10000 0 -0.57 27 27
HGF/MET/CIN85/CBL/ENDOPHILINS -0.071 0.18 -10000 0 -0.56 88 88
AP1 -0.053 0.19 -10000 0 -0.51 123 123
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.015 0.022 -10000 0 -0.65 1 1
apoptosis -0.05 0.23 -10000 0 -0.85 60 60
STAT3 (dimer) 0.007 0.12 -10000 0 -0.57 2 2
GAB1/CRKL/SHP2/PI3K -0.033 0.094 -10000 0 -0.69 7 7
INPP5D 0.009 0.076 -10000 0 -0.85 7 7
CBL/CRK 0.018 0.11 -10000 0 -0.7 4 4
PTPN11 0.015 0.029 -10000 0 -0.85 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
PTEN 0.016 0 -10000 0 -10000 0 0
ELK1 -0.002 0.03 0.26 2 -0.27 8 10
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.025 0.064 -10000 0 -0.37 7 7
PAK1 0.009 0.03 -10000 0 -0.5 3 3
HGF/MET/RANBP10 -0.075 0.18 -10000 0 -0.57 88 88
HRAS -0.011 0.16 -10000 0 -0.71 9 9
DOCK1 0.018 0.11 -10000 0 -0.61 5 5
GAB1 0 0.11 -10000 0 -0.44 11 11
CRK 0.009 0.11 -10000 0 -0.59 5 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.069 0.18 -10000 0 -0.6 88 88
JUN 0.01 0.069 -10000 0 -0.76 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.036 0.091 -10000 0 -0.28 91 91
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
cell morphogenesis 0.036 0.14 -10000 0 -0.68 7 7
GRB2/SHC 0.002 0.089 -10000 0 -0.44 4 4
FOS -0.086 0.26 -10000 0 -0.74 120 120
GLMN -0.001 0.016 -10000 0 -0.33 2 2
cell motility -0.002 0.03 0.26 2 -0.27 8 10
HGF/MET/MUC20 -0.076 0.19 -10000 0 -0.52 129 129
cell migration 0.002 0.087 -10000 0 -0.43 4 4
GRB2 0.016 0 -10000 0 -10000 0 0
CBL 0.015 0.029 -10000 0 -0.85 1 1
MET/RANBP10 -0.005 0.056 -10000 0 -0.59 8 8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.002 0.12 -10000 0 -0.62 2 2
MET/MUC20 -0.005 0.057 -10000 0 -0.6 8 8
RAP1B 0.028 0.096 -10000 0 -0.6 2 2
RAP1A 0.028 0.096 -10000 0 -0.83 1 1
HGF/MET/RANBP9 -0.075 0.18 -10000 0 -0.57 88 88
RAF1 0 0.15 -10000 0 -0.68 8 8
STAT3 0.007 0.12 -10000 0 -0.58 2 2
cell proliferation 0.008 0.16 -10000 0 -0.53 10 10
RPS6KB1 0.003 0.037 -10000 0 -10000 0 0
MAPK3 -0.008 0.037 0.8 1 -10000 0 1
MAPK1 -0.008 0.039 0.91 1 -0.26 5 6
RANBP9 0.016 0 -10000 0 -10000 0 0
MAPK8 0.028 0.14 -10000 0 -0.61 18 18
SRC 0.008 0.12 -10000 0 -0.57 2 2
PI3K -0.004 0.11 -10000 0 -0.53 13 13
MET/Glomulin 0.01 0.054 -10000 0 -0.54 8 8
SOS1 0.016 0 -10000 0 -10000 0 0
MAP2K1 0.01 0.14 -10000 0 -0.64 7 7
MET 0.009 0.075 -10000 0 -0.77 8 8
MAP4K1 -0.001 0.15 -10000 0 -0.59 28 28
PTK2 0.016 0 -10000 0 -10000 0 0
MAP2K2 0.009 0.14 -10000 0 -0.66 11 11
BAD 0.007 0.053 -10000 0 -0.67 5 5
MAP2K4 0.019 0.13 -10000 0 -0.5 27 27
SHP2/GRB2/SOS1/GAB1 -0.031 0.085 -10000 0 -0.57 8 8
INPPL1 0.014 0.041 -10000 0 -0.85 2 2
PXN 0.016 0 -10000 0 -10000 0 0
SH3KBP1 0.01 0.071 -10000 0 -0.85 6 6
HGS -0.009 0.094 -10000 0 -0.39 13 13
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.094 0.28 -10000 0 -0.78 122 122
RASA1 0.013 0.05 -10000 0 -0.85 3 3
NCK1 0.014 0.041 -10000 0 -0.85 2 2
PTPRJ 0.011 0.063 -10000 0 -0.75 6 6
NCK/PLCgamma1 0 0.1 -10000 0 -0.51 5 5
PDPK1 -0.012 0.027 -10000 0 -0.58 2 2
HGF/MET/SHIP -0.079 0.2 -10000 0 -0.6 90 90
TCGA08_rtk_signaling

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
PDGFRA -0.18 0.34 -10000 0 -0.75 228 228
HRAS 0.012 0.059 -10000 0 -0.77 5 5
EGFR -0.021 0.17 -10000 0 -0.78 41 41
AKT 0.033 0.055 -10000 0 -0.51 5 5
FOXO3 0.016 0 -10000 0 -10000 0 0
AKT1 0.015 0.029 -10000 0 -0.85 1 1
FOXO1 0.012 0.055 -10000 0 -0.65 6 6
AKT3 0.008 0.082 -10000 0 -0.85 8 8
FOXO4 0.016 0 -10000 0 -10000 0 0
MET 0.009 0.075 -10000 0 -0.77 8 8
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
PIK3CB 0.015 0.022 -10000 0 -0.65 1 1
NRAS 0.016 0 -10000 0 -10000 0 0
PIK3CG -0.052 0.23 -10000 0 -0.83 71 71
PIK3R3 0.001 0.11 -10000 0 -0.82 16 16
PIK3R2 0.015 0.029 -10000 0 -0.85 1 1
NF1 0.016 0 -10000 0 -10000 0 0
RAS -0.021 0.097 -10000 0 -0.39 20 20
ERBB2 0.012 0.055 -10000 0 -0.8 4 4
proliferation/survival/translation -0.032 0.043 0.27 3 -0.19 1 4
PI3K -0.017 0.1 -10000 0 -0.28 51 51
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
KRAS 0.016 0 -10000 0 -10000 0 0
FOXO 0.042 0.039 -10000 0 -0.44 1 1
AKT2 0.015 0.029 -10000 0 -0.85 1 1
PTEN 0.016 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.039 0.087 -10000 0 -0.49 15 15
adherens junction organization 0.009 0.12 -10000 0 -0.52 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.12 -10000 0 -0.6 11 11
FMN1 -0.017 0.17 -10000 0 -0.52 62 62
mol:IP3 -0.019 0.068 -10000 0 -0.45 14 14
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.017 0.1 -10000 0 -0.75 4 4
CTNNB1 0.017 0.004 -10000 0 -10000 0 0
AKT1 0.035 0.09 -10000 0 -0.59 5 5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.005 0.15 -10000 0 -0.59 44 44
CTNND1 0.017 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.026 0.099 -10000 0 -0.66 5 5
VASP 0.026 0.099 -10000 0 -0.7 4 4
ZYX 0.024 0.11 -10000 0 -0.73 7 7
JUB 0.009 0.14 -10000 0 -0.53 35 35
EGFR(dimer) 0.004 0.14 -10000 0 -0.54 33 33
E-cadherin/beta catenin-gamma catenin -0.047 0.15 -10000 0 -0.5 84 84
mol:PI-3-4-5-P3 -0.022 0.077 -10000 0 -0.49 14 14
PIK3CA 0.011 0.071 -10000 0 -0.85 6 6
PI3K -0.023 0.079 -10000 0 -0.5 14 14
FYN -0.066 0.19 -10000 0 -0.58 34 34
mol:Ca2+ 0.029 0.08 -10000 0 -0.44 14 14
JUP 0.01 0.076 -10000 0 -0.85 7 7
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
mol:DAG -0.019 0.068 -10000 0 -0.45 14 14
CDH1 -0.054 0.22 -10000 0 -0.76 80 80
RhoA/GDP 0.028 0.12 -10000 0 -0.6 11 11
establishment of polarity of embryonic epithelium 0.026 0.097 -10000 0 -0.68 4 4
SRC 0.015 0.022 -10000 0 -0.65 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR -0.021 0.17 -10000 0 -0.78 41 41
CASR -0.094 0.22 -10000 0 -0.61 35 35
RhoA/GTP -0.016 0.059 -10000 0 -0.48 4 4
AKT2 0.035 0.09 -10000 0 -0.59 5 5
actin cable formation -0.007 0.17 -10000 0 -0.5 62 62
apoptosis 0.021 0.075 0.48 15 -10000 0 15
CTNNA1 0.017 0.003 -10000 0 -10000 0 0
mol:GDP 0.019 0.13 -10000 0 -0.63 13 13
PIP5K1A 0.026 0.1 -10000 0 -0.68 5 5
PLCG1 -0.019 0.069 -10000 0 -0.47 14 14
Rac1/GTP -0.039 0.11 -10000 0 -0.48 33 33
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.016 0.15 -9999 0 -0.46 36 36
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.046 0.11 -9999 0 -0.79 4 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.008 0.028 -9999 0 -0.67 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.05 0.099 -9999 0 -0.42 27 27
CaM/Ca2+ -0.051 0.12 -9999 0 -0.85 1 1
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.005 0.15 -9999 0 -0.64 7 7
AKT1 0.009 0.14 -9999 0 -0.84 2 2
MAP2K1 0.009 0.14 -9999 0 -0.8 1 1
MAP3K11 -0.005 0.14 -9999 0 -0.59 5 5
IFNGR1 0.013 0.012 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.11 0.14 -9999 0 -0.61 21 21
Rap1/GTP -0.036 0.085 -9999 0 -0.79 1 1
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.059 0.13 -9999 0 -0.46 39 39
CEBPB 0.031 0.16 -9999 0 -0.75 4 4
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.1 0.23 -9999 0 -1.2 24 24
STAT1 -0.004 0.15 -9999 0 -0.63 7 7
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.27 -9999 0 -0.69 151 151
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
STAT1 (dimer)/PIAS1 0.006 0.14 -9999 0 -0.66 5 5
CEBPB/PTGES2/Cbp/p300 -0.032 0.074 -9999 0 -0.49 5 5
mol:Ca2+ -0.055 0.13 -9999 0 -0.45 36 36
MAPK3 0.022 0.13 -9999 0 -0.77 2 2
STAT1 (dimer) -0.067 0.14 -9999 0 -0.64 27 27
MAPK1 0.023 0.13 -9999 0 -1.1 1 1
JAK2 0.012 0.033 -9999 0 -0.9 1 1
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
JAK1 0.013 0.012 -9999 0 -10000 0 0
CAMK2D 0.016 0 -9999 0 -10000 0 0
DAPK1 0.025 0.18 -9999 0 -0.67 45 45
SMAD7 0.017 0.078 -9999 0 -0.4 1 1
CBL/CRKL/C3G -0.045 0.11 -9999 0 -1.1 1 1
PI3K -0.054 0.12 -9999 0 -1.2 1 1
IFNG -0.1 0.27 -9999 0 -0.69 151 151
apoptosis 0.014 0.14 -9999 0 -0.48 45 45
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.022 0.15 -9999 0 -0.66 46 46
CAMK2B -0.25 0.35 -9999 0 -0.7 326 326
FRAP1 0.011 0.13 -9999 0 -0.74 2 2
PRKCD -0.01 0.16 -9999 0 -0.79 5 5
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.05 0.099 -9999 0 -0.42 27 27
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.015 0.041 -9999 0 -0.85 2 2
IRF1 0.028 0.14 -9999 0 -0.65 8 8
STAT1 (dimer)/PIASy -0.041 0.13 -9999 0 -0.67 6 6
SOCS1 -0.054 0.25 -9999 0 -1.6 16 16
mol:GDP -0.043 0.1 -9999 0 -0.98 1 1
CASP1 0.009 0.1 -9999 0 -0.39 34 34
PTGES2 0.01 0.068 -9999 0 -0.7 8 8
IRF9 0.05 0.06 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.052 0.12 -9999 0 -0.78 2 2
RAP1/GDP -0.037 0.086 -9999 0 -0.8 1 1
CBL -0.004 0.14 -9999 0 -1.3 1 1
MAP3K1 -0.003 0.14 -9999 0 -0.59 3 3
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.014 0.041 -9999 0 -0.85 2 2
antigen processing and presentation of peptide antigen via MHC class II -0.05 0.099 -9999 0 -0.42 27 27
PTPN11 -0.014 0.14 -9999 0 -0.45 36 36
CREBBP 0.017 0.001 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.031 0.17 -10000 0 -0.63 63 63
TP53 -0.013 0.051 0.26 1 -0.41 1 2
Senescence -0.013 0.051 0.26 1 -0.41 1 2
Apoptosis -0.013 0.051 0.26 1 -0.41 1 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.085 0.34 52 -10000 0 52
MDM4 0.015 0.022 -10000 0 -0.65 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.009 0.15 -9999 0 -0.6 44 44
KLHL20 -0.022 0.061 -9999 0 -0.34 10 10
CYFIP2 0.008 0.078 -9999 0 -0.76 9 9
Rac1/GDP 0.047 0.1 -9999 0 -10000 0 0
ENAH 0.007 0.15 -9999 0 -0.6 47 47
AP1M1 0.015 0.029 -9999 0 -0.85 1 1
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.021 0.07 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.042 -9999 0 -0.23 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.045 0.15 -9999 0 -0.56 50 50
RAPGEF1 0.03 0.13 -9999 0 -0.5 44 44
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.041 0.14 -9999 0 -0.63 44 44
CRK 0.02 0.14 -9999 0 -0.55 44 44
E-cadherin/gamma catenin/alpha catenin -0.048 0.16 -9999 0 -0.6 48 48
alphaE/beta7 Integrin -0.007 0.065 -9999 0 -0.65 9 9
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.009 0.15 -9999 0 -0.6 44 44
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.054 -9999 0 -0.32 1 1
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.008 0.061 -9999 0 -0.49 14 14
PI3K -0.023 0.07 -9999 0 -0.44 1 1
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.056 0.18 -9999 0 -0.6 84 84
TIAM1 0.005 0.098 -9999 0 -0.83 12 12
E-cadherin(dimer)/Ca2+ -0.038 0.12 -9999 0 -0.49 44 44
AKT1 -0.013 0.04 -9999 0 -0.28 1 1
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
CDH1 -0.054 0.22 -9999 0 -0.76 80 80
RhoA/GDP 0.047 0.1 -9999 0 -10000 0 0
actin cytoskeleton organization -0.015 0.045 -9999 0 -0.24 9 9
CDC42/GDP 0.047 0.1 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.001 0.1 -9999 0 -0.37 48 48
ITGB7 0.008 0.082 -9999 0 -0.85 8 8
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.04 0.13 -9999 0 -0.51 44 44
E-cadherin/Ca2+/beta catenin/alpha catenin -0.039 0.12 -9999 0 -0.5 44 44
mol:GDP 0.04 0.12 -9999 0 -0.44 8 8
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.009 0.076 -9999 0 -0.85 7 7
p120 catenin/RhoA/GDP -0.024 0.082 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 -0.002 0.045 -9999 0 -0.92 2 2
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.024 0.073 -9999 0 -0.27 42 42
NME1 0.015 0.032 -9999 0 -0.65 2 2
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.009 0.15 -9999 0 -0.6 44 44
regulation of cell-cell adhesion -0.019 0.061 -9999 0 -10000 0 0
WASF2 -0.007 0.021 -9999 0 -10000 0 0
Rap1/GTP -0.025 0.081 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.045 0.15 -9999 0 -0.55 53 53
CCND1 0.026 0.091 -9999 0 -0.35 42 42
VAV2 0.026 0.14 -9999 0 -0.53 44 44
RAP1/GDP -0.022 0.082 -9999 0 -10000 0 0
adherens junction assembly 0.011 0.14 -9999 0 -0.58 44 44
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0.041 -9999 0 -0.85 2 2
regulation of heterotypic cell-cell adhesion -0.043 0.14 -9999 0 -1 7 7
E-cadherin/beta catenin -0.038 0.12 -9999 0 -0.41 82 82
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.009 0.15 -9999 0 -0.6 44 44
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
Rac1/GTP -0.035 0.1 -9999 0 -0.65 9 9
E-cadherin/beta catenin/alpha catenin -0.044 0.14 -9999 0 -0.56 44 44
ITGAE 0.015 0.029 -9999 0 -0.85 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.042 0.14 -9999 0 -0.64 44 44
FoxO family signaling

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
G6PC -0.31 0.58 -9999 0 -1.5 147 147
PLK1 0.063 0.24 -9999 0 -1.1 17 17
CDKN1B 0.093 0.13 -9999 0 -0.38 3 3
FOXO3 0.073 0.2 -9999 0 -0.84 16 16
KAT2B 0.026 0.035 -9999 0 -0.9 1 1
FOXO1/SIRT1 -0.088 0.16 -9999 0 -0.56 5 5
CAT 0.075 0.2 -9999 0 -1 12 12
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 0.014 0.041 -9999 0 -0.86 1 1
FOXO1 -0.077 0.19 -9999 0 -0.42 147 147
MAPK10 0.032 0.086 -9999 0 -0.5 22 22
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.066 -9999 0 -0.51 1 1
response to oxidative stress -0.002 0.033 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.038 0.16 -9999 0 -0.77 13 13
XPO1 0.017 0 -9999 0 -10000 0 0
EP300 0.002 0.047 -9999 0 -0.87 2 2
BCL2L11 0.038 0.038 -9999 0 -10000 0 0
FOXO1/SKP2 -0.067 0.18 -9999 0 -0.55 9 9
mol:GDP -0.002 0.033 -9999 0 -10000 0 0
RAN 0.018 0.001 -9999 0 -10000 0 0
GADD45A 0.14 0.088 -9999 0 -0.63 1 1
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.01 0.098 -9999 0 -0.48 2 2
MST1 -0.019 0.19 -9999 0 -0.75 53 53
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family -0.011 0.13 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.039 0.062 -9999 0 -0.49 11 11
MAPK9 0.045 0.015 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.017 0.038 -9999 0 -0.84 1 1
SOD2 0.094 0.17 -9999 0 -0.73 11 11
RBL2 0.099 0.15 -9999 0 -1.2 3 3
RAL/GDP 0.024 0.024 -9999 0 -10000 0 0
CHUK 0.026 0.033 -9999 0 -0.83 1 1
Ran/GTP 0.018 0.003 -9999 0 -10000 0 0
CSNK1G2 0.013 0.05 -9999 0 -0.85 3 3
RAL/GTP 0.038 0.021 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.15 0.5 -9999 0 -1.1 153 153
SKP2 0.012 0.055 -9999 0 -0.8 4 4
USP7 0.018 0.001 -9999 0 -10000 0 0
IKBKB 0.027 0.016 -9999 0 -10000 0 0
CCNB1 0.074 0.2 -9999 0 -0.84 20 20
FOXO1-3a-4/beta catenin -0.011 0.088 -9999 0 -0.43 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.066 0.18 -9999 0 -0.54 9 9
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.004 0.14 -9999 0 -0.84 24 24
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.005 -9999 0 -10000 0 0
ZFAND5 0.12 0.062 -9999 0 -10000 0 0
SFN -0.23 0.35 -9999 0 -0.72 299 299
CDK2 -0.006 0.036 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.006 0.13 -9999 0 -0.44 9 9
CREBBP -0.006 0.036 -9999 0 -10000 0 0
FBXO32 0.073 0.2 -9999 0 -0.8 17 17
BCL6 0.097 0.16 -9999 0 -1.1 6 6
RALB 0.018 0.001 -9999 0 -10000 0 0
RALA 0.018 0.001 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.001 -9999 0 -10000 0 0
HDAC2 0.016 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.032 0.13 -9999 0 -0.55 51 51
forebrain development -0.023 0.19 -9999 0 -0.57 52 52
GNAO1 -0.054 0.22 -9999 0 -0.76 79 79
SMO/beta Arrestin2 0.011 0.092 -9999 0 -0.62 18 18
SMO -0.002 0.12 -9999 0 -0.82 18 18
ARRB2 0.015 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.043 0.091 -9999 0 -0.64 4 4
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.013 0.03 -9999 0 -0.85 1 1
SIN3/HDAC complex -0.012 0.1 -9999 0 -0.51 33 33
GNAI1 0.003 0.1 -9999 0 -0.85 12 12
XPO1 0.017 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.057 0.14 -9999 0 -0.93 11 11
SAP30 -0.014 0.16 -9999 0 -0.85 31 31
mol:GDP -0.002 0.12 -9999 0 -0.81 18 18
MIM/GLI2A 0.005 0.1 -9999 0 -0.75 16 16
IFT88 0.01 0.071 -9999 0 -0.85 6 6
GNAI3 0.015 0.006 -9999 0 -10000 0 0
GLI2 0.02 0.091 -9999 0 -10000 0 0
GLI3 0.035 0.096 -9999 0 -0.49 12 12
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.01 0.071 -9999 0 -0.85 6 6
GNG2 -0.016 0.16 -9999 0 -0.85 33 33
Gi family/GTP 0 0.13 -9999 0 -0.4 57 57
SIN3B 0.014 0.041 -9999 0 -0.85 2 2
SIN3A 0.016 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.048 0.085 -9999 0 -0.65 4 4
GLI2/Su(fu) 0.029 0.089 -9999 0 -10000 0 0
FOXA2 -0.12 0.29 -9999 0 -1.1 49 49
neural tube patterning -0.023 0.19 -9999 0 -0.57 52 52
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.03 0.045 -9999 0 -0.48 1 1
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0.05 -9999 0 -0.85 3 3
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.005 0.1 -9999 0 -0.75 16 16
embryonic limb morphogenesis -0.023 0.19 -9999 0 -0.57 52 52
SUFU 0.026 0.049 -9999 0 -0.53 1 1
LGALS3 -0.023 0.16 -9999 0 -0.68 50 50
catabolic process 0.049 0.11 -9999 0 -0.49 8 8
GLI3A/CBP -0.017 0.12 -9999 0 -0.38 65 65
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 -0.024 0.2 -9999 0 -0.59 52 52
RAB23 0.015 0.022 -9999 0 -0.65 1 1
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.015 0.029 -9999 0 -0.85 1 1
RBBP7 0.016 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.007 0.11 -9999 0 -0.57 13 13
GNAZ 0.006 0.085 -9999 0 -0.79 10 10
RBBP4 0.015 0.029 -9999 0 -0.85 1 1
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.026 0.085 -9999 0 -10000 0 0
STK36 0.016 0.03 -9999 0 -0.85 1 1
Gi family/GNB1/GNG2/GDP 0.002 0.14 -9999 0 -0.57 28 28
PTCH1 -0.011 0.18 -9999 0 -0.9 11 11
MIM/GLI1 -0.049 0.24 -9999 0 -0.65 66 66
CREBBP -0.017 0.12 -9999 0 -0.38 65 65
Su(fu)/SIN3/HDAC complex 0.051 0.061 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.038 0.13 -9999 0 -0.79 6 6
TC10/GTP -0.023 0.1 -9999 0 -0.81 2 2
Insulin Receptor/Insulin/IRS1/Shp2 -0.018 0.089 -9999 0 -0.55 14 14
HRAS 0.012 0.059 -9999 0 -0.77 5 5
APS homodimer 0 0.12 -9999 0 -0.82 17 17
GRB14 -0.087 0.25 -9999 0 -0.7 128 128
FOXO3 -0.029 0.13 -9999 0 -0.83 23 23
AKT1 -0.006 0.17 -9999 0 -0.67 19 19
INSR 0.016 0.041 -9999 0 -0.84 2 2
Insulin Receptor/Insulin -0.002 0.04 -9999 0 -0.86 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.014 0.041 -9999 0 -0.85 2 2
SORBS1 -0.013 0.16 -9999 0 -0.85 30 30
CRK 0.015 0.022 -9999 0 -0.65 1 1
PTPN1 0.042 0.042 -9999 0 -0.84 1 1
CAV1 -0.043 0.19 -9999 0 -0.52 107 107
CBL/APS/CAP/Crk-II/C3G -0.026 0.11 -9999 0 -0.5 45 45
Insulin Receptor/Insulin/IRS1/NCK2 -0.017 0.087 -9999 0 -0.55 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.095 -9999 0 -0.52 21 21
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.064 -9999 0 -0.76 2 2
RPS6KB1 0.006 0.15 -9999 0 -0.59 19 19
PARD6A 0.007 0.082 -9999 0 -0.72 11 11
CBL 0.015 0.029 -9999 0 -0.85 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.006 0.083 -9999 0 -1 6 6
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.053 0.13 -9999 0 -0.61 19 19
HRAS/GTP -0.018 0.078 -9999 0 -0.65 2 2
Insulin Receptor 0.016 0.041 -9999 0 -0.84 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.016 0.081 -9999 0 -0.52 12 12
PRKCI -0.022 0.085 -9999 0 -0.75 10 10
Insulin Receptor/Insulin/GRB14/PDK1 -0.066 0.16 -9999 0 -0.75 19 19
SHC1 0.015 0.022 -9999 0 -0.65 1 1
negative regulation of MAPKKK cascade -0.008 0.086 -9999 0 -0.84 9 9
PI3K -0.021 0.096 -9999 0 -0.53 21 21
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.003 0.045 -9999 0 -0.59 5 5
AKT2 -0.006 0.17 -9999 0 -0.67 19 19
PRKCZ -0.028 0.12 -9999 0 -0.86 16 16
SH2B2 0 0.12 -9999 0 -0.82 17 17
SHC/SHIP 0.022 0.097 -9999 0 -0.5 19 19
F2RL2 -0.12 0.3 -9999 0 -0.77 152 152
TRIP10 0.006 0.091 -9999 0 -0.85 10 10
Insulin Receptor/Insulin/Shc -0.003 0.033 -9999 0 -0.46 3 3
TC10/GTP/CIP4/Exocyst -0.006 0.061 -9999 0 -0.57 10 10
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.002 0.03 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.013 0.05 -9999 0 -0.85 3 3
NCK1 0.014 0.041 -9999 0 -0.85 2 2
CBL/APS/CAP/Crk-II -0.028 0.12 -9999 0 -0.53 45 45
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.004 0.041 -9999 0 -0.51 4 4
INPP5D 0.013 0.1 -9999 0 -0.53 20 20
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.034 0.18 -9999 0 -1.2 23 23
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0.029 -9999 0 -0.85 1 1
IRS1 -0.01 0.14 -9999 0 -0.72 31 31
p62DOK/RasGAP -0.008 0.087 -9999 0 -0.86 9 9
INS 0.002 0.038 -9999 0 -0.64 3 3
mol:PI-3-4-P2 0.013 0.1 -9999 0 -0.52 20 20
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 -0.007 0.18 -9999 0 -0.68 32 32
PTPRA 0.018 0.003 -9999 0 -10000 0 0
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
TC10/GTP/CIP4 -0.006 0.061 -9999 0 -0.57 10 10
PDPK1 0.014 0.041 -9999 0 -0.85 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.031 0.06 -9999 0 -0.56 1 1
Insulin Receptor/Insulin/IRS1 -0.018 0.089 -9999 0 -0.56 13 13
Insulin Receptor/Insulin/IRS3 -0.003 0.041 -9999 0 -0.54 5 5
Par3/Par6 -0.083 0.19 -9999 0 -0.53 101 101
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.031 0.12 -10000 0 -0.45 60 60
MAPK9 0.011 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.019 0.11 -10000 0 -0.49 43 43
GNB1/GNG2 -0.021 0.11 -10000 0 -0.57 33 33
GNB1 0.016 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 0.011 0 -10000 0 -10000 0 0
Gs family/GTP -0.013 0.077 -10000 0 -0.44 27 27
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 0.003 0.018 0.1 27 -10000 0 27
GNAL -0.006 0.13 -10000 0 -0.72 27 27
GNG2 -0.016 0.16 -10000 0 -0.85 33 33
CRH -0.026 0.14 -10000 0 -0.65 43 43
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.053 -10000 0 -0.47 11 11
MAPK11 0.003 0.061 -10000 0 -0.46 15 15
Aurora C signaling

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
INCENP 0.014 0.041 -9999 0 -0.85 2 2
Aurora C/Aurora B/INCENP -0.036 0.12 -9999 0 -0.54 24 24
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.01 0.032 -9999 0 -10000 0 0
AURKB -0.03 0.18 -9999 0 -0.71 57 57
AURKC 0.001 0.1 -9999 0 -0.7 19 19
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.004 0.052 0.23 39 -10000 0 39
BUB1B 0.016 0.077 -10000 0 -0.39 27 27
PLK1 0.019 0.03 -10000 0 -0.18 11 11
PLK1S1 0.018 0.015 -10000 0 -10000 0 0
KIF2A 0.021 0.065 -10000 0 -0.42 15 15
regulation of mitotic centrosome separation 0.019 0.029 -10000 0 -0.18 11 11
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.012 0.17 -10000 0 -0.52 79 79
WEE1 0.025 0.039 -10000 0 -10000 0 0
cytokinesis -0.005 0.16 -10000 0 -0.59 49 49
PP2A-alpha B56 0.022 0.11 -10000 0 -0.75 12 12
AURKA 0.017 0.027 -10000 0 -0.2 10 10
PICH/PLK1 0.026 0.12 -10000 0 -0.63 22 22
CENPE 0.005 0.11 -10000 0 -0.46 47 47
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.021 0.064 -10000 0 -0.42 15 15
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.014 0.041 -10000 0 -0.85 2 2
TPX2 0.01 0.051 -10000 0 -0.23 35 35
PAK1 0.016 0.001 -10000 0 -10000 0 0
SPC24 -0.021 0.16 -10000 0 -0.74 43 43
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN 0.005 0.07 -10000 0 -0.31 40 40
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase 0 0.003 -10000 0 -0.017 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.011 0.015 -10000 0 -0.089 9 9
G2 phase of mitotic cell cycle 0 0.001 0.02 1 -0.011 8 9
STAG2 0.012 0.058 -10000 0 -0.85 4 4
GRASP65/GM130/RAB1/GTP 0.001 0.007 -10000 0 -10000 0 0
spindle elongation 0.019 0.029 -10000 0 -0.18 11 11
ODF2 0.015 0.029 -10000 0 -0.86 1 1
BUB1 -0.022 0.11 -10000 0 -0.84 12 12
TPT1 0.018 0.015 -10000 0 -10000 0 0
CDC25C -0.003 0.093 -10000 0 -0.33 56 56
CDC25B 0.01 0.068 -10000 0 -0.66 9 9
SGOL1 0.004 0.052 -10000 0 -0.24 39 39
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.012 0.07 -10000 0 -0.47 16 16
CDC14B 0.015 0.002 -10000 0 -10000 0 0
CDC20 -0.012 0.14 -10000 0 -0.67 36 36
PLK1/PBIP1 -0.007 0.041 -10000 0 -0.48 5 5
mitosis 0 0.003 0.03 3 -10000 0 3
FBXO5 0.024 0.028 -10000 0 -0.36 1 1
CDC2 0.001 0.003 -10000 0 -0.018 19 19
NDC80 -0.028 0.19 -10000 0 -0.81 47 47
metaphase plate congression 0.018 0.019 -10000 0 -10000 0 0
ERCC6L -0.019 0.1 -10000 0 -0.65 19 19
NLP/gamma Tubulin 0.015 0.02 -10000 0 -0.2 3 3
microtubule cytoskeleton organization 0.018 0.015 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.016 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.001 0.15 -10000 0 -0.49 66 66
GRASP65/GM130/RAB1/GTP/PLK1 -0.002 0.014 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.024 0.023 -10000 0 -10000 0 0
mitotic prometaphase 0 0.002 -10000 0 -0.012 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.043 -10000 0 -0.56 2 2
microtubule-based process -0.006 0.13 -10000 0 -0.47 64 64
Golgi organization 0.019 0.029 -10000 0 -0.18 11 11
Cohesin/SA2 -0.006 0.039 -10000 0 -0.49 4 4
PPP1CB/MYPT1 0 0.001 -10000 0 -10000 0 0
KIF20A -0.038 0.2 -10000 0 -0.73 64 64
APC/C/CDC20 0.01 0.098 -10000 0 -0.46 36 36
PPP2R1A 0.015 0.029 -10000 0 -0.85 1 1
chromosome segregation -0.006 0.041 -10000 0 -0.47 5 5
PRC1 0.007 0.081 -10000 0 -0.75 10 10
ECT2 0.025 0.047 -10000 0 -0.46 6 6
C13orf34 0.024 0.023 -10000 0 -10000 0 0
NUDC 0.018 0.02 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.016 0.076 -10000 0 -0.39 27 27
spindle assembly 0.019 0.026 -10000 0 -0.16 10 10
spindle stabilization 0.018 0.015 -10000 0 -10000 0 0
APC/C/HCDH1 0.021 0.028 -10000 0 -0.58 2 2
MKLP2/PLK1 -0.006 0.13 -10000 0 -0.47 64 64
CCNB1 0.005 0.089 -10000 0 -0.67 15 15
PPP1CB 0.016 0.001 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 0.01 0.1 -10000 0 -0.53 29 29
TUBG1 0.017 0.024 -10000 0 -0.29 3 3
G2/M transition of mitotic cell cycle -0.012 0.068 -10000 0 -0.46 16 16
MLF1IP 0.011 0.052 -10000 0 -0.67 5 5
INCENP 0.014 0.041 -10000 0 -0.85 2 2
Signaling events mediated by HDAC Class III

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
EP300 0.014 0.041 -10000 0 -0.85 2 2
HDAC4 0.015 0.029 -10000 0 -0.85 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.024 0.038 0.52 4 -10000 0 4
CDKN1A -0.007 0.083 -10000 0 -1 6 6
KAT2B 0.015 0.029 -10000 0 -0.85 1 1
BAX 0.014 0.041 -10000 0 -0.85 2 2
FOXO3 0.001 0.03 0.63 2 -10000 0 2
FOXO1 0.012 0.055 -10000 0 -0.65 6 6
FOXO4 0.028 0.019 -10000 0 -0.37 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT -0.025 0.15 -10000 0 -0.65 50 50
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.007 0.075 -10000 0 -0.49 20 20
PPARGC1A -0.071 0.25 -10000 0 -0.75 102 102
FHL2 -0.05 0.23 -10000 0 -0.83 69 69
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.026 -10000 0 -0.65 1 1
HIST2H4A 0.024 0.038 -10000 0 -0.52 4 4
SIRT1/FOXO3a 0.001 0.02 0.35 1 -0.32 1 2
SIRT1 0.001 0.034 -10000 0 -0.85 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.03 -10000 0 -0.56 2 2
SIRT1/Histone H1b -0.006 0.047 -10000 0 -0.84 1 1
apoptosis 0.001 0.035 0.56 3 -10000 0 3
SIRT1/PGC1A -0.056 0.16 -10000 0 -0.49 103 103
p53/SIRT1 0.002 0.048 0.45 6 -0.65 2 8
SIRT1/FOXO4 0 0.034 -10000 0 -0.84 1 1
FOXO1/FHL2/SIRT1 -0.042 0.15 -10000 0 -0.55 64 64
HIST1H1E 0.019 0.05 -10000 0 -0.38 2 2
SIRT1/p300 -0.001 0.047 -10000 0 -0.92 2 2
muscle cell differentiation 0.009 0.065 0.42 21 -10000 0 21
TP53 0.001 0.034 -10000 0 -0.85 1 1
KU70/SIRT1/BAX -0.001 0.035 -10000 0 -0.56 3 3
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.027 0.11 -10000 0 -0.48 51 51
ACSS2 0.019 0.063 -10000 0 -0.49 13 13
SIRT1/PCAF/MYOD -0.009 0.065 -10000 0 -0.42 21 21
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.01 0.14 -10000 0 -0.55 24 24
BAG4 0.011 0.065 -10000 0 -0.85 5 5
BAD 0.022 0.06 -10000 0 -0.51 4 4
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.066 0.25 -10000 0 -0.81 89 89
BAX 0.022 0.056 -10000 0 -0.64 2 2
EnzymeConsortium:3.1.4.12 0.007 0.035 -10000 0 -0.12 25 25
IKBKB 0.019 0.13 -10000 0 -0.55 19 19
MAP2K2 0.031 0.083 -10000 0 -0.44 18 18
MAP2K1 0.032 0.077 -10000 0 -0.43 15 15
SMPD1 0.014 0.036 -10000 0 -0.17 2 2
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.02 0.14 -10000 0 -0.58 17 17
MAP2K4 0.031 0.049 -10000 0 -0.34 1 1
protein ubiquitination 0.021 0.14 -10000 0 -0.55 21 21
EnzymeConsortium:2.7.1.37 0.037 0.083 -10000 0 -0.44 16 16
response to UV 0 0.001 -10000 0 -0.003 16 16
RAF1 0.025 0.08 -10000 0 -0.46 15 15
CRADD 0.016 0 -10000 0 -10000 0 0
mol:ceramide 0.015 0.05 -10000 0 -0.17 21 21
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.023 0.05 -10000 0 -0.31 2 2
TRADD 0.015 0.029 -10000 0 -0.85 1 1
RELA/p50 0.016 0 -10000 0 -10000 0 0
MAPK3 0.035 0.081 -10000 0 -0.44 16 16
MAPK1 0.035 0.078 -10000 0 -0.42 16 16
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.01 0.14 -10000 0 -0.55 22 22
KSR1 0.016 0.083 -10000 0 -0.47 17 17
MAPK8 0.034 0.068 -10000 0 -0.4 12 12
TRAF2 0.014 0.041 -10000 0 -0.85 2 2
response to radiation 0 0 -10000 0 -0.003 1 1
CHUK 0.019 0.14 -10000 0 -0.56 20 20
TNF R/SODD -0.004 0.049 -10000 0 -0.65 5 5
TNF -0.062 0.23 -10000 0 -0.75 90 90
CYCS 0.023 0.063 0.16 10 -0.39 5 15
IKBKG 0.018 0.14 -10000 0 -0.57 21 21
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.001 0.15 -10000 0 -0.58 23 23
RELA 0.016 0 -10000 0 -10000 0 0
RIPK1 0.016 0.001 -10000 0 -10000 0 0
AIFM1 0.025 0.058 0.16 9 -0.51 3 12
TNF/TNF R/SODD -0.052 0.15 -10000 0 -0.49 95 95
TNFRSF1A 0.016 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.003 1 1
CASP8 0.024 0.051 -10000 0 -1.1 1 1
NSMAF 0.011 0.14 -10000 0 -0.55 22 22
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 16 16
BCL2 0.002 0.11 -10000 0 -0.85 14 14
Atypical NF-kappaB 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
BCL3/RelA -0.007 0.064 -9999 0 -0.6 10 10
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.014 0.11 -9999 0 -0.55 30 30
NF kappa B1 p50/RelA/I kappa B alpha 0.023 0.11 -9999 0 -0.63 13 13
NFKBIA -0.005 0.13 -9999 0 -0.34 85 85
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.033 0.02 -9999 0 -0.56 1 1
ARRB2 0.022 0 -9999 0 -10000 0 0
REL -0.012 0.15 -9999 0 -0.83 29 29
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.062 -9999 0 -0.52 11 11
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.033 0.02 -9999 0 -0.56 1 1
PIK3CA 0.01 0.071 -9999 0 -0.85 6 6
NF kappa B1 p50 dimer 0.025 0.023 -9999 0 -0.65 1 1
PIK3R1 0.011 0.066 -9999 0 -0.78 6 6
NFKB1 0.028 0.023 -9999 0 -0.65 1 1
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.007 0.11 -9999 0 -0.53 12 12
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.028 0.11 -9999 0 -0.63 12 12
SRC 0.015 0.022 -9999 0 -0.65 1 1
PI3K -0.008 0.072 -9999 0 -0.62 12 12
NF kappa B1 p50/RelA 0.006 0.11 -9999 0 -0.54 12 12
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK -0.001 0.12 -9999 0 -0.8 19 19
I kappa B alpha/PIK3R1 0.001 0.13 -9999 0 -0.7 16 16
cell death 0.027 0.11 -9999 0 -0.59 12 12
NF kappa B1 p105/c-Rel 0.014 0.11 -9999 0 -0.55 30 30
LCK -0.08 0.26 -9999 0 -0.8 104 104
BCL3 0.007 0.085 -9999 0 -0.79 10 10
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.022 0.11 -10000 0 -0.54 36 36
HDAC3 0.016 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.014 -10000 0 -0.43 1 1
GATA1/HDAC4 -0.017 0.09 -10000 0 -0.48 32 32
GATA1/HDAC5 -0.019 0.095 -10000 0 -0.49 34 34
GATA2/HDAC5 -0.066 0.18 -10000 0 -0.55 106 106
HDAC5/BCL6/BCoR -0.005 0.058 -10000 0 -0.64 7 7
HDAC9 -0.008 0.14 -10000 0 -0.84 25 25
Glucocorticoid receptor/Hsp90/HDAC6 -0.002 0.035 -10000 0 -0.56 3 3
HDAC4/ANKRA2 -0.001 0.022 -10000 0 -0.65 1 1
HDAC5/YWHAB -0.002 0.038 -10000 0 -0.65 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.027 0.016 -10000 0 -0.29 2 2
GATA2 -0.07 0.24 -10000 0 -0.73 103 103
HDAC4/RFXANK -0.003 0.041 -10000 0 -0.61 4 4
BCOR 0.015 0.029 -10000 0 -0.85 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.013 0.05 -10000 0 -0.85 3 3
HDAC5 0.013 0.05 -10000 0 -0.85 3 3
GNB1/GNG2 -0.024 0.12 -10000 0 -0.65 33 33
Histones 0.037 0.093 -10000 0 -1.5 2 2
ADRBK1 0.014 0.041 -10000 0 -0.85 2 2
HDAC4 0.015 0.029 -10000 0 -0.85 1 1
XPO1 0.016 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.002 0.038 -10000 0 -0.65 3 3
HDAC4/Ubc9 -0.001 0.022 -10000 0 -0.65 1 1
HDAC7 0.014 0.041 -10000 0 -0.85 2 2
HDAC5/14-3-3 E -0.002 0.038 -10000 0 -0.65 3 3
TUBA1B 0.016 0 -10000 0 -10000 0 0
HDAC6 0.016 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.004 0.062 -10000 0 -0.87 4 4
CAMK4 -0.05 0.23 -10000 0 -0.84 69 69
Tubulin/HDAC6 -0.007 0.055 -10000 0 -0.42 15 15
SUMO1 0.016 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
GATA1 -0.01 0.12 -10000 0 -0.65 31 31
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.016 0 -10000 0 -10000 0 0
NR3C1 0.012 0.055 -10000 0 -0.8 4 4
SUMO1/HDAC4 0.037 0.023 -10000 0 -0.47 1 1
SRF 0.016 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.022 -10000 0 -0.65 1 1
Tubulin -0.008 0.065 -10000 0 -0.5 15 15
HDAC4/14-3-3 E -0.001 0.022 -10000 0 -0.65 1 1
GNB1 0.016 0 -10000 0 -10000 0 0
RANGAP1 0.013 0.047 -10000 0 -0.78 3 3
BCL6/BCoR -0.004 0.055 -10000 0 -0.78 4 4
HDAC4/HDAC3/SMRT (N-CoR2) -0.002 0.033 -10000 0 -0.56 3 3
HDAC4/SRF -0.044 0.15 -10000 0 -0.56 66 66
HDAC4/ER alpha -0.042 0.16 -10000 0 -0.63 59 59
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.037 0.09 -10000 0 -1.4 2 2
cell motility -0.007 0.055 -10000 0 -0.42 15 15
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
HDAC7/HDAC3 -0.001 0.031 -10000 0 -0.65 2 2
BCL6 0.012 0.058 -10000 0 -0.85 4 4
HDAC4/CaMK II delta B 0.015 0.029 -10000 0 -0.85 1 1
Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
ESR1 -0.038 0.21 -10000 0 -0.82 58 58
HDAC6/HDAC11 -0.003 0.041 -10000 0 -0.55 5 5
Ran/GTP/Exportin 1 -0.001 0.012 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.024 0.18 -10000 0 -0.84 41 41
RAN 0.016 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.023 0.1 -10000 0 -0.48 43 43
GNG2 -0.016 0.16 -10000 0 -0.85 33 33
NCOR2 0.014 0.041 -10000 0 -0.85 2 2
TUBB2A 0.004 0.09 -10000 0 -0.68 15 15
HDAC11 0.012 0.056 -10000 0 -0.73 5 5
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RANBP2 0.016 0 -10000 0 -10000 0 0
ANKRA2 0.016 0 -10000 0 -10000 0 0
RFXANK 0.013 0.047 -10000 0 -0.78 3 3
nuclear import 0.002 0.03 0.45 4 -10000 0 4
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR -0.028 0.17 -10000 0 -0.66 58 58
Cbp/p300/PCAF -0.002 0.041 -10000 0 -0.82 2 2
EP300 0.014 0.041 -10000 0 -0.85 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.047 0.048 -10000 0 -0.52 2 2
KAT2B 0.015 0.029 -10000 0 -0.85 1 1
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 0.025 0.06 0.25 9 -0.36 9 18
RAR alpha/9cRA/Cyclin H -0.014 0.053 -10000 0 -0.47 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.044 0.05 -10000 0 -0.51 2 2
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.002 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.009 0.094 -10000 0 -0.68 13 13
NCOR2 0.014 0.041 -10000 0 -0.85 2 2
VDR/VDR/Vit D3 -0.033 0.12 -10000 0 -0.5 58 58
RXRs/RARs/NRIP1/9cRA 0.045 0.097 -10000 0 -0.58 6 6
NCOA2 -0.039 0.21 -10000 0 -0.85 57 57
NCOA3 0.016 0 -10000 0 -10000 0 0
NCOA1 0.016 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.028 0.17 -10000 0 -0.66 58 58
RARG 0.015 0.047 -10000 0 -0.78 3 3
RAR gamma1/9cRA -0.002 0.03 -10000 0 -0.52 3 3
MAPK3 0.016 0.029 -10000 0 -0.86 1 1
MAPK1 0.015 0.029 -10000 0 -0.85 1 1
MAPK8 0.007 0.096 -10000 0 -0.85 11 11
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.1 -10000 0 -0.44 22 22
RARA 0.014 0.076 -10000 0 -0.38 15 15
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.023 0.11 -10000 0 -0.44 22 22
PRKCA 0.019 0.032 -10000 0 -0.65 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 0.038 0.095 -10000 0 -0.5 11 11
RXRG -0.003 0.096 -10000 0 -0.28 96 96
RXRA 0.024 0.074 -10000 0 -0.45 8 8
RXRB 0.009 0.085 -10000 0 -0.52 2 2
VDR/Vit D3/DNA -0.033 0.12 -10000 0 -0.5 58 58
RBP1 -0.005 0.13 -10000 0 -0.74 25 25
CRBP1/9-cic-RA -0.016 0.096 -10000 0 -0.57 25 25
RARB 0.012 0.077 -10000 0 -0.85 7 7
PRKCG -0.038 0.18 -10000 0 -0.65 68 68
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.04 0.094 -10000 0 -0.44 7 7
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.045 0.089 -10000 0 -0.51 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.064 -10000 0 -0.38 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 0.038 0.095 -10000 0 -0.5 11 11
positive regulation of DNA binding -0.014 0.05 -10000 0 -0.44 5 5
NRIP1 0.035 0.12 -10000 0 -1.3 5 5
RXRs/RARs 0.031 0.089 -10000 0 -0.43 11 11
RXRs/RXRs/DNA/9cRA -0.024 0.073 -10000 0 -0.48 6 6
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.009 0.037 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.023 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification -0.007 0.031 -10000 0 -0.58 1 1
CLOCK -0.012 0.16 -10000 0 -0.84 33 33
TIMELESS/CRY2 0.041 0.047 -10000 0 -10000 0 0
DEC1/BMAL1 -0.003 0.038 -10000 0 -0.57 4 4
ATR 0.015 0.029 -10000 0 -0.85 1 1
NR1D1 0.036 0.088 -10000 0 -1.5 2 2
ARNTL 0.018 0.041 -10000 0 -0.85 2 2
TIMELESS 0.039 0.05 -10000 0 -0.51 1 1
NPAS2 -0.05 0.24 -10000 0 -0.84 73 73
CRY2 0.015 0.022 -10000 0 -0.65 1 1
mol:CO -0.017 0.009 0.12 4 -10000 0 4
CHEK1 0.016 0 -10000 0 -10000 0 0
mol:HEME 0.017 0.009 -10000 0 -0.12 4 4
PER1 0.012 0.055 -10000 0 -0.8 4 4
BMAL/CLOCK/NPAS2 -0.019 0.2 -10000 0 -0.56 105 105
BMAL1/CLOCK 0.029 0.12 -10000 0 -1 4 4
S phase of mitotic cell cycle -0.007 0.031 -10000 0 -0.58 1 1
TIMELESS/CHEK1/ATR -0.007 0.032 -10000 0 -0.59 1 1
mol:NADPH 0.017 0.009 -10000 0 -0.12 4 4
PER1/TIMELESS 0.039 0.059 -10000 0 -0.84 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.002 0.032 -10000 0 -0.65 2 2
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.029 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.002 0.032 -10000 0 -0.51 3 3
CDKN1B 0.047 0.022 -10000 0 -0.52 1 1
CDKN1A 0.043 0.047 -10000 0 -0.47 7 7
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
FOXO3 0.047 0.022 -10000 0 -0.52 1 1
AKT1 -0.001 0.02 -10000 0 -0.56 1 1
BAD 0.012 0.055 -10000 0 -0.8 4 4
AKT3 0.017 0.051 -10000 0 -0.46 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.047 0.022 -10000 0 -0.52 1 1
AKT1/ASK1 -0.002 0.028 -10000 0 -0.46 3 3
BAD/YWHAZ -0.002 0.035 -10000 0 -0.52 4 4
RICTOR 0.015 0.029 -10000 0 -0.85 1 1
RAF1 0.016 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.027 0.45 3 -10000 0 3
TSC1 0.047 0.022 -10000 0 -0.52 1 1
YWHAZ 0.016 0 -10000 0 -10000 0 0
AKT1/RAF1 0.046 0.022 -10000 0 -0.52 1 1
EP300 0.014 0.041 -10000 0 -0.85 2 2
mol:GDP 0.038 0.022 -10000 0 -0.55 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.045 0.043 -10000 0 -0.63 3 3
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.027 0.04 -10000 0 -0.39 8 8
MAP3K5 0.014 0.041 -10000 0 -0.85 2 2
MAPKAP1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.008 0.072 0.34 1 -10000 0 1
YWHAH 0.016 0 -10000 0 -10000 0 0
AKT1S1 0.046 0.036 -10000 0 -0.98 1 1
CASP9 0.047 0.022 -10000 0 -0.52 1 1
YWHAB 0.016 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.054 0.021 -10000 0 -0.48 1 1
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.002 0.03 -10000 0 -0.51 3 3
YWHAE 0.016 0 -10000 0 -10000 0 0
SRC 0.015 0.022 -10000 0 -0.65 1 1
AKT2/p21CIP1 -0.004 0.044 -10000 0 -0.46 7 7
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.006 -10000 0 -10000 0 0
CHUK 0.046 0.027 -10000 0 -0.49 2 2
BAD/BCL-XL 0.06 0.043 -10000 0 -0.67 2 2
mTORC2 -0.001 0.018 -10000 0 -0.53 1 1
AKT2 0.02 0.028 -10000 0 -0.46 3 3
FOXO1-3a-4/14-3-3 family 0.021 0.084 -10000 0 -0.57 1 1
PDPK1 0.014 0.041 -10000 0 -0.85 2 2
MDM2 0.047 0.022 -10000 0 -0.52 1 1
MAPKKK cascade -0.045 0.021 0.51 1 -10000 0 1
MDM2/Cbp/p300 0.06 0.035 -10000 0 -0.54 3 3
TSC1/TSC2 0.053 0.042 -10000 0 -0.6 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.03 -10000 0 -0.51 3 3
glucose import -0.015 0.15 -10000 0 -0.41 108 108
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.04 0.018 -10000 0 -0.44 1 1
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.015 0.15 -10000 0 -0.41 106 106
GSK3A 0.047 0.022 -10000 0 -0.52 1 1
FOXO1 0.044 0.036 -10000 0 -0.52 1 1
GSK3B 0.047 0.022 -10000 0 -0.52 1 1
SFN -0.23 0.35 -10000 0 -0.72 299 299
G1/S transition of mitotic cell cycle 0.055 0.021 -10000 0 -0.5 1 1
p27Kip1/14-3-3 family -0.01 0.1 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
KPNA1 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.042 0.13 -9999 0 -0.52 48 48
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.12 -9999 0 -0.43 48 48
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.004 0.094 -9999 0 -0.74 14 14
NPC/RanGAP1/SUMO1/Ubc9 0.027 0.016 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones -0.017 0.052 -9999 0 -10000 0 0
YY1/LSF 0.037 0.037 -9999 0 -0.69 2 2
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.009 0.11 -9999 0 -0.37 47 47
I kappa B alpha/HDAC1 0.016 0.076 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.018 0.095 -9999 0 -0.32 47 47
HDAC1/Smad7 -0.001 0.019 -9999 0 -0.56 1 1
RANGAP1 0.013 0.047 -9999 0 -0.78 3 3
HDAC3/TR2 0.016 0.076 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.058 0.028 -9999 0 -0.41 1 1
NF kappa B1 p50/RelA 0.023 0.09 -9999 0 -0.75 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.07 0.24 -9999 0 -0.73 103 103
GATA1 -0.01 0.12 -9999 0 -0.65 31 31
Mad/Max -0.001 0.023 -9999 0 -0.48 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.061 0.058 -9999 0 -0.5 5 5
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.015 0.029 -9999 0 -0.85 1 1
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA 0.009 0.084 -9999 0 -10000 0 0
KAT2B 0.015 0.029 -9999 0 -0.85 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.044 0.06 -9999 0 -10000 0 0
SIN3 complex -0.019 0.097 -9999 0 -0.51 33 33
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.013 0.05 -9999 0 -0.85 3 3
SAP30 -0.014 0.16 -9999 0 -0.85 31 31
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.015 0.029 -9999 0 -0.85 1 1
YY1/HDAC3 0.032 0.076 -9999 0 -0.75 1 1
YY1/HDAC2 0.038 0.032 -9999 0 -0.84 1 1
YY1/HDAC1 0.038 0.032 -9999 0 -0.84 1 1
NuRD/MBD2 Complex (MeCP1) 0.06 0.018 -9999 0 -10000 0 0
PPARG -0.039 0.12 -9999 0 -0.46 52 52
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.015 0.081 -9999 0 -0.64 2 2
MBD3L2 0 0.002 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.019 -9999 0 -0.56 1 1
CREBBP 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.062 0.031 -9999 0 -0.46 1 1
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 0.009 0.084 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.037 0.035 -9999 0 -0.65 2 2
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.015 0.029 -9999 0 -0.85 1 1
NCOR2 0.014 0.041 -9999 0 -0.85 2 2
MXD1 0.015 0.032 -9999 0 -0.65 2 2
STAT3 0.032 0.023 -9999 0 -0.45 2 2
NFKB1 0.015 0.029 -9999 0 -0.85 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.002 0.032 -9999 0 -0.64 2 2
YY1/SAP30/HDAC1 -0.019 0.095 -9999 0 -0.51 32 32
EP300 0.014 0.041 -9999 0 -0.85 2 2
STAT3 (dimer non-phopshorylated) 0.032 0.023 -9999 0 -0.45 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.084 -9999 0 -10000 0 0
histone deacetylation 0.06 0.017 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.028 0.073 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.036 0.17 -9999 0 -0.46 103 103
GATA1/HDAC1 -0.017 0.087 -9999 0 -0.48 31 31
GATA1/HDAC3 -0.004 0.1 -9999 0 -0.53 1 1
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.058 0.17 -9999 0 -0.57 90 90
SIN3/HDAC complex/Mad/Max 0.051 0.051 -9999 0 -10000 0 0
NuRD Complex 0.069 0.029 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.017 0.051 -9999 0 -10000 0 0
SIN3B 0.014 0.041 -9999 0 -0.85 2 2
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.037 0.015 -9999 0 -10000 0 0
HDAC complex -0.001 0.017 -9999 0 -0.51 1 1
GATA1/Fog1 -0.025 0.11 -9999 0 -0.5 45 45
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.062 0.23 -9999 0 -0.75 90 90
negative regulation of cell growth 0.051 0.05 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.06 0.018 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 -0.001 0.012 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.035 0.11 -9999 0 -0.45 47 47
SIN3/HDAC complex/NCoR1 0.048 0.051 -9999 0 -10000 0 0
TFCP2 0.015 0.029 -9999 0 -0.85 1 1
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.011 0.062 -9999 0 -0.81 5 5
MBD2 0.016 0 -9999 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.095 0.053 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.041 0.15 -9999 0 -0.6 61 61
NFKBIA 0.059 0.018 -9999 0 -10000 0 0
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.015 0.022 -9999 0 -0.65 1 1
IKBKG -0.017 0.063 -9999 0 -0.47 3 3
IKK complex/A20 -0.047 0.13 -9999 0 -0.67 15 15
NEMO/A20/RIP2 0.015 0.022 -9999 0 -0.65 1 1
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM 0.044 0.077 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.013 0.05 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.001 0.019 -9999 0 -0.56 1 1
NOD2 -0.038 0.2 -9999 0 -0.79 60 60
NFKB1 0.019 0.029 -9999 0 -0.84 1 1
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.015 0.029 -9999 0 -0.85 1 1
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0.041 -9999 0 -0.85 2 2
TNF/TNFR1A -0.058 0.17 -9999 0 -0.57 90 90
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.015 0.032 -9999 0 -0.65 2 2
CHUK 0.015 0.029 -9999 0 -0.85 1 1
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF -0.062 0.23 -9999 0 -0.75 90 90
NF kappa B1 p50/RelA -0.001 0.018 -9999 0 -0.55 1 1
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.018 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex -0.015 0.056 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.014 0.053 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.024 0.18 -10000 0 -0.81 31 31
regulation of axonogenesis -0.03 0.045 0.35 7 -10000 0 7
myoblast fusion -0.01 0.077 0.35 31 -10000 0 31
mol:GTP -0.007 0.038 -10000 0 -0.26 10 10
regulation of calcium-dependent cell-cell adhesion -0.028 0.08 0.52 14 -10000 0 14
ARF1/GTP -0.005 0.026 -10000 0 -10000 0 0
mol:GM1 0.008 0.031 -10000 0 -0.26 2 2
mol:Choline 0.028 0.059 -10000 0 -0.57 7 7
lamellipodium assembly -0.012 0.071 -10000 0 -0.5 11 11
MAPK3 0.026 0.062 -10000 0 -0.39 11 11
ARF6/GTP/NME1/Tiam1 0.029 0.081 -10000 0 -0.52 14 14
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP 0.01 0.078 -10000 0 -0.35 31 31
ARF1/GDP 0.022 0.073 -10000 0 -0.49 10 10
ARF6 0.011 0.021 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 0.006 0.098 -10000 0 -0.83 12 12
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.026 0.062 -10000 0 -0.38 12 12
actin filament bundle formation 0.012 0.066 0.49 10 -10000 0 10
KALRN -0.014 0.08 -10000 0 -0.46 21 21
RAB11FIP3/RAB11A -0.001 0.031 -10000 0 -0.65 2 2
RhoA/GDP -0.012 0.066 -10000 0 -0.5 10 10
NME1 0.016 0.032 -10000 0 -0.65 2 2
Rac1/GDP -0.012 0.066 -10000 0 -0.5 10 10
substrate adhesion-dependent cell spreading -0.007 0.038 -10000 0 -0.26 10 10
cortical actin cytoskeleton organization -0.012 0.071 -10000 0 -0.5 11 11
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.007 0.038 -10000 0 -0.26 10 10
ARF6/GTP -0.007 0.038 -10000 0 -0.26 10 10
RhoA/GTP -0.005 0.026 -10000 0 -10000 0 0
mol:GDP -0.012 0.075 -10000 0 -0.52 11 11
ARF6/GTP/RAB11FIP3/RAB11A -0.005 0.035 -10000 0 -0.61 2 2
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.022 0.031 -10000 0 -10000 0 0
RAB11FIP3 0.014 0.041 -10000 0 -0.85 2 2
tube morphogenesis -0.012 0.071 -10000 0 -0.5 11 11
ruffle organization 0.03 0.045 -10000 0 -0.35 7 7
regulation of epithelial cell migration -0.007 0.038 -10000 0 -0.26 10 10
PLD2 0.017 0.066 -10000 0 -0.64 7 7
PIP5K1A 0.03 0.045 -10000 0 -0.35 7 7
mol:Phosphatidic acid 0.028 0.059 -10000 0 -0.57 7 7
Rac1/GTP -0.012 0.072 -10000 0 -0.5 11 11
Arf6 trafficking events

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
SLC2A4 -0.068 0.24 -10000 0 -0.71 102 102
CLTC 0.04 0.016 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.033 0.02 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.017 -10000 0 -0.36 2 2
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.036 0.016 -10000 0 -10000 0 0
CPE -0.055 0.19 -10000 0 -0.52 129 129
CTNNB1 0.016 0 -10000 0 -10000 0 0
membrane fusion 0.032 0.021 -10000 0 -10000 0 0
CTNND1 0.04 0.018 -10000 0 -10000 0 0
DNM2 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.04 0.023 -10000 0 -0.37 2 2
TSHR -0.071 0.21 -10000 0 -0.52 152 152
INS 0.014 0.014 -10000 0 -10000 0 0
BIN1 -0.022 0.16 -10000 0 -0.68 48 48
mol:Choline 0.032 0.021 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.021 -10000 0 -0.41 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.017 -10000 0 -0.36 2 2
JUP 0.034 0.031 -10000 0 -0.39 1 1
ASAP2/amphiphysin II -0.023 0.096 -10000 0 -0.52 12 12
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.012 0.078 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.003 0.1 -10000 0 -0.79 14 14
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.016 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.054 0.026 -10000 0 -0.73 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.014 0.046 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.024 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.008 0.066 -10000 0 -0.53 14 14
ACAP1 0.023 0.041 -10000 0 -0.33 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.029 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.044 0.023 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0.054 0.027 -10000 0 -0.75 1 1
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 0.04 0.018 -10000 0 -10000 0 0
NME1 0.023 0.021 -10000 0 -0.41 2 2
clathrin coat assembly 0.04 0.016 -10000 0 -10000 0 0
IL2RA -0.004 0.097 -10000 0 -10000 0 0
VAMP3 0.024 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.04 0.11 -10000 0 -0.43 39 39
EXOC6 0.016 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 -0.003 0.031 -10000 0 -0.35 7 7
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.04 0.023 -10000 0 -0.37 2 2
SDC1 0.029 0.044 -10000 0 -0.39 1 1
ARF6/GDP 0.022 0.02 -10000 0 -0.41 2 2
EXOC7 0.015 0.029 -10000 0 -0.85 1 1
E-cadherin/beta catenin -0.015 0.047 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.032 0.021 -10000 0 -10000 0 0
endocytosis 0.023 0.095 0.52 12 -10000 0 12
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 0.026 0.091 -10000 0 -0.45 11 11
EXOC3 0.015 0.029 -10000 0 -0.85 1 1
ASAP2 0.012 0.058 -10000 0 -0.85 4 4
Dynamin 2/GDP 0.031 0.019 -10000 0 -0.36 2 2
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 -0.014 0.15 -10000 0 -0.46 50 50
RALA 0.016 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.012 0.04 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.021 0.12 -9999 0 -0.65 29 29
FBXW11 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
CHUK 0.015 0.029 -9999 0 -0.85 1 1
NF kappa B2 p100/RelB -0.016 0.088 -9999 0 -0.49 28 28
NFKB1 0.015 0.029 -9999 0 -0.85 1 1
MAP3K14 -0.011 0.15 -9999 0 -0.84 28 28
NF kappa B1 p50/RelB -0.001 0.031 -9999 0 -0.65 2 2
RELB 0.015 0.029 -9999 0 -0.85 1 1
NFKB2 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.001 0.019 -9999 0 -0.57 1 1
regulation of B cell activation -0.001 0.019 -9999 0 -0.57 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.014 0.073 -10000 0 -0.43 21 21
FRAP1 0.016 0.024 -10000 0 -10000 0 0
AKT1 0.022 0.076 -10000 0 -0.52 11 11
INSR 0.014 0.041 -10000 0 -0.85 2 2
Insulin Receptor/Insulin -0.003 0.036 -10000 0 -0.48 5 5
mol:GTP -0.011 0.06 -10000 0 -0.57 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.003 0.016 -10000 0 -10000 0 0
TSC2 0.013 0.05 -10000 0 -0.85 3 3
RHEB/GDP -0.009 0.053 -10000 0 -0.51 5 5
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.009 0.066 -10000 0 -0.46 13 13
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.02 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.028 0.043 -10000 0 -0.38 3 3
MAP3K5 0.013 0.023 -10000 0 -0.46 2 2
PIK3R1 0.011 0.066 -10000 0 -0.78 6 6
apoptosis 0.013 0.023 -10000 0 -0.46 2 2
mol:LY294002 0 0 0.001 1 -0.001 29 30
EIF4B 0.036 0.039 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.005 0.032 -10000 0 -0.4 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.012 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.014 0.082 -10000 0 -0.45 22 22
mTOR/RHEB/GTP/Raptor/GBL 0.034 0.033 -10000 0 -0.27 3 3
FKBP1A 0.016 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.009 0.052 -10000 0 -0.5 5 5
mol:Amino Acids 0 0 0.001 1 -0.001 29 30
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.014 0.076 -10000 0 -0.56 10 10
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.024 0.037 -10000 0 -0.65 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.022 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.012 0.066 -10000 0 -0.63 5 5
tumor necrosis factor receptor activity 0 0 0.001 29 -0.001 1 30
RPS6 0.015 0.032 -10000 0 -0.65 2 2
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0 0.064 -10000 0 -0.31 31 31
INS -0.002 0.038 -10000 0 -0.65 3 3
PTEN 0.016 0 -10000 0 -10000 0 0
PDK2 -0.013 0.07 -10000 0 -0.51 11 11
EIF4EBP1 -0.014 0.18 -10000 0 -1.2 18 18
PIK3CA 0.01 0.071 -10000 0 -0.85 6 6
PPP2R5D 0.024 0.027 -10000 0 -10000 0 0
peptide biosynthetic process 0.018 0.043 -10000 0 -0.46 7 7
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -0.003 11 11
EEF2 0.018 0.043 -10000 0 -0.46 7 7
eIF4E/4E-BP1 -0.004 0.17 -10000 0 -1.1 18 18
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD2 0.017 0.018 -9999 0 -0.32 2 2
SMAD3 0.052 0.021 -9999 0 -10000 0 0
SMAD3/SMAD4 0.058 0.024 -9999 0 -0.39 1 1
SMAD4/Ubc9/PIASy -0.001 0.027 -9999 0 -0.56 2 2
SMAD2/SMAD2/SMAD4 -0.002 0.027 -9999 0 -10000 0 0
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.025 0.017 -9999 0 -10000 0 0
MAP3K1 0.015 0.022 -9999 0 -0.65 1 1
TRAP-1/SMAD4 -0.018 0.11 -9999 0 -0.65 24 24
MAPK3 0.015 0.029 -9999 0 -0.85 1 1
MAPK1 0.015 0.029 -9999 0 -0.85 1 1
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.015 0.029 -9999 0 -0.85 1 1
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.015 0.022 -9999 0 -0.65 1 1
KPNB1 0.015 0.029 -9999 0 -0.85 1 1
TGFBRAP1 -0.007 0.14 -9999 0 -0.85 24 24
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.015 0.029 -9999 0 -0.85 1 1
KPNA2 0.013 0.045 -9999 0 -0.65 4 4
PIAS4 0.014 0.041 -9999 0 -0.85 2 2
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 -0.002 0.037 -9999 0 -0.57 3 3
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0.026 -9999 0 -0.39 2 2
AP2 -0.001 0.022 -9999 0 -0.65 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.02 -9999 0 -0.6 1 1
CLTB 0.014 0.041 -9999 0 -0.85 2 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.032 0.02 -9999 0 -0.38 2 2
CD4 -0.008 0.14 -9999 0 -0.85 25 25
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
ARFGAP1 0.013 0.028 -9999 0 -0.58 2 2
mol:PI-4-5-P2 -0.003 0.029 -9999 0 -0.29 8 8
ARF1/GTP -0.002 0.026 -9999 0 -0.46 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.034 0.029 -9999 0 -0.54 2 2
mol:Choline -0.003 0.029 -9999 0 -0.3 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0.001 -9999 0 -10000 0 0
DDEF1 -0.003 0.029 -9999 0 -0.29 8 8
ARF1/GDP -0.002 0.025 -9999 0 -0.48 2 2
AP2M1 0.016 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.002 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.022 -9999 0 -0.44 2 2
ARFIP2 -0.001 0.028 -9999 0 -0.83 1 1
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.031 0.019 -9999 0 -0.32 2 2
ARF1/GTP/ARHGAP10 0 0.002 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin -0.001 0.011 -9999 0 -10000 0 0
AP2A1 0.015 0.029 -9999 0 -0.85 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.033 0.034 -9999 0 -0.62 2 2
ARF1/GDP/Membrin -0.001 0.01 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.02 -9999 0 -0.58 1 1
CYTH2 0.014 0.041 -9999 0 -0.84 2 2
ARF1/GTP/GGA3 0 0.003 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.036 0.057 -9999 0 -0.41 2 2
PLD2 -0.003 0.029 -9999 0 -0.3 8 8
ARF-GAP1/v-SNARE 0.013 0.028 -9999 0 -0.57 2 2
PIP5K1A -0.003 0.029 -9999 0 -0.29 8 8
ARF1/GTP/Membrin/GBF1/p115 -0.002 0.021 -9999 0 -0.35 2 2
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.003 0.029 -9999 0 -0.3 8 8
KDEL Receptor/Ligand/ARF-GAP1 0.013 0.028 -9999 0 -0.57 2 2
GOSR2 -0.001 0.011 -9999 0 -10000 0 0
USO1 -0.002 0.031 -9999 0 -0.86 1 1
GBF1 -0.002 0.031 -9999 0 -0.86 1 1
ARF1/GTP/Arfaptin 2 -0.001 0.022 -9999 0 -0.64 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.016 0.095 -9999 0 -0.56 26 26
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.015 -9999 0 -0.4 1 1
MDM2/SUMO1 0.037 0.015 -9999 0 -10000 0 0
HDAC4 0.015 0.029 -9999 0 -0.85 1 1
Ran/GTP/Exportin 1/HDAC1 0 0.007 -9999 0 -10000 0 0
SUMO1 0.016 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.021 0.02 -9999 0 -0.36 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.036 0.015 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.037 0.023 -9999 0 -0.47 1 1
SUMO1/HDAC1 0.037 0.015 -9999 0 -10000 0 0
RANGAP1 0.013 0.047 -9999 0 -0.78 3 3
MDM2/SUMO1/SUMO1 -0.001 0.017 -9999 0 -0.51 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.027 0.016 -9999 0 -0.29 2 2
Ran/GTP -0.001 0.013 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 -0.001 0.012 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.015 0.029 -9999 0 -0.85 1 1
PIAS1 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 889 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Y8.A8S1 TCGA.Y8.A8S0 TCGA.Y8.A8RZ TCGA.Y8.A8RY
109_MAP3K5 0.07 0.07 -0.21 0.07
47_PPARGC1A 0.016 0.016 0.016 0.016
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 -0.65 -0.65 0.016 0.016
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR 0 -0.36 0 -0.36
30_TGFB1/TGF beta receptor Type II 0.016 0.016 0.016 0.016
84_STAT5B 0.06 -0.058 -0.23 0.057
84_STAT5A 0.06 -0.058 -0.23 0.057
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIPAN-TP/14527269/KIPAN-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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