PARADIGM pathway analysis of mRNA expression and copy number data
Colorectal Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C15M6522
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C15M6522
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 32 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
TCGA08_retinoblastoma 122
Signaling events mediated by Stem cell factor receptor (c-Kit) 69
Fc-epsilon receptor I signaling in mast cells 56
BCR signaling pathway 55
HIF-1-alpha transcription factor network 50
IGF1 pathway 40
FAS signaling pathway (CD95) 36
Syndecan-1-mediated signaling events 34
Visual signal transduction: Rods 27
Arf6 signaling events 26
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 222 . 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 ( 222 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_retinoblastoma 0.5495 122 979 8 -0.35 0.19 1000 -1000 -0.007 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3108 69 5444 78 -1.1 0.28 1000 -1000 -0.063 -1000
Fc-epsilon receptor I signaling in mast cells 0.2523 56 5450 97 -0.35 0.043 1000 -1000 -0.059 -1000
BCR signaling pathway 0.2477 55 5510 99 -0.39 0.034 1000 -1000 -0.064 -1000
HIF-1-alpha transcription factor network 0.2252 50 3868 76 -0.74 0.041 1000 -1000 -0.062 -1000
IGF1 pathway 0.1802 40 2330 57 -0.28 0.088 1000 -1000 -0.051 -1000
FAS signaling pathway (CD95) 0.1622 36 1700 47 -0.19 0.12 1000 -1000 -0.043 -1000
Syndecan-1-mediated signaling events 0.1532 34 1164 34 -0.32 0.033 1000 -1000 -0.037 -1000
Visual signal transduction: Rods 0.1216 27 1406 52 -0.35 0.067 1000 -1000 -0.038 -1000
Arf6 signaling events 0.1171 26 1621 62 -0.19 0.081 1000 -1000 -0.017 -1000
Glypican 1 network 0.0946 21 1030 48 -0.26 0.055 1000 -1000 -0.029 -1000
HIF-2-alpha transcription factor network 0.0946 21 915 43 -0.56 0.32 1000 -1000 -0.046 -1000
Wnt signaling 0.0901 20 145 7 -0.051 0.032 1000 -1000 -0.022 -1000
FOXM1 transcription factor network 0.0901 20 1066 51 -0.52 0.032 1000 -1000 -0.13 -1000
EGFR-dependent Endothelin signaling events 0.0856 19 413 21 -0.091 0.048 1000 -1000 -0.046 -1000
Reelin signaling pathway 0.0811 18 1044 56 -0.28 0.089 1000 -1000 -0.037 -1000
Visual signal transduction: Cones 0.0766 17 680 38 -0.14 0.054 1000 -1000 -0.011 -1000
IL4-mediated signaling events 0.0766 17 1564 91 -0.49 0.32 1000 -1000 -0.1 -1000
BMP receptor signaling 0.0766 17 1410 81 -0.18 0.063 1000 -1000 -0.06 -1000
Endothelins 0.0766 17 1694 96 -0.38 0.096 1000 -1000 -0.047 -1000
TRAIL signaling pathway 0.0721 16 796 48 -0.1 0.034 1000 -1000 -0.041 -1000
IL12-mediated signaling events 0.0676 15 1365 87 -0.37 0.064 1000 -1000 -0.071 -1000
IL1-mediated signaling events 0.0676 15 958 62 -0.22 0.058 1000 -1000 -0.044 -1000
TCGA08_p53 0.0631 14 98 7 -0.061 0.033 1000 -1000 -0.008 -1000
FOXA2 and FOXA3 transcription factor networks 0.0586 13 599 46 -0.74 0.038 1000 -1000 -0.1 -1000
Syndecan-3-mediated signaling events 0.0586 13 478 35 -0.3 0.07 1000 -1000 -0.026 -1000
IL2 signaling events mediated by PI3K 0.0586 13 797 58 -0.59 0.038 1000 -1000 -0.041 -1000
IL6-mediated signaling events 0.0586 13 1032 75 -0.25 0.061 1000 -1000 -0.05 -1000
Signaling events mediated by PRL 0.0586 13 458 34 -0.079 0.094 1000 -1000 -0.044 -1000
Signaling events mediated by the Hedgehog family 0.0541 12 675 52 -0.13 0.087 1000 -1000 -0.041 -1000
Syndecan-2-mediated signaling events 0.0541 12 830 69 -0.3 0.055 1000 -1000 -0.038 -1000
Ceramide signaling pathway 0.0541 12 923 76 -0.27 0.088 1000 -1000 -0.041 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0495 11 618 54 -0.28 0.042 1000 -1000 -0.045 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0495 11 937 85 -0.13 0.055 1000 -1000 -0.045 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0495 11 617 52 -0.43 0.12 1000 -1000 -0.047 -1000
Regulation of nuclear SMAD2/3 signaling 0.0450 10 1381 136 -1.1 0.12 1000 -1000 -0.049 -1000
Thromboxane A2 receptor signaling 0.0450 10 1136 105 -0.35 0.067 1000 -1000 -0.053 -1000
p75(NTR)-mediated signaling 0.0450 10 1276 125 -0.32 0.079 1000 -1000 -0.054 -1000
TCR signaling in naïve CD8+ T cells 0.0450 10 945 93 -0.06 0.048 1000 -1000 -0.053 -1000
Canonical Wnt signaling pathway 0.0450 10 555 51 -0.23 0.18 1000 -1000 -0.06 -1000
Cellular roles of Anthrax toxin 0.0405 9 374 39 -0.032 0.033 1000 -1000 -0.025 -1000
Presenilin action in Notch and Wnt signaling 0.0405 9 597 61 -0.23 0.12 1000 -1000 -0.051 -1000
PLK1 signaling events 0.0405 9 829 85 -0.11 0.065 1000 -1000 -0.055 -1000
Glucocorticoid receptor regulatory network 0.0405 9 1115 114 -0.3 0.22 1000 -1000 -0.056 -1000
Glypican 2 network 0.0405 9 36 4 0 0.011 1000 -1000 0 -1000
PLK2 and PLK4 events 0.0360 8 26 3 0.004 0.023 1000 -1000 -0.012 -1000
Osteopontin-mediated events 0.0360 8 323 38 -0.21 0.048 1000 -1000 -0.045 -1000
PDGFR-alpha signaling pathway 0.0360 8 357 44 -0.096 0.075 1000 -1000 -0.049 -1000
amb2 Integrin signaling 0.0360 8 666 82 -0.25 0.053 1000 -1000 -0.038 -1000
Ephrin B reverse signaling 0.0360 8 394 48 -0.096 0.048 1000 -1000 -0.036 -1000
Integrins in angiogenesis 0.0360 8 705 84 -0.27 0.078 1000 -1000 -0.046 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0360 8 607 68 -0.38 0.052 1000 -1000 -0.084 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0360 8 274 33 -0.13 0.077 1000 -1000 -0.043 -1000
Regulation of Androgen receptor activity 0.0360 8 584 70 -0.53 0.062 1000 -1000 -0.057 -1000
Ras signaling in the CD4+ TCR pathway 0.0360 8 140 17 -0.016 0.054 1000 -1000 -0.019 -1000
Aurora B signaling 0.0360 8 573 67 -0.14 0.049 1000 -1000 -0.053 -1000
Signaling events mediated by PTP1B 0.0315 7 546 76 -0.27 0.058 1000 -1000 -0.047 -1000
EPO signaling pathway 0.0315 7 426 55 -0.53 0.033 1000 -1000 -0.049 -1000
Regulation of p38-alpha and p38-beta 0.0315 7 416 54 -0.083 0.063 1000 -1000 -0.05 -1000
Calcium signaling in the CD4+ TCR pathway 0.0315 7 239 31 -0.15 0.039 1000 -1000 -0.045 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0315 7 524 74 -0.27 0.065 1000 -1000 -0.072 -1000
Plasma membrane estrogen receptor signaling 0.0315 7 613 86 -0.27 0.1 1000 -1000 -0.068 -1000
Noncanonical Wnt signaling pathway 0.0270 6 172 26 -0.051 0.033 1000 -1000 -0.049 -1000
Nectin adhesion pathway 0.0270 6 412 63 -0.31 0.074 1000 -1000 -0.053 -1000
ceramide signaling pathway 0.0270 6 314 49 -0.19 0.068 1000 -1000 -0.045 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0270 6 523 83 -0.19 0.088 1000 -1000 -0.037 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0270 6 281 45 -0.1 0.058 1000 -1000 -0.053 -1000
Nongenotropic Androgen signaling 0.0270 6 353 52 -0.056 0.073 1000 -1000 -0.037 -1000
IL27-mediated signaling events 0.0270 6 320 51 -0.15 0.033 1000 -1000 -0.054 -1000
TCGA08_rtk_signaling 0.0270 6 156 26 -0.12 0.064 1000 -1000 -0.011 -1000
Class I PI3K signaling events 0.0270 6 456 73 -0.23 0.057 1000 -1000 -0.046 -1000
Syndecan-4-mediated signaling events 0.0270 6 441 67 -0.36 0.11 1000 -1000 -0.049 -1000
IL23-mediated signaling events 0.0270 6 412 60 -0.27 0.034 1000 -1000 -0.09 -1000
VEGFR1 specific signals 0.0270 6 352 56 0 0.1 1000 -1000 -0.057 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0225 5 149 28 -0.032 0.043 1000 -1000 -0.02 -1000
a4b1 and a4b7 Integrin signaling 0.0225 5 26 5 0.011 0.044 1000 -1000 0.004 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0225 5 208 37 -0.084 0.076 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class III 0.0225 5 222 40 -0.2 0.062 1000 -1000 -0.021 -1000
EPHB forward signaling 0.0225 5 478 85 -0.096 0.11 1000 -1000 -0.073 -1000
Regulation of Telomerase 0.0225 5 577 102 -0.16 0.079 1000 -1000 -0.06 -1000
E-cadherin signaling events 0.0225 5 28 5 0.018 0.047 1000 -1000 0.006 -1000
Canonical NF-kappaB pathway 0.0180 4 160 39 -0.042 0.073 1000 -1000 -0.04 -1000
ErbB4 signaling events 0.0180 4 343 69 -0.22 0.096 1000 -1000 -0.043 -1000
Class I PI3K signaling events mediated by Akt 0.0180 4 304 68 -0.057 0.069 1000 -1000 -0.041 -1000
S1P1 pathway 0.0180 4 166 36 -0.034 0.034 1000 -1000 -0.042 -1000
FoxO family signaling 0.0180 4 286 64 -0.12 0.067 1000 -1000 -0.066 -1000
Signaling mediated by p38-alpha and p38-beta 0.0180 4 211 44 -0.15 0.033 1000 -1000 -0.023 -1000
Effects of Botulinum toxin 0.0180 4 120 26 -0.014 0.062 1000 -1000 -0.018 -1000
Arf6 trafficking events 0.0180 4 339 71 -0.1 0.056 1000 -1000 -0.028 -1000
S1P3 pathway 0.0180 4 171 42 -0.031 0.043 1000 -1000 -0.033 -1000
Caspase cascade in apoptosis 0.0135 3 263 74 -0.09 0.046 1000 -1000 -0.051 -1000
BARD1 signaling events 0.0135 3 185 57 -0.052 0.065 1000 -1000 -0.049 -1000
JNK signaling in the CD4+ TCR pathway 0.0135 3 58 17 -0.015 0.075 1000 -1000 -0.036 -1000
Aurora A signaling 0.0135 3 193 60 -0.003 0.085 1000 -1000 -0.025 -1000
Arf6 downstream pathway 0.0135 3 142 43 -0.048 0.049 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 0.0135 3 108 32 -0.07 0.052 1000 -1000 -0.024 -1000
mTOR signaling pathway 0.0135 3 204 53 -0.056 0.046 1000 -1000 -0.043 -1000
IFN-gamma pathway 0.0135 3 257 68 -0.044 0.054 1000 -1000 -0.056 -1000
LPA receptor mediated events 0.0135 3 357 102 -0.11 0.044 1000 -1000 -0.081 -1000
E-cadherin signaling in the nascent adherens junction 0.0135 3 294 76 -0.03 0.097 1000 -1000 -0.064 -1000
IL2 signaling events mediated by STAT5 0.0135 3 67 22 -0.02 0.07 1000 -1000 -0.043 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0135 3 276 88 -0.18 0.11 1000 -1000 -0.067 -1000
PDGFR-beta signaling pathway 0.0135 3 318 97 -0.17 0.098 1000 -1000 -0.052 -1000
S1P4 pathway 0.0135 3 81 25 -0.032 0.043 1000 -1000 -0.028 -1000
LPA4-mediated signaling events 0.0090 2 25 12 -0.006 0.028 1000 -1000 -0.019 -1000
ErbB2/ErbB3 signaling events 0.0090 2 142 65 -0.028 0.052 1000 -1000 -0.058 -1000
Coregulation of Androgen receptor activity 0.0090 2 227 76 -0.078 0.067 1000 -1000 -0.028 -1000
Ephrin A reverse signaling 0.0090 2 14 7 0 0.039 1000 -1000 -0.01 -1000
Hedgehog signaling events mediated by Gli proteins 0.0090 2 181 65 -0.057 0.062 1000 -1000 -0.057 -1000
S1P5 pathway 0.0090 2 38 17 -0.032 0.033 1000 -1000 -0.017 -1000
Signaling mediated by p38-gamma and p38-delta 0.0090 2 43 15 -0.013 0.033 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 0.0090 2 116 58 -0.017 0.068 1000 -1000 -0.043 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0090 2 290 125 -0.019 0.13 1000 -1000 -0.055 -1000
Insulin Pathway 0.0090 2 161 74 -0.026 0.1 1000 -1000 -0.042 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0090 2 240 120 -0.019 0.091 1000 -1000 -0.054 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0045 1 34 23 0.012 0.041 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class II 0.0045 1 148 75 -0.051 0.065 1000 -1000 -0.025 -1000
Circadian rhythm pathway 0.0045 1 29 22 -0.011 0.078 1000 -1000 -0.033 -1000
Signaling events regulated by Ret tyrosine kinase 0.0045 1 97 82 0 0.067 1000 -1000 -0.072 -1000
Paxillin-dependent events mediated by a4b1 0.0045 1 58 36 -0.065 0.07 1000 -1000 -0.047 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0000 0 27 34 -0.046 0.093 1000 -1000 -0.032 -1000
Aurora C signaling 0.0000 0 4 7 0 0.047 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class I 0.0000 0 81 104 -0.064 0.078 1000 -1000 -0.036 -1000
Atypical NF-kappaB pathway 0.0000 0 9 31 0 0.068 1000 -1000 -0.022 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 8 27 0 0.06 1000 -1000 -0.037 -1000
Rapid glucocorticoid signaling 0.0000 0 3 20 0 0.039 1000 -1000 -0.008 -1000
E-cadherin signaling in keratinocytes 0.0000 0 32 43 -0.053 0.097 1000 -1000 -0.04 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.033 0.033 1000 -1000 -0.011 -1000
p38 MAPK signaling pathway 0.0000 0 34 44 0 0.065 1000 -1000 -0.024 -1000
Arf1 pathway 0.0000 0 38 54 -0.001 0.064 1000 -1000 -0.021 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 0 0.089 1000 -1000 0 -1000
Total NA 1333 79136 7203 -23 9.4 131000 -131000 -5.6 -131000
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.35 0.22 -10000 0 -0.47 163 163
CDKN2C 0.041 0.029 -10000 0 -10000 0 0
CDKN2A -0.081 0.17 -10000 0 -0.33 66 66
CCND2 0.17 0.1 0.22 161 -0.22 1 162
RB1 -0.15 0.1 0.22 1 -0.23 129 130
CDK4 0.18 0.099 0.23 161 -0.23 1 162
CDK6 0.19 0.1 0.25 161 -10000 0 161
G1/S progression 0.16 0.1 0.23 134 -0.22 1 135
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.25 0.18 0.28 1 -0.42 106 107
CRKL -0.27 0.19 -10000 0 -0.44 108 108
HRAS -0.23 0.18 -10000 0 -0.39 80 80
mol:PIP3 -0.24 0.18 -10000 0 -0.41 102 102
SPRED1 0.031 0.008 -10000 0 -10000 0 0
SPRED2 0.034 0 -10000 0 -10000 0 0
GAB1 -0.29 0.2 -10000 0 -0.46 111 111
FOXO3 -0.26 0.2 -10000 0 -0.44 100 100
AKT1 -0.28 0.22 -10000 0 -0.47 103 103
BAD -0.26 0.2 -10000 0 -0.43 102 102
megakaryocyte differentiation -0.3 0.2 -10000 0 -0.46 117 117
GSK3B -0.26 0.2 -10000 0 -0.44 100 100
RAF1 -0.19 0.14 -10000 0 -0.34 55 55
SHC1 0.033 0.006 -10000 0 -10000 0 0
STAT3 -0.28 0.2 -10000 0 -0.46 108 108
STAT1 -0.77 0.53 -10000 0 -1.1 142 142
HRAS/SPRED1 -0.18 0.15 -10000 0 -0.34 54 54
cell proliferation -0.28 0.2 -10000 0 -0.45 109 109
PIK3CA 0.032 0.004 -10000 0 -10000 0 0
TEC 0.033 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.28 0.21 -10000 0 -0.46 109 109
HRAS/SPRED2 -0.18 0.15 -10000 0 -0.37 27 27
LYN/TEC/p62DOK -0.25 0.2 -10000 0 -0.44 94 94
MAPK3 -0.13 0.1 -10000 0 -0.28 15 15
STAP1 -0.43 0.25 -10000 0 -0.58 144 144
GRAP2 0.031 0.009 -10000 0 -10000 0 0
JAK2 -0.59 0.42 -10000 0 -0.95 110 110
STAT1 (dimer) -0.75 0.51 -10000 0 -1 148 148
mol:Gleevec 0.012 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.28 0.22 -10000 0 -0.46 110 110
actin filament polymerization -0.28 0.2 -10000 0 -0.45 111 111
LYN 0.029 0.012 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.54 0.31 -10000 0 -0.73 143 143
PIK3R1 0.032 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.24 0.19 -10000 0 -0.4 106 106
PI3K -0.26 0.21 -10000 0 -0.44 108 108
PTEN 0.027 0.052 -10000 0 -0.5 2 2
SCF/KIT/EPO/EPOR -0.84 0.66 -10000 0 -1.5 108 108
MAPK8 -0.29 0.2 -10000 0 -0.46 109 109
STAT3 (dimer) -0.28 0.2 -10000 0 -0.45 108 108
positive regulation of transcription -0.11 0.085 -10000 0 -0.23 10 10
mol:GDP -0.24 0.19 -10000 0 -0.4 105 105
PIK3C2B -0.28 0.2 -10000 0 -0.46 107 107
CBL/CRKL -0.26 0.19 -10000 0 -0.42 107 107
FER -0.29 0.2 -10000 0 -0.46 111 111
SH2B3 -0.29 0.2 -10000 0 -0.46 108 108
PDPK1 -0.23 0.17 -10000 0 -0.38 98 98
SNAI2 -0.28 0.2 -10000 0 -0.45 105 105
positive regulation of cell proliferation -0.51 0.34 -10000 0 -0.8 115 115
KITLG -0.023 0.051 -10000 0 -0.45 2 2
cell motility -0.51 0.34 -10000 0 -0.8 115 115
PTPN6 0.048 0.013 -10000 0 -10000 0 0
EPOR -0.21 0.18 -10000 0 -0.99 3 3
STAT5A (dimer) -0.41 0.28 -10000 0 -0.64 112 112
SOCS1 0.031 0.025 -10000 0 -0.32 1 1
cell migration 0.28 0.19 0.45 107 -10000 0 107
SOS1 0.033 0.002 -10000 0 -10000 0 0
EPO -0.01 0.033 -10000 0 -0.34 1 1
VAV1 -0.014 0.15 -10000 0 -0.5 19 19
GRB10 -0.28 0.2 -10000 0 -0.45 108 108
PTPN11 0.044 0.027 -10000 0 -0.33 1 1
SCF/KIT -0.3 0.21 -10000 0 -0.48 111 111
GO:0007205 0.017 0.01 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.3 20 20
CBL 0.033 0.006 -10000 0 -10000 0 0
KIT -0.79 0.7 -10000 0 -1.5 109 109
MAP2K2 -0.15 0.11 -10000 0 -0.3 15 15
SHC/Grb2/SOS1 -0.26 0.21 -10000 0 -0.44 103 103
STAT5A -0.42 0.29 -10000 0 -0.67 112 112
GRB2 0.032 0.006 -10000 0 -10000 0 0
response to radiation -0.27 0.2 -10000 0 -0.44 105 105
SHC/GRAP2 0.045 0.015 -10000 0 -10000 0 0
PTPRO -0.31 0.21 -10000 0 -0.47 117 117
SH2B2 -0.29 0.2 -10000 0 -0.46 111 111
DOK1 0.032 0.024 -10000 0 -0.32 1 1
MATK -0.29 0.2 -10000 0 -0.46 107 107
CREBBP -0.079 0.079 -10000 0 -10000 0 0
BCL2 -1.1 0.7 -10000 0 -1.5 148 148
Fc-epsilon receptor I signaling in mast cells

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A -0.017 0.16 -10000 0 -0.5 20 20
LAT2 -0.22 0.2 -10000 0 -0.37 125 125
AP1 -0.28 0.29 -10000 0 -0.55 94 94
mol:PIP3 -0.28 0.25 0.26 1 -0.52 95 96
IKBKB -0.14 0.14 0.19 7 -0.27 85 92
AKT1 -0.21 0.18 0.33 3 -0.41 80 83
IKBKG -0.15 0.13 0.18 3 -0.27 96 99
MS4A2 -0.3 0.26 -10000 0 -0.5 135 135
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.004 -10000 0 -10000 0 0
MAP3K1 -0.22 0.21 0.27 1 -0.43 89 90
mol:Ca2+ -0.21 0.18 0.22 3 -0.38 95 98
LYN 0.025 0.011 -10000 0 -10000 0 0
CBLB -0.22 0.2 -10000 0 -0.37 125 125
SHC1 0.033 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.031 0.1 -10000 0 -0.28 19 19
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.24 0.21 0.34 2 -0.44 95 97
PTPN13 -0.26 0.23 -10000 0 -0.57 36 36
PTPN11 0.006 0.039 -10000 0 -0.35 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.17 0.15 0.38 1 -0.33 78 79
SYK 0.028 0.026 -10000 0 -0.34 1 1
GRB2 0.031 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.28 0.26 -10000 0 -0.53 96 96
LAT -0.22 0.2 -10000 0 -0.37 122 122
PAK2 -0.25 0.24 0.28 1 -0.48 89 90
NFATC2 -0.065 0.066 -10000 0 -10000 0 0
HRAS -0.27 0.26 -10000 0 -0.52 92 92
GAB2 0.033 0.004 -10000 0 -10000 0 0
PLA2G1B 0.036 0.14 -10000 0 -0.88 5 5
Fc epsilon R1 -0.29 0.26 -10000 0 -0.46 146 146
Antigen/IgE/Fc epsilon R1 -0.26 0.24 -10000 0 -0.41 146 146
mol:GDP -0.29 0.28 -10000 0 -0.56 93 93
JUN 0.025 0.054 -10000 0 -0.32 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.031 0.005 -10000 0 -10000 0 0
FOS -0.027 0.16 -10000 0 -0.49 24 24
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.23 0.21 -10000 0 -0.38 130 130
CHUK -0.15 0.13 0.19 2 -0.27 94 96
KLRG1 -0.2 0.18 -10000 0 -0.39 84 84
VAV1 -0.24 0.22 -10000 0 -0.44 98 98
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.22 0.2 -10000 0 -0.37 122 122
negative regulation of mast cell degranulation -0.19 0.17 -10000 0 -0.37 84 84
BTK -0.3 0.32 -10000 0 -0.61 90 90
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.35 0.33 -10000 0 -0.63 108 108
GAB2/PI3K/SHP2 -0.22 0.19 -10000 0 -0.44 82 82
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.24 0.22 -10000 0 -0.49 86 86
RAF1 0.039 0.16 -10000 0 -0.98 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.3 0.29 -10000 0 -0.46 149 149
FCER1G 0.043 0.013 -10000 0 -10000 0 0
FCER1A -0.22 0.27 -10000 0 -0.52 99 99
Antigen/IgE/Fc epsilon R1/Fyn -0.24 0.24 -10000 0 -0.39 143 143
MAPK3 0.036 0.15 -10000 0 -0.9 5 5
MAPK1 0.03 0.15 -10000 0 -0.9 5 5
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 -0.18 0.33 -10000 0 -0.77 45 45
DUSP1 -0.012 0.15 -10000 0 -0.5 18 18
NF-kappa-B/RelA -0.082 0.09 -10000 0 -0.2 9 9
actin cytoskeleton reorganization -0.23 0.22 -10000 0 -0.45 74 74
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.24 0.24 -10000 0 -0.47 89 89
FER -0.23 0.2 -10000 0 -0.38 126 126
RELA 0.033 0.006 -10000 0 -10000 0 0
ITK -0.049 0.056 -10000 0 -0.34 2 2
SOS1 0.034 0.002 -10000 0 -10000 0 0
PLCG1 -0.24 0.28 0.27 2 -0.52 90 92
cytokine secretion -0.063 0.06 -10000 0 -10000 0 0
SPHK1 -0.24 0.2 -10000 0 -0.41 104 104
PTK2 -0.24 0.23 -10000 0 -0.51 33 33
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.29 0.28 0.24 2 -0.54 104 106
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.29 0.25 0.25 1 -0.52 99 100
MAP2K2 0.032 0.14 -10000 0 -0.89 5 5
MAP2K1 0.03 0.15 -10000 0 -0.92 5 5
MAP2K7 0.033 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.17 0.17 -10000 0 -0.35 83 83
MAP2K4 -0.2 0.43 -10000 0 -0.96 50 50
Fc epsilon R1/FcgammaRIIB -0.31 0.31 -10000 0 -0.49 149 149
mol:Choline -0.23 0.21 0.34 2 -0.44 95 97
SHC/Grb2/SOS1 -0.19 0.21 -10000 0 -0.41 82 82
FYN 0.03 0.037 -10000 0 -0.5 1 1
DOK1 0.032 0.024 -10000 0 -0.32 1 1
PXN -0.22 0.21 -10000 0 -0.54 14 14
HCLS1 -0.23 0.21 -10000 0 -0.38 126 126
PRKCB -0.21 0.18 0.21 2 -0.38 98 100
FCGR2B -0.086 0.22 -10000 0 -0.5 48 48
IGHE -0.007 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.19 0.17 -10000 0 -0.37 84 84
LCP2 0.025 0.056 -10000 0 -0.37 4 4
PLA2G4A -0.28 0.23 0.19 1 -0.43 132 133
RASA1 0.03 0.035 -10000 0 -0.32 2 2
mol:Phosphatidic acid -0.23 0.21 0.34 2 -0.44 95 97
IKK complex -0.099 0.11 0.17 8 -0.21 67 75
WIPF1 0.031 0.036 -10000 0 -0.5 1 1
BCR signaling pathway

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.21 0.26 -10000 0 -0.49 85 85
IKBKB -0.095 0.13 -10000 0 -0.3 15 15
AKT1 -0.11 0.15 0.28 3 -0.27 77 80
IKBKG -0.1 0.13 -10000 0 -0.29 24 24
CALM1 -0.28 0.31 -10000 0 -0.59 99 99
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
MAP3K1 -0.27 0.37 0.48 1 -0.68 90 91
MAP3K7 0.033 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.31 0.33 -10000 0 -0.62 101 101
DOK1 0.032 0.024 -10000 0 -0.32 1 1
AP-1 -0.14 0.14 -10000 0 -0.28 86 86
LYN 0.029 0.012 -10000 0 -10000 0 0
BLNK 0.017 0.088 -10000 0 -0.5 6 6
SHC1 0.033 0.006 -10000 0 -10000 0 0
BCR complex -0.25 0.31 -10000 0 -0.55 107 107
CD22 -0.32 0.4 -10000 0 -0.77 86 86
CAMK2G -0.26 0.28 -10000 0 -0.54 97 97
CSNK2A1 0.027 0.014 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.16 0.22 -10000 0 -0.44 67 67
GO:0007205 -0.31 0.34 -10000 0 -0.64 101 101
SYK 0.031 0.025 -10000 0 -0.32 1 1
ELK1 -0.29 0.32 -10000 0 -0.6 100 100
NFATC1 -0.31 0.35 0.36 1 -0.66 101 102
B-cell antigen/BCR complex -0.25 0.31 -10000 0 -0.55 107 107
PAG1/CSK -0.068 0.18 -10000 0 -0.36 57 57
NFKBIB -0.02 0.054 -10000 0 -0.14 8 8
HRAS -0.24 0.27 0.22 1 -0.52 96 97
NFKBIA -0.018 0.052 -10000 0 -0.13 6 6
NF-kappa-B/RelA/I kappa B beta -0.009 0.045 -10000 0 -10000 0 0
RasGAP/Csk -0.22 0.31 -10000 0 -0.49 111 111
mol:GDP -0.29 0.32 -10000 0 -0.6 101 101
PTEN 0.026 0.052 -10000 0 -0.5 2 2
CD79B -0.16 0.26 -10000 0 -0.5 78 78
NF-kappa-B/RelA/I kappa B alpha -0.008 0.044 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.31 0.35 -10000 0 -0.65 104 104
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 -0.32 0.35 -10000 0 -0.65 101 101
CSK 0.031 0.009 -10000 0 -10000 0 0
FOS -0.3 0.3 -10000 0 -0.58 101 101
CHUK -0.11 0.14 -10000 0 -0.32 23 23
IBTK 0.032 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.23 0.28 -10000 0 -0.52 91 91
PTPN6 -0.3 0.37 -10000 0 -0.73 84 84
RELA 0.033 0.006 -10000 0 -10000 0 0
BCL2A1 -0.005 0.033 -10000 0 -10000 0 0
VAV2 -0.38 0.46 0.45 1 -0.84 100 101
ubiquitin-dependent protein catabolic process -0.015 0.052 -10000 0 -0.13 6 6
BTK -0.18 0.45 -10000 0 -1.2 35 35
CD19 -0.39 0.46 -10000 0 -0.83 102 102
MAP4K1 0.032 0.006 -10000 0 -10000 0 0
CD72 0.024 0.062 -10000 0 -0.41 4 4
PAG1 -0.12 0.24 -10000 0 -0.5 58 58
MAPK14 -0.22 0.3 0.38 2 -0.56 86 88
SH3BP5 0.03 0.037 -10000 0 -0.5 1 1
PIK3AP1 -0.32 0.35 -10000 0 -0.66 98 98
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.36 0.4 -10000 0 -0.76 98 98
RAF1 -0.23 0.25 -10000 0 -0.49 95 95
RasGAP/p62DOK/SHIP -0.22 0.3 -10000 0 -0.47 116 116
CD79A -0.21 0.27 -10000 0 -0.5 99 99
re-entry into mitotic cell cycle -0.14 0.14 -10000 0 -0.28 87 87
RASA1 0.03 0.035 -10000 0 -0.32 2 2
MAPK3 -0.19 0.21 -10000 0 -0.43 79 79
MAPK1 -0.19 0.21 -10000 0 -0.43 80 80
CD72/SHP1 -0.26 0.36 0.61 1 -0.69 82 83
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 -0.22 0.3 0.45 1 -0.56 86 87
actin cytoskeleton organization -0.29 0.37 0.32 4 -0.66 100 104
NF-kappa-B/RelA -0.01 0.086 -10000 0 -10000 0 0
Calcineurin -0.23 0.27 -10000 0 -0.52 85 85
PI3K -0.26 0.29 -10000 0 -0.56 95 95
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.34 0.37 -10000 0 -0.69 101 101
SOS1 0.033 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.32 0.43 -10000 0 -0.83 82 82
DAPP1 -0.38 0.49 -10000 0 -0.97 82 82
cytokine secretion -0.28 0.32 0.35 1 -0.59 101 102
mol:DAG -0.32 0.35 -10000 0 -0.65 101 101
PLCG2 -0.23 0.27 -10000 0 -0.5 104 104
MAP2K1 -0.21 0.23 -10000 0 -0.46 92 92
B-cell antigen/BCR complex/FcgammaRIIB -0.26 0.34 -10000 0 -0.55 115 115
mol:PI-3-4-5-P3 -0.17 0.19 -10000 0 -0.38 90 90
ETS1 -0.24 0.25 -10000 0 -0.49 96 96
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.16 0.26 -10000 0 -0.41 103 103
B-cell antigen/BCR complex/LYN -0.33 0.43 -10000 0 -0.8 89 89
MALT1 0.023 0.016 -10000 0 -10000 0 0
TRAF6 0.034 0.003 -10000 0 -10000 0 0
RAC1 -0.32 0.4 0.32 4 -0.73 100 104
B-cell antigen/BCR complex/LYN/SYK -0.27 0.37 -10000 0 -0.7 84 84
CARD11 -0.29 0.32 -10000 0 -0.6 100 100
FCGR2B -0.086 0.22 -10000 0 -0.5 48 48
PPP3CA 0.033 0.006 -10000 0 -10000 0 0
BCL10 0.033 0.005 -10000 0 -10000 0 0
IKK complex -0.029 0.055 0.12 2 -0.13 1 3
PTPRC 0.003 0.12 -10000 0 -0.5 12 12
PDPK1 -0.11 0.14 0.25 3 -0.26 75 78
PPP3CB 0.032 0.007 -10000 0 -10000 0 0
PPP3CC 0.023 0.039 -10000 0 -0.5 1 1
POU2F2 -0.003 0.032 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.52 0.33 -9999 0 -0.88 77 77
HDAC7 -0.001 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.41 0.28 -9999 0 -0.79 49 49
SMAD4 0.021 0.039 -9999 0 -0.5 1 1
ID2 -0.52 0.35 -9999 0 -0.89 76 76
AP1 -0.013 0.13 -9999 0 -0.34 28 28
ABCG2 -0.74 0.35 -9999 0 -0.93 140 140
HIF1A -0.086 0.065 -9999 0 -0.44 2 2
TFF3 -0.52 0.35 -9999 0 -0.9 76 76
GATA2 0.031 0.017 -9999 0 -10000 0 0
AKT1 -0.079 0.057 -9999 0 -10000 0 0
response to hypoxia -0.091 0.045 -9999 0 -10000 0 0
MCL1 -0.52 0.35 -9999 0 -0.89 76 76
NDRG1 -0.53 0.38 -9999 0 -0.93 80 80
SERPINE1 -0.54 0.35 -9999 0 -0.9 82 82
FECH -0.51 0.35 -9999 0 -0.9 73 73
FURIN -0.51 0.35 -9999 0 -0.89 75 75
NCOA2 0.03 0.012 -9999 0 -10000 0 0
EP300 -0.084 0.075 -9999 0 -0.25 17 17
HMOX1 -0.54 0.37 -9999 0 -0.95 76 76
BHLHE40 -0.52 0.33 -9999 0 -0.88 77 77
BHLHE41 -0.52 0.33 -9999 0 -0.88 77 77
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.1 0.091 -9999 0 -0.34 1 1
ENG -0.097 0.081 -9999 0 -10000 0 0
JUN 0.023 0.055 -9999 0 -0.32 5 5
RORA -0.52 0.35 -9999 0 -0.9 75 75
ABCB1 -0.57 0.6 -9999 0 -1.3 91 91
TFRC -0.52 0.35 -9999 0 -0.89 76 76
CXCR4 -0.52 0.35 -9999 0 -0.91 75 75
TF -0.52 0.34 -9999 0 -0.89 74 74
CITED2 -0.52 0.34 -9999 0 -0.89 76 76
HIF1A/ARNT -0.58 0.39 -9999 0 -1 73 73
LDHA -0.042 0.073 -9999 0 -0.89 1 1
ETS1 -0.52 0.34 -9999 0 -0.89 76 76
PGK1 -0.52 0.35 -9999 0 -0.9 76 76
NOS2 -0.52 0.33 -9999 0 -0.88 77 77
ITGB2 -0.52 0.35 -9999 0 -0.91 73 73
ALDOA -0.52 0.34 -9999 0 -0.9 71 71
Cbp/p300/CITED2 -0.52 0.35 -9999 0 -0.93 68 68
FOS -0.029 0.16 -9999 0 -0.49 24 24
HK2 -0.52 0.34 -9999 0 -0.9 73 73
SP1 -0.019 0.071 -9999 0 -10000 0 0
GCK -0.091 0.11 -9999 0 -10000 0 0
HK1 -0.52 0.34 -9999 0 -0.9 72 72
NPM1 -0.52 0.34 -9999 0 -0.9 73 73
EGLN1 -0.52 0.35 -9999 0 -0.89 74 74
CREB1 0.041 0 -9999 0 -10000 0 0
PGM1 -0.55 0.37 -9999 0 -0.91 84 84
SMAD3 0.032 0.01 -9999 0 -10000 0 0
EDN1 -0.15 0.29 -9999 0 -1.3 11 11
IGFBP1 -0.52 0.35 -9999 0 -0.91 75 75
VEGFA -0.38 0.25 -9999 0 -0.73 46 46
HIF1A/JAB1 -0.042 0.053 -9999 0 -0.32 2 2
CP -0.56 0.38 -9999 0 -0.96 80 80
CXCL12 -0.7 0.38 -9999 0 -0.95 129 129
COPS5 0.03 0.012 -9999 0 -10000 0 0
SMAD3/SMAD4 0.032 0.039 -9999 0 -0.36 1 1
BNIP3 -0.54 0.36 -9999 0 -0.92 77 77
EGLN3 -0.59 0.39 -9999 0 -0.93 104 104
CA9 -0.58 0.34 -9999 0 -0.9 88 88
TERT -0.51 0.35 -9999 0 -0.88 76 76
ENO1 -0.52 0.34 -9999 0 -0.89 76 76
PFKL -0.52 0.34 -9999 0 -0.89 76 76
NCOA1 0.029 0.051 -9999 0 -0.5 2 2
ADM -0.52 0.35 -9999 0 -0.91 72 72
ARNT -0.091 0.052 -9999 0 -10000 0 0
HNF4A 0.02 0.019 -9999 0 -10000 0 0
ADFP -0.52 0.33 -9999 0 -0.88 77 77
SLC2A1 -0.39 0.25 -9999 0 -0.73 50 50
LEP -0.52 0.34 -9999 0 -0.89 75 75
HIF1A/ARNT/Cbp/p300 -0.43 0.28 -9999 0 -0.81 50 50
EPO -0.27 0.21 -9999 0 -0.8 15 15
CREBBP -0.084 0.076 -9999 0 -0.26 16 16
HIF1A/ARNT/Cbp/p300/HDAC7 -0.42 0.28 -9999 0 -0.82 48 48
PFKFB3 -0.52 0.35 -9999 0 -0.89 78 78
NT5E -0.53 0.36 -9999 0 -0.92 74 74
IGF1 pathway

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.034 0 -10000 0 -10000 0 0
PTK2 0.027 0.013 -10000 0 -10000 0 0
CRKL -0.14 0.14 -10000 0 -0.26 121 121
GRB2/SOS1/SHC 0.064 0.017 -10000 0 -10000 0 0
HRAS 0.033 0.004 -10000 0 -10000 0 0
IRS1/Crk -0.14 0.15 -10000 0 -0.26 123 123
IGF-1R heterotetramer/IGF1/PTP1B -0.096 0.14 -10000 0 -0.3 69 69
AKT1 -0.12 0.12 0.28 1 -0.34 4 5
BAD -0.12 0.11 0.27 1 -0.32 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.14 0.14 -10000 0 -0.26 123 123
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.15 -10000 0 -0.27 123 123
RAF1 -0.11 0.14 -10000 0 -0.56 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.11 0.16 -10000 0 -0.26 106 106
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.16 -10000 0 -0.29 123 123
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.12 0.12 0.28 1 -0.34 4 5
GNB2L1 0.033 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.076 0.12 0.27 2 -0.43 3 5
PXN 0.033 0.003 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.14 -10000 0 -0.35 4 4
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.09 0.16 -10000 0 -0.27 4 4
IGF-1R heterotetramer -0.028 0.055 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.13 0.16 -10000 0 -0.27 123 123
Crk/p130 Cas/Paxillin -0.1 0.16 -10000 0 -0.35 5 5
IGF1R -0.028 0.056 -10000 0 -10000 0 0
IGF1 -0.28 0.27 -10000 0 -0.52 124 124
IRS2/Crk -0.09 0.13 -10000 0 -0.26 68 68
PI3K -0.11 0.16 -10000 0 -0.25 108 108
apoptosis 0.088 0.11 0.29 4 -0.21 1 5
HRAS/GDP 0.025 0.003 -10000 0 -10000 0 0
PRKCD -0.19 0.19 -10000 0 -0.36 118 118
RAF1/14-3-3 E -0.088 0.13 0.28 1 -0.46 5 6
BAD/14-3-3 -0.092 0.11 0.22 1 -0.3 4 5
PRKCZ -0.12 0.12 0.27 1 -0.34 4 5
Crk/p130 Cas/Paxillin/FAK1 -0.086 0.12 -10000 0 -10000 0 0
PTPN1 0.018 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.2 0.2 -10000 0 -0.37 123 123
BCAR1 0.033 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.16 -10000 0 -0.26 109 109
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.033 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.13 0.15 -10000 0 -0.26 123 123
GRB10 0.016 0.072 -10000 0 -0.32 9 9
PTPN11 -0.14 0.14 -10000 0 -0.27 123 123
IRS1 -0.16 0.15 -10000 0 -0.29 123 123
IRS2 -0.099 0.14 -10000 0 -0.27 86 86
IGF-1R heterotetramer/IGF1 -0.2 0.21 -10000 0 -0.38 123 123
GRB2 0.032 0.006 -10000 0 -10000 0 0
PDPK1 -0.12 0.13 0.28 1 -0.36 4 5
YWHAE 0.027 0.014 -10000 0 -10000 0 0
PRKD1 -0.2 0.19 -10000 0 -0.36 118 118
SHC1 0.033 0.006 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.1 0.1 0.21 80 -10000 0 80
RFC1 0.1 0.1 0.21 80 -10000 0 80
PRKDC 0.11 0.13 0.25 83 -10000 0 83
RIPK1 0.034 0.006 -10000 0 -10000 0 0
CASP7 -0.11 0.27 -10000 0 -0.7 35 35
FASLG/FAS/FADD/FAF1 -0.026 0.13 0.21 1 -0.31 28 29
MAP2K4 -0.075 0.16 0.29 1 -0.43 22 23
mol:ceramide -0.052 0.14 -10000 0 -0.37 26 26
GSN 0.077 0.12 0.21 73 -0.29 4 77
FASLG/FAS/FADD/FAF1/Caspase 8 -0.034 0.14 -10000 0 -0.39 19 19
FAS -0.021 0.15 -10000 0 -0.5 20 20
BID -0.022 0.035 0.19 1 -10000 0 1
MAP3K1 -0.046 0.18 -10000 0 -0.49 24 24
MAP3K7 0.031 0.006 -10000 0 -10000 0 0
RB1 0.12 0.15 0.28 83 -10000 0 83
CFLAR 0.035 0.002 -10000 0 -10000 0 0
HGF/MET -0.1 0.16 -10000 0 -0.35 38 38
ARHGDIB 0.1 0.11 0.22 78 -10000 0 78
FADD 0.03 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.061 0.14 0.29 4 -0.21 73 77
NFKB1 -0.034 0.13 -10000 0 -0.74 6 6
MAPK8 -0.088 0.15 0.28 1 -0.45 17 18
DFFA 0.097 0.1 0.21 77 -10000 0 77
DNA fragmentation during apoptosis 0.095 0.1 0.21 77 -10000 0 77
FAS/FADD/MET -0.077 0.14 -10000 0 -0.34 20 20
CFLAR/RIP1 0.051 0.009 -10000 0 -10000 0 0
FAIM3 0.03 0.035 -10000 0 -0.32 2 2
FAF1 0.028 0.008 -10000 0 -10000 0 0
PARP1 0.1 0.1 0.21 80 -10000 0 80
DFFB 0.095 0.1 0.21 77 -10000 0 77
CHUK -0.032 0.12 -10000 0 -0.69 6 6
FASLG -0.03 0.16 -10000 0 -0.49 24 24
FAS/FADD 0.003 0.12 -10000 0 -0.36 20 20
HGF 0.029 0.035 -10000 0 -0.32 2 2
LMNA 0.09 0.091 0.31 2 -10000 0 2
CASP6 0.1 0.1 0.21 80 -10000 0 80
CASP10 0.03 0.005 -10000 0 -10000 0 0
CASP3 0.096 0.13 0.26 81 -10000 0 81
PTPN13 -0.08 0.17 -10000 0 -0.34 66 66
CASP8 -0.022 0.015 -10000 0 -10000 0 0
IL6 -0.089 0.15 -10000 0 -0.94 2 2
MET -0.12 0.18 -10000 0 -0.33 90 90
ICAD/CAD 0.065 0.097 0.22 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.053 0.14 -10000 0 -0.37 26 26
activation of caspase activity by cytochrome c -0.022 0.034 0.19 1 -10000 0 1
PAK2 0.1 0.1 0.21 81 -10000 0 81
BCL2 -0.19 0.25 -10000 0 -0.5 87 87
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.033 0.006 -10000 0 -10000 0 0
CCL5 -0.09 0.22 -10000 0 -0.5 49 49
SDCBP 0.029 0.011 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.12 0.1 0.39 1 -0.31 33 34
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.091 0.095 -10000 0 -0.32 20 20
Syndecan-1/Syntenin -0.11 0.098 0.35 1 -0.3 27 28
MAPK3 -0.11 0.096 0.33 1 -0.31 15 16
HGF/MET -0.069 0.13 -10000 0 -0.22 92 92
TGFB1/TGF beta receptor Type II 0.032 0.006 -10000 0 -10000 0 0
BSG 0.033 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.09 0.094 -10000 0 -0.31 20 20
Syndecan-1/RANTES -0.17 0.15 0.35 1 -0.38 63 64
Syndecan-1/CD147 -0.12 0.1 0.35 1 -0.33 13 14
Syndecan-1/Syntenin/PIP2 -0.1 0.094 0.33 1 -0.29 27 28
LAMA5 0.009 0.059 -10000 0 -0.32 6 6
positive regulation of cell-cell adhesion -0.1 0.092 0.32 1 -0.29 27 28
MMP7 -0.32 0.064 -10000 0 -0.33 209 209
HGF 0.029 0.035 -10000 0 -0.32 2 2
Syndecan-1/CASK -0.12 0.093 -10000 0 -0.3 34 34
Syndecan-1/HGF/MET -0.17 0.12 0.3 1 -0.37 29 30
regulation of cell adhesion -0.1 0.098 0.28 2 -0.31 11 13
HPSE -0.052 0.2 -10000 0 -0.5 34 34
positive regulation of cell migration -0.12 0.1 0.39 1 -0.31 33 34
SDC1 -0.12 0.1 0.39 1 -0.31 33 34
Syndecan-1/Collagen -0.12 0.1 0.39 1 -0.31 33 34
PPIB 0.025 0.049 -10000 0 -0.32 4 4
MET -0.12 0.18 -10000 0 -0.33 90 90
PRKACA 0.033 0.005 -10000 0 -10000 0 0
MMP9 0.008 0.064 -10000 0 -0.36 6 6
MAPK1 -0.11 0.096 0.33 1 -0.31 14 15
homophilic cell adhesion -0.12 0.1 0.39 1 -0.31 33 34
MMP1 -0.29 0.11 -10000 0 -0.33 192 192
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.032 0.008 -10000 0 -10000 0 0
GNAT1/GTP 0.025 0.003 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin -0.21 0.16 -10000 0 -0.31 152 152
PDE6G/GNAT1/GTP 0.043 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.033 0.004 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.18 0.2 -10000 0 -0.46 43 43
mol:Na + -0.086 0.15 -10000 0 -0.39 5 5
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.062 0.17 -10000 0 -0.3 69 69
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.081 0.16 -10000 0 -0.4 5 5
CNGB1 0.033 0.005 -10000 0 -10000 0 0
RDH5 -0.11 0.24 -10000 0 -0.5 57 57
SAG -0.35 0.24 -10000 0 -0.5 153 153
mol:Ca2+ -0.09 0.15 0.42 4 -0.38 5 9
Na + (4 Units) -0.084 0.14 -10000 0 -0.37 5 5
RGS9 -0.14 0.25 -10000 0 -0.5 67 67
GNB1/GNGT1 -0.069 0.13 -10000 0 -0.22 91 91
GNAT1/GDP -0.041 0.15 -10000 0 -0.27 64 64
GUCY2D 0.027 0.013 -10000 0 -10000 0 0
GNGT1 -0.12 0.18 -10000 0 -0.32 91 91
GUCY2F 0.026 0.057 -10000 0 -0.44 3 3
GNB5 0.026 0.043 -10000 0 -0.32 3 3
mol:GMP (4 units) -0.081 0.14 -10000 0 -0.26 83 83
mol:11-cis-retinal -0.11 0.24 -10000 0 -0.5 57 57
mol:cGMP 0.048 0.065 -10000 0 -0.27 4 4
GNB1 0.032 0.008 -10000 0 -10000 0 0
Rhodopsin -0.059 0.18 -10000 0 -0.36 56 56
SLC24A1 0.032 0.008 -10000 0 -10000 0 0
CNGA1 -0.21 0.26 -10000 0 -0.5 98 98
Metarhodopsin II 0.021 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.058 0.06 -10000 0 -0.28 2 2
RGS9BP 0.024 0.054 -10000 0 -0.32 5 5
Metarhodopsin II/Transducin -0.017 0.055 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.054 0.049 -10000 0 -0.28 2 2
PDE6A/B -0.11 0.2 -10000 0 -0.36 84 84
mol:Pi -0.062 0.17 -10000 0 -0.3 69 69
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.038 0.11 -10000 0 -10000 0 0
PDE6B 0.032 0.006 -10000 0 -10000 0 0
PDE6A -0.18 0.26 -10000 0 -0.5 84 84
PDE6G 0.033 0.006 -10000 0 -10000 0 0
RHO 0.033 0.004 -10000 0 -10000 0 0
PDE6 -0.14 0.21 -10000 0 -0.49 34 34
GUCA1A 0.031 0.025 -10000 0 -0.32 1 1
GC2/GCAP Family 0.067 0.066 -10000 0 -0.28 4 4
GUCA1C 0.025 0.062 -10000 0 -0.41 4 4
GUCA1B 0.029 0.035 -10000 0 -0.32 2 2
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.015 0.025 -10000 0 -0.31 1 1
ARNO/beta Arrestin1-2 -0.071 0.14 -10000 0 -0.24 81 81
EGFR 0.02 0.072 -10000 0 -0.5 4 4
EPHA2 0.015 0.075 -10000 0 -0.32 10 10
USP6 0.027 0.013 -10000 0 -10000 0 0
IQSEC1 0.033 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.052 0.16 -10000 0 -0.3 57 57
ARRB2 0.013 0.037 -10000 0 -0.48 1 1
mol:GTP 0.007 0.02 0.12 4 -10000 0 4
ARRB1 0.026 0.063 -10000 0 -0.5 3 3
FBXO8 0.032 0.006 -10000 0 -10000 0 0
TSHR 0.03 0.01 -10000 0 -10000 0 0
EGF -0.091 0.21 -10000 0 -0.43 58 58
somatostatin receptor activity 0 0 0.001 2 -0.001 52 54
ARAP2 0 0 0 2 0 51 53
mol:GDP -0.098 0.12 0.19 1 -0.27 52 53
mol:PI-3-4-5-P3 0 0 0.001 2 -0.001 52 54
ITGA2B 0.032 0.006 -10000 0 -10000 0 0
ARF6 0.031 0.009 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.059 -10000 0 -10000 0 0
ADAP1 0 0 0 1 0 23 24
KIF13B 0.023 0.039 -10000 0 -0.5 1 1
HGF/MET -0.069 0.13 -10000 0 -0.22 92 92
PXN 0.033 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.084 0.12 0.25 1 -0.24 52 53
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.029 0.14 -10000 0 -0.31 32 32
ADRB2 -0.16 0.26 -10000 0 -0.5 78 78
receptor agonist activity 0 0 0 1 0 45 46
actin filament binding 0 0 0 2 0 57 59
SRC 0.019 0.017 -10000 0 -10000 0 0
ITGB3 0.032 0.007 -10000 0 -10000 0 0
GNAQ 0 0 0.001 3 -0.001 31 34
EFA6/PI-4-5-P2 0 0 0.002 2 -0.001 32 34
ARF6/GDP -0.05 0.11 -10000 0 -0.36 19 19
ARF6/GDP/GULP/ACAP1 -0.1 0.15 -10000 0 -0.33 48 48
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.021 -10000 0 -10000 0 0
ACAP1 0 0 0 1 -10000 0 1
ACAP2 0 0 0 2 0 45 47
LHCGR/beta Arrestin2 0.014 0.047 -10000 0 -0.43 1 1
EFNA1 0.033 0.006 -10000 0 -10000 0 0
HGF 0.029 0.035 -10000 0 -0.32 2 2
CYTH3 0 0 0.001 2 -0.001 46 48
CYTH2 -0.002 0.002 -10000 0 -0.004 57 57
NCK1 0.033 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0 6 0 28 34
endosomal lumen acidification 0 0 0 8 0 23 31
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.022 0.16 -10000 0 -0.49 23 23
GNAQ/ARNO -0.002 0.003 0.01 2 -0.006 30 32
mol:Phosphatidic acid 0 0 0 2 0 45 47
PIP3-E 0 0 -10000 0 0 42 42
MET -0.12 0.18 -10000 0 -0.33 90 90
GNA14 0.011 0.11 -10000 0 -0.5 9 9
GNA15 0.021 0.064 -10000 0 -0.32 7 7
GIT1 0.032 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 2 -0.001 39 41
GNA11 0.018 0.088 -10000 0 -0.5 6 6
LHCGR 0.027 0.05 -10000 0 -0.38 3 3
AGTR1 -0.19 0.26 -10000 0 -0.5 89 89
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.047 -10000 0 -0.43 1 1
IPCEF1/ARNO -0.03 0.1 -10000 0 -0.2 57 57
alphaIIb/beta3 Integrin 0.048 0.01 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.036 0.085 -10000 0 -0.31 8 8
fibroblast growth factor receptor signaling pathway 0.035 0.084 -10000 0 -0.31 8 8
LAMA1 0.026 0.014 -10000 0 -10000 0 0
PRNP 0.026 0.014 -10000 0 -10000 0 0
GPC1/SLIT2 -0.19 0.2 -10000 0 -0.36 125 125
SMAD2 0.01 0.037 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.029 0.04 -10000 0 -0.18 6 6
GPC1/Laminin alpha1 0.027 0.054 -10000 0 -0.22 8 8
TDGF1 -0.21 0.17 -10000 0 -0.33 145 145
CRIPTO/GPC1 -0.14 0.13 -10000 0 -0.23 148 148
APP/GPC1 0.035 0.053 -10000 0 -0.22 8 8
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.12 0.1 -10000 0 -0.34 7 7
FLT1 0.006 0.078 -10000 0 -0.32 11 11
GPC1/TGFB/TGFBR1/TGFBR2 0.055 0.05 -10000 0 -10000 0 0
SERPINC1 0.031 0.025 -10000 0 -0.32 1 1
FYN -0.12 0.1 -10000 0 -0.33 8 8
FGR -0.12 0.1 -10000 0 -0.34 7 7
positive regulation of MAPKKK cascade -0.04 0.13 0.29 2 -0.35 9 11
SLIT2 -0.26 0.27 -10000 0 -0.5 119 119
GPC1/NRG 0.028 0.053 -10000 0 -0.22 8 8
NRG1 0.026 0.014 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.018 0.085 -10000 0 -0.35 2 2
LYN -0.11 0.11 -10000 0 -0.34 7 7
mol:Spermine 0.001 0.044 -10000 0 -0.22 8 8
cell growth 0.035 0.084 -10000 0 -0.31 8 8
BMP signaling pathway -0.02 0.068 0.32 8 -10000 0 8
SRC -0.059 0.097 -10000 0 -0.33 4 4
TGFBR1 0.033 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.058 0.19 -10000 0 -0.44 41 41
GPC1 0.02 0.068 -10000 0 -0.32 8 8
TGFBR1 (dimer) 0.033 0.005 -10000 0 -10000 0 0
VEGFA 0.004 0.096 -10000 0 -0.32 17 17
BLK -0.19 0.16 -10000 0 -0.39 59 59
HCK -0.069 0.11 -10000 0 -0.38 10 10
FGF2 0.011 0.1 -10000 0 -0.48 9 9
FGFR1 0.03 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer 0.006 0.078 -10000 0 -0.32 11 11
TGFBR2 0.033 0.003 -10000 0 -10000 0 0
cell death 0.035 0.053 -10000 0 -0.22 8 8
ATIII/GPC1 0.036 0.055 -10000 0 -0.22 9 9
PLA2G2A/GPC1 -0.034 0.15 -10000 0 -0.32 46 46
LCK -0.13 0.11 -10000 0 -0.2 139 139
neuron differentiation 0.028 0.053 -10000 0 -0.22 8 8
PrPc/Cu2+ 0.02 0.01 -10000 0 -10000 0 0
APP 0.031 0.009 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.033 0.003 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.066 0.22 -10000 0 -0.78 17 17
oxygen homeostasis -0.013 0.009 -10000 0 -10000 0 0
TCEB2 0.033 0.006 -10000 0 -10000 0 0
TCEB1 0.027 0.027 -10000 0 -0.32 1 1
VHL/Elongin B/Elongin C/HIF2A -0.13 0.13 -10000 0 -0.39 16 16
EPO -0.25 0.18 -10000 0 -0.57 18 18
FIH (dimer) 0.003 0.026 -10000 0 -10000 0 0
APEX1 0.001 0.029 -10000 0 -10000 0 0
SERPINE1 -0.31 0.23 -10000 0 -0.67 38 38
FLT1 -0.025 0.13 -10000 0 -0.73 5 5
ADORA2A -0.28 0.19 -10000 0 -0.61 27 27
germ cell development -0.29 0.19 -10000 0 -0.61 28 28
SLC11A2 -0.31 0.21 -10000 0 -0.64 37 37
BHLHE40 -0.3 0.2 -10000 0 -0.56 49 49
HIF1AN 0.003 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.2 0.15 -10000 0 -0.42 34 34
ETS1 0.042 0.019 -10000 0 -10000 0 0
CITED2 -0.022 0.14 -10000 0 -0.79 6 6
KDR -0.016 0.15 -10000 0 -0.81 6 6
PGK1 -0.3 0.21 -10000 0 -0.65 31 31
SIRT1 0.032 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.33 0.24 -10000 0 -0.66 47 47
EPAS1 -0.16 0.14 -10000 0 -0.33 70 70
SP1 0.036 0.017 -10000 0 -10000 0 0
ABCG2 -0.56 0.25 -10000 0 -0.7 139 139
EFNA1 -0.3 0.2 -10000 0 -0.63 28 28
FXN -0.29 0.19 -10000 0 -0.61 29 29
POU5F1 -0.3 0.2 -10000 0 -0.63 28 28
neuron apoptosis 0.32 0.23 0.64 47 -10000 0 47
EP300 0.031 0.008 -10000 0 -10000 0 0
EGLN3 -0.15 0.24 -10000 0 -0.51 65 65
EGLN2 0.007 0.025 -10000 0 -10000 0 0
EGLN1 0.003 0.026 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.054 0.035 -10000 0 -10000 0 0
VHL 0.031 0.025 -10000 0 -0.32 1 1
ARNT 0.002 0.029 -10000 0 -10000 0 0
SLC2A1 -0.3 0.21 -10000 0 -0.63 38 38
TWIST1 -0.3 0.21 -10000 0 -0.64 37 37
ELK1 0.035 0.042 -10000 0 -0.32 3 3
HIF2A/ARNT/Cbp/p300 -0.2 0.15 -10000 0 -0.42 34 34
VEGFA -0.3 0.21 -10000 0 -0.62 36 36
CREBBP 0.032 0.006 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.045 0.1 -9999 0 -0.34 8 8
FZD6 0.018 0.065 -9999 0 -0.36 6 6
WNT6 0.032 0.024 -9999 0 -0.32 1 1
WNT4 0.013 0.094 -9999 0 -0.46 8 8
FZD3 -0.051 0.15 -9999 0 -0.34 45 45
WNT5A -0.022 0.13 -9999 0 -0.33 33 33
WNT11 -0.04 0.14 -9999 0 -0.32 44 44
FOXM1 transcription factor network

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
NFATC3 -0.32 0.37 -9999 0 -1.1 18 18
PLK1 0.002 0.12 -9999 0 -1 3 3
BIRC5 -0.037 0.19 -9999 0 -1 6 6
HSPA1B -0.33 0.37 -9999 0 -1 25 25
MAP2K1 -0.009 0.041 -9999 0 -10000 0 0
BRCA2 -0.31 0.4 -9999 0 -1.1 20 20
FOXM1 -0.38 0.45 -9999 0 -1.3 24 24
XRCC1 -0.32 0.37 -9999 0 -1.1 19 19
FOXM1B/p19 -0.4 0.41 -9999 0 -1.1 34 34
Cyclin D1/CDK4 -0.33 0.36 -9999 0 -0.96 27 27
CDC2 -0.34 0.39 -9999 0 -1.1 25 25
TGFA -0.33 0.37 -9999 0 -0.98 27 27
SKP2 -0.33 0.38 -9999 0 -1.1 19 19
CCNE1 0.005 0.09 -9999 0 -0.34 14 14
CKS1B -0.33 0.37 -9999 0 -1 25 25
RB1 -0.13 0.19 -9999 0 -0.92 3 3
FOXM1C/SP1 -0.39 0.44 -9999 0 -1.2 30 30
AURKB -0.19 0.43 -9999 0 -1.1 38 38
CENPF -0.32 0.38 -9999 0 -1.1 23 23
CDK4 -0.012 0.095 -9999 0 -0.34 16 16
MYC -0.35 0.36 -9999 0 -0.95 32 32
CHEK2 -0.01 0.041 -9999 0 -10000 0 0
ONECUT1 -0.34 0.38 -9999 0 -0.99 30 30
CDKN2A -0.079 0.16 -9999 0 -0.33 66 66
LAMA4 -0.32 0.37 -9999 0 -1 22 22
FOXM1B/HNF6 -0.37 0.43 -9999 0 -1.2 29 29
FOS -0.41 0.49 -9999 0 -1.3 41 41
SP1 0.028 0.015 -9999 0 -10000 0 0
CDC25B -0.34 0.39 -9999 0 -1.1 22 22
response to radiation -0.016 0.021 -9999 0 -10000 0 0
CENPB -0.3 0.37 -9999 0 -1 21 21
CENPA -0.34 0.39 -9999 0 -1.1 26 26
NEK2 -0.36 0.4 -9999 0 -1.1 24 24
HIST1H2BA -0.32 0.37 -9999 0 -1 22 22
CCNA2 -0.025 0.13 -9999 0 -0.34 32 32
EP300 0.031 0.008 -9999 0 -10000 0 0
CCNB1/CDK1 -0.37 0.43 -9999 0 -1.2 23 23
CCNB2 -0.32 0.37 -9999 0 -1.1 20 20
CCNB1 -0.35 0.4 -9999 0 -1.1 23 23
ETV5 -0.34 0.38 -9999 0 -1.1 21 21
ESR1 -0.33 0.4 -9999 0 -1.2 21 21
CCND1 -0.33 0.36 -9999 0 -0.98 26 26
GSK3A -0.005 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.038 0.14 -9999 0 -0.4 13 13
CDK2 -0.01 0.11 -9999 0 -0.33 23 23
G2/M transition of mitotic cell cycle -0.02 0.025 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.33 0.41 -9999 0 -1.1 25 25
GAS1 -0.52 0.57 -9999 0 -1.3 64 64
MMP2 -0.32 0.37 -9999 0 -1.1 19 19
RB1/FOXM1C -0.32 0.37 -9999 0 -1 25 25
CREBBP 0.032 0.006 -9999 0 -10000 0 0
EGFR-dependent Endothelin signaling events

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.033 0.004 -9999 0 -10000 0 0
EGFR 0.021 0.072 -9999 0 -0.5 4 4
EGF/EGFR -0.07 0.15 -9999 0 -0.3 44 44
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.001 0.14 -9999 0 -0.27 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.048 0.15 -9999 0 -0.33 49 49
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.091 0.21 -9999 0 -0.43 58 58
EGF/EGFR dimer/SHC -0.028 0.14 -9999 0 -0.31 33 33
mol:GDP -0.006 0.14 -9999 0 -0.26 31 31
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.002 0.12 -9999 0 -0.48 13 13
GRB2/SOS1 0.048 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.017 0.12 -9999 0 -10000 0 0
SHC1 0.033 0.006 -9999 0 -10000 0 0
HRAS/GDP -0.004 0.13 -9999 0 -10000 0 0
FRAP1 -0.061 0.093 -9999 0 -0.25 32 32
EGF/EGFR dimer -0.052 0.16 -9999 0 -0.3 57 57
SOS1 0.033 0.002 -9999 0 -10000 0 0
GRB2 0.032 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.037 0.14 -9999 0 -0.25 61 61
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.043 0.029 -10000 0 -0.22 2 2
VLDLR -0.078 0.22 -10000 0 -0.5 45 45
CRKL 0.031 0.009 -10000 0 -10000 0 0
LRPAP1 0.032 0.006 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.5 1 1
ITGA3 0.03 0.025 -10000 0 -0.32 1 1
RELN/VLDLR/Fyn -0.015 0.15 -10000 0 -0.32 40 40
MAPK8IP1/MKK7/MAP3K11/JNK1 0.089 0.038 -10000 0 -10000 0 0
AKT1 -0.026 0.096 -10000 0 -0.36 1 1
MAP2K7 0.033 0.004 -10000 0 -10000 0 0
RAPGEF1 0.033 0.005 -10000 0 -10000 0 0
DAB1 0.033 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.13 0.078 -10000 0 -0.19 2 2
LRPAP1/LRP8 -0.19 0.087 -10000 0 -0.22 190 190
RELN/LRP8/DAB1/Fyn -0.12 0.08 -10000 0 -0.41 1 1
DAB1/alpha3/beta1 Integrin -0.16 0.12 -10000 0 -0.38 36 36
long-term memory -0.14 0.099 -10000 0 -0.3 26 26
DAB1/LIS1 -0.16 0.13 -10000 0 -0.39 36 36
DAB1/CRLK/C3G -0.16 0.12 -10000 0 -0.38 35 35
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
DAB1/NCK2 -0.17 0.13 -10000 0 -0.39 36 36
ARHGEF2 0.031 0.025 -10000 0 -0.32 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.033 0.006 -10000 0 -10000 0 0
CDK5R1 0.032 0.007 -10000 0 -10000 0 0
RELN 0.032 0.008 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.15 0.088 -10000 0 -0.31 3 3
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.086 -10000 0 -0.41 1 1
MAPK8 0.032 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.009 0.13 -10000 0 -0.28 40 40
ITGB1 0.032 0.025 -10000 0 -0.32 1 1
MAP1B -0.17 0.14 -10000 0 -0.4 51 51
RELN/LRP8 -0.15 0.085 -10000 0 -0.22 2 2
GRIN2B/RELN/LRP8/DAB1/Fyn -0.14 0.1 -10000 0 -0.31 26 26
PI3K 0.048 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.045 0.028 -10000 0 -0.22 2 2
RAP1A -0.15 0.11 -10000 0 -0.37 33 33
PAFAH1B1 0.027 0.013 -10000 0 -10000 0 0
MAPK8IP1 0.032 0.025 -10000 0 -0.32 1 1
CRLK/C3G 0.046 0.014 -10000 0 -10000 0 0
GRIN2B -0.016 0.12 -10000 0 -0.32 29 29
NCK2 0.034 0 -10000 0 -10000 0 0
neuron differentiation -0.035 0.059 -10000 0 -0.31 4 4
neuron adhesion -0.14 0.12 0.36 1 -0.36 32 33
LRP8 -0.28 0.12 -10000 0 -0.33 190 190
GSK3B -0.027 0.094 -10000 0 -0.34 1 1
RELN/VLDLR/DAB1/Fyn 0.002 0.14 -10000 0 -0.27 40 40
MAP3K11 0.033 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.021 0.11 -10000 0 -0.24 39 39
CDK5 0.029 0.035 -10000 0 -0.32 2 2
MAPT 0.023 0.13 0.79 6 -10000 0 6
neuron migration -0.12 0.12 0.25 1 -0.35 35 36
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.035 0.06 -10000 0 -0.31 4 4
RELN/VLDLR -0.19 0.14 -10000 0 -0.39 47 47
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.05 0.032 -9999 0 -10000 0 0
RGS9BP 0.024 0.054 -9999 0 -0.32 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.069 0.16 -9999 0 -0.3 65 65
mol:ADP 0.009 0.016 -9999 0 -0.22 1 1
GNAT2 0.028 0.042 -9999 0 -0.32 3 3
RGS9-1/Gbeta5/R9AP -0.062 0.17 -9999 0 -0.3 69 69
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.038 0.037 -9999 0 -0.22 4 4
GRK7 0.031 0.025 -9999 0 -0.32 1 1
CNGB3 0.022 0.049 -9999 0 -0.32 4 4
Cone Metarhodopsin II/X-Arrestin 0.025 0.002 -9999 0 -10000 0 0
mol:Ca2+ -0.05 0.16 -9999 0 -0.28 59 59
Cone PDE6 -0.033 0.16 -9999 0 -0.27 64 64
Cone Metarhodopsin II 0.02 0.013 -9999 0 -0.16 1 1
Na + (4 Units) -0.05 0.15 -9999 0 -0.28 59 59
GNAT2/GDP -0.044 0.16 -9999 0 -0.27 64 64
GNB5 0.026 0.043 -9999 0 -0.32 3 3
mol:GMP (4 units) 0.018 0.04 -9999 0 -0.28 1 1
Cone Transducin 0.054 0.034 -9999 0 -10000 0 0
SLC24A2 0.033 0.006 -9999 0 -10000 0 0
GNB3/GNGT2 0.045 0.018 -9999 0 -10000 0 0
GNB3 0.032 0.006 -9999 0 -10000 0 0
GNAT2/GTP 0.021 0.029 -9999 0 -0.22 3 3
CNGA3 -0.14 0.25 -9999 0 -0.5 69 69
ARR3 0.033 0.002 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.07 0.16 -9999 0 -0.3 65 65
mol:Pi -0.062 0.17 -9999 0 -0.3 69 69
Cone CNG Channel -0.039 0.15 -9999 0 -0.49 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.032 0.006 -9999 0 -10000 0 0
RGS9 -0.14 0.25 -9999 0 -0.5 67 67
PDE6C 0.03 0.025 -9999 0 -0.32 1 1
GNGT2 0.03 0.037 -9999 0 -0.5 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.03 0.037 -9999 0 -0.5 1 1
IL4-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
BCL2L1 -0.22 0.46 -10000 0 -1.1 25 25
STAT6 (cleaved dimer) -0.33 0.46 -10000 0 -1.1 40 40
IGHG1 -0.079 0.18 -10000 0 -10000 0 0
IGHG3 -0.28 0.43 -10000 0 -1.1 33 33
AKT1 -0.13 0.26 -10000 0 -0.7 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.23 -10000 0 -0.79 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.13 0.25 -10000 0 -0.74 9 9
THY1 -0.3 0.45 -10000 0 -1.1 29 29
MYB 0.027 0.052 -10000 0 -0.5 2 2
HMGA1 0.033 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.22 0.33 -10000 0 -0.76 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.25 -10000 0 -0.66 14 14
SP1 0.024 0.034 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.045 0.028 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.31 0.47 -10000 0 -1.1 38 38
SOCS1 -0.2 0.32 -10000 0 -0.73 29 29
SOCS3 -0.18 0.28 -10000 0 -0.78 14 14
FCER2 -0.25 0.41 -10000 0 -1.1 24 24
PARP14 0.031 0.035 -10000 0 -0.32 2 2
CCL17 -0.3 0.44 -10000 0 -1.1 29 29
GRB2 0.032 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.1 0.2 -10000 0 -0.65 4 4
T cell proliferation -0.28 0.45 -10000 0 -1.1 34 34
IL4R/JAK1 -0.29 0.45 -10000 0 -1.1 32 32
EGR2 -0.32 0.5 -10000 0 -1.3 31 31
JAK2 -0.01 0.065 -10000 0 -0.36 3 3
JAK3 0.02 0.033 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
JAK1 0.011 0.03 -10000 0 -10000 0 0
COL1A2 -0.095 0.18 -10000 0 -10000 0 0
CCL26 -0.31 0.44 -10000 0 -1.2 28 28
IL4R -0.31 0.47 -10000 0 -1.2 29 29
PTPN6 0.038 0.017 -10000 0 -10000 0 0
IL13RA2 -0.33 0.45 -10000 0 -1.2 30 30
IL13RA1 -0.005 0.051 -10000 0 -10000 0 0
IRF4 -0.34 0.62 -10000 0 -1.4 51 51
ARG1 -0.013 0.15 -10000 0 -10000 0 0
CBL -0.21 0.31 -10000 0 -0.75 32 32
GTF3A -0.1 0.15 -10000 0 -0.37 53 53
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.004 0.079 -10000 0 -0.31 2 2
IRF4/BCL6 -0.31 0.58 -10000 0 -1.3 51 51
CD40LG 0 0.081 -10000 0 -0.5 2 2
MAPK14 -0.2 0.31 -10000 0 -0.78 27 27
mitosis -0.13 0.25 -10000 0 -0.66 13 13
STAT6 -0.32 0.5 -10000 0 -1.3 32 32
SPI1 0.038 0.015 -10000 0 -10000 0 0
RPS6KB1 -0.12 0.24 -10000 0 -0.66 11 11
STAT6 (dimer) -0.32 0.5 -10000 0 -1.3 32 32
STAT6 (dimer)/PARP14 -0.3 0.47 -10000 0 -1.2 33 33
mast cell activation 0.007 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.27 -10000 0 -0.72 19 19
FRAP1 -0.13 0.26 -10000 0 -0.71 13 13
LTA -0.29 0.44 -10000 0 -1.2 25 25
FES 0.027 0.044 -10000 0 -0.41 2 2
T-helper 1 cell differentiation 0.32 0.49 1.2 32 -10000 0 32
CCL11 -0.39 0.6 -10000 0 -1.4 45 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.26 -10000 0 -0.68 18 18
IL2RG 0.013 0.07 -10000 0 -0.51 3 3
IL10 -0.29 0.44 -10000 0 -1.1 29 29
IRS1 0.027 0.048 -10000 0 -0.32 4 4
IRS2 0.025 0.015 -10000 0 -10000 0 0
IL4 -0.045 0.12 -10000 0 -10000 0 0
IL5 -0.3 0.44 -10000 0 -1.2 27 27
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.36 -10000 0 -0.86 28 28
COL1A1 -0.21 0.22 -10000 0 -1 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.29 0.45 -10000 0 -1.2 29 29
IL2R gamma/JAK3 0.025 0.067 -10000 0 -0.38 3 3
TFF3 -0.3 0.46 -10000 0 -1.2 30 30
ALOX15 -0.29 0.45 -10000 0 -1.1 30 30
MYBL1 0.024 0.043 -10000 0 -0.32 3 3
T-helper 2 cell differentiation -0.23 0.37 -10000 0 -0.86 36 36
SHC1 0.033 0.006 -10000 0 -10000 0 0
CEBPB 0.015 0.045 -10000 0 -0.32 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.11 0.24 -10000 0 -0.67 11 11
mol:PI-3-4-5-P3 -0.13 0.26 -10000 0 -0.71 13 13
PI3K -0.14 0.28 -10000 0 -0.74 14 14
DOK2 0.023 0.039 -10000 0 -0.5 1 1
ETS1 0.039 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.096 0.19 -10000 0 -0.65 4 4
ITGB3 -0.29 0.44 -10000 0 -1.1 28 28
PIGR -0.33 0.52 -10000 0 -1.3 37 37
IGHE 0.066 0.074 0.19 18 -10000 0 18
MAPKKK cascade -0.095 0.18 -10000 0 -0.63 4 4
BCL6 0.028 0.044 -10000 0 -0.42 2 2
OPRM1 -0.29 0.44 -10000 0 -1.1 30 30
RETNLB -0.49 0.68 -10000 0 -1.5 63 63
SELP -0.38 0.6 -10000 0 -1.5 41 41
AICDA -0.34 0.51 -10000 0 -1.2 39 39
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.016 0.12 -9999 0 -0.3 1 1
SMAD6-7/SMURF1 0.039 0.052 -9999 0 -0.31 1 1
NOG 0.032 0.007 -9999 0 -10000 0 0
SMAD9 -0.069 0.2 -9999 0 -0.5 35 35
SMAD4 0.02 0.039 -9999 0 -0.5 1 1
SMAD5 -0.094 0.15 -9999 0 -0.4 28 28
BMP7/USAG1 -0.15 0.19 -9999 0 -0.36 85 85
SMAD5/SKI -0.084 0.15 -9999 0 -0.4 23 23
SMAD1 -0.008 0.095 -9999 0 -0.47 5 5
BMP2 -0.038 0.17 -9999 0 -0.5 26 26
SMAD1/SMAD1/SMAD4 0.007 0.092 -9999 0 -0.44 4 4
BMPR1A 0.032 0.008 -9999 0 -10000 0 0
BMPR1B 0.028 0.042 -9999 0 -0.32 3 3
BMPR1A-1B/BAMBI 0.028 0.087 -9999 0 -10000 0 0
AHSG 0.033 0.004 -9999 0 -10000 0 0
CER1 0.031 0.025 -9999 0 -0.32 1 1
BMP2-4/CER1 -0.069 0.16 -9999 0 -0.38 32 32
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.025 0.11 -9999 0 -0.35 8 8
BMP2-4 (homodimer) -0.092 0.18 -9999 0 -0.31 76 76
RGMB 0.024 0.054 -9999 0 -0.32 5 5
BMP6/BMPR2/BMPR1A-1B -0.061 0.18 -9999 0 -0.28 81 81
RGMA 0.024 0.063 -9999 0 -0.5 3 3
SMURF1 0.032 0.007 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.036 0.11 -9999 0 -0.34 8 8
BMP2-4/USAG1 -0.18 0.22 -9999 0 -0.4 93 93
SMAD6/SMURF1/SMAD5 -0.085 0.15 -9999 0 -0.42 20 20
SOSTDC1 -0.17 0.26 -9999 0 -0.5 80 80
BMP7/BMPR2/BMPR1A-1B -0.028 0.096 -9999 0 -0.32 1 1
SKI 0.032 0.008 -9999 0 -10000 0 0
BMP6 (homodimer) -0.17 0.26 -9999 0 -0.5 82 82
HFE2 0.032 0.006 -9999 0 -10000 0 0
ZFYVE16 0.033 0.005 -9999 0 -10000 0 0
MAP3K7 0.033 0.006 -9999 0 -10000 0 0
BMP2-4/CHRD -0.067 0.16 -9999 0 -0.38 31 31
SMAD5/SMAD5/SMAD4 -0.08 0.15 -9999 0 -0.42 19 19
MAPK1 0.031 0.008 -9999 0 -10000 0 0
TAK1/TAB family -0.022 0.1 -9999 0 -0.32 6 6
BMP7 (homodimer) -0.08 0.15 -9999 0 -0.32 59 59
NUP214 0.033 0.005 -9999 0 -10000 0 0
BMP6/FETUA -0.11 0.2 -9999 0 -0.36 80 80
SMAD1/SKI -0.002 0.1 -9999 0 -0.48 5 5
SMAD6 0.021 0.059 -9999 0 -0.32 6 6
CTDSP2 0.028 0.051 -9999 0 -0.5 2 2
BMP2-4/FETUA -0.067 0.16 -9999 0 -0.38 31 31
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.006 0.095 -9999 0 -0.34 15 15
BMPR2 (homodimer) 0.033 0.002 -9999 0 -10000 0 0
GADD34/PP1CA 0.063 0.023 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) 0.042 0.034 -9999 0 -0.22 3 3
CHRDL1 0.029 0.044 -9999 0 -0.41 2 2
ENDOFIN/SMAD1 -0.001 0.1 -9999 0 -0.48 5 5
SMAD6-7/SMURF1/SMAD1 0.017 0.11 -9999 0 -0.49 4 4
SMAD6/SMURF1 0.032 0.007 -9999 0 -10000 0 0
BAMBI -0.013 0.12 -9999 0 -0.32 28 28
SMURF2 0.01 0.085 -9999 0 -0.32 13 13
BMP2-4/CHRDL1 -0.071 0.17 -9999 0 -0.38 33 33
BMP2-4/GREM1 -0.083 0.17 -9999 0 -0.4 35 35
SMAD7 0.021 0.039 -9999 0 -0.5 1 1
SMAD8A/SMAD8A/SMAD4 -0.069 0.2 -9999 0 -0.46 39 39
SMAD1/SMAD6 -0.002 0.1 -9999 0 -0.48 5 5
TAK1/SMAD6 0.046 0.013 -9999 0 -10000 0 0
BMP7 -0.08 0.15 -9999 0 -0.32 59 59
BMP6 -0.17 0.26 -9999 0 -0.5 82 82
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.042 0.12 -9999 0 -0.37 16 16
PPM1A 0.031 0.01 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.01 0.11 -9999 0 -0.51 5 5
SMAD7/SMURF1 0.032 0.036 -9999 0 -0.36 1 1
CTDSPL 0.028 0.051 -9999 0 -0.5 2 2
PPP1CA 0.031 0.025 -9999 0 -0.32 1 1
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.033 0.002 -9999 0 -10000 0 0
PPP1R15A 0.033 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.028 0.11 -9999 0 -0.34 8 8
CHRD 0.033 0.004 -9999 0 -10000 0 0
BMPR2 0.033 0.002 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.032 0.11 -9999 0 -0.37 7 7
BMP4 -0.091 0.17 -9999 0 -0.33 72 72
FST 0.033 0.004 -9999 0 -10000 0 0
BMP2-4/NOG -0.067 0.16 -9999 0 -0.37 32 32
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.013 0.12 -9999 0 -0.3 1 1
Endothelins

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
AKT1 -0.014 0.14 -10000 0 -0.37 5 5
PTK2B 0.026 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.17 -10000 0 -0.79 4 4
EDN1 0.037 0.14 -10000 0 -0.48 13 13
EDN3 -0.16 0.24 -10000 0 -0.5 71 71
EDN2 -0.38 0.22 -10000 0 -0.5 166 166
HRAS/GDP 0.012 0.17 0.36 4 -0.51 7 11
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.005 0.13 0.23 2 -0.37 10 12
ADCY4 -0.021 0.11 -10000 0 -0.31 4 4
ADCY5 -0.018 0.11 -10000 0 -0.31 4 4
ADCY6 -0.018 0.11 -10000 0 -0.31 4 4
ADCY7 -0.019 0.11 -10000 0 -0.31 4 4
ADCY1 -0.016 0.1 -10000 0 -0.3 5 5
ADCY2 -0.02 0.11 -10000 0 -0.31 4 4
ADCY3 -0.027 0.12 -10000 0 -0.3 6 6
ADCY8 -0.022 0.1 -10000 0 -0.3 5 5
ADCY9 -0.022 0.11 -10000 0 -0.32 6 6
arachidonic acid secretion -0.068 0.23 0.36 4 -0.55 28 32
ETB receptor/Endothelin-1/Gq/GTP -0.024 0.13 -10000 0 -0.37 18 18
GNAO1 0.033 0.005 -10000 0 -10000 0 0
HRAS 0.033 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.095 0.17 -10000 0 -0.34 5 5
ETA receptor/Endothelin-1/Gs/GTP 0.063 0.16 -10000 0 -0.32 5 5
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.013 0.15 -10000 0 -0.43 6 6
EDNRB -0.026 0.14 -10000 0 -0.51 16 16
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.013 0.13 -10000 0 -0.37 5 5
CYSLTR1 -0.014 0.16 -10000 0 -0.45 6 6
SLC9A1 0.008 0.087 -10000 0 -0.34 1 1
mol:GDP 0 0.17 0.31 7 -0.53 8 15
SLC9A3 -0.34 0.32 -10000 0 -0.71 60 60
RAF1 -0.032 0.19 0.35 4 -0.48 17 21
JUN 0.024 0.16 -10000 0 -0.66 2 2
JAK2 -0.012 0.15 -10000 0 -0.34 14 14
mol:IP3 -0.014 0.14 0.24 3 -0.44 10 13
ETA receptor/Endothelin-1 0.094 0.21 -10000 0 -0.38 15 15
PLCB1 -0.05 0.14 -10000 0 -0.33 45 45
PLCB2 0.03 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.13 0.21 -10000 0 -0.39 77 77
FOS -0.11 0.36 0.4 2 -0.93 33 35
Gai/GDP 0.014 0.13 -10000 0 -0.74 4 4
CRK 0.027 0.014 -10000 0 -10000 0 0
mol:Ca ++ -0.023 0.18 0.39 1 -0.49 12 13
BCAR1 0.033 0.006 -10000 0 -10000 0 0
PRKCB1 -0.01 0.14 0.23 7 -0.42 10 17
GNAQ 0.001 0.005 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
GNAL 0.026 0.014 -10000 0 -10000 0 0
Gs family/GDP 0.001 0.15 0.34 4 -0.5 7 11
ETA receptor/Endothelin-1/Gq/GTP 0.008 0.12 -10000 0 -0.35 8 8
MAPK14 -0.03 0.12 -10000 0 -0.38 13 13
TRPC6 0.022 0.18 -10000 0 -0.96 3 3
GNAI2 0.033 0.004 -10000 0 -10000 0 0
GNAI3 0.033 0.006 -10000 0 -10000 0 0
GNAI1 -0.032 0.17 -10000 0 -0.5 26 26
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.029 0.13 -10000 0 -0.39 14 14
ETB receptor/Endothelin-2 -0.25 0.19 -10000 0 -0.4 123 123
ETB receptor/Endothelin-3 -0.13 0.2 -10000 0 -0.41 65 65
ETB receptor/Endothelin-1 -0.009 0.16 -10000 0 -0.4 25 25
MAPK3 -0.081 0.29 0.4 2 -0.72 32 34
MAPK1 -0.09 0.31 0.38 3 -0.75 32 35
Rac1/GDP 0.004 0.16 0.34 2 -0.52 7 9
cAMP biosynthetic process 0.006 0.11 0.43 2 -10000 0 2
MAPK8 0.025 0.17 -10000 0 -0.57 9 9
SRC 0.019 0.017 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.012 0.12 -10000 0 -0.37 9 9
p130Cas/CRK/Src/PYK2 0.024 0.18 0.38 9 -0.55 7 16
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.004 0.16 0.34 2 -0.52 7 9
COL1A2 -0.012 0.21 -10000 0 -0.55 10 10
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.3 0.21 -10000 0 -0.4 170 170
mol:DAG -0.014 0.14 0.24 3 -0.44 10 13
MAP2K2 -0.055 0.23 0.38 4 -0.54 30 34
MAP2K1 -0.058 0.23 0.34 4 -0.55 30 34
EDNRA -0.012 0.18 -10000 0 -0.33 49 49
positive regulation of muscle contraction 0.005 0.13 0.29 9 -0.32 5 14
Gq family/GDP -0.014 0.15 -10000 0 -0.47 10 10
HRAS/GTP -0.015 0.16 0.33 4 -0.46 11 15
PRKCH -0.013 0.14 0.25 3 -0.47 8 11
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCA -0.003 0.14 0.26 7 -0.44 8 15
PRKCB -0.011 0.14 0.23 7 -0.42 10 17
PRKCE -0.011 0.14 0.24 4 -0.49 7 11
PRKCD -0.012 0.14 0.24 4 -0.47 8 12
PRKCG -0.014 0.14 0.25 4 -0.46 9 13
regulation of vascular smooth muscle contraction -0.14 0.42 0.49 1 -1.1 33 34
PRKCQ -0.014 0.14 0.24 4 -0.47 8 12
PLA2G4A -0.076 0.25 0.37 4 -0.6 28 32
GNA14 0.011 0.11 -10000 0 -0.5 9 9
GNA15 0.021 0.064 -10000 0 -0.32 7 7
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.018 0.088 -10000 0 -0.5 6 6
Rac1/GTP 0.096 0.17 -10000 0 -0.34 5 5
MMP1 -0.23 0.097 0.34 1 -10000 0 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.016 0.16 -9999 0 -0.5 20 20
positive regulation of NF-kappaB transcription factor activity -0.004 0.12 -9999 0 -0.35 23 23
MAP2K4 -0.008 0.092 -9999 0 -0.33 11 11
IKBKB 0.029 0.011 -9999 0 -10000 0 0
TNFRSF10B -0.024 0.12 -9999 0 -0.32 30 30
TNFRSF10A -0.009 0.1 -9999 0 -0.32 21 21
SMPD1 -0.1 0.2 -9999 0 -0.41 56 56
IKBKG 0.033 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.019 0.049 -9999 0 -0.32 4 4
TRAIL/TRAILR2 -0.035 0.15 -9999 0 -0.3 45 45
TRAIL/TRAILR3 -0.029 0.14 -9999 0 -0.3 42 42
TRAIL/TRAILR1 -0.024 0.14 -9999 0 -0.31 38 38
TRAIL/TRAILR4 -0.004 0.12 -9999 0 -0.35 23 23
TRAIL/TRAILR1/DAP3/GTP -0.003 0.11 -9999 0 -0.3 19 19
IKK complex -0.001 0.077 -9999 0 -0.56 1 1
RIPK1 0.033 0.005 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.024 0.004 -9999 0 -10000 0 0
MAPK3 -0.018 0.12 -9999 0 -0.38 20 20
MAP3K1 -0.005 0.092 -9999 0 -0.33 10 10
TRAILR4 (trimer) 0.019 0.049 -9999 0 -0.32 4 4
TRADD 0.033 0.005 -9999 0 -10000 0 0
TRAILR1 (trimer) -0.009 0.1 -9999 0 -0.32 21 21
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.093 -9999 0 -0.28 19 19
CFLAR 0.034 0 -9999 0 -10000 0 0
MAPK1 -0.012 0.1 -9999 0 -0.36 17 17
TRAIL/TRAILR1/FADD/TRADD/RIP 0.021 0.12 -9999 0 -0.28 19 19
mol:ceramide -0.1 0.2 -9999 0 -0.41 56 56
FADD 0.033 0.004 -9999 0 -10000 0 0
MAPK8 -0.009 0.09 -9999 0 -0.34 8 8
TRAF2 0.033 0.005 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.11 -9999 0 -0.32 24 24
CHUK 0.032 0.007 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.005 0.13 -9999 0 -0.33 20 20
DAP3 0.033 0.006 -9999 0 -10000 0 0
CASP10 -0.036 0.1 -9999 0 -0.36 15 15
JNK cascade -0.004 0.12 -9999 0 -0.35 23 23
TRAIL (trimer) -0.016 0.16 -9999 0 -0.5 20 20
TNFRSF10C -0.014 0.11 -9999 0 -0.32 24 24
TRAIL/TRAILR1/DAP3/GTP/FADD 0.008 0.11 -9999 0 -0.28 19 19
TRAIL/TRAILR2/FADD -0.015 0.13 -9999 0 -0.34 20 20
cell death -0.1 0.2 -9999 0 -0.4 56 56
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.009 0.094 -9999 0 -0.28 19 19
TRAILR2 (trimer) -0.024 0.12 -9999 0 -0.32 30 30
CASP8 0.026 0.033 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.01 0.13 -9999 0 -0.3 19 19
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 0.006 0.086 -10000 0 -0.31 1 1
TBX21 -0.37 0.67 -10000 0 -1.3 67 67
B2M 0.012 0.1 -10000 0 -0.5 8 8
TYK2 0.013 0.04 -10000 0 -10000 0 0
IL12RB1 0.014 0.04 -10000 0 -10000 0 0
GADD45B -0.14 0.36 -10000 0 -0.9 28 28
IL12RB2 0.013 0.048 -10000 0 -0.37 1 1
GADD45G -0.14 0.36 -10000 0 -0.88 29 29
natural killer cell activation -0.006 0.024 -10000 0 -0.045 38 38
RELB 0.033 0.005 -10000 0 -10000 0 0
RELA 0.033 0.006 -10000 0 -10000 0 0
IL18 -0.026 0.17 -10000 0 -0.5 24 24
IL2RA 0.021 0.064 -10000 0 -0.32 7 7
IFNG -0.045 0.15 -10000 0 -0.32 47 47
STAT3 (dimer) -0.11 0.32 -10000 0 -0.73 33 33
HLA-DRB5 -0.002 0.007 -10000 0 -0.023 11 11
FASLG -0.2 0.5 -10000 0 -1.3 28 28
NF kappa B2 p52/RelB -0.14 0.38 -10000 0 -0.83 37 37
CD4 0.028 0.018 -10000 0 -10000 0 0
SOCS1 0.031 0.025 -10000 0 -0.32 1 1
EntrezGene:6955 0 0.008 -10000 0 -0.025 17 17
CD3D 0.007 0.11 -10000 0 -0.5 9 9
CD3E 0.029 0.018 -10000 0 -10000 0 0
CD3G 0.006 0.11 -10000 0 -0.49 10 10
IL12Rbeta2/JAK2 0.018 0.068 -10000 0 -0.25 4 4
CCL3 -0.15 0.37 -10000 0 -0.94 26 26
CCL4 -0.15 0.4 -10000 0 -1 26 26
HLA-A 0.001 0.002 -10000 0 -10000 0 0
IL18/IL18R -0.037 0.21 -10000 0 -0.36 59 59
NOS2 -0.16 0.38 -10000 0 -0.84 38 38
IL12/IL12R/TYK2/JAK2/SPHK2 0.006 0.085 -10000 0 -0.31 1 1
IL1R1 -0.17 0.41 -10000 0 -1.1 28 28
IL4 0.037 0.036 -10000 0 -0.32 1 1
JAK2 0.008 0.056 -10000 0 -0.34 3 3
EntrezGene:6957 0 0.007 -10000 0 -0.023 9 9
TCR/CD3/MHC I/CD8 -0.012 0.16 -10000 0 -0.62 10 10
RAB7A -0.11 0.31 -10000 0 -0.81 19 19
lysosomal transport -0.1 0.3 -10000 0 -0.75 20 20
FOS -0.24 0.54 -10000 0 -1.3 41 41
STAT4 (dimer) -0.13 0.36 -10000 0 -0.84 30 30
STAT5A (dimer) -0.16 0.37 -10000 0 -0.85 35 35
GZMA -0.15 0.37 -10000 0 -0.81 39 39
GZMB -0.15 0.37 -10000 0 -0.96 26 26
HLX 0.033 0.005 -10000 0 -10000 0 0
LCK -0.16 0.4 -10000 0 -0.89 38 38
TCR/CD3/MHC II/CD4 -0.022 0.15 -10000 0 -0.45 17 17
IL2/IL2R 0.064 0.066 -10000 0 -0.28 3 3
MAPK14 -0.15 0.38 -10000 0 -0.88 33 33
CCR5 -0.2 0.5 -10000 0 -1.3 30 30
IL1B -0.051 0.14 -10000 0 -0.32 40 40
STAT6 -0.019 0.12 -10000 0 -0.76 1 1
STAT4 0.031 0.036 -10000 0 -0.5 1 1
STAT3 0.033 0.006 -10000 0 -10000 0 0
STAT1 0.002 0.1 -10000 0 -0.32 19 19
NFKB1 0.033 0.006 -10000 0 -10000 0 0
NFKB2 0.03 0.025 -10000 0 -0.32 1 1
IL12B 0.012 0.051 -10000 0 -0.31 2 2
CD8A 0.001 0.002 -10000 0 -10000 0 0
CD8B 0.035 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.006 0.085 0.31 1 -10000 0 1
IL2RB 0.032 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.11 0.33 -10000 0 -0.76 30 30
IL2RG 0.026 0.063 -10000 0 -0.5 3 3
IL12 0.015 0.073 -10000 0 -0.25 2 2
STAT5A 0.033 0.006 -10000 0 -10000 0 0
CD247 0.002 0.12 -10000 0 -0.5 11 11
IL2 0.033 0.005 -10000 0 -10000 0 0
SPHK2 0.03 0.037 -10000 0 -0.5 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.068 -10000 0 -0.32 6 6
IL12/IL12R/TYK2/JAK2 -0.17 0.43 -10000 0 -0.96 38 38
MAP2K3 -0.17 0.4 -10000 0 -0.91 36 36
RIPK2 -0.013 0.11 -10000 0 -0.32 25 25
MAP2K6 -0.14 0.38 -10000 0 -0.89 33 33
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.008 -10000 0 -0.026 17 17
IL18RAP -0.073 0.22 -10000 0 -0.51 43 43
IL12Rbeta1/TYK2 0.022 0.054 -10000 0 -10000 0 0
EOMES 0.025 0.063 -10000 0 -10000 0 0
STAT1 (dimer) -0.12 0.3 -10000 0 -0.75 28 28
T cell proliferation -0.1 0.27 -10000 0 -0.64 29 29
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.031 0.039 -10000 0 -0.51 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.12 0.31 -10000 0 -0.7 32 32
ATF2 -0.13 0.35 -10000 0 -0.8 33 33
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.032 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.002 0.058 -10000 0 -10000 0 0
IRAK/TOLLIP 0.036 0.022 -10000 0 -10000 0 0
IKBKB 0.029 0.011 -10000 0 -10000 0 0
IKBKG 0.033 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.22 0.2 -10000 0 -0.33 156 156
IL1A -0.12 0.18 -10000 0 -0.32 95 95
IL1B -0.049 0.12 -10000 0 -0.25 53 53
IRAK/TRAF6/p62/Atypical PKCs 0.058 0.042 -10000 0 -10000 0 0
IL1R2 -0.18 0.26 -10000 0 -0.5 87 87
IL1R1 0.014 0.1 -10000 0 -0.5 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.064 -10000 0 -10000 0 0
TOLLIP 0.033 0.004 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.008 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.038 0.058 -10000 0 -10000 0 0
JUN -0.015 0.053 0.32 1 -10000 0 1
MAP3K7 0.033 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.005 0.13 -10000 0 -0.29 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.042 0.14 -10000 0 -0.31 12 12
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.029 0.14 -10000 0 -0.29 12 12
IL1 beta fragment/IL1R1/IL1RAP -0.022 0.12 -10000 0 -0.29 22 22
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 0.001 0.055 0.34 1 -0.24 9 10
IRAK1 0.017 0.02 -10000 0 -0.18 2 2
IL1RN/IL1R1 -0.044 0.14 -10000 0 -0.24 70 70
IRAK4 0.033 0.004 -10000 0 -10000 0 0
PRKCI 0.025 0.054 -10000 0 -0.32 5 5
TRAF6 0.033 0.003 -10000 0 -10000 0 0
PI3K 0.048 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.072 -10000 0 -10000 0 0
CHUK 0.032 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.022 0.12 -10000 0 -0.29 22 22
IL1 beta/IL1R2 -0.16 0.19 -10000 0 -0.35 91 91
IRAK/TRAF6/TAK1/TAB1/TAB2 0.045 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.005 0.12 -10000 0 -10000 0 0
IRAK3 0.021 0.064 -10000 0 -0.32 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.008 0.12 -10000 0 -0.26 22 22
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.016 0.072 -10000 0 -0.3 2 2
IL1 alpha/IL1R1/IL1RAP -0.061 0.14 -10000 0 -0.34 12 12
RELA 0.033 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.033 0.004 -10000 0 -10000 0 0
MYD88 0.033 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.053 0.029 -10000 0 -10000 0 0
IL1RAP 0.023 0.059 -10000 0 -0.32 6 6
UBE2N 0.033 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.024 0.1 -10000 0 -10000 0 0
CASP1 -0.001 0.12 -10000 0 -0.44 15 15
IL1RN/IL1R2 -0.19 0.19 -10000 0 -0.32 141 141
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.006 0.13 -10000 0 -0.28 22 22
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.006 0.08 -10000 0 -0.32 8 8
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
IL1RN -0.069 0.16 -10000 0 -0.32 62 62
TRAF6/TAK1/TAB1/TAB2 0.047 0.011 -10000 0 -10000 0 0
MAP2K6 0.009 0.058 0.35 1 -0.25 9 10
TCGA08_p53

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
CDKN2A -0.061 0.11 -10000 0 -0.22 66 66
TP53 -0.023 0.056 -10000 0 -0.25 10 10
Senescence -0.023 0.056 -10000 0 -0.25 10 10
Apoptosis -0.023 0.056 -10000 0 -0.25 10 10
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.031 0.064 0.38 2 -10000 0 2
MDM4 0.033 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.075 0.23 -10000 0 -0.9 5 5
PCK1 -0.68 0.66 -10000 0 -1.2 123 123
HNF4A -0.054 0.25 0.59 3 -0.98 4 7
KCNJ11 -0.062 0.24 -10000 0 -0.97 3 3
AKT1 -0.029 0.14 -10000 0 -0.69 1 1
response to starvation -0.015 0.034 -10000 0 -0.26 2 2
DLK1 -0.059 0.24 -10000 0 -0.97 3 3
NKX2-1 0.036 0.18 0.42 17 -0.38 2 19
ACADM -0.077 0.24 -10000 0 -0.98 5 5
TAT -0.12 0.21 -10000 0 -0.74 8 8
CEBPB -0.007 0.047 -10000 0 -0.33 3 3
CEBPA -0.007 0.043 -10000 0 -10000 0 0
TTR -0.74 0.67 0.58 2 -1.3 122 124
PKLR -0.077 0.23 -10000 0 -0.98 4 4
APOA1 -0.061 0.3 -10000 0 -1.2 6 6
CPT1C -0.077 0.23 -10000 0 -0.98 4 4
ALAS1 -0.016 0.14 -10000 0 -0.64 1 1
TFRC -0.11 0.25 -10000 0 -0.96 5 5
FOXF1 0.015 0.095 -10000 0 -0.5 7 7
NF1 0.038 0.009 -10000 0 -10000 0 0
HNF1A (dimer) 0.032 0.042 -10000 0 -10000 0 0
CPT1A -0.077 0.23 -10000 0 -0.95 4 4
HMGCS1 -0.076 0.23 -10000 0 -0.95 4 4
NR3C1 -0.024 0.17 -10000 0 -0.5 24 24
CPT1B -0.074 0.22 -10000 0 -0.95 4 4
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.023 -10000 0 -10000 0 0
GCK -0.068 0.22 -10000 0 -0.95 4 4
CREB1 -0.12 0.15 -10000 0 -0.28 68 68
IGFBP1 -0.064 0.16 -10000 0 -0.63 2 2
PDX1 -0.004 0.14 -10000 0 -10000 0 0
UCP2 -0.074 0.23 -10000 0 -0.95 4 4
ALDOB -0.11 0.34 -10000 0 -1.1 15 15
AFP -0.13 0.15 -10000 0 -0.43 23 23
BDH1 -0.074 0.24 -10000 0 -1.1 4 4
HADH -0.063 0.24 -10000 0 -0.97 3 3
F2 -0.046 0.27 -10000 0 -1.1 3 3
HNF1A 0.032 0.042 -10000 0 -10000 0 0
G6PC -0.072 0.14 -10000 0 -10000 0 0
SLC2A2 -0.032 0.17 -10000 0 -10000 0 0
INS 0.026 0.022 -10000 0 -10000 0 0
FOXA1 -0.12 0.22 -10000 0 -0.51 53 53
FOXA3 -0.13 0.16 -10000 0 -0.39 30 30
FOXA2 -0.07 0.28 -10000 0 -0.96 5 5
ABCC8 -0.098 0.32 -10000 0 -1 14 14
ALB -0.14 0.15 -10000 0 -0.51 5 5
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.033 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.06 0.15 -9999 0 -0.44 13 13
Syndecan-3/Neurocan 0.013 0.1 -9999 0 -0.37 13 13
POMC 0.031 0.036 -9999 0 -0.5 1 1
EGFR 0.021 0.072 -9999 0 -0.5 4 4
Syndecan-3/EGFR 0.005 0.11 -9999 0 -0.36 15 15
AGRP 0.031 0.025 -9999 0 -0.32 1 1
NCSTN 0.033 0.006 -9999 0 -10000 0 0
PSENEN 0.032 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.03 0.026 -9999 0 -0.32 1 1
APH1A 0.016 0.091 -9999 0 -0.48 7 7
NCAN 0.033 0.004 -9999 0 -10000 0 0
long-term memory 0.027 0.1 -9999 0 -0.35 13 13
Syndecan-3/IL8 -0.14 0.11 -9999 0 -0.48 14 14
PSEN1 0.031 0.01 -9999 0 -10000 0 0
Src/Cortactin 0.027 0.025 -9999 0 -10000 0 0
FYN 0.03 0.037 -9999 0 -0.5 1 1
limb bud formation -0.008 0.096 -9999 0 -0.38 13 13
MC4R 0.023 0.016 -9999 0 -10000 0 0
SRC 0.019 0.017 -9999 0 -10000 0 0
PTN -0.16 0.26 -9999 0 -0.5 79 79
FGFR/FGF/Syndecan-3 -0.008 0.097 -9999 0 -0.39 13 13
neuron projection morphogenesis -0.022 0.18 -9999 0 -0.44 12 12
Syndecan-3/AgRP 0.012 0.1 -9999 0 -0.37 13 13
Syndecan-3/AgRP/MC4R 0.017 0.099 -9999 0 -0.34 13 13
Fyn/Cortactin 0.045 0.03 -9999 0 -0.36 1 1
SDC3 -0.009 0.098 -9999 0 -0.39 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.14 0.11 -9999 0 -0.48 14 14
IL8 -0.3 0.1 -9999 0 -0.33 197 197
Syndecan-3/Fyn/Cortactin 0.028 0.1 -9999 0 -0.36 13 13
Syndecan-3/CASK -0.01 0.093 -9999 0 -0.37 13 13
alpha-MSH/MC4R 0.032 0.036 -9999 0 -0.36 1 1
Gamma Secretase 0.07 0.071 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.075 0.097 -10000 0 -10000 0 0
UGCG -0.014 0.077 -10000 0 -0.76 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT -0.2 0.19 -10000 0 -0.42 56 56
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.015 0.076 -10000 0 -0.75 2 2
mol:DAG 0.023 0.17 -10000 0 -0.79 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.28 0.22 -10000 0 -0.46 109 109
FRAP1 -0.32 0.25 -10000 0 -0.49 139 139
FOXO3 -0.19 0.16 -10000 0 -0.4 39 39
AKT1 -0.2 0.17 -10000 0 -0.42 44 44
GAB2 0.027 0.005 -10000 0 -10000 0 0
SMPD1 -0.17 0.32 -10000 0 -0.79 46 46
SGMS1 -0.031 0.13 -10000 0 -0.74 7 7
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 -0.012 0.012 -10000 0 -10000 0 0
CALM1 0.03 0.01 -10000 0 -10000 0 0
cell proliferation -0.043 0.13 -10000 0 -0.55 7 7
EIF3A 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.038 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.02 0.14 -10000 0 -0.98 4 4
mol:sphingomyelin 0.023 0.17 -10000 0 -0.79 7 7
natural killer cell activation -0.007 0.004 -10000 0 -0.013 30 30
JAK3 0.029 0.007 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
JAK1 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MYC -0.19 0.16 -10000 0 -0.51 6 6
MYB 0.013 0.13 -10000 0 -1.3 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.095 0.11 -10000 0 -0.44 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.019 0.13 -10000 0 -0.9 4 4
mol:PI-3-4-5-P3 -0.094 0.11 -10000 0 -0.43 4 4
Rac1/GDP 0.002 0.023 -10000 0 -10000 0 0
T cell proliferation -0.089 0.099 -10000 0 -0.4 4 4
SHC1 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.03 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.007 -10000 0 -0.065 2 2
PRKCZ -0.092 0.1 -10000 0 -0.42 4 4
NF kappa B1 p50/RelA -0.28 0.22 -10000 0 -0.47 100 100
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.015 0.053 -10000 0 -0.41 1 1
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
RELA 0.033 0.006 -10000 0 -10000 0 0
IL2RA 0.015 0.063 -10000 0 -0.33 7 7
IL2RB 0.027 0.009 -10000 0 -10000 0 0
TERT 0.032 0.007 -10000 0 -10000 0 0
E2F1 0.012 0.058 -10000 0 -0.43 2 2
SOS1 0.027 0.004 -10000 0 -10000 0 0
RPS6 0.029 0.035 -10000 0 -0.32 2 2
mol:cAMP -0.002 0.003 0.031 2 -10000 0 2
PTPN11 0.024 0.025 -10000 0 -0.33 1 1
IL2RG 0.021 0.063 -10000 0 -0.51 3 3
actin cytoskeleton organization -0.089 0.099 -10000 0 -0.4 4 4
GRB2 0.026 0.006 -10000 0 -10000 0 0
IL2 0.027 0.007 -10000 0 -10000 0 0
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.033 -10000 0 -10000 0 0
LCK 0.023 0.045 -10000 0 -0.42 2 2
BCL2 -0.59 0.42 -10000 0 -0.89 143 143
IL6-mediated signaling events

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.036 0.15 -10000 0 -10000 0 0
CRP -0.097 0.14 -10000 0 -10000 0 0
cell cycle arrest -0.11 0.14 -10000 0 -0.62 1 1
TIMP1 -0.14 0.15 -10000 0 -0.74 2 2
IL6ST 0.033 0.009 -10000 0 -10000 0 0
Rac1/GDP -0.15 0.16 -10000 0 -0.41 30 30
AP1 0.005 0.12 -10000 0 -0.58 2 2
GAB2 0.037 0.01 -10000 0 -10000 0 0
TNFSF11 -0.076 0.16 -10000 0 -10000 0 0
HSP90B1 0.015 0.046 -10000 0 -10000 0 0
GAB1 0.03 0.052 -10000 0 -0.5 2 2
MAPK14 -0.14 0.15 -10000 0 -0.46 14 14
AKT1 0.042 0.042 -10000 0 -10000 0 0
FOXO1 0.061 0.089 -10000 0 -10000 0 0
MAP2K6 -0.15 0.15 -10000 0 -0.4 28 28
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
MAP2K4 -0.15 0.15 -10000 0 -0.46 19 19
MITF -0.15 0.14 -10000 0 -0.36 31 31
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.033 0.005 -10000 0 -10000 0 0
A2M -0.17 0.52 -10000 0 -1.4 31 31
CEBPB 0.016 0.046 -10000 0 -0.32 3 3
GRB2/SOS1/GAB family/SHP2 0.003 0.085 -10000 0 -0.45 2 2
STAT3 -0.12 0.14 -10000 0 -0.64 1 1
STAT1 0.008 0.026 -10000 0 -10000 0 0
CEBPD -0.083 0.13 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
PI3K 0.05 0.01 -10000 0 -10000 0 0
JUN 0.025 0.054 -10000 0 -0.33 5 5
PIAS3/MITF -0.14 0.14 -10000 0 -0.37 19 19
MAPK11 -0.14 0.15 -10000 0 -0.47 14 14
STAT3 (dimer)/FOXO1 -0.072 0.16 -10000 0 -0.56 4 4
GRB2/SOS1/GAB family -0.078 0.16 0.32 1 -0.43 6 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.15 -10000 0 -0.35 43 43
GRB2 0.035 0.008 -10000 0 -10000 0 0
JAK2 0.027 0.042 -10000 0 -0.32 3 3
LBP 0.002 0.14 0.5 1 -10000 0 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
JAK1 0.032 0.01 -10000 0 -10000 0 0
MYC -0.12 0.16 -10000 0 -0.64 1 1
FGG -0.1 0.13 -10000 0 -10000 0 0
macrophage differentiation -0.11 0.14 -10000 0 -0.62 1 1
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.18 0.18 -10000 0 -0.36 81 81
JUNB -0.098 0.13 -10000 0 -10000 0 0
FOS -0.028 0.16 -10000 0 -0.49 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.16 0.15 -10000 0 -0.35 48 48
STAT1/PIAS1 -0.11 0.13 -10000 0 -0.38 8 8
GRB2/SOS1/GAB family/SHP2/PI3K 0.048 0.035 -10000 0 -10000 0 0
STAT3 (dimer) -0.12 0.14 -10000 0 -0.64 1 1
PRKCD -0.14 0.16 0.38 2 -0.5 9 11
IL6R -0.25 0.27 -10000 0 -0.5 114 114
SOCS3 -0.12 0.15 -10000 0 -0.59 2 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.053 0.061 -10000 0 -0.29 2 2
Rac1/GTP -0.16 0.16 -10000 0 -0.43 26 26
HCK 0.005 0.087 -10000 0 -0.5 6 6
MAPKKK cascade 0.037 0.094 -10000 0 -0.52 2 2
bone resorption -0.073 0.16 0.49 1 -10000 0 1
IRF1 -0.1 0.14 -10000 0 -1.1 1 1
mol:GDP -0.17 0.16 -10000 0 -0.41 38 38
SOS1 0.037 0.009 -10000 0 -10000 0 0
VAV1 -0.17 0.16 -10000 0 -0.41 38 38
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.22 0.21 -10000 0 -0.48 50 50
PTPN11 0.017 0.017 -10000 0 -10000 0 0
IL6/IL6RA -0.25 0.21 -10000 0 -0.38 145 145
gp130 (dimer)/TYK2/TYK2/LMO4 0.053 0.059 -10000 0 -0.3 2 2
gp130 (dimer)/JAK2/JAK2/LMO4 0.051 0.069 -10000 0 -0.33 5 5
IL6 -0.12 0.18 -10000 0 -0.33 93 93
PIAS3 0.031 0.025 -10000 0 -0.32 1 1
PTPRE 0.031 0.026 -10000 0 -0.32 1 1
PIAS1 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.03 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.15 0.14 -10000 0 -0.32 58 58
LMO4 0.016 0.081 -10000 0 -0.36 9 9
STAT3 (dimer)/PIAS3 -0.11 0.14 -10000 0 -0.62 1 1
MCL1 0.044 0.049 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.009 0.088 -10000 0 -0.32 14 14
mol:Halofuginone 0.005 0 -10000 0 -10000 0 0
ITGA1 0.032 0.024 -10000 0 -0.32 1 1
CDKN1A 0.006 0.059 -10000 0 -0.32 6 6
PRL-3/alpha Tubulin -0.016 0.11 -10000 0 -0.22 44 44
mol:Ca2+ -0.07 0.12 -10000 0 -0.26 41 41
AGT -0.079 0.17 -10000 0 -0.33 67 67
CCNA2 -0.011 0.052 -10000 0 -10000 0 0
TUBA1B 0.033 0.004 -10000 0 -10000 0 0
EGR1 0.006 0.071 -10000 0 -0.35 7 7
CDK2/Cyclin E1 0.048 0.12 -10000 0 -0.35 2 2
MAPK3 -0.013 0.13 0.23 22 -0.23 45 67
PRL-2 /Rab GGTase beta 0.047 0.012 -10000 0 -10000 0 0
MAPK1 -0.011 0.12 0.23 22 -0.22 44 66
PTP4A1 0.002 0.034 -10000 0 -10000 0 0
PTP4A3 -0.046 0.14 -10000 0 -0.32 44 44
PTP4A2 0.032 0.007 -10000 0 -10000 0 0
ITGB1 -0.012 0.13 0.23 22 -10000 0 22
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1 0.014 0.041 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.044 0.016 -10000 0 -10000 0 0
PRL-1/ATF-5 0.091 0.096 0.37 1 -10000 0 1
RABGGTA 0.031 0.009 -10000 0 -10000 0 0
BCAR1 0.013 0.059 -10000 0 -10000 0 0
RHOC 0.008 0.062 -10000 0 -0.42 1 1
RHOA 0.015 0.041 -10000 0 -10000 0 0
cell motility 0.04 0.12 0.41 1 -0.41 3 4
PRL-1/alpha Tubulin 0.094 0.098 0.37 2 -10000 0 2
PRL-3/alpha1 Integrin -0.015 0.11 -10000 0 -0.22 43 43
ROCK1 0.042 0.12 0.41 1 -0.43 2 3
RABGGTB 0.033 0.006 -10000 0 -10000 0 0
CDK2 -0.005 0.11 -10000 0 -0.32 23 23
mitosis 0.002 0.034 -10000 0 -10000 0 0
ATF5 0.033 0.005 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.023 0.1 -10000 0 -0.51 4 4
IHH 0.034 0.055 -10000 0 -0.62 1 1
SHH Np/Cholesterol/GAS1 -0.087 0.17 -10000 0 -0.31 71 71
LRPAP1 0.032 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.087 0.16 0.31 71 -10000 0 71
SMO/beta Arrestin2 0.036 0.074 -10000 0 -0.54 1 1
SMO 0.025 0.067 -10000 0 -0.56 1 1
AKT1 0.01 0.11 -10000 0 -0.4 2 2
ARRB2 0.027 0.013 -10000 0 -10000 0 0
BOC 0.033 0.004 -10000 0 -10000 0 0
ADRBK1 0.033 0.005 -10000 0 -10000 0 0
heart looping 0.025 0.067 -10000 0 -0.55 1 1
STIL -0.017 0.12 0.37 1 -0.36 8 9
DHH N/PTCH2 0.048 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.045 0.067 -10000 0 -0.5 1 1
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
DHH 0.033 0.004 -10000 0 -10000 0 0
PTHLH 0.023 0.1 -10000 0 -0.88 1 1
determination of left/right symmetry 0.025 0.067 -10000 0 -0.55 1 1
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
skeletal system development 0.023 0.1 -10000 0 -0.87 1 1
IHH N/Hhip -0.041 0.19 -10000 0 -0.4 44 44
DHH N/Hhip -0.037 0.17 -10000 0 -0.36 44 44
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.025 0.067 -10000 0 -0.55 1 1
pancreas development -0.076 0.22 -10000 0 -0.5 44 44
HHAT -0.019 0.16 -10000 0 -0.5 21 21
PI3K 0.048 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.13 0.24 -10000 0 -0.49 67 67
somite specification 0.025 0.067 -10000 0 -0.55 1 1
SHH Np/Cholesterol/PTCH1 0.006 0.099 -10000 0 -0.37 3 3
SHH Np/Cholesterol/PTCH2 0.001 0.095 -10000 0 -0.29 20 20
SHH Np/Cholesterol/Megalin 0.001 0.096 -10000 0 -0.29 20 20
SHH -0.018 0.12 0.23 1 -0.36 21 22
catabolic process 0.03 0.07 -10000 0 -0.55 1 1
SMO/Vitamin D3 0.007 0.099 -10000 0 -0.5 1 1
SHH Np/Cholesterol/Hhip -0.059 0.16 -10000 0 -0.32 54 54
LRP2 0.032 0.024 -10000 0 -0.32 1 1
receptor-mediated endocytosis 0.003 0.098 -10000 0 -0.46 1 1
SHH Np/Cholesterol/BOC 0.003 0.093 -10000 0 -0.29 19 19
SHH Np/Cholesterol/CDO 0.001 0.095 -10000 0 -0.29 20 20
mesenchymal cell differentiation 0.059 0.16 0.32 54 -10000 0 54
mol:Vitamin D3 0.011 0.11 0.39 1 -0.37 3 4
IHH N/PTCH2 0.049 0.035 -10000 0 -0.38 1 1
CDON 0.033 0.006 -10000 0 -10000 0 0
IHH N/PTCH1 0.038 0.073 -10000 0 -0.55 1 1
Megalin/LRPAP1 0.047 0.021 -10000 0 -0.22 1 1
PTCH2 0.033 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.011 0.091 -10000 0 -0.29 20 20
PTCH1 0.03 0.07 -10000 0 -0.55 1 1
HHIP -0.076 0.22 -10000 0 -0.5 44 44
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.008 0.068 -10000 0 -10000 0 0
EPHB2 0.02 0.065 -10000 0 -0.36 6 6
Syndecan-2/TACI 0.021 0.039 -10000 0 -0.3 2 2
LAMA1 0.026 0.014 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.021 0.1 -10000 0 -0.28 2 2
HRAS 0.033 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK 0.01 0.015 -10000 0 -0.18 1 1
ITGA5 0.025 0.054 -10000 0 -0.32 5 5
BAX 0.009 0.021 -10000 0 -10000 0 0
EPB41 0.031 0.009 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.027 0.019 -10000 0 -10000 0 0
LAMA3 0.019 0.051 -10000 0 -0.38 3 3
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.018 0.073 -10000 0 -0.35 8 8
Syndecan-2/MMP2 0.028 0.029 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.048 0.13 -10000 0 -0.23 76 76
dendrite morphogenesis 0.021 0.044 -10000 0 -0.3 1 1
Syndecan-2/GM-CSF -0.066 0.11 -10000 0 -0.18 102 102
determination of left/right symmetry 0.013 0.018 -10000 0 -0.21 1 1
Syndecan-2/PKC delta 0.03 0.021 -10000 0 -10000 0 0
GNB2L1 0.033 0.004 -10000 0 -10000 0 0
MAPK3 -0.052 0.12 0.2 17 -0.31 4 21
MAPK1 -0.049 0.12 0.2 17 -0.27 2 19
Syndecan-2/RACK1 0.044 0.025 -10000 0 -10000 0 0
NF1 0.032 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.013 0.018 -10000 0 -0.21 1 1
ITGA2 -0.095 0.17 -10000 0 -0.32 77 77
MAPK8 0.014 0.018 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.017 0.1 -10000 0 -0.3 1 1
Syndecan-2/Kininogen 0.023 0.051 -10000 0 -0.26 6 6
ITGB1 0.032 0.025 -10000 0 -0.32 1 1
SRC 0.02 0.038 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.026 0.02 -10000 0 -10000 0 0
extracellular matrix organization 0.03 0.021 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.008 0.068 -10000 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.036 0.05 -10000 0 -0.28 1 1
Syndecan-2/Laminin alpha3 0.019 0.038 -10000 0 -0.3 1 1
Syndecan-2/RasGAP 0.055 0.037 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.041 0.045 -10000 0 -10000 0 0
PRKCD 0.033 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.044 -10000 0 -0.3 1 1
GO:0007205 0.003 0.004 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.031 -10000 0 -10000 0 0
RHOA 0.033 0.005 -10000 0 -10000 0 0
SDCBP 0.029 0.011 -10000 0 -10000 0 0
TNFRSF13B 0.019 0.063 -10000 0 -0.5 3 3
RASA1 0.03 0.035 -10000 0 -0.32 2 2
alpha2/beta1 Integrin -0.048 0.13 -10000 0 -0.23 76 76
Syndecan-2/Synbindin 0.03 0.021 -10000 0 -10000 0 0
TGFB1 0.033 0.006 -10000 0 -10000 0 0
CASP3 0.042 0.06 0.2 26 -10000 0 26
FN1 -0.006 0.11 -10000 0 -0.32 24 24
Syndecan-2/IL8 -0.13 0.1 -10000 0 -0.26 3 3
SDC2 0.013 0.018 -10000 0 -0.21 1 1
KNG1 0.019 0.084 -10000 0 -0.47 6 6
Syndecan-2/Neurofibromin 0.029 0.022 -10000 0 -10000 0 0
TRAPPC4 0.033 0.005 -10000 0 -10000 0 0
CSF2 -0.16 0.18 -10000 0 -0.33 117 117
Syndecan-2/TGFB1 0.03 0.021 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.027 0.019 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.028 0.019 -10000 0 -10000 0 0
PRKACA 0.047 0.065 0.2 32 -10000 0 32
angiogenesis -0.13 0.1 -10000 0 -0.26 3 3
MMP2 0.03 0.035 -10000 0 -0.32 2 2
IL8 -0.3 0.1 -10000 0 -0.33 197 197
calcineurin-NFAT signaling pathway 0.021 0.039 -10000 0 -0.3 2 2
Ceramide signaling pathway

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
SPHK2 0.007 0.063 -10000 0 -0.36 6 6
MAP4K4 0.016 0.061 -10000 0 -0.36 1 1
BAG4 0.03 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.04 0.095 0.15 1 -0.25 22 23
NFKBIA 0.031 0.01 -10000 0 -10000 0 0
BIRC3 0.008 0.11 -10000 0 -0.45 11 11
BAX -0.005 0.047 -10000 0 -0.29 3 3
RIPK1 0.033 0.005 -10000 0 -10000 0 0
AKT1 0.005 0.013 -10000 0 -10000 0 0
BAD -0.04 0.096 0.16 1 -0.25 22 23
SMPD1 -0.027 0.12 0.33 1 -0.26 39 40
RB1 0.008 0.11 0.2 27 -0.27 10 37
FADD/Caspase 8 0.029 0.052 -10000 0 -10000 0 0
MAP2K4 -0.038 0.094 0.16 1 -0.33 11 12
NSMAF 0.029 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.033 0.096 0.19 2 -0.33 9 11
EGF -0.091 0.21 -10000 0 -0.43 58 58
mol:ceramide -0.042 0.1 0.15 5 -0.27 22 27
MADD 0.033 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.007 0.052 -10000 0 -0.36 4 4
ASAH1 0.026 0.014 -10000 0 -10000 0 0
negative regulation of cell cycle 0.008 0.11 0.2 27 -0.27 10 37
cell proliferation -0.14 0.14 -10000 0 -0.32 37 37
BID -0.008 0.16 -10000 0 -0.61 13 13
MAP3K1 -0.04 0.096 0.16 1 -0.25 22 23
EIF2A -0.054 0.096 -10000 0 -0.45 5 5
TRADD 0.033 0.005 -10000 0 -10000 0 0
CRADD 0.028 0.051 -10000 0 -0.5 2 2
MAPK3 -0.027 0.091 -10000 0 -0.53 3 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.032 0.091 -10000 0 -0.42 5 5
Cathepsin D/ceramide -0.029 0.11 0.17 1 -0.26 22 23
FADD 0.021 0.049 -10000 0 -0.25 1 1
KSR1 -0.035 0.1 0.18 5 -0.26 20 25
MAPK8 -0.035 0.094 0.16 1 -0.28 13 14
PRKRA -0.041 0.096 0.16 1 -0.25 22 23
PDGFA 0.018 0.081 -10000 0 -0.5 5 5
TRAF2 0.033 0.005 -10000 0 -10000 0 0
IGF1 -0.27 0.26 -10000 0 -0.5 124 124
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.042 0.1 0.15 5 -0.26 22 27
CTSD 0.031 0.037 -10000 0 -0.5 1 1
regulation of nitric oxide biosynthetic process 0.047 0.011 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.14 0.15 -10000 0 -0.34 37 37
PRKCD 0.033 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.007 0.052 -10000 0 -0.36 4 4
RelA/NF kappa B1 0.047 0.011 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.033 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.029 0.053 -10000 0 -0.27 2 2
TNFR1A/BAG4/TNF-alpha 0.058 0.025 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.063 -10000 0 -0.36 6 6
MAP2K1 -0.031 0.091 -10000 0 -0.46 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.033 0.006 -10000 0 -10000 0 0
CYCS 0.088 0.076 0.17 48 -0.21 1 49
TNFRSF1A 0.032 0.007 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.043 0.017 -10000 0 -10000 0 0
EIF2AK2 -0.044 0.094 -10000 0 -0.31 12 12
TNF-alpha/TNFR1A/FAN 0.056 0.026 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.033 0.069 -10000 0 -0.4 2 2
MAP2K2 -0.031 0.091 -10000 0 -0.46 4 4
SMPD3 0.018 0.071 -10000 0 -0.3 8 8
TNF 0.033 0.005 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.003 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.038 0.095 0.22 33 -0.15 2 35
NF kappa B1/RelA/I kappa B alpha 0.069 0.028 -10000 0 -10000 0 0
AIFM1 0.08 0.082 0.16 48 -0.29 1 49
BCL2 -0.19 0.25 -10000 0 -0.5 87 87
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.01 -9999 0 -10000 0 0
VLDLR -0.078 0.22 -9999 0 -0.5 45 45
LRPAP1 0.032 0.006 -9999 0 -10000 0 0
NUDC 0.031 0.01 -9999 0 -10000 0 0
RELN/LRP8 -0.15 0.085 -9999 0 -0.22 2 2
CaM/Ca2+ 0.022 0.008 -9999 0 -10000 0 0
KATNA1 0.032 0.007 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.13 0.072 -9999 0 -10000 0 0
IQGAP1/CaM 0.042 0.018 -9999 0 -10000 0 0
DAB1 0.033 0.006 -9999 0 -10000 0 0
IQGAP1 0.031 0.009 -9999 0 -10000 0 0
PLA2G7 0.001 0.13 -9999 0 -0.5 13 13
CALM1 0.03 0.01 -9999 0 -10000 0 0
DYNLT1 0.032 0.007 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.19 0.087 -9999 0 -0.22 190 190
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.033 0.003 -9999 0 -10000 0 0
CDK5R1 0.032 0.007 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.007 -9999 0 -10000 0 0
CDK5R2 0.033 0.002 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.012 0.15 -9999 0 -0.31 40 40
YWHAE 0.027 0.014 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.097 0.083 -9999 0 -10000 0 0
MAP1B -0.008 0.064 -9999 0 -0.28 11 11
RAC1 0.013 0.01 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.07 -9999 0 -0.28 2 2
RELN 0.032 0.008 -9999 0 -10000 0 0
PAFAH/LIS1 0.01 0.074 -9999 0 -0.3 11 11
LIS1/CLIP170 0.027 0.018 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.077 0.066 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.028 0.13 -9999 0 -0.34 11 11
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.1 0.081 -9999 0 -10000 0 0
LIS1/IQGAP1 0.026 0.019 -9999 0 -10000 0 0
RHOA 0.014 0.01 -9999 0 -10000 0 0
PAFAH1B1 0.013 0.009 -9999 0 -10000 0 0
PAFAH1B3 -0.004 0.11 -9999 0 -0.32 22 22
PAFAH1B2 0.033 0.005 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.009 0.057 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.098 0.082 -9999 0 -10000 0 0
LRP8 -0.28 0.12 -9999 0 -0.33 190 190
NDEL1/Katanin 60 -0.1 0.081 -9999 0 -10000 0 0
P39/CDK5 -0.12 0.068 -9999 0 -0.28 2 2
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.019 -9999 0 -10000 0 0
CDK5 -0.13 0.064 -9999 0 -0.3 2 2
PPP2R5D 0.033 0.006 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.016 -9999 0 -10000 0 0
CSNK2A1 0.027 0.014 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.002 0.13 -9999 0 -0.27 30 30
RELN/VLDLR -0.19 0.14 -9999 0 -0.39 47 47
CDC42 0.013 0.01 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.066 0.13 -10000 0 -0.22 90 90
CRKL 0.019 0.099 0.32 4 -0.43 5 9
mol:PIP3 0.003 0.051 0.44 2 -10000 0 2
AKT1 0.001 0.042 0.3 2 -10000 0 2
PTK2B 0.026 0.014 -10000 0 -10000 0 0
RAPGEF1 0.02 0.098 0.31 5 -0.44 4 9
RANBP10 0.033 0.005 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.044 0.12 -10000 0 -0.23 1 1
MAP3K5 0.03 0.1 0.4 4 -0.48 3 7
HGF/MET/CIN85/CBL/ENDOPHILINS -0.032 0.13 -10000 0 -0.39 4 4
AP1 -0.048 0.13 -10000 0 -0.33 27 27
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
apoptosis -0.13 0.31 -10000 0 -0.74 42 42
STAT3 (dimer) 0.003 0.053 0.22 1 -10000 0 1
GAB1/CRKL/SHP2/PI3K 0.055 0.1 0.32 3 -0.47 2 5
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.034 0.095 0.32 2 -0.47 3 5
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.017 0.029 -10000 0 -0.32 1 1
PTEN 0.026 0.052 -10000 0 -0.5 2 2
ELK1 -0.038 0.13 0.4 10 -10000 0 10
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.005 0.042 -10000 0 -0.22 1 1
PAK1 0.001 0.039 0.28 1 -10000 0 1
HGF/MET/RANBP10 -0.044 0.12 -10000 0 -0.23 1 1
HRAS 0.008 0.076 -10000 0 -0.45 3 3
DOCK1 0.017 0.096 0.31 4 -0.47 3 7
GAB1 0.006 0.087 -10000 0 -0.46 5 5
CRK 0.016 0.094 0.32 3 -0.43 5 8
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.066 -10000 0 -0.47 1 1
JUN 0.025 0.054 -10000 0 -0.32 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.046 0.058 -10000 0 -0.21 1 1
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.052 0.11 0.42 6 -10000 0 6
GRB2/SHC -0.022 0.076 -10000 0 -10000 0 0
FOS -0.027 0.16 -10000 0 -0.49 24 24
GLMN 0.001 0.015 -10000 0 -0.16 1 1
cell motility -0.038 0.13 0.39 10 -10000 0 10
HGF/MET/MUC20 -0.055 0.11 -10000 0 -0.18 92 92
cell migration -0.022 0.074 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
CBL 0.033 0.006 -10000 0 -10000 0 0
MET/RANBP10 -0.066 0.13 -10000 0 -0.22 90 90
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.016 0.066 -10000 0 -0.27 2 2
MET/MUC20 -0.079 0.12 -10000 0 -0.22 90 90
RAP1B 0.022 0.098 0.32 6 -0.42 4 10
RAP1A 0.02 0.094 0.3 5 -0.42 4 9
HGF/MET/RANBP9 -0.044 0.12 -10000 0 -0.23 1 1
RAF1 0.008 0.075 0.32 1 -0.42 3 4
STAT3 0.003 0.054 0.22 1 -10000 0 1
cell proliferation 0.023 0.074 0.3 2 -10000 0 2
RPS6KB1 -0.019 0.058 -10000 0 -0.34 4 4
MAPK3 -0.052 0.14 0.59 6 -10000 0 6
MAPK1 -0.023 0.19 0.61 15 -10000 0 15
RANBP9 0.033 0.005 -10000 0 -10000 0 0
MAPK8 0.036 0.11 0.4 4 -0.45 3 7
SRC 0.008 0.06 -10000 0 -10000 0 0
PI3K -0.023 0.076 -10000 0 -10000 0 0
MET/Glomulin -0.093 0.11 -10000 0 -0.22 92 92
SOS1 0.033 0.002 -10000 0 -10000 0 0
MAP2K1 0.011 0.076 0.34 2 -0.42 2 4
MET -0.12 0.18 -10000 0 -0.33 90 90
MAP4K1 0.032 0.1 0.32 4 -0.52 3 7
PTK2 0.027 0.013 -10000 0 -10000 0 0
MAP2K2 0.012 0.078 0.34 2 -0.42 2 4
BAD 0.001 0.039 0.28 1 -10000 0 1
MAP2K4 0.022 0.095 0.38 4 -0.44 3 7
SHP2/GRB2/SOS1/GAB1 0.033 0.095 -10000 0 -0.44 3 3
INPPL1 0.033 0.004 -10000 0 -10000 0 0
PXN 0.033 0.003 -10000 0 -10000 0 0
SH3KBP1 0.023 0.072 -10000 0 -0.5 4 4
HGS -0.042 0.053 -10000 0 -0.2 1 1
PLCgamma1/PKC 0.013 0.02 -10000 0 -0.22 1 1
HGF 0.029 0.035 -10000 0 -0.32 2 2
RASA1 0.03 0.035 -10000 0 -0.32 2 2
NCK1 0.033 0.004 -10000 0 -10000 0 0
PTPRJ 0.033 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.003 0.054 -10000 0 -10000 0 0
PDPK1 0.002 0.047 0.35 2 -10000 0 2
HGF/MET/SHIP -0.055 0.11 -10000 0 -0.18 92 92
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.018 0.059 -10000 0 -10000 0 0
VDR 0.018 0.088 -10000 0 -0.5 6 6
FAM120B 0.032 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.057 0.028 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.064 0.037 -10000 0 -0.37 1 1
MED1 0.032 0.008 -10000 0 -10000 0 0
mol:9cRA 0.006 0.004 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.024 0.067 -10000 0 -0.45 1 1
RXRs/NUR77 0.09 0.037 -10000 0 -10000 0 0
RXRs/PPAR 0.035 0.049 -10000 0 -10000 0 0
NCOR2 0.033 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.064 -10000 0 -0.36 6 6
RARs/VDR/DNA/Vit D3 0.061 0.064 -10000 0 -0.26 6 6
RARA 0.032 0.008 -10000 0 -10000 0 0
NCOA1 0.029 0.051 -10000 0 -0.5 2 2
VDR/VDR/DNA 0.018 0.088 -10000 0 -0.5 6 6
RARs/RARs/DNA/9cRA 0.055 0.027 -10000 0 -10000 0 0
RARG 0.03 0.035 -10000 0 -0.32 2 2
RPS6KB1 0.024 0.085 0.53 6 -10000 0 6
RARs/THRs/DNA/SMRT 0.026 0.059 -10000 0 -10000 0 0
THRA 0.032 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.064 -10000 0 -0.36 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.077 0.026 -10000 0 -10000 0 0
NR1H4 -0.43 0.19 -10000 0 -0.5 185 185
RXRs/LXRs/DNA 0.12 0.042 -10000 0 -10000 0 0
NR1H2 0.038 0.008 -10000 0 -10000 0 0
NR1H3 0.039 0.009 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.076 0.062 -10000 0 -0.26 5 5
NR4A1 0.03 0.035 -10000 0 -0.32 2 2
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.18 0.096 -10000 0 -0.32 9 9
RXRG 0.038 0.008 -10000 0 -10000 0 0
RXR alpha/CCPG 0.05 0.014 -10000 0 -10000 0 0
RXRA 0.038 0.008 -10000 0 -10000 0 0
RXRB 0.038 0.01 -10000 0 -10000 0 0
THRB 0.006 0.12 -10000 0 -0.5 11 11
PPARG 0.018 0.088 -10000 0 -0.5 6 6
PPARD 0.033 0.004 -10000 0 -10000 0 0
TNF 0.056 0.035 -10000 0 -10000 0 0
mol:Oxysterols 0.006 0.004 -10000 0 -10000 0 0
cholesterol transport 0.064 0.037 -10000 0 -0.37 1 1
PPARA 0.029 0.037 -10000 0 -0.5 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.033 0.005 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.11 0.11 -10000 0 -0.23 83 83
SREBF1 0.045 0.042 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.077 0.026 -10000 0 -10000 0 0
ABCA1 0.052 0.08 -10000 0 -1.1 1 1
RARs/THRs 0.072 0.084 -10000 0 -0.27 10 10
RXRs/FXR -0.22 0.13 -10000 0 -0.27 174 174
BCL2 -0.19 0.25 -10000 0 -0.5 87 87
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.045 0.017 -10000 0 -10000 0 0
HSPA8 0.029 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.01 0.096 -10000 0 -0.36 6 6
AKT1 -0.053 0.056 -10000 0 -10000 0 0
GSC -0.048 0.14 -10000 0 -0.65 2 2
NKX2-5 -0.009 0.026 -10000 0 -10000 0 0
muscle cell differentiation 0.12 0.18 0.59 15 -10000 0 15
SMAD2-3/SMAD4/SP1 -0.099 0.12 -10000 0 -0.41 3 3
SMAD4 -0.024 0.062 -10000 0 -0.53 1 1
CBFB 0.028 0.042 -10000 0 -0.32 3 3
SAP18 0.024 0.014 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.052 0.091 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.053 0.093 -10000 0 -10000 0 0
MYC -0.061 0.14 -10000 0 -0.23 52 52
CDKN2B -1.1 0.62 -10000 0 -1.4 169 169
AP1 -0.027 0.11 -10000 0 -0.37 7 7
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.042 0.14 -10000 0 -0.4 17 17
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.31 0.22 -10000 0 -0.46 117 117
SP3 0.035 0.002 -10000 0 -10000 0 0
CREB1 0.034 0 -10000 0 -10000 0 0
FOXH1 0.015 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.048 0.13 -10000 0 -0.37 25 25
GATA3 0.03 0.032 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.017 0.076 -10000 0 -0.46 2 2
MEF2C/TIF2 -0.069 0.19 0.28 1 -0.51 29 30
endothelial cell migration -0.026 0.1 -10000 0 -10000 0 0
MAX 0.032 0.012 -10000 0 -10000 0 0
RBBP7 0.032 0.005 -10000 0 -10000 0 0
RBBP4 0.031 0.007 -10000 0 -10000 0 0
RUNX2 0.033 0.005 -10000 0 -10000 0 0
RUNX3 0.002 0.12 -10000 0 -0.45 13 13
RUNX1 -0.077 0.17 -10000 0 -0.33 65 65
CTBP1 0.032 0.006 -10000 0 -10000 0 0
NR3C1 -0.025 0.17 -10000 0 -0.5 24 24
VDR 0.018 0.088 -10000 0 -0.5 6 6
CDKN1A -0.068 0.18 -10000 0 -1.3 4 4
KAT2B 0.004 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.043 0.084 -10000 0 -0.29 1 1
DCP1A 0.033 0.005 -10000 0 -10000 0 0
SKI 0.03 0.008 -10000 0 -10000 0 0
SERPINE1 0.026 0.1 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.014 0.069 -10000 0 -0.32 1 1
SMAD3/SMAD4/ATF3 -0.017 0.075 -10000 0 -0.31 3 3
SAP30 0.031 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.091 0.051 -10000 0 -10000 0 0
JUN -0.041 0.1 -10000 0 -0.37 7 7
SMAD3/SMAD4/IRF7 -0.004 0.068 -10000 0 -0.32 1 1
TFE3 0.036 0.008 -10000 0 -10000 0 0
COL1A2 -0.033 0.11 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.012 0.067 0.32 1 -10000 0 1
DLX1 0.03 0.034 -10000 0 -0.32 2 2
TCF3 0.032 0.006 -10000 0 -10000 0 0
FOS -0.032 0.17 -10000 0 -0.5 24 24
SMAD3/SMAD4/Max -0.01 0.073 -10000 0 -0.32 1 1
Cbp/p300/SNIP1 0.071 0.027 -10000 0 -10000 0 0
ZBTB17 0.073 0.034 -10000 0 -10000 0 0
LAMC1 -0.018 0.051 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.007 0.061 -10000 0 -10000 0 0
IRF7 0.036 0.004 -10000 0 -10000 0 0
ESR1 0.021 0.081 -10000 0 -0.5 5 5
HNF4A 0.018 0.017 -10000 0 -10000 0 0
MEF2C -0.079 0.2 -10000 0 -0.51 33 33
SMAD2-3/SMAD4 -0.072 0.098 -10000 0 -0.34 3 3
Cbp/p300/Src-1 0.078 0.049 -10000 0 -0.3 2 2
IGHV3OR16-13 -0.008 0.028 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.007 0.063 -10000 0 -0.32 7 7
CREBBP 0.042 0.012 -10000 0 -10000 0 0
SKIL 0.025 0.054 -10000 0 -0.32 5 5
HDAC1 0.031 0.007 -10000 0 -10000 0 0
HDAC2 0.031 0.007 -10000 0 -10000 0 0
SNIP1 0.03 0.006 -10000 0 -10000 0 0
GCN5L2 0.012 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.005 0.067 -10000 0 -0.31 1 1
MSG1/HSC70 0.009 0.089 -10000 0 -0.22 27 27
SMAD2 -0.042 0.06 -10000 0 -0.23 1 1
SMAD3 -0.024 0.045 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.021 0.078 0.27 1 -0.32 2 3
SMAD2/SMAD2/SMAD4 -0.064 0.08 -10000 0 -0.22 19 19
NCOR1 0.025 0.013 -10000 0 -10000 0 0
NCOA2 0.029 0.012 -10000 0 -10000 0 0
NCOA1 0.029 0.051 -10000 0 -0.5 2 2
MYOD/E2A 0.044 0.033 -10000 0 -0.22 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 -0.098 0.12 -10000 0 -0.37 4 4
IFNB1 -0.018 0.047 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.091 0.2 -10000 0 -0.52 32 32
CITED1 -0.012 0.12 -10000 0 -0.32 27 27
SMAD2-3/SMAD4/ARC105 -0.056 0.095 -10000 0 -0.32 2 2
RBL1 0.007 0.063 -10000 0 -0.32 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.39 0.28 -10000 0 -0.57 137 137
RUNX1-3/PEBPB2 -0.035 0.13 -10000 0 -0.3 14 14
SMAD7 -0.087 0.17 -10000 0 -0.56 9 9
MYC/MIZ-1 0.091 0.12 -10000 0 -0.23 14 14
SMAD3/SMAD4 0.055 0.11 0.33 1 -0.36 1 2
IL10 -0.018 0.06 -10000 0 -10000 0 0
PIASy/HDAC complex 0.003 0.026 -10000 0 -10000 0 0
PIAS3 0.035 0.026 -10000 0 -0.33 1 1
CDK2 0.004 0.11 -10000 0 -0.32 23 23
IL5 -0.03 0.092 -10000 0 -0.35 1 1
CDK4 0.018 0.094 -10000 0 -0.31 16 16
PIAS4 0.003 0.026 -10000 0 -10000 0 0
ATF3 0.026 0.049 -10000 0 -0.32 4 4
SMAD3/SMAD4/SP1 -0.049 0.088 -10000 0 -0.36 3 3
FOXG1 -0.015 0.12 -10000 0 -0.33 27 27
FOXO3 -0.071 0.064 -10000 0 -10000 0 0
FOXO1 -0.06 0.088 -10000 0 -0.45 6 6
FOXO4 -0.07 0.062 -10000 0 -10000 0 0
heart looping -0.078 0.2 -10000 0 -0.5 33 33
CEBPB -0.02 0.053 -10000 0 -0.38 3 3
SMAD3/SMAD4/DLX1 -0.016 0.072 -10000 0 -0.3 2 2
MYOD1 0.028 0.042 -10000 0 -0.32 3 3
SMAD3/SMAD4/HNF4 0 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 -0.004 0.08 -10000 0 -0.31 1 1
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.054 -10000 0 -0.32 5 5
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.057 0.13 -10000 0 -0.35 8 8
SMAD3/SMAD4/SP1-3 -0.032 0.086 -10000 0 -0.32 2 2
MED15 0.031 0.009 -10000 0 -10000 0 0
SP1 -0.025 0.04 -10000 0 -10000 0 0
SIN3B 0.032 0.005 -10000 0 -10000 0 0
SIN3A 0.03 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.052 0.11 -10000 0 -0.32 23 23
ITGB5 -0.043 0.062 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.02 0.073 -10000 0 -0.49 2 2
SMAD3/SMAD4/AR -0.015 0.07 -10000 0 -0.3 2 2
AR 0.032 0.024 -10000 0 -0.32 1 1
negative regulation of cell growth -0.037 0.097 -10000 0 -0.38 5 5
SMAD3/SMAD4/MYOD -0.016 0.072 -10000 0 -0.3 2 2
E2F5 -0.081 0.16 -10000 0 -0.32 66 66
E2F4 0.031 0.025 -10000 0 -0.32 1 1
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.01 0.085 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.32 0.24 -10000 0 -0.47 138 138
TFDP1 0.018 0.049 -10000 0 -0.32 4 4
SMAD3/SMAD4/AP1 -0.021 0.12 -10000 0 -0.37 7 7
SMAD3/SMAD4/RUNX2 -0.012 0.068 -10000 0 -0.32 1 1
TGIF2 0.007 0.063 -10000 0 -0.32 7 7
TGIF1 -0.012 0.11 -10000 0 -0.33 23 23
ATF2 0.033 0.002 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.003 0.071 -10000 0 -0.33 9 9
GNB1/GNG2 -0.051 0.049 -10000 0 -0.19 7 7
AKT1 -0.023 0.1 0.23 4 -0.31 7 11
EGF -0.091 0.21 -10000 0 -0.43 58 58
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.12 0.085 -10000 0 -0.27 1 1
mol:Ca2+ -0.025 0.11 0.31 1 -0.32 6 7
LYN -0.1 0.091 -10000 0 -0.26 3 3
RhoA/GTP -0.007 0.046 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.027 0.11 0.31 2 -0.36 5 7
GNG2 0.03 0.01 -10000 0 -10000 0 0
ARRB2 0.027 0.013 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.059 0.14 -10000 0 -0.54 12 12
G beta5/gamma2 -0.063 0.065 -10000 0 -0.25 7 7
PRKCH -0.033 0.12 0.3 1 -0.42 5 6
DNM1 0.03 0.035 -10000 0 -0.32 2 2
TXA2/TP beta/beta Arrestin3 -0.011 0.052 -10000 0 -0.68 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.35 0.24 -10000 0 -0.5 154 154
G12 family/GTP -0.028 0.093 -10000 0 -0.32 5 5
ADRBK1 0.033 0.005 -10000 0 -10000 0 0
ADRBK2 0.032 0.007 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.035 0.019 -10000 0 -10000 0 0
mol:GDP 0.067 0.095 0.33 10 -10000 0 10
mol:NADP 0.031 0.025 -10000 0 -0.32 1 1
RAB11A 0.032 0.008 -10000 0 -10000 0 0
PRKG1 0.03 0.01 -10000 0 -10000 0 0
mol:IP3 -0.035 0.13 0.33 1 -0.39 8 9
cell morphogenesis 0.034 0.019 -10000 0 -10000 0 0
PLCB2 -0.05 0.16 -10000 0 -0.54 8 8
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.16 0.12 -10000 0 -0.36 39 39
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.075 0.099 -10000 0 -0.34 6 6
RHOA 0.033 0.005 -10000 0 -10000 0 0
PTGIR 0.033 0.006 -10000 0 -10000 0 0
PRKCB1 -0.03 0.12 0.32 1 -0.39 6 7
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.031 0.025 -10000 0 -0.32 1 1
TXA2/TXA2-R family -0.045 0.15 -10000 0 -0.56 5 5
LCK -0.12 0.086 -10000 0 -0.27 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.15 0.11 -10000 0 -0.3 4 4
TXA2-R family/G12 family/GDP/G beta/gamma -0.045 0.13 -10000 0 -0.53 12 12
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.15 0.1 -10000 0 -0.3 4 4
MAPK14 -0.015 0.086 0.28 4 -0.25 3 7
TGM2/GTP -0.041 0.13 0.4 1 -0.47 3 4
MAPK11 -0.017 0.082 0.26 2 -0.25 4 6
ARHGEF1 -0.01 0.067 0.3 1 -0.2 3 4
GNAI2 0.033 0.004 -10000 0 -10000 0 0
JNK cascade -0.032 0.12 0.31 1 -0.41 5 6
RAB11/GDP 0.032 0.008 -10000 0 -10000 0 0
ICAM1 -0.017 0.098 0.27 1 -0.29 5 6
cAMP biosynthetic process -0.035 0.12 0.32 1 -0.38 5 6
Gq family/GTP/EBP50 0 0.068 -10000 0 -0.22 17 17
actin cytoskeleton reorganization 0.034 0.019 -10000 0 -10000 0 0
SRC -0.067 0.09 -10000 0 -0.26 2 2
GNB5 0.026 0.043 -10000 0 -0.32 3 3
GNB1 0.032 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.096 0.11 0.24 3 -0.3 22 25
VCAM1 -0.018 0.1 0.28 1 -0.41 5 6
TP beta/Gq family/GDP/G beta5/gamma2 -0.059 0.14 -10000 0 -0.54 12 12
platelet activation -0.024 0.11 0.32 4 -0.33 3 7
PGI2/IP 0.024 0.004 -10000 0 -10000 0 0
PRKACA -0.18 0.12 -10000 0 -0.25 148 148
Gq family/GDP/G beta5/gamma2 -0.071 0.13 -10000 0 -0.51 13 13
TXA2/TP beta/beta Arrestin2 -0.036 0.068 -10000 0 -0.43 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.17 0.1 -10000 0 -0.24 146 146
mol:DAG -0.037 0.14 0.34 1 -0.44 7 8
EGFR 0.021 0.072 -10000 0 -0.5 4 4
TXA2/TP alpha -0.048 0.16 0.37 1 -0.52 5 6
Gq family/GTP -0.003 0.071 0.22 2 -0.22 18 20
YES1 -0.12 0.088 -10000 0 -0.26 3 3
GNAI2/GTP -0.13 0.095 -10000 0 -0.29 3 3
PGD2/DP -0.26 0.16 -10000 0 -0.36 154 154
SLC9A3R1 0.025 0.063 -10000 0 -0.5 3 3
FYN -0.12 0.088 -10000 0 -0.31 3 3
mol:NO 0.031 0.025 -10000 0 -0.32 1 1
GNA15 0.021 0.064 -10000 0 -0.32 7 7
PGK/cGMP 0.038 0.022 -10000 0 -10000 0 0
RhoA/GDP 0.034 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.097 0.11 -10000 0 -0.34 5 5
NOS3 0.031 0.025 -10000 0 -0.33 1 1
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCA -0.026 0.12 0.3 1 -0.36 6 7
PRKCB -0.029 0.11 0.28 1 -0.37 6 7
PRKCE -0.028 0.12 0.28 1 -0.38 5 6
PRKCD -0.029 0.12 0.31 1 -0.4 5 6
PRKCG -0.03 0.13 0.32 1 -0.4 6 7
muscle contraction -0.039 0.15 0.35 1 -0.5 6 7
PRKCZ -0.028 0.11 0.29 1 -0.36 5 6
ARR3 0.033 0.002 -10000 0 -10000 0 0
TXA2/TP beta -0.14 0.11 -10000 0 -0.32 3 3
PRKCQ -0.03 0.12 0.33 2 -0.37 6 8
MAPKKK cascade -0.042 0.14 0.33 1 -0.47 7 8
SELE -0.027 0.11 0.28 1 -0.31 7 8
TP beta/GNAI2/GDP/G beta/gamma -0.14 0.12 -10000 0 -0.31 4 4
ROCK1 0.026 0.014 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.5 9 9
chemotaxis -0.041 0.16 -10000 0 -0.63 5 5
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
GNA11 0.018 0.088 -10000 0 -0.5 6 6
Rac1/GTP 0.022 0.007 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.03 -10000 0 -0.36 1 1
Necdin/E2F1 -0.039 0.14 -10000 0 -0.35 30 30
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.055 0.056 -10000 0 -0.26 4 4
NGF (dimer)/p75(NTR)/BEX1 0.04 0.035 -10000 0 -0.31 2 2
NT-4/5 (dimer)/p75(NTR) 0.024 0.005 -10000 0 -10000 0 0
IKBKB 0.029 0.011 -10000 0 -10000 0 0
AKT1 0.023 0.029 -10000 0 -10000 0 0
IKBKG 0.033 0.006 -10000 0 -10000 0 0
BDNF 0.007 0.094 -10000 0 -0.32 16 16
MGDIs/NGR/p75(NTR)/LINGO1 0.043 0.066 -10000 0 -0.35 1 1
FURIN 0.031 0.009 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.042 0.072 -10000 0 -0.31 1 1
LINGO1 0.025 0.049 -10000 0 -0.32 4 4
Sortilin/TRAF6/NRIF 0.028 0.055 -10000 0 -10000 0 0
proBDNF (dimer) 0.007 0.094 -10000 0 -0.32 16 16
NTRK1 0.033 0.006 -10000 0 -10000 0 0
RTN4R 0.015 0.075 -10000 0 -0.32 10 10
neuron apoptosis 0.014 0.087 -10000 0 -0.43 1 1
IRAK1 0.029 0.035 -10000 0 -0.32 2 2
SHC1 0.019 0.005 -10000 0 -10000 0 0
ARHGDIA 0.033 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.024 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.07 0.071 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.041 0.077 -10000 0 -0.28 11 11
MAGEH1 0.008 0.11 -10000 0 -0.5 10 10
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.01 0.14 -10000 0 -0.29 40 40
Mammalian IAPs/DIABLO 0.046 0.071 -10000 0 -0.28 8 8
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.031 0.025 -10000 0 -0.32 1 1
APP 0.031 0.009 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.045 0.011 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.003 0.042 0.21 6 -0.28 1 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.025 0.043 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.043 0.01 -10000 0 -10000 0 0
NCSTN 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.049 0.15 -10000 0 -0.31 55 55
PSENEN 0.032 0.007 -10000 0 -10000 0 0
mol:ceramide 0.023 0.035 -10000 0 -0.28 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.022 0.039 -10000 0 -10000 0 0
p75(NTR)/beta APP 0.045 0.015 -10000 0 -10000 0 0
BEX1 0.028 0.051 -10000 0 -0.5 2 2
mol:GDP 0.004 0.001 -10000 0 -10000 0 0
NGF (dimer) -0.16 0.048 -10000 0 -0.2 6 6
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.059 0.068 -10000 0 -0.32 1 1
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.035 0.013 -10000 0 -10000 0 0
MYD88 0.033 0.004 -10000 0 -10000 0 0
CHUK 0.032 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.049 0.15 -10000 0 -0.31 55 55
RHOB 0.012 0.085 -10000 0 -0.32 13 13
RHOA 0.033 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.02 0.047 -10000 0 -0.22 6 6
NT3 (dimer) 0.029 0.035 -10000 0 -0.32 2 2
TP53 0.001 0.057 -10000 0 -10000 0 0
PRDM4 0.024 0.035 -10000 0 -0.28 1 1
BDNF (dimer) -0.32 0.069 -10000 0 -0.34 193 193
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
SORT1 0.03 0.037 -10000 0 -0.5 1 1
activation of caspase activity 0.049 0.053 -10000 0 -0.26 4 4
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.058 0.029 -10000 0 -0.28 1 1
RHOC 0.032 0.007 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.021 0.077 0.31 5 -10000 0 5
DIABLO 0.033 0.003 -10000 0 -10000 0 0
SMPD2 0.023 0.035 -10000 0 -0.28 1 1
APH1B 0.03 0.026 -10000 0 -0.32 1 1
APH1A 0.016 0.091 -10000 0 -0.48 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.04 0.027 -10000 0 -0.31 1 1
PSEN1 0.031 0.01 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.044 0.028 -10000 0 -0.21 2 2
NT3 (dimer)/p75(NTR) 0.043 0.029 -10000 0 -0.22 2 2
MAPK8 0.024 0.073 0.31 5 -10000 0 5
MAPK9 0.023 0.072 0.33 4 -10000 0 4
APAF1 0.03 0.034 -10000 0 -0.32 2 2
NTF3 0.029 0.035 -10000 0 -0.32 2 2
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.07 0.21 -10000 0 -0.5 41 41
RAC1/GDP 0.023 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.025 0.14 -10000 0 -0.26 51 51
p75 CTF/Sortilin/TRAF6/NRIF 0.079 0.033 -10000 0 -0.28 1 1
RhoA-B-C/GTP -0.05 0.15 -10000 0 -0.31 55 55
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.069 0.075 -10000 0 -0.27 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.059 0.072 -10000 0 -0.28 1 1
PRKACB -0.1 0.23 -10000 0 -0.5 55 55
proBDNF (dimer)/p75 ECD 0.029 0.072 -10000 0 -0.22 16 16
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.008 0.11 -10000 0 -0.45 11 11
BIRC2 0.033 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.092 0.14 -10000 0 -0.39 25 25
BAD 0.018 0.079 0.37 3 -10000 0 3
RIPK2 -0.013 0.11 -10000 0 -0.32 25 25
NGFR 0.032 0.007 -10000 0 -10000 0 0
CYCS 0.018 0.04 -10000 0 -0.26 2 2
ADAM17 0.033 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.025 0.074 -10000 0 -10000 0 0
BCL2L11 0.018 0.079 0.37 3 -10000 0 3
BDNF (dimer)/p75(NTR) 0.027 0.072 -10000 0 -0.22 16 16
PI3K 0.059 0.018 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.053 0.035 -10000 0 -0.28 1 1
NDNL2 0.03 0.026 -10000 0 -0.32 1 1
YWHAE 0.027 0.014 -10000 0 -10000 0 0
PRKCI 0.025 0.054 -10000 0 -0.32 5 5
NGF (dimer)/p75(NTR) 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.056 0.033 -10000 0 -0.28 1 1
TRAF6 0.033 0.003 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.032 0.007 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.014 0.047 -10000 0 -0.3 1 1
SQSTM1 0.033 0.004 -10000 0 -10000 0 0
NGFRAP1 0.024 0.072 -10000 0 -0.5 4 4
CASP3 0.017 0.077 0.36 3 -10000 0 3
E2F1 0.011 0.054 -10000 0 -0.32 5 5
CASP9 0.031 0.009 -10000 0 -10000 0 0
IKK complex 0.047 0.05 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0.024 0.004 -10000 0 -10000 0 0
MMP7 -0.32 0.064 -10000 0 -0.33 209 209
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.034 -10000 0 -0.26 1 1
MMP3 -0.3 0.091 -10000 0 -0.33 201 201
APAF-1/Caspase 9 0.005 0.053 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.011 0.14 0.28 5 -0.48 11 16
FYN -0.037 0.17 -10000 0 -0.62 12 12
LAT/GRAP2/SLP76 0.003 0.14 -10000 0 -0.5 10 10
IKBKB 0.029 0.011 -10000 0 -10000 0 0
AKT1 -0.023 0.13 0.27 2 -0.4 16 18
B2M 0.011 0.1 -10000 0 -0.51 8 8
IKBKG 0 0.044 0.093 4 -0.14 4 8
MAP3K8 -0.015 0.12 -10000 0 -0.32 29 29
mol:Ca2+ -0.009 0.019 0.09 3 -0.087 3 6
integrin-mediated signaling pathway 0.042 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.035 0.18 0.25 2 -0.52 20 22
TRPV6 0.037 0.22 1.2 8 -10000 0 8
CD28 -0.033 0.18 -10000 0 -0.5 27 27
SHC1 -0.021 0.17 0.29 5 -0.55 14 19
receptor internalization -0.024 0.19 -10000 0 -0.57 18 18
PRF1 -0.019 0.2 -10000 0 -0.79 9 9
KRAS 0.033 0.006 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
COT/AKT1 -0.02 0.12 0.26 2 -0.32 17 19
LAT -0.023 0.16 0.28 1 -0.55 13 14
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.011 0.11 -10000 0 -0.51 9 9
CD3E 0.033 0.006 -10000 0 -10000 0 0
CD3G 0.009 0.11 -10000 0 -0.49 10 10
RASGRP2 0.004 0.036 -10000 0 -0.16 8 8
RASGRP1 0.004 0.14 0.32 2 -0.39 14 16
HLA-A 0 0.003 -10000 0 -10000 0 0
RASSF5 0.033 0.005 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.042 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.025 0.065 0.24 5 -0.12 8 13
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.019 0.059 -10000 0 -0.22 9 9
PRKCA 0.024 0.099 0.16 12 -0.26 10 22
GRAP2 0.031 0.009 -10000 0 -10000 0 0
mol:IP3 -0.024 0.11 -10000 0 -0.39 12 12
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.014 0.16 -10000 0 -0.55 13 13
ORAI1 -0.028 0.18 -10000 0 -1 7 7
CSK -0.027 0.16 -10000 0 -0.52 15 15
B7 family/CD28 -0.02 0.23 -10000 0 -0.61 20 20
CHUK 0.032 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.03 0.19 -10000 0 -0.57 17 17
PTPN6 -0.027 0.16 0.21 1 -0.54 15 16
VAV1 -0.043 0.19 0.25 1 -0.59 18 19
Monovalent TCR/CD3 -0.012 0.16 -10000 0 -0.49 17 17
CBL 0.033 0.006 -10000 0 -10000 0 0
LCK -0.035 0.18 -10000 0 -0.61 13 13
PAG1 -0.06 0.19 -10000 0 -0.51 17 17
RAP1A 0.032 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.031 0.19 -10000 0 -0.58 17 17
CD80 0.026 0.049 -10000 0 -0.33 4 4
CD86 0.006 0.12 -10000 0 -0.49 11 11
PDK1/CARD11/BCL10/MALT1 -0.014 0.075 -10000 0 -0.27 9 9
HRAS 0.033 0.004 -10000 0 -10000 0 0
GO:0035030 -0.044 0.17 -10000 0 -0.49 21 21
CD8A 0 0.003 -10000 0 -10000 0 0
CD8B 0.034 0.003 -10000 0 -10000 0 0
PTPRC 0.003 0.12 -10000 0 -0.51 12 12
PDK1/PKC theta -0.016 0.16 0.31 3 -0.49 14 17
CSK/PAG1 -0.056 0.18 -10000 0 -0.54 13 13
SOS1 0.033 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.008 0.075 -10000 0 -0.34 9 9
GRAP2/SLP76 0.001 0.17 -10000 0 -0.54 13 13
STIM1 -0.004 0.11 1.2 1 -0.94 1 2
RAS family/GTP 0.028 0.07 0.21 5 -0.18 2 7
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.027 0.2 -10000 0 -0.61 18 18
mol:DAG -0.032 0.092 -10000 0 -0.35 12 12
RAP1A/GDP 0.016 0.032 0.12 5 -10000 0 5
PLCG1 0.017 0.029 -10000 0 -0.32 1 1
CD247 0.006 0.12 -10000 0 -0.51 11 11
cytotoxic T cell degranulation -0.017 0.19 -10000 0 -0.75 9 9
RAP1A/GTP 0.002 0.014 -10000 0 -0.062 8 8
mol:PI-3-4-5-P3 -0.026 0.15 0.24 2 -0.44 19 21
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.026 0.14 -10000 0 -0.5 12 12
NRAS 0.029 0.035 -10000 0 -0.32 2 2
ZAP70 0.033 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.018 0.16 0.23 2 -0.5 15 17
MALT1 0.023 0.016 -10000 0 -10000 0 0
TRAF6 0.033 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.025 0.009 -10000 0 -10000 0 0
CARD11 0.006 0.091 -10000 0 -0.32 15 15
PRKCB -0.024 0.065 -10000 0 -0.24 12 12
PRKCE 0.025 0.1 0.16 12 -0.26 9 21
PRKCQ -0.021 0.17 0.29 2 -0.52 16 18
LCP2 0.026 0.055 -10000 0 -0.37 4 4
BCL10 0.033 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.018 0.12 0.26 2 -0.34 16 18
IKK complex 0.037 0.07 0.12 58 -0.12 2 60
RAS family/GDP -0.001 0.01 -10000 0 -0.054 1 1
MAP3K14 -0.017 0.092 0.22 2 -0.25 15 17
PDPK1 -0.018 0.12 0.26 3 -0.37 15 18
TCR/CD3/MHC I/CD8/Fyn -0.029 0.18 -10000 0 -0.6 14 14
Canonical Wnt signaling pathway

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
HDAC1 0.058 0.026 -10000 0 -10000 0 0
AES 0.055 0.021 -10000 0 -10000 0 0
FBXW11 0.033 0.004 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.045 0.022 -10000 0 -0.22 1 1
SMAD4 0.02 0.039 -10000 0 -0.5 1 1
DKK2 -0.11 0.18 -10000 0 -0.33 86 86
TLE1 0.054 0.019 -10000 0 -10000 0 0
MACF1 0.033 0.005 -10000 0 -10000 0 0
CTNNB1 0.06 0.084 0.41 4 -10000 0 4
WIF1 -0.02 0.13 -10000 0 -0.32 32 32
beta catenin/RanBP3 0.18 0.13 0.36 44 -10000 0 44
KREMEN2 -0.034 0.14 -10000 0 -0.32 40 40
DKK1 -0.058 0.16 -10000 0 -0.33 54 54
beta catenin/beta TrCP1 0.077 0.081 0.41 4 -10000 0 4
FZD1 0.032 0.007 -10000 0 -10000 0 0
AXIN2 -0.16 0.18 -10000 0 -1.6 1 1
AXIN1 0.033 0.007 -10000 0 -10000 0 0
RAN 0.033 0.025 -10000 0 -0.32 1 1
Axin1/APC/GSK3/beta catenin 0.048 0.074 -10000 0 -0.52 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.002 0.15 0.37 2 -0.6 4 6
Axin1/APC/GSK3 0.066 0.059 0.31 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.039 0.071 -10000 0 -0.36 1 1
HNF1A 0.055 0.02 -10000 0 -10000 0 0
CTBP1 0.054 0.022 -10000 0 -10000 0 0
MYC -0.064 0.24 0.61 7 -10000 0 7
RANBP3 0.034 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.074 0.15 -10000 0 -0.35 19 19
NKD1 -0.23 0.16 -10000 0 -0.33 160 160
TCF4 0.038 0.031 -10000 0 -10000 0 0
TCF3 0.054 0.022 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.078 0.032 -10000 0 -10000 0 0
Ran/GTP 0.026 0.017 -10000 0 -0.22 1 1
CtBP/CBP/TCF/TLE1/AES 0.14 0.15 0.45 15 -0.45 1 16
LEF1 -0.02 0.15 -10000 0 -0.3 46 46
DVL1 0.05 0.06 -10000 0 -0.48 1 1
CSNK2A1 0.027 0.014 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.009 0.084 -10000 0 -0.56 2 2
DKK1/LRP6/Kremen 2 -0.042 0.14 -10000 0 -0.34 13 13
LRP6 0.031 0.025 -10000 0 -0.32 1 1
CSNK1A1 0.061 0.024 -10000 0 -10000 0 0
NLK 0.028 0.008 -10000 0 -10000 0 0
CCND1 -0.093 0.11 -10000 0 -10000 0 0
WNT1 0.033 0.004 -10000 0 -10000 0 0
GSK3A 0.033 0.006 -10000 0 -10000 0 0
GSK3B 0.032 0.025 -10000 0 -0.33 1 1
FRAT1 0.029 0.037 -10000 0 -0.5 1 1
PPP2R5D 0.13 0.076 0.25 4 -10000 0 4
APC 0.027 0.09 0.56 3 -0.26 1 4
WNT1/LRP6/FZD1 0.047 0.046 0.32 1 -10000 0 1
CREBBP 0.054 0.022 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.082 -10000 0 -0.32 12 12
ANTXR2 0.025 0.063 -10000 0 -0.5 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.012 -10000 0 -0.044 15 15
monocyte activation 0.003 0.093 -10000 0 -0.34 14 14
MAP2K2 0.009 0.08 -10000 0 -0.57 4 4
MAP2K1 -0.004 0.011 -10000 0 -10000 0 0
MAP2K7 -0.004 0.011 -10000 0 -10000 0 0
MAP2K6 -0.015 0.054 -10000 0 -0.27 9 9
CYAA -0.014 0.045 -10000 0 -0.18 15 15
MAP2K4 -0.005 0.02 -10000 0 -0.26 1 1
IL1B -0.032 0.062 -10000 0 -0.16 38 38
Channel 0.026 0.06 -10000 0 -0.19 15 15
NLRP1 -0.004 0.015 -10000 0 -0.15 1 1
CALM1 0.03 0.01 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.028 0.12 -10000 0 -0.39 22 22
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.012 0.044 15 -10000 0 15
MAPK3 -0.006 0.028 0.13 1 -0.26 2 3
MAPK1 -0.004 0.011 -10000 0 -10000 0 0
PGR -0.004 0.011 -10000 0 -10000 0 0
PA/Cellular Receptors 0.026 0.066 -10000 0 -0.21 15 15
apoptosis -0.003 0.012 -10000 0 -0.044 15 15
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.055 -10000 0 -0.17 15 15
macrophage activation -0.001 0.041 0.18 6 -0.25 2 8
TNF 0.033 0.005 -10000 0 -10000 0 0
VCAM1 0.004 0.089 -10000 0 -0.34 13 13
platelet activation -0.028 0.12 -10000 0 -0.39 22 22
MAPKKK cascade 0.003 0.024 0.1 1 -0.13 1 2
IL18 -0.032 0.082 -10000 0 -0.26 24 24
negative regulation of macrophage activation -0.003 0.012 -10000 0 -0.044 15 15
LEF -0.003 0.012 -10000 0 -0.044 15 15
CASP1 -0.004 0.02 -10000 0 -0.078 11 11
mol:cAMP -0.028 0.12 -10000 0 -0.39 22 22
necrosis -0.003 0.012 -10000 0 -0.044 15 15
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.057 -10000 0 -0.18 15 15
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.025 0.12 -10000 0 -10000 0 0
HDAC1 0.038 0.012 -10000 0 -10000 0 0
AES 0.035 0.006 -10000 0 -10000 0 0
FBXW11 0.033 0.004 -10000 0 -10000 0 0
DTX1 0.033 0.003 -10000 0 -10000 0 0
LRP6/FZD1 0.045 0.022 -10000 0 -0.22 1 1
TLE1 0.035 0.005 -10000 0 -10000 0 0
AP1 -0.099 0.12 0.21 1 -0.31 45 46
NCSTN 0.033 0.006 -10000 0 -10000 0 0
ADAM10 0.032 0.009 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.11 -10000 0 -0.69 4 4
NICD/RBPSUH 0.022 0.12 -10000 0 -10000 0 0
WIF1 -0.02 0.13 -10000 0 -0.32 32 32
NOTCH1 0.001 0.12 -10000 0 -10000 0 0
PSENEN 0.032 0.007 -10000 0 -10000 0 0
KREMEN2 -0.034 0.14 -10000 0 -0.32 40 40
DKK1 -0.058 0.16 -10000 0 -0.33 54 54
beta catenin/beta TrCP1 0.075 0.07 0.33 2 -10000 0 2
APH1B 0.03 0.025 -10000 0 -0.32 1 1
APH1A 0.016 0.091 -10000 0 -0.48 7 7
AXIN1 -0.024 0.078 -10000 0 -0.41 4 4
CtBP/CBP/TCF1/TLE1/AES 0.058 0.04 -10000 0 -10000 0 0
PSEN1 0.031 0.009 -10000 0 -10000 0 0
FOS -0.027 0.16 -10000 0 -0.49 24 24
JUN 0.025 0.054 -10000 0 -0.32 5 5
MAP3K7 0.035 0.008 -10000 0 -10000 0 0
CTNNB1 0.06 0.072 0.3 3 -10000 0 3
MAPK3 0.028 0.052 -10000 0 -0.5 2 2
DKK2/LRP6/Kremen 2 -0.075 0.14 -10000 0 -0.35 19 19
HNF1A 0.035 0.004 -10000 0 -10000 0 0
CTBP1 0.034 0.007 -10000 0 -10000 0 0
MYC -0.11 0.12 -10000 0 -10000 0 0
NKD1 -0.23 0.16 -10000 0 -0.32 160 160
FZD1 0.032 0.007 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.023 0.12 -10000 0 -10000 0 0
apoptosis -0.097 0.12 0.2 2 -0.3 45 47
Delta 1/NOTCHprecursor 0.022 0.12 -10000 0 -10000 0 0
DLL1 0.032 0.006 -10000 0 -10000 0 0
PPARD 0.016 0.064 -10000 0 -0.86 1 1
Gamma Secretase 0.069 0.071 -10000 0 -0.27 1 1
APC -0.053 0.14 -10000 0 -0.46 18 18
DVL1 0.013 0.068 -10000 0 -0.59 2 2
CSNK2A1 0.026 0.013 -10000 0 -10000 0 0
MAP3K7IP1 0.003 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.043 0.14 -10000 0 -0.34 13 13
LRP6 0.031 0.025 -10000 0 -0.33 1 1
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
NLK 0.025 0.011 -10000 0 -10000 0 0
CCND1 -0.022 0.13 -10000 0 -0.8 3 3
WNT1 0.033 0.004 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.009 0.13 0.42 3 -0.43 6 9
DKK2 -0.11 0.18 -10000 0 -0.33 86 86
NOTCH1 precursor/DVL1 0.002 0.15 -10000 0 -0.52 9 9
GSK3B 0.032 0.025 -10000 0 -0.32 1 1
FRAT1 0.031 0.037 -10000 0 -0.5 1 1
NOTCH/Deltex homolog 1 0.027 0.12 -10000 0 -10000 0 0
PPP2R5D 0.12 0.072 0.27 1 -10000 0 1
MAPK1 0.031 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.044 0.088 -10000 0 -10000 0 0
RBPJ 0.033 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.008 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.006 0.03 0.13 3 -0.11 1 4
BUB1B -0.017 0.072 0.14 1 -0.21 7 8
PLK1 0.018 0.034 0.11 3 -10000 0 3
PLK1S1 0.007 0.018 0.056 4 -10000 0 4
KIF2A 0.014 0.03 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.018 0.034 0.11 3 -10000 0 3
GOLGA2 0.033 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.024 0.034 -10000 0 -0.17 2 2
WEE1 0.015 0.049 -10000 0 -0.32 1 1
cytokinesis 0.01 0.065 -10000 0 -0.28 2 2
PP2A-alpha B56 0.022 0.12 -10000 0 -0.59 6 6
AURKA 0.025 0.032 0.13 1 -10000 0 1
PICH/PLK1 -0.092 0.14 0.18 10 -0.29 53 63
CENPE 0.008 0.045 -10000 0 -0.17 7 7
RhoA/GTP 0.024 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.014 0.03 -10000 0 -10000 0 0
PPP2CA 0.033 0.004 -10000 0 -10000 0 0
FZR1 0.033 0.006 -10000 0 -10000 0 0
TPX2 0.041 0.053 0.12 36 -10000 0 36
PAK1 0.033 0.004 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.004 -10000 0 -10000 0 0
CLSPN 0.013 0.044 -10000 0 -0.22 6 6
GORASP1 0.033 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.019 5 -0.011 1 6
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.007 0.018 0.056 4 -10000 0 4
G2 phase of mitotic cell cycle 0.001 0.003 0.017 3 -10000 0 3
STAG2 0.023 0.059 -10000 0 -0.32 6 6
GRASP65/GM130/RAB1/GTP 0.008 0.07 -10000 0 -0.57 3 3
spindle elongation 0.018 0.034 0.11 3 -10000 0 3
ODF2 0.035 0.006 -10000 0 -10000 0 0
BUB1 -0.014 0.11 -10000 0 -0.64 6 6
TPT1 0.025 0.038 0.13 2 -0.19 2 4
CDC25C 0.015 0.041 -10000 0 -0.25 3 3
CDC25B -0.11 0.17 -10000 0 -0.32 80 80
SGOL1 0.006 0.03 0.11 1 -0.13 3 4
RHOA 0.033 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 -0.043 0.096 -10000 0 -0.22 21 21
CDC14B 0.01 0.003 -10000 0 -10000 0 0
CDC20 0.023 0.059 -10000 0 -0.32 6 6
PLK1/PBIP1 0 0.055 0.1 2 -0.15 18 20
mitosis -0.003 0.003 -10000 0 -10000 0 0
FBXO5 -0.001 0.049 0.22 2 -0.14 6 8
CDC2 -0.002 0.006 0.01 13 -0.011 27 40
NDC80 0.023 0.036 -10000 0 -0.32 2 2
metaphase plate congression 0.001 0.074 -10000 0 -0.23 19 19
ERCC6L -0.086 0.14 0.19 1 -0.29 42 43
NLP/gamma Tubulin 0.008 0.019 0.078 3 -10000 0 3
microtubule cytoskeleton organization 0.025 0.038 0.13 2 -0.19 2 4
G2/M transition DNA damage checkpoint 0 0.002 0.015 2 -10000 0 2
PPP1R12A 0.034 0.004 -10000 0 -10000 0 0
interphase 0 0.002 0.015 2 -10000 0 2
PLK1/PRC1-2 0.023 0.085 -10000 0 -0.29 3 3
GRASP65/GM130/RAB1/GTP/PLK1 0.065 0.032 -10000 0 -10000 0 0
RAB1A 0.034 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.023 0.035 0.078 25 -10000 0 25
mitotic prometaphase 0.001 0.005 0.018 19 -10000 0 19
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.046 -10000 0 -0.47 1 1
microtubule-based process 0.012 0.075 -10000 0 -0.18 22 22
Golgi organization 0.018 0.034 0.11 3 -10000 0 3
Cohesin/SA2 0.028 0.037 -10000 0 -0.15 1 1
PPP1CB/MYPT1 0.05 0.006 -10000 0 -10000 0 0
KIF20A -0.012 0.12 -10000 0 -0.33 27 27
APC/C/CDC20 0.029 0.049 -10000 0 -0.18 6 6
PPP2R1A 0.033 0.005 -10000 0 -10000 0 0
chromosome segregation 0 0.055 0.1 2 -0.15 18 20
PRC1 0.023 0.054 -10000 0 -0.32 5 5
ECT2 -0.081 0.093 0.18 2 -0.17 88 90
C13orf34 0.018 0.03 0.089 4 -10000 0 4
NUDC 0.001 0.074 -10000 0 -0.23 19 19
regulation of attachment of spindle microtubules to kinetochore -0.017 0.071 0.14 1 -0.21 7 8
spindle assembly 0.013 0.029 0.1 5 -10000 0 5
spindle stabilization 0.007 0.018 0.056 4 -10000 0 4
APC/C/HCDH1 0.031 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.012 0.075 -10000 0 -0.18 22 22
CCNB1 -0.046 0.15 -10000 0 -0.33 47 47
PPP1CB 0.034 0.001 -10000 0 -10000 0 0
BTRC 0.032 0.007 -10000 0 -10000 0 0
ROCK2 0.026 0.034 -10000 0 -0.27 1 1
TUBG1 0.016 0.022 -10000 0 -0.15 1 1
G2/M transition of mitotic cell cycle -0.041 0.1 0.17 13 -0.22 20 33
MLF1IP -0.014 0.072 -10000 0 -0.23 22 22
INCENP 0.027 0.042 -10000 0 -0.33 3 3
Glucocorticoid receptor regulatory network

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
PCK2 0.057 0.096 -10000 0 -0.74 1 1
SMARCC2 0.033 0.004 -10000 0 -10000 0 0
SMARCC1 0.027 0.048 -10000 0 -0.32 4 4
TBX21 -0.3 0.39 -10000 0 -0.84 69 69
SUMO2 0.032 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.008 0.1 -10000 0 -0.32 19 19
FKBP4 0.032 0.007 -10000 0 -10000 0 0
FKBP5 0.033 0.005 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.09 0.14 0.32 12 -0.31 10 22
PRL -0.03 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.23 0.54 39 -10000 0 39
RELA -0.077 0.059 -10000 0 -10000 0 0
FGG 0.13 0.19 0.46 22 -10000 0 22
GR beta/TIF2 0.081 0.15 0.31 18 -0.34 12 30
IFNG -0.16 0.19 -10000 0 -0.57 17 17
apoptosis 0.039 0.13 0.53 2 -0.53 2 4
CREB1 0.042 0 -10000 0 -10000 0 0
histone acetylation -0.054 0.1 -10000 0 -0.32 10 10
BGLAP -0.049 0.12 -10000 0 -10000 0 0
GR/PKAc 0.015 0.21 0.34 7 -0.35 26 33
NF kappa B1 p50/RelA -0.13 0.098 -10000 0 -0.37 5 5
SMARCD1 0.033 0.004 -10000 0 -10000 0 0
MDM2 0.075 0.069 0.23 21 -10000 0 21
GATA3 0.038 0.028 -10000 0 -10000 0 0
AKT1 0.026 0.017 0.24 1 -10000 0 1
CSF2 -0.13 0.14 -10000 0 -0.5 5 5
GSK3B 0.031 0.026 -10000 0 -0.32 1 1
NR1I3 0.043 0.13 0.57 1 -10000 0 1
CSN2 0.095 0.15 0.38 17 -0.32 1 18
BRG1/BAF155/BAF170/BAF60A 0.077 0.039 -10000 0 -10000 0 0
NFATC1 0.027 0.031 -10000 0 -0.32 1 1
POU2F1 0.039 0.01 -10000 0 -10000 0 0
CDKN1A -0.032 0.21 -10000 0 -1.6 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.005 -10000 0 -10000 0 0
SFN 0.026 0.052 -10000 0 -0.5 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.092 0.14 0.33 9 -0.32 8 17
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.018 0.19 0.55 1 -0.86 7 8
JUN -0.096 0.13 -10000 0 -0.42 8 8
IL4 -0.049 0.11 -10000 0 -0.47 4 4
CDK5R1 0.032 0.008 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.039 0.14 -10000 0 -0.33 15 15
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.14 0.33 10 -0.28 9 19
cortisol/GR alpha (monomer) 0.22 0.28 0.62 45 -0.42 1 46
NCOA2 0.029 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.067 0.16 -10000 0 -0.5 24 24
AP-1/NFAT1-c-4 -0.16 0.16 -10000 0 -0.56 9 9
AFP -0.061 0.1 -10000 0 -10000 0 0
SUV420H1 0.033 0.005 -10000 0 -10000 0 0
IRF1 0.1 0.15 0.47 2 -1 1 3
TP53 0.024 0.083 -10000 0 -0.45 2 2
PPP5C 0.031 0.025 -10000 0 -0.32 1 1
KRT17 -0.13 0.17 -10000 0 -0.6 9 9
KRT14 -0.065 0.11 -10000 0 -0.5 1 1
TBP 0.041 0.008 -10000 0 -10000 0 0
CREBBP 0.035 0.016 -10000 0 -10000 0 0
HDAC1 0.03 0.016 -10000 0 -10000 0 0
HDAC2 0.042 0.014 -10000 0 -10000 0 0
AP-1 -0.16 0.17 -10000 0 -0.56 9 9
MAPK14 0.033 0.006 -10000 0 -10000 0 0
MAPK10 0.025 0.062 -10000 0 -0.41 4 4
MAPK11 0.029 0.027 -10000 0 -0.32 1 1
KRT5 -0.13 0.17 -10000 0 -0.61 6 6
interleukin-1 receptor activity 0.01 0.011 -10000 0 -10000 0 0
NCOA1 0.03 0.053 -10000 0 -0.5 2 2
STAT1 0.008 0.1 -10000 0 -0.32 19 19
CGA -0.052 0.12 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.081 0.15 0.4 10 -0.39 1 11
MAPK3 0.028 0.052 -10000 0 -0.5 2 2
MAPK1 0.032 0.009 -10000 0 -10000 0 0
ICAM1 -0.16 0.18 -10000 0 -0.56 18 18
NFKB1 -0.076 0.058 -10000 0 -0.24 1 1
MAPK8 -0.094 0.14 0.42 1 -0.4 19 20
MAPK9 0.033 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.038 0.13 0.53 2 -0.55 2 4
BAX -0.013 0.085 -10000 0 -10000 0 0
POMC -0.075 0.16 -10000 0 -1.3 1 1
EP300 0.035 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.17 0.24 0.56 34 -10000 0 34
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.074 0.28 11 -10000 0 11
SGK1 0.034 0.065 -10000 0 -10000 0 0
IL13 -0.097 0.15 -10000 0 -0.76 1 1
IL6 -0.21 0.21 -10000 0 -0.59 24 24
PRKACG 0.033 0.005 -10000 0 -10000 0 0
IL5 -0.093 0.14 -10000 0 -0.69 1 1
IL2 -0.13 0.17 -10000 0 -0.6 5 5
CDK5 0.029 0.035 -10000 0 -0.32 2 2
PRKACB -0.1 0.23 -10000 0 -0.5 55 55
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
IL8 -0.29 0.17 -10000 0 -0.62 23 23
CDK5R1/CDK5 0.043 0.029 -10000 0 -0.22 2 2
NF kappa B1 p50/RelA/PKAc -0.14 0.15 -10000 0 -0.43 28 28
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.22 0.52 37 -10000 0 37
SMARCA4 0.033 0.006 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.15 0.35 24 -0.34 2 26
NF kappa B1 p50/RelA/Cbp -0.076 0.089 -10000 0 -0.35 1 1
JUN (dimer) -0.096 0.13 -10000 0 -0.42 8 8
YWHAH 0.032 0.008 -10000 0 -10000 0 0
VIPR1 -0.16 0.3 -10000 0 -0.87 29 29
NR3C1 0.1 0.22 0.44 25 -0.43 21 46
NR4A1 0.033 0.061 -10000 0 -0.45 3 3
TIF2/SUV420H1 0.042 0.018 -10000 0 -10000 0 0
MAPKKK cascade 0.039 0.13 0.53 2 -0.53 2 4
cortisol/GR alpha (dimer)/Src-1 0.21 0.24 0.54 44 -0.45 1 45
PBX1 0.029 0.073 -10000 0 -0.5 4 4
POU1F1 0.037 0.037 -10000 0 -0.5 1 1
SELE -0.19 0.21 -10000 0 -0.6 25 25
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.15 0.36 24 -0.34 2 26
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.22 0.52 37 -10000 0 37
mol:cortisol 0.12 0.13 0.35 40 -10000 0 40
MMP1 -0.22 0.13 -10000 0 -0.79 4 4
Glypican 2 network

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.013 0.082 -9999 0 -0.32 12 12
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.011 0.057 -9999 0 -0.22 12 12
neuron projection morphogenesis 0.011 0.056 -9999 0 -0.22 12 12
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.022 0.064 -9999 0 -0.32 7 7
PLK4 0.023 0.059 -9999 0 -0.32 6 6
regulation of centriole replication 0.004 0.058 -9999 0 -0.22 13 13
Osteopontin-mediated events

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
IKK alpha homodimer -0.089 0.1 -9999 0 -0.34 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.079 0.11 -9999 0 -0.38 1 1
alphaV/beta3 Integrin/Osteopontin/Src -0.13 0.13 -9999 0 -0.24 52 52
AP1 -0.1 0.13 -9999 0 -0.41 2 2
ILK -0.096 0.095 -9999 0 -0.34 1 1
bone resorption -0.079 0.098 -9999 0 -10000 0 0
PTK2B 0.026 0.014 -9999 0 -10000 0 0
PYK2/p130Cas -0.073 0.11 -9999 0 -0.31 1 1
ITGAV 0.033 0.025 -9999 0 -0.33 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.039 0.052 -9999 0 -0.22 8 8
alphaV/beta3 Integrin/Osteopontin -0.097 0.12 -9999 0 -0.37 1 1
MAP3K1 -0.096 0.096 -9999 0 -0.34 1 1
JUN 0.025 0.054 -9999 0 -0.32 5 5
MAPK3 -0.1 0.1 -9999 0 -0.41 3 3
MAPK1 -0.1 0.096 -9999 0 -0.36 1 1
Rac1/GDP 0.023 0.007 -9999 0 -10000 0 0
NFKB1 0.033 0.006 -9999 0 -10000 0 0
MAPK8 -0.092 0.089 -9999 0 -0.32 1 1
ITGB3 0.033 0.008 -9999 0 -10000 0 0
NFKBIA -0.091 0.093 -9999 0 -0.35 2 2
FOS -0.027 0.16 -9999 0 -0.49 24 24
CD44 0.02 0.068 -9999 0 -0.32 8 8
CHUK 0.032 0.007 -9999 0 -10000 0 0
PLAU -0.12 0.15 -9999 0 -0.58 2 2
NF kappa B1 p50/RelA -0.084 0.13 -9999 0 -0.4 2 2
BCAR1 0.033 0.006 -9999 0 -10000 0 0
RELA 0.033 0.006 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.048 0.023 -9999 0 -0.23 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.097 0.095 -9999 0 -0.34 1 1
VAV3 -0.13 0.14 -9999 0 -0.42 29 29
MAP3K14 -0.1 0.099 -9999 0 -0.36 1 1
ROCK2 0.033 0.002 -9999 0 -10000 0 0
SPP1 -0.21 0.17 -9999 0 -0.32 145 145
RAC1 0.031 0.01 -9999 0 -10000 0 0
Rac1/GTP -0.11 0.14 -9999 0 -0.39 27 27
MMP2 -0.1 0.1 -9999 0 -0.43 2 2
PDGFR-alpha signaling 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
PDGFRA 0.02 0.07 -10000 0 -0.5 3 3
PDGF/PDGFRA/CRKL 0.041 0.05 -10000 0 -0.36 3 3
positive regulation of JUN kinase activity 0.072 0.048 -10000 0 -0.27 3 3
CRKL 0.031 0.009 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.043 0.05 -10000 0 -0.36 3 3
AP1 -0.069 0.29 -10000 0 -0.8 26 26
mol:IP3 0.011 0.072 0.23 11 -0.34 4 15
PLCG1 0.011 0.072 0.23 11 -0.34 4 15
PDGF/PDGFRA/alphaV Integrin 0.042 0.053 -10000 0 -0.32 4 4
RAPGEF1 0.033 0.005 -10000 0 -10000 0 0
CRK 0.027 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.072 0.23 11 -0.34 4 15
CAV3 0.033 0.006 -10000 0 -10000 0 0
CAV1 0.025 0.056 -10000 0 -0.37 4 4
SHC/Grb2/SOS1 0.075 0.049 -10000 0 -0.27 3 3
PDGF/PDGFRA/Shf -0.006 0.12 -10000 0 -0.24 39 39
FOS -0.096 0.28 0.32 5 -0.78 26 31
JUN -0.016 0.043 -10000 0 -0.22 4 4
oligodendrocyte development 0.042 0.053 -10000 0 -0.32 4 4
GRB2 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:DAG 0.011 0.072 0.23 11 -0.34 4 15
PDGF/PDGFRA 0.02 0.069 -10000 0 -0.5 3 3
actin cytoskeleton reorganization 0.033 0.071 -10000 0 -0.26 11 11
SRF 0.011 0.017 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.062 0.04 -10000 0 -0.3 2 2
PDGF/PDGFRA/Crk/C3G 0.049 0.051 -10000 0 -0.3 3 3
JAK1 0.012 0.048 -10000 0 -0.35 3 3
ELK1/SRF 0.041 0.088 0.3 4 -0.28 4 8
SHB 0.02 0.068 -10000 0 -0.32 8 8
SHF -0.03 0.13 -10000 0 -0.32 37 37
CSNK2A1 0.02 0.028 -10000 0 -10000 0 0
GO:0007205 0.011 0.08 0.26 11 -0.39 3 14
SOS1 0.033 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.072 0.048 -10000 0 -0.27 3 3
PDGF/PDGFRA/SHB 0.033 0.071 -10000 0 -0.26 11 11
PDGF/PDGFRA/Caveolin-1 0.036 0.065 -10000 0 -0.3 7 7
ITGAV 0.031 0.025 -10000 0 -0.32 1 1
ELK1 0.004 0.084 0.28 9 -0.32 5 14
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.035 0.051 -10000 0 -0.36 3 3
JAK-STAT cascade 0.012 0.047 -10000 0 -0.35 3 3
cell proliferation -0.006 0.12 -10000 0 -0.24 39 39
amb2 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
alphaM/beta2 Integrin/proMMP-2 0.033 0.075 -10000 0 -0.37 4 4
alphaM/beta2 Integrin/GPIbA 0.028 0.07 -10000 0 -0.36 4 4
alphaM/beta2 Integrin/proMMP-9 0.017 0.064 -10000 0 -0.32 3 3
PLAUR 0.031 0.025 -10000 0 -0.32 1 1
HMGB1 0.003 0.036 -10000 0 -0.35 1 1
alphaM/beta2 Integrin/Talin 0.035 0.071 -10000 0 -0.37 4 4
AGER 0.004 0.034 -10000 0 -10000 0 0
RAP1A 0.032 0.007 -10000 0 -10000 0 0
SELPLG 0.026 0.063 -10000 0 -0.5 3 3
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.004 0.09 -10000 0 -0.34 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.008 0.064 -10000 0 -0.36 6 6
CYR61 0.004 0.098 -10000 0 -0.33 17 17
TLN1 0.033 0.006 -10000 0 -10000 0 0
Rap1/GTP 0.02 0.091 -10000 0 -0.48 3 3
RHOA 0.033 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.034 0.18 -10000 0 -0.5 27 27
MYH2 0.002 0.088 -10000 0 -0.44 4 4
MST1R 0.033 0.004 -10000 0 -10000 0 0
leukocyte activation during inflammatory response 0.047 0.062 -10000 0 -0.32 4 4
APOB 0.034 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.03 0.035 -10000 0 -0.32 2 2
JAM3 0.033 0.006 -10000 0 -10000 0 0
GP1BA 0.027 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.032 0.075 -10000 0 -0.37 4 4
alphaM/beta2 Integrin 0.003 0.091 -10000 0 -0.55 3 3
JAM3 homodimer 0.033 0.006 -10000 0 -10000 0 0
ICAM2 0.023 0.067 -10000 0 -0.46 4 4
ICAM1 0.013 0.082 -10000 0 -0.32 12 12
phagocytosis triggered by activation of immune response cell surface activating receptor 0.003 0.09 -10000 0 -0.55 3 3
cell adhesion 0.028 0.069 -10000 0 -0.36 4 4
NFKB1 0.002 0.14 0.43 3 -0.37 1 4
THY1 -0.012 0.12 -10000 0 -0.33 27 27
RhoA/GDP 0.024 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.044 0.009 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.048 0.074 -10000 0 -0.32 5 5
IL6 -0.057 0.16 -10000 0 -0.48 1 1
ITGB2 -0.005 0.075 -10000 0 -0.49 4 4
elevation of cytosolic calcium ion concentration -0.014 0.13 -10000 0 -0.34 5 5
alphaM/beta2 Integrin/JAM2/JAM3 -0.13 0.18 -10000 0 -0.3 107 107
JAM2 -0.25 0.26 -10000 0 -0.5 115 115
alphaM/beta2 Integrin/ICAM1 0.045 0.1 -10000 0 -0.38 3 3
alphaM/beta2 Integrin/uPA/Plg -0.013 0.13 -10000 0 -0.33 5 5
RhoA/GTP 0.003 0.09 -10000 0 -0.36 7 7
positive regulation of phagocytosis -0.001 0.086 -10000 0 -0.52 3 3
Ron/MSP 0.037 0.058 -10000 0 -0.22 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.013 0.13 -10000 0 -0.34 5 5
alphaM/beta2 Integrin/uPAR 0.034 0.073 -10000 0 -0.37 4 4
PLAU -0.071 0.16 -10000 0 -0.33 62 62
PLAT 0.025 0.045 -10000 0 -0.41 2 2
actin filament polymerization 0.001 0.087 -10000 0 -0.42 4 4
MST1 0.017 0.075 -10000 0 -0.32 10 10
alphaM/beta2 Integrin/lipoprotein(a) 0.053 0.064 -10000 0 -0.32 4 4
TNF -0.005 0.12 0.39 1 -10000 0 1
RAP1B 0.033 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.033 0.13 -10000 0 -0.32 8 8
fibrinolysis -0.014 0.13 -10000 0 -0.32 5 5
HCK 0.004 0.087 -10000 0 -0.5 6 6
dendritic cell antigen processing and presentation 0.003 0.09 -10000 0 -0.55 3 3
VTN 0.032 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.016 0.098 -10000 0 -0.33 6 6
LPA 0.032 0.007 -10000 0 -10000 0 0
LRP1 0.033 0.004 -10000 0 -10000 0 0
cell migration 0.013 0.064 -10000 0 -0.31 5 5
FN1 -0.006 0.11 -10000 0 -0.32 24 24
alphaM/beta2 Integrin/Thy1 0.005 0.11 -10000 0 -0.32 7 7
MPO 0.011 0.085 -10000 0 -0.32 13 13
KNG1 0.019 0.084 -10000 0 -0.47 6 6
RAP1/GDP 0.043 0.011 -10000 0 -10000 0 0
ROCK1 0.004 0.083 -10000 0 -0.43 3 3
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.032 0.007 -10000 0 -10000 0 0
CTGF 0.029 0.035 -10000 0 -0.32 2 2
alphaM/beta2 Integrin/Hck 0.016 0.078 -10000 0 -0.35 7 7
ITGAM 0 0.059 -10000 0 -0.5 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.012 0.14 -10000 0 -0.32 30 30
HP 0.033 0.006 -10000 0 -10000 0 0
leukocyte adhesion -0.14 0.14 -10000 0 -0.41 9 9
SELP -0.034 0.18 -10000 0 -0.5 27 27
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 0.022 0.039 -10000 0 -0.5 1 1
EPHB2 0.02 0.065 -10000 0 -0.36 6 6
EFNB1 0.015 0.025 -10000 0 -0.23 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.008 0.11 -10000 0 -0.35 3 3
Ephrin B2/EPHB1-2 -0.021 0.099 -10000 0 -0.3 4 4
neuron projection morphogenesis -0.019 0.099 -10000 0 -0.31 5 5
Ephrin B1/EPHB1-2/Tiam1 -0.022 0.12 -10000 0 -0.33 7 7
DNM1 0.029 0.035 -10000 0 -0.33 2 2
cell-cell signaling -0.001 0.005 -10000 0 -10000 0 0
MAP2K4 -0.012 0.071 -10000 0 -0.52 3 3
YES1 -0.029 0.13 -10000 0 -0.68 6 6
Ephrin B1/EPHB1-2/NCK2 -0.018 0.12 -10000 0 -0.3 6 6
PI3K 0.015 0.093 -10000 0 -0.44 5 5
mol:GDP -0.023 0.12 -10000 0 -0.32 8 8
ITGA2B 0.032 0.006 -10000 0 -10000 0 0
endothelial cell proliferation 0.001 0.078 -10000 0 -0.19 29 29
FYN -0.02 0.12 -10000 0 -0.66 7 7
MAP3K7 -0.02 0.079 -10000 0 -0.49 5 5
FGR -0.019 0.11 -10000 0 -0.67 5 5
TIAM1 0.026 0.052 -10000 0 -0.5 2 2
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
RGS3 0.033 0.005 -10000 0 -10000 0 0
cell adhesion 0.01 0.081 -10000 0 -0.43 4 4
LYN -0.016 0.12 -10000 0 -0.67 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.02 0.1 -10000 0 -0.6 6 6
Ephrin B1/EPHB1-2 -0.02 0.074 -10000 0 -0.59 3 3
SRC -0.02 0.11 -10000 0 -0.64 6 6
ITGB3 0.032 0.007 -10000 0 -10000 0 0
EPHB1 -0.096 0.17 -10000 0 -0.32 78 78
EPHB4 -0.023 0.13 -10000 0 -0.32 33 33
RAC1 0.031 0.01 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.001 0.078 -10000 0 -0.19 29 29
alphaIIb/beta3 Integrin 0.048 0.01 -10000 0 -10000 0 0
BLK -0.056 0.13 -10000 0 -0.79 4 4
HCK -0.019 0.096 -10000 0 -0.74 3 3
regulation of stress fiber formation 0.019 0.11 0.29 6 -10000 0 6
MAPK8 -0.015 0.08 -10000 0 -0.47 4 4
Ephrin B1/EPHB1-2/RGS3 -0.019 0.12 -10000 0 -0.3 6 6
endothelial cell migration 0.006 0.13 0.37 6 -0.5 3 9
NCK2 0.034 0 -10000 0 -10000 0 0
PTPN13 -0.075 0.16 -10000 0 -0.31 66 66
regulation of focal adhesion formation 0.019 0.11 0.29 6 -10000 0 6
chemotaxis 0.02 0.11 0.29 6 -10000 0 6
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.013 0.11 -10000 0 -0.33 4 4
angiogenesis -0.02 0.074 -10000 0 -0.59 3 3
LCK -0.02 0.12 -10000 0 -0.67 6 6
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.026 0.073 -10000 0 -0.22 17 17
alphaV beta3 Integrin 0.048 0.075 -10000 0 -0.31 8 8
PTK2 0.059 0.11 0.36 7 -0.35 1 8
IGF1R 0.031 0.009 -10000 0 -10000 0 0
PI4KB 0.033 0.005 -10000 0 -10000 0 0
MFGE8 0.031 0.009 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
CDKN1B 0.025 0.029 -10000 0 -10000 0 0
VEGFA 0.004 0.096 -10000 0 -0.32 17 17
ILK 0.026 0.029 -10000 0 -10000 0 0
ROCK1 0.026 0.014 -10000 0 -10000 0 0
AKT1 0.018 0.027 -10000 0 -10000 0 0
PTK2B 0.012 0.051 -10000 0 -10000 0 0
alphaV/beta3 Integrin/JAM-A 0.058 0.072 -10000 0 -0.27 7 7
CBL 0.033 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.062 0.024 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.13 0.18 -10000 0 -0.29 123 123
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.023 0.057 -10000 0 -0.35 2 2
alphaV/beta3 Integrin/Syndecan-1 0.064 0.023 -10000 0 -10000 0 0
PI4KA 0.031 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.18 -10000 0 -0.42 23 23
PI4 Kinase 0.046 0.014 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.1 0.12 -10000 0 -0.26 3 3
RPS6KB1 -0.15 0.15 -10000 0 -0.4 23 23
TLN1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 -0.057 0.14 -10000 0 -0.54 14 14
GPR124 0.026 0.036 -10000 0 -0.32 2 2
MAPK1 -0.059 0.15 -10000 0 -0.54 15 15
PXN 0.033 0.003 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.061 0.033 -10000 0 -10000 0 0
cell adhesion 0.055 0.027 -10000 0 -10000 0 0
ANGPTL3 0.033 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.028 0.054 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.031 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.007 -10000 0 -10000 0 0
TGFBR2 0.033 0.003 -10000 0 -10000 0 0
ITGB3 0.032 0.007 -10000 0 -10000 0 0
IGF1 -0.27 0.26 -10000 0 -0.5 124 124
RAC1 0.031 0.01 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.053 0.038 -10000 0 -10000 0 0
apoptosis 0.031 0.025 -10000 0 -0.32 1 1
CD47 0.033 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.063 0.024 -10000 0 -10000 0 0
VCL 0.032 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.022 0.12 -10000 0 -0.31 23 23
CSF1 0.033 0.006 -10000 0 -10000 0 0
PIK3C2A 0.022 0.037 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.017 0.071 -10000 0 -0.35 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.058 0.07 -10000 0 -10000 0 0
FAK1/Vinculin 0.075 0.099 0.31 9 -10000 0 9
alphaV beta3/Integrin/ppsTEM5 0.054 0.038 -10000 0 -10000 0 0
RHOA 0.033 0.005 -10000 0 -10000 0 0
VTN 0.032 0.007 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
FGF2 0.011 0.1 -10000 0 -0.48 9 9
F11R 0.003 0.074 -10000 0 -0.35 9 9
alphaV/beta3 Integrin/Lactadherin 0.06 0.027 -10000 0 -10000 0 0
alphaV/beta3 Integrin/TGFBR2 0.063 0.024 -10000 0 -0.19 1 1
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.078 0.03 -10000 0 -10000 0 0
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
alphaV/beta3 Integrin/Talin 0.059 0.023 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.006 0.11 -10000 0 -0.32 24 24
alphaV/beta3 Integrin/Pyk2 0.036 0.065 -10000 0 -10000 0 0
SDC1 0.034 0 -10000 0 -10000 0 0
VAV3 -0.022 0.1 -10000 0 -0.27 31 31
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
IRS1 0.027 0.048 -10000 0 -0.32 4 4
FAK1/Paxillin 0.075 0.097 0.31 7 -10000 0 7
cell migration 0.067 0.093 0.29 8 -10000 0 8
ITGAV 0.031 0.025 -10000 0 -0.32 1 1
PI3K 0.07 0.073 -10000 0 -10000 0 0
SPP1 -0.21 0.17 -10000 0 -0.33 145 145
KDR 0.033 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.031 0.025 -10000 0 -0.32 1 1
COL4A3 0.03 0.034 -10000 0 -0.32 2 2
angiogenesis -0.045 0.15 0.28 1 -0.54 14 15
Rac1/GTP -0.006 0.1 -10000 0 -0.38 1 1
EDIL3 -0.026 0.17 -10000 0 -0.5 24 24
cell proliferation 0.062 0.023 -10000 0 -0.19 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.037 0.021 -10000 0 -10000 0 0
NFATC2 0.001 0.11 -10000 0 -10000 0 0
NFATC3 -0.024 0.086 -10000 0 -0.31 4 4
CD40LG -0.26 0.28 -10000 0 -0.88 15 15
ITCH 0.017 0.042 -10000 0 -10000 0 0
CBLB 0.034 0.039 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.11 0.16 -10000 0 -1 1 1
JUNB 0.028 0.042 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.05 -10000 0 -0.27 4 4
T cell anergy 0.044 0.081 -10000 0 -0.38 3 3
TLE4 0.003 0.074 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.11 0.2 -10000 0 -0.84 8 8
AP-1/NFAT1-c-4 -0.28 0.3 -10000 0 -0.97 16 16
IKZF1 0 0.088 -10000 0 -0.76 1 1
T-helper 2 cell differentiation -0.058 0.13 -10000 0 -0.93 1 1
AP-1/NFAT1 -0.061 0.14 -10000 0 -0.46 9 9
CALM1 0.036 0.035 -10000 0 -10000 0 0
EGR2 -0.068 0.28 -10000 0 -1.4 8 8
EGR3 -0.071 0.25 -10000 0 -1.3 6 6
NFAT1/FOXP3 0.015 0.087 -10000 0 -10000 0 0
EGR1 0.012 0.1 -10000 0 -0.45 10 10
JUN -0.043 0.066 -10000 0 -0.36 5 5
EGR4 0.001 0 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.026 -10000 0 -10000 0 0
GBP3 -0.046 0.22 -10000 0 -0.74 19 19
FOSL1 0.011 0.085 -10000 0 -0.32 13 13
NFAT1-c-4/MAF/IRF4 -0.17 0.28 -10000 0 -0.95 14 14
DGKA 0.003 0.074 -10000 0 -10000 0 0
CREM 0.032 0.003 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.067 0.2 -10000 0 -0.84 7 7
CTLA4 0.011 0.079 -10000 0 -10000 0 0
NFAT1-c-4 (dimer)/EGR1 -0.062 0.21 -10000 0 -0.9 7 7
NFAT1-c-4 (dimer)/EGR4 -0.063 0.19 -10000 0 -0.81 8 8
FOS -0.089 0.16 -10000 0 -0.52 24 24
IFNG -0.2 0.26 -10000 0 -0.69 27 27
T cell activation -0.048 0.15 -10000 0 -10000 0 0
MAF -0.15 0.25 -10000 0 -0.5 73 73
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.052 0.17 0.71 6 -10000 0 6
TNF -0.061 0.18 -10000 0 -0.81 7 7
FASLG -0.18 0.51 -10000 0 -1.4 27 27
TBX21 -0.14 0.23 -10000 0 -0.5 63 63
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.018 0.06 -10000 0 -0.32 4 4
PTPN1 0.003 0.074 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 -0.061 0.2 -10000 0 -0.84 7 7
GATA3 0.035 0.007 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.19 0.26 -10000 0 -0.68 27 27
IL2RA -0.12 0.16 -10000 0 -0.81 2 2
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.002 0.073 -10000 0 -10000 0 0
E2F1 0.009 0.057 -10000 0 -0.32 5 5
PPARG 0.018 0.088 -10000 0 -0.5 6 6
SLC3A2 0.001 0.081 -10000 0 -0.45 1 1
IRF4 -0.084 0.22 -10000 0 -0.5 47 47
PTGS2 -0.29 0.3 -10000 0 -0.84 25 25
CSF2 -0.33 0.31 -10000 0 -0.85 28 28
JunB/Fra1/NFAT1-c-4 -0.059 0.2 -10000 0 -0.8 7 7
IL4 -0.06 0.14 -10000 0 -0.98 1 1
IL5 -0.27 0.28 -10000 0 -0.84 18 18
IL2 -0.048 0.15 -10000 0 -10000 0 0
IL3 -0.017 0.092 -10000 0 -1 1 1
RNF128 0.022 0.093 -10000 0 -0.59 4 4
NFATC1 -0.052 0.17 -10000 0 -0.72 6 6
CDK4 0.017 0.11 -10000 0 -10000 0 0
PTPRK 0.002 0.072 -10000 0 -10000 0 0
IL8 -0.38 0.29 -10000 0 -0.86 29 29
POU2F1 0.04 0.006 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.033 0.006 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.033 0.006 -10000 0 -10000 0 0
TCEB1 0.027 0.027 -10000 0 -0.32 1 1
HIF1A/p53 -0.015 0.089 0.27 1 -0.32 10 11
HIF1A -0.021 0.075 -10000 0 -0.34 8 8
COPS5 0.029 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.077 0.047 -10000 0 -10000 0 0
FIH (dimer) 0.032 0.007 -10000 0 -10000 0 0
CDKN2A -0.077 0.16 -10000 0 -0.32 66 66
ARNT/IPAS 0.048 0.01 -10000 0 -10000 0 0
HIF1AN 0.032 0.007 -10000 0 -10000 0 0
GNB2L1 0.033 0.004 -10000 0 -10000 0 0
HIF1A/ARNT -0.02 0.087 -10000 0 -0.33 10 10
CUL2 0.033 0.003 -10000 0 -10000 0 0
OS9 0.033 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.056 0.03 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.012 0.088 0.27 1 -0.33 10 11
PHD1-3/OS9 -0.039 0.16 -10000 0 -0.28 61 61
HIF1A/RACK1/Elongin B/Elongin C 0.002 0.093 -10000 0 -0.39 5 5
VHL 0.031 0.025 -10000 0 -0.32 1 1
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
HIF1A/JAB1 -0.014 0.087 0.27 1 -0.34 9 10
EGLN3 -0.13 0.24 -10000 0 -0.5 65 65
EGLN2 0.033 0.006 -10000 0 -10000 0 0
EGLN1 0.032 0.007 -10000 0 -10000 0 0
TP53 0.013 0.068 -10000 0 -0.32 8 8
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.027 0.094 -10000 0 -0.53 5 5
ARNT 0.033 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.031 0.008 -10000 0 -10000 0 0
HIF1A/p19ARF -0.063 0.11 0.27 1 -0.35 10 11
Regulation of Androgen receptor activity

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
HDAC1 0.019 0.005 -10000 0 -10000 0 0
SMARCC1 0.009 0.069 -10000 0 -0.82 1 1
REL 0.033 0 -10000 0 -10000 0 0
HDAC7 -0.089 0.13 -10000 0 -0.44 9 9
JUN 0.025 0.054 -10000 0 -0.32 5 5
EP300 0.032 0.008 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.019 0.081 -10000 0 -0.39 9 9
FOXO1 0.01 0.088 -10000 0 -0.5 6 6
T-DHT/AR -0.074 0.15 -10000 0 -0.46 9 9
MAP2K6 -0.004 0.11 -10000 0 -0.52 9 9
BRM/BAF57 0.047 0.014 -10000 0 -10000 0 0
MAP2K4 0.011 0.041 -10000 0 -0.5 1 1
SMARCA2 0.033 0.006 -10000 0 -10000 0 0
PDE9A -0.53 0.57 -10000 0 -1.1 108 108
NCOA2 0.029 0.012 -10000 0 -10000 0 0
CEBPA 0.032 0.007 -10000 0 -10000 0 0
EHMT2 0.033 0.005 -10000 0 -10000 0 0
cell proliferation 0.006 0.17 0.4 8 -0.38 9 17
NR0B1 0.025 0.054 -10000 0 -0.32 5 5
EGR1 0.011 0.1 -10000 0 -0.45 10 10
RXRs/9cRA 0.062 0.016 -10000 0 -10000 0 0
AR/RACK1/Src 0.047 0.12 0.31 5 -0.34 7 12
AR/GR -0.035 0.11 -10000 0 -0.29 21 21
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
PKN1 0.033 0.005 -10000 0 -10000 0 0
RCHY1 0.033 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.003 0.034 -10000 0 -0.35 1 1
T-DHT/AR/TIF2/CARM1 -0.02 0.096 -10000 0 -0.35 8 8
SRC 0.006 0.1 0.22 2 -0.31 8 10
NR3C1 -0.026 0.17 -10000 0 -0.5 24 24
KLK3 -0.067 0.1 -10000 0 -10000 0 0
APPBP2 0.008 0.028 -10000 0 -10000 0 0
TRIM24 0.033 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.047 0.081 -10000 0 -0.34 10 10
TMPRSS2 -0.075 0.19 -10000 0 -0.76 10 10
RXRG 0.033 0.005 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -0.003 1 1
RXRA 0.033 0.005 -10000 0 -10000 0 0
RXRB 0.033 0.005 -10000 0 -10000 0 0
CARM1 0.034 0.004 -10000 0 -10000 0 0
NR2C2 0.033 0.005 -10000 0 -10000 0 0
KLK2 0.028 0.086 0.31 1 -10000 0 1
AR -0.005 0.054 -10000 0 -0.27 1 1
SENP1 0.033 0.005 -10000 0 -10000 0 0
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
MDM2 0.032 0.004 -10000 0 -10000 0 0
SRY -0.001 0.001 -10000 0 -10000 0 0
GATA2 0.033 0.004 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.25 0.14 -10000 0 -0.32 172 172
T-DHT/AR/RACK1/Src 0.045 0.13 0.32 5 -0.35 7 12
positive regulation of transcription 0.033 0.004 -10000 0 -10000 0 0
DNAJA1 0.007 0.037 -10000 0 -0.35 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.008 -10000 0 -10000 0 0
NCOA1 0.032 0.061 -10000 0 -0.58 2 2
SPDEF -0.14 0.25 -10000 0 -0.5 68 68
T-DHT/AR/TIF2 0.002 0.084 0.25 5 -0.42 2 7
T-DHT/AR/Hsp90 -0.03 0.093 -10000 0 -0.36 8 8
GSK3B 0.03 0.025 -10000 0 -0.32 1 1
NR2C1 0.027 0.048 -10000 0 -0.33 4 4
mol:T-DHT -0.031 0.078 0.22 2 -0.33 10 12
SIRT1 0.032 0.007 -10000 0 -10000 0 0
ZMIZ2 0.03 0.009 -10000 0 -10000 0 0
POU2F1 -0.025 0.072 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.038 0.096 -10000 0 -0.36 8 8
CREBBP 0.032 0.006 -10000 0 -10000 0 0
SMARCE1 0.033 0.008 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.003 0.15 -9999 0 -0.44 8 8
MAP3K8 -0.016 0.12 -9999 0 -0.33 29 29
FOS 0.002 0.1 -9999 0 -0.38 5 5
PRKCA 0.024 0.031 -9999 0 -0.34 1 1
PTPN7 0.012 0.07 -9999 0 -0.32 8 8
HRAS 0.033 0.004 -9999 0 -10000 0 0
PRKCB -0.002 0.006 -9999 0 -0.016 33 33
NRAS 0.029 0.035 -9999 0 -0.33 2 2
RAS family/GTP 0.054 0.03 -9999 0 -10000 0 0
MAPK3 0.017 0.077 -9999 0 -0.45 4 4
MAP2K1 0.004 0.056 -9999 0 -0.26 2 2
ELK1 0.02 0.048 -9999 0 -0.34 3 3
BRAF 0.014 0.021 -9999 0 -10000 0 0
mol:GTP -0.001 0.002 -9999 0 -0.005 33 33
MAPK1 0.001 0.12 -9999 0 -0.42 12 12
RAF1 0.014 0.021 -9999 0 -10000 0 0
KRAS 0.032 0.006 -9999 0 -10000 0 0
Aurora B 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
Condensin I complex 0.005 0.055 -9999 0 -0.24 2 2
STMN1 0.014 0.019 -9999 0 -0.23 1 1
Aurora B/RasGAP/Survivin 0.03 0.078 -9999 0 -0.35 1 1
Chromosomal passenger complex/Cul3 protein complex -0.062 0.12 -9999 0 -0.33 19 19
BIRC5 -0.003 0.11 -9999 0 -0.33 21 21
DES -0.13 0.32 -9999 0 -0.69 50 50
Aurora C/Aurora B/INCENP 0.046 0.037 -9999 0 -10000 0 0
Aurora B/TACC1 0.034 0.02 -9999 0 -10000 0 0
Aurora B/PP2A 0.039 0.021 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.01 0.01 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.003 0.004 -9999 0 -10000 0 0
NDC80 0.012 0.025 -9999 0 -10000 0 0
Cul3 protein complex -0.046 0.16 -9999 0 -0.31 55 55
KIF2C -0.003 0.061 -9999 0 -0.35 3 3
PEBP1 0.033 0.004 -9999 0 -10000 0 0
KIF20A -0.009 0.12 -9999 0 -0.32 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.037 0.033 -9999 0 -0.23 2 2
SEPT1 0.033 0.006 -9999 0 -10000 0 0
SMC2 0.015 0.079 -9999 0 -0.32 11 11
SMC4 0.03 0.035 -9999 0 -0.32 2 2
NSUN2/NPM1/Nucleolin -0.078 0.21 -9999 0 -0.49 41 41
PSMA3 0.031 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B 0.016 0.008 -9999 0 -10000 0 0
AURKB 0.027 0.014 -9999 0 -10000 0 0
AURKC 0.033 0.006 -9999 0 -10000 0 0
CDCA8 0.028 0.036 -9999 0 -0.33 2 2
cytokinesis -0.029 0.13 -9999 0 -0.42 15 15
Aurora B/Septin1 -0.026 0.14 -9999 0 -0.41 13 13
AURKA 0.012 0.049 -9999 0 -0.32 4 4
INCENP 0.027 0.043 -9999 0 -0.33 3 3
KLHL13 -0.14 0.24 -9999 0 -0.47 72 72
BUB1 -0.1 0.18 -9999 0 -0.32 82 82
hSgo1/Aurora B/Survivin 0.02 0.085 -9999 0 -0.32 4 4
EVI5 0.033 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.011 0.13 -9999 0 -0.35 11 11
SGOL1 0.014 0.079 -9999 0 -0.32 11 11
CENPA 0.004 0.092 -9999 0 -0.3 7 7
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.04 0.02 -9999 0 -10000 0 0
NCAPD2 0.032 0.007 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.04 0.02 -9999 0 -10000 0 0
RHOA 0.033 0.005 -9999 0 -10000 0 0
NCAPH 0.02 0.068 -9999 0 -0.32 8 8
NPM1 -0.041 0.13 -9999 0 -0.94 1 1
RASA1 0.03 0.035 -9999 0 -0.32 2 2
KLHL9 0.033 0.006 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.02 -9999 0 -10000 0 0
PPP1CC 0.033 0.002 -9999 0 -10000 0 0
Centraspindlin -0.022 0.13 -9999 0 -0.34 17 17
RhoA/GDP 0.024 0.003 -9999 0 -10000 0 0
NSUN2 -0.038 0.13 -9999 0 -0.84 1 1
MYLK -0.023 0.12 -9999 0 -0.37 22 22
KIF23 -0.02 0.13 -9999 0 -0.33 31 31
VIM 0.01 0.046 -9999 0 -0.37 3 3
RACGAP1 0.016 0.076 -9999 0 -0.33 10 10
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.04 0.13 -9999 0 -0.38 9 9
Chromosomal passenger complex -0.018 0.087 -9999 0 -0.32 7 7
Chromosomal passenger complex/EVI5 0.049 0.09 -9999 0 -0.31 3 3
TACC1 0.029 0.011 -9999 0 -10000 0 0
PPP2R5D 0.033 0.006 -9999 0 -10000 0 0
CUL3 0.033 0.002 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.033 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.036 0.08 -10000 0 -0.35 2 2
PTP1B/AKT1 0.01 0.083 -10000 0 -0.32 3 3
FYN 0.03 0.037 -10000 0 -0.5 1 1
p210 bcr-abl/PTP1B 0.002 0.089 0.21 3 -0.33 4 7
EGFR 0.014 0.075 -10000 0 -0.51 4 4
EGF/EGFR -0.036 0.14 -10000 0 -0.32 27 27
CSF1 0.033 0.006 -10000 0 -10000 0 0
AKT1 0.031 0.01 -10000 0 -10000 0 0
INSR 0.026 0.063 -10000 0 -0.5 3 3
PTP1B/N-cadherin 0.001 0.085 0.22 1 -0.38 2 3
Insulin Receptor/Insulin 0.035 0.085 -10000 0 -0.36 3 3
HCK 0.004 0.087 -10000 0 -0.5 6 6
CRK 0.027 0.013 -10000 0 -10000 0 0
TYK2 0.003 0.09 0.28 4 -0.38 2 6
EGF -0.091 0.21 -10000 0 -0.43 58 58
YES1 0.027 0.013 -10000 0 -10000 0 0
CAV1 0.015 0.12 0.28 6 -0.35 4 10
TXN 0.031 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.025 0.096 -10000 0 -0.36 2 2
cell migration -0.002 0.089 0.33 4 -0.21 3 7
STAT3 0.033 0.006 -10000 0 -10000 0 0
PRLR 0.031 0.042 -10000 0 -0.32 3 3
ITGA2B 0.031 0.006 -10000 0 -10000 0 0
CSF1R 0.033 0.004 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.051 0.039 -10000 0 -0.22 3 3
FGR 0.031 0.009 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.011 0.09 0.22 1 -0.34 3 4
Crk/p130 Cas 0.017 0.086 -10000 0 -0.36 2 2
DOK1 0.011 0.081 0.22 1 -0.32 3 4
JAK2 0.029 0.075 0.24 1 -0.34 3 4
Jak2/Leptin Receptor/Leptin 0.027 0.11 -10000 0 -0.37 1 1
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
PTPN1 0.002 0.089 0.21 3 -0.33 4 7
LYN 0.029 0.012 -10000 0 -10000 0 0
CDH2 0.018 0.052 -10000 0 -0.34 4 4
SRC 0.018 0.096 -10000 0 -0.46 4 4
ITGB3 0.031 0.007 -10000 0 -10000 0 0
CAT1/PTP1B 0.005 0.17 0.27 17 -0.39 14 31
CAPN1 0.031 0.005 -10000 0 -10000 0 0
CSK 0.031 0.009 -10000 0 -10000 0 0
PI3K 0.049 0.083 -10000 0 -0.34 3 3
mol:H2O2 -0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.1 -10000 0 -0.33 1 1
negative regulation of transcription 0.029 0.074 0.24 1 -0.34 3 4
FCGR2A 0.009 0.088 -10000 0 -0.32 14 14
FER 0.018 0.067 -10000 0 -0.32 8 8
alphaIIb/beta3 Integrin 0.045 0.01 -10000 0 -10000 0 0
BLK -0.083 0.21 -10000 0 -0.5 44 44
Insulin Receptor/Insulin/Shc 0.058 0.042 -10000 0 -0.31 2 2
RHOA 0.032 0.005 -10000 0 -10000 0 0
LEPR 0.025 0.063 -10000 0 -0.5 3 3
BCAR1 0.033 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.032 0.006 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.059 0.21 0.24 7 -0.46 29 36
PRL 0.035 0.025 -10000 0 -0.32 1 1
SOCS3 -0.011 0.19 -10000 0 -1.1 6 6
SPRY2 0.019 0.052 -10000 0 -0.39 3 3
Insulin Receptor/Insulin/IRS1 0.055 0.053 -10000 0 -0.31 2 2
CSF1/CSF1R 0.03 0.093 0.23 1 -0.37 2 3
Ras protein signal transduction 0.002 0.06 0.45 3 -10000 0 3
IRS1 0.027 0.048 -10000 0 -0.32 4 4
INS 0.032 0.007 -10000 0 -10000 0 0
LEP 0.028 0.052 -10000 0 -0.5 2 2
STAT5B 0.019 0.082 0.23 2 -0.33 3 5
STAT5A 0.019 0.082 0.23 2 -0.33 3 5
GRB2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.091 0.22 1 -0.34 3 4
CSN2 0.024 0.042 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
LAT 0.027 0.071 -10000 0 -0.55 2 2
YBX1 0.043 0.009 -10000 0 -10000 0 0
LCK 0.028 0.044 -10000 0 -0.41 2 2
SHC1 0.033 0.006 -10000 0 -10000 0 0
NOX4 -0.27 0.13 -10000 0 -0.33 180 180
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.13 0.15 -10000 0 -10000 0 0
CRKL -0.033 0.079 0.29 2 -10000 0 2
mol:DAG -0.019 0.064 -10000 0 -10000 0 0
HRAS -0.03 0.085 0.47 1 -10000 0 1
MAPK8 0.014 0.071 -10000 0 -10000 0 0
RAP1A -0.036 0.077 0.34 1 -10000 0 1
GAB1 -0.039 0.084 0.29 2 -0.34 2 4
MAPK14 0.013 0.07 -10000 0 -10000 0 0
EPO 0.008 0.036 -10000 0 -0.34 1 1
PLCG1 -0.02 0.065 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.01 0.028 -10000 0 -10000 0 0
RAPGEF1 0.033 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.015 0.064 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 -0.022 0.09 -10000 0 -0.31 2 2
EPO/EPOR (dimer) 0.009 0.043 -10000 0 -0.24 1 1
IRS2 -0.027 0.067 0.24 1 -10000 0 1
STAT1 -0.095 0.13 -10000 0 -0.36 9 9
STAT5B -0.064 0.1 -10000 0 -10000 0 0
cell proliferation 0.011 0.073 0.28 2 -10000 0 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.032 0.075 -10000 0 -0.3 2 2
TEC -0.037 0.078 0.29 2 -10000 0 2
SOCS3 0.017 0.072 -10000 0 -0.32 9 9
STAT1 (dimer) -0.093 0.13 -10000 0 -0.36 9 9
JAK2 0.021 0.044 -10000 0 -0.33 3 3
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.027 0.094 -10000 0 -10000 0 0
EPO/EPOR 0.009 0.043 -10000 0 -0.24 1 1
LYN 0.006 0.026 -10000 0 -10000 0 0
TEC/VAV2 -0.038 0.082 -10000 0 -0.34 2 2
elevation of cytosolic calcium ion concentration 0.01 0.028 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.003 0.054 -10000 0 -10000 0 0
mol:IP3 -0.019 0.064 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.02 0.068 -10000 0 -10000 0 0
SH2B3 0.027 0.015 -10000 0 -10000 0 0
NFKB1 0.013 0.07 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.036 -10000 0 -0.24 1 1
PTPN6 -0.042 0.074 0.22 1 -10000 0 1
TEC/VAV2/GRB2 -0.031 0.09 -10000 0 -0.33 2 2
EPOR 0.01 0.028 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.023 0.091 -10000 0 -0.32 2 2
SOS1 0.033 0.002 -10000 0 -10000 0 0
PLCG2 -0.23 0.27 -10000 0 -0.5 104 104
CRKL/CBL/C3G -0.025 0.084 -10000 0 -10000 0 0
VAV2 -0.041 0.086 0.29 2 -0.34 2 4
CBL -0.038 0.079 0.29 2 -10000 0 2
SHC/Grb2/SOS1 -0.032 0.075 -10000 0 -10000 0 0
STAT5A -0.064 0.1 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
STAT5 (dimer) -0.13 0.16 -10000 0 -10000 0 0
LYN/PLCgamma2 -0.14 0.19 -10000 0 -0.37 89 89
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
BTK -0.077 0.12 0.24 1 -0.34 24 25
BCL2 -0.53 0.42 -10000 0 -0.82 143 143
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.042 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.033 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.01 0.11 -10000 0 -0.5 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.024 0.039 -10000 0 -0.5 1 1
RAC1-CDC42/GTP/PAK family 0.022 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.013 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.008 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.5 1 1
MAP3K12 0.033 0.004 -10000 0 -10000 0 0
FGR 0.031 0.009 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.078 0.14 -10000 0 -0.34 39 39
PRKG1 0.03 0.01 -10000 0 -10000 0 0
DUSP8 0.031 0.037 -10000 0 -0.5 1 1
PGK/cGMP/p38 alpha -0.027 0.17 0.19 2 -0.36 29 31
apoptosis -0.075 0.13 -10000 0 -0.32 38 38
RAL/GTP 0.041 0.014 -10000 0 -10000 0 0
LYN 0.029 0.012 -10000 0 -10000 0 0
DUSP1 -0.012 0.15 -10000 0 -0.5 18 18
PAK1 0.033 0.004 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.063 0.039 -10000 0 -10000 0 0
TRAF6 0.033 0.003 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.031 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.038 0.017 -10000 0 -10000 0 0
MAPK11 -0.012 0.18 0.3 11 -0.42 17 28
BLK -0.083 0.21 -10000 0 -0.5 44 44
HCK 0.004 0.087 -10000 0 -0.5 6 6
MAP2K3 0.028 0.013 -10000 0 -10000 0 0
DUSP16 0.032 0.006 -10000 0 -10000 0 0
DUSP10 -0.006 0.11 -10000 0 -0.32 23 23
TRAF6/MEKK3 0.04 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.029 0.19 0.24 13 -0.38 36 49
positive regulation of innate immune response -0.027 0.21 0.34 9 -0.46 23 32
LCK 0.028 0.044 -10000 0 -0.41 2 2
p38alpha-beta/MKP7 -0.018 0.2 0.32 7 -0.45 22 29
p38alpha-beta/MKP5 -0.031 0.21 0.32 8 -0.46 22 30
PGK/cGMP 0.022 0.008 -10000 0 -10000 0 0
PAK2 0.033 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.033 0.23 0.32 8 -0.49 27 35
CDC42 0.031 0.009 -10000 0 -10000 0 0
RALB 0.034 0 -10000 0 -10000 0 0
RALA 0.03 0.01 -10000 0 -10000 0 0
PAK3 0.033 0.004 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.015 0.04 -10000 0 -0.21 1 1
NFATC2 -0.011 0.028 -10000 0 -10000 0 0
NFATC3 -0.016 0.041 -10000 0 -10000 0 0
CD40LG -0.084 0.22 0.43 1 -0.56 13 14
PTGS2 -0.11 0.25 0.43 1 -0.56 30 31
JUNB 0.028 0.042 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.032 -10000 0 -10000 0 0
CaM/Ca2+ -0.004 0.032 -10000 0 -10000 0 0
CALM1 0.014 0.027 -10000 0 -10000 0 0
JUN 0.009 0.059 -10000 0 -0.33 5 5
mol:Ca2+ -0.011 0.013 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.013 -10000 0 -10000 0 0
FOSL1 0.011 0.085 -10000 0 -0.32 13 13
CREM 0.033 0.003 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.044 0.11 -10000 0 -10000 0 0
FOS -0.043 0.16 -10000 0 -0.5 24 24
IFNG -0.11 0.25 0.43 1 -0.56 27 28
AP-1/NFAT1-c-4 -0.1 0.24 -10000 0 -0.54 26 26
FASLG -0.1 0.24 0.43 1 -0.55 22 23
NFAT1-c-4/ICER1 -0.026 0.068 -10000 0 -10000 0 0
IL2RA -0.087 0.23 -10000 0 -0.59 12 12
FKBP12/FK506 0.02 0.01 -10000 0 -10000 0 0
CSF2 -0.15 0.26 0.43 1 -0.54 38 39
JunB/Fra1/NFAT1-c-4 0.003 0.12 -10000 0 -0.34 1 1
IL4 -0.083 0.22 0.43 1 -0.55 12 13
IL2 -0.002 0.14 -10000 0 -0.91 5 5
IL3 0.023 0.086 -10000 0 -0.91 1 1
FKBP1A 0.027 0.014 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.039 0.006 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.003 0.09 -10000 0 -0.25 21 21
epithelial cell differentiation 0.054 0.066 -10000 0 -0.26 6 6
CYFIP2 0.028 0.051 -10000 0 -0.5 2 2
ENAH -0.016 0.056 -10000 0 -10000 0 0
EGFR 0.021 0.072 -10000 0 -0.5 4 4
EPHA2 0.015 0.075 -10000 0 -0.32 10 10
MYO6 0.008 0.052 -10000 0 -10000 0 0
CTNNB1 0.025 0.054 -10000 0 -0.32 5 5
ABI1/Sra1/Nap1 0.062 0.041 -10000 0 -0.31 2 2
AQP5 0.006 0.056 -10000 0 -0.38 1 1
CTNND1 0.033 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.01 0.054 -10000 0 -0.25 6 6
regulation of calcium-dependent cell-cell adhesion 0.001 0.074 -10000 0 -0.27 12 12
EGF -0.091 0.21 -10000 0 -0.43 58 58
NCKAP1 0.032 0.024 -10000 0 -0.32 1 1
AQP3 0.007 0.053 -10000 0 -10000 0 0
cortical microtubule organization 0.054 0.066 -10000 0 -0.26 6 6
GO:0000145 -0.012 0.048 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.06 0.068 -10000 0 -0.26 6 6
MLLT4 0.032 0.007 -10000 0 -10000 0 0
ARF6/GDP -0.022 0.057 -10000 0 -0.35 2 2
ARF6 0.031 0.01 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.059 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.003 0.045 -10000 0 -10000 0 0
PVRL2 0.031 0.025 -10000 0 -0.32 1 1
ZYX 0.007 0.052 -10000 0 -0.25 6 6
ARF6/GTP 0.065 0.062 -10000 0 -10000 0 0
CDH1 0.018 0.088 -10000 0 -0.5 6 6
EGFR/EGFR/EGF/EGF -0.027 0.13 -10000 0 -0.38 3 3
RhoA/GDP 0.056 0.064 -10000 0 -0.25 6 6
actin cytoskeleton organization 0 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.031 0.009 -10000 0 -10000 0 0
GIT1 0.032 0.007 -10000 0 -10000 0 0
IGF1R 0.031 0.009 -10000 0 -10000 0 0
IGF1 -0.27 0.26 -10000 0 -0.5 124 124
DIAPH1 0.056 0.11 -10000 0 -0.68 2 2
Wnt receptor signaling pathway -0.054 0.066 0.26 6 -10000 0 6
RHOA 0.033 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.023 0.057 -10000 0 -0.35 2 2
CTNNA1 0.033 0.004 -10000 0 -10000 0 0
VCL 0 0.049 -10000 0 -10000 0 0
EFNA1 0.033 0.006 -10000 0 -10000 0 0
LPP 0.001 0.051 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.035 0.081 -10000 0 -0.32 5 5
SEC6/SEC8 0.006 0.049 -10000 0 -10000 0 0
MGAT3 0.001 0.075 -10000 0 -0.28 12 12
HGF/MET -0.042 0.11 -10000 0 -0.36 4 4
HGF 0.029 0.035 -10000 0 -0.32 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.003 0.09 -10000 0 -0.25 21 21
actin cable formation 0.013 0.082 0.32 5 -0.31 1 6
KIAA1543 -0.012 0.049 -10000 0 -10000 0 0
KIFC3 0.005 0.059 -10000 0 -0.29 2 2
NCK1 0.033 0.004 -10000 0 -10000 0 0
EXOC3 0.032 0.007 -10000 0 -10000 0 0
ACTN1 0.01 0.054 -10000 0 -10000 0 0
NCK1/GIT1 0.047 0.012 -10000 0 -10000 0 0
mol:GDP 0.054 0.066 -10000 0 -0.26 6 6
EXOC4 0.032 0.008 -10000 0 -10000 0 0
STX4 0.009 0.05 -10000 0 -10000 0 0
PIP5K1C 0.01 0.055 -10000 0 -0.25 6 6
LIMA1 -0.009 0.14 -10000 0 -0.5 17 17
ABI1 0.033 0.004 -10000 0 -10000 0 0
ROCK1 0.002 0.069 0.3 2 -10000 0 2
adherens junction assembly 0.008 0.061 0.28 3 -10000 0 3
IGF-1R heterotetramer/IGF1 -0.12 0.16 -10000 0 -0.45 6 6
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.046 0.021 -10000 0 -0.22 1 1
MET -0.12 0.18 -10000 0 -0.33 90 90
PLEKHA7 0.01 0.055 -10000 0 -10000 0 0
mol:GTP 0.06 0.058 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.015 0.064 0.33 1 -10000 0 1
cortical actin cytoskeleton stabilization 0.003 0.09 -10000 0 -0.25 21 21
regulation of cell-cell adhesion 0 0.048 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.003 0.09 -10000 0 -0.25 21 21
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.058 0.058 -10000 0 -0.26 5 5
ER alpha/Gai/GDP/Gbeta gamma -0.013 0.12 -10000 0 -0.5 6 6
AKT1 0.007 0.19 -10000 0 -0.74 12 12
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.011 0.19 -10000 0 -0.74 12 12
mol:Ca2+ -0.019 0.12 0.23 2 -0.38 9 11
IGF1R 0.031 0.009 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.033 0.058 -10000 0 -0.27 7 7
SHC1 0.033 0.006 -10000 0 -10000 0 0
apoptosis -0.008 0.18 0.7 12 -10000 0 12
RhoA/GTP 0.021 0.045 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.056 0.13 0.26 2 -0.38 5 7
regulation of stress fiber formation -0.002 0.056 -10000 0 -0.31 1 1
E2/ERA-ERB (dimer) 0.032 0.054 -10000 0 -0.31 5 5
KRAS 0.033 0.006 -10000 0 -10000 0 0
G13/GTP 0.031 0.049 -10000 0 -0.28 5 5
pseudopodium formation 0.002 0.056 0.31 1 -10000 0 1
E2/ER alpha (dimer)/PELP1 0.028 0.054 -10000 0 -0.3 5 5
GRB2 0.032 0.006 -10000 0 -10000 0 0
GNG2 0.031 0.01 -10000 0 -10000 0 0
GNAO1 0.033 0.005 -10000 0 -10000 0 0
HRAS 0.033 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.004 0.14 0.3 1 -0.46 10 11
E2/ER beta (dimer) 0.023 0.007 -10000 0 -10000 0 0
mol:GDP 0.008 0.073 -10000 0 -0.39 5 5
mol:NADP 0.004 0.14 0.3 1 -0.46 10 11
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 -0.03 0.11 0.24 1 -0.39 9 10
IGF-1R heterotetramer 0.031 0.009 -10000 0 -10000 0 0
PLCB1 -0.034 0.12 -10000 0 -0.35 14 14
PLCB2 -0.009 0.094 -10000 0 -0.4 9 9
IGF1 -0.27 0.26 -10000 0 -0.5 124 124
mol:L-citrulline 0.004 0.14 0.3 1 -0.46 10 11
RHOA 0.033 0.005 -10000 0 -10000 0 0
Gai/GDP 0.012 0.12 -10000 0 -0.66 4 4
JNK cascade 0.023 0.007 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
ESR2 0.031 0.01 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 0.02 0.081 -10000 0 -0.5 5 5
Gq family/GDP/Gbeta gamma -0.013 0.15 -10000 0 -0.58 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.038 0.1 -10000 0 -0.51 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.054 0.13 0.26 2 -0.38 6 8
GNAZ 0.032 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.015 0.058 -10000 0 -0.36 5 5
STRN 0.03 0.034 -10000 0 -0.32 2 2
GNAL 0.026 0.014 -10000 0 -10000 0 0
PELP1 0.027 0.013 -10000 0 -10000 0 0
MAPK11 0.016 0.015 -10000 0 -0.18 1 1
GNAI2 0.033 0.004 -10000 0 -10000 0 0
GNAI3 0.033 0.006 -10000 0 -10000 0 0
GNAI1 -0.032 0.17 -10000 0 -0.5 26 26
HBEGF 0.1 0.17 0.34 52 -0.41 2 54
cAMP biosynthetic process 0.023 0.044 -10000 0 -0.24 5 5
SRC 0.047 0.13 -10000 0 -0.44 2 2
PI3K 0.048 0.009 -10000 0 -10000 0 0
GNB1 0.032 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.04 0.076 -10000 0 -0.35 5 5
SOS1 0.033 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.098 0.12 -10000 0 -0.39 13 13
Gs family/GTP 0.03 0.048 -10000 0 -0.25 5 5
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.057 0.028 -10000 0 -10000 0 0
vasodilation 0.005 0.13 0.3 1 -0.44 10 11
mol:DAG -0.03 0.11 0.24 1 -0.39 9 10
Gs family/GDP/Gbeta gamma 0.015 0.065 -10000 0 -0.33 5 5
MSN 0.001 0.058 0.32 1 -10000 0 1
Gq family/GTP -0.006 0.1 -10000 0 -0.35 14 14
mol:PI-3-4-5-P3 0.012 0.18 -10000 0 -0.71 12 12
NRAS 0.029 0.035 -10000 0 -0.32 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.005 0.13 0.44 10 -0.3 1 11
GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.027 0.078 -10000 0 -0.37 5 5
NOS3 0.003 0.14 0.31 1 -0.48 10 11
GNA11 0.018 0.088 -10000 0 -0.5 6 6
MAPKKK cascade 0.037 0.16 0.45 1 -0.5 10 11
E2/ER alpha (dimer)/PELP1/Src 0.055 0.13 0.28 2 -0.39 6 8
ruffle organization 0.002 0.056 0.31 1 -10000 0 1
ROCK2 0.021 0.06 0.33 1 -10000 0 1
GNA14 0.011 0.11 -10000 0 -0.5 9 9
GNA15 0.021 0.064 -10000 0 -0.32 7 7
GNA13 0.032 0.008 -10000 0 -10000 0 0
MMP9 0.085 0.18 0.39 48 -0.42 2 50
MMP2 0.044 0.13 0.28 2 -0.41 3 5
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.018 0.017 -10000 0 -10000 0 0
GNB1/GNG2 -0.032 0.1 -10000 0 -0.35 3 3
mol:DAG -0.024 0.071 -10000 0 -0.32 1 1
PLCG1 -0.025 0.072 -10000 0 -0.33 1 1
YES1 -0.035 0.082 -10000 0 -0.31 4 4
FZD3 -0.051 0.15 -10000 0 -0.34 45 45
FZD6 0.018 0.065 -10000 0 -0.36 6 6
G protein 0.03 0.12 0.3 2 -0.34 1 3
MAP3K7 -0.02 0.065 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.069 -10000 0 -0.32 1 1
mol:IP3 -0.024 0.071 -10000 0 -0.32 1 1
NLK -0.002 0.1 -10000 0 -0.76 4 4
GNB1 0.032 0.008 -10000 0 -10000 0 0
CAMK2A -0.021 0.069 -10000 0 -0.3 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.045 0.1 -10000 0 -0.34 8 8
CSNK1A1 0.033 0.004 -10000 0 -10000 0 0
GNAS -0.008 0.088 -10000 0 -0.31 5 5
GO:0007205 -0.025 0.067 -10000 0 -0.31 1 1
WNT6 0.032 0.024 -10000 0 -0.32 1 1
WNT4 0.013 0.094 -10000 0 -0.46 8 8
NFAT1/CK1 alpha -0.016 0.078 -10000 0 -0.33 1 1
GNG2 0.031 0.01 -10000 0 -10000 0 0
WNT5A -0.022 0.13 -10000 0 -0.33 33 33
WNT11 -0.04 0.14 -10000 0 -0.32 44 44
CDC42 -0.036 0.078 -10000 0 -0.34 1 1
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.004 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.046 0.021 -9999 0 -0.22 1 1
PTK2 0.014 0.095 -9999 0 -0.39 8 8
positive regulation of JNK cascade 0.023 0.093 -9999 0 -0.36 1 1
CDC42/GDP 0.059 0.13 -9999 0 -0.41 6 6
Rac1/GDP 0.052 0.13 -9999 0 -0.41 6 6
RAP1B 0.033 0.005 -9999 0 -10000 0 0
RAP1A 0.032 0.007 -9999 0 -10000 0 0
CTNNB1 0.025 0.054 -9999 0 -0.32 5 5
CDC42/GTP 0.043 0.12 -9999 0 -0.45 1 1
nectin-3/I-afadin 0.026 0.091 -9999 0 -0.36 11 11
RAPGEF1 0.031 0.12 -9999 0 -0.44 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0.12 -9999 0 -0.48 7 7
PDGFB-D/PDGFRB 0.033 0.004 -9999 0 -10000 0 0
TLN1 -0.002 0.048 -9999 0 -0.38 2 2
Rap1/GTP 0.019 0.087 -9999 0 -0.32 5 5
IQGAP1 0.031 0.009 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.059 0.019 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.026 0.091 -9999 0 -0.36 11 11
PVR 0.033 0.005 -9999 0 -10000 0 0
Necl-5(dimer) 0.033 0.005 -9999 0 -10000 0 0
mol:GDP 0.049 0.14 -9999 0 -0.5 6 6
MLLT4 0.032 0.007 -9999 0 -10000 0 0
PIK3CA 0.033 0.004 -9999 0 -10000 0 0
PI3K 0.074 0.083 -9999 0 -0.27 11 11
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.047 0.012 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly 0.028 0.1 -9999 0 -0.33 5 5
PVRL1 0.033 0.005 -9999 0 -10000 0 0
PVRL3 0.006 0.12 -9999 0 -0.5 11 11
PVRL2 0.031 0.025 -9999 0 -0.32 1 1
PIK3R1 0.033 0.005 -9999 0 -10000 0 0
CDH1 0.018 0.088 -9999 0 -0.5 6 6
CLDN1 -0.31 0.073 -9999 0 -0.32 206 206
JAM-A/CLDN1 -0.16 0.077 -9999 0 -0.4 11 11
SRC -0.002 0.13 -9999 0 -0.51 9 9
ITGB3 0.032 0.007 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.047 0.012 -9999 0 -10000 0 0
FARP2 0.047 0.15 -9999 0 -0.68 1 1
RAC1 0.031 0.01 -9999 0 -10000 0 0
CTNNA1 0.033 0.004 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.046 0.081 -9999 0 -0.31 10 10
nectin-1/I-afadin 0.047 0.012 -9999 0 -10000 0 0
nectin-2/I-afadin 0.046 0.021 -9999 0 -0.22 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.039 0.016 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.044 0.084 -9999 0 -0.31 11 11
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.015 -9999 0 -10000 0 0
F11R 0.033 0.006 -9999 0 -10000 0 0
positive regulation of filopodium formation 0.023 0.093 -9999 0 -0.36 1 1
alphaV/beta3 Integrin/Talin 0.009 0.081 -9999 0 -0.35 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.046 0.021 -9999 0 -0.22 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.046 0.021 -9999 0 -0.22 1 1
PIP5K1C 0 0.053 -9999 0 -0.4 2 2
VAV2 0.043 0.16 -9999 0 -0.54 5 5
RAP1/GDP 0.063 0.12 -9999 0 -0.38 5 5
ITGAV 0.031 0.025 -9999 0 -0.32 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.045 0.082 -9999 0 -0.31 10 10
nectin-3(dimer)/I-afadin/I-afadin 0.026 0.091 -9999 0 -0.36 11 11
Rac1/GTP 0.035 0.12 -9999 0 -0.41 5 5
PTPRM 0.003 0.059 -9999 0 -0.24 10 10
E-cadherin/beta catenin/alpha catenin 0.074 0.075 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.031 0.009 -9999 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.02 0.078 -10000 0 -0.35 2 2
BAG4 0.03 0.01 -10000 0 -10000 0 0
BAD -0.004 0.056 0.21 1 -0.18 3 4
NFKBIA 0.031 0.01 -10000 0 -10000 0 0
BIRC3 0.008 0.11 -10000 0 -0.45 11 11
BAX -0.003 0.064 0.3 2 -0.2 3 5
EnzymeConsortium:3.1.4.12 0.01 0.023 0.12 2 -0.076 1 3
IKBKB 0.035 0.088 0.28 2 -0.37 1 3
MAP2K2 0.003 0.06 0.21 5 -10000 0 5
MAP2K1 0.002 0.057 0.22 4 -10000 0 4
SMPD1 -0.035 0.097 0.18 1 -0.22 45 46
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.028 0.077 -10000 0 -0.33 1 1
MAP2K4 -0.004 0.051 0.21 1 -0.22 1 2
protein ubiquitination 0.029 0.083 0.32 2 -0.37 1 3
EnzymeConsortium:2.7.1.37 0.005 0.06 0.21 5 -10000 0 5
response to UV 0 0 0.002 7 -10000 0 7
RAF1 0.002 0.061 0.2 7 -10000 0 7
CRADD 0.028 0.052 -10000 0 -0.5 2 2
mol:ceramide -0.005 0.059 0.22 1 -0.16 5 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0.04 0.014 -10000 0 -10000 0 0
MADD 0.033 0.003 -10000 0 -10000 0 0
MAP3K1 -0.005 0.056 0.22 1 -0.18 2 3
TRADD 0.033 0.005 -10000 0 -10000 0 0
RELA/p50 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.007 0.061 0.21 5 -10000 0 5
MAPK1 0.003 0.063 0.21 4 -10000 0 4
p50/RELA/I-kappa-B-alpha 0.044 0.016 -10000 0 -10000 0 0
FADD 0.023 0.074 -10000 0 -0.32 1 1
KSR1 0 0.062 0.21 6 -0.19 2 8
MAPK8 -0.003 0.053 0.2 2 -0.2 1 3
TRAF2 0.033 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 3 -10000 0 3
CHUK 0.018 0.073 -10000 0 -0.37 1 1
TNF R/SODD 0.043 0.017 -10000 0 -10000 0 0
TNF 0.033 0.005 -10000 0 -10000 0 0
CYCS 0.068 0.079 0.17 32 -0.17 1 33
IKBKG 0.023 0.08 0.23 1 -0.34 2 3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.025 0.078 -10000 0 -0.32 2 2
RELA 0.033 0.006 -10000 0 -10000 0 0
RIPK1 0.033 0.005 -10000 0 -10000 0 0
AIFM1 0.064 0.075 0.17 23 -0.17 1 24
TNF/TNF R/SODD 0.058 0.025 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.007 -10000 0 -10000 0 0
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.029 0.11 -10000 0 -0.59 6 6
NSMAF 0.041 0.09 0.25 4 -0.29 1 5
response to hydrogen peroxide 0 0 0.002 7 -10000 0 7
BCL2 -0.19 0.25 -10000 0 -0.5 87 87
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.02 0.017 -10000 0 -10000 0 0
NFATC1 -0.018 0.14 0.31 3 -0.38 17 20
NFATC2 0.042 0.047 0.17 4 -10000 0 4
NFATC3 0.015 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.014 0.063 -10000 0 -0.29 2 2
Exportin 1/Ran/NUP214 0.066 0.021 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.047 0.066 -10000 0 -0.29 1 1
BCL2/BAX -0.16 0.18 -10000 0 -0.36 86 86
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.009 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.009 -10000 0 -10000 0 0
BAX 0.031 0.025 -10000 0 -0.32 1 1
MAPK14 0.033 0.005 -10000 0 -10000 0 0
BAD 0.033 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.028 0.065 -10000 0 -0.32 1 1
Calcineurin A alpha-beta B1/BCL2 -0.19 0.25 -10000 0 -0.5 87 87
FKBP8 0.033 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.027 0.064 0.31 1 -10000 0 1
KPNB1 0.022 0.059 -10000 0 -0.32 6 6
KPNA2 0.019 0.068 -10000 0 -0.32 8 8
XPO1 0.034 0 -10000 0 -10000 0 0
SFN 0.026 0.052 -10000 0 -0.5 2 2
MAP3K8 -0.015 0.12 -10000 0 -0.32 29 29
NFAT4/CK1 alpha 0.034 0.025 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.088 0.055 -10000 0 -10000 0 0
CABIN1 0.014 0.061 -10000 0 -0.29 2 2
CALM1 0.031 0.01 -10000 0 -10000 0 0
RAN 0.032 0.025 -10000 0 -0.32 1 1
MAP3K1 0.033 0.004 -10000 0 -10000 0 0
CAMK4 0.033 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.028 0.052 -10000 0 -0.5 2 2
YWHAH 0.032 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.037 0.057 -10000 0 -0.36 4 4
YWHAB 0.018 0.017 -10000 0 -10000 0 0
MAPK8 0.033 0.006 -10000 0 -10000 0 0
MAPK9 0.033 0.004 -10000 0 -10000 0 0
YWHAG 0.032 0.007 -10000 0 -10000 0 0
FKBP1A 0.027 0.014 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.011 0.13 0.44 1 -0.36 5 6
PRKCH 0.026 0.052 -10000 0 -0.5 2 2
CABIN1/Cbp/p300 0.046 0.015 -10000 0 -10000 0 0
CASP3 0.032 0.008 -10000 0 -10000 0 0
PIM1 0.033 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.009 -10000 0 -10000 0 0
apoptosis -0.018 0.053 -10000 0 -0.33 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.041 0.047 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.033 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.03 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.029 0.025 -10000 0 -10000 0 0
PRKCD 0.033 0.005 -10000 0 -10000 0 0
NUP214 0.033 0.005 -10000 0 -10000 0 0
PRKCZ 0 0.001 -10000 0 -10000 0 0
PRKCA 0.029 0.026 -10000 0 -0.32 1 1
PRKCG 0.026 0.049 -10000 0 -0.32 4 4
PRKCQ 0.026 0.049 -10000 0 -0.32 4 4
FKBP38/BCL2 -0.16 0.18 -10000 0 -0.36 86 86
EP300 0.032 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.014 -10000 0 -10000 0 0
NFATc/JNK1 -0.002 0.14 0.34 2 -0.35 17 19
CaM/Ca2+/FKBP38 0.041 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.01 -10000 0 -10000 0 0
CSNK1A1 0.019 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.041 0.016 -10000 0 -10000 0 0
NFATc/ERK1 -0.006 0.14 0.42 1 -0.36 16 17
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.049 0.067 -10000 0 -0.29 1 1
NR4A1 0.055 0.058 0.3 2 -10000 0 2
GSK3B 0.032 0.025 -10000 0 -0.32 1 1
positive T cell selection 0.015 0.006 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.037 0.038 -10000 0 -10000 0 0
RCH1/ KPNB1 0.03 0.07 -10000 0 -0.24 13 13
YWHAQ 0.033 0.002 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
AKAP5 0.021 0.072 -10000 0 -0.5 4 4
MEF2D 0.033 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
NFATc/p38 alpha -0.005 0.14 0.43 1 -0.35 17 18
CREBBP 0.033 0.006 -10000 0 -10000 0 0
BCL2 -0.19 0.25 -10000 0 -0.5 87 87
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.03 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.006 0.13 -10000 0 -0.39 10 10
NEF -0.012 0.047 -10000 0 -10000 0 0
NFKBIA 0.026 0.031 -10000 0 -10000 0 0
BIRC3 0.003 0.11 -10000 0 -0.48 11 11
CYCS -0.017 0.13 -10000 0 -0.4 10 10
RIPK1 0.033 0.005 -10000 0 -10000 0 0
CD247 -0.011 0.15 -10000 0 -0.6 11 11
MAP2K7 0.004 0.14 -10000 0 -0.68 4 4
protein ubiquitination 0.037 0.065 0.34 3 -10000 0 3
CRADD 0.028 0.051 -10000 0 -0.5 2 2
DAXX 0.033 0.005 -10000 0 -10000 0 0
FAS -0.018 0.16 -10000 0 -0.5 20 20
BID -0.024 0.13 0.2 4 -0.42 11 15
NF-kappa-B/RelA/I kappa B alpha 0.051 0.075 -10000 0 -0.28 7 7
TRADD 0.033 0.005 -10000 0 -10000 0 0
MAP3K5 0.029 0.035 -10000 0 -0.32 2 2
CFLAR 0.034 0 -10000 0 -10000 0 0
FADD 0.033 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.075 -10000 0 -0.28 7 7
MAPK8 0.006 0.13 0.44 1 -0.71 3 4
APAF1 0.03 0.034 -10000 0 -0.32 2 2
TRAF1 0.033 0.005 -10000 0 -10000 0 0
TRAF2 0.033 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.018 0.13 0.2 4 -0.33 26 30
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.039 0.056 -10000 0 -0.36 1 1
CHUK 0.039 0.064 0.35 3 -10000 0 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.057 0.11 -10000 0 -0.27 18 18
TCRz/NEF -0.02 0.15 -10000 0 -0.39 26 26
TNF 0.033 0.005 -10000 0 -10000 0 0
FASLG -0.052 0.22 -10000 0 -0.59 28 28
NFKB1 0.029 0.029 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.058 0.025 -10000 0 -10000 0 0
CASP6 0.021 0.13 -10000 0 -0.66 3 3
CASP7 -0.045 0.19 0.46 1 -0.49 22 23
RELA 0.029 0.029 -10000 0 -10000 0 0
CASP2 0.032 0.006 -10000 0 -10000 0 0
CASP3 -0.012 0.15 0.46 1 -0.53 10 11
TNFRSF1A 0.032 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.043 0.017 -10000 0 -10000 0 0
CASP8 0.034 0 -10000 0 -10000 0 0
CASP9 0.031 0.009 -10000 0 -10000 0 0
MAP3K14 0.038 0.061 0.24 1 -0.32 1 2
APAF-1/Caspase 9 -0.01 0.13 -10000 0 -0.37 12 12
BCL2 -0.1 0.15 -10000 0 -0.44 16 16
Nongenotropic Androgen signaling

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
PTK2 0.008 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.054 0.027 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.017 0.018 -10000 0 -10000 0 0
GNAO1 0.033 0.005 -10000 0 -10000 0 0
HRAS 0.033 0.004 -10000 0 -10000 0 0
SHBG/T-DHT 0.018 0.009 -10000 0 -10000 0 0
PELP1 0.027 0.013 -10000 0 -10000 0 0
AKT1 0.009 0.003 -10000 0 -10000 0 0
MAP2K1 0.058 0.091 0.22 1 -10000 0 1
T-DHT/AR 0.023 0.017 -10000 0 -0.22 1 1
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 33 33
GNAI2 0.033 0.004 -10000 0 -10000 0 0
GNAI3 0.032 0.006 -10000 0 -10000 0 0
GNAI1 -0.032 0.17 -10000 0 -0.5 26 26
mol:GDP 0.006 0.007 -10000 0 -10000 0 0
cell proliferation 0.022 0.17 0.28 5 -0.41 15 20
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
FOS -0.056 0.31 -10000 0 -0.81 31 31
mol:Ca2+ -0.005 0.026 -10000 0 -0.073 20 20
MAPK3 0.042 0.13 0.3 5 -0.33 3 8
MAPK1 0.009 0.12 -10000 0 -0.42 7 7
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.005 33 33
cAMP biosynthetic process 0.003 0.02 -10000 0 -10000 0 0
GNG2 0.031 0.01 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 33 33
HRAS/GTP 0.027 0.039 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.042 0.021 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 33 33
PI3K 0.044 0.009 -10000 0 -10000 0 0
apoptosis -0.013 0.17 0.36 29 -0.24 2 31
T-DHT/AR/PELP1 0.035 0.023 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.023 -10000 0 -10000 0 0
CREB1 0.011 0.18 0.24 2 -0.38 29 31
RAC1-CDC42/GTP 0.053 0.026 -10000 0 -10000 0 0
AR 0.031 0.024 -10000 0 -0.32 1 1
GNB1 0.032 0.008 -10000 0 -10000 0 0
RAF1 0.073 0.089 0.22 1 -10000 0 1
RAC1-CDC42/GDP 0.068 0.045 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0.031 0.032 -10000 0 -10000 0 0
MAP2K2 0.06 0.091 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0.017 0.018 -10000 0 -10000 0 0
GNAZ 0.031 0.008 -10000 0 -10000 0 0
SHBG 0.027 0.014 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.007 0.093 -10000 0 -0.5 2 2
mol:T-DHT -0.001 0.002 -10000 0 -0.004 27 27
RAC1 0.031 0.01 -10000 0 -10000 0 0
GNRH1 0.008 0.004 -10000 0 -10000 0 0
Gi family/GTP -0.012 0.085 -10000 0 -0.25 14 14
CDC42 0.031 0.009 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.039 0.012 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.016 0.083 0.46 1 -10000 0 1
IL27/IL27R/JAK1 -0.018 0.11 -10000 0 -10000 0 0
TBX21 -0.15 0.2 -10000 0 -0.43 58 58
IL12B 0.029 0.035 -10000 0 -0.33 2 2
IL12A 0.001 0.039 -10000 0 -0.23 6 6
IL6ST 0.029 0.007 -10000 0 -10000 0 0
IL27RA/JAK1 0.004 0.046 -10000 0 -10000 0 0
IL27 -0.005 0.13 -10000 0 -0.46 15 15
TYK2 0.022 0.021 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.008 0.14 1.1 2 -10000 0 2
T-helper 2 cell differentiation 0.016 0.083 0.46 1 -10000 0 1
T cell proliferation during immune response 0.016 0.083 0.46 1 -10000 0 1
MAPKKK cascade -0.016 0.083 -10000 0 -0.46 1 1
STAT3 0.033 0.006 -10000 0 -10000 0 0
STAT2 0.033 0.004 -10000 0 -10000 0 0
STAT1 0.001 0.1 -10000 0 -0.32 19 19
IL12RB1 0.033 0.004 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.082 0.13 0.38 1 -0.46 3 4
IL27/IL27R/JAK2/TYK2 -0.016 0.083 -10000 0 -0.46 1 1
positive regulation of T cell mediated cytotoxicity -0.016 0.083 -10000 0 -0.46 1 1
STAT1 (dimer) -0.081 0.17 -10000 0 -0.6 2 2
JAK2 0.024 0.044 -10000 0 -0.34 3 3
JAK1 0.031 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.007 0.09 -10000 0 -0.44 1 1
T cell proliferation -0.074 0.12 -10000 0 -0.45 4 4
IL12/IL12R/TYK2/JAK2 0.012 0.13 -10000 0 -0.73 5 5
IL17A 0.008 0.14 1.1 2 -10000 0 2
mast cell activation 0.016 0.083 0.46 1 -10000 0 1
IFNG -0.002 0.029 -10000 0 -0.087 3 3
T cell differentiation -0.005 0.005 -10000 0 -0.017 8 8
STAT3 (dimer) -0.006 0.091 -10000 0 -0.44 1 1
STAT5A (dimer) -0.006 0.091 -10000 0 -0.44 1 1
STAT4 (dimer) -0.006 0.093 -10000 0 -0.44 1 1
STAT4 0.031 0.036 -10000 0 -0.5 1 1
T cell activation -0.007 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.005 0.069 -10000 0 -10000 0 0
GATA3 0.008 0.057 0.55 2 -10000 0 2
IL18 -0.031 0.12 -10000 0 -0.36 24 24
positive regulation of mast cell cytokine production -0.006 0.09 -10000 0 -0.44 1 1
IL27/EBI3 0.012 0.098 -10000 0 -0.34 15 15
IL27RA -0.002 0.04 -10000 0 -10000 0 0
IL6 -0.12 0.17 -10000 0 -0.32 93 93
STAT5A 0.033 0.006 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.007 0.019 -10000 0 -10000 0 0
IL1B -0.033 0.091 -10000 0 -0.22 40 40
EBI3 0.028 0.007 -10000 0 -10000 0 0
TNF 0.01 0.002 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.025 0.063 -10000 0 -0.5 3 3
HRAS 0.033 0.004 -10000 0 -10000 0 0
EGFR 0.021 0.072 -10000 0 -0.5 4 4
AKT 0.037 0.08 0.31 6 -10000 0 6
FOXO3 0.032 0.007 -10000 0 -10000 0 0
AKT1 0.03 0.01 -10000 0 -10000 0 0
FOXO1 0.01 0.088 -10000 0 -0.5 6 6
AKT3 0.033 0.006 -10000 0 -10000 0 0
FOXO4 0.033 0.002 -10000 0 -10000 0 0
MET -0.12 0.18 -10000 0 -0.33 90 90
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
PIK3CB 0.033 0.005 -10000 0 -10000 0 0
NRAS 0.029 0.035 -10000 0 -0.32 2 2
PIK3CG 0.02 0.081 -10000 0 -0.5 5 5
PIK3R3 0.033 0.005 -10000 0 -10000 0 0
PIK3R2 0.033 0.004 -10000 0 -10000 0 0
NF1 0.032 0.007 -10000 0 -10000 0 0
RAS 0.005 0.07 0.24 6 -0.21 4 10
ERBB2 0.029 0.037 -10000 0 -0.5 1 1
proliferation/survival/translation -0.031 0.075 0.3 3 -0.27 2 5
PI3K 0.025 0.083 0.27 11 -0.17 2 13
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
KRAS 0.033 0.006 -10000 0 -10000 0 0
FOXO 0.064 0.071 0.25 9 -10000 0 9
AKT2 0.032 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.052 -10000 0 -0.5 2 2
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.02 0.035 0.28 1 -10000 0 1
DAPP1 -0.014 0.17 0.24 9 -0.41 20 29
Src family/SYK family/BLNK-LAT/BTK-ITK -0.054 0.22 0.3 1 -0.58 21 22
mol:DAG -0.025 0.11 0.19 19 -0.24 12 31
HRAS 0.035 0.006 -10000 0 -10000 0 0
RAP1A 0.033 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.049 0.092 0.25 1 -0.3 3 4
PLCG2 -0.23 0.27 -10000 0 -0.5 104 104
PLCG1 0.017 0.029 -10000 0 -0.32 1 1
ARF5 0.032 0.007 -10000 0 -10000 0 0
mol:GTP -0.007 0.039 0.22 3 -10000 0 3
ARF1/GTP 0.001 0.034 0.22 3 -10000 0 3
RHOA 0.033 0.005 -10000 0 -10000 0 0
YES1 0.027 0.013 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.037 0.21 2 -10000 0 2
ADAP1 -0.006 0.037 0.21 3 -10000 0 3
ARAP3 -0.006 0.038 0.22 3 -10000 0 3
INPPL1 0.033 0.004 -10000 0 -10000 0 0
PREX1 0.019 0.017 -10000 0 -10000 0 0
ARHGEF6 0.028 0.051 -10000 0 -0.5 2 2
ARHGEF7 0.025 0.015 -10000 0 -10000 0 0
ARF1 0.033 0.006 -10000 0 -10000 0 0
NRAS 0.03 0.035 -10000 0 -0.33 2 2
FYN 0.03 0.037 -10000 0 -0.5 1 1
ARF6 0.031 0.01 -10000 0 -10000 0 0
FGR 0.031 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.062 0.16 5 -10000 0 5
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.026 0.052 -10000 0 -0.5 2 2
ZAP70 0.033 0.002 -10000 0 -10000 0 0
mol:IP3 -0.016 0.081 0.15 20 -0.2 3 23
LYN 0.029 0.012 -10000 0 -10000 0 0
ARF1/GDP 0.049 0.093 0.25 1 -0.29 4 5
RhoA/GDP 0.052 0.061 0.23 5 -10000 0 5
PDK1/Src/Hsp90 0.035 0.037 -10000 0 -10000 0 0
BLNK 0.017 0.088 -10000 0 -0.5 6 6
actin cytoskeleton reorganization 0.049 0.088 0.29 5 -0.39 1 6
SRC 0.019 0.017 -10000 0 -10000 0 0
PLEKHA2 0.005 0.019 0.2 1 -10000 0 1
RAC1 0.031 0.01 -10000 0 -10000 0 0
PTEN 0.026 0.05 -10000 0 -0.48 2 2
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
ARF6/GTP 0.02 0.037 0.24 3 -10000 0 3
RhoA/GTP -0.003 0.045 0.23 3 -10000 0 3
Src family/SYK family/BLNK-LAT -0.031 0.12 -10000 0 -0.44 11 11
BLK -0.083 0.21 -10000 0 -0.5 44 44
PDPK1 0.033 0.006 -10000 0 -10000 0 0
CYTH1 -0.006 0.037 0.21 3 -10000 0 3
HCK 0.004 0.087 -10000 0 -0.5 6 6
CYTH3 -0.006 0.037 0.21 3 -10000 0 3
CYTH2 -0.006 0.037 0.21 3 -10000 0 3
KRAS 0.034 0.008 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.009 0.031 0.19 1 -10000 0 1
SGK1 0.009 0.032 0.2 1 -10000 0 1
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.038 0.091 0.25 1 -0.3 4 5
SOS1 0.033 0.002 -10000 0 -10000 0 0
SYK 0.031 0.025 -10000 0 -0.32 1 1
ARF6/GDP 0.038 0.06 0.25 4 -10000 0 4
mol:PI-3-4-5-P3 -0.006 0.041 0.26 3 -10000 0 3
ARAP3/RAP1A/GTP 0.019 0.037 0.21 2 -10000 0 2
VAV1 -0.014 0.15 -10000 0 -0.5 19 19
mol:PI-3-4-P2 0.01 0.001 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.057 0.048 -10000 0 -10000 0 0
PLEKHA1 0.006 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.046 0.089 0.25 1 -0.29 4 5
LAT 0.031 0.025 -10000 0 -0.32 1 1
Rac1/GTP 0.006 0.064 -10000 0 -0.42 2 2
ITK -0.007 0.034 0.23 2 -10000 0 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.042 0.14 0.22 18 -0.33 16 34
LCK 0.028 0.044 -10000 0 -0.41 2 2
BTK -0.043 0.091 0.19 2 -0.26 29 31
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.032 0.057 -10000 0 -0.36 1 1
Syndecan-4/Syndesmos 0.1 0.11 0.37 1 -10000 0 1
positive regulation of JNK cascade -0.07 0.14 -10000 0 -0.57 2 2
Syndecan-4/ADAM12 0.063 0.15 0.37 1 -0.47 2 3
CCL5 -0.09 0.22 -10000 0 -0.5 49 49
Rac1/GDP 0.023 0.007 -10000 0 -10000 0 0
DNM2 0.033 0.004 -10000 0 -10000 0 0
ITGA5 0.025 0.054 -10000 0 -0.32 5 5
SDCBP 0.029 0.011 -10000 0 -10000 0 0
PLG 0.005 0.031 -10000 0 -10000 0 0
ADAM12 -0.1 0.18 -10000 0 -0.33 82 82
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.033 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.021 0.026 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.077 0.1 -10000 0 -10000 0 0
Syndecan-4/CXCL12/CXCR4 -0.073 0.15 -10000 0 -0.61 2 2
Syndecan-4/Laminin alpha3 0.076 0.11 -10000 0 -10000 0 0
MDK 0.013 0.082 -10000 0 -0.32 12 12
Syndecan-4/FZD7 0.1 0.12 0.37 1 -0.43 1 2
Syndecan-4/Midkine 0.1 0.12 0.37 1 -0.43 1 2
FZD7 0.019 0.078 -10000 0 -0.37 8 8
Syndecan-4/FGFR1/FGF 0.095 0.12 0.36 1 -10000 0 1
THBS1 0.027 0.044 -10000 0 -0.41 2 2
integrin-mediated signaling pathway 0.1 0.11 -10000 0 -0.42 1 1
positive regulation of MAPKKK cascade -0.07 0.14 -10000 0 -0.57 2 2
Syndecan-4/TACI 0.083 0.11 0.37 1 -10000 0 1
CXCR4 0.015 0.079 -10000 0 -0.32 11 11
cell adhesion 0.011 0.053 0.2 7 -10000 0 7
Syndecan-4/Dynamin 0.11 0.11 0.37 1 -0.43 1 2
Syndecan-4/TSP1 0.1 0.11 0.37 1 -10000 0 1
Syndecan-4/GIPC 0.11 0.11 0.37 1 -10000 0 1
Syndecan-4/RANTES 0.049 0.14 0.37 1 -0.65 1 2
ITGB1 0.032 0.025 -10000 0 -0.32 1 1
LAMA1 0.026 0.014 -10000 0 -10000 0 0
LAMA3 0.019 0.051 -10000 0 -0.38 3 3
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCA 0.023 0.14 0.68 9 -10000 0 9
Syndecan-4/alpha-Actinin 0.098 0.11 -10000 0 -0.43 1 1
TFPI 0.032 0.024 -10000 0 -0.32 1 1
F2 0.053 0.023 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.041 0.045 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.065 0.1 -10000 0 -10000 0 0
ACTN1 0.031 0.01 -10000 0 -10000 0 0
TNC 0.025 0.054 -10000 0 -0.32 5 5
Syndecan-4/CXCL12 -0.068 0.14 -10000 0 -0.63 2 2
FGF6 0.03 0.025 -10000 0 -0.32 1 1
RHOA 0.033 0.005 -10000 0 -10000 0 0
CXCL12 -0.36 0.23 -10000 0 -0.5 160 160
TNFRSF13B 0.019 0.063 -10000 0 -0.5 3 3
FGF2 0.011 0.1 -10000 0 -0.48 9 9
FGFR1 0.03 0.011 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.012 0.059 -10000 0 -0.43 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.035 0.11 -10000 0 -0.34 24 24
cell migration -0.012 0.014 -10000 0 -10000 0 0
PRKCD 0.006 0.031 -10000 0 -10000 0 0
vasculogenesis 0.1 0.11 0.37 1 -10000 0 1
SDC4 0.017 0.054 -10000 0 -0.45 1 1
Syndecan-4/Tenascin C 0.1 0.11 -10000 0 -0.43 1 1
Syndecan-4/PI-4-5-P2/PKC alpha -0.017 0.021 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.089 0.1 0.37 1 -10000 0 1
MMP9 0.009 0.064 -10000 0 -0.35 6 6
Rac1/GTP 0.011 0.054 0.2 7 -10000 0 7
cytoskeleton organization 0.1 0.1 0.37 1 -0.42 1 2
GIPC1 0.03 0.037 -10000 0 -0.5 1 1
Syndecan-4/TFPI 0.11 0.11 0.37 1 -10000 0 1
IL23-mediated signaling events

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
CCL2 -0.23 0.36 -10000 0 -1.2 17 17
IL23A -0.26 0.3 -10000 0 -1.2 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.2 0.29 -10000 0 -1.2 6 6
positive regulation of T cell mediated cytotoxicity -0.21 0.3 -10000 0 -1.3 6 6
ITGA3 -0.2 0.28 -10000 0 -1.2 5 5
IL17F -0.14 0.21 -10000 0 -0.72 6 6
IL12B -0.003 0.053 -10000 0 -0.36 2 2
STAT1 (dimer) -0.21 0.31 -10000 0 -1.1 9 9
CD4 -0.19 0.27 -10000 0 -1.1 5 5
IL23 -0.25 0.29 -10000 0 -1.1 6 6
IL23R -0.057 0.26 -10000 0 -1.3 8 8
IL1B -0.24 0.3 -10000 0 -1.3 5 5
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.2 0.29 -10000 0 -1.1 6 6
TYK2 0.001 0.033 -10000 0 -10000 0 0
STAT4 0.031 0.036 -10000 0 -0.5 1 1
STAT3 0.033 0.006 -10000 0 -10000 0 0
IL18RAP -0.074 0.21 -10000 0 -0.5 43 43
IL12RB1 0.001 0.033 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.009 0.043 -10000 0 -10000 0 0
IL23R/JAK2 -0.058 0.25 -10000 0 -1.3 7 7
positive regulation of chronic inflammatory response -0.21 0.3 -10000 0 -1.3 6 6
natural killer cell activation 0.004 0.013 0.081 5 -10000 0 5
JAK2 -0.004 0.058 -10000 0 -0.36 3 3
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
NFKB1 0.031 0.006 -10000 0 -10000 0 0
RELA 0.031 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.24 0.28 -10000 0 -1.1 6 6
ALOX12B -0.19 0.27 -10000 0 -1.1 5 5
CXCL1 -0.27 0.29 -10000 0 -1.1 7 7
T cell proliferation -0.21 0.3 -10000 0 -1.3 6 6
NFKBIA 0.029 0.01 -10000 0 -10000 0 0
IL17A -0.11 0.17 -10000 0 -0.57 4 4
PI3K -0.18 0.29 -10000 0 -1.2 6 6
IFNG -0.023 0.04 0.14 4 -0.11 3 7
STAT3 (dimer) -0.16 0.29 -10000 0 -1.1 6 6
IL18R1 0.03 0.036 -10000 0 -0.5 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.12 0.19 -10000 0 -0.79 5 5
IL18/IL18R -0.062 0.19 -10000 0 -0.34 60 60
macrophage activation -0.019 0.015 -10000 0 -0.045 3 3
TNF -0.23 0.29 -10000 0 -1.2 5 5
STAT3/STAT4 -0.19 0.29 -10000 0 -1.2 6 6
STAT4 (dimer) -0.2 0.3 -10000 0 -1.2 6 6
IL18 -0.027 0.17 -10000 0 -0.49 24 24
IL19 -0.19 0.27 -10000 0 -1.1 5 5
STAT5A (dimer) -0.2 0.3 -10000 0 -1.2 6 6
STAT1 0.002 0.1 -10000 0 -0.32 19 19
SOCS3 0.017 0.072 -10000 0 -0.32 9 9
CXCL9 -0.26 0.38 -10000 0 -1.2 20 20
MPO -0.19 0.28 -10000 0 -1.2 5 5
positive regulation of humoral immune response -0.21 0.3 -10000 0 -1.3 6 6
IL23/IL23R/JAK2/TYK2 -0.21 0.32 -10000 0 -1.4 6 6
IL6 -0.23 0.31 -10000 0 -1.2 5 5
STAT5A 0.033 0.006 -10000 0 -10000 0 0
IL2 0.03 0.017 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.013 0.081 5 -10000 0 5
CD3E -0.19 0.27 -10000 0 -1.1 5 5
keratinocyte proliferation -0.21 0.3 -10000 0 -1.3 6 6
NOS2 -0.19 0.27 -10000 0 -1.1 6 6
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.015 0.069 -10000 0 -0.41 2 2
VEGFR1 homodimer/NRP1 0 0.062 -10000 0 -0.41 2 2
mol:DAG 0.012 0.087 -10000 0 -0.41 3 3
VEGFR1 homodimer/NRP1/VEGFR 121 0.006 0.077 -10000 0 -0.42 3 3
CaM/Ca2+ 0.024 0.088 -10000 0 -0.42 2 2
HIF1A 0.025 0.062 -10000 0 -0.47 2 2
GAB1 0.028 0.051 -10000 0 -0.5 2 2
AKT1 0.037 0.096 0.34 1 -0.53 1 2
PLCG1 0.012 0.088 -10000 0 -0.42 3 3
NOS3 0.083 0.12 0.31 23 -0.43 1 24
CBL 0.033 0.006 -10000 0 -10000 0 0
mol:NO 0.09 0.12 0.32 27 -0.42 1 28
FLT1 0.001 0.075 -10000 0 -0.48 2 2
PGF 0.016 0.073 -10000 0 -0.33 9 9
VEGFR1 homodimer/NRP2/VEGFR121 0.019 0.089 -10000 0 -0.46 3 3
CALM1 0.03 0.01 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 0.1 0.12 0.32 26 -0.41 1 27
endothelial cell proliferation 0.084 0.14 0.34 27 -0.44 1 28
mol:Ca2+ 0.012 0.087 -10000 0 -0.41 3 3
MAPK3 0.012 0.099 0.34 4 -0.44 2 6
MAPK1 0.015 0.094 0.34 5 -0.46 1 6
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.016 0.073 -10000 0 -0.33 9 9
PRKACA 0.033 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.025 0.056 -10000 0 -0.37 4 4
VEGFA homodimer 0.004 0.096 -10000 0 -0.32 17 17
VEGFR1 homodimer/VEGFA homodimer 0.007 0.084 -10000 0 -0.45 3 3
platelet activating factor biosynthetic process 0.064 0.14 0.34 21 -0.43 2 23
PI3K 0.071 0.1 -10000 0 -0.42 2 2
PRKCA 0.018 0.1 0.36 5 -0.42 2 7
PRKCB 0.006 0.081 -10000 0 -0.38 3 3
VEGFR1 homodimer/PLGF homodimer 0.01 0.083 -10000 0 -0.45 3 3
VEGFA 0.004 0.096 -10000 0 -0.32 17 17
VEGFB 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 0.012 0.087 -10000 0 -0.41 3 3
RASA1 0.045 0.1 -10000 0 -0.37 2 2
NRP2 0.032 0.024 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.001 0.074 -10000 0 -0.47 2 2
VEGFB homodimer 0.033 0.005 -10000 0 -10000 0 0
NCK1 0.033 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.092 0.12 0.31 20 -0.41 1 21
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
mol:PI-3-4-5-P3 0.033 0.083 -10000 0 -0.39 3 3
mol:L-citrulline 0.09 0.12 0.32 27 -0.42 1 28
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.069 0.1 -10000 0 -0.4 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.019 0.084 -10000 0 -0.42 3 3
CD2AP 0.033 0.005 -10000 0 -10000 0 0
PI3K/GAB1 0.079 0.11 -10000 0 -0.7 1 1
PDPK1 0.038 0.099 0.35 1 -0.47 1 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.02 0.084 -10000 0 -0.42 3 3
mol:NADP 0.09 0.12 0.32 27 -0.42 1 28
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
ubiquitin-dependent protein catabolic process 0.03 0.085 -10000 0 -0.39 3 3
VEGFR1 homodimer/NRP2 0.015 0.074 -10000 0 -0.49 2 2
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.03 0.037 -10000 0 -0.5 1 1
SPHK1 -0.012 0.12 -10000 0 -0.32 27 27
GNAI2 0.033 0.004 -10000 0 -10000 0 0
mol:S1P -0.003 0.052 0.16 1 -0.28 2 3
GNAO1 0.033 0.005 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.013 0.087 -10000 0 -0.24 27 27
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.023 0.054 -10000 0 -0.29 1 1
GNAI3 0.033 0.006 -10000 0 -10000 0 0
G12/G13 0.043 0.017 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.008 0.044 -10000 0 -0.33 1 1
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.032 0.17 -10000 0 -0.5 26 26
S1P/S1P5/G12 0.01 0.05 -10000 0 -0.3 1 1
S1P/S1P3/Gq -0.003 0.088 -10000 0 -0.29 13 13
S1P/S1P4/Gi -0.011 0.095 -10000 0 -0.34 6 6
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.5 9 9
GNA15 0.021 0.064 -10000 0 -0.32 7 7
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
GNA11 0.018 0.088 -10000 0 -0.5 6 6
ABCC1 -0.002 0.11 -10000 0 -0.32 21 21
a4b1 and a4b7 Integrin 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
ITGB1 0.032 0.025 -9999 0 -0.32 1 1
ITGB7 0.011 0.11 -9999 0 -0.5 9 9
ITGA4 0.028 0.051 -9999 0 -0.5 2 2
alpha4/beta7 Integrin 0.028 0.091 -9999 0 -0.36 11 11
alpha4/beta1 Integrin 0.044 0.044 -9999 0 -0.32 3 3
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.066 -9999 0 -0.28 10 10
CRKL 0.031 0.009 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.007 -9999 0 -10000 0 0
DOCK1 0.03 0.037 -9999 0 -0.5 1 1
ITGA4 0.028 0.051 -9999 0 -0.5 2 2
alpha4/beta7 Integrin/MAdCAM1 -0.013 0.17 -9999 0 -0.31 51 51
EPO 0.031 0.025 -9999 0 -0.32 1 1
alpha4/beta7 Integrin 0.028 0.091 -9999 0 -0.36 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.044 0.044 -9999 0 -0.32 3 3
EPO/EPOR (dimer) 0.046 0.022 -9999 0 -0.22 1 1
lamellipodium assembly 0.011 0.08 -9999 0 -10000 0 0
PIK3CA 0.033 0.004 -9999 0 -10000 0 0
PI3K 0.048 0.009 -9999 0 -10000 0 0
ARF6 0.031 0.01 -9999 0 -10000 0 0
JAK2 0.029 0.039 -9999 0 -0.25 1 1
PXN 0.033 0.003 -9999 0 -10000 0 0
PIK3R1 0.033 0.005 -9999 0 -10000 0 0
MADCAM1 -0.084 0.22 -9999 0 -0.5 47 47
cell adhesion -0.015 0.17 -9999 0 -0.31 51 51
CRKL/CBL 0.046 0.014 -9999 0 -10000 0 0
ITGB1 0.032 0.025 -9999 0 -0.32 1 1
SRC 0.005 0.053 -9999 0 -0.34 4 4
ITGB7 0.011 0.11 -9999 0 -0.5 9 9
RAC1 0.031 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.052 0.074 -9999 0 -0.36 6 6
p130Cas/Crk/Dock1 0.064 0.087 -9999 0 -0.47 1 1
VCAM1 0.02 0.081 -9999 0 -0.5 5 5
RHOA 0.033 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.076 0.044 -9999 0 -0.28 2 2
BCAR1 -0.002 0.049 -9999 0 -0.51 1 1
EPOR 0.033 0.005 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.033 0.006 -9999 0 -10000 0 0
GIT1 0.032 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.01 0.082 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.031 0.008 -10000 0 -10000 0 0
HDAC4 0.033 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.009 0.013 -10000 0 -10000 0 0
CDKN1A -0.01 0.066 0.31 1 -0.64 2 3
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.031 0.025 -10000 0 -0.32 1 1
FOXO3 -0.007 0.004 -10000 0 -10000 0 0
FOXO1 0.01 0.088 -10000 0 -0.5 6 6
FOXO4 0.02 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.031 0.008 -10000 0 -10000 0 0
TAT 0.033 0.005 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.007 0.027 -10000 0 -0.22 3 3
PPARGC1A -0.2 0.26 -10000 0 -0.5 92 92
FHL2 0.032 0.024 -10000 0 -0.32 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.043 0.016 -10000 0 -10000 0 0
HIST2H4A 0.009 0.013 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.023 0.028 0.27 1 -10000 0 1
SIRT1 0.03 0.017 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.062 0.02 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.027 0.041 -10000 0 -10000 0 0
apoptosis -0.057 0.028 -10000 0 -10000 0 0
SIRT1/PGC1A -0.11 0.17 -10000 0 -0.31 90 90
p53/SIRT1 0.021 0.058 0.41 1 -0.23 1 2
SIRT1/FOXO4 0.03 0.038 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.035 0.065 -10000 0 -0.31 6 6
HIST1H1E 0.019 0.012 -10000 0 -10000 0 0
SIRT1/p300 0.043 0.016 -10000 0 -10000 0 0
muscle cell differentiation -0.017 0.027 0.18 3 -10000 0 3
TP53 0.011 0.069 0.22 1 -0.33 8 9
KU70/SIRT1/BAX 0.057 0.028 -10000 0 -10000 0 0
CREBBP 0.032 0.006 -10000 0 -10000 0 0
MEF2D 0.033 0.006 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.045 0.016 -10000 0 -10000 0 0
ACSS2 0.009 0.036 0.36 1 -0.37 1 2
SIRT1/PCAF/MYOD 0.017 0.027 -10000 0 -0.19 3 3
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.032 0.049 -10000 0 -0.22 7 7
cell-cell adhesion 0.05 0.084 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.05 0.066 -10000 0 -0.27 1 1
ITSN1 0.032 0.007 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.016 0.08 -10000 0 -0.2 25 25
Ephrin B1/EPHB1 -0.039 0.11 -10000 0 -0.18 78 78
HRAS/GDP -0.041 0.12 -10000 0 -0.4 4 4
Ephrin B/EPHB1/GRB7 0.007 0.1 -10000 0 -10000 0 0
Endophilin/SYNJ1 0.054 0.081 -10000 0 -10000 0 0
KRAS 0.033 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.011 0.08 -10000 0 -10000 0 0
endothelial cell migration 0.02 0.078 -10000 0 -0.26 1 1
GRB2 0.032 0.006 -10000 0 -10000 0 0
GRB7 0.03 0.026 -10000 0 -0.32 1 1
PAK1 0.062 0.088 0.36 2 -10000 0 2
HRAS 0.033 0.004 -10000 0 -10000 0 0
RRAS 0.057 0.082 -10000 0 -10000 0 0
DNM1 0.03 0.035 -10000 0 -0.32 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.002 0.098 0.36 1 -0.3 1 2
lamellipodium assembly -0.05 0.084 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.056 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
EPHB2 0.02 0.065 -10000 0 -0.36 6 6
EPHB3 -0.011 0.12 -10000 0 -0.35 25 25
EPHB1 -0.096 0.17 -10000 0 -0.32 78 78
EPHB4 -0.023 0.13 -10000 0 -0.32 33 33
mol:GDP -0.031 0.11 -10000 0 -0.4 4 4
Ephrin B/EPHB2 0.04 0.054 -10000 0 -0.26 2 2
Ephrin B/EPHB3 0.026 0.075 -10000 0 -0.26 3 3
JNK cascade -0.046 0.11 0.36 3 -0.32 7 10
Ephrin B/EPHB1 -0.008 0.094 -10000 0 -0.25 1 1
RAP1/GDP -0.016 0.12 0.36 1 -0.38 3 4
EFNB2 0.022 0.039 -10000 0 -0.5 1 1
EFNB3 0.027 0.013 -10000 0 -10000 0 0
EFNB1 0.033 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.021 0.1 -10000 0 -0.3 4 4
RAP1B 0.033 0.005 -10000 0 -10000 0 0
RAP1A 0.032 0.007 -10000 0 -10000 0 0
CDC42/GTP -0.014 0.094 -10000 0 -10000 0 0
Rap1/GTP -0.025 0.077 -10000 0 -10000 0 0
axon guidance 0.031 0.049 -10000 0 -0.22 7 7
MAPK3 0.011 0.055 -10000 0 -10000 0 0
MAPK1 0.014 0.049 -10000 0 -10000 0 0
Rac1/GDP -0.025 0.12 -10000 0 -0.4 3 3
actin cytoskeleton reorganization -0.053 0.083 -10000 0 -0.3 2 2
CDC42/GDP -0.019 0.12 0.36 2 -0.39 3 5
PI3K 0.024 0.081 -10000 0 -0.26 1 1
EFNA5 0.03 0.037 -10000 0 -0.5 1 1
Ephrin B2/EPHB4 0.002 0.078 -10000 0 -0.19 29 29
Ephrin B/EPHB2/Intersectin/N-WASP 0.019 0.041 -10000 0 -0.31 1 1
CDC42 0.031 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.028 0.075 -10000 0 -10000 0 0
PTK2 0.11 0.22 0.6 36 -10000 0 36
MAP4K4 -0.046 0.11 0.36 3 -0.32 7 10
SRC 0.019 0.017 -10000 0 -10000 0 0
KALRN 0.033 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.044 0.031 -10000 0 -0.36 1 1
neuron projection morphogenesis -0.018 0.1 0.3 3 -10000 0 3
MAP2K1 0.017 0.054 -10000 0 -10000 0 0
WASL 0.03 0.037 -10000 0 -0.5 1 1
Ephrin B1/EPHB1-2/NCK1 -0.017 0.13 -10000 0 -0.31 5 5
cell migration 0.045 0.091 0.38 3 -10000 0 3
NRAS 0.029 0.035 -10000 0 -0.32 2 2
SYNJ1 0.055 0.082 -10000 0 -10000 0 0
PXN 0.033 0.003 -10000 0 -10000 0 0
TF 0.047 0.081 -10000 0 -10000 0 0
HRAS/GTP -0.014 0.09 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 -0.029 0.12 -10000 0 -0.31 5 5
cell adhesion mediated by integrin -0.044 0.093 0.25 1 -0.2 48 49
RAC1 0.031 0.01 -10000 0 -10000 0 0
mol:GTP -0.014 0.095 -10000 0 -0.28 2 2
RAC1-CDC42/GTP -0.042 0.085 -10000 0 -0.36 3 3
RASA1 0.03 0.035 -10000 0 -0.32 2 2
RAC1-CDC42/GDP -0.019 0.12 -10000 0 -0.38 3 3
ruffle organization -0.007 0.14 0.45 6 -10000 0 6
NCK1 0.033 0.004 -10000 0 -10000 0 0
receptor internalization 0.045 0.083 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.052 0.063 -10000 0 -10000 0 0
ROCK1 0.001 0.058 -10000 0 -0.28 3 3
RAS family/GDP -0.051 0.077 -10000 0 -0.34 1 1
Rac1/GTP -0.049 0.091 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.007 0.041 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.005 0.11 -10000 0 -10000 0 0
RAD9A 0.033 0.005 -10000 0 -10000 0 0
AP1 -0.009 0.13 -10000 0 -0.34 28 28
IFNAR2 0.033 0.008 -10000 0 -10000 0 0
AKT1 0.021 0.043 -10000 0 -0.43 1 1
ER alpha/Oestrogen 0.015 0.058 -10000 0 -0.36 5 5
NFX1/SIN3/HDAC complex 0.047 0.051 -10000 0 -10000 0 0
EGF -0.09 0.21 -10000 0 -0.43 58 58
SMG5 0.033 0.006 -10000 0 -10000 0 0
SMG6 0.027 0.013 -10000 0 -10000 0 0
SP3/HDAC2 0.049 0.012 -10000 0 -10000 0 0
TERT/c-Abl 0.012 0.1 -10000 0 -10000 0 0
SAP18 0.025 0.015 -10000 0 -10000 0 0
MRN complex 0.056 0.026 -10000 0 -10000 0 0
WT1 -0.16 0.18 -10000 0 -0.32 117 117
WRN 0.026 0.014 -10000 0 -10000 0 0
SP1 0.034 0.006 -10000 0 -10000 0 0
SP3 0.034 0.003 -10000 0 -10000 0 0
TERF2IP 0.033 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.003 0.12 -10000 0 -10000 0 0
Mad/Max 0.024 0.095 -10000 0 -0.36 12 12
TERT 0.005 0.11 -10000 0 -10000 0 0
CCND1 -0.01 0.12 -10000 0 -10000 0 0
MAX 0.031 0.01 -10000 0 -10000 0 0
RBBP7 0.033 0.005 -10000 0 -10000 0 0
RBBP4 0.032 0.007 -10000 0 -10000 0 0
TERF2 0.03 0.011 -10000 0 -10000 0 0
PTGES3 0.033 0.004 -10000 0 -10000 0 0
SIN3A 0.032 0.008 -10000 0 -10000 0 0
Telomerase/911 0.026 0.064 0.28 2 -10000 0 2
CDKN1B -0.017 0.091 -10000 0 -0.31 3 3
RAD1 0.022 0.059 -10000 0 -0.32 6 6
XRCC5 0.033 0.002 -10000 0 -10000 0 0
XRCC6 0.031 0.008 -10000 0 -10000 0 0
SAP30 0.032 0.007 -10000 0 -10000 0 0
TRF2/PARP2 0.044 0.017 -10000 0 -10000 0 0
UBE3A 0.032 0.008 -10000 0 -10000 0 0
JUN 0.025 0.054 -10000 0 -0.32 5 5
E6 0 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.024 0.007 -10000 0 -10000 0 0
FOS -0.027 0.16 -10000 0 -0.49 24 24
IFN-gamma/IRF1 -0.005 0.12 -10000 0 -0.37 2 2
PARP2 0.031 0.01 -10000 0 -10000 0 0
BLM 0.028 0.035 -10000 0 -0.32 2 2
Telomerase -0.019 0.12 -10000 0 -0.68 3 3
IRF1 0.033 0.045 -10000 0 -0.41 2 2
ESR1 0.02 0.081 -10000 0 -0.5 5 5
KU/TER 0.047 0.012 -10000 0 -10000 0 0
ATM/TRF2 0.047 0.012 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.069 -10000 0 -0.3 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.041 0.068 -10000 0 -0.3 2 2
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC2 0.033 0.008 -10000 0 -10000 0 0
ATM 0.012 0.005 -10000 0 -10000 0 0
SMAD3 0.017 0.006 -10000 0 -10000 0 0
ABL1 0.033 0.005 -10000 0 -10000 0 0
MXD1 0.004 0.12 -10000 0 -0.5 12 12
MRE11A 0.033 0.005 -10000 0 -10000 0 0
HUS1 0.031 0.01 -10000 0 -10000 0 0
RPS6KB1 0.032 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.023 0.12 -10000 0 -10000 0 0
NR2F2 0.031 0.009 -10000 0 -10000 0 0
MAPK3 0.016 0.037 -10000 0 -0.36 2 2
MAPK1 0.019 0.006 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.032 0.006 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
HNRNPC 0.031 0.009 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.005 -10000 0 -10000 0 0
NBN 0.029 0.012 -10000 0 -10000 0 0
EGFR 0.021 0.073 -10000 0 -0.5 4 4
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.051 0.16 -10000 0 -0.3 57 57
MYC -0.13 0.17 -10000 0 -0.32 97 97
IL2 0.034 0.007 -10000 0 -10000 0 0
KU 0.047 0.012 -10000 0 -10000 0 0
RAD50 0.033 0.004 -10000 0 -10000 0 0
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
TGFB1 0.032 0.006 -10000 0 -10000 0 0
TRF2/BLM 0.043 0.029 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.027 0.11 -10000 0 -10000 0 0
SP1/HDAC2 0.05 0.014 -10000 0 -10000 0 0
PINX1 0.024 0.028 -10000 0 -0.32 1 1
Telomerase/EST1A -0.008 0.12 -10000 0 -10000 0 0
Smad3/Myc -0.068 0.11 -10000 0 -0.26 1 1
911 complex 0.052 0.047 -10000 0 -10000 0 0
IFNG -0.04 0.15 -10000 0 -0.32 47 47
Telomerase/PinX1 -0.012 0.12 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K -0.007 0.11 0.29 1 -0.48 5 6
SIN3B 0.033 0.005 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
Telomerase/EST1B -0.004 0.12 -10000 0 -10000 0 0
response to DNA damage stimulus 0.002 0.022 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.079 0.038 -10000 0 -10000 0 0
TRF2/WRN 0.038 0.021 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.003 0.12 -10000 0 -10000 0 0
E2F1 0.011 0.055 -10000 0 -0.32 5 5
ZNFX1 0.019 0.017 -10000 0 -10000 0 0
PIF1 0.025 0.049 -10000 0 -0.32 4 4
NCL 0.033 0.003 -10000 0 -10000 0 0
DKC1 -0.07 0.16 -10000 0 -0.32 62 62
telomeric DNA binding 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.047 0.073 -9999 0 -0.31 6 6
E-cadherin/beta catenin 0.03 0.079 -9999 0 -0.3 11 11
CTNNB1 0.025 0.054 -9999 0 -0.32 5 5
JUP 0.032 0.006 -9999 0 -10000 0 0
CDH1 0.018 0.088 -9999 0 -0.5 6 6
Canonical NF-kappaB 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
FBXW11 0.036 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.056 0.083 0.37 3 -10000 0 3
ERC1 0.032 0.007 -10000 0 -10000 0 0
RIP2/NOD2 -0.036 0.13 -10000 0 -0.24 59 59
NFKBIA 0.021 0.008 -10000 0 -10000 0 0
BIRC2 0.033 0.006 -10000 0 -10000 0 0
IKBKB 0.029 0.011 -10000 0 -10000 0 0
RIPK2 -0.013 0.11 -10000 0 -0.32 25 25
IKBKG 0.016 0.052 -10000 0 -10000 0 0
IKK complex/A20 0.052 0.063 -10000 0 -10000 0 0
NEMO/A20/RIP2 -0.013 0.11 -10000 0 -0.32 25 25
XPO1 0.034 0 -10000 0 -10000 0 0
NEMO/ATM 0.038 0.064 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.032 0.025 -10000 0 -0.32 1 1
Exportin 1/RanGTP 0.044 0.016 -10000 0 -0.18 1 1
IKK complex/ELKS 0.042 0.054 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.046 0.032 -10000 0 -10000 0 0
NOD2 -0.042 0.15 -10000 0 -0.32 45 45
NFKB1 0.035 0.006 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
MALT1 0.023 0.016 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.047 0.011 -10000 0 -10000 0 0
ATM 0.032 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.047 0.012 -10000 0 -10000 0 0
TRAF6 0.033 0.003 -10000 0 -10000 0 0
PRKCA 0.029 0.026 -10000 0 -0.32 1 1
CHUK 0.032 0.007 -10000 0 -10000 0 0
UBE2D3 0.033 0.006 -10000 0 -10000 0 0
TNF 0.033 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.073 0.019 -10000 0 -10000 0 0
BCL10 0.033 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.007 -10000 0 -10000 0 0
IKK complex 0.035 0.065 -10000 0 -10000 0 0
CYLD 0.033 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.05 0.064 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.067 0.047 -10000 0 -10000 0 0
epithelial cell differentiation 0.062 0.06 -10000 0 -10000 0 0
ITCH 0.021 0.019 -10000 0 -10000 0 0
WWP1 0.02 0.038 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.5 1 1
EGFR 0.021 0.072 -10000 0 -0.5 4 4
PRL 0.031 0.025 -10000 0 -0.32 1 1
neuron projection morphogenesis 0.049 0.057 0.32 3 -10000 0 3
PTPRZ1 -0.021 0.16 -10000 0 -0.49 22 22
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.068 0.053 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.042 0.034 -10000 0 -10000 0 0
ADAM17 0.03 0.01 -10000 0 -10000 0 0
ErbB4/ErbB4 0.02 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.068 0.046 -10000 0 -10000 0 0
NCOR1 0.026 0.014 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.052 0.043 -10000 0 -10000 0 0
GRIN2B 0.022 0.068 0.29 1 -10000 0 1
ErbB4/ErbB2/betacellulin 0.061 0.061 -10000 0 -10000 0 0
STAT1 0.002 0.1 -10000 0 -0.32 19 19
HBEGF 0.028 0.042 -10000 0 -0.32 3 3
PRLR 0.027 0.042 -10000 0 -0.32 3 3
E4ICDs/ETO2 -0.036 0.15 -10000 0 -10000 0 0
axon guidance 0.02 0.058 -10000 0 -10000 0 0
NEDD4 0.017 0.059 -10000 0 -0.33 6 6
Prolactin receptor/Prolactin receptor/Prolactin 0.043 0.038 -10000 0 -0.22 4 4
CBFA2T3 -0.16 0.26 -10000 0 -0.5 77 77
ErbB4/ErbB2/HBEGF 0.066 0.05 -10000 0 -10000 0 0
MAPK3 0.044 0.053 0.28 2 -10000 0 2
STAT1 (dimer) 0.054 0.073 -10000 0 -10000 0 0
MAPK1 0.047 0.046 0.28 1 -10000 0 1
JAK2 0.027 0.042 -10000 0 -0.32 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.036 0.042 -10000 0 -10000 0 0
NRG1 0.014 0.008 -10000 0 -10000 0 0
NRG3 0.03 0.037 -10000 0 -0.5 1 1
NRG2 0.021 0.081 -10000 0 -0.5 5 5
NRG4 0.019 0.075 -10000 0 -0.41 6 6
heart development 0.02 0.058 -10000 0 -10000 0 0
neural crest cell migration 0.035 0.042 -10000 0 -10000 0 0
ERBB2 0.022 0.044 0.23 6 -0.37 1 7
WWOX/E4ICDs 0.063 0.044 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.062 0.071 -10000 0 -10000 0 0
apoptosis -0.05 0.078 0.37 4 -10000 0 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.064 0.06 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.04 0.11 -10000 0 -0.39 1 1
ErbB4/ErbB4/betacellulin/betacellulin 0.063 0.056 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.096 0.063 -10000 0 -10000 0 0
MDM2 0.016 0.021 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.023 0.026 -10000 0 -10000 0 0
STAT5A 0.036 0.063 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.045 0.052 -10000 0 -10000 0 0
DLG4 0.027 0.014 -10000 0 -10000 0 0
GRB2/SHC 0.047 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.05 0.04 -10000 0 -10000 0 0
STAT5A (dimer) 0.082 0.074 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.064 0.067 -10000 0 -10000 0 0
LRIG1 0.011 0.11 -10000 0 -0.5 9 9
EREG -0.22 0.17 -10000 0 -0.33 147 147
BTC 0.02 0.081 -10000 0 -0.5 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.019 0.056 -10000 0 -10000 0 0
ERBB4 0.02 0.025 -10000 0 -10000 0 0
STAT5B 0.033 0.006 -10000 0 -10000 0 0
YAP1 0.011 0.069 -10000 0 -0.39 5 5
GRB2 0.032 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.059 0.062 -10000 0 -10000 0 0
glial cell differentiation -0.05 0.04 -10000 0 -10000 0 0
WWOX 0.029 0.011 -10000 0 -10000 0 0
cell proliferation 0.042 0.075 0.32 3 -10000 0 3
Class I PI3K signaling events mediated by Akt

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.012 0.018 0.23 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.032 0.031 -10000 0 -10000 0 0
CDKN1B 0.034 0.084 0.28 1 -0.63 1 2
CDKN1A 0.03 0.086 -10000 0 -0.63 1 1
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.054 -10000 0 -0.32 5 5
FOXO3 0.037 0.065 -10000 0 -10000 0 0
AKT1 0.027 0.08 -10000 0 -0.66 1 1
BAD 0.033 0.005 -10000 0 -10000 0 0
AKT3 0.019 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.032 0.084 -10000 0 -0.63 1 1
AKT1/ASK1 0.045 0.11 0.28 1 -0.6 1 2
BAD/YWHAZ 0.054 0.028 -10000 0 -10000 0 0
RICTOR 0.03 0.025 -10000 0 -0.32 1 1
RAF1 0.033 0.006 -10000 0 -10000 0 0
JNK cascade -0.043 0.1 0.57 1 -0.27 1 2
TSC1 0.032 0.084 -10000 0 -0.63 1 1
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
AKT1/RAF1 0.053 0.11 0.29 2 -0.63 1 3
EP300 0.031 0.008 -10000 0 -10000 0 0
mol:GDP 0.028 0.079 -10000 0 -0.64 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.032 0.082 -10000 0 -0.63 1 1
YWHAQ 0.033 0.002 -10000 0 -10000 0 0
TBC1D4 0.062 0.1 0.24 51 -0.29 1 52
MAP3K5 0.029 0.035 -10000 0 -0.32 2 2
MAPKAP1 0.03 0.035 -10000 0 -0.32 2 2
negative regulation of cell cycle -0.057 0.1 0.29 4 -0.25 16 20
YWHAH 0.032 0.008 -10000 0 -10000 0 0
AKT1S1 0.035 0.084 0.28 1 -0.63 1 2
CASP9 0.031 0.079 -10000 0 -0.63 1 1
YWHAB 0.018 0.017 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.054 0.11 0.36 4 -0.59 1 5
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.035 0.037 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
AKT2/p21CIP1 0.02 0.084 -10000 0 -0.57 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.035 -10000 0 -10000 0 0
CHUK 0.037 0.065 -10000 0 -10000 0 0
BAD/BCL-XL 0.023 0.078 -10000 0 -0.59 1 1
mTORC2 0.037 0.026 -10000 0 -0.17 3 3
AKT2 0.019 0.005 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.069 0.14 0.32 16 -0.41 4 20
PDPK1 0.033 0.006 -10000 0 -10000 0 0
MDM2 0.034 0.083 0.28 1 -0.63 1 2
MAPKKK cascade -0.053 0.11 0.61 1 -0.29 2 3
MDM2/Cbp/p300 0.056 0.11 0.28 1 -0.58 1 2
TSC1/TSC2 0.032 0.082 0.35 1 -0.61 1 2
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.1 0.27 1 -0.55 1 2
glucose import -0.025 0.13 0.21 24 -0.27 40 64
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.037 0.063 0.25 3 -0.35 1 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.025 0.14 0.21 24 -0.27 40 64
GSK3A 0.036 0.085 0.28 1 -0.63 1 2
FOXO1 0.052 0.12 0.28 16 -0.63 1 17
GSK3B 0.032 0.086 -10000 0 -0.63 1 1
SFN 0.026 0.052 -10000 0 -0.5 2 2
G1/S transition of mitotic cell cycle 0.041 0.11 0.35 5 -0.61 1 6
p27Kip1/14-3-3 family 0.054 0.061 0.28 1 -10000 0 1
PRKACA 0.033 0.005 -10000 0 -10000 0 0
KPNA1 0.033 0.005 -10000 0 -10000 0 0
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
YWHAG 0.032 0.007 -10000 0 -10000 0 0
RHEB 0.033 0.006 -10000 0 -10000 0 0
CREBBP 0.032 0.006 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.024 0.073 -10000 0 -0.22 17 17
PDGFRB 0.034 0.006 -10000 0 -10000 0 0
SPHK1 -0.011 0.085 -10000 0 -0.6 4 4
mol:S1P -0.009 0.09 -10000 0 -0.5 4 4
S1P1/S1P/Gi -0.015 0.11 -10000 0 -0.32 6 6
GNAO1 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 0.026 0.14 0.34 4 -0.32 1 5
PLCG1 -0.016 0.088 0.28 2 -0.31 4 6
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.033 0.008 -10000 0 -10000 0 0
GNAI1 -0.033 0.17 -10000 0 -0.5 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.011 0.053 0.18 1 -0.18 17 18
S1P1/S1P -0.015 0.091 -10000 0 -0.44 2 2
negative regulation of cAMP metabolic process -0.014 0.1 -10000 0 -0.31 6 6
MAPK3 -0.03 0.12 0.27 1 -0.37 3 4
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.003 -10000 0 -10000 0 0
KDR 0.032 0.006 -10000 0 -10000 0 0
PLCB2 -0.003 0.1 0.36 3 -0.4 2 5
RAC1 0.031 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.079 -10000 0 -0.38 2 2
receptor internalization -0.014 0.086 -10000 0 -0.34 4 4
PTGS2 -0.034 0.15 0.48 2 -10000 0 2
Rac1/GTP -0.014 0.076 -10000 0 -0.38 2 2
RHOA 0.033 0.005 -10000 0 -10000 0 0
VEGFA 0.004 0.096 -10000 0 -0.33 17 17
negative regulation of T cell proliferation -0.014 0.1 -10000 0 -0.31 6 6
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.009 -10000 0 -10000 0 0
MAPK1 -0.019 0.11 0.42 1 -0.34 1 2
S1P1/S1P/PDGFB-D/PDGFRB 0.01 0.12 0.35 5 -0.38 2 7
ABCC1 -0.001 0.11 -10000 0 -0.32 21 21
FoxO family 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
G6PC 0.035 0.091 0.48 1 -10000 0 1
PLK1 -0.012 0.19 -10000 0 -0.84 3 3
CDKN1B 0.051 0.15 0.37 3 -0.38 2 5
FOXO3 -0.016 0.2 -10000 0 -0.68 9 9
KAT2B -0.001 0.019 -10000 0 -0.054 9 9
FOXO1/SIRT1 0.045 0.088 0.33 3 -0.33 1 4
CAT -0.019 0.2 -10000 0 -0.97 4 4
CTNNB1 0.025 0.054 -10000 0 -0.32 5 5
AKT1 0.028 0.032 -10000 0 -10000 0 0
FOXO1 0.036 0.098 0.43 3 -0.36 1 4
MAPK10 0.041 0.062 0.2 20 -0.25 2 22
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.065 0.078 0.33 5 -10000 0 5
response to oxidative stress 0.004 0.019 -10000 0 -0.053 6 6
FOXO3A/SIRT1 0.014 0.18 -10000 0 -0.6 7 7
XPO1 0.034 0 -10000 0 -10000 0 0
EP300 0.034 0.009 -10000 0 -10000 0 0
BCL2L11 0.033 0.033 -10000 0 -10000 0 0
FOXO1/SKP2 0.029 0.1 0.28 2 -0.34 2 4
mol:GDP 0.004 0.019 -10000 0 -0.053 6 6
RAN 0.033 0.025 -10000 0 -0.32 1 1
GADD45A 0.051 0.14 -10000 0 -0.56 4 4
YWHAQ 0.033 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.054 0.13 0.35 2 -0.49 4 6
MST1 0.01 0.08 -10000 0 -0.32 10 10
CSNK1D 0.033 0.006 -10000 0 -10000 0 0
CSNK1E 0.03 0.026 -10000 0 -0.32 1 1
FOXO4/14-3-3 family -0.009 0.12 -10000 0 -0.38 8 8
YWHAB 0.018 0.017 -10000 0 -10000 0 0
MAPK8 0.046 0.053 0.2 21 -10000 0 21
MAPK9 0.046 0.053 0.2 19 -10000 0 19
YWHAG 0.032 0.007 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
SIRT1 0.034 0.019 -10000 0 -10000 0 0
SOD2 0.044 0.16 0.58 1 -0.51 2 3
RBL2 0.033 0.14 -10000 0 -10000 0 0
RAL/GDP 0.045 0.024 -10000 0 -10000 0 0
CHUK 0.025 0.032 -10000 0 -10000 0 0
Ran/GTP 0.027 0.017 -10000 0 -0.22 1 1
CSNK1G2 0.033 0.006 -10000 0 -10000 0 0
RAL/GTP 0.049 0.024 -10000 0 -10000 0 0
CSNK1G1 0.032 0.008 -10000 0 -10000 0 0
FASLG -0.12 0.46 -10000 0 -1.5 22 22
SKP2 0.002 0.099 -10000 0 -0.32 18 18
USP7 0.031 0.037 -10000 0 -0.5 1 1
IKBKB 0.023 0.031 -10000 0 -10000 0 0
CCNB1 -0.036 0.2 -10000 0 -0.88 4 4
FOXO1-3a-4/beta catenin 0.067 0.16 0.4 9 -0.44 1 10
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.1 0.28 2 -0.34 2 4
CSNK1A1 0.033 0.004 -10000 0 -10000 0 0
SGK1 -0.001 0.019 -10000 0 -0.054 9 9
CSNK1G3 0.033 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.049 0.017 -10000 0 -0.18 1 1
ZFAND5 0.062 0.073 -10000 0 -10000 0 0
SFN 0.026 0.052 -10000 0 -0.5 2 2
CDK2 -0.002 0.11 -10000 0 -0.32 23 23
FOXO3A/14-3-3 -0.009 0.11 -10000 0 -0.5 4 4
CREBBP 0.035 0.007 -10000 0 -10000 0 0
FBXO32 -0.057 0.41 -10000 0 -1.3 19 19
BCL6 0.028 0.16 -10000 0 -1.3 1 1
RALB 0.035 0.001 -10000 0 -10000 0 0
RALA 0.031 0.01 -10000 0 -10000 0 0
YWHAH 0.032 0.008 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.039 0.13 -10000 0 -0.43 1 1
MKNK1 0.033 0.005 -10000 0 -10000 0 0
MAPK14 -0.003 0.07 -10000 0 -10000 0 0
ATF2/c-Jun -0.004 0.068 -10000 0 -0.39 2 2
MAPK11 -0.003 0.07 -10000 0 -0.31 1 1
MITF -0.006 0.067 -10000 0 -0.27 1 1
MAPKAPK5 -0.005 0.067 -10000 0 -0.27 1 1
KRT8 -0.008 0.074 -10000 0 -0.29 4 4
MAPKAPK3 0.033 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.033 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.002 0.093 -10000 0 -10000 0 0
CEBPB -0.006 0.059 -10000 0 -10000 0 0
SLC9A1 -0.008 0.067 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.005 0.072 -10000 0 -0.33 1 1
p38alpha-beta/MNK1 0.014 0.085 -10000 0 -10000 0 0
JUN -0.006 0.067 -10000 0 -0.39 2 2
PPARGC1A -0.15 0.19 -10000 0 -0.36 92 92
USF1 -0.012 0.078 -10000 0 -0.27 1 1
RAB5/GDP/GDI1 0.005 0.055 -10000 0 -10000 0 0
NOS2 -0.013 0.066 -10000 0 -0.22 7 7
DDIT3 -0.006 0.068 -10000 0 -0.27 1 1
RAB5A 0.033 0.005 -10000 0 -10000 0 0
HSPB1 -0.001 0.074 0.29 6 -0.27 1 7
p38alpha-beta/HBP1 0.014 0.084 -10000 0 -10000 0 0
CREB1 -0.001 0.062 -10000 0 -10000 0 0
RAB5/GDP 0.024 0.004 -10000 0 -10000 0 0
EIF4E -0.007 0.059 -10000 0 -10000 0 0
RPS6KA4 -0.003 0.064 -10000 0 -10000 0 0
PLA2G4A -0.076 0.13 -10000 0 -0.29 37 37
GDI1 -0.003 0.064 -10000 0 -0.27 1 1
TP53 -0.022 0.067 -10000 0 -10000 0 0
RPS6KA5 -0.011 0.077 -10000 0 -0.35 4 4
ESR1 -0.011 0.08 -10000 0 -0.31 6 6
HBP1 0.032 0.006 -10000 0 -10000 0 0
MEF2C -0.055 0.14 -10000 0 -0.34 32 32
MEF2A -0.005 0.067 -10000 0 -0.27 1 1
EIF4EBP1 -0.007 0.071 -10000 0 -0.32 2 2
KRT19 -0.012 0.082 -10000 0 -0.34 5 5
ELK4 -0.004 0.07 -10000 0 -0.27 1 1
ATF6 -0.003 0.066 -10000 0 -0.27 1 1
ATF1 -0.001 0.062 -10000 0 -10000 0 0
p38alpha-beta/MAPKAPK2 0.018 0.082 -10000 0 -10000 0 0
p38alpha-beta/MAPKAPK3 0.014 0.085 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.001 0.044 -10000 0 -0.22 8 8
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.046 0.013 -10000 0 -10000 0 0
STXBP1 0.011 0.085 -10000 0 -0.32 13 13
ACh/CHRNA1 0.017 0.04 -10000 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.062 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.032 0.007 -10000 0 -10000 0 0
mol:ACh 0 0.045 0.11 7 -0.11 13 20
RAB3GAP2 0.033 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.019 0.08 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.017 0.04 -10000 0 -10000 0 0
UNC13B 0.033 0.006 -10000 0 -10000 0 0
CHRNA1 0.033 0.002 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.011 0.078 -10000 0 -0.19 27 27
SNAP25 0.003 0.029 -10000 0 -0.22 3 3
VAMP2 0.005 0.003 -10000 0 -10000 0 0
SYT1 -0.014 0.12 -10000 0 -0.32 28 28
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.009 0.064 -10000 0 -0.18 21 21
STX1A/SNAP25 fragment 1/VAMP2 0.019 0.08 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.1 0.23 -10000 0 -0.5 53 53
CLTC -0.004 0.12 -10000 0 -0.4 16 16
calcium ion-dependent exocytosis -0.004 0.08 -10000 0 -0.33 5 5
Dynamin 2/GTP 0.03 0.022 -10000 0 -10000 0 0
EXOC4 0.032 0.008 -10000 0 -10000 0 0
CD59 -0.002 0.089 -10000 0 -0.34 13 13
CPE -0.013 0.093 -10000 0 -0.28 22 22
CTNNB1 0.025 0.054 -10000 0 -0.32 5 5
membrane fusion 0.01 0.055 -10000 0 -0.33 1 1
CTNND1 0.019 0.028 -10000 0 -10000 0 0
DNM2 0.033 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.001 0.07 -10000 0 -0.28 5 5
TSHR 0.018 0.006 -10000 0 -10000 0 0
INS 0.015 0.047 -10000 0 -0.57 1 1
BIN1 0.034 0 -10000 0 -10000 0 0
mol:Choline 0.01 0.055 -10000 0 -0.33 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.02 -10000 0 -0.18 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.022 -10000 0 -10000 0 0
JUP -0.002 0.087 -10000 0 -0.33 13 13
ASAP2/amphiphysin II 0.039 0.012 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.007 -10000 0 -10000 0 0
CDH1 -0.008 0.095 -10000 0 -0.33 14 14
clathrin-independent pinocytosis 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP3 0.032 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.007 -10000 0 -10000 0 0
EXOC2 0.033 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.03 0.047 -10000 0 -0.31 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.015 0.12 0.34 16 -10000 0 16
positive regulation of phagocytosis 0.017 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.04 0.015 -10000 0 -10000 0 0
ACAP1 0.012 0.048 -10000 0 -0.3 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.011 0.1 -10000 0 -0.35 14 14
clathrin heavy chain/ACAP1 -0.004 0.1 -10000 0 -0.33 14 14
JIP4/KLC1 0.056 0.022 -10000 0 -10000 0 0
EXOC1 0.033 0.006 -10000 0 -10000 0 0
exocyst 0.035 0.038 -10000 0 -0.31 1 1
RALA/GTP 0.022 0.008 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.04 0.015 -10000 0 -10000 0 0
receptor recycling 0.023 0.007 -10000 0 -10000 0 0
CTNNA1 0.019 0.028 -10000 0 -10000 0 0
NME1 0.016 0.02 -10000 0 -0.18 2 2
clathrin coat assembly -0.005 0.12 -10000 0 -0.39 16 16
IL2RA -0.004 0.088 -10000 0 -0.33 13 13
VAMP3 0.017 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.058 0.13 -10000 0 -0.35 11 11
EXOC6 0.032 0.007 -10000 0 -10000 0 0
PLD1 -0.013 0.09 -10000 0 -0.29 20 20
PLD2 0.015 0.011 -10000 0 -10000 0 0
EXOC5 0.031 0.01 -10000 0 -10000 0 0
PIP5K1C 0.004 0.064 -10000 0 -0.26 3 3
SDC1 -0.001 0.088 -10000 0 -0.33 13 13
ARF6/GDP 0.027 0.022 -10000 0 -0.18 2 2
EXOC7 0.032 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.016 0.12 -10000 0 -0.35 16 16
mol:Phosphatidic acid 0.01 0.055 -10000 0 -0.33 1 1
endocytosis -0.038 0.012 -10000 0 -10000 0 0
SCAMP2 0.031 0.009 -10000 0 -10000 0 0
ADRB2 -0.094 0.18 0.39 1 -0.49 21 22
EXOC3 0.032 0.007 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.034 0.023 -10000 0 -10000 0 0
KLC1 0.03 0.01 -10000 0 -10000 0 0
AVPR2 -0.001 0.12 0.37 2 -0.37 16 18
RALA 0.03 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.014 0.11 -10000 0 -0.43 4 4
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.004 -10000 0 -10000 0 0
mol:S1P 0.001 0 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.001 0.087 -10000 0 -0.24 25 25
GNAO1 0.035 0.005 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.039 0.016 -10000 0 -10000 0 0
AKT1 -0.008 0.13 -10000 0 -0.48 7 7
AKT3 0.023 0.051 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.033 0.004 -10000 0 -10000 0 0
GNAI2 0.035 0.004 -10000 0 -10000 0 0
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GNAI1 -0.031 0.17 -10000 0 -0.5 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.002 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.087 -10000 0 -0.36 3 3
MAPK3 -0.002 0.084 -10000 0 -0.35 3 3
MAPK1 0.004 0.078 -10000 0 -0.34 3 3
JAK2 0.042 0.097 0.23 2 -0.31 3 5
CXCR4 -0.008 0.087 -10000 0 -0.34 4 4
FLT1 0.008 0.078 -10000 0 -0.32 11 11
RhoA/GDP 0.024 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.007 -10000 0 -10000 0 0
SRC 0.005 0.05 -10000 0 -0.26 1 1
S1P/S1P3/Gi 0.004 0.088 -10000 0 -0.37 3 3
RAC1 0.031 0.01 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.087 -10000 0 -0.38 2 2
VEGFA 0.007 0.097 -10000 0 -0.32 17 17
S1P/S1P2/Gi 0.001 0.088 -10000 0 -0.37 3 3
VEGFR1 homodimer/VEGFA homodimer 0.016 0.085 -10000 0 -0.24 19 19
RHOA 0.033 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.001 0.073 -10000 0 -0.26 14 14
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.033 0.008 -10000 0 -10000 0 0
G12/G13 0.043 0.017 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.5 9 9
GNA15 0.021 0.064 -10000 0 -0.32 7 7
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
GNA11 0.018 0.088 -10000 0 -0.5 6 6
Rac1/GTP 0.014 0.085 -10000 0 -0.34 3 3
Caspase cascade in apoptosis

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
TOP1 0.011 0.07 -10000 0 -0.33 4 4
ACTA1 -0.016 0.071 -10000 0 -0.33 1 1
NUMA1 0.016 0.089 -10000 0 -0.52 3 3
SPTAN1 0 0.059 -10000 0 -10000 0 0
LIMK1 0 0.075 0.33 3 -10000 0 3
BIRC3 0.008 0.11 -10000 0 -0.45 11 11
BIRC2 0.032 0.006 -10000 0 -10000 0 0
BAX 0.031 0.025 -10000 0 -0.32 1 1
CASP10 -0.002 0.042 -10000 0 -0.23 1 1
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 -10000 0 -0.001 6 6
PTK2 0.015 0.073 -10000 0 -0.36 3 3
DIABLO 0.033 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0 0.059 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.028 0.051 -10000 0 -0.5 2 2
GSN -0.041 0.11 -10000 0 -0.34 12 12
MADD 0.033 0.003 -10000 0 -10000 0 0
TFAP2A 0.027 0.085 -10000 0 -0.61 3 3
BID 0.003 0.033 -10000 0 -0.29 1 1
MAP3K1 0.011 0.049 -10000 0 -0.33 3 3
TRADD 0.033 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.044 0.028 -10000 0 -0.21 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.001 0.064 0.33 1 -10000 0 1
CASP9 0.031 0.009 -10000 0 -10000 0 0
DNA repair 0.002 0.054 0.21 1 -0.18 4 5
neuron apoptosis -0.011 0.18 -10000 0 -0.63 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.007 0.084 -10000 0 -0.83 1 1
APAF1 0.03 0.034 -10000 0 -0.32 2 2
CASP6 0.017 0.14 -10000 0 -0.81 5 5
TRAF2 0.033 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.003 0.056 -10000 0 -10000 0 0
CASP7 -0.049 0.16 0.25 4 -0.43 28 32
KRT18 0.024 0.047 -10000 0 -0.51 1 1
apoptosis -0.006 0.09 0.3 2 -0.41 4 6
DFFA 0 0.055 -10000 0 -10000 0 0
DFFB -0.002 0.058 -10000 0 -10000 0 0
PARP1 -0.002 0.055 0.18 4 -0.21 1 5
actin filament polymerization 0.005 0.069 -10000 0 -0.31 1 1
TNF 0.033 0.005 -10000 0 -10000 0 0
CYCS 0.019 0.041 0.19 1 -0.28 1 2
SATB1 -0.004 0.14 -10000 0 -0.78 5 5
SLK 0 0.056 -10000 0 -10000 0 0
p15 BID/BAX 0.013 0.052 -10000 0 -0.26 1 1
CASP2 0.023 0.056 0.22 4 -0.26 1 5
JNK cascade -0.011 0.049 0.33 3 -10000 0 3
CASP3 0 0.06 -10000 0 -10000 0 0
LMNB2 0.033 0.1 0.37 3 -0.66 2 5
RIPK1 0.033 0.005 -10000 0 -10000 0 0
CASP4 0.033 0.006 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.046 0.071 -10000 0 -0.28 8 8
negative regulation of DNA binding 0.027 0.084 -10000 0 -0.6 3 3
stress fiber formation 0 0.056 -10000 0 -10000 0 0
GZMB 0.006 0.052 -10000 0 -0.23 10 10
CASP1 0 0.074 -10000 0 -0.32 10 10
LMNB1 0.025 0.086 0.35 3 -0.43 3 6
APP -0.011 0.18 -10000 0 -0.64 15 15
TNFRSF1A 0.032 0.007 -10000 0 -10000 0 0
response to stress 0 0 0.001 15 -0.001 3 18
CASP8 0.01 0 -10000 0 -10000 0 0
VIM -0.005 0.094 0.32 2 -0.43 4 6
LMNA 0.039 0.074 0.36 3 -0.41 2 5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.023 0.054 -10000 0 -0.26 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.003 0.05 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.005 0.16 -10000 0 -0.58 14 14
nuclear fragmentation during apoptosis 0.016 0.087 -10000 0 -0.5 3 3
CFL2 -0.006 0.069 0.31 1 -10000 0 1
GAS2 -0.09 0.092 -10000 0 -0.39 1 1
positive regulation of apoptosis 0.036 0.089 0.37 3 -0.54 2 5
PRF1 0.025 0.049 -10000 0 -0.32 4 4
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.027 0.025 -10000 0 -10000 0 0
ATM 0.032 0.007 -10000 0 -10000 0 0
UBE2D3 0.033 0.006 -10000 0 -10000 0 0
PRKDC 0.021 0.054 -10000 0 -0.32 5 5
ATR 0.031 0.025 -10000 0 -0.32 1 1
UBE2L3 0.031 0.009 -10000 0 -10000 0 0
FANCD2 0.027 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.04 0.099 -10000 0 -0.3 4 4
XRCC5 0.033 0.002 -10000 0 -10000 0 0
XRCC6 0.031 0.008 -10000 0 -10000 0 0
M/R/N Complex 0.056 0.026 -10000 0 -10000 0 0
MRE11A 0.033 0.005 -10000 0 -10000 0 0
DNA-PK 0.05 0.045 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.017 0.072 -10000 0 -0.43 2 2
FANCF 0.028 0.051 -10000 0 -0.5 2 2
BRCA1 0.028 0.042 -10000 0 -0.32 3 3
CCNE1 0.009 0.088 -10000 0 -0.32 14 14
CDK2/Cyclin E1 0.002 0.11 -10000 0 -0.25 33 33
FANCG 0.019 0.068 -10000 0 -0.32 8 8
BRCA1/BACH1/BARD1 0.044 0.033 -10000 0 -0.22 3 3
FANCE 0.031 0.025 -10000 0 -0.32 1 1
FANCC 0.033 0.006 -10000 0 -10000 0 0
NBN 0.029 0.012 -10000 0 -10000 0 0
FANCA -0.047 0.15 -10000 0 -0.32 48 48
DNA repair 0.03 0.089 0.32 2 -10000 0 2
BRCA1/BARD1/ubiquitin 0.044 0.033 -10000 0 -0.22 3 3
BARD1/DNA-PK 0.065 0.049 -10000 0 -10000 0 0
FANCL 0.034 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.027 0.025 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.029 0.053 -10000 0 -0.26 2 2
BRCA1/BACH1/BARD1/TopBP1 0.062 0.033 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.055 0.066 -10000 0 -0.32 1 1
BARD1/CSTF1/BRCA1 0.036 0.034 -10000 0 -10000 0 0
BRCA1/BACH1 0.028 0.042 -10000 0 -0.32 3 3
BARD1 0.033 0.002 -10000 0 -10000 0 0
PCNA 0.021 0.043 -10000 0 -0.32 3 3
BRCA1/BARD1/UbcH5C 0.061 0.033 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.058 0.035 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.057 0.05 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.065 0.071 -10000 0 -0.3 1 1
BRCA1/BARD1/Ubiquitin 0.044 0.033 -10000 0 -0.22 3 3
BRCA1/BARD1/CTIP 0.04 0.035 -10000 0 -10000 0 0
FA complex 0.014 0.059 -10000 0 -0.28 2 2
BARD1/EWS 0.046 0.022 -10000 0 -0.22 1 1
RBBP8 0.014 0.009 -10000 0 -10000 0 0
TP53 0.013 0.068 -10000 0 -0.32 8 8
TOPBP1 0.033 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.052 0.064 0.32 1 -10000 0 1
BRCA1/BARD1 0.046 0.1 -10000 0 -0.3 4 4
CSTF1 0.018 0.017 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.025 0.002 -10000 0 -10000 0 0
CDK2 -0.005 0.11 -10000 0 -0.32 23 23
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.031 0.009 -10000 0 -10000 0 0
RAD50 0.033 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.044 0.033 -10000 0 -0.22 3 3
EWSR1 0.03 0.026 -10000 0 -0.32 1 1
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.07 0.049 -10000 0 -0.28 1 1
MAP4K1 0.032 0.006 -10000 0 -10000 0 0
MAP3K8 -0.015 0.12 -10000 0 -0.32 29 29
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.031 0.01 -10000 0 -10000 0 0
CRKL 0.031 0.009 -10000 0 -10000 0 0
MAP3K1 0.02 0.048 -10000 0 -0.29 1 1
JUN -0.004 0.11 -10000 0 -0.58 7 7
MAP3K7 0.021 0.046 -10000 0 -0.29 1 1
GRAP2 0.031 0.009 -10000 0 -10000 0 0
CRK 0.027 0.013 -10000 0 -10000 0 0
MAP2K4 0.011 0.077 0.34 3 -0.31 2 5
LAT 0.031 0.025 -10000 0 -0.32 1 1
LCP2 0.026 0.055 -10000 0 -0.37 4 4
MAPK8 0.002 0.11 -10000 0 -0.6 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.026 0.051 -10000 0 -0.31 1 1
LAT/GRAP2/SLP76/HPK1/HIP-55 0.075 0.056 -10000 0 -0.27 1 1
Aurora A signaling

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
Aurora A/GADD45A 0.067 0.048 -10000 0 -10000 0 0
BIRC5 -0.003 0.11 -10000 0 -0.32 21 21
NFKBIA 0.019 0.04 -10000 0 -10000 0 0
CPEB1 0.002 0.12 -10000 0 -0.5 12 12
AKT1 0.019 0.039 -10000 0 -10000 0 0
NDEL1 0.027 0.013 -10000 0 -10000 0 0
Aurora A/BRCA1 0.034 0.039 -10000 0 -10000 0 0
NDEL1/TACC3 0.06 0.052 -10000 0 -10000 0 0
GADD45A 0.03 0.035 -10000 0 -0.32 2 2
GSK3B 0.031 0.024 -10000 0 -0.31 1 1
PAK1/Aurora A 0.071 0.042 -10000 0 -10000 0 0
MDM2 0.033 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.043 0.11 0.23 44 -0.22 13 57
TP53 0.018 0.047 -10000 0 -0.26 1 1
DLG7 0.019 0.039 -10000 0 -10000 0 0
AURKAIP1 0.032 0.008 -10000 0 -10000 0 0
ARHGEF7 0.025 0.015 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.064 0.055 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.034 0.039 -10000 0 -10000 0 0
AURKA 0.032 0.052 -10000 0 -10000 0 0
AURKB 0.006 0.038 -10000 0 -0.17 7 7
CDC25B -0.003 0.051 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.013 -10000 0 -10000 0 0
mRNA polyadenylation 0.018 0.07 -10000 0 -0.27 6 6
Aurora A/CPEB 0.018 0.07 -10000 0 -0.27 6 6
Aurora A/TACC1/TRAP/chTOG 0.085 0.052 -10000 0 -10000 0 0
BRCA1 0.028 0.042 -10000 0 -0.32 3 3
centrosome duplication 0.071 0.042 -10000 0 -10000 0 0
regulation of centrosome cycle 0.059 0.051 -10000 0 -10000 0 0
spindle assembly 0.082 0.05 -10000 0 -10000 0 0
TDRD7 0.033 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.071 0.078 -10000 0 -0.28 1 1
CENPA 0.012 0.029 -10000 0 -10000 0 0
Aurora A/PP2A 0.069 0.042 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.044 0.048 0.21 1 -10000 0 1
negative regulation of DNA binding 0.009 0.062 -10000 0 -0.25 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.035 0.023 -10000 0 -10000 0 0
RASA1 0.03 0.035 -10000 0 -0.32 2 2
Ajuba/Aurora A 0.008 0.013 -10000 0 -10000 0 0
mitotic prometaphase 0.012 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.052 -10000 0 -10000 0 0
TACC1 0.029 0.011 -10000 0 -10000 0 0
TACC3 0.027 0.042 -10000 0 -0.32 3 3
Aurora A/Antizyme1 0.08 0.043 -10000 0 -10000 0 0
Aurora A/RasGAP 0.069 0.048 -10000 0 -10000 0 0
OAZ1 0.033 0.006 -10000 0 -10000 0 0
RAN 0.032 0.025 -10000 0 -0.32 1 1
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GIT1 0.032 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.031 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.043 0.11 0.23 44 -0.22 13 57
PPP2R5D 0.033 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.02 0.071 0.27 9 -0.24 2 11
PAK1 0.033 0.004 -10000 0 -10000 0 0
CKAP5 0.033 0.003 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.023 0.041 -10000 0 -10000 0 0
regulation of axonogenesis 0.003 0.07 0.38 3 -10000 0 3
myoblast fusion -0.029 0.022 -10000 0 -10000 0 0
mol:GTP 0.015 0.044 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.048 0.061 0.3 3 -10000 0 3
ARF1/GTP 0.032 0.044 -10000 0 -10000 0 0
mol:GM1 0.005 0.033 -10000 0 -10000 0 0
mol:Choline -0.009 0.082 -10000 0 -0.29 17 17
lamellipodium assembly -0.001 0.092 -10000 0 -0.34 14 14
MAPK3 0.022 0.045 -10000 0 -0.32 2 2
ARF6/GTP/NME1/Tiam1 0.049 0.062 -10000 0 -0.3 3 3
ARF1 0.033 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.029 0.022 -10000 0 -10000 0 0
ARF1/GDP 0.022 0.067 -10000 0 -0.27 2 2
ARF6 0.037 0.014 -10000 0 -10000 0 0
RAB11A 0.032 0.008 -10000 0 -10000 0 0
TIAM1 0.028 0.052 -10000 0 -0.5 2 2
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.031 -10000 0 -10000 0 0
actin filament bundle formation -0.028 0.069 0.26 2 -10000 0 2
KALRN 0.019 0.015 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.045 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.028 0.069 -10000 0 -0.26 2 2
NME1 0.03 0.035 -10000 0 -0.32 2 2
Rac1/GDP 0.025 0.067 -10000 0 -0.27 1 1
substrate adhesion-dependent cell spreading 0.015 0.044 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.001 0.092 -10000 0 -0.34 14 14
RAC1 0.031 0.01 -10000 0 -10000 0 0
liver development 0.015 0.044 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.044 -10000 0 -10000 0 0
RhoA/GTP 0.033 0.044 -10000 0 -10000 0 0
mol:GDP 0.007 0.056 -10000 0 -0.28 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.048 0.045 -10000 0 -10000 0 0
RHOA 0.033 0.005 -10000 0 -10000 0 0
PLD1 -0.021 0.11 -10000 0 -0.33 23 23
RAB11FIP3 0.032 0.007 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.092 -10000 0 -0.34 14 14
ruffle organization -0.003 0.07 -10000 0 -0.38 3 3
regulation of epithelial cell migration 0.015 0.044 -10000 0 -10000 0 0
PLD2 0.022 0.016 -10000 0 -10000 0 0
PIP5K1A -0.004 0.07 -10000 0 -0.38 3 3
mol:Phosphatidic acid -0.009 0.082 -10000 0 -0.29 17 17
Rac1/GTP -0.001 0.093 -10000 0 -0.34 14 14
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.047 0.14 -10000 0 -0.28 17 17
CaM/Ca2+ 0.022 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.01 -10000 0 -10000 0 0
AKT2 0.032 0.007 -10000 0 -10000 0 0
STXBP4 0.032 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.063 0.14 0.18 2 -0.26 33 35
YWHAZ 0.028 0.012 -10000 0 -10000 0 0
CALM1 0.03 0.01 -10000 0 -10000 0 0
YWHAQ 0.033 0.002 -10000 0 -10000 0 0
TBC1D4 0.017 0.057 0.23 8 -0.26 4 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.032 0.008 -10000 0 -10000 0 0
YWHAB 0.018 0.017 -10000 0 -10000 0 0
SNARE/Synip 0.052 0.029 -10000 0 -10000 0 0
YWHAG 0.032 0.007 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.025 0.054 -10000 0 -0.32 5 5
AS160/CaM/Ca2+ 0.022 0.008 -10000 0 -10000 0 0
RHOQ 0.033 0.004 -10000 0 -10000 0 0
GYS1 0.016 0.01 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.033 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.044 0.007 -10000 0 -10000 0 0
AS160/14-3-3 0.013 0.052 -10000 0 -0.28 3 3
VAMP2 0.027 0.013 -10000 0 -10000 0 0
SLC2A4 -0.07 0.14 0.19 1 -0.29 33 34
STX4 0.033 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.014 -10000 0 -10000 0 0
SFN 0.026 0.052 -10000 0 -0.5 2 2
LNPEP 0.033 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.033 0.005 -10000 0 -10000 0 0
mol:PIP3 0.01 0.03 0.25 2 -10000 0 2
FRAP1 -0.013 0.13 -10000 0 -0.44 16 16
AKT1 0.009 0.044 0.2 2 -10000 0 2
INSR 0.026 0.063 -10000 0 -0.5 3 3
Insulin Receptor/Insulin 0.039 0.036 -10000 0 -0.31 2 2
mol:GTP 0.04 0.053 0.27 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.007 0.046 -10000 0 -0.22 2 2
TSC2 0.032 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.024 0.034 -10000 0 -10000 0 0
TSC1 0.033 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.042 -10000 0 -0.23 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.058 -10000 0 -0.25 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.033 0.006 -10000 0 -10000 0 0
RPS6KB1 0.013 0.091 0.24 2 -0.39 4 6
MAP3K5 0.005 0.04 0.19 2 -0.18 7 9
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
apoptosis 0.005 0.04 0.19 2 -0.18 7 9
mol:LY294002 0 0 -10000 0 -0.001 1 1
EIF4B 0.014 0.086 0.3 3 -0.37 3 6
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.085 0.24 2 -0.34 4 6
eIF4E/eIF4G1/eIF4A1 0.002 0.077 -10000 0 -0.27 15 15
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.046 0.032 -10000 0 -0.2 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.042 0.19 5 -10000 0 5
FKBP1A 0.027 0.014 -10000 0 -10000 0 0
RHEB/GTP 0.045 0.049 0.24 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 1 1
FKBP12/Rapamycin 0.02 0.01 -10000 0 -10000 0 0
PDPK1 -0.001 0.032 0.21 2 -10000 0 2
EIF4E 0.033 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0 0.16 -10000 0 -0.46 20 20
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.036 -10000 0 -10000 0 0
TSC1/TSC2 0.044 0.058 0.29 1 -10000 0 1
tumor necrosis factor receptor activity 0 0 0.001 1 -10000 0 1
RPS6 0.029 0.035 -10000 0 -0.32 2 2
PPP5C 0.031 0.025 -10000 0 -0.32 1 1
EIF4G1 0.033 0.004 -10000 0 -10000 0 0
IRS1 0.007 0.025 -10000 0 -0.21 2 2
INS 0.032 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.052 -10000 0 -0.5 2 2
PDK2 0 0.033 0.21 2 -10000 0 2
EIF4EBP1 -0.056 0.29 -10000 0 -1 17 17
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
PPP2R5D -0.007 0.12 0.28 1 -0.4 16 17
peptide biosynthetic process 0.023 0.043 0.19 7 -0.28 2 9
RHEB 0.033 0.006 -10000 0 -10000 0 0
EIF4A1 0.027 0.013 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 6 -10000 0 6
EEF2 0.024 0.043 0.19 7 -0.28 2 9
eIF4E/4E-BP1 -0.036 0.27 -10000 0 -0.97 17 17
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.03 0.094 -10000 0 -0.26 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.009 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.015 0.11 0.32 1 -0.37 4 5
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.054 0.041 -10000 0 -0.22 3 3
antigen processing and presentation of peptide antigen via MHC class I -0.005 0.068 -10000 0 -0.27 1 1
CaM/Ca2+ 0.027 0.091 -10000 0 -0.25 3 3
RAP1A 0.032 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.004 0.11 -10000 0 -0.3 15 15
AKT1 -0.003 0.076 0.33 3 -10000 0 3
MAP2K1 -0.009 0.074 0.36 2 -10000 0 2
MAP3K11 -0.003 0.08 0.36 2 -0.25 1 3
IFNGR1 0.031 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.027 0.067 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.06 -10000 0 -10000 0 0
CRKL/C3G 0.046 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.023 0.1 -10000 0 -0.29 3 3
CEBPB 0.046 0.12 0.46 2 -0.72 1 3
STAT3 0.033 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.037 0.13 -10000 0 -0.73 3 3
STAT1 -0.016 0.1 0.36 2 -0.3 15 17
CALM1 0.03 0.01 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.043 0.15 -10000 0 -0.32 47 47
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.003 0.11 0.36 2 -0.36 4 6
CEBPB/PTGES2/Cbp/p300 0.043 0.08 -10000 0 -0.41 1 1
mol:Ca2+ 0.027 0.092 -10000 0 -0.26 3 3
MAPK3 0.004 0.12 0.4 1 -0.83 3 4
STAT1 (dimer) 0.003 0.096 -10000 0 -0.38 1 1
MAPK1 -0.025 0.18 0.42 1 -0.72 12 13
JAK2 0.027 0.045 -10000 0 -0.34 3 3
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
JAK1 0.032 0.012 -10000 0 -10000 0 0
CAMK2D 0.033 0.005 -10000 0 -10000 0 0
DAPK1 0.045 0.092 0.37 3 -0.38 1 4
SMAD7 0.006 0.05 0.22 2 -0.27 1 3
CBL/CRKL/C3G 0.02 0.087 0.36 2 -10000 0 2
PI3K 0.03 0.09 -10000 0 -10000 0 0
IFNG -0.044 0.15 -10000 0 -0.32 47 47
apoptosis 0.028 0.1 0.36 2 -0.39 5 7
CAMK2G 0.032 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.032 0.006 -10000 0 -10000 0 0
CAMK2A 0.033 0.004 -10000 0 -10000 0 0
CAMK2B 0.029 0.026 -10000 0 -0.32 1 1
FRAP1 -0.012 0.068 0.31 3 -10000 0 3
PRKCD -0.003 0.078 0.34 3 -10000 0 3
RAP1B 0.033 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.005 0.068 -10000 0 -0.27 1 1
PTPN2 0.026 0.014 -10000 0 -10000 0 0
EP300 0.032 0.008 -10000 0 -10000 0 0
IRF1 -0.008 0.095 0.37 3 -0.45 2 5
STAT1 (dimer)/PIASy -0.005 0.1 0.42 1 -0.36 4 5
SOCS1 0.022 0.13 -10000 0 -1 3 3
mol:GDP 0.017 0.083 0.34 2 -10000 0 2
CASP1 -0.003 0.075 0.22 2 -0.25 12 14
PTGES2 0.033 0.005 -10000 0 -10000 0 0
IRF9 0.037 0.056 0.25 4 -10000 0 4
mol:PI-3-4-5-P3 0.016 0.08 -10000 0 -10000 0 0
RAP1/GDP 0.016 0.073 -10000 0 -10000 0 0
CBL -0.005 0.079 0.36 2 -10000 0 2
MAP3K1 -0.003 0.08 0.36 2 -0.25 3 5
PIAS1 0.031 0.008 -10000 0 -10000 0 0
PIAS4 0.032 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.005 0.068 -10000 0 -0.27 1 1
PTPN11 -0.007 0.074 -10000 0 -0.26 3 3
CREBBP 0.033 0.006 -10000 0 -10000 0 0
RAPGEF1 0.033 0.005 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.04 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.058 -10000 0 -10000 0 0
AP1 -0.036 0.079 -10000 0 -0.25 23 23
mol:PIP3 0.003 0.043 -10000 0 -0.24 6 6
AKT1 0.037 0.041 0.26 1 -10000 0 1
PTK2B -0.026 0.079 -10000 0 -0.17 46 46
RHOA 0.021 0.052 0.25 1 -0.27 3 4
PIK3CB 0.033 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.04 0.21 3 -0.22 1 4
MAGI3 0.03 0.037 -10000 0 -0.5 1 1
RELA 0.032 0.005 -10000 0 -10000 0 0
apoptosis 0.017 0.013 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.019 0.077 0.2 5 -0.27 1 6
NF kappa B1 p50/RelA -0.012 0.027 -10000 0 -10000 0 0
endothelial cell migration 0.02 0.03 -10000 0 -0.29 2 2
ADCY4 -0.002 0.063 -10000 0 -0.27 3 3
ADCY5 0.002 0.054 -10000 0 -10000 0 0
ADCY6 0.001 0.056 -10000 0 -10000 0 0
ADCY7 0.001 0.057 -10000 0 -10000 0 0
ADCY1 -0.001 0.053 -10000 0 -10000 0 0
ADCY2 0.003 0.054 -10000 0 -10000 0 0
ADCY3 -0.001 0.056 -10000 0 -10000 0 0
ADCY8 0.005 0.046 -10000 0 -10000 0 0
ADCY9 -0.002 0.059 -10000 0 -10000 0 0
GSK3B -0.024 0.079 0.19 2 -0.22 5 7
arachidonic acid secretion 0.002 0.056 -10000 0 -0.25 1 1
GNG2 0.03 0.01 -10000 0 -10000 0 0
TRIP6 0.014 0.016 -10000 0 -10000 0 0
GNAO1 0.021 0.015 -10000 0 -10000 0 0
HRAS 0.033 0.004 -10000 0 -10000 0 0
NFKBIA 0.004 0.05 0.19 1 -10000 0 1
GAB1 0.028 0.051 -10000 0 -0.5 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.02 0.25 -10000 0 -0.83 18 18
JUN 0.024 0.054 -10000 0 -0.33 5 5
LPA/LPA2/NHERF2 0.022 0.009 -10000 0 -10000 0 0
TIAM1 -0.044 0.28 -10000 0 -0.95 19 19
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 0.001 0.039 0.22 3 -0.23 1 4
PLCB3 0.024 0.027 0.19 5 -10000 0 5
FOS -0.028 0.16 -10000 0 -0.49 24 24
positive regulation of mitosis 0.002 0.056 -10000 0 -0.25 1 1
LPA/LPA1-2-3 -0.001 0.012 -10000 0 -0.12 2 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade -0.001 0 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
stress fiber formation 0.01 0.049 -10000 0 -0.24 1 1
GNAZ 0.02 0.016 -10000 0 -10000 0 0
EGFR/PI3K-beta/Gab1 0.01 0.046 -10000 0 -0.25 6 6
positive regulation of dendritic cell cytokine production -0.001 0.012 -10000 0 -0.12 2 2
LPA/LPA2/MAGI-3 0.021 0.025 -10000 0 -0.3 1 1
ARHGEF1 0.044 0.058 0.26 3 -10000 0 3
GNAI2 0.021 0.015 -10000 0 -10000 0 0
GNAI3 0.021 0.016 -10000 0 -10000 0 0
GNAI1 -0.018 0.1 -10000 0 -0.3 26 26
LPA/LPA3 -0.001 0.006 -10000 0 -0.064 2 2
LPA/LPA2 -0.001 0.006 -10000 0 -0.064 2 2
LPA/LPA1 -0.001 0.016 -10000 0 -0.16 2 2
HB-EGF/EGFR 0.007 0.055 -10000 0 -0.31 3 3
HBEGF 0 0.049 -10000 0 -0.24 8 8
mol:DAG 0.001 0.039 0.22 3 -0.23 1 4
cAMP biosynthetic process 0.003 0.069 0.29 3 -10000 0 3
NFKB1 0.032 0.005 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
LYN 0.027 0.056 0.23 3 -10000 0 3
GNAQ 0.001 0.005 -10000 0 -0.046 2 2
LPAR2 -0.001 0 -10000 0 -10000 0 0
LPAR3 -0.001 0 -10000 0 -10000 0 0
LPAR1 0.003 0.01 -10000 0 -0.1 2 2
IL8 -0.11 0.1 -10000 0 -0.43 6 6
PTK2 0.019 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.007 -10000 0 -10000 0 0
CASP3 0.017 0.013 -10000 0 -10000 0 0
EGFR 0.019 0.072 -10000 0 -0.5 4 4
PLCG1 0 0.031 -10000 0 -0.13 10 10
PLD2 0.019 0.016 -10000 0 -10000 0 0
G12/G13 0.041 0.024 -10000 0 -10000 0 0
PI3K-beta 0.018 0.028 -10000 0 -10000 0 0
cell migration 0.019 0.084 -10000 0 -0.24 13 13
SLC9A3R2 0.032 0.006 -10000 0 -10000 0 0
PXN 0.01 0.05 -10000 0 -0.24 1 1
HRAS/GTP 0.001 0.057 -10000 0 -0.25 1 1
RAC1 0.031 0.01 -10000 0 -10000 0 0
MMP9 0.007 0.064 -10000 0 -0.36 6 6
PRKCE 0.033 0.004 -10000 0 -10000 0 0
PRKCD 0.009 0.043 0.21 4 -0.22 1 5
Gi(beta/gamma) 0 0.065 -10000 0 -0.3 2 2
mol:LPA 0.003 0.01 -10000 0 -0.1 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.027 0.043 -10000 0 -10000 0 0
MAPKKK cascade 0.002 0.056 -10000 0 -0.25 1 1
contractile ring contraction involved in cytokinesis 0.022 0.053 0.25 1 -0.27 3 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.002 0.059 -10000 0 -0.28 9 9
GNA15 0.009 0.025 -10000 0 -0.12 6 6
GNA12 0.03 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
MAPT -0.019 0.078 0.2 5 -0.28 1 6
GNA11 0.006 0.048 -10000 0 -0.28 6 6
Rac1/GTP -0.023 0.26 -10000 0 -0.88 18 18
MMP2 0.02 0.03 -10000 0 -0.29 2 2
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.014 0.091 -10000 0 -0.46 6 6
KLHL20 0.041 0.091 0.23 9 -0.23 4 13
CYFIP2 0.028 0.051 -10000 0 -0.5 2 2
Rac1/GDP 0.073 0.1 0.31 4 -10000 0 4
ENAH 0.01 0.094 -10000 0 -0.46 6 6
AP1M1 0.033 0.004 -10000 0 -10000 0 0
RAP1B 0.033 0.005 -10000 0 -10000 0 0
RAP1A 0.032 0.007 -10000 0 -10000 0 0
CTNNB1 0.025 0.054 -10000 0 -0.32 5 5
CDC42/GTP 0.02 0.051 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.036 -10000 0 -0.18 5 5
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.099 -10000 0 -0.28 15 15
RAPGEF1 0.055 0.11 0.34 3 -0.4 5 8
CTNND1 0.033 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.021 0.095 -10000 0 -0.45 7 7
CRK 0.05 0.11 -10000 0 -0.44 5 5
E-cadherin/gamma catenin/alpha catenin 0.053 0.064 -10000 0 -0.31 6 6
alphaE/beta7 Integrin 0.023 0.082 -10000 0 -0.36 9 9
IQGAP1 0.031 0.009 -10000 0 -10000 0 0
NCKAP1 0.032 0.024 -10000 0 -0.32 1 1
Rap1/GTP/I-afadin 0.059 0.019 -10000 0 -10000 0 0
DLG1 0.014 0.091 -10000 0 -0.44 7 7
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.028 -10000 0 -10000 0 0
MLLT4 0.032 0.007 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.049 0.044 -10000 0 -0.27 2 2
PI3K 0.002 0.037 -10000 0 -10000 0 0
ARF6 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.035 0.069 -10000 0 -0.36 6 6
TIAM1 0.026 0.052 -10000 0 -0.5 2 2
E-cadherin(dimer)/Ca2+ 0.059 0.068 -10000 0 -0.26 6 6
AKT1 0.036 0.053 0.19 3 -10000 0 3
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
CDH1 0.018 0.088 -10000 0 -0.5 6 6
RhoA/GDP 0.088 0.11 0.33 7 -10000 0 7
actin cytoskeleton organization 0.038 0.076 0.21 11 -0.17 4 15
CDC42/GDP 0.083 0.11 0.34 7 -10000 0 7
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.019 0.044 -10000 0 -0.24 6 6
ITGB7 0.011 0.11 -10000 0 -0.5 9 9
RAC1 0.03 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.064 0.073 -10000 0 -0.28 6 6
E-cadherin/Ca2+/beta catenin/alpha catenin 0.043 0.062 -10000 0 -0.26 6 6
mol:GDP 0.077 0.12 0.34 7 -0.32 1 8
CDC42/GTP/IQGAP1 0.04 0.015 -10000 0 -10000 0 0
JUP 0.032 0.006 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.097 0.11 0.33 7 -10000 0 7
RAC1/GTP/IQGAP1 0.038 0.016 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.049 0.008 -10000 0 -10000 0 0
RHOA 0.033 0.005 -10000 0 -10000 0 0
CDC42 0.031 0.009 -10000 0 -10000 0 0
CTNNA1 0.033 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.023 0.079 0.18 15 -0.16 2 17
NME1 0.029 0.035 -10000 0 -0.32 2 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.012 0.091 -10000 0 -0.46 6 6
regulation of cell-cell adhesion 0.008 0.037 -10000 0 -10000 0 0
WASF2 0.017 0.04 0.11 7 -0.13 1 8
Rap1/GTP 0.082 0.091 0.32 2 -10000 0 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.054 0.095 -10000 0 -0.27 2 2
CCND1 0.025 0.093 0.2 15 -0.2 2 17
VAV2 0.072 0.17 0.42 1 -0.72 4 5
RAP1/GDP 0.093 0.1 0.34 5 -10000 0 5
adherens junction assembly 0.012 0.089 -10000 0 -0.45 6 6
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.033 0.004 -10000 0 -10000 0 0
PIP5K1C 0.033 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.035 0.091 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.006 0.063 -10000 0 -0.36 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.004 0.08 -10000 0 -0.46 5 5
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.03 0.074 -10000 0 -0.36 5 5
E-cadherin/beta catenin/alpha catenin 0.048 0.073 -10000 0 -0.31 6 6
ITGAE 0.027 0.013 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.097 -10000 0 -0.46 7 7
IL2 signaling events mediated by STAT5

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
GAB2 0.034 0.004 -10000 0 -10000 0 0
ELF1 0.025 0.035 -10000 0 -10000 0 0
CCNA2 -0.02 0.13 -10000 0 -0.32 32 32
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
JAK3 0.034 0.004 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
JAK1 0.034 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.07 0.068 -10000 0 -0.53 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
SP1 0.023 0.071 -10000 0 -0.32 7 7
IL2RA 0.013 0.051 -10000 0 -10000 0 0
IL2RB 0.032 0.008 -10000 0 -10000 0 0
SOS1 0.034 0.002 -10000 0 -10000 0 0
IL2RG 0.027 0.063 -10000 0 -0.5 3 3
G1/S transition of mitotic cell cycle 0.006 0.13 0.4 2 -0.67 5 7
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
CCND2 0 0.13 -10000 0 -0.5 11 11
LCK 0.029 0.044 -10000 0 -0.41 2 2
GRB2 0.033 0.006 -10000 0 -10000 0 0
IL2 0.034 0.005 -10000 0 -10000 0 0
CDK6 0.03 0.025 -10000 0 -0.32 1 1
CCND3 0.07 0.074 0.43 1 -0.46 1 2
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.071 0.082 -10000 0 -10000 0 0
NCK1/PAK1/Dok-R -0.005 0.021 -10000 0 -10000 0 0
NCK1/Dok-R 0.076 0.063 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
mol:beta2-estradiol -0.011 0.008 -10000 0 -10000 0 0
RELA 0.033 0.006 -10000 0 -10000 0 0
SHC1 0.034 0.006 -10000 0 -10000 0 0
Rac/GDP 0.023 0.007 -10000 0 -10000 0 0
F2 0.005 0.026 -10000 0 -10000 0 0
TNIP2 0.032 0.007 -10000 0 -10000 0 0
NF kappa B/RelA 0.11 0.051 -10000 0 -10000 0 0
FN1 -0.006 0.11 -10000 0 -0.32 24 24
PLD2 0.034 0.037 -10000 0 -10000 0 0
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
GRB14 -0.026 0.15 -10000 0 -0.38 31 31
ELK1 0.065 0.059 -10000 0 -10000 0 0
GRB7 0.03 0.026 -10000 0 -0.32 1 1
PAK1 0.033 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.094 0.08 -10000 0 -10000 0 0
CDKN1A 0.032 0.14 -10000 0 -0.82 3 3
ITGA5 0.025 0.054 -10000 0 -0.32 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.074 0.065 -10000 0 -10000 0 0
CRK 0.027 0.013 -10000 0 -10000 0 0
mol:NO 0.081 0.092 0.5 2 -10000 0 2
PLG 0.038 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.072 0.07 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
ANGPT2 -0.067 0.15 -10000 0 -10000 0 0
BMX -0.098 0.12 -10000 0 -10000 0 0
ANGPT1 0.035 0.03 -10000 0 -10000 0 0
tube development 0.029 0.11 0.42 1 -10000 0 1
ANGPT4 0.028 0.014 -10000 0 -10000 0 0
response to hypoxia 0.002 0.007 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.065 0.083 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.041 0.045 -10000 0 -10000 0 0
FGF2 0.01 0.1 -10000 0 -0.48 9 9
STAT5A (dimer) 0.042 0.13 -10000 0 -0.62 1 1
mol:L-citrulline 0.081 0.092 0.5 2 -10000 0 2
AGTR1 -0.18 0.26 -10000 0 -0.5 89 89
MAPK14 0.059 0.072 -10000 0 -10000 0 0
Tie2/SHP2 0.069 0.036 -10000 0 -10000 0 0
TEK 0.043 0.032 -10000 0 -10000 0 0
RPS6KB1 0.073 0.08 -10000 0 -10000 0 0
Angiotensin II/AT1 -0.13 0.19 -10000 0 -0.36 89 89
Tie2/Ang1/GRB2 0.085 0.047 -10000 0 -10000 0 0
MAPK3 0.03 0.044 -10000 0 -10000 0 0
MAPK1 0.033 0.038 -10000 0 -10000 0 0
Tie2/Ang1/GRB7 0.083 0.048 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 0.038 0.037 -10000 0 -10000 0 0
PI3K 0.068 0.079 -10000 0 -10000 0 0
FES 0.048 0.088 -10000 0 -10000 0 0
Crk/Dok-R 0.068 0.063 -10000 0 -10000 0 0
Tie2/Ang1/ABIN2 0.085 0.048 -10000 0 -10000 0 0
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.077 0.081 -10000 0 -10000 0 0
STAT5A 0.033 0.006 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.097 0.1 0.45 2 -10000 0 2
Tie2/Ang2 0.012 0.1 -10000 0 -10000 0 0
Tie2/Ang1 0.043 0.04 -10000 0 -10000 0 0
FOXO1 0.092 0.11 -10000 0 -10000 0 0
ELF1 0.031 0.019 -10000 0 -10000 0 0
ELF2 0.04 0.039 -10000 0 -10000 0 0
mol:Choline 0.034 0.037 -10000 0 -10000 0 0
cell migration -0.002 0.021 -10000 0 -10000 0 0
FYN 0.029 0.11 -10000 0 -10000 0 0
DOK2 0.023 0.039 -10000 0 -0.5 1 1
negative regulation of cell cycle 0.036 0.13 0.42 1 -0.72 3 4
ETS1 0.043 0.012 -10000 0 -10000 0 0
PXN 0.095 0.1 0.42 3 -10000 0 3
ITGB1 0.032 0.025 -10000 0 -0.32 1 1
NOS3 0.08 0.088 0.44 1 -10000 0 1
RAC1 0.031 0.01 -10000 0 -10000 0 0
TNF 0.044 0.012 -10000 0 -10000 0 0
MAPKKK cascade 0.034 0.037 -10000 0 -10000 0 0
RASA1 0.03 0.035 -10000 0 -0.32 2 2
Tie2/Ang1/Shc 0.086 0.048 -10000 0 -10000 0 0
NCK1 0.033 0.004 -10000 0 -10000 0 0
vasculogenesis 0.079 0.089 0.49 2 -10000 0 2
mol:Phosphatidic acid 0.034 0.037 -10000 0 -10000 0 0
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.081 0.092 0.5 2 -10000 0 2
Rac1/GTP 0.069 0.07 -10000 0 -10000 0 0
MMP2 0.037 0.04 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.019 0.098 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SLAP 0.04 0.019 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.043 0.009 -10000 0 -10000 0 0
AKT1 0.062 0.099 0.32 5 -10000 0 5
mol:PI-4-5-P2 0.001 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.05 0.12 0.28 1 -10000 0 1
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
FGR -0.007 0.14 -10000 0 -0.48 14 14
mol:Ca2+ 0.047 0.11 0.27 2 -0.35 1 3
MYC -0.02 0.17 0.4 5 -0.4 3 8
SHC1 0.033 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.07 0.074 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.06 0.025 -10000 0 -10000 0 0
GRB10 0.016 0.072 -10000 0 -0.32 9 9
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
GO:0007205 0.047 0.11 0.27 1 -0.36 1 2
PTEN 0.026 0.052 -10000 0 -0.5 2 2
GRB2 0.032 0.006 -10000 0 -10000 0 0
GRB7 0.03 0.026 -10000 0 -0.32 1 1
PDGFB-D/PDGFRB/SHP2 0.046 0.02 -10000 0 -0.22 1 1
PDGFB-D/PDGFRB/GRB10 0.032 0.056 -10000 0 -0.23 9 9
cell cycle arrest 0.04 0.019 -10000 0 -10000 0 0
HRAS 0.033 0.004 -10000 0 -10000 0 0
HIF1A 0.053 0.096 0.3 5 -0.33 1 6
GAB1 0.008 0.12 -10000 0 -0.37 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.023 0.11 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.026 0.03 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.048 0.007 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.02 0.059 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.046 0.02 -10000 0 -0.22 1 1
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 0.047 0.11 0.27 1 -0.36 1 2
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.03 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.044 0.023 -10000 0 -0.22 1 1
SHB 0.02 0.068 -10000 0 -0.32 8 8
BLK -0.17 0.27 -10000 0 -0.53 70 70
PTPN2 0.026 0.014 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.047 0.01 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
VAV2 0.001 0.14 0.32 2 -0.38 4 6
CBL 0.033 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.048 0.008 -10000 0 -10000 0 0
LCK 0.007 0.13 -10000 0 -0.46 11 11
PDGFRB 0.032 0.005 -10000 0 -10000 0 0
ACP1 0.033 0.002 -10000 0 -10000 0 0
HCK -0.012 0.12 -10000 0 -0.54 9 9
ABL1 0.011 0.13 0.28 1 -0.41 4 5
PDGFB-D/PDGFRB/CBL 0 0.13 -10000 0 -0.38 4 4
PTPN1 0.017 0.016 -10000 0 -10000 0 0
SNX15 0.033 0.006 -10000 0 -10000 0 0
STAT3 0.033 0.006 -10000 0 -10000 0 0
STAT1 0.002 0.1 -10000 0 -0.32 19 19
cell proliferation -0.017 0.16 0.37 7 -0.37 3 10
SLA 0.028 0.013 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.098 0.083 0.34 3 -10000 0 3
SRC 0.007 0.036 -10000 0 -10000 0 0
PI3K 0 0.037 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.059 0.026 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.051 0.12 -10000 0 -10000 0 0
LYN 0.016 0.086 -10000 0 -0.52 3 3
LRP1 0.033 0.004 -10000 0 -10000 0 0
SOS1 0.033 0.002 -10000 0 -10000 0 0
STAT5B 0.033 0.006 -10000 0 -10000 0 0
STAT5A 0.033 0.006 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.043 0.048 -10000 0 -10000 0 0
SPHK1 -0.01 0.12 -10000 0 -0.32 27 27
EDG1 0.002 0.004 -10000 0 -10000 0 0
mol:DAG 0.047 0.11 0.27 1 -0.36 1 2
PLCG1 0.047 0.11 -10000 0 -0.37 1 1
NHERF/PDGFRB 0.056 0.048 -10000 0 -0.31 3 3
YES1 -0.034 0.18 -10000 0 -0.5 24 24
cell migration 0.055 0.048 -10000 0 -0.31 3 3
SHC/Grb2/SOS1 0.041 0.048 -10000 0 -10000 0 0
SLC9A3R2 0.032 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.025 0.063 -10000 0 -0.5 3 3
NHERF1-2/PDGFRB/PTEN 0.064 0.063 -10000 0 -0.28 5 5
FYN 0.01 0.12 -10000 0 -0.53 7 7
DOK1 0.066 0.08 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.003 -10000 0 -10000 0 0
PDGFB 0.03 0.026 -10000 0 -0.32 1 1
RAC1 -0.013 0.15 0.38 2 -0.41 6 8
PRKCD 0.064 0.081 -10000 0 -10000 0 0
FER 0.057 0.088 -10000 0 -10000 0 0
MAPKKK cascade 0.074 0.097 0.36 5 -10000 0 5
RASA1 0.062 0.084 -10000 0 -10000 0 0
NCK1 0.033 0.004 -10000 0 -10000 0 0
NCK2 0.034 0 -10000 0 -10000 0 0
p62DOK/Csk 0.076 0.076 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.037 0.052 -10000 0 -0.22 8 8
chemotaxis 0.011 0.13 0.26 2 -0.4 4 6
STAT1-3-5/STAT1-3-5 0.017 0.063 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.023 0.005 -10000 0 -10000 0 0
PTPRJ 0.033 0.003 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.033 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.008 0.087 -10000 0 -0.34 3 3
PLCG1 0.008 0.063 0.19 9 -0.27 1 10
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.033 0.004 -10000 0 -10000 0 0
GNAI3 0.033 0.006 -10000 0 -10000 0 0
G12/G13 0.043 0.017 -10000 0 -10000 0 0
cell migration 0.008 0.085 -10000 0 -0.33 3 3
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.011 0.084 -10000 0 -0.31 5 5
MAPK1 -0.004 0.078 -10000 0 -0.35 3 3
S1P/S1P5/Gi -0.005 0.088 -10000 0 -0.38 3 3
GNAI1 -0.032 0.17 -10000 0 -0.5 26 26
CDC42/GDP 0.023 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0.021 0.007 -10000 0 -10000 0 0
RHOA 0.04 0.058 0.2 25 -10000 0 25
S1P/S1P4/Gi -0.005 0.088 -10000 0 -0.38 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.008 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.037 0.015 -10000 0 -10000 0 0
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
CDC42 0.031 0.009 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.004 0.021 -10000 0 -0.31 1 1
ADCY5 0.006 0.001 -10000 0 -10000 0 0
ADCY6 0.006 0.001 -10000 0 -10000 0 0
ADCY7 0.006 0.001 -10000 0 -10000 0 0
ADCY1 0.005 0.002 -10000 0 -10000 0 0
ADCY2 0.005 0.013 -10000 0 -0.18 1 1
ADCY3 -0.006 0.045 -10000 0 -0.18 13 13
ADCY8 0.004 0.013 -10000 0 -0.18 1 1
PRKCE 0.01 0.001 -10000 0 -10000 0 0
ADCY9 0.001 0.037 -10000 0 -0.31 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.028 0.063 0.25 6 -10000 0 6
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.004 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.072 -10000 0 -10000 0 0
NFATC4 -0.004 0.046 0.25 2 -10000 0 2
ERBB2IP 0.025 0.062 -10000 0 -0.5 3 3
HSP90 (dimer) 0.029 0.026 -10000 0 -0.32 1 1
mammary gland morphogenesis 0.032 0.046 -10000 0 -10000 0 0
JUN 0.025 0.073 0.25 2 -10000 0 2
HRAS 0.033 0.004 -10000 0 -10000 0 0
DOCK7 0.009 0.042 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.052 0.048 0.27 2 -0.28 1 3
AKT1 0.009 0.004 -10000 0 -10000 0 0
BAD 0.004 0.005 -10000 0 -10000 0 0
MAPK10 0.016 0.053 0.24 4 -10000 0 4
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.035 0.049 -10000 0 -10000 0 0
RAF1 0.026 0.068 0.32 2 -10000 0 2
ErbB2/ErbB3/neuregulin 2 0.038 0.066 0.26 3 -0.3 6 9
STAT3 0.017 0.083 -10000 0 -0.81 2 2
cell migration 0.02 0.056 0.22 7 -10000 0 7
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.001 0.18 0.4 2 -0.56 6 8
FOS -0.028 0.21 0.35 2 -0.49 31 33
NRAS 0.029 0.035 -10000 0 -0.33 2 2
mol:Ca2+ 0.032 0.046 -10000 0 -10000 0 0
MAPK3 0.017 0.13 0.37 2 -0.66 1 3
MAPK1 0.002 0.16 0.38 2 -0.7 5 7
JAK2 0.007 0.046 -10000 0 -10000 0 0
NF2 0.009 0.063 -10000 0 -0.64 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.022 0.026 -10000 0 -10000 0 0
NRG1 0.027 0.014 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
MAPK8 0.011 0.068 -10000 0 -10000 0 0
MAPK9 0.019 0.05 0.24 4 -10000 0 4
ERBB2 -0.011 0.063 0.26 9 -0.38 1 10
ERBB3 0.033 0.004 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
apoptosis -0.003 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.017 0.082 -10000 0 -0.79 2 2
RNF41 -0.003 0.005 -10000 0 -10000 0 0
FRAP1 0.002 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.006 0.027 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.025 0.047 0.26 3 -0.26 2 5
CHRNA1 0.024 0.11 0.36 2 -0.41 1 3
myelination 0.002 0.055 0.3 3 -10000 0 3
PPP3CB 0.009 0.041 -10000 0 -10000 0 0
KRAS 0.033 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.037 0.057 -10000 0 -10000 0 0
NRG2 0.021 0.081 -10000 0 -0.5 5 5
mol:GDP 0.022 0.026 -10000 0 -10000 0 0
SOS1 0.034 0.002 -10000 0 -10000 0 0
MAP2K2 0.019 0.066 0.39 1 -10000 0 1
SRC 0.019 0.017 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.009 0.044 -10000 0 -10000 0 0
MAP2K1 -0.014 0.2 0.38 1 -0.63 14 15
heart morphogenesis 0.032 0.046 -10000 0 -10000 0 0
RAS family/GDP 0.05 0.072 0.26 1 -10000 0 1
GRB2 0.032 0.006 -10000 0 -10000 0 0
PRKACA 0.012 0.067 -10000 0 -0.68 2 2
CHRNE 0.015 0.018 -10000 0 -10000 0 0
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
activation of caspase activity -0.009 0.004 -10000 0 -10000 0 0
nervous system development 0.032 0.046 -10000 0 -10000 0 0
CDC42 0.031 0.009 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.032 0.011 -9999 0 -10000 0 0
SVIL 0.029 0.052 -9999 0 -0.5 2 2
ZNF318 0.03 0.006 -9999 0 -10000 0 0
JMJD2C 0.007 0.001 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.051 0.027 -9999 0 -10000 0 0
CARM1 0.033 0.004 -9999 0 -10000 0 0
PRDX1 0.033 0.005 -9999 0 -10000 0 0
PELP1 0.027 0.013 -9999 0 -10000 0 0
CTNNB1 0.026 0.054 -9999 0 -0.32 5 5
AKT1 0.03 0.01 -9999 0 -10000 0 0
PTK2B 0.026 0.015 -9999 0 -10000 0 0
MED1 0.031 0.008 -9999 0 -10000 0 0
MAK 0.024 0.049 -9999 0 -0.33 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.032 0.025 -9999 0 -0.32 1 1
GSN -0.053 0.2 -9999 0 -0.5 35 35
NCOA2 0.029 0.012 -9999 0 -10000 0 0
NCOA6 0.02 0.018 -9999 0 -10000 0 0
DNA-PK 0.048 0.044 -9999 0 -10000 0 0
NCOA4 0.032 0.007 -9999 0 -10000 0 0
PIAS3 0.032 0.025 -9999 0 -0.32 1 1
cell proliferation 0.019 0.043 -9999 0 -0.37 2 2
XRCC5 0.033 0.002 -9999 0 -10000 0 0
UBE3A 0.033 0.01 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.032 0.017 -9999 0 -0.17 1 1
FHL2 0.042 0.023 -9999 0 -10000 0 0
RANBP9 0.034 0.006 -9999 0 -10000 0 0
JMJD1A 0.007 0.01 -9999 0 -0.14 1 1
CDK6 0.03 0.025 -9999 0 -0.32 1 1
TGFB1I1 0.034 0.005 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 0.02 0.085 -9999 0 -10000 0 0
XRCC6 0.031 0.008 -9999 0 -10000 0 0
T-DHT/AR 0.067 0.028 -9999 0 -10000 0 0
CTDSP1 0.034 0.002 -9999 0 -10000 0 0
CTDSP2 0.026 0.051 -9999 0 -0.5 2 2
BRCA1 0.029 0.042 -9999 0 -0.32 3 3
TCF4 0.022 0.015 -9999 0 -10000 0 0
CDKN2A -0.078 0.16 -9999 0 -0.33 66 66
SRF 0.038 0.01 -9999 0 -10000 0 0
NKX3-1 0.014 0.018 -9999 0 -0.23 1 1
KLK3 0.019 0.044 -9999 0 -10000 0 0
TMF1 0.033 0.006 -9999 0 -10000 0 0
HNRNPA1 0.032 0.004 -9999 0 -10000 0 0
AOF2 0.002 0.001 -9999 0 -10000 0 0
APPL1 0.016 0.006 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.053 0.02 -9999 0 -10000 0 0
AR 0.037 0.026 -9999 0 -0.32 1 1
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.031 0.008 -9999 0 -10000 0 0
PAWR 0.033 0.004 -9999 0 -10000 0 0
PRKDC 0.02 0.054 -9999 0 -0.33 5 5
PA2G4 0.03 0.025 -9999 0 -0.33 1 1
UBE2I 0.031 0.025 -9999 0 -0.32 1 1
T-DHT/AR/Cyclin D3/CDK11 p58 0.049 0.02 -9999 0 -10000 0 0
RPS6KA3 0.034 0.006 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.053 0.021 -9999 0 -10000 0 0
LATS2 0.024 0.014 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.049 0.019 -9999 0 -10000 0 0
Cyclin D3/CDK11 p58 0.024 0.004 -9999 0 -10000 0 0
VAV3 -0.046 0.19 -9999 0 -0.5 32 32
KLK2 0.031 0.012 -9999 0 -10000 0 0
CASP8 0.033 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.063 0.032 -9999 0 -10000 0 0
TMPRSS2 0.025 0.071 -9999 0 -0.94 1 1
CCND1 -0.021 0.13 -9999 0 -0.32 33 33
PIAS1 0.033 0.01 -9999 0 -10000 0 0
mol:T-DHT 0.005 0.005 -9999 0 -0.063 1 1
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.035 0.008 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.05 0.027 -9999 0 -10000 0 0
CMTM2 0.026 0.049 -9999 0 -0.33 4 4
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.037 0.012 -9999 0 -10000 0 0
CCND3 0.033 0.006 -9999 0 -10000 0 0
TGIF1 -0.013 0.11 -9999 0 -0.33 23 23
FKBP4 0.034 0.007 -9999 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.038 0.034 -9999 0 -0.22 3 3
EFNA5 0.03 0.037 -9999 0 -0.5 1 1
FYN 0.016 0.036 -9999 0 -0.28 2 2
neuron projection morphogenesis 0.038 0.034 -9999 0 -0.22 3 3
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.039 0.034 -9999 0 -0.23 3 3
EPHA5 0.029 0.035 -9999 0 -0.32 2 2
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC2 0.032 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.05 0.046 -10000 0 -0.31 1 1
forebrain development -0.018 0.16 -10000 0 -0.63 8 8
GNAO1 0.033 0.005 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.032 0.047 -10000 0 -0.26 4 4
SMO 0.024 0.056 -10000 0 -0.37 4 4
ARRB2 0.027 0.013 -10000 0 -10000 0 0
GLI3/SPOP 0.054 0.097 0.28 1 -10000 0 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.031 0.025 -10000 0 -0.32 1 1
GNAI2 0.033 0.004 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.041 -10000 0 -10000 0 0
GNAI1 -0.032 0.17 -10000 0 -0.5 26 26
XPO1 0.032 0.012 -10000 0 -10000 0 0
GLI1/Su(fu) -0.018 0.14 -10000 0 -0.74 4 4
SAP30 0.032 0.007 -10000 0 -10000 0 0
mol:GDP 0.024 0.056 -10000 0 -0.37 4 4
MIM/GLI2A 0.007 0.07 -10000 0 -0.5 3 3
IFT88 0.025 0.015 -10000 0 -10000 0 0
GNAI3 0.032 0.006 -10000 0 -10000 0 0
GLI2 0.022 0.063 -10000 0 -0.35 2 2
GLI3 0.043 0.1 0.32 2 -0.33 2 4
CSNK1D 0.033 0.006 -10000 0 -10000 0 0
CSNK1E 0.03 0.026 -10000 0 -0.32 1 1
SAP18 0.025 0.015 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.015 -10000 0 -10000 0 0
GNG2 0.031 0.01 -10000 0 -10000 0 0
Gi family/GTP -0.004 0.092 -10000 0 -0.32 5 5
SIN3B 0.033 0.005 -10000 0 -10000 0 0
SIN3A 0.031 0.008 -10000 0 -10000 0 0
GLI3/Su(fu) 0.051 0.087 0.37 1 -10000 0 1
GLI2/Su(fu) 0.026 0.069 -10000 0 -0.42 2 2
FOXA2 -0.057 0.2 -10000 0 -0.86 7 7
neural tube patterning -0.018 0.16 -10000 0 -0.63 8 8
SPOP 0.032 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.03 0.052 -10000 0 -10000 0 0
GNB1 0.032 0.008 -10000 0 -10000 0 0
CSNK1G2 0.033 0.006 -10000 0 -10000 0 0
CSNK1G3 0.033 0.005 -10000 0 -10000 0 0
MTSS1 0.007 0.07 -10000 0 -0.5 3 3
embryonic limb morphogenesis -0.018 0.16 -10000 0 -0.63 8 8
SUFU 0.021 0.027 -10000 0 -10000 0 0
LGALS3 0.013 0.095 -10000 0 -0.5 7 7
catabolic process 0.062 0.11 -10000 0 -0.36 2 2
GLI3A/CBP 0.018 0.088 -10000 0 -0.34 12 12
KIF3A 0.031 0.025 -10000 0 -0.32 1 1
GLI1 -0.019 0.16 -10000 0 -0.65 8 8
RAB23 0.02 0.068 -10000 0 -0.32 8 8
CSNK1A1 0.033 0.004 -10000 0 -10000 0 0
IFT172 0.031 0.036 -10000 0 -0.5 1 1
RBBP7 0.033 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.022 0.076 -10000 0 -0.29 7 7
GNAZ 0.031 0.008 -10000 0 -10000 0 0
RBBP4 0.032 0.007 -10000 0 -10000 0 0
CSNK1G1 0.032 0.008 -10000 0 -10000 0 0
PIAS1 0.031 0.008 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.037 0.062 -10000 0 -0.32 2 2
STK36 0.03 0.027 -10000 0 -0.32 1 1
Gi family/GNB1/GNG2/GDP -0.002 0.094 -10000 0 -0.39 5 5
PTCH1 -0.013 0.15 -10000 0 -0.74 3 3
MIM/GLI1 -0.028 0.18 -10000 0 -0.66 9 9
CREBBP 0.018 0.088 -10000 0 -0.34 12 12
Su(fu)/SIN3/HDAC complex 0.032 0.096 -10000 0 -0.39 6 6
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.009 0.086 0.33 3 -10000 0 3
GNAI2 0.033 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.021 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.033 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.009 0.088 -10000 0 -0.34 3 3
negative regulation of cAMP metabolic process -0.005 0.087 -10000 0 -0.37 3 3
GNAZ 0.032 0.008 -10000 0 -10000 0 0
GNAI3 0.033 0.006 -10000 0 -10000 0 0
GNA12 0.031 0.01 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.005 0.088 -10000 0 -0.38 3 3
RhoA/GDP 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.033 0.005 -10000 0 -10000 0 0
GNAI1 -0.032 0.17 -10000 0 -0.5 26 26
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.007 0.003 -10000 0 -10000 0 0
SNTA1 0.019 0.017 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.006 0.014 -10000 0 -10000 0 0
MAPK12 -0.013 0.063 -10000 0 -0.29 9 9
CCND1 -0.002 0.046 -10000 0 -0.32 1 1
p38 gamma/SNTA1 0.003 0.064 -10000 0 -0.27 8 8
MAP2K3 0.028 0.013 -10000 0 -10000 0 0
PKN1 0.033 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.009 0.069 0.21 4 -0.28 9 13
MAP2K6 -0.007 0.06 -10000 0 -0.3 9 9
MAPT 0.005 0.046 0.22 3 -10000 0 3
MAPK13 0.016 0.008 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.002 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC3 0.033 0.004 -10000 0 -10000 0 0
VDR 0.018 0.088 -10000 0 -0.5 6 6
Cbp/p300/PCAF 0.041 0.013 -10000 0 -10000 0 0
EP300 0.031 0.008 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.018 0.039 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.033 0.005 -10000 0 -10000 0 0
AKT1 0.027 0.061 0.22 8 -0.23 1 9
RAR alpha/9cRA/Cyclin H 0.06 0.061 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.033 0.043 0.2 2 -10000 0 2
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.039 0.042 -10000 0 -0.32 1 1
NCOR2 0.033 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.064 -10000 0 -0.36 6 6
RXRs/RARs/NRIP1/9cRA 0.044 0.069 0.4 1 -10000 0 1
NCOA2 0.029 0.012 -10000 0 -10000 0 0
NCOA3 0.019 0.017 -10000 0 -10000 0 0
NCOA1 0.029 0.051 -10000 0 -0.5 2 2
VDR/VDR/DNA 0.018 0.088 -10000 0 -0.5 6 6
RARG 0.031 0.035 -10000 0 -0.32 2 2
RAR gamma1/9cRA 0.042 0.023 -10000 0 -0.18 2 2
MAPK3 0.028 0.052 -10000 0 -0.5 2 2
MAPK1 0.031 0.008 -10000 0 -10000 0 0
MAPK8 0.033 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.043 0.075 -10000 0 -0.43 1 1
RARA 0.024 0.023 -10000 0 -0.18 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.028 0.04 0.2 2 -10000 0 2
PRKCA 0.032 0.026 -10000 0 -0.32 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 0.048 0.068 0.37 1 -10000 0 1
RXRG 0.028 0.022 -10000 0 -10000 0 0
RXRA 0.026 0.037 -10000 0 -0.22 2 2
RXRB 0.028 0.022 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.064 -10000 0 -0.36 6 6
RBP1 -0.017 0.14 -10000 0 -0.4 25 25
CRBP1/9-cic-RA -0.011 0.1 -10000 0 -0.28 25 25
RARB 0.035 0.005 -10000 0 -10000 0 0
PRKCG 0.029 0.049 -10000 0 -0.32 4 4
MNAT1 0.031 0.01 -10000 0 -10000 0 0
RAR alpha/RXRs 0.038 0.073 0.35 1 -10000 0 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.046 0.067 0.4 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.068 0.28 5 -0.31 1 6
RXRs/RARs/NRIP1/9cRA/HDAC3 0.049 0.068 0.37 1 -10000 0 1
positive regulation of DNA binding 0.044 0.051 -10000 0 -10000 0 0
NRIP1 0.05 0.065 -10000 0 -10000 0 0
RXRs/RARs 0.048 0.064 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.028 0.052 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
CDK7 0.033 0.005 -10000 0 -10000 0 0
TFIIH 0.061 0.021 -10000 0 -10000 0 0
RAR alpha/9cRA 0.068 0.051 -10000 0 -10000 0 0
CCNH 0.033 0.003 -10000 0 -10000 0 0
CREBBP 0.032 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.057 0.031 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.046 0.021 -10000 0 -0.22 1 1
AKT1 0.083 0.12 0.4 7 -10000 0 7
PTK2B 0.006 0.067 -10000 0 -10000 0 0
VEGFR2 homodimer/Frs2 0.03 0.062 -10000 0 -10000 0 0
CAV1 0.025 0.056 -10000 0 -0.37 4 4
CALM1 0.03 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.03 0.088 -10000 0 -0.32 1 1
endothelial cell proliferation 0.13 0.14 0.36 33 -10000 0 33
mol:Ca2+ -0.005 0.065 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.084 -10000 0 -10000 0 0
RP11-342D11.1 -0.013 0.083 -10000 0 -0.42 2 2
CDH5 0.033 0.005 -10000 0 -10000 0 0
VEGFA homodimer 0.053 0.077 -10000 0 -0.32 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
SHC2 0.014 0.079 -10000 0 -0.32 11 11
HRAS/GDP 0.023 0.086 -10000 0 -0.37 2 2
SH2D2A 0.023 0.059 -10000 0 -0.32 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.092 0.11 0.34 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.024 0.092 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.006 0.078 -10000 0 -0.32 11 11
SHC/GRB2/SOS1 0.047 0.11 -10000 0 -0.41 2 2
GRB10 -0.004 0.092 -10000 0 -0.42 1 1
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
GRB2 0.032 0.006 -10000 0 -10000 0 0
PAK1 0.033 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.1 -10000 0 -0.38 1 1
HRAS 0.033 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.008 0.099 -10000 0 -0.35 4 4
HIF1A 0.027 0.035 -10000 0 -0.32 2 2
FRS2 0.033 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.041 0.082 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.033 0.004 -10000 0 -10000 0 0
Nck/Pak 0.049 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.028 0.091 -10000 0 -0.34 2 2
mol:GDP 0.032 0.097 -10000 0 -0.4 2 2
mol:NADP 0.083 0.1 0.35 5 -10000 0 5
eNOS/Hsp90 0.087 0.1 0.35 5 -10000 0 5
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 -0.005 0.065 -10000 0 -10000 0 0
HIF1A/ARNT 0.042 0.03 -10000 0 -0.22 2 2
SHB 0.02 0.068 -10000 0 -0.32 8 8
VEGFA 0.002 0.099 -10000 0 -0.33 17 17
VEGFC 0.025 0.063 -10000 0 -0.5 3 3
FAK1/Vinculin 0.053 0.096 0.31 1 -10000 0 1
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.033 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.044 0.091 -10000 0 -10000 0 0
PTPN6 0.033 0.006 -10000 0 -10000 0 0
EPAS1 0.022 0.089 -10000 0 -0.49 6 6
mol:L-citrulline 0.083 0.1 0.35 5 -10000 0 5
ITGAV 0.031 0.025 -10000 0 -0.32 1 1
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.046 0.09 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.022 0.11 -10000 0 -0.46 2 2
VEGFR2/3 heterodimer 0.03 0.061 -10000 0 -0.29 5 5
VEGFB 0.033 0.005 -10000 0 -10000 0 0
MAPK11 -0.019 0.085 -10000 0 -0.42 3 3
VEGFR2 homodimer 0.014 0.066 -10000 0 -0.35 6 6
FLT1 0.006 0.078 -10000 0 -0.32 11 11
NEDD4 0.018 0.064 -10000 0 -0.33 6 6
MAPK3 0.038 0.11 0.33 3 -10000 0 3
MAPK1 0.038 0.11 0.33 3 -10000 0 3
VEGFA145/NRP2 0.026 0.079 -10000 0 -0.24 17 17
VEGFR1/2 heterodimer 0.01 0.072 -10000 0 -10000 0 0
KDR 0.014 0.066 -10000 0 -0.35 6 6
VEGFA165/NRP1/VEGFR2 homodimer 0.026 0.1 -10000 0 -0.42 2 2
SRC 0.019 0.017 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.05 0.11 0.34 4 -10000 0 4
PI3K 0.042 0.092 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.031 0.086 -10000 0 -0.32 1 1
FES -0.001 0.097 -10000 0 -0.55 2 2
GAB1 0.01 0.079 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.016 0.068 -10000 0 -10000 0 0
CTNNB1 0.025 0.054 -10000 0 -0.32 5 5
SOS1 0.033 0.002 -10000 0 -10000 0 0
ARNT 0.033 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.084 0.1 0.34 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Yes 0.021 0.085 -10000 0 -0.31 1 1
PI3K/GAB1 0.047 0.082 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.061 0.093 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.072 -10000 0 -10000 0 0
HSP90AA1 0.029 0.026 -10000 0 -0.32 1 1
CDC42 0 0.09 -10000 0 -0.43 2 2
actin cytoskeleton reorganization 0.024 0.091 -10000 0 -0.32 1 1
PTK2 0.028 0.073 -10000 0 -10000 0 0
EDG1 -0.013 0.083 -10000 0 -0.42 2 2
mol:DAG -0.005 0.065 -10000 0 -10000 0 0
CaM/Ca2+ 0.003 0.066 -10000 0 -10000 0 0
MAP2K3 -0.008 0.08 -10000 0 -0.4 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.033 0.12 -10000 0 -0.43 1 1
PLCG1 -0.005 0.066 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.02 0.076 -10000 0 -10000 0 0
IQGAP1 0.031 0.009 -10000 0 -10000 0 0
YES1 0.027 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.029 0.089 -10000 0 -0.32 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.029 0.088 -10000 0 -0.32 1 1
cell migration 0.06 0.095 0.3 2 -10000 0 2
mol:PI-3-4-5-P3 0.041 0.089 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.5 1 1
VEGFB/NRP1 0.004 0.086 -10000 0 -0.4 2 2
mol:NO 0.083 0.1 0.35 5 -10000 0 5
PXN 0.033 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.076 -10000 0 -0.37 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.015 0.1 -10000 0 -0.42 1 1
VHL 0.031 0.025 -10000 0 -0.32 1 1
ITGB3 0.032 0.007 -10000 0 -10000 0 0
NOS3 0.085 0.11 0.37 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Sck 0.02 0.1 -10000 0 -0.36 2 2
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCA -0.004 0.07 -10000 0 -10000 0 0
PRKCB -0.011 0.058 -10000 0 -10000 0 0
VCL 0.032 0.007 -10000 0 -10000 0 0
VEGFA165/NRP1 0.002 0.09 -10000 0 -0.43 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.013 0.087 -10000 0 -0.31 2 2
VEGFA165/NRP2 0.026 0.079 -10000 0 -0.24 17 17
MAPKKK cascade 0.016 0.09 -10000 0 -10000 0 0
NRP2 0.032 0.024 -10000 0 -0.32 1 1
VEGFC homodimer 0.025 0.063 -10000 0 -0.5 3 3
NCK1 0.033 0.004 -10000 0 -10000 0 0
ROCK1 0.026 0.014 -10000 0 -10000 0 0
FAK1/Paxillin 0.051 0.097 0.31 1 -10000 0 1
MAP3K13 0.001 0.09 -10000 0 -0.43 2 2
PDPK1 0.065 0.11 0.39 1 -10000 0 1
Insulin Pathway

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
CBL/APS/CAP 0.037 0.091 -10000 0 -0.3 10 10
TC10/GTP 0.023 0.072 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.087 0.062 -10000 0 -0.26 2 2
HRAS 0.033 0.004 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.026 0.15 -10000 0 -0.38 31 31
FOXO3 -0.002 0.1 -10000 0 -0.55 7 7
AKT1 0.005 0.085 -10000 0 -0.36 1 1
INSR 0.039 0.065 -10000 0 -0.49 3 3
Insulin Receptor/Insulin 0.091 0.086 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.016 0.072 -10000 0 -0.32 9 9
SORBS1 -0.002 0.13 -10000 0 -0.49 14 14
CRK 0.027 0.013 -10000 0 -10000 0 0
PTPN1 0.009 0.032 -10000 0 -10000 0 0
CAV1 0.031 0.063 -10000 0 -0.31 3 3
CBL/APS/CAP/Crk-II/C3G 0.039 0.085 -10000 0 -0.26 13 13
Insulin Receptor/Insulin/IRS1/NCK2 0.089 0.06 -10000 0 -0.26 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.068 0.051 -10000 0 -0.23 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.071 0.092 -10000 0 -0.46 3 3
RPS6KB1 -0.01 0.075 0.21 2 -0.33 1 3
PARD6A 0.018 0.072 -10000 0 -0.32 9 9
CBL 0.033 0.006 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.024 0.015 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.026 0.087 -10000 0 -0.34 1 1
HRAS/GTP 0.016 0.034 -10000 0 -10000 0 0
Insulin Receptor 0.039 0.065 -10000 0 -0.49 3 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.096 0.064 -10000 0 -10000 0 0
PRKCI 0.032 0.059 -10000 0 -0.38 1 1
Insulin Receptor/Insulin/GRB14/PDK1 0.012 0.085 -10000 0 -0.38 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.053 0.034 -10000 0 -10000 0 0
PI3K 0.083 0.057 -10000 0 -10000 0 0
NCK2 0.034 0 -10000 0 -10000 0 0
RHOQ 0.033 0.004 -10000 0 -10000 0 0
mol:H2O2 0.001 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.003 -10000 0 -10000 0 0
AKT2 0.005 0.083 -10000 0 -0.36 1 1
PRKCZ 0.016 0.05 -10000 0 -0.39 1 1
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP 0.036 0.048 -10000 0 -0.23 2 2
F2RL2 0.027 0.048 -10000 0 -0.32 4 4
TRIP10 0.033 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.072 0.045 -10000 0 -0.26 2 2
TC10/GTP/CIP4/Exocyst 0.044 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.1 0.054 -10000 0 -10000 0 0
RAPGEF1 0.033 0.005 -10000 0 -10000 0 0
RASA1 0.03 0.035 -10000 0 -0.32 2 2
NCK1 0.033 0.004 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.028 0.084 -10000 0 -0.28 13 13
TC10/GDP 0.025 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.073 0.071 -10000 0 -0.26 2 2
INPP5D 0.011 0.039 -10000 0 -0.24 2 2
SOS1 0.033 0.002 -10000 0 -10000 0 0
SGK1 -0.003 0.007 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
IRS1 0.027 0.048 -10000 0 -0.32 4 4
p62DOK/RasGAP 0.054 0.035 -10000 0 -10000 0 0
INS 0.044 0.018 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.011 0.039 -10000 0 -0.24 2 2
GRB2 0.032 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.012 0.079 0.21 2 -0.33 1 3
PTPRA 0.034 0.021 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.044 0.007 -10000 0 -10000 0 0
PDPK1 0.033 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.044 0.04 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.069 0.055 -10000 0 -0.26 2 2
Insulin Receptor/Insulin/IRS3 0.062 0.051 -10000 0 -0.36 2 2
Par3/Par6 0.062 0.057 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.031 0.009 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.027 0.031 -10000 0 -10000 0 0
NT3 (dimer)/TRKC 0.042 0.03 -10000 0 -0.22 2 2
NT3 (dimer)/TRKB 0.042 0.08 -10000 0 -0.3 8 8
SHC/Grb2/SOS1/GAB1/PI3K 0.036 0.029 -10000 0 -10000 0 0
RAPGEF1 0.033 0.005 -10000 0 -10000 0 0
BDNF 0.007 0.094 -10000 0 -0.32 16 16
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
DYNLT1 0.032 0.007 -10000 0 -10000 0 0
NTRK1 0.033 0.006 -10000 0 -10000 0 0
NTRK2 0.006 0.11 -10000 0 -0.45 12 12
NTRK3 0.031 0.009 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.027 0.071 -10000 0 -0.27 11 11
neuron apoptosis -0.019 0.078 0.32 2 -10000 0 2
SHC 2-3/Grb2 0.02 0.083 -10000 0 -0.34 2 2
SHC1 0.033 0.006 -10000 0 -10000 0 0
SHC2 0.01 0.067 -10000 0 -0.31 4 4
SHC3 0.008 0.077 -10000 0 -0.41 4 4
STAT3 (dimer) 0.01 0.07 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.059 0.031 -10000 0 -10000 0 0
RIN/GDP 0.052 0.078 0.31 7 -10000 0 7
GIPC1 0.03 0.037 -10000 0 -0.5 1 1
KRAS 0.033 0.006 -10000 0 -10000 0 0
DNAJA3 0.011 0.029 -10000 0 -10000 0 0
RIN/GTP 0.017 0.012 -10000 0 -10000 0 0
CCND1 -0.019 0.11 -10000 0 -10000 0 0
MAGED1 0.031 0.025 -10000 0 -0.32 1 1
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.064 0.017 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.043 0.01 -10000 0 -10000 0 0
TRKA/NEDD4-2 -0.001 0.11 -10000 0 -0.36 15 15
ELMO1 0.03 0.01 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.037 0.03 -10000 0 -0.31 1 1
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.033 0.004 -10000 0 -10000 0 0
DOCK1 0.03 0.037 -10000 0 -0.5 1 1
GAB2 0.033 0.004 -10000 0 -10000 0 0
RIT2 0.023 0.016 -10000 0 -10000 0 0
RIT1 0.033 0.006 -10000 0 -10000 0 0
FRS2 0.033 0.004 -10000 0 -10000 0 0
DNM1 0.03 0.035 -10000 0 -0.32 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.013 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.03 0.031 -10000 0 -10000 0 0
mol:GDP 0.068 0.1 0.36 8 -0.36 2 10
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.022 0.008 -10000 0 -10000 0 0
RIT1/GDP 0.059 0.067 0.22 6 -0.25 1 7
TIAM1 0.026 0.052 -10000 0 -0.5 2 2
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.025 0.1 -10000 0 -0.3 10 10
KIDINS220/CRKL/C3G 0.046 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.045 0.028 -10000 0 -0.22 2 2
FRS2 family/SHP2 0.065 0.021 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.076 0.042 -10000 0 -0.28 2 2
RIT1/GTP 0.024 0.004 -10000 0 -10000 0 0
NT3 (dimer) 0.029 0.035 -10000 0 -0.32 2 2
RAP1/GDP 0.045 0.052 0.16 2 -10000 0 2
KIDINS220/CRKL 0.031 0.009 -10000 0 -10000 0 0
BDNF (dimer) 0.007 0.094 -10000 0 -0.32 16 16
ubiquitin-dependent protein catabolic process 0.001 0.09 -10000 0 -0.31 15 15
Schwann cell development -0.004 0.014 -10000 0 -10000 0 0
EHD4 0.031 0.009 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.08 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.05 -10000 0 -10000 0 0
RAP1B 0.033 0.005 -10000 0 -10000 0 0
RAP1A 0.032 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.076 -10000 0 -10000 0 0
ABL1 0.033 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
Rap1/GTP 0.016 0.09 -10000 0 -0.44 3 3
STAT3 0.01 0.07 -10000 0 -10000 0 0
axon guidance 0.007 0.068 -10000 0 -10000 0 0
MAPK3 0.023 0.041 -10000 0 -0.28 2 2
MAPK1 0.025 0.028 -10000 0 -10000 0 0
CDC42/GDP 0.066 0.082 0.3 9 -0.25 1 10
NTF3 0.029 0.035 -10000 0 -0.32 2 2
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.042 0.018 -10000 0 -0.18 1 1
PI3K 0.048 0.009 -10000 0 -10000 0 0
FRS3 0.033 0.006 -10000 0 -10000 0 0
FAIM 0.03 0.035 -10000 0 -0.32 2 2
GAB1 0.028 0.051 -10000 0 -0.5 2 2
RASGRF1 0 0.041 -10000 0 -10000 0 0
SOS1 0.033 0.002 -10000 0 -10000 0 0
MCF2L 0.014 0.022 -10000 0 -10000 0 0
RGS19 0.019 0.017 -10000 0 -10000 0 0
CDC42 0.031 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.052 0.082 0.49 2 -10000 0 2
Rac1/GDP 0.055 0.072 0.29 5 -0.25 1 6
NGF (dimer)/TRKA/GRIT 0.022 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.028 0.095 -10000 0 -0.86 2 2
NGF (dimer)/TRKA/NEDD4-2 0.001 0.091 -10000 0 -0.31 15 15
MAP2K1 0.023 0.043 -10000 0 -0.26 2 2
NGFR 0.032 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.026 -10000 0 -0.23 1 1
RAS family/GTP/PI3K 0.031 0.022 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.091 0.032 -10000 0 -10000 0 0
NRAS 0.029 0.035 -10000 0 -0.32 2 2
GRB2/SOS1 0.048 0.01 -10000 0 -10000 0 0
PRKCI 0.025 0.054 -10000 0 -0.32 5 5
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.011 0.026 -10000 0 -10000 0 0
RASA1 0.03 0.035 -10000 0 -0.32 2 2
TRKA/c-Abl 0.047 0.011 -10000 0 -10000 0 0
SQSTM1 0.033 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.042 0.1 -10000 0 -0.32 8 8
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.032 -10000 0 -10000 0 0
MATK 0.033 0.006 -10000 0 -10000 0 0
NEDD4L -0.014 0.13 -10000 0 -0.5 15 15
RAS family/GDP -0.006 0.023 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0.018 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.042 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family 0.075 0.046 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.02 0.039 -9999 0 -0.5 1 1
SMAD2 0.014 0.045 -9999 0 -0.24 2 2
SMAD3 0.02 0.057 -9999 0 -0.56 1 1
SMAD3/SMAD4 0.014 0.097 -9999 0 -0.46 6 6
SMAD4/Ubc9/PIASy 0.041 0.045 -9999 0 -0.31 1 1
SMAD2/SMAD2/SMAD4 0.034 0.072 -9999 0 -10000 0 0
PPM1A 0.031 0.01 -9999 0 -10000 0 0
CALM1 0.03 0.01 -9999 0 -10000 0 0
SMAD2/SMAD4 0.012 0.046 -9999 0 -0.26 1 1
MAP3K1 0.033 0.004 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.031 0.038 -9999 0 -0.36 1 1
MAPK3 0.028 0.052 -9999 0 -0.5 2 2
MAPK1 0.031 0.008 -9999 0 -10000 0 0
NUP214 0.033 0.005 -9999 0 -10000 0 0
CTDSP1 0.033 0.002 -9999 0 -10000 0 0
CTDSP2 0.028 0.051 -9999 0 -0.5 2 2
CTDSPL 0.028 0.051 -9999 0 -0.5 2 2
KPNB1 0.022 0.059 -9999 0 -0.32 6 6
TGFBRAP1 0.034 0 -9999 0 -10000 0 0
UBE2I 0.031 0.025 -9999 0 -0.32 1 1
NUP153 0.033 0.005 -9999 0 -10000 0 0
KPNA2 0.019 0.068 -9999 0 -0.32 8 8
PIAS4 0.033 0.006 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.071 0.033 -9999 0 -10000 0 0
HDAC3 0.033 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.008 0.014 -9999 0 -10000 0 0
GATA1/HDAC4 0.047 0.02 -9999 0 -0.22 1 1
GATA1/HDAC5 0.046 0.021 -9999 0 -0.22 1 1
GATA2/HDAC5 0.047 0.011 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.061 0.035 -9999 0 -0.31 1 1
HDAC9 0.03 0.01 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.018 0.12 -9999 0 -0.31 24 24
HDAC4/ANKRA2 0.049 0.008 -9999 0 -10000 0 0
HDAC5/YWHAB 0.026 0.025 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.013 -9999 0 -10000 0 0
GATA2 0.033 0.004 -9999 0 -10000 0 0
HDAC4/RFXANK 0.049 0.008 -9999 0 -10000 0 0
BCOR 0.033 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.026 0.043 -9999 0 -0.32 3 3
HDAC5 0.032 0.006 -9999 0 -10000 0 0
GNB1/GNG2 0.042 0.018 -9999 0 -10000 0 0
Histones 0.031 0.045 -9999 0 -0.25 2 2
ADRBK1 0.033 0.005 -9999 0 -10000 0 0
HDAC4 0.033 0.004 -9999 0 -10000 0 0
XPO1 0.034 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.047 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.046 0.022 -9999 0 -0.22 1 1
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.04 0.02 -9999 0 -10000 0 0
TUBA1B 0.033 0.004 -9999 0 -10000 0 0
HDAC6 0.033 0.004 -9999 0 -10000 0 0
HDAC5/RFXANK 0.048 0.01 -9999 0 -10000 0 0
CAMK4 0.033 0.006 -9999 0 -10000 0 0
Tubulin/HDAC6 0.065 0.014 -9999 0 -10000 0 0
SUMO1 0.034 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.018 0.017 -9999 0 -10000 0 0
GATA1 0.031 0.025 -9999 0 -0.32 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.027 0.014 -9999 0 -10000 0 0
NR3C1 -0.026 0.17 -9999 0 -0.5 24 24
SUMO1/HDAC4 0.045 0.04 -9999 0 -10000 0 0
SRF 0.033 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.027 0.025 -9999 0 -10000 0 0
Tubulin 0.048 0.009 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.039 0.02 -9999 0 -10000 0 0
GNB1 0.032 0.008 -9999 0 -10000 0 0
RANGAP1 0.026 0.043 -9999 0 -0.32 3 3
BCL6/BCoR 0.045 0.034 -9999 0 -0.29 2 2
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.064 0.017 -9999 0 -10000 0 0
HDAC4/ER alpha 0.038 0.063 -9999 0 -0.36 5 5
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.03 0.045 -9999 0 -0.25 2 2
cell motility 0.064 0.014 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.031 0.025 -9999 0 -0.32 1 1
HDAC7/HDAC3 0.025 0.003 -9999 0 -10000 0 0
BCL6 0.029 0.044 -9999 0 -0.41 2 2
HDAC4/CaMK II delta B 0.033 0.004 -9999 0 -10000 0 0
Hsp90/HDAC6 0.043 0.024 -9999 0 -0.22 1 1
ESR1 0.02 0.081 -9999 0 -0.5 5 5
HDAC6/HDAC11 0.048 0.009 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.042 -9999 0 -10000 0 0
NPC 0.019 0.012 -9999 0 -0.15 1 1
MEF2C -0.051 0.2 -9999 0 -0.5 34 34
RAN 0.032 0.025 -9999 0 -0.32 1 1
HDAC4/MEF2C 0.039 0.13 -9999 0 -0.27 31 31
GNG2 0.031 0.01 -9999 0 -10000 0 0
NCOR2 0.033 0.005 -9999 0 -10000 0 0
TUBB2A 0.033 0.005 -9999 0 -10000 0 0
HDAC11 0.033 0.006 -9999 0 -10000 0 0
HSP90AA1 0.029 0.026 -9999 0 -0.32 1 1
RANBP2 0.032 0.024 -9999 0 -0.32 1 1
ANKRA2 0.033 0.004 -9999 0 -10000 0 0
RFXANK 0.033 0.004 -9999 0 -10000 0 0
nuclear import -0.021 0.023 -9999 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.041 0.071 -9999 0 -10000 0 0
CLOCK 0.034 0.01 -9999 0 -10000 0 0
TIMELESS/CRY2 0.048 0.034 -9999 0 -10000 0 0
DEC1/BMAL1 0.049 0.023 -9999 0 -0.27 1 1
ATR 0.031 0.025 -9999 0 -0.32 1 1
NR1D1 0.028 0.028 -9999 0 -10000 0 0
ARNTL 0.035 0.009 -9999 0 -10000 0 0
TIMELESS 0.029 0.031 -9999 0 -10000 0 0
NPAS2 0.035 0.009 -9999 0 -10000 0 0
CRY2 0.033 0.003 -9999 0 -10000 0 0
mol:CO -0.011 0.009 -9999 0 -10000 0 0
CHEK1 -0.011 0.12 -9999 0 -0.32 26 26
mol:HEME 0.011 0.009 -9999 0 -10000 0 0
PER1 0.027 0.013 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.078 0.024 -9999 0 -10000 0 0
BMAL1/CLOCK 0.041 0.047 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.041 0.071 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.042 0.072 -9999 0 -10000 0 0
mol:NADPH 0.011 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.038 0.037 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.031 0.029 -9999 0 -0.39 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.023 0.042 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin 0.003 0.04 -10000 0 -10000 0 0
JUN 0.015 0.049 -10000 0 -10000 0 0
HRAS 0.033 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.052 0.079 -10000 0 -0.29 4 4
RAP1A 0.032 0.007 -10000 0 -10000 0 0
FRS2 0.033 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.024 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.065 0.069 -10000 0 -0.28 5 5
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.025 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.058 0.024 -10000 0 -10000 0 0
RHOA 0.033 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.058 0.067 -10000 0 -0.25 4 4
GRB7 0.03 0.026 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF 0.065 0.068 -10000 0 -0.28 5 5
MAPKKK cascade 0.038 0.057 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.055 0.035 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.045 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC 0.064 0.068 -10000 0 -0.28 5 5
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.059 0.019 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3 0.056 0.022 -10000 0 -10000 0 0
MAPK3 0.01 0.062 -10000 0 -10000 0 0
DOK1 0.032 0.024 -10000 0 -0.32 1 1
DOK6 0.023 0.016 -10000 0 -10000 0 0
PXN 0.033 0.003 -10000 0 -10000 0 0
neurite development 0.001 0.051 -10000 0 -0.32 2 2
DOK5 0.01 0.054 -10000 0 -0.32 5 5
GFRA1 0.032 0.006 -10000 0 -10000 0 0
MAPK8 0.02 0.041 -10000 0 -10000 0 0
HRAS/GTP 0.061 0.066 -10000 0 -10000 0 0
tube development 0.055 0.029 -10000 0 -10000 0 0
MAPK1 0.014 0.064 0.35 2 -10000 0 2
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.032 0.013 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.007 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
PDLIM7 0.031 0.025 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/Dok6 0.035 0.061 -10000 0 -0.27 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.063 0.073 -10000 0 -0.28 6 6
RET51/GFRalpha1/GDNF/Dok5 0.03 0.065 -10000 0 -0.28 2 2
PRKCA 0.029 0.026 -10000 0 -0.32 1 1
HRAS/GDP 0.025 0.003 -10000 0 -10000 0 0
CREB1 0.032 0.031 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.029 0.028 -10000 0 -0.23 2 2
RET51/GFRalpha1/GDNF/Grb7 0.06 0.071 -10000 0 -0.28 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.014 0.093 -10000 0 -0.42 9 9
DOK4 0.026 0.063 -10000 0 -0.5 3 3
JNK cascade 0.015 0.048 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/FRS2 0.06 0.017 -10000 0 -10000 0 0
SHANK3 0.031 0.009 -10000 0 -10000 0 0
RASA1 0.03 0.035 -10000 0 -0.32 2 2
NCK1 0.033 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.031 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.029 0.045 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.031 0.043 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.029 0.045 -10000 0 -10000 0 0
PI3K 0.022 0.061 -10000 0 -10000 0 0
SOS1 0.033 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.067 0.029 -10000 0 -10000 0 0
GRB10 0.016 0.072 -10000 0 -0.32 9 9
activation of MAPKK activity 0.031 0.045 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2 0.066 0.067 -10000 0 -0.28 5 5
GAB1 0.028 0.051 -10000 0 -0.5 2 2
IRS1 0.027 0.048 -10000 0 -0.32 4 4
IRS2 0.025 0.015 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.026 0.051 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/PKC alpha 0.06 0.07 -10000 0 -0.28 5 5
GRB2 0.032 0.006 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
GDNF 0.032 0.007 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.061 0.075 -10000 0 -0.28 5 5
Rac1/GTP 0.023 0.057 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF 0.042 0.012 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.046 0.013 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.031 0.009 -9999 0 -10000 0 0
Rac1/GDP 0.029 0.011 -9999 0 -10000 0 0
DOCK1 0.03 0.037 -9999 0 -0.5 1 1
ITGA4 0.028 0.051 -9999 0 -0.5 2 2
RAC1 0.031 0.01 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.028 0.091 -9999 0 -0.36 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.061 0.042 -9999 0 -0.31 2 2
alpha4/beta7 Integrin/Paxillin 0.04 0.075 -9999 0 -0.28 11 11
lamellipodium assembly 0.021 0.072 -9999 0 -0.42 3 3
PIK3CA 0.033 0.004 -9999 0 -10000 0 0
PI3K 0.048 0.009 -9999 0 -10000 0 0
ARF6 0.031 0.01 -9999 0 -10000 0 0
TLN1 0.033 0.006 -9999 0 -10000 0 0
PXN 0.019 0.003 -9999 0 -10000 0 0
PIK3R1 0.033 0.005 -9999 0 -10000 0 0
ARF6/GTP 0.06 0.042 -9999 0 -10000 0 0
cell adhesion 0.066 0.04 -9999 0 -0.26 2 2
CRKL/CBL 0.046 0.014 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.052 0.038 -9999 0 -0.28 2 2
ITGB1 0.032 0.025 -9999 0 -0.32 1 1
ITGB7 0.011 0.11 -9999 0 -0.5 9 9
ARF6/GDP 0.028 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.063 0.07 -9999 0 -0.51 1 1
p130Cas/Crk/Dock1 0.05 0.04 -9999 0 -0.31 1 1
VCAM1 0.02 0.081 -9999 0 -0.5 5 5
alpha4/beta1 Integrin/Paxillin/Talin 0.07 0.042 -9999 0 -0.27 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.07 0.043 -9999 0 -10000 0 0
BCAR1 0.033 0.006 -9999 0 -10000 0 0
mol:GDP -0.065 0.041 -9999 0 -10000 0 0
CBL 0.033 0.006 -9999 0 -10000 0 0
PRKACA 0.033 0.005 -9999 0 -10000 0 0
GIT1 0.032 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.07 0.042 -9999 0 -0.27 2 2
Rac1/GTP 0.019 0.077 -9999 0 -0.46 3 3
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.046 0.03 0.22 2 -10000 0 2
KIRREL 0.035 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.046 0.03 -10000 0 -0.22 2 2
PLCG1 0.017 0.029 -10000 0 -0.32 1 1
ARRB2 0.027 0.013 -10000 0 -10000 0 0
WASL 0.03 0.037 -10000 0 -0.5 1 1
Nephrin/NEPH1/podocin/CD2AP 0.077 0.035 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.036 0.024 -10000 0 -10000 0 0
FYN 0.029 0.05 0.31 4 -0.21 1 5
mol:Ca2+ 0.043 0.046 -10000 0 -10000 0 0
mol:DAG 0.044 0.047 -10000 0 -10000 0 0
NPHS2 0.035 0.011 -10000 0 -10000 0 0
mol:IP3 0.044 0.047 -10000 0 -10000 0 0
regulation of endocytosis 0.053 0.039 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol 0.058 0.029 -10000 0 -10000 0 0
establishment of cell polarity 0.046 0.03 -10000 0 -0.22 2 2
Nephrin/NEPH1/podocin/NCK1-2 0.093 0.037 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.056 0.041 -10000 0 -10000 0 0
NPHS1 0.031 0.036 -10000 0 -0.32 2 2
Nephrin/NEPH1/podocin 0.059 0.03 -10000 0 -0.21 1 1
TJP1 0.031 0.008 -10000 0 -10000 0 0
NCK1 0.033 0.004 -10000 0 -10000 0 0
NCK2 0.034 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.045 0.048 -10000 0 -10000 0 0
CD2AP 0.033 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.075 0.037 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.029 0.064 0.32 6 -0.28 2 8
cytoskeleton organization 0.027 0.032 0.22 3 -10000 0 3
Nephrin/NEPH1 0.039 0.022 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.058 0.032 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.028 0.042 -9999 0 -0.32 3 3
Aurora C/Aurora B/INCENP 0.047 0.037 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.013 0.023 -9999 0 -0.3 1 1
AURKB 0.027 0.013 -9999 0 -10000 0 0
AURKC 0.033 0.006 -9999 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 0.072 0.048 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.008 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.041 0.06 -10000 0 -0.3 1 1
SUMO1 0.034 0 -10000 0 -10000 0 0
ZFPM1 0.033 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.013 -10000 0 -10000 0 0
FKBP3 0.03 0.01 -10000 0 -10000 0 0
Histones 0.077 0.037 -10000 0 -10000 0 0
YY1/LSF 0.019 0.056 -10000 0 -0.29 1 1
SMG5 0.033 0.006 -10000 0 -10000 0 0
RAN 0.032 0.025 -10000 0 -0.32 1 1
I kappa B alpha/HDAC3 0.033 0.014 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.031 0.057 -10000 0 -10000 0 0
SAP18 0.025 0.015 -10000 0 -10000 0 0
RELA 0.032 0.021 -10000 0 -10000 0 0
HDAC1/Smad7 0.044 0.04 -10000 0 -0.31 1 1
RANGAP1 0.026 0.043 -10000 0 -0.32 3 3
HDAC3/TR2 0.044 0.039 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.027 0.052 -10000 0 -0.33 1 1
NF kappa B1 p50/RelA 0.038 0.069 0.32 1 -0.34 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.033 0.004 -10000 0 -10000 0 0
GATA1 0.031 0.025 -10000 0 -0.32 1 1
Mad/Max 0.023 0.094 -10000 0 -0.36 12 12
NuRD/MBD3 Complex/GATA1/Fog1 0.024 0.075 -10000 0 -0.45 1 1
RBBP7 0.033 0.005 -10000 0 -10000 0 0
NPC 0.019 0.012 -10000 0 -10000 0 0
RBBP4 0.032 0.007 -10000 0 -10000 0 0
MAX 0.031 0.01 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.004 -10000 0 -10000 0 0
NFKBIA 0.028 0.012 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.049 0.045 -10000 0 -0.35 1 1
SIN3 complex 0.059 0.041 -10000 0 -10000 0 0
SMURF1 0.032 0.007 -10000 0 -10000 0 0
CHD3 0.025 0.031 -10000 0 -0.39 1 1
SAP30 0.032 0.007 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.014 -10000 0 -10000 0 0
YY1/HDAC3 0.024 0.042 -10000 0 -10000 0 0
YY1/HDAC2 0.021 0.053 -10000 0 -0.29 1 1
YY1/HDAC1 0.019 0.055 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.017 0.065 -10000 0 -0.45 2 2
PPARG 0.02 0.063 -10000 0 -0.3 6 6
HDAC8/hEST1B 0.065 0.015 -10000 0 -10000 0 0
UBE2I 0.031 0.025 -10000 0 -0.32 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.047 0.03 -10000 0 -10000 0 0
MBD3L2 0.033 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.04 -10000 0 -0.31 1 1
CREBBP 0.032 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.025 0.08 -10000 0 -0.5 1 1
HDAC1 0.032 0.007 -10000 0 -10000 0 0
HDAC3 0.031 0.009 -10000 0 -10000 0 0
HDAC2 0.032 0.007 -10000 0 -10000 0 0
YY1 0.018 0.009 -10000 0 -10000 0 0
HDAC8 0.033 0.002 -10000 0 -10000 0 0
SMAD7 0.021 0.039 -10000 0 -0.5 1 1
NCOR2 0.033 0.005 -10000 0 -10000 0 0
MXD1 0.004 0.12 -10000 0 -0.5 12 12
STAT3 0.026 0.01 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.032 0.024 -10000 0 -0.32 1 1
YY1/LSF/HDAC1 0.035 0.058 -10000 0 -0.25 1 1
YY1/SAP30/HDAC1 0.035 0.057 -10000 0 -0.25 1 1
EP300 0.031 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.026 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.012 -10000 0 -10000 0 0
histone deacetylation 0.012 0.075 -10000 0 -0.45 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.042 0.019 -10000 0 -10000 0 0
nuclear export -0.064 0.015 -10000 0 -10000 0 0
PRKACA 0.033 0.005 -10000 0 -10000 0 0
GATAD2B 0.033 0.005 -10000 0 -10000 0 0
GATAD2A 0.033 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.047 0.03 -10000 0 -10000 0 0
GATA1/HDAC1 0.046 0.022 -10000 0 -0.22 1 1
GATA1/HDAC3 0.046 0.033 -10000 0 -10000 0 0
CHD4 0.032 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.047 0.012 -10000 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.03 0.073 -10000 0 -0.33 2 2
NuRD Complex -0.006 0.11 -10000 0 -0.33 9 9
positive regulation of chromatin silencing 0.074 0.036 -10000 0 -10000 0 0
SIN3B 0.033 0.005 -10000 0 -10000 0 0
MTA2 0.033 0.006 -10000 0 -10000 0 0
SIN3A 0.031 0.008 -10000 0 -10000 0 0
XPO1 0.034 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.044 0.04 -10000 0 -10000 0 0
HDAC complex 0.078 0.026 -10000 0 -10000 0 0
GATA1/Fog1 0.047 0.021 -10000 0 -0.22 1 1
FKBP25/HDAC1/HDAC2 0.057 0.026 -10000 0 -10000 0 0
TNF 0.033 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.028 0.076 -10000 0 -0.33 2 2
NuRD/MBD2/PRMT5 Complex 0.017 0.065 -10000 0 -0.45 2 2
Ran/GTP/Exportin 1 0.045 0.042 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.027 0.047 -10000 0 -0.31 1 1
SIN3/HDAC complex/NCoR1 0.017 0.048 -10000 0 -0.36 1 1
TFCP2 0.033 0.004 -10000 0 -10000 0 0
NR2C1 0.027 0.048 -10000 0 -0.32 4 4
MBD3 0.032 0.006 -10000 0 -10000 0 0
MBD2 0.023 0.016 -10000 0 -10000 0 0
Atypical 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
BCL3/RelA 0.047 0.011 -10000 0 -10000 0 0
FBXW11 0.033 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.034 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.065 0.056 0.26 1 -10000 0 1
NFKBIA 0.053 0.053 -10000 0 -10000 0 0
MAPK14 0.033 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.034 0.018 -10000 0 -10000 0 0
ARRB2 0.016 0.008 -10000 0 -10000 0 0
REL 0.034 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.034 0.018 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.033 0.018 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.024 0.01 -10000 0 -10000 0 0
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
NFKB1 0.017 0.016 0.23 1 -10000 0 1
RELA 0.033 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.045 0.043 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.056 0.058 0.23 1 -10000 0 1
SRC 0.019 0.017 -10000 0 -10000 0 0
PI3K 0.048 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.045 0.043 -10000 0 -10000 0 0
IKBKB 0.029 0.011 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.004 -10000 0 -10000 0 0
SYK 0.031 0.025 -10000 0 -0.32 1 1
I kappa B alpha/PIK3R1 0.068 0.057 0.24 2 -10000 0 2
cell death 0.054 0.056 0.22 1 -10000 0 1
NF kappa B1 p105/c-Rel 0.034 0.018 -10000 0 -10000 0 0
LCK 0.028 0.044 -10000 0 -0.41 2 2
BCL3 0.033 0.005 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.032 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.005 0.019 -9999 0 -10000 0 0
MDM2/SUMO1 0.045 0.04 -9999 0 -10000 0 0
HDAC4 0.033 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.005 0.019 -9999 0 -10000 0 0
SUMO1 0.034 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.015 0.013 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.014 0.012 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.032 0.025 -9999 0 -0.32 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.032 0.024 -9999 0 -0.32 1 1
SUMO1/HDAC4 0.045 0.04 -9999 0 -10000 0 0
SUMO1/HDAC1 0.044 0.04 -9999 0 -10000 0 0
RANGAP1 0.026 0.043 -9999 0 -0.32 3 3
MDM2/SUMO1/SUMO1 0.06 0.04 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.018 0.013 -9999 0 -10000 0 0
Ran/GTP 0.029 0.038 -9999 0 -0.21 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.033 0.004 -9999 0 -10000 0 0
UBE2I 0.031 0.025 -9999 0 -0.32 1 1
Ran/GTP/Exportin 1 0.028 0.037 -9999 0 -10000 0 0
NPC 0.019 0.012 -9999 0 -0.15 1 1
PIAS2 0.023 0.015 -9999 0 -10000 0 0
PIAS1 0.031 0.008 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.044 0.026 -9999 0 -10000 0 0
MAPK9 0.01 0.001 -9999 0 -10000 0 0
adrenocorticotropin secretion 0.008 0.016 -9999 0 -0.22 1 1
GNB1/GNG2 0.039 0.016 -9999 0 -10000 0 0
GNB1 0.032 0.008 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.01 0.001 -9999 0 -10000 0 0
Gs family/GTP 0.017 0.009 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.026 0.014 -9999 0 -10000 0 0
GNG2 0.031 0.01 -9999 0 -10000 0 0
CRH 0.027 0.027 -9999 0 -0.32 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.002 -9999 0 -10000 0 0
MAPK11 0.009 0.009 -9999 0 -0.12 1 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.019 0.041 -9999 0 -10000 0 0
adherens junction organization 0.04 0.063 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.024 0.055 -9999 0 -10000 0 0
FMN1 0.04 0.058 -9999 0 -10000 0 0
mol:IP3 0.012 0.032 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.045 0.061 -9999 0 -10000 0 0
CTNNB1 0.025 0.054 -9999 0 -0.33 5 5
AKT1 0.058 0.062 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.064 0.1 -9999 0 -0.4 6 6
CTNND1 0.036 0.006 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.042 0.06 -9999 0 -10000 0 0
VASP 0.041 0.06 -9999 0 -10000 0 0
ZYX 0.04 0.06 -9999 0 -10000 0 0
JUB 0.04 0.058 -9999 0 -10000 0 0
EGFR(dimer) 0.048 0.075 -9999 0 -0.29 1 1
E-cadherin/beta catenin-gamma catenin 0.044 0.07 -9999 0 -0.29 6 6
mol:PI-3-4-5-P3 0.095 0.076 -9999 0 -10000 0 0
PIK3CA 0.037 0.006 -9999 0 -10000 0 0
PI3K 0.097 0.077 -9999 0 -10000 0 0
FYN 0.017 0.051 -9999 0 -0.3 2 2
mol:Ca2+ 0.012 0.032 -9999 0 -10000 0 0
JUP 0.033 0.007 -9999 0 -10000 0 0
PIK3R1 0.037 0.007 -9999 0 -10000 0 0
mol:DAG 0.012 0.032 -9999 0 -10000 0 0
CDH1 0.019 0.088 -9999 0 -0.5 6 6
RhoA/GDP 0.026 0.057 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.041 0.059 -9999 0 -10000 0 0
SRC 0.019 0.017 -9999 0 -10000 0 0
RAC1 0.031 0.01 -9999 0 -10000 0 0
RHOA 0.033 0.005 -9999 0 -10000 0 0
EGFR 0.021 0.072 -9999 0 -0.5 4 4
CASR 0.014 0.047 -9999 0 -0.36 1 1
RhoA/GTP 0.021 0.038 -9999 0 -10000 0 0
AKT2 0.062 0.062 -9999 0 -10000 0 0
actin cable formation 0.038 0.058 -9999 0 -10000 0 0
apoptosis -0.053 0.06 -9999 0 -0.24 1 1
CTNNA1 0.037 0.006 -9999 0 -10000 0 0
mol:GDP 0.009 0.043 -9999 0 -10000 0 0
PIP5K1A 0.042 0.06 -9999 0 -10000 0 0
PLCG1 0.012 0.033 -9999 0 -10000 0 0
Rac1/GTP 0.055 0.073 -9999 0 -10000 0 0
homophilic cell adhesion 0.003 0.004 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.033 0.003 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.033 0.003 -9999 0 -9999 0 0
PDE3B 0.033 0.003 -9999 0 -9999 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.024 0.02 -10000 0 -0.15 2 2
TRAF2/ASK1 0.04 0.024 -10000 0 -0.18 2 2
ATM 0.032 0.007 -10000 0 -10000 0 0
MAP2K3 0.02 0.078 0.31 2 -0.28 4 6
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.019 0.085 0.27 3 -0.36 3 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.025 0.054 -10000 0 -0.32 5 5
TXN 0.01 0.001 -10000 0 -10000 0 0
CALM1 0.03 0.01 -10000 0 -10000 0 0
GADD45A 0.03 0.035 -10000 0 -0.32 2 2
GADD45B 0.033 0.006 -10000 0 -10000 0 0
MAP3K1 0.033 0.004 -10000 0 -10000 0 0
MAP3K6 0.031 0.009 -10000 0 -10000 0 0
MAP3K7 0.033 0.006 -10000 0 -10000 0 0
MAP3K4 0.032 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.041 0.03 -10000 0 -0.22 2 2
TAK1/TAB family 0 0.017 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.055 0.023 -10000 0 -10000 0 0
TRAF2 0.033 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.032 0.067 -10000 0 -10000 0 0
TRAF6 0.01 0.001 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.029 0.026 -10000 0 -0.32 1 1
CCM2 0.031 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.036 0.023 -10000 0 -0.18 1 1
MAPK11 0.029 0.026 -10000 0 -0.32 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.049 0.036 -10000 0 -10000 0 0
OSM/MEKK3 0.043 0.017 -10000 0 -10000 0 0
TAOK1 0.017 0.024 -10000 0 -0.32 1 1
TAOK2 0.019 0.005 -10000 0 -10000 0 0
TAOK3 0.019 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.033 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.029 0.035 -10000 0 -0.32 2 2
MAP3K10 0.031 0.025 -10000 0 -0.32 1 1
MAP3K3 0.032 0.008 -10000 0 -10000 0 0
TRX/ASK1 0.028 0.024 -10000 0 -0.17 2 2
GADD45/MTK1/MTK1 0.065 0.047 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.065 0.069 0.17 9 -10000 0 9
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.013 0.036 0.14 3 -10000 0 3
AP2 0.048 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.039 0.015 -10000 0 -10000 0 0
CLTB 0.033 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.026 0.008 -10000 0 -10000 0 0
CD4 0.032 0.006 -10000 0 -10000 0 0
CLTA 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.006 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.022 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.016 0.031 0.18 7 -10000 0 7
mol:Choline 0.007 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.033 0.006 -10000 0 -10000 0 0
DDEF1 0.006 0.006 -10000 0 -10000 0 0
ARF1/GDP 0.007 0.029 0.17 6 -10000 0 6
AP2M1 0.033 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.016 0.006 -10000 0 -10000 0 0
Rac/GTP 0.023 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.033 0.037 -10000 0 -10000 0 0
ARFIP2 0.02 0.023 -10000 0 -10000 0 0
COPA 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.01 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0.021 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.022 0.005 -10000 0 -10000 0 0
GGA3 0.032 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.023 0.038 -10000 0 -0.25 4 4
AP2A1 0.033 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.017 0.026 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.023 0.045 -10000 0 -0.3 4 4
Arfaptin 2/Rac/GDP 0.039 0.014 -10000 0 -10000 0 0
CYTH2 -0.001 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.042 0.012 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.023 0.007 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.032 0.02 -10000 0 -10000 0 0
PLD2 0.007 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.005 -10000 0 -10000 0 0
PIP5K1A 0.007 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.029 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.005 -10000 0 -10000 0 0
GOSR2 0.014 0.008 -10000 0 -10000 0 0
USO1 0.012 0.023 -10000 0 -0.31 1 1
GBF1 0.008 0.044 -10000 0 -0.31 4 4
ARF1/GTP/Arfaptin 2 0.042 0.01 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.064 0.017 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.046 0.013 -9999 0 -10000 0 0
FBXW11 0.033 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.004 -9999 0 -10000 0 0
CHUK 0.032 0.007 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.089 0.035 -9999 0 -10000 0 0
NFKB1 0.033 0.006 -9999 0 -10000 0 0
MAP3K14 0.033 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.048 0.01 -9999 0 -10000 0 0
RELB 0.033 0.005 -9999 0 -10000 0 0
NFKB2 0.03 0.025 -9999 0 -0.32 1 1
NF kappa B2 p52/RelB 0.041 0.019 -9999 0 -0.18 1 1
regulation of B cell activation 0.041 0.019 -9999 0 -0.18 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 216 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.AY.4071 TCGA.AY.4070 TCGA.AG.A032 TCGA.AG.A02X
109_MAP3K5 0.16 0.13 0.024 -0.12
47_PPARGC1A 0.034 -0.5 0.034 -0.5
105_BMP4 0.034 0.034 0.034 0.034
105_BMP6 0.034 0.034 -0.5 -0.5
105_BMP7 0 0 0 0.034
105_BMP2 0 0.034 0.034 0.034
131_RELN/VLDLR -0.43 0 -0.17 -0.17
30_TGFB1/TGF beta receptor Type II 0.033 0.036 0.033 0.033
84_STAT5B 0.084 0.021 0.073 0.062
84_STAT5A 0.084 0.021 0.073 0.062
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD-TP/22214508/GDAC_MergeDataFiles_12183681/COADREAD-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/COADREAD-TP/22506542/Gistic2_Analysis_22507117/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
Copyright © 2016 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle