PARADIGM pathway analysis of mRNA expression data
Colon/Rectal Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C16971KQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression data. Broad Institute of MIT and Harvard. doi:10.7908/C16971KQ
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 43 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 132
Syndecan-1-mediated signaling events 73
Signaling events mediated by Stem cell factor receptor (c-Kit) 65
FAS signaling pathway (CD95) 58
BCR signaling pathway 54
FOXM1 transcription factor network 48
Fc-epsilon receptor I signaling in mast cells 47
Glypican 1 network 44
HIF-1-alpha transcription factor network 40
Reelin signaling pathway 35
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 0.5946 132 1057 8 -0.48 0.25 1000 -1000 -0.021 -1000
Syndecan-1-mediated signaling events 0.3288 73 2498 34 -0.7 0.017 1000 -1000 -0.099 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2928 65 5093 78 -0.99 0.28 1000 -1000 -0.093 -1000
FAS signaling pathway (CD95) 0.2613 58 2743 47 -0.41 0.2 1000 -1000 -0.07 -1000
BCR signaling pathway 0.2432 54 5404 99 -0.48 0.017 1000 -1000 -0.11 -1000
FOXM1 transcription factor network 0.2162 48 2495 51 -0.69 0.017 1000 -1000 -0.18 -1000
Fc-epsilon receptor I signaling in mast cells 0.2117 47 4573 97 -0.44 0.064 1000 -1000 -0.12 -1000
Glypican 1 network 0.1982 44 2153 48 -0.48 0.03 1000 -1000 -0.064 -1000
HIF-1-alpha transcription factor network 0.1802 40 3045 76 -0.82 0.028 1000 -1000 -0.11 -1000
Reelin signaling pathway 0.1577 35 1981 56 -0.64 0.017 1000 -1000 -0.11 -1000
IL23-mediated signaling events 0.1441 32 1962 60 -0.64 0.018 1000 -1000 -0.17 -1000
Endothelins 0.1306 29 2842 96 -0.53 0.084 1000 -1000 -0.077 -1000
Osteopontin-mediated events 0.1216 27 1029 38 -0.48 0.018 1000 -1000 -0.13 -1000
Canonical Wnt signaling pathway 0.1171 26 1327 51 -0.54 0.37 1000 -1000 -0.072 -1000
Visual signal transduction: Rods 0.1126 25 1326 52 -0.45 0.017 1000 -1000 -0.1 -1000
Arf6 signaling events 0.1081 24 1547 62 -0.31 0.018 1000 -1000 -0.081 -1000
BMP receptor signaling 0.1081 24 2015 81 -0.45 0.032 1000 -1000 -0.12 -1000
Wnt signaling 0.1081 24 174 7 -0.14 0.014 1000 -1000 -0.03 -1000
IL6-mediated signaling events 0.1081 24 1848 75 -0.49 0.072 1000 -1000 -0.1 -1000
TCGA08_p53 0.1036 23 167 7 -0.16 0.087 1000 -1000 -0.012 -1000
Syndecan-2-mediated signaling events 0.0991 22 1523 69 -0.67 0.053 1000 -1000 -0.084 -1000
IL4-mediated signaling events 0.0991 22 2046 91 -0.56 0.38 1000 -1000 -0.16 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0946 21 1165 54 -0.64 0.036 1000 -1000 -0.12 -1000
HIF-2-alpha transcription factor network 0.0946 21 914 43 -0.67 0.38 1000 -1000 -0.097 -1000
Signaling events mediated by PRL 0.0946 21 743 34 -0.22 0.11 1000 -1000 -0.082 -1000
Syndecan-3-mediated signaling events 0.0901 20 728 35 -0.67 0.017 1000 -1000 -0.088 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0856 19 1619 85 -0.31 0.023 1000 -1000 -0.1 -1000
Glucocorticoid receptor regulatory network 0.0856 19 2171 114 -0.69 0.34 1000 -1000 -0.079 -1000
IL1-mediated signaling events 0.0811 18 1145 62 -0.41 0.082 1000 -1000 -0.12 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0811 18 1228 68 -0.84 0.076 1000 -1000 -0.14 -1000
Presenilin action in Notch and Wnt signaling 0.0766 17 1083 61 -0.54 0.24 1000 -1000 -0.094 -1000
Aurora A signaling 0.0766 17 1065 60 -0.69 0.021 1000 -1000 -0.084 -1000
IGF1 pathway 0.0766 17 1004 57 -0.36 0.077 1000 -1000 -0.13 -1000
TRAIL signaling pathway 0.0721 16 787 48 -0.15 0.017 1000 -1000 -0.081 -1000
Calcium signaling in the CD4+ TCR pathway 0.0676 15 473 31 -0.38 0.028 1000 -1000 -0.09 -1000
Regulation of nuclear SMAD2/3 signaling 0.0631 14 1930 136 -1.1 0.069 1000 -1000 -0.096 -1000
PLK1 signaling events 0.0631 14 1252 85 -0.38 0.02 1000 -1000 -0.071 -1000
IL2 signaling events mediated by PI3K 0.0631 14 863 58 -0.61 0.043 1000 -1000 -0.1 -1000
EGFR-dependent Endothelin signaling events 0.0631 14 313 21 -0.21 0.017 1000 -1000 -0.1 -1000
IL12-mediated signaling events 0.0586 13 1191 87 -0.34 0.031 1000 -1000 -0.14 -1000
FOXA2 and FOXA3 transcription factor networks 0.0586 13 641 46 -0.8 0.034 1000 -1000 -0.047 -1000
Noncanonical Wnt signaling pathway 0.0541 12 317 26 -0.14 0.017 1000 -1000 -0.11 -1000
p75(NTR)-mediated signaling 0.0541 12 1587 125 -0.81 0.066 1000 -1000 -0.12 -1000
Thromboxane A2 receptor signaling 0.0495 11 1186 105 -0.49 0.12 1000 -1000 -0.099 -1000
amb2 Integrin signaling 0.0495 11 973 82 -0.36 0.017 1000 -1000 -0.11 -1000
Ephrin B reverse signaling 0.0495 11 555 48 -0.26 0.15 1000 -1000 -0.098 -1000
S1P1 pathway 0.0495 11 403 36 -0.14 0.017 1000 -1000 -0.099 -1000
Visual signal transduction: Cones 0.0450 10 382 38 -0.2 0.025 1000 -1000 -0.086 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0450 10 847 83 -0.41 0.088 1000 -1000 -0.087 -1000
EPHB forward signaling 0.0450 10 910 85 -0.26 0.17 1000 -1000 -0.13 -1000
Aurora B signaling 0.0450 10 698 67 -0.27 0.03 1000 -1000 -0.097 -1000
Signaling events mediated by the Hedgehog family 0.0405 9 489 52 -0.19 0.16 1000 -1000 -0.1 -1000
PDGFR-alpha signaling pathway 0.0405 9 400 44 -0.18 0.033 1000 -1000 -0.072 -1000
Glypican 2 network 0.0405 9 36 4 -0.03 0 1000 -1000 -0.026 -1000
Regulation of Telomerase 0.0405 9 931 102 -0.42 0.062 1000 -1000 -0.13 -1000
Syndecan-4-mediated signaling events 0.0405 9 625 67 -0.48 0.03 1000 -1000 -0.11 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0360 8 230 28 -0.073 0.017 1000 -1000 -0.062 -1000
PLK2 and PLK4 events 0.0360 8 26 3 -0.006 -0.002 1000 -1000 -0.023 -1000
EPO signaling pathway 0.0360 8 460 55 -0.57 0.024 1000 -1000 -0.12 -1000
Ceramide signaling pathway 0.0360 8 631 76 -0.41 0.09 1000 -1000 -0.077 -1000
Integrins in angiogenesis 0.0360 8 721 84 -0.48 0.064 1000 -1000 -0.13 -1000
TCR signaling in naïve CD8+ T cells 0.0360 8 749 93 -0.096 0.045 1000 -1000 -0.1 -1000
Cellular roles of Anthrax toxin 0.0315 7 290 39 -0.063 0.017 1000 -1000 -0.039 -1000
Signaling events mediated by PTP1B 0.0315 7 557 76 -0.6 0.11 1000 -1000 -0.1 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0315 7 404 52 -0.54 0.1 1000 -1000 -0.082 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0315 7 258 33 -0.23 0.038 1000 -1000 -0.087 -1000
Regulation of Androgen receptor activity 0.0315 7 531 70 -0.59 0.041 1000 -1000 -0.085 -1000
Ras signaling in the CD4+ TCR pathway 0.0315 7 129 17 -0.088 0.017 1000 -1000 -0.058 -1000
Nectin adhesion pathway 0.0270 6 415 63 -0.7 0.057 1000 -1000 -0.094 -1000
Signaling events mediated by HDAC Class III 0.0270 6 246 40 -0.27 0.031 1000 -1000 -0.059 -1000
Signaling mediated by p38-alpha and p38-beta 0.0270 6 288 44 -0.2 0.017 1000 -1000 -0.071 -1000
IL27-mediated signaling events 0.0270 6 326 51 -0.31 0.025 1000 -1000 -0.1 -1000
VEGFR1 specific signals 0.0270 6 344 56 -0.068 0.04 1000 -1000 -0.1 -1000
E-cadherin signaling in keratinocytes 0.0270 6 282 43 -0.35 0.045 1000 -1000 -0.085 -1000
E-cadherin signaling events 0.0270 6 33 5 -0.025 0.017 1000 -1000 -0.058 -1000
Canonical NF-kappaB pathway 0.0225 5 219 39 -0.21 0.064 1000 -1000 -0.11 -1000
ErbB4 signaling events 0.0225 5 386 69 -0.49 0.088 1000 -1000 -0.1 -1000
BARD1 signaling events 0.0225 5 310 57 -0.16 0.052 1000 -1000 -0.091 -1000
a4b1 and a4b7 Integrin signaling 0.0225 5 26 5 -0.023 0.011 1000 -1000 -0.049 -1000
Signaling mediated by p38-gamma and p38-delta 0.0225 5 82 15 -0.031 0.039 1000 -1000 -0.041 -1000
Nongenotropic Androgen signaling 0.0225 5 311 52 -0.068 0.048 1000 -1000 -0.08 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0225 5 672 125 -0.1 0.078 1000 -1000 -0.14 -1000
TCGA08_rtk_signaling 0.0225 5 154 26 -0.31 0.036 1000 -1000 -0.028 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0225 5 415 74 -0.35 0.087 1000 -1000 -0.12 -1000
Class I PI3K signaling events 0.0225 5 384 73 -0.31 0.033 1000 -1000 -0.07 -1000
Plasma membrane estrogen receptor signaling 0.0225 5 474 86 -0.35 0.062 1000 -1000 -0.11 -1000
Coregulation of Androgen receptor activity 0.0180 4 332 76 -0.22 0.063 1000 -1000 -0.058 -1000
IFN-gamma pathway 0.0180 4 326 68 -0.15 0.056 1000 -1000 -0.13 -1000
ceramide signaling pathway 0.0180 4 222 49 -0.41 0.085 1000 -1000 -0.071 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0180 4 218 45 -0.16 0.089 1000 -1000 -0.11 -1000
Effects of Botulinum toxin 0.0180 4 119 26 -0.08 0.017 1000 -1000 -0.089 -1000
PDGFR-beta signaling pathway 0.0180 4 442 97 -0.26 0.066 1000 -1000 -0.12 -1000
Caspase cascade in apoptosis 0.0135 3 280 74 -0.22 0.061 1000 -1000 -0.06 -1000
Circadian rhythm pathway 0.0135 3 71 22 -0.073 0.066 1000 -1000 -0.069 -1000
FoxO family signaling 0.0135 3 239 64 -0.12 0.13 1000 -1000 -0.071 -1000
Regulation of p38-alpha and p38-beta 0.0135 3 195 54 -0.16 0.037 1000 -1000 -0.077 -1000
LPA receptor mediated events 0.0135 3 312 102 -0.32 0.044 1000 -1000 -0.099 -1000
E-cadherin signaling in the nascent adherens junction 0.0135 3 245 76 -0.054 0.062 1000 -1000 -0.1 -1000
IL2 signaling events mediated by STAT5 0.0135 3 76 22 -0.093 0.11 1000 -1000 -0.053 -1000
S1P3 pathway 0.0135 3 161 42 -0.066 0.03 1000 -1000 -0.072 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0135 3 290 88 -0.26 0.099 1000 -1000 -0.15 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0090 2 90 34 -0.033 0.059 1000 -1000 -0.086 -1000
Ephrin A reverse signaling 0.0090 2 14 7 -0.006 0.027 1000 -1000 -0.045 -1000
JNK signaling in the CD4+ TCR pathway 0.0090 2 43 17 -0.086 0.056 1000 -1000 -0.086 -1000
Hedgehog signaling events mediated by Gli proteins 0.0090 2 156 65 -0.15 0.067 1000 -1000 -0.072 -1000
Arf6 downstream pathway 0.0090 2 88 43 -0.036 0.037 1000 -1000 -0.061 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0090 2 110 37 -0.13 0.042 1000 -1000 -0.1 -1000
Retinoic acid receptors-mediated signaling 0.0090 2 141 58 -0.069 0.079 1000 -1000 -0.094 -1000
Arf6 trafficking events 0.0090 2 165 71 -0.17 0.059 1000 -1000 -0.092 -1000
Insulin Pathway 0.0090 2 168 74 -0.082 0.052 1000 -1000 -0.12 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0090 2 334 120 -0.059 0.1 1000 -1000 -0.11 -1000
LPA4-mediated signaling events 0.0045 1 19 12 -0.002 0.045 1000 -1000 -0.02 -1000
ErbB2/ErbB3 signaling events 0.0045 1 104 65 -0.017 0.091 1000 -1000 -0.09 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0045 1 38 23 -0.02 0.045 1000 -1000 -0.092 -1000
Signaling events mediated by HDAC Class II 0.0045 1 124 75 -0.083 0.044 1000 -1000 -0.085 -1000
Insulin-mediated glucose transport 0.0045 1 32 32 -0.054 0.051 1000 -1000 -0.078 -1000
mTOR signaling pathway 0.0045 1 77 53 -0.007 0.068 1000 -1000 -0.08 -1000
Class I PI3K signaling events mediated by Akt 0.0045 1 74 68 -0.094 0.062 1000 -1000 -0.094 -1000
Signaling events regulated by Ret tyrosine kinase 0.0045 1 139 82 -0.041 0.067 1000 -1000 -0.11 -1000
S1P5 pathway 0.0045 1 29 17 -0.068 0.024 1000 -1000 -0.065 -1000
Paxillin-dependent events mediated by a4b1 0.0045 1 39 36 -0.023 0.031 1000 -1000 -0.093 -1000
S1P4 pathway 0.0045 1 45 25 -0.068 0.033 1000 -1000 -0.064 -1000
Arf1 pathway 0.0045 1 56 54 -0.014 0.048 1000 -1000 -0.062 -1000
Aurora C signaling 0.0000 0 6 7 -0.006 0.017 1000 -1000 -0.057 -1000
Signaling events mediated by HDAC Class I 0.0000 0 54 104 -0.025 0.078 1000 -1000 -0.11 -1000
Atypical NF-kappaB pathway 0.0000 0 11 31 -0.003 0.065 1000 -1000 -0.091 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 16 27 -0.005 0.035 1000 -1000 -0.071 -1000
Rapid glucocorticoid signaling 0.0000 0 3 20 0 0.017 1000 -1000 -0.062 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.017 0.017 1000 -1000 -0.021 -1000
p38 MAPK signaling pathway 0.0000 0 32 44 -0.012 0.064 1000 -1000 -0.086 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 -0.002 0.017 1000 -1000 -0.086 -1000
Total NA 1642 95593 7203 -38 8.6 131000 -131000 -12 -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 -0.48 0.25 -10000 0 -0.61 175 175
CDKN2C 0.034 0.048 -10000 0 -10000 0 0
CDKN2A -0.23 0.34 -10000 0 -0.74 70 70
CCND2 0.22 0.12 0.28 160 -10000 0 160
RB1 -0.23 0.12 -10000 0 -0.28 159 159
CDK4 0.23 0.12 0.28 162 -10000 0 162
CDK6 0.25 0.13 0.3 172 -10000 0 172
G1/S progression 0.23 0.12 0.28 159 -10000 0 159
Syndecan-1-mediated signaling events

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
TGFB1 0.017 0 -9999 0 -10000 0 0
CCL5 -0.14 0.28 -9999 0 -0.64 52 52
SDCBP 0.017 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.41 0.14 -9999 0 -0.44 198 198
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.41 0.17 -9999 0 -0.66 51 51
Syndecan-1/Syntenin -0.39 0.13 -9999 0 -0.61 41 41
MAPK3 -0.35 0.13 -9999 0 -0.57 41 41
HGF/MET -0.24 0.27 -9999 0 -0.54 101 101
TGFB1/TGF beta receptor Type II 0.017 0 -9999 0 -10000 0 0
BSG 0.014 0.044 -9999 0 -0.64 1 1
keratinocyte migration -0.4 0.16 -9999 0 -0.65 51 51
Syndecan-1/RANTES -0.46 0.21 -9999 0 -0.71 75 75
Syndecan-1/CD147 -0.37 0.14 -9999 0 -0.6 44 44
Syndecan-1/Syntenin/PIP2 -0.37 0.13 -9999 0 -0.59 41 41
LAMA5 -0.026 0.17 -9999 0 -0.72 13 13
positive regulation of cell-cell adhesion -0.37 0.12 -9999 0 -0.57 41 41
MMP7 -0.7 0.12 -9999 0 -0.72 216 216
HGF 0.01 0.07 -9999 0 -0.72 2 2
Syndecan-1/CASK -0.4 0.13 -9999 0 -0.43 198 198
Syndecan-1/HGF/MET -0.54 0.22 -9999 0 -0.72 121 121
regulation of cell adhesion -0.33 0.13 -9999 0 -0.56 39 39
HPSE -0.083 0.24 -9999 0 -0.64 34 34
positive regulation of cell migration -0.41 0.14 -9999 0 -0.44 198 198
SDC1 -0.42 0.14 -9999 0 -0.45 198 198
Syndecan-1/Collagen -0.41 0.14 -9999 0 -0.44 198 198
PPIB 0.004 0.098 -9999 0 -0.72 4 4
MET -0.31 0.37 -9999 0 -0.72 99 99
PRKACA 0.017 0 -9999 0 -10000 0 0
MMP9 -0.006 0.13 -9999 0 -0.71 7 7
MAPK1 -0.35 0.13 -9999 0 -0.59 39 39
homophilic cell adhesion -0.41 0.13 -9999 0 -0.44 198 198
MMP1 -0.64 0.23 -9999 0 -0.72 197 197
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.24 0.18 -10000 0 -0.41 77 77
CRKL -0.26 0.2 -10000 0 -0.43 112 112
HRAS -0.21 0.18 -10000 0 -0.5 16 16
mol:PIP3 -0.26 0.19 -10000 0 -0.42 109 109
SPRED1 0.017 0 -10000 0 -10000 0 0
SPRED2 0.017 0 -10000 0 -10000 0 0
GAB1 -0.29 0.2 -10000 0 -0.46 113 113
FOXO3 -0.24 0.19 -10000 0 -0.4 106 106
AKT1 -0.27 0.2 -10000 0 -0.44 116 116
BAD -0.24 0.19 -10000 0 -0.4 106 106
megakaryocyte differentiation -0.33 0.24 -10000 0 -0.51 124 124
GSK3B -0.25 0.19 -10000 0 -0.41 106 106
RAF1 -0.16 0.15 -10000 0 -0.4 13 13
SHC1 0.017 0 -10000 0 -10000 0 0
STAT3 -0.29 0.2 -10000 0 -0.46 111 111
STAT1 -0.8 0.56 -10000 0 -1.3 113 113
HRAS/SPRED1 -0.18 0.12 -10000 0 -0.39 16 16
cell proliferation -0.28 0.2 -10000 0 -0.45 111 111
PIK3CA 0.016 0.001 -10000 0 -10000 0 0
TEC 0.017 0 -10000 0 -10000 0 0
RPS6KB1 -0.29 0.2 -10000 0 -0.46 117 117
HRAS/SPRED2 -0.18 0.12 -10000 0 -0.39 16 16
LYN/TEC/p62DOK -0.27 0.17 -10000 0 -0.42 111 111
MAPK3 -0.11 0.11 -10000 0 -10000 0 0
STAP1 -0.48 0.28 -10000 0 -0.65 150 150
GRAP2 0.017 0 -10000 0 -10000 0 0
JAK2 -0.62 0.39 -10000 0 -0.97 112 112
STAT1 (dimer) -0.77 0.54 -10000 0 -1.2 113 113
mol:Gleevec 0.012 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.3 0.2 -10000 0 -0.46 115 115
actin filament polymerization -0.29 0.2 -10000 0 -0.46 111 111
LYN 0.017 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.59 0.34 -10000 0 -0.79 152 152
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.24 0.15 -10000 0 -0.51 4 4
PI3K -0.28 0.17 -10000 0 -0.43 110 110
PTEN 0 0.11 -10000 0 -0.63 6 6
SCF/KIT/EPO/EPOR -0.86 0.67 -10000 0 -1.5 111 111
MAPK8 -0.29 0.2 -10000 0 -0.46 111 111
STAT3 (dimer) -0.28 0.2 -10000 0 -0.45 111 111
positive regulation of transcription -0.086 0.097 -10000 0 -10000 0 0
mol:GDP -0.24 0.16 -10000 0 -0.56 16 16
PIK3C2B -0.29 0.2 -10000 0 -0.46 111 111
CBL/CRKL -0.24 0.18 -10000 0 -0.41 77 77
FER -0.3 0.21 -10000 0 -0.48 115 115
SH2B3 -0.29 0.2 -10000 0 -0.46 111 111
PDPK1 -0.23 0.17 -10000 0 -0.38 109 109
SNAI2 -0.3 0.22 -10000 0 -0.48 113 113
positive regulation of cell proliferation -0.52 0.35 -10000 0 -0.82 115 115
KITLG -0.002 0.069 -10000 0 -0.71 2 2
cell motility -0.52 0.35 -10000 0 -0.82 115 115
PTPN6 0.031 0.015 -10000 0 -10000 0 0
EPOR -0.23 0.17 -10000 0 -10000 0 0
STAT5A (dimer) -0.42 0.29 -10000 0 -0.66 114 114
SOCS1 0.014 0.05 -10000 0 -0.72 1 1
cell migration 0.28 0.2 0.45 111 -10000 0 111
SOS1 0.017 0 -10000 0 -10000 0 0
EPO 0.001 0.051 -10000 0 -0.74 1 1
VAV1 -0.042 0.19 -10000 0 -0.64 20 20
GRB10 -0.31 0.23 -10000 0 -0.49 118 118
PTPN11 0.023 0.052 -10000 0 -0.73 1 1
SCF/KIT -0.32 0.2 0.26 1 -0.5 111 112
GO:0007205 0.016 0.01 -10000 0 -10000 0 0
MAP2K1 -0.12 0.12 -10000 0 -10000 0 0
CBL 0.017 0 -10000 0 -10000 0 0
KIT -0.81 0.72 -10000 0 -1.5 111 111
MAP2K2 -0.12 0.12 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.27 0.17 -10000 0 -0.42 102 102
STAT5A -0.44 0.3 -10000 0 -0.69 114 114
GRB2 0.017 0 -10000 0 -10000 0 0
response to radiation -0.29 0.21 -10000 0 -0.47 113 113
SHC/GRAP2 0 0 -10000 0 -10000 0 0
PTPRO -0.34 0.25 -10000 0 -0.52 124 124
SH2B2 -0.3 0.2 -10000 0 -0.47 111 111
DOK1 0.014 0.05 -10000 0 -0.72 1 1
MATK -0.29 0.2 -10000 0 -0.46 111 111
CREBBP 0.011 0.021 -10000 0 -10000 0 0
BCL2 -0.99 0.69 -10000 0 -1.5 145 145
FAS signaling pathway (CD95)

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
SPTAN1 0.17 0.13 0.26 145 -0.33 1 146
RFC1 0.17 0.13 0.26 145 -0.33 1 146
PRKDC 0.13 0.19 0.26 131 -0.51 5 136
RIPK1 0.019 0.005 -10000 0 -10000 0 0
CASP7 -0.12 0.26 -10000 0 -0.73 31 31
FASLG/FAS/FADD/FAF1 -0.006 0.18 0.43 1 -0.44 14 15
MAP2K4 -0.067 0.17 -10000 0 -0.47 18 18
mol:ceramide -0.063 0.16 -10000 0 -0.51 14 14
GSN 0.099 0.19 0.27 69 -0.38 8 77
FASLG/FAS/FADD/FAF1/Caspase 8 -0.021 0.17 -10000 0 -0.5 12 12
FAS -0.055 0.19 -10000 0 -0.64 22 22
BID -0.013 0.086 -10000 0 -0.48 7 7
MAP3K1 -0.031 0.19 0.28 1 -0.55 19 20
MAP3K7 0.01 0.009 -10000 0 -10000 0 0
RB1 0.17 0.13 0.26 145 -0.33 1 146
CFLAR 0.019 0.005 -10000 0 -10000 0 0
HGF/MET -0.34 0.32 -10000 0 -0.57 132 132
ARHGDIB 0.17 0.13 0.26 144 -0.33 1 145
FADD 0.01 0.009 -10000 0 -10000 0 0
actin filament polymerization -0.099 0.19 0.38 8 -0.27 72 80
NFKB1 -0.076 0.07 -10000 0 -10000 0 0
MAPK8 -0.097 0.2 -10000 0 -0.53 14 14
DFFA 0.17 0.13 0.26 145 -0.33 1 146
DNA fragmentation during apoptosis 0.17 0.14 0.26 144 -0.39 2 146
FAS/FADD/MET -0.24 0.26 -10000 0 -0.49 111 111
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 0.012 0.07 -10000 0 -0.72 2 2
FAF1 0.01 0.009 -10000 0 -10000 0 0
PARP1 0.17 0.13 0.26 145 -0.33 1 146
DFFB 0.17 0.14 0.27 98 -0.39 2 100
CHUK -0.062 0.059 -10000 0 -10000 0 0
FASLG -0.061 0.2 -10000 0 -0.65 24 24
FAS/FADD -0.046 0.14 -10000 0 -0.46 22 22
HGF 0.01 0.07 -10000 0 -0.72 2 2
LMNA 0.16 0.12 0.34 2 -10000 0 2
CASP6 0.17 0.13 0.26 145 -0.33 1 146
CASP10 0.01 0.009 -10000 0 -10000 0 0
CASP3 0.2 0.15 0.31 145 -0.38 1 146
PTPN13 -0.22 0.34 -10000 0 -0.72 70 70
CASP8 0.003 0.032 0.34 2 -10000 0 2
IL6 -0.23 0.29 -10000 0 -0.54 103 103
MET -0.31 0.37 -10000 0 -0.72 99 99
ICAD/CAD 0.16 0.13 0.34 2 -0.42 1 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.064 0.16 -10000 0 -0.52 14 14
activation of caspase activity by cytochrome c -0.013 0.086 -10000 0 -0.48 7 7
PAK2 0.17 0.13 0.26 145 -0.33 1 146
BCL2 -0.41 0.31 -10000 0 -0.63 145 145
BCR signaling pathway

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
JUN -0.19 0.28 -10000 0 -0.52 85 85
IKBKB -0.096 0.14 -10000 0 -0.29 9 9
AKT1 -0.093 0.17 0.24 2 -0.29 65 67
IKBKG -0.1 0.15 -10000 0 -0.29 36 36
CALM1 -0.32 0.34 -10000 0 -0.66 98 98
PIK3CA 0.017 0 -10000 0 -10000 0 0
MAP3K1 -0.28 0.4 -10000 0 -0.74 89 89
MAP3K7 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ -0.35 0.37 -10000 0 -0.7 104 104
DOK1 0.014 0.05 -10000 0 -0.72 1 1
AP-1 -0.12 0.16 -10000 0 -0.3 81 81
LYN 0.017 0 -10000 0 -10000 0 0
BLNK -0.001 0.11 -10000 0 -0.64 6 6
SHC1 0.017 0 -10000 0 -10000 0 0
BCR complex -0.36 0.38 -10000 0 -0.72 113 113
CD22 -0.38 0.48 -10000 0 -0.91 90 90
CAMK2G -0.28 0.31 -10000 0 -0.6 98 98
CSNK2A1 0.017 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.24 0.26 -10000 0 -0.58 76 76
GO:0007205 -0.36 0.38 -10000 0 -0.72 104 104
SYK 0.014 0.049 -10000 0 -0.72 1 1
ELK1 -0.33 0.35 -10000 0 -0.67 102 102
NFATC1 -0.29 0.38 -10000 0 -0.68 100 100
B-cell antigen/BCR complex -0.36 0.38 -10000 0 -0.72 113 113
PAG1/CSK -0.14 0.21 -10000 0 -0.46 65 65
NFKBIB -0.019 0.049 -10000 0 -10000 0 0
HRAS -0.28 0.32 -10000 0 -0.62 98 98
NFKBIA -0.018 0.048 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta -0.005 0.039 -10000 0 -10000 0 0
RasGAP/Csk -0.35 0.37 -10000 0 -0.79 83 83
mol:GDP -0.33 0.35 -10000 0 -0.67 104 104
PTEN -0.001 0.11 -10000 0 -0.64 6 6
CD79B -0.23 0.32 -10000 0 -0.63 84 84
NF-kappa-B/RelA/I kappa B alpha -0.004 0.039 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.31 0.37 -10000 0 -0.68 107 107
PIK3R1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.36 0.39 -10000 0 -0.73 104 104
CSK 0.017 0 -10000 0 -10000 0 0
FOS -0.33 0.35 -10000 0 -0.66 107 107
CHUK -0.1 0.15 -10000 0 -0.3 27 27
IBTK 0.017 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.29 0.28 -10000 0 -0.63 79 79
PTPN6 -0.35 0.44 -10000 0 -0.87 85 85
RELA 0.017 0 -10000 0 -10000 0 0
BCL2A1 -0.004 0.039 -10000 0 -0.12 7 7
VAV2 -0.44 0.52 -10000 0 -0.99 99 99
ubiquitin-dependent protein catabolic process -0.012 0.047 -10000 0 -10000 0 0
BTK -0.18 0.43 -10000 0 -1.2 34 34
CD19 -0.48 0.56 -10000 0 -1 101 101
MAP4K1 0.017 0 -10000 0 -10000 0 0
CD72 0.004 0.093 -10000 0 -0.68 4 4
PAG1 -0.17 0.3 -10000 0 -0.64 65 65
MAPK14 -0.22 0.33 -10000 0 -0.6 85 85
SH3BP5 0.014 0.044 -10000 0 -0.64 1 1
PIK3AP1 -0.36 0.39 -10000 0 -0.74 102 102
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.42 0.45 -10000 0 -0.87 99 99
RAF1 -0.26 0.3 -10000 0 -0.57 97 97
RasGAP/p62DOK/SHIP -0.34 0.36 -10000 0 -0.77 84 84
CD79A -0.28 0.32 -10000 0 -0.64 103 103
re-entry into mitotic cell cycle -0.12 0.16 -10000 0 -0.3 87 87
RASA1 0.01 0.07 -10000 0 -0.72 2 2
MAPK3 -0.19 0.25 -10000 0 -0.51 68 68
MAPK1 -0.19 0.24 -10000 0 -0.51 68 68
CD72/SHP1 -0.3 0.42 -10000 0 -0.8 83 83
NFKB1 0.017 0 -10000 0 -10000 0 0
MAPK8 -0.22 0.33 -10000 0 -0.6 85 85
actin cytoskeleton organization -0.32 0.42 -10000 0 -0.76 99 99
NF-kappa-B/RelA -0.002 0.076 -10000 0 -10000 0 0
Calcineurin -0.26 0.26 -10000 0 -0.6 72 72
PI3K -0.29 0.31 -10000 0 -0.64 93 93
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.4 0.4 -10000 0 -0.8 101 101
SOS1 0.017 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.33 0.44 -10000 0 -0.84 87 87
DAPP1 -0.41 0.5 -10000 0 -0.99 87 87
cytokine secretion -0.26 0.34 -10000 0 -0.62 100 100
mol:DAG -0.36 0.39 -10000 0 -0.73 104 104
PLCG2 -0.31 0.33 -10000 0 -0.64 110 110
MAP2K1 -0.22 0.27 -10000 0 -0.55 80 80
B-cell antigen/BCR complex/FcgammaRIIB -0.4 0.43 -10000 0 -0.75 118 118
mol:PI-3-4-5-P3 -0.19 0.2 0.33 2 -0.42 84 86
ETS1 -0.24 0.28 -10000 0 -0.56 84 84
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.28 0.3 -10000 0 -0.67 76 76
B-cell antigen/BCR complex/LYN -0.41 0.52 -10000 0 -0.98 90 90
MALT1 0.017 0 -10000 0 -10000 0 0
TRAF6 0.017 0 -10000 0 -10000 0 0
RAC1 -0.36 0.47 -10000 0 -0.85 99 99
B-cell antigen/BCR complex/LYN/SYK -0.36 0.41 -10000 0 -0.86 83 83
CARD11 -0.35 0.37 -10000 0 -0.7 106 106
FCGR2B -0.13 0.27 -10000 0 -0.64 50 50
PPP3CA 0.017 0 -10000 0 -10000 0 0
BCL10 0.017 0 -10000 0 -10000 0 0
IKK complex -0.023 0.062 -10000 0 -10000 0 0
PTPRC -0.018 0.15 -10000 0 -0.64 12 12
PDPK1 -0.088 0.17 0.23 2 -0.28 64 66
PPP3CB 0.017 0 -10000 0 -10000 0 0
PPP3CC 0.002 0.097 -10000 0 -0.64 5 5
POU2F2 0.004 0.029 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.46 0.54 -9999 0 -1.2 57 57
PLK1 0.013 0.054 -9999 0 -10000 0 0
BIRC5 -0.048 0.2 -9999 0 -0.61 23 23
HSPA1B -0.47 0.54 -9999 0 -1.1 69 69
MAP2K1 0.007 0.033 -9999 0 -10000 0 0
BRCA2 -0.55 0.58 -9999 0 -1.2 71 71
FOXM1 -0.63 0.76 -9999 0 -1.6 69 69
XRCC1 -0.46 0.54 -9999 0 -1.2 56 56
FOXM1B/p19 -0.69 0.57 -9999 0 -1.3 88 88
Cyclin D1/CDK4 -0.5 0.52 -9999 0 -1.1 71 71
CDC2 -0.51 0.59 -9999 0 -1.3 60 60
TGFA -0.45 0.5 -9999 0 -1.1 60 60
SKP2 -0.48 0.57 -9999 0 -1.2 63 63
CCNE1 -0.041 0.19 -9999 0 -0.74 15 15
CKS1B -0.47 0.55 -9999 0 -1.2 58 58
RB1 -0.25 0.22 -9999 0 -0.65 34 34
FOXM1C/SP1 -0.62 0.67 -9999 0 -1.4 77 77
AURKB 0.013 0.054 -9999 0 -10000 0 0
CENPF -0.47 0.55 -9999 0 -1.2 58 58
CDK4 -0.053 0.2 -9999 0 -0.74 18 18
MYC -0.61 0.5 -9999 0 -1.1 91 91
CHEK2 0.007 0.033 -9999 0 -10000 0 0
ONECUT1 -0.5 0.54 -9999 0 -1.2 66 66
CDKN2A -0.22 0.34 -9999 0 -0.73 70 70
LAMA4 -0.46 0.54 -9999 0 -1.2 57 57
FOXM1B/HNF6 -0.6 0.67 -9999 0 -1.5 67 67
FOS -0.54 0.6 -9999 0 -1.2 73 73
SP1 0.011 0.013 -9999 0 -10000 0 0
CDC25B -0.58 0.59 -9999 0 -1.2 86 86
response to radiation -0.016 0.032 -9999 0 -10000 0 0
CENPB -0.46 0.54 -9999 0 -1.2 57 57
CENPA -0.5 0.59 -9999 0 -1.2 66 66
NEK2 -0.56 0.61 -9999 0 -1.3 73 73
HIST1H2BA -0.46 0.54 -9999 0 -1.2 57 57
CCNA2 -0.1 0.26 -9999 0 -0.74 33 33
EP300 0.017 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.57 0.68 -9999 0 -1.5 61 61
CCNB2 -0.46 0.54 -9999 0 -1.2 58 58
CCNB1 -0.52 0.61 -9999 0 -1.3 63 63
ETV5 -0.49 0.56 -9999 0 -1.2 64 64
ESR1 -0.47 0.56 -9999 0 -1.2 58 58
CCND1 -0.5 0.53 -9999 0 -1.1 68 68
GSK3A 0.011 0.025 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.14 0.3 -9999 0 -0.61 55 55
CDK2 -0.071 0.23 -9999 0 -0.73 24 24
G2/M transition of mitotic cell cycle -0.02 0.039 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.55 0.54 -9999 0 -1.2 76 76
GAS1 -0.64 0.65 -9999 0 -1.3 97 97
MMP2 -0.46 0.54 -9999 0 -1.2 57 57
RB1/FOXM1C -0.51 0.55 -9999 0 -1.2 71 71
CREBBP 0.017 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.042 0.19 -9999 0 -0.64 20 20
LAT2 -0.24 0.23 -9999 0 -0.49 88 88
AP1 -0.31 0.29 -9999 0 -0.7 59 59
mol:PIP3 -0.3 0.3 -9999 0 -0.61 93 93
IKBKB -0.14 0.16 -9999 0 -0.32 49 49
AKT1 -0.22 0.24 -9999 0 -0.61 5 5
IKBKG -0.14 0.16 -9999 0 -0.3 89 89
MS4A2 -0.39 0.32 -9999 0 -0.64 137 137
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.002 -9999 0 -10000 0 0
MAP3K1 -0.21 0.24 -9999 0 -0.59 35 35
mol:Ca2+ -0.21 0.22 -9999 0 -0.43 93 93
LYN 0.007 0.009 -9999 0 -10000 0 0
CBLB -0.24 0.23 -9999 0 -0.48 88 88
SHC1 0.017 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.036 0.12 -9999 0 -0.38 21 21
positive regulation of cell migration -0.013 0.12 -9999 0 -0.47 13 13
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.3 0.28 -9999 0 -0.6 88 88
PTPN13 -0.34 0.29 -9999 0 -0.59 111 111
PTPN11 0.006 0.051 -9999 0 -0.75 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.16 0.2 -9999 0 -0.39 19 19
SYK 0.004 0.05 -9999 0 -0.73 1 1
GRB2 0.016 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.34 0.28 -9999 0 -0.62 99 99
LAT -0.24 0.24 -9999 0 -0.49 88 88
PAK2 -0.24 0.28 -9999 0 -0.52 90 90
NFATC2 -0.1 0.078 -9999 0 -10000 0 0
HRAS -0.28 0.3 -9999 0 -0.57 96 96
GAB2 0.017 0 -9999 0 -10000 0 0
PLA2G1B 0.064 0.028 -9999 0 -10000 0 0
Fc epsilon R1 -0.4 0.31 -9999 0 -0.7 102 102
Antigen/IgE/Fc epsilon R1 -0.37 0.29 -9999 0 -0.69 89 89
mol:GDP -0.3 0.33 -9999 0 -0.62 96 96
JUN 0 0.11 -9999 0 -0.72 5 5
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.015 0.002 -9999 0 -10000 0 0
FOS -0.081 0.23 -9999 0 -0.64 33 33
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.28 0.22 -9999 0 -0.52 88 88
CHUK -0.14 0.16 -9999 0 -0.32 48 48
KLRG1 -0.22 0.22 -9999 0 -0.46 88 88
VAV1 -0.27 0.27 -9999 0 -0.54 90 90
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.24 0.23 -9999 0 -0.48 88 88
negative regulation of mast cell degranulation -0.22 0.18 -9999 0 -0.43 88 88
BTK -0.34 0.34 -9999 0 -0.66 95 95
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.43 0.42 -9999 0 -0.86 98 98
GAB2/PI3K/SHP2 -0.27 0.23 -9999 0 -0.54 88 88
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.28 0.28 -9999 0 -0.6 88 88
RAF1 0.053 0.033 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.41 0.35 -9999 0 -0.78 96 96
FCER1G 0.026 0.011 -9999 0 -10000 0 0
FCER1A -0.29 0.33 -9999 0 -0.65 102 102
Antigen/IgE/Fc epsilon R1/Fyn -0.34 0.28 -9999 0 -0.65 88 88
MAPK3 0.062 0.03 -9999 0 -10000 0 0
MAPK1 0.062 0.029 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 -0.057 0.12 -9999 0 -0.66 4 4
DUSP1 -0.039 0.18 -9999 0 -0.64 19 19
NF-kappa-B/RelA -0.096 0.072 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.25 0.24 -9999 0 -0.49 88 88
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.27 0.24 -9999 0 -0.68 35 35
FER -0.25 0.24 -9999 0 -0.5 93 93
RELA 0.017 0 -9999 0 -10000 0 0
ITK -0.057 0.044 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
PLCG1 -0.32 0.35 -9999 0 -0.65 99 99
cytokine secretion -0.07 0.052 -9999 0 -10000 0 0
SPHK1 -0.29 0.25 -9999 0 -0.5 109 109
PTK2 -0.26 0.24 -9999 0 -0.52 88 88
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.36 0.29 -9999 0 -0.66 93 93
EDG1 -0.013 0.12 -9999 0 -0.48 13 13
mol:DAG -0.3 0.31 -9999 0 -0.61 96 96
MAP2K2 0.058 0.029 -9999 0 -10000 0 0
MAP2K1 0.058 0.029 -9999 0 -10000 0 0
MAP2K7 0.017 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.21 0.18 -9999 0 -0.41 88 88
MAP2K4 -0.006 0.14 -9999 0 -1 4 4
Fc epsilon R1/FcgammaRIIB -0.44 0.37 -9999 0 -0.82 96 96
mol:Choline -0.29 0.28 -9999 0 -0.59 88 88
SHC/Grb2/SOS1 -0.23 0.19 -9999 0 -0.44 88 88
FYN 0.014 0.044 -9999 0 -0.64 1 1
DOK1 0.014 0.05 -9999 0 -0.72 1 1
PXN -0.23 0.23 -9999 0 -0.47 88 88
HCLS1 -0.25 0.26 -9999 0 -0.52 88 88
PRKCB -0.22 0.22 -9999 0 -0.43 93 93
FCGR2B -0.13 0.27 -9999 0 -0.64 50 50
IGHE -0.008 0.008 -9999 0 -10000 0 0
KLRG1/SHIP -0.23 0.19 -9999 0 -0.44 88 88
LCP2 0.003 0.096 -9999 0 -0.7 4 4
PLA2G4A -0.33 0.29 -9999 0 -0.57 114 114
RASA1 0.01 0.07 -9999 0 -0.72 2 2
mol:Phosphatidic acid -0.29 0.28 -9999 0 -0.59 88 88
IKK complex -0.091 0.13 -9999 0 -0.27 1 1
WIPF1 0.014 0.044 -9999 0 -0.64 1 1
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.032 0.11 -10000 0 -0.42 17 17
fibroblast growth factor receptor signaling pathway -0.032 0.11 -10000 0 -0.42 17 17
LAMA1 0.017 0 -10000 0 -10000 0 0
PRNP 0.017 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.28 0.24 -10000 0 -0.47 132 132
SMAD2 0.03 0.084 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.017 0.087 -10000 0 -0.47 8 8
GPC1/Laminin alpha1 -0.019 0.1 -10000 0 -0.54 8 8
TDGF1 -0.48 0.35 -10000 0 -0.72 148 148
CRIPTO/GPC1 -0.38 0.27 -10000 0 -0.55 151 151
APP/GPC1 -0.019 0.1 -10000 0 -0.54 8 8
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.31 0.24 -10000 0 -0.47 151 151
FLT1 -0.02 0.16 -10000 0 -0.72 11 11
GPC1/TGFB/TGFBR1/TGFBR2 -0.016 0.085 -10000 0 -0.46 8 8
SERPINC1 0.014 0.05 -10000 0 -0.72 1 1
FYN -0.31 0.24 -10000 0 -0.47 149 149
FGR -0.31 0.24 -10000 0 -0.47 151 151
positive regulation of MAPKKK cascade -0.26 0.22 -10000 0 -0.54 53 53
SLIT2 -0.35 0.32 -10000 0 -0.64 126 126
GPC1/NRG -0.019 0.1 -10000 0 -0.54 8 8
NRG1 0.017 0 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.081 0.2 -10000 0 -0.53 34 34
LYN -0.31 0.24 -10000 0 -0.47 151 151
mol:Spermine -0.005 0.11 -10000 0 -0.55 8 8
cell growth -0.032 0.11 -10000 0 -0.42 17 17
BMP signaling pathway 0.01 0.14 0.72 8 -10000 0 8
SRC -0.31 0.24 -10000 0 -0.47 151 151
TGFBR1 0.017 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.12 0.27 -10000 0 -0.66 45 45
GPC1 -0.01 0.14 -10000 0 -0.72 8 8
TGFBR1 (dimer) 0.017 0 -10000 0 -10000 0 0
VEGFA -0.053 0.22 -10000 0 -0.72 21 21
BLK -0.41 0.31 -10000 0 -0.56 167 167
HCK -0.34 0.27 -10000 0 -0.51 149 149
FGF2 -0.01 0.13 -10000 0 -0.64 9 9
FGFR1 0.017 0 -10000 0 -10000 0 0
VEGFR1 homodimer -0.02 0.16 -10000 0 -0.72 11 11
TGFBR2 0.017 0 -10000 0 -10000 0 0
cell death -0.019 0.1 -10000 0 -0.54 8 8
ATIII/GPC1 -0.022 0.11 -10000 0 -0.54 9 9
PLA2G2A/GPC1 -0.12 0.22 -10000 0 -0.52 50 50
LCK -0.31 0.25 -10000 0 -0.47 152 152
neuron differentiation -0.019 0.1 -10000 0 -0.54 8 8
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.017 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.017 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.54 0.46 -9999 0 -1.2 57 57
HDAC7 -0.003 0.011 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.38 0.29 -9999 0 -0.83 38 38
SMAD4 0.01 0.075 -9999 0 -0.63 3 3
ID2 -0.53 0.45 -9999 0 -1.1 56 56
AP1 -0.081 0.18 -9999 0 -0.48 37 37
ABCG2 -0.82 0.46 -9999 0 -1.2 100 100
HIF1A -0.075 0.09 -9999 0 -0.87 2 2
TFF3 -0.54 0.45 -9999 0 -1.1 57 57
GATA2 0.018 0.005 -9999 0 -10000 0 0
AKT1 -0.059 0.058 -9999 0 -10000 0 0
response to hypoxia -0.089 0.064 -9999 0 -10000 0 0
MCL1 -0.53 0.45 -9999 0 -1.1 56 56
NDRG1 -0.58 0.48 -9999 0 -1.2 66 66
SERPINE1 -0.59 0.49 -9999 0 -1.2 72 72
FECH -0.54 0.45 -9999 0 -1.1 56 56
FURIN -0.53 0.45 -9999 0 -1.1 56 56
NCOA2 0.019 0.002 -9999 0 -10000 0 0
EP300 -0.053 0.078 -9999 0 -10000 0 0
HMOX1 -0.57 0.48 -9999 0 -1.2 62 62
BHLHE40 -0.54 0.45 -9999 0 -1.1 58 58
BHLHE41 -0.54 0.45 -9999 0 -1.1 58 58
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.072 0.085 -9999 0 -0.48 5 5
ENG -0.04 0.1 -9999 0 -0.51 2 2
JUN 0.001 0.11 -9999 0 -0.72 5 5
RORA -0.54 0.46 -9999 0 -1.2 56 56
ABCB1 -0.6 0.63 -9999 0 -1.3 94 94
TFRC -0.54 0.46 -9999 0 -1.2 57 57
CXCR4 -0.55 0.47 -9999 0 -1.2 57 57
TF -0.53 0.45 -9999 0 -1.1 56 56
CITED2 -0.53 0.45 -9999 0 -1.1 56 56
HIF1A/ARNT -0.63 0.53 -9999 0 -1.3 70 70
LDHA -0.047 0.043 -9999 0 -10000 0 0
ETS1 -0.53 0.45 -9999 0 -1.1 56 56
PGK1 -0.55 0.46 -9999 0 -1.2 59 59
NOS2 -0.54 0.45 -9999 0 -1.1 58 58
ITGB2 -0.54 0.46 -9999 0 -1.2 57 57
ALDOA -0.53 0.45 -9999 0 -1.1 56 56
Cbp/p300/CITED2 -0.52 0.43 -9999 0 -1.1 53 53
FOS -0.08 0.23 -9999 0 -0.64 33 33
HK2 -0.53 0.45 -9999 0 -1.1 56 56
SP1 0.009 0.036 -9999 0 -10000 0 0
GCK -0.072 0.11 -9999 0 -10000 0 0
HK1 -0.53 0.45 -9999 0 -1.1 56 56
NPM1 -0.53 0.45 -9999 0 -1.1 56 56
EGLN1 -0.53 0.45 -9999 0 -1.1 56 56
CREB1 0.028 0 -9999 0 -10000 0 0
PGM1 -0.58 0.47 -9999 0 -1.2 63 63
SMAD3 0.013 0.061 -9999 0 -0.63 2 2
EDN1 -0.099 0.3 -9999 0 -1.3 11 11
IGFBP1 -0.56 0.48 -9999 0 -1.2 65 65
VEGFA -0.37 0.34 -9999 0 -1 26 26
HIF1A/JAB1 -0.034 0.066 -9999 0 -0.67 2 2
CP -0.59 0.5 -9999 0 -1.2 66 66
CXCL12 -0.77 0.48 -9999 0 -1.2 97 97
COPS5 0.019 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.01 0.068 -9999 0 -0.46 5 5
BNIP3 -0.58 0.48 -9999 0 -1.2 69 69
EGLN3 -0.65 0.51 -9999 0 -1.2 77 77
CA9 -0.7 0.48 -9999 0 -1.2 83 83
TERT -0.53 0.45 -9999 0 -1.1 56 56
ENO1 -0.54 0.45 -9999 0 -1.2 56 56
PFKL -0.53 0.45 -9999 0 -1.1 56 56
NCOA1 0.011 0.062 -9999 0 -0.63 2 2
ADM -0.54 0.45 -9999 0 -1.1 56 56
ARNT -0.068 0.049 -9999 0 -10000 0 0
HNF4A 0.023 0 -9999 0 -10000 0 0
ADFP -0.55 0.46 -9999 0 -1.2 61 61
SLC2A1 -0.38 0.34 -9999 0 -0.95 33 33
LEP -0.54 0.45 -9999 0 -1.1 56 56
HIF1A/ARNT/Cbp/p300 -0.4 0.3 -9999 0 -0.86 41 41
EPO -0.24 0.22 -9999 0 -0.82 2 2
CREBBP -0.053 0.078 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.41 0.33 -9999 0 -0.86 55 55
PFKFB3 -0.55 0.47 -9999 0 -1.2 60 60
NT5E -0.55 0.46 -9999 0 -1.2 57 57
Reelin signaling pathway

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
CDK5R1/CDK5 -0.005 0.051 -9999 0 -0.54 2 2
VLDLR -0.12 0.27 -9999 0 -0.64 48 48
CRKL 0.017 0 -9999 0 -10000 0 0
LRPAP1 0.017 0 -9999 0 -10000 0 0
FYN 0.014 0.044 -9999 0 -0.64 1 1
ITGA3 0.014 0.05 -9999 0 -0.72 1 1
RELN/VLDLR/Fyn -0.085 0.16 -9999 0 -0.4 48 48
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.003 0.036 -9999 0 -10000 0 0
AKT1 -0.01 0.12 -9999 0 -10000 0 0
MAP2K7 0.017 0 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
DAB1 0.017 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.37 0.14 -9999 0 -0.42 196 196
LRPAP1/LRP8 -0.48 0.17 -9999 0 -0.54 196 196
RELN/LRP8/DAB1/Fyn -0.34 0.13 -9999 0 -0.39 196 196
DAB1/alpha3/beta1 Integrin -0.36 0.17 -9999 0 -0.66 44 44
long-term memory -0.37 0.18 -9999 0 -0.74 30 30
DAB1/LIS1 -0.38 0.18 -9999 0 -0.68 43 43
DAB1/CRLK/C3G -0.36 0.17 -9999 0 -0.66 43 43
PIK3CA 0.017 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.38 0.18 -9999 0 -0.68 43 43
ARHGEF2 0.014 0.05 -9999 0 -0.72 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.017 0 -9999 0 -10000 0 0
CDK5R1 0.017 0 -9999 0 -10000 0 0
RELN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.4 0.15 -9999 0 -0.46 196 196
GRIN2A/RELN/LRP8/DAB1/Fyn -0.33 0.12 -9999 0 -0.72 1 1
MAPK8 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.076 0.15 -9999 0 -0.35 48 48
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
MAP1B -0.38 0.22 -9999 0 -0.71 53 53
RELN/LRP8 -0.4 0.15 -9999 0 -0.46 196 196
GRIN2B/RELN/LRP8/DAB1/Fyn -0.39 0.19 -9999 0 -0.78 30 30
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.005 0.051 -9999 0 -0.54 2 2
RAP1A -0.33 0.18 -9999 0 -0.6 43 43
PAFAH1B1 0.017 0 -9999 0 -10000 0 0
MAPK8IP1 0.014 0.05 -9999 0 -0.72 1 1
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.086 0.26 -9999 0 -0.72 31 31
NCK2 0.017 0 -9999 0 -10000 0 0
neuron differentiation -0.12 0.069 -9999 0 -0.36 2 2
neuron adhesion -0.3 0.17 -9999 0 -0.56 44 44
LRP8 -0.64 0.24 -9999 0 -0.72 196 196
GSK3B -0.001 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/Fyn -0.071 0.14 -9999 0 -0.52 2 2
MAP3K11 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.023 0.12 -9999 0 -10000 0 0
CDK5 0.01 0.07 -9999 0 -0.72 2 2
MAPT 0.014 0.026 -9999 0 -10000 0 0
neuron migration -0.25 0.16 -9999 0 -0.5 43 43
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.12 0.069 -9999 0 -0.36 2 2
RELN/VLDLR -0.44 0.2 -9999 0 -0.48 196 196
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.47 0.49 -10000 0 -1.1 55 55
IL23A -0.59 0.52 -10000 0 -1.3 59 59
NF kappa B1 p50/RelA/I kappa B alpha -0.48 0.45 -10000 0 -1.1 63 63
positive regulation of T cell mediated cytotoxicity -0.49 0.51 -10000 0 -1.2 63 63
ITGA3 -0.46 0.45 -10000 0 -1.1 45 45
IL17F -0.27 0.31 -10000 0 -0.76 23 23
IL12B 0.004 0.077 -10000 0 -0.77 2 2
STAT1 (dimer) -0.49 0.52 -10000 0 -1.2 61 61
CD4 -0.42 0.44 -10000 0 -1.1 44 44
IL23 -0.57 0.48 -10000 0 -1.2 59 59
IL23R -0.078 0.24 -10000 0 -1.6 5 5
IL1B -0.55 0.52 -10000 0 -1.3 51 51
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.44 0.47 -10000 0 -1.1 49 49
TYK2 0.006 0.014 -10000 0 -10000 0 0
STAT4 0.014 0.044 -10000 0 -0.64 1 1
STAT3 0.017 0.001 -10000 0 -10000 0 0
IL18RAP -0.11 0.26 -10000 0 -0.63 43 43
IL12RB1 0.006 0.014 -10000 0 -10000 0 0
PIK3CA 0.017 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.001 0.017 -10000 0 -10000 0 0
IL23R/JAK2 -0.092 0.25 -10000 0 -1.2 8 8
positive regulation of chronic inflammatory response -0.49 0.51 -10000 0 -1.2 63 63
natural killer cell activation 0.006 0.013 0.078 5 -10000 0 5
JAK2 -0.003 0.11 -10000 0 -0.77 4 4
PIK3R1 0.017 0.001 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.013 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.54 0.45 -10000 0 -1.1 59 59
ALOX12B -0.42 0.44 -10000 0 -1.1 46 46
CXCL1 -0.64 0.48 -10000 0 -1.2 78 78
T cell proliferation -0.49 0.51 -10000 0 -1.2 63 63
NFKBIA 0.013 0.003 -10000 0 -10000 0 0
IL17A -0.21 0.26 -10000 0 -0.61 10 10
PI3K -0.44 0.45 -10000 0 -1 63 63
IFNG -0.038 0.048 0.16 2 -0.12 2 4
STAT3 (dimer) -0.41 0.43 -10000 0 -1 53 53
IL18R1 0.012 0.044 -10000 0 -0.63 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.24 0.26 -10000 0 -0.78 15 15
IL18/IL18R -0.095 0.22 -10000 0 -0.5 30 30
macrophage activation -0.031 0.017 -10000 0 -0.046 17 17
TNF -0.52 0.48 -10000 0 -1.2 51 51
STAT3/STAT4 -0.46 0.44 -10000 0 -1 63 63
STAT4 (dimer) -0.46 0.49 -10000 0 -1.1 60 60
IL18 -0.059 0.21 -10000 0 -0.64 25 25
IL19 -0.43 0.45 -10000 0 -1.1 39 39
STAT5A (dimer) -0.46 0.49 -10000 0 -1.1 63 63
STAT1 -0.05 0.21 -10000 0 -0.72 20 20
SOCS3 -0.013 0.15 -10000 0 -0.72 9 9
CXCL9 -0.52 0.52 -10000 0 -1.2 69 69
MPO -0.44 0.45 -10000 0 -1.1 49 49
positive regulation of humoral immune response -0.49 0.51 -10000 0 -1.2 63 63
IL23/IL23R/JAK2/TYK2 -0.52 0.56 -10000 0 -1.2 63 63
IL6 -0.58 0.52 -10000 0 -1.2 71 71
STAT5A 0.017 0 -10000 0 -10000 0 0
IL2 0.018 0.011 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.013 0.078 5 -10000 0 5
CD3E -0.42 0.44 -10000 0 -1.1 44 44
keratinocyte proliferation -0.49 0.51 -10000 0 -1.2 63 63
NOS2 -0.43 0.44 -10000 0 -1 63 63
Endothelins

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
AKT1 -0.001 0.28 -10000 0 -0.57 23 23
PTK2B 0.017 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.04 0.18 -10000 0 -0.92 3 3
EDN1 0.073 0.19 -10000 0 -0.62 13 13
EDN3 -0.33 0.32 -10000 0 -0.64 117 117
EDN2 -0.49 0.27 -10000 0 -0.64 173 173
HRAS/GDP -0.062 0.19 -10000 0 -0.51 14 14
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.016 0.16 -10000 0 -0.36 16 16
ADCY4 -0.02 0.21 -10000 0 -0.47 23 23
ADCY5 -0.019 0.21 -10000 0 -0.7 4 4
ADCY6 -0.019 0.21 -10000 0 -0.64 5 5
ADCY7 -0.019 0.21 -10000 0 -0.64 5 5
ADCY1 -0.019 0.21 -10000 0 -0.7 4 4
ADCY2 -0.02 0.21 -10000 0 -0.7 4 4
ADCY3 -0.043 0.23 -10000 0 -0.62 13 13
ADCY8 -0.02 0.21 -10000 0 -0.7 4 4
ADCY9 -0.023 0.21 -10000 0 -0.62 7 7
arachidonic acid secretion -0.095 0.25 -10000 0 -0.61 29 29
ETB receptor/Endothelin-1/Gq/GTP -0.006 0.17 -10000 0 -0.5 14 14
GNAO1 0.017 0 -10000 0 -10000 0 0
HRAS 0.015 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.083 0.32 0.33 118 -0.53 23 141
ETA receptor/Endothelin-1/Gs/GTP 0.077 0.3 0.31 116 -0.5 23 139
mol:GTP 0.001 0.005 -10000 0 -10000 0 0
COL3A1 -0.006 0.29 -10000 0 -0.86 7 7
EDNRB -0.047 0.18 -10000 0 -0.64 18 18
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0 0.27 -10000 0 -0.56 23 23
CYSLTR1 -0.004 0.28 -10000 0 -0.77 6 6
SLC9A1 0.03 0.15 -10000 0 -0.35 3 3
mol:GDP -0.076 0.2 -10000 0 -0.49 21 21
SLC9A3 -0.38 0.36 -10000 0 -0.71 88 88
RAF1 -0.075 0.21 -10000 0 -0.5 26 26
JUN 0.043 0.17 -10000 0 -0.58 4 4
JAK2 -0.01 0.28 -10000 0 -0.58 25 25
mol:IP3 -0.04 0.17 -10000 0 -0.44 13 13
ETA receptor/Endothelin-1 0.082 0.39 0.39 118 -0.65 24 142
PLCB1 -0.2 0.34 -10000 0 -0.72 65 65
PLCB2 0.015 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.3 0.35 -10000 0 -0.54 138 138
FOS -0.13 0.37 -10000 0 -0.95 34 34
Gai/GDP -0.002 0.1 -10000 0 -10000 0 0
CRK 0.014 0.044 -10000 0 -0.63 1 1
mol:Ca ++ -0.064 0.27 -10000 0 -0.6 24 24
BCAR1 0.017 0 -10000 0 -10000 0 0
PRKCB1 -0.22 0.24 -10000 0 -0.51 63 63
GNAQ 0.002 0.006 -10000 0 -10000 0 0
GNAZ 0.017 0 -10000 0 -10000 0 0
GNAL 0.017 0 -10000 0 -10000 0 0
Gs family/GDP -0.1 0.14 -10000 0 -0.47 16 16
ETA receptor/Endothelin-1/Gq/GTP 0.024 0.18 -10000 0 -0.47 9 9
MAPK14 -0.029 0.15 -10000 0 -0.43 14 14
TRPC6 0.038 0.18 -10000 0 -1 3 3
GNAI2 0.017 0 -10000 0 -10000 0 0
GNAI3 0.017 0 -10000 0 -10000 0 0
GNAI1 -0.068 0.22 -10000 0 -0.64 29 29
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.043 0.16 -10000 0 -0.45 16 16
ETB receptor/Endothelin-2 -0.4 0.21 -10000 0 -0.49 179 179
ETB receptor/Endothelin-3 -0.28 0.27 -10000 0 -0.51 122 122
ETB receptor/Endothelin-1 0.008 0.22 -10000 0 -0.5 28 28
MAPK3 -0.11 0.32 -10000 0 -0.8 34 34
MAPK1 -0.11 0.32 -10000 0 -0.8 34 34
Rac1/GDP -0.062 0.19 -10000 0 -0.52 13 13
cAMP biosynthetic process 0.017 0.19 -10000 0 -0.57 4 4
MAPK8 0.037 0.17 -10000 0 -0.58 4 4
SRC 0.017 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.003 0.13 -10000 0 -0.44 6 6
p130Cas/CRK/Src/PYK2 -0.069 0.2 -10000 0 -0.58 11 11
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.062 0.19 -10000 0 -0.51 14 14
COL1A2 -0.065 0.38 -10000 0 -0.82 30 30
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.42 0.32 -10000 0 -0.55 178 178
mol:DAG -0.04 0.17 -10000 0 -0.44 13 13
MAP2K2 -0.085 0.25 -10000 0 -0.58 36 36
MAP2K1 -0.085 0.25 -10000 0 -0.59 34 34
EDNRA -0.047 0.35 -10000 0 -0.68 49 49
positive regulation of muscle contraction 0.013 0.24 -10000 0 -0.73 4 4
Gq family/GDP -0.097 0.18 -10000 0 -0.56 17 17
HRAS/GTP -0.072 0.18 -10000 0 -0.46 19 19
PRKCH -0.034 0.17 -10000 0 -0.59 7 7
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.031 0.17 -10000 0 -0.59 6 6
PRKCB -0.039 0.16 -10000 0 -0.42 13 13
PRKCE -0.028 0.16 -10000 0 -0.58 5 5
PRKCD -0.029 0.16 -10000 0 -0.58 5 5
PRKCG -0.036 0.17 -10000 0 -0.55 8 8
regulation of vascular smooth muscle contraction -0.15 0.43 -10000 0 -1.1 34 34
PRKCQ -0.037 0.18 -10000 0 -0.58 9 9
PLA2G4A -0.1 0.27 -10000 0 -0.68 29 29
GNA14 -0.009 0.13 -10000 0 -0.64 9 9
GNA15 -0.006 0.13 -10000 0 -0.72 7 7
GNA12 0.017 0 -10000 0 -10000 0 0
GNA11 -0.001 0.11 -10000 0 -0.63 6 6
Rac1/GTP 0.084 0.32 0.34 116 -0.52 23 139
MMP1 -0.53 0.2 -10000 0 -0.6 197 197
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.24 0.22 -9999 0 -0.46 46 46
NF kappa B1 p50/RelA/I kappa B alpha -0.23 0.17 -9999 0 -0.57 4 4
alphaV/beta3 Integrin/Osteopontin/Src -0.36 0.26 -9999 0 -0.54 150 150
AP1 -0.26 0.19 -9999 0 -0.62 26 26
ILK -0.25 0.22 -9999 0 -0.61 3 3
bone resorption -0.22 0.17 -9999 0 -0.68 8 8
PTK2B 0.017 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.24 0.17 -9999 0 -0.78 1 1
ITGAV 0.015 0.05 -9999 0 -0.73 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.022 0.11 -9999 0 -0.54 9 9
alphaV/beta3 Integrin/Osteopontin -0.31 0.22 -9999 0 -0.46 150 150
MAP3K1 -0.26 0.22 -9999 0 -0.46 50 50
JUN 0 0.11 -9999 0 -0.72 5 5
MAPK3 -0.25 0.23 -9999 0 -0.52 52 52
MAPK1 -0.25 0.23 -9999 0 -0.51 50 50
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 -0.23 0.21 -9999 0 -0.6 3 3
ITGB3 0.018 0.005 -9999 0 -10000 0 0
NFKBIA -0.23 0.23 -9999 0 -0.52 52 52
FOS -0.081 0.23 -9999 0 -0.64 33 33
CD44 -0.013 0.15 -9999 0 -0.72 9 9
CHUK 0.017 0 -9999 0 -10000 0 0
PLAU -0.3 0.32 -9999 0 -0.8 51 51
NF kappa B1 p50/RelA -0.24 0.18 -9999 0 -0.63 5 5
BCAR1 0.017 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.002 0.037 -9999 0 -0.55 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.26 0.22 -9999 0 -0.46 50 50
VAV3 -0.28 0.27 -9999 0 -0.74 31 31
MAP3K14 -0.26 0.23 -9999 0 -0.5 51 51
ROCK2 0.017 0 -9999 0 -10000 0 0
SPP1 -0.48 0.35 -9999 0 -0.72 150 150
RAC1 0.017 0 -9999 0 -10000 0 0
Rac1/GTP -0.27 0.22 -9999 0 -0.68 31 31
MMP2 -0.19 0.2 -9999 0 -0.64 7 7
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.082 0.052 -10000 0 -10000 0 0
AES 0.071 0.044 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
mol:GTP 0.003 0.002 -10000 0 -10000 0 0
LRP6/FZD1 -0.002 0.036 -10000 0 -0.54 1 1
SMAD4 0.008 0.075 -10000 0 -0.64 3 3
DKK2 -0.27 0.36 -10000 0 -0.72 87 87
TLE1 0.069 0.044 -10000 0 -10000 0 0
MACF1 0.018 0.001 -10000 0 -10000 0 0
CTNNB1 0.094 0.11 0.31 9 -10000 0 9
WIF1 -0.092 0.26 -10000 0 -0.72 33 33
beta catenin/RanBP3 0.31 0.2 0.49 104 -10000 0 104
KREMEN2 -0.13 0.29 -10000 0 -0.72 43 43
DKK1 -0.17 0.32 -10000 0 -0.72 56 56
beta catenin/beta TrCP1 0.1 0.099 0.33 2 -10000 0 2
FZD1 0.016 0.003 -10000 0 -10000 0 0
AXIN2 -0.45 0.32 -10000 0 -0.75 85 85
AXIN1 0.019 0.001 -10000 0 -10000 0 0
RAN 0.016 0.05 -10000 0 -0.72 1 1
Axin1/APC/GSK3/beta catenin 0.062 0.058 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.1 0.12 0.32 1 -10000 0 1
Axin1/APC/GSK3 0.14 0.084 0.24 23 -10000 0 23
Axin1/APC/GSK3/beta catenin/Macf1 0.092 0.07 -10000 0 -10000 0 0
HNF1A 0.072 0.046 -10000 0 -10000 0 0
CTBP1 0.073 0.047 -10000 0 -10000 0 0
MYC -0.42 0.33 -10000 0 -0.69 126 126
RANBP3 0.019 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.27 0.28 -10000 0 -0.52 113 113
NKD1 -0.54 0.32 -10000 0 -0.72 167 167
TCF4 0.075 0.047 -10000 0 -10000 0 0
TCF3 0.069 0.065 -10000 0 -0.61 1 1
WNT1/LRP6/FZD1/Axin1 0.001 0.029 -10000 0 -0.41 1 1
Ran/GTP 0.008 0.039 -10000 0 -0.55 1 1
CtBP/CBP/TCF/TLE1/AES 0.37 0.26 0.6 105 -10000 0 105
LEF1 -0.083 0.31 -10000 0 -0.66 48 48
DVL1 0.085 0.049 -10000 0 -10000 0 0
CSNK2A1 0.018 0.001 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.076 0.12 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.2 0.26 -10000 0 -0.51 89 89
LRP6 0.013 0.05 -10000 0 -0.72 1 1
CSNK1A1 0.082 0.051 -10000 0 -10000 0 0
NLK 0.003 0.007 -10000 0 -10000 0 0
CCND1 -0.24 0.25 -10000 0 -0.8 25 25
WNT1 0.016 0.003 -10000 0 -10000 0 0
GSK3A 0.017 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.05 -10000 0 -0.73 1 1
FRAT1 0.012 0.044 -10000 0 -0.63 1 1
PPP2R5D 0.27 0.14 0.35 167 -10000 0 167
APC 0.034 0.078 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.044 0.093 0.26 33 -10000 0 33
CREBBP 0.072 0.046 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.017 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.29 0.18 -9999 0 -0.4 160 160
PDE6G/GNAT1/GTP 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.017 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.25 0.22 -9999 0 -0.61 44 44
mol:Na + -0.14 0.16 -9999 0 -0.62 7 7
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.15 0.2 -9999 0 -0.54 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.14 0.16 -9999 0 -0.64 7 7
CNGB1 0.017 0 -9999 0 -10000 0 0
RDH5 -0.16 0.29 -9999 0 -0.64 59 59
SAG -0.45 0.29 -9999 0 -0.64 160 160
mol:Ca2+ -0.094 0.18 -9999 0 -0.59 7 7
Na + (4 Units) -0.13 0.14 -9999 0 -0.57 7 7
RGS9 -0.2 0.31 -9999 0 -0.64 74 74
GNB1/GNGT1 -0.24 0.27 -9999 0 -0.54 98 98
GNAT1/GDP -0.12 0.17 -9999 0 -0.46 9 9
GUCY2D 0.017 0 -9999 0 -10000 0 0
GNGT1 -0.31 0.37 -9999 0 -0.72 98 98
GUCY2F 0.008 0.079 -9999 0 -0.66 3 3
GNB5 0.007 0.085 -9999 0 -0.72 3 3
mol:GMP (4 units) -0.1 0.18 -9999 0 -10000 0 0
mol:11-cis-retinal -0.16 0.29 -9999 0 -0.63 59 59
mol:cGMP -0.019 0.08 -9999 0 -10000 0 0
GNB1 0.017 0 -9999 0 -10000 0 0
Rhodopsin -0.12 0.2 -9999 0 -0.46 59 59
SLC24A1 0.017 0 -9999 0 -10000 0 0
CNGA1 -0.29 0.33 -9999 0 -0.64 104 104
Metarhodopsin II 0 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.016 0.078 -9999 0 -0.41 7 7
RGS9BP -0.003 0.12 -9999 0 -0.72 6 6
Metarhodopsin II/Transducin -0.08 0.13 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.016 0.08 -9999 0 -0.4 9 9
PDE6A/B -0.18 0.23 -9999 0 -0.46 88 88
mol:Pi -0.15 0.2 -9999 0 -0.53 9 9
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.18 0.21 -9999 0 -0.42 98 98
PDE6B 0.017 0 -9999 0 -10000 0 0
PDE6A -0.24 0.32 -9999 0 -0.64 88 88
PDE6G 0.017 0 -9999 0 -10000 0 0
RHO 0.017 0 -9999 0 -10000 0 0
PDE6 -0.23 0.23 -9999 0 -0.65 37 37
GUCA1A 0.014 0.05 -9999 0 -0.72 1 1
GC2/GCAP Family -0.021 0.088 -9999 0 -0.41 8 8
GUCA1C 0.004 0.093 -9999 0 -0.68 4 4
GUCA1B 0.004 0.098 -9999 0 -0.72 4 4
Arf6 signaling events

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
CENTA1/KIF3B -0.004 0.039 -9999 0 -0.41 2 2
ARNO/beta Arrestin1-2 -0.11 0.14 -9999 0 -0.3 82 82
EGFR 0.002 0.099 -9999 0 -0.65 5 5
EPHA2 -0.016 0.15 -9999 0 -0.72 10 10
USP6 0.017 0 -9999 0 -10000 0 0
IQSEC1 0.017 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.15 0.23 -9999 0 -0.5 68 68
ARRB2 0.018 0.041 -9999 0 -0.33 3 3
mol:GTP 0.009 0.007 -9999 0 -10000 0 0
ARRB1 0.008 0.075 -9999 0 -0.64 3 3
FBXO8 0.017 0 -9999 0 -10000 0 0
TSHR 0.017 0 -9999 0 -10000 0 0
EGF -0.18 0.31 -9999 0 -0.68 64 64
somatostatin receptor activity 0 0 -9999 0 -0.001 50 50
ARAP2 0 0 -9999 0 0 53 53
mol:GDP -0.13 0.14 -9999 0 -0.3 69 69
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 50 50
ITGA2B 0.017 0 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.085 -9999 0 -10000 0 0
ADAP1 0 0 -9999 0 0 23 23
KIF13B 0.011 0.062 -9999 0 -0.64 2 2
HGF/MET -0.24 0.27 -9999 0 -0.54 101 101
PXN 0.017 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.12 -9999 0 -0.28 51 51
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.13 0.2 -9999 0 -0.47 30 30
ADRB2 -0.22 0.31 -9999 0 -0.64 80 80
receptor agonist activity 0 0 -9999 0 0 47 47
actin filament binding 0 0 -9999 0 -0.001 51 51
SRC 0.017 0 -9999 0 -10000 0 0
ITGB3 0.017 0 -9999 0 -10000 0 0
GNAQ 0 0 -9999 0 -0.001 26 26
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 34 34
ARF6/GDP -0.017 0.058 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.14 0.17 -9999 0 -0.49 32 32
alphaIIb/beta3 Integrin/paxillin/GIT1 0 0 -9999 0 -10000 0 0
ACAP1 0 0 -9999 0 -10000 0 0
ACAP2 0 0 -9999 0 0 49 49
LHCGR/beta Arrestin2 -0.007 0.056 -9999 0 -0.48 3 3
EFNA1 0.017 0 -9999 0 -10000 0 0
HGF 0.01 0.07 -9999 0 -0.72 2 2
CYTH3 0 0 -9999 0 -0.001 47 47
CYTH2 -0.002 0.002 -9999 0 -0.004 62 62
NCK1 0.017 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 26 26
endosomal lumen acidification 0 0 -9999 0 0 25 25
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.051 0.2 -9999 0 -0.64 23 23
GNAQ/ARNO -0.003 0.003 -9999 0 -0.007 24 24
mol:Phosphatidic acid 0 0 -9999 0 0 49 49
PIP3-E 0.01 0.066 -9999 0 -0.68 2 2
MET -0.31 0.37 -9999 0 -0.72 99 99
GNA14 -0.01 0.13 -9999 0 -0.64 9 9
GNA15 -0.007 0.13 -9999 0 -0.72 7 7
GIT1 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 45 45
GNA11 -0.001 0.11 -9999 0 -0.64 6 6
LHCGR 0.007 0.082 -9999 0 -0.69 3 3
AGTR1 -0.26 0.32 -9999 0 -0.64 95 95
desensitization of G-protein coupled receptor protein signaling pathway -0.007 0.056 -9999 0 -0.48 3 3
IPCEF1/ARNO -0.093 0.17 -9999 0 -0.38 32 32
alphaIIb/beta3 Integrin 0 0 -9999 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.2 0.19 -9999 0 -0.78 1 1
SMAD6-7/SMURF1 -0.014 0.078 -9999 0 -0.46 6 6
NOG 0.017 0 -9999 0 -10000 0 0
SMAD9 -0.1 0.19 -9999 0 -0.54 31 31
SMAD4 0.008 0.075 -9999 0 -0.64 3 3
SMAD5 -0.15 0.19 -9999 0 -0.5 27 27
BMP7/USAG1 -0.45 0.31 -9999 0 -0.61 164 164
SMAD5/SKI -0.13 0.18 -9999 0 -0.49 22 22
SMAD1 0.023 0.083 -9999 0 -0.55 3 3
BMP2 -0.095 0.24 -9999 0 -0.64 38 38
SMAD1/SMAD1/SMAD4 -0.02 0.076 -9999 0 -0.47 1 1
BMPR1A 0.017 0 -9999 0 -10000 0 0
BMPR1B 0.007 0.085 -9999 0 -0.72 3 3
BMPR1A-1B/BAMBI -0.066 0.16 -9999 0 -0.46 32 32
AHSG 0.017 0 -9999 0 -10000 0 0
CER1 0.014 0.05 -9999 0 -0.72 1 1
BMP2-4/CER1 -0.22 0.28 -9999 0 -0.51 93 93
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.038 0.14 -9999 0 -0.42 2 2
BMP2-4 (homodimer) -0.25 0.31 -9999 0 -0.59 93 93
RGMB 0 0.11 -9999 0 -0.72 5 5
BMP6/BMPR2/BMPR1A-1B -0.14 0.17 -9999 0 -0.52 3 3
RGMA 0.005 0.087 -9999 0 -0.64 4 4
SMURF1 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.062 0.15 -9999 0 -0.37 24 24
BMP2-4/USAG1 -0.36 0.34 -9999 0 -0.59 138 138
SMAD6/SMURF1/SMAD5 -0.13 0.18 -9999 0 -0.49 22 22
SOSTDC1 -0.25 0.32 -9999 0 -0.64 90 90
BMP7/BMPR2/BMPR1A-1B -0.22 0.21 -9999 0 -0.82 1 1
SKI 0.017 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.24 0.32 -9999 0 -0.63 86 86
HFE2 0.017 0 -9999 0 -10000 0 0
ZFYVE16 0.017 0 -9999 0 -10000 0 0
MAP3K7 0.017 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.21 0.27 -9999 0 -0.55 71 71
SMAD5/SMAD5/SMAD4 -0.14 0.18 -9999 0 -0.49 23 23
MAPK1 0.014 0.044 -9999 0 -0.64 1 1
TAK1/TAB family -0.063 0.089 -9999 0 -10000 0 0
BMP7 (homodimer) -0.36 0.37 -9999 0 -0.72 115 115
NUP214 0.017 0 -9999 0 -10000 0 0
BMP6/FETUA -0.18 0.22 -9999 0 -0.46 86 86
SMAD1/SKI 0.032 0.079 -9999 0 -0.51 3 3
SMAD6 -0.003 0.12 -9999 0 -0.72 6 6
CTDSP2 0.008 0.075 -9999 0 -0.64 3 3
BMP2-4/FETUA -0.21 0.27 -9999 0 -0.51 93 93
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
GREM1 -0.033 0.18 -9999 0 -0.72 15 15
BMPR2 (homodimer) 0.017 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.002 0.031 -9999 0 -0.46 1 1
BMPR1A-1B (homodimer) -0.007 0.062 -9999 0 -0.54 3 3
CHRDL1 0.011 0.066 -9999 0 -0.68 2 2
ENDOFIN/SMAD1 0.032 0.079 -9999 0 -0.51 3 3
SMAD6-7/SMURF1/SMAD1 -0.013 0.085 -9999 0 -0.53 1 1
SMAD6/SMURF1 0.017 0 -9999 0 -10000 0 0
BAMBI -0.08 0.25 -9999 0 -0.72 29 29
SMURF2 -0.03 0.18 -9999 0 -0.72 14 14
BMP2-4/CHRDL1 -0.22 0.28 -9999 0 -0.51 94 94
BMP2-4/GREM1 -0.24 0.3 -9999 0 -0.54 99 99
SMAD7 0.014 0.044 -9999 0 -0.64 1 1
SMAD8A/SMAD8A/SMAD4 -0.07 0.19 -9999 0 -0.5 32 32
SMAD1/SMAD6 0.032 0.079 -9999 0 -0.51 3 3
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.37 0.37 -9999 0 -0.72 115 115
BMP6 -0.24 0.32 -9999 0 -0.64 86 86
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.04 0.13 -9999 0 -0.42 2 2
PPM1A 0.017 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.007 0.13 -9999 0 -0.63 3 3
SMAD7/SMURF1 -0.002 0.031 -9999 0 -0.46 1 1
CTDSPL 0.011 0.062 -9999 0 -0.64 2 2
PPP1CA 0.014 0.05 -9999 0 -0.72 1 1
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.017 0 -9999 0 -10000 0 0
PPP1R15A 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.055 0.14 -9999 0 -0.37 23 23
CHRD 0.017 0 -9999 0 -10000 0 0
BMPR2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.065 0.16 -9999 0 -0.4 24 24
BMP4 -0.22 0.35 -9999 0 -0.72 73 73
FST 0.017 0 -9999 0 -10000 0 0
BMP2-4/NOG -0.21 0.27 -9999 0 -0.51 93 93
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.2 0.19 -9999 0 -0.78 1 1
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.12 0.18 -9999 0 -0.47 25 25
FZD6 -0.029 0.18 -9999 0 -0.72 14 14
WNT6 0.014 0.05 -9999 0 -0.72 1 1
WNT4 -0.01 0.13 -9999 0 -0.65 9 9
FZD3 -0.14 0.3 -9999 0 -0.72 47 47
WNT5A -0.093 0.26 -9999 0 -0.72 33 33
WNT11 -0.13 0.3 -9999 0 -0.72 45 45
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.22 -9999 0 -0.68 14 14
CRP -0.24 0.22 -9999 0 -0.74 5 5
cell cycle arrest -0.28 0.24 -9999 0 -0.75 21 21
TIMP1 -0.38 0.27 -9999 0 -0.72 52 52
IL6ST 0.012 0.011 -9999 0 -10000 0 0
Rac1/GDP -0.28 0.21 -9999 0 -0.55 55 55
AP1 -0.058 0.15 -9999 0 -0.65 2 2
GAB2 0.021 0.008 -9999 0 -10000 0 0
TNFSF11 -0.3 0.28 -9999 0 -0.84 27 27
HSP90B1 -0.024 0.093 -9999 0 -0.6 3 3
GAB1 0.013 0.062 -9999 0 -0.63 2 2
MAPK14 -0.23 0.22 -9999 0 -0.56 37 37
AKT1 0.065 0.027 -9999 0 -10000 0 0
FOXO1 0.058 0.075 -9999 0 -0.46 1 1
MAP2K6 -0.26 0.22 -9999 0 -0.54 62 62
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
MAP2K4 -0.28 0.22 -9999 0 -0.6 39 39
MITF -0.26 0.2 -9999 0 -0.53 54 54
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.017 0 -9999 0 -10000 0 0
A2M -0.16 0.51 -9999 0 -1.5 29 29
CEBPB 0.008 0.12 -9999 0 -0.71 6 6
GRB2/SOS1/GAB family/SHP2 -0.064 0.092 -9999 0 -10000 0 0
STAT3 -0.29 0.26 -9999 0 -0.79 21 21
STAT1 -0.047 0.09 -9999 0 -0.34 13 13
CEBPD -0.24 0.22 -9999 0 -0.77 5 5
PIK3CA 0.019 0 -9999 0 -10000 0 0
PI3K 0.008 0.013 -9999 0 -10000 0 0
JUN 0 0.11 -9999 0 -0.72 5 5
PIAS3/MITF -0.24 0.2 -9999 0 -0.52 44 44
MAPK11 -0.23 0.22 -9999 0 -0.55 45 45
STAT3 (dimer)/FOXO1 -0.22 0.22 -9999 0 -0.76 9 9
GRB2/SOS1/GAB family -0.22 0.18 -9999 0 -0.52 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.29 0.22 -9999 0 -0.54 75 75
GRB2 0.019 0.005 -9999 0 -10000 0 0
JAK2 0.004 0.098 -9999 0 -0.72 4 4
LBP -0.18 0.19 -9999 0 -0.72 5 5
PIK3R1 0.018 0 -9999 0 -10000 0 0
JAK1 0.013 0.01 -9999 0 -10000 0 0
MYC -0.4 0.3 -9999 0 -0.78 48 48
FGG -0.24 0.22 -9999 0 -0.77 6 6
macrophage differentiation -0.28 0.24 -9999 0 -0.75 21 21
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.38 0.27 -9999 0 -0.74 62 62
JUNB -0.24 0.21 -9999 0 -0.71 7 7
FOS -0.081 0.23 -9999 0 -0.64 33 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.29 0.21 -9999 0 -0.53 71 71
STAT1/PIAS1 -0.26 0.19 -9999 0 -0.52 48 48
GRB2/SOS1/GAB family/SHP2/PI3K 0.047 0.032 -9999 0 -10000 0 0
STAT3 (dimer) -0.29 0.26 -9999 0 -0.78 21 21
PRKCD -0.27 0.22 -9999 0 -0.66 23 23
IL6R -0.34 0.33 -9999 0 -0.64 122 122
SOCS3 -0.21 0.22 -9999 0 -0.79 13 13
gp130 (dimer)/JAK1/JAK1/LMO4 -0.003 0.095 -9999 0 -0.45 8 8
Rac1/GTP -0.29 0.2 -9999 0 -0.54 61 61
HCK -0.044 0.19 -9999 0 -0.63 21 21
MAPKKK cascade -0.014 0.079 -9999 0 -10000 0 0
bone resorption -0.28 0.27 -9999 0 -0.78 27 27
IRF1 -0.25 0.22 -9999 0 -0.78 8 8
mol:GDP -0.29 0.22 -9999 0 -0.54 70 70
SOS1 0.02 0.008 -9999 0 -10000 0 0
VAV1 -0.3 0.22 -9999 0 -0.55 70 70
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.3 0.26 -9999 0 -0.63 62 62
PTPN11 -0.017 0.026 -9999 0 -10000 0 0
IL6/IL6RA -0.49 0.32 -9999 0 -0.63 173 173
gp130 (dimer)/TYK2/TYK2/LMO4 -0.008 0.092 -9999 0 -0.44 9 9
gp130 (dimer)/JAK2/JAK2/LMO4 -0.016 0.13 -9999 0 -0.57 10 10
IL6 -0.33 0.37 -9999 0 -0.73 103 103
PIAS3 0.014 0.05 -9999 0 -0.72 1 1
PTPRE 0.015 0.05 -9999 0 -0.71 1 1
PIAS1 0.017 0 -9999 0 -10000 0 0
RAC1 0.016 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.27 0.19 -9999 0 -0.52 60 60
LMO4 -0.017 0.14 -9999 0 -0.71 9 9
STAT3 (dimer)/PIAS3 -0.29 0.22 -9999 0 -0.74 21 21
MCL1 0.072 0.026 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.16 0.26 -10000 0 -0.55 70 70
TP53 -0.058 0.082 -10000 0 -0.27 9 9
Senescence -0.058 0.082 -10000 0 -0.27 9 9
Apoptosis -0.058 0.082 -10000 0 -0.27 9 9
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.087 0.13 0.28 70 -10000 0 70
MDM4 0.017 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.027 0.16 -9999 0 -0.46 27 27
EPHB2 -0.003 0.12 -9999 0 -0.71 6 6
Syndecan-2/TACI 0.023 0.065 -9999 0 -0.4 5 5
LAMA1 0.017 0 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.14 0.19 -9999 0 -0.64 2 2
HRAS 0.017 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.003 0.032 -9999 0 -0.46 1 1
ITGA5 0 0.11 -9999 0 -0.72 5 5
BAX 0.051 0.05 -9999 0 -0.55 1 1
EPB41 0.017 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.029 -9999 0 -0.41 1 1
LAMA3 0.001 0.1 -9999 0 -0.67 5 5
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.009 0.14 -9999 0 -0.71 8 8
Syndecan-2/MMP2 0.026 0.057 -9999 0 -0.46 3 3
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.19 0.26 -9999 0 -0.55 77 77
dendrite morphogenesis 0.017 0.084 -9999 0 -0.45 7 7
Syndecan-2/GM-CSF -0.24 0.25 -9999 0 -0.46 120 120
determination of left/right symmetry 0.024 0.04 -9999 0 -0.54 1 1
Syndecan-2/PKC delta 0.03 0.034 -9999 0 -0.45 1 1
GNB2L1 0.017 0 -9999 0 -10000 0 0
MAPK3 -0.21 0.23 -9999 0 -0.42 120 120
MAPK1 -0.2 0.23 -9999 0 -0.41 120 120
Syndecan-2/RACK1 -0.002 0.026 -9999 0 -0.38 1 1
NF1 0.017 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.024 0.04 -9999 0 -0.54 1 1
ITGA2 -0.24 0.35 -9999 0 -0.72 77 77
MAPK8 0.044 0.039 -9999 0 -0.45 1 1
Syndecan-2/alpha2/beta1 Integrin -0.14 0.19 -9999 0 -0.64 2 2
Syndecan-2/Kininogen 0.017 0.082 -9999 0 -0.4 8 8
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
SRC 0.048 0.028 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 -0.002 0.029 -9999 0 -0.42 1 1
extracellular matrix organization 0.03 0.034 -9999 0 -0.45 1 1
actin cytoskeleton reorganization -0.027 0.16 -9999 0 -0.46 27 27
Syndecan-2/Caveolin-2/Ras -0.017 0.08 -9999 0 -0.41 8 8
Syndecan-2/Laminin alpha3 0.02 0.075 -9999 0 -0.42 6 6
Syndecan-2/RasGAP -0.005 0.042 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.015 0.087 -9999 0 -0.54 6 6
PRKCD 0.017 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.017 0.085 -9999 0 -0.45 7 7
GO:0007205 0.004 0.008 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.053 0.047 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
SDCBP 0.017 0 -9999 0 -10000 0 0
TNFRSF13B 0.005 0.087 -9999 0 -0.64 4 4
RASA1 0.01 0.07 -9999 0 -0.72 2 2
alpha2/beta1 Integrin -0.19 0.26 -9999 0 -0.55 77 77
Syndecan-2/Synbindin 0.03 0.034 -9999 0 -0.45 1 1
TGFB1 0.017 0 -9999 0 -10000 0 0
CASP3 0.04 0.041 -9999 0 -0.4 1 1
FN1 -0.07 0.24 -9999 0 -0.72 26 26
Syndecan-2/IL8 -0.42 0.14 -9999 0 -0.46 205 205
SDC2 0.024 0.04 -9999 0 -0.54 1 1
KNG1 -0.004 0.12 -9999 0 -0.65 7 7
Syndecan-2/Neurofibromin 0.03 0.034 -9999 0 -0.45 1 1
TRAPPC4 0.017 0 -9999 0 -10000 0 0
CSF2 -0.38 0.37 -9999 0 -0.72 120 120
Syndecan-2/TGFB1 0.03 0.034 -9999 0 -0.45 1 1
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.029 -9999 0 -0.42 1 1
Syndecan-2/Ezrin -0.002 0.029 -9999 0 -0.42 1 1
PRKACA 0.042 0.031 -9999 0 -0.4 1 1
angiogenesis -0.42 0.13 -9999 0 -0.46 205 205
MMP2 0.01 0.07 -9999 0 -0.72 2 2
IL8 -0.67 0.2 -9999 0 -0.72 205 205
calcineurin-NFAT signaling pathway 0.023 0.065 -9999 0 -0.4 5 5
IL4-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
BCL2L1 -0.34 0.52 -10000 0 -1.1 41 41
STAT6 (cleaved dimer) -0.44 0.47 -10000 0 -1.1 63 63
IGHG1 -0.1 0.2 -10000 0 -0.55 3 3
IGHG3 -0.34 0.49 -10000 0 -1 56 56
AKT1 -0.14 0.3 -10000 0 -0.72 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.25 -10000 0 -0.91 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.28 -10000 0 -0.91 4 4
THY1 -0.37 0.55 -10000 0 -1.2 41 41
MYB 0.011 0.062 -10000 0 -0.64 2 2
HMGA1 0.017 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.37 -10000 0 -0.85 32 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.28 -10000 0 -0.78 7 7
SP1 0.023 0.013 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.03 0.024 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.42 0.46 -10000 0 -1.1 53 53
SOCS1 -0.21 0.36 -10000 0 -0.8 18 18
SOCS3 -0.19 0.33 -10000 0 -0.86 16 16
FCER2 -0.28 0.45 -10000 0 -1.1 29 29
PARP14 0.012 0.07 -10000 0 -0.72 2 2
CCL17 -0.36 0.54 -10000 0 -1.2 41 41
GRB2 0.017 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.1 0.23 -10000 0 -0.76 3 3
T cell proliferation -0.34 0.52 -10000 0 -1.2 41 41
IL4R/JAK1 -0.34 0.51 -10000 0 -1.2 40 40
EGR2 -0.36 0.57 -10000 0 -1.3 41 41
JAK2 -0.001 0.1 -10000 0 -0.74 4 4
JAK3 0.016 0.014 -10000 0 -10000 0 0
PIK3R1 0.017 0 -10000 0 -10000 0 0
JAK1 0.012 0.019 -10000 0 -10000 0 0
COL1A2 -0.17 0.31 -10000 0 -0.77 32 32
CCL26 -0.4 0.55 -10000 0 -1.2 46 46
IL4R -0.36 0.55 -10000 0 -1.2 40 40
PTPN6 0.023 0.015 -10000 0 -10000 0 0
IL13RA2 -0.44 0.56 -10000 0 -1.2 52 52
IL13RA1 0.013 0.03 -10000 0 -10000 0 0
IRF4 -0.34 0.63 -10000 0 -1.5 50 50
ARG1 -0.054 0.18 -10000 0 -0.76 4 4
CBL -0.21 0.35 -10000 0 -0.8 32 32
GTF3A -0.38 0.4 -10000 0 -0.81 101 101
PIK3CA 0.017 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.001 0.093 -10000 0 -0.57 4 4
IRF4/BCL6 -0.35 0.56 -10000 0 -1.4 50 50
CD40LG 0.013 0.067 -10000 0 -0.63 2 2
MAPK14 -0.21 0.35 -10000 0 -0.82 30 30
mitosis -0.13 0.28 -10000 0 -0.67 13 13
STAT6 -0.43 0.55 -10000 0 -1.3 42 42
SPI1 0.024 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.12 0.28 -10000 0 -0.68 8 8
STAT6 (dimer) -0.41 0.57 -10000 0 -1.3 45 45
STAT6 (dimer)/PARP14 -0.36 0.55 -10000 0 -1.2 43 43
mast cell activation 0.007 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.15 0.29 -10000 0 -0.78 10 10
FRAP1 -0.14 0.3 -10000 0 -0.72 13 13
LTA -0.34 0.51 -10000 0 -1.2 36 36
FES 0.011 0.066 -10000 0 -0.68 2 2
T-helper 1 cell differentiation 0.38 0.57 1.3 45 -10000 0 45
CCL11 -0.44 0.64 -10000 0 -1.4 57 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.29 -10000 0 -0.76 10 10
IL2RG 0.007 0.078 -10000 0 -0.64 3 3
IL10 -0.34 0.51 -10000 0 -1.2 36 36
IRS1 0.004 0.098 -10000 0 -0.72 4 4
IRS2 0.014 0.05 -10000 0 -0.72 1 1
IL4 -0.049 0.15 -10000 0 -0.81 1 1
IL5 -0.36 0.54 -10000 0 -1.2 43 43
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.27 0.42 -10000 0 -0.89 36 36
COL1A1 -0.56 0.35 -10000 0 -0.85 106 106
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.34 0.52 -10000 0 -1.2 35 35
IL2R gamma/JAK3 0.017 0.063 -10000 0 -0.48 3 3
TFF3 -0.34 0.53 -10000 0 -1.2 37 37
ALOX15 -0.34 0.52 -10000 0 -1.2 41 41
MYBL1 0.004 0.098 -10000 0 -0.72 4 4
T-helper 2 cell differentiation -0.28 0.42 -10000 0 -0.91 40 40
SHC1 0.017 0 -10000 0 -10000 0 0
CEBPB 0.004 0.12 -10000 0 -0.71 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.27 -10000 0 -0.91 4 4
mol:PI-3-4-5-P3 -0.14 0.3 -10000 0 -0.72 13 13
PI3K -0.15 0.31 -10000 0 -0.77 13 13
DOK2 0.008 0.075 -10000 0 -0.64 3 3
ETS1 0.025 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.091 0.22 -10000 0 -0.71 3 3
ITGB3 -0.34 0.51 -10000 0 -1.2 36 36
PIGR -0.38 0.58 -10000 0 -1.3 41 41
IGHE 0.027 0.069 -10000 0 -0.3 2 2
MAPKKK cascade -0.089 0.21 -10000 0 -0.7 3 3
BCL6 0.009 0.066 -10000 0 -0.68 2 2
OPRM1 -0.34 0.51 -10000 0 -1.2 36 36
RETNLB -0.53 0.72 -10000 0 -1.5 67 67
SELP -0.44 0.65 -10000 0 -1.4 55 55
AICDA -0.38 0.57 -10000 0 -1.2 51 51
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.017 0 -9999 0 -10000 0 0
VLDLR -0.12 0.27 -9999 0 -0.64 48 48
LRPAP1 0.017 0 -9999 0 -10000 0 0
NUDC 0.017 0 -9999 0 -10000 0 0
RELN/LRP8 -0.4 0.15 -9999 0 -0.46 196 196
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.017 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.35 0.15 -9999 0 -0.41 196 196
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.017 0 -9999 0 -10000 0 0
IQGAP1 0.017 0 -9999 0 -10000 0 0
PLA2G7 -0.024 0.16 -9999 0 -0.64 14 14
CALM1 0.017 0 -9999 0 -10000 0 0
DYNLT1 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.48 0.17 -9999 0 -0.54 196 196
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.017 0 -9999 0 -10000 0 0
CDK5R1 0.017 0 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.017 0 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.084 0.16 -9999 0 -0.39 48 48
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
NDEL1/14-3-3 E -0.25 0.12 -9999 0 -0.61 2 2
MAP1B -0.025 0.087 -9999 0 -0.33 17 17
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.3 0.14 -9999 0 -0.73 2 2
RELN 0.017 0 -9999 0 -10000 0 0
PAFAH/LIS1 0.009 0.1 -9999 0 -0.38 14 14
LIS1/CLIP170 0.036 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.19 0.073 -9999 0 -0.46 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.034 0.14 -9999 0 -0.56 3 3
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.27 0.13 -9999 0 -0.66 2 2
LIS1/IQGAP1 0.036 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.031 0 -9999 0 -10000 0 0
PAFAH1B3 -0.063 0.23 -9999 0 -0.72 24 24
PAFAH1B2 0.017 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.016 0.061 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.24 0.093 -9999 0 -0.58 2 2
LRP8 -0.64 0.24 -9999 0 -0.72 196 196
NDEL1/Katanin 60 -0.25 0.12 -9999 0 -0.61 2 2
P39/CDK5 -0.3 0.14 -9999 0 -0.73 2 2
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.036 0 -9999 0 -10000 0 0
CDK5 -0.32 0.14 -9999 0 -0.77 2 2
PPP2R5D 0.017 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.068 0.13 -9999 0 -10000 0 0
RELN/VLDLR -0.44 0.2 -9999 0 -0.48 196 196
CDC42 0 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.041 0.14 -10000 0 -0.62 11 11
oxygen homeostasis -0.014 0.014 -10000 0 -10000 0 0
TCEB2 0.017 0 -10000 0 -10000 0 0
TCEB1 0.01 0.07 -10000 0 -0.72 2 2
VHL/Elongin B/Elongin C/HIF2A -0.14 0.16 -10000 0 -0.48 11 11
EPO -0.27 0.25 -10000 0 -0.72 22 22
FIH (dimer) 0.002 0.009 -10000 0 -10000 0 0
APEX1 0.002 0.013 -10000 0 -10000 0 0
SERPINE1 -0.37 0.37 -10000 0 -0.93 49 49
FLT1 -0.032 0.14 -10000 0 -0.62 10 10
ADORA2A -0.31 0.29 -10000 0 -0.84 27 27
germ cell development -0.31 0.29 -10000 0 -0.82 29 29
SLC11A2 -0.36 0.34 -10000 0 -0.87 47 47
BHLHE40 -0.33 0.3 -10000 0 -0.79 41 41
HIF1AN 0.002 0.008 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.21 0.17 -10000 0 -0.48 41 41
ETS1 0.037 0.008 -10000 0 -10000 0 0
CITED2 -0.015 0.045 -10000 0 -10000 0 0
KDR -0.008 0.043 -10000 0 -10000 0 0
PGK1 -0.33 0.32 -10000 0 -0.9 31 31
SIRT1 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.39 0.38 -10000 0 -0.98 42 42
EPAS1 -0.18 0.18 -10000 0 -0.44 42 42
SP1 0.026 0.006 -10000 0 -10000 0 0
ABCG2 -0.67 0.31 -10000 0 -0.83 151 151
EFNA1 -0.32 0.3 -10000 0 -0.87 27 27
FXN -0.31 0.3 -10000 0 -0.85 28 28
POU5F1 -0.32 0.31 -10000 0 -0.87 29 29
neuron apoptosis 0.38 0.36 0.92 42 -10000 0 42
EP300 0.017 0 -10000 0 -10000 0 0
EGLN3 -0.25 0.32 -10000 0 -0.65 85 85
EGLN2 0.004 0.01 -10000 0 -10000 0 0
EGLN1 0.002 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.006 0.053 -10000 0 -0.46 3 3
VHL 0.014 0.05 -10000 0 -0.72 1 1
ARNT 0.002 0.013 -10000 0 -10000 0 0
SLC2A1 -0.35 0.34 -10000 0 -0.88 43 43
TWIST1 -0.36 0.35 -10000 0 -0.95 41 41
ELK1 0.018 0.086 -10000 0 -0.72 3 3
HIF2A/ARNT/Cbp/p300 -0.21 0.17 -10000 0 -0.54 16 16
VEGFA -0.35 0.34 -10000 0 -0.89 40 40
CREBBP 0.017 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.033 0.19 -10000 0 -0.72 15 15
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.01 0.07 -10000 0 -0.72 2 2
CDKN1A 0.031 0.063 -10000 0 -0.39 3 3
PRL-3/alpha Tubulin -0.17 0.25 -10000 0 -0.54 70 70
mol:Ca2+ -0.1 0.29 0.34 35 -0.5 68 103
AGT -0.21 0.34 -10000 0 -0.72 68 68
CCNA2 -0.025 0.17 -10000 0 -0.7 1 1
TUBA1B 0.017 0 -10000 0 -10000 0 0
EGR1 0.008 0.11 -10000 0 -0.48 11 11
CDK2/Cyclin E1 -0.073 0.16 -10000 0 -0.69 6 6
MAPK3 -0.15 0.27 -10000 0 -0.54 72 72
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 -0.15 0.27 -10000 0 -0.54 70 70
PTP4A1 0.031 0.088 -10000 0 -10000 0 0
PTP4A3 -0.22 0.34 -10000 0 -0.72 70 70
PTP4A2 0.017 0 -10000 0 -10000 0 0
ITGB1 -0.15 0.27 -10000 0 -0.54 71 71
SRC 0.017 0 -10000 0 -10000 0 0
RAC1 -0.033 0.11 -10000 0 -0.36 4 4
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.037 0.082 -10000 0 -10000 0 0
RABGGTA 0.017 0 -10000 0 -10000 0 0
BCAR1 0.11 0.16 0.34 70 -10000 0 70
RHOC -0.033 0.11 -10000 0 -0.36 4 4
RHOA -0.033 0.11 -10000 0 -10000 0 0
cell motility -0.028 0.11 -10000 0 -0.37 4 4
PRL-1/alpha Tubulin 0.037 0.082 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.17 0.26 -10000 0 -0.55 71 71
ROCK1 -0.029 0.12 -10000 0 -0.37 4 4
RABGGTB 0.017 0 -10000 0 -10000 0 0
CDK2 -0.063 0.23 -10000 0 -0.72 24 24
mitosis 0.031 0.088 -10000 0 -10000 0 0
ATF5 0.017 0 -10000 0 -10000 0 0
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 0.017 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.12 0.14 -9999 0 -0.56 1 1
Syndecan-3/Neurocan -0.003 0.021 -9999 0 -10000 0 0
POMC 0.014 0.044 -9999 0 -0.64 1 1
EGFR 0.002 0.099 -9999 0 -0.65 5 5
Syndecan-3/EGFR -0.011 0.058 -9999 0 -0.4 3 3
AGRP 0.014 0.05 -9999 0 -0.72 1 1
NCSTN 0.017 0 -9999 0 -10000 0 0
PSENEN 0.017 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0.05 -9999 0 -0.72 1 1
APH1A -0.004 0.12 -9999 0 -0.65 7 7
NCAN 0.017 0 -9999 0 -10000 0 0
long-term memory -0.004 0.027 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.36 0.11 -9999 0 -0.39 205 205
PSEN1 0.017 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.014 0.044 -9999 0 -0.64 1 1
limb bud formation -0.004 0.023 -9999 0 -10000 0 0
MC4R 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
PTN -0.24 0.32 -9999 0 -0.64 89 89
FGFR/FGF/Syndecan-3 -0.004 0.023 -9999 0 -10000 0 0
neuron projection morphogenesis -0.11 0.13 -9999 0 -0.53 1 1
Syndecan-3/AgRP -0.005 0.033 -9999 0 -0.38 1 1
Syndecan-3/AgRP/MC4R -0.004 0.03 -9999 0 -10000 0 0
Fyn/Cortactin -0.002 0.031 -9999 0 -0.46 1 1
SDC3 -0.004 0.023 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.35 0.1 -9999 0 -0.38 205 205
IL8 -0.67 0.2 -9999 0 -0.72 205 205
Syndecan-3/Fyn/Cortactin -0.004 0.027 -9999 0 -10000 0 0
Syndecan-3/CASK -0.004 0.022 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.002 0.031 -9999 0 -0.46 1 1
Gamma Secretase -0.012 0.061 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.24 0.27 -10000 0 -0.54 99 99
CRKL -0.048 0.12 -10000 0 -0.52 2 2
mol:PIP3 -0.01 0.095 0.56 6 -10000 0 6
AKT1 0.014 0.064 0.4 6 -10000 0 6
PTK2B 0.017 0 -10000 0 -10000 0 0
RAPGEF1 -0.036 0.11 -10000 0 -0.6 1 1
RANBP10 0.017 0 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.21 0.23 -10000 0 -0.46 101 101
MAP3K5 -0.024 0.11 -10000 0 -0.54 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS -0.19 0.21 -10000 0 -0.76 3 3
AP1 -0.13 0.18 -10000 0 -0.5 37 37
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.017 0 -10000 0 -10000 0 0
apoptosis -0.14 0.27 -10000 0 -0.76 32 32
STAT3 (dimer) -0.051 0.12 -10000 0 -0.38 1 1
GAB1/CRKL/SHP2/PI3K -0.061 0.078 -10000 0 -0.52 2 2
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.038 0.11 -10000 0 -0.6 1 1
PTPN11 0.014 0.05 -10000 0 -0.72 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 -0.033 0.19 -10000 0 -0.72 15 15
PTEN -0.001 0.11 -10000 0 -0.64 6 6
ELK1 -0.11 0.13 0.24 1 -0.26 97 98
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.049 0.064 -10000 0 -0.29 1 1
PAK1 0.023 0.059 0.37 6 -10000 0 6
HGF/MET/RANBP10 -0.21 0.23 -10000 0 -0.46 101 101
HRAS -0.083 0.15 -10000 0 -10000 0 0
DOCK1 -0.039 0.12 -10000 0 -0.54 2 2
GAB1 -0.061 0.12 -10000 0 -0.56 2 2
CRK -0.05 0.12 -10000 0 -0.52 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.12 0.13 -10000 0 -10000 0 0
JUN 0 0.11 -10000 0 -0.72 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.11 0.12 -10000 0 -0.25 90 90
PIK3R1 0.017 0 -10000 0 -10000 0 0
cell morphogenesis -0.009 0.12 -10000 0 -10000 0 0
GRB2/SHC -0.084 0.1 -10000 0 -10000 0 0
FOS -0.081 0.23 -10000 0 -0.64 33 33
GLMN 0.006 0.043 -10000 0 -0.23 3 3
cell motility -0.11 0.13 0.23 1 -0.26 97 98
HGF/MET/MUC20 -0.21 0.23 -10000 0 -0.47 101 101
cell migration -0.083 0.099 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
CBL 0.017 0 -10000 0 -10000 0 0
MET/RANBP10 -0.24 0.27 -10000 0 -0.54 99 99
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.07 0.13 -10000 0 -0.42 1 1
MET/MUC20 -0.25 0.27 -10000 0 -0.55 99 99
RAP1B -0.024 0.11 -10000 0 -0.55 1 1
RAP1A -0.024 0.11 -10000 0 -0.55 1 1
HGF/MET/RANBP9 -0.21 0.23 -10000 0 -0.46 101 101
RAF1 -0.067 0.14 -10000 0 -10000 0 0
STAT3 -0.051 0.12 -10000 0 -0.38 1 1
cell proliferation -0.049 0.14 -10000 0 -10000 0 0
RPS6KB1 -0.023 0.057 -10000 0 -0.22 2 2
MAPK3 -0.1 0.14 0.7 2 -10000 0 2
MAPK1 -0.11 0.13 0.68 1 -0.24 97 98
RANBP9 0.017 0 -10000 0 -10000 0 0
MAPK8 0 0.1 -10000 0 -0.42 1 1
SRC -0.054 0.12 -10000 0 -10000 0 0
PI3K -0.084 0.1 -10000 0 -10000 0 0
MET/Glomulin -0.21 0.25 -10000 0 -0.49 99 99
SOS1 0.017 0 -10000 0 -10000 0 0
MAP2K1 -0.053 0.14 -10000 0 -10000 0 0
MET -0.31 0.37 -10000 0 -0.72 99 99
MAP4K1 -0.032 0.11 -10000 0 -0.48 2 2
PTK2 0.014 0.05 -10000 0 -0.72 1 1
MAP2K2 -0.053 0.14 -10000 0 -10000 0 0
BAD 0.023 0.059 0.37 6 -10000 0 6
MAP2K4 -0.018 0.11 -10000 0 -0.44 3 3
SHP2/GRB2/SOS1/GAB1 -0.12 0.13 -10000 0 -0.57 2 2
INPPL1 0.017 0 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
SH3KBP1 0.005 0.087 -10000 0 -0.64 4 4
HGS -0.077 0.12 -10000 0 -10000 0 0
PLCgamma1/PKC -0.037 0.14 -10000 0 -0.55 15 15
HGF 0.01 0.07 -10000 0 -0.72 2 2
RASA1 0.01 0.07 -10000 0 -0.72 2 2
NCK1 0.017 0 -10000 0 -10000 0 0
PTPRJ 0.017 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.092 0.16 -10000 0 -0.52 15 15
PDPK1 0.002 0.074 0.44 6 -10000 0 6
HGF/MET/SHIP -0.21 0.23 -10000 0 -0.47 101 101
Glucocorticoid receptor regulatory network

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
PCK2 0.038 0.12 0.35 1 -0.76 1 2
SMARCC2 0.017 0 -10000 0 -10000 0 0
SMARCC1 0.004 0.098 -10000 0 -0.72 4 4
TBX21 -0.35 0.45 -10000 0 -0.92 80 80
SUMO2 0.017 0.007 -10000 0 -10000 0 0
STAT1 (dimer) -0.039 0.21 -10000 0 -0.72 20 20
FKBP4 0.01 0.07 -10000 0 -0.72 2 2
FKBP5 0.017 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.1 0.18 0.35 22 -0.39 4 26
PRL -0.046 0.14 -10000 0 -0.77 1 1
cortisol/GR alpha (dimer)/TIF2 0.29 0.29 0.6 72 -10000 0 72
RELA -0.11 0.073 -10000 0 -10000 0 0
FGG 0.22 0.24 0.59 27 -10000 0 27
GR beta/TIF2 0.11 0.2 0.38 23 -0.44 12 35
IFNG -0.35 0.36 -10000 0 -0.87 56 56
apoptosis 0.068 0.14 0.58 4 -10000 0 4
CREB1 0.029 0.001 -10000 0 -10000 0 0
histone acetylation -0.072 0.14 -10000 0 -0.39 13 13
BGLAP -0.081 0.16 -10000 0 -0.59 1 1
GR/PKAc -0.002 0.24 0.36 9 -0.61 9 18
NF kappa B1 p50/RelA -0.21 0.14 -10000 0 -0.48 15 15
SMARCD1 0.017 0 -10000 0 -10000 0 0
MDM2 0.12 0.093 0.32 24 -10000 0 24
GATA3 0.029 0.027 -10000 0 -10000 0 0
AKT1 0.001 0.018 -10000 0 -10000 0 0
CSF2 -0.29 0.28 -10000 0 -0.62 61 61
GSK3B 0.014 0.05 -10000 0 -0.72 1 1
NR1I3 0.095 0.12 0.55 4 -10000 0 4
CSN2 0.18 0.19 0.47 21 -10000 0 21
BRG1/BAF155/BAF170/BAF60A -0.007 0.054 -10000 0 -0.41 4 4
NFATC1 0.025 0.05 -10000 0 -0.7 1 1
POU2F1 0.027 0.009 -10000 0 -10000 0 0
CDKN1A 0.005 0.19 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.011 0.062 -10000 0 -0.64 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.17 0.35 19 -0.67 1 20
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.068 0.21 0.54 3 -0.83 8 11
JUN -0.18 0.21 -10000 0 -0.59 24 24
IL4 -0.085 0.17 -10000 0 -0.72 3 3
CDK5R1 0.017 0.005 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.074 0.27 0.26 1 -0.57 20 21
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.17 0.34 20 -10000 0 20
cortisol/GR alpha (monomer) 0.34 0.36 0.73 72 -0.53 1 73
NCOA2 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.13 0.24 -10000 0 -0.68 33 33
AP-1/NFAT1-c-4 -0.32 0.28 -10000 0 -0.77 36 36
AFP -0.11 0.16 -10000 0 -0.88 1 1
SUV420H1 0.017 0 -10000 0 -10000 0 0
IRF1 0.15 0.21 0.5 15 -1 2 17
TP53 0.009 0.16 -10000 0 -0.63 12 12
PPP5C 0.014 0.05 -10000 0 -0.72 1 1
KRT17 -0.28 0.29 -10000 0 -0.85 27 27
KRT14 -0.13 0.17 -10000 0 -0.88 3 3
TBP 0.029 0.001 -10000 0 -10000 0 0
CREBBP 0.03 0.031 -10000 0 -10000 0 0
HDAC1 0.009 0.031 -10000 0 -10000 0 0
HDAC2 0.041 0.025 -10000 0 -10000 0 0
AP-1 -0.32 0.29 -10000 0 -0.77 36 36
MAPK14 0.017 0.006 -10000 0 -10000 0 0
MAPK10 0.005 0.093 -10000 0 -0.68 4 4
MAPK11 0.014 0.05 -10000 0 -0.72 1 1
KRT5 -0.26 0.26 -10000 0 -0.8 21 21
interleukin-1 receptor activity 0.025 0.026 -10000 0 -10000 0 0
NCOA1 0.015 0.063 -10000 0 -0.63 2 2
STAT1 -0.039 0.21 -10000 0 -0.72 20 20
CGA -0.081 0.16 -10000 0 -0.59 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.19 0.23 0.49 50 -10000 0 50
MAPK3 0.011 0.062 -10000 0 -0.64 2 2
MAPK1 0.014 0.044 -10000 0 -0.64 1 1
ICAM1 -0.32 0.32 -10000 0 -0.92 31 31
NFKB1 -0.11 0.073 -10000 0 -10000 0 0
MAPK8 -0.17 0.2 -10000 0 -0.53 30 30
MAPK9 0.017 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.046 0.14 0.58 4 -10000 0 4
BAX 0.019 0.087 -10000 0 -10000 0 0
POMC -0.13 0.19 -10000 0 -1.3 1 1
EP300 0.036 0.036 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.28 0.32 0.62 70 -0.67 1 71
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.07 0.27 3 -10000 0 3
SGK1 0.082 0.073 0.32 3 -10000 0 3
IL13 -0.2 0.23 -10000 0 -1 6 6
IL6 -0.49 0.44 -10000 0 -0.92 105 105
PRKACG 0.017 0 -10000 0 -10000 0 0
IL5 -0.21 0.25 -10000 0 -0.86 17 17
IL2 -0.26 0.25 -10000 0 -0.77 19 19
CDK5 0.01 0.07 -10000 0 -0.72 2 2
PRKACB -0.16 0.29 -10000 0 -0.64 60 60
HSP90AA1 0.014 0.05 -10000 0 -0.72 1 1
IL8 -0.69 0.32 -10000 0 -0.83 158 158
CDK5R1/CDK5 -0.003 0.052 -10000 0 -0.54 2 2
NF kappa B1 p50/RelA/PKAc -0.21 0.2 -10000 0 -0.58 30 30
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.28 0.28 0.57 70 -0.5 1 71
SMARCA4 0.017 0 -10000 0 -10000 0 0
chromatin remodeling 0.18 0.2 0.42 45 -0.53 3 48
NF kappa B1 p50/RelA/Cbp -0.12 0.1 -10000 0 -0.52 1 1
JUN (dimer) -0.18 0.2 -10000 0 -0.59 24 24
YWHAH 0.017 0 -10000 0 -10000 0 0
VIPR1 -0.19 0.36 -10000 0 -1 31 31
NR3C1 0.16 0.3 0.52 43 -0.55 21 64
NR4A1 0.018 0.084 -10000 0 -0.7 3 3
TIF2/SUV420H1 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.068 0.14 0.58 4 -10000 0 4
cortisol/GR alpha (dimer)/Src-1 0.3 0.3 0.61 72 -0.51 1 73
PBX1 0.015 0.087 -10000 0 -0.63 4 4
POU1F1 0.024 0.045 -10000 0 -0.63 1 1
SELE -0.4 0.4 -10000 0 -0.96 62 62
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.18 0.2 0.42 45 -0.54 3 48
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.28 0.28 0.57 70 -0.5 1 71
mol:cortisol 0.22 0.19 0.44 72 -10000 0 72
MMP1 -0.55 0.22 -10000 0 -0.68 114 114
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
ERC1 0.017 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.052 0.088 -9999 0 -0.37 4 4
IRAK/TOLLIP 0.03 0.043 -9999 0 -0.42 2 2
IKBKB 0.014 0.05 -9999 0 -0.72 1 1
IKBKG 0.017 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.41 0.29 -9999 0 -0.57 161 161
IL1A -0.32 0.37 -9999 0 -0.72 100 100
IL1B -0.11 0.25 -9999 0 -0.54 55 55
IRAK/TRAF6/p62/Atypical PKCs -0.013 0.065 -9999 0 -10000 0 0
IL1R2 -0.24 0.32 -9999 0 -0.64 87 87
IL1R1 -0.007 0.12 -9999 0 -0.64 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.043 0.078 -9999 0 -10000 0 0
TOLLIP 0.017 0 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.082 0.035 -9999 0 -10000 0 0
JUN 0.056 0.083 -9999 0 -10000 0 0
MAP3K7 0.017 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.11 0.18 -9999 0 -0.74 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.21 0.22 -9999 0 -0.43 101 101
PIK3R1 0.017 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.19 0.21 -9999 0 -0.77 6 6
IL1 beta fragment/IL1R1/IL1RAP -0.12 0.21 -9999 0 -0.46 47 47
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 0.056 0.065 -9999 0 -10000 0 0
IRAK1 0.021 0.047 -9999 0 -0.47 2 2
IL1RN/IL1R1 -0.17 0.25 -9999 0 -0.53 72 72
IRAK4 0.017 0 -9999 0 -10000 0 0
PRKCI -0.003 0.12 -9999 0 -0.72 6 6
TRAF6 0.017 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.021 0.12 -9999 0 -0.39 4 4
CHUK 0.017 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.12 0.21 -9999 0 -0.46 47 47
IL1 beta/IL1R2 -0.26 0.26 -9999 0 -0.58 52 52
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.003 0.032 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.095 0.16 -9999 0 -0.66 6 6
IRAK3 -0.01 0.14 -9999 0 -0.72 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.11 0.18 -9999 0 -0.75 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.082 0.14 -9999 0 -0.43 6 6
IL1 alpha/IL1R1/IL1RAP -0.23 0.25 -9999 0 -0.48 108 108
RELA 0.017 0 -9999 0 -10000 0 0
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
SQSTM1 0.017 0 -9999 0 -10000 0 0
MYD88 0.017 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.003 0.036 -9999 0 -0.39 2 2
IL1RAP -0.003 0.12 -9999 0 -0.72 6 6
UBE2N 0.017 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.092 0.15 -9999 0 -0.61 7 7
CASP1 -0.032 0.18 -9999 0 -0.67 16 16
IL1RN/IL1R2 -0.33 0.26 -9999 0 -0.52 143 143
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.12 0.19 -9999 0 -0.78 6 6
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.051 0.12 -9999 0 -0.38 6 6
PIK3CA 0.017 0 -9999 0 -10000 0 0
IL1RN -0.2 0.34 -9999 0 -0.72 64 64
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.047 0.067 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.023 0.026 -10000 0 -10000 0 0
NFATC2 -0.005 0.17 -10000 0 -0.7 3 3
NFATC3 -0.024 0.094 -10000 0 -10000 0 0
CD40LG -0.52 0.39 -10000 0 -0.98 66 66
ITCH 0.055 0.049 -10000 0 -10000 0 0
CBLB 0.055 0.049 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.19 0.22 -10000 0 -0.89 8 8
JUNB 0.007 0.085 -10000 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.049 -10000 0 -10000 0 0
T cell anergy 0.076 0.084 -10000 0 -0.46 1 1
TLE4 0.017 0.14 -10000 0 -1.2 1 1
Jun/NFAT1-c-4/p21SNFT -0.21 0.27 -10000 0 -0.87 19 19
AP-1/NFAT1-c-4 -0.59 0.49 -10000 0 -1.1 71 71
IKZF1 0.008 0.17 -10000 0 -0.96 4 4
T-helper 2 cell differentiation -0.085 0.14 -10000 0 -0.76 2 2
AP-1/NFAT1 -0.16 0.21 -10000 0 -0.58 33 33
CALM1 0.03 0.031 -10000 0 -10000 0 0
EGR2 -0.084 0.36 -10000 0 -1.4 11 11
EGR3 -0.088 0.34 -10000 0 -1.2 11 11
NFAT1/FOXP3 0.017 0.12 -10000 0 -0.8 1 1
EGR1 -0.015 0.15 -10000 0 -0.66 11 11
JUN -0.049 0.12 -10000 0 -0.76 5 5
EGR4 0.002 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.035 -10000 0 -10000 0 0
GBP3 -0.1 0.34 -10000 0 -0.82 40 40
FOSL1 -0.026 0.17 -10000 0 -0.72 13 13
NFAT1-c-4/MAF/IRF4 -0.28 0.37 -10000 0 -1.1 28 28
DGKA 0.019 0.12 -10000 0 -0.8 1 1
CREM 0.016 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.12 0.26 -10000 0 -0.84 16 16
CTLA4 0.02 0.13 -10000 0 -0.67 4 4
NFAT1-c-4 (dimer)/EGR1 -0.12 0.29 -10000 0 -0.96 14 14
NFAT1-c-4 (dimer)/EGR4 -0.11 0.26 -10000 0 -0.85 15 15
FOS -0.14 0.24 -10000 0 -0.69 33 33
IFNG -0.32 0.32 -10000 0 -0.75 43 43
T cell activation -0.14 0.17 -10000 0 -0.71 3 3
MAF -0.21 0.31 -10000 0 -0.63 78 78
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.057 0.21 0.66 10 -10000 0 10
TNF -0.085 0.26 -10000 0 -0.87 11 11
FASLG -0.22 0.54 -10000 0 -1.5 30 30
TBX21 -0.19 0.29 -10000 0 -0.63 67 67
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.001 0.11 -10000 0 -0.74 5 5
PTPN1 0.019 0.12 -10000 0 -0.8 1 1
NFAT1-c-4/ICER1 -0.11 0.25 -10000 0 -0.86 14 14
GATA3 0.022 0.002 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.32 0.32 -10000 0 -0.72 46 46
IL2RA -0.2 0.21 -10000 0 -0.8 10 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.016 0.13 -10000 0 -0.8 2 2
E2F1 -0.031 0.18 -10000 0 -0.71 14 14
PPARG -0.001 0.11 -10000 0 -0.63 6 6
SLC3A2 -0.002 0.18 -10000 0 -0.65 10 10
IRF4 -0.13 0.27 -10000 0 -0.63 50 50
PTGS2 -0.61 0.48 -10000 0 -1.1 83 83
CSF2 -0.7 0.49 -10000 0 -1.1 104 104
JunB/Fra1/NFAT1-c-4 -0.12 0.26 -10000 0 -0.86 11 11
IL4 -0.088 0.14 -10000 0 -0.8 2 2
IL5 -0.54 0.41 -10000 0 -1 65 65
IL2 -0.14 0.17 -10000 0 -0.72 3 3
IL3 -0.056 0.052 -10000 0 -10000 0 0
RNF128 0.038 0.13 -10000 0 -0.67 7 7
NFATC1 -0.057 0.21 -10000 0 -0.66 10 10
CDK4 -0.003 0.21 -10000 0 -0.63 8 8
PTPRK 0.019 0.12 -10000 0 -0.8 1 1
IL8 -0.84 0.4 -10000 0 -1.1 120 120
POU2F1 0.028 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.007 -10000 0 -10000 0 0
HDAC1 0.028 0.022 -10000 0 -10000 0 0
AES 0.021 0.006 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
DTX1 0.017 0 -10000 0 -10000 0 0
LRP6/FZD1 -0.002 0.036 -10000 0 -0.54 1 1
TLE1 0.02 0.005 -10000 0 -10000 0 0
AP1 -0.24 0.2 -10000 0 -0.57 39 39
NCSTN 0.017 0 -10000 0 -10000 0 0
ADAM10 0.018 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.046 0.099 -10000 0 -10000 0 0
NICD/RBPSUH -0.001 0.007 -10000 0 -10000 0 0
WIF1 -0.093 0.26 -10000 0 -0.72 33 33
NOTCH1 -0.002 0.01 -10000 0 -10000 0 0
PSENEN 0.017 0 -10000 0 -10000 0 0
KREMEN2 -0.13 0.29 -10000 0 -0.72 43 43
DKK1 -0.17 0.32 -10000 0 -0.72 56 56
beta catenin/beta TrCP1 0.12 0.083 -10000 0 -10000 0 0
APH1B 0.013 0.049 -10000 0 -0.72 1 1
APH1A -0.004 0.12 -10000 0 -0.65 7 7
AXIN1 -0.045 0.039 0.29 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.093 0.072 -10000 0 -10000 0 0
PSEN1 0.017 0 -10000 0 -10000 0 0
FOS -0.081 0.23 -10000 0 -0.64 33 33
JUN 0 0.11 -10000 0 -0.72 5 5
MAP3K7 0.024 0.008 -10000 0 -10000 0 0
CTNNB1 0.12 0.089 0.28 1 -10000 0 1
MAPK3 0.011 0.062 -10000 0 -0.64 2 2
DKK2/LRP6/Kremen 2 -0.27 0.28 -10000 0 -0.52 113 113
HNF1A 0.021 0.006 -10000 0 -10000 0 0
CTBP1 0.021 0.006 -10000 0 -10000 0 0
MYC -0.32 0.29 -10000 0 -0.57 131 131
NKD1 -0.54 0.32 -10000 0 -0.72 167 167
FZD1 0.017 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.001 0.007 -10000 0 -10000 0 0
apoptosis -0.23 0.2 -10000 0 -0.57 39 39
Delta 1/NOTCHprecursor -0.001 0.007 -10000 0 -10000 0 0
DLL1 0.017 0 -10000 0 -10000 0 0
PPARD -0.011 0.039 -10000 0 -10000 0 0
Gamma Secretase -0.012 0.061 -10000 0 -10000 0 0
APC -0.063 0.099 0.29 1 -0.5 9 10
DVL1 -0.009 0.021 -10000 0 -10000 0 0
CSNK2A1 0.008 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.024 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.2 0.26 -10000 0 -0.51 89 89
LRP6 0.013 0.05 -10000 0 -0.72 1 1
CSNK1A1 0.008 0.008 -10000 0 -10000 0 0
NLK 0.052 0.018 -10000 0 -10000 0 0
CCND1 -0.091 0.21 -10000 0 -0.63 19 19
WNT1 0.017 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.061 0.073 0.35 1 -10000 0 1
DKK2 -0.27 0.36 -10000 0 -0.72 87 87
NOTCH1 precursor/DVL1 -0.002 0.009 -10000 0 -10000 0 0
GSK3B 0.016 0.049 -10000 0 -0.72 1 1
FRAT1 0.018 0.044 -10000 0 -0.64 1 1
NOTCH/Deltex homolog 1 -0.001 0.007 -10000 0 -10000 0 0
PPP2R5D 0.24 0.14 0.31 167 -10000 0 167
MAPK1 0.014 0.044 -10000 0 -0.64 1 1
WNT1/LRP6/FZD1 -0.063 0.15 -10000 0 -0.41 34 34
RBPJ 0.017 0 -10000 0 -10000 0 0
CREBBP 0.008 0.011 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0 0.1 -9999 0 -0.44 3 3
BIRC5 -0.06 0.22 -9999 0 -0.72 23 23
NFKBIA 0.01 0.098 -9999 0 -0.42 1 1
CPEB1 -0.021 0.15 -9999 0 -0.64 13 13
AKT1 0.01 0.098 -9999 0 -0.42 1 1
NDEL1 0.017 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.026 0.1 -9999 0 -0.5 5 5
NDEL1/TACC3 -0.02 0.088 -9999 0 -0.44 3 3
GADD45A 0.01 0.07 -9999 0 -0.72 2 2
GSK3B 0.017 0.05 -9999 0 -0.71 1 1
PAK1/Aurora A 0.004 0.095 -9999 0 -0.42 1 1
MDM2 0.017 0 -9999 0 -10000 0 0
JUB -0.69 0.16 -9999 0 -0.72 211 211
TPX2 -0.12 0.25 -9999 0 -0.54 58 58
TP53 0.011 0.083 -9999 0 -0.36 3 3
DLG7 -0.024 0.15 -9999 0 -0.47 16 16
AURKAIP1 0.017 0 -9999 0 -10000 0 0
ARHGEF7 0.017 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.021 0.093 -9999 0 -0.46 3 3
G2/M transition of mitotic cell cycle -0.026 0.1 -9999 0 -0.49 5 5
AURKA -0.003 0.12 -9999 0 -0.5 1 1
AURKB -0.02 0.038 -9999 0 -0.2 1 1
CDC25B -0.24 0.15 -9999 0 -0.37 110 110
G2/M transition checkpoint -0.42 0.12 -9999 0 -0.44 211 211
mRNA polyadenylation -0.039 0.12 -9999 0 -0.38 14 14
Aurora A/CPEB -0.04 0.12 -9999 0 -0.38 14 14
Aurora A/TACC1/TRAP/chTOG -0.011 0.072 -9999 0 -10000 0 0
BRCA1 0.004 0.098 -9999 0 -0.72 4 4
centrosome duplication 0.004 0.095 -9999 0 -0.42 1 1
regulation of centrosome cycle -0.02 0.087 -9999 0 -0.41 4 4
spindle assembly -0.011 0.071 -9999 0 -10000 0 0
TDRD7 0.017 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.062 0.16 -9999 0 -0.63 8 8
CENPA -0.035 0.065 -9999 0 -0.24 13 13
Aurora A/PP2A 0.004 0.095 -9999 0 -0.42 1 1
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.008 0.11 -9999 0 -0.38 3 3
negative regulation of DNA binding 0.011 0.083 -9999 0 -0.36 3 3
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.01 0.07 -9999 0 -0.72 2 2
Ajuba/Aurora A -0.42 0.12 -9999 0 -0.44 211 211
mitotic prometaphase -0.002 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.12 -9999 0 -0.5 1 1
TACC1 0.017 0 -9999 0 -10000 0 0
TACC3 0.007 0.085 -9999 0 -0.72 3 3
Aurora A/Antizyme1 -0.015 0.078 -9999 0 -0.37 1 1
Aurora A/RasGAP 0 0.1 -9999 0 -0.44 3 3
OAZ1 0.017 0 -9999 0 -10000 0 0
RAN 0.014 0.05 -9999 0 -0.72 1 1
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.021 0.011 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.12 0.25 -9999 0 -0.54 58 58
PPP2R5D 0.017 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.098 0.24 -9999 0 -0.5 48 48
PAK1 0.017 0 -9999 0 -10000 0 0
CKAP5 0.017 0 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.017 0 -9999 0 -10000 0 0
PTK2 0.014 0.05 -9999 0 -0.72 1 1
CRKL -0.16 0.18 -9999 0 -0.68 4 4
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0.017 0 -9999 0 -10000 0 0
IRS1/Crk -0.17 0.19 -9999 0 -0.68 5 5
IGF-1R heterotetramer/IGF1/PTP1B -0.2 0.18 -9999 0 -0.47 4 4
AKT1 -0.11 0.16 -9999 0 -0.57 4 4
BAD -0.097 0.15 -9999 0 -0.52 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.17 0.19 -9999 0 -0.68 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.18 0.17 -9999 0 -0.7 5 5
RAF1 -0.087 0.15 -9999 0 -0.49 4 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.17 0.16 -9999 0 -0.65 4 4
YWHAZ 0.017 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.2 0.18 -9999 0 -0.36 125 125
PIK3CA 0.017 0 -9999 0 -10000 0 0
RPS6KB1 -0.11 0.16 -9999 0 -0.58 5 5
GNB2L1 0.017 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.079 0.13 -9999 0 -0.41 4 4
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.14 0.13 -9999 0 -0.58 4 4
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.15 0.14 -9999 0 -10000 0 0
IGF-1R heterotetramer -0.027 0.04 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.18 0.17 -9999 0 -0.69 4 4
Crk/p130 Cas/Paxillin -0.16 0.15 -9999 0 -0.61 5 5
IGF1R -0.027 0.04 -9999 0 -10000 0 0
IGF1 -0.36 0.33 -9999 0 -0.65 125 125
IRS2/Crk -0.15 0.18 -9999 0 -0.65 6 6
PI3K -0.17 0.15 -9999 0 -0.65 4 4
apoptosis 0.077 0.14 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD -0.2 0.22 -9999 0 -0.39 125 125
RAF1/14-3-3 E -0.069 0.13 -9999 0 -10000 0 0
BAD/14-3-3 -0.081 0.14 -9999 0 -10000 0 0
PRKCZ -0.12 0.16 -9999 0 -0.57 4 4
Crk/p130 Cas/Paxillin/FAK1 -0.11 0.11 -9999 0 -0.5 2 2
PTPN1 0.017 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.22 0.24 -9999 0 -0.42 125 125
BCAR1 0.017 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.2 0.19 -9999 0 -0.58 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.16 0.18 -9999 0 -0.68 4 4
GRB10 -0.03 0.18 -9999 0 -0.72 14 14
PTPN11 -0.17 0.19 -9999 0 -0.69 5 5
IRS1 -0.19 0.2 -9999 0 -0.36 125 125
IRS2 -0.17 0.19 -9999 0 -0.69 5 5
IGF-1R heterotetramer/IGF1 -0.27 0.24 -9999 0 -0.48 125 125
GRB2 0.017 0 -9999 0 -10000 0 0
PDPK1 -0.13 0.17 -9999 0 -0.61 4 4
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
PRKD1 -0.2 0.23 -9999 0 -0.4 125 125
SHC1 0.017 0 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.042 0.19 -9999 0 -0.64 20 20
positive regulation of NF-kappaB transcription factor activity -0.051 0.15 -9999 0 -0.49 23 23
MAP2K4 0.003 0.12 -9999 0 -0.52 4 4
IKBKB 0.014 0.05 -9999 0 -0.72 1 1
TNFRSF10B -0.083 0.25 -9999 0 -0.72 30 30
TNFRSF10A -0.053 0.22 -9999 0 -0.72 21 21
SMPD1 -0.15 0.23 -9999 0 -0.52 50 50
IKBKG 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.004 0.098 -9999 0 -0.72 4 4
TRAIL/TRAILR2 -0.11 0.23 -9999 0 -0.56 45 45
TRAIL/TRAILR3 -0.1 0.21 -9999 0 -0.52 44 44
TRAIL/TRAILR1 -0.091 0.21 -9999 0 -0.53 38 38
TRAIL/TRAILR4 -0.051 0.15 -9999 0 -0.49 23 23
TRAIL/TRAILR1/DAP3/GTP -0.071 0.16 -9999 0 -0.42 38 38
IKK complex -0.033 0.063 -9999 0 -10000 0 0
RIPK1 0.017 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 -0.017 0.15 -9999 0 -0.48 21 21
MAP3K1 -0.044 0.095 -9999 0 -0.42 6 6
TRAILR4 (trimer) 0.004 0.098 -9999 0 -0.72 4 4
TRADD 0.017 0 -9999 0 -10000 0 0
TRAILR1 (trimer) -0.053 0.22 -9999 0 -0.72 21 21
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.12 -9999 0 -0.49 3 3
CFLAR 0.017 0 -9999 0 -10000 0 0
MAPK1 -0.015 0.14 -9999 0 -0.46 21 21
TRAIL/TRAILR1/FADD/TRADD/RIP -0.064 0.15 -9999 0 -0.72 3 3
mol:ceramide -0.15 0.23 -9999 0 -0.51 50 50
FADD 0.017 0 -9999 0 -10000 0 0
MAPK8 0.014 0.12 -9999 0 -0.48 4 4
TRAF2 0.017 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.07 0.24 -9999 0 -0.72 26 26
CHUK 0.017 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.078 0.18 -9999 0 -0.45 38 38
DAP3 0.017 0 -9999 0 -10000 0 0
CASP10 -0.08 0.16 -9999 0 -0.46 24 24
JNK cascade -0.051 0.15 -9999 0 -0.49 23 23
TRAIL (trimer) -0.042 0.19 -9999 0 -0.63 20 20
TNFRSF10C -0.07 0.24 -9999 0 -0.72 26 26
TRAIL/TRAILR1/DAP3/GTP/FADD -0.066 0.15 -9999 0 -0.44 21 21
TRAIL/TRAILR2/FADD -0.096 0.2 -9999 0 -0.47 45 45
cell death -0.15 0.23 -9999 0 -0.51 50 50
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.011 0.13 -9999 0 -0.49 5 5
TRAILR2 (trimer) -0.083 0.25 -9999 0 -0.72 30 30
CASP8 0.013 0.044 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.08 0.17 -9999 0 -0.72 5 5
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.004 0.055 -9999 0 -0.5 1 1
NFATC2 -0.002 0.044 -9999 0 -10000 0 0
NFATC3 -0.002 0.044 -9999 0 -10000 0 0
CD40LG -0.21 0.33 -9999 0 -0.74 38 38
PTGS2 -0.3 0.43 -9999 0 -0.86 67 67
JUNB 0.007 0.085 -9999 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.013 0.016 -9999 0 -10000 0 0
CALM1 0.01 0.012 -9999 0 -10000 0 0
JUN -0.005 0.11 -9999 0 -0.72 5 5
mol:Ca2+ -0.017 0.015 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.004 -9999 0 -10000 0 0
FOSL1 -0.026 0.17 -9999 0 -0.72 13 13
CREM 0.016 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.12 0.13 -9999 0 -0.55 3 3
FOS -0.087 0.24 -9999 0 -0.65 33 33
IFNG -0.28 0.41 -9999 0 -0.88 53 53
AP-1/NFAT1-c-4 -0.26 0.4 -9999 0 -0.93 38 38
FASLG -0.24 0.36 -9999 0 -0.76 44 44
NFAT1-c-4/ICER1 -0.054 0.068 -9999 0 -0.44 1 1
IL2RA -0.22 0.34 -9999 0 -0.77 39 39
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.38 0.45 -9999 0 -0.86 88 88
JunB/Fra1/NFAT1-c-4 -0.069 0.13 -9999 0 -0.57 9 9
IL4 -0.21 0.33 -9999 0 -0.73 38 38
IL2 0.011 0.013 -9999 0 -10000 0 0
IL3 0.001 0.021 -9999 0 -10000 0 0
FKBP1A 0.017 0 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.028 0 -9999 0 -10000 0 0
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 0.031 0.017 -10000 0 -10000 0 0
HSPA8 0.008 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.004 0.12 -10000 0 -0.47 7 7
AKT1 -0.043 0.036 -10000 0 -10000 0 0
GSC -0.01 0.12 -10000 0 -0.57 8 8
NKX2-5 0.006 0.055 -10000 0 -0.72 1 1
muscle cell differentiation 0.068 0.13 0.45 8 -10000 0 8
SMAD2-3/SMAD4/SP1 -0.085 0.12 -10000 0 -0.52 2 2
SMAD4 -0.025 0.087 -10000 0 -0.63 3 3
CBFB 0.007 0.085 -10000 0 -0.72 3 3
SAP18 0.012 0.049 -10000 0 -0.72 1 1
Cbp/p300/MSG1 -0.008 0.17 -10000 0 -0.45 28 28
SMAD3/SMAD4/VDR 0 0.08 -10000 0 -10000 0 0
MYC -0.32 0.33 -10000 0 -0.6 131 131
CDKN2B -1.1 0.62 -10000 0 -1.4 175 175
AP1 -0.045 0.17 -10000 0 -0.7 7 7
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.01 0.054 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.26 0.19 -10000 0 -0.53 34 34
SP3 0.02 0.001 -10000 0 -10000 0 0
CREB1 0.017 0 -10000 0 -10000 0 0
FOXH1 0.011 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.059 0.16 -10000 0 -0.45 26 26
GATA3 0.016 0.039 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.021 0.035 -10000 0 -10000 0 0
MEF2C/TIF2 -0.078 0.23 -10000 0 -0.6 34 34
endothelial cell migration 0.042 0.24 0.57 26 -10000 0 26
MAX 0.021 0.014 -10000 0 -10000 0 0
RBBP7 0.015 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.002 -10000 0 -10000 0 0
RUNX2 0.017 0 -10000 0 -10000 0 0
RUNX3 -0.026 0.16 -10000 0 -0.66 14 14
RUNX1 -0.2 0.34 -10000 0 -0.72 66 66
CTBP1 0.017 0 -10000 0 -10000 0 0
NR3C1 -0.05 0.21 -10000 0 -0.64 24 24
VDR -0.001 0.11 -10000 0 -0.64 6 6
CDKN1A -0.031 0.19 -10000 0 -1.5 3 3
KAT2B 0.005 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.042 0.089 -10000 0 -10000 0 0
DCP1A 0.017 0 -10000 0 -10000 0 0
SKI 0.015 0.002 -10000 0 -10000 0 0
SERPINE1 -0.05 0.24 -10000 0 -0.58 24 24
SMAD3/SMAD4/ATF2 -0.017 0.072 -10000 0 -0.53 1 1
SMAD3/SMAD4/ATF3 -0.026 0.1 -10000 0 -0.54 5 5
SAP30 0.015 0.002 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.069 0.062 -10000 0 -0.49 1 1
JUN -0.027 0.18 -10000 0 -0.7 7 7
SMAD3/SMAD4/IRF7 -0.013 0.071 -10000 0 -0.52 1 1
TFE3 0.021 0.01 -10000 0 -10000 0 0
COL1A2 -0.11 0.25 -10000 0 -0.6 44 44
mesenchymal cell differentiation 0.017 0.072 0.53 1 -10000 0 1
DLX1 0.01 0.07 -10000 0 -0.72 2 2
TCF3 0.014 0.05 -10000 0 -0.72 1 1
FOS -0.08 0.24 -10000 0 -0.64 33 33
SMAD3/SMAD4/Max -0.012 0.079 -10000 0 -0.53 1 1
Cbp/p300/SNIP1 0.005 0.016 -10000 0 -10000 0 0
ZBTB17 0.043 0.023 -10000 0 -10000 0 0
LAMC1 0.011 0.07 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.12 0.22 -10000 0 -0.52 50 50
IRF7 0.022 0.001 -10000 0 -10000 0 0
ESR1 0.004 0.11 -10000 0 -0.64 6 6
HNF4A 0.017 0 -10000 0 -10000 0 0
MEF2C -0.077 0.25 -10000 0 -0.64 34 34
SMAD2-3/SMAD4 -0.061 0.094 -10000 0 -0.45 4 4
Cbp/p300/Src-1 0.047 0.053 -10000 0 -10000 0 0
IGHV3OR16-13 -0.034 0.046 -10000 0 -10000 0 0
TGIF2/HDAC complex -0.14 0.3 -10000 0 -0.72 48 48
CREBBP 0.027 0.013 -10000 0 -10000 0 0
SKIL 0 0.11 -10000 0 -0.72 5 5
HDAC1 0.015 0.002 -10000 0 -10000 0 0
HDAC2 0.015 0.002 -10000 0 -10000 0 0
SNIP1 0.009 0.008 -10000 0 -10000 0 0
GCN5L2 -0.17 0.32 -10000 0 -0.7 60 60
SMAD3/SMAD4/TFE3 -0.017 0.068 -10000 0 -0.52 1 1
MSG1/HSC70 -0.066 0.18 -10000 0 -0.54 28 28
SMAD2 -0.049 0.049 -10000 0 -10000 0 0
SMAD3 -0.015 0.075 -10000 0 -0.66 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.15 0.19 -10000 0 -0.51 29 29
SMAD2/SMAD2/SMAD4 -0.014 0.05 -10000 0 -0.36 3 3
NCOR1 0.012 0.043 -10000 0 -0.63 1 1
NCOA2 0.017 0 -10000 0 -10000 0 0
NCOA1 0.011 0.062 -10000 0 -0.64 2 2
MYOD/E2A -0.01 0.072 -10000 0 -0.54 4 4
SMAD2-3/SMAD4/SP1/MIZ-1 -0.094 0.12 -10000 0 -0.53 2 2
IFNB1 0.003 0.068 -10000 0 -0.45 1 1
SMAD3/SMAD4/MEF2C -0.095 0.24 -10000 0 -0.64 30 30
CITED1 -0.079 0.24 -10000 0 -0.72 28 28
SMAD2-3/SMAD4/ARC105 -0.041 0.083 -10000 0 -0.51 1 1
RBL1 -0.07 0.24 -10000 0 -0.72 26 26
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.44 0.28 -10000 0 -0.58 173 173
RUNX1-3/PEBPB2 -0.17 0.23 -10000 0 -0.48 70 70
SMAD7 -0.062 0.17 -10000 0 -0.85 3 3
MYC/MIZ-1 -0.18 0.26 -10000 0 -0.38 130 130
SMAD3/SMAD4 0.045 0.19 0.36 3 -0.47 6 9
IL10 -0.007 0.092 -10000 0 -10000 0 0
PIASy/HDAC complex 0.007 0.011 -10000 0 -10000 0 0
PIAS3 0.018 0.051 -10000 0 -0.73 1 1
CDK2 -0.054 0.23 -10000 0 -0.72 24 24
IL5 -0.041 0.19 -10000 0 -0.64 18 18
CDK4 -0.031 0.2 -10000 0 -0.71 18 18
PIAS4 0.007 0.011 -10000 0 -10000 0 0
ATF3 0.004 0.098 -10000 0 -0.72 4 4
SMAD3/SMAD4/SP1 -0.052 0.097 -10000 0 -0.62 1 1
FOXG1 -0.074 0.24 -10000 0 -0.72 27 27
FOXO3 -0.051 0.048 -10000 0 -10000 0 0
FOXO1 -0.071 0.11 -10000 0 -0.56 9 9
FOXO4 -0.05 0.048 -10000 0 -10000 0 0
heart looping -0.075 0.24 -10000 0 -0.63 34 34
CEBPB -0.033 0.13 -10000 0 -0.78 6 6
SMAD3/SMAD4/DLX1 -0.022 0.088 -10000 0 -0.54 3 3
MYOD1 0.007 0.085 -10000 0 -0.72 3 3
SMAD3/SMAD4/HNF4 -0.017 0.072 -10000 0 -0.53 1 1
SMAD3/SMAD4/GATA3 -0.026 0.099 -10000 0 -0.51 1 1
SnoN/SIN3/HDAC complex/NCoR1 0 0.11 -10000 0 -0.72 5 5
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.16 0.22 -10000 0 -0.58 19 19
SMAD3/SMAD4/SP1-3 -0.037 0.08 -10000 0 -0.55 1 1
MED15 0.017 0 -10000 0 -10000 0 0
SP1 -0.015 0.055 -10000 0 -10000 0 0
SIN3B 0.015 0.002 -10000 0 -10000 0 0
SIN3A 0.015 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.053 0.13 -10000 0 -0.44 1 1
ITGB5 -0.009 0.085 -10000 0 -0.49 1 1
TGIF/SIN3/HDAC complex/CtBP 0.035 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.019 0.081 -10000 0 -0.56 2 2
AR 0.014 0.05 -10000 0 -0.72 1 1
negative regulation of cell growth -0.13 0.17 -10000 0 -0.49 22 22
SMAD3/SMAD4/MYOD -0.024 0.091 -10000 0 -0.46 6 6
E2F5 -0.3 0.36 -10000 0 -0.72 94 94
E2F4 0.014 0.05 -10000 0 -0.72 1 1
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.007 0.07 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.27 0.19 -10000 0 -0.45 49 49
TFDP1 -0.043 0.2 -10000 0 -0.72 18 18
SMAD3/SMAD4/AP1 -0.052 0.17 -10000 0 -0.71 7 7
SMAD3/SMAD4/RUNX2 -0.017 0.072 -10000 0 -0.53 1 1
TGIF2 -0.14 0.3 -10000 0 -0.72 48 48
TGIF1 -0.07 0.24 -10000 0 -0.72 26 26
ATF2 0.017 0 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.003 0.048 0.21 11 -10000 0 11
BUB1B -0.098 0.15 -10000 0 -0.38 45 45
PLK1 -0.015 0.042 -10000 0 -0.13 10 10
PLK1S1 -0.008 0.021 -10000 0 -0.078 2 2
KIF2A -0.002 0.038 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.015 0.042 -10000 0 -0.13 10 10
GOLGA2 0.017 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.015 0.051 -10000 0 -0.46 2 2
WEE1 -0.05 0.077 -10000 0 -0.34 3 3
cytokinesis -0.033 0.13 -10000 0 -0.38 27 27
PP2A-alpha B56 -0.1 0.13 -10000 0 -0.5 3 3
AURKA -0.02 0.061 -10000 0 -0.17 30 30
PICH/PLK1 -0.38 0.36 -10000 0 -0.72 95 95
CENPE -0.019 0.1 -10000 0 -0.48 9 9
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.001 0.038 -10000 0 -10000 0 0
PPP2CA 0.017 0 -10000 0 -10000 0 0
FZR1 0.017 0 -10000 0 -10000 0 0
TPX2 -0.04 0.077 -10000 0 -0.17 57 57
PAK1 0.015 0.002 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
CLSPN -0.005 0.038 -10000 0 -0.2 5 5
GORASP1 0.017 0 -10000 0 -10000 0 0
metaphase -0.001 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.008 0.021 -10000 0 -0.078 2 2
G2 phase of mitotic cell cycle -0.003 0.004 -10000 0 -0.013 20 20
STAG2 -0.006 0.13 -10000 0 -0.72 7 7
GRASP65/GM130/RAB1/GTP -0.012 0.024 -10000 0 -10000 0 0
spindle elongation -0.015 0.042 -10000 0 -0.13 10 10
ODF2 0.01 0.049 -10000 0 -0.72 1 1
BUB1 -0.13 0.15 -10000 0 -0.56 3 3
TPT1 0 0.021 -10000 0 -10000 0 0
CDC25C -0.011 0.058 -10000 0 -0.23 13 13
CDC25B -0.34 0.37 -10000 0 -0.72 105 105
SGOL1 -0.003 0.048 -10000 0 -0.21 11 11
RHOA 0.017 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.26 0.26 -10000 0 -0.52 82 82
CDC14B 0.013 0.005 -10000 0 -10000 0 0
CDC20 -0.003 0.12 -10000 0 -0.72 6 6
PLK1/PBIP1 -0.05 0.13 -10000 0 -0.42 22 22
mitosis 0.002 0.012 0.033 30 -0.026 1 31
FBXO5 -0.04 0.088 -10000 0 -0.39 9 9
CDC2 -0.062 0.22 -10000 0 -0.73 21 21
NDC80 0.01 0.07 -10000 0 -0.72 2 2
metaphase plate congression -0.003 0.025 -10000 0 -10000 0 0
ERCC6L -0.38 0.33 -10000 0 -0.72 92 92
NLP/gamma Tubulin -0.004 0.022 -10000 0 -0.11 1 1
microtubule cytoskeleton organization 0 0.021 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.002 0.002 -10000 0 -10000 0 0
PPP1R12A 0.016 0.001 -10000 0 -10000 0 0
interphase -0.002 0.002 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.053 0.17 -10000 0 -0.47 31 31
GRASP65/GM130/RAB1/GTP/PLK1 -0.004 0.02 -10000 0 -10000 0 0
RAB1A 0.017 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.01 0.054 -10000 0 -0.43 1 1
mitotic prometaphase -0.002 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.027 -10000 0 -10000 0 0
microtubule-based process -0.055 0.16 -10000 0 -0.47 27 27
Golgi organization -0.015 0.042 -10000 0 -0.13 10 10
Cohesin/SA2 -0.027 0.073 -10000 0 -0.41 7 7
PPP1CB/MYPT1 0 0.002 -10000 0 -10000 0 0
KIF20A -0.073 0.24 -10000 0 -0.72 27 27
APC/C/CDC20 -0.014 0.085 -10000 0 -0.48 6 6
PPP2R1A 0.017 0 -10000 0 -10000 0 0
chromosome segregation -0.05 0.12 -10000 0 -0.42 22 22
PRC1 -0.003 0.12 -10000 0 -0.72 6 6
ECT2 -0.28 0.23 -10000 0 -0.45 137 137
C13orf34 -0.007 0.048 -10000 0 -0.44 1 1
NUDC -0.003 0.025 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.097 0.15 -10000 0 -0.37 45 45
spindle assembly -0.008 0.032 -10000 0 -0.13 1 1
spindle stabilization -0.008 0.021 -10000 0 -0.078 2 2
APC/C/HCDH1 0.02 0.008 -10000 0 -10000 0 0
MKLP2/PLK1 -0.055 0.16 -10000 0 -0.47 27 27
CCNB1 -0.15 0.3 -10000 0 -0.73 48 48
PPP1CB 0.016 0.001 -10000 0 -10000 0 0
BTRC 0.017 0 -10000 0 -10000 0 0
ROCK2 0.006 0.028 -10000 0 -10000 0 0
TUBG1 0 0.021 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.26 0.25 -10000 0 -0.51 82 82
MLF1IP -0.042 0.17 -10000 0 -0.56 22 22
INCENP 0 0.086 -10000 0 -0.73 3 3
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.032 0.062 -10000 0 -0.53 1 1
UGCG -0.021 0.025 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT -0.19 0.17 -10000 0 -0.39 13 13
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.015 0.034 -10000 0 -10000 0 0
mol:DAG 0.043 0.083 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.31 0.2 -10000 0 -0.52 92 92
FRAP1 -0.34 0.27 -10000 0 -0.62 92 92
FOXO3 -0.21 0.19 -10000 0 -0.41 86 86
AKT1 -0.24 0.2 -10000 0 -0.45 88 88
GAB2 0.003 0.007 -10000 0 -10000 0 0
SMPD1 -0.19 0.33 -10000 0 -0.82 47 47
SGMS1 -0.021 0.025 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.012 -10000 0 -10000 0 0
CALM1 0.017 0 -10000 0 -10000 0 0
cell proliferation -0.073 0.11 -10000 0 -10000 0 0
EIF3A 0.017 0 -10000 0 -10000 0 0
PI3K 0.005 0.012 -10000 0 -10000 0 0
RPS6KB1 -0.011 0.038 -10000 0 -10000 0 0
mol:sphingomyelin 0.043 0.083 -10000 0 -10000 0 0
natural killer cell activation -0.009 0.005 -10000 0 -0.014 83 83
JAK3 0.004 0.008 -10000 0 -10000 0 0
PIK3R1 0.003 0.008 -10000 0 -10000 0 0
JAK1 0.003 0.008 -10000 0 -10000 0 0
NFKB1 0.017 0 -10000 0 -10000 0 0
MYC -0.35 0.28 -10000 0 -0.63 90 90
MYB 0.007 0.14 -10000 0 -1.3 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.084 0.12 -10000 0 -0.42 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.002 0.07 -10000 0 -0.4 5 5
mol:PI-3-4-5-P3 -0.083 0.12 -10000 0 -0.41 1 1
Rac1/GDP 0.006 0.014 -10000 0 -10000 0 0
T cell proliferation -0.088 0.11 -10000 0 -0.39 1 1
SHC1 0.003 0.007 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.007 0.007 -10000 0 -0.066 2 2
PRKCZ -0.091 0.11 -10000 0 -0.4 1 1
NF kappa B1 p50/RelA -0.3 0.2 -10000 0 -0.52 88 88
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.05 -10000 0 -10000 0 0
HSP90AA1 0.014 0.05 -10000 0 -0.72 1 1
RELA 0.017 0 -10000 0 -10000 0 0
IL2RA -0.021 0.13 -10000 0 -0.73 7 7
IL2RB 0.001 0.044 -10000 0 -0.64 1 1
TERT 0.017 0 -10000 0 -10000 0 0
E2F1 0.005 0.071 -10000 0 -0.46 2 2
SOS1 0.003 0.007 -10000 0 -10000 0 0
RPS6 0 0.11 -10000 0 -0.72 5 5
mol:cAMP -0.004 0.003 0.031 2 -10000 0 2
PTPN11 -0.001 0.05 -10000 0 -0.73 1 1
IL2RG -0.005 0.075 -10000 0 -0.64 3 3
actin cytoskeleton organization -0.088 0.11 -10000 0 -0.39 1 1
GRB2 0.003 0.007 -10000 0 -10000 0 0
IL2 0.003 0.008 -10000 0 -10000 0 0
PIK3CA 0.003 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.018 -10000 0 -10000 0 0
LCK -0.003 0.066 -10000 0 -0.69 2 2
BCL2 -0.61 0.44 -10000 0 -0.93 145 145
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.017 0 -9999 0 -10000 0 0
EGFR 0.002 0.099 -9999 0 -0.65 5 5
EGF/EGFR -0.21 0.22 -9999 0 -0.7 18 18
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.11 0.16 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.15 0.31 -9999 0 -0.72 49 49
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.18 0.31 -9999 0 -0.68 64 64
EGF/EGFR dimer/SHC -0.13 0.2 -9999 0 -0.47 30 30
mol:GDP -0.1 0.16 -9999 0 -0.7 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.022 0.16 -9999 0 -0.65 13 13
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.095 0.14 -9999 0 -0.65 1 1
SHC1 0.017 0 -9999 0 -10000 0 0
HRAS/GDP -0.096 0.15 -9999 0 -0.66 1 1
FRAP1 -0.054 0.18 -9999 0 -0.67 1 1
EGF/EGFR dimer -0.15 0.23 -9999 0 -0.5 68 68
SOS1 0.017 0 -9999 0 -10000 0 0
GRB2 0.017 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.15 0.24 -9999 0 -0.53 61 61
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.031 0.097 -10000 0 -0.38 1 1
TBX21 -0.34 0.69 -10000 0 -1.4 67 67
B2M -0.007 0.13 -10000 0 -0.63 9 9
TYK2 0.019 0.021 -10000 0 -10000 0 0
IL12RB1 0.019 0.021 -10000 0 -10000 0 0
GADD45B -0.097 0.37 -10000 0 -0.91 24 24
IL12RB2 0.017 0.057 -10000 0 -0.77 1 1
GADD45G -0.1 0.38 -10000 0 -0.96 22 22
natural killer cell activation -0.001 0.028 -10000 0 -10000 0 0
RELB 0.017 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
IL18 -0.053 0.21 -10000 0 -0.64 25 25
IL2RA -0.006 0.13 -10000 0 -0.72 7 7
IFNG -0.15 0.31 -10000 0 -0.72 50 50
STAT3 (dimer) -0.061 0.33 -10000 0 -0.77 23 23
HLA-DRB5 -0.005 0.11 -10000 0 -0.63 7 7
FASLG -0.17 0.52 -10000 0 -1.4 25 25
NF kappa B2 p52/RelB -0.19 0.31 -10000 0 -0.88 29 29
CD4 0.016 0.007 -10000 0 -10000 0 0
SOCS1 0.014 0.05 -10000 0 -0.72 1 1
EntrezGene:6955 0 0.01 -10000 0 -10000 0 0
CD3D -0.011 0.14 -10000 0 -0.64 10 10
CD3E 0.018 0.008 -10000 0 -10000 0 0
CD3G -0.015 0.14 -10000 0 -0.65 11 11
IL12Rbeta2/JAK2 0.017 0.094 -10000 0 -0.55 5 5
CCL3 -0.12 0.39 -10000 0 -1 17 17
CCL4 -0.11 0.41 -10000 0 -1.1 18 18
HLA-A 0.005 0.097 -10000 0 -0.63 5 5
IL18/IL18R -0.064 0.25 -10000 0 -0.46 51 51
NOS2 -0.12 0.39 -10000 0 -0.81 39 39
IL12/IL12R/TYK2/JAK2/SPHK2 0.031 0.096 -10000 0 -0.38 1 1
IL1R1 -0.13 0.43 -10000 0 -1.1 22 22
IL4 0.018 0.055 -10000 0 -0.71 1 1
JAK2 0.006 0.1 -10000 0 -0.72 4 4
EntrezGene:6957 0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.003 0.2 -10000 0 -0.74 11 11
RAB7A -0.057 0.32 -10000 0 -0.83 14 14
lysosomal transport -0.051 0.31 -10000 0 -0.78 14 14
FOS -0.18 0.53 -10000 0 -1.3 39 39
STAT4 (dimer) -0.11 0.38 -10000 0 -0.88 28 28
STAT5A (dimer) -0.26 0.31 -10000 0 -0.82 38 38
GZMA -0.12 0.38 -10000 0 -0.89 29 29
GZMB -0.11 0.38 -10000 0 -0.98 22 22
HLX 0.017 0 -10000 0 -10000 0 0
LCK -0.12 0.41 -10000 0 -0.95 30 30
TCR/CD3/MHC II/CD4 -0.017 0.22 -10000 0 -0.65 17 17
IL2/IL2R -0.019 0.084 -10000 0 -0.41 7 7
MAPK14 -0.093 0.38 -10000 0 -0.9 27 27
CCR5 -0.17 0.52 -10000 0 -1.3 30 30
IL1B -0.12 0.28 -10000 0 -0.71 41 41
STAT6 -0.006 0.12 -10000 0 -0.25 1 1
STAT4 0.014 0.044 -10000 0 -0.64 1 1
STAT3 0.017 0 -10000 0 -10000 0 0
STAT1 -0.05 0.21 -10000 0 -0.72 20 20
NFKB1 0.017 0 -10000 0 -10000 0 0
NFKB2 0.014 0.05 -10000 0 -0.72 1 1
IL12B 0.013 0.071 -10000 0 -0.7 2 2
CD8A 0.002 0.003 -10000 0 -10000 0 0
CD8B 0.019 0.002 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.031 0.097 0.38 1 -10000 0 1
IL2RB 0.014 0.044 -10000 0 -0.64 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.095 0.35 -10000 0 -0.8 27 27
IL2RG 0.008 0.075 -10000 0 -0.64 3 3
IL12 0.007 0.11 -10000 0 -0.51 9 9
STAT5A 0.017 0 -10000 0 -10000 0 0
CD247 -0.014 0.14 -10000 0 -0.64 11 11
IL2 0.017 0 -10000 0 -10000 0 0
SPHK2 0.014 0.044 -10000 0 -0.64 1 1
FRAP1 0.017 0 -10000 0 -10000 0 0
IL12A -0.004 0.13 -10000 0 -0.71 7 7
IL12/IL12R/TYK2/JAK2 -0.13 0.44 -10000 0 -1 29 29
MAP2K3 -0.097 0.38 -10000 0 -0.91 27 27
RIPK2 -0.12 0.29 -10000 0 -0.72 42 42
MAP2K6 -0.11 0.39 -10000 0 -0.92 27 27
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.007 0.075 -10000 0 -0.63 3 3
IL18RAP -0.11 0.26 -10000 0 -0.64 43 43
IL12Rbeta1/TYK2 0.027 0.033 -10000 0 -10000 0 0
EOMES 0.023 0.066 -10000 0 -10000 0 0
STAT1 (dimer) -0.14 0.32 -10000 0 -0.74 29 29
T cell proliferation -0.085 0.3 -10000 0 -0.66 27 27
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.045 -10000 0 -0.64 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.18 0.26 -10000 0 -0.72 31 31
ATF2 -0.074 0.35 -10000 0 -0.83 25 25
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.07 0.3 -9999 0 -1 9 9
PCK1 -0.73 0.7 -9999 0 -1.3 132 132
HNF4A -0.083 0.31 -9999 0 -1.1 7 7
KCNJ11 -0.058 0.32 -9999 0 -1.1 7 7
AKT1 0.012 0.11 -9999 0 -10000 0 0
response to starvation -0.008 0.022 -9999 0 -10000 0 0
DLK1 -0.058 0.32 -9999 0 -1.1 7 7
NKX2-1 0.034 0.25 -9999 0 -0.77 6 6
ACADM -0.076 0.32 -9999 0 -1 12 12
TAT -0.083 0.24 -9999 0 -0.74 13 13
CEBPB -0.014 0.12 -9999 0 -0.72 6 6
CEBPA 0.011 0.013 -9999 0 -10000 0 0
TTR -0.8 0.67 -9999 0 -1.3 132 132
PKLR -0.081 0.31 -9999 0 -1 10 10
APOA1 -0.08 0.36 -9999 0 -1.2 10 10
CPT1C -0.075 0.31 -9999 0 -1.1 8 8
ALAS1 -0.006 0.16 -9999 0 -10000 0 0
TFRC -0.074 0.29 -9999 0 -0.98 8 8
FOXF1 -0.008 0.12 -9999 0 -0.64 7 7
NF1 0.027 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.02 0.057 -9999 0 -10000 0 0
CPT1A -0.071 0.31 -9999 0 -1.1 9 9
HMGCS1 -0.077 0.31 -9999 0 -1 9 9
NR3C1 -0.045 0.2 -9999 0 -0.62 24 24
CPT1B -0.068 0.3 -9999 0 -0.95 11 11
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.021 0.027 -9999 0 -10000 0 0
GCK -0.068 0.3 -9999 0 -1 8 8
CREB1 -0.095 0.11 -9999 0 -10000 0 0
IGFBP1 -0.088 0.25 -9999 0 -0.74 16 16
PDX1 -0.018 0.2 -9999 0 -0.81 4 4
UCP2 -0.068 0.3 -9999 0 -1 8 8
ALDOB -0.12 0.42 -9999 0 -1.1 24 24
AFP -0.12 0.16 -9999 0 -0.47 13 13
BDH1 -0.069 0.31 -9999 0 -1.1 8 8
HADH -0.058 0.32 -9999 0 -1.1 7 7
F2 -0.065 0.32 -9999 0 -1.1 7 7
HNF1A 0.02 0.056 -9999 0 -10000 0 0
G6PC -0.076 0.13 -9999 0 -10000 0 0
SLC2A2 -0.062 0.25 -9999 0 -0.77 5 5
INS 0.012 0.038 -9999 0 -10000 0 0
FOXA1 -0.16 0.29 -9999 0 -0.62 62 62
FOXA3 -0.093 0.16 -9999 0 -0.63 8 8
FOXA2 -0.074 0.38 -9999 0 -1.1 12 12
ABCC8 -0.11 0.42 -9999 0 -1.1 21 21
ALB -0.12 0.17 -9999 0 -0.53 11 11
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.017 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.12 0.13 -9999 0 -0.51 6 6
mol:DAG -0.098 0.18 -9999 0 -0.55 12 12
PLCG1 -0.1 0.18 -9999 0 -0.57 12 12
YES1 -0.1 0.17 -9999 0 -0.43 25 25
FZD3 -0.14 0.3 -9999 0 -0.72 47 47
FZD6 -0.029 0.18 -9999 0 -0.72 14 14
G protein -0.11 0.12 -9999 0 -0.55 3 3
MAP3K7 -0.064 0.16 -9999 0 -0.51 3 3
mol:Ca2+ -0.095 0.17 -9999 0 -0.53 12 12
mol:IP3 -0.098 0.18 -9999 0 -0.55 12 12
NLK 0.004 0.007 -9999 0 -10000 0 0
GNB1 0.017 0 -9999 0 -10000 0 0
CAMK2A -0.079 0.16 -9999 0 -0.49 12 12
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.12 0.18 -9999 0 -0.47 25 25
CSNK1A1 0.017 0 -9999 0 -10000 0 0
GNAS -0.1 0.17 -9999 0 -0.43 25 25
GO:0007205 -0.093 0.17 -9999 0 -0.52 12 12
WNT6 0.014 0.05 -9999 0 -0.72 1 1
WNT4 -0.01 0.13 -9999 0 -0.65 9 9
NFAT1/CK1 alpha -0.1 0.12 -9999 0 -0.54 3 3
GNG2 0.017 0 -9999 0 -10000 0 0
WNT5A -0.093 0.26 -9999 0 -0.72 33 33
WNT11 -0.13 0.3 -9999 0 -0.72 45 45
CDC42 -0.087 0.16 -9999 0 -0.5 6 6
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.002 0.031 -9999 0 -0.46 1 1
Necdin/E2F1 -0.13 0.23 -9999 0 -0.51 57 57
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.009 0.054 -9999 0 -0.39 1 1
NGF (dimer)/p75(NTR)/BEX1 -0.004 0.037 -9999 0 -0.4 2 2
NT-4/5 (dimer)/p75(NTR) 0 0 -9999 0 -10000 0 0
IKBKB 0.014 0.05 -9999 0 -0.72 1 1
AKT1 0.043 0 -9999 0 -10000 0 0
IKBKG 0.017 0 -9999 0 -10000 0 0
BDNF -0.036 0.19 -9999 0 -0.72 16 16
MGDIs/NGR/p75(NTR)/LINGO1 -0.029 0.12 -9999 0 -0.49 13 13
FURIN 0.017 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.035 0.12 -9999 0 -0.45 17 17
LINGO1 0.004 0.098 -9999 0 -0.72 4 4
Sortilin/TRAF6/NRIF -0.011 0.052 -9999 0 -10000 0 0
proBDNF (dimer) -0.036 0.19 -9999 0 -0.72 16 16
NTRK1 0.017 0 -9999 0 -10000 0 0
RTN4R -0.016 0.15 -9999 0 -0.72 10 10
neuron apoptosis 0.028 0.1 -9999 0 -10000 0 0
IRAK1 0.01 0.07 -9999 0 -0.72 2 2
SHC1 0.026 0 -9999 0 -10000 0 0
ARHGDIA 0.017 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.012 0.061 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.017 0.076 -9999 0 -0.35 11 11
MAGEH1 -0.012 0.14 -9999 0 -0.64 10 10
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.076 0.15 -9999 0 -0.36 47 47
Mammalian IAPs/DIABLO -0.02 0.084 -9999 0 -0.42 3 3
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.014 0.05 -9999 0 -0.72 1 1
APP 0.017 0 -9999 0 -10000 0 0
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.017 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI 0 0 -9999 0 -10000 0 0
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest 0 0.029 -9999 0 -0.34 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.009 0.1 -9999 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0 0 -9999 0 -10000 0 0
NCSTN 0.017 0 -9999 0 -10000 0 0
mol:GTP -0.11 0.18 -9999 0 -0.4 60 60
PSENEN 0.017 0 -9999 0 -10000 0 0
mol:ceramide 0.033 0.026 -9999 0 -0.35 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.002 0.092 -9999 0 -0.39 2 2
p75(NTR)/beta APP 0 0 -9999 0 -10000 0 0
BEX1 0.011 0.062 -9999 0 -0.64 2 2
mol:GDP 0.012 0 -9999 0 -10000 0 0
NGF (dimer) -0.41 0.068 -9999 0 -0.42 216 216
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.026 0.11 -9999 0 -0.82 1 1
PIK3R1 0.017 0 -9999 0 -10000 0 0
RAC1/GTP 0 0 -9999 0 -10000 0 0
MYD88 0.017 0 -9999 0 -10000 0 0
CHUK 0.017 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.11 0.18 -9999 0 -0.4 60 60
RHOB -0.03 0.18 -9999 0 -0.72 14 14
RHOA 0.017 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.036 0.14 -9999 0 -0.54 15 15
NT3 (dimer) 0.01 0.07 -9999 0 -0.72 2 2
TP53 0.014 0.13 -9999 0 -10000 0 0
PRDM4 0.033 0.026 -9999 0 -0.35 1 1
BDNF (dimer) -0.81 0.16 -9999 0 -0.85 202 202
PIK3CA 0.017 0 -9999 0 -10000 0 0
SORT1 0.014 0.044 -9999 0 -0.64 1 1
activation of caspase activity -0.009 0.054 -9999 0 -0.38 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.002 0.024 -9999 0 -10000 0 0
RHOC 0.017 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 0.054 0.089 -9999 0 -10000 0 0
DIABLO 0.017 0 -9999 0 -10000 0 0
SMPD2 0.033 0.026 -9999 0 -0.35 1 1
APH1B 0.014 0.05 -9999 0 -0.72 1 1
APH1A -0.004 0.12 -9999 0 -0.65 7 7
proNGF (dimer)/p75(NTR)/Sortilin -0.002 0.027 -9999 0 -0.4 1 1
PSEN1 0.017 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.005 0.051 -9999 0 -0.54 2 2
NT3 (dimer)/p75(NTR) -0.005 0.051 -9999 0 -0.54 2 2
MAPK8 0.059 0.081 -9999 0 -10000 0 0
MAPK9 0.059 0.081 -9999 0 -10000 0 0
APAF1 0.01 0.07 -9999 0 -0.72 2 2
NTF3 0.01 0.07 -9999 0 -0.72 2 2
NTF4 0 0 -9999 0 -10000 0 0
NDN -0.12 0.27 -9999 0 -0.64 47 47
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.1 0.16 -9999 0 -0.67 4 4
p75 CTF/Sortilin/TRAF6/NRIF -0.002 0.023 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.11 0.18 -9999 0 -0.39 60 60
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.029 0.099 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.031 0.11 -9999 0 -10000 0 0
PRKACB -0.16 0.29 -9999 0 -0.64 60 60
proBDNF (dimer)/p75 ECD -0.039 0.14 -9999 0 -0.54 16 16
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.02 0.15 -9999 0 -0.66 12 12
BIRC2 0.017 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.12 0.17 -9999 0 -0.52 23 23
BAD 0.066 0.082 -9999 0 -10000 0 0
RIPK2 -0.12 0.29 -9999 0 -0.72 42 42
NGFR 0.017 0 -9999 0 -10000 0 0
CYCS 0.038 0.045 -9999 0 -10000 0 0
ADAM17 0.017 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.079 0.16 -9999 0 -0.42 42 42
BCL2L11 0.066 0.082 -9999 0 -10000 0 0
BDNF (dimer)/p75(NTR) -0.039 0.14 -9999 0 -0.54 16 16
PI3K 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.003 0.037 -9999 0 -0.39 2 2
NDNL2 0.014 0.05 -9999 0 -0.72 1 1
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
PRKCI -0.003 0.12 -9999 0 -0.72 6 6
NGF (dimer)/p75(NTR) 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.003 0.037 -9999 0 -0.39 2 2
TRAF6 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 0.014 0.099 -9999 0 -0.36 1 1
SQSTM1 0.017 0 -9999 0 -10000 0 0
NGFRAP1 0.005 0.087 -9999 0 -0.64 4 4
CASP3 0.066 0.077 -9999 0 -10000 0 0
E2F1 -0.03 0.18 -9999 0 -0.72 14 14
CASP9 0.017 0 -9999 0 -10000 0 0
IKK complex -0.022 0.052 -9999 0 -0.46 1 1
NGF (dimer)/TRKA 0 0 -9999 0 -10000 0 0
MMP7 -0.7 0.12 -9999 0 -0.72 216 216
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.001 0.022 -9999 0 -10000 0 0
MMP3 -0.68 0.18 -9999 0 -0.72 208 208
APAF-1/Caspase 9 -0.018 0.064 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.059 0.22 -10000 0 -0.72 22 22
GNB1/GNG2 -0.093 0.063 -10000 0 -0.21 11 11
AKT1 -0.052 0.089 -10000 0 -10000 0 0
EGF -0.18 0.31 -10000 0 -0.68 64 64
mol:TXA2 -0.001 0 -10000 0 -10000 0 0
FGR -0.12 0.095 -10000 0 -10000 0 0
mol:Ca2+ -0.092 0.12 -10000 0 -0.32 11 11
LYN -0.12 0.095 -10000 0 -10000 0 0
RhoA/GTP -0.041 0.039 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.097 0.14 -10000 0 -0.37 5 5
GNG2 0.017 0 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.034 0.11 -10000 0 -0.56 6 6
G beta5/gamma2 -0.12 0.087 -10000 0 -0.28 14 14
PRKCH -0.099 0.14 -10000 0 -0.43 8 8
DNM1 0.01 0.07 -10000 0 -0.72 2 2
TXA2/TP beta/beta Arrestin3 -0.031 0.027 -10000 0 -0.26 1 1
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.49 0.27 -10000 0 -0.64 174 174
G12 family/GTP -0.11 0.096 -10000 0 -0.31 11 11
ADRBK1 0.017 0 -10000 0 -10000 0 0
ADRBK2 0.017 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.12 0.1 0.29 26 -10000 0 26
mol:NADP 0.013 0.049 -10000 0 -0.72 1 1
RAB11A 0.017 0 -10000 0 -10000 0 0
PRKG1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.12 0.15 -10000 0 -0.4 13 13
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.15 0.19 -10000 0 -0.53 16 16
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.2 0.17 -10000 0 -0.45 55 55
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.14 0.13 -10000 0 -0.45 19 19
RHOA 0.017 0 -10000 0 -10000 0 0
PTGIR 0.017 0 -10000 0 -10000 0 0
PRKCB1 -0.17 0.18 -10000 0 -0.46 34 34
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0.049 -10000 0 -0.72 1 1
TXA2/TXA2-R family -0.15 0.2 -10000 0 -0.55 13 13
LCK -0.12 0.1 -10000 0 -0.48 2 2
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.17 0.091 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma -0.027 0.038 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.17 0.091 -10000 0 -10000 0 0
MAPK14 -0.058 0.099 -10000 0 -10000 0 0
TGM2/GTP -0.14 0.18 -10000 0 -0.48 14 14
MAPK11 -0.059 0.1 -10000 0 -0.41 1 1
ARHGEF1 -0.045 0.077 -10000 0 -10000 0 0
GNAI2 0.017 0 -10000 0 -10000 0 0
JNK cascade -0.12 0.15 -10000 0 -0.4 13 13
RAB11/GDP 0.018 0.001 -10000 0 -10000 0 0
ICAM1 -0.083 0.13 -10000 0 -0.39 9 9
cAMP biosynthetic process -0.12 0.14 -10000 0 -0.38 13 13
Gq family/GTP/EBP50 0.003 0.085 -10000 0 -0.28 10 10
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.12 0.095 -10000 0 -10000 0 0
GNB5 0.007 0.085 -10000 0 -0.72 3 3
GNB1 0.017 0 -10000 0 -10000 0 0
EGF/EGFR -0.13 0.11 -10000 0 -0.41 5 5
VCAM1 -0.077 0.12 -10000 0 -0.43 5 5
TP beta/Gq family/GDP/G beta5/gamma2 -0.034 0.11 -10000 0 -0.56 6 6
platelet activation -0.08 0.13 -10000 0 -0.34 4 4
PGI2/IP 0 0 -10000 0 -10000 0 0
PRKACA -0.22 0.13 -10000 0 -0.3 174 174
Gq family/GDP/G beta5/gamma2 -0.052 0.11 -10000 0 -0.45 11 11
TXA2/TP beta/beta Arrestin2 -0.019 0.03 -10000 0 -0.31 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.2 0.13 -10000 0 -10000 0 0
mol:DAG -0.12 0.16 -10000 0 -0.44 14 14
EGFR 0.002 0.099 -10000 0 -0.65 5 5
TXA2/TP alpha -0.16 0.19 -10000 0 -0.52 15 15
Gq family/GTP 0.001 0.077 -10000 0 -0.25 14 14
YES1 -0.12 0.095 -10000 0 -10000 0 0
GNAI2/GTP -0.15 0.081 -10000 0 -10000 0 0
PGD2/DP -0.37 0.2 -10000 0 -0.48 174 174
SLC9A3R1 0.005 0.087 -10000 0 -0.64 4 4
FYN -0.12 0.098 -10000 0 -0.46 1 1
mol:NO 0.013 0.049 -10000 0 -0.72 1 1
GNA15 -0.006 0.13 -10000 0 -0.72 7 7
PGK/cGMP -0.002 0.031 -10000 0 -0.47 1 1
RhoA/GDP 0.018 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.2 0.14 -10000 0 -0.58 16 16
NOS3 0.013 0.05 -10000 0 -0.72 1 1
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.097 0.14 -10000 0 -0.38 8 8
PRKCB -0.1 0.14 -10000 0 -0.36 14 14
PRKCE -0.095 0.14 -10000 0 -0.38 7 7
PRKCD -0.098 0.14 -10000 0 -0.4 5 5
PRKCG -0.11 0.15 -10000 0 -0.44 11 11
muscle contraction -0.14 0.18 -10000 0 -0.5 13 13
PRKCZ -0.1 0.14 -10000 0 -0.36 13 13
ARR3 0.017 0 -10000 0 -10000 0 0
TXA2/TP beta -0.18 0.092 -10000 0 -10000 0 0
PRKCQ -0.1 0.14 -10000 0 -0.4 8 8
MAPKKK cascade -0.13 0.17 -10000 0 -0.48 13 13
SELE -0.1 0.15 -10000 0 -0.36 33 33
TP beta/GNAI2/GDP/G beta/gamma -0.16 0.087 -10000 0 -10000 0 0
ROCK1 0.017 0 -10000 0 -10000 0 0
GNA14 -0.01 0.13 -10000 0 -0.64 9 9
chemotaxis -0.16 0.21 -10000 0 -0.6 14 14
GNA12 0.017 0 -10000 0 -10000 0 0
GNA13 0.017 0 -10000 0 -10000 0 0
GNA11 -0.001 0.11 -10000 0 -0.64 6 6
Rac1/GTP 0 0 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.023 0.087 -9999 0 -0.54 4 4
alphaM/beta2 Integrin/GPIbA -0.019 0.074 -9999 0 -0.58 2 2
alphaM/beta2 Integrin/proMMP-9 -0.034 0.11 -9999 0 -0.46 13 13
PLAUR 0.014 0.05 -9999 0 -0.72 1 1
HMGB1 0 0.054 -9999 0 -0.74 1 1
alphaM/beta2 Integrin/Talin -0.019 0.074 -9999 0 -0.44 6 6
AGER 0.003 0.02 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
SELPLG 0.008 0.075 -9999 0 -0.64 3 3
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.071 0.1 -9999 0 -0.8 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.006 0.13 -9999 0 -0.71 7 7
CYR61 -0.043 0.2 -9999 0 -0.72 18 18
TLN1 0.017 0 -9999 0 -10000 0 0
Rap1/GTP -0.033 0.074 -9999 0 -0.47 2 2
RHOA 0.017 0 -9999 0 -10000 0 0
P-selectin oligomer -0.068 0.22 -9999 0 -0.63 29 29
MYH2 0.002 0.14 -9999 0 -0.55 3 3
MST1R 0.017 0 -9999 0 -10000 0 0
leukocyte activation during inflammatory response -0.008 0.063 -9999 0 -0.64 1 1
APOB 0.017 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.01 0.07 -9999 0 -0.72 2 2
JAM3 0.017 0 -9999 0 -10000 0 0
GP1BA 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.023 0.087 -9999 0 -0.46 8 8
alphaM/beta2 Integrin -0.002 0.12 -9999 0 -0.48 4 4
JAM3 homodimer 0.017 0 -9999 0 -10000 0 0
ICAM2 0.005 0.09 -9999 0 -0.66 4 4
ICAM1 -0.023 0.17 -9999 0 -0.72 12 12
phagocytosis triggered by activation of immune response cell surface activating receptor -0.002 0.12 -9999 0 -0.48 4 4
cell adhesion -0.019 0.074 -9999 0 -0.57 2 2
NFKB1 -0.071 0.18 -9999 0 -0.8 2 2
THY1 -0.076 0.24 -9999 0 -0.72 28 28
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.012 0.077 -9999 0 -0.57 2 2
IL6 -0.21 0.32 -9999 0 -0.55 104 104
ITGB2 -0.011 0.096 -9999 0 -0.63 5 5
elevation of cytosolic calcium ion concentration -0.14 0.21 -9999 0 -0.46 53 53
alphaM/beta2 Integrin/JAM2/JAM3 -0.22 0.2 -9999 0 -0.74 6 6
JAM2 -0.36 0.32 -9999 0 -0.64 130 130
alphaM/beta2 Integrin/ICAM1 -0.044 0.15 -9999 0 -0.76 3 3
alphaM/beta2 Integrin/uPA/Plg -0.14 0.2 -9999 0 -0.46 53 53
RhoA/GTP 0.002 0.12 -9999 0 -0.43 4 4
positive regulation of phagocytosis -0.054 0.12 -9999 0 -0.68 5 5
Ron/MSP -0.024 0.11 -9999 0 -0.54 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.21 -9999 0 -0.46 53 53
alphaM/beta2 Integrin/uPAR -0.021 0.081 -9999 0 -0.55 3 3
PLAU -0.19 0.33 -9999 0 -0.72 63 63
PLAT 0.011 0.066 -9999 0 -0.68 2 2
actin filament polymerization 0.003 0.13 -9999 0 -0.52 3 3
MST1 -0.016 0.15 -9999 0 -0.72 10 10
alphaM/beta2 Integrin/lipoprotein(a) -0.008 0.064 -9999 0 -0.65 1 1
TNF -0.053 0.17 -9999 0 -0.87 1 1
RAP1B 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.16 0.22 -9999 0 -0.5 65 65
fibrinolysis -0.13 0.2 -9999 0 -0.45 53 53
HCK -0.045 0.19 -9999 0 -0.64 21 21
dendritic cell antigen processing and presentation -0.002 0.12 -9999 0 -0.48 4 4
VTN 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.058 0.15 -9999 0 -0.5 20 20
LPA 0.017 0 -9999 0 -10000 0 0
LRP1 0.017 0 -9999 0 -10000 0 0
cell migration -0.026 0.12 -9999 0 -0.59 7 7
FN1 -0.07 0.24 -9999 0 -0.72 26 26
alphaM/beta2 Integrin/Thy1 -0.079 0.17 -9999 0 -0.49 30 30
MPO -0.03 0.18 -9999 0 -0.72 14 14
KNG1 -0.004 0.12 -9999 0 -0.65 7 7
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 0.013 0.12 -9999 0 -0.42 2 2
ELA2 0.017 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
CTGF 0.01 0.07 -9999 0 -0.72 2 2
alphaM/beta2 Integrin/Hck -0.055 0.15 -9999 0 -0.75 6 6
ITGAM -0.003 0.063 -9999 0 -0.63 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.059 0.16 -9999 0 -0.76 5 5
HP 0.017 0 -9999 0 -10000 0 0
leukocyte adhesion -0.25 0.19 -9999 0 -0.7 11 11
SELP -0.068 0.22 -9999 0 -0.64 29 29
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.011 0.066 -10000 0 -0.68 2 2
EPHB2 -0.005 0.12 -10000 0 -0.71 6 6
EFNB1 0.022 0.054 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.19 -10000 0 -0.7 7 7
Ephrin B2/EPHB1-2 -0.17 0.22 -10000 0 -0.44 84 84
neuron projection morphogenesis -0.14 0.18 -10000 0 -0.66 7 7
Ephrin B1/EPHB1-2/Tiam1 -0.16 0.21 -10000 0 -0.76 7 7
DNM1 0.009 0.07 -10000 0 -0.72 2 2
cell-cell signaling -0.003 0.004 -10000 0 -10000 0 0
MAP2K4 -0.065 0.15 -10000 0 -0.75 5 5
YES1 -0.094 0.18 -10000 0 -1 4 4
Ephrin B1/EPHB1-2/NCK2 -0.15 0.2 -10000 0 -0.77 5 5
PI3K -0.059 0.15 -10000 0 -0.81 4 4
mol:GDP -0.16 0.21 -10000 0 -0.74 7 7
ITGA2B 0.017 0 -10000 0 -10000 0 0
endothelial cell proliferation -0.084 0.18 -10000 0 -0.48 39 39
FYN -0.095 0.18 -10000 0 -0.91 5 5
MAP3K7 -0.082 0.15 -10000 0 -0.85 4 4
FGR -0.096 0.18 -10000 0 -1 4 4
TIAM1 0.011 0.062 -10000 0 -0.64 2 2
PIK3R1 0.017 0 -10000 0 -10000 0 0
RGS3 0.017 0 -10000 0 -10000 0 0
cell adhesion -0.034 0.14 -10000 0 -0.73 4 4
LYN -0.094 0.18 -10000 0 -1 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.089 0.17 -10000 0 -0.97 4 4
Ephrin B1/EPHB1-2 -0.099 0.16 -10000 0 -0.92 4 4
SRC -0.096 0.18 -10000 0 -1 4 4
ITGB3 0.017 0 -10000 0 -10000 0 0
EPHB1 -0.26 0.36 -10000 0 -0.72 82 82
EPHB4 -0.11 0.28 -10000 0 -0.72 38 38
RAC1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.084 0.18 -10000 0 -0.48 39 39
alphaIIb/beta3 Integrin 0 0 -10000 0 -10000 0 0
BLK -0.14 0.2 -10000 0 -0.56 21 21
HCK -0.11 0.19 -10000 0 -0.78 8 8
regulation of stress fiber formation 0.15 0.2 0.76 5 -10000 0 5
MAPK8 -0.051 0.14 -10000 0 -0.7 5 5
Ephrin B1/EPHB1-2/RGS3 -0.15 0.2 -10000 0 -0.77 5 5
endothelial cell migration -0.14 0.2 -10000 0 -0.49 41 41
NCK2 0.017 0 -10000 0 -10000 0 0
PTPN13 -0.2 0.32 -10000 0 -0.68 70 70
regulation of focal adhesion formation 0.15 0.2 0.76 5 -10000 0 5
chemotaxis 0.15 0.2 0.76 5 -10000 0 5
PIK3CA 0.017 0 -10000 0 -10000 0 0
Rac1/GTP -0.14 0.19 -10000 0 -0.69 7 7
angiogenesis -0.099 0.16 -10000 0 -0.91 4 4
LCK -0.097 0.18 -10000 0 -1 4 4
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.068 0.18 -9999 0 -0.56 21 21
PDGFRB 0.013 0.007 -9999 0 -10000 0 0
SPHK1 -0.048 0.087 -9999 0 -0.3 18 18
mol:S1P -0.087 0.14 -9999 0 -0.42 24 24
S1P1/S1P/Gi -0.086 0.2 -9999 0 -0.55 15 15
GNAO1 0.012 0.008 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.13 0.16 -9999 0 -0.58 12 12
PLCG1 -0.096 0.21 -9999 0 -0.57 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.007 -9999 0 -10000 0 0
GNAI2 0.012 0.008 -9999 0 -10000 0 0
GNAI3 0.012 0.008 -9999 0 -10000 0 0
GNAI1 -0.073 0.22 -9999 0 -0.64 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.052 0.23 -9999 0 -0.69 19 19
S1P1/S1P -0.14 0.22 -9999 0 -0.68 21 21
negative regulation of cAMP metabolic process -0.083 0.19 -9999 0 -0.53 15 15
MAPK3 -0.1 0.22 -9999 0 -0.57 15 15
calcium-dependent phospholipase C activity -0.003 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.011 0.043 -9999 0 -10000 0 0
PLCB2 -0.078 0.21 -9999 0 -0.58 21 21
RAC1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.11 0.18 -9999 0 -0.54 21 21
receptor internalization -0.12 0.2 -9999 0 -0.62 21 21
PTGS2 -0.14 0.28 -9999 0 -0.64 19 19
Rac1/GTP -0.11 0.18 -9999 0 -0.54 21 21
RHOA 0.017 0 -9999 0 -10000 0 0
VEGFA -0.059 0.22 -9999 0 -0.73 21 21
negative regulation of T cell proliferation -0.083 0.19 -9999 0 -0.53 15 15
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.012 0.008 -9999 0 -10000 0 0
MAPK1 -0.1 0.22 -9999 0 -0.56 14 14
S1P1/S1P/PDGFB-D/PDGFRB -0.1 0.25 -9999 0 -0.7 21 21
ABCC1 -0.061 0.23 -9999 0 -0.73 23 23
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.007 0.051 -9999 0 -0.4 3 3
RGS9BP -0.003 0.12 -9999 0 -0.72 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.14 0.2 -9999 0 -0.41 77 77
mol:ADP 0.013 0.038 -9999 0 -0.55 1 1
GNAT2 0.007 0.085 -9999 0 -0.72 3 3
RGS9-1/Gbeta5/R9AP -0.15 0.2 -9999 0 -0.54 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.008 0.06 -9999 0 -0.45 4 4
GRK7 0.014 0.05 -9999 0 -0.72 1 1
CNGB3 -0.007 0.13 -9999 0 -0.72 7 7
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.1 0.19 -9999 0 -0.47 7 7
Cone PDE6 -0.12 0.16 -9999 0 -0.71 2 2
Cone Metarhodopsin II -0.002 0.029 -9999 0 -0.44 1 1
Na + (4 Units) -0.12 0.17 -9999 0 -0.46 7 7
GNAT2/GDP -0.13 0.17 -9999 0 -0.72 3 3
GNB5 0.007 0.085 -9999 0 -0.72 3 3
mol:GMP (4 units) 0.025 0.065 -9999 0 -0.4 5 5
Cone Transducin -0.007 0.054 -9999 0 -0.42 3 3
SLC24A2 0.017 0 -9999 0 -10000 0 0
GNB3/GNGT2 -0.002 0.031 -9999 0 -0.46 1 1
GNB3 0.017 0 -9999 0 -10000 0 0
GNAT2/GTP -0.007 0.064 -9999 0 -0.55 3 3
CNGA3 -0.19 0.3 -9999 0 -0.64 71 71
ARR3 0.017 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.14 0.2 -9999 0 -0.41 77 77
mol:Pi -0.15 0.2 -9999 0 -0.53 9 9
Cone CNG Channel -0.12 0.16 -9999 0 -0.66 2 2
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.017 0 -9999 0 -10000 0 0
RGS9 -0.2 0.31 -9999 0 -0.64 74 74
PDE6C 0.014 0.05 -9999 0 -0.72 1 1
GNGT2 0.014 0.044 -9999 0 -0.64 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.014 0.044 -9999 0 -0.64 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.014 0.05 -10000 0 -0.72 1 1
NFATC1 0.058 0.046 -10000 0 -10000 0 0
NFATC2 0.035 0.047 -10000 0 -10000 0 0
NFATC3 0.021 0.002 -10000 0 -10000 0 0
YWHAE 0.014 0.05 -10000 0 -0.72 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.1 0.14 -10000 0 -0.45 9 9
Exportin 1/Ran/NUP214 -0.002 0.031 -10000 0 -0.46 1 1
mol:DAG 0.001 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.092 0.091 -10000 0 -0.46 4 4
BCL2/BAX -0.3 0.22 -10000 0 -0.46 146 146
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.002 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.002 -10000 0 -10000 0 0
BAX 0.014 0.05 -10000 0 -0.72 1 1
MAPK14 0.017 0.002 -10000 0 -10000 0 0
BAD 0.017 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.089 0.14 -10000 0 -0.42 9 9
Calcineurin A alpha-beta B1/BCL2 -0.41 0.31 -10000 0 -0.63 145 145
FKBP8 0.017 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.088 0.14 0.41 9 -10000 0 9
KPNB1 -0.003 0.12 -10000 0 -0.72 6 6
KPNA2 -0.013 0.15 -10000 0 -0.72 9 9
XPO1 0.017 0 -10000 0 -10000 0 0
SFN 0.011 0.062 -10000 0 -0.64 2 2
MAP3K8 -0.086 0.26 -10000 0 -0.72 31 31
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.005 0.027 -10000 0 -10000 0 0
CABIN1 -0.1 0.14 -10000 0 -0.45 9 9
CALM1 0.018 0.002 -10000 0 -10000 0 0
RAN 0.014 0.05 -10000 0 -0.72 1 1
MAP3K1 0.017 0 -10000 0 -10000 0 0
CAMK4 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.002 -10000 0 -10000 0 0
MAPK3 0.011 0.062 -10000 0 -0.64 2 2
YWHAH 0.017 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.008 0.061 -10000 0 -0.46 4 4
YWHAB 0.017 0 -10000 0 -10000 0 0
MAPK8 0.018 0.002 -10000 0 -10000 0 0
MAPK9 0.017 0 -10000 0 -10000 0 0
YWHAG 0.017 0 -10000 0 -10000 0 0
FKBP1A 0.017 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.023 -10000 0 -10000 0 0
PRKCH 0.008 0.075 -10000 0 -0.64 3 3
CABIN1/Cbp/p300 0 0 -10000 0 -10000 0 0
CASP3 0.014 0.044 -10000 0 -0.63 1 1
PIM1 0.017 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.09 0.066 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.057 0.024 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.017 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.029 0.003 -10000 0 -10000 0 0
BAD/BCL-XL -0.002 0.036 -10000 0 -0.54 1 1
PRKCD 0.017 0 -10000 0 -10000 0 0
NUP214 0.017 0 -10000 0 -10000 0 0
PRKCZ 0.001 0.001 -10000 0 -10000 0 0
PRKCA 0.014 0.05 -10000 0 -0.72 1 1
PRKCG 0.004 0.098 -10000 0 -0.72 4 4
PRKCQ 0 0.11 -10000 0 -0.72 5 5
FKBP38/BCL2 -0.3 0.22 -10000 0 -0.46 145 145
EP300 0.018 0.001 -10000 0 -10000 0 0
PRKCB1 -0.36 0.32 -10000 0 -0.64 127 127
CSNK2A1 0.017 0 -10000 0 -10000 0 0
NFATc/JNK1 0.066 0.045 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.028 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0 0 -10000 0 -10000 0 0
NFATc/ERK1 0.062 0.054 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.093 0.091 -10000 0 -0.46 4 4
NR4A1 0.073 0.072 -10000 0 -0.57 2 2
GSK3B 0.014 0.05 -10000 0 -0.72 1 1
positive T cell selection 0.021 0.002 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.008 0.021 -10000 0 -10000 0 0
RCH1/ KPNB1 -0.036 0.14 -10000 0 -0.57 14 14
YWHAQ 0.017 0 -10000 0 -10000 0 0
PRKACA 0.017 0.002 -10000 0 -10000 0 0
AKAP5 0.005 0.087 -10000 0 -0.64 4 4
MEF2D 0.018 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.017 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.066 0.045 -10000 0 -10000 0 0
CREBBP 0.018 0.001 -10000 0 -10000 0 0
BCL2 -0.41 0.31 -10000 0 -0.64 145 145
EPHB forward 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
Ephrin A5/EPHB2 -0.014 0.078 -10000 0 -0.45 7 7
cell-cell adhesion 0.17 0.2 0.63 21 -10000 0 21
Ephrin B/EPHB2/RasGAP -0.016 0.076 -10000 0 -10000 0 0
ITSN1 0.017 0 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
SHC1 0.017 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.052 0.14 -10000 0 -0.46 25 25
Ephrin B1/EPHB1 -0.17 0.23 -10000 0 -0.47 82 82
HRAS/GDP -0.16 0.2 -10000 0 -0.63 19 19
Ephrin B/EPHB1/GRB7 -0.16 0.2 -10000 0 -0.78 5 5
Endophilin/SYNJ1 0.038 0.073 -10000 0 -10000 0 0
KRAS 0.017 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.14 0.19 -10000 0 -0.78 1 1
endothelial cell migration -0.068 0.15 -10000 0 -0.39 38 38
GRB2 0.017 0 -10000 0 -10000 0 0
GRB7 -0.01 0.14 -10000 0 -0.72 8 8
PAK1 0.048 0.074 -10000 0 -10000 0 0
HRAS 0.017 0 -10000 0 -10000 0 0
RRAS 0.038 0.074 -10000 0 -10000 0 0
DNM1 0.01 0.07 -10000 0 -0.72 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.1 0.2 -10000 0 -0.68 2 2
lamellipodium assembly -0.17 0.2 -10000 0 -0.63 21 21
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.042 0.13 -10000 0 -0.42 1 1
PIK3R1 0.017 0 -10000 0 -10000 0 0
EPHB2 -0.003 0.12 -10000 0 -0.71 6 6
EPHB3 -0.065 0.23 -10000 0 -0.71 25 25
EPHB1 -0.26 0.36 -10000 0 -0.72 82 82
EPHB4 -0.11 0.28 -10000 0 -0.72 38 38
mol:GDP -0.14 0.2 -10000 0 -0.59 19 19
Ephrin B/EPHB2 -0.013 0.069 -10000 0 -10000 0 0
Ephrin B/EPHB3 -0.046 0.12 -10000 0 -10000 0 0
JNK cascade -0.12 0.23 -10000 0 -0.75 7 7
Ephrin B/EPHB1 -0.15 0.19 -10000 0 -0.79 1 1
RAP1/GDP -0.11 0.18 -10000 0 -0.51 18 18
EFNB2 0.011 0.066 -10000 0 -0.68 2 2
EFNB3 0.017 0 -10000 0 -10000 0 0
EFNB1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.17 0.22 -10000 0 -0.44 83 83
RAP1B 0.017 0 -10000 0 -10000 0 0
RAP1A 0.017 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.16 -10000 0 -0.62 5 5
Rap1/GTP -0.12 0.16 -10000 0 -0.6 6 6
axon guidance -0.014 0.078 -10000 0 -0.44 7 7
MAPK3 -0.02 0.12 -10000 0 -10000 0 0
MAPK1 -0.018 0.12 -10000 0 -0.5 1 1
Rac1/GDP -0.09 0.21 -10000 0 -0.54 18 18
actin cytoskeleton reorganization -0.13 0.16 -10000 0 -0.48 23 23
CDC42/GDP -0.09 0.21 -10000 0 -0.54 18 18
PI3K -0.069 0.15 -10000 0 -0.4 38 38
EFNA5 0.014 0.044 -10000 0 -0.64 1 1
Ephrin B2/EPHB4 -0.084 0.18 -10000 0 -0.48 39 39
Ephrin B/EPHB2/Intersectin/N-WASP 0.04 0.054 -10000 0 -10000 0 0
CDC42 0.017 0 -10000 0 -10000 0 0
RAS family/GTP -0.12 0.16 -10000 0 -0.6 7 7
PTK2 0.035 0.07 -10000 0 -0.71 1 1
MAP4K4 -0.12 0.23 -10000 0 -0.76 7 7
SRC 0.017 0 -10000 0 -10000 0 0
KALRN 0.017 0 -10000 0 -10000 0 0
Intersectin/N-WASP -0.002 0.031 -10000 0 -0.46 1 1
neuron projection morphogenesis -0.066 0.19 -10000 0 -0.57 2 2
MAP2K1 -0.029 0.12 -10000 0 -10000 0 0
WASL 0.014 0.044 -10000 0 -0.64 1 1
Ephrin B1/EPHB1-2/NCK1 -0.16 0.21 -10000 0 -0.82 4 4
cell migration -0.02 0.13 -10000 0 -10000 0 0
NRAS 0.007 0.085 -10000 0 -0.72 3 3
SYNJ1 0.038 0.074 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
TF 0.048 0.071 -10000 0 -10000 0 0
HRAS/GTP -0.13 0.17 -10000 0 -0.66 5 5
Ephrin B1/EPHB1-2 -0.17 0.22 -10000 0 -0.44 83 83
cell adhesion mediated by integrin -0.012 0.076 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
mol:GTP -0.14 0.18 -10000 0 -0.72 5 5
RAC1-CDC42/GTP -0.15 0.18 -10000 0 -0.62 13 13
RASA1 0.01 0.07 -10000 0 -0.72 2 2
RAC1-CDC42/GDP -0.11 0.18 -10000 0 -0.51 18 18
ruffle organization -0.13 0.24 -10000 0 -0.64 22 22
NCK1 0.017 0 -10000 0 -10000 0 0
receptor internalization 0.044 0.08 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN -0.013 0.067 -10000 0 -10000 0 0
ROCK1 -0.015 0.14 -10000 0 -0.41 25 25
RAS family/GDP -0.12 0.14 -10000 0 -0.45 20 20
Rac1/GTP -0.18 0.22 -10000 0 -0.69 21 21
Ephrin B/EPHB1/Src/Paxillin -0.047 0.13 -10000 0 -0.42 1 1
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.014 0.086 -9999 0 -0.42 4 4
STMN1 0.03 0.039 -9999 0 -0.55 1 1
Aurora B/RasGAP/Survivin -0.033 0.16 -9999 0 -0.47 24 24
Chromosomal passenger complex/Cul3 protein complex -0.066 0.15 -9999 0 -0.45 14 14
BIRC5 -0.062 0.23 -9999 0 -0.73 23 23
DES -0.032 0.15 -9999 0 -0.67 11 11
Aurora C/Aurora B/INCENP 0.013 0.054 -9999 0 -0.42 3 3
Aurora B/TACC1 0.015 0.015 -9999 0 -10000 0 0
Aurora B/PP2A 0.016 0.016 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.02 0.029 -9999 0 -0.23 3 3
mitotic metaphase/anaphase transition 0.003 0.006 -9999 0 -10000 0 0
NDC80 0.027 0.055 -9999 0 -0.55 2 2
Cul3 protein complex -0.14 0.19 -9999 0 -0.4 76 76
KIF2C -0.03 0.093 -9999 0 -0.28 18 18
PEBP1 0.012 0.008 -9999 0 -10000 0 0
KIF20A -0.071 0.24 -9999 0 -0.72 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.011 0.056 -9999 0 -0.55 2 2
SEPT1 0.017 0 -9999 0 -10000 0 0
SMC2 -0.023 0.17 -9999 0 -0.72 12 12
SMC4 0.007 0.085 -9999 0 -0.72 3 3
NSUN2/NPM1/Nucleolin 0.02 0.049 -9999 0 -10000 0 0
PSMA3 0.017 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.001 0.005 -9999 0 -10000 0 0
H3F3B 0.025 0.003 -9999 0 -10000 0 0
AURKB 0.021 0.008 -9999 0 -10000 0 0
AURKC 0.017 0 -9999 0 -10000 0 0
CDCA8 0.007 0.071 -9999 0 -0.74 2 2
cytokinesis -0.09 0.17 -9999 0 -0.57 18 18
Aurora B/Septin1 -0.073 0.16 -9999 0 -0.55 15 15
AURKA -0.084 0.25 -9999 0 -0.72 30 30
INCENP 0.003 0.087 -9999 0 -0.74 3 3
KLHL13 -0.21 0.32 -9999 0 -0.65 76 76
BUB1 -0.27 0.36 -9999 0 -0.72 85 85
hSgo1/Aurora B/Survivin -0.049 0.18 -9999 0 -0.48 30 30
EVI5 0.017 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.12 0.22 -9999 0 -0.6 34 34
SGOL1 -0.02 0.16 -9999 0 -0.72 11 11
CENPA -0.058 0.14 -9999 0 -0.36 27 27
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.016 0.016 -9999 0 -10000 0 0
NCAPD2 0.01 0.07 -9999 0 -0.72 2 2
Aurora B/PP1-gamma 0.016 0.016 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
NCAPH -0.01 0.14 -9999 0 -0.72 8 8
NPM1 0.004 0.024 -9999 0 -10000 0 0
RASA1 0.01 0.07 -9999 0 -0.72 2 2
KLHL9 0.017 0 -9999 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.016 -9999 0 -10000 0 0
PPP1CC 0.017 0 -9999 0 -10000 0 0
Centraspindlin -0.14 0.25 -9999 0 -0.64 36 36
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.003 0.03 -9999 0 -10000 0 0
MYLK -0.02 0.12 -9999 0 -0.37 25 25
KIF23 -0.088 0.26 -9999 0 -0.73 31 31
VIM 0.021 0.075 -9999 0 -0.47 5 5
RACGAP1 -0.02 0.16 -9999 0 -0.73 10 10
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.006 0.015 -9999 0 -10000 0 0
Chromosomal passenger complex -0.062 0.15 -9999 0 -0.41 22 22
Chromosomal passenger complex/EVI5 -0.02 0.16 -9999 0 -0.79 3 3
TACC1 0.017 0 -9999 0 -10000 0 0
PPP2R5D 0.017 0 -9999 0 -10000 0 0
CUL3 0.017 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.016 0.23 -10000 0 -0.69 19 19
IHH 0.02 0.063 -10000 0 -0.79 1 1
SHH Np/Cholesterol/GAS1 -0.16 0.21 -10000 0 -0.61 17 17
LRPAP1 0.017 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.16 0.21 0.61 17 -10000 0 17
SMO/beta Arrestin2 0.046 0.1 -10000 0 -0.7 1 1
SMO 0.04 0.11 -10000 0 -0.75 1 1
AKT1 0.05 0.053 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
BOC 0.017 0 -10000 0 -10000 0 0
ADRBK1 0.017 0 -10000 0 -10000 0 0
heart looping 0.04 0.1 -10000 0 -0.74 1 1
STIL -0.048 0.21 -10000 0 -0.62 13 13
DHH N/PTCH2 0 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.04 0.1 -10000 0 -0.7 1 1
PIK3CA 0.017 0 -10000 0 -10000 0 0
DHH 0.017 0 -10000 0 -10000 0 0
PTHLH 0.027 0.21 -10000 0 -1.2 4 4
determination of left/right symmetry 0.04 0.1 -10000 0 -0.74 1 1
PIK3R1 0.017 0 -10000 0 -10000 0 0
skeletal system development 0.028 0.21 -10000 0 -1.1 4 4
IHH N/Hhip -0.087 0.23 -10000 0 -0.51 48 48
DHH N/Hhip -0.1 0.19 -10000 0 -0.46 48 48
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.04 0.1 -10000 0 -0.74 1 1
pancreas development -0.12 0.27 -10000 0 -0.63 48 48
HHAT -0.054 0.2 -10000 0 -0.64 24 24
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.19 0.31 -10000 0 -0.64 71 71
somite specification 0.04 0.1 -10000 0 -0.74 1 1
SHH Np/Cholesterol/PTCH1 0.004 0.15 -10000 0 -0.57 4 4
SHH Np/Cholesterol/PTCH2 -0.044 0.12 -10000 0 -0.53 3 3
SHH Np/Cholesterol/Megalin -0.045 0.12 -10000 0 -0.5 4 4
SHH -0.029 0.17 -10000 0 -0.48 26 26
catabolic process 0.036 0.11 -10000 0 -0.5 4 4
SMO/Vitamin D3 0.015 0.15 -10000 0 -0.56 4 4
SHH Np/Cholesterol/Hhip -0.12 0.21 -10000 0 -0.72 12 12
LRP2 0.014 0.05 -10000 0 -0.72 1 1
receptor-mediated endocytosis -0.051 0.11 -10000 0 -0.53 4 4
SHH Np/Cholesterol/BOC -0.044 0.12 -10000 0 -0.53 3 3
SHH Np/Cholesterol/CDO -0.044 0.12 -10000 0 -0.53 3 3
mesenchymal cell differentiation 0.12 0.2 0.71 12 -10000 0 12
mol:Vitamin D3 0.009 0.15 -10000 0 -0.57 4 4
IHH N/PTCH2 0.028 0.039 -10000 0 -0.51 1 1
CDON 0.017 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.035 0.11 -10000 0 -0.5 4 4
Megalin/LRPAP1 -0.002 0.036 -10000 0 -0.54 1 1
PTCH2 0.017 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.045 0.13 -10000 0 -0.38 26 26
PTCH1 0.036 0.11 -10000 0 -0.5 4 4
HHIP -0.12 0.27 -10000 0 -0.64 48 48
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.004 0.076 -9999 0 -0.63 3 3
PDGF/PDGFRA/CRKL -0.006 0.051 -9999 0 -0.45 3 3
positive regulation of JUN kinase activity -0.004 0.037 -9999 0 -10000 0 0
CRKL 0.017 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.006 0.051 -9999 0 -0.45 3 3
AP1 -0.18 0.37 -9999 0 -1 36 36
mol:IP3 -0.019 0.16 -9999 0 -0.54 18 18
PLCG1 -0.019 0.16 -9999 0 -0.54 18 18
PDGF/PDGFRA/alphaV Integrin -0.008 0.063 -9999 0 -0.47 4 4
RAPGEF1 0.017 0 -9999 0 -10000 0 0
CRK 0.014 0.044 -9999 0 -0.64 1 1
mol:Ca2+ -0.019 0.16 -9999 0 -0.54 18 18
CAV3 0.017 0 -9999 0 -10000 0 0
CAV1 0.004 0.096 -9999 0 -0.7 4 4
SHC/Grb2/SOS1 -0.004 0.037 -9999 0 -10000 0 0
PDGF/PDGFRA/Shf -0.1 0.22 -9999 0 -0.55 41 41
FOS -0.13 0.39 -9999 0 -0.98 36 36
JUN -0.023 0.086 -9999 0 -0.57 5 5
oligodendrocyte development -0.008 0.063 -9999 0 -0.47 4 4
GRB2 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
mol:DAG -0.019 0.16 -9999 0 -0.54 18 18
PDGF/PDGFRA 0.004 0.075 -9999 0 -0.63 3 3
actin cytoskeleton reorganization -0.031 0.12 -9999 0 -0.53 13 13
SRF 0.033 0.01 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
PI3K -0.005 0.042 -9999 0 -0.37 3 3
PDGF/PDGFRA/Crk/C3G -0.007 0.05 -9999 0 -0.38 4 4
JAK1 0.022 0.056 -9999 0 -0.44 3 3
ELK1/SRF 0.014 0.13 -9999 0 -0.49 7 7
SHB -0.016 0.15 -9999 0 -0.72 10 10
SHF -0.11 0.28 -9999 0 -0.72 39 39
CSNK2A1 0.013 0.024 -9999 0 -10000 0 0
GO:0007205 -0.016 0.15 -9999 0 -0.51 18 18
SOS1 0.017 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.004 0.037 -9999 0 -10000 0 0
PDGF/PDGFRA/SHB -0.031 0.12 -9999 0 -0.53 13 13
PDGF/PDGFRA/Caveolin-1 -0.016 0.086 -9999 0 -0.49 7 7
ITGAV 0.014 0.05 -9999 0 -0.72 1 1
ELK1 -0.013 0.16 -9999 0 -0.49 19 19
PIK3CA 0.017 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.008 0.06 -9999 0 -0.45 4 4
JAK-STAT cascade 0.022 0.055 -9999 0 -0.44 3 3
cell proliferation -0.1 0.22 -9999 0 -0.55 41 41
Glypican 2 network

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
MDK -0.023 0.17 -9999 0 -0.72 12 12
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.03 0.12 -9999 0 -0.55 12 12
neuron projection morphogenesis -0.03 0.12 -9999 0 -0.55 12 12
Regulation of Telomerase

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
Telomerase catalytic core complex -0.093 0.15 -9999 0 -10000 0 0
RAD9A 0.017 0 -9999 0 -10000 0 0
AP1 -0.081 0.18 -9999 0 -0.49 37 37
IFNAR2 0.017 0.007 -9999 0 -10000 0 0
AKT1 0.025 0.043 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.013 0.077 -9999 0 -0.47 6 6
NFX1/SIN3/HDAC complex 0.056 0.029 -9999 0 -10000 0 0
EGF -0.18 0.31 -9999 0 -0.67 64 64
SMG5 0.017 0 -9999 0 -10000 0 0
SMG6 0.017 0 -9999 0 -10000 0 0
SP3/HDAC2 0.019 0.015 -9999 0 -10000 0 0
TERT/c-Abl -0.09 0.13 -9999 0 -10000 0 0
SAP18 0.014 0.049 -9999 0 -0.72 1 1
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.39 0.37 -9999 0 -0.72 122 122
WRN 0.017 0 -9999 0 -10000 0 0
SP1 0.018 0.008 -9999 0 -10000 0 0
SP3 0.016 0.005 -9999 0 -10000 0 0
TERF2IP 0.017 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.18 0.2 -9999 0 -0.64 12 12
Mad/Max -0.025 0.1 -9999 0 -0.46 12 12
TERT -0.095 0.15 -9999 0 -10000 0 0
CCND1 -0.12 0.22 -9999 0 -0.69 13 13
MAX 0.016 0.006 -9999 0 -10000 0 0
RBBP7 0.017 0.001 -9999 0 -10000 0 0
RBBP4 0.017 0.001 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.017 0 -9999 0 -10000 0 0
SIN3A 0.017 0.001 -9999 0 -10000 0 0
Telomerase/911 -0.059 0.14 -9999 0 -0.5 1 1
CDKN1B -0.063 0.21 -9999 0 -0.75 2 2
RAD1 -0.013 0.15 -9999 0 -0.72 9 9
XRCC5 0.017 0 -9999 0 -10000 0 0
XRCC6 0.017 0 -9999 0 -10000 0 0
SAP30 0.017 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.016 0.005 -9999 0 -10000 0 0
JUN 0 0.11 -9999 0 -0.72 5 5
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.013 0.006 -9999 0 -10000 0 0
FOS -0.081 0.23 -9999 0 -0.64 33 33
IFN-gamma/IRF1 -0.12 0.22 -9999 0 -0.52 51 51
PARP2 0.017 0 -9999 0 -10000 0 0
BLM 0.007 0.085 -9999 0 -0.72 3 3
Telomerase -0.063 0.15 -9999 0 -0.49 1 1
IRF1 0.015 0.067 -9999 0 -0.67 2 2
ESR1 0 0.11 -9999 0 -0.64 6 6
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.061 0.033 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.062 0.033 -9999 0 -10000 0 0
HDAC1 0.017 0.001 -9999 0 -10000 0 0
HDAC2 0.017 0.007 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.026 0.047 -9999 0 -0.46 2 2
ABL1 0.017 0 -9999 0 -10000 0 0
MXD1 -0.019 0.15 -9999 0 -0.64 12 12
MRE11A 0.017 0 -9999 0 -10000 0 0
HUS1 0.017 0 -9999 0 -10000 0 0
RPS6KB1 0.014 0.05 -9999 0 -0.72 1 1
TERT/NF kappa B1/14-3-3 -0.064 0.12 -9999 0 -10000 0 0
NR2F2 0.016 0.005 -9999 0 -10000 0 0
MAPK3 0.027 0.047 -9999 0 -0.46 2 2
MAPK1 0.029 0.034 -9999 0 -0.47 1 1
TGFB1/TGF beta receptor Type II 0.017 0.001 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
HNRNPC 0.017 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.017 0 -9999 0 -10000 0 0
EGFR 0.002 0.1 -9999 0 -0.65 5 5
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.15 0.23 -9999 0 -0.5 68 68
MYC -0.42 0.36 -9999 0 -0.72 131 131
IL2 0.018 0.008 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
TGFB1 0.017 0.001 -9999 0 -10000 0 0
TRF2/BLM -0.007 0.058 -9999 0 -0.5 3 3
FRAP1 0.017 0 -9999 0 -10000 0 0
KU/TERT -0.083 0.13 -9999 0 -10000 0 0
SP1/HDAC2 0.029 0.012 -9999 0 -10000 0 0
PINX1 0.014 0.05 -9999 0 -0.72 1 1
Telomerase/EST1A -0.18 0.2 -9999 0 -0.64 12 12
Smad3/Myc -0.26 0.25 -9999 0 -0.46 131 131
911 complex -0.019 0.09 -9999 0 -0.46 9 9
IFNG -0.14 0.3 -9999 0 -0.71 50 50
Telomerase/PinX1 -0.18 0.2 -9999 0 -0.64 12 12
Telomerase/AKT1/mTOR/p70S6K -0.044 0.12 -9999 0 -10000 0 0
SIN3B 0.017 0.001 -9999 0 -10000 0 0
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
Telomerase/EST1B -0.18 0.2 -9999 0 -0.64 12 12
response to DNA damage stimulus 0.005 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.18 0.2 -9999 0 -0.64 12 12
E2F1 -0.03 0.18 -9999 0 -0.72 14 14
ZNFX1 0.014 0.05 -9999 0 -0.72 1 1
PIF1 0.004 0.098 -9999 0 -0.72 4 4
NCL 0.017 0 -9999 0 -10000 0 0
DKC1 -0.2 0.34 -9999 0 -0.72 66 66
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.003 0.12 -9999 0 -0.39 3 3
Syndecan-4/Syndesmos 0.027 0.11 -9999 0 -0.48 4 4
positive regulation of JNK cascade -0.23 0.14 -9999 0 -0.54 25 25
Syndecan-4/ADAM12 -0.12 0.25 -9999 0 -0.61 25 25
CCL5 -0.14 0.28 -9999 0 -0.64 52 52
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.017 0 -9999 0 -10000 0 0
ITGA5 0 0.11 -9999 0 -0.72 5 5
SDCBP 0.017 0 -9999 0 -10000 0 0
PLG 0.013 0.006 -9999 0 -10000 0 0
ADAM12 -0.26 0.36 -9999 0 -0.72 83 83
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.017 0.042 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.027 0.11 -9999 0 -0.48 4 4
Syndecan-4/CXCL12/CXCR4 -0.24 0.15 -9999 0 -0.64 15 15
Syndecan-4/Laminin alpha3 0.019 0.13 -9999 0 -0.56 5 5
MDK -0.023 0.17 -9999 0 -0.72 12 12
Syndecan-4/FZD7 0.013 0.13 -9999 0 -0.48 4 4
Syndecan-4/Midkine 0.006 0.15 -9999 0 -0.53 7 7
FZD7 -0.009 0.13 -9999 0 -0.7 8 8
Syndecan-4/FGFR1/FGF -0.04 0.09 -9999 0 -10000 0 0
THBS1 0.011 0.066 -9999 0 -0.68 2 2
integrin-mediated signaling pathway 0.019 0.14 -9999 0 -0.56 7 7
positive regulation of MAPKKK cascade -0.23 0.14 -9999 0 -0.54 25 25
Syndecan-4/TACI 0.021 0.12 -9999 0 -0.5 5 5
CXCR4 -0.02 0.16 -9999 0 -0.72 11 11
cell adhesion -0.035 0.094 -9999 0 -0.38 4 4
Syndecan-4/Dynamin 0.027 0.11 -9999 0 -0.48 4 4
Syndecan-4/TSP1 0.024 0.12 -9999 0 -0.57 4 4
Syndecan-4/GIPC 0.026 0.12 -9999 0 -0.49 5 5
Syndecan-4/RANTES -0.051 0.18 -9999 0 -0.54 12 12
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
LAMA1 0.017 0 -9999 0 -10000 0 0
LAMA3 0.001 0.1 -9999 0 -0.67 5 5
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCA 0.011 0.058 -9999 0 -0.7 1 1
Syndecan-4/alpha-Actinin 0.027 0.11 -9999 0 -0.48 4 4
TFPI 0.014 0.05 -9999 0 -0.72 1 1
F2 0.019 0.004 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.015 0.087 -9999 0 -0.54 6 6
positive regulation of cell adhesion 0.03 0.13 -9999 0 -0.65 2 2
ACTN1 0.017 0 -9999 0 -10000 0 0
TNC 0 0.11 -9999 0 -0.72 5 5
Syndecan-4/CXCL12 -0.23 0.16 -9999 0 -0.53 18 18
FGF6 0.014 0.05 -9999 0 -0.72 1 1
RHOA 0.017 0 -9999 0 -10000 0 0
CXCL12 -0.48 0.28 -9999 0 -0.64 168 168
TNFRSF13B 0.005 0.087 -9999 0 -0.64 4 4
FGF2 -0.01 0.13 -9999 0 -0.64 9 9
FGFR1 0.017 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.016 0.11 -9999 0 -0.49 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.074 0.24 -9999 0 -0.74 26 26
cell migration -0.006 0.016 -9999 0 -10000 0 0
PRKCD 0.013 0.006 -9999 0 -10000 0 0
vasculogenesis 0.024 0.12 -9999 0 -0.55 4 4
SDC4 0.018 0.12 -9999 0 -0.52 4 4
Syndecan-4/Tenascin C 0.019 0.14 -9999 0 -0.59 7 7
Syndecan-4/PI-4-5-P2/PKC alpha -0.014 0.033 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.027 0.11 -9999 0 -0.48 4 4
MMP9 -0.003 0.13 -9999 0 -0.7 7 7
Rac1/GTP -0.036 0.096 -9999 0 -0.42 3 3
cytoskeleton organization 0.027 0.11 -9999 0 -0.47 4 4
GIPC1 0.014 0.044 -9999 0 -0.64 1 1
Syndecan-4/TFPI 0.026 0.12 -9999 0 -0.5 5 5
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.014 0.044 -9999 0 -0.64 1 1
SPHK1 -0.073 0.24 -9999 0 -0.72 27 27
GNAI2 0.017 0 -9999 0 -10000 0 0
mol:S1P -0.032 0.12 -9999 0 -0.25 49 49
GNAO1 0.017 0 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.04 0.19 -9999 0 -0.55 27 27
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.037 0.074 -9999 0 -0.42 2 2
GNAI3 0.017 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.021 0.15 -9999 0 -0.64 13 13
S1P1/S1P -0.042 0.14 -9999 0 -0.43 15 15
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.068 0.22 -9999 0 -0.64 29 29
S1P/S1P5/G12 -0.041 0.082 -9999 0 -0.45 2 2
S1P/S1P3/Gq -0.019 0.12 -9999 0 -0.34 15 15
S1P/S1P4/Gi -0.008 0.099 -9999 0 -0.35 5 5
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.017 0 -9999 0 -10000 0 0
GNA14 -0.01 0.13 -9999 0 -0.64 9 9
GNA15 -0.006 0.13 -9999 0 -0.72 7 7
GNA12 0.017 0 -9999 0 -10000 0 0
GNA13 0.017 0 -9999 0 -10000 0 0
GNA11 -0.001 0.11 -9999 0 -0.64 6 6
ABCC1 -0.06 0.22 -9999 0 -0.72 23 23
PLK2 and PLK4 events

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
PLK2 -0.006 0.13 -9999 0 -0.72 7 7
PLK4 -0.003 0.12 -9999 0 -0.72 6 6
regulation of centriole replication -0.002 0.13 -9999 0 -0.54 13 13
EPO signaling pathway

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
BCL2L1 -0.16 0.18 -9999 0 -0.56 2 2
CRKL -0.01 0.072 -9999 0 -10000 0 0
mol:DAG -0.054 0.12 -9999 0 -0.46 11 11
HRAS 0.024 0.07 -9999 0 -10000 0 0
MAPK8 0.016 0.039 -9999 0 -0.42 1 1
RAP1A -0.01 0.072 -9999 0 -10000 0 0
GAB1 -0.013 0.08 -9999 0 -10000 0 0
MAPK14 0.016 0.039 -9999 0 -0.42 1 1
EPO 0.004 0.051 -9999 0 -0.74 1 1
PLCG1 -0.056 0.13 -9999 0 -0.47 11 11
EPOR/TRPC2/IP3 Receptors 0.007 0.011 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.022 0.1 -9999 0 -0.48 10 10
GAB1/SHC/GRB2/SOS1 -0.014 0.051 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.008 0.042 -9999 0 -0.56 1 1
IRS2 -0.012 0.078 -9999 0 -0.45 1 1
STAT1 -0.12 0.16 -9999 0 -0.56 11 11
STAT5B -0.064 0.11 -9999 0 -0.47 1 1
cell proliferation 0.019 0.04 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.015 0.052 -9999 0 -10000 0 0
TEC -0.01 0.072 -9999 0 -10000 0 0
SOCS3 -0.013 0.15 -9999 0 -0.72 9 9
STAT1 (dimer) -0.12 0.16 -9999 0 -0.55 11 11
JAK2 -0.006 0.097 -9999 0 -0.72 4 4
PIK3R1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.016 0.081 -9999 0 -0.45 1 1
EPO/EPOR 0.008 0.042 -9999 0 -0.56 1 1
LYN 0.007 0.009 -9999 0 -10000 0 0
TEC/VAV2 -0.005 0.082 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.007 0.011 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.015 0.041 -9999 0 -0.48 1 1
mol:IP3 -0.054 0.12 -9999 0 -0.46 11 11
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.026 0.052 -9999 0 -10000 0 0
SH2B3 0.006 0.01 -9999 0 -10000 0 0
NFKB1 0.016 0.039 -9999 0 -0.42 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.013 0.054 -9999 0 -0.43 1 1
PTPN6 -0.022 0.075 -9999 0 -0.44 1 1
TEC/VAV2/GRB2 0.004 0.079 -9999 0 -10000 0 0
EPOR 0.007 0.011 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.015 0.051 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
PLCG2 -0.31 0.33 -9999 0 -0.64 110 110
CRKL/CBL/C3G 0.01 0.068 -9999 0 -10000 0 0
VAV2 -0.016 0.084 -9999 0 -10000 0 0
CBL -0.01 0.072 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.018 0.044 -9999 0 -10000 0 0
STAT5A -0.064 0.11 -9999 0 -0.47 1 1
GRB2 0.017 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.12 0.17 -9999 0 -0.59 1 1
LYN/PLCgamma2 -0.23 0.23 -9999 0 -0.47 110 110
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
BTK -0.063 0.15 -9999 0 -10000 0 0
BCL2 -0.57 0.47 -9999 0 -0.9 145 145
Ceramide signaling 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
SPHK2 0.018 0.08 -10000 0 -0.46 6 6
MAP4K4 0.045 0.084 -10000 0 -0.58 1 1
BAG4 0.017 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.042 0.056 0.18 1 -10000 0 1
NFKBIA 0.017 0 -10000 0 -10000 0 0
BIRC3 -0.02 0.15 -10000 0 -0.66 12 12
BAX -0.011 0.032 -10000 0 -0.23 1 1
RIPK1 0.017 0 -10000 0 -10000 0 0
AKT1 0.034 0.011 -10000 0 -10000 0 0
BAD -0.03 0.057 0.2 1 -10000 0 1
SMPD1 -0.028 0.13 -10000 0 -0.27 47 47
RB1 -0.03 0.057 0.2 1 -10000 0 1
FADD/Caspase 8 0.066 0.054 -10000 0 -10000 0 0
MAP2K4 -0.025 0.072 -10000 0 -0.38 4 4
NSMAF 0.017 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.018 0.054 -10000 0 -10000 0 0
EGF -0.18 0.31 -10000 0 -0.68 64 64
mol:ceramide -0.044 0.061 0.18 5 -10000 0 5
MADD 0.017 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.02 0.073 -10000 0 -0.46 5 5
ASAH1 0.017 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.03 0.057 0.2 1 -10000 0 1
cell proliferation -0.16 0.14 -10000 0 -0.34 37 37
BID 0.023 0.068 -10000 0 -0.4 1 1
MAP3K1 -0.03 0.057 0.2 1 -10000 0 1
EIF2A -0.055 0.14 -10000 0 -0.42 25 25
TRADD 0.017 0 -10000 0 -10000 0 0
CRADD 0.011 0.062 -10000 0 -0.64 2 2
MAPK3 -0.003 0.052 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.002 0.05 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.032 0.063 0.19 1 -0.47 1 2
FADD 0.053 0.057 -10000 0 -10000 0 0
KSR1 -0.03 0.057 0.2 1 -10000 0 1
MAPK8 -0.022 0.061 0.2 1 -0.25 3 4
PRKRA -0.03 0.057 0.2 1 -10000 0 1
PDGFA 0.002 0.097 -10000 0 -0.64 5 5
TRAF2 0.017 0 -10000 0 -10000 0 0
IGF1 -0.35 0.32 -10000 0 -0.64 125 125
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.044 0.061 0.18 5 -10000 0 5
CTSD 0.014 0.044 -10000 0 -0.64 1 1
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.16 0.16 -10000 0 -0.37 34 34
PRKCD 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.02 0.073 -10000 0 -0.46 5 5
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.017 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.044 0.06 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.018 0.08 -10000 0 -0.46 6 6
MAP2K1 -0.007 0.052 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
CYCS 0.089 0.088 0.29 2 -10000 0 2
TNFRSF1A 0.017 0 -10000 0 -10000 0 0
NFKB1 0.017 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 -0.031 0.089 -10000 0 -0.45 6 6
TNF-alpha/TNFR1A/FAN 0 0 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.052 0.036 -10000 0 -10000 0 0
MAP2K2 -0.007 0.052 -10000 0 -10000 0 0
SMPD3 0.029 0.072 -10000 0 -0.35 7 7
TNF 0.017 0 -10000 0 -10000 0 0
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.059 0.11 0.23 64 -10000 0 64
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.09 0.09 0.3 3 -10000 0 3
BCL2 -0.41 0.31 -10000 0 -0.64 145 145
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.051 0.16 -9999 0 -0.54 21 21
alphaV beta3 Integrin -0.018 0.083 -9999 0 -0.4 10 10
PTK2 0.05 0.12 -9999 0 -10000 0 0
IGF1R 0.017 0 -9999 0 -10000 0 0
PI4KB 0.017 0 -9999 0 -10000 0 0
MFGE8 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
CDKN1B -0.008 0.036 -9999 0 -10000 0 0
VEGFA -0.053 0.22 -9999 0 -0.72 21 21
ILK -0.006 0.029 -9999 0 -10000 0 0
ROCK1 0.017 0 -9999 0 -10000 0 0
AKT1 -0.005 0.024 -9999 0 -10000 0 0
PTK2B 0.012 0.13 -9999 0 -10000 0 0
alphaV/beta3 Integrin/JAM-A -0.015 0.067 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.002 0.031 -9999 0 -0.46 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.2 0.19 -9999 0 -0.76 5 5
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.038 0.063 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Syndecan-1 -0.002 0.031 -9999 0 -0.46 1 1
PI4KA 0.017 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.22 0.2 -9999 0 -0.67 23 23
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.31 0.22 -9999 0 -0.46 150 150
RPS6KB1 -0.17 0.22 -9999 0 -0.62 24 24
TLN1 0.017 0 -9999 0 -10000 0 0
MAPK3 -0.078 0.13 -9999 0 -0.72 7 7
GPR124 0.01 0.07 -9999 0 -0.72 2 2
MAPK1 -0.077 0.13 -9999 0 -0.72 7 7
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.006 0.053 -9999 0 -0.46 3 3
cell adhesion -0.002 0.025 -9999 0 -10000 0 0
ANGPTL3 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.043 0.13 -9999 0 -0.46 21 21
IGF-1R heterotetramer 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.017 0 -9999 0 -10000 0 0
ITGB3 0.017 0 -9999 0 -10000 0 0
IGF1 -0.35 0.32 -9999 0 -0.64 125 125
RAC1 0.017 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.006 0.052 -9999 0 -0.46 3 3
apoptosis 0.014 0.049 -9999 0 -0.72 1 1
CD47 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.002 0.031 -9999 0 -0.46 1 1
VCL 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.044 0.12 -9999 0 -0.39 25 25
CSF1 0.017 0 -9999 0 -10000 0 0
PIK3C2A -0.016 0.065 -9999 0 -0.47 1 1
PI4 Kinase/Pyk2 -0.039 0.11 -9999 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.04 0.12 -9999 0 -0.41 22 22
FAK1/Vinculin 0.054 0.1 -9999 0 -10000 0 0
alphaV beta3/Integrin/ppsTEM5 -0.006 0.053 -9999 0 -0.46 3 3
RHOA 0.017 0 -9999 0 -10000 0 0
VTN 0.017 0 -9999 0 -10000 0 0
BCAR1 0.017 0 -9999 0 -10000 0 0
FGF2 -0.01 0.13 -9999 0 -0.64 9 9
F11R 0.011 0.099 -9999 0 -0.47 9 9
alphaV/beta3 Integrin/Lactadherin -0.002 0.031 -9999 0 -0.46 1 1
alphaV/beta3 Integrin/TGFBR2 -0.002 0.031 -9999 0 -0.46 1 1
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.027 -9999 0 -0.41 1 1
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
alphaV/beta3 Integrin/Talin -0.002 0.028 -9999 0 -0.42 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.07 0.24 -9999 0 -0.72 26 26
alphaV/beta3 Integrin/Pyk2 -0.037 0.11 -9999 0 -10000 0 0
SDC1 0.017 0 -9999 0 -10000 0 0
VAV3 -0.004 0.14 -9999 0 -0.71 1 1
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
IRS1 0.004 0.098 -9999 0 -0.72 4 4
FAK1/Paxillin 0.054 0.1 -9999 0 -10000 0 0
cell migration 0.064 0.097 -9999 0 -10000 0 0
ITGAV 0.014 0.05 -9999 0 -0.72 1 1
PI3K -0.013 0.058 -9999 0 -10000 0 0
SPP1 -0.48 0.35 -9999 0 -0.72 150 150
KDR 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.014 0.049 -9999 0 -0.72 1 1
COL4A3 0.01 0.07 -9999 0 -0.72 2 2
angiogenesis -0.034 0.15 -9999 0 -0.7 7 7
Rac1/GTP -0.044 0.11 -9999 0 -0.65 1 1
EDIL3 -0.054 0.2 -9999 0 -0.64 24 24
cell proliferation -0.002 0.03 -9999 0 -0.46 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.042 0.13 -10000 0 -0.55 11 11
FYN -0.016 0.22 -10000 0 -0.71 14 14
LAT/GRAP2/SLP76 -0.043 0.14 -10000 0 -0.58 10 10
IKBKB 0.014 0.05 -10000 0 -0.72 1 1
AKT1 0.022 0.15 -10000 0 -0.48 12 12
B2M -0.009 0.13 -10000 0 -0.64 9 9
IKBKG -0.017 0.037 -10000 0 -0.18 1 1
MAP3K8 -0.086 0.26 -10000 0 -0.72 31 31
mol:Ca2+ -0.003 0.021 -10000 0 -0.14 4 4
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.006 0.21 -10000 0 -0.74 12 12
TRPV6 -0.01 0.099 -10000 0 -0.74 4 4
CD28 -0.062 0.21 -10000 0 -0.64 27 27
SHC1 0.008 0.2 -10000 0 -0.7 12 12
receptor internalization -0.007 0.21 -10000 0 -0.73 14 14
PRF1 0.013 0.18 -10000 0 -0.77 7 7
KRAS 0.017 0 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
COT/AKT1 -0.014 0.16 -10000 0 -0.38 19 19
LAT 0.005 0.2 -10000 0 -0.7 12 12
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.011 0.14 -10000 0 -0.64 10 10
CD3E 0.017 0.006 -10000 0 -10000 0 0
CD3G -0.015 0.14 -10000 0 -0.65 11 11
RASGRP2 0.01 0.033 -10000 0 -0.19 4 4
RASGRP1 0.027 0.15 -10000 0 -0.46 12 12
HLA-A 0.003 0.098 -10000 0 -0.64 5 5
RASSF5 0.017 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.036 0.055 -10000 0 -0.14 2 2
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.032 0.066 -10000 0 -0.26 5 5
PRKCA -0.039 0.083 -10000 0 -0.31 12 12
GRAP2 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.057 0.14 0.24 2 -0.49 13 15
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.001 0.2 -10000 0 -0.71 12 12
ORAI1 0.01 0.05 0.37 4 -10000 0 4
CSK -0.002 0.2 -10000 0 -0.71 12 12
B7 family/CD28 -0.096 0.23 -10000 0 -0.73 20 20
CHUK 0.017 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.012 0.23 -10000 0 -0.84 12 12
PTPN6 0.002 0.2 -10000 0 -0.73 12 12
VAV1 -0.017 0.24 -10000 0 -0.82 14 14
Monovalent TCR/CD3 -0.012 0.2 -10000 0 -0.74 12 12
CBL 0.017 0 -10000 0 -10000 0 0
LCK -0.014 0.22 -10000 0 -0.71 14 14
PAG1 -0.065 0.24 -10000 0 -0.64 20 20
RAP1A 0.017 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.016 0.23 -10000 0 -0.86 12 12
CD80 0.004 0.099 -10000 0 -0.72 4 4
CD86 -0.016 0.14 -10000 0 -0.65 11 11
PDK1/CARD11/BCL10/MALT1 -0.04 0.081 -10000 0 -0.29 9 9
HRAS 0.017 0 -10000 0 -10000 0 0
GO:0035030 -0.015 0.21 -10000 0 -0.6 19 19
CD8A 0.001 0.004 -10000 0 -10000 0 0
CD8B 0.017 0.005 -10000 0 -10000 0 0
PTPRC -0.018 0.15 -10000 0 -0.64 12 12
PDK1/PKC theta 0.023 0.18 -10000 0 -0.61 12 12
CSK/PAG1 -0.056 0.23 -10000 0 -0.65 17 17
SOS1 0.017 0 -10000 0 -10000 0 0
peptide-MHC class I -0.01 0.14 -10000 0 -0.57 11 11
GRAP2/SLP76 -0.05 0.17 -10000 0 -0.69 11 11
STIM1 0.007 0.026 -10000 0 -10000 0 0
RAS family/GTP 0.045 0.07 -10000 0 -0.24 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.011 0.24 -10000 0 -0.8 14 14
mol:DAG -0.055 0.12 -10000 0 -0.42 14 14
RAP1A/GDP 0.018 0.024 -10000 0 -10000 0 0
PLCG1 -0.033 0.19 -10000 0 -0.72 15 15
CD247 -0.014 0.14 -10000 0 -0.64 11 11
cytotoxic T cell degranulation 0.015 0.18 -10000 0 -0.67 10 10
RAP1A/GTP -0.002 0.009 -10000 0 -0.068 3 3
mol:PI-3-4-5-P3 0.014 0.18 -10000 0 -0.59 12 12
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.073 0.17 0.3 1 -0.63 14 15
NRAS 0.007 0.085 -10000 0 -0.72 3 3
ZAP70 0.017 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.059 0.16 -10000 0 -0.64 12 12
MALT1 0.017 0 -10000 0 -10000 0 0
TRAF6 0.017 0 -10000 0 -10000 0 0
CD8 heterodimer 0.012 0.009 -10000 0 -10000 0 0
CARD11 -0.046 0.21 -10000 0 -0.72 19 19
PRKCB -0.04 0.082 -10000 0 -0.29 14 14
PRKCE -0.038 0.08 -10000 0 -0.29 12 12
PRKCQ 0.009 0.21 -10000 0 -0.71 12 12
LCP2 0.004 0.096 -10000 0 -0.7 4 4
BCL10 0.017 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.13 -10000 0 -0.4 12 12
IKK complex 0.039 0.058 -10000 0 -0.13 1 1
RAS family/GDP -0.003 0.011 -10000 0 -0.081 3 3
MAP3K14 0.003 0.13 -10000 0 -0.3 12 12
PDPK1 0.027 0.14 -10000 0 -0.45 12 12
TCR/CD3/MHC I/CD8/Fyn -0.01 0.22 -10000 0 -0.81 12 12
Cellular roles of Anthrax toxin

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
ANTXR1 -0.026 0.17 -10000 0 -0.72 13 13
ANTXR2 0.008 0.075 -10000 0 -0.64 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.022 -10000 0 -0.086 16 16
monocyte activation 0.01 0.066 -10000 0 -0.42 5 5
MAP2K2 -0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.005 0.018 -10000 0 -10000 0 0
MAP2K7 -0.005 0.018 -10000 0 -10000 0 0
MAP2K6 -0.019 0.072 -10000 0 -0.36 9 9
CYAA -0.009 0.11 -10000 0 -0.39 16 16
MAP2K4 -0.011 0.049 -10000 0 -0.35 4 4
IL1B -0.063 0.17 -10000 0 -0.42 41 41
Channel -0.03 0.11 -10000 0 -0.42 16 16
NLRP1 -0.007 0.033 -10000 0 -0.41 1 1
CALM1 0.017 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.007 0.026 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.022 0.086 16 -10000 0 16
MAPK3 -0.008 0.037 -10000 0 -0.35 2 2
MAPK1 -0.007 0.029 -10000 0 -0.35 1 1
PGR -0.005 0.018 -10000 0 -10000 0 0
PA/Cellular Receptors -0.033 0.12 -10000 0 -0.45 16 16
apoptosis -0.006 0.022 -10000 0 -0.086 16 16
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.007 0.1 -10000 0 -0.38 16 16
macrophage activation 0.017 0.045 -10000 0 -0.32 3 3
TNF 0.017 0 -10000 0 -10000 0 0
VCAM1 0.01 0.067 -10000 0 -0.42 5 5
platelet activation -0.007 0.026 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.031 0.16 1 -10000 0 1
IL18 -0.026 0.12 -10000 0 -0.35 25 25
negative regulation of macrophage activation -0.006 0.022 -10000 0 -0.086 16 16
LEF -0.006 0.022 -10000 0 -0.086 16 16
CASP1 -0.009 0.025 -10000 0 -0.2 1 1
mol:cAMP -0.007 0.026 -10000 0 -10000 0 0
necrosis -0.006 0.022 -10000 0 -0.086 16 16
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.028 0.1 -10000 0 -0.4 16 16
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.017 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.05 0.066 -10000 0 -0.39 2 2
PTP1B/AKT1 -0.089 0.068 -10000 0 -0.34 1 1
FYN 0.014 0.044 -10000 0 -0.64 1 1
p210 bcr-abl/PTP1B -0.11 0.076 -10000 0 -0.33 2 2
EGFR -0.006 0.1 -10000 0 -0.66 5 5
EGF/EGFR -0.19 0.18 -10000 0 -0.47 60 60
CSF1 0.017 0 -10000 0 -10000 0 0
AKT1 0.017 0.002 -10000 0 -10000 0 0
INSR 0.008 0.075 -10000 0 -0.64 3 3
PTP1B/N-cadherin -0.11 0.093 -10000 0 -0.44 7 7
Insulin Receptor/Insulin -0.058 0.057 -10000 0 -0.46 2 2
HCK -0.045 0.19 -10000 0 -0.64 21 21
CRK 0.014 0.044 -10000 0 -0.64 1 1
TYK2 -0.096 0.073 -10000 0 -0.33 1 1
EGF -0.19 0.32 -10000 0 -0.68 64 64
YES1 0.017 0 -10000 0 -10000 0 0
CAV1 -0.1 0.1 -10000 0 -0.4 3 3
TXN 0.01 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.09 0.09 -10000 0 -0.51 4 4
cell migration 0.11 0.076 0.33 2 -10000 0 2
STAT3 0.016 0.001 -10000 0 -10000 0 0
PRLR 0.01 0.098 -10000 0 -0.71 4 4
ITGA2B 0.015 0.001 -10000 0 -10000 0 0
CSF1R 0.017 0 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.026 0.084 -10000 0 -0.52 5 5
FGR 0.017 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.096 0.073 -10000 0 -0.33 1 1
Crk/p130 Cas -0.084 0.075 -10000 0 -0.5 1 1
DOK1 -0.073 0.068 -10000 0 -0.38 1 1
JAK2 -0.048 0.062 -10000 0 -0.34 2 2
Jak2/Leptin Receptor/Leptin -0.071 0.12 -10000 0 -0.59 9 9
PIK3R1 0.017 0 -10000 0 -10000 0 0
PTPN1 -0.11 0.077 -10000 0 -0.34 2 2
LYN 0.017 0 -10000 0 -10000 0 0
CDH2 -0.005 0.12 -10000 0 -0.68 7 7
SRC -0.025 0.031 -10000 0 -10000 0 0
ITGB3 0.015 0.001 -10000 0 -10000 0 0
CAT1/PTP1B -0.12 0.12 -10000 0 -0.43 9 9
CAPN1 0.011 0.007 -10000 0 -10000 0 0
CSK 0.017 0 -10000 0 -10000 0 0
PI3K -0.037 0.052 -10000 0 -0.46 1 1
mol:H2O2 0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.064 0.12 -10000 0 -0.58 9 9
negative regulation of transcription -0.048 0.061 -10000 0 -0.33 2 2
FCGR2A -0.03 0.18 -10000 0 -0.72 14 14
FER -0.016 0.14 -10000 0 -0.72 8 8
alphaIIb/beta3 Integrin 0 0 -10000 0 -10000 0 0
BLK -0.16 0.29 -10000 0 -0.64 61 61
Insulin Receptor/Insulin/Shc -0.005 0.044 -10000 0 -0.38 3 3
RHOA 0.011 0.007 -10000 0 -10000 0 0
LEPR 0.005 0.086 -10000 0 -0.63 4 4
BCAR1 0.017 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.017 0 -10000 0 -10000 0 0
mol:NADPH -0.003 0.003 -10000 0 -10000 0 0
TRPV6 -0.056 0.16 -10000 0 -0.5 11 11
PRL 0.019 0.049 -10000 0 -0.72 1 1
SOCS3 0.007 0.12 -10000 0 -0.56 9 9
SPRY2 0.002 0.11 -10000 0 -0.71 5 5
Insulin Receptor/Insulin/IRS1 -0.014 0.075 -10000 0 -0.46 4 4
CSF1/CSF1R -0.083 0.07 -10000 0 -10000 0 0
Ras protein signal transduction 0.058 0.023 -10000 0 -10000 0 0
IRS1 0.004 0.098 -10000 0 -0.72 4 4
INS 0.017 0.002 -10000 0 -10000 0 0
LEP 0.011 0.062 -10000 0 -0.64 2 2
STAT5B -0.081 0.068 -10000 0 -0.28 3 3
STAT5A -0.081 0.068 -10000 0 -0.28 3 3
GRB2 0.017 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.096 0.073 -10000 0 -10000 0 0
CSN2 0.062 0.03 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
LAT -0.042 0.069 -10000 0 -0.3 6 6
YBX1 0.025 0.002 -10000 0 -10000 0 0
LCK 0.011 0.066 -10000 0 -0.68 2 2
SHC1 0.017 0 -10000 0 -10000 0 0
NOX4 -0.6 0.27 -10000 0 -0.72 185 185
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.002 0.035 -9999 0 -10000 0 0
VDR -0.001 0.11 -9999 0 -0.64 6 6
FAM120B 0.017 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.086 0.025 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.097 0.037 -9999 0 -10000 0 0
MED1 0.007 0.085 -9999 0 -0.72 3 3
mol:9cRA 0.01 0.005 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.028 0.079 -9999 0 -10000 0 0
RXRs/NUR77 0.061 0.044 -9999 0 -0.39 2 2
RXRs/PPAR 0.054 0.053 -9999 0 -10000 0 0
NCOR2 0.017 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.013 0.077 -9999 0 -0.47 6 6
RARs/VDR/DNA/Vit D3 -0.014 0.068 -9999 0 -0.39 3 3
RARA 0.014 0.05 -9999 0 -0.72 1 1
NCOA1 0.011 0.062 -9999 0 -0.64 2 2
VDR/VDR/DNA -0.001 0.11 -9999 0 -0.63 6 6
RARs/RARs/DNA/9cRA -0.005 0.045 -9999 0 -0.39 3 3
RARG 0.01 0.07 -9999 0 -0.72 2 2
RPS6KB1 -0.003 0.047 -9999 0 -0.69 1 1
RARs/THRs/DNA/SMRT 0.031 0.074 -9999 0 -10000 0 0
THRA 0.017 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.013 0.077 -9999 0 -0.47 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.062 0.014 -9999 0 -10000 0 0
NR1H4 -0.54 0.23 -9999 0 -0.64 190 190
RXRs/LXRs/DNA 0.092 0.018 -9999 0 -10000 0 0
NR1H2 0.026 0.003 -9999 0 -10000 0 0
NR1H3 0.027 0.004 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.05 0.06 -9999 0 -10000 0 0
NR4A1 0.01 0.07 -9999 0 -0.72 2 2
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.2 0.11 -9999 0 -0.4 4 4
RXRG 0.026 0.003 -9999 0 -10000 0 0
RXR alpha/CCPG 0.032 0.003 -9999 0 -10000 0 0
RXRA 0.026 0.003 -9999 0 -10000 0 0
RXRB 0.026 0.004 -9999 0 -10000 0 0
THRB -0.018 0.15 -9999 0 -0.64 12 12
PPARG -0.001 0.11 -9999 0 -0.64 6 6
PPARD 0.017 0 -9999 0 -10000 0 0
TNF 0.1 0.034 -9999 0 -10000 0 0
mol:Oxysterols 0.01 0.005 -9999 0 -10000 0 0
cholesterol transport 0.097 0.036 -9999 0 -10000 0 0
PPARA 0.014 0.044 -9999 0 -0.64 1 1
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.017 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 -0.15 0.14 -9999 0 -10000 0 0
SREBF1 0.1 0.049 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.062 0.014 -9999 0 -10000 0 0
ABCA1 0.099 0.083 -9999 0 -1.1 1 1
RARs/THRs -0.022 0.082 -9999 0 -10000 0 0
RXRs/FXR -0.27 0.14 -9999 0 -0.4 2 2
BCL2 -0.41 0.31 -9999 0 -0.64 145 145
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.017 0 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.017 0 -9999 0 -10000 0 0
TCEB1 0.01 0.07 -9999 0 -0.72 2 2
HIF1A/p53 -0.016 0.1 -9999 0 -0.38 9 9
HIF1A -0.01 0.073 -9999 0 -10000 0 0
COPS5 0.017 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.005 0.043 -9999 0 -10000 0 0
FIH (dimer) 0.017 0 -9999 0 -10000 0 0
CDKN2A -0.22 0.34 -9999 0 -0.72 70 70
ARNT/IPAS 0 0 -9999 0 -10000 0 0
HIF1AN 0.017 0 -9999 0 -10000 0 0
GNB2L1 0.017 0 -9999 0 -10000 0 0
HIF1A/ARNT 0 0.07 -9999 0 -10000 0 0
CUL2 0.017 0 -9999 0 -10000 0 0
OS9 0.017 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.004 0.043 -9999 0 -0.46 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.074 -9999 0 -0.35 1 1
PHD1-3/OS9 -0.13 0.17 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.024 0.052 -9999 0 -0.41 1 1
VHL 0.014 0.05 -9999 0 -0.72 1 1
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
HIF1A/JAB1 0 0.07 -9999 0 -10000 0 0
EGLN3 -0.23 0.32 -9999 0 -0.64 85 85
EGLN2 0.017 0 -9999 0 -10000 0 0
EGLN1 0.017 0 -9999 0 -10000 0 0
TP53 -0.013 0.15 -9999 0 -0.72 9 9
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.038 0.031 -9999 0 -10000 0 0
ARNT 0.017 0 -9999 0 -10000 0 0
ARD1A -0.006 0.13 -9999 0 -0.72 7 7
RBX1 0.017 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.12 0.19 -9999 0 -0.39 70 70
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.032 0 -9999 0 -10000 0 0
SMARCC1 0.002 0.085 -9999 0 -10000 0 0
REL 0.016 0.001 -9999 0 -10000 0 0
HDAC7 -0.034 0.15 -9999 0 -0.49 10 10
JUN 0.001 0.11 -9999 0 -0.72 5 5
EP300 0.017 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0 0.1 -9999 0 -0.49 9 9
FOXO1 -0.009 0.13 -9999 0 -0.64 9 9
T-DHT/AR -0.033 0.16 -9999 0 -0.51 10 10
MAP2K6 -0.016 0.13 -9999 0 -0.65 9 9
BRM/BAF57 -0.005 0.051 -9999 0 -0.54 2 2
MAP2K4 -0.001 0.086 -9999 0 -0.64 4 4
SMARCA2 0.018 0.001 -9999 0 -10000 0 0
PDE9A -0.56 0.57 -9999 0 -1.1 111 111
NCOA2 0.018 0 -9999 0 -10000 0 0
CEBPA 0.017 0 -9999 0 -10000 0 0
EHMT2 0.018 0.001 -9999 0 -10000 0 0
cell proliferation 0.014 0.15 -9999 0 -0.47 1 1
NR0B1 0 0.11 -9999 0 -0.72 5 5
EGR1 -0.016 0.15 -9999 0 -0.67 11 11
RXRs/9cRA 0 0 -9999 0 -10000 0 0
AR/RACK1/Src 0.031 0.1 -9999 0 -10000 0 0
AR/GR -0.016 0.13 -9999 0 -0.35 24 24
GNB2L1 0.017 0 -9999 0 -10000 0 0
PKN1 0.017 0 -9999 0 -10000 0 0
RCHY1 0.017 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0 -9999 0 -10000 0 0
MAPK8 0.011 0.067 -9999 0 -0.46 4 4
T-DHT/AR/TIF2/CARM1 0.029 0.1 -9999 0 -10000 0 0
SRC 0.016 0.097 -9999 0 -10000 0 0
NR3C1 -0.054 0.2 -9999 0 -0.64 24 24
KLK3 -0.14 0.12 -9999 0 -0.62 2 2
APPBP2 0.01 0.01 -9999 0 -10000 0 0
TRIM24 0.018 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.035 0.089 -9999 0 -0.42 9 9
TMPRSS2 -0.063 0.11 -9999 0 -1.4 1 1
RXRG 0.017 0 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -0.006 1 1
RXRA 0.017 0 -9999 0 -10000 0 0
RXRB 0.017 0 -9999 0 -10000 0 0
CARM1 0.018 0 -9999 0 -10000 0 0
NR2C2 0.017 0 -9999 0 -10000 0 0
KLK2 0.04 0.091 -9999 0 -10000 0 0
AR 0.02 0.07 -9999 0 -10000 0 0
SENP1 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
MDM2 0.015 0.001 -9999 0 -10000 0 0
SRY 0.012 0.05 -9999 0 -0.72 1 1
GATA2 0.017 0 -9999 0 -10000 0 0
MYST2 0.017 0 -9999 0 -10000 0 0
HOXB13 -0.59 0.28 -9999 0 -0.72 183 183
T-DHT/AR/RACK1/Src 0.024 0.1 -9999 0 -10000 0 0
positive regulation of transcription 0.017 0 -9999 0 -10000 0 0
DNAJA1 0.007 0.052 -9999 0 -0.75 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.04 0 -9999 0 -10000 0 0
NCOA1 0.016 0.067 -9999 0 -0.66 2 2
SPDEF -0.19 0.3 -9999 0 -0.64 71 71
T-DHT/AR/TIF2 0.041 0.063 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.006 0.11 -9999 0 -0.44 1 1
GSK3B 0.012 0.049 -9999 0 -0.72 1 1
NR2C1 0.003 0.098 -9999 0 -0.72 4 4
mol:T-DHT 0.002 0.1 -9999 0 -0.41 9 9
SIRT1 0.017 0 -9999 0 -10000 0 0
ZMIZ2 0.015 0.001 -9999 0 -10000 0 0
POU2F1 0.019 0.019 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.001 0.12 -9999 0 -0.44 4 4
CREBBP 0.017 0 -9999 0 -10000 0 0
SMARCE1 0.011 0.07 -9999 0 -0.72 2 2
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.012 0.16 -9999 0 -0.48 6 6
MAP3K8 -0.088 0.26 -9999 0 -0.72 31 31
FOS 0.004 0.1 -9999 0 -0.42 2 2
PRKCA 0.013 0.051 -9999 0 -0.74 1 1
PTPN7 -0.01 0.14 -9999 0 -0.72 8 8
HRAS 0.017 0.001 -9999 0 -10000 0 0
PRKCB -0.001 0.007 -9999 0 -0.019 33 33
NRAS 0.007 0.086 -9999 0 -0.72 3 3
RAS family/GTP -0.006 0.049 -9999 0 -0.42 3 3
MAPK3 0.008 0.075 -9999 0 -0.42 2 2
MAP2K1 0.011 0.076 -9999 0 -0.51 1 1
ELK1 0.005 0.087 -9999 0 -0.73 3 3
BRAF -0.006 0.025 -9999 0 -0.33 1 1
mol:GTP -0.001 0.002 -9999 0 -0.006 33 33
MAPK1 0.01 0.076 -9999 0 -0.64 1 1
RAF1 -0.006 0.025 -9999 0 -0.33 1 1
KRAS 0.017 0.001 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.017 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.002 0.036 -9999 0 -0.54 1 1
PTK2 -0.021 0.085 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.015 0.063 -9999 0 -10000 0 0
CDC42/GDP 0.055 0.1 -9999 0 -0.39 11 11
Rac1/GDP 0.057 0.1 -9999 0 -0.39 11 11
RAP1B 0.017 0 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
CTNNB1 0 0.11 -9999 0 -0.72 5 5
CDC42/GTP -0.018 0.076 -9999 0 -0.35 11 11
nectin-3/I-afadin -0.023 0.1 -9999 0 -0.46 11 11
RAPGEF1 0.051 0.11 -9999 0 -0.43 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.041 0.12 -9999 0 -0.49 11 11
PDGFB-D/PDGFRB 0.017 0 -9999 0 -10000 0 0
TLN1 0.036 0.047 -9999 0 -10000 0 0
Rap1/GTP -0.016 0.065 -9999 0 -10000 0 0
IQGAP1 0.017 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.023 0.1 -9999 0 -0.46 11 11
PVR 0.014 0.05 -9999 0 -0.72 1 1
Necl-5(dimer) 0.014 0.049 -9999 0 -0.72 1 1
mol:GDP 0.051 0.12 -9999 0 -0.48 11 11
MLLT4 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
PI3K -0.015 0.067 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.019 0.074 -9999 0 -0.32 11 11
PVRL1 0.017 0 -9999 0 -10000 0 0
PVRL3 -0.015 0.14 -9999 0 -0.64 11 11
PVRL2 0.014 0.05 -9999 0 -0.72 1 1
PIK3R1 0.017 0 -9999 0 -10000 0 0
CDH1 -0.001 0.11 -9999 0 -0.64 6 6
CLDN1 -0.7 0.14 -9999 0 -0.72 214 214
JAM-A/CLDN1 -0.41 0.11 -9999 0 -0.76 11 11
SRC -0.028 0.12 -9999 0 -0.55 11 11
ITGB3 0.017 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
FARP2 0.047 0.12 -9999 0 -0.46 11 11
RAC1 0.017 0 -9999 0 -10000 0 0
CTNNA1 0.017 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.021 0.089 -9999 0 -0.46 1 1
nectin-1/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2/I-afadin -0.002 0.036 -9999 0 -0.54 1 1
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.019 0.084 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.017 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.015 0.063 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.05 0.051 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.036 -9999 0 -0.54 1 1
nectin-2(dimer)/I-afadin/I-afadin -0.002 0.036 -9999 0 -0.54 1 1
PIP5K1C 0.026 0.051 -9999 0 -10000 0 0
VAV2 0.037 0.14 -9999 0 -0.5 14 14
RAP1/GDP -0.019 0.077 -9999 0 -0.42 1 1
ITGAV 0.014 0.05 -9999 0 -0.72 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.021 0.089 -9999 0 -0.46 1 1
nectin-3(dimer)/I-afadin/I-afadin -0.023 0.1 -9999 0 -0.46 11 11
Rac1/GTP -0.023 0.09 -9999 0 -0.38 11 11
PTPRM -0.011 0.05 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.017 0.073 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.017 0 -10000 0 -10000 0 0
HDAC4 0.017 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.002 0.015 -10000 0 -10000 0 0
CDKN1A -0.007 0.097 -10000 0 -0.82 3 3
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.014 0.05 -10000 0 -0.72 1 1
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 -0.01 0.13 -10000 0 -0.64 9 9
FOXO4 0.031 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
TAT 0.017 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.008 0.066 -10000 0 -0.55 3 3
PPARGC1A -0.27 0.32 -10000 0 -0.64 99 99
FHL2 0.014 0.05 -10000 0 -0.72 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.002 0.018 -10000 0 -10000 0 0
HIST2H4A 0.002 0.015 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.002 0.016 -10000 0 -10000 0 0
SIRT1 0.003 0.024 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.002 0.018 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.001 0.027 -10000 0 -10000 0 0
apoptosis 0 0.035 0.46 1 -10000 0 1
SIRT1/PGC1A -0.18 0.2 -10000 0 -0.4 99 99
p53/SIRT1 -0.017 0.12 0.42 3 -0.55 9 12
SIRT1/FOXO4 0.002 0.02 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.014 0.085 -10000 0 -0.77 1 1
HIST1H1E 0.029 0.026 -10000 0 -10000 0 0
SIRT1/p300 0.002 0.018 -10000 0 -10000 0 0
muscle cell differentiation 0.004 0.057 0.47 3 -10000 0 3
TP53 -0.027 0.15 -10000 0 -0.73 9 9
KU70/SIRT1/BAX 0 0.036 -10000 0 -0.46 1 1
CREBBP 0.017 0 -10000 0 -10000 0 0
MEF2D 0.017 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.002 0.018 -10000 0 -10000 0 0
ACSS2 0.027 0.036 -10000 0 -0.46 1 1
SIRT1/PCAF/MYOD -0.004 0.057 -10000 0 -0.47 3 3
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.13 0.28 -9999 0 -0.56 65 65
MKNK1 0.017 0 -9999 0 -10000 0 0
MAPK14 -0.034 0.1 -9999 0 -10000 0 0
ATF2/c-Jun -0.008 0.13 -9999 0 -0.7 5 5
MAPK11 -0.037 0.11 -9999 0 -0.68 1 1
MITF -0.022 0.12 -9999 0 -10000 0 0
MAPKAPK5 -0.022 0.12 -9999 0 -10000 0 0
KRT8 -0.029 0.12 -9999 0 -0.33 4 4
MAPKAPK3 0.017 0 -9999 0 -10000 0 0
MAPKAPK2 0.017 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.051 0.15 -9999 0 -0.44 3 3
CEBPB -0.032 0.13 -9999 0 -0.55 2 2
SLC9A1 -0.022 0.12 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.018 0.12 -9999 0 -0.42 2 2
p38alpha-beta/MNK1 -0.059 0.091 -9999 0 -10000 0 0
JUN -0.007 0.13 -9999 0 -0.7 5 5
PPARGC1A -0.2 0.25 -9999 0 -0.44 100 100
USF1 -0.046 0.16 -9999 0 -0.55 10 10
RAB5/GDP/GDI1 -0.038 0.059 -9999 0 -10000 0 0
NOS2 -0.035 0.12 -9999 0 -0.31 3 3
DDIT3 -0.028 0.12 -9999 0 -0.55 1 1
RAB5A 0.017 0 -9999 0 -10000 0 0
HSPB1 -0.008 0.1 -9999 0 -0.46 2 2
p38alpha-beta/HBP1 -0.059 0.091 -9999 0 -0.39 1 1
CREB1 -0.021 0.12 -9999 0 -0.41 3 3
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.007 0.1 -9999 0 -10000 0 0
RPS6KA4 -0.022 0.12 -9999 0 -10000 0 0
PLA2G4A -0.12 0.21 -9999 0 -0.59 16 16
GDI1 -0.022 0.12 -9999 0 -10000 0 0
TP53 -0.044 0.15 -9999 0 -0.57 2 2
RPS6KA5 -0.033 0.14 -9999 0 -0.48 6 6
ESR1 -0.033 0.13 -9999 0 -0.38 6 6
HBP1 0.017 0 -9999 0 -10000 0 0
MEF2C -0.083 0.18 -9999 0 -0.38 34 34
MEF2A -0.022 0.12 -9999 0 -10000 0 0
EIF4EBP1 -0.025 0.12 -9999 0 -0.41 3 3
KRT19 -0.035 0.14 -9999 0 -0.46 7 7
ELK4 -0.03 0.14 -9999 0 -0.55 4 4
ATF6 -0.022 0.12 -9999 0 -10000 0 0
ATF1 -0.021 0.12 -9999 0 -0.41 3 3
p38alpha-beta/MAPKAPK2 -0.059 0.091 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK3 -0.059 0.091 -9999 0 -10000 0 0
IL27-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
TGFB1 0.028 0.016 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.025 0.12 0.86 1 -10000 0 1
IL27/IL27R/JAK1 -0.057 0.11 -10000 0 -0.82 1 1
TBX21 -0.16 0.27 -10000 0 -0.66 7 7
IL12B 0.008 0.071 -10000 0 -0.73 2 2
IL12A -0.005 0.1 -10000 0 -0.56 7 7
IL6ST 0.009 0.009 -10000 0 -10000 0 0
IL27RA/JAK1 0.003 0.053 -10000 0 -0.53 1 1
IL27 -0.04 0.18 -10000 0 -0.67 16 16
TYK2 0.014 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.093 0.14 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.025 0.12 0.86 1 -10000 0 1
T cell proliferation during immune response 0.025 0.12 0.86 1 -10000 0 1
MAPKKK cascade -0.025 0.12 -10000 0 -0.86 1 1
STAT3 0.017 0 -10000 0 -10000 0 0
STAT2 0.017 0 -10000 0 -10000 0 0
STAT1 -0.051 0.21 -10000 0 -0.72 20 20
IL12RB1 0.014 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.072 0.18 -10000 0 -0.64 4 4
IL27/IL27R/JAK2/TYK2 -0.025 0.12 -10000 0 -0.88 1 1
positive regulation of T cell mediated cytotoxicity -0.025 0.12 -10000 0 -0.86 1 1
STAT1 (dimer) -0.14 0.18 -10000 0 -0.9 3 3
JAK2 -0.001 0.1 -10000 0 -0.75 4 4
JAK1 0.015 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.014 0.11 -10000 0 -0.83 1 1
T cell proliferation -0.2 0.24 -10000 0 -0.54 41 41
IL12/IL12R/TYK2/JAK2 -0.008 0.12 -10000 0 -0.56 1 1
IL17A -0.094 0.14 -10000 0 -10000 0 0
mast cell activation 0.025 0.12 0.86 1 -10000 0 1
IFNG -0.012 0.046 -10000 0 -0.1 16 16
T cell differentiation -0.007 0.007 -10000 0 -0.025 1 1
STAT3 (dimer) -0.014 0.11 -10000 0 -0.83 1 1
STAT5A (dimer) -0.014 0.11 -10000 0 -0.83 1 1
STAT4 (dimer) -0.016 0.11 -10000 0 -0.83 1 1
STAT4 0.014 0.044 -10000 0 -0.64 1 1
T cell activation -0.01 0.01 0.084 2 -10000 0 2
IL27R/JAK2/TYK2 -0.024 0.087 -10000 0 -0.92 1 1
GATA3 0.021 0.032 -10000 0 -10000 0 0
IL18 -0.041 0.16 -10000 0 -0.48 25 25
positive regulation of mast cell cytokine production -0.014 0.11 -10000 0 -0.8 1 1
IL27/EBI3 -0.036 0.13 -10000 0 -0.5 16 16
IL27RA -0.01 0.052 -10000 0 -0.59 1 1
IL6 -0.31 0.37 -10000 0 -0.71 103 103
STAT5A 0.017 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.007 0.033 -10000 0 -10000 0 0
IL1B -0.09 0.22 -10000 0 -0.55 41 41
EBI3 0.008 0.009 -10000 0 -10000 0 0
TNF 0.015 0.002 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.011 0.15 -9999 0 -0.62 11 11
VEGFR1 homodimer/NRP1 -0.031 0.14 -9999 0 -0.63 11 11
mol:DAG -0.023 0.21 -9999 0 -0.68 13 13
VEGFR1 homodimer/NRP1/VEGFR 121 -0.067 0.2 -9999 0 -0.72 11 11
CaM/Ca2+ -0.013 0.2 -9999 0 -0.88 6 6
HIF1A 0.005 0.12 -9999 0 -1 2 2
GAB1 0.011 0.062 -9999 0 -0.64 2 2
AKT1 0.04 0.15 -9999 0 -0.87 3 3
PLCG1 -0.024 0.22 -9999 0 -0.69 13 13
NOS3 0.033 0.16 -9999 0 -0.76 4 4
CBL 0.017 0 -9999 0 -10000 0 0
mol:NO 0.034 0.15 -9999 0 -0.71 4 4
FLT1 0.004 0.17 -9999 0 -0.71 11 11
PGF -0.013 0.15 -9999 0 -0.72 9 9
VEGFR1 homodimer/NRP2/VEGFR121 -0.068 0.2 -9999 0 -1.1 5 5
CALM1 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.04 0.15 -9999 0 -0.68 4 4
endothelial cell proliferation -0.001 0.18 -9999 0 -0.79 6 6
mol:Ca2+ -0.023 0.21 -9999 0 -0.67 13 13
MAPK3 -0.003 0.2 -9999 0 -0.79 7 7
MAPK1 -0.002 0.19 -9999 0 -0.8 6 6
PIK3R1 0.017 0 -9999 0 -10000 0 0
PLGF homodimer -0.013 0.15 -9999 0 -0.72 9 9
PRKACA 0.017 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.004 0.096 -9999 0 -0.7 4 4
VEGFA homodimer -0.053 0.22 -9999 0 -0.72 21 21
VEGFR1 homodimer/VEGFA homodimer -0.034 0.22 -9999 0 -0.77 11 11
platelet activating factor biosynthetic process 0.005 0.19 -9999 0 -0.76 7 7
PI3K -0.041 0.15 -9999 0 -1 3 3
PRKCA -0.012 0.2 -9999 0 -0.85 6 6
PRKCB -0.021 0.2 -9999 0 -0.64 13 13
VEGFR1 homodimer/PLGF homodimer -0.008 0.19 -9999 0 -0.6 18 18
VEGFA -0.053 0.22 -9999 0 -0.72 21 21
VEGFB 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.023 0.21 -9999 0 -0.68 13 13
RASA1 0.02 0.15 -9999 0 -0.56 11 11
NRP2 0.014 0.05 -9999 0 -0.72 1 1
VEGFR1 homodimer 0.005 0.17 -9999 0 -0.71 11 11
VEGFB homodimer 0.017 0 -9999 0 -10000 0 0
NCK1 0.017 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.035 0.15 -9999 0 -0.68 4 4
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
mol:PI-3-4-5-P3 -0.04 0.15 -9999 0 -0.97 3 3
mol:L-citrulline 0.034 0.15 -9999 0 -0.71 4 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.061 0.18 -9999 0 -0.94 5 5
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.066 0.19 -9999 0 -0.99 5 5
CD2AP 0.017 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.041 0.15 -9999 0 -1 3 3
PDPK1 0.026 0.16 -9999 0 -0.91 3 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.068 0.19 -9999 0 -0.99 5 5
mol:NADP 0.034 0.15 -9999 0 -0.71 4 4
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
ubiquitin-dependent protein catabolic process -0.061 0.18 -9999 0 -0.92 5 5
VEGFR1 homodimer/NRP2 0.009 0.16 -9999 0 -0.66 11 11
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.042 0.081 -9999 0 -10000 0 0
adherens junction organization -0.087 0.068 -9999 0 -0.39 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.038 0.11 -9999 0 -0.55 2 2
FMN1 0.029 0.067 -9999 0 -0.31 2 2
mol:IP3 -0.026 0.083 -9999 0 -0.44 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.03 0.07 -9999 0 -0.32 2 2
CTNNB1 0 0.11 -9999 0 -0.72 5 5
AKT1 0.045 0.064 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.037 0.09 -9999 0 -0.42 6 6
CTNND1 0.017 0.005 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0.066 -9999 0 -10000 0 0
VASP 0.04 0.067 -9999 0 -10000 0 0
ZYX 0.038 0.072 -9999 0 -0.35 1 1
JUB -0.35 0.1 -9999 0 -0.37 211 211
EGFR(dimer) 0.03 0.091 -9999 0 -0.43 3 3
E-cadherin/beta catenin-gamma catenin -0.018 0.091 -9999 0 -0.41 11 11
mol:PI-3-4-5-P3 -0.016 0.049 -9999 0 -10000 0 0
PIK3CA 0.017 0.005 -9999 0 -10000 0 0
PI3K -0.016 0.05 -9999 0 -10000 0 0
FYN 0.043 0.098 -9999 0 -0.5 1 1
mol:Ca2+ -0.026 0.081 -9999 0 -0.42 2 2
JUP 0.017 0.003 -9999 0 -10000 0 0
PIK3R1 0.017 0.005 -9999 0 -10000 0 0
mol:DAG -0.026 0.083 -9999 0 -0.44 2 2
CDH1 -0.001 0.1 -9999 0 -0.63 6 6
RhoA/GDP 0.038 0.11 -9999 0 -0.55 2 2
establishment of polarity of embryonic epithelium 0.04 0.066 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
EGFR 0.002 0.099 -9999 0 -0.65 5 5
CASR 0.032 0.11 -9999 0 -0.45 4 4
RhoA/GTP -0.023 0.073 -9999 0 -0.38 2 2
AKT2 0.045 0.064 -9999 0 -10000 0 0
actin cable formation 0.039 0.065 -9999 0 -10000 0 0
apoptosis 0.014 0.044 -9999 0 -10000 0 0
CTNNA1 0.017 0.005 -9999 0 -10000 0 0
mol:GDP 0.029 0.12 -9999 0 -0.51 4 4
PIP5K1A 0.04 0.067 -9999 0 -10000 0 0
PLCG1 -0.027 0.085 -9999 0 -0.44 2 2
Rac1/GTP -0.019 0.067 -9999 0 -0.44 1 1
homophilic cell adhesion 0.001 0.003 -9999 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.021 0.091 -9999 0 -0.42 11 11
E-cadherin/beta catenin -0.025 0.11 -9999 0 -0.5 11 11
CTNNB1 0 0.11 -9999 0 -0.72 5 5
JUP 0.017 0 -9999 0 -10000 0 0
CDH1 -0.001 0.11 -9999 0 -0.64 6 6
Canonical NF-kappaB pathway

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
FBXW11 0.022 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.062 0.078 -9999 0 -10000 0 0
ERC1 0.017 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.21 0.3 -9999 0 -0.6 79 79
NFKBIA 0.064 0 -9999 0 -10000 0 0
BIRC2 0.017 0 -9999 0 -10000 0 0
IKBKB 0.014 0.05 -9999 0 -0.72 1 1
RIPK2 -0.12 0.29 -9999 0 -0.72 42 42
IKBKG -0.057 0.08 -9999 0 -10000 0 0
IKK complex/A20 -0.042 0.069 -9999 0 -0.58 1 1
NEMO/A20/RIP2 -0.12 0.29 -9999 0 -0.72 42 42
XPO1 0.017 0 -9999 0 -10000 0 0
NEMO/ATM -0.006 0.1 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0.05 -9999 0 -0.72 1 1
Exportin 1/RanGTP -0.002 0.031 -9999 0 -0.47 1 1
IKK complex/ELKS -0.041 0.067 -9999 0 -0.56 1 1
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.14 0.3 -9999 0 -0.72 47 47
NFKB1 0.022 0 -9999 0 -10000 0 0
RELA 0.022 0 -9999 0 -10000 0 0
MALT1 0.017 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.017 0 -9999 0 -10000 0 0
TNF/TNFR1A 0 0 -9999 0 -10000 0 0
TRAF6 0.017 0 -9999 0 -10000 0 0
PRKCA 0.014 0.05 -9999 0 -0.72 1 1
CHUK 0.017 0 -9999 0 -10000 0 0
UBE2D3 0.017 0 -9999 0 -10000 0 0
TNF 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.017 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.064 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0 -9999 0 -10000 0 0
TNFRSF1A 0.017 0 -9999 0 -10000 0 0
IKK complex -0.047 0.075 -9999 0 -0.61 1 1
CYLD 0.017 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.044 0.075 -9999 0 -0.53 2 2
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.041 0.058 -10000 0 -0.42 3 3
epithelial cell differentiation -0.016 0.058 -10000 0 -10000 0 0
ITCH 0.018 0.006 -10000 0 -10000 0 0
WWP1 0.049 0.022 -10000 0 -10000 0 0
FYN 0.014 0.044 -10000 0 -0.64 1 1
EGFR 0.002 0.099 -10000 0 -0.65 5 5
PRL 0.014 0.05 -10000 0 -0.72 1 1
neuron projection morphogenesis 0.088 0.04 -10000 0 -10000 0 0
PTPRZ1 -0.057 0.21 -10000 0 -0.64 25 25
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0 0.003 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.052 0.018 -10000 0 -10000 0 0
ADAM17 0.018 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4 0.049 0.026 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.045 0.034 -10000 0 -10000 0 0
NCOR1 0.014 0.044 -10000 0 -0.64 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.002 0.021 -10000 0 -10000 0 0
GRIN2B 0.008 0.15 -10000 0 -10000 0 0
ErbB4/ErbB2/betacellulin -0.02 0.079 -10000 0 -0.46 1 1
STAT1 -0.05 0.21 -10000 0 -0.72 20 20
HBEGF 0.007 0.085 -10000 0 -0.72 3 3
PRLR 0.004 0.098 -10000 0 -0.72 4 4
E4ICDs/ETO2 -0.1 0.2 -10000 0 -0.45 2 2
axon guidance 0.056 0.068 -10000 0 -10000 0 0
NEDD4 -0.003 0.12 -10000 0 -0.72 6 6
Prolactin receptor/Prolactin receptor/Prolactin -0.012 0.08 -10000 0 -0.54 5 5
CBFA2T3 -0.22 0.32 -10000 0 -0.64 82 82
ErbB4/ErbB2/HBEGF -0.018 0.078 -10000 0 -0.46 1 1
MAPK3 0.08 0.035 -10000 0 -10000 0 0
STAT1 (dimer) 0.005 0.14 -10000 0 -0.42 20 20
MAPK1 0.082 0.027 -10000 0 -10000 0 0
JAK2 0.004 0.098 -10000 0 -0.72 4 4
ErbB4/ErbB2/neuregulin 1 beta -0.013 0.066 -10000 0 -0.46 1 1
NRG1 0.032 0.003 -10000 0 -10000 0 0
NRG3 0.014 0.044 -10000 0 -0.64 1 1
NRG2 0.002 0.097 -10000 0 -0.64 5 5
NRG4 -0.005 0.12 -10000 0 -0.67 7 7
heart development 0.056 0.068 -10000 0 -10000 0 0
neural crest cell migration -0.013 0.065 -10000 0 -0.46 1 1
ERBB2 0.014 0.099 -10000 0 -0.53 7 7
WWOX/E4ICDs 0.047 0.021 -10000 0 -10000 0 0
SHC1 0.017 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.02 0.079 -10000 0 -0.43 1 1
apoptosis 0.044 0.052 0.62 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.038 0.063 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.27 0.19 -10000 0 -0.65 10 10
ErbB4/ErbB4/betacellulin/betacellulin 0.038 0.063 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.019 0.075 -10000 0 -10000 0 0
MDM2 0.054 0.022 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.004 -10000 0 -10000 0 0
STAT5A 0.063 0.063 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.008 0.048 -10000 0 -10000 0 0
DLG4 0.017 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.003 0.023 -10000 0 -10000 0 0
STAT5A (dimer) -0.017 0.062 -10000 0 -10000 0 0
MAP3K7IP2 0.017 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.059 0.059 -10000 0 -10000 0 0
LRIG1 -0.01 0.13 -10000 0 -0.64 9 9
EREG -0.49 0.34 -10000 0 -0.72 153 153
BTC 0.002 0.097 -10000 0 -0.64 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.056 0.068 -10000 0 -10000 0 0
ERBB4 0.049 0.026 -10000 0 -10000 0 0
STAT5B 0.017 0 -10000 0 -10000 0 0
YAP1 -0.003 0.026 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.023 0.088 -10000 0 -0.46 1 1
glial cell differentiation 0.003 0.023 -10000 0 -10000 0 0
WWOX 0.017 0 -10000 0 -10000 0 0
cell proliferation 0.055 0.089 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0 0 -10000 0 -10000 0 0
ATM 0.017 0 -10000 0 -10000 0 0
UBE2D3 0.017 0 -10000 0 -10000 0 0
PRKDC -0.046 0.21 -10000 0 -0.72 19 19
ATR 0.014 0.05 -10000 0 -0.72 1 1
UBE2L3 0.017 0 -10000 0 -10000 0 0
FANCD2 0.032 0.032 -10000 0 -10000 0 0
protein ubiquitination -0.072 0.17 -10000 0 -0.76 6 6
XRCC5 0.017 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.017 0 -10000 0 -10000 0 0
DNA-PK -0.039 0.13 -10000 0 -0.46 19 19
FA complex/FANCD2/Ubiquitin -0.045 0.099 -10000 0 -0.48 6 6
FANCF 0.011 0.062 -10000 0 -0.64 2 2
BRCA1 0.004 0.098 -10000 0 -0.72 4 4
CCNE1 -0.033 0.19 -10000 0 -0.72 15 15
CDK2/Cyclin E1 -0.093 0.22 -10000 0 -0.59 35 35
FANCG -0.016 0.15 -10000 0 -0.72 10 10
BRCA1/BACH1/BARD1 -0.01 0.072 -10000 0 -0.54 4 4
FANCE 0.014 0.05 -10000 0 -0.72 1 1
FANCC 0.017 0 -10000 0 -10000 0 0
NBN 0.017 0 -10000 0 -10000 0 0
FANCA -0.16 0.31 -10000 0 -0.72 52 52
DNA repair 0.013 0.15 -10000 0 -0.6 4 4
BRCA1/BARD1/ubiquitin -0.01 0.072 -10000 0 -0.54 4 4
BARD1/DNA-PK -0.035 0.11 -10000 0 -10000 0 0
FANCL 0.017 0 -10000 0 -10000 0 0
mRNA polyadenylation 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.052 0.022 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.008 0.061 -10000 0 -0.46 4 4
BRCA1/BARD1/P53 -0.026 0.11 -10000 0 -0.44 13 13
BARD1/CSTF1/BRCA1 -0.008 0.061 -10000 0 -0.46 4 4
BRCA1/BACH1 0.004 0.098 -10000 0 -0.72 4 4
BARD1 0.017 0 -10000 0 -10000 0 0
PCNA -0.01 0.14 -10000 0 -0.72 8 8
BRCA1/BARD1/UbcH5C -0.008 0.061 -10000 0 -0.46 4 4
BRCA1/BARD1/UbcH7 -0.008 0.061 -10000 0 -0.46 4 4
BRCA1/BARD1/RAD51/PCNA -0.022 0.11 -10000 0 -0.49 10 10
BARD1/DNA-PK/P53 -0.048 0.14 -10000 0 -0.78 2 2
BRCA1/BARD1/Ubiquitin -0.01 0.072 -10000 0 -0.54 4 4
BRCA1/BARD1/CTIP -0.007 0.054 -10000 0 -0.41 4 4
FA complex -0.02 0.13 -10000 0 -0.42 9 9
BARD1/EWS -0.002 0.036 -10000 0 -0.54 1 1
RBBP8 0.031 0 -10000 0 -10000 0 0
TP53 -0.013 0.15 -10000 0 -0.72 9 9
TOPBP1 0.017 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.026 0.11 0.44 13 -10000 0 13
BRCA1/BARD1 -0.073 0.17 -10000 0 -0.77 6 6
CSTF1 0.017 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0 0 -10000 0 -10000 0 0
CDK2 -0.063 0.23 -10000 0 -0.72 24 24
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.017 0 -10000 0 -10000 0 0
RAD50 0.017 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.01 0.072 -10000 0 -0.54 4 4
EWSR1 0.014 0.05 -10000 0 -0.72 1 1
a4b1 and a4b7 Integrin 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
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
ITGB7 -0.01 0.13 -9999 0 -0.64 9 9
ITGA4 0.011 0.062 -9999 0 -0.64 2 2
alpha4/beta7 Integrin -0.023 0.1 -9999 0 -0.46 11 11
alpha4/beta1 Integrin -0.007 0.056 -9999 0 -0.49 3 3
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.041 0 -9999 0 -10000 0 0
SNTA1 0.017 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.039 0.033 -9999 0 -0.46 1 1
MAPK12 -0.025 0.14 -9999 0 -0.4 14 14
CCND1 -0.031 0.1 -9999 0 -0.35 10 10
p38 gamma/SNTA1 -0.014 0.13 -9999 0 -0.71 1 1
MAP2K3 0.017 0 -9999 0 -10000 0 0
PKN1 0.017 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.024 0.14 -9999 0 -0.39 14 14
MAP2K6 -0.026 0.13 -9999 0 -0.38 9 9
MAPT 0.022 0.045 -9999 0 -10000 0 0
MAPK13 0.031 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.026 0.12 -9999 0 -0.31 33 33
Nongenotropic Androgen signaling

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
PTK2 0.013 0.038 -10000 0 -0.55 1 1
GNB1/GNG2 -0.002 0.028 -10000 0 -0.42 1 1
regulation of S phase of mitotic cell cycle 0.04 0.018 -10000 0 -10000 0 0
GNAO1 0.017 0 -10000 0 -10000 0 0
HRAS 0.017 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0.017 0.002 -10000 0 -10000 0 0
AKT1 0.016 0.001 -10000 0 -10000 0 0
MAP2K1 0.048 0.053 -10000 0 -10000 0 0
T-DHT/AR -0.001 0.037 -10000 0 -0.55 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 0.017 0 -10000 0 -10000 0 0
GNAI3 0.017 0 -10000 0 -10000 0 0
GNAI1 -0.068 0.22 -10000 0 -0.64 29 29
mol:GDP -0.002 0.023 -10000 0 -0.34 1 1
cell proliferation 0.029 0.16 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
FOS -0.049 0.32 -10000 0 -0.81 33 33
mol:Ca2+ -0.009 0.023 -10000 0 -0.079 13 13
MAPK3 0.04 0.11 -10000 0 -10000 0 0
MAPK1 0.02 0.088 -10000 0 -0.41 1 1
PIK3R1 0.017 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 33 33
cAMP biosynthetic process 0.008 0.02 -10000 0 -10000 0 0
GNG2 0.017 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 33 33
HRAS/GTP -0.004 0.025 -10000 0 -0.36 1 1
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.017 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 33 33
PI3K 0 0 -10000 0 -10000 0 0
apoptosis -0.014 0.16 0.37 31 -10000 0 31
T-DHT/AR/PELP1 0 0.032 -10000 0 -0.47 1 1
HRAS/GDP -0.001 0.021 -10000 0 -10000 0 0
CREB1 0.011 0.17 -10000 0 -0.4 31 31
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR 0.013 0.049 -10000 0 -0.72 1 1
GNB1 0.017 0 -10000 0 -10000 0 0
RAF1 0.042 0.043 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.001 0.019 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0 0.028 -10000 0 -0.42 1 1
MAP2K2 0.048 0.053 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0.04 0.018 -10000 0 -10000 0 0
GNAZ 0.017 0 -10000 0 -10000 0 0
SHBG 0.017 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.033 0.082 -10000 0 -10000 0 0
mol:T-DHT 0 0.001 -10000 0 -0.003 33 33
RAC1 0.017 0 -10000 0 -10000 0 0
GNRH1 0.015 0.001 -10000 0 -10000 0 0
Gi family/GTP -0.029 0.073 -10000 0 -10000 0 0
CDC42 0.017 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.002 0.036 -9999 0 -0.54 1 1
AKT1 0.039 0.17 -9999 0 -0.66 2 2
PTK2B 0.019 0.15 -9999 0 -10000 0 0
VEGFR2 homodimer/Frs2 -0.01 0.068 -9999 0 -10000 0 0
CAV1 0.004 0.096 -9999 0 -0.7 4 4
CALM1 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.06 0.14 -9999 0 -0.57 7 7
endothelial cell proliferation 0.039 0.18 -9999 0 -0.65 3 3
mol:Ca2+ -0.031 0.24 -9999 0 -0.73 14 14
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.055 0.13 -9999 0 -0.54 6 6
RP11-342D11.1 -0.016 0.2 -9999 0 -0.66 10 10
CDH5 0.017 0 -9999 0 -10000 0 0
VEGFA homodimer -0.045 0.14 -9999 0 -0.44 23 23
SHC1 0.017 0 -9999 0 -10000 0 0
SHC2 -0.02 0.16 -9999 0 -0.72 11 11
HRAS/GDP -0.063 0.14 -9999 0 -0.58 7 7
SH2D2A -0.01 0.14 -9999 0 -0.72 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.06 0.12 -9999 0 -0.66 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.074 0.15 -9999 0 -0.58 6 6
VEGFR1 homodimer -0.02 0.16 -9999 0 -0.72 11 11
SHC/GRB2/SOS1 -0.071 0.15 -9999 0 -0.65 7 7
GRB10 -0.027 0.26 -9999 0 -0.77 17 17
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
GRB2 0.017 0 -9999 0 -10000 0 0
PAK1 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.059 0.14 -9999 0 -0.55 8 8
HRAS 0.017 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.039 0.081 -9999 0 -10000 0 0
HIF1A 0.01 0.07 -9999 0 -0.72 2 2
FRS2 0.017 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.054 0.13 -9999 0 -0.53 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.017 0 -9999 0 -10000 0 0
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.062 0.14 -9999 0 -0.57 8 8
mol:GDP -0.069 0.15 -9999 0 -0.63 7 7
mol:NADP 0.031 0.16 -9999 0 -0.56 3 3
eNOS/Hsp90 0.036 0.15 -9999 0 -0.55 2 2
PIK3R1 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.032 0.25 -9999 0 -0.75 14 14
HIF1A/ARNT -0.005 0.051 -9999 0 -0.54 2 2
SHB -0.016 0.15 -9999 0 -0.72 10 10
VEGFA -0.054 0.22 -9999 0 -0.74 21 21
VEGFC 0.008 0.075 -9999 0 -0.64 3 3
FAK1/Vinculin 0.048 0.14 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.056 0.13 -9999 0 -0.54 6 6
PTPN6 0.017 0 -9999 0 -10000 0 0
EPAS1 0.008 0.11 -9999 0 -0.61 7 7
mol:L-citrulline 0.031 0.16 -9999 0 -0.56 3 3
ITGAV 0.014 0.05 -9999 0 -0.72 1 1
PIK3CA 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.055 0.13 -9999 0 -0.54 6 6
VEGFR2 homodimer/VEGFA homodimer -0.088 0.18 -9999 0 -0.72 10 10
VEGFR2/3 heterodimer -0.01 0.068 -9999 0 -10000 0 0
VEGFB 0.017 0 -9999 0 -10000 0 0
MAPK11 0.004 0.2 -9999 0 -0.64 10 10
VEGFR2 homodimer 0.03 0.093 -9999 0 -0.56 1 1
FLT1 -0.02 0.16 -9999 0 -0.72 11 11
NEDD4 -0.003 0.12 -9999 0 -0.73 6 6
MAPK3 -0.019 0.22 -9999 0 -0.66 14 14
MAPK1 -0.019 0.22 -9999 0 -0.66 14 14
VEGFA145/NRP2 -0.055 0.17 -9999 0 -0.57 21 21
VEGFR1/2 heterodimer -0.033 0.12 -9999 0 -0.47 2 2
KDR 0.03 0.093 -9999 0 -0.56 1 1
VEGFA165/NRP1/VEGFR2 homodimer -0.08 0.17 -9999 0 -0.65 11 11
SRC 0.017 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.017 0.23 -9999 0 -0.67 14 14
PI3K -0.08 0.16 -9999 0 -0.94 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.06 0.14 -9999 0 -0.58 6 6
FES -0.009 0.22 -9999 0 -0.7 10 10
GAB1 -0.069 0.14 -9999 0 -0.71 2 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.06 0.14 -9999 0 -0.58 6 6
CTNNB1 0 0.11 -9999 0 -0.72 5 5
SOS1 0.017 0 -9999 0 -10000 0 0
ARNT 0.017 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.032 0.16 -9999 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.06 0.14 -9999 0 -0.57 7 7
PI3K/GAB1 0.04 0.17 -9999 0 -0.79 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.051 0.12 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.017 0.072 -9999 0 -10000 0 0
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
CDC42 -0.006 0.21 -9999 0 -0.67 10 10
actin cytoskeleton reorganization -0.073 0.15 -9999 0 -0.57 6 6
PTK2 0.04 0.14 -9999 0 -10000 0 0
EDG1 -0.027 0.26 -9999 0 -0.77 17 17
mol:DAG -0.032 0.25 -9999 0 -0.75 14 14
CaM/Ca2+ -0.093 0.19 -9999 0 -0.68 14 14
MAP2K3 0.007 0.2 -9999 0 -0.67 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.1 0.23 -9999 0 -0.79 17 17
PLCG1 -0.034 0.25 -9999 0 -0.76 14 14
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.072 0.15 -9999 0 -0.57 7 7
IQGAP1 0.017 0 -9999 0 -10000 0 0
YES1 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.062 0.14 -9999 0 -0.58 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.06 0.14 -9999 0 -0.57 7 7
cell migration 0.078 0.12 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.075 0.14 -9999 0 -0.82 2 2
FYN 0.014 0.044 -9999 0 -0.64 1 1
VEGFB/NRP1 -0.075 0.16 -9999 0 -0.62 10 10
mol:NO 0.031 0.16 -9999 0 -0.56 3 3
PXN 0.017 0 -9999 0 -10000 0 0
HRAS/GTP -0.063 0.14 -9999 0 -0.58 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.1 0.23 -9999 0 -0.79 17 17
VHL 0.014 0.05 -9999 0 -0.72 1 1
ITGB3 0.017 0 -9999 0 -10000 0 0
NOS3 0.028 0.17 -9999 0 -0.65 3 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.081 0.17 -9999 0 -0.6 10 10
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCA -0.019 0.23 -9999 0 -0.7 13 13
PRKCB -0.028 0.23 -9999 0 -0.69 14 14
VCL 0.017 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.018 0.2 -9999 0 -0.67 10 10
VEGFR1/2 heterodimer/VEGFA homodimer -0.08 0.18 -9999 0 -0.67 10 10
VEGFA165/NRP2 -0.055 0.17 -9999 0 -0.57 21 21
MAPKKK cascade -0.08 0.18 -9999 0 -0.81 7 7
NRP2 0.014 0.05 -9999 0 -0.72 1 1
VEGFC homodimer 0.008 0.075 -9999 0 -0.63 3 3
NCK1 0.017 0 -9999 0 -10000 0 0
ROCK1 0.017 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.048 0.14 -9999 0 -10000 0 0
MAP3K13 -0.006 0.21 -9999 0 -0.67 10 10
PDPK1 0.026 0.18 -9999 0 -0.69 2 2
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.008 0.075 -10000 0 -0.64 3 3
HRAS 0.017 0 -10000 0 -10000 0 0
EGFR 0.002 0.099 -10000 0 -0.65 5 5
AKT 0.033 0.038 -10000 0 -10000 0 0
FOXO3 0.017 0 -10000 0 -10000 0 0
AKT1 0.017 0 -10000 0 -10000 0 0
FOXO1 -0.01 0.13 -10000 0 -0.64 9 9
AKT3 0.017 0 -10000 0 -10000 0 0
FOXO4 0.017 0 -10000 0 -10000 0 0
MET -0.31 0.37 -10000 0 -0.72 99 99
PIK3CA 0.017 0 -10000 0 -10000 0 0
PIK3CB 0.014 0.05 -10000 0 -0.72 1 1
NRAS 0.007 0.085 -10000 0 -0.72 3 3
PIK3CG -0.001 0.11 -10000 0 -0.64 6 6
PIK3R3 0.017 0 -10000 0 -10000 0 0
PIK3R2 0.017 0 -10000 0 -10000 0 0
NF1 0.017 0 -10000 0 -10000 0 0
RAS -0.043 0.084 -10000 0 -0.31 4 4
ERBB2 -0.006 0.13 -10000 0 -0.71 7 7
proliferation/survival/translation -0.013 0.054 -10000 0 -10000 0 0
PI3K 0.015 0.068 0.22 4 -0.24 7 11
PIK3R1 0.017 0 -10000 0 -10000 0 0
KRAS 0.017 0 -10000 0 -10000 0 0
FOXO 0.036 0.042 -10000 0 -10000 0 0
AKT2 0.017 0 -10000 0 -10000 0 0
PTEN -0.001 0.11 -10000 0 -0.64 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.004 0.11 -10000 0 -0.74 1 1
epithelial cell differentiation -0.017 0.076 -10000 0 -0.38 5 5
CYFIP2 0.011 0.062 -10000 0 -0.64 2 2
ENAH 0.062 0.1 -10000 0 -10000 0 0
EGFR 0.002 0.099 -10000 0 -0.65 5 5
EPHA2 -0.016 0.15 -10000 0 -0.72 10 10
MYO6 0.032 0.086 -10000 0 -10000 0 0
CTNNB1 0 0.11 -10000 0 -0.72 5 5
ABI1/Sra1/Nap1 -0.006 0.047 -10000 0 -0.46 1 1
AQP5 -0.033 0.089 -10000 0 -0.57 1 1
CTNND1 0.017 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.081 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.018 0.11 -10000 0 -0.62 1 1
EGF -0.18 0.31 -10000 0 -0.68 64 64
NCKAP1 0.014 0.05 -10000 0 -0.72 1 1
AQP3 -0.031 0.086 -10000 0 -0.53 1 1
cortical microtubule organization -0.017 0.076 -10000 0 -0.38 5 5
GO:0000145 0.033 0.077 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.017 0.077 -10000 0 -0.39 5 5
MLLT4 0.017 0 -10000 0 -10000 0 0
ARF6/GDP -0.026 0.1 -10000 0 -0.59 5 5
ARF6 0.017 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.085 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.048 0.079 -10000 0 -10000 0 0
PVRL2 0.014 0.05 -10000 0 -0.72 1 1
ZYX 0.032 0.086 -10000 0 -10000 0 0
ARF6/GTP -0.017 0.077 -10000 0 -10000 0 0
CDH1 -0.001 0.11 -10000 0 -0.64 6 6
EGFR/EGFR/EGF/EGF -0.11 0.16 -10000 0 -0.66 4 4
RhoA/GDP -0.016 0.07 -10000 0 -10000 0 0
actin cytoskeleton organization 0.041 0.082 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.017 0 -10000 0 -10000 0 0
GIT1 0.017 0 -10000 0 -10000 0 0
IGF1R 0.017 0 -10000 0 -10000 0 0
IGF1 -0.35 0.32 -10000 0 -0.64 125 125
DIAPH1 -0.007 0.069 -10000 0 -0.71 2 2
Wnt receptor signaling pathway 0.017 0.076 0.38 5 -10000 0 5
RHOA 0.017 0 -10000 0 -10000 0 0
RhoA/GTP -0.026 0.1 -10000 0 -0.6 5 5
CTNNA1 0.017 0 -10000 0 -10000 0 0
VCL 0.041 0.084 -10000 0 -10000 0 0
EFNA1 0.017 0 -10000 0 -10000 0 0
LPP 0.042 0.082 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.031 0.12 -10000 0 -0.7 5 5
SEC6/SEC8 -0.015 0.062 -10000 0 -10000 0 0
MGAT3 0.018 0.11 -10000 0 -0.63 1 1
HGF/MET -0.17 0.18 -10000 0 -0.68 4 4
HGF 0.01 0.07 -10000 0 -0.72 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.004 0.11 -10000 0 -0.75 1 1
actin cable formation 0.087 0.09 -10000 0 -0.41 1 1
KIAA1543 0.042 0.087 -10000 0 -0.6 1 1
KIFC3 0.026 0.11 -10000 0 -0.75 2 2
NCK1 0.017 0 -10000 0 -10000 0 0
EXOC3 0.017 0 -10000 0 -10000 0 0
ACTN1 0.034 0.082 -10000 0 -10000 0 0
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.017 0.076 -10000 0 -0.38 5 5
EXOC4 0.017 0 -10000 0 -10000 0 0
STX4 0.034 0.082 -10000 0 -10000 0 0
PIP5K1C 0.034 0.082 -10000 0 -10000 0 0
LIMA1 -0.033 0.17 -10000 0 -0.64 17 17
ABI1 0.017 0 -10000 0 -10000 0 0
ROCK1 -0.023 0.088 -10000 0 -0.5 5 5
adherens junction assembly 0.059 0.1 -10000 0 -0.58 3 3
IGF-1R heterotetramer/IGF1 -0.17 0.16 -10000 0 -0.62 6 6
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.036 -10000 0 -0.54 1 1
MET -0.31 0.37 -10000 0 -0.72 99 99
PLEKHA7 0.034 0.082 -10000 0 -10000 0 0
mol:GTP -0.018 0.084 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.067 0.077 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.004 0.11 -10000 0 -0.74 1 1
regulation of cell-cell adhesion 0.041 0.082 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.004 0.11 -10000 0 -0.75 1 1
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.003 0.057 0.27 6 -10000 0 6
DAPP1 -0.037 0.16 -10000 0 -0.56 11 11
Src family/SYK family/BLNK-LAT/BTK-ITK -0.037 0.21 -10000 0 -0.66 11 11
mol:DAG -0.036 0.13 0.23 1 -0.28 13 14
HRAS 0.018 0.003 -10000 0 -10000 0 0
RAP1A 0.017 0.003 -10000 0 -10000 0 0
ARF5/GDP 0.033 0.069 -10000 0 -0.28 3 3
PLCG2 -0.31 0.33 -10000 0 -0.64 110 110
PLCG1 -0.033 0.19 -10000 0 -0.72 15 15
ARF5 0.017 0 -10000 0 -10000 0 0
mol:GTP 0.002 0.057 -10000 0 -10000 0 0
ARF1/GTP 0.002 0.055 0.25 6 -10000 0 6
RHOA 0.017 0 -10000 0 -10000 0 0
YES1 0.017 0 -10000 0 -10000 0 0
RAP1A/GTP 0.002 0.055 -10000 0 -10000 0 0
ADAP1 0.002 0.054 -10000 0 -10000 0 0
ARAP3 0.002 0.056 -10000 0 -10000 0 0
INPPL1 0.017 0 -10000 0 -10000 0 0
PREX1 0.017 0 -10000 0 -10000 0 0
ARHGEF6 0.011 0.062 -10000 0 -0.64 2 2
ARHGEF7 0.017 0 -10000 0 -10000 0 0
ARF1 0.017 0 -10000 0 -10000 0 0
NRAS 0.008 0.085 -10000 0 -0.72 3 3
FYN 0.014 0.044 -10000 0 -0.64 1 1
ARF6 0.017 0 -10000 0 -10000 0 0
FGR 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.071 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.011 0.062 -10000 0 -0.64 2 2
ZAP70 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.019 0.095 -10000 0 -0.28 1 1
LYN 0.017 0 -10000 0 -10000 0 0
ARF1/GDP 0.033 0.069 -10000 0 -0.28 3 3
RhoA/GDP -0.002 0.058 0.26 5 -10000 0 5
PDK1/Src/Hsp90 -0.002 0.031 -10000 0 -0.46 1 1
BLNK -0.001 0.11 -10000 0 -0.64 6 6
actin cytoskeleton reorganization 0.055 0.079 -10000 0 -0.4 1 1
SRC 0.017 0 -10000 0 -10000 0 0
PLEKHA2 0.023 0.047 -10000 0 -0.47 2 2
RAC1 0.017 0 -10000 0 -10000 0 0
PTEN -0.016 0.099 -10000 0 -0.61 6 6
HSP90AA1 0.014 0.05 -10000 0 -0.72 1 1
ARF6/GTP 0.003 0.057 0.27 6 -10000 0 6
RhoA/GTP 0.002 0.054 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.02 0.16 -10000 0 -0.45 13 13
BLK -0.16 0.29 -10000 0 -0.64 61 61
PDPK1 0.017 0 -10000 0 -10000 0 0
CYTH1 0.002 0.054 -10000 0 -10000 0 0
HCK -0.045 0.19 -10000 0 -0.64 21 21
CYTH3 0.002 0.054 -10000 0 -10000 0 0
CYTH2 0.002 0.054 -10000 0 -10000 0 0
KRAS 0.018 0.003 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.003 0.039 0.2 6 -10000 0 6
SGK1 0.003 0.04 0.21 6 -10000 0 6
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.072 -10000 0 -0.31 3 3
SOS1 0.017 0 -10000 0 -10000 0 0
SYK 0.014 0.05 -10000 0 -0.72 1 1
ARF6/GDP -0.002 0.058 0.27 5 -10000 0 5
mol:PI-3-4-5-P3 0.004 0.066 0.32 6 -10000 0 6
ARAP3/RAP1A/GTP 0.002 0.056 -10000 0 -10000 0 0
VAV1 -0.042 0.19 -10000 0 -0.64 20 20
mol:PI-3-4-P2 0.015 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.027 0.044 -10000 0 -0.35 3 3
PLEKHA1 0.027 0 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.069 -10000 0 -10000 0 0
LAT 0.01 0.07 -10000 0 -0.72 2 2
Rac1/GTP 0.029 0.089 -10000 0 -0.51 2 2
ITK 0.002 0.055 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.058 0.17 0.26 1 -0.4 14 15
LCK 0.011 0.066 -10000 0 -0.68 2 2
BTK -0.044 0.13 -10000 0 -0.64 2 2
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.009 0.052 -10000 0 -10000 0 0
ER alpha/Gai/GDP/Gbeta gamma 0.022 0.11 -10000 0 -0.58 3 3
AKT1 0.025 0.14 -10000 0 -0.82 6 6
PIK3CA 0.017 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.021 0.14 -10000 0 -0.84 6 6
mol:Ca2+ -0.092 0.19 -10000 0 -0.43 14 14
IGF1R 0.017 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.015 0.077 -10000 0 -0.42 8 8
SHC1 0.017 0 -10000 0 -10000 0 0
apoptosis -0.026 0.14 0.78 6 -10000 0 6
RhoA/GTP -0.012 0.058 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.028 0.088 -10000 0 -0.58 3 3
regulation of stress fiber formation -0.06 0.058 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.011 0.064 -10000 0 -0.4 6 6
KRAS 0.017 0 -10000 0 -10000 0 0
G13/GTP -0.01 0.059 -10000 0 -0.36 6 6
pseudopodium formation 0.06 0.058 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.011 0.064 -10000 0 -0.4 6 6
GRB2 0.017 0 -10000 0 -10000 0 0
GNG2 0.017 0 -10000 0 -10000 0 0
GNAO1 0.017 0 -10000 0 -10000 0 0
HRAS 0.017 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.04 0.11 -10000 0 -0.54 6 6
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.071 -10000 0 -0.42 6 6
mol:NADP 0.04 0.11 -10000 0 -0.54 6 6
PIK3R1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.096 0.2 -10000 0 -0.44 14 14
IGF-1R heterotetramer 0.017 0 -10000 0 -10000 0 0
PLCB1 -0.11 0.2 -10000 0 -0.38 74 74
PLCB2 0.009 0.11 -10000 0 -0.44 9 9
IGF1 -0.35 0.32 -10000 0 -0.64 125 125
mol:L-citrulline 0.04 0.11 -10000 0 -0.54 6 6
RHOA 0.017 0 -10000 0 -10000 0 0
Gai/GDP -0.03 0.078 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.017 0 -10000 0 -10000 0 0
ESR2 0.017 0 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.001 0.11 -10000 0 -0.64 6 6
Gq family/GDP/Gbeta gamma 0.017 0.11 -10000 0 -0.48 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.042 0.056 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.028 0.088 -10000 0 -0.58 3 3
GNAZ 0.017 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.013 0.077 -10000 0 -0.47 6 6
STRN 0.01 0.07 -10000 0 -0.72 2 2
GNAL 0.017 0 -10000 0 -10000 0 0
PELP1 0.017 0 -10000 0 -10000 0 0
MAPK11 0.023 0.033 -10000 0 -0.47 1 1
GNAI2 0.017 0 -10000 0 -10000 0 0
GNAI3 0.017 0 -10000 0 -10000 0 0
GNAI1 -0.068 0.22 -10000 0 -0.64 29 29
HBEGF 0.037 0.11 -10000 0 -0.48 3 3
cAMP biosynthetic process -0.008 0.051 -10000 0 -10000 0 0
SRC 0.032 0.11 -10000 0 -0.54 3 3
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.017 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.011 0.06 -10000 0 -10000 0 0
SOS1 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.14 0.14 -10000 0 -0.59 6 6
Gs family/GTP -0.009 0.051 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.048 -10000 0 -0.42 3 3
vasodilation 0.04 0.11 -10000 0 -0.51 6 6
mol:DAG -0.096 0.2 -10000 0 -0.44 14 14
Gs family/GDP/Gbeta gamma -0.011 0.056 -10000 0 -10000 0 0
MSN 0.062 0.061 -10000 0 -10000 0 0
Gq family/GTP -0.034 0.1 -10000 0 -0.47 9 9
mol:PI-3-4-5-P3 0.022 0.14 -10000 0 -0.8 6 6
NRAS 0.007 0.085 -10000 0 -0.72 3 3
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.04 0.11 0.51 6 -10000 0 6
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.013 0.066 -10000 0 -0.39 6 6
NOS3 0.04 0.12 -10000 0 -0.57 6 6
GNA11 -0.001 0.11 -10000 0 -0.64 6 6
MAPKKK cascade 0.047 0.12 -10000 0 -0.62 6 6
E2/ER alpha (dimer)/PELP1/Src -0.03 0.095 -10000 0 -0.52 6 6
ruffle organization 0.06 0.058 -10000 0 -10000 0 0
ROCK2 0.053 0.065 -10000 0 -10000 0 0
GNA14 -0.01 0.13 -10000 0 -0.64 9 9
GNA15 -0.006 0.13 -10000 0 -0.72 7 7
GNA13 0.017 0 -10000 0 -10000 0 0
MMP9 0.029 0.12 -10000 0 -0.5 3 3
MMP2 0.038 0.11 -10000 0 -0.5 3 3
Coregulation of Androgen receptor activity

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
NRIP1 0.019 0.001 -9999 0 -10000 0 0
SVIL 0.013 0.062 -9999 0 -0.63 2 2
ZNF318 -0.002 0.049 -9999 0 -0.73 1 1
JMJD2C 0.027 0.001 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.004 0.043 -9999 0 -0.45 2 2
CARM1 0.017 0 -9999 0 -10000 0 0
PRDX1 0.017 0 -9999 0 -10000 0 0
PELP1 0.016 0.001 -9999 0 -10000 0 0
CTNNB1 0.002 0.11 -9999 0 -0.72 5 5
AKT1 0.016 0.002 -9999 0 -10000 0 0
PTK2B 0.018 0.001 -9999 0 -10000 0 0
MED1 0.005 0.085 -9999 0 -0.72 3 3
MAK -0.012 0.097 -9999 0 -0.73 4 4
response to oxidative stress -0.001 0.001 -9999 0 -10000 0 0
HIP1 0.012 0.07 -9999 0 -0.72 2 2
GSN -0.09 0.24 -9999 0 -0.63 37 37
NCOA2 0.017 0 -9999 0 -10000 0 0
NCOA6 0.016 0.049 -9999 0 -0.72 1 1
DNA-PK -0.039 0.13 -9999 0 -0.46 19 19
NCOA4 0.017 0 -9999 0 -10000 0 0
PIAS3 0.015 0.05 -9999 0 -0.72 1 1
cell proliferation -0.007 0.054 -9999 0 -0.4 4 4
XRCC5 0.016 0.001 -9999 0 -10000 0 0
UBE3A 0.02 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.027 0.034 -9999 0 -0.46 1 1
FHL2 -0.003 0.04 -9999 0 -0.56 1 1
RANBP9 0.019 0.001 -9999 0 -10000 0 0
JMJD1A 0.028 0.01 -9999 0 -10000 0 0
CDK6 0.01 0.07 -9999 0 -0.72 2 2
TGFB1I1 0.019 0.001 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.069 0.16 -9999 0 -0.45 34 34
XRCC6 0.016 0.001 -9999 0 -10000 0 0
T-DHT/AR 0.063 0.038 -9999 0 -0.43 1 1
CTDSP1 0.018 0.001 -9999 0 -10000 0 0
CTDSP2 0.003 0.075 -9999 0 -0.64 3 3
BRCA1 0.006 0.098 -9999 0 -0.72 4 4
TCF4 0.015 0.003 -9999 0 -10000 0 0
CDKN2A -0.22 0.34 -9999 0 -0.72 70 70
SRF 0.026 0.008 -9999 0 -10000 0 0
NKX3-1 -0.002 0.018 -9999 0 -10000 0 0
KLK3 0.032 0.061 -9999 0 -10000 0 0
TMF1 0.017 0.001 -9999 0 -10000 0 0
HNRNPA1 0.015 0.002 -9999 0 -10000 0 0
AOF2 0.012 0.07 -9999 0 -0.72 2 2
APPL1 0.029 0.004 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.002 0.031 -9999 0 -0.45 1 1
AR 0.022 0.049 -9999 0 -0.71 1 1
UBA3 0.001 0.001 -9999 0 -10000 0 0
PATZ1 0.015 0.002 -9999 0 -10000 0 0
PAWR 0.017 0.001 -9999 0 -10000 0 0
PRKDC -0.047 0.21 -9999 0 -0.72 19 19
PA2G4 0.012 0.05 -9999 0 -0.72 1 1
UBE2I 0.014 0.05 -9999 0 -0.72 1 1
T-DHT/AR/Cyclin D3/CDK11 p58 -0.002 0.028 -9999 0 -0.41 1 1
RPS6KA3 0.019 0.001 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.002 0.03 -9999 0 -0.44 1 1
LATS2 0.015 0.002 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.002 0.029 -9999 0 -0.41 1 1
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.081 0.24 -9999 0 -0.63 34 34
KLK2 0 0.01 -9999 0 -10000 0 0
CASP8 0.016 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.049 0.032 -9999 0 -0.4 1 1
TMPRSS2 0.056 0.073 -9999 0 -1 1 1
CCND1 -0.092 0.26 -9999 0 -0.72 33 33
PIAS1 0.02 0.003 -9999 0 -10000 0 0
mol:T-DHT 0.009 0.007 -9999 0 -0.065 2 2
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.021 0.005 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.006 0.052 -9999 0 -0.45 3 3
CMTM2 0 0.11 -9999 0 -0.72 5 5
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.026 0.006 -9999 0 -10000 0 0
CCND3 0.017 0 -9999 0 -10000 0 0
TGIF1 -0.071 0.24 -9999 0 -0.72 26 26
FKBP4 0.012 0.07 -9999 0 -0.72 2 2
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.082 0.16 -9999 0 -0.71 4 4
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.017 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.095 0.2 -9999 0 -0.69 17 17
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.019 0.073 -9999 0 -0.54 4 4
antigen processing and presentation of peptide antigen via MHC class I -0.045 0.084 -9999 0 -0.34 6 6
CaM/Ca2+ -0.076 0.14 -9999 0 -0.65 4 4
RAP1A 0.017 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.065 0.25 -9999 0 -0.78 17 17
AKT1 -0.008 0.16 -9999 0 -0.57 4 4
MAP2K1 -0.011 0.17 -9999 0 -0.62 4 4
MAP3K11 -0.027 0.17 -9999 0 -0.66 4 4
IFNGR1 0.012 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.023 0.049 -9999 0 -10000 0 0
Rap1/GTP -0.054 0.1 -9999 0 -0.48 4 4
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.088 0.17 -9999 0 -0.75 4 4
CEBPB 0.036 0.16 -9999 0 -0.52 1 1
STAT3 0.017 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.076 0.15 -9999 0 -0.67 4 4
STAT1 -0.061 0.25 -9999 0 -0.78 17 17
CALM1 0.017 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.15 0.31 -9999 0 -0.72 50 50
PIK3CA 0.017 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.052 0.24 -9999 0 -0.72 17 17
CEBPB/PTGES2/Cbp/p300 -0.029 0.06 -9999 0 -10000 0 0
mol:Ca2+ -0.082 0.16 -9999 0 -0.7 4 4
MAPK3 0.01 0.17 -9999 0 -0.77 3 3
STAT1 (dimer) -0.061 0.12 -9999 0 -0.55 3 3
MAPK1 0.013 0.16 -9999 0 -0.56 5 5
JAK2 -0.001 0.1 -9999 0 -0.76 4 4
PIK3R1 0.017 0 -9999 0 -10000 0 0
JAK1 0.012 0.014 -9999 0 -10000 0 0
CAMK2D 0.017 0 -9999 0 -10000 0 0
DAPK1 0.05 0.12 -9999 0 -0.5 1 1
SMAD7 0.044 0.082 -9999 0 -0.29 1 1
CBL/CRKL/C3G -0.067 0.13 -9999 0 -0.59 4 4
PI3K -0.072 0.14 -9999 0 -0.64 4 4
IFNG -0.15 0.31 -9999 0 -0.72 50 50
apoptosis 0.033 0.1 -9999 0 -0.36 1 1
CAMK2G 0.017 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.017 0 -9999 0 -10000 0 0
CAMK2A 0.017 0 -9999 0 -10000 0 0
CAMK2B 0.014 0.05 -9999 0 -0.72 1 1
FRAP1 0.008 0.15 -9999 0 -0.52 4 4
PRKCD -0.007 0.16 -9999 0 -0.59 4 4
RAP1B 0.017 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.045 0.084 -9999 0 -0.34 6 6
PTPN2 0.017 0 -9999 0 -10000 0 0
EP300 0.018 0.001 -9999 0 -10000 0 0
IRF1 0.011 0.19 -9999 0 -0.62 6 6
STAT1 (dimer)/PIASy -0.1 0.21 -9999 0 -0.73 17 17
SOCS1 0.008 0.043 -9999 0 -0.57 1 1
mol:GDP -0.064 0.12 -9999 0 -0.56 4 4
CASP1 0.03 0.12 -9999 0 -0.3 16 16
PTGES2 0.017 0 -9999 0 -10000 0 0
IRF9 0.056 0.06 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.07 0.14 -9999 0 -0.61 4 4
RAP1/GDP -0.054 0.1 -9999 0 -0.48 4 4
CBL -0.028 0.17 -9999 0 -0.66 4 4
MAP3K1 -0.026 0.17 -9999 0 -0.66 4 4
PIAS1 0.017 0 -9999 0 -10000 0 0
PIAS4 0.016 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.045 0.084 -9999 0 -0.34 6 6
PTPN11 -0.04 0.18 -9999 0 -0.7 4 4
CREBBP 0.018 0.001 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.046 0.093 -9999 0 -0.63 1 1
BAG4 0.017 0 -9999 0 -10000 0 0
BAD 0.012 0.063 -9999 0 -10000 0 0
NFKBIA 0.017 0 -9999 0 -10000 0 0
BIRC3 -0.02 0.15 -9999 0 -0.66 12 12
BAX 0.011 0.071 -9999 0 -0.48 1 1
EnzymeConsortium:3.1.4.12 0.019 0.018 -9999 0 -10000 0 0
IKBKB 0.053 0.092 -9999 0 -0.58 1 1
MAP2K2 0.034 0.054 -9999 0 -10000 0 0
MAP2K1 0.034 0.054 -9999 0 -10000 0 0
SMPD1 -0.032 0.12 -9999 0 -0.26 47 47
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.062 0.069 -9999 0 -10000 0 0
MAP2K4 0.018 0.075 -9999 0 -0.39 2 2
protein ubiquitination 0.056 0.09 -9999 0 -0.59 1 1
EnzymeConsortium:2.7.1.37 0.041 0.055 -9999 0 -10000 0 0
response to UV 0.001 0 -9999 0 -10000 0 0
RAF1 0.025 0.058 -9999 0 -10000 0 0
CRADD 0.011 0.062 -9999 0 -0.64 2 2
mol:ceramide 0.002 0.066 -9999 0 -0.22 4 4
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.017 0 -9999 0 -10000 0 0
MAP3K1 0.013 0.063 -9999 0 -10000 0 0
TRADD 0.017 0 -9999 0 -10000 0 0
RELA/p50 0.017 0 -9999 0 -10000 0 0
MAPK3 0.037 0.055 -9999 0 -10000 0 0
MAPK1 0.037 0.053 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.053 0.071 -9999 0 -10000 0 0
KSR1 0.014 0.062 -9999 0 -10000 0 0
MAPK8 0.028 0.071 -9999 0 -0.35 2 2
TRAF2 0.017 0 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.055 0.089 -9999 0 -0.58 1 1
TNF R/SODD 0 0 -9999 0 -10000 0 0
TNF 0.017 0 -9999 0 -10000 0 0
CYCS 0.084 0.084 -9999 0 -0.27 1 1
IKBKG 0.055 0.089 -9999 0 -0.58 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.044 0.074 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
RIPK1 0.017 0 -9999 0 -10000 0 0
AIFM1 0.085 0.084 -9999 0 -0.27 1 1
TNF/TNF R/SODD 0 0 -9999 0 -10000 0 0
TNFRSF1A 0.017 0 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.037 0.02 -9999 0 -10000 0 0
NSMAF 0.054 0.07 -9999 0 -10000 0 0
response to hydrogen peroxide 0.001 0 -9999 0 -10000 0 0
BCL2 -0.41 0.31 -9999 0 -0.64 145 145
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.017 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.047 0.11 -9999 0 -0.46 8 8
NEF -0.011 0.057 -9999 0 -10000 0 0
NFKBIA 0.015 0.026 -9999 0 -10000 0 0
BIRC3 0.024 0.16 -9999 0 -0.64 12 12
CYCS -0.002 0.16 -9999 0 -0.52 9 9
RIPK1 0.017 0 -9999 0 -10000 0 0
CD247 -0.029 0.17 -9999 0 -0.75 11 11
MAP2K7 0.027 0.11 -9999 0 -0.37 3 3
protein ubiquitination 0.087 0.04 -9999 0 -10000 0 0
CRADD 0.011 0.062 -9999 0 -0.64 2 2
DAXX 0.017 0 -9999 0 -10000 0 0
FAS -0.048 0.2 -9999 0 -0.64 22 22
BID -0.012 0.17 -9999 0 -0.46 17 17
NF-kappa-B/RelA/I kappa B alpha -0.015 0.064 -9999 0 -10000 0 0
TRADD 0.017 0 -9999 0 -10000 0 0
MAP3K5 0.01 0.07 -9999 0 -0.72 2 2
CFLAR 0.017 0 -9999 0 -10000 0 0
FADD 0.017 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.015 0.065 -9999 0 -10000 0 0
MAPK8 0.037 0.1 -9999 0 -0.37 1 1
APAF1 0.01 0.07 -9999 0 -0.72 2 2
TRAF1 0.017 0 -9999 0 -10000 0 0
TRAF2 0.017 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.011 0.15 -9999 0 -0.5 11 11
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.075 0.046 -9999 0 -10000 0 0
CHUK 0.089 0.042 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.034 0.1 -9999 0 -0.72 1 1
TCRz/NEF -0.058 0.17 -9999 0 -0.46 28 28
TNF 0.017 0 -9999 0 -10000 0 0
FASLG -0.059 0.27 -9999 0 -0.81 24 24
NFKB1 0.015 0.026 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0 0 -9999 0 -10000 0 0
CASP6 -0.03 0.079 -9999 0 -10000 0 0
CASP7 0 0.22 -9999 0 -0.6 13 13
RELA 0.015 0.026 -9999 0 -10000 0 0
CASP2 0.017 0 -9999 0 -10000 0 0
CASP3 0.043 0.17 -9999 0 -0.57 10 10
TNFRSF1A 0.017 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0 0 -9999 0 -10000 0 0
CASP8 0.017 0 -9999 0 -10000 0 0
CASP9 0.017 0 -9999 0 -10000 0 0
MAP3K14 0.083 0.044 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.054 0.12 -9999 0 -0.53 7 7
BCL2 -0.16 0.2 -9999 0 -0.46 35 35
Effects of Botulinum toxin

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
STX1A -0.007 0.11 -9999 0 -0.55 9 9
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0 0 -9999 0 -10000 0 0
STXBP1 -0.026 0.17 -9999 0 -0.72 13 13
ACh/CHRNA1 0.017 0.022 -9999 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.017 0 -9999 0 -10000 0 0
mol:ACh 0.007 0.03 -9999 0 -0.12 10 10
RAB3GAP2 0.017 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.033 0.099 -9999 0 -0.47 2 2
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.017 0.022 -9999 0 -10000 0 0
UNC13B 0.017 0 -9999 0 -10000 0 0
CHRNA1 0.017 0 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.051 0.18 -9999 0 -0.5 29 29
SNAP25 0.006 0.037 -9999 0 -0.31 3 3
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.08 0.25 -9999 0 -0.72 29 29
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.025 0.15 -9999 0 -0.47 22 22
STX1A/SNAP25 fragment 1/VAMP2 -0.033 0.099 -9999 0 -0.47 2 2
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.084 0.14 -9999 0 -0.46 10 10
PDGFB-D/PDGFRB/SLAP 0.001 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0 0.003 -9999 0 -10000 0 0
AKT1 0.061 0.063 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.06 0.13 -9999 0 -0.39 10 10
PIK3CA 0.017 0 -9999 0 -10000 0 0
FGR -0.01 0.028 -9999 0 -10000 0 0
mol:Ca2+ -0.027 0.079 -9999 0 -0.38 2 2
MYC -0.26 0.25 -9999 0 -0.52 54 54
SHC1 0.017 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.035 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.002 0.031 -9999 0 -0.46 1 1
GRB10 -0.03 0.18 -9999 0 -0.72 14 14
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
GO:0007205 -0.027 0.08 -9999 0 -0.38 2 2
PTEN -0.001 0.11 -9999 0 -0.64 6 6
GRB2 0.017 0 -9999 0 -10000 0 0
GRB7 -0.01 0.14 -9999 0 -0.72 8 8
PDGFB-D/PDGFRB/SHP2 -0.002 0.037 -9999 0 -0.55 1 1
PDGFB-D/PDGFRB/GRB10 -0.034 0.13 -9999 0 -0.55 14 14
cell cycle arrest 0.001 0.004 -9999 0 -10000 0 0
HRAS 0.017 0 -9999 0 -10000 0 0
HIF1A 0.066 0.073 -9999 0 -0.53 1 1
GAB1 -0.064 0.1 -9999 0 -0.41 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.062 0.11 -9999 0 -0.44 2 2
PDGFB-D/PDGFRB 0.005 0.013 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.001 0.004 -9999 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.11 0.14 -9999 0 -0.5 11 11
positive regulation of MAPKKK cascade -0.002 0.037 -9999 0 -0.55 1 1
PIK3R1 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.028 0.08 -9999 0 -0.38 2 2
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.018 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.019 0.1 -9999 0 -0.55 8 8
SHB -0.016 0.15 -9999 0 -0.72 10 10
BLK -0.18 0.29 -9999 0 -0.64 61 61
PTPN2 0.007 0.008 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.001 0.004 -9999 0 -10000 0 0
BCAR1 0.017 0 -9999 0 -10000 0 0
VAV2 -0.1 0.13 -9999 0 -0.54 6 6
CBL 0.017 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.001 0.004 -9999 0 -10000 0 0
LCK -0.014 0.059 -9999 0 -0.74 1 1
PDGFRB 0.006 0.009 -9999 0 -10000 0 0
ACP1 0.017 0 -9999 0 -10000 0 0
HCK -0.066 0.2 -9999 0 -0.68 21 21
ABL1 -0.049 0.091 -9999 0 -0.41 2 2
PDGFB-D/PDGFRB/CBL -0.064 0.1 -9999 0 -0.42 4 4
PTPN1 0.007 0.008 -9999 0 -10000 0 0
SNX15 0.017 0 -9999 0 -10000 0 0
STAT3 0.017 0 -9999 0 -10000 0 0
STAT1 -0.05 0.21 -9999 0 -0.72 20 20
cell proliferation -0.24 0.23 -9999 0 -0.47 54 54
SLA 0.017 0 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.005 0.083 -9999 0 -10000 0 0
SRC -0.008 0.027 -9999 0 -10000 0 0
PI3K -0.011 0.052 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.017 0.086 -9999 0 -0.46 8 8
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.062 0.13 -9999 0 -0.41 10 10
LYN -0.008 0.027 -9999 0 -10000 0 0
LRP1 0.017 0 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
STAT5B 0.017 0 -9999 0 -10000 0 0
STAT5A 0.017 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0.001 0.009 -9999 0 -10000 0 0
SPHK1 -0.075 0.24 -9999 0 -0.72 27 27
EDG1 -0.023 0.15 -9999 0 -0.64 13 13
mol:DAG -0.028 0.08 -9999 0 -0.38 2 2
PLCG1 -0.028 0.082 -9999 0 -0.39 2 2
NHERF/PDGFRB -0.007 0.052 -9999 0 -0.39 4 4
YES1 -0.009 0.028 -9999 0 -10000 0 0
cell migration -0.007 0.051 -9999 0 -0.39 4 4
SHC/Grb2/SOS1 0.001 0.009 -9999 0 -10000 0 0
SLC9A3R2 0.017 0 -9999 0 -10000 0 0
SLC9A3R1 0.005 0.087 -9999 0 -0.64 4 4
NHERF1-2/PDGFRB/PTEN -0.015 0.071 -9999 0 -10000 0 0
FYN -0.011 0.06 -9999 0 -0.81 1 1
DOK1 0.017 0.036 -9999 0 -0.42 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.014 0.05 -9999 0 -0.72 1 1
RAC1 -0.16 0.18 -9999 0 -0.54 11 11
PRKCD 0.018 0.022 -9999 0 -10000 0 0
FER 0.002 0.085 -9999 0 -0.42 8 8
MAPKKK cascade 0.001 0.016 -9999 0 -10000 0 0
RASA1 0.014 0.046 -9999 0 -0.41 2 2
NCK1 0.017 0 -9999 0 -10000 0 0
NCK2 0.017 0 -9999 0 -10000 0 0
p62DOK/Csk 0.044 0.036 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.024 0.11 -9999 0 -0.55 10 10
chemotaxis -0.048 0.089 -9999 0 -0.4 2 2
STAT1-3-5/STAT1-3-5 -0.031 0.097 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.002 0.005 -9999 0 -10000 0 0
PTPRJ 0.017 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.037 0.062 -10000 0 -10000 0 0
ACTA1 0.003 0.092 -10000 0 -0.36 6 6
NUMA1 0.037 0.062 -10000 0 -10000 0 0
SPTAN1 0.03 0.074 -10000 0 -10000 0 0
LIMK1 0.009 0.11 -10000 0 -0.41 8 8
BIRC3 -0.02 0.15 -10000 0 -0.66 12 12
BIRC2 0.017 0 -10000 0 -10000 0 0
BAX 0.014 0.05 -10000 0 -0.72 1 1
CASP10 0.019 0.1 -10000 0 -0.46 10 10
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.036 0.063 -10000 0 -10000 0 0
DIABLO 0.017 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.03 0.073 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.011 0.062 -10000 0 -0.64 2 2
GSN -0.03 0.15 -10000 0 -0.57 3 3
MADD 0.017 0 -10000 0 -10000 0 0
TFAP2A 0.001 0.083 -10000 0 -10000 0 0
BID 0.016 0.073 -10000 0 -0.48 2 2
MAP3K1 0.021 0.032 -10000 0 -10000 0 0
TRADD 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.005 0.051 -10000 0 -0.54 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.028 0.074 -10000 0 -10000 0 0
CASP9 0.017 0.001 -10000 0 -10000 0 0
DNA repair -0.003 0.062 0.24 2 -0.21 6 8
neuron apoptosis 0.035 0.011 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.036 0.084 -10000 0 -0.56 1 1
APAF1 0.01 0.07 -10000 0 -0.72 2 2
CASP6 0.048 0.043 -10000 0 -10000 0 0
TRAF2 0.017 0 -10000 0 -10000 0 0
ICAD/CAD 0.035 0.085 -10000 0 -0.56 1 1
CASP7 -0.06 0.19 0.31 9 -0.52 28 37
KRT18 0.023 0.033 -10000 0 -10000 0 0
apoptosis 0.03 0.092 -10000 0 -0.45 1 1
DFFA 0.03 0.074 -10000 0 -10000 0 0
DFFB 0.026 0.088 -10000 0 -0.49 2 2
PARP1 0.003 0.062 0.21 6 -0.24 2 8
actin filament polymerization -0.005 0.12 0.51 2 -10000 0 2
TNF 0.017 0 -10000 0 -10000 0 0
CYCS 0.028 0.052 -10000 0 -0.24 2 2
SATB1 0.025 0.11 -10000 0 -0.48 2 2
SLK 0.028 0.079 -10000 0 -0.38 1 1
p15 BID/BAX 0.02 0.072 -10000 0 -0.42 3 3
CASP2 0.056 0.051 -10000 0 -10000 0 0
JNK cascade -0.021 0.032 -10000 0 -10000 0 0
CASP3 0.02 0.078 -10000 0 -0.36 5 5
LMNB2 0.058 0.042 -10000 0 -10000 0 0
RIPK1 0.017 0 -10000 0 -10000 0 0
CASP4 0.017 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.02 0.084 -10000 0 -0.42 3 3
negative regulation of DNA binding 0.001 0.083 -10000 0 -10000 0 0
stress fiber formation 0.028 0.078 -10000 0 -0.38 1 1
GZMB 0.006 0.12 -10000 0 -0.54 10 10
CASP1 -0.003 0.097 -10000 0 -0.35 16 16
LMNB1 0.025 0.065 -10000 0 -10000 0 0
APP 0.035 0.011 -10000 0 -10000 0 0
TNFRSF1A 0.017 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM 0.023 0.09 0.28 1 -0.4 3 4
LMNA 0.061 0.037 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.048 0.054 -10000 0 -10000 0 0
LRDD 0.014 0.05 -10000 0 -0.72 1 1
SREBF1 0.028 0.079 -10000 0 -0.38 1 1
APAF-1/Caspase 9 0.004 0.039 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.037 0.062 -10000 0 -10000 0 0
CFL2 0.005 0.12 -10000 0 -0.53 2 2
GAS2 -0.22 0.22 -10000 0 -0.4 117 117
positive regulation of apoptosis 0.046 0.048 -10000 0 -10000 0 0
PRF1 0.004 0.098 -10000 0 -0.72 4 4
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.054 0.14 -10000 0 -0.55 4 4
CLOCK 0.021 0.005 -10000 0 -10000 0 0
TIMELESS/CRY2 0.048 0.076 -10000 0 -0.49 4 4
DEC1/BMAL1 -0.002 0.036 -10000 0 -0.54 1 1
ATR 0.014 0.05 -10000 0 -0.72 1 1
NR1D1 0.05 0.067 -10000 0 -0.54 2 2
ARNTL 0.021 0.005 -10000 0 -10000 0 0
TIMELESS 0.047 0.083 -10000 0 -0.54 4 4
NPAS2 0.021 0.005 -10000 0 -10000 0 0
CRY2 0.017 0 -10000 0 -10000 0 0
mol:CO -0.016 0.019 0.097 6 -10000 0 6
CHEK1 -0.073 0.24 -10000 0 -0.72 27 27
mol:HEME 0.016 0.019 -10000 0 -0.097 6 6
PER1 0.017 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.055 0.018 -10000 0 -10000 0 0
BMAL1/CLOCK 0.066 0.064 -10000 0 -10000 0 0
S phase of mitotic cell cycle -0.054 0.14 -10000 0 -0.55 4 4
TIMELESS/CHEK1/ATR -0.055 0.14 -10000 0 -0.85 1 1
mol:NADPH 0.016 0.019 -10000 0 -0.097 6 6
PER1/TIMELESS 0.048 0.076 -10000 0 -0.49 4 4
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.014 0.05 -10000 0 -0.72 1 1
FoxO family signaling

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
G6PC 0.031 0.1 -9999 0 -10000 0 0
PLK1 0.032 0.2 -9999 0 -0.72 4 4
CDKN1B 0.089 0.15 -9999 0 -10000 0 0
FOXO3 0.021 0.22 -9999 0 -0.71 8 8
KAT2B 0.002 0.025 -9999 0 -0.058 8 8
FOXO1/SIRT1 -0.004 0.098 -9999 0 -0.56 1 1
CAT 0.027 0.22 -9999 0 -0.88 4 4
CTNNB1 0 0.11 -9999 0 -0.72 5 5
AKT1 0.026 0.022 -9999 0 -10000 0 0
FOXO1 0.021 0.11 -9999 0 -0.61 1 1
MAPK10 0.043 0.056 -9999 0 -0.38 2 2
mol:GTP 0.003 0.002 -9999 0 -10000 0 0
FOXO4 0.12 0.059 -9999 0 -10000 0 0
response to oxidative stress 0.01 0.025 -9999 0 -0.054 7 7
FOXO3A/SIRT1 -0.034 0.16 -9999 0 -0.6 7 7
XPO1 0.018 0.001 -9999 0 -10000 0 0
EP300 0.021 0.002 -9999 0 -10000 0 0
BCL2L11 0.034 0.039 -9999 0 -10000 0 0
FOXO1/SKP2 -0.02 0.19 -9999 0 -0.49 24 24
mol:GDP 0.01 0.025 -9999 0 -0.054 7 7
RAN 0.016 0.049 -9999 0 -0.72 1 1
GADD45A 0.1 0.11 -9999 0 -0.56 2 2
YWHAQ 0.017 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.091 0.038 -9999 0 -10000 0 0
MST1 -0.011 0.15 -9999 0 -0.71 10 10
CSNK1D 0.017 0 -9999 0 -10000 0 0
CSNK1E 0.014 0.05 -9999 0 -0.72 1 1
FOXO4/14-3-3 family 0.076 0.037 -9999 0 -10000 0 0
YWHAB 0.017 0 -9999 0 -10000 0 0
MAPK8 0.05 0.018 -9999 0 -10000 0 0
MAPK9 0.05 0.017 -9999 0 -10000 0 0
YWHAG 0.017 0 -9999 0 -10000 0 0
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
YWHAZ 0.017 0 -9999 0 -10000 0 0
SIRT1 0.014 0.023 -9999 0 -10000 0 0
SOD2 0.074 0.21 -9999 0 -0.64 7 7
RBL2 0.07 0.15 -9999 0 -10000 0 0
RAL/GDP 0.03 0.025 -9999 0 -10000 0 0
CHUK 0.022 0.02 -9999 0 -10000 0 0
Ran/GTP 0.015 0.038 -9999 0 -0.55 1 1
CSNK1G2 0.017 0 -9999 0 -10000 0 0
RAL/GTP 0.045 0.022 -9999 0 -10000 0 0
CSNK1G1 0.017 0 -9999 0 -10000 0 0
FASLG -0.12 0.46 -9999 0 -1.4 24 24
SKP2 -0.06 0.22 -9999 0 -0.72 23 23
USP7 0.016 0.044 -9999 0 -0.63 1 1
IKBKB 0.019 0.052 -9999 0 -0.7 1 1
CCNB1 -0.033 0.29 -9999 0 -0.83 9 9
FOXO1-3a-4/beta catenin -0.018 0.095 -9999 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.019 0.18 -9999 0 -0.49 24 24
CSNK1A1 0.017 0 -9999 0 -10000 0 0
SGK1 0.002 0.025 -9999 0 -0.058 8 8
CSNK1G3 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.034 -9999 0 -0.46 1 1
ZFAND5 0.13 0.054 -9999 0 -10000 0 0
SFN 0.011 0.062 -9999 0 -0.64 2 2
CDK2 -0.058 0.23 -9999 0 -0.72 24 24
FOXO3A/14-3-3 0.062 0.058 -9999 0 -10000 0 0
CREBBP 0.022 0.002 -9999 0 -10000 0 0
FBXO32 -0.047 0.41 -9999 0 -1.3 19 19
BCL6 0.064 0.18 -9999 0 -1.3 1 1
RALB 0.019 0.001 -9999 0 -10000 0 0
RALA 0.019 0.001 -9999 0 -10000 0 0
YWHAH 0.017 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.017 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.01 0.13 -9999 0 -0.64 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.005 0.087 -9999 0 -0.64 4 4
RAC1-CDC42/GTP/PAK family 0.037 0 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.017 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0 -9999 0 -10000 0 0
FYN 0.014 0.044 -9999 0 -0.64 1 1
MAP3K12 0.017 0 -9999 0 -10000 0 0
FGR 0.017 0 -9999 0 -10000 0 0
p38 alpha/TAB1 -0.035 0.066 -9999 0 -0.41 2 2
PRKG1 0.017 0 -9999 0 -10000 0 0
DUSP8 0.014 0.044 -9999 0 -0.64 1 1
PGK/cGMP/p38 alpha -0.034 0.064 -9999 0 -0.4 2 2
apoptosis -0.034 0.063 -9999 0 -0.39 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.017 0 -9999 0 -10000 0 0
DUSP1 -0.039 0.18 -9999 0 -0.64 19 19
PAK1 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.017 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0 0.14 -9999 0 -0.38 12 12
BLK -0.16 0.29 -9999 0 -0.64 61 61
HCK -0.045 0.19 -9999 0 -0.64 21 21
MAP2K3 0.017 0 -9999 0 -10000 0 0
DUSP16 0.017 0 -9999 0 -10000 0 0
DUSP10 -0.066 0.23 -9999 0 -0.72 25 25
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
MAPK14 0.011 0.11 -9999 0 -0.45 2 2
positive regulation of innate immune response 0.005 0.15 -9999 0 -0.52 3 3
LCK 0.011 0.066 -9999 0 -0.68 2 2
p38alpha-beta/MKP7 0.014 0.14 -9999 0 -0.55 2 2
p38alpha-beta/MKP5 -0.026 0.18 -9999 0 -0.5 12 12
PGK/cGMP 0 0 -9999 0 -10000 0 0
PAK2 0.017 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.011 0.18 -9999 0 -0.46 15 15
CDC42 0.017 0 -9999 0 -10000 0 0
RALB 0.017 0 -9999 0 -10000 0 0
RALA 0.017 0 -9999 0 -10000 0 0
PAK3 0.017 0 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.002 0.022 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.016 -9999 0 -10000 0 0
AP1 -0.059 0.13 -9999 0 -0.35 37 37
mol:PIP3 -0.012 0.061 -9999 0 -0.47 1 1
AKT1 0.044 0.042 -9999 0 -10000 0 0
PTK2B 0.018 0.02 -9999 0 -10000 0 0
RHOA -0.002 0.023 -9999 0 -10000 0 0
PIK3CB 0.013 0.05 -9999 0 -0.72 1 1
mol:Ca2+ 0.017 0.042 -9999 0 -10000 0 0
MAGI3 0.011 0.062 -9999 0 -0.64 2 2
RELA 0.017 0 -9999 0 -10000 0 0
apoptosis 0.015 0.032 -9999 0 -0.26 3 3
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.035 0.031 -9999 0 -0.34 1 1
NF kappa B1 p50/RelA -0.009 0.027 -9999 0 -10000 0 0
endothelial cell migration 0.019 0.066 -9999 0 -0.67 2 2
ADCY4 0.022 0.073 -9999 0 -0.33 1 1
ADCY5 0.023 0.07 -9999 0 -10000 0 0
ADCY6 0.023 0.07 -9999 0 -10000 0 0
ADCY7 0.023 0.07 -9999 0 -10000 0 0
ADCY1 0.023 0.07 -9999 0 -10000 0 0
ADCY2 0.022 0.07 -9999 0 -10000 0 0
ADCY3 0.014 0.078 -9999 0 -0.27 1 1
ADCY8 0.022 0.07 -9999 0 -10000 0 0
ADCY9 0.02 0.073 -9999 0 -10000 0 0
GSK3B 0.026 0.033 -9999 0 -0.38 1 1
arachidonic acid secretion 0.031 0.065 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
TRIP6 0.012 0.067 -9999 0 -0.33 8 8
GNAO1 0.022 0.027 -9999 0 -0.26 2 2
HRAS 0.017 0 -9999 0 -10000 0 0
NFKBIA 0.03 0.035 -9999 0 -10000 0 0
GAB1 0.011 0.062 -9999 0 -0.64 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.008 0.089 -9999 0 -0.94 2 2
JUN 0 0.11 -9999 0 -0.72 5 5
LPA/LPA2/NHERF2 -0.001 0.008 -9999 0 -10000 0 0
TIAM1 -0.01 0.11 -9999 0 -1.1 2 2
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.017 0.043 -9999 0 -10000 0 0
PLCB3 0.024 0.009 -9999 0 -10000 0 0
FOS -0.082 0.23 -9999 0 -0.64 33 33
positive regulation of mitosis 0.031 0.065 -9999 0 -10000 0 0
LPA/LPA1-2-3 -0.002 0.024 -9999 0 -0.25 2 2
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade -0.001 0.001 -9999 0 -10000 0 0
BCAR1 0.017 0 -9999 0 -10000 0 0
stress fiber formation 0.026 0.022 -9999 0 -10000 0 0
GNAZ 0.022 0.027 -9999 0 -0.26 2 2
EGFR/PI3K-beta/Gab1 -0.013 0.064 -9999 0 -0.5 1 1
positive regulation of dendritic cell cytokine production -0.002 0.024 -9999 0 -0.25 2 2
LPA/LPA2/MAGI-3 -0.004 0.039 -9999 0 -0.4 2 2
ARHGEF1 0.04 0.023 -9999 0 -10000 0 0
GNAI2 0.022 0.027 -9999 0 -0.26 2 2
GNAI3 0.022 0.027 -9999 0 -0.26 2 2
GNAI1 -0.033 0.14 -9999 0 -0.39 31 31
LPA/LPA3 -0.001 0.012 -9999 0 -0.12 2 2
LPA/LPA2 -0.001 0.012 -9999 0 -0.12 2 2
LPA/LPA1 -0.003 0.031 -9999 0 -0.33 2 2
HB-EGF/EGFR -0.026 0.12 -9999 0 -0.46 14 14
HBEGF 0.004 0.12 -9999 0 -0.58 9 9
mol:DAG 0.017 0.043 -9999 0 -10000 0 0
cAMP biosynthetic process 0.028 0.071 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
LYN 0.03 0.035 -9999 0 -10000 0 0
GNAQ 0 0.009 -9999 0 -0.091 2 2
LPAR2 -0.002 0.001 -9999 0 -10000 0 0
LPAR3 -0.002 0.001 -9999 0 -10000 0 0
LPAR1 0.004 0.018 -9999 0 -0.19 2 2
IL8 -0.32 0.13 -9999 0 -0.41 68 68
PTK2 0.014 0.037 -9999 0 -0.29 3 3
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 0.015 0.033 -9999 0 -0.26 3 3
EGFR -0.001 0.099 -9999 0 -0.65 5 5
PLCG1 -0.017 0.043 -9999 0 -0.15 14 14
PLD2 0.016 0.023 -9999 0 -10000 0 0
G12/G13 -0.002 0.022 -9999 0 -10000 0 0
PI3K-beta -0.004 0.026 -9999 0 -10000 0 0
cell migration -0.002 0.032 -9999 0 -0.27 2 2
SLC9A3R2 0.017 0 -9999 0 -10000 0 0
PXN 0.026 0.022 -9999 0 -10000 0 0
HRAS/GTP -0.018 0.046 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
MMP9 -0.007 0.13 -9999 0 -0.71 7 7
PRKCE 0.017 0.002 -9999 0 -10000 0 0
PRKCD 0.024 0.041 -9999 0 -10000 0 0
Gi(beta/gamma) -0.02 0.05 -9999 0 -10000 0 0
mol:LPA -0.001 0.018 -9999 0 -0.19 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.004 0.046 -9999 0 -10000 0 0
MAPKKK cascade 0.031 0.065 -9999 0 -10000 0 0
contractile ring contraction involved in cytokinesis 0.029 0.025 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.003 0.071 -9999 0 -0.35 9 9
GNA15 0 0.062 -9999 0 -0.34 7 7
GNA12 0.017 0 -9999 0 -10000 0 0
GNA13 0.017 0 -9999 0 -10000 0 0
MAPT 0.035 0.032 -9999 0 -0.35 1 1
GNA11 0.002 0.059 -9999 0 -0.35 6 6
Rac1/GTP -0.008 0.095 -9999 0 -1 2 2
MMP2 0.019 0.066 -9999 0 -0.68 2 2
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.029 0.097 -9999 0 -0.48 6 6
KLHL20 -0.034 0.066 -9999 0 -0.3 1 1
CYFIP2 0.011 0.062 -9999 0 -0.64 2 2
Rac1/GDP 0.062 0.071 -9999 0 -10000 0 0
ENAH 0.024 0.1 -9999 0 -0.48 6 6
AP1M1 0.017 0 -9999 0 -10000 0 0
RAP1B 0.017 0 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
CTNNB1 0 0.11 -9999 0 -0.72 5 5
CDC42/GTP -0.01 0.043 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.023 0.046 -9999 0 -0.22 3 3
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.032 0.1 -9999 0 -0.41 5 5
RAPGEF1 0.052 0.087 -9999 0 -0.4 6 6
CTNND1 0.017 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.019 0.089 -9999 0 -0.5 6 6
CRK 0.043 0.093 -9999 0 -0.44 6 6
E-cadherin/gamma catenin/alpha catenin -0.01 0.063 -9999 0 -0.38 6 6
alphaE/beta7 Integrin -0.019 0.091 -9999 0 -0.46 9 9
IQGAP1 0.017 0 -9999 0 -10000 0 0
NCKAP1 0.014 0.05 -9999 0 -0.72 1 1
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.029 0.097 -9999 0 -0.48 6 6
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.03 -9999 0 -10000 0 0
MLLT4 0.017 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.058 -9999 0 -0.42 3 3
PI3K -0.009 0.038 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.012 0.075 -9999 0 -0.46 6 6
TIAM1 0.011 0.062 -9999 0 -0.64 2 2
E-cadherin(dimer)/Ca2+ -0.017 0.077 -9999 0 -0.39 5 5
AKT1 -0.005 0.022 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
CDH1 -0.001 0.11 -9999 0 -0.64 6 6
RhoA/GDP 0.062 0.07 -9999 0 -10000 0 0
actin cytoskeleton organization -0.025 0.049 -9999 0 -0.22 1 1
CDC42/GDP 0.062 0.07 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.025 0.05 -9999 0 -0.27 6 6
ITGB7 -0.01 0.13 -9999 0 -0.64 9 9
RAC1 0.017 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.018 0.081 -9999 0 -0.41 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin -0.018 0.079 -9999 0 -0.36 11 11
mol:GDP 0.057 0.079 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.017 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP -0.013 0.051 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
CTNNA1 0.017 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.001 0.1 -9999 0 -0.24 33 33
NME1 0.007 0.085 -9999 0 -0.72 3 3
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.029 0.097 -9999 0 -0.48 6 6
regulation of cell-cell adhesion -0.009 0.038 -9999 0 -10000 0 0
WASF2 -0.012 0.026 -9999 0 -0.2 1 1
Rap1/GTP -0.012 0.05 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.021 0.078 -9999 0 -10000 0 0
CCND1 -0.002 0.13 -9999 0 -0.3 33 33
VAV2 0.033 0.13 -9999 0 -0.54 10 10
RAP1/GDP -0.003 0.055 -9999 0 -10000 0 0
adherens junction assembly 0.036 0.093 -9999 0 -0.46 6 6
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.017 0 -9999 0 -10000 0 0
PIP5K1C 0.017 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.027 0.088 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.013 0.067 -9999 0 -0.41 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.029 0.097 -9999 0 -0.48 6 6
PIK3CA 0.017 0 -9999 0 -10000 0 0
Rac1/GTP -0.054 0.11 -9999 0 -0.46 2 2
E-cadherin/beta catenin/alpha catenin -0.021 0.091 -9999 0 -0.42 11 11
ITGAE 0.017 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.091 -9999 0 -0.51 6 6
IL2 signaling events mediated by STAT5

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
GAB2 0.018 0 -9999 0 -10000 0 0
ELF1 0.015 0.072 -9999 0 -0.7 1 1
CCNA2 -0.093 0.26 -9999 0 -0.72 33 33
PIK3CA 0.018 0 -9999 0 -10000 0 0
JAK3 0.018 0 -9999 0 -10000 0 0
PIK3R1 0.018 0 -9999 0 -10000 0 0
JAK1 0.018 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.1 0.047 -9999 0 -10000 0 0
SHC1 0.018 0 -9999 0 -10000 0 0
SP1 0.007 0.081 -9999 0 -0.35 5 5
IL2RA 0.02 0.12 -9999 0 -0.6 8 8
IL2RB 0.015 0.044 -9999 0 -0.63 1 1
SOS1 0.018 0 -9999 0 -10000 0 0
IL2RG 0.009 0.075 -9999 0 -0.63 3 3
G1/S transition of mitotic cell cycle -0.017 0.17 -9999 0 -0.67 6 6
PTPN11 0.015 0.049 -9999 0 -0.72 1 1
CCND2 -0.005 0.18 -9999 0 -0.71 14 14
LCK 0.012 0.066 -9999 0 -0.68 2 2
GRB2 0.018 0 -9999 0 -10000 0 0
IL2 0.018 0 -9999 0 -10000 0 0
CDK6 0.01 0.07 -9999 0 -0.72 2 2
CCND3 0.11 0.044 -9999 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.017 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0 0.12 -9999 0 -0.49 4 4
GNAO1 0.019 0 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.008 0.023 -9999 0 -10000 0 0
AKT3 0.027 0.079 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0 -9999 0 -10000 0 0
GNAI2 0.019 0 -9999 0 -10000 0 0
GNAI3 0.019 0 -9999 0 -10000 0 0
GNAI1 -0.066 0.22 -9999 0 -0.63 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.002 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.021 0.15 -9999 0 -0.64 13 13
mol:Ca2+ 0.02 0.087 -9999 0 -10000 0 0
MAPK3 0.027 0.089 -9999 0 -10000 0 0
MAPK1 0.028 0.086 -9999 0 -10000 0 0
JAK2 0.023 0.096 -9999 0 -0.38 1 1
CXCR4 0.009 0.12 -9999 0 -0.38 11 11
FLT1 -0.016 0.16 -9999 0 -0.72 11 11
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.03 0.083 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.02 0.088 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.023 0.06 -9999 0 -10000 0 0
VEGFA -0.049 0.22 -9999 0 -0.72 21 21
S1P/S1P2/Gi 0.015 0.088 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.043 0.22 -9999 0 -0.6 28 28
RHOA 0.017 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.001 0.092 -9999 0 -0.28 21 21
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.019 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.01 0.13 -9999 0 -0.64 9 9
GNA15 -0.006 0.13 -9999 0 -0.72 7 7
GNA12 0.017 0 -9999 0 -10000 0 0
GNA13 0.017 0 -9999 0 -10000 0 0
GNA11 -0.001 0.11 -9999 0 -0.64 6 6
Rac1/GTP -0.023 0.06 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.095 0.079 -9999 0 -10000 0 0
NCK1/PAK1/Dok-R -0.007 0.031 -9999 0 -10000 0 0
NCK1/Dok-R -0.01 0.056 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
mol:beta2-estradiol -0.015 0.012 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
SHC1 0.018 0.001 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
F2 0.001 0.012 -9999 0 -10000 0 0
TNIP2 0.017 0 -9999 0 -10000 0 0
NF kappa B/RelA -0.006 0.045 -9999 0 -10000 0 0
FN1 -0.07 0.24 -9999 0 -0.72 26 26
PLD2 0.091 0.066 -9999 0 -10000 0 0
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
GRB14 -0.082 0.25 -9999 0 -0.69 31 31
ELK1 0.099 0.065 -9999 0 -10000 0 0
GRB7 -0.01 0.14 -9999 0 -0.72 8 8
PAK1 0.017 0 -9999 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.048 0.12 -9999 0 -10000 0 0
CDKN1A 0.052 0.14 -9999 0 -0.83 3 3
ITGA5 0 0.11 -9999 0 -0.72 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
RasGAP/Dok-R -0.013 0.062 -9999 0 -10000 0 0
CRK 0.014 0.044 -9999 0 -0.64 1 1
mol:NO 0.097 0.075 -9999 0 -10000 0 0
PLG 0.091 0.066 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
chemokinesis 0.093 0.071 -9999 0 -10000 0 0
GRB2 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.018 0.001 -9999 0 -10000 0 0
ANGPT2 -0.043 0.14 -9999 0 -10000 0 0
BMX -0.18 0.17 -9999 0 -10000 0 0
ANGPT1 0.054 0.04 -9999 0 -10000 0 0
tube development 0.053 0.1 -9999 0 -10000 0 0
ANGPT4 0.018 0.001 -9999 0 -10000 0 0
response to hypoxia 0.007 0.008 -9999 0 -10000 0 0
Tie2/Ang1/GRB14 0.032 0.15 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.015 0.087 -9999 0 -0.54 6 6
FGF2 -0.011 0.13 -9999 0 -0.64 9 9
STAT5A (dimer) 0.058 0.12 -9999 0 -10000 0 0
mol:L-citrulline 0.097 0.075 -9999 0 -10000 0 0
AGTR1 -0.26 0.32 -9999 0 -0.63 95 95
MAPK14 0.08 0.066 -9999 0 -10000 0 0
Tie2/SHP2 -0.005 0.031 -9999 0 -10000 0 0
TEK 0.067 0.041 -9999 0 -10000 0 0
RPS6KB1 0.091 0.081 -9999 0 -10000 0 0
Angiotensin II/AT1 -0.19 0.24 -9999 0 -0.47 95 95
Tie2/Ang1/GRB2 0.087 0.066 -9999 0 -10000 0 0
MAPK3 0.094 0.071 -9999 0 -10000 0 0
MAPK1 0.096 0.067 -9999 0 -10000 0 0
Tie2/Ang1/GRB7 0.072 0.1 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 0.091 0.066 -9999 0 -10000 0 0
PI3K 0.086 0.078 -9999 0 -10000 0 0
FES 0.077 0.073 -9999 0 -10000 0 0
Crk/Dok-R -0.011 0.058 -9999 0 -10000 0 0
Tie2/Ang1/ABIN2 0.087 0.066 -9999 0 -10000 0 0
blood circulation 0 0 -9999 0 -10000 0 0
negative regulation of caspase activity 0.094 0.076 -9999 0 -10000 0 0
STAT5A 0.017 0.002 -9999 0 -10000 0 0
mol:ROS 0 0 -9999 0 -10000 0 0
PTK2 0.091 0.077 -9999 0 -10000 0 0
Tie2/Ang2 0.046 0.11 -9999 0 -10000 0 0
Tie2/Ang1 0.084 0.069 -9999 0 -10000 0 0
FOXO1 0.096 0.097 -9999 0 -10000 0 0
ELF1 0.026 0.05 -9999 0 -0.71 1 1
ELF2 0.084 0.077 -9999 0 -10000 0 0
mol:Choline 0.09 0.065 -9999 0 -10000 0 0
cell migration -0.015 0.037 -9999 0 -10000 0 0
FYN 0.053 0.11 -9999 0 -10000 0 0
DOK2 0.008 0.075 -9999 0 -0.64 3 3
negative regulation of cell cycle 0.053 0.13 -9999 0 -0.73 3 3
ETS1 0.031 0.011 -9999 0 -10000 0 0
PXN 0.097 0.072 -9999 0 -10000 0 0
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
NOS3 0.099 0.078 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
TNF 0.032 0.011 -9999 0 -10000 0 0
MAPKKK cascade 0.09 0.065 -9999 0 -10000 0 0
RASA1 0.01 0.07 -9999 0 -0.72 2 2
Tie2/Ang1/Shc 0.085 0.068 -9999 0 -10000 0 0
NCK1 0.017 0 -9999 0 -10000 0 0
vasculogenesis 0.095 0.072 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.09 0.065 -9999 0 -10000 0 0
mol:Angiotensin II 0.002 0.002 -9999 0 -10000 0 0
mol:NADP 0.097 0.075 -9999 0 -10000 0 0
Rac1/GTP -0.009 0.039 -9999 0 -10000 0 0
MMP2 0.087 0.078 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.005 0.05 0.53 2 -10000 0 2
KIRREL 0.018 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.005 0.05 -10000 0 -0.53 2 2
PLCG1 -0.033 0.19 -10000 0 -0.72 15 15
ARRB2 0.017 0 -10000 0 -10000 0 0
WASL 0.014 0.044 -10000 0 -0.64 1 1
Nephrin/NEPH1/podocin/CD2AP -0.004 0.036 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.048 0.032 -10000 0 -10000 0 0
FYN 0.032 0.041 -10000 0 -10000 0 0
mol:Ca2+ -0.033 0.12 -10000 0 -0.46 15 15
mol:DAG -0.033 0.12 -10000 0 -0.46 15 15
NPHS2 0.018 0.005 -10000 0 -10000 0 0
mol:IP3 -0.033 0.12 -10000 0 -0.46 15 15
regulation of endocytosis -0.004 0.034 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol -0.004 0.037 -10000 0 -0.39 2 2
establishment of cell polarity -0.005 0.05 -10000 0 -0.53 2 2
Nephrin/NEPH1/podocin/NCK1-2 -0.003 0.032 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 -0.004 0.034 -10000 0 -10000 0 0
NPHS1 0.012 0.069 -10000 0 -0.71 2 2
Nephrin/NEPH1/podocin -0.004 0.037 -10000 0 -10000 0 0
TJP1 0.017 0 -10000 0 -10000 0 0
NCK1 0.017 0 -10000 0 -10000 0 0
NCK2 0.017 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.033 0.12 -10000 0 -0.47 15 15
CD2AP 0.017 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.004 0.036 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.035 0.052 -10000 0 -10000 0 0
cytoskeleton organization 0.059 0.036 -10000 0 -10000 0 0
Nephrin/NEPH1 -0.004 0.037 -10000 0 -0.39 2 2
Nephrin/NEPH1/ZO-1 -0.004 0.04 -10000 0 -0.42 2 2
Ephrin A reverse signaling

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
MAPKKK cascade -0.006 0.051 -9999 0 -0.44 3 3
EFNA5 0.014 0.044 -9999 0 -0.64 1 1
FYN 0.027 0.056 -9999 0 -0.42 2 2
neuron projection morphogenesis -0.006 0.051 -9999 0 -0.44 3 3
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.006 0.051 -9999 0 -0.44 3 3
EPHA5 0.01 0.07 -9999 0 -0.72 2 2
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.011 0.065 -9999 0 -10000 0 0
MAP4K1 0.017 0 -9999 0 -10000 0 0
MAP3K8 -0.086 0.26 -9999 0 -0.72 31 31
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.017 0 -9999 0 -10000 0 0
CRKL 0.017 0 -9999 0 -10000 0 0
MAP3K1 0.056 0.042 -9999 0 -10000 0 0
JUN 0.026 0.065 -9999 0 -0.38 5 5
MAP3K7 0.056 0.042 -9999 0 -10000 0 0
GRAP2 0.017 0 -9999 0 -10000 0 0
CRK 0.014 0.044 -9999 0 -0.64 1 1
MAP2K4 0.045 0.069 -9999 0 -10000 0 0
LAT 0.01 0.07 -9999 0 -0.72 2 2
LCP2 0.004 0.096 -9999 0 -0.7 4 4
MAPK8 0.027 0.021 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.047 0.044 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.01 0.059 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.017 0.001 -9999 0 -10000 0 0
HDAC2 0.017 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.008 0.059 -9999 0 -0.46 3 3
forebrain development -0.006 0.17 -9999 0 -0.67 7 7
GNAO1 0.015 0.007 -9999 0 -10000 0 0
SMO/beta Arrestin2 0.014 0.074 -9999 0 -0.53 4 4
SMO 0.002 0.096 -9999 0 -0.7 4 4
ARRB2 0.014 0.008 -9999 0 -10000 0 0
GLI3/SPOP 0.03 0.098 -9999 0 -0.4 2 2
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.014 0.05 -9999 0 -0.72 1 1
GNAI2 0.015 0.007 -9999 0 -10000 0 0
SIN3/HDAC complex -0.002 0.027 -9999 0 -0.41 1 1
GNAI1 -0.07 0.22 -9999 0 -0.64 29 29
XPO1 0.017 0.009 -9999 0 -10000 0 0
GLI1/Su(fu) -0.051 0.11 -9999 0 -0.63 4 4
SAP30 0.017 0.001 -9999 0 -10000 0 0
mol:GDP 0.002 0.096 -9999 0 -0.7 4 4
MIM/GLI2A 0.007 0.098 -9999 0 -0.63 5 5
IFT88 -0.003 0.12 -9999 0 -0.72 6 6
GNAI3 0.014 0.007 -9999 0 -10000 0 0
GLI2 0.057 0.034 -9999 0 -10000 0 0
GLI3 0.021 0.1 -9999 0 -0.43 2 2
CSNK1D 0.017 0 -9999 0 -10000 0 0
CSNK1E 0.014 0.05 -9999 0 -0.72 1 1
SAP18 0.014 0.05 -9999 0 -0.72 1 1
embryonic digit morphogenesis -0.003 0.12 -9999 0 -0.72 6 6
GNG2 0.017 0 -9999 0 -10000 0 0
Gi family/GTP 0.005 0.097 -9999 0 -10000 0 0
SIN3B 0.017 0.001 -9999 0 -10000 0 0
SIN3A 0.017 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.037 0.084 -9999 0 -10000 0 0
GLI2/Su(fu) 0.059 0.053 -9999 0 -10000 0 0
FOXA2 -0.15 0.27 -9999 0 -0.7 19 19
neural tube patterning -0.006 0.17 -9999 0 -0.67 7 7
SPOP 0.017 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.031 0.041 -9999 0 -10000 0 0
GNB1 0.017 0 -9999 0 -10000 0 0
CSNK1G2 0.017 0 -9999 0 -10000 0 0
CSNK1G3 0.017 0 -9999 0 -10000 0 0
MTSS1 0.007 0.098 -9999 0 -0.63 5 5
embryonic limb morphogenesis -0.006 0.17 -9999 0 -0.67 7 7
SUFU 0.027 0.044 -9999 0 -10000 0 0
LGALS3 -0.004 0.11 -9999 0 -0.64 7 7
catabolic process 0.065 0.093 -9999 0 -10000 0 0
GLI3A/CBP 0.002 0.088 -9999 0 -10000 0 0
KIF3A 0.014 0.05 -9999 0 -0.72 1 1
GLI1 -0.007 0.17 -9999 0 -0.69 7 7
RAB23 -0.01 0.14 -9999 0 -0.72 8 8
CSNK1A1 0.017 0 -9999 0 -10000 0 0
IFT172 0.014 0.044 -9999 0 -0.64 1 1
RBBP7 0.017 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.019 0.076 -9999 0 -10000 0 0
GNAZ 0.014 0.007 -9999 0 -10000 0 0
RBBP4 0.017 0.001 -9999 0 -10000 0 0
CSNK1G1 0.017 0 -9999 0 -10000 0 0
PIAS1 0.017 0 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GLI2/SPOP 0.062 0.031 -9999 0 -10000 0 0
STK36 0.013 0.05 -9999 0 -0.72 1 1
Gi family/GNB1/GNG2/GDP 0.014 0.092 -9999 0 -10000 0 0
PTCH1 0.006 0.16 -9999 0 -0.62 6 6
MIM/GLI1 -0.041 0.23 -9999 0 -0.8 7 7
CREBBP 0.002 0.088 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.067 0.017 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.052 0.053 -10000 0 -0.55 1 1
regulation of axonogenesis -0.013 0.081 -10000 0 -10000 0 0
myoblast fusion 0.002 0.02 -10000 0 -10000 0 0
mol:GTP 0 0.013 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.036 0.068 0.4 5 -10000 0 5
ARF1/GTP 0 0.01 -10000 0 -10000 0 0
mol:GM1 0.015 0.01 -10000 0 -10000 0 0
mol:Choline -0.002 0.12 -10000 0 -0.37 23 23
lamellipodium assembly 0.001 0.027 -10000 0 -10000 0 0
MAPK3 0.034 0.047 -10000 0 -0.42 2 2
ARF6/GTP/NME1/Tiam1 0.036 0.068 -10000 0 -0.4 5 5
ARF1 0.017 0 -10000 0 -10000 0 0
ARF6/GDP -0.002 0.02 -10000 0 -10000 0 0
ARF1/GDP 0.036 0.023 -10000 0 -10000 0 0
ARF6 0.016 0.007 -10000 0 -10000 0 0
RAB11A 0.017 0 -10000 0 -10000 0 0
TIAM1 0.013 0.062 -10000 0 -0.63 2 2
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.037 0.036 -10000 0 -0.42 1 1
actin filament bundle formation 0.002 0.017 -10000 0 -10000 0 0
KALRN 0.001 0.02 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.002 0.017 -10000 0 -10000 0 0
NME1 0.009 0.085 -10000 0 -0.72 3 3
Rac1/GDP -0.002 0.017 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.013 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.001 0.027 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
liver development 0 0.013 -10000 0 -10000 0 0
ARF6/GTP 0 0.013 -10000 0 -10000 0 0
RhoA/GTP 0 0.01 -10000 0 -10000 0 0
mol:GDP 0 0.026 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.009 -10000 0 -10000 0 0
RHOA 0.017 0 -10000 0 -10000 0 0
PLD1 -0.018 0.14 -10000 0 -0.43 23 23
RAB11FIP3 0.017 0 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.027 -10000 0 -10000 0 0
ruffle organization 0.013 0.081 -10000 0 -10000 0 0
regulation of epithelial cell migration 0 0.013 -10000 0 -10000 0 0
PLD2 0.029 0.009 -10000 0 -10000 0 0
PIP5K1A 0.013 0.082 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.12 -10000 0 -0.37 23 23
Rac1/GTP 0.001 0.027 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.021 0.088 -9999 0 -0.42 2 2
CRKL 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.011 0.062 -9999 0 -0.64 2 2
ITGA4 0.011 0.062 -9999 0 -0.64 2 2
alpha4/beta7 Integrin/MAdCAM1 -0.093 0.17 -9999 0 -0.69 6 6
EPO 0.014 0.05 -9999 0 -0.72 1 1
alpha4/beta7 Integrin -0.023 0.1 -9999 0 -0.46 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0.044 -9999 0 -0.64 1 1
alpha4/beta1 Integrin -0.007 0.056 -9999 0 -0.49 3 3
EPO/EPOR (dimer) -0.002 0.036 -9999 0 -0.54 1 1
lamellipodium assembly 0.001 0.008 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
JAK2 -0.01 0.054 -9999 0 -10000 0 0
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
MADCAM1 -0.13 0.27 -9999 0 -0.64 49 49
cell adhesion -0.092 0.17 -9999 0 -0.69 6 6
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
SRC 0.032 0.081 -9999 0 -0.55 2 2
ITGB7 -0.01 0.13 -9999 0 -0.64 9 9
RAC1 0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.014 0.081 -9999 0 -0.45 7 7
p130Cas/Crk/Dock1 -0.014 0.066 -9999 0 -0.58 1 1
VCAM1 0.002 0.097 -9999 0 -0.64 5 5
RHOA 0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.042 -9999 0 -10000 0 0
BCAR1 0.042 0.076 -9999 0 -0.64 1 1
EPOR 0.017 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
Rac1/GTP 0.002 0.008 -9999 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.017 0 -10000 0 -10000 0 0
HDAC3 0.017 0 -10000 0 -10000 0 0
VDR -0.001 0.11 -10000 0 -0.64 6 6
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.017 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.052 0.032 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.017 0 -10000 0 -10000 0 0
AKT1 0.055 0.06 0.24 9 -10000 0 9
RAR alpha/9cRA/Cyclin H -0.012 0.039 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.049 0.033 -10000 0 -10000 0 0
CDC2 -0.052 0.22 -10000 0 -0.72 21 21
response to UV 0.002 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.004 0.024 -10000 0 -10000 0 0
NCOR2 0.017 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.013 0.077 -10000 0 -0.47 6 6
RXRs/RARs/NRIP1/9cRA 0.077 0.062 -10000 0 -10000 0 0
NCOA2 0.017 0 -10000 0 -10000 0 0
NCOA3 0.004 0.098 -10000 0 -0.72 4 4
NCOA1 0.011 0.062 -10000 0 -0.64 2 2
VDR/VDR/DNA -0.001 0.11 -10000 0 -0.63 6 6
RARG 0.012 0.07 -10000 0 -0.72 2 2
RAR gamma1/9cRA -0.004 0.044 -10000 0 -0.47 2 2
MAPK3 0.012 0.062 -10000 0 -0.63 2 2
MAPK1 0.014 0.044 -10000 0 -0.64 1 1
MAPK8 0.019 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.022 0.067 -10000 0 -0.4 2 2
RARA 0.037 0.037 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.051 0.023 -10000 0 -10000 0 0
PRKCA 0.019 0.05 -10000 0 -0.72 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 0.069 0.052 -10000 0 -10000 0 0
RXRG 0.035 0.05 -10000 0 -0.3 5 5
RXRA 0.033 0.079 -10000 0 -0.41 2 2
RXRB 0.034 0.05 -10000 0 -0.3 5 5
VDR/Vit D3/DNA -0.013 0.077 -10000 0 -0.47 6 6
RBP1 -0.069 0.23 -10000 0 -0.69 27 27
CRBP1/9-cic-RA -0.064 0.17 -10000 0 -0.52 27 27
RARB 0.021 0 -10000 0 -10000 0 0
PRKCG 0.008 0.098 -10000 0 -0.72 4 4
MNAT1 0.017 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.079 0.079 -10000 0 -10000 0 0
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.076 0.059 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.035 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.069 0.052 -10000 0 -10000 0 0
positive regulation of DNA binding -0.011 0.037 -10000 0 -10000 0 0
NRIP1 0.068 0.046 -10000 0 -10000 0 0
RXRs/RARs 0.061 0.05 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.016 0.051 -10000 0 -0.38 1 1
PRKACA 0.017 0 -10000 0 -10000 0 0
CDK7 0.017 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.002 0.014 -10000 0 -10000 0 0
CCNH 0.017 0 -10000 0 -10000 0 0
CREBBP 0.017 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.003 0.032 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.17 0.3 -10000 0 -0.64 65 65
CLTC 0.034 0.037 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.017 0.057 -10000 0 -10000 0 0
Dynamin 2/GTP -0.006 0.048 -10000 0 -0.42 3 3
EXOC4 0.017 0 -10000 0 -10000 0 0
CD59 0.029 0.034 -10000 0 -10000 0 0
CPE -0.02 0.13 -10000 0 -0.41 23 23
CTNNB1 0 0.11 -10000 0 -0.72 5 5
membrane fusion -0.017 0.049 -10000 0 -10000 0 0
CTNND1 0.038 0.049 -10000 0 -10000 0 0
DNM2 0.017 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.035 -10000 0 -10000 0 0
TSHR 0.026 0 -10000 0 -10000 0 0
INS 0.023 0.012 -10000 0 -10000 0 0
BIN1 0.017 0 -10000 0 -10000 0 0
mol:Choline -0.017 0.049 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.057 -10000 0 -0.47 3 3
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.048 -10000 0 -0.42 3 3
JUP 0.029 0.034 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0 0 -10000 0 -10000 0 0
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.022 0.062 -10000 0 -0.43 2 2
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.017 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.017 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.059 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.017 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.014 0.079 0.61 2 -10000 0 2
positive regulation of phagocytosis 0.025 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.016 0.048 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.009 0.075 -10000 0 -0.3 2 2
clathrin heavy chain/ACAP1 0.035 0.047 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.017 0 -10000 0 -10000 0 0
exocyst 0.059 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.038 0.049 -10000 0 -0.38 3 3
NME1 0.019 0.057 -10000 0 -0.47 3 3
clathrin coat assembly 0.034 0.037 -10000 0 -10000 0 0
IL2RA 0.022 0.051 -10000 0 -10000 0 0
VAMP3 0.026 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.088 0.13 -10000 0 -0.45 4 4
EXOC6 0.017 0 -10000 0 -10000 0 0
PLD1 -0.03 0.089 -10000 0 -0.29 23 23
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.017 0 -10000 0 -10000 0 0
PIP5K1C 0.033 0.035 -10000 0 -10000 0 0
SDC1 0.029 0.034 -10000 0 -10000 0 0
ARF6/GDP 0.017 0.057 -10000 0 -0.47 3 3
EXOC7 0.017 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.014 0.081 -10000 0 -0.64 2 2
mol:Phosphatidic acid -0.017 0.049 -10000 0 -10000 0 0
endocytosis 0 0 -10000 0 -10000 0 0
SCAMP2 0.017 0 -10000 0 -10000 0 0
ADRB2 -0.081 0.17 -10000 0 -0.35 14 14
EXOC3 0.017 0 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.052 -10000 0 -0.42 3 3
KLC1 0.017 0 -10000 0 -10000 0 0
AVPR2 0.043 0.035 -10000 0 -10000 0 0
RALA 0.017 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.074 -10000 0 -0.58 2 2
Insulin 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
CBL/APS/CAP -0.03 0.11 -9999 0 -0.65 3 3
TC10/GTP -0.021 0.075 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.014 0.071 -9999 0 -10000 0 0
HRAS 0.017 0 -9999 0 -10000 0 0
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.082 0.25 -9999 0 -0.69 31 31
FOXO3 -0.009 0.02 -9999 0 -10000 0 0
AKT1 0.018 0.14 -9999 0 -0.58 1 1
INSR 0.011 0.075 -9999 0 -0.63 3 3
Insulin Receptor/Insulin -0.005 0.037 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 -0.03 0.18 -9999 0 -0.72 14 14
SORBS1 -0.028 0.16 -9999 0 -0.64 15 15
CRK 0.014 0.044 -9999 0 -0.64 1 1
PTPN1 0.052 0.044 -9999 0 -10000 0 0
CAV1 0.027 0.1 -9999 0 -0.51 6 6
CBL/APS/CAP/Crk-II/C3G -0.023 0.084 -9999 0 -0.39 1 1
Insulin Receptor/Insulin/IRS1/NCK2 -0.012 0.066 -9999 0 -0.42 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.01 0.056 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.049 0.074 -9999 0 -0.52 3 3
RPS6KB1 0.028 0.13 -9999 0 -0.52 1 1
PARD6A -0.013 0.15 -9999 0 -0.72 9 9
CBL 0.017 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.006 0.037 -9999 0 -0.36 1 1
PIK3R1 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.042 0.095 -9999 0 -0.54 1 1
HRAS/GTP -0.008 0.048 -9999 0 -10000 0 0
Insulin Receptor 0.011 0.075 -9999 0 -0.63 3 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.011 0.06 -9999 0 -10000 0 0
PRKCI -0.017 0.048 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.052 0.12 -9999 0 -0.63 1 1
SHC1 0.017 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.002 0.058 -9999 0 -0.54 2 2
PI3K -0.01 0.057 -9999 0 -10000 0 0
NCK2 0.017 0 -9999 0 -10000 0 0
RHOQ 0.017 0 -9999 0 -10000 0 0
mol:H2O2 -0.001 0.005 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 0.018 0.14 -9999 0 -0.58 1 1
PRKCZ -0.012 0.028 -9999 0 -10000 0 0
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.01 0.058 -9999 0 -0.37 4 4
F2RL2 0.004 0.098 -9999 0 -0.72 4 4
TRIP10 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.004 0.038 -9999 0 -0.32 3 3
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.004 0.033 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
RASA1 0.01 0.07 -9999 0 -0.72 2 2
NCK1 0.017 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.026 0.092 -9999 0 -0.36 16 16
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.031 0.11 -9999 0 -0.42 14 14
INPP5D 0.022 0.069 -9999 0 -0.4 4 4
SOS1 0.017 0 -9999 0 -10000 0 0
SGK1 -0.005 0.011 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
IRS1 0.004 0.098 -9999 0 -0.72 4 4
p62DOK/RasGAP 0.002 0.059 -9999 0 -0.69 1 1
INS 0.019 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.022 0.068 -9999 0 -0.4 4 4
GRB2 0.017 0 -9999 0 -10000 0 0
EIF4EBP1 0.013 0.15 -9999 0 -0.57 2 2
PTPRA 0.017 0.043 -9999 0 -0.63 1 1
PIK3CA 0.017 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.045 0.049 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.012 0.068 -9999 0 -0.43 4 4
Insulin Receptor/Insulin/IRS3 -0.006 0.053 -9999 0 -0.46 3 3
Par3/Par6 -0.023 0.091 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.017 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.006 0.035 -10000 0 -10000 0 0
NT3 (dimer)/TRKC -0.005 0.051 -10000 0 -0.54 2 2
NT3 (dimer)/TRKB -0.028 0.1 -10000 0 -0.42 15 15
SHC/Grb2/SOS1/GAB1/PI3K 0.048 0.029 -10000 0 -10000 0 0
RAPGEF1 0.017 0 -10000 0 -10000 0 0
BDNF -0.036 0.19 -10000 0 -0.72 16 16
PIK3CA 0.017 0 -10000 0 -10000 0 0
DYNLT1 0.017 0 -10000 0 -10000 0 0
NTRK1 0.017 0 -10000 0 -10000 0 0
NTRK2 -0.023 0.16 -10000 0 -0.67 13 13
NTRK3 0.017 0 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB -0.025 0.1 -10000 0 -0.42 13 13
neuron apoptosis 0.039 0.081 0.41 1 -0.22 1 2
SHC 2-3/Grb2 -0.042 0.086 -10000 0 -0.44 1 1
SHC1 0.017 0 -10000 0 -10000 0 0
SHC2 -0.024 0.067 -10000 0 -0.4 1 1
SHC3 -0.032 0.081 -10000 0 -0.4 3 3
STAT3 (dimer) -0.019 0.11 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.004 0.043 -10000 0 -0.46 2 2
RIN/GDP 0.084 0.029 -10000 0 -10000 0 0
GIPC1 0.014 0.044 -10000 0 -0.64 1 1
KRAS 0.017 0 -10000 0 -10000 0 0
DNAJA3 -0.002 0.039 -10000 0 -0.38 2 2
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 -0.056 0.24 -10000 0 -0.62 33 33
MAGED1 0.014 0.05 -10000 0 -0.72 1 1
PTPN11 0.014 0.05 -10000 0 -0.72 1 1
RICS 0.017 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0 0 -10000 0 -10000 0 0
TRKA/NEDD4-2 -0.054 0.15 -10000 0 -0.46 26 26
ELMO1 0.017 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 -0.004 0.037 -10000 0 -0.4 2 2
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.017 0 -10000 0 -10000 0 0
DOCK1 0.011 0.062 -10000 0 -0.64 2 2
GAB2 0.017 0 -10000 0 -10000 0 0
RIT2 0.017 0 -10000 0 -10000 0 0
RIT1 0.017 0 -10000 0 -10000 0 0
FRS2 0.017 0 -10000 0 -10000 0 0
DNM1 0.01 0.07 -10000 0 -0.72 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0.044 -10000 0 -0.64 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.001 0.016 0.24 1 -10000 0 1
mol:GDP 0.1 0.039 -10000 0 -10000 0 0
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP 0.084 0.029 -10000 0 -10000 0 0
TIAM1 0.011 0.062 -10000 0 -0.64 2 2
PIK3R1 0.017 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.057 0.15 -10000 0 -0.48 20 20
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.005 0.051 -10000 0 -0.54 2 2
FRS2 family/SHP2 -0.002 0.031 -10000 0 -0.46 1 1
SHC/GRB2/SOS1/GAB1 -0.003 0.032 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) 0.01 0.07 -10000 0 -0.72 2 2
RAP1/GDP -0.001 0.008 -10000 0 -10000 0 0
KIDINS220/CRKL 0.017 0 -10000 0 -10000 0 0
BDNF (dimer) -0.036 0.19 -10000 0 -0.72 16 16
ubiquitin-dependent protein catabolic process -0.046 0.13 -10000 0 -0.4 26 26
Schwann cell development -0.009 0.02 -10000 0 -10000 0 0
EHD4 0.017 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.053 0.024 -10000 0 -10000 0 0
RAP1B 0.017 0 -10000 0 -10000 0 0
RAP1A 0.017 0 -10000 0 -10000 0 0
CDC42/GTP -0.043 0.12 -10000 0 -0.69 2 2
ABL1 0.017 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.017 0.045 -10000 0 -10000 0 0
STAT3 -0.019 0.11 -10000 0 -10000 0 0
axon guidance -0.042 0.11 -10000 0 -0.65 2 2
MAPK3 0.031 0.037 -10000 0 -0.35 2 2
MAPK1 0.033 0.026 -10000 0 -0.35 1 1
CDC42/GDP 0.084 0.029 -10000 0 -10000 0 0
NTF3 0.01 0.07 -10000 0 -0.72 2 2
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM -0.006 0.054 -10000 0 -0.47 3 3
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0.017 0 -10000 0 -10000 0 0
FAIM 0.007 0.085 -10000 0 -0.72 3 3
GAB1 0.011 0.062 -10000 0 -0.64 2 2
RASGRF1 -0.023 0.094 0.23 1 -0.38 14 15
SOS1 0.017 0 -10000 0 -10000 0 0
MCF2L 0.034 0.047 -10000 0 -0.46 2 2
RGS19 0.017 0 -10000 0 -10000 0 0
CDC42 0.017 0 -10000 0 -10000 0 0
RAS family/GTP 0.07 0.043 -10000 0 -10000 0 0
Rac1/GDP 0.084 0.029 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.029 0.053 -10000 0 -10000 0 0
NGF (dimer)/TRKA/NEDD4-2 -0.046 0.13 -10000 0 -0.4 26 26
MAP2K1 0.051 0.034 -10000 0 -10000 0 0
NGFR 0.017 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GIPC/GAIP 0.039 0.032 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.039 0.03 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.002 0.025 -10000 0 -10000 0 0
NRAS 0.007 0.085 -10000 0 -0.72 3 3
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI -0.003 0.12 -10000 0 -0.72 6 6
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.012 0.031 -10000 0 -10000 0 0
RASA1 0.01 0.07 -10000 0 -0.72 2 2
TRKA/c-Abl 0 0 -10000 0 -10000 0 0
SQSTM1 0.017 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.053 0.14 -10000 0 -0.44 21 21
NGF (dimer)/TRKA/p62/Atypical PKCs -0.011 0.064 -10000 0 -0.4 6 6
MATK 0.017 0 -10000 0 -10000 0 0
NEDD4L -0.059 0.21 -10000 0 -0.64 26 26
RAS family/GDP -0.003 0.022 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0.001 0.017 0.26 1 -10000 0 1
Rac1/GTP -0.016 0.055 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family -0.003 0.033 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.025 0.028 -9999 0 -0.4 1 1
ADCY5 0.027 0 -9999 0 -10000 0 0
ADCY6 0.027 0 -9999 0 -10000 0 0
ADCY7 0.027 0 -9999 0 -10000 0 0
ADCY1 0.027 0 -9999 0 -10000 0 0
ADCY2 0.025 0.033 -9999 0 -0.47 1 1
ADCY3 -0.002 0.12 -9999 0 -0.47 13 13
ADCY8 0.025 0.033 -9999 0 -0.47 1 1
PRKCE 0.016 0 -9999 0 -10000 0 0
ADCY9 0.022 0.049 -9999 0 -0.4 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.045 0.03 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.029 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.039 -10000 0 -10000 0 0
NFATC4 0.054 0.062 -10000 0 -10000 0 0
ERBB2IP 0.007 0.075 -10000 0 -0.63 3 3
HSP90 (dimer) 0.014 0.049 -10000 0 -0.72 1 1
mammary gland morphogenesis -0.005 0.057 0.26 3 -10000 0 3
JUN 0.079 0.071 -10000 0 -10000 0 0
HRAS 0.017 0.001 -10000 0 -10000 0 0
DOCK7 0.052 0.065 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.008 0.073 0.26 3 -0.38 6 9
AKT1 0.017 0.002 -10000 0 -10000 0 0
BAD 0.028 0.002 -10000 0 -10000 0 0
MAPK10 -0.008 0.038 -10000 0 -0.33 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.046 0.071 -10000 0 -10000 0 0
RAF1 0.08 0.063 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 2 -0.017 0.094 0.26 3 -0.39 12 15
STAT3 0.001 0.003 -10000 0 -10000 0 0
cell migration 0.07 0.045 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.001 0.001 -10000 0 -10000 0 0
cell proliferation 0.086 0.16 -10000 0 -10000 0 0
FOS 0.04 0.23 -10000 0 -0.51 32 32
NRAS 0.007 0.085 -10000 0 -0.72 3 3
mol:Ca2+ -0.005 0.057 0.26 3 -10000 0 3
MAPK3 0.09 0.12 -10000 0 -10000 0 0
MAPK1 0.091 0.12 -10000 0 -0.44 1 1
JAK2 0.045 0.081 -10000 0 -10000 0 0
NF2 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.041 0.028 -10000 0 -10000 0 0
NRG1 0.018 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 0.059 0.055 -10000 0 -10000 0 0
MAPK9 -0.004 0.022 -10000 0 -10000 0 0
ERBB2 -0.011 0.11 0.42 3 -0.55 7 10
ERBB3 0.018 0.002 -10000 0 -10000 0 0
SHC1 0.017 0.001 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
apoptosis 0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.001 0.003 -10000 0 -10000 0 0
RNF41 0.039 0.004 -10000 0 -10000 0 0
FRAP1 0.028 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.006 0.031 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.093 0.28 3 -0.46 8 11
CHRNA1 0.091 0.1 -10000 0 -10000 0 0
myelination 0.071 0.057 -10000 0 -10000 0 0
PPP3CB 0.05 0.062 -10000 0 -10000 0 0
KRAS 0.017 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.002 0.01 -10000 0 -10000 0 0
NRG2 0.002 0.097 -10000 0 -0.64 5 5
mol:GDP 0.041 0.028 -10000 0 -10000 0 0
SOS1 0.017 0.001 -10000 0 -10000 0 0
MAP2K2 0.091 0.064 -10000 0 -10000 0 0
SRC 0.017 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.049 0.069 -10000 0 -10000 0 0
MAP2K1 0.08 0.11 -10000 0 -10000 0 0
heart morphogenesis -0.005 0.057 0.26 3 -10000 0 3
RAS family/GDP -0.006 0.04 -10000 0 -10000 0 0
GRB2 0.017 0.001 -10000 0 -10000 0 0
PRKACA 0 0.003 -10000 0 -10000 0 0
CHRNE 0.035 0.018 -10000 0 -10000 0 0
HSP90AA1 0.014 0.05 -10000 0 -0.72 1 1
activation of caspase activity -0.017 0.002 -10000 0 -10000 0 0
nervous system development -0.005 0.057 0.26 3 -10000 0 3
CDC42 0.017 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.008 0.075 -9999 0 -0.64 3 3
SMAD2 0.018 0.034 -9999 0 -10000 0 0
SMAD3 0.045 0.063 -9999 0 -0.49 1 1
SMAD3/SMAD4 0.041 0.067 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.007 0.054 -9999 0 -0.4 4 4
SMAD2/SMAD2/SMAD4 -0.02 0.076 -9999 0 -10000 0 0
PPM1A 0.017 0 -9999 0 -10000 0 0
CALM1 0.017 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0.052 -9999 0 -0.35 3 3
MAP3K1 0.017 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.006 0.053 -9999 0 -0.46 3 3
MAPK3 0.011 0.062 -9999 0 -0.64 2 2
MAPK1 0.014 0.044 -9999 0 -0.64 1 1
NUP214 0.017 0 -9999 0 -10000 0 0
CTDSP1 0.017 0 -9999 0 -10000 0 0
CTDSP2 0.008 0.075 -9999 0 -0.64 3 3
CTDSPL 0.011 0.062 -9999 0 -0.64 2 2
KPNB1 -0.003 0.12 -9999 0 -0.72 6 6
TGFBRAP1 0.017 0 -9999 0 -10000 0 0
UBE2I 0.014 0.05 -9999 0 -0.72 1 1
NUP153 0.017 0 -9999 0 -10000 0 0
KPNA2 -0.013 0.15 -9999 0 -0.72 9 9
PIAS4 0.017 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0 0 -9999 0 -10000 0 0
HDAC3 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.003 0.032 -9999 0 -0.34 2 2
GATA1/HDAC4 -0.002 0.036 -9999 0 -0.54 1 1
GATA1/HDAC5 -0.002 0.036 -9999 0 -0.54 1 1
GATA2/HDAC5 0 0 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.004 0.04 -9999 0 -0.42 2 2
HDAC9 0.017 0 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.044 0.12 -9999 0 -0.39 25 25
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0.031 -9999 0 -10000 0 0
GATA2 0.017 0 -9999 0 -10000 0 0
HDAC4/RFXANK 0 0 -9999 0 -10000 0 0
BCOR 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.007 0.085 -9999 0 -0.72 3 3
HDAC5 0.017 0 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
Histones 0.044 0.024 -9999 0 -10000 0 0
ADRBK1 0.017 0 -9999 0 -10000 0 0
HDAC4 0.017 0 -9999 0 -10000 0 0
XPO1 0.017 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 -0.002 0.036 -9999 0 -0.54 1 1
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E -0.002 0.036 -9999 0 -0.54 1 1
TUBA1B 0.017 0 -9999 0 -10000 0 0
HDAC6 0.017 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 0.017 0 -9999 0 -10000 0 0
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.017 0 -9999 0 -10000 0 0
GATA1 0.014 0.05 -9999 0 -0.72 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
NR3C1 -0.054 0.2 -9999 0 -0.64 24 24
SUMO1/HDAC4 -0.003 0.022 -9999 0 -10000 0 0
SRF 0.017 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin 0 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E -0.002 0.036 -9999 0 -0.54 1 1
GNB1 0.017 0 -9999 0 -10000 0 0
RANGAP1 0.007 0.085 -9999 0 -0.72 3 3
BCL6/BCoR -0.005 0.047 -9999 0 -0.5 2 2
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF 0 0 -9999 0 -10000 0 0
HDAC4/ER alpha -0.012 0.075 -9999 0 -0.46 6 6
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.044 0.024 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0.05 -9999 0 -0.72 1 1
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.011 0.066 -9999 0 -0.68 2 2
HDAC4/CaMK II delta B 0.017 0 -9999 0 -10000 0 0
Hsp90/HDAC6 -0.002 0.036 -9999 0 -0.54 1 1
ESR1 -0.001 0.11 -9999 0 -0.64 6 6
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 -0.005 0.031 -9999 0 -0.35 1 1
NPC -0.002 0.028 -9999 0 -0.42 1 1
MEF2C -0.083 0.24 -9999 0 -0.64 34 34
RAN 0.014 0.05 -9999 0 -0.72 1 1
HDAC4/MEF2C -0.05 0.12 -9999 0 -0.72 1 1
GNG2 0.017 0 -9999 0 -10000 0 0
NCOR2 0.017 0 -9999 0 -10000 0 0
TUBB2A 0.017 0 -9999 0 -10000 0 0
HDAC11 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
RANBP2 0.014 0.05 -9999 0 -0.72 1 1
ANKRA2 0.017 0 -9999 0 -10000 0 0
RFXANK 0.017 0 -9999 0 -10000 0 0
nuclear import 0.001 0.021 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.054 0.086 -9999 0 -0.36 3 3
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0.017 0 -9999 0 -10000 0 0
AKT2 0.017 0 -9999 0 -10000 0 0
STXBP4 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.017 0.13 -9999 0 -0.4 3 3
YWHAZ 0.017 0 -9999 0 -10000 0 0
CALM1 0.017 0 -9999 0 -10000 0 0
YWHAQ 0.017 0 -9999 0 -10000 0 0
TBC1D4 0.001 0.13 -9999 0 -0.53 12 12
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.017 0 -9999 0 -10000 0 0
YWHAB 0.017 0 -9999 0 -10000 0 0
SNARE/Synip 0 0 -9999 0 -10000 0 0
YWHAG 0.017 0 -9999 0 -10000 0 0
ASIP 0 0 -9999 0 -10000 0 0
PRKCI -0.003 0.12 -9999 0 -0.72 6 6
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0.017 0 -9999 0 -10000 0 0
GYS1 0.042 0.019 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0.017 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 0.051 0.05 -9999 0 -10000 0 0
VAMP2 0.017 0 -9999 0 -10000 0 0
SLC2A4 -0.021 0.14 -9999 0 -0.4 4 4
STX4 0.017 0 -9999 0 -10000 0 0
GSK3B 0.034 0.023 -9999 0 -0.3 1 1
SFN 0.011 0.062 -9999 0 -0.64 2 2
LNPEP 0.017 0 -9999 0 -10000 0 0
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.017 0 -10000 0 -10000 0 0
MKNK1 0.017 0 -10000 0 -10000 0 0
mol:PIP3 0.005 0.055 0.3 6 -10000 0 6
FRAP1 0.032 0.019 -10000 0 -10000 0 0
AKT1 0.004 0.044 0.25 6 -10000 0 6
INSR 0.008 0.075 -10000 0 -0.64 3 3
Insulin Receptor/Insulin -0.005 0.046 -10000 0 -0.4 3 3
mol:GTP -0.002 0.012 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.002 -10000 0 -10000 0 0
TSC2 0.017 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.01 -10000 0 -10000 0 0
TSC1 0.017 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.013 0.052 -10000 0 -0.34 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.017 0 -10000 0 -10000 0 0
RPS6KB1 0.047 0.031 -10000 0 -10000 0 0
MAP3K5 0.011 0.031 -10000 0 -0.32 2 2
PIK3R1 0.017 0 -10000 0 -10000 0 0
apoptosis 0.011 0.031 -10000 0 -0.32 2 2
mol:LY294002 0 0 -10000 0 -0.001 4 4
EIF4B 0.054 0.03 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.007 0.042 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -10000 0 -10000 0 0
KIAA1303 0.017 0 -10000 0 -10000 0 0
PI3K 0.028 0.03 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.068 0.025 -10000 0 -10000 0 0
FKBP1A 0.017 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.001 0.01 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 4 4
FKBP12/Rapamycin 0.001 0.004 -10000 0 -10000 0 0
PDPK1 0.004 0.046 0.25 6 -10000 0 6
EIF4E 0.017 0 -10000 0 -10000 0 0
ASK1/PP5C 0.035 0.03 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.045 0.007 -10000 0 -10000 0 0
TSC1/TSC2 -0.002 0.013 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 4 -10000 0 4
RPS6 0 0.11 -10000 0 -0.72 5 5
PPP5C 0.014 0.05 -10000 0 -0.72 1 1
EIF4G1 0.017 0 -10000 0 -10000 0 0
IRS1 0.008 0.034 -10000 0 -0.24 4 4
INS 0.017 0 -10000 0 -10000 0 0
PTEN -0.001 0.1 -10000 0 -0.63 6 6
PDK2 0.004 0.046 0.25 6 -10000 0 6
EIF4EBP1 0.002 0.065 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
PPP2R5D 0.041 0.018 -10000 0 -10000 0 0
peptide biosynthetic process 0.029 0.044 -10000 0 -0.35 3 3
RHEB 0.017 0 -10000 0 -10000 0 0
EIF4A1 0.017 0 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.004 6 -10000 0 6
EEF2 0.029 0.044 -10000 0 -0.35 3 3
eIF4E/4E-BP1 0.012 0.058 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.029 0.038 -9999 0 -0.54 1 1
BAD/BCL-XL/YWHAZ -0.002 0.027 -9999 0 -10000 0 0
CDKN1B 0.031 0.08 -9999 0 -10000 0 0
CDKN1A 0.029 0.084 -9999 0 -10000 0 0
FRAP1 0.017 0 -9999 0 -10000 0 0
PRKDC -0.046 0.21 -9999 0 -0.72 19 19
FOXO3 0.033 0.076 -9999 0 -10000 0 0
AKT1 -0.021 0.065 -9999 0 -0.32 1 1
BAD 0.017 0 -9999 0 -10000 0 0
AKT3 0.023 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.033 0.076 -9999 0 -10000 0 0
AKT1/ASK1 -0.021 0.065 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.014 0.05 -9999 0 -0.72 1 1
RAF1 0.017 0 -9999 0 -10000 0 0
JNK cascade 0.021 0.064 -9999 0 -10000 0 0
TSC1 0.033 0.076 -9999 0 -10000 0 0
YWHAZ 0.017 0 -9999 0 -10000 0 0
AKT1/RAF1 0.032 0.075 -9999 0 -10000 0 0
EP300 0.017 0 -9999 0 -10000 0 0
mol:GDP -0.02 0.064 -9999 0 -0.32 1 1
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.033 0.076 -9999 0 -10000 0 0
YWHAQ 0.017 0 -9999 0 -10000 0 0
TBC1D4 0.008 0.11 -9999 0 -0.45 12 12
MAP3K5 0.01 0.07 -9999 0 -0.72 2 2
MAPKAP1 0.01 0.07 -9999 0 -0.72 2 2
negative regulation of cell cycle -0.051 0.036 -9999 0 -10000 0 0
YWHAH 0.017 0 -9999 0 -10000 0 0
AKT1S1 0.033 0.076 -9999 0 -10000 0 0
CASP9 0.033 0.076 -9999 0 -10000 0 0
YWHAB 0.017 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.04 0.076 -9999 0 -10000 0 0
GBL 0.017 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.002 0.031 -9999 0 -0.46 1 1
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
SRC 0.017 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.021 0.061 -9999 0 -10000 0 0
KIAA1303 0.017 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.042 0.026 -9999 0 -10000 0 0
CHUK 0.033 0.076 -9999 0 -10000 0 0
BAD/BCL-XL 0.049 0.076 -9999 0 -10000 0 0
mTORC2 -0.006 0.047 -9999 0 -0.41 3 3
AKT2 0.023 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.062 0.063 -9999 0 -10000 0 0
PDPK1 0.017 0 -9999 0 -10000 0 0
MDM2 0.033 0.076 -9999 0 -10000 0 0
MAPKKK cascade -0.032 0.074 -9999 0 -10000 0 0
MDM2/Cbp/p300 -0.015 0.05 -9999 0 -10000 0 0
TSC1/TSC2 0.042 0.074 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.048 -9999 0 -10000 0 0
glucose import -0.093 0.2 -9999 0 -0.51 12 12
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.05 0.053 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.094 0.2 -9999 0 -0.52 12 12
GSK3A 0.033 0.076 -9999 0 -10000 0 0
FOXO1 0.019 0.1 -9999 0 -0.54 1 1
GSK3B 0.032 0.085 -9999 0 -0.6 1 1
SFN 0.011 0.062 -9999 0 -0.64 2 2
G1/S transition of mitotic cell cycle 0.041 0.083 -9999 0 -0.57 1 1
p27Kip1/14-3-3 family 0.058 0.032 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
KPNA1 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
YWHAG 0.017 0 -9999 0 -10000 0 0
RHEB 0.017 0 -9999 0 -10000 0 0
CREBBP 0.017 0 -9999 0 -10000 0 0
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 -0.005 0.027 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.012 0.044 -9999 0 -10000 0 0
JUN 0.045 0.084 -9999 0 -10000 0 0
HRAS 0.017 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.041 0.14 -9999 0 -0.47 17 17
RAP1A 0.017 0 -9999 0 -10000 0 0
FRS2 0.017 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.017 0.078 -9999 0 -0.41 5 5
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0.044 -9999 0 -0.64 1 1
RET9/GFRalpha1/GDNF/Enigma -0.002 0.028 -9999 0 -0.42 1 1
RHOA 0.017 0 -9999 0 -10000 0 0
RAP1A/GTP -0.017 0.072 -9999 0 -10000 0 0
GRB7 -0.01 0.14 -9999 0 -0.72 8 8
RET51/GFRalpha1/GDNF -0.015 0.073 -9999 0 -0.41 4 4
MAPKKK cascade -0.013 0.059 -9999 0 -10000 0 0
BCAR1 0.017 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.008 0.056 -9999 0 -0.42 4 4
lamellipodium assembly -0.011 0.04 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC -0.015 0.073 -9999 0 -0.41 4 4
PIK3CA 0.017 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3 0 0 -9999 0 -10000 0 0
MAPK3 0.038 0.086 -9999 0 -10000 0 0
DOK1 0.014 0.05 -9999 0 -0.72 1 1
DOK6 0.017 0 -9999 0 -10000 0 0
PXN 0.017 0 -9999 0 -10000 0 0
neurite development 0.054 0.088 -9999 0 -10000 0 0
DOK5 -0.01 0.14 -9999 0 -0.72 8 8
GFRA1 0.017 0 -9999 0 -10000 0 0
MAPK8 0.046 0.063 -9999 0 -0.39 1 1
HRAS/GTP -0.016 0.07 -9999 0 -0.48 1 1
tube development 0 0 -9999 0 -10000 0 0
MAPK1 0.04 0.083 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.041 0.017 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
PDLIM7 0.014 0.05 -9999 0 -0.72 1 1
RET51/GFRalpha1/GDNF/Dok6 -0.014 0.067 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.02 0.083 -9999 0 -0.41 4 4
RET51/GFRalpha1/GDNF/Dok5 -0.03 0.1 -9999 0 -0.41 12 12
PRKCA 0.014 0.05 -9999 0 -0.72 1 1
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 0.048 0.029 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.04 0.029 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.03 0.1 -9999 0 -0.41 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.011 0.14 -9999 0 -0.67 9 9
DOK4 0.008 0.075 -9999 0 -0.64 3 3
JNK cascade 0.045 0.083 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/FRS2 0 0 -9999 0 -10000 0 0
SHANK3 0.017 0 -9999 0 -10000 0 0
RASA1 0.01 0.07 -9999 0 -0.72 2 2
NCK1 0.017 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.042 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.038 0.059 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.036 0.066 -9999 0 -0.42 1 1
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.039 0.056 -9999 0 -10000 0 0
PI3K 0.067 0.08 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0 0 -9999 0 -10000 0 0
GRB10 -0.03 0.18 -9999 0 -0.72 14 14
activation of MAPKK activity 0.041 0.044 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2 -0.015 0.073 -9999 0 -0.41 4 4
GAB1 0.011 0.062 -9999 0 -0.64 2 2
IRS1 0.004 0.098 -9999 0 -0.72 4 4
IRS2 0.014 0.05 -9999 0 -0.72 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.037 0.063 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/PKC alpha -0.017 0.078 -9999 0 -0.41 5 5
GRB2 0.017 0 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GDNF 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.022 0.09 -9999 0 -0.41 8 8
Rac1/GTP -0.013 0.046 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF 0 0 -9999 0 -10000 0 0
GFRalpha1/GDNF 0 0 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.024 0.063 -9999 0 -10000 0 0
GNAI2 0.017 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.025 0.064 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process 0.005 0.087 -9999 0 -10000 0 0
GNAZ 0.017 0 -9999 0 -10000 0 0
GNAI3 0.017 0 -9999 0 -10000 0 0
GNA12 0.017 0 -9999 0 -10000 0 0
S1PR5 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi 0.005 0.088 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
GNAI1 -0.068 0.22 -9999 0 -0.64 29 29
Paxillin-dependent events mediated by a4b1

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
CRKL 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0.001 0.007 -9999 0 -10000 0 0
DOCK1 0.011 0.062 -9999 0 -0.64 2 2
ITGA4 0.011 0.062 -9999 0 -0.64 2 2
RAC1 0.017 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.023 0.1 -9999 0 -0.46 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0.044 -9999 0 -0.64 1 1
alpha4/beta1 Integrin -0.006 0.047 -9999 0 -0.41 3 3
alpha4/beta7 Integrin/Paxillin -0.017 0.074 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.033 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
TLN1 0.017 0 -9999 0 -10000 0 0
PXN 0.031 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
ARF6/GTP -0.004 0.034 -9999 0 -10000 0 0
cell adhesion -0.004 0.038 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.005 0.042 -9999 0 -0.41 1 1
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
ITGB7 -0.01 0.13 -9999 0 -0.64 9 9
ARF6/GDP 0.001 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.012 0.068 -9999 0 -0.65 1 1
p130Cas/Crk/Dock1 -0.005 0.044 -9999 0 -0.38 3 3
VCAM1 0.002 0.097 -9999 0 -0.64 5 5
alpha4/beta1 Integrin/Paxillin/Talin -0.005 0.039 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.039 -9999 0 -10000 0 0
BCAR1 0.017 0 -9999 0 -10000 0 0
mol:GDP 0.004 0.038 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.005 0.039 -9999 0 -10000 0 0
Rac1/GTP -0.003 0.036 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.017 0 -9999 0 -10000 0 0
CDC42/GTP -0.025 0.064 -9999 0 -10000 0 0
PLCG1 -0.012 0.14 -9999 0 -0.44 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.017 0 -9999 0 -10000 0 0
GNAI3 0.017 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.024 0.063 -9999 0 -10000 0 0
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0.013 0.089 -9999 0 -10000 0 0
MAPK1 0.015 0.086 -9999 0 -0.31 1 1
S1P/S1P5/Gi 0.005 0.088 -9999 0 -10000 0 0
GNAI1 -0.068 0.22 -9999 0 -0.64 29 29
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0 0 -9999 0 -10000 0 0
RHOA 0.033 0 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.005 0.088 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.017 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 0 0 -9999 0 -10000 0 0
GNA12 0.017 0 -9999 0 -10000 0 0
GNA13 0.017 0 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex -0.013 0.065 -9999 0 -0.35 8 8
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.017 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.034 0 -9999 0 -10000 0 0
CD4 0.017 0 -9999 0 -10000 0 0
CLTA 0.017 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 -0.005 0.11 -9999 0 -0.55 8 8
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.022 0.076 -9999 0 -0.37 8 8
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 0 0.001 -9999 0 -10000 0 0
ARF1/GDP -0.014 0.075 -9999 0 -0.4 8 8
AP2M1 0.017 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.014 0.075 -9999 0 -0.4 8 8
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.032 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.017 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.017 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.028 0.044 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.001 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.048 0 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE -0.005 0.1 -9999 0 -0.55 8 8
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.005 0.1 -9999 0 -0.55 8 8
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0.007 0.085 -9999 0 -0.72 3 3
Aurora C/Aurora B/INCENP -0.006 0.048 -9999 0 -0.42 3 3
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.002 0.013 -9999 0 -10000 0 0
AURKB 0.017 0 -9999 0 -10000 0 0
AURKC 0.017 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.003 0.032 -9999 0 -0.34 2 2
NF kappa B1 p50/RelA/I kappa B alpha 0 0 -9999 0 -10000 0 0
SUMO1 0.017 0 -9999 0 -10000 0 0
ZFPM1 0.017 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0.031 -9999 0 -10000 0 0
FKBP3 0.017 0 -9999 0 -10000 0 0
Histones 0 0 -9999 0 -10000 0 0
YY1/LSF 0.035 0 -9999 0 -10000 0 0
SMG5 0.017 0 -9999 0 -10000 0 0
RAN 0.014 0.05 -9999 0 -0.72 1 1
I kappa B alpha/HDAC3 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0 0 -9999 0 -10000 0 0
SAP18 0.014 0.05 -9999 0 -0.72 1 1
RELA 0.053 0 -9999 0 -10000 0 0
HDAC1/Smad7 -0.002 0.026 -9999 0 -0.38 1 1
RANGAP1 0.007 0.085 -9999 0 -0.72 3 3
HDAC3/TR2 -0.007 0.054 -9999 0 -0.4 4 4
NuRD/MBD3 Complex 0.064 0.011 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.055 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.017 0 -9999 0 -10000 0 0
GATA1 0.014 0.05 -9999 0 -0.72 1 1
Mad/Max -0.025 0.1 -9999 0 -0.46 12 12
NuRD/MBD3 Complex/GATA1/Fog1 0.078 0.025 -9999 0 -10000 0 0
RBBP7 0.017 0 -9999 0 -10000 0 0
NPC -0.002 0.028 -9999 0 -0.42 1 1
RBBP4 0.017 0 -9999 0 -10000 0 0
MAX 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.017 0 -9999 0 -10000 0 0
NFKBIA 0.039 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.058 0.014 -9999 0 -10000 0 0
SIN3 complex -0.002 0.027 -9999 0 -0.41 1 1
SMURF1 0.017 0 -9999 0 -10000 0 0
CHD3 0.014 0.05 -9999 0 -0.72 1 1
SAP30 0.017 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.014 0.044 -9999 0 -0.64 1 1
YY1/HDAC3 0 0 -9999 0 -10000 0 0
YY1/HDAC2 0.035 0 -9999 0 -10000 0 0
YY1/HDAC1 0.035 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.063 0.019 -9999 0 -10000 0 0
PPARG -0.009 0.052 -9999 0 -10000 0 0
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0.05 -9999 0 -0.72 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.017 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
MBD3L2 0.017 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.026 -9999 0 -0.38 1 1
CREBBP 0.017 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.075 0.013 -9999 0 -10000 0 0
HDAC1 0.017 0 -9999 0 -10000 0 0
HDAC3 0.039 0 -9999 0 -10000 0 0
HDAC2 0.017 0 -9999 0 -10000 0 0
YY1 0.031 0 -9999 0 -10000 0 0
HDAC8 0.017 0 -9999 0 -10000 0 0
SMAD7 0.014 0.044 -9999 0 -0.64 1 1
NCOR2 0.017 0 -9999 0 -10000 0 0
MXD1 -0.018 0.15 -9999 0 -0.64 12 12
STAT3 0.035 0 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0.05 -9999 0 -0.72 1 1
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0 0 -9999 0 -10000 0 0
EP300 0.017 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.035 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.039 0 -9999 0 -10000 0 0
histone deacetylation 0.063 0.019 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0 0 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GATAD2B 0.017 0 -9999 0 -10000 0 0
GATAD2A 0.017 0 -9999 0 -10000 0 0
GATA2/HDAC3 0 0 -9999 0 -10000 0 0
GATA1/HDAC1 -0.002 0.036 -9999 0 -0.54 1 1
GATA1/HDAC3 -0.002 0.027 -9999 0 -0.4 1 1
CHD4 0.017 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.052 0.051 -9999 0 -10000 0 0
NuRD Complex 0.074 0.02 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0 0 -9999 0 -10000 0 0
SIN3B 0.017 0 -9999 0 -10000 0 0
MTA2 0.017 0 -9999 0 -10000 0 0
SIN3A 0.017 0 -9999 0 -10000 0 0
XPO1 0.017 0 -9999 0 -10000 0 0
SUMO1/HDAC1 -0.003 0.022 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.002 0.036 -9999 0 -0.54 1 1
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF 0.017 0 -9999 0 -10000 0 0
negative regulation of cell growth 0.052 0.051 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.063 0.019 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 -0.005 0.031 -9999 0 -0.35 1 1
NF kappa B/RelA/I kappa B alpha 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.06 0.02 -9999 0 -10000 0 0
TFCP2 0.017 0 -9999 0 -10000 0 0
NR2C1 0.004 0.098 -9999 0 -0.72 4 4
MBD3 0.017 0 -9999 0 -10000 0 0
MBD2 0.014 0.044 -9999 0 -0.64 1 1
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0 0 -9999 0 -10000 0 0
FBXW11 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.034 0.033 -9999 0 -0.46 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.061 0.035 -9999 0 -10000 0 0
NFKBIA 0.038 0.026 -9999 0 -10000 0 0
MAPK14 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.033 0.033 -9999 0 -0.46 1 1
ARRB2 0.023 0 -9999 0 -10000 0 0
REL 0.017 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.034 0.033 -9999 0 -0.46 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.034 0.033 -9999 0 -0.46 1 1
PIK3CA 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.025 0.038 -9999 0 -0.54 1 1
PIK3R1 0.017 0 -9999 0 -10000 0 0
NFKB1 0.029 0.038 -9999 0 -0.54 1 1
RELA 0.017 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.046 0.029 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.065 0.034 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.046 0.029 -9999 0 -10000 0 0
IKBKB 0.014 0.05 -9999 0 -0.72 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
SYK 0.014 0.05 -9999 0 -0.72 1 1
I kappa B alpha/PIK3R1 0.044 0.025 -9999 0 -10000 0 0
cell death -0.003 0.025 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.034 0.033 -9999 0 -0.46 1 1
LCK 0.011 0.066 -9999 0 -0.68 2 2
BCL3 0.017 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.004 0.031 -9999 0 -0.31 1 1
MDM2/SUMO1 -0.003 0.022 -9999 0 -10000 0 0
HDAC4 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.004 0.031 -9999 0 -0.31 1 1
SUMO1 0.017 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.019 0.033 -9999 0 -0.23 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.035 0.029 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.014 0.05 -9999 0 -0.72 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0.05 -9999 0 -0.72 1 1
SUMO1/HDAC4 -0.003 0.022 -9999 0 -10000 0 0
SUMO1/HDAC1 -0.003 0.022 -9999 0 -10000 0 0
RANGAP1 0.007 0.085 -9999 0 -0.72 3 3
MDM2/SUMO1/SUMO1 -0.002 0.027 -9999 0 -0.41 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.025 0.031 -9999 0 -10000 0 0
Ran/GTP -0.005 0.033 -9999 0 -0.37 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.017 0 -9999 0 -10000 0 0
UBE2I 0.014 0.05 -9999 0 -0.72 1 1
Ran/GTP/Exportin 1 -0.005 0.031 -9999 0 -0.35 1 1
NPC -0.002 0.028 -9999 0 -0.42 1 1
PIAS2 0.014 0.05 -9999 0 -0.72 1 1
PIAS1 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0 0 -9999 0 -10000 0 0
MAPK9 0.012 0 -9999 0 -10000 0 0
adrenocorticotropin secretion 0.013 0.038 -9999 0 -0.55 1 1
GNB1/GNG2 0 0 -9999 0 -10000 0 0
GNB1 0.017 0 -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 0.012 0 -9999 0 -10000 0 0
Gs family/GTP 0 0 -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 0.017 0 -9999 0 -10000 0 0
GNG2 0.017 0 -9999 0 -10000 0 0
CRH 0.014 0.05 -9999 0 -0.72 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.012 0 -9999 0 -10000 0 0
MAPK11 0.01 0.022 -9999 0 -0.32 1 1
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.017 0 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.017 0 -9999 0 -9999 0 0
PDE3B 0.017 0 -9999 0 -9999 0 0
p38 MAPK signaling 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
TRAF6/ASK1 -0.004 0.038 -9999 0 -0.4 2 2
TRAF2/ASK1 -0.004 0.044 -9999 0 -0.47 2 2
ATM 0.017 0 -9999 0 -10000 0 0
MAP2K3 0.064 0.023 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.059 0.055 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0 0.11 -9999 0 -0.72 5 5
TXN 0.012 0 -9999 0 -10000 0 0
CALM1 0.017 0 -9999 0 -10000 0 0
GADD45A 0.01 0.07 -9999 0 -0.72 2 2
GADD45B 0.017 0 -9999 0 -10000 0 0
MAP3K1 0.017 0 -9999 0 -10000 0 0
MAP3K6 0.017 0 -9999 0 -10000 0 0
MAP3K7 0.017 0 -9999 0 -10000 0 0
MAP3K4 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.005 0.051 -9999 0 -0.54 2 2
TAK1/TAB family 0.001 0.013 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.017 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.008 -9999 0 -10000 0 0
TRAF6 0.023 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.014 0.05 -9999 0 -0.72 1 1
CCM2 0.017 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.002 0.031 -9999 0 -0.47 1 1
MAPK11 0.014 0.05 -9999 0 -0.72 1 1
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.006 0.048 -9999 0 -0.42 3 3
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.022 0.026 -9999 0 -0.37 1 1
TAOK2 0.023 0 -9999 0 -10000 0 0
TAOK3 0.023 0 -9999 0 -10000 0 0
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
MAPK14 0.017 0 -9999 0 -10000 0 0
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
MAP3K5 0.01 0.07 -9999 0 -0.72 2 2
MAP3K10 0.014 0.05 -9999 0 -0.72 1 1
MAP3K3 0.017 0 -9999 0 -10000 0 0
TRX/ASK1 0.017 0.045 -9999 0 -0.46 2 2
GADD45/MTK1/MTK1 -0.012 0.068 -9999 0 -0.39 7 7
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.017 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
CHUK 0.017 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.002 0.025 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
MAP3K14 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0 0 -9999 0 -10000 0 0
RELB 0.017 0 -9999 0 -10000 0 0
NFKB2 0.014 0.05 -9999 0 -0.72 1 1
NF kappa B2 p52/RelB -0.002 0.031 -9999 0 -0.47 1 1
regulation of B cell activation -0.002 0.031 -9999 0 -0.47 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 222 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.AY.4071 TCGA.AY.4070 TCGA.AG.A032 TCGA.AG.A02X
109_MAP3K5 0.075 0.075 -0.089 -0.31
47_PPARGC1A 0.017 -0.63 0.017 -0.63
105_BMP4 0.017 0.017 0.017 0.017
105_BMP6 0.017 0.017 -0.63 -0.63
105_BMP7 0.017 -0.72 -0.72 0.017
105_BMP2 0.017 0.017 0.017 0.017
131_RELN/VLDLR -0.76 -0.41 -0.41 -0.41
30_TGFB1/TGF beta receptor Type II 0.016 0.02 0.016 0.016
84_STAT5B -0.087 -0.16 -0.14 0.054
84_STAT5A -0.087 -0.16 -0.14 0.054
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/3348409/GDAC_MergeDataFiles_3202301/COADREAD-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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