PARADIGM pathway analysis of mRNASeq expression and copy number data
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1KD1VZR
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 59 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
HIF-1-alpha transcription factor network 26
TCGA08_retinoblastoma 26
Thromboxane A2 receptor signaling 25
Angiopoietin receptor Tie2-mediated signaling 25
Osteopontin-mediated events 23
Fc-epsilon receptor I signaling in mast cells 23
Endothelins 23
Integrins in angiogenesis 22
Signaling events mediated by VEGFR1 and VEGFR2 22
TCGA08_p53 21
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 173 . 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 ( 173 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 0.1503 26 1992 76 -0.13 0.038 1000 -1000 -0.003 -1000
TCGA08_retinoblastoma 0.1503 26 210 8 -0.041 0.027 1000 -1000 -0.004 -1000
Thromboxane A2 receptor signaling 0.1445 25 2698 105 -0.16 0.063 1000 -1000 -0.019 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1445 25 2263 88 -0.22 0.055 1000 -1000 -0.043 -1000
Osteopontin-mediated events 0.1329 23 893 38 -0.096 0.04 1000 -1000 -0.013 -1000
Fc-epsilon receptor I signaling in mast cells 0.1329 23 2292 97 -0.2 0.054 1000 -1000 -0.041 -1000
Endothelins 0.1329 23 2233 96 -0.13 0.032 1000 -1000 -0.021 -1000
Integrins in angiogenesis 0.1272 22 1906 84 -0.12 0.043 1000 -1000 -0.025 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1272 22 2800 125 -0.15 0.061 1000 -1000 -0.018 -1000
TCGA08_p53 0.1214 21 148 7 -0.042 0.032 1000 -1000 -0.007 -1000
E-cadherin signaling in keratinocytes 0.1214 21 913 43 -0.097 0.033 1000 -1000 -0.01 -1000
Syndecan-1-mediated signaling events 0.1156 20 696 34 -0.075 0.031 1000 -1000 -0.013 -1000
Ephrin B reverse signaling 0.1156 20 966 48 -0.065 0.032 1000 -1000 -0.031 -1000
LPA receptor mediated events 0.1156 20 2070 102 -0.097 0.031 1000 -1000 -0.059 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.1156 20 1523 74 -0.055 0.049 1000 -1000 -0.043 -1000
E-cadherin signaling events 0.1156 20 103 5 -0.033 0.031 1000 -1000 0.02 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1098 19 676 34 -0.052 0.032 1000 -1000 -0.03 -1000
IL4-mediated signaling events 0.1098 19 1778 91 -0.4 0.32 1000 -1000 -0.043 -1000
EPHB forward signaling 0.1040 18 1591 85 -0.058 0.042 1000 -1000 -0.034 -1000
Syndecan-4-mediated signaling events 0.1040 18 1239 67 -0.11 0.047 1000 -1000 -0.026 -1000
amb2 Integrin signaling 0.0983 17 1405 82 -0.074 0.041 1000 -1000 -0.013 -1000
p75(NTR)-mediated signaling 0.0925 16 2041 125 -0.092 0.086 1000 -1000 -0.036 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0925 16 1116 68 -0.25 0.099 1000 -1000 -0.037 -1000
E-cadherin signaling in the nascent adherens junction 0.0925 16 1290 76 -0.092 0.044 1000 -1000 -0.03 -1000
IGF1 pathway 0.0925 16 938 57 -0.053 0.06 1000 -1000 -0.018 -1000
Nectin adhesion pathway 0.0867 15 991 63 -0.12 0.047 1000 -1000 -0.037 -1000
Signaling mediated by p38-alpha and p38-beta 0.0867 15 673 44 -0.058 0.031 1000 -1000 -0.007 -1000
Syndecan-2-mediated signaling events 0.0809 14 984 69 -0.033 0.047 1000 -1000 -0.022 -1000
Syndecan-3-mediated signaling events 0.0809 14 508 35 -0.075 0.086 1000 -1000 -0.01 -1000
Nongenotropic Androgen signaling 0.0809 14 762 52 -0.07 0.052 1000 -1000 -0.012 -1000
IL23-mediated signaling events 0.0809 14 862 60 -0.32 0.034 1000 -1000 -0.027 -1000
S1P3 pathway 0.0809 14 589 42 -0.069 0.039 1000 -1000 -0.011 -1000
PDGFR-alpha signaling pathway 0.0751 13 577 44 -0.055 0.048 1000 -1000 -0.025 -1000
Retinoic acid receptors-mediated signaling 0.0751 13 769 58 -0.12 0.06 1000 -1000 -0.01 -1000
TCR signaling in naïve CD8+ T cells 0.0751 13 1236 93 -0.036 0.045 1000 -1000 -0.028 -1000
PDGFR-beta signaling pathway 0.0751 13 1350 97 -0.098 0.062 1000 -1000 -0.029 -1000
IL12-mediated signaling events 0.0694 12 1113 87 -0.2 0.039 1000 -1000 -0.037 -1000
Noncanonical Wnt signaling pathway 0.0694 12 330 26 -0.039 0.031 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 0.0694 12 486 39 -0.086 0.032 1000 -1000 -0.013 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0694 12 1049 85 -0.077 0.039 1000 -1000 -0.025 -1000
IL1-mediated signaling events 0.0694 12 756 62 -0.049 0.048 1000 -1000 -0.018 -1000
Signaling events regulated by Ret tyrosine kinase 0.0694 12 1029 82 -0.075 0.032 1000 -1000 -0.026 -1000
Wnt signaling 0.0694 12 85 7 -0.025 0.031 1000 -1000 0.002 -1000
VEGFR1 specific signals 0.0694 12 683 56 -0.057 0.04 1000 -1000 -0.023 -1000
Arf6 signaling events 0.0636 11 735 62 -0.047 0.041 1000 -1000 -0.019 -1000
HIF-2-alpha transcription factor network 0.0636 11 503 43 -0.11 0.054 1000 -1000 -0.039 -1000
S1P1 pathway 0.0636 11 420 36 -0.091 0.031 1000 -1000 -0.014 -1000
Plasma membrane estrogen receptor signaling 0.0636 11 987 86 -0.092 0.056 1000 -1000 -0.026 -1000
FOXM1 transcription factor network 0.0636 11 566 51 -0.17 0.046 1000 -1000 -0.033 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0636 11 912 78 -0.061 0.033 1000 -1000 -0.029 -1000
Caspase cascade in apoptosis 0.0578 10 794 74 -0.2 0.07 1000 -1000 -0.025 -1000
Signaling events mediated by PTP1B 0.0578 10 792 76 -0.063 0.046 1000 -1000 -0.023 -1000
Glucocorticoid receptor regulatory network 0.0578 10 1149 114 -0.22 0.1 1000 -1000 -0.032 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0578 10 372 37 -0.098 0.072 1000 -1000 -0.014 -1000
EGFR-dependent Endothelin signaling events 0.0578 10 218 21 -0.03 0.045 1000 -1000 -0.025 -1000
LPA4-mediated signaling events 0.0520 9 111 12 -0.034 0.004 1000 -1000 -0.017 -1000
BMP receptor signaling 0.0520 9 771 81 -0.042 0.057 1000 -1000 -0.014 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0520 9 498 52 -0.061 0.07 1000 -1000 -0.018 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0520 9 1166 120 -0.098 0.087 1000 -1000 -0.025 -1000
Regulation of nuclear SMAD2/3 signaling 0.0462 8 1209 136 -0.13 0.1 1000 -1000 -0.03 -1000
Ceramide signaling pathway 0.0462 8 644 76 -0.036 0.044 1000 -1000 -0.016 -1000
Reelin signaling pathway 0.0462 8 502 56 -0.042 0.078 1000 -1000 -0.011 -1000
Canonical Wnt signaling pathway 0.0462 8 432 51 -0.052 0.064 1000 -1000 -0.024 -1000
Effects of Botulinum toxin 0.0462 8 226 26 -0.051 0.032 1000 -1000 0 -1000
Calcium signaling in the CD4+ TCR pathway 0.0462 8 254 31 -0.046 0.032 1000 -1000 -0.028 -1000
S1P4 pathway 0.0462 8 215 25 -0.021 0.048 1000 -1000 -0.007 -1000
Ras signaling in the CD4+ TCR pathway 0.0462 8 138 17 -0.025 0.056 1000 -1000 -0.004 -1000
Coregulation of Androgen receptor activity 0.0405 7 593 76 -0.052 0.055 1000 -1000 -0.014 -1000
Glypican 1 network 0.0405 7 381 48 -0.092 0.06 1000 -1000 -0.021 -1000
S1P5 pathway 0.0405 7 121 17 -0.021 0.032 1000 -1000 -0.005 -1000
Signaling mediated by p38-gamma and p38-delta 0.0405 7 108 15 -0.016 0.03 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 0.0405 7 260 36 -0.098 0.063 1000 -1000 -0.03 -1000
IL6-mediated signaling events 0.0405 7 585 75 -0.16 0.064 1000 -1000 -0.019 -1000
Class I PI3K signaling events 0.0405 7 524 73 -0.078 0.036 1000 -1000 -0.023 -1000
Signaling events mediated by PRL 0.0405 7 264 34 -0.033 0.046 1000 -1000 -0.024 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0347 6 179 28 -0.046 0.045 1000 -1000 -0.007 -1000
Signaling events mediated by the Hedgehog family 0.0347 6 314 52 -0.015 0.045 1000 -1000 -0.011 -1000
Presenilin action in Notch and Wnt signaling 0.0347 6 371 61 -0.026 0.086 1000 -1000 -0.031 -1000
Arf6 downstream pathway 0.0347 6 259 43 -0.032 0.054 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class III 0.0347 6 243 40 -0.059 0.066 1000 -1000 -0.036 -1000
Glypican 2 network 0.0347 6 27 4 0.014 0.024 1000 -1000 0.019 -1000
BCR signaling pathway 0.0347 6 648 99 -0.025 0.067 1000 -1000 -0.041 -1000
Visual signal transduction: Cones 0.0289 5 212 38 -0.009 0.048 1000 -1000 -0.007 -1000
Hedgehog signaling events mediated by Gli proteins 0.0289 5 376 65 -0.04 0.069 1000 -1000 -0.016 -1000
Insulin-mediated glucose transport 0.0289 5 160 32 -0.073 0.057 1000 -1000 -0.009 -1000
ceramide signaling pathway 0.0289 5 274 49 -0.001 0.045 1000 -1000 -0.026 -1000
FAS signaling pathway (CD95) 0.0289 5 265 47 -0.024 0.053 1000 -1000 -0.023 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0289 5 226 45 -0.025 0.09 1000 -1000 -0.037 -1000
Insulin Pathway 0.0289 5 386 74 -0.068 0.074 1000 -1000 -0.023 -1000
Visual signal transduction: Rods 0.0289 5 264 52 -0.02 0.058 1000 -1000 -0.01 -1000
Class IB PI3K non-lipid kinase events 0.0289 5 15 3 -0.02 0.02 1000 -1000 -0.021 -1000
ErbB2/ErbB3 signaling events 0.0231 4 269 65 -0.1 0.065 1000 -1000 -0.049 -1000
Canonical NF-kappaB pathway 0.0231 4 163 39 -0.036 0.067 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class II 0.0231 4 333 75 -0.037 0.064 1000 -1000 -0.019 -1000
PLK2 and PLK4 events 0.0231 4 14 3 0.004 0.027 1000 -1000 -0.005 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0231 4 221 54 -0.042 0.045 1000 -1000 -0.012 -1000
JNK signaling in the CD4+ TCR pathway 0.0231 4 82 17 0.005 0.057 1000 -1000 -0.017 -1000
FOXA2 and FOXA3 transcription factor networks 0.0231 4 192 46 -0.078 0.035 1000 -1000 -0.037 -1000
EPO signaling pathway 0.0231 4 245 55 0 0.07 1000 -1000 -0.014 -1000
PLK1 signaling events 0.0231 4 342 85 -0.016 0.054 1000 -1000 -0.023 -1000
IFN-gamma pathway 0.0231 4 312 68 -0.031 0.08 1000 -1000 -0.025 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0231 4 375 83 -0.026 0.062 1000 -1000 -0.006 -1000
Regulation of p38-alpha and p38-beta 0.0231 4 251 54 -0.05 0.068 1000 -1000 -0.036 -1000
Regulation of Telomerase 0.0231 4 456 102 -0.08 0.074 1000 -1000 -0.014 -1000
Aurora B signaling 0.0231 4 303 67 -0.085 0.073 1000 -1000 -0.03 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0173 3 77 23 -0.016 0.058 1000 -1000 -0.006 -1000
ErbB4 signaling events 0.0173 3 268 69 -0.062 0.074 1000 -1000 -0.014 -1000
mTOR signaling pathway 0.0173 3 181 53 -0.017 0.041 1000 -1000 -0.022 -1000
TRAIL signaling pathway 0.0173 3 147 48 0 0.073 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class I 0.0173 3 371 104 -0.056 0.074 1000 -1000 -0.037 -1000
FoxO family signaling 0.0173 3 214 64 -0.067 0.081 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 0.0173 3 117 31 -0.007 0.045 1000 -1000 -0.006 -1000
IL2 signaling events mediated by PI3K 0.0173 3 190 58 -0.008 0.062 1000 -1000 -0.023 -1000
TCGA08_rtk_signaling 0.0173 3 88 26 -0.035 0.051 1000 -1000 -0.013 -1000
IL2 signaling events mediated by STAT5 0.0173 3 86 22 -0.037 0.034 1000 -1000 -0.015 -1000
Arf6 trafficking events 0.0173 3 270 71 -0.022 0.057 1000 -1000 -0.035 -1000
Arf1 pathway 0.0173 3 178 54 -0.011 0.046 1000 -1000 -0.005 -1000
Regulation of Androgen receptor activity 0.0173 3 244 70 -0.041 0.043 1000 -1000 -0.021 -1000
Class I PI3K signaling events mediated by Akt 0.0116 2 167 68 -0.04 0.052 1000 -1000 -0.018 -1000
IL27-mediated signaling events 0.0116 2 134 51 -0.058 0.072 1000 -1000 -0.041 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0116 2 77 33 -0.047 0.078 1000 -1000 -0.018 -1000
Rapid glucocorticoid signaling 0.0116 2 43 20 -0.006 0.03 1000 -1000 -0.001 -1000
BARD1 signaling events 0.0058 1 58 57 -0.066 0.076 1000 -1000 -0.039 -1000
Circadian rhythm pathway 0.0058 1 31 22 -0.008 0.058 1000 -1000 -0.026 -1000
a4b1 and a4b7 Integrin signaling 0.0058 1 8 5 0.023 0.047 1000 -1000 0.018 -1000
p38 MAPK signaling pathway 0.0058 1 49 44 -0.006 0.061 1000 -1000 -0.009 -1000
Ephrin A reverse signaling 0.0000 0 5 7 -0.012 0.028 1000 -1000 0 -1000
Aurora A signaling 0.0000 0 58 60 0 0.06 1000 -1000 -0.003 -1000
Aurora C signaling 0.0000 0 5 7 0 0.049 1000 -1000 -0.006 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 6 27 0 0.077 1000 -1000 -0.019 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 0 0.083 1000 -1000 0 -1000
Total NA 1226 77914 7203 -8.6 7.2 131000 -131000 -2.6 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.023 0.31 0.52 4 -0.49 35 39
HDAC7 0.03 0.014 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.028 0.28 0.48 1 -0.47 20 21
SMAD4 0.026 0.02 -10000 0 -10000 0 0
ID2 -0.024 0.32 0.49 5 -0.51 35 40
AP1 0.014 0.092 -10000 0 -0.26 15 15
ABCG2 -0.053 0.32 0.59 1 -0.54 37 38
HIF1A 0.011 0.082 -10000 0 -0.14 10 10
TFF3 -0.045 0.29 0.47 2 -0.48 36 38
GATA2 -0.008 0.11 -10000 0 -0.34 16 16
AKT1 0.013 0.081 -10000 0 -0.13 6 6
response to hypoxia -0.005 0.063 0.13 1 -0.11 16 17
MCL1 -0.024 0.3 0.53 1 -0.48 36 37
NDRG1 -0.039 0.29 0.47 2 -0.48 34 36
SERPINE1 -0.052 0.3 0.51 2 -0.51 35 37
FECH -0.022 0.3 0.48 4 -0.48 36 40
FURIN -0.021 0.31 0.52 4 -0.49 35 39
NCOA2 0.027 0.03 -10000 0 -0.34 1 1
EP300 0.018 0.082 0.2 2 -0.18 2 4
HMOX1 -0.057 0.3 -10000 0 -0.5 40 40
BHLHE40 -0.024 0.31 0.52 4 -0.49 35 39
BHLHE41 -0.022 0.32 0.52 4 -0.5 36 40
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.033 0.16 -10000 0 -0.24 20 20
ENG -0.021 0.15 0.28 4 -0.38 15 19
JUN 0.005 0.088 -10000 0 -0.34 10 10
RORA -0.023 0.31 0.52 4 -0.49 36 40
ABCB1 -0.13 0.34 -10000 0 -0.85 28 28
TFRC -0.025 0.3 0.51 3 -0.48 36 39
CXCR4 -0.019 0.31 0.52 4 -0.49 36 40
TF -0.051 0.31 0.56 2 -0.52 37 39
CITED2 -0.017 0.31 0.49 5 -0.48 36 41
HIF1A/ARNT 0.005 0.37 -10000 0 -0.59 25 25
LDHA 0.022 0.074 -10000 0 -0.55 1 1
ETS1 -0.025 0.3 0.48 3 -0.49 34 37
PGK1 -0.03 0.3 0.52 2 -0.49 34 36
NOS2 -0.039 0.3 0.54 3 -0.49 35 38
ITGB2 -0.041 0.3 0.51 3 -0.49 36 39
ALDOA -0.023 0.31 0.51 4 -0.48 36 40
Cbp/p300/CITED2 -0.017 0.31 0.49 2 -0.53 27 29
FOS 0.013 0.075 -10000 0 -0.34 7 7
HK2 -0.014 0.31 0.49 5 -0.48 36 41
SP1 0.012 0.055 -10000 0 -0.11 24 24
GCK 0.014 0.12 -10000 0 -0.32 1 1
HK1 -0.023 0.3 0.49 3 -0.49 36 39
NPM1 -0.023 0.3 0.49 5 -0.49 35 40
EGLN1 -0.031 0.31 0.46 2 -0.5 37 39
CREB1 0.038 0.003 -10000 0 -10000 0 0
PGM1 -0.032 0.3 0.46 2 -0.5 36 38
SMAD3 0.024 0.034 -10000 0 -0.34 1 1
EDN1 -0.038 0.25 0.45 2 -0.93 9 11
IGFBP1 -0.046 0.29 0.46 2 -0.49 34 36
VEGFA -0.011 0.25 0.46 3 -0.43 25 28
HIF1A/JAB1 0.022 0.064 -10000 0 -0.12 1 1
CP -0.044 0.3 0.51 3 -0.48 39 42
CXCL12 -0.088 0.33 0.53 1 -0.52 46 47
COPS5 0.029 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.037 -10000 0 -0.23 1 1
BNIP3 -0.021 0.3 0.47 4 -0.48 35 39
EGLN3 -0.04 0.31 0.42 1 -0.5 36 37
CA9 -0.027 0.3 0.51 4 -0.49 35 39
TERT -0.036 0.32 0.49 5 -0.49 38 43
ENO1 -0.026 0.3 0.52 1 -0.48 36 37
PFKL -0.034 0.3 0.51 3 -0.48 36 39
NCOA1 0.032 0.004 -10000 0 -10000 0 0
ADM -0.053 0.32 0.48 3 -0.54 38 41
ARNT 0.009 0.081 -10000 0 -0.13 15 15
HNF4A 0.02 0.008 -10000 0 -10000 0 0
ADFP -0.041 0.29 0.41 4 -0.48 36 40
SLC2A1 -0.001 0.24 0.45 2 -0.42 20 22
LEP -0.047 0.29 0.5 2 -0.49 34 36
HIF1A/ARNT/Cbp/p300 0.016 0.29 0.48 1 -0.48 21 22
EPO -0.005 0.19 -10000 0 -0.42 5 5
CREBBP 0.021 0.082 0.2 3 -0.14 2 5
HIF1A/ARNT/Cbp/p300/HDAC7 0.025 0.29 0.48 1 -0.47 20 21
PFKFB3 -0.019 0.3 0.47 4 -0.48 36 40
NT5E -0.026 0.32 0.52 4 -0.5 37 41
TCGA08_retinoblastoma

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
CDKN2B 0 0.088 -10000 0 -0.3 12 12
CDKN2C 0.027 0.048 -10000 0 -0.3 3 3
CDKN2A -0.041 0.14 -10000 0 -0.32 34 34
CCND2 0.015 0.074 0.16 27 -0.1 10 37
RB1 -0.024 0.091 0.31 1 -0.19 31 32
CDK4 0.027 0.086 0.19 30 -10000 0 30
CDK6 0.023 0.084 0.19 28 -0.13 2 30
G1/S progression 0.027 0.092 0.19 31 -0.3 1 32
Thromboxane A2 receptor signaling

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
TGM2 -0.014 0.12 -10000 0 -0.34 19 19
GNB1/GNG2 -0.069 0.076 -10000 0 -0.17 53 53
AKT1 -0.048 0.11 0.24 3 -0.2 44 47
EGF -0.026 0.12 -10000 0 -0.34 23 23
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.042 0.12 0.28 6 -0.25 22 28
mol:Ca2+ -0.083 0.16 0.22 1 -0.29 55 56
LYN -0.023 0.099 0.28 5 -0.25 9 14
RhoA/GTP -0.034 0.065 -10000 0 -0.13 48 48
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.093 0.17 0.36 1 -0.31 53 54
GNG2 0.003 0.099 -10000 0 -0.34 13 13
ARRB2 0.029 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.03 0.12 0.23 2 -0.33 15 17
G beta5/gamma2 -0.085 0.11 -10000 0 -0.23 52 52
PRKCH -0.098 0.18 -10000 0 -0.33 56 56
DNM1 -0.007 0.11 -10000 0 -0.34 17 17
TXA2/TP beta/beta Arrestin3 -0.026 0.11 -10000 0 -0.5 6 6
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.02 0.057 -10000 0 -0.34 4 4
G12 family/GTP -0.085 0.14 -10000 0 -0.28 54 54
ADRBK1 0.031 0.007 -10000 0 -10000 0 0
ADRBK2 0.025 0.041 -10000 0 -0.34 2 2
RhoA/GTP/ROCK1 0.041 0.01 -10000 0 -10000 0 0
mol:GDP 0.063 0.12 0.28 22 -10000 0 22
mol:NADP 0.006 0.083 -10000 0 -0.34 9 9
RAB11A 0.031 0.006 -10000 0 -10000 0 0
PRKG1 0.012 0.019 -10000 0 -10000 0 0
mol:IP3 -0.11 0.19 -10000 0 -0.36 55 55
cell morphogenesis 0.04 0.01 -10000 0 -10000 0 0
PLCB2 -0.15 0.25 -10000 0 -0.48 55 55
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.034 0.096 0.28 2 -0.26 10 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.026 0.13 0.42 5 -0.27 14 19
RHOA 0.031 0.007 -10000 0 -10000 0 0
PTGIR -0.018 0.12 -10000 0 -0.34 20 20
PRKCB1 -0.1 0.19 -10000 0 -0.34 57 57
GNAQ 0.031 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.006 0.083 -10000 0 -0.34 9 9
TXA2/TXA2-R family -0.15 0.24 -10000 0 -0.47 54 54
LCK -0.026 0.11 0.29 5 -0.25 10 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.024 0.1 -10000 0 -0.18 42 42
TXA2-R family/G12 family/GDP/G beta/gamma -0.03 0.13 -10000 0 -0.41 15 15
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.021 0.1 -10000 0 -0.18 42 42
MAPK14 -0.061 0.12 0.24 2 -0.21 51 53
TGM2/GTP -0.13 0.22 -10000 0 -0.42 55 55
MAPK11 -0.057 0.12 0.23 4 -0.21 48 52
ARHGEF1 -0.045 0.092 0.18 3 -0.17 51 54
GNAI2 0.031 0.007 -10000 0 -10000 0 0
JNK cascade -0.1 0.18 -10000 0 -0.35 55 55
RAB11/GDP 0.032 0.006 -10000 0 -10000 0 0
ICAM1 -0.077 0.14 0.2 1 -0.27 53 54
cAMP biosynthetic process -0.1 0.18 -10000 0 -0.34 56 56
Gq family/GTP/EBP50 -0.005 0.074 0.25 1 -0.18 22 23
actin cytoskeleton reorganization 0.04 0.01 -10000 0 -10000 0 0
SRC -0.031 0.14 0.39 6 -0.27 17 23
GNB5 0.022 0.057 -10000 0 -0.34 4 4
GNB1 0.03 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.043 0.15 0.31 10 -0.24 35 45
VCAM1 -0.089 0.17 -10000 0 -0.32 52 52
TP beta/Gq family/GDP/G beta5/gamma2 -0.03 0.12 0.23 2 -0.33 15 17
platelet activation -0.08 0.15 0.28 3 -0.28 54 57
PGI2/IP -0.011 0.082 -10000 0 -0.23 20 20
PRKACA -0.01 0.071 -10000 0 -0.18 24 24
Gq family/GDP/G beta5/gamma2 -0.023 0.1 0.17 1 -0.28 15 16
TXA2/TP beta/beta Arrestin2 -0.042 0.14 -10000 0 -0.43 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.044 0.099 -10000 0 -0.2 44 44
mol:DAG -0.12 0.21 -10000 0 -0.38 57 57
EGFR 0.021 0.011 -10000 0 -10000 0 0
TXA2/TP alpha -0.14 0.24 -10000 0 -0.46 55 55
Gq family/GTP -0.016 0.071 -10000 0 -0.17 27 27
YES1 -0.025 0.13 0.37 6 -0.28 14 20
GNAI2/GTP -0.029 0.095 -10000 0 -0.18 43 43
PGD2/DP 0.015 0.039 -10000 0 -0.23 4 4
SLC9A3R1 0.03 0.008 -10000 0 -10000 0 0
FYN -0.017 0.13 0.35 8 -0.25 10 18
mol:NO 0.006 0.083 -10000 0 -0.34 9 9
GNA15 0.027 0.03 -10000 0 -0.34 1 1
PGK/cGMP 0.017 0.054 -10000 0 -0.2 9 9
RhoA/GDP 0.031 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.039 0.13 -10000 0 -0.25 32 32
NOS3 0.006 0.083 -10000 0 -0.34 9 9
RAC1 0.028 0.011 -10000 0 -10000 0 0
PRKCA -0.11 0.18 0.3 1 -0.33 56 57
PRKCB -0.096 0.17 -10000 0 -0.32 55 55
PRKCE -0.098 0.18 -10000 0 -0.33 53 53
PRKCD -0.1 0.18 0.26 1 -0.34 55 56
PRKCG -0.1 0.19 0.26 1 -0.35 55 56
muscle contraction -0.14 0.23 -10000 0 -0.44 54 54
PRKCZ -0.1 0.17 0.28 2 -0.33 54 56
ARR3 0.024 0.01 -10000 0 -10000 0 0
TXA2/TP beta -0.023 0.11 -10000 0 -0.19 43 43
PRKCQ -0.098 0.18 0.23 1 -0.33 55 56
MAPKKK cascade -0.13 0.22 -10000 0 -0.42 55 55
SELE -0.073 0.14 -10000 0 -0.26 52 52
TP beta/GNAI2/GDP/G beta/gamma -0.022 0.12 -10000 0 -0.21 40 40
ROCK1 0.031 0.006 -10000 0 -10000 0 0
GNA14 0.008 0.083 -10000 0 -0.34 9 9
chemotaxis -0.16 0.27 -10000 0 -0.53 51 51
GNA12 0.028 0.011 -10000 0 -10000 0 0
GNA13 0.03 0.008 -10000 0 -10000 0 0
GNA11 0.005 0.092 -10000 0 -0.34 11 11
Rac1/GTP 0.02 0.008 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.15 0.38 0.42 1 -0.78 42 43
NCK1/PAK1/Dok-R -0.1 0.17 -10000 0 -0.39 42 42
NCK1/Dok-R -0.18 0.42 -10000 0 -0.88 42 42
PIK3CA 0.032 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.035 0.088 0.22 29 -10000 0 29
RELA 0.031 0.007 -10000 0 -10000 0 0
SHC1 0.031 0.005 -10000 0 -10000 0 0
Rac/GDP 0.021 0.008 -10000 0 -10000 0 0
F2 0.055 0.097 0.26 29 -10000 0 29
TNIP2 0.031 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.15 0.41 -10000 0 -0.84 42 42
FN1 0.021 0.05 -10000 0 -0.34 3 3
PLD2 -0.22 0.42 -10000 0 -0.93 42 42
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GRB14 0.02 0.007 -10000 0 -10000 0 0
ELK1 -0.2 0.39 -10000 0 -0.86 42 42
GRB7 0.018 0.008 -10000 0 -10000 0 0
PAK1 0.029 0.029 -10000 0 -0.34 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.15 0.43 -10000 0 -0.86 42 42
CDKN1A -0.11 0.3 -10000 0 -0.56 47 47
ITGA5 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.18 0.42 -10000 0 -0.88 42 42
CRK 0.029 0.01 -10000 0 -10000 0 0
mol:NO -0.11 0.3 0.37 2 -0.59 42 44
PLG -0.21 0.42 -10000 0 -0.91 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.36 -10000 0 -0.75 42 42
GRB2 0.03 0.008 -10000 0 -10000 0 0
PIK3R1 0.03 0.007 -10000 0 -10000 0 0
ANGPT2 -0.067 0.2 -10000 0 -0.51 11 11
BMX -0.21 0.42 -10000 0 -0.91 42 42
ANGPT1 -0.18 0.41 -10000 0 -1.1 29 29
tube development -0.12 0.29 -10000 0 -0.58 42 42
ANGPT4 0.018 0.018 -10000 0 -10000 0 0
response to hypoxia -0.015 0.029 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.2 0.44 -10000 0 -0.93 42 42
alpha5/beta1 Integrin 0.047 0.007 -10000 0 -10000 0 0
FGF2 0.021 0.057 -10000 0 -0.34 4 4
STAT5A (dimer) -0.13 0.34 -10000 0 -0.64 47 47
mol:L-citrulline -0.11 0.3 0.37 2 -0.59 42 44
AGTR1 0.005 0.087 -10000 0 -0.34 10 10
MAPK14 -0.19 0.44 -10000 0 -0.92 42 42
Tie2/SHP2 -0.081 0.31 -10000 0 -0.95 17 17
TEK -0.11 0.33 -10000 0 -1 17 17
RPS6KB1 -0.14 0.37 -10000 0 -0.75 42 42
Angiotensin II/AT1 0.006 0.061 -10000 0 -0.21 11 11
Tie2/Ang1/GRB2 -0.19 0.44 -10000 0 -0.93 42 42
MAPK3 -0.21 0.39 -10000 0 -0.87 42 42
MAPK1 -0.21 0.4 -10000 0 -0.87 42 42
Tie2/Ang1/GRB7 -0.2 0.44 -10000 0 -0.93 42 42
NFKB1 0.031 0.006 -10000 0 -10000 0 0
MAPK8 -0.2 0.42 -10000 0 -0.91 42 42
PI3K -0.18 0.42 -10000 0 -0.87 42 42
FES -0.2 0.44 -10000 0 -0.91 43 43
Crk/Dok-R -0.18 0.42 -10000 0 -0.88 42 42
Tie2/Ang1/ABIN2 -0.19 0.45 -10000 0 -0.93 42 42
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.13 0.34 0.41 1 -0.7 42 43
STAT5A 0.03 0.009 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.15 0.38 0.4 4 -0.77 42 46
Tie2/Ang2 -0.17 0.38 -10000 0 -0.76 42 42
Tie2/Ang1 -0.22 0.45 -10000 0 -0.97 42 42
FOXO1 -0.14 0.35 0.48 1 -0.71 42 43
ELF1 0.012 0.05 -10000 0 -0.12 17 17
ELF2 -0.2 0.42 -10000 0 -0.91 42 42
mol:Choline -0.22 0.41 -10000 0 -0.89 42 42
cell migration -0.051 0.1 -10000 0 -0.22 42 42
FYN -0.14 0.33 -10000 0 -0.66 42 42
DOK2 0.019 0.057 -10000 0 -0.34 4 4
negative regulation of cell cycle -0.097 0.27 -10000 0 -0.51 47 47
ETS1 -0.014 0.1 -10000 0 -0.23 28 28
PXN -0.12 0.33 0.37 6 -0.64 42 48
ITGB1 0.032 0.004 -10000 0 -10000 0 0
NOS3 -0.13 0.33 0.38 2 -0.67 42 44
RAC1 0.028 0.011 -10000 0 -10000 0 0
TNF -0.041 0.14 -10000 0 -0.27 39 39
MAPKKK cascade -0.22 0.41 -10000 0 -0.89 42 42
RASA1 0.03 0.008 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.19 0.45 -10000 0 -0.93 42 42
NCK1 0.031 0.006 -10000 0 -10000 0 0
vasculogenesis -0.094 0.27 0.35 3 -0.53 42 45
mol:Phosphatidic acid -0.22 0.41 -10000 0 -0.89 42 42
mol:Angiotensin II 0.001 0.003 -10000 0 -10000 0 0
mol:NADP -0.11 0.3 0.37 2 -0.59 42 44
Rac1/GTP -0.13 0.34 -10000 0 -0.7 42 42
MMP2 -0.22 0.43 -10000 0 -0.93 42 42
Osteopontin-mediated events

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
IKK alpha homodimer -0.046 0.12 0.19 1 -0.19 55 56
NF kappa B1 p50/RelA/I kappa B alpha -0.036 0.13 0.32 2 -0.29 18 20
alphaV/beta3 Integrin/Osteopontin/Src -0.022 0.12 -10000 0 -0.25 35 35
AP1 -0.068 0.18 0.34 1 -0.34 33 34
ILK -0.057 0.12 0.19 1 -0.22 38 39
bone resorption -0.041 0.13 0.19 6 -0.3 14 20
PTK2B 0.029 0.01 -10000 0 -10000 0 0
PYK2/p130Cas -0.039 0.13 -10000 0 -0.19 57 57
ITGAV -0.004 0.11 -10000 0 -0.34 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.04 0.039 -10000 0 -0.24 3 3
alphaV/beta3 Integrin/Osteopontin -0.049 0.14 -10000 0 -0.22 59 59
MAP3K1 -0.061 0.12 0.18 2 -0.21 54 56
JUN 0.006 0.088 -10000 0 -0.34 10 10
MAPK3 -0.065 0.11 0.19 1 -0.27 22 23
MAPK1 -0.066 0.11 -10000 0 -0.27 22 22
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
NFKB1 0.031 0.006 -10000 0 -10000 0 0
MAPK8 -0.061 0.12 0.23 4 -0.22 37 41
ITGB3 -0.048 0.14 -10000 0 -0.33 32 32
NFKBIA -0.061 0.12 0.32 2 -0.3 18 20
FOS 0.015 0.075 -10000 0 -0.34 7 7
CD44 0.031 0.007 -10000 0 -10000 0 0
CHUK 0.032 0.005 -10000 0 -10000 0 0
PLAU -0.089 0.25 0.63 1 -0.85 12 13
NF kappa B1 p50/RelA -0.037 0.14 -10000 0 -0.33 17 17
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
RELA 0.031 0.007 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.037 0.13 -10000 0 -0.24 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.057 0.12 0.18 3 -0.2 58 61
VAV3 -0.058 0.12 0.23 5 -0.21 37 42
MAP3K14 -0.059 0.12 0.19 1 -0.2 56 57
ROCK2 0.025 0.049 -10000 0 -0.34 3 3
SPP1 -0.03 0.13 -10000 0 -0.34 24 24
RAC1 0.028 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.047 0.11 0.24 3 -0.2 36 39
MMP2 -0.096 0.18 0.32 1 -0.39 34 35
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.018 0.069 -10000 0 -0.34 6 6
LAT2 -0.064 0.13 0.21 1 -0.26 44 45
AP1 -0.048 0.17 0.28 2 -0.37 22 24
mol:PIP3 -0.069 0.17 0.36 7 -0.28 47 54
IKBKB -0.024 0.13 0.32 11 -0.2 17 28
AKT1 -0.045 0.13 0.36 9 -0.25 14 23
IKBKG -0.031 0.12 0.28 12 -0.2 18 30
MS4A2 -0.044 0.15 -10000 0 -0.34 33 33
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
MAP3K1 -0.042 0.15 0.34 8 -0.32 16 24
mol:Ca2+ -0.05 0.14 0.3 9 -0.22 45 54
LYN 0.027 0.014 -10000 0 -10000 0 0
CBLB -0.064 0.13 -10000 0 -0.24 46 46
SHC1 0.032 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.054 0.031 -10000 0 -0.18 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.032 0.003 -10000 0 -10000 0 0
PLD2 -0.081 0.13 0.26 4 -0.25 42 46
PTPN13 -0.19 0.3 -10000 0 -0.66 41 41
PTPN11 0.026 0.021 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.087 0.19 0.37 11 -0.32 45 56
SYK 0.03 0.012 -10000 0 -10000 0 0
GRB2 0.03 0.008 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.077 0.15 -10000 0 -0.28 47 47
LAT -0.066 0.13 -10000 0 -0.25 46 46
PAK2 -0.049 0.16 0.33 7 -0.33 19 26
NFATC2 -0.031 0.098 -10000 0 -0.44 7 7
HRAS -0.055 0.16 0.28 5 -0.26 46 51
GAB2 0.031 0.007 -10000 0 -10000 0 0
PLA2G1B 0.016 0.15 -10000 0 -0.9 4 4
Fc epsilon R1 -0.051 0.14 -10000 0 -0.22 62 62
Antigen/IgE/Fc epsilon R1 -0.042 0.13 -10000 0 -0.2 62 62
mol:GDP -0.06 0.16 0.27 3 -0.37 19 22
JUN 0.008 0.088 -10000 0 -0.34 10 10
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
FOS 0.016 0.074 -10000 0 -0.34 7 7
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.06 0.14 -10000 0 -0.25 46 46
CHUK -0.035 0.12 0.32 8 -0.2 19 27
KLRG1 -0.048 0.11 -10000 0 -0.19 51 51
VAV1 -0.063 0.12 -10000 0 -0.25 44 44
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.06 0.12 -10000 0 -0.24 44 44
negative regulation of mast cell degranulation -0.031 0.12 0.2 5 -0.28 16 21
BTK -0.071 0.16 0.22 1 -0.39 20 21
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.073 0.15 -10000 0 -0.3 35 35
GAB2/PI3K/SHP2 -0.068 0.087 -10000 0 -0.21 29 29
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.045 0.12 -10000 0 -0.2 52 52
RAF1 0.014 0.15 -10000 0 -0.93 4 4
Fc epsilon R1/FcgammaRIIB/SHIP -0.033 0.15 -10000 0 -0.2 66 66
FCER1G -0.014 0.12 -10000 0 -0.33 22 22
FCER1A -0.024 0.13 -10000 0 -0.35 22 22
Antigen/IgE/Fc epsilon R1/Fyn -0.033 0.13 -10000 0 -0.18 65 65
MAPK3 0.015 0.15 -10000 0 -0.9 4 4
MAPK1 0.014 0.15 -10000 0 -0.9 4 4
NFKB1 0.031 0.006 -10000 0 -10000 0 0
MAPK8 -0.022 0.17 -10000 0 -0.57 11 11
DUSP1 0.027 0.041 -10000 0 -0.34 2 2
NF-kappa-B/RelA -0.015 0.069 0.14 7 -0.14 15 22
actin cytoskeleton reorganization -0.19 0.31 -10000 0 -0.66 43 43
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.036 0.15 0.31 3 -0.25 43 46
FER -0.07 0.13 -10000 0 -0.25 47 47
RELA 0.031 0.007 -10000 0 -10000 0 0
ITK -0.022 0.071 -10000 0 -0.26 9 9
SOS1 0.032 0.003 -10000 0 -10000 0 0
PLCG1 -0.063 0.17 0.31 6 -0.35 21 27
cytokine secretion -0.017 0.044 -10000 0 -0.1 10 10
SPHK1 -0.064 0.13 -10000 0 -0.25 44 44
PTK2 -0.2 0.33 -10000 0 -0.71 42 42
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.078 0.15 -10000 0 -0.29 46 46
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.068 0.17 0.36 8 -0.27 46 54
MAP2K2 0.012 0.14 -10000 0 -0.86 4 4
MAP2K1 0.007 0.14 -10000 0 -0.87 4 4
MAP2K7 0.029 0.009 -10000 0 -10000 0 0
KLRG1/SHP2 -0.03 0.1 0.21 1 -0.23 22 23
MAP2K4 -0.057 0.28 -10000 0 -0.84 18 18
Fc epsilon R1/FcgammaRIIB -0.045 0.15 -10000 0 -0.22 66 66
mol:Choline -0.08 0.13 0.26 4 -0.25 42 46
SHC/Grb2/SOS1 -0.026 0.15 0.22 1 -0.23 44 45
FYN 0.026 0.049 -10000 0 -0.34 3 3
DOK1 0.032 0.003 -10000 0 -10000 0 0
PXN -0.18 0.3 0.37 1 -0.67 40 41
HCLS1 -0.064 0.13 -10000 0 -0.24 46 46
PRKCB -0.052 0.14 0.33 7 -0.26 21 28
FCGR2B 0.004 0.091 -10000 0 -0.34 11 11
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.031 0.12 0.2 5 -0.28 16 21
LCP2 0.031 0.007 -10000 0 -10000 0 0
PLA2G4A -0.076 0.13 -10000 0 -0.26 48 48
RASA1 0.03 0.008 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.08 0.13 0.26 4 -0.25 42 46
IKK complex -0.007 0.14 0.34 14 -0.16 12 26
WIPF1 0.032 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.055 0.14 -10000 0 -0.26 43 43
PTK2B 0.029 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.044 0.17 -10000 0 -0.51 7 7
EDN1 -0.045 0.13 -10000 0 -0.21 52 52
EDN3 0.019 0.009 -10000 0 -10000 0 0
EDN2 0.02 0.007 -10000 0 -10000 0 0
HRAS/GDP -0.078 0.17 0.3 3 -0.36 24 27
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.058 0.13 -10000 0 -0.31 25 25
ADCY4 -0.049 0.12 -10000 0 -0.22 42 42
ADCY5 -0.051 0.11 -10000 0 -0.22 40 40
ADCY6 -0.063 0.13 -10000 0 -0.23 50 50
ADCY7 -0.05 0.12 -10000 0 -0.22 43 43
ADCY1 -0.051 0.11 -10000 0 -0.22 38 38
ADCY2 -0.065 0.12 -10000 0 -0.24 44 44
ADCY3 -0.049 0.12 -10000 0 -0.22 44 44
ADCY8 -0.045 0.11 -10000 0 -0.23 36 36
ADCY9 -0.067 0.14 -10000 0 -0.24 49 49
arachidonic acid secretion -0.069 0.19 0.4 5 -0.41 24 29
ETB receptor/Endothelin-1/Gq/GTP -0.056 0.12 -10000 0 -0.25 37 37
GNAO1 0.026 0.041 -10000 0 -0.34 2 2
HRAS 0.03 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.031 0.14 -10000 0 -0.23 46 46
ETA receptor/Endothelin-1/Gs/GTP -0.028 0.14 -10000 0 -0.22 46 46
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.1 0.21 -10000 0 -0.41 43 43
EDNRB -0.024 0.11 -10000 0 -0.26 24 24
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.072 0.17 -10000 0 -0.32 44 44
CYSLTR1 -0.059 0.14 -10000 0 -0.28 41 41
SLC9A1 -0.032 0.087 -10000 0 -0.2 21 21
mol:GDP -0.087 0.18 0.31 5 -0.36 28 33
SLC9A3 -0.12 0.26 -10000 0 -0.57 32 32
RAF1 -0.069 0.18 0.32 5 -0.39 22 27
JUN -0.08 0.26 -10000 0 -0.84 14 14
JAK2 -0.06 0.14 -10000 0 -0.26 47 47
mol:IP3 -0.065 0.14 -10000 0 -0.34 24 24
ETA receptor/Endothelin-1 -0.06 0.17 -10000 0 -0.3 51 51
PLCB1 0.021 0.063 -10000 0 -0.34 5 5
PLCB2 0.013 0.079 -10000 0 -0.34 8 8
ETA receptor/Endothelin-3 -0.01 0.073 -10000 0 -0.14 25 25
FOS -0.065 0.22 0.42 5 -0.74 10 15
Gai/GDP -0.033 0.18 -10000 0 -0.74 8 8
CRK 0.029 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.099 0.18 -10000 0 -0.38 37 37
BCAR1 0.003 0.087 -10000 0 -0.34 10 10
PRKCB1 -0.063 0.14 -10000 0 -0.33 24 24
GNAQ 0.029 0.016 -10000 0 -10000 0 0
GNAZ 0.013 0.069 -10000 0 -0.34 6 6
GNAL 0.029 0.029 -10000 0 -0.34 1 1
Gs family/GDP -0.077 0.16 0.27 4 -0.34 27 31
ETA receptor/Endothelin-1/Gq/GTP -0.053 0.14 -10000 0 -0.29 27 27
MAPK14 -0.06 0.12 -10000 0 -0.26 28 28
TRPC6 -0.046 0.17 -10000 0 -0.55 6 6
GNAI2 0.031 0.007 -10000 0 -10000 0 0
GNAI3 0.032 0.004 -10000 0 -10000 0 0
GNAI1 -0.021 0.12 -10000 0 -0.34 21 21
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.059 0.12 -10000 0 -0.27 29 29
ETB receptor/Endothelin-2 -0.005 0.084 -10000 0 -0.23 16 16
ETB receptor/Endothelin-3 -0.006 0.083 -10000 0 -0.25 14 14
ETB receptor/Endothelin-1 -0.05 0.14 -10000 0 -0.24 46 46
MAPK3 -0.071 0.22 0.42 5 -0.66 12 17
MAPK1 -0.073 0.22 0.42 5 -0.68 12 17
Rac1/GDP -0.076 0.16 0.3 3 -0.35 26 29
cAMP biosynthetic process -0.082 0.14 -10000 0 -0.3 35 35
MAPK8 -0.06 0.19 -10000 0 -0.5 17 17
SRC -0.007 0.11 -10000 0 -0.34 17 17
ETB receptor/Endothelin-1/Gi/GTP -0.052 0.11 -10000 0 -0.23 30 30
p130Cas/CRK/Src/PYK2 -0.084 0.19 0.35 5 -0.41 24 29
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.076 0.16 0.3 3 -0.35 26 29
COL1A2 -0.13 0.26 -10000 0 -0.6 34 34
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.008 0.072 -10000 0 -0.13 36 36
mol:DAG -0.065 0.14 -10000 0 -0.34 24 24
MAP2K2 -0.066 0.2 0.44 5 -0.53 14 19
MAP2K1 -0.071 0.19 0.5 2 -0.55 13 15
EDNRA -0.03 0.096 -10000 0 -0.18 41 41
positive regulation of muscle contraction -0.04 0.13 0.22 5 -0.23 39 44
Gq family/GDP -0.066 0.17 -10000 0 -0.38 23 23
HRAS/GTP -0.07 0.16 0.29 5 -0.37 22 27
PRKCH -0.071 0.15 -10000 0 -0.33 28 28
RAC1 0.028 0.011 -10000 0 -10000 0 0
PRKCA -0.083 0.15 -10000 0 -0.32 32 32
PRKCB -0.066 0.14 -10000 0 -0.33 23 23
PRKCE -0.067 0.14 -10000 0 -0.33 25 25
PRKCD -0.067 0.14 -10000 0 -0.34 23 23
PRKCG -0.064 0.14 -10000 0 -0.34 22 22
regulation of vascular smooth muscle contraction -0.079 0.25 0.45 5 -0.88 10 15
PRKCQ -0.069 0.15 0.22 1 -0.34 26 27
PLA2G4A -0.076 0.21 0.4 5 -0.44 24 29
GNA14 0.005 0.084 -10000 0 -0.34 9 9
GNA15 0.025 0.032 -10000 0 -0.34 1 1
GNA12 0.028 0.011 -10000 0 -10000 0 0
GNA11 0.003 0.092 -10000 0 -0.34 11 11
Rac1/GTP -0.031 0.14 -10000 0 -0.24 43 43
MMP1 0.032 0.1 0.44 4 -10000 0 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.004 0.1 -10000 0 -0.24 26 26
alphaV beta3 Integrin -0.02 0.13 -10000 0 -0.22 45 45
PTK2 -0.12 0.23 0.29 9 -0.42 46 55
IGF1R -0.001 0.1 -10000 0 -0.34 14 14
PI4KB 0.032 0.004 -10000 0 -10000 0 0
MFGE8 0.021 0.057 -10000 0 -0.34 4 4
SRC -0.007 0.11 -10000 0 -0.34 17 17
CDKN1B -0.014 0.097 -10000 0 -0.47 5 5
VEGFA 0.009 0.083 -10000 0 -0.34 9 9
ILK -0.014 0.097 -10000 0 -0.47 5 5
ROCK1 0.031 0.006 -10000 0 -10000 0 0
AKT1 -0.018 0.089 -10000 0 -0.44 5 5
PTK2B -0.056 0.11 0.24 3 -0.2 47 50
alphaV/beta3 Integrin/JAM-A -0.016 0.13 -10000 0 -0.2 48 48
CBL 0.03 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.024 0.13 -10000 0 -0.22 48 48
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.027 0.11 -10000 0 -0.2 30 30
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.051 0.12 -10000 0 -0.35 14 14
alphaV/beta3 Integrin/Syndecan-1 -0.041 0.14 -10000 0 -0.23 54 54
PI4KA 0.029 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.044 0.14 -10000 0 -0.2 64 64
PI4 Kinase 0.043 0.014 -10000 0 -10000 0 0
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.049 0.14 -10000 0 -0.22 59 59
RPS6KB1 -0.075 0.11 0.18 1 -0.32 15 16
TLN1 0.029 0.029 -10000 0 -0.34 1 1
MAPK3 -0.1 0.19 -10000 0 -0.39 44 44
GPR124 -0.019 0.12 -10000 0 -0.34 21 21
MAPK1 -0.099 0.19 -10000 0 -0.4 43 43
PXN 0.027 0.04 -10000 0 -0.34 2 2
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.021 0.13 -10000 0 -0.22 45 45
cell adhesion -0.035 0.13 -10000 0 -0.22 51 51
ANGPTL3 0.014 0.074 -10000 0 -0.34 7 7
VEGFR2 homodimer/VEGFA homodimer/Src -0.009 0.11 -10000 0 -0.2 41 41
IGF-1R heterotetramer -0.001 0.1 -10000 0 -0.34 14 14
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
TGFBR2 0.031 0.007 -10000 0 -10000 0 0
ITGB3 -0.047 0.14 -10000 0 -0.34 32 32
IGF1 0 0.099 -10000 0 -0.34 13 13
RAC1 0.028 0.011 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.04 0.14 -10000 0 -0.24 51 51
apoptosis -0.001 0.11 -10000 0 -0.34 15 15
CD47 0.031 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.014 0.12 -10000 0 -0.21 43 43
VCL 0.027 0.041 -10000 0 -0.34 2 2
alphaV/beta3 Integrin/Del1 -0.023 0.12 -10000 0 -0.21 45 45
CSF1 0.012 0.079 -10000 0 -0.34 8 8
PIK3C2A -0.015 0.097 -10000 0 -0.47 5 5
PI4 Kinase/Pyk2 -0.04 0.12 -10000 0 -0.2 46 46
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.035 0.14 -10000 0 -0.21 60 60
FAK1/Vinculin -0.092 0.19 0.26 8 -0.34 44 52
alphaV beta3/Integrin/ppsTEM5 -0.04 0.14 -10000 0 -0.24 51 51
RHOA 0.031 0.007 -10000 0 -10000 0 0
VTN 0.021 0.057 -10000 0 -0.34 4 4
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
FGF2 0.021 0.057 -10000 0 -0.34 4 4
F11R 0.003 0.05 -10000 0 -0.24 7 7
alphaV/beta3 Integrin/Lactadherin -0.021 0.12 -10000 0 -0.21 47 47
alphaV/beta3 Integrin/TGFBR2 -0.014 0.12 -10000 0 -0.21 43 43
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.023 0.1 -10000 0 -0.18 32 32
HSP90AA1 0.032 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.011 0.11 -10000 0 -0.19 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.05 -10000 0 -0.34 3 3
alphaV/beta3 Integrin/Pyk2 -0.036 0.12 -10000 0 -0.2 54 54
SDC1 -0.013 0.12 -10000 0 -0.34 19 19
VAV3 -0.033 0.079 0.19 7 -0.17 28 35
PTPN11 0.032 0.004 -10000 0 -10000 0 0
IRS1 0.018 0.069 -10000 0 -0.34 6 6
FAK1/Paxillin -0.089 0.19 0.28 9 -0.36 40 49
cell migration -0.087 0.17 0.25 8 -0.33 40 48
ITGAV -0.001 0.11 -10000 0 -0.34 15 15
PI3K -0.005 0.13 -10000 0 -0.19 47 47
SPP1 -0.028 0.13 -10000 0 -0.34 24 24
KDR -0.016 0.11 -10000 0 -0.34 18 18
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 -0.001 0.11 -10000 0 -0.34 15 15
COL4A3 0.018 0.069 -10000 0 -0.34 6 6
angiogenesis -0.1 0.2 -10000 0 -0.42 43 43
Rac1/GTP -0.004 0.077 0.18 3 -0.16 25 28
EDIL3 0.016 0.049 -10000 0 -0.34 3 3
cell proliferation -0.014 0.12 -10000 0 -0.21 43 43
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.035 0.13 -10000 0 -0.25 43 43
AKT1 -0.082 0.19 0.58 1 -0.41 33 34
PTK2B -0.092 0.17 0.35 1 -0.4 31 32
VEGFR2 homodimer/Frs2 -0.047 0.18 -10000 0 -0.37 33 33
CAV1 -0.012 0.11 -10000 0 -0.34 16 16
CALM1 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.043 0.18 -10000 0 -0.4 28 28
endothelial cell proliferation -0.11 0.2 0.36 2 -0.4 41 43
mol:Ca2+ -0.076 0.17 -10000 0 -0.39 33 33
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.027 0.18 -10000 0 -0.43 23 23
RP11-342D11.1 -0.079 0.16 0.18 2 -0.39 30 32
CDH5 -0.035 0.14 -10000 0 -0.34 28 28
VEGFA homodimer 0.061 0.063 -10000 0 -0.18 9 9
SHC1 0.032 0.004 -10000 0 -10000 0 0
SHC2 0.025 0.011 -10000 0 -10000 0 0
HRAS/GDP -0.041 0.16 -10000 0 -0.35 30 30
SH2D2A 0.013 0.079 -10000 0 -0.34 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.1 0.23 -10000 0 -0.43 43 43
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.051 0.18 -10000 0 -0.33 42 42
VEGFR1 homodimer 0.013 0.074 -10000 0 -0.34 7 7
SHC/GRB2/SOS1 -0.026 0.19 -10000 0 -0.38 30 30
GRB10 -0.074 0.19 -10000 0 -0.45 29 29
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GRB2 0.03 0.008 -10000 0 -10000 0 0
PAK1 0.029 0.029 -10000 0 -0.34 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.048 0.21 -10000 0 -0.44 29 29
HRAS 0.03 0.008 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.076 0.16 -10000 0 -0.34 34 34
HIF1A 0.032 0.005 -10000 0 -10000 0 0
FRS2 0.032 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.028 0.18 -10000 0 -0.42 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.004 0.098 -10000 0 -0.34 13 13
Nck/Pak 0.043 0.025 -10000 0 -0.24 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.046 0.18 -10000 0 -0.4 29 29
mol:GDP -0.035 0.18 -10000 0 -0.37 30 30
mol:NADP -0.11 0.2 -10000 0 -0.4 42 42
eNOS/Hsp90 -0.092 0.2 -10000 0 -0.38 41 41
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
mol:IP3 -0.077 0.17 -10000 0 -0.39 33 33
HIF1A/ARNT 0.046 0.009 -10000 0 -10000 0 0
SHB 0.025 0.049 -10000 0 -0.34 3 3
VEGFA 0.005 0.087 -10000 0 -0.3 11 11
VEGFC 0.011 0.074 -10000 0 -0.34 7 7
FAK1/Vinculin -0.13 0.25 0.3 1 -0.52 39 40
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.031 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.084 0.2 -10000 0 -0.41 34 34
PTPN6 0.032 0.005 -10000 0 -10000 0 0
EPAS1 -0.049 0.16 -10000 0 -0.35 34 34
mol:L-citrulline -0.11 0.2 -10000 0 -0.4 42 42
ITGAV -0.001 0.11 -10000 0 -0.34 15 15
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.026 0.18 -10000 0 -0.42 23 23
VEGFR2 homodimer/VEGFA homodimer -0.056 0.2 -10000 0 -0.43 30 30
VEGFR2/3 heterodimer -0.066 0.18 -10000 0 -0.35 40 40
VEGFB 0.029 0.029 -10000 0 -0.34 1 1
MAPK11 -0.084 0.18 -10000 0 -0.43 29 29
VEGFR2 homodimer -0.075 0.19 -10000 0 -0.43 33 33
FLT1 0.013 0.074 -10000 0 -0.34 7 7
NEDD4 0.01 0.086 -10000 0 -0.33 9 9
MAPK3 -0.094 0.16 0.26 1 -0.37 33 34
MAPK1 -0.09 0.16 0.32 1 -0.37 33 34
VEGFA145/NRP2 -0.01 0.11 -10000 0 -0.24 29 29
VEGFR1/2 heterodimer -0.057 0.18 -10000 0 -0.39 34 34
KDR -0.076 0.2 -10000 0 -0.43 33 33
VEGFA165/NRP1/VEGFR2 homodimer -0.071 0.19 -10000 0 -0.4 34 34
SRC -0.007 0.11 -10000 0 -0.34 17 17
platelet activating factor biosynthetic process -0.091 0.16 0.28 1 -0.38 33 34
PI3K -0.084 0.2 -10000 0 -0.44 35 35
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.042 0.18 -10000 0 -0.41 27 27
FES -0.072 0.18 -10000 0 -0.4 30 30
GAB1 -0.075 0.2 -10000 0 -0.47 30 30
VEGFR2 homodimer/VEGFA homodimer/Src -0.063 0.19 -10000 0 -0.39 33 33
CTNNB1 0.031 0.007 -10000 0 -10000 0 0
SOS1 0.032 0.003 -10000 0 -10000 0 0
ARNT 0.032 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.1 0.19 -10000 0 -0.38 42 42
VEGFR2 homodimer/VEGFA homodimer/Yes -0.055 0.19 -10000 0 -0.4 31 31
PI3K/GAB1 -0.08 0.2 -10000 0 -0.42 36 36
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.013 0.18 -10000 0 -0.41 23 23
PRKACA 0.029 0.009 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.058 0.18 -10000 0 -0.32 42 42
HSP90AA1 0.032 0.005 -10000 0 -10000 0 0
CDC42 -0.069 0.17 -10000 0 -0.4 30 30
actin cytoskeleton reorganization -0.051 0.18 -10000 0 -0.33 42 42
PTK2 -0.15 0.25 0.3 1 -0.53 41 42
EDG1 -0.079 0.16 0.18 2 -0.39 30 32
mol:DAG -0.077 0.17 -10000 0 -0.39 33 33
CaM/Ca2+ -0.058 0.17 -10000 0 -0.36 33 33
MAP2K3 -0.085 0.16 -10000 0 -0.39 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.054 0.21 -10000 0 -0.45 30 30
PLCG1 -0.078 0.18 -10000 0 -0.4 33 33
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.049 0.19 -10000 0 -0.41 29 29
IQGAP1 0.029 0.029 -10000 0 -0.34 1 1
YES1 0.004 0.096 -10000 0 -0.34 12 12
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.043 0.18 -10000 0 -0.38 30 30
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.043 0.18 -10000 0 -0.45 23 23
cell migration -0.12 0.22 0.28 1 -0.48 38 39
mol:PI-3-4-5-P3 -0.078 0.19 -10000 0 -0.41 35 35
FYN 0.026 0.049 -10000 0 -0.34 3 3
VEGFB/NRP1 -0.061 0.17 -10000 0 -0.38 30 30
mol:NO -0.11 0.2 -10000 0 -0.4 42 42
PXN 0.027 0.04 -10000 0 -0.34 2 2
HRAS/GTP -0.056 0.15 -10000 0 -0.35 30 30
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.069 0.2 -10000 0 -0.45 30 30
VHL 0.031 0.006 -10000 0 -10000 0 0
ITGB3 -0.047 0.14 -10000 0 -0.34 32 32
NOS3 -0.12 0.22 -10000 0 -0.45 42 42
VEGFR2 homodimer/VEGFA homodimer/Sck -0.044 0.18 -10000 0 -0.34 36 36
RAC1 0.028 0.011 -10000 0 -10000 0 0
PRKCA -0.11 0.16 -10000 0 -0.37 38 38
PRKCB -0.087 0.16 0.19 2 -0.38 32 34
VCL 0.027 0.041 -10000 0 -0.34 2 2
VEGFA165/NRP1 -0.066 0.17 -10000 0 -0.39 30 30
VEGFR1/2 heterodimer/VEGFA homodimer -0.05 0.18 -10000 0 -0.43 27 27
VEGFA165/NRP2 -0.01 0.11 -10000 0 -0.24 29 29
MAPKKK cascade -0.058 0.17 0.37 1 -0.4 29 30
NRP2 -0.019 0.12 -10000 0 -0.34 21 21
VEGFC homodimer 0.011 0.074 -10000 0 -0.34 7 7
NCK1 0.031 0.006 -10000 0 -10000 0 0
ROCK1 0.031 0.006 -10000 0 -10000 0 0
FAK1/Paxillin -0.13 0.25 0.3 1 -0.5 41 42
MAP3K13 -0.07 0.18 0.2 1 -0.4 30 31
PDPK1 -0.079 0.17 -10000 0 -0.38 34 34
TCGA08_p53

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
CDKN2A -0.042 0.096 -10000 0 -0.23 34 34
TP53 -0.009 0.04 -10000 0 -0.097 27 27
Senescence -0.009 0.04 -10000 0 -0.097 27 27
Apoptosis -0.009 0.04 -10000 0 -0.097 27 27
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.026 0.071 0.17 33 -10000 0 33
MDM4 0.032 0.005 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.027 0.091 -10000 0 -0.26 15 15
adherens junction organization -0.06 0.14 -10000 0 -0.27 42 42
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.021 0.094 -10000 0 -0.24 14 14
FMN1 -0.063 0.14 -10000 0 -0.26 45 45
mol:IP3 -0.027 0.093 -10000 0 -0.22 22 22
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.056 0.14 -10000 0 -0.26 42 42
CTNNB1 0.033 0.008 -10000 0 -10000 0 0
AKT1 -0.031 0.1 -10000 0 -0.25 17 17
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.097 0.19 -10000 0 -0.37 46 46
CTNND1 0.024 0.05 -10000 0 -0.34 3 3
mol:PI-4-5-P2 -0.056 0.13 -10000 0 -0.25 42 42
VASP -0.049 0.12 -10000 0 -0.24 38 38
ZYX -0.054 0.13 -10000 0 -0.25 39 39
JUB -0.055 0.13 -10000 0 -0.25 42 42
EGFR(dimer) -0.05 0.14 -10000 0 -0.26 41 41
E-cadherin/beta catenin-gamma catenin -0.003 0.11 -10000 0 -0.21 35 35
mol:PI-3-4-5-P3 -0.018 0.12 -10000 0 -0.25 19 19
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
PI3K -0.018 0.12 -10000 0 -0.26 19 19
FYN -0.028 0.093 -10000 0 -0.26 15 15
mol:Ca2+ -0.027 0.091 -10000 0 -0.21 22 22
JUP -0.007 0.11 -10000 0 -0.34 17 17
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
mol:DAG -0.027 0.093 -10000 0 -0.22 22 22
CDH1 -0.032 0.13 -10000 0 -0.34 26 26
RhoA/GDP -0.019 0.099 0.18 3 -0.24 14 17
establishment of polarity of embryonic epithelium -0.048 0.12 -10000 0 -0.24 38 38
SRC -0.007 0.11 -10000 0 -0.34 17 17
RAC1 0.028 0.011 -10000 0 -10000 0 0
RHOA 0.031 0.007 -10000 0 -10000 0 0
EGFR 0.021 0.011 -10000 0 -10000 0 0
CASR -0.03 0.083 -10000 0 -0.24 13 13
RhoA/GTP -0.016 0.092 -10000 0 -0.23 14 14
AKT2 -0.027 0.095 -10000 0 -0.28 11 11
actin cable formation -0.058 0.13 -10000 0 -0.26 40 40
apoptosis 0.029 0.096 0.28 13 -10000 0 13
CTNNA1 0.02 0.058 -10000 0 -0.34 4 4
mol:GDP -0.034 0.09 -10000 0 -0.23 19 19
PIP5K1A -0.057 0.13 -10000 0 -0.26 42 42
PLCG1 -0.028 0.094 -10000 0 -0.22 22 22
Rac1/GTP -0.037 0.14 -10000 0 -0.24 40 40
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 0.01 -10000 0 -10000 0 0
CCL5 0.018 0.063 -10000 0 -0.34 5 5
SDCBP 0.024 0.041 -10000 0 -0.34 2 2
FGFR/FGF2/Syndecan-1 -0.063 0.13 0.21 4 -0.24 40 44
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.06 0.14 0.23 5 -0.31 21 26
Syndecan-1/Syntenin -0.056 0.14 0.2 5 -0.24 36 41
MAPK3 -0.06 0.12 0.19 3 -0.35 13 16
HGF/MET -0.001 0.093 -10000 0 -0.24 22 22
TGFB1/TGF beta receptor Type II 0.029 0.01 -10000 0 -10000 0 0
BSG 0.029 0.01 -10000 0 -10000 0 0
keratinocyte migration -0.059 0.14 0.23 5 -0.31 21 26
Syndecan-1/RANTES -0.061 0.14 0.21 6 -0.25 40 46
Syndecan-1/CD147 -0.05 0.14 0.22 4 -0.36 13 17
Syndecan-1/Syntenin/PIP2 -0.055 0.13 0.19 4 -0.26 26 30
LAMA5 0.02 0.057 -10000 0 -0.34 4 4
positive regulation of cell-cell adhesion -0.055 0.13 0.19 4 -0.24 33 37
MMP7 0.005 0.083 -10000 0 -0.34 9 9
HGF -0.024 0.12 -10000 0 -0.34 22 22
Syndecan-1/CASK -0.075 0.12 -10000 0 -0.23 40 40
Syndecan-1/HGF/MET -0.071 0.14 0.21 4 -0.34 22 26
regulation of cell adhesion -0.056 0.13 0.26 6 -0.34 13 19
HPSE -0.034 0.14 -10000 0 -0.34 29 29
positive regulation of cell migration -0.063 0.13 0.21 4 -0.24 40 44
SDC1 -0.07 0.12 -10000 0 -0.21 59 59
Syndecan-1/Collagen -0.063 0.13 0.21 4 -0.24 40 44
PPIB 0.031 0.006 -10000 0 -10000 0 0
MET 0.025 0.012 -10000 0 -10000 0 0
PRKACA 0.029 0.009 -10000 0 -10000 0 0
MMP9 -0.034 0.13 -10000 0 -0.34 26 26
MAPK1 -0.057 0.12 0.19 4 -0.35 13 17
homophilic cell adhesion -0.067 0.14 0.21 5 -0.24 40 45
MMP1 0.018 0.007 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.006 0.087 -10000 0 -0.34 10 10
EPHB2 -0.036 0.13 -10000 0 -0.34 25 25
EFNB1 -0.023 0.091 -10000 0 -0.25 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.12 -10000 0 -0.18 47 47
Ephrin B2/EPHB1-2 -0.002 0.095 -10000 0 -0.18 35 35
neuron projection morphogenesis -0.024 0.1 -10000 0 -0.18 47 47
Ephrin B1/EPHB1-2/Tiam1 -0.019 0.12 0.18 1 -0.19 49 50
DNM1 -0.007 0.11 -10000 0 -0.34 17 17
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.035 0.13 -10000 0 -0.53 11 11
YES1 -0.045 0.2 -10000 0 -0.73 12 12
Ephrin B1/EPHB1-2/NCK2 -0.003 0.11 0.18 4 -0.18 44 48
PI3K 0.005 0.15 -10000 0 -0.5 13 13
mol:GDP -0.019 0.12 0.18 2 -0.19 49 51
ITGA2B -0.008 0.11 -10000 0 -0.34 16 16
endothelial cell proliferation 0.011 0.071 -10000 0 -0.19 18 18
FYN -0.037 0.19 -10000 0 -0.73 12 12
MAP3K7 -0.038 0.14 -10000 0 -0.54 12 12
FGR -0.065 0.19 -10000 0 -0.69 13 13
TIAM1 0.003 0.091 -10000 0 -0.34 11 11
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
RGS3 0.025 0.049 -10000 0 -0.34 3 3
cell adhesion -0.057 0.16 -10000 0 -0.44 18 18
LYN -0.04 0.2 -10000 0 -0.7 13 13
Ephrin B1/EPHB1-2/Src Family Kinases -0.044 0.18 -10000 0 -0.66 13 13
Ephrin B1/EPHB1-2 -0.035 0.15 -10000 0 -0.59 11 11
SRC -0.055 0.2 -10000 0 -0.7 13 13
ITGB3 -0.047 0.14 -10000 0 -0.34 32 32
EPHB1 0.022 0.032 -10000 0 -0.33 1 1
EPHB4 0.01 0.079 -10000 0 -0.34 8 8
RAC1 0.028 0.011 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.011 0.071 -10000 0 -0.19 18 18
alphaIIb/beta3 Integrin -0.039 0.14 -10000 0 -0.26 42 42
BLK -0.045 0.19 -10000 0 -0.7 13 13
HCK -0.047 0.2 -10000 0 -0.7 13 13
regulation of stress fiber formation 0.005 0.11 0.18 44 -0.18 4 48
MAPK8 -0.033 0.13 0.26 1 -0.49 12 13
Ephrin B1/EPHB1-2/RGS3 -0.009 0.11 -10000 0 -0.18 46 46
endothelial cell migration -0.036 0.14 0.2 5 -0.49 11 16
NCK2 0.032 0 -10000 0 -10000 0 0
PTPN13 -0.003 0.12 -10000 0 -0.45 11 11
regulation of focal adhesion formation 0.005 0.11 0.18 44 -0.18 4 48
chemotaxis 0.01 0.11 0.18 46 -10000 0 46
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.017 0.11 -10000 0 -0.18 47 47
angiogenesis -0.035 0.15 -10000 0 -0.59 11 11
LCK -0.041 0.19 -10000 0 -0.7 13 13
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.014 0.12 -10000 0 -0.19 48 48
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.1 0.32 1 -0.28 9 10
AP1 -0.02 0.11 -10000 0 -0.19 44 44
mol:PIP3 -0.02 0.074 -10000 0 -0.17 28 28
AKT1 -0.017 0.11 0.35 3 -0.26 11 14
PTK2B -0.022 0.1 0.29 2 -0.23 17 19
RHOA -0.008 0.094 0.25 2 -0.48 4 6
PIK3CB 0.031 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.1 0.26 6 -0.28 8 14
MAGI3 0.029 0.029 -10000 0 -0.34 1 1
RELA 0.031 0.007 -10000 0 -10000 0 0
apoptosis -0.023 0.094 -10000 0 -0.2 36 36
HRAS/GDP 0.022 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.018 0.099 0.26 6 -0.23 13 19
NF kappa B1 p50/RelA -0.043 0.12 -10000 0 -0.28 21 21
endothelial cell migration -0.067 0.17 -10000 0 -0.36 37 37
ADCY4 -0.06 0.13 -10000 0 -0.28 34 34
ADCY5 -0.059 0.12 -10000 0 -0.28 34 34
ADCY6 -0.077 0.15 -10000 0 -0.31 36 36
ADCY7 -0.062 0.13 -10000 0 -0.29 34 34
ADCY1 -0.059 0.13 -10000 0 -0.29 33 33
ADCY2 -0.069 0.13 -10000 0 -0.29 36 36
ADCY3 -0.063 0.13 -10000 0 -0.28 36 36
ADCY8 -0.055 0.12 -10000 0 -0.28 30 30
ADCY9 -0.075 0.14 -10000 0 -0.3 37 37
GSK3B -0.022 0.099 0.36 2 -0.24 15 17
arachidonic acid secretion -0.058 0.12 -10000 0 -0.25 37 37
GNG2 0.002 0.099 -10000 0 -0.34 13 13
TRIP6 -0.025 0.1 -10000 0 -0.29 22 22
GNAO1 -0.03 0.1 -10000 0 -0.21 38 38
HRAS 0.03 0.008 -10000 0 -10000 0 0
NFKBIA -0.032 0.12 0.48 2 -0.29 12 14
GAB1 0.027 0.041 -10000 0 -0.34 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.037 0.25 -10000 0 -0.8 16 16
JUN 0.008 0.088 -10000 0 -0.34 10 10
LPA/LPA2/NHERF2 -0.001 0.083 -10000 0 -0.18 23 23
TIAM1 -0.054 0.28 -10000 0 -0.92 16 16
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
mol:IP3 -0.026 0.084 0.19 3 -0.32 6 9
PLCB3 -0.013 0.075 0.15 3 -0.19 19 22
FOS 0.016 0.074 -10000 0 -0.34 7 7
positive regulation of mitosis -0.058 0.12 -10000 0 -0.25 37 37
LPA/LPA1-2-3 0.002 0.1 -10000 0 -0.19 35 35
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
stress fiber formation -0.045 0.13 0.34 2 -0.32 13 15
GNAZ -0.031 0.1 -10000 0 -0.22 35 35
EGFR/PI3K-beta/Gab1 -0.009 0.082 -10000 0 -0.17 30 30
positive regulation of dendritic cell cytokine production 0.001 0.1 -10000 0 -0.19 35 35
LPA/LPA2/MAGI-3 0.025 0.045 -10000 0 -0.1 6 6
ARHGEF1 -0.009 0.091 0.19 5 -0.18 30 35
GNAI2 -0.025 0.1 -10000 0 -0.21 35 35
GNAI3 -0.027 0.1 -10000 0 -0.21 37 37
GNAI1 -0.047 0.11 -10000 0 -0.21 48 48
LPA/LPA3 0.003 0.04 -10000 0 -0.093 21 21
LPA/LPA2 0.009 0.04 -10000 0 -0.096 18 18
LPA/LPA1 -0.036 0.12 -10000 0 -0.24 38 38
HB-EGF/EGFR -0.029 0.11 -10000 0 -0.23 34 34
HBEGF -0.046 0.12 -10000 0 -0.27 34 34
mol:DAG -0.026 0.084 0.19 3 -0.32 6 9
cAMP biosynthetic process -0.062 0.14 0.28 3 -0.28 37 40
NFKB1 0.031 0.006 -10000 0 -10000 0 0
SRC -0.007 0.11 -10000 0 -0.34 17 17
GNB1 0.03 0.009 -10000 0 -10000 0 0
LYN -0.022 0.12 0.46 3 -0.29 10 13
GNAQ 0.007 0.033 -10000 0 -0.11 2 2
LPAR2 0.029 0.01 -10000 0 -10000 0 0
LPAR3 0.023 0.012 -10000 0 -10000 0 0
LPAR1 -0.029 0.12 -10000 0 -0.24 37 37
IL8 -0.096 0.18 0.66 1 -0.42 30 31
PTK2 -0.049 0.096 -10000 0 -0.18 49 49
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
CASP3 -0.023 0.094 -10000 0 -0.2 36 36
EGFR 0.02 0.013 -10000 0 -10000 0 0
PLCG1 -0.006 0.049 -10000 0 -0.17 5 5
PLD2 -0.037 0.11 0.28 2 -0.19 45 47
G12/G13 0.004 0.1 -10000 0 -0.19 33 33
PI3K-beta -0.03 0.1 -10000 0 -0.28 13 13
cell migration -0.05 0.094 -10000 0 -0.26 16 16
SLC9A3R2 -0.014 0.12 -10000 0 -0.34 20 20
PXN -0.046 0.13 0.34 2 -0.33 13 15
HRAS/GTP -0.06 0.12 -10000 0 -0.25 37 37
RAC1 0.028 0.011 -10000 0 -10000 0 0
MMP9 -0.034 0.13 -10000 0 -0.34 26 26
PRKCE 0.025 0.05 -10000 0 -0.34 3 3
PRKCD -0.026 0.11 0.25 7 -0.3 8 15
Gi(beta/gamma) -0.062 0.13 -10000 0 -0.26 38 38
mol:LPA -0.02 0.051 -10000 0 -0.13 26 26
TRIP6/p130 Cas/FAK1/Paxillin -0.097 0.16 -10000 0 -0.32 43 43
MAPKKK cascade -0.058 0.12 -10000 0 -0.25 37 37
contractile ring contraction involved in cytokinesis -0.011 0.1 0.24 2 -0.43 6 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.005 0.056 -10000 0 -0.18 11 11
GNA15 0.007 0.038 -10000 0 -0.18 2 2
GNA12 0.028 0.011 -10000 0 -10000 0 0
GNA13 0.03 0.008 -10000 0 -10000 0 0
MAPT -0.019 0.1 0.26 6 -0.24 13 19
GNA11 -0.005 0.062 -10000 0 -0.19 13 13
Rac1/GTP -0.04 0.27 -10000 0 -0.84 16 16
MMP2 -0.068 0.17 -10000 0 -0.36 37 37
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.015 0.086 -10000 0 -0.19 31 31
epithelial cell differentiation 0.014 0.093 -10000 0 -0.17 31 31
CYFIP2 0.026 0.041 -10000 0 -0.34 2 2
ENAH -0.044 0.091 0.22 4 -0.25 12 16
EGFR 0.021 0.011 -10000 0 -10000 0 0
EPHA2 -0.006 0.1 -10000 0 -0.34 14 14
MYO6 -0.03 0.088 0.2 6 -0.18 32 38
CTNNB1 0.031 0.007 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.035 0.078 -10000 0 -0.21 14 14
AQP5 -0.021 0.078 -10000 0 -0.33 3 3
CTNND1 0.024 0.05 -10000 0 -0.34 3 3
mol:PI-4-5-P2 -0.025 0.073 0.2 5 -0.16 26 31
regulation of calcium-dependent cell-cell adhesion -0.039 0.097 0.2 4 -0.22 30 34
EGF -0.026 0.12 -10000 0 -0.34 23 23
NCKAP1 -0.001 0.099 -10000 0 -0.34 13 13
AQP3 -0.018 0.088 -10000 0 -0.43 3 3
cortical microtubule organization 0.014 0.093 -10000 0 -0.17 31 31
GO:0000145 -0.026 0.068 0.19 5 -0.15 27 32
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.018 0.096 -10000 0 -0.17 31 31
MLLT4 0.008 0.083 -10000 0 -0.34 9 9
ARF6/GDP -0.055 0.079 -10000 0 -0.18 40 40
ARF6 0.032 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.041 0.087 -10000 0 -0.19 18 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.022 0.072 0.18 2 -0.27 5 7
PVRL2 0.007 0.088 -10000 0 -0.34 10 10
ZYX -0.026 0.073 0.2 4 -0.17 27 31
ARF6/GTP 0.049 0.087 -10000 0 -0.18 18 18
CDH1 -0.033 0.13 -10000 0 -0.34 26 26
EGFR/EGFR/EGF/EGF -0.022 0.1 -10000 0 -0.18 48 48
RhoA/GDP 0.016 0.092 -10000 0 -0.17 31 31
actin cytoskeleton organization -0.033 0.087 0.19 6 -0.18 29 35
IGF-1R heterotetramer -0.001 0.1 -10000 0 -0.34 14 14
GIT1 0.03 0.008 -10000 0 -10000 0 0
IGF1R -0.001 0.1 -10000 0 -0.34 14 14
IGF1 0 0.099 -10000 0 -0.34 13 13
DIAPH1 -0.014 0.2 -10000 0 -0.57 18 18
Wnt receptor signaling pathway -0.014 0.093 0.17 31 -10000 0 31
RHOA 0.031 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.055 0.079 -10000 0 -0.18 40 40
CTNNA1 0.021 0.057 -10000 0 -0.34 4 4
VCL -0.035 0.087 0.19 5 -0.19 29 34
EFNA1 0.014 0.069 -10000 0 -0.34 6 6
LPP -0.03 0.078 0.2 6 -0.16 31 37
Ephrin A1/EPHA2 -0.013 0.11 -10000 0 -0.19 43 43
SEC6/SEC8 -0.051 0.077 -10000 0 -0.18 34 34
MGAT3 -0.039 0.099 0.2 4 -0.22 30 34
HGF/MET -0.019 0.1 -10000 0 -0.17 47 47
HGF -0.024 0.12 -10000 0 -0.34 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.015 0.087 -10000 0 -0.19 31 31
actin cable formation -0.031 0.11 0.39 4 -0.24 15 19
KIAA1543 -0.034 0.07 0.19 2 -0.17 29 31
KIFC3 -0.034 0.086 0.2 4 -0.19 31 35
NCK1 0.031 0.006 -10000 0 -10000 0 0
EXOC3 0.031 0.007 -10000 0 -10000 0 0
ACTN1 -0.025 0.084 0.21 7 -0.17 31 38
NCK1/GIT1 0.044 0.013 -10000 0 -10000 0 0
mol:GDP 0.014 0.093 -10000 0 -0.17 31 31
EXOC4 0.028 0.012 -10000 0 -10000 0 0
STX4 -0.028 0.078 0.19 5 -0.17 31 36
PIP5K1C -0.025 0.074 0.21 5 -0.16 26 31
LIMA1 0.03 0.029 -10000 0 -0.34 1 1
ABI1 0.032 0.004 -10000 0 -10000 0 0
ROCK1 -0.029 0.11 0.29 8 -0.27 7 15
adherens junction assembly -0.037 0.13 0.31 3 -0.4 10 13
IGF-1R heterotetramer/IGF1 -0.019 0.11 -10000 0 -0.18 49 49
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.011 0.086 -10000 0 -0.23 18 18
MET 0.025 0.012 -10000 0 -10000 0 0
PLEKHA7 -0.033 0.075 0.2 2 -0.17 29 31
mol:GTP 0.039 0.086 -10000 0 -0.19 18 18
establishment of epithelial cell apical/basal polarity -0.026 0.12 0.32 8 -0.28 7 15
cortical actin cytoskeleton stabilization -0.015 0.086 -10000 0 -0.19 31 31
regulation of cell-cell adhesion -0.033 0.087 0.19 6 -0.18 29 35
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.015 0.087 -10000 0 -0.19 31 31
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.006 0.12 -9999 0 -0.23 35 35
E-cadherin/beta catenin -0.001 0.099 -9999 0 -0.24 25 25
CTNNB1 0.031 0.007 -9999 0 -10000 0 0
JUP -0.008 0.11 -9999 0 -0.34 17 17
CDH1 -0.033 0.13 -9999 0 -0.34 26 26
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.021 0.1 0.25 29 -10000 0 29
KIRREL -0.052 0.14 -10000 0 -0.34 30 30
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.021 0.1 -10000 0 -0.25 29 29
PLCG1 0.019 0.063 -10000 0 -0.34 5 5
ARRB2 0.029 0.01 -10000 0 -10000 0 0
WASL 0.028 0.012 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.009 0.093 -10000 0 -0.19 29 29
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.018 0.081 -10000 0 -0.19 29 29
FYN -0.024 0.086 0.24 6 -0.17 29 35
mol:Ca2+ 0 0.097 -10000 0 -0.19 33 33
mol:DAG 0 0.098 -10000 0 -0.19 33 33
NPHS2 -0.001 0.028 -10000 0 -10000 0 0
mol:IP3 0 0.098 -10000 0 -0.19 33 33
regulation of endocytosis 0.004 0.084 -10000 0 -0.16 32 32
Nephrin/NEPH1/podocin/Cholesterol -0.005 0.081 -10000 0 -0.18 29 29
establishment of cell polarity -0.021 0.1 -10000 0 -0.25 29 29
Nephrin/NEPH1/podocin/NCK1-2 0.025 0.091 -10000 0 -0.17 29 29
Nephrin/NEPH1/beta Arrestin2 0.005 0.085 -10000 0 -0.16 32 32
NPHS1 0 0.029 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin -0.004 0.084 0.18 1 -0.17 32 33
TJP1 -0.002 0.094 -10000 0 -0.34 12 12
NCK1 0.031 0.006 -10000 0 -10000 0 0
NCK2 0.032 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.002 0.099 -10000 0 -0.19 33 33
CD2AP 0.03 0.029 -10000 0 -0.34 1 1
Nephrin/NEPH1/podocin/GRB2 0.009 0.09 -10000 0 -0.18 29 29
GRB2 0.03 0.008 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.032 0.066 0.16 3 -0.16 29 32
cytoskeleton organization -0.03 0.084 0.2 2 -0.2 29 31
Nephrin/NEPH1 -0.01 0.072 -10000 0 -0.16 29 29
Nephrin/NEPH1/ZO-1 -0.02 0.1 -10000 0 -0.2 40 40
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.29 0.49 -10000 0 -1.1 30 30
STAT6 (cleaved dimer) -0.3 0.5 -10000 0 -1 40 40
IGHG1 -0.1 0.23 -10000 0 -0.42 30 30
IGHG3 -0.28 0.47 -10000 0 -0.91 46 46
AKT1 -0.12 0.27 -10000 0 -0.64 18 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.097 0.25 -10000 0 -0.75 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.13 0.26 -10000 0 -0.58 24 24
THY1 -0.34 0.58 -10000 0 -1.3 34 34
MYB 0.03 0.029 -10000 0 -0.34 1 1
HMGA1 0.032 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.16 0.31 -10000 0 -0.64 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.26 -10000 0 -0.59 20 20
SP1 0.009 0.058 -10000 0 -0.12 21 21
INPP5D 0.032 0.003 -10000 0 -10000 0 0
SOCS5 0.025 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.28 0.5 -10000 0 -1.1 32 32
SOCS1 -0.18 0.33 -10000 0 -0.74 28 28
SOCS3 -0.15 0.3 -10000 0 -0.85 13 13
FCER2 -0.31 0.54 -10000 0 -1.1 40 40
PARP14 0.03 0.014 -10000 0 -10000 0 0
CCL17 -0.29 0.49 -10000 0 -1.1 30 30
GRB2 0.03 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.092 0.2 -10000 0 -0.49 12 12
T cell proliferation -0.28 0.5 -10000 0 -1.2 30 30
IL4R/JAK1 -0.29 0.5 -10000 0 -1.1 32 32
EGR2 -0.38 0.59 -10000 0 -1.2 45 45
JAK2 0 0.058 -10000 0 -10000 0 0
JAK3 0.03 0.017 -10000 0 -10000 0 0
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
JAK1 0.016 0.031 -10000 0 -10000 0 0
COL1A2 -0.3 0.54 -10000 0 -1.3 35 35
CCL26 -0.29 0.49 -10000 0 -1.1 30 30
IL4R -0.31 0.53 -10000 0 -1.2 31 31
PTPN6 0.034 0.02 -10000 0 -10000 0 0
IL13RA2 -0.29 0.49 -10000 0 -1.1 29 29
IL13RA1 -0.029 0.1 -10000 0 -0.34 11 11
IRF4 -0.1 0.32 -10000 0 -0.9 16 16
ARG1 -0.093 0.28 -10000 0 -1.1 9 9
CBL -0.14 0.29 -10000 0 -0.62 28 28
GTF3A 0.007 0.061 -10000 0 -0.11 34 34
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.012 0.092 -10000 0 -0.22 9 9
IRF4/BCL6 -0.098 0.31 -10000 0 -0.86 16 16
CD40LG 0.009 0.083 -10000 0 -0.26 12 12
MAPK14 -0.15 0.3 -10000 0 -0.64 28 28
mitosis -0.11 0.26 -10000 0 -0.6 18 18
STAT6 -0.34 0.58 -10000 0 -1.1 44 44
SPI1 0.029 0.036 -10000 0 -0.14 7 7
RPS6KB1 -0.11 0.25 -10000 0 -0.61 15 15
STAT6 (dimer) -0.34 0.58 -10000 0 -1.1 44 44
STAT6 (dimer)/PARP14 -0.32 0.55 -10000 0 -1 46 46
mast cell activation 0.005 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.12 0.28 -10000 0 -0.71 16 16
FRAP1 -0.12 0.27 -10000 0 -0.65 17 17
LTA -0.31 0.52 -10000 0 -1.2 32 32
FES 0.031 0.006 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.32 0.56 1.1 45 -10000 0 45
CCL11 -0.28 0.46 -10000 0 -1.1 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.12 0.28 -10000 0 -0.69 16 16
IL2RG 0.023 0.051 -10000 0 -0.33 3 3
IL10 -0.31 0.53 -10000 0 -1.2 34 34
IRS1 0.018 0.069 -10000 0 -0.34 6 6
IRS2 0.028 0.029 -10000 0 -0.34 1 1
IL4 -0.073 0.16 -10000 0 -0.56 5 5
IL5 -0.29 0.48 -10000 0 -1.1 30 30
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.23 0.39 -10000 0 -0.85 31 31
COL1A1 -0.3 0.56 -10000 0 -1.3 38 38
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.3 0.51 -10000 0 -1.2 31 31
IL2R gamma/JAK3 0.037 0.045 -10000 0 -0.23 3 3
TFF3 -0.28 0.5 -10000 0 -1.1 29 29
ALOX15 -0.29 0.49 -10000 0 -1.1 30 30
MYBL1 0.028 0.012 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.22 0.39 -10000 0 -0.85 31 31
SHC1 0.032 0.004 -10000 0 -10000 0 0
CEBPB 0.019 0.066 -10000 0 -0.21 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.26 -10000 0 -0.6 20 20
mol:PI-3-4-5-P3 -0.12 0.27 -10000 0 -0.65 17 17
PI3K -0.13 0.29 -10000 0 -0.7 17 17
DOK2 0.019 0.057 -10000 0 -0.34 4 4
ETS1 0.027 0.03 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.086 0.2 -10000 0 -0.46 14 14
ITGB3 -0.4 0.62 -10000 0 -1.3 46 46
PIGR -0.29 0.49 -10000 0 -1.1 31 31
IGHE -0.006 0.062 0.15 1 -0.2 5 6
MAPKKK cascade -0.085 0.19 -10000 0 -0.45 14 14
BCL6 0.003 0.099 -10000 0 -0.34 13 13
OPRM1 -0.29 0.49 -10000 0 -1.1 30 30
RETNLB -0.29 0.49 -10000 0 -1.1 30 30
SELP -0.34 0.55 -10000 0 -1.2 38 38
AICDA -0.28 0.47 -10000 0 -1.1 29 29
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.003 0.082 -10000 0 -0.2 25 25
cell-cell adhesion 0.042 0.071 0.17 33 -10000 0 33
Ephrin B/EPHB2/RasGAP 0.013 0.1 -10000 0 -0.17 38 38
ITSN1 0.012 0.079 -10000 0 -0.34 8 8
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
SHC1 0.032 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.014 0.1 -10000 0 -0.21 33 33
Ephrin B1/EPHB1 0.027 0.052 -10000 0 -0.22 6 6
HRAS/GDP 0.011 0.086 0.16 1 -0.22 13 14
Ephrin B/EPHB1/GRB7 0.041 0.078 -10000 0 -0.18 15 15
Endophilin/SYNJ1 -0.012 0.11 0.25 14 -0.17 23 37
KRAS 0.031 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.024 0.099 -10000 0 -0.17 30 30
endothelial cell migration 0.032 0.072 -10000 0 -0.16 18 18
GRB2 0.03 0.008 -10000 0 -10000 0 0
GRB7 0.018 0.008 -10000 0 -10000 0 0
PAK1 -0.029 0.11 0.2 15 -0.2 17 32
HRAS 0.03 0.008 -10000 0 -10000 0 0
RRAS -0.033 0.094 0.19 9 -0.18 27 36
DNM1 -0.007 0.11 -10000 0 -0.34 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.004 0.076 0.2 10 -0.18 12 22
lamellipodium assembly -0.042 0.071 -10000 0 -0.17 33 33
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.009 0.083 -10000 0 -0.2 12 12
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
EPHB2 -0.032 0.13 -10000 0 -0.34 25 25
EPHB3 -0.045 0.14 -10000 0 -0.34 32 32
EPHB1 0.024 0.03 -10000 0 -0.34 1 1
EPHB4 0.01 0.079 -10000 0 -0.34 8 8
mol:GDP -0.011 0.088 0.21 4 -0.24 13 17
Ephrin B/EPHB2 0.002 0.095 -10000 0 -0.16 39 39
Ephrin B/EPHB3 -0.004 0.11 -10000 0 -0.18 40 40
JNK cascade -0.015 0.11 0.28 12 -0.19 27 39
Ephrin B/EPHB1 0.033 0.073 -10000 0 -0.17 16 16
RAP1/GDP 0.012 0.1 0.26 3 -0.24 10 13
EFNB2 0.006 0.087 -10000 0 -0.34 10 10
EFNB3 0.02 0.013 -10000 0 -10000 0 0
EFNB1 0.016 0.069 -10000 0 -0.34 6 6
Ephrin B2/EPHB1-2 -0.002 0.094 -10000 0 -0.18 35 35
RAP1B 0.031 0.006 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.007 0.11 -10000 0 -0.2 34 34
Rap1/GTP -0.015 0.079 -10000 0 -0.16 34 34
axon guidance -0.003 0.082 -10000 0 -0.2 25 25
MAPK3 -0.018 0.075 -10000 0 -0.26 4 4
MAPK1 -0.016 0.073 -10000 0 -0.26 4 4
Rac1/GDP 0.003 0.088 0.26 2 -0.24 8 10
actin cytoskeleton reorganization -0.034 0.066 -10000 0 -0.18 19 19
CDC42/GDP 0.003 0.097 0.26 3 -0.24 11 14
PI3K 0.037 0.075 -10000 0 -0.16 18 18
EFNA5 0.025 0.011 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.011 0.071 -10000 0 -0.19 18 18
Ephrin B/EPHB2/Intersectin/N-WASP -0.032 0.11 -10000 0 -0.21 40 40
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.018 0.076 -10000 0 -0.16 34 34
PTK2 -0.006 0.22 0.56 15 -0.33 30 45
MAP4K4 -0.015 0.12 0.28 12 -0.19 27 39
SRC -0.007 0.11 -10000 0 -0.34 17 17
KALRN 0.001 0.095 -10000 0 -0.34 12 12
Intersectin/N-WASP 0.026 0.06 -10000 0 -0.23 8 8
neuron projection morphogenesis -0.031 0.11 0.32 4 -0.28 8 12
MAP2K1 -0.014 0.079 -10000 0 -0.27 4 4
WASL 0.028 0.012 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.02 0.099 -10000 0 -0.18 30 30
cell migration -0.015 0.11 0.32 2 -0.34 7 9
NRAS 0.032 0.005 -10000 0 -10000 0 0
SYNJ1 -0.013 0.11 0.26 14 -0.17 23 37
PXN 0.027 0.04 -10000 0 -0.34 2 2
TF -0.026 0.12 0.25 14 -0.21 25 39
HRAS/GTP 0.001 0.091 -10000 0 -0.16 36 36
Ephrin B1/EPHB1-2 0.005 0.09 -10000 0 -0.18 30 30
cell adhesion mediated by integrin 0.024 0.08 0.18 17 -0.19 9 26
RAC1 0.028 0.011 -10000 0 -10000 0 0
mol:GTP 0.003 0.094 -10000 0 -0.16 36 36
RAC1-CDC42/GTP -0.058 0.092 -10000 0 -0.21 33 33
RASA1 0.03 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.012 0.092 0.26 2 -0.24 8 10
ruffle organization -0.022 0.11 0.26 7 -0.28 6 13
NCK1 0.031 0.006 -10000 0 -10000 0 0
receptor internalization -0.031 0.12 0.25 13 -0.2 23 36
Ephrin B/EPHB2/KALRN -0.003 0.11 -10000 0 -0.17 47 47
ROCK1 -0.015 0.096 0.19 8 -0.19 32 40
RAS family/GDP -0.041 0.065 -10000 0 -0.18 21 21
Rac1/GTP -0.025 0.083 -10000 0 -0.18 33 33
Ephrin B/EPHB1/Src/Paxillin -0.015 0.093 -10000 0 -0.2 32 32
Syndecan-4-mediated signaling events

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
PTK2 -0.047 0.16 -10000 0 -0.33 34 34
Syndecan-4/Syndesmos -0.07 0.23 -10000 0 -0.46 36 36
positive regulation of JNK cascade -0.1 0.22 -10000 0 -0.46 37 37
Syndecan-4/ADAM12 -0.073 0.23 -10000 0 -0.46 36 36
CCL5 0.018 0.063 -10000 0 -0.34 5 5
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
DNM2 0.029 0.009 -10000 0 -10000 0 0
ITGA5 0.032 0.004 -10000 0 -10000 0 0
SDCBP 0.024 0.041 -10000 0 -0.34 2 2
PLG 0.009 0.022 -10000 0 -10000 0 0
ADAM12 0.02 0.063 -10000 0 -0.34 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.032 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.026 0.015 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.078 0.23 -10000 0 -0.46 36 36
Syndecan-4/CXCL12/CXCR4 -0.11 0.24 -10000 0 -0.49 37 37
Syndecan-4/Laminin alpha3 -0.086 0.23 -10000 0 -0.48 36 36
MDK 0.019 0.063 -10000 0 -0.34 5 5
Syndecan-4/FZD7 -0.072 0.24 -10000 0 -0.46 36 36
Syndecan-4/Midkine -0.075 0.23 -10000 0 -0.46 36 36
FZD7 0.023 0.057 -10000 0 -0.34 4 4
Syndecan-4/FGFR1/FGF -0.073 0.22 -10000 0 -0.43 38 38
THBS1 -0.034 0.13 -10000 0 -0.34 27 27
integrin-mediated signaling pathway -0.078 0.22 -10000 0 -0.44 37 37
positive regulation of MAPKKK cascade -0.1 0.22 -10000 0 -0.46 37 37
Syndecan-4/TACI -0.078 0.23 -10000 0 -0.46 37 37
CXCR4 0.027 0.04 -10000 0 -0.34 2 2
cell adhesion -0.002 0.066 0.2 3 -0.19 8 11
Syndecan-4/Dynamin -0.07 0.23 -10000 0 -0.46 35 35
Syndecan-4/TSP1 -0.089 0.23 -10000 0 -0.47 37 37
Syndecan-4/GIPC -0.072 0.23 -10000 0 -0.46 35 35
Syndecan-4/RANTES -0.074 0.23 -10000 0 -0.45 36 36
ITGB1 0.032 0.004 -10000 0 -10000 0 0
LAMA1 0.018 0.006 -10000 0 -10000 0 0
LAMA3 -0.009 0.11 -10000 0 -0.34 16 16
RAC1 0.028 0.011 -10000 0 -10000 0 0
PRKCA -0.018 0.17 0.84 4 -0.3 21 25
Syndecan-4/alpha-Actinin -0.072 0.23 -10000 0 -0.46 36 36
TFPI -0.022 0.13 -10000 0 -0.34 24 24
F2 0.017 0.028 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.047 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.091 0.22 -10000 0 -0.47 36 36
ACTN1 0.032 0.005 -10000 0 -10000 0 0
TNC 0.006 0.083 -10000 0 -0.34 9 9
Syndecan-4/CXCL12 -0.1 0.24 -10000 0 -0.5 37 37
FGF6 0.018 0.006 -10000 0 -10000 0 0
RHOA 0.031 0.007 -10000 0 -10000 0 0
CXCL12 -0.082 0.16 -10000 0 -0.34 48 48
TNFRSF13B 0.004 0.091 -10000 0 -0.34 11 11
FGF2 0.021 0.057 -10000 0 -0.34 4 4
FGFR1 -0.005 0.098 -10000 0 -0.34 13 13
Syndecan-4/PI-4-5-P2 -0.088 0.22 -10000 0 -0.46 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.049 -10000 0 -0.31 3 3
cell migration -0.011 0.013 -10000 0 -10000 0 0
PRKCD 0.019 0.068 -10000 0 -0.32 6 6
vasculogenesis -0.085 0.22 -10000 0 -0.45 37 37
SDC4 -0.085 0.23 -10000 0 -0.48 35 35
Syndecan-4/Tenascin C -0.082 0.23 -10000 0 -0.46 37 37
Syndecan-4/PI-4-5-P2/PKC alpha -0.021 0.012 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.074 0.22 -10000 0 -0.45 36 36
MMP9 -0.034 0.13 -10000 0 -0.34 26 26
Rac1/GTP -0.002 0.067 0.21 3 -0.2 8 11
cytoskeleton organization -0.067 0.22 -10000 0 -0.44 36 36
GIPC1 0.023 0.05 -10000 0 -0.34 3 3
Syndecan-4/TFPI -0.081 0.24 -10000 0 -0.47 37 37
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.018 0.12 -10000 0 -0.21 43 43
alphaM/beta2 Integrin/GPIbA 0.016 0.097 -10000 0 -0.22 21 21
alphaM/beta2 Integrin/proMMP-9 -0.025 0.13 -10000 0 -0.23 43 43
PLAUR 0.02 0.057 -10000 0 -0.34 4 4
HMGB1 0.026 0.024 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.015 0.1 -10000 0 -0.23 21 21
AGER 0.027 0.023 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
SELPLG 0.023 0.057 -10000 0 -0.34 4 4
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.026 0.12 -10000 0 -0.21 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.034 0.13 -10000 0 -0.34 26 26
CYR61 0.013 0.079 -10000 0 -0.34 8 8
TLN1 0.029 0.029 -10000 0 -0.34 1 1
Rap1/GTP -0.054 0.14 0.2 1 -0.29 30 31
RHOA 0.031 0.007 -10000 0 -10000 0 0
P-selectin oligomer 0 0.099 -10000 0 -0.34 13 13
MYH2 -0.068 0.14 -10000 0 -0.36 22 22
MST1R 0.005 0.083 -10000 0 -0.34 9 9
leukocyte activation during inflammatory response 0.005 0.092 -10000 0 -0.18 28 28
APOB 0.008 0.073 -10000 0 -0.34 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.033 0.13 -10000 0 -0.34 26 26
JAM3 0.028 0.011 -10000 0 -10000 0 0
GP1BA 0.029 0.01 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.021 0.12 -10000 0 -0.22 43 43
alphaM/beta2 Integrin -0.069 0.14 -10000 0 -0.34 26 26
JAM3 homodimer 0.028 0.011 -10000 0 -10000 0 0
ICAM2 0.03 0.008 -10000 0 -10000 0 0
ICAM1 0.014 0.074 -10000 0 -0.34 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.069 0.14 -10000 0 -0.34 26 26
cell adhesion 0.015 0.097 -10000 0 -0.22 21 21
NFKB1 -0.001 0.13 0.21 4 -0.35 13 17
THY1 -0.021 0.12 -10000 0 -0.34 20 20
RhoA/GDP 0.023 0.005 -10000 0 -10000 0 0
Lipoprotein(a) 0.019 0.046 -10000 0 -0.2 7 7
alphaM/beta2 Integrin/LRP/tPA -0.03 0.14 -10000 0 -0.23 49 49
IL6 -0.018 0.11 0.2 1 -0.33 13 14
ITGB2 0.007 0.079 -10000 0 -0.33 8 8
elevation of cytosolic calcium ion concentration 0.007 0.11 -10000 0 -0.2 33 33
alphaM/beta2 Integrin/JAM2/JAM3 0.028 0.092 -10000 0 -0.19 20 20
JAM2 0.024 0.012 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 0.013 0.12 -10000 0 -0.19 34 34
alphaM/beta2 Integrin/uPA/Plg 0.01 0.1 -10000 0 -0.2 30 30
RhoA/GTP -0.074 0.16 -10000 0 -0.37 26 26
positive regulation of phagocytosis -0.06 0.15 0.21 2 -0.28 38 40
Ron/MSP 0.023 0.066 -10000 0 -0.23 10 10
alphaM/beta2 Integrin/uPAR/uPA 0.009 0.11 -10000 0 -0.2 33 33
alphaM/beta2 Integrin/uPAR 0.009 0.1 -10000 0 -0.22 24 24
PLAU 0.011 0.084 -10000 0 -0.34 9 9
PLAT 0.017 0.063 -10000 0 -0.34 5 5
actin filament polymerization -0.065 0.13 -10000 0 -0.34 22 22
MST1 0.025 0.031 -10000 0 -0.34 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.009 0.095 -10000 0 -0.18 28 28
TNF -0.036 0.18 -10000 0 -0.55 15 15
RAP1B 0.031 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.002 0.11 -10000 0 -0.21 30 30
fibrinolysis 0.008 0.1 -10000 0 -0.2 30 30
HCK 0.007 0.092 -10000 0 -0.34 11 11
dendritic cell antigen processing and presentation -0.069 0.14 -10000 0 -0.34 26 26
VTN 0.021 0.057 -10000 0 -0.34 4 4
alphaM/beta2 Integrin/CYR61 0.003 0.11 -10000 0 -0.21 29 29
LPA 0.02 0.006 -10000 0 -10000 0 0
LRP1 -0.065 0.16 -10000 0 -0.34 42 42
cell migration -0.048 0.13 -10000 0 -0.21 60 60
FN1 0.021 0.05 -10000 0 -0.34 3 3
alphaM/beta2 Integrin/Thy1 -0.016 0.12 -10000 0 -0.23 37 37
MPO -0.066 0.16 -10000 0 -0.34 41 41
KNG1 0.028 0.008 -10000 0 -10000 0 0
RAP1/GDP 0.041 0.01 -10000 0 -10000 0 0
ROCK1 -0.07 0.14 -10000 0 -0.36 23 23
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.017 0.002 -10000 0 -10000 0 0
CTGF -0.029 0.13 -10000 0 -0.34 25 25
alphaM/beta2 Integrin/Hck 0.002 0.12 -10000 0 -0.24 28 28
ITGAM -0.01 0.11 -10000 0 -0.35 16 16
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.009 0.12 -10000 0 -0.22 33 33
HP -0.01 0.11 -10000 0 -0.34 17 17
leukocyte adhesion -0.008 0.12 -10000 0 -0.23 33 33
SELP 0 0.099 -10000 0 -0.34 13 13
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.027 0.12 -10000 0 -0.23 42 42
Necdin/E2F1 -0.023 0.11 -10000 0 -0.23 37 37
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.046 0.15 -10000 0 -0.21 68 68
NGF (dimer)/p75(NTR)/BEX1 -0.014 0.1 -10000 0 -0.21 36 36
NT-4/5 (dimer)/p75(NTR) 0.015 0.065 -10000 0 -0.24 10 10
IKBKB 0.029 0.01 -10000 0 -10000 0 0
AKT1 -0.011 0.068 0.2 10 -0.17 10 20
IKBKG 0.029 0.01 -10000 0 -10000 0 0
BDNF 0.023 0.05 -10000 0 -0.34 3 3
MGDIs/NGR/p75(NTR)/LINGO1 0.008 0.095 -10000 0 -0.2 28 28
FURIN 0.031 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.023 0.13 -10000 0 -0.22 47 47
LINGO1 0.026 0.01 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.008 0.086 -10000 0 -0.16 36 36
proBDNF (dimer) 0.023 0.05 -10000 0 -0.34 3 3
NTRK1 -0.025 0.12 -10000 0 -0.34 22 22
RTN4R -0.01 0.11 -10000 0 -0.34 17 17
neuron apoptosis -0.064 0.16 0.34 1 -0.43 15 16
IRAK1 0.029 0.01 -10000 0 -10000 0 0
SHC1 -0.022 0.05 -10000 0 -0.2 11 11
ARHGDIA 0.03 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.023 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.086 0.031 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.008 0.12 -10000 0 -0.2 43 43
MAGEH1 0.029 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.054 0.14 -10000 0 -0.22 67 67
Mammalian IAPs/DIABLO 0.07 0.039 -10000 0 -0.18 2 2
proNGF (dimer) 0.018 0.005 -10000 0 -10000 0 0
MAGED1 0.016 0.069 -10000 0 -0.34 6 6
APP -0.092 0.17 -10000 0 -0.34 55 55
NT-4/5 (dimer) 0.016 0.006 -10000 0 -10000 0 0
ZNF274 0.029 0.01 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.025 0.054 -10000 0 -0.17 11 11
NGF 0.018 0.005 -10000 0 -10000 0 0
cell cycle arrest -0.039 0.11 0.27 3 -0.2 34 37
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.012 0.051 -10000 0 -0.18 10 10
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.033 0.059 -10000 0 -0.2 9 9
NCSTN 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0.03 0.067 -10000 0 -0.2 12 12
PSENEN 0.029 0.009 -10000 0 -10000 0 0
mol:ceramide -0.058 0.095 0.18 2 -0.2 45 47
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.007 0.093 -10000 0 -0.42 4 4
p75(NTR)/beta APP -0.067 0.14 -10000 0 -0.24 62 62
BEX1 -0.038 0.13 -10000 0 -0.34 27 27
mol:GDP -0.021 0.047 -10000 0 -0.2 11 11
NGF (dimer) 0.042 0.058 -10000 0 -0.19 9 9
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.024 0.096 -10000 0 -0.18 28 28
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
RAC1/GTP 0.024 0.055 -10000 0 -0.17 11 11
MYD88 0.031 0.007 -10000 0 -10000 0 0
CHUK 0.032 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.031 0.067 -10000 0 -0.2 12 12
RHOB 0.009 0.088 -10000 0 -0.34 10 10
RHOA 0.031 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.042 0.033 -10000 0 -0.24 2 2
NT3 (dimer) 0.017 0.004 -10000 0 -10000 0 0
TP53 -0.05 0.085 0.19 1 -0.19 35 36
PRDM4 -0.057 0.095 0.18 2 -0.2 44 46
BDNF (dimer) 0.037 0.064 -10000 0 -0.18 12 12
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
SORT1 -0.064 0.16 -10000 0 -0.34 42 42
activation of caspase activity -0.049 0.14 -10000 0 -0.2 68 68
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.008 0.12 -10000 0 -0.2 44 44
RHOC 0.027 0.041 -10000 0 -0.34 2 2
XIAP 0.029 0.01 -10000 0 -10000 0 0
MAPK10 -0.067 0.15 0.38 6 -0.3 22 28
DIABLO 0.032 0.004 -10000 0 -10000 0 0
SMPD2 -0.058 0.096 0.18 2 -0.2 45 47
APH1B 0.031 0.006 -10000 0 -10000 0 0
APH1A 0.032 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.026 0.12 -10000 0 -0.22 45 45
PSEN1 0.032 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.016 0.065 -10000 0 -0.24 10 10
MAPK8 -0.068 0.15 0.44 5 -0.3 22 27
MAPK9 -0.066 0.15 0.4 6 -0.29 22 28
APAF1 0.032 0.004 -10000 0 -10000 0 0
NTF3 0.017 0.004 -10000 0 -10000 0 0
NTF4 0.016 0.006 -10000 0 -10000 0 0
NDN -0.056 0.15 -10000 0 -0.34 35 35
RAC1/GDP 0.021 0.008 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.037 0.087 -10000 0 -0.18 21 21
p75 CTF/Sortilin/TRAF6/NRIF 0.012 0.11 -10000 0 -0.18 39 39
RhoA-B-C/GTP 0.03 0.066 -10000 0 -0.2 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.005 0.12 -10000 0 -0.19 46 46
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.006 0.13 -10000 0 -0.2 47 47
PRKACB 0.029 0.029 -10000 0 -0.34 1 1
proBDNF (dimer)/p75 ECD 0.039 0.039 -10000 0 -0.24 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.024 0.05 -10000 0 -0.34 3 3
BIRC2 0.031 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.058 0.12 0.12 8 -0.23 40 48
BAD -0.064 0.17 0.48 7 -0.31 22 29
RIPK2 0.028 0.011 -10000 0 -10000 0 0
NGFR 0.003 0.091 -10000 0 -0.34 11 11
CYCS -0.04 0.12 0.31 8 -0.21 35 43
ADAM17 0.032 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.042 0.065 -10000 0 -0.18 10 10
BCL2L11 -0.069 0.17 0.45 7 -0.31 23 30
BDNF (dimer)/p75(NTR) 0.018 0.076 -10000 0 -0.24 13 13
PI3K 0.047 0.066 -10000 0 -0.18 11 11
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.008 0.12 -10000 0 -0.2 44 44
NDNL2 0.031 0.007 -10000 0 -10000 0 0
YWHAE 0.029 0.01 -10000 0 -10000 0 0
PRKCI 0.031 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.015 0.069 -10000 0 -0.24 11 11
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.016 0.13 -10000 0 -0.21 46 46
TRAF6 0.031 0.007 -10000 0 -10000 0 0
RAC1 0.028 0.011 -10000 0 -10000 0 0
PRKCZ -0.025 0.13 -10000 0 -0.34 25 25
PLG 0.017 0.002 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.047 0.12 0.15 1 -0.23 46 47
SQSTM1 0.03 0.008 -10000 0 -10000 0 0
NGFRAP1 -0.053 0.15 -10000 0 -0.34 37 37
CASP3 -0.061 0.16 0.46 7 -0.28 23 30
E2F1 0.027 0.041 -10000 0 -0.34 2 2
CASP9 0.031 0.006 -10000 0 -10000 0 0
IKK complex -0.013 0.12 -10000 0 -0.32 8 8
NGF (dimer)/TRKA -0.005 0.092 -10000 0 -0.24 22 22
MMP7 0.005 0.083 -10000 0 -0.34 9 9
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.004 0.12 -10000 0 -0.19 43 43
MMP3 0.016 0.004 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.057 0.078 -10000 0 -0.28 9 9
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.019 0.056 -10000 0 -0.19 8 8
NFATC2 0.004 0.18 -10000 0 -0.47 11 11
NFATC3 -0.022 0.13 -10000 0 -0.25 35 35
CD40LG -0.17 0.38 -10000 0 -0.78 40 40
ITCH 0.027 0.006 -10000 0 -10000 0 0
CBLB 0.026 0.007 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.35 -10000 0 -0.77 28 28
JUNB 0.027 0.03 -10000 0 -0.34 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.007 -10000 0 -10000 0 0
T cell anergy 0.012 0.035 0.24 1 -10000 0 1
TLE4 -0.011 0.14 -10000 0 -0.47 8 8
Jun/NFAT1-c-4/p21SNFT -0.12 0.42 -10000 0 -0.84 36 36
AP-1/NFAT1-c-4 -0.14 0.46 -10000 0 -0.89 38 38
IKZF1 -0.011 0.12 -10000 0 -0.37 6 6
T-helper 2 cell differentiation -0.063 0.23 -10000 0 -0.66 15 15
AP-1/NFAT1 0.003 0.16 -10000 0 -0.33 16 16
CALM1 0.038 0.006 -10000 0 -10000 0 0
EGR2 -0.18 0.49 -10000 0 -1.1 32 32
EGR3 -0.18 0.49 -10000 0 -1.1 31 31
NFAT1/FOXP3 0.009 0.15 -10000 0 -0.36 13 13
EGR1 0.001 0.092 -10000 0 -0.34 11 11
JUN 0.001 0.092 -10000 0 -0.34 10 10
EGR4 0.02 0.018 -10000 0 -10000 0 0
mol:Ca2+ 0.007 0.001 -10000 0 -10000 0 0
GBP3 -0.008 0.13 -10000 0 -0.46 6 6
FOSL1 0.019 0.063 -10000 0 -0.34 5 5
NFAT1-c-4/MAF/IRF4 -0.1 0.41 -10000 0 -0.8 37 37
DGKA -0.006 0.13 -10000 0 -0.39 8 8
CREM 0.032 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.41 -10000 0 -0.86 35 35
CTLA4 -0.013 0.15 0.24 5 -0.43 12 17
NFAT1-c-4 (dimer)/EGR1 -0.12 0.42 -10000 0 -0.86 36 36
NFAT1-c-4 (dimer)/EGR4 -0.11 0.41 -10000 0 -0.84 35 35
FOS 0.009 0.079 -10000 0 -0.34 7 7
IFNG -0.048 0.24 -10000 0 -0.78 10 10
T cell activation -0.084 0.21 -10000 0 -0.57 12 12
MAF 0.02 0.063 -10000 0 -0.34 5 5
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.099 0.3 0.7 29 -10000 0 29
TNF -0.15 0.38 -10000 0 -0.77 40 40
FASLG -0.25 0.61 -10000 0 -1.3 38 38
TBX21 0.022 0.061 -10000 0 -0.31 5 5
BATF3 0.014 0.074 -10000 0 -0.34 7 7
PRKCQ 0.013 0.075 -10000 0 -0.22 12 12
PTPN1 -0.002 0.12 -10000 0 -0.34 8 8
NFAT1-c-4/ICER1 -0.1 0.41 -10000 0 -0.82 36 36
GATA3 0.013 0.079 -10000 0 -0.34 8 8
T-helper 1 cell differentiation -0.045 0.23 -10000 0 -0.76 10 10
IL2RA -0.1 0.33 -10000 0 -0.68 31 31
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.002 0.12 -10000 0 -0.37 6 6
E2F1 0.031 0.041 -10000 0 -0.34 2 2
PPARG -0.047 0.14 -10000 0 -0.34 31 31
SLC3A2 -0.004 0.12 0.32 1 -0.37 6 7
IRF4 0.017 0.069 -10000 0 -0.34 6 6
PTGS2 -0.17 0.39 0.46 1 -0.78 41 42
CSF2 -0.16 0.37 0.48 1 -0.77 40 41
JunB/Fra1/NFAT1-c-4 -0.1 0.4 -10000 0 -0.82 34 34
IL4 -0.068 0.24 -10000 0 -0.69 15 15
IL5 -0.16 0.37 0.49 1 -0.77 40 41
IL2 -0.086 0.21 -10000 0 -0.59 11 11
IL3 -0.013 0.079 -10000 0 -10000 0 0
RNF128 0.017 0.007 -10000 0 -10000 0 0
NFATC1 -0.1 0.31 -10000 0 -0.71 29 29
CDK4 0.062 0.19 0.48 19 -10000 0 19
PTPRK -0.02 0.16 -10000 0 -0.53 10 10
IL8 -0.17 0.39 0.48 2 -0.77 43 45
POU2F1 0.032 0.005 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.071 0.18 -10000 0 -0.43 31 31
KLHL20 -0.022 0.098 0.17 1 -0.21 23 24
CYFIP2 0.026 0.041 -10000 0 -0.34 2 2
Rac1/GDP -0.04 0.12 -10000 0 -0.25 29 29
ENAH -0.063 0.17 -10000 0 -0.4 31 31
AP1M1 0.029 0.009 -10000 0 -10000 0 0
RAP1B 0.031 0.006 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
CTNNB1 0.031 0.007 -10000 0 -10000 0 0
CDC42/GTP -0.02 0.094 -10000 0 -0.19 28 28
ABI1/Sra1/Nap1 -0.038 0.06 -10000 0 -0.16 26 26
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.096 -10000 0 -0.18 28 28
RAPGEF1 -0.065 0.15 -10000 0 -0.34 31 31
CTNND1 0.024 0.049 -10000 0 -0.34 3 3
regulation of calcium-dependent cell-cell adhesion -0.052 0.17 -10000 0 -0.39 31 31
CRK -0.064 0.16 -10000 0 -0.37 29 29
E-cadherin/gamma catenin/alpha catenin -0.014 0.12 -10000 0 -0.22 40 40
alphaE/beta7 Integrin 0.036 0.044 -10000 0 -0.23 4 4
IQGAP1 0.029 0.029 -10000 0 -0.34 1 1
NCKAP1 -0.001 0.099 -10000 0 -0.34 13 13
Rap1/GTP/I-afadin 0.044 0.055 -10000 0 -0.18 9 9
DLG1 -0.053 0.16 -10000 0 -0.39 29 29
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.063 -10000 0 -0.14 28 28
MLLT4 0.008 0.083 -10000 0 -0.34 9 9
ARF6/GTP/NME1/Tiam1 0.038 0.061 -10000 0 -0.18 11 11
PI3K -0.032 0.082 -10000 0 -0.18 28 28
ARF6 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.028 0.13 -10000 0 -0.27 36 36
TIAM1 0.003 0.091 -10000 0 -0.34 11 11
E-cadherin(dimer)/Ca2+ 0.018 0.096 -10000 0 -0.18 31 31
AKT1 -0.026 0.049 -10000 0 -0.15 9 9
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
CDH1 -0.033 0.13 -10000 0 -0.34 26 26
RhoA/GDP -0.041 0.12 -10000 0 -0.24 31 31
actin cytoskeleton organization -0.013 0.076 0.14 4 -0.16 22 26
CDC42/GDP -0.042 0.12 0.27 1 -0.24 32 33
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.04 0.11 -10000 0 -0.21 43 43
ITGB7 0.023 0.057 -10000 0 -0.34 4 4
RAC1 0.028 0.011 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.02 0.1 -10000 0 -0.19 31 31
E-cadherin/Ca2+/beta catenin/alpha catenin 0.01 0.085 -10000 0 -0.17 28 28
mol:GDP -0.06 0.12 -10000 0 -0.28 32 32
CDC42/GTP/IQGAP1 0.04 0.021 -10000 0 -0.2 1 1
JUP -0.008 0.11 -10000 0 -0.34 17 17
p120 catenin/RhoA/GDP -0.037 0.12 -10000 0 -0.25 30 30
RAC1/GTP/IQGAP1 0.036 0.022 -10000 0 -0.17 1 1
PIP5K1C/AP1M1 0.044 0.014 -10000 0 -10000 0 0
RHOA 0.031 0.007 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
CTNNA1 0.021 0.057 -10000 0 -0.34 4 4
positive regulation of S phase of mitotic cell cycle -0.013 0.052 -10000 0 -0.14 14 14
NME1 0.03 0.008 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.063 0.17 -10000 0 -0.39 31 31
regulation of cell-cell adhesion -0.024 0.079 -10000 0 -0.17 28 28
WASF2 -0.01 0.042 0.082 1 -0.094 18 19
Rap1/GTP -0.023 0.1 0.18 2 -0.21 28 30
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.01 0.12 -10000 0 -0.19 41 41
CCND1 -0.016 0.063 -10000 0 -0.17 14 14
VAV2 -0.092 0.22 -10000 0 -0.55 21 21
RAP1/GDP -0.028 0.11 -10000 0 -0.23 24 24
adherens junction assembly -0.062 0.16 -10000 0 -0.38 31 31
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.032 0.004 -10000 0 -10000 0 0
PIP5K1C 0.03 0.009 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.002 0.11 -10000 0 -0.19 39 39
E-cadherin/beta catenin -0.027 0.1 -10000 0 -0.27 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.07 0.17 -10000 0 -0.39 32 32
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.063 0.13 -10000 0 -0.33 24 24
E-cadherin/beta catenin/alpha catenin 0.01 0.1 -10000 0 -0.2 28 28
ITGAE 0.028 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.053 0.17 -10000 0 -0.4 31 31
IGF1 pathway

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
NCK2 0.032 0 -10000 0 -10000 0 0
PTK2 -0.047 0.14 -10000 0 -0.34 31 31
CRKL -0.018 0.078 -10000 0 -0.19 25 25
GRB2/SOS1/SHC 0.06 0.018 -10000 0 -10000 0 0
HRAS 0.03 0.008 -10000 0 -10000 0 0
IRS1/Crk -0.01 0.083 -10000 0 -0.18 30 30
IGF-1R heterotetramer/IGF1/PTP1B 0.017 0.096 -10000 0 -0.2 26 26
AKT1 -0.032 0.077 0.28 3 -0.18 24 27
BAD -0.033 0.072 0.26 3 -0.17 23 26
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.019 0.079 -10000 0 -0.18 30 30
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.004 0.086 -10000 0 -0.18 30 30
RAF1 -0.012 0.075 -10000 0 -0.39 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.024 0.098 -10000 0 -0.19 26 26
YWHAZ 0.028 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.003 0.093 -10000 0 -0.19 30 30
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.035 0.067 0.18 2 -0.18 24 26
GNB2L1 0.031 0.007 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.004 0.093 0.37 3 -10000 0 3
PXN 0.027 0.04 -10000 0 -0.34 2 2
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.045 0.012 -10000 0 -10000 0 0
HRAS/GTP 0 0.079 -10000 0 -0.18 25 25
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.045 0.095 -10000 0 -0.16 26 26
IGF-1R heterotetramer -0.01 0.11 -10000 0 -0.32 16 16
IGF-1R heterotetramer/IGF1/IRS/Nck 0.013 0.095 -10000 0 -0.18 30 30
Crk/p130 Cas/Paxillin 0.007 0.11 0.23 1 -0.19 34 35
IGF1R -0.01 0.11 -10000 0 -0.32 16 16
IGF1 -0.01 0.11 -10000 0 -0.34 14 14
IRS2/Crk -0.011 0.081 -10000 0 -0.18 27 27
PI3K 0.026 0.097 -10000 0 -0.17 29 29
apoptosis 0.026 0.061 0.24 3 -0.17 2 5
HRAS/GDP 0.022 0.006 -10000 0 -10000 0 0
PRKCD -0.025 0.1 -10000 0 -0.25 26 26
RAF1/14-3-3 E 0 0.079 -10000 0 -0.28 4 4
BAD/14-3-3 -0.027 0.064 0.17 2 -0.25 3 5
PRKCZ -0.053 0.092 0.32 2 -0.18 40 42
Crk/p130 Cas/Paxillin/FAK1 -0.039 0.1 -10000 0 -0.18 49 49
PTPN1 0.031 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.024 0.11 -10000 0 -0.25 29 29
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.014 0.11 -10000 0 -0.19 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.032 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.001 0.088 0.14 1 -0.18 30 31
GRB10 0.006 0.087 -10000 0 -0.34 10 10
PTPN11 -0.018 0.079 -10000 0 -0.19 26 26
IRS1 -0.017 0.085 0.14 1 -0.21 26 27
IRS2 -0.019 0.079 -10000 0 -0.19 26 26
IGF-1R heterotetramer/IGF1 -0.006 0.11 -10000 0 -0.27 26 26
GRB2 0.03 0.008 -10000 0 -10000 0 0
PDPK1 -0.014 0.084 0.28 3 -0.18 25 28
YWHAE 0.029 0.01 -10000 0 -10000 0 0
PRKD1 -0.026 0.11 0.2 1 -0.24 29 30
SHC1 0.032 0.004 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.009 0.11 -10000 0 -0.34 16 16
alphaV beta3 Integrin -0.035 0.13 -10000 0 -0.25 43 43
PTK2 -0.1 0.2 -10000 0 -0.42 41 41
positive regulation of JNK cascade -0.059 0.13 -10000 0 -0.33 20 20
CDC42/GDP -0.074 0.19 0.33 1 -0.46 21 22
Rac1/GDP -0.075 0.18 0.29 1 -0.45 22 23
RAP1B 0.031 0.006 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
CTNNB1 0.031 0.007 -10000 0 -10000 0 0
CDC42/GTP -0.068 0.16 -10000 0 -0.41 20 20
nectin-3/I-afadin 0.025 0.067 -10000 0 -0.23 10 10
RAPGEF1 -0.088 0.18 0.27 1 -0.48 20 21
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.2 -10000 0 -0.55 19 19
PDGFB-D/PDGFRB -0.009 0.11 -10000 0 -0.34 16 16
TLN1 -0.038 0.11 0.19 2 -0.25 29 31
Rap1/GTP -0.067 0.13 -10000 0 -0.34 20 20
IQGAP1 0.029 0.029 -10000 0 -0.34 1 1
Rap1/GTP/I-afadin 0.044 0.055 -10000 0 -0.18 9 9
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.025 0.067 -10000 0 -0.23 10 10
PVR -0.009 0.11 -10000 0 -0.34 17 17
Necl-5(dimer) -0.009 0.11 -10000 0 -0.34 17 17
mol:GDP -0.1 0.22 0.32 2 -0.56 22 24
MLLT4 0.008 0.083 -10000 0 -0.34 9 9
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
PI3K 0.047 0.1 -10000 0 -0.21 19 19
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.016 0.083 -10000 0 -0.24 15 15
positive regulation of lamellipodium assembly -0.071 0.14 -10000 0 -0.35 23 23
PVRL1 0.009 0.083 -10000 0 -0.34 9 9
PVRL3 0.026 0.03 -10000 0 -0.34 1 1
PVRL2 0.007 0.088 -10000 0 -0.34 10 10
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
CDH1 -0.033 0.13 -10000 0 -0.34 26 26
CLDN1 0.018 0.006 -10000 0 -10000 0 0
JAM-A/CLDN1 0.046 0.069 -10000 0 -0.18 13 13
SRC -0.12 0.22 -10000 0 -0.58 22 22
ITGB3 -0.047 0.14 -10000 0 -0.34 32 32
nectin-1(dimer)/I-afadin/I-afadin 0.016 0.083 -10000 0 -0.24 15 15
FARP2 -0.093 0.21 -10000 0 -0.56 19 19
RAC1 0.028 0.011 -10000 0 -10000 0 0
CTNNA1 0.021 0.057 -10000 0 -0.34 4 4
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.016 0.097 -10000 0 -0.21 24 24
nectin-1/I-afadin 0.016 0.083 -10000 0 -0.24 15 15
nectin-2/I-afadin 0.011 0.086 -10000 0 -0.23 18 18
RAC1/GTP/IQGAP1/filamentous actin 0.036 0.022 -10000 0 -0.17 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.031 0.078 -10000 0 -0.2 15 15
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.021 -10000 0 -0.2 1 1
F11R 0.025 0.049 -10000 0 -0.34 3 3
positive regulation of filopodium formation -0.059 0.13 -10000 0 -0.33 20 20
alphaV/beta3 Integrin/Talin -0.057 0.15 0.2 2 -0.27 43 45
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.011 0.086 -10000 0 -0.23 18 18
nectin-2(dimer)/I-afadin/I-afadin 0.011 0.086 -10000 0 -0.23 18 18
PIP5K1C -0.037 0.11 -10000 0 -0.26 29 29
VAV2 -0.12 0.24 0.3 1 -0.59 24 25
RAP1/GDP -0.067 0.18 0.33 1 -0.42 21 22
ITGAV -0.001 0.11 -10000 0 -0.34 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.026 0.082 -10000 0 -0.2 19 19
nectin-3(dimer)/I-afadin/I-afadin 0.025 0.067 -10000 0 -0.23 10 10
Rac1/GTP -0.085 0.18 -10000 0 -0.44 23 23
PTPRM -0.041 0.12 -10000 0 -0.29 31 31
E-cadherin/beta catenin/alpha catenin 0.005 0.12 -10000 0 -0.19 42 42
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.047 0.25 -10000 0 -0.85 14 14
MKNK1 0.031 0.006 -10000 0 -10000 0 0
MAPK14 0.012 0.092 -10000 0 -0.28 13 13
ATF2/c-Jun -0.024 0.14 -10000 0 -0.33 22 22
MAPK11 0.002 0.1 -10000 0 -0.3 15 15
MITF -0.021 0.14 -10000 0 -0.36 20 20
MAPKAPK5 -0.003 0.1 -10000 0 -0.31 15 15
KRT8 -0.058 0.15 -10000 0 -0.29 46 46
MAPKAPK3 0.031 0.007 -10000 0 -10000 0 0
MAPKAPK2 0.031 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.007 0.13 -10000 0 -0.39 15 15
CEBPB -0.01 0.11 -10000 0 -0.32 18 18
SLC9A1 -0.003 0.1 -10000 0 -0.31 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.008 0.11 0.23 1 -0.3 18 19
p38alpha-beta/MNK1 0.026 0.12 -10000 0 -0.31 15 15
JUN -0.026 0.13 -10000 0 -0.33 22 22
PPARGC1A -0.039 0.13 -10000 0 -0.27 37 37
USF1 -0.003 0.1 -10000 0 -0.31 15 15
RAB5/GDP/GDI1 0.004 0.084 -10000 0 -0.23 15 15
NOS2 -0.005 0.097 -10000 0 -0.32 13 13
DDIT3 -0.003 0.1 -10000 0 -0.31 15 15
RAB5A 0.031 0.007 -10000 0 -10000 0 0
HSPB1 -0.006 0.1 0.29 6 -0.26 18 24
p38alpha-beta/HBP1 0.018 0.11 -10000 0 -0.31 15 15
CREB1 -0.005 0.11 -10000 0 -0.32 17 17
RAB5/GDP 0.023 0.005 -10000 0 -10000 0 0
EIF4E 0.001 0.096 0.37 1 -0.29 13 14
RPS6KA4 -0.004 0.1 -10000 0 -0.31 15 15
PLA2G4A -0.02 0.12 0.37 1 -0.26 24 25
GDI1 -0.005 0.1 -10000 0 -0.31 15 15
TP53 -0.021 0.12 0.21 1 -0.39 15 16
RPS6KA5 -0.003 0.1 -10000 0 -0.31 15 15
ESR1 -0.023 0.12 -10000 0 -0.29 27 27
HBP1 0.028 0.011 -10000 0 -10000 0 0
MEF2C -0.025 0.14 -10000 0 -0.34 23 23
MEF2A -0.004 0.1 -10000 0 -0.31 15 15
EIF4EBP1 -0.007 0.11 -10000 0 -0.32 17 17
KRT19 -0.008 0.097 -10000 0 -0.32 14 14
ELK4 -0.004 0.1 -10000 0 -0.31 15 15
ATF6 -0.003 0.1 -10000 0 -0.31 15 15
ATF1 -0.005 0.11 -10000 0 -0.32 17 17
p38alpha-beta/MAPKAPK2 0.024 0.12 -10000 0 -0.31 15 15
p38alpha-beta/MAPKAPK3 0.023 0.12 -10000 0 -0.31 15 15
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.001 0.068 -10000 0 -0.19 18 18
EPHB2 -0.032 0.13 -10000 0 -0.34 25 25
Syndecan-2/TACI -0.009 0.085 -10000 0 -0.2 25 25
LAMA1 0.018 0.006 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.006 0.097 -10000 0 -0.17 35 35
HRAS 0.03 0.008 -10000 0 -10000 0 0
Syndecan-2/CASK -0.012 0.057 -10000 0 -0.19 16 16
ITGA5 0.032 0.004 -10000 0 -10000 0 0
BAX -0.009 0.05 -10000 0 -10000 0 0
EPB41 0.031 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.005 0.061 -10000 0 -0.17 18 18
LAMA3 -0.009 0.11 -10000 0 -0.34 16 16
EZR 0.028 0.04 -10000 0 -0.34 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.013 0.11 -10000 0 -0.34 16 16
Syndecan-2/MMP2 -0.031 0.097 -10000 0 -0.2 39 39
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.031 0.057 -10000 0 -0.24 7 7
dendrite morphogenesis -0.026 0.096 -10000 0 -0.21 33 33
Syndecan-2/GM-CSF -0.002 0.063 -10000 0 -0.19 16 16
determination of left/right symmetry -0.014 0.069 -10000 0 -0.22 16 16
Syndecan-2/PKC delta 0.001 0.076 -10000 0 -0.2 20 20
GNB2L1 0.031 0.007 -10000 0 -10000 0 0
MAPK3 0.006 0.076 0.19 13 -0.18 15 28
MAPK1 0.003 0.073 0.19 11 -0.18 15 26
Syndecan-2/RACK1 0.021 0.062 -10000 0 -0.16 16 16
NF1 0.029 0.01 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.014 0.069 -10000 0 -0.22 16 16
ITGA2 0.011 0.074 -10000 0 -0.34 7 7
MAPK8 -0.007 0.057 -10000 0 -0.19 15 15
Syndecan-2/alpha2/beta1 Integrin 0.021 0.078 -10000 0 -0.17 22 22
Syndecan-2/Kininogen 0.006 0.065 -10000 0 -0.19 16 16
ITGB1 0.032 0.004 -10000 0 -10000 0 0
SRC 0.008 0.1 0.21 16 -0.17 25 41
Syndecan-2/CASK/Protein 4.1 0.007 0.059 -10000 0 -0.17 16 16
extracellular matrix organization 0.006 0.065 -10000 0 -0.19 16 16
actin cytoskeleton reorganization 0.001 0.068 -10000 0 -0.19 18 18
Syndecan-2/Caveolin-2/Ras -0.002 0.085 -10000 0 -0.18 28 28
Syndecan-2/Laminin alpha3 -0.015 0.085 -10000 0 -0.19 30 30
Syndecan-2/RasGAP 0.032 0.066 -10000 0 -0.16 16 16
alpha5/beta1 Integrin 0.047 0.007 -10000 0 -10000 0 0
PRKCD 0.017 0.069 -10000 0 -0.34 6 6
Syndecan-2 dimer -0.026 0.097 -10000 0 -0.21 33 33
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.006 0.078 0.19 2 -0.16 25 27
RHOA 0.031 0.007 -10000 0 -10000 0 0
SDCBP 0.024 0.041 -10000 0 -0.34 2 2
TNFRSF13B 0.004 0.091 -10000 0 -0.34 11 11
RASA1 0.03 0.008 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.031 0.057 -10000 0 -0.24 7 7
Syndecan-2/Synbindin 0.006 0.065 -10000 0 -0.19 16 16
TGFB1 0.029 0.01 -10000 0 -10000 0 0
CASP3 0.013 0.087 0.2 16 -0.18 18 34
FN1 0.021 0.05 -10000 0 -0.34 3 3
Syndecan-2/IL8 -0.012 0.089 -10000 0 -0.2 27 27
SDC2 -0.014 0.069 -10000 0 -0.23 16 16
KNG1 0.028 0.008 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.006 0.065 -10000 0 -0.19 16 16
TRAPPC4 0.03 0.008 -10000 0 -10000 0 0
CSF2 0.016 0.005 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.006 0.065 -10000 0 -0.19 16 16
Syndecan-2/Syntenin/PI-4-5-P2 0.005 0.062 -10000 0 -0.17 18 18
Syndecan-2/Ezrin 0.023 0.067 -10000 0 -0.17 16 16
PRKACA 0.011 0.077 0.2 13 -0.17 16 29
angiogenesis -0.012 0.089 -10000 0 -0.2 27 27
MMP2 -0.033 0.13 -10000 0 -0.34 26 26
IL8 -0.007 0.11 -10000 0 -0.34 16 16
calcineurin-NFAT signaling pathway -0.009 0.084 -10000 0 -0.2 25 25
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.013 0.11 -9999 0 -0.34 18 18
Syndecan-3/Src/Cortactin -0.06 0.21 -9999 0 -0.51 25 25
Syndecan-3/Neurocan -0.047 0.18 -9999 0 -0.48 25 25
POMC -0.036 0.13 -9999 0 -0.34 27 27
EGFR 0.021 0.011 -9999 0 -10000 0 0
Syndecan-3/EGFR -0.05 0.18 -9999 0 -0.49 25 25
AGRP 0.03 0.008 -9999 0 -10000 0 0
NCSTN 0.032 0.004 -9999 0 -10000 0 0
PSENEN 0.029 0.009 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.031 0.006 -9999 0 -10000 0 0
APH1A 0.032 0.004 -9999 0 -10000 0 0
NCAN 0.023 0.01 -9999 0 -10000 0 0
long-term memory -0.049 0.2 -9999 0 -0.51 24 24
Syndecan-3/IL8 -0.06 0.19 -9999 0 -0.51 24 24
PSEN1 0.032 0.005 -9999 0 -10000 0 0
Src/Cortactin -0.017 0.12 -9999 0 -0.24 34 34
FYN 0.026 0.049 -9999 0 -0.34 3 3
limb bud formation -0.063 0.18 -9999 0 -0.5 25 25
MC4R 0.022 0.008 -9999 0 -10000 0 0
SRC -0.007 0.11 -9999 0 -0.34 17 17
PTN 0.017 0.009 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-3 -0.064 0.19 -9999 0 -0.5 25 25
neuron projection morphogenesis -0.075 0.19 -9999 0 -0.51 24 24
Syndecan-3/AgRP -0.045 0.19 -9999 0 -0.49 25 25
Syndecan-3/AgRP/MC4R -0.033 0.19 -9999 0 -0.48 25 25
Fyn/Cortactin 0.007 0.093 -9999 0 -0.24 21 21
SDC3 -0.065 0.19 -9999 0 -0.51 25 25
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.058 0.19 -9999 0 -0.5 24 24
IL8 -0.007 0.11 -9999 0 -0.34 16 16
Syndecan-3/Fyn/Cortactin -0.05 0.2 -9999 0 -0.53 24 24
Syndecan-3/CASK -0.062 0.18 -9999 0 -0.48 25 25
alpha-MSH/MC4R -0.011 0.1 -9999 0 -0.24 27 27
Gamma Secretase 0.086 0.031 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.039 0.092 -10000 0 -0.23 31 31
GNB1/GNG2 -0.01 0.11 -10000 0 -0.2 38 38
regulation of S phase of mitotic cell cycle -0.036 0.097 -10000 0 -0.18 47 47
GNAO1 0.026 0.041 -10000 0 -0.34 2 2
HRAS 0.03 0.008 -10000 0 -10000 0 0
SHBG/T-DHT 0.015 0.007 -10000 0 -10000 0 0
PELP1 0.029 0.01 -10000 0 -10000 0 0
AKT1 0.008 0.001 -10000 0 -10000 0 0
MAP2K1 -0.03 0.097 0.21 11 -0.4 1 12
T-DHT/AR -0.033 0.095 -10000 0 -0.23 31 31
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.006 7 7
GNAI2 0.031 0.007 -10000 0 -10000 0 0
GNAI3 0.032 0.004 -10000 0 -10000 0 0
GNAI1 -0.021 0.12 -10000 0 -0.34 21 21
mol:GDP -0.07 0.13 -10000 0 -0.3 36 36
cell proliferation -0.028 0.14 0.34 6 -0.37 10 16
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
FOS -0.021 0.17 0.43 2 -0.73 7 9
mol:Ca2+ -0.01 0.021 -10000 0 -0.047 32 32
MAPK3 -0.031 0.12 0.31 5 -0.3 8 13
MAPK1 -0.011 0.11 0.27 3 -0.44 6 9
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 7 7
cAMP biosynthetic process 0.006 0.027 0.27 1 -10000 0 1
GNG2 0.003 0.099 -10000 0 -0.34 13 13
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 7 7
HRAS/GTP -0.012 0.094 -10000 0 -0.16 44 44
actin cytoskeleton reorganization 0.042 0.02 -10000 0 -10000 0 0
SRC -0.007 0.11 -10000 0 -0.34 17 17
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 7 7
PI3K 0.041 0.01 -10000 0 -10000 0 0
apoptosis 0.013 0.12 0.39 9 -0.31 4 13
T-DHT/AR/PELP1 -0.012 0.088 -10000 0 -0.19 31 31
HRAS/GDP -0.051 0.13 -10000 0 -0.29 36 36
CREB1 -0.015 0.13 0.32 4 -0.42 9 13
RAC1-CDC42/GTP 0.052 0.025 -10000 0 -10000 0 0
AR -0.049 0.14 -10000 0 -0.34 31 31
GNB1 0.03 0.008 -10000 0 -10000 0 0
RAF1 -0.021 0.1 0.22 11 -0.16 33 44
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.29 34 34
T-DHT/AR/PELP1/Src -0.018 0.1 -10000 0 -0.18 46 46
MAP2K2 -0.036 0.082 0.17 7 -0.4 1 8
T-DHT/AR/PELP1/Src/PI3K -0.036 0.098 -10000 0 -0.18 47 47
GNAZ 0.013 0.069 -10000 0 -0.34 6 6
SHBG 0.022 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.046 0.13 -10000 0 -0.35 18 18
mol:T-DHT 0 0 -10000 0 -0.002 5 5
RAC1 0.028 0.011 -10000 0 -10000 0 0
GNRH1 0.007 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.034 0.079 -10000 0 -0.17 30 30
CDC42 0.031 0.006 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.16 0.34 -10000 0 -0.9 16 16
IL23A -0.19 0.39 -10000 0 -0.89 27 27
NF kappa B1 p50/RelA/I kappa B alpha -0.14 0.35 -10000 0 -0.82 21 21
positive regulation of T cell mediated cytotoxicity -0.18 0.37 -10000 0 -0.89 22 22
ITGA3 -0.17 0.36 -10000 0 -0.88 21 21
IL17F -0.12 0.25 0.44 1 -0.57 22 23
IL12B -0.003 0.047 -10000 0 -10000 0 0
STAT1 (dimer) -0.17 0.36 -10000 0 -0.86 22 22
CD4 -0.19 0.38 -10000 0 -0.95 23 23
IL23 -0.19 0.37 -10000 0 -0.87 27 27
IL23R -0.009 0.093 -10000 0 -0.69 1 1
IL1B -0.2 0.4 -10000 0 -0.95 27 27
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.19 0.39 -10000 0 -0.98 22 22
TYK2 0.005 0.041 -10000 0 -10000 0 0
STAT4 0.009 0.088 -10000 0 -0.34 10 10
STAT3 0.03 0.009 -10000 0 -10000 0 0
IL18RAP 0.016 0.069 -10000 0 -0.34 6 6
IL12RB1 -0.026 0.11 -10000 0 -0.35 14 14
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.013 0.086 -10000 0 -0.24 14 14
IL23R/JAK2 -0.009 0.11 -10000 0 -0.54 1 1
positive regulation of chronic inflammatory response -0.18 0.37 -10000 0 -0.89 22 22
natural killer cell activation 0.002 0.007 -10000 0 -10000 0 0
JAK2 0.005 0.049 -10000 0 -10000 0 0
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
NFKB1 0.031 0.006 -10000 0 -10000 0 0
RELA 0.03 0.008 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.18 0.36 -10000 0 -0.83 27 27
ALOX12B -0.16 0.33 -10000 0 -0.86 17 17
CXCL1 -0.21 0.42 -10000 0 -1 26 26
T cell proliferation -0.18 0.37 -10000 0 -0.89 22 22
NFKBIA 0.031 0.006 -10000 0 -10000 0 0
IL17A -0.077 0.21 0.38 1 -0.48 15 16
PI3K -0.16 0.35 -10000 0 -0.83 22 22
IFNG -0.004 0.029 -10000 0 -0.12 5 5
STAT3 (dimer) -0.15 0.34 -10000 0 -0.8 22 22
IL18R1 0.006 0.092 -10000 0 -0.34 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 -0.1 0.24 0.5 1 -0.54 18 19
IL18/IL18R 0.034 0.088 -10000 0 -0.22 16 16
macrophage activation -0.012 0.018 -10000 0 -0.04 29 29
TNF -0.2 0.42 -10000 0 -1 23 23
STAT3/STAT4 -0.17 0.35 -10000 0 -0.84 22 22
STAT4 (dimer) -0.18 0.36 -10000 0 -0.87 22 22
IL18 0.028 0.03 -10000 0 -0.33 1 1
IL19 -0.16 0.33 -10000 0 -0.85 18 18
STAT5A (dimer) -0.17 0.36 -10000 0 -0.85 22 22
STAT1 0.032 0 -10000 0 -10000 0 0
SOCS3 0.023 0.05 -10000 0 -0.34 3 3
CXCL9 -0.19 0.38 -10000 0 -0.95 21 21
MPO -0.32 0.5 0.56 1 -0.99 51 52
positive regulation of humoral immune response -0.18 0.37 -10000 0 -0.89 22 22
IL23/IL23R/JAK2/TYK2 -0.18 0.38 -10000 0 -0.92 22 22
IL6 -0.16 0.34 -10000 0 -0.83 21 21
STAT5A 0.03 0.009 -10000 0 -10000 0 0
IL2 0.01 0.022 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.007 -10000 0 -10000 0 0
CD3E -0.16 0.35 -10000 0 -0.83 23 23
keratinocyte proliferation -0.18 0.37 -10000 0 -0.89 22 22
NOS2 -0.16 0.33 0.56 1 -0.87 16 17
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.009 0.11 -10000 0 -0.34 16 16
mol:S1P 0 0.005 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.017 0.081 -10000 0 -0.18 30 30
GNAO1 0.024 0.043 -10000 0 -0.34 2 2
S1P/S1P3/G12/G13 0.005 0.09 -10000 0 -0.18 30 30
AKT1 -0.053 0.18 -10000 0 -0.48 21 21
AKT3 -0.068 0.26 -10000 0 -0.85 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.009 0.11 -10000 0 -0.34 16 16
GNAI2 0.029 0.017 -10000 0 -10000 0 0
GNAI3 0.03 0.014 -10000 0 -10000 0 0
GNAI1 -0.023 0.12 -10000 0 -0.34 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.047 0.15 -10000 0 -0.34 33 33
S1PR2 0.025 0.041 -10000 0 -0.34 2 2
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.051 0.13 -10000 0 -0.25 35 35
MAPK3 -0.053 0.12 -10000 0 -0.24 35 35
MAPK1 -0.049 0.12 -10000 0 -0.24 32 32
JAK2 -0.06 0.13 0.2 1 -0.32 25 26
CXCR4 -0.055 0.13 -10000 0 -0.26 33 33
FLT1 0.012 0.076 -10000 0 -0.34 7 7
RhoA/GDP 0.023 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
SRC -0.069 0.14 -10000 0 -0.27 40 40
S1P/S1P3/Gi -0.052 0.13 -10000 0 -0.26 35 35
RAC1 0.028 0.011 -10000 0 -10000 0 0
RhoA/GTP -0.042 0.13 -10000 0 -0.31 19 19
VEGFA 0.009 0.085 -10000 0 -0.34 9 9
S1P/S1P2/Gi -0.013 0.084 -10000 0 -0.17 29 29
VEGFR1 homodimer/VEGFA homodimer 0.019 0.087 -10000 0 -0.24 15 15
RHOA 0.031 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.038 0.12 -10000 0 -0.22 43 43
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.011 0.07 -10000 0 -0.34 6 6
G12/G13 0.039 0.019 -10000 0 -10000 0 0
GNA14 0.008 0.083 -10000 0 -0.34 9 9
GNA15 0.027 0.03 -10000 0 -0.34 1 1
GNA12 0.028 0.011 -10000 0 -10000 0 0
GNA13 0.03 0.008 -10000 0 -10000 0 0
GNA11 0.005 0.092 -10000 0 -0.34 11 11
Rac1/GTP -0.041 0.13 -10000 0 -0.31 19 19
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.012 0.11 -10000 0 -0.35 16 16
PDGF/PDGFRA/CRKL 0.012 0.08 -10000 0 -0.23 15 15
positive regulation of JUN kinase activity 0.046 0.076 -10000 0 -0.18 16 16
CRKL 0.029 0.009 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.009 0.082 -10000 0 -0.23 16 16
AP1 -0.054 0.17 0.31 1 -0.77 7 8
mol:IP3 -0.021 0.088 0.12 1 -0.24 21 22
PLCG1 -0.021 0.088 0.12 1 -0.24 21 22
PDGF/PDGFRA/alphaV Integrin -0.008 0.11 -10000 0 -0.25 28 28
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
CRK 0.029 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.088 0.12 1 -0.24 21 22
CAV3 0.025 0.009 -10000 0 -10000 0 0
CAV1 -0.012 0.11 -10000 0 -0.34 16 16
SHC/Grb2/SOS1 0.048 0.077 -10000 0 -0.18 16 16
PDGF/PDGFRA/Shf 0.01 0.087 -10000 0 -0.23 18 18
FOS -0.055 0.17 0.32 2 -0.76 7 9
JUN -0.035 0.056 -10000 0 -0.25 9 9
oligodendrocyte development -0.008 0.11 -10000 0 -0.25 28 28
GRB2 0.03 0.008 -10000 0 -10000 0 0
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
mol:DAG -0.021 0.088 0.12 1 -0.24 21 22
PDGF/PDGFRA -0.012 0.11 -10000 0 -0.34 16 16
actin cytoskeleton reorganization 0.01 0.087 -10000 0 -0.23 18 18
SRF 0.014 0.012 -10000 0 -10000 0 0
SHC1 0.032 0.004 -10000 0 -10000 0 0
PI3K 0.033 0.076 -10000 0 -0.19 16 16
PDGF/PDGFRA/Crk/C3G 0.031 0.074 -10000 0 -0.2 15 15
JAK1 -0.015 0.073 -10000 0 -0.23 16 16
ELK1/SRF -0.025 0.081 0.19 8 -0.2 21 29
SHB 0.025 0.049 -10000 0 -0.34 3 3
SHF 0.027 0.041 -10000 0 -0.34 2 2
CSNK2A1 0.031 0.021 -10000 0 -10000 0 0
GO:0007205 -0.03 0.094 0.12 1 -0.27 21 22
SOS1 0.032 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.046 0.076 -10000 0 -0.18 16 16
PDGF/PDGFRA/SHB 0.01 0.087 -10000 0 -0.24 18 18
PDGF/PDGFRA/Caveolin-1 -0.017 0.11 -10000 0 -0.24 30 30
ITGAV -0.001 0.11 -10000 0 -0.34 15 15
ELK1 -0.025 0.097 0.24 7 -0.24 21 28
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.011 0.082 -10000 0 -0.23 16 16
JAK-STAT cascade -0.015 0.073 -10000 0 -0.23 16 16
cell proliferation 0.01 0.087 -10000 0 -0.23 18 18
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.031 0.006 -10000 0 -10000 0 0
HDAC3 0.029 0.009 -10000 0 -10000 0 0
VDR -0.001 0.1 -10000 0 -0.34 14 14
Cbp/p300/PCAF 0.058 0.021 -10000 0 -10000 0 0
EP300 0.03 0.009 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.013 0.079 0.17 4 -0.37 4 8
KAT2B 0.031 0.007 -10000 0 -10000 0 0
MAPK14 0.032 0.003 -10000 0 -10000 0 0
AKT1 -0.003 0.065 0.18 3 -0.24 4 7
RAR alpha/9cRA/Cyclin H -0.013 0.13 0.22 3 -0.23 37 40
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.003 0.092 0.16 2 -0.34 7 9
CDC2 -0.001 0.005 -10000 0 -10000 0 0
response to UV -0.002 0.008 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.013 0.087 0.16 1 -0.17 30 31
NCOR2 0.032 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.001 0.071 -10000 0 -0.23 14 14
RXRs/RARs/NRIP1/9cRA -0.076 0.21 0.33 2 -0.42 42 44
NCOA2 0.026 0.03 -10000 0 -0.34 1 1
NCOA3 0.031 0.006 -10000 0 -10000 0 0
NCOA1 0.032 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA -0.001 0.1 -10000 0 -0.34 14 14
RARG 0.025 0.033 -10000 0 -0.34 1 1
RAR gamma1/9cRA 0.037 0.023 -10000 0 -0.2 1 1
MAPK3 0.027 0.018 -10000 0 -10000 0 0
MAPK1 0.029 0.009 -10000 0 -10000 0 0
MAPK8 0.026 0.02 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.073 0.18 -10000 0 -0.34 45 45
RARA -0.015 0.073 -10000 0 -0.19 22 22
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.002 0.091 0.16 2 -0.37 6 8
PRKCA -0.025 0.12 -10000 0 -0.23 36 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.085 0.23 0.27 3 -0.43 45 48
RXRG -0.027 0.093 -10000 0 -0.19 36 36
RXRA -0.026 0.089 -10000 0 -0.18 39 39
RXRB -0.022 0.092 -10000 0 -0.25 22 22
VDR/Vit D3/DNA 0.001 0.071 -10000 0 -0.23 14 14
RBP1 0.028 0.009 -10000 0 -10000 0 0
CRBP1/9-cic-RA 0.021 0.007 -10000 0 -10000 0 0
RARB 0.023 0.035 -10000 0 -0.34 1 1
PRKCG 0.016 0.028 -10000 0 -0.073 1 1
MNAT1 0.032 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.067 0.18 -10000 0 -0.36 40 40
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.037 0.15 0.26 3 -0.28 38 41
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.12 0.2 5 -0.38 10 15
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.089 0.23 0.25 3 -0.44 45 48
positive regulation of DNA binding -0.022 0.12 -10000 0 -0.22 37 37
NRIP1 -0.12 0.34 0.32 2 -0.82 25 27
RXRs/RARs -0.07 0.19 0.25 1 -0.38 42 43
RXRs/RXRs/DNA/9cRA -0.073 0.16 -10000 0 -0.32 46 46
PRKACA 0.029 0.009 -10000 0 -10000 0 0
CDK7 0.031 0.007 -10000 0 -10000 0 0
TFIIH 0.06 0.019 -10000 0 -10000 0 0
RAR alpha/9cRA 0.023 0.09 0.18 1 -0.17 14 15
CCNH 0.03 0.008 -10000 0 -10000 0 0
CREBBP 0.031 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.055 0.028 -10000 0 -0.16 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.014 0.16 0.3 8 -0.38 16 24
FYN 0.002 0.18 0.32 10 -0.43 16 26
LAT/GRAP2/SLP76 -0.008 0.16 0.22 3 -0.42 16 19
IKBKB 0.029 0.01 -10000 0 -10000 0 0
AKT1 0.004 0.15 0.3 12 -0.33 17 29
B2M 0.03 0.013 -10000 0 -10000 0 0
IKBKG -0.001 0.045 0.089 7 -0.12 12 19
MAP3K8 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.013 -10000 0 -0.05 7 7
integrin-mediated signaling pathway 0.041 0.02 -10000 0 -0.19 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.006 0.2 0.34 12 -0.47 17 29
TRPV6 0.03 0.21 1.2 5 -10000 0 5
CD28 0.008 0.088 -10000 0 -0.34 10 10
SHC1 -0.012 0.18 0.28 8 -0.44 17 25
receptor internalization -0.022 0.18 0.26 1 -0.44 20 21
PRF1 -0.022 0.25 0.34 1 -0.78 13 14
KRAS 0.031 0.006 -10000 0 -10000 0 0
GRB2 0.03 0.008 -10000 0 -10000 0 0
COT/AKT1 0.016 0.12 0.26 11 -0.27 17 28
LAT -0.014 0.18 0.29 7 -0.45 17 24
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D 0 0.097 -10000 0 -0.34 12 12
CD3E 0.021 0.052 -10000 0 -0.35 3 3
CD3G 0 0.096 -10000 0 -0.34 12 12
RASGRP2 0.005 0.015 -10000 0 -10000 0 0
RASGRP1 0.01 0.16 0.33 14 -0.34 16 30
HLA-A 0.032 0.013 -10000 0 -10000 0 0
RASSF5 0.029 0.029 -10000 0 -0.34 1 1
RAP1A/GTP/RAPL 0.041 0.02 -10000 0 -0.2 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.03 0.082 0.2 17 -0.11 5 22
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.018 0.064 -10000 0 -0.18 18 18
PRKCA -0.014 0.091 0.16 7 -0.23 17 24
GRAP2 0.006 0.087 -10000 0 -0.34 10 10
mol:IP3 -0.023 0.12 0.18 2 -0.32 17 19
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.019 0.15 0.15 1 -0.44 15 16
ORAI1 -0.027 0.18 -10000 0 -1 5 5
CSK -0.008 0.18 0.31 8 -0.45 17 25
B7 family/CD28 -0.022 0.19 0.31 5 -0.43 20 25
CHUK 0.032 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.027 0.19 0.28 2 -0.47 19 21
PTPN6 -0.014 0.17 0.26 8 -0.45 16 24
VAV1 -0.014 0.18 0.28 9 -0.44 17 26
Monovalent TCR/CD3 -0.021 0.12 -10000 0 -0.29 23 23
CBL 0.03 0.008 -10000 0 -10000 0 0
LCK -0.005 0.18 0.31 6 -0.44 16 22
PAG1 -0.007 0.19 0.24 13 -0.46 17 30
RAP1A 0.032 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.03 0.18 -10000 0 -0.48 17 17
CD80 0.02 0.057 -10000 0 -0.34 4 4
CD86 -0.036 0.14 -10000 0 -0.34 29 29
PDK1/CARD11/BCL10/MALT1 -0.012 0.081 -10000 0 -0.22 18 18
HRAS 0.03 0.008 -10000 0 -10000 0 0
GO:0035030 -0.036 0.16 0.29 6 -0.37 20 26
CD8A 0.023 0.052 -10000 0 -0.34 3 3
CD8B 0.012 0.082 -10000 0 -0.34 8 8
PTPRC 0.032 0.006 -10000 0 -10000 0 0
PDK1/PKC theta -0.002 0.18 0.34 12 -0.4 17 29
CSK/PAG1 -0.002 0.19 0.29 11 -0.44 17 28
SOS1 0.032 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.045 0.02 -10000 0 -10000 0 0
GRAP2/SLP76 -0.005 0.18 0.24 2 -0.46 17 19
STIM1 0.036 0.22 1.2 6 -10000 0 6
RAS family/GTP 0.03 0.096 0.26 12 -0.15 8 20
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.025 0.19 0.26 1 -0.46 20 21
mol:DAG -0.031 0.098 -10000 0 -0.28 18 18
RAP1A/GDP 0.016 0.033 0.09 13 -0.053 4 17
PLCG1 0.019 0.063 -10000 0 -0.34 5 5
CD247 0.016 0.07 -10000 0 -0.34 6 6
cytotoxic T cell degranulation -0.019 0.24 0.34 1 -0.74 13 14
RAP1A/GTP 0.002 0.007 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.001 0.17 0.32 12 -0.39 17 29
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.019 0.15 0.2 2 -0.4 17 19
NRAS 0.032 0.005 -10000 0 -10000 0 0
ZAP70 0.014 0.079 -10000 0 -0.34 8 8
GRB2/SOS1 0.045 0.012 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.018 0.15 0.29 2 -0.4 16 18
MALT1 0.032 0.005 -10000 0 -10000 0 0
TRAF6 0.031 0.007 -10000 0 -10000 0 0
CD8 heterodimer 0.027 0.077 -10000 0 -0.26 10 10
CARD11 0.007 0.083 -10000 0 -0.34 9 9
PRKCB -0.004 0.087 0.16 9 -0.22 15 24
PRKCE -0.005 0.087 0.16 9 -0.22 15 24
PRKCQ -0.005 0.2 0.34 13 -0.44 18 31
LCP2 0.031 0.007 -10000 0 -10000 0 0
BCL10 0.032 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.009 0.13 0.29 12 -0.28 17 29
IKK complex 0.019 0.09 0.22 17 -0.1 8 25
RAS family/GDP 0 0.011 -10000 0 -0.035 1 1
MAP3K14 0.003 0.092 0.21 7 -0.21 17 24
PDPK1 0.003 0.14 0.3 12 -0.32 17 29
TCR/CD3/MHC I/CD8/Fyn -0.02 0.2 0.28 1 -0.51 17 18
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.045 0.15 0.24 1 -0.31 31 32
PDGFB-D/PDGFRB/SLAP 0.004 0.09 -10000 0 -0.23 20 20
PDGFB-D/PDGFRB/APS/CBL 0.031 0.073 -10000 0 -0.21 12 12
AKT1 -0.029 0.09 0.27 4 -0.27 5 9
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.049 0.16 0.21 1 -0.35 31 32
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
FGR -0.098 0.21 -10000 0 -0.5 31 31
mol:Ca2+ -0.064 0.17 -10000 0 -0.38 33 33
MYC -0.017 0.17 0.31 5 -0.5 9 14
SHC1 0.032 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.014 0.058 -10000 0 -0.16 15 15
LRP1/PDGFRB/PDGFB -0.041 0.15 -10000 0 -0.24 51 51
GRB10 0.006 0.087 -10000 0 -0.34 10 10
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GO:0007205 -0.065 0.17 -10000 0 -0.38 33 33
PTEN 0.031 0.006 -10000 0 -10000 0 0
GRB2 0.03 0.008 -10000 0 -10000 0 0
GRB7 0.018 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.015 0.083 -10000 0 -0.23 16 16
PDGFB-D/PDGFRB/GRB10 -0.002 0.1 -10000 0 -0.25 23 23
cell cycle arrest 0.004 0.09 -10000 0 -0.23 20 20
HRAS 0.03 0.008 -10000 0 -10000 0 0
HIF1A -0.031 0.082 0.25 4 -0.25 5 9
GAB1 -0.053 0.16 0.27 1 -0.38 24 25
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.047 0.14 0.27 3 -0.35 21 24
PDGFB-D/PDGFRB 0.032 0.081 -10000 0 -0.2 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.015 0.081 -10000 0 -0.24 15 15
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.034 0.13 0.2 1 -0.32 21 22
positive regulation of MAPKKK cascade 0.015 0.082 -10000 0 -0.23 16 16
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
mol:IP3 -0.066 0.18 -10000 0 -0.38 33 33
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.031 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.008 0.078 -10000 0 -0.24 15 15
SHB 0.025 0.049 -10000 0 -0.34 3 3
BLK -0.033 0.13 -10000 0 -0.43 11 11
PTPN2 0.031 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.014 0.083 -10000 0 -0.24 16 16
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
VAV2 -0.057 0.17 0.3 1 -0.4 23 24
CBL 0.03 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.01 0.12 -10000 0 -0.26 28 28
LCK -0.025 0.12 -10000 0 -0.47 7 7
PDGFRB -0.009 0.11 -10000 0 -0.34 16 16
ACP1 0.031 0.006 -10000 0 -10000 0 0
HCK -0.05 0.17 -10000 0 -0.49 16 16
ABL1 -0.053 0.15 0.2 1 -0.34 24 25
PDGFB-D/PDGFRB/CBL -0.066 0.18 0.26 1 -0.44 26 27
PTPN1 0.031 0.006 -10000 0 -10000 0 0
SNX15 0.031 0.007 -10000 0 -10000 0 0
STAT3 0.03 0.009 -10000 0 -10000 0 0
STAT1 0.032 0 -10000 0 -10000 0 0
cell proliferation -0.013 0.16 0.28 9 -0.45 9 18
SLA 0.014 0.069 -10000 0 -0.34 6 6
actin cytoskeleton reorganization -0.009 0.078 0.21 1 -0.18 23 24
SRC -0.078 0.21 -10000 0 -0.57 22 22
PI3K -0.027 0.076 -10000 0 -0.19 27 27
PDGFB-D/PDGFRB/GRB7/SHC 0.026 0.073 -10000 0 -0.2 15 15
SH2B2 0.025 0.03 -10000 0 -0.34 1 1
PLCgamma1/SPHK1 -0.05 0.17 0.22 1 -0.36 31 32
LYN -0.011 0.073 -10000 0 -0.26 2 2
LRP1 -0.065 0.16 -10000 0 -0.34 42 42
SOS1 0.032 0.003 -10000 0 -10000 0 0
STAT5B 0.03 0.009 -10000 0 -10000 0 0
STAT5A 0.03 0.009 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.046 0.098 -10000 0 -0.17 25 25
SPHK1 0.023 0.05 -10000 0 -0.34 3 3
EDG1 -0.001 0.003 -10000 0 -10000 0 0
mol:DAG -0.066 0.18 -10000 0 -0.38 33 33
PLCG1 -0.067 0.18 -10000 0 -0.39 33 33
NHERF/PDGFRB 0.006 0.11 -10000 0 -0.22 29 29
YES1 -0.062 0.18 -10000 0 -0.53 18 18
cell migration 0.006 0.11 -10000 0 -0.22 29 29
SHC/Grb2/SOS1 0.062 0.08 -10000 0 -0.17 15 15
SLC9A3R2 -0.014 0.12 -10000 0 -0.34 20 20
SLC9A3R1 0.03 0.008 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.021 0.11 -10000 0 -0.2 29 29
FYN -0.017 0.091 -10000 0 -0.37 5 5
DOK1 -0.006 0.06 -10000 0 -0.18 16 16
HRAS/GTP 0.022 0.006 -10000 0 -10000 0 0
PDGFB 0.003 0.091 -10000 0 -0.34 11 11
RAC1 -0.048 0.17 0.3 1 -0.41 20 21
PRKCD -0.011 0.068 -10000 0 -0.19 19 19
FER -0.012 0.072 -10000 0 -0.2 19 19
MAPKKK cascade -0.023 0.057 0.19 4 -0.18 3 7
RASA1 -0.006 0.06 -10000 0 -0.18 16 16
NCK1 0.031 0.006 -10000 0 -10000 0 0
NCK2 0.032 0 -10000 0 -10000 0 0
p62DOK/Csk 0.016 0.062 -10000 0 -0.17 16 16
PDGFB-D/PDGFRB/SHB 0.01 0.089 -10000 0 -0.23 19 19
chemotaxis -0.052 0.14 0.2 1 -0.33 24 25
STAT1-3-5/STAT1-3-5 0.05 0.072 -10000 0 -0.17 13 13
Bovine Papilomavirus E5/PDGFRB -0.005 0.075 -10000 0 -0.23 16 16
PTPRJ -0.003 0.11 -10000 0 -0.34 15 15
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.024 0.13 -10000 0 -0.33 15 15
TBX21 -0.13 0.37 0.48 1 -0.86 26 27
B2M 0.029 0.019 -10000 0 -10000 0 0
TYK2 0.012 0.04 -10000 0 -10000 0 0
IL12RB1 -0.017 0.11 -10000 0 -0.36 14 14
GADD45B -0.079 0.29 0.44 1 -0.67 20 21
IL12RB2 0.007 0.046 -10000 0 -0.33 1 1
GADD45G -0.085 0.29 -10000 0 -0.64 23 23
natural killer cell activation -0.004 0.022 -10000 0 -10000 0 0
RELB 0.029 0.01 -10000 0 -10000 0 0
RELA 0.031 0.007 -10000 0 -10000 0 0
IL18 0.026 0.033 -10000 0 -0.32 1 1
IL2RA 0.001 0.095 -10000 0 -0.34 12 12
IFNG 0.022 0.05 -10000 0 -0.34 3 3
STAT3 (dimer) -0.099 0.29 -10000 0 -0.62 30 30
HLA-DRB5 -0.03 0.13 -10000 0 -0.34 25 25
FASLG -0.17 0.43 0.54 1 -0.97 31 32
NF kappa B2 p52/RelB -0.12 0.34 -10000 0 -0.75 30 30
CD4 0.011 0.08 -10000 0 -0.34 8 8
SOCS1 0.017 0.069 -10000 0 -0.34 6 6
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D -0.001 0.098 -10000 0 -0.34 12 12
CD3E 0.019 0.055 -10000 0 -0.21 6 6
CD3G -0.002 0.097 -10000 0 -0.34 12 12
IL12Rbeta2/JAK2 0.021 0.058 -10000 0 -0.23 1 1
CCL3 -0.15 0.41 0.48 1 -0.89 32 33
CCL4 -0.14 0.39 0.48 1 -0.88 28 29
HLA-A 0.029 0.018 -10000 0 -10000 0 0
IL18/IL18R 0.039 0.1 -10000 0 -0.23 16 16
NOS2 -0.1 0.31 -10000 0 -0.69 26 26
IL12/IL12R/TYK2/JAK2/SPHK2 -0.017 0.12 -10000 0 -0.33 11 11
IL1R1 -0.2 0.46 -10000 0 -0.99 36 36
IL4 0.007 0.038 -10000 0 -10000 0 0
JAK2 0.014 0.041 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.056 0.29 -10000 0 -0.87 15 15
RAB7A -0.059 0.26 -10000 0 -0.59 18 18
lysosomal transport -0.055 0.26 -10000 0 -0.56 18 18
FOS -0.088 0.31 -10000 0 -0.89 15 15
STAT4 (dimer) -0.1 0.33 0.64 1 -0.67 30 31
STAT5A (dimer) -0.12 0.34 -10000 0 -0.75 30 30
GZMA -0.15 0.4 -10000 0 -0.91 29 29
GZMB -0.17 0.43 0.52 1 -0.97 31 32
HLX 0.012 0.084 -10000 0 -0.34 9 9
LCK -0.14 0.36 -10000 0 -0.8 31 31
TCR/CD3/MHC II/CD4 -0.07 0.2 -10000 0 -0.4 32 32
IL2/IL2R 0.035 0.079 -10000 0 -0.18 18 18
MAPK14 -0.08 0.3 0.43 1 -0.67 22 23
CCR5 -0.13 0.39 -10000 0 -0.97 23 23
IL1B -0.007 0.095 -10000 0 -0.35 10 10
STAT6 -0.017 0.13 -10000 0 -1 1 1
STAT4 0.009 0.088 -10000 0 -0.34 10 10
STAT3 0.03 0.009 -10000 0 -10000 0 0
STAT1 0.032 0 -10000 0 -10000 0 0
NFKB1 0.031 0.006 -10000 0 -10000 0 0
NFKB2 0.029 0.029 -10000 0 -0.34 1 1
IL12B 0.004 0.039 -10000 0 -10000 0 0
CD8A 0.022 0.054 -10000 0 -0.24 5 5
CD8B 0.01 0.082 -10000 0 -0.34 8 8
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.024 0.12 0.32 15 -10000 0 15
IL2RB 0.022 0.05 -10000 0 -0.34 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.09 0.31 0.51 2 -0.62 30 32
IL2RG 0.023 0.05 -10000 0 -0.34 3 3
IL12 0.007 0.07 -10000 0 -0.19 7 7
STAT5A 0.03 0.009 -10000 0 -10000 0 0
CD247 0.013 0.072 -10000 0 -0.34 6 6
IL2 0.019 0.006 -10000 0 -10000 0 0
SPHK2 0.029 0.01 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0 0.077 -10000 0 -0.34 6 6
IL12/IL12R/TYK2/JAK2 -0.14 0.38 -10000 0 -0.82 32 32
MAP2K3 -0.086 0.31 0.42 1 -0.66 23 24
RIPK2 0.028 0.011 -10000 0 -10000 0 0
MAP2K6 -0.085 0.31 0.42 1 -0.66 23 24
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.018 0.12 -10000 0 -0.34 22 22
IL18RAP 0.013 0.072 -10000 0 -0.34 6 6
IL12Rbeta1/TYK2 0 0.095 -10000 0 -0.26 14 14
EOMES -0.043 0.26 -10000 0 -0.92 12 12
STAT1 (dimer) -0.083 0.3 -10000 0 -0.62 29 29
T cell proliferation -0.06 0.26 0.51 3 -0.52 27 30
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.094 -10000 0 -0.34 11 11
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.088 0.27 -10000 0 -0.58 25 25
ATF2 -0.077 0.28 0.41 1 -0.62 22 23
Noncanonical Wnt signaling pathway

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
NFATC2 0.018 0.069 -10000 0 -0.34 6 6
GNB1/GNG2 -0.011 0.12 -10000 0 -0.32 9 9
mol:DAG -0.024 0.12 0.22 8 -0.37 8 16
PLCG1 -0.025 0.13 0.23 8 -0.38 8 16
YES1 -0.039 0.11 -10000 0 -0.21 34 34
FZD3 -0.004 0.098 -10000 0 -0.34 13 13
FZD6 0.011 0.069 -10000 0 -0.34 6 6
G protein -0.006 0.13 0.28 3 -0.36 7 10
MAP3K7 -0.031 0.12 0.25 7 -0.32 8 15
mol:Ca2+ -0.024 0.12 0.22 8 -0.36 8 16
mol:IP3 -0.024 0.12 0.22 8 -0.37 8 16
NLK -0.013 0.14 -10000 0 -0.67 7 7
GNB1 0.03 0.008 -10000 0 -10000 0 0
CAMK2A -0.029 0.12 0.28 6 -0.34 8 14
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.025 0.11 -10000 0 -0.2 37 37
CSNK1A1 0.029 0.009 -10000 0 -10000 0 0
GNAS -0.03 0.098 -10000 0 -0.2 34 34
GO:0007205 -0.019 0.16 0.34 11 -0.35 10 21
WNT6 -0.022 0.13 -10000 0 -0.34 23 23
WNT4 0.031 0.006 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.018 0.12 0.22 1 -0.35 9 10
GNG2 0.003 0.099 -10000 0 -0.34 13 13
WNT5A 0.022 0.01 -10000 0 -10000 0 0
WNT11 0.013 0.069 -10000 0 -0.34 6 6
CDC42 -0.038 0.1 0.19 1 -0.36 7 8
Cellular roles of Anthrax toxin

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
ANTXR1 -0.029 0.13 -10000 0 -0.34 26 26
ANTXR2 0.031 0.006 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.008 0.017 -10000 0 -0.047 26 26
monocyte activation -0.085 0.19 -10000 0 -0.4 41 41
MAP2K2 -0.015 0.13 -10000 0 -0.55 9 9
MAP2K1 -0.01 0.016 -10000 0 -10000 0 0
MAP2K7 -0.01 0.015 -10000 0 -10000 0 0
MAP2K6 -0.011 0.02 -10000 0 -0.16 1 1
CYAA -0.029 0.058 -10000 0 -0.16 26 26
MAP2K4 -0.01 0.016 -10000 0 -10000 0 0
IL1B -0.02 0.042 0.11 1 -0.14 14 15
Channel 0.004 0.078 -10000 0 -0.18 26 26
NLRP1 -0.016 0.032 -10000 0 -0.16 6 6
CALM1 0.032 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.007 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.008 0.017 0.047 26 -10000 0 26
MAPK3 -0.01 0.016 -10000 0 -10000 0 0
MAPK1 -0.01 0.015 -10000 0 -10000 0 0
PGR -0.012 0.016 -10000 0 -10000 0 0
PA/Cellular Receptors 0.003 0.086 -10000 0 -0.2 26 26
apoptosis -0.008 0.017 -10000 0 -0.047 26 26
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.075 -10000 0 -0.17 26 26
macrophage activation -0.004 0.041 0.17 8 -10000 0 8
TNF -0.002 0.098 -10000 0 -0.34 13 13
VCAM1 -0.086 0.19 -10000 0 -0.4 41 41
platelet activation 0.007 0.019 -10000 0 -10000 0 0
MAPKKK cascade 0.007 0.024 0.086 1 -0.09 4 5
IL18 -0.011 0.024 0.11 1 -10000 0 1
negative regulation of macrophage activation -0.008 0.017 -10000 0 -0.047 26 26
LEF -0.008 0.017 -10000 0 -0.047 26 26
CASP1 -0.01 0.023 -10000 0 -0.052 34 34
mol:cAMP 0.007 0.02 -10000 0 -10000 0 0
necrosis -0.008 0.017 -10000 0 -0.047 26 26
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.005 0.073 -10000 0 -0.16 26 26
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.039 0.017 -10000 0 -10000 0 0
CRKL -0.037 0.16 0.39 3 -0.45 11 14
mol:PIP3 -0.006 0.1 -10000 0 -0.76 3 3
AKT1 -0.006 0.09 0.24 2 -0.61 3 5
PTK2B 0.029 0.01 -10000 0 -10000 0 0
RAPGEF1 -0.032 0.16 0.38 5 -0.44 10 15
RANBP10 0.031 0.006 -10000 0 -10000 0 0
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.016 0.087 -10000 0 -0.2 22 22
MAP3K5 -0.028 0.15 0.34 4 -0.45 9 13
HGF/MET/CIN85/CBL/ENDOPHILINS 0.03 0.085 -10000 0 -0.18 20 20
AP1 0.013 0.079 0.14 1 -0.22 15 16
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.032 0.004 -10000 0 -10000 0 0
apoptosis -0.032 0.22 -10000 0 -0.72 15 15
STAT3 (dimer) -0.063 0.13 -10000 0 -0.37 16 16
GAB1/CRKL/SHP2/PI3K -0.013 0.16 0.37 3 -0.42 10 13
INPP5D 0.032 0.003 -10000 0 -10000 0 0
CBL/CRK -0.032 0.14 -10000 0 -0.46 9 9
PTPN11 0.032 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.019 0.063 -10000 0 -0.34 5 5
PTEN 0.031 0.006 -10000 0 -10000 0 0
ELK1 0.006 0.1 0.38 8 -10000 0 8
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.029 0.094 -10000 0 -0.23 22 22
PAK1 -0.002 0.088 0.23 1 -0.53 3 4
HGF/MET/RANBP10 0.016 0.087 -10000 0 -0.2 22 22
HRAS -0.045 0.15 -10000 0 -0.43 15 15
DOCK1 -0.077 0.18 0.42 5 -0.38 21 26
GAB1 -0.047 0.15 -10000 0 -0.47 11 11
CRK -0.046 0.14 -10000 0 -0.46 10 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.068 0.18 -10000 0 -0.41 34 34
JUN 0.008 0.088 -10000 0 -0.34 10 10
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.025 0.085 -10000 0 -0.18 33 33
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
cell morphogenesis -0.06 0.16 0.38 4 -0.39 17 21
GRB2/SHC -0.003 0.1 0.18 3 -0.16 42 45
FOS 0.016 0.074 -10000 0 -0.34 7 7
GLMN 0.007 0.015 0.09 5 -10000 0 5
cell motility 0.006 0.1 0.37 8 -10000 0 8
HGF/MET/MUC20 0.002 0.079 -10000 0 -0.2 22 22
cell migration -0.003 0.1 0.18 3 -0.16 42 45
GRB2 0.03 0.008 -10000 0 -10000 0 0
CBL 0.03 0.008 -10000 0 -10000 0 0
MET/RANBP10 0.038 0.018 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.044 0.12 -10000 0 -0.22 46 46
MET/MUC20 0.018 0.009 -10000 0 -10000 0 0
RAP1B -0.03 0.15 0.34 6 -0.42 10 16
RAP1A -0.03 0.15 0.43 5 -0.42 10 15
HGF/MET/RANBP9 0.017 0.088 -10000 0 -0.2 22 22
RAF1 -0.037 0.15 -10000 0 -0.41 15 15
STAT3 -0.06 0.13 -10000 0 -0.38 14 14
cell proliferation -0.074 0.17 0.34 2 -0.35 34 36
RPS6KB1 -0.006 0.058 -10000 0 -0.26 5 5
MAPK3 0.003 0.13 0.62 5 -10000 0 5
MAPK1 0.008 0.14 0.74 5 -10000 0 5
RANBP9 0.032 0.004 -10000 0 -10000 0 0
MAPK8 -0.01 0.14 0.37 4 -0.39 9 13
SRC -0.06 0.12 -10000 0 -0.23 40 40
PI3K -0.002 0.1 0.18 3 -0.16 43 46
MET/Glomulin 0.024 0.015 0.11 1 -10000 0 1
SOS1 0.032 0.003 -10000 0 -10000 0 0
MAP2K1 -0.042 0.14 -10000 0 -0.4 15 15
MET 0.025 0.012 -10000 0 -10000 0 0
MAP4K1 -0.029 0.16 0.35 4 -0.47 10 14
PTK2 -0.047 0.14 -10000 0 -0.34 31 31
MAP2K2 -0.035 0.14 0.34 1 -0.4 13 14
BAD -0.001 0.088 0.23 1 -0.53 3 4
MAP2K4 -0.025 0.14 0.32 4 -0.41 9 13
SHP2/GRB2/SOS1/GAB1 -0.031 0.13 -10000 0 -0.41 10 10
INPPL1 0.029 0.029 -10000 0 -0.34 1 1
PXN 0.027 0.04 -10000 0 -0.34 2 2
SH3KBP1 0.029 0.01 -10000 0 -10000 0 0
HGS -0.028 0.079 -10000 0 -0.17 34 34
PLCgamma1/PKC 0.015 0.044 -10000 0 -0.23 5 5
HGF -0.024 0.12 -10000 0 -0.34 22 22
RASA1 0.03 0.008 -10000 0 -10000 0 0
NCK1 0.031 0.006 -10000 0 -10000 0 0
PTPRJ -0.003 0.11 -10000 0 -0.34 15 15
NCK/PLCgamma1 -0.014 0.11 0.18 2 -0.18 48 50
PDPK1 -0.008 0.098 0.26 1 -0.7 3 4
HGF/MET/SHIP 0.017 0.088 -10000 0 -0.2 22 22
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.033 0.049 -10000 0 -0.24 5 5
PRKCZ -0.025 0.13 -10000 0 -0.34 25 25
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.031 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.017 0.055 -10000 0 -0.19 6 6
IRAK/TOLLIP 0.027 0.041 0.18 1 -0.18 5 6
IKBKB 0.029 0.01 -10000 0 -10000 0 0
IKBKG 0.029 0.01 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.004 0.093 -10000 0 -0.23 22 22
IL1A 0.019 0.063 -10000 0 -0.34 5 5
IL1B -0.003 0.068 -10000 0 -0.25 11 11
IRAK/TRAF6/p62/Atypical PKCs 0.028 0.092 0.2 1 -0.16 27 28
IL1R2 -0.014 0.11 -10000 0 -0.34 17 17
IL1R1 -0.017 0.12 -10000 0 -0.34 21 21
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.082 -10000 0 -0.21 19 19
TOLLIP 0.031 0.007 -10000 0 -10000 0 0
TICAM2 0.002 0.095 -10000 0 -0.34 12 12
MAP3K3 0.03 0.008 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.014 0.056 -10000 0 -0.3 1 1
JUN -0.024 0.047 0.15 3 -10000 0 3
MAP3K7 0.032 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.032 0.11 -10000 0 -0.18 32 32
IL1 alpha/IL1R1/IL1RAP/MYD88 0.035 0.1 -10000 0 -0.19 25 25
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.1 -10000 0 -0.18 25 25
IL1 beta fragment/IL1R1/IL1RAP 0.002 0.096 -10000 0 -0.19 32 32
NFKB1 0.031 0.006 -10000 0 -10000 0 0
MAPK8 -0.015 0.036 0.16 3 -10000 0 3
IRAK1 0 0.038 -10000 0 -0.2 5 5
IL1RN/IL1R1 -0.047 0.14 -10000 0 -0.26 50 50
IRAK4 0.032 0.004 -10000 0 -10000 0 0
PRKCI 0.031 0.006 -10000 0 -10000 0 0
TRAF6 0.031 0.007 -10000 0 -10000 0 0
PI3K 0.045 0.011 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.079 -10000 0 -0.18 23 23
CHUK 0.032 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.002 0.096 -10000 0 -0.19 32 32
IL1 beta/IL1R2 -0.005 0.092 -10000 0 -0.21 27 27
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.039 0.16 1 -0.16 5 6
NF kappa B1 p50/RelA 0.017 0.092 -10000 0 -0.17 30 30
IRAK3 0.027 0.041 -10000 0 -0.34 2 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.013 0.12 -10000 0 -0.19 38 38
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.082 -10000 0 -0.19 24 24
IL1 alpha/IL1R1/IL1RAP 0.019 0.1 -10000 0 -0.21 25 25
RELA 0.031 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.03 0.008 -10000 0 -10000 0 0
MYD88 0.031 0.007 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.041 0.044 0.19 1 -0.17 5 6
IL1RAP 0.029 0.029 -10000 0 -0.34 1 1
UBE2N 0.032 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.016 0.096 -10000 0 -0.19 33 33
CASP1 0.024 0.05 -10000 0 -0.34 3 3
IL1RN/IL1R2 -0.045 0.14 -10000 0 -0.26 46 46
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.021 0.1 0.18 5 -0.18 32 37
TMEM189-UBE2V1 0.014 0.063 -10000 0 -0.34 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.015 0.11 -10000 0 -0.28 20 20
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
IL1RN -0.049 0.15 -10000 0 -0.34 36 36
TRAF6/TAK1/TAB1/TAB2 0.048 0.041 -10000 0 -0.16 5 5
MAP2K6 -0.011 0.04 0.17 4 -10000 0 4
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.075 0.19 -10000 0 -0.46 31 31
Crk/p130 Cas/Paxillin -0.042 0.091 -10000 0 -0.22 25 25
JUN -0.024 0.079 0.18 2 -0.32 2 4
HRAS 0.03 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.007 0.1 -10000 0 -0.19 32 32
RAP1A 0.032 0.005 -10000 0 -10000 0 0
FRS2 0.032 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.023 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.027 0.09 -10000 0 -0.19 23 23
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.026 0.062 -10000 0 -0.18 13 13
RHOA 0.031 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.02 0.093 -10000 0 -0.18 27 27
GRB7 0.018 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.025 0.088 -10000 0 -0.19 22 22
MAPKKK cascade -0.027 0.1 -10000 0 -0.23 20 20
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
RET9/GFRalpha1/GDNF/IRS1 0.018 0.073 -10000 0 -0.18 19 19
lamellipodium assembly -0.023 0.083 -10000 0 -0.23 15 15
RET51/GFRalpha1/GDNF/SHC 0.026 0.09 -10000 0 -0.19 23 23
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.027 0.062 -10000 0 -0.18 13 13
RET9/GFRalpha1/GDNF/Shank3 -0.017 0.11 -10000 0 -0.2 39 39
MAPK3 -0.024 0.094 0.29 6 -0.3 3 9
DOK1 0.032 0.003 -10000 0 -10000 0 0
DOK6 0.016 0.069 -10000 0 -0.34 6 6
PXN 0.027 0.04 -10000 0 -0.34 2 2
neurite development -0.034 0.078 0.26 2 -0.26 6 8
DOK5 0.02 0.008 -10000 0 -10000 0 0
GFRA1 -0.007 0.1 -10000 0 -0.34 14 14
MAPK8 -0.013 0.072 -10000 0 -0.18 23 23
HRAS/GTP 0.023 0.095 -10000 0 -0.21 22 22
tube development -0.016 0.1 0.21 1 -0.19 38 39
MAPK1 -0.031 0.075 0.26 2 -0.3 3 5
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.006 0.055 -10000 0 -0.18 13 13
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
SRC -0.007 0.11 -10000 0 -0.34 17 17
PDLIM7 0.031 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.004 0.12 -10000 0 -0.2 41 41
SHC1 0.032 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.018 0.1 -10000 0 -0.2 27 27
RET51/GFRalpha1/GDNF/Dok5 0.02 0.087 -10000 0 -0.19 23 23
PRKCA -0.019 0.12 -10000 0 -0.34 22 22
HRAS/GDP 0.022 0.006 -10000 0 -10000 0 0
CREB1 0.003 0.07 -10000 0 -0.22 13 13
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.004 0.065 -10000 0 -0.2 14 14
RET51/GFRalpha1/GDNF/Grb7 0.018 0.086 -10000 0 -0.19 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.004 0.091 -10000 0 -0.34 11 11
DOK4 0.018 0.069 -10000 0 -0.34 6 6
JNK cascade -0.023 0.078 0.18 2 -0.32 2 4
RET9/GFRalpha1/GDNF/FRS2 0.027 0.062 -10000 0 -0.18 13 13
SHANK3 -0.042 0.14 -10000 0 -0.34 31 31
RASA1 0.03 0.008 -10000 0 -10000 0 0
NCK1 0.031 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.006 0.056 -10000 0 -0.18 13 13
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.001 0.075 -10000 0 -0.19 22 22
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.003 0.077 -10000 0 -0.19 24 24
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.001 0.077 -10000 0 -0.19 22 22
PI3K -0.032 0.12 0.23 2 -0.32 16 18
SOS1 0.032 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.005 0.11 -10000 0 -0.19 38 38
GRB10 0.006 0.087 -10000 0 -0.34 10 10
activation of MAPKK activity -0.002 0.067 -10000 0 -0.18 13 13
RET51/GFRalpha1/GDNF/FRS2 0.027 0.09 -10000 0 -0.19 23 23
GAB1 0.027 0.041 -10000 0 -0.34 2 2
IRS1 0.018 0.069 -10000 0 -0.34 6 6
IRS2 0.028 0.029 -10000 0 -0.34 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.005 0.084 -10000 0 -0.2 24 24
RET51/GFRalpha1/GDNF/PKC alpha -0.008 0.11 -10000 0 -0.2 42 42
GRB2 0.03 0.008 -10000 0 -10000 0 0
PRKACA 0.029 0.009 -10000 0 -10000 0 0
GDNF 0.017 0.005 -10000 0 -10000 0 0
RAC1 0.028 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.017 0.097 -10000 0 -0.19 29 29
Rac1/GTP -0.025 0.098 -10000 0 -0.26 15 15
RET9/GFRalpha1/GDNF 0.009 0.061 -10000 0 -0.2 13 13
GFRalpha1/GDNF 0.008 0.073 -10000 0 -0.24 13 13
Wnt 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
Noncanonical Wnts/FZD -0.025 0.11 -9999 0 -0.2 37 37
FZD6 0.011 0.069 -9999 0 -0.34 6 6
WNT6 -0.022 0.13 -9999 0 -0.34 23 23
WNT4 0.031 0.006 -9999 0 -10000 0 0
FZD3 -0.004 0.098 -9999 0 -0.34 13 13
WNT5A 0.022 0.01 -9999 0 -10000 0 0
WNT11 0.013 0.069 -9999 0 -0.34 6 6
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.012 0.12 -10000 0 -0.48 8 8
VEGFR1 homodimer/NRP1 -0.008 0.11 -10000 0 -0.52 7 7
mol:DAG -0.023 0.12 0.2 3 -0.37 12 15
VEGFR1 homodimer/NRP1/VEGFR 121 0.002 0.12 -10000 0 -0.34 14 14
CaM/Ca2+ -0.003 0.12 0.2 4 -0.26 24 28
HIF1A 0.024 0.068 -10000 0 -0.3 7 7
GAB1 0.027 0.041 -10000 0 -0.34 2 2
AKT1 -0.014 0.12 0.25 2 -0.46 7 9
PLCG1 -0.023 0.12 0.2 3 -0.37 12 15
NOS3 -0.041 0.15 0.48 1 -0.41 16 17
CBL 0.03 0.008 -10000 0 -10000 0 0
mol:NO -0.039 0.16 0.6 2 -0.39 18 20
FLT1 -0.004 0.12 -10000 0 -0.6 7 7
PGF -0.001 0.1 -10000 0 -0.34 14 14
VEGFR1 homodimer/NRP2/VEGFR121 -0.01 0.14 -10000 0 -0.26 32 32
CALM1 0.032 0.005 -10000 0 -10000 0 0
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
eNOS/Hsp90 -0.036 0.15 -10000 0 -0.38 18 18
endothelial cell proliferation -0.046 0.16 0.41 3 -0.48 13 16
mol:Ca2+ -0.023 0.12 0.2 3 -0.36 12 15
MAPK3 -0.054 0.14 0.29 5 -0.42 12 17
MAPK1 -0.057 0.13 0.24 3 -0.42 12 15
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
PLGF homodimer -0.001 0.1 -10000 0 -0.34 14 14
PRKACA 0.029 0.009 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.012 0.11 -10000 0 -0.34 16 16
VEGFA homodimer 0.009 0.083 -10000 0 -0.34 9 9
VEGFR1 homodimer/VEGFA homodimer 0.002 0.12 -10000 0 -0.37 14 14
platelet activating factor biosynthetic process -0.049 0.14 0.21 11 -0.42 12 23
PI3K 0.033 0.12 -10000 0 -0.28 19 19
PRKCA -0.053 0.14 0.3 5 -0.44 12 17
PRKCB -0.03 0.13 0.3 7 -0.47 7 14
VEGFR1 homodimer/PLGF homodimer -0.004 0.13 -10000 0 -0.32 19 19
VEGFA 0.009 0.083 -10000 0 -0.34 9 9
VEGFB 0.029 0.029 -10000 0 -0.34 1 1
mol:IP3 -0.023 0.12 0.2 3 -0.37 12 15
RASA1 -0.001 0.11 0.2 5 -0.48 7 12
NRP2 -0.019 0.12 -10000 0 -0.34 21 21
VEGFR1 homodimer -0.004 0.12 -10000 0 -0.6 7 7
VEGFB homodimer 0.029 0.029 -10000 0 -0.34 1 1
NCK1 0.031 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.039 0.15 -10000 0 -0.39 20 20
PTPN11 0.032 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.031 0.12 -10000 0 -0.27 19 19
mol:L-citrulline -0.039 0.16 0.6 2 -0.39 18 20
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.04 0.12 -10000 0 -0.33 14 14
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.021 0.12 -10000 0 -0.34 13 13
CD2AP 0.03 0.029 -10000 0 -0.34 1 1
PI3K/GAB1 0.04 0.13 -10000 0 -0.27 20 20
PDPK1 -0.004 0.12 0.28 8 -0.43 7 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.021 0.12 -10000 0 -0.34 14 14
mol:NADP -0.039 0.16 0.6 2 -0.39 18 20
HSP90AA1 0.032 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.12 -10000 0 -0.32 14 14
VEGFR1 homodimer/NRP2 -0.017 0.14 -10000 0 -0.29 26 26
Arf6 signaling events

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
CENTA1/KIF3B 0.029 0.039 -10000 0 -0.2 4 4
ARNO/beta Arrestin1-2 -0.001 0.18 -10000 0 -0.71 10 10
EGFR 0.021 0.011 -10000 0 -10000 0 0
EPHA2 -0.006 0.1 -10000 0 -0.34 14 14
USP6 0.027 0.012 -10000 0 -10000 0 0
IQSEC1 0.027 0.041 -10000 0 -0.34 2 2
EGFR/EGFR/EGF/EGF -0.005 0.092 -10000 0 -0.24 22 22
ARRB2 0.011 0.004 -10000 0 -10000 0 0
mol:GTP -0.015 0.065 0.12 1 -0.18 14 15
ARRB1 0.031 0.007 -10000 0 -10000 0 0
FBXO8 0.031 0.006 -10000 0 -10000 0 0
TSHR 0.022 0.057 -10000 0 -0.34 4 4
EGF -0.026 0.12 -10000 0 -0.34 23 23
somatostatin receptor activity 0 0 0.001 11 -0.001 18 29
ARAP2 0.007 0.092 -10000 0 -0.34 11 11
mol:GDP -0.036 0.11 0.17 5 -0.29 20 25
mol:PI-3-4-5-P3 0 0 0.001 5 -0.001 13 18
ITGA2B -0.008 0.11 -10000 0 -0.34 16 16
ARF6 0.032 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.041 0.087 -10000 0 -0.19 18 18
ADAP1 0.017 0.063 -10000 0 -0.34 5 5
KIF13B 0.029 0.01 -10000 0 -10000 0 0
HGF/MET -0.001 0.094 -10000 0 -0.24 22 22
PXN 0.027 0.04 -10000 0 -0.34 2 2
ARF6/GTP -0.032 0.11 0.22 10 -0.22 22 32
EGFR/EGFR/EGF/EGF/ARFGEP100 0.011 0.089 -10000 0 -0.2 24 24
ADRB2 0.02 0.057 -10000 0 -0.34 4 4
receptor agonist activity 0 0 0 9 0 17 26
actin filament binding 0 0 0.001 11 0 19 30
SRC -0.007 0.11 -10000 0 -0.34 17 17
ITGB3 -0.047 0.14 -10000 0 -0.34 32 32
GNAQ 0.031 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 11 -0.001 15 26
ARF6/GDP -0.033 0.15 0.23 1 -0.44 14 15
ARF6/GDP/GULP/ACAP1 -0.006 0.12 0.22 1 -0.25 19 20
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.002 0.12 -10000 0 -0.2 43 43
ACAP1 0.029 0.01 -10000 0 -10000 0 0
ACAP2 0.031 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.021 -10000 0 -10000 0 0
EFNA1 0.014 0.069 -10000 0 -0.34 6 6
HGF -0.024 0.12 -10000 0 -0.34 22 22
CYTH3 0.007 0.003 -10000 0 -10000 0 0
CYTH2 -0.036 0.23 -10000 0 -0.94 10 10
NCK1 0.031 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0 11 0 15 26
endosomal lumen acidification 0 0 0.001 10 0 18 28
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.023 0.009 -10000 0 -10000 0 0
GNAQ/ARNO -0.016 0.22 -10000 0 -0.87 10 10
mol:Phosphatidic acid 0 0 0 4 -10000 0 4
PIP3-E 0 0 0 4 0 7 11
MET 0.025 0.012 -10000 0 -10000 0 0
GNA14 0.007 0.083 -10000 0 -0.34 9 9
GNA15 0.027 0.03 -10000 0 -0.34 1 1
GIT1 0.03 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 10 -0.001 15 25
GNA11 0.005 0.092 -10000 0 -0.34 11 11
LHCGR 0.019 0.007 -10000 0 -10000 0 0
AGTR1 0.004 0.087 -10000 0 -0.34 10 10
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.021 -10000 0 -10000 0 0
IPCEF1/ARNO -0.031 0.2 -10000 0 -0.77 10 10
alphaIIb/beta3 Integrin -0.039 0.14 -10000 0 -0.26 42 42
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.11 0.37 -10000 0 -0.99 25 25
oxygen homeostasis 0.002 0.013 -10000 0 -10000 0 0
TCEB2 0.031 0.006 -10000 0 -10000 0 0
TCEB1 0.028 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.01 0.13 -10000 0 -0.29 14 14
EPO -0.015 0.2 -10000 0 -0.45 17 17
FIH (dimer) 0.029 0.023 -10000 0 -10000 0 0
APEX1 0.023 0.03 -10000 0 -10000 0 0
SERPINE1 -0.036 0.23 -10000 0 -0.47 25 25
FLT1 -0.024 0.22 -10000 0 -1 7 7
ADORA2A -0.022 0.21 0.39 2 -0.48 16 18
germ cell development -0.015 0.22 0.31 2 -0.47 19 21
SLC11A2 -0.014 0.22 0.32 1 -0.5 16 17
BHLHE40 -0.018 0.22 -10000 0 -0.49 17 17
HIF1AN 0.029 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.006 0.17 -10000 0 -0.36 15 15
ETS1 0.019 0.052 -10000 0 -0.1 24 24
CITED2 0.019 0.1 -10000 0 -0.58 4 4
KDR -0.082 0.31 -10000 0 -0.93 19 19
PGK1 -0.017 0.22 0.32 1 -0.47 18 19
SIRT1 0.032 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.007 0.26 -10000 0 -0.54 18 18
EPAS1 -0.017 0.13 0.21 1 -0.28 23 24
SP1 0.017 0.052 -10000 0 -0.1 26 26
ABCG2 -0.036 0.25 -10000 0 -0.51 26 26
EFNA1 -0.021 0.23 0.4 1 -0.52 18 19
FXN -0.02 0.21 0.37 4 -0.48 16 20
POU5F1 -0.017 0.22 0.32 1 -0.48 19 20
neuron apoptosis -0.007 0.26 0.52 18 -10000 0 18
EP300 0.03 0.009 -10000 0 -10000 0 0
EGLN3 0.006 0.081 -10000 0 -0.34 8 8
EGLN2 0.026 0.024 -10000 0 -10000 0 0
EGLN1 0.013 0.076 -10000 0 -0.33 7 7
VHL/Elongin B/Elongin C 0.054 0.025 -10000 0 -10000 0 0
VHL 0.031 0.006 -10000 0 -10000 0 0
ARNT 0.023 0.03 -10000 0 -10000 0 0
SLC2A1 -0.015 0.21 0.39 3 -0.48 16 19
TWIST1 -0.025 0.2 0.35 2 -0.47 17 19
ELK1 0.034 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.009 0.17 0.31 1 -0.36 15 16
VEGFA -0.027 0.23 0.32 1 -0.51 20 21
CREBBP 0.031 0.006 -10000 0 -10000 0 0
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 -0.007 0.1 -9999 0 -0.24 26 26
PDGFRB -0.01 0.11 -9999 0 -0.34 16 16
SPHK1 -0.031 0.17 -9999 0 -0.71 9 9
mol:S1P -0.03 0.14 -9999 0 -0.64 8 8
S1P1/S1P/Gi -0.057 0.15 -9999 0 -0.4 20 20
GNAO1 0.022 0.043 -9999 0 -0.34 2 2
PDGFB-D/PDGFRB/PLCgamma1 -0.065 0.14 -9999 0 -0.35 25 25
PLCG1 -0.062 0.14 -9999 0 -0.37 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.01 0.11 -9999 0 -0.34 16 16
GNAI2 0.027 0.016 -9999 0 -10000 0 0
GNAI3 0.027 0.016 -9999 0 -10000 0 0
GNAI1 -0.024 0.12 -9999 0 -0.34 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.034 0.071 -9999 0 -0.2 26 26
S1P1/S1P -0.049 0.12 -9999 0 -0.32 17 17
negative regulation of cAMP metabolic process -0.056 0.15 -9999 0 -0.39 20 20
MAPK3 -0.072 0.18 -9999 0 -0.55 18 18
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.021 0.008 -9999 0 -10000 0 0
RhoA/GDP 0.023 0.005 -9999 0 -10000 0 0
KDR -0.017 0.11 -9999 0 -0.34 18 18
PLCB2 -0.045 0.11 -9999 0 -0.32 14 14
RAC1 0.028 0.011 -9999 0 -10000 0 0
RhoA/GTP -0.039 0.1 -9999 0 -0.28 16 16
receptor internalization -0.047 0.11 -9999 0 -0.3 17 17
PTGS2 -0.091 0.26 -9999 0 -0.82 17 17
Rac1/GTP -0.04 0.1 -9999 0 -0.28 17 17
RHOA 0.031 0.007 -9999 0 -10000 0 0
VEGFA 0.009 0.084 -9999 0 -0.34 9 9
negative regulation of T cell proliferation -0.056 0.15 -9999 0 -0.39 20 20
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.009 0.07 -9999 0 -0.34 6 6
MAPK1 -0.067 0.18 -9999 0 -0.54 17 17
S1P1/S1P/PDGFB-D/PDGFRB -0.051 0.13 -9999 0 -0.3 23 23
ABCC1 0.031 0.005 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.029 0.091 -10000 0 -0.18 26 26
ER alpha/Gai/GDP/Gbeta gamma -0.041 0.13 -10000 0 -0.33 22 22
AKT1 -0.043 0.21 -10000 0 -0.66 17 17
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.039 0.22 -10000 0 -0.68 17 17
mol:Ca2+ -0.031 0.1 -10000 0 -0.31 14 14
IGF1R -0.001 0.1 -10000 0 -0.34 14 14
E2/ER alpha (dimer)/Striatin 0.019 0.07 -10000 0 -0.21 14 14
SHC1 0.032 0.004 -10000 0 -10000 0 0
apoptosis 0.041 0.2 0.64 17 -10000 0 17
RhoA/GTP 0.013 0.051 -10000 0 -0.16 13 13
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.053 0.14 -10000 0 -0.32 27 27
regulation of stress fiber formation 0.015 0.056 0.25 1 -0.15 9 10
E2/ERA-ERB (dimer) 0.017 0.068 -10000 0 -0.2 15 15
KRAS 0.031 0.006 -10000 0 -10000 0 0
G13/GTP 0.018 0.06 -10000 0 -0.17 14 14
pseudopodium formation -0.015 0.056 0.15 9 -0.25 1 10
E2/ER alpha (dimer)/PELP1 0.017 0.066 -10000 0 -0.2 14 14
GRB2 0.03 0.008 -10000 0 -10000 0 0
GNG2 0.003 0.099 -10000 0 -0.34 13 13
GNAO1 0.026 0.041 -10000 0 -0.34 2 2
HRAS 0.03 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.055 0.17 0.32 2 -0.41 23 25
E2/ER beta (dimer) 0.021 0.021 -10000 0 -0.23 1 1
mol:GDP -0.005 0.09 -10000 0 -0.28 15 15
mol:NADP -0.055 0.17 0.32 2 -0.41 23 25
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
mol:IP3 -0.032 0.1 -10000 0 -0.32 14 14
IGF-1R heterotetramer -0.001 0.1 -10000 0 -0.34 14 14
PLCB1 -0.02 0.1 -10000 0 -0.32 14 14
PLCB2 -0.023 0.1 -10000 0 -0.34 12 12
IGF1 0 0.099 -10000 0 -0.34 13 13
mol:L-citrulline -0.055 0.17 0.32 2 -0.41 23 25
RHOA 0.031 0.007 -10000 0 -10000 0 0
Gai/GDP -0.015 0.14 -10000 0 -0.55 8 8
JNK cascade 0.021 0.021 -10000 0 -0.23 1 1
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
ESR2 0.028 0.03 -10000 0 -0.34 1 1
GNAQ 0.031 0.006 -10000 0 -10000 0 0
ESR1 -0.004 0.1 -10000 0 -0.34 14 14
Gq family/GDP/Gbeta gamma -0.053 0.19 0.21 1 -0.48 22 23
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.004 0.13 -10000 0 -0.54 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.042 0.14 -10000 0 -0.32 27 27
GNAZ 0.013 0.069 -10000 0 -0.34 6 6
E2/ER alpha (dimer) -0.001 0.07 -10000 0 -0.23 14 14
STRN 0.03 0.029 -10000 0 -0.34 1 1
GNAL 0.029 0.029 -10000 0 -0.34 1 1
PELP1 0.029 0.01 -10000 0 -10000 0 0
MAPK11 0.011 0.029 -10000 0 -0.2 3 3
GNAI2 0.031 0.007 -10000 0 -10000 0 0
GNAI3 0.032 0.004 -10000 0 -10000 0 0
GNAI1 -0.021 0.12 -10000 0 -0.34 21 21
HBEGF -0.092 0.16 0.38 1 -0.39 23 24
cAMP biosynthetic process 0.014 0.057 -10000 0 -0.16 16 16
SRC -0.053 0.14 -10000 0 -0.32 27 27
PI3K 0.045 0.011 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.014 0.1 -10000 0 -0.27 15 15
SOS1 0.032 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.068 0.12 -10000 0 -0.28 30 30
Gs family/GTP 0.021 0.06 -10000 0 -0.16 16 16
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.056 0.019 -10000 0 -10000 0 0
vasodilation -0.052 0.16 0.32 2 -0.39 23 25
mol:DAG -0.032 0.1 -10000 0 -0.32 14 14
Gs family/GDP/Gbeta gamma -0.006 0.093 -10000 0 -0.27 14 14
MSN -0.016 0.059 0.16 9 -0.27 1 10
Gq family/GTP -0.009 0.1 -10000 0 -0.34 12 12
mol:PI-3-4-5-P3 -0.037 0.21 -10000 0 -0.65 17 17
NRAS 0.032 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.052 0.16 0.39 23 -0.32 2 25
GRB2/SOS1 0.045 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.011 0.092 -10000 0 -0.28 14 14
NOS3 -0.058 0.18 0.43 1 -0.43 23 24
GNA11 0.005 0.092 -10000 0 -0.34 11 11
MAPKKK cascade -0.041 0.17 0.35 1 -0.5 17 18
E2/ER alpha (dimer)/PELP1/Src -0.048 0.15 -10000 0 -0.33 27 27
ruffle organization -0.015 0.056 0.15 9 -0.25 1 10
ROCK2 -0.005 0.08 0.2 14 -0.29 1 15
GNA14 0.008 0.083 -10000 0 -0.34 9 9
GNA15 0.027 0.03 -10000 0 -0.34 1 1
GNA13 0.03 0.008 -10000 0 -10000 0 0
MMP9 -0.071 0.15 0.23 1 -0.32 33 34
MMP2 -0.069 0.14 0.24 1 -0.33 25 26
FOXM1 transcription factor network

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
NFATC3 -0.07 0.37 0.68 1 -1 11 12
PLK1 -0.004 0.22 -10000 0 -1 7 7
BIRC5 -0.016 0.24 -10000 0 -0.95 9 9
HSPA1B -0.082 0.38 0.68 1 -0.99 14 15
MAP2K1 0.014 0.051 -10000 0 -10000 0 0
BRCA2 -0.065 0.37 0.68 1 -1 11 12
FOXM1 -0.096 0.45 0.76 1 -1.3 11 12
XRCC1 -0.063 0.37 0.93 1 -1 11 12
FOXM1B/p19 -0.13 0.37 -10000 0 -1 15 15
Cyclin D1/CDK4 -0.078 0.36 -10000 0 -0.94 13 13
CDC2 -0.074 0.39 0.75 1 -1.1 11 12
TGFA -0.083 0.36 0.69 1 -0.86 16 17
SKP2 -0.066 0.37 0.93 1 -1 11 12
CCNE1 0.025 0.034 -10000 0 -0.35 1 1
CKS1B -0.067 0.37 0.68 1 -1 11 12
RB1 -0.007 0.21 -10000 0 -0.88 4 4
FOXM1C/SP1 -0.079 0.41 0.67 1 -1.2 11 12
AURKB -0.06 0.32 -10000 0 -1 14 14
CENPF -0.08 0.39 0.68 1 -1 14 15
CDK4 0.025 0.028 -10000 0 -10000 0 0
MYC -0.08 0.32 -10000 0 -0.87 12 12
CHEK2 0.013 0.051 0.18 1 -10000 0 1
ONECUT1 -0.083 0.36 -10000 0 -0.95 13 13
CDKN2A -0.048 0.15 -10000 0 -0.34 34 34
LAMA4 -0.17 0.5 0.68 1 -1 34 35
FOXM1B/HNF6 -0.1 0.41 -10000 0 -1.1 13 13
FOS -0.089 0.41 0.68 1 -1.1 16 17
SP1 0.032 0.011 -10000 0 -10000 0 0
CDC25B -0.068 0.37 0.68 1 -1 11 12
response to radiation 0.004 0.029 0.095 1 -10000 0 1
CENPB -0.068 0.37 0.68 1 -1 11 12
CENPA -0.083 0.4 0.68 1 -1.1 14 15
NEK2 -0.067 0.37 0.68 1 -1 11 12
HIST1H2BA -0.075 0.36 0.68 1 -1 11 12
CCNA2 0.028 0.033 -10000 0 -0.35 1 1
EP300 0.03 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 -0.087 0.42 0.79 1 -1.2 11 12
CCNB2 -0.069 0.37 0.93 1 -1 11 12
CCNB1 -0.074 0.39 0.81 1 -1.1 11 12
ETV5 -0.09 0.41 0.93 1 -1.1 15 16
ESR1 -0.12 0.44 0.69 1 -1 22 23
CCND1 -0.091 0.36 -10000 0 -0.96 13 13
GSK3A 0.013 0.045 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.046 0.063 -10000 0 -0.4 1 1
CDK2 0.031 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.033 0.14 1 -10000 0 1
FOXM1B/Cbp/p300 -0.081 0.39 0.64 1 -1.1 11 12
GAS1 -0.12 0.44 0.93 1 -1 21 22
MMP2 -0.17 0.5 0.68 1 -1 32 33
RB1/FOXM1C -0.08 0.36 -10000 0 -0.99 13 13
CREBBP 0.031 0.006 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.02 0.12 0.3 2 -0.36 15 17
CRKL -0.024 0.13 0.2 3 -0.37 16 19
HRAS -0.011 0.12 -10000 0 -0.33 15 15
mol:PIP3 -0.024 0.12 0.26 1 -0.35 15 16
SPRED1 -0.027 0.12 -10000 0 -0.34 23 23
SPRED2 0.012 0.084 -10000 0 -0.34 9 9
GAB1 -0.027 0.13 -10000 0 -0.39 16 16
FOXO3 -0.015 0.12 -10000 0 -0.38 13 13
AKT1 -0.013 0.13 -10000 0 -0.4 13 13
BAD -0.008 0.13 -10000 0 -0.38 13 13
megakaryocyte differentiation -0.043 0.13 -10000 0 -0.36 20 20
GSK3B -0.011 0.13 0.36 1 -0.38 13 14
RAF1 -0.008 0.1 0.29 1 -0.27 15 16
SHC1 0.032 0.004 -10000 0 -10000 0 0
STAT3 -0.025 0.13 -10000 0 -0.38 16 16
STAT1 -0.058 0.26 -10000 0 -0.83 16 16
HRAS/SPRED1 -0.017 0.11 -10000 0 -0.27 18 18
cell proliferation -0.021 0.12 -10000 0 -0.37 16 16
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
TEC 0.029 0.029 -10000 0 -0.34 1 1
RPS6KB1 -0.021 0.14 -10000 0 -0.38 16 16
HRAS/SPRED2 -0.003 0.11 -10000 0 -0.28 16 16
LYN/TEC/p62DOK 0.017 0.14 -10000 0 -0.36 14 14
MAPK3 0.005 0.093 0.3 4 -0.21 14 18
STAP1 -0.034 0.14 -10000 0 -0.4 16 16
GRAP2 0.006 0.088 -10000 0 -0.34 10 10
JAK2 -0.044 0.23 -10000 0 -0.7 16 16
STAT1 (dimer) -0.056 0.26 -10000 0 -0.81 16 16
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.014 0.14 -10000 0 -0.38 15 15
actin filament polymerization -0.026 0.12 -10000 0 -0.39 14 14
LYN 0.028 0.011 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.044 0.17 -10000 0 -0.53 16 16
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.007 0.13 -10000 0 -0.38 13 13
PI3K 0.005 0.14 -10000 0 -0.39 14 14
PTEN 0.031 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.061 0.33 -10000 0 -1 16 16
MAPK8 -0.022 0.13 -10000 0 -0.38 16 16
STAT3 (dimer) -0.024 0.12 -10000 0 -0.37 16 16
positive regulation of transcription 0.005 0.083 0.29 4 -0.18 10 14
mol:GDP -0.005 0.13 -10000 0 -0.35 15 15
PIK3C2B -0.024 0.13 -10000 0 -0.38 16 16
CBL/CRKL -0.002 0.13 0.38 1 -0.37 14 15
FER -0.03 0.13 -10000 0 -0.38 16 16
SH2B3 -0.025 0.13 -10000 0 -0.38 16 16
PDPK1 -0.023 0.11 0.25 1 -0.33 15 16
SNAI2 -0.033 0.13 -10000 0 -0.39 17 17
positive regulation of cell proliferation -0.038 0.2 -10000 0 -0.62 16 16
KITLG -0.001 0.099 -10000 0 -0.35 12 12
cell motility -0.038 0.2 -10000 0 -0.62 16 16
PTPN6 0.032 0.009 -10000 0 -10000 0 0
EPOR -0.031 0.23 -10000 0 -0.88 8 8
STAT5A (dimer) -0.031 0.17 -10000 0 -0.51 16 16
SOCS1 0.017 0.069 -10000 0 -0.34 6 6
cell migration 0.028 0.13 0.4 16 -10000 0 16
SOS1 0.032 0.003 -10000 0 -10000 0 0
EPO 0.018 0.021 -10000 0 -10000 0 0
VAV1 0.03 0.009 -10000 0 -10000 0 0
GRB10 -0.032 0.14 -10000 0 -0.44 14 14
PTPN11 0.032 0.006 -10000 0 -10000 0 0
SCF/KIT -0.022 0.13 -10000 0 -0.39 16 16
GO:0007205 0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.003 0.09 0.28 2 -0.22 14 16
CBL 0.03 0.008 -10000 0 -10000 0 0
KIT -0.048 0.3 -10000 0 -1.1 12 12
MAP2K2 -0.004 0.09 0.41 1 -0.22 14 15
SHC/Grb2/SOS1 0.021 0.14 -10000 0 -0.38 13 13
STAT5A -0.031 0.17 -10000 0 -0.53 16 16
GRB2 0.03 0.008 -10000 0 -10000 0 0
response to radiation -0.032 0.13 -10000 0 -0.38 17 17
SHC/GRAP2 0.026 0.068 -10000 0 -0.24 10 10
PTPRO -0.044 0.14 -10000 0 -0.37 20 20
SH2B2 -0.026 0.12 -10000 0 -0.4 14 14
DOK1 0.032 0.003 -10000 0 -10000 0 0
MATK -0.029 0.14 -10000 0 -0.41 16 16
CREBBP 0.033 0.045 -10000 0 -0.11 2 2
BCL2 0.005 0.13 -10000 0 -0.55 3 3
Caspase cascade in apoptosis

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
TOP1 -0.004 0.11 0.3 1 -0.35 8 9
ACTA1 -0.023 0.11 0.25 3 -0.28 18 21
NUMA1 0.001 0.098 0.3 1 -0.38 5 6
SPTAN1 -0.021 0.11 0.27 4 -0.28 18 22
LIMK1 -0.017 0.11 0.23 6 -0.28 17 23
BIRC3 0.024 0.05 -10000 0 -0.34 3 3
BIRC2 0.031 0.007 -10000 0 -10000 0 0
BAX 0.029 0.01 -10000 0 -10000 0 0
CASP10 -0.032 0.072 -10000 0 -0.23 18 18
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.029 0.01 -10000 0 -10000 0 0
PTK2 -0.05 0.13 0.26 1 -0.39 11 12
DIABLO 0.032 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.021 0.11 0.27 4 -0.28 18 22
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.029 -10000 0 -0.34 1 1
GSN -0.028 0.11 0.29 3 -0.28 18 21
MADD 0.031 0.007 -10000 0 -10000 0 0
TFAP2A -0.011 0.16 -10000 0 -0.52 14 14
BID -0.009 0.052 -10000 0 -0.16 17 17
MAP3K1 -0.001 0.073 0.2 1 -0.37 4 5
TRADD 0.031 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.024 0.11 0.23 3 -0.28 18 21
CASP9 0.031 0.006 -10000 0 -10000 0 0
DNA repair -0.002 0.047 0.18 3 -0.14 3 6
neuron apoptosis -0.2 0.31 -10000 0 -0.61 58 58
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.006 0.11 0.31 3 -0.42 5 8
APAF1 0.032 0.004 -10000 0 -10000 0 0
CASP6 0.009 0.12 -10000 0 -0.93 2 2
TRAF2 0.031 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.018 0.12 0.36 5 -0.27 17 22
CASP7 -0.01 0.098 0.21 3 -0.33 9 12
KRT18 -0.14 0.25 -10000 0 -0.51 49 49
apoptosis -0.012 0.12 0.46 3 -0.42 5 8
DFFA -0.02 0.11 0.32 3 -0.28 18 21
DFFB -0.02 0.11 0.32 3 -0.28 18 21
PARP1 0.002 0.047 0.14 3 -0.18 3 6
actin filament polymerization 0.013 0.11 0.27 17 -0.27 7 24
TNF -0.002 0.098 -10000 0 -0.34 13 13
CYCS -0.01 0.074 0.2 3 -0.17 19 22
SATB1 0.009 0.12 -10000 0 -0.86 2 2
SLK -0.021 0.12 0.39 3 -0.28 18 21
p15 BID/BAX 0.012 0.062 0.2 1 -0.15 17 18
CASP2 0.012 0.063 0.21 4 -0.24 4 8
JNK cascade 0.001 0.072 0.37 4 -0.2 1 5
CASP3 -0.023 0.12 0.23 3 -0.29 18 21
LMNB2 0.009 0.11 -10000 0 -0.43 6 6
RIPK1 0.032 0.005 -10000 0 -10000 0 0
CASP4 0.031 0.007 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.07 0.039 -10000 0 -0.18 2 2
negative regulation of DNA binding -0.011 0.16 -10000 0 -0.51 14 14
stress fiber formation -0.021 0.12 0.39 3 -0.28 18 21
GZMB -0.016 0.091 -10000 0 -0.27 18 18
CASP1 0.011 0.035 -10000 0 -0.25 3 3
LMNB1 0.005 0.12 -10000 0 -0.41 7 7
APP -0.2 0.31 -10000 0 -0.62 58 58
TNFRSF1A 0.032 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.001 -10000 0 -10000 0 0
VIM -0.011 0.11 0.34 2 -0.43 5 7
LMNA 0.002 0.11 0.29 1 -0.37 7 8
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.015 0.06 -10000 0 -0.25 4 4
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.025 0.11 0.24 2 -0.28 18 20
APAF-1/Caspase 9 0.013 0.068 -10000 0 -0.51 2 2
nuclear fragmentation during apoptosis 0.001 0.097 0.3 1 -0.38 5 6
CFL2 -0.014 0.12 0.27 7 -0.27 17 24
GAS2 -0.027 0.11 0.32 2 -0.28 18 20
positive regulation of apoptosis 0.005 0.11 -10000 0 -0.44 6 6
PRF1 0.017 0.069 -10000 0 -0.34 6 6
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.009 0.11 -10000 0 -0.34 16 16
Jak2/Leptin Receptor -0.034 0.12 -10000 0 -0.27 16 16
PTP1B/AKT1 -0.008 0.085 0.2 2 -0.23 10 12
FYN 0.026 0.049 -10000 0 -0.34 3 3
p210 bcr-abl/PTP1B -0.02 0.088 0.25 3 -0.26 10 13
EGFR 0.014 0.02 -10000 0 -10000 0 0
EGF/EGFR -0.026 0.098 -10000 0 -0.2 32 32
CSF1 0.012 0.079 -10000 0 -0.34 8 8
AKT1 0.032 0.005 -10000 0 -10000 0 0
INSR 0.026 0.041 -10000 0 -0.34 2 2
PTP1B/N-cadherin -0.029 0.093 0.18 1 -0.23 19 20
Insulin Receptor/Insulin 0.005 0.084 -10000 0 -0.29 4 4
HCK 0.007 0.092 -10000 0 -0.34 11 11
CRK 0.029 0.01 -10000 0 -10000 0 0
TYK2 -0.015 0.096 0.31 5 -0.26 7 12
EGF -0.027 0.13 -10000 0 -0.34 23 23
YES1 0.004 0.096 -10000 0 -0.34 12 12
CAV1 -0.045 0.11 0.29 2 -0.25 19 21
TXN 0.031 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.008 0.096 0.27 2 -0.24 10 12
cell migration 0.02 0.088 0.26 10 -0.25 3 13
STAT3 0.03 0.009 -10000 0 -10000 0 0
PRLR -0.063 0.15 -10000 0 -0.34 39 39
ITGA2B -0.009 0.11 -10000 0 -0.34 16 16
CSF1R 0.009 0.083 -10000 0 -0.34 9 9
Prolactin Receptor/Prolactin -0.03 0.11 -10000 0 -0.24 39 39
FGR -0.034 0.14 -10000 0 -0.34 28 28
PTP1B/p130 Cas -0.019 0.091 0.23 3 -0.24 12 15
Crk/p130 Cas -0.015 0.093 0.31 1 -0.23 11 12
DOK1 -0.031 0.11 0.34 2 -0.29 14 16
JAK2 -0.044 0.12 -10000 0 -0.28 17 17
Jak2/Leptin Receptor/Leptin -0.019 0.092 -10000 0 -0.28 6 6
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
PTPN1 -0.02 0.089 0.25 3 -0.26 10 13
LYN 0.028 0.011 -10000 0 -10000 0 0
CDH2 -0.025 0.12 -10000 0 -0.34 20 20
SRC -0.045 0.18 -10000 0 -0.45 25 25
ITGB3 -0.047 0.14 -10000 0 -0.34 32 32
CAT1/PTP1B -0.046 0.16 0.5 3 -0.32 23 26
CAPN1 0.031 0.007 -10000 0 -10000 0 0
CSK 0.031 0.006 -10000 0 -10000 0 0
PI3K 0.024 0.084 -10000 0 -0.29 3 3
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.014 0.089 -10000 0 -0.28 6 6
negative regulation of transcription -0.043 0.12 -10000 0 -0.27 17 17
FCGR2A -0.009 0.12 -10000 0 -0.34 18 18
FER 0.016 0.07 -10000 0 -0.34 6 6
alphaIIb/beta3 Integrin -0.04 0.14 -10000 0 -0.26 42 42
BLK 0.011 0.074 -10000 0 -0.34 7 7
Insulin Receptor/Insulin/Shc 0.046 0.033 -10000 0 -0.2 2 2
RHOA 0.032 0.008 -10000 0 -10000 0 0
LEPR 0.028 0.029 -10000 0 -0.33 1 1
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
p210 bcr-abl/Grb2 0.03 0.008 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.038 0.16 0.38 4 -0.36 18 22
PRL 0.013 0.018 -10000 0 -10000 0 0
SOCS3 -0.036 0.27 -10000 0 -1.1 10 10
SPRY2 0.008 0.089 -10000 0 -0.34 10 10
Insulin Receptor/Insulin/IRS1 0.036 0.057 -10000 0 -0.2 8 8
CSF1/CSF1R -0.02 0.1 0.2 1 -0.28 10 11
Ras protein signal transduction 0.01 0.079 0.48 4 -10000 0 4
IRS1 0.018 0.069 -10000 0 -0.34 6 6
INS 0.01 0.015 -10000 0 -10000 0 0
LEP 0.017 0.015 -10000 0 -10000 0 0
STAT5B -0.028 0.1 0.19 3 -0.35 8 11
STAT5A -0.028 0.1 0.19 3 -0.35 8 11
GRB2 0.03 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.024 0.095 0.18 1 -0.25 16 17
CSN2 -0.017 0.066 0.34 1 -10000 0 1
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
LAT -0.042 0.16 -10000 0 -0.43 23 23
YBX1 0.038 0.008 -10000 0 -10000 0 0
LCK 0.024 0.05 -10000 0 -0.34 3 3
SHC1 0.032 0.004 -10000 0 -10000 0 0
NOX4 0.003 0.018 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.04 0.067 0.26 1 -10000 0 1
SMARCC2 0.023 0.032 -10000 0 -0.1 1 1
SMARCC1 0.022 0.031 -10000 0 -0.084 4 4
TBX21 -0.038 0.14 0.35 2 -0.52 7 9
SUMO2 0.035 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.039 0 -10000 0 -10000 0 0
FKBP4 0.031 0.006 -10000 0 -10000 0 0
FKBP5 0.029 0.029 -10000 0 -0.34 1 1
GR alpha/HSP90/FKBP51/HSP90 0.087 0.077 0.23 18 -10000 0 18
PRL -0.037 0.097 -10000 0 -0.44 1 1
cortisol/GR alpha (dimer)/TIF2 0.084 0.18 0.39 26 -10000 0 26
RELA 0.017 0.066 -10000 0 -0.16 20 20
FGG 0.065 0.15 0.33 22 -10000 0 22
GR beta/TIF2 0.049 0.092 0.21 22 -0.25 1 23
IFNG -0.064 0.19 -10000 0 -0.69 7 7
apoptosis 0.096 0.23 0.53 26 -0.41 6 32
CREB1 0.032 0.003 -10000 0 -10000 0 0
histone acetylation -0.055 0.13 -10000 0 -0.33 22 22
BGLAP -0.025 0.11 -10000 0 -0.46 4 4
GR/PKAc 0.09 0.078 0.26 8 -0.14 1 9
NF kappa B1 p50/RelA 0.027 0.11 -10000 0 -0.25 21 21
SMARCD1 0.023 0.031 -10000 0 -10000 0 0
MDM2 0.038 0.064 0.15 24 -10000 0 24
GATA3 0.019 0.08 -10000 0 -0.33 8 8
AKT1 0.027 0.004 -10000 0 -10000 0 0
CSF2 -0.063 0.099 -10000 0 -0.38 2 2
GSK3B 0.036 0.017 -10000 0 -10000 0 0
NR1I3 0.092 0.22 0.5 26 -0.59 2 28
CSN2 0.053 0.12 0.3 14 -10000 0 14
BRG1/BAF155/BAF170/BAF60A 0.051 0.089 -10000 0 -0.2 16 16
NFATC1 0.031 0.03 -10000 0 -0.34 1 1
POU2F1 0.034 0.006 -10000 0 -10000 0 0
CDKN1A -0.055 0.27 -10000 0 -1.2 9 9
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.006 0.016 -10000 0 -10000 0 0
SFN 0.027 0.03 -10000 0 -0.34 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.096 0.078 0.25 12 -10000 0 12
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.051 0.26 0.48 26 -0.54 15 41
JUN -0.033 0.12 0.66 1 -0.32 11 12
IL4 -0.035 0.091 -10000 0 -0.34 4 4
CDK5R1 0.033 0.012 -10000 0 -10000 0 0
PRKACA 0.029 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.03 0.049 -10000 0 -0.21 5 5
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.096 0.078 0.25 12 -10000 0 12
cortisol/GR alpha (monomer) 0.1 0.21 0.45 30 -10000 0 30
NCOA2 0.026 0.03 -10000 0 -0.34 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.006 0.087 -10000 0 -0.29 9 9
AP-1/NFAT1-c-4 -0.041 0.17 -10000 0 -0.43 18 18
AFP -0.017 0.1 0.43 1 -10000 0 1
SUV420H1 0.031 0.007 -10000 0 -10000 0 0
IRF1 0.069 0.1 0.34 6 -10000 0 6
TP53 0.021 0.1 -10000 0 -0.45 7 7
PPP5C 0.029 0.01 -10000 0 -10000 0 0
KRT17 -0.12 0.3 -10000 0 -0.88 20 20
KRT14 -0.029 0.11 -10000 0 -10000 0 0
TBP 0.036 0.031 -10000 0 -0.35 1 1
CREBBP 0.01 0.084 -10000 0 -0.25 16 16
HDAC1 0.027 0.008 -10000 0 -10000 0 0
HDAC2 0.032 0.003 -10000 0 -10000 0 0
AP-1 -0.041 0.17 -10000 0 -0.43 18 18
MAPK14 0.037 0.017 -10000 0 -10000 0 0
MAPK10 0.029 0.023 0.12 2 -10000 0 2
MAPK11 0.029 0.045 -10000 0 -0.34 2 2
KRT5 -0.059 0.14 -10000 0 -0.45 8 8
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.033 0.004 -10000 0 -10000 0 0
STAT1 0.039 0 -10000 0 -10000 0 0
CGA -0.036 0.087 -10000 0 -0.37 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.042 0.11 0.3 6 -0.26 3 9
MAPK3 0.036 0.02 0.12 2 -10000 0 2
MAPK1 0.035 0.018 -10000 0 -10000 0 0
ICAM1 -0.063 0.2 -10000 0 -0.66 12 12
NFKB1 0.016 0.068 -10000 0 -0.16 16 16
MAPK8 -0.026 0.098 0.35 1 -0.31 7 8
MAPK9 0.035 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.095 0.23 0.53 26 -0.42 6 32
BAX -0.007 0.086 -10000 0 -0.43 2 2
POMC -0.22 0.46 -10000 0 -1.2 28 28
EP300 0.01 0.082 -10000 0 -0.25 15 15
cortisol/GR alpha (dimer)/p53 0.088 0.19 0.43 27 -0.36 1 28
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.055 0.18 7 -10000 0 7
SGK1 -0.075 0.35 -10000 0 -1.1 17 17
IL13 -0.058 0.14 -10000 0 -0.6 4 4
IL6 -0.037 0.11 -10000 0 -0.32 10 10
PRKACG 0.025 0.01 -10000 0 -10000 0 0
IL5 -0.05 0.12 -10000 0 -0.51 4 4
IL2 -0.06 0.14 -10000 0 -0.51 6 6
CDK5 0.03 0.014 -10000 0 -10000 0 0
PRKACB 0.029 0.029 -10000 0 -0.34 1 1
HSP90AA1 0.032 0.005 -10000 0 -10000 0 0
IL8 -0.093 0.26 -10000 0 -0.79 18 18
CDK5R1/CDK5 0.044 0.027 0.15 1 -10000 0 1
NF kappa B1 p50/RelA/PKAc 0.059 0.1 -10000 0 -0.2 17 17
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.099 0.18 0.39 34 -10000 0 34
SMARCA4 0.021 0.031 -10000 0 -0.082 6 6
chromatin remodeling 0.034 0.15 0.3 11 -0.37 10 21
NF kappa B1 p50/RelA/Cbp 0.026 0.16 -10000 0 -0.29 28 28
JUN (dimer) -0.033 0.12 0.66 1 -0.32 11 12
YWHAH 0.03 0.009 -10000 0 -10000 0 0
VIPR1 -0.087 0.22 0.34 1 -0.64 20 21
NR3C1 0.059 0.13 0.28 26 -10000 0 26
NR4A1 -0.081 0.21 -10000 0 -0.44 40 40
TIF2/SUV420H1 0.039 0.028 -10000 0 -0.24 1 1
MAPKKK cascade 0.096 0.23 0.53 26 -0.41 6 32
cortisol/GR alpha (dimer)/Src-1 0.099 0.19 0.41 31 -10000 0 31
PBX1 -0.013 0.11 -10000 0 -0.34 18 18
POU1F1 0.021 0.009 -10000 0 -10000 0 0
SELE -0.038 0.12 -10000 0 -0.33 8 8
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.034 0.15 0.3 11 -0.37 10 21
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.099 0.18 0.39 34 -10000 0 34
mol:cortisol 0.048 0.11 0.24 29 -10000 0 29
MMP1 -0.004 0.046 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.022 0.087 -10000 0 -0.19 34 34
CRKL 0.029 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
DOCK1 -0.098 0.17 -10000 0 -0.34 56 56
ITGA4 0.032 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.064 0.047 -10000 0 -0.18 4 4
EPO 0.023 0.012 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.04 0.044 -10000 0 -0.24 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.047 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.029 0.043 -10000 0 -0.22 4 4
lamellipodium assembly 0.014 0.021 -10000 0 -10000 0 0
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
PI3K 0.045 0.011 -10000 0 -10000 0 0
ARF6 0.032 0.005 -10000 0 -10000 0 0
JAK2 0.022 0.03 -10000 0 -0.18 3 3
PXN 0.027 0.04 -10000 0 -0.34 2 2
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
MADCAM1 0.026 0.011 -10000 0 -10000 0 0
cell adhesion 0.062 0.046 -10000 0 -0.18 4 4
CRKL/CBL 0.041 0.017 -10000 0 -10000 0 0
ITGB1 0.032 0.004 -10000 0 -10000 0 0
SRC -0.041 0.097 0.19 2 -0.19 48 50
ITGB7 0.023 0.057 -10000 0 -0.34 4 4
RAC1 0.028 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.007 0.1 -10000 0 -0.2 33 33
p130Cas/Crk/Dock1 -0.092 0.13 -10000 0 -0.21 83 83
VCAM1 -0.048 0.14 -10000 0 -0.34 33 33
RHOA 0.031 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.072 0.037 -10000 0 -0.18 2 2
BCAR1 -0.059 0.1 0.24 3 -0.2 49 52
EPOR 0.02 0.057 -10000 0 -0.34 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.03 0.008 -10000 0 -10000 0 0
GIT1 0.03 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.021 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.03 0.008 -9999 0 -10000 0 0
EGFR 0.021 0.011 -9999 0 -10000 0 0
EGF/EGFR 0.005 0.082 -9999 0 -0.16 30 30
EGF/EGFR dimer/SHC/GRB2/SOS1 0.038 0.088 -9999 0 -0.17 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.023 0.011 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.026 0.12 -9999 0 -0.34 23 23
EGF/EGFR dimer/SHC 0.013 0.086 -9999 0 -0.2 22 22
mol:GDP 0.033 0.084 -9999 0 -0.17 21 21
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.013 0.079 -9999 0 -0.34 8 8
GRB2/SOS1 0.045 0.012 -9999 0 -10000 0 0
HRAS/GTP 0.018 0.073 -9999 0 -0.16 21 21
SHC1 0.032 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.032 0.082 -9999 0 -0.17 21 21
FRAP1 -0.03 0.052 -9999 0 -0.16 21 21
EGF/EGFR dimer -0.005 0.092 -9999 0 -0.24 22 22
SOS1 0.032 0.003 -9999 0 -10000 0 0
GRB2 0.03 0.008 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.027 0.06 -9999 0 -0.23 8 8
LPA4-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
ADCY4 -0.015 0.045 -10000 0 -0.22 7 7
ADCY5 -0.013 0.025 -10000 0 -0.2 3 3
ADCY6 -0.033 0.065 -10000 0 -0.2 23 23
ADCY7 -0.017 0.048 -10000 0 -0.25 6 6
ADCY1 -0.01 0.037 -10000 0 -0.2 6 6
ADCY2 -0.026 0.068 -10000 0 -0.2 20 20
ADCY3 -0.017 0.04 -10000 0 -0.2 8 8
ADCY8 -0.012 0.02 -10000 0 -0.18 2 2
PRKCE 0.004 0.032 -10000 0 -0.23 3 3
ADCY9 -0.034 0.069 -10000 0 -0.2 23 23
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.014 0.088 0.25 4 -0.28 6 10
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.007 0.11 -10000 0 -0.19 38 38
SMAD6-7/SMURF1 0.028 0.081 -10000 0 -0.19 18 18
NOG -0.022 0.12 -10000 0 -0.34 22 22
SMAD9 0.01 0.047 -10000 0 -10000 0 0
SMAD4 0.031 0.006 -10000 0 -10000 0 0
SMAD5 -0.038 0.12 -10000 0 -0.33 15 15
BMP7/USAG1 0.027 0.014 -10000 0 -10000 0 0
SMAD5/SKI -0.033 0.13 -10000 0 -0.3 19 19
SMAD1 -0.022 0.11 -10000 0 -0.32 11 11
BMP2 0.008 0.073 -10000 0 -0.34 7 7
SMAD1/SMAD1/SMAD4 -0.017 0.11 -10000 0 -0.28 10 10
BMPR1A 0.014 0.069 -10000 0 -0.34 6 6
BMPR1B -0.023 0.12 -10000 0 -0.34 21 21
BMPR1A-1B/BAMBI -0.007 0.11 -10000 0 -0.21 35 35
AHSG 0.019 0.007 -10000 0 -10000 0 0
CER1 0.017 0.005 -10000 0 -10000 0 0
BMP2-4/CER1 0.032 0.052 -10000 0 -0.2 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.034 0.12 -10000 0 -0.3 19 19
BMP2-4 (homodimer) 0.023 0.056 -10000 0 -0.24 7 7
RGMB 0.023 0.05 -10000 0 -0.34 3 3
BMP6/BMPR2/BMPR1A-1B 0.007 0.12 -10000 0 -0.2 38 38
RGMA -0.001 0.095 -10000 0 -0.34 12 12
SMURF1 0.028 0.012 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.041 0.12 -10000 0 -0.33 18 18
BMP2-4/USAG1 0.032 0.053 -10000 0 -0.2 7 7
SMAD6/SMURF1/SMAD5 -0.027 0.12 0.32 1 -0.3 17 18
SOSTDC1 0.022 0.013 -10000 0 -10000 0 0
BMP7/BMPR2/BMPR1A-1B 0 0.12 -10000 0 -0.2 38 38
SKI 0.03 0.008 -10000 0 -10000 0 0
BMP6 (homodimer) 0.026 0.041 -10000 0 -0.34 2 2
HFE2 0.029 0.007 -10000 0 -10000 0 0
ZFYVE16 0.03 0.008 -10000 0 -10000 0 0
MAP3K7 0.032 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.036 0.053 -10000 0 -0.2 7 7
SMAD5/SMAD5/SMAD4 -0.034 0.13 0.32 1 -0.31 18 19
MAPK1 0.029 0.009 -10000 0 -10000 0 0
TAK1/TAB family -0.019 0.12 -10000 0 -0.27 18 18
BMP7 (homodimer) 0.017 0.004 -10000 0 -10000 0 0
NUP214 0.031 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.033 0.032 -10000 0 -0.24 2 2
SMAD1/SKI -0.013 0.11 -10000 0 -0.31 11 11
SMAD6 0.01 0.084 -10000 0 -0.34 9 9
CTDSP2 0.032 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.033 0.052 -10000 0 -0.2 7 7
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.019 0.01 -10000 0 -10000 0 0
BMPR2 (homodimer) -0.003 0.11 -10000 0 -0.34 16 16
GADD34/PP1CA 0.057 0.023 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.007 0.1 -10000 0 -0.23 27 27
CHRDL1 -0.032 0.13 -10000 0 -0.34 24 24
ENDOFIN/SMAD1 -0.012 0.11 0.26 1 -0.31 11 12
SMAD6-7/SMURF1/SMAD1 -0.008 0.12 -10000 0 -0.3 10 10
SMAD6/SMURF1 0.027 0.012 -10000 0 -10000 0 0
BAMBI -0.001 0.095 -10000 0 -0.34 12 12
SMURF2 0.03 0.008 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.003 0.1 -10000 0 -0.22 28 28
BMP2-4/GREM1 0.033 0.051 -10000 0 -0.19 7 7
SMAD7 0.011 0.084 -10000 0 -0.34 9 9
SMAD8A/SMAD8A/SMAD4 0.022 0.066 0.27 1 -0.35 1 2
SMAD1/SMAD6 -0.011 0.11 0.26 1 -0.31 9 10
TAK1/SMAD6 0.041 0.017 -10000 0 -10000 0 0
BMP7 0.017 0.004 -10000 0 -10000 0 0
BMP6 0.026 0.041 -10000 0 -0.34 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.041 0.12 -10000 0 -0.32 19 19
PPM1A 0.032 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.013 0.11 0.26 1 -0.31 11 12
SMAD7/SMURF1 0.025 0.065 -10000 0 -0.24 9 9
CTDSPL -0.016 0.12 -10000 0 -0.34 21 21
PPP1CA 0.031 0.007 -10000 0 -10000 0 0
XIAP 0.029 0.01 -10000 0 -10000 0 0
CTDSP1 0.032 0.003 -10000 0 -10000 0 0
PPP1R15A 0.029 0.01 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.04 0.12 -10000 0 -0.35 15 15
CHRD 0.024 0.009 -10000 0 -10000 0 0
BMPR2 -0.003 0.11 -10000 0 -0.34 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.042 0.13 -10000 0 -0.38 14 14
BMP4 0.023 0.012 -10000 0 -10000 0 0
FST 0.022 0.011 -10000 0 -10000 0 0
BMP2-4/NOG 0.006 0.095 -10000 0 -0.2 28 28
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.011 0.11 -10000 0 -0.19 34 34
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.023 0.11 0.53 6 -10000 0 6
VDR -0.001 0.1 -10000 0 -0.34 14 14
FAM120B 0.031 0.007 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.005 0.12 -10000 0 -0.28 24 24
RXRs/LXRs/DNA/Oxysterols -0.019 0.16 -10000 0 -0.39 25 25
MED1 0.03 0.009 -10000 0 -10000 0 0
mol:9cRA -0.003 0.018 -10000 0 -0.083 1 1
RARs/THRs/DNA/Src-1 0.021 0.049 -10000 0 -0.18 9 9
RXRs/NUR77 0.028 0.1 -10000 0 -0.21 19 19
RXRs/PPAR -0.023 0.11 -10000 0 -0.22 34 34
NCOR2 0.032 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.001 0.071 -10000 0 -0.23 14 14
RARs/VDR/DNA/Vit D3 0.046 0.071 -10000 0 -0.16 15 15
RARA 0.03 0.009 -10000 0 -10000 0 0
NCOA1 0.032 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA -0.001 0.1 -10000 0 -0.34 14 14
RARs/RARs/DNA/9cRA 0.046 0.032 -10000 0 -0.16 2 2
RARG 0.03 0.029 -10000 0 -0.34 1 1
RPS6KB1 0.025 0.089 0.58 4 -10000 0 4
RARs/THRs/DNA/SMRT 0.021 0.049 -10000 0 -0.18 9 9
THRA 0.03 0.009 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.001 0.071 -10000 0 -0.23 14 14
RXRs/PPAR/9cRA/PGJ2/DNA 0.031 0.087 -10000 0 -0.17 25 25
NR1H4 0.017 0.002 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.051 0.11 -10000 0 -0.21 23 23
NR1H2 0.022 0.03 -10000 0 -0.082 1 1
NR1H3 0.021 0.042 -10000 0 -0.21 2 2
RXRs/VDR/DNA/Vit D3 0.026 0.098 -10000 0 -0.2 19 19
NR4A1 -0.002 0.1 -10000 0 -0.34 14 14
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.004 0.061 -10000 0 -0.23 6 6
RXRG 0.011 0.029 -10000 0 -0.09 1 1
RXR alpha/CCPG 0.028 0.06 -10000 0 -0.24 6 6
RXRA 0.011 0.076 -10000 0 -0.36 6 6
RXRB 0.024 0.033 -10000 0 -0.094 1 1
THRB 0.012 0.074 -10000 0 -0.34 7 7
PPARG -0.047 0.14 -10000 0 -0.34 31 31
PPARD 0.026 0.049 -10000 0 -0.34 3 3
TNF -0.061 0.27 -10000 0 -0.67 23 23
mol:Oxysterols -0.002 0.016 -10000 0 -0.072 1 1
cholesterol transport -0.018 0.16 -10000 0 -0.39 25 25
PPARA 0.028 0.03 -10000 0 -0.34 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.028 0.03 -10000 0 -0.34 1 1
RXRs/NUR77/BCL2 -0.004 0.074 -10000 0 -0.2 19 19
SREBF1 -0.02 0.15 -10000 0 -0.37 23 23
RXRs/RXRs/DNA/9cRA 0.031 0.087 -10000 0 -0.17 25 25
ABCA1 -0.06 0.26 -10000 0 -0.85 14 14
RARs/THRs 0.07 0.065 -10000 0 -0.17 9 9
RXRs/FXR 0.041 0.077 -10000 0 -0.21 7 7
BCL2 0.031 0.006 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.029 0.009 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.009 0.051 -10000 0 -0.17 10 10
NT3 (dimer)/TRKC 0.029 0.01 -10000 0 -10000 0 0
NT3 (dimer)/TRKB -0.003 0.098 -10000 0 -0.21 30 30
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.026 -10000 0 -0.18 2 2
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
BDNF 0.023 0.05 -10000 0 -0.34 3 3
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
DYNLT1 0.032 0.004 -10000 0 -10000 0 0
NTRK1 -0.025 0.12 -10000 0 -0.34 22 22
NTRK2 -0.021 0.12 -10000 0 -0.34 21 21
NTRK3 0.022 0.012 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB -0.002 0.097 -10000 0 -0.21 29 29
neuron apoptosis 0.033 0.12 0.29 17 -10000 0 17
SHC 2-3/Grb2 -0.036 0.13 -10000 0 -0.32 17 17
SHC1 0.032 0.004 -10000 0 -10000 0 0
SHC2 -0.044 0.13 -10000 0 -0.36 18 18
SHC3 -0.038 0.12 -10000 0 -0.34 14 14
STAT3 (dimer) 0.026 0.058 -10000 0 -0.3 5 5
NT3 (dimer)/TRKA -0.003 0.1 -10000 0 -0.21 30 30
RIN/GDP 0.009 0.079 0.3 2 -0.25 4 6
GIPC1 0.023 0.05 -10000 0 -0.34 3 3
KRAS 0.031 0.006 -10000 0 -10000 0 0
DNAJA3 -0.031 0.094 0.18 4 -0.2 30 34
RIN/GTP 0.012 0.002 -10000 0 -10000 0 0
CCND1 0.002 0.11 -10000 0 -0.6 5 5
MAGED1 0.016 0.069 -10000 0 -0.34 6 6
PTPN11 0.032 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.016 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.06 0.018 -10000 0 -10000 0 0
GRB2 0.03 0.008 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.005 0.097 -10000 0 -0.21 26 26
TRKA/NEDD4-2 -0.017 0.11 -10000 0 -0.24 32 32
ELMO1 0.028 0.011 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 -0.044 0.11 -10000 0 -0.19 55 55
NGF 0.018 0.005 -10000 0 -10000 0 0
HRAS 0.03 0.008 -10000 0 -10000 0 0
DOCK1 -0.098 0.17 -10000 0 -0.34 56 56
GAB2 0.031 0.007 -10000 0 -10000 0 0
RIT2 0.017 0.003 -10000 0 -10000 0 0
RIT1 0.032 0.004 -10000 0 -10000 0 0
FRS2 0.032 0.004 -10000 0 -10000 0 0
DNM1 -0.007 0.11 -10000 0 -0.34 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.017 0.098 0.19 3 -0.2 29 32
mol:GDP 0.006 0.11 0.32 3 -0.35 5 8
NGF (dimer) 0.018 0.005 -10000 0 -10000 0 0
RhoG/GDP 0.021 0.008 -10000 0 -10000 0 0
RIT1/GDP 0.012 0.076 0.26 1 -0.25 4 5
TIAM1 0.003 0.091 -10000 0 -0.34 11 11
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.013 0.096 -10000 0 -0.2 26 26
KIDINS220/CRKL/C3G 0.043 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.044 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.063 0.022 -10000 0 -0.2 1 1
SHC/GRB2/SOS1/GAB1 0.072 0.037 -10000 0 -0.18 2 2
RIT1/GTP 0.024 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.017 0.004 -10000 0 -10000 0 0
RAP1/GDP 0.009 0.063 -10000 0 -0.21 4 4
KIDINS220/CRKL 0.029 0.009 -10000 0 -10000 0 0
BDNF (dimer) 0.023 0.05 -10000 0 -0.34 3 3
ubiquitin-dependent protein catabolic process -0.004 0.099 -10000 0 -0.2 32 32
Schwann cell development -0.022 0.023 -10000 0 -10000 0 0
EHD4 0.023 0.057 -10000 0 -0.34 4 4
FRS2 family/GRB2/SOS1 0.075 0.031 -10000 0 -0.18 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.027 0.038 -10000 0 -0.19 3 3
RAP1B 0.031 0.006 -10000 0 -10000 0 0
RAP1A 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.003 0.1 -10000 0 -0.19 35 35
ABL1 0.031 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.045 0.012 -10000 0 -10000 0 0
Rap1/GTP 0.023 0.052 -10000 0 -0.24 1 1
STAT3 0.026 0.058 -10000 0 -0.3 5 5
axon guidance -0.012 0.093 -10000 0 -0.18 35 35
MAPK3 -0.033 0.078 0.18 3 -0.2 26 29
MAPK1 -0.032 0.078 0.18 3 -0.2 26 29
CDC42/GDP 0.014 0.075 0.23 2 -0.24 4 6
NTF3 0.017 0.004 -10000 0 -10000 0 0
NTF4 0.016 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.013 0.087 -10000 0 -0.2 23 23
PI3K 0.045 0.011 -10000 0 -10000 0 0
FRS3 0.03 0.029 -10000 0 -0.34 1 1
FAIM 0.029 0.029 -10000 0 -0.34 1 1
GAB1 0.027 0.041 -10000 0 -0.34 2 2
RASGRF1 -0.032 0.1 0.18 4 -0.21 32 36
SOS1 0.032 0.003 -10000 0 -10000 0 0
MCF2L -0.026 0.059 -10000 0 -0.2 16 16
RGS19 0.031 0.006 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.085 0.28 1 -0.34 4 5
Rac1/GDP 0.01 0.079 0.27 3 -0.24 4 7
NGF (dimer)/TRKA/GRIT -0.002 0.077 -10000 0 -0.2 22 22
neuron projection morphogenesis -0.052 0.2 -10000 0 -0.76 9 9
NGF (dimer)/TRKA/NEDD4-2 -0.004 0.1 -10000 0 -0.2 32 32
MAP2K1 -0.004 0.06 0.22 9 -0.17 2 11
NGFR 0.003 0.091 -10000 0 -0.34 11 11
NGF (dimer)/TRKA/GIPC/GAIP -0.026 0.12 -10000 0 -0.23 35 35
RAS family/GTP/PI3K 0.027 0.011 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.087 0.034 -10000 0 -0.17 1 1
NRAS 0.032 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.045 0.012 -10000 0 -10000 0 0
PRKCI 0.031 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.028 0.011 -10000 0 -10000 0 0
PRKCZ -0.025 0.13 -10000 0 -0.34 25 25
MAPKKK cascade -0.048 0.18 -10000 0 -0.46 25 25
RASA1 0.03 0.008 -10000 0 -10000 0 0
TRKA/c-Abl 0.004 0.094 -10000 0 -0.24 22 22
SQSTM1 0.03 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.027 0.095 -10000 0 -0.19 25 25
NGF (dimer)/TRKA/p62/Atypical PKCs 0.004 0.11 -10000 0 -0.18 44 44
MATK 0.016 0.069 -10000 0 -0.34 6 6
NEDD4L 0.002 0.091 -10000 0 -0.34 11 11
RAS family/GDP -0.015 0.041 -10000 0 -0.18 4 4
NGF (dimer)/TRKA -0.025 0.099 0.19 4 -0.21 30 34
Rac1/GTP -0.055 0.085 -10000 0 -0.2 27 27
FRS2 family/SHP2/CRK family 0.081 0.04 -10000 0 -0.17 1 1
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.026 0.022 -10000 0 -10000 0 0
HSPA8 0.03 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.018 0.13 0.22 11 -0.24 20 31
AKT1 0.025 0.031 -10000 0 -0.1 2 2
GSC 0.012 0.034 -10000 0 -10000 0 0
NKX2-5 0.012 0.024 -10000 0 -0.093 1 1
muscle cell differentiation 0.014 0.1 0.27 5 -10000 0 5
SMAD2-3/SMAD4/SP1 -0.006 0.15 -10000 0 -0.26 25 25
SMAD4 -0.007 0.078 -10000 0 -0.16 15 15
CBFB 0.031 0.007 -10000 0 -10000 0 0
SAP18 0.031 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.048 0.038 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.019 0.11 -10000 0 -0.2 19 19
MYC 0.024 0.054 -10000 0 -0.34 3 3
CDKN2B -0.086 0.32 -10000 0 -1.1 13 13
AP1 -0.018 0.13 -10000 0 -0.3 21 21
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.023 0.083 -10000 0 -0.41 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.017 0.095 -10000 0 -0.3 12 12
SP3 0.028 0.023 -10000 0 -10000 0 0
CREB1 0.032 0.003 -10000 0 -10000 0 0
FOXH1 0.013 0.06 -10000 0 -0.34 4 4
SMAD3/SMAD4/GR 0.011 0.1 0.2 1 -0.19 14 15
GATA3 0.01 0.085 -10000 0 -0.22 16 16
SKI/SIN3/HDAC complex/NCoR1 0.027 0.075 -10000 0 -0.81 1 1
MEF2C/TIF2 -0.021 0.11 0.27 1 -0.34 13 14
endothelial cell migration 0.1 0.33 0.76 29 -10000 0 29
MAX 0.034 0.014 -10000 0 -10000 0 0
RBBP7 0.029 0.01 -10000 0 -10000 0 0
RBBP4 0.031 0.006 -10000 0 -10000 0 0
RUNX2 0.026 0.049 -10000 0 -0.34 3 3
RUNX3 0.013 0.079 -10000 0 -0.34 8 8
RUNX1 0.031 0.007 -10000 0 -10000 0 0
CTBP1 0.031 0.006 -10000 0 -10000 0 0
NR3C1 0.032 0.016 -10000 0 -10000 0 0
VDR -0.001 0.1 -10000 0 -0.34 14 14
CDKN1A -0.07 0.26 -10000 0 -1.1 9 9
KAT2B 0.028 0.015 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.015 0.081 -10000 0 -0.18 8 8
DCP1A 0.031 0.007 -10000 0 -10000 0 0
SKI 0.03 0.008 -10000 0 -10000 0 0
SERPINE1 -0.11 0.33 -10000 0 -0.77 29 29
SMAD3/SMAD4/ATF2 0.01 0.1 -10000 0 -0.2 15 15
SMAD3/SMAD4/ATF3 0.001 0.11 -10000 0 -0.2 22 22
SAP30 0.027 0.041 -10000 0 -0.34 2 2
Cbp/p300/PIAS3 0.054 0.041 -10000 0 -10000 0 0
JUN -0.03 0.12 -10000 0 -0.32 18 18
SMAD3/SMAD4/IRF7 0.01 0.098 -10000 0 -0.21 11 11
TFE3 0.005 0.057 -10000 0 -0.11 24 24
COL1A2 -0.13 0.3 -10000 0 -0.72 34 34
mesenchymal cell differentiation -0.006 0.1 0.19 17 -10000 0 17
DLX1 0.028 0.009 -10000 0 -10000 0 0
TCF3 0.029 0.01 -10000 0 -10000 0 0
FOS 0.005 0.084 -10000 0 -0.36 7 7
SMAD3/SMAD4/Max 0.012 0.1 0.2 1 -0.19 15 16
Cbp/p300/SNIP1 0.054 0.032 -10000 0 -10000 0 0
ZBTB17 0.034 0.018 -10000 0 -10000 0 0
LAMC1 -0.065 0.17 0.21 1 -0.42 28 29
TGIF2/HDAC complex/SMAD3/SMAD4 0.01 0.1 -10000 0 -0.19 15 15
IRF7 0.03 0.011 -10000 0 -10000 0 0
ESR1 0.011 0.097 -10000 0 -0.34 11 11
HNF4A 0.019 0.008 -10000 0 -10000 0 0
MEF2C -0.015 0.12 0.21 11 -0.36 13 24
SMAD2-3/SMAD4 0.007 0.11 -10000 0 -0.21 16 16
Cbp/p300/Src-1 0.053 0.036 -10000 0 -10000 0 0
IGHV3OR16-13 0.005 0.021 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.031 0.006 -10000 0 -10000 0 0
CREBBP 0.028 0.018 -10000 0 -10000 0 0
SKIL 0.027 0.041 -10000 0 -0.34 2 2
HDAC1 0.031 0.006 -10000 0 -10000 0 0
HDAC2 0.032 0.003 -10000 0 -10000 0 0
SNIP1 0.031 0.006 -10000 0 -10000 0 0
GCN5L2 0 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.009 0.13 -10000 0 -0.25 30 30
MSG1/HSC70 0.041 0.016 -10000 0 -10000 0 0
SMAD2 0.018 0.04 -10000 0 -0.13 1 1
SMAD3 -0.006 0.08 -10000 0 -0.17 16 16
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.002 0.07 -10000 0 -0.21 9 9
SMAD2/SMAD2/SMAD4 -0.014 0.051 -10000 0 -0.28 3 3
NCOR1 0.03 0.009 -10000 0 -10000 0 0
NCOA2 0.026 0.03 -10000 0 -0.34 1 1
NCOA1 0.032 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.033 0.012 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.002 0.15 -10000 0 -0.26 23 23
IFNB1 -0.005 0.083 0.25 4 -0.21 6 10
SMAD3/SMAD4/MEF2C -0.005 0.15 0.26 6 -0.31 18 24
CITED1 0.027 0.011 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.016 0.1 -10000 0 -0.2 12 12
RBL1 0.029 0.029 -10000 0 -0.34 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.03 0.14 -10000 0 -0.46 13 13
RUNX1-3/PEBPB2 0.046 0.057 -10000 0 -0.19 8 8
SMAD7 -0.067 0.22 -10000 0 -0.56 19 19
MYC/MIZ-1 0.04 0.054 0.18 10 -0.24 3 13
SMAD3/SMAD4 -0.016 0.12 0.2 1 -0.39 12 13
IL10 -0.035 0.13 0.2 1 -0.35 17 18
PIASy/HDAC complex 0.028 0.018 -10000 0 -10000 0 0
PIAS3 0.029 0.015 -10000 0 -10000 0 0
CDK2 0.028 0.017 -10000 0 -10000 0 0
IL5 -0.021 0.1 0.26 2 -0.24 18 20
CDK4 0.029 0.018 -10000 0 -10000 0 0
PIAS4 0.028 0.018 -10000 0 -10000 0 0
ATF3 0.017 0.069 -10000 0 -0.34 6 6
SMAD3/SMAD4/SP1 -0.019 0.15 -10000 0 -0.24 33 33
FOXG1 -0.009 0.016 -10000 0 -10000 0 0
FOXO3 0.007 0.033 -10000 0 -0.13 2 2
FOXO1 -0.002 0.057 -10000 0 -0.2 9 9
FOXO4 0.008 0.028 -10000 0 -0.11 2 2
heart looping -0.015 0.12 0.21 11 -0.35 13 24
CEBPB 0.017 0.06 -10000 0 -0.34 4 4
SMAD3/SMAD4/DLX1 0.01 0.099 -10000 0 -0.19 15 15
MYOD1 0.017 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.005 0.097 -10000 0 -0.2 14 14
SMAD3/SMAD4/GATA3 -0.002 0.13 -10000 0 -0.26 22 22
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.041 -10000 0 -0.34 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.021 0.11 -10000 0 -0.18 17 17
SMAD3/SMAD4/SP1-3 -0.004 0.15 -10000 0 -0.26 28 28
MED15 0.029 0.009 -10000 0 -10000 0 0
SP1 -0.006 0.068 -10000 0 -0.12 28 28
SIN3B 0.03 0.009 -10000 0 -10000 0 0
SIN3A 0.031 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.021 0.096 -10000 0 -0.21 16 16
ITGB5 -0.05 0.14 0.22 1 -0.35 21 22
TGIF/SIN3/HDAC complex/CtBP 0.03 0.059 -10000 0 -0.42 2 2
SMAD3/SMAD4/AR -0.038 0.13 -10000 0 -0.22 44 44
AR -0.049 0.14 -10000 0 -0.34 31 31
negative regulation of cell growth -0.003 0.093 -10000 0 -0.27 7 7
SMAD3/SMAD4/MYOD 0 0.096 -10000 0 -0.2 15 15
E2F5 0.017 0.063 -10000 0 -0.34 5 5
E2F4 0.031 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.038 0.083 -10000 0 -0.17 5 5
SMAD2-3/SMAD4/FOXO1-3a-4 -0.008 0.11 0.18 2 -0.33 12 14
TFDP1 0.028 0.029 -10000 0 -0.34 1 1
SMAD3/SMAD4/AP1 -0.001 0.14 0.25 2 -0.3 21 23
SMAD3/SMAD4/RUNX2 0.007 0.1 -10000 0 -0.19 17 17
TGIF2 0.031 0.006 -10000 0 -10000 0 0
TGIF1 0.027 0.041 -10000 0 -0.34 2 2
ATF2 0.03 0.029 -10000 0 -0.34 1 1
Ceramide signaling pathway

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
SPHK2 -0.003 0.059 -10000 0 -0.24 10 10
MAP4K4 0.006 0.065 -10000 0 -0.28 4 4
BAG4 0.029 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.021 0.087 -10000 0 -0.19 31 31
NFKBIA 0.032 0.005 -10000 0 -10000 0 0
BIRC3 0.024 0.05 -10000 0 -0.34 3 3
BAX -0.015 0.094 -10000 0 -0.35 11 11
RIPK1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.008 0.1 0.76 3 -10000 0 3
BAD -0.009 0.068 0.21 5 -0.19 12 17
SMPD1 0.018 0.062 0.18 6 -0.18 4 10
RB1 -0.01 0.06 0.2 3 -0.18 11 14
FADD/Caspase 8 0.017 0.061 -10000 0 -0.29 3 3
MAP2K4 -0.017 0.055 0.22 1 -0.18 11 12
NSMAF 0.028 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.013 0.054 0.18 2 -0.18 10 12
EGF -0.026 0.12 -10000 0 -0.34 23 23
mol:ceramide -0.015 0.063 0.1 6 -0.2 14 20
MADD 0.031 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.002 0.057 -10000 0 -0.24 9 9
ASAH1 0.029 0.01 -10000 0 -10000 0 0
negative regulation of cell cycle -0.01 0.059 0.2 3 -0.18 11 14
cell proliferation 0 0.072 0.18 1 -0.16 12 13
BID 0.013 0.1 -10000 0 -0.55 4 4
MAP3K1 -0.014 0.06 0.18 2 -0.19 13 15
EIF2A -0.018 0.058 0.18 3 -0.19 9 12
TRADD 0.031 0.006 -10000 0 -10000 0 0
CRADD 0.029 0.029 -10000 0 -0.34 1 1
MAPK3 -0.007 0.053 0.16 4 -0.17 6 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.007 0.055 0.16 4 -0.19 6 10
Cathepsin D/ceramide 0.002 0.064 -10000 0 -0.19 13 13
FADD 0.008 0.062 -10000 0 -0.28 4 4
KSR1 -0.012 0.056 0.16 2 -0.19 11 13
MAPK8 -0.036 0.093 -10000 0 -0.22 25 25
PRKRA -0.017 0.059 -10000 0 -0.19 14 14
PDGFA 0 0.091 -10000 0 -0.34 11 11
TRAF2 0.031 0.006 -10000 0 -10000 0 0
IGF1 0 0.099 -10000 0 -0.34 13 13
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.015 0.063 0.1 6 -0.2 14 20
CTSD 0.03 0.009 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.044 0.013 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0 0.077 0.19 1 -0.18 11 12
PRKCD 0.017 0.069 -10000 0 -0.34 6 6
PRKCZ -0.025 0.13 -10000 0 -0.34 25 25
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.002 0.057 -10000 0 -0.24 9 9
RelA/NF kappa B1 0.044 0.013 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.002 0.086 -10000 0 -0.34 10 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.066 -10000 0 -0.29 4 4
TNFR1A/BAG4/TNF-alpha 0.038 0.066 -10000 0 -0.2 11 11
mol:Sphingosine-1-phosphate -0.003 0.059 -10000 0 -0.24 10 10
MAP2K1 -0.014 0.052 0.17 2 -0.18 9 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.031 0.007 -10000 0 -10000 0 0
CYCS -0.013 0.058 -10000 0 -0.19 10 10
TNFRSF1A 0.032 0.005 -10000 0 -10000 0 0
NFKB1 0.031 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.042 0.016 -10000 0 -10000 0 0
EIF2AK2 -0.018 0.059 0.22 1 -0.19 13 14
TNF-alpha/TNFR1A/FAN 0.036 0.066 -10000 0 -0.2 11 11
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.033 0.043 -10000 0 -10000 0 0
MAP2K2 -0.01 0.051 0.18 4 -0.17 8 12
SMPD3 0.015 0.058 -10000 0 -0.21 4 4
TNF -0.002 0.098 -10000 0 -0.34 13 13
PKC zeta/PAR4 -0.02 0.11 -10000 0 -0.24 33 33
mol:PHOSPHOCHOLINE 0.022 0.087 0.2 23 -0.16 8 31
NF kappa B1/RelA/I kappa B alpha 0.032 0.1 -10000 0 -0.17 29 29
AIFM1 -0.01 0.062 0.14 3 -0.18 12 15
BCL2 0.031 0.006 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.039 0.019 -10000 0 -10000 0 0
VLDLR -0.042 0.14 -10000 0 -0.34 30 30
CRKL 0.029 0.009 -10000 0 -10000 0 0
LRPAP1 0.031 0.006 -10000 0 -10000 0 0
FYN 0.026 0.049 -10000 0 -0.34 3 3
ITGA3 0.02 0.05 -10000 0 -0.34 3 3
RELN/VLDLR/Fyn -0.001 0.097 -10000 0 -0.2 32 32
MAPK8IP1/MKK7/MAP3K11/JNK1 0.078 0.048 -10000 0 -0.17 3 3
AKT1 -0.019 0.077 -10000 0 -0.19 27 27
MAP2K7 0.029 0.009 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
DAB1 0.022 0.009 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.039 0.036 -10000 0 -0.18 3 3
LRPAP1/LRP8 0.04 0.039 -10000 0 -0.24 3 3
RELN/LRP8/DAB1/Fyn 0.047 0.049 -10000 0 -0.17 6 6
DAB1/alpha3/beta1 Integrin 0.009 0.094 -10000 0 -0.17 31 31
long-term memory 0.047 0.051 -10000 0 -0.18 6 6
DAB1/LIS1 0.022 0.095 -10000 0 -0.16 31 31
DAB1/CRLK/C3G 0.014 0.087 -10000 0 -0.16 29 29
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
DAB1/NCK2 0.023 0.097 -10000 0 -0.17 32 32
ARHGEF2 0.032 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.022 0.008 -10000 0 -10000 0 0
CDK5R1 0.03 0.009 -10000 0 -10000 0 0
RELN 0.02 0.013 -10000 0 -10000 0 0
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.041 0.052 -10000 0 -0.2 6 6
GRIN2A/RELN/LRP8/DAB1/Fyn 0.058 0.055 -10000 0 -0.18 6 6
MAPK8 0.031 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0 0.083 -10000 0 -0.18 29 29
ITGB1 0.032 0.004 -10000 0 -10000 0 0
MAP1B -0.018 0.083 0.17 7 -0.17 34 41
RELN/LRP8 0.045 0.041 -10000 0 -0.2 3 3
GRIN2B/RELN/LRP8/DAB1/Fyn 0.054 0.054 -10000 0 -0.18 6 6
PI3K 0.045 0.011 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.04 -10000 0 -0.24 3 3
RAP1A -0.006 0.12 0.3 13 -10000 0 13
PAFAH1B1 0.029 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.05 -10000 0 -0.34 3 3
CRLK/C3G 0.043 0.015 -10000 0 -10000 0 0
GRIN2B 0.018 0.007 -10000 0 -10000 0 0
NCK2 0.032 0 -10000 0 -10000 0 0
neuron differentiation 0.016 0.049 0.17 1 -10000 0 1
neuron adhesion -0.006 0.13 0.34 13 -0.29 2 15
LRP8 0.025 0.049 -10000 0 -0.34 3 3
GSK3B -0.017 0.071 -10000 0 -0.18 24 24
RELN/VLDLR/DAB1/Fyn 0.008 0.089 -10000 0 -0.17 32 32
MAP3K11 0.031 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.014 0.083 -10000 0 -0.2 27 27
CDK5 0.028 0.012 -10000 0 -10000 0 0
MAPT 0.016 0.11 0.73 4 -10000 0 4
neuron migration -0.033 0.089 0.24 3 -0.21 12 15
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.015 0.047 -10000 0 -10000 0 0
RELN/VLDLR 0.013 0.097 -10000 0 -0.18 32 32
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.024 0.2 1 -10000 0 1
AES 0.032 0.022 0.17 1 -10000 0 1
FBXW11 0.031 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.006 0.1 -10000 0 -0.24 24 24
SMAD4 0.031 0.006 -10000 0 -10000 0 0
DKK2 -0.026 0.12 -10000 0 -0.34 22 22
TLE1 -0.002 0.11 0.18 1 -0.34 15 16
MACF1 0.031 0.006 -10000 0 -10000 0 0
CTNNB1 -0.037 0.14 0.25 1 -0.4 12 13
WIF1 0.018 0.011 -10000 0 -10000 0 0
beta catenin/RanBP3 -0.01 0.14 0.31 10 -0.4 8 18
KREMEN2 0.027 0.041 -10000 0 -0.34 2 2
DKK1 0.02 0.009 -10000 0 -10000 0 0
beta catenin/beta TrCP1 -0.019 0.13 0.26 1 -0.36 11 12
FZD1 0.018 0.057 -10000 0 -0.34 4 4
AXIN2 -0.033 0.26 0.47 3 -1.2 7 10
AXIN1 0.031 0.006 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.007 0.16 -10000 0 -0.75 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.038 0.19 -10000 0 -0.54 14 14
Axin1/APC/GSK3 -0.005 0.095 0.26 1 -0.42 5 6
Axin1/APC/GSK3/beta catenin/Macf1 -0.023 0.14 -10000 0 -0.48 8 8
HNF1A 0.032 0.035 0.18 1 -0.34 1 2
CTBP1 0.033 0.02 0.18 1 -10000 0 1
MYC 0.064 0.29 0.63 23 -1.3 3 26
RANBP3 0.03 0.009 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.017 0.11 -10000 0 -0.2 42 42
NKD1 0.012 0.074 -10000 0 -0.34 7 7
TCF4 0.013 0.085 0.18 1 -0.33 9 10
TCF3 0.032 0.022 0.18 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.024 0.093 -10000 0 -0.19 24 24
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.001 0.14 0.41 12 -0.35 5 17
LEF1 0.009 0.087 0.18 1 -0.33 10 11
DVL1 0.01 0.063 -10000 0 -0.42 2 2
CSNK2A1 0.032 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.052 0.2 0.26 2 -0.54 17 19
DKK1/LRP6/Kremen 2 0.011 0.087 -10000 0 -0.2 23 23
LRP6 -0.026 0.12 -10000 0 -0.34 21 21
CSNK1A1 0.032 0.024 0.19 1 -10000 0 1
NLK 0.029 0.012 -10000 0 -10000 0 0
CCND1 -0.006 0.25 0.64 7 -1.1 6 13
WNT1 0.028 0.012 -10000 0 -10000 0 0
GSK3A 0.029 0.01 -10000 0 -10000 0 0
GSK3B 0.031 0.007 -10000 0 -10000 0 0
FRAT1 0.032 0.005 -10000 0 -10000 0 0
PPP2R5D 0.021 0.052 0.2 6 -0.29 1 7
APC -0.016 0.083 0.23 6 -0.18 23 29
WNT1/LRP6/FZD1 -0.009 0.075 -10000 0 -0.18 18 18
CREBBP 0.033 0.02 0.18 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A 0.004 0.026 -10000 0 -0.23 2 2
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.023 0.11 -10000 0 -0.24 35 35
STXBP1 0.009 0.079 -10000 0 -0.34 8 8
ACh/CHRNA1 0.013 0.021 -10000 0 -0.087 1 1
RAB3GAP2/RIMS1/UNC13B -0.003 0.1 -10000 0 -0.2 35 35
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.02 0.008 -10000 0 -10000 0 0
mol:ACh 0.003 0.025 0.082 8 -0.1 1 9
RAB3GAP2 0.032 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.012 0.097 -10000 0 -0.17 38 38
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.013 0.021 -10000 0 -0.086 1 1
UNC13B -0.051 0.15 -10000 0 -0.34 35 35
CHRNA1 0.019 0.005 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.006 0.046 -10000 0 -0.18 7 7
SNAP25 0.002 0.002 -10000 0 -10000 0 0
VAMP2 0.005 0.002 -10000 0 -10000 0 0
SYT1 0.006 0.073 -10000 0 -0.34 7 7
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.009 0.053 -10000 0 -0.2 10 10
STX1A/SNAP25 fragment 1/VAMP2 -0.012 0.097 -10000 0 -0.17 38 38
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.007 0.033 -10000 0 -0.21 1 1
NFATC2 0.001 0.05 -10000 0 -0.22 6 6
NFATC3 0.008 0.028 -10000 0 -10000 0 0
CD40LG -0.046 0.16 0.33 1 -0.42 17 18
PTGS2 -0.043 0.18 0.45 3 -0.38 25 28
JUNB 0.027 0.03 -10000 0 -0.34 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.023 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.023 -10000 0 -10000 0 0
CALM1 0.028 0.016 -10000 0 -10000 0 0
JUN 0.005 0.089 -10000 0 -0.34 10 10
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.008 -10000 0 -10000 0 0
FOSL1 0.019 0.063 -10000 0 -0.34 5 5
CREM 0.032 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.001 0.13 -10000 0 -0.27 18 18
FOS 0.013 0.076 -10000 0 -0.34 7 7
IFNG -0.034 0.16 0.4 3 -0.39 17 20
AP-1/NFAT1-c-4 -0.007 0.18 -10000 0 -0.42 17 17
FASLG -0.043 0.18 0.45 3 -0.43 21 24
NFAT1-c-4/ICER1 0.012 0.079 -10000 0 -0.18 12 12
IL2RA -0.044 0.17 0.39 3 -0.41 22 25
FKBP12/FK506 0.024 0.003 -10000 0 -10000 0 0
CSF2 -0.044 0.14 0.32 1 -0.38 16 17
JunB/Fra1/NFAT1-c-4 0.015 0.093 -10000 0 -0.24 9 9
IL4 -0.043 0.14 0.32 1 -0.37 17 18
IL2 0.009 0.062 -10000 0 -0.78 1 1
IL3 -0.008 0.13 -10000 0 -0.52 10 10
FKBP1A 0.032 0.004 -10000 0 -10000 0 0
BATF3 0.014 0.074 -10000 0 -0.34 7 7
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.032 0.005 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.026 0.041 -10000 0 -0.34 2 2
CDC42/GTP 0 0.085 -10000 0 -0.21 6 6
PLCG1 -0.018 0.071 -10000 0 -0.15 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.031 0.007 -10000 0 -10000 0 0
GNAI3 0.032 0.004 -10000 0 -10000 0 0
G12/G13 0.039 0.019 -10000 0 -10000 0 0
cell migration 0 0.083 -10000 0 -0.21 6 6
S1PR5 0.019 0.057 -10000 0 -0.34 4 4
S1PR4 0.027 0.03 -10000 0 -0.34 1 1
MAPK3 -0.015 0.074 -10000 0 -0.16 31 31
MAPK1 -0.012 0.066 -10000 0 -0.15 28 28
S1P/S1P5/Gi -0.013 0.082 -10000 0 -0.16 33 33
GNAI1 -0.021 0.12 -10000 0 -0.34 21 21
CDC42/GDP 0.023 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.039 -10000 0 -0.2 4 4
RHOA 0.028 0.059 0.21 13 -0.17 1 14
S1P/S1P4/Gi -0.01 0.079 -10000 0 -0.16 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.013 0.069 -10000 0 -0.34 6 6
S1P/S1P4/G12/G13 0.048 0.031 -10000 0 -0.18 1 1
GNA12 0.028 0.011 -10000 0 -10000 0 0
GNA13 0.03 0.008 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0 0.15 -10000 0 -0.42 12 12
MAP3K8 0.032 0.005 -10000 0 -10000 0 0
FOS -0.01 0.14 0.33 1 -0.54 7 8
PRKCA -0.02 0.12 -10000 0 -0.34 22 22
PTPN7 0.026 0.042 -10000 0 -0.34 2 2
HRAS 0.03 0.008 -10000 0 -10000 0 0
PRKCB 0.031 0.011 -10000 0 -10000 0 0
NRAS 0.032 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.056 0.02 -10000 0 -10000 0 0
MAPK3 -0.001 0.13 -10000 0 -0.57 6 6
MAP2K1 -0.025 0.12 0.25 1 -0.3 25 26
ELK1 0.028 0.015 -10000 0 -10000 0 0
BRAF -0.025 0.11 -10000 0 -0.3 24 24
mol:GTP 0 0.001 -10000 0 -0.004 7 7
MAPK1 -0.001 0.14 0.27 1 -0.56 7 8
RAF1 -0.02 0.11 -10000 0 -0.3 23 23
KRAS 0.031 0.006 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 -0.007 0.11 -9999 0 -0.34 16 16
SVIL 0.032 0.004 -9999 0 -10000 0 0
ZNF318 0.032 0.003 -9999 0 -10000 0 0
JMJD2C 0.002 0.003 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.012 0.092 -9999 0 -0.18 36 36
CARM1 0.029 0.009 -9999 0 -10000 0 0
PRDX1 0.031 0.007 -9999 0 -10000 0 0
PELP1 0.029 0.01 -9999 0 -10000 0 0
CTNNB1 0.031 0.007 -9999 0 -10000 0 0
AKT1 0.032 0.005 -9999 0 -10000 0 0
PTK2B 0.029 0.01 -9999 0 -10000 0 0
MED1 0.03 0.009 -9999 0 -10000 0 0
MAK 0.027 0.04 -9999 0 -0.34 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.019 0.057 -9999 0 -0.34 4 4
GSN 0.021 0.063 -9999 0 -0.34 5 5
NCOA2 0.026 0.03 -9999 0 -0.34 1 1
NCOA6 0.031 0.006 -9999 0 -10000 0 0
DNA-PK 0.055 0.024 -9999 0 -10000 0 0
NCOA4 0.031 0.006 -9999 0 -10000 0 0
PIAS3 0.032 0.004 -9999 0 -10000 0 0
cell proliferation 0.001 0.082 -9999 0 -0.56 3 3
XRCC5 0.032 0.003 -9999 0 -10000 0 0
UBE3A 0.031 0.006 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.028 0.1 -9999 0 -0.19 42 42
FHL2 -0.021 0.17 -9999 0 -0.74 8 8
RANBP9 0.032 0.004 -9999 0 -10000 0 0
JMJD1A 0 0.03 -9999 0 -0.13 9 9
CDK6 0.023 0.041 -9999 0 -0.34 2 2
TGFB1I1 -0.005 0.1 -9999 0 -0.34 15 15
T-DHT/AR/CyclinD1 -0.022 0.094 -9999 0 -0.17 43 43
XRCC6 0.03 0.009 -9999 0 -10000 0 0
T-DHT/AR -0.011 0.1 -9999 0 -0.18 43 43
CTDSP1 0.032 0.003 -9999 0 -10000 0 0
CTDSP2 0.032 0.004 -9999 0 -10000 0 0
BRCA1 0.025 0.041 -9999 0 -0.34 2 2
TCF4 0.01 0.084 -9999 0 -0.34 9 9
CDKN2A -0.047 0.15 -9999 0 -0.34 34 34
SRF 0.03 0.04 -9999 0 -0.15 8 8
NKX3-1 -0.043 0.18 -9999 0 -0.77 9 9
KLK3 0.002 0.053 -9999 0 -10000 0 0
TMF1 0.031 0.007 -9999 0 -10000 0 0
HNRNPA1 0.032 0.004 -9999 0 -10000 0 0
AOF2 0 0 -9999 0 -10000 0 0
APPL1 0.014 0.004 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.013 0.092 -9999 0 -0.19 32 32
AR -0.052 0.14 -9999 0 -0.33 31 31
UBA3 0.031 0.007 -9999 0 -10000 0 0
PATZ1 0.03 0.009 -9999 0 -10000 0 0
PAWR -0.002 0.086 -9999 0 -0.34 10 10
PRKDC 0.029 0.01 -9999 0 -10000 0 0
PA2G4 0.032 0.004 -9999 0 -10000 0 0
UBE2I 0.032 0.005 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.01 0.084 -9999 0 -0.15 40 40
RPS6KA3 0.029 0.01 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.013 0.092 -9999 0 -0.18 36 36
LATS2 0.031 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.01 0.083 -9999 0 -0.15 39 39
Cyclin D3/CDK11 p58 0.024 0.002 -9999 0 -10000 0 0
VAV3 0.032 0.004 -9999 0 -10000 0 0
KLK2 -0.011 0.048 -9999 0 -0.33 1 1
CASP8 0.032 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.005 0.09 -9999 0 -0.17 31 31
TMPRSS2 -0.015 0.062 -9999 0 -0.25 2 2
CCND1 0.015 0.063 -9999 0 -0.34 5 5
PIAS1 0.031 0.006 -9999 0 -10000 0 0
mol:T-DHT -0.002 0.019 -9999 0 -0.063 14 14
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.03 0.009 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.019 0.096 -9999 0 -0.18 38 38
CMTM2 0.011 0.079 -9999 0 -0.34 8 8
SNURF -0.002 0.094 -9999 0 -0.34 12 12
ZMIZ1 0.025 0.031 -9999 0 -0.12 1 1
CCND3 0.032 0.003 -9999 0 -10000 0 0
TGIF1 0.027 0.041 -9999 0 -0.34 2 2
FKBP4 0.031 0.006 -9999 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.027 0.079 -10000 0 -0.21 15 15
fibroblast growth factor receptor signaling pathway 0.026 0.079 -10000 0 -0.21 15 15
LAMA1 0.018 0.006 -10000 0 -10000 0 0
PRNP 0.027 0.04 -10000 0 -0.34 2 2
GPC1/SLIT2 0.04 0.011 -10000 0 -10000 0 0
SMAD2 0.02 0.024 0.19 3 -10000 0 3
GPC1/PrPc/Cu2+ 0.039 0.027 -10000 0 -0.2 2 2
GPC1/Laminin alpha1 0.036 0.009 -10000 0 -10000 0 0
TDGF1 0.017 0.006 -10000 0 -10000 0 0
CRIPTO/GPC1 0.035 0.01 -10000 0 -10000 0 0
APP/GPC1 -0.05 0.13 -10000 0 -0.23 55 55
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.024 0.05 -10000 0 -0.2 12 12
FLT1 0.013 0.074 -10000 0 -0.34 7 7
GPC1/TGFB/TGFBR1/TGFBR2 0.06 0.018 -10000 0 -10000 0 0
SERPINC1 0.027 0.008 -10000 0 -10000 0 0
FYN -0.014 0.028 -10000 0 -0.2 3 3
FGR -0.041 0.073 -10000 0 -0.2 28 28
positive regulation of MAPKKK cascade -0.027 0.11 0.24 9 -0.25 20 29
SLIT2 0.024 0.01 -10000 0 -10000 0 0
GPC1/NRG 0.035 0.016 -10000 0 -10000 0 0
NRG1 0.02 0.012 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.035 0.077 -10000 0 -0.21 14 14
LYN -0.009 0.012 -10000 0 -10000 0 0
mol:Spermine 0.008 0.002 -10000 0 -10000 0 0
cell growth 0.026 0.079 -10000 0 -0.21 15 15
BMP signaling pathway -0.031 0.007 -10000 0 -10000 0 0
SRC -0.029 0.057 -10000 0 -0.2 16 16
TGFBR1 0.031 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.017 0.005 -10000 0 -10000 0 0
GPC1 0.031 0.007 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.031 0.006 -10000 0 -10000 0 0
VEGFA 0.009 0.083 -10000 0 -0.34 9 9
BLK -0.015 0.038 -10000 0 -0.2 6 6
HCK -0.023 0.049 -10000 0 -0.2 11 11
FGF2 0.021 0.057 -10000 0 -0.34 4 4
FGFR1 -0.005 0.098 -10000 0 -0.34 13 13
VEGFR1 homodimer 0.013 0.074 -10000 0 -0.34 7 7
TGFBR2 0.031 0.007 -10000 0 -10000 0 0
cell death -0.05 0.13 -10000 0 -0.23 55 55
ATIII/GPC1 0.042 0.01 -10000 0 -10000 0 0
PLA2G2A/GPC1 0.035 0.01 -10000 0 -10000 0 0
LCK -0.013 0.028 -10000 0 -0.2 3 3
neuron differentiation 0.035 0.016 -10000 0 -10000 0 0
PrPc/Cu2+ 0.02 0.028 -10000 0 -0.23 2 2
APP -0.092 0.17 -10000 0 -0.34 55 55
TGFBR2 (dimer) 0.031 0.007 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.005 0.087 0.2 9 -10000 0 9
GNAI2 0.031 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.039 -10000 0 -0.2 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.026 0.041 -10000 0 -0.34 2 2
RhoA/GTP -0.005 0.088 -10000 0 -0.2 9 9
negative regulation of cAMP metabolic process -0.013 0.081 -10000 0 -0.16 33 33
GNAZ 0.013 0.069 -10000 0 -0.34 6 6
GNAI3 0.032 0.004 -10000 0 -10000 0 0
GNA12 0.028 0.011 -10000 0 -10000 0 0
S1PR5 0.019 0.057 -10000 0 -0.34 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.013 0.082 -10000 0 -0.16 33 33
RhoA/GDP 0.023 0.005 -10000 0 -10000 0 0
RHOA 0.031 0.007 -10000 0 -10000 0 0
GNAI1 -0.021 0.12 -10000 0 -0.34 21 21
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.029 -10000 0 -0.2 4 4
SNTA1 0.027 0.041 -10000 0 -0.34 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.016 0.032 -10000 0 -0.2 5 5
MAPK12 -0.007 0.061 0.21 4 -0.19 12 16
CCND1 -0.012 0.09 -10000 0 -0.42 7 7
p38 gamma/SNTA1 0.009 0.076 0.22 5 -0.19 15 20
MAP2K3 0.03 0.008 -10000 0 -10000 0 0
PKN1 0.029 0.009 -10000 0 -10000 0 0
G2/M transition checkpoint -0.007 0.061 0.21 4 -0.19 12 16
MAP2K6 -0.009 0.065 0.24 1 -0.23 12 13
MAPT 0.003 0.05 0.25 3 -0.16 5 8
MAPK13 0.008 0.039 -10000 0 -0.24 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.005 0.071 -10000 0 -0.25 13 13
Paxillin-dependent events mediated by a4b1

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
CRKL 0.029 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.027 0.014 -10000 0 -10000 0 0
DOCK1 -0.098 0.17 -10000 0 -0.34 56 56
ITGA4 0.032 0 -10000 0 -10000 0 0
RAC1 0.028 0.011 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.04 0.044 -10000 0 -0.24 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.059 0.02 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.04 0.046 -10000 0 -0.18 6 6
lamellipodium assembly -0.059 0.12 -10000 0 -0.33 10 10
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
PI3K 0.045 0.011 -10000 0 -10000 0 0
ARF6 0.032 0.005 -10000 0 -10000 0 0
TLN1 0.029 0.029 -10000 0 -0.34 1 1
PXN 0.011 0.028 -10000 0 -0.24 2 2
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
ARF6/GTP 0.059 0.035 -10000 0 -0.16 2 2
cell adhesion 0.061 0.041 0.18 3 -0.17 3 6
CRKL/CBL 0.041 0.017 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.046 0.03 -10000 0 -0.18 2 2
ITGB1 0.032 0.004 -10000 0 -10000 0 0
ITGB7 0.023 0.057 -10000 0 -0.34 4 4
ARF6/GDP 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.015 0.097 0.18 1 -0.18 32 33
p130Cas/Crk/Dock1 -0.048 0.12 -10000 0 -0.2 63 63
VCAM1 -0.048 0.14 -10000 0 -0.34 33 33
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.041 0.18 3 -0.17 3 6
alpha4/beta1 Integrin/Paxillin/GIT1 0.061 0.036 0.18 1 -0.17 2 3
BCAR1 0.004 0.087 -10000 0 -0.34 10 10
mol:GDP -0.059 0.036 0.17 2 -0.18 1 3
CBL 0.03 0.008 -10000 0 -10000 0 0
PRKACA 0.029 0.009 -10000 0 -10000 0 0
GIT1 0.03 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.063 0.041 0.18 3 -0.17 3 6
Rac1/GTP -0.065 0.13 -10000 0 -0.36 10 10
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.028 0.21 -10000 0 -0.68 8 8
CRP -0.031 0.21 0.5 2 -0.66 9 11
cell cycle arrest -0.04 0.23 -10000 0 -0.72 11 11
TIMP1 -0.032 0.24 -10000 0 -0.65 16 16
IL6ST 0.01 0.081 -10000 0 -0.34 8 8
Rac1/GDP 0.003 0.11 -10000 0 -0.35 7 7
AP1 0.064 0.11 -10000 0 -0.38 3 3
GAB2 0.034 0.011 -10000 0 -10000 0 0
TNFSF11 -0.029 0.21 -10000 0 -0.62 11 11
HSP90B1 -0.001 0.18 -10000 0 -0.78 7 7
GAB1 0.029 0.041 -10000 0 -0.33 2 2
MAPK14 -0.013 0.12 -10000 0 -0.52 6 6
AKT1 0.042 0.064 0.25 2 -0.61 1 3
FOXO1 0.036 0.076 0.36 2 -0.58 1 3
MAP2K6 -0.008 0.1 0.2 1 -0.37 8 9
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.008 0.13 0.42 1 -0.38 9 10
MITF -0.017 0.11 -10000 0 -0.32 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.009 -10000 0 -10000 0 0
A2M -0.16 0.44 -10000 0 -1.2 27 27
CEBPB 0.024 0.059 -10000 0 -0.34 4 4
GRB2/SOS1/GAB family/SHP2 0.043 0.082 0.23 3 -0.4 2 5
STAT3 -0.044 0.24 -10000 0 -0.77 11 11
STAT1 0.022 0.02 -10000 0 -10000 0 0
CEBPD -0.076 0.35 0.43 1 -0.9 23 24
PIK3CA 0.032 0.006 -10000 0 -10000 0 0
PI3K 0.047 0.012 -10000 0 -10000 0 0
JUN 0.008 0.088 -10000 0 -0.34 10 10
PIAS3/MITF -0.007 0.11 0.22 2 -0.33 9 11
MAPK11 -0.012 0.12 -10000 0 -0.51 6 6
STAT3 (dimer)/FOXO1 -0.04 0.23 0.35 1 -0.55 19 20
GRB2/SOS1/GAB family 0.042 0.12 0.23 4 -0.3 8 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.006 0.11 -10000 0 -0.25 21 21
GRB2 0.033 0.01 -10000 0 -10000 0 0
JAK2 0.031 0.006 -10000 0 -10000 0 0
LBP -0.077 0.29 -10000 0 -0.74 23 23
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
JAK1 0.031 0.014 -10000 0 -10000 0 0
MYC -0.018 0.24 0.43 1 -0.67 12 13
FGG -0.033 0.2 -10000 0 -0.61 11 11
macrophage differentiation -0.04 0.23 -10000 0 -0.72 11 11
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.048 0.095 -10000 0 -0.19 17 17
JUNB -0.028 0.22 0.48 1 -0.79 7 8
FOS 0.016 0.074 -10000 0 -0.34 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.002 0.11 0.23 1 -0.33 9 10
STAT1/PIAS1 0.007 0.12 0.25 1 -0.32 8 9
GRB2/SOS1/GAB family/SHP2/PI3K 0.043 0.074 -10000 0 -0.81 1 1
STAT3 (dimer) -0.044 0.24 -10000 0 -0.76 11 11
PRKCD -0.01 0.18 0.36 6 -0.48 11 17
IL6R 0.029 0.034 -10000 0 -0.37 1 1
SOCS3 -0.014 0.18 0.45 1 -0.9 5 6
gp130 (dimer)/JAK1/JAK1/LMO4 0.035 0.089 -10000 0 -0.21 16 16
Rac1/GTP -0.001 0.12 -10000 0 -0.35 8 8
HCK 0.007 0.092 -10000 0 -0.34 11 11
MAPKKK cascade 0.058 0.086 -10000 0 -0.48 2 2
bone resorption -0.024 0.2 0.42 1 -0.59 11 12
IRF1 -0.03 0.21 -10000 0 -0.62 11 11
mol:GDP -0.006 0.1 0.21 2 -0.32 9 11
SOS1 0.035 0.008 -10000 0 -10000 0 0
VAV1 -0.008 0.1 0.21 1 -0.32 9 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.003 0.12 -10000 0 -0.53 6 6
PTPN11 0.019 0.057 -10000 0 -0.66 1 1
IL6/IL6RA 0.032 0.039 -10000 0 -0.29 1 1
gp130 (dimer)/TYK2/TYK2/LMO4 0.033 0.085 -10000 0 -0.21 16 16
gp130 (dimer)/JAK2/JAK2/LMO4 0.033 0.086 -10000 0 -0.21 16 16
IL6 0.019 0.024 -10000 0 -10000 0 0
PIAS3 0.032 0.004 -10000 0 -10000 0 0
PTPRE 0.027 0.032 -10000 0 -0.34 1 1
PIAS1 0.031 0.006 -10000 0 -10000 0 0
RAC1 0.028 0.011 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.003 0.085 0.21 1 -0.22 18 19
LMO4 0.008 0.086 -10000 0 -0.34 9 9
STAT3 (dimer)/PIAS3 -0.032 0.24 -10000 0 -0.72 11 11
MCL1 0.043 0.073 0.44 1 -0.55 1 2
Class I PI3K signaling events

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
ARF5/GTP -0.037 0.057 0.16 1 -10000 0 1
DAPP1 -0.031 0.16 0.37 4 -0.34 23 27
Src family/SYK family/BLNK-LAT/BTK-ITK -0.078 0.2 0.29 1 -0.42 32 33
mol:DAG -0.031 0.1 0.35 3 -0.22 18 21
HRAS 0.03 0.009 -10000 0 -10000 0 0
RAP1A 0.031 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.011 0.082 0.36 1 -0.24 6 7
PLCG2 0.031 0.006 -10000 0 -10000 0 0
PLCG1 0.019 0.063 -10000 0 -0.34 5 5
ARF5 0.028 0.012 -10000 0 -10000 0 0
mol:GTP -0.038 0.057 0.14 4 -10000 0 4
ARF1/GTP -0.029 0.066 0.23 1 -0.17 1 2
RHOA 0.031 0.007 -10000 0 -10000 0 0
YES1 0.004 0.096 -10000 0 -0.34 12 12
RAP1A/GTP -0.036 0.059 0.16 4 -10000 0 4
ADAP1 -0.037 0.078 0.3 3 -0.29 3 6
ARAP3 -0.038 0.057 0.14 4 -10000 0 4
INPPL1 0.029 0.029 -10000 0 -0.34 1 1
PREX1 0.031 0.006 -10000 0 -10000 0 0
ARHGEF6 0.03 0.009 -10000 0 -10000 0 0
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
ARF1 0.032 0.005 -10000 0 -10000 0 0
NRAS 0.031 0.007 -10000 0 -10000 0 0
FYN 0.026 0.049 -10000 0 -0.34 3 3
ARF6 0.032 0.005 -10000 0 -10000 0 0
FGR -0.034 0.14 -10000 0 -0.34 28 28
mol:Ca2+ -0.014 0.077 0.3 4 -0.12 11 15
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.003 0.091 -10000 0 -0.34 11 11
ZAP70 0.014 0.079 -10000 0 -0.34 8 8
mol:IP3 -0.024 0.092 0.37 3 -0.16 14 17
LYN 0.028 0.011 -10000 0 -10000 0 0
ARF1/GDP 0.007 0.086 -10000 0 -0.22 15 15
RhoA/GDP 0.006 0.083 0.23 2 -0.22 4 6
PDK1/Src/Hsp90 0.036 0.078 -10000 0 -0.2 16 16
BLNK -0.025 0.13 -10000 0 -0.34 24 24
actin cytoskeleton reorganization -0.011 0.1 0.45 2 -0.25 6 8
SRC -0.007 0.11 -10000 0 -0.34 17 17
PLEKHA2 -0.011 0.015 -10000 0 -0.2 1 1
RAC1 0.028 0.011 -10000 0 -10000 0 0
PTEN 0.032 0.015 -10000 0 -10000 0 0
HSP90AA1 0.032 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.038 0.062 0.22 2 -10000 0 2
RhoA/GTP -0.038 0.057 0.16 4 -10000 0 4
Src family/SYK family/BLNK-LAT -0.073 0.18 -10000 0 -0.38 35 35
BLK 0.011 0.074 -10000 0 -0.34 7 7
PDPK1 0.032 0.005 -10000 0 -10000 0 0
CYTH1 -0.035 0.063 0.2 3 -10000 0 3
HCK 0.007 0.092 -10000 0 -0.34 11 11
CYTH3 -0.033 0.071 0.3 3 -10000 0 3
CYTH2 -0.037 0.055 0.15 2 -10000 0 2
KRAS 0.031 0.01 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.051 0.16 -10000 0 -0.45 19 19
SGK1 -0.052 0.17 -10000 0 -0.48 19 19
INPP5D 0.032 0.003 -10000 0 -10000 0 0
mol:GDP -0.003 0.087 0.37 1 -0.22 15 16
SOS1 0.032 0.003 -10000 0 -10000 0 0
SYK 0.031 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.01 0.076 0.2 3 -0.22 4 7
mol:PI-3-4-5-P3 -0.038 0.057 0.15 1 -10000 0 1
ARAP3/RAP1A/GTP -0.037 0.06 0.16 4 -10000 0 4
VAV1 0.03 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.013 0.02 -10000 0 -0.24 1 1
RAS family/GTP/PI3K Class I 0.01 0.076 0.2 1 -0.15 29 30
PLEKHA1 -0.015 0.025 -10000 0 -0.2 3 3
Rac1/GDP 0.01 0.085 0.36 1 -0.24 8 9
LAT 0.025 0.049 -10000 0 -0.34 3 3
Rac1/GTP -0.013 0.12 -10000 0 -0.31 18 18
ITK -0.043 0.064 0.15 1 -0.24 5 6
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.054 0.12 0.23 1 -0.3 18 19
LCK 0.024 0.05 -10000 0 -0.34 3 3
BTK -0.034 0.063 0.2 3 -10000 0 3
Signaling events mediated by PRL

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
CCNE1 0.027 0.03 -10000 0 -0.34 1 1
mol:Halofuginone 0.003 0.016 -10000 0 -0.2 1 1
ITGA1 -0.008 0.11 -10000 0 -0.34 16 16
CDKN1A -0.009 0.1 -10000 0 -0.41 9 9
PRL-3/alpha Tubulin 0.023 0.068 -10000 0 -0.24 10 10
mol:Ca2+ -0.002 0.09 0.3 11 -0.25 4 15
AGT 0.013 0.063 -10000 0 -0.34 5 5
CCNA2 -0.033 0.072 -10000 0 -0.42 2 2
TUBA1B 0.032 0.004 -10000 0 -10000 0 0
EGR1 -0.003 0.066 -10000 0 -0.24 12 12
CDK2/Cyclin E1 0.014 0.12 -10000 0 -0.4 10 10
MAPK3 -0.004 0.062 -10000 0 -0.24 11 11
PRL-2 /Rab GGTase beta 0.046 0.01 -10000 0 -10000 0 0
MAPK1 -0.004 0.062 -10000 0 -0.24 11 11
PTP4A1 -0.029 0.086 -10000 0 -0.54 2 2
PTP4A3 0.003 0.091 -10000 0 -0.34 11 11
PTP4A2 0.031 0.006 -10000 0 -10000 0 0
ITGB1 -0.003 0.062 -10000 0 -0.24 11 11
SRC -0.007 0.11 -10000 0 -0.34 17 17
RAC1 -0.03 0.12 -10000 0 -0.37 18 18
Rab GGTase beta/Rab GGTase alpha 0.045 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.009 0.083 -10000 0 -0.42 2 2
RABGGTA 0.031 0.006 -10000 0 -10000 0 0
BCAR1 -0.01 0.098 0.3 11 -0.25 9 20
RHOC -0.017 0.11 -10000 0 -0.39 12 12
RHOA -0.015 0.11 -10000 0 -0.4 11 11
cell motility -0.019 0.12 -10000 0 -0.36 16 16
PRL-1/alpha Tubulin -0.011 0.089 -10000 0 -0.51 2 2
PRL-3/alpha1 Integrin -0.004 0.1 -10000 0 -0.25 24 24
ROCK1 -0.013 0.12 -10000 0 -0.38 13 13
RABGGTB 0.031 0.006 -10000 0 -10000 0 0
CDK2 0.032 0.004 -10000 0 -10000 0 0
mitosis -0.028 0.086 -10000 0 -0.53 2 2
ATF5 0.029 0.01 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.029 0.01 -10000 0 -10000 0 0
SPHK1 0.023 0.05 -10000 0 -0.34 3 3
GNAI2 0.031 0.007 -10000 0 -10000 0 0
mol:S1P 0.012 0.031 -10000 0 -0.21 3 3
GNAO1 0.026 0.041 -10000 0 -0.34 2 2
mol:Sphinganine-1-P 0.009 0.034 -10000 0 -0.24 3 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.045 0.063 -10000 0 -0.17 9 9
GNAI3 0.032 0.004 -10000 0 -10000 0 0
G12/G13 0.039 0.019 -10000 0 -10000 0 0
S1PR3 -0.046 0.15 -10000 0 -0.34 33 33
S1PR2 0.025 0.041 -10000 0 -0.34 2 2
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.003 0.051 -10000 0 -0.2 9 9
S1PR5 0.019 0.057 -10000 0 -0.34 4 4
S1PR4 0.027 0.03 -10000 0 -0.34 1 1
GNAI1 -0.021 0.12 -10000 0 -0.34 21 21
S1P/S1P5/G12 0.029 0.062 0.19 1 -0.16 13 14
S1P/S1P3/Gq -0.036 0.13 -10000 0 -0.32 18 18
S1P/S1P4/Gi -0.015 0.1 -10000 0 -0.19 30 30
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.013 0.069 -10000 0 -0.34 6 6
GNA14 0.008 0.083 -10000 0 -0.34 9 9
GNA15 0.027 0.03 -10000 0 -0.34 1 1
GNA12 0.028 0.011 -10000 0 -10000 0 0
GNA13 0.03 0.008 -10000 0 -10000 0 0
GNA11 0.005 0.092 -10000 0 -0.34 11 11
ABCC1 0.032 0.004 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.022 0.071 -10000 0 -0.36 5 5
IHH 0.034 0.037 -10000 0 -0.15 5 5
SHH Np/Cholesterol/GAS1 0.004 0.058 -10000 0 -0.18 15 15
LRPAP1 0.031 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.004 0.058 0.18 15 -10000 0 15
SMO/beta Arrestin2 -0.007 0.13 -10000 0 -0.42 7 7
SMO -0.015 0.12 -10000 0 -0.29 20 20
AKT1 0.017 0.068 -10000 0 -0.43 1 1
ARRB2 0.029 0.01 -10000 0 -10000 0 0
BOC 0.029 0.029 -10000 0 -0.34 1 1
ADRBK1 0.031 0.007 -10000 0 -10000 0 0
heart looping -0.015 0.12 -10000 0 -0.31 16 16
STIL 0.008 0.067 0.18 2 -0.31 5 7
DHH N/PTCH2 0.04 0.033 -10000 0 -0.24 2 2
DHH N/PTCH1 0.033 0.071 -10000 0 -0.36 5 5
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
DHH 0.028 0.008 -10000 0 -10000 0 0
PTHLH 0.017 0.086 -10000 0 -0.45 5 5
determination of left/right symmetry -0.015 0.12 -10000 0 -0.31 16 16
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
skeletal system development 0.018 0.085 -10000 0 -0.44 5 5
IHH N/Hhip 0.019 0.079 -10000 0 -0.26 11 11
DHH N/Hhip 0.02 0.07 -10000 0 -0.24 11 11
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.015 0.12 -10000 0 -0.31 16 16
pancreas development 0 0.091 -10000 0 -0.34 11 11
HHAT 0.025 0.049 -10000 0 -0.34 3 3
PI3K 0.045 0.011 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0 0.095 -10000 0 -0.34 12 12
somite specification -0.015 0.12 -10000 0 -0.31 16 16
SHH Np/Cholesterol/PTCH1 0.014 0.064 -10000 0 -0.3 6 6
SHH Np/Cholesterol/PTCH2 0.019 0.036 -10000 0 -0.18 5 5
SHH Np/Cholesterol/Megalin 0.019 0.027 -10000 0 -0.16 3 3
SHH -0.001 0.029 -10000 0 -0.24 2 2
catabolic process 0.013 0.075 -10000 0 -0.4 5 5
SMO/Vitamin D3 -0.007 0.089 -10000 0 -0.43 5 5
SHH Np/Cholesterol/Hhip 0.003 0.056 -10000 0 -0.18 14 14
LRP2 0.026 0.01 -10000 0 -10000 0 0
receptor-mediated endocytosis 0.001 0.092 -10000 0 -0.48 5 5
SHH Np/Cholesterol/BOC 0.02 0.032 -10000 0 -0.17 4 4
SHH Np/Cholesterol/CDO 0.015 0.039 -10000 0 -0.18 6 6
mesenchymal cell differentiation -0.003 0.055 0.18 14 -10000 0 14
mol:Vitamin D3 0.015 0.069 0.19 4 -0.33 5 9
IHH N/PTCH2 0.041 0.043 -10000 0 -0.26 2 2
CDON 0.02 0.05 -10000 0 -0.34 3 3
IHH N/PTCH1 0.023 0.078 -10000 0 -0.4 5 5
Megalin/LRPAP1 0.042 0.01 -10000 0 -10000 0 0
PTCH2 0.027 0.041 -10000 0 -0.34 2 2
SHH Np/Cholesterol 0.016 0.027 -10000 0 -0.17 3 3
PTCH1 0.013 0.075 -10000 0 -0.4 5 5
HHIP 0 0.091 -10000 0 -0.34 11 11
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.029 0.078 -10000 0 -0.34 4 4
HDAC1 0.031 0.011 -10000 0 -10000 0 0
AES 0.029 0.009 -10000 0 -10000 0 0
FBXW11 0.031 0.007 -10000 0 -10000 0 0
DTX1 0.004 0.091 -10000 0 -0.34 11 11
LRP6/FZD1 -0.006 0.1 -10000 0 -0.24 24 24
TLE1 -0.004 0.1 -10000 0 -0.34 15 15
AP1 -0.008 0.079 -10000 0 -0.2 21 21
NCSTN 0.032 0.004 -10000 0 -10000 0 0
ADAM10 0.031 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.001 0.12 -10000 0 -0.52 5 5
NICD/RBPSUH 0.041 0.073 -10000 0 -0.35 5 5
WIF1 0.018 0.01 -10000 0 -10000 0 0
NOTCH1 0.021 0.069 -10000 0 -0.37 5 5
PSENEN 0.029 0.009 -10000 0 -10000 0 0
KREMEN2 0.027 0.041 -10000 0 -0.34 2 2
DKK1 0.02 0.009 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.024 0.06 -10000 0 -0.22 2 2
APH1B 0.031 0.006 -10000 0 -10000 0 0
APH1A 0.032 0.004 -10000 0 -10000 0 0
AXIN1 0.002 0.065 -10000 0 -0.35 3 3
CtBP/CBP/TCF1/TLE1/AES 0.009 0.069 0.16 1 -0.19 13 14
PSEN1 0.032 0.005 -10000 0 -10000 0 0
FOS 0.016 0.074 -10000 0 -0.34 7 7
JUN 0.008 0.088 -10000 0 -0.34 10 10
MAP3K7 0.032 0.005 -10000 0 -10000 0 0
CTNNB1 0.003 0.065 -10000 0 -0.26 3 3
MAPK3 0.032 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.017 0.11 -10000 0 -0.2 42 42
HNF1A 0.029 0.029 -10000 0 -0.34 1 1
CTBP1 0.031 0.006 -10000 0 -10000 0 0
MYC 0.002 0.16 -10000 0 -1.1 3 3
NKD1 0.012 0.074 -10000 0 -0.34 7 7
FZD1 0.018 0.057 -10000 0 -0.34 4 4
NOTCH1 precursor/Deltex homolog 1 0.025 0.082 -10000 0 -0.34 5 5
apoptosis -0.008 0.079 -10000 0 -0.2 21 21
Delta 1/NOTCHprecursor 0.023 0.077 -10000 0 -0.34 4 4
DLL1 -0.005 0.1 -10000 0 -0.34 14 14
PPARD 0.006 0.16 -10000 0 -1.1 3 3
Gamma Secretase 0.086 0.031 -10000 0 -10000 0 0
APC -0.019 0.12 -10000 0 -0.42 10 10
DVL1 0.012 0.062 -10000 0 -0.47 2 2
CSNK2A1 0.032 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.011 0.087 -10000 0 -0.2 23 23
LRP6 -0.026 0.12 -10000 0 -0.34 21 21
CSNK1A1 0.03 0.009 -10000 0 -10000 0 0
NLK 0.015 0.01 -10000 0 -10000 0 0
CCND1 -0.017 0.22 -10000 0 -1.1 7 7
WNT1 0.029 0.008 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.004 0.1 0.25 1 -0.37 8 9
DKK2 -0.026 0.12 -10000 0 -0.34 22 22
NOTCH1 precursor/DVL1 0.021 0.11 -10000 0 -0.51 5 5
GSK3B 0.031 0.007 -10000 0 -10000 0 0
FRAT1 0.032 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.03 0.082 -10000 0 -0.34 5 5
PPP2R5D 0.025 0.049 0.21 7 -0.29 1 8
MAPK1 0.029 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.019 0.091 -10000 0 -0.19 24 24
RBPJ 0.031 0.006 -10000 0 -10000 0 0
CREBBP 0.031 0.011 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.001 0.14 -10000 0 -0.9 4 4
regulation of axonogenesis 0.008 0.053 0.2 4 -10000 0 4
myoblast fusion -0.012 0.073 0.35 5 -10000 0 5
mol:GTP 0.016 0.04 -10000 0 -0.21 4 4
regulation of calcium-dependent cell-cell adhesion -0.032 0.075 0.19 15 -10000 0 15
ARF1/GTP 0.037 0.034 -10000 0 -0.16 4 4
mol:GM1 0.006 0.028 -10000 0 -0.16 4 4
mol:Choline -0.021 0.074 -10000 0 -0.19 26 26
lamellipodium assembly 0.007 0.072 -10000 0 -0.38 5 5
MAPK3 0.017 0.056 -10000 0 -0.29 5 5
ARF6/GTP/NME1/Tiam1 0.033 0.076 -10000 0 -0.19 15 15
ARF1 0.032 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.012 0.073 -10000 0 -0.36 5 5
ARF1/GDP 0.019 0.071 -10000 0 -0.33 5 5
ARF6 0.035 0.029 -10000 0 -0.12 5 5
RAB11A 0.031 0.006 -10000 0 -10000 0 0
TIAM1 0.002 0.092 -10000 0 -0.34 11 11
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.054 -10000 0 -0.32 4 4
actin filament bundle formation -0.025 0.07 0.33 5 -10000 0 5
KALRN 0 0.066 -10000 0 -0.2 15 15
RAB11FIP3/RAB11A 0.045 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.071 -10000 0 -0.33 5 5
NME1 0.029 0.014 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.071 -10000 0 -0.33 5 5
substrate adhesion-dependent cell spreading 0.016 0.04 -10000 0 -0.21 4 4
cortical actin cytoskeleton organization 0.007 0.072 -10000 0 -0.39 5 5
RAC1 0.028 0.011 -10000 0 -10000 0 0
liver development 0.016 0.04 -10000 0 -0.21 4 4
ARF6/GTP 0.016 0.04 -10000 0 -0.21 4 4
RhoA/GTP 0.036 0.035 -10000 0 -0.16 4 4
mol:GDP 0.006 0.065 -10000 0 -0.38 4 4
ARF6/GTP/RAB11FIP3/RAB11A 0.054 0.036 -10000 0 -0.14 4 4
RHOA 0.031 0.007 -10000 0 -10000 0 0
PLD1 0.01 0.046 -10000 0 -0.18 8 8
RAB11FIP3 0.031 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.072 -10000 0 -0.38 5 5
ruffle organization -0.008 0.053 -10000 0 -0.2 4 4
regulation of epithelial cell migration 0.016 0.04 -10000 0 -0.21 4 4
PLD2 -0.014 0.083 -10000 0 -0.22 23 23
PIP5K1A -0.008 0.053 -10000 0 -0.2 4 4
mol:Phosphatidic acid -0.021 0.074 -10000 0 -0.19 26 26
Rac1/GTP 0.007 0.072 -10000 0 -0.39 5 5
Signaling events mediated by HDAC Class III

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
EP300 0.03 0.009 -10000 0 -10000 0 0
HDAC4 0.032 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.003 0.037 0.24 1 -0.13 9 10
CDKN1A -0.036 0.12 -10000 0 -0.53 9 9
KAT2B 0.031 0.007 -10000 0 -10000 0 0
BAX 0.029 0.01 -10000 0 -10000 0 0
FOXO3 -0.008 0.008 -10000 0 -10000 0 0
FOXO1 0.017 0.069 -10000 0 -0.34 6 6
FOXO4 0.016 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
TAT 0.02 0.008 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.013 0.005 -10000 0 -10000 0 0
PPARGC1A -0.045 0.14 -10000 0 -0.34 30 30
FHL2 0.009 0.079 -10000 0 -0.34 8 8
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.047 0.029 0.16 8 -10000 0 8
HIST2H4A -0.003 0.038 0.13 9 -0.24 1 10
SIRT1/FOXO3a 0.016 0.058 0.14 9 -0.2 8 17
SIRT1 0.037 0.037 0.2 8 -10000 0 8
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.066 0.027 0.17 8 -10000 0 8
SIRT1/Histone H1b 0.037 0.047 -10000 0 -0.19 3 3
apoptosis -0.059 0.033 -10000 0 -0.17 8 8
SIRT1/PGC1A -0.003 0.091 0.14 5 -0.19 29 34
p53/SIRT1 0.049 0.068 0.36 7 -10000 0 7
SIRT1/FOXO4 0.039 0.053 0.17 2 -0.22 3 5
FOXO1/FHL2/SIRT1 0.039 0.072 0.16 8 -0.18 14 22
HIST1H1E 0.013 0.031 -10000 0 -0.21 3 3
SIRT1/p300 0.047 0.029 0.16 8 -10000 0 8
muscle cell differentiation -0.045 0.036 -10000 0 -0.22 3 3
TP53 0.033 0.035 0.2 7 -10000 0 7
KU70/SIRT1/BAX 0.06 0.033 0.17 8 -10000 0 8
CREBBP 0.031 0.006 -10000 0 -10000 0 0
MEF2D 0.032 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.041 0.027 0.15 8 -10000 0 8
ACSS2 -0.005 0.041 0.13 8 -0.24 2 10
SIRT1/PCAF/MYOD 0.045 0.036 0.22 3 -10000 0 3
Glypican 2 network

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
MDK 0.019 0.063 -9999 0 -0.34 5 5
GPC2 0.014 0.069 -9999 0 -0.34 6 6
GPC2/Midkine 0.024 0.073 -9999 0 -0.28 8 8
neuron projection morphogenesis 0.024 0.073 -9999 0 -0.28 8 8
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.003 0.13 0.45 3 -0.34 9 12
IKBKB 0.029 0.084 0.38 3 -0.26 2 5
AKT1 -0.001 0.093 0.39 5 -0.21 3 8
IKBKG 0.011 0.1 0.37 2 -0.31 8 10
CALM1 0 0.1 0.25 4 -0.34 7 11
PIK3CA 0.031 0.006 -10000 0 -10000 0 0
MAP3K1 0.008 0.13 0.45 1 -0.45 7 8
MAP3K7 0.032 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.11 0.22 3 -0.38 7 10
DOK1 0.032 0.003 -10000 0 -10000 0 0
AP-1 0.007 0.1 0.33 6 -0.22 6 12
LYN 0.028 0.011 -10000 0 -10000 0 0
BLNK -0.025 0.13 -10000 0 -0.34 24 24
SHC1 0.032 0.004 -10000 0 -10000 0 0
BCR complex 0.038 0.034 -10000 0 -0.24 2 2
CD22 0.004 0.068 -10000 0 -0.43 3 3
CAMK2G 0 0.1 0.32 4 -0.32 7 11
CSNK2A1 0.032 0.004 -10000 0 -10000 0 0
INPP5D 0.032 0.003 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.012 0.064 -10000 0 -0.16 15 15
GO:0007205 -0.002 0.11 0.22 3 -0.39 7 10
SYK 0.031 0.006 -10000 0 -10000 0 0
ELK1 0.006 0.11 0.3 6 -0.41 5 11
NFATC1 -0.004 0.13 0.32 5 -0.32 12 17
B-cell antigen/BCR complex 0.038 0.034 -10000 0 -0.24 2 2
PAG1/CSK 0.034 0.046 -10000 0 -0.24 4 4
NFKBIB 0.03 0.044 0.22 3 -0.13 3 6
HRAS 0.006 0.11 0.27 4 -0.35 6 10
NFKBIA 0.03 0.044 0.22 3 -0.13 3 6
NF-kappa-B/RelA/I kappa B beta 0.033 0.041 0.22 3 -10000 0 3
RasGAP/Csk 0.061 0.075 -10000 0 -0.18 12 12
mol:GDP 0 0.11 0.22 2 -0.39 7 9
PTEN 0.031 0.006 -10000 0 -10000 0 0
CD79B 0.026 0.041 -10000 0 -0.34 2 2
NF-kappa-B/RelA/I kappa B alpha 0.033 0.041 0.22 3 -10000 0 3
GRB2 0.03 0.008 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.001 0.14 0.45 2 -0.47 7 9
PIK3R1 0.031 0.007 -10000 0 -10000 0 0
mol:IP3 -0.005 0.11 0.23 2 -0.37 8 10
CSK 0.031 0.006 -10000 0 -10000 0 0
FOS 0.001 0.12 0.32 6 -0.41 5 11
CHUK 0.019 0.082 0.4 2 -0.28 4 6
IBTK 0.032 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.027 0.1 0.23 2 -0.31 6 8
PTPN6 0 0.06 -10000 0 -0.48 2 2
RELA 0.031 0.007 -10000 0 -10000 0 0
BCL2A1 0.02 0.035 0.3 1 -10000 0 1
VAV2 -0.016 0.12 -10000 0 -0.41 11 11
ubiquitin-dependent protein catabolic process 0.033 0.044 0.22 3 -0.13 3 6
BTK -0.014 0.19 -10000 0 -0.92 7 7
CD19 0.004 0.073 -10000 0 -0.41 4 4
MAP4K1 0.029 0.01 -10000 0 -10000 0 0
CD72 0.024 0.05 -10000 0 -0.34 3 3
PAG1 0.019 0.057 -10000 0 -0.34 4 4
MAPK14 0.011 0.12 0.49 2 -0.37 7 9
SH3BP5 -0.001 0.1 -10000 0 -0.34 14 14
PIK3AP1 0 0.11 0.26 1 -0.37 7 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.003 0.1 -10000 0 -0.36 8 8
RAF1 0.006 0.1 0.3 4 -0.32 6 10
RasGAP/p62DOK/SHIP 0.062 0.075 -10000 0 -0.18 12 12
CD79A 0.029 0.01 -10000 0 -10000 0 0
re-entry into mitotic cell cycle 0.007 0.1 0.33 6 -0.22 6 12
RASA1 0.03 0.008 -10000 0 -10000 0 0
MAPK3 0.005 0.092 0.32 4 -0.28 5 9
MAPK1 0.012 0.1 0.38 5 -0.27 5 10
CD72/SHP1 0.009 0.086 0.44 1 -0.34 5 6
NFKB1 0.031 0.006 -10000 0 -10000 0 0
MAPK8 0.014 0.12 0.48 3 -0.39 7 10
actin cytoskeleton organization -0.007 0.12 0.36 2 -0.36 11 13
NF-kappa-B/RelA 0.067 0.074 0.37 3 -0.21 2 5
Calcineurin 0.025 0.095 0.23 1 -0.32 5 6
PI3K -0.01 0.089 -10000 0 -0.28 9 9
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.004 0.11 0.21 7 -0.39 7 14
SOS1 0.032 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.006 0.18 -10000 0 -0.66 11 11
DAPP1 -0.014 0.2 -10000 0 -0.74 11 11
cytokine secretion -0.003 0.12 0.31 5 -0.3 12 17
mol:DAG -0.005 0.11 0.23 2 -0.37 8 10
PLCG2 0.031 0.006 -10000 0 -10000 0 0
MAP2K1 0.006 0.1 0.33 4 -0.29 6 10
B-cell antigen/BCR complex/FcgammaRIIB 0.035 0.073 -10000 0 -0.21 12 12
mol:PI-3-4-5-P3 -0.025 0.071 0.27 2 -0.26 5 7
ETS1 0.011 0.11 0.3 7 -0.35 4 11
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.042 0.087 -10000 0 -0.17 20 20
B-cell antigen/BCR complex/LYN 0.011 0.073 -10000 0 -0.37 5 5
MALT1 0.032 0.005 -10000 0 -10000 0 0
TRAF6 0.031 0.007 -10000 0 -10000 0 0
RAC1 -0.013 0.12 0.27 1 -0.38 11 12
B-cell antigen/BCR complex/LYN/SYK 0.033 0.083 -10000 0 -0.32 5 5
CARD11 -0.006 0.11 0.2 7 -0.37 7 14
FCGR2B 0.004 0.091 -10000 0 -0.34 11 11
PPP3CA 0.031 0.006 -10000 0 -10000 0 0
BCL10 0.032 0.005 -10000 0 -10000 0 0
IKK complex 0.029 0.076 0.24 10 -0.12 4 14
PTPRC 0.031 0.006 -10000 0 -10000 0 0
PDPK1 -0.015 0.06 0.18 7 -0.2 4 11
PPP3CB 0.032 0.005 -10000 0 -10000 0 0
PPP3CC 0.029 0.01 -10000 0 -10000 0 0
POU2F2 0.027 0.038 0.21 4 -10000 0 4
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.018 0.082 -10000 0 -0.18 23 23
RGS9BP -0.003 0.098 -10000 0 -0.34 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.008 -10000 0 -10000 0 0
mol:Na + 0.024 0.011 -10000 0 -10000 0 0
mol:ADP -0.008 0.012 -10000 0 -10000 0 0
GNAT2 0.029 0.029 -10000 0 -0.34 1 1
RGS9-1/Gbeta5/R9AP 0.028 0.077 -10000 0 -0.2 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.037 0.022 -10000 0 -0.2 1 1
GRK7 0.029 0.008 -10000 0 -10000 0 0
CNGB3 0.021 0.011 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.018 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.061 0.17 19 -10000 0 19
Cone PDE6 0.047 0.083 -10000 0 -0.17 18 18
Cone Metarhodopsin II 0.03 0.011 -10000 0 -10000 0 0
Na + (4 Units) 0.032 0.014 -10000 0 -10000 0 0
GNAT2/GDP 0.038 0.074 -10000 0 -0.17 17 17
GNB5 0.023 0.057 -10000 0 -0.34 4 4
mol:GMP (4 units) 0.007 0.04 0.19 3 -0.18 4 7
Cone Transducin 0.02 0.088 -10000 0 -0.19 23 23
SLC24A2 0.018 0.005 -10000 0 -10000 0 0
GNB3/GNGT2 0.003 0.1 -10000 0 -0.25 22 22
GNB3 0.014 0.074 -10000 0 -0.34 7 7
GNAT2/GTP 0.022 0.02 -10000 0 -0.23 1 1
CNGA3 0.018 0.003 -10000 0 -10000 0 0
ARR3 0.024 0.01 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.025 0.011 -10000 0 -10000 0 0
mol:Pi 0.028 0.076 -10000 0 -0.2 16 16
Cone CNG Channel 0.048 0.043 -10000 0 -0.17 4 4
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.018 0.005 -10000 0 -10000 0 0
RGS9 0.026 0.011 -10000 0 -10000 0 0
PDE6C 0.024 0.049 -10000 0 -0.34 3 3
GNGT2 -0.009 0.11 -10000 0 -0.34 17 17
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.027 0.01 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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 I