MoonlightR: Identify oncogenes and tumor suppressor genes from omics data

Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MoonlightR")
AuthorAntonio Colaprico*, Catharina Olsen*, Claudia Cava, Thilde Terkelsen, Laura Cantini, Andre Olsen, Gloria Bertoli, Andrei Zinovyev, Emmanuel Barillot, Isabella Castiglioni, Elena Papaleo, Gianluca Bontempi
Bioconductor views DNAMethylation DifferentialExpression DifferentialMethylation GeneExpression GeneRegulation GeneSetEnrichment MethylationArray Network NetworkEnrichment Pathways Survival
Date of publicationNone
MaintainerAntonio Colaprico <antonio.colaprico@ulb.ac.be>, Catharina Olsen <colsen@ulb.ac.be>
LicenseGPL (>= 3)
Version1.0.0
https://github.com/torongs82/Moonlight

View on Bioconductor

Functions

dataFilt Man page
dataGRN Man page
dataURA Man page
DEGsmatrix Man page
DiseaseList Man page
DPA Man page
EAGenes Man page
FEA Man page
GDCprojects Man page
geneInfo Man page
GEO_TCGAtab Man page
getDataGEO Man page
getDataTCGA Man page
GRN Man page
GSEA Man page
knownDriverGenes Man page
listMoonlight Man page
LPA Man page
moonlight Man page
MoonlightR Man page
MoonlightR-package Man page
plotCircos Man page
plotFEA Man page
plotNetworkHive Man page
plotURA Man page
PRA Man page
tabGrowBlock Man page
URA Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/DPA.R R/FEA.R R/GRN.R R/GSEA.R R/LPA.R R/MoonlightR.R R/PRA.R R/URA.R R/getDataGEO.R R/getDataTCGA.R R/moonlight.R R/plotCircos.R R/plotFEA.R R/plotNetworkHive.R R/plotURA.R
README.md
build
build/vignette.rds
data
data/DEGsmatrix.rda
data/DiseaseList.rda
data/EAGenes.rda
data/GDCprojects.rda
data/GEO_TCGAtab.rda
data/dataFilt.rda
data/dataGRN.rda
data/dataURA.rda
data/datalist
data/geneInfo.rda
data/knownDriverGenes.rda
data/listMoonlight.rda
data/tabGrowBlock.rda
inst
inst/CITATION
inst/doc
inst/doc/Moonlight.R
inst/doc/Moonlight.Rmd
inst/doc/Moonlight.html
man
man/DEGsmatrix.Rd man/DPA.Rd man/DiseaseList.Rd man/EAGenes.Rd man/FEA.Rd man/GDCprojects.Rd man/GEO_TCGAtab.Rd man/GRN.Rd man/GSEA.Rd man/LPA.Rd man/MoonlightR.Rd man/PRA.Rd man/URA.Rd man/dataFilt.Rd man/dataGRN.Rd man/dataURA.Rd man/geneInfo.Rd man/getDataGEO.Rd man/getDataTCGA.Rd man/knownDriverGenes.Rd man/listMoonlight.Rd man/moonlight.Rd man/plotCircos.Rd man/plotFEA.Rd man/plotNetworkHive.Rd man/plotURA.Rd man/tabGrowBlock.Rd
vignettes
vignettes/Case1_URA.png
vignettes/FEAplot.png
vignettes/GSEAplot.png
vignettes/Moonlight.Rmd
vignettes/Moonlight_Pipeline.png
vignettes/URAplot.png
vignettes/circos_ocg_tsg_ncancer5.png
vignettes/circos_ocg_tsg_stages.png
vignettes/networkHive.png

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