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.

AuthorAntonio Colaprico*, Catharina Olsen*, Claudia Cava, Thilde Terkelsen, Laura Cantini, Andre Olsen, Gloria Bertoli, Andrei Zinovyev, Emmanuel Barillot, Isabella Castiglioni, Elena Papaleo, Gianluca Bontempi
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

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

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