MoonlightR: Identify oncogenes and tumor suppressor genes from omics data
Version 1.2.0

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.

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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)
Version1.2.0
URL https://github.com/torongs82/Moonlight
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MoonlightR")

Man pages

dataFilt: Gene Expression (Rnaseqv2) data from TCGA LUAD
dataGRN: GRN gene regulatory network output
dataURA: Output example from function Upstram Regulator Analysis
DEGsmatrix: DEG Differentially expressed genes
DiseaseList: Information on 101 biological processes
DPA: DPA
EAGenes: Information about genes
FEA: FEA
GDCprojects: Information on GDC projects
geneInfo: Information about genes for normalization
GEO_TCGAtab: Information on GEO data (and overlap with TCGA)#' A data set...
getDataGEO: getDataGEO
getDataTCGA: getDataTCGA
GRN: Generate network
GSEA: GSEA
knownDriverGenes: Information on known cancer driver gene from COSMIC
listMoonlight: Output list from Moonlight
LPA: LPA
moonlight: moonlight pipeline
MoonlightR: MoonlightR
plotCircos: plotCircos
plotFEA: plotFEA
plotNetworkHive: plotNetworkHive: Hive network plot
plotURA: plotURA: Upstream regulatory analysis heatmap plot
PRA: Pattern Recognition Analysis (PRA)
tabGrowBlock: Information growing/blocking characteristics for 101 selected...
URA: URA Upstream Regulator Analysis

Functions

DEGsmatrix Man page
DPA Man page Source code
DiseaseList Man page
EAGenes Man page
FEA Man page Source code
GDCprojects Man page
GEO_TCGAtab Man page
GRN Man page Source code
GSEA Man page Source code
LPA Man page Source code
MoonlightR Man page
MoonlightR-package Man page
PRA Man page Source code
URA Man page Source code
dataFilt Man page
dataGRN Man page
dataURA Man page
geneInfo Man page
getDataGEO Man page Source code
getDataTCGA Man page Source code
knownDriverGenes Man page
listMoonlight Man page
moonlight Man page Source code
plotCircos Man page Source code
plotFEA Man page Source code
plotNetworkHive Man page Source code
plotURA Man page Source code
tabGrowBlock 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
MoonlightR documentation built on May 20, 2017, 10:44 p.m.