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.

Author
Antonio 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 publication
None
Maintainer
Antonio Colaprico <antonio.colaprico@ulb.ac.be>, Catharina Olsen <colsen@ulb.ac.be>
License
GPL (>= 3)
Version
1.0.0
URLs

View on Bioconductor

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

Files in this package

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