Package: MoonlightR 1.31.0

Matteo Tiberti

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.

Authors:Antonio Colaprico [aut], Catharina Olsen [aut], Matthew H. Bailey [aut], Gabriel J. Odom [aut], Thilde Terkelsen [aut], Mona Nourbakhsh [aut], Astrid Saksager [aut], Tiago C. Silva [aut], André V. Olsen [aut], Laura Cantini [aut], Andrei Zinovyev [aut], Emmanuel Barillot [aut], Houtan Noushmehr [aut], Gloria Bertoli [aut], Isabella Castiglioni [aut], Claudia Cava [aut], Gianluca Bontempi [aut], Xi Steven Chen [aut], Elena Papaleo [aut], Matteo Tiberti [cre, aut]

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NEWS

# Install 'MoonlightR' in R:
install.packages('MoonlightR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/elelab/moonlightr/issues

Datasets:
  • DEGsmatrix - DEG Differentially expressed genes
  • DiseaseList - Information on 101 biological processes
  • EAGenes - Information about genes
  • GDCprojects - Information on GDC projects
  • GEO_TCGAtab - Information on GEO data (and overlap with TCGA)#' A data set containing the following data:
  • dataFilt - Gene Expression (Rnaseqv2) data from TCGA LUAD
  • dataGRN - GRN gene regulatory network output
  • dataURA - Output example from function Upstram Regulator Analysis
  • geneInfo - Information about genes for normalization
  • knownDriverGenes - Information on known cancer driver gene from COSMIC
  • listMoonlight - Output list from Moonlight
  • tabGrowBlock - Information growing/blocking characteristics for 101 selected biological processes

On BioConductor:MoonlightR-1.31.0(bioc 3.20)MoonlightR-1.30.0(bioc 3.19)

bioconductor-package

14 exports 1.38 score 183 dependencies 2 mentions

Last updated 2 months agofrom:bba1442278

Exports:DPAFEAgetDataGEOgetDataTCGAGRNGSEALPAmoonlightplotCircosplotFEAplotNetworkHiveplotURAPRAURA

Dependencies:abindAnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcaToolscirclizeclicliprclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdoParallelDOSEdownloaderdplyrenrichplotevaluatefansifarverfastmapfastmatchfgseafilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOqueryggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeGlobalOptionsglueGO.dbGOSemSimgplotsgraphlayoutsgridExtragridGraphicsgsongtablegtoolsHDO.dbhighrHiveRhmshtmltoolshtmlwidgetshttrhttr2igraphIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslparmigenepatchworkpillarpkgconfigplogrplyrpngpolyclipprettyunitsprogresspurrrqvalueR.methodsS3R.ooR.utilsR6randomForestrappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadrreshape2rglRISmedrlangrmarkdownRSQLitervestS4ArraysS4VectorssassscalesscatterpieselectrshadowtextshapesnowSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontsTCGAbiolinksTCGAbiolinksGUI.datatibbletidygraphtidyrtidyselecttidytreetinytextreeiotweenrtzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlyulab.utilszlibbioc

Moonlight: an approach to identify multiple role of biomarkers as oncogene or tumorsuppressor in different tumor types and stages.

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

Rendered fromMoonlight.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2022-10-11
Started: 2016-09-24