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 <email@example.com>, Catharina Olsen <firstname.lastname@example.org>|
|License||GPL (>= 3)|
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
EAGenes: Information about genes
GDCprojects: Information on GDC projects
geneInfo: Information about genes for normalization
GEO_TCGAtab: Information on GEO data (and overlap with TCGA)#' A data set...
GRN: Generate network
knownDriverGenes: Information on known cancer driver gene from COSMIC
listMoonlight: Output list from Moonlight
moonlight: moonlight pipeline
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