title: MiRComb: An R Package to Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers.
abstract: MicroRNAs (miRNAs) are small RNAs that regulate the expression of target mRNAs by specific binding on the mRNA 3'UTR and promoting mRNA degradation in the majority of cases. It is often of interest to know the specific targets of a miRNA in order to study them in a particular disease context. In that sense, some databases have been designed to predict potential miRNA-mRNA interactions based on hybridization sequences. However, one of the main limitations is that these databases have too many false positives and do not take into account disease-specific interactions. We have developed an R package (miRComb) able to combine miRNA and mRNA expression data with hybridization information, in order to find potential miRNA-mRNA targets that are more reliable to occur in a specific physiological or disease context. This article summarizes the pipeline and the main outputs of this package by using as example TCGA data from five gastrointestinal cancers (colon cancer, rectal cancer, liver cancer, stomach cancer and esophageal cancer). The obtained results can be used to develop a huge number of testable hypotheses by other authors. Globally, we show that the miRComb package is a useful tool to deal with miRNA and mRNA expression data, that helps to filter the high amount of miRNA-mRNA interactions obtained from the pre-existing miRNA target prediction databases and it presents the results in a standardised way (pdf report). Moreover, an integrative analysis of the miRComb miRNA-mRNA interactions from the five digestive cancers is presented. Therefore, miRComb is a very useful tool to start understanding miRNA gene regulation in a specific context. The package can be downloaded in http://mircomb.sourceforge.net.
authors.affiliation: Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.|Gastrointestinal and Pancreatic Oncology Group, Hospital Clínic of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Vila-Casadesús
authors.affiliation: Gastrointestinal and Pancreatic Oncology Group, Hospital Clínic of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.
authors.forename: Meritxell
authors.initials: M
authors.lastname: Gironella
authors.affiliation: Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Catalonia, Spain.|Gastrointestinal and Pancreatic Oncology Group, Hospital Clínic of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.
authors.forename: Juan José
authors.initials: JJ
authors.lastname: Lozano
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D004067:Digestive System Neoplasms / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D012984:Software
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger