title: RGmatch: matching genomic regions to proximal genes in omics data integration.
abstract: BACKGROUND
  The integrative analysis of multiple genomics data often requires that genome coordinates-based signals have to be associated with proximal genes. The relative location of a genomic region with respect to the gene (gene area) is important for functional data interpretation; hence algorithms that match regions to genes should be able to deliver insight into this information.
  
  
  RESULTS
  In this work we review the tools that are publicly available for making region-to-gene associations. We also present a novel method, RGmatch, a flexible and easy-to-use Python tool that computes associations either at the gene, transcript, or exon level, applying a set of rules to annotate each region-gene association with the region location within the gene. RGmatch can be applied to any organism as long as genome annotation is available. Furthermore, we qualitatively and quantitatively compare RGmatch to other tools.
  
  
  CONCLUSIONS
  RGmatch simplifies the association of a genomic region with its closest gene. At the same time, it is a powerful tool because the rules used to annotate these associations are very easy to modify according to the researcher's specific interests. Some important differences between RGmatch and other similar tools already in existence are RGmatch's flexibility, its wide range of user options, compatibility with any annotatable organism, and its comprehensive and user-friendly output.
authors.affiliation: Genomics of Gene Expression Laboratory, Gene Expression and Epigenomics Program, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012, Valencia, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Furió-Tarí
authors.affiliation: Genomics of Gene Expression Laboratory, Gene Expression and Epigenomics Program, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012, Valencia, Spain. aconesa@cipf.es.|Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32603, USA. aconesa@cipf.es.
authors.forename: Ana
authors.initials: A
authors.lastname: Conesa
authors.affiliation: Genomics of Gene Expression Laboratory, Gene Expression and Epigenomics Program, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012, Valencia, Spain. starazona@cipf.es.|Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, Camí de Vera, 46022, Valencia, Spain. starazona@cipf.es.
authors.forename: Sonia
authors.initials: S
authors.lastname: Tarazona
mesh_terms: D000465:Algorithms; D005091:Exons; D023281:Genomics / Q000379:methods*; D020407:Internet; D011401:Promoter Regions, Genetic; D014584:User-Computer Interface
keywords: Associations; Gene; Genomic region; NGS; Omics integration; Peak