title: spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
abstract: Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been identified where a lncRNA acts by sequestering miRNAs. This implies the down-regulation in the interaction of the miRNAs with their mRNA targets, what has been called a sponge effect. Multiple approaches exist for the prediction of miRNA targets in mRNAs. However, few methods exist for the prediction of miRNA response elements (MREs) in lncRNAs acting as ceRNAs (sponges). Here, we present spongeScan (http://spongescan.rc.ufl.edu), a graphical web tool to compute and visualize putative MREs in lncRNAs, along with different measures to assess their likely behavior as ceRNAs.
authors.affiliation: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Furió-Tarí
authors.affiliation: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, Camí de Vera, 46022 Valencia, Spain.
authors.forename: Sonia
authors.initials: S
authors.lastname: Tarazona
authors.affiliation: Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB4 1GU, UK aconesa@cipf.es.
authors.forename: Anton J
authors.initials: AJ
authors.lastname: Enright
authors.affiliation: Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain Microbiology and Cell Science, IFAS, University of Florida, Gainesville, USA aconesa@cipf.es.
authors.forename: Ana
authors.initials: A
authors.lastname: Conesa
mesh_terms: D001667:Binding, Competitive; D003196:Computer Graphics; D015536:Down-Regulation; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D059372:Nucleotide Motifs; D009928:Organ Specificity; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D020218:Response Elements; D012984:Software
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger