title: rMAPS: RNA map analysis and plotting server for alternative exon regulation.
abstract: RNA-binding proteins (RBPs) play a critical role in the regulation of alternative splicing (AS), a prevalent mechanism for generating transcriptomic and proteomic diversity in eukaryotic cells. Studies have shown that AS can be regulated by RBPs in a binding-site-position dependent manner. Depending on where RBPs bind, splicing of an alternative exon can be enhanced or suppressed. Therefore, spatial analyses of RBP motifs and binding sites around alternative exons will help elucidate splicing regulation by RBPs. The development of high-throughput sequencing technologies has allowed transcriptome-wide analyses of AS and RBP-RNA interactions. Given a set of differentially regulated alternative exons obtained from RNA sequencing (RNA-seq) experiments, the rMAPS web server (http://rmaps.cecsresearch.org) performs motif analyses of RBPs in the vicinity of alternatively spliced exons and creates RNA maps that depict the spatial patterns of RBP motifs. Similarly, rMAPS can also perform spatial analyses of RBP-RNA binding sites identified by cross-linking immunoprecipitation sequencing (CLIP-seq) experiments. We anticipate rMAPS will be a useful tool for elucidating RBP regulation of alternative exon splicing using high-throughput sequencing data.
authors.affiliation: Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA juw.park@louisville.edu.
authors.forename: Juw Won
authors.initials: JW
authors.lastname: Park
authors.affiliation: Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA.
authors.forename: Sungbo
authors.initials: S
authors.lastname: Jung
authors.affiliation: Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA.
authors.forename: Eric C
authors.initials: EC
authors.lastname: Rouchka
authors.affiliation: Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA.
authors.forename: Yu-Ting
authors.initials: YT
authors.lastname: Tseng
authors.affiliation: Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA yxing@ucla.edu.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xing
mesh_terms: D017398:Alternative Splicing; D001665:Binding Sites; D003196:Computer Graphics; D005057:Eukaryotic Cells / Q000378:metabolism; D005091:Exons; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D007438:Introns; D011485:Protein Binding; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D014584:User-Computer Interface
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA