title: SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions.
abstract: SomamiR 2.0 (http://compbio.uthsc.edu/SomamiR) is a database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA) including mRNAs, circular RNAs (circRNA) and long noncoding RNAs (lncRNA). Here, we describe the recent major updates to the SomamiR database. We expanded the scope of the database by including somatic mutations that impact the interactions between miRNAs and two classes of non-coding RNAs, circRNAs and lncRNAs. Recently, a large number of miRNA target sites have been discovered by newly emerged high-throughput technologies for mapping the miRNA interactome. We have mapped 388 247 somatic mutations to the experimentally identified miRNA target sites. The updated database also includes a list of somatic mutations in the miRNA seed regions, which contain the most important guiding information for miRNA target recognition. A recently developed webserver, miR2GO, was integrated with the database to provide a seamless pipeline for assessing functional impacts of somatic mutations in miRNA seed regions. Data and functions from multiple sources including biological pathways and genome-wide association studies were updated and integrated with SomamiR 2.0 to make it a better platform for functional analysis of somatic mutations altering miRNA-ceRNA interactions.
authors.affiliation: Machine Intelligence Unit, Indian Statistical Institute, Kolkata, WB 700108, India anindyamail123@gmail.com.
authors.forename: Anindya
authors.initials: A
authors.lastname: Bhattacharya
authors.affiliation: Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN 38163, USA ycui2@uthsc.edu.
authors.forename: Yan
authors.initials: Y
authors.lastname: Cui
mesh_terms: D001665:Binding Sites / Q000235:genetics; D030561:Databases, Nucleic Acid; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D000079962:RNA, Circular; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D000079962:RNA, Circular; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D012313:RNA