SomamiR 2.0

A database of cancer somatic mutations altering microRNA-ceRNA interactions

Anindya Bhattacharya, Yan Cui

Research output: Contribution to journalArticle

33 Citations (Scopus)

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 web-server, 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.

Original languageEnglish (US)
Pages (from-to)D1005-D1010
JournalNucleic acids research
Volume44
Issue numberD1
DOIs
StatePublished - Jan 4 2016

Fingerprint

MicroRNAs
Databases
RNA
Mutation
Neoplasms
Long Noncoding RNA
Seeds
Untranslated RNA
Genome-Wide Association Study
Technology
Messenger RNA

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

SomamiR 2.0 : A database of cancer somatic mutations altering microRNA-ceRNA interactions. / Bhattacharya, Anindya; Cui, Yan.

In: Nucleic acids research, Vol. 44, No. D1, 04.01.2016, p. D1005-D1010.

Research output: Contribution to journalArticle

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