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Nucleic Acids Res. 2016 Jan 4;44(D1):D1005-10. doi: 10.1093/nar/gkv1220. Epub 2015 Nov 17.

SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions.

Author information

1
Machine Intelligence Unit, Indian Statistical Institute, Kolkata, WB 700108, India anindyamail123@gmail.com.
2
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.

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.

PMID:
26578591
PMCID:
PMC4702864
DOI:
10.1093/nar/gkv1220
[Indexed for MEDLINE]
Free PMC Article

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