|SomamiR DB 2.0
Somatic mutations altering microRNA-ceRNA interactions
|About the database:|
|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). It also provides an integrated platform for the functional analysis of these somatic mutations. The SomamiR DB can be browsed in several ways:
1. Somatic mutations in miRNA sequences displays somatic mutations in miRNA sequences. Users can use miR2GO to analyze the functional impacts of somatic mutations in miRNA seed regions.
2. Somatic mutations in experimentally identified miRNA target sites: CLASH displays the somatic mutations in miRNA target sites identified from CLASH experiments.
3. Somatic mutations in experimentally identified miRNA target sites: PAR-CLIP and HITS-CLIP displays the somatic mutations in miRNA target sites identified from PAR-CLIP and HITS-CLIP experiments.
4. Somatic mutations in predicted miRNA target sites displays somatic mutations within 3' UTRs of genes, lncRNAs and circRNAs that create or disrupt putative miRNA target sites.
5. Biological pathways impacted by somatic mutations in miRNA target sites displays genes in cancer related KEGG pathways that contain somatic mutations in miRNA target sites.
6. Genes associated with cancer risk that contain miRNA related somatic mutations displays cancer-associated genes that contain somatic mutations in miRNA target sites.
Additionally, the SomamiR DB contains a collection of somatic and germline mutations in miRNAs or their target sites that have been strongly linked with cancer. Specifically, the majority of these mutations met the following criteria (a) they have been associated with cancer risk in GWAS or CGAS and (b) there is experimental evidence indicating that the mutation alters miRNA function. Mutations in miRNAs and their target sites that fit these criteria can be browsed by clicking on Experimental evidence linking miRNA related polymorphisms with cancer or Experimental evidence linking polymorphisms in miRNA with cancer, respectively.
|How to cite the SomamiR database:|
|1. Bhattacharya A, Cui Y. SomamiR 2.0: a database of cancer somatic mutations altering microRNA–ceRNA interactions. Nucleic Acids Res. 2016; 44(D1): D1005-D1010. PMID: 26578591|
|2. Bhattacharya A, Ziebarth JD, Cui Y. SomamiR: a database for somatic mutations impacting microRNA function in cancer. Nucleic Acids Res. 2013; 41(D1):D977-D982. PMID: 23180788.|