dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation

被引：55

作者：

Hariharan, Manoj ^{[1
]}

Scaria, Vinod ^{[1
]}

Brahmachari, Samir K. ^{[1
]}

机构：

[1] CSIR, Inst Genom & Integrat Biol, GN Ramachandran Knowledge Ctr Genome Informat, Delhi, India

来源：

BMC BIOINFORMATICS | 2009年 / 10卷

关键词：

TARGET SITES; POLYMORPHISM; PREDICTION; BINDING; REPRESSION; DUPLEXES;

D O I：

10.1186/1471-2105-10-108

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: MicroRNAs (miRNAs) regulate several biological processes through post-transcriptional gene silencing. The efficiency of binding of miRNAs to target transcripts depends on the sequence as well as intramolecular structure of the transcript. Single Nucleotide Polymorphisms (SNPs) can contribute to alterations in the structure of regions flanking them, thereby influencing the accessibility for miRNA binding. Description: The entire human genome was analyzed for SNPs in and around predicted miRNA target sites. Polymorphisms within 200 nucleotides that could alter the intramolecular structure at the target site, thereby altering regulation were annotated. Collated information was ported in a MySQL database with a user-friendly interface accessible through the URL: http://miracle.igib.res.in/dbSMR. Conclusion: The database has a user-friendly interface where the information can be queried using either the gene name, microRNA name, polymorphism ID or transcript ID. Combination queries using 'AND' or 'OR' is also possible along with specifying the degree of change of intramolecular bonding with and without the polymorphism. Such a resource would enable researchers address questions like the role of regulatory SNPs in the 3' UTRs and population specific regulatory modulations in the context of microRNA targets.

引用

页数：6

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