OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer

BMC Bioinformatics

Rimpi Khurana³  Vinod Kumar Verma³  Abdul Rawoof³  Shrish Tiwari²  Rekha A Nair¹  Ganesh Mahidhara³  Mohammed M Idris³  Alan R Clarke⁴  Lekha Dinesh Kumar³ 

[1] Department of Pathology, Regional Cancer Centre, Trivandrum, Kerala, India

[2] Bioinformatics, Centre for Cellular & Molecular Biology, Council of scientific and Industrial Research, Hyderabad, A.P, India

[3] Cancer Biology, Centre for Cellular & Molecular Biology, Council of scientific and Industrial Research, Hyderabad, A.P, India

[4] School of Biosciences, Cardiff University, Cardiff, South Glamorgan, UK

关键词: TLDA;    miRanda;    3'UTR;    Targets;    Breast cancer;    MicroRNAs;   

Others  :  1087652
DOI  :  10.1186/1471-2105-15-15

 received in 2013-08-14, accepted in 2014-01-02,  发布年份 2014

【 摘 要 】

Background

Given the estimate that 30% of our genes are controlled by microRNAs, it is essential that we understand the precise relationship between microRNAs and their targets. OncomiRs are microRNAs (miRNAs) that have been frequently shown to be deregulated in cancer. However, although several oncomiRs have been identified and characterized, there is as yet no comprehensive compilation of this data which has rendered it underutilized by cancer biologists. There is therefore an unmet need in generating bioinformatic platforms to speed the identification of novel therapeutic targets.

Description

We describe here OncomiRdbB, a comprehensive database of oncomiRs mined from different existing databases for mouse and humans along with novel oncomiRs that we have validated in human breast cancer samples. The database also lists their respective predicted targets, identified using miRanda, along with their IDs, sequences, chromosome location and detailed description. This database facilitates querying by search strings including microRNA name, sequence, accession number, target genes and organisms. The microRNA networks and their hubs with respective targets at 3'UTR, 5'UTR and exons of different pathway genes were also deciphered using the 'R' algorithm.

Conclusion

OncomiRdbB is a comprehensive and integrated database of oncomiRs and their targets in breast cancer with multiple query options which will help enhance both understanding of the biology of breast cancer and the development of new and innovative microRNA based diagnostic tools and targets of therapeutic significance. OncomiRdbB is freely available for download through the URL link http://tdb.ccmb.res.in/OncomiRdbB/index.htm webcite.

【 授权许可】

   
2014 Khurana et al.; licensee BioMed Central Ltd.

【 图 表 】

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