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

Rimpi Khurana1, Vinod Kumar Verma1, Abdul Rawoof1, Shrish Tiwari2, Rekha A Nair3, Ganesh Mahidhara1, Mohammed M Idris1, Alan R Clarke4* and Lekha Dinesh Kumar1*

Author Affiliations

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

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

3 Department of Pathology, Regional Cancer Centre, Trivandrum, Kerala, India

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

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BMC Bioinformatics 2014, 15:15  doi:10.1186/1471-2105-15-15

Published: 15 January 2014

Abstract

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.

Keywords:
MicroRNAs; Breast cancer; Targets; 3'UTR; miRanda; TLDA