A database of breast oncogenic specific siRNAs

Atul Tyagi,Ashok Sharma,Manoj Semwal

doi:10.1038/s41598-017-08948-1

Atul Tyagi, Ashok Sharma + Show 1 more

Open Access

https://doi.org/10.1038/s41598-017-08948-1

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Abstract

Breast cancer is a serious problem causing the death of women across the world. At present, one of the major challenges is to design drugs to target breast cancer specific gene(s). RNA interference (RNAi) is an important technique for targeted gene silencing that may lead to promising novel therapeutic strategies for breast cancer. Therefore, identification of such molecules having high oncogene specificity is the need of the hour. Here, we have developed a database named as Breast Oncogenic Specific siRNAs (BOSS, http://bioinformatics.cimap.res.in/sharma/boss/) on the basis of the current research status on siRNA-mediated repression of oncogenes in different breast cancer cell lines. BOSS is a resource of experimentally validated breast oncogenic siRNAs, collected from research articles and patents published yet. The present database contains information on 865 breast oncogenic siRNA entries. Each entry provides comprehensive information of an siRNA that includes its name, sequence, target gene, type of cells, and inhibition value, etc. Additionally, some useful tools like siRNAMAP and BOSS BLAST were also developed and linked with the database. siRNAMAP can be used for the selection of best siRNA against a target gene while BOSS BLAST tool helps to locate the siRNA sequences in deferent oncogenes.

Highlights

Breast cancer is a serious problem causing the death of women across the world
BOSS database maintains the comprehensive information of breast oncogenic specific short interfering RNAs (siRNAs) and comprises information about siRNAs name, target genes, inhibition value, cell line, siRNA sequence, NCBI Accession No, transfection reagent, test method, test objective and Pubmed ID etc. which are directly linked to essential databases
BOSS database consists of 865 entries for 195 unique breast oncogene-specific siRNAs/short hairpin RNAs (shRNAs)

Summary

Introduction

Breast cancer is a serious problem causing the death of women across the world. At present, one of the major challenges is to design drugs to target breast cancer specific gene(s). To the best of our knowledge, there is no comprehensive database of siRNAs/shRNAs targeting breast oncogenes which is required to search and analyse the data from the literature With this in mind, a manually curated specialised databank, “BOSS”, has been developed on the basis of information from experimentally validated and published siRNAs and shRNAs targeting various breast oncogenes to facilitate research on RNAi-based cancer therapy. Most of the siRNA or shRNA entries have been provided with the inhibition value, qualitative representations were considered and included in the database if the quantitative values for siRNAs or shRNA were not given in the corresponding reports These reports have evaluated the expression level of different test targets (i.e. mRNA, protein, etc) in breast cancer samples[14,15,16,17,18,19,20,21,22,23,24,25].

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