Using Bioinformatics Tools to Study the Role of microRNA in Cancer
High-throughput sequencing (HTS) has emerged as a promising method to study gene expression in neoplastic and normal tissues. Using HTS, many research groups have described transcript variants as well as discovering new transcribed loci and noncoding RNAs, including microRNAs. In oncology, expression profiling of microRNAs in matched tumor and normal tissues has been used to detect differential expression of microRNAs in cancer. We present one approach for laboratories with few bioinformatics support to assist in the analysis of microRNA HTS data focused in oncology. This approach can also be adapted to study other systems.
Key wordsBioinformatics High-throughput sequencing microRNA miRNA databases miRNA target
F.P. acknowledges the support of Fundação Carlos Chagas de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) and Fundação do Câncer. F.P. and A.D. acknowledge the support of Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). N.A.N.J. is supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).
- 3.Blankenberg D, Von Kuster G, Coraor N et al (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 19(10):1–21Google Scholar