IsomiRage: from functional classification to differential expression of miRNAs and their isoforms

ABSTRACT: Characterization and analysis of miRNAs and their variants (called "IsomiRs") in next-generation sequencing datasets in breast epithelium. Our pipeline, called IsomiRage, allows distinguishing canonical miRNAs from templated and non-templated isomiRs by alignment to a custom database, which comprises all possible 3’-, 5’- and trimmed variants. Functionally equivalent isomiRs can be grouped together according to the type of modification (e.g. uridylation, adenylation, trimming...) to assess which miRNAs are more intensively modified in a given biological context. When applied to the analysis of primary epithelial breast cancer cells, our methodology provided a 40% increase in the number of detected miRNA species and allowed to easily identify and classify more than 1000 variants.

ORGANISM(S): Homo sapiens

SUBMITTER: Heiko Muller 

PROVIDER: E-GEOD-61165 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress