PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs.

Genome Biol 2013 Aug 16;14(8):R84. Epub 2013 Aug 16.

The regulation of intragenic miRNAs by their own intronic promoters is one of the open problems of miRNA biogenesis. Here, we describe PROmiRNA, a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features. We validate our results with existing annotation, PolII occupancy data and read coverage from RNA-seq data. Compared to previous methods PROmiRNA increases the detection rate of intronic promoters by 30%, allowing us to perform a large-scale analysis of their genomic features, as well as elucidate their contribution to tissue-specific regulation. PROmiRNA can be downloaded from http://promirna.molgen.mpg.de.

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2013-14-8-r84DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053815PMC
August 2013
18 Reads

Publication Analysis

Top Keywords

mirna promoter
8
intronic promoters
8
data read
4
occupancy data
4
polii occupancy
4
read coverage
4
rna-seq data
4
compared previous
4
data compared
4
annotation polii
4
coverage rna-seq
4
validate existing
4
trained deepcage
4
model trained
4
statistical model
4
semi-supervised statistical
4
deepcage data
4
data sequence
4
previous methods
4
features validate
4

References

(Supplied by CrossRef)

Similar Publications