[Bioc-devel] Roar - detecting 3'UTR shortening with standard RNAseq data

Elena Grassi grassi.e at gmail.com
Thu Mar 27 10:45:30 CET 2014

Dear BioC developers,

post-transcriptional regulation is a complex mechanism that plays a
central role in defining multiple cellular identities starting from a
common genome - recently modifications in the 3'UTR lengths of
transcripts have been found to have a role in this conundrum: a
shorter 3'UTR could lead to  miRNAs targeting escape, different
cellular localizations and so on.

A tendency toward expressing genes with shorter UTRs has been found in
proliferating tissues and cancers; being able to identify the genes
that change their lengths in physiological and pathological conditions
could lead to interesting insights about their nature.
We have developed a package to identify those genes using RNA
sequencing data obtained from standard libraries, thus widely
applicable on data that are obtained to perform classical differential
expression analyses.

The approach is based on Fisher test to detect dis-equilibriums in the
number of reads falling over the 3'UTRs when comparing two conditions.
The name roar means "ratio of a ratio": counts and fragments lengths
are used to calculate the prevalence of the short isoform over the
long one in both conditions, therefore the ratio of these ratios
represents the relative "shortening" (or lengthening) in one condition
with respect to the other. As input, roar uses alignments files for
the two conditions and coordinates of the 3'UTRs with alternative
polyadenylation sites.

Any comment will be greatly appreciated,
Elena Grassi

PhD student at the Molecular Biotechnology Center - http://www.mbcunito.it/
$ pom

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