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