SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements.

ABSTRACT:

Background

Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called exonization), or the element inserts into the exon, leading to a new transcript. Several examples in the literature show that isoforms generated by an exonization are specific to a certain tissue (for example the heart muscle) or inflict a disease. Thus, exonizations can have negative effects for the transcriptome of an organism.

Results

As we aimed at detecting other tissue- or tumor-specific isoforms in human and mouse genomes which were generated through exonization of a transposed element, we designed the automated analysis pipeline SERpredict (SER = Specific Exonized Retroelement) making use of Bayesian Statist

SUBMITTER: Mersch B 

PROVIDER: S-EPMC2194731 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature