SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elementsReport as inadecuate




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BMC Genetics

, 8:78

First Online: 06 November 2007Received: 24 May 2007Accepted: 06 November 2007

Abstract

BackgroundTransposed 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.

ResultsAs 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 = S pecific E xonized R etroelement making use of Bayesian Statistics. With this pipeline, we found several genes in which a transposed element formed a tissue- or tumor-specific isoform.

ConclusionOur results show that SERpredict produces relevant results, demonstrating the importance of transposed elements in shaping both the human and the mouse transcriptomes. The effect of transposed elements on the human transcriptome is several times higher than the effect on the mouse transcriptome, due to the contribution of the primate-specific Alu elements.

AbbreviationsTEtransposed element

SINEshort interspersed element

LINElong interspersed element

MIRmammalian interspersed repeat

ESTexpressed sequence tag

TS scoretissue specificity score

LOD scorelog-odd score

HUSARHeidelberg Unix Sequence Analysis Resources

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2156-8-78 contains supplementary material, which is available to authorized users.

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Author: Britta Mersch - Noa Sela - Gil Ast - Sándor Suhai - Agnes Hotz-Wagenblatt

Source: https://link.springer.com/article/10.1186/1471-2156-8-78







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