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Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.

Rowsell, J and da Silva Camargo, R and Langdon, WB and Stalteri, MA and Harrison, AP (2010) 'Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.' Journal of integrative bioinformatics, 7 (3). ISSN 1613-4516

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Abstract

BACKGROUND: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras. RESULTS: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript. CONCLUSIONS: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras.

Item Type: Article
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health > Mathematical Sciences, Department of
Depositing User: Jim Jamieson
Date Deposited: 09 Dec 2011 15:22
Last Modified: 20 Feb 2019 00:15
URI: http://repository.essex.ac.uk/id/eprint/1746

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