J Integr Bioinform - Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.

Tópicos

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Resumo

CKGROUND: 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.

Resumo Limpo

ckground chimer transcript singl rna sequenc result transcript two adjac gene recent studi estim least tandem human gene pair may form chimer transcript affymetrix genechip data use studi express pattern ten thousand gene probe sequenc use microarray can potenti map exot rna sequenc chimerasresult studi human chimera investig express pattern use larg survey affymetrix microarray data obtain gene express omnibus show six probe set uniqu probe map transcript produc one adjac gene can use identifi express pattern readthrough transcript furthermor uniqu probe map intergen exon present maskbp chimera can use direct studi express level transcriptconclus attempt implement new method identifi tandem chimer analysi unambigu probe need measur runoff transcript probe map intergen exon particular valuabl identifi express chimera

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