Abstract:
BACKGROUND:Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results using an updated mapping of probes to genes, taking into account the latest biological knowledge available. METHODS:We investigated how probes found on recent commercial microarrays for human genes (Affymetrix HG-U133A) were matching a recent curated collection of human transcripts: the NCBI RefSeq database. We also built mappings and used them in place of the original probe to genes associations provided by the manufacturer of the arrays. RESULTS:In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data. CONCLUSIONS:While the probes on Affymetrix arrays remain the same for several years, the biological knowledge concerning the genomic sequences evolves rapidly. Using up-to-date knowledge can apparently change the outcome of an analysis.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Gautier L,Møller M,Friis-Hansen L,Knudsen Sdoi
10.1186/1471-2105-5-111keywords:
subject
Has Abstractpub_date
2004-08-14 00:00:00pages
111issn
1471-2105pii
1471-2105-5-111journal_volume
5pub_type
杂志文章abstract:BACKGROUND:Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is ne...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
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更新日期:2009-03-06 00:00:00
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2019-05-28 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2005-04-27 00:00:00
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pub_type: 杂志文章
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更新日期:2008-10-06 00:00:00
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更新日期:2017-12-28 00:00:00