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Related Articles Cross-Hybridization Modeling on Affymetrix Exon Arrays.
Bioinformatics. 2008 Nov 4;
Authors: Kapur K, Jiang H, Xing Y, Wong WH
MOTIVATION: Microarray designs have become increasingly proberich, enabling targeting of specific features, such as individual exons or SNPs. These arrays have the potential to achieve quantitative highthroughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts. RESULTS: To study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion-deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct for crosshybridization biases of gene-level expression estimates. Comparison with Solexa ultra-high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improvement of gene expression estimates. AVAILABILITY: We provide mappings between human and mouse exon array probes and off-target transcripts and provide software extending the GeneBASE program for generating gene-level expression estimates including the cross-hybridization correction http://biogibbs.stanford.edu/~kkapur/GeneBase/. CONTACT: [email protected].
PMID: 18984598 [PubMed - as supplied by publisher]
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Related Articles Cross-Hybridization Modeling on Affymetrix Exon Arrays.
Bioinformatics. 2008 Nov 4;
Authors: Kapur K, Jiang H, Xing Y, Wong WH
MOTIVATION: Microarray designs have become increasingly proberich, enabling targeting of specific features, such as individual exons or SNPs. These arrays have the potential to achieve quantitative highthroughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts. RESULTS: To study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion-deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct for crosshybridization biases of gene-level expression estimates. Comparison with Solexa ultra-high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improvement of gene expression estimates. AVAILABILITY: We provide mappings between human and mouse exon array probes and off-target transcripts and provide software extending the GeneBASE program for generating gene-level expression estimates including the cross-hybridization correction http://biogibbs.stanford.edu/~kkapur/GeneBase/. CONTACT: [email protected].
PMID: 18984598 [PubMed - as supplied by publisher]
More...