Name
Abstract | ||
|---|---|---|
Microarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms. These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts.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 cross-hybridization 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.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/. |
Year | DOI | Venue |
|---|---|---|
2008 | 10.1093/bioinformatics/btn571 | Bioinformatics |
Keywords | Field | DocType |
gene-level expression estimate,annotated mrna transcript,solexa ultra high-throughput,mouse exon array probe,gene-level expression,cross-hybridization modeling,gene expression estimate,cross-hybridization correction,affymetrix exon array probe,cross-hybridization bias,off-target transcript,gene expression profiling,gene expression,high throughput,computational biology,exons,molecular probes,single nucleotide polymorphism | Molecular probe,Microarray,Biology,Exon,Gene expression,Single-nucleotide polymorphism,Bioinformatics,Genetics,Gene expression profiling | Journal |
Volume | Issue | ISSN |
24 | 24 | 1367-4811 |
Citations | PageRank | References |
8 | 5.20 | 7 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Karen Kapur | 1 | 29 | 6.97 |
| Hui Jiang | 2 | 201 | 39.94 |
| Yi Xing | 3 | 8 | 5.20 |
| Wing Hung Wong | 4 | 607 | 96.45 |