ArticleNucleic acids research2004
Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 18 citations in OpenAlex.
- Article
- Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.BMC bioinformatics · 2009Article
- Detecting genetic variation in microarray expression data.Genome research · 2007Article
- Cross-species analysis of gene expression in non-model mammals: reproducibility of hybridization on high density oligonucleotide microarrays.BMC genomics · 2007Article
- Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.Genome research · 2005Article
- Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.Nucleic acids research · 2005Article
- Microarray and EST database estimates of mRNA expression levels differ: the protein length versus expression curve for C. elegans.BMC genomics · 2004Article
- A method for cross-species gene expression analysis with high-density oligonucleotide arrays.Nucleic acids research · 2004Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
DNA microarrays are powerful tools for comparing gene expression profiles from closely related organisms. However, a single microarray design is frequently used in these studies. Therefore, the levels of certain transcripts can be grossly underestimated due to sequence differences between the transcripts and the arrayed DNA probes. Here, we seek to improve the sensitivity and specificity of oligonucleotide microarray-based gene expression analysis by using genomic sequence information to predict the hybridization efficiency of orthologous transcripts to a given microarray. To test our approach, we examine hybridization patterns from three Escherichia coli strains on E.coli K-12 MG1655 gene expression microarrays. We create electronic mask files to discard data from probes predicted to have poor hybridization sensitivity and specificity to cDNA targets from each strain. We increased the accuracy of gene expression analysis and identified genes that cannot be accurately interrogated in each strain using these microarrays. Overall, these studies provide guidelines for designing effective electronic masks for gene expression analysis in organisms where substantial genome sequence information is available.
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Registered trials
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