ArticleNucleic acids research2004
A method for cross-species gene expression analysis with high-density oligonucleotide arrays.
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 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa.BMC genomics · 2009Pooled it
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- Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae).BMC molecular biology · 2011Article
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- Gene expression profiles in a rabbit model of systemic lupus erythematosus autoantibody production.Journal of immunology (Baltimore, Md. : 1950) · 2010Article
- Molecular characterization of in vivo adjuvant activity in ferrets vaccinated against influenza virus.Journal of virology · 2010Article
- Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes.BMC genomics · 2010Article
- Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes.BMC plant biology · 2010Article
- A Method to Detect Differential Gene expression in Cross-Species Hybridization Experiments at Gene and Probe Level.Biomedical informatics insights · 2010Article
- Comparative genomics using microarrays reveals divergence and loss of virulence-associated genes in host-specific strains of the insect pathogen Metarhizium anisopliae.Eukaryotic cell · 2009Article
- Nuclear reprogramming in heterokaryons is rapid, extensive, and bidirectional.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2009Article
- Single-species microarrays and comparative transcriptomics.PloS one · 2008Article
- Genome-wide screen for temperature-regulated genes of the obligate intracellular bacterium, Rickettsia typhi.BMC microbiology · 2008Article
- Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection.BMC genomics · 2007Article
- AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.BMC bioinformatics · 2007Article
- Biomarker discovery in animal health and disease: the application of post-genomic technologies.Biomarker insights · 2007Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA microarrays have been widely used in gene expression analysis of biological processes. Due to a lack of sequence information, the applications have been largely restricted to humans and a few model organisms. Presented within this study are results of the cross-species hybridization with Affymetrix human high-density oligonucleotide arrays or GeneChip using distantly related mammalian species; cattle, pig and dog. Based on the unique feature of the Affymetrix GeneChip where every gene is represented by multiple probes, we hypothesized that sequence conservation within mammals is high enough to generate sufficient signals from some of the probes for expression analysis. We demonstrated that while overall hybridization signals are low for cross-species hybridization, a few probes of most genes still generated signals equivalent to the same-species hybridization. By masking the poorly hybridized probes electronically, the remaining probes provided reliable data for gene expression analysis. We developed an algorithm to select the reliable probes for analysis utilizing the match/mismatch feature of GeneChip. When comparing gene expression between two tissues using the selected probes, we found a linear correlation between the cross-species and same-species hybridization. In addition, we validated cross-species hybridization results by quantitative PCR using randomly selected genes. The method shown herein could be applied to both plant and animal research.
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