ArticlePloS one2008
Single-species microarrays and comparative transcriptomics.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis.BMC genomics · 2014Article
- Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks.Genesis (New York, N.Y. : 2000) · 2012Review
- Expression divergence measured by transcriptome sequencing of four yeast species.BMC genomics · 2011Article
- Article
- Comparative functional genomic analysis of Solanum glandular trichome types.Plant physiology · 2011Article
- 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
- A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.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
- Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens.PLoS computational biology · 2009Article
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Authors and funding
3 authors.
Funding
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Abstract
backgroundPrefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes. METHODOLOGY/PRINCIPAL
findingsHere we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes. CONCLUSIONS/SIGNIFICANCE: Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species.
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