Single-species microarrays and comparative transcriptomics.
BACKGROUND: Prefabricated 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 FINDINGS: Here we demonstrate that the hybridization intensity of genomic DNA is...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2008-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2533705?pdf=render |
| _version_ | 1818619342983528448 |
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| author | Frédéric J J Chain Dora Ilieva Ben J Evans |
| author_facet | Frédéric J J Chain Dora Ilieva Ben J Evans |
| author_sort | Frédéric J J Chain |
| collection | DOAJ |
| description | BACKGROUND: Prefabricated 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 FINDINGS: Here 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. |
| first_indexed | 2024-12-16T17:35:58Z |
| format | Article |
| id | doaj.art-1d608065aedf47e2b8af994d1b1cd862 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-16T17:35:58Z |
| publishDate | 2008-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-1d608065aedf47e2b8af994d1b1cd8622022-12-21T22:22:46ZengPublic Library of Science (PLoS)PLoS ONE1932-62032008-01-0139e327910.1371/journal.pone.0003279Single-species microarrays and comparative transcriptomics.Frédéric J J ChainDora IlievaBen J EvansBACKGROUND: Prefabricated 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 FINDINGS: Here 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.http://europepmc.org/articles/PMC2533705?pdf=render |
| spellingShingle | Frédéric J J Chain Dora Ilieva Ben J Evans Single-species microarrays and comparative transcriptomics. PLoS ONE |
| title | Single-species microarrays and comparative transcriptomics. |
| title_full | Single-species microarrays and comparative transcriptomics. |
| title_fullStr | Single-species microarrays and comparative transcriptomics. |
| title_full_unstemmed | Single-species microarrays and comparative transcriptomics. |
| title_short | Single-species microarrays and comparative transcriptomics. |
| title_sort | single species microarrays and comparative transcriptomics |
| url | http://europepmc.org/articles/PMC2533705?pdf=render |
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