A method for cross-species gene expression analysis with high-density oligonucleotide arrays

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 Affymet...

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Main Authors: Ji, Wan, Zhou, Wenli, Gregg, Keqin, Yu, Nan, Davis, Scott, Davis, Sara
Formato: Artigo
Idioma:en
Publicado em: Oxford University Press 2004
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NAR Methods Online
Acesso em linha:https://ncbi.nlm.nih.gov/pmc/articles/PMC443552/
https://ncbi.nlm.nih.gov/pubmed/15247326
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1093/nar/gnh084
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spelling pubmed-4435522004-07-23 A method for cross-species gene expression analysis with high-density oligonucleotide arrays Ji, Wan Zhou, Wenli Gregg, Keqin Yu, Nan Davis, Scott Davis, Sara Nucleic Acids Res NAR Methods Online 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. Oxford University Press 2004 2004-07-01 /pmc/articles/PMC443552/ /pubmed/15247326 http://dx.doi.org/10.1093/nar/gnh084 Text en Copyright © 2004 Oxford University Press
institution US National Library of Medicine
collection PubMed Central
language en
format Article
topic NAR Methods Online
spellingShingle NAR Methods Online
Ji, Wan
Zhou, Wenli
Gregg, Keqin
Yu, Nan
Davis, Scott
Davis, Sara
A method for cross-species gene expression analysis with high-density oligonucleotide arrays
description 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.
author Ji, Wan
Zhou, Wenli
Gregg, Keqin
Yu, Nan
Davis, Scott
Davis, Sara
author_facet Ji, Wan
Zhou, Wenli
Gregg, Keqin
Yu, Nan
Davis, Scott
Davis, Sara
author_sort Ji, Wan
title A method for cross-species gene expression analysis with high-density oligonucleotide arrays
title_short A method for cross-species gene expression analysis with high-density oligonucleotide arrays
title_full A method for cross-species gene expression analysis with high-density oligonucleotide arrays
title_fullStr A method for cross-species gene expression analysis with high-density oligonucleotide arrays
title_full_unstemmed A method for cross-species gene expression analysis with high-density oligonucleotide arrays
title_sort method for cross-species gene expression analysis with high-density oligonucleotide arrays
publisher Oxford University Press
publisher_facet Oxford University Press
publishDate 2004
url https://ncbi.nlm.nih.gov/pmc/articles/PMC443552/
https://ncbi.nlm.nih.gov/pubmed/15247326
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1093/nar/gnh084
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