Skip Navigation

Nucleic Acids Research 2004 32(11):e93; doi:10.1093/nar/gnh084
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (786K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Ji, W.
Right arrow Articles by Davis, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ji, W.
Right arrow Articles by Davis, S.
Related Collections
Right arrow Microarray
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 1 July 2004

Nucleic Acids Research, Vol. 32 No. 11 © Oxford University Press 2004; all rights reserved

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

Wan Ji*, Wenli Zhou, Keqin Gregg, Nan Yu, Scott Davis and Sara Davis

ViaGen Inc., 12357-A Riata Trace Parkway, Suite 100, Austin, TX 78727, USA

* To whom correspondence should be addressed. Tel: +1 512 401 5904; Fax: +1 512 401 5919; Email: wan.ji{at}viagen.com

Received January 22, 2004; Revised April 7, 2004; Accepted May 26, 2004

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 ReproductionHome page
M. Vallee, K. Aiba, Y. Piao, M.-F. Palin, M. S H Ko, and M.-A. Sirard
Comparative analysis of oocyte transcript profiles reveals a high degree of conservation among species
Reproduction, April 1, 2008; 135(4): 439 - 448.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
A. N. Starr, T. R. Famula, N. J. Markward, J. V. Baldwin, K. D. Fowler, D. E. Klumb, N. L. Simpson, and K. E. Murphy
Hereditary Evaluation of Multiple Developmental Abnormalities in the Havanese Dog Breed
J. Hered., July 9, 2007; (2007) esm049v1.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
D. P. Chandler, A. E. Jarrell, E. R. Roden, J. Golova, B. Chernov, M. J. Schipma, A. D. Peacock, and P. E. Long
Suspension Array Analysis of 16S rRNA from Fe- and SO42-Reducing Bacteria in Uranium-Contaminated Sediments Undergoing Bioremediation.
Appl. Envir. Microbiol., July 1, 2006; 72(7): 4672 - 4687.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
P. Klener, M. Szynal, Y. Cleuter, M. Merimi, H. Duvillier, F. Lallemand, C. Bagnis, P. Griebel, C. Sotiriou, A. Burny, et al.
Insights into Gene Expression Changes Impacting B-Cell Transformation: Cross-Species Microarray Analysis of Bovine Leukemia Virus Tax-Responsive Genes in Ovine B Cells
J. Virol., February 15, 2006; 80(4): 1922 - 1938.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
L. I. Brodsky, J. Jacob-Hirsch, A. Avivi, L. Trakhtenbrot, S. Zeligson, N. Amariglio, A. Paz, A. B. Korol, M. Band, G. Rechavi, et al.
Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression
PNAS, November 22, 2005; 102(47): 17047 - 17052.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.