Cross-species hybridisation of pig RNA to human nylon microarrays

被引:75
作者
Moody, DE
Zou, Z
McIntyre, L
机构
[1] Purdue Univ, Dept Agron, W Lafayette, IN 47907 USA
[2] Purdue Univ, Dept Anim Sci, W Lafayette, IN 47907 USA
关键词
D O I
10.1186/1471-2164-3-27
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Comparisons between same- and cross-species hybridisations were also made. Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed. Three replicate hybridisations of two different amounts of pig RNA, and of human skeletal muscle RNA were completed on three additional microarrays. Results: Reproducibility of microarray hybridisations of pig cDNA to human microarrays was high, as determined by Spearman and Pearson correlation coefficients and a Kappa statistic. Variability among replicate hybridisations was similar for human and pig data, indicating the reproducibility of results were not compromised in cross-species hybridisations. The concordance between data generated from hybridisations using pig and human skeletal muscle RNA was high, further supporting the use of human microarrays for the analysis of gene expression in the pig. No systematic effect of stripping and re-using nylon microarrays was found, and variability across microarrays was minimal. Conclusion: The majority of genes generated highly reproducible data in cross-species microarray hybridisations, although approximately 6% were identified as highly variable. Experimental designs that include at least three replicate hybridisations for each experimental treatment will enable the variability of individual genes to be considered appropriately. The use of cross-species microarray analysis looks promising. However, additional validation is needed to determine the specificity of cross-species hybridisations, and the validity of results.
引用
收藏
页数:11
相关论文
共 15 条
[1]  
Agresti A., 1990, Analysis of categorical data
[2]   Upregulation of M-creatine kinase and glyceraldehyde-3-phosphate dehydrogenase:: two markers of muscle disuse [J].
Cros, N ;
Muller, J ;
Bouju, S ;
Piétu, G ;
Jacquet, C ;
Dechesne, CA .
AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY, 1999, 276 (02) :R308-R316
[3]   Analysis of expressed sequence tags of porcine skeletal muscle [J].
Davoli, R ;
Zambonelli, P ;
Bigi, D ;
Fontanesi, L ;
Russo, V .
GENE, 1999, 233 (1-2) :181-188
[4]   Cluster analysis and display of genome-wide expression patterns [J].
Eisen, MB ;
Spellman, PT ;
Brown, PO ;
Botstein, D .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (25) :14863-14868
[5]  
Fleiss JL, 1981, STAT METHODS RATES P
[6]   Differential gene expression of livers from ApoE deficient mice [J].
Huang, GS ;
Yang, SM ;
Hong, MY ;
Yang, PC ;
Liu, YC .
LIFE SCIENCES, 2000, 68 (01) :19-28
[7]   The transcriptional program in the response of human fibroblasts to serum [J].
Iyer, VR ;
Eisen, MB ;
Ross, DT ;
Schuler, G ;
Moore, T ;
Lee, JCF ;
Trent, JM ;
Staudt, LM ;
Hudson, J ;
Boguski, MS ;
Lashkari, D ;
Shalon, D ;
Botstein, D ;
Brown, PO .
SCIENCE, 1999, 283 (5398) :83-87
[8]   Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations [J].
Lee, MLT ;
Kuo, FC ;
Whitmore, GA ;
Sklar, J .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (18) :9834-9839
[9]   Upregulation of collagens detected by gene array in a model of flow-induced pulmonary vascular remodeling [J].
Medhora, M ;
Bousamra, M ;
Zhu, DL ;
Somberg, L ;
Jacobs, ER .
AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY, 2002, 282 (02) :H414-H422
[10]   Cross-hybridization of closely related Genes on high-density macroarrays [J].
Miller, NA ;
Gong, Q ;
Bryan, R ;
Ruvolo, M ;
Turner, LA ;
LaBrie, ST .
BIOTECHNIQUES, 2002, 32 (03) :620-625