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ISSN
1672-9145
Acta Biochim Biophys Sin
2005, 37(5): 341–348
CN 31-1940/Q
Comparative Study of Apoptosis-related Gene Loci in Human, Mouse and
Rat Genomes
Yan-Bin YIN, Yong ZHANG, Peng YU, Jing-Chu LUO, Ying JIANG*, and Song-Gang LI*
Center of Bioinformatics, National Laboratory of Genetic Engineering
and Protein Engineering, College of Life Sciences,
Peking University, Beijing 100871, China
Abstract Many
genes are involved in mammalian cell apoptosis pathway. These apoptosis genes
often contain characteristic functional domains, and can be classified into at
least 15 functional groups, according to previous reports. Using an integrated
bioinformatics platform for motif or domain search from three public mammalian
proteomes (International Protein Index database for human, mouse, and rat), we
systematically cataloged all of the proteins involved in mammalian apoptosis
pathway. By localizing those proteins onto the genomes, we obtained a gene
locus centric apoptosis gene catalog for human, mouse and rat. Further
phylogenetic analysis showed that most of the apoptosis related gene loci are
conserved among these three mammals. Interestingly, about one-third of apoptosis
gene loci form gene clusters on mammal chromosomes, and exist in the three
species, which indicated that mammalian apoptosis gene orders are also
conserved. In addition, some tandem duplicated gene loci were revealed by
comparing gene loci clusters in the three species. All data produced in this
work were stored in a relational database and may be viewed at
http://pcas.cbi.pku.edu.cn/database/apd.php.
Key words apoptosis; gene cluster;
comparative genomics; bioinformatics
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Received: December 30, 2004 Accepted: March 23, 2005
This work was supported by a grant from the National High Technology
Research and Development Program of China (No. 2002AA231051)
*Corresponding authors:
Ying JIANG: Tel, 86-215-6521442; Fax, 86-10-62759001; E-mail, [email protected]
Song-Gang LI: Tel, 86-10-62756803; Fax, 86-10-62759001; E-mail, [email protected]