Ying Zheng1, Dalong Ma. 1. Center for Human Disease Genomics, Peking University, Beijing 100083, China. zy@bjmu.edu.cn
Abstract
OBJECTIVE: To lay foundation for the functional studies of programmed cell death 5 (PDCD5) and develop new technical pathway for bioinformatics analysis of human functional genes. METHODS: Using PDCD5 as the target molecule, intensive bioinformatics analysis of the nucleic acid and protein sequences were conducted. Data mining and comprehensive analysis by sequence against database similarity searching, ortholog structure comparison, expression profile analysis and gene "neighbor" listing were performed. RESULTS: Two human putative pseudogenes on chromosomes 12 and 5, and one mouse putative pseudogene on chromosome 1 were identified. The methanobacterium thermoautotrophicum ortholog was classified as the same fold as ubiquitin and ribosomal protein S13. The C. elegans ortholog, ubiquitin and IAP (inhibitor of apoptosis proteins) belonged to the same expression profile cluster. This cluster was related to biosynthesis and protein synthesis. PDCD5 orthologs in various genomes were adjacent to various ribosomal proteins on the chromosome. CONCLUSION: The human genome contains at least two processed pseudogenes of PDCD5. Besides the relationship with cell apoptosis, PDCD5 is predicted to have functional relationship with ubiquitin and participate in the translation regulation.
OBJECTIVE: To lay foundation for the functional studies of programmed cell death 5 (PDCD5) and develop new technical pathway for bioinformatics analysis of human functional genes. METHODS: Using PDCD5 as the target molecule, intensive bioinformatics analysis of the nucleic acid and protein sequences were conducted. Data mining and comprehensive analysis by sequence against database similarity searching, ortholog structure comparison, expression profile analysis and gene "neighbor" listing were performed. RESULTS: Two human putative pseudogenes on chromosomes 12 and 5, and one mouse putative pseudogene on chromosome 1 were identified. The methanobacterium thermoautotrophicum ortholog was classified as the same fold as ubiquitin and ribosomal protein S13. The C. elegans ortholog, ubiquitin and IAP (inhibitor of apoptosis proteins) belonged to the same expression profile cluster. This cluster was related to biosynthesis and protein synthesis. PDCD5 orthologs in various genomes were adjacent to various ribosomal proteins on the chromosome. CONCLUSION: The human genome contains at least two processed pseudogenes of PDCD5. Besides the relationship with cell apoptosis, PDCD5 is predicted to have functional relationship with ubiquitin and participate in the translation regulation.