NAR Molecular Biology Database Collection entry number 1266
Kim, D.-S.1, Cho, C.-Y.3, Huh, J-W.4, Kim, H.-S.2, Cho, H.-G.3
1Korean BioInformation Center (KOBIC), KRIBB, Daejeon 305-806, Korea.2Division of Biological Sciences, Pusan National University, Busan 609-735, Korea.3School of Computer Science and Engineering, Pusan National University, Busan 609-735, Korea.4National Primate Research Center (NPRC), KRIBB, Ochang, Chungbuk 363-883, Republic of Korea.
Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not yet been clearly determined. We have implemented EVOG (Evolution Visualizer for Overlapping Genes), a Web-based database with a novel visualization interface, to investigate the evolutionary relationship between overlapping genes. Here we study comparatively the extent of overlapping genes in thirteen genomes by analyzing the public databases of expressed sequences using a set of computational tools designed to identify overlapping genes on opposite DNA strands of the same genomic locus. Using this technique, we collected and analyzed all overlapping genes in human, chimpanzee, orangutan, marmoset, rhesus, cow, dog, mouse, rat, chicken, Xenopus, zebrafish, and Drosophila. This integrated service provides a manually curated database that displays the evolutionary features of overlapping genes. The EVOG database components included a number of overlapping genes (10074 in human, 10009 in chimpanzee, 67039 in orangutan, 51001 in marmoset, 219 in rhesus, 3627 in cow, 209 in dog, 10700 in mouse, 7987 in rat, 1439 in chicken, 597 in Xenopus, 2457 in zebrafish and 4115 in Drosophila). The EVOG database is very effective and easy to use for the analysis of the evolutionary process of overlapping genes when comparing different species. Therefore, EVOG could potentially be used as the main tool to investigate the evolution of the human genome in relation disease by comparing the expression profiles of overlapping genes.
Yelin, R., Dahary, D., Sorek, R., Levanon, E. Y., Goldstein, O., Shoshan, A., Diber, A., Biton, S., Tamir, Y., Khosravi, R., Nemzer, S., Pinner, E., Walach, S., Bernstein, J., Savitsky, K. and Rotman, G. (2003) Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol., 21, 379-386.
Category: Human and other Vertebrate Genomes
Subcategory: Model organisms, comparative genomics
Go to the abstract in the NAR 2009 Database Issue.
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