Kim DS et al. (2009), EVOG: a database for evolutionary analysis of o...

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Nucleic Acids Res 2009 Jan 01;37Database issue:D698-702. doi: 10.1093/nar/gkn813.

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EVOG: a database for evolutionary analysis of overlapping genes.

Kim DS , Cho CY , Huh JW , Kim HS , Cho HG .

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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. In this study, we implemented evolutionary visualizer for overlapping genes (EVOG), a Web-based DB with a novel visualization interface, to investigate the evolutionary relationship between overlapping genes. 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 database provides a manually curated database that displays the evolutionary features of overlapping genes. The EVOG DB components included a number of overlapping genes (10074 in human, 10,009 in chimpanzee, 67,039 in orangutan, 51,001 in marmoset, 219 in rhesus, 3627 in cow, 209 in dog, 10,700 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 to disease by comparing the expression profiles of overlapping genes. EVOG is available at http://neobio.cs.pusan.ac.kr/evog/.

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	Figure 1. Computing the similarity of gene proximity between two different species.
	Figure 2. Computing the maximal common interval. Sy was slightly moved to the right in order to maximize the common intervals.
	Figure 3. (A) Overlapping genes web retrieval interface. The web interface allows users to access the database contents via three different searching options. This is useful for finding organisms with overlapping genes specified by the users. (B) The results page from the EvOG database. The results page is very effective and easy to use for the comparative analysis and investigation of the evolutionary process of overlapping genes. (C) The users can search interesting overlapping genes by click genome listed on the main page. (D) The distance matrix was calculated by the number of overlapping genes between each two-genome pair.