• Journal of the Korea Academia-Industrial cooperation Society
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• v.9 no.5
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• pp.1218-1224
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• 2008

Located on the upstream of a gene, the promoter region that plays a very important role in the control of gene expression as a signal part has various binding sites for transcription factors. These binding sites are present in various parts of the promoter region and assume an aspect of highly conserved consensus sequence pattern. This paper deals with the introductions of search methods for consensus pattern, including Wataru method, EM algorithm, MEME algorithm, Genetic algorithm and Phylogenetic Footprinting method, and intends to give future prospects of research on this field.

• BMB Reports
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• v.42 no.12
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• pp.823-828
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• 2009

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

• Journal of Marine Bioscience and Biotechnology
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• v.7 no.2
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• pp.35-41
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• 2015

Whales are marine mammals that are fully adapted to aquatic environment. Whales breathe by lungs so they require adaptive system to low oxygen concentration (hypoxia) while deep and prolonged diving. However, the study for the molecular mechanism underlying cetacean adaptation to hypoxia has been limited. Hypoxia-inducible factor (HIF) is the central transcription factor that regulates hypoxia-related gene expression. Here we identified HIF-binding sites in whale genome by phylogenetic footprinting and analyzed HIF-target genes to understand how whales cope with hypoxia. By comparison with the HIF-target genes of terrestrial mammals, it was suggested that whales may retain unique adaptation mechanisms to hypoxia.