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In Silico Biol. 2004;4(2):109-25.

Content analysis of the core promoter region of human genes.

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Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore.


We analyzed an extended core promoter regions covering [-70,+60] segment relative to the transcription start site of human promoters contained in the Eukaryotic Promoter Database. The analysis was made by using the Match program ver. 1.9 with an optimized setting and the TRANSFAC Professional database ver. 7.2. This analysis revealed that the most common transcription factor binding site in the examined collection of core promoters appears to be initiator (characterized by GEN_INI), which is expected. The other less obvious sites found were Spz1, E2F-1, ZF5, and C/EBP. The 'cap' site was also in this most common group. Over-representation of these sites relative to the non-promoter background data ranged from 0.3167 to 32.1645. These sites were characterized by being present in more than 60% of promoter sequences. Interestingly, the TATA-box has been found in only 11.63% of all examined promoters. The study is complemented by separate analyses of promoter groups having different GC content. These additional analyses revealed that the most common promoter elements found also include AP-2, CdxA, Pax-2, SRY, STAT1 and STAT5A. It was also observed that a number of promoter elements show strong preference either for the GC-rich or the GC-poor core promoters.

[Indexed for MEDLINE]

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