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Database (Oxford). 2013 Jul 26;2013:bat057. doi: 10.1093/database/bat057. Print 2013.

BGDB: a database of bivalent genes.

Author information

1
Department of Electronics, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou 510006, China.

Abstract

Bivalent gene is a gene marked with both H3K4me3 and H3K27me3 epigenetic modification in the same area, and is proposed to play a pivotal role related to pluripotency in embryonic stem (ES) cells. Identification of these bivalent genes and understanding their functions are important for further research of lineage specification and embryo development. So far, lots of genome-wide histone modification data were generated in mouse and human ES cells. These valuable data make it possible to identify bivalent genes, but no comprehensive data repositories or analysis tools are available for bivalent genes currently. In this work, we develop BGDB, the database of bivalent genes. The database contains 6897 bivalent genes in human and mouse ES cells, which are manually collected from scientific literature. Each entry contains curated information, including genomic context, sequences, gene ontology and other relevant information. The web services of BGDB database were implemented with PHP + MySQL + JavaScript, and provide diverse query functions. Database URL: http://dailab.sysu.edu.cn/bgdb/.

PMID:
23894186
PMCID:
PMC3724367
DOI:
10.1093/database/bat057
[Indexed for MEDLINE]
Free PMC Article

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