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Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

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Published on: October 11, 2018

BGDB: a database of bivalent genes.

Qingyan Li¹, Shuabin Lian, Zhiming Dai

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

Database : the Journal of Biological Databases and Curation

|July 30, 2013

Summary

This summary is machine-generated.

We developed BGDB, a database of bivalent genes, which are crucial for embryonic stem cell pluripotency. This resource aids research into lineage specification and embryo development by providing curated data on 6897 bivalent genes from human and mouse studies.

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Area of Science:

Epigenetics and Developmental Biology
Genomics and Bioinformatics

Background:

Bivalent genes, marked by H3K4me3 and H3K27me3, are critical for embryonic stem cell (ES) pluripotency and lineage specification.
Existing genome-wide histone modification data in human and mouse ES cells offer potential for identifying these genes.
A lack of centralized repositories and analysis tools hinders comprehensive study of bivalent genes.

Purpose of the Study:

To develop BGDB, a comprehensive database for bivalent genes.
To curate and integrate data on bivalent genes from scientific literature.
To provide web services for querying and analyzing bivalent gene information.

Main Methods:

Manual curation of bivalent genes from scientific literature.
Integration of genomic context, sequences, and gene ontology data for each gene.
Development of a web-based platform using PHP, MySQL, and JavaScript for data access.

Main Results:

BGDB contains 6897 manually curated bivalent genes from human and mouse ES cells.
The database provides detailed information including genomic location, sequences, and functional annotations (Gene Ontology).
Web services enable diverse query functions for researchers.

Conclusions:

BGDB serves as a valuable, centralized resource for bivalent genes.
This database facilitates further research into the roles of bivalent genes in pluripotency, lineage specification, and embryo development.
BGDB supports the analysis of epigenetic modifications and their impact on gene regulation in stem cells.