Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Jan;35(Database issue):D732-6.
doi: 10.1093/nar/gkl816. Epub 2006 Nov 7.

KBERG: KnowledgeBase for Estrogen Responsive Genes

Affiliations

KBERG: KnowledgeBase for Estrogen Responsive Genes

Suisheng Tang et al. Nucleic Acids Res. 2007 Jan.

Abstract

Estrogen has a profound impact on human physiology affecting transcription of numerous genes. To decipher functional characteristics of estrogen responsive genes, we developed KnowledgeBase for Estrogen Responsive Genes (KBERG). Genes in KBERG were derived from Estrogen Responsive Gene Database (ERGDB) and were analyzed from multiple aspects. We explored the possible transcription regulation mechanism by capturing highly conserved promoter motifs across orthologous genes, using promoter regions that cover the range of [-1200, +500] relative to the transcription start sites. The motif detection is based on ab initio discovery of common cis-elements from the orthologous gene cluster from human, mouse and rat, thus reflecting a degree of promoter sequence preservation during evolution. The identified motifs are linked to transcription factor binding sites based on the TRANSFAC database. In addition, KBERG uses two established ontology systems, GO and eVOC, to associate genes with their function. Users may assess gene functionality through the description terms in GO. Alternatively, they can gain gene co-expression information through evidence from human EST libraries via eVOC. KBERG is a user-friendly system that provides links to other relevant resources such as ERGDB, UniGene, Entrez Gene, HomoloGene, GO, eVOC and GenBank, and thus offers a platform for functional exploration and potential annotation of genes responsive to estrogen. KBERG database can be accessed at http://research.i2r.a-star.edu.sg/kberg.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Flow chart for promoter extraction.

References

    1. Nilsson S., Gustafsson J.A. Estrogen receptor transcription and transactivation: basic aspects of estrogen action. Breast Cancer Res. 2000;2:360–366. - PMC - PubMed
    1. Harrington W.R., Kim S.H., Funk C.C., Madak-Erdogan Z., Schiff R., Katzenellenbogen J.A., Katzenellenbogen B.S. Estrogen dendrimer conjugates that preferentially activate extranuclear, nongenomic versus genomic pathways of estrogen action. Mol. Endocrinol. 2006;20:491–502. - PubMed
    1. Tang S., Han H., Bajic V.B. ERGDB: Estrogen Responsive Genes DataBase. Nucleic Acids Res. 2004;32:D533–D536. - PMC - PubMed
    1. Werner T., Fessele S., Maier H., Nelson P.J. Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J. 2003;17:1228–1237. - PubMed
    1. Claverie J.M. Gene number. What if there are only 30,000 human genes? Science. 2001;291:1255–1257. - PubMed

Publication types