title: KBERG: KnowledgeBase for Estrogen Responsive Genes.
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.
authors.affiliation: Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613. suisheng@i2r.a-star.edu.sg
authors.forename: Suisheng
authors.initials: S
authors.lastname: Tang
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Zhang
authors.forename: Sin Lam
authors.initials: SL
authors.lastname: Tan
authors.forename: Man-Hung Eric
authors.initials: MH
authors.lastname: Tang
authors.forename: Arun Prashanth
authors.initials: AP
authors.lastname: Kumar
authors.forename: Suresh Kumar
authors.initials: SK
authors.lastname: Ramadoss
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D004967:Estrogens / Q000502:physiology*; D006801:Humans; D020407:Internet; D051379:Mice; D011401:Promoter Regions, Genetic; D051381:Rats; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D004967:Estrogens; D014157:Transcription Factors