TY - JOUR
T1 - KBERG: KnowledgeBase for Estrogen Responsive Genes.
AU - Tang, Suisheng
AU - Zhang, Zhuo
AU - Tan, Sin Lam
AU - Tang, Man-Hung Eric
AU - Kumar, Arun Prashanth
AU - Ramadoss, Suresh Kumar
AU - Bajic, Vladimir B
N1 - Keywords: Animals; Base Sequence; Binding Sites; Conserved Sequence; Databases, Nucleic Acid; Estrogens; Humans; Internet; Mice; Promoter Regions (Genetics); Rats; Sequence Analysis, DNA; Transcription Factors; Transcription, Genetic; User-Computer Interface
PY - 2007
Y1 - 2007
N2 - 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.
AB - 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.
U2 - 10.1093/nar/gkl816
DO - 10.1093/nar/gkl816
M3 - Journal article
C2 - 17090589
SN - 0305-1048
VL - 35
SP - D732-6
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - Database issue
ER -