SayaMatcher: genome scale organization and systematic analysis of nuclear receptor response elements.
The availability of genome sequences enables us to make experiments in silico to find biological features encoded in the genome. In order to study gene expression regulation network by nuclear receptors that function as ligand-activated transcription, nuclear receptor response elements (NREs) in genomes were computationally explored by integration of computational prediction and experimental data. Dealing with expansion of available genome sequences and continuous update of these genomic sequences, the computation needed for these searches is organized to form a 'pipeline', called SayaMatcher. The information of genomic position for those NREs is served using the Distributed Annotation System (DAS) to be shown in Ensembl genome browser. Utilizing the SayaMatcher system, binding activity in vivo was studied for androgen response elements in human.
Bono
Hidemasa U
HU
Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical School, 1397-1 Yamane, Hidaka, Saitama 350-1241, Japan. bono@saitama-med.ac.jp
D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics; D005826:Genetics, Medical; D016678:Genome; D015894:Genome, Human; D049750:Genome, Insect; D023281:Genomics / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid