title: Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.
abstract: Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.
authors.affiliation: Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei, Taiwan, ROC. aptsou@ym.edu.tw
authors.forename: Ann-Ping
authors.initials: AP
authors.lastname: Tsou
authors.forename: Yi-Ming
authors.initials: YM
authors.lastname: Sun
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Liu
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
authors.forename: Jorng-Tzong
authors.initials: JT
authors.lastname: Horng
authors.forename: Meng-Feng
authors.initials: MF
authors.lastname: Tsai
authors.forename: Baw-Juine
authors.initials: BJ
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D049490:Systems Biology / Q000379:methods; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors