Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data

Ann Ping Tsou, Yi Ming Sun, Chia Lin Liu, Hsien Da Huang, Jorng Tzong Horng, Meng Feng Tsai, Baw Juine Liu

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

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.

Original languageEnglish
Pages (from-to)550-558
Number of pages9
JournalIEEE Transactions on Information Technology in Biomedicine
Volume10
Issue number3
DOIs
StatePublished - Jul 2006

Keywords

  • Data warehouse
  • Databases
  • Gene expression
  • Gene regulation
  • Microarray
  • Regulatory sites
  • Synexpression group
  • Transcription factor

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