Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining

Background: Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cisregulatory elements have been well studied, the combinations of transcription factors that regulate normal expression levels for the vast majority of the 20,000 genes in the human genome are unknown. We hypothesized that it should be possible to discover transcription factor combinations that regulate gene expression in concert by identifying over-represented combinations of sequence motifs that occur together in the genome. In order to detect combinations of transcription factor binding motifs, we developed a data mining approach based on the use of association rules, which are typically used in market basket analysis. We scored each segment of the genome for the presence or absence of each of 83 transcription factor binding motifs, then used association rule mining algorithms to mine this dataset,...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Xochitl C. Morgan, Shulin Ni, Daniel P. Miranker, Vishwanath R. Iyer
• Keywords: BMCBI 2007, Combinations, Genome, Transcription Factor