A cis-regulatory logic simulator

Background: A major goal of computational studies of gene regulation is to accurately predict the expression of genes based on the cis-regulatory content of their promoters. The development of computational methods to decode the interactions among cis-regulatory elements has been slow, in part, because it is difficult to know, without extensive experimental validation, whether a particular method identifies the correct cis-regulatory interactions that underlie a given set of expression data. There is an urgent need for test expression data in which the interactions among cis-regulatory sites that produce the data are known. The ability to rapidly generate such data sets would facilitate the development and comparison of computational methods that predict gene expression patterns from promoter sequence. Results: We developed a gene expression simulator which generates expression data using userdefined interactions between cis-regulatory sites. The simulator can incorporate additive, co...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Robert D. Zeigler, Jason Gertz, Barak A. Cohen
• Keywords: BMCBI 2007, Cis-regulatory, Expression Data, Gene Expression