Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

Background: A major goal of molecular biology is determining the mechanisms that control the transcription of genes. Motif Enrichment Analysis (MEA) seeks to determine which DNA-binding transcription factors control the transcription of a set of genes by detecting enrichment of known binding motifs in the genes' regulatory regions. Typically, the biologist specifies a set of genes believed to be co-regulated and a library of known DNA-binding models for transcription factors, and MEA determines which (if any) of the factors may be direct regulators of the genes. Since the number of factors with known DNA-binding models is rapidly increasing as a result of high-throughput technologies, MEA is becoming increasingly useful. In this paper, we explore ways to make MEA applicable in more settings, and evaluate the efficacy of a number of MEA approaches. Results: We first define a mathematical framework for Motif Enrichment Analysis that relaxes the requirement that the biologist input ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Robert C. McLeay, Timothy L. Bailey
• Keywords: BMCBI 2010, DNA-binding Models, Enrichment Analysis, Transcription Factors