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- Title
Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data.
- Authors
Seifert, Michael; Keilwagen, Jens; Strickert, Marc; Grosse, Ivo
- Abstract
Array-based analysis of chromatin immunoprecipitation (ChIP-chip) data is a powerful technique for identifying DNA target regions of individual transcription factors. The identification of these target regions from comprehensive promoter array ChIP-chip data is challenging. Here, three approaches for the identification of transcription factor target genes from promoter array ChIP-chip data are presented. We compare (i) a standard log-fold-change analysis (LFC); (ii) a basic method based on a Hidden Markov Model (HMM); and (iii) a new extension of the HMM approach to an HMM with scaled transition matrices (SHMM) that incorporates information about the relative orientation of adjacent gene pairs on DNA.
- Publication
Bioinformatics (Oxford, England), 2009, Vol 25, Issue 16, p2118
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/btp276