Dec 9, 2008

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation

Nucleic Acids Research
Alessandro CoppeStefania Bortoluzzi

Abstract

Genes co-expressed may be under similar promoter-based and/or position-based regulation. Although data on expression, position and function of human genes are available, their true integration still represents a challenge for computational biology, hampering the identification of regulatory mechanisms. We carried out an integrative analysis of genomic position, functional annotation and promoters of genes expressed in myeloid cells. Promoter analysis was conducted by a novel multi-step method for discovering putative regulatory elements, i.e. over-represented motifs, in a selected set of promoters, as compared with a background model. The combination of transcriptional, structural and functional data allowed the identification of sets of promoters pertaining to groups of genes co-expressed and co-localized in regions of the human genome. The application of motif discovery to 26 groups of genes co-expressed in myeloid cells differentiation and co-localized in the genome showed that there are more over-represented motifs in promoters of co-expressed and co-localized genes than in promoters of simply co-expressed genes (CEG). Motifs, which are similar to the binding sequences of known transcription factors, non-uniformly distribut...Continue Reading

Mentioned in this Paper

Myelopoiesis
Genome
Transcription, Genetic
Promoter
Myeloid Cells
Genomics
Sequence Determinations, DNA
Protein Domain
Computational Biology
Transcription Factor

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