title: Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs.
abstract: Comprehensive motif discovery under experimental conditions is critical for the global understanding of gene regulation. To generate a nearly complete list of human DNA motifs under given conditions, we employed a novel approach to de novo discover significant co-occurring DNA motifs in 349 human DNase I hypersensitive site datasets. We predicted 845 to 1325 motifs in each dataset, for a total of 2684 non-redundant motifs. These 2684 motifs contained 54.02 to 75.95% of the known motifs in seven large collections including TRANSFAC. In each dataset, we also discovered 43 663 to 2 013 288 motif modules, groups of motifs with their binding sites co-occurring in a significant number of short DNA regions. Compared with known interacting transcription factors in eight resources, the predicted motif modules on average included 84.23% of known interacting motifs. We further showed new features of the predicted motifs, such as motifs enriched in proximal regions rarely overlapped with motifs enriched in distal regions, motifs enriched in 5' distal regions were often enriched in 3' distal regions, etc. Finally, we observed that the 2684 predicted motifs classified the cell or tissue types of the datasets with an accuracy of 81.29%. The resources generated in this study are available at http://server.cs.ucf.edu/predrem/.
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA.
authors.forename: Yiyu
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA xiaoman@mail.ucf.edu.
authors.forename: Xiaoman
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA xiaoman@mail.ucf.edu.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Hu
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D023281:Genomics; D006801:Humans; D059372:Nucleotide Motifs; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA