title: CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
abstract: CompleteMOTIFs (cMOTIFs) is an integrated web tool developed to facilitate systematic discovery of overrepresented transcription factor binding motifs from high-throughput chromatin immunoprecipitation experiments. Comprehensive annotations and Boolean logic operations on multiple peak locations enable users to focus on genomic regions of interest for de novo motif discovery using tools such as MEME, Weeder and ChIPMunk. The pipeline incorporates a scanning tool for known motifs from TRANSFAC and JASPAR databases, and performs an enrichment test using local or precalculated background models that significantly improve the motif scanning result. Furthermore, using the cMOTIFs pipeline, we demonstrated that multiple transcription factors could cooperatively bind to the upstream of important stem cell differentiation regulators.
  
  
  BACKGROUND
  http://cmotifs.tchlab.org.
authors.affiliation: Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, USA.
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Kuttippurathu
authors.forename: Michael
authors.initials: M
authors.lastname: Hsing
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Liu
authors.forename: Bertil
authors.initials: B
authors.lastname: Schmidt
authors.forename: Douglas L
authors.initials: DL
authors.lastname: Maskell
authors.forename: Kyungjoon
authors.initials: K
authors.lastname: Lee
authors.forename: Aibin
authors.initials: A
authors.lastname: He
authors.forename: William T
authors.initials: WT
authors.lastname: Pu
authors.forename: Sek Won
authors.initials: SW
authors.lastname: Kong
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D030561:Databases, Nucleic Acid; D020407:Internet; D015233:Models, Statistical; D058977:Molecular Sequence Annotation; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA