title: TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species.
abstract: Genome-wide transcription factors (TFs) binding data has been extensively generated in the past few years, which poses a great challenge to data interpretation. Therefore, comprehensive and dedicated functional annotation databases for TF-DNA interaction are in great demands to manage, explore and utilize those invaluable data resources. Here, we constructed a platform 'TFBSbank' which houses the annotation of 1870 chromatin immunoprecipitation (ChIP) datasets of 585 TFs in five species (human, mouse, fly, worm and yeast). There are mainly five functional modules in TFBSbank aimed at characterizing ChIP peaks, identifying putative targets, predicting TF responsive enhancers, revealing potential cofactors/collaborators and discovering enriched TF motifs. TFBSbank has two distinctive features compared to the existing databases. Firstly, we provided putative cofactors/collaborators analysis (for Drosophila melanogaster), as they are crucial for the in vivo functions of TFs. Additionally, this database predicted the enrichment of both known and de novo motifs based on ChIP data. TFBSbank is freely accessible at http://tfbsbank.co.uk.
authors.affiliation: Fitzwilliam College, University of Cambridge, Storey's Way, Cambridge CB3 0DG, UK dc571@cam.ac.uk dschen2016@gmail.com.
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Chen
authors.affiliation: St Edmund's College, University of Cambridge, Mount Pleasant, Cambridge CB3 0BN, UK.
authors.forename: Sanjie
authors.initials: S
authors.lastname: Jiang
authors.affiliation: Downing College, University of Cambridge, Regent St, Cambridge CB2 1DQ, UK.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Ma
authors.affiliation: Department of Gynaecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, China fang_li@tongji.edu.cn.
authors.forename: Fang
authors.initials: F
authors.lastname: Li
mesh_terms: D000818:Animals; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D059372:Nucleotide Motifs; D064878:Web Browser
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA