title: NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse.
abstract: CONCLUSIONS
  Nuclear receptors (NRs) are a class of transcription factors playing important roles in various biological processes. An NR often impacts numerous genes and different NRs share overlapped target networks. To fulfil the need for a database incorporating binding sites of different NRs at various conditions for easy comparison and visualization to improve our understanding of NR binding mechanisms, we have developed NURBS, a database for experimental and predicted nuclear receptor binding sites of mouse (NURBS). NURBS currently contains binding sites across the whole-mouse genome of 8 NRs identified in 40 chromatin immunoprecipitation with massively parallel DNA sequencing experiments. All datasets are processed using a widely used procedure and same statistical criteria to ensure the binding sites derived from different datasets are comparable. NURBS also provides predicted binding sites using NR-HMM, a Hidden Markov Model (HMM) model.
  
  
  BACKGROUND
  The GBrowse-based user interface of NURBS is freely accessible at http://shark.abl.ku.edu/nurbs/. NR-HMM and all results can be downloaded for free at the website.
  
  
  BACKGROUND
  jwfang@ku.edu
authors.affiliation: Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA. jwfang@ku.edu
authors.forename: Yaping
authors.initials: Y
authors.lastname: Fang
authors.forename: Hui-Xin
authors.initials: HX
authors.lastname: Liu
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.forename: Grace L
authors.initials: GL
authors.lastname: Guo
authors.forename: Yu-Jui Yvonne
authors.initials: YJ
authors.lastname: Wan
authors.forename: Jianwen
authors.initials: J
authors.lastname: Fang
mesh_terms: D000818:Animals; D001665:Binding Sites; D002467:Cell Nucleus / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D030541:Databases, Genetic; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008390:Markov Chains; D051379:Mice; D018160:Receptors, Cytoplasmic and Nuclear / Q000378:metabolism*; D017422:Sequence Analysis, DNA
chemical_list: D018160:Receptors, Cytoplasmic and Nuclear