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Bioinformatics. 2013 Jan 15;29(2):295-7. doi: 10.1093/bioinformatics/bts693. Epub 2012 Nov 29.

NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse.

Author information

1
Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA. jwfang@ku.edu

Abstract

SUMMARY:

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.

AVAILABILITY:

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.

CONTACT:

jwfang@ku.edu

PMID:
23196988
PMCID:
PMC3546791
DOI:
10.1093/bioinformatics/bts693
[Indexed for MEDLINE]
Free PMC Article
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