NURBS

A database of experimental and predicted nuclear receptor binding sites of mouse

Yaping Fang, Hui Xin Liu, Ning Zhang, Grace L. Guo, Yu-Jui Yvonne Wan, Jianwen Fang

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)295-297
Number of pages3
JournalBioinformatics
Volume29
Issue number2
DOIs
StatePublished - Jan 15 2013

Fingerprint

Binding sites
Cytoplasmic and Nuclear Receptors
Receptor
Mouse
Binding Sites
Databases
Hidden Markov models
Markov Model
Genes
Biological Phenomena
High-Throughput Nucleotide Sequencing
DNA Sequencing
Transcription factors
Chromatin Immunoprecipitation
Chromatin
Transcription Factor
DNA Sequence Analysis
Genome
DNA
Transcription Factors

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

NURBS : A database of experimental and predicted nuclear receptor binding sites of mouse. / Fang, Yaping; Liu, Hui Xin; Zhang, Ning; Guo, Grace L.; Wan, Yu-Jui Yvonne; Fang, Jianwen.

In: Bioinformatics, Vol. 29, No. 2, 15.01.2013, p. 295-297.

Research output: Contribution to journalArticle

Fang, Yaping ; Liu, Hui Xin ; Zhang, Ning ; Guo, Grace L. ; Wan, Yu-Jui Yvonne ; Fang, Jianwen. / NURBS : A database of experimental and predicted nuclear receptor binding sites of mouse. In: Bioinformatics. 2013 ; Vol. 29, No. 2. pp. 295-297.
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