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 language | English (US) |
|---|---|
| Pages (from-to) | 295-297 |
| Number of pages | 3 |
| Journal | Bioinformatics |
| Volume | 29 |
| Issue number | 2 |
| DOIs | |
| State | Published - Jan 15 2013 |
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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 journal › Article
}
TY - JOUR
T1 - NURBS
T2 - A database of experimental and predicted nuclear receptor binding sites of mouse
AU - Fang, Yaping
AU - Liu, Hui Xin
AU - Zhang, Ning
AU - Guo, Grace L.
AU - Wan, Yu-Jui Yvonne
AU - Fang, Jianwen
PY - 2013/1/15
Y1 - 2013/1/15
N2 - 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.
AB - 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.
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U2 - 10.1093/bioinformatics/bts693
DO - 10.1093/bioinformatics/bts693
M3 - Article
C2 - 23196988
AN - SCOPUS:84872581119
VL - 29
SP - 295
EP - 297
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 2
ER -