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Nucleic Acids Research Advance Access published online on October 11, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm790
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice

Ling V. Sun1,2,*, Ke Jin2, Yiming Liu3, Wenwei Yang1,2, Xing Xie3, Lin Ye2, Li Wang2,4, Lin Zhu3, Sheng Ding1,2, Yi Su3, Jie Zhou2, Min Han1,2,5, Yuan Zhuang1,2,6, Tian Xu1,2,7, Xiaohui Wu1,2, Ning Gu3,* and Yang Zhong2,4,*

1Institute of Developmental Biology and Molecular Medicine, 2School of Life Sciences, 3School of Information Science and Engineering, Fudan University, Shanghai 200433, 4Shanghai Center for Bioinformation Technology, Shanghai 200235, China, 5Howard Hughes Medical Institute, Department of MCDB, University of Colorado at Boulder, Boulder, CO 80309, 6Department of Immunology, Duke University Medical Center, Durham, NC 27710 and 7Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, Boyer Center for Molecular Medicine, New Haven, CT 06536, USA

* To whom correspondence should be addressed. Tel: +86 21 55664436; Fax: +86 21 65642468; Email: yangzhong{at}fudan.edu.cn Correspondence may be addressed to Ling V. Sun – Tel: +86 21 65642244; Fax: +86 21 65643770; Email: lingsun{at}fudan.edu.cn and Ning Gu – Tel: +86 21 55664462; Fax: +86 21 55664456; Email: ninggu{at}fudan.edu.cn

Received August 13, 2007. Revised September 13, 2007. Accepted September 17, 2007.

DNA transposon piggyBac (PB) is a newly established mutagen for large-scale mutagenesis in mice. We have designed and implemented an integrated database system called PBmice (PB Mutagenesis Information CEnter) for storing, retrieving and displaying the information derived from PB insertions (INSERTs) in the mouse genome. This system is centered on INSERTs with information including their genomic locations and flanking genomic sequences, the expression levels of the hit genes, and the expression patterns of the trapped genes if a trapping vector was used. It also archives mouse phenotyping data linked to INSERTs, and allows users to conduct quick and advanced searches for genotypic and phenotypic information relevant to a particular or a set of INSERT(s). Sequence-based information can be cross-referenced with other genomic databases such as Ensembl, BLAST and GBrowse tools used in PBmice offer enhanced search and display for additional information relevant to INSERTs. The total number and genomic distribution of PB INSERTs, as well as the availability of each PB insertional LINE can also be viewed with user-friendly interfaces. PBmice is freely available at http://www.idmshanghai.cn/PBmice or http://www.scbit.org/PBmice/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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