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 mutagenfor large-scale mutagenesis in mice. We have designed and implementedan integrated database system called PBmice (PB MutagenesisInformation CEnter) for storing, retrieving and displaying theinformation derived from PB insertions (INSERTs) in the mousegenome. This system is centered on INSERTs with informationincluding their genomic locations and flanking genomic sequences,the expression levels of the hit genes, and the expression patternsof the trapped genes if a trapping vector was used. It alsoarchives mouse phenotyping data linked to INSERTs, and allowsusers to conduct quick and advanced searches for genotypic andphenotypic information relevant to a particular or a set ofINSERT(s). Sequence-based information can be cross-referencedwith other genomic databases such as Ensembl, BLAST and GBrowsetools used in PBmice offer enhanced search and display for additionalinformation relevant to INSERTs. The total number and genomicdistribution of PB INSERTs, as well as the availability of eachPB insertional LINE can also be viewed with user-friendly interfaces.PBmice is freely available at http://www.idmshanghai.cn/PBmiceor http://www.scbit.org/PBmice/.

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

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