PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice.
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/.
Sun
Ling V
LV
Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433, Shanghai Center for Bioinformation Technology, Shanghai 200235, China. lingsun@fudan.edu.cn
Jin
Ke
K
Liu
Yiming
Y
Yang
Wenwei
W
Xie
Xing
X
Ye
Lin
L
Wang
Li
L
Zhu
Lin
L
Ding
Sheng
S
Su
Yi
Y
Zhou
Jie
J
Han
Min
M
Zhuang
Yuan
Y
Xu
Tian
T
Wu
Xiaohui
X
Gu
Ning
N
Zhong
Yang
Y
D000818:Animals; D004251:DNA Transposable Elements; D030541:Databases, Genetic; D015870:Gene Expression; D023281:Genomics; D020407:Internet; D051379:Mice / Q000235:genetics*; D016254:Mutagenesis, Insertional; D010641:Phenotype; D018511:Systems Integration; D014584:User-Computer Interface
D004251:DNA Transposable Elements