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

Sun LV, Jin K, Liu Y, Yang W, Xie X, Ye L, Wang L, Zhu L, Ding S, Su Y, Zhou J, Han M, Zhuang Y, Xu T, Wu X, Gu N, Zhong Y - Nucleic Acids Res. (2007)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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

ABSTRACT
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/.

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An example of the LINE interface. Information is based on LINE Pkd2.
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Figure 3: An example of the LINE interface. Information is based on LINE Pkd2.

Mentions: In the PBmice database, the information of a LINE is associated with the INSERT(s) it carries. The LINE Detail interface reveals the properties of a LINE carrying one or more INSERTs, including the status, expression pattern and phenotyping data of the LINE (Figure 3). In this interface, the Status item indicates the storage status of the LINE (live animal, frozen sperm and/or frozen embryo) and related information for strain distribution. When a LINE carries trapping vector-related INSERT(s), the Expression pattern item will indicate any information that was characterized to some extent for the expression of the reporter protein. The Phenotype item provides clickable categories of phenotypes characterized for this LINE. The detailed phenotypic data contains not only the description of the phenotype and assays used to depict the phenotype, but also the sample information, such as the heterozygosity or homozygosity, the developmental stage, the sex of the animals or the organ examined. Users can also retrieve related INSERTs/LINEs based on similarity of phenotypes through advanced search (Figure 1b).Figure 3.


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

Sun LV, Jin K, Liu Y, Yang W, Xie X, Ye L, Wang L, Zhu L, Ding S, Su Y, Zhou J, Han M, Zhuang Y, Xu T, Wu X, Gu N, Zhong Y - Nucleic Acids Res. (2007)

An example of the LINE interface. Information is based on LINE Pkd2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238892&req=5

Figure 3: An example of the LINE interface. Information is based on LINE Pkd2.
Mentions: In the PBmice database, the information of a LINE is associated with the INSERT(s) it carries. The LINE Detail interface reveals the properties of a LINE carrying one or more INSERTs, including the status, expression pattern and phenotyping data of the LINE (Figure 3). In this interface, the Status item indicates the storage status of the LINE (live animal, frozen sperm and/or frozen embryo) and related information for strain distribution. When a LINE carries trapping vector-related INSERT(s), the Expression pattern item will indicate any information that was characterized to some extent for the expression of the reporter protein. The Phenotype item provides clickable categories of phenotypes characterized for this LINE. The detailed phenotypic data contains not only the description of the phenotype and assays used to depict the phenotype, but also the sample information, such as the heterozygosity or homozygosity, the developmental stage, the sex of the animals or the organ examined. Users can also retrieve related INSERTs/LINEs based on similarity of phenotypes through advanced search (Figure 1b).Figure 3.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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

ABSTRACT
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/.

Show MeSH
Related in: MedlinePlus