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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 Search Result interface, using search term Pkd2.
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Figure 5: An example of the Search Result interface, using search term Pkd2.

Mentions: Taking the INSERT AF0-47T6 that hits into the gene Pkd2 as an example to navigate PBmice. Pkd2 was cloned in 1996 and proved to contribute to autosomal dominant polycystic kidney disease (ADPKD) when mutated (43). Patients suffering from ADPKD grow cysts in their kidneys eventually leading to kidney failure. ADPKD is the most common inherited disease affecting about half a million Americans and more than 1.5 million Chinese (44,45). To search for any INSERT existing that hits Pkd2, either quick search or advanced search can be used (Figure 1). Input Pkd2 in the search box in the Quick Search interface (Figure 1a) will lead to a Search Result interface displaying the following information (Figure 5): (i) INSERT Name AF0-47T6, which is clickable to display the INSERT Detail interface for AF0-47T6 (Figure 2); (ii) Mouse strain FVB/NJ carrying AF0-47T6; (iii) Chromosome 5 on which AF0-47T6 is located; (iv) LINE Name Pkd2 carrying AF0-47T6, which is also a link to exhibit the LINE Detail interface for Pkd2 (Figure 3) and (v) Gene hit by AF0-47T6 in its Ensembl ID ENSMUSG00000034462, which leads to the Gene Information and Transcript interface for the Pkd2 gene (Figure 4a and b). In the LINE Detail interface for Pkd2, two types of phenotypes have been characterized for this LINE, including detailed information that LINE Pkd2 has phenotypes similar to those of the previously described Pkd2 knockout mice (29,46). Advanced Search can also be used to retrieve any INSERT relevant to Pkd2 (Figure 1b). Currently, three options are available in the Advanced Search interface to reach this goal: (i) search for any INSERT within 0 kb of the Gene Pkd2; (ii) search for any INSERT on Chromosome 5 within 104 699 752–104 746 120 bp and (iii) search for any INSERT associated with any phenotype falling into either category Gross Anatomy or category Growth/Size/Lethality. Submission of the query using option 1 will lead to an intermediate interface to let users choose the right gene of interest to continue, because more than one gene name contains the four characters, pkd2. Submission of the query using options 2 or 3 directly leads to a Search Result interface similar as shown in Figure 5.Figure 5.


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 Search Result interface, using search term Pkd2.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: An example of the Search Result interface, using search term Pkd2.
Mentions: Taking the INSERT AF0-47T6 that hits into the gene Pkd2 as an example to navigate PBmice. Pkd2 was cloned in 1996 and proved to contribute to autosomal dominant polycystic kidney disease (ADPKD) when mutated (43). Patients suffering from ADPKD grow cysts in their kidneys eventually leading to kidney failure. ADPKD is the most common inherited disease affecting about half a million Americans and more than 1.5 million Chinese (44,45). To search for any INSERT existing that hits Pkd2, either quick search or advanced search can be used (Figure 1). Input Pkd2 in the search box in the Quick Search interface (Figure 1a) will lead to a Search Result interface displaying the following information (Figure 5): (i) INSERT Name AF0-47T6, which is clickable to display the INSERT Detail interface for AF0-47T6 (Figure 2); (ii) Mouse strain FVB/NJ carrying AF0-47T6; (iii) Chromosome 5 on which AF0-47T6 is located; (iv) LINE Name Pkd2 carrying AF0-47T6, which is also a link to exhibit the LINE Detail interface for Pkd2 (Figure 3) and (v) Gene hit by AF0-47T6 in its Ensembl ID ENSMUSG00000034462, which leads to the Gene Information and Transcript interface for the Pkd2 gene (Figure 4a and b). In the LINE Detail interface for Pkd2, two types of phenotypes have been characterized for this LINE, including detailed information that LINE Pkd2 has phenotypes similar to those of the previously described Pkd2 knockout mice (29,46). Advanced Search can also be used to retrieve any INSERT relevant to Pkd2 (Figure 1b). Currently, three options are available in the Advanced Search interface to reach this goal: (i) search for any INSERT within 0 kb of the Gene Pkd2; (ii) search for any INSERT on Chromosome 5 within 104 699 752–104 746 120 bp and (iii) search for any INSERT associated with any phenotype falling into either category Gross Anatomy or category Growth/Size/Lethality. Submission of the query using option 1 will lead to an intermediate interface to let users choose the right gene of interest to continue, because more than one gene name contains the four characters, pkd2. Submission of the query using options 2 or 3 directly leads to a Search Result interface similar as shown in Figure 5.Figure 5.

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