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Web-based database and viewer of East asian copy number variations.

Kim JH, Hu HJ, Chung YJ - Genomics Inform (2012)

Bottom Line: We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study.To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information.This system helps researchers browsing these variants with gene and structure variant annotations.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine, Seoul 137-701, Korea.

ABSTRACT
We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.

No MeSH data available.


Database search page and genome browser.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
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Figure 2: Database search page and genome browser.

Mentions: Our web-based database viewer can display previously discovered CNVs by their positions (Fig. 2). Users can also filter out CNVs based on the DGV overlapped regions, CNV type (Gain/Loss/Complex), or their frequencies. Each selected region could be diagnosed in detail by clicking on it. DGV and OMIM ID columns are linked with corresponding websites, and CNVR position columns are linked with the genome browser. The genome browser is integrated based on the open source project GBrowse2. Users can seek or zoom in/out of CNVs across the chromosome by entering positions or clicking zoom buttons. GBrowse2 can also display interesting areas by dragging the region bar without reloading the entire page. Gene information of the selected area is also displayed, and details will be given on separate pop-up page by clicking on it.


Web-based database and viewer of East asian copy number variations.

Kim JH, Hu HJ, Chung YJ - Genomics Inform (2012)

Database search page and genome browser.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3475484&req=5

Figure 2: Database search page and genome browser.
Mentions: Our web-based database viewer can display previously discovered CNVs by their positions (Fig. 2). Users can also filter out CNVs based on the DGV overlapped regions, CNV type (Gain/Loss/Complex), or their frequencies. Each selected region could be diagnosed in detail by clicking on it. DGV and OMIM ID columns are linked with corresponding websites, and CNVR position columns are linked with the genome browser. The genome browser is integrated based on the open source project GBrowse2. Users can seek or zoom in/out of CNVs across the chromosome by entering positions or clicking zoom buttons. GBrowse2 can also display interesting areas by dragging the region bar without reloading the entire page. Gene information of the selected area is also displayed, and details will be given on separate pop-up page by clicking on it.

Bottom Line: We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study.To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information.This system helps researchers browsing these variants with gene and structure variant annotations.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine, Seoul 137-701, Korea.

ABSTRACT
We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.

No MeSH data available.