GPViz: dynamic visualization of genomic regions and variants affecting protein domains

被引:3
作者
Snajder, Rene [1 ,2 ]
Trajanoski, Zlatko [1 ]
Hackl, Hubert [1 ]
机构
[1] Med Univ Innsbruck, Bioctr, Div Bioinformat, A-6020 Innsbruck, Austria
[2] Oncotyrol Ctr Personalized Canc Med GmbH, A-6020 Innsbruck, Austria
关键词
D O I
10.1093/bioinformatics/btt354
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
GPViz is a versatile Java-based software for dynamic gene-centered visualization of genomic regions and/or variants. User-defined data can be loaded in common formats as resulting from analysis workflows used in sequencing applications and studied in the context of the gene, the corresponding transcript isoforms, proteins and their domains or other protein features. Both the genomic regions and variants can be also defined interactively. Various gene filter options are provided to enable an intersection of variants, genomic regions and affected protein features. Finally, by using GPViz, we identified differentially expressed exons, which could indicate alternative splicing events, and found somatic variants in different cancer types affecting metabolic proteins. GPViz is freely available at http://icbi.at/gpviz (released under GNU general public license), is based on Java 7 and can be used as a stand-alone or Web Start application.
引用
收藏
页码:2195 / 2196
页数:2
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