{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:43:46Z","timestamp":1773290626037,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/icbi.at\/gpviz<\/jats:p>\n               <jats:p>Contact: \u00a0hubert.hackl@i-med.ac.at<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt354","type":"journal-article","created":{"date-parts":[[2013,6,20]],"date-time":"2013-06-20T00:15:39Z","timestamp":1371687339000},"page":"2195-2196","source":"Crossref","is-referenced-by-count":3,"title":["GPViz: dynamic visualization of genomic regions and variants affecting protein domains"],"prefix":"10.1093","volume":"29","author":[{"given":"Rene","family":"Snajder","sequence":"first","affiliation":[{"name":"1 Biocenter, Division of Bioinformatics, Innsbruck Medical University and 2Oncotyrol Center for Personalized Cancer Medicine GmbH, 6020 Innsbruck, Austria"},{"name":"1 Biocenter, Division of Bioinformatics, Innsbruck Medical University and 2Oncotyrol Center for Personalized Cancer Medicine GmbH, 6020 Innsbruck, Austria"}]},{"given":"Zlatko","family":"Trajanoski","sequence":"additional","affiliation":[{"name":"1 Biocenter, Division of Bioinformatics, Innsbruck Medical University and 2Oncotyrol Center for Personalized Cancer Medicine GmbH, 6020 Innsbruck, Austria"}]},{"given":"Hubert","family":"Hackl","sequence":"additional","affiliation":[{"name":"1 Biocenter, Division of Bioinformatics, Innsbruck Medical University and 2Oncotyrol Center for Personalized Cancer Medicine GmbH, 6020 Innsbruck, Austria"}]}],"member":"286","published-online":{"date-parts":[[2013,6,19]]},"reference":[{"key":"2023012810463368300_btt354-B1","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res."},{"key":"2023012810463368300_btt354-B2","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1101\/gr.134635.111","article-title":"MuSiC: identifying mutational significance in cancer genomes","volume":"22","author":"Dees","year":"2012","journal-title":"Genome Res."},{"key":"2023012810463368300_btt354-B3","doi-asserted-by":"crossref","first-page":"W755","DOI":"10.1093\/nar\/gkq405","article-title":"AltAnalyze and DomainGraph: analyzing and visualizing exon expression data","volume":"38","author":"Emig","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012810463368300_btt354-B4","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gks1236","article-title":"Ensembl 2013","volume":"41","author":"Flicek","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810463368300_btt354-B5","article-title":"A survey of tools for variant analysis of next-generation genome sequencing data","author":"Pabinger","year":"2013","journal-title":"Brief Bioinform"},{"key":"2023012810463368300_btt354-B6","doi-asserted-by":"crossref","first-page":"2458","DOI":"10.1093\/bioinformatics\/btq447","article-title":"DMDM: domain mapping of disease mutations","volume":"26","author":"Peterson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810463368300_btt354-B7","doi-asserted-by":"crossref","first-page":"2281","DOI":"10.1093\/bioinformatics\/btp381","article-title":"FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci","volume":"25","author":"Rambaldi","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810463368300_btt354-B8","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/gm413","article-title":"Visualizing multidimensional cancer genomics data","volume":"5","author":"Schroeder","year":"2013","journal-title":"Genome Med."},{"key":"2023012810463368300_btt354-B9","doi-asserted-by":"crossref","first-page":"2059","DOI":"10.1056\/NEJMoa1301689","article-title":"Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia","volume":"368","author":"TCGA","year":"2013","journal-title":"N. 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