{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,23]],"date-time":"2025-09-23T13:21:39Z","timestamp":1758633699474},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Genome-wide association studies (GWAS) have revolutionized the search for the variants underlying human complex diseases. However, in a typical GWAS, only a minority of the single-nucleotide polymorphisms (SNPs) with the strongest evidence of association is explained. One possible reason of complex diseases is the alterations in the activity of several biological pathways. Here we present a web server called Pathway and Network-Oriented GWAS Analysis to devise functionally important pathways through the identification of SNP-targeted genes within these pathways. The strength of our methodology stems from its multidimensional perspective, where we combine evidence from the following five resources: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein\u2013protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways.<\/jats:p>\n               <jats:p>Availability: PANOGA web server is freely available at: http:\/\/panoga.sabanciuniv.edu\/. The source code is available to academic users \u2018as is\u2019 on request.<\/jats:p>\n               <jats:p>Contact: \u00a0burcub@gatech.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt743","type":"journal-article","created":{"date-parts":[[2014,1,12]],"date-time":"2014-01-12T01:28:34Z","timestamp":1389490114000},"page":"1287-1289","source":"Crossref","is-referenced-by-count":25,"title":["PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data"],"prefix":"10.1093","volume":"30","author":[{"given":"Burcu","family":"Bakir-Gungor","sequence":"first","affiliation":[{"name":"1 Department of Genetics and Bioinformatics, Faculty of Arts and Sciences, Bahcesehir University, 34353, Besiktas, Istanbul, Turkey, 2Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, 38039, Kayseri, Turkey, 3Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey and 4Department of Biological Sciences and Bioengineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey"},{"name":"1 Department of Genetics and Bioinformatics, Faculty of Arts and Sciences, Bahcesehir University, 34353, Besiktas, Istanbul, Turkey, 2Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, 38039, Kayseri, Turkey, 3Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey and 4Department of Biological Sciences and Bioengineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey"}]},{"given":"Ece","family":"Egemen","sequence":"additional","affiliation":[{"name":"1 Department of Genetics and Bioinformatics, Faculty of Arts and Sciences, Bahcesehir University, 34353, Besiktas, Istanbul, Turkey, 2Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, 38039, Kayseri, Turkey, 3Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey and 4Department of Biological Sciences and Bioengineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey"}]},{"given":"Osman Ugur","family":"Sezerman","sequence":"additional","affiliation":[{"name":"1 Department of Genetics and Bioinformatics, Faculty of Arts and Sciences, Bahcesehir University, 34353, Besiktas, Istanbul, Turkey, 2Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, 38039, Kayseri, Turkey, 3Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey and 4Department of Biological Sciences and Bioengineering, Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey"}]}],"member":"286","published-online":{"date-parts":[[2014,1,11]]},"reference":[{"key":"2023012710511227900_btt743-B1","doi-asserted-by":"crossref","first-page":"e57022","DOI":"10.1371\/journal.pone.0057022","article-title":"The identification of pathway markers in intracranial aneurysm using genome-wide association data from two different populations","volume":"8","author":"Bakir-Gungor","year":"2013","journal-title":"Plos One"},{"key":"2023012710511227900_btt743-B2","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.eplepsyres.2013.02.008","article-title":"Identifying SNP targeted pathways in partial epilepsies with genome-wide association study data","volume":"105","author":"Bakir-Gungor","year":"2013","journal-title":"Epilepsy Res."},{"key":"2023012710511227900_btt743-B3","volume-title":"The Identification of Pathway Markers in Beh\u00e7et's Disease Using GWA Data From Two Different Populations, Scientific Meeting of the American College of Rheumatology, November 9\u201314","author":"Bakir-Gungor","year":"2012"},{"key":"2023012710511227900_btt743-B4","doi-asserted-by":"crossref","DOI":"10.1038\/protex.2012.019","article-title":"Identification of SNP targeted pathways from GWAS data","author":"Bakir-Gungor","year":"2012","journal-title":"Nature Protocol Exchange"},{"key":"2023012710511227900_btt743-B5","doi-asserted-by":"crossref","first-page":"e26277","DOI":"10.1371\/journal.pone.0026277","article-title":"A new methodology to associate SNPs with human diseases according to their pathway related context","volume":"6","author":"Bakir-Gungor","year":"2011","journal-title":"PLos One"},{"key":"2023012710511227900_btt743-B6","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1534\/genetics.111.131698","article-title":"Experimental designs for robust detection of effects in genome-wide 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Mutat."},{"key":"2023012710511227900_btt743-B9","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nrg2779","article-title":"Uncovering the roles of rare variants in common disease through whole-genome sequencing, Nat","volume":"11","author":"Cirulli","year":"2010","journal-title":"Rev. Genet."},{"key":"2023012710511227900_btt743-B10","doi-asserted-by":"crossref","first-page":"D820","DOI":"10.1093\/nar\/gkm904","article-title":"F-SNP: computationally predicted functional SNPs for disease association studies","volume":"36","author":"Lee","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012710511227900_btt743-B11","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1038\/ejhg.2009.115","article-title":"Gene and pathway-based second-wave analysis of genome-wide association studies","volume":"18","author":"Peng","year":"2010","journal-title":"Eur. J. Hum. Genet."},{"key":"2023012710511227900_btt743-B12","doi-asserted-by":"crossref","first-page":"W201","DOI":"10.1093\/nar\/gkq513","article-title":"SPOT: a web-based tool for using biological databases to prioritize SNPs after a GWA study","volume":"38","author":"Saccone","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012710511227900_btt743-B13","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3002132","article-title":"NEW: network-enabled wisdom in biology, medicine, and health care","volume":"4","author":"Schadt","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"2023012710511227900_btt743-B14","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.ajhg.2011.11.029","article-title":"Five years of GWAS discovery","volume":"90","author":"Visscher","year":"2012","journal-title":"Am. J. Hum. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/9\/1287\/48922717\/bioinformatics_30_9_1287.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/9\/1287\/48922717\/bioinformatics_30_9_1287.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:30:02Z","timestamp":1674819002000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/9\/1287\/234082"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1,11]]},"references-count":14,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2014,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt743","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,5,1]]},"published":{"date-parts":[[2014,1,11]]}}}