{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:18Z","timestamp":1740185118391,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2018,6,7]],"date-time":"2018-06-07T00:00:00Z","timestamp":1528329600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centre of Excellence in Molecular Systems Immunology and Physiology Research","award":["250114","292832"],"award-info":[{"award-number":["250114","292832"]}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["292335","294337","292482","31444"],"award-info":[{"award-number":["292335","294337","292482","31444"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000901","name":"JDRF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000901","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006306","name":"Sigrid Jus\u00e9lius Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100006306","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Finnish Cancer Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Co-localization of trait associated SNPs for specific transcription-factor binding sites or regulatory regions in the genome can yield profound insight into underlying causal mechanisms. Analysis is complicated because the truly causal SNPs are generally unknown and can be either SNPs reported in GWAS studies or other proxy SNPs in their linkage disequilibrium. Hence, a comprehensive pipeline for SNP co-localization analysis that utilizes all relevant information about both the genotyped SNPs and their proxies is needed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed an R package snpEnrichR for SNP co-localization analysis. The software integrates different tools for random SNP generation and genome co-localization analysis to automatize and help users to create custom SNP co-localization analysis. We show via an example that including proxy SNPs in SNP co-localization analysis enhances the sensitivity of co-localization detection.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software is available at https:\/\/github.com\/kartiek\/snpEnrichR.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty460","type":"journal-article","created":{"date-parts":[[2018,6,5]],"date-time":"2018-06-05T19:22:32Z","timestamp":1528226552000},"page":"4112-4114","source":"Crossref","is-referenced-by-count":2,"title":["snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions"],"prefix":"10.1093","volume":"34","author":[{"given":"Kari","family":"Nousiainen","sequence":"first","affiliation":[{"name":"Department of Computer Science, Aalto University School of Science, FI-00076 Aalto, Finland"}]},{"given":"Kartiek","family":"Kanduri","sequence":"additional","affiliation":[{"name":"Turku Centre for Biotechnology, University of Turku and \u00c5bo Akademi University, Turku, Finland"}]},{"given":"Isis","family":"Rica\u00f1o-Ponce","sequence":"additional","affiliation":[{"name":"Department of Genetics, UMCG, University of Groningen, AB Groningen, the Netherlands"}]},{"given":"Cisca","family":"Wijmenga","sequence":"additional","affiliation":[{"name":"Department of Genetics, UMCG, University of Groningen, AB Groningen, the Netherlands"},{"name":"Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway"}]},{"given":"Riitta","family":"Lahesmaa","sequence":"additional","affiliation":[{"name":"Turku Centre for Biotechnology, University of Turku and \u00c5bo Akademi University, Turku, Finland"}]},{"given":"Vinod","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Genetics, UMCG, University of Groningen, AB Groningen, the Netherlands"},{"name":"Department of Internal Medicine, Radboud University Medical Center, GA Nijmegen, the Netherlands"}]},{"given":"Harri","family":"L\u00e4hdesm\u00e4ki","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Aalto University School of Science, FI-00076 Aalto, Finland"},{"name":"Turku Centre for Biotechnology, University of Turku and \u00c5bo Akademi University, Turku, Finland"}]}],"member":"286","published-online":{"date-parts":[[2018,6,7]]},"reference":[{"key":"2023012712310989400_bty460-B1","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"2023012712310989400_bty460-B2","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.immuni.2010.06.011","article-title":"Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming","volume":"32","author":"Elo","year":"2010","journal-title":"Immunity"},{"key":"2023012712310989400_bty460-B3","doi-asserted-by":"crossref","first-page":"D896","DOI":"10.1093\/nar\/gkw1133","article-title":"The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)","volume":"45","author":"MacArthur","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012712310989400_bty460-B4","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1093\/bioinformatics\/btu655","article-title":"SNPsnap: a Web-based tool for identification and annotation of matched SNPs","volume":"31","author":"Pers","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712310989400_bty460-B5","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"The 1000 Genomes Project Consortium","year":"2015","journal-title":"Nature"},{"key":"2023012712310989400_bty460-B6","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.celrep.2017.05.013","article-title":"Genome-wide analysis of STAT3 mediated transcription during early human Th17 cell differentiation","volume":"19","author":"Tripathi","year":"2017","journal-title":"Cell Rep"},{"key":"2023012712310989400_bty460-B7","doi-asserted-by":"crossref","first-page":"2094","DOI":"10.1016\/j.celrep.2018.01.070","article-title":"Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells","volume":"22","author":"Ullah","year":"2018","journal-title":"Cell Rep"},{"key":"2023012712310989400_bty460-B8","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkw951","article-title":"GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments","volume":"45","author":"Yevshin","year":"2017","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/23\/4112\/48921157\/bioinformatics_34_23_4112.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/23\/4112\/48921157\/bioinformatics_34_23_4112.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:18:05Z","timestamp":1674825485000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/23\/4112\/5034433"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,7]]},"references-count":8,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2018,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty460","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,12,1]]},"published":{"date-parts":[[2018,6,7]]}}}