{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T21:46:36Z","timestamp":1722721596676},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":139,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Expression quantitative trait loci (eQTLs) are genetic variants that affect gene expression. In eQTL studies, one important task is to find eGenes or genes whose expressions are associated with at least one eQTL. The standard statistical method to determine whether a gene is an eGene requires association testing at all nearby variants and the permutation test to correct for multiple testing. The standard method however does not consider genomic annotation of the variants. In practice, variants near gene transcription start sites (TSSs) or certain histone modifications are likely to regulate gene expression. In this article, we introduce a novel eGene detection method that considers this empirical evidence and thereby increases the statistical power.<\/jats:p>\n               <jats:p>Results: We applied our method to the liver Genotype-Tissue Expression (GTEx) data using distance from TSSs, DNase hypersensitivity sites, and six histone modifications as the genomic annotations for the variants. Each of these annotations helped us detected more candidate eGenes. Distance from TSS appears to be the most important annotation; specifically, using this annotation, our method discovered 50% more candidate eGenes than the standard permutation method.<\/jats:p>\n               <jats:p>Contact: \u00a0buhm.han@amc.seoul.kr or eeskin@cs.ucla.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw272","type":"journal-article","created":{"date-parts":[[2016,6,15]],"date-time":"2016-06-15T15:43:52Z","timestamp":1466005432000},"page":"i156-i163","source":"Crossref","is-referenced-by-count":12,"title":["Using genomic annotations increases statistical power to detect eGenes"],"prefix":"10.1093","volume":"32","author":[{"given":"Dat","family":"Duong","sequence":"first","affiliation":[{"name":"1 Department of Computer Science"}]},{"given":"Jennifer","family":"Zou","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science"}]},{"given":"Farhad","family":"Hormozdiari","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science"}]},{"given":"Jae Hoon","family":"Sul","sequence":"additional","affiliation":[{"name":"4 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"}]},{"given":"Jason","family":"Ernst","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science"},{"name":"2 Department of Biological Chemistry"}]},{"given":"Buhm","family":"Han","sequence":"additional","affiliation":[{"name":"5 Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea"}]},{"given":"Eleazar","family":"Eskin","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science"},{"name":"3 Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,6,11]]},"reference":[{"key":"2023020112322670800_btw272-B1","first-page":"btw018","article-title":"FINEMAP: efficient variable selection using summary data from genome-wide association studies","author":"Benner","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020112322670800_btw272-B2","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1073\/pnas.0408709102","article-title":"The landscape of genetic complexity across 5,700 gene expression traits in yeast","volume":"102","author":"Brem","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020112322670800_btw272-B3","doi-asserted-by":"crossref","first-page":"e1004461","DOI":"10.1371\/journal.pgen.1004461","article-title":"Cis and trans effects of human genomic variants on gene expression","volume":"10","author":"Bryois","year":"2014","journal-title":"PLoS Genetics"},{"key":"2023020112322670800_btw272-B4","doi-asserted-by":"crossref","first-page":"i147","DOI":"10.1093\/bioinformatics\/bts235","article-title":"Incorporating prior information into association studies","volume":"28","author":"Darnell","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020112322670800_btw272-B5","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1016\/j.ajhg.2015.11.021","article-title":"An efficient multiple-testing adjustment for eQTL studies that accounts for linkage disequilibrium between variants","volume":"98","author":"Davis","year":"2016","journal-title":"Am. J. Hum. Genet"},{"key":"2023020112322670800_btw272-B6","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1038\/nbt.3157","article-title":"Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues","volume":"33","author":"Ernst","year":"2015","journal-title":"Nat. Biotechnol"},{"key":"2023020112322670800_btw272-B7","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1101\/gr.072785.107","article-title":"Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information","volume":"18","author":"Eskin","year":"2008","journal-title":"Gen. Res"},{"key":"2023020112322670800_btw272-B8","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1016\/j.tig.2008.06.001","article-title":"Revealing the architecture of gene regulation: the promise of eQTL studies","volume":"24","author":"Gilad","year":"2008","journal-title":"Trends Genet"},{"key":"2023020112322670800_btw272-B9","first-page":"004309","article-title":"Regulatory variants explain much more heritability than coding variants across 11 common diseases","author":"Gusev","year":"2014","journal-title":"BioRxiv"},{"key":"2023020112322670800_btw272-B10","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1534\/genetics.114.167908","article-title":"Identifying causal variants at loci with multiple signals of association","volume":"198","author":"Hormozdiari","year":"2014","journal-title":"Genetics"},{"key":"2023020112322670800_btw272-B11","doi-asserted-by":"crossref","first-page":"i206","DOI":"10.1093\/bioinformatics\/btv240","article-title":"Identification of causal genes for complex traits","volume":"31","author":"Hormozdiari","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020112322670800_btw272-B12","article-title":"A method to increase the power of multiple testing procedures through sample splitting","volume":"5","author":"Rubin","year":"2006","journal-title":"Stat. App. Genet. Mol. Biol"},{"key":"2023020112322670800_btw272-B13","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/nprot.2011.457","article-title":"Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses","volume":"7","author":"Stegle","year":"2012","journal-title":"Nat. Protoc"},{"key":"2023020112322670800_btw272-B14","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","article-title":"Statistical significance for genomewide studies","volume":"100","author":"Storey","year":"2003","journal-title":"Proc. Natl. Acad. Sci"},{"key":"2023020112322670800_btw272-B15","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1016\/j.ajhg.2015.04.012","article-title":"Accurate and fast multiple-testing correction in eQTL studies","volume":"96","author":"Sul","year":"2015","journal-title":"Am. J. Hum. Genet"},{"key":"2023020112322670800_btw272-B16","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans","volume":"348","author":"The GTEx Consortium","year":"2015","journal-title":"Science"},{"key":"2023020112322670800_btw272-B17","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nature14248","article-title":"Integrative analysis of 111 reference human epigenomes","volume":"518","author":"The Roadmap Epigenomics Mapping Consortium","year":"2015","journal-title":"Nature"},{"key":"2023020112322670800_btw272-B18","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nmeth.3582","article-title":"WASP: allele-specific software for robust molecular quantitative trait locus discovery","volume":"12","author":"van de Geijn","year":"2015","journal-title":"Nat. Met"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/12\/i156\/49022935\/bioinformatics_32_12_i156.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/12\/i156\/49022935\/bioinformatics_32_12_i156.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:41:06Z","timestamp":1675291266000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/12\/i156\/2288856"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,6,11]]},"references-count":18,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2016,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw272","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,6,15]]},"published":{"date-parts":[[2016,6,11]]}}}