{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T11:40:32Z","timestamp":1675338032844},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Genes often regulate multiple traits. Identifying clusters of traits influenced by a common group of genes helps elucidate regulatory networks and can improve linkage mapping.<\/jats:p>\n               <jats:p>Methods: We show that the Pearson correlation coefficient, \u03c1\u2227L, between two LOD score profiles can, with high specificity and sensitivity, identify pairs of genes that have their transcription regulated by shared quantitative trait loci (QTL). Furthermore, using theoretical and\/or empirical methods, we can approximate the distribution of \u03c1\u2227L under the null hypothesis of no common QTL. Therefore, it is possible to calculate P-values and false discovery rates for testing whether two traits share common QTL. We then examine the properties of \u03c1\u2227L through simulation and use \u03c1\u2227L to cluster genes in a genetical genomics experiment examining Saccharomyces cerevisiae.<\/jats:p>\n               <jats:p>Results: Simulations show that \u03c1\u2227L can have more power than the clustering methods currently used in genetical genomics. Combining experimental results with Gene Ontology (GO) annotations show that genes within a purported cluster often share similar function.<\/jats:p>\n               <jats:p>Software: R-code included in online Supplementary Material.<\/jats:p>\n               <jats:p>Contact: \u00a0joshua.sampson@yale.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary materials are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn064","type":"journal-article","created":{"date-parts":[[2008,3,2]],"date-time":"2008-03-02T01:23:46Z","timestamp":1204421026000},"page":"958-964","source":"Crossref","is-referenced-by-count":3,"title":["Identifying trait clusters by linkage profiles: application in genetical genomics"],"prefix":"10.1093","volume":"24","author":[{"given":"Joshua N.","family":"Sampson","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, University of Washington and 2Statistical Center for HIV\/AIDS Research and Prevention, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven G.","family":"Self","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, University of Washington and 2Statistical Center for HIV\/AIDS Research and Prevention, Seattle, WA, USA"},{"name":"1 Department of Biostatistics, University of Washington and 2Statistical Center for HIV\/AIDS Research and Prevention, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,2,29]]},"reference":[{"key":"2023020209532680900_B1","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1073\/pnas.0408709102","article-title":"The landscape of genetic complexity across, 5700 gene expression traits in yeast","volume":"102","author":"Brem","year":"2005","journal-title":"PNAS"},{"key":"2023020209532680900_B2","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1126\/science.1069516","article-title":"Genetic dissection of transcriptional regulation in budding yeast","volume":"296","author":"Brem","year":"2002","journal-title":"Science"},{"key":"2023020209532680900_B3","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1111\/j.1541-0420.2005.00327.x","article-title":"The full em algorithm for the mles of qtl effects and positions and their estimated variances in multiple-interval mapping","volume":"61","author":"Chen","year":"2005","journal-title":"Biometrics"},{"key":"2023020209532680900_B4","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome-wide expression patterns","volume":"95","author":"Eisen","year":"1998","journal-title":"Proc. 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