{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T13:26:45Z","timestamp":1791466005865,"version":"4.3.4"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: RNA sequencing enables allele-specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression (GTEx) project is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data.<\/jats:p>\n                  <jats:p>Results: We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally.<\/jats:p>\n                  <jats:p>Availability and implementation: http:\/\/www.well.ox.ac.uk\/~rivas\/mamba\/. R-sources and data examples http:\/\/www.iki.fi\/mpirinen\/<\/jats:p>\n                  <jats:p>Contact: matti.pirinen@helsinki.fi or rivas@well.ox.ac.uk<\/jats:p>\n                  <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv074","type":"journal-article","created":{"date-parts":[[2015,3,28]],"date-time":"2015-03-28T23:44:55Z","timestamp":1427586295000},"page":"2497-2504","source":"Crossref","is-referenced-by-count":74,"title":["Assessing allele-specific expression across multiple tissues from RNA-seq read data"],"prefix":"10.1093","volume":"31","author":[{"given":"Matti","family":"Pirinen","sequence":"first","affiliation":[{"name":"1 Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tuuli","family":"Lappalainen","sequence":"additional","affiliation":[{"name":"2 Department of Genetic Medicine and Development and,"},{"name":"3 Institute for Genetics and Genomics in Geneva (iG3), University of Geneva, Geneva, Switzerland,"},{"name":"4 Swiss Institute of Bioinformatics, Geneva, Switzerland,"},{"name":"5 Department of Genetics, Stanford University, Palo Alto, CA, USA,"},{"name":"6 New York Genome Center, New York, NY, USA,"},{"name":"7 Department of Systems Biology, Columbia University, New York, NY, USA,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noah A.","family":"Zaitlen","sequence":"additional","affiliation":[{"name":"8 Department of Medicine, University of California, San Francisco, CA, USA,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"GTEx Consortium","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanouil T.","family":"Dermitzakis","sequence":"additional","affiliation":[{"name":"2 Department of Genetic Medicine and Development and,"},{"name":"3 Institute for Genetics and Genomics in Geneva (iG3), University of Geneva, Geneva, Switzerland,"},{"name":"4 Swiss Institute of Bioinformatics, Geneva, Switzerland,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Donnelly","sequence":"additional","affiliation":[{"name":"9 Wellcome Trust Centre for Human Genetics and"},{"name":"10 Department of Statistics, University of Oxford, Oxford, UK and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark I.","family":"McCarthy","sequence":"additional","affiliation":[{"name":"9 Wellcome Trust Centre for Human Genetics and"},{"name":"11 Oxford Centre for Diabetes, Endocrinology and Metabolism, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel A.","family":"Rivas","sequence":"additional","affiliation":[{"name":"9 Wellcome Trust Centre for Human Genetics and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,3,27]]},"reference":[{"key":"2023051308484656500_btv074-B1","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1016\/j.cub.2008.09.044","article-title":"Global survey of genomic imprinting by transcriptome sequencing","volume":"18","author":"Babak","year":"2008","journal-title":"Curr. 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