{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T12:22:36Z","timestamp":1772626956488,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Translational control of gene expression has emerged as a major mechanism that regulates many biological processes and shows dysregulation in human diseases including cancer. When studying differential translation, levels of both actively translating mRNAs and total cytosolic mRNAs are obtained where the latter is used to correct for a possible contribution of differential cytosolic mRNA levels to the observed differential levels of actively translated mRNAs. We have recently shown that analysis of partial variance (APV) corrects for cytosolic mRNA levels more effectively than the commonly applied log ratio approach. APV provides a high degree of specificity and sensitivity for detecting biologically meaningful translation changes, especially when combined with a variance shrinkage method for estimating random error. Here we describe the anota (analysis of translational activity) R-package which implements APV, allows scrutiny of associated statistical assumptions and provides biologically motivated filters for analysis of genome wide datasets. Although the package was developed for analysis of differential translation in polysome microarray or ribosome-profiling datasets, any high-dimensional data that result in paired controls, such as RNP immunoprecipitation-microarray (RIP-CHIP) datasets, can be successfully analyzed with anota.<\/jats:p>\n               <jats:p>Availability: The anota Bioconductor package, www.bioconductor.org.<\/jats:p>\n               <jats:p>Contact: \u00a0ola.larsson@ki.se; robert.nadon@mcgill.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr146","type":"journal-article","created":{"date-parts":[[2011,3,22]],"date-time":"2011-03-22T02:35:42Z","timestamp":1300761342000},"page":"1440-1441","source":"Crossref","is-referenced-by-count":60,"title":["<i>anota<\/i>: analysis of differential translation in genome-wide studies"],"prefix":"10.1093","volume":"27","author":[{"given":"Ola","family":"Larsson","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, 2Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1 and 3McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nahum","family":"Sonenberg","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, 2Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1 and 3McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Nadon","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, 2Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1 and 3McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A4, Canada"},{"name":"1 Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, 2Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1 and 3McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,3,21]]},"reference":[{"key":"2023012511023613800_B1","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"2023012511023613800_B2","doi-asserted-by":"crossref","first-page":"77","DOI":"10.5661\/bger-25-77","article-title":"Gene expression - time to change point of view?","volume":"25","author":"Larsson","year":"2008","journal-title":"Biotechnol. Genet. Eng. Rev."},{"key":"2023012511023613800_B3","doi-asserted-by":"crossref","first-page":"21487","DOI":"10.1073\/pnas.1006821107","article-title":"Identification of differential translation in genome wide studies","volume":"107","author":"Larsson","year":"2010","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511023613800_B4","volume-title":"Translational Control in Biology and Medicine.","author":"Mathews","year":"2007"},{"key":"2023012511023613800_B5","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1038\/nrc2824","article-title":"Translational control in cancer","volume":"10","author":"Silvera","year":"2010","journal-title":"Nat. Rev. Cancer"},{"key":"2023012511023613800_B6","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1016\/j.cell.2009.01.042","article-title":"Regulation of translation initiation in eukaryotes: mechanisms and biological targets","volume":"136","author":"Sonenberg","year":"2009","journal-title":"Cell"},{"key":"2023012511023613800_B7","doi-asserted-by":"crossref","first-page":"2448","DOI":"10.1093\/bioinformatics\/btg345","article-title":"A random variance model for detection of differential gene expression in small microarray experiments","volume":"19","author":"Wright","year":"2003","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/10\/1440\/48861085\/bioinformatics_27_10_1440.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/10\/1440\/48861085\/bioinformatics_27_10_1440.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:08:17Z","timestamp":1674644897000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/10\/1440\/259940"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,3,21]]},"references-count":7,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2011,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr146","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,5,15]]},"published":{"date-parts":[[2011,3,21]]}}}