{"id":2588,"date":"2013-01-05T20:27:21","date_gmt":"2013-01-05T20:27:21","guid":{"rendered":"http:\/\/www.cytognomix.com\/?p=2588"},"modified":"2025-12-01T22:41:06","modified_gmt":"2025-12-01T22:41:06","slug":"2588","status":"publish","type":"post","link":"https:\/\/www.cytognomix.com\/?p=2588","title":{"rendered":"January 4, 2013. Paper: “Predicting mRNA transcript isoforms derived from splicing mutations”, ASSEDA server"},"content":{"rendered":"

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guaranteed lendingfast cash online payday loans<\/a><\/div>\n
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Volume 34, Issue 4<\/p><\/div>\n

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\u201cPrediction of mutant mRNA splice isoforms by information theory-based exon definition,\u201d<\/strong> by Eliseos Mucaki, Ben Shirley and Peter Rogan has been accepted for publication by the journal Human Mutation.<\/span><\/span><\/p>\n

Abstract<\/em>.\u00a0 Mutations that affect mRNA splicing often produce multiple mRNA isoforms, resulting in complex molecular phenotypes. Definition of an exon and its inclusion in mature mRNA relies on joint recognition of both acceptor and donor splice sites. This study predicts cryptic and exon skipping isoforms in mRNA produced by splicing mutations from the combined information contents (Ri<\/sub>, which measures binding site affinity) and distribution of the splice sites defining these exons. The total information content of an exon (Ri,total<\/sub>) is the sum of the Ri<\/sub> values of its acceptor and donor splice sites, adjusted for the distance separating these sites, ie. the gap surprisal. Differences between total exon information contents (\u0394Ri,total<\/sub>) are predictive of the relative abundance of these exons in distinct processed mRNAs. Constraints on splice site and exon selection are used to eliminate non-conforming and poorly expressed isoforms. Molecular phenotypes are computed by the Automated Splice Site and Exon Definition Analysis server (ASSEDA; http:\/\/splice.uwo.ca). <\/em>Predictions of splicing mutations were highly concordant (85.2%; n=61) with published expression data. In silico<\/em> exon definition analysis will contribute to streamlining assessment of abnormal and normal splice isoforms resulting from mutations.<\/p>\n

Update: The paper is now available online from the Journal website: DOI:\u00a010.1002\/humu.22277 and is cited on PubMed<\/a>.<\/p>\n

Update 2: John Mucaki has produced a Video Tutorial on using the ASSEDA server on YouTube.<\/p>\n

Update 3: \u00a0The accepted paper has now been copyedited, \u00a0typeset and published online: \u00a0http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/humu.22277\/abstract. Supplementary data are available as well. \u00a0(2-21-2013)<\/p>\n

Update 4: \u00a0Annual subscriptions<\/a> to the Automated Splice Site and Exon Definition server are available through Cytognomix \u00a0(2-22-2013).<\/p>\n

Update 5: The paper has been highlighted in the April 2013 issue of the Journal, where it appeared. \u00a0Bing Yu, University of Sydney, authored the commentary (Vol\u00a034[4], page v).<\/p>\n

Update 6:\u00a0\u00a0Mucaki EJ., Shirley BC, and Rogan PK. Prediction of Mutant mRNA Splice Isoforms by Information Theory-Based Exon Definition has been published in print. Human Mutation, April 2013, Volume 34 (4), pages 557\u2013565. The\u00a0journal has made the paper FREE for anyone to download. <\/em><\/p>\n","protected":false},"excerpt":{"rendered":"

guaranteed lendingfast cash online payday loans \u201cPrediction of mutant mRNA splice isoforms by information theory-based exon definition,\u201d by Eliseos Mucaki, Ben Shirley and Peter Rogan has been accepted for publication by the journal Human Mutation. Abstract.\u00a0 Mutations that affect mRNA splicing often produce multiple mRNA isoforms, resulting in complex molecular phenotypes. Definition of an exon […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[142],"tags":[120,127,130,129,122,131,128,125,106,133],"_links":{"self":[{"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/posts\/2588"}],"collection":[{"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2588"}],"version-history":[{"count":26,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/posts\/2588\/revisions"}],"predecessor-version":[{"id":5182,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/posts\/2588\/revisions\/5182"}],"wp:attachment":[{"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2588"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2588"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2588"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}