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dc.contributor.advisorChristopher Burge.en_US
dc.contributor.authorRothman, Craig Jeremyen_US
dc.contributor.otherMassachusetts Institute of Technology. Biological Engineering Division.en_US
dc.date.accessioned2008-01-10T16:01:20Z
dc.date.available2008-01-10T16:01:20Z
dc.date.copyright2007en_US
dc.date.issued2007en_US
dc.identifier.urihttp://hdl.handle.net/1721.1/39920
dc.descriptionThesis (M. Eng.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007.en_US
dc.descriptionIncludes bibliographical references (p. 53-57).en_US
dc.description.abstractAlternative splicing is involved in numerous cellular functions and is often disrupted and involved in disease. Previous research has identified methods to distinguish alternative conserved exons (ACEs) in human and mouse. However, the cellular machinery, the spliceosome, does not use comparative genomics to decide when to include and when to exclude an exon. Human RefSeq exons obtained from the University of California Santa Cruz (UCSC) genome browser were analyzed for tissue-specific skipping. Expressed sequence tags (ESTs) were aligned to exons and their tissue of origin and histology were identified. ACEs were also identified as a subset of the skipped exons. About 18% of the exons were identified as tissue-specifically skipped in one of sixteen different tissues at four stringency levels. The different datasets were analyzed for both general features such as exon and intron length, splice site strength, base composition, conservation, modularity, and susceptibility to nonsense-mediated mRNA decay caused by skipping. Cis-element motifs that might bind protein factors that affect splicing were identified using overrepresentation analysis and conserved occurrence rate between human and mouse.en_US
dc.description.abstract(cont.) Tissue-specific skipped exons were then classified with both a decision-tree based classifier (Random ForestsTM) and a support vector machine. Classification results were better for tissue-specific skipped exons vs. constitutive exons than for tissue-specific skipped exons vs. exons skipped in other tissues.en_US
dc.description.statementofresponsibilityby Craig Jeremy Rothman.en_US
dc.format.extent57 p.en_US
dc.language.isoengen_US
dc.publisherMassachusetts Institute of Technologyen_US
dc.rightsMIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided.en_US
dc.rights.urihttp://dspace.mit.edu/handle/1721.1/7582
dc.subjectBiological Engineering Division.en_US
dc.titleTissue-specific classification of alternatively spliced human exonsen_US
dc.typeThesisen_US
dc.description.degreeM.Eng.en_US
dc.contributor.departmentMassachusetts Institute of Technology. Biological Engineering Division.en_US
dc.identifier.oclc182622079en_US


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