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dc.contributor.advisorMarth L. Bulyk.en_US
dc.contributor.authorHe, Fangxueen_US
dc.contributor.otherHarvard University--MIT Division of Health Sciences and Technology.en_US
dc.date.accessioned2006-06-19T17:38:52Z
dc.date.available2006-06-19T17:38:52Z
dc.date.copyright2005en_US
dc.date.issued2005en_US
dc.identifier.urihttp://hdl.handle.net/1721.1/33081
dc.descriptionThesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2005.en_US
dc.descriptionIncludes bibliographical references (leaves 55-57).en_US
dc.description.abstractRegulation of gene expression occurs largely through the binding of sequence- specific transcription factors (TFs) to genomic DNA binding sites (BSs). This thesis presents a rigorous scoring scheme, implemented as a C program termed "ModuleFinder", that evaluates the likelihood that a given genomic region is a cis regulatory module (CRM) for an input set of TFs according to its degree of: (1) homotypic site clustering; (2) heterotypic site clustering; and (3) evolutionary conservation across multiple genomes. Importantly, ModuleFinder obtains all parameters needed to appropriately weight the relative contributions of these sequence features directly from the input sequences and TFBS motifs, and does not need to first be trained. Using two previously described collections of experimentally verified CRMs in mammals as validation datasets, we show that ModuleFinder is able to identify CRMs with great sensitivity and specificity. We also evaluated ModuleFinder on a set of DNA binding site data for the human TFs Hepatocyte Nuclear Factor HNF1 [alpha], HNF4 [alpha] and HNF6 and compared its performance with logistic regression and neural network models.en_US
dc.description.statementofresponsibilityby Fangxue He.en_US
dc.format.extent57 leavesen_US
dc.format.extent2423925 bytes
dc.format.extent2425194 bytes
dc.format.mimetypeapplication/pdf
dc.format.mimetypeapplication/pdf
dc.language.isoengen_US
dc.publisherMassachusetts Institute of Technologyen_US
dc.rightsM.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.en_US
dc.rights.urihttp://dspace.mit.edu/handle/1721.1/7582
dc.subjectHarvard University--MIT Division of Health Sciences and Technology.en_US
dc.titleModuleFinder : a computational model for the identification of Cis regulatory modulesen_US
dc.title.alternativeModule Finder : a computational model for the identification of Cis regulatory modulesen_US
dc.typeThesisen_US
dc.description.degreeS.M.en_US
dc.contributor.departmentHarvard University--MIT Division of Health Sciences and Technology.en_US
dc.identifier.oclc62171687en_US


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