Comparison of Transcription Factor Binding Site Models

Handle URI:
http://hdl.handle.net/10754/244613
Title:
Comparison of Transcription Factor Binding Site Models
Authors:
Bhuyan, Sharifulislam
Abstract:
Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.
Advisors:
Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Committee Member:
Gao, Xin ( 0000-0002-7108-3574 ) ; Zhang, Xiangliang ( 0000-0002-3574-5665 )
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Program:
Computer Science
Issue Date:
May-2012
Type:
Thesis
Appears in Collections:
Theses; Computer Science Program; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.advisorBajic, Vladimir B.en
dc.contributor.authorBhuyan, Sharifulislamen
dc.date.accessioned2012-09-18T09:11:45Z-
dc.date.available2012-09-18T09:11:45Z-
dc.date.issued2012-05en
dc.identifier.urihttp://hdl.handle.net/10754/244613en
dc.description.abstractModeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.en
dc.language.isoenen
dc.titleComparison of Transcription Factor Binding Site Modelsen
dc.typeThesisen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberGao, Xinen
dc.contributor.committeememberZhang, Xiangliangen
thesis.degree.disciplineComputer Scienceen
thesis.degree.nameMaster of Scienceen
dc.person.id113311en
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