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dc.contributor.advisorBajic, Vladimir B.
dc.contributor.authorAshoor, Haitham
dc.date.accessioned2011-07-24T07:51:56Z
dc.date.available2011-07-24T07:51:56Z
dc.date.issued2011-06
dc.identifier.doi10.25781/KAUST-D30U6
dc.identifier.urihttp://hdl.handle.net/10754/136689
dc.description.abstractThis thesis presents a computational methodology for ab-initio identification of transcription factor binding sites based on ChIP-seq data. This method consists of three main steps, namely ChIP-seq data processing, motif discovery and models selection. A novel method for ranking the models of motifs identified in this process is proposed. This method combines multiple factors in order to rank the provided candidate motifs. It combines the model coverage of the ChIP-seq fragments that contain motifs from which that model is built, the suitable background data made up of shuffled ChIP-seq fragments, and the p-value that resulted from evaluating the model on actual and background data. Two ChIP-seq datasets retrieved from ENCODE project are used to evaluate and demonstrate the ability of the method to predict correct TFBSs with high precision. The first dataset relates to neuron-restrictive silencer factor, NRSF, while the second one corresponds to growth-associated binding protein, GABP. The pipeline system shows high precision prediction for both datasets, as in both cases the top ranked motif closely resembles the known motifs for the respective transcription factors.
dc.language.isoen
dc.titlePipeline for the Analysis of ChIP-seq Data and New Motif Ranking Procedure
dc.typeThesis
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
thesis.degree.grantorKing Abdullah University of Science and Technology
dc.contributor.committeememberMoshkov, Mikhail
dc.contributor.committeememberZhang, Xiangliang
thesis.degree.disciplineComputer Science
thesis.degree.nameMaster of Science


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