Pipeline for the Analysis of ChIP-seq Data and New Motif Ranking Procedure

Handle URI:
http://hdl.handle.net/10754/136689
Title:
Pipeline for the Analysis of ChIP-seq Data and New Motif Ranking Procedure
Authors:
Ashoor, Haitham
Abstract:
This 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.
Advisors:
Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Committee Member:
Moshkov, Mikhail ( 0000-0003-0085-9483 ) ; Zhang, Xiangliang ( 0000-0002-3574-5665 )
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Program:
Computer Science
Issue Date:
Jun-2011
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.authorAshoor, Haithamen
dc.date.accessioned2011-07-24T07:51:56Z-
dc.date.available2011-07-24T07:51:56Z-
dc.date.issued2011-06en
dc.identifier.urihttp://hdl.handle.net/10754/136689en
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.en
dc.language.isoenen
dc.titlePipeline for the Analysis of ChIP-seq Data and New Motif Ranking Procedureen
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.committeememberMoshkov, Mikhailen
dc.contributor.committeememberZhang, Xiangliangen
thesis.degree.disciplineComputer Scienceen
thesis.degree.nameMaster of Scienceen
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