000000675 001__ 675 000000675 005__ 20250424232539.0 000000675 0247_ $$2DOI$$a10.6083/M4NC5Z6P 000000675 037__ $$aETD 000000675 245__ $$aAn evaluation of the extensibility and application of occupancy prediction of transcription factor binding sites 000000675 260__ $$bOregon Health and Science University 000000675 269__ $$a2010 000000675 336__ $$aDissertation 000000675 502__ $$bPh.D. 000000675 520__ $$aIdentification of biologically relevant high-occupancy transcription factor binding sites (TFBS) in silico has historically been a difficult problem with a high error rate. Methods that utilize information in addition to the sequence of binding sites (e.g. chromatin information) have been shown to improve performance over strictly sequence-based methods; however, several questions about such methods remain unanswered: whether such models are suitable for multiple transcription factors, whether a general model or generalizable approach to the problem is possible, and what the effect of such prediction on biological inference is. In this work, we construct and evaluate several classifiers of position weight matrix-predicted TFBS (“occupancy classifiers”) based on four distinct transcription factors and demonstrate that such classifiers identify biochemically confirmed high--occupancy sites at a high rate. 000000675 540__ $$fCC BY 000000675 542__ $$fIn copyright - single owner 000000675 650__ $$aArtificial Intelligence$$015109 000000675 650__ $$aNeoplasms$$022758 000000675 650__ $$aComputational Biology$$031511 000000675 650__ $$aTranscription Factors$$027255 000000675 650__ $$aEpigenesis, Genetic$$035405 000000675 650__ $$aBinding Sites$$015545 000000675 6531_ $$acancer 000000675 691__ $$aSchool of Medicine$$041369 000000675 692__ $$aDepartment of Medical Informatics and Clinical Epidemiology$$041422 000000675 7001_ $$aWright, Hollis$$uOregon Health and Science University$$041354 000000675 7201_ $$aMcWeeney, Shannon$$uOregon Health and Science University$$041354$$7Personal$$eAdvisor$$eCommittee chair 000000675 8564_ $$98f288d66-69a5-4d01-9b6d-a063a94b4fd9$$s900117$$uhttps://digitalcollections.ohsu.edu/record/675/files/676_etd.pdf$$ePublic$$2576dc2b06551f4bd9f686949f0e4a827$$31 000000675 905__ $$a/rest/prod/6m/31/1p/33/6m311p33r 000000675 909CO $$ooai:digitalcollections.ohsu.edu:675$$pstudent-work 000000675 980__ $$aBiomedical Informatics