000000157 001__ 157
000000157 005__ 20260410124443.0
000000157 0247_ $$2DOI$$a10.6083/M4PZ56RX
000000157 037__ $$aETD
000000157 245__ $$aA data cleaning and annotation framework for genome-wide studies
000000157 260__ $$bOregon Health and Science University
000000157 269__ $$a2007
000000157 336__ $$aThesis
000000157 502__ $$bM.S.
000000157 502__ $$gComputer Science & Electrical Engineering (sunsetting)
000000157 520__ $$aGenome-wide studies depend heavily on the quality and consistency of integrated annotation data from diverse computational and experimental sources. This thesis presents a generalized framework for detecting and managing discrepancies within and between annotation datasets by addressing biological identity, data relationships, source independence, and conflicts. The workflow identifies errors and either resolves or incorporates inconsistencies into downstream analyses. The framework’s utility is demonstrated through construction of a genome-wide mouse transcription factor binding map and classification of single nucleotide polymorphisms. We further examine the impact of annotation discrepancies on downstream analyses and discuss future extensions for biologically meaningful summarization of inconsistencies.
000000157 540__ $$fCC BY
000000157 542__ $$fIn copyright - single owner
000000157 650__ $$aGenomics$$033016
000000157 650__ $$aWorkflow$$038890
000000157 650__ $$aTranscription Factors
000000157 650__ $$aMice$$036842
000000157 650__ $$aPolymorphism, Single Nucleotide$$032570
000000157 650__ $$aComputational Biology$$031511
000000157 650__ $$aGenome-Wide Association Study$$038168
000000157 6531_ $$aannotations
000000157 6531_ $$abiological data source
000000157 6531_ $$adata cleaning
000000157 691__ $$aOGI School of Science and Engineering$$041365
000000157 692__ $$aDepartment of Computer Science and Engineering$$041405
000000157 7001_ $$aRamakrishnan, Ranjani$$uOregon Health and Science University$$041354
000000157 7201_ $$aMcWeeney, Shannon$$uOregon Health and Science University$$041354$$7Personal$$eAdvisor
000000157 8564_ $$99e2340f6-6a9c-4215-8f43-8de69b580775$$s550824$$uhttps://digitalcollections.ohsu.edu/record/157/files/157_etd.pdf$$ePublic$$29ef8a816adf8e0d1e8a8b3e420f27616$$31
000000157 901__ $$a<p>These documents are archival records. They are retained for historical reference only. </p><p><b>Need an accessible version? Use the ‘Get Accessible Copy’ link above.</b></p>
000000157 905__ $$a/rest/prod/vq/27/zn/41/vq27zn41g
000000157 909CO $$ooai:digitalcollections.ohsu.edu:157$$pstudent-work
000000157 956__ $$aGet Accessible Copy$$uhttps://ohsu.libwizard.com/f/requestaccessibledocument
000000157 980__ $$aTheses and Dissertations