Integrating biological pathways and genomic profiles with ChiBE 2

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buir.advisorDoğrusöz, Uğur
dc.contributor.authorÇakır, Merve
dc.date.accessioned2016-01-08T20:05:57Z
dc.date.available2016-01-08T20:05:57Z
dc.date.issued2013
dc.descriptionAnkara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent Univ., 2013.en_US
dc.descriptionThesis (Master's) -- Bilkent University, 2013.en_US
dc.descriptionIncludes bibliographical references leaves 78-83.en_US
dc.description.abstractBiological pathways store information about spatial and temporal organization of interactions taking place in an organism. They hold valuable information that can assist scientific community in understanding the details of a particular mechanism or deciphering the reasons of disruption when the system goes wrong. However, extracting knowledge from these pathways is not trivial as they can be huge and complicated. Additionally, simple visualization of pathways will only reveal limited knowledge, whereas their integration with experimental results can identify distinct and intriguing relationships. Therefore, it is critical to have tools that are specialized in analyzing and understanding biological pathways. ChiBE is one such tool that can visualize, manipulate and analyze pathway data stored in BioPAX format. While preparing the second version of the tool, there have been improvements regarding pathway searches, high throughput data integration, and database connections. Visual notation has also been updated in order to follow standards in visualizations defined by the SBGN community. Previously defined pathway query algorithms have been adapted to be compatible with the BioPAX model. New query types have also been designed to offer a wider range of options. With these queries, ChiBE now offers a variety of ways of pathway decomposition and thorough analysis of complex pathway views. There has also been improvements in integration of high throughput experimental results. To offer easy access to expression microarrays, a gateway to the GEO database has been added. The cBio Cancer Genomics Portal is also now reachable within ChiBE in order to obtain information about genomic status of various cancer cells. After simply asking for an identifier of a particular experiment, ChiBE retrieves the results from databases and then integrates them with the available pathway view through color codes. Furthermore, a connection to DAVID database is available, in case users want to annotate a list of genes with respect to biological terms associated with them. With these new features and improvements, ChiBE 2 has become a comprehensive tool that offers a wide range of analysis options with a genomics-oriented workflow to deepen our understanding of biological pathways.en_US
dc.description.provenanceMade available in DSpace on 2016-01-08T20:05:57Z (GMT). No. of bitstreams: 1 0007034.pdf: 3308951 bytes, checksum: 333269500ab574c2b0819d4fc1bcca1e (MD5)en
dc.description.statementofresponsibilityÇakır, Merveen_US
dc.format.extentxiv, 83 leaves, illustrationsen_US
dc.identifier.itemidB147820
dc.identifier.urihttp://hdl.handle.net/11693/17061
dc.language.isoEnglishen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectComputational biologyen_US
dc.subjectBioinformaticsen_US
dc.subjectPathway informaticsen_US
dc.subjectPathway visualizationen_US
dc.subjectGenomicsen_US
dc.subject.lccQH324.2 .C35 2013en_US
dc.subject.lcshBioinformatics.en_US
dc.subject.lcshComputational biology.en_US
dc.subject.lcshVisualization.en_US
dc.subject.lcshComputer graphics.en_US
dc.subject.lcshGenomics.en_US
dc.titleIntegrating biological pathways and genomic profiles with ChiBE 2en_US
dc.typeThesisen_US
thesis.degree.disciplineComputer Engineering
thesis.degree.grantorBilkent University
thesis.degree.levelMaster's
thesis.degree.nameMS (Master of Science)

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