dc.contributor.advisor | Doğrusöz, Uğur | |
dc.contributor.author | Çakır, Merve | |
dc.date.accessioned | 2016-01-08T20:05:57Z | |
dc.date.available | 2016-01-08T20:05:57Z | |
dc.date.issued | 2013 | |
dc.identifier.uri | http://hdl.handle.net/11693/17061 | |
dc.description | Ankara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent Univ., 2013. | en_US |
dc.description | Thesis (Master's) -- Bilkent University, 2013. | en_US |
dc.description | Includes bibliographical references leaves 78-83. | en_US |
dc.description.abstract | Biological 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.statementofresponsibility | Çakır, Merve | en_US |
dc.format.extent | xiv, 83 leaves, illustrations | en_US |
dc.language.iso | English | en_US |
dc.rights | info:eu-repo/semantics/openAccess | en_US |
dc.subject | Computational biology | en_US |
dc.subject | Bioinformatics | en_US |
dc.subject | Pathway informatics | en_US |
dc.subject | Pathway visualization | en_US |
dc.subject | Genomics | en_US |
dc.subject.lcc | QH324.2 .C35 2013 | en_US |
dc.subject.lcsh | Bioinformatics. | en_US |
dc.subject.lcsh | Computational biology. | en_US |
dc.subject.lcsh | Visualization. | en_US |
dc.subject.lcsh | Computer graphics. | en_US |
dc.subject.lcsh | Genomics. | en_US |
dc.title | Integrating biological pathways and genomic profiles with ChiBE 2 | en_US |
dc.type | Thesis | en_US |
dc.department | Department of Computer Engineering | en_US |
dc.publisher | Bilkent University | en_US |
dc.description.degree | M.S. | en_US |
dc.identifier.itemid | B147820 | |