Bilkent University
Department of Computer Engineering
MS Thesis Presentation


Integrating biological pathways and genomic profiles with ChiBE 2


Merve Çakır
MS Student
Computer Engineering Department
Bilkent University

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 graph searches, high throughput data integration and database connections. Visual notation has also been updated in order to follow standards in visualizations defined by SBGN community.

Previously defined graph query algorithms have been adapted to be compatible with BioPAX structure. New query approaches 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 GEO database has been added. 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 updates, ChiBE 2 has become a comprehensive tool that offers a wide range of analysis options with a genomics-oriented workflow in order to deepen our understanding of biological pathways.


DATE: 26 July, 2013, Friday @ 11:00