Biyolojik yolakların ve genomik profillerin ChiBE 2 yoluyla entegrasyonu

Biological pathways store information about spatial and temporal organization of interactions taking place in an organism. 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. 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. There have been improvements in ChiBE regarding pathway searches, high throughput data integration, and database connections. Visual notation has been updated to follow standards in visualizations defined by the SBGN. 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. 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 to obtain information about genomic status of various cancer cells. 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.