Browsing by Subject "Pathway informatics"

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    Integrating biological pathways and genomic profiles with ChiBE 2
    (2013) Çakır, Merve
    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.
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    ItemOpen Access
    Integrating biological pathways and genomic profiles with ChiBE 2
    (BioMed Central Ltd., 2014) Babur, O.; Dogrusoz, U.; Çakır, M.; Aksoy, B. A.; Schultz, N.; Sander, C.; Demir, E.
    Background: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets.Results: ChiBE is a free, open-source software tool for visualizing, querying, and analyzing human biological pathways in BioPAX format. The recently released version 2 can search for neighborhoods, paths between molecules, and common regulators/targets of molecules, on large integrated cellular networks in the Pathway Commons database as well as in local BioPAX models. Resulting networks can be automatically laid out for visualization using a graphically rich, process-centric notation. Profiling data from the cBioPortal for Cancer Genomics and expression data from the Gene Expression Omnibus can be overlaid on these networks.Conclusions: ChiBE's new capabilities are organized around a genomics-oriented workflow and offer a unique comprehensive pathway analysis solution for genomics researchers. The software is freely available at http://code.google.com/p/chibe. © 2014 Babur et al.; licensee BioMed Central Ltd.