Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Aug 3;15(1):642.
doi: 10.1186/1471-2164-15-642.

Integrating biological pathways and genomic profiles with ChiBE 2

Özgün Babur  1 , Ugur Dogrusoz, Merve Çakır, Bülent Arman Aksoy, Nikolaus Schultz, Chris Sander, Emek Demir
Affiliations

Integrating biological pathways and genomic profiles with ChiBE 2

Özgün Babur et al. BMC Genomics. .

Abstract

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
ChiBE data flow. Diagram showing the data flow between ChiBE and related resources.
Figure 2
Figure 2
Steps in sample use case 1. A) A reconstruction of the pathway published in the manuscript by the TCGA network [16]. In the original figure, alteration frequencies are shown for three subgroups of cases, but we merge these into one in this version. B) Dialog to retrieve alteration data from the cBioPortal. C) Paths from ERBB2 to KRAS in Pathway Commons, overlayed with alteration data of endometrial cancer from the cBioPortal. This diagram is part of the result that was automatically generated by ChiBE using the menu item "Query | Pathway Commons (Level 3) | Paths From To". D) Oncoprint of the related genes, generated by the cBioPortal. Genes from C are shown above the black line, and altered genes from A are shown under the black line.
Figure 3
Figure 3
Paths between frequently mutated genes. The paths-between query result, with alteration data overlaid.
Figure 4
Figure 4
Steps of sample use case 2. A) The reaction of interest in a separate view displaying compartments and detailed properties of GAB2. B) Oncoprint of altered genes, provided by the cBioPortal. C) The same reaction but this time expression data is overlaid on involved molecules.
Figure 5
Figure 5
ChiBE overview. ChiBE views are organized in canvasses, each displaying one or more BioPAX pathways in a graphically rich, interactive manner. In this example, an Interferon Gamma Signaling pathway is displayed in process description notation.
Figure 6
Figure 6
SIF views with ChiBE. A process diagram view (left) and its SIF view (right), showing controls-state-change relations.
Figure 7
Figure 7
Notation. Notation for process description diagrams in ChiBE.
See this image and copyright information in PMC

References

    1. Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, Leonardson A, Castellini LW, Wang S, Champy M-F, Zhang B, Emilsson V, Doss S, Ghazalpour A, Horvath S, Drake TA, Lusis AJ, Schadt EE. Variations in DNA elucidate molecular networks that cause disease. Nature. 2008;452(7186):429–435. - PMC - PubMed
    1. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, Mouy M, Steinthorsdottir V, Eiriksdottir GH, Bjornsdottir G, Reynisdottir I, Gudbjartsson D, Helgadottir A, Jonasdottir A, Jonasdottir A, Styrkarsdottir U, Gretarsdottir S, Magnusson KP, Stefansson H, Fossdal R, Kristjansson K, Gislason HG, Stefansson T, Leifsson BG, Thorsteinsdottir U, Lamb JR, et al. Genetics of gene expression and its effect on disease. Nature. 2008;452(7186):423–428. - PubMed
    1. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D’Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, et al. The biopax community standard for pathway data sharing. Nat Biotechnol. 2010;28(9):935–942. - PMC - PubMed
    1. Bader GD, Cary MP, Sander C. Pathguide: a pathway resource list. Nucleic Acids Res. 2006;34(suppl 1):504–506. - PMC - PubMed
    1. Diez D, Wheelock AM, Goto S, Haeggström JZ, Paulsson-Berne G, Hansson GK, Hedin U, Gabrielsen A, Wheelock CE. The use of network analyses for elucidating mechanisms in cardiovascular disease. Mol Biosyst. 2010;6(2):289–304. - PubMed

Publication types

LinkOut - more resources