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. 2017 Nov 1;33(21):3461-3467.
doi: 10.1093/bioinformatics/btx441.

Reactome enhanced pathway visualization

Konstantinos Sidiropoulos  1 , Guilherme Viteri  1 , Cristoffer Sevilla  1 , Steve Jupe  1 , Marissa Webber  2 , Marija Orlic-Milacic  2 , Bijay Jassal  2 , Bruce May  2 , Veronica Shamovsky  3 , Corina Duenas  1 , Karen Rothfels  2 , Lisa Matthews  3 , Heeyeon Song  2 , Lincoln Stein  2   4 , Robin Haw  2 , Peter D'Eustachio  3 , Peipei Ping  5 , Henning Hermjakob  6   7 , Antonio Fabregat  6   8
Affiliations

Reactome enhanced pathway visualization

Konstantinos Sidiropoulos et al. Bioinformatics. .

Abstract

Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications.

Results: For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like 'mitochondrion' or 'receptor' are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects.

Availability and implementation: http://reactome.org.

Contact: [email protected] or [email protected].

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Reactome’s previous approach to scalable visualization (a) Pathways overview (b) HLDs were shown as a set of green boxes (c) Static images of biological processes illustrations were provided for some of the diagrams (d) SBGN-compliant diagrams containing molecular details of a reaction sequence
Fig. 2.
Fig. 2.
Different levels of visualization address different scenarios. The top row shows navigation from the entirety of reaction space to focus on Cell Cycle. The middle row presents EHLDs displaying successively narrower aspects of the cell cycle process. The bottom row presents navigation down to molecular details of individual reactions involved in mitotic prophase, and the optional export of this view to Microsoft PowerPoint
Fig. 3.
Fig. 3.
Correspondence between the hierarchy and EHLD. (a) Pathway hierarchy view for Haemostasis. (b) Haemostasis as an EHLD representation. (c) Haemostasis EHLD overlaid with pathway enrichment analysis results. The width of the yellow bar under the pathway label indicates the proportion of pathway entities contained in the analysed dataset. (d) A closer view to ‘Platelet Homeostasis’ label with analysis results overlaid. http://reactome.org/PathwayBrowser/#/R-HSA-109582
Fig. 4.
Fig. 4.
Example of different elements provided in the iconography library. http://reactome.org/icon-lib
Fig. 5.
Fig. 5.
Pathway diagram for Gene silencing by RNA. (a) As it was displayed prior to the inclusion of the subpathways highlighting. (b) After adding the feature of highlighting the existing subpathways in the zoomed-out view (where the text in the entity icons is also omitted). http://reactome.org/PathwayBrowser/#/R-HSA-211000
Fig. 6.
Fig. 6.
The pathway diagram for Striated Muscle Contraction exported to Microsoft PowerPoint. (http://reactome.org/PathwayBrowser/#/R-HSA-390522)
See this image and copyright information in PMC

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References

    1. Ashburner M. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25–29. - PMC - PubMed
    1. Battiato S. et al. (2005) SVG rendering for Internet imaging In: Proceedings of the Seventh International Workshop on Computer Architecture for Machine Perception, CAMP'05, July 04-06, 2005, Palermo, Italy, pp. 333–338
    1. Cerami E.G. et al. (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res., 39, D685–D690. - PMC - PubMed
    1. Fabregat A. et al. (2016) The Reactome pathway Knowledgebase. Nucleic. Acids. Res, 44, D481–D487. - PMC - PubMed
    1. Gawron P. et al. (2016) MINERVA – a platform for visualisation and curation of molecular interaction networks. Syst. Biol. Appl., 2, 16020. - PMC - PubMed