Reactome Pathways Portal

Reactome is a free, open-source, curated and peer-
reviewed knowledge-base of biomolecular pathways.
Its aim is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education.

1. Pathways Portal

Diagram Viewer | Pathways Overview
Analysis Service | Developer’s Zone
Antonio Fabregat Mundo
Senior Software Engineer
European Bioinformatics Institute
[email protected]

February 22, 2016

2. Introduction
• Reactome is a free, open-source, curated and peer-
reviewed knowledge-base of biomolecular pathways.
• Its aim is to provide intuitive bioinformatics tools for the
visualization, interpretation and analysis of pathway
knowledge to support basic research, genome analysis,
modelling, systems biology and education.

3. Introduction
• Reactome has grown to include entries for 8,701 human
genes reaching 43% of the 20,296 predicted human protein-
coding genes and 9,052 reactions annotated based on 20,708
literature references.
• Aiming to improve the user experience in terms of usability,
responsiveness and data visualisation, all major
components of the Reactome web interface have been re-
designed and re-implemented.

4. Pathways Overview
Pathways:
• Organised hierarchically.
• Grouping detailed pathways like translation, protein folding, and post-
translational modification into larger domains of biological function like
protein metabolism.

5. Pathways Overview
• Provides a bird’s-eye view of all Reactome pathways.
• Highlights parent-child relationships.
• Shares conserved modular processes between pathways.
• Constitutes an entry point to Reactome’s progressively increasing content.

6. Pathway Diagram Viewer
Features:
• Fast loading times for a more responsive and interactive user experience.
• Visual feedback for common user actions (e.g. hovering and focusing).
• Smooth zooming or selection transitions and efficient navigation and searching.
• The amount of detail displayed depends on the level of zoom.

7. Pathway Diagram Viewer - MI Overlay
• Molecular Interactions Overlay
• Interaction data:
• IntAct (static) à processed during release and stored locally.
• PSICQUIC à retrieved on demand on user request.
• Loading times improved to achieve a more responsive and
interactive user experience.
• Included an option to easily filter the displayed interactors by
confidence score.
• The interactors data has been included into the diagram search
feature, as well as in the Reactome main search.
• Protein and chemical structures displayed for closer views.
• Layout kept within the session per diagram and resource.

8. Pathway Diagram Viewer - MI Overlay
• Molecular Interactions Overlay
Interacts with itself
Interacts with another protein present in the diagram
Interacts with another protein
Number of interactors
for the selected Resource
Selected Resource

9. Pathway Diagram Viewer - MI Overlay
PCH2 is not present in Reactome but the
main search provides the list of proteins
present in Reactome which interacts with it.
e.g. PARK2 (from the previous slide)

10. Pathway Diagram Viewer
Zoomed-out view
• Subpathway shades
• No text in the glyphs
• No trivial molecules displayed
Close view
• No Shades
• Text is placed in the glyphs
• Trivial molecules and interactors summary items appear
Closer view
• Stoichiometry shown
• Node attachments appear
• Interactors show gene name or chemical name
Zoomed-in view
• Interactors show structures and protein details
• Diagram proteins and chemicals show extra info

11. Pathway Browser
It has been updated to feature
• Re-designed user interface with a clean and colour consistent look & feel.
• Tight integration among its visual components.

12. Pathway Analysis Module
• The analysis module generates detailed results for genome-wide
expression datasets with more than 20.000 identifiers in less that 3
seconds.
• Users can submit their datasets through the analysis submission
interface integrated in the pathway browser.
http://www.reactome.org/PathwayBrowser/#/TOOL=AT
• Pathway analysis is accessible via a web service, which allows the
use of the Reactome server for batch analysis of user datasets.
http://www.reactome.org/AnalysisService/

13. Pathway Analysis Module
• Analysis results are now better displayed by both the pathways
overview and the diagram viewer modules.

14. Short introduction demo

15. Developer’s Zone
• Third parties can integrate the presented tools
http://www.reactome.org/pages/documentation/developer-guide/

16. Third parties integrating Reactome #1
• BLUEPRINT is a high
impact FP7 project aiming to
produce a blueprint of
haemopoetic epigenomes.


• Integrates the Analysis
Service providing a button to
perform a pathway analysis
and show the results in
Reactome.

17. Third parties integrating Reactome #2
• The PRIDE database is a
centralized, standards
compliant, public data
repository for proteomics
data.

• Integrates the Analysis
Service providing a button to
perform a pathway analysis
and show the results in
Reactome.

18. Third parties integrating Reactome #3
• Chemical Entities of
Biological Interest (ChEBI) is
a freely available dictionary
of molecular entities focused
on ‘small’ chemical
compounds.

• Integrates the diagram
viewer to visualise the target
reactions in the context of
Reactome pathways.

19. Third parties integrating Reactome #4
• CTTV aims to provide evidence
on the biological validity of
therapeutic targets and provide
an initial assessment of the
likely effectiveness of
pharmacological intervention
on these targets, using
genome-scale experiments and
analysis.

• Integrates the diagram viewer
to visualise the target
Reactome pathways.

20. Acknowledgments
• Henning Hermjakob, EBI (UK)
• Kostas Sidiropoulos, EBI
• Guilherme Viteri, EBI
• Florian Korninger, EBI
• Reactome Curators
• Lincoln Stein, OICR (Canada)
• Peter D’Eustachio, NYU (USA)
• Guanming Wu, OICR
• Steve Jupe, EBI
• Phani Garapati, EBI
• Bijay Jassal, OICR
• Funders:
• NIH BD2K Center of Excellence
UCLA Grant number 1U54GM114833-01, NHLBI
Proteomics Center Award HHSN268201000035C
• Centre for Therapeutic Target
Validation (CTTV)
• EMBL core funding

21. Thank you very much