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REACTOMEgsa

Extending the REACTOME Pathway Database for multi-omics biomedical data analysis

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

REACTOMEgsa project word cloud

Explore the words cloud of the REACTOMEgsa project. It provides you a very rough idea of what is the project "REACTOMEgsa" about.

form replace group doctor gained throughput basis bottleneck biology technologies clinical attributed successful career popular stringent algorithms additional web communication sophisticated amounts version datasets biomedical omics envisaged bioinformatician existence resource transcriptomics skills prime samples big phenotype unprecedented proteomics despite supporting rely correlated start gene metabolomics microarray powerful interpretation scientific biological derive simplistic incorporate manual expression peer curation extend extended interdisciplinary ora reactome completion interface techniques data representation model medical anticipate integrate me ideal precision foundation regulated medicine review platform

Project "REACTOMEgsa" data sheet

The following table provides information about the project.

Coordinator	EUROPEAN MOLECULAR BIOLOGY LABORATORY Organization address address: Meyerhofstrasse 1 city: HEIDELBERG postcode: 69117 website: http://www.embl.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Germany [DE]
Project website	https://reactome.github.io/ReactomeGSA
Total cost	97˙727 €
EC max contribution	97˙727 € (100%)
Programme	1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
Code Call	H2020-MSCA-IF-2017
Funding Scheme	MSCA-IF-EF-ST
Starting year	2018
Duration (year-month-day)	from 2018-08-01 to 2019-07-31

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	EUROPEAN MOLECULAR BIOLOGY LABORATORY EUROPEAN MOLECULAR BIOLOGY LABORATORY Organization address address: Meyerhofstrasse 1 city: HEIDELBERG postcode: 69117 website: http://www.embl.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (HEIDELBERG)	coordinator	97˙727.00

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Project objective

The increasing availability of high-throughput ‘omics technologies results in unprecedented opportunities for precision medicine and biomedical research. With the increasing availability of large amounts of data (‘big data’), data analysis and interpretation have become a major bottleneck.

Pathway analysis techniques are used to incorporate existing biological knowledge into the data analysis and allow researchers to focus on the interpretation of regulated biological processes. Despite the existence of many advanced pathway analysis algorithms, most leading pathway analysis resources still rely on simplistic ‘gene set over representation’ analyses (ORA) and cannot integrate data from different ‘omics approaches. Reactome is one of the most popular resources for pathway information. Its open-access data model, powerful web interface, and stringent manual curation and peer-review provide an ideal foundation for this project’s developments.

In this project, I will extend Reactome towards an analysis platform for multi-omics biomedical studies. I will replace its current ORA approach with more sophisticated pathway algorithms supporting transcriptomics, microarray, proteomics, and metabolomics data. Next, I will extend Reactome to analyse datasets of samples that cannot be attributed to a phenotype. The extended version of Reactome will be able to derive one expression value per pathway which can then be correlated with clinical parameters to identify clinical relevant biological processes. This will make Reactome a prime resource for multi-omics biomedical studies. I anticipate that the successful completion of this project will allow me to integrate and extend my current skills as a medical doctor and a bioinformatician towards systems biology studies. The additional gained experience in project management and communication of scientific results will form the basis for my envisaged career to start my own interdisciplinary biomedical research group.

Publications

List of publications.
year	authors and title	journal	last update
2019	Johannes Griss, Wolfgang Bauer, Christine Wagner, Martin Simon, Minyi Chen, Katharina Grabmeier-Pfistershammer, Margarita Maurer-Granofszky, Florian Roka, Thomas Penz, Christoph Bock, Gao Zhang, Meenhard Herlyn, Katharina Glatz, Heinz LÃ¤ubli, Kirsten D. Mertz, Peter Petzelbauer, Thomas Wiesner, Markus Hartl, Winfried F. Pickl, Rajasekharan Somasundaram, Peter Steinberger, Stephan N. Wagner B cells sustain inflammation and predict response to immune checkpoint blockade in human melanoma published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-019-12160-2	Nature Communications 10/1	2020-01-22
2019	Johannes Griss, Goran Vinterhalter, Veit SchwÃ¤mmle IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments published pages: 1751-1759, ISSN: 1535-3893, DOI: 10.1021/acs.jproteome.8b00968	Journal of Proteome Research 18/4	2020-01-22
2019	Johannes Griss, Florian Stanek, Otto Hudecz, Gerhard DÃ¼rnberger, Yasset Perez-Riverol, Juan Antonio VizcaÃno, Karl Mechtler Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins published pages: 1477-1485, ISSN: 1535-3893, DOI: 10.1021/acs.jproteome.8b00377	Journal of Proteome Research 18/4	2020-01-22

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The information about "REACTOMEGSA" are provided by the European Opendata Portal: CORDIS opendata.