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RAMONA: A web application for gene set analysis on multilevel omics data.
Bioinformatics 31, 128-130 (2015)
SUMMARY: Decreasing costs of modern high-throughput experiments allow for the simultaneous analysis of altered gene activity on various molecular levels. However, these multi-omics approaches lead to a large amount of data which is hard to interpret for a non-bioinformatician. Here, we present the remotely accessible multilevel ontology analysis (RAMONA). It offers an easy-to-use interface for the simultaneous gene set analysis of combined omics datasets and is an extension of the previously introduced MONA approach. RAMONA is based on a Bayesian enrichment method for the inference of overrepresented biological processes among given gene sets. Overrepresentation is quantified by interpretable term probabilities. It is able to handle data from various molecular levels, while in parallel coping with redundancies arising from gene set overlaps and related multiple testing problems. The comprehensive output of RAMONA is easy to interpret and thus allows for functional insight into the affected biological processes. With RAMONA, we provide an efficient implementation of the Bayesian inference problem such that ontologies consisting of thousands of terms can be processed in the order of seconds. Availability and Implementation: RAMONA is implemented as ASP.NET web application and publicly available at http://icb.helmholtz-muenchen.de/ramona. CONTACT: steffen.sass@helmholtz-muenchen.de.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Ontology; Biology
ISSN (print) / ISBN
1367-4803
Journal
Bioinformatics
Quellenangaben
Volume: 31,
Issue: 1,
Pages: 128-130
Publisher
Oxford University Press
Publishing Place
Oxford
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Computational Biology (ICB)