On the performance of de novo pathway enrichment

Richa Batra, Nicolas Alcaraz, Kevin Gitzhofer, Josch Pauling, Henrik J. Ditzel, Marc Hellmuth, Jan Baumbach, Markus List

Research output: Contribution to journalArticlepeer-review

38 Scopus citations

Abstract

De novo pathway enrichment is a powerful approach to discover previously uncharacterized molecular mechanisms in addition to already known pathways. To achieve this, condition-specific functional modules are extracted from large interaction networks. Here, we give an overview of the state of the art and present the first framework for assessing the performance of existing methods. We identified 19 tools and selected seven representative candidates for a comparative analysis with more than 12,000 runs, spanning different biological networks, molecular profiles, and parameters. Our results show that none of the methods consistently outperforms the others. To mitigate this issue for biomedical researchers, we provide guidelines to choose the appropriate tool for a given dataset. Moreover, our framework is the first attempt for a quantitative evaluation of de novo methods, which will allow the bioinformatics community to objectively compare future tools against the state of the art.

Original languageEnglish
Article number6
Journalnpj Systems Biology and Applications
Volume3
Issue number1
DOIs
StatePublished - 1 Dec 2017
Externally publishedYes

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