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PheNetic: Network-based interpretation of unstructured gene lists in E. coli
Center of Microbial and Plant Genetics, Leuven, Belgium .
Department of Computer Science, Katholieke Universiteit Leuven, Heverlee, Belgium.
Center of Microbial and Plant Genetics, Leuven, Belgium .
Department of Computer Science, Katholieke Universiteit Leuven, Heverlee, Belgium.ORCID iD: 0000-0002-6860-6303
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2013 (English)In: Molecular Biosystems, ISSN 1742-206X, E-ISSN 1742-2051, Vol. 9, no 7, p. 1594-1603Article in journal (Refereed) Published
Abstract [en]

At the present time, omics experiments are commonly used in wet lab practice to identify leads involved in interesting phenotypes. These omics experiments often result in unstructured gene lists, the interpretation of which in terms of pathways or the mode of action is challenging. To aid in the interpretation of such gene lists, we developed PheNetic, a decision theoretic method that exploits publicly available information, captured in a comprehensive interaction network to obtain a mechanistic view of the listed genes. PheNetic selects from an interaction network the sub-networks highlighted by these gene lists. We applied PheNetic to an Escherichia coli interaction network to reanalyse a previously published KO compendium, assessing gene expression of 27 E. coli knock-out mutants under mild acidic conditions. Being able to unveil previously described mechanisms involved in acid resistance demonstrated both the performance of our method and the added value of our integrated E. coli network.

Place, publisher, year, edition, pages
Cambridge: Royal Society of Chemistry, 2013. Vol. 9, no 7, p. 1594-1603
National Category
Bioinformatics and Systems Biology Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:oru:diva-87106DOI: 10.1039/c3mb25551dISI: 000319882200006PubMedID: 23591551Scopus ID: 2-s2.0-84878686232OAI: oai:DiVA.org:oru-87106DiVA, id: diva2:1485477
Note

Funding Agencies:

KU Leuven GOA/08/011 PF/10/010 (NATAR) CREA/08/023

Agentschap voor Innovatie door Wetenschap en Technologie (IWT): SBO-BioFrame  

Agentschap voor Innovatie door Wetenschap en Technologie (IWT): SBO-NEMOA  

FWO G.0329.09

Ghent University [Multidisciplinary Research Partnership "M2N"] 

Available from: 2020-11-02 Created: 2020-11-02 Last updated: 2020-11-10Bibliographically approved

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De Raedt, Luc

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