KeyPathwayMinerWeb: online multi-omics network enrichment

Markus List; Nicolas Alcaraz; Martin Dissing-Hansen; Henrik J Ditzel; Jan Mollenhauer; Jan Baumbach

doi:10.1093/nar/gkw373

KeyPathwayMinerWeb: online multi-omics network enrichment

Nucleic Acids Res. 2016 Jul 8;44(W1):W98-W104. doi: 10.1093/nar/gkw373. Epub 2016 May 5.

Authors

Markus List¹, Nicolas Alcaraz², Martin Dissing-Hansen³, Henrik J Ditzel⁴, Jan Mollenhauer⁵, Jan Baumbach⁶

Affiliations

¹ Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark Institute of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
² Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.
³ Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark.
⁴ Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark Department of Oncology, Odense University Hospital, 5000 Odense, Denmark.
⁵ Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.
⁶ Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany jan.baumbach@imada.sdu.dk.

Abstract

We present KeyPathwayMinerWeb, the first online platform for de novo pathway enrichment analysis directly in the browser. Given a biological interaction network (e.g. protein-protein interactions) and a series of molecular profiles derived from one or multiple OMICS studies (gene expression, for instance), KeyPathwayMiner extracts connected sub-networks containing a high number of active or differentially regulated genes (proteins, metabolites) in the molecular profiles. The web interface at (http://keypathwayminer.compbio.sdu.dk) implements all core functionalities of the KeyPathwayMiner tool set such as data integration, input of background knowledge, batch runs for parameter optimization and visualization of extracted pathways. In addition to an intuitive web interface, we also implemented a RESTful API that now enables other online developers to integrate network enrichment as a web service into their own platforms.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Case-Control Studies
Computational Biology / methods*
Computational Biology / statistics & numerical data
Datasets as Topic
Gene Expression Profiling
Gene Expression Regulation
Gene Regulatory Networks*
Humans
Huntingtin Protein / genetics*
Huntington Disease / diagnosis
Huntington Disease / genetics*
Internet
Protein Interaction Mapping
User-Computer Interface*

Substances

HTT protein, human
Huntingtin Protein