KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape

Nicolas Alcaraz, Josch Pauling, Richa Batra, Eudes Barbosa, Alexander Junge, Anne GL Christensen, Vasco Azevedo, Henrik J Ditzel, Jan Baumbach
2014 BMC Systems Biology  
Over the last decade network enrichment analysis has become popular in computational systems biology to elucidate aberrant network modules. Traditionally, these approaches focus on combining gene expression data with protein-protein interaction (PPI) networks. Nowadays, the so-called omics technologies allow for inclusion of many more data sets, e.g. protein phosphorylation or epigenetic modifications. This creates a need for analysis methods that can combine these various sources of data to
more » ... ain a systems-level view on aberrant biological networks. Results: We present a new release of KeyPathwayMiner (version 4.0) that is not limited to analyses of single omics data sets, e.g. gene expression, but is able to directly combine several different omics data types. Version 4.0 can further integrate existing knowledge by adding a search bias towards sub-networks that contain (avoid) genes provided in a positive (negative) list. Finally the new release now also provides a set of novel visualization features and has been implemented as an app for the standard bioinformatics network analysis tool: Cytoscape. Conclusion: With KeyPathwayMiner 4.0, we publish a Cytoscape app for multi-omics based sub-network extraction. It is available in Cytoscape's app store
doi:10.1186/s12918-014-0099-x pmid:25134827 pmcid:PMC4236746 fatcat:yvm544tkpvh7jdoqccrf4ipcg4