title: KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.
abstract: BACKGROUND
  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 obtain 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.
  
  
  CONCLUSIONS
  With KeyPathwayMiner 4.0, we publish a Cytoscape app for multi-omics based sub-network extraction. It is available in Cytoscape's app store http://apps.cytoscape.org/apps/keypathwayminer or via http://keypathwayminer.mpi-inf.mpg.de.
authors.affiliation: Max Planck Institute for Informatics, Saarbrücken, Germany. nalcaraz@imada.sdu.dk.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Alcaraz
authors.forename: Josch
authors.initials: J
authors.lastname: Pauling
authors.forename: Richa
authors.initials: R
authors.lastname: Batra
authors.forename: Eudes
authors.initials: E
authors.lastname: Barbosa
authors.forename: Alexander
authors.initials: A
authors.lastname: Junge
authors.forename: Anne G L
authors.initials: AG
authors.lastname: Christensen
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
authors.forename: Henrik J
authors.initials: HJ
authors.lastname: Ditzel
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D025941:Protein Interaction Mapping; D012984:Software