title: Efficient key pathway mining: combining networks and OMICS data.
abstract: Systems biology has emerged over the last decade. Driven by the advances in sophisticated measurement technology the research community generated huge molecular biology data sets. These comprise rather static data on the interplay of biological entities, for instance protein-protein interaction network data, as well as quite dynamic data collected for studying the behavior of individual cells or tissues in accordance with changing environmental conditions, such as DNA microarrays or RNA sequencing. Here we bring the two different data types together in order to gain higher level knowledge. We introduce a significantly improved version of the KeyPathwayMiner software framework. Given a biological network modelled as a graph and a set of expression studies, KeyPathwayMiner efficiently finds and visualizes connected sub-networks where most components are expressed in most cases. It finds all maximal connected sub-networks where all nodes but k exceptions are expressed in all experimental studies but at most l exceptions. We demonstrate the power of the new approach by comparing it to similar approaches with gene expression data previously used to study Huntington's disease. In addition, we demonstrate KeyPathwayMiner's flexibility and applicability to non-array data by analyzing genome-scale DNA methylation profiles from colorectal tumor cancer patients. KeyPathwayMiner release 2 is available as a Cytoscape plugin and online at http://keypathwayminer.mpi-inf.mpg.de.
authors.affiliation: Max Planck Institute for Informatics-Computational Systems Biology, Saarbrucken 66123, Germany.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Alcaraz
authors.forename: Tobias
authors.initials: T
authors.lastname: Friedrich
authors.forename: Timo
authors.initials: T
authors.lastname: Kötzing
authors.forename: Anton
authors.initials: A
authors.lastname: Krohmer
authors.forename: Joachim
authors.initials: J
authors.lastname: Müller
authors.forename: Josch
authors.initials: J
authors.lastname: Pauling
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
mesh_terms: D000465:Algorithms; D003110:Colonic Neoplasms / Q000235:genetics; D019295:Computational Biology; D003198:Computer Simulation; D019175:DNA Methylation; D057225:Data Mining; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods*; D006801:Humans; D006816:Huntington Disease / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D060066:Protein Interaction Maps; D012984:Software; D049490:Systems Biology / Q000379:methods*