Efficient algorithms for extracting biological key pathways with global constraints

Jan Baumbach, T. Friedrich, T. Kötzing, Jens Müller, J. Pauling, A. Krohmer

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

Abstract

The integrated analysis of data of different types and with various interdependencies is one of the major challenges in computational biology. Recently, we developed KeyPathwayMiner, a method that combines biological networks modeled as graphs with disease-specific genetic expression data gained from a set of cases (patients, cell lines, tissues, etc.). We aimed for finding all maximal connected sub-graphs where all nodes but K are expressed in all cases but at most L, i.e. key pathways. Thereby, we combined biological networks with OMICS data, instead of analyzing these data sets in isolation. Here we present an alternative approach that avoids a certain bias towards hub nodes: We now aim for extracting all maximal connected sub-networks where all but at most K nodes are expressed in all cases but in total (!) at most L, i.e. accumulated over all cases and all nodes in a solution. We call this strategy GLONE (global node exceptions); the previous problem we call INES (individual node exceptions). Since finding GLONE-components is computationally hard, we developed an Ant Colony Optimization algorithm and implemented it with the KeyPathwayMiner Cytoscape framework as an alternative to the INES algorithms. KeyPathwayMiner 3.0 now offers both the INES and the GLONE algorithms. It is available as plugin from Cytoscape and online at http://keypathwayminer.mpi-inf. mpg.de.
Original languageEnglish
Title of host publicationGECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation
Number of pages7
Publication date1. Jan 2012
Pages169-175
ISBN (Print)9781450311779
DOIs
Publication statusPublished - 1. Jan 2012

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