title: EcmPred: prediction of extracellular matrix proteins based on random forest with maximum relevance minimum redundancy feature selection.
abstract: The extracellular matrix (ECM) is a major component of tissues of multicellular organisms. It consists of secreted macromolecules, mainly polysaccharides and glycoproteins. Malfunctions of ECM proteins lead to severe disorders such as marfan syndrome, osteogenesis imperfecta, numerous chondrodysplasias, and skin diseases. In this work, we report a random forest approach, EcmPred, for the prediction of ECM proteins from protein sequences. EcmPred was trained on a dataset containing 300 ECM and 300 non-ECM and tested on a dataset containing 145 ECM and 4187 non-ECM proteins. EcmPred achieved 83% accuracy on the training and 77% on the test dataset. EcmPred predicted 15 out of 20 experimentally verified ECM proteins. By scanning the entire human proteome, we predicted novel ECM proteins validated with gene ontology and InterPro. The dataset and standalone version of the EcmPred software is available at http://www.inb.uni-luebeck.de/tools-demos/Extracellular_matrix_proteins/EcmPred.
authors.affiliation: Institute for Neuro- and Bioinformatics, University of Luebeck, Germany. Krishna.Kandaswamy@age.mpg.de
authors.forename: Krishna Kumar
authors.initials: KK
authors.lastname: Kandaswamy
authors.forename: Ganesan
authors.initials: G
authors.lastname: Pugalenthi
authors.forename: Kai-Uwe
authors.initials: KU
authors.lastname: Kalies
authors.forename: Enno
authors.initials: E
authors.lastname: Hartmann
authors.forename: Thomas
authors.initials: T
authors.lastname: Martinetz
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D016326:Extracellular Matrix Proteins / Q000378:metabolism*; D006801:Humans; D020543:Proteome / Q000378:metabolism; D012372:ROC Curve
chemical_list: D016326:Extracellular Matrix Proteins; D020543:Proteome