title: WeGET: predicting new genes for molecular systems by weighted co-expression.
abstract: We have developed the Weighted Gene Expression Tool and database (WeGET, http://weget.cmbi.umcn.nl) for the prediction of new genes of a molecular system by correlated gene expression. WeGET utilizes a compendium of 465 human and 560 murine gene expression datasets that have been collected from multiple tissues under a wide range of experimental conditions. It exploits this abundance of expression data by assigning a high weight to datasets in which the known genes of a molecular system are harmoniously up- and down-regulated. WeGET ranks new candidate genes by calculating their weighted co-expression with that system. A weighted rank is calculated for human genes and their mouse orthologs. Then, an integrated gene rank and p-value is computed using a rank-order statistic. We applied our method to predict novel genes that have a high degree of co-expression with Gene Ontology terms and pathways from KEGG and Reactome. For each query set we provide a list of predicted novel genes, computed weights for transcription datasets used and cell and tissue types that contributed to the final predictions. The performance for each query set is assessed by 10-fold cross-validation. Finally, users can use the WeGET to predict novel genes that co-express with a custom query set.
authors.affiliation: Maastricht University Medical Centre, P. Debyelaan 25, 6226XM Maastricht, The Netherlands Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, Nijmegen, The Netherlands radek.szklarczyk@maastrichtuniversity.nl.
authors.forename: Radek
authors.initials: R
authors.lastname: Szklarczyk
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, Nijmegen, The Netherlands Institute for Computing and Information Sciences (ICIS), Radboud University, Toernooiveld 212, 6525 EC Nijmegen, The Netherlands Centre for Systems Biology and Bioenergetics (CSBB), Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6500 HB Nijmegen, Nijmegen, The Netherlands.
authors.forename: Wout
authors.initials: W
authors.lastname: Megchelenbrink
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, Nijmegen, The Netherlands.
authors.forename: Pavel
authors.initials: P
authors.lastname: Cizek
authors.affiliation: Maastricht University Medical Centre, P. Debyelaan 25, 6226XM Maastricht, The Netherlands.
authors.forename: Marie
authors.initials: M
authors.lastname: Ledent
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, Nijmegen, The Netherlands.
authors.forename: Gonny
authors.initials: G
authors.lastname: Velemans
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Damian
authors.initials: D
authors.lastname: Szklarczyk
authors.affiliation: Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, Nijmegen, The Netherlands Centre for Systems Biology and Bioenergetics (CSBB), Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6500 HB Nijmegen, Nijmegen, The Netherlands Martijn.Huijnen@radboudumc.nl.
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Huynen
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D009437:Neuralgia / Q000235:genetics; D012984:Software