title: Predicting pathway membership via domain signatures.
abstract: BACKGROUND
  Functional characterization of genes is of great importance for the understanding of complex cellular processes. Valuable information for this purpose can be obtained from pathway databases, like KEGG. However, only a small fraction of genes is annotated with pathway information up to now. In contrast, information on contained protein domains can be obtained for a significantly higher number of genes, e.g. from the InterPro database.
  
  
  RESULTS
  We present a classification model, which for a specific gene of interest can predict the mapping to a KEGG pathway, based on its domain signature. The classifier makes explicit use of the hierarchical organization of pathways in the KEGG database. Furthermore, we take into account that a specific gene can be mapped to different pathways at the same time. The classification method produces a scoring of all possible mapping positions of the gene in the KEGG hierarchy. Evaluations of our model, which is a combination of a SVM and ranking perceptron approach, show a high prediction performance. Moreover, for signaling pathways we reveal that it is even possible to forecast accurately the membership to individual pathway components.
  
  
  BACKGROUND
  The R package gene2pathway is a supplement to this article.
authors.affiliation: German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany. h.froehlich@dkfz-heidelberg.de
authors.forename: Holger
authors.initials: H
authors.lastname: Fröhlich
authors.forename: Mark
authors.initials: M
authors.lastname: Fellmann
authors.forename: Holger
authors.initials: H
authors.lastname: Sültmann
authors.forename: Annemarie
authors.initials: A
authors.lastname: Poustka
authors.forename: Tim
authors.initials: T
authors.lastname: Beissbarth
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D011506:Proteins