title: Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients.
abstract: BACKGROUND
  One of the main goals of high-throughput gene-expression studies in cancer research is to identify prognostic gene signatures, which have the potential to predict the clinical outcome. It is common practice to investigate these questions using classification methods. However, standard methods merely rely on gene-expression data and assume the genes to be independent. Including pathway knowledge a priori into the classification process has recently been indicated as a promising way to increase classification accuracy as well as the interpretability and reproducibility of prognostic gene signatures.
  
  
  RESULTS
  We propose a new method called Reweighted Recursive Feature Elimination. It is based on the hypothesis that a gene with a low fold-change should have an increased influence on the classifier if it is connected to differentially expressed genes. We used a modified version of Google's PageRank algorithm to alter the ranking criterion of the SVM-RFE algorithm. Evaluations of our method on an integrated breast cancer dataset comprising 788 samples showed an improvement of the area under the receiver operator characteristic curve as well as in the reproducibility and interpretability of selected genes.
  
  
  BACKGROUND
  The R code of the proposed algorithm is given in Supplementary Material.
authors.affiliation: German Cancer Research Center, Cancer Genome Research, Im Neuenheimer Feld 280, 69120 Heidelberg. m.johannes@DKFZ-heidelberg.de
authors.forename: Marc
authors.initials: M
authors.lastname: Johannes
authors.forename: Jan C
authors.initials: JC
authors.lastname: Brase
authors.forename: Holger
authors.initials: H
authors.lastname: Fröhlich
authors.forename: Stephan
authors.initials: S
authors.lastname: Gade
authors.forename: Mathias
authors.initials: M
authors.lastname: Gehrmann
authors.forename: Maria
authors.initials: M
authors.lastname: Fälth
authors.forename: Holger
authors.initials: H
authors.lastname: Sültmann
authors.forename: Tim
authors.initials: T
authors.lastname: Beissbarth
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D011379:Prognosis; D012372:ROC Curve; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics; D012307:Risk Factors
chemical_list: D018719:Erb-b2 Receptor Tyrosine Kinases; C508053:ERBB2 protein, human