title: AGRA: analysis of gene ranking algorithms.
abstract: Often, the most informative genes have to be selected from different gene sets and several computer gene ranking algorithms have been developed to cope with the problem. To help researchers decide which algorithm to use, we developed the analysis of gene ranking algorithms (AGRA) system that offers a novel technique for comparing ranked lists of genes. The most important feature of AGRA is that no previous knowledge of gene ranking algorithms is needed for their comparison. Using the text mining system finding-associated concepts with text analysis. AGRA defines what we call biomedical concept space (BCS) for each gene list and offers a comparison of the gene lists in six different BCS categories. The uploaded gene lists can be compared using two different methods. In the first method, the overlap between each pair of two gene lists of BCSs is calculated. The second method offers a text field where a specific biomedical concept can be entered. AGRA searches for this concept in each gene lists' BCS, highlights the rank of the concept and offers a visual representation of concepts ranked above and below it.
  
  
  METHODS
  Available at http://agra.fzv.uni-mb.si/, implemented in Java and running on the Glassfish server.
  
  
  BACKGROUND
  simon.kocbek@uni-mb.si.
authors.affiliation: Faculty of Health Sciences, University of Maribor, Maribor, Slovenia. simon.kocbek@uni-mb.si
authors.forename: Simon
authors.initials: S
authors.lastname: Kocbek
authors.forename: Rune
authors.initials: R
authors.lastname: Sætre
authors.forename: Gregor
authors.initials: G
authors.lastname: Stiglic
authors.forename: Jin-Dong
authors.initials: JD
authors.lastname: Kim
authors.forename: Igor
authors.initials: I
authors.lastname: Pernek
authors.forename: Yoshimasa
authors.initials: Y
authors.lastname: Tsuruoka
authors.forename: Peter
authors.initials: P
authors.lastname: Kokol
authors.forename: Sophia
authors.initials: S
authors.lastname: Ananiadou
authors.forename: Jun'ichi
authors.initials: J
authors.lastname: Tsujii
mesh_terms: D000465:Algorithms; D057225:Data Mining; D005796:Genes; D012984:Software