title: GeneTools--application for functional annotation and statistical hypothesis testing.
abstract: BACKGROUND
  Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions.
  
  
  RESULTS
  GeneTools is a web-service providing access to a database that brings together information from a broad range of resources. The annotation data are updated weekly, guaranteeing that users get data most recently available. Data submitted by the user are stored in the database, where it can easily be updated, shared between users and exported in various formats. GeneTools provides three different tools: i) NMC Annotation Tool, which offers annotations from several databases like UniGene, Entrez Gene, SwissProt and GeneOntology, in both single- and batch search mode. ii) GO Annotator Tool, where users can add new gene ontology (GO) annotations to genes of interest. These user defined GO annotations can be used in further analysis or exported for public distribution. iii) eGOn, a tool for visualization and statistical hypothesis testing of GO category representation. As the first GO tool, eGOn supports hypothesis testing for three different situations (master-target situation, mutually exclusive target-target situation and intersecting target-target situation). An important additional function is an evidence-code filter that allows users, to select the GO annotations for the analysis.
  
  
  CONCLUSIONS
  GeneTools is the first "all in one" annotation tool, providing users with a rapid extraction of highly relevant gene annotation data for e.g. thousands of genes or clones at once. It allows a user to define and archive new GO annotations and it supports hypothesis testing related to GO category representations. GeneTools is freely available through www.genetools.no
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway. vidar.beisvag@ntnu.no
authors.forename: Vidar
authors.initials: V
authors.lastname: Beisvag
authors.forename: Frode K R
authors.initials: FK
authors.lastname: Jünge
authors.forename: Hallgeir
authors.initials: H
authors.lastname: Bergum
authors.forename: Lars
authors.initials: L
authors.lastname: Jølsum
authors.forename: Stian
authors.initials: S
authors.lastname: Lydersen
authors.forename: Clara-Cecilie
authors.initials: CC
authors.lastname: Günther
authors.forename: Heri
authors.initials: H
authors.lastname: Ramampiaro
authors.forename: Mette
authors.initials: M
authors.lastname: Langaas
authors.forename: Arne K
authors.initials: AK
authors.lastname: Sandvik
authors.forename: Astrid
authors.initials: A
authors.lastname: Laegreid
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface