title: GOAL: a software tool for assessing biological significance of genes groups.
abstract: BACKGROUND
  Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functional relevance among the genes in each group is usually characterized by utilizing available biological knowledge in public databases such as Gene Ontology (GO), KEGG pathways, association between a transcription factor (TF) and its target genes, and/or gene networks.
  
  
  RESULTS
  We developed
  
  
  OBJECTIVE
  Gene Ontology AnaLyzer, a software tool specifically designed for the functional evaluation of gene groups. GOAL implements and supports efficient and statistically rigorous functional interpretations of gene groups through its integration with available GO, TF-gene association data, and association with KEGG pathways. In order to facilitate more specific functional characterization of a gene group, we implement three GO-tree search strategies rather than one as in most existing GO analysis tools. Furthermore, GOAL offers flexibility in deployment. It can be used as a standalone tool, a plug-in to other computational biology tools, or a web server application.
  
  
  CONCLUSIONS
  We developed a functional evaluation software tool, GOAL, to perform functional characterization of a gene group. GOAL offers three GO-tree search strategies and combines its strength in function integration, portability and visualization, and its flexibility in deployment. Furthermore, GOAL can be used to evaluate and compare gene groups as the output from computational biology tools such as clustering algorithms.
authors.affiliation: Knowledge Discovery Group, Institute for Information Technology, National Research Council, Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6 Canada. alain.tchagang@nrc-cnrc.gc.ca
authors.forename: Alain B
authors.initials: AB
authors.lastname: Tchagang
authors.forename: Alexander
authors.initials: A
authors.lastname: Gawronski
authors.forename: Hugo
authors.initials: H
authors.lastname: Bérubé
authors.forename: Sieu
authors.initials: S
authors.lastname: Phan
authors.forename: Fazel
authors.initials: F
authors.lastname: Famili
authors.forename: Youlian
authors.initials: Y
authors.lastname: Pan
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks; D005796:Genes; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software
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