title: Handling multiple testing while interpreting microarrays with the Gene Ontology Database.
abstract: BACKGROUND
  The development of software tools that analyze microarray data in the context of genetic knowledgebases is being pursued by multiple research groups using different methods. A common problem for many of these tools is how to correct for multiple statistical testing since simple corrections are overly conservative and more sophisticated corrections are currently impractical. A careful study of the nature of the distribution one would expect by chance, such as by a simulation study, may be able to guide the development of an appropriate correction that is not overly time consuming computationally.
  
  
  RESULTS
  We present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from Drosophila, S. cerevisiae, Wormbase, and Gramene databases using the Gene Ontology Database.
  
  
  CONCLUSIONS
  We found that the estimated distribution is not regular and is not predictable outside of a particular set of genes. Permutation-based simulations may be necessary to determine the confidence in results of such analyses.
authors.affiliation: Department of Biological Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623, USA. michael@bioinformatics.rit.edu
authors.forename: Michael V
authors.initials: MV
authors.lastname: Osier
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.forename: Kei-Hoi
authors.initials: KH
authors.lastname: Cheung
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000706:statistics & numerical data; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic / Q000706:statistics & numerical data*; D004330:Drosophila / Q000235:genetics; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D006376:Helminths / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software / Q000706:statistics & numerical data