title: Validation of MIMGO: a method to identify differentially expressed GO terms in a microarray dataset.
abstract: BACKGROUND
  We previously proposed an algorithm for the identification of GO terms that commonly annotate genes whose expression is upregulated or downregulated in some microarray data compared with in other microarray data. We call these "differentially expressed GO terms" and have named the algorithm "matrix-assisted identification method of differentially expressed GO terms" (MIMGO). MIMGO can also identify microarray data in which genes annotated with a differentially expressed GO term are upregulated or downregulated. However, MIMGO has not yet been validated on a real microarray dataset using all available GO terms.
  
  
  RESULTS
  We combined Gene Set Enrichment Analysis (GSEA) with MIMGO to identify differentially expressed GO terms in a yeast cell cycle microarray dataset. GSEA followed by MIMGO (GSEA + MIMGO) correctly identified (p < 0.05) microarray data in which genes annotated to differentially expressed GO terms are upregulated. We found that GSEA + MIMGO was slightly less effective than, or comparable to, GSEA (Pearson), a method that uses Pearson's correlation as a metric, at detecting true differentially expressed GO terms. However, unlike other methods including GSEA (Pearson), GSEA + MIMGO can comprehensively identify the microarray data in which genes annotated with a differentially expressed GO term are upregulated or downregulated.
  
  
  CONCLUSIONS
  MIMGO is a reliable method to identify differentially expressed GO terms comprehensively.
authors.affiliation: Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan. youichi@t.kanazawa-u.ac.jp
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Yamada
authors.forename: Hiroki
authors.initials: H
authors.lastname: Sawada
authors.forename: Ken-Ichi
authors.initials: K
authors.lastname: Hirotani
authors.forename: Masanobu
authors.initials: M
authors.lastname: Oshima
authors.forename: Kenji
authors.initials: K
authors.lastname: Satou
mesh_terms: D000465:Algorithms; D002453:Cell Cycle / Q000235:genetics; D019295:Computational Biology; D030541:Databases, Genetic; D005656:Fungal Proteins / Q000235:genetics*; D020869:Gene Expression Profiling / Q000592:standards*; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D005656:Fungal Proteins