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Open Access Technical Note

Validation of MIMGO: a method to identify differentially expressed GO terms in a microarray dataset

Yoichi Yamada1*, Hiroki Sawada2, Ken-ichi Hirotani2, Masanobu Oshima3 and Kenji Satou1

Author Affiliations

1 Institute of Science and Engineering, Faculty of Electrical and Computer Engineering, Kanazawa University, Kanazawa 920-1192, Japan

2 Division of Electrical and Computer Engineering, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, 920-1192, Japan

3 Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan

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BMC Research Notes 2012, 5:680  doi:10.1186/1756-0500-5-680

Published: 12 December 2012

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.

Findings

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.