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Open Access Highly Accessed Open Badges Research article

Unsupervised clustering of gene expression data points at hypoxia as possible trigger for metabolic syndrome

Andrey Ptitsyn1*, Matthew Hulver2, William Cefalu3, David York4 and Steven R Smith3

Author Affiliations

1 Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA

2 Virginia Polytechnic Institute and State University, Department of Human Nutrition, Foods and Exercise Corporate Research Center, Blacksburg, VA 24061, USA

3 Pennington Biomedical Research Center, 6400 Perkins Rd. Baton Rouge, LA 70808, USA

4 Center for Advanced Nutrition, Utah State University, 4715 Old Main Hill, Logan, UT 84322, USA

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BMC Genomics 2006, 7:318  doi:10.1186/1471-2164-7-318

Published: 19 December 2006



Classification of large volumes of data produced in a microarray experiment allows for the extraction of important clues as to the nature of a disease.


Using multi-dimensional unsupervised FOREL (FORmal ELement) algorithm we have re-analyzed three public datasets of skeletal muscle gene expression in connection with insulin resistance and type 2 diabetes (DM2). Our analysis revealed the major line of variation between expression profiles of normal, insulin resistant, and diabetic skeletal muscle. A cluster of most "metabolically sound" samples occupied one end of this line. The distance along this line coincided with the classic markers of diabetes risk, namely obesity and insulin resistance, but did not follow the accepted clinical diagnosis of DM2 as defined by the presence or absence of hyperglycemia. Genes implicated in this expression pattern are those controlling skeletal muscle fiber type and glycolytic metabolism. Additionally myoglobin and hemoglobin were upregulated and ribosomal genes deregulated in insulin resistant patients.


Our findings are concordant with the changes seen in skeletal muscle with altitude hypoxia. This suggests that hypoxia and shift to glycolytic metabolism may also drive insulin resistance.