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. 2014:2014:452891.
doi: 10.1155/2014/452891. Epub 2014 Jun 24.

Coexpression within Integrated Mitochondrial Pathways Reveals Different Networks in Normal and Chemically Treated Transcriptomes

Cong Chen  1 , Tae Kyung Hyun  2 , Xiao Han  2 , Zhihui Feng  1 , Yuan Li  1 , Xiaolong Liu  3 , Jiankang Liu  1
Affiliations

Coexpression within Integrated Mitochondrial Pathways Reveals Different Networks in Normal and Chemically Treated Transcriptomes

Cong Chen et al. Int J Genomics. 2014.

Abstract

As energy producers, mitochondria play a pivotal role in multiple cellular processes. Although several lines of evidence suggest that differential expression of mitochondrial respiratory complexes (MRCs) has a significant impact on mitochondrial function, the role of integrated MRCs in the whole coexpression network has yet to be revealed. In this study, we construct coexpression networks based on microarray datasets from different tissues and chemical treatments to explore the role of integrated MRCs in the coexpression network and the effects of different chemicals on the mitochondrial network. By grouping MRCs as one seed target, the hypergeometric distribution allowed us to identify genes that are significantly coexpress with whole MRCs. Coexpression among 46 MRC genes (approximately 78% of MRC genes tested) was significant in the normal tissue transcriptome dataset. These MRC genes are coexpressed with genes involved in the categories "muscle system process," "metabolic process," and "neurodegenerative disease pathways," whereas, in the chemically treated tissues, coexpression of these genes mostly disappeared. These results indicate that chemical stimuli alter the normal coexpression network of MRC genes. Taken together, the datasets obtained from the different coexpression networks are informative about mitochondrial biogenesis and should contribute to understanding the side effects of drugs on mitochondrial function.

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Figures

Figure 1
Figure 1
Genes significantly coexpressed with MRCs in normal and chemically treated tissues. (a) Self-connections among mitochondrial respiratory complexes. (b) Coexpressed cellular genes.
Figure 2
Figure 2
Genes coexpressed with MRCs in (a) the tissue-based network and (b) the chemical treatment-based network.
Figure 3
Figure 3
PANTHER analysis of the functional categories of genes coexpressed with MRCs. (a) Genes coexpressed in both normal tissues and chemically treated tissues. (b) Genes coexpressed with MRCs only in the tissue-based network. (c) Genes coexpressed with MRCs only in the chemically treated tissue.
See this image and copyright information in PMC

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