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Biclustering Analysis of Co-regulation Patterns in Nuclear-Encoded Mitochondrial Genes and Metabolic Pathways

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Cancer Metabolism

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1928))

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Abstract

Transcription of a large set of nuclear-encoded genes underlies biogenesis of mitochondria, regulated by a complex network of transcription factors and co-regulators. A remarkable heterogeneity can be detected in the expression of these genes in different cell types and tissues, and the recent availability of large gene expression compendiums allows the quantification of specific mitochondrial biogenesis patterns. We have developed a method to effectively perform this task. Massively correlated biclustering (MCbiclust) is a novel bioinformatics method that has been successfully applied to identify co-regulation patterns in large genesets, underlying essential cellular functions and determining cell types. The method has been recently evaluated and made available as a package in Bioconductor for R. One of the potential applications of the method is to compare expression of nuclear-encoded mitochondrial genes or larger sets of metabolism-related genes between different cell types or cellular metabolic states. Here we describe the essential steps to use MCbiclust as a tool to investigate co-regulation of mitochondrial genes and metabolic pathways.

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Acknowledgment

Funding was provided by the University College London COMPLeX/British Heart Foundation Fund (SP/08/004), the Biochemical and Biophysical Research Council (BB/L020874/1, BB/P018726/1), the Wellcome Trust (097815/Z/11/Z) in the UK, and the Association for Cancer Research (AIRC, IG13447) in Italy.

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Authors and Affiliations

  1. Department of Cell and Developmental Biology, Consortium for Mitochondrial Research, University College London, London, UK

    Robert B. Bentham & Gyorgy Szabadkai

  2. Department of Computer Sciences, University College London, London, UK

    Kevin Bryson

  3. Department of Biomedical Sciences, University of Padua, Padua, Italy

    Gyorgy Szabadkai

  4. The Francis Crick Institute, London, UK

    Gyorgy Szabadkai

Authors
  1. Robert B. Bentham
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  2. Kevin Bryson
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  3. Gyorgy Szabadkai
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Corresponding author

Correspondence to Robert B. Bentham .

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Editors and Affiliations

  1. National Cancer Institute, North Bethesda, MD, USA

    Majda Haznadar

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Bentham, R.B., Bryson, K., Szabadkai, G. (2019). Biclustering Analysis of Co-regulation Patterns in Nuclear-Encoded Mitochondrial Genes and Metabolic Pathways. In: Haznadar, M. (eds) Cancer Metabolism. Methods in Molecular Biology, vol 1928. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9027-6_24

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  • DOI: https://doi.org/10.1007/978-1-4939-9027-6_24

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9026-9

  • Online ISBN: 978-1-4939-9027-6

  • eBook Packages: Springer Protocols

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