Developing the ‘omic toolkit of comparative physiologists

Ripley, Daniel M.; Garner, Terence; Stevens, Adam

doi:10.1016/j.cbd.2024.101287

Comparative Biochemistry and Physiology Part D: Genomics and Pr

2024

DOI: 10.1016/j.cbd.2024.101287

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Developing the ‘omic toolkit of comparative physiologists

Daniel M. Ripley,

Terence Garner,

Adam Stevens

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2024

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Cited by 2 publications

References 67 publications

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Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome

Cuvertino,

Garner,

Martirosian

et al. 2024

Briefings in Bioinformatics

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Complex direct and indirect relationships between multiple variables, termed higher order interactions (HOIs), are characteristics of all natural systems. Traditional differential and network analyses fail to account for the omic datasets richness and miss HOIs. We investigated peripheral blood DNA methylation data from Kabuki syndrome type 1 (KS1) and control individuals, identified 2,002 differentially methylated points (DMPs), and inferred 17 differentially methylated regions, which represent only 189 DMPs. We applied hypergraph models to measure HOIs on all the CpGs and revealed differences in the coordination of DMPs with lower entropy and higher coordination of the peripheral epigenome in KS1 implying reduced network complexity. Hypergraphs also capture epigenomic trans-relationships, and identify biologically relevant pathways that escape the standard analyses. These findings construct the basis of a suitable model for the analysis of organization in the epigenome in rare diseases, which can be applied to investigate mechanism in big data.

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Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome

Cuvertino,

Garner,

Martirosian

et al. 2024

Briefings in Bioinformatics

View full text Add to dashboard Cite

show abstract

The integrative biology of the heart: mechanisms enabling cardiac plasticity

Joyce,

Shiels,

Franklin

2024

Journal of Experimental Biology

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Cardiac phenotypic plasticity, the remodelling of heart structure and function, is a response to any sustained (or repeated) stimulus or stressor that results in a change in heart performance. Cardiac plasticity can be either adaptive (beneficial) or maladaptive (pathological), depending on the nature and intensity of the stimulus. Here, we draw on articles published in this Special Issue of Journal of Experimental Biology, and from the broader comparative physiology literature, to highlight the core components that enable cardiac plasticity, including structural remodelling, excitation–contraction coupling remodelling and metabolic rewiring. We discuss when and how these changes occur, with a focus on the underlying molecular mechanisms, from the regulation of gene transcription by epigenetic processes to post-translational modifications of cardiac proteins. Looking to the future, we anticipate that the growing use of -omics technologies in integration with traditional comparative physiology approaches will allow researchers to continue to uncover the vast scope for plasticity in cardiac function across animals.

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Developing the ‘omic toolkit of comparative physiologists

Cited by 2 publications

References 67 publications

Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome

Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome

The integrative biology of the heart: mechanisms enabling cardiac plasticity

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