Construction of Functional Gene Networks Using Phylogenetic Profiles

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1526)

Abstract

Functional constraints between genes display similar patterns of gain or loss during speciation. Similar phylogenetic profiles, therefore, can be an indication of a functional association between genes. The phylogenetic profiling method has been applied successfully to the reconstruction of gene pathways and the inference of unknown gene functions. This method requires only sequence data to generate phylogenetic profiles. This method therefore has the potential to take advantage of the recent explosion in available sequence data to reveal a significant number of functional associations between genes. Since the initial development of phylogenetic profiling, many modifications to improve this method have been proposed, including improvements in the measurement of profile similarity and the selection of reference species. Here, we describe the existing methods of phylogenetic profiling for the inference of functional associations and discuss their technical limitations and caveats.

Key words

Phylogenetic profiling Functional association Gene network 
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Notes

Acknowledgements

This work was supported by grants from the National Research Foundation of Korea (2015R1A2A1A15055859, 2012M3A9B4028641, 2012M3A9C7050151).

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeoulSouth Korea

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