Construction of functional gene networks using phylogenetic profiles

Junha Shin, Insuk Lee

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Citations (Scopus)

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages87-98
Number of pages12
DOIs
Publication statusPublished - 2017 Jan 1

Publication series

NameMethods in Molecular Biology
Volume1526
ISSN (Print)1064-3745

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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    Shin, J., & Lee, I. (2017). Construction of functional gene networks using phylogenetic profiles. In Methods in Molecular Biology (pp. 87-98). (Methods in Molecular Biology; Vol. 1526). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-6613-4_5