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Phylogenetic profiling

Part 4. Bioinformatics

4.4. Comparative Analysis and Phylogeny

Introductory Review

  1. Matteo Pellegrini1,
  2. Sorel T. Fitz-Gibbon2,
  3. Todd O. Yeates1,
  4. David Eisenberg1

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g404104

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Pellegrini, M., Fitz-Gibbon, S. T., Yeates, T. O. and Eisenberg, D. 2005. Phylogenetic profiling. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.4:41.

Author Information

  1. 1

    Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA

  2. 2

    IGPP Center for Astrobiology, University of California at Los Angeles, Los Angeles, CA, USA

Publication History

  1. Published Online: 15 APR 2005

Abstract

Phylogenetic profiling involves the study of the occurrence of gene families across fully sequenced genomes. For any gene, it is possible to create a phylogenetic profile, which encodes the presence or absence of homologs of the gene across organisms. Phylogenetic profiles may be used to measure the evolutionary distance between organisms, leading to the reconstruction of phylogenetic trees. The pairwise comparison of phylogenetic profiles allows us to identify genes that co-occur across organisms and are likely to participate within the same pathway or protein complex. Finally, by comparing phylogenetic profiles to phenotypic profiles that encode the presence or absence of phenotypes across organisms, it is possible to infer that a gene is partially responsible for establishing a phenotype. These techniques are currently used to survey about 100 fully sequenced genomes that are currently determined. However, they promise to become more informative as the number of fully sequenced genomes increases by orders of magnitude.

Keywords:

  • phylogenetic profiling;
  • phylogenetic profiles;
  • phylogeny;
  • functional genomics;
  • phenotypic profiles;
  • comparative genomics