Phylogenetic profiling

Figure 6.1. Phylogenetic profile method. Four genomes are shown, each containing a subset of proteins (PI, .P7). The presence or absence of a protein is given by 1 or 0 in the phylogenetic profile shown at lower left. Identical profiles are shown clustered on the right. In this example, the P2 and P7 are functionally linked because they exhibit the same phylogenetic profile. The P3 and P6 protein are similarly linked. Figure adapted from Pellegrini et al. (1999).

A phylogenetic profile is a description of the presence or absence of a particular protein in a set of organisms whose genome has been sequenced. The profile is a string with n entries, each one bit, where n is the number of... 

Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., and Yeates, T. O. (1999). Assigning protein functions by comparative genome analysis Protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96, 4285-4288. 

Pellegrini, M., E.M. Marcotte, M.J. Thompson, D. Eisenberg, and T.O. Yeates, Assigning protein functions by comparative genome analysis protein phylogenetic profiles. Proc Natl Acad Sci USA, 1999. 96(8) 4285-8. 

Hover on the Phylogenetic Profiler in the drop down menu and then select the Single Genes button. 

Acad. Sci. V.S.A., 96, 4285 (1999). Assigning Protein Functions by Comparative Genome Analysis Protein Phylogenetic Profiles. 

The phylogenetic profile method analyzes the co-occurrence of genes in the genomes of different organisms, for the same purpose [96],... 

In the example shown in Fig. 6, the Phylogenetic Profiler is used to find genes from a Burkholderia mallei strain that have no homologs in a Burkholderia pseudomallei strain. Similarity cutoffs can be used to fine-tune the selection. The list of genes with the specified profile is then provided as a selectable list as shown in Fig. 6. 

Marcotte, E. M., I. Xenarios, A. M. van der Bliek, and D. Eisenberg. Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci USA 97 12115-20. 

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