A Web Interface to analyse SOM of

Bipartitions of Gene Phylogenies - A Walk Through

J. Peter Gogarten, Maria Poptsova Dept. of Molecular and Cell Biology

University of Connecticut

Neha Nahar, Lutz Hamel Department of Computer Science and Statistics

University of Rhode Island

BranchClust

n Genomes

Super Families

Gene Families

Reconstruct Phylogenetic History for Each Family

Data Matrix

Biapartiton #1 (**….….)

… Biapartiton #k(*******..)

Support value vector for a set #1 of orthologous genes P11 … P1k

Support value vector for a set #2 of orthologous genes P21 … P2k

… … … …

Support value vector for a set #m of orthologous genes Pn1 … Pnk

Number of bipartitions (k) for N genomes is equal to 2(N-1)-N-1.

Visualizing Multiple Genomes: SOMs

SOM Self-Organizing Map An artificial neural network approach to clustering

we are looking for clusters of genes which favor certain tree topologies

Advantages over other clustering approaches: No a priori knowledge of how many clusters to expect Explicit summary of commonalities and differences between

clusters Visually appealing representation

T. Kohonen, Self-organizing maps, 3rd ed. Berlin ; New York: Springer, 2001.

All clusters selected => ATV tree viewer applet (Zmasek & Eddy, Bioinformatics, 17, 383-384 2001) displays plurality consensus of all gene families.

ATV allows to modify display

Select branch to place root

Select to re-root tree

Cren-

archaeotaE

uryarchaeota

Root

List of strongly supported bipartitions, including conflicts

click to open map as pdf

select clusters that support bipartition

“well behaved” gene families

gene families that group Archaeoglobus with Methanosarcina

prolyl-tRNA synthetase, a gene family that groups the Halobacteria with the

outgroup.

This gene was acquired by the halobacterial lineage from the bacteria. These rare inter-domain gene transfers allow to correlate evolution in the three domains of life. (see Huang & Gogarten: Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends in Genetics 22 (7): 361-366. 2006)