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 ConnecticutNeha 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)
