The Table view shows the evolutionary scenario of each bystander-target gene pair in tabular form, using a defined code for each scenario. The following is a screenshot of the table view, using PAX2 as an example.
The table lists all genes in the PAX2 GRB, ordered in 5' to 3' direction on the chromosome, with one row per gene. The gene highlighted in red is the putative target gene. In the example, the reference genome is human, and it is compared to all five fish genomes. The rightmost column contains links to the idealized gene tree for the corresponding gene(
), and the tree for the whole protein family from Ensembl(
). The method used to extract a gene tree from the Ensembl protein family tree is described here.
We define the evolutionary scenario for each bystander gene using a three-digit code ("XYZ"). This describes the number of orthologs for a bystander gene in each compared species, and their location in the genome relative to the target gene, as follows:
X: the number of the target gene orthologs in the compared species
Y: the number of the bystander gene orthologs in the compared species (for the target gene itself, X=Y)
Z: the number of the bystander gene orthologs which are in synteny with the target gene (0 <= Z <= Y)
For example, scenario code "211" tells us this is a 1-to-2 scenario for the main target gene (alternatively called a 1-to-2 GRB case). The bystander gene in this example has one ortholog in the teleost genome, and that copy is in synteny with (on copy of) the target gene.
