Tree view maps all orthologs for genes in the given GRB onto an ideal gene tree based on complete teleost whole-genome duplication. This provides a visual overview of how the genes in the ancestral GRB have been lost or reallocated to a position outside of the GRB in all considered species.
The method used to map genes onto the ideal tree is described in the method section.
Here's a sample results page for PAX2, along with brief explanations:
| A. | Ideal Gene Tree based on teleost whole genome duplication The ideal gene tree includes all considered species, currently human, mouse, chicken, frog and teleost fish (zebrafish, fugu, tetradon, medaka, stickleback). It assumes a whole genome duplication event in teleost, that resulted in doubling of all genes. Note: the branch length of tree is set to unit, not scaled to the phylogenetic distance. |
| B. | Orthologous gene position For better view, all species are marked with different color (the color itself has no meaning). All protein-coding genes in the GRB are ordered at the top by transcription start position, from 5' to 3'. All genes in one row are in one synteny block; all genes in one duplication branch are closer in evolutionary distance to each other than to the ortholog in the other branch. If a duplicate of a bystander gene is closer to branch1, but not in synteny with the target gene in branch1, it will be put at the second level of bystander gene at branch1. For example, the zebrafish SCD ortholog in branch1 is closer to the other orthologs of SCD in branch1, but not in synteny with the zebrafish PAX2 target gene, so it is shown at the second level in branch1. |
| C. | Pop-up gene tree When moving the mouse pointer on top of an underlined gene name, a window showing the ideal gene tree will pop up. Genes not present in the tree are shown in gray, and not underlined. The method used to map genes onto the ideal tree is described in the Method section. |