A comparison of the mouse and human X chromosomes and the MAGE gene phylogeny. Dot plot on the left shows the mouse X chromosome on the horizontal axis and the human X chromosome on the vertical axis, with the 5'-end of both chromosomes at the upper left corner of the dot plot. Syntenic regions predicted by DiagHunter [36, 72] are highlighted in blue and numbered in the order that the program identified them. The locations of MAGE [25, 26] genes are shown with short green lines on the axes. Where two of these genes from mouse and human intersect with a diagonal, they are highlighted with bulls-eyes, both on the diagonal and both axes. These points represent candidate orthologs. OrthoMap uses these diagonal names to annotate the phylogeny, shown on the right. Names in the phylogeny have the form "Mx-0035427_69351 9a". First character indicates Mouse or Human; second character or digit(s) indicates chromosome number (with u being undetermined); middle digits (after the dash) are the last seven digits of the Ensembl gene ID; digits after the underscore are the gene midpoint position in Kb; and last characters (e.g. 9a) correspond to diagonal numbers from the dot plot on, with a or b signifying horizontal or vertical axis/chromosome origin, respectively. In the tree, S indicates inferred speciation, and t indicates inferred tandem duplication (as inferred by ParaMap). Lines drawn between the middle dot plot and nodes in the phylogeny show where segmental duplications have been "mapped" between the genomic dot plot and the phylogenetic analysis. Two cases of ancient (pre-speciation) tandem gene duplications are indicated on the tree, as are cases of tandem duplications that have occurred in mouse and human after speciation.