Figure 2

Sample from list of all eLRR genes, hierarchically clustered at e^-40 cutoff. Proteins have been sorted in this table based on the clustering output from TribeMCL. This has been done hierarchically across inflation parameters, starting at 1.2, then 2, 3, 4 and 5. For most proteins this yields a tree-like structure with cluster stringency increasing (and membership decreasing) from low inflation parameters to high. Numbers used to identify clusters are generated by TribeMCL with larger clusters having lower numbers. Proteins are colour-coded by species: black, mammalian; blue, fly; red, worm. For the mammalian proteins, only the mouse orthologue is listed. The table shows examples of clusters in the LRR_Ig/FN3 group with mouse, fly and worm orthologues (the Lrig subfamily) and with mouse paralogues only (the Lrrn6, Lrrn1–3 and Lrrc4 subfamilies, which cluster together at level 1.2). It also shows many of the proteins in the LRR_Tollkin group, with the hierarchical clustering apparent across inflation parameters and indicated by shading. One subfamily containing a known and novel member is shown at the bottom. Proteins encoded by genes located in tandem in the genome are boxed in the right-hand column. A complete list of all eLRR proteins is provided [see Additional File 3]. Lists clustered at the e^-25 and e^-10 cutoff levels are given [see Additional Files 4 and 5].