Xenbase Image ID: 130293

Fig. S9. To rule out the possibility that phenolog intersections arise predominantly from “deep paralogs,” we measured the pair-wise BLAST E-values between genes in phenolog intersections (I) and genes in the same phenotypes but not the phenolog intersections (the differential gene sets D1 or D2), comparing the Evalue distributions on a species-by-species basis for each species pair (see SI Materials and Methods for details). Distributions are plotted above; box plots represent first quartile, median, and third quartile, whiskers 1.5 × interquartile range, and stars represent outliers >3 IQR [thus, the majority of pair-wise sequence comparisons show no significant similarity with –log10(Eval) = 3]. In general, genes in phenolog intersections were no more likely to encode similar protein sequences than genes in the phenologs but outside the intersections (i.e., associated with the phenotype in only one species), indicating that deep paralogy is not a dominant factor in identifying phenologs. Across 20 such comparisons (10 species pairs, performing tests on a per species basis for each comparison), in 14 cases gene pairs in the I sets showed less significant BLAST E-values than those in the D sets (one-tailed P < 0.0001 for each; Wilcoxon-Mann- Whitney); in 3 cases gene pairs in the I sets showed more significant BLAST E-values than in the D sets (1 tailed P < 0.0001, P < 0.02, P < 0.03); and in 3 cases the sets were not significantly biased in either direction. Image published in: McGary KL et al. (2010) Copyright © 2010. Image reproduced with permission of the publisher and the copyright holder. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. Larger Image Printer Friendly View

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