S-Figure 3. An introduction to what is considered a chromosomally clustered gene. How we assessed if genes are clustered along the chromosome is illustrated with three different hypothetical examples. In each example (A-C), the organization of the hypothetical genome (genome organization) is given on the top line with 10 kb intervals marked.  The bent arrows represent the genes within the genome and the vertical line of the bent arrows represents their respective start codons. The position of the genes obtained from the query list of genes is shown on the second line (query list of genes).  Those genes considered clustered from the query list is given on the third line (genes considered clustered). A gene is considered clustered if the start codon is within 10 kb of another gene’s start codon from the same query list.  A. In this genome, there are no operons or potential paralogs.  All genes that are within 10 kb of another gene from the queried list are considered clustered.  The resulting number of clustered genes is nine.  B. A second hypothetical genome with the same organization as the first, but with genes in two operons (blue bent arrows). Note that the genes in the query list have the same positions as in example (A).  The genes considered clustered in (B), however, is different than that in (A) because only the start codon of the most upstream gene in the operon is considered in the clustering analysis (unify operons).  The resulting number of clustered genes is four.  C. A third hypothetical genome with the same organization as the first two, but it contains genes that are predicted to be paralogs of each other (red bent arrows). Note that the genes that are considered are of the same positions as in example (A&B). The genes considered clustered in (C) are different than that in (A&B) because if the relationship between two neighboring potential paralogs is never considered clustered (purple diagonal lines). If a member of a paralog group, however, is within 10kb of non-paralogous neighbor, both are considered clustered. The resulting number of clustered genes is six.  For more details on how we incorporated these principles into the cluster analysis of both the experimental lists and the random sampled lists, see the experimental procedures and S-Fig4 (this supplemental web site).