Scatter-plot of GDDI rank vs. promiscuity, scenario D shuffled domains, Pe = 1.0.

<p>Mixed architecture proteins play a critical role in the ability of non-attribute-reduced concept lattices to rank promiscuous GDDIs highly. All the 194,752 putative DDIs were ranked as described in the text, and the ranks of GDDIs were extracted to create the plots. Promiscuity of a domain pair (<i>a</i>, <i>b</i>) = [N(<i>a</i>)+N(<i>b</i>)]/2 where N(<i>d</i>) is the number of times domain <i>d</i> occurs in a protein set. The concept lattices which are not attribute-reduced (<b>OA</b> and <b>oA</b>) <i>no longer exhibit the desired negative relationship</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088943#pone-0088943-g011" target="_blank">Figure 11</a>). Instead, they tend to rank promiscuous GDDIs less highly. The relationship is still strongly positive when the <b>Oa</b> rankings are used. <b>Oa</b> results are identical to the Associative method which is known to penalize promiscuous domain-pairs. There is still also a tendency for the <b>oa</b> concept lattice to rank promiscuous GDDIs less highly, but this positive relationship is not so apparent because scoreless GDDIs are included in the plot (they start at rank 28,457 and onwards to the right of the plot). When the <b>oa</b> concept lattice is used, only 59 of the 214 GDDIs have CB scores; the remaining GDDIs are scoreless and are ranked randomly but below the GDDIs with CB scores.