Degree

Figure 4. The vertical axis shows the average number of genomes (± one s.d.) among six folly sequenced genomes that contain at least one protein homologous to proteins whose degree is indicated on the horizontal axis. The analysis is based on two different data sets on yeast protein interactions, one ('two hybrid') from a high-throughput experiment using the yeast-two hybrid assay to identify such interactions,38 the other ('non-two hybrid') from a publicly available database on protein interactions from which I eliminated all data generated with the two-hybrid assay.39 Protein comparisons are based on the following six maximally diverse fully sequenced and publicly available genomes: Schizosaccharomyces pombe (www.sanger.ac.uk), Plasmodium falciparum (www.plasmodb.org), Arabidopsis thaliana (www.tigr.org), Drosophila melanogaster (www.fruitfly.org), Escherichia coli K12-MG1655 (www.tigr.org), Methanococcus janaschii DSM2661 (www.tigr.org). I used gapped BLAST37 with a threshold protein alignment score of E < 10"5 to identify homology. Results (not shown) are qualitatively identical for threshold scores of E < 10'2 and E < 10'10.

these six species contain a recognizable homologue of the yeast proteins. The data in Figure 4 show the results of this analysis for a BLAST protein alignment score threshold of E < 10"5 to identify homology. Specifically, the figure shows the average number of taxa that contain at least one homologue to a yeast protein (vertical axis) plotted against the degree of this protein in the protein interaction network. The analysis shown is based on two different data sets of yeast protein interactions.38'39 If highly connected proteins are phylogenetically old, then highly connected proteins should occur in significantly more of the six taxa than lowly connected proteins. The data of Figure 4, however, does not support this pattern. Figure 5 shows a complementary analysis, where I plotted average protein degree against the number of the six taxa in which a proteins homologue is found. If more widely distributed proteins are more highly connected, then they should have a higher degree. The data does not support this association either. Alignment score thresholds of E < 10"2 and E < 1010 yield the same conclusion (data not shown).

In a second analysis, I cast my net wider than just the above six fully sequenced genome. I arbitrarily chose 15 highly connected proteins (degree > 4) and 15 proteins with low connectivity (degree one) from the yeast protein interaction network.38 For each of these thirty proteins, I asked whether it has at least one homologue in any of six broad taxonomic groups:

Widely distributed proteins are not more highly connected

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