Global multiple protein-protein interaction network alignment by combining pairwise network alignments

BMC Bioinformatics

Table 2 Pairwise algorithm performance

max-scores (sum over pairs)	NA _s	NF _s	NH _s	*NForH* _s	EA-2	EA _s	EF _s	EH _s	EForH _s
IsoRankN highest	Human 20054	Human 8264	Human 2874	Human 8997	Human 1865	Arabi 7067	Arabi 1678	Human 213	Arabi 1767
IsoRankN second	Droso 17968	Mouse 7047	Mouse 2411	Mouse 7633	Yeast 1630	Yeast 5586	Yeast 1370	Mouse 162	Yeast 1374
SMETANA highest	Human 62172	Human 32028	Human 6774	Human 33942	Human 7099	Human 32344	Arabi 17783	Human 996	Arabi 17881
SMETANA second	Droso 57266	Droso 27410	Droso 5290	Droso 29144	Yeast 5082	Arabi 25013	Yeast 7185	Yeast 741	Yeast 7477
PINALOG highest	Human 17764	Human 7005	Human 4385	Human 8130	Yeast 10179	Yeast 10202	Human 1267	Human 832	Human 1516
PINALOG second	Droso 17173	Droso 5711	Mouse 2984	Droso 6586	Human 8866	Human 8870	Yeast 1024	Yeast 477	Yeast 1220
NETAL highest	Human 27869	Human 796	Droso 3	Human 797	Human 37852	Human 37852	Human 123	Droso 1	Human 123
NETAL second	Droso 27283	Droso 448	Celeg, Human 1	Droso 449	Droso 23888	Droso 23888	Droso, Mouse 29	-,0	Droso 30

For a given algorithm and measure, the species PPIN with the highest (bold) and second highest (underlined) score sum over all pairwise alignments is presented, along with the score obtained. The highest scoring network for a given algorithm and measure of choice is the one our methodology would designate as the scaffolding PPIN. Note that NETAL found only one conserved interaction with endpoint proteins homologous to their aligned counterparts (EH). We thus only present one value in the corresponding cell.

ISSN: 1471-2105