Statistics

Datasets

We used IsoRank & IsoRankN on five eukaryotic PPI networks: H. sapiens (Human), M. musculus (Mouse), D. melanogaster (Fly), C. elegans (Worm), and S. cerevisiae (Yeast). Two forms of data were required as inputs, PPI networks and sequence similarity scores. The PPI networks were constructed by combining data from the DIP, BioGRID, and HPRD databases. In total, these five networks contained 87,737 proteins and 98,945 known interactions. The sequence similarity scores of pairs of proteins were the BLAST Bit-values of the sequences as retrieved from Ensembl.

Species	Number of Proteins	Number of Interactions
H. sapiens	22369	36387
M. musculus	24855	255
D. melanogaster	14098	25831
C. elegans	19756	4752
S. cerevisiae	6659	31899

Evaluation

We evaluated the biological relevance of our results against two gene ontology databases: GO and KEGG. We first measured the consistency of the predicted network alignment by computing the mean entropy of the predicted clusters. The entropy of a given cluster S*_v is:

where p_i is the fraction of S*_v with GO or KEGG group ID i. Thus a cluster has lower entropy if its GO and KEGG annotations are more within-cluster consistent. We also measured the fraction of clusters which are exact, i.e. those in which all proteins have the same GO or KEGG ID. For GO annotation, we restricted to the deepest categories, removing questions of multiplicity and specificity of annotations. Note that only 60-70% of the proteins in any of the aligned networks have an assigned GO or KEGG ID, comparable to the fraction of all known proteins included in GO or KEGG. Additionally the relative performance under either consistency measure does not change when restricted to GO or KEGG individually.

Consistency	IsoRank & IsoRankN
Mean entropy	0.274
Exact cluster ratio*	0.380(3079 of 8095)
Exact protein ratio*	0.261(9284 of 35604)

*The fraction of predicted clusters (proteins) which are exact.

Coverage* (# of species)	IsoRank & IsoRankN
Total	12848/48978

2	3844/8739
3	4022/13533
4	2926/13991
5	2056/12715

*The number of predicted clusters containing exactly # species and number of constituent proteins in those clusters (#cluster / #proteins)

GO/KEGG	IsoRank & IsoRankN
p-value	1.28 e-90
GO/KEGG category	712/2490

Human	632/2200
Mouse	605/2124
Fly	574/1787
Worm	552/1698
Yeast	368/938

The number of GO/KEGG categories enriched by IsoRank & IsoRankN. As computed by GO TermFinder, we remark that this excludes those proteins tagged IEA (inferred from electronic annotation).