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

BMC Bioinformatics

Table 1 funSim scores and homolgene ID matches in RNA Polymerase complex compared to manual classification

Scaffold	Gene	Aligned	Gene	FunSim	Homologene	Manual
P52435	Polr2j	A1Z9J6	mRpL53	0	mismatch	mismatch
P19387	POLR2C	Q9V3G9	BACR37P7.5	0	mismatch	mismatch
P53803	Polr2k	Q9VG44	CG6225	0.02	mismatch	mismatch
P52434	POLR2H	Q9VKS9	CG18284	0.03	mismatch	mismatch
P62487	POLR2G	Q9VJB3	CG5681	0.04	mismatch	mismatch
P62875	POLR2l	P14284	REV3	0.09	mismatch	match
P19388	POLR2e	Q8SXU3	CG8207	0.12	mismatch	mismatch
O15514	POLR2d	P20433	RPB4	0.31	match	match
P52434	POLR2H	P20436	RPB8	0.34	match	match
P19387	POLR2C	P16370	RPB3	0.43	match	match
P62487	POLR2G	P34087	RPB7	0.47	match	match
P52435	Polr2j	P38902	RPB11	0.48	match	match
P19388	POLR2e	P20434	RPB5	0.48	match	match
P24928	POLR2a	P04050	RPO21	0.51	match	match
P61218	POLR2F	P20435	RPO26	0.6	mismatch	match
P30876	POLR2B	P08518	RPB2	0.6	match	match
O15514	POLR2d	Q9VEA5	Rpb4	0.73	match	match
P24928	POLR2a	P04052	RpII215	0.77	match	match
P61218	POLR2F	Q24320	RpII18	0.77	match	match
P30876	POLR2B	P08266	RpII140	0.87	match	match
P19387	POLR2C	P97760	Polr2c	0.93	match	match
P62875	POLR2l	Q9VC49	Rpb10	0.93	match	match
P30876	POLR2B	Q8CFI7	Polr2b	0.95	match	match

A threshold of 0.2 for NF would better cover the biologically relevant protein mappings than the currently used value of 0.5. While NH has both high coverage and accuracy in this complex, it is in general also missing many valid correspondences. NForH is most consistent with manual classification.

ISSN: 1471-2105