genomebiology.com

Table 1
Top binding site predictions in human
Protein	Partner	Binding site	OMIM disease	Pubmed

Using only reliable protein-protein interactions
*PROC*	*PROS1*	*PS01187*	*Protein C deficiency*	*1615482*
*PROC*	*PROS1*	*PS50026*	*Protein C deficiency*	*1615482*
*BAX*	*BCL2L1*	*PS01259*	*Leukemia*	*9531611*
MMP2	BCAN	PS00142	Winchester syndrome	10986281
STAT1	SRC	PS50001	STAT1 deficiency	9344858
VAPB	VAMP2	PS50202	Amyotrophic lateral sclerosis	9920726
VAPB	VAMP1	PS50202	Amyotrophic lateral sclerosis	9920726
MMP2	BCAN	PS00546	Multicentric osteolysis	10986281
PLAU	PLAT	PS50070	Alzheimer disease	7721771
UCHL1	S100A7	PS00140	Parkinson disease	12032852

Integrating high-throughput interactions
*PROC*	*PROS1*	*PS01187*	*Protein C deficiency*	*1615482*
*PROC*	*PROS1*	*PS50026*	*Protein C deficiency*	*1615482*
*BAX*	*BCL2L1*	*PS01259*	*Leukemia*	*9531611*
MMP2	BCAN	PS00142	Winchester syndrome	10986281
PTPN11	TIE1	PS50055	Noonan syndrome 1	10949653
VAPB	VAMP2	PS50202	Amyotrophic lateral sclerosis	9920726
MMP2	BCAN	PS00546	Multicentric osteolysis	10986281
EFNB1	SRC	PS01299	Craniofrontonasal syndrome	8878483
PLAU	PLAT	PS50070	Alzheimer disease	7721771
UCHL1	S100A7	PS00140	Parkinson disease	12032852

We list the top 10 binding site predictions in human that contain disease causing mutations. The top part lists the predictions when using only reliable protein-protein interactions. The bottom part lists the predictions when integrating high-throughput interactions. Eight predictions appear in both panels, showing our method is robust to the change in the input data. Shown are the protein, its interacting partner, the motif that is predicted to be the binding sites to its partner, the disease caused by the mutations inside the motif, and the Pubmed reference to the interaction. Three of top predictions are verified by literature (in bold and italics), four in the top panel and three in the bottom panel are supported by existing evidence (in bold), one in the top panel and two in the bottom panel are confirmed to be wrong (in italics), and the remaining two predictions do not have literature information. In some cases, it is possible that the mutations at the binding site disrupt the interaction, and thus lead to the disease. PS01187, calcium-binding EGF-like domain; PS50026, EGF-like domain; PS01259, BH3 motif; PS00142, metallopeptidase zinc-binding region; PS50001, SH2 domain; PS50055, PTP type protein phosphatase; PS50202, major sperm protein (MSP) domain; PS00546, cysteine switch; PS01299, ephrins signature; PS50070, Kringle domain; PS00140, ubiquitin carboxy-terminal hydrolase cysteine active-site.
Wang et al. Genome Biology 2007 8:R192 doi:10.1186/gb-2007-8-9-r192

Table 1