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

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