A survey of protein interaction data and multigenic inherited disorders

BMC Bioinformatics

Table 1 DiGs related only to complexes found in n-ary data

DiG ID	DiG name	# Genes	Best match (icrigid)	Complex span	# significant p-values (raw)	# significant p-values (FDR)
6	3-methylcrotonyl-coa carboxylase	2	1209480	9	9	2
65	Albinism	3	1209579	1	1	1
80	alport syndrome	3	781937	4	4	1
89	Amyloidosis	6	1221863	26	22	9
168	bethlem myopathy	3	1027975	5	5	1
192	Bradyopsia	2	969965	1	1	1
259	Ceroid	8	1232651	6	3	1
302	combined cellular and humoral immune defects	2	1220789	1	1	1
313	congenital disorder of glycosylation	23	725907	28	26	4
578	Hematuria	2	781937	4	4	1
595	hereditary hemorrhagic telangiectasia	2	618400	1	1	1
690	immune dysfunction	2	1122614	5	5	2
758	leigh syndrome	14	1211293	44	36	13
812	maple syrup urine disease	4	1225549	12	11	1
870	mitochondrial complex	16	1211293	28	24	5
975	omenn syndrome	3	1220789	1	1	1
998	Osteoporosis	5	869728	5	5	2
1108	Propionicacidemia	2	1209480	5	5	2
1266	stickler syndrome	3	878437	4	4	1
1341	tumoral calcinosis	4	682939	3	3	1
1345	ullrich congenital muscular dystrophy	3	1027975	5	5	1
1477	celiac disease	4	1220318	2	1	1
1512	intervertebral disc disease	2	893696	1	1	1
1520	Leprosy	4	651466	7	7	1

Summary of the 24 DiGs that can be related to protein complexes but can only be found in iRefIndex n-ary data: Mitochondrial complex deficiency (DiG ID = 870) is a DiG that groups 16 genes. At least one of the 16 genes in this DiG was present in 28 complexes present in iRefIndex n-ary data (complex span = 28) and 24 of them could be considered as significantly similar after a hypergeometric test with a p-value < 0.05. After adjusting the p-values for multiple testing using the FDR method, only 5 of those complexes could be considered significantly similar to the DiG, and therefore, their subunits related to the diseases involved in the DiG. The best match, among those 5, is the complex with the icrigid = 1211293, which corresponds to the complex in the CORUM database with interaction identifier = 15317750.
“3-methylcrotonyl-coa carboxylase” stands for “3-methylcrotonyl-coa carboxylase 1 deficiency” and “3-methylcrotonyl-coa carboxylase 2 deficiency”, while “Ceroid” stands for “Ceroid lipofuscinosis” and “Mitochondrial complex” stands for Mitochondrial complex I, II, III and IV deficiencies.

ISSN: 1471-2105