Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships

Zhang, Wangshu; Coba, Marcelo P.; Sun, Fengzhu

doi:10.1186/s12918-015-0247-y

BMC Systems Biology

Table 3 Novel predictions of domain-disease and gene-disease associations

From: Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships

Rank	Disease	OMIM_d	Module Index	Domain	Pfam	Gene	OMIM_g
1	APNEA, OBSTRUCTIVE SLEEP	107650	152	Acetyltransf_1	PF00583	NAA10	300013
1	APNEA, OBSTRUCTIVE SLEEP	107650	152	Acetyltransf_1	PF00583	AANAT	600950
2	ARTERIES, ANOMALIES OF	108000	182	Sugar_tr	PF00083	SLC2A1	138140
						SLC2A2	138160
						SLC2A9	606142
						SLC2A10	606145
3	ATRESIA OF EXTERNAL AUDITORY CANAL AND CONDUCTIVE DEAFNESS	108760	133	zf-C2H2_2	PF12756	TSHZ1	614427
4	CELIAC ARTERY STENOSIS FROM COMPRESSION BY MEDIAN ARCUATE LIGAMENT OF DIAPHRAGM	116870	182	Sugar_tr	PF00083	SLC2A1	138140
						SLC2A2	138160
						SLC2A9	606142
						SLC2A10	606145
5	SCHNYDER CORNEAL DYSTROPHY; SCCD	121800	77	Fasciclin	PF02469	TGFBI	601692
6	CORNEAL DYSTROPHY, EPITHELIAL BASEMENT MEMBRANE; EBMD	121820	77	Fasciclin	PF02469	TGFBI	601692
7	CORNEAL DYSTROPHY, GROENOUW TYPE I; CDGG1	121900	77	Fasciclin	PF02469	TGFBI	601692
8	CORNEAL DYSTROPHY, MEESMANN; MECD	122100	77	Fasciclin	PF02469	TGFBI	601692
9	CORNEAL DYSTROPHY, LATTICE TYPE I; LCD1	122200	77	Fasciclin	PF02469	TGFBI	601692
10	CORONARY ARTERY DISSECTION, SPONTANEOUS	122455	182	Sugar_tr	PF00083	SLC2A1	138140
						SLC2A2	138160
						SLC2A9	606142
						SLC2A10	606145
11	DEAFNESS, CONDUCTIVE STAPEDIAL, WITH EAR MALFORMATION AND FACIAL PALSY	124490	137	Endothelin	PF00322	EDN1	131240
11		124490	137	Endothelin	PF00322	EDN3	131242
12	EAR FOLDING	128500	137	Endothelin	PF00322	EDN1	131240
12	EAR FOLDING	128500	137	Endothelin	PF00322	EDN3	131242
13	PREAURICULAR FISTULAE, CONGENITAL	128700	137	Endothelin	PF00322	EDN1	131240
13	PREAURICULAR FISTULAE, CONGENITAL	128700	137	Endothelin	PF00322	EDN3	131242
14	EAR PITS, POSTERIOR HELICAL	128710	137	Endothelin	PF00322	EDN1	131240
14	EAR PITS, POSTERIOR HELICAL	128710	137	Endothelin	PF00322	EDN3	131242
15	EAR WITHOUT HELIX	128800	137	Endothelin	PF00322	EDN1	131240
15	EAR WITHOUT HELIX	128800	137	Endothelin	PF00322	EDN3	131242
16	EXTERNAL AUDITORY CANAL, BILATERAL ATRESIA OF, WITH CONGENITAL VERTICAL TALUS	133705	133	zf-C2H2_2	PF12756	TSHZ1	614427
17	FIBROMUSCULAR DYSPLASIA OF ARTERIES	135580	182	Sugar_tr	PF00083	SLC2A1	138140
						SLC2A2	138160
						SLC2A9	606142
						SLC2A10	606145
18	GLAUCOMA AND SLEEP APNEA	137763	152	Acetyltransf_1	PF00583	NAA10	300013
18	GLAUCOMA AND SLEEP APNEA	137763	152	Acetyltransf_1	PF00583	AANAT	600950
19	LUBS X-LINKED MENTAL RETARDATION SYNDROME; MRXSL	300260	66	MBD	PF01429	MECP2	300005
20	ALPHA-THALASSEMIA	604131	188	Globin	PF00042	HBA1	141800
						HBA2	141850
						HBB	141900
21	HOLT-ORAM SYNDROME; HOS	142900	140	LMBR1	PF04791	LMBR1	605522
22	INTERNAL CAROTID ARTERY, SPONTANEOUS DISSECTION OF	147820	182	Sugar_tr	PF00083	SLC2A1	138140
						SLC2A2	138160
						SLC2A9	606142
						SLC2A10	606145
23	LITHIUM TRANSPORT	152420	180	SNF	PF00209	SLC6A3	126455
23	LITHIUM TRANSPORT	152420	180	SNF	PF00209	SLC6A19	608893
24	MACULAR DYSTROPHY, FENESTRATED SHEEN TYPE	153890	77	Fasciclin	PF02469	TGFBI	601692
25	MULLERIAN APLASIA AND HYPERANDROGENISM	158330	199	wnt	PF00110	WNT5A	164975
						WNT10B	601906
						WNT4	603490
						WNT10A	606268
26	OSSIFIED EAR CARTILAGES	165670	137	Endothelin	PF00322	EDN1	131240
26	OSSIFIED EAR CARTILAGES	165670	137	Endothelin	PF00322	EDN3	131242
27	ENCHONDROMATOSIS, MULTIPLE, OLLIER TYPE	166000	166	Iso_dh	PF00180	IDH2	147650
						IDH1	147700
						IDH3B	604526
28	MACULAR DYSTROPHY, PATTERNED, 1; MDPT1	169150	77	Fasciclin	PF02469	TGFBI	601692
29	RADIAL RAY HYPOPLASIA WITH CHOANAL ATRESIA	179270	140	LMBR1	PF04791	LMBR1	605522
30	QUESTION MARK EARS, ISOLATED; QME	612798	137	Endothelin	PF00322	EDN1	131240
30	QUESTION MARK EARS, ISOLATED; QME	612798	137	Endothelin	PF00322	EDN3	131242
31	THUMB DEFORMITY	188100	140	LMBR1	PF04791	LMBR1	605522
32	THYROID HORMONE PLASMA MEMBRANE TRANSPORT DEFECT	188560	180	SNF	PF00209	SLC6A3	126455
32	THYROID HORMONE PLASMA MEMBRANE TRANSPORT DEFECT	188560	180	SNF	PF00209	SLC6A19	608893
33	TRACHEOESOPHAGEAL FISTULA WITH OR WITHOUT ESOPHAGEAL ATRESIA	189960	133, 181	zf-C2H2_2	PF12756	TSHZ1	614427
34	TRIGGER THUMB	190410	140	LMBR1	PF04791	LMBR1	605522
35	TRIPHALANGEAL THUMB WITH DOUBLE PHALANGES	190500	140	LMBR1	PF04791	LMBR1	605522
36	TRIPHALANGEAL THUMB, NONOPPOSABLE	190600	140	LMBR1	PF04791	LMBR1	605522
37	UTERINE ANOMALIES	192000	199	wnt	PF00110	WNT5A	164975
						WNT10B	601906
						WNT4	603490
						WNT10A	606268
38	UTERUS BICORNIS BICOLLIS WITH PARTIAL VAGINAL SEPTUM AND UNILATERAL HEMATOCOLPOS WITH IPSILATERAL RENAL AGENESIS	192050	199	wnt	PF00110	WNT5A	164975
						WNT10B	601906
						WNT4	603490
						WNT10A	606268
39	ACRORENAL-MANDIBULAR SYNDROME	200980	199	wnt	PF00110	WNT5A	164975
						WNT10B	601906
						WNT4	603490
						WNT10A	606268
40	ADDUCTED THUMBS SYNDROME	201550	140	LMBR1	PF04791	LMBR1	605522
41	APNEA, CENTRAL SLEEP	207720	152	Acetyltransf_1	PF00583	NAA10	300013
41	APNEA, CENTRAL SLEEP	207720	152	Acetyltransf_1	PF00583	AANAT	600950
42	ARTERIAL TORTUOSITY SYNDROME; ATS	208050	182	Sugar_tr	PF00083	SLC2A1	138140
						SLC2A2	138160
						SLC2A9	606142
						SLC2A10	606145
43	AURAL ATRESIA, MULTIPLE CONGENITAL ANOMALIES, AND MENTAL RETARDATION	209770	133, 181	zf-C2H2_2	PF12756	TSHZ1	614427
44	BILIARY ATRESIA, EXTRAHEPATIC; EHBA	210500	133, 181	zf-C2H2_2	PF12756	TSHZ1	614427
45	CITRULLINE TRANSPORT DEFECT	215720	180	SNF	PF00209	SLC6A3	126455
45	CITRULLINE TRANSPORT DEFECT	215720	180	SNF	PF00209	SLC6A19	608893
46	CENTRAL CLOUDY DYSTROPHY OF FRANCOIS; CCDF	217600	77	Fasciclin	PF02469	TGFBI	601692
47	DEAFNESS, CONDUCTIVE, WITH MALFORMED EXTERNAL EAR	221300	137	Endothelin	PF00322	EDN1	131240
47	DEAFNESS, CONDUCTIVE, WITH MALFORMED EXTERNAL EAR	221300	137	Endothelin	PF00322	EDN3	131242
48	DICARBOXYLIC AMINOACIDURIA; DCBXA	222730	180	SNF	PF00209	SLC6A3	126455
48	DICARBOXYLIC AMINOACIDURIA; DCBXA	222730	180	SNF	PF00209	SLC6A19	608893
49	DUODENAL ATRESIA	223400	181	zf-C2H2_2	PF12756	TSHZ1	614427
50	HARTNUP DISORDER; HND	234500	180	SNF	PF00209	SLC6A3	126455
50	HARTNUP DISORDER; HND	234500	180	SNF	PF00209	SLC6A19	608893

“Rank” is the rank of predicted domain-disease associations in terms of Bayesian scores; “Disease” is the name of the disease phenotype, “OMIM_d” is ID of disease phenotype in the OMIM database; “Module Index” is the index of module including the disease; “Domain” is the name of domain; “Pfam” is the domain ID in the Pfam database; “Gene” is mapped gene from corresponding domain; and “OMIM_g” is the gene ID in the OMIM database. The bold rows represent known domain-disease associations compiled by the Ensembl BioMart tool. The italic rows represent domain-disease associations that are unknown in our study but have at least one known genes in the OMIM database. The bold italic elements in the “OMIM_g” column represent that the predicted genes are known as disease genes in the OMIM database

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