Benchmark disease table

Benchmark disease table

In order to benchmark the performance of our system, we randomly selected from the EntrezGene database 100 genes for which disease causing mutations had already been reported.

The associations used to analyse this set were derived from a version of MEDLINE from which we removed the sets of papers related to the 100 diseases altogether. This was done in order to ensure that we would not find a relation between the disease and the known related gene directly from the papers that describe the connection.

A chromosomal region of about 30Mb (corresponding to the average size of the regions where the uncharacterized diseases examined were mapped) was taken around each of the 100 genes, and the procedure used in analysis 1.0 was aplied.

Click on the disease Id(s) (e.g. 001) to see details about each analysis.

DISEASE		.	REGION ANALYSED				.	RESPONSIBLE GENE				.
Id	Description	.	Chr	From	To	Size (Mb)	.	Id	Chr	From	To	.
001	acyl coA dehydrogenase deficiency medium chain	.	1	57350000	87350000	30.0	.	[4557231\|NP_000007]	1	75902302	75941204	.
002	oculocutaneous albinism	.	15	7000000	37000000	30.0	.	[4557811\|NP_000266]	15	25673627	26018061	.
003	hereditary renal amyloidosis	.	4	117050000	147050000	30.0	.	[4503689\|NP_000499]	4	155861884	155869470	.
004	anxiety related personality traits	.	17	13700000	43700000	30.0	.	[4507043\|NP_001036]	17	25549031	25586831	.
005	sporadic b cell non hodgkin lymphoma	.	11	93800000	123800000	30.0	.	[4502267\|NP_000042]	11	107599052	107741966	.
006	primary bile acid malabsorption	.	13	89800000	119800000	30.0	.	[4506973\|NP_000443]	13	102494350	102517197	.
007	brunner syndrome	.	X	27300000	57300000	30.0	.	[4557735\|NP_000231]	X	43271662	43362321	.
008	hepatic CPT deficiency type II	.	1	40250000	70250000	30.0	.	n.a.	n.a.	n.a.	n.a.	.
009	carnitine acetyltransferase deficiency	.	9	115150000	145150000	30.0	.	[4557487\|NP_000746]	9	128936628	128952637	.
010	infantile neuronal ceroid lipofuscinosis	.	1	40250000	70250000	30.0	.	[4506031\|NP_000301]	1	40207476	40232061	.
011	x linked chronic granulomatous disease	.	X	19350000	49350000	30.0	.	[6996021\|NP_000388]	X	37395536	37428931	.
012	coproporphyria	.	3	86750000	116750000	30.0	.	[4503017\|NP_000088]	3	99780981	99795131	.
013	nephropathic cystinosis	.	17	0	30000000	30.0	.	[4826682\|NP_004928]	17	3486764	3511581	.
014	autosomal recessive deafness	.	2	15950000	45950000	30.0	.	[4758856\|NP_004793]	2	26591722	26612561	.
015	dicarboxylic aminoaciduria	.	9	0	30000000	30.0	.	[4759122\|NP_004161]	9	4480439	4577258	.
016	ehlers danlos syndrome type III	.	2	161200000	191200000	30.0	.	[4502951\|NP_000081]	2	189664604	189702978	.
017	dominant epidermolysis bullosa dystrophica	.	3	38350000	68350000	30.0	.	[4502961\|NP_000085]	3	48576509	48607689	.
018	progressive myoclonic epilepsy	.	21	29172162	59172161	30.0	.	[4503117\|NP_000091]	21	44018259	44020687	.
019	factor X deficiency	.	13	96621490	126621490	30.0	.	[4503625\|NP_000495]	13	112825145	112851842	.
020	friedreich ataxia retained reflexes	.	9	56950000	86950000	30.0	.	[4503785\|NP_000135]	9	68879897	68918506	.
021	variant form gaucher disease	.	10	52600000	82900000	30.3	.	[11386147\|NP_002769]	10	73246063	73281015	.
022	glycerol kinase deficiency	.	X	11950000	41950000	30.0	.	n.a.	n.a.	n.a.	n.a.	.
023	growth hormone deficient dwarfism	.	7	21700000	51700000	30.0	.	[4503997\|NP_000814]	7	30776875	30792381	.
024	hemolytic anemia adenosine deaminase	.	20	24350000	54350000	30.0	.	[4557249\|NP_000013]	20	42681577	42713790	.
025	systemic hemosiderosis aceruloplasminemia	.	3	136300000	166300000	30.0	.	[4557485\|NP_000087]	3	150374073	150422277	.
026	autosomal recessive hypoparathyroidism	.	11	1150000	31150000	30.0	.	[4506267\|NP_000306]	11	13470177	13474143	.
027	fatal familial insomnia	.	20	0	30000000	30.0	.	[4506113\|NP_000302]	20	4615068	4630233	.
028	krabbe disease	.	14	68250000	98250000	30.0	.	[4557613\|NP_000144]	14	87469112	87529596	.
029	acute pre B cell leukemia	.	1	142850000	172850000	30.0	.	[4505623\|NP_002576]	1	161260594	161547967	.
030	liddle syndrome	.	16	7150000	37150000	30.0	.	[4506821\|NP_001030]	16	23101540	23135701	.
031	mental retardation x linked	.	X	50750000	80750000	30.0	.	[4505507\|NP_002538]	X	67045735	67436668	.
032	mucopolysaccharidosis IVA	.	16	73013627	103013627	30.0	.	[4503899\|NP_000503]	16	87407643	87450885	.
033	muscular dystrophy limb-girdle	.	4	41450000	71450000	30.0	.	[4506913\|NP_000223]	4	52727799	52745374	.
034	myotonya atypical acetazolamide responsive	.	17	49837371	79837371	30.0	.	[4506807\|NP_000325]	17	59369645	59404010	.
035	norrie disease	.	X	24750000	54750000	30.0	.	[4557789\|NP_000257]	X	43564279	43589004	.
036	idiopathic osteoporosis	.	17	29550000	59550000	30.0	.	[4502945\|NP_000079]	17	45616455	45633992	.
037	paraneoplastic sensory neuropathy	.	1	25400000	55400000	30.0	.	[11386163\|NP_068771]	1	50286657	50379074	.
038	phenylketonuria dihydropteridine reductase deficiency	.	4	5650000	35650000	30.0	.	[4506359\|NP_000311]	4	17164291	17189982	.
039	porphyria variegata	.	1	137400000	167400000	30.0	.	[4506001\|NP_000300]	1	157949266	157954085	.
040	pycnodysostosis	.	1	131500000	161500000	30.0	.	[4503151\|NP_000387]	1	147581759	147593885	.
041	autosomal recessive retinitis pigmentosa	.	3	121850000	151850000	30.0	.	[4506527\|NP_000530]	3	130730179	130736885	.
042	rhizomelic chondrodysplasia punctata type I	.	6	96850000	126850000	30.0	.	[4505731\|NP_000279]	6	137185415	137276752	.
043	X-linked severe combined immunodeficiency	.	X	54750000	84750000	30.0	.	[4557882\|NP_000197]	X	70110279	70114424	.
044	spherocytosis	.	14	50050000	80050000	30.0	.	[4507193\|NP_000338]	14	64302870	64416308	.
045	thrombophilia plasminogen activator inhibitor	.	7	84650000	114650000	30.0	.	[10835159\|NP_000593]	7	100363886	100375741	.
046	trifunctional protein deficiency type II	.	2	13000000	43000000	30.0	.	[4504327\|NP_000174]	2	26379471	26424983	.
047	vohwinkel syndrome	.	1	131500000	161500000	30.0	.	[4557725\|NP_000418]	1	150046475	150047671	.
048	novelty seeking personality	.	11	0	30000000	30.0	.	[4503389\|NP_000788]	11	627304	630703	.
049	autoimmune lymphoproliferative syndrome	.	10	83150000	113150000	30.0	.	[4507583\|NP_000034]	10	90740267	90765521	.
050	susceptibility to myocardial infarction	.	17	40400000	70400000	30.0	.	[4503273\|NP_000780]	17	58908165	58928711	.
051	3-beta-hydroxysteroid dehydrogenase deficiency	.	1	101200000	131200000	30.0	.	[4504509\|NP_000189]	1	119669814	119677693	.
052	Adhalinopathy	.	17	26350000	56350000	30.0	.	[4506911\|NP_000014]	17	45598389	45608288	.
053	Alport syndrome	.	X	88350000	118350000	30.0	.	[4502955\|NP_000486]	X	107489298	107746920	.
054	Angelman syndrome	.	15	9200000	39200000	30.0	.	[4507799\|NP_000453]	15	23133488	23204888	.
055	Autoimmune polyglandular disease	.	21	29172162	59172161	30.0	.	[4557291\|NP_000374]	21	44530190	44542530	.
056	Biotinidase deficiency	.	3	640293	30640293	30.0	.	[4557373\|NP_000051]	3	15618258	15662328	.
057	C1r C1s deficiency	.	12	0	30000000	30.0	.	[4502493\|NP_001724]	12	7057771	7058863	.
058	Cardiomopathy hypertrophic	.	3	32950000	62950000	30.0	.	[4557777\|NP_000249]	3	46874370	46879935	.
059	Centrocytic lymphoma	.	11	55250000	85250000	30.0	.	n.a.	n.a.	n.a.	n.a.	.
060	Choroideremia	.	X	70250000	100250000	30.0	.	[9966761\|NP_000381]	X	84925656	85108711	.
061	Colorectal cancer	.	5	91250000	121250000	30.0	.	[4505129\|NP_002378]	5	112389427	112658201	.
062	Cortisol resistance	.	5	123350000	153350000	30.0	.	[4504133\|NP_000167]	5	142639324	142763087	.
063	Deafness autosomal dominant	.	11	104452384	134452384	30.0	.	[4885627\|NP_005413]	11	120478584	120566725	.
064	Diabetes mellitus noninsulin-dependent	.	2	211100000	241100000	30.0	.	[5031805\|NP_005535]	2	227425442	227489980	.
065	Ehlers-Danlos syndrome	.	9	120714634	150714634	30.0	.	[4502957\|NP_000084]	9	134759596	134960684	.
066	Episodic ataxia myokymia syndrome	.	12	0	30000000	30.0	.	[4557685\|NP_000208]	12	4890805	4892293	.
067	Fanconi-Bickel syndrome	.	3	152500000	182500000	30.0	.	[4557851\|NP_000331]	3	172196838	172227470	.
068	Galactose epimerase deficiency	.	1	8869867	38869867	30.0	.	[4503891\|NP_000394]	1	23867394	23872340	.
069	Glutaricaciduria	.	19	37050000	67050000	30.0	.	[4503609\|NP_001976]	19	56540220	56561484	.
070	Growth retardation deafness mental	.	12	84350000	114350000	30.0	.	[11024682\|NP_000609]	12	101292143	101376791	.
071	Hemolytic anemia bisphosphoglycerate mutase	.	7	118805314	148805314	30.0	.	[4502445\|NP_001715]	7	133788809	133821820	.
072	Hirschsprung disease	.	10	32250000	62250000	30.0	.	[10862705\|NP_000314]	n.a.	n.a.	n.a.	.
073	Hyperlipoproteinemia 1	.	19	30750000	60750000	30.0	.	[4502159\|NP_000474]	19	50141082	50144657	.
074	Hypokalemic paralysis	.	1	188250000	218250000	30.0	.	[4557401\|NP_000060]	1	197740298	197813351	.
075	Insulin-dependent diabetes mellitus	.	12	102449811	132449811	30.0	.	[4507393\|NP_000536]	12	119879268	119903032	.
076	Lactoferrin deficiency neutrophils	.	3	31466949	61466949	30.0	.	[4505043\|NP_002334]	3	46452500	46481399	.
077	Leukemia myeloid lymphoid	.	11	100600000	130600000	30.0	.	[5174569\|NP_005924]	11	117812414	117901146	.
078	Lung cancer small cell	.	17	49150000	79150000	30.0	.	[4557859\|NP_001041]	17	68672754	68679655	.
079	Maple syrup urine	.	1	57350000	87350000	30.0	.	[4503265\|NP_001909]	1	100371756	100427411	.
080	Mephenytoin poor	.	10	86350000	116350000	30.0	.	[4503219\|NP_000760]	10	96512452	96602661	.
081	Mucopolysaccharidosis	.	7	66550000	96550000	30.0	.	[4504223\|NP_000172]	7	64869824	64891346	.
082	Myelogenous leukemia	.	5	119700000	149700000	30.0	.	[4504721\|NP_002189]	5	131846683	131854326	.
083	Nephrolithiasis	.	X	35850000	65850000	30.0	.	[4557473\|NP_000075]	X	49537191	49560557	.
084	Non-insulin-dependent diabetes mellitus 2	.	12	101050000	131050000	30.0	.	[4507393\|NP_000536]	12	119879268	119903032	.
085	Osteoporosis idiopathic	.	7	85500000	115500000	30.0	.	[4502947\|NP_000080]	7	93668523	93705195	.
086	Pelizaeus-Merzbacher	.	X	88350000	118350000	30.0	.	[10834970\|NP_000524]	X	102837898	102853690	.
087	Pituitary hormone deficiency	.	5	150857866	180857866	30.0	.	[5453982\|NP_006252]	5	177351841	177355849	.
088	Prolactinoma hyperparathyroidism	.	11	55250000	85250000	30.0	.	[4557745\|NP_000235]	11	64327571	64334764	.
089	Pulmonary alveolar proteinosis	.	22	22550000	52550000	30.0	.	[4559408\|NP_000386]	22	35642721	35659318	.
090	Retinitis pigmentosa	.	15	78619458	108619457	30.0	.	[4506541\|NP_000317]	15	87554102	87565926	.
091	SED congenita	.	12	34750000	64750000	30.0	.	[13435125\|NP_001835]	12	46653017	46684528	.
092	BETA-THALASSEMIA	.	11	0	30000000	30.0	.	[4504349\|NP_000509]	11	5203271	5204877	.
093	Stargardt disease	.	1	84300000	114300000	30.0	.	[4557876\|NP_000341]	1	94170416	94298700	.
094	Thrombocytopenia	.	X	31950000	61950000	30.0	.	[4507909\|NP_000368]	X	48298458	48306065	.
095	Trypsinogen deficiency	.	7	130150000	160150000	30.0	.	[4506145\|NP_002760]	7	141943618	141947210	.
096	Waardenburg syndrome ocular albinism	.	11	71900000	101900000	30.0	.	[4507753\|NP_000363]	11	88550687	88668474	.
097	Zellweger syndrome	.	8	64500000	94500000	30.0	.	[4506343\|NP_000309]	8	78057712	78074994	.
098	Hyperproreninemia	.	1	188250000	218250000	30.0	.	[4506475\|NP_000528]	1	200855604	200867122	.
099	Asthma nocturnal	.	5	126000000	156000000	30.0	.	[4501969\|NP_000015]	5	148186368	148188379	.
100	Nicotine addiction	.	19	30750000	60750000	30.0	.	[4503215\|NP_000753]	19	46041283	46048180	.

Meaning of the column headers

DISEASE

Details about an inherited disease whose responsible gene is known. We used 100 of these as benchmark of the system.

Id: Genes2Diseases identifier given to the disease.
Description: Name of the disease.

REGION ANALYSED

Chromosomal region generated around the responsible gene that was used to test the system.

Chr: Chromosome in which the region is located.
From: Start position (in bp) of the region analysed.
To: Stop position (in bp) of the region analysed.
Size (Mb): Size of the region analysed in magabases (Mb). Note that we generated regions of about 30Mb with the responsible gene in the middle.

RESPONSIBLE GENE

Information about the gene responsible of the disease.

Id: the RefSeq identifier of the gene.
Chr: Chromosome in which the responsible gene is located.
From: Start position (in bp) of the responsible gene.
To: Stop position (in bp) of the responsible gene.
(n.a. = non available) It can happen that the gene was not in the band in the version of the human genome used.