Andrew Su immediately mentioned on Twitter that he was working on GeneWiki+, an integration of GeneWiki on Semantic-MediaWiki that could answer the same question.
@yokofakun Nice... FYI, we also created genewikiplus.org to map gene-disease (and -SNP) links based on Gene Wiki + SNPedia #inpress
— Andrew Su (@andrewsu) April 13, 2012
@yokofakun yes, reasoning leverages MW cat system. see genewikiplus.org/wiki/Craniofac… as example query orofacial_cleft --> cleft lip, cleft palate
— Andrew Su (@andrewsu) April 13, 2012
Later, Benjamin Good announced that a SPARQL endpoint for GeneWiki+ was now available:
Gene Wiki SPARQL endpoint ff.im/V9UEf
— Benjamin Good (@bgood) April 23, 2012
The following java code uses the Jena/ARQ API to query this SPARQL endpoint. For a given Disease Ontology accession identifier, it fetches all the genes associated to this disease and run recursively with the sub-classes of this disease.
Here is the output (gene-name, gene-id, disease) with DOID:114 ("Heart Disease"):
Protein C 5624 Heart disease HMG-CoA reductase 3156 Heart disease SCARB1 949 Heart disease Coagulation factor II receptor 2149 Heart disease Cathepsin S 1520 Heart disease ABCA1 19 Heart disease CHD7 55636 Heart disease GJA5 2702 Heart disease ENTPD1 953 Heart disease PEDF 5176 Heart disease HMG CoA reductase 3156 Heart disease PROC 5624 Heart disease F2R 2149 Heart disease SERPINF1 5176 Heart disease HMGCR 3156 Heart disease CTSS 1520 Heart disease Cytochrome c 54205 Heart failure FOXP1 27086 Heart failure Vasoactive intestinal peptide 7432 Heart failure Angiotensin-converting enzyme 1636 Heart failure PPP1CA 5499 Heart failure Transferrin 7018 Heart failure Natriuretic peptide precursor C 4880 Heart failure Insulin-like growth factor 1 3479 Heart failure CA-125 94025 Heart failure Myosin binding protein C, cardiac 4607 Heart failure MYH7 4625 Heart failure Tafazzin 6901 Heart failure 5-HT2B receptor 3357 Heart failure Beta-1 adrenergic receptor 153 Heart failure PTGS2 5743 Heart failure EPAS1 2034 Heart failure Nociceptin receptor 4987 Heart failure Cystatin C 1471 Heart failure Ryanodine receptor 2 6262 Heart failure Multidrug resistance-associated protein 2 1244 Heart failure KCNA5 3741 Heart failure ANXA6 309 Heart failure CMA1 1215 Heart failure KLF15 28999 Heart failure IL1RL1 9173 Heart failure JPH2 57158 Heart failure Heart-type fatty acid binding protein 2170 Heart failure TF 7018 Heart failure ABCC2 1244 Heart failure Cytochrome-c 54205 Heart failure HTR2B 3357 Heart failure Cytochrome C 54205 Heart failure Hif2a 2034 Heart failure FABP3 2170 Heart failure MYBPC3 4607 Heart failure Angiotensin converting enzyme 1636 Heart failure IGF-1 3479 Heart failure Insulin-like growth factor-1 3479 Heart failure Stress-induced polymorphic ventricular tachycardia 6262 Heart failure C-type natriuretic peptide 4880 Heart failure OPRL1 4987 Heart failure CYCS 54205 Heart failure ADRB1 153 Heart failure TAZ 6901 Heart failure VIP 7432 Heart failure IGF1 3479 Heart failure NPPC 4880 Heart failure ACE 1636 Heart failure CST3 1471 Heart failure MUC16 94025 Heart failure RYR2 6262 Heart failure Aquaporin-2 359 Congestive heart failure Aquaporin 2 359 Congestive heart failure Atrial natriuretic peptide 4878 Congestive heart failure Brain natriuretic peptide 4879 Congestive heart failure Phospholamban 5350 Congestive heart failure CYP2C9 1559 Congestive heart failure RAGE (receptor) 177 Congestive heart failure Angiotensin II receptor type 1 185 Congestive heart failure Programmed cell death 1 5133 Congestive heart failure AGTR1 185 Congestive heart failure Atrial natriuretic factor 4878 Congestive heart failure PDCD1 5133 Congestive heart failure AGER 177 Congestive heart failure AQP2 359 Congestive heart failure PLN 5350 Congestive heart failure NPPB 4879 Congestive heart failure NPPA 4878 Congestive heart failure GroEL 3329 Endocarditis Ornithine transcarbamylase 5009 Endocarditis Valosin-containing protein 7415 Endocarditis Parathyroid hormone 1 receptor 5745 Endocarditis VDAC1 7416 Endocarditis RuvB-like 1 8607 Endocarditis TUBB2A 7280 Endocarditis ACTG1 71 Endocarditis ACTC1 70 Endocarditis PRDX6 9588 Endocarditis Hyaluronan-mediated motility receptor 3161 Endocarditis HSPB6 126393 Endocarditis Parathyroid hormone receptor 1 5745 Endocarditis VCP 7415 Endocarditis OTC 5009 Endocarditis PTH1R 5745 Endocarditis HSPD1 3329 Endocarditis HMMR 3161 Endocarditis RUVBL1 8607 Endocarditis HCN4 10021 Sick sinus syndrome Heparin-binding EGF-like growth factor 1839 Aortic valve disease HBEGF 1839 Aortic valve disease Von Willebrand factor 7450 Aortic valve stenosis ADAMTS13 11093 Aortic valve stenosis VWF 7450 Aortic valve stenosis Elastin 2006 Supravalvular aortic stenosis ELN 2006 Supravalvular aortic stenosis PRG4 10216 Pericarditis Histamine H3 receptor 11255 Myocardial ischemia MAP3K7IP1 10454 Myocardial ischemia Vascular endothelial growth factor A 7422 Myocardial ischemia Cathepsin L1 1514 Myocardial ischemia VEGF-A 7422 Myocardial ischemia VEGFA 7422 Myocardial ischemia CTSL1 1514 Myocardial ischemia TAB1 10454 Myocardial ischemia HRH3 11255 Myocardial ischemia APOA1 335 Coronary heart disease APOC3 345 Coronary heart disease Lipoprotein(a) 4018 Coronary heart disease Brain natriuretic peptide 4879 Coronary heart disease Beta-3 adrenergic receptor 155 Coronary heart disease Insulin-like growth factor 1 3479 Coronary heart disease Perlecan 3339 Coronary heart disease PCSK9 255738 Coronary heart disease Cholesterylester transfer protein 1071 Coronary heart disease Arachidonate 5-lipoxygenase 240 Coronary heart disease Apolipoprotein B 338 Coronary heart disease Apolipoprotein A1 335 Coronary heart disease Beta-1 adrenergic receptor 153 Coronary heart disease Apolipoprotein C3 345 Coronary heart disease Lipoprotein-associated phospholipase A2 7941 Coronary heart disease NEUROG3 50674 Coronary heart disease 5-lipoxygenase 240 Coronary heart disease ApoA1 335 Coronary heart disease CETP 1071 Coronary heart disease ApoB 338 Coronary heart disease IGF-1 3479 Coronary heart disease Insulin-like growth factor-1 3479 Coronary heart disease ApoCIII 345 Coronary heart disease PLA2G7 7941 Coronary heart disease ADRB3 155 Coronary heart disease ADRB1 153 Coronary heart disease APOB 338 Coronary heart disease ALOX5 240 Coronary heart disease IGF1 3479 Coronary heart disease NPPB 4879 Coronary heart disease HSPG2 3339 Coronary heart disease LPA 4018 Coronary heart disease CYP7A1 1581 Myocardial infarction Caspase 3 836 Myocardial infarction C-reactive protein 1401 Myocardial infarction Renin 5972 Myocardial infarction Factor VII 2155 Myocardial infarction Factor H 3075 Myocardial infarction Hepatic lipase 3990 Myocardial infarction Myeloperoxidase 4353 Myocardial infarction Endothelial protein C receptor 10544 Myocardial infarction ALDH2 217 Myocardial infarction C1-inhibitor 710 Myocardial infarction Basic fibroblast growth factor 2247 Myocardial infarction Myocyte-specific enhancer factor 2A 4205 Myocardial infarction 5-Lipoxygenase-activating protein 241 Myocardial infarction RAGE (receptor) 177 Myocardial infarction OLR1 4973 Myocardial infarction Beta-1 adrenergic receptor 153 Myocardial infarction PTGS2 5743 Myocardial infarction Cholesterol 7 alpha-hydroxylase 1581 Myocardial infarction GPVI 51206 Myocardial infarction Adrenomedullin 133 Myocardial infarction Prostacyclin synthase 5740 Myocardial infarction Cystatin C 1471 Myocardial infarction Tenascin X 7148 Myocardial infarction Thymosin beta-4 7114 Myocardial infarction GCLM 2730 Myocardial infarction S100A9 6280 Myocardial infarction IL1RL1 9173 Myocardial infarction LGALS2 3957 Myocardial infarction CKM (gene) 1158 Myocardial infarction ABCC9 10060 Myocardial infarction Renalase 55328 Myocardial infarction VTI1A 143187 Myocardial infarction MIAT (gene) 440823 Myocardial infarction BFGF 2247 Myocardial infarction TMSB4X 7114 Myocardial infarction CASP3 836 Myocardial infarction Caspase-3 836 Myocardial infarction Complement factor H 3075 Myocardial infarction MEF2A 4205 Myocardial infarction 5-lipoxygenase activating protein 241 Myocardial infarction Factor VIIa 2155 Myocardial infarction PROCR 10544 Myocardial infarction GP6 51206 Myocardial infarction F7 2155 Myocardial infarction AGER 177 Myocardial infarction ADRB1 153 Myocardial infarction MIAT 440823 Myocardial infarction CFH 3075 Myocardial infarction CKM 1158 Myocardial infarction CRP 1401 Myocardial infarction LIPC 3990 Myocardial infarction RNLS 55328 Myocardial infarction PTGIS 5740 Myocardial infarction TNXB 7148 Myocardial infarction SERPING1 710 Myocardial infarction FGF2 2247 Myocardial infarction REN 5972 Myocardial infarction ADM 133 Myocardial infarction CST3 1471 Myocardial infarction MPO 4353 Myocardial infarction ALOX5AP 241 Myocardial infarction Myoglobin 4151 Acute myocardial infarction Tissue plasminogen activator 5327 Acute myocardial infarction MIRN21 406991 Acute myocardial infarction Apolipoprotein B 338 Acute myocardial infarction Endothelin 1 1906 Acute myocardial infarction MMP3 4314 Acute myocardial infarction Heart-type fatty acid binding protein 2170 Acute myocardial infarction Alteplase 5327 Acute myocardial infarction FABP3 2170 Acute myocardial infarction ApoB 338 Acute myocardial infarction MB 4151 Acute myocardial infarction APOB 338 Acute myocardial infarction PLAT 5327 Acute myocardial infarction EDN1 1906 Acute myocardial infarction MIR21 406991 Acute myocardial infarction Adenosine A1 receptor 134 Myocardial stunning SOD2 6648 Myocardial stunning ADORA1 134 Myocardial stunning MYH7 4625 Endocardial fibroelastosis Tafazzin 6901 Endocardial fibroelastosis TAZ 6901 Endocardial fibroelastosis Nav1.5 6331 Conduction disease SCN5A 6331 Conduction disease PRKAG2 51422 Wolff-Parkinson-White syndrome TNNT2 7139 Restrictive cardiomyopathy Titin 7273 Hypertrophic cardiomyopathy CSRP3 8048 Hypertrophic cardiomyopathy CD36 948 Hypertrophic cardiomyopathy Myosin binding protein C, cardiac 4607 Hypertrophic cardiomyopathy MYH7 4625 Hypertrophic cardiomyopathy MYL9 10398 Hypertrophic cardiomyopathy TNNT2 7139 Hypertrophic cardiomyopathy ACTC1 70 Hypertrophic cardiomyopathy Endothelin 2 1907 Hypertrophic cardiomyopathy MYL2 4633 Hypertrophic cardiomyopathy MYH6 4624 Hypertrophic cardiomyopathy MYBPC1 4604 Hypertrophic cardiomyopathy MYL3 4634 Hypertrophic cardiomyopathy JPH2 57158 Hypertrophic cardiomyopathy MYLK2 85366 Hypertrophic cardiomyopathy MYBPC3 4607 Hypertrophic cardiomyopathy CD-36 948 Hypertrophic cardiomyopathy TTN 7273 Hypertrophic cardiomyopathy EDN2 1907 Hypertrophic cardiomyopathy Titin 7273 Dilated cardiomyopathy CSRP3 8048 Dilated cardiomyopathy Phospholamban 5350 Dilated cardiomyopathy Tafazzin 6901 Dilated cardiomyopathy Beta-1 adrenergic receptor 153 Dilated cardiomyopathy LMNA 4000 Dilated cardiomyopathy Palladin 23022 Dilated cardiomyopathy Fukutin 2218 Dilated cardiomyopathy TNNT2 7139 Dilated cardiomyopathy ACTC1 70 Dilated cardiomyopathy SGCD 6444 Dilated cardiomyopathy Programmed cell death 1 5133 Dilated cardiomyopathy LDB3 11155 Dilated cardiomyopathy ABCC9 10060 Dilated cardiomyopathy PDCD1 5133 Dilated cardiomyopathy ADRB1 153 Dilated cardiomyopathy TTN 7273 Dilated cardiomyopathy TAZ 6901 Dilated cardiomyopathy PLN 5350 Dilated cardiomyopathy PALLD 23022 Dilated cardiomyopathy FKTN 2218 Dilated cardiomyopathy
Note: In my previous post ADA was found to be associated to DOID:3363 (coronary arteriosclerosis). This result was not retrieved using SPARQL and this information is not available on the GeneWiki+ page for ADA. But keep in mind that GeneWiki+ is still under development.
That's it,
Pierre
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