How to Build CHD@ZJU

CHD related Articles were retrieved from Pubmed, by entering keywords "coronary heart disease" and constrict the publish date from 2000/1/1 to now (2013/1/23). As a result, totally 115898 articles were found and their abstracts were downloaded for text mining. Since some articles didn't contain abstracts, only 88396 abstracts remained.
The text-mining process to get CHD related genes could be divided in to 5 following steps:

  • 1) Extracting all keywords from abstracts and ignoring those keywords start with numbers. 101402 keywords were extracted.

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  • 2) Input these keywords into Gene library in ArrayTrack and find possible related genes. 4674 genes were then found.

  • 3) Put these 4674 genes again into pubmed abstracts to find related aticles. Only genes which offical name or there keyword description (such as prolactin for gene PRL) could be found in the abstract would be remained. As a result, 1247 genes were remained.

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  • 4) Manually examined on the 1247 genes to validate it was acutally related to CHD. Some genes would be filtered if it represents other meanings (such as gene CAD, Entrez ID:790, carbamoyl-phosphate synthetase 2, is mostly meant coronary arterial disease in articles). 681 genes were then validated with at least one reference.

  • 5) All genes was compared with 1078 CHD genes in RGD database, and 370 genes were overlapped. These 370 genes were labels as "RGD_Supported" and the other 293 genes were labels as "REFERED". All 663 genes had supported references in CHD@ZJU which were examined by step 4.

    • How To contact Us

    Collaboration Information: Prof. Xiaohui Fan (fanxh@zju.edu.cn)

    Website using assistance : Leihong Wu (11019004@zju.edu.cn)



    Basic Information

    Gene Name: GLA

    Description: "galactosidase, alpha"

    Entrez Gene ID: 2717

    SwissProt Acc Number: P06280

    RefSeq: NM_000169

    It was suspected to be CHD related:

    ..Fabry's disease (FD) is a rare hereditary disorder caused by the loss of alpha galactosidase A activity leading to accumulation of glycosphingolipids in various organs including hypertrophy of the heart...

    From PMID: 20730727, in Journal Kardiol Pol , 2010


    References

    There were 29 potential papers with GLA and CHD.

    PMIDTitleJournalsDetails
    23877986 Matrix Gla protein species and risk of cardiovascular events in type 2 diabetic patients.Diabetes careMore Details
    23563003 No association between MGP rs1800802 polymorphism and stenosis of the coronary artery.Annals of Saudi medicineMore Details
    23307874 Matrix gla protein gene polymorphism is associated with increased coronary artery calcification progression."Arteriosclerosis, thrombosis, and vascular biology"More Details
    23677904 Common genetic variants of MGP are associated with calcification on the arterial wall but not with calcification present in the atherosclerotic plaques.Circulation. Cardiovascular geneticsMore Details
    22516723 Vitamin K status and vascular calcification: evidence from observational and clinical studies."Advances in nutrition (Bethesda, Md.)"More Details
    22558451 Globotriaosylsphingosine accumulation and not alpha-galactosidase-A deficiency causes endothelial dysfunction in Fabry disease.PloS oneMore Details
    21628633 "Circulating uncarboxylated matrix gla protein is associated with vitamin K nutritional status, but not coronary artery calcium, in older adults."The Journal of nutritionMore Details
    21747998 Endothelin but Not Angiotensin II May Mediate Hypertension-Induced Coronary Vascular Calcification in Chronic Kidney Disease.International journal of nephrologyMore Details
    20479029 The associations of fibroblast growth factor 23 and uncarboxylated matrix Gla protein with mortality in coronary artery disease: the Heart and Soul Study.Annals of internal medicineMore Details
    22767366 Cardiac involvement in Anderson-Fabry disease.BMJ case reportsMore Details
    19816015 "Coronary calcifications in end-stage renal disease patients: a new link between osteoprotegerin, diabetes and body mass index?"Blood purificationMore Details
    19386744 Vitamin K supplementation and progression of coronary artery calcium in older men and women.The American journal of clinical nutritionMore Details
    19847375 Does prolonged warfarin exposure potentiate coronary calcification in humans? Results of the warfarin and coronary calcification study.Calcified tissue internationalMore Details
    18348729 Can essential fatty acids reduce the burden of disease(s)?Lipids in health and diseaseMore Details
    18401181 The circulating inactive form of matrix Gla Protein (ucMGP) as a biomarker for cardiovascular calcification.Journal of vascular researchMore Details
    17074310 Activin-like kinase receptor 1 (ALK1) in atherosclerotic lesions and vascular mesenchymal cells.Cardiovascular researchMore Details
    17374084 Inhibitors of calcification in blood and urine.Seminars in dialysisMore Details
    17339737 [Calcified coronary artery disease and serum markers].Clinical calciumMore Details
    17259697 Serum levels of calcification inhibition proteins and coronary artery calcium score: comparison between transplantation and dialysis.American journal of nephrologyMore Details
    16484598 Optical imaging of hydroxyapatite in the calcified vasculature of transgenic animals."Arteriosclerosis, thrombosis, and vascular biology"More Details
    16458467 Proatherogenic pathways leading to vascular calcification.European journal of radiologyMore Details
    16973975 Matrix Gla protein is associated with risk factors for atherosclerosis but not with coronary artery calcification."Arteriosclerosis, thrombosis, and vascular biology"More Details
    16502129 Vascular calcification in chronic kidney disease.Journal of bone and mineral metabolismMore Details
    16169351 Relation of oral anticoagulation to cardiac valvular and coronary calcium assessed by multislice spiral computed tomography.The American journal of cardiologyMore Details
    15744522 Matrix Gla protein and osteopontin genetic associations with coronary artery calcification and bone density: the CARDIA study.Human geneticsMore Details
    15882271 Role of calcification inhibitors in the pathogenesis of vascular calcification in chronic kidney disease (CKD).Kidney internationalMore Details
    15961706 Novel conformation-specific antibodies against matrix gamma-carboxyglutamic acid (Gla) protein: undercarboxylated matrix Gla protein as marker for vascular calcification."Arteriosclerosis, thrombosis, and vascular biology"More Details
    15576949 [Risk factors of atherosclerosis in end-stage renal disease patients].Clinical calciumMore Details
    15045141 Matrix Gla protein is associated with coronary artery calcification as assessed by electron-beam computed tomography.Thrombosis and haemostasisMore Details

    NOTEs: These result is mostly from TEXT-MINING and there might have mismatches.



    PPI interactions

    There were totally 4 unique genes interacted with GLA. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GLA in vitro15003450 CHD related
    OTUD4 Affinity Capture-MS19615732 No
    UBC Affinity Capture-MS21987572|21139048|21890473|21906983 No
    FBXO6 Affinity Capture-MS22268729 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02944Alpha-D-Mannose