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.

  • 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.

  • 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: MGP

    Description: matrix Gla protein

    Entrez Gene ID: 4256

    SwissProt Acc Number: P08493

    RefSeq: NM_000900

    It was suspected to be CHD related:

    ..Matrix gamma-carboxyglutamate (Gla) protein (MGP) is a vitamin K-dependent protein and a strong inhibitor of vascular calcification...

    From PMID: 18401181, in Journal J Vasc Res , 2008


    References

    There were 20 potential papers with MGP and CHD.

    PMIDTitleJournalsDetails
    24072176 Research Progress of Warfarin-associated Vascular Calcification and its Possible Therapy.Journal of cardiovascular pharmacologyMore Details
    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
    23317172 Calcification of coronary arteries and abdominal aorta in relation to traditional and novel risk factors of atherosclerosis in hemodialysis patients.BMC nephrologyMore Details
    22516723 Vitamin K status and vascular calcification: evidence from observational and clinical studies."Advances in nutrition (Bethesda, Md.)"More 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
    20592751 Human lipoxygenase pathway gene variation and association with markers of subclinical atherosclerosis in the diabetes heart study.Mediators of inflammationMore 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
    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
    17259697 Serum levels of calcification inhibition proteins and coronary artery calcium score: comparison between transplantation and dialysis.American journal of nephrologyMore 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
    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
    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 1 unique genes interacted with MGP. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BMP2 Affinity Capture-Western11741887 CHD related


    Involved FDA drugs

    There was no drug associated with MGP