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: MTR

    Description: 5-methyltetrahydrofolate-homocysteine methyltransferase

    Entrez Gene ID: 4548

    SwissProt Acc Number: Q99707

    RefSeq: NM_000254

    It was suspected to be CHD related:

    .."Alcohol intake in subjects with MTR 2756G allele was found to inflate the risk for CAD [OR: 4.15, 95% CI: 1.35-12.69]."..

    From PMID: 19394322, in Journal Clin Chim Acta , 2009


    References

    There were 9 potential papers with MTR and CHD.

    PMIDTitleJournalsDetails
    23824729 Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.The American journal of clinical nutritionMore Details
    22339686 "Folate gene polymorphisms MTR A2756G, MTRR A66G, and BHMT G742A and risk for coronary artery disease: a meta-analysis."Genetic testing and molecular biomarkersMore Details
    21780915 Three genetic polymorphisms of homocysteine-metabolizing enzymes and risk of coronary heart disease: a meta-analysis based on 23 case-control studies.DNA and cell biologyMore Details
    21567207 Tetra primer ARMS-PCR relates folate/homocysteine pathway genes and ACE gene polymorphism with coronary artery disease.Molecular and cellular biochemistryMore Details
    19283448 Genetic polymorphisms involved in folate metabolism and concentrations of methylmalonic acid and folate on plasma homocysteine and risk of coronary artery disease.Journal of thrombosis and thrombolysisMore Details
    19394322 Genetic and environmental influences on total plasma homocysteine and coronary artery disease (CAD) risk among South Indians.Clinica chimica acta; international journal of clinical chemistryMore Details
    18844488 Association between the 2756A> G variant in the gene encoding methionine synthase and myocardial infarction in Tunisian patients.Clinical chemistry and laboratory medicine : CCLM / FESCCMore Details
    17822659 "Relation between plasma homocysteine, gene polymorphisms of homocysteine metabolism-related enzymes, and angiographically proven coronary artery disease."European journal of internal medicineMore Details
    16268464 "Association of MTRRA66G polymorphism (but not of MTHFR C677T and A1298C, MTRA2756G, TCN C776G) with homocysteine and coronary artery disease in the French population."Thrombosis and haemostasisMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with MTR. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NAPG Co-fractionation22939629 No
    TSC22D1 Affinity Capture-MS17353931 No
    UBC Affinity Capture-MS16196087|21963094|21139048|21890473|21906983|22053931|22505724 No
    CDKN2A Affinity Capture-MS17955473 CHD related
    ELAVL1 Affinity Capture-RNA19322201 No
    UBD Affinity Capture-MS22797925 No
    LSM4 Co-fractionation22939629 No
    DHX16 Co-fractionation22939629 No
    ILF2 Co-fractionation22939629 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00115CyanocobalaminFor treatment of pernicious anemia (due to lack of or inhibition of intrinsic factor) and for prevention and treatment of vitamin B 12 deficiency.B03BB01;B03BA01
    approved;nutraceuticalDB00116Tetrahydrofolic acid"For nutritional supplementation, also for treating dietary shortage or imbalance."
    approved;nutraceuticalDB00134L-Methionine"Used for protein synthesis including the formation of SAMe, L-homocysteine, L-cysteine, taurine, and sulfate."V03AB26
    approvedDB00200Hydroxocobalamin"For treatment of pernicious anemia and the prevention and treatment of vitamin B12 deficiency arising from alcoholism, malabsorption, tapeworm infestation, celiac, hyperthyroidism, hepatic-biliary tract disease, persistent diarrhea, ileal resection, pancreatic cancer, renal disease, prolonged stress, vegan diets, macrobiotic diets or other restrictive diets. Also for the treatment of known or suspected cyanide poisoning."B03BA03;V03AB33