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: BHMT

    Description: betaine-homocysteine methyltransferase

    Entrez Gene ID: 635

    SwissProt Acc Number: Q93088

    RefSeq: NM_001713

    It was supported literatures to be a novel CHD related gene:

    ..Our study suggests that the Q allele of the R239Q mutation may decrease the risk of CAD and that this variant warrants additional investigation of its relationship with the development of CAD as well as other homocysteine-dependent disorders...

    From PMID: 12818402, in Journal Atherosclerosis. , 2003


    References

    There were 2 potential papers with BHMT and CHD.

    PMIDTitleJournalsDetails
    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
    21876361 Gene polymorphisms and low dietary intake of micronutrients in coronary artery disease.Journal of nutrigenetics and nutrigenomicsMore Details

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



    PPI interactions

    There were totally 1 unique genes interacted with BHMT. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BHMT Two-hybrid16189514|11223523|12071701,11223523,12220488,16189514 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00134L-Methionine"Used for protein synthesis including the formation of SAMe, L-homocysteine, L-cysteine, taurine, and sulfate."V03AB26
    experimentalDB02337S-(D-Carboxybutyl)-L-Homocysteine
    experimentalDB04272Citric AcidA09AB04