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: MYBPC3

    Description: "myosin binding protein C, cardiac"

    Entrez Gene ID: 4607

    SwissProt Acc Number: Q14896

    RefSeq: NM_000256

    It was suspected to be CHD related:

    ..Association of 25 bp deletion in MYBPC3 gene with left ventricle dysfunction in coronary artery disease patients...

    From PMID: 21915287, in Journal PLoS One. , 2011


    References

    There were 4 potential papers with MYBPC3 and CHD.

    PMIDTitleJournalsDetails
    22869457 Coronary telangiectasia associated with hypertrophic cardiomyopathy.European journal of heart failureMore Details
    22021246 Carriers of the hypertrophic cardiomyopathy MYBPC3 mutation are characterized by reduced myocardial efficiency in the absence of hypertrophy and microvascular dysfunction.European journal of heart failureMore Details
    21915287 Association of 25 bp deletion in MYBPC3 gene with left ventricle dysfunction in coronary artery disease patients.PloS oneMore Details
    20435227 Clinical assessment incorporating a personal genome.LancetMore Details

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



    PPI interactions

    There were totally 11 unique genes interacted with MYBPC3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TRIM63 Two-hybrid19850579 No
    MYBPC3 yeast 2-hybrid12386147 CHD related
    MYH9 in vitro;in vivo6448079,352343,10672519 No
    TNNI3K Two-hybrid12721663|12721663 No
    TTN Far Western8631348 CHD related
    ALK Affinity Capture-MS14968112 No
    BLNK Affinity Capture-MS21822214 No
    FBXO32 Affinity Capture-Western19850579 No
    CUL1 Affinity Capture-MS21145461 No
    NCF1 Two-hybrid16052631|16052631 CHD related
    CAPN1 yeast 2-hybrid12358155 No


    Involved FDA drugs

    There was no drug associated with MYBPC3