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: MYH7

    Description: "myosin, heavy chain 7, cardiac muscle, beta"

    Entrez Gene ID: 4625

    SwissProt Acc Number: P12883

    RefSeq: NM_000257

    It was suspected to be CHD related:

    .."The entire coding sequences of 9 genes (MYH7,MYBPC3,TNNI3,TNNT2,MYL2,MYL3,TPM1,ACTC, and TNNC1) were analyzed in 197 unrelated index cases with familial or sporadic hypertrophic cardiomyopathy"..

    From PMID: 12707239, in Journal Circulation. , 2003


    References

    There were 2 potential papers with MYH7 and CHD.

    PMIDTitleJournalsDetails
    22869457 Coronary telangiectasia associated with hypertrophic cardiomyopathy.European journal of heart failureMore Details
    18374998 Hypertrophic cardiomyopathy due to beta-myosin heavy chain mutation with extreme phenotypic variability within a family.International journal of cardiologyMore Details

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



    PPI interactions

    There were totally 8 unique genes interacted with MYH7. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-Western20035047 No
    TEAD4 in vitro;yeast 2-hybrid12861002 No
    TEAD3 in vitro12861002 No
    NTHL1 Affinity Capture-MS17353931 No
    PSMD4 Affinity Capture-MS12601813 No
    YWHAQ Affinity Capture-MS20618440 No
    KIAA0368 Two-hybrid20682791|20682791|20682791 No
    TEAD1 in vitro;yeast 2-hybrid8253797,12861002 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB08378"4-[4-(2,5-DIOXO-PYRROLIDIN-1-YL)-PHENYLAMINO]-4-HYDROXY-BUTYRIC ACID"