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: MMP13

    Description: matrix metallopeptidase 13 (collagenase 3)

    Entrez Gene ID: 4322

    SwissProt Acc Number: P45452

    RefSeq: NM_002427

    It was suspected to be CHD related:

    .."Functional polymorphisms in the MMP1, MMP2, MMP7, MMP9, MMP12, and MMP13 genes have also been related to coronary artery disease, arterial stiffness, and/or abdominal aortic aneurysm."..

    From PMID: 16122719, in Journal Cardiovasc Res , 2006


    References

    There were 2 potential papers with MMP13 and CHD.

    PMIDTitleJournalsDetails
    19233360 Activation of MMP8 and MMP13 by angiotensin II correlates to severe intra-plaque hemorrhages and collagen breakdown in atherosclerotic lesions with a vulnerable phenotype.AtherosclerosisMore Details
    16122719 Influence of matrix metalloproteinase genotype on cardiovascular disease susceptibility and outcome.Cardiovascular researchMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with MMP13. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BCAN Biochemical Activity10986281|10986281 No
    LRP1 in vitro;in vivo10514495 CHD related
    TIMP3 in vitro9065415 CHD related
    F12 in vivo10930399 CHD related
    MMP13 in vitro10074939 CHD related
    COL2A1 in vitro8609233 No
    CCL7 in vitro;in vivo12149192,10947989 CHD related
    MMP14 in vivo8663255 CHD related
    ADAMTS5 in vitro11032846 No


    Involved FDA drugs

    There was no drug associated with MMP13