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: MMP8

    Description: matrix metallopeptidase 8 (neutrophil collagenase)

    Entrez Gene ID: 4317

    SwissProt Acc Number: P22894

    RefSeq: NM_002424

    It was suspected to be CHD related:

    .."Angiotensin II (Ang II)-mediated hypertension increases the risk for acute coronary syndrome, a consequence of atherosclerotic plaque rupture, which may be caused by matrix metalloproteinases (MMPs)."..

    From PMID: 15817699, in Journal J Leukoc Biol. , 2005


    References

    There were 2 potential papers with MMP8 and CHD.

    PMIDTitleJournalsDetails
    19745165 A role of matrix metalloproteinase-8 in atherosclerosis.Circulation researchMore Details
    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

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



    PPI interactions

    There were totally 7 unique genes interacted with MMP8. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BCAN Biochemical Activity10986281 No
    CCL2 in vitro;in vivo12149192,9558113 CHD related
    UBC Reconstituted Complex19850743 No
    TIMP2 in vitro10353844 CHD related
    UMOD in vitro8397318 No
    TFPI in vitro12117418 No
    ACAN in vitro8216228,7998967 No


    Involved FDA drugs

    There was no drug associated with MMP8