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: MMP12

    Description: matrix metallopeptidase 12 (macrophage elastase)

    Entrez Gene ID: 4321

    SwissProt Acc Number: P39900

    RefSeq: NM_002426

    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 4 potential papers with MMP12 and CHD.

    PMIDTitleJournalsDetails
    23599440 Impaired coronary collateral growth in the metabolic syndrome is in part mediated by matrix metalloproteinase 12-dependent production of endostatin and angiostatin."Arteriosclerosis, thrombosis, and vascular biology"More Details
    22388798 Gene panels to help identify subgroups at high and low risk of coronary heart disease among those randomized to antihypertensive treatment: the GenHAT study.Pharmacogenetics and genomicsMore Details
    21887284 Pharmacogenetic associations of MMP9 and MMP12 variants with cardiovascular disease in patients with hypertension.PloS oneMore 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 5 unique genes interacted with MMP12. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APP Reconstituted Complex21832049 No
    PLAUR in vitro;in vivo12195704 CHD related
    F12 in vivo10930399 CHD related
    LPA in vitro10187779 CHD related
    TFPI in vitro10859319 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00551Acetohydroxamic Acid"Used, in addition to antibiotics or medical procedures, to treat chronic urea-splitting urinary infections."G04BX03
    approvedDB00786MarimastatFor the treatment of various cancers
    experimentalDB02118CP-271485
    experimentalDB03367PF-00356231
    experimentalDB03880Batimastat
    experimentalDB04405"2-[2-(1,3-Dioxo-1,3-Dihydro-2h-Isoindol-2-Yl)Ethyl]-4-(4'-Ethoxy-1,1'-Biphenyl-4-Yl)-4-Oxobutanoic Acid"
    experimentalDB07026"(1S,5S,7R)-N~7~-(BIPHENYL-4-YLMETHYL)-N~3~-HYDROXY-6,8-DIOXA-3-AZABICYCLO[3.2.1]OCTANE-3,7-DICARBOXAMIDE"
    experimentalDB07446N-(biphenyl-4-ylsulfonyl)-D-leucine
    experimentalDB07556N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE
    experimentalDB07683"N-(dibenzo[b,d]thiophen-3-ylsulfonyl)-L-valine"
    experimentalDB07920N-oxo-2-[(4-phenylphenyl)sulfonylamino]ethanamide
    experimentalDB079212-[(4-fluorophenyl)sulfonylamino]-N-oxo-ethanamide
    experimentalDB07922N-oxo-2-(phenylsulfonylamino)ethanamide
    experimentalDB08271N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID
    experimentalDB08599N-[(4-methoxyphenyl)sulfonyl]-D-alanine