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: MMP2

    Description: "matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"

    Entrez Gene ID: 4313

    SwissProt Acc Number: P08253

    RefSeq: NM_001127891

    It was suspected to be CHD related:

    ..The results suggest that the MMP2-1575 (rs243866) gene polymorphism could be involved in the risk of developing myocardial infarction in Mexican individuals...

    From PMID: 16122719, in Journal Cardiovasc Res.? , 2006


    References

    There were 13 potential papers with MMP2 and CHD.

    PMIDTitleJournalsDetails
    24137286 Rosuvastatin suppresses platelet-derived growth factor-BB-induced vascular smooth muscle cell proliferation and migration via the MAPK signaling pathway.Experimental and therapeutic medicineMore Details
    23146278 Heavy smoking before coronary surgical procedures affects the native matrix metalloproteinase-2 and matrix metalloproteinase-9 gene expression in saphenous vein conduits.The Annals of thoracic surgeryMore Details
    22664146 "Association of matrix metalloproteinases (MMP2, MMP7 and MMP9) genetic variants with left ventricular dysfunction in coronary artery disease patients."Clinica chimica acta; international journal of clinical chemistryMore Details
    22950427 Tissue inhibitor of matrix metalloproteinase-3 or vascular endothelial growth factor transfection of aged human mesenchymal stem cells enhances cell therapy after myocardial infarction.Rejuvenation researchMore 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
    21142815 The role of matrix metalloproteinase-2 promoter polymorphisms in coronary artery disease and myocardial infarction.Genetic testing and molecular biomarkersMore Details
    21206012 Matrix metalloproteinases 2 and 3 gene polymorphisms and the risk of target vessel revascularization after percutaneous coronary intervention: Is there still room for determining genetic variation of MMPs for assessment of an increased risk of restenosis?Disease markersMore Details
    19040207 Local matrix metalloproteinase 2 gene knockdown in balloon-injured rabbit carotid arteries using nonviral-small interfering RNA transfection.The journal of gene medicineMore Details
    17312010 Robust immunohistochemical staining of several classes of proteins in tissues subjected to autolysis.The journal of histochemistry and cytochemistry : official journal of theMore Details
    18035073 "Matrix metalloproteinase circulating levels, genetic polymorphisms, and susceptibility to acute myocardial infarction among patients with coronary artery disease."American heart journalMore Details
    16122719 Influence of matrix metalloproteinase genotype on cardiovascular disease susceptibility and outcome.Cardiovascular researchMore Details
    15958085 Sustained activation of neutrophils in the course of Kawasaki disease: an association with matrix metalloproteinases.Clinical and experimental immunologyMore Details
    10828225 Marimastat inhibits neointimal thickening in a model of human arterial intimal hyperplasia.European journal of vascular and endovascular surgery : the official journal ofMore Details

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



    PPI interactions

    There were totally 39 unique genes interacted with MMP2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TIMP2 Co-crystal Structure12032297|12374789 CHD related
    TIMP3 Reconstituted Complex10196161 CHD related
    TGFB1 Biochemical Activity10652271 CHD related
    PZP Reconstituted Complex9344465|9344465 No
    A2M Reconstituted Complex9344465|9344465 No
    CCL7 Two-hybrid10947989|10947989|10947989|10947989|10947989,12149192 CHD related
    LCN2 Affinity Capture-Western7683678 No
    BCAN Biochemical Activity10986281|10986281 No
    ITGAV Affinity Capture-Western22349830 CHD related
    ITGB1 Affinity Capture-Western22349830 CHD related
    HAPLN1 in vitro7694569 No
    COL7A1 in vivo10652000 No
    COL6A3 in vitro8862926 No
    COL18A1 in vitro;in vivo12023034 No
    FGFR1 in vitro;in vivo8692946 No
    IGFBP3 in vitro7523391 CHD related
    IL1B in vitro8663297 CHD related
    LGALS3 in vitro7947821 No
    KISS1 in vitro;in vivo12879005 No
    DCN in vitro9148753 CHD related
    EPHB2 in vitro18713744 No
    COL1A1 Reconstituted Complex11368514 CHD related
    TIMP4 Reconstituted Complex9182583|9182583,12374789 CHD related
    THBS1 Two-hybrid10900205|10900205 CHD related
    THBS2 Two-hybrid10900205|10900205 CHD related
    USP12 Affinity Capture-MS19615732 No
    OSBPL10 Affinity Capture-MS19615732 No
    KIAA0101 Affinity Capture-MS21628590 No
    CAND1 Affinity Capture-MS21145461 No
    TIMP1 in vitro12475252 CHD related
    MMP14 in vitro8663332,14583471 CHD related
    CXCL12 in vitro11571304 CHD related
    MMP17 in vitro10551873 No
    CLDN1 in vivo11382769 No
    MMP25 in vitro8663332,14583471 No
    BACE1 in vitro12586836 No
    SPOCK1 in vitro12810672 No
    ACAN in vitro7998967 No
    HSP90AA1 in vivo15146192 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00786MarimastatFor the treatment of various cancers
    approvedDB01197Captopril"For the treatment of essential or renovascular hypertension (usually administered with other drugs, particularly thiazide diuretics). May be used to treat congestive heart failure in combination with other drugs (e.g. cardiac glycosides, diuretics, β-adrenergic blockers). May improve survival in patients with left ventricular dysfunction following myocardial infarction. May be used to treat nephropathy, including diabetic nephropathy. "C09AA01
    experimentalDB01630SC-74020