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: MMP9

    Description: "matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"

    Entrez Gene ID: 4318

    SwissProt Acc Number: P14780

    RefSeq: NM_004994

    It was suspected to be CHD related:

    ..The functional genetic polymorphisms present in the promoters of stromelysin-1 (MMP3) and gelatinase B (MMP9) have been shown to be associated with angiographically measured atherosclerosis..

    From PMID: 19438845, in Journal Ann Hum Genet , 2009


    References

    There were 25 potential papers with MMP9 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
    23377317 "Variations in matrix metalloproteinase-1, -3, and -9 genes and the risk of acute coronary syndrome and coronary artery disease in the Chinese Han population."Coronary artery diseaseMore 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
    23328249 Meta-analysis of MMP9-562C/T and the risk of coronary heart disease.CardiologyMore Details
    22878829 Intake of fermented beverages protect against acute myocardial injury: target organ cardiac effects and vasculoprotective effects.Basic research in cardiologyMore Details
    22738689 Peripheral blood gene expression profile of atherosclerotic coronary artery disease in patients of different ethnicity in Malaysia.Journal of cardiologyMore 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
    22689717 Matrix metalloproteinase family gene polymorphisms and risk for coronary artery disease: systematic review and meta-analysis.Heart (British Cardiac Society)More 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
    21462131 [Association of MMP9 gene -1562 C/T polymorphism with myocardial infarction in Uighur population of Xinjiang].Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = ChineseMore Details
    21887284 Pharmacogenetic associations of MMP9 and MMP12 variants with cardiovascular disease in patients with hypertension.PloS oneMore Details
    19438845 Haplotype analysis of the stromelysin-1 (MMP3) and gelatinase B (MMP9) genes in relation to coronary heart disease.Annals of human geneticsMore 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
    19751510 MMP-1 serum levels predict coronary atherosclerosis in humans.Cardiovascular diabetologyMore Details
    17275003 Genetic risk for restenosis after coronary stenting.AtherosclerosisMore 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
    17927738 Release of protein as well as activity of MMP-9 from unstable atherosclerotic plaques during percutaneous coronary intervention.Journal of internal medicineMore Details
    16424352 Modulation of hepatic inflammatory risk markers of cardiovascular diseases by PPAR-alpha activators: clinical and experimental evidence."Arteriosclerosis, thrombosis, and vascular biology"More Details
    16122719 Influence of matrix metalloproteinase genotype on cardiovascular disease susceptibility and outcome.Cardiovascular researchMore Details
    16905683 The role of genetic variants of matrix metalloproteinases in coronary and carotid atherosclerosis.Journal of medical geneticsMore Details
    15823277 Matrix metalloproteinase3 and 9 gene promoter polymorphisms: joint action of two loci as a risk factor for coronary artery complicated plaques.AtherosclerosisMore 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 33 unique genes interacted with MMP9. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CXCL5 Biochemical Activity12950257|12950257,10095777 CHD related
    CXCL6 Biochemical Activity12950257 No
    TGFB1 Biochemical Activity10652271 CHD related
    THBS1 Affinity Capture-Western10900205 CHD related
    THBS2 Affinity Capture-Western10900205 CHD related
    HAPLN1 in vitro7694569 No
    MMP9 in vitro12051944 CHD related
    COL4A3 in vivo9878537 No
    COL4A2 in vivo9878537 No
    COL4A1 in vivo9878537 CHD related
    COL4A4 in vivo9878537 No
    COL1A1 in vivo9878537 CHD related
    COL1A2 in vivo9878537 CHD related
    IL8 in vitro11023497 CHD related
    CXCL1 in vitro11023497 CHD related
    PLG in vitro9360944 No
    KISS1 in vitro;in vivo12879005 No
    PZP in vitro9344465 No
    TFPI in vitro10859319 No
    EPHB2 in vivo18713744 No
    AREG in vivo10389762 No
    CD44 in vivo10652271,17912438 CHD related
    FN1 in vitro11134254 CHD related
    MMP7 in vivo7896811 CHD related
    TIMP3 in vitro;in vivo11827795 CHD related
    COL4A5 in vivo9878537 No
    COL4A6 in vivo9878537 No
    LCN2 in vitro10339412,1281792 No
    BTC in vitro;in vivo10706134 No
    RECK in vitro9789069 No
    MMP26 in vivo12586837 No
    PRSS2 in vitro9578462,9261109 No
    MMP10 in vitro9578462 No


    Involved FDA drugs

    There was no drug associated with MMP9