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: MMP3

    Description: "matrix metallopeptidase 3 (stromelysin 1, progelatinase)"

    Entrez Gene ID: 4314

    SwissProt Acc Number: P08254

    RefSeq: NM_002422

    It was suspected to be CHD related:

    ..The results provided strong evidence regarding the susceptibility of MMP3 and MMP9 genes to the development of CAD. ..

    From PMID: 22689717, in Journal Heart , 2012


    References

    There were 18 potential papers with MMP3 and CHD.

    PMIDTitleJournalsDetails
    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
    22689717 Matrix metalloproteinase family gene polymorphisms and risk for coronary artery disease: systematic review and meta-analysis.Heart (British Cardiac Society)More Details
    19762026 Haplotypes and 5A/6A polymorphism of the matrix metalloproteinase-3 gene in coronary disease: case-control study and a meta-analysis.AtherosclerosisMore Details
    20740392 Risk of coronary artery stenosis in Iranian type 2 diabetics: is there a role for matrix metalloproteinase-3 gene (-1612 5A/6A) polymorphism?Journal of physiology and biochemistryMore Details
    22371740 Genetic variability and the risk of myocardial infarction in Poles under 45 years of age.Archives of medical science : AMSMore 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
    20082876 Influence of genetic polymorphism in matrix metalloproteinase-3 on extent of coronary atherosclerosis and risk of coronary artery stenosis.Archives of medical researchMore Details
    19221176 Matrix metalloproteinase-1 and matrix metalloproteinase-3 gene promoter polymorphisms are associated with mortality in haemodialysis patients."Nephrology, dialysis, transplantation : official publication of the European"More 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
    17719307 Connexin37 (GJA4) genotype predicts survival after an acute coronary syndrome.American heart journalMore 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
    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
    15341739 Positive selection on MMP3 regulation has shaped heart disease risk.Current biology : CBMore Details
    12485468 Interaction between smoking and the stromelysin-1 (MMP3) gene 5A/6A promoter polymorphism and risk of coronary heart disease in healthy men.Annals of human geneticsMore Details
    11977998 The 5A6A polymorphism in the promoter of the stromelysin-1 (MMP3) gene as a risk factor for restenosis.European heart journalMore Details

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



    PPI interactions

    There were totally 18 unique genes interacted with MMP3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BCAN Biochemical Activity10986281 No
    SERPINE1 in vitro10967118 CHD related
    CCL13 in vitro12149192 No
    CCL8 in vitro12149192 No
    HAPLN1 in vitro7694569 No
    MMP3 in vitro10543949,10639284,10669564,10877850,11297453,11327577,9733482,9873489,9888835 CHD related
    DCN in vitro9148753 CHD related
    SPP1 in vitro11375993 CHD related
    IGFBP3 in vitro7523391 CHD related
    CCL2 in vitro;in vivo12149192,9558113 CHD related
    CCL7 in vitro;in vivo12149192,10947989 CHD related
    TIMP1 Co-crystal Structure9288970|9288970,12834347 CHD related
    SPOCK3 Affinity Capture-Western11751414|11751414 No
    TIMP3 in vitro;in vivo11827795 CHD related
    SPOCK1 in vitro12810672 No
    TNFSF11 in vitro15894268 CHD related
    PLG in vitro9548733 No
    ACAN in vitro7998967 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00786MarimastatFor the treatment of various cancers
    experimentalDB01877"N-Hydroxy 1n(4-Methoxyphenyl)Sulfonyl-4-(Z,E-N-Methoxyimino)Pyrrolidine-2r-Carboxamide"
    experimentalDB019963-Methylpyridine
    experimentalDB02090A Disubstituted Succinyl Caprolactam Hydroxymate Mmp3inhibitor
    experimentalDB02350"N-Hydroxy-4-[(4-Methoxylphenyl)Sulfonyl]-2,2-Dimethyl-Hexahydro-1,4-Thiazepine-3(S)-Carboxamide"
    experimentalDB02367(1n)-4-N-Butoxyphenylsulfonyl-(2r)-N-Hydroxycarboxamido-(4s)-Methanesulfonylamino-Pyrrolidine
    experimentalDB024493-(1h-Indol-3-Yl)-2-[4-(4-Phenyl-Piperidin-1-Yl)-Benzenesulfonylamino]-Propionic Acid
    experimentalDB02697Hydroxyaminovaline
    experimentalDB030331-Methyloxy-4-Sulfone-Benzene
    experimentalDB03368"5-Methyl-5-(4-Phenoxy-Phenyl)-Pyrimidine-2,4,6-Trione"
    experimentalDB041401-Benzyl-3-(4-Methoxy-Benzenesulfonyl)-6-Oxo-Hexahydro-Pyrimidine-4-Carboxylic Acid Hydroxyamide
    experimentalDB04232N-Hydroxy-1-(4-Methoxyphenyl)Sulfonyl-4-Benzyloxycarbonyl-Piperazine-2-Carboxamide
    experimentalDB04416"R-2-{[4'-Methoxy-(1,1'-Biphenyl)-4-Yl]-Sulfonyl}-Amino-6-Methoxy-Hex-4-Ynoic Acid"
    experimentalDB07390"2-[3-(5-MERCAPTO-[1,3,4]THIADIAZOL-2-YL)-UREIDO]-N-METHYL-3-PHENYL-PROPIONAMIDE"
    experimentalDB07986[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-ACETIC ACID
    experimentalDB07987"[2-(5-MERCAPTO-[1,3,4]THIADIAZOL-2-YLCARBAMOYL)-1-PHENYL-ETHYL]-CARBAMIC ACID BENZYL ESTER"
    experimentalDB07988"2-[3-(5-MERCAPTO-[1,3,4]THIADIAZOL-2YL)-UREIDO]-N-METHYL-3-PENTAFLUOROPHENYL-PROPIONAMIDE"
    experimentalDB08029N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~-(2-hydroxyethyl)glycinamide
    experimentalDB080303-[(4'-cyanobiphenyl-4-yl)oxy]-N-hydroxypropanamide
    experimentalDB08271N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID
    experimentalDB08507N-[[2-METHYL-4-HYDROXYCARBAMOYL]BUT-4-YL-N]-BENZYL-P-[PHENYL]-P-[METHYL]PHOSPHINAMID
    experimentalDB086432-(2-{2-[(BIPHENYL-4-YLMETHYL)-AMINO]-3-MERCAPTO-PENTANOYLAMINO}-ACETYLAMINO)-3-METHYL-BUTYRIC ACID METHYL ESTER