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: MMP1

    Description: matrix metallopeptidase 1 (interstitial collagenase)

    Entrez Gene ID: 4312

    SwissProt Acc Number: P03956

    RefSeq: NM_001145938

    It was suspected to be CHD related:

    .."Our data shows MMP1 gene -519A/G polymorphism is associated with the risk of CHD, "..

    From PMID: 19099971, in Journal Zhonghua Xin Xue Guan Bing Za Zhi. , 2008


    References

    There were 8 potential papers with MMP1 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
    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
    22371740 Genetic variability and the risk of myocardial infarction in Poles under 45 years of age.Archives of medical science : AMSMore 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
    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
    16210545 Haplotype effect of the matrix metalloproteinase-1 gene on risk of myocardial infarction.Circulation researchMore Details

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



    PPI interactions

    There were totally 17 unique genes interacted with MMP1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BCAN Biochemical Activity10986281 No
    SERPINA3 in vitro;in vivo1311327 CHD related
    IGFBP3 in vitro7523391 CHD related
    CCL2 in vitro;in vivo12149192,9558113 CHD related
    CCL7 in vitro;in vivo12149192,10947989 CHD related
    CCL13 in vitro;in vivo12149192 No
    TNFSF11 in vivo10224132 CHD related
    TFPI in vitro10859319 No
    COL2A1 in vitro8609233 No
    CD44 in vitro11381077 CHD related
    ITGA2 Reconstituted Complex11359774|11359774,11359786 CHD related
    TIMP1 Reconstituted Complex9063449|9063449 CHD related
    BSG Affinity Capture-Western10706100 No
    UBC Affinity Capture-MS21890473 No
    CMA1 in vitro;in vivo8027075 CHD related
    MMP7 in vitro7896811 CHD related
    ACAN in vitro8216228 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00786MarimastatFor the treatment of various cancers
    experimentalDB07556N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE
    experimentalDB07926N-[3-(N'-HYDROXYCARBOXAMIDO)-2-(2-METHYLPROPYL)-PROPANOYL]-O-TYROSINE-N-METHYLAMIDE
    experimentalDB08403METHYLAMINO-PHENYLALANYL-LEUCYL-HYDROXAMIC ACID
    experimentalDB08482[[1-[N-HYDROXY-ACETAMIDYL]-3-METHYL-BUTYL]-CARBONYL-LEUCINYL]-ALANINE ETHYL ESTER
    experimentalDB08491N-HYDROXY-2-[4-(4-PHENOXY-BENZENESULFONYL)-TETRAHYDRO-PYRAN-4-YL]-ACETAMIDE