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: COL1A1

    Description: "collagen, type I, alpha 1"

    Entrez Gene ID: 1277

    SwissProt Acc Number: P02452

    RefSeq: NM_000088

    It was suspected to be CHD related:

    .."The ""SS"" genotype of the COL1A1 gene was found to occur significantly more frequently in patients surviving a MI,"..

    From PMID: 16869454, in Journal Acta Cardiol. , 2006


    References

    There were 5 potential papers with COL1A1 and CHD.

    PMIDTitleJournalsDetails
    23344661 "Integrins alpha4 and alphaM, collagen1A1, and matrix metalloproteinase 7 are upregulated in acute Kawasaki disease vasculopathy."Pediatric researchMore Details
    21077732 Gene expression profiles following intracoronary injection of mesenchymal stromal cells using a porcine model of chronic myocardial infarction.CytotherapyMore Details
    20117381 Growth differentiation factor 5 regulates cardiac repair after myocardial infarction.Journal of the American College of CardiologyMore Details
    19715896 Gene expression profiles in a porcine model of infarction: differential expression after intracoronary injection of heterologous bone marrow mesenchymal cells.Transplantation proceedingsMore Details
    15811432 Gene variants for osteoporosis and their pleiotropic effects in aging.Molecular aspects of medicineMore Details

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



    PPI interactions

    There were totally 39 unique genes interacted with COL1A1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ITGA2 Co-purification2156854 CHD related
    ITGB1 Co-purification2156854 CHD related
    NID1 Reconstituted Complex9733643 No
    NID2 Reconstituted Complex9733643 No
    SPARC Reconstituted Complex2745554 CHD related
    MMP2 Reconstituted Complex11368514 CHD related
    RNH1 Co-fractionation22939629 No
    CD44 in vitro1730778 CHD related
    IGFBP3 Two-hybrid12735930|12735930|12735930 CHD related
    TXN Two-hybrid12099690|12099690|12099690 CHD related
    PRELP Reconstituted Complex11847210|11847210 No
    PKD1 Reconstituted Complex11752017 CHD related
    VWF Co-fractionation3490481|3490481|3490481 CHD related
    THBS1 Reconstituted Complex3571333|3571333 CHD related
    COL7A1 Reconstituted Complex9169408 No
    MATN2 Reconstituted Complex12180907|12180907 No
    MAG Reconstituted Complex2446864 No
    ACHE Reconstituted Complex12524166 No
    UBC Affinity Capture-MS21139048 No
    ELAVL1 Affinity Capture-RNA19322201 No
    ATP13A2 Two-hybrid22645275 No
    C12orf57 Co-fractionation22939629 No
    BMP1 in vivo11283002 No
    CAPN1 yeast 2-hybrid12358155 No
    MMP9 in vivo9878537 CHD related
    CD93 in vitro1377218 CHD related
    DCN in vitro9675033,1468447 CHD related
    FN1 in vivo8468356 CHD related
    ITGA5 in vitro;in vivo1693626 CHD related
    FGF7 in vitro11973338 No
    CD36 in vitro2468670 CHD related
    PDGFB in vitro10446987 CHD related
    DDR2 in vitro9659899 No
    BGN in vitro7852349 No
    TGFBI in vitro12034705,11867580 No
    PAK1 in vitro10772928 CHD related
    P4HB in vitro1339453 No
    TMPRSS6 in vitro12149247 No
    HTRA1 yeast 2-hybrid15101818 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00048CollagenaseUsed to promote debridement of necrotic tissue in the treatment of severe burns and dermal ulcers including decubitus ulcers.D03BA02