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: PLA2G4A

    Description: "phospholipase A2, group IVA (cytosolic, calcium-dependent)"

    Entrez Gene ID: 5321

    SwissProt Acc Number: P47712

    RefSeq: NM_024420

    It was suspected to be CHD related:

    .."a PLA2G4A SNP (rs12746200) that decreased risk of CAD (OR = 0.7, 95% CI 0.6-0.9"..

    From PMID: 21293878, in Journal Hum Genet , 2011


    References

    There were 1 potential papers with PLA2G4A and CHD.

    PMIDTitleJournalsDetails
    21293878 Genetic contribution of the leukotriene pathway to coronary artery disease.Human geneticsMore Details

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



    PPI interactions

    There were totally 15 unique genes interacted with PLA2G4A. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    VIM in vitro10625659 CHD related
    PLA2G5 in vitro12124392 CHD related
    PLA2G4A in vitro9430701 CHD related
    KAT5 Affinity Capture-Western11416127|11416127 No
    UBC Affinity Capture-MS18781797|21139048|21906983 No
    SHBG Two-hybrid15862967 CHD related
    CKB Co-fractionation22939629 No
    CASP3 in vitro9875225 CHD related
    RPS6KA5 in vitro10978317 No
    MAPKAPK5 in vitro;in vivo10978317,9468497,8636128 No
    MKNK1 in vitro;in vivo10978317,9468497,8636128 No
    CASP4 in vivo9875225 No
    JAK1 in vivo8612580 CHD related
    MAPK14 in vivo9468497 CHD related
    CASP1 in vitro9875225 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00588Fluticasone PropionateFor the maintenance treatment of asthma as prophylactic therapy and for patients requiring oral corticosteroid therapy for asthma.D07AC17;R01AD08;R03BA05
    approvedDB01103QuinacrineFor the treatment of giardiasis and cutaneous leishmaniasis and the management of malignant effusions.
    approvedDB04552Niflumic AcidUsed in the treatment of rheumatoid arthritis.M02AA17;M01AX02