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: LGALS2

    Description: "lectin, galactoside-binding, soluble, 2"

    Entrez Gene ID: 3957

    SwissProt Acc Number: P05162

    RefSeq: NM_006498

    It was suspected to be CHD related:

    .."we have identified additional MI susceptible genes, LGALS2, PSMA6 and BRAP, so far."..

    From PMID: 20387550, in Journal Nihon Rinsho , 2010


    References

    There were 9 potential papers with LGALS2 and CHD.

    PMIDTitleJournalsDetails
    21831908 Galectin-2 expression is dependent on the rs7291467 polymorphism and acts as an inhibitor of arteriogenesis.European heart journalMore Details
    22310064 "Polymorphisms of LTA, LGALS2, and PSMA6 genes and coronary atherosclerosis: a pathological study of 1503 consecutive autopsy cases."AtherosclerosisMore Details
    19726041 "Lack of association between lymphotoxin-alpha, galectin-2 polymorphisms and coronary artery disease: a meta-analysis."AtherosclerosisMore Details
    19198608 SNPs in BRAP associated with risk of myocardial infarction in Asian populations.Nature geneticsMore Details
    17040205 "Effects of lymphotoxin-alpha gene and galectin-2 gene polymorphisms on inflammatory biomarkers, cellular adhesion molecules and risk of coronary heart disease.""Clinical science (London, England : 1979)"More Details
    17493152 Lack of association between LTA and LGALS2 polymorphisms and myocardial infarction in Japanese and Korean populations.Tissue antigensMore Details
    17517687 Association of variants in the BAT1-NFKBIL1-LTA genomic region with protection against myocardial infarction in Europeans.Human molecular geneticsMore Details
    16987874 Genetic susceptibility to myocardial infarction and coronary artery disease.Human molecular geneticsMore Details
    15129282 Functional variation in LGALS2 confers risk of myocardial infarction and regulates lymphotoxin-alpha secretion in vitro.NatureMore Details

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



    PPI interactions

    There were totally 5 unique genes interacted with LGALS2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APP Reconstituted Complex21832049 No
    TUBA4A in vivo15129282 No
    LGALS2 in vitro8262940,8411163 CHD related
    LTA in vitro;in vivo15129282 CHD related
    IKBKG Reconstituted Complex20098747 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02379Beta-D-Glucose