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: AGER

    Description: advanced glycosylation end product-specific receptor

    Entrez Gene ID: 177

    SwissProt Acc Number: Q15109

    RefSeq: NM_001136

    It was suspected to be CHD related:

    ..AGER 82S allele showed a protective effect on CAD severity in the presence of T2DM in Chinese Han population...

    From PMID: 21521347, in Journal Clin Endocrinol (Oxf) , 2011


    References

    There were 5 potential papers with AGER and CHD.

    PMIDTitleJournalsDetails
    23894685 Association of four genetic polymorphisms of AGER and its circulating forms with coronary artery disease: a meta-analysis.PloS oneMore Details
    21521347 Association of AGER gene G82S polymorphism with the severity of coronary artery disease in Chinese Han population.Clinical endocrinologyMore Details
    21282351 Receptor for advanced glycation end-products expression in subcutaneous adipose tissue is related to coronary artery disease.European journal of endocrinology / European Federation of Endocrine SocietiesMore Details
    17700210 Genetic polymorphism in the pregnancy-associated plasma protein-A associated with acute myocardial infarction.Coronary artery diseaseMore 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

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



    PPI interactions

    There were totally 9 unique genes interacted with AGER. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CANX Affinity Capture-Western10601334 No
    APP Reconstituted Complex21832049 No
    S100A1 in vivo11007787 CHD related
    S100B in vivo10399917 CHD related
    HMGB1 in vitro9812979 CHD related
    S100P Affinity Capture-Western14617629|14617629 CHD related
    SEC61B Affinity Capture-Western10601334 No
    S100A12 in vitro;in vivo10399917 CHD related
    TTR in vitro16716307 No


    Involved FDA drugs

    There was no drug associated with AGER