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: GPC3

    Description: glypican 3

    Entrez Gene ID: 2719

    SwissProt Acc Number: P51654

    RefSeq: NM_001164617

    It was suspected to be CHD related:

    ..Gpc3-deficient mice display a high incidence of congenital cardiac malformations..

    From PMID: 19733558, in Journal Dev Biol , 2009


    References

    There were 2 potential papers with GPC3 and CHD.

    PMIDTitleJournalsDetails
    22318994 Human gene copy number spectra analysis in congenital heart malformations.Physiological genomicsMore Details
    19733558 Loss of glypican-3 function causes growth factor-dependent defects in cardiac and coronary vascular development.Developmental biologyMore Details

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



    PPI interactions

    There were totally 5 unique genes interacted with GPC3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    FGF2 Affinity Capture-Western12478660|12478660 CHD related
    WNT3A in vivo16227623 CHD related
    WNT7B in vivo16227623 No
    IGF2 in vivo8589713 CHD related
    UBC Affinity Capture-MS21890473|21906983 No


    Involved FDA drugs

    There was no drug associated with GPC3