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: GP6

    Description: glycoprotein VI (platelet)

    Entrez Gene ID: 51206

    SwissProt Acc Number: Q9HCN6

    RefSeq: NM_001083899

    It was supported literatures to be a novel CHD related gene:

    .."Furthermore, HT increased the HR of CHD events in patients with the GP1BA -5TT plus GP6 13254TC+CC genotypes by 57% and reduced the HR in patients with the GP1BA -5TC+CC plus GP6 13254TT genotypes by 55% (adj interaction P < .001). "..

    From PMID: 17105818, in Journal Blood. , 2007


    References

    There were 2 potential papers with GP6 and CHD.

    PMIDTitleJournalsDetails
    17105818 Effect of genetic variations in platelet glycoproteins Ibalpha and VI on the risk for coronary heart disease events in postmenopausal women taking hormone therapy.BloodMore Details
    16706959 Definition of novel GP6 polymorphisms and major difference in haplotype frequencies between populations by a combination of in-depth exon resequencing and genotyping with tag single nucleotide polymorphisms.Journal of thrombosis and haemostasis : JTHMore Details

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



    PPI interactions

    There were totally 12 unique genes interacted with GP6. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    LYN Reconstituted Complex11943772|11943772|12594225|20946164|11943772,1715582 No
    FYN Reconstituted Complex11943772|11943772,1715582 No
    CALM1 Affinity Capture-Western12594225|20946164 No
    FCER1G Affinity Capture-Western12594225|10825177,9280292 No
    TRAF4 Affinity Capture-Western20946164 No
    TGFB1I1 Affinity Capture-Western20946164 No
    NCF1 Affinity Capture-Western20946164 CHD related
    PTK2B Affinity Capture-Western20946164 No
    YES1 in vivo1715582 No
    CRP in vitro11027634 CHD related
    FCGR3A in vivo10961879,11027634 CHD related
    FCGR2A in vivo9295288,9280292 CHD related


    Involved FDA drugs

    There was no drug associated with GP6