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: PTAFR

    Description: platelet-activating factor receptor

    Entrez Gene ID: 5724

    SwissProt Acc Number: P25105

    RefSeq: NM_000952

    It was suspected to be CHD related:

    ..PAF-AH activity has been postulated to be a risk factor for coronary artery disease..

    From PMID: 15115767, in Journal Hum Mol Genet , 2004


    References

    There were 1 potential papers with PTAFR and CHD.

    PMIDTitleJournalsDetails
    15115767 Platelet-activating factor-acetylhydrolase and PAF-receptor gene haplotypes in relation to future cardiovascular event in patients with coronary artery disease.Human molecular geneticsMore Details

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



    PPI interactions

    There were totally 6 unique genes interacted with PTAFR. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ARRB2 Affinity Capture-Western11729201|11729201,9037196 No
    ARR3 Affinity Capture-Western11729201 No
    UBC Affinity Capture-Western14500726 No
    PTK2 Affinity Capture-Western20576130 No
    TYK2 in vivo14500680 No
    RGS4 in vitro11297424 CHD related


    Involved FDA drugs

    There was no drug associated with PTAFR