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: PKP2

    Description: plakophilin 2

    Entrez Gene ID: 5318

    SwissProt Acc Number: Q99959

    RefSeq: NM_001005242

    It was suspected to be CHD related:

    .."We present such a method that extracts G x E information in longitudinal data of endophenotypes, and apply the method to repeated measures of multiple phenotypes related to coronary heart disease in Genetic Analysis Workshop 16 Problem 2. The new method identified many genes, including SCNN1B (sodium channel nonvoltage-gated 1 beta) and PKP2 (plakophilin 2), with potential time-dependent G x E interactions;"..

    From PMID: 20018082, in Journal BMC Proc. , 2009


    References

    There were 0 potential papers with PKP2 and CHD.

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



    PPI interactions

    There were totally 19 unique genes interacted with PKP2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    DSP Affinity Capture-Western11790773|11790773|11790773 No
    JUP Affinity Capture-Western11790773|11790773|11790773 CHD related
    DSG1 Affinity Capture-Western11790773|11790773|11790773 No
    DSG2 Affinity Capture-Western11790773|11790773 No
    DSC1 Two-hybrid11790773|11790773 No
    DSC2 Two-hybrid11790773|11790773 No
    POLR3A Reconstituted Complex11416169|11416169 No
    KRT18 Reconstituted Complex10852826|10852826 No
    KRT5 Reconstituted Complex10852826|10852826 No
    MARK3 Affinity Capture-Western12941695 No
    SMAD9 yeast 2-hybrid15231748 No
    PKP2 in vitro10852826 CHD related
    CTNNB1 in vivo;yeast 2-hybrid11790773 CHD related
    SFN Affinity Capture-MS15778465 No
    GTF2B Affinity Capture-Western11416169 No
    UBC Affinity Capture-MS21139048|21906983 No
    CUL3 Affinity Capture-MS21145461 No
    YWHAQ Affinity Capture-Western12941695 No
    YWHAG in vivo15324660 No


    Involved FDA drugs

    There was no drug associated with PKP2