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: JUP

    Description: junction plakoglobin

    Entrez Gene ID: 3728

    SwissProt Acc Number: P14923

    RefSeq: NM_002230

    It was suspected to be CHD related:

    ..Antibody phage display assisted identification of junction plakoglobin as a potential biomarker for atherosclerosis...

    From PMID: 23110151, in Journal PLoS One. , 2012


    References

    There were 1 potential papers with JUP and CHD.

    PMIDTitleJournalsDetails
    23110151 Antibody phage display assisted identification of junction plakoglobin as a potential biomarker for atherosclerosis.PloS oneMore Details

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



    PPI interactions

    There were totally 70 unique genes interacted with JUP. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    WDYHV1 Two-hybrid16189514|16189514 No
    RIBC2 Two-hybrid16189514|16189514 No
    NFKBIE Two-hybrid16189514|16189514 No
    CTNNBIP1 Two-hybrid16189514|16189514 No
    CTNNA1 Affinity Capture-Western9762469|9110993|7650039,9110993,7890674 CHD related
    APC Reconstituted Complex8074697 No
    ERBB2 Far Western7702605|7702605 CHD related
    Dsc1 Affinity Capture-Western12847106 No
    Dsg1a Affinity Capture-Western12847106 No
    PLEC Co-fractionation22939629 No
    PTRH2 Co-fractionation22939629 No
    RPL21 Co-fractionation22939629 No
    SLC25A44 Co-fractionation22939629 No
    IARS2 Co-fractionation22939629 No
    ZFYVE9 yeast 2-hybrid15231748 No
    CDH15 in vitro9168809 No
    BIRC2 Two-hybrid16189514 No
    PHB2 Affinity Capture-MS17353931 No
    LGALS9 Affinity Capture-MS17353931 No
    CTNNB1 Affinity Capture-Western9535896|11712088 CHD related
    CDH1 Affinity Capture-Western7542250|9535896|8207061|1639850|8207061,7542250,10959047,1639850,7890674,11226248,8074697 No
    EGFR Reconstituted Complex9535896 CHD related
    MUC1 Affinity Capture-Western12939402|12939402 No
    CDH3 Affinity Capture-Western10910767|10910767 No
    CDH5 Affinity Capture-Western9434630|12003790|9739078,12003790 CHD related
    CDH2 Affinity Capture-MS14625392|7650039|22939629 No
    PTPN14 Affinity Capture-MS12808048|12808048 No
    PKP3 Two-hybrid12707304 No
    RAB8B Affinity Capture-Western12639940 No
    ARHGDIA Two-hybrid16169070|16169070 No
    DSG3 Affinity Capture-Western7738346 No
    PKP2 Affinity Capture-Western11790773|11790773|11790773 CHD related
    DSG2 Affinity Capture-Western11710948 No
    BTRC Affinity Capture-Western10803460|10803460 No
    DSC2 Affinity Capture-Western9443898 No
    GJB1 Affinity Capture-Western7971964 No
    DSC3 Affinity Capture-Western10769211|10769211 No
    PECAM1 Affinity Capture-Western10801826|10801826 CHD related
    TCF7L2 Reconstituted Complex11711551|11711551 CHD related
    DSP Affinity Capture-Western9739078 No
    DSG1 Reconstituted Complex9606214 No
    PTPRF Reconstituted Complex9245795|9245795 No
    PTPRK Reconstituted Complex8663237|8663237|8663237 No
    USP1 Affinity Capture-MS19615732 No
    UBC Affinity Capture-MS16335966|18781797|21987572|21963094|21139048|21906983 No
    INSIG2 Affinity Capture-MS19815544 No
    KIAA0101 Affinity Capture-MS21628590 No
    CUL4B Affinity Capture-MS21145461 No
    CUL2 Affinity Capture-MS21145461 No
    CDK2 Affinity Capture-MS21319273 No
    COPS5 Affinity Capture-MS21145461 No
    GRK5 Affinity Capture-MS22952844 CHD related
    UBD Affinity Capture-MS22797925 No
    ILF3 Co-fractionation22939629 No
    ITGB4 Co-fractionation22939629 No
    B4GALT1 Co-fractionation22939629 No
    DBN1 Co-fractionation22939629 No
    ABCC2 Co-fractionation22939629 No
    NENF Co-fractionation22939629 No
    ILF2 Co-fractionation22939629 No
    DES Co-fractionation22939629 No
    PTPRJ in vitro12370829 No
    CTNND1 in vivo7876318 No
    PKD1 in vitro;in vivo11274246 CHD related
    AXIN1 in vitro;in vivo10488109 No
    SRC in vitro14517306 CHD related
    FER in vitro14517306 No
    FYN in vitro14517306 No
    PSEN1 in vitro;in vivo16306047,11226248 No
    TCF4 in vitro;in vivo16306047 No


    Involved FDA drugs

    There was no drug associated with JUP