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: PRKCH

    Description: "protein kinase C, eta"

    Entrez Gene ID: 5583

    SwissProt Acc Number: P24723

    RefSeq: NM_006255

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

    .."In conclusion, weobserved that there was a remarkable association of minor alleles (1425G/A and _15) in the PRKCH gene with an elevated risk of CAD and increased levels of LDL-C in this Chinese population."..

    From PMID: 21625852, in Journal Mol Biol Rep. , 2012


    References

    There were 2 potential papers with PRKCH and CHD.

    PMIDTitleJournalsDetails
    21625852 The role of PRKCH gene variants in coronary artery disease in a Chinese population.Molecular biology reportsMore Details
    17206144 A nonsynonymous SNP in PRKCH (protein kinase C eta) increases the risk of cerebral infarction.Nature geneticsMore Details

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



    PPI interactions

    There were totally 14 unique genes interacted with PRKCH. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ZBTB8OS Two-hybrid20936779 No
    NFE2L2 Biochemical Activity19920073 CHD related
    PRKCH Biochemical Activity19920073 CHD related
    PTPN11 in vivo11781100 CHD related
    ITGB2 in vitro11700305 CHD related
    PRKD1 in vitro;in vivo10867018,11741879 No
    SRC in vitro8621384 CHD related
    FYN in vitro8621384 No
    CDK2 Affinity Capture-Western11175348 No
    MGMT Affinity Capture-MS16226712 No
    UBC Affinity Capture-MS21139048|21906983|22505724 No
    VHL Affinity Capture-Western10491320 No
    PARD6A in vivo17335965 No
    NUMB in vitro17203073 No


    Involved FDA drugs

    There was no drug associated with PRKCH