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: BAT3

    Description: HLA-B associated transcript 3

    Entrez Gene ID: 7917

    SwissProt Acc Number: P46379

    RefSeq: NM_001098534

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

    .."BAT2 -8671, BAT3 8854, and BAT5 22655, 9569 polymorphisms as well as BAT haplotypes (ATTGTG and ATCATG) might be associated with higher KD susceptibility and CAA formation. "..

    From PMID: 20626023, in Journal J Clin Lab Anal , 2010


    References

    There were 2 potential papers with BAT3 and CHD.

    PMIDTitleJournalsDetails
    21815799 Major histocompatibility complex class I chain-related gene polymorphisms: associated with susceptibility to Kawasaki disease and coronary artery aneurysms.Genetic testing and molecular biomarkersMore Details
    20626023 "Human lymphocyte antigen B-associated transcript 2, 3, and 5 polymorphisms and haplotypes are associated with susceptibility of Kawasaki disease and coronary artery aneurysm."Journal of clinical laboratory analysisMore Details

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



    PPI interactions

    There were totally 52 unique genes interacted with BAT3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SMN1 yeast 2-hybrid16169070 No
    CSTF2 yeast 2-hybrid16169070 No
    IMMT yeast 2-hybrid16169070 No
    TOMM20 yeast 2-hybrid16169070 No
    STX5 yeast 2-hybrid16169070 No
    IKBKAP yeast 2-hybrid16169070 No
    EFEMP2 yeast 2-hybrid16189514 No
    SETDB1 yeast 2-hybrid16169070 No
    ARPC3 yeast 2-hybrid16169070 No
    KLHL12 yeast 2-hybrid16189514 No
    FAM173A yeast 2-hybrid16169070 No
    PPAP2C yeast 2-hybrid16169070 No
    DNAJB11 yeast 2-hybrid16169070 No
    - yeast 2-hybrid16169070 No
    C19orf10 yeast 2-hybrid16169070 No
    PELP1 yeast 2-hybrid16169070 No
    NOMO1 yeast 2-hybrid16169070 No
    IQCG yeast 2-hybrid16169070 No
    UBQLN4 yeast 2-hybrid16713569 No
    EP300 in vivo17403783 CHD related
    HSPA8 in vitro11230127 CHD related
    PRPF40A yeast 2-hybrid15231748 No
    ATN1 yeast 2-hybrid16713569 No
    ZFYVE9 yeast 2-hybrid15231748 No
    CDK4 yeast 2-hybrid16169070 CHD related
    ATXN2 yeast 2-hybrid16713569 No
    B2M yeast 2-hybrid16169070 CHD related
    CTSB yeast 2-hybrid16169070 CHD related
    CTSE yeast 2-hybrid16169070 No
    DPT yeast 2-hybrid16169070 No
    IGFBP5 yeast 2-hybrid16169070 CHD related
    RAB8A yeast 2-hybrid16169070 No
    REG1B yeast 2-hybrid16169070 No
    PTH yeast 2-hybrid16169070 CHD related
    PRNP yeast 2-hybrid16169070 No
    FKBP2 yeast 2-hybrid16169070 No
    TDGF1 yeast 2-hybrid16169070 No
    GLRA2 yeast 2-hybrid16169070 No
    CDK16 yeast 2-hybrid16169070 No
    RCN2 yeast 2-hybrid16169070 No
    CHN2 yeast 2-hybrid16169070 No
    EDN1 yeast 2-hybrid16169070 CHD related
    TAC1 yeast 2-hybrid16169070 No
    NDUFA6 yeast 2-hybrid16169070 No
    S100A4 yeast 2-hybrid16169070 No
    SGTA yeast 2-hybrid14667819 No
    NBL1 yeast 2-hybrid10390159 No
    XRN1 yeast 2-hybrid15231747 No
    RNF126 yeast 2-hybrid14667819 No
    UBL7 yeast 2-hybrid14667819 No
    FAM46A yeast 2-hybrid15231748 No
    PTPN12 yeast 2-hybrid15231748 No


    Involved FDA drugs

    There was no drug associated with BAT3