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: BAT2

    Description: HLA-B associated transcript 2

    Entrez Gene ID: 7916

    SwissProt Acc Number: P48634

    RefSeq: NM_080686

    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. HLA-B region polymorphisms might contribute to the pathogenesis of KD and CAA."..

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


    References

    There were 2 potential papers with BAT2 and CHD.

    PMIDTitleJournalsDetails
    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
    19023099 Gene variants associated with ischemic stroke: the cardiovascular health study.Stroke; a journal of cerebral circulationMore Details

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



    PPI interactions

    There were totally 24 unique genes interacted with BAT2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GRB2 yeast 2-hybrid14667819 CHD related
    - yeast 2-hybrid16713569 No
    FGA yeast 2-hybrid14667819 CHD related
    QARS yeast 2-hybrid14667819 No
    ATN1 yeast 2-hybrid16713569 No
    ATXN1 yeast 2-hybrid16713569 No
    RERE yeast 2-hybrid16713569 No
    MAN2C1 yeast 2-hybrid14667819 No
    HNRNPM yeast 2-hybrid14667819 No
    HNRNPA1 yeast 2-hybrid14667819 No
    PSMA3 yeast 2-hybrid14667819 No
    CCR10 yeast 2-hybrid14667819 No
    IMMT yeast 2-hybrid14667819 No
    C1QBP yeast 2-hybrid14667819 No
    GANAB yeast 2-hybrid14667819 No
    EIF3E yeast 2-hybrid14667819 CHD related
    CPSF1 yeast 2-hybrid14667819 No
    DDX20 yeast 2-hybrid14667819 No
    UBAP2L yeast 2-hybrid14667819 No
    MAD2L2 yeast 2-hybrid14667819 No
    IFT88 yeast 2-hybrid14667819 No
    PRMT2 yeast 2-hybrid14667819 No
    P4HA2 yeast 2-hybrid14667819 No
    SSR3 yeast 2-hybrid14667819 No


    Involved FDA drugs

    There was no drug associated with BAT2