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: BAT5

    Description: HLA-B associated transcript 5

    Entrez Gene ID: 7920

    SwissProt Acc Number: O95870

    RefSeq: NM_021160

    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 1 potential papers with BAT5 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

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



    PPI interactions

    There were totally 16 unique genes interacted with BAT5. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PTGS2 yeast 2-hybrid14667819 CHD related
    UPF1 yeast 2-hybrid15231747 No
    RNF5 yeast 2-hybrid14667819 No
    ATP5G3 yeast 2-hybrid14667819 No
    SAFB yeast 2-hybrid14667819 No
    IFITM1 yeast 2-hybrid14667819 No
    HM13 yeast 2-hybrid14667819 No
    PILRB yeast 2-hybrid14667819 No
    MT-ND3 yeast 2-hybrid14667819 No
    MT-ND4 yeast 2-hybrid14667819 No
    DNAJC1 yeast 2-hybrid14667819 No
    SPAG7 yeast 2-hybrid14667819 No
    TMEM222 yeast 2-hybrid14667819 No
    HNRNPA1 yeast 2-hybrid14667819 No
    GPRC5C yeast 2-hybrid14667819 No
    TMEM147 yeast 2-hybrid14667819 No


    Involved FDA drugs

    There was no drug associated with BAT5