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: NOD2

    Description: nucleotide-binding oligomerization domain containing 2

    Entrez Gene ID: 64127

    SwissProt Acc Number: Q9HC29

    RefSeq: NM_022162

    It was suspected to be CHD related:

    .."The NOD2 up-regulation in atheroma lesions indicates an involvement of this protein in the pathology of CHD. Although NOD2 could be important in local immune response mechanisms, none of the analyzed CARD15 variants seem to play a significant role in the etiology of CHD."..

    From PMID: 17980027, in Journal BMC Genet , 2007


    References

    There were 2 potential papers with NOD2 and CHD.

    PMIDTitleJournalsDetails
    17980027 Role of NOD2/CARD15 in coronary heart disease.BMC geneticsMore Details
    15653568 Nod1-mediated endothelial cell activation by Chlamydophila pneumoniae.Circulation researchMore Details

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



    PPI interactions

    There were totally 25 unique genes interacted with NOD2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    RIPK2 Affinity Capture-Western11087742|19592251|15620648|21123652|22607974|21097508|11087742 No
    BIRC2 Affinity Capture-Western22607974 No
    BIRC3 Affinity Capture-Western22607974 No
    NAT16 Affinity Capture-Western22607974 No
    XIAP Affinity Capture-Western22607974 CHD related
    IKBKG Affinity Capture-Western22607974 No
    RIPK1 Affinity Capture-Western22607974 No
    RNF31 Affinity Capture-Western22607974 No
    RBCK1 Affinity Capture-Western22607974 No
    Sharpin Affinity Capture-Western22607974 No
    GALNT2 Two-hybrid21699783|21699783 CHD related
    FIS1 Two-hybrid21699783|21699783 No
    TLE1 Two-hybrid21699783|21699783 No
    VIM Two-hybrid21699783|21699783 CHD related
    KAT5 Two-hybrid21699783|21699783 No
    PPP2R5E Two-hybrid21699783|21699783 No
    CASP12 Affinity Capture-Western18329614 CHD related
    TRIM27 Affinity Capture-Western22829933 No
    COPS6 Affinity Capture-Western17337451 No
    MAP3K7 Affinity Capture-Western17965022 No
    NLRC4 Affinity Capture-Western15107016|11472070|11472070 No
    CASP1 Affinity Capture-Western15107016 CHD related
    UBC Affinity Capture-MS21906983 No
    TRAF4 Affinity Capture-Western21097508 No
    ERBB2IP in vivo;yeast 2-hybrid16203728 No


    Involved FDA drugs

    There was no drug associated with NOD2