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: S100A9

    Description: S100 calcium binding protein A9

    Entrez Gene ID: 6280

    SwissProt Acc Number: P06702

    RefSeq: NM_002965

    It was suspected to be CHD related:

    ..S100A8 and S100A9 were accumulated in atherosclerotic lesions..

    From PMID: 22333479, in Journal Diabetes Res Clin Pract , 2012


    References

    There were 4 potential papers with S100A9 and CHD.

    PMIDTitleJournalsDetails
    24202303 "Plasma S100A8/A9 Correlates With Blood Neutrophil Counts, Traditional Risk Factors, and Cardiovascular Disease in Middle-Aged Healthy Individuals.""Arteriosclerosis, thrombosis, and vascular biology"More Details
    22333479 High serum S100A8/A9 levels and high cardiovascular complication rate in type 2 diabetics with ultrasonographic low carotid plaque density.Diabetes research and clinical practiceMore Details
    21536666 Mechanisms of urokinase plasminogen activator (uPA)-mediated atherosclerosis: role of the uPA receptor and S100A8/A9 proteins.The Journal of biological chemistryMore Details
    19620505 Myeloid-related protein-8/14 is critical for the biological response to vascular injury.CirculationMore Details

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



    PPI interactions

    There were totally 74 unique genes interacted with S100A9. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    S100A9 Co-crystal Structure11851337|11851337 CHD related
    S100A8 Two-hybrid20936779|12553726 CHD related
    SRSF10 Co-fractionation22939629 No
    GTF3C1 Co-fractionation22939629 No
    U2AF1 Co-fractionation22939629 No
    SMARCA5 Co-fractionation22939629 No
    SART1 Co-fractionation22939629 No
    THRAP3 Co-fractionation22939629 No
    TOP1 Co-fractionation22939629 No
    TRA2A Co-fractionation22939629 No
    TRA2B Co-fractionation22939629 No
    VTN Co-fractionation22939629 CHD related
    SAP18 Co-fractionation22939629 No
    UTP14A Co-fractionation22939629 No
    TPBG Co-fractionation22939629 No
    ZC3H18 Co-fractionation22939629 No
    SRRT Co-fractionation22939629 No
    SUPT16H Co-fractionation22939629 No
    SON Co-fractionation22939629 No
    SRSF5 Co-fractionation22939629 No
    TRIM55 Co-fractionation22939629 No
    SRSF7 Co-fractionation22939629 No
    SSRP1 Co-fractionation22939629 No
    SRSF3 Co-fractionation22939629 No
    ZNF326 Co-fractionation22939629 No
    SRSF11 Co-fractionation22939629 No
    TOP2B Co-fractionation22939629 No
    U2AF2 Co-fractionation22939629 No
    SURF4 Co-fractionation22939629 No
    SSSCA1 Co-fractionation22939629 No
    TLE3 Co-fractionation22939629 No
    UNK Co-fractionation22939629 No
    TPR Co-fractionation22939629 No
    TAGLN Affinity Capture-MS17353931 No
    ASB3 Affinity Capture-MS17353931 No
    USF2 Affinity Capture-MS17353931 No
    PAK7 Affinity Capture-MS17353931 No
    NUAK1 Affinity Capture-MS17353931 No
    ILK Affinity Capture-MS17353931 CHD related
    CDC42 Two-hybrid20936779 CHD related
    TOPORS Affinity Capture-MS17803295 No
    UBC Affinity Capture-MS16196087|21139048 No
    PPP2R1A Affinity Capture-MS19156129 No
    PPP2R2B Affinity Capture-MS19156129 No
    KIAA0101 Affinity Capture-MS21628590 No
    RAD21 Affinity Capture-Western22145905 No
    ARRB1 Affinity Capture-MS17620599|17620599 No
    ARRB2 Affinity Capture-MS17620599|17620599 No
    CUL5 Affinity Capture-MS21145461 No
    CUL2 Affinity Capture-MS21145461 No
    COPS5 Affinity Capture-MS21145461 No
    SHC1 Affinity Capture-MS19380743 No
    RBM39 Co-fractionation22939629 No
    SF3B14 Co-fractionation22939629 No
    EIF4A3 Co-fractionation22939629 No
    CD2BP2 Co-fractionation22939629 No
    PSMA5 Co-fractionation22939629 No
    DHX15 Co-fractionation22939629 No
    NCSTN Co-fractionation22939629 No
    MATR3 Co-fractionation22939629 No
    RBM14 Co-fractionation22939629 No
    ACIN1 Co-fractionation22939629 No
    PSRC1 Co-fractionation22939629 CHD related
    CPLX1 Co-fractionation22939629 No
    PSMB7 Co-fractionation22939629 No
    DEK Co-fractionation22939629 No
    RNPS1 Co-fractionation22939629 No
    PRPF8 Co-fractionation22939629 No
    LUC7L3 Co-fractionation22939629 No
    DSTN Co-fractionation22939629 No
    HNRNPU Co-fractionation22939629 No
    DDX21 Co-fractionation22939629 No
    NUBP2 Co-fractionation22939629 No
    EGFR in vivo16799092 CHD related


    Involved FDA drugs

    There was no drug associated with S100A9