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: S100A8

    Description: S100 calcium binding protein A8

    Entrez Gene ID: 6279

    SwissProt Acc Number: P05109

    RefSeq: NM_002964

    It was suspected to be CHD related:

    ..The pattern of cytokine and S100A9/S100A8 up-regulation characterizes atherosclerosis as a proinflammatory disorder..

    From PMID: 19134193, in Journal BMC Genomics , 2009


    References

    There were 5 potential papers with S100A8 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
    21938407 Proteomic analysis of circulating human monocytes in coronary artery disease.Molecular and cellular biochemistryMore 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 39 unique genes interacted with S100A8. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    C14orf1 Two-hybrid16169070|16169070 No
    PRMT1 Two-hybrid16169070 No
    PDCD11 Two-hybrid16169070|16169070 No
    PPIA Two-hybrid16169070 CHD related
    CHGB Two-hybrid16169070 No
    GDF9 Two-hybrid16169070 No
    IGSF21 Two-hybrid16169070|16169070 No
    TP53 Two-hybrid16169070|16169070 CHD related
    Tuba1a Two-hybrid16169070 No
    LRIF1 Two-hybrid16169070 No
    UNC119 Two-hybrid16169070|16169070 No
    S100A8 Co-crystal Structure10771424|10771424 CHD related
    APP Reconstituted Complex21832049 No
    C1orf103 yeast 2-hybrid16169070 No
    TUBA4A yeast 2-hybrid16169070 No
    RAB17 yeast 2-hybrid16169070 No
    KLC2 yeast 2-hybrid16169070 No
    MOB1A Affinity Capture-MS17353931 No
    LRRK1 Affinity Capture-MS17353931 No
    PPM1B Affinity Capture-MS17353931 No
    NUAK1 Affinity Capture-MS17353931 No
    ASB3 Affinity Capture-MS17353931 No
    USF2 Affinity Capture-MS17353931 No
    DMWD Affinity Capture-MS19615732 No
    SLX1B Affinity Capture-MS19596235 No
    S100A9 Two-hybrid20936779|12553726 CHD related
    TERF1 Affinity Capture-MS20811636 No
    TERF2 Affinity Capture-MS20811636 No
    POT1 Affinity Capture-MS20811636 No
    CDKN1A Two-hybrid21900206 CHD related
    KIAA0101 Affinity Capture-MS21628590 No
    UBC Affinity Capture-MS21139048 No
    SIRT7 Affinity Capture-MS22586326 No
    TFAP4 Affinity Capture-MS19505873 No
    CDK2 Affinity Capture-MS21319273 No
    COPS5 Affinity Capture-MS21145461 No
    SHC1 Affinity Capture-MS19380743 No
    NCF2 in vitro15642721 No
    CEACAM3 in vivo11708798 No


    Involved FDA drugs

    There was no drug associated with S100A8