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: PTEN

    Description: phosphatase and tensin homolog

    Entrez Gene ID: 5728

    SwissProt Acc Number: P60484

    RefSeq: NM_000314

    It was suspected to be CHD related:

    .."Taken together, PTEN could be a possible downstream regulator of AMPK, and the AMPK-PTEN pathway might be important in the regulation of the inflammatory response in VSMCs."..

    From PMID: 22898050, in Journal Biochem Biophys Res Commun , 2012


    References

    There were 7 potential papers with PTEN and CHD.

    PMIDTitleJournalsDetails
    22898050 Metformin inhibits inflammatory response via AMPK-PTEN pathway in vascular smooth muscle cells.Biochemical and biophysical research communicationsMore Details
    22936458 Phosphodiesterase III inhibition increases cAMP levels and augments the infarct size limiting effect of a DPP-4 inhibitor in mice with type-2 diabetes mellitus.Cardiovascular drugs and therapy / sponsored by the International Society ofMore Details
    20112301 Green tea polyphenols improve cardiac muscle mRNA and protein levels of signal pathways related to insulin and lipid metabolism and inflammation in insulin-resistant rats.Molecular nutrition & food researchMore Details
    18544045 Regulation of cell cycle entry by PTEN in smooth muscle cell proliferation of human coronary artery bypass conduits.Journal of cellular and molecular medicineMore Details
    19276401 "Inhibition of vascular smooth-muscle cell proliferation and arterial restenosis by HO-3867, a novel synthetic curcuminoid, through up-regulation of PTEN expression."The Journal of pharmacology and experimental therapeuticsMore Details
    18689499 Myocardial ischemic postconditioning against ischemia-reperfusion is impaired in ob/ob mice.American journal of physiology. Heart and circulatory physiologyMore Details
    15905966 "Biomedicine and diseases: the Klippel-Trenaunay syndrome, vascular anomalies and vascular morphogenesis."Cellular and molecular life sciences : CMLSMore Details

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



    PPI interactions

    There were totally 76 unique genes interacted with PTEN. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    AR Reconstituted Complex15205473|15205473 CHD related
    ESR1 Reconstituted Complex15205473 CHD related
    UBE2L3 Affinity Capture-Western12620973 No
    UBE2I Affinity Capture-Western12620973 No
    TP53 Affinity Capture-Western12620407|14559824|12620407 CHD related
    UTP14A Two-hybrid16169070|16169070 No
    ANG Two-hybrid16169070 CHD related
    CHGB Two-hybrid16169070 No
    COPS6 Two-hybrid16169070|16169070 No
    HBA1 Two-hybrid16169070 No
    PTK2 Affinity Capture-Western10400703|11857088|15717329 No
    MVP Two-hybrid12177006|12177006 No
    CAV1 Affinity Capture-Western12176037|12176037 CHD related
    PXN Affinity Capture-Western11857088 No
    UBC Reconstituted Complex18498243|21532586|19345329|20605778|21990315|22427670 No
    XIAP Affinity Capture-Western19473982|22427670 CHD related
    WWP1 Affinity Capture-Western21532586|21532586 No
    CASP8 Affinity Capture-Western15717329|15717329 CHD related
    CCNE2 Affinity Capture-Western15717329|15717329 No
    IRS4 Affinity Capture-Western15717329|15717329 No
    PPP2R4 Affinity Capture-Western15717329 No
    WNT4 Affinity Capture-MS15717329 No
    QRFPR Affinity Capture-MS15717329 No
    ARHGAP26 Affinity Capture-MS15717329 No
    G3BP2 Affinity Capture-MS15717329 No
    CENPC1 Affinity Capture-MS15717329 No
    DBF4B Affinity Capture-MS15717329 No
    GPR113 Affinity Capture-MS15717329 No
    INHBE Affinity Capture-MS15717329 No
    GFRA2 Affinity Capture-MS15717329 No
    SMTN Affinity Capture-MS15717329 No
    KRT14 Affinity Capture-MS15717329 No
    AMHR2 Affinity Capture-MS15717329 No
    PTK2B Affinity Capture-MS15717329 No
    CRKL Affinity Capture-MS15717329 No
    MAP2K6 Affinity Capture-MS15717329 CHD related
    PKN2 Affinity Capture-MS15717329 No
    PDGFRA Affinity Capture-MS15717329 No
    PINK1 Affinity Capture-MS15717329 No
    LEPREL4 Affinity Capture-MS15717329 No
    PTPN14 Affinity Capture-MS15717329 No
    TCEB3C Affinity Capture-MS15717329 No
    BAP1 Affinity Capture-MS15717329 No
    WWP2 Affinity Capture-MS15717329|22427670 No
    MED12 Affinity Capture-MS15717329 No
    ZNF787 Affinity Capture-MS15717329 No
    FBN2 Affinity Capture-MS15717329 No
    TTBK2 Affinity Capture-MS15717329 No
    RPL14 Affinity Capture-MS15717329 No
    EEF1A2 Affinity Capture-MS15717329 No
    FRK Affinity Capture-MS19345329|19345329 No
    AKT1 Affinity Capture-Western20605778 CHD related
    SLC9A3R1 Reconstituted Complex21990315|21990315|21990315|16456542 No
    STUB1 Reconstituted Complex22427670|22427670 No
    BMI1 Affinity Capture-Western19903340 No
    KAT2B Affinity Capture-Western16829519 No
    MAST2 in vitro;yeast 2-hybrid15951562 No
    MAST1 in vitro;yeast 2-hybrid15951562 No
    STK11 in vitro;in vivo;yeast 2-hybrid15987703 CHD related
    SLC9A3R2 in vivo16456542 No
    CSNK2A1 Biochemical Activity12297295|12297295 CHD related
    CSNK2A2 Biochemical Activity12297295|12297295 No
    MAGI3 Two-hybrid10748157|10748157|10748157 No
    NEDD4 Biochemical Activity18498243|21986318 No
    NDFIP1 Affinity Capture-Western20534535|22213801 No
    NDFIP2 Affinity Capture-Western20534535 No
    PPP3CA Affinity Capture-Western20605778 CHD related
    EGR1 Affinity Capture-Western21354147 No
    ELAVL1 Affinity Capture-RNA19322201 No
    HDAC4 Negative Genetic22318606 CHD related
    PPP1CA Affinity Capture-Western17274640|17274640 No
    Sharpin Affinity Capture-Western20458142 No
    PARK7 Affinity Capture-Western21426932|19885556|19885556 No
    MAGI2 in vivo;yeast 2-hybrid10760291 No
    DLG1 in vitro;yeast 2-hybrid10646847 No
    MAST3 in vitro;yeast 2-hybrid15951562 No


    Involved FDA drugs

    There was no drug associated with PTEN