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: ILK

    Description: integrin-linked kinase

    Entrez Gene ID: 3611

    SwissProt Acc Number: Q13418

    RefSeq: NM_001014794

    It was supported literatures to be a novel CHD related gene:

    .."ILK gene therapy improves cardiac remodeling and function in rats after myocardial infarction and is associated with increased angiogenesis, reduced apoptosis, and increased cardiomyocyte proliferation."..

    From PMID: 19687354, in Journal Circulation. , 2009


    References

    There were 5 potential papers with ILK and CHD.

    PMIDTitleJournalsDetails
    19687354 Increased expression of integrin-linked kinase attenuates left ventricular remodeling and improves cardiac function after myocardial infarction.CirculationMore Details
    18505769 Serial analysis of the vascular endothelial transcriptome under static and shear stress conditions.Physiological genomicsMore Details
    18823942 Role of integrin-linked kinase for functional capacity of endothelial progenitor cells in patients with stable coronary artery disease.Biochemical and biophysical research communicationsMore Details
    17600280 Thymosin beta4 is cardioprotective after myocardial infarction.Annals of the New York Academy of SciencesMore Details
    15565145 "Thymosin beta4 activates integrin-linked kinase and promotes cardiac cell migration, survival and cardiac repair."NatureMore Details

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



    PPI interactions

    There were totally 64 unique genes interacted with ILK. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ILKAP Two-hybrid11331582|11331582 No
    LIMS1 Two-hybrid10022929|12167643 CHD related
    PARVA Two-hybrid16189514 No
    HEATR1 Affinity Capture-MS17353931 No
    OTUD4 Affinity Capture-MS17353931 No
    FANCI Affinity Capture-MS17353931 No
    GEMIN4 Affinity Capture-MS17353931 No
    DDX3X Affinity Capture-MS17353931 No
    MMS19 Affinity Capture-MS17353931 No
    MYO1D Affinity Capture-MS17353931 No
    HEATR2 Affinity Capture-MS17353931 No
    RSU1 Affinity Capture-MS17353931 No
    PARVB Affinity Capture-MS17353931 No
    AUP1 Affinity Capture-MS17353931 No
    NOC2L Affinity Capture-MS17353931 No
    IGF2BP1 Affinity Capture-MS17353931 No
    COPG Affinity Capture-MS17353931 No
    S100A9 Affinity Capture-MS17353931 CHD related
    EWSR1 Affinity Capture-MS17353931 No
    PUF60 Affinity Capture-MS17353931 No
    MARS Affinity Capture-MS17353931 No
    PRPSAP1 Affinity Capture-MS17353931 No
    DHX36 Affinity Capture-MS17353931 No
    COPB2 Affinity Capture-MS17353931 No
    ERH Affinity Capture-MS17353931 No
    HSPB1 Affinity Capture-MS17353931 No
    ILK Biochemical Activity8538749 CHD related
    ITGB3 Affinity Capture-Western12372433|12372433 CHD related
    AKT1 Affinity Capture-Western11825911|9736715|11313365|9736715,12176337,12149249,11445557,11546794,14500673,11278835 CHD related
    LIMS2 Affinity Capture-Western12167643 CHD related
    RPL13 Two-hybrid21900206 No
    ZBTB48 Two-hybrid21900206 No
    SHC1 Two-hybrid21900206 No
    MIPEP Two-hybrid21900206 No
    ZNF579 Two-hybrid21900206 No
    SERPINA4 Two-hybrid21900206 No
    ZNF746 Two-hybrid21900206 No
    SNRNP35 Two-hybrid21900206 No
    CKB Two-hybrid21900206 No
    RNF19A Two-hybrid21900206 No
    ZNF133 Two-hybrid21900206 No
    ZNF205 Two-hybrid21900206 No
    NOTCH1 Biochemical Activity17526737 CHD related
    TMSB4X in vitro15565145 No
    ITGB2 in vivo9736715 CHD related
    PPP1R12A in vitro12600888,10601309,11931630,12220642 No
    CASP9 in vivo16936772 CHD related
    CASP8 in vivo16936772 CHD related
    ACP6 Affinity Capture-MS17353931 No
    ITGA5 Affinity Capture-Western8538749 CHD related
    ITGB1 Affinity Capture-Western8538749 CHD related
    VTNR Affinity Capture-Western8538749 No
    PXN Reconstituted Complex11304546|11694518,11304546,16936772 No
    NCK2 Reconstituted Complex10022929 No
    PDPK1 Affinity Capture-Western11313365|11313365 CHD related
    UBC Affinity Capture-MS21987572|21139048|21890473|21906983|22053931 No
    KIAA0101 Affinity Capture-MS21628590 No
    CUL3 Affinity Capture-MS21145461 No
    CUL5 Affinity Capture-MS21145461 No
    CUL1 Affinity Capture-MS21145461 No
    COPS5 Affinity Capture-MS21145461 No
    GSK3B in vitro9736715,16936772 CHD related
    CAV1 in vitro;in vivo15722199 CHD related
    PARVG in vitro;in vivo;yeast 2-hybrid16517730 No


    Involved FDA drugs

    There was no drug associated with ILK