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: DDR1

    Description: discoidin domain receptor tyrosine kinase 1

    Entrez Gene ID: 780

    SwissProt Acc Number: Q08345

    RefSeq: NM_001954

    It was suspected to be CHD related:

    .."The discoidin domain receptor 1 (DDR1) is a collagen receptor that is emerging as a critical mediator of atherosclerosis. Taken together, our results demonstrate that DDR1 mediates an important mechanism for atherosclerotic calcification."..

    From PMID: 19893047, in Journal Am J Pathol.? , 2009


    References

    There were 2 potential papers with DDR1 and CHD.

    PMIDTitleJournalsDetails
    19893047 Discoidin domain receptor-1 deficiency attenuates atherosclerotic calcification and smooth muscle cell-mediated mineralization.The American journal of pathologyMore Details
    16497176 Regulation of neuronal type genes in congestive heart failure rats."Acta physiologica (Oxford, England)"More Details

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



    PPI interactions

    There were totally 19 unique genes interacted with DDR1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SNRNP40 Two-hybrid16169070|16169070 No
    SNAPIN Two-hybrid16169070|16169070 No
    TTR Two-hybrid16169070 No
    PLCG1 in vitro;in vivo10783152 CHD related
    DDR1 in vitro9659899 CHD related
    COL2A1 in vivo9659900 No
    COL3A1 in vivo9659900 CHD related
    COL5A2 in vivo9659900 No
    COL11A1 in vivo9659900 No
    BEND5 yeast 2-hybrid16169070 No
    NCK2 yeast 2-hybrid16337946 No
    PTPN11 in vivo;yeast 2-hybrid16337946 CHD related
    RGS2 Two-hybrid16169070|21900206 No
    TM4SF1 Two-hybrid16169070|16169070 No
    SHC1 Reconstituted Complex9659899|10783152 No
    NUDT3 Two-hybrid21900206 No
    MAPK6 Two-hybrid21900206 No
    UBC Affinity Capture-MS21139048|21906983 No
    FRS2 in vitro;in vivo10783152 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00619ImatinibFor the treatment Philadelphia chromosome positive chronic myeloid leukemia (CML) and malignant gastrointestinal stromal tumors (GIST).L01XE01