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.
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    Collaboration Information: Prof. Xiaohui Fan (

    Website using assistance : Leihong Wu (

    Basic Information

    Gene Name: RTN3

    Description: reticulon 3

    Entrez Gene ID: 10313

    SwissProt Acc Number: O95197

    RefSeq: NM_006054

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

    .."Our research group found Reticulon3 (RTN3), a member of the reticulon family, may be a candidate pathogenic element in the progress of AS"..

    From PMID: 21964562, in Journal Mol Cell Biochem. , 2012


    There were 1 potential papers with RTN3 and CHD.

    21964562 The potential role of RTN3 in monocyte recruitment and atherosclerosis.Molecular and cellular biochemistryMore Details

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

    PPI interactions

    There were totally 14 unique genes interacted with RTN3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    FAM160A2 Two-hybrid16189514 No
    RTN4 Two-hybrid16189514|12811824 No
    PLEKHF2 Two-hybrid16189514 No
    RTN3 Two-hybrid16189514|16189514 CHD related
    FXR2 Two-hybrid16189514|16189514 No
    PTPN9 Two-hybrid16189514|16189514 No
    COL4A3BP Two-hybrid16189514|16189514 No
    RAB33A Two-hybrid16189514|16189514 No
    SPOP Two-hybrid16189514|16189514 No
    UGCG Two-hybrid12873973 No
    UBC Affinity Capture-MS16196087|21139048|21906983|22505724 No
    TERF1 Two-hybrid21044950 No
    PRTFDC1 Co-fractionation22939629 No
    FGFR1 in vitro;in vivo15117958 No

    Involved FDA drugs

    There was no drug associated with RTN3