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.

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  • 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.

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  • 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: KALRN

    Description: "kalirin, RhoGEF kinase"

    Entrez Gene ID: 8997

    SwissProt Acc Number: O60229

    RefSeq: NM_001024660

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

    .."The strongest associations were found in three SNPs from the kalirin (KALRN) gene, especially in patients with early-onset CAD"..

    From PMID: 22965072, in Journal Diab Vasc Dis Res. , 2012


    References

    There were 3 potential papers with KALRN and CHD.

    PMIDTitleJournalsDetails
    23907653 Gene-smoking interactions in multiple Rho-GTPase pathway genes in an early-onset coronary artery disease cohort.Human geneticsMore Details
    19706030 Validation study of genetic associations with coronary artery disease on chromosome 3q13-21 and potential effect modification by smoking.Annals of human geneticsMore Details
    17357071 Peakwide mapping on chromosome 3q13 identifies the kalirin gene as a novel candidate gene for coronary artery disease.American journal of human geneticsMore Details

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



    PPI interactions

    There were totally 16 unique genes interacted with KALRN. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PAM Two-hybrid9139723|9139723 No
    GNB1 Affinity Capture-Western10518015 No
    RAC1 Reconstituted Complex9139723 CHD related
    SUMO2 Affinity Capture-MS16620772|16620772 No
    SUMO3 Affinity Capture-MS16620772|16620772 No
    ATXN7 Two-hybrid21078624 No
    CACNA1A Two-hybrid21078624 No
    CDC5L Two-hybrid17043677 No
    DISC1 Two-hybrid17043677 No
    DTNBP1 Two-hybrid17043677 No
    NDEL1 Two-hybrid17043677 No
    LNX1 Two-hybrid22889411 No
    FASLG Protein-peptide19807924 No
    COIL Two-hybrid16713569|16713569 No
    GFI1B Two-hybrid16713569|16713569 No
    EPHB2 in vitro12546821 No


    Involved FDA drugs

    There was no drug associated with KALRN