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: NR4A2

    Description: nuclear receptor subfamily 4, group A, member 2

    This suspected gene is newly curated in the Version 2.0

    It was suspected to be CHD related:

    ..The tumor necrosis factor-alpha-induced proinflammatory response of SMCs is inhibited by Nurr1, as reflected by reduced interleukin-1beta, tumor necrosis factor-alpha, and monocyte chemoattractant protein-1 expression...

    From PMID: 20421523, in Journal Circulation. 2010;121:2023-2032 ,


    References

    There were 2 potential papers with NR4A2 and CHD.

    PMIDTitleJournalsDetails
    19156841 Haplotypes of the NR4A2/NURR1 gene and cardiovascular disease: the Rotterdam Study.Human mutationMore Details
    17885421 NR4A nuclear orphan receptors: protective in vascular disease?Current opinion in lipidologyMore Details

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



    PPI interactions

    There were totally 16 unique genes interacted with NR4A2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    RARA Two-hybrid7705655|7705655 No
    RARB Two-hybrid7705655|7705655 No
    SFPQ Affinity Capture-Western19144721 No
    NCOR2 Affinity Capture-Western19144721 No
    SIN3A Affinity Capture-Western19144721 No
    SMARCA4 Affinity Capture-Western17043312|17043312 No
    SMARCA2 Affinity Capture-Western17043312|17043312 No
    RUNX1 Affinity Capture-Western21468021 CHD related
    RXRA Two-hybrid15604093|7758108,7705655,15604093 CHD related
    COPS5 Two-hybrid15604093|15604093 No
    RXRB Two-hybrid15604093|7758108,7705655,15604093 No
    CDKN1C in vitro14671317 No
    PIAS4 in vitro;in vivo;yeast 2-hybrid14559918 No
    ELAVL1 Affinity Capture-RNA19322201 No
    RPS6KA1 in vivo16223362 CHD related
    VHL in vivo18305400 No


    Involved FDA drugs

    There was no drug associated with NR4A2