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: HSPB8

    Description: heat shock 22kDa protein 8

    This suspected gene is newly curated in the Version 2.0

    It was suspected to be CHD related:

    ..Silencing and overexpression experiments in isolated neonatal rat cardiomyocytes showed that Hsp22 activates STAT3 via production of interleukin-6 by the transcription factor nuclear factor-κB. ..

    From PMID: 21747053, in Journal Circulation. 2011;124:406-415 ,


    References

    There were 0 potential papers with HSPB8 and CHD.

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



    PPI interactions

    There were totally 14 unique genes interacted with HSPB8. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    HSPB1 Two-hybrid14594798|15122253 No
    HSPB7 Two-hybrid16189514|14594798|16189514 CHD related
    HSPB8 Two-hybrid14594798|14594798|14594798 CHD related
    HSPB2 Two-hybrid14594798|11342557 No
    HSPB6 Two-hybrid16225851|16225851 CHD related
    CRYAB Two-hybrid16225851|16225851 No
    HSPB3 Two-hybrid16225851 No
    CSNK2A1 in vitro11342557 CHD related
    BAG3 Two-hybrid16189514 No
    SNCA Reconstituted Complex21905118 No
    CIAPIN1 Co-fractionation22939629 No
    DSTN Co-fractionation22939629 No
    PRKCA in vitro11342557 CHD related
    MAPK3 in vitro11342557 CHD related


    Involved FDA drugs

    There was no drug associated with HSPB8