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: GFAP

    Description: glial fibrillary acidic protein

    Entrez Gene ID: 2670

    SwissProt Acc Number: P14136

    RefSeq: NM_001131019

    It was suspected to be CHD related:

    .."Interestingly, the levels of iNOS and GFAP were increased in the gallbladders of cholesterol-fed hamsters."..

    From PMID: 19784582, in Journal Arch Pharm Res , 2009


    References

    There were 2 potential papers with GFAP and CHD.

    PMIDTitleJournalsDetails
    22471436 Cardiac neuroendocrine tumor with absence of sustentacular cells: immunohistochemical and ultrastructural findings.Ultrastructural pathologyMore Details
    19784582 Alteration of sphingolipid metabolism and pSTAT3 expression by dietary cholesterol in the gallbladder of hamsters.Archives of pharmacal researchMore Details

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



    PPI interactions

    There were totally 33 unique genes interacted with GFAP. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PDLIM1 Two-hybrid16189514|16189514 No
    KIAA0408 Two-hybrid16189514|16189514 No
    PDLIM7 Two-hybrid16189514|16189514 No
    VIM Two-hybrid16189514|16189514 CHD related
    SH3YL1 Two-hybrid16189514|16189514 No
    POM121 Two-hybrid16189514|16189514 No
    GRAP2 Two-hybrid16189514|16189514 No
    RIBC2 Two-hybrid16189514|16189514 No
    PDZK1 Two-hybrid16189514|16189514 CHD related
    MYO15B Two-hybrid16189514 No
    TUBGCP4 Two-hybrid16189514|16189514 No
    CEP76 Two-hybrid16189514|16189514 No
    UBC Affinity Capture-Western19427371 No
    PDCD6IP Affinity Capture-Western12771190 No
    APP Reconstituted Complex21832049 No
    PSEN1 Two-hybrid12058025|12058025 No
    PSEN2 Two-hybrid12058025 No
    MEN1 Affinity Capture-Western12169273|12169273 No
    HGS Reconstituted Complex19019082 No
    STAT1 Two-hybrid20936779 CHD related
    CEBPA Affinity Capture-MS18239623 No
    FBXO25 Affinity Capture-MS20473970 No
    CRYAB Reconstituted Complex17590381 No
    UBD Affinity Capture-MS22797925 No
    Htt Affinity Capture-MS17500595 No
    CDK1 in vitro;in vivo7822264,12177195 CHD related
    S100A1 in vitro10510252 CHD related
    PRKCA in vitro;in vivo2155236,9099667,7822264,2114109 CHD related
    S100B in vitro10510252 CHD related
    SRC in vivo11379820 CHD related
    PRKACA in vitro;in vivo2155236,9099667,7822264,2114109 CHD related
    ROCK1 in vitro;in vivo9099667,2155236,7822264,2114109 CHD related
    CAMK2A in vitro;in vivo2155236,9099667,7822264,2114109 CHD related


    Involved FDA drugs

    There was no drug associated with GFAP