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: GCH1

    Description: GTP cyclohydrolase 1

    Entrez Gene ID: 2643

    SwissProt Acc Number: P30793

    RefSeq: NM_000161

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

    ..The ability to increase vascular GCH1 expression and BH4 synthesis in response to inflammation preserves endothelial function in inflammatory states...

    From PMID: 21969008, in Journal Circulation. , 2011


    References

    There were 2 potential papers with GCH1 and CHD.

    PMIDTitleJournalsDetails
    21969008 Induction of vascular GTP-cyclohydrolase I and endogenous tetrahydrobiopterin synthesis protect against inflammation-induced endothelial dysfunction in human atherosclerosis.CirculationMore Details
    18598896 GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function.Journal of the American College of CardiologyMore Details

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



    PPI interactions

    There were totally 13 unique genes interacted with GCH1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GCH1 Two-hybrid16696853|11087827 CHD related
    GCHFR Two-hybrid16696853 No
    AHSA1 Two-hybrid16696853|16696853|16696853 No
    RLF Two-hybrid16696853|16696853 No
    HSPA8 Two-hybrid16696853|16696853 CHD related
    SP3 Two-hybrid16696853 No
    CNRIP1 Two-hybrid16696853 No
    RAB26 Two-hybrid16696853|16696853 No
    ATP1B1 Two-hybrid16696853|16696853 No
    RPH3A Affinity Capture-Western7802677|7802677 No
    OSBPL9 Affinity Capture-MS19615732 No
    SH3GL2 Two-hybrid21900206 No
    CDC37 Two-hybrid21900206 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02377Guanine