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: GHRL

    Description: ghrelin/obestatin prepropeptide

    Entrez Gene ID: 51738

    SwissProt Acc Number: Q9UBU3

    RefSeq: NM_001134941

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

    .."The combined group samples identified 6 up regulated differential expression (DE) genes (GHRL, LTA, CBS, HP, ITGA2B, and OLR1) and 12 down regulated DE genes (IL18R1, ITGA2B, IL18RAP, HP, OLR1, SOD2 ITGB3, IL1B, MMP9, PLA2G7, UTS2, and CBS) to be involved in CAD at the fold change of 1.3 with fault discovery rate (FDR) of 1%."..

    From PMID: 22738689, in Journal J Cardiol. , 2012


    References

    There were 2 potential papers with GHRL and CHD.

    PMIDTitleJournalsDetails
    22738689 Peripheral blood gene expression profile of atherosclerotic coronary artery disease in patients of different ethnicity in Malaysia.Journal of cardiologyMore Details
    17324965 Epistatic interaction between haplotypes of the ghrelin ligand and receptor genes influence susceptibility to myocardial infarction and coronary artery disease.Human molecular geneticsMore Details

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



    PPI interactions

    There were totally 7 unique genes interacted with GHRL. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GHSR in vivo10604470,11227737 No
    GHRHR in vivo10461027 No
    NPY in vivo11196643,12663466 CHD related
    LEP in vivo11196643 CHD related
    MLNR Reconstituted Complex12606621 No
    ACE2 in vitro11815627 CHD related
    AGRP in vivo11196643 No


    Involved FDA drugs

    There was no drug associated with GHRL