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: PCSK5

    Description: proprotein convertase subtilisin/kexin type 5

    Entrez Gene ID: 5125

    SwissProt Acc Number: Q92824

    RefSeq: NM_006200

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

    .."We conclude that variability at the PCSK5 locus influences HDL-C levels, possibly through the inactivation of endothelial lipase activity, and,consequently, atherosclerotic cardiovascular disease risk."..

    From PMID: 20031622, in Journal Circ Cardiovasc Genet. , 2009


    References

    There were 2 potential papers with PCSK5 and CHD.

    PMIDTitleJournalsDetails
    21681612 Inactivation of endothelial proprotein convertase 5/6 decreases collagen deposition in the cardiovascular system: role of fibroblast autophagy."Journal of molecular medicine (Berlin, Germany)"More Details
    20031622 Genetic variation at the proprotein convertase subtilisin/kexin type 5 gene modulates high-density lipoprotein cholesterol levels.Circulation. Cardiovascular geneticsMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with PCSK5. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APPBP2 Two-hybrid16189514 No
    REN in vitro8901832 CHD related
    AMH in vitro;in vivo8755541 No
    ITGA6 in vitro10657249 No
    PMCH in vivo10037747 No
    CACNA1A Two-hybrid21078624 No
    UBC Affinity Capture-MS21890473 No
    ATN1 Two-hybrid16713569|16713569 No
    PTPRM in vitro8620001 No


    Involved FDA drugs

    There was no drug associated with PCSK5