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: PTPRD

    Description: "protein tyrosine phosphatase, receptor type, D"

    Entrez Gene ID: 5789

    SwissProt Acc Number: P23468

    RefSeq: NM_001040712

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

    .."This approach replicated HNRNPA3P1-CXCL12 association with CAD and identified new significant associations of CDKAL1, ST6GAL1, and PTPRD with CAD."..

    From PMID: 22216278, in Journal PLoS One , 2011


    References

    There were 2 potential papers with PTPRD and CHD.

    PMIDTitleJournalsDetails
    22216278 Large scale association analysis identifies three susceptibility loci for coronary artery disease.PloS oneMore Details
    19525478 Identification of ZNF366 and PTPRD as novel determinants of plasma homocysteine in a family-based genome-wide association study.BloodMore Details

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



    PPI interactions

    There were totally 8 unique genes interacted with PTPRD. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PPFIA1 Two-hybrid8524829|8524829 No
    PTPRA in vivo;yeast 2-hybrid10777529 No
    PTPRE in vivo12376545 No
    PTPRF in vivo12376545 No
    PTPRS Two-hybrid9566880|9566880 No
    PPFIA2 in vitro9624153 No
    PPFIA3 in vitro9624153 No
    MTSS1 in vitro;yeast 2-hybrid12570871 No


    Involved FDA drugs

    There was no drug associated with PTPRD