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: PPAP2B

    Description: phosphatidic acid phosphatase type 2B

    Entrez Gene ID: 8613

    SwissProt Acc Number: O14495

    RefSeq: NM_003713

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

    ..These findings may provide a mechanistic link to explain the association between a PPAP2B polymorphism and coronary artery disease risk...

    From PMID: 23104851, in Journal Arterioscler Thromb Vasc Biol. , 2013


    References

    There were 3 potential papers with PPAP2B and CHD.

    PMIDTitleJournalsDetails
    23667179 Identification of CAD candidate genes in GWAS loci and their expression in vascular cells.Journal of lipid researchMore Details
    22835522 Lipid phosphate phosphatase (LPP3) and vascular development.Biochimica et biophysica actaMore Details
    23104851 Lipid phosphate phosphatase 3 negatively regulates smooth muscle cell phenotypic modulation to limit intimal hyperplasia."Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 5 unique genes interacted with PPAP2B. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APP Reconstituted Complex21832049 No
    BCAR1 in vitro16099422 No
    SHC1 in vitro16099422 No
    BCL6 Affinity Capture-MS16147992 No
    UBC Affinity Capture-MS21987572|21139048|21906983 No


    Involved FDA drugs

    There was no drug associated with PPAP2B