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: PECAM1

    Description: platelet/endothelial cell adhesion molecule

    Entrez Gene ID: 5175

    SwissProt Acc Number: P16284

    RefSeq: NM_000442

    It was suspected to be CHD related:

    .."it was found an association between young AMI and polymorphism C-260T in the CD14 gene, between coronarics atherosclerosis and polymorphism A516C in the E Selectin gene or polymorphisms Leu125Val and Ser563Asn in the PECAM1 gene."..

    From PMID: 15284679, in Journal Minerva Cardioangiol , 2004


    References

    There were 3 potential papers with PECAM1 and CHD.

    PMIDTitleJournalsDetails
    23906684 Genetic associations with coronary heart disease: meta-analyses of 12 candidate genetic variants.GeneMore Details
    21130994 Strong association of the APOA5-1131T>C gene variant and early-onset acute myocardial infarction.AtherosclerosisMore Details
    17130180 "Candidate gene genotypes, along with conventional risk factor assessment, improve estimation of coronary heart disease risk in healthy UK men."Clinical chemistryMore Details

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



    PPI interactions

    There were totally 24 unique genes interacted with PECAM1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    XRCC6 Two-hybrid16169070 No
    CTNNB1 Affinity Capture-Western10801826|10801826 CHD related
    PTPN11 Affinity Capture-Western10801826|10350061|10350061|9774457|9774457|9054388|9054388 CHD related
    MAPK1 Affinity Capture-Western10801826 CHD related
    DSP Affinity Capture-Western10801826|10801826 No
    JUP Affinity Capture-Western10801826|10801826 CHD related
    PIK3R1 Affinity Capture-Western9774384|9774384 CHD related
    PLCG1 Reconstituted Complex10350061|10350061|10350061 CHD related
    INPP5D Reconstituted Complex10350061|10350061 No
    PTPN6 Reconstituted Complex10350061|10350061|9774457|9774457 No
    PECAM1 Reconstituted Complex10425179|10350061,10425179 CHD related
    CD38 in vitro9551996 CHD related
    ITGA5 in vivo10982404 CHD related
    PRPF40A yeast 2-hybrid15231748 No
    FYN Affinity Capture-Western10858437 No
    SRC Affinity Capture-Western10858437|10858437 CHD related
    LYN Affinity Capture-Western10858437 No
    YES1 Affinity Capture-Western10858437 No
    HCK Affinity Capture-Western10858437 No
    ITGB3 Co-localization10982404|10982404 CHD related
    LCK Biochemical Activity9624175 No
    CSK Biochemical Activity9624175 No
    PRKCE in vitro10801826 CHD related
    EFNB2 in vivo16357318 No


    Involved FDA drugs

    There was no drug associated with PECAM1