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: F13A1

    Description: "coagulation factor XIII, A1 polypeptide"

    Entrez Gene ID: 2162

    SwissProt Acc Number: P00488

    RefSeq: NM_000129

    It was suspected to be CHD related:

    .."Our study provides the first evidence of an association between these polymorphisms and myocardial perfusion, suggesting that the process of coronary artery disease and also patients' prognosis, may be modified by the FV:c.1691G>A, FII:c.20210G>A, PAI-1 -675 (4G/5G), -fibrinogen FGB:c.4577G>A and F13A1:c.103G>T genotypes."..

    From PMID: 21332313, in Journal Pharmacogenomics , 2011


    References

    There were 2 potential papers with F13A1 and CHD.

    PMIDTitleJournalsDetails
    21332313 "Sequence variations in the FII, FV, F13A1, FGB and PAI-1 genes are associated with differences in myocardial perfusion."PharmacogenomicsMore Details
    12923221 Genome-wide scan for quantitative trait loci influencing LDL size and plasma triglyceride in familial hypertriglyceridemia.Journal of lipid researchMore Details

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



    PPI interactions

    There were totally 14 unique genes interacted with F13A1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    F13A1 Co-purification2491853|2491853|2184890,2365049,7660355,7913750,7920263,9515726,9988734 CHD related
    F13B Co-purification2491853|2491853|8905624 CHD related
    FN1 Reconstituted Complex8905624 CHD related
    FGA Co-crystal Structure10956659 CHD related
    NUDT21 Two-hybrid21900206 No
    UFD1L Two-hybrid21900206 No
    SH3GL2 Two-hybrid21900206 No
    TK1 Two-hybrid21900206 No
    PTK2 Two-hybrid21900206 No
    CDKN1A Two-hybrid21900206 CHD related
    ANXA7 Two-hybrid21900206 No
    SERPINF2 in vitro10958788 CHD related
    FGG in vitro8905624,10828988 CHD related
    F2 in vitro9546612 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB01839"1,2-Propanediol"
    experimentalDB02340N-Acetyl-Serine