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.

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  • 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.

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  • 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: F12

    Description: coagulation factor XII (Hageman factor)

    Entrez Gene ID: 2161

    SwissProt Acc Number: P00748

    RefSeq: NM_000505

    It was suspected to be CHD related:

    .."we identified a panel of genetic variants that collectively improved the prediction of CHD to a small but statistically significant extent. Chlorthalidone (A): NOS3 rs3918226; SELE rs5361; ICAM1 rs1799969; AGT rs5051; GNAS rs7121; ROC comparison, P=0.004; Amlodipine (B): MMP1 rs1799750; Factor5 (F5) rs6025; NPPA rs5065; PDE4D rs6450512; MMP9 rs2274756; ROC comparison, P=0.006; Lisinopril (C): AGT rs5051; PON1 rs705379; MMP12 rs652438; F12 rs1801020; GP1BA rs6065; PDE4D rs27653; ROC comparison, P=0.01; Doxazosin (D): F2 rs1799963; PAI1 rs1799768; MMP7 rs11568818; AGT rs5051; ACE rs4343; MMP2 rs243865; ROC comparison, P=0.007. "..

    From PMID: 22388798, in Journal Pharmacogenet Genomics. , 2012


    References

    There were 4 potential papers with F12 and CHD.

    PMIDTitleJournalsDetails
    22388798 Gene panels to help identify subgroups at high and low risk of coronary heart disease among those randomized to antihypertensive treatment: the GenHAT study.Pharmacogenetics and genomicsMore Details
    22703881 "Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease."American journal of human geneticsMore Details
    19422815 "Rapid triplex asymmetric real-time PCR hybridization probe assay for the joint genotyping of F2, F5 and F12."Clinical biochemistryMore Details
    19204433 Factor XII 46C --> T gene polymorphism in Chilean subjects with coronary artery disease and controls."Medical principles and practice : international journal of the Kuwait University,"More Details

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



    PPI interactions

    There were totally 17 unique genes interacted with F12. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-Western18838541 No
    CD93 in vitro11204562,8710908 CHD related
    APOH in vitro3361230 CHD related
    KRT1 in vitro11204562 No
    APP in vivo11589915 No
    GP1BA Reconstituted Complex10801853 CHD related
    EPAS1 Affinity Capture-Western21512133 CHD related
    HIF1A Affinity Capture-Western18838541 CHD related
    UBE2D1 Biochemical Activity18838541 No
    UBE2D2 Biochemical Activity18838541 No
    UBE2D3 Biochemical Activity18838541 No
    UBE2E1 Biochemical Activity18838541 No
    UBE2N Biochemical Activity18838541 No
    MMP13 in vivo10930399 CHD related
    MMP14 in vitro10930399 CHD related
    MMP12 in vivo10930399 CHD related
    KLKB1 in vitro3521732 No


    Involved FDA drugs

    There was no drug associated with F12