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: F5

    Description: "coagulation factor V (proaccelerin, labile factor)"

    Entrez Gene ID: 2153

    SwissProt Acc Number: P12259

    RefSeq: NM_000130

    It was suspected to be CHD related:

    ..Gain-of-function variants of genes encoding coagulation factor V (F5 G1691A) and prothrombin (F2 G20210A) cause hypercoagulability and are established risk factors for venous thrombosis...

    From PMID: 20626623, in Journal J Thromb Haemost , 2010


    References

    There were 7 potential papers with F5 and CHD.

    PMIDTitleJournalsDetails
    23690342 "Pharmacogenomic association of nonsynonymous SNPs in SIGLEC12, A1BG, and the selectin region and cardiovascular outcomes."HypertensionMore Details
    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
    20626623 The association of factor V Leiden with myocardial infarction is replicated in 1880 patients with premature disease.Journal of thrombosis and haemostasis : JTHMore Details
    20216324 Predicting cardiac rehabilitation attendance in a gender-tailored randomized clinical trial.Journal of cardiopulmonary rehabilitation and preventionMore Details
    19422815 "Rapid triplex asymmetric real-time PCR hybridization probe assay for the joint genotyping of F2, F5 and F12."Clinical biochemistryMore Details
    17683517 The Mediterranean paradox for susceptibility factors in coronary heart disease extends to genetics.Annals of human geneticsMore Details

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



    PPI interactions

    There were totally 13 unique genes interacted with F5. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    F5 Co-crystal Structure10586886|10586886 CHD related
    SERPINA3 in vitro8216224 CHD related
    CTSG in vitro9718313 No
    F10 Reconstituted Complex2303476|2303476 No
    CALR Affinity Capture-Western9525969 No
    PROS1 Reconstituted Complex10593904 CHD related
    F2 Reconstituted Complex9032460 CHD related
    POT1 Affinity Capture-MS20811636 No
    PROC in vitro1615482,7989361,10026263 CHD related
    EPR1 in vitro9079657 No
    CSNK2A1 in vivo9525959 CHD related
    MMRN1 in vitro15452129 No
    ELANE in vitro9242537 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00055Drotrecogin alfaFor reduction of mortality in patients with severe sepsis.B01AD10
    experimentalDB04558Phenylmercury