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: HNF1A

    Description: HNF1 homeobox A

    Entrez Gene ID: 6927

    SwissProt Acc Number: P20823

    RefSeq: NM_000545

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

    .."Five single-nucleotide polymorphisms, rs4977574 (CDKN2A/2B), rs12526453 (PHACTR1), rs646776 (CELSR2-PSRC1-SORT1), rs2259816 (HNF1A), and rs11206510 (PCSK9) showed directionally consistent associations with CHD in the 3 studies, with combined odds ratios (ORs) ranging from 1.17 to 1.25 (p = 0.03 to 0.0002).//In the LURIC Study cohort the A-allele of rs2259816 is associated with decreased CRP but not with coronary artery disease."..

    From PMID: 22152955, in Journal J Am Coll Cardiol. , 2011


    References

    There were 8 potential papers with HNF1A and CHD.

    PMIDTitleJournalsDetails
    23824729 Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.The American journal of clinical nutritionMore Details
    22643178 A novel missense mutation in the signal peptide of the human POMC gene: a possible additional link between early-onset type 2 diabetes and obesity.European journal of human genetics : EJHGMore Details
    21300955 Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.CirculationMore Details
    22152955 Genetic susceptibility to coronary heart disease in type 2 diabetes: 3 independent studies.Journal of the American College of CardiologyMore Details
    21094359 "Effect of central obesity, low high-density lipoprotein cholesterol and C-reactive protein polymorphisms on C-reactive protein levels during treatment with Rosuvastatin (10 mg Daily)."The American journal of cardiologyMore Details
    21062467 Effect of the rs2259816 polymorphism in the HNF1A gene on circulating levels of c-reactive protein and coronary artery disease (the ludwigshafen risk and cardiovascular health study).BMC medical geneticsMore Details
    20031592 Common coding variants of the HNF1A gene are associated with multiple cardiovascular risk phenotypes in community-based samples of younger and older European-American adults: the Coronary Artery Risk Development in Young Adults Study and The Cardiovascular Health Study.Circulation. Cardiovascular geneticsMore Details
    19567438 Genetic Loci associated with C-reactive protein levels and risk of coronary heart disease.JAMA : the journal of the American Medical AssociationMore Details

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



    PPI interactions

    There were totally 26 unique genes interacted with HNF1A. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PCBD1 Affinity Capture-MS17353931|9092652|9092652|9092652|21047120|9092652 No
    PCBD2 Affinity Capture-MS17353931 No
    CALM3 Affinity Capture-MS17353931 No
    SNRPA1 Affinity Capture-MS17353931 No
    RHPN2 Affinity Capture-MS17353931 No
    HNF1B Reconstituted Complex2044952 No
    HNF1A Reconstituted Complex2044952|12453420 CHD related
    FOS Affinity Capture-Western11134330 CHD related
    STAT3 Affinity Capture-Western11134330|11134330 CHD related
    CTNNB1 in vivo12107263,11266540,16442529 CHD related
    CEBPA in vitro8288579 No
    BCR in vivo16442529 CHD related
    ALB in vitro2460858 CHD related
    CREBBP Affinity Capture-Western10777539|15598887|10777539 No
    KAT2B Affinity Capture-Western10777539|10777539 No
    SRC Affinity Capture-Western10777539|10777539 CHD related
    RAC3 Affinity Capture-Western10777539|10777539 No
    EP300 Affinity Capture-Western11978637|11978637|15598887|11978637 CHD related
    CDX2 Reconstituted Complex10677375|10677375 No
    AES Two-hybrid11266540 No
    SIRT1 Reconstituted Complex21176092|21176092 CHD related
    BCL6 Affinity Capture-MS16147992 No
    POU2F1 in vitro10779377 No
    TLE1 in vitro10209158 No
    HNF4A in vitro9792724 No
    GATA5 in vitro;in vivo12011060,14715527 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB04419Norleucine