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: NLRP3

    Description: "NLR family, pyrin domain containing 3"

    Entrez Gene ID: 114548

    SwissProt Acc Number: Q96P20

    RefSeq: NM_001079821

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

    ..Monosodium urate (MSU) crystals increase gout associated coronary heart disease (CHD) risk through the activation of NLRP3 inflammasome...

    From PMID: 22726397, in Journal Int J Cardiol. , 2012


    References

    There were 8 potential papers with NLRP3 and CHD.

    PMIDTitleJournalsDetails
    23944632 NLRP3 inflammasome activation in coronary artery disease: results from prospective and randomized study of treatment with atorvastatin or rosuvastatin."Clinical science (London, England : 1979)"More Details
    23462287 NLRP3 inflammasomes show high expression in aorta of patients with atherosclerosis."Heart, lung & circulation"More Details
    23471228 Epicardial adipose tissue volume and adipocytokine imbalance are strongly linked to human coronary atherosclerosis."Arteriosclerosis, thrombosis, and vascular biology"More Details
    24244322 Ethanol Inhibits Activation of NLRP3 and AIM2 Inflammasomes in Human Macrophages-A Novel Anti-Inflammatory Action of Alcohol.PloS oneMore Details
    22361326 Interleukin-1beta is crucial for the induction of coronary artery inflammation in a mouse model of Kawasaki disease.CirculationMore Details
    22246178 Statins and pulmonary fibrosis: the potential role of NLRP3 inflammasome activation.American journal of respiratory and critical care medicineMore Details
    21300955 Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.CirculationMore Details
    20671522 Monogenic autoinflammatory diseases: new insights into clinical aspects and pathogenesis.Current opinion in rheumatologyMore Details

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



    PPI interactions

    There were totally 6 unique genes interacted with NLRP3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SUGT1 Affinity Capture-Western17435760 No
    HSP90AA1 Affinity Capture-Western17435760 CHD related
    FAF1 Two-hybrid17046979|17046979 No
    NLRC4 Affinity Capture-Western15107016 No
    PYCARD in vitro11786556 CHD related
    CARD8 in vivo15030775 No


    Involved FDA drugs

    There was no drug associated with NLRP3