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: PON2

    Description: paraoxonase 2

    Entrez Gene ID: 5445

    SwissProt Acc Number: Q15165

    RefSeq: NM_000305

    It was suspected to be CHD related:

    ..Polymorphisms in PON2 gene have been associated with the level of plasma lipoproteins and glucose and are thought to play a role in atherosclerosis...

    From PMID: 16185677, in Journal Clin Chim Acta , 2006


    References

    There were 18 potential papers with PON2 and CHD.

    PMIDTitleJournalsDetails
    23742759 Associations between genetic polymorphisms of paraoxonase genes and coronary artery disease in a Taiwanese population.Clinical biochemistryMore Details
    23053877 Association of PON1 and PON2 polymorphisms with PON1 activity and significant coronary stenosis in a Tunisian population.Biochemical geneticsMore Details
    21867409 The human paraoxonase gene cluster as a target in the treatment of atherosclerosis.Antioxidants & redox signalingMore Details
    22548179 Regulation of hepatic paraoxonase-1 expression.Journal of lipidsMore Details
    21231776 C-reactive protein levels are associated with paraoxonase polymorphism L55M in patients undergoing cardiac SPECT imaging.Scandinavian journal of clinical and laboratory investigationMore Details
    21620813 Polymorphisms of pon1 and pon2 genes in hemodialyzed patients.Clinical biochemistryMore Details
    21223581 Association analysis of PON2 genetic variants with serum paraoxonase activity and systemic lupus erythematosus.BMC medical geneticsMore Details
    19939821 The role of polymorphisms within paraoxonases (192 Gln/Arg in PON1 and 311Ser/Cys in PON2) in the modulation of cardiovascular risk: a pilot study.AngiologyMore Details
    20536507 "Independent predictive roles of eotaxin Ala23Thr, paraoxonase 2 Ser311Cys and beta-adrenergic receptor Trp64Arg polymorphisms on cardiac disease in Type 2 Diabetes--an 8-year prospective cohort analysis of 1297 patients."Diabetic medicine : a journal of the British Diabetic AssociationMore Details
    19426787 Molecular characterization and expression analysis of the porcine paraoxonase 3 (PON3) gene.GeneMore Details
    16185677 Detecting the polymorphisms of paraoxonase (PON) cluster in Chinese Han population based on a rapid method.Clinica chimica acta; international journal of clinical chemistryMore Details
    16319130 Polymorphisms in the PON gene cluster are associated with Alzheimer disease.Human molecular geneticsMore Details
    16239632 Evaluation of the paraoxonases as candidate genes for stroke: Gln192Arg polymorphism in the paraoxonase 1 gene is associated with increased risk of stroke.Stroke; a journal of cerebral circulationMore Details
    14996478 PON1 M/L55 mutation protects high-risk patients against coronary artery disease.International journal of cardiologyMore Details
    15001326 Four paraoxonase gene polymorphisms in 11212 cases of coronary heart disease and 12786 controls: meta-analysis of 43 studies.LancetMore Details
    12454802 "Association between the severity of angiographic coronary artery disease and paraoxonase gene polymorphisms in the National Heart, Lung, and Blood Institute-sponsored Women's Ischemia Syndrome Evaluation (WISE) study."American journal of human geneticsMore Details
    14551701 "Paraoxonase gene polymorphisms, oxidative stress, and diseases.""Journal of molecular medicine (Berlin, Germany)"More Details
    11803456 Codon 311 (Cys --> Ser) polymorphism of paraoxonase-2 gene is associated with apolipoprotein E4 allele in both Alzheimer's and vascular dementias.Molecular psychiatryMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with PON2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    RUVBL2 Affinity Capture-MS17353931 No
    RHOA Co-fractionation22939629 CHD related
    RAP1A Co-fractionation22939629 No
    STOM Co-fractionation22939629 No
    UBC Affinity Capture-MS18781797|21139048|21906983 No
    TCF3 Affinity Capture-MS22354994 No
    CUL3 Affinity Capture-MS21145461 No
    FBXO6 Affinity Capture-MS22268729 No
    HTR2A yeast 2-hybrid16537434 No


    Involved FDA drugs

    There was no drug associated with PON2