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: COX2

    Description: cytochrome c oxidase subunit II

    Entrez Gene ID: 4513

    SwissProt Acc Number: P00403

    RefSeq:

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

    .."For RD patients, serum creatinine (p<0.001) and CRP levels, VEGF levels, and NSAID/COX2 inhibitor use (all p<0.05) were independently associated with CHD risk"..

    From PMID: 19185362, in Journal Int J Cardiol. , 2010


    References

    There were 8 potential papers with COX2 and CHD.

    PMIDTitleJournalsDetails
    21852616 Accumulation of dietary docosahexaenoic acid in the brain attenuates acute immune response and development of postischemic neuronal damage.Stroke; a journal of cerebral circulationMore Details
    20606121 Relation of platelet and leukocyte inflammatory transcripts to body mass index in the Framingham heart study.CirculationMore Details
    18469150 "The role of eNOS, iNOS, and NF-kappaB in upregulation and activation of cyclooxygenase-2 and infarct size reduction by atorvastatin."American journal of physiology. Heart and circulatory physiologyMore Details
    18931027 Pioglitazone protects the myocardium against ischemia-reperfusion injury in eNOS and iNOS knockout mice.American journal of physiology. Heart and circulatory physiologyMore Details
    18022214 Cellular senescence in endothelial cells from atherosclerotic patients is accelerated by oxidative stress associated with cardiovascular risk factors.Mechanisms of ageing and developmentMore Details
    17277020 Aspirin before reperfusion blunts the infarct size limiting effect of atorvastatin.American journal of physiology. Heart and circulatory physiologyMore Details
    17008926 Primer: managing NSAID-induced ulcer complications--balancing gastrointestinal and cardiovascular risks.Nature clinical practice. Gastroenterology & hepatologyMore Details
    16265533 Drug insight: cyclo-oxygenase 2 inhibitors and cardiovascular risk--where are we now?Nature clinical practice. Cardiovascular medicineMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with COX2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BCAP31 Co-localization15254227 No
    TH1L Affinity Capture-MS17353931 No
    SNCA Affinity Capture-MS18614564 No
    YWHAE Two-hybrid20936779 No
    ICT1 Affinity Capture-MS20186120 No
    RAD21 Two-hybrid22145905 No
    UBC Affinity Capture-MS21139048|21890473 No
    CDK2 Affinity Capture-MS21319273 No
    Htt Affinity Capture-MS17500595 No


    Involved FDA drugs

    There was no drug associated with COX2