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: PTX3

    Description: "pentraxin-related gene, rapidly induced by IL-1 beta"

    Entrez Gene ID: 5806

    SwissProt Acc Number: P26022

    RefSeq: NM_002852

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

    ..Pentraxin 3 (PTX3) is a novel candidate immunoinflammatory marker that has been reported to be associated with cardiometabolic risk factors and to predict adverse outcomes in patients with coronary artery disease...

    From PMID: 22617341, in Journal CoronArteryDis. , 2012


    References

    There were 16 potential papers with PTX3 and CHD.

    PMIDTitleJournalsDetails
    24215445 Obesity and high waist circumference are associated with low circulating pentraxin-3 in acute coronary syndrome.Cardiovascular diabetologyMore Details
    23414296 Plasma pentraxin 3 may be a more sensitive marker of inflammatory response than high-sensitivity C-reactive protein after bare-metal stent compared to drug-eluting stent implantation.Journal of interferon & cytokine research : the official journal of theMore Details
    23468517 Incremental diagnostic value of circulating pentraxin in patients with intermediate risk of coronary artery disease.Heart (British Cardiac Society)More Details
    22305847 "Associations of pentraxin-3 with cardiovascular events, incident heart failure, and mortality among persons with coronary heart disease: data from the Heart and Soul Study."American heart journalMore Details
    22617341 Plasma pentraxin-3 levels are associated with coronary plaque vulnerability and are decreased by statin.Coronary artery diseaseMore Details
    22577258 Pentraxin 3(PTX 3): an endogenous modulator of the inflammatory response.Mediators of inflammationMore Details
    21676590 Elevated concentrations of pentraxin 3 are associated with coronary plaque vulnerability.Journal of cardiologyMore Details
    21939648 Novel serum biomarkers in carotid artery stenosis: useful to identify the vulnerable plaque?Clinical biochemistryMore Details
    21677138 Early and transient release of leukocyte pentraxin 3 during acute myocardial infarction."Journal of immunology (Baltimore, Md. : 1950)"More Details
    20692380 Usefulness of cardiovascular biomarkers and cardiac imaging in systemic rheumatic diseases.Autoimmunity reviewsMore Details
    20391484 "Increased levels of serum pentraxin 3, a novel cardiovascular biomarker, in patients with inflammatory rheumatic disease."Arthritis care & researchMore Details
    20656213 The long pentraxin PTX3: a modulator of the immunoinflammatory response in atherosclerosis and cardiovascular diseases.Trends in cardiovascular medicineMore Details
    17640648 Pentraxin3 is a novel marker for stent-induced inflammation and neointimal thickening.AtherosclerosisMore Details
    18268142 Cardioprotective function of the long pentraxin PTX3 in acute myocardial infarction.CirculationMore Details
    17095712 Establishment of a high sensitivity plasma assay for human pentraxin3 as a marker for unstable angina pectoris."Arteriosclerosis, thrombosis, and vascular biology"More Details
    17496115 Pentraxin 3 is elevated in haemodialysis patients and is associated with cardiovascular disease."Nephrology, dialysis, transplantation : official publication of the European"More Details

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



    PPI interactions

    There were totally 5 unique genes interacted with PTX3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    FGF2 in vitro16020751 CHD related
    C1QA in vitro;in vivo12645945 CHD related
    C1QB in vitro12645945 CHD related
    C1QC in vitro12645945 No
    CFH in vitro19050261 CHD related


    Involved FDA drugs

    There was no drug associated with PTX3