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: PF4

    Description: platelet factor 4

    Entrez Gene ID: 5196

    SwissProt Acc Number: P02776

    RefSeq: NM_002619

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

    ..PF4 deficiency accelerated endothelial regeneration and protected mice from neointima formation after arterial injury...

    From PMID: 19372458, in Journal Arterioscler Thromb Vasc Biol. , 2009


    References

    There were 12 potential papers with PF4 and CHD.

    PMIDTitleJournalsDetails
    23611535 Persistence of subsyndromal residual symptoms after remission of major depression in patients without cardiovascular disease may condition maintenance of elevated platelet factor 4 and beta-thromboglobulin plasma levels.Journal of affective disordersMore Details
    24267260 Quantitative and qualitative pleiotropic differences between Simvastatin single and Vytorin combination therapy in hypercholesterolemic subjects.AtherosclerosisMore Details
    22614874 Impact of clopidogrel and aspirin treatment on the expression of proteins in platelets from type-2 diabetic patients with stable coronary ischemia.Journal of pharmaceutical sciencesMore Details
    20034674 Depression and platelet activation in outpatients with stable coronary heart disease: findings from the Heart and Soul Study.Psychiatry researchMore Details
    18521540 Selective thromboxane inhibition after vascular protectant AGI-1067: results of assessment of lipoprotein profiles (ALPS) biomarkers in vitro and in vivo substudy.Journal of thrombosis and thrombolysisMore Details
    19249435 Heparin/PF4 antibodies formation after heparin treatment: temporal aspects and long-term follow-up.American heart journalMore Details
    19372458 Core2 1-6-N-glucosaminyltransferase-I deficiency protects injured arteries from neointima formation in ApoE-deficient mice."Arteriosclerosis, thrombosis, and vascular biology"More Details
    19419582 Relevance of hemostatic risk factors on coronary morphology in patients with diabetes mellitus type 2.Cardiovascular diabetologyMore Details
    17700216 Increased platelet activity in patients with isolated coronary artery ectasia.Coronary artery diseaseMore Details
    17495016 Increased plasma concentrations of soluble CD40 ligand in acute coronary syndrome depend on in vitro platelet activation.Clinical chemistryMore Details
    16875910 Prevalence of heparin-induced thrombocytopenia in patients undergoing cardiac catheterization.American heart journalMore Details
    15932816 Relationship between release of platelet/endothelial biomarkers and plasma levels of sertraline and N-desmethylsertraline in acute coronary syndrome patients receiving SSRI treatment for depression.The American journal of psychiatryMore Details

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



    PPI interactions

    There were totally 12 unique genes interacted with PF4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    THBD Reconstituted Complex9395524 CHD related
    PROC Reconstituted Complex9395524 CHD related
    PF4 Co-crystal Structure8031770|7547867|7835432|7547867,8031770 CHD related
    LDLR Reconstituted Complex11986215 CHD related
    CXCL12 Reconstituted Complex10233851 CHD related
    CCL5 in vitro15459010 CHD related
    FGF2 in vitro;in vivo9558385 CHD related
    SDC2 in vitro7524669 No
    CXCR3 Reconstituted Complex12782716|12782716 CHD related
    VCAN Reconstituted Complex11083865 CHD related
    SRGN in vitro;in vivo8613703 No
    IL8 in vitro;in vivo15531763,12586630 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00055Drotrecogin alfaFor reduction of mortality in patients with severe sepsis.B01AD10