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.

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  • 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.

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  • 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: CD28

    Description: CD28 molecule

    Entrez Gene ID: 940

    SwissProt Acc Number: P10747

    RefSeq: NM_006139

    It was suspected to be CHD related:

    .."In DM patients, CD4+CD28(null)T-cells are expanded and are associated with poor glycaemic control"..

    From PMID: 21217142, in Journal Eur Heart J , 2011


    References

    There were 7 potential papers with CD28 and CHD.

    PMIDTitleJournalsDetails
    22882906 Persistent accumulation of interferon-gamma-producing CD8+CD56+ T cells in blood from patients with coronary artery disease.AtherosclerosisMore Details
    22282196 High levels of costimulatory receptors OX40 and 4-1BB characterize CD4+CD28null T cells in patients with acute coronary syndrome.Circulation researchMore Details
    18818214 CD4+ CD28 null T cells in coronary artery disease: when helpers become killers.Cardiovascular researchMore Details
    18281862 Behcet's disease.Current opinion in rheumatologyMore Details
    15864782 Endothelial inducible costimulator ligand expression is increased during human cardiac allograft rejection and regulates endothelial cell-dependent allo-activation of CD8+ T cells in vitro.European journal of immunologyMore Details
    15621570 CTLA4Ig prevents initiation but not evolution of anti-phospholipid syndrome in NZW/BXSB mice.AutoimmunityMore Details
    15374847 Blockade of the interaction between PD-1 and PD-L1 accelerates graft arterial disease in cardiac allografts."Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 19 unique genes interacted with CD28. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CD80 Reconstituted Complex7545666|7545666 CHD related
    GRAP2 Affinity Capture-Western10820259|10820259|10820259 No
    LRRC23 Reconstituted Complex1847722 No
    DUSP14 Two-hybrid11123293|11123293|11123293 No
    PIK3R2 Affinity Capture-Western19190244|7509360,8080844 No
    PIK3CA Affinity Capture-Western9915850 CHD related
    PLCG1 in vivo8386518 CHD related
    NSF in vivo11680900 No
    PIK3CG in vivo9915850 CHD related
    PTPRC in vivo1355979 CHD related
    LCK in vitro10430626 No
    IL12A in vitro;in vivo7516408 CHD related
    GRB2 Reconstituted Complex9694876 CHD related
    PIK3R1 Protein-peptide8621607 CHD related
    UBC Affinity Capture-MS22505724 No
    CD247 in vivo8760790 No
    CD4 in vitro7539755 CHD related
    ITK in vitro;in vivo10586033,8992971,15144186 No
    CD86 in vivo11021528,7513726 CHD related


    Involved FDA drugs

    There was no drug associated with CD28