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: CD40LG

    Description: CD40 ligand

    Entrez Gene ID: 959

    SwissProt Acc Number: P29965

    RefSeq: NM_000074

    It was suspected to be CHD related:

    ..Soluble CD40L levels are regulated by the -3459 A>G polymorphism and predict myocardial infarction and the efficacy of antithrombotic treatment in non-ST elevation acute coronary syndrome. We identified a SNP in the CD40LG gene as a novel regulator of sCD40L plasma concentrations...

    From PMID: 16627810, in Journal Arterioscler Thromb Vasc Biol. , 2006


    References

    There were 2 potential papers with CD40LG and CHD.

    PMIDTitleJournalsDetails
    21889313 Chlamydia pneumoniae heat shock protein 60 is associated with apoptotic signaling pathway in human atheromatous plaques of coronary artery disease patients.Journal of cardiologyMore Details
    16627810 Soluble CD40L levels are regulated by the -3459 A>G polymorphism and predict myocardial infarction and the efficacy of antithrombotic treatment in non-ST elevation acute coronary syndrome."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 11 unique genes interacted with CD40LG. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    HPR Affinity Capture-Western10085035 CHD related
    APOA1 Affinity Capture-Western10085035 CHD related
    RNF128 Affinity Capture-Western18641297 No
    UBC Affinity Capture-Western18641297 No
    CD40 in vitro;in vivo10647992,7516405,7543281 CHD related
    CD40LG in vitro11525169 CHD related
    IGKC in vitro11525169 No
    CRYAB Affinity Capture-MS21357544 No
    CD5L in vivo11981870 No
    IGHG1 in vitro11525169 No
    TP53 in vivo12011072 CHD related


    Involved FDA drugs

    There was no drug associated with CD40LG