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: IL4

    Description: interleukin 4

    Entrez Gene ID: 3565

    SwissProt Acc Number: P05112

    RefSeq: NM_000589

    It was suspected to be CHD related:

    ..Many studies have suggested an imbalance between proinflammatory and anti-inflammatory markers in acute myocardial infarction (AMI). Interleukin 4 (IL-4) shows mainly anti-inflammatory activities...

    From PMID: 21127885, in Journal Heart Vessels. , 2011


    References

    There were 4 potential papers with IL4 and CHD.

    PMIDTitleJournalsDetails
    22984364 A Multinomial Ordinal Probit Model with Singular Value Decomposition Method for a Multinomial Trait.Journal of probability and statisticsMore Details
    17924848 Cytokines and growth factors in mostly atherosclerotic patients on hemodialysis determined by biochip array technology.Clinical chemistry and laboratory medicine : CCLM / FESCCMore Details
    15302839 Endogenous angiotensin II induces atherosclerotic plaque vulnerability and elicits a Th1 response in ApoE-/- mice.HypertensionMore Details
    10945940 Graft vasculopathy and tolerance: does the balance of Th cells contribute to graft vasculopathy?The Journal of surgical researchMore Details

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



    PPI interactions

    There were totally 6 unique genes interacted with IL4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    IL4R Co-crystal Structure11786020 CHD related
    A2M Reconstituted Complex10714547 No
    CD53 in vivo7963560 No
    IL13RA2 in vitro;in vivo9130652 No
    IL2RG in vivo8266078 No
    PIK3CD in vivo9113989 No


    Involved FDA drugs

    There was no drug associated with IL4