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: KLF2

    Description: Kruppel-like factor 2 (lung)

    Entrez Gene ID: 10365

    SwissProt Acc Number: Q9Y5W3

    RefSeq: NM_016270

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

    ..Kruppel-like factor 2 as a novel mediator of statin effects in endothelial cells..

    From PMID: 16043642, in Journal Circulation. , 2005


    References

    There were 5 potential papers with KLF2 and CHD.

    PMIDTitleJournalsDetails
    23723375 Histone and DNA methylation-mediated epigenetic downregulation of endothelial Kruppel-like factor 2 by low-density lipoprotein cholesterol."Arteriosclerosis, thrombosis, and vascular biology"More Details
    24107715 Kruppel-like factor 2 regulates dendritic cell activation in patients with acute coronary syndrome.Cellular physiology and biochemistry : international journal of experimentalMore Details
    20494899 Kruppel-like factor 2 improves neovascularization capacity of aged proangiogenic cells.European heart journalMore Details
    20551377 Discovery of novel mechanosensitive genes in vivo using mouse carotid artery endothelium exposed to disturbed flow.BloodMore Details
    16617118 Kruppel-like factor 2 (KLF2) regulates proinflammatory activation of monocytes.Proceedings of the National Academy of Sciences of the United States of AmericaMore Details

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



    PPI interactions

    There were totally 7 unique genes interacted with KLF2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-Western15003522|21382345 No
    SMURF1 Reconstituted Complex21382345|21382345 No
    EP300 in vitro15136591 CHD related
    GATA5 Two-hybrid11375995 CHD related
    GATA6 Two-hybrid11375995 CHD related
    WWP1 Two-hybrid11375995|11375995 No
    ELAVL1 Affinity Capture-RNA19322201 No


    Involved FDA drugs

    There was no drug associated with KLF2