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: ELN

    Description: elastin

    Entrez Gene ID: 2006

    SwissProt Acc Number: P15502

    RefSeq: NM_000501

    It was suspected to be CHD related:

    .."Matrix metalloproteinase-2 degrades a number of extracellular substrates, including elastin and has been shown to play a critical role in the development of abdominal aortic aneurysms"..

    From PMID: 21039989, in Journal Int J Exp Pathol , 2011


    References

    There were 4 potential papers with ELN and CHD.

    PMIDTitleJournalsDetails
    22318994 Human gene copy number spectra analysis in congenital heart malformations.Physiological genomicsMore Details
    23250899 Supravalvular aortic stenosis: elastin arteriopathy.Circulation. Cardiovascular geneticsMore Details
    21179441 Effects of an alpha-4 integrin inhibitor on restenosis in a new porcine model combining endothelial denudation and stent placement.PloS oneMore Details
    16930010 Congenital heart disease: Molecular diagnostics of supravalvular aortic stenosis.Methods in molecular medicineMore Details

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



    PPI interactions

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

    Gene nameInteraction typereference PMIDCHD relation
    BGN Reconstituted Complex11723132 No
    DCN Reconstituted Complex11723132|11723132 CHD related
    FBN1 Reconstituted Complex10825173 CHD related
    FBN2 Reconstituted Complex10825173|10825173 No
    FBLN1 Reconstituted Complex10544250 CHD related
    FBLN2 Reconstituted Complex10544250 No
    NID2 Reconstituted Complex10544250 No
    CLU Reconstituted Complex17872975 No
    LOXL1 in vitro;yeast 2-hybrid16251195 No
    ELANE in vitro10471600 CHD related
    PRTN3 Biochemical Activity11867344|11867344 No
    LGALS3 Affinity Capture-Western10536372|10536372|10536372 No
    FCN1 Reconstituted Complex8947836|8947836 No
    LYZ in vivo9745729 No
    LOX in vivo6912069 CHD related
    MFAP2 in vivo8761465,11723132 No
    SPINK1 in vitro2093478 No
    ASS1 in vivo1372742 No
    FKBP10 in vitro;in vivo11071917 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    withdrawnDB00533Rofecoxib"For the treatment of osteoarthritis, rheumatoid arthritis, acute pain in adults, and primary dysmenorrhea, as well as acute treatment of migraine attacks with or without auras."M01AH02