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: DCN

    Description: decorin

    Entrez Gene ID: 1634

    SwissProt Acc Number: P07585

    RefSeq: NM_001920

    It was suspected to be CHD related:

    .."postinfarction decorin gene therapy mitigated cardiac remodeling and dysfunction by altering infarct tissue noncardiomyocyte dynamics and preventing cardiac fibrosis, accompanying inhibition of Smad2/3 activation."..

    From PMID: 19684189, in Journal Am J Physiol?Heart?Circ Physiol. , 2009


    References

    There were 2 potential papers with DCN and CHD.

    PMIDTitleJournalsDetails
    23951402 An integrative computational analysis provides evidence for FBN1-associated network deregulation in trisomy 21.Biology openMore Details
    20876586 Role of the autonomic nervous system in cardioprotection by remote preconditioning in isoflurane-anaesthetized dogs.Cardiovascular researchMore Details

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



    PPI interactions

    There were totally 29 unique genes interacted with DCN. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    EGFR Two-hybrid12105206|12105206|9988678 CHD related
    FLNA Reconstituted Complex12106908 No
    COL6A1 Reconstituted Complex1544908 No
    AHSG Reconstituted Complex12071714 CHD related
    COL5A1 in vitro8440685 No
    COL4A3 in vivo10382266 No
    COL4A1 in vivo10382266 CHD related
    COL4A4 in vivo10382266 No
    COL1A1 in vitro9675033,1468447 CHD related
    COL1A2 in vitro;in vivo9675033,1468447,2375748 CHD related
    SFTPD Reconstituted Complex12730206|12730206 CHD related
    COL14A1 Reconstituted Complex9252349 No
    TGFB1 Reconstituted Complex8093006|7638106,7798269 CHD related
    TNF Reconstituted Complex12387878|12387878 CHD related
    ELN Reconstituted Complex11723132|11723132 CHD related
    C1QA Reconstituted Complex1431141 CHD related
    TGFB2 Reconstituted Complex9675033 CHD related
    PLA2G2A Reconstituted Complex10747008|10747008 CHD related
    MET Affinity Capture-Western19433454|19433454 No
    DPT in vitro9895299 No
    MMP2 in vitro9148753 CHD related
    MMP3 in vitro9148753 CHD related
    FBN1 in vivo10793130 CHD related
    FN1 in vitro1468447 CHD related
    MMP7 in vitro9148753 CHD related
    THBS1 in vitro;in vivo9328841,1550960 CHD related
    COL4A5 in vivo10382266 No
    COL4A6 in vivo10382266 No
    WISP1 in vitro11598131 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB03754Tris(Hydroxymethyl)Aminomethane