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: DUSP1

    Description: dual specificity phosphatase 1

    Entrez Gene ID: 1843

    SwissProt Acc Number: P28562

    RefSeq: NM_004417

    It was suspected to be CHD related:

    .."Taken together, these results indicate that blood levels of the anti-inflammatory protein DUSP1 can be used as a biomarker for post-operative complications leading to prolonged hospitalization after CABG and therefore merit further testing in longitudinal studies of patients eligible for CABG."..

    From PMID: 21424112, in Journal Int J Mol Med. , 2011


    References

    There were 2 potential papers with DUSP1 and CHD.

    PMIDTitleJournalsDetails
    21424112 Blood levels of dual-specificity phosphatase-1 independently predict risk for post-operative morbidities causing prolonged hospitalization after coronary artery bypass grafting.International journal of molecular medicineMore Details
    15364876 Differences in gene expression profiles of diabetic and nondiabetic patients undergoing cardiopulmonary bypass and cardioplegic arrest.CirculationMore Details

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



    PPI interactions

    There were totally 17 unique genes interacted with DUSP1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    MAPK9 Affinity Capture-Western11359773 CHD related
    MAPK10 Affinity Capture-Western11359773 No
    MAPK3 Two-hybrid11278799 CHD related
    MAPK1 Two-hybrid11278799|18519678 CHD related
    MAPK8 Two-hybrid11278799 CHD related
    SKP2 Affinity Capture-Western18519678|18519678 No
    UBC Affinity Capture-Western18519678|12676937|19117950|16286470 No
    CKS1B Affinity Capture-Western18519678|18519678 No
    CHUK Affinity Capture-Western10022904 CHD related
    IKBKB Affinity Capture-Western10022904 CHD related
    PRKCI Affinity Capture-Western10022904 No
    HSPA4 in vivo15677475 No
    MAPK14 Affinity Capture-Western11359773|11278799|20936779 CHD related
    FBXO32 Affinity Capture-Western19117950 No
    UBD Affinity Capture-MS22797925 No
    UBB in vitro;in vivo16286470 No
    MAPK12 in vitro;in vivo11062068 No


    Involved FDA drugs

    There was no drug associated with DUSP1