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: DKK1

    Description: dickkopf homolog 1 (Xenopus laevis)

    Entrez Gene ID: 22943

    SwissProt Acc Number: O94907

    RefSeq: NM_012242

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

    ..Serum DKK1 concentrations correlate with the coronary atherosclerosis and play an independent role in predicting the presence of coronary atherosclerosis...

    From PMID: 21935273, in Journal J Korean Med Sci. , 2011


    References

    There were 4 potential papers with DKK1 and CHD.

    PMIDTitleJournalsDetails
    21935273 A novel biomarker of coronary atherosclerosis: serum DKK1 concentration correlates with coronary artery calcification and atherosclerotic plaques.Journal of Korean medical scienceMore Details
    19720407 Levels of DKK1 in patients with acute myocardial infarction and response to atorvastatin.International journal of cardiologyMore Details
    20665672 Chondro/osteoblastic and cardiovascular gene modulation in human artery smooth muscle cells that calcify in the presence of phosphate and calcitriol or paricalcitol.Journal of cellular biochemistryMore Details
    16831933 Osteogenic regulation of vascular calcification.Annals of the New York Academy of SciencesMore Details

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



    PPI interactions

    There were totally 6 unique genes interacted with DKK1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CORO1A Affinity Capture-MS17353931 No
    SMAD9 yeast 2-hybrid15231748 No
    LRP5 in vivo11516963 CHD related
    MDFI Two-hybrid16189514 No
    LRP6 Affinity Capture-Western11448771 CHD related
    KREMEN1 in vitro;in vivo12050670 No


    Involved FDA drugs

    There was no drug associated with DKK1