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: BMP2

    Description: bone morphogenetic protein 2

    Entrez Gene ID: 650

    SwissProt Acc Number: P12643

    RefSeq: NM_001200

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

    .."We conclude that there is a balance between the actions of BMP-2 and MGP in the initiation of vascular mesenchymal cell condensation and SMC differentiation, and that targeting ALK1, BMP2 and/or MGP may lead to novel concepts of atherosclerosis treatment."..

    From PMID: 17074310, in Journal Cardiovasc Res. , 2007


    References

    There were 5 potential papers with BMP2 and CHD.

    PMIDTitleJournalsDetails
    23372767 Identification of temporal and region-specific myocardial gene expression patterns in response to infarction in swine.PloS oneMore Details
    19453255 Bone morphogenetic protein 7 (BMP7) gene polymorphisms are associated with inverse relationships between vascular calcification and BMD: the Diabetes Heart Study.Journal of bone and mineral research : the official journal of the AmericanMore Details
    17074310 Activin-like kinase receptor 1 (ALK1) in atherosclerotic lesions and vascular mesenchymal cells.Cardiovascular researchMore Details
    16831933 Osteogenic regulation of vascular calcification.Annals of the New York Academy of SciencesMore Details
    15911698 Smad1 protects cardiomyocytes from ischemia-reperfusion injury.CirculationMore Details

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



    PPI interactions

    There were totally 20 unique genes interacted with BMP2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BMPR2 Affinity Capture-Western7791754|10880444|10712517 No
    COL2A1 Affinity Capture-Western10085302|10085302 No
    ACTR2 Reconstituted Complex10880444 No
    MGP Affinity Capture-Western11741887 CHD related
    BMPR1B Reconstituted Complex10712517 No
    ACVR1 in vivo8006002 No
    ASCL1 in vitro9197246 No
    BMP2 in vitro10074410,10692589,10881198 CHD related
    CHRD in vitro15064755 No
    GREM1 in vitro15064755 No
    ACVR2B in vitro15064755 No
    BMPR1A Co-crystal Structure11263668|11263668,10881198,10692589,15064755 No
    SOSTDC1 Affinity Capture-Western15020244|15020244,14623234 No
    ENG Affinity Capture-Western9872992|9872992 CHD related
    TGFB1 in vivo11456401 CHD related
    TGFB2 in vivo9493905 CHD related
    NOG in vitro;in vivo10657699,15064755 No
    CHRDL2 in vivo14660436 No
    BMPER in vivo12897139 No
    GREM2 in vivo15039429 No


    Involved FDA drugs

    There was no drug associated with BMP2