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: BMP7

    Description: bone morphogenetic protein 7

    Entrez Gene ID: 655

    SwissProt Acc Number: P18075

    RefSeq: NM_001719

    It was suspected to be CHD related:

    .."Our results suggest that BMP7 has neuroprotective effects against Aβ, which may be mediated through inhibition of Bax gene expression during cell apoptosis and elevation of SOD activities during the oxidative stress response. "..

    From PMID: 21496477, in Journal Neuroscience. , 2011


    References

    There were 3 potential papers with BMP7 and CHD.

    PMIDTitleJournalsDetails
    22681982 [Hypertension-induced fibrosis: a balance story].Annales de cardiologie et d'angeiologieMore 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
    19696925 Restoration of podocyte structure and improvement of chronic renal disease in transgenic mice overexpressing renin.PloS oneMore Details

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



    PPI interactions

    There were totally 17 unique genes interacted with BMP7. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BMPR2 Affinity Capture-Western7791754 No
    BMP7 Co-purification12478285 CHD related
    BMPR1A Reconstituted Complex8006002 No
    BMPR1B Reconstituted Complex8006002 No
    ACVR1 Reconstituted Complex8006002|8006002 No
    ACVR2A Affinity Capture-Western9748228|9748228,12667445 No
    ACVR2B Affinity Capture-Western9748228 No
    SMAD1 Phenotypic Suppression11438941 CHD related
    SOSTDC1 Affinity Capture-Western15020244|15020244,14623234 No
    NOG Co-crystal Structure12478285|12478285|12478285 No
    ENG Affinity Capture-Western9872992|9872992 CHD related
    SMAD3 Co-localization20093492 CHD related
    UBC Reconstituted Complex19850743|21906983 No
    SIRT5 Negative Genetic22318606 No
    NCOA3 in vivo7791754 No
    GDF7 in vitro12741987 No
    CHRDL2 in vivo14660436 No


    Involved FDA drugs

    There was no drug associated with BMP7