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: NPPB

    Description: natriuretic peptide precursor B

    Entrez Gene ID: 4879

    SwissProt Acc Number: P16860

    RefSeq: NM_002521

    It was suspected to be CHD related:

    .."Atrial natriuretic peptide (ANP, also known as NPPA) and brain natriuretic peptide (BNP, also known as NPPB) have been determined as genetic factors for several diseases, including stroke and myocardial infarction, in human and rat models."..

    From PMID: 22400494, in Journal DNA Cell Biol , 2012


    References

    There were 5 potential papers with NPPB and CHD.

    PMIDTitleJournalsDetails
    24104878 A transgenic mouse model for the simultaneous monitoring of ANF and BNP gene activity during heart development and disease.Cardiovascular researchMore Details
    23847679 Expression of angiogenesis-related genes in right atrial appendages from patients with advanced myocardial ischemia - preliminary results.Archives of medical science : AMSMore Details
    22400494 Potential association between frequent nonsynonymous variant of NPPA and cardioembolic stroke.DNA and cell biologyMore Details
    21276798 Association of genetic variation in the natriuretic peptide system with cardiovascular outcomes.Journal of molecular and cellular cardiologyMore Details
    15964927 Electrophysiological effects of O2*- on the plasma membrane in vascular endothelial cells.American journal of physiology. Heart and circulatory physiologyMore Details

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



    PPI interactions

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

    Gene nameInteraction typereference PMIDCHD relation
    HDAC4 Reconstituted Complex21464227 CHD related
    NPR1 in vitro;in vivo7901875,1309330 CHD related
    EWSR1 Two-hybrid16189514|16189514 No
    NPR3 Reconstituted Complex1309330 CHD related
    NPR2 Reconstituted Complex1309330 CHD related
    UBD Affinity Capture-MS22797925 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB01136CarvedilolFor the treatment of mild or moderate (NYHA class II or III) heart failure of ischemic or cardiomyopathic origin.C07AG02