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: CASQ2

    Description: calsequestrin 2 (cardiac muscle)

    Entrez Gene ID: 845

    SwissProt Acc Number: O14958

    RefSeq: NM_001232

    It was suspected to be CHD related:

    ..Westaway et al. have revealed a significant association between common variants of calsequestrin-2 (CASQ2) and nitric oxide synthase 1 (neuronal) adaptor protein (NOS1AP) and the risk of sudden death in patients of coronary heart disease (CHD)...

    From PMID: 23171141, in Journal Genet Test Mol Biomarkers , 2013


    References

    There were 3 potential papers with CASQ2 and CHD.

    PMIDTitleJournalsDetails
    23171141 Positive association between rs10918859 of the NOS1AP gene and coronary heart disease in male Han Chinese.Genetic testing and molecular biomarkersMore Details
    22733215 Inherited calcium channelopathies in the pathophysiology of arrhythmias.Nature reviews. CardiologyMore Details
    21685173 "Common variants in CASQ2, GPD1L, and NOS1AP are significantly associated with risk of sudden death in patients with coronary artery disease."Circulation. Cardiovascular geneticsMore Details

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



    PPI interactions

    There were totally 4 unique genes interacted with CASQ2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TRDN Reconstituted Complex7721813|10748065|14638677,11113462,11069905,10748065,9287354,7721813 No
    ANKRD1 in vitro15698842 CHD related
    CSNK2A1 in vitro;in vivo1985907 CHD related
    CSNK2A2 in vitro;in vivo1985907 No


    Involved FDA drugs

    There was no drug associated with CASQ2