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: PLN

    Description: phospholamban

    Entrez Gene ID: 5350

    SwissProt Acc Number: P26678

    RefSeq: NM_002667

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

    ..Human hibernating myocardium (HHM) is characterized by reversible contractile dysfunction during chronic ischemia.In HHM a decreased activity of SERCA2a due to an impaired phosphorylation of PLN contributes to contractile dysfunction...

    From PMID: 16317512, in Journal Mol Cell Biochem. , 2006


    References

    There were 1 potential papers with PLN and CHD.

    PMIDTitleJournalsDetails
    16317512 Reduced sarcoplasmic reticulum Ca2+ -ATPase activity and dephosphorylated phospholamban contribute to contractile dysfunction in human hibernating myocardium.Molecular and cellular biochemistryMore Details

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



    PPI interactions

    There were totally 8 unique genes interacted with PLN. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ATP2A1 Affinity Capture-Western12032137|10551848|11526231|11526231,10551848 No
    ATP2A2 Affinity Capture-Western12032137|10809745|11854448,11526231,10809745 CHD related
    PPP1R3A Reconstituted Complex9845327 No
    PLN in vitro16043693 CHD related
    DMPK in vitro;in vivo15598648 No
    SLN Affinity Capture-Western12692302|12032137|12692302,12032137 No
    S100A1 in vitro;in vivo12804600 CHD related
    PRKACA in vitro;in vivo3759968,9468536 CHD related


    Involved FDA drugs

    There was no drug associated with PLN