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: COG6

    Description: component of oligomeric golgi complex 6

    Entrez Gene ID: 57511

    SwissProt Acc Number: Q9Y2V7

    RefSeq: NM_001145079

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

    .."The polymorphism of miRNA-1 target gene COG6 rs9548934C->T is associated with lower risk of pCAD, especially in female subjects and subjects with lower serum lipid levels."..

    From PMID: 22883088, in Journal Zhonghua Xin Xue Guan Bing Za Zhi. , 2012


    References

    There were 0 potential papers with COG6 and CHD.

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



    PPI interactions

    There were totally 9 unique genes interacted with COG6. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    COG7 Co-fractionation22939629 No
    COG8 Co-fractionation22939629 No
    COG3 Affinity Capture-Western11929878|22939629 No
    SNCA Synthetic Growth Defect14657499 No
    ATXN7 Two-hybrid21078624 No
    UBD Affinity Capture-MS22797925 No
    COG1 Co-fractionation22939629 No
    COG5 Co-fractionation22939629 No
    COG2 Co-fractionation22939629 No


    Involved FDA drugs

    There was no drug associated with COG6