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: GOSR2

    Description: golgi SNAP receptor complex member 2

    Entrez Gene ID: 9570

    SwissProt Acc Number: O14653

    RefSeq: NM_001012511

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

    ..We found evidence that a SNP in GOSR2 is modestly associated with hypertension in whites from the ARIC study and the WGHS...

    From PMID: 19057520, in Journal Am J Hypertens. , 2009


    References

    There were 2 potential papers with GOSR2 and CHD.

    PMIDTitleJournalsDetails
    21909115 Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.NatureMore Details
    19057520 GOSR2 Lys67Arg is associated with hypertension in whites.American journal of hypertensionMore Details

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



    PPI interactions

    There were totally 6 unique genes interacted with GOSR2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APP Reconstituted Complex21832049 No
    NAPA in vitro;in vivo9349823 No
    ARF1 in vitro;in vivo15781476 No
    STX5 Co-purification9094723|11927603 No
    USO1 Co-purification11927603|10903204|10903204 No
    UBC Affinity Capture-MS21139048 No


    Involved FDA drugs

    There was no drug associated with GOSR2