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: SELS

    Description: selenoprotein S

    Entrez Gene ID: 55829

    SwissProt Acc Number: Q9BQE4

    RefSeq: NM_018445

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

    ..These results suggest a potential role for the SELS region in the development subclinical CVD in this sample enriched for T2DM...

    From PMID: 23161441, in Journal Acta Diabetol , 2012


    References

    There were 1 potential papers with SELS and CHD.

    PMIDTitleJournalsDetails
    23161441 Polymorphisms in the Selenoprotein S gene and subclinical cardiovascular disease in the Diabetes Heart Study.Acta diabetologicaMore Details

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



    PPI interactions

    There were totally 14 unique genes interacted with SELS. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    VCP Reconstituted Complex15215856|15215856|17872946|16289116|21832065|21832065 No
    UFD1L Affinity Capture-Western15215856 No
    HSPA4 Affinity Capture-Western15215856 No
    DERL1 Affinity Capture-Western15215856|17872946|16289116|16186510|16186509|21832065 No
    SAA1 Reconstituted Complex12031974 CHD related
    SYVN1 Affinity Capture-Western17872946|16289116 No
    AMFR Affinity Capture-Western17872946|21832065 No
    NPLOC4 Affinity Capture-Western17872946 No
    DERL2 Affinity Capture-Western16186509 No
    KPNB1 Affinity Capture-MS21832065|21832065|21832065 No
    SVIP Affinity Capture-Western17872946 No
    HERPUD1 Affinity Capture-Western16289116 No
    UBC Affinity Capture-MS21906983|22505724 No
    APOB Affinity Capture-Western19164805 CHD related


    Involved FDA drugs

    There was no drug associated with SELS