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: IL6ST

    Description: "interleukin 6 signal transducer (gp130, oncostatin M receptor)"

    Entrez Gene ID: 3572

    SwissProt Acc Number: P40189

    RefSeq: NM_002184

    It was suspected to be CHD related:

    .."we show that genetic variation within the human gp130 homologue, interleukin 6 signal transducer (IL6ST), is significantly associated with coronary artery disease (CAD; P < 0.05). "..

    From PMID: 17664290, in Journal J Exp Med.? , 2007


    References

    There were 1 potential papers with IL6ST and CHD.

    PMIDTitleJournalsDetails
    17664290 Signal transducer of inflammation gp130 modulates atherosclerosis in mice and man.The Journal of experimental medicineMore Details

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



    PPI interactions

    There were totally 32 unique genes interacted with IL6ST. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TLE1 Two-hybrid12030375|12030375|12030375 No
    CNTFR Reconstituted Complex12707266|11285233 No
    PTPN11 Affinity Capture-Western12403768|10946280|9388212|10777583 CHD related
    SOCS3 Affinity Capture-Western12403768|12403768|10777583 CHD related
    ERBB2 Affinity Capture-Western11821958|11821958 CHD related
    ERBB3 Affinity Capture-Western11821958|11821958 No
    VAV1 Reconstituted Complex9013873|9013873 No
    GRB2 Reconstituted Complex9013873|9013873 CHD related
    OSMR Affinity Capture-Western8999038 No
    JAK2 Affinity Capture-Western9388212 CHD related
    TYK2 Affinity Capture-Western9388212|9388212 No
    PRKCD Affinity Capture-Western12361954 CHD related
    STAT3 Affinity Capture-Western12361954|12361954 CHD related
    PIK3R1 Affinity Capture-Western10579793 CHD related
    PTPN6 Affinity Capture-Western10800945|10800945 No
    UBC Affinity Capture-Western18519587 No
    OSM in vitro8999038,16051226 CHD related
    CTF1 in vivo11834704 No
    PLAUR in vitro9353320 CHD related
    IL6ST in vitro11251120 CHD related
    CNTF in vitro12643274,16051226 CHD related
    IL6 in vivo14557255 CHD related
    AR Affinity Capture-Western15129430|15129430 CHD related
    JAK1 Affinity Capture-Western11468294|11468294 CHD related
    IL6R Affinity Capture-Western2788034 CHD related
    LIFR Affinity Capture-Western12047380 No
    CDK9 Reconstituted Complex12386808|12386808 No
    HCK Affinity Capture-Western11689697 No
    SHC1 Affinity Capture-Western9126968|9126968 No
    PIK3CG in vivo10579793 CHD related
    LIF in vivo12707269 CHD related
    IL31RA in vivo14504285,15184896 No


    Involved FDA drugs

    There was no drug associated with IL6ST