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: IRS2

    Description: insulin receptor substrate 2

    Entrez Gene ID: 8660

    SwissProt Acc Number: Q9Y4H2

    RefSeq: NM_003749

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

    ..we conclude that elevated IRS2 gene expression in macrophages may be associated with an increased risk of CHD...

    From PMID: 18506362, in Journal Int J Mol Med. , 2008


    References

    There were 2 potential papers with IRS2 and CHD.

    PMIDTitleJournalsDetails
    22347652 Insulin receptor substrate-1 expression is increased in circulating leukocytes of patients with acute coronary syndrome.ISRN cardiologyMore Details
    20112301 Green tea polyphenols improve cardiac muscle mRNA and protein levels of signal pathways related to insulin and lipid metabolism and inflammation in insulin-resistant rats.Molecular nutrition & food researchMore Details

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



    PPI interactions

    There were totally 49 unique genes interacted with IRS2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PIK3R1 Affinity Capture-Western8910607|9334184|9852124|12107746|15514089|19561084|12107746,9852124 CHD related
    PTPN11 Affinity Capture-Western8910607|8910607 CHD related
    PIK3R3 Affinity Capture-Western10417350|10417350 No
    EPOR Affinity Capture-Western9334184|9334184 No
    JAK1 Affinity Capture-Western7499365|7499365 CHD related
    TYK2 Reconstituted Complex8550573|8550573 No
    UBTF Affinity Capture-Western12554758|12554758 No
    UBC Affinity Capture-Western12821935 No
    PIK3CA Affinity Capture-Western12933652 CHD related
    SOCS3 Affinity Capture-Western15514089 CHD related
    RPTOR Reconstituted Complex19561084 No
    ATP2A1 in vitro;in vivo9295312 No
    BCL2L1 in vivo10679027 CHD related
    JAK3 in vivo7499365 No
    SHC1 in vitro11505033 No
    PTPN6 in vivo12198247 No
    PIK3CD in vitro;in vivo9113989 No
    PIK3R2 in vitro;in vivo9651378,10594015 No
    SOCS7 in vitro12052866 No
    NTRK1 in vitro;yeast 2-hybrid11147812 No
    IGF1R in vivo;yeast 2-hybrid9852124,8662806 CHD related
    IL4R in vitro8954948 CHD related
    YWHAB Affinity Capture-MS17353931|15324660|15324660 No
    YWHAG Affinity Capture-MS17353931|15324660|15324660 No
    YWHAQ Affinity Capture-MS17353931|15161933 No
    SFN Affinity Capture-MS15778465 No
    SOCS1 Affinity Capture-Western12228220 CHD related
    INSR Two-hybrid8626379|8626379,8662806,9195949 No
    BCL2 Affinity Capture-Western10679027 CHD related
    NISCH Affinity Capture-Western11912194 No
    PLCG1 Affinity Capture-Western9535722 CHD related
    IRS1 Co-fractionation12554758 CHD related
    ESR1 Affinity Capture-Western12821935 CHD related
    SUMO2 Affinity Capture-MS21693764 No
    ELAVL1 Affinity Capture-RNA19322201 No
    MYC Dosage Lethality22623531 CHD related
    GRB10 Affinity Capture-Western12783867 No
    EGFR Affinity Capture-MS18271526 CHD related
    COPS2 Co-fractionation22939629 No
    PTPRF in vitro8732688,15588985 No
    GRB2 in vivo7559579,9852124 CHD related
    YWHAZ in vivo9312143 No
    YWHAE in vivo9312143 No
    SOCS6 in vitro12052866 No
    JAK2 in vivo12960006 CHD related
    ATP2A2 in vitro;in vivo9295312 CHD related
    MPL in vivo11054408 No
    CRK in vitro8621590 No
    FES in vitro10856136 No


    Involved FDA drugs

    There was no drug associated with IRS2