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: CIITA

    Description: "class II, major histocompatibility complex, transactivator"

    Entrez Gene ID: 4261

    SwissProt Acc Number: P33076

    RefSeq: NM_000246

    It was suspected to be CHD related:

    ..simvastatin selectively decreases IFN-gamma-induced MHC class II expression in human primary endothelial cells through actions on the CIITA promoter IV..

    From PMID: 11219190, in Journal Swiss Med Wkly. , 2001


    References

    There were 1 potential papers with CIITA and CHD.

    PMIDTitleJournalsDetails
    11219190 The HMG-CoA reductase inhibitor simvastatin inhibits IFN-gamma induced MHC class II expression in human vascular endothelial cells.Swiss medical weeklyMore Details

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



    PPI interactions

    There were totally 24 unique genes interacted with CIITA. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NCOA1 Affinity Capture-Western12933903|12933903 No
    RFX5 Affinity Capture-Western11003667 No
    MAPK3 Affinity Capture-Western18245089 CHD related
    HDAC2 Affinity Capture-Western19041327|17991736 CHD related
    SIN3B Affinity Capture-Western17991736 No
    GTF2B Reconstituted Complex9177216 No
    TAF9 Reconstituted Complex9177216 No
    NFYB in vivo11003667 No
    ZXDC in vivo;yeast 2-hybrid16600381 No
    RFXANK Reconstituted Complex11463838|11463838|11463838 No
    XPO1 Reconstituted Complex12517958|18245089|12517958 No
    MAPK1 Biochemical Activity18245089|18245089 CHD related
    CDK1 Biochemical Activity18245089 CHD related
    HDAC1 Reconstituted Complex12697811 CHD related
    SMARCA4 Reconstituted Complex12077331 No
    HDAC4 Affinity Capture-Western15964851|15964851 CHD related
    HDAC5 Affinity Capture-Western15964851|15964851 No
    GSK3B Biochemical Activity17991736 CHD related
    PSMC5 Reconstituted Complex20351748|20351748|18215421 No
    PSMC2 Affinity Capture-Western20351748 No
    PSMC3 Affinity Capture-Western20351748 No
    PRKACA in vitro;in vivo11416140 CHD related
    KAT2B in vitro;in vivo11046145 No
    TAF6 in vitro9177216 No


    Involved FDA drugs

    There was no drug associated with CIITA