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: GATA2

    Description: GATA binding protein 2

    Entrez Gene ID: 2624

    SwissProt Acc Number: P23769

    RefSeq: NM_001145661

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

    .."The CATHGEN study reported associations of chromosome 3q13-21 genes (KALRN, MYLK, CDGAP, and GATA2) with early-onset coronary?artery disease (CAD)"..

    From PMID: 19706030, in Journal Ann Hum Genet. , 2009


    References

    There were 4 potential papers with GATA2 and CHD.

    PMIDTitleJournalsDetails
    19864173 Association study of GATA-2 transcription factor gene (GATA2) polymorphism and Parkinson's disease.Parkinsonism & related disordersMore Details
    19885677 The transcription factor GATA-2 does not associate with angiographic coronary artery disease in the Ottawa Heart Genomics and Cleveland Clinic GeneBank Studies.Human geneticsMore Details
    19706030 Validation study of genetic associations with coronary artery disease on chromosome 3q13-21 and potential effect modification by smoking.Annals of human geneticsMore Details
    16934006 GATA2 is associated with familial early-onset coronary artery disease.PLoS geneticsMore Details

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



    PPI interactions

    There were totally 24 unique genes interacted with GATA2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PML Two-hybrid10938104|10938104|10938104|10938104 No
    HDAC3 Affinity Capture-Western11567998 CHD related
    HDAC5 Affinity Capture-Western11567998 No
    ZBTB16 Affinity Capture-Western11964310|11964310 No
    ZBTB32 Affinity Capture-Western11964310 No
    JUN Reconstituted Complex11278891|11278891 CHD related
    ZFPM1 Affinity Capture-Western12483298 No
    SMAD4 Two-hybrid20211142 No
    POU2AF1 Two-hybrid20211142 No
    MED1 Reconstituted Complex16396960 No
    CEBPA in vitro1563207 No
    MAPK1 in vitro7876160 CHD related
    HHEX in vitro15016828 No
    RARA in vitro;in vivo;yeast 2-hybrid15254248 No
    RXRA in vivo15254248 CHD related
    SPI1 Affinity Capture-Western10411939|10411939|10411939|18250304|10411939 No
    POU1F1 Affinity Capture-Western10367888|10367888|16396960|10367888 No
    LMO2 Two-hybrid7568177 No
    TAL1 Two-hybrid7568177 No
    EP300 Biochemical Activity15001660 CHD related
    KAT2A Biochemical Activity15001660 No
    ELAVL1 Affinity Capture-RNA19322201 No
    AKT1 in vivo15837948 CHD related
    STAT3 in vitro;in vivo15673499 CHD related


    Involved FDA drugs

    There was no drug associated with GATA2