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.
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    Collaboration Information: Prof. Xiaohui Fan (

    Website using assistance : Leihong Wu (

    Basic Information

    Gene Name: GATA6

    Description: GATA binding protein 6

    Entrez Gene ID: 2627

    SwissProt Acc Number: Q92908

    RefSeq: NM_005257

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

    ..GATA6?mutations cause human cardiac outflow tract defects by disrupting semaphorin-plexin signaling..

    From PMID: 19666519, in Journal Proc Natl Acad Sci U S A. , 2009


    There were 1 potential papers with GATA6 and CHD.

    22318994 Human gene copy number spectra analysis in congenital heart malformations.Physiological genomicsMore Details

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

    PPI interactions

    There were totally 8 unique genes interacted with GATA6. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    EP300 Affinity Capture-Western10851229|10851229 CHD related
    KLF2 Two-hybrid11375995 CHD related
    SP1 Affinity Capture-Western14988427|21076612 No
    NKX2-1 in vitro;yeast 2-hybrid11733512 No
    CRIP2 in vitro;in vivo12530967 No
    MED1 in vitro11724781 No
    HHEX yeast 2-hybrid15016828 No
    CDK9 Affinity Capture-Western20081228 No

    Involved FDA drugs

    There was no drug associated with GATA6