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: GATA5

    Description: GATA binding protein 5

    Entrez Gene ID: 140628

    SwissProt Acc Number: Q9BWX5

    RefSeq: NM_080473

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

    ..The results unravel a critical cell-autonomous role for endocardial Gata5 in aortic valve formation and identify GATA5 as a potential gene responsible for congenital heart disease in humans...

    From PMID: 21633169, in Journal J Clin Invest , 2011


    There were 1 potential papers with GATA5 and CHD.

    21633169 Loss of Gata5 in mice leads to bicuspid aortic valve.The Journal of clinical investigationMore Details

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

    PPI interactions

    There were totally 3 unique genes interacted with GATA5. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    KLF2 Two-hybrid11375995 CHD related
    HNF1A in vitro;in vivo12011060,14715527 CHD related
    EP300 in vitro;in vivo10567378 CHD related

    Involved FDA drugs

    There was no drug associated with GATA5