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: BNIP3

    Description: BCL2/adenovirus E1B 19kDa interacting protein 3

    Entrez Gene ID: 664

    SwissProt Acc Number: Q12983

    RefSeq: NM_004052

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

    .."Chronic hypoxia induced the expression and accumulation of BNIP3 mRNA and protein in cardiac myocytes, but acidosis was required to activate the death pathway. "..

    From PMID: 12226479, in Journal Proc Natl Acad Sci U S A. , 2002


    There were 3 potential papers with BNIP3 and CHD.

    23160801 Oxidative stress in coronary artery disease: epigenetic perspective.Molecular and cellular biochemistryMore Details
    20559783 Mitochondrial pruning by Nix and BNip3: an essential function for cardiac-expressed death factors.Journal of cardiovascular translational researchMore Details
    12226479 Hypoxia and acidosis activate cardiac myocyte death through the Bcl-2 family protein BNIP3.Proceedings of the National Academy of Sciences of the United States of AmericaMore Details

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

    PPI interactions

    There were totally 9 unique genes interacted with BNIP3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TMEM11 Two-hybrid16189514|16189514|16189514 No
    BNIP3L Two-hybrid16189514|16189514 No
    BNIP3 Two-hybrid16189514|9396766|9396766|10625696|9396766,16169070 CHD related
    HDAC1 Affinity Capture-Western19339613 CHD related
    BCL2L1 Two-hybrid10625696|10625696 CHD related
    CD47 Two-hybrid12690108|12690108 No
    BCL2 Two-hybrid7954800|10625696 CHD related
    NCBP1 Two-hybrid7478990 No
    UBC Affinity Capture-MS21963094|21139048|21906983 No

    Involved FDA drugs

    There was no drug associated with BNIP3