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: HDAC10

    Description: histone deacetylase 10

    Entrez Gene ID: 83933

    SwissProt Acc Number: Q969S8

    RefSeq: NM_001159286

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

    .."Vasospastic angina (VA) is a specific type of coronary artery disease and develops as a result of coronary artery spasm. The fold change levels were highest in the CTDP1 (18q23), HDAC10 (22q13.33), KCNQ1 (11p15.5-p15.4), NINJ2 (12p13.33), NOTCH2 (1p12-p11.2), PCSK6 (15q26.3), SDHA (5p15.33), and MUC17 (7q22.1) genes."..

    From PMID: 21860640, in Journal Korean Circ J. , 2011


    References

    There were 1 potential papers with HDAC10 and CHD.

    PMIDTitleJournalsDetails
    21860640 Deoxyribonucleic Acid copy number aberrations in vasospastic angina patients using an array comparative genomic hybridization.Korean circulation journalMore Details

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



    PPI interactions

    There were totally 13 unique genes interacted with HDAC10. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    HDAC3 Affinity Capture-Western11861901|11861901 CHD related
    NCOR2 Affinity Capture-Western11739383|11739383 No
    HSPA8 Affinity Capture-Western20032463|20032463 CHD related
    TRIM28 Affinity Capture-Western20032463|20032463 No
    JDP2 Affinity Capture-Western22989952 No
    ATF3 Affinity Capture-Western22989952 No
    MDC1 Protein-peptide14578343 No
    HDAC2 Affinity Capture-Western11739383 CHD related
    PAX3 Affinity Capture-Western20032463|20032463 No
    NUDT21 Affinity Capture-Western17172643 No
    PAPOLA Affinity Capture-Western17172643 No
    PPP1CC Co-purification14670976 No
    UBC Affinity Capture-MS22505724 No


    Involved FDA drugs

    There was no drug associated with HDAC10