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: NOX5

    Description: "NADPH oxidase, EF-hand calcium binding domain 5"

    Entrez Gene ID: 79400

    SwissProt Acc Number: Q96PH1

    RefSeq: NM_024505

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

    .."The expression level of?Nox5?is altered in cardiovascular disease. In particular,?coronary artery disease?is associated with increased expression of?Nox5"..

    From PMID: 19331545, in Journal Antioxid Redox Signal. , 2009


    References

    There were 2 potential papers with NOX5 and CHD.

    PMIDTitleJournalsDetails
    22503554 NOX5 expression is increased in intramyocardial blood vessels and cardiomyocytes after acute myocardial infarction in humans.The American journal of pathologyMore Details
    19022160 Calcium-dependent NOX5 nicotinamide adenine dinucleotide phosphate oxidase contributes to vascular oxidative stress in human coronary artery disease.Journal of the American College of CardiologyMore Details

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



    PPI interactions

    There were totally 4 unique genes interacted with NOX5. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    HSPA4 Affinity Capture-Western23023377 No
    HSP90AA1 Affinity Capture-Western23023377 CHD related
    SUMO1 Affinity Capture-Western21527745 No
    UBC Affinity Capture-Western23023377 No


    Involved FDA drugs

    There was no drug associated with NOX5