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.

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  • 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.

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  • 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: HFE

    Description: hemochromatosis

    Entrez Gene ID: 3077

    SwissProt Acc Number: Q30201

    RefSeq: NM_000410

    It was suspected to be CHD related:

    ..The SNP rs9366637 in HFE gene was associated with higher CHD risk in Chinese Han population...

    From PMID: 21696736, in Journal Atherosclerosis. , 2011


    References

    There were 11 potential papers with HFE and CHD.

    PMIDTitleJournalsDetails
    23792061 Meta-analyses of HFE variants in coronary heart disease.GeneMore Details
    23303523 Loci influencing blood pressure identified using a cardiovascular gene-centric array.Human molecular geneticsMore Details
    22552896 Pathology supported genetic testing and treatment of cardiovascular disease in middle age for prevention of Alzheimer's disease.Metabolic brain diseaseMore Details
    21696736 "Plasma ferritin levels, genetic variations in HFE gene, and coronary heart disease in Chinese: a case-control study."AtherosclerosisMore Details
    20640879 HFE gene mutations increase the risk of coronary heart disease in women.European journal of epidemiologyMore Details
    20031565 HFE C282Y homozygosity is associated with lower total and low-density lipoprotein cholesterol: The hemochromatosis and iron overload screening study.Circulation. Cardiovascular geneticsMore Details
    18810584 HFE mutations in heart disease.Heart and vesselsMore Details
    20031541 Mutations in the HFE gene and cardiovascular disease risk: an individual patient data meta-analysis of 53 880 subjects.Circulation. Cardiovascular geneticsMore Details
    18593631 HFE C282Y homozygotes have reduced low-density lipoprotein cholesterol: the Atherosclerosis Risk in Communities (ARIC) Study.Translational research : the journal of laboratory and clinical medicineMore Details
    16968463 HFE mutations and risk of coronary heart disease in middle-aged women.European journal of clinical investigationMore Details
    10854101 Haemochromatosis gene mutations and risk of coronary artery disease.European journal of human genetics : EJHGMore Details

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



    PPI interactions

    There were totally 5 unique genes interacted with HFE. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TFRC Affinity Capture-Western9465039|9465039 No
    TFR2 Co-crystal Structure10638746 No
    UBC Affinity Capture-Western21245296 No
    SYVN1 Affinity Capture-Western21245296 No
    B2M Affinity Capture-Western20618438 CHD related


    Involved FDA drugs

    There was no drug associated with HFE