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: FTO

    Description: fat mass and obesity associated

    Entrez Gene ID: 79068

    SwissProt Acc Number: Q9C0B1

    RefSeq: NM_001080432

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

    .."Single nucleotide polymorphisms (SNPs) in several genes including ApoE, MTHFR, HFE and FTO are known to increase the risk of both conditions."..

    From PMID: 22552896, in Journal Metab Brain Dis. , 2012


    There were 6 potential papers with FTO and CHD.

    22552896 Pathology supported genetic testing and treatment of cardiovascular disease in middle age for prevention of Alzheimer's disease.Metabolic brain diseaseMore Details
    23104008 Bayesian refinement of association signals for 14 loci in 3 common diseases.Nature geneticsMore Details
    21491999 Correlates of the FTO gene variant (rs9939609) and growth of American Indian infants.Genetic testing and molecular biomarkersMore Details
    21706003 Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.Nature geneticsMore Details
    20362563 A FTO variant and risk of acute coronary syndrome.Clinica chimica acta; international journal of clinical chemistryMore Details
    19955787 Gene-environment interactions in obesity.Forum of nutritionMore Details

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

    PPI interactions

    There were totally 1 unique genes interacted with FTO. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-MS21890473|21906983 No

    Involved FDA drugs

    There was no drug associated with FTO