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: FGF4

    Description: fibroblast growth factor 4

    Entrez Gene ID: 2249

    SwissProt Acc Number: P08620

    RefSeq: NM_002007

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

    .."Alferminogene tadenovec, an angiogenic FGF4 gene therapy for coronary artery disease."..

    From PMID: 18379964, in Journal IDrugs , 2008


    References

    There were 3 potential papers with FGF4 and CHD.

    PMIDTitleJournalsDetails
    22297612 "The original family revisited after 37 years: odontoma-dysphagia syndrome is most likely caused by a microduplication of chromosome 11q13.3, including the FGF3 and FGF4 genes."Clinical oral investigationsMore Details
    17058153 Intravenous injection of phagocytes transfected ex vivo with FGF4 DNA/biodegradable gelatin complex promotes angiogenesis in a rat myocardial ischemia/reperfusion injury model.Basic research in cardiologyMore Details
    15212716 Increased regional function and perfusion after intracoronary delivery of adenovirus encoding fibroblast growth factor 4: report of preclinical data.Human gene therapyMore Details

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



    PPI interactions

    There were totally 5 unique genes interacted with FGF4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NRP1 in vitro15695515 CHD related
    FGFR2 in vitro8663044 No
    FGFR3 in vitro8663044 No
    FGFR4 in vitro8663044 CHD related
    FGFR1 in vitro11486033 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00686Pentosan PolysulfateFor the relief of bladder pain or discomfort associated with interstitial cystitis.C05BA04