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: HCN4

    Description: hyperpolarization activated cyclic nucleotide-gated potassium channel 4

    Entrez Gene ID: 10021

    SwissProt Acc Number: Q9Y3Q4

    RefSeq: NM_005477

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

    .."The expression of the HCN2, HCN4, as well as KCNE1, and KCNE2 genes in ventricular cells from AMI rat hearts underwent dynamic changes, reaching peak levels at 1 or 2weeks post-AMI. The increased expression maybe related to ventricular arrhythmogenesis after AMI."..

    From PMID: 20381460, in Journal Biochem Biophys Res Commun. , 2010


    References

    There were 3 potential papers with HCN4 and CHD.

    PMIDTitleJournalsDetails
    20381460 "Dynamic changes in HCN2, HCN4, KCNE1, and KCNE2 expression in ventricular cells from acute myocardial infarction rat hearts."Biochemical and biophysical research communicationsMore Details
    20933199 I(f) inhibition in cardiovascular diseases."Advances in pharmacology (San Diego, Calif.)"More Details
    17261653 Direct inhibition of cardiac hyperpolarization-activated cyclic nucleotide-gated pacemaker channels by clonidine.CirculationMore Details

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



    PPI interactions

    There were totally 3 unique genes interacted with HCN4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    HCN3 Affinity Capture-Western12928435 No
    HCN2 Affinity Capture-Western12928435|12928435 CHD related
    HCN1 Affinity Capture-Western12928435 No


    Involved FDA drugs

    There was no drug associated with HCN4