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: KCNN3

    Description: "potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3"

    Entrez Gene ID: 3782

    SwissProt Acc Number: Q9UGI6

    RefSeq: NM_002249

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

    .."Atrial fibrillation (AF) is the most common cardiac rhythm disorder at the clinical setting and accounts for up to 15% of all strokes. rs13376333 in KCNN3 (encoding a potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3) that showed significant association with AF in multiple populations of European ancestry."..

    From PMID: 21107608, in Journal Hum Genet. , 2011


    References

    There were 1 potential papers with KCNN3 and CHD.

    PMIDTitleJournalsDetails
    21107608 Significant association of SNP rs2106261 in the ZFHX3 gene with atrial fibrillation in a Chinese Han GeneID population.Human geneticsMore Details

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



    PPI interactions

    There were totally 3 unique genes interacted with KCNN3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CALM1 Reconstituted Complex10026195 No
    APP Reconstituted Complex21832049 No
    UBC Affinity Capture-MS21906983 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB01110Miconazole"For topical application in the treatment of tinea pedis (athlete’s foot), tinea cruris, and tinea corporis caused by <i>Trichophyton rubrum</i>, <i>Trichophyton mentagrophytes</i>, and <i>Epidermophyton floccosum</i>, in the treatment of cutaneous candidiasis (moniliasis), and in the treatment of tinea versicolor."A01AB09;A07AC01;D01AC02;G01AF04;J02AB01;S02AA13