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: KCNJ2

    Description: "potassium inwardly-rectifying channel, subfamily J, member 2"

    Entrez Gene ID: 3759

    SwissProt Acc Number: P63252

    RefSeq: NM_000891

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

    ..The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2...

    From PMID: 17401374, in Journal Nat Med. , 2007


    References

    There were 1 potential papers with KCNJ2 and CHD.

    PMIDTitleJournalsDetails
    17401374 The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2.Nature medicineMore Details

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



    PPI interactions

    There were totally 14 unique genes interacted with KCNJ2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CASK in vitro15024025 No
    KCNJ4 in vitro;in vivo12032359 No
    DLG2 in vitro;yeast 2-hybrid15304517 No
    FLNA in vitro;yeast 2-hybrid12923176 No
    DLG3 in vitro16637659 No
    INADL in vitro16637659 No
    DLG4 Two-hybrid10627592|10627592|10627592 No
    TRAK2 Affinity Capture-Western16895905|16895905|16895905 No
    DLG1 Reconstituted Complex11181181|11181181 No
    IL16 Two-hybrid10479680|10479680|10479680 No
    KCNJ8 in vitro;in vivo10559219 CHD related
    AKAP5 in vitro;in vivo11287423 No
    KCNJ11 in vitro10559219 No
    KCNJ16 in vitro11240146 No


    Involved FDA drugs

    There was no drug associated with KCNJ2