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: APPL2

    Description: "adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2"

    Entrez Gene ID: 55198

    SwissProt Acc Number: Q8NEU8

    RefSeq: NM_018171

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

    ..APPL1 or APPL2 as an adaptor for adiponectin receptors mediates the signaling pathway of adiponectin which acts as an anti-atherosclerotic adipokine...

    From PMID: 22340213, in Journal Chin Med J (Engl) , 2011


    References

    There were 0 potential papers with APPL2 and CHD.

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



    PPI interactions

    There were totally 8 unique genes interacted with APPL2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    RAB22A Two-hybrid16189514 No
    RBBP7 Reconstituted Complex15016378 No
    MTA2 Reconstituted Complex15016378|15016378 No
    APPL1 Two-hybrid16189514|16189514 CHD related
    RUVBL2 Affinity Capture-Western19433865 No
    RAB5A Reconstituted Complex15016378|15016378 No
    TINF2 Two-hybrid21044950 No
    POT1 Two-hybrid21044950 No


    Involved FDA drugs

    There was no drug associated with APPL2