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: APPL1

    Description: "adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1"

    Entrez Gene ID: 26060

    SwissProt Acc Number: Q9UKG1

    RefSeq: NM_012096

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

    ..Genetic variation(s) in APPL1/2 may be associated with CAD risk in T2DM in Chinese population...

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


    References

    There were 0 potential papers with APPL1 and CHD.

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



    PPI interactions

    There were totally 18 unique genes interacted with APPL1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APPL2 Two-hybrid16189514|16189514 CHD related
    MTA2 Affinity Capture-Western19686092|15016378|15016378 No
    HDAC1 Affinity Capture-Western19686092|19686092 CHD related
    HDAC2 Affinity Capture-Western19686092|19686092|19686092 CHD related
    RBBP4 Affinity Capture-Western19686092 No
    RBBP7 Affinity Capture-Western19686092|15016378 No
    ADIPOR1 Two-hybrid16622416|16622416|16622416|16622416 CHD related
    PIK3CA in vitro;in vivo;yeast 2-hybrid10490823 CHD related
    AKT2 Two-hybrid10490823|10490823 CHD related
    TRAF2 Two-hybrid16189514|16189514 No
    DCC Two-hybrid12011067 No
    RUVBL2 Affinity Capture-Western19433865 No
    RAB5A Affinity Capture-MS15016378|15016378|15016378 No
    UBC Affinity Capture-MS20639865|21139048|21890473|21906983|22053931|22505724 No
    ELAVL1 Affinity Capture-RNA19322201 No
    FSHR Two-hybrid15196694|15070827|15070827 No
    ADIPOR2 Affinity Capture-Western16622416 CHD related
    AKT1 in vitro;in vivo12621049 CHD related


    Involved FDA drugs

    There was no drug associated with APPL1