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: PLD2

    Description: phospholipase D2

    Entrez Gene ID: 5338

    SwissProt Acc Number: O14939

    RefSeq: NM_002663

    It was suspected to be CHD related:

    ..The results suggest that heart failure is associated with increased activities of both PLD2 and PAP2 in the SL membrane and the beneficial effect of imidapril on heart function may be due to its ability to prevent these changes in the phospholipid signaling molecules in the cardiac SL membrane...

    From PMID: 12213494, in Journal Biochim Biophys Acta. , 2002


    References

    There were 1 potential papers with PLD2 and CHD.

    PMIDTitleJournalsDetails
    22359512 Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.PLoS geneticsMore Details

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



    PPI interactions

    There were totally 30 unique genes interacted with PLD2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    AQP3 Affinity Capture-Western14675200 No
    GAPDH Affinity Capture-Western12753082|12753082|12753082 No
    PLCG1 Affinity Capture-Western12646582|12646582 CHD related
    ARF1 Reconstituted Complex11373276|10801846|12519790,10801846 No
    Actb Reconstituted Complex11373276 No
    PRKCA Affinity Capture-Western11042115|11042115 CHD related
    AMPH Phenotypic Suppression10764771|10764771|10764771 No
    BIN1 Phenotypic Suppression10764771|10764771 No
    PEA15 Affinity Capture-Western10926929 No
    CAV2 Co-fractionation10675563 No
    ALDOA Reconstituted Complex11876650|11876650|11876650 No
    PRKCD Affinity Capture-Western11744693|11744693|11744693 CHD related
    GM2A in vitro11672434 No
    ALDOC in vitro11876650 No
    ACTN1 in vitro;in vivo10801846 No
    STXBP1 in vitro;in vivo14744865 No
    CSK in vitro;in vivo12697812 No
    FYN in vivo12697812 No
    LCK in vivo12697812 No
    CAV1 Affinity Capture-Western14675200 CHD related
    SRC Biochemical Activity12697812|12697812 CHD related
    MTOR Affinity Capture-Western16837165|16837165 CHD related
    RPTOR Affinity Capture-Western16837165 No
    EGFR Affinity Capture-Western9837959|9837959 CHD related
    OPRM1 Affinity Capture-Western12519790 No
    UBC Affinity Capture-MS21987572|21139048|21906983 No
    CUL3 Affinity Capture-MS21145461 No
    RPS6KB1 Affinity Capture-Western16837165 CHD related
    DPYSL2 in vitro;in vivo11741937 No
    PIP5K1A in vitro;in vivo11032811 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00122Choline"For nutritional supplementation, also for treating dietary shortage or imbalance"N02BA03;N07AX02;R03DA02;V03AB29;S01EB09