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: MAP4K4

    Description: mitogen-activated protein kinase kinase kinase kinase 4

    Entrez Gene ID: 9448

    SwissProt Acc Number: O95819

    RefSeq: NM_004834

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

    .."Adjusting for these variables,two SNPs, one on chromosome 2 for MAP4K4 gene (rs2236935, = 0.037, p-value = 2.36x10(-06)), and one on chromosome 5 for IL5 gene (rs739318, = 0.051, p-value = 5.02x10(-05)) associated positively with CIMT;"..

    From PMID: 23188791, in Journal Physiol Genomics. , 2013


    References

    There were 1 potential papers with MAP4K4 and CHD.

    PMIDTitleJournalsDetails
    23188791 Genetic polymorphisms associated with carotid artery intima-media thickness and coronary artery calcification in women of the Kronos Early Estrogen Prevention Study.Physiological genomicsMore Details

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



    PPI interactions

    There were totally 20 unique genes interacted with MAP4K4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    RASA1 Affinity Capture-Western10669731|10669731 No
    MAP3K1 Affinity Capture-Western9135144 No
    GBP3 Reconstituted Complex12387898|12387898 No
    KIF5A Two-hybrid20936779 No
    PRKCE Two-hybrid20936779 CHD related
    SLC9A1 Two-hybrid20936779|11369779 CHD related
    HIST2H2BE Two-hybrid20936779 No
    KIF26B Two-hybrid20936779 No
    CASP8 in vivo11002417 CHD related
    DOK1 in vivo10669731 No
    RAP2A yeast 2-hybrid14966141 No
    BRCA1 Protein-peptide14578343 CHD related
    ITGB1 Two-hybrid11967148|11967148|11967148 CHD related
    NCK1 Reconstituted Complex9135144 No
    MAP3K7 Affinity Capture-Western10807933 No
    ZRANB1 Affinity Capture-MS19615732 No
    UBC Affinity Capture-MS21139048|21890473|21906983|22505724 No
    PPP1CA Two-hybrid22321011 No
    TRAPPC9 Affinity Capture-Western15951441 No
    GRK5 Affinity Capture-MS22952844 CHD related


    Involved FDA drugs

    There was no drug associated with MAP4K4