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: AAMP

    Description: "angio-associated, migratory cell protein"

    Entrez Gene ID: 14

    SwissProt Acc Number: Q13685

    RefSeq: NM_001087

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

    .."These data reveal an important functional role of AAMP in the migration of SMCs, identifying AAMP as a potential target to limit lesion formation after injury."..

    From PMID: 18634987, in Journal J Am Coll Cardiol. , 2008


    References

    There were 1 potential papers with AAMP and CHD.

    PMIDTitleJournalsDetails
    18634987 Blockade of angio-associated migratory cell protein inhibits smooth muscle cell migration and neointima formation in accelerated atherosclerosis.Journal of the American College of CardiologyMore Details

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



    PPI interactions

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

    Gene nameInteraction typereference PMIDCHD relation
    TH1L yeast 2-hybrid16169070 No
    GABARAPL2 Two-hybrid21900206 No
    TK1 Two-hybrid21900206 No
    MAP1LC3B Two-hybrid21900206 No
    C8orf33 Two-hybrid21900206 No
    UBC Affinity Capture-MS21139048|21890473|21906983|22505724 No
    UBD Affinity Capture-MS22797925 No
    PSEN2 Two-hybrid21163940 No


    Involved FDA drugs

    There was no drug associated with AAMP