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: F11R

    Description: F11 receptor

    Entrez Gene ID: 50848

    SwissProt Acc Number: Q9Y624

    RefSeq: NM_016946

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

    .."Plasma F11R is independently associated with the presence and severity of angiographically defined CAD. By virtue of its strong correlation to plasma TNF-alpha, F11R may be an important mediator of the effects of inflammation on the vessel wall. Strategies that block F11R may represent a novel approach to the treatment of human atherosclerosis."..

    From PMID: 17964041, in Journal J Am Coll Cardiol. , 2007


    References

    There were 3 potential papers with F11R and CHD.

    PMIDTitleJournalsDetails
    20627246 Silencing of the F11R gene reveals a role for F11R/JAM-A in the migration of inflamed vascular smooth muscle cells and in atherosclerosis.AtherosclerosisMore Details
    17964041 Association of plasma levels of F11 receptor/junctional adhesion molecule-A (F11R/JAM-A) with human atherosclerosis.Journal of the American College of CardiologyMore Details
    17885212 "USF1 gene variants, cardiovascular risk, and mortality in European Americans: analysis of two US cohort studies.""Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 17 unique genes interacted with F11R. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TJP1 Two-hybrid10856295|10856295|10856295|10856295,11489913 No
    Pard3 Two-hybrid11447115|11447115 No
    MLLT4 Reconstituted Complex10856295|10856295|10856295 No
    PTPRB in vivo12234928 No
    ITGAL in vivo;yeast 2-hybrid11812992 No
    MPDZ in vitro;in vivo11689568 No
    F11R in vitro;in vivo14749337 CHD related
    ASIP in vitro;in vivo;yeast 2-hybrid11447115 No
    SGTA Two-hybrid16189514|16189514 No
    PARD3 Reconstituted Complex12953056 No
    UBC Affinity Capture-MS21139048|21890473|21906983 No
    ELAVL1 Affinity Capture-RNA19322201 No
    CGN in vitro;in vivo10877843 No
    CSNK2A1 in vitro7646439 CHD related
    PRKCA in vitro7646439 CHD related
    PICK1 in vivo15811349 No
    F2RL2 in vitro17057644 No


    Involved FDA drugs

    There was no drug associated with F11R