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: OSM

    Description: oncostatin M

    Entrez Gene ID: 5008

    SwissProt Acc Number: P13725

    RefSeq: NM_020530

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

    .."The pleiotropic cytokine oncostatin M (OSM), a member of the glycoprotein (gp)130 ligand family, plays a key role in inflammation and cardiovascular disease. "..

    From PMID: 21174212, in Journal Basic Res Cardiol. , 2011


    References

    There were 2 potential papers with OSM and CHD.

    PMIDTitleJournalsDetails
    21174212 "Oncostatin M-enhanced vascular endothelial growth factor expression in human vascular smooth muscle cells involves PI3K-, p38 MAPK-, Erk1/2- and STAT1/STAT3-dependent pathways and is attenuated by interferon-gamma."Basic research in cardiologyMore Details
    17604327 The inflammatory cytokine oncostatin M induces PAI-1 in human vascular smooth muscle cells in vitro via PI 3-kinase and ERK1/2-dependent pathways.American journal of physiology. Heart and circulatory physiologyMore Details

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



    PPI interactions

    There were totally 11 unique genes interacted with OSM. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APP Reconstituted Complex21832049 No
    COL4A3 in vitro11711546 No
    COL4A2 in vitro11711546 No
    COL4A1 in vitro11711546 CHD related
    COL4A4 in vitro11711546 No
    LIFR Affinity Capture-Western1536831 No
    TNNT1 Two-hybrid21900206 No
    COL4A5 in vitro11711546 No
    COL4A6 in vitro11711546 No
    IL6ST in vitro8999038,16051226 CHD related
    OSMR in vitro;in vivo10997905,8999038 No


    Involved FDA drugs

    There was no drug associated with OSM