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: LIF

    Description: leukemia inhibitory factor (cholinergic differentiation factor)

    Entrez Gene ID: 3976

    SwissProt Acc Number: P15018

    RefSeq: NM_002309

    It was suspected to be CHD related:

    .."Leukemia inhibitory factor (LIF), an IL-6 class cytokine, is reported to be antiatherosclerotic."..

    From PMID: 18480664, in Journal Coron Artery Dis , 2008


    References

    There were 4 potential papers with LIF and CHD.

    PMIDTitleJournalsDetails
    23231902 Intrinsic versus laser-induced fluorescence spectroscopy for coronary atherosclerosis: a generational comparison model for testing diagnostic accuracy.Applied spectroscopyMore Details
    18480664 Leukemia inhibitory factor is upregulated in coronary arteries of Ossabaw miniature swine after stent placement.Coronary artery diseaseMore 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
    16263353 Estimation of radiation dose received during treatment of in-stent restenosis using ionizing radiation.Cardiovascular revascularization medicine : including molecular interventionsMore Details

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



    PPI interactions

    There were totally 2 unique genes interacted with LIF. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    IL6ST in vivo12707269 CHD related
    LIFR Reconstituted Complex12601009 No


    Involved FDA drugs

    There was no drug associated with LIF