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: LBP

    Description: lipopolysaccharide binding protein

    Entrez Gene ID: 3929

    SwissProt Acc Number: P18428

    RefSeq: NM_004139

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

    ..Lipopolysaccharide-binding protein (LBP) is associated with total and cardiovascular mortality in individuals with or without stable?coronary?artery disease--results from the Ludwigshafen Risk and Cardiovascular Health Study (LURIC)...

    From PMID: 21722903, in Journal Atherosclerosis. , 2011


    References

    There were 5 potential papers with LBP and CHD.

    PMIDTitleJournalsDetails
    24075748 Serum lipopolysaccharide-binding protein as a marker of atherosclerosis.AtherosclerosisMore Details
    22009184 Increased systemic elastase and C-reactive protein in aggressive periodontitis (CLOI-D-00160R2).Clinical oral investigationsMore Details
    21722903 Lipopolysaccharide-binding protein (LBP) is associated with total and cardiovascular mortality in individuals with or without stable coronary artery disease--results from the Ludwigshafen Risk and Cardiovascular Health Study (LURIC).AtherosclerosisMore Details
    17601541 Association of lipopolysaccharide-binding protein and coronary artery disease in men.Journal of the American College of CardiologyMore Details
    15186959 Effects of heparin-mediated extracorporeal low-density lipoprotein precipitation beyond lowering proatherogenic lipoproteins--reduction of circulating proinflammatory and procoagulatory markers.AtherosclerosisMore Details

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



    PPI interactions

    There were totally 6 unique genes interacted with LBP. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    IRF6 Reconstituted Complex11544322 No
    CFHR1 Affinity Capture-Western8663389|8663389 No
    APOA1 Affinity Capture-Western8663389 CHD related
    RPS21 in vitro;yeast 2-hybrid10079194 No
    CAMP in vitro11544322 No
    CD14 Reconstituted Complex12417309|7583357 CHD related


    Involved FDA drugs

    There was no drug associated with LBP