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: LTBP1

    Description: latent transforming growth factor beta binding protein 1

    Entrez Gene ID: 4052

    SwissProt Acc Number: Q14766

    RefSeq: NM_000627

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

    ..The proportion of LTBP1Δ41 ranged from 2% of total LTBP1 mRNA in early coronary atherosclerotic lesions to 54% in advanced lesions...

    From PMID: 21161366, in Journal Biochem Genet. , 2011


    References

    There were 1 potential papers with LTBP1 and CHD.

    PMIDTitleJournalsDetails
    21161366 Expression of mRNA isoforms of latent transforming growth factor-beta binding protein-1 in coronary atherosclerosis and human tissues.Biochemical geneticsMore Details

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



    PPI interactions

    There were totally 10 unique genes interacted with LTBP1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TGFB1 Affinity Capture-Western10930463|10930463 CHD related
    LTBP1 in vitro;in vivo8617200,10930463 CHD related
    FBN1 in vitro;in vivo12429738 CHD related
    FBN2 in vitro;in vivo12429738 No
    FN1 in vitro8756760 CHD related
    IGFBP3 yeast 2-hybrid12962157 CHD related
    ITGB5 in vitro;in vivo12358597 No
    CACNA1A Two-hybrid21078624 No
    ATN1 Two-hybrid16713569|16713569 No
    TGM2 in vitro9060478 CHD related


    Involved FDA drugs

    There was no drug associated with LTBP1