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: LRP8

    Description: "low density lipoprotein receptor-related protein 8, apolipoprotein e receptor"

    Entrez Gene ID: 7804

    SwissProt Acc Number: Q14114

    RefSeq: NM_001018054

    It was suspected to be CHD related:

    .."This extensive study, involving multiple independent populations, provides the first evidence that genetic variants in LRP8 may contribute to the development of premature and familial CAD and MI."..

    From PMID: 17847002, in Journal Am J Hum Genet.? , 2007


    References

    There were 4 potential papers with LRP8 and CHD.

    PMIDTitleJournalsDetails
    23524007 Multi-allelic haplotype association identifies novel information different from single-SNP analysis: a new protective haplotype in the LRP8 gene is against familial and early-onset CAD and MI.GeneMore Details
    22404453 Genetic variant R952Q in LRP8 is associated with increased plasma triglyceride levels in patients with early-onset CAD and MI.Annals of human geneticsMore Details
    18592168 Lack of association of genetic variants in the LRP8 gene with familial and sporadic myocardial infarction."Journal of molecular medicine (Berlin, Germany)"More Details
    17847002 An LRP8 variant is associated with familial and premature coronary artery disease and myocardial infarction.American journal of human geneticsMore Details

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



    PPI interactions

    There were totally 20 unique genes interacted with LRP8. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GIPC1 Two-hybrid10827173 No
    MAPK8IP1 Two-hybrid10827173 No
    DLG4 Two-hybrid10827173|16332682 No
    MAPK8IP2 Two-hybrid10827173 No
    SYNJ2BP Two-hybrid10827173 No
    NOS1AP Two-hybrid10827173 CHD related
    SCN3A Two-hybrid10827173 No
    APBA2 Two-hybrid10827173 No
    DAB1 Two-hybrid10827173 No
    ITGB1BP1 Two-hybrid10827173 No
    ANAPC10 Two-hybrid10827173 No
    CLU in vitro;in vivo12824284 No
    GRIN1 in vivo16332682 No
    APOE Reconstituted Complex12950167 CHD related
    LRPAP1 Reconstituted Complex12899622 CHD related
    RELN Reconstituted Complex12899622|12670700 No
    APOH Affinity Capture-Western12807892 CHD related
    SNX17 Affinity Capture-Western12169628|12169628 No
    UBC Affinity Capture-MS21906983 No
    MYLIP Protein-peptide22109552 No


    Involved FDA drugs

    There was no drug associated with LRP8