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: LEPR

    Description: leptin receptor

    Entrez Gene ID: 3953

    SwissProt Acc Number: P48357

    RefSeq: NM_001003679

    It was suspected to be CHD related:

    ..The LEPR Q223R TT genotype was associated with low high-density lipoprotein (HDL) cholesterol levels..

    From PMID: 21298202, in Journal Cardiovasc J Afr , 2011


    References

    There were 6 potential papers with LEPR and CHD.

    PMIDTitleJournalsDetails
    24140454 Leptin receptor Arg109 homozygotes display decreased total mortality as well as lower incidence of cardiovascular disease and related death.GeneMore Details
    21584748 "Leptin, leptin gene and leptin receptor gene polymorphism in heart failure with preserved ejection fraction."Heart and vesselsMore Details
    21300955 Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.CirculationMore Details
    19567438 Genetic Loci associated with C-reactive protein levels and risk of coronary heart disease.JAMA : the journal of the American Medical AssociationMore Details
    18854995 The 223A>G polymorphism of the leptin receptor gene and lipid-lowering efficacy of simvastatin in Chinese patients with coronary heart disease.European journal of clinical pharmacologyMore Details
    15189365 Tyrosine phosphatase 1B and leptin receptor genes and their interaction in type 2 diabetes.Journal of internal medicineMore Details

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



    PPI interactions

    There were totally 17 unique genes interacted with LEPR. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PIN1 Two-hybrid16169070|16169070 No
    JAK3 Affinity Capture-Western11585385 No
    APOD in vitro;in vivo;yeast 2-hybrid11344130 No
    PTPN11 in vivo11018044 CHD related
    STAT3 in vivo8608603 CHD related
    LEPR in vivo15771593 CHD related
    JAK2 in vitro8608603 CHD related
    LEP in vivo8608603 CHD related
    SOCS3 Reconstituted Complex11018044|11018044 CHD related
    SNX6 Affinity Capture-Western11279102|11279102 No
    SNX1 Affinity Capture-Western9819414|9819414 No
    SNX2 Affinity Capture-Western9819414|9819414 No
    SNX4 Affinity Capture-Western9819414|9819414 No
    CSNK2B Two-hybrid21900206 No
    RNF41 PCA21378310 No
    DGKZ in vitro;in vivo;yeast 2-hybrid11078732 CHD related
    CLU in vitro12824284 No


    Involved FDA drugs

    There was no drug associated with LEPR