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: CUBN

    Description: cubilin (intrinsic factor-cobalamin receptor)

    Entrez Gene ID: 8029

    SwissProt Acc Number: O60494

    RefSeq: NM_001081

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

    .."After adjustment for multiple testing within each gene, single-nucleotide polymorphisms (SNP) significantly associated with case status were identified in the genes encoding LIPC (rs4775065, P<0.0001); CETP (rs5882, P=0.0002); RXRA (rs11185660, P=0.0021); ABCA1 (rs2249891, P=0.0126); ABCC6 (rs150468, P=0.0206; rs212077, P=0.0443); CUBN (rs7893395, P=0.0246); APOA2 (rs3813627, P=0.0324); SELP (rs732314, P=0.0376); and APOC4 (rs10413089, P=0.0425). "..

    From PMID: 20855565, in Journal J Lipid Res , 2010


    References

    There were 2 potential papers with CUBN and CHD.

    PMIDTitleJournalsDetails
    23824729 Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.The American journal of clinical nutritionMore Details
    20855565 Common genetic variation in multiple metabolic pathways influences susceptibility to low HDL-cholesterol and coronary heart disease.Journal of lipid researchMore Details

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



    PPI interactions

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

    Gene nameInteraction typereference PMIDCHD relation
    GIF Reconstituted Complex9572993|9572993 No
    CUBN Reconstituted Complex20237569 CHD related
    LRP2 in vitro;in vivo11994745,11595644 No
    TF in vitro11606717 No
    ALB in vivo10811843 CHD related
    LGALS3 in vitro11856751 No
    GC Affinity Capture-Western11717447 No
    SCGB1A1 Reconstituted Complex11278724 No
    RRP1B Affinity Capture-MS19710015 No
    CBL Protein-peptide15736970 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00200Hydroxocobalamin"For treatment of pernicious anemia and the prevention and treatment of vitamin B12 deficiency arising from alcoholism, malabsorption, tapeworm infestation, celiac, hyperthyroidism, hepatic-biliary tract disease, persistent diarrhea, ileal resection, pancreatic cancer, renal disease, prolonged stress, vegan diets, macrobiotic diets or other restrictive diets. Also for the treatment of known or suspected cyanide poisoning."B03BA03;V03AB33