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: GALNT2

    Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)

    Entrez Gene ID: 2590

    SwissProt Acc Number: Q10471

    RefSeq: NM_004481

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

    .."In addition, using recessive models of inheritance, polymorphisms on chromosome 19 adjacent to the CILP2 and PBX4 loci (rs16996148) and on chromosome 1 at the GALNT2 locus (rs4846914) were associated with elevated HDL-C (P = 0.005) and lower LDL-C (P = 0.048), respectively."..

    From PMID: 18987386, in Journal J Lipid Res. , 2009


    References

    There were 5 potential papers with GALNT2 and CHD.

    PMIDTitleJournalsDetails
    23382687 Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network.PLoS geneticsMore Details
    22952570 "Segregation of LIPG, CETP, and GALNT2 mutations in Caucasian families with extremely high HDL cholesterol."PloS oneMore Details
    18987386 Polymorphisms at newly identified lipid-associated loci are associated with blood lipids and cardiovascular disease in an Asian Malay population.Journal of lipid researchMore Details
    18193044 "Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans."Nature geneticsMore Details
    18193043 Newly identified loci that influence lipid concentrations and risk of coronary artery disease.Nature geneticsMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with GALNT2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    RPS15A Co-fractionation22939629 No
    MRPS5 Co-fractionation22939629 No
    PRPF40A Co-fractionation22939629 No
    MUC1 in vitro;in vivo12754287,9295285,12925576,9312074 No
    UBC Affinity Capture-MS21139048|21906983 No
    NOD2 Two-hybrid21699783|21699783 CHD related
    FAM3C Co-fractionation22939629 No
    SLC25A4 Co-fractionation22939629 No
    ZMPSTE24 Co-fractionation22939629 No


    Involved FDA drugs

    There was no drug associated with GALNT2