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: PDZK1

    Description: PDZ domain containing 1

    Entrez Gene ID: 5174

    SwissProt Acc Number: Q5T2W1

    RefSeq: NM_002614

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

    ..Loss of PDZK1 Causes Coronary Artery Occlusion and Myocardial Infarction in Paigen Diet-Fed Apolipoprotein E Deficient Mice..

    From PMID: 19956623, in Journal PLoS One. , 2009


    References

    There were 4 potential papers with PDZK1 and CHD.

    PMIDTitleJournalsDetails
    20884846 Multiple genetic loci influence serum urate levels and their relationship with gout and cardiovascular disease risk factors.Circulation. Cardiovascular geneticsMore Details
    19956623 Loss of PDZK1 causes coronary artery occlusion and myocardial infarction in Paigen diet-fed apolipoprotein E deficient mice.PloS oneMore Details
    19890391 "Common polymorphisms influencing serum uric acid levels contribute to susceptibility to gout, but not to coronary artery disease."PloS oneMore Details
    18342019 Influence of PDZK1 on lipoprotein metabolism and atherosclerosis.Biochimica et biophysica actaMore Details

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



    PPI interactions

    There were totally 29 unique genes interacted with PDZK1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SLC9A3 Two-hybrid14531806|14531806 No
    SLC17A1 Two-hybrid14531806|14531806 No
    ABCC2 Two-hybrid10496535|10496535,12615054 No
    SLC22A4 Two-hybrid14531806|14531806 No
    AKAP10 Two-hybrid14531806|14531806 No
    SLC22A12 Two-hybrid14531806|14531806 No
    PEX5 Two-hybrid16189514 No
    UBE2I Two-hybrid14531806 No
    SLC9A3R2 Two-hybrid14531806 No
    FARP2 Two-hybrid14531806|14531806 No
    SLK Two-hybrid14531806|14531806 No
    SLC9A3R1 Two-hybrid14531806|14531806 No
    SLC34A3 Reconstituted Complex14531806|14531806 No
    SCARB1 Affinity Capture-Western12119305|10829064,14551195,12119305 CHD related
    CLCN3 Reconstituted Complex12471024|12471024|12471024 No
    CFTR Reconstituted Complex12471024|12471024|11051556|11051556,12471024,12615054,15553237 CHD related
    Klhl17 Two-hybrid12063253 No
    Syngap1 Two-hybrid12063253 No
    Dlg4 Two-hybrid12063253 No
    APP Reconstituted Complex21832049 No
    SLC26A6 in vitro;yeast 2-hybrid14531806 No
    SSTR5 in vitro;in vivo;yeast 2-hybrid16012170 No
    SLC22A5 in vitro;yeast 2-hybrid15523054,15553237 No
    SLC15A2 in vitro;in vivo;yeast 2-hybrid15553237 No
    SLCO1A2 yeast 2-hybrid15553237 No
    PDZK1IP1 Two-hybrid14531806|12837682|9461128,14531806,12837682,12754212 No
    GFAP Two-hybrid16189514|16189514 CHD related
    SLC22A11 in vitro;in vivo;yeast 2-hybrid16236806,15553237 No
    ABCA1 in vitro16192282 CHD related


    Involved FDA drugs

    There was no drug associated with PDZK1