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: PSMD9

    Description: "proteasome (prosome, macropain) 26S subunit, non-ATPase, 9"

    Entrez Gene ID: 5715

    SwissProt Acc Number: O00233

    RefSeq: NM_002813

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

    .."In summary, the PSMD9 IVS3+nt460A/G, +nt437C/T and exon E197G A/G SNPs are linked to CAD, stroke/TIA and macrovascular pathology of T2D in Italians."..

    From PMID: 21496327, in Journal Cardiovasc Diabetol. , 2011


    References

    There were 1 potential papers with PSMD9 and CHD.

    PMIDTitleJournalsDetails
    21496327 Proteasome modulator 9 and macrovascular pathology of T2D.Cardiovascular diabetologyMore Details

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



    PPI interactions

    There were totally 17 unique genes interacted with PSMD9. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SKP2 FRET17409098 No
    CKS1B FRET17409098 No
    YY1 Reconstituted Complex22440256 No
    PSMC3 Co-fractionation19490896|19490896 No
    UBE2I Co-fractionation22939629 No
    TCF3 in vivo10567574 No
    PSMC6 Two-hybrid16189514|16189514 No
    MGMT Affinity Capture-MS16226712 No
    UBC Affinity Capture-MS21139048|21890473|21906983|22440256|22053931|22505724 No
    CDK2 Affinity Capture-Western12684681 No
    CDK4 Affinity Capture-Western12684681 CHD related
    ELAVL1 Affinity Capture-RNA19322201 No
    DCLRE1C Reconstituted Complex22134138 No
    CD2BP2 Co-fractionation22939629 No
    NUDCD2 Co-fractionation22939629 No
    CPLX1 Co-fractionation22939629 No
    DSTN Co-fractionation22939629 No


    Involved FDA drugs

    There was no drug associated with PSMD9