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: PSMA6

    Description: "proteasome (prosome, macropain) subunit, alpha type, 6"

    Entrez Gene ID: 5687

    SwissProt Acc Number: P60900

    RefSeq: NM_002791

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

    .."we have identified additional MI susceptible genes, LGALS2, PSMA6 and BRAP, so far."..

    From PMID: 20387550, in Journal Nihon Rinsho. , 2010


    References

    There were 6 potential papers with PSMA6 and CHD.

    PMIDTitleJournalsDetails
    22882272 Genetic variants associated with myocardial infarction in the PSMA6 gene and Chr9p21 are also associated with ischaemic stroke.European journal of neurology : the official journal of the European FederationMore Details
    23111455 Quantitative assessment of the influence of PSMA6 variant (rs1048990) on coronary artery disease risk.Molecular biology reportsMore Details
    22310064 "Polymorphisms of LTA, LGALS2, and PSMA6 genes and coronary atherosclerosis: a pathological study of 1503 consecutive autopsy cases."AtherosclerosisMore Details
    19624571 Haplotypes encompassing the KIAA0391 and PSMA6 gene cluster confer a genetic link for myocardial infarction and coronary artery disease.Annals of human geneticsMore Details
    18157711 Association between inflammatory gene polymorphisms and coronary artery disease in an Indian population.Journal of thrombosis and thrombolysisMore Details
    19282875 Replication studies for the association of PSMA6 polymorphism with coronary artery disease in East Asian populations.Journal of human geneticsMore Details

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



    PPI interactions

    There were totally 83 unique genes interacted with PSMA6. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PSMA3 Two-hybrid16169070|9451443 No
    CUL1 Affinity Capture-Western16759355|16759355 No
    RBX1 Affinity Capture-Western16759355 No
    PSMD4 Co-fractionation19781552|22939629 No
    PSMD14 Co-fractionation19781552|22939629 No
    ADRM1 Co-fractionation19781552 No
    PSMD1 Co-fractionation19781552|22939629 No
    TXNL1 Co-fractionation19781552 No
    PSME1 Affinity Capture-Western12419264|22939629 No
    tat Affinity Capture-Western12419264 No
    PSMA7 Two-hybrid15225636|15225636|14733938|17948026|22939629|15225636,14733938 No
    CCND1 Affinity Capture-Western22158041 CHD related
    CCNE1 Affinity Capture-Western22158041 CHD related
    CCNA2 Affinity Capture-Western22158041 CHD related
    CCNB1 Affinity Capture-Western22158041 No
    CDK4 Affinity Capture-Western22158041 CHD related
    CDK1 Affinity Capture-Western22158041 CHD related
    CDK2 Affinity Capture-Western22158041 No
    CCNF Affinity Capture-Western22158041 No
    GPS1 Affinity Capture-Western16045761 No
    COPS5 Affinity Capture-Western16045761 No
    PSMD6 Affinity Capture-Western16045761|22939629 No
    PSMC1 Affinity Capture-Western16045761 No
    PSMB5 Two-hybrid17948026|22939629 No
    PSMB8 Two-hybrid17948026|22939629 No
    PSMB1 Co-fractionation22939629 No
    PSMB2 Co-fractionation22939629 No
    PSMB3 Co-fractionation22939629 No
    PSMB4 Co-fractionation22939629 No
    PSMB7 Co-fractionation22939629 No
    PSMD2 Co-fractionation22939629 No
    PSMD3 Co-fractionation22939629 No
    PSMD8 Co-fractionation22939629 No
    PSMD12 Co-fractionation22939629 No
    PSMD11 Co-fractionation22939629 No
    PSMD7 Co-fractionation22939629 No
    PSMD5 Co-fractionation22939629 No
    PSME2 Co-fractionation22939629 No
    PSME3 Co-fractionation22939629 No
    PSMA8 Co-fractionation22939629 No
    SF3A1 Co-fractionation22939629 No
    CCT5 Co-fractionation22939629 No
    SNRPA1 Co-fractionation22939629 No
    TPM4 Co-fractionation22939629 No
    CCT4 Co-fractionation22939629 No
    CCT3 Co-fractionation22939629 No
    CCT8 Co-fractionation22939629 No
    TARDBP Co-fractionation22939629 No
    PSMD13 Affinity Capture-MS17353931 No
    PLK1 Affinity Capture-MS11205743|11205743 No
    UBQLN2 Affinity Capture-Western10983987 No
    USP14 Affinity Capture-MS19615732 No
    USP53 Affinity Capture-MS19615732 No
    SLX1B Affinity Capture-MS19596235 No
    PSMA4 Affinity Capture-Western16759355|15225636|9311996|22939629|15225636 No
    PSMA2 Affinity Capture-Western16759355|12376572|19193609|22939629 No
    RNF185 Affinity Capture-MS17558393 No
    UBC Affinity Capture-MS16196087|18781797|21987572|21963094|12938929|21139048|21890473|21906983|22053931|21853274|22505724 No
    XBP1 Affinity Capture-Western19941857 No
    UBD Affinity Capture-Western22072791|16707496 No
    KIAA0101 Affinity Capture-MS21628590 No
    RAD23A Affinity Capture-MS19013454 No
    SHFM1 Affinity Capture-MS18775730 No
    PSMA1 Two-hybrid14733938|22939629 No
    PPP3CA Two-hybrid21420386|21420386 CHD related
    FKBP8 Affinity Capture-MS17573772 No
    NEDD8 Affinity Capture-MS16503656 No
    PSMG1 Co-fractionation17189198 No
    PSMG3 Co-fractionation17189198 No
    POMP Co-fractionation17189198|17948026 No
    DNAJB2 Affinity Capture-Western15936278 No
    KIAA0368 Co-localization20682791 No
    COPS2 Affinity Capture-MS19535905|19535905 No
    UCHL5 Affinity Capture-MS18922472 No
    PSMB6 Two-hybrid17948026 No
    USP4 Two-hybrid23022198 No
    PSMA5 Co-fractionation22939629 No
    PSMC6 Co-fractionation22939629 No
    PSMC3 Co-fractionation22939629 No
    PSMC4 Co-fractionation22939629 No
    PSMC2 Co-fractionation22939629 No
    PSMC5 Co-fractionation22939629 No
    EEF1A1 Co-fractionation22939629 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB07475N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
    experimentalDB08515"(3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE"