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: SDHA

    Description: "succinate dehydrogenase complex, subunit A, flavoprotein (Fp)"

    Entrez Gene ID: 6389

    SwissProt Acc Number: P31040

    RefSeq: NM_004168

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

    .."Vasospastic angina (VA) is a specific type of coronary artery disease and develops as a result of coronary artery spasm. The fold change levels were highest in the CTDP1 (18q23), HDAC10 (22q13.33), KCNQ1(11p15.5-p15.4), NINJ2 (12p13.33), NOTCH2 (1p12-p11.2), PCSK6 (15q26.3), SDHA (5p15.33), and MUC17 (7q22.1) genes."..

    From PMID: 21860640, in Journal Korean Circ J. , 2011


    References

    There were 1 potential papers with SDHA and CHD.

    PMIDTitleJournalsDetails
    21860640 Deoxyribonucleic Acid copy number aberrations in vasospastic angina patients using an array comparative genomic hybridization.Korean circulation journalMore Details

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



    PPI interactions

    There were totally 59 unique genes interacted with SDHA. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SDHB Co-fractionation22939629 No
    SUCLA2 Co-fractionation22939629 No
    SUCLG1 Co-fractionation22939629 No
    SUCLG2 Co-fractionation22939629 No
    UQCRFS1 Co-fractionation22939629 No
    UQCRB Co-fractionation22939629 No
    SYNE2 Co-fractionation22939629 No
    MTERFD1 Co-fractionation22939629 No
    RAVER1 Co-fractionation22939629 No
    TIMM50 Co-fractionation22939629 No
    LRRC8A Co-fractionation22939629 No
    MDH1 Co-fractionation22939629 No
    SAMM50 Co-fractionation22939629 No
    DHODH Co-fractionation22939629 No
    TOMM70A Co-fractionation22939629 No
    TAP1 Co-fractionation22939629 CHD related
    TMEM14B Co-fractionation22939629 No
    HIGD1A Co-fractionation22939629 No
    NDUFS2 Co-fractionation22939629 No
    OXCT1 Co-fractionation22939629 No
    MRPL1 Co-fractionation22939629 No
    MRPS9 Co-fractionation22939629 No
    ZC3H4 Co-fractionation22939629 No
    NDUFS3 Co-fractionation22939629 No
    CYB5R3 Co-fractionation22939629 No
    NDUFS6 Co-fractionation22939629 No
    NDUFS8 Co-fractionation22939629 No
    NDUFV2 Co-fractionation22939629 No
    EIF4A1 Co-fractionation22939629 No
    XRCC6 Co-fractionation22939629 No
    MARC1 Co-fractionation22939629 No
    IMPAD1 Co-fractionation22939629 No
    ACAT1 Co-fractionation22939629 CHD related
    GCN1L1 Co-fractionation22939629 No
    PSMD1 Co-fractionation22939629 No
    PROCR Co-fractionation22939629 CHD related
    SLC2A14 Co-fractionation22939629 No
    SLC27A2 Co-fractionation22939629 No
    SQSTM1 Co-fractionation22939629 No
    PDHA1 Co-fractionation22939629 No
    NDUFV1 Co-fractionation22939629 No
    UBC Affinity Capture-MS16196087|18781797|21987572|21963094|21139048|21890473|21906983|22505724 No
    ICT1 Affinity Capture-MS20186120 No
    CSNK2B Two-hybrid21900206 No
    KIAA0101 Affinity Capture-MS21628590 No
    ARRB2 Affinity Capture-MS17620599 No
    SIRT7 Affinity Capture-MS22586326 No
    CUL3 Affinity Capture-MS21145461 No
    CUL4A Affinity Capture-MS21145461 No
    CUL5 Affinity Capture-MS21145461 No
    CUL2 Affinity Capture-MS21145461 No
    CUL1 Affinity Capture-MS21145461 No
    COPS5 Affinity Capture-MS21145461 No
    COPS6 Affinity Capture-MS21145461 No
    DCUN1D1 Affinity Capture-MS21145461 No
    CAND1 Affinity Capture-MS21145461 No
    NEDD8 Affinity Capture-MS21145461 No
    UBD Affinity Capture-MS22797925 No
    ATP5F1 Co-fractionation22939629 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00139Succinic acid"For nutritional supplementation, also for treating dietary shortage or imbalance"
    experimentalDB04141"2-Hexyloxy-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol"
    experimentalDB04657Carboxin
    experimentalDB04795Thenoyltrifluoroacetone
    experimentalDB08689UBIQUINONE-1