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: RPA1

    Description: "replication protein A1, 70kDa"

    Entrez Gene ID: 6117

    SwissProt Acc Number: P27694

    RefSeq: NM_002945

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

    ..RPA1 thus apparently functions as a repressor protein in the -786T-->C mutation-related reduction of eNOS gene transcription associated with the development of coronary artery disease..

    From PMID: 11063722, in Journal Hum Mol Genet. , 2000


    References

    There were 0 potential papers with RPA1 and CHD.

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



    PPI interactions

    There were totally 101 unique genes interacted with RPA1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    MCM2 Two-hybrid12614612|12614612 No
    ORC2 Two-hybrid12614612 No
    ORC6 Two-hybrid12614612 No
    MCM4 Two-hybrid12614612 No
    MCM6 Two-hybrid12614612 No
    RPA2 Affinity Capture-Western10064605|11927569|21504906|22939629 No
    RAD52 Reconstituted Complex12077133 No
    RPA1 Co-crystal Structure11927569|11927569 CHD related
    CCNA2 Reconstituted Complex8798463 CHD related
    PRIM1 Affinity Capture-Western17035231 No
    C1orf124 Co-localization22894931 No
    SMARCAL1 Affinity Capture-MS21504906 No
    MCM3 Affinity Capture-MS21504906 No
    SMC2 Affinity Capture-MS21504906 No
    XPC Reconstituted Complex15914671 No
    RAD23B Reconstituted Complex15914671 No
    UBXN1 Co-fractionation22939629 No
    HELB in vitro12181327 No
    C8orf30A yeast 2-hybrid16169070 No
    MCM7 Two-hybrid12614612|12614612 No
    BRCA2 Reconstituted Complex12527904|12527904|12527904 No
    TP53 Reconstituted Complex15489903|15489903|11751427|11751427,8361542,15735006,15489903 CHD related
    BLM Reconstituted Complex10825162|12181313|12724401|12724401|10825162 No
    ATR Protein-peptide10608806|18162465 No
    TP53BP1 Affinity Capture-Western15856006|15856006 No
    FANCA Affinity Capture-MS12973351|12724401|12724401|22705371 No
    TIPIN Affinity Capture-Western17296725|17296725 No
    KIN Co-fractionation12754299 No
    TCEA2 Two-hybrid16169070 No
    ASCC2 Two-hybrid16169070 No
    CPE Two-hybrid16169070|16169070 CHD related
    AKTIP Two-hybrid16169070 No
    FAM203A Two-hybrid16169070 No
    RBM23 Two-hybrid16169070 No
    SELENBP1 Two-hybrid16169070 No
    PRKDC Reconstituted Complex10064605|10064605 No
    ATRIP Co-localization12791985 No
    RPA4 Two-hybrid7760808|7760808|7760808 No
    RPA3 Co-purification9461578|9461578 No
    MUTYH Affinity Capture-Western11092888|11092888|11092888 No
    RAD51 Reconstituted Complex12077133 No
    MSH4 Co-localization11950880|11950880 No
    XPA Two-hybrid7565690|7565690|19446504|7565690 No
    PCNA Affinity Capture-MS12171929|20227374|11254741 CHD related
    SMARCA4 Co-fractionation9443979 No
    RAD9A Affinity Capture-Western15897895|15897895 No
    RAD1 Affinity Capture-Western15897895|15897895 No
    HUS1 Affinity Capture-Western15897895|15897895 No
    FANCM Affinity Capture-MS20347428 No
    YOL086W-A Affinity Capture-MS20347428 No
    C12orf44 Affinity Capture-MS20562859 No
    FYCO1 Affinity Capture-MS20562859 No
    RB1CC1 Affinity Capture-MS20562859 No
    CHAF1A Affinity Capture-Western19059499 No
    CHD1L Affinity Capture-MS19661379 No
    MCPH1 Co-localization16872911 No
    HNRNPUL1 Affinity Capture-Western18480432|18480432 No
    BRCA1 Affinity Capture-Western21240188|19766185 CHD related
    TOPBP1 Co-localization20159562 No
    BRIP1 Co-localization20159562|17596542 No
    EBNA-1 Affinity Capture-Western19748364 No
    TOP3A Affinity Capture-Western12724401 No
    FANCG Affinity Capture-Western12724401 No
    POLK Affinity Capture-Western20227374|20227374 No
    RFWD3 Affinity Capture-MS21558276|21558276|21504906|21504906 No
    CENPA Affinity Capture-MS19410544 No
    DYRK2 Affinity Capture-MS19287380 No
    CSNK2B Two-hybrid21900206 No
    TK1 Two-hybrid21900206 No
    ANXA1 Two-hybrid21900206 CHD related
    RCC1 Two-hybrid21900206 No
    ANXA7 Two-hybrid21900206 No
    UBC Affinity Capture-MS20639865|18781797|21963094|21139048|21890473|21906983|22053931|22505724 No
    GTF2H1 Affinity Capture-Western11259578 No
    KIAA0101 Affinity Capture-MS21628590 No
    HDGF Affinity Capture-MS21907836 No
    SUMO2 Affinity Capture-MS19471022|21252943 No
    PSMD4 Affinity Capture-Western22661229 No
    RNF4 Affinity Capture-Western22661229 No
    ARRB2 Affinity Capture-MS17620599 No
    SH3KBP1 Affinity Capture-MS19531213 No
    HHV8GK18_gp81 Far Western22379092|22379092 No
    CDK2 Biochemical Activity8397207|8397206 No
    CCNB1 Biochemical Activity8397207|8397206 No
    CDK1 Biochemical Activity8397207|8397206 CHD related
    CCNA1 Biochemical Activity8397207|8397206 No
    BID Reconstituted Complex21859891|21859891 CHD related
    POLR2A Affinity Capture-Western16916636 No
    ERCC6 Affinity Capture-Western16916636 No
    HERC2 Affinity Capture-MS22261722 No
    NEURL4 Affinity Capture-MS22261722 No
    POLD1 Co-fractionation22939629 No
    MSH3 Co-fractionation22939629 No
    PPME1 Co-fractionation22939629 No
    ORC2L yeast 2-hybrid12614612 No
    WRN in vitro;in vivo10373438,15735006 CHD related
    TREX1 in vitro12791985 No
    AICDA in vitro16251902 No
    DMC1 in vitro9826763 No
    RECQL in vitro;in vivo15096578 No
    POLL in vitro17507928 No


    Involved FDA drugs

    There was no drug associated with RPA1