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: BRCA1

    Description: "breast cancer 1, early onset"

    Entrez Gene ID: 672

    SwissProt Acc Number: P38398

    RefSeq: NM_007294

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

    ..The single nucleotide polymorphisms (SNPs) in the gene of breast cancer suppressor protein (BRCA1)-associated protein (BRAP) are significantly associated with coronary artery disease..

    From PMID: 22965072, in Journal Diab Vasc Dis Res. , 2012


    References

    There were 7 potential papers with BRCA1 and CHD.

    PMIDTitleJournalsDetails
    22965072 The single nucleotide polymorphisms in BRAP decrease the risk of metabolic syndrome in a Chinese young adult population.Diabetes & vascular disease research : official journal of the InternationalMore Details
    24009820 Blood cellular mutant LXR-alpha protein stability governs initiation of coronary heart disease.World journal of cardiologyMore Details
    21898151 Non-cancer endpoints in BRCA1/2 carriers after risk-reducing salpingo-oophorectomy.Familial cancerMore Details
    21596366 Loss of BRCC3 deubiquitinating enzyme leads to abnormal angiogenesis and is associated with syndromic moyamoya.American journal of human geneticsMore Details
    21192737 "Chlamydia pneumoniae heat shock protein 60 enhances expression of ERK, TLR-4 and IL-8 in atheromatous plaques of coronary artery disease patients."Immunological investigationsMore Details
    18037339 Genetic polymorphisms and micronucleus formation: a review of the literature.Mutation researchMore Details
    18030340 Negative selection on BRCA1 susceptibility alleles sheds light on the population genetics of late-onset diseases and aging theory.PloS oneMore Details

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



    PPI interactions

    There were totally 264 unique genes interacted with BRCA1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ATF1 Two-hybrid10945975|10945975|10945975 No
    MSH2 Two-hybrid11498787|11498787|10783165|16260778|16260778|15886699 No
    BARD1 Two-hybrid8944023|11498787|11498787|12485996|11278247|11925436|14647430|12732733|14638690|14636569|14636569|11504724|8944023|11526114|10026184|12438698|11927591|11278247|15159397|11573085|9738006|9342365|10635334|12951069|12732733|10026184|11301010|19176389|19117993|20215511|16489000|18936166|17664283|20060929|20351172|21901007|11927591|11927591|19369211|19369211|20681793|20681793|19766185|15569676|15855157|18493658|19916563|23086937 No
    MSH6 Two-hybrid11498787|11498787|10783165|16260778 No
    MAP3K3 Two-hybrid15205325|15205325|15205325 No
    KPNA2 Two-hybrid8955125 No
    SMARCA4 Affinity Capture-Western15034933|10943845|10943845 No
    SMARCA2 Affinity Capture-Western15034933 No
    H2AFX Reconstituted Complex12485996|11927591|19766185|20681793 No
    UBE2D1 Reconstituted Complex12485996|12732733|14638690|12438698|11927591|14636569|12890688|11278247|19712108|19712108|19712108|12887909|16403807 No
    MYC Affinity Capture-Western11916966|14612409|14612409|9788437|9788437|20215511|20215511|12646176 CHD related
    BRCA1 Protein-peptide14578343|11573086|9525870|16818604|20351172|21965653|11927591|21880590|16403807|15448696|12611903,11751867,9159119,555 CHD related
    CTCFL Protein-peptide14578343 No
    KIF1B Protein-peptide14578343 No
    MSH3 Protein-peptide14578343|11498787 No
    NCOA2 Protein-peptide14578343|11085509 No
    NCOA3 Protein-peptide14578343|16860316 No
    MAP4K4 Protein-peptide14578343 CHD related
    NUP153 Protein-peptide14578343 No
    RBBP8 Protein-peptide14578343|10196224|10196224|10196224|9811458|9811458|11689934|9738006|9738006|10764811|17525342|16818604|16818604|21908405|17525340|17525340|16843262|19452558|18285836|10910365|18171670 No
    DNAJA3 Protein-peptide14578343 No
    POLR2A Affinity Capture-Western14506230|9159119|9159119|11504724|11504724|12955082|15886201|10725406|12955082|12955082 No
    CDK8 Co-purification9159119 No
    MED21 Co-purification9159119|9159119 No
    TUBG1 Co-localization11691781|11691781|11691781|9789027|9789027|9789027|15367667|22262852 No
    FHL2 Reconstituted Complex14550570|14550570|14986435|14986435|14986435|14550570|14550570 No
    ELK4 Reconstituted Complex11313879|11313879 No
    JUN Affinity Capture-Western12080089|12080089 CHD related
    RB1 Affinity Capture-Western10518542|11521194|11521194|11521194 CHD related
    RAD51 Reconstituted Complex9008167|14636569|14636569|14636569|11498787|9774970|19766185|9008167 No
    TP53 Affinity Capture-Western14710355|9482880|14636569|14636569|9926942|9926942|9582019|14636569|16677609|16969499|9582019|15571721 CHD related
    BLM Co-purification10783165 No
    MRE11A Co-purification10783165|11353843|11504724|11504724|10426999|16391231 No
    NBN Co-purification10783165|11504724|10426999|18171670 No
    RAD50 Co-purification10783165|11504724|10426999|10426999|10426999|10426999|16260778|18171670 No
    HSPA8 Two-hybrid9738006 CHD related
    CDK16 Two-hybrid9738006 No
    ESR1 Co-localization11493692|11244506|11244506|12400015|11782371|16260778|16061635|20060929|19887647|15674350|17505062 CHD related
    XIST Co-localization15065664|12419249 No
    CSTF1 Reconstituted Complex11257228 No
    CSTF2 Co-purification11257228|11257228|10477523|10477523 No
    MED17 Co-purification11504724|15208681 No
    RBL1 Co-localization11521194|11521194 No
    RBL2 Co-localization11521194|11521194 No
    SP1 Affinity Capture-Western12706836|17766039|12706836 No
    UBE2L3 Reconstituted Complex12732733|19712108|19712108|19712108 No
    APLP2 Far Western11746496 No
    PEG3 Far Western11746496 No
    RPL31 Far Western11746496|11746496 No
    WNT2B Far Western11746496 No
    COBRA1 Reconstituted Complex11739404|11739404|11739404 No
    ACACA Affinity Capture-MS12360400|12360400|16326698|19061860|18452305|16698035 CHD related
    HIST2H2AC Reconstituted Complex11927591|11927591|19916563 No
    AR Reconstituted Complex11085509|11016951|11016951 CHD related
    CREB1 Phenotypic Enhancement10945975 No
    RELA Reconstituted Complex12700228|12700228|21908405 CHD related
    HIST2H3C Co-localization12419249 No
    H2AFY Co-localization12419249|12419249 No
    AKT1 Reconstituted Complex10542266|19074868|19074868 CHD related
    UBE3A Reconstituted Complex12890688 No
    CTBP1 Affinity Capture-Western10196224 No
    MED23 Affinity Capture-MS15208681 No
    ETS1 Reconstituted Complex11313879 CHD related
    FLI1 Reconstituted Complex11313879 No
    MLH1 Co-purification10783165|21240188 No
    NUFIP1 Two-hybrid15107825|15107825|15107825|15107825 No
    RFC1 Co-purification10783165|10783165 No
    GTF2E1 Co-purification9159119 No
    GTF2F1 Co-purification9159119 No
    GTF2H4 Co-purification9159119 No
    MED24 Affinity Capture-Western15208681|15208681 No
    MED13 Affinity Capture-MS15208681 No
    HDAC1 Reconstituted Complex10220405 CHD related
    HDAC2 Reconstituted Complex10220405|21946536 CHD related
    SMARCC2 Co-purification10943845 No
    SMARCC1 Co-purification10943845 No
    SMARCD2 Co-purification10943845 No
    DHH1 Synthetic Rescue18197258 No
    CCR4 Synthetic Rescue18197258 CHD related
    DEF1 Synthetic Rescue18197258 No
    SPT4 Synthetic Rescue18197258 No
    SPT5 Synthetic Rescue18197258 No
    SUB1 Synthetic Rescue18197258 No
    MLP2 Synthetic Rescue18197258 No
    ASM4 Synthetic Rescue18197258 No
    NUP2 Synthetic Rescue18197258 No
    NUP120 Synthetic Rescue18197258 No
    NUP133 Synthetic Rescue18197258 No
    NUP170 Synthetic Rescue18197258 No
    NUP188 Synthetic Rescue18197258 No
    POM34 Synthetic Rescue18197258 No
    MRPL39 Synthetic Rescue18197258 No
    JAK1 Affinity Capture-Western11163768 CHD related
    JAK2 Affinity Capture-Western11163768 CHD related
    STAT5A Affinity Capture-Western12459499 No
    VCP Affinity Capture-Western10855792 No
    FANCA Two-hybrid12354784|12354784|12354784|21240188 No
    CCNE1 Affinity Capture-Western17525332 CHD related
    CDK4 Reconstituted Complex9244350 CHD related
    CDK5 Reconstituted Complex9244350 No
    E2F4 Reconstituted Complex9244350 No
    CDK1 Reconstituted Complex9244350 CHD related
    CCNA1 Reconstituted Complex9244350|10373534,9244350 No
    CCNB1 Reconstituted Complex9244350 No
    CCND1 Reconstituted Complex9244350 CHD related
    BACH1 Affinity Capture-Western11301010|11301010|17664283|15125843|15125843|16391231|19369211|17525340|17525340|15242590|15242590|15208681 No
    STAT1 Affinity Capture-Western10792030|10792030 CHD related
    NFYA Affinity Capture-Western11777930 No
    POU2F1 Affinity Capture-Western11777930|18000219|11777930 No
    BRAP Two-hybrid9497340|8955125 CHD related
    ZNF350 Reconstituted Complex11090615|11090615|16843262 No
    UIMC1 Affinity Capture-MS17525342|17525342|17525341|21622030|19261748|17525340|17525340|19305427|19766185 No
    BRD7 Two-hybrid20215511|20215511|20215511 No
    PIAS4 Co-localization20016603|20016594 No
    PIAS1 Co-localization20016603|20016594 No
    SUMO1 FRET20016594|18025037|18025037|18025037 No
    UBE2I FRET20016594|19287951 No
    TOP2A Affinity Capture-Western15965487|15965487|15965487 No
    TERF1 Affinity Capture-Western19797051 No
    TERF2 Affinity Capture-Western19797051 No
    SRC Affinity Capture-Western16860316 CHD related
    ARNT Affinity Capture-Western16567799|16567799 No
    TRRAP Affinity Capture-MS16260778|16260778|16260778|16260778|16260778 No
    KAT2A Affinity Capture-MS16260778|16260778|16260778 No
    RPA1 Affinity Capture-Western21240188|19766185 CHD related
    UBE2D2 Two-hybrid21113135|19712108|19712108|19712108 No
    UBE2D3 Two-hybrid21113135|16628214|19712108|19712108|19712108|21531767|20351172|16818604|15886201|22863316|15367667|21756275|17283126|21965653 No
    HERC2 Affinity Capture-Western20631078 No
    POLR2H Biochemical Activity17283126 No
    PGR Biochemical Activity21531767|16109739|16109739 No
    TOPBP1 Affinity Capture-Western16391231|19766185 No
    TUBB Affinity Capture-Western12353262|12353262 No
    UBE2E1 Two-hybrid19712108|19712108|19712108|17873885|21965653 No
    UBE2E2 Two-hybrid19712108|19712108|19712108|17873885|21965653 No
    UBE2E3 Two-hybrid19712108|19712108|19712108|17873885|21965653 No
    UBE2W Two-hybrid19712108|19712108|19712108|17873885|21965653 No
    UBE2K Two-hybrid19712108|19712108|19712108|17873885 No
    UBE2N Two-hybrid19712108|19712108|19712108|17873885|21965653 No
    SUMO3 Affinity Capture-Western21147198 No
    E2F1 Affinity Capture-Western21880590 CHD related
    PAX2 Affinity Capture-Western21880590 No
    ZFP161 Affinity Capture-Western21880590 No
    AP2A1 Affinity Capture-Western21880590 No
    TP63 Affinity Capture-Western21363924 No
    TFAP2A Affinity Capture-Western21363924 No
    TFAP2C Affinity Capture-Western21363924 No
    ETV5 FRET21282464 No
    RDX Affinity Capture-MS21282464 No
    MSN Affinity Capture-MS21282464 No
    ATRIP Affinity Capture-Western17616665 No
    BRAT1 Affinity Capture-Western16452482 No
    TRIM74 Two-hybrid22493164 No
    TP73 Affinity Capture-Western20807817 No
    KIAA0101 Affinity Capture-Western21673012 No
    SRSF1 Affinity Capture-RNA18391021 No
    TARDBP Affinity Capture-RNA18391021 No
    HNRNPA1 Affinity Capture-RNA18391021 No
    HNRNPA2B1 Affinity Capture-RNA18391021 No
    DAZAP1 Affinity Capture-RNA18391021 No
    HIF1A Affinity Capture-Western16543242 CHD related
    AHR Affinity Capture-Western18259752|18259752 No
    GTF2I Reconstituted Complex21407215|21407215|21407215 No
    PABPC1 Far Western16782705|16782705|16782705 No
    MAPK3 Affinity Capture-Western18593910 CHD related
    MAPK1 Affinity Capture-Western18593910 CHD related
    IFI16 Affinity Capture-Western14654789|14654789 No
    CTNNB1 Affinity Capture-Western20215423|20215423 CHD related
    BAP1 Two-hybrid9528852|9528852 No
    SKP1 Affinity Capture-Western23086937 No
    FBXO44 Affinity Capture-Western23086937 No
    SKP2 Affinity Capture-Western23086937 No
    FBXO5 Affinity Capture-Western23086937 No
    STAT3 in vivo11163768 CHD related
    YY1 in vitro11777930 No
    PSAP in vitro;in vivo11313879 No
    TUBA4A in vivo12353262 No
    KPNA6 yeast 2-hybrid8955125 No
    SMAD2 in vitro15735739 CHD related
    SMAD4 in vitro15735739 No
    UBB in vitro11320250 No
    BRIP1 Affinity Capture-Western15242590|21240188|20173781|17581638|17581638|17596542|22032289|11301010,15242590,11877378 No
    BRCA2 Affinity Capture-Western11477095|14499622|19369211|19369211|9774970,11477095 No
    ATM Affinity Capture-Western10866324|10866324|10608806|10550055|10550055|11114888|18344987|10866324|10866324|10866324|10550055,10866324,11114888 No
    ATR Reconstituted Complex11114888|10608806|11016625|11016625|11114888|11278964|11278964|11114888,11278964 No
    CSNK2B Reconstituted Complex10403822|10403822 No
    USF2 Affinity Capture-Western14502648|14502648 No
    NMI Affinity Capture-Western11916966|11916966 No
    Ifi204 Affinity Capture-Western14654789 No
    AURKA Affinity Capture-Western14990569|14990569|22110403|14990569|14990569 No
    JUNB Two-hybrid12080089|12080089|12080089|12080089 No
    JUND Two-hybrid12080089|12080089|12080089|12080089 No
    CREBBP Affinity Capture-Western10655477|10655477|9443979|16860316|16417649|9926942|10655477 No
    EP300 Affinity Capture-Western10655477|10655477|21212407|10655477 CHD related
    ABL1 Affinity Capture-Western12024016|12024016|12024016 No
    CLSPN Affinity Capture-Western15096610 No
    BRE Affinity Capture-MS14636569|14636569|14636569 No
    BRCC3 Affinity Capture-MS14636569|14636569|14636569|17664283 CHD related
    CHEK2 Reconstituted Complex10724175|10724175|18804494|12438214|17380128|10724175,12111733 No
    CSNK2A1 Reconstituted Complex10403822|10403822 CHD related
    MED1 Affinity Capture-Western15208681|15208681|15208681|15208681 No
    RBBP7 Affinity Capture-Western11394910|11394910|10220405|10220405,11394910 No
    PRKDC Protein-peptide10608806 No
    CDK2 Affinity Capture-Western10373534|10373534|10373534|8764100|10373534 No
    CCNA2 Affinity Capture-Western10373534|9244350,10373534 CHD related
    FANCD2 Two-hybrid14499622|11239454|11239454 No
    LMO4 Affinity Capture-Western11751867|11751867|11751867|12925972|11751867,12925972 No
    DHX9 Affinity Capture-Western12592385|12592385,9662397 No
    RBBP4 Reconstituted Complex10220405|10220405|10220405 No
    SMARCB1 Co-purification10943845 No
    MDC1 Affinity Capture-Western17525332|21622030|12611903|12607005 No
    TP53BP1 Affinity Capture-Western17525332|21552324|12364621 No
    ZCCHC8 Affinity Capture-Western17525332 No
    ORC2 Affinity Capture-Western17525332 No
    ORC3 Affinity Capture-Western17525332 No
    UBC Reconstituted Complex17525341|17185394|21890473|21906983|23086937 No
    PPP1CA Affinity Capture-Western17511879|12438214|12438214 No
    PPP1CB Affinity Capture-Western17511879 No
    PPP1R3A Affinity Capture-Western17511879 No
    WDR48 Affinity Capture-MS19615732 No
    UBE2J1 Two-hybrid19690564 No
    SUMO2 Affinity Capture-Western20016594|21693764|22689573 No
    XRCC5 Affinity Capture-Western18936166|18936166 No
    NPM1 Affinity Capture-Western15184379 No
    SMAD3 Reconstituted Complex15735739|15735739|19768112 CHD related
    FOXO3 Affinity Capture-Western18344987 CHD related
    CDKN2D Affinity Capture-Western17334399|17334399|17334399 No
    PRMT1 Biochemical Activity20614009|20614009 No
    MORF4L1 Affinity Capture-Western20332121 No
    PALB2 Affinity Capture-Western19584259|19553677|19268590|19268590|19369211|19369211|19369211|23038782 No
    MRPL36 Affinity Capture-Western16462773 No
    UBE2T Reconstituted Complex19887602 No
    SMC1A Affinity Capture-Western11877377|11877377 No
    MTA2 Affinity Capture-MS19703393 No
    BABAM1 Affinity Capture-Western19261749|19261746 No
    FAM175A Affinity Capture-MS19261749|19261746|21282113|19261748|17525340|17643121|17643122|17525340 No
    UBXN1 Affinity Capture-Western20351172|20351172 No
    SHFM1 Two-hybrid17563742 No
    SIRT1 Negative Genetic22318606 CHD related
    SIRT2 Negative Genetic22318606 No
    EZR Affinity Capture-Western21282464 No
    VDR Affinity Capture-Western19074549 CHD related
    TFAP4 Affinity Capture-MS19505873 No
    PIK3R1 Reconstituted Complex16135792 CHD related
    ERCC6 Affinity Capture-Western21756275 No
    CHEK1 Affinity Capture-Western11836499|17380128 No
    KIAA1967 Affinity Capture-Western20160719 No
    CDKN2A Affinity Capture-Western18703154|18703154 CHD related
    HMMR Affinity Capture-Western22110403 No
    TPX2 Affinity Capture-Western22110403 No
    MNAT1 Two-hybrid22493164|15282296 No
    BCL2 FRET21444675 CHD related
    DCLRE1C Affinity Capture-Western15456891|15456891 No
    NINL Affinity Capture-Western19509300 No
    CDK7 Affinity Capture-Western15282296 No
    CCNH Affinity Capture-Western15282296 No
    GFI1B Two-hybrid16713569 No
    RAD23B Affinity Capture-MS16712842 No
    RBX1 Biochemical Activity23086937 No
    NFKB1 in vitro;in vivo12700228 CHD related
    XRCC1 in vitro11352725 CHD related
    ELK1 in vitro;in vivo11313879 No
    CASP3 in vitro;in vivo12149654 CHD related
    POLR2K in vitro10725406 No
    ANTXR1 in vivo20566643 No


    Involved FDA drugs

    There was no drug associated with BRCA1