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: NFKB1

    Description: nuclear factor of kappa light polypeptide gene enhancer in B-cells 1

    Entrez Gene ID: 4790

    SwissProt Acc Number: P19838

    RefSeq: NM_001165412

    It was suspected to be CHD related:

    ..Our results suggest that NFKB1-94ATTG ins/del polymorphism is associated with CV disease in patients with RA...

    From PMID: 22742859, in Journal Atherosclerosis , 2012


    References

    There were 4 potential papers with NFKB1 and CHD.

    PMIDTitleJournalsDetails
    23357300 Role of inflammatory gene polymorphisms in left ventricular dysfunction (LVD) susceptibility in coronary artery disease (CAD) patients.CytokineMore Details
    23671649 Interaction between obesity and the NFKB1 - 94ins/delATTG promoter polymorphism in relation to incident acute coronary syndrome: a follow up study in three independent cohorts.PloS oneMore Details
    22742859 NFKB1-94ATTG ins/del polymorphism (rs28362491) is associated with cardiovascular disease in patients with rheumatoid arthritis.AtherosclerosisMore Details
    21726863 The NFKB1 ATTG ins/del polymorphism and risk of coronary heart disease in three independent populations.AtherosclerosisMore Details

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



    PPI interactions

    There were totally 132 unique genes interacted with NFKB1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    LYL1 Two-hybrid10023675|10023675 No
    COPB2 Affinity Capture-MS14743216 No
    REL Affinity Capture-MS14743216|17962807|17962807|15143182,17962807 No
    SPAG9 Affinity Capture-MS14743216 No
    NFKB2 Affinity Capture-MS14743216|17962807|14743216 No
    RELA Affinity Capture-MS14743216|8798655|16740634|16319923|16204234|16105840|20237821|2050119|17962807|11976329|11970949,8246997,15657065,8428580,17962807 CHD related
    KPNA3 Affinity Capture-MS14743216|14743216 No
    NFKB1 Affinity Capture-MS14743216|8428580|8428580|8428580|11943214,8428580,14678988,8139561,9738011 CHD related
    RELB Affinity Capture-MS14743216|17962807|17962807|14743216,17962807 No
    TP53BP1 Affinity Capture-Western10646849 No
    IKBKG Affinity Capture-MS14743216|14743216 No
    TBK1 Affinity Capture-MS14743216 No
    TNIP2 Affinity Capture-MS14743216|15169888|15169888 No
    TNIP3 Affinity Capture-MS14743216 No
    RSF1 Affinity Capture-Western15242768 No
    KLF5 Affinity Capture-Western14573617 CHD related
    HMGB1 Reconstituted Complex12604365|12604365 CHD related
    BTRC Affinity Capture-Western11158290|12482991|12482991|12482991,10835356 No
    MEN1 Affinity Capture-Western11526476|11526476|16651450|11526476 No
    NOTCH1 Affinity Capture-Western8642313 CHD related
    CHUK Affinity Capture-Western10469655|11976329|11976329 CHD related
    RXRA Reconstituted Complex10075655 CHD related
    PPP4C Affinity Capture-Western9837938 No
    IRF8 Reconstituted Complex8550813 No
    IRF2 Reconstituted Complex8550813|8550813 No
    IRF9 Reconstituted Complex8550813 No
    ZFP36 Affinity Capture-Western19738286 No
    PCBD1 Two-hybrid20211142 No
    ZBTB9 Two-hybrid20211142 No
    EP300 Affinity Capture-Western14662860|20065107|22013068 CHD related
    POLR2A Co-localization16319923 No
    NCOR2 Co-localization15494311 No
    PSMD10 Affinity Capture-Western17904523 No
    HDAC2 Affinity Capture-Western17827154 CHD related
    CLU Affinity Capture-Western20068069 No
    HDAC5 Reconstituted Complex12917325 No
    KAT5 Co-localization15829968|15829968 No
    CTNNB1 Co-localization15829968|15829968 CHD related
    RUVBL2 Co-localization15829968|15829968 No
    SIN3A Affinity Capture-Western17962807 No
    STAT5A Affinity Capture-Western21763497 No
    BRCA1 in vitro;in vivo12700228 CHD related
    UBE2D3 in vitro10835356 No
    CFLAR in vivo;yeast 2-hybrid13679070 No
    NFKBIB in vitro;in vivo14743216 No
    PDCD11 in vitro;yeast 2-hybrid14624448 No
    IRF1 in vitro8746784 CHD related
    IL2RA in vitro;in vivo2497520 CHD related
    MAP3K8 Two-hybrid9950430|14743216|9950430|9950430|15169888|9950430,16291755 No
    NCOA6 Reconstituted Complex10847592 No
    NCOA1 Reconstituted Complex10847592|9556555 No
    BCL3 Affinity Capture-Western14678988|14678988|8428580|8428580|8428580|10469655|20547759|20558726|20800578 No
    UNC5CL Affinity Capture-Western14769797|14769797 No
    HMGA2 Reconstituted Complex12693954|12693954|12693954 No
    NCOR1 Affinity Capture-Western12150997 No
    TAB2 Reconstituted Complex12150997 No
    HDAC1 Affinity Capture-Western11931769|11931769|12972430|16319923|11931769,14678988 CHD related
    IKBKB Biochemical Activity11158290|11976329|11976329|10469655,11158290,11976329 CHD related
    ELF1 Reconstituted Complex7862168|9094628|7862168 No
    GSK3B Biochemical Activity11425860|11425860 CHD related
    ITGB3BP Affinity Capture-Western12244126|12244126|12244126 No
    ELF3 Reconstituted Complex11036073|11036073 No
    SP1 Reconstituted Complex7933095 No
    NR3C1 Reconstituted Complex7823959|16380507 CHD related
    NFKBIE Two-hybrid9315679|9315679|9315679 No
    NFKBIA Affinity Capture-Western11313474|20980497|20558726|11020244 CHD related
    NFKBIZ Affinity Capture-Western11356851|11356851,15241416 No
    NKRF Reconstituted Complex10562553|10562553 No
    STAT6 Affinity Capture-Western9584180|9584180|9584180 CHD related
    TXN Co-crystal Structure7788295|7788295 CHD related
    TSC22D3 Affinity Capture-Western11468175|11468175|11468175 No
    CEBPB Reconstituted Complex1518839|1518839 No
    E2F1 Reconstituted Complex9368006|9368006 CHD related
    MTPN Reconstituted Complex11971907|11971907 No
    STAT3 Affinity Capture-Western12057007|12057007 CHD related
    BANP Affinity Capture-Western18981184 No
    BRMS1 Affinity Capture-Western17000776 No
    HDAC3 Affinity Capture-Western12972430 CHD related
    PARP1 Reconstituted Complex16204234|11590148 CHD related
    SUMO1 Affinity Capture-MS17549794 No
    ANXA4 Affinity Capture-Western20237821 No
    RPS3 Affinity Capture-Western18045535|18045535 No
    HMGA1 Reconstituted Complex9809067 CHD related
    CARM1 Co-purification14729568 No
    DPF2 Reconstituted Complex20460684|22334708|22334708 No
    PPME1 Affinity Capture-MS19156129 No
    SF1 Affinity Capture-Western12917325 No
    HDAC4 Affinity Capture-Western12917325 CHD related
    NCOA3 Affinity Capture-Western15383283 No
    gag-pol Biochemical Activity2017258 No
    HSPA4 Reconstituted Complex9250404 No
    UBC Affinity Capture-MS21139048|21906983 No
    tat Reconstituted Complex7690421 No
    PSMA4 Affinity Capture-Western8692272 No
    DPF3 Reconstituted Complex22334708|22334708 No
    PHF10 Affinity Capture-Western22334708 No
    DPF1 Affinity Capture-Western22334708 No
    TNIP1 Affinity Capture-Western19695220 No
    CUL3 Affinity Capture-MS21145461 No
    CUL4A Affinity Capture-MS21145461 No
    CUL4B Affinity Capture-MS21145461 No
    CUL5 Affinity Capture-MS21145461 No
    COPS5 Affinity Capture-MS21145461 No
    COPS6 Affinity Capture-MS21145461 No
    DCUN1D1 Affinity Capture-MS21145461 No
    COMMD1 Affinity Capture-Western15799966 No
    COMMD2 Affinity Capture-Western15799966 No
    COMMD4 Affinity Capture-Western15799966 No
    COMMD5 Affinity Capture-Western15799966 No
    COMMD8 Affinity Capture-Western15799966 No
    COMMD9 Affinity Capture-Western15799966 No
    COMMD3 Affinity Capture-Western15799966 No
    COMMD10 Affinity Capture-Western15799966 No
    COMMD6 Affinity Capture-Western15799966 No
    SOCS3 Affinity Capture-Western21451109 CHD related
    FBXW11 Affinity Capture-MS22017875 No
    RPS6KA5 Affinity Capture-Western20129940 No
    ESR1 in vitro7651415 CHD related
    RIPK1 in vivo16291755 No
    NFRKB in vitro2050119 No
    ETS1 in vitro9094628 CHD related
    FOS in vivo9468519 CHD related
    SPI1 in vitro9094628 No
    NCF1 in vitro;in vivo12618429 CHD related
    AR in vitro;in vivo8798655 CHD related
    PRKACA in vitro12947093 CHD related
    TNFSF11 in vitro;in vivo10635328 CHD related
    UBE2K in vitro9535861 No
    ATF3 in vitro7692236 No
    TRIP4 in vitro12077347 No
    G3BP2 in vitro;in vivo10969074 No
    CDK9 in vitro;in vivo12173051 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;withdrawnDB01041ThalidomideFor the acute treatment of the cutaneous manifestations of moderate to severe erythema nodosum leprosum (ENL). Also for use as maintenance therapy for prevention and suppression of the cutaneous manifestations of ENL recurrence.L04AX02
    approvedDB01411PranlukastUsed as an adjunct to the standard therapy of inhaled steroids with inhaled long- and/or short-acting beta-agonists. R03DC02
    approvedDB08814TriflusalB01AC18