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: RXRA

    Description: "retinoid X receptor, alpha"

    Entrez Gene ID: 6256

    SwissProt Acc Number: P19793

    RefSeq: NM_002957

    It was suspected to be CHD related:

    .."After adjustment for multiple testing within each gene, single-nucleotide polymorphisms (SNP) significantly associated with case status were identified in the genes encoding LIPC (rs4775065, P<0.0001); CETP (rs5882, P=0.0002); RXRA (rs11185660, P=0.0021); ABCA1 (rs2249891, P=0.0126);"..

    From PMID: 20855565, in Journal J Lipid Res. , 2010


    References

    There were 1 potential papers with RXRA and CHD.

    PMIDTitleJournalsDetails
    20855565 Common genetic variation in multiple metabolic pathways influences susceptibility to low HDL-cholesterol and coronary heart disease.Journal of lipid researchMore Details

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



    PPI interactions

    There were totally 116 unique genes interacted with RXRA. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BRD8 Two-hybrid10517671 No
    CTNNB1 Affinity Capture-Western12771132 CHD related
    RNF8 Two-hybrid14981089|14981089|14981089 No
    HDAC3 Reconstituted Complex12943985 CHD related
    HDAC4 Reconstituted Complex12943985 CHD related
    RARA Reconstituted Complex12052862 No
    MYOD1 Reconstituted Complex9692544|9692544 No
    NR2F6 Two-hybrid10318855 No
    NR1H3 Reconstituted Complex8621574|9013544,12117567,15604093 CHD related
    Parp1 Reconstituted Complex10082530 No
    PPARGC1A Affinity Capture-Western11714715|11714715 CHD related
    SP1 Reconstituted Complex10361124 No
    PPARG Co-purification7838715 CHD related
    NPAS2 Two-hybrid11439184|11439184 No
    CLOCK Two-hybrid11439184|11439184 No
    ARNTL Reconstituted Complex11439184 No
    NR1I3 Reconstituted Complex8114692 No
    NCOA2 Reconstituted Complex11851396|11514567|15657427 No
    SNW1 Reconstituted Complex11514567 No
    NCOA1 Reconstituted Complex9171239|11027271|10935544|10935544|11124027 No
    IGFBP3 Reconstituted Complex10874028|10874028|10874028 CHD related
    MED1 Co-localization15863722|11027271 No
    POLR2A Co-localization15863722 No
    SMARCA4 Affinity Capture-Western15774904 No
    GRIP1 Reconstituted Complex11027271 No
    KIF1A Two-hybrid15604093|15604093 No
    PSMC5 Reconstituted Complex8598193|8603043 No
    TRIM32 Affinity Capture-Western21984809 No
    ESR1 Far Western9121466 CHD related
    ESR2 Far Western9121466 CHD related
    BHLHE40 Affinity Capture-Western19786558 No
    BHLHE41 Affinity Capture-Western19786558 No
    ARID5A Two-hybrid15941852 No
    NR2F1 in vitro;in vivo1311101 No
    NRBF2 Two-hybrid10786636|10786636 No
    NCOA6 Reconstituted Complex10567404|10567404|11158331|14578865|14578865|10866662|10866662|10866662,11158331 No
    GADD45G Reconstituted Complex10872826|10872826 No
    GADD45A Affinity Capture-Western10872826|21900206 No
    Gadd45b Reconstituted Complex10872826 No
    DNTTIP2 Reconstituted Complex15047147|15047147 No
    NR4A1 Reconstituted Complex14980220|17761950 CHD related
    TDG Reconstituted Complex12874288|12874288 No
    SRC Reconstituted Complex10517671|15140878|15116119|17363140|15140878 CHD related
    Pparg Two-hybrid10517671|10517671 No
    THRB Reconstituted Complex9368056|9415406|15604093|7746322,15604093 No
    PML Reconstituted Complex10610177|16540467 No
    UBQLN4 Two-hybrid16169070 No
    TMPRSS3 Two-hybrid16169070 No
    POU2F1 Reconstituted Complex10480874|10383413 No
    NCOA3 Reconstituted Complex9267036|9267036 No
    NRIP1 Reconstituted Complex12549917|8887632 No
    NR0B2 Two-hybrid10594021|12198243|10594021 No
    EDF1 Reconstituted Complex12040021|12040021 No
    CTSL1 Biochemical Activity9837884 No
    TADA3 Reconstituted Complex12235159|12235159 No
    BCL3 Reconstituted Complex9812988|9812988 No
    NR1H2 Two-hybrid7760852|15604093|7760852,15604093 CHD related
    NR1H4 Two-hybrid7760852|19883617|19883617|7760852 No
    NFKBIB Two-hybrid9452433|9452433|9452433,7776974 No
    RELA Reconstituted Complex10075655 CHD related
    NFKB1 Reconstituted Complex10075655 CHD related
    TBP Reconstituted Complex7667283|7667283|7667283 No
    POU2F2 Reconstituted Complex10383413 No
    PPARA Reconstituted Complex10195690 CHD related
    TRIM24 Reconstituted Complex9115274|11851396,9115274,9632676 No
    ITGB3BP Reconstituted Complex10490654|10490654 No
    THRA Co-purification1314167|11117530|15604093|1331778,15604093 CHD related
    NR2E3 Reconstituted Complex10611353 No
    VDR Reconstituted Complex9632709|11514567|15890193|15805579|15647825|11075811|10224118|10037600|17786964|15604093|15829977|12796488,15604093 CHD related
    MED24 Reconstituted Complex9653119|9653119 No
    FUS Reconstituted Complex9440806 No
    NCOR2 Two-hybrid9878542|10082574|9415406|15604093|12665583,15604093 No
    TAF1B Reconstituted Complex12511607 No
    RARB Co-crystal Structure15528208|7565739 No
    NCOR1 Reconstituted Complex15116119 No
    CTCF Reconstituted Complex20404925 No
    MAPK3 Biochemical Activity20371703 CHD related
    MAPK1 Biochemical Activity20371703|12048211 CHD related
    RARG Two-hybrid15604093 No
    PPARD Two-hybrid15604093|15604093 CHD related
    NR1I2 Two-hybrid15604093|9727070,9489701,15604093 No
    NR4A2 Two-hybrid15604093|7758108,7705655,15604093 CHD related
    MED25 Two-hybrid17641689|17641689|17641689|17641689 No
    GSK3B Two-hybrid21900206 CHD related
    CSNK2B Two-hybrid21900206 No
    CASP2 Two-hybrid21900206 No
    TK1 Two-hybrid21900206 No
    PLK1 Two-hybrid21900206 No
    RPS6KA6 Two-hybrid21900206 No
    SMN1 Two-hybrid21900206 No
    ROBO4 Reconstituted Complex14761960 No
    EP300 Affinity Capture-Western17761950 CHD related
    HDAC1 Negative Genetic22318606 CHD related
    SUMO1 Affinity Capture-Western19046432 No
    RAD54L2 Reconstituted Complex19692572 No
    SRF in vitro;yeast 2-hybrid11641790 CHD related
    NCOA4 in vitro;in vivo10347167 No
    MAPK7 in vitro;in vivo12048211 No
    ZNHIT3 yeast 2-hybrid7776974 No
    TRIP4 yeast 2-hybrid7776974 No
    JMJD1C yeast 2-hybrid7776974 No
    TRIP10 yeast 2-hybrid7776974 No
    COPS2 in vitro;yeast 2-hybrid7776974 No
    PRMT2 in vitro12039952 No
    NSD1 in vitro9628876 No
    ZBTB16 in vitro8622986 No
    TAF11 in vitro8670810 No
    PSMC3IP in vitro;yeast 2-hybrid11739747 No
    ACVR1 in vitro;yeast 2-hybrid9267036 No
    MPG in vitro14761960 No
    CHD9 in vitro16554032 No
    SMARCD3 in vitro14701856 No
    CNOT1 in vitro;yeast 2-hybrid16778766 No
    GATA2 in vivo15254248 CHD related
    HMGA1 yeast 2-hybrid10428836 CHD related
    SMAD2 yeast 2-hybrid15231748 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00210Adapalene"For the topical treatment of comedo, papular and pustular acne (acne vulgaris) of the face, chest or back."D10AD03
    approvedDB00307BexaroteneUsed orally for the treatment of skin manifestations of cutaneous T-cell lymphoma (CTCL) in patients who are refractory to at least one prior systemic therapy. Also used topically for the treatment of skin lesions in early (stage IA and IB) CTCL in patients who experience refractory or persistent disease with the use of other therapies or are intolerant of other therapies.L01XX25
    approvedDB00459AcitretinFor the treatment of severe psoriasis in adults.D05BB02
    approvedDB00523AlitretinoinFor topical treatment of cutaneous lesions in patients with AIDS-related Kaposi's sarcoma.L01XX22;D11AH04
    approvedDB00749Etodolac"For acute and long-term management of signs and symptoms of osteoarthritis and rheumatoid arthritis, as well as for the management of pain."M01AB08
    withdrawnDB00926EtretinateFor the treatment of severe psoriasis in adults.D05BB01
    experimentalDB07557"(5BETA)-PREGNANE-3,20-DIONE"
    experimentalDB078632-chloro-5-nitro-N-phenylbenzamide
    experimentalDB08063"1-BENZYL-3-(4-METHOXYPHENYLAMINO)-4-PHENYLPYRROLE-2,5-DIONE"
    experimentalDB08402"2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID"
    experimentalDB08601tributylstannanyl