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: ESR2

    Description: estrogen receptor 2 (ER beta)

    Entrez Gene ID: 2100

    SwissProt Acc Number: Q92731

    RefSeq: NM_001040275

    It was suspected to be CHD related:

    ..ESR2 Alu I polymorphism may have a favorable influence on risk factors for cardiovascular disease such as obesity indices and cholesterol levels...

    From PMID: 19938352, in Journal Exp Clin Endocrinol Diabetes , 2009


    References

    There were 3 potential papers with ESR2 and CHD.

    PMIDTitleJournalsDetails
    19948975 Integrative predictive model of coronary artery calcification in atherosclerosis.CirculationMore Details
    17941906 Polymorphism of the oestrogen receptor beta gene (ESR2) is associated with susceptibility to Graves' disease.Clinical endocrinologyMore Details
    16099331 Genetic polymorphisms of estrogen receptors in patients with premature coronary artery disease.Archives of medical researchMore Details

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



    PPI interactions

    There were totally 93 unique genes interacted with ESR2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ESR1 Reconstituted Complex9473491|9473491|9473491 CHD related
    MED12 Reconstituted Complex11867769 No
    MED1 Reconstituted Complex11867769|11500849|10770935 No
    MED14 Reconstituted Complex11867769 No
    MED23 Reconstituted Complex11867769 No
    MED24 Reconstituted Complex11867769 No
    MED16 Reconstituted Complex11867769 No
    MED17 Reconstituted Complex11867769 No
    MED7 Reconstituted Complex11867769 No
    MED6 Reconstituted Complex11867769 No
    MED20 Reconstituted Complex11867769 No
    MED21 Reconstituted Complex11867769 No
    MED10 Reconstituted Complex11867769 No
    CCNC Reconstituted Complex11867769 No
    CDK8 Reconstituted Complex11867769 No
    DDX17 Reconstituted Complex11250900 No
    DDX5 Reconstituted Complex11250900 No
    MKNK2 Two-hybrid11013076 No
    UBC Affinity Capture-Western17962381|22349818 No
    UBE3A Affinity Capture-Western17962381 No
    SP1 Affinity Capture-Western18765668|10681512 No
    CREBBP Affinity Capture-Western18765668 No
    EP300 Affinity Capture-Western18765668|11500849 CHD related
    MSH2 Affinity Capture-Western15886699|15886699 No
    NCOA2 FRET11500849|12630920|12554772|11376110|11014206|11014206 No
    ZNHIT3 FRET11500849 No
    TRIP4 FRET11500849 No
    JMJD1C FRET11500849 No
    NFKBIB FRET11500849 No
    NRIP1 FRET11500849|15604093|15604093 No
    SERPINH1 FRET11500849 No
    TRIM24 FRET11500849 No
    ESR2 Affinity Capture-Luminescence20353944|15231873,12456792 CHD related
    HSP90AA1 Affinity Capture-Western20353944 CHD related
    KLF5 Reconstituted Complex21487105|21487105 CHD related
    WWP1 Affinity Capture-Western21487105 No
    EIF3I Two-hybrid15604093 No
    PNRC1 Two-hybrid15604093|15604093 No
    PPARGC1A Two-hybrid15604093|15784253,15604093 CHD related
    PNRC2 Two-hybrid15604093|15604093 No
    TRAM1 Two-hybrid11014206|11014206 No
    MDM2 Affinity Capture-Western22349818 CHD related
    ARID5A Two-hybrid15941852 No
    YWHAH in vitro11266503 No
    PELP1 in vitro12415108 No
    CALM1 in vivo11981030 No
    CALM2 in vivo11981030 No
    CALM3 in vivo11981030 No
    MAPK11 in vitro11579095 No
    SMAD3 in vitro11555647 CHD related
    AKAP13 in vitro;in vivo11579095 No
    NR0B1 in vitro;in vivo11053406 No
    PRMT2 in vitro;in vivo12039952 No
    NCOA7 in vitro;in vivo11971969,8197458 No
    TRIM59 in vitro;in vivo;yeast 2-hybrid15941852 No
    ZBTB17 in vitro11117529 No
    PIAS1 in vitro;in vivo11117529 No
    PIAS3 in vitro;in vivo11117529 No
    MAD2L1 Two-hybrid10706629|10706629 No
    NCOA6 Two-hybrid11158331|11773444|11773444,11158331,15604093 No
    SRC Affinity Capture-Western11032808|12095943 CHD related
    RBM39 Two-hybrid11704680|11704680|11704680 No
    DNTTIP2 Reconstituted Complex15047147|15047147 No
    SMARCE1 Reconstituted Complex12145209|12145209 No
    YWHAQ Reconstituted Complex11266503 No
    STAT5A Reconstituted Complex11682624 No
    RBFOX2 Reconstituted Complex11875103 No
    DAP3 Reconstituted Complex10903152 No
    REXO4 Reconstituted Complex10908561|10908561 No
    NCOA1 Two-hybrid10809226|14715875|10809226 No
    NCOA3 Reconstituted Complex11389589|10681591|17158759|10681591,11389589 No
    DDX54 Reconstituted Complex12466272|12466272 No
    PIAS2 Reconstituted Complex11117529 No
    MYOD1 Affinity Capture-Western18765668 No
    MAPK1 Biochemical Activity11358671 CHD related
    NCOR2 Affinity Capture-Western14715875|12904255 No
    KAT5 Two-hybrid11591700 No
    RXRA Far Western9121466 CHD related
    PPARG Far Western9121466 CHD related
    CAND1 Affinity Capture-MS21145461 No
    NR0B2 in vitro;yeast 2-hybrid10648597,9773978 No
    OXT in vitro9501254 CHD related
    RBM9 in vitro11875103 No
    PSMC3IP in vitro;yeast 2-hybrid11739747 No
    MMS19 in vitro;yeast 2-hybrid11279242 No
    BCAS2 in vitro15694360 No
    LCK in vitro12415108 No
    AKT1 in vivo15001646 CHD related
    SREBF1 in vitro;in vivo12021179 No
    NCOR1 in vitro;yeast 2-hybrid12904255 No
    SMAD4 in vitro11555647 No
    SMAD2 in vitro11555647 CHD related
    WIPI1 in vitro15602573 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB00255DiethylstilbestrolUsed in the treatment of prostate cancer. Previously used in the prevention of miscarriage or premature delivery in pregnant women prone to miscarriage or premature delivery.G03CB02;G03CC05;L02AA01
    approvedDB00481Raloxifene"For the prevention and treatment of osteoporosis in post-menopausal women, as well as prevention and treatment of corticosteroid-induced bone loss. Also for the reduction in the incidence of invasive breast cancer in postmenopausal women with osteoporosis or have a high risk for developing breast cancer."G03XC01
    approvedDB00675TamoxifenFor the treatment of breast cancer.L02BA01
    approvedDB00783Estradiol"For the treatment of urogenital symptoms associated with post-menopausal atrophy of the vagina (such as dryness, burning, pruritus and dyspareunia) and/or the lower urinary tract (urinary urgency and dysuria)."G03CA01;G03CA03;L02AA02;L02AA03
    approved;withdrawnDB01108TrilostaneUsed in the treatment of Cushing's syndrome. It is normally used in short-term treatment until permanent therapy is possible.H02CA01
    approvedDB01196EstramustineFor the palliative treatment of patients with metastatic and/or progressive carcinoma of the prostateL01XX11
    experimentalDB01645Genistein
    experimentalDB02983Para-Mercury-Benzenesulfonic Acid
    experimentalDB03860"N-Butyl-11-[(7r,8r,9s,13s,14s,17s)-3,17-Dihydroxy-13-Methyl-7,8,9,11,12,13,14,15,16,17-Decahydro-6h-Cyclopenta[a]Phenanthren-7-Yl]-N-Methylundecanamide"
    experimentalDB03882"5-Alpha-Androstane-3-Beta,17beta-Diol"
    experimentalDB04020"4-(2-{[4-{[3-(4-Chlorophenyl)Propyl]Sulfanyl}-6-(1-Piperazinyl)-1,3,5-Triazin-2-Yl]Amino}Ethyl)Phenol"
    approvedDB04573EstriolUsed as a test to determine the general health of an unborn fetus.G03CC06;G03CA04
    approvedDB04574Estropipate"Estropipate is used for the treatment of moderate to severe vasomotor symptoms associated with the monopause, and moderate to severe symptoms of vulval and vaginal atrophy associated with the menopause. It is also used to treat hypoestrogenism due to hypogonadism, castration or primary ovarian failure, and prevent postmenopausal osteoporosis."
    experimentalDB06832"2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL"
    experimentalDB068753-(3-FLUORO-4-HYDROXYPHENYL)-7-HYDROXY-1-NAPHTHONITRILE
    experimentalDB06927[5-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-YL]ACETONITRILE
    experimentalDB06937"4-(6-HYDROXY-BENZO[D]ISOXAZOL-3-YL)BENZENE-1,3-DIOL"
    experimentalDB07009"2-(5-HYDROXY-NAPHTHALEN-1-YL)-1,3-BENZOOXAZOL-6-OL"
    experimentalDB070322-(4-HYDROXY-PHENYL)BENZOFURAN-5-OL
    experimentalDB07036"(3aS,4R,9bR)-2,2-difluoro-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol"
    experimentalDB071191-CHLORO-6-(4-HYDROXYPHENYL)-2-NAPHTHOL
    experimentalDB071504-(4-HYDROXYPHENYL)-1-NAPHTHALDEHYDE OXIME
    experimentalDB071985-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-CARBONITRILE
    experimentalDB072303-BROMO-6-HYDROXY-2-(4-HYDROXYPHENYL)-1H-INDEN-1-ONE
    experimentalDB072363-(6-HYDROXY-NAPHTHALEN-2-YL)-BENZO[D]ISOOXAZOL-6-OL
    experimentalDB07638"(3AS,4R,9BR)-2,2-DIFLUORO-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL"
    experimentalDB07702"(16ALPHA,17ALPHA)-ESTRA-1,3,5(10)-TRIENE-3,16,17-TRIOL"
    experimentalDB07757"(9aS)-4-bromo-9a-butyl-7-hydroxy-1,2,9,9a-tetrahydro-3H-fluoren-3-one"
    experimentalDB07933"(3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL"
    experimentalDB08020"(3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-6-(METHOXYMETHYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL"