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: CASP3

    Description: "caspase 3, apoptosis-related cysteine peptidase"

    Entrez Gene ID: 836

    SwissProt Acc Number: P42574

    RefSeq: NM_004346

    It was suspected to be CHD related:

    ..ITPKC and CASP3 polymorphisms and risks for IVIG unresponsiveness and coronary artery lesion formation in Kawasaki disease...

    From PMID: 21987091, in Journal Pharmacogenomics J. , 2013


    References

    There were 5 potential papers with CASP3 and CHD.

    PMIDTitleJournalsDetails
    24162006 Management of Kawasaki disease.Archives of disease in childhoodMore Details
    21987091 ITPKC and CASP3 polymorphisms and risks for IVIG unresponsiveness and coronary artery lesion formation in Kawasaki disease.The pharmacogenomics journalMore Details
    23568731 [Association of CASP3 gene single nucleotide polymorphisms with Kawasaki disease in Chinese children patients].Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = ChineseMore Details
    23894522 A replication study for association of ITPKC and CASP3 two-locus analysis in IVIG unresponsiveness and coronary artery lesion in Kawasaki disease.PloS oneMore Details
    21160486 CASP3 gene single-nucleotide polymorphism (rs72689236) and Kawasaki disease in Taiwanese children.Journal of human geneticsMore Details

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



    PPI interactions

    There were totally 151 unique genes interacted with CASP3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BCL2 Biochemical Activity11752215|11948397,9395403 CHD related
    BLM Biochemical Activity11470874|11470874 No
    MCL1 Biochemical Activity15637055|15637055 No
    TRAF3 Biochemical Activity11261798|11098060|11261798 No
    HCLS1 Biochemical Activity11988074|11689006 No
    CASP2 Biochemical Activity11399776 No
    BID Biochemical Activity11399776|10364179 CHD related
    PARG Biochemical Activity11053413 No
    GORASP1 Biochemical Activity11815631 No
    CASP6 Biochemical Activity8900201 No
    CTTN Biochemical Activity11689006 No
    DBNL Biochemical Activity11689006 No
    BMX Biochemical Activity11278797|11278797 No
    HSPE1 Affinity Capture-Western10205158|10205158 No
    CASP3 Co-crystal Structure11257232|11257232 CHD related
    USO1 Biochemical Activity12438416 No
    MAP3K14 Affinity Capture-Western11002417 No
    SRP72 Biochemical Activity9857079 No
    GRIPAP1 Biochemical Activity10896157|12207967 No
    NDUFS1 Biochemical Activity15186778 No
    RNF2 Biochemical Activity17379327 No
    GMNN Biochemical Activity17261582 No
    HEY2 Affinity Capture-Western17217622 CHD related
    RBX1 Affinity Capture-Western17217622 No
    FBXW11 Affinity Capture-Western17217622 No
    BTRC Affinity Capture-Western17217622 No
    UBC Reconstituted Complex19258326 No
    THAP11 Two-hybrid18585351 No
    MDC1 Biochemical Activity21148072 No
    COPS6 Biochemical Activity17337451 No
    CASP9 Biochemical Activity15507451|17437405 CHD related
    MDM2 Biochemical Activity9278461|9278461 CHD related
    LYN in vitro;in vivo11526478 No
    DSG3 in vitro;in vivo11500511 No
    TFAP2A in vitro;in vivo11438643 No
    EIF2AK2 in vitro;in vivo11555640 No
    PRKCZ in vitro;in vivo11016947 No
    RAD51 in vitro;in vivo10082566,10998058 No
    RB1 in vitro11420704 CHD related
    PTMA in vitro10675528,9334214 No
    SP1 in vitro10103059 No
    TGM2 in vitro10556977 CHD related
    CDH1 in vitro;in vivo11076937 No
    VIM in vitro;in vivo10469173,11423904,11514563 CHD related
    BCAP31 in vitro;in vivo9334338 No
    PRKCQ in vitro9252332 No
    NFE2L2 in vitro;in vivo;yeast 2-hybrid10510468 CHD related
    SRF in vitro11387340 CHD related
    MEF2A in vitro;in vivo11904443 CHD related
    PTBP1 in vitro;in vivo12004072 No
    PSEN2 in vivo9990034,9219695,10069390 No
    PRKDC in vivo8804412 No
    IL18 in vitro9334240 CHD related
    PKN1 in vitro;in vivo9751706 No
    TRAF1 in vitro;in vivo11098060 CHD related
    DFFA in vitro11752060,9108473 No
    MAP4K1 in vitro10602493 No
    NEDD4 in vitro;in vivo9593687 No
    PXN in vitro11825902 No
    PKN2 in vitro;in vivo9368003 No
    GOLGA3 in vitro;in vivo10791974 No
    MDM4 in vitro;in vivo11840332 CHD related
    HNRNPU in vitro;in vivo10671544 No
    BCAR1 in vitro;in vivo10712510 No
    IL16 in vitro10479680,9422780 No
    PIP5K1A in vitro;in vivo11042212 No
    RABEP1 in vitro10608812 No
    PSIP1 in vitro12181742 No
    EIF2S1 in vitro10734073,10432301 CHD related
    EIF3J in vitro10672017 No
    EIF4B in vitro;in vivo11274152,10672017 No
    ACIN1 in vitro;in vivo10490026 No
    KCNIP3 in vitro;in vivo11278424 No
    PAK2 in vitro;in vivo9786869,16204230 No
    STK3 in vitro;in vivo11278283 No
    PSME3 in vitro;yeast 2-hybrid11859414 No
    ATN1 in vitro9361003 No
    CAD in vitro11854437 No
    STK24 in vivo12107159 No
    UBE4B in vitro11802788 No
    MAPK8IP3 in vitro10629060 No
    CAST in vivo9705209 CHD related
    PLA2G4A in vitro9875225 CHD related
    ARHGDIB in vitro8626669 No
    EIF4G2 in vitro;in vivo11175261 No
    ROCK1 in vitro;in vivo11283607 CHD related
    VAV1 in vitro10713703 No
    BRCA1 in vitro;in vivo12149654 CHD related
    PPP3CA in vitro11478781 CHD related
    RFC1 in vitro;in vivo9235961,9351817 No
    CTNNB1 in vivo9348292 CHD related
    CDKN1A in vivo9660939,10022118,9799125 CHD related
    CDC2L2 in vivo9632733,9115219 No
    CDC42 in vitro;in vivo11278572 CHD related
    MLH1 in vitro15087450 No
    RAC1 in vitro11278572 CHD related
    CDK11B in vitro9632733 No
    YWHAE in vitro;yeast 2-hybrid12657644 No
    TOP1 in vitro;in vivo9933635 No
    ADD1 in vitro10823823 CHD related
    FYN in vitro;in vivo10435619 No
    GSN in vitro;in vivo9323209,9671712 No
    RASA1 in vitro10200531 No
    HTT in vitro10770929 No
    PSEN1 in vitro;in vivo10069390 No
    LMNB1 in vivo11901153 No
    APP in vitro;in vivo8943232,15178331 No
    MAPT in vitro;in vivo12888622,11162250 No
    MYL3 in vitro;in vivo12186978 No
    HMGB1 in vitro11748221 CHD related
    AKT1 in vitro;in vivo12124386 CHD related
    CFLAR Affinity Capture-Western9208847|9326610|9326610|9208847 No
    DCC Two-hybrid11248093 No
    XIAP Affinity Capture-Western11447297|11447297|11927604|11257232|9384571|9230442|11359776|15200957|22072751|15507451|12624662|18521960|15650747|16543147|17069460|11257230|17291493|19698783 CHD related
    BIRC7 Reconstituted Complex11024045|11024045,11084335 No
    SREBF2 Biochemical Activity8605870 CHD related
    BIRC5 Reconstituted Complex9850056|11170436|11170436|9850056 CHD related
    HSPD1 Affinity Capture-Western10205158 CHD related
    CASP8 Biochemical Activity11832478|8962078|15254227|11437602 CHD related
    BIRC3 Reconstituted Complex9384571|17069460|9384571 No
    BIRC2 Reconstituted Complex9384571|19258326|19258326|17069460|9384571,11084335 No
    CASP10 Biochemical Activity8962078|8755496 No
    HSPB1 Affinity Capture-Western22238643 No
    ELAVL1 Affinity Capture-RNA19322201 No
    BIRC6 Affinity Capture-Western15200957|15507451|15200957 No
    CDK2 Affinity Capture-MS21319273 No
    ZBTB16 Biochemical Activity17340613 No
    CRYAB Affinity Capture-Western18669646 No
    BAX Co-localization15254227 CHD related
    CASP4 in vitro;in vivo9233763,9694885 No
    PICALM in vitro10926122 No
    PDE5A in vitro11602184 CHD related
    DEDD in vivo12235123 No
    DCTN1 in vivo11425872 No
    SLK in vitro;in vivo10611247 No
    SARS2 in vitro11331419 No
    PDE10A in vitro11602184 No
    AKAP8 in vivo;yeast 2-hybrid16227597 No
    CDC27 in vitro9618490 No
    MET in vitro;in vivo15542841 No
    SPTAN1 in vitro9811849 No
    WEE1 in vitro9618490 No
    AIFM1 in vitro9206994 No
    AR in vitro;in vivo9535906,8626669,9208847 CHD related
    APAF1 in vitro11550094 No
    GZMB in vitro;in vivo9233763,9694885 No
    STK4 in vitro;in vivo11278283,11278782,9545236 No
    KRT18 in vitro11356849,9298992,12235123 No
    NMT2 in vivo16530191 No
    HIP1 in vivo16979168 No
    GATA1 in vitro17167422 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB01017Minocycline"For the treatment of infections caused by susceptible strains of microorganisms, such as Rocky Mountain spotted fever, typhus fever and the typhus group, Q fever, rickettsial pox and tick fevers caused by Rickettsiae, upper respiratory tract infections caused by <i>Streptococcus pneumoniae</i> and for the treatment of asymptomatic carriers of <i>Neisseria meningitidis</i>."A01AB23;J01AA08
    experimentalDB031245-[4-(1-Carboxymethyl-2-Oxo-Propylcarbamoyl)-Benzylsulfamoyl]-2-Hydroxy-Benzoic Acid
    experimentalDB068622-HYDROXY-5-(2-MERCAPTO-ETHYLSULFAMOYL)-BENZOIC ACID
    experimentalDB07696methyl (3S)-3-[(tert-butoxycarbonyl)amino]-4-oxopentanoate
    experimentalDB08213"1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE"
    experimentalDB08229[N-(3-DIBENZYLCARBAMOYL-OXIRANECARBONYL)-HYDRAZINO]-ACETIC ACID
    experimentalDB082514-[5-(2-CARBOXY-1-FORMYL-ETHYLCARBAMOYL)-PYRIDIN-3-YL]-BENZOIC ACID
    experimentalDB08497"(1S)-2-oxo-1-phenyl-2-[(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-5-yl)amino]ethyl acetate"
    experimentalDB08498"(1S)-1-(3-chlorophenyl)-2-oxo-2-[(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-5-yl)amino]ethyl acetate"
    experimentalDB08499"N-[3-(2-fluoroethoxy)phenyl]-N'-(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-6-yl)butanediamide"