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: HDAC4

    Description: histone deacetylase 4

    Entrez Gene ID: 9759

    SwissProt Acc Number: P56524

    RefSeq: NM_006037

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

    .."In vitro, siRNA knockdown experiments implicate HDAC4 as a mediator of the effects in ischemic cardiac myocytes."..

    From PMID: 18606865, in Journal FASEB J. , 2008


    References

    There were 1 potential papers with HDAC4 and CHD.

    PMIDTitleJournalsDetails
    18606865 Histone deacetylase inhibition reduces myocardial ischemia-reperfusion injury in mice.FASEB journal : official publication of the Federation of American Societies for More Details

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



    PPI interactions

    There were totally 188 unique genes interacted with HDAC4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CTBP1 Reconstituted Complex11022042 No
    MEF2A Affinity Capture-Western10487761|10487761|10487761,11792813 CHD related
    MEF2C Affinity Capture-Western10523670|15964851|18332106|10523670,11504882,11792813 No
    MEF2D Affinity Capture-Western10523670|16356933|10523670 No
    HDAC4 Reconstituted Complex11486037|18332106|11486037,10898795,11509672 CHD related
    RBBP4 Affinity Capture-Western10220385|10220385 No
    HDAC3 Affinity Capture-Western10220385|11804585|11804585|11804585|11466315|10869435 CHD related
    NCOR1 Reconstituted Complex11804585|10640275 No
    NCOR2 Reconstituted Complex11804585|10640275|22318606|11804585 No
    YWHAB Affinity Capture-Western10869435|10958686 No
    MECOM Affinity Capture-Western11568182|11568182 No
    SUV39H1 Affinity Capture-Western12242305 No
    MAPK3 Affinity Capture-Western11114188|11114188 CHD related
    MAPK1 Affinity Capture-Western11114188|11114188 CHD related
    FOXP3 Co-localization19276356 CHD related
    SENP1 Co-localization20079608 No
    CDK5 Affinity Capture-Western16356933 No
    PARK2 Affinity Capture-Western16332688 No
    NR1H2 Biochemical Activity17218271|17218271 CHD related
    YY1 Affinity Capture-Western19013255|18558095 No
    SS18L1 Two-hybrid20211142 No
    REST Affinity Capture-Western17011572 No
    MARK3 Affinity Capture-Western16980613 No
    CAMK1 Affinity Capture-Western16767219 No
    NUP214 Affinity Capture-Western16356933 No
    DNAJB5 Affinity Capture-Western18555775 No
    ESCO2 Affinity Capture-Western18501190 No
    GNB1 Affinity Capture-Western16221676|16221676 No
    TP53BP1 Affinity Capture-Western12668657|22318606 No
    HNF4A Reconstituted Complex12205093 No
    YWHAQ Two-hybrid15964851|11470791|22466704 No
    ANKRA2 Two-hybrid15964851|15964851|15964851 No
    ATRX Two-hybrid15964851|15964851 No
    REV3L Two-hybrid15964851|15964851 No
    MAP1S Two-hybrid15964851|15964851 No
    RFXANK Reconstituted Complex15964851|15964851|15964851 No
    CIITA Affinity Capture-Western15964851|15964851 CHD related
    PPP2CA Affinity Capture-Western18339811|22466704 CHD related
    NFKBIA Affinity Capture-Western15536134 CHD related
    RL2 Affinity Capture-Western15194749|15194749 No
    NUP155 Two-hybrid21464227|21464227 No
    ATXN1 Affinity Capture-Western17646162 No
    Twist1 Affinity Capture-Western19950203 No
    NFKB1 Affinity Capture-Western12917325 CHD related
    SF1 Affinity Capture-Western12917325 No
    KDM5B Affinity Capture-Western17373667|22318606 No
    PPP2R1A Affinity Capture-Western22466704 No
    ARNT Negative Genetic22318606 No
    ASNS Negative Genetic22318606 No
    ATR Negative Genetic22318606 No
    BCL2A1 Negative Genetic22318606 CHD related
    BNIPL Negative Genetic22318606 No
    CAB39 Negative Genetic22318606 No
    CDC26 Negative Genetic22318606 No
    CEP55 Negative Genetic22318606 No
    CHFR Negative Genetic22318606 No
    CKAP5 Negative Genetic22318606 No
    CLIP3 Negative Genetic22318606 No
    COG2 Negative Genetic22318606 No
    DHRS1 Negative Genetic22318606 No
    EIF4E Negative Genetic22318606 No
    HSPG2 Negative Genetic22318606 No
    HTR3C Negative Genetic22318606 No
    HTRA3 Negative Genetic22318606 No
    JUN Negative Genetic22318606 CHD related
    MECP2 Negative Genetic22318606 No
    MYLK Negative Genetic22318606 CHD related
    KAT7 Negative Genetic22318606 No
    KAT6A Negative Genetic22318606 No
    NXF1 Negative Genetic22318606 No
    PDHA2 Negative Genetic22318606 No
    PGK1 Negative Genetic22318606 No
    PHKB Negative Genetic22318606 No
    PLK1 Negative Genetic22318606 No
    PLK4 Negative Genetic22318606 No
    POLR1A Negative Genetic22318606 No
    POLR2C Negative Genetic22318606 No
    POLR2K Negative Genetic22318606 No
    PTCHD3 Negative Genetic22318606 No
    PTEN Negative Genetic22318606 CHD related
    RANBP3 Negative Genetic22318606 No
    RASSF8 Negative Genetic22318606 No
    RCOR1 Negative Genetic22318606 No
    RHO Negative Genetic22318606 No
    RPL3 Negative Genetic22318606 No
    RPS28 Negative Genetic22318606 No
    RUNX3 Negative Genetic22318606|15138260 No
    SLITRK3 Negative Genetic22318606 No
    SMN1 Negative Genetic22318606 No
    SNW1 Negative Genetic22318606 No
    STK16 Negative Genetic22318606 No
    TAF9B Negative Genetic22318606 No
    TCF7L2 Negative Genetic22318606 CHD related
    THBS2 Negative Genetic22318606 CHD related
    TP53 Negative Genetic22318606 CHD related
    TP53BP2 Negative Genetic22318606 No
    TWF2 Negative Genetic22318606 No
    UBA1 Negative Genetic22318606 No
    UCN Negative Genetic22318606 CHD related
    VAMP2 Negative Genetic22318606 No
    WNT2 Negative Genetic22318606 No
    WNT3 Negative Genetic22318606 No
    CLEC1A Positive Genetic22318606 No
    ELF4 Positive Genetic22318606 No
    INO80D Positive Genetic22318606 No
    KDM3B Positive Genetic22318606 No
    LOC391746 Positive Genetic22318606 No
    SKAP1 Positive Genetic22318606 No
    TSPO Positive Genetic22318606 No
    UBN1 Positive Genetic22318606 No
    STAT1 Affinity Capture-Western21571862 CHD related
    NFATC1 Affinity Capture-Western19218564 CHD related
    JDP2 Reconstituted Complex22989952 No
    ATF3 Reconstituted Complex22989952 No
    APP Reconstituted Complex21832049 No
    TNFRSF14 in vivo11463856 CHD related
    RUVBL2 in vitro15829968 No
    ZBTB16 Reconstituted Complex15467736|15467736,11929873 No
    SFN Affinity Capture-MS15778465 No
    GATA1 Affinity Capture-Western14668799|14668799 No
    RARA Reconstituted Complex12943985 No
    RXRA Reconstituted Complex12943985 CHD related
    NR2C1 Reconstituted Complex12943985|11463856 No
    NR2C2 Reconstituted Complex12943985 No
    AR Reconstituted Complex12943985|21242980|21242980 CHD related
    PPARD Reconstituted Complex12943985 CHD related
    PPARG Reconstituted Complex12943985 CHD related
    IKZF2 Reconstituted Complex12943985 No
    ZNF354A Reconstituted Complex12943985 No
    HDAC9 Reconstituted Complex12590135|12590135 No
    YWHAE Reconstituted Complex11504882|20936779 No
    YWHAG Reconstituted Complex11504882|15324660|15324660 No
    YWHAZ Reconstituted Complex11504882 No
    BCL6 Affinity Capture-Western11929873|16147992 No
    BCOR Affinity Capture-Western10898795|10898795 No
    IKZF1 Affinity Capture-Western12015313 No
    IKZF3 Affinity Capture-Western12015313 No
    IKZF4 Affinity Capture-Western12015313 No
    CBX5 Reconstituted Complex12242305 No
    UBE2I Biochemical Activity18691969|16166628 No
    SUMO2 Affinity Capture-Western16955485|17491593 No
    DNAJB6 Affinity Capture-Western20159555|18163532 No
    DNAJB8 Affinity Capture-Western20159555 No
    ATF2 Affinity Capture-Western20116378 CHD related
    MORC2 Co-localization20110259 No
    RUNX2 Affinity Capture-Western20097749|16613856|15537544 No
    SUMO1 Affinity Capture-Western16332688|17491593 No
    SIN3A Affinity Capture-Western17210713 No
    HIF1A Affinity Capture-Western19071119 CHD related
    CAMK2D Biochemical Activity17179159|16767219 CHD related
    ESR1 Reconstituted Complex19893013|16051668|16051668 CHD related
    LZTR1 Two-hybrid20211142 No
    SP1 Affinity Capture-Western18850004|18632985 No
    GATA3 Affinity Capture-Western16922677 No
    GCM1 Affinity Capture-Western16528103|16528103 No
    SYK Reconstituted Complex16288017 No
    CTNNB1 Affinity Capture-Western16204248 CHD related
    SRF Affinity Capture-Western12663674|12663674 CHD related
    SIRT1 Affinity Capture-Western16166628 CHD related
    LCOR Reconstituted Complex12535528 No
    CDKN1A Reconstituted Complex16082198 CHD related
    RANBP2 Biochemical Activity12032081|12032081 No
    SMAD3 Affinity Capture-Western15990875|15990875 CHD related
    RFX5 Affinity Capture-Western15964851 No
    RFXAP Affinity Capture-Western15964851 No
    IFRD1 Reconstituted Complex15743821 No
    NFKBIE Reconstituted Complex15536134 No
    HDAC5 Affinity Capture-Western18332106 No
    CAMK4 Biochemical Activity11470791|11470791 No
    CSRP3 Affinity Capture-Western18250163 No
    HDAC7 Reconstituted Complex11279209 No
    PPP2R4 Reconstituted Complex18045992 No
    AHRR Affinity Capture-Western17949687 No
    CEBPD Reconstituted Complex17910034 No
    BCORL1 Affinity Capture-Western17379597 No
    ACTA1 Reconstituted Complex21464227 CHD related
    NPPB Reconstituted Complex21464227 CHD related
    CACNA1C Reconstituted Complex21464227 CHD related
    HIC1 Affinity Capture-Western17283066 No
    ELAVL1 Affinity Capture-RNA19322201 No
    ZEB2 Affinity Capture-Western16061479 No
    BRMS1 Affinity Capture-Western16919237|16919237 No
    NACC1 Two-hybrid16033423|16033423|16033423 No
    Btg2 Reconstituted Complex17371797 No
    ANKRD11 in vitro15184363 No
    MEGF10 yeast 2-hybrid12421765 No
    NFKB2 in vitro;in vivo12917325 No
    MEF2B in vitro15567413 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB07879"N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide"
    experimentalDB08613"2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL"