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: CDK1

    Description: cyclin-dependent kinase 1

    Entrez Gene ID: 983

    SwissProt Acc Number: P06493

    RefSeq: NM_001130829

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

    ..These finding provide the evidence that radiation inhibits VSMC proliferation through cell cycle arrest by enhancing p21 expression and suppressing CDK1 and 2..

    From PMID: 15380677, in Journal J MolCellCardiol. , 2004


    References

    There were 1 potential papers with CDK1 and CHD.

    PMIDTitleJournalsDetails
    15380677 The essential role of p21 in radiation-induced cell cycle arrest of vascular smooth muscle cell.Journal of molecular and cellular cardiologyMore Details

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



    PPI interactions

    There were totally 184 unique genes interacted with CDK1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    FANCG Reconstituted Complex15367677|15367677|15367677 No
    DAB2 Affinity Capture-Western12881709|12881709 CHD related
    FEN1 Reconstituted Complex12853968|12853968 No
    NSFL1C Biochemical Activity12810701|12810701 No
    CDKN3 Two-hybrid8127873|8127873 No
    TP53 Biochemical Activity10884347|11327730 CHD related
    CUX1 Biochemical Activity11584018|11584018 No
    MKI67 Biochemical Activity10502411 CHD related
    TSC1 Reconstituted Complex14551205|11444800,14551205 No
    SPAG5 Biochemical Activity11549262 No
    CCNF Affinity Capture-Western10716937 No
    MAP4 Biochemical Activity7876309|9398320,11683421 No
    CIITA Biochemical Activity18245089 CHD related
    CDKN1A Affinity Capture-Western17679094|21308745|9467962 CHD related
    HIST1H1A Biochemical Activity9247342|10362260|9053846|8397207|8397206|11836499|7790358 No
    HMGB1 Biochemical Activity2013279|2013279 CHD related
    CDCA2 Biochemical Activity16998479 No
    TSPYL2 Biochemical Activity11395479 No
    FOXM1 Affinity Capture-Western15024056|15024056|15024056 No
    MLL5 Biochemical Activity20439461 No
    EZH2 Biochemical Activity20935635|21135039|21135039|21131960|21131960|21123648 No
    HIST1H1D Biochemical Activity21131960 No
    RUNX1 Biochemical Activity21059642 CHD related
    KAT5 Biochemical Activity12468530 No
    PAH1 Biochemical Activity21081492 No
    NCAPD2 Biochemical Activity11136719 No
    NCAPG Biochemical Activity11136719 No
    NCAPH Biochemical Activity11136719 No
    HIST1H1B Biochemical Activity16205633|18560763 No
    RPO21 Biochemical Activity22689984 No
    MARCKS Biochemical Activity10359664 No
    Lmnb1 Biochemical Activity9053846 No
    RB1 Biochemical Activity9053846|1756735|1756735 CHD related
    RPA1 Biochemical Activity8397207|8397206 CHD related
    KIF26B Biochemical Activity22768111 No
    FZR1 Biochemical Activity20581839 No
    UBE2I Biochemical Activity22407595 No
    FBXO5 Biochemical Activity21454540 No
    H1F0 Biochemical Activity12190313|15147269 No
    CSN2 Biochemical Activity7790358 No
    BUB1 Biochemical Activity16760428|16760428 No
    REPS2 Biochemical Activity10764745 No
    EPN1 Biochemical Activity10764745|10764745 No
    MBP Biochemical Activity17906618 No
    HTRA2 Biochemical Activity17906618 CHD related
    KIF11 Biochemical Activity8548803|9235942,8548803 No
    TFDP1 Biochemical Activity9199321 No
    E2F1 Biochemical Activity9199321|8087847 CHD related
    RACGAP1 Biochemical Activity18201571 No
    RUNX2 in vitro16407259 No
    CALD1 in vitro12613668 No
    CSNK2B in vitro;in vivo7578274 No
    CDC25A in vitro;in vivo12411508 No
    CREM in vitro;in vivo8404858 CHD related
    TOP2A in vitro;in vivo7635160,12569090 No
    EEF1D in vitro8051108,12551973 No
    GFAP in vitro;in vivo7822264,12177195 CHD related
    ITPR1 in vitro;in vivo14635192,16237118 No
    KRT18 in vivo9524113,15368451 No
    LMNA in vitro;in vivo7925482,2344612 CHD related
    STMN1 in vivo8376365,11135364,8325880 No
    NPM1 in vitro;in vivo12058066,11278991 No
    PTPN1 in vitro8491187,9600099 CHD related
    RAB4A in vitro1425574 No
    RAB5B in vitro10403367 No
    RPA2 in vitro;in vivo1318195,9295339 No
    RRM2 in vitro9990288 No
    ABL1 in vitro;in vivo2183353 No
    VIM in vitro7983050,15345747 CHD related
    UBE2A in vivo11953320 No
    UBA1 in vitro;in vivo7724583,7673335 No
    RAP1GAP in vitro1406653 No
    AMPH in vitro11113134 No
    HMGA2 in vitro10636877 No
    HMGA1 in vitro;in vivo1939057 CHD related
    DUT in vitro;in vivo8631817 No
    PLEC1 in vitro;in vivo8626512 No
    TP73 in vitro;in vivo12676926 No
    KHDRBS1 in vitro;in vivo9315091 No
    GOLGA2 in vitro;in vivo10769027,9753325 No
    IL16 in vitro;in vivo12450396 No
    BIRC5 in vitro;in vivo11069302,11861764 CHD related
    PTTG1 in vitro;in vivo10656688 No
    NUP210 in vitro8672508 No
    PTPN2 in vitro;in vivo15030318 No
    STMN2 in vitro9525956,9126608 No
    NES in vitro;in vivo12832492,11278541 No
    KIF20B in vitro;in vivo11470801 No
    RPS6KB1 in vitro;in vivo12586835,9271440 CHD related
    NDE1 in vitro12556484 No
    PBK in vitro15541388 No
    C13orf15 in vitro;in vivo11687586 No
    MAPT in vitro9614189 No
    RCC1 in vitro15014043 No
    TK1 in vitro9575153,14697231 No
    TGFBR2 in vitro;in vivo9926943 CHD related
    AR in vitro;in vivo;yeast 2-hybrid12569365,9725910 CHD related
    PTCH1 in vitro;in vivo11331587 No
    PITPNM1 in vitro;in vivo15125835 No
    MDM4 in vitro15735705 CHD related
    MEF2C in vitro16478538 No
    MCM4 in vivo16519687 No
    ECT2 in vitro16247472 No
    APLP2 in vitro;in vivo9109675 No
    GADD45A Reconstituted Complex10362260|10973963|12124778|10973963,10362260 No
    FANCA Affinity Capture-MS15082718|15367677|15367677 No
    FANCC Two-hybrid14499622|9242535|9242535 No
    CCNA2 Affinity Capture-Western12853968|17679094|19483727|9053846|21308745|10924145 CHD related
    CCNE1 Affinity Capture-Western9891079|1388288|1388288|9053846|1388288 CHD related
    CCNB1 Affinity Capture-Western9891079|2570636|17679094|9247342|16784539|16159883|20228808|17431037|20733055|20956543|2570636,10362260 No
    CCNA1 Affinity Capture-Western8565853|8565853 No
    LYN Affinity Capture-Western8051175|8051175|8910336|8910336,8051175,8084605,10564259 No
    LATS1 Two-hybrid9988268|9988268 No
    CNOT7 Affinity Capture-Western10602502|10602502 No
    FYN Affinity Capture-Western8910336|8910336 No
    BCL2 Affinity Capture-Western11774038|11326318 CHD related
    LZTS1 Affinity Capture-Western11504921|11504921 No
    BRCA1 Reconstituted Complex9244350 CHD related
    SFN Affinity Capture-Western10524633|10524633 No
    PRKCB Affinity Capture-Western11901153 CHD related
    ZBTB16 Affinity Capture-Western10497277|10497277 No
    CDC25C Reconstituted Complex10864927|11836499,9585407,9733650,9268380,9141461,8440392,8119945,17349584 No
    GADD45B Reconstituted Complex12124778|10973963 No
    GADD45G Reconstituted Complex12124778|10973963 No
    UBC Affinity Capture-MS18655026|18655026|16196087|18781797|21987572|21139048|21890473|21906983|22053931|22505724 No
    HSPA4 Affinity Capture-Western9247342 No
    USP19 Affinity Capture-MS19615732 No
    USP32 Affinity Capture-MS19615732 No
    USP45 Affinity Capture-MS19615732 No
    UIMC1 Affinity Capture-MS19615732 No
    DLGAP5 Affinity Capture-Western15145941 No
    MGMT Affinity Capture-Western16226712 No
    tat Reconstituted Complex19454010 No
    RYK Affinity Capture-MS21875946 No
    CSNK2A1 Biochemical Activity1400350 CHD related
    ARID4A Biochemical Activity21148318 No
    PPP2R1B Affinity Capture-Western17540176|17540176|17540176 No
    PPP2R1A Affinity Capture-Western17540176|17540176|17540176 No
    HDAC5 Affinity Capture-MS21081666 No
    UHRF2 Far Western21952639 No
    Cep55 Affinity Capture-MS20360068 No
    Cdk1 Affinity Capture-MS20360068 No
    Cep72 Affinity Capture-MS20360068 No
    Espl1 Affinity Capture-MS20360068 No
    Dctn1 Affinity Capture-MS20360068 No
    AI837181 Affinity Capture-MS20360068 No
    Mprip Affinity Capture-MS20360068 No
    EBNA-LP Affinity Capture-MS18457437 No
    KIAA0101 Affinity Capture-MS21628590 No
    SUMO2 Affinity Capture-MS21693764|19471022 No
    CCND1 Affinity Capture-Western7903056 CHD related
    HDGF Affinity Capture-MS21907836 No
    CKS1B Affinity Capture-MS19786724 No
    CKS2 Affinity Capture-MS19786724 No
    E2F4 Co-localization15782160 No
    PSMA6 Affinity Capture-Western22158041 CHD related
    SP1 Co-localization22266860|22266860 No
    PPP1CA Affinity Capture-Western17274640 No
    PPP1CC Affinity Capture-Western17274640 No
    CDK2 Affinity Capture-MS21319273 No
    KCND3 Affinity Capture-Western17725712 No
    CDT1 Affinity Capture-Western14993212|14993212|14993212 No
    EGFR Affinity Capture-MS18271526 CHD related
    MYC in vivo1748630 CHD related
    CDC25B in vitro9585407,9733650,9268380,9141461,8440392,12107172 No
    ERCC2 in vivo8652557 No
    PCNA in vitro7949095 CHD related
    PTMA in vitro11310559 No
    WEE1 in vitro;in vivo10564259,9268380,12186947,8428596 No
    POLA1 in vitro;in vivo11259605 No
    TLE1 in vitro12397081 No
    MYT1 in vitro;in vivo9001210,9268380 No
    PIN1 in vivo11774038 No
    CHAF1B in vitro10938080 No
    DNM2 in vitro;in vivo7590285 No
    PKMYT1 in vitro;in vivo10373560,10504341,9001210,9268380,12912980 No
    CCNB2 in vitro;in vivo9926943 No
    GORASP1 in vitro12839990 No
    USP16 in vitro;in vivo10077596 No
    HSPA2 in vitro9247342 No
    CDK7 in vitro7944411,11113184 No
    MNDA in vitro16458891 No
    BRCA2 in vitro15800651 No
    BIRC6 in vivo18329369 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02052Indirubin-3'-Monoxime
    experimentalDB02116Olomoucine
    experimentalDB02950Hymenialdisine
    experimentalDB03428SU9516
    experimentalDB03496Flavopiridol"Investigated for use/treatment in esophageal cancer, leukemia (lymphoid), lung cancer, liver cancer, and lymphoma (unspecified)."
    experimentalDB04014Alsterpaullone