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: CDK4

    Description: cyclin-dependent kinase 4

    Entrez Gene ID: 1019

    SwissProt Acc Number: P11802

    RefSeq: NM_000075

    It was suspected to be CHD related:

    ..Expression of Skp2 enhanced the effect of D1NLS and CDK4 on the proliferation of cardiomyocytes and further contributed to improved post-ischaemic cardiac function...

    From PMID: 18596061, in Journal Cardiovasc Res , 2008


    References

    There were 7 potential papers with CDK4 and CHD.

    PMIDTitleJournalsDetails
    20978019 CDKN2BAS is associated with periodontitis in different European populations and is activated by bacterial infection.Journal of medical geneticsMore Details
    18845646 "Mutant parathyroid hormone-related protein, devoid of the nuclear localization signal, markedly inhibits arterial smooth muscle cell cycle and neointima formation by coordinate up-regulation of p15Ink4b and p27kip1."EndocrinologyMore Details
    18596061 Cardiomyocyte proliferation and protection against post-myocardial infarction heart failure by cyclin D1 and Skp2 ubiquitin ligase.Cardiovascular researchMore Details
    17507429 "PKCdelta mediates anti-proliferative, pro-apoptic effects of testosterone on coronary smooth muscle."American journal of physiology. Cell physiologyMore Details
    16115478 Roxithromycin is an inhibitor of human coronary artery smooth muscle cells proliferation: a potential ability to prevent coronary heart disease.AtherosclerosisMore Details
    15380677 The essential role of p21 in radiation-induced cell cycle arrest of vascular smooth muscle cell.Journal of molecular and cellular cardiologyMore Details
    12048257 3-Hydroxy-3-methylglutaryl CoA reductase inhibitors prevent high glucose-induced proliferation of mesangial cells via modulation of Rho GTPase/ p21 signaling pathway: Implications for diabetic nephropathy.Proceedings of the National Academy of Sciences of the United States of AmericaMore Details

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



    PPI interactions

    There were totally 98 unique genes interacted with CDK4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CDKN2D Two-hybrid16189514 No
    VTA1 Two-hybrid16189514|16189514 No
    CDKN2B Two-hybrid16189514|16169070|21900206 CHD related
    CDC37 Affinity Capture-MS17353931|8703009|9150368|8666233|11867521 No
    CDKN2A Affinity Capture-MS17353931|8259215|8259215|8259215|9228064|17881001|11900540|10719365 CHD related
    SMC3 Affinity Capture-MS17353931 No
    GEMIN4 Affinity Capture-MS17353931 No
    UBXN1 Affinity Capture-MS17353931 No
    SMC1A Affinity Capture-MS17353931 No
    LYN Affinity Capture-MS17353931 No
    BAG6 Two-hybrid16169070 No
    SETDB1 Two-hybrid16169070|21900206|16169070 No
    CAPNS1 Two-hybrid16169070 No
    CCND1 Reconstituted Complex10580009|8259215|11360184|10908655|9228064|18537972|9372967|20837141|8867812|16985050 CHD related
    PCNA Affinity Capture-Western8259215|8101826 CHD related
    CCND2 Affinity Capture-Western11360184|15169570 CHD related
    RFC1 Affinity Capture-Western10353443|10353443 No
    RB1 Biochemical Activity19225156|15003538|16205633|15169570|12949733|12519773|10198259|8647086|8867812|15998794|12190313|11900540|16985050|19556892|12509456|15147269|15922743|9199321|9464540|9003781,11254678,9190208,9315635,9139732,8626527 CHD related
    TSPYL2 Biochemical Activity11395479 No
    APLP1 Two-hybrid21900206 No
    DDAH2 Two-hybrid21900206 No
    ZBTB16 Two-hybrid21900206 No
    QARS Two-hybrid21900206 No
    HMGXB3 Two-hybrid21900206 No
    TRMT2A Two-hybrid21900206 No
    ATP5B Two-hybrid21900206 No
    PKM2 Two-hybrid21900206 No
    LUC7L2 Two-hybrid21900206 No
    HIST1H1D Biochemical Activity18850315 No
    PSMD9 Affinity Capture-Western12684681 CHD related
    HIST1H1A Biochemical Activity11132966|10447003|9464540 No
    CDK5R1 Affinity Capture-Western22654103 No
    MARCKS Biochemical Activity10359664 No
    H1F0 Biochemical Activity12383116 No
    APP Reconstituted Complex21832049 No
    RFC4 in vivo10353443 No
    MCM2 in vitro15232106 No
    TGFBR1 in vivo15761153 CHD related
    RBL1 in vivo12006580 No
    SMAD3 in vitro;in vivo15241418 CHD related
    BAT3 yeast 2-hybrid16169070 CHD related
    SMAD2 in vitro15241418 CHD related
    ZNF655 in vitro;in vivo15558030 No
    NOL12 yeast 2-hybrid16169070 No
    CCND3 Two-hybrid16189514|14641107|9716181|16782892|10342870,15232106,11896535 No
    CDKN2C Affinity Capture-MS17353931|8001816|8001816|8001816|8001816 No
    RPRM Affinity Capture-MS17353931 No
    ACTR3B Affinity Capture-MS17353931 No
    DBNL Affinity Capture-MS17353931 No
    SERTAD1 Reconstituted Complex15065884|10580009|15065884,10580009 No
    CDKN1B Reconstituted Complex11360184|8978686|9311993|11940657|18285702|16782892|10908655,16326706 CHD related
    CNOT7 Affinity Capture-Western10602502|10602502 No
    BRCA1 Reconstituted Complex9244350 CHD related
    CEBPA Co-fractionation11684017|11684017|11684017 No
    MYOD1 Reconstituted Complex10601020|10022835|10022835|10601020,10022835 No
    BIRC5 Affinity Capture-Western10713676|10713676 CHD related
    IME2 Phenotypic Suppression19197163 No
    CDKN1A Affinity Capture-Western20102411|17556661|15169570|12383116 CHD related
    SP1 Affinity Capture-Western18769160 No
    SAP25 Affinity Capture-MS16449650 No
    CDT1 Affinity Capture-Western15004027 No
    HSPA8 Affinity Capture-Western18537972 CHD related
    NCOA2 Reconstituted Complex12130539|12130539 No
    HSP82 Affinity Capture-Western21419342 No
    WDR77 Affinity Capture-Western20951943 No
    PRMT5 Affinity Capture-Western20951943 No
    ARID4A Biochemical Activity21148318 No
    PPP2R1B Affinity Capture-Western17540176|17540176|17540176 No
    PPP2R1A Affinity Capture-Western17540176 No
    UHRF2 Far Western21952639 No
    IRF8 Affinity Capture-MS21903422 No
    DAZAP2 Two-hybrid21900206 No
    SNCA Two-hybrid21900206 No
    TK1 Two-hybrid21900206 No
    ANXA7 Two-hybrid21900206 No
    UBC Affinity Capture-MS18781797|21139048|21890473|21906983|22053931|22505724 No
    KIAA0101 Affinity Capture-MS21628590 No
    HSP90AA1 Affinity Capture-Western22315411 CHD related
    ARRB2 Affinity Capture-MS17620599 No
    RPL34 Reconstituted Complex10049762 No
    PSMA6 Affinity Capture-Western22158041 CHD related
    CCNE1 Affinity Capture-Western9716181 CHD related
    CCNA2 Affinity Capture-Western9716181 CHD related
    SIRT2 Negative Genetic22318606 No
    PSMD10 Affinity Capture-Western17881001|11900540|11900540|11779854 No
    PPP1CA Affinity Capture-Western17274640 No
    CUL3 Affinity Capture-MS21145461 No
    CUL4B Affinity Capture-MS21145461 No
    CUL1 Affinity Capture-MS21145461 No
    COPS5 Affinity Capture-MS21145461 No
    COPS6 Affinity Capture-MS21145461 No
    PTMA in vitro11310559 No
    IFI27 in vivo9837900 No
    CDKN1C in vivo9106657 No
    ORC3L in vitro15232106 No
    CDC45L in vitro15232106 No
    CDC7 in vitro15232106 No
    PRKAR1A in vivo16582606 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02733Purvalanol
    experimentalDB03496Flavopiridol"Investigated for use/treatment in esophageal cancer, leukemia (lymphoid), lung cancer, liver cancer, and lymphoma (unspecified)."