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: CDKN2A

    Description: "cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"

    Entrez Gene ID: 1029

    SwissProt Acc Number: P42771

    RefSeq: NM_000077

    It was suspected to be CHD related:

    .."In contrast with previous studies demonstrating cancer resistance in Super-Ink4/Arf mice carrying an additional transgenic copy of the entire Ink4/Arf locus, our results cast doubt on the potential of Ink4/Arf activation as a strategy for the treatment of atherosclerotic disease.(the neighboring Ink4/Arf tumor-suppressor locus HI3L1 chitinase 3-like 1 (cartilage glycoprotein-39) gp38k (CHI3L1) is a novel adhesion and migration factor for vascular cells.//CHI3L1-329G>A and -131G>C polymorphisms are associated with serum YKL-40 levels, but not with the prevalence or severity of CAD."..

    From PMID: 22226369, in Journal Atherosclerosis. , 2012


    References

    There were 21 potential papers with CDKN2A and CHD.

    PMIDTitleJournalsDetails
    23199516 Interferon-gamma activates expression of p15 and p16 regardless of 9p21.3 coronary artery disease risk genotype.Journal of the American College of CardiologyMore Details
    23086272 "Association between 9p21.3 genomic markers and coronary artery disease in East Asians: a meta-analysis involving 9,813 cases and 10,710 controls."Molecular biology reportsMore Details
    23315372 Resequencing and clinical associations of the 9p21.3 region: a comprehensive investigation in the Framingham heart study.CirculationMore Details
    23665474 "A distant, cis-acting enhancer drives induction of Arf by Tgfbeta in the developing eye."Developmental biologyMore Details
    22706276 Functional analyses of coronary artery disease associated variation on chromosome 9p21 in vascular smooth muscle cells.Human molecular geneticsMore Details
    22952318 Effect of 9p21.3 coronary artery disease locus neighboring genes on atherosclerosis in mice.CirculationMore Details
    22768093 The chromosome 9p21.3 coronary heart disease risk allele is associated with altered gene expression in normal heart and vascular tissues.PloS oneMore Details
    21868699 Cdkn2a is an atherosclerosis modifier locus that regulates monocyte/macrophage proliferation."Arteriosclerosis, thrombosis, and vascular biology"More Details
    21550161 "[Genetic variants, cardiovascular risk and genome-wide association studies]."Revista espanola de cardiologiaMore Details
    20978019 CDKN2BAS is associated with periodontitis in different European populations and is activated by bacterial infection.Journal of medical geneticsMore Details
    20637465 "Expression of Chr9p21 genes CDKN2B (p15(INK4b)), CDKN2A (p16(INK4a), p14(ARF)) and MTAP in human atherosclerotic plaque."AtherosclerosisMore Details
    22144573 Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction.CirculationMore Details
    20173736 Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice.NatureMore Details
    20056914 ANRIL expression is associated with atherosclerosis risk at chromosome 9p21."Arteriosclerosis, thrombosis, and vascular biology"More Details
    20386740 Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression.PLoS geneticsMore Details
    19578363 New common variants affecting susceptibility to basal cell carcinoma.Nature geneticsMore Details
    19888323 Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants.PloS oneMore Details
    18599554 Replication study of 10 genetic polymorphisms associated with coronary heart disease in a specific high-risk population with familial hypercholesterolemia.European heart journalMore Details
    18340101 Whole genome analyses suggest ischemic stroke and heart disease share an association with polymorphisms on chromosome 9p21.Stroke; a journal of cerebral circulationMore Details
    17478681 A common allele on chromosome 9 associated with coronary heart disease."Science (New York, N.Y.)"More Details
    17478679 A common variant on chromosome 9p21 affects the risk of myocardial infarction."Science (New York, N.Y.)"More Details

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



    PPI interactions

    There were totally 122 unique genes interacted with CDKN2A. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CDK6 Protein-peptide8805225|17955473|17881001|10491434 No
    CCND2 Reconstituted Complex15065884|11900540 CHD related
    TP53 Affinity Capture-Western14612427|9529249|20395212 CHD related
    CCND1 Reconstituted Complex10580009 CHD related
    E4F1 Two-hybrid12446718 No
    DAXX Reconstituted Complex18583933|18583933 No
    TOP1 Affinity Capture-Western15361825 No
    SMARCA4 Two-hybrid19149898|19149898 No
    PIAS2 Two-hybrid19901969|19901969|20308430 No
    KAT5 Affinity Capture-Western16705183|16705183 No
    YY1 Affinity Capture-Western15210108 No
    NPM1 Affinity Capture-Western16679321|16679321|15989956|15989956|14636574|14636574|22561347|20308430 No
    UBC Affinity Capture-Western20208519|20395212|15289458|22561347|23034180 No
    HUWE1 Affinity Capture-Western15989956|15989956|15989956|22561347 No
    ACTB Affinity Capture-MS17955473 No
    ACTG1 Affinity Capture-MS17955473 No
    ACTN4 Affinity Capture-MS17955473 No
    ACLY Affinity Capture-MS17955473 No
    MCM6 Affinity Capture-MS17955473|17955473 No
    EEF2 Affinity Capture-MS17955473 No
    EPHA3 Affinity Capture-MS17955473 No
    GAPDH Affinity Capture-MS17955473 No
    HSP90AA1 Affinity Capture-MS17955473 CHD related
    HSP90AB1 Affinity Capture-MS17955473|16582619 CHD related
    HSPA8 Affinity Capture-MS17955473 CHD related
    HSPA4 Affinity Capture-MS17955473 No
    HNRNPA2B1 Affinity Capture-MS17955473 No
    HNRNPC Affinity Capture-MS17955473 No
    MTR Affinity Capture-MS17955473 CHD related
    MYL12A Affinity Capture-MS17955473 No
    MMRN1 Affinity Capture-MS17955473 No
    PDCD6 Affinity Capture-MS17955473 No
    PCNA Affinity Capture-MS17955473|17955473 CHD related
    RIN2 Affinity Capture-MS17955473 No
    RUVBL2 Affinity Capture-MS17955473 No
    SNRPB Affinity Capture-MS17955473 No
    HSPA9 Affinity Capture-MS17955473 No
    TUBB Affinity Capture-MS17955473 No
    TUBA1A Affinity Capture-MS17955473 No
    TUBB4B Affinity Capture-MS17955473 No
    TUBA1C Affinity Capture-MS17955473 No
    SNRPA Affinity Capture-MS17955473 No
    USP26 Affinity Capture-MS17955473 No
    UBE4B Affinity Capture-MS17955473 No
    UCHL1 Affinity Capture-Western20395212 No
    SP1 Affinity Capture-Western21555589 No
    ARFIP2 Two-hybrid11792819|11792819 No
    GGA1 Two-hybrid11792819 No
    WRN Reconstituted Complex15355988|15355988|15355988 CHD related
    TP63 Affinity Capture-Western15367673|15367673 No
    NCL Affinity Capture-Western14636574|16582619 No
    COMMD1 Two-hybrid18305112|18305112 No
    TRADD Affinity Capture-Western22561347 No
    SENP3 Affinity Capture-Western18948745 No
    CDK5RAP3 Two-hybrid16173922|16173922 No
    CTBP2 Affinity Capture-Western16508011|16508011 No
    MYC Affinity Capture-Western20308430|15361884 CHD related
    BRCA1 Affinity Capture-Western18703154|18703154 CHD related
    IKBKB Affinity Capture-Western20152798 CHD related
    GGA3 FRET21517092 No
    NMI Two-hybrid23034180|23034180|23034180 No
    ATR Affinity Capture-Western15775976 No
    RPS7 yeast 2-hybrid16582619 No
    TBRG1 in vitro;in vivo;yeast 2-hybrid16582619 No
    GSPT1 in vitro;in vivo;yeast 2-hybrid16582619 No
    KIAA1984 in vitro;in vivo;yeast 2-hybrid16582619 No
    ANKRD12 in vitro;yeast 2-hybrid16582619 No
    ZNF227 yeast 2-hybrid16582619 No
    PEX19 yeast 2-hybrid16582619 No
    ZFP91 in vitro;yeast 2-hybrid16582619 No
    TPI1 yeast 2-hybrid16582619 No
    AHNAK yeast 2-hybrid16582619 No
    MCM2 in vitro15232106 No
    GMNN in vitro15232106 No
    HIF1A in vivo11382768 CHD related
    E2F1 in vitro11314038 CHD related
    CDKN2A in vitro;in vivo;yeast 2-hybrid8755727,8910511 CHD related
    PPP1R9B Two-hybrid11278317|11278317 No
    CDK4 Affinity Capture-MS17353931|8259215|8259215|8259215|9228064|17881001|11900540|10719365 CHD related
    AURKA Affinity Capture-MS17353931 No
    PLEKHA8 Reconstituted Complex15107860 No
    SERTAD1 Reconstituted Complex15065884|10580009,15065884 No
    MDM2 Affinity Capture-MS14612427|14612427|9529249|9529249|12085228|12085228|9529248|18583933|16107876|11223036|10822382|20395212|22120712|18541670|17116689|10801444|16173922|18813780|18467333 CHD related
    RPL11 Affinity Capture-Western14612427 No
    UBE2A Affinity Capture-Western12640129 No
    FKBP2 Affinity Capture-Western12606707 No
    CCNG1 Reconstituted Complex12556559|12556559 No
    MDM4 Affinity Capture-Western11297540 CHD related
    ING4 Affinity Capture-Western18775696 No
    PSME3 Affinity Capture-Western17588519 No
    PSMC3 Affinity Capture-Western17334400|14665636|14665636|14665636 No
    LAMTOR3 Co-crystal Structure20655927 No
    ING1 Affinity Capture-Western19085961 No
    SAP25 Affinity Capture-MS16449650 No
    TRIP12 Affinity Capture-Western20208519|23034180 No
    Tubb5 Affinity Capture-MS20360068 No
    VHL Affinity Capture-MS21942715|7604013 No
    KIAA0101 Affinity Capture-MS21628590 No
    TTF1 Affinity Capture-Western22383580 No
    HIST3H2BB Affinity Capture-MS21846774|21846774|21846774 No
    HDAC1 Reconstituted Complex21846774|21846774 CHD related
    PPP1CB Affinity Capture-Western17274640 No
    PPP1CC Affinity Capture-Western17274640 No
    UBE2I Affinity Capture-Western15876874 No
    CUL2 Affinity Capture-MS21145461 No
    COPS5 Affinity Capture-MS21145461 No
    RNF2 Affinity Capture-Western22910419 No
    EIF3A Affinity Capture-Western16582619 No
    CDKN2AIP Affinity Capture-Western17460193|12154087 No
    tat Co-fractionation18418067 No
    CDC6 in vitro15232106 No
    MCM5 in vitro15232106 No
    CDC5L in vitro15232106 No
    CDKN2C in vitro8259215 No
    ORC4L in vitro15232106 No
    CDC45L in vitro15232106 No
    CDC7 in vitro15232106 No
    ALS2CR8 in vivo;yeast 2-hybrid12154087 No
    MCM10 in vitro15232106 No
    ZNF410 in vitro;yeast 2-hybrid12370286 No
    SLC4A1 in vitro;in vivo;yeast 2-hybrid15811326 No
    EGR1 in vitro19057511 No


    Involved FDA drugs

    There was no drug associated with CDKN2A