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: CDKN2B

    Description: "cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)"

    Entrez Gene ID: 1030

    SwissProt Acc Number: P42772

    RefSeq: NM_004936

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

    ..provide further support for the hypothesis that complex regulatory variation affecting ANRIL and CDKN2B gene expression may contribute to increased risk for clinically apparent and subclinical coronary artery disease and aortic disease...

    From PMID: 23315372, in Journal Circulation. , 2013


    References

    There were 25 potential papers with CDKN2B 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
    23162013 Loss of CDKN2B promotes p53-dependent smooth muscle cell apoptosis and aneurysm formation."Arteriosclerosis, thrombosis, and vascular biology"More 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
    22199011 Association between chromosome 9p21 variants and the ankle-brachial index identified by a meta-analysis of 21 genome-wide association studies.Circulation. Cardiovascular geneticsMore 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
    21270820 A common variant in the CDKN2B gene on chromosome 9p21 protects against coronary artery disease in Americans of African ancestry.Journal of human geneticsMore 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
    19592466 Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus."Arteriosclerosis, thrombosis, and vascular biology"More 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 9 unique genes interacted with CDKN2B. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    MAGEA11 Two-hybrid16189514 No
    IKBKAP Two-hybrid16169070|16169070 No
    CCDC90B Two-hybrid16169070|16169070 No
    KIAA1377 Two-hybrid16169070|16169070 No
    APP Reconstituted Complex21832049 No
    CDK4 Two-hybrid16189514|16169070|21900206 CHD related
    ARPC3 Two-hybrid16169070 No
    CDK8 in vitro12007796 No
    ZBTB17 in vitro;in vivo11283613 No


    Involved FDA drugs

    There was no drug associated with CDKN2B