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: LMNA

    Description: lamin A/C

    Entrez Gene ID: 4000

    SwissProt Acc Number: P02545

    RefSeq: NM_005572

    It was suspected to be CHD related:

    .."Rare?LMNA?mutations that underlie FPLD with insulin resistance and hyperinsulinemia are also associated with early CHD, notably in women."..

    From PMID: 11342468, in Journal Circulation. , 2001


    References

    There were 11 potential papers with LMNA and CHD.

    PMIDTitleJournalsDetails
    23846499 Lipodystrophy-linked LMNA p.R482W mutation induces clinical early atherosclerosis and in vitro endothelial dysfunction."Arteriosclerosis, thrombosis, and vascular biology"More Details
    23372767 Identification of temporal and region-specific myocardial gene expression patterns in response to infarction in swine.PloS oneMore Details
    23213444 Naive adult stem cells from patients with Hutchinson-Gilford progeria syndrome express low levels of progerin in vivo.Biology openMore Details
    22065502 "Coronary artery disease in a Werner syndrome-like form of progeria characterized by low levels of progerin, a splice variant of lamin A."American journal of medical genetics. Part AMore Details
    18339564 Progeria caused by a rare LMNA mutation p.S143F associated with mild myopathy and atrial fibrillation.European journal of paediatric neurology : EJPN : official journal of theMore Details
    18060063 The mutant form of lamin A that causes Hutchinson-Gilford progeria is a biomarker of cellular aging in human skin.PloS oneMore Details
    16386954 Genetic and phenotypic analysis of dilated cardiomyopathy with conduction system disease: demand for strategies in the management of presymptomatic lamin A/C mutant carriers.European journal of heart failureMore Details
    16117820 Association of LMNA 1908C/T polymorphism with cerebral vascular disease and diabetic nephropathy in Japanese men with type 2 diabetes.Clinical endocrinologyMore Details
    16262891 Aging syndrome genes and premature coronary artery disease.BMC medical geneticsMore Details
    16208517 Correction of cellular phenotypes of Hutchinson-Gilford Progeria cells by RNA interference.Human geneticsMore Details
    12768443 LMNA is mutated in Hutchinson-Gilford progeria (MIM 176670) but not in Wiedemann-Rautenstrauch progeroid syndrome (MIM 264090).Journal of human geneticsMore Details

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



    PPI interactions

    There were totally 68 unique genes interacted with LMNA. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    LMNB1 Two-hybrid11792809|21346760 No
    SREBF1 Two-hybrid11929849|11929849|11929849 No
    NARF Two-hybrid10514485 No
    KAT5 Two-hybrid16169070 No
    ZNF239 Two-hybrid12409453|12409453 No
    SYNE1 Affinity Capture-Western11801724 No
    RB1 Reconstituted Complex8278403 CHD related
    TOR1AIP1 Reconstituted Complex8324822 No
    RBBP4 Two-hybrid19734887|19734887 No
    CTNNB1 Affinity Capture-Western15355978 CHD related
    PRKDC Affinity Capture-Western21346760 No
    DBNL Two-hybrid17306257 No
    SH3KBP1 Two-hybrid17306257 No
    VAV1 Two-hybrid17306257 No
    LMNA Two-hybrid16248985|16248985|11792809 CHD related
    SF3B3 Co-fractionation22939629 No
    WDR18 Co-fractionation22939629 No
    PMS2 Co-fractionation22939629 No
    NONO Co-fractionation22939629 No
    SMAD3 in vitro15527767 CHD related
    ACTB in vitro9563518 No
    EMD Two-hybrid12755701|12755701|12670476|11173535|17620012|10673356,11173535 No
    TMPO Affinity Capture-Western12475961|10984438|10984438|10984438|19727227|10984438,12475961 No
    ALOX12 Two-hybrid10727209|10727209|10727209 CHD related
    PRKCA Protein-peptide12112001|12112001,7925482,8477740 CHD related
    TOR1A Reconstituted Complex8324822 No
    FYCO1 Affinity Capture-MS20562859 No
    BANF1 Affinity Capture-MS19759913 No
    ING1 Affinity Capture-Western18836436 No
    SRRM1 Affinity Capture-MS16159877 No
    SRRM2 Affinity Capture-MS16159877 No
    MORF4L1 Affinity Capture-MS17573780 No
    MORF4L2 Affinity Capture-MS17573780 No
    C20orf20 Affinity Capture-MS17573780 No
    H2AFX Affinity Capture-MS20000738 No
    MYC Affinity Capture-MS17314511 CHD related
    UCHL5 Reconstituted Complex21800051 No
    YWHAQ Affinity Capture-MS20618440|15161933 No
    MME Affinity Capture-MS17342744 No
    CTCF Affinity Capture-MS14759373 No
    UBC Reconstituted Complex19850743|22178446|21987572|21963094|21139048|21890473|21906983|21853274|22505724 No
    SUMO1 Affinity Capture-MS19596686|19596686|21098080 No
    SVIL Two-hybrid20309963|20309963 No
    KIAA0101 Affinity Capture-MS21628590 No
    SUMO2 Affinity Capture-MS21693764|19471022 No
    SUMO4 Affinity Capture-MS16236267|16236267 CHD related
    STAC Two-hybrid18654987 No
    SIRT7 Affinity Capture-MS22586326 No
    ISG15 Affinity Capture-MS16009940 No
    PPP1CC Affinity Capture-MS17683050 No
    CDK2 Affinity Capture-MS21319273 No
    PCBP1 Two-hybrid16248985|16248985|19727227 No
    EGF Two-hybrid16248985 CHD related
    GFM1 Two-hybrid16248985|16248985 No
    UBE2I Two-hybrid16248985|16248985 No
    PCGF2 Two-hybrid16248985|16248985 No
    MRPS26 Two-hybrid16248985 No
    FLNA Two-hybrid16248985 No
    UNC13D Two-hybrid16248985 No
    HNRNPM Co-fractionation22939629 No
    SLC25A6 Co-fractionation22939629 No
    SLC25A5 Co-fractionation22939629 No
    CDK1 in vitro;in vivo7925482,2344612 CHD related
    FOS in vitro;in vivo;yeast 2-hybrid16452503 CHD related
    CASP1 in vitro;in vivo8978814,11953316 CHD related
    CASP6 in vitro;in vivo8978814,11953316 No
    ALOX12B in vitro;in vivo;yeast 2-hybrid10727209 No
    URB2 in vitro15265697 No


    Involved FDA drugs

    There was no drug associated with LMNA