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: PPARD

    Description: peroxisome proliferator-activated receptor delta

    Entrez Gene ID: 5467

    SwissProt Acc Number: Q03181

    RefSeq: NM_006238

    It was suspected to be CHD related:

    ..PPARD plays a role in cholesterol metabolism in man...

    From PMID: 14641801, in Journal J Intern Med , 2003


    References

    There were 4 potential papers with PPARD and CHD.

    PMIDTitleJournalsDetails
    23906684 Genetic associations with coronary heart disease: meta-analyses of 12 candidate genetic variants.GeneMore Details
    22277050 Investigation of polymorphic variants of PPARD and APOE genes in Turkish coronary heart disease patients.DNA and cell biologyMore Details
    20512451 "Association of the CYBA, PPARGC1A, PPARG3, and PPARD gene variants with coronary artery disease and metabolic risk factors of coronary atherosclerosis in a Russian population."Heart and vesselsMore Details
    19935834 Genome scan for loci regulating HDL cholesterol levels in Finnish extended pedigrees with early coronary heart disease.European journal of human genetics : EJHGMore Details

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



    PPI interactions

    There were totally 34 unique genes interacted with PPARD. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    HDAC4 Reconstituted Complex12943985 CHD related
    HDAC3 Reconstituted Complex12943985|11867749 CHD related
    NCOR2 Two-hybrid11867749 No
    NCOR1 Two-hybrid11867749|15001550 No
    SPEN Affinity Capture-Western11867749 No
    PPARD Affinity Capture-Western17803688|10198642 CHD related
    SRC Reconstituted Complex16930961|15001550 CHD related
    NCOA2 Reconstituted Complex16930961 No
    EP300 Reconstituted Complex16930961 CHD related
    RELA Affinity Capture-Western18037904 CHD related
    GLUL Two-hybrid15604093 No
    ITGB5 Two-hybrid15604093 No
    PROX1 Two-hybrid15604093|15604093 No
    EIF3I Two-hybrid15604093 No
    RXRA Two-hybrid15604093|15604093 CHD related
    NCOA1 Two-hybrid15604093 No
    PRDX6 Two-hybrid15604093|15604093 No
    SHMT2 Two-hybrid15604093 No
    RANBP9 Two-hybrid15604093|15604093 No
    RXRG Two-hybrid15604093|15604093 No
    NR0B2 Two-hybrid15604093|15604093 No
    RXRB Two-hybrid15604093|15604093 No
    TNP1 Two-hybrid21967852 No
    SMAD9 yeast 2-hybrid15231748 No
    PEBP1 in vitro15001550 CHD related
    NRIP1 in vitro15001550 No
    GADD45G Reconstituted Complex10872826|10872826 No
    Gadd45b Reconstituted Complex10872826 No
    HDAC1 Affinity Capture-Western11867749|11867749 CHD related
    HDAC2 Affinity Capture-Western11867749|11867749 CHD related
    Nedd4 Reconstituted Complex19953087 No
    PSMG1 Affinity Capture-Western18793612 No
    HDAC7 in vitro12970571 No
    DUT in vitro;in vivo8910358 No


    Involved FDA drugs

    There was no drug associated with PPARD