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: PDE4D

    Description: "phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila)"

    Entrez Gene ID: 5144

    SwissProt Acc Number: Q08499

    RefSeq: NM_001104631

    It was suspected to be CHD related:

    ..Previous reports have shown ambiguous findings regarding the possible associations between ischaemic stroke (IS) and single nucleotide polymorphisms (SNPs) in the phosphodiesterase 4D (PDE4D) gene region. No effect from rs12188950 on IS was found from either our pooled multi-centre data or the performed meta-analysis. ..

    From PMID: 22274584, in Journal Eur J Hum Genet. , 2012


    References

    There were 4 potential papers with PDE4D and CHD.

    PMIDTitleJournalsDetails
    23852788 PDE4D gene polymorphisms and coronary heart disease: a case-control study in a north Indian population.Journal of clinical laboratory analysisMore Details
    22388798 Gene panels to help identify subgroups at high and low risk of coronary heart disease among those randomized to antihypertensive treatment: the GenHAT study.Pharmacogenetics and genomicsMore Details
    22274584 A large-sample assessment of possible association between ischaemic stroke and rs12188950 in the PDE4D gene.European journal of human genetics : EJHGMore Details
    18157711 Association between inflammatory gene polymorphisms and coronary artery disease in an Indian population.Journal of thrombosis and thrombolysisMore Details

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



    PPI interactions

    There were totally 20 unique genes interacted with PDE4D. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PDE4D Reconstituted Complex12387865|12387865 CHD related
    AKAP6 Affinity Capture-Western11296225 No
    GNB2L1 Two-hybrid10329691|19372219|10329691,11516626 No
    UBC Affinity Capture-Western19372219|20647544 No
    PAFAH1B1 Affinity Capture-Western21652625 No
    APP Reconstituted Complex21832049 No
    PDE4DIP Two-hybrid11134006|11134006|11134006 No
    Bub1 Affinity Capture-MS20360068 No
    ARRB1 Affinity Capture-Western19372219 No
    MDM2 Affinity Capture-Western19372219|19372219 CHD related
    SUMO2 Affinity Capture-MS19471022 No
    ITSN1 PCA22558309|22558309 No
    ARRB2 Affinity Capture-MS17620599 No
    PPP3CA Affinity Capture-Western20647544 CHD related
    PPP3CB Affinity Capture-Western20647544 CHD related
    PPP3R1 Affinity Capture-Western20647544 CHD related
    GSK3B Biochemical Activity20647544 CHD related
    CSNK1A1 Biochemical Activity20647544 No
    CDK2 Affinity Capture-MS21319273 No
    PRKACA Biochemical Activity9639573|8663227 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00131Adenosine monophosphate"For nutritional supplementation, also for treating dietary shortage or imbalance"
    approvedDB00651DyphyllineFor relief of acute bronchial asthma and for reversible bronchospasm associated with chronic bronchitis and emphysema.R03DA01
    approvedDB00920KetotifenIndicated as an add-on or prophylactic oral medication in the chronic treatment of mild atopic asthmatic children. Also used as self-medication for the temporary relief of itching of the eye due to allergic conjunctivitis (ophthalmic).R06AX17;S01GX08
    approvedDB01088IloprostUsed for the treatment of pulmonary arterial hypertension.B01AC11
    experimentalDB01791Piclamilast
    experimentalDB019544-[3-(Cyclopentyloxy)-4-Methoxyphenyl]-2-Pyrrolidinone
    experimentalDB01959"3,5-Dimethyl-1-(3-Nitrophenyl)-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester"
    experimentalDB02676"2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol"
    experimentalDB029186-(4-Difluoromethoxy-3-Methoxy-Phenyl)-2h-Pyridazin-3-One
    experimentalDB03183"1-(4-Aminophenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester"
    experimentalDB03606(S)-Rolipram
    experimentalDB03849Cis-4-Cyano-4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]Cyclohexanecarboxylic Acid
    experimentalDB04149(R)-Rolipram
    experimentalDB04271"3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester"
    experimentalDB04469"1-(4-Methoxyphenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester"
    approvedDB05266Ibudilast"For the treatment of multiple sclerosis, asthma, and cerebrovascular disease."R03DC04
    experimentalDB06842(4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one
    experimentalDB07051"3,5-DIMETHYL-1-PHENYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER"
    experimentalDB079543-ISOBUTYL-1-METHYLXANTHINE
    experimentalDB08299"4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid"