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.

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  • 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.

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  • 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: MIF

    Description: macrophage migration inhibitory factor (glycosylation-inhibiting factor)

    Entrez Gene ID: 4282

    SwissProt Acc Number: P14174

    RefSeq: NM_002415

    It was suspected to be CHD related:

    .."Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine which can inhibit the random migration of macrophages and concentrate macrophages at the inflammatory site, and is thought to play an important role in cell mediated immunity."..

    From PMID: 17029206, in Journal Zhonghua Yi Xue Yi Chuan Xue Za Zhi , 2006


    References

    There were 17 potential papers with MIF and CHD.

    PMIDTitleJournalsDetails
    23707455 Assessment of macrophage migration inhibitory factor in humans: protocol for accurate and reproducible levels.Free radical biology & medicineMore Details
    23922522 Chlamydia pneumoniae and helicobacter pylori serology - importance in patients with coronary heart disease.Materia socio-medicaMore Details
    22693633 Macrophage migration inhibitory factor is enhanced in acute coronary syndromes and is associated with the inflammatory response.PloS oneMore Details
    21674000 Immunological and cardiometabolic risk factors in the prediction of type 2 diabetes and coronary events: MONICA/KORA Augsburg case-cohort study.PloS oneMore Details
    20934703 High plasma levels of macrophage migration inhibitory factor are associated with adverse long-term outcome in patients with stable coronary artery disease and impaired glucose tolerance or type 2 diabetes mellitus.AtherosclerosisMore Details
    18242614 "Macrophage migration inhibitory factor (MIF) and risk for coronary heart disease: results from the MONICA/KORA Augsburg case-cohort study, 1984-2002."AtherosclerosisMore Details
    18235500 Macrophage migration inhibitory factor stimulates AMP-activated protein kinase in the ischaemic heart.NatureMore Details
    17244850 Exhaustion is associated with low macrophage migration inhibitory factor expression in patients with coronary artery disease.Psychosomatic medicineMore Details
    16846847 Chlamydia pneumoniae and coronary artery disease: controversial results of serological studies.International immunopharmacologyMore Details
    16546716 "Relationship between Chlamydia pneumoniae infection, inflammatory markers, and coronary heart diseases."International immunopharmacologyMore Details
    16527487 A single nucleotide polymorphism of macrophage migration inhibitory factor is related to inflammatory response in coronary bypass surgery using cardiopulmonary bypass.European journal of cardio-thoracic surgery : official journal of the EuropeanMore Details
    15550518 Haptoglobin expression and activity during coronary collateralization.American journal of physiology. Heart and circulatory physiologyMore Details
    15893396 Low prevalence of antibodies against heat shock protein 10 of Chlamydophila pneumoniae in patients with coronary heart disease.Journal of microbiological methodsMore Details
    15325761 Evaluation and optimization of ELISA for detection of anti-Chlamydophila pneumoniae IgG and IgA in patients with coronary heart diseases.Journal of microbiological methodsMore Details
    15136506 Chronic hyperglycemia attenuates coronary collateral development and impairs proliferative properties of myocardial interstitial fluid by production of angiostatin.CirculationMore Details
    12851610 Neopterin levels in patients with coronary artery disease are independent of Chlamydia pneumoniae seropositivity.American heart journalMore Details
    12881477 Migration inhibitory factor mediates angiogenesis via mitogen-activated protein kinase and phosphatidylinositol kinase.Circulation researchMore Details

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



    PPI interactions

    There were totally 18 unique genes interacted with MIF. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GORASP2 Two-hybrid16189514|16189514 No
    COPS5 Affinity Capture-Western11089976|11089976|15757663|15757663|15757663|15757663 No
    STUB1 Affinity Capture-Western22271573 No
    HSP90AA1 Affinity Capture-Western22271573 CHD related
    TP53 Affinity Capture-Western18815136|18815136 CHD related
    MIF in vitro10353846,11170644,11997397,8610159 CHD related
    STRN4 yeast 2-hybrid16169070 No
    FIBP Affinity Capture-MS17353931 No
    CD74 Reconstituted Complex12782713|12782713 No
    BNIPL Two-hybrid12681488|12681488|12681488|12681488 No
    VHL Affinity Capture-MS21942715 No
    UBC Affinity Capture-MS21139048|21890473|21906983|22053931|22505724 No
    CDK2 Affinity Capture-MS21319273 No
    NME1 Affinity Capture-Western18815136 No
    IGBP1 Co-fractionation22939629 No
    CLNS1A Co-fractionation22939629 No
    COPS6 in vivo15757663 No
    ZNF408 yeast 2-hybrid15231747 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB01880"3,4-Dihydroxycinnamic Acid"
    experimentalDB027287-Hydroxy-2-Oxo-Chromene-3-Carboxylic Acid Ethyl Ester
    experimentalDB04272Citric AcidA09AB04
    experimentalDB077183-(4-HYDROXY-PHENYL)PYRUVIC ACID
    experimentalDB07888"3-(4-HYDROXYPHENYL)-4,5-DIHYDRO-5-ISOXAZOLE-ACETIC ACID METHYL ESTER"
    experimentalDB083334-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME
    experimentalDB083343-FLUORO-4-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME
    experimentalDB08335"4-HYDROXYBENZALDEHYDE O-(3,3-DIMETHYLBUTANOYL)OXIME"
    experimentalDB08765"6-HYDROXY-1,3-BENZOTHIAZOLE-2-SULFONAMIDE"