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: HMGB1

    Description: high-mobility group box 1

    Entrez Gene ID: 3146

    SwissProt Acc Number: P09429

    RefSeq: NM_002128

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

    ..HMGB1 expression by activated vascular smooth muscle cells in advanced human atherosclerosis plaques...

    From PMID: 17502242, in Journal Cardiovasc Pathol. , 2007


    References

    There were 13 potential papers with HMGB1 and CHD.

    PMIDTitleJournalsDetails
    23935732 Correlation between serum high-mobility group box-1 levels and high-sensitivity C-reactive protein and troponin I in patients with coronary artery disease.Experimental and therapeutic medicineMore Details
    23188125 Intramyocardial delivery of HMGB1 by a novel thermosensitive hydrogel attenuates cardiac remodeling and improves cardiac function after myocardial infarction.Journal of cardiovascular pharmacologyMore Details
    22495229 HMGB1 in vascular diseases: Its role in vascular inflammation and atherosclerosis.Autoimmunity reviewsMore Details
    21698364 High mobility group box-1 induces migration of vascular smooth muscle cells via TLR4-dependent PI3K/Akt pathway activation.Molecular biology reportsMore Details
    22179023 2-methoxycinnamaldehyde from Cinnamomum cassia reduces rat myocardial ischemia and reperfusion injury in vivo due to HO-1 induction.Journal of ethnopharmacologyMore Details
    22128087 CD36 overexpression predisposes to arrhythmias but reduces infarct size in spontaneously hypertensive rats: gene expression profile analysis.Physiological genomicsMore Details
    23226786 Atorvastatin reduces serum HMGB1 levels in patients with hyperlipidemia.Experimental and therapeutic medicineMore Details
    23284878 HMGB1 is associated with atherosclerotic plaque composition and burden in patients with stable coronary artery disease.PloS oneMore Details
    19545550 Increased serum HMGB1 is related to the severity of coronary artery stenosis.Clinica chimica acta; international journal of clinical chemistryMore Details
    19150066 Increased serum HMGB1 level is associated with coronary artery disease in nondiabetic and type 2 diabetic patients.AtherosclerosisMore Details
    18824741 Modulated inflammation by injection of high-mobility group box 1 recovers post-infarction chronically failing heart.CirculationMore Details
    17502242 HMGB1 expression by activated vascular smooth muscle cells in advanced human atherosclerosis plaques.Cardiovascular pathology : the official journal of the Society for CardiovascularMore Details
    16721263 Elevated high-mobility group box 1 levels in patients with cerebral and myocardial ischemia."Shock (Augusta, Ga.)"More Details

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



    PPI interactions

    There were totally 86 unique genes interacted with HMGB1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    C14orf1 Two-hybrid16169070|16169070 No
    CRMP1 Two-hybrid16169070 No
    LRIF1 Two-hybrid16169070 No
    UNC119 Two-hybrid16169070|16169070 No
    HOXB1 Reconstituted Complex8890171 No
    HOXB3 Reconstituted Complex8890171 No
    HOXC6 Reconstituted Complex8890171 No
    HOXD3 Reconstituted Complex8890171 No
    HOXD8 Reconstituted Complex8890171 No
    HOXD9 Reconstituted Complex8890171|8890171 No
    HOXD10 Reconstituted Complex8890171 No
    HOXD11 Reconstituted Complex8890171 No
    NCAN Reconstituted Complex9507007 No
    PTPRZ1 Reconstituted Complex9507007 No
    PLAT Co-purification8366113 CHD related
    RAG1 Reconstituted Complex10490593 No
    TP73 Reconstituted Complex11748232 No
    HMGB2 Affinity Capture-Western12517784 No
    PDIA3 Affinity Capture-Western12517784 No
    HSPA8 Affinity Capture-Western12517784 CHD related
    HHV8GK18_gp81 Affinity Capture-Western22379092 No
    XPC Reconstituted Complex19446504|19446504 No
    RAD23B Reconstituted Complex19446504 No
    SSRP1 Co-fractionation22939629 No
    SMARCE1 Co-fractionation22939629 No
    CUX1 in vitro11748221 No
    C1orf103 yeast 2-hybrid16169070 No
    TLR4 in vivo16267105 CHD related
    DNMT1 in vitro11748221 No
    HES1 in vitro11748221 No
    RBPJ in vitro11748221 No
    IRF2 in vitro11748221 No
    RELA Affinity Capture-Western12665595|12665595 CHD related
    NFKB1 Reconstituted Complex12604365|12604365 CHD related
    CSNK1A1 Co-purification12062430|12062430 No
    TP53 Affinity Capture-Western11106654|11106654|11748221|9472015,11106654,11748221 CHD related
    PLG Reconstituted Complex1909331|1909331 No
    POU5F1 Affinity Capture-Western11099378|21151833|11099378 No
    RB1 Reconstituted Complex11748221|11748221 CHD related
    HNRNPK Reconstituted Complex11748221|11748221 No
    MECP2 Reconstituted Complex11748221|11748221 No
    TLE1 Reconstituted Complex11748221|11748221 No
    AES Reconstituted Complex11748221|11748221 No
    TBP Reconstituted Complex9880542|8006019|9880542 No
    GTF2A1 Reconstituted Complex9880542 No
    PGR Reconstituted Complex9671457 No
    NR3C1 Reconstituted Complex9671457 CHD related
    AR Reconstituted Complex9671457|9671457,11748221 CHD related
    UBC Affinity Capture-MS18655026|21139048|21890473|21906983|22505724 No
    CDK1 Biochemical Activity2013279|2013279 CHD related
    CREBBP Biochemical Activity15005629 No
    H3F3A Affinity Capture-MS17403666 No
    Ccdc15 Affinity Capture-MS20360068 No
    DNM2 Two-hybrid21900206 No
    FCP1 Affinity Capture-MS12591939 No
    SUMO2 Affinity Capture-MS19471022 No
    TERF2IP Two-hybrid21044950 No
    TERF2 Two-hybrid21044950 No
    TFAP4 Affinity Capture-MS19505873|19505873 No
    CDK2 Affinity Capture-MS21319273 No
    XPA Affinity Capture-Western19446504 No
    PSEN1 Two-hybrid21163940 No
    PRKCA in vitro10617144 CHD related
    TLR2 in vitro;in vivo16267105 CHD related
    CEBPB in vitro11748221 No
    ZFP36 in vitro11748221 No
    TAF1 in vitro9880542,11748221 No
    TFE3 in vitro11748221 No
    RFX1 in vitro11748221 No
    AGER in vitro9812979 CHD related
    CASP3 in vitro11748221 CHD related
    PRKDC in vitro9722660 No
    TLE2 in vitro11748221 No
    FOXC1 in vitro11748221 CHD related
    ATOH1 in vitro11748221 No
    FOXA3 in vitro11748221 No
    HR in vitro11748221 No
    TGIF1 in vitro11748221 No
    MNT in vitro11748221 No
    CTCF in vitro11748221 No
    SOX18 in vitro11748221 CHD related
    SIX5 in vitro11748221 No
    PPP2R3A in vitro11748221 No
    ERF in vitro11748221 No
    NEUROD6 in vitro11748221 No
    RASSF4 in vitro11748221 No


    Involved FDA drugs

    There was no drug associated with HMGB1