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: PTN

    Description: pleiotrophin

    Entrez Gene ID: 5764

    SwissProt Acc Number: P21246

    RefSeq: NM_002825

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

    ..We have recently demonstrated the effective use of Pleiotrophin (PTN) as a therapeutic agent for treatment of ischemic myocardium...

    From PMID: 15451633, in Journal Biomaterials. , 2005


    References

    There were 2 potential papers with PTN and CHD.

    PMIDTitleJournalsDetails
    24267260 Quantitative and qualitative pleiotropic differences between Simvastatin single and Vytorin combination therapy in hypercholesterolemic subjects.AtherosclerosisMore Details
    15451633 Enhanced neovasculature formation in ischemic myocardium following delivery of pleiotrophin plasmid in a biopolymer.BiomaterialsMore Details

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



    PPI interactions

    There were totally 95 unique genes interacted with PTN. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CHD3 Two-hybrid16169070 No
    PTPRZ1 Affinity Capture-Western10706604 No
    CTNNB1 Affinity Capture-Western10706604 CHD related
    SDC1 Reconstituted Complex8175719 CHD related
    GADD45G Two-hybrid15383276 No
    FEZ1 Two-hybrid15383276 No
    PTN Two-hybrid15383276|10600521,15383276 CHD related
    PIAS4 Two-hybrid15383276 No
    GPRASP2 Two-hybrid15383276 No
    C8orf30A yeast 2-hybrid16169070 No
    SPIN1 yeast 2-hybrid16169070 No
    ACTB in vivo9739080 No
    APOBEC3G Two-hybrid16169070 No
    CGA Two-hybrid16169070|16169070 No
    DFNA5 Two-hybrid16169070|16169070 No
    HSPBAP1 Two-hybrid16169070 No
    TAF1D Two-hybrid16169070|21900206 No
    MKKS Two-hybrid16169070 No
    PLXNB2 Two-hybrid16169070 No
    SUPT7L Two-hybrid16169070 No
    WFDC2 Two-hybrid16169070 No
    ATRX Two-hybrid16169070|16169070 No
    BMI1 Two-hybrid16169070|16169070 No
    BTBD2 Two-hybrid16169070 No
    C9orf82 Two-hybrid16169070 No
    CACNB4 Two-hybrid16169070|16169070 No
    CDH10 Two-hybrid16169070|16169070 No
    CDK5RAP2 Two-hybrid16169070 No
    COX6C Two-hybrid16169070|16169070 No
    DUSP12 Two-hybrid16169070 No
    FAM176A Two-hybrid16169070 No
    FTL Two-hybrid16169070|16169070 No
    BLOC1S1 Two-hybrid16169070|16169070 No
    GLYAT Two-hybrid16169070 No
    GTF2F1 Two-hybrid16169070|16169070 No
    ITSN2 Two-hybrid16169070 No
    MLLT3 Two-hybrid16169070|16169070 No
    MYCBP Two-hybrid16169070 No
    NAP1L5 Two-hybrid16169070 No
    CRCT1 Two-hybrid16169070 No
    PMF1 Two-hybrid16169070 No
    PSMB10 Two-hybrid16169070|16169070 No
    RIT1 Two-hybrid16169070 No
    RBM23 Two-hybrid16169070 No
    SNCAIP Two-hybrid16169070 No
    STC2 Two-hybrid16169070 No
    TAC3 Two-hybrid16169070 No
    TBRG4 Two-hybrid16169070 No
    TXNDC9 Two-hybrid16169070 No
    ARL15 Two-hybrid16169070 No
    ATP5C1 Two-hybrid16169070|16169070 No
    CAPZB Two-hybrid16169070 No
    CCDC53 Two-hybrid16169070 No
    CRELD1 Two-hybrid16169070 No
    DNAJB11 Two-hybrid16169070|21900206 No
    EIF3F Two-hybrid16169070 No
    SLC25A36 Two-hybrid16169070 No
    GPD1 Two-hybrid16169070|16169070 No
    GSTP1 Two-hybrid16169070|16169070 No
    LAMA4 Two-hybrid16169070 No
    LUC7L2 Two-hybrid16169070 No
    MAD2L1BP Two-hybrid16169070 No
    P4HB Two-hybrid16169070 No
    UTP3 Two-hybrid16169070 No
    SAT1 Two-hybrid16169070 No
    SSR1 Two-hybrid16169070 No
    TP53BP2 Two-hybrid16169070 No
    ARIH2 Two-hybrid16169070 No
    GIPC2 Two-hybrid16169070 No
    GNB2L1 Two-hybrid16169070 No
    FAM203A Two-hybrid16169070 No
    PPP2CA Two-hybrid16169070 CHD related
    PSMD11 Two-hybrid16169070 No
    PTPRS Two-hybrid16169070 No
    RPLP1 Two-hybrid16169070 No
    SGSM2 Two-hybrid16169070 No
    TOMM20 Two-hybrid16169070 No
    UBQLN4 Two-hybrid16169070|16713569 No
    PSMD2 Two-hybrid16169070 No
    SGTA Two-hybrid16169070 No
    BCCIP Two-hybrid16169070 No
    ALK Reconstituted Complex11278720 No
    NUDT21 Two-hybrid21900206 No
    GSK3B Two-hybrid21900206 CHD related
    MRPL44 Two-hybrid21900206 No
    C7orf25 Two-hybrid21900206 No
    BCL2L1 Two-hybrid21900206 CHD related
    PFDN1 Two-hybrid21900206 No
    GADD45A Two-hybrid21900206 No
    C11orf58 Two-hybrid21900206 No
    BARD1 Two-hybrid15383276|15383276 No
    KPNB1 Two-hybrid15383276|15383276 No
    CSTA yeast 2-hybrid16169070 No
    SDC3 in vitro8175719 No
    NCAN in vitro9507007 No


    Involved FDA drugs

    There was no drug associated with PTN