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: CTDP1

    Description: "CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1"

    Entrez Gene ID: 9150

    SwissProt Acc Number: Q9Y5B0

    RefSeq: NM_004715

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

    .."Vasospastic angina (VA) is a specific type of coronary artery disease and develops as a result of coronary artery spasm. The fold change levels were highest in the CTDP1 (18q23), HDAC10 (22q13.33), KCNQ1 (11p15.5-p15.4), NINJ2 (12p13.33), NOTCH2 (1p12-p11.2), PCSK6 (15q26.3), SDHA (5p15.33), and MUC17 (7q22.1) genes."..

    From PMID: 21860640, in Journal Korean Circ J. , 2011


    References

    There were 1 potential papers with CTDP1 and CHD.

    PMIDTitleJournalsDetails
    21860640 Deoxyribonucleic Acid copy number aberrations in vasospastic angina patients using an array comparative genomic hybridization.Korean circulation journalMore Details

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



    PPI interactions

    There were totally 48 unique genes interacted with CTDP1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    WDR77 Affinity Capture-Western12560496|12560496|12560496|12560496,15670829 No
    HIST1H4A Biochemical Activity15670829 No
    HIST2H2AC Biochemical Activity15670829 No
    INTS1 Reconstituted Complex16239144 No
    INTS3 Reconstituted Complex16239144 No
    INTS6 Reconstituted Complex16239144 No
    INTS7 Reconstituted Complex16239144 No
    INTS8 Reconstituted Complex16239144 No
    MED1 Reconstituted Complex16239144 No
    MED14 Reconstituted Complex16239144 No
    MED23 Reconstituted Complex16239144 No
    MED15 Reconstituted Complex16239144 No
    MED24 Reconstituted Complex16239144 No
    MED16 Reconstituted Complex16239144 No
    MED25 Reconstituted Complex16239144 No
    MED17 Reconstituted Complex16239144 No
    MED26 Reconstituted Complex16239144 No
    MED4 Reconstituted Complex16239144 No
    MED7 Reconstituted Complex16239144 No
    MED6 Reconstituted Complex16239144 No
    MED8 Reconstituted Complex16239144 No
    SNRNP70 in vivo12560496 No
    SNRPB in vivo12560496 No
    E2F1 in vitro14576433 CHD related
    NDRG2 in vivo15670829 No
    POLR2A Co-purification9159119|9159119|9159119|12560496 No
    GTF2F1 Two-hybrid9765293|9765293|9765293 No
    TCEA1 Reconstituted Complex9765293 No
    CHD8 Affinity Capture-Western19255092 No
    POLR2J Affinity Capture-MS17643375|15282305 No
    GTF2F2 Affinity Capture-MS17643375 No
    GTF2B Affinity Capture-MS17643375 No
    POLR2B Reconstituted Complex15670829 No
    STK38 Affinity Capture-Western15670829 No
    ERH Affinity Capture-Western15670829 No
    PRMT5 Affinity Capture-Western15670829 No
    CDK9 Biochemical Activity19914168 No
    CDK8 Biochemical Activity19914168 No
    CDK7 Biochemical Activity19914168 No
    UBC Affinity Capture-MS21906983 No
    PRKDC Biochemical Activity21450944|21450944 No
    SUMO2 Affinity Capture-MS21252943 No
    ELP2 Reconstituted Complex11818576 No
    ELP3 Reconstituted Complex11818576 No
    GRK5 Affinity Capture-MS22952844 CHD related
    CSNK2A1 in vitro;in vivo12591939 CHD related
    CSNK2B in vitro;in vivo12591939 No
    CSNK2A2 in vitro;in vivo12591939 No


    Involved FDA drugs

    There was no drug associated with CTDP1