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: CALU

    Description: calumenin

    Entrez Gene ID: 813

    SwissProt Acc Number: O43852

    RefSeq: NM_001130674

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

    ..Our results suggest that CALU A29809G is associated with arterial calcification and short-term prognosis of the outcome of patients with nSTACS...

    From PMID: 20673165, in Journal Ann Med. , 2010


    References

    There were 1 potential papers with CALU and CHD.

    PMIDTitleJournalsDetails
    20673165 CALU A29809G polymorphism in coronary atherothrombosis: Implications for coronary calcification and prognosis.Annals of medicineMore Details

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



    PPI interactions

    There were totally 22 unique genes interacted with CALU. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APCS Reconstituted Complex10631319|10631319 No
    GAA Co-fractionation22939629 No
    SARS2 Co-fractionation22939629 No
    C17orf61 Co-fractionation22939629 No
    FAF2 Co-fractionation22939629 No
    PTBP3 Co-fractionation22939629 No
    DBN1 Co-fractionation22939629 No
    KIAA0090 Co-fractionation22939629 No
    ICT1 Co-fractionation22939629 No
    TMEM165 Co-fractionation22939629 No
    RPL32 Co-fractionation22939629 No
    PRPH Co-fractionation22939629 No
    PPT2 Co-fractionation22939629 No
    EGFR Co-fractionation22939629 CHD related
    RPL21 Co-fractionation22939629 No
    IARS2 Co-fractionation22939629 No
    PRKCDBP Co-fractionation22939629 No
    Trim28 Affinity Capture-MS20360068 No
    AURKA Affinity Capture-MS20360068 No
    Mad2l2 Affinity Capture-MS20360068 No
    Mis12 Affinity Capture-MS20360068 No
    UBC Affinity Capture-MS21139048|21890473|21906983 No


    Involved FDA drugs

    There was no drug associated with CALU