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: BRCC3

    Description: "BRCA1/BRCA2-containing complex, subunit 3"

    Entrez Gene ID: 79184

    SwissProt Acc Number: P46736

    RefSeq: NM_001018055

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

    .."altogether,these data strongly suggest that BRCC3, a deubiquitinating enzyme that is part of the cellular BRCA1 and BRISC complexes, is an important player in angiogenesis and that BRCC3 loss-of-function mutations are associated with moyamoya angiopathy."..

    From PMID: 21596366, in Journal Am J Hum Genet , 2011


    References

    There were 1 potential papers with BRCC3 and CHD.

    PMIDTitleJournalsDetails
    21596366 Loss of BRCC3 deubiquitinating enzyme leads to abnormal angiogenesis and is associated with syndromic moyamoya.American journal of human geneticsMore Details

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



    PPI interactions

    There were totally 28 unique genes interacted with BRCC3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    BARD1 Affinity Capture-MS14636569|14636569|17664283 No
    BRCA1 Affinity Capture-MS14636569|14636569|14636569|17664283 CHD related
    RAD51 Affinity Capture-MS14636569|14636569|14636569 No
    TP53 Affinity Capture-Western14636569|14636569|14636569 CHD related
    UBE2D1 Reconstituted Complex14636569 No
    ATP5O Affinity Capture-MS19615732 No
    DDOST Affinity Capture-MS19615732 No
    E2F5 Affinity Capture-MS19615732 No
    MCM2 Affinity Capture-MS19615732 No
    NDUFA10 Affinity Capture-MS19615732 No
    SHMT2 Affinity Capture-MS19615732 No
    SUPT16H Affinity Capture-MS19615732 No
    FAM175B Affinity Capture-MS19615732|20032457|21282113 No
    BABAM1 Affinity Capture-MS19615732|19261749|20032457|21282113|19261748 No
    CAND1 Affinity Capture-MS19615732 No
    FAM175A Affinity Capture-MS19615732|18077395|19261749|21282113|20656689|19261748|19261748 No
    EXOC8 Affinity Capture-MS19615732 No
    BACH1 Affinity Capture-Western17664283 No
    BRCC3 Affinity Capture-Western21282113 CHD related
    SNAPC5 Two-hybrid16189514 No
    BRE Affinity Capture-MS17353931|19615732|19261749|19261746|21282113|20656689|19261748|19261748 No
    BRCA2 Co-purification14636569|14636569|14636569 No
    UIMC1 Affinity Capture-MS17525341|19615732|18077395|19261749|19261746|19261748|19261748|19261748|19305427|19015238 No
    USP7 Affinity Capture-MS19615732 No
    COPS5 Affinity Capture-Western19214193 No
    UBC Reconstituted Complex19261749|21987572|21963094|21139048|21890473|21906983|20656690|22505724 No
    SUMO2 Reconstituted Complex22689573 No
    GRB2 Affinity Capture-MS19380743 CHD related


    Involved FDA drugs

    There was no drug associated with BRCC3