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: CYLD

    Description: cylindromatosis (turban tumor syndrome)

    Entrez Gene ID: 1540

    SwissProt Acc Number: Q9NQC7

    RefSeq: NM_001042355

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

    .."our results uncover an unexpected role of CYLD in promoting inflammatory responses in VSMCs via a mechanism involving MAPK activation but independent of NF- B activity,contributing to the pathogenesis of vascular disease."..

    From PMID: 22406061, in Journal Biochem Biophys Res Commun. , 2012


    References

    There were 1 potential papers with CYLD and CHD.

    PMIDTitleJournalsDetails
    22406061 A pro-inflammatory role of deubiquitinating enzyme cylindromatosis (CYLD) in vascular smooth muscle cells.Biochemical and biophysical research communicationsMore Details

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



    PPI interactions

    There were totally 37 unique genes interacted with CYLD. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PLK1 Affinity Capture-MS17495026 No
    CAMK2D Affinity Capture-MS19615732 CHD related
    MYO6 Affinity Capture-MS19615732 No
    MGEA5 Affinity Capture-MS19615732 No
    Cep192 Affinity Capture-MS19615732 No
    SPATA2L Affinity Capture-MS19615732 No
    TRPA1 Affinity Capture-Western16500080 No
    HDAC6 Affinity Capture-Western19893491|19893491|20593489 No
    TRAIP Two-hybrid14676304|14676304|14676304 No
    TRAF6 Biochemical Activity12917691|20622874 No
    DVL1 Affinity Capture-Western20227366 CHD related
    SQSTM1 Affinity Capture-Western19201866 No
    UBE2S Biochemical Activity20622874 No
    TUBA1A Reconstituted Complex18222923|18222923 No
    AURKB Affinity Capture-Western20593489|20593489 No
    TRAF7 in vivo16230348 No
    PPIP5K1 Affinity Capture-Western18636086 No
    TBK1 Affinity Capture-Western18636086 No
    IKBKE Affinity Capture-Western18636086 No
    DDX58 Affinity Capture-Western18636086 No
    MAP3K7 Affinity Capture-Western18332137 No
    RIPK1 Affinity Capture-Western17981138 No
    USP32P2 Affinity Capture-MS19615732 No
    USP13 Affinity Capture-MS19615732 No
    SPATA2 Affinity Capture-MS19615732 No
    PMS2 Affinity Capture-MS17148452 No
    PMS1 Affinity Capture-Western17148452 No
    BCL3 Affinity Capture-Western19893491 No
    IKBKG Two-hybrid12917691|12917690|12917689 No
    TRAF2 Two-hybrid12917691 No
    OPTN Two-hybrid21408173|21408173 No
    DVL3 Affinity Capture-Western20227366 No
    ITCH Affinity Capture-Western22057290|22057290 No
    UBC Affinity Capture-Western17851586|21139048|22505724 No
    HDAC3 Positive Genetic22318606 CHD related
    CLIP3 Affinity Capture-Western22297296 No
    PPP2R4 Affinity Capture-Western20593489|20593489 No


    Involved FDA drugs

    There was no drug associated with CYLD