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.

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  • 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.

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  • 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: CD209

    Description: CD209 molecule

    Entrez Gene ID: 30835

    SwissProt Acc Number: Q9NNX6

    RefSeq: NM_001144893

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

    ..CD209 positivity early after HTx was an independent marker for coronary endothelial dysfunction during follow-up...

    From PMID: 18374874, in Journal JHeartLung Transplant. , 2008


    References

    There were 2 potential papers with CD209 and CHD.

    PMIDTitleJournalsDetails
    22629172 DC-SIGN (CD209) promoter -336 A/G (rs4804803) polymorphism associated with susceptibility of Kawasaki disease.TheScientificWorldJournalMore Details
    18374874 Graft-infiltrating dendritic cells and coronary endothelial dysfunction after human heart transplantation.The Journal of heart and lung transplantation : the official publication of theMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with CD209. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CD209 Co-crystal Structure11739956|11384997|11739956,11384997 CHD related
    CLEC4M Reconstituted Complex11384997|11384997 No
    LGALS3BP Affinity Capture-MS21515679|21515679 No
    CEACAM5 Affinity Capture-Western21515679 No
    CEACAM1 in vivo16246332 No
    ITGAM in vivo16246332 CHD related
    ICAM2 in vitro11017109 No
    ICAM3 in vitro;in vivo10721994,11017109,11799126 No
    CLU Affinity Capture-Western22013110|22013110 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02944Alpha-D-Mannose