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: CTLA4

    Description: cytotoxic T-lymphocyte-associated protein 4

    Entrez Gene ID: 1493

    SwissProt Acc Number: P16410

    RefSeq: NM_001037631

    It was suspected to be CHD related:

    ..In a Polish population the ESR2 A allele is associated with GD with a strength comparable to polymorphisms of PTPN22 and CTLA4 CT60 loci (OR approximately 1.7)..

    From PMID: 17941906, in Journal Clin Endocrinol (Oxf).? , 2008


    References

    There were 2 potential papers with CTLA4 and CHD.

    PMIDTitleJournalsDetails
    23104008 Bayesian refinement of association signals for 14 loci in 3 common diseases.Nature geneticsMore Details
    17941906 Polymorphism of the oestrogen receptor beta gene (ESR2) is associated with susceptibility to Graves' disease.Clinical endocrinologyMore Details

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



    PPI interactions

    There were totally 16 unique genes interacted with CTLA4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CD80 Reconstituted Complex7545666|7545666 CHD related
    CD86 Co-crystal Structure11279501 CHD related
    CTLA4 Co-crystal Structure11279502|11279501 CHD related
    FYN Affinity Capture-Western9712716 No
    LCK Affinity Capture-Western9712716 No
    LYN Affinity Capture-Western9712716 No
    PPP2R5A Affinity Capture-Western11994459|11994459|11994459 No
    AP1M1 Co-crystal Structure9812899 No
    JAK2 Affinity Capture-Western10842319 CHD related
    STAT5A in vivo;yeast 2-hybrid16476059 No
    AP2M1 Co-crystal Structure11583591|9200449,9256472,11583591 No
    ELAVL1 Affinity Capture-RNA19322201 No
    STAT5B in vivo;yeast 2-hybrid16476059 No
    PIK3R1 in vitro;in vivo7807015 CHD related
    PTPN11 in vitro;in vivo8638161 CHD related
    TXK in vitro;in vivo9813138 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02944Alpha-D-Mannose