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: MT2A

    Description: metallothionein 2A

    Entrez Gene ID: 4502

    SwissProt Acc Number: P02795

    RefSeq: NM_005953

    It was suspected to be CHD related:

    .."risk, Novel -209A/G MT2A Polymorphism in Old Patients with Type 2 Diabetes and Atherosclerosis: Relationship with Inflammation (IL-6) and Zinc"..

    From PMID: 16518702, in Journal Biogerontology.? , 2005


    References

    There were 1 potential papers with MT2A and CHD.

    PMIDTitleJournalsDetails
    17098305 "CD14 C (-260)T polymorphism, atherosclerosis, elderly: role of cytokines and metallothioneins."International journal of cardiologyMore Details

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



    PPI interactions

    There were totally 7 unique genes interacted with MT2A. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    PRKD1 Two-hybrid14550308|14550308|14550308 No
    SPINK7 Two-hybrid12970870|12646258|12646258|12646258|12646258,12970870 No
    USP25 Two-hybrid16501887 No
    NEDD4L Two-hybrid19664597|19664597 No
    SHBG Two-hybrid15862967 CHD related
    ADAMTS4 yeast 2-hybrid16099106 CHD related
    CXorf40A in vivo;yeast 2-hybrid15541360 No


    Involved FDA drugs

    There was no drug associated with MT2A