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: LAMA3

    Description: "laminin, alpha 3"

    Entrez Gene ID: 3909

    SwissProt Acc Number: Q16787

    RefSeq: NM_000227

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

    .."An initial screen by the chi-square test revealed that the A-->G polymorphism of SEMA3F (rs12632110), the C-->T polymorphism of CLEC16A (rs9925481), the A-->G polymorphism of LAMA3 (rs12373237), and the C-->G polymorphism of PCSK2 (rs6080699) were significantly (false discovery rate for allele frequencies of <0.05) associated with MI."..

    From PMID: 20036365, in Journal Atherosclerosis , 2010


    References

    There were 1 potential papers with LAMA3 and CHD.

    PMIDTitleJournalsDetails
    20036365 "Association of genetic variants in SEMA3F, CLEC16A, LAMA3, and PCSK2 with myocardial infarction in Japanese individuals."AtherosclerosisMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with LAMA3. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    SDC2 Affinity Capture-Western11373281|11373281|11373281 No
    PLG in vitro10956663 No
    PLAT in vitro10956663 CHD related
    BMP1 in vitro;in vivo10806203 No
    SLC35E1 yeast 2-hybrid16169070 No
    LAMB3 in vitro7775432 No
    P2rx7 Affinity Capture-MS11707406|11707406 No
    APC Two-hybrid20936779 No
    SIRT1 Affinity Capture-MS19343720 CHD related


    Involved FDA drugs

    There was no drug associated with LAMA3