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: ALOX12

    Description: arachidonate 12-lipoxygenase

    Entrez Gene ID: 239

    SwissProt Acc Number: P18054

    RefSeq: NM_000697

    It was suspected to be CHD related:

    .."Polymorphisms within ALOX12, ALOX5, and ALOX5AP are genetically associated with subclinical atherosclerosis and with biomarkers of disease in families with type 2 diabetes."..

    From PMID: 20592751, in Journal Mediators Inflamm , 2010


    References

    There were 2 potential papers with ALOX12 and CHD.

    PMIDTitleJournalsDetails
    20592751 Human lipoxygenase pathway gene variation and association with markers of subclinical atherosclerosis in the diabetes heart study.Mediators of inflammationMore Details
    19046748 "Variation in eicosanoid genes, non-fatal myocardial infarction and ischemic stroke."AtherosclerosisMore Details

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



    PPI interactions

    There were totally 7 unique genes interacted with ALOX12. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    LMNA Two-hybrid10727209|10727209|10727209 CHD related
    ITGB4 Two-hybrid10727209|10727209 No
    TRIB1 Two-hybrid10727209|10727209 CHD related
    KRT5 Two-hybrid10727209|10727209|10727209 No
    PLA2G2A in vivo15474031 CHD related
    KAT5 in vivo15474031 No
    KRT85 yeast 2-hybrid10727209 No


    Involved FDA drugs

    There was no drug associated with ALOX12