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: FABP5

    Description: fatty acid binding protein 5 (psoriasis-associated)

    Entrez Gene ID: 2171

    SwissProt Acc Number: Q01469

    RefSeq: NM_001444

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

    ..These findings suggest that FABP4 and FABP5 may represent mediators of and biomarkers for metabolic and cardiovascular disease in type 2 diabetes mellitus...

    From PMID: 20920650, in Journal Am J Cardiol. , 2010


    References

    There were 1 potential papers with FABP5 and CHD.

    PMIDTitleJournalsDetails
    20920650 "Relation of plasma fatty acid binding proteins 4 and 5 with the metabolic syndrome, inflammation and coronary calcium in patients with type-2 diabetes mellitus."The American journal of cardiologyMore Details

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



    PPI interactions

    There were totally 4 unique genes interacted with FABP5. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    STK24 Affinity Capture-MS17353931 No
    S100A7 Affinity Capture-Western12839573|10331666 No
    PPP2R2A Affinity Capture-MS19156129 No
    UBC Affinity Capture-MS21139048|21890473|21906983|22505724 No


    Involved FDA drugs

    There was no drug associated with FABP5