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: FABP4

    Description: "fatty acid binding protein 4, adipocyte"

    Entrez Gene ID: 2167

    SwissProt Acc Number: P15090

    RefSeq: NM_001442

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

    .."Among CAD patients in the present study, the fasting level of FABP4 positively correlated with MetS and serum levels of FABP4 correlated with a number of MetS criteria.// Serum FABP4 levels increased as the numbers of stenotic coronary artery increased, although these differences were attenuated after adjustment for age and fasting glucose levels."..

    From PMID: 19001529, in Journal Eur J Endocrinol. , 2009


    References

    There were 3 potential papers with FABP4 and CHD.

    PMIDTitleJournalsDetails
    22109668 "The effects of 3-month atorvastatin therapy on arterial inflammation, calcification, abdominal adipose tissue and circulating biomarkers."European journal of nuclear medicine and molecular imagingMore Details
    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
    19001529 The association of serum adipocyte fatty acid-binding protein with coronary artery disease in Korean adults.European journal of endocrinology / European Federation of Endocrine SocietiesMore Details

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



    PPI interactions

    There were totally 13 unique genes interacted with FABP4. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    OSTF1 Affinity Capture-MS17353931 No
    SNCG Affinity Capture-MS17353931 No
    EXT2 Affinity Capture-MS17353931 No
    VIM Two-hybrid16169070|21900206|16169070 CHD related
    ACTB Two-hybrid21900206 No
    CHD3 Two-hybrid21900206 No
    ZBED1 Two-hybrid21900206 No
    PRKCI Two-hybrid21900206 No
    LIPE in vitro;in vivo;yeast 2-hybrid10318917 No
    USP15 Affinity Capture-MS19615732 No
    TNK2 Reconstituted Complex19144635|19144635 No
    ACP1 in vitro1304913 CHD related
    INSR in vitro;in vivo1648089,8463311 No


    Involved FDA drugs

    There was no drug associated with FABP4