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: ABCG2

    Description: "ATP-binding cassette, sub-family G (WHITE), member 2"

    Entrez Gene ID: 9429

    SwissProt Acc Number: Q9UNQ0

    RefSeq: NM_004827

    It was suspected to be CHD related:

    ..The Val12Met SNP in ABCG2 (encoding a transporter of sterols and xenobiotics) was associated with incident ischemic stroke in white and black participants of CHS...

    From PMID: 19023099, in Journal Stroke , 2009


    References

    There were 5 potential papers with ABCG2 and CHD.

    PMIDTitleJournalsDetails
    21425956 Impact of SLCO1B1 (OATP1B1) and ABCG2 (BCRP) genetic polymorphisms and inhibition on LDL-C lowering and myopathy of statins.Xenobiotica; the fate of foreign compounds in biological systemsMore Details
    20884846 Multiple genetic loci influence serum urate levels and their relationship with gout and cardiovascular disease risk factors.Circulation. Cardiovascular geneticsMore Details
    19023099 Gene variants associated with ischemic stroke: the cardiovascular health study.Stroke; a journal of cerebral circulationMore Details
    19890391 "Common polymorphisms influencing serum uric acid levels contribute to susceptibility to gout, but not to coronary artery disease."PloS oneMore Details
    17569884 A polymorphism in the protease-like domain of apolipoprotein(a) is associated with severe coronary artery disease."Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 3 unique genes interacted with ABCG2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    UBC Affinity Capture-Western19909340 No
    Trim69 Affinity Capture-MS20360068 No
    HDAC1 Negative Genetic22318606 CHD related


    Involved FDA drugs

    There was no drug associated with ABCG2