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: APOA2

    Description: apolipoprotein A-II

    Entrez Gene ID: 336

    SwissProt Acc Number: P02652

    RefSeq: NM_001643

    It was suspected to be CHD related:

    .."After adjustment for multiple testing within each gene, single-nucleotide polymorphisms (SNP) significantly associated with case status were identified in the genes encoding LIPC (rs4775065, P <0.0001); CETP (rs5882, P = 0.0002); RXRA (rs11185660, P = 0.0021); ABCA1(rs2249891, P = 0.0126); ABCC6 (rs150468, P = 0.0206; rs212077, P = 0.0443); CUBN (rs7893395, P = 0.0246); APOA2 (rs3813627, P = 0.0324); SELP (rs732314, P =0.0376); and APOC4 (rs10413089, P = 0.0425)."..

    From PMID: 20855565, in Journal J Lipid Res. , 2010


    References

    There were 4 potential papers with APOA2 and CHD.

    PMIDTitleJournalsDetails
    22498810 Using bioinformatics and systems genetics to dissect HDL-cholesterol genetics in an MRL/MpJ x SM/J intercross.Journal of lipid researchMore Details
    20855565 Common genetic variation in multiple metabolic pathways influences susceptibility to low HDL-cholesterol and coronary heart disease.Journal of lipid researchMore Details
    20667078 Novel proteins associated with risk for coronary heart disease or stroke among postmenopausal women identified by in-depth plasma proteome profiling.Genome medicineMore Details
    19878569 Candidate genetic analysis of plasma high-density lipoprotein-cholesterol and severity of coronary atherosclerosis.BMC medical geneticsMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with APOA2. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    APOA2 in vitro12269810 CHD related
    APOD Co-purification7918467|7918467 No
    APOF Co-purification6816269|6816269 No
    PLTP Reconstituted Complex9469594|9469594 CHD related
    SCARB1 Reconstituted Complex10764676 CHD related
    ABCA13 Reconstituted Complex11162594 No
    APOC1 in vitro6789904 CHD related
    C4A in vitro;in vivo7518568 No
    APOA1BP in vitro11991719 No


    Involved FDA drugs

    There was no drug associated with APOA2