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: LTA4H

    Description: leukotriene A4 hydrolase

    Entrez Gene ID: 4048

    SwissProt Acc Number: P09960

    RefSeq: NM_000895

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

    .."whereas a haplotype of LTA4H (HapK) was associated with CAD in Caucasians (OR = 1.2, 95% CI 1.01-1.4; p = 0.03)"..

    From PMID: 21293878, in Journal Hum Genet. , 2011


    References

    There were 3 potential papers with LTA4H and CHD.

    PMIDTitleJournalsDetails
    21293878 Genetic contribution of the leukotriene pathway to coronary artery disease.Human geneticsMore Details
    19130089 Genetic effects in the leukotriene biosynthesis pathway and association with atherosclerosis.Human geneticsMore Details
    18318662 Genetic variation in the arachidonate 5-lipoxygenase-activating protein (ALOX5AP) is associated with myocardial infarction in the German population."Clinical science (London, England : 1979)"More Details

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



    PPI interactions

    There were totally 13 unique genes interacted with LTA4H. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    TMEM62 Two-hybrid16169070|16169070 No
    SIRT1 Co-fractionation22939629 CHD related
    ZNF593 Co-fractionation22939629 No
    ARPC3 yeast 2-hybrid16169070 No
    GH1 Affinity Capture-MS17353931 CHD related
    MCC Affinity Capture-MS17353931 No
    DDA1 Affinity Capture-MS20562859 No
    UBA5 Affinity Capture-MS20562859 No
    HDAC5 Affinity Capture-MS21081666 No
    UBC Affinity Capture-MS18781797|21987572|21139048|21890473|21906983|22053931|22505724 No
    ELAVL1 Affinity Capture-RNA19322201 No
    SIRT7 Affinity Capture-MS22586326 No
    TINF2 Two-hybrid21044950 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    experimentalDB02062"N-[3-[(1-Aminoethyl)(Hydroxy)Phosphoryl]-2-(1,1'-Biphenyl-4-Ylmethyl)Propanoyl]Alanine"
    experimentalDB023523-(Benzyloxy)Pyridin-2-Amine
    experimentalDB03424Bestatin
    experimentalDB068285-[2-(1H-pyrrol-1-yl)ethoxy]-1H-indole
    experimentalDB06851N-(pyridin-3-ylmethyl)aniline
    experimentalDB06917(4-fluorophenyl)(pyridin-4-yl)methanone
    experimentalDB07094"1-(2,2'-bithiophen-5-yl)methanamine"
    experimentalDB07099N-[4-(benzyloxy)phenyl]glycinamide
    experimentalDB07102(2S)-2-amino-5-oxo-5-[(4-phenylmethoxyphenyl)amino]pentanoic acid
    experimentalDB071044-amino-N-[4-(benzyloxy)phenyl]butanamide
    experimentalDB07196N-methyl-1-(2-thiophen-2-ylphenyl)methanamine
    experimentalDB07237{4-[(2R)-pyrrolidin-2-ylmethoxy]phenyl}(4-thiophen-3-ylphenyl)methanone
    experimentalDB07258(R)-pyridin-4-yl[4-(2-pyrrolidin-1-ylethoxy)phenyl]methanol
    experimentalDB072591-(4-thiophen-2-ylphenyl)methanamine
    experimentalDB07260N-benzyl-4-[(2R)-pyrrolidin-2-ylmethoxy]aniline
    experimentalDB07292"4-(2-amino-1,3-thiazol-4-yl)phenol"
    experimentalDB08040N-[(2R)-2-benzyl-4-(hydroxyamino)-4-oxobutanoyl]-L-alanine
    experimentalDB08466"5-[2-(4-hydroxyphenyl)ethyl]benzene-1,3-diol"