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: HMOX1

    Description: heme oxygenase (decycling) 1

    Entrez Gene ID: 3162

    SwissProt Acc Number: P09601

    RefSeq: NM_002133

    It was suspected to be CHD related:

    ..A (GT)n dinucleotide repeat and a -413A>T single nucleotide polymorphism have been reported in the promoter region of HMOX1 to both influence the occurrence of coronary artery disease and myocardial infarction...

    From PMID: 19389234, in Journal BMC Med Genet , 2009


    References

    There were 5 potential papers with HMOX1 and CHD.

    PMIDTitleJournalsDetails
    22403797 Impact of salt on cardiac differential gene expression and coronary lesion in normotensive mineralocorticoid-treated mice."American journal of physiology. Regulatory, integrative and comparative"More Details
    22780915 A novel multiplex polymerase chain reaction assay for profile analyses of gene expression in peripheral blood.BMC cardiovascular disordersMore Details
    19238116 Common variants of four bilirubin metabolism genes and their association with serum bilirubin and coronary artery disease in Chinese Han population.Pharmacogenetics and genomicsMore Details
    19389234 Genetic variants of the promoter of the heme oxygenase-1 gene and their influence on cardiovascular disease (the Ludwigshafen Risk and Cardiovascular Health study).BMC medical geneticsMore Details
    18505769 Serial analysis of the vascular endothelial transcriptome under static and shear stress conditions.Physiological genomicsMore Details

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



    PPI interactions

    There were totally 12 unique genes interacted with HMOX1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    HMOX1 Co-crystal Structure12500973|12500973 CHD related
    UBC Affinity Capture-Western18544348 No
    UFD1L Affinity Capture-Western18544348 No
    PSMD2 Affinity Capture-Western18544348 No
    POR in vitro12626517 No
    BLVRB in vitro12626517 No
    HMX1 Dosage Rescue21081499 No
    ELAVL1 Affinity Capture-RNA19322201 No
    TERF1 Two-hybrid21044950 No
    POT1 Two-hybrid21044950 No
    AKT1 in vitro;in vivo15581622 CHD related
    NOS1 in vivo11849436 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approved;nutraceuticalDB00157NADH"Some evidence suggests that NADH might be useful in treating Parkinson's disease, chronic fatigue syndrome, Alzheimer's disease and cardiovascular disease."
    experimentalDB01942Formic Acid
    experimentalDB02073Biliverdine Ix Alpha
    experimentalDB0246812-Phenylheme
    experimentalDB03014Heme
    experimentalDB039062-Phenylheme
    experimentalDB04803Verdoheme
    experimentalDB06914"1-({2-[2-(4-CHLOROPHENYL)ETHYL]-1,3-DIOXOLAN-2-YL}METHYL)-1H-IMIDAZOLE"
    experimentalDB073421-(adamantan-1-yl)-2-(1H-imidazol-1-yl)ethanone