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: ODC1

    Description: ornithine decarboxylase 1

    Entrez Gene ID: 4953

    SwissProt Acc Number: P11926

    RefSeq: NM_002539

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

    .."In conclusion, these results show that patients at an early stage of CRF have a specific gene expression profile of aortic tissue and suggest that genes implicated in collagen fibrillogenesis, and VSMCs migration and proliferation, particularly LUM and ODC1, may play a role."..

    From PMID: 18327085, in Journal J Hypertens , 2008


    References

    There were 1 potential papers with ODC1 and CHD.

    PMIDTitleJournalsDetails
    18327085 Accelerated arterial stiffening and gene expression profile of the aorta in patients with coronary artery disease.Journal of hypertensionMore Details

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



    PPI interactions

    There were totally 9 unique genes interacted with ODC1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    ODC1 Co-crystal Structure10623504|10623504 CHD related
    AZI1 Reconstituted Complex12359729|18062773 No
    AZI2 Reconstituted Complex12359729 No
    UBC Affinity Capture-Western18062773 No
    OAZ3 Affinity Capture-Western18062773 No
    CSNK2B Two-hybrid21900206 No
    TK1 Two-hybrid21900206 No
    OAZ1 in vitro12359729,8185631 No
    OAZ2 in vitro12359729 No


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    nutraceuticalDB00114Pyridoxal PhosphateFor nutritional supplementation and for treating dietary shortage or imbalance.A11HA02;A11HA06
    approved;nutraceuticalDB00127Spermine"For nutritional supplementation, also for treating dietary shortage or imbalance"
    experimentalDB01917Putrescine
    experimentalDB02209Pyridoxine-5'-Phosphate
    experimentalDB02824N-Pyridoxyl-Glycine-5-Monophosphate
    experimentalDB03856Alpha-Difluoromethylornithine
    experimentalDB04083N'-Pyridoxyl-Lysine-5'-Monophosphate
    experimentalDB04263G418