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: NOD1

    Description: nucleotide-binding oligomerization domain containing 1

    Entrez Gene ID: 10392

    SwissProt Acc Number: Q9Y239

    RefSeq: NM_006092

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

    ..We have reported that oral administration of a pure NOD1 ligand induces coronary arteritis in mice without fail..

    From PMID: 22507623, in Journal Hum Immunol. , 2012


    References

    There were 5 potential papers with NOD1 and CHD.

    PMIDTitleJournalsDetails
    22507623 Genetic susceptibility to Kawasaki disease: analysis of pattern recognition receptor genes.Human immunologyMore Details
    23029284 Comprehensive exploration of the effects of miRNA SNPs on monocyte gene expression.PloS oneMore Details
    21330608 Nod1 ligands induce site-specific vascular inflammation."Arteriosclerosis, thrombosis, and vascular biology"More Details
    16893397 A functional variant in the CARD4 gene and risk of premature coronary heart disease.International journal of immunogeneticsMore Details
    15653568 Nod1-mediated endothelial cell activation by Chlamydophila pneumoniae.Circulation researchMore Details

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



    PPI interactions

    There were totally 17 unique genes interacted with NOD1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    NOD1 Affinity Capture-Western10329646|10329646,10880512 CHD related
    CASP1 Affinity Capture-Western10329646|10329646,12459189 CHD related
    CASP2 Affinity Capture-Western10329646|10329646 No
    CASP4 Affinity Capture-Western10329646|10329646 No
    CASP8 Affinity Capture-Western10329646|10329646 CHD related
    CASP9 Affinity Capture-Western10329646|10329646 CHD related
    RIPK2 Affinity Capture-Western10329646|10329646,12459189,10224040 No
    CFLAR Affinity Capture-Western10329646 No
    HSP90AA1 Affinity Capture-Western17435760 CHD related
    SUGT1 Affinity Capture-Western17435760 No
    NLRC4 Affinity Capture-Western15107016 No
    CARD6 Affinity Capture-Western12775719|12775719 No
    COPS6 Affinity Capture-Western17337451 No
    GPS1 Affinity Capture-Western17337451 No
    TRAF4 Affinity Capture-Western21097508 No
    XIAP Reconstituted Complex19667203 CHD related
    NLRP1 in vitro11113115 No


    Involved FDA drugs

    There was no drug associated with NOD1