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: NFKBIL1

    Description: nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1

    Entrez Gene ID: 4795

    SwissProt Acc Number: Q9UBC1

    RefSeq: NM_001144961

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

    ..Our finding that protective effects are linked with minor homozygous genotypes and haplotype 1 of the BAT1-NFKBIL1-LTA region in Europeans is opposite to the observation of associated risks in Japanese...

    From PMID: 17517687, in Journal Hum Mol Genet. , 2007


    References

    There were 2 potential papers with NFKBIL1 and CHD.

    PMIDTitleJournalsDetails
    17517687 Association of variants in the BAT1-NFKBIL1-LTA genomic region with protection against myocardial infarction in Europeans.Human molecular geneticsMore Details
    12426569 Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction.Nature geneticsMore Details

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



    PPI interactions

    There were totally 10 unique genes interacted with NFKBIL1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    GEMIN4 Affinity Capture-MS17353931 No
    MRPS22 Affinity Capture-MS17353931 No
    RFXANK Affinity Capture-MS17353931 No
    LUC7L Affinity Capture-MS17353931 No
    PNN Affinity Capture-MS17353931 No
    MRPS34 Affinity Capture-MS17353931 No
    MRPL44 Affinity Capture-MS17353931 No
    MRPS18B Affinity Capture-MS17353931 No
    KRT77 Affinity Capture-MS17353931 No
    CXorf56 Affinity Capture-MS17353931 No


    Involved FDA drugs

    There was no drug associated with NFKBIL1