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: IRF1

    Description: interferon regulatory factor 1

    Entrez Gene ID: 3659

    SwissProt Acc Number: P10914

    RefSeq: NM_002198

    It was suspected to be CHD related:

    .."Our data support the hypothesis that oxLDL is a proinflammatory stimulus that induces the expression of TLR2 and IRF1, 2 important gene regulators of innate immune response, and inhibits the expression of the antioxidant SOD1."..

    From PMID: 16690872, in Journal Arterioscler Thromb Vasc Biol , 2006


    References

    There were 3 potential papers with IRF1 and CHD.

    PMIDTitleJournalsDetails
    21300955 Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.CirculationMore Details
    17922810 Oxidized low-density lipoprotein-induced expression of ABCA1 in blood monocytes precedes coronary atherosclerosis and is associated with plaque complexity in hypercholesterolemic pigs.Journal of thrombosis and haemostasis : JTHMore Details
    16690872 Oxidized low-density lipoprotein correlates positively with toll-like receptor 2 and interferon regulatory factor-1 and inversely with superoxide dismutase-1 expression: studies in hypercholesterolemic swine and THP-1 cells."Arteriosclerosis, thrombosis, and vascular biology"More Details

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



    PPI interactions

    There were totally 24 unique genes interacted with IRF1. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    KAT2B Reconstituted Complex10022868 No
    KAT2A Reconstituted Complex10022868 No
    UBC Co-fractionation17942705 No
    IRF9 Two-hybrid20211142 No
    EP300 Affinity Capture-Western14662860|10438822 CHD related
    STUB1 Reconstituted Complex20947504|20947504 No
    TRAF3 Affinity Capture-MS21903422|21903422 No
    HCFC1 Affinity Capture-MS21903422 No
    KEAP1 Affinity Capture-MS21903422|21903422 No
    SEC63 Affinity Capture-MS21903422 No
    TRMT2A Affinity Capture-MS21903422 No
    NPM1 Affinity Capture-Western21245151|21245151 No
    YBX1 Reconstituted Complex21245151|21245151 CHD related
    TRIM28 Reconstituted Complex21245151|21245151 No
    SP2 Affinity Capture-Western19482358 No
    STAT1 Affinity Capture-Western10764778|10764778|10764778 CHD related
    IRF8 Two-hybrid9742224|7768900|7768900,9742224 No
    HMGA1 Reconstituted Complex10357819|10357819 CHD related
    SMARCA4 Co-localization16195385 No
    tat Reconstituted Complex12021315|12021315 No
    CREBBP Reconstituted Complex9659924 No
    SPI1 Reconstituted Complex9593745 No
    NFKB1 in vitro8746784 CHD related
    RELA in vivo8746784 CHD related


    Involved FDA drugs

    There was no drug associated with IRF1