Identification of a Serum-Induced Transcriptional Signature Associated With Type 1 Diabetes in the BioBreeding Rat

TABLE 1

Significantly regulated gene ontology biological processes

Biological process* Count Percentage P value
Day 60 DRlyp/lyp:DR+/+ intersection (n = 912 probe sets)
    Antigen processing and presentation of exogenous antigen 7 0.76 2.55 × 10−4
    Immune system process 49 5.31 2.28 × 10−3
    Antigen processing and presentation 10 1.08 4.57 × 10−3
    Antigen processing and presentation of peptide antigen 8 0.87 8.62 × 10−3
    Immune response 33 3.58 1.21 × 10−2
    Regulation of transcription 87 9.44 1.89 × 10−2
    Regulation of signal transduction 33 3.58 2.68 × 10−2
    Regulation of transcription, DNA dependent 79 8.57 2.71 × 10−2
    Regulation of gene expression 91 9.87 3.54 × 10−2
    Myeloid leukocyte mediated immunity 4 0.43 3.65 × 10−2
    I-κB kinase/NFκB cascade 11 1.19 6.94 × 10−2
Day 60 DRlyp/lyp (n = 1,979 probe sets)
    Antigen processing and presentation of exogenous antigen 14 0.71 6.54 × 10−9
    Antigen processing and presentation 22 1.11 4.47 × 10−6
    Antigen processing and presentation of peptide antigen 17 0.86 3.55 × 10−5
    Immune system process 95 4.80 3.50 × 10−3
    I-κB kinase/NFκB cascade 24 1.21 6.23 × 10−3
    Immune response 65 3.28 1.00 × 10−2
    Myeloid leukocyte mediated immunity 6 0.30 2.15 × 10−2
    Leukocyte migration 9 0.45 8.73 × 10−2
Day 60 DR+/+ (n = 2,904 probe sets)
    Regulation of transcription 260 9.33 8.75 × 10−8
    Regulation of gene expression 276 9.90 2.13 × 10−7
    Regulation of transcription, DNA dependent 237 8.50 3.84 × 10−7
    Regulation of signal transduction 91 3.27 1.83 × 10−4
    Regulation of transcription from RNA polymerase II promoter 81 2.91 2.64 × 10−3
    Negative regulation of transcription, DNA dependent 38 1.36 9.95 × 10−3
    Antigen processing and presentation of exogenous antigen 8 0.29 1.21 × 10−2
    Negative regulation of transcription 49 1.76 1.34 × 10−2
    Antigen processing and presentation 17 0.61 1.40 × 10−2
    Negative regulation of gene expression, epigenetic 5 0.18 2.17 × 10−2
    I-κB kinase/NFκB cascade 25 0.90 3.33 × 10−2
    Immune system process 105 3.77 3.75 × 10−2
Day 40 PBS-treated DRlyp/lyp (n = 1,526 probe sets)
    Antigen processing and presentation 27 1.73 2.63 × 10−11
    Antigen processing and presentation of peptide antigen 21 1.35 1.89 × 10−9
    Immune system process 96 6.17 1.96 × 10−6
    Immune response 67 4.30 2.31 × 10−5
    Antigen processing and presentation of exogenous antigen 9 0.58 1.92 × 10−4
    I-κB kinase/NFκB cascade 25 1.61 1.98 × 10−4
  • *Genes identified in Figs. 1, 2, and 4 were analyzed for significantly regulated annotations by DAVID. If an annotation was identified in more than one of the analyses, it is listed accordingly. Complete lists of annotations are provided in supplement B. The P value defines the significance of the association of a particular biological process with the gene list analyzed.

This Article

  1. Diabetes vol. 59 no. 10 2375-2385