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Table 2 GO categories enriched for upregulated and downregulated genes

From: Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation

GO ID Term Annotated genes Significant Expected Rank in downregulated genes p value (FDR) for upregulated genes p value (FDR) for downregulated genes
(A) Top GO categories enriched for upregulated genes
 GO:0009408 Response to heat 70 13 1.51 2483 5.7 × 10−8 (2.3 × 10−4) 0.87 (1)
 GO:0006986 Response to unfolded protein 97 15 2.09 2757 7.1 × 10−8 (2.7 × 10−4) 1 (1)
 GO:0006457 Protein folding 133 17 2.87 1600 1.7 × 10−7 (6.4 × 10−4) 0.52 (1)
 GO:0035966 Response to topologically incorrect protein 106 15 2.29 2368 2.4 × 10−7 (9.4 × 10−4) 0.81 (1)
 GO:0009266 Response to temperature stimulus 96 13 2.07 2257 2.5 × 10−6 (9.8 × 10−3) 0.76 (1)
 GO:0042026 Protein refolding 11 5 0.24 2758 6.7 × 10−6 (0.028) 1 (1)
 GO:0034605 Cellular response to heat 50 9 1.08 2759 8.6 × 10−6 (0.035) 1 (1)
 GO:0043618 Regulation of transcription from RNA polymerase II promoter in response to stress 35 7 0.76 1907 4.3 × 10−5 (0.18) 0.63 (1)
 GO:1900034 Regulation of cellular response to heat 26 6 0.56 2760 6.6 × 10−5 (0.27) 1 (1)
 GO:0043620 Regulation of DNA-templated transcription in response to stress 39 7 0.84 2008 9 × 10−5 (0.37) 0.67 (1)
(B) Top GO categories enriched for down regulated genes
 GO:0051225 Spindle assembly 37 6 0.82 1 1 (1) 5.4 × 10−4 (1)
 GO:0043207 Response to external biotic stimulus 342 20 7.59 2 0.63 (1) 1.6 × 10−3 (1)
 GO:0051707 Response to other organism 342 20 7.59 3 0.63 (1) 1.6 × 10−3 (1)
 GO:0045931 Positive regulation of mitotic cell cycle 64 7 1.42 4 1 (1) 2.1 × 10−3 (1)
 GO:0007049 Cell cycle 1037 45 23.02 5 0.69 (1) 2.2 × 10−3 (1)
 GO:0007143 Female meiotic division 10 3 0.22 6 1 (1) 2.3 × 10−3 (1)
 GO:0009607 Response to biotic stimulus 355 20 7.88 7 0.54 (1) 2.6 × 10−3 (1)
 GO:0032496 Response to lipopolysaccharide 128 10 2.84 8 0.49 (1) 3.3 × 10−3 (1)
 GO:1903047 Mitotic cell cycle process 552 27 12.26 9 0.78 (1) 3.7 × 10−3 (1)
 GO:0002237 Response to molecule of bacterial origin 134 10 2.98 10 0.52 (1) 4.6 × 10−3 (1)
 GO:0008219 Cell death 1022 43 22.69 11 4.3 × 10−3 (1) 4.9 × 10−3 (1)
  1. The most significant GO categories for differentially expressed genes following heat shock in LCLs are shown. Numbers of significant and expected genes shown, together with p values (Fisher’s exact test)