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Table 10 Induced ESR gene set: comparison between NEAT and LA+S (GO Slim sets)

From: NEAT: an efficient network enrichment analysis test

   μ 0 log10 (p-value)
  GO Slim BP set NEAT LA+S NEAT LA+S
1 Response to oxidative stress 242.2 248.5 –202.7 –253.7
2 Carbohydrate metabolic process 671.2 663.9 –110.9 –123.3
3 Response to chemical stimulus 885.1 912.4 –83.4 –92.8
4 Oligosaccharide metabolic process 165.3 158.1 –77.3 –104.5
5 Cofactor metabolic process 219.0 225.6 –73.7 –76.2
6 Generation of precursor metabolites and energy 294.8 293.4 –54.0 –56.1
7 Nucleobase-containing small molecule metabolic process 404.5 417.4 –49.2 –41.0
8 Carbohydrate transport 65.8 77.7 –45.0 –52.8
9 Membrane invagination 120.6 118.3 –37.0 –51.7
10 Transmembrane transport 644.4 684.7 –24.2 –16.2
11 Protein folding 296.9 296.3 –22.7 –26.6
12 Lipid metabolic process 484.4 495.7 –19.9 –23.3
13 Endocytosis 245.5 248.7 –19.3 –19.3
14 Vacuole organization 200.2 199.7 –18.9 –22.4
15 Cellular respiration 118.4 125.2 –14.5 –14.1
16 Response to starvation 331.4 318.4 –11.2 –15.8
17 Protein targeting 478.8 485.1 –10.9 –15.8
18 Proteolysis involved in cellular protein catabolic process 488.5 494.1 –10.9 –9.8
19 Peroxisome organization 124.8 123.5 –6.0 –6.0
20 Lipid transport 79.7 90.4 –4.9 –2.8
21 Ion transport 380.2 410.7 –4.8 –2.1
22 Protein maturation 27.7 30.9 –3.9 –3.0
23 Cell morphogenesis 79.4 80.8 –3.6 –3.7
24 Sporulation 306.4 301.7 –2.1 –2.5
25 Amino acid transport 109.4 113.0 –2.1 –1.6
26 Response to osmotic stress 181.8 178.3 –1.6 –2.1
27 Protein phosphorylation 587.6 564.3 –1.4 –2.7
  1. The table reports the gene sets that are found to be over-enriched (α=1 %) by at least one of the two methods. μ 0 denotes the expected value of N AB in the absence of enrichment. The last two columns report log 10 p-values for the proposed NEAT and the LA+S test of [19], respectively