Skip to main content

Table 9 Repressed ESR gene set: comparison between NEAT and LA+S

From: NEAT: an efficient network enrichment analysis test

   μ 0 log10 (p-value)
  Gene set NEAT LA+S NEAT LA+S
  GO Slim BP sets:     
1 Cytoplasmic translation 2641.9 3583.5 <-300 –290.9
2 Ribosomal large subunit biogenesis 1097.8 1602.4 <-300 –269.2
3 Ribosomal small subunit biogenesis 2073.7 3013.2 <-300 –236.8
4 Ribosome assembly 621.9 872.1 <-300 –95.9
5 RNA modification 1062.0 1422.7 <-300 –213.7
6 rRNA processing 3290.2 4623.2 <-300 <-300
7 tRNA processing 901.0 1137.6 <-300 –103.3
8 Translational elongation 782.3 1019.5 –283.8 –71.2
9 Ribosomal subunit export from nucleus 561.4 693.4 –281.8 –151.2
10 Nuclear transport 2003.5 2452.5 –162.4 –33.0
11 Translational initiation 462.5 594.8 –112.1 –33.6
12 Transcription from RNA polymerase III promoter 228.4 281.6 –107.7 –43.6
13 Organelle assembly 1362.7 1719.2 –96.1 –8.0
14 SnoRNA processing 303.3 349.8 –82.0 –26.5
15 Regulation of translation 1328.6 1577.5 –73.5 –12.9
16 DNA-dependent transcription, termination 447.0 575.2 –57.5 –11.7
17 Transcription from RNA polymerase I promoter 646.4 874.2 –49.5 –5.2
18 tRNA aminoacylation for protein translation 233.1 256.7 –29.4 –11.2
19 Protein alkylation 759.4 1000.0 –31.4 –1.2
20 Nucleobase-containing compound transport 1155.4 1445.1 –20.8 –0.1
21 Cytokinesis 806.9 925.9 –16.0 –1.8
22 Peptidyl-amino acid modification 883.0 1102.4 –13.2 –0.1
23 Vitamin metabolic process 274.0 245.8 –3.1 –5.5
  KEGG pathways:     
24 Ribosome biogenesis in eukaryotes 3661.0 5212.5 <-300 <-300
25 Ribosome 8731.7 11954.0 <-300 –283.3
26 RNA polymerase 1541.2 2058.0 <-300 –76.1
27 Purine metabolism 3623.0 4136.9 –263.6 –66.9
28 Pyrimidine metabolism 2884.5 3402.5 –234.9 –61.0
29 RNA transport 2906.4 3193.2 –177.6 –75.4
30 Aminoacyl-tRNA biosynthesis 960.9 934.2 –58.2 –49.8
31 RNA degradation 1939.3 2051.3 –51.9 –19.9
32 mRNA surveillance pathway 1413.5 1477.3 –24.0 –12.7
33 One carbon pool by folate 392.5 344.2 –15.0 –19.5
34 Pentose phosphate pathway 947.1 979.2 –9.7 –4.6
35 Cyanoamino acid metabolism 158.8 132.2 –6.3 –7.2
36 Sulfur relay system 196.5 172.7 –2.9 –3.9
37 Carbapenem biosynthesis 89.8 75.1 –2.7 –4.1
38 Spliceosome 2523.6 2432.2 –2.3 –4.1
39 Synthesis and degradation of ketone bodies 39.8 29.8 –0.3 –2.2
  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