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Table 6 Network enrichment analysis of the repressed ESR gene set

From: NEAT: an efficient network enrichment analysis test

  Gene set n AB μ 0 log 10 (p-value)
  Go Slim BP sets:    
1 Cytoplasmic translation 6878 2641.9 <-300
2 Ribosomal large subunit biogenesis 3408 1097.8 <-300
3 Ribosomal small subunit biogenesis 5861 2073.7 <-300
4 Ribosome assembly 1782 621.9 <-300
5 RNA modification 2944 1062.0 <-300
6 rRNA processing 9187 3290.2 <-300
7 tRNA processing 2037 901.0 <-300
8 Translational elongation 1786 782.3 –283.8
9 Ribosomal subunit export from nucleus 1420 561.4 –281.8
10 Translational initiation 939 462.5 –112.1
11 Transcription from RNA polymerase III promoter 565 228.4 –107.7
12 SnoRNA processing 634 303.3 –82.0
13 Regulation of translation 1952 1328.6 –73.5
14 DNA-dependent transcription, termination 774 447.0 –57.5
15 Transcription from RNA polymerase I promoter 1005 646.4 –49.5
16 Protein alkylation 1063 759.4 –31.4
17 tRNA aminoacylation for protein translation 400 233.1 –29.4
18 Peptidyl-amino acid modification 1088 883.0 –13.2
19 Nuclear transport 3154 2003.5 –162.4
20 Organelle assembly 2090 1362.7 –96.1
21 Nucleobase-containing compound transport 1453 1155.4 –20.8
22 Cytokinesis 1024 806.9 –16.0
23 Vitamin metabolic process 325 274.0 –3.1
  KEGG pathways:    
24 Ribosome biogenesis in eukaryotes 9824 3661.0 <-300
25 Ribosome 18640 8731.7 <-300
26 RNA polymerase 3057 1541.2 <-300
27 RNA transport 4341 2906.4 –177.6
28 Aminoacyl-tRNA biosynthesis 1433 960.9 –58.2
29 RNA degradation 2560 1939.3 –51.9
30 mRNA surveillance pathway 1768 1413.5 –24.0
31 Pentose phosphate pathway 1126 947.1 –9.7
32 Spliceosome 2649 2523.6 –2.3
33 Purine metabolism 5579 3623.0 –263.6
34 Pyrimidine metabolism 4541 2884.5 –234.9
35 Cyanoamino acid metabolism 218 158.8 –6.3
36 One carbon pool by folate 541 392.5 –15.0
37 Sulfur relay system 238 196.5 –2.9
38 Carbapenem biosynthesis 117 89.8 –2.7
  1. The table lists the 23 Go Slim BP gene sets and the 15 KEGG pathways which the set of repressed ESR genes is found to be over-enriched with at 1 % significance level