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