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Table 2 Functional modules in a yeast co-expression network

From: A general co-expression network-based approach to gene expression analysis: comparison and applications

Cluster Size Category1 Term Count Enrichment2 P-value
1 361 BP protein catabolism 32 4.2 2.0E-12
   BP protein folding 21 5.9 1.6E-11
2 498 BP ribosome biogenesis 133 9.2 2.0E-106
3 18 BP chromatin assembly or disassembly 9 36.4 5.3E-13
   TF HIR2 6 129.8 2.3E-12
   TF HIR1 6 62.9 3.0E-10
   TF HIR3 6 57.7 5.3E-10
4 25 BP telomerase-independent telomere maintenance 4 82.3 1.1E-07
   BP biological process unknown 16 2.9 7.6E-06
   TF GAT3 13 56.8 3.5E-21
   TF YAP5 15 43.5 5.8E-17
   TF PDR1 9 25.8 3.1E-11
   TF MSN4 8 35.0 3.8E-11
5 422 BP spore wall assembly 16 7.0 1.6E-10
   BP biological process unknown 138 1.5 1.2E-07
   TF NRG1 21 4.2 1.4E-08
   TF SUM1 16 3.9 2.3E-06
   TF PHD1 15 3.4 3.2E-05
6 99 - - - - -
7 463 BP carbohydrate metabolism 41 2.9 4.6E-10
   BP biological process unknown 178 1.7 9.5E-17
   BP response to stimulus 62 1.7 2.0E-05
   TF UME6 25 2.5 2.6E-05
   TF NRG1 15 2.8 3.6E-04
8 108 BP nitrogen compound metabolism 25 7.0 5.2E-15
   TF MET31 4 9.6 8.0E-04
   TF MET32 5 5.7 2.1E-03
9 192 BP generation of precursor metabolites and energy 50 8.2 7.5E-33
   TF HAP4 22 9.2 5.1E-16
10 22 BP Ty element transposition 17 58.6 6.2E-29
   TF SUM1 4 18.9 5.8E-05
11 604 BP carboxylic acid metabolism 76 3.0 2.4E-19
   BP cell organization and biogenesis 212 1.6 3.7E-15
   TF SWI6 45 2.9 3.6E-11
   TF SWI4 44 2.8 2.7E-10
   TF FKH2 35 3.0 4.7E-09
   TF MBP1 36 2.8 1.9E-08
   TF STE12 22 3.6 7.9E-08
   TF NDD1 30 2.9 1.1E-07
   TF FKH1 34 2.5 9.6E-07
   TF MCM1 22 2.9 3.9E-06
12 186 BP protein biosynthesis 131 6.4 6.4E-85
   TF FHL1 96 17.1 3.3E-105
   TF RAP1 58 11.5 2.2E-48
  1. 1 For each cluster, significantly enriched biological process GO terms (BP) or binding of transcription factors (TF) are counted.
  2. 2Fold of enrichment is calculated as: .