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Table 2 Functionally enriched modules found in the yeast osmotic shock data

From: Identification of functional modules using network topology and high-throughput data

JACS Size Front Enriched GO terms p-value TFs p-value
1 120 119 processing of 20S pre-rRNA < 0.001 Fhl1 4.82·10-16
    rRNA processing < 0.001 Rap1 2.89·10-11
    35S primary transcript processing < 0.001 Sfp1 2.98·10-8
    ribosomal large subunit assembly and maintenance 0.019   
    rRNA modification < 0.001   
    ribosome biogenesis 0.029   
2 120 118 translational elongation < 0.001 Fhl1 1.03·10-5
3 120 118 processing of 20S pre-rRNA < 0.001   
    rRNA processing 0.030   
    35S primary transcript processing 0.011   
    ribosomal large subunit assembly and maintenance 0.019   
    ribosomal large subunit biogenesis < 0.001   
5 120 112 signal transduction during filamentous growth 0.010 Ste12 5.41·10-13
    conjugation with cellular fusion < 0.001 Dig1 5.41·10-13
6 120 99 transcription from RNA polymerase III promoter < 0.001   
    transcription from RNA polymerase I promoter 0.006   
7 120 107 ergosterol biosynthesis < 0.001   
    hexose transport 0.019   
8 114 85 chromatin remodeling 0.050   
11 120 114 pseudohyphal growth 0.010 Msn2 3.17·10-4
    response to stress < 0.001 Msn4 1.82·10-12
14 120 102 ubiquitin-dependent protein catabolism 0.047   
15 120 96 nuclear mRNA splicing, via spliceosome < 0.001   
16 89 61 ubiquitin-dependent protein catabolism < 0.001 Rpn4 6.44·10-6
17 120 109 response to stress < 0.001 Msn4 1.74·10-3
    mitochondrial electron transport < 0.001   
18 87 59 nuclear mRNA splicing, via spliceosome 0.012   
20 46 35 pyridoxine metabolism 0.045   
  1. The GO p-value was adjusted for multiple testing using the TANGO algorithm (see Methods). Enriched TF binding site motifs were detected using the PRIMA algorithm [35]. TF p-values were Bonferroni corrected for multiple testing.