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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.