Table 2

Functionally enriched modules found in the yeast osmotic shock 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


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.

Ulitsky and Shamir BMC Systems Biology 2007 1:8   doi:10.1186/1752-0509-1-8

Open Data