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 |
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