Table 1 |
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|
Significance values relating genomic properties to clusters defined by the TBP regulatory network* |
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|
Cluster number† |
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|
|
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|
Row‡ |
Property |
0 |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
|
|
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|
Environmental stress |
|||||||||||
|
1 |
Induced during heat stress |
-25 |
-6 |
... |
8 |
... |
30 |
35 |
... |
... |
... |
|
2 |
Repressed during heat stress |
-7 |
106 |
... |
... |
... |
... |
... |
... |
... |
... |
|
Gene ontology§ |
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|
3 |
RB genes¶ |
... |
69 |
... |
... |
... |
... |
... |
... |
... |
... |
|
4 |
RP genes¶ |
... |
... |
... |
... |
-4 |
... |
... |
... |
31 |
14 |
|
5 |
Oxidative phosphorylation {GO:6119} |
... |
... |
... |
... |
... |
... |
... |
... |
... |
13 |
|
6 |
Amine metabolism {GO:9308} |
... |
... |
... |
8 |
... |
... |
... |
... |
... |
... |
|
7 |
Alcohol metabolism {GO:6066} |
... |
... |
... |
5 |
... |
9 |
4 |
... |
... |
... |
|
8 |
Energy derivation {GO:15980} |
... |
... |
... |
... |
... |
6 |
13 |
... |
... |
5 |
|
9 |
Sporulation {GO:30435} |
... |
... |
... |
... |
4 |
... |
... |
... |
... |
... |
|
10 |
Ty element transposition {GO:6319} |
... |
... |
... |
... |
... |
... |
... |
6 |
... |
... |
|
11 |
Proteolysis {GO:6508} |
... |
... |
6 |
... |
... |
... |
... |
... |
... |
... |
|
General properties |
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|
12 |
Lowly transcribed |
84 |
... |
... |
... |
89 |
... |
... |
10 |
... |
... |
|
13 |
Highly transcribed |
... |
... |
... |
... |
-7 |
... |
... |
... |
12 |
21 |
|
14 |
Low mRNA levels |
14 |
... |
... |
... |
28 |
-5 |
-6 |
... |
... |
... |
|
15 |
High mRNA levels |
-7 |
-6 |
... |
... |
-7 |
... |
32 |
... |
8 |
21 |
|
16 |
SAGA-dominated |
-46 |
... |
... |
9 |
... |
53 |
43 |
... |
... |
... |
|
17 |
TATA-containing |
-52 |
-6 |
... |
9 |
12 |
45 |
46 |
... |
... |
4 |
|
18 |
Low H3 K4Me2 in ORF |
... |
... |
... |
... |
58 |
... |
... |
... |
... |
... |
|
19 |
Low H3 K4Me2 in IGR |
... |
... |
... |
... |
28 |
... |
... |
... |
... |
... |
|
Positively regulated by |
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|
20 |
Spt3 (SAGA) |
-31 |
-4 |
-7 |
... |
28 |
5 |
31 |
28 |
... |
... |
|
21 |
Mot1 |
... |
... |
... |
... |
-4 |
-6 |
... |
... |
27 |
8 |
|
22 |
Bur6 (NC2) |
13 |
15 |
... |
... |
... |
-5 |
... |
... |
17 |
... |
|
23 |
Bdf1 (TFIID) |
11 |
... |
... |
... |
... |
... |
... |
10 |
6 |
... |
|
24 |
Bdf2 |
... |
... |
... |
... |
20 |
... |
... |
... |
... |
... |
|
25 |
TAF1 (TFIID) |
... |
... |
... |
... |
... |
... |
... |
... |
10 |
5 |
|
Negatively regulated by |
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|
26 |
RP genes |
... |
¥ |
... |
... |
... |
... |
... |
... |
... |
... |
|
27 |
Spt3 (SAGA) |
-8 |
6 |
27 |
30 |
... |
... |
... |
-5 |
... |
... |
|
28 |
Mot1 |
-25 |
... |
... |
15 |
22 |
36 |
5 |
... |
-6 |
... |
|
29 |
Bur6 (NC2) |
-28 |
... |
... |
5 |
13 |
43 |
9 |
... |
-4 |
... |
|
30 |
Bdf1 (TFIID) |
-21 |
... |
... |
10 |
... |
25 |
8 |
... |
... |
... |
|
31 |
Hda1 |
-23 |
... |
... |
... |
25 |
11 |
5 |
5 |
... |
... |
|
32 |
Tup1 (SSN6-TUP1) |
-31 |
... |
-4 |
... |
52 |
12 |
11 |
17 |
... |
... |
|
33 |
Set1 (COMPASS) |
-8 |
... |
-6 |
... |
60 |
... |
... |
15 |
... |
... |
|
|
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|
*Values represent -log10 p values, using the extreme most 10% of the data points (n > approximately 3,000) as identified in Additional data file 4, and are calculated using the CHITEST formula in EXCEL. Negative signs are inserted where relationships are anti-correlated. For clarity, any absolute value less than 4 was replaced with a period. †Cluster numbers refer to clusters shown in Figure 3. Cluster 0 includes all genes not clustered in Figure 3. ‡Row identifier in the text. References are provided in Additional data file 4. §Gene Ontology term identifier is provided in brackets. P values were derived using 'GO term finder' [62]. ¶RP genes are defined here as genes defined by the following Gene Ontology terms: ribosomal protein, mitochondrial ribosomal protein, translational elongation, translational initiation, translational termination, protein biosynthesis. RB genes are defined here by the following Gene Ontology terms: 35S primary transcript processing, ribosomal large subunit assembly and maintenance, rRNA metabolism, rRNA modification, rRNA processing, rRNA nucleus export, transcription from Pol I promoter, tRNA methylation, tRNA modification, tRNA processing, tRNA splicing, tRNA nucleus export, regulation of translation, processing of 20S pre-rRNA. ¥Up-regulated upon deletion of RPL12A (p < 10-24), RPL27A (p < 10-26), RPL34A (p < 10-8), RPL6B (p < 10-9), RPL8A (p < 10-63), or RPL24A (p < 10-20); see entries R135T, R137T, R138T, R139T, R140T, R141T in Additional data file 4. |
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|
Huisinga and Pugh Genome Biology 2007 8:R46 doi:10.1186/gb-2007-8-4-r46 |
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