Table 1. Enrichment of clusters for ORFs within functional categories.
|
Cluster |
Periodicity index |
Number of ORFs (n) |
Functional category (total ORFs) |
ORFs within functional category (k) |
P-value |
|
1 |
0.07 |
164 |
Ribosomal proteins (206) Organization of cytoplasm (555) Organization of chromosome structure (41) |
64 79 7 |
10-54 10-39 10-4 |
|
2 |
0.38 |
186 |
DNA synthesis and replication (82) Cell cycle control and mitosis (312) Recombination and DNA repair (84) Nuclear organization (720) |
23 30 11 40 |
10-16 10-8 10-5 10-4 |
|
3 |
0.08 |
104 |
NA |
|
|
|
4 |
0.14 |
170 |
Mitochondrial organization (339) Respiration (79) |
32 10 |
10-10 10-5 |
|
5 |
0.18
|
152 |
Cell rescue, defense, cell death (331) Carbohydrate metabolism (411) Stress response (149) Energy (236) Metabolism of energy reserves (37) |
22 24 12 16 6 |
10-5 10-4 10-4 10-4 10-4 |
|
6 |
0.09 |
104 |
NA |
|
|
|
7 |
0.35 |
101 |
Cell cycle control and mitosis (312) Budding, cell polarity, filament formation (161) DNA synthesis and replication (82) |
17 10 7 |
10-5 10-4 10-4 |
|
8 |
0.09 |
148 |
Carbohydrate metabolism (411) TCA pathway (22) |
22 5 |
10-4 10-4 |
|
9 |
0.18 |
147 |
NA |
|
|
|
10 |
0.09 |
89 |
NA |
|
|
|
11 |
0.44 |
94 |
NA |
|
|
|
12 |
0.15 |
80 |
NA |
|
|
|
13 |
0.11 |
99 |
NA |
|
|
|
14 |
0.45 |
74 |
Organization of centrosome (28) Nuclear biogenesis (5) Organization of cytoskeleton (93) |
6 3 7 |
10-6 10-5 10-4 |
|
15 |
0.13 |
115 |
NA |
|
|
|
16 |
0.20 |
99 |
NA |
|
|
|
17 |
0.16 |
83 |
Transcription (722) |
21 |
10-4 |
|
18 |
0.05 |
101 |
Organization of cytoplasm (555) Ribosomal proteins (206) Protein synthesis (343) Cellular organization (2105) |
30 16 20 55 |
10-9 10-7 10-7 10-5 |
|
19 |
0.09 |
73 |
NA |
|
|
|
20 |
0.19 |
84 |
NA |
|
|
|
21 |
0.12 |
70 |
Protein synthesis (343) Organization of cytoplasm (555) Ribosomal proteins (206) |
14 18 10 |
10-5 10-5 10-4 |
|
22 |
0.26 |
85 |
NA |
|
|
|
23 |
0.31 |
69 |
NA |
|
|
|
24 |
0.13 |
85 |
NA |
|
|
|
25 |
0.12 |
76 |
NA |
|
|
|
26 |
0.13 |
50 |
NA |
|
|
|
27 |
0.11 |
64 |
NA |
|
|
|
28 |
0.22 |
68 |
NA |
|
|
|
29 |
0.09 |
51 |
NA |
|
|
|
30 |
0.24 |
60 |
Nitrogen and sulfur metabolism (75) Amino acid metabolism (203) |
9 12 |
10-8 10-7 |
Periodicity index is a quantitative measure of cell cycle periodicity. (see methods). The most highly enriched functional categories are given for each cluster. P values were calculated using the cumulative hypergeometric probability distribution for finding at least (k) ORFs from a particular functional category within a cluster of size (n) (see Methods). Since 199 MIPS functional categories were tested for each cluster, P values greater than 3 x 10-4 are not reported, as their total expectation within the cluster would be greater than 0.05. Also, since all 30 clusters are being tested independently, P values with asterisks may have marginal significance.