Table 2 |
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|
The seven most significant linear ICA clusters from the yeast cell cycle data (Dataset 2) |
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|
Cluster |
Number of ORFs |
GO/KEGG functional categories |
Number of ORFs within functional category |
p value (log10) |
|
|
||||
|
1 |
215 |
Protein biosynthesis (175) |
93 |
-60.1 |
|
217 |
Structural constituent of ribosome (118) |
83 |
-67.6 |
|
|
157 |
Cytosolic ribosome (94) |
83 |
-73.1 |
|
|
229 |
Ribosome (96) |
83 |
-82.5 |
|
|
5 |
208 |
Cell cycle (220) |
61 |
-19.5 |
|
202 |
DNA-directed DNA polymerase (13) |
7 |
-4.7 |
|
|
115 |
Replication fork (30) |
16 |
-9.6 |
|
|
229 |
Cell cycle (58) |
18 |
-6.6 |
|
|
11 |
2,072 |
Sulfur amino acid metabolism (12) |
11 |
-11.1 |
|
211 |
Structural constituent of cytoskeleton (25) |
11 |
-5.9 |
|
|
125 |
Spindle (32) |
18 |
-10.62 |
|
|
9 |
209 |
Ribosome biogenesis (38) |
15 |
-7.1 |
|
207 |
RNA binding (75) |
7 |
-3.4 |
|
|
111 |
Nucleus (334) |
54 |
-7.3 |
|
|
7 |
198 |
Glutamine family amino acid biosynthesis (11) |
8 |
-6.8 |
|
99 |
Mitochondrion (353) |
22 |
-3.8 |
|
|
3 |
209 |
Protein folding (26) |
11 |
-5.7 |
|
212 |
Heat shock protein (14) |
9 |
-6.7 |
|
|
11 |
199 |
DNA unwinding (10) |
6 |
-4.5 |
|
192 |
ATP-dependent DNA helicase (7) |
6 |
-6.0 |
|
|
85 |
Pre-replicative complex (8) |
6 |
-5.7 |
|
|
216 |
Cell cycle (58) |
13 |
-3.6 |
|
|
|
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|
The cluster IDs are shown, where cluster Ci,1in Equation 3 is denoted by 2i-1 and a cluster Ci,2 is denoted by 2i. The number of genes in the cluster that have at least one annotation in GO or KEGG are listed along with the functional category with the smallest p-value among those in each annotation system. Four annotation systems are used: biological process (GO), molecular function (GO), cellular component (GO) and KEGG. Numbers in parentheses show the number of genes within the functional category that are present in the microarray data. Functional categories with p-values higher than 10-3 are discarded, and those with values higher than 10-7 are not considered to be significant. The number of genes shared by the cluster and the functional category is shown with the log10 of the p-values corresponding to each functional category for the cluster. |
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|
Lee and Batzoglou Genome Biology 2003 4:R76 doi:10.1186/gb-2003-4-11-r76 |
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