Enriched clinical annotations |
For each of the clinical annotations, we tested whether it was enriched in the set of arrays in which the module is significantly induced (or repressed). Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of induced (or repressed) module's arrays in which they appear. We also show the fraction of the module's induced (or repressed) arrays with the given annotation ('Hits (%)' column). For completeness, we also list the total number of relevant induced arrays in the module ('Module hits in category' column), total number of arrays in the compendium in which the corresponding annotation is present ('Arrays in annotation' column), and the total number of relevant arrays in the compendium ('Arrays' column). Note that the 'relevant' arrays may be different for each annotation, since it includes only arrays in which the annotation was relevant (i.e., present or not present) and excludes arrays where the value of the annotation was not known. Rows that correspond to annotations that were enriched in the induced arrays of the module have a red background, while rows corresponding to annotations enriched in the repressed arrays have a green background. For each annotation, we also list the other modules in which it was enriched. |
Clinical annotation |
Category |
P-value |
Hits |
Hits(%) |
Module hits in category |
Arrays in annotation |
Arrays |
Liver tissue (Liver cancer*) |
Liver cancer* |
4.7e-32 |
52 |
57.1 |
91 |
187 |
1945 |
Liver tissue, cancer or cell line (Liver cancer*) |
Liver cancer* |
8.8e-31 |
52 |
57.1 |
91 |
197 |
1945 |
Hepatitis infected liver (Liver cancer*) |
Liver cancer* |
5.2e-18 |
36 |
39.5 |
91 |
156 |
1945 |
Liver tissue, cancer or cell line (Liver cancer*) |
Liver cancer* |
4.3e-17 |
32 |
51.6 |
62 |
197 |
1945 |
Cancer and cell line (Liver cancer) |
Liver cancer |
3.3e-11 |
42 |
100 |
42 |
126 |
207 |
Non-tumor liver tissue (Liver cancer) |
Liver cancer |
6.3e-10 |
38 |
73.0 |
52 |
76 |
207 |
Liver tissue (Liver cancer*) |
Liver cancer* |
1.4e-08 |
22 |
35.4 |
62 |
187 |
1945 |
Liver cancer cell line (Liver cancer) |
Liver cancer |
4.6e-08 |
10 |
23.8 |
42 |
10 |
207 |
Metastasis (Liver cancer) |
Liver cancer |
4.6e-08 |
10 |
23.8 |
42 |
10 |
207 |
Hepatitis infected liver (Liver cancer*) |
Liver cancer* |
1.0e-07 |
19 |
30.6 |
62 |
156 |
1945 |
Cell line (Liver cancer) |
Liver cancer |
4.3e-07 |
10 |
23.8 |
42 |
11 |
207 |
Normal tissue (Liver cancer) |
Liver cancer |
2.0e-05 |
11 |
21.1 |
52 |
14 |
207 |
Lung carcinoid (Lung cancer) |
Lung cancer |
9.7e-05 |
4 |
80 |
5 |
20 |
276 |
Colon cancer (Liver cancer) |
Liver cancer |
0.0002 |
5 |
11.9 |
42 |
5 |
207 |
Colon cancer metastasis to liver (Liver cancer) |
Liver cancer |
0.0002 |
5 |
11.9 |
42 |
5 |
207 |
Colon cancer or cell line (Liver cancer) |
Liver cancer |
0.0002 |
5 |
11.9 |
42 |
5 |
207 |
Colon tissue, cancer or cell line (Liver cancer) |
Liver cancer |
0.0002 |
5 |
11.9 |
42 |
5 |
207 |
Enriched GO annotations |
For each GO annotation, we tested whether it was enriched in the set of genes of the module. Below we list all such annotations that were enriched in this module with an FDR corrected p-value of 0.05 ('P-value' column), along with the number ('Hits' column) of the module's genes in which they appear. We also show the fraction of the module's genes with the given GO annotation that are included in this module ('Hits (%)' column). For completeness, we also list the total number of genes in the module ('Module genes' column), total number of genes in the compendium in which the corresponding annotation is present ('Genes in annotation' column), and the total number of genes in the compendium ('Genes' column). |
GO annotation |
P-value |
Hits |
Hits(%) |
Module genes |
Genes in annotation |
Genes |
oxidoreductase activity\, acting on the CH-CH group of donors |
1.4e-27 |
13 |
46.4 |
28 |
17 |
4566 |
oxidoreductase activity\, acting on the CH-CH group of donors\, other acceptors |
2.9e-20 |
9 |
32.1 |
28 |
10 |
4566 |
fatty acid metabolism |
1.3e-18 |
13 |
46.4 |
28 |
57 |
4566 |
oxidoreductase activity |
1.1e-16 |
18 |
64.2 |
28 |
254 |
4566 |
electron transporter activity |
9.0e-15 |
17 |
60.7 |
28 |
269 |
4566 |
fatty acid beta-oxidation |
1.7e-14 |
7 |
25 |
28 |
10 |
4566 |
fatty acid oxidation |
1.7e-14 |
7 |
25 |
28 |
10 |
4566 |
catalytic activity |
5.7e-13 |
28 |
100 |
28 |
1677 |
4566 |
carboxylic acid metabolism |
7.2e-12 |
12 |
42.8 |
28 |
138 |
4566 |
organic acid metabolism |
7.9e-12 |
12 |
42.8 |
28 |
139 |
4566 |
energy pathways |
3.1e-11 |
13 |
46.4 |
28 |
200 |
4566 |
acyl-CoA dehydrogenase activity |
3.5e-11 |
5 |
17.8 |
28 |
6 |
4566 |
mitochondrion |
4.8e-11 |
13 |
46.4 |
28 |
207 |
4566 |
photosynthesis |
4.9e-11 |
12 |
42.8 |
28 |
162 |
4566 |
oxidoreductase activity\, acting on the CH-CH group of donors\, oxygen as acceptor |
5.6e-09 |
4 |
14.2 |
28 |
5 |
4566 |
photosynthesis\, light reaction |
1.3e-08 |
9 |
32.1 |
28 |
115 |
4566 |
electron transport |
3.5e-08 |
9 |
32.1 |
28 |
128 |
4566 |
lipid metabolism |
9.3e-08 |
9 |
32.1 |
28 |
143 |
4566 |
regulation of metabolism |
5.3e-07 |
12 |
42.8 |
28 |
365 |
4566 |
oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor |
1.0e-06 |
4 |
14.2 |
28 |
14 |
4566 |
oxidoreductase activity\, acting on the aldehyde or oxo group of donors |
2.5e-06 |
4 |
14.2 |
28 |
17 |
4566 |
ligase activity\, forming carbon-sulfur bonds |
4.0e-06 |
3 |
10.7 |
28 |
6 |
4566 |
response to xenobiotic stimulus |
1.0e-05 |
7 |
25 |
28 |
133 |
4566 |
aldehyde dehydrogenase activity |
2.4e-05 |
3 |
10.7 |
28 |
10 |
4566 |
peroxisome |
2.7e-05 |
4 |
14.2 |
28 |
30 |
4566 |