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 >4x |
Module 344 |
| General Properties | |
|---|---|
| Below we list the number of gene sets from which the module was composed was originally composed, and the number of genes and experiments that it contains. Clicking on the number of genes will display a detailed list of all the genes in the module. Clicking on the number of experiments will display a detailed list of all the experiments in the module. | |
| Num gene sets: | 4 |
| Num genes: | 92 (see 999 additional genes for this module) |
| Num experiments: | 268 (117 induced, 151 repressed) |
| Parent module: | 403 |
| Children modules: | 302 303 |
| Gene sets | |
|---|---|
| Below we list the gene sets from which the module was originally composed. Clicking on a gene set will display all the genes associated with that gene set. Also listed are all the other modules in which the gene set participates. | |
| response to DNA damage stimulus | |
| Perou00 45 | |
| Nicotinate_and_nicotinamide_metabolism | |
| Benzoate_degradation | |
| 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 |
| Normal lung tissue (Lung cancer) | Lung cancer | 4.4e-18 | 19 | 59.3 | 32 | 22 | 276 |
| Normal tissue (Lung cancer) | Lung cancer | 2.4e-17 | 19 | 59.3 | 32 | 23 | 276 |
| Hematologic cancer and cell line (Stimulated PBMC) | Stimulated PBMC | 5.2e-12 | 15 | 88.2 | 17 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 5.2e-12 | 15 | 88.2 | 17 | 30 | 182 |
| Leukemia (General compendium) | General compendium | 1.7e-09 | 40 | 26.4 | 151 | 198 | 1946 |
| Leukemia or leukemia cell line (General compendium) | General compendium | 1.4e-08 | 40 | 26.4 | 151 | 212 | 1946 |
| Small cell lung cancer (Lung cancer) | Lung cancer | 9.7e-07 | 6 | 42.8 | 14 | 10 | 276 |
| Breast tissue or cancer (NCI60) | NCI60 | 1.0e-06 | 4 | 66.6 | 6 | 4 | 139 |
| Female hormonal tissue or cancer (NCI60) | NCI60 | 1.0e-06 | 4 | 66.6 | 6 | 4 | 139 |
| Acute myelogeous leukemia (Leukemia) | Leukemia | 6.2e-06 | 20 | 74.0 | 27 | 50 | 141 |
| Non-tumor liver tissue (Liver cancer) | Liver cancer | 1.2e-05 | 16 | 84.2 | 19 | 76 | 207 |
| Macrophages (General compendium) | General compendium | 1.7e-05 | 16 | 13.6 | 117 | 83 | 1946 |
| EWS/FLI expressing fibroblasts (General compendium) | EWS/FLI expressing fibroblasts (General compendium) | 3.2e-05 | 6 | 3.9 | 151 | 10 | 1946 |
| Breast cancer (NCI60) | NCI60 | 4.5e-05 | 3 | 50 | 6 | 3 | 139 |
| Cell line (B lymphoma) | B lymphoma | 6.3e-05 | 6 | 37.5 | 16 | 14 | 245 |
| Hematologic cancer (General compendium) | General compendium | 7.2e-05 | 48 | 31.7 | 151 | 372 | 1946 |
| Chronic lymphocytic leukemia (B lymphoma) | B lymphoma | 0.0001 | 13 | 50 | 26 | 46 | 245 |
| Leukemia (B lymphoma) | B lymphoma | 0.0001 | 13 | 50 | 26 | 46 | 245 |
| Leukemia or leukemia cell line (B lymphoma) | B lymphoma | 0.0001 | 13 | 50 | 26 | 46 | 245 |
| Hematologic cancer and cell line (General compendium) | General compendium | 0.0001 | 47 | 40.1 | 117 | 486 | 1946 |
| Invasive liver tumor (Liver cancer) | Liver cancer | 0.0001 | 8 | 66.6 | 12 | 38 | 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 |
| response to DNA damage stimulus | 1.5e-77 | 69 | 93.2 | 74 | 313 | 4609 |
| response to stress | 1.2e-47 | 69 | 93.2 | 74 | 796 | 4609 |
| ATP binding | 5.6e-30 | 45 | 60.8 | 74 | 401 | 4609 |
| nucleotidyltransferase activity | 1.5e-27 | 44 | 59.4 | 74 | 427 | 4609 |
| protein amino acid phosphorylation | 7.0e-27 | 35 | 47.2 | 74 | 231 | 4609 |
| DNA metabolism | 4.4e-22 | 28 | 37.8 | 74 | 171 | 4609 |
| DNA repair | 1.2e-20 | 22 | 29.7 | 74 | 96 | 4609 |
| protein serine/threonine kinase activity | 7.1e-19 | 22 | 29.7 | 74 | 114 | 4609 |
| catalytic activity | 1.1e-12 | 57 | 77.0 | 74 | 1691 | 4609 |
| endomembrane system | 6.0e-12 | 44 | 59.4 | 74 | 1040 | 4609 |
| kinase regulator activity | 5.3e-11 | 13 | 17.5 | 74 | 72 | 4609 |
| nucleus | 8.4e-11 | 41 | 55.4 | 74 | 976 | 4609 |
| cell cycle | 1.9e-10 | 16 | 21.6 | 74 | 135 | 4609 |
| regulation of cell cycle | 4.4e-10 | 17 | 22.9 | 74 | 165 | 4609 |
| DNA recombination | 4.7e-10 | 9 | 12.1 | 74 | 30 | 4609 |
| protein kinase regulator activity | 1.2e-09 | 11 | 14.8 | 74 | 59 | 4609 |
| protein tyrosine kinase activity | 4.1e-09 | 14 | 18.9 | 74 | 121 | 4609 |
| DNA damage response\, signal transduction | 5.6e-09 | 7 | 9.4 | 74 | 18 | 4609 |
| cell cycle checkpoint | 2.1e-08 | 6 | 8.1 | 74 | 13 | 4609 |
| cytokinesis | 7.6e-08 | 9 | 12.1 | 74 | 51 | 4609 |
| signal transducer activity | 1.5e-07 | 37 | 50 | 74 | 1035 | 4609 |
| DNA dependent DNA replication | 2.4e-07 | 7 | 9.4 | 74 | 29 | 4609 |
| chromosome organization and biogenesis (sensu Eukarya) | 1.7e-06 | 8 | 10.8 | 74 | 54 | 4609 |
| cGMP biosynthesis | 2.0e-06 | 4 | 5.4 | 74 | 7 | 4609 |
| transcription\, DNA-dependent | 1.0e-05 | 12 | 16.2 | 74 | 167 | 4609 |
| mitosis | 1.1e-05 | 7 | 9.4 | 74 | 50 | 4609 |
| guanylate cyclase activity | 1.1e-05 | 4 | 5.4 | 74 | 10 | 4609 |
| cAMP-dependent protein kinase activity | 1.8e-05 | 6 | 8.1 | 74 | 36 | 4609 |
| cyclic nucleotide biosynthesis | 2.7e-05 | 4 | 5.4 | 74 | 12 | 4609 |
| cyclin-dependent protein kinase activity | 2.7e-05 | 4 | 5.4 | 74 | 12 | 4609 |
| transcription | 3.0e-05 | 12 | 16.2 | 74 | 185 | 4609 |
| damaged DNA binding | 3.1e-05 | 5 | 6.7 | 74 | 24 | 4609 |
| cyclic nucleotide metabolism | 3.9e-05 | 4 | 5.4 | 74 | 13 | 4609 |
| Visual display | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Below is a visual display of the module. Shown are those arrays in which the module's genes significantly change, and the direction of change (induction/repression) in each array is indicated (middle, labeled 'Module changes'; red/green row). The arrays that correspond to the significant clinical attributes are also shown (top; brown rows). The gene sets that compose the module are also shown (left) along with an indication of the membership of the module genes in these gene sets. | |||||||||
| You can also view the images within GeneXPress by loading the module gxp file file. | |||||||||
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