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 >4x |
Module 158 -- DNA replication |
| 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: | 5 |
| Num genes: | 43 (see 1172 additional genes for this module) |
| Num experiments: | 404 (184 induced, 220 repressed) |
| Parent module: | None |
| Children modules: | 125 |
| 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. | |
| replication fork | |
| DNA dependent DNA replication | |
| S phase of mitotic cell cycle | |
| DNA replication and chromosome cycle | |
| DNA replication | |
| 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 |
| Non-tumor liver tissue (Liver cancer) | Liver cancer | 2.6e-18 | 49 | 83.0 | 59 | 76 | 207 |
| Hematologic cancer and cell line (Stimulated PBMC) | Stimulated PBMC | 3.4e-16 | 17 | 100 | 17 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 3.4e-16 | 17 | 100 | 17 | 30 | 182 |
| Liver tissue (Liver cancer*) | Liver cancer* | 1.6e-15 | 59 | 26.8 | 220 | 187 | 1945 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 2.4e-14 | 59 | 26.8 | 220 | 197 | 1945 |
| Hepatitis infected liver (Liver cancer*) | Liver cancer* | 1.6e-11 | 47 | 21.3 | 220 | 156 | 1945 |
| Normal lung tissue (Lung cancer) | Lung cancer | 2.8e-11 | 16 | 42.1 | 38 | 22 | 276 |
| Normal tissue (Lung cancer) | Lung cancer | 8.7e-11 | 16 | 42.1 | 38 | 23 | 276 |
| Cancer and cell line (Liver cancer) | Liver cancer | 4.7e-10 | 38 | 100 | 38 | 126 | 207 |
| Liver cancer cell line (Liver cancer) | Liver cancer | 1.4e-08 | 10 | 26.3 | 38 | 10 | 207 |
| Small cell lung cancer (Lung cancer) | Lung cancer | 8.2e-08 | 8 | 30.7 | 26 | 10 | 276 |
| Cell line (Liver cancer) | Liver cancer | 1.4e-07 | 10 | 26.3 | 38 | 11 | 207 |
| Hematologic samples and cell lines (Various tumors) | Various tumors | 2.0e-06 | 10 | 90.9 | 11 | 37 | 154 |
| Hematologic samples (Various tumors) | Various tumors | 2.0e-06 | 10 | 90.9 | 11 | 37 | 154 |
| Breast tissue or cancer (NCI60) | NCI60 | 4.7e-06 | 4 | 50 | 8 | 4 | 139 |
| Female hormonal tissue or cancer (NCI60) | NCI60 | 4.7e-06 | 4 | 50 | 8 | 4 | 139 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 1.1e-05 | 37 | 20.2 | 183 | 197 | 1945 |
| Invasive liver tumor (Liver cancer) | Liver cancer | 2.1e-05 | 17 | 44.7 | 38 | 38 | 207 |
| Grade 3 (Breast cancer) | Breast cancer | 5.6e-05 | 11 | 100 | 11 | 38 | 85 |
| Centroblasts (Various tumors) | Various tumors | 7.0e-05 | 4 | 36.3 | 11 | 5 | 154 |
| GC B like DLBCL (Various tumors) | Various tumors | 7.0e-05 | 4 | 36.3 | 11 | 5 | 154 |
| T cells (Various tumors) | Various tumors | 7.0e-05 | 4 | 36.3 | 11 | 5 | 154 |
| Breast cancer (NCI60) | NCI60 | 0.0001 | 3 | 37.5 | 8 | 3 | 139 |
| Follicular lymphoma (B lymphoma) | B lymphoma | 0.0001 | 13 | 30.2 | 43 | 28 | 245 |
| Cell line (Breast cancer) | Breast cancer | 0.0002 | 12 | 50 | 24 | 30 | 152 |
| Cancer and cell line (Fibroblast EWS-FLI*) | Fibroblast EWS-FLI* | 0.0002 | 6 | 2.7 | 220 | 10 | 1945 |
| Cell line (Fibroblast EWS-FLI*) | Fibroblast EWS-FLI* | 0.0002 | 6 | 2.7 | 220 | 10 | 1945 |
| EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*) | Fibroblast EWS-FLI* | 0.0002 | 6 | 2.7 | 220 | 10 | 1945 |
| Fibroblasts (Fibroblast EWS-FLI*) | Fibroblast EWS-FLI* | 0.0002 | 6 | 2.7 | 220 | 10 | 1945 |
| Skin fibroblasts (Fibroblast EWS-FLI*) | Fibroblast EWS-FLI* | 0.0002 | 6 | 2.7 | 220 | 10 | 1945 |
| 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 |
| DNA replication | 2.5e-70 | 36 | 83.7 | 43 | 52 | 4566 |
| DNA metabolism | 1.4e-61 | 42 | 97.6 | 43 | 169 | 4566 |
| DNA replication and chromosome cycle | 1.5e-36 | 20 | 46.5 | 43 | 29 | 4566 |
| S phase of mitotic cell cycle | 2.8e-30 | 17 | 39.5 | 43 | 26 | 4566 |
| DNA dependent DNA replication | 1.0e-26 | 16 | 37.2 | 43 | 29 | 4566 |
| replication fork | 5.4e-22 | 12 | 27.9 | 43 | 17 | 4566 |
| DNA binding | 4.2e-20 | 27 | 62.7 | 43 | 357 | 4566 |
| nucleus | 1.0e-19 | 37 | 86.0 | 43 | 966 | 4566 |
| DNA repair | 3.9e-17 | 16 | 37.2 | 43 | 93 | 4566 |
| nucleoplasm | 6.4e-16 | 15 | 34.8 | 43 | 89 | 4566 |
| DNA-directed DNA polymerase activity | 3.1e-14 | 7 | 16.2 | 43 | 8 | 4566 |
| endomembrane system | 5.1e-14 | 33 | 76.7 | 43 | 1029 | 4566 |
| nucleotidyltransferase activity | 1.8e-13 | 23 | 53.4 | 43 | 425 | 4566 |
| cell cycle | 1.2e-10 | 13 | 30.2 | 43 | 135 | 4566 |
| nu DNA polymerase activity | 3.4e-10 | 5 | 11.6 | 43 | 6 | 4566 |
| DNA replication initiation | 1.4e-08 | 5 | 11.6 | 43 | 10 | 4566 |
| nucleotide binding | 2.7e-08 | 8 | 18.6 | 43 | 55 | 4566 |
| transcription regulator activity | 4.1e-08 | 22 | 51.1 | 43 | 703 | 4566 |
| DNA replication factor C complex | 1.0e-07 | 4 | 9.3 | 43 | 6 | 4566 |
| single-stranded DNA binding | 8.1e-07 | 5 | 11.6 | 43 | 20 | 4566 |
| exonuclease activity | 6.3e-06 | 4 | 9.3 | 43 | 14 | 4566 |
| ribonuclease activity | 6.9e-06 | 5 | 11.6 | 43 | 30 | 4566 |
| 3'-5' exonuclease activity | 7.6e-06 | 3 | 6.9 | 43 | 5 | 4566 |
| chromatin remodeling complex | 7.6e-06 | 3 | 6.9 | 43 | 5 | 4566 |
| chromosome | 2.0e-05 | 6 | 13.9 | 43 | 62 | 4566 |
| exoribonuclease activity | 2.6e-05 | 3 | 6.9 | 43 | 7 | 4566 |
| catalytic activity | 3.9e-05 | 29 | 67.4 | 43 | 1677 | 4566 |
| ATP binding | 4.5e-05 | 13 | 30.2 | 43 | 399 | 4566 |
| DNA dependent ATPase activity | 0.0001 | 4 | 9.3 | 43 | 28 | 4566 |
| 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. | |||||||||
| Note: Since there are 404 experiments, this image does not display the individual experiment names, but rather condenses each experiment to a single pixel without displaying its name. You can fully view the image for this module within GeneXPress, by loading any of the four files mentioned in the line above | |||||||||
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