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Module 124 -- Transcription |
| 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: | 2 |
| Num genes: | 96 (see 1672 additional genes for this module) |
| Num experiments: | 384 (190 induced, 194 repressed) |
| Parent module: | None |
| Children modules: | None |
| 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. | |
| transcription, DNA_dependent | |
| transcription | |
| 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 |
| Hematologic cancer and cell line (Stimulated PBMC) | Stimulated PBMC | 1.6e-23 | 28 | 77.7 | 36 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 1.6e-23 | 28 | 77.7 | 36 | 30 | 182 |
| Chronic lymphocytic leukemia (B lymphoma) | B lymphoma | 9.9e-17 | 34 | 59.6 | 57 | 46 | 245 |
| Leukemia (B lymphoma) | B lymphoma | 9.9e-17 | 34 | 59.6 | 57 | 46 | 245 |
| Leukemia or leukemia cell line (B lymphoma) | B lymphoma | 9.9e-17 | 34 | 59.6 | 57 | 46 | 245 |
| Lymphocytes (B lymphoma*) | B lymphoma* | 1.9e-11 | 57 | 29.5 | 193 | 244 | 1945 |
| B cells (B lymphoma*) | B lymphoma* | 2.1e-11 | 55 | 28.4 | 193 | 231 | 1945 |
| Cell line (B lymphoma) | B lymphoma | 3.2e-11 | 12 | 42.8 | 28 | 14 | 245 |
| Cancer (B lymphoma*) | B lymphoma* | 1.6e-09 | 47 | 24.3 | 193 | 200 | 1945 |
| Hematologic cancer (B lymphoma*) | B lymphoma* | 1.6e-09 | 47 | 24.3 | 193 | 200 | 1945 |
| Non-tumor liver tissue (Liver cancer) | Liver cancer | 2.7e-09 | 24 | 88.8 | 27 | 76 | 207 |
| Cancer and cell line (B lymphoma*) | B lymphoma* | 1.7e-08 | 47 | 24.3 | 193 | 214 | 1945 |
| Hematologic cancer and cell line (B lymphoma*) | B lymphoma* | 1.7e-08 | 47 | 24.3 | 193 | 214 | 1945 |
| Liver cancer cell line (Liver cancer) | Liver cancer | 5.6e-08 | 9 | 31.0 | 29 | 10 | 207 |
| Cancer and cell line (Liver cancer) | Liver cancer | 1.3e-07 | 29 | 100 | 29 | 126 | 207 |
| Cell line (Liver cancer) | Liver cancer | 2.8e-07 | 9 | 31.0 | 29 | 11 | 207 |
| Breast tissue or cancer (NCI60) | NCI60 | 3.3e-07 | 4 | 80 | 5 | 4 | 139 |
| Female hormonal tissue or cancer (NCI60) | NCI60 | 3.3e-07 | 4 | 80 | 5 | 4 | 139 |
| Acute myelogeous leukemia (Leukemia) | Leukemia | 4.3e-07 | 15 | 93.7 | 16 | 50 | 141 |
| Small cell lung cancer (Lung cancer) | Lung cancer | 9.7e-07 | 6 | 42.8 | 14 | 10 | 276 |
| B. petrussis stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 1.4e-06 | 23 | 88.4 | 26 | 67 | 144 |
| Invasive liver tumor (Liver cancer) | Liver cancer | 8.6e-06 | 15 | 51.7 | 29 | 38 | 207 |
| Hematologic samples and cell lines (Stimulated PBMC*) | Stimulated PBMC* | 1.0e-05 | 36 | 19.0 | 189 | 182 | 1945 |
| Monocytes (Stimulated PBMC*) | Stimulated PBMC* | 1.0e-05 | 36 | 19.0 | 189 | 182 | 1945 |
| Breast cancer (NCI60) | NCI60 | 2.2e-05 | 3 | 60 | 5 | 3 | 139 |
| Grade 3 (Breast cancer) | Breast cancer | 5.6e-05 | 11 | 100 | 11 | 38 | 85 |
| Gram negative bacteria stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 5.9e-05 | 23 | 88.4 | 26 | 78 | 144 |
| B. petrussis A2 stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 0.0001 | 5 | 19.2 | 26 | 5 | 144 |
| B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 0.0001 | 5 | 19.2 | 26 | 5 | 144 |
| Normal lung tissue (Lung cancer) | Lung cancer | 0.0002 | 6 | 42.8 | 14 | 22 | 276 |
| Normal tissue (Lung cancer) | Lung cancer | 0.0003 | 6 | 42.8 | 14 | 23 | 276 |
| Renal cancer or cell line (Neuro tumors) | Neuro tumors | 0.0003 | 4 | 40 | 10 | 5 | 90 |
| Renal tissue (Neuro tumors) | Neuro tumors | 0.0003 | 4 | 40 | 10 | 5 | 90 |
| Hematologic cancer and cell line (Stimulated immune*) | Stimulated immune* | 0.0004 | 14 | 7.2 | 193 | 53 | 1945 |
| Hematologic samples and cell lines (Stimulated immune*) | Stimulated immune* | 0.0004 | 14 | 7.2 | 193 | 53 | 1945 |
| Macrophages (Stimulated immune*) | Stimulated immune* | 0.0004 | 14 | 7.2 | 193 | 53 | 1945 |
| Monocytes (Stimulated immune*) | Stimulated immune* | 0.0004 | 14 | 7.2 | 193 | 53 | 1945 |
| Breast tissue, cancer or cell line (NCI60) | NCI60 | 0.0004 | 5 | 100 | 5 | 31 | 139 |
| 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 |
| transcription | 1.5e-147 | 96 | 100 | 96 | 184 | 4566 |
| transcription\, DNA-dependent | 9.9e-140 | 92 | 95.8 | 96 | 167 | 4566 |
| regulation of transcription | 3.0e-56 | 43 | 44.7 | 96 | 76 | 4566 |
| mitosis | 3.3e-50 | 35 | 36.4 | 96 | 50 | 4566 |
| regulation of transcription\, DNA-dependent | 1.1e-43 | 71 | 73.9 | 96 | 595 | 4566 |
| transcription from Pol I promoter | 1.2e-26 | 21 | 21.8 | 96 | 38 | 4566 |
| cell cycle | 6.8e-24 | 30 | 31.2 | 96 | 135 | 4566 |
| cytokinesis | 2.4e-20 | 19 | 19.7 | 96 | 49 | 4566 |
| transcription from Pol II promoter | 2.0e-19 | 26 | 27.0 | 96 | 130 | 4566 |
| regulation of cell cycle | 4.9e-19 | 28 | 29.1 | 96 | 163 | 4566 |
| nucleus | 8.5e-19 | 60 | 62.5 | 96 | 966 | 4566 |
| endomembrane system | 1.3e-16 | 59 | 61.4 | 96 | 1029 | 4566 |
| regulation of transcription from Pol II promoter | 9.6e-13 | 21 | 21.8 | 96 | 146 | 4566 |
| transcription initiation | 5.5e-12 | 9 | 9.3 | 96 | 16 | 4566 |
| RNA processing | 9.8e-12 | 17 | 17.7 | 96 | 99 | 4566 |
| nucleoplasm | 2.0e-11 | 16 | 16.6 | 96 | 89 | 4566 |
| nuclear division | 7.6e-11 | 9 | 9.3 | 96 | 20 | 4566 |
| M phase of mitotic cell cycle | 5.9e-10 | 8 | 8.3 | 96 | 17 | 4566 |
| M phase | 1.2e-09 | 9 | 9.3 | 96 | 26 | 4566 |
| transcription initiation from Pol II promoter | 2.2e-09 | 7 | 7.2 | 96 | 13 | 4566 |
| viral host cell process manipulation | 1.6e-08 | 14 | 14.5 | 96 | 102 | 4566 |
| G1/S transition of mitotic cell cycle | 3.1e-08 | 6 | 6.2 | 96 | 11 | 4566 |
| kinetochore | 3.1e-08 | 6 | 6.2 | 96 | 11 | 4566 |
| mitotic anaphase | 3.1e-08 | 6 | 6.2 | 96 | 11 | 4566 |
| mitotic cell cycle | 6.5e-08 | 10 | 10.4 | 96 | 51 | 4566 |
| heterogeneous nuclear ribonucleoprotein | 1.1e-07 | 6 | 6.2 | 96 | 13 | 4566 |
| mitotic checkpoint | 1.9e-07 | 5 | 5.2 | 96 | 8 | 4566 |
| general RNA polymerase II transcription factor activity | 7.5e-07 | 6 | 6.2 | 96 | 17 | 4566 |
| transcription termination | 8.5e-07 | 5 | 5.2 | 96 | 10 | 4566 |
| transcription factor complex | 9.1e-07 | 7 | 7.2 | 96 | 27 | 4566 |
| response to DNA damage stimulus | 1.0e-06 | 21 | 21.8 | 96 | 310 | 4566 |
| nucleotidyltransferase activity | 1.2e-06 | 25 | 26.0 | 96 | 425 | 4566 |
| cyclin-dependent protein kinase activity | 2.6e-06 | 5 | 5.2 | 96 | 12 | 4566 |
| RNA binding | 2.9e-06 | 18 | 18.7 | 96 | 249 | 4566 |
| regulation of mitosis | 4.1e-06 | 5 | 5.2 | 96 | 13 | 4566 |
| regulation of CDK activity | 7.3e-06 | 6 | 6.2 | 96 | 24 | 4566 |
| nuclease activity | 7.7e-06 | 16 | 16.6 | 96 | 215 | 4566 |
| host-pathogen interaction | 1.2e-05 | 15 | 15.6 | 96 | 198 | 4566 |
| nucleolus | 2.5e-05 | 7 | 7.2 | 96 | 43 | 4566 |
| DNA-directed RNA polymerase I activity | 3.4e-05 | 4 | 4.1 | 96 | 10 | 4566 |
| DNA-directed RNA polymerase II activity | 3.4e-05 | 4 | 4.1 | 96 | 10 | 4566 |
| DNA binding | 3.6e-05 | 20 | 20.8 | 96 | 357 | 4566 |
| RNA polymerase II transcription factor activity | 4.5e-05 | 10 | 10.4 | 96 | 102 | 4566 |
| obsolete | 4.5e-05 | 38 | 39.5 | 96 | 990 | 4566 |
| DNA-directed RNA polymerase II\, core complex | 5.4e-05 | 4 | 4.1 | 96 | 11 | 4566 |
| DNA-directed RNA polymerase III activity | 5.4e-05 | 4 | 4.1 | 96 | 11 | 4566 |
| ATP binding | 5.7e-05 | 21 | 21.8 | 96 | 399 | 4566 |
| DNA-directed RNA polymerase activity | 7.9e-05 | 4 | 4.1 | 96 | 12 | 4566 |
| single-stranded RNA binding | 7.9e-05 | 4 | 4.1 | 96 | 12 | 4566 |
| oncogenesis | 0.0001 | 13 | 13.5 | 96 | 184 | 4566 |
| kinase regulator activity | 0.0001 | 8 | 8.3 | 96 | 72 | 4566 |
| cell cycle checkpoint | 0.0001 | 4 | 4.1 | 96 | 13 | 4566 |
| DNA-directed RNA polymerase II\, holoenzyme | 0.0001 | 4 | 4.1 | 96 | 13 | 4566 |
| conjugation with cellular fusion | 0.0001 | 5 | 5.2 | 96 | 24 | 4566 |
| nucleolar preribosome | 0.0001 | 5 | 5.2 | 96 | 24 | 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. | |||||||||
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