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 >4x |
Module 252 -- TFs and nuclear |
| 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: | 7 |
| Num genes: | 237 (see 1067 additional genes for this module) |
| Num experiments: | 660 (280 induced, 380 repressed) |
| Parent module: | None |
| Children modules: | 198 197 |
| 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. | |
| sensory perception | |
| chemosensory perception | |
| regulation of transcription, DNA_dependent | |
| nucleus | |
| endomembrane system | |
| transcription regulator activity | |
| DNA binding | |
| 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 | 2.0e-28 | 63 | 85.1 | 74 | 76 | 207 |
| Hematologic cancer and cell line (Stimulated PBMC) | Stimulated PBMC | 2.6e-27 | 28 | 90.3 | 31 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 2.6e-27 | 28 | 90.3 | 31 | 30 | 182 |
| Chronic lymphocytic leukemia (B lymphoma) | B lymphoma | 1.5e-17 | 39 | 52 | 75 | 46 | 245 |
| Leukemia (B lymphoma) | B lymphoma | 1.5e-17 | 39 | 52 | 75 | 46 | 245 |
| Leukemia or leukemia cell line (B lymphoma) | B lymphoma | 1.5e-17 | 39 | 52 | 75 | 46 | 245 |
| Cell line (B lymphoma) | B lymphoma | 1.2e-14 | 14 | 45.1 | 31 | 14 | 245 |
| Cancer and cell line (Liver cancer) | Liver cancer | 4.0e-13 | 53 | 98.1 | 54 | 126 | 207 |
| Normal lung tissue (Lung cancer) | Lung cancer | 1.2e-11 | 19 | 32.2 | 59 | 22 | 276 |
| Liver tissue (Liver cancer*) | Liver cancer* | 1.6e-11 | 74 | 19.4 | 380 | 187 | 1945 |
| Normal tissue (Lung cancer) | Lung cancer | 6.2e-11 | 19 | 32.2 | 59 | 23 | 276 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 3.2e-10 | 74 | 19.4 | 380 | 197 | 1945 |
| Invasive liver tumor (Liver cancer) | Liver cancer | 8.7e-10 | 26 | 48.1 | 54 | 38 | 207 |
| Hepatitis infected liver (Liver cancer*) | Liver cancer* | 1.6e-07 | 57 | 15 | 380 | 156 | 1945 |
| Cell line (Liver cancer) | Liver cancer | 1.6e-07 | 11 | 20.3 | 54 | 11 | 207 |
| Hematologic cancer and cell line (Stimulated immune*) | Stimulated immune* | 1.8e-07 | 23 | 8.2 | 279 | 53 | 1945 |
| Hematologic samples and cell lines (Stimulated immune*) | Stimulated immune* | 1.8e-07 | 23 | 8.2 | 279 | 53 | 1945 |
| Macrophages (Stimulated immune*) | Stimulated immune* | 1.8e-07 | 23 | 8.2 | 279 | 53 | 1945 |
| Monocytes (Stimulated immune*) | Stimulated immune* | 1.8e-07 | 23 | 8.2 | 279 | 53 | 1945 |
| Grade 3 (Breast cancer) | Breast cancer | 2.8e-07 | 16 | 100 | 16 | 38 | 85 |
| Acute myelogeous leukemia (Leukemia) | Leukemia | 4.1e-07 | 18 | 85.7 | 21 | 50 | 141 |
| Liver cancer cell line (Liver cancer) | Liver cancer | 7.4e-07 | 10 | 18.5 | 54 | 10 | 207 |
| Small cell lung cancer (Lung cancer) | Lung cancer | 9.0e-07 | 8 | 23.5 | 34 | 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 |
| B cells (B lymphoma*) | B lymphoma* | 2.0e-06 | 73 | 19.2 | 380 | 231 | 1945 |
| Lymphocytes (B lymphoma*) | B lymphoma* | 4.8e-06 | 75 | 19.7 | 380 | 244 | 1945 |
| Normal tissue (Liver cancer) | Liver cancer | 7.4e-06 | 13 | 17.5 | 74 | 14 | 207 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 1.0e-05 | 50 | 17.9 | 279 | 197 | 1945 |
| B. petrussis stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 1.7e-05 | 20 | 86.9 | 23 | 67 | 144 |
| Breast cancer (NCI60) | NCI60 | 4.5e-05 | 3 | 50 | 6 | 3 | 139 |
| Adenocarcinoma (Liver cancer) | Liver cancer | 4.8e-05 | 38 | 70.3 | 54 | 97 | 207 |
| Cancer (B lymphoma*) | B lymphoma* | 5.8e-05 | 61 | 16.0 | 380 | 200 | 1945 |
| Hematologic cancer (B lymphoma*) | B lymphoma* | 5.8e-05 | 61 | 16.0 | 380 | 200 | 1945 |
| B. petrussis A2 stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 6.9e-05 | 5 | 21.7 | 23 | 5 | 144 |
| B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 6.9e-05 | 5 | 21.7 | 23 | 5 | 144 |
| p53 positive hepatocellular carcinoma (Liver cancer) | Liver cancer | 8.2e-05 | 17 | 68 | 25 | 23 | 60 |
| Cancer (Liver cancer) | Liver cancer | 8.8e-05 | 42 | 77.7 | 54 | 115 | 207 |
| Hematologic samples and cell lines (Various tumors) | Various tumors | 0.0001 | 9 | 75 | 12 | 37 | 154 |
| Hematologic samples (Various tumors) | Various tumors | 0.0001 | 9 | 75 | 12 | 37 | 154 |
| 1X dose immune stimulation (Stimulated PBMC) | Stimulated PBMC | 0.0001 | 9 | 60 | 15 | 13 | 59 |
| Acute lymphocytic leukemia (Leukemia) | Leukemia | 0.0002 | 19 | 100 | 19 | 99 | 149 |
| Gram negative bacteria stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 0.0003 | 20 | 86.9 | 23 | 78 | 144 |
| Lymphoma or lymphoma cell line (B lymphoma) | B lymphoma | 0.0004 | 29 | 93.5 | 31 | 167 | 245 |
| 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 |
| nucleus | 9.0e-152 | 229 | 96.6 | 237 | 966 | 4566 |
| endomembrane system | 1.0e-117 | 214 | 90.2 | 237 | 1029 | 4566 |
| DNA metabolism | 4.1e-31 | 55 | 23.2 | 237 | 169 | 4566 |
| DNA binding | 1.0e-28 | 75 | 31.6 | 237 | 357 | 4566 |
| transcription regulator activity | 1.3e-24 | 100 | 42.1 | 237 | 703 | 4566 |
| regulation of transcription\, DNA-dependent | 2.3e-24 | 91 | 38.3 | 237 | 595 | 4566 |
| DNA repair | 4.6e-20 | 33 | 13.9 | 237 | 93 | 4566 |
| cell cycle | 5.6e-19 | 38 | 16.0 | 237 | 135 | 4566 |
| DNA replication | 5.4e-18 | 24 | 10.1 | 237 | 52 | 4566 |
| nucleoplasm | 1.4e-16 | 29 | 12.2 | 237 | 89 | 4566 |
| replication fork | 2.8e-14 | 13 | 5.4 | 237 | 17 | 4566 |
| DNA replication and chromosome cycle | 6.2e-14 | 16 | 6.7 | 237 | 29 | 4566 |
| mitosis | 1.0e-13 | 20 | 8.4 | 237 | 50 | 4566 |
| nucleotidyltransferase activity | 3.0e-13 | 59 | 24.8 | 237 | 425 | 4566 |
| RNA splicing | 1.7e-12 | 21 | 8.8 | 237 | 63 | 4566 |
| RNA metabolism | 2.1e-12 | 25 | 10.5 | 237 | 92 | 4566 |
| regulation of cell cycle | 4.3e-12 | 33 | 13.9 | 237 | 163 | 4566 |
| cytokinesis | 1.0e-11 | 18 | 7.5 | 237 | 49 | 4566 |
| mRNA splicing | 1.0e-11 | 18 | 7.5 | 237 | 49 | 4566 |
| RNA processing | 1.3e-11 | 25 | 10.5 | 237 | 99 | 4566 |
| chemosensory perception | 1.7e-11 | 75 | 31.6 | 237 | 682 | 4566 |
| DNA dependent DNA replication | 2.7e-11 | 14 | 5.9 | 237 | 29 | 4566 |
| transcription | 2.9e-11 | 34 | 14.3 | 237 | 184 | 4566 |
| transcription\, DNA-dependent | 4.4e-11 | 32 | 13.5 | 237 | 167 | 4566 |
| mRNA binding | 5.5e-11 | 17 | 7.1 | 237 | 47 | 4566 |
| sensory perception | 6.6e-11 | 75 | 31.6 | 237 | 700 | 4566 |
| response to DNA damage stimulus | 7.9e-11 | 45 | 18.9 | 237 | 310 | 4566 |
| DNA recombination | 1.5e-10 | 13 | 5.4 | 237 | 27 | 4566 |
| chromatin | 1.7e-10 | 17 | 7.1 | 237 | 50 | 4566 |
| pre-mRNA splicing factor activity | 9.6e-10 | 14 | 5.9 | 237 | 36 | 4566 |
| ATP binding | 1.3e-09 | 50 | 21.0 | 237 | 399 | 4566 |
| S phase of mitotic cell cycle | 1.4e-09 | 12 | 5.0 | 237 | 26 | 4566 |
| DNA packaging | 1.7e-09 | 16 | 6.7 | 237 | 50 | 4566 |
| transcription factor activity | 1.8e-09 | 45 | 18.9 | 237 | 340 | 4566 |
| nucleic acid binding | 2.2e-09 | 53 | 22.3 | 237 | 444 | 4566 |
| regulation of transcription | 5.1e-09 | 19 | 8.0 | 237 | 76 | 4566 |
| mitotic cell cycle | 2.0e-08 | 15 | 6.3 | 237 | 51 | 4566 |
| primary active transporter activity | 3.0e-08 | 7 | 2.9 | 237 | 9 | 4566 |
| M phase of mitotic cell cycle | 3.9e-08 | 9 | 3.7 | 237 | 17 | 4566 |
| DNA dependent ATPase activity | 5.7e-08 | 11 | 4.6 | 237 | 28 | 4566 |
| RNA binding | 1.0e-07 | 34 | 14.3 | 237 | 249 | 4566 |
| transcription from Pol II promoter | 1.3e-07 | 23 | 9.7 | 237 | 130 | 4566 |
| chromosome organization and biogenesis (sensu Eukarya) | 2.1e-07 | 14 | 5.9 | 237 | 52 | 4566 |
| M phase | 2.9e-07 | 10 | 4.2 | 237 | 26 | 4566 |
| establishment and/or maintenance of chromatin architecture | 3.1e-07 | 13 | 5.4 | 237 | 46 | 4566 |
| chromosome | 3.5e-07 | 15 | 6.3 | 237 | 62 | 4566 |
| DNA-directed DNA polymerase activity | 4.7e-07 | 6 | 2.5 | 237 | 8 | 4566 |
| P-P-bond-hydrolysis-driven transporter activity | 5.8e-07 | 7 | 2.9 | 237 | 12 | 4566 |
| RNA polymerase II transcription factor activity | 7.9e-07 | 19 | 8.0 | 237 | 102 | 4566 |
| chromatin assembly/disassembly | 8.0e-07 | 11 | 4.6 | 237 | 35 | 4566 |
| nuclear chromosome | 1.4e-06 | 14 | 5.9 | 237 | 60 | 4566 |
| damaged DNA binding | 1.5e-06 | 9 | 3.7 | 237 | 24 | 4566 |
| oncogenesis | 2.0e-06 | 26 | 10.9 | 237 | 184 | 4566 |
| chromatin binding | 2.1e-06 | 8 | 3.3 | 237 | 19 | 4566 |
| nuclear division | 3.4e-06 | 8 | 3.3 | 237 | 20 | 4566 |
| single-stranded DNA binding | 3.4e-06 | 8 | 3.3 | 237 | 20 | 4566 |
| mRNA processing | 3.5e-06 | 11 | 4.6 | 237 | 40 | 4566 |
| transcription factor complex | 4.8e-06 | 9 | 3.7 | 237 | 27 | 4566 |
| pore complex | 1.2e-05 | 9 | 3.7 | 237 | 30 | 4566 |
| nucleosome assembly | 1.6e-05 | 8 | 3.3 | 237 | 24 | 4566 |
| regulation of mitosis | 2.3e-05 | 6 | 2.5 | 237 | 13 | 4566 |
| regulation of transcription from Pol II promoter | 5.1e-05 | 20 | 8.4 | 237 | 146 | 4566 |
| nuclear pore | 5.7e-05 | 7 | 2.9 | 237 | 21 | 4566 |
| DNA replication initiation | 7.3e-05 | 5 | 2.1 | 237 | 10 | 4566 |
| transcription initiation | 9.4e-05 | 6 | 2.5 | 237 | 16 | 4566 |
| mitotic recombination | 9.7e-05 | 4 | 1.6 | 237 | 6 | 4566 |
| nu DNA polymerase activity | 9.7e-05 | 4 | 1.6 | 237 | 6 | 4566 |
| nuclease activity | 9.8e-05 | 25 | 10.5 | 237 | 215 | 4566 |
| nucleocytoplasmic transport | 0.0001 | 7 | 2.9 | 237 | 23 | 4566 |
| mitotic anaphase | 0.0001 | 5 | 2.1 | 237 | 11 | 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 660 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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