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 >4x |
Module 198 |
| 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: | 303 (see 1394 additional genes for this module) |
| Num experiments: | 641 (273 induced, 368 repressed) |
| Parent module: | 252 |
| Children modules: | 98 |
| 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. | |
| 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 |
| Hematologic cancer and cell line (Stimulated PBMC) | Stimulated PBMC | 2.6e-28 | 28 | 93.3 | 30 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 2.6e-28 | 28 | 93.3 | 30 | 30 | 182 |
| Non-tumor liver tissue (Liver cancer) | Liver cancer | 4.7e-21 | 52 | 85.2 | 61 | 76 | 207 |
| Chronic lymphocytic leukemia (B lymphoma) | B lymphoma | 6.4e-14 | 35 | 50 | 70 | 46 | 245 |
| Leukemia (B lymphoma) | B lymphoma | 6.4e-14 | 35 | 50 | 70 | 46 | 245 |
| Leukemia or leukemia cell line (B lymphoma) | B lymphoma | 6.4e-14 | 35 | 50 | 70 | 46 | 245 |
| Normal lung tissue (Lung cancer) | Lung cancer | 3.5e-13 | 20 | 33.8 | 59 | 22 | 276 |
| Normal tissue (Lung cancer) | Lung cancer | 2.3e-12 | 20 | 33.8 | 59 | 23 | 276 |
| Cancer and cell line (Liver cancer) | Liver cancer | 6.8e-12 | 49 | 98 | 50 | 126 | 207 |
| Invasive liver tumor (Liver cancer) | Liver cancer | 7.6e-11 | 26 | 52 | 50 | 38 | 207 |
| Cell line (B lymphoma) | B lymphoma | 1.0e-09 | 11 | 40.7 | 27 | 14 | 245 |
| Hematologic cancer and cell line (Stimulated immune*) | Stimulated immune* | 2.1e-08 | 24 | 8.8 | 272 | 53 | 1945 |
| Hematologic samples and cell lines (Stimulated immune*) | Stimulated immune* | 2.1e-08 | 24 | 8.8 | 272 | 53 | 1945 |
| Macrophages (Stimulated immune*) | Stimulated immune* | 2.1e-08 | 24 | 8.8 | 272 | 53 | 1945 |
| Monocytes (Stimulated immune*) | Stimulated immune* | 2.1e-08 | 24 | 8.8 | 272 | 53 | 1945 |
| Liver cancer cell line (Liver cancer) | Liver cancer | 3.2e-07 | 10 | 20 | 50 | 10 | 207 |
| Acute myelogeous leukemia (Leukemia) | Leukemia | 4.1e-07 | 18 | 85.7 | 21 | 50 | 141 |
| Small cell lung cancer (Lung cancer) | Lung cancer | 6.9e-07 | 8 | 24.2 | 33 | 10 | 276 |
| Grade 3 (Breast cancer) | Breast cancer | 8.6e-07 | 15 | 100 | 15 | 38 | 85 |
| Liver tissue (Liver cancer*) | Liver cancer* | 1.6e-06 | 61 | 16.5 | 368 | 187 | 1945 |
| Cell line (Liver cancer) | Liver cancer | 2.8e-06 | 10 | 20 | 50 | 11 | 207 |
| 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 |
| B cells (B lymphoma*) | B lymphoma* | 1.1e-05 | 69 | 18.7 | 368 | 231 | 1945 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 1.1e-05 | 61 | 16.5 | 368 | 197 | 1945 |
| Adenocarcinoma (Liver cancer) | Liver cancer | 3.7e-05 | 36 | 72 | 50 | 97 | 207 |
| B. petrussis stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 3.8e-05 | 19 | 86.3 | 22 | 67 | 144 |
| Lymphocytes (B lymphoma*) | B lymphoma* | 4.6e-05 | 70 | 19.0 | 368 | 244 | 1945 |
| B. petrussis A2 stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 5.4e-05 | 5 | 22.7 | 22 | 5 | 144 |
| B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 5.4e-05 | 5 | 22.7 | 22 | 5 | 144 |
| CNS tissue, cancer or cell line (Neuro tumors*) | Neuro tumors* | 7.5e-05 | 31 | 8.4 | 368 | 85 | 1945 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 0.0001 | 46 | 16.9 | 272 | 197 | 1945 |
| Breast cancer (NCI60) | NCI60 | 0.0001 | 3 | 37.5 | 8 | 3 | 139 |
| Acute lymphocytic leukemia (Leukemia) | Leukemia | 0.0001 | 20 | 100 | 20 | 99 | 149 |
| Hepatitis infected liver (Liver cancer*) | Liver cancer* | 0.0001 | 48 | 13.0 | 368 | 156 | 1945 |
| Cancer (Liver cancer) | Liver cancer | 0.0001 | 39 | 78 | 50 | 115 | 207 |
| Lymphoma or lymphoma cell line (B lymphoma) | B lymphoma | 0.0002 | 26 | 96.2 | 27 | 167 | 245 |
| Cancer (B lymphoma*) | B lymphoma* | 0.0003 | 57 | 15.4 | 368 | 200 | 1945 |
| Hematologic cancer (B lymphoma*) | B lymphoma* | 0.0003 | 57 | 15.4 | 368 | 200 | 1945 |
| Lymphocytes (Leukemia) | Leukemia | 0.0003 | 17 | 100 | 17 | 91 | 141 |
| 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 | 2.1e-207 | 297 | 98.0 | 303 | 966 | 4566 |
| endomembrane system | 5.6e-164 | 280 | 92.4 | 303 | 1029 | 4566 |
| DNA binding | 7.0e-40 | 99 | 32.6 | 303 | 357 | 4566 |
| DNA metabolism | 3.6e-37 | 67 | 22.1 | 303 | 169 | 4566 |
| transcription regulator activity | 9.5e-34 | 131 | 43.2 | 303 | 703 | 4566 |
| regulation of transcription\, DNA-dependent | 8.6e-32 | 117 | 38.6 | 303 | 595 | 4566 |
| DNA repair | 1.0e-22 | 39 | 12.8 | 303 | 93 | 4566 |
| DNA replication | 1.6e-21 | 29 | 9.5 | 303 | 52 | 4566 |
| nucleoplasm | 2.2e-20 | 36 | 11.8 | 303 | 89 | 4566 |
| cell cycle | 1.4e-18 | 42 | 13.8 | 303 | 135 | 4566 |
| transcription | 7.7e-17 | 47 | 15.5 | 303 | 184 | 4566 |
| replication fork | 1.8e-16 | 15 | 4.9 | 303 | 17 | 4566 |
| transcription\, DNA-dependent | 2.4e-16 | 44 | 14.5 | 303 | 167 | 4566 |
| mitosis | 5.5e-16 | 24 | 7.9 | 303 | 50 | 4566 |
| chemosensory perception | 1.7e-15 | 98 | 32.3 | 303 | 682 | 4566 |
| nucleotidyltransferase activity | 6.6e-15 | 72 | 23.7 | 303 | 425 | 4566 |
| sensory perception | 1.0e-14 | 98 | 32.3 | 303 | 700 | 4566 |
| RNA processing | 5.2e-14 | 31 | 10.2 | 303 | 99 | 4566 |
| DNA replication and chromosome cycle | 1.5e-13 | 17 | 5.6 | 303 | 29 | 4566 |
| RNA metabolism | 2.9e-13 | 29 | 9.5 | 303 | 92 | 4566 |
| RNA splicing | 3.2e-13 | 24 | 7.9 | 303 | 63 | 4566 |
| DNA recombination | 6.4e-13 | 16 | 5.2 | 303 | 27 | 4566 |
| cytokinesis | 6.6e-13 | 21 | 6.9 | 303 | 49 | 4566 |
| DNA packaging | 1.0e-12 | 21 | 6.9 | 303 | 50 | 4566 |
| transcription factor activity | 1.1e-12 | 59 | 19.4 | 303 | 340 | 4566 |
| DNA dependent DNA replication | 2.9e-12 | 16 | 5.2 | 303 | 29 | 4566 |
| mRNA splicing | 7.2e-12 | 20 | 6.6 | 303 | 49 | 4566 |
| regulation of cell cycle | 1.0e-11 | 37 | 12.2 | 303 | 163 | 4566 |
| chromatin | 1.0e-10 | 19 | 6.2 | 303 | 50 | 4566 |
| response to DNA damage stimulus | 1.1e-10 | 52 | 17.1 | 303 | 310 | 4566 |
| ATP binding | 1.2e-10 | 61 | 20.1 | 303 | 399 | 4566 |
| establishment and/or maintenance of chromatin architecture | 1.9e-10 | 18 | 5.9 | 303 | 46 | 4566 |
| regulation of transcription | 2.4e-10 | 23 | 7.5 | 303 | 76 | 4566 |
| chromosome organization and biogenesis (sensu Eukarya) | 2.4e-10 | 19 | 6.2 | 303 | 52 | 4566 |
| mRNA binding | 2.9e-10 | 18 | 5.9 | 303 | 47 | 4566 |
| S phase of mitotic cell cycle | 1.7e-09 | 13 | 4.2 | 303 | 26 | 4566 |
| pre-mRNA splicing factor activity | 2.3e-09 | 15 | 4.9 | 303 | 36 | 4566 |
| nucleic acid binding | 3.7e-09 | 62 | 20.4 | 303 | 444 | 4566 |
| DNA dependent ATPase activity | 5.6e-09 | 13 | 4.2 | 303 | 28 | 4566 |
| chromatin assembly/disassembly | 1.5e-08 | 14 | 4.6 | 303 | 35 | 4566 |
| M phase of mitotic cell cycle | 1.8e-08 | 10 | 3.3 | 303 | 17 | 4566 |
| M phase | 2.4e-08 | 12 | 3.9 | 303 | 26 | 4566 |
| RNA polymerase II transcription factor activity | 2.5e-08 | 24 | 7.9 | 303 | 102 | 4566 |
| DNA-directed DNA polymerase activity | 4.0e-08 | 7 | 2.3 | 303 | 8 | 4566 |
| transcription factor complex | 4.1e-08 | 12 | 3.9 | 303 | 27 | 4566 |
| chromosome | 4.8e-08 | 18 | 5.9 | 303 | 62 | 4566 |
| RNA binding | 7.6e-08 | 40 | 13.2 | 303 | 249 | 4566 |
| chromatin binding | 7.7e-08 | 10 | 3.3 | 303 | 19 | 4566 |
| mitotic cell cycle | 8.1e-08 | 16 | 5.2 | 303 | 51 | 4566 |
| mRNA processing | 1.1e-07 | 14 | 4.6 | 303 | 40 | 4566 |
| nuclear division | 1.4e-07 | 10 | 3.3 | 303 | 20 | 4566 |
| primary active transporter activity | 1.7e-07 | 7 | 2.3 | 303 | 9 | 4566 |
| nuclear chromosome | 1.7e-07 | 17 | 5.6 | 303 | 60 | 4566 |
| regulation of transcription from Pol II promoter | 1.9e-07 | 28 | 9.2 | 303 | 146 | 4566 |
| transcription from Pol II promoter | 2.3e-07 | 26 | 8.5 | 303 | 130 | 4566 |
| pore complex | 1.6e-06 | 11 | 3.6 | 303 | 30 | 4566 |
| oncogenesis | 2.7e-06 | 30 | 9.9 | 303 | 184 | 4566 |
| transcription initiation | 2.7e-06 | 8 | 2.6 | 303 | 16 | 4566 |
| P-P-bond-hydrolysis-driven transporter activity | 3.1e-06 | 7 | 2.3 | 303 | 12 | 4566 |
| nuclear pore | 3.2e-06 | 9 | 2.9 | 303 | 21 | 4566 |
| histone acetyltransferase complex | 5.7e-06 | 6 | 1.9 | 303 | 9 | 4566 |
| cell cycle checkpoint | 6.4e-06 | 7 | 2.3 | 303 | 13 | 4566 |
| transcription initiation from Pol II promoter | 6.4e-06 | 7 | 2.3 | 303 | 13 | 4566 |
| DNA replication factor C complex | 7.0e-06 | 5 | 1.6 | 303 | 6 | 4566 |
| nu DNA polymerase activity | 7.0e-06 | 5 | 1.6 | 303 | 6 | 4566 |
| nucleotide binding | 8.6e-06 | 14 | 4.6 | 303 | 55 | 4566 |
| damaged DNA binding | 1.1e-05 | 9 | 2.9 | 303 | 24 | 4566 |
| nucleosome assembly | 1.1e-05 | 9 | 2.9 | 303 | 24 | 4566 |
| regulation of CDK activity | 1.1e-05 | 9 | 2.9 | 303 | 24 | 4566 |
| regulation of transcription by pheromones | 1.3e-05 | 22 | 7.2 | 303 | 123 | 4566 |
| single-stranded DNA binding | 2.1e-05 | 8 | 2.6 | 303 | 20 | 4566 |
| nuclease activity | 2.4e-05 | 31 | 10.2 | 303 | 215 | 4566 |
| mitotic anaphase | 2.8e-05 | 6 | 1.9 | 303 | 11 | 4566 |
| ATPase activity\, coupled | 4.7e-05 | 11 | 3.6 | 303 | 41 | 4566 |
| protein-nucleus import | 4.8e-05 | 8 | 2.6 | 303 | 22 | 4566 |
| general RNA polymerase II transcription factor activity | 5.7e-05 | 7 | 2.3 | 303 | 17 | 4566 |
| transcription factor TFIID complex | 5.9e-05 | 5 | 1.6 | 303 | 8 | 4566 |
| nucleocytoplasmic transport | 6.9e-05 | 8 | 2.6 | 303 | 23 | 4566 |
| 3'-5' exonuclease activity | 9.0e-05 | 4 | 1.3 | 303 | 5 | 4566 |
| chromatin remodeling complex | 9.0e-05 | 4 | 1.3 | 303 | 5 | 4566 |
| regulation of mitosis | 9.3e-05 | 6 | 1.9 | 303 | 13 | 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 641 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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