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 >4x |
Module 98 |
| 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: | 393 (see 1813 additional genes for this module) |
| Num experiments: | 615 (257 induced, 358 repressed) |
| Parent module: | 198 |
| 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. | |
| nucleus | |
| endomembrane system | |
| 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 | 1.2e-25 | 27 | 90 | 30 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 1.2e-25 | 27 | 90 | 30 | 30 | 182 |
| Non-tumor liver tissue (Liver cancer) | Liver cancer | 2.4e-18 | 48 | 84.2 | 57 | 76 | 207 |
| 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 |
| Chronic lymphocytic leukemia (B lymphoma) | B lymphoma | 3.4e-12 | 32 | 50 | 64 | 46 | 245 |
| Leukemia (B lymphoma) | B lymphoma | 3.4e-12 | 32 | 50 | 64 | 46 | 245 |
| Leukemia or leukemia cell line (B lymphoma) | B lymphoma | 3.4e-12 | 32 | 50 | 64 | 46 | 245 |
| Cell line (B lymphoma) | B lymphoma | 6.1e-10 | 11 | 42.3 | 26 | 14 | 245 |
| Cancer and cell line (Liver cancer) | Liver cancer | 7.2e-10 | 42 | 97.6 | 43 | 126 | 207 |
| Hematologic cancer and cell line (Stimulated immune*) | Stimulated immune* | 6.4e-09 | 24 | 9.3 | 257 | 53 | 1945 |
| Hematologic samples and cell lines (Stimulated immune*) | Stimulated immune* | 6.4e-09 | 24 | 9.3 | 257 | 53 | 1945 |
| Macrophages (Stimulated immune*) | Stimulated immune* | 6.4e-09 | 24 | 9.3 | 257 | 53 | 1945 |
| Monocytes (Stimulated immune*) | Stimulated immune* | 6.4e-09 | 24 | 9.3 | 257 | 53 | 1945 |
| Small cell lung cancer (Lung cancer) | Lung cancer | 8.2e-08 | 8 | 30.7 | 26 | 10 | 276 |
| Invasive liver tumor (Liver cancer) | Liver cancer | 1.2e-07 | 21 | 48.8 | 43 | 38 | 207 |
| Acute myelogeous leukemia (Leukemia) | Leukemia | 4.1e-07 | 18 | 85.7 | 21 | 50 | 141 |
| Liver cancer cell line (Liver cancer) | Liver cancer | 2.9e-06 | 9 | 20.9 | 43 | 10 | 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 |
| Grade 3 (Breast cancer) | Breast cancer | 7.3e-06 | 13 | 100 | 13 | 38 | 85 |
| Cell line (Liver cancer) | Liver cancer | 1.3e-05 | 9 | 20.9 | 43 | 11 | 207 |
| CNS tissue, cancer or cell line (Neuro tumors*) | Neuro tumors* | 1.5e-05 | 32 | 8.9 | 358 | 85 | 1945 |
| Liver tissue (Liver cancer*) | Liver cancer* | 1.6e-05 | 57 | 15.9 | 358 | 187 | 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 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 9.1e-05 | 57 | 15.9 | 358 | 197 | 1945 |
| Breast cancer (NCI60) | NCI60 | 0.0001 | 3 | 37.5 | 8 | 3 | 139 |
| p53 positive hepatocellular carcinoma (Liver cancer) | Liver cancer | 0.0001 | 14 | 73.6 | 19 | 23 | 60 |
| Acute lymphocytic leukemia (Leukemia) | Leukemia | 0.0002 | 19 | 100 | 19 | 99 | 149 |
| B cells (B lymphoma*) | B lymphoma* | 0.0002 | 63 | 17.5 | 358 | 231 | 1945 |
| B. petrussis stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 0.0002 | 18 | 81.8 | 22 | 67 | 144 |
| Hepatitis infected liver (Liver cancer*) | Liver cancer* | 0.0002 | 46 | 12.8 | 358 | 156 | 1945 |
| CNS cancer or cell line (Neuro tumors*) | Neuro tumors* | 0.0002 | 28 | 7.8 | 358 | 81 | 1945 |
| CNS tumor (Neuro tumors*) | Neuro tumors* | 0.0002 | 28 | 7.8 | 358 | 81 | 1945 |
| Lymphoma or lymphoma cell line (B lymphoma) | B lymphoma | 0.0003 | 25 | 96.1 | 26 | 167 | 245 |
| Cancer and cell line (Neuro tumors*) | Neuro tumors* | 0.0003 | 29 | 8.1 | 358 | 86 | 1945 |
| Cancer (Neuro tumors*) | Neuro tumors* | 0.0003 | 29 | 8.1 | 358 | 86 | 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 |
| nucleus | 2.0e-281 | 387 | 98.4 | 393 | 966 | 4566 |
| endomembrane system | 1.7e-216 | 362 | 92.1 | 393 | 1029 | 4566 |
| transcription regulator activity | 1.3e-53 | 182 | 46.3 | 393 | 703 | 4566 |
| DNA binding | 5.0e-51 | 126 | 32.0 | 393 | 357 | 4566 |
| regulation of transcription\, DNA-dependent | 2.2e-47 | 159 | 40.4 | 393 | 595 | 4566 |
| DNA metabolism | 2.0e-37 | 75 | 19.0 | 393 | 169 | 4566 |
| chemosensory perception | 1.5e-27 | 141 | 35.8 | 393 | 682 | 4566 |
| sensory perception | 7.6e-27 | 142 | 36.1 | 393 | 700 | 4566 |
| DNA repair | 1.8e-24 | 45 | 11.4 | 393 | 93 | 4566 |
| nucleoplasm | 2.5e-22 | 42 | 10.6 | 393 | 89 | 4566 |
| transcription factor activity | 1.8e-21 | 85 | 21.6 | 393 | 340 | 4566 |
| DNA replication | 1.7e-19 | 30 | 7.6 | 393 | 52 | 4566 |
| RNA processing | 3.4e-19 | 41 | 10.4 | 393 | 99 | 4566 |
| cell cycle | 5.3e-19 | 48 | 12.2 | 393 | 135 | 4566 |
| RNA metabolism | 8.5e-18 | 38 | 9.6 | 393 | 92 | 4566 |
| replication fork | 1.0e-16 | 16 | 4.0 | 393 | 17 | 4566 |
| RNA splicing | 2.3e-16 | 30 | 7.6 | 393 | 63 | 4566 |
| transcription | 2.7e-16 | 53 | 13.4 | 393 | 184 | 4566 |
| transcription\, DNA-dependent | 1.8e-15 | 49 | 12.4 | 393 | 167 | 4566 |
| DNA packaging | 1.9e-14 | 25 | 6.3 | 393 | 50 | 4566 |
| mRNA splicing | 1.1e-13 | 24 | 6.1 | 393 | 49 | 4566 |
| RNA polymerase II transcription factor activity | 1.4e-13 | 35 | 8.9 | 393 | 102 | 4566 |
| chromatin | 2.0e-13 | 24 | 6.1 | 393 | 50 | 4566 |
| mitosis | 2.0e-13 | 24 | 6.1 | 393 | 50 | 4566 |
| regulation of cell cycle | 3.3e-13 | 45 | 11.4 | 393 | 163 | 4566 |
| DNA replication and chromosome cycle | 6.6e-13 | 18 | 4.5 | 393 | 29 | 4566 |
| chromosome | 1.0e-12 | 26 | 6.6 | 393 | 62 | 4566 |
| DNA recombination | 2.1e-12 | 17 | 4.3 | 393 | 27 | 4566 |
| nucleic acid binding | 2.2e-12 | 82 | 20.8 | 393 | 444 | 4566 |
| establishment and/or maintenance of chromatin architecture | 2.3e-12 | 22 | 5.5 | 393 | 46 | 4566 |
| nuclear chromosome | 3.4e-12 | 25 | 6.3 | 393 | 60 | 4566 |
| DNA dependent DNA replication | 1.1e-11 | 17 | 4.3 | 393 | 29 | 4566 |
| cytokinesis | 1.1e-11 | 22 | 5.5 | 393 | 49 | 4566 |
| RNA binding | 1.4e-11 | 55 | 13.9 | 393 | 249 | 4566 |
| nucleotidyltransferase activity | 3.3e-11 | 77 | 19.5 | 393 | 425 | 4566 |
| transcription factor complex | 3.6e-11 | 16 | 4.0 | 393 | 27 | 4566 |
| chromosome organization and biogenesis (sensu Eukarya) | 5.0e-11 | 22 | 5.5 | 393 | 52 | 4566 |
| mRNA processing | 9.1e-11 | 19 | 4.8 | 393 | 40 | 4566 |
| response to DNA damage stimulus | 5.0e-10 | 60 | 15.2 | 393 | 310 | 4566 |
| chromatin assembly/disassembly | 5.9e-10 | 17 | 4.3 | 393 | 35 | 4566 |
| nuclease activity | 7.4e-10 | 47 | 11.9 | 393 | 215 | 4566 |
| pre-mRNA splicing factor activity | 1.0e-09 | 17 | 4.3 | 393 | 36 | 4566 |
| nuclear pore | 1.2e-09 | 13 | 3.3 | 393 | 21 | 4566 |
| mRNA binding | 2.7e-09 | 19 | 4.8 | 393 | 47 | 4566 |
| regulation of transcription from Pol II promoter | 2.8e-09 | 36 | 9.1 | 393 | 146 | 4566 |
| S phase of mitotic cell cycle | 3.6e-09 | 14 | 3.5 | 393 | 26 | 4566 |
| transcription from Pol II promoter | 6.1e-09 | 33 | 8.3 | 393 | 130 | 4566 |
| regulation of transcription | 7.7e-09 | 24 | 6.1 | 393 | 76 | 4566 |
| DNA dependent ATPase activity | 1.2e-08 | 14 | 3.5 | 393 | 28 | 4566 |
| response to abiotic stimulus | 1.8e-08 | 154 | 39.1 | 393 | 1228 | 4566 |
| regulation of transcription by pheromones | 2.1e-08 | 31 | 7.8 | 393 | 123 | 4566 |
| pore complex | 3.9e-08 | 14 | 3.5 | 393 | 30 | 4566 |
| M phase | 4.3e-08 | 13 | 3.3 | 393 | 26 | 4566 |
| mitotic cell cycle | 8.9e-08 | 18 | 4.5 | 393 | 51 | 4566 |
| transcription initiation | 9.9e-08 | 10 | 2.5 | 393 | 16 | 4566 |
| transcription initiation from Pol II promoter | 1.2e-07 | 9 | 2.2 | 393 | 13 | 4566 |
| ATP binding | 1.2e-07 | 65 | 16.5 | 393 | 399 | 4566 |
| transcription factor binding | 1.4e-07 | 29 | 7.3 | 393 | 119 | 4566 |
| nucleosome assembly | 1.4e-07 | 12 | 3.0 | 393 | 24 | 4566 |
| general RNA polymerase II transcription factor activity | 2.2e-07 | 10 | 2.5 | 393 | 17 | 4566 |
| M phase of mitotic cell cycle | 2.2e-07 | 10 | 2.5 | 393 | 17 | 4566 |
| DNA-directed DNA polymerase activity | 2.4e-07 | 7 | 1.7 | 393 | 8 | 4566 |
| protein-nucleus import | 4.9e-07 | 11 | 2.7 | 393 | 22 | 4566 |
| nucleocytoplasmic transport | 8.7e-07 | 11 | 2.7 | 393 | 23 | 4566 |
| histone acetyltransferase complex | 1.0e-06 | 7 | 1.7 | 393 | 9 | 4566 |
| primary active transporter activity | 1.0e-06 | 7 | 1.7 | 393 | 9 | 4566 |
| transcription cofactor activity | 1.0e-06 | 28 | 7.1 | 393 | 123 | 4566 |
| 26S proteasome | 1.1e-06 | 12 | 3.0 | 393 | 28 | 4566 |
| regulation of CDK activity | 1.4e-06 | 11 | 2.7 | 393 | 24 | 4566 |
| nuclear division | 1.6e-06 | 10 | 2.5 | 393 | 20 | 4566 |
| proteasome complex (sensu Eukarya) | 2.9e-06 | 10 | 2.5 | 393 | 21 | 4566 |
| oncogenesis | 4.2e-06 | 35 | 8.9 | 393 | 184 | 4566 |
| nucleosome disassembly | 5.0e-06 | 10 | 2.5 | 393 | 22 | 4566 |
| transcription factor TFIID complex | 9.4e-06 | 6 | 1.5 | 393 | 8 | 4566 |
| chromatin binding | 1.0e-05 | 9 | 2.2 | 393 | 19 | 4566 |
| damaged DNA binding | 1.2e-05 | 10 | 2.5 | 393 | 24 | 4566 |
| P-P-bond-hydrolysis-driven transporter activity | 1.7e-05 | 7 | 1.7 | 393 | 12 | 4566 |
| condensed chromosome | 1.9e-05 | 8 | 2.0 | 393 | 16 | 4566 |
| DNA replication factor C complex | 2.5e-05 | 5 | 1.2 | 393 | 6 | 4566 |
| nu DNA polymerase activity | 2.5e-05 | 5 | 1.2 | 393 | 6 | 4566 |
| cell cycle checkpoint | 3.6e-05 | 7 | 1.7 | 393 | 13 | 4566 |
| regulation of mitosis | 3.6e-05 | 7 | 1.7 | 393 | 13 | 4566 |
| nucleotide binding | 3.8e-05 | 15 | 3.8 | 393 | 55 | 4566 |
| transcription co-repressor activity | 3.8e-05 | 13 | 3.3 | 393 | 43 | 4566 |
| DNA replication initiation | 6.0e-05 | 6 | 1.5 | 393 | 10 | 4566 |
| phosphorus metabolism | 8.9e-05 | 26 | 6.6 | 393 | 138 | 4566 |
| ATPase activity\, coupled | 0.0001 | 12 | 3.0 | 393 | 41 | 4566 |
| kinetochore | 0.0001 | 6 | 1.5 | 393 | 11 | 4566 |
| mitotic anaphase | 0.0001 | 6 | 1.5 | 393 | 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 615 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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