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Module 223 -- Immune (defense) response |
| 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: | 3 |
| Num genes: | 142 (see 2325 additional genes for this module) |
| Num experiments: | 736 (277 induced, 459 repressed) |
| Parent module: | None |
| Children modules: | 121 |
| 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. | |
| lymphocyte activation | |
| T_cell activation | |
| defense response | |
| 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 |
| Cancer and cell line (Lung cancer*) | Lung cancer* | 7.9e-32 | 139 | 30.3 | 458 | 252 | 1945 |
| Cancer (Lung cancer*) | Lung cancer* | 7.9e-32 | 139 | 30.3 | 458 | 252 | 1945 |
| Liver tissue (Liver cancer*) | Liver cancer* | 5.2e-30 | 87 | 31.4 | 277 | 187 | 1945 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 6.9e-28 | 87 | 31.4 | 277 | 197 | 1945 |
| Lung cancer (Lung cancer*) | Lung cancer* | 1.5e-27 | 128 | 27.9 | 458 | 238 | 1945 |
| Lung cancer or cell line (Lung cancer*) | Lung cancer* | 1.5e-27 | 128 | 27.9 | 458 | 238 | 1945 |
| Lung tissue, cancer or cell line (Lung cancer*) | Lung cancer* | 7.5e-27 | 140 | 30.5 | 458 | 276 | 1945 |
| Hepatitis infected liver (Liver cancer*) | Liver cancer* | 8.7e-22 | 69 | 24.9 | 277 | 156 | 1945 |
| Stimulated immune cells (Stimulated PBMC*) | Stimulated PBMC* | 9.4e-17 | 59 | 21.2 | 277 | 143 | 1945 |
| Non-tumor liver tissue (Liver cancer) | Liver cancer | 1.0e-16 | 60 | 68.9 | 87 | 76 | 207 |
| Non small cell lung cancer and cell line (Lung cancer*) | Lung cancer* | 1.6e-16 | 99 | 21.6 | 458 | 205 | 1945 |
| Non small cell lung cancer (Lung cancer*) | Lung cancer* | 1.6e-16 | 99 | 21.6 | 458 | 205 | 1945 |
| Hematologic cancer and cell line (Stimulated PBMC) | Stimulated PBMC | 2.2e-15 | 24 | 64.8 | 37 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 2.2e-15 | 24 | 64.8 | 37 | 30 | 182 |
| Hematologic samples (Stimulated PBMC*) | Stimulated PBMC* | 2.9e-15 | 59 | 21.2 | 277 | 152 | 1945 |
| Lymphocytes (Stimulated PBMC*) | Stimulated PBMC* | 2.9e-15 | 59 | 21.2 | 277 | 152 | 1945 |
| Primary blood mononuclear cells (Stimulated PBMC*) | Stimulated PBMC* | 2.9e-15 | 59 | 21.2 | 277 | 152 | 1945 |
| Cancer and cell line (Liver cancer) | Liver cancer | 1.7e-14 | 61 | 96.8 | 63 | 126 | 207 |
| Hematologic samples and cell lines (Stimulated PBMC*) | Stimulated PBMC* | 8.8e-12 | 60 | 21.6 | 277 | 182 | 1945 |
| Monocytes (Stimulated PBMC*) | Stimulated PBMC* | 8.8e-12 | 60 | 21.6 | 277 | 182 | 1945 |
| Cell line (Breast cancer) | Breast cancer | 1.5e-09 | 17 | 70.8 | 24 | 30 | 152 |
| Cell line (B lymphoma) | B lymphoma | 1.1e-07 | 8 | 50 | 16 | 14 | 245 |
| Cancer (Liver cancer) | Liver cancer | 6.2e-07 | 51 | 80.9 | 63 | 115 | 207 |
| Breast cancer cell line (Breast cancer) | Breast cancer | 1.0e-06 | 11 | 45.8 | 24 | 17 | 152 |
| Activated B like DLBCL (B lymphoma) | B lymphoma | 1.1e-06 | 11 | 55 | 20 | 30 | 245 |
| Primary blood mononuclear cells (B lymphoma) | B lymphoma | 3.2e-06 | 7 | 43.7 | 16 | 14 | 245 |
| Liver cancer cell line (Liver cancer) | Liver cancer | 4.0e-06 | 10 | 15.8 | 63 | 10 | 207 |
| Prostate (Prostate cancer*) | Prostate cancer* | 2.7e-05 | 42 | 9.1 | 458 | 101 | 1945 |
| Cell line (Liver cancer) | Liver cancer | 3.3e-05 | 10 | 15.8 | 63 | 11 | 207 |
| Female hormonal cancer cell line (Breast cancer) | Breast cancer | 3.8e-05 | 9 | 37.5 | 24 | 15 | 152 |
| B. petrussis A2 stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 4.2e-05 | 5 | 23.8 | 21 | 5 | 144 |
| B. petrussis stimulated immune cells (Stimulated PBMC) | Stimulated PBMC | 8.4e-05 | 18 | 85.7 | 21 | 67 | 144 |
| Adenocarcinoma (Liver cancer) | Liver cancer | 0.0001 | 42 | 66.6 | 63 | 97 | 207 |
| Breast tissue, cancer or cell line (NCI60) | NCI60 | 0.0001 | 11 | 61.1 | 18 | 31 | 139 |
| Lung carcinoid (Lung cancer) | Lung cancer | 0.0001 | 18 | 12.8 | 140 | 20 | 276 |
| Breast tissue or cancer (NCI60) | NCI60 | 0.0002 | 4 | 22.2 | 18 | 4 | 139 |
| Female hormonal tissue or cancer (NCI60) | NCI60 | 0.0002 | 4 | 22.2 | 18 | 4 | 139 |
| Bone marrow (Leukemia) | Leukemia | 0.0002 | 13 | 38.2 | 34 | 23 | 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 |
| defense response | 1.5e-193 | 142 | 100 | 142 | 272 | 4566 |
| response to biotic stimulus | 8.1e-133 | 142 | 100 | 142 | 600 | 4566 |
| lymphocyte activation | 5.8e-123 | 106 | 74.6 | 142 | 209 | 4566 |
| T-cell activation | 1.7e-121 | 105 | 73.9 | 142 | 207 | 4566 |
| immune response | 3.9e-101 | 120 | 84.5 | 142 | 469 | 4566 |
| regulation of T-cell proliferation | 8.1e-33 | 33 | 23.2 | 142 | 69 | 4566 |
| lymphocyte proliferation | 1.5e-32 | 33 | 23.2 | 142 | 70 | 4566 |
| positive regulation of cell proliferation | 1.5e-31 | 32 | 22.5 | 142 | 68 | 4566 |
| response to stress | 2.0e-20 | 72 | 50.7 | 142 | 792 | 4566 |
| signal transducer activity | 3.0e-18 | 79 | 55.6 | 142 | 1026 | 4566 |
| receptor binding | 2.2e-17 | 37 | 26.0 | 142 | 235 | 4566 |
| growth factor activity | 3.5e-15 | 23 | 16.1 | 142 | 95 | 4566 |
| antigen presentation\, peptide antigen | 6.0e-15 | 11 | 7.7 | 142 | 14 | 4566 |
| antigen processing | 6.0e-15 | 11 | 7.7 | 142 | 14 | 4566 |
| cytokine activity | 1.5e-12 | 17 | 11.9 | 142 | 61 | 4566 |
| receptor activity | 1.2e-10 | 47 | 33.0 | 142 | 582 | 4566 |
| antigen presentation\, endogenous antigen | 1.8e-10 | 7 | 4.9 | 142 | 8 | 4566 |
| antigen processing\, endogenous antigen via MHC class I | 1.8e-10 | 7 | 4.9 | 142 | 8 | 4566 |
| cell-cell signaling | 6.3e-10 | 25 | 17.6 | 142 | 194 | 4566 |
| MHC class I receptor activity | 8.3e-10 | 7 | 4.9 | 142 | 9 | 4566 |
| secretion | 2.6e-09 | 27 | 19.0 | 142 | 240 | 4566 |
| transmembrane receptor activity | 3.5e-09 | 38 | 26.7 | 142 | 448 | 4566 |
| development | 4.1e-08 | 41 | 28.8 | 142 | 554 | 4566 |
| cell communication | 8.2e-08 | 60 | 42.2 | 142 | 1030 | 4566 |
| signal transduction | 2.7e-07 | 51 | 35.9 | 142 | 831 | 4566 |
| viral host cell process manipulation | 2.3e-06 | 14 | 9.8 | 142 | 102 | 4566 |
| integral to plasma membrane | 4.9e-06 | 39 | 27.4 | 142 | 612 | 4566 |
| extracellular space | 6.5e-06 | 20 | 14.0 | 142 | 212 | 4566 |
| host-pathogen interaction | 8.8e-06 | 19 | 13.3 | 142 | 198 | 4566 |
| antigen processing\, exogenous antigen via MHC class II | 1.2e-05 | 4 | 2.8 | 142 | 6 | 4566 |
| EGF receptor signaling pathway | 1.2e-05 | 4 | 2.8 | 142 | 6 | 4566 |
| antigen binding | 2.9e-05 | 4 | 2.8 | 142 | 7 | 4566 |
| response to pest/pathogen/parasite | 3.6e-05 | 16 | 11.2 | 142 | 163 | 4566 |
| cell surface receptor linked signal transduction | 3.9e-05 | 21 | 14.7 | 142 | 259 | 4566 |
| pathogenesis | 9.5e-05 | 7 | 4.9 | 142 | 36 | 4566 |
| response to extracellular stimulus | 0.0001 | 31 | 21.8 | 142 | 500 | 4566 |
| regulation of cytokine biosynthesis | 0.0001 | 3 | 2.1 | 142 | 4 | 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 736 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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