Module 169 -- Immune response

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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: 97 (see 2324 additional genes for this module)
Num experiments: 499 (200 induced, 299 repressed)
Parent module: None
Children modules: None


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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.
Rosenwald01 36
Alizadeh00 19


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 2.6e-26 45 56.9 79 46 245
Leukemia (B lymphoma) B lymphoma 2.6e-26 45 56.9 79 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 2.6e-26 45 56.9 79 46 245
Lymphocytes (B lymphoma*) B lymphoma* 5.0e-23 76 38 200 244 1945
Cancer (B lymphoma*) B lymphoma* 1.0e-19 64 32 200 200 1945
Hematologic cancer (B lymphoma*) B lymphoma* 1.0e-19 64 32 200 200 1945
Cancer and cell line (B lymphoma*) B lymphoma* 2.1e-19 66 33 200 214 1945
Hematologic cancer and cell line (B lymphoma*) B lymphoma* 2.1e-19 66 33 200 214 1945
B cells (B lymphoma*) B lymphoma* 9.1e-19 68 34 200 231 1945
Lymphocytes (B lymphoma*) B lymphoma* 1.6e-12 78 26.0 299 244 1945
B cells (B lymphoma*) B lymphoma* 6.5e-12 74 24.7 299 231 1945
Activated B like DLBCL (B lymphoma) B lymphoma 4.3e-09 24 31.5 76 30 245
Cancer and cell line (B lymphoma*) B lymphoma* 1.8e-08 63 21.0 299 214 1945
Hematologic cancer and cell line (B lymphoma*) B lymphoma* 1.8e-08 63 21.0 299 214 1945
Stimulated immune cells (Stimulated PBMC*) Stimulated PBMC* 2.2e-08 37 18.5 200 143 1945
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 3.4e-08 19 48.7 39 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 3.4e-08 19 48.7 39 30 182
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 1.0e-07 58 76.3 76 126 245
Hematologic samples (Stimulated PBMC*) Stimulated PBMC* 1.3e-07 37 18.5 200 152 1945
Lymphocytes (Stimulated PBMC*) Stimulated PBMC* 1.3e-07 37 18.5 200 152 1945
Primary blood mononuclear cells (Stimulated PBMC*) Stimulated PBMC* 1.3e-07 37 18.5 200 152 1945
Cell line (Breast cancer) Breast cancer 2.5e-07 13 72.2 18 30 152
Stimulated B cells (B lymphoma) B lymphoma 6.8e-07 12 15.1 79 12 245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 7.8e-07 59 77.6 76 134 245
Female hormonal cancer cell line (Breast cancer) Breast cancer 1.8e-06 9 50 18 15 152
GC B like DLBCL (B lymphoma) B lymphoma 2.3e-06 31 40.7 76 53 245
Liver cancer cell line (Liver cancer) Liver cancer 2.9e-06 8 26.6 30 10 207
Lung carcinoid (Lung cancer) Lung cancer 4.3e-06 13 24.0 54 20 276
Breast cancer cell line (Breast cancer) Breast cancer 7.8e-06 9 50 18 17 152
Cell line (Liver cancer) Liver cancer 9.7e-06 8 26.6 30 11 207
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 1.0e-05 66 86.8 76 167 245
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 1.5e-05 37 18.5 200 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 1.5e-05 37 18.5 200 182 1945
Cancer and cell line (Liver cancer) Liver cancer 2.3e-05 28 93.3 30 126 207
Cancer (B lymphoma*) B lymphoma* 2.6e-05 52 17.3 299 200 1945
Hematologic cancer (B lymphoma*) B lymphoma* 2.6e-05 52 17.3 299 200 1945
Hematologic samples (B lymphoma) B lymphoma 5.3e-05 16 20.2 79 22 245
Unstimulated immune cells (Stimulated PBMC) Stimulated PBMC 6.9e-05 18 46.1 39 39 182
Cell line (B lymphoma) B lymphoma 0.0003 11 13.9 79 14 245


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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
humoral defense mechanism (sensu Invertebrata) 2.6e-06 8 13.7 58 72 4566
immune response 1.0e-05 18 31.0 58 469 4566
response to stress 1.3e-05 24 41.3 58 792 4566
humoral immune response 1.3e-05 9 15.5 58 118 4566
response to pest/pathogen/parasite 3.0e-05 10 17.2 58 163 4566
signal transducer activity 3.9e-05 27 46.5 58 1026 4566
response to biotic stimulus 8.6e-05 19 32.7 58 600 4566


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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 499 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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