Module 84 -- Immune (humoral) and inflammatory 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: 15
Num genes: 552 (see 1962 additional genes for this module)
Num experiments: 1548 (498 induced, 1050 repressed)
Parent module: None
Children modules: 45 44


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.
Spleen
Thymus_2
Thymus_1
Whole_Blood_6
Whole_Blood_3
Whole_Blood_4
Whole_Blood_1
Whole_Blood_5
Whole_Blood_2
Perou00 42
Bhattacharjee01 7
Perou00 18
Garber01 45
Chen02 50
Sorlie01 20


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
Liver tissue (Liver cancer*) Liver cancer* 8.7e-26 112 22.4 498 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 4.6e-23 112 22.4 498 197 1945
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 5.2e-23 30 65.2 46 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 5.2e-23 30 65.2 46 30 182
Cancer and cell line (Liver cancer) Liver cancer 1.0e-20 81 96.4 84 126 207
Hepatitis infected liver (Liver cancer*) Liver cancer* 2.4e-18 89 17.8 498 156 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 3.6e-18 70 61.9 113 76 207
Hematologic samples (Stimulated PBMC*) Stimulated PBMC* 4.8e-18 87 17.4 498 152 1945
Lymphocytes (Stimulated PBMC*) Stimulated PBMC* 4.8e-18 87 17.4 498 152 1945
Primary blood mononuclear cells (Stimulated PBMC*) Stimulated PBMC* 4.8e-18 87 17.4 498 152 1945
Activated B like DLBCL (B lymphoma) B lymphoma 9.5e-14 26 40.6 64 30 245
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 1.9e-12 44 34.3 128 46 245
Leukemia (B lymphoma) B lymphoma 1.9e-12 44 34.3 128 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 1.9e-12 44 34.3 128 46 245
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 3.1e-12 56 87.5 64 126 245
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 8.5e-12 87 17.4 498 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 8.5e-12 87 17.4 498 182 1945
Prostate (Prostate cancer*) Prostate cancer* 9.8e-12 86 8.1 1049 101 1945
Cancer (Liver cancer) Liver cancer 1.0e-11 70 83.3 84 115 207
Cancer and cell line (Lung cancer*) Lung cancer* 1.5e-10 182 17.3 1049 252 1945
Cancer (Lung cancer*) Lung cancer* 1.5e-10 182 17.3 1049 252 1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 1.6e-10 56 87.5 64 134 245
Stimulated immune cells (Stimulated PBMC*) Stimulated PBMC* 1.0e-09 69 13.8 498 143 1945
Acute leukemia (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Cancer and cell line (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Cancer (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Hematologic cancer and cell line (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Hematologic cancer (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Hematologic samples and cell lines (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Leukemia (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Leukemia or leukemia cell line (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Monocytes (Leukemia*) Leukemia* 2.2e-09 109 10.3 1049 141 1945
Cancer and cell line (Various tumors*) Various tumors* 2.6e-09 85 8.1 1049 105 1945
Cancer (Various tumors*) Various tumors* 2.6e-09 85 8.1 1049 105 1945
Lung cancer (Lung cancer*) Lung cancer* 3.1e-09 170 16.2 1049 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 3.1e-09 170 16.2 1049 238 1945
Acute lymphocytic leukemia (Leukemia) Leukemia 5.5e-09 92 78.6 117 99 149
Lymphocytes (Leukemia) Leukemia 2.2e-08 84 77.0 109 91 141
Hepatocellular carcinoma (Liver cancer) Liver cancer 7.7e-08 61 72.6 84 104 207
Adenocarcinoma (Liver cancer) Liver cancer 4.7e-07 57 67.8 84 97 207
Cell line (NCI60*) NCI60* 5.1e-07 100 9.5 1049 135 1945
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 1.3e-06 28 82.3 34 67 144
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 1.7e-06 58 90.6 64 167 245
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 2.5e-06 184 17.5 1049 276 1945
Cancer and cell line (NCI60*) NCI60* 2.9e-06 100 9.5 1049 138 1945
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 4.4e-06 29 5.8 498 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 4.4e-06 29 5.8 498 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 4.4e-06 29 5.8 498 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 4.4e-06 29 5.8 498 53 1945
Adenocarcinoma (Breast cancer*) Breast cancer* 5.1e-06 50 10.0 498 112 1945
Breast cancer (Breast cancer*) Breast cancer* 5.1e-06 50 10.0 498 112 1945
Cancer (Breast cancer*) Breast cancer* 5.1e-06 50 10.0 498 112 1945
Female hormonal cancer (Breast cancer*) Breast cancer* 5.1e-06 50 10.0 498 112 1945
Breast tissue or cancer (Breast cancer*) Breast cancer* 5.2e-06 52 10.4 498 118 1945
Female hormonal tissue or cancer (Breast cancer*) Breast cancer* 5.2e-06 52 10.4 498 118 1945
Epithelial cell line (NCI60) NCI60 7.0e-06 32 31.6 101 32 139
Breast cancer cell line (Breast cancer) Breast cancer 1.2e-05 14 28 50 17 152
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 1.4e-05 139 13.2 1049 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 1.4e-05 139 13.2 1049 205 1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 1.8e-05 29 85.2 34 78 144
Cell line (Breast cancer) Breast cancer 2.3e-05 20 40 50 30 152
B cells (Leukemia) Leukemia 2.3e-05 58 53.2 109 62 141
Cell line (Liver cancer) Liver cancer 3.2e-05 11 13.0 84 11 207
Malignant glioblastoma (Neuro tumors) Neuro tumors 5.9e-05 6 60 10 10 90
Cell line (B lymphoma) B lymphoma 7.8e-05 14 10.9 128 14 245
Liver cancer cell line (Liver cancer) Liver cancer 8.6e-05 10 11.9 84 10 207
Female hormonal cancer cell line (Breast cancer) Breast cancer 0.0001 12 24 50 15 152
GC B like DLBCL (B lymphoma) B lymphoma 0.0001 25 39.0 64 53 245
Lung carcinoid (Lung cancer) Lung cancer 0.0002 20 10.8 184 20 276
Female hormonal cancer or cell line (Breast cancer*) Breast cancer* 0.0002 50 10.0 498 127 1945
Breast cancer or cell line (Breast cancer*) Breast cancer* 0.0003 50 10.0 498 128 1945


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
response to biotic stimulus 4.0e-33 135 36.2 372 600 4566
response to stress 1.0e-20 136 36.5 372 792 4566
immune response 1.4e-20 98 26.3 372 469 4566
inflammatory response 1.9e-13 35 9.4 372 108 4566
thermoregulation 1.4e-11 32 8.6 372 105 4566
response to pest/pathogen/parasite 1.7e-11 41 11.0 372 163 4566
defense/immunity protein activity 2.3e-08 27 7.2 372 103 4566
chemotaxis 1.6e-07 21 5.6 372 73 4566
energy taxis 2.0e-07 21 5.6 372 74 4566
chemokine receptor binding 2.1e-07 14 3.7 372 35 4566
taxis 3.4e-07 21 5.6 372 76 4566
receptor activity 5.6e-07 80 21.5 372 582 4566
extracellular space 6.7e-07 39 10.4 372 212 4566
cell communication 7.7e-07 123 33.0 372 1030 4566
cellular defense response 1.0e-06 16 4.3 372 50 4566
transmembrane receptor activity 1.2e-06 65 17.4 372 448 4566
interleukin binding 1.4e-06 11 2.9 372 25 4566
cell adhesion 2.2e-06 39 10.4 372 222 4566
signal transducer activity 3.6e-06 120 32.2 372 1026 4566
interleukin receptor activity 5.4e-06 11 2.9 372 28 4566
humoral immune response 5.8e-06 25 6.7 372 118 4566
hematopoietin/interferon-class (D200-domain) cytokine receptor activity 1.6e-05 13 3.4 372 42 4566
integral to plasma membrane 1.6e-05 78 20.9 372 612 4566
antiviral response protein activity 2.2e-05 8 2.1 372 17 4566
response to viruses 3.8e-05 8 2.1 372 18 4566
receptor binding 5.4e-05 37 9.9 372 235 4566
defense response 5.9e-05 41 11.0 372 272 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 552 genes, this image does not display the individual gene names, but rather condenses each gene 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.
Note: Since there are 1548 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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