Module 128

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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: 3
Num genes: 98 (see 2229 additional genes for this module)
Num experiments: 1031 (421 induced, 610 repressed)
Parent module: 170
Children modules: 79


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.
Alizadeh00 29
Rosenwald01 6
Alizadeh00 25


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
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 1.3e-23 70 97.2 72 126 245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 5.3e-21 70 97.2 72 134 245
Hematologic samples (Stimulated PBMC*) Stimulated PBMC* 6.3e-20 82 19.4 421 152 1945
Lymphocytes (Stimulated PBMC*) Stimulated PBMC* 6.3e-20 82 19.4 421 152 1945
Primary blood mononuclear cells (Stimulated PBMC*) Stimulated PBMC* 6.3e-20 82 19.4 421 152 1945
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 2.8e-17 88 20.9 421 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 2.8e-17 88 20.9 421 182 1945
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 6.6e-14 44 36.6 120 46 245
Leukemia (B lymphoma) B lymphoma 6.6e-14 44 36.6 120 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 6.6e-14 44 36.6 120 46 245
Activated B like DLBCL (B lymphoma) B lymphoma 1.4e-13 27 37.5 72 30 245
Stimulated immune cells (Stimulated PBMC*) Stimulated PBMC* 6.6e-13 68 16.1 421 143 1945
Lung carcinoid (Lung cancer) Lung cancer 1.4e-12 20 25.6 78 20 276
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 2.6e-12 70 97.2 72 167 245
Acute lymphocytic leukemia (Leukemia) Leukemia 2.9e-12 65 94.2 69 99 149
Cancer and cell line (Liver cancer) Liver cancer 3.7e-12 57 95 60 126 207
B cells (Leukemia) Leukemia 3.0e-11 46 75.4 61 62 141
Lymphocytes (Leukemia) Leukemia 5.2e-11 57 93.4 61 91 141
Non-tumor liver tissue (Liver cancer) Liver cancer 6.2e-10 44 67.6 65 76 207
Lymphocytes (B lymphoma*) B lymphoma* 7.0e-10 119 19.5 608 244 1945
Cell line (Breast cancer) Breast cancer 1.2e-08 20 55.5 36 30 152
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 1.5e-08 22 43.1 51 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 1.5e-08 22 43.1 51 30 182
Hematologic samples (B lymphoma) B lymphoma 5.1e-08 22 18.3 120 22 245
Breast cancer cell line (Breast cancer) Breast cancer 7.2e-08 14 38.8 36 17 152
B cells (B lymphoma*) B lymphoma* 1.0e-07 108 17.7 608 231 1945
Normal lymphocytes (B lymphoma) B lymphoma 3.1e-07 28 23.3 120 31 245
Cell line (NCI60*) NCI60* 5.0e-07 69 11.3 608 135 1945
Cancer and cell line (NCI60*) NCI60* 1.4e-06 69 11.3 608 138 1945
Female hormonal cancer cell line (Breast cancer) Breast cancer 1.6e-06 12 33.3 36 15 152
GC B like DLBCL (B lymphoma) B lymphoma 2.2e-06 30 41.6 72 53 245
Liver cancer cell line (Liver cancer) Liver cancer 2.3e-06 10 16.6 60 10 207
Cancer (B lymphoma*) B lymphoma* 2.9e-06 70 16.6 421 200 1945
Hematologic cancer (B lymphoma*) B lymphoma* 2.9e-06 70 16.6 421 200 1945
Bone marrow (Leukemia) Leukemia 3.5e-06 20 32.7 61 23 141
Cancer (Liver cancer) Liver cancer 1.6e-05 47 78.3 60 115 207
Fast doubling (20-40) cell lines (NCI60) NCI60 1.9e-05 59 89.3 66 90 122
Liver tissue (Liver cancer*) Liver cancer* 1.9e-05 64 15.2 421 187 1945
Cell line (Liver cancer) Liver cancer 1.9e-05 10 16.6 60 11 207
Cell line (B lymphoma) B lymphoma 3.0e-05 14 11.6 120 14 245
Primary blood mononuclear cells (B lymphoma) B lymphoma 3.0e-05 14 11.6 120 14 245
Colon cancer cell line (NCI60) NCI60 3.2e-05 14 20 70 14 139
Colon cancer or cell line (NCI60) NCI60 3.2e-05 14 20 70 14 139
Colon tissue, cancer or cell line (NCI60) NCI60 3.2e-05 14 20 70 14 139
Cancer and cell line (B lymphoma*) B lymphoma* 4.4e-05 70 16.6 421 214 1945
Hematologic cancer and cell line (B lymphoma*) B lymphoma* 4.4e-05 70 16.6 421 214 1945
Cancer and cell line (B lymphoma*) B lymphoma* 8.3e-05 92 15.1 608 214 1945
Hematologic cancer and cell line (B lymphoma*) B lymphoma* 8.3e-05 92 15.1 608 214 1945
Normal lung tissue (Lung cancer) Lung cancer 0.0001 12 22.6 53 22 276
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 0.0001 64 15.2 421 197 1945
Stimulated B cells (B lymphoma) B lymphoma 0.0001 12 10 120 12 245
Normal tissue (Lung cancer) Lung cancer 0.0002 12 22.6 53 23 276
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 0.0002 23 5.4 421 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 0.0002 23 5.4 421 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 0.0002 23 5.4 421 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 0.0002 23 5.4 421 53 1945
Hepatitis infected liver (Liver cancer*) Liver cancer* 0.0002 52 12.3 421 156 1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0003 31 77.5 40 78 144
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0004 28 70 40 67 144


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
inflammatory response 4.0e-14 18 24 75 108 4566
thermoregulation 3.7e-13 17 22.6 75 105 4566
response to biotic stimulus 5.8e-12 34 45.3 75 600 4566
immune response 8.4e-09 26 34.6 75 469 4566
response to stress 1.2e-08 34 45.3 75 792 4566
chemotaxis 1.7e-08 11 14.6 75 73 4566
energy taxis 2.0e-08 11 14.6 75 74 4566
taxis 2.7e-08 11 14.6 75 76 4566
chemokine receptor binding 1.1e-06 7 9.3 75 35 4566
cellular defense response 1.3e-05 7 9.3 75 50 4566
chemokine binding 2.0e-05 4 5.3 75 11 4566
G-protein chemoattractant receptor activity 5.9e-05 4 5.3 75 14 4566
invasive growth 7.9e-05 4 5.3 75 15 4566
calcium ion homeostasis 0.0001 4 5.3 75 16 4566
metal ion homeostasis 0.0001 5 6.6 75 30 4566
cation homeostasis 0.0001 5 6.6 75 31 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 1031 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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