Module 44 -- Thymus genes

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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: 328 (see 3070 additional genes for this module)
Num experiments: 1234 (371 induced, 863 repressed)
Parent module: 84
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.
Thymus_2
Thymus_1


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
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 2.5e-27 30 78.9 38 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 2.5e-27 30 78.9 38 30 182
Liver tissue (Liver cancer*) Liver cancer* 4.0e-23 92 24.7 371 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 4.8e-21 92 24.7 371 197 1945
Prostate (Prostate cancer*) Prostate cancer* 2.4e-17 85 9.8 862 101 1945
Hepatitis infected liver (Liver cancer*) Liver cancer* 1.2e-16 73 19.6 371 156 1945
Cancer and cell line (Liver cancer) Liver cancer 2.1e-15 67 95.7 70 126 207
Cell line (NCI60*) NCI60* 6.4e-11 96 11.1 862 135 1945
Cancer and cell line (NCI60*) NCI60* 4.7e-10 96 11.1 862 138 1945
Cancer and cell line (Lung cancer*) Lung cancer* 1.4e-09 156 18.0 862 252 1945
Cancer (Lung cancer*) Lung cancer* 1.4e-09 156 18.0 862 252 1945
Activated B like DLBCL (B lymphoma) B lymphoma 2.6e-08 18 40.9 44 30 245
Lung cancer (Lung cancer*) Lung cancer* 6.4e-08 144 16.7 862 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 6.4e-08 144 16.7 862 238 1945
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 1.1e-07 27 7.2 371 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 1.1e-07 27 7.2 371 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 1.1e-07 27 7.2 371 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 1.1e-07 27 7.2 371 53 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 2.0e-07 52 55.9 93 76 207
Cancer (Liver cancer) Liver cancer 2.3e-07 56 80 70 115 207
Cancer and cell line (Various tumors*) Various tumors* 6.4e-07 71 8.2 862 105 1945
Cancer (Various tumors*) Various tumors* 6.4e-07 71 8.2 862 105 1945
Cell line (Breast cancer) Breast cancer 9.1e-07 20 46.5 43 30 152
Cell line (B lymphoma) B lymphoma 1.2e-06 13 17.1 76 14 245
Breast cancer cell line (Breast cancer) Breast cancer 1.2e-06 14 32.5 43 17 152
Epithelial cell line (NCI60) NCI60 1.4e-06 32 32.9 97 32 139
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 2.6e-06 24 85.7 28 67 144
Breast tissue or cancer (Breast cancer*) Breast cancer* 3.5e-06 43 11.5 371 118 1945
Female hormonal tissue or cancer (Breast cancer*) Breast cancer* 3.5e-06 43 11.5 371 118 1945
Cell line (Liver cancer) Liver cancer 3.7e-06 11 15.7 70 11 207
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 4.1e-06 157 18.2 862 276 1945
Lung carcinoid (Lung cancer) Lung cancer 7.1e-06 20 12.7 157 20 276
Liver cancer cell line (Liver cancer) Liver cancer 1.2e-05 10 14.2 70 10 207
Adenocarcinoma (Breast cancer*) Breast cancer* 1.4e-05 40 10.7 371 112 1945
Breast cancer (Breast cancer*) Breast cancer* 1.4e-05 40 10.7 371 112 1945
Cancer (Breast cancer*) Breast cancer* 1.4e-05 40 10.7 371 112 1945
Female hormonal cancer (Breast cancer*) Breast cancer* 1.4e-05 40 10.7 371 112 1945
Female hormonal cancer cell line (Breast cancer) Breast cancer 1.7e-05 12 27.9 43 15 152
Hematologic samples (Stimulated PBMC*) Stimulated PBMC* 3.7e-05 49 13.2 371 152 1945
Lymphocytes (Stimulated PBMC*) Stimulated PBMC* 3.7e-05 49 13.2 371 152 1945
Primary blood mononuclear cells (Stimulated PBMC*) Stimulated PBMC* 3.7e-05 49 13.2 371 152 1945
Adenocarcinoma (Liver cancer) Liver cancer 8.6e-05 46 65.7 70 97 207
Medulloblastoma (Neuro tumors) Neuro tumors 0.0001 42 84 50 60 90
Vincristine chemotherapy (Neuro tumors) Neuro tumors 0.0001 42 84 50 60 90
Malignant glioblastoma (Neuro tumors) Neuro tumors 0.0001 5 71.4 7 10 90
Acute leukemia (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Cancer and cell line (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Cancer (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Hematologic cancer and cell line (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Hematologic cancer (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Hematologic samples and cell lines (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Leukemia (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Leukemia or leukemia cell line (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Monocytes (Leukemia*) Leukemia* 0.0001 84 9.7 862 141 1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0001 24 85.7 28 78 144
Hepatocellular carcinoma (Liver cancer) Liver cancer 0.0001 48 68.5 70 104 207
B. petrussis 537 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0002 5 17.8 28 5 144
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0002 5 17.8 28 5 144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0002 5 17.8 28 5 144
CNS tissue, cancer or cell line (Various tumors) Various tumors 0.0003 21 19.4 108 21 154
Female hormonal cancer or cell line (Breast cancer*) Breast cancer* 0.0003 40 10.7 371 127 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 0.0003 114 13.2 862 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 0.0003 114 13.2 862 205 1945
Breast cancer or cell line (Breast cancer*) Breast cancer* 0.0004 40 10.7 371 128 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 5.7e-14 71 31.9 222 600 4566
immune response 4.1e-09 52 23.4 222 469 4566
response to stress 5.8e-09 73 32.8 222 792 4566
response to pest/pathogen/parasite 3.1e-05 21 9.4 222 163 4566
cell adhesion molecule activity 0.0001 16 7.2 222 114 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 1234 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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