Module 34

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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: 19 (see 1715 additional genes for this module)
Num experiments: 321 (133 induced, 188 repressed)
Parent module: 191
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.
metal ion homeostasis
cation homeostasis


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
Non-tumor liver tissue (Liver cancer) Liver cancer 6.0e-17 41 89.1 46 76 207
Liver tissue (General compendium) General compendium 1.0e-16 46 34.5 133 187 1946
Liver tissue, cancer or cell line (General compendium) General compendium 9.5e-16 46 34.5 133 197 1946
Hepatitis infected liver (General compendium) General compendium 8.7e-13 37 27.8 133 156 1946
Cell line (Breast cancer) Breast cancer 2.7e-08 16 66.6 24 30 152
Breast cancer cell line (Breast cancer) Breast cancer 5.4e-08 12 50 24 17 152
Lung tissue, cancer or cell line (General compendium) General compendium 1.0e-06 54 28.7 188 304 1946
Lung cancer (General compendium) General compendium 1.5e-06 46 24.4 188 244 1946
Ionomycin PMA stimulated immune cells (Stimulated PBMC) Stimulated PBMC 1.7e-06 6 42.8 14 7 144
Female hormonal cancer cell line (Breast cancer) Breast cancer 2.7e-06 10 41.6 24 15 152
Lung cancer or cell line (General compendium) General compendium 5.0e-06 47 25 188 262 1946
Cancer and cell line (Liver cancer) Liver cancer 0.0002 20 95.2 21 126 207


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
metal ion homeostasis 1.6e-45 19 100 19 30 4609
cation homeostasis 4.3e-45 19 100 19 31 4609
cell ion homeostasis 2.5e-44 19 100 19 33 4609
calcium ion homeostasis 6.6e-25 11 57.8 19 16 4609
chemokine receptor binding 1.8e-17 10 52.6 19 36 4609
transition metal ion homeostasis 1.9e-17 8 42.1 19 13 4609
iron ion homeostasis 6.8e-16 7 36.8 19 10 4609
chemotaxis 3.0e-12 9 47.3 19 73 4609
energy taxis 3.5e-12 9 47.3 19 74 4609
taxis 4.4e-12 9 47.3 19 76 4609
iron ion transport 1.4e-11 5 26.3 19 7 4609
receptor binding 2.9e-10 11 57.8 19 238 4609
response to biotic stimulus 2.2e-09 14 73.6 19 602 4609
di-\, tri-valent inorganic cation transport 2.8e-09 5 26.3 19 16 4609
thermoregulation 3.6e-09 8 42.1 19 106 4609
inflammatory response 4.6e-09 8 42.1 19 109 4609
cell-cell signaling 2.4e-08 9 47.3 19 196 4609
binding 5.1e-08 16 84.2 19 1108 4609
secretion 1.5e-07 9 47.3 19 242 4609
metal ion transport 1.7e-07 5 26.3 19 34 4609
immune response 4.0e-07 11 57.8 19 471 4609
extracellular space 8.5e-07 8 42.1 19 212 4609
response to pest/pathogen/parasite 2.2e-06 7 36.8 19 164 4609
response to stress 1.0e-05 12 63.1 19 796 4609
iron ion binding 1.6e-05 3 15.7 19 13 4609
signal transducer activity 2.3e-05 13 68.4 19 1035 4609
antiviral response protein activity 3.8e-05 3 15.7 19 17 4609
response to extracellular stimulus 7.6e-05 9 47.3 19 509 4609
humoral immune response 9.1e-05 5 26.3 19 119 4609
cation transport 9.9e-05 5 26.3 19 121 4609


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.
 
 





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