Module 481

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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: 90 (see 1390 additional genes for this module)
Num experiments: 250 (115 induced, 135 repressed)
Parent module: 544
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.
Boldrick02 26
Boldrick02 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
Liver tissue (Liver cancer*) Liver cancer* 7.6e-14 39 33.9 115 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 4.7e-13 39 33.9 115 197 1945
Hematologic samples (Stimulated PBMC*) Stimulated PBMC* 5.6e-10 30 26.0 115 152 1945
Lymphocytes (Stimulated PBMC*) Stimulated PBMC* 5.6e-10 30 26.0 115 152 1945
Primary blood mononuclear cells (Stimulated PBMC*) Stimulated PBMC* 5.6e-10 30 26.0 115 152 1945
Hepatitis infected liver (Liver cancer*) Liver cancer* 2.3e-08 28 24.3 115 156 1945
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 5.2e-08 30 26.0 115 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 5.2e-08 30 26.0 115 182 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 3.2e-07 29 72.5 40 76 207
Cancer and cell line (Liver cancer) Liver cancer 1.8e-06 29 96.6 30 126 207
Stimulated immune cells (Stimulated PBMC*) Stimulated PBMC* 4.1e-06 23 20 115 143 1945
Cancer and cell line (Breast cancer*) Breast cancer* 6.6e-06 25 18.5 135 143 1945
Breast cancer or cell line (Breast cancer*) Breast cancer* 3.4e-05 22 16.2 135 128 1945
Breast tissue, cancer or cell line (Breast cancer*) Breast cancer* 6.0e-05 23 17.0 135 142 1945
Cancer (Liver cancer) Liver cancer 0.0001 26 86.6 30 115 207
Normal tissue (Liver cancer) Liver cancer 0.0001 9 22.5 40 14 207
Female hormonal cancer or cell line (Breast cancer*) Breast cancer* 0.0002 20 14.8 135 127 1945
Adenocarcinoma (Liver cancer) Liver cancer 0.0003 23 76.6 30 97 207
Female hormonal tissue, cancer or cell line (Breast cancer*) Breast cancer* 0.0004 21 15.5 135 141 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).


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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