Module 432

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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: 15 (see 800 additional genes for this module)
Num experiments: 70 (48 induced, 22 repressed)
Parent module: None
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.
cholesterol biosynthesis
Sterol_biosynthesis
Cholesterol Biosynthesis


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
Cancer and cell line (Fibroblast serum*) Fibroblast serum* 1.7e-08 6 27.2 22 18 1945
Cell line (Fibroblast serum*) Fibroblast serum* 1.7e-08 6 27.2 22 18 1945
Skin fibroblasts (Fibroblast serum*) Fibroblast serum* 1.7e-08 6 27.2 22 18 1945
Fibroblasts (Fibroblast serum*) Fibroblast serum* 6.4e-07 5 22.7 22 17 1945
Serum response in epithelial cells (Fibroblast serum*) Fibroblast serum* 1.1e-05 4 18.1 22 14 1945
Liver tissue (Liver cancer*) Liver cancer* 2.0e-05 15 31.2 48 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 3.8e-05 15 31.2 48 197 1945
Cell line (Breast cancer) Breast cancer 3.8e-05 6 100 6 30 152
Breast cancer cell line (Breast cancer) Breast cancer 5.4e-05 5 83.3 6 17 152
Hepatitis infected liver (Liver cancer*) Liver cancer* 5.6e-05 13 27.0 48 156 1945
Metastasis (Liver cancer) Liver cancer 0.0001 4 50 8 10 207
Hepatocellular carcinoma (Liver cancer) Liver cancer 0.0003 14 93.3 15 104 207


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
cholesterol biosynthesis 6.7e-28 10 83.3 12 11 4566
regulation of biosynthesis 7.9e-21 10 83.3 12 34 4566
regulation of metabolism 5.4e-10 10 83.3 12 365 4566
lipid metabolism 1.7e-08 7 58.3 12 143 4566
carbon-carbon lyase activity 7.6e-06 3 25 12 16 4566
steroid biosynthesis 1.5e-05 3 25 12 20 4566
carboxylic acid metabolism 1.5e-05 5 41.6 12 138 4566
organic acid metabolism 1.6e-05 5 41.6 12 139 4566
lyase activity 3.1e-05 4 33.3 12 76 4566
peroxisome 5.4e-05 3 25 12 30 4566
organic acid biosynthesis 7.2e-05 3 25 12 33 4566
carboxylic acid biosynthesis 7.9e-05 3 25 12 34 4566
lipid biosynthesis 0.0001 3 25 12 37 4566
catalytic activity 0.0001 11 91.6 12 1677 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.
 
 





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