Module 13

Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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: 8
Num genes: 519 (see 1319 additional genes for this module)
Num experiments: 268 (78 induced, 190 repressed)
Parent module: 41
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.
Lessnick02 25
Singh02 5
Singh02 2
Singh02 3
Armstrong01 12
Nutt03 43
Singh02 20
Singh02 13


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
Prostate (Prostate cancer*) Prostate cancer* 3.1e-38 60 31.5 190 101 1945
Prostate (Prostate cancer*) Prostate cancer* 8.1e-13 23 29.4 78 101 1945
Lymphoma (B lymphoma) B lymphoma 1.1e-06 16 84.2 19 77 245
Cancer and cell line (Gliomas*) Gliomas* 3.6e-06 16 8.4 190 47 1945
Cancer (Gliomas*) Gliomas* 3.6e-06 16 8.4 190 47 1945
CNS cancer or cell line (Gliomas*) Gliomas* 3.6e-06 16 8.4 190 47 1945
CNS tissue, cancer or cell line (Gliomas*) Gliomas* 3.6e-06 16 8.4 190 47 1945
CNS tumor (Gliomas*) Gliomas* 3.6e-06 16 8.4 190 47 1945
Hematologic samples and cell lines (B lymphoma) B lymphoma 1.6e-05 18 94.7 19 121 245
Cancer and cell line (Neuro tumors*) Neuro tumors* 3.9e-05 21 11.0 190 86 1945
Cancer (Neuro tumors*) Neuro tumors* 3.9e-05 21 11.0 190 86 1945
Acute myelogeous leukemia (Leukemia) Leukemia 0.0001 8 100 8 50 141
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 0.0004 11 14.1 78 85 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
integral to plasma membrane 1.8e-05 72 21.3 337 612 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 519 genes, this image does not display the individual gene names, but rather condenses each gene 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.
 
 





 >4x