Module 547

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:	15
Num genes:	16 (see 63 additional genes for this module)
Num experiments:	95 (49 induced, 46 repressed)
Parent module:	None
Children modules:	313

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.
Perou99 26
Perou99 45
Perou99 35
Perou99 5
Perou99 43
Perou99 27
Perou99 4
Perou99 13
Perou99 17
Perou99 20
Perou99 41
Perou99 3
Perou99 18
Perou99 6
Perou99 42

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
B cells (B lymphoma*)	B lymphoma*	9.4e-16	29	59.1	49	231	1945
Lymphocytes (B lymphoma*)	B lymphoma*	4.4e-15	29	59.1	49	244	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.7e-14	23	79.3	29	46	245
Leukemia (B lymphoma)	B lymphoma	1.7e-14	23	79.3	29	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.7e-14	23	79.3	29	46	245
Cancer (B lymphoma*)	B lymphoma*	3.3e-12	24	48.9	49	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	3.3e-12	24	48.9	49	200	1945
Cancer and cell line (B lymphoma*)	B lymphoma*	1.5e-11	24	48.9	49	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	1.5e-11	24	48.9	49	214	1945
T cells (B lymphoma)	B lymphoma	2.2e-06	5	41.6	12	7	245
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	6.0e-05	12	26.0	46	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	6.4e-05	12	26.0	46	142	1945
Cancer and cell line (Breast cancer*)	Breast cancer*	6.9e-05	12	26.0	46	143	1945
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	0.0001	11	23.9	46	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	0.0001	11	23.9	46	128	1945
Live bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	3	60	5	5	148

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).

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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