Module 56

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:	6
Num genes:	12 (see 1195 additional genes for this module)
Num experiments:	113 (56 induced, 57 repressed)
Parent module:	102
Children modules:	31 21

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.
ribonucleoside monophosphate metabolism
nucleoside monophosphate biosynthesis
ribonucleoside monophosphate biosynthesis
purine ribonucleoside monophosphate metabolism
purine nucleoside monophosphate biosynthesis
purine ribonucleoside monophosphate biosynthesis

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
Normal lung tissue (Lung cancer)	Lung cancer	9.1e-15	16	61.5	26	22	276
Normal tissue (Lung cancer)	Lung cancer	2.8e-14	16	61.5	26	23	276
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	4.8e-11	14	87.5	16	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	4.8e-11	14	87.5	16	30	182
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	5.8e-09	26	45.6	57	276	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	2.6e-05	16	28.5	56	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	2.6e-05	16	28.5	56	182	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	0.0001	12	100	12	121	245
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	0.0002	8	66.6	12	46	245
Leukemia (B lymphoma)	B lymphoma	0.0002	8	66.6	12	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	0.0002	8	66.6	12	46	245

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
ribonucleoside monophosphate biosynthesis	3.2e-31	11	91.6	12	12	4566
ribonucleotide metabolism	5.1e-28	12	100	12	30	4566
nucleoside monophosphate biosynthesis	6.7e-28	10	83.3	12	11	4566
nucleotide biosynthesis	1.6e-26	12	100	12	38	4566
ribonucleotide biosynthesis	1.8e-26	11	91.6	12	22	4566
ribonucleoside monophosphate metabolism	9.3e-25	9	75	12	10	4566
nucleotide metabolism	1.9e-23	12	100	12	64	4566
purine ribonucleoside monophosphate biosynthesis	9.5e-22	8	66.6	12	9	4566
purine nucleoside monophosphate biosynthesis	9.6e-20	7	58.3	12	7	4566
purine ribonucleoside monophosphate metabolism	9.6e-20	7	58.3	12	7	4566
purine ribonucleotide biosynthesis	7.6e-17	7	58.3	12	12	4566
regulation of nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism	1.2e-13	6	50	12	13	4566
nucleoside metabolism	3.7e-11	5	41.6	12	12	4566
purine nucleotide biosynthesis	1.3e-10	4	33.3	12	5	4566
nucleobase metabolism	9.5e-10	4	33.3	12	7	4566
heterocycle metabolism	5.6e-09	4	33.3	12	10	4566
ligase activity\, forming carbon-nitrogen bonds	9.5e-08	5	41.6	12	50	4566
aromatic compound metabolism	3.3e-07	4	33.3	12	25	4566
transferase activity\, transferring pentosyl groups	7.7e-07	3	25	12	8	4566
catalytic activity	5.8e-06	12	100	12	1677	4566
magnesium ion binding	1.0e-05	4	33.3	12	57	4566
regulation of metabolism	1.0e-05	7	58.3	12	365	4566

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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