Module 126 -- Lymphoma and immune response expression clusters

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:	5
Num genes:	186 (see 1003 additional genes for this module)
Num experiments:	507 (241 induced, 266 repressed)
Parent module:	None
Children modules:	61

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.
Rosenwald01 45
Alizadeh00 42
Boldrick02 28
Boldrick02 16
Boldrick02 12

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
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	4.0e-23	43	55.8	77	46	245
Leukemia (B lymphoma)	B lymphoma	4.0e-23	43	55.8	77	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	4.0e-23	43	55.8	77	46	245
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.4e-22	30	63.8	47	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.4e-22	30	63.8	47	30	182
Lymphocytes (B lymphoma*)	B lymphoma*	4.3e-15	77	28.9	266	244	1945
B cells (B lymphoma*)	B lymphoma*	9.7e-14	72	27.0	266	231	1945
Cancer (B lymphoma*)	B lymphoma*	3.8e-11	61	22.9	266	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	3.8e-11	61	22.9	266	200	1945
Cell line (B lymphoma)	B lymphoma	3.3e-10	13	30.2	43	14	245
Cancer and cell line (B lymphoma*)	B lymphoma*	9.0e-10	61	22.9	266	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	9.0e-10	61	22.9	266	214	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	4.0e-08	23	85.1	27	76	207
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	5.5e-08	22	9.1	240	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	5.5e-08	22	9.1	240	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	5.5e-08	22	9.1	240	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	5.5e-08	22	9.1	240	53	1945
Liver cancer cell line (Liver cancer)	Liver cancer	5.6e-08	9	31.0	29	10	207
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	5.7e-08	30	85.7	35	67	144
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	1.1e-07	47	19.5	240	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	1.1e-07	47	19.5	240	182	1945
Cancer and cell line (Liver cancer)	Liver cancer	1.3e-07	29	100	29	126	207
Cell line (Liver cancer)	Liver cancer	2.8e-07	9	31.0	29	11	207
Breast tissue or cancer (NCI60)	NCI60	3.3e-07	4	80	5	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	3.3e-07	4	80	5	4	139
Normal lung tissue (Lung cancer)	Lung cancer	1.0e-06	12	33.3	36	22	276
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	1.6e-06	42	15.7	266	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	1.6e-06	42	15.7	266	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	1.6e-06	42	15.7	266	152	1945
Normal tissue (Lung cancer)	Lung cancer	1.9e-06	12	33.3	36	23	276
Lung carcinoid (Lung cancer)	Lung cancer	3.0e-06	11	30.5	36	20	276
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	9.3e-06	30	85.7	35	78	144
Breast cancer (NCI60)	NCI60	2.2e-05	3	60	5	3	139
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	2.2e-05	35	14.5	240	143	1945
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	3.0e-05	19	7.1	266	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	3.0e-05	19	7.1	266	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	3.0e-05	19	7.1	266	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	3.0e-05	19	7.1	266	53	1945
Grade 3 (Breast cancer)	Breast cancer	5.6e-05	11	100	11	38	85
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	9.2e-05	36	13.5	266	143	1945
Hematologic cancer and cell line (NCI60)	NCI60	9.3e-05	5	71.4	7	14	139
Hematologic samples and cell lines (NCI60)	NCI60	9.3e-05	5	71.4	7	14	139
Leukemia cell line (NCI60)	NCI60	9.3e-05	5	71.4	7	14	139
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	0.0002	42	15.7	266	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	0.0002	42	15.7	266	182	1945
Hematologic samples (B lymphoma)	B lymphoma	0.0002	15	19.4	77	22	245
Invasive liver tumor (Liver cancer)	Liver cancer	0.0003	13	44.8	29	38	207
Breast tissue, cancer or cell line (NCI60)	NCI60	0.0004	5	100	5	31	139

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
ribonucleotide biosynthesis	6.3e-11	10	8.1	122	22	4566
purine ribonucleotide biosynthesis	9.3e-11	8	6.5	122	12	4566
ribonucleotide metabolism	2.4e-09	10	8.1	122	30	4566
cytokinesis	3.0e-09	12	9.8	122	49	4566
mitosis	3.9e-09	12	9.8	122	50	4566
nucleotide biosynthesis	3.2e-08	10	8.1	122	38	4566
regulation of cell cycle	3.8e-08	19	15.5	122	163	4566
ribonucleoside monophosphate metabolism	6.1e-08	6	4.9	122	10	4566
cell cycle	6.7e-08	17	13.9	122	135	4566
nucleoside monophosphate biosynthesis	1.3e-07	6	4.9	122	11	4566
purine nucleoside monophosphate biosynthesis	2.5e-07	5	4.0	122	7	4566
purine ribonucleoside monophosphate metabolism	2.5e-07	5	4.0	122	7	4566
ribonucleoside monophosphate biosynthesis	2.6e-07	6	4.9	122	12	4566
purine ribonucleoside monophosphate biosynthesis	1.4e-06	5	4.0	122	9	4566
regulation of CDK activity	1.9e-06	7	5.7	122	24	4566
purine nucleotide biosynthesis	2.3e-06	4	3.2	122	5	4566
regulation of transcription	4.1e-06	11	9.0	122	76	4566
nucleotide metabolism	5.7e-06	10	8.1	122	64	4566
cyclin-dependent protein kinase activity	8.5e-06	5	4.0	122	12	4566
nucleotidyltransferase activity	1.2e-05	27	22.1	122	425	4566
nucleobase metabolism	1.5e-05	4	3.2	122	7	4566
transcription\, DNA-dependent	3.0e-05	15	12.2	122	167	4566
ATP binding	3.6e-05	25	20.4	122	399	4566
replication fork	6.0e-05	5	4.0	122	17	4566
heterocycle metabolism	8.9e-05	4	3.2	122	10	4566
transcription	9.4e-05	15	12.2	122	184	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.

Note: Since there are 507 experiments, this image does not display the individual experiment names, but rather condenses each experiment 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

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