Module 128

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:	98 (see 2229 additional genes for this module)
Num experiments:	1031 (421 induced, 610 repressed)
Parent module:	170
Children modules:	79

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.
Alizadeh00 29
Rosenwald01 6
Alizadeh00 25

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
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	1.3e-23	70	97.2	72	126	245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	5.3e-21	70	97.2	72	134	245
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	6.3e-20	82	19.4	421	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	6.3e-20	82	19.4	421	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	6.3e-20	82	19.4	421	152	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	2.8e-17	88	20.9	421	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	2.8e-17	88	20.9	421	182	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	6.6e-14	44	36.6	120	46	245
Leukemia (B lymphoma)	B lymphoma	6.6e-14	44	36.6	120	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	6.6e-14	44	36.6	120	46	245
Activated B like DLBCL (B lymphoma)	B lymphoma	1.4e-13	27	37.5	72	30	245
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	6.6e-13	68	16.1	421	143	1945
Lung carcinoid (Lung cancer)	Lung cancer	1.4e-12	20	25.6	78	20	276
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	2.6e-12	70	97.2	72	167	245
Acute lymphocytic leukemia (Leukemia)	Leukemia	2.9e-12	65	94.2	69	99	149
Cancer and cell line (Liver cancer)	Liver cancer	3.7e-12	57	95	60	126	207
B cells (Leukemia)	Leukemia	3.0e-11	46	75.4	61	62	141
Lymphocytes (Leukemia)	Leukemia	5.2e-11	57	93.4	61	91	141
Non-tumor liver tissue (Liver cancer)	Liver cancer	6.2e-10	44	67.6	65	76	207
Lymphocytes (B lymphoma*)	B lymphoma*	7.0e-10	119	19.5	608	244	1945
Cell line (Breast cancer)	Breast cancer	1.2e-08	20	55.5	36	30	152
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.5e-08	22	43.1	51	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.5e-08	22	43.1	51	30	182
Hematologic samples (B lymphoma)	B lymphoma	5.1e-08	22	18.3	120	22	245
Breast cancer cell line (Breast cancer)	Breast cancer	7.2e-08	14	38.8	36	17	152
B cells (B lymphoma*)	B lymphoma*	1.0e-07	108	17.7	608	231	1945
Normal lymphocytes (B lymphoma)	B lymphoma	3.1e-07	28	23.3	120	31	245
Cell line (NCI60*)	NCI60*	5.0e-07	69	11.3	608	135	1945
Cancer and cell line (NCI60*)	NCI60*	1.4e-06	69	11.3	608	138	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	1.6e-06	12	33.3	36	15	152
GC B like DLBCL (B lymphoma)	B lymphoma	2.2e-06	30	41.6	72	53	245
Liver cancer cell line (Liver cancer)	Liver cancer	2.3e-06	10	16.6	60	10	207
Cancer (B lymphoma*)	B lymphoma*	2.9e-06	70	16.6	421	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	2.9e-06	70	16.6	421	200	1945
Bone marrow (Leukemia)	Leukemia	3.5e-06	20	32.7	61	23	141
Cancer (Liver cancer)	Liver cancer	1.6e-05	47	78.3	60	115	207
Fast doubling (20-40) cell lines (NCI60)	NCI60	1.9e-05	59	89.3	66	90	122
Liver tissue (Liver cancer*)	Liver cancer*	1.9e-05	64	15.2	421	187	1945
Cell line (Liver cancer)	Liver cancer	1.9e-05	10	16.6	60	11	207
Cell line (B lymphoma)	B lymphoma	3.0e-05	14	11.6	120	14	245
Primary blood mononuclear cells (B lymphoma)	B lymphoma	3.0e-05	14	11.6	120	14	245
Colon cancer cell line (NCI60)	NCI60	3.2e-05	14	20	70	14	139
Colon cancer or cell line (NCI60)	NCI60	3.2e-05	14	20	70	14	139
Colon tissue, cancer or cell line (NCI60)	NCI60	3.2e-05	14	20	70	14	139
Cancer and cell line (B lymphoma*)	B lymphoma*	4.4e-05	70	16.6	421	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	4.4e-05	70	16.6	421	214	1945
Cancer and cell line (B lymphoma*)	B lymphoma*	8.3e-05	92	15.1	608	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	8.3e-05	92	15.1	608	214	1945
Normal lung tissue (Lung cancer)	Lung cancer	0.0001	12	22.6	53	22	276
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	0.0001	64	15.2	421	197	1945
Stimulated B cells (B lymphoma)	B lymphoma	0.0001	12	10	120	12	245
Normal tissue (Lung cancer)	Lung cancer	0.0002	12	22.6	53	23	276
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	0.0002	23	5.4	421	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	0.0002	23	5.4	421	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	0.0002	23	5.4	421	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	0.0002	23	5.4	421	53	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	0.0002	52	12.3	421	156	1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0003	31	77.5	40	78	144
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0004	28	70	40	67	144

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
inflammatory response	4.0e-14	18	24	75	108	4566
thermoregulation	3.7e-13	17	22.6	75	105	4566
response to biotic stimulus	5.8e-12	34	45.3	75	600	4566
immune response	8.4e-09	26	34.6	75	469	4566
response to stress	1.2e-08	34	45.3	75	792	4566
chemotaxis	1.7e-08	11	14.6	75	73	4566
energy taxis	2.0e-08	11	14.6	75	74	4566
taxis	2.7e-08	11	14.6	75	76	4566
chemokine receptor binding	1.1e-06	7	9.3	75	35	4566
cellular defense response	1.3e-05	7	9.3	75	50	4566
chemokine binding	2.0e-05	4	5.3	75	11	4566
G-protein chemoattractant receptor activity	5.9e-05	4	5.3	75	14	4566
invasive growth	7.9e-05	4	5.3	75	15	4566
calcium ion homeostasis	0.0001	4	5.3	75	16	4566
metal ion homeostasis	0.0001	5	6.6	75	30	4566
cation homeostasis	0.0001	5	6.6	75	31	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 1031 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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