Module 241

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:	14
Num genes:	73 (see 1234 additional genes for this module)
Num experiments:	770 (151 induced, 619 repressed)
Parent module:	291
Children modules:	175 174

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.
Shipp02 12
Shipp02 32
Shipp02 45
Shipp02 27
Pomeroy02 21
Shipp02 37
Golub99 30
Golub99 43
Golub99 41
Golub99 19
Golub99 42
Golub99 12
Golub99 1
Golub99 24

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
Acute leukemia (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Cancer (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Leukemia (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Monocytes (Leukemia*)	Leukemia*	9.1e-35	113	18.2	618	141	1945
Cancer and cell line (Various tumors*)	Various tumors*	1.7e-18	76	12.2	618	105	1945
Cancer (Various tumors*)	Various tumors*	1.7e-18	76	12.2	618	105	1945
Lymphoma (B lymphoma)	B lymphoma	1.4e-16	63	58.8	107	77	245
Hematologic samples and cell lines (B lymphoma)	B lymphoma	1.9e-13	81	75.7	107	121	245
Lung carcinoid (Lung cancer)	Lung cancer	2.3e-13	20	27.7	72	20	276
Acute lymphocytic leukemia (Leukemia)	Leukemia	5.3e-09	94	77.6	121	99	149
Follicular lymphoma (B lymphoma)	B lymphoma	9.9e-09	26	24.2	107	28	245
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.5e-08	12	80	15	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.5e-08	12	80	15	30	182
Lymphocytes (Leukemia)	Leukemia	1.9e-08	86	76.1	113	91	141
Cell line (Breast cancer)	Breast cancer	2.1e-08	15	71.4	21	30	152
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	9.8e-08	34	89.4	38	126	245
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	1.4e-07	31	20.5	151	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	1.4e-07	31	20.5	151	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	1.4e-07	31	20.5	151	152	1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	8.4e-07	34	89.4	38	134	245
Cancer (B lymphoma*)	B lymphoma*	1.4e-06	94	15.2	618	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	1.4e-06	94	15.2	618	200	1945
Cancer (B lymphoma*)	B lymphoma*	3.2e-06	34	22.5	151	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	3.2e-06	34	22.5	151	200	1945
Cancer and cell line (B lymphoma*)	B lymphoma*	3.7e-06	98	15.8	618	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	3.7e-06	98	15.8	618	214	1945
B cells (B lymphoma*)	B lymphoma*	4.7e-06	104	16.8	618	231	1945
Cancer and cell line (B lymphoma*)	B lymphoma*	5.7e-06	35	23.1	151	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	5.7e-06	35	23.1	151	214	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	9.4e-06	31	20.5	151	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	9.4e-06	31	20.5	151	182	1945
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	1.0e-05	46	7.4	618	85	1945
Lymphocytes (B lymphoma*)	B lymphoma*	1.5e-05	107	17.3	618	244	1945
Lymphocytes (B lymphoma*)	B lymphoma*	1.8e-05	37	24.5	151	244	1945
Small cell lung cancer (Lung cancer)	Lung cancer	2.9e-05	9	12.5	72	10	276
B cells (B lymphoma*)	B lymphoma*	3.4e-05	35	23.1	151	231	1945
Breast cancer cell line (Breast cancer)	Breast cancer	4.0e-05	9	42.8	21	17	152
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	5.1e-05	25	16.5	151	143	1945
Epithelial cell line (NCI60)	NCI60	0.0001	21	42	50	32	139
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	0.0001	42	6.7	618	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	0.0001	42	6.7	618	81	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	8	38.0	21	15	152
Cancer and cell line (Gliomas*)	Gliomas*	0.0002	27	4.3	618	47	1945
Cancer (Gliomas*)	Gliomas*	0.0002	27	4.3	618	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	0.0002	27	4.3	618	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	0.0002	27	4.3	618	47	1945
CNS tumor (Gliomas*)	Gliomas*	0.0002	27	4.3	618	47	1945
Cancer and cell line (Neuro tumors*)	Neuro tumors*	0.0002	43	6.9	618	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	0.0002	43	6.9	618	86	1945
Activated B like DLBCL (B lymphoma)	B lymphoma	0.0004	12	31.5	38	30	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
inflammatory response	4.9e-06	9	16.0	56	108	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 770 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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