Module 165

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:	10
Num genes:	82 (see 1090 additional genes for this module)
Num experiments:	778 (154 induced, 624 repressed)
Parent module:	None
Children modules:	None

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.
Ramaswamy01 15
Ramaswamy01 26
Ramaswamy01 34
Ramaswamy01 38
Ramaswamy01 12
Ramaswamy01 10
Ramaswamy01 5
Ramaswamy01 36
Ramaswamy01 32
Ramaswamy01 37

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
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	3.3e-54	204	32.6	624	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	1.3e-48	186	29.8	624	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.3e-48	186	29.8	624	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	4.2e-44	174	27.8	624	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	4.2e-44	174	27.8	624	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	4.5e-41	154	24.6	624	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	4.5e-41	154	24.6	624	205	1945
Cancer and cell line (Various tumors*)	Various tumors*	1.0e-40	97	15.5	624	105	1945
Cancer (Various tumors*)	Various tumors*	1.0e-40	97	15.5	624	105	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.1e-24	59	38.3	154	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	4.7e-23	59	38.3	154	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.0e-20	50	32.4	154	156	1945
Acute leukemia (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Cancer (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Leukemia (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Monocytes (Leukemia*)	Leukemia*	1.4e-14	88	14.1	624	141	1945
Lymphoma (B lymphoma)	B lymphoma	6.1e-13	39	73.5	53	77	245
Hematologic samples and cell lines (B lymphoma)	B lymphoma	2.1e-10	46	86.7	53	121	245
Liver cancer cell line (Liver cancer)	Liver cancer	9.9e-08	10	22.2	45	10	207
Cell line (Liver cancer)	Liver cancer	9.2e-07	10	22.2	45	11	207
Breast cancer cell line (Breast cancer)	Breast cancer	1.3e-06	12	40	30	17	152
Cell line (Breast cancer)	Breast cancer	2.7e-06	16	53.3	30	30	152
Cancer and cell line (Liver cancer)	Liver cancer	4.4e-06	40	88.8	45	126	207
Female hormonal cancer cell line (Breast cancer)	Breast cancer	3.3e-05	10	33.3	30	15	152
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	3.3e-05	14	9.0	154	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	3.3e-05	14	9.0	154	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	3.3e-05	14	9.0	154	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	3.3e-05	14	9.0	154	53	1945
Acute lymphocytic leukemia (Leukemia)	Leukemia	5.7e-05	75	78.1	96	99	149
Live bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	3	60	5	5	148
p53 positive hepatocellular carcinoma (Liver cancer)	Liver cancer	0.0002	13	76.4	17	23	60
Lymphocytes (Leukemia)	Leukemia	0.0002	67	76.1	88	91	141

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
response to stress	3.5e-07	31	42.4	73	792	4566
response to biotic stimulus	7.2e-07	26	35.6	73	600	4566
cellular defense response	1.1e-05	7	9.5	73	50	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 778 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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