Module 5 -- Lung genes

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:	2
Num genes:	435 (see 3084 additional genes for this module)
Num experiments:	1433 (449 induced, 984 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.
Lung_2
Lung_1

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
Liver tissue (Liver cancer*)	Liver cancer*	5.5e-23	102	22.7	449	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.1e-20	102	22.7	449	197	1945
Cancer and cell line (Liver cancer)	Liver cancer	6.6e-20	76	97.4	78	126	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.5e-18	84	18.7	449	156	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	2.9e-18	67	65.0	103	76	207
Normal lung tissue (Lung cancer)	Lung cancer	9.2e-15	21	35	60	22	276
Acute lymphocytic leukemia (Leukemia)	Leukemia	1.6e-14	97	81.5	119	99	149
Normal tissue (Lung cancer)	Lung cancer	9.0e-14	21	35	60	23	276
Lymphocytes (Leukemia)	Leukemia	9.1e-14	89	80.1	111	91	141
Cancer and cell line (Lung cancer*)	Lung cancer*	1.4e-13	181	18.4	982	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.4e-13	181	18.4	982	252	1945
Acute leukemia (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Cancer (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Leukemia (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Monocytes (Leukemia*)	Leukemia*	7.5e-13	111	11.3	982	141	1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	8.0e-12	44	93.6	47	126	245
Lung cancer (Lung cancer*)	Lung cancer*	1.5e-11	168	17.1	982	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	1.5e-11	168	17.1	982	238	1945
Cancer (Liver cancer)	Liver cancer	1.4e-10	65	83.3	78	115	207
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	1.7e-10	44	93.6	47	134	245
Prostate (Prostate cancer*)	Prostate cancer*	2.3e-10	81	8.2	982	101	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	7.7e-09	38	34.5	110	46	245
Leukemia (B lymphoma)	B lymphoma	7.7e-09	38	34.5	110	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	7.7e-09	38	34.5	110	46	245
Activated B like DLBCL (B lymphoma)	B lymphoma	9.3e-09	19	40.4	47	30	245
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.0e-08	19	51.3	37	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.0e-08	19	51.3	37	30	182
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	3.5e-08	181	18.4	982	276	1945
B cells (Leukemia)	Leukemia	5.2e-08	61	54.9	111	62	141
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	2.0e-07	138	14.0	982	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	2.0e-07	138	14.0	982	205	1945
Medulloblastoma (Neuro tumors)	Neuro tumors	7.8e-07	53	82.8	64	60	90
Vincristine chemotherapy (Neuro tumors)	Neuro tumors	7.8e-07	53	82.8	64	60	90
Cell line (Breast cancer)	Breast cancer	9.1e-07	20	46.5	43	30	152
Cell line (NCI60*)	NCI60*	9.5e-07	95	9.6	982	135	1945
Epithelial cell line (NCI60)	NCI60	9.9e-07	32	33.3	96	32	139
Hepatocellular carcinoma (Liver cancer)	Liver cancer	1.1e-06	56	71.7	78	104	207
Breast cancer cell line (Breast cancer)	Breast cancer	1.2e-06	14	32.5	43	17	152
Adenocarcinoma (Liver cancer)	Liver cancer	1.9e-06	53	67.9	78	97	207
Cancer and cell line (Various tumors*)	Various tumors*	2.2e-06	76	7.7	982	105	1945
Cancer (Various tumors*)	Various tumors*	2.2e-06	76	7.7	982	105	1945
Cancer and cell line (NCI60*)	NCI60*	4.6e-06	95	9.6	982	138	1945
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	4.7e-06	63	6.4	982	85	1945
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	5.8e-06	44	93.6	47	167	245
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	9.4e-06	58	12.9	449	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	9.4e-06	58	12.9	449	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	9.4e-06	58	12.9	449	152	1945
Cell line (Liver cancer)	Liver cancer	1.3e-05	11	14.1	78	11	207
Female hormonal cancer cell line (Breast cancer)	Breast cancer	1.7e-05	12	27.9	43	15	152
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	2.4e-05	59	6.0	982	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	2.4e-05	59	6.0	982	81	1945
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	2.4e-05	26	5.7	449	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	2.4e-05	26	5.7	449	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	2.4e-05	26	5.7	449	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	2.4e-05	26	5.7	449	53	1945
Liver cancer cell line (Liver cancer)	Liver cancer	3.9e-05	10	12.8	78	10	207
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.8e-05	5	20.8	24	5	144
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	0.0001	52	11.5	449	143	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	0.0001	63	14.0	449	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	0.0001	63	14.0	449	182	1945
Lung carcinoid (Lung cancer)	Lung cancer	0.0001	20	11.0	181	20	276
Cancer and cell line (Neuro tumors*)	Neuro tumors*	0.0001	60	6.1	982	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	0.0001	60	6.1	982	86	1945
Cell line (B lymphoma)	B lymphoma	0.0001	13	11.8	110	14	245
CNS tissue, cancer or cell line (Various tumors)	Various tumors	0.0001	21	19.8	106	21	154
Hematologic samples and cell lines (Various tumors)	Various tumors	0.0002	34	32.0	106	37	154
Hematologic samples (Various tumors)	Various tumors	0.0002	34	32.0	106	37	154
Hematologic cancer and cell line (Various tumors)	Various tumors	0.0003	29	27.3	106	31	154
Hematologic cancer (Various tumors)	Various tumors	0.0003	29	27.3	106	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	0.0003	29	27.3	106	31	154
After doxorubicin chemotherapy (Breast cancer)	Breast cancer	0.0004	16	84.2	19	21	38

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 biotic stimulus	1.5e-09	80	25.0	319	600	4566
immune response	1.7e-08	65	20.3	319	469	4566
cell adhesion	3.5e-07	37	11.5	319	222	4566
cell communication	5.7e-07	109	34.1	319	1030	4566
inflammatory response	9.1e-07	23	7.2	319	108	4566
response to pest/pathogen/parasite	1.8e-06	29	9.0	319	163	4566
cell adhesion molecule activity	2.4e-06	23	7.2	319	114	4566
extracellular space	2.7e-06	34	10.6	319	212	4566
response to stress	2.9e-06	87	27.2	319	792	4566
thermoregulation	7.9e-06	21	6.5	319	105	4566
extracellular matrix structural constituent	9.2e-06	26	8.1	319	149	4566
phospholipase inhibitor activity	3.0e-05	5	1.5	319	7	4566
protein kinase activity	6.1e-05	19	5.9	319	102	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 1433 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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