Module 154 -- Intermediate filaments

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:	75 (see 2487 additional genes for this module)
Num experiments:	727 (201 induced, 526 repressed)
Parent module:	297
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.
Garber01 4
Ross01 39
Perou00 41

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*	1.4e-90	221	42.0	525	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	3.8e-79	200	38.0	525	252	1945
Cancer (Lung cancer*)	Lung cancer*	3.8e-79	200	38.0	525	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	8.0e-72	187	35.6	525	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	8.0e-72	187	35.6	525	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	2.7e-58	159	30.2	525	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	2.7e-58	159	30.2	525	205	1945
Squamous cell lung cancer (Lung cancer)	Lung cancer	1.7e-22	29	65.9	44	35	276
Lymphoma (B lymphoma)	B lymphoma	4.9e-14	24	100	24	77	245
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	9.7e-14	55	27.3	201	197	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.8e-12	51	25.3	201	187	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.2e-09	41	20.3	201	156	1945
Hematologic samples and cell lines (Various tumors)	Various tumors	2.3e-09	30	50	60	37	154
Hematologic samples (Various tumors)	Various tumors	2.3e-09	30	50	60	37	154
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	4.5e-09	38	18.9	201	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	5.6e-09	38	18.9	201	142	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	1.2e-08	24	100	24	121	245
Hematologic cancer and cell line (Various tumors)	Various tumors	1.3e-08	26	43.3	60	31	154
Hematologic cancer (Various tumors)	Various tumors	1.3e-08	26	43.3	60	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	1.3e-08	26	43.3	60	31	154
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	4.1e-08	34	16.9	201	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	5.1e-08	34	16.9	201	128	1945
Breast tissue or cancer (Breast cancer*)	Breast cancer*	7.8e-08	32	15.9	201	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	7.8e-08	32	15.9	201	118	1945
Adenocarcinoma (Lung cancer)	Lung cancer	1.9e-07	150	67.8	221	166	276
Cell line (NCI60*)	NCI60*	2.9e-07	63	12	525	135	1945
Lymphocytes (Various tumors)	Various tumors	3.2e-07	23	38.3	60	28	154
Monocytes (Various tumors)	Various tumors	3.2e-07	23	38.3	60	28	154
Cancer and cell line (NCI60*)	NCI60*	7.9e-07	63	12	525	138	1945
Cancer and cell line (Breast cancer*)	Breast cancer*	9.5e-07	34	16.9	201	143	1945
Cancer and cell line (Liver cancer)	Liver cancer	1.4e-06	52	85.2	61	126	207
Cancer (Liver cancer)	Liver cancer	2.0e-06	49	80.3	61	115	207
Acute lymphocytic leukemia (Leukemia)	Leukemia	2.3e-06	28	100	28	99	149
CNS tissue, cancer or cell line (Various tumors)	Various tumors	3.2e-06	18	30	60	21	154
Adenocarcinoma (Breast cancer*)	Breast cancer*	3.4e-06	28	13.9	201	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	3.4e-06	28	13.9	201	112	1945
Cancer (Breast cancer*)	Breast cancer*	3.4e-06	28	13.9	201	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	3.4e-06	28	13.9	201	112	1945
Hepatocellular carcinoma (Liver cancer)	Liver cancer	9.2e-06	45	73.7	61	104	207
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	2.0e-05	40	19.9	201	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	2.0e-05	40	19.9	201	205	1945
B cells (Various tumors)	Various tumors	4.0e-05	18	30	60	23	154
Non-tumor liver tissue (Liver cancer)	Liver cancer	4.3e-05	35	58.3	60	76	207
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	5.7e-05	24	100	24	167	245
B cells (Leukemia)	Leukemia	6.6e-05	17	85	20	62	141
Lymphocytes (Leukemia)	Leukemia	6.7e-05	20	100	20	91	141
Lung cancer (Lung cancer*)	Lung cancer*	7.1e-05	43	21.3	201	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	7.1e-05	43	21.3	201	238	1945
Adenocarcinoma (Liver cancer)	Liver cancer	0.0001	41	67.2	61	97	207
Cancer and cell line (Various tumors*)	Various tumors*	0.0002	45	8.5	525	105	1945
Cancer (Various tumors*)	Various tumors*	0.0002	45	8.5	525	105	1945
Human mammary epithelial cells (HMECs) or normal breast tissue (Various tumors)	Various tumors	0.0002	3	42.8	7	4	154
Normal breast tissue (Various tumors)	Various tumors	0.0002	3	42.8	7	4	154
Cancer and cell line (Lung cancer*)	Lung cancer*	0.0002	43	21.3	201	252	1945
Cancer (Lung cancer*)	Lung cancer*	0.0002	43	21.3	201	252	1945
CNS cancer or cell line (Various tumors)	Various tumors	0.0003	13	21.6	60	16	154
CNS tumor (Various tumors)	Various tumors	0.0003	13	21.6	60	16	154
Diffuse large B cell lymphoma - DLBCL (Various tumors)	Various tumors	0.0003	10	16.6	60	11	154
Diffuse large B cell lymphoma tumor or cell line (Various tumors)	Various tumors	0.0003	10	16.6	60	11	154

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
ectoderm development	3.6e-11	10	19.6	51	46	4566
histogenesis	1.3e-10	10	19.6	51	52	4566
epidermal differentiation	2.7e-10	9	17.6	51	40	4566
nuclear lamina	2.1e-06	6	11.7	51	36	4566
intermediate filament	3.0e-06	6	11.7	51	38	4566
serine protease inhibitor activity	4.7e-06	6	11.7	51	41	4566
endopeptidase inhibitor activity	6.0e-06	7	13.7	51	65	4566
nuclear membrane	8.3e-06	6	11.7	51	45	4566
organogenesis	0.0001	12	23.5	51	315	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 727 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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