Module 47 -- ECM and collagens

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:	5
Num genes:	227 (see 2220 additional genes for this module)
Num experiments:	1138 (380 induced, 758 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.
Sorlie01 48
Ross01 7
Garber01 31
Bhattacharjee01 22
Perou00 31

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
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	5.6e-17	70	9.2	757	85	1945
Cancer and cell line (Neuro tumors*)	Neuro tumors*	1.3e-15	69	9.1	757	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	1.3e-15	69	9.1	757	86	1945
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	1.3e-15	66	8.7	757	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	1.3e-15	66	8.7	757	81	1945
Cancer and cell line (Liver cancer)	Liver cancer	1.3e-13	70	92.1	76	126	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	2.8e-13	48	94.1	51	126	245
Hematologic samples and cell lines (Various tumors)	Various tumors	3.6e-13	35	50.7	69	37	154
Hematologic samples (Various tumors)	Various tumors	3.6e-13	35	50.7	69	37	154
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	3.8e-12	78	20.5	380	197	1945
Liver tissue (Liver cancer*)	Liver cancer*	5.1e-12	75	19.7	380	187	1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	9.2e-12	48	94.1	51	134	245
Cell line (NCI60*)	NCI60*	4.4e-11	89	11.7	757	135	1945
Hepatocellular carcinoma (Liver cancer)	Liver cancer	1.6e-10	60	78.9	76	104	207
Cancer and cell line (NCI60*)	NCI60*	2.6e-10	89	11.7	757	138	1945
Hematologic cancer and cell line (Various tumors)	Various tumors	2.8e-10	29	42.0	69	31	154
Hematologic cancer (Various tumors)	Various tumors	2.8e-10	29	42.0	69	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	2.8e-10	29	42.0	69	31	154
Cancer (Liver cancer)	Liver cancer	6.4e-10	63	82.8	76	115	207
Lung carcinoid (Lung cancer)	Lung cancer	4.8e-09	20	17.8	112	20	276
Lymphocytes (Various tumors)	Various tumors	6.0e-09	26	37.6	69	28	154
Monocytes (Various tumors)	Various tumors	6.0e-09	26	37.6	69	28	154
Adenocarcinoma (Liver cancer)	Liver cancer	1.6e-08	55	72.3	76	97	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.1e-08	59	15.5	380	156	1945
Breast tissue or cancer (Breast cancer*)	Breast cancer*	3.6e-08	48	12.6	380	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	3.6e-08	48	12.6	380	118	1945
Acute leukemia (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
Cancer (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
Leukemia (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
Monocytes (Leukemia*)	Leukemia*	8.2e-08	85	11.2	757	141	1945
B cells (Leukemia)	Leukemia	2.4e-07	52	61.1	85	62	141
Non-tumor liver tissue (Liver cancer)	Liver cancer	2.6e-07	48	57.8	83	76	207
Hematologic samples and cell lines (B lymphoma)	B lymphoma	4.7e-07	67	69.0	97	121	245
Adenocarcinoma (Breast cancer*)	Breast cancer*	4.7e-07	44	11.5	380	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	4.7e-07	44	11.5	380	112	1945
Cancer (Breast cancer*)	Breast cancer*	4.7e-07	44	11.5	380	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	4.7e-07	44	11.5	380	112	1945
B cells (Various tumors)	Various tumors	7.1e-07	21	30.4	69	23	154
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	1.0e-06	48	94.1	51	167	245
Cancer and cell line (Gliomas*)	Gliomas*	2.6e-06	34	4.4	757	47	1945
Cancer (Gliomas*)	Gliomas*	2.6e-06	34	4.4	757	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	2.6e-06	34	4.4	757	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	2.6e-06	34	4.4	757	47	1945
CNS tumor (Gliomas*)	Gliomas*	2.6e-06	34	4.4	757	47	1945
Acute lymphocytic leukemia (Leukemia)	Leukemia	2.8e-06	75	80.6	93	99	149
Normal female hormonal tissue and cells (Various tumors)	Various tumors	7.0e-06	7	29.1	24	8	154
Normal female hormonal tissue (Various tumors)	Various tumors	7.0e-06	7	29.1	24	8	154
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	7.2e-06	49	12.8	380	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	9.0e-06	49	12.8	380	142	1945
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	9.9e-06	45	11.8	380	127	1945
Lymphoma (Various tumors)	Various tumors	1.0e-05	18	26.0	69	20	154
Breast cancer or cell line (Breast cancer*)	Breast cancer*	1.2e-05	45	11.8	380	128	1945
Lymphocytes (Leukemia)	Leukemia	1.3e-05	67	78.8	85	91	141
Cell line (Breast cancer)	Breast cancer	1.7e-05	19	42.2	45	30	152
Breast cancer cell line (Breast cancer)	Breast cancer	3.0e-05	13	28.8	45	17	152
Female hormonal tissue, cancer or cell line (Various tumors)	Various tumors	5.0e-05	10	41.6	24	19	154
Female hormonal tissue or cancer (Various tumors)	Various tumors	5.0e-05	10	41.6	24	19	154
Primary blood mononuclear cells (Leukemia)	Leukemia	0.0001	20	23.5	85	21	141
Normal tissue (Prostate cancer)	Prostate cancer	0.0002	17	85	20	49	102
Invasive liver tumor (Liver cancer)	Liver cancer	0.0002	24	31.5	76	38	207
Epithelial cell line (NCI60)	NCI60	0.0002	29	32.2	90	32	139
Cancer and cell line (Breast cancer*)	Breast cancer*	0.0002	45	11.8	380	143	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0002	11	24.4	45	15	152
Normal prostate tissue (Prostate cancer)	Prostate cancer	0.0002	17	85	20	50	102

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
extracellular matrix structural constituent	4.0e-11	24	16	150	149	4566
collagen	1.6e-09	11	7.3	150	31	4566
skeletal development	1.1e-08	15	10	150	75	4566
bone remodeling	9.2e-08	14	9.3	150	75	4566
cell adhesion	1.5e-07	24	16	150	222	4566
cell adhesion molecule activity	3.5e-06	15	10	150	114	4566
extracellular matrix glycoprotein	1.4e-05	5	3.3	150	11	4566
growth factor binding	2.3e-05	5	3.3	150	12	4566
development	3.0e-05	36	24	150	554	4566
cell communication	4.7e-05	55	36.6	150	1030	4566
extracellular space	5.1e-05	19	12.6	150	212	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 1138 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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