Module 234 -- Bone remodeling

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:	54 (see 2330 additional genes for this module)
Num experiments:	533 (172 induced, 361 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.
skeletal development
bone remodeling

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*	1.0e-40	140	38.7	361	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	1.4e-37	129	35.7	361	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.4e-37	129	35.7	361	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	1.0e-33	120	33.2	361	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	1.0e-33	120	33.2	361	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	1.7e-27	102	28.2	361	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	1.7e-27	102	28.2	361	205	1945
Liver tissue (Liver cancer*)	Liver cancer*	1.0e-26	65	37.7	172	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	3.4e-25	65	37.7	172	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	5.6e-20	52	30.2	172	156	1945
Breast tissue or cancer (Breast cancer*)	Breast cancer*	1.0e-14	39	22.6	172	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	1.0e-14	39	22.6	172	118	1945
Cancer and cell line (Liver cancer)	Liver cancer	2.1e-14	57	98.2	58	126	207
Adenocarcinoma (Breast cancer*)	Breast cancer*	5.6e-14	37	21.5	172	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	5.6e-14	37	21.5	172	112	1945
Cancer (Breast cancer*)	Breast cancer*	5.6e-14	37	21.5	172	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	5.6e-14	37	21.5	172	112	1945
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	4.7e-12	37	21.5	172	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	6.2e-12	37	21.5	172	128	1945
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	6.9e-12	39	22.6	172	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	8.9e-12	39	22.6	172	142	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.2e-10	47	67.1	70	76	207
Cancer and cell line (Breast cancer*)	Breast cancer*	2.3e-10	37	21.5	172	143	1945
Cancer (Liver cancer)	Liver cancer	1.1e-09	51	87.9	58	115	207
Hepatocellular carcinoma (Liver cancer)	Liver cancer	2.4e-09	48	82.7	58	104	207
Adenocarcinoma (Liver cancer)	Liver cancer	1.4e-07	44	75.8	58	97	207
B cells (Leukemia)	Leukemia	3.7e-07	21	91.3	23	62	141
Cell line (Breast cancer)	Breast cancer	1.8e-05	18	43.9	41	30	152
Epithelial cell line (NCI60)	NCI60	4.1e-05	18	48.6	37	32	139
Breast cancer cell line (Breast cancer)	Breast cancer	8.2e-05	12	29.2	41	17	152
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	0.0002	56	15.5	361	197	1945
Lymphocytes (Leukemia)	Leukemia	0.0002	22	95.6	23	91	141
Acute lymphocytic leukemia (Leukemia)	Leukemia	0.0003	23	95.8	24	99	149
Centroblasts (Various tumors)	Various tumors	0.0003	3	50	6	5	154
GC B like DLBCL (Various tumors)	Various tumors	0.0003	3	50	6	5	154
Invasive liver tumor (Liver cancer)	Liver cancer	0.0003	20	34.4	58	38	207

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
skeletal development	9.2e-101	52	96.2	54	75	4566
bone remodeling	1.6e-87	48	88.8	54	75	4566
ossification	3.7e-15	10	18.5	54	20	4566
mesoderm development	1.5e-08	6	11.1	54	16	4566
collagen	4.5e-08	7	12.9	54	31	4566
extracellular matrix structural constituent	9.8e-08	12	22.2	54	149	4566
growth factor activity	1.0e-07	10	18.5	54	95	4566
development	4.3e-07	21	38.8	54	554	4566
cytokine activity	5.7e-06	7	12.9	54	61	4566
death	2.7e-05	14	25.9	54	342	4566
morphogenesis	5.8e-05	14	25.9	54	366	4566
receptor binding	7.1e-05	11	20.3	54	235	4566
regulation of bone remodeling	8.3e-05	3	5.5	54	8	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 533 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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