Module 234 -- Bone remodeling

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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


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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


Jump to: Home | General properties | Gene sets | Enriched clinical annotations | Enriched Go annotations | Visual display
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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