Module 47 -- ECM and collagens

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


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
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


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
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


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 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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