Module 12 -- Spinal cord (neuro-development) genes

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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: 360 (see 3082 additional genes for this module)
Num experiments: 1322 (357 induced, 965 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.
Spinal_cord_2
Spinal_cord_1


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
Cancer and cell line (Lung cancer*) Lung cancer* 4.3e-26 201 20.8 964 252 1945
Cancer (Lung cancer*) Lung cancer* 4.3e-26 201 20.8 964 252 1945
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 1.6e-23 212 21.9 964 276 1945
Lung cancer (Lung cancer*) Lung cancer* 2.5e-23 188 19.5 964 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 2.5e-23 188 19.5 964 238 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 2.4e-21 164 17.0 964 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 2.4e-21 164 17.0 964 205 1945
Liver tissue (Liver cancer*) Liver cancer* 2.0e-18 83 23.3 356 187 1945
Cancer and cell line (Neuro tumors*) Neuro tumors* 9.8e-18 79 8.1 964 86 1945
Cancer (Neuro tumors*) Neuro tumors* 9.8e-18 79 8.1 964 86 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 1.1e-16 83 23.3 356 197 1945
Cancer and cell line (Liver cancer) Liver cancer 1.7e-16 73 94.8 77 126 207
CNS cancer or cell line (Neuro tumors*) Neuro tumors* 2.6e-16 74 7.6 964 81 1945
CNS tumor (Neuro tumors*) Neuro tumors* 2.6e-16 74 7.6 964 81 1945
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 1.9e-15 76 7.8 964 85 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 1.0e-14 57 67.8 84 76 207
Hepatitis infected liver (Liver cancer*) Liver cancer* 1.1e-11 63 17.6 356 156 1945
Prostate (Prostate cancer*) Prostate cancer* 7.1e-11 81 8.4 964 101 1945
Hematologic samples and cell lines (Various tumors) Various tumors 1.4e-09 37 38.1 97 37 154
Hematologic samples (Various tumors) Various tumors 1.4e-09 37 38.1 97 37 154
Cancer (Liver cancer) Liver cancer 2.1e-09 63 81.8 77 115 207
Acute leukemia (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Cancer and cell line (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Cancer (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Hematologic cancer and cell line (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Hematologic cancer (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Hematologic samples and cell lines (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Leukemia (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Leukemia or leukemia cell line (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Monocytes (Leukemia*) Leukemia* 9.9e-09 102 10.5 964 141 1945
Hematologic cancer and cell line (Various tumors) Various tumors 6.9e-08 31 31.9 97 31 154
Hematologic cancer (Various tumors) Various tumors 6.9e-08 31 31.9 97 31 154
Primary blood mononuclear cells (Various tumors) Various tumors 6.9e-08 31 31.9 97 31 154
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 1.1e-07 36 87.8 41 126 245
Cancer and cell line (Various tumors*) Various tumors* 3.0e-07 77 7.9 964 105 1945
Cancer (Various tumors*) Various tumors* 3.0e-07 77 7.9 964 105 1945
Lymphocytes (Various tumors) Various tumors 4.3e-07 28 28.8 97 28 154
Monocytes (Various tumors) Various tumors 4.3e-07 28 28.8 97 28 154
Adenocarcinoma (Liver cancer) Liver cancer 9.2e-07 53 68.8 77 97 207
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 1.0e-06 36 87.8 41 134 245
Breast tissue or cancer (Breast cancer*) Breast cancer* 1.0e-06 43 12.0 356 118 1945
Female hormonal tissue or cancer (Breast cancer*) Breast cancer* 1.0e-06 43 12.0 356 118 1945
Cell line (NCI60*) NCI60* 1.9e-06 93 9.6 964 135 1945
Hepatocellular carcinoma (Liver cancer) Liver cancer 2.1e-06 55 71.4 77 104 207
Malignant glioblastoma (Neuro tumors) Neuro tumors 2.2e-06 6 85.7 7 10 90
Acute lymphocytic leukemia (Leukemia) Leukemia 4.8e-06 85 77.2 110 99 149
B cells (Various tumors) Various tumors 7.9e-06 23 23.7 97 23 154
Cancer and cell line (NCI60*) NCI60* 8.7e-06 93 9.6 964 138 1945
Epithelial cell line (NCI60) NCI60 1.0e-05 31 32.9 94 32 139
Breast cancer cell line (Breast cancer) Breast cancer 1.2e-05 14 28 50 17 152
Adenocarcinoma (Breast cancer*) Breast cancer* 1.3e-05 39 10.9 356 112 1945
Breast cancer (Breast cancer*) Breast cancer* 1.3e-05 39 10.9 356 112 1945
Cancer (Breast cancer*) Breast cancer* 1.3e-05 39 10.9 356 112 1945
Female hormonal cancer (Breast cancer*) Breast cancer* 1.3e-05 39 10.9 356 112 1945
Lymphocytes (Leukemia) Leukemia 1.6e-05 77 75.4 102 91 141
Unstimulated immune cells (Stimulated PBMC) Stimulated PBMC 1.8e-05 13 61.9 21 39 182
Cell line (Breast cancer) Breast cancer 2.3e-05 20 40 50 30 152
CNS tissue, cancer or cell line (Various tumors) Various tumors 3.0e-05 7 70 10 21 154
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 3.0e-05 29 32.9 88 46 245
Leukemia (B lymphoma) B lymphoma 3.0e-05 29 32.9 88 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 3.0e-05 29 32.9 88 46 245
Cancer and cell line (Gliomas*) Gliomas* 3.1e-05 37 3.8 964 47 1945
Cancer (Gliomas*) Gliomas* 3.1e-05 37 3.8 964 47 1945
CNS cancer or cell line (Gliomas*) Gliomas* 3.1e-05 37 3.8 964 47 1945
CNS tissue, cancer or cell line (Gliomas*) Gliomas* 3.1e-05 37 3.8 964 47 1945
CNS tumor (Gliomas*) Gliomas* 3.1e-05 37 3.8 964 47 1945
Liver cancer cell line (Liver cancer) Liver cancer 3.4e-05 10 12.9 77 10 207
Lymphoma (Various tumors) Various tumors 4.2e-05 20 20.6 97 20 154
B cells (Leukemia) Leukemia 8.0e-05 55 53.9 102 62 141
Female hormonal tissue, cancer or cell line (Breast cancer*) Breast cancer* 8.1e-05 44 12.3 356 141 1945
Breast tissue, cancer or cell line (Breast cancer*) Breast cancer* 9.8e-05 44 12.3 356 142 1945
Cancer and cell line (Various tumors) Various tumors 0.0001 77 79.3 97 105 154
Cancer (Various tumors) Various tumors 0.0001 77 79.3 97 105 154
Female hormonal cancer cell line (Breast cancer) Breast cancer 0.0001 12 24 50 15 152
Activated B like DLBCL (B lymphoma) B lymphoma 0.0001 13 31.7 41 30 245
Cancer and cell line (NCI60*) NCI60* 0.0002 42 11.7 356 138 1945
Cell line (Liver cancer) Liver cancer 0.0002 10 12.9 77 11 207
Female hormonal cancer or cell line (Breast cancer*) Breast cancer* 0.0003 39 10.9 356 127 1945
Breast cancer or cell line (Breast cancer*) Breast cancer* 0.0003 39 10.9 356 128 1945


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 4.9e-10 29 11.9 243 149 4566
cell adhesion 1.4e-06 30 12.3 243 222 4566
collagen 2.4e-06 10 4.1 243 31 4566
cell adhesion molecule activity 6.6e-06 19 7.8 243 114 4566
organogenesis 6.7e-06 36 14.8 243 315 4566
neurogenesis 7.2e-06 24 9.8 243 169 4566
morphogenesis 1.4e-05 39 16.0 243 366 4566
development 8.0e-05 50 20.5 243 554 4566
fibrillar collagen 0.0001 4 1.6 243 6 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 1322 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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