Module 426

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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: 3
Num genes: 88 (see 2231 additional genes for this module)
Num experiments: 457 (92 induced, 365 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.
tumor necrosis factor receptor binding
Shipp02 4
Iyer99 9


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* 4.7e-74 175 47.9 365 276 1945
Cancer and cell line (Lung cancer*) Lung cancer* 2.0e-65 159 43.5 365 252 1945
Cancer (Lung cancer*) Lung cancer* 2.0e-65 159 43.5 365 252 1945
Lung cancer (Lung cancer*) Lung cancer* 7.6e-60 149 40.8 365 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 7.6e-60 149 40.8 365 238 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 4.2e-53 131 35.8 365 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 4.2e-53 131 35.8 365 205 1945
Liver tissue (Liver cancer*) Liver cancer* 1.1e-21 43 46.7 92 187 1945
Hepatitis infected liver (Liver cancer*) Liver cancer* 7.7e-21 39 42.3 92 156 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 1.1e-20 43 46.7 92 197 1945
Cell line (NCI60*) NCI60* 1.1e-14 63 17.2 365 135 1945
Cancer and cell line (NCI60*) NCI60* 4.2e-14 63 17.2 365 138 1945
Liver cancer cell line (Liver cancer) Liver cancer 1.6e-10 10 38.4 26 10 207
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 4.0e-10 11 100 11 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 4.0e-10 11 100 11 30 182
Cell line (Liver cancer) Liver cancer 1.6e-09 10 38.4 26 11 207
Cell line (NCI60*) NCI60* 9.1e-08 22 23.9 92 135 1945
Cancer and cell line (NCI60*) NCI60* 1.3e-07 22 23.9 92 138 1945
B cells (Leukemia) Leukemia 3.6e-07 30 78.9 38 62 141
Non-tumor liver tissue (Liver cancer) Liver cancer 7.6e-07 30 69.7 43 76 207
Bone marrow (Leukemia) Leukemia 3.0e-06 16 42.1 38 23 141
Acute lymphocytic leukemia (Leukemia) Leukemia 3.2e-06 40 93.0 43 99 149
Lymphocytes (Leukemia) Leukemia 1.0e-05 35 92.1 38 91 141
Cell line (Breast cancer) Breast cancer 3.3e-05 10 66.6 15 30 152
Cancer and cell line (Liver cancer) Liver cancer 0.0001 24 92.3 26 126 207
Hematologic samples and cell lines (Various tumors) Various tumors 0.0002 10 66.6 15 37 154
Hematologic samples (Various tumors) Various tumors 0.0002 10 66.6 15 37 154
T cells (Various tumors) Various tumors 0.0002 4 26.6 15 5 154
Stage T1 (Lung cancer) Lung cancer 0.0004 117 85.4 137 153 195


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).


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 457 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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