Module 280 -- Metal ion (zinc) binding

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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: 45 (see 1057 additional genes for this module)
Num experiments: 212 (84 induced, 128 repressed)
Parent module: 371
Children modules: None


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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.
zinc ion binding
transition metal ion binding


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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* 7.2e-12 48 37.5 128 276 1945
Cancer and cell line (Lung cancer*) Lung cancer* 5.2e-08 39 30.4 128 252 1945
Cancer (Lung cancer*) Lung cancer* 5.2e-08 39 30.4 128 252 1945
Lung cancer (Lung cancer*) Lung cancer* 2.8e-05 32 25 128 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 2.8e-05 32 25 128 238 1945
B. petrussis 537 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 5.9e-05 4 40 10 5 144
Bone marrow (Leukemia) Leukemia 0.0002 6 75 8 23 141
Cancer and cell line (Breast cancer*) Breast cancer* 0.0002 21 16.4 128 143 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 0.0002 20 23.8 84 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 0.0002 20 23.8 84 205 1945
Lung cancer (Lung cancer*) Lung cancer* 0.0002 22 26.1 84 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 0.0002 22 26.1 84 238 1945
Adenocarcinoma - metastasis (Lung cancer) Lung cancer 0.0004 3 13.6 22 3 276


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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
transition metal ion binding 4.1e-69 45 100 45 160 4566
metal ion binding 7.9e-49 45 100 45 410 4566
zinc ion binding 1.4e-48 34 75.5 45 108 4566
binding 8.6e-29 45 100 45 1103 4566
metallopeptidase activity 6.4e-26 20 44.4 45 70 4566
metalloendopeptidase activity 3.2e-22 16 35.5 45 46 4566
proteolysis and peptidolysis 2.4e-17 20 44.4 45 176 4566
peptidase activity 1.5e-16 20 44.4 45 193 4566
collagen catabolism 5.7e-14 8 17.7 45 13 4566
protein catabolism 2.0e-11 8 17.7 45 23 4566
macromolecule catabolism 4.4e-11 8 17.7 45 25 4566
endopeptidase activity 8.7e-11 12 26.6 45 99 4566
catalytic activity 3.0e-09 36 80 45 1677 4566
catabolism 7.8e-09 14 31.1 45 215 4566
regulation of catabolism 2.7e-08 12 26.6 45 162 4566
hydrolase activity 3.0e-08 24 53.3 45 783 4566
carbonate dehydratase activity 5.5e-08 5 11.1 45 12 4566
amino acid biosynthesis 1.2e-07 6 13.3 45 26 4566
sterol regulatory element-binding protease activity 1.3e-06 5 11.1 45 21 4566
sulfur amino acid metabolism 1.6e-06 8 17.7 45 88 4566
one-carbon compound metabolism 2.1e-06 5 11.1 45 23 4566
sulfur amino acid biosynthesis 2.7e-06 5 11.1 45 24 4566
extracellular space 4.2e-06 11 24.4 45 212 4566
hydro-lyase activity 7.3e-06 5 11.1 45 29 4566
carbon-oxygen lyase activity 1.9e-05 5 11.1 45 35 4566
amino acid metabolism 5.0e-05 8 17.7 45 139 4566
alcohol dehydrogenase activity\, zinc-dependent 0.0001 3 6.6 45 10 4566
iron ion homeostasis 0.0001 3 6.6 45 10 4566


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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.
 
 





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