Module 293

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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: 12 (see 1773 additional genes for this module)
Num experiments: 191 (80 induced, 111 repressed)
Parent module: 345
Children modules: 144 143


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.
antigen processing
antigen presentation, peptide antigen
MHC class I receptor activity
antigen processing, endogenous antigen via MHC class I
antigen presentation, endogenous antigen


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
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 5.3e-22 23 95.8 24 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 5.3e-22 23 95.8 24 30 182
Lung carcinoid (Lung cancer) Lung cancer 2.2e-11 13 54.1 24 20 276
Cell line (B lymphoma) B lymphoma 1.2e-08 7 77.7 9 14 245
Breast cancer cell line (Breast cancer) Breast cancer 8.7e-08 10 62.5 16 17 152
Female hormonal cancer cell line (Breast cancer) Breast cancer 4.6e-07 9 56.2 16 15 152
Cell line (Breast cancer) Breast cancer 4.6e-07 12 75 16 30 152
Lymphoma (Various tumors) Various tumors 1.6e-06 7 87.5 8 20 154
B cells (Various tumors) Various tumors 4.9e-06 7 87.5 8 23 154
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 9.0e-06 5 31.2 16 5 144
Lymphocytes (Various tumors) Various tumors 2.3e-05 7 87.5 8 28 154
Monocytes (Various tumors) Various tumors 2.3e-05 7 87.5 8 28 154
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 4.0e-05 15 93.7 16 67 144
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 4.5e-05 24 21.6 111 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 4.5e-05 24 21.6 111 182 1945
Hematologic cancer and cell line (Various tumors) Various tumors 5.0e-05 7 87.5 8 31 154
Hematologic cancer (Various tumors) Various tumors 5.0e-05 7 87.5 8 31 154
Primary blood mononuclear cells (Various tumors) Various tumors 5.0e-05 7 87.5 8 31 154
Hematologic samples and cell lines (Various tumors) Various tumors 0.0001 7 87.5 8 37 154
Hematologic samples (Various tumors) Various tumors 0.0001 7 87.5 8 37 154
Liver tissue (Liver cancer*) Liver cancer* 0.0003 18 22.5 80 187 1945
Breast cancer (NCI60) NCI60 0.0003 3 27.2 11 3 139
Hepatitis infected liver (Liver cancer*) Liver cancer* 0.0003 16 20 80 156 1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0004 15 93.7 16 78 144


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
antigen presentation\, peptide antigen 5.3e-34 12 100 12 14 4566
antigen processing 5.3e-34 12 100 12 14 4566
antigen presentation\, endogenous antigen 7.7e-19 7 58.3 12 8 4566
antigen processing\, endogenous antigen via MHC class I 7.7e-19 7 58.3 12 8 4566
MHC class I receptor activity 3.4e-18 7 58.3 12 9 4566
defense response 1.5e-15 12 100 12 272 4566
antigen processing\, exogenous antigen via MHC class II 2.8e-13 5 41.6 12 6 4566
transmembrane receptor activity 6.9e-13 12 100 12 448 4566
immune response 1.2e-12 12 100 12 469 4566
receptor activity 1.6e-11 12 100 12 582 4566
response to biotic stimulus 2.4e-11 12 100 12 600 4566
signal transducer activity 1.5e-08 12 100 12 1026 4566
response to stress 4.0e-08 11 91.6 12 792 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.
 
 





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