Module 303

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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: 28 (see 830 additional genes for this module)
Num experiments: 150 (75 induced, 75 repressed)
Parent module: 403
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.
Nicotinate_and_nicotinamide_metabolism
Benzoate_degradation


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 2.0e-18 19 100 19 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 2.0e-18 19 100 19 30 182
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 1.9e-08 16 69.5 23 46 245
Leukemia (B lymphoma) B lymphoma 1.9e-08 16 69.5 23 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 1.9e-08 16 69.5 23 46 245
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 9.6e-07 5 45.4 11 5 144
Cell line (B lymphoma) B lymphoma 1.8e-06 7 46.6 15 14 245
Hematologic samples (Stimulated PBMC*) Stimulated PBMC* 1.9e-06 19 25.3 75 152 1945
Lymphocytes (Stimulated PBMC*) Stimulated PBMC* 1.9e-06 19 25.3 75 152 1945
Primary blood mononuclear cells (Stimulated PBMC*) Stimulated PBMC* 1.9e-06 19 25.3 75 152 1945
Stimulated immune cells (Stimulated PBMC*) Stimulated PBMC* 1.5e-05 17 22.6 75 143 1945
Lymphocytes (B lymphoma*) B lymphoma* 1.8e-05 23 30.6 75 244 1945
B cells (B lymphoma*) B lymphoma* 2.6e-05 22 29.3 75 231 1945
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 2.9e-05 19 25.3 75 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 2.9e-05 19 25.3 75 182 1945
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 2.9e-05 19 25.3 75 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 2.9e-05 19 25.3 75 182 1945
Cancer and cell line (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0003 4 5.3 75 10 1945
Cell line (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0003 4 5.3 75 10 1945
EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0003 4 5.3 75 10 1945
Fibroblasts (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0003 4 5.3 75 10 1945
Skin fibroblasts (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0003 4 5.3 75 10 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
protein amino acid phosphorylation 1.3e-28 23 92 25 230 4566
protein serine/threonine kinase activity 1.4e-24 18 72 25 114 4566
response to DNA damage stimulus 1.8e-23 22 88 25 310 4566
ATP binding 6.3e-23 23 92 25 399 4566
nucleotidyltransferase activity 2.7e-22 23 92 25 425 4566
response to stress 5.1e-16 23 92 25 792 4566
protein kinase regulator activity 9.2e-12 9 36 25 59 4566
catalytic activity 1.1e-11 25 100 25 1677 4566
kinase regulator activity 6.0e-11 9 36 25 72 4566
signal transducer activity 1.5e-09 20 80 25 1026 4566
cyclin-dependent protein kinase activity 2.4e-09 5 20 25 12 4566
cytokinesis 4.3e-09 7 28 25 49 4566
regulation of cell cycle 5.2e-09 10 40 25 163 4566
cell cycle 1.8e-08 9 36 25 135 4566
protein tyrosine kinase activity 1.3e-07 8 32 25 120 4566
mitosis 1.9e-07 6 24 25 50 4566
oncogenesis 3.5e-06 8 32 25 184 4566
enzyme regulator activity 1.1e-05 9 36 25 287 4566
transcription\, DNA-dependent 2.1e-05 7 28 25 167 4566
cAMP-dependent protein kinase activity 3.6e-05 4 16 25 36 4566
transcription 3.9e-05 7 28 25 184 4566
regulation of mitosis 4.0e-05 3 12 25 13 4566
regulation of transcription 4.5e-05 5 20 25 76 4566
receptor signaling protein serine/threonine kinase activity 6.3e-05 3 12 25 15 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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