Module 219

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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: 13
Num genes: 27 (see 857 additional genes for this module)
Num experiments: 236 (122 induced, 114 repressed)
Parent module: None
Children modules: 102


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.
ribonucleotide metabolism
nucleotide metabolism
purine nucleotide biosynthesis
ribonucleoside monophosphate metabolism
nucleoside monophosphate biosynthesis
ribonucleoside monophosphate biosynthesis
purine ribonucleoside monophosphate metabolism
purine nucleoside monophosphate biosynthesis
purine ribonucleoside monophosphate biosynthesis
purine ribonucleotide biosynthesis
ribonucleotide biosynthesis
nucleotide biosynthesis
Purine_metabolism


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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
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 1.2e-26 27 93.1 29 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 1.2e-26 27 93.1 29 30 182
Lymphocytes (B lymphoma*) B lymphoma* 1.1e-15 47 41.2 114 244 1945
B cells (B lymphoma*) B lymphoma* 2.3e-14 44 38.5 114 231 1945
Cancer (B lymphoma*) B lymphoma* 1.0e-13 40 35.0 114 200 1945
Hematologic cancer (B lymphoma*) B lymphoma* 1.0e-13 40 35.0 114 200 1945
Cancer and cell line (B lymphoma*) B lymphoma* 1.1e-12 40 35.0 114 214 1945
Hematologic cancer and cell line (B lymphoma*) B lymphoma* 1.1e-12 40 35.0 114 214 1945
Normal lung tissue (Lung cancer) Lung cancer 9.1e-10 10 71.4 14 22 276
Normal tissue (Lung cancer) Lung cancer 1.5e-09 10 71.4 14 23 276
Cell line (B lymphoma) B lymphoma 2.9e-09 10 45.4 22 14 245
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 7.9e-08 23 48.9 47 46 245
Leukemia (B lymphoma) B lymphoma 7.9e-08 23 48.9 47 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 7.9e-08 23 48.9 47 46 245
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 8.1e-07 29 23.7 122 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 8.1e-07 29 23.7 122 182 1945
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors) Neuro tumors 5.7e-06 5 100 5 10 90
Renal cancer or cell line (Neuro tumors) Neuro tumors 9.6e-06 4 80 5 5 90
Renal tissue (Neuro tumors) Neuro tumors 9.6e-06 4 80 5 5 90
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 3.1e-05 12 10.5 114 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 3.1e-05 12 10.5 114 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 3.1e-05 12 10.5 114 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 3.1e-05 12 10.5 114 53 1945
Liver cancer cell line (Liver cancer) Liver cancer 3.4e-05 5 45.4 11 10 207
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 4.2e-05 5 23.8 21 5 144
Cell line (Liver cancer) Liver cancer 6.0e-05 5 45.4 11 11 207
Follicular lymphoma (B lymphoma) B lymphoma 7.9e-05 14 29.7 47 28 245
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 8.4e-05 18 85.7 21 67 144
Stimulated immune cells (Stimulated PBMC*) Stimulated PBMC* 0.0001 21 17.2 122 143 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
nucleotide metabolism 7.8e-45 24 92.3 26 64 4566
ribonucleotide metabolism 1.3e-39 19 73.0 26 30 4566
ribonucleotide biosynthesis 1.8e-37 17 65.3 26 22 4566
nucleotide biosynthesis 8.4e-37 19 73.0 26 38 4566
purine ribonucleotide biosynthesis 2.0e-25 11 42.3 26 12 4566
nucleoside monophosphate biosynthesis 5.4e-23 10 38.4 26 11 4566
ribonucleoside monophosphate biosynthesis 3.2e-22 10 38.4 26 12 4566
ribonucleoside monophosphate metabolism 1.3e-20 9 34.6 26 10 4566
purine ribonucleoside monophosphate biosynthesis 3.0e-18 8 30.7 26 9 4566
purine nucleoside monophosphate biosynthesis 8.0e-17 7 26.9 26 7 4566
purine ribonucleoside monophosphate metabolism 8.0e-17 7 26.9 26 7 4566
nucleoside triphosphate biosynthesis 1.2e-13 6 23.0 26 7 4566
purine nucleotide biosynthesis 3.9e-12 5 19.2 26 5 4566
pyrimidine ribonucleotide biosynthesis 3.9e-12 5 19.2 26 5 4566
ribonucleoside triphosphate biosynthesis 2.3e-11 5 19.2 26 6 4566
regulation of nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism 3.0e-11 6 23.0 26 13 4566
phosphotransferase activity\, phosphate group as acceptor 5.3e-11 6 23.0 26 14 4566
ribonucleoside triphosphate metabolism 8.3e-11 5 19.2 26 7 4566
kinase activity 2.2e-09 8 30.7 26 69 4566
nucleoside metabolism 3.0e-09 5 19.2 26 12 4566
catalytic activity 4.4e-09 24 92.3 26 1677 4566
pyrimidine nucleotide biosynthesis 1.2e-08 4 15.3 26 6 4566
nucleobase metabolism 2.8e-08 4 15.3 26 7 4566
other carbon-nitrogen ligase activity 1.0e-07 4 15.3 26 9 4566
pyrimidine ribonucleoside triphosphate biosynthesis 1.6e-07 3 11.5 26 3 4566
heterocycle metabolism 1.6e-07 4 15.3 26 10 4566
ligase activity\, forming carbon-nitrogen bonds 2.4e-07 6 23.0 26 50 4566
GTP biosynthesis 6.5e-07 3 11.5 26 4 4566
purine ribonucleoside triphosphate metabolism 1.6e-06 3 11.5 26 5 4566
pyrimidine nucleotide metabolism 1.6e-06 3 11.5 26 5 4566
nucleoside monophosphate phosphorylation 2.3e-06 4 15.3 26 18 4566
transferase activity\, transferring pentosyl groups 9.0e-06 3 11.5 26 8 4566
aromatic compound metabolism 9.6e-06 4 15.3 26 25 4566
proton transport 3.8e-05 4 15.3 26 35 4566
mitochondrion 0.0001 7 26.9 26 207 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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