| | ||||
 |
|
|||
 >4x |
Module 102 -- Nucleotide (purine) biosynthesis |
| 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: | 9 |
| Num genes: | 19 (see 1102 additional genes for this module) |
| Num experiments: | 173 (93 induced, 80 repressed) |
| Parent module: | 219 |
| Children modules: | 56 |
| 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. | |
| 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 | |
| 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 | 4.5e-15 | 18 | 90 | 20 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 4.5e-15 | 18 | 90 | 20 | 30 | 182 |
| Normal lung tissue (Lung cancer) | Lung cancer | 2.4e-13 | 14 | 66.6 | 21 | 22 | 276 |
| Normal tissue (Lung cancer) | Lung cancer | 6.1e-13 | 14 | 66.6 | 21 | 23 | 276 |
| Lymphocytes (B lymphoma*) | B lymphoma* | 9.9e-10 | 31 | 38.7 | 80 | 244 | 1945 |
| Chronic lymphocytic leukemia (B lymphoma) | B lymphoma | 1.1e-09 | 20 | 64.5 | 31 | 46 | 245 |
| Leukemia (B lymphoma) | B lymphoma | 1.1e-09 | 20 | 64.5 | 31 | 46 | 245 |
| Leukemia or leukemia cell line (B lymphoma) | B lymphoma | 1.1e-09 | 20 | 64.5 | 31 | 46 | 245 |
| B cells (B lymphoma*) | B lymphoma* | 5.9e-09 | 29 | 36.2 | 80 | 231 | 1945 |
| Cancer (B lymphoma*) | B lymphoma* | 1.0e-07 | 25 | 31.2 | 80 | 200 | 1945 |
| Hematologic cancer (B lymphoma*) | B lymphoma* | 1.0e-07 | 25 | 31.2 | 80 | 200 | 1945 |
| Cancer and cell line (B lymphoma*) | B lymphoma* | 4.3e-07 | 25 | 31.2 | 80 | 214 | 1945 |
| Hematologic cancer and cell line (B lymphoma*) | B lymphoma* | 4.3e-07 | 25 | 31.2 | 80 | 214 | 1945 |
| Cell line (B lymphoma) | B lymphoma | 5.3e-06 | 7 | 41.1 | 17 | 14 | 245 |
| 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 samples and cell lines (Stimulated PBMC*) | Stimulated PBMC* | 0.0002 | 20 | 21.5 | 93 | 182 | 1945 |
| Monocytes (Stimulated PBMC*) | Stimulated PBMC* | 0.0002 | 20 | 21.5 | 93 | 182 | 1945 |
| Liver cancer cell line (Liver cancer) | Liver cancer | 0.0003 | 3 | 75 | 4 | 10 | 207 |
| Cell line (Liver cancer) | Liver cancer | 0.0004 | 3 | 75 | 4 | 11 | 207 |
| 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 |
| ribonucleotide biosynthesis | 1.2e-45 | 18 | 94.7 | 19 | 22 | 4566 |
| ribonucleotide metabolism | 2.0e-45 | 19 | 100 | 19 | 30 | 4566 |
| nucleotide biosynthesis | 1.3e-42 | 19 | 100 | 19 | 38 | 4566 |
| nucleotide metabolism | 3.2e-37 | 19 | 100 | 19 | 64 | 4566 |
| purine ribonucleotide biosynthesis | 2.0e-27 | 11 | 57.8 | 19 | 12 | 4566 |
| ribonucleoside monophosphate biosynthesis | 2.0e-27 | 11 | 57.8 | 19 | 12 | 4566 |
| ribonucleoside monophosphate metabolism | 3.9e-22 | 9 | 47.3 | 19 | 10 | 4566 |
| nucleoside monophosphate biosynthesis | 2.1e-21 | 9 | 47.3 | 19 | 11 | 4566 |
| purine ribonucleoside monophosphate biosynthesis | 1.4e-19 | 8 | 42.1 | 19 | 9 | 4566 |
| purine nucleoside monophosphate biosynthesis | 6.1e-18 | 7 | 36.8 | 19 | 7 | 4566 |
| purine ribonucleoside monophosphate metabolism | 6.1e-18 | 7 | 36.8 | 19 | 7 | 4566 |
| regulation of nucleobase\, nucleoside\, nucleotide and nucleic acid metabolism | 1.0e-14 | 7 | 36.8 | 19 | 13 | 4566 |
| nucleoside triphosphate biosynthesis | 1.5e-14 | 6 | 31.5 | 19 | 7 | 4566 |
| purine nucleotide biosynthesis | 7.0e-13 | 5 | 26.3 | 19 | 5 | 4566 |
| pyrimidine ribonucleotide biosynthesis | 7.0e-13 | 5 | 26.3 | 19 | 5 | 4566 |
| nucleoside metabolism | 1.9e-12 | 6 | 31.5 | 19 | 12 | 4566 |
| ribonucleoside triphosphate biosynthesis | 4.2e-12 | 5 | 26.3 | 19 | 6 | 4566 |
| ribonucleoside triphosphate metabolism | 1.4e-11 | 5 | 26.3 | 19 | 7 | 4566 |
| kinase activity | 1.1e-10 | 8 | 42.1 | 19 | 69 | 4566 |
| ligase activity\, forming carbon-nitrogen bonds | 5.5e-10 | 7 | 36.8 | 19 | 50 | 4566 |
| phosphotransferase activity\, phosphate group as acceptor | 1.3e-09 | 5 | 26.3 | 19 | 14 | 4566 |
| catalytic activity | 5.0e-09 | 19 | 100 | 19 | 1677 | 4566 |
| nucleobase metabolism | 7.4e-09 | 4 | 21.0 | 19 | 7 | 4566 |
| other carbon-nitrogen ligase activity | 2.6e-08 | 4 | 21.0 | 19 | 9 | 4566 |
| heterocycle metabolism | 4.4e-08 | 4 | 21.0 | 19 | 10 | 4566 |
| pyrimidine ribonucleoside triphosphate biosynthesis | 6.1e-08 | 3 | 15.7 | 19 | 3 | 4566 |
| GTP biosynthesis | 2.4e-07 | 3 | 15.7 | 19 | 4 | 4566 |
| purine ribonucleoside triphosphate metabolism | 6.0e-07 | 3 | 15.7 | 19 | 5 | 4566 |
| pyrimidine nucleotide biosynthesis | 1.2e-06 | 3 | 15.7 | 19 | 6 | 4566 |
| aromatic compound metabolism | 2.5e-06 | 4 | 21.0 | 19 | 25 | 4566 |
| transferase activity\, transferring pentosyl groups | 3.3e-06 | 3 | 15.7 | 19 | 8 | 4566 |
| regulation of metabolism | 5.3e-05 | 8 | 42.1 | 19 | 365 | 4566 |
| magnesium ion binding | 7.3e-05 | 4 | 21.0 | 19 | 57 | 4566 |
| 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. | |||||||||
|
|||||||||
