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Module 114 -- Protein biosynthesis and ribosomes |
| 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: | 28 |
| Num genes: | 339 (see 1811 additional genes for this module) |
| Num experiments: | 364 (182 induced, 182 repressed) |
| Parent module: | 151 |
| Children modules: | 83 |
| 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. | |
| Lessnick02 4 | |
| Garber01 43 | |
| nucleic acid binding | |
| nuclease activity | |
| RNA binding | |
| ribonucleoprotein complex | |
| small ribosomal subunit | |
| cytosolic small ribosomal subunit (sensu Eukarya) | |
| ribosome | |
| Perou00 22 | |
| Singh02 38 | |
| protein biosynthesis | |
| Singh02 22 | |
| Armstrong01 27 | |
| Nutt03 15 | |
| structural constituent of ribosome | |
| Ribosome | |
| Cytoplasmic Ribosomal Proteins | |
| Staunton01 40 | |
| Golub99 17 | |
| Shipp02 13 | |
| Pomeroy02 14 | |
| Ramaswamy01 33 | |
| Bhattacharjee01 20 | |
| large ribosomal subunit | |
| cytosolic large ribosomal subunit (sensu Eukarya) | |
| Armstrong01 32 | |
| Detweiler01 8 | |
| 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 | 3.4e-16 | 17 | 100 | 17 | 30 | 182 |
| Macrophages (Stimulated PBMC) | Stimulated PBMC | 3.4e-16 | 17 | 100 | 17 | 30 | 182 |
| Prostate (Prostate cancer*) | Prostate cancer* | 8.6e-15 | 37 | 20.3 | 182 | 101 | 1945 |
| Hematologic cancer and cell line (Stimulated immune*) | Stimulated immune* | 2.9e-14 | 26 | 14.3 | 181 | 53 | 1945 |
| Hematologic samples and cell lines (Stimulated immune*) | Stimulated immune* | 2.9e-14 | 26 | 14.3 | 181 | 53 | 1945 |
| Macrophages (Stimulated immune*) | Stimulated immune* | 2.9e-14 | 26 | 14.3 | 181 | 53 | 1945 |
| Monocytes (Stimulated immune*) | Stimulated immune* | 2.9e-14 | 26 | 14.3 | 181 | 53 | 1945 |
| CNS tissue, cancer or cell line (Neuro tumors*) | Neuro tumors* | 8.0e-11 | 29 | 15.9 | 182 | 85 | 1945 |
| CNS cancer or cell line (Neuro tumors*) | Neuro tumors* | 1.2e-10 | 28 | 15.3 | 182 | 81 | 1945 |
| CNS tumor (Neuro tumors*) | Neuro tumors* | 1.2e-10 | 28 | 15.3 | 182 | 81 | 1945 |
| Cancer and cell line (Neuro tumors*) | Neuro tumors* | 6.2e-10 | 28 | 15.3 | 182 | 86 | 1945 |
| Cancer (Neuro tumors*) | Neuro tumors* | 6.2e-10 | 28 | 15.3 | 182 | 86 | 1945 |
| CNS cancer or cell line (Various tumors) | Various tumors | 7.7e-10 | 12 | 60 | 20 | 16 | 154 |
| CNS tumor (Various tumors) | Various tumors | 7.7e-10 | 12 | 60 | 20 | 16 | 154 |
| CNS tissue, cancer or cell line (Various tumors) | Various tumors | 4.1e-09 | 13 | 65 | 20 | 21 | 154 |
| Cancer and cell line (Liver cancer) | Liver cancer | 3.9e-08 | 31 | 100 | 31 | 126 | 207 |
| Hematologic cancer and cell line (Stimulated immune*) | Stimulated immune* | 7.9e-08 | 19 | 10.4 | 182 | 53 | 1945 |
| Hematologic samples and cell lines (Stimulated immune*) | Stimulated immune* | 7.9e-08 | 19 | 10.4 | 182 | 53 | 1945 |
| Macrophages (Stimulated immune*) | Stimulated immune* | 7.9e-08 | 19 | 10.4 | 182 | 53 | 1945 |
| Monocytes (Stimulated immune*) | Stimulated immune* | 7.9e-08 | 19 | 10.4 | 182 | 53 | 1945 |
| Malignant glioblastoma (Various tumors) | Various tumors | 1.6e-07 | 8 | 40 | 20 | 9 | 154 |
| Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors) | Neuro tumors | 4.6e-06 | 7 | 63.6 | 11 | 10 | 90 |
| Prostate (Prostate cancer*) | Prostate cancer* | 7.4e-06 | 24 | 13.2 | 181 | 101 | 1945 |
| Breast tissue or cancer (NCI60) | NCI60 | 9.0e-05 | 3 | 60 | 5 | 4 | 139 |
| Female hormonal tissue or cancer (NCI60) | NCI60 | 9.0e-05 | 3 | 60 | 5 | 4 | 139 |
| Adenocarcinoma (Prostate cancer) | Prostate cancer | 0.0002 | 20 | 83.3 | 24 | 52 | 102 |
| Cancer and cell line (Prostate cancer) | Prostate cancer | 0.0002 | 20 | 83.3 | 24 | 52 | 102 |
| Cancer (Prostate cancer) | Prostate cancer | 0.0002 | 20 | 83.3 | 24 | 52 | 102 |
| Prostate cancer or cell line (Prostate cancer) | Prostate cancer | 0.0002 | 20 | 83.3 | 24 | 52 | 102 |
| Prostate cancer (Prostate cancer) | Prostate cancer | 0.0002 | 20 | 83.3 | 24 | 52 | 102 |
| Breast tissue, cancer or cell line (NCI60) | NCI60 | 0.0004 | 5 | 100 | 5 | 31 | 139 |
| 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 |
| structural constituent of ribosome | 2.8e-50 | 53 | 22.3 | 237 | 81 | 4566 |
| protein biosynthesis | 6.1e-50 | 68 | 28.6 | 237 | 151 | 4566 |
| ribosome | 1.5e-43 | 70 | 29.5 | 237 | 194 | 4566 |
| ribonucleoprotein complex | 4.7e-41 | 80 | 33.7 | 237 | 283 | 4566 |
| large ribosomal subunit | 1.8e-29 | 27 | 11.3 | 237 | 34 | 4566 |
| cytosolic large ribosomal subunit (sensu Eukarya) | 4.3e-29 | 25 | 10.5 | 237 | 29 | 4566 |
| RNA binding | 8.7e-28 | 62 | 26.1 | 237 | 249 | 4566 |
| nucleic acid binding | 3.4e-25 | 79 | 33.3 | 237 | 444 | 4566 |
| nuclease activity | 3.5e-25 | 55 | 23.2 | 237 | 215 | 4566 |
| cytosolic small ribosomal subunit (sensu Eukarya) | 4.3e-16 | 17 | 7.1 | 237 | 27 | 4566 |
| monovalent inorganic cation transporter activity | 6.4e-16 | 27 | 11.3 | 237 | 80 | 4566 |
| small ribosomal subunit | 2.3e-14 | 17 | 7.1 | 237 | 32 | 4566 |
| hydrogen ion transporter activity | 1.3e-12 | 19 | 8.0 | 237 | 50 | 4566 |
| ion transporter activity | 1.1e-10 | 29 | 12.2 | 237 | 144 | 4566 |
| mitochondrion | 1.9e-10 | 35 | 14.7 | 237 | 207 | 4566 |
| hydrolase activity | 9.1e-10 | 78 | 32.9 | 237 | 783 | 4566 |
| sodium ion transporter activity | 1.7e-09 | 16 | 6.7 | 237 | 50 | 4566 |
| metal ion transporter activity | 3.2e-08 | 16 | 6.7 | 237 | 60 | 4566 |
| translational elongation | 3.9e-08 | 9 | 3.7 | 237 | 17 | 4566 |
| inner membrane | 8.8e-08 | 11 | 4.6 | 237 | 29 | 4566 |
| mitochondrial membrane | 3.5e-07 | 14 | 5.9 | 237 | 54 | 4566 |
| electron transporter activity | 7.1e-07 | 34 | 14.3 | 237 | 269 | 4566 |
| oxidoreductase activity | 1.6e-06 | 32 | 13.5 | 237 | 254 | 4566 |
| translation elongation factor activity | 4.1e-06 | 7 | 2.9 | 237 | 15 | 4566 |
| mitochondrial inner membrane | 4.6e-06 | 11 | 4.6 | 237 | 41 | 4566 |
| regulation of translational initiation | 5.2e-06 | 8 | 3.3 | 237 | 21 | 4566 |
| proton transport | 6.8e-06 | 10 | 4.2 | 237 | 35 | 4566 |
| cation transporter activity | 1.2e-05 | 11 | 4.6 | 237 | 45 | 4566 |
| cbb3-type cytochrome c oxidase | 1.3e-05 | 6 | 2.5 | 237 | 12 | 4566 |
| cytochrome c oxidase activity | 2.3e-05 | 6 | 2.5 | 237 | 13 | 4566 |
| NADH dehydrogenase (ubiquinone) activity | 3.2e-05 | 8 | 3.3 | 237 | 26 | 4566 |
| ubiquinol-cytochrome c reductase activity | 3.3e-05 | 4 | 1.6 | 237 | 5 | 4566 |
| proteasome complex (sensu Eukarya) | 5.7e-05 | 7 | 2.9 | 237 | 21 | 4566 |
| 26S proteasome | 5.8e-05 | 8 | 3.3 | 237 | 28 | 4566 |
| translational initiation | 5.8e-05 | 8 | 3.3 | 237 | 28 | 4566 |
| energy pathways | 8.2e-05 | 24 | 10.1 | 237 | 200 | 4566 |
| mRNA binding | 0.0001 | 10 | 4.2 | 237 | 47 | 4566 |
| translation initiation factor activity | 0.0001 | 8 | 3.3 | 237 | 31 | 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. | |||||||||
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