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Module 220 -- Developmental processes |
| 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: | 3 |
| Num genes: | 333 (see 2857 additional genes for this module) |
| Num experiments: | 1042 (237 induced, 805 repressed) |
| Parent module: | None |
| Children modules: | None |
| 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. | |
| development | |
| organogenesis | |
| morphogenesis | |
| 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 |
| Lymphoma (B lymphoma) | B lymphoma | 1.3e-30 | 57 | 89.0 | 64 | 77 | 245 |
| Lung tissue, cancer or cell line (Lung cancer*) | Lung cancer* | 1.0e-27 | 197 | 24.5 | 804 | 276 | 1945 |
| Cancer and cell line (Lung cancer*) | Lung cancer* | 1.5e-24 | 179 | 22.2 | 804 | 252 | 1945 |
| Cancer (Lung cancer*) | Lung cancer* | 1.5e-24 | 179 | 22.2 | 804 | 252 | 1945 |
| Lung cancer (Lung cancer*) | Lung cancer* | 4.7e-23 | 169 | 21.0 | 804 | 238 | 1945 |
| Lung cancer or cell line (Lung cancer*) | Lung cancer* | 4.7e-23 | 169 | 21.0 | 804 | 238 | 1945 |
| Hematologic samples and cell lines (B lymphoma) | B lymphoma | 1.9e-21 | 62 | 96.8 | 64 | 121 | 245 |
| Non small cell lung cancer and cell line (Lung cancer*) | Lung cancer* | 3.1e-21 | 148 | 18.4 | 804 | 205 | 1945 |
| Non small cell lung cancer (Lung cancer*) | Lung cancer* | 3.1e-21 | 148 | 18.4 | 804 | 205 | 1945 |
| Cancer and cell line (Liver cancer) | Liver cancer | 1.5e-11 | 55 | 94.8 | 58 | 126 | 207 |
| Lymphoma or lymphoma cell line (B lymphoma) | B lymphoma | 1.8e-10 | 62 | 96.8 | 64 | 167 | 245 |
| Cancer (Liver cancer) | Liver cancer | 1.1e-09 | 51 | 87.9 | 58 | 115 | 207 |
| Hepatocellular carcinoma (Liver cancer) | Liver cancer | 2.4e-09 | 48 | 82.7 | 58 | 104 | 207 |
| Acute leukemia (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Cancer and cell line (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Cancer (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Hematologic cancer and cell line (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Hematologic cancer (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Hematologic samples and cell lines (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Leukemia (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Leukemia or leukemia cell line (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Monocytes (Leukemia*) | Leukemia* | 5.1e-08 | 89 | 11.0 | 804 | 141 | 1945 |
| Cancer and cell line (Various tumors*) | Various tumors* | 6.5e-08 | 70 | 8.7 | 804 | 105 | 1945 |
| Cancer (Various tumors*) | Various tumors* | 6.5e-08 | 70 | 8.7 | 804 | 105 | 1945 |
| Cell line (NCI60*) | NCI60* | 1.2e-07 | 85 | 10.5 | 804 | 135 | 1945 |
| Adenocarcinoma (Liver cancer) | Liver cancer | 1.4e-07 | 44 | 75.8 | 58 | 97 | 207 |
| Prostate (Prostate cancer*) | Prostate cancer* | 1.7e-07 | 67 | 8.3 | 804 | 101 | 1945 |
| Cancer and cell line (NCI60*) | NCI60* | 5.2e-07 | 85 | 10.5 | 804 | 138 | 1945 |
| Cancer and cell line (NCI60*) | NCI60* | 2.5e-06 | 36 | 15.1 | 237 | 138 | 1945 |
| Breast tissue or cancer (Breast cancer*) | Breast cancer* | 4.0e-06 | 32 | 13.5 | 237 | 118 | 1945 |
| Female hormonal tissue or cancer (Breast cancer*) | Breast cancer* | 4.0e-06 | 32 | 13.5 | 237 | 118 | 1945 |
| B cells (Leukemia) | Leukemia | 4.1e-06 | 52 | 58.4 | 89 | 62 | 141 |
| Acute lymphocytic leukemia (Leukemia) | Leukemia | 6.6e-06 | 77 | 79.3 | 97 | 99 | 149 |
| Liver tissue, cancer or cell line (Liver cancer*) | Liver cancer* | 6.6e-06 | 45 | 18.9 | 237 | 197 | 1945 |
| Diffuse large B cell lymphoma - DLBCL (B lymphoma) | B lymphoma | 7.9e-06 | 48 | 75 | 64 | 126 | 245 |
| Liver tissue (Liver cancer*) | Liver cancer* | 9.3e-06 | 43 | 18.1 | 237 | 187 | 1945 |
| Diffuse large B cell lymphoma tumor or cell line (B lymphoma) | B lymphoma | 2.8e-05 | 49 | 76.5 | 64 | 134 | 245 |
| Lymphocytes (Leukemia) | Leukemia | 2.8e-05 | 69 | 77.5 | 89 | 91 | 141 |
| Cell line (NCI60*) | NCI60* | 3.1e-05 | 33 | 13.9 | 237 | 135 | 1945 |
| Cell line (Breast cancer) | Breast cancer | 4.1e-05 | 19 | 40.4 | 47 | 30 | 152 |
| Breast cancer cell line (Breast cancer) | Breast cancer | 5.4e-05 | 13 | 27.6 | 47 | 17 | 152 |
| Hepatitis C virus (HCV) infected liver (Liver cancer) | Liver cancer | 8.0e-05 | 8 | 23.5 | 34 | 10 | 156 |
| Female hormonal tissue, cancer or cell line (Breast cancer*) | Breast cancer* | 8.2e-05 | 33 | 13.9 | 237 | 141 | 1945 |
| Adenocarcinoma (Breast cancer*) | Breast cancer* | 8.7e-05 | 28 | 11.8 | 237 | 112 | 1945 |
| Breast cancer (Breast cancer*) | Breast cancer* | 8.7e-05 | 28 | 11.8 | 237 | 112 | 1945 |
| Cancer (Breast cancer*) | Breast cancer* | 8.7e-05 | 28 | 11.8 | 237 | 112 | 1945 |
| Female hormonal cancer (Breast cancer*) | Breast cancer* | 8.7e-05 | 28 | 11.8 | 237 | 112 | 1945 |
| Breast tissue, cancer or cell line (Breast cancer*) | Breast cancer* | 9.5e-05 | 33 | 13.9 | 237 | 142 | 1945 |
| Activated B like DLBCL (B lymphoma) | B lymphoma | 0.0001 | 8 | 50 | 16 | 30 | 245 |
| Bone marrow (Leukemia) | Leukemia | 0.0001 | 22 | 24.7 | 89 | 23 | 141 |
| Cancer and cell line (Neuro tumors*) | Neuro tumors* | 0.0001 | 52 | 6.4 | 804 | 86 | 1945 |
| Cancer (Neuro tumors*) | Neuro tumors* | 0.0001 | 52 | 6.4 | 804 | 86 | 1945 |
| Hepatitis infected liver (Liver cancer*) | Liver cancer* | 0.0002 | 34 | 14.3 | 237 | 156 | 1945 |
| Female hormonal cancer or cell line (Breast cancer*) | Breast cancer* | 0.0003 | 29 | 12.2 | 237 | 127 | 1945 |
| Hematologic samples and cell lines (Various tumors) | Various tumors | 0.0003 | 33 | 32.3 | 102 | 37 | 154 |
| Hematologic samples (Various tumors) | Various tumors | 0.0003 | 33 | 32.3 | 102 | 37 | 154 |
| Primary blood mononuclear cells (Leukemia) | Leukemia | 0.0003 | 20 | 22.4 | 89 | 21 | 141 |
| Breast cancer or cell line (Breast cancer*) | Breast cancer* | 0.0004 | 29 | 12.2 | 237 | 128 | 1945 |
| 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 |
| development | 0 | 331 | 99.3 | 333 | 554 | 4566 |
| morphogenesis | 4.6e-175 | 213 | 63.9 | 333 | 366 | 4566 |
| organogenesis | 1.6e-154 | 189 | 56.7 | 333 | 315 | 4566 |
| neurogenesis | 4.2e-80 | 104 | 31.2 | 333 | 169 | 4566 |
| death | 4.4e-73 | 135 | 40.5 | 333 | 342 | 4566 |
| histogenesis | 2.0e-28 | 35 | 10.5 | 333 | 52 | 4566 |
| ectoderm development | 2.7e-28 | 33 | 9.9 | 333 | 46 | 4566 |
| muscle development | 1.1e-23 | 35 | 10.5 | 333 | 65 | 4566 |
| epidermal differentiation | 1.2e-23 | 28 | 8.4 | 333 | 40 | 4566 |
| post-embryonic morphogenesis | 3.6e-23 | 28 | 8.4 | 333 | 41 | 4566 |
| post-embryonic development | 1.0e-22 | 28 | 8.4 | 333 | 42 | 4566 |
| eye photoreceptor cell fate commitment | 1.2e-21 | 26 | 7.8 | 333 | 38 | 4566 |
| compound eye morphogenesis (sensu Drosophila) | 2.4e-20 | 26 | 7.8 | 333 | 41 | 4566 |
| transmembrane receptor protein tyrosine kinase signaling pathway | 2.4e-20 | 29 | 8.7 | 333 | 52 | 4566 |
| central nervous system development | 5.1e-17 | 24 | 7.2 | 333 | 43 | 4566 |
| pattern specification | 4.8e-14 | 19 | 5.7 | 333 | 33 | 4566 |
| cell differentiation | 8.2e-13 | 18 | 5.4 | 333 | 33 | 4566 |
| transmembrane receptor protein tyrosine kinase activity | 1.7e-12 | 24 | 7.2 | 333 | 62 | 4566 |
| embryonic development | 2.8e-12 | 16 | 4.8 | 333 | 27 | 4566 |
| growth factor activity | 8.3e-12 | 29 | 8.7 | 333 | 95 | 4566 |
| transmembrane receptor protein kinase activity | 1.7e-11 | 24 | 7.2 | 333 | 68 | 4566 |
| T-cell activation | 2.9e-11 | 44 | 13.2 | 333 | 207 | 4566 |
| lymphocyte activation | 4.1e-11 | 44 | 13.2 | 333 | 209 | 4566 |
| receptor binding | 5.5e-11 | 47 | 14.1 | 333 | 235 | 4566 |
| transcription factor activity | 7.0e-11 | 59 | 17.7 | 333 | 340 | 4566 |
| embryonic pattern specification | 9.2e-11 | 14 | 4.2 | 333 | 24 | 4566 |
| cell communication | 4.4e-10 | 123 | 36.9 | 333 | 1030 | 4566 |
| sexual reproduction | 2.8e-09 | 10 | 3.0 | 333 | 14 | 4566 |
| angiogenesis | 3.0e-09 | 12 | 3.6 | 333 | 21 | 4566 |
| skeletal development | 7.0e-09 | 22 | 6.6 | 333 | 75 | 4566 |
| cell-cell signaling | 8.5e-09 | 38 | 11.4 | 333 | 194 | 4566 |
| peripheral nervous system development | 1.0e-08 | 7 | 2.1 | 333 | 7 | 4566 |
| brain development | 2.9e-08 | 8 | 2.4 | 333 | 10 | 4566 |
| nuclear lamina | 7.9e-08 | 14 | 4.2 | 333 | 36 | 4566 |
| protein kinase activity | 1.6e-07 | 24 | 7.2 | 333 | 102 | 4566 |
| intermediate filament | 1.7e-07 | 14 | 4.2 | 333 | 38 | 4566 |
| positive regulation of cell proliferation | 1.8e-07 | 19 | 5.7 | 333 | 68 | 4566 |
| histogenesis and organogenesis | 2.1e-07 | 15 | 4.5 | 333 | 44 | 4566 |
| defense response | 2.1e-07 | 44 | 13.2 | 333 | 272 | 4566 |
| signal transducer activity | 2.2e-07 | 114 | 34.2 | 333 | 1026 | 4566 |
| regulation of transcription\, DNA-dependent | 2.2e-07 | 76 | 22.8 | 333 | 595 | 4566 |
| regulation of T-cell proliferation | 2.3e-07 | 19 | 5.7 | 333 | 69 | 4566 |
| signal transduction | 2.6e-07 | 97 | 29.1 | 333 | 831 | 4566 |
| embryogenesis and morphogenesis | 2.6e-07 | 18 | 5.4 | 333 | 63 | 4566 |
| lymphocyte proliferation | 3.0e-07 | 19 | 5.7 | 333 | 70 | 4566 |
| chemosensory perception | 4.6e-07 | 83 | 24.9 | 333 | 682 | 4566 |
| sensory perception | 7.1e-07 | 84 | 25.2 | 333 | 700 | 4566 |
| nuclear membrane | 1.9e-06 | 14 | 4.2 | 333 | 45 | 4566 |
| hemopoiesis | 2.0e-06 | 5 | 1.5 | 333 | 5 | 4566 |
| ephrin receptor activity | 2.6e-06 | 7 | 2.1 | 333 | 11 | 4566 |
| gametogenesis | 2.6e-06 | 7 | 2.1 | 333 | 11 | 4566 |
| secretion | 2.7e-06 | 38 | 11.4 | 333 | 240 | 4566 |
| regulation of cell differentiation | 3.5e-06 | 6 | 1.8 | 333 | 8 | 4566 |
| cytokine activity | 4.3e-06 | 16 | 4.8 | 333 | 61 | 4566 |
| bone remodeling | 4.4e-06 | 18 | 5.4 | 333 | 75 | 4566 |
| Wnt receptor signaling pathway | 5.9e-06 | 7 | 2.1 | 333 | 12 | 4566 |
| extracellular space | 7.2e-06 | 34 | 10.2 | 333 | 212 | 4566 |
| immune response | 1.1e-05 | 59 | 17.7 | 333 | 469 | 4566 |
| axonogenesis | 2.2e-05 | 7 | 2.1 | 333 | 14 | 4566 |
| transcription regulator activity | 2.2e-05 | 79 | 23.7 | 333 | 703 | 4566 |
| heart development | 2.3e-05 | 6 | 1.8 | 333 | 10 | 4566 |
| lymph gland development | 4.8e-05 | 6 | 1.8 | 333 | 11 | 4566 |
| kinesin complex | 7.2e-05 | 25 | 7.5 | 333 | 151 | 4566 |
| response to extracellular stimulus | 7.9e-05 | 59 | 17.7 | 333 | 500 | 4566 |
| oogenesis | 9.1e-05 | 6 | 1.8 | 333 | 12 | 4566 |
| cell surface receptor linked signal transduction | 9.5e-05 | 36 | 10.8 | 333 | 259 | 4566 |
| oocyte construction | 0.0001 | 4 | 1.2 | 333 | 5 | 4566 |
| cytoskeleton | 0.0001 | 36 | 10.8 | 333 | 263 | 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. | |||||||||
| Note: Since there are 1042 experiments, this image does not display the individual experiment names, but rather condenses each experiment to a single pixel without displaying its name. You can fully view the image for this module within GeneXPress, by loading any of the four files mentioned in the line above | |||||||||
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