Module 405

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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: 3
Num genes: 62 (see 851 additional genes for this module)
Num experiments: 343 (117 induced, 226 repressed)
Parent module: None
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.
tropomyosin binding
cytoskeleton
Golub99 9


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
Lung tissue, cancer or cell line (General compendium) General compendium 2.5e-20 88 39.1 225 304 1946
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 2.7e-17 18 100 18 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 2.7e-17 18 100 18 30 182
Lung cancer (General compendium) General compendium 7.2e-15 69 30.6 225 244 1946
Lung cancer or cell line (General compendium) General compendium 4.0e-13 69 30.6 225 262 1946
Non small cell lung cancer (General compendium) General compendium 2.0e-12 58 25.7 225 205 1946
Non small cell lung cancer and cell line (General compendium) General compendium 1.0e-10 58 25.7 225 223 1946
CNS tissue, cancer or cell line (General compendium) General compendium 3.3e-09 45 20 225 164 1946
Macrophages (General compendium) General compendium 4.3e-09 21 17.9 117 83 1946
CNS tumor (General compendium) General compendium 5.8e-09 41 18.2 225 144 1946
CNS cancer or cell line (General compendium) General compendium 1.9e-08 42 18.6 225 155 1946
Cell line (General compendium) General compendium 1.6e-07 42 35.8 117 325 1946
Adenocarcinoma (General compendium) General compendium 2.4e-07 86 38.2 225 466 1946
Cancer (General compendium) General compendium 6.4e-07 162 72 225 1110 1946
Liver cancer cell line (Liver cancer) Liver cancer 8.1e-06 7 30.4 23 10 207
Cell line (Liver cancer) Liver cancer 2.0e-05 7 30.4 23 11 207
Adenocarcinoma - extrapulmonary metastasis (Lung cancer) Lung cancer 3.1e-05 12 13.6 88 14 276
Cell line (B lymphoma) B lymphoma 6.0e-05 5 50 10 14 245
Hematologic samples (B lymphoma) B lymphoma 0.0003 5 55.5 9 22 245
Cancer and cell line (General compendium) General compendium 0.0003 186 82.6 225 1429 1946


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
cytoskeleton 3.7e-72 59 95.1 62 266 4609
microtubule cytoskeleton 2.0e-50 44 70.9 62 177 4609
microtubule associated complex 4.1e-44 40 64.5 62 168 4609
kinesin complex 1.9e-42 38 61.2 62 152 4609
structural constituent of cytoskeleton 3.3e-17 16 25.8 62 63 4609
motor activity 1.7e-12 11 17.7 62 40 4609
cytoskeletal protein binding 4.8e-12 14 22.5 62 89 4609
actin binding 2.0e-11 13 20.9 62 80 4609
intermediate filament 9.5e-10 9 14.5 62 38 4609
actin cytoskeleton 7.9e-09 11 17.7 62 83 4609
nuclear lamina 1.5e-08 8 12.9 62 36 4609
spindle 2.1e-08 6 9.6 62 15 4609
nuclear membrane 9.8e-08 8 12.9 62 45 4609
actomyosin 4.4e-07 5 8.0 62 13 4609
protein binding 3.7e-06 16 25.8 62 326 4609
synaptosome 2.2e-05 3 4.8 62 5 4609
ectoderm development 2.8e-05 6 9.6 62 46 4609
condensed chromosome 4.7e-05 4 6.4 62 16 4609
histogenesis 5.8e-05 6 9.6 62 52 4609
cytoskeleton-dependent intracellular transport 8.9e-05 5 8.0 62 35 4609
cytoskeleton organization and biogenesis 0.0001 7 11.2 62 84 4609


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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