Module 108

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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: 56 (see 2566 additional genes for this module)
Num experiments: 661 (252 induced, 409 repressed)
Parent module: 263
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.
taxis
energy taxis
chemotaxis


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 (Lung cancer*) Lung cancer* 2.3e-24 127 31.0 409 276 1945
Lung cancer (Lung cancer*) Lung cancer* 1.7e-23 114 27.8 409 238 1945
Lung cancer or cell line (Lung cancer*) Lung cancer* 1.7e-23 114 27.8 409 238 1945
Cancer and cell line (Lung cancer*) Lung cancer* 1.1e-22 117 28.6 409 252 1945
Cancer (Lung cancer*) Lung cancer* 1.1e-22 117 28.6 409 252 1945
Non small cell lung cancer and cell line (Lung cancer*) Lung cancer* 1.2e-18 96 23.4 409 205 1945
Non small cell lung cancer (Lung cancer*) Lung cancer* 1.2e-18 96 23.4 409 205 1945
Liver tissue (Liver cancer*) Liver cancer* 1.2e-17 67 26.5 252 187 1945
Non-tumor liver tissue (Liver cancer) Liver cancer 3.2e-17 52 77.6 67 76 207
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 3.1e-16 67 26.5 252 197 1945
Cancer and cell line (Liver cancer) Liver cancer 4.5e-14 56 98.2 57 126 207
Hepatitis infected liver (Liver cancer*) Liver cancer* 3.7e-12 52 20.6 252 156 1945
Hematologic samples (Stimulated PBMC*) Stimulated PBMC* 2.6e-10 48 19.0 252 152 1945
Lymphocytes (Stimulated PBMC*) Stimulated PBMC* 2.6e-10 48 19.0 252 152 1945
Primary blood mononuclear cells (Stimulated PBMC*) Stimulated PBMC* 2.6e-10 48 19.0 252 152 1945
Stimulated immune cells (Stimulated PBMC*) Stimulated PBMC* 1.4e-08 43 17.0 252 143 1945
Cell line (Breast cancer) Breast cancer 6.7e-08 16 64 25 30 152
Hematologic samples and cell lines (Stimulated PBMC*) Stimulated PBMC* 7.1e-08 49 19.4 252 182 1945
Monocytes (Stimulated PBMC*) Stimulated PBMC* 7.1e-08 49 19.4 252 182 1945
Acute lymphocytic leukemia (Leukemia) Leukemia 1.3e-06 34 97.1 35 99 149
Breast cancer cell line (Breast cancer) Breast cancer 1.7e-06 11 44 25 17 152
Lymphocytes (Leukemia) Leukemia 3.5e-06 30 96.7 31 91 141
Cancer (Liver cancer) Liver cancer 4.1e-06 46 80.7 57 115 207
Female hormonal cancer cell line (Breast cancer) Breast cancer 4.3e-06 10 40 25 15 152
Activated B like DLBCL (B lymphoma) B lymphoma 1.0e-05 12 42.8 28 30 245
Cell line (Liver cancer) Liver cancer 1.1e-05 10 17.5 57 11 207
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 1.3e-05 19 7.5 252 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 1.3e-05 19 7.5 252 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 1.3e-05 19 7.5 252 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 1.3e-05 19 7.5 252 53 1945
Liver cancer cell line (Liver cancer) Liver cancer 4.3e-05 9 15.7 57 10 207
Diffuse large B cell lymphoma - DLBCL (B lymphoma) B lymphoma 7.0e-05 24 85.7 28 126 245
Live bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 7.6e-05 5 20.8 24 5 148
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 0.0002 14 38.8 36 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 0.0002 14 38.8 36 30 182
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0002 21 87.5 24 78 144
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 0.0002 24 85.7 28 134 245
Hepatocellular carcinoma (Liver cancer) Liver cancer 0.0003 40 70.1 57 104 207
Normal tissue (Liver cancer) Liver cancer 0.0003 11 16.4 67 14 207


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
taxis 1.2e-112 56 100 56 76 4566
chemotaxis 2.8e-110 55 98.2 56 73 4566
energy taxis 1.1e-109 55 98.2 56 74 4566
chemokine receptor binding 1.0e-56 30 53.5 56 35 4566
inflammatory response 2.6e-45 35 62.5 56 108 4566
thermoregulation 8.2e-44 34 60.7 56 105 4566
response to biotic stimulus 4.8e-29 44 78.5 56 600 4566
receptor binding 1.0e-27 32 57.1 56 235 4566
immune response 4.8e-24 37 66.0 56 469 4566
response to stress 8.1e-24 44 78.5 56 792 4566
cell-cell signaling 3.8e-23 27 48.2 56 194 4566
secretion 1.3e-20 27 48.2 56 240 4566
signal transducer activity 3.3e-20 45 80.3 56 1026 4566
conjugation without cellular fusion 1.1e-17 21 37.5 56 152 4566
calcium ion homeostasis 2.5e-16 10 17.8 56 16 4566
signal transduction 2.7e-16 38 67.8 56 831 4566
cell communication 7.2e-16 41 73.2 56 1030 4566
response to pest/pathogen/parasite 9.1e-16 20 35.7 56 163 4566
G-protein coupled receptor protein signaling pathway 1.4e-15 23 41.0 56 245 4566
metal ion homeostasis 8.2e-13 10 17.8 56 30 4566
peptide receptor activity 9.8e-13 12 21.4 56 55 4566
cation homeostasis 1.2e-12 10 17.8 56 31 4566
peptide receptor activity\, G-protein coupled 1.9e-12 12 21.4 56 58 4566
cell ion homeostasis 2.4e-12 10 17.8 56 33 4566
extracellular space 2.1e-11 18 32.1 56 212 4566
G-protein chemoattractant receptor activity 9.1e-11 7 12.5 56 14 4566
response to extracellular stimulus 1.1e-10 25 44.6 56 500 4566
cytosolic calcium ion concentration elevation 1.9e-10 8 14.2 56 24 4566
G-protein signaling\, coupled to IP3 second messenger (phospholipase C activating) 3.7e-09 9 16.0 56 48 4566
cellular defense response 5.4e-09 9 16.0 56 50 4566
cell motility 6.5e-09 12 21.4 56 113 4566
rhodopsin-like receptor activity 1.3e-08 13 23.2 56 147 4566
response to viruses 4.2e-08 6 10.7 56 18 4566
G-protein coupled receptor activity 7.8e-08 13 23.2 56 170 4566
chemokine binding 1.0e-07 5 8.9 56 11 4566
binding 1.0e-07 32 57.1 56 1103 4566
humoral immune response 1.2e-07 11 19.6 56 118 4566
humoral defense mechanism (sensu Invertebrata) 1.5e-07 9 16.0 56 72 4566
heparin binding 3.8e-07 7 12.5 56 40 4566
glycosaminoglycan binding 7.6e-07 7 12.5 56 44 4566
sensory perception 2.6e-06 23 41.0 56 700 4566
chemosensory perception 6.8e-06 22 39.2 56 682 4566
activation of MAPK 9.3e-06 4 7.1 56 12 4566
invasive growth 2.5e-05 4 7.1 56 15 4566
cell adhesion 6.0e-05 11 19.6 56 222 4566
cellular morphogenesis 6.8e-05 4 7.1 56 19 4566
MAPKKK cascade (osmolarity sensing) 0.0001 4 7.1 56 21 4566


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.
Note: Since there are 661 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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