Module 287

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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: 2
Num genes: 50 (see 1405 additional genes for this module)
Num experiments: 228 (90 induced, 138 repressed)
Parent module: 373
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.
vision
perception of light


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
Liver tissue (Liver cancer*) Liver cancer* 1.2e-15 36 40.4 89 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 7.6e-15 36 40.4 89 197 1945
Hepatitis infected liver (Liver cancer*) Liver cancer* 3.3e-11 28 31.4 89 156 1945
Cancer and cell line (Liver cancer) Liver cancer 2.4e-10 39 100 39 126 207
B cells (Leukemia) Leukemia 4.4e-08 25 89.2 28 62 141
Acute leukemia (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Cancer and cell line (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Cancer (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Hematologic cancer and cell line (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Hematologic cancer (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Hematologic samples and cell lines (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Leukemia (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Leukemia or leukemia cell line (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Monocytes (Leukemia*) Leukemia* 1.6e-07 28 20.2 138 141 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 2.2e-07 34 24.6 138 197 1945
Cancer and cell line (NCI60*) NCI60* 3.5e-07 21 23.5 89 138 1945
Cell line (NCI60*) NCI60* 1.1e-06 20 22.4 89 135 1945
Cancer (Liver cancer) Liver cancer 4.2e-06 34 87.1 39 115 207
Hepatitis infected liver (Liver cancer*) Liver cancer* 1.6e-05 26 18.8 138 156 1945
Liver tissue (Liver cancer*) Liver cancer* 2.0e-05 29 21.0 138 187 1945
Primary blood mononuclear cells (Leukemia) Leukemia 3.6e-05 12 42.8 28 21 141
Cell line (Breast cancer) Breast cancer 7.7e-05 10 62.5 16 30 152
Adenocarcinoma (Liver cancer) Liver cancer 0.0001 29 74.3 39 97 207
Bone marrow (Leukemia) Leukemia 0.0001 12 42.8 28 23 141
Lymphocytes (Leukemia) Leukemia 0.0001 26 92.8 28 91 141
Acute lymphocytic leukemia - relapse (Leukemia) Leukemia 0.0002 6 21.4 28 7 141
Acute lymphocytic leukemia (Leukemia) Leukemia 0.0002 27 93.1 29 99 149


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
vision 4.2e-90 50 100 50 100 4566
perception of light 3.1e-89 50 100 50 103 4566
response to light 2.1e-65 50 100 50 256 4566
response to radiation 9.4e-65 50 100 50 263 4566
response to abiotic stimulus 1.4e-29 50 100 50 1228 4566
phototransduction 1.6e-14 10 20 50 24 4566
rhodopsin mediated phototransduction 7.3e-11 7 14 50 15 4566
rhodopsin mediated signaling 2.0e-09 6 12 50 13 4566
structural constituent of eye lens 2.5e-06 4 8 50 10 4566
rhodopsin-like receptor activity 2.9e-06 10 20 50 147 4566
G-protein signaling\, coupled to IP3 second messenger (phospholipase C activating) 1.0e-05 6 12 50 48 4566
G-protein coupled receptor activity 1.1e-05 10 20 50 170 4566
G-protein coupled photoreceptor activity 1.2e-05 3 6 50 5 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.
 
 





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