Module 83

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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: 27
Num genes: 320 (see 1369 additional genes for this module)
Num experiments: 303 (147 induced, 156 repressed)
Parent module: 114
Children modules: 32 29


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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


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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
Prostate (Prostate cancer*) Prostate cancer* 3.2e-18 38 24.5 155 101 1945
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 1.3e-16 26 17.6 147 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 1.3e-16 26 17.6 147 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 1.3e-16 26 17.6 147 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 1.3e-16 26 17.6 147 53 1945
CNS cancer or cell line (Neuro tumors*) Neuro tumors* 6.0e-10 25 16.1 155 81 1945
CNS tumor (Neuro tumors*) Neuro tumors* 6.0e-10 25 16.1 155 81 1945
CNS tissue, cancer or cell line (Neuro tumors*) Neuro tumors* 1.8e-09 25 16.1 155 85 1945
Cancer and cell line (Neuro tumors*) Neuro tumors* 2.4e-09 25 16.1 155 86 1945
Cancer (Neuro tumors*) Neuro tumors* 2.4e-09 25 16.1 155 86 1945
Prostate (Prostate cancer*) Prostate cancer* 6.1e-09 26 17.6 147 101 1945
CNS cancer or cell line (Various tumors) Various tumors 1.2e-08 11 57.8 19 16 154
CNS tumor (Various tumors) Various tumors 1.2e-08 11 57.8 19 16 154
Hematologic cancer and cell line (Stimulated immune*) Stimulated immune* 3.6e-08 18 11.6 155 53 1945
Hematologic samples and cell lines (Stimulated immune*) Stimulated immune* 3.6e-08 18 11.6 155 53 1945
Macrophages (Stimulated immune*) Stimulated immune* 3.6e-08 18 11.6 155 53 1945
Monocytes (Stimulated immune*) Stimulated immune* 3.6e-08 18 11.6 155 53 1945
CNS tissue, cancer or cell line (Various tumors) Various tumors 4.0e-08 12 63.1 19 21 154
Malignant glioblastoma (Various tumors) Various tumors 9.7e-08 8 42.1 19 9 154
Adenocarcinoma (Prostate cancer) Prostate cancer 4.3e-07 24 92.3 26 52 102
Cancer and cell line (Prostate cancer) Prostate cancer 4.3e-07 24 92.3 26 52 102
Cancer (Prostate cancer) Prostate cancer 4.3e-07 24 92.3 26 52 102
Prostate cancer or cell line (Prostate cancer) Prostate cancer 4.3e-07 24 92.3 26 52 102
Prostate cancer (Prostate cancer) Prostate cancer 4.3e-07 24 92.3 26 52 102
Cancer and cell line (Liver cancer) Liver cancer 2.5e-06 24 100 24 126 207
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors) Neuro tumors 4.6e-06 7 63.6 11 10 90
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
Breast tissue, cancer or cell line (NCI60) NCI60 0.0004 5 100 5 31 139


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
protein biosynthesis 2.4e-71 84 34.2 245 151 4566
ribonucleoprotein complex 8.6e-68 105 42.8 245 283 4566
structural constituent of ribosome 3.8e-65 62 25.3 245 81 4566
ribosome 4.1e-62 86 35.1 245 194 4566
nucleic acid binding 6.6e-61 120 48.9 245 444 4566
RNA binding 1.7e-53 88 35.9 245 249 4566
nuclease activity 1.0e-46 77 31.4 245 215 4566
cytosolic large ribosomal subunit (sensu Eukarya) 4.5e-33 27 11.0 245 29 4566
large ribosomal subunit 6.1e-33 29 11.8 245 34 4566
small ribosomal subunit 7.7e-25 24 9.7 245 32 4566
cytosolic small ribosomal subunit (sensu Eukarya) 2.8e-24 22 8.9 245 27 4566
hydrolase activity 7.0e-22 104 42.4 245 783 4566
regulation of translational initiation 3.1e-12 13 5.3 245 21 4566
translation factor activity\, nucleic acid binding 1.9e-11 30 12.2 245 139 4566
26S proteasome 2.3e-11 14 5.7 245 28 4566
proteasome complex (sensu Eukarya) 8.3e-11 12 4.8 245 21 4566
translation initiation factor activity 1.3e-10 14 5.7 245 31 4566
translational initiation 4.0e-10 13 5.3 245 28 4566
monovalent inorganic cation transporter activity 5.3e-10 21 8.5 245 80 4566
translational elongation 2.3e-09 10 4.0 245 17 4566
translation regulator activity 4.6e-09 30 12.2 245 172 4566
proteasome endopeptidase activity 5.0e-09 9 3.6 245 14 4566
proteasome core complex (sensu Eukarya) 1.2e-08 9 3.6 245 15 4566
RNA processing 3.3e-08 21 8.5 245 99 4566
mRNA binding 7.8e-08 14 5.7 245 47 4566
catalytic activity 1.2e-07 129 52.6 245 1677 4566
eukaryotic translation initiation factor 3 complex 1.5e-07 6 2.4 245 7 4566
hydrogen ion transporter activity 1.8e-07 14 5.7 245 50 4566
translation elongation factor activity 2.8e-07 8 3.2 245 15 4566
cbb3-type cytochrome c oxidase 7.3e-07 7 2.8 245 12 4566
RNA metabolism 1.1e-06 18 7.3 245 92 4566
cytochrome c oxidase activity 1.5e-06 7 2.8 245 13 4566
eukaryotic 43S pre-initiation complex 1.6e-06 6 2.4 245 9 4566
RNA splicing 3.9e-06 14 5.7 245 63 4566
mRNA processing 4.8e-06 11 4.4 245 40 4566
mitochondrion 1.1e-05 27 11.0 245 207 4566
pre-mRNA splicing factor activity 1.2e-05 10 4.0 245 36 4566
inner membrane 1.2e-05 9 3.6 245 29 4566
single-stranded RNA binding 1.5e-05 6 2.4 245 12 4566
ion transporter activity 2.1e-05 21 8.5 245 144 4566
ubiquitin-dependent protein catabolism 3.0e-05 9 3.6 245 32 4566
mRNA splicing 4.0e-05 11 4.4 245 49 4566
endoplasmic reticulum 4.3e-05 21 8.5 245 151 4566
sodium ion transporter activity 4.9e-05 11 4.4 245 50 4566
single-stranded DNA binding 4.9e-05 7 2.8 245 20 4566
oxidoreductase activity 6.9e-05 29 11.8 245 254 4566
small nucleolar ribonucleoprotein complex 8.6e-05 5 2.0 245 10 4566
cation transporter activity 9.9e-05 10 4.0 245 45 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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