Module 158 -- DNA replication

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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: 5
Num genes: 43 (see 1172 additional genes for this module)
Num experiments: 404 (184 induced, 220 repressed)
Parent module: None
Children modules: 125


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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.
replication fork
DNA dependent DNA replication
S phase of mitotic cell cycle
DNA replication and chromosome cycle
DNA replication


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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
Non-tumor liver tissue (Liver cancer) Liver cancer 2.6e-18 49 83.0 59 76 207
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 3.4e-16 17 100 17 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 3.4e-16 17 100 17 30 182
Liver tissue (Liver cancer*) Liver cancer* 1.6e-15 59 26.8 220 187 1945
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 2.4e-14 59 26.8 220 197 1945
Hepatitis infected liver (Liver cancer*) Liver cancer* 1.6e-11 47 21.3 220 156 1945
Normal lung tissue (Lung cancer) Lung cancer 2.8e-11 16 42.1 38 22 276
Normal tissue (Lung cancer) Lung cancer 8.7e-11 16 42.1 38 23 276
Cancer and cell line (Liver cancer) Liver cancer 4.7e-10 38 100 38 126 207
Liver cancer cell line (Liver cancer) Liver cancer 1.4e-08 10 26.3 38 10 207
Small cell lung cancer (Lung cancer) Lung cancer 8.2e-08 8 30.7 26 10 276
Cell line (Liver cancer) Liver cancer 1.4e-07 10 26.3 38 11 207
Hematologic samples and cell lines (Various tumors) Various tumors 2.0e-06 10 90.9 11 37 154
Hematologic samples (Various tumors) Various tumors 2.0e-06 10 90.9 11 37 154
Breast tissue or cancer (NCI60) NCI60 4.7e-06 4 50 8 4 139
Female hormonal tissue or cancer (NCI60) NCI60 4.7e-06 4 50 8 4 139
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 1.1e-05 37 20.2 183 197 1945
Invasive liver tumor (Liver cancer) Liver cancer 2.1e-05 17 44.7 38 38 207
Grade 3 (Breast cancer) Breast cancer 5.6e-05 11 100 11 38 85
Centroblasts (Various tumors) Various tumors 7.0e-05 4 36.3 11 5 154
GC B like DLBCL (Various tumors) Various tumors 7.0e-05 4 36.3 11 5 154
T cells (Various tumors) Various tumors 7.0e-05 4 36.3 11 5 154
Breast cancer (NCI60) NCI60 0.0001 3 37.5 8 3 139
Follicular lymphoma (B lymphoma) B lymphoma 0.0001 13 30.2 43 28 245
Cell line (Breast cancer) Breast cancer 0.0002 12 50 24 30 152
Cancer and cell line (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0002 6 2.7 220 10 1945
Cell line (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0002 6 2.7 220 10 1945
EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0002 6 2.7 220 10 1945
Fibroblasts (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0002 6 2.7 220 10 1945
Skin fibroblasts (Fibroblast EWS-FLI*) Fibroblast EWS-FLI* 0.0002 6 2.7 220 10 1945


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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
DNA replication 2.5e-70 36 83.7 43 52 4566
DNA metabolism 1.4e-61 42 97.6 43 169 4566
DNA replication and chromosome cycle 1.5e-36 20 46.5 43 29 4566
S phase of mitotic cell cycle 2.8e-30 17 39.5 43 26 4566
DNA dependent DNA replication 1.0e-26 16 37.2 43 29 4566
replication fork 5.4e-22 12 27.9 43 17 4566
DNA binding 4.2e-20 27 62.7 43 357 4566
nucleus 1.0e-19 37 86.0 43 966 4566
DNA repair 3.9e-17 16 37.2 43 93 4566
nucleoplasm 6.4e-16 15 34.8 43 89 4566
DNA-directed DNA polymerase activity 3.1e-14 7 16.2 43 8 4566
endomembrane system 5.1e-14 33 76.7 43 1029 4566
nucleotidyltransferase activity 1.8e-13 23 53.4 43 425 4566
cell cycle 1.2e-10 13 30.2 43 135 4566
nu DNA polymerase activity 3.4e-10 5 11.6 43 6 4566
DNA replication initiation 1.4e-08 5 11.6 43 10 4566
nucleotide binding 2.7e-08 8 18.6 43 55 4566
transcription regulator activity 4.1e-08 22 51.1 43 703 4566
DNA replication factor C complex 1.0e-07 4 9.3 43 6 4566
single-stranded DNA binding 8.1e-07 5 11.6 43 20 4566
exonuclease activity 6.3e-06 4 9.3 43 14 4566
ribonuclease activity 6.9e-06 5 11.6 43 30 4566
3'-5' exonuclease activity 7.6e-06 3 6.9 43 5 4566
chromatin remodeling complex 7.6e-06 3 6.9 43 5 4566
chromosome 2.0e-05 6 13.9 43 62 4566
exoribonuclease activity 2.6e-05 3 6.9 43 7 4566
catalytic activity 3.9e-05 29 67.4 43 1677 4566
ATP binding 4.5e-05 13 30.2 43 399 4566
DNA dependent ATPase activity 0.0001 4 9.3 43 28 4566


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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 404 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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