Module 54 -- Cell cycle (expression clusters)

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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: 9
Num genes: 263 (see 1989 additional genes for this module)
Num experiments: 944 (349 induced, 595 repressed)
Parent module: None
Children modules: None


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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.
Armstrong01 31
Lessnick02 20
Rosenwald01 46
Alizadeh00 20
Iyer99 17
Whitfield02 34
Perou00 6
Garber01 23
Sorlie01 33


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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 6.8e-26 73 68.8 106 76 207
Hematologic cancer and cell line (Stimulated PBMC) Stimulated PBMC 6.0e-24 30 68.1 44 30 182
Macrophages (Stimulated PBMC) Stimulated PBMC 6.0e-24 30 68.1 44 30 182
Chronic lymphocytic leukemia (B lymphoma) B lymphoma 1.4e-20 44 48.3 91 46 245
Leukemia (B lymphoma) B lymphoma 1.4e-20 44 48.3 91 46 245
Leukemia or leukemia cell line (B lymphoma) B lymphoma 1.4e-20 44 48.3 91 46 245
Cancer and cell line (Liver cancer) Liver cancer 1.9e-19 67 100 67 126 207
Liver tissue (Liver cancer*) Liver cancer* 1.9e-13 103 17.3 595 187 1945
Cell line (B lymphoma) B lymphoma 1.5e-11 14 29.7 47 14 245
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 1.6e-11 103 17.3 595 197 1945
B. petrussis stimulated immune cells (Stimulated PBMC) Stimulated PBMC 2.5e-11 30 96.7 31 67 144
Hepatitis infected liver (Liver cancer*) Liver cancer* 5.4e-09 81 13.6 595 156 1945
Invasive liver tumor (Liver cancer) Liver cancer 7.2e-09 28 41.7 67 38 207
Gram negative bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 7.6e-09 30 96.7 31 78 144
Cancer (Liver cancer) Liver cancer 7.8e-09 56 83.5 67 115 207
Hepatocellular carcinoma (Liver cancer) Liver cancer 1.8e-07 51 76.1 67 104 207
Normal lung tissue (Lung cancer) Lung cancer 4.8e-07 20 17.8 112 22 276
Adenocarcinoma (Liver cancer) Liver cancer 6.5e-07 48 71.6 67 97 207
Liver tissue, cancer or cell line (Liver cancer*) Liver cancer* 6.7e-07 62 17.8 348 197 1945
Grade 3 (Breast cancer) Breast cancer 9.1e-07 19 90.4 21 38 85
Hematologic samples (B lymphoma) B lymphoma 9.4e-07 19 20.8 91 22 245
Normal tissue (Various tumors) Various tumors 1.2e-06 25 64.1 39 49 154
Small cell lung cancer (Lung cancer) Lung cancer 1.6e-06 9 16.9 53 10 276
Cell line (Liver cancer) Liver cancer 2.2e-06 11 16.4 67 11 207
Breast tissue or cancer (NCI60) NCI60 2.3e-06 4 57.1 7 4 139
Female hormonal tissue or cancer (NCI60) NCI60 2.3e-06 4 57.1 7 4 139
Normal tissue (Lung cancer) Lung cancer 2.4e-06 20 17.8 112 23 276
Acute myelogeous leukemia (Leukemia) Leukemia 6.2e-06 26 65 40 50 141
Liver cancer cell line (Liver cancer) Liver cancer 7.7e-06 10 14.9 67 10 207
Breast tissue, cancer or cell line (NCI60) NCI60 1.5e-05 7 100 7 31 139
Prostate (Various tumors) Various tumors 1.8e-05 10 25.6 39 12 154
Hepatitis infected liver (Liver cancer*) Liver cancer* 2.9e-05 48 13.7 348 156 1945
p53 positive hepatocellular carcinoma (Liver cancer) Liver cancer 3.3e-05 20 62.5 32 23 60
Diffuse large B cell lymphoma tumor or cell line (B lymphoma) B lymphoma 3.6e-05 38 80.8 47 134 245
Lymphoma or lymphoma cell line (B lymphoma) B lymphoma 4.0e-05 43 91.4 47 167 245
Normal prostate tissue (Various tumors) Various tumors 4.3e-05 7 17.9 39 7 154
Normal tissue (Liver cancer) Liver cancer 5.4e-05 14 13.2 106 14 207
Cell line (Breast cancer) Breast cancer 7.1e-05 17 42.5 40 30 152
Breast cancer (NCI60) NCI60 7.9e-05 3 42.8 7 3 139
Lung tissue, cancer or cell line (Lung cancer*) Lung cancer* 8.9e-05 112 18.8 595 276 1945
Hematologic samples and cell lines (Various tumors) Various tumors 0.0001 8 80 10 37 154
Hematologic samples (Various tumors) Various tumors 0.0001 8 80 10 37 154
Female hormonal tissue, cancer or cell line (NCI60) NCI60 0.0001 7 100 7 43 139
Live bacteria stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0002 5 16.6 30 5 148
Liver tissue (Liver cancer*) Liver cancer* 0.0002 52 14.9 348 187 1945
Wild type p53 tumor (Breast cancer) Breast cancer 0.0003 15 93.7 16 43 78
B. petrussis 537 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0003 5 16.1 31 5 144
B. petrussis A2 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0003 5 16.1 31 5 144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC) Stimulated PBMC 0.0003 5 16.1 31 5 144
Breast cancer or cell line (NCI60) NCI60 0.0003 6 85.7 7 30 139


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
cell cycle 1.3e-28 40 26.1 153 135 4566
DNA metabolism 2.5e-19 35 22.8 153 169 4566
mitosis 7.8e-19 21 13.7 153 50 4566
DNA replication 2.1e-18 21 13.7 153 52 4566
regulation of cell cycle 5.1e-16 31 20.2 153 163 4566
DNA replication and chromosome cycle 6.2e-14 14 9.1 153 29 4566
cytokinesis 1.4e-12 16 10.4 153 49 4566
S phase of mitotic cell cycle 8.4e-12 12 7.8 153 26 4566
nucleus 4.0e-11 68 44.4 153 966 4566
regulation of transcription 2.4e-10 17 11.1 153 76 4566
nucleotidyltransferase activity 5.7e-10 40 26.1 153 425 4566
transcription\, DNA-dependent 7.3e-10 24 15.6 153 167 4566
M phase of mitotic cell cycle 8.1e-10 9 5.8 153 17 4566
DNA dependent DNA replication 8.6e-10 11 7.1 153 29 4566
DNA repair 8.7e-10 18 11.7 153 93 4566
endomembrane system 2.2e-09 67 43.7 153 1029 4566
M phase 4.4e-09 10 6.5 153 26 4566
nuclear division 5.1e-09 9 5.8 153 20 4566
transcription 5.4e-09 24 15.6 153 184 4566
mitotic cell cycle 6.3e-09 13 8.4 153 51 4566
replication fork 2.4e-08 8 5.2 153 17 4566
ATP binding 5.6e-08 35 22.8 153 399 4566
regulation of mitosis 5.9e-08 7 4.5 153 13 4566
spindle 2.1e-07 7 4.5 153 15 4566
regulation of CDK activity 6.1e-07 8 5.2 153 24 4566
viral host cell process manipulation 1.0e-06 15 9.8 153 102 4566
DNA replication initiation 8.7e-06 5 3.2 153 10 4566
response to DNA damage stimulus 9.0e-06 26 16.9 153 310 4566
catalytic activity 1.1e-05 82 53.5 153 1677 4566
mitotic anaphase 1.5e-05 5 3.2 153 11 4566
nucleoplasm 3.3e-05 12 7.8 153 89 4566
oncogenesis 3.3e-05 18 11.7 153 184 4566
cell cycle checkpoint 4.0e-05 5 3.2 153 13 4566
ribonucleotide metabolism 4.3e-05 7 4.5 153 30 4566
DNA-directed DNA polymerase activity 7.6e-05 4 2.6 153 8 4566
mitotic checkpoint 7.6e-05 4 2.6 153 8 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 944 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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