Module 57 -- Cell cycle (KEGG, GenMapp)

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:	56 (see 2103 additional genes for this module)
Num experiments:	487 (229 induced, 258 repressed)
Parent module:	None
Children modules:	None

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.
Cell_cycle
Cell cycle

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
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	1.7e-29	30	85.7	35	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.7e-29	30	85.7	35	30	182
Non-tumor liver tissue (Liver cancer)	Liver cancer	5.7e-25	54	90	60	76	207
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	7.2e-23	40	62.5	64	46	245
Leukemia (B lymphoma)	B lymphoma	7.2e-23	40	62.5	64	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	7.2e-23	40	62.5	64	46	245
Cell line (B lymphoma)	B lymphoma	6.3e-14	14	41.1	34	14	245
Liver tissue (Liver cancer*)	Liver cancer*	9.5e-13	60	23.3	257	187	1945
Cancer and cell line (Liver cancer)	Liver cancer	8.6e-12	44	100	44	126	207
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.2e-11	60	23.3	257	197	1945
Normal lung tissue (Lung cancer)	Lung cancer	1.8e-09	12	52.1	23	22	276
B cells (B lymphoma*)	B lymphoma*	2.0e-09	62	24.1	257	231	1945
Lymphocytes (B lymphoma*)	B lymphoma*	3.0e-09	64	24.9	257	244	1945
Normal tissue (Lung cancer)	Lung cancer	3.6e-09	12	52.1	23	23	276
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.1e-08	24	96	25	67	144
Hepatitis infected liver (Liver cancer*)	Liver cancer*	5.2e-08	45	17.5	257	156	1945
Liver cancer cell line (Liver cancer)	Liver cancer	7.7e-08	10	22.7	44	10	207
Small cell lung cancer (Lung cancer)	Lung cancer	8.2e-08	8	30.7	26	10	276
Invasive liver tumor (Liver cancer)	Liver cancer	2.1e-07	21	47.7	44	38	207
Breast tissue or cancer (NCI60)	NCI60	3.3e-07	4	80	5	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	3.3e-07	4	80	5	4	139
Cancer (B lymphoma*)	B lymphoma*	5.0e-07	51	19.8	257	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	5.0e-07	51	19.8	257	200	1945
Cell line (Liver cancer)	Liver cancer	7.2e-07	10	22.7	44	11	207
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.3e-07	24	96	25	78	144
p53 positive hepatocellular carcinoma (Liver cancer)	Liver cancer	4.0e-06	16	80	20	23	60
Cancer and cell line (B lymphoma*)	B lymphoma*	4.7e-06	51	19.8	257	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	4.7e-06	51	19.8	257	214	1945
Normal tissue (Liver cancer)	Liver cancer	8.1e-06	12	20	60	14	207
Grade 3 (Breast cancer)	Breast cancer	9.5e-06	15	93.7	16	38	85
Breast cancer (NCI60)	NCI60	2.2e-05	3	60	5	3	139
Hematologic samples and cell lines (Various tumors)	Various tumors	4.3e-05	8	88.8	9	37	154
Hematologic samples (Various tumors)	Various tumors	4.3e-05	8	88.8	9	37	154
Cancer and cell line (Breast cancer*)	Breast cancer*	4.9e-05	33	14.4	228	143	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	7.5e-05	41	17.9	228	197	1945
Cell line (Breast cancer)	Breast cancer	0.0001	15	45.4	33	30	152
B. petrussis 537 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	5	20	25	5	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	5	20	25	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	5	20	25	5	144
Acute myelogeous leukemia (Leukemia)	Leukemia	0.0003	16	69.5	23	50	141
Adenocarcinoma (Liver cancer)	Liver cancer	0.0003	31	70.4	44	97	207
Breast tissue, cancer or cell line (NCI60)	NCI60	0.0004	5	100	5	31	139

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
regulation of cell cycle	7.7e-37	31	72.0	43	163	4566
cytokinesis	4.4e-22	16	37.2	43	49	4566
mitosis	6.4e-22	16	37.2	43	50	4566
cell cycle	9.6e-22	21	48.8	43	135	4566
transcription\, DNA-dependent	1.0e-19	21	48.8	43	167	4566
transcription	8.0e-19	21	48.8	43	184	4566
nucleus	2.0e-18	36	83.7	43	966	4566
endomembrane system	1.8e-17	36	83.7	43	1029	4566
regulation of transcription	5.1e-17	15	34.8	43	76	4566
viral host cell process manipulation	1.8e-16	16	37.2	43	102	4566
regulation of transcription\, DNA-dependent	2.5e-14	27	62.7	43	595	4566
host-pathogen interaction	8.0e-12	16	37.2	43	198	4566
regulation of CDK activity	2.0e-11	8	18.6	43	24	4566
S phase of mitotic cell cycle	4.2e-11	8	18.6	43	26	4566
DNA replication initiation	9.9e-11	6	13.9	43	10	4566
DNA dependent DNA replication	1.1e-10	8	18.6	43	29	4566
DNA replication and chromosome cycle	1.1e-10	8	18.6	43	29	4566
cell cycle checkpoint	7.9e-10	6	13.9	43	13	4566
regulation of mitosis	7.9e-10	6	13.9	43	13	4566
mitotic checkpoint	3.1e-09	5	11.6	43	8	4566
DNA replication	1.7e-08	8	18.6	43	52	4566
response to DNA damage stimulus	4.2e-07	14	32.5	43	310	4566
DNA damage response\, signal transduction	4.5e-07	5	11.6	43	18	4566
oncogenesis	6.2e-07	11	25.5	43	184	4566
protein serine/threonine kinase activity	7.6e-07	9	20.9	43	114	4566
transcription from Pol II promoter	2.3e-06	9	20.9	43	130	4566
DNA metabolism	2.4e-06	10	23.2	43	169	4566
kinase regulator activity	3.6e-06	7	16.2	43	72	4566
protein amino acid phosphorylation	5.7e-06	11	25.5	43	230	4566
regulation of transcription from Pol II promoter	6.0e-06	9	20.9	43	146	4566
nucleotidyltransferase activity	1.8e-05	14	32.5	43	425	4566
ATP binding	4.5e-05	13	30.2	43	399	4566
G1/S transition of mitotic cell cycle	0.0001	3	6.9	43	11	4566
kinetochore	0.0001	3	6.9	43	11	4566

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 487 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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