Module 54 -- Cell cycle (expression clusters)

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

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

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

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

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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