Module 53 -- Cell line expressed genes

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:	22
Num genes:	406 (see 1271 additional genes for this module)
Num experiments:	1298 (422 induced, 876 repressed)
Parent module:	118
Children modules:	16 15

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.
HL60_2
HL60_1
THY__2
THY__1
THY+
Lymphoblastic_molt_4_2
Lymphoblastic_molt_4_3
Lymphoblastic_molt_4_1
GA10_1
K422_2
Ramos_2
Ramos_1
GA10_2
WSU_2
WSU_1
DOHH2_2
DOHH2_1
K422_1
Burkitts_Daudi_2
Burkitts_Daudi_1
Burkitts_Raji_2
Burkitts_Raji_1

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	1.6e-19	30	54.5	55	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	1.6e-19	30	54.5	55	30	182
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.0e-17	44	43.1	102	46	245
Leukemia (B lymphoma)	B lymphoma	1.0e-17	44	43.1	102	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.0e-17	44	43.1	102	46	245
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.4e-14	88	20.9	421	197	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	2.8e-11	175	19.9	876	276	1945
Liver tissue (Liver cancer*)	Liver cancer*	5.1e-11	78	18.5	421	187	1945
Activated B like DLBCL (B lymphoma)	B lymphoma	4.1e-10	23	36.5	63	30	245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	2.6e-09	54	85.7	63	134	245
Hepatitis infected liver (Liver cancer*)	Liver cancer*	8.7e-09	64	15.2	421	156	1945
Follicular lymphoma (B lymphoma)	B lymphoma	4.1e-08	25	24.5	102	28	245
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	4.9e-08	59	93.6	63	167	245
Lung cancer (Lung cancer*)	Lung cancer*	5.1e-08	146	16.6	876	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	5.1e-08	146	16.6	876	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	9.1e-08	128	14.6	876	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	9.1e-08	128	14.6	876	205	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	1.3e-07	152	17.3	876	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.3e-07	152	17.3	876	252	1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	7.5e-07	49	77.7	63	126	245
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	1.7e-06	27	6.4	421	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	1.7e-06	27	6.4	421	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	1.7e-06	27	6.4	421	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	1.7e-06	27	6.4	421	53	1945
Prostate (Prostate cancer*)	Prostate cancer*	2.9e-06	68	7.7	876	101	1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	3.3e-06	37	82.2	45	78	144
Mutated p53 tumor (Breast cancer)	Breast cancer	5.4e-06	20	83.3	24	35	78
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.2e-05	33	73.3	45	67	144
Hematologic samples and cell lines (Various tumors)	Various tumors	2.9e-05	7	100	7	37	154
Hematologic samples (Various tumors)	Various tumors	2.9e-05	7	100	7	37	154
Hematologic samples (B lymphoma)	B lymphoma	7.0e-05	18	17.6	102	22	245
Breast cancer cell line (Breast cancer)	Breast cancer	0.0001	12	28.5	42	17	152
Grade 1 (Breast cancer)	Breast cancer	0.0001	7	41.1	17	9	85
Cell line (Liver cancer)	Liver cancer	0.0001	11	11.7	94	11	207
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	11	26.1	42	15	152
Grade 3 (Breast cancer)	Breast cancer	0.0002	20	74.0	27	38	85
Normal tissue (Lung cancer)	Lung cancer	0.0002	22	12.5	175	23	276
Cancer and cell line (Various tumors*)	Various tumors*	0.0002	65	7.4	876	105	1945
Cancer (Various tumors*)	Various tumors*	0.0002	65	7.4	876	105	1945
p53 positive hepatocellular carcinoma (Liver cancer)	Liver cancer	0.0002	18	62.0	29	23	60
Liver cancer cell line (Liver cancer)	Liver cancer	0.0002	10	10.6	94	10	207
Cell line (B lymphoma)	B lymphoma	0.0002	10	15.8	63	14	245
Epithelial cell line (NCI60)	NCI60	0.0004	25	35.2	71	32	139
Normal lung tissue (Lung cancer)	Lung cancer	0.0004	21	12	175	22	276

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 metabolism	2.5e-12	37	13.2	279	169	4566
mitosis	2.5e-11	19	6.8	279	50	4566
DNA replication	5.7e-11	19	6.8	279	52	4566
DNA replication and chromosome cycle	3.5e-09	13	4.6	279	29	4566
S phase of mitotic cell cycle	9.5e-09	12	4.3	279	26	4566
DNA dependent DNA replication	4.3e-08	12	4.3	279	29	4566
regulation of transcription	4.0e-07	18	6.4	279	76	4566
cell cycle	1.4e-06	24	8.6	279	135	4566
replication fork	2.6e-06	8	2.8	279	17	4566
transcription\, DNA-dependent	2.0e-05	25	8.9	279	167	4566
cytokinesis	2.5e-05	12	4.3	279	49	4566
regulation of cell cycle	4.0e-05	24	8.6	279	163	4566
host-pathogen interaction	5.3e-05	27	9.6	279	198	4566
nucleus	0.0001	85	30.4	279	966	4566
transcription	0.0001	25	8.9	279	184	4566
DNA repair	0.0001	16	5.7	279	93	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 1298 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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