Module 118 -- 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:	31
Num genes:	411 (see 1251 additional genes for this module)
Num experiments:	1519 (458 induced, 1061 repressed)
Parent module:	None
Children modules:	52 53

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.
A2058_2
A2058_1
Myelogenous_k_562_2
Myelogenous_k_562_1
HUVEC_1
HUVEC_3
HUVEC_2
Hep3b_2
Hep3b_1
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	7.3e-20	30	55.5	54	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	7.3e-20	30	55.5	54	30	182
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	2.4e-16	96	20.9	458	197	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.1e-14	208	19.6	1060	276	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.8e-13	87	18.9	458	187	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	5.6e-13	44	35.2	125	46	245
Leukemia (B lymphoma)	B lymphoma	5.6e-13	44	35.2	125	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	5.6e-13	44	35.2	125	46	245
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	1.4e-12	76	7.1	1060	85	1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	9.1e-12	62	87.3	71	134	245
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	1.1e-11	72	6.7	1060	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	1.1e-11	72	6.7	1060	81	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	3.2e-11	185	17.4	1060	252	1945
Cancer (Lung cancer*)	Lung cancer*	3.2e-11	185	17.4	1060	252	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	3.7e-11	155	14.6	1060	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	3.7e-11	155	14.6	1060	205	1945
Lung cancer (Lung cancer*)	Lung cancer*	3.8e-11	176	16.6	1060	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	3.8e-11	176	16.6	1060	238	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.4e-10	71	15.5	458	156	1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	5.8e-10	58	81.6	71	126	245
Activated B like DLBCL (B lymphoma)	B lymphoma	7.1e-10	24	33.8	71	30	245
Cancer and cell line (Neuro tumors*)	Neuro tumors*	5.0e-09	72	6.7	1060	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	5.0e-09	72	6.7	1060	86	1945
Epithelial cell line (NCI60)	NCI60	8.0e-08	32	35.5	90	32	139
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	8.8e-08	65	91.5	71	167	245
Prostate (Prostate cancer*)	Prostate cancer*	1.0e-07	80	7.5	1060	101	1945
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	6.7e-07	29	6.3	458	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	6.7e-07	29	6.3	458	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	6.7e-07	29	6.3	458	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	6.7e-07	29	6.3	458	53	1945
Follicular lymphoma (B lymphoma)	B lymphoma	7.3e-07	26	20.8	125	28	245
Mutated p53 tumor (Breast cancer)	Breast cancer	8.0e-06	22	78.5	28	35	78
Hematologic samples and cell lines (B lymphoma)	B lymphoma	8.0e-06	79	63.2	125	121	245
Classical malignant glioblastoma (Gliomas)	Gliomas	0.0001	10	100	10	14	27
Non-classic malignant glioblastoma (Gliomas)	Gliomas	0.0001	13	76.4	17	13	27
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	31	70.4	44	67	144
Wild type p53 tumor (Breast cancer)	Breast cancer	0.0001	16	94.1	17	43	78
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	34	77.2	44	78	144
Large cell lung cancer (Lung cancer)	Lung cancer	0.0003	4	10.5	38	4	276
GC B like DLBCL (B lymphoma)	B lymphoma	0.0003	26	36.6	71	53	245

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
mitosis	3.2e-08	16	5.5	290	50	4566
DNA replication	2.5e-06	14	4.8	290	52	4566
cell cycle	2.8e-06	24	8.2	290	135	4566
regulation of transcription	3.4e-06	17	5.8	290	76	4566
DNA metabolism	5.6e-06	27	9.3	290	169	4566
DNA replication and chromosome cycle	4.8e-05	9	3.1	290	29	4566
regulation of cell cycle	7.5e-05	24	8.2	290	163	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 1519 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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