Module 52 -- 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:	9
Num genes:	433 (see 1859 additional genes for this module)
Num experiments:	1406 (402 induced, 1004 repressed)
Parent module:	118
Children modules:	8 18 17 3

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

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	2.8e-31	30	90.9	33	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	2.8e-31	30	90.9	33	30	182
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	3.4e-20	95	23.6	402	197	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.9e-19	210	20.9	1003	276	1945
Liver tissue (Liver cancer*)	Liver cancer*	5.8e-16	85	21.1	402	187	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	3.2e-15	187	18.6	1003	252	1945
Cancer (Lung cancer*)	Lung cancer*	3.2e-15	187	18.6	1003	252	1945
Prostate (Prostate cancer*)	Prostate cancer*	9.5e-15	88	8.7	1003	101	1945
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	2.4e-13	75	7.4	1003	85	1945
Lung cancer (Lung cancer*)	Lung cancer*	4.0e-13	174	17.3	1003	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	4.0e-13	174	17.3	1003	238	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.5e-12	43	35.8	120	46	245
Leukemia (B lymphoma)	B lymphoma	1.5e-12	43	35.8	120	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.5e-12	43	35.8	120	46	245
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	2.3e-12	71	7.0	1003	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	2.3e-12	71	7.0	1003	81	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.9e-12	69	17.1	402	156	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	2.1e-11	150	14.9	1003	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	2.1e-11	150	14.9	1003	205	1945
Hematologic samples and cell lines (Various tumors)	Various tumors	1.5e-10	36	42.3	85	37	154
Hematologic samples (Various tumors)	Various tumors	1.5e-10	36	42.3	85	37	154
Cancer and cell line (Neuro tumors*)	Neuro tumors*	1.9e-10	72	7.1	1003	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	1.9e-10	72	7.1	1003	86	1945
Hematologic cancer and cell line (Various tumors)	Various tumors	1.9e-08	30	35.2	85	31	154
Hematologic cancer (Various tumors)	Various tumors	1.9e-08	30	35.2	85	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	1.9e-08	30	35.2	85	31	154
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	1.5e-07	28	6.9	402	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	1.5e-07	28	6.9	402	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	1.5e-07	28	6.9	402	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	1.5e-07	28	6.9	402	53	1945
Lymphocytes (Various tumors)	Various tumors	1.8e-07	27	31.7	85	28	154
Monocytes (Various tumors)	Various tumors	1.8e-07	27	31.7	85	28	154
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	2.2e-07	45	84.9	53	134	245
Activated B like DLBCL (B lymphoma)	B lymphoma	9.6e-07	18	33.9	53	30	245
Epithelial cell line (NCI60)	NCI60	1.2e-06	30	36.5	82	32	139
Follicular lymphoma (B lymphoma)	B lymphoma	2.7e-06	25	20.8	120	28	245
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	3.7e-06	49	92.4	53	167	245
Cell line (B lymphoma)	B lymphoma	4.2e-06	11	20.7	53	14	245
Lymphoma (B lymphoma)	B lymphoma	5.7e-06	54	45	120	77	245
B cells (Various tumors)	Various tumors	6.4e-06	22	25.8	85	23	154
Hematologic samples and cell lines (B lymphoma)	B lymphoma	4.5e-05	75	62.5	120	121	245
Lymphoma (Various tumors)	Various tumors	4.8e-05	19	22.3	85	20	154
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.6e-05	20	83.3	24	67	144
Invasive liver tumor (Liver cancer)	Liver cancer	8.3e-05	29	29.2	99	38	207
B. petrussis 537 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.8e-05	5	20.8	24	5	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.8e-05	5	20.8	24	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.8e-05	5	20.8	24	5	144
Mutated p53 tumor (Breast cancer)	Breast cancer	0.0001	17	80.9	21	35	78
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	0.0001	39	73.5	53	126	245
Cell line (Liver cancer)	Liver cancer	0.0002	11	11.1	99	11	207
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	0.0002	5	62.5	8	10	90
Large cell lung cancer (Lung cancer)	Lung cancer	0.0002	4	10.8	37	4	276
Dead prognosis (Breast cancer)	Breast cancer	0.0003	16	72.7	22	34	86
Cancer and cell line (Gliomas*)	Gliomas*	0.0003	36	3.5	1003	47	1945
Cancer (Gliomas*)	Gliomas*	0.0003	36	3.5	1003	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	0.0003	36	3.5	1003	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	0.0003	36	3.5	1003	47	1945
CNS tumor (Gliomas*)	Gliomas*	0.0003	36	3.5	1003	47	1945
Hematologic cancer and cell line (NCI60)	NCI60	0.0003	14	17.0	82	14	139
Hematologic samples and cell lines (NCI60)	NCI60	0.0003	14	17.0	82	14	139
Leukemia cell line (NCI60)	NCI60	0.0003	14	17.0	82	14	139
Classical malignant glioblastoma (Gliomas)	Gliomas	0.0004	9	100	9	14	27
Non-classic malignant glioblastoma (Gliomas)	Gliomas	0.0004	13	72.2	18	13	27

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	9.4e-08	16	5.1	313	50	4566
DNA replication	1.0e-06	15	4.7	313	52	4566
regulation of transcription	9.7e-06	17	5.4	313	76	4566
cell cycle	1.0e-05	24	7.6	313	135	4566
DNA metabolism	2.3e-05	27	8.6	313	169	4566
regulation of cell cycle	3.4e-05	26	8.3	313	163	4566
T-cell activation	5.6e-05	30	9.5	313	207	4566
lymphocyte activation	6.7e-05	30	9.5	313	209	4566
DNA replication and chromosome cycle	8.7e-05	9	2.8	313	29	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 1406 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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