Module 55

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:	10
Num genes:	834 (see 2799 additional genes for this module)
Num experiments:	1420 (389 induced, 1031 repressed)
Parent module:	88
Children modules:	24 23

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.
Fetal_liver_2
Fetal_liver_1
Salivary_gland_2
Pancreas_2
Pancreas_1
Kidney_3
Kidney_1
Kidney_2
Liver_1
Liver_2

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
Liver tissue (Liver cancer*)	Liver cancer*	7.5e-44	119	30.5	389	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	2.2e-40	119	30.5	389	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	3.9e-31	94	24.1	389	156	1945
Cancer and cell line (Liver cancer)	Liver cancer	1.4e-25	82	100	82	126	207
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.0e-23	75	63.0	119	76	207
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	2.9e-23	220	21.3	1030	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	1.8e-22	203	19.7	1030	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.8e-22	203	19.7	1030	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	4.5e-20	190	18.4	1030	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	4.5e-20	190	18.4	1030	238	1945
Cancer and cell line (Various tumors*)	Various tumors*	1.9e-19	97	9.4	1030	105	1945
Cancer (Various tumors*)	Various tumors*	1.9e-19	97	9.4	1030	105	1945
Acute lymphocytic leukemia (Leukemia)	Leukemia	3.3e-19	90	90.9	99	99	149
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	1.1e-18	166	16.1	1030	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	1.1e-18	166	16.1	1030	205	1945
Lymphocytes (Leukemia)	Leukemia	4.3e-18	82	90.1	91	91	141
Cancer (Liver cancer)	Liver cancer	4.7e-15	72	87.8	82	115	207
B cells (Leukemia)	Leukemia	3.7e-10	57	62.6	91	62	141
Adenocarcinoma (Liver cancer)	Liver cancer	5.7e-10	60	73.1	82	97	207
Activated B like DLBCL (B lymphoma)	B lymphoma	1.6e-09	17	50	34	30	245
Hepatocellular carcinoma (Liver cancer)	Liver cancer	2.1e-09	62	75.6	82	104	207
Breast tissue or cancer (Breast cancer*)	Breast cancer*	2.4e-09	51	13.1	389	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	2.4e-09	51	13.1	389	118	1945
Prostate (Prostate cancer*)	Prostate cancer*	4.9e-09	81	7.8	1030	101	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	7.3e-09	73	70.8	103	121	245
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	1.1e-08	32	94.1	34	126	245
Adenocarcinoma (Breast cancer*)	Breast cancer*	3.4e-08	47	12.0	389	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	3.4e-08	47	12.0	389	112	1945
Cancer (Breast cancer*)	Breast cancer*	3.4e-08	47	12.0	389	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	3.4e-08	47	12.0	389	112	1945
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	9.7e-08	32	94.1	34	134	245
Cell line (NCI60*)	NCI60*	4.1e-07	99	9.6	1030	135	1945
Invasive liver tumor (Liver cancer)	Liver cancer	4.2e-07	29	35.3	82	38	207
Cancer and cell line (Neuro tumors*)	Neuro tumors*	9.1e-07	67	6.5	1030	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	9.1e-07	67	6.5	1030	86	1945
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	2.1e-06	63	6.1	1030	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	2.1e-06	63	6.1	1030	81	1945
Cancer and cell line (NCI60*)	NCI60*	2.3e-06	99	9.6	1030	138	1945
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	2.4e-06	51	13.1	389	141	1945
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	3.0e-06	47	12.0	389	127	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	3.1e-06	51	13.1	389	142	1945
Lymphoma (B lymphoma)	B lymphoma	3.5e-06	49	47.5	103	77	245
Breast cancer or cell line (Breast cancer*)	Breast cancer*	3.9e-06	47	12.0	389	128	1945
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	4.3e-06	65	6.3	1030	85	1945
Epithelial cell line (NCI60)	NCI60	4.7e-06	32	32	100	32	139
After doxorubicin chemotherapy (Breast cancer)	Breast cancer	3.2e-05	18	85.7	21	21	38
Primary blood mononuclear cells (Leukemia)	Leukemia	3.9e-05	21	23.0	91	21	141
Liver cancer cell line (Liver cancer)	Liver cancer	6.7e-05	10	12.1	82	10	207
Metastasis (Liver cancer)	Liver cancer	6.7e-05	10	12.1	82	10	207
Cancer and cell line (Breast cancer*)	Breast cancer*	0.0001	47	12.0	389	143	1945
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	0.0001	32	94.1	34	167	245
Toxoplasma infected skin fibroblasts (Fibroblast infection*)	Fibroblast infection*	0.0001	9	2.3	389	13	1945
Fibroblasts (Fibroblast infection*)	Fibroblast infection*	0.0002	10	2.5	389	16	1945
Bone marrow (Leukemia)	Leukemia	0.0002	22	24.1	91	23	141
Normal tissue (Liver cancer)	Liver cancer	0.0003	14	11.7	119	14	207
Breast cancer cell line (Breast cancer)	Breast cancer	0.0003	13	24.0	54	17	152
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	0.0003	10	47.6	21	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	0.0003	10	47.6	21	30	182

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
extracellular space	3.6e-13	67	11.2	594	212	4566
plasma protein	1.7e-11	18	3.0	594	25	4566
response to chemical substance	5.8e-09	76	12.7	594	308	4566
complement activation	8.4e-08	15	2.5	594	26	4566
oxidoreductase activity	1.0e-07	63	10.6	594	254	4566
microsome	1.8e-07	24	4.0	594	61	4566
regulation of complement activation	3.8e-07	14	2.3	594	25	4566
response to xenobiotic stimulus	1.0e-06	38	6.3	594	133	4566
complement activity	2.2e-06	11	1.8	594	18	4566
serine-type endopeptidase activity	9.6e-06	23	3.8	594	69	4566
electron transporter activity	9.8e-06	60	10.1	594	269	4566
endopeptidase inhibitor activity	1.1e-05	22	3.7	594	65	4566
plasma glycoprotein	1.2e-05	12	2.0	594	24	4566
chymotrypsin activity	1.4e-05	18	3.0	594	48	4566
oxidoreductase activity\, acting on paired donors\, with incorporation or reduction of molecular oxygen	1.5e-05	17	2.8	594	44	4566
trypsin activity	2.7e-05	18	3.0	594	50	4566
complement activation\, classical pathway	2.9e-05	11	1.8	594	22	4566
complement activation\, alternative pathway	5.1e-05	7	1.1	594	10	4566
response to pathogenic bacteria	5.1e-05	7	1.1	594	10	4566
heparin binding	7.5e-05	15	2.5	594	40	4566
xenobiotic metabolism	0.0001	14	2.3	594	37	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 834 genes, this image does not display the individual gene names, but rather condenses each gene 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.

Note: Since there are 1420 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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