Module 24 -- Fetal liver genes - Metabolism and xenobiotics

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:	2
Num genes:	453 (see 3218 additional genes for this module)
Num experiments:	1221 (335 induced, 886 repressed)
Parent module:	55
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.
Fetal_liver_2
Fetal_liver_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
Liver tissue (Liver cancer*)	Liver cancer*	5.5e-59	125	37.3	335	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	5.6e-55	125	37.3	335	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.2e-42	99	29.5	335	156	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.4e-34	218	24.6	885	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	9.3e-33	201	22.7	885	252	1945
Cancer (Lung cancer*)	Lung cancer*	9.3e-33	201	22.7	885	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	2.0e-29	188	21.2	885	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	2.0e-29	188	21.2	885	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	1.2e-26	164	18.5	885	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	1.2e-26	164	18.5	885	205	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	2.8e-21	75	60	125	76	207
Cancer and cell line (Liver cancer)	Liver cancer	5.8e-21	71	100	71	126	207
Acute lymphocytic leukemia (Leukemia)	Leukemia	1.6e-15	82	91.1	90	99	149
Prostate (Prostate cancer*)	Prostate cancer*	7.5e-15	83	9.3	885	101	1945
Lymphocytes (Leukemia)	Leukemia	2.2e-14	74	90.2	82	91	141
Cancer (Liver cancer)	Liver cancer	5.3e-11	61	85.9	71	115	207
Cancer and cell line (Various tumors*)	Various tumors*	2.6e-09	77	8.7	885	105	1945
Cancer (Various tumors*)	Various tumors*	2.6e-09	77	8.7	885	105	1945
B cells (Leukemia)	Leukemia	2.3e-08	52	63.4	82	62	141
Adenocarcinoma (Liver cancer)	Liver cancer	3.1e-08	52	73.2	71	97	207
Breast tissue or cancer (Breast cancer*)	Breast cancer*	1.7e-07	43	12.8	335	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	1.7e-07	43	12.8	335	118	1945
Hematologic samples and cell lines (Various tumors)	Various tumors	1.9e-07	36	36	100	37	154
Hematologic samples (Various tumors)	Various tumors	1.9e-07	36	36	100	37	154
Cell line (NCI60*)	NCI60*	5.9e-07	89	10.0	885	135	1945
Invasive liver tumor (Liver cancer)	Liver cancer	2.0e-06	26	36.6	71	38	207
Cancer and cell line (NCI60*)	NCI60*	2.5e-06	89	10.0	885	138	1945
Adenocarcinoma (Breast cancer*)	Breast cancer*	2.6e-06	39	11.6	335	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	2.6e-06	39	11.6	335	112	1945
Cancer (Breast cancer*)	Breast cancer*	2.6e-06	39	11.6	335	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	2.6e-06	39	11.6	335	112	1945
Cell line (Breast cancer)	Breast cancer	4.3e-06	19	45.2	42	30	152
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	4.6e-06	59	6.6	885	85	1945
Hematologic cancer and cell line (Various tumors)	Various tumors	5.3e-06	30	30	100	31	154
Hematologic cancer (Various tumors)	Various tumors	5.3e-06	30	30	100	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	5.3e-06	30	30	100	31	154
Hepatocellular carcinoma (Liver cancer)	Liver cancer	5.6e-06	51	71.8	71	104	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	7.1e-06	23	92	25	126	245
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	9.9e-06	56	6.3	885	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	9.9e-06	56	6.3	885	81	1945
Breast cancer cell line (Breast cancer)	Breast cancer	1.1e-05	13	30.9	42	17	152
Liver cancer cell line (Liver cancer)	Liver cancer	1.4e-05	10	14.0	71	10	207
Metastasis (Liver cancer)	Liver cancer	1.4e-05	10	14.0	71	10	207
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	1.6e-05	44	13.1	335	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	2.0e-05	44	13.1	335	142	1945
Activated B like DLBCL (B lymphoma)	B lymphoma	2.1e-05	11	44	25	30	245
Cancer and cell line (Neuro tumors*)	Neuro tumors*	2.2e-05	58	6.5	885	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	2.2e-05	58	6.5	885	86	1945
Lymphocytes (Various tumors)	Various tumors	2.5e-05	27	27	100	28	154
Monocytes (Various tumors)	Various tumors	2.5e-05	27	27	100	28	154
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	2.9e-05	23	92	25	134	245
CNS tissue, cancer or cell line (Various tumors)	Various tumors	5.0e-05	21	21	100	21	154
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	7.8e-05	39	11.6	335	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	9.4e-05	39	11.6	335	128	1945
Cell line (Liver cancer)	Liver cancer	0.0001	10	14.0	71	11	207
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	11	26.1	42	15	152
Bone marrow (Leukemia)	Leukemia	0.0002	21	25.6	82	23	141
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	0.0002	23	34.3	67	46	245
Leukemia (B lymphoma)	B lymphoma	0.0002	23	34.3	67	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	0.0002	23	34.3	67	46	245
B cells (Various tumors)	Various tumors	0.0002	22	22	100	23	154

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
plasma protein	5.5e-13	16	4.7	335	25	4566
endopeptidase inhibitor activity	9.1e-08	19	5.6	335	65	4566
extracellular space	1.2e-07	38	11.3	335	212	4566
complement activation	8.0e-07	11	3.2	335	26	4566
plasma glycoprotein	3.0e-06	10	2.9	335	24	4566
serine protease inhibitor activity	3.7e-06	13	3.8	335	41	4566
regulation of complement activation	4.7e-06	10	2.9	335	25	4566
blood coagulation	4.8e-06	14	4.1	335	48	4566
chymotrypsin activity	4.8e-06	14	4.1	335	48	4566
serine-type endopeptidase activity	6.0e-06	17	5.0	335	69	4566
hemostasis	8.2e-06	14	4.1	335	50	4566
trypsin activity	8.2e-06	14	4.1	335	50	4566
oxidoreductase activity\, acting on paired donors\, with incorporation or reduction of molecular oxygen\, reduced flavin or flavoprotein as one donor\, and incorporation of one atom of oxygen	1.0e-05	6	1.7	335	9	4566
heparin binding	1.7e-05	12	3.5	335	40	4566
complement activity	1.7e-05	8	2.3	335	18	4566
blood coagulation factor activity	2.4e-05	6	1.7	335	10	4566
response to chemical substance	4.3e-05	42	12.5	335	308	4566
glycosaminoglycan binding	4.9e-05	12	3.5	335	44	4566
enzyme inhibitor activity	5.6e-05	20	5.9	335	105	4566
oxidoreductase activity	7.1e-05	36	10.7	335	254	4566
complement activation\, classical pathway	9.9e-05	8	2.3	335	22	4566
lipid transport	0.0001	9	2.6	335	28	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 1221 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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