Module 45 -- Whole blood 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:	6
Num genes:	584 (see 2800 additional genes for this module)
Num experiments:	1222 (393 induced, 829 repressed)
Parent module:	84
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.
Whole_Blood_6
Whole_Blood_3
Whole_Blood_4
Whole_Blood_1
Whole_Blood_5
Whole_Blood_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*	3.7e-23	95	24.1	393	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	5.4e-21	95	24.1	393	197	1945
Cancer and cell line (Liver cancer)	Liver cancer	6.3e-18	74	96.1	77	126	207
Non-tumor liver tissue (Liver cancer)	Liver cancer	6.3e-18	64	67.3	95	76	207
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	5.3e-17	26	63.4	41	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	5.3e-17	26	63.4	41	30	182
Cancer and cell line (Various tumors*)	Various tumors*	1.4e-16	85	10.2	828	105	1945
Cancer (Various tumors*)	Various tumors*	1.4e-16	85	10.2	828	105	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.3e-16	75	19.0	393	156	1945
Acute lymphocytic leukemia (Leukemia)	Leukemia	8.9e-11	80	86.0	93	99	149
Lymphocytes (Leukemia)	Leukemia	1.1e-10	74	85.0	87	91	141
Cell line (NCI60*)	NCI60*	1.4e-10	93	11.2	828	135	1945
Cancer and cell line (NCI60*)	NCI60*	9.4e-10	93	11.2	828	138	1945
Cancer (Liver cancer)	Liver cancer	2.1e-09	63	81.8	77	115	207
Breast cancer cell line (Breast cancer)	Breast cancer	1.7e-07	14	36.8	38	17	152
Cancer and cell line (Lung cancer*)	Lung cancer*	4.3e-07	144	17.3	828	252	1945
Cancer (Lung cancer*)	Lung cancer*	4.3e-07	144	17.3	828	252	1945
Cell line (Breast cancer)	Breast cancer	5.0e-07	19	50	38	30	152
Acute leukemia (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Cancer (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Leukemia (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Monocytes (Leukemia*)	Leukemia*	1.6e-06	87	10.5	828	141	1945
Prostate (Prostate cancer*)	Prostate cancer*	1.8e-06	66	7.9	828	101	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	3.4e-06	12	31.5	38	15	152
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	6.9e-06	25	6.3	393	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	6.9e-06	25	6.3	393	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	6.9e-06	25	6.3	393	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	6.9e-06	25	6.3	393	53	1945
Lung cancer (Lung cancer*)	Lung cancer*	7.1e-06	133	16.0	828	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	7.1e-06	133	16.0	828	238	1945
Hepatocellular carcinoma (Liver cancer)	Liver cancer	8.4e-06	54	70.1	77	104	207
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.0e-05	24	82.7	29	67	144
Epithelial cell line (NCI60)	NCI60	1.0e-05	31	32.9	94	32	139
Cell line (Liver cancer)	Liver cancer	1.1e-05	11	14.2	77	11	207
Activated B like DLBCL (B lymphoma)	B lymphoma	1.2e-05	16	32.6	49	30	245
Adenocarcinoma (Liver cancer)	Liver cancer	1.4e-05	51	66.2	77	97	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	2.9e-05	38	77.5	49	126	245
Liver cancer cell line (Liver cancer)	Liver cancer	3.4e-05	10	12.9	77	10	207
Cell line (B lymphoma)	B lymphoma	6.1e-05	12	14.4	83	14	245
Squamous cell lung cancer (Lung cancer)	Lung cancer	8.8e-05	29	19.8	146	35	276
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	0.0001	146	17.6	828	276	1945
B cells (Leukemia)	Leukemia	0.0001	49	56.3	87	62	141
Normal tissue (Liver cancer)	Liver cancer	0.0002	13	13.6	95	14	207
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	0.0002	38	77.5	49	134	245
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0002	5	17.2	29	5	144
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	0.0002	111	13.4	828	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	0.0002	111	13.4	828	205	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	0.0003	54	65.0	83	121	245
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	0.0003	48	12.2	393	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	0.0003	48	12.2	393	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	0.0003	48	12.2	393	152	1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0003	24	82.7	29	78	144

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
response to biotic stimulus	2.4e-18	117	28.5	410	600	4566
response to stress	5.1e-16	135	32.9	410	792	4566
immune response	2.6e-11	85	20.7	410	469	4566
integral to plasma membrane	1.8e-10	100	24.3	410	612	4566
signal transducer activity	1.7e-08	139	33.9	410	1026	4566
intracellular signaling cascade	1.4e-07	57	13.9	410	319	4566
cell communication	2.7e-07	135	32.9	410	1030	4566
receptor activity	3.1e-07	87	21.2	410	582	4566
signal transduction	3.2e-07	114	27.8	410	831	4566
transmembrane receptor activity	5.2e-07	71	17.3	410	448	4566
interleukin binding	3.7e-06	11	2.6	410	25	4566
cellular defense response	3.7e-06	16	3.9	410	50	4566
response to red/far-red light	5.1e-06	32	7.8	410	156	4566
cell surface receptor linked signal transduction	7.4e-06	45	10.9	410	259	4566
hematopoietin/interferon-class (D200-domain) cytokine receptor activity	8.9e-06	14	3.4	410	42	4566
response to pest/pathogen/parasite	1.3e-05	32	7.8	410	163	4566
interleukin receptor activity	1.4e-05	11	2.6	410	28	4566
channel/pore class transporter activity	7.0e-05	53	12.9	410	351	4566
porin activity	9.0e-05	39	9.5	410	235	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 584 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 1222 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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