Module 143

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:	14 (see 1847 additional genes for this module)
Num experiments:	180 (75 induced, 105 repressed)
Parent module:	293
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.
antigen processing
antigen presentation, peptide antigen

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	5.3e-22	23	95.8	24	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	5.3e-22	23	95.8	24	30	182
Lung carcinoid (Lung cancer)	Lung cancer	4.5e-14	15	57.6	26	20	276
Cell line (B lymphoma)	B lymphoma	1.2e-08	7	77.7	9	14	245
Lymphoma (Various tumors)	Various tumors	7.5e-08	9	81.8	11	20	154
Hematologic cancer and cell line (Various tumors)	Various tumors	2.7e-07	10	90.9	11	31	154
Hematologic cancer (Various tumors)	Various tumors	2.7e-07	10	90.9	11	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	2.7e-07	10	90.9	11	31	154
B cells (Various tumors)	Various tumors	3.5e-07	9	81.8	11	23	154
Hematologic samples and cell lines (Various tumors)	Various tumors	2.0e-06	10	90.9	11	37	154
Hematologic samples (Various tumors)	Various tumors	2.0e-06	10	90.9	11	37	154
Lymphocytes (Various tumors)	Various tumors	2.7e-06	9	81.8	11	28	154
Monocytes (Various tumors)	Various tumors	2.7e-06	9	81.8	11	28	154
Cell line (Breast cancer)	Breast cancer	6.3e-06	9	81.8	11	30	152
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	9.0e-06	5	31.2	16	5	144
Breast cancer cell line (Breast cancer)	Breast cancer	1.5e-05	7	63.6	11	17	152
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	1.6e-05	24	22.8	105	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	1.6e-05	24	22.8	105	182	1945
Epithelial cell line (Breast cancer)	Breast cancer	2.4e-05	7	63.6	11	18	152
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	4.0e-05	15	93.7	16	67	144
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	6	54.5	11	15	152
Liver tissue (Liver cancer*)	Liver cancer*	0.0001	18	24	75	187	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	0.0001	16	21.3	75	156	1945
Diffuse large B cell lymphoma - DLBCL (Various tumors)	Various tumors	0.0002	5	45.4	11	11	154
Diffuse large B cell lymphoma tumor or cell line (Various tumors)	Various tumors	0.0002	5	45.4	11	11	154
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	0.0002	18	24	75	197	1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0004	15	93.7	16	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
antigen presentation\, peptide antigen	5.1e-41	14	100	14	14	4566
antigen processing	5.1e-41	14	100	14	14	4566
antigen presentation\, endogenous antigen	6.4e-22	8	57.1	14	8	4566
antigen processing\, endogenous antigen via MHC class I	6.4e-22	8	57.1	14	8	4566
MHC class I receptor activity	5.7e-21	8	57.1	14	9	4566
defense response	5.1e-18	14	100	14	272	4566
antigen processing\, exogenous antigen via MHC class II	2.3e-16	6	42.8	14	6	4566
transmembrane receptor activity	6.3e-15	14	100	14	448	4566
immune response	1.2e-14	14	100	14	469	4566
receptor activity	2.6e-13	14	100	14	582	4566
response to biotic stimulus	4.0e-13	14	100	14	600	4566
signal transducer activity	7.8e-10	14	100	14	1026	4566
response to stress	1.3e-09	13	92.8	14	792	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.

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