Module 92 -- Secreted signaling molecules

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:	149 (see 2653 additional genes for this module)
Num experiments:	888 (285 induced, 603 repressed)
Parent module:	None
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.
secretion
cell_cell signaling

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
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.2e-70	217	35.9	603	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	1.4e-65	200	33.1	603	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.4e-65	200	33.1	603	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	2.0e-59	187	31.0	603	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	2.0e-59	187	31.0	603	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	2.8e-51	162	26.8	603	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	2.8e-51	162	26.8	603	205	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	2.6e-21	57	80.2	71	76	207
Stimulated immune cells (Stimulated PBMC*)	Stimulated PBMC*	5.3e-19	63	22.1	285	143	1945
Hematologic samples (Stimulated PBMC*)	Stimulated PBMC*	9.0e-19	65	22.8	285	152	1945
Lymphocytes (Stimulated PBMC*)	Stimulated PBMC*	9.0e-19	65	22.8	285	152	1945
Primary blood mononuclear cells (Stimulated PBMC*)	Stimulated PBMC*	9.0e-19	65	22.8	285	152	1945
Cancer and cell line (Liver cancer)	Liver cancer	4.2e-16	69	95.8	72	126	207
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	7.2e-16	68	23.8	285	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	7.2e-16	68	23.8	285	182	1945
Liver tissue (Liver cancer*)	Liver cancer*	9.0e-16	69	24.2	285	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	2.1e-14	69	24.2	285	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	4.7e-11	54	18.9	285	156	1945
Cancer (Liver cancer)	Liver cancer	1.6e-09	60	83.3	72	115	207
B cells (Leukemia)	Leukemia	2.0e-08	48	66.6	72	62	141
Bone marrow (Leukemia)	Leukemia	2.4e-08	23	31.9	72	23	141
Cell line (Breast cancer)	Breast cancer	3.8e-08	19	55.8	34	30	152
Hepatocellular carcinoma (Liver cancer)	Liver cancer	1.4e-07	54	75	72	104	207
Acute leukemia (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Cancer (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Leukemia (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Monocytes (Leukemia*)	Leukemia*	1.9e-07	72	11.9	603	141	1945
Unstimulated immune cells (Stimulated PBMC)	Stimulated PBMC	2.9e-07	23	50	46	39	182
Breast cancer cell line (Breast cancer)	Breast cancer	5.4e-07	13	38.2	34	17	152
Adenocarcinoma (Liver cancer)	Liver cancer	1.6e-06	50	69.4	72	97	207
Primary blood mononuclear cells (Leukemia)	Leukemia	4.0e-06	20	27.7	72	21	141
Female hormonal cancer cell line (Breast cancer)	Breast cancer	1.1e-05	11	32.3	34	15	152
Hematologic samples and cell lines (Various tumors)	Various tumors	4.8e-05	21	46.6	45	37	154
Hematologic samples (Various tumors)	Various tumors	4.8e-05	21	46.6	45	37	154
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	5.3e-05	17	36.9	46	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	5.3e-05	17	36.9	46	30	182
Normal tissue (Liver cancer)	Liver cancer	6.4e-05	12	16.9	71	14	207
Live bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	5	18.5	27	5	148
Stage T1 (Lung cancer)	Lung cancer	0.0002	139	83.2	167	153	195
Invasive liver tumor (Liver cancer)	Liver cancer	0.0003	23	31.9	72	38	207
Activated B like DLBCL (B lymphoma)	B lymphoma	0.0003	9	40.9	22	30	245
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	0.0004	19	86.3	22	126	245

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
secretion	2.1e-199	144	96.6	149	240	4566
cell-cell signaling	1.0e-169	126	84.5	149	194	4566
receptor binding	3.3e-66	79	53.0	149	235	4566
signal transducer activity	3.8e-34	102	68.4	149	1026	4566
cell communication	1.3e-29	97	65.1	149	1030	4566
chemokine receptor binding	9.9e-29	24	16.1	149	35	4566
signal transduction	4.8e-28	86	57.7	149	831	4566
response to extracellular stimulus	1.5e-24	64	42.9	149	500	4566
response to biotic stimulus	6.3e-24	69	46.3	149	600	4566
immune response	1.3e-23	61	40.9	149	469	4566
chemotaxis	1.4e-22	27	18.1	149	73	4566
energy taxis	2.2e-22	27	18.1	149	74	4566
taxis	5.0e-22	27	18.1	149	76	4566
binding	9.3e-22	90	60.4	149	1103	4566
extracellular space	5.5e-21	40	26.8	149	212	4566
inflammatory response	7.1e-21	30	20.1	149	108	4566
growth factor activity	2.7e-20	28	18.7	149	95	4566
thermoregulation	4.1e-20	29	19.4	149	105	4566
digestion	5.3e-16	16	10.7	149	33	4566
T-cell activation	7.2e-16	34	22.8	149	207	4566
lymphocyte activation	9.8e-16	34	22.8	149	209	4566
cytokine activity	1.6e-14	19	12.7	149	61	4566
defense response	1.6e-14	37	24.8	149	272	4566
hormone activity	8.4e-14	17	11.4	149	50	4566
regulation of T-cell proliferation	2.0e-13	19	12.7	149	69	4566
lymphocyte proliferation	2.7e-13	19	12.7	149	70	4566
positive regulation of cell proliferation	1.9e-12	18	12.0	149	68	4566
calcium ion homeostasis	6.8e-12	10	6.7	149	16	4566
response to stress	5.4e-10	57	38.2	149	792	4566
metal ion homeostasis	1.7e-08	10	6.7	149	30	4566
cation homeostasis	2.4e-08	10	6.7	149	31	4566
cell ion homeostasis	4.9e-08	10	6.7	149	33	4566
transmission of nerve impulse	8.4e-08	6	4.0	149	9	4566
response to pest/pathogen/parasite	2.1e-07	20	13.4	149	163	4566
G-protein coupled receptor protein signaling pathway	8.4e-07	24	16.1	149	245	4566
cell surface receptor linked signal transduction	8.0e-06	23	15.4	149	259	4566
regulation of neurotransmitter levels	1.0e-05	7	4.6	149	25	4566
neurotransmitter secretion	1.0e-05	6	4.0	149	17	4566
humoral immune response	2.3e-05	14	9.3	149	118	4566
development	2.6e-05	36	24.1	149	554	4566
peptide hormone	2.8e-05	6	4.0	149	20	4566
heparin binding	3.3e-05	8	5.3	149	40	4566
toxin activity	3.5e-05	4	2.6	149	7	4566
exocytosis	5.4e-05	5	3.3	149	14	4566
circulation	6.7e-05	9	6.0	149	56	4566
glycosaminoglycan binding	6.9e-05	8	5.3	149	44	4566
humoral defense mechanism (sensu Invertebrata)	9.5e-05	10	6.7	149	72	4566
viral host cell process manipulation	0.0001	12	8.0	149	102	4566
conjugation without cellular fusion	0.0001	15	10.0	149	152	4566
protein secretion	0.0001	4	2.6	149	9	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 888 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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