Module 122 -- Adhesion 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:	3
Num genes:	141 (see 2175 additional genes for this module)
Num experiments:	914 (245 induced, 669 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.
cell adhesion
extracellular matrix structural constituent
cell adhesion molecule activity

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-32	184	27.5	667	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	2.8e-32	172	25.7	667	252	1945
Cancer (Lung cancer*)	Lung cancer*	2.8e-32	172	25.7	667	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	5.3e-30	162	24.2	667	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	5.3e-30	162	24.2	667	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	3.5e-23	136	20.3	667	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	3.5e-23	136	20.3	667	205	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	1.0e-13	51	91.0	56	121	245
Cancer and cell line (Liver cancer)	Liver cancer	3.4e-12	50	98.0	51	126	207
Breast tissue or cancer (Breast cancer*)	Breast cancer*	4.7e-12	43	17.5	245	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	4.7e-12	43	17.5	245	118	1945
Adenocarcinoma (Breast cancer*)	Breast cancer*	1.3e-11	41	16.7	245	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	1.3e-11	41	16.7	245	112	1945
Cancer (Breast cancer*)	Breast cancer*	1.3e-11	41	16.7	245	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	1.3e-11	41	16.7	245	112	1945
B cells (Leukemia)	Leukemia	4.0e-11	52	69.3	75	62	141
Acute lymphocytic leukemia (Leukemia)	Leukemia	3.2e-10	73	87.9	83	99	149
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	3.3e-10	42	17.1	245	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	4.4e-10	42	17.1	245	128	1945
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	1.0e-09	44	17.9	245	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	1.3e-09	44	17.9	245	142	1945
Lymphocytes (Leukemia)	Leukemia	3.2e-09	65	86.6	75	91	141
Lymphoma (B lymphoma)	B lymphoma	5.8e-09	36	64.2	56	77	245
Hematologic samples and cell lines (Various tumors)	Various tumors	1.9e-08	31	45.5	68	37	154
Hematologic samples (Various tumors)	Various tumors	1.9e-08	31	45.5	68	37	154
Cancer and cell line (Breast cancer*)	Breast cancer*	2.0e-08	42	17.1	245	143	1945
Cell line (NCI60*)	NCI60*	4.6e-08	76	11.3	667	135	1945
Hepatocellular carcinoma (Liver cancer)	Liver cancer	6.7e-08	42	82.3	51	104	207
Bone marrow (Leukemia)	Leukemia	7.5e-08	23	30.6	75	23	141
Cancer (Liver cancer)	Liver cancer	1.2e-07	44	86.2	51	115	207
Cancer and cell line (NCI60*)	NCI60*	1.6e-07	76	11.3	667	138	1945
Hematologic cancer and cell line (Various tumors)	Various tumors	5.4e-07	26	38.2	68	31	154
Hematologic cancer (Various tumors)	Various tumors	5.4e-07	26	38.2	68	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	5.4e-07	26	38.2	68	31	154
Cancer and cell line (NCI60*)	NCI60*	6.9e-07	38	15.5	245	138	1945
Adenocarcinoma (Liver cancer)	Liver cancer	8.5e-07	39	76.4	51	97	207
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.1e-06	48	19.5	245	197	1945
Acute leukemia (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Cancer (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Leukemia (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Monocytes (Leukemia*)	Leukemia*	1.3e-06	75	11.2	667	141	1945
Liver tissue (Liver cancer*)	Liver cancer*	1.4e-06	46	18.7	245	187	1945
Cell line (Breast cancer)	Breast cancer	2.6e-06	19	46.3	41	30	152
Lymphocytes (Various tumors)	Various tumors	7.3e-06	23	33.8	68	28	154
Monocytes (Various tumors)	Various tumors	7.3e-06	23	33.8	68	28	154
Breast cancer cell line (Breast cancer)	Breast cancer	8.2e-06	13	31.7	41	17	152
Cell line (NCI60*)	NCI60*	9.2e-06	35	14.2	245	135	1945
Primary blood mononuclear cells (Leukemia)	Leukemia	9.9e-06	20	26.6	75	21	141
Cancer and cell line (Gliomas*)	Gliomas*	2.7e-05	30	4.4	667	47	1945
Cancer (Gliomas*)	Gliomas*	2.7e-05	30	4.4	667	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	2.7e-05	30	4.4	667	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	2.7e-05	30	4.4	667	47	1945
CNS tumor (Gliomas*)	Gliomas*	2.7e-05	30	4.4	667	47	1945
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	2.7e-05	21	91.3	23	126	245
Activated B like DLBCL (B lymphoma)	B lymphoma	6.6e-05	10	43.4	23	30	245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	9.8e-05	21	91.3	23	134	245
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	11	26.8	41	15	152
Hepatitis infected liver (Liver cancer*)	Liver cancer*	0.0001	36	14.6	245	156	1945
Colon cancer cell line (NCI60)	NCI60	0.0001	14	18.1	77	14	139
Colon cancer or cell line (NCI60)	NCI60	0.0001	14	18.1	77	14	139
Colon tissue, cancer or cell line (NCI60)	NCI60	0.0001	14	18.1	77	14	139
Hematologic cancer and cell line (NCI60)	NCI60	0.0001	14	18.1	77	14	139
Hematologic samples and cell lines (NCI60)	NCI60	0.0001	14	18.1	77	14	139
Leukemia cell line (NCI60)	NCI60	0.0001	14	18.1	77	14	139
After doxorubicin chemotherapy (Breast cancer)	Breast cancer	0.0001	18	81.8	22	21	38
Fast doubling (20-40) cell lines (NCI60)	NCI60	0.0002	62	86.1	72	90	122
B cells (Various tumors)	Various tumors	0.0003	18	26.4	68	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
cell adhesion	2.1e-155	122	86.5	141	222	4566
extracellular matrix structural constituent	4.5e-117	93	65.9	141	149	4566
cell adhesion molecule activity	9.7e-82	69	48.9	141	114	4566
cell communication	1.1e-63	124	87.9	141	1030	4566
collagen	1.8e-29	23	16.3	141	31	4566
cell-cell adhesion	7.3e-21	19	13.4	141	34	4566
cell-matrix adhesion	1.9e-14	14	9.9	141	29	4566
cell adhesion receptor activity	2.4e-14	13	9.2	141	24	4566
integrin complex	2.1e-12	11	7.8	141	20	4566
homophilic cell adhesion	8.7e-12	11	7.8	141	22	4566
integrin-mediated signaling pathway	1.6e-11	11	7.8	141	23	4566
calcium ion binding	8.0e-08	22	15.6	141	195	4566
fibrillar collagen	1.5e-07	5	3.5	141	6	4566
histogenesis and organogenesis	5.7e-07	10	7.0	141	44	4566
obsolete	6.5e-07	56	39.7	141	990	4566
regulation of cell adhesion	2.9e-06	5	3.5	141	9	4566
chemotaxis	1.1e-05	11	7.8	141	73	4566
energy taxis	1.2e-05	11	7.8	141	74	4566
bone remodeling	1.4e-05	11	7.8	141	75	4566
skeletal development	1.4e-05	11	7.8	141	75	4566
proteoglycan integral to plasma membrane	1.5e-05	6	4.2	141	19	4566
taxis	1.6e-05	11	7.8	141	76	4566
integral to plasma membrane	2.6e-05	37	26.2	141	612	4566
metal ion binding	3.8e-05	28	19.8	141	410	4566
chemokine receptor binding	7.5e-05	7	4.9	141	35	4566
porin activity	8.9e-05	19	13.4	141	235	4566
integrin binding	9.7e-05	4	2.8	141	9	4566
development	0.0001	33	23.4	141	554	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 914 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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