Module 324 -- metal/Ca ion binding

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:	133 (see 1523 additional genes for this module)
Num experiments:	936 (266 induced, 670 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.
metal ion binding
calcium ion binding

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
Cancer and cell line (Lung cancer*)	Lung cancer*	3.5e-49	193	28.8	669	252	1945
Cancer (Lung cancer*)	Lung cancer*	3.5e-49	193	28.8	669	252	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	4.8e-47	203	30.3	669	276	1945
Lung cancer (Lung cancer*)	Lung cancer*	4.4e-44	180	26.9	669	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	4.4e-44	180	26.9	669	238	1945
Liver tissue (Liver cancer*)	Liver cancer*	4.6e-38	94	35.3	266	187	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	1.1e-35	153	22.8	669	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	1.1e-35	153	22.8	669	205	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.3e-35	94	35.3	266	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.8e-26	73	27.4	266	156	1945
Cancer and cell line (Liver cancer)	Liver cancer	9.6e-16	68	95.7	71	126	207
Non-tumor liver tissue (Liver cancer)	Liver cancer	3.9e-13	60	62.5	96	76	207
Hematologic samples and cell lines (Various tumors)	Various tumors	2.0e-10	34	45.9	74	37	154
Hematologic samples (Various tumors)	Various tumors	2.0e-10	34	45.9	74	37	154
Cancer (Liver cancer)	Liver cancer	3.3e-09	59	83.0	71	115	207
Breast tissue or cancer (Breast cancer*)	Breast cancer*	1.9e-08	39	14.6	266	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	1.9e-08	39	14.6	266	118	1945
Acute lymphocytic leukemia (Leukemia)	Leukemia	2.3e-08	65	87.8	74	99	149
Adenocarcinoma (Breast cancer*)	Breast cancer*	4.8e-08	37	13.9	266	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	4.8e-08	37	13.9	266	112	1945
Cancer (Breast cancer*)	Breast cancer*	4.8e-08	37	13.9	266	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	4.8e-08	37	13.9	266	112	1945
Hematologic cancer and cell line (Various tumors)	Various tumors	5.5e-08	28	37.8	74	31	154
Hematologic cancer (Various tumors)	Various tumors	5.5e-08	28	37.8	74	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	5.5e-08	28	37.8	74	31	154
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	1.9e-07	39	14.6	266	127	1945
Lymphocytes (Leukemia)	Leukemia	2.2e-07	57	86.3	66	91	141
Breast cancer or cell line (Breast cancer*)	Breast cancer*	2.4e-07	39	14.6	266	128	1945
B cells (Leukemia)	Leukemia	3.0e-07	44	66.6	66	62	141
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	4.8e-07	41	15.4	266	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	6.0e-07	41	15.4	266	142	1945
Lymphocytes (Various tumors)	Various tumors	7.2e-07	25	33.7	74	28	154
Monocytes (Various tumors)	Various tumors	7.2e-07	25	33.7	74	28	154
Cancer and cell line (Various tumors*)	Various tumors*	7.8e-07	60	8.9	669	105	1945
Cancer (Various tumors*)	Various tumors*	7.8e-07	60	8.9	669	105	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	1.1e-06	41	78.8	52	121	245
Hepatocellular carcinoma (Liver cancer)	Liver cancer	1.3e-06	52	73.2	71	104	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	3.6e-06	24	92.3	26	126	245
Cancer and cell line (Breast cancer*)	Breast cancer*	5.7e-06	39	14.6	266	143	1945
Adenocarcinoma (Liver cancer)	Liver cancer	1.3e-05	48	67.6	71	97	207
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	1.6e-05	24	92.3	26	134	245
CNS tissue, cancer or cell line (Various tumors)	Various tumors	1.7e-05	19	25.6	74	21	154
B cells (Various tumors)	Various tumors	3.7e-05	20	27.0	74	23	154
CNS cancer or cell line (Various tumors)	Various tumors	7.1e-05	15	20.2	74	16	154
CNS tumor (Various tumors)	Various tumors	7.1e-05	15	20.2	74	16	154
Cell line (Breast cancer)	Breast cancer	7.1e-05	17	42.5	40	30	152
Lymphoma (B lymphoma)	B lymphoma	0.0001	28	53.8	52	77	245
Bone marrow (Leukemia)	Leukemia	0.0001	19	28.7	66	23	141
Liver cancer cell line (Liver cancer)	Liver cancer	0.0003	9	12.6	71	10	207
Lymphoma (Various tumors)	Various tumors	0.0003	17	22.9	74	20	154
Stage T2 (Lung cancer)	Lung cancer	0.0003	8	61.5	13	35	195
Medulloblastoma (Neuro tumors)	Neuro tumors	0.0004	33	86.8	38	60	90
Vincristine chemotherapy (Neuro tumors)	Neuro tumors	0.0004	33	86.8	38	60	90

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
metal ion binding	1.3e-149	133	100	133	410	4566
calcium ion binding	1.7e-86	83	62.4	133	195	4566
binding	1.5e-85	133	100	133	1103	4566
transition metal ion binding	1.4e-24	37	27.8	133	160	4566
zinc ion binding	9.6e-18	26	19.5	133	108	4566
homophilic cell adhesion	1.1e-13	12	9.0	133	22	4566
cell-cell adhesion	7.2e-11	12	9.0	133	34	4566
metallopeptidase activity	7.6e-09	14	10.5	133	70	4566
collagen catabolism	2.2e-08	7	5.2	133	13	4566
metalloendopeptidase activity	4.7e-08	11	8.2	133	46	4566
alcohol dehydrogenase activity\, zinc-dependent	1.0e-07	6	4.5	133	10	4566
calcium-dependent phospholipid binding	1.0e-07	6	4.5	133	10	4566
proteolysis and peptidolysis	1.1e-07	20	15.0	133	176	4566
extracellular matrix structural constituent	2.0e-07	18	13.5	133	149	4566
phospholipase inhibitor activity	3.9e-07	5	3.7	133	7	4566
alcohol dehydrogenase activity	4.3e-07	6	4.5	133	12	4566
magnesium ion binding	4.9e-07	11	8.2	133	57	4566
peptidase activity	5.1e-07	20	15.0	133	193	4566
endopeptidase activity	7.3e-07	14	10.5	133	99	4566
blood coagulation	7.9e-07	10	7.5	133	48	4566
cell adhesion	1.1e-06	21	15.7	133	222	4566
hemostasis	1.1e-06	10	7.5	133	50	4566
extracellular space	2.3e-06	20	15.0	133	212	4566
protein catabolism	2.5e-06	7	5.2	133	23	4566
phospholipid binding	3.4e-06	7	5.2	133	24	4566
cell adhesion molecule activity	4.1e-06	14	10.5	133	114	4566
macromolecule catabolism	4.7e-06	7	5.2	133	25	4566
iron ion binding	2.0e-05	5	3.7	133	13	4566
anticoagulant activity	2.2e-05	4	3.0	133	7	4566
copper ion binding	3.1e-05	5	3.7	133	14	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 936 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

>4x