Module 12 -- Spinal cord (neuro-development) 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:	2
Num genes:	360 (see 3082 additional genes for this module)
Num experiments:	1322 (357 induced, 965 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.
Spinal_cord_2
Spinal_cord_1

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*	4.3e-26	201	20.8	964	252	1945
Cancer (Lung cancer*)	Lung cancer*	4.3e-26	201	20.8	964	252	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.6e-23	212	21.9	964	276	1945
Lung cancer (Lung cancer*)	Lung cancer*	2.5e-23	188	19.5	964	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	2.5e-23	188	19.5	964	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	2.4e-21	164	17.0	964	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	2.4e-21	164	17.0	964	205	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.0e-18	83	23.3	356	187	1945
Cancer and cell line (Neuro tumors*)	Neuro tumors*	9.8e-18	79	8.1	964	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	9.8e-18	79	8.1	964	86	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.1e-16	83	23.3	356	197	1945
Cancer and cell line (Liver cancer)	Liver cancer	1.7e-16	73	94.8	77	126	207
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	2.6e-16	74	7.6	964	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	2.6e-16	74	7.6	964	81	1945
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	1.9e-15	76	7.8	964	85	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.0e-14	57	67.8	84	76	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.1e-11	63	17.6	356	156	1945
Prostate (Prostate cancer*)	Prostate cancer*	7.1e-11	81	8.4	964	101	1945
Hematologic samples and cell lines (Various tumors)	Various tumors	1.4e-09	37	38.1	97	37	154
Hematologic samples (Various tumors)	Various tumors	1.4e-09	37	38.1	97	37	154
Cancer (Liver cancer)	Liver cancer	2.1e-09	63	81.8	77	115	207
Acute leukemia (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Cancer (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Leukemia (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Monocytes (Leukemia*)	Leukemia*	9.9e-09	102	10.5	964	141	1945
Hematologic cancer and cell line (Various tumors)	Various tumors	6.9e-08	31	31.9	97	31	154
Hematologic cancer (Various tumors)	Various tumors	6.9e-08	31	31.9	97	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	6.9e-08	31	31.9	97	31	154
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	1.1e-07	36	87.8	41	126	245
Cancer and cell line (Various tumors*)	Various tumors*	3.0e-07	77	7.9	964	105	1945
Cancer (Various tumors*)	Various tumors*	3.0e-07	77	7.9	964	105	1945
Lymphocytes (Various tumors)	Various tumors	4.3e-07	28	28.8	97	28	154
Monocytes (Various tumors)	Various tumors	4.3e-07	28	28.8	97	28	154
Adenocarcinoma (Liver cancer)	Liver cancer	9.2e-07	53	68.8	77	97	207
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	1.0e-06	36	87.8	41	134	245
Breast tissue or cancer (Breast cancer*)	Breast cancer*	1.0e-06	43	12.0	356	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	1.0e-06	43	12.0	356	118	1945
Cell line (NCI60*)	NCI60*	1.9e-06	93	9.6	964	135	1945
Hepatocellular carcinoma (Liver cancer)	Liver cancer	2.1e-06	55	71.4	77	104	207
Malignant glioblastoma (Neuro tumors)	Neuro tumors	2.2e-06	6	85.7	7	10	90
Acute lymphocytic leukemia (Leukemia)	Leukemia	4.8e-06	85	77.2	110	99	149
B cells (Various tumors)	Various tumors	7.9e-06	23	23.7	97	23	154
Cancer and cell line (NCI60*)	NCI60*	8.7e-06	93	9.6	964	138	1945
Epithelial cell line (NCI60)	NCI60	1.0e-05	31	32.9	94	32	139
Breast cancer cell line (Breast cancer)	Breast cancer	1.2e-05	14	28	50	17	152
Adenocarcinoma (Breast cancer*)	Breast cancer*	1.3e-05	39	10.9	356	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	1.3e-05	39	10.9	356	112	1945
Cancer (Breast cancer*)	Breast cancer*	1.3e-05	39	10.9	356	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	1.3e-05	39	10.9	356	112	1945
Lymphocytes (Leukemia)	Leukemia	1.6e-05	77	75.4	102	91	141
Unstimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.8e-05	13	61.9	21	39	182
Cell line (Breast cancer)	Breast cancer	2.3e-05	20	40	50	30	152
CNS tissue, cancer or cell line (Various tumors)	Various tumors	3.0e-05	7	70	10	21	154
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	3.0e-05	29	32.9	88	46	245
Leukemia (B lymphoma)	B lymphoma	3.0e-05	29	32.9	88	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	3.0e-05	29	32.9	88	46	245
Cancer and cell line (Gliomas*)	Gliomas*	3.1e-05	37	3.8	964	47	1945
Cancer (Gliomas*)	Gliomas*	3.1e-05	37	3.8	964	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	3.1e-05	37	3.8	964	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	3.1e-05	37	3.8	964	47	1945
CNS tumor (Gliomas*)	Gliomas*	3.1e-05	37	3.8	964	47	1945
Liver cancer cell line (Liver cancer)	Liver cancer	3.4e-05	10	12.9	77	10	207
Lymphoma (Various tumors)	Various tumors	4.2e-05	20	20.6	97	20	154
B cells (Leukemia)	Leukemia	8.0e-05	55	53.9	102	62	141
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	8.1e-05	44	12.3	356	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	9.8e-05	44	12.3	356	142	1945
Cancer and cell line (Various tumors)	Various tumors	0.0001	77	79.3	97	105	154
Cancer (Various tumors)	Various tumors	0.0001	77	79.3	97	105	154
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	12	24	50	15	152
Activated B like DLBCL (B lymphoma)	B lymphoma	0.0001	13	31.7	41	30	245
Cancer and cell line (NCI60*)	NCI60*	0.0002	42	11.7	356	138	1945
Cell line (Liver cancer)	Liver cancer	0.0002	10	12.9	77	11	207
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	0.0003	39	10.9	356	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	0.0003	39	10.9	356	128	1945

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
extracellular matrix structural constituent	4.9e-10	29	11.9	243	149	4566
cell adhesion	1.4e-06	30	12.3	243	222	4566
collagen	2.4e-06	10	4.1	243	31	4566
cell adhesion molecule activity	6.6e-06	19	7.8	243	114	4566
organogenesis	6.7e-06	36	14.8	243	315	4566
neurogenesis	7.2e-06	24	9.8	243	169	4566
morphogenesis	1.4e-05	39	16.0	243	366	4566
development	8.0e-05	50	20.5	243	554	4566
fibrillar collagen	0.0001	4	1.6	243	6	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 1322 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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