Module 137 -- CNS 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:	22
Num genes:	546 (see 1632 additional genes for this module)
Num experiments:	1270 (301 induced, 969 repressed)
Parent module:	None
Children modules:	100

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.
Nutt03 23
Nutt03 26
Pomeroy02 31
Corpus_callosum_3
Corpus_callosum_2
Corpus_callosum_1
Fetal_brain_1
Fetal_brain_2
Whole_Brain_2
Cerebellum_2
Cerebellum_1
Amygdala_1
Cortex
Thalamus_2
Thalamus_1
Amygdala_2
Caudate_nucleus_2
Caudate_nucleus_1
Whole_Brain_1
Pituitary_gland
Pomeroy02 32
Nutt03 16

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
Acute leukemia (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Cancer (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Leukemia (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Monocytes (Leukemia*)	Leukemia*	4.8e-26	127	13.1	968	141	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	2.3e-25	170	17.5	968	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	2.3e-25	170	17.5	968	205	1945
Liver tissue (Liver cancer*)	Liver cancer*	1.3e-21	80	26.5	301	187	1945
Lymphoma (B lymphoma)	B lymphoma	2.7e-21	51	79.6	64	77	245
Cancer and cell line (Neuro tumors*)	Neuro tumors*	3.9e-21	82	8.4	968	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	3.9e-21	82	8.4	968	86	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	7.5e-20	80	26.5	301	197	1945
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	1.2e-19	77	7.9	968	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	1.2e-19	77	7.9	968	81	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.1e-18	204	21.0	968	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	2.3e-17	187	19.3	968	252	1945
Cancer (Lung cancer*)	Lung cancer*	2.3e-17	187	19.3	968	252	1945
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	2.7e-16	77	7.9	968	85	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	1.0e-15	58	90.6	64	121	245
Lung cancer (Lung cancer*)	Lung cancer*	1.5e-15	175	18.0	968	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	1.5e-15	175	18.0	968	238	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.3e-15	63	20.9	301	156	1945
Cancer and cell line (Various tumors*)	Various tumors*	1.5e-14	89	9.1	968	105	1945
Cancer (Various tumors*)	Various tumors*	1.5e-14	89	9.1	968	105	1945
Lung carcinoid (Lung cancer)	Lung cancer	7.0e-14	19	33.9	56	20	276
Non-tumor liver tissue (Liver cancer)	Liver cancer	4.6e-13	55	66.2	83	76	207
Cancer and cell line (Liver cancer)	Liver cancer	3.0e-11	65	90.2	72	126	207
CNS tissue, cancer or cell line (Various tumors)	Various tumors	2.2e-10	10	100	10	21	154
Breast tissue or cancer (Breast cancer*)	Breast cancer*	4.3e-10	45	14.9	301	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	4.3e-10	45	14.9	301	118	1945
Adenocarcinoma (Breast cancer*)	Breast cancer*	3.3e-09	42	13.9	301	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	3.3e-09	42	13.9	301	112	1945
Cancer (Breast cancer*)	Breast cancer*	3.3e-09	42	13.9	301	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	3.3e-09	42	13.9	301	112	1945
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	2.3e-07	42	13.9	301	127	1945
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	2.7e-07	45	14.9	301	141	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	3.0e-07	42	13.9	301	128	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	3.4e-07	45	14.9	301	142	1945
Prostate (Prostate cancer*)	Prostate cancer*	6.8e-07	74	7.6	968	101	1945
Cell line (NCI60*)	NCI60*	2.5e-06	93	9.6	968	135	1945
Cancer (Liver cancer)	Liver cancer	7.2e-06	55	76.3	72	115	207
Cancer and cell line (Breast cancer*)	Breast cancer*	8.3e-06	42	13.9	301	143	1945
Epithelial cell line (NCI60)	NCI60	1.0e-05	31	32.9	94	32	139
Cancer and cell line (NCI60*)	NCI60*	1.0e-05	93	9.6	968	138	1945
Liver cancer cell line (Liver cancer)	Liver cancer	1.6e-05	10	13.8	72	10	207
Adenocarcinoma (Lung cancer)	Lung cancer	1.9e-05	138	67.6	204	166	276
Normal cerebellum tissue (Neuro tumors)	Neuro tumors	2.7e-05	4	50	8	4	90
Normal CNS tissue (Neuro tumors)	Neuro tumors	2.7e-05	4	50	8	4	90
Normal tissue (Neuro tumors)	Neuro tumors	2.7e-05	4	50	8	4	90
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	2.8e-05	49	76.5	64	134	245
Normal CNS tissue (Various tumors)	Various tumors	4.5e-05	4	40	10	5	154
Cancer and cell line (NCI60*)	NCI60*	4.9e-05	39	12.9	301	138	1945
CNS cancer or cell line (Various tumors)	Various tumors	7.8e-05	6	60	10	16	154
CNS tumor (Various tumors)	Various tumors	7.8e-05	6	60	10	16	154
Cancer and cell line (Gliomas*)	Gliomas*	0.0001	36	3.7	968	47	1945
Cancer (Gliomas*)	Gliomas*	0.0001	36	3.7	968	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	0.0001	36	3.7	968	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	0.0001	36	3.7	968	47	1945
CNS tumor (Gliomas*)	Gliomas*	0.0001	36	3.7	968	47	1945
Cell line (Liver cancer)	Liver cancer	0.0001	10	13.8	72	11	207
Hepatocellular carcinoma (Liver cancer)	Liver cancer	0.0001	49	68.0	72	104	207
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	0.0001	55	85.9	64	167	245
Normal cerebellum tissue (Various tumors)	Various tumors	0.0002	3	30	10	3	154
Breast cancer cell line (Breast cancer)	Breast cancer	0.0002	13	24.5	53	17	152
Adenocarcinoma (Liver cancer)	Liver cancer	0.0002	46	63.8	72	97	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	0.0003	45	70.3	64	126	245
Cell line (NCI60*)	NCI60*	0.0003	36	11.9	301	135	1945
Cell line (Breast cancer)	Breast cancer	0.0003	19	35.8	53	30	152

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
neurogenesis	1.2e-08	37	9.9	372	169	4566
synaptic transmission	3.4e-07	27	7.2	372	116	4566
microtubule associated complex	6.0e-05	29	7.7	372	167	4566
organogenesis	9.7e-05	45	12.0	372	315	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 546 genes, this image does not display the individual gene names, but rather condenses each gene 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.

Note: Since there are 1270 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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