Module 112

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:	9
Num genes:	260 (see 2053 additional genes for this module)
Num experiments:	1210 (302 induced, 908 repressed)
Parent module:	176
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.
Shipp02 10
Staunton01 15
Ramaswamy01 4
Ramaswamy01 22
Golub99 23
Shipp02 23
Ramaswamy01 44
Shipp02 9
Staunton01 3

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
Liver tissue (Liver cancer*)	Liver cancer*	4.7e-45	107	35.4	302	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	4.9e-42	107	35.4	302	197	1945
Lymphoma (B lymphoma)	B lymphoma	2.1e-33	60	89.5	67	77	245
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.0e-32	85	28.1	302	156	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.0e-31	76	71.0	107	76	207
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	6.2e-29	213	23.4	907	276	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	3.0e-27	196	21.6	907	252	1945
Cancer (Lung cancer*)	Lung cancer*	3.0e-27	196	21.6	907	252	1945
Lung cancer (Lung cancer*)	Lung cancer*	1.4e-25	185	20.3	907	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	1.4e-25	185	20.3	907	238	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	4.3e-25	164	18.0	907	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	4.3e-25	164	18.0	907	205	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	9.6e-25	66	98.5	67	121	245
Cancer and cell line (Liver cancer)	Liver cancer	9.9e-25	84	98.8	85	126	207
Acute leukemia (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Cancer (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Leukemia (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Monocytes (Leukemia*)	Leukemia*	2.4e-20	117	12.8	907	141	1945
Cancer and cell line (Various tumors*)	Various tumors*	1.2e-17	90	9.9	907	105	1945
Cancer (Various tumors*)	Various tumors*	1.2e-17	90	9.9	907	105	1945
Cancer (Liver cancer)	Liver cancer	3.6e-15	74	87.0	85	115	207
Breast tissue or cancer (Breast cancer*)	Breast cancer*	7.3e-12	48	15.8	302	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	7.3e-12	48	15.8	302	118	1945
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	3.9e-11	65	97.0	67	167	245
Adenocarcinoma (Liver cancer)	Liver cancer	2.4e-10	62	72.9	85	97	207
Adenocarcinoma (Breast cancer*)	Breast cancer*	2.4e-10	44	14.5	302	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	2.4e-10	44	14.5	302	112	1945
Cancer (Breast cancer*)	Breast cancer*	2.4e-10	44	14.5	302	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	2.4e-10	44	14.5	302	112	1945
Hepatocellular carcinoma (Liver cancer)	Liver cancer	1.1e-09	64	75.2	85	104	207
Female hormonal tissue, cancer or cell line (Breast cancer*)	Breast cancer*	3.2e-09	49	16.2	302	141	1945
Breast tissue, cancer or cell line (Breast cancer*)	Breast cancer*	4.3e-09	49	16.2	302	142	1945
Female hormonal cancer or cell line (Breast cancer*)	Breast cancer*	7.8e-09	45	14.9	302	127	1945
Breast cancer or cell line (Breast cancer*)	Breast cancer*	1.0e-08	45	14.9	302	128	1945
Cell line (NCI60*)	NCI60*	1.4e-07	92	10.1	907	135	1945
Cancer and cell line (Breast cancer*)	Breast cancer*	4.7e-07	45	14.9	302	143	1945
Cancer and cell line (NCI60*)	NCI60*	6.9e-07	92	10.1	907	138	1945
Acute lymphocytic leukemia (Leukemia)	Leukemia	7.2e-07	94	75.2	125	99	149
Invasive liver tumor (Liver cancer)	Liver cancer	1.2e-06	29	34.1	85	38	207
Lymphocytes (Leukemia)	Leukemia	2.0e-06	86	73.5	117	91	141
Stage T2 (Lung cancer)	Lung cancer	3.8e-05	10	62.5	16	35	195
Normal tissue (Liver cancer)	Liver cancer	6.2e-05	14	13.0	107	14	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	7.6e-05	48	71.6	67	126	245
Liver cancer cell line (Liver cancer)	Liver cancer	9.8e-05	10	11.7	85	10	207
Metastasis (Liver cancer)	Liver cancer	9.8e-05	10	11.7	85	10	207
Cancer and cell line (NCI60*)	NCI60*	0.0001	38	12.5	302	138	1945
Hematologic samples and cell lines (Various tumors)	Various tumors	0.0002	37	29.1	127	37	154
Hematologic samples (Various tumors)	Various tumors	0.0002	37	29.1	127	37	154
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	0.0002	49	73.1	67	134	245
Breast cancer cell line (Breast cancer)	Breast cancer	0.0003	13	24.0	54	17	152
B cells (Leukemia)	Leukemia	0.0004	59	50.4	117	62	141

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
morphogenesis	1.7e-06	38	17.6	215	366	4566
organogenesis	7.8e-06	33	15.3	215	315	4566
development	1.2e-05	48	22.3	215	554	4566
microsome	1.9e-05	12	5.5	215	61	4566
neurogenesis	3.4e-05	21	9.7	215	169	4566
extracellular space	0.0001	23	10.6	215	212	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 1210 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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