Module 113

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:	107 (see 1013 additional genes for this module)
Num experiments:	585 (181 induced, 404 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 11
Golub99 49
Pomeroy02 9

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*	8.3e-38	78	43.0	181	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	8.2e-36	78	43.0	181	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	9.5e-28	62	34.2	181	156	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	6.8e-20	59	75.6	78	76	207
Cancer and cell line (Various tumors*)	Various tumors*	3.0e-14	56	13.8	404	105	1945
Cancer (Various tumors*)	Various tumors*	3.0e-14	56	13.8	404	105	1945
Cancer and cell line (Liver cancer)	Liver cancer	1.2e-13	50	100	50	126	207
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	6.2e-12	83	20.5	404	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	6.2e-12	83	20.5	404	205	1945
Lymphoma (B lymphoma)	B lymphoma	3.6e-11	23	92	25	77	245
Prostate (Prostate cancer*)	Prostate cancer*	5.5e-10	48	11.8	404	101	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.2e-09	97	24.0	404	276	1945
Hematologic samples and cell lines (B lymphoma)	B lymphoma	5.4e-09	25	100	25	121	245
Lung cancer (Lung cancer*)	Lung cancer*	1.8e-08	84	20.7	404	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	1.8e-08	84	20.7	404	238	1945
Lung carcinoid (Lung cancer)	Lung cancer	1.3e-07	10	45.4	22	20	276
Cancer and cell line (Lung cancer*)	Lung cancer*	1.6e-07	85	21.0	404	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.6e-07	85	21.0	404	252	1945
Cancer and cell line (Neuro tumors*)	Neuro tumors*	4.5e-06	36	8.9	404	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	4.5e-06	36	8.9	404	86	1945
Lymphoma (B lymphoma)	B lymphoma	4.7e-06	12	92.3	13	77	245
Cancer (Liver cancer)	Liver cancer	8.6e-06	41	82	50	115	207
Liver cancer cell line (Liver cancer)	Liver cancer	1.2e-05	9	18	50	10	207
B cells (Leukemia)	Leukemia	3.2e-05	26	74.2	35	62	141
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	4.4e-05	10	27.7	36	10	90
Cell line (Liver cancer)	Liver cancer	5.6e-05	9	18	50	11	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	6.4e-05	22	88	25	126	245
Primary blood mononuclear cells (Leukemia)	Leukemia	9.1e-05	13	37.1	35	21	141
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	0.0001	31	7.6	404	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	0.0001	31	7.6	404	81	1945
Normal tissue (Liver cancer)	Liver cancer	0.0001	12	15.3	78	14	207
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	0.0002	22	88	25	134	245
Lymphocytes (Leukemia)	Leukemia	0.0003	31	88.5	35	91	141
Acute lymphocytic leukemia (Leukemia)	Leukemia	0.0003	33	89.1	37	99	149
Small cell lung cancer (Lung cancer)	Lung cancer	0.0003	5	22.7	22	10	276
Invasive liver tumor (Liver cancer)	Liver cancer	0.0004	18	36	50	38	207

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).

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 585 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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