Module 242

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:	48
Num genes:	214 (see 413 additional genes for this module)
Num experiments:	413 (105 induced, 308 repressed)
Parent module:	379
Children modules:	181 157

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 43
Shipp02 41
Pomeroy02 49
Shipp02 42
Ramaswamy01 18
Golub99 31
Shipp02 20
Pomeroy02 10
Golub99 11
Shipp02 47
Ramaswamy01 6
Golub99 18
Ramaswamy01 8
Pomeroy02 13
Golub99 48
Golub99 44
Pomeroy02 40
Ramaswamy01 40
Staunton01 49
Lessnick02 26
Bhattacharjee01 11
Bhattacharjee01 18
Lessnick02 15
Armstrong01 11
Nutt03 38
Bhattacharjee01 25
Armstrong01 48
Singh02 6
Singh02 12
Lessnick02 25
Singh02 5
Singh02 2
Singh02 3
Armstrong01 12
Nutt03 43
Singh02 20
Singh02 13
Nutt03 36
Singh02 42
Singh02 10
Nutt03 41
Armstrong01 4
Lessnick02 3
Singh02 23
Lessnick02 36
Bhattacharjee01 23
Armstrong01 21
Armstrong01 26

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
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	5.0e-42	130	42.2	308	276	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	7.6e-39	107	34.7	308	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	7.6e-39	107	34.7	308	205	1945
Prostate (Prostate cancer*)	Prostate cancer*	3.8e-38	72	23.3	308	101	1945
Lung cancer (Lung cancer*)	Lung cancer*	9.8e-33	109	35.3	308	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	9.8e-33	109	35.3	308	238	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	3.1e-32	112	36.3	308	252	1945
Cancer (Lung cancer*)	Lung cancer*	3.1e-32	112	36.3	308	252	1945
Prostate (Prostate cancer*)	Prostate cancer*	2.3e-13	27	25.7	105	101	1945
Lung carcinoid (Lung cancer)	Lung cancer	1.7e-11	14	48.2	29	20	276
Bone marrow (Leukemia)	Leukemia	5.1e-07	11	68.7	16	23	141
B cells (Leukemia)	Leukemia	5.6e-07	16	100	16	62	141
Lung cancer (Lung cancer*)	Lung cancer*	8.7e-06	29	27.6	105	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	8.7e-06	29	27.6	105	238	1945
Cancer and cell line (Gliomas*)	Gliomas*	8.8e-06	20	6.4	308	47	1945
Cancer (Gliomas*)	Gliomas*	8.8e-06	20	6.4	308	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	8.8e-06	20	6.4	308	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	8.8e-06	20	6.4	308	47	1945
CNS tumor (Gliomas*)	Gliomas*	8.8e-06	20	6.4	308	47	1945
Cancer and cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.2e-05	8	2.5	308	10	1945
Cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.2e-05	8	2.5	308	10	1945
EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.2e-05	8	2.5	308	10	1945
Fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.2e-05	8	2.5	308	10	1945
Skin fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	1.2e-05	8	2.5	308	10	1945
Cancer and cell line (Lung cancer*)	Lung cancer*	2.7e-05	29	27.6	105	252	1945
Cancer (Lung cancer*)	Lung cancer*	2.7e-05	29	27.6	105	252	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	0.0001	29	27.6	105	276	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).

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 413 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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