Module 485

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:	4
Num genes:	52 (see 476 additional genes for this module)
Num experiments:	453 (224 induced, 229 repressed)
Parent module:	None
Children modules:	325

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.
Ross01 30
Pollack99 44
Pollack99 27
Pollack99 23

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
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	3.1e-29	27	100	27	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	3.1e-29	27	100	27	30	182
Liver tissue (Liver cancer*)	Liver cancer*	3.7e-20	67	29.2	229	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.0e-18	67	29.2	229	197	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	4.9e-16	51	76.1	67	76	207
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	8.2e-15	27	69.2	39	46	245
Leukemia (B lymphoma)	B lymphoma	8.2e-15	27	69.2	39	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	8.2e-15	27	69.2	39	46	245
Hepatitis infected liver (Liver cancer*)	Liver cancer*	5.6e-14	52	22.7	229	156	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	7.9e-13	57	25.5	223	197	1945
Cancer and cell line (Liver cancer)	Liver cancer	9.1e-13	59	95.1	62	126	207
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.5e-09	44	19.7	223	156	1945
Liver tissue (Liver cancer*)	Liver cancer*	2.4e-08	47	21.0	223	187	1945
Normal lung tissue (Lung cancer)	Lung cancer	1.2e-07	13	35.1	37	22	276
Normal tissue (Lung cancer)	Lung cancer	2.5e-07	13	35.1	37	23	276
Liver cancer cell line (Liver cancer)	Liver cancer	3.3e-06	10	16.1	62	10	207
Cancer (Liver cancer)	Liver cancer	5.4e-06	49	79.0	62	115	207
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	7.3e-06	17	94.4	18	67	144
Invasive liver tumor (Liver cancer)	Liver cancer	1.3e-05	23	37.0	62	38	207
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.7e-05	5	27.7	18	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.7e-05	5	27.7	18	5	144
Cell line (Liver cancer)	Liver cancer	2.8e-05	10	16.1	62	11	207
p53 positive hepatocellular carcinoma (Liver cancer)	Liver cancer	5.1e-05	18	66.6	27	23	60
Hepatocellular carcinoma (Liver cancer)	Liver cancer	7.6e-05	44	70.9	62	104	207
Cell line (B lymphoma)	B lymphoma	9.5e-05	6	35.2	17	14	245
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0001	17	94.4	18	78	144
Cancer and cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0003	6	2.6	229	10	1945
Cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0003	6	2.6	229	10	1945
EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0003	6	2.6	229	10	1945
Fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0003	6	2.6	229	10	1945
Skin fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0003	6	2.6	229	10	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
DNA replication	0.0001	4	17.3	23	52	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 453 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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