Module 321

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:	113 (see 886 additional genes for this module)
Num experiments:	492 (199 induced, 293 repressed)
Parent module:	None
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.
Perou00 28
Perou00 43
Ross00 50

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
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	1.0e-24	53	18.1	292	85	1945
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	5.1e-23	50	17.1	292	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	5.1e-23	50	17.1	292	81	1945
Cancer and cell line (Neuro tumors*)	Neuro tumors*	2.4e-21	50	17.1	292	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	2.4e-21	50	17.1	292	86	1945
Hematologic cancer and cell line (Stimulated PBMC)	Stimulated PBMC	6.4e-21	23	92	25	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	6.4e-21	23	92	25	30	182
Lung carcinoid (Lung cancer)	Lung cancer	1.8e-10	15	37.5	40	20	276
Cancer and cell line (Liver cancer)	Liver cancer	4.7e-10	38	100	38	126	207
Cell line (NCI60*)	NCI60*	2.0e-09	47	16.0	292	135	1945
Cancer and cell line (NCI60*)	NCI60*	4.7e-09	47	16.0	292	138	1945
Cell line (NCI60*)	NCI60*	1.2e-08	36	18.0	199	135	1945
Hematologic samples and cell lines (Various tumors)	Various tumors	2.3e-08	18	72	25	37	154
Hematologic samples (Various tumors)	Various tumors	2.3e-08	18	72	25	37	154
Cancer and cell line (NCI60*)	NCI60*	2.4e-08	36	18.0	199	138	1945
Hematologic cancer and cell line (NCI60)	NCI60	8.2e-08	14	29.1	48	14	139
Hematologic samples and cell lines (NCI60)	NCI60	8.2e-08	14	29.1	48	14	139
Leukemia cell line (NCI60)	NCI60	8.2e-08	14	29.1	48	14	139
Cancer (Liver cancer)	Liver cancer	1.0e-06	34	89.4	38	115	207
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	5.6e-06	40	20.1	199	197	1945
Hematologic cancer and cell line (Various tumors)	Various tumors	1.1e-05	14	56	25	31	154
Hematologic cancer (Various tumors)	Various tumors	1.1e-05	14	56	25	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	1.1e-05	14	56	25	31	154
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.7e-05	5	27.7	18	5	144
Lymphocytes (Various tumors)	Various tumors	2.0e-05	13	52	25	28	154
Monocytes (Various tumors)	Various tumors	2.0e-05	13	52	25	28	154
Fast doubling (20-40) cell lines (NCI60)	NCI60	5.5e-05	43	93.4	46	90	122
Liver tissue (Liver cancer*)	Liver cancer*	6.3e-05	36	18.0	199	187	1945
Breast cancer cell line (Breast cancer)	Breast cancer	6.4e-05	9	40.9	22	17	152
Small cell lung cancer (Lung cancer)	Lung cancer	7.0e-05	7	17.5	40	10	276
Cell line (Breast cancer)	Breast cancer	7.5e-05	12	54.5	22	30	152
B cells (Various tumors)	Various tumors	9.3e-05	11	44	25	23	154
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	0.0001	6	54.5	11	10	90
Acute lymphocytic leukemia (Leukemia)	Leukemia	0.0001	20	100	20	99	149
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	0.0001	15	7.5	199	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	0.0001	15	7.5	199	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	0.0001	15	7.5	199	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	0.0001	15	7.5	199	53	1945
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	8	36.3	22	15	152
Metastasis (Liver cancer)	Liver cancer	0.0003	7	18.4	38	10	207
Mesenchemal cell line (Breast cancer)	Breast cancer	0.0003	4	18.1	22	4	152
Large cell lung cancer (Lung cancer)	Lung cancer	0.0004	3	21.4	14	4	276
Lymphoma (B lymphoma)	B lymphoma	0.0004	16	64	25	77	245

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
cell-matrix adhesion	0.0001	5	6.1	81	29	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 492 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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