Module 105

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:	200 (see 851 additional genes for this module)
Num experiments:	850 (223 induced, 627 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.
Shipp02 28
Ramaswamy01 28
Shipp02 5
Golub99 15

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	8.7e-28	27	96.4	28	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	8.7e-28	27	96.4	28	30	182
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	1.2e-13	60	9.5	626	85	1945
Cancer and cell line (Various tumors*)	Various tumors*	4.3e-13	69	11.0	626	105	1945
Cancer (Various tumors*)	Various tumors*	4.3e-13	69	11.0	626	105	1945
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	3.6e-12	56	8.9	626	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	3.6e-12	56	8.9	626	81	1945
Epithelial cell line (NCI60)	NCI60	1.2e-11	30	50	60	32	139
Cancer and cell line (Neuro tumors*)	Neuro tumors*	1.4e-10	56	8.9	626	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	1.4e-10	56	8.9	626	86	1945
Acute leukemia (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Cancer (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Leukemia (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Monocytes (Leukemia*)	Leukemia*	1.1e-09	79	12.6	626	141	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.7e-09	38	35.8	106	46	245
Leukemia (B lymphoma)	B lymphoma	1.7e-09	38	35.8	106	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.7e-09	38	35.8	106	46	245
Lymphoma (B lymphoma)	B lymphoma	8.7e-09	54	50.9	106	77	245
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	8.9e-08	8	72.7	11	10	90
Normal tissue (Lung cancer)	Lung cancer	1.1e-06	20	18.5	108	23	276
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	2.5e-06	27	93.1	29	134	245
Normal lung tissue (Lung cancer)	Lung cancer	2.9e-06	19	17.5	108	22	276
Cancer (B lymphoma*)	B lymphoma*	5.7e-06	93	14.8	626	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	5.7e-06	93	14.8	626	200	1945
Cancer and cell line (Liver cancer)	Liver cancer	8.0e-06	30	93.7	32	126	207
B cells (B lymphoma*)	B lymphoma*	1.7e-05	103	16.4	626	231	1945
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	2.4e-05	5	26.3	19	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	2.4e-05	5	26.3	19	5	144
Cell line (B lymphoma)	B lymphoma	2.7e-05	8	27.5	29	14	245
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	4.3e-05	17	89.4	19	67	144
Lymphocytes (B lymphoma*)	B lymphoma*	5.2e-05	106	16.9	626	244	1945
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	0.0001	28	96.5	29	167	245
Hematologic samples and cell lines (B lymphoma)	B lymphoma	0.0001	67	63.2	106	121	245
Cancer and cell line (B lymphoma*)	B lymphoma*	0.0001	93	14.8	626	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	0.0001	93	14.8	626	214	1945
Mesenchemal cell line (Breast cancer)	Breast cancer	0.0002	4	20	20	4	152
Cell line (Liver cancer)	Liver cancer	0.0002	7	21.8	32	11	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).
GO annotation	P-value	Hits	Hits(%)	Module genes	Genes in annotation	Genes
cell cycle	1.5e-06	18	10.7	168	135	4566
mitosis	6.8e-05	9	5.3	168	50	4566
regulation of cell cycle	8.2e-05	17	10.1	168	163	4566
collagen	0.0001	7	4.1	168	31	4566
transcription\, DNA-dependent	0.0001	17	10.1	168	167	4566
transcription	0.0001	18	10.7	168	184	4566
DNA metabolism	0.0001	17	10.1	168	169	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 850 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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