Module 16

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:	2
Num genes:	512 (see 2635 additional genes for this module)
Num experiments:	967 (296 induced, 671 repressed)
Parent module:	53
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.
HL60_2
HL60_1

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	4.4e-26	30	75	40	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	4.4e-26	30	75	40	30	182
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	2.9e-19	42	50	84	46	245
Leukemia (B lymphoma)	B lymphoma	2.9e-19	42	50	84	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	2.9e-19	42	50	84	46	245
Cancer and cell line (Various tumors*)	Various tumors*	4.8e-12	70	10.4	671	105	1945
Cancer (Various tumors*)	Various tumors*	4.8e-12	70	10.4	671	105	1945
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	1.3e-11	29	9.7	296	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	1.3e-11	29	9.7	296	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	1.3e-11	29	9.7	296	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	1.3e-11	29	9.7	296	53	1945
Prostate (Prostate cancer*)	Prostate cancer*	8.3e-11	66	9.8	671	101	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	6.7e-09	60	20.2	296	197	1945
Liver tissue (Liver cancer*)	Liver cancer*	3.4e-07	54	18.2	296	187	1945
Hematologic samples (B lymphoma)	B lymphoma	2.2e-06	18	21.4	84	22	245
Lymphocytes (Leukemia)	Leukemia	3.5e-06	30	96.7	31	91	141
B. petrussis 338 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	3.8e-06	17	73.9	23	44	143
Non-classic malignant glioblastoma (Gliomas)	Gliomas	5.2e-06	13	86.6	15	13	27
Normal lung tissue (Lung cancer)	Lung cancer	5.8e-06	18	18.1	99	22	276
Acute lymphocytic leukemia (Leukemia)	Leukemia	6.5e-06	31	96.8	32	99	149
Grade 3 (Breast cancer)	Breast cancer	7.3e-06	13	100	13	38	85
Epithelial cell line (NCI60)	NCI60	8.9e-06	25	40.9	61	32	139
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.0e-05	24	82.7	29	67	144
Activated B like DLBCL (B lymphoma)	B lymphoma	1.7e-05	14	35.8	39	30	245
Normal tissue (Lung cancer)	Lung cancer	1.8e-05	18	18.1	99	23	276
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	2.1e-05	33	84.6	39	134	245
Hepatitis infected liver (Liver cancer*)	Liver cancer*	0.0001	41	13.8	296	156	1945
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	0.0001	36	92.3	39	167	245
Large cell lung cancer (Lung cancer)	Lung cancer	0.0001	4	12.5	32	4	276
Female hormonal cancer cell line (Breast cancer)	Breast cancer	0.0001	9	32.1	28	15	152
B. petrussis 537 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0002	5	17.2	29	5	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0002	5	17.2	29	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0002	5	17.2	29	5	144
Cell line (B lymphoma)	B lymphoma	0.0003	8	20.5	39	14	245
Cancer and cell line (Gliomas*)	Gliomas*	0.0003	28	4.1	671	47	1945
Cancer (Gliomas*)	Gliomas*	0.0003	28	4.1	671	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	0.0003	28	4.1	671	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	0.0003	28	4.1	671	47	1945
CNS tumor (Gliomas*)	Gliomas*	0.0003	28	4.1	671	47	1945
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0003	24	82.7	29	78	144
Classical malignant glioblastoma (Gliomas)	Gliomas	0.0004	9	100	9	14	27

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
mitosis	3.8e-06	15	4.1	361	50	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 512 genes, this image does not display the individual gene names, but rather condenses each gene 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.

Note: Since there are 967 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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