Module 17

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:	368 (see 2571 additional genes for this module)
Num experiments:	789 (261 induced, 528 repressed)
Parent module:	52
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.
Myelogenous_k_562_2
Myelogenous_k_562_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	2.8e-31	30	90.9	33	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	2.8e-31	30	90.9	33	30	182
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	1.0e-16	59	11.1	528	85	1945
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	5.9e-15	55	10.4	528	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	5.9e-15	55	10.4	528	81	1945
Cancer and cell line (Neuro tumors*)	Neuro tumors*	5.4e-14	56	10.6	528	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	5.4e-14	56	10.6	528	86	1945
Cancer and cell line (Liver cancer)	Liver cancer	2.3e-11	51	96.2	53	126	207
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	1.9e-10	31	46.2	67	46	245
Leukemia (B lymphoma)	B lymphoma	1.9e-10	31	46.2	67	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	1.9e-10	31	46.2	67	46	245
Cell line (B lymphoma)	B lymphoma	2.6e-09	11	37.9	29	14	245
Invasive liver tumor (Liver cancer)	Liver cancer	5.0e-09	25	47.1	53	38	207
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	8.9e-09	24	9.1	261	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	8.9e-09	24	9.1	261	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	8.9e-09	24	9.1	261	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	8.9e-09	24	9.1	261	53	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	5.0e-07	51	19.5	261	197	1945
Normal lung tissue (Lung cancer)	Lung cancer	1.7e-06	19	18.0	105	22	276
Non-tumor liver tissue (Liver cancer)	Liver cancer	3.0e-06	32	65.3	49	76	207
Cell line (Liver cancer)	Liver cancer	5.3e-06	10	18.8	53	11	207
Normal tissue (Lung cancer)	Lung cancer	6.7e-06	19	18.0	105	23	276
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.2e-05	105	19.8	528	276	1945
Liver cancer cell line (Liver cancer)	Liver cancer	2.1e-05	9	16.9	53	10	207
Breast tissue or cancer (NCI60)	NCI60	2.2e-05	4	36.3	11	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	2.2e-05	4	36.3	11	4	139
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	4.3e-05	7	50	14	10	90
Cell line (Breast cancer)	Breast cancer	6.3e-05	13	52	25	30	152
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.6e-05	20	83.3	24	67	144
Hepatitis infected liver (Liver cancer*)	Liver cancer*	8.1e-05	38	14.5	261	156	1945
B. petrussis 537 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.8e-05	5	20.8	24	5	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.8e-05	5	20.8	24	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.8e-05	5	20.8	24	5	144
Adenocarcinoma (Liver cancer)	Liver cancer	8.9e-05	37	69.8	53	97	207
Lung carcinoid (Lung cancer)	Lung cancer	9.1e-05	16	15.2	105	20	276
Acute myelogeous leukemia (Leukemia)	Leukemia	0.0001	22	62.8	35	50	141
Cancer (Liver cancer)	Liver cancer	0.0001	41	77.3	53	115	207
Grade 3 (Breast cancer)	Breast cancer	0.0001	10	100	10	38	85
Prostate (Prostate cancer*)	Prostate cancer*	0.0001	44	8.3	528	101	1945
Hepatocellular carcinoma (Liver cancer)	Liver cancer	0.0002	38	71.6	53	104	207
Liver tissue (Liver cancer*)	Liver cancer*	0.0002	42	16.0	261	187	1945
p53 positive hepatocellular carcinoma (Liver cancer)	Liver cancer	0.0002	16	66.6	24	23	60
Cancer and cell line (Gliomas*)	Gliomas*	0.0003	24	4.5	528	47	1945
Cancer (Gliomas*)	Gliomas*	0.0003	24	4.5	528	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	0.0003	24	4.5	528	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	0.0003	24	4.5	528	47	1945
CNS tumor (Gliomas*)	Gliomas*	0.0003	24	4.5	528	47	1945
Breast cancer (NCI60)	NCI60	0.0003	3	27.2	11	3	139
B. petrussis 338 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0004	11	73.3	15	44	143

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	1.3e-13	21	8.0	261	52	4566
DNA metabolism	3.1e-13	37	14.1	261	169	4566
S phase of mitotic cell cycle	2.7e-10	13	4.9	261	26	4566
DNA dependent DNA replication	2.0e-08	12	4.5	261	29	4566
DNA replication and chromosome cycle	2.0e-08	12	4.5	261	29	4566
nucleus	1.9e-07	90	34.4	261	966	4566
mitosis	4.1e-07	14	5.3	261	50	4566
nucleosome assembly	3.4e-06	9	3.4	261	24	4566
endomembrane system	7.1e-06	89	34.0	261	1029	4566
purine nucleoside monophosphate biosynthesis	1.1e-05	5	1.9	261	7	4566
purine ribonucleoside monophosphate metabolism	1.1e-05	5	1.9	261	7	4566
nucleoside monophosphate biosynthesis	1.1e-05	6	2.2	261	11	4566
nucleosome disassembly	1.6e-05	8	3.0	261	22	4566
cell cycle	2.0e-05	21	8.0	261	135	4566
ribonucleotide metabolism	2.8e-05	9	3.4	261	30	4566
regulation of cell cycle	4.0e-05	23	8.8	261	163	4566
purine nucleotide biosynthesis	4.9e-05	4	1.5	261	5	4566
viral genome	5.1e-05	7	2.6	261	19	4566
viral host cell process manipulation	5.1e-05	17	6.5	261	102	4566
purine ribonucleoside monophosphate biosynthesis	6.1e-05	5	1.9	261	9	4566
nuclear chromatin	7.4e-05	7	2.6	261	20	4566
DNA packaging	8.7e-05	11	4.2	261	50	4566
virion	0.0001	7	2.6	261	21	4566
chromatin assembly/disassembly	0.0001	9	3.4	261	35	4566
nucleotidyltransferase activity	0.0001	43	16.4	261	425	4566
DNA replication initiation	0.0001	5	1.9	261	10	4566
ribonucleoside monophosphate metabolism	0.0001	5	1.9	261	10	4566
26S proteasome	0.0001	8	3.0	261	28	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 789 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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