Module 3

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:	385 (see 2788 additional genes for this module)
Num experiments:	954 (321 induced, 633 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.
HUVEC_3
HUVEC_2

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	2.6e-32	30	93.7	32	30	182
Macrophages (Stimulated PBMC)	Stimulated PBMC	2.6e-32	30	93.7	32	30	182
CNS tissue, cancer or cell line (Neuro tumors*)	Neuro tumors*	3.4e-19	67	10.6	632	85	1945
CNS cancer or cell line (Neuro tumors*)	Neuro tumors*	1.5e-17	63	9.9	632	81	1945
CNS tumor (Neuro tumors*)	Neuro tumors*	1.5e-17	63	9.9	632	81	1945
Cancer and cell line (Neuro tumors*)	Neuro tumors*	2.6e-15	63	9.9	632	86	1945
Cancer (Neuro tumors*)	Neuro tumors*	2.6e-15	63	9.9	632	86	1945
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	2.3e-10	33	43.4	76	46	245
Leukemia (B lymphoma)	B lymphoma	2.3e-10	33	43.4	76	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	2.3e-10	33	43.4	76	46	245
Cell line (B lymphoma)	B lymphoma	4.1e-09	11	36.6	30	14	245
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	1.2e-07	25	7.7	321	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	1.2e-07	25	7.7	321	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	1.2e-07	25	7.7	321	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	1.2e-07	25	7.7	321	53	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.8e-07	60	18.6	321	197	1945
Hematologic cancer and cell line (NCI60)	NCI60	3.0e-07	14	26.9	52	14	139
Hematologic samples and cell lines (NCI60)	NCI60	3.0e-07	14	26.9	52	14	139
Leukemia cell line (NCI60)	NCI60	3.0e-07	14	26.9	52	14	139
Cancer and cell line (Liver cancer)	Liver cancer	1.6e-06	54	84.3	64	126	207
Lung carcinoid (Lung cancer)	Lung cancer	3.4e-06	17	17.3	98	20	276
Liver cancer cell line (Liver cancer)	Liver cancer	4.7e-06	10	15.6	64	10	207
Normal lung tissue (Lung cancer)	Lung cancer	4.8e-06	18	18.3	98	22	276
Grade 3 (Breast cancer)	Breast cancer	7.3e-06	13	100	13	38	85
Normal tissue (Lung cancer)	Lung cancer	1.5e-05	18	18.3	98	23	276
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	1.7e-05	20	86.9	23	67	144
Atypical teratoid/rhabdoid tumour - CNS and other origin (Neuro tumors)	Neuro tumors	2.2e-05	7	53.8	13	10	90
Hematologic cancer and cell line (Various tumors)	Various tumors	2.7e-05	22	37.9	58	31	154
Hematologic cancer (Various tumors)	Various tumors	2.7e-05	22	37.9	58	31	154
Primary blood mononuclear cells (Various tumors)	Various tumors	2.7e-05	22	37.9	58	31	154
Cell line (Liver cancer)	Liver cancer	3.9e-05	10	15.6	64	11	207
Lymphocytes (Various tumors)	Various tumors	6.8e-05	20	34.4	58	28	154
Monocytes (Various tumors)	Various tumors	6.8e-05	20	34.4	58	28	154
B. petrussis 537 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.9e-05	5	21.7	23	5	144
B. petrussis A2 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.9e-05	5	21.7	23	5	144
B. petrussis Tox 6 stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	6.9e-05	5	21.7	23	5	144
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	7.2e-05	29	96.6	30	167	245
Follicular lymphoma (Various tumors)	Various tumors	0.0001	9	15.5	58	9	154
Hematologic samples and cell lines (Various tumors)	Various tumors	0.0001	24	41.3	58	37	154
Hematologic samples (Various tumors)	Various tumors	0.0001	24	41.3	58	37	154
Follicular lymphoma (B lymphoma)	B lymphoma	0.0001	18	23.6	76	28	245
Invasive liver tumor (Liver cancer)	Liver cancer	0.0001	22	34.3	64	38	207
Liver tissue (Liver cancer*)	Liver cancer*	0.0001	50	15.5	321	187	1945
Colon cancer cell line (NCI60)	NCI60	0.0001	12	23.0	52	14	139
Colon cancer or cell line (NCI60)	NCI60	0.0001	12	23.0	52	14	139
Colon tissue, cancer or cell line (NCI60)	NCI60	0.0001	12	23.0	52	14	139
B cells (Various tumors)	Various tumors	0.0001	17	29.3	58	23	154
Cell line (NCI60*)	NCI60*	0.0002	38	11.8	321	135	1945
p53 positive hepatocellular carcinoma (Liver cancer)	Liver cancer	0.0002	16	66.6	24	23	60
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	0.0003	20	86.9	23	78	144

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	6.5e-08	15	5.6	264	50	4566
regulation of transcription	9.3e-07	17	6.4	264	76	4566
regulation of cell cycle	1.5e-06	26	9.8	264	163	4566
viral host cell process manipulation	4.0e-06	19	7.1	264	102	4566
DNA replication	4.9e-06	13	4.9	264	52	4566
ribonucleotide metabolism	3.0e-05	9	3.4	264	30	4566
cell cycle	7.6e-05	20	7.5	264	135	4566
cytokinesis	7.9e-05	11	4.1	264	49	4566
DNA metabolism	8.6e-05	23	8.7	264	169	4566
26S proteasome	0.0001	8	3.0	264	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 954 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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