Module 244 -- Response to DNA damage

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:	187 (see 1540 additional genes for this module)
Num experiments:	411 (189 induced, 222 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.
nucleotidyltransferase activity
ATP binding

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
Normal lung tissue (Lung cancer)	Lung cancer	3.6e-16	18	56.2	32	22	276
Normal tissue (Lung cancer)	Lung cancer	1.5e-15	18	56.2	32	23	276
Cell line (B lymphoma)	B lymphoma	9.1e-11	12	40	30	14	245
Liver cancer cell line (Liver cancer)	Liver cancer	2.9e-09	9	40.9	22	10	207
Non-tumor liver tissue (Liver cancer)	Liver cancer	6.9e-09	26	83.8	31	76	207
Cell line (Liver cancer)	Liver cancer	1.5e-08	9	40.9	22	11	207
B. petrussis stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	8.0e-08	22	95.6	23	67	144
Lymphocytes (B lymphoma*)	B lymphoma*	1.8e-07	54	24.3	222	244	1945
Breast tissue or cancer (NCI60)	NCI60	3.3e-07	4	80	5	4	139
Female hormonal tissue or cancer (NCI60)	NCI60	3.3e-07	4	80	5	4	139
B cells (B lymphoma*)	B lymphoma*	4.8e-07	51	22.9	222	231	1945
Acute myelogeous leukemia (Leukemia)	Leukemia	7.0e-07	23	74.1	31	50	141
Gram negative bacteria stimulated immune cells (Stimulated PBMC)	Stimulated PBMC	3.6e-06	22	95.6	23	78	144
Cancer and cell line (Liver cancer)	Liver cancer	8.1e-06	22	100	22	126	207
Cancer (B lymphoma*)	B lymphoma*	9.9e-06	43	19.3	222	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	9.9e-06	43	19.3	222	200	1945
Breast cancer (NCI60)	NCI60	2.2e-05	3	60	5	3	139
Cancer and cell line (B lymphoma*)	B lymphoma*	6.0e-05	43	19.3	222	214	1945
Hematologic cancer and cell line (B lymphoma*)	B lymphoma*	6.0e-05	43	19.3	222	214	1945
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
Acute leukemia (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Cancer and cell line (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Cancer (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Hematologic cancer and cell line (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Hematologic cancer (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Hematologic samples and cell lines (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Leukemia (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Leukemia or leukemia cell line (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Monocytes (Leukemia*)	Leukemia*	0.0001	31	13.9	222	141	1945
Cancer and cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	6	2.7	222	10	1945
Cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	6	2.7	222	10	1945
EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	6	2.7	222	10	1945
Fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	6	2.7	222	10	1945
Skin fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	6	2.7	222	10	1945
Hematologic samples and cell lines (Stimulated PBMC*)	Stimulated PBMC*	0.0003	32	16.9	189	182	1945
Monocytes (Stimulated PBMC*)	Stimulated PBMC*	0.0003	32	16.9	189	182	1945
Breast tissue, cancer or cell line (NCI60)	NCI60	0.0004	5	100	5	31	139

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
nucleotidyltransferase activity	2.5e-206	185	98.9	187	425	4566
ATP binding	1.9e-174	170	90.9	187	399	4566
catalytic activity	4.4e-85	187	100	187	1677	4566
response to DNA damage stimulus	1.3e-51	84	44.9	187	310	4566
protein serine/threonine kinase activity	3.7e-41	50	26.7	187	114	4566
protein amino acid phosphorylation	4.1e-41	66	35.2	187	230	4566
response to stress	2.9e-21	87	46.5	187	792	4566
ATPase activity\, coupled	3.1e-19	21	11.2	187	41	4566
DNA metabolism	4.8e-19	38	20.3	187	169	4566
DNA replication	8.0e-18	22	11.7	187	52	4566
nucleotide binding	3.4e-17	22	11.7	187	55	4566
DNA repair	1.0e-15	26	13.9	187	93	4566
DNA dependent ATPase activity	2.0e-14	15	8.0	187	28	4566
protein kinase regulator activity	4.4e-14	20	10.6	187	59	4566
cell cycle	3.1e-13	28	14.9	187	135	4566
DNA dependent DNA replication	1.0e-12	14	7.4	187	29	4566
cAMP-dependent protein kinase activity	2.2e-12	15	8.0	187	36	4566
kinase regulator activity	3.1e-12	20	10.6	187	72	4566
S phase of mitotic cell cycle	3.9e-12	13	6.9	187	26	4566
protein tyrosine kinase activity	5.9e-12	25	13.3	187	120	4566
DNA-directed DNA polymerase activity	6.8e-12	8	4.2	187	8	4566
DNA replication and chromosome cycle	2.3e-11	13	6.9	187	29	4566
RNA dependent ATPase activity	2.3e-11	13	6.9	187	29	4566
ATP dependent helicase activity	2.7e-11	12	6.4	187	24	4566
protein kinase CK2 activity	3.9e-11	14	7.4	187	36	4566
nucleus	6.7e-11	78	41.7	187	966	4566
kinase activity	1.2e-10	18	9.6	187	69	4566
cytokinesis	4.0e-10	15	8.0	187	49	4566
mitosis	5.5e-10	15	8.0	187	50	4566
ligase activity\, forming phosphoric ester bonds	7.0e-10	10	5.3	187	19	4566
regulation of cell cycle	1.1e-09	26	13.9	187	163	4566
signal transducer activity	1.4e-09	78	41.7	187	1026	4566
nucleoplasm	1.5e-09	19	10.1	187	89	4566
DNA binding	1.7e-09	40	21.3	187	357	4566
DNA-directed RNA polymerase activity	2.9e-09	8	4.2	187	12	4566
DNA recombination	2.9e-09	11	5.8	187	27	4566
nu DNA polymerase activity	4.3e-09	6	3.2	187	6	4566
endomembrane system	4.4e-09	77	41.1	187	1029	4566
replication fork	4.9e-09	9	4.8	187	17	4566
hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides	7.0e-09	21	11.2	187	118	4566
transcription	1.6e-08	26	13.9	187	184	4566
tRNA ligase activity	6.6e-08	8	4.2	187	16	4566
amino acid activation	1.2e-07	8	4.2	187	17	4566
phosphotransferase activity\, alcohol group as acceptor	1.2e-07	16	8.5	187	82	4566
primary active transporter activity	3.3e-07	6	3.2	187	9	4566
phosphotransferase activity\, phosphate group as acceptor	4.6e-07	7	3.7	187	14	4566
DNA replication factor C complex	6.3e-07	5	2.6	187	6	4566
DNA-directed RNA polymerase I activity	7.9e-07	6	3.2	187	10	4566
DNA-directed RNA polymerase II activity	7.9e-07	6	3.2	187	10	4566
ligase activity\, forming aminoacyl-tRNA and related compounds	8.4e-07	7	3.7	187	15	4566
ATP dependent DNA helicase activity	1.6e-06	6	3.2	187	11	4566
DNA-directed RNA polymerase III activity	1.6e-06	6	3.2	187	11	4566
nucleoside triphosphate biosynthesis	2.1e-06	5	2.6	187	7	4566
transcription\, DNA-dependent	3.1e-06	21	11.2	187	167	4566
P-P-bond-hydrolysis-driven transporter activity	3.2e-06	6	3.2	187	12	4566
mitotic cell cycle	4.5e-06	11	5.8	187	51	4566
DNA-directed RNA polymerase II\, holoenzyme	5.8e-06	6	3.2	187	13	4566
nuclear division	8.5e-06	7	3.7	187	20	4566
pyrimidine ribonucleotide biosynthesis	1.3e-05	4	2.1	187	5	4566
protein kinase activity	1.3e-05	15	8.0	187	102	4566
viral host cell process manipulation	1.3e-05	15	8.0	187	102	4566
nucleotide biosynthesis	1.5e-05	9	4.8	187	38	4566
receptor signaling protein serine/threonine kinase activity	1.6e-05	6	3.2	187	15	4566
ribonucleotide metabolism	1.8e-05	8	4.2	187	30	4566
microtubule motor activity	2.3e-05	5	2.6	187	10	4566
motor activity	2.4e-05	9	4.8	187	40	4566
M phase of mitotic cell cycle	3.6e-05	6	3.2	187	17	4566
ribonucleoside triphosphate biosynthesis	3.8e-05	4	2.1	187	6	4566
DNA-directed RNA polymerase II\, core complex	4.1e-05	5	2.6	187	11	4566
nucleotide metabolism	4.5e-05	11	5.8	187	64	4566
regulation of transcription	4.8e-05	12	6.4	187	76	4566
M phase	5.8e-05	7	3.7	187	26	4566
pyrimidine ribonucleoside triphosphate biosynthesis	6.7e-05	3	1.6	187	3	4566
cyclin-dependent protein kinase activity	6.8e-05	5	2.6	187	12	4566
mismatch repair	8.6e-05	4	2.1	187	7	4566
ribonucleoside triphosphate metabolism	8.6e-05	4	2.1	187	7	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 411 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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