Module 392 -- rRNA processing and DNA repair

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:	18 (see 391 additional genes for this module)
Num experiments:	83 (49 induced, 34 repressed)
Parent module:	457
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.
rRNA processing
chromosome organization and biogenesis (sensu Eukarya)
nucleolus
damaged DNA 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
Normal lung tissue (Lung cancer)	Lung cancer	1.2e-07	6	100	6	22	276
Normal tissue (Lung cancer)	Lung cancer	1.7e-07	6	100	6	23	276
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
Liver cancer cell line (Liver cancer)	Liver cancer	8.8e-06	6	40	15	10	207
Cell line (Liver cancer)	Liver cancer	1.8e-05	6	40	15	11	207
Breast cancer (NCI60)	NCI60	2.2e-05	3	60	5	3	139
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	0.0002	14	28.5	49	197	1945
Cancer and cell line (Liver cancer)	Liver cancer	0.0004	15	100	15	126	207
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
nucleolus	1.0e-14	9	50	18	43	4566
DNA metabolism	3.2e-12	11	61.1	18	169	4566
chromosome organization and biogenesis (sensu Eukarya)	4.7e-10	7	38.8	18	52	4566
chromatin assembly/disassembly	2.2e-09	6	33.3	18	35	4566
establishment and/or maintenance of chromatin architecture	1.2e-08	6	33.3	18	46	4566
damaged DNA binding	2.1e-08	5	27.7	18	24	4566
chromatin	2.1e-08	6	33.3	18	50	4566
DNA packaging	2.1e-08	6	33.3	18	50	4566
nuclear chromosome	6.5e-08	6	33.3	18	60	4566
chromosome	8.0e-08	6	33.3	18	62	4566
ribonucleoprotein complex	3.5e-07	9	50	18	283	4566
viral genome	6.3e-07	4	22.2	18	19	4566
response to DNA damage stimulus	7.7e-07	9	50	18	310	4566
nuclear chromatin	7.8e-07	4	22.2	18	20	4566
virion	9.7e-07	4	22.2	18	21	4566
nucleosome disassembly	1.1e-06	4	22.2	18	22	4566
nucleolar preribosome	1.7e-06	4	22.2	18	24	4566
nucleosome assembly	1.7e-06	4	22.2	18	24	4566
DNA repair	2.1e-05	5	27.7	18	93	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.

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