Module 196

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:	3
Num genes:	23 (see 879 additional genes for this module)
Num experiments:	113 (46 induced, 67 repressed)
Parent module:	253
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.
motor activity
intracellular transport
cytoskeleton_dependent intracellular transport

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
Cancer and cell line (Gliomas*)	Gliomas*	1.1e-10	14	20.8	67	47	1945
Cancer (Gliomas*)	Gliomas*	1.1e-10	14	20.8	67	47	1945
CNS cancer or cell line (Gliomas*)	Gliomas*	1.1e-10	14	20.8	67	47	1945
CNS tissue, cancer or cell line (Gliomas*)	Gliomas*	1.1e-10	14	20.8	67	47	1945
CNS tumor (Gliomas*)	Gliomas*	1.1e-10	14	20.8	67	47	1945
Small cell lung cancer (Lung cancer)	Lung cancer	6.2e-10	7	70	10	10	276
Liver cancer cell line (Liver cancer)	Liver cancer	1.2e-07	7	50	14	10	207
Cell line (Liver cancer)	Liver cancer	3.4e-07	7	50	14	11	207
Hematologic cancer and cell line (Stimulated immune*)	Stimulated immune*	8.5e-07	11	16.4	67	53	1945
Hematologic samples and cell lines (Stimulated immune*)	Stimulated immune*	8.5e-07	11	16.4	67	53	1945
Macrophages (Stimulated immune*)	Stimulated immune*	8.5e-07	11	16.4	67	53	1945
Monocytes (Stimulated immune*)	Stimulated immune*	8.5e-07	11	16.4	67	53	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.2e-06	15	93.7	16	76	207
Cancer and cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	4	5.9	67	10	1945
Cell line (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	4	5.9	67	10	1945
EWS/FLI expressing fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	4	5.9	67	10	1945
Fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	4	5.9	67	10	1945
Skin fibroblasts (Fibroblast EWS-FLI*)	Fibroblast EWS-FLI*	0.0002	4	5.9	67	10	1945
Cancer and cell line (HeLa cell cycle*)	HeLa cell cycle*	0.0002	9	20	45	96	1945
Cell line (HeLa cell cycle*)	HeLa cell cycle*	0.0002	9	20	45	96	1945
Epithelial cell line (HeLa cell cycle*)	HeLa cell cycle*	0.0002	9	20	45	96	1945
HeLa cell line (HeLa cell cycle*)	HeLa cell cycle*	0.0002	9	20	45	96	1945
Liver tissue (Liver cancer*)	Liver cancer*	0.0003	16	23.8	67	187	1945

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
intracellular transport	1.8e-48	22	95.6	23	38	4566
cytoskeleton-dependent intracellular transport	9.3e-43	20	86.9	23	35	4566
microtubule-based process	8.6e-32	16	69.5	23	32	4566
motor activity	9.3e-25	14	60.8	23	40	4566
cytoskeleton	7.1e-19	18	78.2	23	263	4566
microtubule cytoskeleton	2.3e-18	16	69.5	23	176	4566
microtubule associated complex	5.7e-17	15	65.2	23	167	4566
microtubule motor activity	1.6e-12	6	26.0	23	10	4566
kinesin complex	9.2e-10	10	43.4	23	151	4566
microtubule-based movement	9.2e-10	5	21.7	23	11	4566
dynein complex	1.6e-08	4	17.3	23	7	4566
spindle	6.4e-07	4	17.3	23	15	4566
mitosis	3.7e-06	5	21.7	23	50	4566
microtubule	6.1e-06	3	13.0	23	8	4566
condensed chromosome	5.9e-05	3	13.0	23	16	4566
M phase of mitotic cell cycle	7.2e-05	3	13.0	23	17	4566
ATP binding	7.3e-05	9	39.1	23	399	4566
nucleotidyltransferase activity	0.0001	9	39.1	23	425	4566
nuclear division	0.0001	3	13.0	23	20	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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