Module 172

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:	96 (see 1756 additional genes for this module)
Num experiments:	656 (255 induced, 401 repressed)
Parent module:	209
Children modules:	107

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.
catabolism
regulation of catabolism
proteolysis and peptidolysis

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 (Lung cancer*)	Lung cancer*	5.6e-38	137	34.1	401	252	1945
Cancer (Lung cancer*)	Lung cancer*	5.6e-38	137	34.1	401	252	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	2.2e-37	144	35.9	401	276	1945
Liver tissue (Liver cancer*)	Liver cancer*	5.6e-37	91	35.6	255	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.3e-34	91	35.6	255	197	1945
Lung cancer (Lung cancer*)	Lung cancer*	6.4e-33	126	31.4	401	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	6.4e-33	126	31.4	401	238	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	2.5e-23	68	26.6	255	156	1945
Non small cell lung cancer and cell line (Lung cancer*)	Lung cancer*	3.0e-21	99	24.6	401	205	1945
Non small cell lung cancer (Lung cancer*)	Lung cancer*	3.0e-21	99	24.6	401	205	1945
Non-tumor liver tissue (Liver cancer)	Liver cancer	2.8e-17	62	68.1	91	76	207
Cancer and cell line (Liver cancer)	Liver cancer	2.1e-14	57	98.2	58	126	207
Diffuse large B cell lymphoma - DLBCL (B lymphoma)	B lymphoma	8.5e-13	44	95.6	46	126	245
Diffuse large B cell lymphoma tumor or cell line (B lymphoma)	B lymphoma	2.0e-11	44	95.6	46	134	245
Activated B like DLBCL (B lymphoma)	B lymphoma	4.5e-10	20	43.4	46	30	245
CNS tissue, cancer or cell line (Various tumors)	Various tumors	3.1e-09	16	50	32	21	154
Cell line (Breast cancer)	Breast cancer	3.8e-08	19	55.8	34	30	152
B cells (Leukemia)	Leukemia	7.5e-08	18	100	18	62	141
Bone marrow (Leukemia)	Leukemia	1.9e-07	12	66.6	18	23	141
Breast cancer cell line (Breast cancer)	Breast cancer	5.4e-07	13	38.2	34	17	152
Lymphoma or lymphoma cell line (B lymphoma)	B lymphoma	9.4e-07	44	95.6	46	167	245
CNS cancer or cell line (Various tumors)	Various tumors	9.7e-07	12	37.5	32	16	154
CNS tumor (Various tumors)	Various tumors	9.7e-07	12	37.5	32	16	154
Liver cancer cell line (Liver cancer)	Liver cancer	1.6e-06	10	17.2	58	10	207
Metastasis (Liver cancer)	Liver cancer	1.6e-06	10	17.2	58	10	207
Cancer (Liver cancer)	Liver cancer	2.3e-06	47	81.0	58	115	207
Normal tissue (Liver cancer)	Liver cancer	5.5e-06	14	15.3	91	14	207
Female hormonal cancer cell line (Breast cancer)	Breast cancer	1.1e-05	11	32.3	34	15	152
Cell line (Liver cancer)	Liver cancer	1.3e-05	10	17.2	58	11	207
Acute lymphocytic leukemia (Leukemia)	Leukemia	1.8e-05	24	100	24	99	149
Chronic lymphocytic leukemia (B lymphoma)	B lymphoma	3.4e-05	23	37.7	61	46	245
Leukemia (B lymphoma)	B lymphoma	3.4e-05	23	37.7	61	46	245
Leukemia or leukemia cell line (B lymphoma)	B lymphoma	3.4e-05	23	37.7	61	46	245
Adenocarcinoma (Breast cancer*)	Breast cancer*	4.8e-05	30	11.7	255	112	1945
Breast cancer (Breast cancer*)	Breast cancer*	4.8e-05	30	11.7	255	112	1945
Cancer (Breast cancer*)	Breast cancer*	4.8e-05	30	11.7	255	112	1945
Female hormonal cancer (Breast cancer*)	Breast cancer*	4.8e-05	30	11.7	255	112	1945
Breast tissue or cancer (Breast cancer*)	Breast cancer*	0.0001	30	11.7	255	118	1945
Female hormonal tissue or cancer (Breast cancer*)	Breast cancer*	0.0001	30	11.7	255	118	1945
Cancer (B lymphoma*)	B lymphoma*	0.0001	44	17.2	255	200	1945
Hematologic cancer (B lymphoma*)	B lymphoma*	0.0001	44	17.2	255	200	1945
Lymphocytes (Leukemia)	Leukemia	0.0001	18	100	18	91	141
Malignant glioblastoma (Various tumors)	Various tumors	0.0002	7	21.8	32	9	154
Breast cancer cell line (NCI60)	NCI60	0.0002	9	60	15	27	139
Centroblasts (Various tumors)	Various tumors	0.0002	5	15.6	32	5	154
GC B like DLBCL (Various tumors)	Various tumors	0.0002	5	15.6	32	5	154
After doxorubicin chemotherapy (Breast cancer)	Breast cancer	0.0003	13	92.8	14	21	38

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
catabolism	1.1e-112	87	90.6	96	215	4566
proteolysis and peptidolysis	2.4e-98	77	80.2	96	176	4566
peptidase activity	6.6e-84	72	75	96	193	4566
regulation of catabolism	1.9e-82	68	70.8	96	162	4566
regulation of metabolism	2.5e-64	74	77.0	96	365	4566
hydrolase activity	2.7e-48	81	84.3	96	783	4566
endopeptidase activity	2.7e-44	40	41.6	96	99	4566
serine-type endopeptidase activity	1.1e-35	31	32.2	96	69	4566
chymotrypsin activity	1.5e-34	27	28.1	96	48	4566
trypsin activity	7.4e-34	27	28.1	96	50	4566
serine-type peptidase activity	3.4e-33	31	32.2	96	80	4566
catalytic activity	1.0e-32	90	93.7	96	1677	4566
metallopeptidase activity	3.6e-27	26	27.0	96	70	4566
metalloexopeptidase activity	1.2e-17	13	13.5	96	21	4566
exopeptidase activity	9.3e-16	12	12.5	96	21	4566
carboxylic acid catabolism	2.0e-15	14	14.5	96	35	4566
cysteine-type peptidase activity	1.7e-11	11	11.4	96	32	4566
macromolecule catabolism	2.6e-11	10	10.4	96	25	4566
collagen catabolism	3.3e-11	8	8.3	96	13	4566
zinc ion binding	4.2e-11	17	17.7	96	108	4566
metalloendopeptidase activity	8.0e-11	12	12.5	96	46	4566
sterol regulatory element-binding protease activity	1.3e-10	9	9.3	96	21	4566
protein catabolism	3.5e-10	9	9.3	96	23	4566
cysteine-type endopeptidase activity	5.5e-10	9	9.3	96	24	4566
metal ion binding	1.8e-09	29	30.2	96	410	4566
carboxypeptidase activity	2.2e-09	7	7.2	96	13	4566
transition metal ion binding	3.1e-09	18	18.7	96	160	4566
metallocarboxypeptidase activity	3.1e-08	6	6.2	96	11	4566
aminopeptidase activity	7.5e-08	5	5.2	96	7	4566
lipid catabolism	1.1e-07	8	8.3	96	30	4566
carboxylic acid metabolism	1.2e-07	15	15.6	96	138	4566
organic acid metabolism	1.3e-07	15	15.6	96	139	4566
blood coagulation factor activity	8.5e-07	5	5.2	96	10	4566
carboxypeptidase A activity	8.5e-07	5	5.2	96	10	4566
aspartic-type endopeptidase activity	9.0e-07	4	4.1	96	5	4566
extracellular space	1.3e-06	17	17.7	96	212	4566
lysosome	2.1e-06	9	9.3	96	57	4566
blood coagulation	5.3e-06	8	8.3	96	48	4566
lipase activity	6.3e-06	5	5.2	96	14	4566
hemostasis	7.3e-06	8	8.3	96	50	4566
defense/immunity protein activity	8.0e-06	11	11.4	96	103	4566
carboxylic ester hydrolase activity	1.2e-05	6	6.2	96	26	4566
complement activity	2.5e-05	5	5.2	96	18	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 656 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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