Module 40 -- Organic acid metabolism

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:	82 (see 1963 additional genes for this module)
Num experiments:	287 (145 induced, 142 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.
organic acid metabolism
carboxylic acid metabolism

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
Liver tissue (Liver cancer*)	Liver cancer*	1.6e-75	98	67.5	145	187	1945
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.5e-72	98	67.5	145	197	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	1.4e-50	75	51.7	145	156	1945
Cancer and cell line (Liver cancer)	Liver cancer	1.4e-15	56	100	56	126	207
Non-tumor liver tissue (Liver cancer)	Liver cancer	1.5e-15	63	64.2	98	76	207
Liver tissue, cancer or cell line (Liver cancer*)	Liver cancer*	1.7e-14	46	32.3	142	197	1945
Lung tissue, cancer or cell line (Lung cancer*)	Lung cancer*	1.9e-09	47	33.0	142	276	1945
Hepatitis infected liver (Liver cancer*)	Liver cancer*	3.7e-09	33	23.2	142	156	1945
Liver tissue (Liver cancer*)	Liver cancer*	9.6e-09	36	25.3	142	187	1945
Liver cancer cell line (Liver cancer)	Liver cancer	1.1e-06	10	17.8	56	10	207
Metastasis (Liver cancer)	Liver cancer	1.1e-06	10	17.8	56	10	207
Cancer and cell line (Lung cancer*)	Lung cancer*	1.1e-06	39	27.4	142	252	1945
Cancer (Lung cancer*)	Lung cancer*	1.1e-06	39	27.4	142	252	1945
Cancer (Liver cancer)	Liver cancer	1.4e-06	46	82.1	56	115	207
Lung cancer (Lung cancer*)	Lung cancer*	5.8e-06	36	25.3	142	238	1945
Lung cancer or cell line (Lung cancer*)	Lung cancer*	5.8e-06	36	25.3	142	238	1945
Cell line (Liver cancer)	Liver cancer	9.6e-06	10	17.8	56	11	207
Invasive liver tumor (Liver cancer)	Liver cancer	0.0001	20	35.7	56	38	207
Follicular lymphoma (Various tumors)	Various tumors	0.0001	4	57.1	7	9	154
Adenocarcinoma (Liver cancer)	Liver cancer	0.0001	38	67.8	56	97	207
Normal tissue (Liver cancer)	Liver cancer	0.0003	13	13.2	98	14	207

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
carboxylic acid metabolism	1.0e-134	81	98.7	82	138	4566
organic acid metabolism	2.5e-134	81	98.7	82	139	4566
amine metabolism	5.3e-31	21	25.6	82	31	4566
catalytic activity	7.5e-27	76	92.6	82	1677	4566
carboxylic acid catabolism	2.4e-25	19	23.1	82	35	4566
amino acid and derivative metabolism	1.0e-24	17	20.7	82	26	4566
oxidoreductase activity	2.1e-23	35	42.6	82	254	4566
fatty acid metabolism	7.5e-22	20	24.3	82	57	4566
electron transporter activity	2.6e-20	33	40.2	82	269	4566
organic acid biosynthesis	1.3e-18	15	18.2	82	33	4566
carboxylic acid biosynthesis	2.4e-18	15	18.2	82	34	4566
aldehyde metabolism	1.2e-15	9	10.9	82	10	4566
lipid catabolism	3.2e-14	12	14.6	82	30	4566
amino acid metabolism	1.4e-13	20	24.3	82	139	4566
eicosanoid metabolism	1.6e-13	10	12.1	82	19	4566
fatty acid beta-oxidation	3.3e-13	8	9.7	82	10	4566
fatty acid oxidation	3.3e-13	8	9.7	82	10	4566
lipid metabolism	2.9e-12	19	23.1	82	143	4566
aromatic amino acid family metabolism	3.6e-12	7	8.5	82	8	4566
phenylalanine catabolism	3.6e-12	7	8.5	82	8	4566
fatty acid biosynthesis	5.2e-12	10	12.1	82	25	4566
eicosanoid biosynthesis	5.3e-12	9	10.9	82	18	4566
phenylalanine metabolism	1.6e-11	7	8.5	82	9	4566
aromatic compound metabolism	2.0e-10	9	10.9	82	25	4566
lipid biosynthesis	4.6e-10	10	12.1	82	37	4566
catabolism	5.5e-10	20	24.3	82	215	4566
oxidoreductase activity\, acting on the aldehyde or oxo group of donors\, NAD or NADP as acceptor	1.4e-09	7	8.5	82	14	4566
mitochondrion	2.0e-09	19	23.1	82	207	4566
oxidoreductase activity\, acting on the aldehyde or oxo group of donors	7.8e-09	7	8.5	82	17	4566
response to xenobiotic stimulus	7.9e-09	15	18.2	82	133	4566
response to chemical substance	1.0e-08	22	26.8	82	308	4566
lyase activity	7.0e-08	11	13.4	82	76	4566
lipase activity	7.4e-08	6	7.3	82	14	4566
carboxylic ester hydrolase activity	2.3e-07	7	8.5	82	26	4566
oxidoreductase activity\, acting on CH-OH group of donors	2.9e-07	9	10.9	82	53	4566
oxidoreductase activity\, acting on the CH-OH group of donors\, NAD or NADP as acceptor	2.9e-07	9	10.9	82	53	4566
energy pathways	3.2e-07	16	19.5	82	200	4566
aldehyde dehydrogenase activity	3.8e-07	5	6.0	82	10	4566
sulfur metabolism	4.5e-07	16	19.5	82	205	4566
peroxisome	6.7e-07	7	8.5	82	30	4566
phospholipase activity	1.9e-06	5	6.0	82	13	4566
transferase activity\, transferring one-carbon groups	3.7e-06	6	7.3	82	25	4566
photosynthesis	4.6e-06	13	15.8	82	162	4566
response to toxin	4.8e-06	6	7.3	82	26	4566
leukotriene biosynthesis	6.4e-06	4	4.8	82	8	4566
prostanoid biosynthesis	6.4e-06	4	4.8	82	8	4566
ribosome	6.7e-06	14	17.0	82	194	4566
oxidoreductase activity\, acting on the CH-NH group of donors	1.1e-05	4	4.8	82	9	4566
phospholipid metabolism	1.1e-05	5	6.0	82	18	4566
electron transport	1.4e-05	11	13.4	82	128	4566
phospholipase A2 activity	2.2e-05	3	3.6	82	4	4566
carbon-oxygen lyase activity	2.9e-05	6	7.3	82	35	4566
photosynthesis\, light reaction	3.2e-05	10	12.1	82	115	4566
iron ion binding	6.1e-05	4	4.8	82	13	4566
transaminase activity	8.4e-05	4	4.8	82	14	4566
tricarboxylic acid cycle	0.0001	4	4.8	82	15	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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