Integrating phenotypic and expression profiles to map arsenic-response networks

Table 1 Pathways enriched for genes significantly expressed in response to arsenic

Category	Differentially expressed genes	Pathway size	p-value	Significant
KEGG pathway
Cell cycle reference pathway	8	87	0.9072	False
Galcatose metabolism	5	15	0.0391	False
Glutathione metabolism	6	11	0.0014	True
MAPK signaling pathway	7	55	0.609	False
Methionine metabolism	8	11	1.07E-05	True
Proteasome	9	30	0.0127	False
Purine metabolism	14	139	0.8991	False
Pyrmidine metabolism	8	80	0.8515	False
Sulfur metabolism	7	7	7.15E-07	True
Serine, threonine and glycine metabolism	8	25	0.0125	False
Citrate cycle	4	22	0.3345	False
Starch and sucrose	9	31	0.0159	False
Pyruvate	4	25	0.4292	False
Reductive carboxylate	5	16	0.0508	False
Second messenger signaling	3	19	0.472	False
Valine, leucine, isoleucine	2	13	0.5313	False
Circadian rhythm	2	19	0.7398	False
Porphyrin and chlorophyll metabolism	7	74	0.8782	False
Selenoamino-acid metabolism	10	12	8.36E-08	True
Ubiquitin-mediated proteolysis	2	29	0.9133	False
Cysteine metabolism	2	4	0.088	False
Fructose and mannose	6	15	0.0093	False
Carbon fixation	3	15	0.3207	False
Alanine and aspartate	2	24	0.8477	False
Glutamate	3	19	0.472	False
Methane	2	4	0.088	False
Gene Ontology (biological process)
Biological process	72	436	0.0244	False
Cell communication	72	270	<1.00E-008	True
Cell growth and maintenance	47	268	0.0231	False
Cell surface linked signal transduction	14	91	0.3197	False
Developmental processes	5	32	0.4233	False
Heat-shock response	14	22	5.40E-08	True
Intracellular signaling	9	47	0.1635	False
Serine threonine kinase signaling	5	38	0.5815	False
Signal transduction	26	172	0.2656	False
ATPase	3	78	0.9988	False
Cyclin	4	29	0.5499	False

Transcript profiling reveals that arsenic affects glutathione, methionine, sulfur, selenoamino-acid metabolism, cell communication and heat-shock response. Genes were categorized by KEGG pathway and Simplified Gene Ontology. In total, 829 genes out of 6,240 had a significant alteration in expression in at least one experimental condition. Along with the size of each functional category, a statistical measure for the significance of the enrichment was calculated by using a hypergeometric test. The level of significance for this test (True-shown in bold, False) was determined using the Bonferroni correction, where the α value is set at 0.05 and 27 and 11 tests were done for KEGG pathway and Simplified Gene Ontology, respectively.

ISSN: 1474-760X