Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

BMC Plant Biology

Table 5 Overrepresented Gene Ontology (GO) categories of genes with transient body methylation

GO term	Ontology description		Number in input list	Number in BG/Ref	p-value	FDR
Protein metabolism
GO: 0006886	P	Intracellular protein transport	32	187	8.10E-13	1. 70E-10
GO: 0034613	P	Cellular protein localization	33	199	8.90e-13	1. 90E-10
GO: 0030163	P	protein cataolic process	19	156	6.50E	0.0011
GO: 00065111	P	ubiquitin-dependent protein catabolic process modification-dependent protein catabolic	17	130	7.50E-06	0.0012
GO: 0019941	P	process	17	130	7.50E-06	0.0012
Nucleic acid metabolism
		nucleobase, nucleoside and nucleotide
GO: 0055086	P	metabloic process	28	256	4.80E-07	9.20E-05
GO: 0006259	P	DNA metabolic process	25	214	5.60E-07	0.00011
Go: 0016070	P	RNA metabloic process	87	1366	2.10E-06	0.00037
GO: 0034660	P	nCRNA metablic process	24	141	5.90E-10	1.20E-07
GO: 0006396	P	RNA processing	22	141	3.00E-06	0.00053
GO: 0006399	P	tRNA metabloic process	20	108	3.30E-09	6.60E-07
Cellular signalling
regulation of small GTPase mediated signal
Go: 0051056	P	transduction	13	63	4.80E-07	9.20E-05
GO: 0046578	P	regulation of Ras protein signal transduction	13	63	4.80E-07	9.20E-05
GO: 0007265	P	Ras protein signal transduction	13	63	4.80E-07	9.20E-05
GO: 0009966	P	regulation of signal transduction	13	67	1.00E-07	0.00018
GO: 0023051	P	regulation of signaling process	13	67	1.00E-06	0.00018
GO: 0010646	P	regulation of cell communication	13	37	1.00E-06	0.00018
GO: 0032011	P	ARF protein signal transduction	7	34	0.00022	0.029

Genes were determined to be methylated at their gene bodies compared to a non-immunoprecipitated control using a negative binomial analysis (q < 0.1). GO analysis was performed with the AgriGo Singular Enrichment Analysis tool (http://bioinfo.cau.edu.cn/agriGO/analysis.php).Categories shown are a subset of the total 189 significantly enriched (p < 0.05) categories, all of which are shown in Additional file 3.

ISSN: 1471-2229