. 2013 Oct 18;4:313. doi: 10.3389/fmicb.2013.00313

Table 1.

Numbers of DEGs in gene ontology groups overrepresented or underrepresented in RGSV-infected plants.

Categories	Cene ontology ID¹	Gene ontology term^a	Number of expressed genes	Number of DEG^b	P-value^c	Response of DEG
Categories	Cene ontology ID¹	Gene ontology term^a	Number of expressed genes	Number of DEG^b	P-value^c	Induced	Suppressed
Component	GO:0016020	Membrane	3193	1188	2.53E-05	671	517
	GO:0005618	Cell wall	1645	688	3.25E-10	377	311
	GO:0005623	Cell	233	100	7.88E-03	54	46
	GO:0005622	Intracellular	627	152	1.50E-04	103	49
	GO:0005840	Ribosome	301	43	1.73E-08	18	25
	GO:0005829	Cytosol	264	56	9.08E-04	33	23
Process	GO:0009719	Response to endogenous stimulus	2619	1072	9.56E-13	615	457
	GO:0007582	Physiological process	2105	836	5.78E-08	499	337
	GO:0007165	Signal transduction	2022	785	3.87E-06	485	300
	GO:0006950	Response to stress	1804	694	4.11E-05	411	283
	GO:0009628	Response to abiotic stimulus	1527	676	1.14E-14	404	272
	GO:0008150	Biological process	1388	586	1.63E-09	357	229
	GO:0009607	Response to biotic stimulus	1348	585	2.12E-11	321	264
	GO:0009058	Biosynthetic process	1222	492	7.94E-06	214	278
	GO:0006519	Amino acid and derivative metabolic process	803	331	4.23E-05	152	179
	GO:0019748	Secondary metabolic process	659	317	1.14E-11	133	184
	GO:0006629	Lipid metabolic process	655	272	1.26E-04	132	140
	GO:0006118	Electron transport	481	210	4.12E-05	98	112
	GO: 0005975	Carbohydrate metabolic process	473	226	1.82E-08	107	119
	GO: 0007275	Multicellular organismal development	463	205	2.09E-05	128	77
	GO:0030154	Cell differentiation	426	183	3.10E-04	120	63
	GO:0009908	Flower development	342	164	1.29E-06	92	72
	GO: 00096 53	Anatomical structure morphogenesis	204	95	6.87E-04	61	34
	GO:0016043	Cellular component organization and biogenesis	784	196	1.09E-04	117	79
	GO:0006412	Translation	516	83	2.60E-11	39	44
	GO:0006139	Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	453	95	9.20E-06	59	36
			24911	8204		3896	4307

Based on Rice Genome Annotation Project database Osa1 (rice.plantbiology.msu.edu).

Numbers in bold (or underlined) text indicate that the corresponding ontology groups are overrepresented (or underrepresented) based on a χ²-test between the actual ratio of DEG (the number of DEGs/the number of expressed genes belonging to the corresponding ontology group) and the expected ratio of DEG [the number of total DEGs (8204)/the number of the total expressed genes (24,911)].

From the χ²-test.