Infection and genotype remodel the entire soybean transcriptome

BMC Genomics

Table 2 Differences among sub-groups as revealed by LMMA analyses of data sets preprocessed by GC-RMA (TST-FDR)

FDR^a	Fixed factors^b	2 Sub-Groups^c		6 Sub-Groups^d
		Number significant^e	Percentage significant^f	Number significant^e	Percentage significant^f
0.05	Genotype	26,043	91.9	25,975	91.6
	Treatment	27,191	95.9	27,180	95.9
	Time	4,748	16.7	4,735	16.7
	Genotype × Treatment	24,837	87.6	24,774	87.4
	Sub	45	0.2	235	0.8
	Sub × Genotype	458	1.6	238	0.8
	Sub × Treatment	251	0.9	429	1.5
	Sub × Genotype × Treatment	805	2.8	364	1.3
0.01	Genotype	24,808	87.5	24,732	87.2
	Treatment	26,652	94.0	26,645	94.0
	Time	2,692	9.5	2,692	9.5
	Genotype × Treatment	23,275	82.1	23,213	81.9
	Sub	0	0	20	0.1
	Sub × Genotype	68	0.2	42	0.1
	Sub × Treatment	35	0.1	74	0.3
	Sub × Genotype × Treatment	143	0.5	53	0.2
0.001	Genotype	23,268	82.1	23,150	81.7
	Treatment	25,891	91.3	25,881	91.3
	Time	1,468	5.2	1,465	5.2
	Genotype × Treatment	21,141	74.6	21,056	74.3
	Sub	0	0	0	0
	Sub × Genotype	4	0	3	0
	Sub × Treatment	5	0	9	0
	Sub × Genotype × Treatment	13	0	2	0
0.0001	Genotype	21,694	76.5	21,474	75.7
	Treatment	25,128	88.6	25,073	88.4
	Time	895	3.2	894	3.2
	Genotype × Treatment	19,265	68.0	19,131	67.5
	Sub	0	0	0	0
	Sub × Genotype	0	0	0	0
	Sub × Treatment	2	0	0	0
	Sub × Genotype × Treatment	1	0	0	0
0.00001	Genotype	20,105	71	19,845	70
	Treatment	24,310	86	24,264	86
	Time	585	2	583	2
	Genotype × Treatment	17,518	62	17,377	61
	Sub	0	0	0	0
	Sub × Genotype	0	0	0	0
	Sub × Treatment	0	0	0	0
	Sub × Genotype × Treatment	0	0	0	0

^aFalse discovery rate (FDR) was controlled the two-stage linear step-up method (TST-FDR). ^bThe fixed factors used in the LMMA model included genotype (V71-370, Sloan and VPRIL9), treatment (Upper, Lower, and Mock), time (9 am, 10:30 am, and 12 pm), sub (sub-group), and the interactions (genotype × treatment, sub × genotype, sub × treatment, and sub × genotype × treatment). ^c "2 Sub-Groups" refers to the 12 odd-numbered blocks compared to the 12 even-numbered blocks. ^d "6 Sub-Groups" refers to 6 randomly selected groups of blocks (four blocks in each group). ^eNumber of significant genes for a factor determined by LMMA analysis with FDR control. ^fThe number of significant genes as a percentage of the total number of detectable genes.

ISSN: 1471-2164