. 2017 Jun 13;8:1036. doi: 10.3389/fpls.2017.01036

Table 5.

Selected DEGs that may be beneficial for primocane apex rooting in SAP1-VS-SAP2 and SAP2-VS-SAP3 paired comparisons of Rubus.

Function group	GeneID	log₂FoldChange(SAF-VS-SAP)			log₂FoldChange (SAP-VS-SAP)			Gene annotation
		SAF1-VS-SAP1	SAF2-VS-SAP2	SAF3-VS-SAP3	SAP1-VS-SAP2	SAP2-VS-SAP3	SAP1-VS-SAP3
Circadian rhythm - plant	CL1524.Contig3_All	−0.10	−1.29^*	−0.06	−1.21^*	−0.26	−1.48^*	PHYB, PHYTOCHROME B
	CL2434.Contig1_All	−0.18	−1.45^*	−0.30	−1.71^*	−0.02	−1.72^*	ELF3, EARLY FLOWERING 3
	CL5214.Contig6_All	−0.15	−9.79^**	−4.39	−10.36^**		−10.36^**	APRR5, TWO-COMPONENT RESPONSE REGULATOR APRR5
	Unigene16183_All	0.04	−3.40^**	0.18	−3.45^**	0.16	−3.30^**	CDF1, CYCLING DOF FACTOR 1
	Unigene21192_All	−0.25	3.05^*	−3.88^**	3.22^*	−4.40^**	−1.18	HEC2, HECATE 2
Cysteine and methionine metabolism	Unigene20575_All	−4.00	8.07^*	−0.07	8.07^*	−0.83	7.24^*	ACS, 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE
Plant hormone signal transduction	CL1090.Contig5_All	−0.38	−9.86^**	0.95	−9.79^**	5.91^**	−3.88^**	ARF1, AUXIN RESPONSE FACTOR 1
	CL2444.Contig1_All	−0.07	−8.07^**	−4.58	−7.96^**		−7.96^**	ARF18
	CL1556.Contig5_All	0.14	−7.09^**	−5.17^**	−7.51^**		−7.51^**	ARF7
	Unigene20581_All	0.7	−2.81^*	−0.1	−3.30^**	1.00	−2.30^*	ARF7
	CL5079.Contig1_All	−0.07	−2.86^*	−1.46	−3.16^**	−1.58	−4.74^**	ARF23
	CL1556.Contig2_All	0.42	−3.19^**	0	−3.17^**	0.70	−2.47^*	ARF7
	Unigene24307_All		3.05^**	4.81^**	7.91^**	−3.10^**	4.81	CTR1, THREONINE-PROTEIN KINASE CTR1
	Unigene13079_All	−0.57	4.03^**	−0.53	4.00^**	−0.76	3.23^**	ERF1, ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR1
	Unigene15505_All		4.58	9.12^**	4.58	4.53^**	9.12^**	ARF7
	CL5715.Contig2_All	−0.02	−1.82^*	4.17^**	−1.49	4.03^**	2.54^*	CTR1
	Unigene1657_All	−1.58	−5.95	7.92^**	−3.70	7.92^**	4.22^**	EIN3, ETHYLENE-INSENSITIVE3
Shoot and root development	CL6648.Contig1_All	−0.12	1.11^*	−0.25	1.16^*	−0.24	0.92	STM, SHOOT MERISTEMLESS
	CL6648.Contig3_All	0.05	1.51^*	−0.44	1.84^*	−0.88	0.96	STM
	CL6906.Contig3_All	−0.03	−1.30^*	0.48	−1.25^*	0.59	−0.65	RPD1, ROOT PRIMORDIUM DEFECTIVE 1
	Unigene12164_All	−0.27	−1.14^*	−1.76^*	−1.00^*	−1.57^*	−2.57^*	SGR5, SHOOT GRAVITROPISM 5
	Unigene15061_All	0.08	−2.99^*	−3.81	−2.63^*	−4.86	−7.49^**	RPT3, ROOT PHOTOTROPISM 3
	Unigene16263_All	−0.31	2.51^*	0.67	2.99^*	0.90	3.89^**	LRP, LATERAL ROOT PRIMORDIUM
	Unigene17114_All	3.81	4.61^**	1.94^*	5.13^**	1.53*	6.65^**	RC, ROOT CAP
	Unigene20360_All	0.47	−1.65^*	−0.15	−1.47^*	−0.10	−1.57^*	RPD1
	Unigene331_All	−0.14	−1.59^*	0.04	−1.49^*	0.38	−1.11^*	RPD1
	Unigene7065_All	−1.00^*	7.34^**	3.96^**	4.53^**	3.10^**	7.63^**	RC
	Unigene811_All	−0.27	−0.96	−1.99^*	−0.61	−2.07^*	−2.68^*	RC
	CL1554.Contig3_All	−0.33	0.07	−1.76^*	0.38	−1.65^*	−1.27^*	RPT2
	CL1554.Contig1_All		0.04	−1.62^*	0.11	−1.60^*	−1.50^*	RPT2
	CL1554.Contig2_All	0.39	−0.15	−1.22^*	−0.30	−1.26^*	−1.57^*	RPT2
	CL4872.Contig3_All	1.41^*	1.85	2.58^*	−1.76	3.27^**	1.51	RHD3, ROOT HAIR DEFECTIVE 3
	CL6648.Contig2_All	−0.63	1.31		0.09	−7.65^**	−7.56^**	STM
	Unigene10691_All	−0.01	−0.09	−4.48^**	0.10	−4.70^**	−4.61^**	SGR5
	Unigene10761_All	−0.06	0.85	1.18^*	0.87	1.22^*	2.09	AIR12, AUXIN INDUCED IN ROOTS 12

Asterisk represent DEGs with a threshold of FDR ≤ 0.001 and |log₂Ratio| ≥ 1, and double asterisks represent highly regulated DEGs with a threshold of FDR ≤ 0.001 and |log₂Ratio| ≥ 3.