Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

Table 2 Transcription factor binding sites predicted in the 1000 bp upstream region of the genes using STIFAL with a cut-off > 1.5 and their abundance in 10 different species. The number of occurrences of each TFBS at both family and subfamily level has been indicated in the table

TFBS Statistics		*F. vesca*	*M. domestica*	*P. avium*	*P. bretschneideri*	*P. communis*	*P. dulcis*	*P. mume*	*P. persica*	*R. chinensis*	*R. occidentalis*
Number of genes with TFBS		34	35	57	297	228	177	200	42	189	201
Number of genes without TFBS		1	0	4	8	3	6	7	3	10	8
Predicted TFBS		238	285	426	2265	1654	1464	1584	305	1430	1494
TF family	TF subfamily	TFBS predicted in 1000 bp upstream ≥ 1.5 Z-score
MYB	Myb_box1	16	31	53	245	184	164	162	36	154	164
	Myb_box2	16	26	29	186	145	88	142	26	119	118
	Myb_box3	16	21	26	163	92	103	93	17	103	113
	Myb_box4	8	11	24	88	55	64	69	13	53	45
	Myb_box5	68	81	97	564	424	382	393	76	345	415
bHLH	G_box	12	6	19	103	78	75	71	8	73	55
bHLH	N_box	10	11	24	104	83	64	67	17	65	46
AP2/EREBP	DREB	9	13	24	108	90	67	78	14	69	65
AP2/EREBP	GCC_box	6	14	7	49	53	31	23	3	30	23
WRKY	W_box	24	21	33	184	142	111	124	28	103	131
bZIP	G_box1	1	2	1	5	3	4	4	0	6	3
	G_box2	13	15	20	105	81	61	87	13	85	68
	C_ABRE	2	5	3	35	27	19	22	3	19	23
	G_ABRE	0	3	3	18	12	7	8	0	10	8
ARF	AuxRE	22	10	29	136	86	108	129	22	91	95
NAC	Nac_box	12	13	23	123	80	82	93	23	87	98
HSF	HSE1	3	1	9	33	10	23	13	5	10	16
HB	HBE	0	1	2	15	8	11	6	1	8	8
ABI3/VP1	ABRE	0	0	0	1	1	0	0	0	0	0

ISSN: 1471-2164