. 2016 Aug 3;17:539. doi: 10.1186/s12864-016-2840-x

Table 3.

Motifs discovered de novo ^a and enriched in the upstream regions of the co-regulated genes

Groups of co-regulated genes^b	Enrichment p-value	No. of upstream regions, total	No. of upstream regions with the motif(s)	TFBS database match [database] (q-value ^c)
G > R, 20 h	6.58e-6	86	31	Lactobacillaceae CcpA [RegPrecise] (1e-07)
G > R, 20 h	6.58e-6	86	31	Bacilli CcpA [RegTransBase] (1e-06)
X > R, 20 h	1.76e-10	90	38	Lactobacillaceae CcpA [RegPrecise] (2e-08)
X > R, 20 h	1.76e-10	90	38	Bacilli CcpA [RegTransBase] (4e-07)
G ≈ X > R, 20 h	1.04e-5	42	21	Lactobacillaceae CcpA [RegPrecise] (1e-09)
G ≈ X > R, 20 h	1.04e-5	42	21	Bacilli CcpA [RegTransBase] (2e-07)
G > X, 20 h	1.32e-5	23	11	Bacillales Rex [RegPrecise] (9e-08)
				Lactobacillaceae Rex[RegPrecise] (1e-07)
				Bacillus Fnr [PRODORIC] (2e-03)
G > X, 24 h	1.92e-5	31	13	Bacillales Rex[RegPrecise] (2e-09)
				Lactobacillaceae Rex [RegPrecise] (7e-09)
				Bacillus Fnr [PRODORIC] (6e-05)

^a Sequence logos for the discovered motifs can be found in Additional file 1: Table S6

^b G indicates glucose, R ribose, X xylose. Notation G > R designates the group of genes that have higher expression during growth on glucose than on ribose; G ≈ X > R – the group of genes that has similar expression levels on glucose and xylose, which are higher than on ribose

^c q-value is an adjusted p-value, as given by tomtom tool from MEME suite [33]