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Table 3 Motifs discovered de novo a and enriched in the upstream regions of the co-regulated genes

From: Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase

Groups of co-regulated genesb 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)
Bacilli CcpA [RegTransBase] (1e-06)
X > R, 20 h 1.76e-10 90 38 Lactobacillaceae CcpA [RegPrecise] (2e-08)
Bacilli CcpA [RegTransBase] (4e-07)
G ≈ X > R, 20 h 1.04e-5 42 21 Lactobacillaceae CcpA [RegPrecise] (1e-09)
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)
  1. a Sequence logos for the discovered motifs can be found in Additional file 1: Table S6
  2. 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
  3. c q-value is an adjusted p-value, as given by tomtom tool from MEME suite [33]