BMC Genomics 2006, 7:21 http://www.biomedcentral.com/1471-2164/7/21 Table 1: Identification of DtxR binding sites in the genome sequence of C. glutamicum CDS1 Gene Predicted DtxR binding motif2 Distance to translational start codon3 Differential gene expression in C. glutamicum IB2103 measured by DNA microarray (ratio)4 Real-time RT-PCR (relative expression)5 cg0466* cg0748* cg0771* cg0922* cg0924* cg0926* cg1405* cg1418* cg2234* cg2445* cg2782* cg3327* cg3404* cg0160 cg0445 cg0527 cg1120 cg1930 cg1996 cg2311 cg2796 cg3082 cg3119 cg3156 cg0405 cg0470 cg0591 cg0955 cg1642 cg3247 cg3394 cg1070 cg1088 cg1966 cg2224 cg2399 cg2598 cg2651 cg2842 cg3170 - - - - - - - - - hmuO ftn dps - - sdhCD - ripA - cglIM - - - fpr2 - - - - - - cgtR11 - - - - xerC glk - - phoU - TTAAGTTAGCATAGCCTTA ATAGGATAGGTTAACCTGA GTCGGGCAGCCTAACCTAA TAAGGTTTGCCTAATCTTT TTAGGTAACCTAACCTCAC TTAGGTTAGGCTCTAATAT TTTTGTTAGGCTTGCCTAG TTAGGTAAGGTTTGCATAC TTAGGCAAGGCTACCTTTT GTAGGTGTGGGTAACCTAA TTATGCTGCGCTAACCTAT TCAGGATAGGACAACCTAA TTAGGCTATCCTAACGCAA AATGGTTAGGCTAACCTTA TAAAGTAAGGCTATCCTAA TTAGGCTTGCCATACCTAT TGAGGTTAGCGTAACCTAC TTAGGTAAAGCTTGCCTAT TTAGGATTCTCTCAACTAA TCAAGTAAGGTTTACCTTA GAAGGCAAGCCAAACTTAA TTCTGTGAGGTTAACTTTT TTAGGTTAGGTTCACCGTG TAAGGCAAGCCTAAATTAG TAAGGATAACCTTGCCTTA TTAGGTTAAGCTAATCTAG TTAGTAAAGGCTCACCTAA TTACGTGAGCGTAGCCGAA TTAGGTTAGGCAAGCCATA ATCAGTAAGGCTAGACTAA TTAAGGTAAGTTCAGCTAA ATAGGTTATCCAAGCCTAA TTAAGTCAGTGTTACCTAA TAACTTTGACATAACCTAA GTGTGTGAGGCAAGCCTAA AAAGATTAAATTCACCTAA TTAGGTCAAGCTTGCATTT TTAGGTTGTAAAAACCTTA TTAGGTGATTCAATCTTAA TTAACTTTGCCCTACCTAA 141 25 40 30 63 173 33 30 4 120 37 61 overlap overlap 111 11 32 90 199 overlap 18 254 204 97 28 32 91 200 39 87 37 18 82 67 93 29 20 46 50 190 +3.2 +3.0 +5.3 +4.4 +4.4 +4.0 +4.3 +1.8 +3.2 +5.6 -3.3 -3.4 +3.2 +3.4 -2.5 +3.2 +4.9 +4.8 +1.7 +3.0 +5.3 +1.1 +2.2 +5.0 n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. +1160 +29 +239 +176 +2000 +185 +198 +119 +1980 +203 +0.02 +0.01 +364 +1870 +0.12 +63 +359 +1210 +3.8 +37 +1610 +19 +18 +304 +1010 +978 +310 +2.8 +4.4 +5.5 +4.6 n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. n.d. 1 Asterisks denote genes whose upstream regions were used for initial HMM processing. 2 Bases belonging to predicted translational start codons are underlined. 3 The distance from the last nucleotide of the DtxR binding site to the translational start codon is indicated. 4 n.d., not detected as differentially expressed by using a significance cut-off of ± 1 (ratio). 5 n.d.; not detected as differentially expressed by using a significance cut-off of +2 (up-regulation) or +0.5 (down-regulation). C. glutamicum IB2103. Therefore, genes revealing an enhanced expression in C. glutamicum IB2103 when com- pared to the wild-type are candidates that might belong to the transcriptional regulatory network of DtxR. Cell samples for total RNA preparation were taken from two independently grown C. glutamicum cultures of each strain. The respective RNA preparations were used in two DNA microarray hybridization assays by applying label swapping. Labeling of probes and DNA microarray hybridization were carried out as described previously [20]. To minimize the number of false-positive signals, the data were stringently filtered to obtain genes with at least six statistically significant values out of the eight Page 5 of 19 (page number not for citation purposes)