Table 1

Regulatory networks with significant perturbations
Perturbation Direction Locus tag Name of TF Size FDR q-val
Genome reduction Increased b1951 rcsA 26 0.0000
b2217 rcsB 29 0.0000
b3938 metJ 15 0.0000
b3516 gadX 25 0.0000
b3512 gadE 49 0.0000
b0889 lrp 83 0.0038
b3461 rpoH 150 0.0065
b0761 modE 45 0.0061
b1237 hns 136 0.0145
b3261 fis 216 0.0513
b2193 narP 49 0.0870
b1221 narL 113 0.1043
b3912 cpxR 51 0.0972
b2531 iscR 26 0.1580
b0399 phoB 36 0.1572
b1712 ihfA 191 0.1477
b2741 rpoS 215 0.1448
b0912 ihfB 191 0.1398
b0076 leuO 20 0.1703
b1130 phoP 48 0.1627
b1334 fnr 272 0.1687
b1531 marA 36 0.2127
Decreased b1658 purR 31 0.0071
b0683 fur 81 0.0201
Heat shock Increased b3461 rpoH 150 0.0000
b3912 cpxR 51 0.0004
b3938 metJ 15 0.0026
b2193 narP 49 0.0837
b0399 phoB 36 0.1384
b0761 modE 45 0.2134
b0076 leuO 20 0.2345
Decreased b1658 purR 31 0.0000
b1275 cysB 19 0.0000
b0683 fur 81 0.0000
b3516 gadX 25 0.0123
b3868 glnG 44 0.0118

The information pertaining to transcription factors (TFs), sigma factors and the downstream genes under their control is from RegulonDB. The transcriptional changes in the downstream genes were evaluated with gene set enrichment analysis (GSEA) [36], and the disturbed regulatory networks were determined accordingly (FDR <  0.25). Perturbation and Direction refer to the type of disturbance to the transcriptome and the directionality of the changes in gene expression, respectively. Locus tag, Name of TF, Size and FDR q-val represent the gene ID, the corresponding regulator gene, the number of regulated downstream genes and the statistical significance, respectively.

Ying et al.

Ying et al. BMC Genomics 2013 14:25   doi:10.1186/1471-2164-14-25

Open Data