Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia colitranscriptome

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
	Decreased	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.

ISSN: 1471-2164