Deciphering transcriptional regulations coordinating the response to environmental changes

BMC Bioinformatics

Table 2 E. coli global regulators and their ranking using radiality centrality index in the LOMBARDE output

Gene	Ranking	Ranking for radiality	Ranking for radiality
name	in literature	index in Lombarde	index in Lombarde
		output for \(\mathcal {G}_{\mathcal {A}}\)	output for \(\mathcal {G}_{\mathcal {A}\mathcal {V}}\)
crp	1	25	1
ihfA	2	14	4
ihfB	3	16	5
fnr	4	1	6
fis	5	63	2
arcA	6	13	7
lrp	7	34	87
hns	8	—	14
narL	9	121	126
ompR	10	143	96
fur	11	7	8
phoB	12	9	25
cpxR	13	80	22
soxR	14	69	49
soxS	15	109	18
mtfA	16	—	—
cspA	17	—	42
rob	18	30	95
purR	19	39	47

The first two columns list E. coli gene names and their global rankings as described in the literature. The last two columns show the ranking of the operons that contain each of these genes using the radiality index in the networks obtained by applying Lombarde to \(\mathcal {G}_{\mathcal {A}}\) and \(\mathcal {G}_{\mathcal {AV}}\). The numbers in bold indicate genes that were ranked among the top 30 % of radiality index and were considered central regulators

ISSN: 1471-2105