Stringent response of Escherichia coli: revisiting the bibliome using literature mining

Table 1 Annotations of the genetic components in the corpus.

Class	Concept	Number of Annotations	Number of Documents	% Frequency (Eq. 1)^ψ	Mean (Eq. 2)	Std (Eq. 3)	VMR (Eq. 4)
Genes	relA	3163	138	71.50	22.92	27.23	33.14
	spoT	1315	88	45.60	14.94	27.42	52.07
	lac	354	63	32.64	5.620	19.42	72.20
	lacZ	534	50	25.91	10.68	17.16	28.90
	thi	91	47	24.35	1.940	0.050	4.000
	rel	523	47	24.35	11.13	20.68	36.36
	recA	82	39	20.21	2.100	1.810	0.5000
	rpsL	95	36	18.65	2.640	3.530	4.500
	thr	84	36	18.65	2.330	3.760	4.500
	rpsG	103	34	17.62	3.030	7.250	16.33
	leu	98	34	17.62	2.880	6.800	18.00
	rpoS	205	33	17.10	6.210	10.83	16.67
	kan	308	33	17.10	9.330	16.61	28.44
	glnV	42	31	16.06	1.350	0.7400	0
	rpoB	389	30	15.54	12.97	17.60	24.08
	ptsG	240	30	15.54	8.000	21.54	55.13
	trp	144	25	12.95	5.760	14.73	39.20
	carA	60	20	10.36	3.000	3.810	3.000
	hsdR	23	19	9.840	1.210	0.5600	0
DNAs	DNA	1839	137	70.98	13.42	16.31	19.69
	plasmid DNA	193	36	18.65	5.360	12.31	28.80
	chromosomal DNA	63	24	12.44	2.630	2.440	2.000
	cDNA	125	23	11.92	5.430	5.820	5.000
RNAs	RNA	4193	140	72.54	29.95	38.21	49.79
	uncharged tRNA	1168	117	60.62	9.980	19.64	40.11
	rRNA	1116	97	50.26	11.51	25.97	56.82
	a mRNA	999	91	47.15	10.98	19.52	36.10
	rrnA	911	87	45.08	10.47	22.51	48.40
	stable RNA	430	87	45.08	4.940	8.030	16.00
	a charged tRNA	140	43	22.28	3.260	4.200	5.330
	rrnB	301	26	13.47	11.58	19.30	32.82
	rrn	321	26	13.47	12.35	30.42	75.00
	16s-rRNAs	156	25	12.95	6.240	9.090	13.50

Individual genetic components (i.e. genes, DNAs and RNAs) were evaluated considering the number of documents where these entities were annotated and their number of annotations in the corpus. Statistical measurements are detailed in the Methods and Materials section.
^ψ A threshold of 10% of the frequency of annotation was set for each genetic component category. However, lists of all annotated entities are provided in Additional file 5.
VMR: variance-to-mean
Std: standard deviation