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

Table 2 Annotations of the gene products in the corpus.

Class	Concept	Number of Annotations	Number of Documents	% Frequency (Eq. 1)^ψ	Mean (Eq. 2)	Std (Eq. 3)	VMR (Eq. 4)
Proteins	Ribosome	1643	128	66.32	12.84	23.57	44.08
	Rel	1021	62	32.12	16.50	36.60	81.00
	LacZ	543	53	27.46	10.30	17.44	28.90
	Sigma 38 factor	392	42	21.76	9.330	15.40	25.00
	Sigma factor	112	35	18.13	3.200	5.870	8.330
	UvrD	56	35	18.13	1.600	1.300	1.000
	RpoB	252	35	18.13	7.200	11.50	17.29
	RecA	99	31	16.06	3.190	4.260	5.330
	EF-Tu	223	26	13.47	8.580	17.32	36.13
	Der	51	25	12.95	2.040	2.140	2.000
	Sigma 70 factor	134	21	10.88	6.380	11.19	20.17
Transcription factors	Fis	888	18	9.330	49.33	86.88	150.9
	Fur	56	13	6.740	4.310	9.260	20.25
	CRP	279	12	6.220	23.25	36.28	56.35
	DnaA	121	11	5.700	11.00	23.00	48.09
	H-NS	73	11	5.700	6.640	10.73	16.67
	LexA	101	10	5.180	10.10	18.32	32.40
	IHF	54	9	4.660	6.000	5.250	4.170
Enzymes	RelA	4138	152	78.76	27.22	31.16	35.59
	RNAP	1873	117	60.62	16.01	28.08	49.00
	SpoT	1024	60	31.09	17.07	42.19	103.8
	EcoRI	215	53	27.46	4.060	4.970	4.000
	β-galactosidase	294	47	24.35	6.260	6.550	6.000
	BamHI	149	43	22.28	3.470	5.870	8.330
	HindIII	114	41	21.24	2.780	2.160	2.000
	RNase	109	36	18.65	3.030	4.280	5.330
	YbcS	50	23	11.92	2.170	2.620	2.000
	Reverse transcriptase	34	21	10.88	1.620	1.050	1.000
	tRNA synthetase	54	20	10.36	2.700	2.630	2.000
	Endonuclease I	29	20	10.36	1.450	1.400	1.000

Individual gene products (i.e. enzymes, transcription factors and other proteins) 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 enzymes and other proteins, whereas a threshold of 5% was set for transcription factors. However, lists of all annotated entities are provided in Additional file 6.
VMR: variance-to-mean
Std: standard deviation