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. 2011 Dec 30;1:14. doi: 10.1186/2042-5783-1-14

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