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Table 7 Correspondence between the functional annotations of predicted genes and of known genes.

From: Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coliK12 DNA

Regulon Consensus/Patser Dyad-analysis/sweeping
  Percent with related function Percent without functional annotation Percent with related function Percent without functional annotation
AraC 73.33 (66.67) 37.50 (42.86) 53.75 (51.32) 36.51 (37.70)
ArcA 72.61 (70.75) 45.86 (47.50) 74.07 (70.83) 40.88 (43.75)
ArgR 100.00 (100.00) 18.18 (33.33) 56.25 (36.36) 51.52 (60.71)
CRP 93.90 (93.38) 40.87 (43.63) - -
CysB 56.78 (56.56) 43.03 (43.16) - -
CytR 53.90 (53.58) 38.56 (38.72) - -
FIS 45.52 (45.11) 41.23 (41.28) - -
FNR 82.85 (81.99) 45.85 (47.06) 83.77 (83.43) 41.43 (41.92)
FruR 51.96 (51.29) 36.57 (36.89) - -
IHF 80.95 (80.33) 46.34 (47.14) - -
LexA 69.70 (61.54) 42.11 (48.00) 65.79 (58.06) 38.71 (43.64)
Lrp 82.61 (81.95) 43.67 (44.58) - -
NarL 73.38 (72.11) 45.20 (46.35) - -
PurR 95.24 (92.31) 8.70 (7.14) 77.14 (70.37) 22.22 (25.00)
TrpR 85.71 (50.00) 30.00 (60.00) 46.94 (40.91) 42.35 (45.00)
TyrR 69.23 (50.00) 18.75 (27.27) 73.68 (61.54) 32.14 (40.91)
  1. A comparison between the functional annotations of genes known to be regulated by a given protein and the functional annotations of the predicted set of genes. The percentage with related function is calculated against all the genes with functional annotations, while the percentage without functional annotations is calculated against the whole set of predicted genes. The number in parentheses excludes genes known to be part of the corresponding regulon. In cases with high correlation of functional annotations we can propose a related function for genes without functional annotations, as in the Consensus/Patser predictions of ArgR, CRP and PurR (all with correspondences above 90%). Detailed tables are provided as Additional data files.