Factors Influencing the Identification of Transcription Factor Binding Sites by Cross-Species Comparison

Table 2.

Orthologous Data for Each Species

Species Study set orthologs TF orthologs Mean % identity of intergenic regions
Escherichia coli 166 48 100
Salmonella typhi 161 46 70.0 ± 12.4
Yersinia pestis 138 40 48.1 ± 7.9
Buchnera sp. 27 1 39.6 ± 3.4
Haemophilus influenzae 72 21 41.5 ± 4.9
Vibrio cholerae 112 31 41.6 ± 6.0
Shewanella oneidensis 91 24 41.1 ± 5.0
Pseudomonas aeruginosa 92 25 37.7 ± 3.7
Acidithiobacillus ferrooxidans 46 11 39.2 ± 3.7
Xylella fastidiosa 50 7 38.7 ± 3.4

  • ↵Transcription factors (TF) that regulate expression of the study set genes in E. coli.

  • ↵GAP (GCG Wisconsin Package version 10.2) was used to calculate the % identity (relative to E. coli) of the available orthologous intergenic sequences.

This Article

  1. Published in Advance September 13, 2002, doi: 10.1101/gr.323602 Genome Res. 12: 1523-1532

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