S1 File. This file contains the following sections:
- Selection of a similarity measure to quantify coexpression
- Rank-based similarity measures compensate for conditional dependency
- The degree of coexpression of genes that are coregulated in E. coli is generally low
- Evidence of horizontal gene co-transfer in genes with strong distance conservation (https://doi.org/10.1371/journal.pone.0174887.s001)
S1 Table. List of TFs that control the pairs of coregulated genes used in this study. This
table shows all TFs considered in our analysis with at least one pair of coregulated genes (see
Materials and methods for the definition of coregulated genes). For each TF we showed the
number of pairs of genes coregulated by that TF, the mean distance between every two genes
in a pair (in base pairs), and the mean coexpression (as measured by SCR). (https://doi.org/10.1371/journal.pone.0174887.s002)
S2 Table. List of so-called non-coregulated genes that are potentially coregulated as
derived from SELEX. This table shows an excerpt of pairs of genes that belong to the negative
control of genes not known to be coregulated but highly coexpressed and located nearby and
that were predicted to be coregulated according to SELEX. Gene 1 and gene 2 correspond to a
pair of genes selected from the set of so-called non-coregulated genes with selection criteria 1)
small distance (< 10 kb) 2) high degree of coexpression (SCR<10) and 3) at least one common
TF in their respective set of TFs as predicted by SELEX. The coexpression degree between gene
1 and gene 2 is given in SCR. One or more predicted common TF(s) was (were) given. The
numbers between brackets refer to the Nth best hit (which means Nth highest % similarity of
that TF for that gene) that TF was for respectively gene 1 and gene 2. (https://doi.org/10.1371/journal.pone.0174887.s003)
S3 Table. List of all coregulated genes with their genomic distances and coexpression
degrees. This table contains the following fields: TF (coregulating TF), gene 1 (first gene in the
pair), gene 2 (second gene in the pair), distance (genomic distance between gene 1 and gene 2),
TF-gene1_distance (genomic distance between the TF and the first gene), TF-gene2_distance
(genomic distance between the TF and the second gene), role (a = activator, r = repressor,
d = dual), SCR (Spearman Correlation Rank as a measure of coexpression degree). (https://doi.org/10.1371/journal.pone.0174887.s004)