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. 2018 Apr 3;8:5550. doi: 10.1038/s41598-018-23858-6

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Gene expression profiles in presence or absence of ICEclc. (A) Log2–fold change of gene expression between P. putida with ICEclc (strain 2737) and that with clc genes only (strain 3227) in exponential (upper) and REG phase (lower). Only genes with an a.value (mean expression values, calculated using the trimmed mean of M values (TMM) normalization method) >4.0 are plotted, according to their positions on the chromosome. Differentially expressed genes with a q-value < 0.05 are coloured in red. (B) Pathway activity in the presence/absence of ICEclc. Activities were inferred from significantly induced or repressed KEGG Pathways identified for each dataset comparison (p < 0.05 in two-tailed Welch t test). Blue/red blocks indicate pathways (rows) that are up/down regulated in quadruplicate samples (columns) of specific strains and growth phases (top). Pathways are clustered based on the similarity of their activities across samples. (C) Venn diagram showing overlap among differentially expressed genes (DEGs) among transcriptome datasets. The intersection shows the DEGs at a q-value < 0.05 that were common to both comparisons and with the same direction of expression change.