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Table 3 Genes significantly up-regulated in Escherichia coli O26:H11 21,765 in samples with microbiota compared to those without microbiota

From: Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat

Locus (ECO26H_v1_ #) Gene name Mean of normalized counts FCa adj. p b Function or product
Unknown or hypothetical proteins
260022 ymgB 101 2.1 0.0001 Hypothetical protein
310027 ydfP 34 2.5 0.003 Conserved hypothetical protein; Qin prophage
340082 ydhS 506 2.0 0.0002 Conserved hypothetical protein; putative FAD/NAD(P)-binding domain
400008 yecT 105 2.1 0.0002 Hypothetical protein
420013 yeeE 55 2.3 0.001 Conserved hypothetical protein; putative inner membrane protein
50014 _ 102 2.1 0.002 Conserved protein of unknown function
510037 _ 162 2.5 3.6E-06 Protein of unknown function
590009 _ 61 2.1 0.004 Conserved protein of unknown function
p40014 _ 591 2.0 0.0002 Conserved protein of unknown function
Other up-regulated genes
250005 _ 48 2.3 0.001 T3SS secreted effector NleG-like protein
270179 ydcX 105 2.3 8.8E-06 Putative inner membrane protein
500243 yfhR 250 2.0 7.1E-05 Putative peptidase
50040 yhhI 106 2.1 0.0007 Putative transposase
p40035 _ 99 2.3 0.0002 Pilus assembly protein
  1. aFC is the fold change of the genes that exhibit significant (FC ≥ 2, false discovery rate (FDR) ≤ 0.005, minimum normalized read count = 10) differential expression. Only genes passed the filter are shown on this table. Expected genes to be differentially expressed due to the possibility of spurious alignment, and crosstalk between the reference genome and other similar genomes identified at genus level by 16S meta-genomic analysis, were discarded from this study (For discarded genes see Additional file 6: Table S6)
  2. bAdjusted p-value for multiple testing with the Benjamini-Hochberg procedure which controls FDR