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

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

Locus (ECO26H_v1_ #)	Gene name	Mean of normalized counts	FC^a	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

^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)
^bAdjusted p-value for multiple testing with the Benjamini-Hochberg procedure which controls FDR

ISSN: 1471-2164