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Table 4 Genes significantly up-regulated in E. coli O157:H7 EDL933 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 (Z #) Gene name Mean of normalized counts FCa adj. p b Function or product
Antibiotic resistance
2169 marB 78 2.6 8.2E-06 Conserved hypothetical protein associated with multiple antibiotic resistance operon
2170 marA 133 2.1 2.1E-05 DNA-binding transcriptional dual activator of multiple antibiotic resistance
Response to stress
2478 pspD 74 2.6 2.2E-05 Peripheral inner membrane phage-shock protein
Hypothetical proteins
1402 ymcB 102 2.1 0.0004 Conserved hypothetical protein
2695 ydhS 1115 2.0 0.0001 Conserved hypothetical protein; putative FAD/NAD(P)-binding domain
2774 ydjR 206 2.3 0.0004 Conserved hypothetical protein
3175 yeeE 143 2.8 1.7E-07 Conserved hypothetical protein; putative inner membrane protein
5712 yjcZ 173 2.1 0.0002 Conserved hypothetical protein
Other up-regulated genes
0043 caiC 204 2.0 0.0005 Putative crotonobetaine CoA ligase:carnitine CoA ligase
1987 ldrB 176 2.0 0.001 Fragment of small toxic polypeptide (partial)
3266 yegX 100 2.3 0.0002 Putative membrane-bound hydrolase
3660 yfeA 3551 2.0 2.9E-05 Putative diguanylate cyclase
  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 8: Table S8)
  2. bAdjusted p-value for multiple testing with the Benjamini-Hochberg procedure which controls FDR