Table 1.

Summary of top 20 genes with expression upregulated in wild type strain 110.58 by exposure to ORF 2 ligand peptide FPPQSV

Gene number	Gene name	Function	Ratioa	q
SpnNT_02141		tRNA-Phe	infiniteb	0.03
SpnNT_02309		tRNA-Asn	infiniteb	0.03
SpnNT_01742	afr	1,5-anhydro-D-fructose reductase	20.2	0.001
SpnNT_01743	nanB	Sialidase	11.9	0.001
SpnNT_01746	yesO_2	Putative ABC transporter for carbohydrate	10.1	0.001
SpnNT_01745	ycjO	Putative ABC transporter for carbohydrate	7.5	0.001
SpnNT_01744	ycjP	Putative ABC transporter for carbohydrate	7.5	0.001
SpnNT_00088	sorB_1	Sorbose-specific phosphotransferase enzyme IIB component	6.6	0.04
SpnNT_01738	yesO_1	Putative ABC transporter for carbohydrate	6.3	0.001
SpnNT_01747	tabA	Toxin-antitoxin biofilm protein TabA	6.2	0.001
SpnNT_01751	nanA_3	Sialidase	5.3	0.001
SpnNT_01537		CsbD-like protein, general stress response protein	4.6	0.001
SpnNT_01944		tRNA-Leu	4.5	0.005
SpnNT_00467	grpE	HSP-70 cofactor, heat shock protein	4.4	0.001
SpnNT_01021	pyrP	Uracil transporter	4.2	0.001
SpnNT_00091	manX_1	EIIAB-Man, carbohydrate transport	4.1	0.001
SpnNT_00092	agaS	Putative tagatose-6-phosphate ketose/aldose isomerase	4.1	0.001
SpnNT_00089	agaC_1	PTS system N-acetylgalactosamine-specific EIIC component 1	4.1	0.001
SpnNT_02080	adhE	Aldehyde-alcohol dehydrogenase	4.1	0.001
SpnNT_01032	pyrR	Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase	3.8	0.001

Genes names in bold indicate an association with carbohydrate metabolism or uptake. For the complete dataset for the wild type and ΔORF 2 mutant see Additional files 2: Table S1, Additional file 3: Table S2, Additional file 4: Table S3, Additional file 5: Table S4

^aRatio represents the fold increase in the expression of genes in the presence of peptide FPPQSV compared to in its absence

^bExpression in the absence of peptide was 0 so fold increase in the presence of peptide could not be calculated