Probiotic bacteria change Escherichia coli-induced gene expression in cultured colonocytes: Implications in intestinal pathophysiology

Table 2 Modulation of gene expression during mixed (E. coli and L. plantarum) infection

Biological process	Gene symbol	Gene ID NCBI	Gene name	Fold change
Category 1: Regulation of transcription	HOXD10	3236	Homeobox D10	2.50
	PHF7	51533	PHD finger protein 7 (Zinc ion binding)	2.44
	EGR1	1958	Early growth response 1	-2.08
	TRIM24	8805	Tripartite motif-containing 24 (Zinc ion and DNA binding)	-2.15
	ENO1	2023	Enolase 1, (alpha) (DNA binding)	-2.34
Category 2: RNA processing	SSB	6741	Sjogren syndrome antigen B (autoantigen La)	-2.08
	FUSIP1	10772	FUS interacting protein (serine/arginine-rich) 1	-2.21
	NOLA5	10528	Nucleolar protein 5A (56 kDa with KKE/D repeat)	-2.27
	DDX5	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	-2.71
Category 3: Protein biosynthesis, folding, binding and transport	NEURL	9148	Neuralized homolog (Intracellular protein transport)	2.91
	WDR36	134430	WD repeat domain 36	2.37
	MTFMT	123263	Mitochondrial methionyl-tRNA formyltransferase	2.04
	ARF4	378	ADP-ribosylation factor 4	-2.03
	CEP57	9702	Centrosomal protein 57 kDa	-2.11
	ETF1	2107	Eukaryotic translation termination factor 1	-2.27
	HSPA1A	3303	Heat shock 70 kDa protein 1A	-2.28
	LGALS3	3958	Lectin, galactoside-binding, soluble, 3 (galectin 3)	-2.75
	HSPH1	10808	Heat shock 105 kDa/110 kDa protein 1	-2.93
	HSPA8	3312	Heat shock 70 kDa protein 8	-2.97
Category 4: Structural protein	AMPH	273	Amphiphysin (Actin cytoskeleton)	3.04
	MAP1B	4131	Microtubule-associated protein 1B	2.13
	ABCC10	89845	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	-2.05
	SLC26A2	1836	Solute carrier family 26 (sulfate transporter), member 2	-2.06
	TUBB2A	7280	Tubulin, beta 2A	-2.15
Category 5: Metabolism	C5orf14	79770	Chromosome 5 open reading frame 14	2.91
	NAV2	89797	Neuron navigator 2	2.83
	SLC24A4	123041	Solute carrier family 24 (sodium/potassium/calcium), member 4	2.35
	PLEKHM2	23207	Pleckstrin homology domain containing, family M, member 2	2.10
	TWF1	5756	Twinfilin, actin-binding protein, homolog 1 (Tyrosin kinase)	-2.01
	AKR1C1	1645	Aldo-keto reductase 1, member C1 (Bile acid binding)	-2.09
	HMGCR	3156	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	-2.10
	DC2	58505	DC2 protein (Glycotransferase activity)	-2.12
	GSTA1	2938	Glutathione S-transferase A1	-2.15
	GAPD	2597	Glyceraldehyde-3-phosphate dehydrogenase	-2.16
	GCLC	2729	Glutamate-cysteine ligase, catalytic subunit	-2.21
	SRM	6723	Spermidine synthase	-2.39
	HSP90AA1	3320	Heat shock protein 90 kDa alpha (cytosolic), class A member 1	-2.46
	AHCY	191	S-adenosylhomocysteine hydrolase	-2.48
	MAT2A	4144	Methionine adenosyltransferase II, alpha	-2.74
Category 6: Cell physiology	NCF4	4689	Neutrophil cytosolic factor 4, 40 kDa	2.39
	CYCS	54205	Cytochrome c, somatic	-2.02
	DBI	1622	GABA receptor modulator, acyl-Coenzyme A binding protein	-2.25
	ATP5G3	518	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3	-2.26
	HSPA1L	3305	Heat shock 70 kDa protein 1-like	-2.26
Category 7: Cell proliferation	FOSL1	8061	FOS-like antigen 1 (transcription factor activity)	-2.09
	FGG	2266	Fibrinogen gamma chain	-2.36
	FGG	2244	Fibrinogen beta chain	-2.45
Category 8: Cell adhesion	NELL2	4753	NEL-like 2 (Calcium ion binding)	2.25
	ITGB3	3690	Integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	2.11
	RHOB	388	Ras homolog gene family, member B	-2.19
	ADRM1	11047	Adhesion regulating molecule 1	-2.25
Category 9: Ubiquitination	UBE2N	7334	Ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)	-2.02
	UBE2S	27338	Ubiquitin-conjugating enzyme E2S	-2.05
	ANAPC7	51434	Anaphase promoting complex subunit 7	-2.15
	CACYBP	27101	Calcyclin binding protein	-2.18
	UBA52	7311	Ubiquitin A-52 residue ribosomal protein fusion product 1	-2.29
	COL6A3	1293	Collagen, type VI, alpha 3	2.33
	RPS3A	6189	Ribosomal protein S3A	-2.08
	TWF1	5756	Twinfilin, actin-binding protein, homolog 1 (Tyrosin kinase)	-2.01
	AKR1C1	1645	Aldo-keto reductase 1, member C1 (Bile acid binding)	-2.09

Negative value indicates reduction in gene expression.