Identification of differentially expressed genes in ulcerative colitis and verification in a colitis mouse model by bioinformatics analyses

Table 1 Sequences of primers

Gene	Sequence, 5’ to 3’
β-actin	Forward: GAGATTACTGCTCTGGCTCCTA
	Reverse: GGACTCATCGTACTCCTGCTTG
CXCL13	Forward: CCCAACCCACATCCTTGTTCCTT
	Reverse: CTGAAGTCCATCTCGCAAACCTCT
NPY1R	Forward: CCAGTGAGACCAAGCGAATCAACA
	Reverse: GCGGTGAGGTGACAGAGCAGAA
CXCR2	Forward: ATGGTGGAACTTGTGGCTCTAGC
	Reverse: CCATTCCTGGTCCTGGCATTCC

CXCL13: C-X-C motif chemokine ligand 13; NPY1R: Neuropeptide Y receptor Y1; CXCR2: C-X-C motif chemokine receptor 2.

Table 2 Top three enriched terms in the respective categories of upregulated differentially expressed genes identified in ulcerative colitis (P < 0.05)

Category	Term	Count	Genes
BP	Defense response (GO: 0006952)	40	CXCL1, KYNU, S100A8, FGR, C3, CXCL3, CXCL2, S100A9, CXCL9, CXCR2, CXCL6, DEFB4A, CXCL11, CXCL10, REG3A, SERPINA3, CSF3R, VNN1, IL1B, LTF, SERPINA1, CFI, SPP1, SELP, CR1, PDPN, CFB, IL1RN, C4BPB, IDO1, CCL18, S100A12, LILRB2, TNFAIP6, PROK2, DEFA6, CXCL13, DEFA5, PLA2G2D, DMBT1.
BP	Inflammatory response (GO: 0006954)	31	CXCL1, S100A8, C3, CXCL3, CXCL2, S100A9, CXCL9, CXCR2, CXCL6, CXCL11, CXCL10, REG3A, SERPINA3, VNN1, IL1B, SERPINA1, CFI, SPP1, SELP, CR1, PDPN, CFB, IL1RN, C4BPB, IDO1, CCL18, S100A12, TNFAIP6, PROK2, CXCL13, PLA2G2D.
BP	Response to wounding (GO: 0009611)	33	CXCL1, S100A8, C3, TNC, CXCL3, CXCL2, S100A9, CXCL9, CXCR2, CXCL6, CXCL11, CDH3, CXCL10, REG3A, SERPINA3, VNN1, IL1B, SERPINA1, CFI, SPP1, SELP, CR1, PDPN, CFB, IL1RN, C4BPB, IDO1, CCL18, S100A12, TNFAIP6, PROK2, CXCL13, PLA2G2D.
CC	Extracellular region (GO: 0005576)	55	REG4, MMP9, MMP7, CXCL11, MMP3, MMP1, CXCL10, REG3A, SERPINA3, CSF3R, IL1B, LTF, SERPINA1, KLK10, CFI, FCGR3B, CYR61, IL13RA2, EGFL6, IL24, TCN1, MMP12, MMP10, PROK2, GZMK, DEFA6, SERPINB5, DEFA5, STC1, PLA2G2D, CXCL1, CXCL5, C3, CXCL3, TNC, CXCL2, CXCL9, CXCL6, DEFB4A, GREM1, TIMP1, THBS2, OLFM1, SPP1, SELP, CFB, IL1RN, CHI3L1, CHI3L2, C4BPB, CCL18, LCN2, CXCL13, PI3, DMBT1.
CC	Extracellular region part (GO: 0044421)	38	CXCL1, CXCL5, C3, MMP9, TNC, CXCL3, CXCL2, MMP7, CXCL9, CXCL6, CXCL11, MMP3, GREM1, MMP1, CXCL10, TIMP1, REG3A, IL1B, SERPINA1, CFI, OLFM1, SPP1, IL13RA2, SELP, EGFL6, IL1RN, CHI3L1, CHI3L2, IL24, CCL18, MMP12, MMP10, SERPINB5, DEFA6, CXCL13, DEFA5, PI3, STC1.
CC	Extracellular space (GO: 0005615)	33	CXCL1, CXCL5, C3, MMP9, CXCL3, CXCL2, MMP7, CXCL9, CXCL6, GREM1, CXCL11, MMP3, CXCL10, REG3A, IL1B, SERPINA1, CFI, OLFM1, IL13RA2, SPP1, SELP, EGFL6, IL1RN, CHI3L1, CHI3L2, IL24, CCL18, MMP10, SERPINB5, DEFA6, CXCL13, DEFA5, STC1.
MF	Cytokine activity (GO: 0005125)	16	CXCL1, NAMPT, CXCL5, CXCL3, IL1RN, CXCL2, CXCL9, CXCL6, IL24, GREM1, CXCL11, CCL18, CXCL10, CXCL13, IL1B, SPP1.
MF	Chemokine activity (GO: 0008009)	10	CXCL1, CXCL5, CXCL13, CXCL3, CXCL2, CXCL9, CXCL6, CXCL11, CCL18, CXCL10.
MF	Chemokine receptor binding (GO: 0042379)	10	CXCL1, CXCL5, CXCL13, CXCL3, CXCL2, CXCL9, CXCL6, CXCL11, CCL18, CXCL10.

MF: Molecular function; CC: Cellular component; BP: Biological process.

Table 3 Top three enriched terms in the respective categories of downregulated differentially expressed genes identified in ulcerative colitis (P < 0.05)

Category	Term	Count	Genes
BP	Transmembrane transport (GO: 0055085)	9	TRPM6, SLC23A1, SLC16A1, SLC25A34, SLC17A4, ABCB1, AQP7, SLC30A10, SLC26A2.
BP	Carboxylic acid transport (GO: 0046942)	5	SLC38A4, SLC23A1, SLC16A1, AQP8, SLC3A1.
BP	Organic acid transport (GO: 0015849)	5	SLC38A4, SLC23A1, SLC16A1, AQP8, SLC3A1.
CC	Cell fraction (GO: 0000267)	12	HSD3B2, SLC23A1, SLC16A1, AQP8, SLC17A4, CYP2B6, MEP1B, ABCB1, ANPEP, SLC3A1, SLC26A2, PCK1.
CC	Membrane fraction (GO: 0005624)	10	HSD3B2, SLC23A1, SLC16A1, AQP8, SLC17A4, CYP2B6, MEP1B, ABCB1, SLC3A1, SLC26A2.
CC	Insoluble fraction (GO: 0005626)	10	HSD3B2, SLC23A1, SLC16A1, AQP8, SLC17A4, CYP2B6, MEP1B, ABCB1, SLC3A1, SLC26A2.
MF	Symporter activity (GO: 0015293)	4	SLC38A4, SLC23A1, SLC16A1, SLC17A4.
MF	Xenobiotic-transporting ATPase activity (GO: 0008559)	2	ABCB1, ABCG2.
MF	Multidrug transporter activity (GO: 0015239)	2	ABCB1, ABCG2.

MF: Molecular function; CC: Cellular component; BP: Biological process.

Table 4 Enriched terms in the Kyoto Encyclopedia of Genes and Genomes pathways for differentially expressed genes identified in ulcerative colitis (P < 0.05)

Pathway ID	Term	Genes
hsa04062	Chemokine signaling pathway	CXCL1, FGR, CXCL5, CXCL3, CXCL2, CXCL9, CXCR2, CXCL6, CXCL11, CCL18, CXCL10, CXCL13, JAK3.
hsa04060	Cytokine-cytokine receptor interaction	CXCL1, CXCL5, CXCL3, CXCL2, CXCL9, CXCR2, CXCL6, IL24, CXCL11, CCL18, CXCL10, CXCL13, CSF3R, IL1B.
hsa04610	Complement and coagulation cascades	CR1, C3, CFB, C4BPB, SERPINA1, CFI.
hsa04514	Cell adhesion molecules	SELP, SELL, CD274, CTLA4, CLDN2, CDH3.
hsa00830	Retinol metabolism	CYP2B6, ADH1C, UGT2A3.
hsa00980	Metabolism of xenobiotics by cytochrome P450	CYP2B6, ADH1C, UGT2A3.
hsa04620	Toll-like receptor signaling pathway	CXCL9, IL1B, CXCL11, SPP1, CXCL10.
hsa00982	Drug metabolism	CYP2B6, ADH1C, UGT2A3.
hsa03320	PPAR signaling pathway	HMGCS2, AQP7, PCK1.

PPAR: Peroxisome proliferator-activated receptor.

Table 5 Repeated Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of 18 core genes in the first cluster (P < 0.05)

Category	Term	Count, %	Genes
KEGG pathway	hsa04060, cytokine-cytokine receptor interaction.	12, 6.06	CXCL1, CXCL5, CXCL13, CXCL3, CXCL2, CXCL9, IL1B, CXCR2, CXCL6, CXCL11, CCL18, CXCL10.
KEGG pathway	hsa04062, chemokine signaling pathway.	11, 5.56	CXCL1, CXCL5, CXCL13, CXCL3, CXCL2, CXCL9, CXCR2, CXCL6, CXCL11, CCL18, CXCL10.
KEGG pathway	hsa04620, toll-like receptor signaling pathway.	4, 2.02	CXCL9, IL1B, CXCL11, CXCL10.
KEGG pathway	hsa04621, NOD-like receptor signaling pathway.	3, 1.52	CXCL1, CXCL2, IL1B.

KEGG: Kyoto Encyclopedia of Genes and Genomes.