Parallel mRNA, proteomics and miRNA expression analysis in cell line models of the intestine

Table 3 Overlap of DE genes, proteins, microRNAs with other HT-29/Caco-2 profiling studies

Identifier	Symbol	Description/Family	LinFC	P value	Overlapping study	Dataset
hsa-miR-196a_st	hsa-miR-196a	miR-196abc	-5.06	8.53E-05	88	microRNA
hsa-let-7a_st	hsa-let-7a	let-7/98/4458/4500	-2.72	6.34E-04	57
hsa-miR-10a_st	hsa-miR-10a	miR-10abc/10a-5p	-46.76	7.40E-06	57
hsa-miR-98_st	hsa-miR-98_st	miR-98	-11.90	4.50E-06	57
P17931	LGALS3	Galectin-3	2.09	1.10E-03	89; 90	Protein
P06576	ATP5B	ATP synthase subunit beta, mitochondrial	2.07	1.20E-03	89
P27797	CALR	Calreticulin	1.62	3.35E-02	89
P23528	CFL1	Cofilin-1	1.53	5.94E-03	89
P07858	CTSB	Cathepsin B	5.15	5.36E-05	89
P06733	ENO1	Alpha-enolase	2.06	4.65E-03	89
P22626	HNRNPA2B1	Heterogeneous nuclear ribonucleoproteins A2/B1	1.72	9.62E-03	89
P61978	HNRNPK	Heterogeneous nuclear ribonucleoprotein K	1.38	4.38E-04	89
P14866	HNRNPL	Heterogeneous nuclear ribonucleoprotein L	1.69	4.02E-03	89
P05787	KRT8	Keratin, type II cytoskeletal 8	2.21	1.81E-03	89
P07237	P4HB	Protein disulfide-isomerase	1.41	3.49E-03	89
P30101	PDIA3	Protein disulfide-isomerase A3	1.84	7.49E-05	89
P18669	PGAM1	Phosphoglycerate mutase 1	1.93	1.42E-04	89
P12429	ANXA3	Annexin A3	2.53	1.55E-06	90
P19338	NCL	Nucleolin	2.74	4.80E-03	90
P06748	NPM1	Nucleophosmin	1.51	1.15E-02	90
Q00796	SORD	Sorbitol dehydrogenase	4.21	7.73E-05	90
16779311	ATP7B	ATPase, Cu++ transporting, beta polypeptide	3.60	1.57E-05	91; 92	Gene
16823109	ABCA3	ATP-binding cassette, sub-family A (ABC1), member 3	10.07	1.75E-05	91
17059491	ABCB1	ATP-binding cassette, sub-family B (MDR/TAP), member 1	36.64	2.14E-06
16701957	AKR1E2	aldo-keto reductase family 1, member E2	4.56	1.09E-05
17005368	ALDH5A1	aldehyde dehydrogenase 5 family, member A1	3.38	4.08E-06
16794632	ALDH6A1	aldehyde dehydrogenase 6 family, member A1	2.27	7.54E-05
17067102	CDCA2	carboxylesterase 1	2.32	2.28E-03
16889762	CYP20A1	cytochrome P450, family 20, subfamily A, polypeptide 1	2.78	8.71E-04
16891082	CYP27A1	cytochrome P450, family 27, subfamily A, polypeptide 1	20.68	2.05E-06
17067284	EPHX2	epoxide hydrolase 2, cytoplasmic	6.51	3.62E-06
17020103	GSTA4	glutathione S-transferase alpha 4	2.25	4.04E-04
16877728	NCOA1	nuclear receptor coactivator 1	2.99	7.90E-04
16675638	NR5A2	nuclear receptor subfamily 5, group A, member 2	2.33	1.73E-03
16959797	RBP2	retinol binding protein 2, cellular	27.20	2.06E-06
16780481	SLC15A1	solute carrier family 15 (oligopeptide transporter), member 1	20.05	1.95E-06
16909257	SLC19A3	solute carrier family 19 (thiamine transporter), member 3	35.13	6.97E-08
16984056	SLC1A3	solute carrier family 1 (glial high affinity glutamate transporter), member 3	50.97	1.62E-07
16989018	SLC22A5	solute carrier family 22 (organic cation/carnitine transporter), member 5	2.21	5.49E-04
16843078	SLC6A4	solute carrier family 6 (neurotransmitter transporter), member 4	9.33	1.33E-06
16820398	SLC7A6	solute carrier family 7 (amino acid transporter light chain, y+L system), member 6	4.71	5.00E-06
16790744	SLC7A8	solute carrier family 7 (amino acid transporter light chain, L system), member 8	11.99	4.99E-06
16729064	SLCO2B1	solute carrier organic anion transporter family, member 2B1	10.15	8.38E-06
16998551	SLCO4C1	solute carrier organic anion transporter family, member 4C1	11.95	2.59E-03
16884050	SULT1C4	sulfotransferase family, cytosolic, 1C, member 4	15.89	2.49E-07
16951567	THRB	thyroid hormone receptor, beta	4.38	1.90E-04
17068541	VDAC3	voltage-dependent anion channel 3	2.28	3.11E-04

List of 49 gene, protein and miRNA annotated candidates (6 microRNAs, 17 proteins, 26 genes) which are differentially expressed between the HT-29 and Caco-2 cell lines in this and other published profiling studies that combine both cell lines.