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

Table 1 Twenty-seven downregulated proteins with no DE mRNA targeted by 19 upregulated miRNAs

Protein					microRNA
Uniprot	Symbol	Title	Linear FC	Adj. P value	miRBase ID	logFC	LinFC	AveExpr	P value	Adj. P value
Q09666	AHNAK	Neuroblast differentiation-associated protein AHNAK	1.66	0.02036	hsa-miR-30b	1.39	2.62	10.38	5.04E-04	0.011296975
					hsa-miR-30d	1.36	2.56	11.05	1.17E-04	0.003668745
					hsa-miR-372	12.21	4743.91	7.03	6.55E-11	2.27E-07
					hsa-miR-373	12.12	4451.32	7.23	2.25E-11	1.88E-07
P04075	ALDOA	Fructose-bisphosphate aldolase A	2.03	0.00001	hsa-miR-122	5.85	57.63	5.04	3.71E-05	0.001621788
P50995	ANXA11	Annexin A11	4.57	0.00012	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
Q14444	CAPRIN1	Caprin-1	1.42	0.00658	hsa-miR-28-5p	1.16	2.24	9.32	7.05E-05	0.002531521
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
					hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
P23528	CFL1	Cofilin-1	1.53	0.00962	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
P62633	CNBP	Cellular nucleic acid-binding protein	1.79	0.00064	hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
Q14247	CTTN	Src substrate cortactin	1.33	0.00716	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
P68104	EEF1A1	Elongation factor 1-alpha 1	1.46	0.01148	hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
P06733	ENO1	Alpha-enolase	2.06	0.00015	hsa-miR-22	1.96	3.9	10.84	1.01E-04	0.003309338
Q96AE4	FUBP1	Far upstream element-binding protein 1	2.17	0.00290	hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
P22626	HNRNPA2B1	Heterogeneous nuclear ribonucleoproteins A2/B1	1.72	0.00053	hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
Q00839	HNRNPU	Heterogeneous nuclear ribonucleoprotein U	4.51	0.00152	hsa-miR-92b	1.22	2.33	6.95	4.51E-04	0.010275397
					hsa-miR-122	5.85	57.63	5.04	3.71E-05	0.001621788
P31153	MAT2A	S-adenosylmethionine synthase isoform type-2	1.92	0.00023	hsa-miR-30b	1.39	2.62	10.38	5.04E-04	0.011296975
					hsa-miR-30d	1.36	2.56	11.05	1.17E-04	0.003668745
Q15233	NONO	Non-POU domain-containing octamer-binding protein	2.74	0.00522	hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
P06748	NPM1	Nucleophosmin	1.51	0.01869	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
P30101	PDIA3	Protein disulfide-isomerase A3	1.84	0.00465	hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
P13667	PDIA4	Protein disulfide-isomerase A4	1.74	0.00006	hsa-miR-378	1.35	2.55	11.31	7.79E-05	0.002720502
					hsa-miR-378c	1.17	2.25	10.21	5.74E-04	0.012576882
					hsa-miR-378i	0.85	1.80	9.00	7.98E-04	0.01627753
O15212	PFDN6	Prefoldin subunit 6	2.26	0.02810	hsa-miR-22	1.96	3.90	10.84	1.01E-04	0.003309338
P14618	PKM	Pyruvate kinase PKM	1.91	0.00020	hsa-miR-122	5.85	57.63	5.04	3.71E-05	0.001621788
P62491	RAB11A	Ras-related protein Rab-11A	1.74	0.00318	hsa-miR-138	5.84	57.23	4.36	6.08E-08	2.62E-05
					hsa-miR-30b	1.39	2.62	10.38	5.04E-04	0.011296975
					hsa-miR-30d	1.36	2.56	11.05	1.17E-04	0.003668745
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
					hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
					hsa-miR-372	12.21	4743.91	7.03	6.55E-11	2.27E-07
					hsa-miR-373	12.12	4451.32	7.23	2.25E-11	1.88E-07
Q09028	RBBP4	Histone-binding protein RBBP4	1.76	0.00339	hsa-miR-138	5.84	57.23	4.36	6.08E-08	2.62E-05
					hsa-miR-138	5.84	57.23	4.36	6.08E-08	2.62E-05
					hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
					hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
Q9UHD8	9-Sep	Septin-9	1.98	0.00016	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
Q8NC51	SERBP1	Plasminogen activator inhibitor 1 RNA-binding protein	2.35	0.00473	hsa-miR-130b	1.77	3.42	11.03	2.57E-05	0.00127274
					hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
P29401	TKT	Transketolase	1.56	0.00000	hsa-miR-371-5p	11.89	3799.61	7.79	1.04E-10	2.62E-07
P31946	YWHAB	14-3-3 protein beta/alpha	1.35	0.01490	hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
P61981	YWHAG	14-3-3 protein gamma	2.05	0.00007	hsa-miR-182	1.09	2.13	12.01	2.48E-04	0.006341084
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768
P63104	YWHAZ	14-3-3 protein zeta/delta	2.52	0.00005	hsa-miR-155	1.85	3.61	9.51	5.54E-05	0.002127503
					hsa-miR-22	1.96	3.90	10.84	1.01E-04	0.003309338
					hsa-miR-28-5p	1.16	2.24	9.32	7.05E-05	0.002531521
					hsa-miR-30b	1.39	2.62	10.38	5.04E-04	0.011296975
					hsa-miR-30d	1.36	2.56	11.05	1.17E-04	0.003668745
					hsa-miR-320a	1.46	2.76	12.49	2.74E-05	0.001333363
					hsa-miR-320b	1.46	2.76	12.49	4.80E-05	0.001959043
					hsa-miR-320c	1.46	2.74	12.35	5.43E-05	0.002111768

Twenty-seven proteins found downregulated in the Caco-2 cell line relative to the HT-29 cell line and predicted to be targeted by 19 unique anti-correlated/upregulated microRNAs.