Dysregulation of microRNA in cholangiocarcinoma identified through a meta-analysis of microRNA profiling

Table 1 Summary of microRNA microarray datasets used in this study

Dataset	Sample type	Number of samples		Microarray platform
		CCA	Normal
GSE32958	Tissue	19	5	Nanostring nCounter human miRNA expression
GSE47396	Cell lines	2		miRCURY LNA miRNA Array, 5th generation
GSE47764	Tissue	3	3	Agilent-021827 human miRNA microarray
GSE50894	Tissue	16		Exiqon miRCURY LNA miRNA array version 10.0 extended and version 11.0 (condensed version)
GSE51429	Tissue	29		Applied Biosystems human miRNA array version 2.0
GSE53870	Tissue	63	9	State Key Laboratory human miRNA array 1104
GSE53992	Tissue	16	30	Agilent-031181 unrestricted human miRNA version 16.0
GSE59856	Serum	98	150	3D-Gene human miRNA version 20_1.0.0
Total		246	197

CCA: Cholangiocarcinoma; miRNA: MicroRNA.

Table 2 List of 10-fold-cross-validated differentially-expressed microRNAs which were up-regulated in cholangiocarcinoma

miRNA	FC	Abs. t value	DF	Adj. P value	FDR
hsa-let-7b-3p	1.482	6.603	74	0.000	0.000
hsa-miR-1193	1.579	7.409	112	0.000	0.000
hsa-miR-1207-3p	1.516	10.533	120	0.000	0.000
hsa-miR-1224-3p	5.164	7.024	66	0.000	0.000
hsa-miR-1227-3p	2.039	7.963	117	0.000	0.000
hsa-miR-1237-3p	1.594	5.7	355	0.000	0.000
hsa-miR-1247-5p	1.781	7.406	126	0.000	0.000
hsa-miR-1249-3p	3.877	9.138	137	0.000	0.000
hsa-miR-1267	2.433	7.758	119	0.000	0.000
hsa-miR-1269a	1.647	7.209	72	0.000	0.000
hsa-miR-1273d	1.665	7.159	80	0.000	0.000
hsa-miR-1284	1.606	7.019	127	0.000	0.000
hsa-miR-1304-5p	1.651	6.863	89	0.000	0.000
hsa-miR-1322	1.731	9.986	132	0.000	0.000
hsa-miR-147b	2.727	8.195	52	0.000	0.000
hsa-miR-149-3p	3.022	8.11	88	0.000	0.000
hsa-miR-181a-2-3p	1.476	7.004	90	0.000	0.000
hsa-miR-185-3p	5.044	9.684	113	0.000	0.000
hsa-miR-1908-5p	9.384	7.977	150	0.000	0.000
hsa-miR-1909-3p	2.19	6.502	129	0.000	0.000
hsa-miR-1913	2.222	6.861	137	0.000	0.000
hsa-miR-1914-5p	1.575	6.615	140	0.000	0.000
hsa-miR-1972	2.043	8.605	111	0.000	0.000
hsa-miR-2113	1.634	7.74	358	0.000	0.000
hsa-miR-2116-3p	1.656	9.782	115	0.000	0.000
hsa-miR-219a-2-3p	1.6	6.436	125	0.000	0.000
hsa-miR-2355-5p	2.762	9.902	113	0.000	0.000
hsa-miR-30c-1-3p	1.976	7.144	114	0.000	0.000
hsa-miR-3131	2.446	6.211	114	0.000	0.000
hsa-miR-3147	1.371	7.617	115	0.000	0.000
hsa-miR-3150a-3p	1.894	7.004	112	0.000	0.000
hsa-miR-3151-5p	1.387	6.831	115	0.000	0.000
hsa-miR-3153	1.994	9.741	115	0.000	0.000
hsa-miR-3178	4.752	8.999	97	0.000	0.000
hsa-miR-3180	4.161	9.232	92	0.000	0.000
hsa-miR-3184-5p	4.809	6.949	81	0.000	0.000
hsa-miR-3185	3.193	8.217	96	0.000	0.000
hsa-miR-3186-3p	1.446	6.611	104	0.000	0.000
hsa-miR-3197	4.454	13.341	95	0.000	0.000
hsa-miR-325	1.498	5.994	168	0.000	0.000
hsa-miR-330-5p	1.808	8.061	161	0.000	0.000
hsa-miR-412-3p	1.933	7.414	144	0.000	0.000
hsa-miR-423-3p	1.784	8.826	81	0.000	0.000
hsa-miR-4258	3.644	8.72	99	0.000	0.000
hsa-miR-4270	3.705	6.216	113	0.000	0.000
hsa-miR-4288	2.393	7.991	84	0.000	0.000
hsa-miR-4292	2.93	7.318	83	0.000	0.000
hsa-miR-4301	2.558	8.404	93	0.000	0.000
hsa-miR-4310	2.22	8.196	99	0.000	0.000
hsa-miR-4312	1.462	7.004	115	0.000	0.000
hsa-miR-4323	1.915	9.85	109	0.000	0.000
hsa-miR-512-5p	1.484	6.579	172	0.000	0.000
hsa-miR-515-3p	1.833	7.931	97	0.000	0.000
hsa-miR-517c-3p	1.635	6.22	186	0.000	0.000
hsa-miR-519d-3p	1.833	7.499	164	0.000	0.000
hsa-miR-520a-5p	1.627	6.71	151	0.000	0.000
hsa-miR-520d-5p	5.392	7.514	342	0.000	0.000
hsa-miR-520g-3p	2.047	6.687	119	0.000	0.000
hsa-miR-548a-5p	1.79	6.719	131	0.000	0.000
hsa-miR-548d-3p	2.938	6.573	62	0.000	0.000
hsa-miR-612	1.79	6.952	376	0.000	0.000
hsa-miR-615-5p	1.691	7.028	116	0.000	0.000
hsa-miR-625-3p	3.763	8.618	104	0.000	0.000
hsa-miR-637	2.081	7.404	159	0.000	0.000
hsa-miR-668-3p	1.437	6.341	153	0.000	0.000
hsa-miR-765	2.014	7.266	338	0.000	0.000
hsa-miR-891a-5p	2.297	13.332	105	0.000	0.000
hsa-miR-891b	2.052	7.342	117	0.000	0.000
hsa-miR-92b-5p	2.802	6.499	106	0.000	0.000
hsa-miR-938	1.556	8.445	155	0.000	0.000

The P value was set to lower than 0.001 (P < 0.001). miRNA: MicroRNA; FC: Fold change (ratio of mean signal intensities of cholangiocarcinoma to those of normal samples); DF: Degree of freedom; Abs. t value: Absolute t value; Adj. P value: Adjusted P value; FDR: False discovery rate.

Table 3 List of 10-fold-cross-validated differentially-expressed microRNAs which were down-regulated in cholangiocarcinoma

miRNA	FC	Abs. t value	DF	Adj. P value	FDR
hsa-let-7b-5p	0.336	6.655	186	0.000	0.000
hsa-let-7c-3p	0.686	9.519	138	0.000	0.000
hsa-let-7f-5p	0.226	6.65	89	0.000	0.000
hsa-miR-100-5p	0.424	7.984	144	0.000	0.000
hsa-miR-10a-5p	0.458	5.943	196	0.000	0.000
hsa-miR-10b-3p	0.352	8.834	72	0.000	0.000
hsa-miR-1225-5p	0.097	6.448	88	0.000	0.000
hsa-miR-127-3p	0.62	6.167	84	0.000	0.000
hsa-miR-1288-3p	0.394	7.17	61	0.000	0.000
hsa-miR-1305	0.311	7.255	66	0.000	0.000
hsa-miR-130a-3p	0.459	7.775	101	0.000	0.000
hsa-miR-136-5p	0.51	7.184	191	0.000	0.000
hsa-miR-139-3p	0.626	7.227	95	0.000	0.000
hsa-miR-145-5p	0.359	7.026	129	0.000	0.000
hsa-miR-150-3p	0.51	7.109	139	0.000	0.000
hsa-miR-17-3p	0.638	7.108	115	0.000	0.000
hsa-miR-181c-3p	0.602	6.651	133	0.000	0.000
hsa-miR-181d-5p	0.598	7.741	138	0.000	0.000
hsa-miR-192-5p	0.267	7.582	69	0.000	0.000
hsa-miR-194-5p	0.283	8.454	90	0.000	0.000
hsa-miR-195-5p	0.449	7.441	101	0.000	0.000
hsa-miR-20a-5p	0.386	6.929	99	0.000	0.000
hsa-miR-215-5p	0.271	8.404	70	0.000	0.000
hsa-miR-26b-5p	0.305	7.657	121	0.000	0.000
hsa-miR-27b-3p	0.317	8.02	146	0.000	0.000
hsa-miR-29b-3p	0.432	6.216	110	0.000	0.000
hsa-miR-29c-3p	0.25	9.578	93	0.000	0.000
hsa-miR-29c-5p	0.755	6.521	122	0.000	0.000
hsa-miR-3120-3p	0.673	6.341	90	0.000	0.000
hsa-miR-330-3p	0.691	6.605	99	0.000	0.000
hsa-miR-339-3p	0.746	7.662	90	0.000	0.000
hsa-miR-342-3p	0.516	8.228	193	0.000	0.000
hsa-miR-345-5p	0.531	8.154	69	0.000	0.000
hsa-miR-374a-5p	0.439	8.25	99	0.000	0.000
hsa-miR-374b-5p	0.568	6.771	117	0.000	0.000
hsa-miR-378b	0.489	7.181	101	0.000	0.000
hsa-miR-4294	0.471	7.279	96	0.000	0.000
hsa-miR-4326	0.69	6.513	115	0.000	0.000
hsa-miR-451a	0.143	7.636	85	0.000	0.000
hsa-miR-483-5p	0.412	7.272	166	0.000	0.000
hsa-miR-505-3p	0.625	6.612	105	0.000	0.000
hsa-miR-575	0.311	7.35	62	0.000	0.000
hsa-miR-614	0.341	7.8	412	0.000	0.000
hsa-miR-627-5p	0.601	6.504	190	0.000	0.000
hsa-miR-650	0.252	9.369	148	0.000	0.000
hsa-miR-671-5p	0.594	6.372	402	0.000	0.000
hsa-miR-922	0.323	8.522	148	0.000	0.000
hsa-miR-99a-5p	0.328	9.611	117	0.000	0.000

The P value was set to lower than 0.001 (P < 0.001). miRNA: MicroRNA; FC: Fold change (ratio of mean signal intensities of cholangiocarcinoma to those of normal samples); DF: Degree of freedom; Abs. t value: Absolute t value; Adj. P value: Adjusted P value; FDR: False discovery rate.