Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing

Chang, Yao-Yin; Kuo, Wen-Hung; Hung, Jui-Hui; Lee, Chien-Yueh; Lee, Yung-Hua; Chang, Ya-Chu; Lin, Wen-Chun; Shen, Cheng-Ying; Huang, Chiun-Sheng; Hsieh, Fon-Jou; Lai, Liang-Chuan; Tsai, Mong-Hsun; Chang, King-Jen; Chuang, Eric Y

doi:10.1186/s12943-015-0301-9

Molecular Cancer

Table 3 Polycistronic miRNA clusters harboring deregulated miRNAs between triple-negative breast cancers and adjacent normal tissues ^a

From: Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing

miRNA	p value	Triple-negative breast cancer			Adjacent normal tissue			Fold change ^b in expression
		Mean	Range		Mean	Range
		Normalized	Min	Max	Normalized	Min	Max
Down-regulated miRNAs in triple-negative breast cancer
miR-143-145 cluster (Chromosome 5 q32, intergenic)
hsa-miR-143-5p	3.91E-04	43060	3104	99397	102717	29650	364644	2.4
hsa-miR-145-3p	7.36E-03	128335	8310	287564	404278	43410	1212945	3.2
hsa-miR-145-5p	1.47E-04	256	9	603	877	202	2457	3.4
miR-497-195 cluster (Chromosome 17 p13.1, MIR497HG intron 1)
hsa-miR-497-5p	2.43E-06	1980	354	6215	6520	2335	18692	3.3
hsa-miR-195-5p	3.18E-03	239	52	504	721	128	2492	3.0
Up-regulated miRNAs in triple-negative breast cancer
miR-17-92 cluster (Chromosome 13 q31.3, *C13orf25* intron 3)
has-miR-17-3p	2.66E-02	40467	7676	137962	21080	5047	67282	1.9
has-miR-18a-3p	1.43E-02	6362	904	26300	2141	0	11488	3.0
has-miR-19b-3p	9.93E-05	569	0	3214	0	0	0	N/A
has-miR-92a-3p	2.43E-04	182	0	1151	0	0	0	N/A
miR-183-182 cluster (Chromosome 7 q32.2, intergenic)
hsa-miR-183-3p	5.42E-03	160	29	431	63	0	155	2.5
hsa-miR-183-5p	5.13E-05	6223	1305	24697	1928	602	5753	3.2
hsa-miR-96-3p	2.70E-03	65	0	163	26	0	106	2.5
hsa-miR-96-5p	1.34E-05	4568	898	12421	1545	494	3892	3.0
hsa-miR-182-5p	4.76E-03	13189	2441	40871	3501	7	7623	3.8
miR-200b-429 cluster (Chromosome 1 p36.33, intergenic)
hsa-miR-200b-3p	2.65E-02	694	156	2348	398	35	1061	1.7
hsa-miR-200a-3p	2.46E-02	77	0	362	40	0	296	1.9
hsa-miR-200a-5p	1.25E-03	46665	1800	160398	15886	2412	46254	2.9
hsa-miR-429-5p	1.91E-04	6416	1486	23455	2082	406	8716	3.1
miR-301b-130b cluster (Chromosome 22 q11.21, *PPIL2* exon 2)
hsa-miR-301b-5p	1.41E-03	323	103	1483	89	0	244	3.6
hsa-miR-130b-3p	1.23E-04	550	204	1683	246	110	579	2.2
hsa-miR-130b-5p	7.64E-05	3729	1413	10634	1352	159	2856	2.8
miR-532-502 cluster (Chromosome X p11.23, *CLCN5* intron 3)
hsa-miR-532-5p	1.58E-02	514	125	2731	253	31	990	2.0
hsa-miR-188-3p	2.72E-02	1159	509	5061	520	0	1258	2.2
hsa-miR-362-3p	2.56E-04	1043	565	2168	448	43	845	2.3
hsa-miR-362-5p	1.69E-04	2216	1186	5092	1006	297	2303	2.2
hsa-miR-501-3p	2.13E-02	335	125	1439	143	0	258	2.3
hsa-miR-660-3p	3.00E-02	11371	5546	23930	4438	0	9196	2.6
hsa-miR-502-3p	1.01E-02	144	60	339	68	0	129	2.1
hsa-miR-502-5p	2.55E-02	354	98	717	174	0	351	2.0

^aNormalized miRNA reads from each sample were obtained after quantile-quantile scaling. The p-value is calculated using the log₁₀-scaled miRNA expression data without the Holm adjustment. Relative expression levels are shown.
^bFold change was obtained by comparing the mean normalized miRNA expression reads between the triple-negative breast cancers and adjacent normal tissues.

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