Alternative splicing in osteoclasts and Paget’s disease of bone

Klinck, Roscoe; Laberge, Gino; Bisson, Martine; McManus, Stephen; Michou, Laëtitia; Brown, Jacques P; Roux, Sophie

doi:10.1186/s12881-014-0098-1

BMC Medical Genetics

Table 2 Validation of the selected 21 alternative splicing events in the whole cohort

From: Alternative splicing in osteoclasts and Paget’s disease of bone

Gene	Forward Primer	Reverse Primer	all PDBvsHD		all PDBvsHD^wt		PDB^wt vsHD^wt		PDB^wt vsHD^P392L		PDB^wt vsPDB^P392L		HD^wt vsHD^P392L
			(n =19 vs 16)		(n =19 vs 11)		(n =12 vs 11)		(n =12 vs 5)		(n =12 vs 7)		(n =11 vs 5)
			p*	q	p	q	p	q	p	q	p	q	p	q
*LGALS8*	ACACTCTGGGCATTTATGGC	TTTAACGACGACAGTTCGTCC	0.00001	0.0002	0.0005	0.009	0.0004	0.004	0.001	0.008	0.64	0.55	0.71	0.55
*USP4*	AGCTATTCAACATCCCTGCG	GGTGGCTCCTGACAATTATACG	0.0002	0.0012	0.0019	0.013	0.002	0.006	0.033	0.054	0.73	0.55	0.48	0.51
*CASC4*	GAGGTGGTGATGCAGGGATGC	GATCCATTTGAAGCTCTCGTTCTTC	0.001	0.004	0.001	0.009	0.001	0.004	0.050	0.07	0.15	0.27	0.22	0.39
*RHOT1*	TCCACCACAAGCCTTCACTT	GTGCACATACAGCGTAACCG	0.001	0.004	0.018	0.061	0.021	0.042	0.003	0.0019	0.88	0.59	0.89	0.66
*PIDD*	ATGTTCGAGGGCGAAGAGTT	CGCCACGGTAGAAGGACAC	0.01	0.03	0.03	0.08	0.03	0.04	0.03	0.05	0.68	0.55	0.62	0.51
*LGALS9*	GTGATGGTGAACGGGATCCT	GTTGGCAGGCCACACGCC	0.02	0.03	0.053	0.11	0.14	0.18	0.10	0.12	0.38	0.42	0.81	0.68
*TBC1D25*	AATGTGAGAGCTTCTTGCCG	AGGATGGACTGTGTAAAGGGC	0.03	0.05	0.04	0.10	0.01	0.02	0.02	0.05	0.04	0.24	0.35	0.39
*THAP1*	AGGACAAGCCCGTTTCTTTC	TCCAATAGCAGCATCAACCTG	0.04	0.09	0.01	0.051	0.01	0.04	0.43	0.44	0.53	0.49	0.27	0.39
*ABTB1*	GAGCAGCGAGACGTGGAG	GCTTGTAATCGCGTAGAGCC	0.09	0.33	0.01	0.057	0.02	0.08	0.56	0.44	0.12	0.27	0.08	0.39
*WARS*	AGCGTGACCAGTGGCCAC	GCCTTTTGCACTGCTTGTCT	0.28	0.39	0.51	0.67	0.84	0.85	0.48	0.44	0.15	0.27	0.50	0.55
*PIDD*	CTGAGCTTGGACCTGTACCC	AGGCCACTCAGACCAGCG	0.23	0.39	0.42	0.65	0.47	0.59	0.73	0.47	0.03	0.24	0.27	0.39
*METTL13*	CATGCGTGCGTTTGTCGT	ATGTCGATGTTCACTATATCCCG	0.42	0.56	0.78	0.87	0.50	0.50	0.01	0.05	0.11	0.27	0.29	0.39
*L3MBTL*	CCAAGTGGACCATCGATGAG	AGCAAATGAGTGGGTAGAGAGC	0.34	0.56	0.22	0.43	0.24	0.49	1.00	0.56	0.82	0.59	0.22	0.39
*BTC*	ACCACCACACAATCAAAGCG	TTACGACGTTTCCGAAGAGG	0.41	0.56	0.57	0.70	0.80	0.79	0.75	0.47	0.19	0.29	0.51	0.51
*NLRP12*	TCAGTGTGAACCAGAGCCTG	CAGGTAAAGGTCGGTCAAGG	0.41	0.56	0.80	0.87	0.38	0.50	0.03	0.05	0.22	0.29	0.25	0.39
*CASC4*	GCTCAAACTTGGACAGTGAACC	GCAGGATCCATTTGAAGCTC	0.66	0.92	0.42	0.65	0.24	0.48	0.87	0.52	0.37	0.42	0.21	0.39
*ABI1*	AGTTCTGGATGATGTGGGCC	TGGCGGTTTCTGAGTAGGAGGA	0.85	0.94	0.46	0.65	0.37	0.50	0.52	0.44	0.48	0.49	0.20	0.39
*RAB3IP*	TGGGATTACAACCTATCCGG	CCCTGCTGAATGTATCGAATG	0.89	0.94	0.44	0.65	0.50	0.53	0.44	0.44	0.98	0.63	0.24	0.39
*PRMT2*	GCTCCTGGAAAGGACCGTC	TTAGGCTCTGCCTCATAACTGC	0.85	0.97	0.93	0.87	0.93	0.85	0.70	0.47	n/a	n/a	0.28	0.39
*BCL2L12*	TCCTAGCTGCCTTCCTTAG	GTATGGCTTCCTTCTCTGTC	0.87	0.92	0.86	0.87	0.48	0.61	0.58	0.44	0.14	0.27	0.95	0.68
*BCL2L15*	TTGAGGAACAAACGGAATGC	AGCTAAGCTGGAATCCTGAGC	0.98	0.98	0.91	0.87	0.87	0.82	n/a	n/a	n/a	n/a	n/a	n/a

*Student’s t-test of Ψ (PSI) values for each AS event in each group (p-value) with a correction for multiple testing using the false discovery rate (q-value).
HD^wt healthy donors exempt from SQSTM1/p62 mutation (n=11); HD^P392L healthy donors carrying p62^P392L (n=5); PBD (Paget’s disease of bone); PBD^wt patients exempt from SQSTM1/p62 mutation (n=12); PDB^P392L patients carrying the p62^P392L (n=7). n/a: missing data (inadequate RNA samples).

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