Table 3 Genes in t(4;14) samples that... | American Society of Hematology

Table 3

Genes in t(4;14) samples that are both differentially methylated and differentially expressed compared with samples with no split IGH locus

Gene	Chr.	Expression changes (U133 Plus 2.0)					Methylation changes (humanmethylation27)						Description
Gene	Chr.	Probe	t(4;14)	No split	Fold change	P	Probe	CpG island	t(4;14)	No split	Difference	P	Description
C20orf103	20	219463_at	8.038	10.772	−6.656	.008991	cg09119967	False	0.472	0.231	0.241	.001135	Chromosome 20 open reading frame 103
CD79A	19	1555779_a_at	7.168	8.408	−2.362	.006872	cg04790874	False	0.484	0.222	0.262	4.11 × 10⁻⁵	CD79A
CD79A	19	205049_s_at	7.652	8.722	−2.100	.040305	cg04790874	False	0.484	0.222	0.262	4.11 × 10⁻⁵	CD79A
FAM49A	2	208092_s_at	6.461	7.775	−2.487	.009265	cg10106284	False	0.287	0.167	0.12	.033294	Family with sequence similarity 49, member A
		209683_at	5.631	6.891	−2.396	.019702
		230276_at	7.031	7.898	−1.823	.023463
GLTSCR2	19	234339_s_at	10.806	12.216	−2.658	1.05 × 10⁻⁷	cg16791686	True	0.307	0.159	0.148	3.36 × 10⁻⁵	Glioma tumor suppressor candidate region gene 2
GLTSCR2	19	217807_s_at	13.126	14.083	−1.942	1.06 × 10⁻⁷	cg16791686	True	0.307	0.159	0.148	3.36 × 10⁻⁵	Glioma tumor suppressor candidate region gene 2
GPX1	3	200736_s_at	9.846	11.311	−2.760	.000267	cg06613840	True	0.442	0.177	0.265	2.46 × 10⁻⁸	Glutathione peroxidase 1
GPX1	3	200736_s_at	9.846	11.311	−2.760	.000267	cg15900980	True	0.386	0.082	0.304	1.16 × 10⁻⁶	Glutathione peroxidase 1
GRM8	7	216992_s_at	4.346	4.896	−1.464	.002383	cg09868882	False	0.532	0.267	0.265	4.34 × 10⁻⁸	Glutamate receptor, metabotropic 8
MAB21L1	13	206163_at	3.443	4.138	−1.619	.037692	cg05093686	True	0.538	0.207	0.271	4.86 × 10⁻⁷	mab-21-like 1
MAB21L1	13	206163_at	3.443	4.138	−1.619	.037692	cg12029639	True	0.560	0.225	0.335	1.20 × 10⁻⁷	mab-21-like 1
MBP	18	209072_at	6.539	7.032	−1.407	.000475	cg12555907	True	0.841	0.411	0.43	2.61 × 10⁻⁸	Myelin basic protein
NME4	16	212739_s_at	8.007	8.658	−1.570	.012902	cg18676162	True	0.321	0.178	0.143	.027662	Nonmetastic cells 4
OSBPL10	3	231656_x_at	5.979	6.995	−2.023	.002011	cg15840985	True	0.329	0.170	0.159	.00022	Oxysterol binding protein-like 10
RPS2	16	212433_x_at	13.275	14.107	−1.781	.000313	cg18279742	True	0.344	0.205	0.139	.041014	Ribosomal protein S2
		203107_x_at	13.825	14.543	−1.645	.000254
		217466_x_at	10.499	11.145	−1.564	.001184
SOCS2	12	203373_at	7.734	8.405	−1.593	.041561	cg04797323	True	0.450	0.140	0.31	.000257	Suppressor of cytokine signalling 2
							cg06630241	True	0.637	0.285	0.352	7.18 × 10⁻¹⁰
							cg11738543	True	0.353	0.103	0.25	5.05 × 10⁻⁵
							cg23412850	True	0.330	0.059	0.271	4.24 × 10⁻⁶
ACADVL	17	200710_at	10.904	10.024	1.840	.000336	cg24825722	False	0.121	0.305	−0.184	.007423	Acyl-CoA dehydrogenase, very long chain
ACADVL	17	200710_at	10.904	10.024	1.840	.000336	cg21636577	False	0.221	0.472	−0.251	.000713	Acyl-CoA dehydrogenase, very long chain
CTHRC1	8	225681_at	12.349	8.766	11.984	4.57 × 10⁻⁵	cg19188612	True	0.620	0.840	−0.22	.00053	Collagen triple helix containing 1
DNMT3A	2	222640_at	6.557	6.273	1.218	.037539	cg21629895	False	0.339	0.491	−0.152	.042813	DNA methyl-transferase 3A
GALNT1	18	201724_s_at	8.838	8.011	1.774	.041426	cg05714729	False	0.212	0.383	−0.171	.034844	UDP-N-acetyl-alpha-D-galactosamine
GNPTG	16	224887_at	9.518	8.917	1.516	.008847	cg18146152	True	0.534	0.748	−0.214	.000131	N-acetyl-glucosamine-1-phosphate transferase, gamma subunit
IRS2	13	209184_s_at	7.470	6.309	2.236	4.05 × 10⁻⁵	cg14341579	True	0.037	0.285	−0.248	.011963	Insulin receptor substrate 2
IRS2	13	209185_s_at	7.711	5.849	3.636	4.90 × 10⁻⁶	cg25802424	True	0.037	0.265	−0.228	.003687	Insulin receptor substrate 2
LRIG1	3	211596_s_at	6.472	5.568	1.872	.009466	cg26131019	True	0.057	0.310	−0.253	.001657	Leucine-rich repeats and Ig-like domains 1
LRP12	8	220253_s_at	4.404	3.418	1.981	1.74 × 10⁻⁸	cg09531892	True	0.224	0.429	−0.205	.03994	Low-density lipoprotein-related protein 12
LRP12	8	219631_at	5.758	4.230	2.883	8.52 × 10⁻⁷	cg09531892	True	0.224	0.429	−0.205	.03994	Low-density lipoprotein-related protein 12
PELI1	2	218319_at	12.686	11.809	1.836	.033075	cg15309578	False	0.299	0.421	−0.122	.006695	Pellino homolog 1
PELI1	2	232213_at	9.231	8.255	1.966	.034372	cg15309578	False	0.299	0.421	−0.122	.006695	Pellino homolog 1
PTPRA	20	213795_s_at	7.332	6.753	1.493	.02016	cg03115886	False	0.443	0.601	−0.158	.025021	Protein tyrosine phosphatase receptor type A
PTPRCAP	11	204960_at	9.872	8.598	2.419	.004979	cg05751148	False	0.111	0.319	−0.208	.036243	Protein tyrosine phosphatase receptor type C associated protein
PTPRCAP	11	204960_at	9.872	8.598	2.419	.004979	cg20792833	False	0.191	0.465	−0.274	.003583
SBNO1	12	218737_at	5.164	4.624	1.454	.003605	cg04398275	False	0.438	0.700	−0.262	2.95 × 10⁻⁶	Strawberry notch homolog 1
SNRK	3	209481_at	8.785	8.049	1.666	.009873	cg04008913	False	0.171	0.314	−0.143	.031077	SNF-related kinase
ZNF75A	16	227670_at	5.386	4.892	1.409	.02804	cg02825709	True	0.322	0.575	−0.253	.000649	Zinc finger protein 75A

Gene	Chr.	Expression changes (U133 Plus 2.0)					Methylation changes (humanmethylation27)						Description
Gene	Chr.	Probe	t(4;14)	No split	Fold change	P	Probe	CpG island	t(4;14)	No split	Difference	P	Description
C20orf103	20	219463_at	8.038	10.772	−6.656	.008991	cg09119967	False	0.472	0.231	0.241	.001135	Chromosome 20 open reading frame 103
CD79A	19	1555779_a_at	7.168	8.408	−2.362	.006872	cg04790874	False	0.484	0.222	0.262	4.11 × 10⁻⁵	CD79A
CD79A	19	205049_s_at	7.652	8.722	−2.100	.040305	cg04790874	False	0.484	0.222	0.262	4.11 × 10⁻⁵	CD79A
FAM49A	2	208092_s_at	6.461	7.775	−2.487	.009265	cg10106284	False	0.287	0.167	0.12	.033294	Family with sequence similarity 49, member A
		209683_at	5.631	6.891	−2.396	.019702
		230276_at	7.031	7.898	−1.823	.023463
GLTSCR2	19	234339_s_at	10.806	12.216	−2.658	1.05 × 10⁻⁷	cg16791686	True	0.307	0.159	0.148	3.36 × 10⁻⁵	Glioma tumor suppressor candidate region gene 2
GLTSCR2	19	217807_s_at	13.126	14.083	−1.942	1.06 × 10⁻⁷	cg16791686	True	0.307	0.159	0.148	3.36 × 10⁻⁵	Glioma tumor suppressor candidate region gene 2
GPX1	3	200736_s_at	9.846	11.311	−2.760	.000267	cg06613840	True	0.442	0.177	0.265	2.46 × 10⁻⁸	Glutathione peroxidase 1
GPX1	3	200736_s_at	9.846	11.311	−2.760	.000267	cg15900980	True	0.386	0.082	0.304	1.16 × 10⁻⁶	Glutathione peroxidase 1
GRM8	7	216992_s_at	4.346	4.896	−1.464	.002383	cg09868882	False	0.532	0.267	0.265	4.34 × 10⁻⁸	Glutamate receptor, metabotropic 8
MAB21L1	13	206163_at	3.443	4.138	−1.619	.037692	cg05093686	True	0.538	0.207	0.271	4.86 × 10⁻⁷	mab-21-like 1
MAB21L1	13	206163_at	3.443	4.138	−1.619	.037692	cg12029639	True	0.560	0.225	0.335	1.20 × 10⁻⁷	mab-21-like 1
MBP	18	209072_at	6.539	7.032	−1.407	.000475	cg12555907	True	0.841	0.411	0.43	2.61 × 10⁻⁸	Myelin basic protein
NME4	16	212739_s_at	8.007	8.658	−1.570	.012902	cg18676162	True	0.321	0.178	0.143	.027662	Nonmetastic cells 4
OSBPL10	3	231656_x_at	5.979	6.995	−2.023	.002011	cg15840985	True	0.329	0.170	0.159	.00022	Oxysterol binding protein-like 10
RPS2	16	212433_x_at	13.275	14.107	−1.781	.000313	cg18279742	True	0.344	0.205	0.139	.041014	Ribosomal protein S2
		203107_x_at	13.825	14.543	−1.645	.000254
		217466_x_at	10.499	11.145	−1.564	.001184
SOCS2	12	203373_at	7.734	8.405	−1.593	.041561	cg04797323	True	0.450	0.140	0.31	.000257	Suppressor of cytokine signalling 2
							cg06630241	True	0.637	0.285	0.352	7.18 × 10⁻¹⁰
							cg11738543	True	0.353	0.103	0.25	5.05 × 10⁻⁵
							cg23412850	True	0.330	0.059	0.271	4.24 × 10⁻⁶
ACADVL	17	200710_at	10.904	10.024	1.840	.000336	cg24825722	False	0.121	0.305	−0.184	.007423	Acyl-CoA dehydrogenase, very long chain
ACADVL	17	200710_at	10.904	10.024	1.840	.000336	cg21636577	False	0.221	0.472	−0.251	.000713	Acyl-CoA dehydrogenase, very long chain
CTHRC1	8	225681_at	12.349	8.766	11.984	4.57 × 10⁻⁵	cg19188612	True	0.620	0.840	−0.22	.00053	Collagen triple helix containing 1
DNMT3A	2	222640_at	6.557	6.273	1.218	.037539	cg21629895	False	0.339	0.491	−0.152	.042813	DNA methyl-transferase 3A
GALNT1	18	201724_s_at	8.838	8.011	1.774	.041426	cg05714729	False	0.212	0.383	−0.171	.034844	UDP-N-acetyl-alpha-D-galactosamine
GNPTG	16	224887_at	9.518	8.917	1.516	.008847	cg18146152	True	0.534	0.748	−0.214	.000131	N-acetyl-glucosamine-1-phosphate transferase, gamma subunit
IRS2	13	209184_s_at	7.470	6.309	2.236	4.05 × 10⁻⁵	cg14341579	True	0.037	0.285	−0.248	.011963	Insulin receptor substrate 2
IRS2	13	209185_s_at	7.711	5.849	3.636	4.90 × 10⁻⁶	cg25802424	True	0.037	0.265	−0.228	.003687	Insulin receptor substrate 2
LRIG1	3	211596_s_at	6.472	5.568	1.872	.009466	cg26131019	True	0.057	0.310	−0.253	.001657	Leucine-rich repeats and Ig-like domains 1
LRP12	8	220253_s_at	4.404	3.418	1.981	1.74 × 10⁻⁸	cg09531892	True	0.224	0.429	−0.205	.03994	Low-density lipoprotein-related protein 12
LRP12	8	219631_at	5.758	4.230	2.883	8.52 × 10⁻⁷	cg09531892	True	0.224	0.429	−0.205	.03994	Low-density lipoprotein-related protein 12
PELI1	2	218319_at	12.686	11.809	1.836	.033075	cg15309578	False	0.299	0.421	−0.122	.006695	Pellino homolog 1
PELI1	2	232213_at	9.231	8.255	1.966	.034372	cg15309578	False	0.299	0.421	−0.122	.006695	Pellino homolog 1
PTPRA	20	213795_s_at	7.332	6.753	1.493	.02016	cg03115886	False	0.443	0.601	−0.158	.025021	Protein tyrosine phosphatase receptor type A
PTPRCAP	11	204960_at	9.872	8.598	2.419	.004979	cg05751148	False	0.111	0.319	−0.208	.036243	Protein tyrosine phosphatase receptor type C associated protein
PTPRCAP	11	204960_at	9.872	8.598	2.419	.004979	cg20792833	False	0.191	0.465	−0.274	.003583
SBNO1	12	218737_at	5.164	4.624	1.454	.003605	cg04398275	False	0.438	0.700	−0.262	2.95 × 10⁻⁶	Strawberry notch homolog 1
SNRK	3	209481_at	8.785	8.049	1.666	.009873	cg04008913	False	0.171	0.314	−0.143	.031077	SNF-related kinase
ZNF75A	16	227670_at	5.386	4.892	1.409	.02804	cg02825709	True	0.322	0.575	−0.253	.000649	Zinc finger protein 75A

Expression values are log-transformed and methylation numbers are β-values.

IGH indicates immunoglobulin heavy; and SNF, sucrose nonfermenting.

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