Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas

Renner, Marcus; Wolf, Thomas; Meyer, Hannah; Hartmann, Wolfgang; Penzel, Roland; Ulrich, Alexis; Lehner, Burkhard; Hovestadt, Volker; Czwan, Esteban; Egerer, Gerlinde; Schmitt, Thomas; Alldinger, Ingo; Renker, Eva Kristin; Ehemann, Volker; Eils, Roland; Wardelmann, Eva; Büttner, Reinhard; Lichter, Peter; Brors, Benedikt; Schirmacher, Peter; Mechtersheimer, Gunhild

doi:10.1186/gb-2013-14-12-r137

Table 3 Characteristics of the selected CpG sites

From: Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas

Short name	CpG number	Gene symbol	1/FC	1/FC	Correlation	CpG region	Hypomethylated	Hypermethylated	Absolute d	Kruskal–Wallis
Short name	CpG number	Gene symbol	(Gene expression)	(Methylation)	Correlation	CpG region	(β value)	(β value)	(β value)	Pvalue
Negative correlation
4–09	cg19510698	ALDH1A3	6.3	6.9	-0.49	GB	0.339	0.748	0.41	3.5 × 10^–5
3–13	cg27652350	ALDH1A3	6.0	31.4	-0.44^a	GB	0.181	0.830	0.65	1.5 × 10^–5
1–26	cg21359747	ALDH1A3	5.7	28.8	-0.38	P	0.121	0.751	0.63	2.5 × 10^–5
2–37	cg23352695	EVI2A	1.8	8.4	-0.47^a	P	0.235	0.694	0.46	6.5 × 10^–5
3–30	cg00250430	DMRT2	2.7	14.5	-0.41^b	P	0.138	0.652	0.51	1.2 × 10^–4
2–18	cg20955688	TMEM71	1.6	11.6	-0.41	P	0.090	0.490	0.40	5.1 × 10^–5
1–39	cg08687163	MST1R	1.6	19.0	-0.39^b	P	0.566	0.951	0.39	1.2 × 10^–4
2–43	cg09874127	UBA7	4.5	6.8	-0.37	P	0.094	0.406	0.31	1.6 × 10^–3
1–34	cg23418591	APCDD1L	5.9	36.6	-0.33	P	0.097	0.739	0.64	5.8 × 10^–5
1–31	cg14546153	APCDD1L	5.2	22.2	-0.33	P	0.057	0.549	0.49	1.1 × 10^–5
5–01	cg00201234	FBLN2	3.4	31.9	-0.32	P	0.075	0.662	0.59	1.1 × 10^–4
4–21	cg22736323	PDGFRA	6.3	11.7	-0.31	P	0.182	0.679	0.50	4.8 × 10^–2
1–24	cg01035422	PLIN	4.9	5.0	-0.31	P	0.167	0.544	0.38	1.4 × 10^–3
1–01	cg22298088	NNAT	24.7	9.3	-0.30^b	P	0.492	0.876	0.38	1.1 × 10^–5
1–13	cg12862537	NNAT	41.4	16.6	-0.27	P	0.548	0.940	0.39	2.0 × 10^–4
2–16	cg22502502	TRIM38	1.7	7.2	-0.30	P	0.120	0.468	0.35	1.1 × 10^–2
5–36	cg22836229	EFCAB1	1.6	16.1	-0.30	P	0.167	0.708	0.54	3.0 × 10^–3
4–15	cg11391732	HSPB3	2.4	9.4	-0.30	P	0.361	0.795	0.43	6.7 × 10^–3
1–03	cg18508525	CD36	13.5	17.4	-0.30	P	0.246	0.811	0.56	9.7 × 10^–5
3–38	cg20786074	EFEMP1	1.9	11.0	-0.28^a	P	0.167	0.658	0.49	6.0 × 10^–5
2–02	cg10150813	SEL1L3	1.5	14.1	-0.27	P	0.232	0.771	0.54	9.6 × 10^–5
1–27	cg08278554	C15orf48	1.7	10.1	-0.27	P	0.183	0.640	0.46	1.3 × 10^–5
2–01	cg08397758	PYROXD2	1.6	17.4	-0.26	P	0.159	0.709	0.55	3.2 × 10^–4
4–06	cg00476577	ZNF217	1.6	9.7	-0.26	P	0.094	0.486	0.39	1.9 × 10^–4
1–02	cg16907566	COL14A1	1.7	13.8	-0.26	P	0.120	0.606	0.49	9.6 × 10^–5
1–20	cg01473816	ELF5	2.3	4.2	-0.25	P	0.461	0.758	0.30	6.3 × 10^–4
1–11	cg25181284	GPD1	3.6	9.9	-0.25	P	0.524	0.910	0.39	1.5 × 10^–4
4–07	cg26205432	PLN	3.4	3.8	-0.24	P	0.302	0.581	0.28	3.1 × 10^–3
3–42	cg12567315	TSPAN13	1.5	19.8	-0.23	P	0.053	0.494	0.44	1.6 × 10^–2
4–02	cg10062065	SPEG	2.4	15.2	-0.20	P	0.364	0.870	0.51	7.3 × 10^–4
*Positive correlation*
3–07	cg10895543	CDKN2A	0.3	17.9	0.58	GB	0.188	0.758	0.57	2.8 × 10^–6
1–35	cg24690731	SOX7	0.6	12.1	0.30	P	0.217	0.735	0.52	4.3 × 10^–4
1–14	cg04396791	SHANK2	0.4	52.7	0.25	P	0.079	0.759	0.68	8.9 × 10^–4
1–18	cg10362475	SHANK2	0.5	18.1	0.25	GB	0.221	0.792	0.57	8.0 × 10^–4
5–33	cg01820777	MICALL2	0.6	5.3	0.20	P	0.089	0.345	0.26	7.8 × 10^–3

^aSignificant correlation of gene expression within the range of DNA hypermethylation.
^bSignificant correlation of gene expression within the range of DNA hypomethylation.
GB, gene body; P, promoter.
1/FC is defined as the inverse value of the fold change.

Back to article page

ISSN: 1474-760X

Contact us

Submission enquiries: editorial@genomebiology.com
General enquiries: info@biomedcentral.com

Genome Biology

Contact us