Table 1 Integrated RNA sequencing, DNA methylation and DNA copy number alteration(CNA) analysis.

From: Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes

Gene symbol	Genomic region	Enhancer	Gene expression^a	DNA methylation^b	DNA copy number alteration^c
CCC case vs MC control
FAM20A	17q24.2-q24.3	NA	overexpressed	hypomethylated	genomic gain
LAMB1	7q22.3-q31.1	NA	overexpressed	hypomethylated	genomic gain
EC case vs CCC control
CLMN	14q32.13	NA	overexpressed	hypomethylated	genomic gain
HGSC case vs CCC control
CACNA1A	19p13.13	yes	overexpressed	hypomethylated	genomic gain
CACNB1	17q12	yes	overexpressed	hypomethylated	genomic gain
CELF4	18q12.2	NA	overexpressed	hypomethylated	genomic gain
CLMN	14q32.13	yes	overexpressed	hypomethylated	genomic gain
COL14A1	8q24.12	yes	overexpressed	hypomethylated	genomic gain
EBF4	20p13	NA	overexpressed	hypomethylated	genomic gain
EHF	11p13	yes	overexpressed	hypomethylated	genomic gain
HMGA2	12q14.3	yes	overexpressed	hypomethylated	genomic gain
IDH3B	20p13	NA	overexpressed	hypomethylated	genomic gain
KCNMB2	3q26.32	NA	overexpressed	hypomethylated	genomic gain
LINC00578	3q26.32	yes	overexpressed	hypomethylated	genomic gain
MAPK4	18q21.1-q21.2	NA	overexpressed	hypomethylated	genomic gain
MEIS2	15q14	NA	overexpressed	hypomethylated	genomic gain
MTBP	8q24.12	NA	overexpressed	hypomethylated	genomic gain
MYLK2	20q11.21	NA	overexpressed	hypomethylated	genomic gain
NRSN2	20p13	NA	overexpressed	hypomethylated	genomic gain
PDYN	20p13	yes	overexpressed	hypomethylated	genomic gain
PPP1R1B	17q12	yes	overexpressed	hypomethylated	genomic gain
PROKR2	20p12.3	NA	overexpressed	hypomethylated	genomic gain
RASSF2	20p13-p12.3	NA	overexpressed	hypomethylated	genomic gain
RPL22L1	3q26.2	NA	overexpressed	hypomethylated	genomic gain
TP63	3q28	NA	overexpressed	hypomethylated	genomic gain
ELP3	8p21.1	NA	underexpressed	hypermethylated	genomic loss
HGSC case vs EC control
AARD	8q24.11	NA	overexpressed	hypomethylated	genomic gain
CCNE1	19q12	NA	overexpressed	hypomethylated	genomic gain
CTCFL	20q13.31	NA	overexpressed	hypomethylated	genomic gain
LINC00578	3q26.32	yes	overexpressed	hypomethylated	genomic gain
LINC01532	19q12	NA	overexpressed	hypomethylated	genomic gain
RBM38	20q13.31	yes	overexpressed	hypomethylated	genomic gain
RSPO4	20p13	NA	overexpressed	hypomethylated	genomic gain
UQCRFS1	19q12	NA	overexpressed	hypomethylated	genomic gain
URI1	19q12	NA	overexpressed	hypomethylated	genomic gain
PDE8B	5q13.3	NA	underexpressed	hypermethylated	genomic loss
HGSC case vs MC control
ANKS1B	12q23.1	yes	overexpressed	hypomethylated	genomic gain
COLEC10	8q24.12	yes	overexpressed	hypomethylated	genomic gain
EGFEM1P	3q26.2	NA	overexpressed	hypomethylated	genomic gain
KCNMB2-AS1	3q26.32	NA	overexpressed	hypomethylated	genomic gain
LINC00578	3q26.32	yes	overexpressed	hypomethylated	genomic gain
MYEF2	15q21.1	NA	overexpressed	hypomethylated	genomic gain
PDYN	20p13	NA	overexpressed	hypomethylated	genomic gain
RBFOX1	16p13.3	yes	overexpressed	hypomethylated	genomic gain
SNAP25	20p12.3-p12.2	NA	overexpressed	hypomethylated	genomic gain
STON2	14q31.1	yes	overexpressed	hypomethylated	genomic gain
SULF1	8q13.2-q13.3	NA	overexpressed	hypomethylated	genomic gain
TSHR	14q31.1	yes	overexpressed	hypomethylated	genomic gain
TGFBR2	3p24.1	NA	underexpressed	hypermethylated	genomic loss

The table shows putative oncogenes and tumor suppressor genes that were found to be deregulated using three different methods (RNA-seq, DNA methylation, CNA analyses). Generally, the genes were overexpressed, hypomethylated and showed genomic gain. A few genes were also underexpressed, hypermethylated and showed genomic loss. No biomarkers were found to be deregulated in all three methods when comparing EC with MC.
^aGene expression log2 ratios greater than 0.58 (i.e. 1.5 fold change) are indicated by overexpression and less than -0.58 (i.e. 1.5 fold change) by underexpression.
^bDNA methylation delta beta values greater than 0.2 are indicated by hypermethylation and less than -0.2 by hypomethylation.
^cDNA copy number alteration values greater than 0.3 are indicated by genomic gain and less than -0.3 by genomic loss.

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Table 1 Integrated RNA sequencing, DNA methylation and DNA copy number alteration(CNA) analysis.

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