An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer

BMC Medical Genomics

Table 2 Characteristics of epigenetic marks that were increased or decreased over 3 fold in the PANC-1 as compared to the hTERT-HPNE cell line

A. Epigenetic marks that were enriched or depleted in PANC-1 as compared to hTERT-HPNE pancreatic cells
		Increased in PANC-1 cells		Decreased in PANC-1 cells
Mark	Fold change	# Increased	% Increased	# Decreased	% Decreased
RNA Pol II	≥ 3	42,809	71.8%	16,841	28.2%
H3K4Me3	≥ 3	4,434	53.7%	3,828	46.3%
H3K4me1	≥ 3	13,999	26.1%	39,556	73.9%
H3K27Me3	≥ 3	2,474	19.0%	10,521	81.0%
B. Differential epigenetic marks (change ≥ 3 fold) in the *ALDH1A3* gene in PANC-1 and hTERT-HPNE pancreatic cell lines
		RNA Pol II		H3K27me3
Gene symbol		ALDH1A3		ALDH1A3
Chromosome		chr15		chr15
Start (bp)		101,420,000		101,435,600
End (bp)		101,420,199		101,439,799
PANC-1 readcount		1.119		1.181
hTERT-HPNE readcount		0.065		5.404
Fold change		12.39		0.23
P value		1.08 x 10^-13		8.55 x 10^-24
FDR		3.16 x 10^-13		1.27 x 10^-22

A. Number and percentages of epigenetic marks that were increased or decreased over 3 fold in the PANC-1 as compared to the hTERT-HPNE cell lines.
B. Epigenetic marks in the ALDH1A3 gene are listed with location (NCBI build 37) of the respective epigenetic mark, normalized read counts, fold change and significance values (P value and False Discovery Rate, FDR).

ISSN: 1755-8794