Cellular and clinical impact of protein phosphatase enzyme epigenetic silencing in multiple cancer tissues

Table 1 Breakdown of the Infinium Human Methylation 450 BeadChip (450 K) samples used and excluded in this study. Initial dataset refers to the number of cancer patients and control datasets downloaded and pre-processed for 450 K DNA methylation analysis. Datasets for analysis is the final number of 450 K patient and control samples analysed in this study. Datasets removed were the number of samples excluded after pre-processing and quality control steps, representing incorrect or mislabeled samples.

Tissue dataset	TCGA cancer	CCL	Organoids	Controls	TCGA healthy test
Dataset source:
Colorectum	100	49	11	10	16
Oesophagus	100	35	4	10	8
Lung	100	61	1	10	16
Pancreas	100	31	7	10	5
Stomach	100	28	2	10*	2
Total:	500	204	25	50	47
Datasets used for analysis:
Colorectum	95	49	11	10	16
Oesophagus	92	35	4	8	8
Lung	94	61	1	10	16
Pancreas	97	31	7	4	5
Stomach	98	28	2	10	2
Total:	476	204	25	42	47
Datasets excluded:	24	0	0	8	0
Colorectum	5	0	0	0	0
Oesophagus	8	0	0	2	0
Lung	6	0	0	0	0
Pancreas	3	0	0	6	0
Stomach	2	0	0	10	0
Total:	24	0	0	8	0

TCGA cancer = Primary tumour samples from The Cancer Genome Atlas data repository, CCL = Cancer Cell Line, Organoids = embedded 3D cultures. Controls = healthy tissue samples used as controls to identify cancer-associated hypermethylation at PPEIP gene promoters. TCGA healthy test = separate subset of healthy tissue samples used to identify non-cancer associated hypermethylation events in PPEIP gene promoters in the healthy population. * = Stomach samples were downloaded from GEO under the accession number: GSE127857 (due to the lack of available samples in TCGA data repository)

ISSN: 1479-7364