Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences

BMC Genomics

Table 2 Editing ratios of constitutive A-to-I sites at one editing box in 18 human samples

chr2:	37,328,008	37,328,012	37,328,013	37,328,016	37,328,034	37,328,075	37,328,082	37,328,087	37,328,100
H9	9.1%		5.6%		43.3%	26.9%		20.0%	8.3%
HeLa	11.5%		24.7%	8.5%	71.8%	45.8%	18.9%	16.7%
Adipose	30.2%		41.5%	20.7%	78.0%	74.2%	63.3%	38.1%	8.8%
Adrenal	41.9%	7.5%	32.3%	25.9%	87.8%	69.5%	53.0%	38.6%
Brain	24.3%	5.6%	42.3%	28.0%	87.2%	63.8%	46.8%	26.6%	14.6%
Breast	9.7%		14.2%	15.5%	63.8%	47.0%	50.0%	12.5%
Colon	19.3%		19.6%	18.1%	91.8%	50.8%	7.0%	26.9%
Heart	9.1%		18.4%		53.3%	13.3%	17.6%	18.4%
Kidney	22.4%	6.4%	29.1%		58.9%	45.9%		15.1%	6.5%
Liver		50.0%	54.2%		76.0%
Lung	26.4%	7.8%	19.6%	13.7%	59.5%				29.3%
Lymph Node			29.8%	14.3%	65.7%	39.1%	20.0%	48.6%
Ovary	11.2%		40.1%	15.4%	71.2%	32.5%	25.8%	23.5%
Prostate	27.8%	7.9%	43.4%	30.3%	79.7%	95.6%	46.7%	33.2%	11.4%
Skeletal Muscle			33.3%		20.9%
Testes	19.6%		16.1%	15.5%	89.0%	42.6%	38.8%	31.1%	5.5%
Thyroid	13.2%	8.2%	31.8%	20.3%	64.8%	17.6%	28.8%	32.0%
White Bllod Cell	7.6%		31.1%	24.5%	66.3%	26.3%	36.7%
PSS	13	5	8	13	10	3	5	12	7
Darned database^a			Yes		Yes	Yes	Yes
Li, et al. 2009²⁴			Yes		Yes	Yes	Yes
Bahn, et al. 2012-BC⁹			Yes		Yes	Yes	Yes	Yes
Bahn, et al. 2012-U87MG⁹					Yes	Yes
Peng, et al. 2012⁸			Yes
Ramaswami, et al. 2012¹⁰			Yes		Yes	Yes	Yes

Predicted editing ratios of nine A-to-I sites in editing box at chr2: 37,328,008 -37,328,100 are listed in all examined cell lines/tissues. Blank indicates either no editing or failure of passing our stringent cutoffs (HPB > 5, etc.). Five annotated sites were reported from different datasets/analyses. ^aDataset of RNA editing at http://darned.ucc.ie/.

ISSN: 1471-2164