Skip to main content

Advertisement

Table 1 The distribution of the ratio of read counts between RefGene and Ensembl annotations (read length = 75 bp)

From: A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification

Sample No Expr Same 1.05 1.10 1.20 1.50 2 5 10 100
Adipose 19.97 16.53 26.16 19.64 14.51 8.81 5.65 1.96 0.94 0.16
Adrenal 16.92 14.04 36.18 27.09 19.07 11.28 7.14 2.45 1.24 0.24
Brain 16.79 15.22 32.94 24.91 17.95 10.78 6.73 2.29 1.08 0.20
Breast 18.04 15.22 29.63 22.21 16.06 9.80 6.52 2.38 1.19 0.20
Colon 20.50 17.41 25.85 19.43 14.30 8.95 6.10 2.30 1.17 0.19
Heart 21.23 16.43 26.39 20.10 14.39 8.88 5.47 1.73 0.82 0.19
Kidney 18.86 16.08 28.88 21.50 15.51 9.55 6.40 2.55 1.30 0.26
Leukocyte 29.53 17.37 20.03 15.29 11.62 7.58 5.37 2.47 1.33 0.26
Liver 24.60 19.16 23.20 17.43 12.84 8.24 5.42 2.00 1.02 0.15
Lung 19.65 16.46 29.22 21.35 15.07 9.09 6.15 2.61 1.43 0.24
Lymph node 20.94 16.79 31.74 24.16 17.21 10.26 6.65 2.69 1.44 0.24
Ovary 16.90 13.42 31.46 23.30 16.72 10.23 6.63 2.31 1.13 0.20
Prostate 18.21 16.29 28.33 21.14 15.17 9.43 6.51 2.49 1.27 0.23
Skeletal muscle 29.60 23.48 18.65 14.40 10.73 6.88 4.81 2.34 1.39 0.21
Testis 10.15 13.35 31.35 22.57 15.84 9.35 5.92 2.08 1.05 0.28
Thyroid 17.41 14.25 30.08 22.23 15.88 9.39 5.88 1.97 1.03 0.24
Average 19.96 16.34 28.13 21.05 15.18 9.28 6.09 2.29 1.18 0.22
  1. Note: Column “No Expr” represents the percentage of genes that do not express at all in both annotations. Column “Same” denotes the percentage of genes that have the same number of reads mapped to them in both gene models. The number in each cell after the column “Same” corresponds to the percentage of genes whose ratio is equal or greater than the threshold represented by the number.