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Table 1 Performance of methylation status prediction using different prediction models

From: Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

Feature set Features Accuracy (%) AUC Specificity (%) Sensitivity (%) MCC R RMSE
Gene_pos a 9 78.6 0.85 72.5 83.6 0.57 0.61 0.39
Gene_pos + seq_property b 13 79.5 0.86 71.6 85.9 0.58 0.66 0.34
Gene_pos + seq_property + TFBSs 93 85.7 0.92 78.4 91.7 0.71 0.80 0.29
Gene_pos + seq_property + CREs c 118 89 0.94 83.9 93.3 0.78 0.86 0.23
Neighbor CpG methylation status + distance d 4 90.7 0.94 87.2 93.5 0.81 0.87 0.24
All features 122 91.9 0.96 87.9 95.1 0.84 0.90 0.19
  1. aGenomic position features including gene region status (promoter, gene body, and intergenic region), CGI status (CGI, CGI shore, CGI shelf, and non-CGI), and proximal SNPs. bDNA sequence properties include GC content, recombination rate, conservation score, and iHSs. cCREs include TFBSs, DHS sites, histone modifications and chromatin state segmentation. dGenomic distance between neighboring CpG sites. AUC, area under ROC curve; CGI, CpG island; CRE, cis-regulatory element; iHS, integrated haplotype score; MCC, Matthew’s correlation coefficient; RMSE, root-mean-square error; SNP, single nucleotide polymorphism; TFBS, transcription factor binding site.