Additional file 1 of CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers
Creators: name: Maruyama, Osamu
name: Li, Yinuo
name: Narita, Hiroki
name: Toh, Hidehiro
name: Au Yeung, Wan Kin
name: Sasaki, Hiroyuki
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Artificial Intelligence and Image Processing
subject: FOS: Computer and information sciences

description: Additional file 1. Fig. S1. Distribution of methylation ratios in the maternal genome of mouse blastocyst of the CGIs that are methylated in FGOs. The lower bound of class M (methylated) for FGOs is set to βM = 0.8 as shown in Table. 2. Fig. S2. Balanced accuracy of CMIC with different pairs of kmin and kmax. The search space of the pairs of kmin and kmax are set to be kmin = 2, . . . , 11 and kmax = 3, . . . , 12 with kmax − kmin ≥ 1. The bars are grouped by kmax. Fig. S3. MCC of CMIC with different pairs of kmin and kmax. The search space of the pairs of kmin and kmax are set to be kmin = 2, ..., 11 and kmax = 3, ..., 12 with kmax − kmin ≥ 1. The bars are grouped by kmax. Fig. S4. AUC of CMIC with different pairs of kmin and kmax. The search space of the pairs of kmin and kmax are set to be kmin = 2, ..., 11 and kmax = 3, ..., 12 with kmax − kmin ≥ 1. The bars are grouped by kmax. Fig. S5. Balanced accuracy with different schemes for embedding vectors shown in Table 3. The x-axis represents the eight methods to be compared: splitDNA2vec-C, splitDNA2vec-V, splitDNA2vec-sh-C, splitDNA2vec-sh-V, dna2vec-C, dna2vec-V, dna2vec-N1000-C, and dna2vec-N1000-V. The y-axis shows the F-measure on test datasets. Fig. S6. MCC with different schemes for embedding vectors shown in Table 3. The x-axis represents the eight methods to be compared: splitDNA2vec-C, splitDNA2vec-V, splitDNA2vec-sh-C, splitDNA2vec-sh-V, dna2vec-C, dna2vec-V, dna2vec-N1000-C, and dna2vec-N1000-V. The y-axis shows the F-measure on test datasets. Fig. S7. AUC with different schemes for embedding vectors shown in Table 3. The x-axis represents the eight methods to be compared: splitDNA2vec-C, splitDNA2vec-V, splitDNA2vec-sh-C, splitDNA2vec-sh-V, dna2vec-C, dna2vec-V, dna2vec-N1000-C, and dna2vec-N1000-V. The y-axis shows the F-measure on test datasets. Fig. S8. Balanced accuracy of CMIC with different numbers of variable-length k-mer sequences generated from an input CGI sequence, N. The x-axis represents values of N. The y-axis shows the F-measure with N. Fig. S9. MCC of CMIC with different numbers of variable-length k-mer sequences generated from an input CGI sequence, N. The x-axis represents values of N. The y-axis shows the F-measure with N. Fig. S10. AUC of CMIC with different numbers of variable-length k-mer sequences generated from an input CGI sequence, N. The x-axis represents values of N. The y-axis shows the F-measure with N. Fig. S11. Balanced accuracy of CMIC trained with short CGIs for long CGIs. The x-axis indicates the range of CGI sequence lengths. The y-axis indicates the F-measure. Fig. S12. MCC of CMIC trained with short CGIs for long CGIs. The x-axis indicates the range of CGI sequence lengths. The y-axis indicates the F-measure. Fig. S13. AUC of CMIC trained with short CGIs for long CGIs. The x-axis indicates the range of CGI sequence lengths. The y-axis indicates the F-measure. Fig. S14. Balanced accuracy of CMIC with alternative recurrent units, RNN, BiRNN, GRU, BiGRU, LSTM, and BiLSTM. Fig. S15. MCC of CMIC with alternative recurrent units, RNN, BiRNN, GRU, BiGRU, LSTM, and BiLSTM. Fig. S16. AUC of CMIC with alternative recurrent units, RNN, BiRNN, GRU, BiGRU, LSTM, and BiLSTM. Fig. S17. Balanced accuracy of KEGRU with various lengths of k-mers and strides. The vector size is set to 20. The x-axis represents a pair of k and stride. Fig. S18. MCC of KEGRU with various lengths of k-mers and strides. The vector size is set to 20. The x-axis represents a pair of k and stride. Fig. S19. AUC of KEGRU with various lengths of k-mers and strides. The vector size is set to 20. The x-axis represents a pair of k and stride. Fig. S20. Balanced accuracy of KEGRU with various lengths of k-mers and strides. The vector size is set to 50. The x-axis represents a pair of k and stride. Fig. S21. MCC of KEGRU with various lengths of k-mers and strides. The vector size is set to 50. The x-axis represents a pair of k and stride. Fig. S22. AUC of KEGRU with various lengths of k-mers and strides. The vector size is set to 50. The x-axis represents a pair of k and stride. Fig. S23. Plot generated by t-SNE with perplexity 10. Fig. S24. Plot generated by t-SNE with perplexity 50.