Average decoding accuracies of the acoustic parameters in layers S5, S6, and S7 with different kernel sizes.

Note that S5 with kernel size 10×10 and S6 with kernel size 10×10 are layers in the original network. Layer S5 with kernel size 20×20 was obtained by fixing layers S1 to C4 of the original network; layer S6 with size 5×5 and layer S7 with kernel size 5×5 were obtained by fixing layers S1 to C5 of the original network. The STRF sizes in these layers are indicated in parentheses.</p

Additional file 5 of Survey of the binding preferences of RNA-binding proteins to RNA editing events

Additional file 5: Table S4. Comparison of the overall editing levels between RBP eCLIP and RNA-seq data in K562 and HepG2

Additional file 1 of Survey of the binding preferences of RNA-binding proteins to RNA editing events

Additional file 1: Fig. S1. Statistics of the RNA editing events. Fig. S2. Cell specificity of the A-to-I RNA editing events in HepG2 and K562. Fig. S3. Statistics of the RNA editing sites falling in the RBP-binding regions. Fig. S4. Distributions of the editing levels in RBP eCLIP and RNA-seq data. Fig. S5. Overlaps between the RBP-associated editing sites identified by comparing RBP eCLIP and RNA-seq of 3 cellular fractions. Fig. S6. Numbers of the RBP-associated RNA editing events. Fig. 7. Summary of the RBP-associated RNA editing events in the same RBP-binding regions. Fig. S8. RBP interaction networks reconstructed with two methods. Fig. S9. The RBP interaction network based on the RBP-associated editing sites, highlighting different RNA processes. Fig. S10. The RBP interaction network based on the overlapping eCLIP peaks, highlighting different RNA processes. Fig. S11. RNA secondary structure differences before and after ADAR knockdown in HepG2

Additional file 8 of Survey of the binding preferences of RNA-binding proteins to RNA editing events

Additional file 8: Table S6. Survival-related RNA editing sites in cancers, data obtained from Han, L., et al., Cancer Cell, 2015

Visualization of the representative bases in layer S2 along with typical STRFs of the inferior colliculus neurons in animals.

(a–d) STRFs of several typical layer S2 units. Curves denote the spectral and temporal profiles obtained by SVD. (a) Two ON-type units. (b) Two OFF-type units. (c) Two localized checkerboard units. (d) Two spectral motion units. Similar STRFs of typical inferior colliculus neurons have been observed in physiological experiments. One can compare (a) with Fig 3E in [34], (b) with Fig 6A in [23], (c) with Fig 7A in [23] and (d) with Fig 6C in [29].</p

Influence of the pooling method used in the model.

(a, b) STRFs of all units in layers S2 and S3 without pooling. (c) PSI vectors of 77 active units in layer S6 without pooling. (d) PSI vectors of 96 active units in layer C6 with average pooling.</p

Additional file 3 of Survey of the binding preferences of RNA-binding proteins to RNA editing events

Additional file 3: Table S2. Summary of RNA editing sites detected in each fraction of K562 and HepG2

Additional file 9 of Survey of the binding preferences of RNA-binding proteins to RNA editing events

Additional file 9: Table S7. Statistics of 3’ UTR energy changes in HepG2 upon ADAR knockdown

Distributions of STRF parameters of layer S2 units.

(a) Best temporal modulation frequency. (b) Response duration. (c) Center frequencies. (d) Spectral bandwidth. These four parameters respectively correspond to the peak and bandwidth with 90% power of the temporal and spectral profiles shown in Fig 3. (e) Tradeoff between temporal modulation (Best T) and spectral modulation. (f–i) Probability distribution of STRF parameters normalized from the corresponding histograms. For comparison, the normalized probability distributions in layers S1 and S3 and the reference distributions of inferior colliculus neurons in cats [30] are also plotted. The horizontal axis in each panel is normalized to [0, 1] by dividing all values by the maximum value.</p

Additional file 7 of Survey of the binding preferences of RNA-binding proteins to RNA editing events

Additional file 7: Table S5. Annotations of the statistically significant RBP-associated RNA editing sites in K562 and HepG2