# A Novel Deep Learning Method for Predicting RNA-Protein Binding Sites
## 3 Results
### Motif Visualizations  
In this research, binding motifs representing binding preferences were automatically extracted according to the parameters and other information in HPNet. Based on the results of a biological study, a database of RBP motifs and specificities has been constructed named the RNA Inferred Sequence Binding Protein Catalog (CISBP-RNA) [42]. Therefore, the patterns retrieved by HPNet can be compared with the motifs in CISBP-RNA. TOMTOM [43] can fulfill this function. It rates the similarity between the input motifs and the pre-existing database of known motifs and selects the p-value as the measure.  
In this experiment, the first-layer output of the GCN represented the importance of the nucleotide nodes. The weights output by the first layer of the CNN represented the importance of the nucleotides in the sequence. The mean value for the node importance and sequence importance for each nucleotide was calculated as the nucleotide-binding affinity and expanded into 7-mer motifs centered on the most significant 5% of nucleotides. Then, the RCK technique was utilized to convert the binding nucleotide sequences into PWM based on the selected nucleotides. We used TOMTOM to visualize and compare experimentally generated motifs.  
Table 4 displays the RBP-binding motifs extracted by HPNet and the motifs in the CISBP-RNA database. It also shows the \"U\" enrichment in the binding motif of TIA1 and HNRNPC proteins. The results of TOMTOM were consistent with the motifs previously found in CISBP-RNA, with \(p\)-values of 0.00046 and 0.00017, respectively. The binding motif of the SFRS1 protein was rich in the segment of \"GAGGA\", which was the same as a result in the CISBP-RNA database. According to the CISBP-RNA database, the \"UGCA\" region was highly typical in the binding motif of the PUM2 protein. The binding motif of the protein QKI contained a \"CUAA\" fragment. However, the outcomes for the IGF2 BP1-3 protein need to be made clearer.  
However, the CISBP-RNA database only contains known experimental RBP binding motifs. Several RBPs have binding motifs that still need to be verified. Therefore, we employed Multiple EM for Motive Elicitation (MEME) [44] to develop the models of untested binding motifs, as given in Table 5, which also compares the results with relevant previous findings. Table 5 demonstrates that the ELAVL1 protein and its related proteins have a high affinity for \"U\"-rich motifs, consistent with the biological experiment results in [45]. The binding motif of the TIAL1 protein and TIA1 protein is rich in \"UU\", consistent with the results from [46]. In addition, the binding motifs of FUS, TAF15, and EWSR1 are  
\begin{table}
\begin{tabular}{c c c c c} \hline \hline
**RBPs** & **Motifs** & **RBPs** & **Motifs** & **RBPs** & **Motifs** \\ \hline \multirow{6}{*}{HNRNPC} & \(p\)-value: 3.22 \(\times\)\(10^{-5}\) & \(p\)-value: 3.58 \(\times\)\(10^{-3}\) & \(p\)-value: 5.70 \(\times\)\(10^{-4}\) \\  & & SRSF1 & TIA1 & \\ \cline{1-1}  & & QKI & IGF2 BP123 & \\ \hline \hline \end{tabular}
\end{table}
Table 4: Comparison of motifs extracted by HPNet (bottom) and motifs in the CISBP-RNA database (top).  
rich in \"AU\", while PTB is rich in \"UC\". The character's height indicates each position's information retention degree (bit) at that point in the illustration.