Prediction of binding property of RNA-binding proteins using multi-sized filters and multi-modal deep convolutional neural network

Cited 4 time in webofscience Cited 4 time in scopus
  • Hit : 448
  • Download : 201
RNA-binding proteins (RBPs) are important in gene expression regulations by post-transcriptional control of RNAs and immune system development and its function. Due to the help of sequencing technology, numerous RNA sequences are newly discovered without knowing their binding partner RBPs. Therefore, demands for accurate prediction method for RBP binding sites are increasing. There are many attempts for RBP binding site predictions using various machine-learning techniques combined with various RNA features. In this work, we present a new deep convolution neural network model trained on CLIP-seq datasets using multi-sized filters and multi-modal features to predict the binding property of RBPs. With this model, we integrated sequence and structure information to extract sequence motifs, structure motifs, and combined motifs at the same time. The RBP binding site prediction on RBP-24 dataset was compared with two multi-modal methods, GraphProt and Deepnet-rbp, using area under curve (AUC) of receiver-operating characteristics (ROC). Our method (average AUC = 0.920) outperformed 20 RBPs with GraphProt (average AUC = 0.888) and 15 RBP with Deepnet-rbp (average AUC = 0.902). The improvement was achieved by using multi-sized convolution filters, where average relative error reduction was 17%. By introducing new RNA structure representation, structure probability matrix, average relative error was reduced by 3% when compared to one-hot encoded secondary structure representation. Interestingly, structure probability matrix was more effective on ALKBH5, where relative error reduction was 30%. We developed new sequence motif enrichment method, which we stated as response enrichment method. We successfully enriched sequence motif for 12 RBPs, which had high resemblance with other literature evidences, RBP group and CISBP-RNA. Finally by analyzing these results altogether, we found intricate interplay between sequence motif and structure motif, which agreed with other researches.
Publisher
PUBLIC LIBRARY SCIENCE
Issue Date
2019-04
Language
English
Article Type
Article
Citation

PLOS ONE, v.14, no.4

ISSN
1932-6203
DOI
10.1371/journal.pone.0216257
URI
http://hdl.handle.net/10203/262205
Appears in Collection
BiS-Journal Papers(저널논문)
Files in This Item
000465846200040.pdf(3.86 MB)Download
This item is cited by other documents in WoS
⊙ Detail Information in WoSⓡ Click to see webofscience_button
⊙ Cited 4 items in WoS Click to see citing articles in records_button

qr_code

  • mendeley

    citeulike


rss_1.0 rss_2.0 atom_1.0