Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets
Abstract
:1. Introduction
2. Materials and Methods
2.1. Downloading CLIP-Seq Datasets
2.2. Linearization of circRNA Library
2.3. Competitive Alignment of CLIP-Seq Reads
2.4. Filtering for CLIP-Seq Reads Supporting RBP-circRNA Interactions
2.5. Software Implementation
2.6. Motif Search
2.7. “Strand Bias” of RBP Binding to circRNAs
2.8. Hierarchical Clustering of RBPs
2.9. Gene Ontology Enrichment Analysis
3. Results
3.1. The Implementation of the Clirc Software
3.2. Profiling circRNAs Bound by RBPs Using Clirc
3.3. Binding Properties of RBPs on circRNAs
3.4. Functional Implications of circRNA-RBP Interactions
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Zhang, M.; Wang, T.; Xiao, G.; Xie, Y. Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Genes 2020, 11, 54. https://doi.org/10.3390/genes11010054
Zhang M, Wang T, Xiao G, Xie Y. Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Genes. 2020; 11(1):54. https://doi.org/10.3390/genes11010054
Chicago/Turabian StyleZhang, Minzhe, Tao Wang, Guanghua Xiao, and Yang Xie. 2020. "Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets" Genes 11, no. 1: 54. https://doi.org/10.3390/genes11010054