CirRNAPL: A web server for the identification of circRNA based on extreme learning machine

https://doi.org/10.1016/j.csbj.2020.03.028Get rights and content
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Abstract

Circular RNA (circRNA) plays an important role in the development of diseases, and it provides a novel idea for drug development. Accurate identification of circRNAs is important for a deeper understanding of their functions. In this study, we developed a new classifier, CirRNAPL, which extracts the features of nucleic acid composition and structure of the circRNA sequence and optimizes the extreme learning machine based on the particle swarm optimization algorithm. We compared CirRNAPL with existing methods, including blast, on three datasets and found CirRNAPL significantly improved the identification accuracy for the three datasets, with accuracies of 0.815, 0.802, and 0.782, respectively. Additionally, we performed sequence alignment on 564 sequences of the independent detection set of the third data set and analyzed the expression level of circRNAs. Results showed the expression level of the sequence is positively correlated with the abundance. A user-friendly CirRNAPL web server is freely available at http://server.malab.cn/CirRNAPL/.

Abbreviations

circRNA
circular RNA
RF
random forest
PSO
particle swarm optimization algorithm
lncRNAs
long non-coding RNAs
PCGs
protein coding genes
DAC
Dinucleotide-based auto-covariance
DCC
Dinucleotide-based cross-covariance
DACC
Dinucleotide-based auto-cross-covariance
MAC
Moran autocorrelation
GAC
Geary autocorrelation
NMBAC
Normalized Moreau–Broto autocorrelation
PC-PseDNC-General
General parallel correlation pseudo-dinucleotide composition
SC-PseDNC-General
General series correlation pseudo-dinucleotide composition
Triplet
Local structure-sequence triplet element
PseSSC
Pseudo-structure status composition
PseDPC
Pseudo-distance structure status pair composition
ELM
extreme learning machine
RBF
radial basis function
CNN
Convolutional Neural Networks
SVM
support vector machine
SE
Sensitivity
SP
Specifity
ACC
Accuracy
MCC
Matthews Correlation Coefficient
MRMD
Maximum-Relevance-Maximum-Distance

Keywords

Circular RNA
Extreme learning machine
Particle swarm optimization algorithm
Identification
Expression level

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These authors contributed equally to this study