Jump to main content
Jump to site search

Issue 8, 2015
Previous Article Next Article

PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features

Author affiliations

Abstract

Recently circular RNA (circularRNA) has been discovered as an increasingly important type of long non-coding RNA (lncRNA), playing an important role in gene regulation, such as functioning as miRNA sponges. So it is very promising to identify circularRNA transcripts from de novo assembled transcripts obtained by high-throughput sequencing, such as RNA-seq data. In this study, we presented a machine learning approach, named as PredcircRNA, focused on distinguishing circularRNA from other lncRNAs using multiple kernel learning. Firstly we extracted different sources of discriminative features, including graph features, conservation information and sequence compositions, ALU and tandem repeats, SNP densities and open reading frames (ORFs) from transcripts. Secondly, to better integrate features from different sources, we proposed a computational approach based on a multiple kernel learning framework to fuse those heterogeneous features. Our preliminary 5-fold cross-validation result showed that our proposed method can classify circularRNA from other types of lncRNAs with an accuracy of 0.778, sensitivity of 0.781, specificity of 0.770, precision of 0.784 and MCC of 0.554 in our constructed gold-standard dataset, respectively. Our feature importance analysis based on Random Forest illustrated some discriminative features, such as conservation features and a GTAG sequence motif. Our PredcircRNA tool is available for download at https://github.com/xypan1232/PredcircRNA.

Graphical abstract: PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features

Back to tab navigation

Supplementary files

Publication details

The article was received on 26 Mar 2015, accepted on 18 May 2015 and first published on 18 May 2015


Article type: Paper
DOI: 10.1039/C5MB00214A
Author version
available:
Download author version (PDF)
Mol. BioSyst., 2015,11, 2219-2226

  •   Request permissions

    PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features

    X. Pan and K. Xiong, Mol. BioSyst., 2015, 11, 2219
    DOI: 10.1039/C5MB00214A

Search articles by author

Spotlight

Advertisements