WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.
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WebCircRNA : Classifying the Circular RNA Potential of Coding and Noncoding RNA. / Pan, Xiaoyong; Xiong, Kai; Anthon, Christian; Hyttel, Poul; Freude, Kristine; Jensen, Lars Juhl; Gorodkin, Jan.
In: Genes, Vol. 9, No. 11, 536, 06.11.2018.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - WebCircRNA
T2 - Classifying the Circular RNA Potential of Coding and Noncoding RNA.
AU - Pan, Xiaoyong
AU - Xiong, Kai
AU - Anthon, Christian
AU - Hyttel, Poul
AU - Freude, Kristine
AU - Jensen, Lars Juhl
AU - Gorodkin, Jan
PY - 2018/11/6
Y1 - 2018/11/6
N2 - Circular RNAs (circRNAs) are increasingly recognized to play crucial roles in post-transcriptional gene regulation including functioning as microRNA (miRNA) sponges or as wide-spread regulators, for example in stem cell differentiation. It is therefore highly relevant to identify if a transcript of interest can also function as a circRNA. Here, we present a user-friendly web server that predicts if coding and noncoding RNAs have circRNA isoforms and whether circRNAs are expressed in stem cells. The predictions are made by random forest models using sequence-derived features as input. The output scores are converted to fractiles, which are used to assess the circRNA and stem cell potential. The performances of the three models are reported as the area under the receiver operating characteristic (ROC) curve and are 0.82 for coding genes, 0.89 for long noncoding RNAs (lncRNAs) and 0.72 for stem cell expression. We present WebCircRNA for quick evaluation of human genes and transcripts for their circRNA potential, which can be essential in several contexts.
AB - Circular RNAs (circRNAs) are increasingly recognized to play crucial roles in post-transcriptional gene regulation including functioning as microRNA (miRNA) sponges or as wide-spread regulators, for example in stem cell differentiation. It is therefore highly relevant to identify if a transcript of interest can also function as a circRNA. Here, we present a user-friendly web server that predicts if coding and noncoding RNAs have circRNA isoforms and whether circRNAs are expressed in stem cells. The predictions are made by random forest models using sequence-derived features as input. The output scores are converted to fractiles, which are used to assess the circRNA and stem cell potential. The performances of the three models are reported as the area under the receiver operating characteristic (ROC) curve and are 0.82 for coding genes, 0.89 for long noncoding RNAs (lncRNAs) and 0.72 for stem cell expression. We present WebCircRNA for quick evaluation of human genes and transcripts for their circRNA potential, which can be essential in several contexts.
KW - Circular RNA
KW - Noncoding RNA
KW - Random forest
U2 - 10.3390/genes9110536
DO - 10.3390/genes9110536
M3 - Journal article
C2 - 30404245
VL - 9
JO - Genes
JF - Genes
SN - 2073-4425
IS - 11
M1 - 536
ER -
ID: 209117159