Inferring disease-associated long non-coding RNAs using genome - wide tissue expression profiles
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
Inferring disease-associated long non-coding RNAs using genome - wide tissue expression profiles. / Pan, Xiaoyong; Jensen, Lars Juhl; Gorodkin, Jan.
In: Bioinformatics, Vol. 35, No. 9, 2019, p. 1494-1502.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Inferring disease-associated long non-coding RNAs using genome - wide tissue expression profiles
AU - Pan, Xiaoyong
AU - Jensen, Lars Juhl
AU - Gorodkin, Jan
PY - 2019
Y1 - 2019
N2 - Motivation: Long non-coding RNAs (lncRNAs) are important regulators in wide variety of biological processes, which are linked to many diseases. Compared to protein-coding genes (PCGs), the association between diseases and lncRNAs is still not well studied. Thus, inferring disease-associated lncRNAs on a genome-wide scale has become imperative.Results: In this study, we propose a machine learning-based method, DislncRF, which infers disease-associated lncRNAs on a genome-wide scale based on tissue expression profiles. DislncRF uses random forest models trained on expression profiles of known disease-associated PCGs across human tissues to extract general patterns between expression profiles and diseases. These models are then applied to score associations between lncRNAs and diseases. DislncRF was benchmarked against a gold standard data set and compared to other methods. The results show that DislncRF yields promising performance and outperforms the existing methods. The utility of DislncRF is further substantiated on two diseases in which we find that top scoring candidates are supported by literature or independent data sets.Availability: https://github.com/xypan1232/DislncRF.Supplementary information: Supplementary data are available at Bioinformatics online.
AB - Motivation: Long non-coding RNAs (lncRNAs) are important regulators in wide variety of biological processes, which are linked to many diseases. Compared to protein-coding genes (PCGs), the association between diseases and lncRNAs is still not well studied. Thus, inferring disease-associated lncRNAs on a genome-wide scale has become imperative.Results: In this study, we propose a machine learning-based method, DislncRF, which infers disease-associated lncRNAs on a genome-wide scale based on tissue expression profiles. DislncRF uses random forest models trained on expression profiles of known disease-associated PCGs across human tissues to extract general patterns between expression profiles and diseases. These models are then applied to score associations between lncRNAs and diseases. DislncRF was benchmarked against a gold standard data set and compared to other methods. The results show that DislncRF yields promising performance and outperforms the existing methods. The utility of DislncRF is further substantiated on two diseases in which we find that top scoring candidates are supported by literature or independent data sets.Availability: https://github.com/xypan1232/DislncRF.Supplementary information: Supplementary data are available at Bioinformatics online.
U2 - 10.1093/bioinformatics/bty859
DO - 10.1093/bioinformatics/bty859
M3 - Journal article
C2 - 30295698
VL - 35
SP - 1494
EP - 1502
JO - Computer Applications in the Biosciences
JF - Computer Applications in the Biosciences
SN - 1471-2105
IS - 9
ER -
ID: 203559337