LncDC: a Machine Learning-based Tool for Long Non-coding RNA Detection from RNA-Seq Data

Overview

Journal Sci Rep

Specialty Science

Date 2022 Nov 9

PMID 36351980

Authors

Minghua Li

Chun Liang

Affiliations

Soon will be listed here.

Abstract

Long non-coding RNAs (lncRNAs) play an essential role in diverse biological processes and disease development. Accurate classification of lncRNAs and mRNAs is important for the identification of tissue- or disease-specific lncRNAs. Here, we present our tool LncDC (Long non-coding RNA detection) that is able to accurately predict lncRNAs with an XGBoost model using features extracted from RNA sequences, secondary structures, and translated proteins. Benchmarking experiments showed that LncDC consistently outperformed six state-of-the-art tools in distinguishing lncRNAs from mRNAs. Notably, the use of sequence and secondary structure (SASS) k-mer score features and flexible ORF features improved the classification capability of LncDC. We anticipate that LncDC will definitely promote the discovery of more and novel disease-specific lncRNAs. LncDC is implemented in Python and freely available at https://github.com/lim74/LncDC .

Citing Articles

Computational Resources for lncRNA Functions and Targetome.

Thakur A, Kumar M Methods Mol Biol. 2024; 2883:299-323.

PMID: 39702714 DOI: 10.1007/978-1-0716-4290-0_13.

Simulated Annealing for RNA Design with SIMARD.

Tsang H Methods Mol Biol. 2024; 2847:95-108.

PMID: 39312138 DOI: 10.1007/978-1-0716-4079-1_6.

Discovering the hidden function in fungal genomes.

Gervais N, Shapiro R Nat Commun. 2024; 15(1):8219.

PMID: 39300175 PMC: 11413187. DOI: 10.1038/s41467-024-52568-z.

Comparison and benchmark of deep learning methods for non-coding RNA classification.

Creux C, Zehraoui F, Radvanyi F, Tahi F PLoS Comput Biol. 2024; 20(9):e1012446.

PMID: 39264986 PMC: 11421803. DOI: 10.1371/journal.pcbi.1012446.

Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration.

Chaudhary U, Banerjee S ACS Pharmacol Transl Sci. 2024; 7(7):1901-1915.

PMID: 39022352 PMC: 11249652. DOI: 10.1021/acsptsci.3c00388.

References

Cabili M, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A . Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25(18):1915-27. PMC: 3185964. DOI: 10.1101/gad.17446611. View

Zhao J, Song X, Wang K . lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts. Sci Rep. 2016; 6:34838. PMC: 5052565. DOI: 10.1038/srep34838. View

Budak H, Kaya S, Cagirici H . Long Non-coding RNA in Plants in the Era of Reference Sequences. Front Plant Sci. 2020; 11:276. PMC: 7080850. DOI: 10.3389/fpls.2020.00276. View

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H . The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012; 22(9):1775-89. PMC: 3431493. DOI: 10.1101/gr.132159.111. View

Zuker M, Stiegler P . Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981; 9(1):133-48. PMC: 326673. DOI: 10.1093/nar/9.1.133. View

Wucher V, Legeai F, Hedan B, Rizk G, Lagoutte L, Leeb T . FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res. 2017; 45(8):e57. PMC: 5416892. DOI: 10.1093/nar/gkw1306. View

Fickett J, Tung C . Assessment of protein coding measures. Nucleic Acids Res. 1992; 20(24):6441-50. PMC: 334555. DOI: 10.1093/nar/20.24.6441. View

Li X, Chen X, Hu X, Shen Y, Xu R, Wu L . Overexpression of GUCY1A2 Correlates With Poor Prognosis in Gastric Cancer Patients. Front Oncol. 2021; 11:632172. PMC: 8185334. DOI: 10.3389/fonc.2021.632172. View

Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S . STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; 29(1):15-21. PMC: 3530905. DOI: 10.1093/bioinformatics/bts635. View

10.

Babajide Mustapha I, Saeed F . Bioactive Molecule Prediction Using Extreme Gradient Boosting. Molecules. 2016; 21(8). PMC: 6273295. DOI: 10.3390/molecules21080983. View

11.

Statello L, Guo C, Chen L, Huarte M . Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol. 2020; 22(2):96-118. PMC: 7754182. DOI: 10.1038/s41580-020-00315-9. View

12.

Li Z, Dou P, Liu T, He S . Application of Long Noncoding RNAs in Osteosarcoma: Biomarkers and Therapeutic Targets. Cell Physiol Biochem. 2017; 42(4):1407-1419. DOI: 10.1159/000479205. View

13.

Tong X, Liu S . CPPred: coding potential prediction based on the global description of RNA sequence. Nucleic Acids Res. 2019; 47(8):e43. PMC: 6486542. DOI: 10.1093/nar/gkz087. View

14.

Li W, Godzik A . Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13):1658-9. DOI: 10.1093/bioinformatics/btl158. View

15.

Pertea M, Kim D, Pertea G, Leek J, Salzberg S . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11(9):1650-67. PMC: 5032908. DOI: 10.1038/nprot.2016.095. View

16.

Schmitz S, Grote P, Herrmann B . Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci. 2016; 73(13):2491-509. PMC: 4894931. DOI: 10.1007/s00018-016-2174-5. View

17.

Bjellqvist B, Hughes G, Pasquali C, Paquet N, Ravier F, Sanchez J . The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis. 1993; 14(10):1023-31. DOI: 10.1002/elps.11501401163. View

18.

Lobry J, Gautier C . Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res. 1994; 22(15):3174-80. PMC: 310293. DOI: 10.1093/nar/22.15.3174. View

19.

Hu L, Xu Z, Hu B, Lu Z . COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features. Nucleic Acids Res. 2016; 45(1):e2. PMC: 5224497. DOI: 10.1093/nar/gkw798. View

20.

Guruprasad K, Reddy B, Pandit M . Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. 1990; 4(2):155-61. DOI: 10.1093/protein/4.2.155. View