Similar Datasets
Project description:The dual functional lncRNAs have been intensively studied and identified to be involved in various fundamental cellular processes recently. It is essential to understand in which context when a dual functional lncRNA serves as a non-coding RNA or a template for coding peptide, particularly in some pathological conditions. However, apart from time consuming and cell type specific experiments, there is virtually no in-silico method for predicting the identity of dual functional lncRNAs. Here, we developed a deep-learning model with multi-head self-attention mechanism, LncReader, to identify dual functional lncRNAs based on their sequence, physicochemical and secondary structural features. Our data demonstrated that LncReader showed multiple advantage compared to various classical machine learning methods. Moreover, to obtain independent in-house datasets for robust testing, mass spectrometry proteomics combined with RNA-seq were applied in four leukemia cell lines. Remarkably, LncReader achieved the best performance among all these datasets. Therefore, LncReader provides a sophisticated and practical tool that enables fast dual functional lncRNAs identification.
2023-04-26 | PXD030066 | Pride
Project description:The dual functional lncRNAs have been intensively studied and identified to be involved in various fundamental cellular processes recently. It is essential to understand in which context when a dual functional lncRNA serves as a non-coding RNA or a template for coding peptide, particularly in some pathological conditions. However, apart from time consuming and cell type specific experiments, there is virtually no in-silico method for predicting the identity of dual functional lncRNAs. Here, we developed a deep-learning model with multi-head self-attention mechanism, LncReader, to identify dual functional lncRNAs based on their sequence, physicochemical and secondary structural features. Our data demonstrated that LncReader showed multiple advantage compared to various classical machine learning methods. Moreover, to obtain independent in-house datasets for robust testing, mass spectrometry proteomics combined with RNA-seq were applied in four leukemia cell lines. Remarkably, LncReader achieved the best performance among all these datasets. Therefore, LncReader provides a sophisticated and practical tool that enables fast dual functional lncRNAs identification.
2021-11-25 | GSE189394 | GEO
Project description:The dual functional lncRNAs have been intensively studied and identified to be involved in various fundamental cellular processes recently. It is essential to understand in which context when a dual functional lncRNA serves as a non-coding RNA or a template for coding peptide, particularly in some pathological conditions. However, apart from time consuming and cell type specific experiments, there is virtually no in-silico method for predicting the identity of dual functional lncRNAs. Here, we developed a deep-learning model with multi-head self-attention mechanism, LncReader, to identify dual functional lncRNAs based on their sequence, physicochemical and secondary structural features. Our data demonstrated that LncReader showed multiple advantage compared to various classical machine learning methods. Moreover, to obtain independent in-house datasets for robust testing, mass spectrometry proteomics combined with RNA-seq were applied in four leukemia cell lines. Remarkably, LncReader achieved the best performance among all these datasets. Therefore, LncReader provides a sophisticated and practical tool that enables fast dual functional lncRNAs identification.
2022-04-26 | GSE201484 | GEO
Project description:LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism
| PRJNA831861 | ENA
Project description:LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [RNA-seq]
| PRJNA782889 | ENA
Project description:LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [Ribo-seq]
| PRJNA831863 | ENA
Project description:Subcellular localization of messenger RNAs (mRNAs), as a prevalent mechanism, gives precise and efficient control for the translation process. There is mounting evidence for the important roles of this process in a variety of cellular events. Computational methods for mRNA subcellular localization prediction provide a useful approach for studying mRNA functions. However, few computational methods were designed for mRNA subcellular localization prediction and their performance have room for improvement. Especially, there is still no available tool to predict for mRNAs that have multiple localization annotations. In this paper, we propose a multi-head self-attention method, DM3Loc, for multi-label mRNA subcellular localization prediction. Evaluation results show that DM3Loc outperforms existing methods and tools in general. Furthermore, DM3Loc has the interpretation ability to analyze RNA-binding protein motifs and key signals on mRNAs for subcellular localization. Our analyses found hundreds of instances of mRNA isoform-specific subcellular localizations and many significantly enriched gene functions for mRNAs in different subcellular localizations.
| S-EPMC8096227 | biostudies-literature
Project description:Anemia is a critical complication in hemodialysis patients, but the response to erythropoietin-stimulating agents (ESA) treatment varies from patient to patient and is not linear across different time points. The aim of this study was to develop deep learning algorithms for individualized anemia management. We retrospectively collected 36,677 data points from 623 hemodialysis patients, including clinical data, laboratory values, hemoglobin levels, and previous ESA doses. To reduce the computational complexity associated with recurrent neural networks (RNN) in processing time-series data, we developed neural networks based on multi-head self-attention mechanisms in an efficient and effective hemoglobin prediction model. Our proposed model achieved a more accurate hemoglobin prediction than the state-of-the-art RNN model, as shown by the smaller mean absolute error (MAE) of hemoglobin (0.451 vs. 0.593 g/dL, p = 0.014). In ESA (including darbepoetin and epoetin) dose recommendation, the simulation results by our model revealed a higher rate of achieved hemoglobin targets (physician prescription vs. model: 86.3 % vs. 92.7 %, p < 0.001), a lower rate of hemoglobin levels below 10 g/dL (13.7 % vs. 7.3 %, p < 0.001) and smaller change in hemoglobin levels (0.6 g/dL vs. 0.4 g/dL, p < 0.001) in all patients. Our model holds great potential for individualized anemia management as a computerized clinical decision support system for hemodialysis patients. Further external validation with other datasets and prospective clinical utility studies are warranted.
| S-EPMC9898283 | biostudies-literature
Project description:Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and human through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.
| S-EPMC6128939 | biostudies-literature
Project description:BackgroundFunctional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing 20 years ago. The last decade of research has seen a tremendous increase in the number of non-coding RNAs identified in various organisms. While we have mechanistic understandings of small non-coding RNA pathways, long non-coding RNAs represent a diverse class of active transcripts whose function remains less well characterised.ResultsBy analysing hundreds of published transcriptome datasets, we annotated 3392 potential lncRNAs including 143 multi-exonic loci that showed increased nucleotide conservation and GC content relative to other non-coding regions. Using CRISPR/Cas9 genome editing, we generated deletion mutants for ten long non-coding RNA loci. Using automated microscopy for in-depth phenotyping, we show that six of the long non-coding RNA loci are required for normal development and fertility. Using RNA interference-mediated gene knock-down, we provide evidence that for two of the long non-coding RNA loci, the observed phenotypes are dependent on the corresponding RNA transcripts.ConclusionsOur results highlight that a large section of the non-coding regions of the C. elegans genome remains unexplored. Based on our in vivo analysis of a selection of high-confidence lncRNA loci, we expect that a significant proportion of these high-confidence regions is likely to have a biological function at either the genomic or the transcript level.
| S-EPMC6378714 | biostudies-literature