ArticleGenome research2011
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 39 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed.
- CGC1, a new reference genome forGenome research · 2025Article
- Detecting gene expression in Caenorhabditis elegans.Genetics · 2025Review
- Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans.The EMBO journal · 2021Article
- Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer.Frontiers in genetics · 2021Review
- The computational approaches of lncRNA identification based on coding potential:Computational and structural biotechnology journal · 2020Review
- Predicting functional long non-coding RNAs validated by low throughput experiments.RNA biology · 2019Article
- Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus.BMC genomics · 2018Article
- Recurrently deregulated lncRNAs in hepatocellular carcinoma.Nature communications · 2017Article
- COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features.Nucleic acids research · 2017Article
- A Review on Recent Computational Methods for Predicting Noncoding RNAs.BioMed research international · 2017Review
- Critical roles of long noncoding RNAs in Drosophila spermatogenesis.Genome research · 2016Article
- The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection.PLoS genetics · 2016Article
- Integrating Epigenomics into the Understanding of Biomedical Insight.Bioinformatics and biology insights · 2016Review
- Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos.BMC genomics · 2015Article
- A common set of distinct features that characterize noncoding RNAs across multiple species.Nucleic acids research · 2015Article
- Computational Approaches for the Analysis of ncRNA through Deep Sequencing Techniques.Frontiers in bioengineering and biotechnology · 2015Review
- ptRNApred: computational identification and classification of post-transcriptional RNA.Nucleic acids research · 2014Article
- Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy.Protein & cell · 2014Article
- Article
- Genome and transcriptome of the porcine whipworm Trichuris suis.Nature genetics · 2014Article
Corrections and comments
- Erratum issued
Authors and funding
17 authors.
Funding
Abstract
We present an integrative machine learning method, incRNA, for whole-genome identification of noncoding RNAs (ncRNAs). It combines a large amount of expression data, RNA secondary-structure stability, and evolutionary conservation at the protein and nucleic-acid level. Using the incRNA model and data from the modENCODE consortium, we are able to separate known C. elegans ncRNAs from coding sequences and other genomic elements with a high level of accuracy (97% AUC on an independent validation set), and find more than 7000 novel ncRNA candidates, among which more than 1000 are located in the intergenic regions of C. elegans genome. Based on the validation set, we estimate that 91% of the approximately 7000 novel ncRNA candidates are true positives. We then analyze 15 novel ncRNA candidates by RT-PCR, detecting the expression for 14. In addition, we characterize the properties of all the novel ncRNA candidates and find that they have distinct expression patterns across developmental stages and tend to use novel RNA structural families. We also find that they are often targeted by specific transcription factors (∼59% of intergenic novel ncRNA candidates). Overall, our study identifies many new potential ncRNAs in C. elegans and provides a method that can be adapted to other organisms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.