ArticleGenome research2017
High-confidence coding and noncoding transcriptome maps.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- A hybrid transcriptome assembly reveals coding and noncoding landscapes in Drosophila hemocytes.Genetics · 2026Article
- GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing.bioRxiv : the preprint server for biology · 2024Article
- Identification of SLC31A1 as a prognostic biomarker and a target for therapeutics in breast cancer.Scientific reports · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Distinct regulatory functions and biological roles of lncRNA splice variants.Molecular therapy. Nucleic acids · 2023Review
- LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations.Nucleic acids research · 2023Article
- GENCODE: reference annotation for the human and mouse genomes in 2023.Nucleic acids research · 2023Article
- TGF-β1 regulates the lncRNA transcriptome of ovarian granulosa cells in a transcription activity-dependent manner.Cell proliferation · 2023Article
- Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities.Cell genomics · 2022Article
- how_are_we_stranded_here: quick determination of RNA-Seq strandedness.BMC bioinformatics · 2022Article
- Tumor immune microenvironment lncRNAs.Briefings in bioinformatics · 2022Review
- RNA editing regulates lncRNA splicing in human early embryo development.PLoS computational biology · 2021Article
- The RNA Atlas expands the catalog of human non-coding RNAs.Nature biotechnology · 2021Article
- Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease.PLoS genetics · 2021Article
- Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells.Nucleic acids research · 2021Article
- lncRNA TRMP-S directs dual mechanisms to regulate p27-mediated cellular senescence.Molecular therapy. Nucleic acids · 2021Article
- LncExpDB: an expression database of human long non-coding RNAs.Nucleic acids research · 2021Article
- Illuminating lncRNA Function Through Target Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae.Scientific reports · 2020Article
- lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA.Scientific data · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes.
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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.