ArticleMolecular systems biology2015
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer.
Article in Molecular systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed.
- Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues.Journal of applied genetics · 2022Article
- The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma.NAR cancer · 2022Article
- EBV-associated diseases: Current therapeutics and emerging technologies.Frontiers in immunology · 2022Review
- Baiting out a full length sequence from unmapped RNA-seq data.BMC genomics · 2021Article
- Host-Virus Chimeric Events in SARS-CoV-2-Infected Cells Are Infrequent and Artifactual.Journal of virology · 2021Article
- Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual.bioRxiv : the preprint server for biology · 2021Article
- A genomic-clinicopathologic nomogram for predicting overall survival of hepatocellular carcinoma.BMC cancer · 2020Article
- Comparative RNA-Seq transcriptome analyses reveal dynamic time-dependent effects ofBMC genomics · 2020Article
- CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.Briefings in bioinformatics · 2020Article
- Transcriptomic signature reveals mechanism of flower bud distortion in witches'-broom disease of soybean (Glycine max).BMC plant biology · 2019Article
- Epigenetic regulation of lateralized fetal spinal gene expression underlies hemispheric asymmetries.eLife · 2017Article
- Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing.Frontiers in plant science · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Crucial parts of the genome including genes encoding microRNAs and noncoding RNAs went unnoticed for years, and even now, despite extensive annotation and assembly of the human genome, RNA-sequencing continues to yield millions of unmappable and thus uncharacterized reads. Here, we examined > 300 billion reads from 536 normal donors and 1,873 patients encompassing 21 cancer types, identified ~300 million such uncharacterized reads, and using a distinctive approach de novo assembled 2,550 novel human transcripts, which mainly represent long noncoding RNAs. Of these, 230 exhibited relatively specific expression or non-expression in certain cancer types, making them potential markers for those cancers, whereas 183 exhibited tissue specificity. Moreover, we used lentiviral-mediated expression of three selected transcripts that had higher expression in normal than in cancer patients and found that each inhibited the growth of HepG2 cells. Our analysis provides a comprehensive and unbiased resource of unmapped human transcripts and reveals their associations with specific cancers, providing potentially important new genes for therapeutic targeting.
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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.