ArticleNucleic acids research2016
deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 137 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
137 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Circ-ABCA1 promotes breast cancer stem cell-mediated malignant progression by modulating miR-33a-5p/EIF4A3 axis.Clinical and experimental medicine · 2026Article
- Identification of Long Noncoding RNA by In Situ Hybridization Approaches.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Elevated cytokines in osteoporotic blood correlate with immune microenvironment shifts and dysregulated circRNA profiles.Frontiers in immunology · 2026Article
- Integrative circRNA landscape of intrauterine adhesions: putative ceRNA axes and circRNA-associated splicing usage linked to contractility and immunity.Frontiers in molecular biosciences · 2026Article
- Online Databases in Circular RNAs.Advances in experimental medicine and biology · 2025Review
- Review
- Review
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- Distinctive physical properties of DNA shared by RNA polymerase II gene promoters and 5'-flanking regions of tRNA genes.Journal of biochemistry · 2024Article
- circAtlas 3.0: a gateway to 3 million curated vertebrate circular RNAs based on a standardized nomenclature scheme.Nucleic acids research · 2024Article
- Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human.Nature genetics · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Emerging roles and potential clinical applications of translatable circular RNAs in cancer and other human diseases.Genes & diseases · 2023Review
- circRNA-SFMBT2 orchestrates ERα activation to drive tamoxifen resistance in breast cancer cells.Cell death & disease · 2023Article
- Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis.NAR cancer · 2023Article
- Exploring circular MET RNA as a potential biomarker in tumors exhibiting high MET activity.Journal of experimental & clinical cancer research : CR · 2023Article
- Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia.Cell reports · 2023Article
- Circular RNAs: implications of signaling pathways and bioinformatics in human cancer.Cancer biology & medicine · 2023Review
- Recent Advances and Future Potential of Long Non-Coding RNAs in Insects.International journal of molecular sciences · 2023Review
77 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small non-coding RNAs (e.g. miRNAs) and long non-coding RNAs (e.g. lincRNAs and circRNAs) are emerging as key regulators of various cellular processes. However, only a very small fraction of these enigmatic RNAs have been well functionally characterized. In this study, we describe deepBase v2.0 (http://biocenter.sysu.edu.cn/deepBase/), an updated platform, to decode evolution, expression patterns and functions of diverse ncRNAs across 19 species. deepBase v2.0 has been updated to provide the most comprehensive collection of ncRNA-derived small RNAs generated from 588 sRNA-Seq datasets. Moreover, we developed a pipeline named lncSeeker to identify 176 680 high-confidence lncRNAs from 14 species. Temporal and spatial expression patterns of various ncRNAs were profiled. We identified approximately 24 280 primate-specific, 5193 rodent-specific lncRNAs, and 55 highly conserved lncRNA orthologs between human and zebrafish. We annotated 14 867 human circRNAs, 1260 of which are orthologous to mouse circRNAs. By combining expression profiles and functional genomic annotations, we developed lncFunction web-server to predict the function of lncRNAs based on protein-lncRNA co-expression networks. This study is expected to provide considerable resources to facilitate future experimental studies and to uncover ncRNA functions.
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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.