ArticleNucleic acids research2017
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 41 citations in OpenAlex.
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- A Deep Learning Model to Predict the ncRNA-Protein Interactions Based on Sequences Information Only.Bioinformatics and biology insights · 2025Article
- ASH2L regulates postnatal neurogenesis through Onecut2-mediated inhibition of TGF-β signaling pathway.Cell death and differentiation · 2023Article
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways.Bioinformatics (Oxford, England) · 2023Article
- Exploring the landscape of tools and resources for the analysis of long non-coding RNAs.Computational and structural biotechnology journal · 2023Review
- COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19.Frontiers in public health · 2023Article
- LncRNA functional annotation with improved false discovery rate achieved by disease associations.Computational and structural biotechnology journal · 2022Article
- LncSEA: a platform for long non-coding RNA related sets and enrichment analysis.Nucleic acids research · 2021Article
- Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer.Frontiers in genetics · 2021Review
- Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives.Non-coding RNA · 2020Review
- Widespread Dysregulation of Long Noncoding Genes Associated With Fatty Acid Metabolism, Cell Division, and Immune Response Gene Networks in Xenobiotic-exposed Rat Liver.Toxicological sciences : an official journal of the Society of Toxicology · 2020Article
- LnCompare: gene set feature analysis for human long non-coding RNAs.Nucleic acids research · 2019Article
- Drug Resistance-Related Competing Interactions of lncRNA and mRNA across 19 Cancer Types.Molecular therapy. Nucleic acids · 2019Article
- LncBook: a curated knowledgebase of human long non-coding RNAs.Nucleic acids research · 2019Article
- Literature-Based Enrichment Insights into Redox Control of Vascular Biology.Oxidative medicine and cellular longevity · 2019Review
- Measures of co-expression for improved function prediction of long non-coding RNAs.BMC bioinformatics · 2018Article
- RNA motifs and combinatorial prediction of interactions, stability and localization of noncoding RNAs.Nature structural & molecular biology · 2018Review
- LncRNA Structural Characteristics in Epigenetic Regulation.International journal of molecular sciences · 2017Review
- DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.RNA biology · 2017Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna.
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