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DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts

2019 Nucleic Acids Research  
DIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts.  ...  Known short variant information, on >67,000 experimentally supported target sites and lncRNA expression profiles in different cellular compartments are catered to users.  ...  We would also like to thank Artemis Fakorelli for her contribution to the final editing of the manuscript and Athanasios Fevgas for the IT support.  ... 
doi:10.1093/nar/gkz1036 pmid:31732741 pmcid:PMC7145509 fatcat:ldtxbr6y3je45drvs3ygjynbv4

DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs

Maria D. Paraskevopoulou, Georgios Georgakilas, Nikos Kostoulas, Martin Reczko, Manolis Maragkakis, Theodore M. Dalamagas, Artemis G. Hatzigeorgiou
2012 Nucleic Acids Research  
DIANA-LncBase hosts transcriptome-wide experimentally verified and computationally predicted miRNA recognition elements (MREs) on human and mouse lncRNAs.  ...  Recently, the attention of the research community has been focused on long non-coding RNAs (lncRNAs) and their physiological/pathological implications.  ...  Results of a submitted query in DIANA-LncBase experimental module.  ... 
doi:10.1093/nar/gks1246 pmid:23193281 pmcid:PMC3531175 fatcat:gfbjbg7cobdftcfjahhbnpvaey

Discovered differentially expressed lncRNA AC010973.2 can act as a diagnostic and prognostic biomarker for colon adenocarcinoma

Xinhong Liu, Caizhi Xiao, Fang Tan, Ruokun Yi, Xin Zhao
2020 Translational Cancer Research  
The potential biofunctions of target lncRNA were investigated through bioinformatic analysis.  ...  The area under the curve (0.758) and the C-index (0.753) further confirmed the prediction accuracy of our model.  ...  This database (www.microrna.gr/LncBase) is a reference repository with experimentally supported miRNA targets on non-coding transcripts.  ... 
doi:10.21037/tcr-20-2011 pmid:35117237 pmcid:PMC8799118 fatcat:zg6ccjmnpndjbaarkjqs7ltcf4

Computational approaches towards understanding human long non-coding RNA biology

Saakshi Jalali, Shruti Kapoor, Ambily Sivadas, Deeksha Bhartiya, Vinod Scaria
2015 Bioinformatics  
Long noncoding RNAs (lncRNAs) form the largest class of nonprotein coding genes in the human genome.  ...  DIANA- Experimentally verified and computationally predicted microRNA targets on www.microrna.gr/LncBase (Paraskevopoulou et LncBase long noncoding RNAs. al., 2013) 11.  ...  DIANA-LncBase is a comprehensive resource for computationally predicted and experimentally annotated miRNA-lncRNA interactions (Paraskevopoulou et al., 2013) .  ... 
doi:10.1093/bioinformatics/btv148 pmid:25777523 fatcat:xgmydv5rjvfqjarbx5oakz2r4a

SPMLMI: predicting lncRNA–miRNA interactions in humans using a structural perturbation method

Mingmin Xu, Yuanyuan Chen, Wei Lu, Lingpeng Kong, Jingya Fang, Zutan Li, Liangyun Zhang, Cong Pian
2021 PeerJ  
Long non-coding RNA (lncRNA)–microRNA (miRNA) interactions are quickly emerging as important mechanisms underlying the functions of non-coding RNAs.  ...  We found that the structural consistency of the bilayer network was higher than that of any single network, supporting the utility of bilayer network construction for the prediction of lncRNA–miRNA interactions  ...  This information was retrieved from DIANA-LncBase v3 (Karagkouni et al., 2020) .  ... 
doi:10.7717/peerj.11426 pmid:34055486 pmcid:PMC8140594 fatcat:6clmjwdja5d2jln57gnxtb4mki

The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders

Carla Liaci, Lucia Prandi, Lisa Pavinato, Alfredo Brusco, Mara Maldotti, Ivan Molineris, Salvatore Oliviero, Giorgio R. Merlo
2022 International Journal of Molecular Sciences  
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their  ...  Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis  ...  An updated resource reporting known miRNA-lncRNA interactions is DIANA-LncBase v3 [203] ; Zang et al. provided an example of a modular approach to identify a lncRNA-related miRNA sponge in breast cancer  ... 
doi:10.3390/ijms23116118 pmid:35682796 fatcat:7lnsaemzwffvzms3ys5piji5pq

(In)Distinctive Role of Long Non-Coding RNAs in Common and Rare Ovarian Cancers

Maja Sabol, Jean Calleja-Agius, Riccardo Di Di Fiore, Sherif Suleiman, Sureyya Ozcan, Mark P. Ward, Petar Ozretić
2021 Cancers  
Long non-coding RNA (lncRNA) are defined as transcribed RNA molecules, more than 200 nucleotides in length which are not translated into proteins.  ...  Dysregulation of the cellular processes that lead to cancer includes gene mutations, epimutations, non-coding RNA (ncRNA) regulation, posttranscriptional and posttranslational modifications.  ...  SnoRNAs, miRNAs, and piRNAs are collectively named small non-coding RNAs (sncRNAs).  ... 
doi:10.3390/cancers13205040 pmid:34680193 fatcat:nn6t4l6rljdp7gcnqyp4cx6yv4

Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease

Lining Su, Sufen Chen, Chenqing Zheng, Huiping Wei, Xiaoqing Song
2019 Frontiers in Neuroscience  
Furthermore, we analyzed the microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and single nucleotide polymorphisms (SNPs) associated with the AD-associated genes, and then identified feed-forward loops  ...  Among them, one important FFL was found between the gene SERPINA3, hsa-miR-27a, and the transcription factor MYC.  ...  DEGs and non-coding RNAs, miRNAs associated with these genes were analyzed using the DIANA-Tarbase v.8.0 database.  ... 
doi:10.3389/fnins.2019.00633 pmid:31333395 pmcid:PMC6616202 fatcat:je2jzuqeavgktkw6pjv5xzumbe

Integrated computational and experimental methods for the characterization of the frequency and functional consequences of RNA editing in microRNAs [article]

Σπυρίδων Ταστσόγλου, University Of Thessaly, Άρτεμις Χατζηγεωργίου
2021
presentation of a small RNA quantification application, three studies related to miRNA targeting, the showcase of a database of experimentally supported microbe-disease associations and two transcriptomic  ...  On 7/12/2016, the State Scholarship Foundation (I.K.Y.) accepted to fund my proposal on the computational and experimental study of RNA editing in microRNAs, in the form of a 36-month scholarship.  ...  DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts.  ... 
doi:10.26253/heal.uth.12635 fatcat:h33i7nerdbfutgpxd4kyhjhemy

ELIXIR Annual Report 2019 [article]

ELIXIR
2020
Scientific breakthroughs in life sciences rest on our ability to connect and compare data across different locations, across different species and over different scales.  ...  DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts, Nucleic Acids Research 2020, 48, pages D101-D110 (https://doi.org/10.1093/nar/gkz1036) 11 Blencowe BJ, Amann  ...  These containers package up code and all additional software needed to run the code.  ... 
doi:10.7490/f1000research.1118022.1 fatcat:ou4prjrrazfwhlbr6sjpsimgsa