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DIANA-TarBase v7: indexing hundreds of thousands experimentally supported miRNA:mRNA interactions

Dimitra Karagkouni
2015 EMBnet journal  
Karagkouni, G. Georgakilas, T. Vergoulis, I. Kanellos, I-L. Anastasopoulos, S. : M. Reczko, M. Maragkakis, P. Alexiou, I. Grosse, and A. G.  ... 
doi:10.14806/ej.21.a.824 fatcat:nq4j3jfbgfalzdtrb44zgbdtei

microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions

Maria D. Paraskevopoulou, Dimitra Karagkouni, Ioannis S. Vlachos, Spyros Tastsoglou, Artemis G. Hatzigeorgiou
2018 Nature Communications  
doi:10.1038/s41467-018-06046-y pmid:30190538 pmcid:PMC6127135 fatcat:ijhhn73m5vb5vpgfyabuocwf2e

DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification

Athanasios Alexiou, Dimitrios Zisis, Ioannis Kavakiotis, Marios Miliotis, Antonis Koussounadis, Dimitra Karagkouni, Artemis G. Hatzigeorgiou
2020 Genes  
microRNAs (miRNAs) are small non-coding RNAs (~22 nts) that are considered central post-transcriptional regulators of gene expression and key components in many pathological conditions. Next-Generation Sequencing (NGS) technologies have led to inexpensive, massive data production, revolutionizing every research aspect in the fields of biology and medicine. Particularly, small RNA-Seq (sRNA-Seq) enables small non-coding RNA quantification on a high-throughput scale, providing a closer look into
more » ... he expression profiles of these crucial regulators within the cell. Here, we present DIANA-microRNA-Analysis-Pipeline (DIANA-mAP), a fully automated computational pipeline that allows the user to perform miRNA NGS data analysis from raw sRNA-Seq libraries to quantification and Differential Expression Analysis in an easy, scalable, efficient, and intuitive way. Emphasis has been given to data pre-processing, an early, critical step in the analysis for the robustness of the final results and conclusions. Through modularity, parallelizability and customization, DIANA-mAP produces high quality expression results, reports and graphs for downstream data mining and statistical analysis. In an extended evaluation, the tool outperforms similar tools providing pre-processing without any adapter knowledge. Closing, DIANA-mAP is a freely available tool. It is available dockerized with no dependency installations or standalone, accompanied by an installation manual through Github.
doi:10.3390/genes12010046 pmid:33396959 pmcid:PMC7823405 fatcat:h5vcowpievbfpcrqypq72hmbvm

DIANA-miRPath v3.0: deciphering microRNA function with experimental support

Ioannis S. Vlachos, Konstantinos Zagganas, Maria D. Paraskevopoulou, Georgios Georgakilas, Dimitra Karagkouni, Thanasis Vergoulis, Theodore Dalamagas, Artemis G. Hatzigeorgiou
2015 Nucleic Acids Research  
The functional characterization of miRNAs is still an open challenge. Here, we present DIANA-miRPath v3.0 (http://www.microrna.gr/miRPathv3) an online software suite dedicated to the assessment of miRNA regulatory roles and the identification of controlled pathways. The new miRPath web server renders possible the functional annotation of one or more miRNAs using standard (hypergeometric distributions), unbiased empirical distributions and/or meta-analysis statistics. DIANA-miRPath v3.0 database
more » ... and functionality have been significantly extended to support all analyses for KEGG molecular pathways, as well as multiple slices of Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio). Importantly, more than 600 000 experimentally supported miRNA targets from DIANA-TarBase v7.0 have been incorporated into the new schema. Users of DIANA-miRPath v3.0 can harness this wealth of information and substitute or combine the available in silico predicted targets from DIANA-microT-CDS and/or TargetScan v6.2 with high quality experimentally supported interactions. A unique feature of DIANA-miRPath v3.0 is its redesigned Reverse Search module, which enables users to identify and visualize miRNAs significantly controlling selected pathways or belonging to specific GO categories based on in silico or experimental data. DIANA-miRPath v3.0 is freely available to all users without any login requirement.
doi:10.1093/nar/gkv403 pmid:25977294 pmcid:PMC4489228 fatcat:thu67ur6qjb3xncaavr226lq2m

NMR-Based Metabolomics in Differential Diagnosis of Chronic Kidney Disease (CKD) Subtypes

Styliani A. Chasapi, Evdokia Karagkouni, Dimitra Kalavrizioti, Sotirios Vamvakas, Aikaterini Zompra, Panteleimon G. Takis, Dimitrios S. Goumenos, Georgios A. Spyroulias
2022 Metabolites  
Chronic Kidney Disease (CKD) is considered as a major public health problem as it can lead to end-stage kidney failure, which requires replacement therapy. A prompt and accurate diagnosis, along with the appropriate treatment, can delay CKD's progression, significantly. Herein, we sought to determine whether CKD etiology can be reflected in urine metabolomics during its early stage. This is achieved through the analysis of the urine metabolic fingerprint from 108 CKD patients by means of
more » ... Magnetic Resonance (NMR) spectroscopy metabolomic analysis. We report the first NMR—metabolomics data regarding the three most common etiologies of CKD: Chronic Glomerulonephritis (IgA and Membranous Nephropathy), Diabetic Nephropathy (DN) and Hypertensive Nephrosclerosis (HN). Analysis aided a moderate glomerulonephritis clustering, providing characterization of the metabolic fluctuations between the CKD subtypes and control disease. The urine metabolome of IgA Nephropathy reveals a specific metabolism, reflecting its different etiology or origin and is useful for determining the origin of the disease. In contrast, urine metabolomes from DN and HN patients did not reveal any indicative metabolic pattern, which is consistent with their fused clinical phenotype. These findings may contribute to improving diagnostics and prognostic approaches for CKD, as well as improving our understanding of its pathology.
doi:10.3390/metabo12060490 fatcat:fwu7jdws5vgxfptnmcukjsfbfe

Cooperative action of miR-124 and ISX9 in instructing direct reprogramming of mouse astrocytes to induced-neurons in vitro and in vivo [article]

Elsa Papadimitriou, Paraskevi N. Koutsoudaki, Timokratis Karamitros, Dimitra Karagkouni, Dafni Chroni-Tzartou, Maria Margariti, Christos Gkemisis, Evangelia Xingi, Irini Thanou, Socrates J Tzartos, Artemis G Hatzigeorgiou, Dimitra Thomaidou
2020 bioRxiv   pre-print
miR-124 plays a major regulatory role in neurogenesis and neuronal differentiation during brain development through control of its multiple non-neuronal targets and has therefore been employed in direct reprogramming protocols supplementary to neurogenic TFs, and other miRNAs to enhance neurogenic conversion. However, its capacity to instruct neurogenic conversion of astrocytes and its independent mechanism of direct reprogramming action have been poorly investigated. Aim of the study was to
more » ... estigate whether miR-124 is a master-regulatory reprogramming agent, potent to drive direct reprogramming of astrocytes to induced-neurons (iNs) on its own and to elucidate its mechanism of reprogramming action. To this end we overexpressed miR-124 either alone or in combination with the small neurogenic compound ISX9 both in vitro and in in vivo in a mouse mechanical cortical trauma model and analyzed their mechanism of reprogramming action. Our data indicate that miR-124 and ISX9 exhibit both unique and convergent molecular contributions in the reprogramming process to iNs. miR-124 is a potent driver of the astrocytic reprogramming switch of astrocytes towards an immature neuronal fate by repressing genes regulating astrocytic function, among which we identified the RNA-binding protein Zfp36l1 as a novel miR-124 direct target. We also provide evidence that ISX9 greatly improves both miR-124-induced reprogramming efficiency and functional maturation of iNs. Importantly, miR-124 either alone or along with ISX9 is potent to guide direct neuronal reprogramming of reactive astrocytes to iNs of cortical identity in vivo, a novel finding confirming the robust direct reprogramming action of the two molecules in activated astrocytes in vivo.
doi:10.1101/2020.06.01.127126 fatcat:p2i7sdofuvb4heszbfm6c7mkou

DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts

Maria D. Paraskevopoulou, Ioannis S. Vlachos, Dimitra Karagkouni, Georgios Georgakilas, Ilias Kanellos, Thanasis Vergoulis, Konstantinos Zagganas, Panayiotis Tsanakas, Evangelos Floros, Theodore Dalamagas, Artemis G. Hatzigeorgiou
2015 Nucleic Acids Research  
microRNAs (miRNAs) are short non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of coding gene expression. Long non-coding RNAs (lncRNAs) have been recently reported to interact with miRNAs. The sponge-like function of lncR- NAs introduces an extra layer of complexity in the miRNA interactome. DIANA-LncBase v1 provided a database of experimentally supported and in silico predicted miRNA Recognition Elements (MREs) on lncRNAs. The second version of LncBase (www.
more » ... ase) presents an extensive collection of miRNA:lncRNA interactions. The significantly enhanced database includes more than 70 000 low and high-throughput, (in)direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of 153 AGO CLIP-Seq libraries. The new experimental module presents a 14-fold increase compared to the previous release. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm. The relevant module provides millions of predicted miRNA binding sites, accompanied with detailed metadata and MRE conservation metrics. LncBase v2 caters information regarding cell type specific miRNA:lncRNA regulation and enables users to easily identify interactions in 66 different cell types, spanning 36 tissues for hu-man and mouse. Database entries are also supported by accurate lncRNA expression information, derived from the analysis of more than 6 billion RNA-Seq reads.
doi:10.1093/nar/gkv1270 pmid:26612864 pmcid:PMC4702897 fatcat:dgtwj7bf5zb37ncghz7xji5y3i

Reporting on the Role of miRNAs and Affected Pathways on the Molecular Backbone of Ovarian Insufficiency: A Systematic Review and Critical Analysis Mapping of Future Research

Anna Rapani, Dimitra Nikiforaki, Dimitra Karagkouni, Konstantinos Sfakianoudis, Petroula Tsioulou, Sokratis Grigoriadis, Evangelos Maziotis, Amelia Pantou, Aikaterini Voutsina, Agni Pantou, Michael Koutsilieris, Artemis Hatzigeorgiou (+2 others)
2021 Frontiers in Cell and Developmental Biology  
Functional Analysis of miRNA Targets Experimentally supported and in silico predicted miRNAtarget pairs were retrieved from DIANA-TarBase (Karagkouni et al., 2018) repository and microT-CDS (Reczko  ... 
doi:10.3389/fcell.2020.590106 pmid:33511114 pmcid:PMC7835544 fatcat:psfzpjlvpfeu5ootxlm73skhgq

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions

Dimitra Karagkouni, Maria D Paraskevopoulou, Serafeim Chatzopoulos, Ioannis S Vlachos, Spyros Tastsoglou, Ilias Kanellos, Dimitris Papadimitriou, Ioannis Kavakiotis, Sofia Maniou, Giorgos Skoufos, Thanasis Vergoulis, Theodore Dalamagas (+1 others)
2017 Nucleic Acids Research  
DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Its eighth version is the first database indexing >1 million entries, corresponding to ∼670 000 unique miRNA-target pairs. The interactions are supported by >33 experimental methodologies, applied to ∼600 cell types/tissues under ∼451 experimental conditions. It integrates information on cell-type specific miRNA-gene regulation, while hundreds
more » ... thousands of miRNA-binding locations are reported. TarBase is coming of age, with more than a decade of continuous support in the non-coding RNA field. A new module has been implemented that enables the browsing of interactions through different filtering combinations. It permits easy retrieval of positive and negative miRNA targets per species, methodology, cell type and tissue. An incorporated ranking system is utilized for the display of interactions based on the robustness of their supporting methodologies. Statistics, pie-charts and interactive barplots depicting the database content are available through a dedicated result page. An intuitive interface is introduced, providing a user-friendly application with flexible options to different queries.
doi:10.1093/nar/gkx1141 pmid:29156006 pmcid:PMC5753203 fatcat:mzgphze3fbatrfsj3setx27vei

DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data

Ioannis S. Vlachos, Thanasis Vergoulis, Maria D. Paraskevopoulou, Filopoimin Lykokanellos, Georgios Georgakilas, Penny Georgiou, Serafeim Chatzopoulos, Dimitra Karagkouni, Foteini Christodoulou, Theodore Dalamagas, Artemis G. Hatzigeorgiou
2016 Nucleic Acids Research  
Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna. gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can
more » ... combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0. The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement.
doi:10.1093/nar/gkw455 pmid:27207881 pmcid:PMC4987956 fatcat:44nz6jw7njf5rbk7nhxdrmfn6i

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

Ioannis S. Vlachos, Maria D. Paraskevopoulou, Dimitra Karagkouni, Georgios Georgakilas, Thanasis Vergoulis, Ilias Kanellos, Ioannis-Laertis Anastasopoulos, Sofia Maniou, Konstantina Karathanou, Despina Kalfakakou, Athanasios Fevgas, Theodore Dalamagas (+1 others)
2014 Nucleic Acids Research  
microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds of thousands of miRNA:gene interactions have been experimentally identified. However, this wealth of information is fragmented and hidden in thousands of manuscripts and raw nextgeneration sequencing data sets. DIANA-TarBase was initially released in 2006 and it was the first database aiming
more » ... o catalog published experimentally validated miRNA:gene interactions. DIANA-TarBase v7.0 (http://www.microrna.gr/tarbase) aims to provide for the first time hundreds of thousands of high-quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. DIANA-TarBase v7.0 enables users to easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments. More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9-to 250-fold more entries than any other relevant database. DIANA-TarBase v7.0 is freely available.
doi:10.1093/nar/gku1215 pmid:25416803 pmcid:PMC4383989 fatcat:c3bxfqdu5bdhjlwif2gldkwlgi

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral Consortium, Blake A Sweeney, Anton I Petrov, Carlos E Ribas, Robert D Finn, Alex Bateman, Maciej Szymanski, Wojciech M Karlowski, Stefan E Seemann, Jan Gorodkin, Jamie J Cannone, Robin R Gutell (+81 others)
2020 Nucleic Acids Research  
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and
more » ... izable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.
doi:10.1093/nar/gkaa921 pmid:33106848 pmcid:PMC7779037 fatcat:nodb7xauq5fbzlw5qdlm66jni4

RNAcentral: a hub of information for non-coding RNA sequences

Blake A Sweeney, Anton I Petrov, Boris Burkov, Robert D Finn, Alex Bateman, Maciej Szymanski, Wojciech M Karlowski, Jan Gorodkin, Stefan E Seemann, Jamie J Cannone, Robin R Gutell, Petra Fey (+49 others)
2018 Nucleic Acids Research  
RNAcentral is a comprehensive database of noncoding RNA (ncRNA) sequences, collating informa-tion on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic lo-cations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family
more » ... ignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org.
doi:10.1093/nar/gky1034 pmid:30395267 fatcat:cpskjl3j6bd5hhpehf6ighpjfa

RNAcentral: a hub of information for non-coding RNA sequences

The RNAcentral Consortium, Blake A Sweeney, Anton I Petrov, Boris Burkov, Robert D Finn, Alex Bateman, Maciej Szymanski, Wojciech M Karlowski, Jan Gorodkin, Stefan E Seemann, Jamie J Cannone, Robin R Gutell (+50 others)
2018 Nucleic Acids Research  
RNAcentral is a comprehensive database of noncoding RNA (ncRNA) sequences, collating informa-tion on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic lo-cations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family
more » ... ignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org.
doi:10.1093/nar/gky1206 pmid:30535383 pmcid:PMC6323998 fatcat:zu6n3hhfqbcznczprmfelptfhy

The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

Alexie Papanicolaou, Marc F. Schetelig, Peter Arensburger, Peter W. Atkinson, Joshua B. Benoit, Kostas Bourtzis, Pedro Castañera, John P. Cavanaugh, Hsu Chao, Christopher Childers, Ingrid Curril, Huyen Dinh (+52 others)
2016 Genome Biology  
The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of
more » ... ly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control. Results: The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A highquality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT.
doi:10.1186/s13059-016-1049-2 pmid:27659211 pmcid:PMC5034548 fatcat:xgpl63wfkbh77bhc36jdi25voi
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