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Insights into Online microRNA Bioinformatics Tools

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Dynamic interplay of microRNA in diseases and therapeutic

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Summary: In this review article, the role of microRNAs in human diseases and recent research in clinical therapeutics are discussed. Network models for microRNAs and their targets have been constructed to understand their relationships and associations with diseases. Future research will provide new strategies for the broader utility of microRNAs.

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Summary: The updated resource provides sequencing data of 188 tissue samples from six humans and 58 samples from Tabula Muris collection, totaling 87,252 non-coding RNAs, to shed light on organ specificity in the non-coding transcriptome.

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miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions

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Summary: miRTarBase is a large biological database that provides experimentally verified miRNA-target interactions, making it one of the most research-friendly MTI databases with comprehensive and experimentally verified annotations.

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The Sequence Read Archive: a decade more of explosive growth

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Summary: The Sequence Read Archive (SRA) plays a vital role in storing raw sequencing data and alignment information to enhance reproducibility and expedite new discoveries through data analysis. Changes have been made in storage to increase access, and analyses are used to augment metadata with taxonomic insight to assist users in selecting data. Three unexpected applications of taxonomic analysis have been introduced, showing the potential of driving scientific research and discovery.

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Ensembl 2022

Fiona Cunningham et al.

Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.

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Summary: In this Review, the authors discuss the functional relevance of non-canonical features of microRNAs in cardiovascular homeostasis and pathophysiology, including atypical microRNA biogenesis and localization, RISC heterogeneity, and non-conventional regulatory functions. They highlight the importance of uncovering these non-conventional properties for translational research in cardiovascular disease.

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dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms

Feng Xu et al.

Summary: MicroRNAs play important roles in gene expression regulation, and their dysregulation is widely reported in pathological cellular states. The dbDEMC database was constructed to store and query differentially expressed miRNAs (DEMs) in human cancers. The updated version, dbDEMC 3.0, contains more data entries and includes data from mice and rats. It provides a valuable resource for studying the molecular functions and regulatory mechanisms of DEMs in human cancers.

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Summary: MicroRNAs (miRNAs) are small non-coding RNAs that posttranscriptionally regulate gene expression. Genetic variations in miRNA genes may affect their functioning and the development of human diseases.

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Laura Adriana de Rooij et al.

Summary: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and play important physiological and pathological roles. Alterations in miRNA biogenesis, target regulation, and function can promote tumor progression. Understanding the lifecycle and regulation of miRNAs is crucial for their potential application as cancer biomarkers.

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miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets

Chun-Jie Liu et al.

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The Gene Ontology resource: enriching a GOld mine

Seth Carbon et al.

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NUCLEIC ACIDS RESEARCH (2021)

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Rfam 14: expanded coverage of metagenomic, viral and microRNA families

Ioanna Kalvari et al.

Summary: Rfam is a database of RNA families with 3444 families, each represented by a multiple sequence alignment of known RNA sequences and a covariance model for searching additional members. Recent developments focused on improving data quality and coverage, adding new families like microRNAs, viral and bacterial RNAs through expert collaborations. The database saw significant growth with 759 new families added in Rfam 14, along with new features such as the Rfam Cloud family curation system.

NUCLEIC ACIDS RESEARCH (2021)

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MiREDiBase, a manually curated database of validated and putative editing events in microRNAs

Gioacchino P. Marceca et al.

Summary: miRNAs are small non-coding RNAs that play a regulatory role in cellular processes. MiRNA editing is a post-transcriptional modification that can impact their biogenesis and target-binding ability. MiREDiBase is a manually curated catalog of miRNA editing events, serving as a valuable tool for cell biology and biomedical research.

SCIENTIFIC DATA (2021)

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miRNA Targets: From Prediction Tools to Experimental Validation

Giulia Riolo et al.

Summary: MicroRNAs are post-transcriptional regulators of gene expression in animals and plants, playing gene-regulatory roles by pairing to microRNA responsive elements on target mRNAs. The identification of miRNA-mRNA target interactions is fundamental for discovering the regulatory network governed by miRNAs.

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Summary: KEGG is a curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information, providing mapping tools for understanding cellular and organism-level functions from genome sequences and other molecular datasets. The network variation maps in the KEGG database show how different pathogens and environmental factors influence cellular signaling pathways.

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

Blake A. Sweeney et al.

Summary: RNAcentral is a comprehensive database of non-coding RNA sequences, providing a single access point to over 18 million ncRNA sequences from diverse organisms and RNA types, as well as information on the secondary structure for over 13 million sequences. The database also includes a fast sequence similarity search tool with filtering options, making it a central data resource for the RNA community.

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miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database

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Computational Methods and Software Tools for Functional Analysis of miRNA Data

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BRIEFINGS IN BIOINFORMATICS (2019)

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JOURNAL OF CELLULAR PHYSIOLOGY (2019)

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HMDD v3.0: a database for experimentally supported human microRNA-disease associations

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ArrayExpress update - from bulk to single-cell expression data

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EVmiRNA: a database of miRNA profiling in extracellular vesicles

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

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The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

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COSMIC: the Catalogue Of Somatic Mutations In Cancer

John G. Tate et al.

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Expression Atlas: gene and protein expression across multiple studies and organisms

Irene Papatheodorou et al.

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miRCarta: a central repository for collecting miRNA candidates

Christina Backes et al.

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miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

Chih-Hung Chou et al.

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

Dimitra Karagkouni et al.

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Comparing miRNA structure of mirtrons and non-mirtrons

Igor I. Titov et al.

BMC GENOMICS (2018)

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Expanding the horizons of microRNA bioinformatics

Rachael P. Huntley et al.

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A novel class of microRNA-recognition elements that function only within open reading frames

Kai Zhang et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

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Jacob O'Brien et al.

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OncomiR: an online resource for exploring pan-cancer microRNA dysregulation

Nathan W. Wong et al.

BIOINFORMATICS (2018)

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miRPathDB: a new dictionary on microRNAs and target pathways

Christina Backes et al.

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KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

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Combining Results from Distinct MicroRNA Target Prediction Tools Enhances the Performance of Analyses

Arthur C. Oliveira et al.

FRONTIERS IN GENETICS (2017)

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Bioinformatic tools for microRNA dissection

Most Mauluda Akhtar et al.

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miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database

Chih-Hung Chou et al.

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Distribution of miRNA expression across human tissues

Nicole Ludwig et al.

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miTALOS v2: Analyzing Tissue Specific microRNA Function

Martin Preusse et al.

PLOS ONE (2016)

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The role of MicroRNAs in human cancer

Yong Peng et al.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2016)

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Tools for Sequence-Based miRNA Target Prediction: What to Choose?

Angela L. Riffo-Campos et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2016)

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NON-CODING RNA Towards a molecular understanding of microRNA-mediated gene silencing

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

Ioannis S. Vlachos et al.

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In vivo, Argonaute-bound microRNAs exist predominantly in a reservoir of low molecular weight complexes not associated with mRNA

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An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools

Jing Gong et al.

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Genetic variants in microRNA genes: impact on microRNA expression, function, and disease

Sophia Cammaerts et al.

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miRDB: an online resource for microRNA target prediction and functional annotations

Nathan Wong et al.

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Regulation of miRNA strand selection: follow the leader?

Hedda A. Meijer et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2014)

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mRNA Destabilization Is the Dominant Effect of Mammalian MicroRNAs by the Time Substantial Repression Ensues

Stephen W. Eichhorn et al.

MOLECULAR CELL (2014)

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Regulation of microRNA biogenesis

Minju Ha et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2014)

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miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

Sheng-Da Hsu et al.

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HMDD v2.0: a database for experimentally supported human microRNA and disease associations

Yang Li et al.

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miRBase: annotating high confidence microRNAs using deep sequencing data

Ana Kozomara et al.

NUCLEIC ACIDS RESEARCH (2014)

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PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways

Anindya Bhattacharya et al.

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Common features of microRNA target prediction tools

Sarah M. Peterson et al.

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RNA decay machines: Deadenylation by the Ccr4-Not and Pan2-Pan3 complexes

Elmar Wahle et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2013)

Article Biochemistry & Molecular Biology

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

Aleksandra Helwak et al.

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miRNAs: Biogenesis, Origin and Evolution, Functions on Virus-Host Interaction

Yang Zhuo et al.

CELLULAR PHYSIOLOGY AND BIOCHEMISTRY (2013)

Editorial Material Genetics & Heredity

The Cancer Genome Atlas Pan-Cancer analysis project

John N. Weinstein et al.

NATURE GENETICS (2013)

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NCBI GEO: archive for functional genomics data sets-update

Tanya Barrett et al.

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miRNASNP: a database of miRNA related SNPs and their effects on miRNA function

Jing Gong et al.

BMC BIOINFORMATICS (2012)

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Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals

Ryuya Fukunaga et al.

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The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC

Marc R. Fabian et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)

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TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

Thanasis Vergoulis et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits

Jesse D. Ziebarth et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Genetics & Heredity

MicroRNAs in Common Human Diseases

Yu Li et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2012)

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Yong Huang et al.

MOLECULAR BIOLOGY REPORTS (2011)

Article Biochemistry & Molecular Biology

miRTarBase: a database curates experimentally validated microRNA-target interactions

Sheng-Da Hsu et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

miRBase: integrating microRNA annotation and deep-sequencing data

Ana Kozomara et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biotechnology & Applied Microbiology

dbDEMC: a database of differentially expressed miRNAs in human cancers

Zhen Yang et al.

BMC GENOMICS (2010)

Article Biochemistry & Molecular Biology

Structure and activity of putative intronic miRNA promoters

Alex Mas Monteys et al.

Article Biochemistry & Molecular Biology

Most mammalian mRNAs are conserved targets of microRNAs

Robin C. Friedman et al.

GENOME RESEARCH (2009)

Article Cell Biology

Chromatin structure analyses identify miRNA promoters

Fatih Ozsolak et al.

GENES & DEVELOPMENT (2008)

Article Multidisciplinary Sciences

An Analysis of Human MicroRNA and Disease Associations

Ming Lu et al.

PLOS ONE (2008)

Article Biochemistry & Molecular Biology

Mammalian mirtron genes

Eugene Berezikov et al.

MOLECULAR CELL (2007)

Article Biochemistry & Molecular Biology

MicroRNA targeting specificity in mammals: Determinants beyond seed pairing

Andrew Grimson et al.

MOLECULAR CELL (2007)

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Human polymorphism at microRNAs and microRNA target sites

Matthew A. Saunders et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits

Lei Bao et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

Identification of microRNAs of the herpesvirus family

S Pfeffer et al.

NATURE METHODS (2005)

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Identification of virus-encoded microRNAs

S Pfeffer et al.

SCIENCE (2004)

Article Multidisciplinary Sciences

Nuclear export of microRNA precursors

E Lund et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

MicroRNA genes are transcribed by RNA polymerase II

Y Lee et al.

EMBO JOURNAL (2004)

Article Multidisciplinary Sciences

The nuclear RNase III Drosha initiates microRNA processing

Y Lee et al.

NATURE (2003)

Article Cell Biology

MicroRNAs in plants

BJ Reinhart et al.

GENES & DEVELOPMENT (2002)

Article Biochemistry & Molecular Biology

dbSNP: the NCBI database of genetic variation

ST Sherry et al.

NUCLEIC ACIDS RESEARCH (2001)