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MicroRNA databases | RNA interference

MicroRNAs (miRNAs) are small non-coding RNA (∼22 nt) involved in the post-transcriptional regulation of gene expression. miRNAs promote the degradation or inhibit the expression of messenger RNA by binding to specific sequences generally located…
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FANTOM5 CAGE
Dataset

FANTOM5 CAGE

Provides an integrated expression collection of miRNAs and their promoters. The…

Provides an integrated expression collection of miRNAs and their promoters. The database contains matching Cap Analysis Gene Expression (CAGE) data from 396 human and 47 mouse RNA samples. It offers…

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miRGen
Dataset

miRGen

Provides a genome-wide map of transcription factor-microRNA (TF–miRNA)…

Provides a genome-wide map of transcription factor-microRNA (TF–miRNA) interactions for multiple tissues and cell-lines in Homo sapiens and Mus musculus. miRGen is a repository that supports…

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deepBase
Dataset

deepBase

A platform for annotating and discovering small (microRNAs, siRNAs, piRNAs...),…

A platform for annotating and discovering small (microRNAs, siRNAs, piRNAs...), long ncRNAs (lncRNAs) and circular RNAs (circRNAs) from next generation sequencing data. deepBase v2.0 provides a set…

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miRBase
Dataset

miRBase

Distributes published microRNA sequences, for browsing and searching by…

Distributes published microRNA sequences, for browsing and searching by sequence and keywords. miRBase is a public repository for all published microRNA sequences and associated annotation. For each…

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doRiNA
Dataset

doRiNA

Focuses in post-transcriptional regulation which integrates information related…

Focuses in post-transcriptional regulation which integrates information related to binding site data between RNA binding proteins (RBPs) and microRNAs. To enable the inclusion of doRiNA into…

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SomamiR
Dataset

SomamiR

A database of cancer somatic mutations in microRNAs (miRNA) and their target…

A database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA) including mRNAs,…

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miRPathDB
Dataset

miRPathDB miRNA Pathway Dictionary Database

Provides easy access to the information which pathways are regulated by a…

Provides easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific the regulations are. miRPathDB contains a large number of miRNAs (2599…

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miRDB
Dataset

miRDB

An online resource for miRNA target prediction and functional annotations. In…

An online resource for miRNA target prediction and functional annotations. In addition to presenting precompiled prediction data, a new feature is the web server interface that allows submission of…

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dbDEMC
Dataset

dbDEMC database of Differentially Expressed MiRNAs in human Cancers

Provides a collection of differentially expressed miRNAs in human cancers…

Provides a collection of differentially expressed miRNAs in human cancers obtained from microarray data. dbDEMC documents 209 expression profiling data sets across 36 cancer types and 73 subtypes,…

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microRNA.org
Dataset

microRNA.org

A comprehensive resource of microRNA target predictions and expression…

A comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge…

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NSDNA
Dataset

NSDNA Nervous System Disease NcRNAome Atlas

A manually curated database that provides comprehensive experimentally…

A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713…

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miRIAD
Dataset

miRIAD Intragenic microRNA database

Provides information regarding genomic context, gene function, gene…

Provides information regarding genomic context, gene function, gene interaction, miRNA targets and gene expression. miRIAD is a database that examines intragenic miRNAs, their host genes and their…

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HMDD
Dataset

HMDD Human MicroRNA and Disease Database

A repository of miRNA-associated diseases, obtained by manual curation from…

A repository of miRNA-associated diseases, obtained by manual curation from literature data. HMDD v2.0 presents more detailed and comprehensive annotations to the human miRNA-disease association…

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PolymiRTS…
Dataset

PolymiRTS Database

An integrated platform for analyzing the functional impact of genetic…

An integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites. The browse and search pages of PolymiRTS allow users to explore the…

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Miratlas
Dataset

Miratlas

A comprehensive catalogue of miRNA expression data and modifications from…

A comprehensive catalogue of miRNA expression data and modifications from already published datasets. Miratlas contains 52 analysed datasets from human and mouse samples. Annotation for the miratlas…

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ncRDeathDB
Dataset

ncRDeathDB

A comprehensive bioinformatics resource to archive non-coding RNA…

A comprehensive bioinformatics resource to archive non-coding RNA (ncRNA)-associated cell death interactions. ncRDeathDB documents a total of more than 4600 ncRNA-mediated programmed cell death (PCD)…

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miREnvironment
Dataset

miREnvironment

A database that curated and collected experimentally supported miRNA, one class…

A database that curated and collected experimentally supported miRNA, one class of newly identified genetic factors, and environmental factor interplays and their associated phenotypes.…

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ASRP
Dataset

ASRP Arabidopsis Small RNA Project

Provides information and tools for the analysis of microRNA, endogenous siRNA…

Provides information and tools for the analysis of microRNA, endogenous siRNA and other small RNA-related features. New search and visualization tools have also been developed to improve access to…

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PlaMoM
Dataset

PlaMoM Plant Mobile Macromolecules

Provides convenient and interactive search tools allowing users to retrieve, to…

Provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM database contains detailed information such…

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microTranspoGen…
Dataset

microTranspoGene

A publicly available database of human, mouse, zebrafish and nematode microRNAs…

A publicly available database of human, mouse, zebrafish and nematode microRNAs which are derived from Transposable elements (TEs) either transcriptionally or structurally.

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miROrtho
Dataset

miROrtho

Presents the results of a comprehensive computational survey of miRNA gene…

Presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. The miROrtho data are conceptually complementary to the…

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ViTa
Dataset

ViTa

A database which collects virus data from miRBase and ICTV, VirGne, VBRC..,…

A database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan.

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miRandb
Dataset

miRandb miRNA algorithmic network database

Presents a survey of more than 180 Web-based miRNA databases which include…

Presents a survey of more than 180 Web-based miRNA databases which include miRNA sequence, discovery, target prediction, target validation, expression and regulation, functions and their roles in…

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RepTar
Dataset

RepTar

Contains genome-wide predictions of human and mouse miRNAs as well as…

Contains genome-wide predictions of human and mouse miRNAs as well as predictions of cellular targets of human and mouse viral miRNAs. These predictions are presented in a user-friendly database,…

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miRCancer
Dataset

miRCancer

Provides comprehensive collection of microRNA (miRNA) expression profiles in…

Provides comprehensive collection of microRNA (miRNA) expression profiles in various human cancers which are automatically extracted from published literatures in PubMed. It utilizes text mining…

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OncomiRDB
Dataset

OncomiRDB oncomiRNA DataBase

Aims at annotating the experimentally verified oncogenic and tumor-suppressive…

Aims at annotating the experimentally verified oncogenic and tumor-suppressive miRNAs from literature. OncomiRDB only collects items having direct functional evidences: 1) the miRNA regulates at…

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PmiRKB
Dataset

PmiRKB Plant microRNA Knowledge Base

Includes the miRNAs of two model plants, Arabidopsis (Arabidopsis thaliana) and…

Includes the miRNAs of two model plants, Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Four major functional modules, "SNPs", "Pri-miRNAs", "MiR—Tar",…

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TissueAtlas
Dataset

TissueAtlas

An atlas of miRNA expression in multiple human tissues. TissueAtlas has been…

An atlas of miRNA expression in multiple human tissues. TissueAtlas has been created by determining the abundance of 1997 miRNAs in 61 tissue biopsies of different organs from two individuals…

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DASHR
Dataset

DASHR Database of small human noncoding RNAs

Contains the most comprehensive information to date on human small non-coding…

Contains the most comprehensive information to date on human small non-coding RNAs (sncRNA) genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence…

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DsTRD
Dataset

DsTRD Danshen Transcriptional Resource Database

A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains…

A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains 76531 transcribed sequences assembled from the RNA-seq data. DsTRD provides information regarding the sequences and…

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Cardio_ncRNA
Dataset

Cardio_ncRNA

Allows users to obtain multiple types of information on interesting…

Allows users to obtain multiple types of information on interesting cardio-ncRNAs. Cardio_ncRNA combines information on about 13 249 curated relationships between about 9503 ncRNAs and 139…

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SEA
Dataset

SEA Small-RNA Expression Atlas

Permits querying, visualization, and analysis of over 2000 published sRNA-seq…

Permits querying, visualization, and analysis of over 2000 published sRNA-seq expression datasets. SEA stores sRNA expression information as well as deep and standardized meta-data on the samples,…

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miRmine
Dataset

miRmine

Contains a collection of expression profiles from different publicly available…

Contains a collection of expression profiles from different publicly available miRNA-seq datasets and detailed information about the different miRNAs. miRmine has options to retrieve expression…

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mimiRNA
Dataset

mimiRNA

A database of miRNA expression profile data across different tissues and cell…

A database of miRNA expression profile data across different tissues and cell lines. mimiRNA incorporates a sample classification algorithm, ExParser, that groups identical miRNA or mRNA experiments…

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miRNeye
Dataset

miRNeye

A high-resolution expression atlas revealing the spatiotemporal distribution of…

A high-resolution expression atlas revealing the spatiotemporal distribution of 221 miRNAs in the developing and adult wild-type mouse eye. The expression patterns were generated by RNA in situ…

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MirSNP
Dataset

MirSNP

A collection of human SNPs in predicted miRNA target sites. MirSNP could…

A collection of human SNPs in predicted miRNA target sites. MirSNP could identify the putative miRNA-related SNPs from GWAS and eQTLs researches and provide the direction for subsequent functional…

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IGDB.NSCLC
Dataset

IGDB.NSCLC Integrated Genomic Database of Non-Small Cell Lung Carcinoma

Aims to facilitate and prioritize identified lung cancer genes and microRNAs…

Aims to facilitate and prioritize identified lung cancer genes and microRNAs for pathological and mechanistic studies of lung tumorigenesis and for developing new strategies for clinical…

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mESAdb
Dataset

mESAdb

A regularly updated database for the multivariate analysis of sequences and…

A regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript…

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mTD
Dataset

mTD MicroRNAs affecting Therapeutic effects of Drugs

Provides comprehensive information about miRNAs affecting drug therapies. mTD…

Provides comprehensive information about miRNAs affecting drug therapies. mTD is a database that provides the sentences describing the drug-miRNA interactions with links to corresponding publications…

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RNAcentral
Dataset

RNAcentral

A resource that provides unified access to the ncRNA sequence data supplied by…

A resource that provides unified access to the ncRNA sequence data supplied by the Expert Databases. A web portal provides free access to data, search functionality, cross-references, source code and…

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PhenomiR
Dataset

PhenomiR

Provides literature studies linking dysregulated miRNA profiles with diseases.…

Provides literature studies linking dysregulated miRNA profiles with diseases. PhenomiR offers an in-depth annotation resource. It includes (i) information like the mode of miRNA expression (up or…

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S-MED
Dataset

S-MED Sarcoma MicroRNA Expression Database

A repository that describes the patterns of miRNA expression in various human…

A repository that describes the patterns of miRNA expression in various human sarcoma types. S-MED provides both Basic and Advanced data search options for exploration of the data in heatmap and text…

SignaFish
Dataset

SignaFish

An integrated resource to analyze signaling pathway cross-talks, miRNAs and…

An integrated resource to analyze signaling pathway cross-talks, miRNAs and regulatory enzymes in zebrafish. SignaFish contains more than 200 curation-based signaling interactions, 132 further…

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ExprTargetDB
Dataset

ExprTargetDB

An online database of human miRNA targets predicted by this approach as well as…

An online database of human miRNA targets predicted by this approach as well as a potential reference resource on miRNA-mediated gene regulation in the HapMap LCLs to facilitate future studies of the…

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Mythology of…
Dataset

Mythology of “micro”-RNAs

Provides a huge volume of experimental data in high quality visualization and…

Provides a huge volume of experimental data in high quality visualization and representation to facilitate the user to have meaningful insights. A user can browse the portal through several entry…

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Pan-ceRNADB
Dataset

Pan-ceRNADB Pan-cancer associated ceRNA database

A freely available resource to investigate mRNA related ceRNA-ceRNA landscape…

A freely available resource to investigate mRNA related ceRNA-ceRNA landscape and significance across 20 major cancer types. By providing mechanistic linkage between known cancer miRNAs, their…

MethHC
Dataset

MethHC

A database comprising a systematic integration of a large collection of DNA…

A database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. MethHC integrates data such as DNA methylation,…

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ViRBase
Dataset

ViRBase

Aims to provide the scientific community with a resource for efficient browsing…

Aims to provide the scientific community with a resource for efficient browsing and visualization of virus-host ncRNA-associated interactions and interaction networks in viral infection. Users can…

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TMREC
Dataset

TMREC Transcription factor and MiRNA Regulatory Cascades in Human Diseases

A database which provides a user-friendly interface for convenient retrieval…

A database which provides a user-friendly interface for convenient retrieval and visualization of TF-miRNA regulatory cascades and clusters in specific disease by TF, miRNA or disease name. TMREC…

RiceATM
Dataset

RiceATM

Can be employed to investigate the association between rice agronomic traits…

Can be employed to investigate the association between rice agronomic traits and miRNA expression. The functions of RiceATM includes phenotype selection, sample grouping, microarray data…

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SlideBase
Dataset

SlideBase

Offers a way of selecting genes, promoters, enhancers and microRNAs that are…

Offers a way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders. SlideBase…

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CircuitsDB
Dataset

CircuitsDB

A resource devoted to the identification and analysis of mixed…

A resource devoted to the identification and analysis of mixed MicroRNA/Transcription Factor Regulatory Circuits in the Human and Mouse genomes. The resulting integrated network can be the starting…

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NetAge
Dataset

NetAge

Gives visitors a wealth of information about the microRNA-regulated…

Gives visitors a wealth of information about the microRNA-regulated protein-protein interaction networks which are involved in complex processes of aging and age-related diseases, and ultimately in…

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miRSel
Dataset

miRSel

Offers a large collection of literature derived miRNA-gene associations. miRSel…

Offers a large collection of literature derived miRNA-gene associations. miRSel combines text-mining results with existing databases and computational predictions. Text mining enables the reliable…

SIFGD
Dataset

SIFGD Setaria italica Functional Genomics Database

Provides search and analysis tools for bioinformatics analyses of gene function…

Provides search and analysis tools for bioinformatics analyses of gene function or regulatory modules. SIFGD was designed to integrate existing data from publications, to improve the proportion of…

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CoGemiR
Dataset

CoGemiR

A publicily available microRNA-centered database whose aim is to offer an…

A publicily available microRNA-centered database whose aim is to offer an overview of the conservation of microRNAs during evolution in different animal species. This database collects information on…

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dPORE
Dataset

dPORE

A database that integrates information from promoter regions of human miRNA…

A database that integrates information from promoter regions of human miRNA genes, SNPs, and predicted TFBSs in the promoter regions. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their…

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mirEX
Dataset

mirEX

Provides a comprehensive platform for the exploration of microRNA expression…

Provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time polymerase chain reaction (PCR) and next generation sequencing (NGS) sequencing…

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ZooMir
Dataset

ZooMir

An online database of homologous microRNA search in animal genomes. The…

An online database of homologous microRNA search in animal genomes. The prediction pipeline allows the rapid and effective discovery of homologous miRNAs in a large number of genomes.

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PuTmiR
Dataset

PuTmiR

Focus on TF to miRNA regulation and provide a novel interface for extracting…

Focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs. The interface provided by the PuTmiR web server provides an important resource…

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µPC
Dataset

µPC MicroPC

An online resource that provides comprehensive information of plant miRNAs from…

An online resource that provides comprehensive information of plant miRNAs from two sources including previously reported miRNAs from miRBase and predicted miRNAs and their targets from our large…

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miRNEST
Dataset

miRNEST

A comprehensive database of animal, plant and virus microRNAs. In its updated…

A comprehensive database of animal, plant and virus microRNAs. In its updated version, named miRNEST 2.0, the database is complemented with our extensive miRNA predictions from deep sequencing…

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TriplexRNA
Dataset

TriplexRNA

A database of cooperating microRNAs and their mutual targets. Using the form on…

A database of cooperating microRNAs and their mutual targets. Using the form on the front page one can be query the database either for human genes or miRNAs to receive information about their…

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miRò
Dataset

miRò

A web-based knowledge base that provides users with miRNA-phenotype…

A web-based knowledge base that provides users with miRNA-phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and…

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MSDD
Dataset

MSDD MiRNA SNP Disease Database

Collects and integrates experimentally supported disease associated miRSNPs…

Collects and integrates experimentally supported disease associated miRSNPs into a comprehensive resource. MSDD is a manually curated database that provides a user-friendly web interface that enables…

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mirTrans
Dataset

mirTrans

Provides comprehensive information about cell-specific transcription of miRNA.…

Provides comprehensive information about cell-specific transcription of miRNA. mirTrans delivers abundant cell-specific data which includes both miRNA transcriptional start sites (TSSs) and…

CirGRDB
Dataset

CirGRDB

Searches, visualizes and interprets circadian genes and multiple…

Searches, visualizes and interprets circadian genes and multiple transcriptional and post-transcriptional regulatory. CirGRDB offers a user-friendly web interface that provides bench researchers…

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miRCarta
Dataset

miRCarta

Collects human MicroRNAs (miRNAs) and miRNA candidates. miRCarta is a database…

Collects human MicroRNAs (miRNAs) and miRNA candidates. miRCarta is a database developed to provide the information of miRBase as well as more recent data stemming from miRNA predictions. It aims to…

ncDR
Dataset

ncDR

Provides experimentally validated ncRNAs involved in drug resistance that were…

Provides experimentally validated ncRNAs involved in drug resistance that were curated from a large-scale of literature. ncDR offers computationally predicted drug resistance-ncRNA associations based…

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bloodmiRs
Dataset

bloodmiRs

Offers a reference dataset for miRNA expression in the different components of…

Offers a reference dataset for miRNA expression in the different components of healthy human blood (cell types, vesicles and fluid). bloodmiRs reports the transcriptional profiles of miRNAs and…

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mirPub
Dataset

mirPub

A database with a powerful and intuitive interface which facilitates searching…

A database with a powerful and intuitive interface which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text…

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EpimiRBase
Dataset

EpimiRBase

A comprehensive manually curated database of over 2,000 microRNA-epilepsy…

A comprehensive manually curated database of over 2,000 microRNA-epilepsy associations from 34 publications to date including 973 unique microRNA (1,191 up and 864 down regulated) from three species:…

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OncomiRdbB
Dataset

OncomiRdbB

Lists miRNAs and their respective targets for breast cancer in both human and…

Lists miRNAs and their respective targets for breast cancer in both human and mouse species. OncomiRdbB is a central resource for cancer biologists and clinicians for further experimental validation…

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miRNApath
Dataset

miRNApath

Online database that uses miRNA target genes to link miRNAs to metabolic…

Online database that uses miRNA target genes to link miRNAs to metabolic pathways. For each search, there is a specific type of input, which can be a list of target genes, miRNAs, or metabolic…

EpimiR
Dataset

EpimiR

Provides a fairly comprehensive repository about the mutual regulation between…

Provides a fairly comprehensive repository about the mutual regulation between epigenetic modifications and miRNAs, which will promote the research on the regulatory mechanism of epigenetics and…

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miRVine
Dataset

miRVine

A genome-wide transcription atlas of miRNAs in grapevine, analyzing the…

A genome-wide transcription atlas of miRNAs in grapevine, analyzing the spatio-temporal distribution of known and newly discovered miRNAs, in the widest range of grapevine samples considered thus…

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Wheat microRNA…
Dataset

Wheat microRNA Portal

Provides a broad repertoire of hexaploid wheat miRNAs associated with abiotic…

Provides a broad repertoire of hexaploid wheat miRNAs associated with abiotic stress responses, tolerance and development. These valuable resources of expressed wheat miRNAs will help in elucidating…

STPD
Dataset

STPD Salinity Tolerant Poplar Database

An integrative database for salt-tolerant poplar genome biology. Currently the…

An integrative database for salt-tolerant poplar genome biology. Currently the STPD contains Populus euphratica genome and its related genetic resources. P. euphratica, with a preference of the salty…

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miRecords
Dataset

miRecords

A resource for animal miRNA–target interactions. miRecords consists of two…

A resource for animal miRNA–target interactions. miRecords consists of two components. The validated targets component is a large, high-quality database of experimentally validated miRNA targets…

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microRNA body…
Dataset

microRNA body map

A repository of RT-qPCR miRNA expression data and functional miRNA annotation…

A repository of RT-qPCR miRNA expression data and functional miRNA annotation in normal and diseased human tissues. The miRNA bodymap enables prioritization of candidate miRNAs based on their…

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Mirsnpscore
Dataset

Mirsnpscore

A computational tool that can help identifying SNPs associated with diseases,…

A computational tool that can help identifying SNPs associated with diseases, by focusing on SNPs affecting miRNA-regulation of genes. The tool predicts the effects of SNPs in miRNA target sites and…

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Vir-Mir db
Dataset

Vir-Mir db

A database containing predicted viral miRNA candidate hairpins. An interface…

A database containing predicted viral miRNA candidate hairpins. An interface for users to query the predicted viral miRNA hairpins based on taxonomic classification, and a host target gene prediction…

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CSRDB
Dataset

CSRDB Cereal small RNAs Database

A bioinformatics resource for cereal crops consisting of large-scale datasets…

A bioinformatics resource for cereal crops consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing.

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DMD
Dataset

DMD Dietary MicroRNA Database

The first repository for archiving and analyzing the published and novel…

The first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. DMD provides a feature generator where a total of 411 descriptive attributes can be…

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GAMBD
Dataset

GAMBD Gerontology-Autophagic-MicroRNA Database

A web resource which contained 836 autophagy-related miRNAs, 197 targeted…

A web resource which contained 836 autophagy-related miRNAs, 197 targeted genes/proteins and 56 aging-related diseases such as Parkinson' disease, Alzheimer's disease and Huntington's…

Psmir
Dataset

Psmir

Presents computationally predicted small molecule-miRNA associations through…

Presents computationally predicted small molecule-miRNA associations through comparison of current gene expression profiles under miRNA perturbation and drug treatment. Psmir also provides detailed…

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PmiRExAt
Dataset

PmiRExAt

A database resource that caters plant miRNA expression atlas. The web-based…

A database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database…

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microPIR
Dataset

microPIR microRNA-Promoter Interaction Resource

Provides comparative analyses of target sites on the promoters of human–mouse…

Provides comparative analyses of target sites on the promoters of human–mouse orthologous genes. microPIR contains over 15 million predicted miRNA target sites located within human promoter…

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ExcellmiRDB
Dataset

ExcellmiRDB

A curated online database that provides integrated information about miRNAs…

A curated online database that provides integrated information about miRNAs levels in biofluids in a user-friendly way. Although many miRNA databases, including disease-oriented databases, have been…

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miRHrt
Dataset

miRHrt

An integrated database of miRNAs function in regulating heart development. This…

An integrated database of miRNAs function in regulating heart development. This database provides a platform to query miRNAs and gene data during the heart development of the major model animals…

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CREAM
Dataset

CREAM Chemotherapy ResistancE-Associated MiRSNP Database

A free online database depositing the functional miRSNP associated with…

A free online database depositing the functional miRSNP associated with chemotherapy resistance. CREAM can constitute an authoritative resource for the chemotherapy research and clinical practice…

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MNDR
Dataset

MNDR

Allows exploration of associations between ncRNAs and diseases. MNDR integrates…

Allows exploration of associations between ncRNAs and diseases. MNDR integrates manual literature curation, experimental resources and prediction algorithms. It contains a confidence score for each…

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HMED
Dataset

HMED Human MiRNA Expression Database

A database that compiles the miRNA expression profiles. HMED can be searched by…

A database that compiles the miRNA expression profiles. HMED can be searched by the miRNA ID or SRA ID of the dataset, as well as browse the data sets by tissue/disease or by miRNA. HMED enables…

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miSolRNA
Dataset

miSolRNA

A database integrating genetic map positions of miRNA-targeted genes, their…

A database integrating genetic map positions of miRNA-targeted genes, their expression profiles and their relations with quantitative fruit metabolic loci and yield associated traits. The MiSolRNA…

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miRandola
Dataset

miRandola

Gathers information about extracellular non-coding RNAs (ncRNAs). miRandola…

Gathers information about extracellular non-coding RNAs (ncRNAs). miRandola allows user to identify and prioritize papers for manual curation. This database aims to present a comprehensive list of…

TGRD
Dataset

TGRD Tomato Genomic Resources Database

Allows interactive browsing of tomato genes, micro RNAs, simple sequence…

Allows interactive browsing of tomato genes, micro RNAs, simple sequence repeats (SSRs), important quantitative trait loci and Tomato-EXPEN 2000 genetic map altogether or separately along twelve…

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miRegulome
Dataset

miRegulome

An integrated resource on the miRNA regulome. miRegulome attempts to facilitate…

An integrated resource on the miRNA regulome. miRegulome attempts to facilitate the exploration and understanding of miRNA regulomics. miRegulome provides details on the entire regulatory modules of…

GPA
Dataset

GPA Gene Perturbation Atlas

A database that includes a comprehensive collection of transcriptome profiles…

A database that includes a comprehensive collection of transcriptome profiles of protein coding genes, miRNAs and lncRNAs perturbed by knockdown or overexpression in human and mouse. GPA offers a…

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miRSponge
Dataset

miRSponge

Provides an experimentally supported resource for microRNA (miRNA) sponges. We…

Provides an experimentally supported resource for microRNA (miRNA) sponges. We have established the experimentally supported miRSponge database that contains data on 599 miRNA-sponge interactions and…

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miReg
Dataset

miReg

A manually curated microRNA Regulation Resource that represents regulatory…

A manually curated microRNA Regulation Resource that represents regulatory relationships among validated upstream regulators, downstream targets, associated biological process, experimental condition…

SM2miR
Dataset

SM2miR

Records 2925 relationships between 151 small molecules and 747 miRNAs in 17…

Records 2925 relationships between 151 small molecules and 747 miRNAs in 17 species after manual curation from nearly 2000 articles. Each entry contains the detailed information about small…

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miRvar
Dataset

miRvar

A community curation resource for genomic variation in miRNA loci. miRvar…

A community curation resource for genomic variation in miRNA loci. miRvar provides a user friendly interface to search variants in different miRNAs and has information about the variant position and…

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RNAimmuno
Dataset

RNAimmuno

A database designed to collect the published data regarding the nonspecific…

A database designed to collect the published data regarding the nonspecific immunological effects of reagents (e.g., siRNAs, shRNAs, sh-miRs, and anti-miRs) observed in investigated cell lines and…

HNOCDB
Dataset

HNOCDB Head Neck and Oral Cancer DataBase

Provides essential information for researchers working on head and neck and…

Provides essential information for researchers working on head and neck and oral cancer (HNOC). HNOCDB serves as a ‘crossroad/junction’ database, where information regarding a particular…

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VIRmiRNA
Dataset

VIRmiRNA

A resource for experimental viral miRNA and their targets. The web interface…

A resource for experimental viral miRNA and their targets. The web interface was developed using Linux-Apache-MySQL-PHP (LAMP) software bundle. User-friendly browse, search, advanced search and…

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IntmiR
Dataset

IntmiR

A manually curated database of published intronic miRNAs of human and mouse…

A manually curated database of published intronic miRNAs of human and mouse genome. Each entry in the database, aims at providing a complete resource of intronic miRNA with their target gene and…

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Antagomirbase
Dataset

Antagomirbase

A database based on putative antagomirs-miRNA heterodimers. In this work, the…

A database based on putative antagomirs-miRNA heterodimers. In this work, the human miRNA dataset was used as template to design putative antagomirs, using GC content and secondary structures as…

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miR2Disease
Dataset

miR2Disease

A manually curated database, aims at providing a comprehensive resource of…

A manually curated database, aims at providing a comprehensive resource of miRNA deregulation in various human diseases. miR2Disease provides a user-friendly interface for a convenient retrieval of…

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PMRD
Dataset

PMRD Plant MicroRNA Database

Integrates available plant miRNA data deposited in public databases, gleaned…

Integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. PMRD provides a global view of plant male reproduction and thus…

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UCbase & miRfunc
Dataset

UCbase & miRfunc Ultraconserved sequences data and miRNA function

Offers information about correlation between micro RNAs (miRNAs),…

Offers information about correlation between micro RNAs (miRNAs), ultraconserved sequences (UCRs) and the disorders related to their aberrant expression. UCbase & miRfunc is a database of human,…

MethmiRbase
Dataset

MethmiRbase

A database that makes use of meta-analysis to identify potential…

A database that makes use of meta-analysis to identify potential epigenetic-regulated miRNAs for three human cancers, i.e. lung adenocarcinoma, lung squamous carcinoma and ovarian cancers.…

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RNAdb
Dataset

RNAdb

Provides a database of mammalian non-protein-coding RNAs (ncRNAs). RNAdb is an…

Provides a database of mammalian non-protein-coding RNAs (ncRNAs). RNAdb is an online resource that (i) provides a searchable sequence repository for mammalian ncRNAs whose function may be regulatory…

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Patrocles
Dataset

Patrocles

Compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb…

Compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: (i) the coverage of seven vertebrate species in its present…

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TransmiR
Dataset

TransmiR

A database for transcription factor-microRNA regulations. TransmiR provides a…

A database for transcription factor-microRNA regulations. TransmiR provides a user-friendly interface by which interested parties can easily retrieve TF-miRNA regulatory pairs by searching for either…

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BBBomics
Dataset

BBBomics Blood Brain Barrier omics

A comprehensive portal for blood-brain barrier transcriptomics data, obtained…

A comprehensive portal for blood-brain barrier transcriptomics data, obtained by sequencing mRNA (mRNA-seq) and microRNA (miRNA-seq) of polarized hCMEC/D3 cell monolayers. This data encompasses…

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miRFANs
Dataset

miRFANs

An integrative database of Arabidopsis thaliana miRNAs and their target genes,…

An integrative database of Arabidopsis thaliana miRNAs and their target genes, expression profiles, function annotations and pathways. A friendly web interface is developed to browse and analyze of…

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miRStress
Dataset

miRStress

Describes the changes in miRNA levels following an array of stress types in…

Describes the changes in miRNA levels following an array of stress types in eukaryotic cells. miRStress can be used to uncover new insight into the biological roles of miRNAs and has the potential to…

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vHoT
Dataset

vHoT

A database that searches for mRNA targets of viral microRNAs. vHoT supports…

A database that searches for mRNA targets of viral microRNAs. vHoT supports target prediction of 271 viral microRNAs from human, mouse, rat, rhesus monkey, cow, and virus genomes.

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TUMIR
Dataset

TUMIR

A manually extracted database of experimentally supported microRNA-cancer…

A manually extracted database of experimentally supported microRNA-cancer relationship. TUMIR aims at providing a large, high-quality, validated comprehensive resource of microRNA deregulation in…

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