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 in the 3′ UTR of their target (Pasquinelli, 2012). Source text: Godard and van Eyll, 2015.
activity of miRNAs
activity of miRNAs
ActMiR
A computational approach for identifying active miRNAs and miRNA-mediated regulatory…
A computational approach for identifying active miRNAs and miRNA-mediated regulatory mechanisms. Applying ActMiR to four cancer datasets in The Cancer Genome Atlas (TCGA), we showed that (1) miRNA activity was tumor subtype specific; (2) genes…
Antagomirbase
Antagomirbase
A database based on putative antagomirs-miRNA heterodimers. In this work, the human miRNA…
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 parameters. The algorithm used predicted the free…
Arabidopsis Small RNA Project
Arabidopsis Small RNA Project
ASRP
Provides information and tools for the analysis of microRNA, endogenous siRNA and other…
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 small RNA classes and their targets.
AtmiRNET
AtmiRNET
A resource geared towards plant scientists for reconstructing regulatory networks of…
A resource geared towards plant scientists for reconstructing regulatory networks of Arabidopsis miRNAs. By means of highlighted miRNA studies in target recognition, functional enrichment of target genes, promoter identification, and detection of…
Blood Brain Barrier omics
Blood Brain Barrier omics
BBBomics
A comprehensive portal for blood-brain barrier transcriptomics data, obtained by…
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 coding (gene expression, alternate splice forms,…
Chemotherapy ResistancE-Associated MiRSNP Database
Chemotherapy ResistancE-Associated MiRSNP Database
CREAM
A free online database depositing the functional miRSNP associated with chemotherapy…
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 community, and spur further research on role of miRNA…
CircuitsDB
CircuitsDB
A resource devoted to the identification and analysis of mixed MicroRNA/Transcription…
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 point for a deeper understanding of their…
CoGemiR
CoGemiR
A publicily available microRNA-centered database whose aim is to offer an overview of the…
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 genomic location, conservation and expression…
Danshen Transcriptional Resource Database
Danshen Transcriptional Resource Database
DsTRD
A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains 76531…
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 functional annotations of the transcripts, including…
database of Differentially Expressed MiRNAs in…
database of Differentially Expressed MiRNAs in human Cancers
dbDEMC
A database to explore aberrantly expressed miRNAs among different cancers. An easy-to-use…
A database to explore aberrantly expressed miRNAs among different cancers. An easy-to-use interface was constructed to facilitate the analysis of the relationship between miRNA signatures and various cancer types. All the data is freely available to…
Database of small human noncoding RNAs
Database of small human noncoding RNAs
DASHR
Contains the most comprehensive information to date on human small non-coding RNAs…
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 and secondary structure, compare expression levels,…
deepBase
deepBase
A platform for annotating and discovering small (microRNAs, siRNAs, piRNAs...), long…
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 of useful tools to decode evolution and expression…
DIANA-miRPath
DIANA-miRPath
A miRNA pathway analysis web-server, providing accurate statistics, while being able to…
A miRNA pathway analysis web-server, providing accurate statistics, while being able to accommodate advanced pipelines. mirPath can utilize predicted miRNA targets (in CDS or 3’-UTR regions) provided by the DIANA-microT-CDS algorithm or even…
doRiNA
doRiNA
Focuses in post-transcriptional regulation which integrates information related to…
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 third-party analysis pipelines, all operations are…
dPORE
dPORE
A database that integrates information from promoter regions of human miRNA genes, SNPs,…
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 targets, or involvement in diseases, or biological…
EpimiR
EpimiR
Provides a fairly comprehensive repository about the mutual regulation between epigenetic…
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 miRNA.
EpimiRBase
EpimiRBase
A comprehensive manually curated database of over 2,000 microRNA-epilepsy associations…
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: human (161), mouse (849) and rat (1,045). We have…
ExcellmiRDB
ExcellmiRDB
A curated online database that provides integrated information about miRNAs levels in…
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 launched before, the ExcellmiRDB is so far the…
ExprTargetDB
ExprTargetDB
An online database of human miRNA targets predicted by this approach as well as a…
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 mechanisms of gene regulation and gene regulatory…
Head, Neck and Oral Cancer DataBase
Head, Neck and Oral Cancer DataBase
HNOCDB
Provides essential information for researchers working on head and neck and oral cancer…
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 gene/miRNA has been extracted from other databases and…
Host gene Opposite Correlated TARgets
Host gene Opposite Correlated TARgets
HOCTAR
A procedure to improve the prediction of miRNA targets. The HOCTAR procedure is based on…
A procedure to improve the prediction of miRNA targets. The HOCTAR procedure is based on the integration of expression profiling and sequence-based miRNA target recognition softwares. HOCTAR database (db) is the first and unique database to use…
Human MicroRNA and Disease Database
Human MicroRNA and Disease Database
HMDD
A repository of miRNA-associated diseases, obtained by manual curation from literature…
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 data, including miRNA-disease association data from…
iMiRNA-PseDPC
iMiRNA-PseDPC
Identifies the real microRNA precursors and false microRNA precursors. For the…
Identifies the real microRNA precursors and false microRNA precursors. For the convenience of most experimental scientists, a user-friendly web server for the new predictor has been established, by which users can easily get their desired results…
Integrated Genomic Database of Non-Small Cell…
Integrated Genomic Database of Non-Small Cell Lung Carcinoma
IGDB.NSCLC
Aims to facilitate and prioritize identified lung cancer genes and microRNAs for…
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 interventions.
IntmiR
IntmiR
A manually curated database of published intronic miRNAs of human and mouse genome. Each…
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 deregulation in various diseases with related tissues…
mESAdb
mESAdb
A regularly updated database for the multivariate analysis of sequences and expression of…
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 and coupled with statistical analysis and…
MethHC
MethHC
A database comprising a systematic integration of a large collection of DNA methylation…
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, mRNA expression, DNA methylation of microRNA gene and…
MicroPC
MicroPC
µPC
An online resource that provides comprehensive information of plant miRNAs from two…
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 scale Expressed Sequence Tags (ESTs) analysis. µPC…
microRNA body map
microRNA body map
A repository of RT-qPCR miRNA expression data and functional miRNA annotation in normal…
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 expression pattern or functional annotation across tissue…
microRNA-Promoter Interaction Resource
microRNA-Promoter Interaction Resource
microPIR
A public database containing over 15 million predicted miRNA target sites located within…
A public database containing over 15 million predicted miRNA target sites located within human promoter sequences. These predicted targets are presented along with their related genomic and experimental data, making the microPIR database the most…
microRNA.org
microRNA.org
A comprehensive resource of microRNA target predictions and expression profiles. Target…
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 on target rules and on the use of an up-to-date…
microRNAviewer
microRNAviewer
miRviewer
Encompasses all known and predicted miRNAs of fully annotated animal genomes.…
Encompasses all known and predicted miRNAs of fully annotated animal genomes. miRviewer's interface provides the user with a graphic outlook of the current miRNA world together with additional information such as sequence alignments and…
microTranspoGene
microTranspoGene
A publicly available database of human, mouse, zebrafish and nematode microRNAs which are…
A publicly available database of human, mouse, zebrafish and nematode microRNAs which are derived from Transposable elements (TEs) either transcriptionally or structurally.
mimiRNA
mimiRNA
A database of miRNA expression profile data across different tissues and cell lines.…
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 from separate sources. This enables mimiRNA to…
miR_Path
miR_Path
A software for inferring cancer-related miRNAs based on gene expression data. It is a…
A software for inferring cancer-related miRNAs based on gene expression data. It is a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles which can effectively identify cancer-related miRNAs…
[email protected]@N
[email protected]@N
An integrative approach based on a meta-regulation network model and a large-scale…
An integrative approach based on a meta-regulation network model and a large-scale database. [email protected]@N uses a graph-based approach to predict novel molecular actors across multiple regulatory processes (i.e. TFs acting on protein-coding or miRNA…
miR2Disease
miR2Disease
A manually curated database, aims at providing a comprehensive resource of miRNA…
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 each entry by microRNA ID, disease name, or target…
miR2GO
miR2GO
A web based platform for comparative analyses of human miRNA functions. miR2GO includes…
A web based platform for comparative analyses of human miRNA functions. miR2GO includes two programs: miRmut2GO and miRpair2GO. miRmut2GO implements a knowledge-based method to assess the functional effects of genetic and somatic mutations in…
mirAct
mirAct
A tool designed to investigate miRNA activity based on gene-expression data by using the…
A tool designed to investigate miRNA activity based on gene-expression data by using the negative regulation relationship between miRNAs and their target genes. mirAct supports multiple-class data and enables clustering analysis based on…
miRandola
miRandola
A comprehensive classification of different extracellular circulating miRNA types. A…
A comprehensive classification of different extracellular circulating miRNA types. A direct link to the knowledge base miRò together with the inclusion of datamining facilities allow users to infer possible biological functions of the circulating…
miRBase
miRBase
A searchable database of published miRNA sequences and annotation. Each entry in the…
A searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence…
miRCancer
miRCancer
Provides comprehensive collection of microRNA (miRNA) expression profiles in various…
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 techniques for information collection. Manual revision…
miRClassify
miRClassify
A machine learning-based web server that can rapidly identify miRNA from the primary…
A machine learning-based web server that can rapidly identify miRNA from the primary sequence and classify it into a miRNA family regardless of similarity in sequence and structure. Additionally, the medical implication of the miRNA family is also…
miRDB
miRDB
An online resource for miRNA target prediction and functional annotations. In addition to…
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 user-provided sequences for miRNA target…
miRecords
miRecords
A resource for animal miRNA-target interactions. miRecords consists of two components.…
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 resulting from meticulous literature curation. The…
miReg
miReg
A manually curated microRNA Regulation Resource that represents regulatory relationships…
A manually curated microRNA Regulation Resource that represents regulatory relationships among validated upstream regulators, downstream targets, associated biological process, experimental condition or disease state.
miREnvironment
miREnvironment
A database that curated and collected experimentally supported microRNA (miRNA), one…
A database that curated and collected experimentally supported microRNA (miRNA), one class of newly identified genetic factors, and environmental factor interplays and their associated phenotypes.
miRFam
miRFam
An alignment-free method to classify miRNA genes with n-grams and a multiclass SVM.…
An alignment-free method to classify miRNA genes with n-grams and a multiclass SVM. miRFam uses only primary information of pre-miRNAs or mature miRNAs and a multiclass SVM, to automatically classify miRNA genes.
miRFANs
miRFANs
An integrative database of Arabidopsis thaliana miRNAs and their target genes, expression…
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 the data. We believe that miRFANs is a useful…
miRGen
miRGen
Provides for the first time accurate cell-line-specific miRNA gene transcription start…
Provides for the first time accurate cell-line-specific miRNA gene transcription start sites (TSSs), coupled with genome-wide maps of transcription factor (TF) binding sites in order to unveil the mechanisms of miRNA transcription regulation. To…
miRHrt
miRHrt
An integrated database of miRNAs function in regulating heart development. This database…
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 (Zebrafish, Chicken, Mouse).
miRiadne
miRiadne
A tool for re-annotating miRNA namelists or datasets. Obsolete annotations (either due to…
A tool for re-annotating miRNA namelists or datasets. Obsolete annotations (either due to older miRBase versions or out-dated profiling platforms) can be converted into newer ones enforcing mature sequence correspondence. miRiadne uses the miRNA…
Mirinho
Mirinho
The predicton of the pre-miRNA hairpin structures is an essential step in the predicton…
The predicton of the pre-miRNA hairpin structures is an essential step in the predicton of miRNAs. However, the cubic complexity algorithms used for that can become very slow in a genome-wide scale. Mirinho was developed to solve this problem.
miRNA SNiPer
miRNA SNiPer
An online tool for the detection of miRNA polymorphisms in vertebrates. miRNA SNiPer…
An online tool for the detection of miRNA polymorphisms in vertebrates. miRNA SNiPer accepts a list of miRNA genes and returns a table of variations within different regions of miRNA genes: pre-miRNA, mature, seed region.
miRNAMap
miRNAMap
In addition to known miRNA targets, three computational tools previously developed, such…
In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3' -UTR of genes. Various criteria for filtering the putative miRNA…
miRNApath
miRNApath
Online database that uses miRNA target genes to link miRNAs to metabolic pathways. For…
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 pathways, which results in different views, depending…
miRNEST
miRNEST
A comprehensive database of animal, plant and virus microRNAs. In its updated version,…
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 libraries, data from plant degradome analyses, results…
miRNeye
miRNeye
A high-resolution expression atlas revealing the spatiotemporal distribution of 221…
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 hybridization (ISH) using Locked Nucleic Acid…
miRò
miRò
A web-based knowledge base that provides users with miRNA-phenotype associations in…
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 targets, into a unified database equipped with an…
miROrtho
miROrtho
Presents the results of a comprehensive computational survey of miRNA gene candidates…
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 miRBase catalog of experimentally verified miRNA…
miRPD
miRPD
An approach in which miRNAs are linked to diseases via proteins, thereby directly…
An approach in which miRNAs are linked to diseases via proteins, thereby directly providing biological hypotheses. Specifically, we infer miRNA–disease associations by network analysis of known or predicted miRNA–protein associations and…
mirPub
mirPub
A database with a powerful and intuitive interface which facilitates searching for miRNA…
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 mining techniques on MEDLINE, integrates data from…
miRSel
miRSel
Offers a large collection of literature derived miRNA-gene associations. miRSel combines…
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 extraction of microRNA, gene and protein occurrences…
MirSNP
MirSNP
A collection of human SNPs in predicted miRNA target sites. MirSNP could identify the…
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 researches.
Mirsnpscore
Mirsnpscore
A computational tool that can help identifying SNPs associated with diseases, by focusing…
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 uses linkage disequilibrium to map these…
miRSponge
miRSponge
Provides an experimentally supported resource for microRNA (miRNA) sponges. We have…
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 463 ceRNA relationships from 11 species following…
MirtronPred
MirtronPred
A web based server to predict mirtrons from intronic sequences. The MirtronPred algorithm…
A web based server to predict mirtrons from intronic sequences. The MirtronPred algorithm predicts and filters probable intronic miRNAs, based on distinct structural and sequence features of known plant miRNAs and mirtrons.
miRvar
miRvar
A community curation resource for genomic variation in miRNA loci. miRvar provides a user…
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 the allele change in the respective miRNA, in…
miRVine
miRVine
A genome-wide transcription atlas of miRNAs in grapevine, analyzing the spatio-temporal…
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 far. miRVine aims at becoming the reference for the…
miSolRNA
miSolRNA
A database integrating genetic map positions of miRNA-targeted genes, their expression…
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 database allows the simple extraction of metadata…
MNDR
MNDR
A comprehensive mammalian ncRNA-disease database. MNDR intends to provide the scientific…
A comprehensive mammalian ncRNA-disease database. MNDR intends to provide the scientific community with a comprehensive tool for efficient browsing and extraction of the relationships between diverse ncRNAs and diseases in three mammalians.
Mythology of “micro”-RNAs
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 points: by searching for terms, browsing for…
NetAge
NetAge
Gives visitors a wealth of information about the microRNA-regulated protein-protein…
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 the determination of longevity. NetAge can provide…
OncomiRDB
OncomiRDB
Aims at annotating the experimentally verified oncogenic and tumor-suppressive miRNAs…
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 least one cancer-related phenotype or cellular process…
OncomiRdbB
OncomiRdbB
An integrated database consisting of the miRNAs of human and mouse genomes, their…
An integrated database consisting of the miRNAs of human and mouse genomes, their sequences, chromosome and gene locations, respective targets and their description, pathways it regulates in breast cancer.
Pan-cancer associated ceRNA database
Pan-cancer associated ceRNA database
Pan-ceRNADB
A freely available resource to investigate mRNA related ceRNA-ceRNA landscape and…
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 mediated ceRNA–ceRNA interactions, and the…
Patrocles
Patrocles
Compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated…
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 release, aiming for more when information becomes…
PhenomiR
PhenomiR
Provides information about differentially regulated miRNA expression in diseases and…
Provides information about differentially regulated miRNA expression in diseases and other biological processes. PhenomiR allows machine-readable access to miRNA and target relations from these studies to study the impact of miRNAs on multifactorial…
Plant MicroRNA Database
Plant MicroRNA Database
PMRD
Integrates available plant miRNA data deposited in public databases, gleaned from the…
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 aids advances in this important area.
Plant microRNA Knowledge Base
Plant microRNA Knowledge Base
PmiRKB
Includes the miRNAs of two model plants, Arabidopsis (Arabidopsis thaliana) and rice…
Includes the miRNAs of two model plants, Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Four major functional modules, "SNPs", "Pri-miRNAs", "MiR—Tar", and "Self-reg", are provided.
PlantMiRNAPred
PlantMiRNAPred
A classification method based on support vector machine (SVM) is proposed specifically…
A classification method based on support vector machine (SVM) is proposed specifically for predicting plant pre-miRNAs. The ability of PlantMiRNAPred to discern real and pseudo pre-miRNAs provides a viable method for discovering new non-homologous…
PmiRExAt
PmiRExAt
A database resource that caters plant miRNA expression atlas. The web-based repository…
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 interface offers open and easy access to miRNA…
PolymiRTS Database
PolymiRTS Database
An integrated platform for analyzing the functional impact of genetic polymorphisms in…
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 relations between the PolymiRTSs and gene…
PuTmiR
PuTmiR
Focus on TF to miRNA regulation and provide a novel interface for extracting the list of…
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 for analyzing the direct and indirect regulation…
RepTar
RepTar
Contains genome-wide predictions of human and mouse miRNAs as well as predictions of…
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, which allows browsing through the putative sites as…
RNAcentral
RNAcentral
A resource that provides unified access to the ncRNA sequence data supplied by the Expert…
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 an integrated genome browser for selected species.
RNAdb
RNAdb
A comprehensive database of mammalian non-protein-coding RNAs (ncRNAs). This website…
A comprehensive database of mammalian non-protein-coding RNAs (ncRNAs). This website serves to archive the final snapshot of the RNAdb 2.0 datasets for legacy purposes. It will remain active indefinitely.
Sarcoma MicroRNA Expression Database
Sarcoma MicroRNA Expression Database
S-MED
A repository that describes the patterns of miRNA expression in various human sarcoma…
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 formats. The database also provides statistical…
SM2miR
SM2miR
Records 2925 relationships between 151 small molecules and 747 miRNAs in 17 species after…
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 molecules, miRNAs and evidences of their relationships,…
SomamiR
SomamiR
A database of cancer somatic mutations in microRNAs (miRNA) and their target sites that…
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, circular RNAs (circRNA) and long noncoding RNAs…
Soybean microRNA Functional Network
Soybean microRNA Functional Network
SmiRFN
A comprehensive web tool about soybean microRNA functional Analysis. SmiRFN measures the…
A comprehensive web tool about soybean microRNA functional Analysis. SmiRFN measures the functional similarity of miRNAs considering both the site accessibility and the interactive context of target genes in functional gene networks.
Targetfinder
Targetfinder
Predicts small RNA targets in a sequence database using a plant-based scoring metric.…
Predicts small RNA targets in a sequence database using a plant-based scoring metric. Deep sequencing and computational methods are used to identify, profile and analyze non-conserved MIRNA genes in Arabidopsis thaliana.
TargetRunningSum
TargetRunningSum
A rank-based algorithm to detect miRNA regulatory activity in cancer-derived tissue…
A rank-based algorithm to detect miRNA regulatory activity in cancer-derived tissue samples which combines measurements of gene and miRNA expression levels and sequence-based target predictions. TargetRunningSum is designed to detect modest but…
TissueAtlas
TissueAtlas
An atlas of miRNA expression in multiple human tissues. TissueAtlas has been created by…
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 collected post-mortem. One thousand three hundred…
tools4miRs
tools4miRs
A platform that gathers currently more than 160 methods for broadly defined miRNA…
A platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods…
TransmiR
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 a miRNA or a TF.
TriplexRNA
TriplexRNA
A database of cooperating microRNAs and their mutual targets. Using the form on the front…
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 possible involvement in RNA triplexes.
vHoT
vHoT
A database that searches for mRNA targets of viral microRNAs. vHoT supports target…
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.
Vir-Mir db
Vir-Mir db
A database containing predicted viral miRNA candidate hairpins. An interface for users to…
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 service based on the RNAhybrid program and the…
ViRBase
ViRBase
Aims to provide the scientific community with a resource for efficient browsing and…
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 query, browse and manipulate these virus-host…
VIRmiRNA
VIRmiRNA
A resource for experimental viral miRNA and their targets. The web interface was…
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 useful analysis tools are also provided on the web…
ViTa
ViTa
A database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc,…
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.
Wheat microRNA Portal
Wheat microRNA Portal
Provides a broad repertoire of hexaploid wheat miRNAs associated with abiotic stress…
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 the regulatory mechanisms involved in freezing and…
ZooMir
ZooMir
An online database of homologous microRNA search in animal genomes. The prediction…
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.