Tag: functional, regulatory and non-coding rna

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence ...

SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provide ...

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More in ...

GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-co ...

The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions in a variety of species. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and dif ...

NONCODE is a database of noncoding RNAs (except tRNAs and rRNAs), including long noncoding (lnc) RNAs. Information contained within the database includes human lncRNA–disease relationships and single nucleotide polymorphism-lncRNA–disease relationshi ...

DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBas ...

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes ...

A database of exosomes, membrane vesicles of endocytic origin released by diverse cell types.

MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that ...

As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to fu ...

H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splici ...

miRNA target prediction and functional annotation

MirGeneDB is a database of microRNA genes that have been validated and annotated as described in "A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome".* The initial version contained 1,434 micro ...

PolymiRTS (Polymorphism in microRNAs and their TargetSites) is a database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational ...

microRNA-mRNA interaction maps

GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications.

LncBook is a curated knowledgebase of human lncRNAs that features a comprehensive collection of human lncRNAs and systematic curation of lncRNAs by multi-omics data integration, functional annotation and disease association. It integrates multi-omics ...

RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of databases representing a broad range of organisms and RNA types.

Long Non-Coding RNA Database

We developed a pipeline to annotate lncRNAs (Long non-coding RNAs) and applied it to 37 plant species and six algae, resulting in the annotation of more than 120 000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the in ...

The Pancreatic Expression Database (PED) is a repository for pancreatic-derived -omics data. With a generic web-based system, the database provides the research community with an open access tool to mine currently available pancreatic cancer experime ...

The RNA Modification Database contains information pertaining to naturally occurring RNA modifications. The database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry pro ...

sORFs.org is a database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are pro ...

miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mi ...

TransmiR is a database for transcription factor-microRNA regulations, which is free for academic usage.

EpiFactors is a web-accessible database that provides broad information about human proteins and complexes involved in epigenetic regulation. It also lists corresponding genes and their expression levels in several samples, in particular 458 human pr ...

Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, di ...

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. Currently has data from 24 cancer projects. Open access data (eg. Somatic mutations, copy number alteratio ...

The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.

Database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs, as well as their relationships with microRNA binding events, disease-related SNPs and RNA-binding proteins (RBP).

The Leaf Senescence Database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. LSD includes data types such as leaf senescence-associated transcriptomics, phenotype and interaction data.

NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can b ...

Deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, C. intestinalis, D. melanogaster, C. elegans and A. thaliana. It facilitates the comprehensive annotation and discovery o ...

T-psi-C is a database of tRNA sequences and 3D tRNA structures. The T-psi-C database can be continuously updated by any member of the scientific community.

The database integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and ...

piRBase stores information on piRNAs and piRNA-associated data to support piRNA functional analysis.

Polymorphic miRNA-mediated gene regulation in vertebrates

Experimentally-determined binding sites of RNA-binding proteins

Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform fo ...

Cervical cancer gene database

Database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships.

VIRsiRNAdb contains information on experimentally validated Viral siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic ...

BSRD is a resource for bacterial sRNA sequences with extensive annotation and expression profiles. BSRD provides combinatorial regulatory networks of transcription factors and sRNAs with their common targets. There is also a novel RNA-Seq analysis pl ...

DriverDB, a database that incorporates >9500 cancer-related RNA-seq datasets and >7000 more exome-seq datasets, in addition to annotation databases and published bioinformatics algorithms dedicated to driver gene/mutation identification. Seven additi ...

MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global orderin ...

Small nucleolar RNA orthological gene database.

Dictionary on miRNAs and their putative target pathways

circAtlas is an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-dept ...

Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multiv ...

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including au ...

Database of Human Lung Cancer Research

RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured ncRNAs, with focus on sequence and structure similarities. RNArchitecture also provides literature information and links to o ...

The noncoding RNAs database is a colection of currently available sequence data on RNAs, which do not have protein-coding capacity and have been implicated in regulation of cellular processes. The RNAs included in the database form very heterogenous ...

Predicted targets of host and viral miRNAs

Plant microRNA knowledge base

Nervous System Disease NcRNAome Atlas

Lnc2Cancer 3.0 includes comprehensive data on experimentally supported long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) associated with human cancers. In addition, web tools for analyzing lncRNA expression by high-throughput RNA sequencing ...

The siRNA database provides a gene-centric view of human siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by siSearch. Linked to these sequences is information including siRNA thermodynamic prope ...

Mammal ncRNA-disease repository with increased coverage and annotation. Mammalian ncRNA-Disease Repository. MNDR v3.1: Mammal NcRNA-Disease Repository. MNDR (Mammalian ncRNA-Disease Repository) is a database that curated associations between ncRNA ...

An integrated database of ncRNA interactions. Noncoding RNAs (ncRNAs) play crucial regulatory roles in a variety of biological circuits. To document regulatory interactions between ncRNAs and biomolecules, we previously created the NPInter database ...

Human lncRNA expression database

Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions.

A manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases. Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple specie ...

microRNA Expression and Sequence Analysis Database

A comprehensive database of genomic variations that disturb ceRNA network regulation. Genomic VA,T,C,G RIATION disturbing ceRNA regulations. LnCeVar is a comprehensive database that aims to infer genomic variations that disturb lncRNA-associated ce ...

Integrates information on RNA helicases. The database allows retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Sacc ...

Reference human lncRNA sets

PmiREN is a comprehensive encyclopedia of plant miRNAs.

Coding and non-coding RNA

miRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation for the functional investigation of miRNA. miRGator v2.0 contains information about : 1) Human miRNA expr ...

lncRNA-associated ceRNA networks

A database of putative RNA binding protein target sites in the transcriptomes of model species. Dashboard - Overview of the database. Welcome to oRNAment - o RNA motifs enrichment in complete transcriptomes. Here, we developed a computational tool ...

Manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNA ...

an interactive database of human snoRNA sequences, abundance and interactions. Tool to visualize expression data in heatmaps. Column Options Reset Filters Refresh Table. snoTHAW is a tool to help visualize snoRNA expression data from snoDB

A database of curated mutual regulation between miRNAs and epigenetic modifications.

Crosstalk among signaling pathways

A database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types | Numerous studies indicate that ncRNAs have critical functions across biological processes, and single nucleotide polymorphisms (SNPs) could c ...

An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes. R-BIND: The RNA-Targeted BIoactive ligaNd Database. The dataset includes only bioactive ligands with demonstrated activity in cell culture and/or animal models. This ...

Deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Search by RsID, Gene, Region or Disease:. Links MeT-DB Whistle DRUM DRRMSDB. A database for the disease-associated genetic variants tha ...

High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides ...

Database of genetic variations associated with long noncoding genes.

A database of experimentally supported non-coding RNAs and drug targets in cancer. NoncoRNA (http: www.ncdtcdb.cn:8080 NoncoRNA ) is a manually curated database of experimentally supported non-coding RNAs (ncRNAs) and drug target associations that a ...

Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. tRFexplorer is a public database through which users may display the expression profile of tRNA-derived ncRNAs in every cel ...

a manually curated database of viral integration sites in the human genome. VISDB, visdb, virus integration site, viral integration, DNA virus, retrovirus, HBV, HPV, HIV, HTLV-1, EBV, AAV2, MCV, MLV, XMRV, gene, fragile site, miRNA, database, resour ...

An atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids.

RNA Localization in the cell

LncRNA Spatial Atlas of Expression across Normal and Cancer Tissues. Knowledge of lncRNA spatial expression patterns across tissues is important for identifying their roles in different tissues that provide important insights into disease mechanisms ...

A comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets. Welcome to the miRNASNP -v3 database. microRNAs (miRNAs) are endogenous and regulatory non-coding RNAs by targeting mRNAs for cleavage or translational re ...

PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables user ...

CoronaVR is a Computational Resource and Analysis of Epitopes and Therapeutics for Severe Acute Respiratory Syndrome Coronavirus-2. It is a comprehensive web resource for SARS-CoV-2 study.

A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides. More and more evidences have shown that non-coding RNAs (ncRNAs), such as lncRNAs, circRNAs and primary miRNAs, could encode proteins or peptides. ncEP is a ...

the small RNA Expression Atlas web application. Sign in with Google or with you SEA account below. If you have not created an account yet, then please register first. If you have received an eMail from Oasis 2 that the classification or DE analysis ...

A comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression

SyntDB: defining orthologues of human long noncoding RNAs across primates. SyntDB - the database of human long non-coding RNAs conserved across primates. Comprehensive collection of long noncoding RNAs (lncRNAs) and their evolutionary relationships ...

a comprehensive database platform for identification and validation of disease related noncoding RNAs. Mar 26, 2020: ncRPheno was published on the journal of RNA Biology... ncRPheno is a comprehensive database that provides experimentally supported ...

Database to discover the regulate relationships in the context of enhancers.

FuncPEP is a database of functional peptides encoded by non-coding RNAs.

Cancer-Specific CircRNA Databse(CSCD) is an integrated interactional database of cancer-specific circular RNAs.

dbMTS is a comprehensive database of putative human microRNA target site (MTS) SNVs and their functional predictions. dbMTS collects all potential SNVs microRNA target seed regions in human 3’UTRs and provides their functional predictions and annotat ...

Predicting circRNA-Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data. March 31, 2018, the CircR2Disease has been updated. Circular RNAs (circRNAs) are widely expressed in diverse eukaryotic spec ...

a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. RNAactDrug a comprehensive database of RNAs associated with Drug sensitivity from multi-omics data. RNAactDrug is a comprehensive resource for querying associa ...

Tissue-specific circRNA expression profiles and regulatory networks

ConsRM is a collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome.

A manually curated database for experimentally supported lncRNAs during various cancer metastatic events. A database for experimentally supported lncRNAs during various cancer metastatic events.

TarDB is a database for conserved miRNA targets, degradome supported miRNA targets and miRNA-triggered phasiRNAs in plants. TarDB is a plant miRNA target repository, which is based on cross-species conservation filter, degradome PARE-seq, and small R ...

A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome. Murine microbiome database (MMDB) contains 16S rRNA gene-based microbiome taxonomic profiles of the healthy mouse gut microbiota with manually curated meta ...

Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells.

Knowledge database of Soybean Functional gene Networks and miRNA functional networks.

Database for ncRNA expression in human extracellular vesicles.

A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases. Jun 1, 2018: Startup of the ncRNAVar project.... Sep 10, 2019: The variant mapping was developed...

Checkpoint Therapeutic Targets and Modulators Database (CKTTD) for Cancer Immunotherapy is a comprehensive database for checkpoint targets and their modulators in cancer immunotherapy. Immune checkpoints are regulators of the immune system which prev ...

A database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.

circ2GO is a comprehensive database compiling and analyzing circular RNAs found in lung cancer cell lines providing the data in tables as well as visualizing it in transcript maps and in heatmaps. Importantly, we also provide easy-to-use online tools ...

A database for plant circRNAs that act as miRNA decoys. Circular RNAs (circRNAs) are a novel type of RNAs that form covalently closed loop structures with neither 5'- 3' polarities nor polyadenylated tails. GreenCircRNA(v1.0) is the most comprehensi ...

Human osteoporosis-related gene database.

A knowledgebase of lncRNA function in human cancer.

An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma.

Multi-omics knowledge database for cytomegaloviruses.

Vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses.

ctcRbase is agene expression database of circulating tumor cells and microemboli Circulating tumor cells/microemboli (CTCs/CTM) are those cells that depart from cancerous lesions and shed into the bloodstream. Enumeration and analysis of CTCs/CTM may ...

circVAR database is genome-wide archive of genetic variants for human circular RNAs Circular RNAs (circRNAs), the 3' and 5' ends of which are covalently linked, are a kind of widely distributed and abundant RNAs found in eukaryotic organisms in recen ...

An online database for exploring over 2,000 Arabidopsis small RNA libraries.

Knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal (GI) cancer.

ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease.

An online transcriptome platform for human circRNA expressions in cancers.

An updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine.

Autophagy and Tumor Database (ATdb) is a database used to compile the published information concerning autophagy and tumor research. Such a database can be used for optaining an in-depth understanding of the complex correlations between autophagy and ...

FGviewer is an online visualization tool for functional features of human fusion genes. FGviewer is aiming for the effective visualization of the functional features of fusion genes for better prioritization of therapeutic target selection. FGviewer ...

a database of the Regulation of the Hippo Pathway in Cancer Genome. Hippo signaling pathway is a highly conserved pathway, which is consisted of a group of kinases. Dysregulation of Hippo signaling pathway is involved in the initiation and progressi ...

A comprehensive database of RNAs involved in liquid-liquid phase separation.

A knowledgebase of human long non-coding RNAs with enhanced curation model and database system.

Fusion gene annotation updates aided by deep learning.

Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A.

CRMarker is a manually curated comprehensive resource of both long noncoding and circular cancer RNA markers.

ExoBCD is a comprehensive database for exosomal biomarker discovery in breast cancer.

A database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.

A manually curated database for experimentally validated non-coding RNAs in inflammation. Non-coding RNAs in Inflammation (ncRI) provides a manually curated database for experimentally validated non-coding RNAs in inflammatary disease. Recently, inf ...

ColorCells is a database of expression, classification and functions of lncRNAs in single cells. Single cell RNA sequencing (scRNA-Seq) technology has revealed significant differences in gene expression levels between different cell groups.

PopTargs is a database for studying population evolutionary genetics of human microRNA target sites. These are the scripts used to create the MySQL database that is used by PopTargs.essex.ac.uk. The pipeline can be altered to create similar database ...

An Alzheimer's Disease Biomarker Comprehensive Database for Humans. It includes the information for all the genetic parameters like mitochondrial genes, polymorphic genes (SNP's), transcription factors, proteins, miRNAs, Associative pathway, and AD b ...

CUBAP (Codon Usage Biases Across Populations) is an interactive web portal for analyzing codon usage biases across populations. Although synonymous codon usage does not change the protein primary structure, codon choice significantly impacts translat ...

TTSurv aims to correlate coding and noncoding genes with cancers by combining high-throughput data with clinical prognosis. The application focuses on the use of high-throughput data to detect ncRNAs, such as lncRNAs and microRNAs, as novel diagnosti ...

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource. OpenProt is the first database that enforces a polycistronic model of eukaryotic genome annotations. Thus, OpenProt annotates known proteins (called RefProts) but also novel ...

A Literature-Curated Database of microRNA Expression Patterns, in Diabetic Microvascular Complications. miR2Diabetes aims to provide a comprehensive resource of miRNA dysregulation in diabetic microvascular complications (DMC). Each entry in the miR2 ...

Cancer drivers at non-coding regions

Computational prediction of animal microRNA genes

Plant transfer RNA-derived non-coding RNAs (tncRNAs) database.

T1TAdb is a database of Type I Toxin-Antitoxin systems.

Plant transfer RNA database.

A manually curated database of noncoding RNAs associated with orthopedics. Harbin Medical University, China

A database of ribozymes.

AlnC is an extensive database of long non-coding RNAs in Angiosperms.

A manually curated database of human and mouse essential lncRNA genes.

A positive miRNA-target regulations database.

A database for cancer A-to-I RNA editing with interactive analysis.

A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans.

Database of cooperating miRNAs and their mutual targets which enables researchers explore novel patterns in gene regulation.

A Knowledgebase of RAG Regulators.

A database for orchid genomics and molecular biology.

the database of immunologically relevant non-coding RNAs | git clone [email protected]:sschmeier/irndb2.git irndb2 | IRNdb - Database of immunologically relevant non-coding RNAs | // © Massey University 2014-2018 // v1.5.8

Full-length transcripts and conservation of plant circRNAs.

A database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data.

A web platform to perform, learn, and discuss gene set analysis

A PIWI-bound piRNAs database to mining NGS sncRNA data and beyond.

An integrated database for sex differences in cancer.

A blood platelets-based gene expression database for disease investigation.

A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.).

A comprehensive database of long inverted repeats in eukaryotic genomes.

An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle.

Human microbiome affect the host epigenome.

A database for comparative co-expression networks analysis of allohexaploid wheat and its progenitors.

A comprehensive and interactive database for transcriptomes from prostate cancer population cohorts.

A Database for Comparing Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.

A database of enhancer mediated feed-forward loops for human and mouse.

A virus and host ncRNA-associated interaction repository with increased coverage and annotation.

An integrated transcriptomic and genomic database for Bombyx mori and related species.

A comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation.

A resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs.

emiRIT is a text-mining based database for microRNA information.

A comprehensive database for regulations of human transcription factors and their targets. Transcription factors (TFs) as key regulators could modulate the expression of target genes by binding to specific DNA sequences of their promoter(s) or enhan ...

piRNAdb it's a piwi-interacting RNA sequences storage and search system, providing some others relevant information like alignments, clusters, datasets and targets of these piRNAs.

GUIdEStaR (G-quadruplex, uORF, IRES, Epigenetics, Small RNA, Repeats) is the integrated metadatabase in conjunction with neural network methods.

dbDEMC (database of Differentially Expressed MiRNAs in human Cancers) is an integrated database that designed to store and display differentially expressed microRNAs cancers detected by high-throughput and low-throughput methods.

A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons. A Database of miRNAs during Muscular Atrophy. Defence Institute of Physiology and Allied Sciences,.

exRNADisease is a database designed for providing the landscape of different types of extracellular RNAs (mRNAs, lncRNAs, miRNAs, circRNAs, tRFRNAs and piRNAs) from body fluids in human diseases.

Provides comprehensive prediction of microRNA target repression strength. MicroRNAs, or miRNAs, post-transcriptionally repress the expression of protein-coding genes. Our resource enables to search precompiled and predict online miRNA targets with mi ...

A comprehensive animal enhancer RNA database.

Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.

Intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.

circR2Cancer is a manually curated database of associations between circRNAs and cancers. circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase.

Buffalo Subclinical Mastitis Methylome–Transcriptome database (BSCM2TDb) is a three-tier architecture-based relational database in Water Buffalo.

A comprehensive database for translatable lncRNAs ( TransLnc) extends immunopeptidome. TransLnc provides both computationally predicted and experimentally supported lncRNA peptides in multiple species.

FishmiRNA is an evolutionarily-supported, manually-curated, genome duplication-aware database for the annotation of ray-finned fish miRNA genes, their mature products and their expression profiles.

A microRNA tissue expression database.

MicroRNA childhood Cancer Catalog (M3Cs) is a high-quality curated collection of published miRNA research studies on 16 pediatric cancer diseases.

An integrated resource for human miRNA-Transcription Factor-Target Gene coregulatory networks and associated Feed Forward Loops. Defence Institute of Physiology and Allied Science. miRNA and Transcription Factors (TFs) are fundamental transcription ...

CancerMIRNome is a web server for cancer miRNome interactive analysis and visualization based on the huamn miRNome data of 33 cancer types from The Cancer Genome Atlas (TCGA), and 40 public cancer circulating miRNome profiling datasets from NCBI Gene ...

In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility.

BDdb is a comprehensive database associated with birth-defect-related diseases. It consists of multi-omics datasets involving tens of common birth-defect diseases, and BDdb supplements more than 2000 biomarkers belonging to 22 types of birth defects.

A web-based application for molecular identification of Prototheca species.

Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types.

A Server Platform For High Altitude Human miRNA-Gene Coregulatory Networks And Associated Regulatory-Circuits. HAHmiR DB (High-Altitude Human miRNA Database) is a unique, comprehensive, curated collection of miRNAs that have been experimentally vali ...

The Chinese Glioma Genome Atlas (CGGA) is a user-friendly web application for data storage and analysis to explore brain tumors datasets. This database includes the whole-exome sequencing, DNA methylation, mRNA sequencing, mRNA microarray and microRN ...

DataBase of Plant Research (DBHR) is an online data resource specifically designed for human research, which provides access to almost all latest human database on easy and friendly finding way, the classification based on data type is informative an ...

A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta-analysis. MetamORF: A repository of unique short Open Reading Frames identified by both experimental and computatio ...

NeuroCirc is an integrative web-based resource of circRNA expression in the human brain, which allows interactive exploration of circRNA expression across multiple datatsets, including circRNA expression in bulk brain tissue, circQTLs, circRNA expres ...

a database repository of uniformly-annotated small RNAs in plants | Abstract Small RNAs (sRNAs) are essential regulatory molecules, including three mayor classes in plants, microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs ...

SPENCER is a catalog of small peptides encoded by ncRNAs. The ncRNA encoding peptides were derived from re-annotation of public mass spectrometry data from over 1,700 patient samples spanning diverse cancers. SPENCER enables the users to simply and c ...