1 - 50 of 137 results

miRGen

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 miRBase and Ensembl nomenclatures, allowing for any combination of pre-miRNA and TF names as valid search terms for querying the database. The database provides several search and filtering options, such as combinations of pre-miRNA/TF names, the supported tissues and cell lines, or a threshold of the expression value for each TF.

deepBase

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 patterns of diverse ncRNAs across 19 species from 5 clades and to infer their functions. We provide accurate annotations of lncRNAs from RNA-seq experiments. By combining expression profiles of protein-coding genes and functional genomic annotations, we predict the function of lncRNAs from co-expression networks derived from RNA-Seq data. deepBase v2.0 also provided an integrative, interactive and versatile web graphical interface to display multidimensional data, and facilitate transcriptomic research and the discovery of novel ncRNAs.

SomamiR

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 (lncRNA). We expanded the scope of the database by including somatic mutations that impact the interactions between miRNAs and two classes of non-coding RNAs, circRNAs and lncRNAs. A recently developed webserver, miR2GO, was integrated with the database to provide a seamless pipeline for assessing functional impacts of somatic mutations in miRNA seed regions. Data and functions from multiple sources including biological pathways and genome-wide association studies were updated and integrated with SomamiR 2.0 to make it a better platform for functional analysis of somatic mutations altering miRNA-ceRNA interactions.

dbDEMC / database 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, and a total of 2224 differentially expressed miRNAs were identified. An easy-to-use web interface allows users to make a quick search of the differentially expressed miRNAs in certain cancer types. In addition, a function of ‘meta-profiling’ allows to view differential expression events according to user-defined miRNAs and cancer types. This database serves as a valuable source for cancer investigation and potential clinical application related to miRNAs.

NSDNA / Nervous System Disease NcRNAome Atlas

A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents a useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.

miRIAD / Intragenic microRNA database

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 functional annotations with a streamlined graphical data representation and an efficient information query system. This online resource integrates all known protein-coding genes, all known miRNAs, miRNAs targets, validated and predicted protein–protein interactions (PPIs) and expression data for miRNAs and coding genes across five and six tissues, respectively.

Miratlas

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 database has been generated manually based on the information that is available in the original databases for each dataset. The curated annotation classes may refer to either a cell line/type/tissue (e.g. liver) or a condition/disease (e.g. cancer). In case both a cell line/type/tissue and a condition/disease are provided for a dataset, only the condition/disease information is used for the annotation of that dataset. Additional information is provided in the miratlas repository as well as the links to the original resources.

ncRDeathDB

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) entries in 12 species. ncRDeathDB provides a user-friendly interface to query, browse and manipulate these ncRNA-associated cell death interactions. Furthermore, this resource will help to visualize and navigate current knowledge of the noncoding RNA component of cell death and autophagy, to uncover the generic organizing principles of ncRNA-associated cell death systems, and to generate valuable biological hypotheses.

miREnvironment

A database that curated and collected experimentally supported miRNA, one class of newly identified genetic factors, and environmental factor interplays and their associated phenotypes. miREnvironment integrated more than 3857 entries, 1242 miRNAs, 394 environmental factors, 305 phenotypes, 24 species from 557 publications. Information such as conditions of environmental factors, samples treated by environmental factors, species, detailed evidences of the experiments and references are also given.

miRandb / miRNA algorithmic network database

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 diseases, interactions in cellular pathways and networks and deep sequencing. miRandb recapitulates the diverse possibilities and facilitates that access to the different categories of miRNA resources. Researchers can easily select the category of miRNA information and desired organism, in result eligible databases with their features are presented. This database introducing an easy-to-follow classification of available resources that can facilitate selection of appropriate resources for miRNA-related bioinformatics tools.

PlaMoM / Plant Mobile Macromolecules

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 as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. The resource provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature.

DsTRD / Danshen Transcriptional Resource Database

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 protein-coding RNAs, lncRNAs, other ncRNA, miRNAs, and phasiRNAs. The database also includes the tissue expression feature for each transcript, which was calculated and shown based on RNA-seq data. As an efficient bioinformatics tool, DsTRD is important in studying various kinds of molecular processes in S. miltiorrhiza.

SEA / Small-RNA Expression Atlas

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, analysis workflows, and databases used. It provides expression information of high-quality predicted miRNAs including the ID, organism, chromosomal location, precursor and mature sequences, structure, read counts, prediction scores, and detailed information on the software and its versions used to predict the miRNA.

PhenomiR

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 down) and the miRNA detection method, (ii) data such as the quantitative fold-change of miRNA expression, the sample size and the origin of the samples (patients or cell culture) analysed. This repository allows a large-scale statistical analysis of aspects such as genomic localization of deregulated miRNAs or the influence of sample origin.

SignaFish

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 interactions listed in other resources, and it also lists potential miRNA-based regulatory connections for seven major signaling pathways. From the SignaFish website, users can reach other web resources, such as ZFIN. SignaFish provides signaling or signaling-related interactions that can be examined for each gene or downloaded for each signaling pathway. SignaFish serves as a navigating point for experimental design and evaluation for the zebrafish community and for researchers focusing on nonmodel fish species, such as cyclids.

Mythology of “micro”-RNAs

Obsolete
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 regulatory sRNAs (rsRNAs) or by directly opting for the various result sections which in turn transfer the user to entire tool sets, look into the pathways details, and select various cancer states. A wall page contains clustering of the rsRNAs on the basis of seed similarities, which provides dynamic image system and enrichment analysis for the targets of the selected clusters and sRNAs. The provisions of dynamic expression analysis is given where any number of experimental conditions could be selected along with sRNA of choice and its targets. Search can be performed using single term as well as in batch mode. Search results may be explored with two options: Annotation Viewer and Expression Search. On selecting Annotation Viewer, an annotation chart with visual genomic representation of the selected query is displayed. From here, all information for a target site and rsRNA can be accessed.

DASHR / Database of small human noncoding 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, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). DASHR is distinct from other existing databases because it integrates annotations for all major classes of sncRNAs with baseline expression profiles in different human tissues and cell types, making it a very useful resource to the broader scientific community.

SlideBase

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 enables users to define custom expression thresholds for individual cell types/tissues, producing sets of genes, enhancers etc. which satisfy these constraints. Changes in slider settings result in simultaneous changes in the selected sets, updated in real time. SlideBase is linked to major databases from genomics consortia, including FANTOM, GTEx, The Human Protein Atlas and BioGPS.

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 extraction of microRNA, gene and protein occurrences as well as their relationships from texts. Comprehensive collections of miRNA-gene associations are important for the development of miRNA target prediction tools and the analysis of regulatory networks. miRSel is updated daily and can be queried using a web-based interface via microRNA identifiers, gene and protein names, PubMed queries as well as gene ontology (GO) terms.