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PAHKB / Pulmonary Arterial Hypertension KnowledgeBase
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A comprehensive database committed to establishing a comprehensive resource for pulmonary arterial hypertension. PAHKB extracts genetic data from all available sources, including those from association studies, genetic mutation, gene expression, animal model, supporting literature, various genomic annotations, gene networks, cellular and regulatory pathways, as well as microRNAs. Moreover, PAHKB provides online tools for data browsing and searching, data integration, pathway graphical presentation, and gene ranking.
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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
Permits users to identify and annotate long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), and to predict the functions of lncRNAs. deepBase is a database that facilitates the display and the annotation and discovery of small RNAs (sRNAs), lncRNAs and circRNAs. It also provides expression and evolution profiles of lncRNAs, circRNAs and small RNAs. Two web-based tools, lncSeeker and lncFunction, can be used to identify high-confidence lncRNAs, and to predict lncRNA functions.
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.
miRecords
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 manual literature curation. As the largest known collection of experimental validated miRNA targets, it emphasizes systematic and structured documentation of experimental support of miRNA–target interactions. This database not only serves the experimental researchers by providing the lists of confirmed targets of the miRNAs of their interest, but also provides a large and high-quality dataset that will facilitate the development of the next-generation miRNA target prediction programs. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. As the most complete integration of predicted miRNA targets, it is expected to provide considerable help to researchers investigating new miRNA targets.
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.
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.
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.
mirEX
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 experiments, covering various developmental stages, from wild-type to mutant plants. The mirEX portal includes mature and pri-miRNA expression levels detected in three plant species (Arabidopsis thaliana, Hordeum vulgare and Pellia endiviifolia), and in A. thaliana miRNA biogenesis pathway mutants. In total, the database contains information about the expression of 461 miRNAs representing 268 families. The data can be explored through the use of advanced web tools, including (i) a graphical query builder system allowing a combination of any given species, developmental stages and tissues, (ii) a modular presentation of the results in the form of thematic windows, and (iii) a number of user-friendly utilities such as a community-building discussion system and extensive tutorial documentation. All data contained within the mirEX database can be downloaded for use in further applications in a context-based way from the result windows or from a dedicated web page.
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.
Comparative Sequencing of Plant Small RNAs database
Consists of a sequence resources of plant small RNAs from representative species across the plant kingdom. Comparative Sequencing of Plant Small RNAs database is a repository containing data that enables studies of microRNAs (miRNA) and short-interfering RNAs (siRNAs). Five analysis tools are available to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function.
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.
microRNA body map
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 or disease subgroup. The miRNA bodymap web tool enables researchers to upload additional data sets of matching mRNA and miRNA expression data to populate the database with additional functional miRNA predictions. In this way, miRNA functions that are predicted in multiple independent data sets can be further prioritized, making the miRNA bodymap a community resource for functional miRNA research.
MethHC
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 microRNA expression to identify correlations between DNA methylation and mRNA/microRNA expression from TCGA (The Cancer Genome Atlas), which includes 18 human cancers in more than 6000 samples, 6548 microarrays and 12 567 RNA sequencing data.
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.
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.
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.
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.
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