Tag: transcriptomics

The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in ...

The Immunology Database and Analysis Portal (ImmPort) data repository was created for the exploration of clinical and basic research data on immunology and associated findings. ImmPort intends to promote effective data sharing across the basic, clini ...

Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositorie ...

Database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.

ProteomicsDB is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of ...

The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

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 ...

ATTED-II is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can find functional gene relationships and design experiments to identify gene functions by reverse gene ...

The Omics Discovery Index (OmicsDI) provides dataset discovery across a heterogeneous, distributed group of Transcriptomics, Genomics, Proteomics and Metabolomics data resources, including both open and controlled access data resources. The resource ...

The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad ...

A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that ...

CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately. This is crucial, as cell-cell communi ...

Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expr ...

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

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 Banana Genome Hub centralises databases of genetic and genomic data for the Musa acuminata crop, and is the official portal for the Musa genome resources.

CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-datas ...

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tis ...

A comprehensive repository for omics data from the red spotted newt Notophthalmus viridescens from high throughput experiments. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive ann ...

Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology. SpatialDB is the first public database that specifically curates spatially resolved tran ...

ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. They provide a source of cross-referenced data across multiple scales of biological organization—from the genome to ...

The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes.

FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them ...

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 ...

Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. ...

A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project

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 ...

An integrated knowledge database and network analysis tool for exploring complex gene regulatory networks involved in cancer. The database content is based on the manually curated annotation of experimentally verified molecular interactions described ...

SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biologica ...

a database of endothelial cell transcriptomics data. EndoDB The endothelial cell database (EndoDB) is a freely accessible added-value database that facilitates bench scientists to unlock the untapped potential of publicly available (single cell) tra ...

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 ...

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator cu ...

CellTalkDB is a manually curated database of ligand-receptor interactions in humans and mice. CellTalkDB contains literature-supported ligand-receptor (LR) pairs for human and mouse, which are curated from protein-protein interactions (PPIs) in STRIN ...

Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.

CRISPR/Cas9 Off-Target Cleavage Assays

RNA Localization in the cell

Sciatic Nerve Atlas (SNAT) is a database med transcriptional profiling of mouse peripheral nerves to the single-cell level.

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 ...

OmicsDB offers an integrated platform for studying biological networks in multiple organisms, as well as accessing gene expression data. By expanding the classic single species databases across species, it is possible to leverage the amount of inform ...

Cell type specificity of genetic traits

Alternative splicing during development in 20 species

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 ...

Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing | Tupaia belangeri (Family Tupaia, Genus Tupaia) | Tupaia ( Tupaia belangeri ) is a small mammal belonging to the family Tupaiidae, whic ...

Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.

Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various types of cDNA data resources ...

Arabidopsis thaliana Multi-omics Association Database

Versatile methodological aid to functional genomics in the neuromuscular field.

A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. A high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosom ...

A gene Expression Browser for RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics.

A database of gene expression patterns in the Drosophila terminalia. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster.

The CGDB (Coriander Genome Database) is mainly contained the coriander genome, transcriptome, and metabolome datasets

Re-annotating oligo sets used for expression microarrays is essential to supply biologists with up-to-date annotations. The tool is a query environment populated with regularly updated annotations for different oligo sets. It permits easy extraction ...

Regeneration Roadmap aims to compile large datasets for gene expression and regulation created by a broad spectrum of high-throughput omics technologies. This one-stop service provides user-friendly functionalities to explore annotated regeneration-r ...

A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue.

CuAS is an integrated database for Cucumber Alternative Splicing, includes genomic annotation, isoform-level functions, isoform-level features and tissue-specific AS events among multiple tissues.

Transcriptomic database for 14 species of scleractinian corals.

TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.

Web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance.

Database to integrate, analyze and visualize human disease-related circRNA transcriptome.

CrustyBase is an interactive online database for crustacean transcriptomes. CrustyBase provides an environment for navigating and visualising crustacean transcriptome datasets. Users can search existing transcriptomes or import new datasets of their ...

The webTWAS integrates large number of GWAS summary level data for disease, and this number will be constantly increasing according to our timely curation. The webTWAS calculates the causal genes using single tissue expression imputation (MetaXcan an ...

ADEx: Autoimmune Diseases Explorer is a comprehensive and centralized database for exploring omics data in Autoimmune Diseases. The database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most ...

The Abalomics community portal is a community driven project to increase genetic knowledge of the abalone species.

An Expertized Knowledge Database for the Model Legume Medicago truncatula. Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biologi ...

A manually curated database of genomics, transcriptomics, proteomics and drug information for interstitial lung diseases. ILDGDB is a manually curated database that provides comprehensive experimentally supported associations between genes and inter ...

Integrated multi-omics database of human and mouse early embryo.

CoFly is a gene coexpression database for the fruit fly Drosophila melanogaster

A database for single-cell screening of virus target cells in the animal kingdom.

A large and standardized collection of transcriptome data sets for human pluripotent stem cell research.

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

Database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale.

Human Antigen Receptor Consortium (huARdb) is a comprehensive database of single cell immune profiling and V(D)J T cell and B cell analysis, enhanced with advanced visualization of single-cell data.

RNAPhaSep is a novel database that collects phase separation related RNAs manually curated from publication and public databases. Various properties of RNAs together with the corresponding phase separation conditions validated by experiments were col ...

Cancer Treatment Response gene signature DataBase (CTR-DB). A database for basic and clinical researchers to access, integrate, and reuse clinical transcriptomes with cancer drug response.

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary in ...

PrimateDatabase.com, a publicly available web-accessible archive of intracellular patch clamp recordings and highly detailed three-dimensional digital reconstructions of neuronal morphology. PrimateDatabase.com is unique because it is currently the l ...

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, a specialized database of 5 ...

GEISHA (Gallus Expression In Situ Hybridization Analysis) is a centralized and comprehensive repository of precise spatial and temporal information on chicken embryonic gene expression created through in situ hybridization. Annotations include probe ...

Comparative transcriptomics and co-expression database for bacterial pathogens.

A secondary database derived from primary data in NCBI's short read archive. Database for corrected read counts and genome mapping on NCBI's transcriptomics archives.

PICEAdatabase is a web database for Picea omics and phenotypic information.

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide ...

Database of Streptocarpus rexii transcriptome.

An Atlas of RNA editing events in human tissues.

A curated repository of cell types with multifaceted characterization.

a comprehensive and interactive database of the silkworm | Silkworm Genome Informatics Database | e.g. FIBH or KWMTBOMO15365 or BGIBMGA005111 or silk fibroin heavy chain &nbspBrowse in Gene Lists | Search by sequence alignment against genomes or gene ...

A collection of functional sequence patterns located in UTR sequences.

A website to browse miRNA target predictions from the ElMMo algorithm

A database for orchid genomics and molecular biology.

Sepsis single-cell whole gene expression database.

The RNA G-quadruplex and RG4-binding proteins database.

A curated and comprehensive resource of plant cell markers.

=== !!!!! Due to changes in technology and funding, the RAD website is no longer available !!!!! ===

A Knowledgebase of RAG Regulators.

Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.

A comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells.

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

Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data.

smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs).

A comprehensive database for alternative splicing in tea plants (Camellia sinensis).

LjaFGD is the Lonicera japonica functional genomics database..

A platform dedicated to the visualization and analysis of protist co-expression and co-function networks.

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

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

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

A Comprehensive Multi-Omics Association Database of Secondary Growth in Response to Stress in Populus trichocarpa.

Community database centralizing genomic and transcriptomic sequence information for ants and related species (e.g., bees and wasps). Provides BLAST search and data download. Updated periodically with latest data and new tools.

A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication.

RNA editing database in organelles.

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

ABC portal provides web-based interactive analysis modules, especially a comprehensive cell-cell communication analysis and disease-related gene signature analysis.

GAIA (G-quAdruplexes In Alive creature) is a user-friendly database with a web interface that can be used to query a data set containing pG4s in diverse species from all three living kingdoms.

A database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species.

The Swiss Portal for Immune Cell Analysis (SPICA) is a web resource dedicated to the exploration and analysis of single-cell RNA-seq data of immune cells.

Gene Expression platform to investigate gene expression and functionalities in the tomato genome. It includes expression data from cultivated specie/variety Heinz 1706, Ailsa Craig e Solanum pimpinellifolium.

The Contraceptive and Infertility Target DataBase. The CITDBase is a tool that provides a gateway for reproductive tissue-specific genes and proteins for research and the discovery of new contraceptive/infertility targets.

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.

Long-read-tools is an interactive database of software tools for the analysis of long read sequencing data.

The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.

Black Pepper Drought Transcriptome Database (BPDRTDb) catalogues all the genomic information like differential expressed genes, microsatellites, variants, transcriptional factors, pathways, domain and families of assembled transcriptome associated wi ...

Database of transcriptomic profiles of human brains of six neuropsychiatric disorders.

Here, we have predicted CasRx guide efficiency for all human and mouse RefSeq genes. We have also enabled custom sequence input for CasRx guide design.

EchinoDB is a database consisting of amino acid sequence othoclusters from 42 echinoderm transcriptomes. We sampled taxa to span the deepest divergences within each of the 5 extant echinoderm classes. Data can be searched by keywords such as annotati ...

This Data Coordination Center web page allows DANIO-CODE consortium members to submit and view their data sets annotated with standard metadata nomenclatures.

a curated lung disease gene expression database | An accessible R package to download PulmonDB data | PulmonDB is a transcriptomic database of IPF and COPD with curated annotation | PulmonDB is a gene expression database with Chronic Obstructive Pulm ...

rPanglaoDB is an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. A meta-analysis database for single cell RNA sequencing data. Search across datasets, studies, download data, and perform advanced visualiz ...

The Open Archive for Miscellaneous Data (OMIX) database is a data repository developed and maintained by the National Genomics Data Center (NGDC). The database specializes in descriptions of biological studies, including genomic, proteomic, and metab ...

A database for exploring N6-methyladenosine methylome. REPIC (RNA Epitranscriptome Collection) is a database dedicated to provide a new resource to investigate potential functions and mechanisms of N6-adenosine methylation (m6A) modifications. Curre ...

METdb is a genomic reference database dedicated to micro-eukaryotic marine species transcriptomes. Most datasets were from Marine Microbial Eukaryote Transcriptome Sequencing Project and others from Roscoff marine station and Tara research projects. ...

Co-expression Network Database for <i>de novo</i> Transcriptome Assembly of <i>Paeonia lactiflora</i> Pall. Paeonia lactiflora Pall., commonly known as the herbaceous peony, is an ornamental flowering plant known around the world. Its oil contains a ...

>>>!!!<<< OMICtools is no longer online >>>!!!<<< We founded OMICtools in 2012 with the vision to drive progress in life science. We wanted to empower life science practitioners all over the world to achieve breakthroughs by getting data to talk. W ...