Tag: gene expression

The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...

Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the re ...

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to dat ...

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

Investigation Study Assay Tabular (ISA-Tab) describes the ISA Abstract Model reference implementation specified using the ISA-Tab format. ISA-Tab files are tab separated value (tsv) files, with specific labeled column structures. The ISA model consis ...

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

The aim of MIQE is to provide authors, reviewers and editors with specifications for the minimum information that must be reported for a qPCR experiment in order to ensure its relevance, accuracy, correct interpretation and repeatability.

MIAME is intended to specify all the information necessary for an unambiguous interpretation of a microarray experiment, and potentially to reproduce it. MIAME defines the content but not the format for this information.

The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, ...

Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...

The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular dia ...

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Expe ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated ...

The NIDDK Information Network provides access to large pools of data relevant to the mission of NIDDK. The dkNET portal contains information about research resources such as antibodies, vectors and mouse strains, data, protocols, and literature.

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrat ...

Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...

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 ...

BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...

The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this in ...

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene pro ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...

Database of RNA interactions in post-transcriptional regulation.

The Ensembl genome annotation system, developed jointly by EMBL-EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented b ...

The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Center ...

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 ...

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 ...

Genotype-Tissue Expression (GTEx) - database which helps to study the relationship between genetic variation and gene expression in human tissues.

ABA Adult Mouse Brain is a standardised collection of the expression patterns of thousands of adult brain genes. This resource can be used for a vast array of research on brain organisation and function. There are lighter versions of this ontology th ...

Characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection of strains for experimental studies. Data sets are voluntarily contributed by researchers or retrieved by us from public so ...

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims ...

Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.1 (GAF 2.1). The annotation flat file format is comprised of 17 tab-delimited fields. Thi ...

ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.

MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication ...

The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements ...

PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank contains over 306,800 primers covering most known human and mouse genes. There are several ways to ...

dbVar is a database of human genomic structural variation where users can search, view, and download data from submitted studies. dbVar stopped supporting data from non-human organisms in 2017, however existing non-human data remains available. In ke ...

PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as w ...

GenePattern GeneSet Table Format is an analytical tool and file format for the analysis of gene expression and network analysis provided by GenePattern.

FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.

Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.2 (GAF 2.2). The annotation flat file format is comprised of 17 tab-delimited fields. Thi ...

The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides lin ...

Plant Transcription Factor Database (PlantTFDB) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, It contains 320 370 TFs, classified into 5 ...

The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature, databases and unpublished data.

The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is e ...

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

TDR Targets integrates chemical and genomic information and allows users to prioritize targets and compounds to develop and repurpose new drugs and chemical tools for human pathogens. The TDR Target Project was started in 2005 after a call for applic ...

FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides access to integrated data at a number of d ...

The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines w ...

Part of the Progenetix project, the arrayMap database facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed ...

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 ...

MaizeGDB is the maize research community's central repository for genetics and genomics information.

Detects this family of direct repeats found in the DNA of many bacteria and archaea.

The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...

The NCBI BioSample database stores submitter-supplied descriptive information, or metadata, about the biological materials from which data stored in NCBI’s primary data archives are derived. NCBI’s archives host data from diverse types of samples fro ...

This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosoma ...

The Chemical Effects in Biological Systems (CEBS) database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial, and governmental laboratories.

The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for who ...

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...

AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transc ...

Overview The NIH Mammalian Gene Collection (MGC) program is a multi-institutional effort to identify and sequence cDNA clones containing a full-length open reading frame (FL-ORF) for human, mouse, and rat genes. To date, the MGC has produced over 324 ...

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to ...

The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.

The e-Mouse Atlas (EMA) is a detailed model of the developing mouse. Its purpose is not only to provide information about the shape, gross anatomy and detailed histological structure of the mouse, but also to provide a framework into which informatio ...

RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In t ...

GigaDB primarily serves as a repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles. GigaDB defines a dataset as a group of files (e. ...

The International Human Epigenome Consortium (IHEC) coordinates the production of reference epigenome maps through the characterization of the regulome, methylome, and transcriptome from a wide range of tissues and cell types. The IHEC Data Portal pr ...

IMGT/GENE-DB is the IMGT® comprehensive genome database for immunoglobulins (IG) and T cell receptors (TR) genes from human and mouse, and, in developement, from other vertebrate species (e.g. rat). IMGT/GENE-DB is part of IMGT®, the international ...

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 ...

This database includes TSS data from adult and embryonic human tissue. DBTSS now contains 491 million TSS tag sequences for collected from a total of 20 tissues and 7 cell cultures.

The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plant ...

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 ...

GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, ...

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...

Fly-FISH documents the expression and localization patterns of Drosophila mRNAs at the cellular and subcellular level during early embryogenesis and third instar larval tissues. A high-resolution, high-throughput fluorescence detection method is used ...

The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for compre ...

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-ref ...

Online GEne Essentiality database

The Princeton University MicroArray database (PUMAdb) stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, PUMAdb provides interfaces for data retrieval, analysis and visualization.

MISFISHIE is the Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments. This specification details the minimum information that should be provided when publishing, making public, or exchanging results from v ...

GWIPS-viz is a freely available on-line genome browser which provides pre-populated ribosome profiling (Ribo-seq) and mRNA-seq tracks from published studies.

The e-Mouse Atlas of Gene Expression (EMAGE) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descripti ...

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 COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research ...

Open TG-GATEs is a public toxicogenomics database developed so that a wider community of researchers could utilize the fruits of TGP and TGP2 research. This database provides public access to data on 170 of the compounds catalogued in TG-GATEs. Data ...

BloodSpot is a database of mRNA expression in healthy and malignant haematopoiesis and includes data from both humans and mice. The core function of BloodSpot is to provide an expression plot of genes in healthy and cancerous haematopoietic cells at ...

ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains availa ...

Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage collaboration in the research community.

canSAR is an integrated cancer research and drug discovery resource that brings together large-scale data from different disciplines and allows query and exploration to help cancer research and drug discovery.

The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of hundreds of organisms with completely sequenced genomes. Each database contains the genome, predicted metabolic pathways, p ...

REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence ...

AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB int ...

Gene expression and neuroanatomical data.

Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.

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 ...

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 ...

Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.

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 GenitoUrinary Development Molecular Anatomy Project (GUDMAP) provides data and tools to facilitate research on the GenitoUrinary (GU) tract for the scientific and medical community. In addition to current GUDMAP data, this resource incorporates d ...

Database for meta-analysis of the prognostic value of genes. It has features of 1) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as 2) a tool for assessing the biological relationship between ge ...

MIAME/Plant is a standard describing which biological details should be captured for describing microarray experiments involving plants. Detailed information is required about biological aspects such as growth conditions, harvesting time or harvested ...

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 ...

AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products.

An ontology of the anatomy of Drosophila melanogaster. It can be used for annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. It was originally developed by FlyBase, who continue to main ...

A suite of Web-based tools for comparative genomics

Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. ...

The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regula ...

The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arab ...

TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. All evidence to common protein identifiers and Brenda Tissue O ...

PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

The Network of Cancer Genes (NCG) contains information on duplicability, evolution, protein-protein and microRNA-gene interaction, function, expression and essentiality of cancer genes from manually curated publications . NCG also provides informatio ...

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 ...

The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and anno ...

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 ...

ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.

ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they mo ...

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

Minimum Information About an RNAi Experiment (MIARE) is a set of reporting guidelines that describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results. MI ...

ViBE-Z, the Virtual Brain Explorer for Zebrafish is an imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with prec ...

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 ...

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 ...

Cyclebase is a database to visualize and download results from genome-wide cell-cycle-related experiments. In addition to genome annotation, Cyclebase also provides mRNA data, protein expression data, and integrated cell-cycle phenotype information f ...

The DGVa team accepts direct submissions from researchers and also curates data from the published literature. As part of a regular exchange, DGVa data is sent to its partner archive, dbVar (hosted by the National Center for Biotechnology Information ...

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 objective of this project is to generate the most comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications.

Online Mendelian Inheritance in Animals is a a database of inherited disorders, other (single-locus) traits, and genes in animal species (other than human and mouse).

The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to mo ...

PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR ...

SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA mi ...

MIAME defines a conceptual structure for defining the core information that is common to most microarray experiments. MIAME/Env is an extension of these guidelines to cover environmental genomics.

Human Gene and Protein Database (HGPD) presents SDS-PAGE patterns and other informations of human genes and proteins.

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that b ...

HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.

The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are high ...

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 ...

GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists togethe ...

The CHD7 database contains locus-specific, anonymised mutation data on both published and unpublished variants of the CHD7 gene related to the CHARGE syndrome phenotype. It can be searched for patients and their clinical phenotype or for mutations. I ...

Collaborative resource for the Bacillus community.

RTPrimerDB is a public database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisa ...

Provides accurate cell-line-specific miRNA gene transcription start sites, coupled with genome-wide maps of transcription factor binding sites in order to unveil the mechanisms of miRNA transcription regulation. The database schema and web interface ...

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

The Generic Feature Format Version 3 (GFF3) format was developed after earlier formats, although widely used, became fragmented into multiple incompatible dialects. The GFF3 format addresses the most common extensions to GFF, while preserving backwar ...

mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface.

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 ...

The Bovine Genome Database project is developed to support the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.

Gene Signature DataBase

Predicted regulons in prokaryotic genomes

Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains. Combining information from different resources, manually checking the retrieved mammalian TF sequences and applying extensive phyloge ...

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 ...

Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum ...

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

Integrated annotation and sequencing-based expression data for all major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs.

SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated b ...

The TFClass Schema is an identifier schema for classifying transcription factors according to a six-level schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene ...

DroID, the Drosophila Interactions Database, assembles gene and protein interaction data from a variety of sources into one easily accessible, comprehensive database. The database includes published and unpublished low and high throughput data sets, ...

T1DBase focuses on two research areas in type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.

A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system ...

The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the lis ...

Gene expression data sorted into two groups: expressed and not expressed genes

The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. The JGA contains exclusive data col ...

Rice transcriptome under natural conditions

Information Commons for Rice (IC4R) is a rice knowledgebase that incorporates rice data through multiple modules such as genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequen ...

Gene Signature DataBase (GeneSigDB) is a database of gene signatures (or gene sets) that have been extracted and manually curated from articles that are indexed by PubMed.

CellFinder maps validated gene and protein expression, phenotype and images related to cell types.The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells ...

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 ...

ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accu ...

VFB is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster. Our goal is to make it easier for researchers to find relevant anatomical information and reagent ...

ChimerDB is a database of fusion sequences encompassing bioinformatics analysis of mRNA and EST sequences in the GenBank, manual collection of literature data and integration with other well known databases. Fusion transcripts with nonoverlapping ali ...

GeneProf Data is an open web resource for analysed functional genomics experiments. We have built up a large collection of completely processed RNA-seq and ChIP-seq studies by carefully and transparently reanalysing and annotating high-profile public ...

Internal Control Genes (ICG) is a wiki-based knowledgebase of internal control genes (or reference genes) for RT-qPCR normalization in a variety of species across three domains of life. Based on community curation, ICG provides curated data from a la ...

DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF incl ...

BioXpress is a curated gene expression and disease association database where the expression levels are mapped to genes.

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 ...

Experimentally-determined binding sites of RNA-binding proteins

Customizable RNA-seq Data Analysis and Visualization Platform.

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarra ...

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 ...

Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed.

The database of human DNA Methylation and Cancer (MethyCancer) is developed to study interplay of DNA methylation, gene expression and cancer. It hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer informati ...

Metabolic gEne RApid Visualizer

Genomic Expression Archive (GEA) is a public database of functional genomics data such as gene expression, epigenetics and genotyping SNP array. Both microarray- and sequence-based data are accepted in the MAGE-TAB format in compliance with MIAME and ...

The dbDEPC is a database of differentially expressed proteins in human cancers.

<<<!!!<<< This repository is no longer available >>>!!!>>>

4DGenome is a public database that archives and disseminates chromatin interaction data. Currently, 4DGenome contains over 8,038,248 interactions curated from both experimental studies (high throughput and individual studies) and computational predic ...

Public repository for gene expression experimental data. The database system is compliant with the MIAME standard.

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.

The KUPKB is a collection of omics datasets that have been extracted from scientific publications and other related renal databases. The iKUP browser provides a single point of entry for you to query and browse these datasets.

The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualising and analysing genomics and transcriptomics data for different plant species. Currently, it includes dedicated web portals for enabling in- ...

The Neural-Immune Gene Ontology (NIGO) is a subset of GO directed for neurological and immunological systems. NIGO was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to ...

Integrated Genomic Database of Non-Small Cell Lung Cancer.

StellaBase is the Nematostella vectensis genomics database.

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 ...

The immune tolerance data management and visualization portal for studies sponsored by the Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies a ...

These are preliminary guidelines describing the Minimum Information About a Peptide-Array Experiment (MIAPepAE). Described is a checklist of data and meta-data that should accompany a peptide-array experiment. The guidelines are maintained by the res ...

WebGesTer Database (DB) is the largest compilation of intrinsic terminators of transcription. It comprises of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. The database is the storehouse for algorithm ...

An integrated Omics data warehouse for Locust, Locusta migratoria

The Mammalian Transcriptomic Database (MTD) was created to store information on mammalian transcriptomes. The MTD allows browsing of genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exo ...

Tissue microarrays (TMA) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential ...

FlyTF (v2) is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified T ...

EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.

The RDML file format is developed by the RDML consortium (http://www.rdml.org) and can be used free of charge. The RDML file format was created to encourage the exchange, publication, revision and re-analysis of raw qPCR data. The core of an RDML fil ...

Regulatory Network in Protein Phosphorylation

Query single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query retur ...

Database for Human Transcription Co-Factors

Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) and mRNA specific codon red ...

HuSiDa is a public database that serves as a depository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at supporting the setup ...

>>>!!! <<< The Epigenomics database was retired on June 1, 2016. All epigenomics data are available in our GEO resource https://www.ncbi.nlm.nih.gov/geo >>> !!! <<< The Epigenomics database provides genomics maps of stable and reprogrammable nucl ...

An InterMine interface to data from Phytozome

The Hardwood Genomics Project is a databases for expressed genes, genetic markers, genetic linkage maps, and reference populations. It provides lasting genomic and biological resources for the discovery and conservation of genes in hardwood trees for ...

Diatoms are photosynthetic unicellular eukaryotes that play an essential role in marine ecosystems. On a global scale, they generate around one fifth of the oxygen we breathe. On this web site we present searchable databases of diatom ESTs (expressed ...

An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.

An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.

WikiCell provides a wiki interface to information about the human transcriptome and stores information on Expressed Sequenced Tags (ESTs). Users can access, curate, and submit database data as well as browse, query, and up- and download sequences. Ge ...

Database of Human Lung Cancer Research

YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene e ...

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 ...

The Heart Disease-related Non-coding RNAs Database (HDncRNA) provides information about common heart diseases and their related noncoding RNAs. The HDncRNA database contains manually annotated associations of ncRNAs with heart disease. Sources of dat ...

WholeCellSimDB is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted: - Metabolite concentrations, - DNA, RNA and protein expression, - DNA-bound ...

Kazusa Plant Pathway Viewer

Plant microRNA knowledge base

DIGGER is an essential resource for studying the mechanistic consequences of alternative splicing such as isoform-specific interaction and consequence of exon skipping. The database integrates information of domain-domain and protein-protein interact ...

ODB (Operon DataBase) is a database of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The first release of ODB conteins about 2000 known operons and 13,000 ...

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 ...

EpoDB (Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.

Standards for “Minimum Information about a Animal Spinal Cord Injury Experiment” (MIASCI) facilitates bioinformatic efforts and allow investigators to more accurately replicate and extend studies.

SalmoBase is an integrated molecular resource for Salmonid species which includes visualizations and analytic tools. The genome of the Atlantic salmon (Salmo salar) has undergone extensive restructuring since a whole genome duplication event ~80 mill ...

Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library.

A structured controlled vocabulary developed and used by FlyBase, including the Drosophila phenotype ontology. It is used in annotation and classification of data related to Drosophila, including phenotypes and expression.

Autosomal monoallelic expression (MAE) refers to mitotically stable, epigenetically controlled allele-specific expression of autosomal genes, with the initial non-predetermined ('random') choice of thetranscriptional activity of the two alleles maint ...

Human lncRNA expression database

Probe-Level Annotation Database for Affymetrix microarrays

Gene Ontology-based functional similarity values for proteins and protein families

The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one ...

Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining targ ...

ViBrism DB is a database for anatomical gene expression maps and topological co-expression network graphs created with original techniques of microtomy-based gene expression measurements, Transcriptome Tomography. The DB is equipped with a WebGL-base ...

The database contains information about the occurrence of methylated cytosines in the DNA.

LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data.

The aim of this Oryza sativa database was first to display sequence information such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the framework of the French genomics initiative Genoplante and the EU consortium Cereal Gene Tags. This ...

EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

Dragon Database of Genes Implicated in Prostate Cancer is a knowledgebase of genes experimentally verified to be involved in prostate cancer (PC). DDPC provides gene-associated data such as protein annotation, molecular pathways, ontologies and trans ...

Coding and non-coding RNA

This site contains data generated by (Re)Building a Kidney (RBK), an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration ...

MINiML (MIAME Notation in Markup Language, pronounced 'minimal') is a data exchange format optimized for microarray gene expression data, as well as many other types of high-throughput molecular abundance data. MINiML assumes only very basic relation ...

The Stem Cell Commons were initiated by the Harvard Stem Cell Institute to develop a community for stem cell bioinformatics. This open source environment for sharing, processing and analyzing stem cell data brings together stem cell data sets with to ...

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 ...

The BCCM/GeneCorner Plasmid Collection warrants the long-term storage and distribution of plasmids, microbial host strains and DNA libraries of fundamental, biotechnological, educational or general scientific importance. The focus is on the collectio ...

H-DBAS is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. RNA-Seq tag information is correlated to the AS exons and splice junctions. A total of 148,376,598 RNA-Seq tags have been generated from R ...

MEPD contains expression data of genes and regulatory elements assayed in the Japanese killifish Medaka (Oryzias latipes).

TF-target relationsips inferred from single cell and bulk RNA-seq datasets

"iModulons", groups of independently-modulated genes

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 ...

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

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 ...

Proteomic signature library of Staphylococcus aureus Pathophysiology for inter-experimental expression data analyses.

The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcript ...

MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.

PeanutMine integrates peanut data from LIS PeanutBase and other sources.

This mine integrates many types of data for string bean built from the LIS chado database.

This mine integrates data for multiple legume species. It is under development by NCGR and is built from the LIS and PeanutBase chado databases as well as exports from other sources.

WormMine integrates many types of data for C. elegans and related nematodes. You can run flexible queries, export results and analyse lists of data.

RatMine integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. You can run flexible queries, export results and analyse lists of data.

If a database is inadequate in terms of its description, unclear with respect to the terms of use, or is not downloadable, it may not be fully used, cited or rightly acknowledged by the (research) communities. This is even true for databases with hig ...

A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling t ...

Breast cancer gene-expression miner (bc-GenExMiner) 4.5 is a mining module computes breast cancer differential gene expression analyses. It is a statistical mining tool of published annotated breast cancer transcriptomic data (DNA microarrays and RNA ...

A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states a ...

Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots | A platform dedicated to the visualization and analysis of plant co-expression and co-function networks

A database of epigenome-wide association studies.

A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

an adaptive immune receptor genotype and haplotype database. The adaptive immune receptor Genotype and Haplotype database. 11-Oct-2019 *NEW* - VDJbase is described in Nucleic Acids Research. VDJbase is a publicly available database that offers eas ...

A system of databases documenting the influence of mutations in regulatory gene regions.

PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including ...

BuG@Sbase is a microbial gene expression and comparative genomic database containing microarray datasets.

Dual RNA-seq host-pathogen sequencing

Laminins (LM) correspond to a large number of heretotrimeric glycoproteins, playing and a major role in several cell functions, including differentiation, proliferation, adhesion, and migration [1-3]. In addition to binding to other extracellular mat ...

CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians.

CellO (Cell Ontology-based classification) is a Python package for performing cell type classification of human RNA-seq data. CellO makes hierarchical predictions against the Cell Ontology. These classifiers were trained on nearly all of the human pr ...

The eQTL Catalogue aims to provide uniformly processed gene expression and splicing QTLs from all available public studies on human. Quantitative trait loci (QTL) are genomic variants that are significantly associated to a measurable phenotype. This ...

Chickspress is a gene expression database for chicken tissues. Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL information. By linking gene models from both NCBI and ...

riboCIRC is a comprehensive database of translatable circRNAs. Translation of circular RNAs (circRNAs) now has drawn increasing attention from researchers due to their emerging roles of the functional peptides encoded by circRNAs as new players invol ...

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ...

Human IRES Atlas is an integrative platform for studying IRES-driven translational regulation in humans.

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 ...

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 ...

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 ...

Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis

Glycan Microarray Database and Analysis Toolset.

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 ...

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 ...

The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individua ...

The NimbleGen Gene Description is a text tabular format that contains descriptive information (annotation) about the genes on an array. Please note that Roche issued a statement in 2012 as follows: "As previously announced in June 2012, Roche has exi ...

NimbleGen Design File Format is a standard data file format. NimbleGen is now a trademark of Roche.

A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein.

The BPMAP file contains information relating to the design of the Affymetrix tiling arrays. The format of the BPMAP file is a binary file with data stored in big-endian format.

The microarray track data Browser Extensible Data Format displays configuration files for microarray annotation tracks displayed on the UCSC Genome Browser.

The GenePix Results Format (GPR) contains general information about microarray image acquisition and analysis, as well as the data extracted from each individual feature. It was originally developed as the output format for GenePix software.

A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database

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 ...

CancerLivER (Liver Cancer Expression Resource) is a database of liver cancer that maintains gene expression datasets and biomarkers curated from public repositories and literature respectively. It contains the following three modules for extracting a ...

Database of single-cell expression map across various human cancers.

Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species.

PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources.

A knowledgebase of cellular drug response.

CNAdbCC is a curated database for copy number aberrations analysis and visualization of cervical cancer. Currently, the database contains about 1,000 dataset samples mainly integrated by affymetrix and aligent platform. Affymetrix is based on light-c ...

A database of cancer associated enhancers. A comprehensive resource on enhancer information for TCGA cancer types. CancerEnD Genome-wide association studies have successfully identified thousands of genomic loci potentially associated with hundreds ...

Taking advantage of a decade of Daphnia '-omics' data for gene annotation | Welcome to the Daphnia Stressor database

MSRdb (Mycobacterial Systems Resource) is a mycobacterial systems resource for the research community. The Mycobacterial Systems Resource (MSR) is a comprehensive, integrated biological and bioinformatic resource for the research community. The MSR u ...

Avian Immunome DB is a user-friendly interface for extracting genetic information about the avian immune system. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes.

Database of fusion transcripts in Arabidopsis thaliana.

A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource. Providing Bioinformatics Data For The Study Of Liver Diseases. a liver disease microarray database, visualization platform and data-mining resource. Hepamine was ...

A database of experimentally supported protein-coding RNAs and drug associations in human cancer.

A comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.

Leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.

Human 51 672 molecular pathways database with tools for activity calculating and visualization.

A major update of the ruminant functional and evolutionary genomics database.

An online transcriptome platform for human circRNA expressions in cancers.

dBMHCC is a comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers.

scAPAdb provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level in six species based on a large volume of scRNA-seq data. Currently, scAPAdb records APA information in animal speci ...

CHDGKB (A knowledgebase of non-syndromic congenital heart disease genetic variations) is a manually curated database of genetic variations associated with non syndromic congenital heart disease. CHDGKB contains a comprehensive information of genetic ...

The LEAFDATA resource collects information from primary research articles focusing on Arabidopsis leaf growth and development. The result section of selected papers is manually annotated and organized into distinct categories. Text fragments of the m ...

The first integrated database of gene annotation and expression profiles for variants related to human diseases. An integrated database of variants and gene expression profiles for genetic diseases.

An interactive online database for analysis of gene expression and viral infection in cancer.

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.

A web service for studying gene expression in human skeletal muscle. MuscleAtlasExplorer(BETA)2.

Cancer Gene and Pathway Explorer (CGPE) provides a highly integrated bioinformatics webserver for investigating, analyzing, and visualizing the TCGA and GEO gene expression data. CGPE provides key interactive and customizable analysis portal

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 ...

Fusion gene annotation updates aided by deep learning.

An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers

A database of human tissue functional gene networks built with a large compendium of curated RNA-seq data.

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

Sequence composition dynamics of genes and genomes.

syngeneic mouse tumor database to model tumor immunity and immunotherapy response.

New Platform for the Analysis of the Molecular Impact of SARS-CoV-2 Viral Infection.

Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma.

A centralized online platform for predicting the m6A methylation degree of mRNA and the SNP-related traits in Maize.

AddictGene is an integrated knowledge base for differentially expressed genes associated with psychostimulants,

User-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.

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 ...

The One-stop Database for COVID-19 Specific Humoral Immunity and Clinical Parameters.

The GENSAT (Gene Expression Nervous System ATlas) database captures information on gene expression in mouse brain at several developmental ages. The project began at Rockefeller University in New York under the direction of Nat Heintz, and has since ...

Gene annotation portal and a resource on gene and protein function

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 ...

Full-length pig cDNA libraries and ESTs

Drosophila transgenic lines created using an intron protein trap strategy

STAB is a comprehensive cell atlas resource for the human brain, containing single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With cell subtypes and their marker genes defined by a unified ...

The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence.

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 ...

Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world. This year's update for EMBL-EBI focuses on data exchanges among ...

Human disease-related phenotypes in model organisms

Huanglongbing (HLB) is a tritrophic disease complex involving citrus host trees, the Asian citrus psyllid (ACP) insect and a phloem restricted, bacterial pathogen Candidatus Liberibacter asiaticus (CLas). HLB is considered to be the most devastating ...

Anti-CRISPRdb is a comprehensive online resource that effectively organizes anti-CRISPR proteins determined by experimental and bioinformatics methods. Additionally, it also provides nucleotide sequences, interactors, three-dimensional structures, ...

AOE (All Of gene Expression) - an integrated index for public gene expression databases.

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

AhNGE is a Database for Arachis hypogaea nodule developmental gene expression.

The Gene Expression Database of Poplar under Stress.

High performance search engine for gene expression. It integrates thousands of manually curated, well described public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts such as diseases, drug ...

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

An integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases.

Databases which contain gene expression levels from next generation sequencing and also drug screening data for a large number of cancer cell lines.

The Kohara lab has been constructing an expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from ...

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 ...

MozAtlas provides gene expression data of adult male and female mosquitoes as tables, expressions, trees and models. MozAtlas also provides sequence orthology relationships with data provided by FlyBase, Vectorbase, Beetlebase, BeeBase, and WormBase.

MtExpress is a comprehensive and curated RNAseq-based gene expression atlas for the model legume medicago truncatula.

An integrated multi-omics database of barley gene families.

ConnecTF is a platform to build gene networks by integrating transcription factor-target gene interactions.

The Erythron Database is a resource dedicated to facilitating better understanding of the cellular and molecular underpinnings of mammalian erythropoiesis. The resource is built upon a searchable database of gene expression in murine primitive and de ...

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 ...

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

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

An integrative database of the expression dynamics of proteins in response to hypoxia in animals.

A microRNA tissue expression database.

Barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.

Provide gene and epigenetics expression data useful for dissecting quantitative trait data in livestock. Future work will providedata tracks for these information sources and will ID tissue specific regulation information that is helpful in dissectin ...

An automated approach to spectral unmixing of fluorescent biological images.

A curated RNA-seq database of palmitoylating and de-palmitoylating enzyme expression in the mouse brain.

Full-length transcripts and conservation of plant circRNAs.

TEx-MST is a novel bioinformatic database for providing the valuable expression information of MANE-select transcripts in normal human tissues.

Encyclopedia of microbiota regulated genes.

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

Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the s ...

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

An integrated omics database for functional genomic analysis of cyanobacteria.

AGODB is a comprehensive domain annotation database of argonaute (Ago) proteins, which contains extensive information about 1902 Ago proteins manually extracted from research articles and public databases.

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

Powerful new framework for interrogation of global pathway relationships.

The NCBI Nucleotide database collects sequences from such sources as GenBank, RefSeq, TPA, and PDB. Sequences collected relate to genome, gene, and transcript sequence data, and provide a foundation for research related to the biomedical field.

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 manually curated database of human and mouse essential lncRNA genes.

An Evidence-based Database of Genes and Phenotypes of Male Infertility.

A comprehensive bipolar disorder database for genetic research.

A database of extrachromosomal circular DNA profiles in human cancers.

An Interactive Web Server to Evaluate Prognostic Biomarkers for Ovarian Cancer.

A comprehensive genome platform for Brassicaceae plants.

Multi-omics molecular biomarkers and database of osteoarthritis.

An Integrated Genetic Database for Hearing Loss.

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

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 ...

A knowledgebase and transparency tool for minimum information in spheroid identity.

NetSlim is a resource of high-confidence signaling pathway maps derived from NetPath pathway reactions. 40-60% of the molecules and their reactions in NetPath pathways are available in NetSlim.

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.

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

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

A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis.

DINAX is a comprehensive database of inherited ataxias.

database for eukaryotic single-exon coding sequences. Single-exon coding sequences (CDSs), also known as 'single-exon genes' (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to det ...

Database of circadian and ultradian transcripts in control tissues of kingdom-wide species.

GPCards is an integrated database of genotype-phenotype correlations in human genetic diseases.

DRscDB is a single-cell RNA-seq resource for data mining and data comparison across species.

A data hub for long genes. Long genes harbor specific genomic and epigenomic features and have been implicated in many human diseases. LongGeneDB is an interactive, visual database containing genomic information of 992 long genes (>200 kb) in 15 spe ...

Quickomics is a tool for exploring omics data in an intuitive, interactive and informative manner.

Exploration and analysis of R-loop mapping data with RLBase.

One-stop and comprehensive annotation system for individual cancer genome at multi-omics level.

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.

BCGene is a online database for brain cancer-implicated genes: exploring the subtype-specific mechanisms of brain cancer

a comprehensive genetic database of Parkinson's disease. Gene4PD: an integrative genomic database and analytic platform for Parkinson's disease. Rare variants identified from PD patients.

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.

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 ...

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

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

An integrated resource for High-Altitude associated genes and proteins, interacting networks and semantic-similarities. Around 140 million people live in High Altitude (HA) conditions and even a larger number visit it for tourism, adventure-seeking ...

A database and web application for analyzing embryonic stem cells differentiation process on mouse model. The data is collected by FunGenES consortium and organized into six clusters to facilitate data mining.

>>>!!!<<< caArray Retirement Announcement >>>!!!<<< The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) instance of the caArray database was retired on March 31st, 2015. All publicly-accessib ...

The database of Allelic Dosage-corrected Allele-Specific human Transcription factor binding sites provides a genomic map of allele-specific binding at hundreds thousands single-nucleotide polymorphisms constructed by meta-analysis of thousands of ChI ...

ZINC Express is a virtual assistant for purchasing compounds annotated in the ZINC Database.

TPA is a database that contains sequences built from the existing primary sequence data in GenBank. TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the se ...

A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.

The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters.

The Bibliome Variant Database is a collection of variants mined from open-access primary literature. All variants included in the database have been mapped to the human genome and are presented in a manner ordered by genomic location. The goal of thi ...

LifeMap Discovery® is a compendium of embryonic development for stem cell research and regenerative medicine, constructed by integrating extensive molecular, cellular, anatomical and medical data curated from scientific literature and high-throughput ...

MedProDB is the first database dedicated to Mediator protein in plants, fungi and animals. It harbors 33,971 entries of different types of Mediator subunits of various organisms. This database is believed to be beneficial for exploring the complex an ...

ATAV is a comprehensive platform for population-scale genomic analyses. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and single ...

A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database.

An integrative platform for comparative and functional genomics of marmots. iMarmot: an integrative Marmot database. Marmots are large Holarctic rodents in the genus Marmota with 14 living species. Most marmot species occupy a harsh environment cha ...

The sequencing of several bird genomes and the anticipated sequencing of many more provided the impetus to develop a model organism database devoted to the taxonomic class: Aves. Birds provide model organisms important to the study of neurobiology, i ...

BART Cancer Database is a web resource designed to display putative transcriptional regulators (TRs) that are responsible for up and downregulation of genes in 15 different cancer types in The Cancer Genome Atlas. BART Cancer uses BART (Binding Analy ...

PaIntDB (Pseudomonas aeruginosa Interactions Database) is a tool for network-based omics integration and visualization using protein–protein interactions in Pseudomonas aeruginosa. PaIntDB contains more than 150K protein-protein (PPI) and protein-met ...

The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle gen ...

The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, functi ...

The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to: Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, ...

The Drosophila Synthetic Population Resource (DSPR) consists of a new panel of over 1700 recombinant inbred lines (RILs) of Drosophila melanogaster, derived from two highly recombined synthetic populations, each created by intercrossing a different s ...

Investigation Study Assay JSON (ISA-JSON) describes the ISA Abstract Model reference implementation specified using the JavaScript Object Notation (JSON) format, a text format for serializing structured data. The ISA model consists of three core enti ...

Sift-PUL database is a public repository providing predicted PULs with specific functional annotations. The key difference between sift-PUL and other PUL databases (e.g. PULDB, CGCs and dbCAN-PUL) is the functional annotation for each predicted PUL.

NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering ...

CoDNaS-RNA is a database of the Conformational Diversity in the Native State of RNA molecules. Each entry in CoDNaS-RNA is a redundant collection of known structures of the same RNA molecule, which can be considered as alternative instances of the RN ...