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It is the leading website and database of Drosophila genes and genomes. FlyBase curates a variety of data from published biological literature, including phenotype, gene expression, interactions (genetic and physical), gene ontology (GO) information and many others. These data are organized in ∼31 different data-type reports such as the Gene Report or the Allele Report. The range of data we provide increases and changes as new types of data become available. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for.

GXD / Gene eXpression Database

Offers an extensive and well-curated community resource of mouse developmental expression information. GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata.


Summarizes analysis-ready expression data for genes, exons, exon–exon splice junctions and base-level coverage. ReCount is an online resource that uses analysis pipelines that are annotation agnostic to process and summarize samples. The data provided allow multiple downstream analyses, including testing for differential expression of potentially unannotated transcribed sequence, enabling studies that individual laboratories would otherwise not have the resources to undertake.

BrainTx / Brain Transcriptome Database

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Provides data on the transcriptome related to mouse cerebellar development. BrainTx is a neuroinformatics database that contains gene expression information related to various stages and states of the brain. This online resource assigns parent ID number to each gene as described above and classifies different expression data for each gene, which are obtained from different transcripts of a gene or obtained by different probes of a gene.

Expression Atlas

Provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. Expression Atlas consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Expression Atlas search interface allows for querying one or more genes or proteins from a selected species. The user can also add search filters for sample attributes and experimental factors, taking full advantage of ontology-driven query expansion.

PATRIC / Pathosystems Resource Integration Center

Aims to assist scientists in infectious-disease research. PATRIC is a National Institute of Health (NIH) supported bioinformatics resource center that has been built to enable comparative genomic analysis of bacterial pathogens. The database provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Tools and services for bacterial infectious disease research are also available.


Provides a central repository and a web-based analytical platform for cancer multi-omics data. OASIS contains sample-level annotations and gene level mutation, copy number variation (CNV) and expression data on primary tumor, normal samples and cell lines across cancers and tissues from The Cancer Genome Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE), the Genotype-Tissue Expression (GTE) project and four published genomics studies of liver, gastric and breast cancers. It also provides a suite of easy-to-use analytical features to help wet-lab biologists perform exploratory analysis of the data.

BCaPE / Breast Cancer PDTX Encyclopaedia

A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. BCaPE provides tools for visualizing, querying and downloading data from a large collection of highly molecularly annotated breast cancer patient-derived tumour xenografts (PDTX). The biobank represents a powerful resource for pre-clinical breast cancer pharmacogenomic studies, including identification of biomarkers of response or resistance.


Provides an expression plot of genes in healthy and cancerous haematopoietic cells at specific differentiation stages. BloodSpot facilitates the easy assessment of gene-expression data and how this links to patient survival, investigation of gene-expression signatures, as well as analysis of user generated data and export of data and figures. Focusing on simplicity, BloodSpot has features that allow clinicians or biologists to quickly retrieve relevant information on the expression of specific genes/pathways, and further explore co-regulated patterns of gene-expression as well as impact on patient survival.


Aims to provide access to all available assembled genomes and transcriptomes. In September 2014, diArk contains about 2600 eukaryotes with 6000 genome and transcriptome assemblies, of which 22% are not available via NCBI/ENA/DDBJ. Several indicators for the quality of the assemblies are provided to facilitate their comparison for selecting the most appropriate dataset for further studies. diArk has a user-friendly web interface with extensive options for filtering and browsing the sequenced eukaryotes.


Consists of a community resource dedicated to the study of parasitic nematodes. Nematode.net is a publicly available resource that provides access to annotation of genomes, expression and related genome-scale data, as well as data-mining tools and their comparative data products. NemaGene hosts annotation for almost 1.1 million genes and transcripts spanning 67 nematode species and NemaBrowse allows displaying of SnpEff-annotated variants from isolates with different phenotypes. The database is a part of Helminth.net, an evolving collection of databases hosting resources for helminths.

PED / Pancreatic Expression database

Provides functions to extract, analyze, and integrate publicly available multi-omics datasets. PED is developed as a data repository to provide researchers with a single-entry point from which to manipulate, mine and integrate the heterogeneous and isolated findings into their own research. It incorporates published findings on pancreatic precursor lesions, including pancreatic intraepithelial neoplasias (PanINs), intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs).

HipSci / human induced pluripotent Stem cells initiative

Generates human induced pluripotent stem cells (iPSCs) from hundreds of healthy individuals as well as patients diagnosed with selected diseases. HipSci is a powerful resource to evaluate and quantify cell responses to chemical, physical and biological stimuli using novel assays and artificial microenvironments. Within this framework, phenotypic data are being collated with genomics, epigenomics and proteomics data to discover the impact of their variation on the cellular phenotype.

AtRTD / Arabidopsis Thaliana Reference Transcript Dataset

Provides a comprehensive high-quality reference transcript dataset about Arabidopsis transcripts. AtRTD contains more than 82 190 unique transcript models. It was generated by integration of transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries. The database contains 37 137 events and those which occurred at least 50 times made up 95.24% of all alternative splicing events.

SZGR / Schizophrenia Gene Resource

A database for candidate variants and genes for schizophrenia. SZGR covers genetic, epigenetic, transcriptomic, translational and many other types of evidence. This tool provides a onestop shop of schizophrenia variants and genes and their function and regulation, providing an important resource in the schizophrenia and other mental disease community. To facilitate interpretation, SZGR includes various functional annotation data, especially brain eQTL (expression quantitative trait loci), methylation QTL, brain expression featured in deep categorization of brain areas and developmental stages and brain-specific promoter and enhancer annotations.


Compiles expression of the genes of Drosophila melanogaster in different tissues. FlyAtlas includes data obtained by hybridization of messenger RNA to Affymetrix Drosophila Genome 2 microarrays. It displays information related to the expression of individual transcripts, microRNAs, and separates data for male and female flies in adult somatic tissues. Results can be browsed by gene, tissue and category and users can also to query a specific gene for finding those with a similar pattern of expression across the different tissues.

SATMD / Staphylococcus aureus Transcriptome Meta-Database

Contains information coming from manually curating papers published on Staphylococcus aureus transcriptome studies. SATMD is the updated version of Staphylococcus aureus microarray meta-database (SAMMD). The database contains tables describing the lists of regulated genes, experiment details, annotations, and references to publications. An additional data column in the experiments table classifies the transcriptome technology that was used to generate the data.


Integrates variety of data from biomedical model genus and archives large data sets that would otherwise be unavailable to the global scientific community. Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks. Xenbase has been designed to facilitate direct comparison of information from Xenopus genes with their human orthologs. Search returns will show all gene pages on which the OMIM entry is linked, and all other OMIM disease associations for that gene.


Provides several types of information about different gene or biological contexts. cMapper is a gene-centric connectivity mapper for the European Bioinformatics Institute-Resource Description Framework (EBI-RDF) platform. It displays data entities connected with the given genes or small molecules of interest, and also visualizes them using a graphical interface. This database aims users to identify gene of interest has a connected entity in six biological databases in the EBI-RDF platform.


A collective resource for rice sheath blight pathogen, Rhizoctonia solani AG1 IA genome and transcritome. RSIADB enables users to search, browse, and download gene sequences for R. solani AG1 IA, and mine the data using BLAST, sequence extractor, browse and construction diagram tools that were integrated into the database. RSIADB is an important genomic resource for scientists working with R. solani AG1 IA and will assist researchers in analysing the annotated genome and transcriptome of this pathogen. This resource facilitates studies on gene function, pathogenesis factors and secreted proteins, as well as provide an avenue for comparative analyses of genes expressed during different stages of infection.

BDGP / Berkeley Drosophila Genome Project

Provides sequence of euchromatic genome of Drosophila melanogaster in high quality. BDGP is a resource developed to (i) produce gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans, (ii) characterize sequence and expression of cDNAs and (iii) develop informatics tools that support the experimental process, identify features of DNA sequence, and allow to present up-to-date information about annotated sequence to the research community.