Related Links for ArrayExpress updateDatabase Content

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BioSample DatabaseDatabase Content

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The BioSample Database at the EBI is designed to hold information about biological samples, particularly samples referenced from other EBI databases. BioSD data will be exchanged with NCBI

Bug@SbaseDatabase Content

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A relational database containing microbial gene expression and comparative genomic hybridisation experimental data. The data is mostly derived from whole genome microarrays designed by the BµG@S group, however data from other microarrays is included and the database is being modified to support RNA-Seq analysis. Public access is available for datasets that have been published and login credentials can be obtained for data submission.

DDBJDatabase Content

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The DNA Data Bank of Japan (DDBJ) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. A new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Other improvements include improved content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline.

European Nucleotide ArchiveDatabase Content

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The European Nucleotide Archive (ENA) is Europe's nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. New features include extended EMBL-Bank and SRA-data submission services, extended ENA Browser functionality, support for submitting data to the European Genome-phenome Archive (EGA) through SRA, and the launch of a new sequence similarity search service.

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Expression ProfilerTool Content

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Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.

Gene Expression AtlasDatabase Content

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The Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.

Gene Expression BarcodeDatabase Content

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Gene Expression Barcode is a database that provides reliable absolute measures of expression for most annotated genes for human and mouse tissue types, including diseased tissue. This is made possible by an algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results.

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GXADatabase Content

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The Gene Expression Atlas is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential gene expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism parts or cell types.

MIAMExpressTool Content

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MIAME (minimum information about a microarray experiment) compliant microarray data submission tool.

Microarray RetrieverTool Content

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Microarray Retriever (MaRe) is a web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download facilitates gene expression meta-analysis.

NCBI GEODatabase Content

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The Gene Expression Omnibus (GEO) database stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies.

Pancreatic Expression databaseDatabase Content

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The Pancreatic Expression database (PED) is a repository for pancreatic-derived -omics data. It includes easurements derived from transcriptomics, proteomics, genomics and miRNA profiles from various pancreas-centred reports on a broad range of specimen and experimental types.

SRADatabase Content

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The Sequence Read Archive (SRA) was established as a public repository for the next-generation sequence data and is operated by the International Nucleotide Sequence Database Collaboration (INSDC). INSDC partners include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ).

This content is being maintained by rasko.