WGE: a CRISPR database for genome engineering.

Unlabelled: The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes.

ArrayExpress update--trends in database growth and links to data analysis tools.

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Gene Expression Atlas (http://www.ebi.ac.

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.

The ArrayExpress Archive (http://www.ebi.ac.

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.

The MAGE-TAB format for microarray data representation and exchange has been proposed by the microarray community to replace the more complex MAGE-ML format. We present a suite of tools to support MAGE-TAB generation and validation, conversion between existing formats for data exchange, visualization of the experiment designs encoded by MAGE-TAB documents and the mining of such documents for semantic content.

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.

ArrayExpress http://www.ebi.ac.

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

Background: Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support.

Results: We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion.

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.

ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data sets represent approximately one-quarter of the experiments in ArrayExpress. The majority are based on Arabidopsis (Arabidopsis thaliana); however, there are other data sets based on Triticum aestivum, Hordeum vulgare, and Populus subsp.

The ArrayExpress gene expression database: a software engineering and implementation perspective.

Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for microarray data ArrayExpress we had to find novel solutions to many non-trivial software engineering problems. Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high-throughput technologies.