Who we are

EMBL’s European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. We help scientists realise the potential of ‘big data’ by enhancing their ability to exploit complex information to make discoveries that benefit humankind.

We are at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis, and data-driven biological discovery; from plant biology to mammalian development and disease. We are part of EMBL and are located on the Wellcome Genome Campus, near Cambridge, UK, one of the world’s largest concentrations of scientific and technical expertise in genomics.

Our role in DIAMONDS

We will process and distribute the results of the transcriptomics data sets and molecular signatures generated by our partners in DIAMONDS through EMBL-EBI’s resource for gene and protein expression, Expression Atlas (https://www.ebi.ac.uk/gxa/home/). As part of Expression Atlas, the DIAMONDS data sets will be integrated with further studies in a way that is easy to discover, query, and interpret by the scientific community.

Expression Atlas is a database and web-service that annotates, re-analyses and displays gene and protein expression data. Currently, we provide results on almost 3700 experiments that include about 120,000 assays from over 60 different organisms. Data sets include large landmark studies, such as GTEx, CCLE, ENCODE, BLUEPRINT, HipSci. Experimental factors are annotated with Experimental Factor Ontology (EFO) terms, therefore enabling searching and combining different experiments according to user-selected diseases or other metadata. RNA-seq experiments are analysed in a uniform way, using our standardised pipelines (iRAP) that enable both bulk and single cell RNA-Seq analyses. Our baseline datasets on expression in different tissues are embedded in other resources to enable integration with different types of data and contribute to the understanding of pathways (with REACTOME), disease targets (Open Targets Platform) or plant functional genomics (Gramene).

Our team

The Gene Expression team at EMBL-EBI develops resources to query and display gene and protein expression in cell types, tissues, under different conditions such as disease or environmental stress. We develop the Expression Atlas and its latest component, the Single Cell Expression Atlas – resources that analyse and display transcriptomics data sets in a systematic way. We are responsible for the ArrayExpress archive and contribute to training in transcriptomics. We also support Open Targets, the Human Cell Atlas and the Cancer Genome Atlas’ Pan-Cancer Project (PCAWG) projects. We analyse and visualise plant data through our collaboration with Gramene database.

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This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 848196