Annual Scientific Report 2015

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Gene Expression The Gene Expression team handles the acquisition, curation, quality control, statistical analysis and visualisation of functional genomics data at EMBL-EBI, focusing on microarray, high-throughput sequencing-based gene expression and related proteomics data. We are responsible for several core EMBL-EBI resources, including the Expression Atlas, which enables users to query for information about gene expression, and the ArrayExpress archive of functional genomics data. We contribute substantially to online and face-to-face training in transcriptomics, in particular relating to our team’s resources but also for related topics such as next-generation sequencing. We are a centre of excellence for RNA-sequencing quality control and analysis, the results of which are used by numerous resources at EMBL-EBI and externally. We are increasingly interested in epigenetic analysis, for example methylation, and work towards placing transcriptomic data in a broader regulatory context. We are part of Open Targets (formerly the Centre for Therapeutic Target Validation, CTTV) and the Cancer Genome Atlas Pan-Cancer analysis project. Analysis and visualisation on plant data is also a major component of our work through our involvement in Gramene project. We collaborate closely with the Brazma, Marioni, Stegle and Teichmann research groups at EMBL-EBI and with the Choudhary group at the Wellcome Trust Sanger Institute, developing new methods and algorithms, integrating new types of data across multiple platforms, and investigating relationships between transcriptomics and proteomics data in the context of cancer genomics. Major achievements ArrayExpress, Expression Atlas and related projects In 2015 we capitalised on the deployment and continual improvement of Annotare, the ArrayExpress submission tool, and focused our curation efforts on datasets in the Expression Atlas, which held 100 000 assays in December 2015 (a six-fold increase compared to 2014). These assays included 157 RNA-seq experiments, over 7000 differential comparisons across 26 organisms, and 568 plant experiments. At the end of 2015 the Baseline Expression Atlas contained 46 RNA-seq studies, including data from many high impact studies (e.g. GTEx and FANTOM5) and its first proteomics study. We improved the Expression Atlas interface substantially, applying many enhancements in its presentation of search results (e.g. faceting). We developed new functionalities that will be available to users in early 2016, for example gene co-expression and a new Bioconductor package for easy access to Atlas data in R language. The Expression Atlas now contributes transcriptomic data and visualisations to many resources, including the Open Targets (formerly CTTV), Ensembl, Reactome, Plant Reactome and International Mouse Phenotyping Consortium portals. We developed an RNA-seq pipeline and adapted it to help analyse public RNA-seq data for major species in the European Nucleotide Archive’s Sequence Read Archive. This functionality resulted in 148 000 processed sequencing runs in 85 species by the end of the year. Where applicable, this data is included in both the Expression Atlas and Ensembl. Future plans In 2016 our development efforts for the biology-centric Expression Atlas will centre on integration of baseline RNA-sequencing gene expression and proteomics data. The BioStudies database, developed by the Sarkans team, will serve as the back-end for dealing with new types of data, including molecular imaging data. We will continue to expand our analyses and develop intuitive visualisation methods for both the existing data in Expression Atlas and for novel data types, such as epigenetic (methylation), genetic (eQTL), single-cell RNA-seq and smallRNA-seq. We will also complete the analysis of public RNA-seq data in major species and make the raw results available publicly. As a part of the pan-cancer project of the ICGC, we will continue to investigate aberrant transcription patterns across many cancer types. 99 2015 EMBL-EBI Annual Scientific Report
Robert Petryszak Gene Expression MPhil in Computer Speech and Language Processing, University of Cambridge, UK. At EMBL-EBI since 2003. Team Leader since 2015. Selected publications Frankish A, et al. (2015) Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics 16 Suppl 8:s2 Kolesnikov N, Hastings E, Keays M, et al. (2015) ArrayExpress update--simplifying data submissions. Nucleic Acids Res. 43:D1113-D1116 Petryszak R, et al. (2016) Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 44:D746-D752 Tello-Ruiz MK, et al. (2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res. 44:D1133-D1140 Expression Atlas: baseline expression in tissues and cell lines for human gene REG1B. 2015 EMBL-EBI Annual Scientific Report 100
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Annual Scientific Report 2015

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