Annual Scientific Report 2015

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Functional Genomics The Functional Genomics team provides bioinformatics services and conducts research in functional genomics data analysis, concentrating on high-throughput sequencing-based gene-expression and related proteomics data. We are responsible for core EMBL-EBI resources including the Expression Atlas, which enables users to query for gene expression; the ArrayExpress archive of functional genomics data; and the emerging BioStudies database. We contribute substantially to training in transcriptomics and other EMBL-EBI bioinformatics tools. The Brazma research group compliments the Functional Genomics service team, developing new methods and algorithms and integrating new types of data across multiple platforms. We are particularly interested in cancer genomics and elucidating relationships between transcriptomics and proteomics. We collaborate closely with several research groups at EMBL-EBI, including the Marioni, and Stegle groups. Major achievements BioStudies Database and the Expression Atlas In 2015 we released BioStudies (McEntyre et al., 2015): a new database that holds descriptions of biological studies, links to data from these studies in other databases and data that do not fit in the structured archives at EMBL-EBI. BioStudies can accept a wide range of study types described using a simple format. Developed jointly with the Literature Services team, it enables authors to submit supplementary information and link to it from the manuscript publication. Data from 558 182 studies are available from BioStudies Database. We increased the content of the RNA-sequencing-based Baseline Expression Atlas significantly, releasing the first large-scale proteomics data on protein expression in human tissues (Petryszak et al, 2015). Taken together, the Baseline and Differential Expression Atlases now offer data from 2620 studies and over 97 484 assays. In addition to the growth of data volume and diversity, we implemented many user interface improvements. Research In research we focused on two related areas: comparison of transcript and protein expression levels, and data integration for cancer genomics. We compared gene expression profiles, in both transcript and protein levels, across multiple human tissues, using several large-scale datasets. Overall we showed a higher level of correlation than has been reported previously, even in cases where different samples were used in transcriptomics and proteomics experiments. We continued our research into isoform-level gene expression, comparing data at transcript and proteome levels. A publication describing this research is under review, and several more are in preparation. Together with colleagues at the University of California Santa Cruz and Memorial Sloan Kettering Cancer Center, we led a working group on RNA and DNA data integration for the Pan-cancer project of the International Cancer Genome Consortium. As a part of this work we also collaborated closely on a number of investigations with the Stegle group at EMBL-EBI and the Korbel group at EMBL Heidelberg, and prepared the results of these analyses for publication. Future plans Integration of baseline RNA sequencing gene expression and proteomics data will be the focus of our development of the Expression Atlas. The new BioStudies database will serve as the back-end for dealing with new types of data, including molecular imaging data. Large-scale data integration and systems biology will remain the focus of our research. We will extend our work on cancer genomics as a part of the pan-cancer project of the ICGC, in which we are co-leading the transcriptomics/genomics integration working group that aims to study aberrant transcription patterns across many cancer types. We will also expand our research into dominant transcripts to protein abundance data. 95 2015 EMBL-EBI Annual Scientific Report
Alvis Brazma Functional Genomics PhD in Computer Science, Moscow State University, 1987. MSc in mathematics, University of Latvia, Riga. At EMBL-EBI since 1997. Joint clustering of cancer and normal tissue samples from RNA sequencing-based gene expression datasets derived from over 3000 samples from the International Cancer Genome Consortium Whole Genome Pan-cancer Project and the Genotype-Tissue Expression project. Selected publications McEntyre J, Sarkans U, Brazma A (2015) The BioStudies database. Mol. Syst. Biol.. 11:847. doi: 10.15252/ msb.20156658 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. doi: 10.1093/nar/gkv1045 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:S2. doi: 10.1186/1471-2164-16-S8-S2 2015 EMBL-EBI Annual Scientific Report 96
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The European Bioinformatics Institu
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SERVICE TEAMS TRAINING PROGRAMME RE
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Foreword We are pleased to present
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awareness amongst some of our stron
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Chemical biology The 17 million nov
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The most extensive catalogue of str
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“ EMBL -EBI services are the back
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European Nucleotide Archive The ENA
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Vertebrate Genomics Paul Flicek Bro
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Functional Genomics Alvis Brazma
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Pfam Pfam is a database of protein
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Protein Data Bank in Europe Gerard
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MetaboLights MetaboLights is a data
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Proteomics Services and Molecular I
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BioSamples The BioSamples database
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EMBL International PhD Programme at
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The Birney group used methods devel
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Marioni group • Improved and exte
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Industry workshops • In silico AD
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Future plans The Industry Programme
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Reporting on usage We further devel
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Petteri Jokinen Systems & Networkin
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Mark Green EMBL-EBI Administration
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Annual Scientific Report 2015

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