Annual Scientific Report 2015

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.
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2015 EMBL-EBI Annual Scientific Report