Annual Scientific Report 2015

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