EMBL-EBI Annual Scientific Report 2012

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Functional genomicsThe Functional Genomics team provides bioinformatics services andconducts research in gene expression and high-throughputsequencing applications.We participate in software development related to biomedical informatics and systems microscopy and are responsible forthe Expression Atlas, which is growing to include proteomics and metabolomics data. Together with our Production andDevelopment teams, we develop ArrayExpress, the archive of functional genomics data and the EBI BioSamples Database.We also contribute substantially to training in transcriptomics and the use of EMBL-EBI bioinformatics tools.Our research efforts centre on developing new methods and algorithms for analysing gene expression data and integratingdifferent types of data across multiple platforms. We are particularly interested in cancer genomics and transcript isoformusage, and collaborate closely with the Marioni group and others throughout EMBL.Major achievementsThe co-ordination of Expression Atlas development was takenover by Robert Petryszak, following the departure of MishaKaphushesky in early 2012. The major focus was on planningand prototype development for the baseline Expression Atlas,which utilises high-throughput-sequencing-based expressiondata to report absolute (rather than relative) gene expressionlevels. We also started working on the close integration ofgene-expression, protein-expression and metabolitemeasurementdata.Major developments in the ArrayExpress Archive and the EBIBioSamples Database are described by Helen Parkinson andUgis Sarkans (see also Rustici et al., 2013 and Gostev atal., 2012).In 2012 we organised and participated in over 25 trainingevents, including Bioinformatics Roadshows and on-sitecourses. These included the EMBO practical course on theanalysis of high-throughput sequencing data, which was themost popular and oversubscribed training event in 2012.Our team developed a prototype database for systemsmicroscopy data and loaded seven datasets from projectpartners in the Systems Microscopy Network of Excellence,which was funded under the EU’s Seventh FrameworkProgramme (FP7).As a part of our participation in the GEUVADIS project(funded by the FP7), we analysed mRNA and small RNAfrom lymphoblastoid cell lines of 465 individuals whoparticipated in the 1000 Genomes Project. Our group led theanalysis of transcript isoform use and fusion gene discovery.By integrating RNA and DNA sequencing data, we wereable to link gene expression and genetic variation, and tocharacterise mRNA and miRNA variation in several humanpopulations. All of the data generated in the project areavailable through ArrayExpress.The human transcriptome contains in excess of 100 000different transcripts. We analysed transcript compositionin 16 human tissues and five cell lines to show that, in agiven condition, most protein coding genes have one majortranscript expressed at significantly higher level than others,and that in human tissues the major transcripts contributealmost 85% to the total mRNA. We also found that thesame major transcript is often expressed in many tissues.These observations can help prioritise candidate targets inproteomics research and help predict the functional impactof the detected changes in variation studies. Our findings,submitted for publication in 2012, point towards a lowerdegree of transcriptome complexity than recently estimated.Other research includes an exploration of the utility of geneexpression data in the public domain (Rung and Brazma,2012).Angela Goncalves, a PhD student in the Functional Genomicsgroup, gained her doctorate in 2012 and published some ofher major findings in Nature Genetics and Genome Research(Goncalves, et al. 2012).22 2012 EMBL-EBI Annual Scientific Report
Alvis BrazmaPhD in Computer Science, Moscow StateUniversity, 1987. Postdoctoral research at NewMexico State University, US.At EMBL-EBI since 1997.Future plansIn 2012 we began the process of integrating ExpressionAtlas data with PRIDE proteomics data, and this processwill continue in 2013. We will also undertake to integratethe metabolomics data in MetaboLights with the ExpressionAtlas. Our research will continue to focus on large-scale dataintegration and systems biology. We will develop methodsfor RNA-seq data analysis and processing, and apply theseto address important biological questions, such as the roleof alternative splicing and splicing mechanisms. Togetherwith our colleagues at the International Cancer GenomeConsortium, we will investigate the impact of cancer genomeson functional changes in cancer development and explorefusion genes and their role in cancer development.References citedRustici, G., et al. (2013) ArrayExpress update—trends indatabase growth and links to data analysis tools. NucleicAcids Res 41(D1), D987-D990.Selected publicationsRung, J. and Brazma, A. (2012) Reuse of public genome-widegene expression data. Nat Rev Genet doi: 10.1038/nrg3394.Fonseca, N.A., et al. (2012) Tools for mapping high-throughputsequencing data. Bioinformatics 28, 3169-3177.Goncalves, A., et al. (2012) Extensive compensatory cis-transregulation in the evolution of mouse gene expression. GenomeRes 22, 2376-2384.Gostev, M., et al. (2012) The BioSample Database (BioSD) atthe European Bioinformatics Institute. Nucleic Acids Res 40(D1), D64-D70. doi: 10.1093/nar/gkr937.Kapushesky, M., et al. (2012) Gene Expression Atlasupdate—a value-added database of microarray andsequencing-based functional genomics experiments. NucleicAcids Res 40 (D1), D1077-D1081.Kutter, C., et al. (2011) Pol III binding in six mammals showsconservation among amino acid isotypes despite divergenceamong tRNA genes. Nat Genet 43, 948-955.Figure. Prototype of thebaseline Expression Atlas.2012 EMBL-EBI Annual Scientific Report23
Page 1 and 2: EMBL-European Bioinformatics Instit
Page 3: Table of contentsIntroduction & ove
Page 6 and 7: EMBL-EBI 2012It was a year of trans
Page 8 and 9: New service developments• Underst
Page 10 and 11: Organisation ofEMBL-EBI Leadership
Page 12 and 13: dGenes, genomes and variationThe Eu
Page 14 and 15: dGenes, genomes and variationSummar
Page 16 and 17: European Nucleotide ArchiveOur team
Page 18 and 19: Vertebrate genomicsThe Vertebrate G
Page 20 and 21: Nonvertebrate genomicsWe provide to
Page 22 and 23: gMolecular atlasLife scientists are
Page 26 and 27: Functional genomics productionOur t
Page 28 and 29: Functional genomics developmentOur
Page 30 and 31: PProteins and protein familiesUniPr
Page 32 and 33: UniProt contentOne of the central a
Page 34 and 35: UniProt developmentOur team provide
Page 36 and 37: InterProOur team co-ordinates the I
Page 38 and 39: sMolecular and cellular structureUn
Page 40 and 41: Protein Data Bank in EuropeThe majo
Page 42 and 43: PDBe content and integrationOur goa
Page 44 and 45: PDBe databases and servicesOur team
Page 46 and 47: yMolecular systemsThe genes and gen
Page 48 and 49: Proteomics servicesThe Proteomics S
Page 50 and 51: Chemical biologyThe importance of s
Page 52 and 53: ChEMBLThe ChEMBL team develops and
Page 54 and 55: Cheminformatics and metabolismOur t
Page 56 and 57: cCross-domain toolsand resourcesSci
Page 58 and 59: Literature servicesScientific liter
Page 60 and 61: Research2012 has seen the further t
Page 62 and 63: Bertone groupPluripotency, reprogra
Page 64 and 65: Birney groupNucleotide dataDNA sequ
Page 66 and 67: Enright groupFunctional genomics an
Page 68 and 69: Goldman groupEvolutionary tools for
Page 70 and 71: Le Novère groupComputational syste
Page 72 and 73: Luscombe groupGenomics and regulato
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Marioni groupComputational and evol
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Rebholz groupPhenotypes and multili
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Saez-Rodriguez groupSystems biomedi
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Thornton groupProteins: structure,
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The EMBL International PhDProgramme
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SupportOur support teams provide fo
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T TrainingAs part of EMBL-EBI’s m
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IIndustry programmeSince 1996 the I
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NExternal relationsAs a European In
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sExternal servicesOur team manages
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SSystems and networkingOur team man
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q AdministrationThe EMBL-EBI Admini
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Funding and resource allocationDesp
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Growth of core resourcesIn 2012 the
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CollaborationsEMBL-EBI is a highly
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Staff growthOur organisational stru
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Scientific advisory commiteesEMBL S
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The International Nucleotide Sequen
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EMDataBank Advisory Committee• Jo
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Major database collaborationsARRAYE
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THE GENE ONTOLOGY CONSORTIUM• Agb
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REACTOME• New York University Med
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Publications in 2012In 2012, EMBL-E
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Doreleijers, J. F., Vranken W. F.,
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Kruger, F. A., Rostom R. and Overin
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Sahakyan, Aleksandr B., Cavalli And
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EMBL - European Bioinformatics Inst
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EMBL-EBI Annual Scientific Report 2012

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