ebi proteomics services team – standards, data, and tools for proteomics henning hermjakob...
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EBI Proteomics Services Team –
Standards, Data, and Tools for Proteomics
Henning HermjakobEuropean Bioinformatics Institute
SME forum 2009Vienna
Annotation
Context
UniProtProteins
Archive PRIDEMass Spec
IntActInteractions
ReactomePathways
Integration and dissemination
EnVision
DAS
The Proteomics Identifications Database
(PRIDE)
•Centralized, standards compliant, public data repository for proteomics identifications
•Open source
•Open data
•50,287,408 spectra
• 2,555,194 protein identifications
• Detailed annotation of meta-data
•Jones, P, et al: PRIDE: new developments and new datasets. Nucleic Acids Res. 2008 Jan;36(Database issue):D878-83.
http://www.ebi.ac.uk/pride
PRIDE data content
[email protected] http://www.ebi.ac.uk/pride
PRIDE web interface – overview
[email protected] http://www.ebi.ac.uk/pride
PRIDE web interface – experiment and protein
[email protected] http://www.ebi.ac.uk/pride
PRIDE web interface – mass spectra
[email protected] http://www.ebi.ac.uk/pride
PRIDE web interface – project comparison
[email protected] http://www.ebi.ac.uk/pride
PRIDE BioMart
[email protected] http://www.ebi.ac.uk/pride
The spectacular bit: across-BioMart queries!Question: “Which proteins, identified in PRIDE experiment 2,
are involved in nucleotide metabolism”PRIDEReactome
The IntAct Molecular Interaction Database
•Centralized, standards compliant, public data repository for protein interactions
•Open source
•Open data
•200.000 binary interaction reports
•S. Kerrien, et al: IntAct – Open Source Resource for Molecular Interaction Data. Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5.
•Orchard, S. et al: The minimum information required for reporting a molecular interaction experiment (MIMIx).Nat Biotechnol. 2007 Aug;25(8):894-8.
http://www.ebi.ac.uk/intact
The IntAct Molecular Interaction Database
The IntAct Molecular Interaction Database
Reactome
•Human pathway knowledgebase•Manually curated•Open source, open data•Collaboration between EBI, OCRI and NYU•Online since 2003•Matthews L, et al: Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2008 Nov 3.
http://www.ebi.ac.uk/pride
• Pathways 870
• Reactions 2900
• Proteins 2900
• Complexes 2250
• References 4200
Reactome content
authors
summary
speciesGO term
other species
Pat
hway
desc
riptio
n
Pat
hway
part
icip
ants
UniProtEnsembl
MIMKEGG
ChEBICompound
Entrez Gene
HapmapUCSC
RefSeq
PubChem
SkyPainter• ‘Painting’ the reaction map with user-
supplied data, e.g. over- and under-expressed genes from a microarray analysis
• Animation for time series experiments• Overrepresentation analysis, e.g. disease
candidate genes concentrated to a pathway
#ID value1P20248 2.381255P14635 2.078063Q01094 1.358003P08319 1.274531O95067 1.251352P12004 1.031162P30305 1.654142P16104 1.274092P33992 1.560363P35249 1.185243O94913 2.410139Q13415 1.085086Q15054 1.148979P30307 2.270973O75496 0.796653P49736 0.998988Q13243 2.634955P50613 1.466119O75419 1.853295P30304 0.863513O96017 0.889464P38398 1.068929P06730 1.789461P15927 0.89531P30038 0.655572P51530 1.060222P17174 1.611088P35250 0.58771…
Usable identifiers:
•UniProt
•RefSeq
•Ensembl
•MIM
•Entrez Gene
•KEGG COMPOUND
•ChEBI
•Affymetrix
•GO
SkyPainter
SkyPaintercoloring according to the numeric values provided
SkyPainterOverrepresentation analysis
The Team• EU:
– ProDaC (to 03/2009)– ProteomeBinders– BioSapiens– Felics– LipidomicNet– APO-SYS– PSIMEx (since 03/2009)
• EMBL• Wellcome Trust• NIH
The Funding
• ?
Lab B
Private Data in
PRIDE “Collaboration”
Comparison
Reviewer
Lab A
Lab C
PRIDE private mode
Publicly available data
•Private mode allows data analysis within a collaboration
•PRIDE tools are already accessible in private mode, in particular experiment comparison (alpha)
•On manuscript submission, reviewers can access the data in standard format
Lab B
Private Data
“Collaboration”
Reviewer
Lab A
Lab C
PRIDE private mode
Publicly available data
•Private mode allows data analysis within a collaboration
•PRIDE tools are already accessible in private mode, in particular experiment comparison (alpha)
•On manuscript submission, reviewers can access the data in standard format
•On manuscript publication, the data becomes public