1 / 31

EBI Proteomics Services Team – Standards, Data, and Tools for Proteomics

EBI Proteomics Services Team – Standards, Data, and Tools for Proteomics. Henning Hermjakob European Bioinformatics Institute SME forum 2009 Vienna. IntAct Interactions. PRIDE Mass Spec. Reactome Pathways. UniProt Proteins. Context. Annotation. Integration and dissemination.

pascha
Download Presentation

EBI Proteomics Services Team – Standards, Data, and Tools for Proteomics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. EBI Proteomics Services Team – Standards, Data, and Tools for Proteomics Henning Hermjakob European Bioinformatics Institute SME forum 2009 Vienna

  2. IntAct Interactions PRIDE Mass Spec Reactome Pathways UniProt Proteins Context Annotation Integration and dissemination EnVision Archive DAS

  3. 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

  4. PRIDE data content

  5. PRIDE web interface – overview

  6. PRIDE web interface – experiment and protein

  7. PRIDE web interface – mass spectra

  8. PRIDE web interface – project comparison

  9. PRIDE BioMart

  10. The spectacular bit: across-BioMart queries! Question:“Which proteins, identified in PRIDE experiment 2, are involved in nucleotide metabolism” PRIDE Reactome

  11. 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

  12. The IntAct Molecular Interaction Database

  13. The IntAct Molecular Interaction Database

  14. 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

  15. Reactome content • Pathways 870 • Reactions 2900 • Proteins 2900 • Complexes 2250 • References 4200

  16. Pathwaydescription authors summary species GO term other species

  17. UniProt ChEBI Ensembl Compound Entrez Gene PubChem MIM KEGG RefSeq Hapmap UCSC Pathwayparticipants

  18. 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

  19. SkyPainter #ID value1 P20248 2.381255 P14635 2.078063 Q01094 1.358003 P08319 1.274531 O95067 1.251352 P12004 1.031162 P30305 1.654142 P16104 1.274092 P33992 1.560363 P35249 1.185243 O94913 2.410139 Q13415 1.085086 Q15054 1.148979 P30307 2.270973 O75496 0.796653 P49736 0.998988 Q13243 2.634955 P50613 1.466119 O75419 1.853295 P30304 0.863513 O96017 0.889464 P38398 1.068929 P06730 1.789461 P15927 0.89531 P30038 0.655572 P51530 1.060222 P17174 1.611088 P35250 0.58771 … • Usable identifiers: • UniProt • RefSeq • Ensembl • MIM • Entrez Gene • KEGG COMPOUND • ChEBI • Affymetrix • GO

  20. SkyPaintercoloring according to the numeric values provided

  21. SkyPainterOverrepresentation analysis

  22. The Funding The Team • EU: • ProDaC (to 03/2009) • ProteomeBinders • BioSapiens • Felics • LipidomicNet • APO-SYS • PSIMEx (since 03/2009) • EMBL • Wellcome Trust • NIH

  23. ?

  24. PRIDE private mode Private Data in PRIDE “Collaboration” • Private mode allows data analysis within a collaboration Lab B Lab A • PRIDE tools are already accessible in private mode, in particular experiment comparison (alpha) Lab C Reviewer • On manuscript submission, reviewers can access the data in standard format Comparison Publicly available data

  25. PRIDE private mode Publicly available data Private Data “Collaboration” • Private mode allows data analysis within a collaboration Lab B Lab A • PRIDE tools are already accessible in private mode, in particular experiment comparison (alpha) Lab C Reviewer • On manuscript submission, reviewers can access the data in standard format • On manuscript publication, the data becomes public

More Related