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PRIDE centric exercise: BioMart interface

PRIDE centric exercise: BioMart interface. Juan Antonio VIZCAINO. PRIDE team, Proteomics Services Group PANDA group European Bioinformatics Institute Hinxton , Cambridge United Kingdom. Overview …. Introduction to the BioMart interface PRIDE BioMart

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PRIDE centric exercise: BioMart interface

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  1. PRIDE centric exercise: BioMart interface Juan Antonio VIZCAINO PRIDE team, Proteomics Services Group PANDA group European Bioinformatics Institute Hinxton, Cambridge United Kingdom

  2. Overview … • Introduction to the BioMart interface • PRIDE BioMart • Presentation of the PRIDE centric exercise (focused in data mining)

  3. BIOMART INTERFACE

  4. Interface developed originally at the EBI to access data at EBI resources. It is another way to access the data… Suitable for making more complex data queries that the web interface. Very powerful: suitable for wet lab scientists without being experts in bioinformatics You can search and integrate data from two resources simultaneously… Introduction to BioMart … www.biomart.org

  5. PRIDE BioMart

  6. PRIDE BioMart

  7. PRIDE BioMart

  8. The spectacular bit: across-BioMart queries! Question:“Which proteins, identified in PRIDE, in blood plasma, are transcribed from genes located in chromosome 11” PRIDE Ensembl

  9. PRIDE CENTRIC EXERCISE

  10. PRIDE centric exercise

  11. You will learn how to use PRIDE for data mining purposes… You will learn how to retrieve data from the PRIDE database using the PRIDE BioMart You will also browse the PRIDE web interface, and learn how to make use of the PICR protein mappings You will learn how to search data combining the PRIDE (Proteomics) and the EnsemblBioMarts (Genomics) In this exercise…

  12. Let’s suppose that you are particularly interested in one protein you obtained in your results after the search with OMSSA: In this exercise… Protein accession O76094 (Signal recognition particle 72 kDa protein)

  13. If this same protein (O76094) has been detected by MS before. If so, how was/were the experiment(s) done? Information about the peptide sequences identified and possible protein modifications (PTMs) You will use PRIDE to find out…

  14. You need to consider all possible mappings of the protein. If there are equivalent protein accessions in other DBs (IPI, Ensembl protein, etc) You will use the PRIDE BioMart (easy way to retrieve data for biologists without bioinformatics/ programming knowledge). Don’t forget…

  15. No direct comparison can be done if the different submitters use different databases to perform the searches Make proteomics results comparable Protein list A (DB Search vs. IPI) IPI000001 IPI000002 IPI000003 … • Protein list B • (DB Search vs. UniProt) P00001 P00002 P00003 …

  16. Make proteomics results comparable • No direct comparison can be done if the different submitters use different databases to perform the searches Protein list A (DB Search vs. IPI) IPI000001 IPI000002 IPI000003 … • Protein list B • (DB Search vs. UniProt) P00001 P00002 P00003 … We will use the PICR tool to be able to make protein identifiers comparable

  17. …and also, across-BioMart queries! You will need to combine the PRIDE and EnsemblBioMarts: easy way to perform data mining using proteomics and genomics data

  18. Time to Work on it…

  19. You have learnt how to use PRIDE for data mining purposes You have learnt to use the BioMart interface (available not only for PRIDE) Hopefully, you have learnt the need to use the PICR service to make proteomics experiments comparable Conclusions

  20. Attila Csordas David Ovelleiro Richard Côté Rui Wang Daniel Ríos FlorianReisinger Joe Foster Johannes Griss Jose A. Dianes Antonio Fabregat Yasset Perez-Riverol Juan Antonio Vizcaíno Henning Hermjakob The PRIDE Team: Who we are

  21. Questions?

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