Web Resources

There are many free web resources available to analyze proteomic data. 

Here are a few:

http://www.uniprot.org/

  • Accession names of proteins identified in proteomic data (gene names are not usually used)
  • Proteomes available for searching
  • GO annotation of each protein
  • PTM/processing
  • Expression, inteaction, structure

 

https://david.ncifcrf.gov/

  • Identify enriched biological themes, particularly GO terms
  • Identify pathways linked to your protein list (KEGG and Biocarta)
  • Multiple species, not just eukaryotes
  • More...

HeLa fmol Endocytosis_1                                    fmol of proteins identified in the endocytic pathway from 200ng HeLa cell lysate mapped unto KEGG pathway

 

http://www.phosphosite.org/homeAction.action

  • Resource for the study of post-translational modifications
  • Phosphorylation, ubiquitination, acetylation and methylation
  • Links to cell signaling antibodies available for specific PTM studied
  • Gives overview of the protein (MW, function, gene name, associated disease...)
  • Gives crystal structure if available

 

http://string-db.org/

  • Protein-Protein interactions network
  • Multiple species, not just eukaryotes
  • GO analysis of proteins in network

String analysis of all 1833 proteins identified in a 200ng HeLa lysate. High Stringency                                                                  String analysis of all 1833 proteins identified in a 200ng HeLa lysate. High Stringency

 

http://www.reactome.org/

  • Reactome is a curated database of pathways and reactions (pathway steps) in human biology
  • Extensively cross-referenced to other resources e.g. NCBI, Ensembl, UniProt, UCSC Genome Browser, HapMap, KEGG (Gene and Compound), ChEBI, PubMed and GO
  • Inferred orthologous reactions are available for over 20 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, Arabidopsis and E.coli

HeLa reactome

Reactome analysis of all 1833 proteins identified in a 200ng HeLa lysate. Overrepresentation of pathways is shown in yellow